Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8764944
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 632878 characters in sequence are not A, C, G, or T
File 30 of 52
Found at i:5217493 original size:34 final size:33
Alignment explanation
Indices: 5217416--5217555 Score: 221
Period size: 33 Copynumber: 4.2 Consensus size: 33
5217406 GGCATCTTTC
*
5217416 ACCCTT-TCTAAAGCCCACACAAGTCGATGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
5217448 AACCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGC-A
5217482 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
5217515 A-CCTTCTTCCAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTC-TCTAAAGCCCACACAAGTCGGTGGCA
5217548 ACCCTTCT
1 ACCCTTCT
5217556 AAGCCCAATA
Statistics
Matches: 100, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
32 10 0.10
33 53 0.53
34 37 0.37
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.19
Consensus pattern (33 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:5217508 original size:67 final size:66
Alignment explanation
Indices: 5217416--5217555 Score: 230
Period size: 67 Copynumber: 2.1 Consensus size: 66
5217406 GGCATCTTTC
*
5217416 ACCCTT-TCTAAAGCCCACACAAGTCGATGGCAAACCTTC-TCTAAAGCCCACACAAGTCGGTGG
1 ACCCTTCTCTAAAGCCCACACAAGTCGATGGC-AACCTTCTTCCAAAGCCCACACAAGTCGGTGG
5217479 CAA
65 C-A
*
5217482 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTCTTCCAAAGCCCACACAAGTCGGTGGC
1 ACCCTTCTCTAAAGCCCACACAAGTCGATGGCAACCTTCTTCCAAAGCCCACACAAGTCGGTGGC
5217547 A
66 A
5217548 ACCCTTCT
1 ACCCTTCT
5217556 AAGCCCAATA
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
66 22 0.31
67 48 0.69
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.19
Consensus pattern (66 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGATGGCAACCTTCTTCCAAAGCCCACACAAGTCGGTGGC
A
Found at i:5217619 original size:49 final size:48
Alignment explanation
Indices: 5217555--5218302 Score: 917
Period size: 49 Copynumber: 15.8 Consensus size: 48
5217545 GCAACCCTTC
* * *
5217555 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
*
5217604 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * * *
5217647 TAAGTCCAATATCGCTGGCCTTGACTCAGCACATTGGCACCTTCAACTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
5217696 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
5217739 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
5217788 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * * *
5217831 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* * *
5217880 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* * *
5217929 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* * *
5217978 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTT-CATCTT
* * * *
5218027 TAAG-CCCATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* *
5218075 TAAGTCCAATGTAGCTAGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTT
* *
5218124 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
5218172 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
* * *
5218215 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--TT-CATCTT
5218267 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
5218303 ACATCCTTTT
Statistics
Matches: 608, Mismatches: 61, Indels: 57
0.84 0.08 0.08
Matches are distributed among these distances:
43 157 0.26
45 4 0.01
47 3 0.00
48 86 0.14
49 321 0.53
50 1 0.00
52 36 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTCATCTT
Found at i:5217717 original size:92 final size:92
Alignment explanation
Indices: 5217550--5218311 Score: 1078
Period size: 92 Copynumber: 8.1 Consensus size: 92
5217540 CGGTGGCAAC
* *
5217550 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
5217615 TAGCTGGCCTTGACTCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
5217643 CCTTTAAGTCCAATATCGCTGGCCTTGACTCAGCACATTGGCACCTTCAACTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
5217708 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
5217735 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
5217800 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
5217827 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
5217892 AGCTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
5217919 CCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTC
1 CC-T-----TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
*
5217984 CAATGTAGCTGGCCTTGACTCAGCACATTGGCACTTGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATT-G-----GCA
* * *
5218023 CCATTAAG-CCCATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
* *
5218087 AGCTAGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * *
5218114 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTC
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTC
5218178 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
5218211 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAA
*
5218276 TGTAGCTGGCCTTGAATCAGCACATTGACA
63 TGTAGCTGGCCTTGAATCAGCACATTGGCA
5218306 TCCTTT
1 -CCTTT
5218312 TTCATCATCT
Statistics
Matches: 612, Mismatches: 33, Indels: 45
0.89 0.05 0.07
Matches are distributed among these distances:
91 44 0.07
92 261 0.43
93 6 0.01
94 1 0.00
95 44 0.07
96 6 0.01
97 125 0.20
98 119 0.19
99 1 0.00
104 5 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:5218290 original size:52 final size:53
Alignment explanation
Indices: 5218212--5218371 Score: 187
Period size: 52 Copynumber: 3.0 Consensus size: 53
5218202 ACATTGGCAC
*
5218212 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCACAT
* * *
5218264 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCA-CAT
* * * * * *
5218320 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCAC
5218372 TTTTCCCATC
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
52 38 0.42
53 2 0.02
54 9 0.10
55 4 0.04
56 37 0.41
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCACAT
Found at i:5219214 original size:33 final size:33
Alignment explanation
Indices: 5219177--5219243 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5219167 TTCAACGATT
5219177 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5219210 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5219243 T
1 T
5219244 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5219215 original size:13 final size:13
Alignment explanation
Indices: 5219197--5219221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5219187 CATAAAATGT
5219197 TGTATCGATACAA
1 TGTATCGATACAA
5219210 TGTATCGATACA
1 TGTATCGATACA
5219222 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5219304 original size:13 final size:13
Alignment explanation
Indices: 5219286--5219310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5219276 ATTACTCACA
5219286 TGTATCGATACAT
1 TGTATCGATACAT
5219299 TGTATCGATACA
1 TGTATCGATACA
5219311 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5219447 original size:52 final size:52
Alignment explanation
Indices: 5219319--5219439 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
5219309 CACTGATCTT
*
5219319 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
5219371 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
5219423 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
5219440 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:5225347 original size:165 final size:161
Alignment explanation
Indices: 5225098--5225393 Score: 405
Period size: 165 Copynumber: 1.8 Consensus size: 161
5225088 AAATCCACCC
* * *
5225098 AAAAAATTATGAAGTAGAAAAAAACGAATTTCGAAAAAAAATTTGAGGAAAAAATTAAAAAACTC
1 AAAAAATTATAAAGTAGAAAAAAACGAATTTCAAAAAAAAATTTAAGGAAAAAATTAAAAAACTC
*
5225163 ATAAAAATGAAATAATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCATGAATTT
66 ATAAAAATGAAATAATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCAAGAATTT
5225228 TAAAAATTAAAAACTAAGAAAAATCTCCCCA
131 TAAAAATTAAAAACTAAGAAAAATCTCCCCA
* * * *
5225259 AAAAAATTATAAAGTAGAAAATAACGTATTTCAAAAAAGGAAAATTTCAAGGAAAAATTTTAAAA
1 AAAAAATTATAAAGTAGAAAAAAACGAATTTC-AAAAA--AAAATTT-AAGGAAAAAATTAAAAA
* * * * * * *
5225324 ATTCATGAAAATG-AATAAATTTTTGAAAACTGATTTAATATGAAATAAATAATGATATTTGAAG
62 ACTCATAAAAATGAAAT-AATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCAAG
5225388 AATTTT
126 AATTTT
5225394 GATGTTTGAA
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
161 29 0.25
162 4 0.03
164 10 0.09
165 72 0.63
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.29
Consensus pattern (161 bp):
AAAAAATTATAAAGTAGAAAAAAACGAATTTCAAAAAAAAATTTAAGGAAAAAATTAAAAAACTC
ATAAAAATGAAATAATTTTTAAAAAATAATTTAATATGAAATAAATAATAATATTTCAAGAATTT
TAAAAATTAAAAACTAAGAAAAATCTCCCCA
Found at i:5226449 original size:60 final size:59
Alignment explanation
Indices: 5226371--5227144 Score: 382
Period size: 60 Copynumber: 12.9 Consensus size: 59
5226361 TGAAGAAAAA
* *
5226371 CTTGACCGAATACT-GTCAAGTAGGGTAAGATTTAACTGAGTACAGTCAAATAAGGATTGT
1 CTTGAACGAATA-TAGTCAA-TAGGGTAAGATTTGACTGAGTACAGTCAAATAAGGATTGT
* * * * * *
5226431 CTTGAATGAATATAGTCAATAGAGATAAGATTT-AATCGAGTACTGTCAAATAAGGGA-AGA
1 CTTGAACGAATATAGTCAATAG-GGTAAGATTTGACT-GAGTACAGTCAAATAA-GGATTGT
* * * * * * *
5226491 CCTGAGA-AAAAATAATCAAGGAGGGTAAGATTTGACTGAGTATAGTCAAATGAGGATTGAT
1 CTTGA-ACGAATATAGTCAA-TAGGGTAAGATTTGACTGAGTACAGTCAAATAAGGATTG-T
* * * * * * * ** * *
5226552 -TTGACCAAAAATAATCAATGGGGGAAGATTTGACCGAGTATTGTCAAATGAGGATTGC
1 CTTGAACGAATATAGTCAATAGGGTAAGATTTGACTGAGTACAGTCAAATAAGGATTGT
* * * * * *
5226610 CTTGACCGAATATAGTCAAAAAAGGTAAAATTTGACTAAGCACAGTCAAATAAGGATTGT
1 CTTGAACGAATATAGTC-AATAGGGTAAGATTTGACTGAGTACAGTCAAATAAGGATTGT
* * * * *
5226670 CTTGATCGAATACAGTCAATAGGGGTAAAATTTGA-TCAAGCACAGTCAAATAAGGATTGT
1 CTTGAACGAATATAGTCAATA-GGGTAAGATTTGACT-GAGTACAGTCAAATAAGGATTGT
* * * * * * * * ** *
5226730 CTTGACCGAATATAGTCAAGAGGGGTAAAATTTGACCGAGCACAATCAAATGAGAAAAGG
1 CTTGAACGAATATAGTCAATA-GGGTAAGATTTGACTGAGTACAGTCAAATAAGGATTGT
* * * * * * * ** *
5226790 CTTGACCGAATACAGTCAAAAGGGGTAAAATTTGACCGAGTACAATCAAATGAGGAAAGA
1 CTTGAACGAATATAGTCAATA-GGGTAAGATTTGACTGAGTACAGTCAAATAAGGATTGT
* ** * * * * * * *
5226850 CTT-AACGAATACAGTTTAGAGGGCTAAAATTTGATTGAGTATAATCAAATGAGGAAATG-
1 CTTGAACGAATATAGTCAATAGGG-TAAGATTTGACTGAGTACAGTCAAATAAGG-ATTGT
* * * * * * * ** *
5226909 CTTGACCGAATATATTCAAAAGTGATAAAATTTGACCGAGTACAGTCAAATGAGGAAAGG
1 CTTGAACGAATATAGTCAATAG-GGTAAGATTTGACTGAGTACAGTCAAATAAGGATTGT
* * * * * ** *
5226969 CTTGACCGAATACAATCAAGAAGGGTAAAATTTGA-TCGAGTACAGTCAAATAAGGAAAGG
1 CTTGAACGAATATAGTCAA-TAGGGTAAGATTTGACT-GAGTACAGTCAAATAAGGATTGT
* * * * * ** *
5227029 CTTGATCGAATACAGTCAAGAGGGGTAAAATTTGA-TCGAGTACAGTCAAATGAGGAAAGG
1 CTTGAACGAATATAGTCAATA-GGGTAAGATTTGACT-GAGTACAGTCAAATAAGGATTGT
* * * * *
5227089 CTTGACCGAATACAGTCAAAAGGGGTAAAATTTGA-TCGAGTACAGTCAAATGAGGA
1 CTTGAACGAATATAGTCAATA-GGGTAAGATTTGACT-GAGTACAGTCAAATAAGGA
5227145 AAGGCCTAAT
Statistics
Matches: 598, Mismatches: 93, Indels: 46
0.81 0.13 0.06
Matches are distributed among these distances:
58 3 0.01
59 107 0.18
60 476 0.80
61 12 0.02
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (59 bp):
CTTGAACGAATATAGTCAATAGGGTAAGATTTGACTGAGTACAGTCAAATAAGGATTGT
Found at i:5226555 original size:30 final size:30
Alignment explanation
Indices: 5226519--5226629 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 30
5226509 AGGAGGGTAA
* *
5226519 GATTTGACTGAGTATAGTCAAATGAGGATT
1 GATTTGACCGAATATAGTCAAATGAGGATT
* * * * *
5226549 GATTTGACCAAAAATAATC-AATGGGGGA-A
1 GATTTGACCGAATATAGTCAAAT-GAGGATT
* *
5226578 GATTTGACCGAGTATTGTCAAATGAGGATT
1 GATTTGACCGAATATAGTCAAATGAGGATT
**
5226608 GCCTTGACCGAATATAGTCAAA
1 GATTTGACCGAATATAGTCAAA
5226630 AAAGGTAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
29 21 0.35
30 39 0.65
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (30 bp):
GATTTGACCGAATATAGTCAAATGAGGATT
Found at i:5226765 original size:30 final size:29
Alignment explanation
Indices: 5226731--5227138 Score: 175
Period size: 30 Copynumber: 13.7 Consensus size: 29
5226721 AAGGATTGTC
*
5226731 TTGACCGAATATAGTCAAGAGGGGTAAAAT
1 TTGACCGAATACAGTCAA-AGGGGTAAAAT
** * * * *
5226761 TTGACCGAGCACAATCAAATGAG-AAAAGGC
1 TTGACCGAATACAGTCAAAGGGGTAAAA--T
5226791 TTGACCGAATACAGTCAAAAGGGGTAAAAT
1 TTGACCGAATACAGTC-AAAGGGGTAAAAT
* * * *
5226821 TTGACCGAGTACAATCAAATGAGG-AAAGAC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
* * * *
5226851 TT-AACGAATACAGTTTAGAGGGCTAAAAT
1 TTGACCGAATACAG-TCAAAGGGGTAAAAT
** * * * *
5226880 TTGATTGAGTATAATCAAATGAGG--AAAT
1 TTGACCGAATACAGTCAAA-GGGGTAAAAT
* * * *
5226908 GCTTGACCGAATATATTCAAAAGTGATAAAAT
1 --TTGACCGAATACAGTC-AAAGGGGTAAAAT
* * **
5226940 TTGACCGAGTACAGTCAAATGAGG-AAAGGC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
* *
5226970 TTGACCGAATACAATCAAGAAGGGTAAAAT
1 TTGACCGAATACAGTCAA-AGGGGTAAAAT
* * ** **
5227000 TTGATCGAGTACAGTCAAATAAGG-AAAGGC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
*
5227030 TTGATCGAATACAGTCAAGAGGGGTAAAAT
1 TTGACCGAATACAGTCAA-AGGGGTAAAAT
* * * **
5227060 TTGATCGAGTACAGTCAAATGAGG-AAAGGC
1 TTGACCGAATACAGTCAAA-GGGGTAAA-AT
5227090 TTGACCGAATACAGTCAAAAGGGGTAAAAT
1 TTGACCGAATACAGTC-AAAGGGGTAAAAT
* *
5227120 TTGATCGAGTACAGTCAAA
1 TTGACCGAATACAGTCAAA
5227139 TGAGGAAAGG
Statistics
Matches: 276, Mismatches: 75, Indels: 55
0.68 0.18 0.14
Matches are distributed among these distances:
28 8 0.03
29 42 0.15
30 196 0.71
31 22 0.08
32 8 0.03
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (29 bp):
TTGACCGAATACAGTCAAAGGGGTAAAAT
Found at i:5227145 original size:60 final size:60
Alignment explanation
Indices: 5226579--5227400 Score: 711
Period size: 60 Copynumber: 13.7 Consensus size: 60
5226569 ATGGGGGAAG
** ** * * **
5226579 ATTTGACCGAGTATTGTCAAATGAGGATTGCCTTGACCGAATATAGTCAAAAAAGGTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
** * * ** * * *
5226639 ATTTGACTAAGCACAGTCAAATAAGGATTGTCTTGATCGAATACAGTCAATAGGGGTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
* * * * ** * * *
5226699 ATTTGATCAAGCACAGTCAAATAAGGATTGTCTTGACCGAATATAGTCAAGAGGGGTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
* * *
5226759 ATTTGACCGAGCACAATCAAATGAGAAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
* * * ** * *
5226819 ATTTGACCGAGTACAATCAAATGAGGAAAGACTT-AACGAATACAGTTTAGAGGGCTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
** * * * * * * *
5226878 ATTTGATTGAGTATAATCAAATGAGGAAATGCTTGACCGAATATATTCAAAAGTGATAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
*
5226938 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAATCAAGAA-GGGTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAA-AAGGGGTAAA
* * * *
5226998 ATTTGATCGAGTACAGTCAAATAAGGAAAGGCTTGATCGAATACAGTCAAGAGGGGTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
*
5227058 ATTTGATCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
* * * * * ***
5227118 ATTTGATCGAGTACAGTCAAATGAGGAAAGGCCTAATCGAATACAATCAAGAA-GGGTTGG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAA-AAGGGGTAAA
* * * * * * * * * * * *
5227178 ATTCGACCGAATATAGTCAAATAAGGAAAGTCTTGACCGAATACAATTAAGAGAGTTGAG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
* * * * ** ** ***
5227238 ATTTGAACGAGTATAGTCAAATGAGGAAAGGCTTAACCGAATACAGTTAAGCGACGTTGG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
* * * * * * *
5227298 ATTCGACTGAATACAGTCAAATAAGG-AAGGTCTTAACCGAATACAGTCAAGCAA--GGTGAG
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGG-CTTGACCGAATACAGTCAA--AAGGGGTAAA
* ** * *
5227358 ATTTGACTGAGTGTAATCAAATGAGGAAAGGCTTAACCGAATA
1 ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATA
5227401 AAGTTAAGTG
Statistics
Matches: 636, Mismatches: 117, Indels: 18
0.82 0.15 0.02
Matches are distributed among these distances:
59 55 0.09
60 573 0.90
61 8 0.01
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (60 bp):
ATTTGACCGAGTACAGTCAAATGAGGAAAGGCTTGACCGAATACAGTCAAAAGGGGTAAA
Found at i:5227157 original size:30 final size:30
Alignment explanation
Indices: 5226940--5227167 Score: 178
Period size: 30 Copynumber: 7.6 Consensus size: 30
5226930 GTGATAAAAT
* *
5226940 TTGACCGAGTACAGTCAAATGAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* * * **
5226970 TTGACCGAATACAATCAAGAAG-GGTAAA-AT
1 TTGATCGAATACAGTCAA-ATGAGG-AAAGGC
* *
5227000 TTGATCGAGTACAGTCAAATAAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* **
5227030 TTGATCGAATACAGTCAAGA-GGGGTAAA-AT
1 TTGATCGAATACAGTCAA-ATGAGG-AAAGGC
*
5227060 TTGATCGAGTACAGTCAAATGAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* * * **
5227090 TTGACCGAATACAGTCAAAAGGGGTAAA-AT
1 TTGATCGAATACAGTCAAATGAGG-AAAGGC
*
5227120 TTGATCGAGTACAGTCAAATGAGGAAAGGC
1 TTGATCGAATACAGTCAAATGAGGAAAGGC
* * *
5227150 CTAATCGAATACAATCAA
1 TTGATCGAATACAGTCAA
5227168 GAAGGGTTGG
Statistics
Matches: 151, Mismatches: 37, Indels: 20
0.73 0.18 0.10
Matches are distributed among these distances:
29 11 0.07
30 128 0.85
31 12 0.08
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (30 bp):
TTGATCGAATACAGTCAAATGAGGAAAGGC
Found at i:5227216 original size:30 final size:30
Alignment explanation
Indices: 5226610--5227222 Score: 156
Period size: 30 Copynumber: 20.5 Consensus size: 30
5226600 TGAGGATTGC
* * *
5226610 CTTGACCGAATATAGTCAAAAAAGGTAAAAT
1 CTTGACCGAATACAGTCAAATAAGG-AAAGT
* * **
5226641 -TTGA-CTAAGCACAGTCAAATAAGGATTGT
1 CTTGACCGAA-TACAGTCAAATAAGGAAAGT
* * *
5226670 CTTGATCGAATACAGTC-AATAGGGGTAAAAT
1 CTTGACCGAATACAGTCAAATA-AGG-AAAGT
* * **
5226701 -TTGATC-AAGCACAGTCAAATAAGGATTGT
1 CTTGACCGAA-TACAGTCAAATAAGGAAAGT
* ** *
5226730 CTTGACCGAATATAGTCAAGA-GGGGTAAAAT
1 CTTGACCGAATACAGTCAA-ATAAGG-AAAGT
** * * * *
5226761 -TTGACCGAGCACAATCAAATGAGAAAAGG
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* *
5226790 CTTGACCGAATACAGTCAAA-AGGGGTAAAAT
1 CTTGACCGAATACAGTCAAATA-AGG-AAAGT
* * * *
5226821 -TTGACCGAGTACAATCAAATGAGGAAAGA
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* ** * * *
5226850 CTT-AACGAATACAGT-TTAGAGGGCTAAAAT
1 CTTGACCGAATACAGTCAAATAAGG--AAAGT
** * * * *
5226880 -TTGATTGAGTATAATCAAATGAGGAAA-T
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* * *
5226908 GCTTGACCGAATATATTC-AA-AAGTGATAAAAT
1 -CTTGACCGAATACAGTCAAATAAG-G--AAAGT
* * *
5226940 -TTGACCGAGTACAGTCAAATGAGGAAAGG
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* * *
5226969 CTTGACCGAATACAATCAAGA-AGGGTAAAAT
1 CTTGACCGAATACAGTCAA-ATAAGG-AAAGT
* * *
5227000 -TTGATCGAGTACAGTCAAATAAGGAAAGG
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* ** *
5227029 CTTGATCGAATACAGTCAAGA-GGGGTAAAAT
1 CTTGACCGAATACAGTCAA-ATAAGG-AAAGT
* * * *
5227060 -TTGATCGAGTACAGTCAAATGAGGAAAGG
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* *
5227089 CTTGACCGAATACAGTCAAA-AGGGGTAAAAT
1 CTTGACCGAATACAGTCAAATA-AGG-AAAGT
* * * *
5227120 -TTGATCGAGTACAGTCAAATGAGGAAAGG
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* * * * * *** *
5227149 CCTAATCGAATACAATC-AAGAAGGGTTGG
1 CTTGACCGAATACAGTCAAATAAGGAAAGT
* *
5227178 ATTCGACCGAATATAGTCAAATAAGGAAAGT
1 CTT-GACCGAATACAGTCAAATAAGGAAAGT
5227209 CTTGACCGAATACA
1 CTTGACCGAATACA
5227223 ATTAAGAGAG
Statistics
Matches: 404, Mismatches: 134, Indels: 89
0.64 0.21 0.14
Matches are distributed among these distances:
28 6 0.01
29 59 0.15
30 290 0.72
31 46 0.11
32 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (30 bp):
CTTGACCGAATACAGTCAAATAAGGAAAGT
Found at i:5228798 original size:18 final size:19
Alignment explanation
Indices: 5228775--5228815 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
5228765 CTTGTTTCTA
5228775 TTTTCATTTC-TTTCATTC
1 TTTTCATTTCTTTTCATTC
*
5228793 TTTTCATTTCTTTTCTTTC
1 TTTTCATTTCTTTTCATTC
5228812 TTTT
1 TTTT
5228816 TTCTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTCATTTCTTTTCATTC
Found at i:5228811 original size:9 final size:9
Alignment explanation
Indices: 5228775--5228831 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
5228765 CTTGTTTCTA
5228775 TTTTCATTTC
1 TTTTC-TTTC
*
5228785 -TTTCATTC
1 TTTTCTTTC
5228793 TTTTCATTTC
1 TTTTC-TTTC
5228803 TTTTCTTTC
1 TTTTCTTTC
5228812 -TTT-TTTC
1 TTTTCTTTC
5228819 TTATT-TTTC
1 TT-TTCTTTC
5228828 TTTT
1 TTTT
5228832 TGCAAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 4 0.10
8 9 0.22
9 20 0.49
10 8 0.20
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:5228820 original size:16 final size:16
Alignment explanation
Indices: 5228799--5228832 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5228789 ATTCTTTTCA
5228799 TTTCTT-TTCTTTCTTT
1 TTTCTTATT-TTTCTTT
5228815 TTTCTTATTTTTCTTT
1 TTTCTTATTTTTCTTT
5228831 TT
1 TT
5228833 GCAAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTATTTTTCTTT
Found at i:5228824 original size:23 final size:22
Alignment explanation
Indices: 5228753--5228824 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 22
5228743 TTTCATGATT
*
5228753 TTTCATTTT-TTTCTTGTTTCTA
1 TTTC-TTTTCTTTCTTTTTTCTA
*
5228775 TTTTCATTTCTTTCATTCTTTTC-A
1 -TTTCTTTTCTTTC-TT-TTTTCTA
5228799 TTTCTTTTCTTTCTTTTTTCTTA
1 TTTCTTTTCTTTCTTTTTTC-TA
5228822 TTT
1 TTT
5228825 TTCTTTTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
21 5 0.12
22 5 0.12
23 24 0.59
24 3 0.07
25 4 0.10
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTTCTA
Found at i:5231565 original size:158 final size:156
Alignment explanation
Indices: 5231227--5231606 Score: 408
Period size: 158 Copynumber: 2.4 Consensus size: 156
5231217 ATAAAAGCGA
* * * * *
5231227 GGTTGGAGTAACCCCAAGATGAAAATTTTAATATTTTTGAAATAAAAACAGGGTTGGAGTATCCT
1 GGTTGAAGTATCCCCAACATGAAAATTTTAATATTTTGGAAATAAAAACAGGGTTAGAGTATCCT
* * ** * *
5231292 CTCGAAAATAATAGGGTTGGAGTATCCCCAAGAAGAAAATTAATATTTTGGAAATAAAAGTGGGG
66 CTCGAAAATAATAGGGTTGGAGTATCCCCAAAAAAAAAATTAATATTTTAAAAATAAAAATAGGG
* * * * *
5231357 TTGGAGTATCCCTTCAGAATTGATGG
131 TTGAAGTATCCCCTCAGAAATAACGG
* * * * *
5231383 GGTTGAAGTATCCCTAAGAAGAAAATTTTAATATTTTGGAAATGAAAA-TGAGGTTAGAGTATCC
1 GGTTGAAGTATCCCCAACATGAAAATTTTAATATTTTGGAAATAAAAACAG-GGTTAGAGTATCC
* * *
5231447 -CTTCGGAATTGAT-GGAGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTAAAAATAAAAA
65 TC-TCGAAAATAATAGG-GTTGGAGTATCCCCAAAA-AAAAAA-TTAATATTTTAAAAATAAAAA
*
5231510 TAGGGTTTAAGTATCCCCTCAGAAATAACGG
126 TAGGGTTGAAGTATCCCCTCAGAAATAACGG
* * * * *
5231541 GGCTTG-AGTATCCCCGACATGAAAATTTCAATATTTTGGAAATAAAAACGGGGTTGGAATATCC
1 GG-TTGAAGTATCCCCAACATGAAAATTTTAATATTTTGGAAATAAAAACAGGGTTAGAGTATCC
5231605 TC
65 TC
5231607 GAGATGAAGA
Statistics
Matches: 184, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
155 4 0.02
156 79 0.43
157 5 0.03
158 91 0.49
159 5 0.03
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (156 bp):
GGTTGAAGTATCCCCAACATGAAAATTTTAATATTTTGGAAATAAAAACAGGGTTAGAGTATCCT
CTCGAAAATAATAGGGTTGGAGTATCCCCAAAAAAAAAATTAATATTTTAAAAATAAAAATAGGG
TTGAAGTATCCCCTCAGAAATAACGG
Found at i:5231595 original size:79 final size:78
Alignment explanation
Indices: 5231227--5231604 Score: 352
Period size: 79 Copynumber: 4.8 Consensus size: 78
5231217 ATAAAAGCGA
* * ** * *
5231227 GGTTGGAGTAACCCCAAGATGAAAATTTTAATATTTTTGAAATAAAAACAGGGTTGGAGTATCCT
1 GGTTGGAGTATCCCCAAGATGAAAA-TTTAATATTTTGGAAATAAAAATGGGGTTGAAGTATCCC
*
5231292 CTC-GAAAATAATAG
65 CTCAG-AAATAATGG
* * * *
5231306 GGTTGGAGTATCCCCAAGAAGAAAA-TTAATATTTTGGAAATAAAAGTGGGGTTGGAGTATCCCT
1 GGTTGGAGTATCCCCAAGATGAAAATTTAATATTTTGGAAATAAAAATGGGGTTGAAGTATCCCC
* *
5231370 TCAGAATTGATGG
66 TCAGAAATAATGG
* * * * *
5231383 GGTTGAAGTATCCCTAAGAAGAAAATTTTAATATTTTGGAAATGAAAATGAGGTT-AGAGTATCC
1 GGTTGGAGTATCCCCAAGATGAAAA-TTTAATATTTTGGAAATAAAAATGGGGTTGA-AGTATCC
* * * *
5231447 CTTCGGAATTGATGG
64 CCTCAGAAATAATGG
* * * ** * *
5231462 AGTTGGAGTATCCCCAAAATAAAAAATTTAATATTTTAAAAATAAAAATAGGGTTTAAGTATCCC
1 GGTTGGAGTATCCCCAAGAT-GAAAATTTAATATTTTGGAAATAAAAATGGGGTTGAAGTATCCC
*
5231527 CTCAGAAATAACGG
65 CTCAGAAATAATGG
* * *
5231541 GGCTT-GAGTATCCCCGACATGAAAATTTCAATATTTTGGAAATAAAAACGGGGTTGGAA-TATC
1 GG-TTGGAGTATCCCCAAGATGAAAATTT-AATATTTTGGAAATAAAAATGGGGTT-GAAGTATC
5231604 C
63 C
5231605 TCGAGATGAA
Statistics
Matches: 247, Mismatches: 43, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
77 64 0.26
78 8 0.03
79 166 0.67
80 9 0.04
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (78 bp):
GGTTGGAGTATCCCCAAGATGAAAATTTAATATTTTGGAAATAAAAATGGGGTTGAAGTATCCCC
TCAGAAATAATGG
Found at i:5234051 original size:20 final size:20
Alignment explanation
Indices: 5234026--5234081 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
5234016 TAAACAGTAA
5234026 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
5234046 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
*
5234066 ATGTATCGATATATTT
1 ATGTATCGATACATTT
5234082 TCTTGGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTTACTT
Found at i:5235108 original size:62 final size:62
Alignment explanation
Indices: 5234898--5235727 Score: 933
Period size: 62 Copynumber: 13.4 Consensus size: 62
5234888 TGGCACACTT
* * * * * *
5234898 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTAT-GGTTTTTAAGAGGAAAAAAGAAAGTGTCCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAA-AAG-AAAAAG--A-CGTCCT
5234962 GC
61 GC
* *
5234964 TCTTTGAGGACTAAAAGGTGTCACCAACTCGTGTGAGG-TTT-AAAAGAAAAAAACGTCCTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTG-GGCTTTGAAAAGAAAAAGACGTCCTGC
* * **
5235025 TCTTTGAGGACAAAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGTGTCCTGC
1 TCTTTGAGGACTAAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* *
5235088 TCTTTGAGGACTAAAAGGTGCAACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTTC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * *
5235150 TCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * * * ** * * * *
5235212 TTTTTGAGAACTAAAGGGTACCACCAACTTATGTAGGCTTTGAAAA-AAAAAGATGACTTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * ** ** *
5235273 TTTTTGAGGACTAAAGGGTGCCATGAACTCGTGTGGGCTTTGAAAAGAAAAAGGTGTCTTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * * * *
5235335 TCTTTGAGGACTAAAGGGTGCCACCAATTCATATGGGCTTTGAAAAGAAAAATG-CTTCCTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA-GACGTCCTGC
* * * * *
5235397 TCTTTGAGGAATAAAAGGTGCCACCAACTCGTGTGAGCTTTGTAAAGAAAAAGGCGTCATGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* * * *
5235459 TCTTTGAGGACTAAAAGGTG-CACCAACTTGTGTGGGCTTTAAAAAGGAAAAGCAC--CTTGC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAG-ACGTCCTGC
* * * ** * * * *
5235519 CCTTTGAGAACTAAAAAGGTGCCACCACCTTATGTGGGCTTTGAAAGGGAAAAGACATCTTGC
1 TCTTTGAGGACT-AAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
*
5235582 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGACGTCCTAC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* *
5235643 TCTTTGAGGACTAGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAATG-CGTCTTGC
1 TCTTTGAGGACTA-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
* *
5235705 TTTTTGAGGACTAAAGGGTGCCA
1 TCTTTGAGGACTAAAAGGTGCCA
5235728 AGGGTGCCAA
Statistics
Matches: 659, Mismatches: 90, Indels: 35
0.84 0.11 0.04
Matches are distributed among these distances:
60 14 0.02
61 149 0.23
62 393 0.60
63 58 0.09
64 5 0.01
65 2 0.00
66 33 0.05
67 3 0.00
68 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (62 bp):
TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTGC
Found at i:5235339 original size:247 final size:247
Alignment explanation
Indices: 5234898--5236566 Score: 1568
Period size: 247 Copynumber: 6.7 Consensus size: 247
5234888 TGGCACACTT
* * * * *
5234898 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTAT-GGTTTTTAAGAGGAAAAAAGAAAGTGTCCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AAG-AAAAAGACA---TCCT
* * * * *
5234962 GCTCTTTGAGGACTAAAAGGTGTCACCAACTCGTGTGAGG-TTT-AAAAGAAAAAAACGTCCTGC
61 GCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGT-AGGCTTTGAAAAGAAAAAGA-GACTTGC
* * *
5235025 TCTTTGAGGACAAAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGTGTCCTGCTC
124 TCTTTGAGGAC-TAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTC
* * * *
5235090 TTTGAGGACTAAAAGGTGCAACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTTC
188 TTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGACATCCTGC
* * * *
5235150 TCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCTGCTTT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCT
* * ** *
5235215 TTGAGAACTAAAGGGTACCACCAACTTATGTAGGCTTTGAAAA-AAAAAGATGACTTGCTTTTTG
66 TTGAGGACTAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGA-GACTTGCTCTTTG
** * *
5235279 AGGACTAAAGGGTGCCATGAACTCGTGTGGGCTTTGAAAAGAAAAAGGTGTCTTGCTCTTTGAGG
130 AGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGG
* * * *
5235344 ACTAAAGGGTGCCACCAATTCATATGGGCTTTGAAAAGAAAAATG-CTTCCTGC
195 ACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAA-GACATCCTGC
* * * * * * *
5235397 TCTTTGAGGAATAAAAGGTGCCACCAACTCGTGTGAGCTTTGTAAAGAAAAAGGCGTCATGCTCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCT
* * * * * * *
5235462 TTGAGGACTAAAAGGTG-CACCAACTTGTGTGGGCTTTAAAAAGGAAAAGCA-CCTTGCCCTTTG
66 TTGAGGACTAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAG-AGACTTGCTCTTTG
* * * ** * * * * *
5235525 AGAACTAAAAAGGTGCCACCACCTTATGTGGGCTTTGAAAGGGAAAAGACATCTTGCTCTTTGAG
130 AGGACT-AAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAG
* * *
5235590 GACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGACGTCCTAC
194 GACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGACATCCTGC
* * * * *
5235643 TCTTTGAGGACTAGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAATG-CGTCTTGCTT
1 TCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTC
** *
5235707 TTTGAGGACTAAAGGGTGCCAAGGGTGCCAAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAA
65 TTTGAGGAC-------T----A-------AAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAA
* * * *
5235772 AAAG-GCATCCTACTCTTTGAGGACTAAAGGGTGCCACCAATTCGTGTGGGTTTTG-AAA-AAAA
112 AAAGAG-A-CTTGCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAA
* * *
5235834 AGGCATCTTGCT-TTTGAGGACT-AAAGAGTGCCACCAACTCATGTGGACTTTGAAAAGAAAAA-
175 AGGCGTCCTGCTCTTTGAGGACTAAAAG-GTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAG
5235896 AGCATCCTGC
239 A-CATCCTGC
* * * * * *
5235906 TCTTTGAAGACTAAAGGGTGCTATCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCT
* * * * * *
5235971 TTGAGGACTAGAAGGGTGCCATCAACTCATTTGGGCTTTGAAAAGAGAAAG-GCATCTTACTCTT
66 TTGAGGACTA-AAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGAG-A-CTTGCTCTT
* * *
5236035 TGAGGACTAAAGGGTGCCACCAACTCGTGTGGGTTTTG-AAA-AAAAAGACGTCCTGCTTTTTGA
128 TGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGA
** *
5236098 GGACT-AAAGAGTGCCACCAACTCATGTGGATTTTGAAAAGAAAAAGGCATCCTGC
193 GGACTAAAAG-GTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGACATCCTGC
* * * * *
5236153 TCTTTGAGGACTAAAGGGTGCCATCAACTTGTGTGGGCTTTGAAAAGAAACAGGCATCCTACTC-
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCT
* * * * *
5236217 TTGAGGACTAAAAGGTGTCACCAACTCGTGT-GAGCTTTGAAAAGAAAAAAGTGTCTTACTCTTT
66 TTGAGGACTAAAGGGTGCCACCAACTCGTGTAG-GCTTTGAAAAG-AAAAAGAGACTTGCTCTTT
* * * * * * * * * *
5236281 GAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAA-TCGCCCTACTCGTTAAA
129 GAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAG
* ** * *
5236345 GACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTAC
194 GACT-AAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGACATCCTGC
* * * * ** * *
5236400 TTTTTGAAGACTTAAAGGTGCCACCAATTTGTGTGGGCTTT-AAAAGAAAAAGATGTCTTACTCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCT
* * * *
5236464 TTGAGGACTAGAAGGGTGTCACC-ACTCGTGTAGGCTTTAAAAAGAAAAAGACGTCCTGCTCTTT
66 TTGAGGACTA-AAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGA-GACTTGCTCTTT
* **
5236528 AAGGACTAAAGGGTGCCACCAACTTATGTGGGCTTTGAA
129 GAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAA
5236567 GAAAGGTTGC
Statistics
Matches: 1201, Mismatches: 168, Indels: 101
0.82 0.11 0.07
Matches are distributed among these distances:
244 1 0.00
245 71 0.06
246 237 0.20
247 560 0.47
248 75 0.06
249 4 0.00
251 8 0.01
252 34 0.03
253 8 0.01
256 1 0.00
257 1 0.00
261 4 0.00
262 68 0.06
263 57 0.05
264 8 0.01
265 51 0.04
266 13 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (247 bp):
TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCT
TTGAGGACTAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGAGACTTGCTCTTTGA
GGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGA
CTAAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGACATCCTGC
Found at i:5235350 original size:185 final size:184
Alignment explanation
Indices: 5234898--5236566 Score: 1573
Period size: 185 Copynumber: 8.9 Consensus size: 184
5234888 TGGCACACTT
* * ** * * *
5234898 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTATGGTTTTTAAGAGGAAA-AAAGAAAGTGTCCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT--GA--AAAGAAA-AAGGCGTCTT
* * * *
5234962 GCTCTTTGAGGACTAAAAGGTGTCACCAACTCGTGTGAGG-TTT-AAAAGAAAAAAACGTCCTGC
61 GCTCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTG-GGCTTTGAAAAGAAAAAGACATCCTGC
* * * *
5235025 TCTTTGAGGACAAAAAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAAGGTGTCCTGC
125 TCTTTGAGGAC-TAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAA-G-GACCTGC
* *
5235088 TCTTTGAGGACTAAAAGGTGCAACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACGTCCTT-CTC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGT-CTTGCTC
* *
5235152 TTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCTGCTTTTT
65 TTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCTTT
* * * * *
5235217 GAGAACTAAAGGGTACCACCAACTTATGTAGGCTTTGAAAA-AAAAAGATGACTTGC
130 GAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG--GACCTGC
* * ** *
5235273 TTTTTGAGGACTAAAGGGTGCCATGAACTCGTGTGGGCTTTGAAAAGAAAAAGGTGTCTTGCTCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTCT
* * * *
5235338 TTGAGGACTAAAGGGTGCCACCAATTCATATGGGCTTTGAAAAGAAAAATG-CTTCCTGCTCTTT
66 TTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAA-GACATCCTGCTCTTT
* * * * *
5235402 GAGGAATAAAAGGTGCCACCAACTCGTGTGAGCTTTGTAAAGAAAAAGG-CGTCATGC
130 GAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGAC--C-TGC
* * * ** *
5235459 TCTTTGAGGACTAAAAGGTG-CACCAACTTGTGTGGGCTTTAAAAAGGAAAA-GCACCTTGCCCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTCT
* * * ** * * *
5235522 TTGAGAACTAAAAAGGTGCCACCACCTTATGTGGGCTTTGAAAGGGAAAAGACATCTTGCTCTTT
66 TTGAGGACT-AAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCTTT
* * * *
5235587 GAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGAAAAAGACGTCCTAC
130 GAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG--GACCTGC
* *
5235643 TCTTTGAGGACTAGAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAG-AAAATGCGTCTTGCTT
1 TCTTTGAGGACTA-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTC
**
5235707 TTTGAGGACTAAAGGGTGCCAAGGGTGCCAAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAA
65 TTTGAGGAC-------T----A-------AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAA
* * *
5235772 AAAGGCATCCTACTCTTTGAGGACTAAAGGGTGCCACCAA-TTCGTGTGGGTTTTG-AAA-AAAA
112 AAAGACATCCTGCTCTTTGAGGACTAAAGGGTGCCACCAACTT-GTGTGGGCTTTGAAAAGAAAA
*
5235834 AGGCATCTTGC
176 AGG-A-CCTGC
* * * * *
5235845 T-TTTGAGGACT-AAAGAGTGCCACCAACTCATGTGGACTTTGAAAAGAAAAAAGCATCCTGCTC
1 TCTTTGAGGACTAAAAG-GTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTC
* * * * * *
5235908 TTTGAAGACTAAAGGGTGCTATCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTT
65 TTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCTTT
* ** * * * *
5235973 GAGGACTAGAAGGGTGCCATCAACTCATTTGGGCTTTGAAAAGAGAAAGGCATCTTAC
130 GAGGACTA-AAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGG-A-CCTGC
* * * * *
5236031 TCTTTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGTTTTG-AAA-AAAAAGACGTCCTGCTTT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTCT
* * ** *
5236094 TTGAGGACTAAAGAGTGCCACCAACTCATGTGGATTTTGAAAAGAAAAAGGCATCCTGCTCTTTG
66 TTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCTTTG
* * *
5236159 AGGACTAAAGGGTGCCATCAACTTGTGTGGGCTTTGAAAAGAAACAGGCATCCTAC
131 AGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGG-A-CCTGC
* * * * *
5236215 TC-TTGAGGACTAAAAGGTGTCACCAACTCGTGTGAGCTTTGAAAAGAAAAAAGTGTCTTACTCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTCT
* * * * * ** * * *
5236279 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAA-TCGCCCTACTCGTTA
66 TTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCTTTG
* * * *
5236343 AAGACTAAAAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTAC
131 AGGACT-AAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGG-A-CCTGC
* * * * * ** *
5236400 TTTTTGAAGACTTAAAGGTGCCACCAATTTGTGTGGGCTTT-AAAAGAAAAAGATGTCTTACTCT
1 TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTCT
* * * *
5236464 TTGAGGACTAGAAGGGTGTCACC-ACTCGTGTAGGCTTTAAAAAGAAAAAGACGTCCTGCTCTTT
66 TTGAGGACTA-AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCTTT
* *
5236528 AAGGACTAAAGGGTGCCACCAACTTATGTGGGCTTTGAA
130 GAGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAA
5236567 GAAAGGTTGC
Statistics
Matches: 1241, Mismatches: 184, Indels: 113
0.81 0.12 0.07
Matches are distributed among these distances:
183 93 0.07
184 131 0.11
185 535 0.43
186 218 0.18
187 65 0.05
188 5 0.00
190 37 0.03
193 1 0.00
194 1 0.00
196 2 0.00
199 4 0.00
200 29 0.02
201 30 0.02
202 11 0.01
203 79 0.06
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (184 bp):
TCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCGTCTTGCTCT
TTGAGGACTAAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGACATCCTGCTCTTTG
AGGACTAAAGGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGACCTGC
Found at i:5235732 original size:9 final size:9
Alignment explanation
Indices: 5235718--5235745 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5235708 TTGAGGACTA
5235718 AAGGGTGCC
1 AAGGGTGCC
5235727 AAGGGTGCC
1 AAGGGTGCC
5235736 AAGGGTGCC
1 AAGGGTGCC
5235745 A
1 A
5235746 CCAACTCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.21, G:0.43, T:0.11
Consensus pattern (9 bp):
AAGGGTGCC
Found at i:5235934 original size:62 final size:62
Alignment explanation
Indices: 5235736--5236566 Score: 928
Period size: 62 Copynumber: 13.5 Consensus size: 62
5235726 CAAGGGTGCC
**
5235736 AAGGGTGCCACCAACTCACGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * *
5235798 AAGGGTGCCACCAATTCGTGTGGGTTTTG-AAA-AAAAAGGCATCTTGCT-TTTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * * * *
5235857 AAGAGTGCCACCAACTCATGTGGACTTTGAAAAGAAAAAAGCATCCTGCTCTTTGAAGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * *
5235919 AAGGGTGCTATCAACTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * * *
5235981 GAAGGGTGCCATCAACTCATTTGGGCTTTGAAAAGAGAAAGGCATCTTACTCTTTGAGGACTA
1 -AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * * *
5236044 AAGGGTGCCACCAACTCGTGTGGGTTTTG-AAA-AAAAAGACGTCCTGCTTTTTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * ** *
5236104 AAGAGTGCCACCAACTCATGTGGATTTTGAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * *
5236166 AAGGGTGCCATCAACTTGTGTGGGCTTTGAAAAGAAACAGGCATCCTACTC-TTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * * ** *
5236227 AAAGGTGTCACCAACTCGTGTGAGCTTTGAAAAGAAAAAAGTGTCTTACTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * ** * * *
5236289 AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAATCGC--CCTACTCGTTAAAGACTAA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGCATCCTACTCTTTGAGGACT-A
* * * * *
5236351 AAAGGTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTTTTTGAAGACTTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGAC-TA
* * *** *
5236414 AA-GGTGCCACCAATTTGTGTGGGCTTT-AAAAGAAAAAGATGTCTTACTCTTTGAGGACTA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
* * * * * * *
5236474 GAAGGGTGTCACC-ACTCGTGTAGGCTTTAAAAAGAAAAAGACGTCCTGCTCTTTAAGGACTA
1 -AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
**
5236536 AAGGGTGCCACCAACTTATGTGGGCTTTGAA
1 AAGGGTGCCACCAACTCGTGTGGGCTTTGAA
5236567 GAAAGGTTGC
Statistics
Matches: 651, Mismatches: 102, Indels: 32
0.83 0.13 0.04
Matches are distributed among these distances:
59 35 0.05
60 67 0.10
61 144 0.22
62 326 0.50
63 78 0.12
64 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (62 bp):
AAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCATCCTACTCTTTGAGGACTA
Found at i:5244504 original size:31 final size:31
Alignment explanation
Indices: 5244461--5244536 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
5244451 TACATTGAGA
* *
5244461 AATGTATTGATACATCTGGGTTAAAACCTAG
1 AATGTATCGATACATCTAGGTTAAAACCTAG
* *
5244492 GATGTATCGATACATCTAGGTTAAAACTTAG
1 AATGTATCGATACATCTAGGTTAAAACCTAG
5244523 AATGTATCGATACA
1 AATGTATCGATACA
5244537 ATGAAAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (31 bp):
AATGTATCGATACATCTAGGTTAAAACCTAG
Found at i:5244596 original size:20 final size:20
Alignment explanation
Indices: 5244568--5244620 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
5244558 ATAGTAAATC
5244568 TATCGATACATTTACTTATG
1 TATCGATACATTTACTTATG
*
5244588 TATCAATACATTTACTTATG
1 TATCGATACATTTACTTATG
5244608 TATCGATACATTT
1 TATCGATACATTT
5244621 CCTTGGCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (20 bp):
TATCGATACATTTACTTATG
Found at i:5249266 original size:149 final size:149
Alignment explanation
Indices: 5249086--5249401 Score: 361
Period size: 159 Copynumber: 2.1 Consensus size: 149
5249076 ATACGAAAAG
* * * * * *
5249086 TTTTTGAAATCTTTTATGCCCTAACAGATGCCCATAGGAATATAAAAAATT-T-AAATTTTTTTT
1 TTTTTGAAACCTTTTATCCCCTAACAGATGCCCATAAGAATATAAAAAATTATAAAATTTATCTC
*
5249149 GAAAATGTTAATTCAACTTAATTTTATTTATTTTTGAAAACACCATTTCATACCCTAATGGAAGC
66 GAAAATATTAATTCAACTTAATTTTATTTATTTTTGAAAACACCATTTCATACCCTAATGGAAGC
5249214 CTG-AAAGGATACAGAATGT
131 C-GAAAAGGATACAGAATGT
** *
5249233 TTTTTGGAAACCTTTTATACCCCTAATGGATGCCCATAAGAATATAAAAGATTAGAAAAAAATAA
1 TTTTT-GAAACCTTTTAT-CCCCTAACAGATGCCCATAAGAATATAAAAAATT--------ATAA
* * * * *
5249298 AATTTATCTCGAAAGTATTAATTCAATTTAATTTTATTTATTTTTGAAAATATCATTTCGTACCC
56 AATTTATCTCGAAAATATTAATTCAACTTAATTTTATTTATTTTTGAAAACACCATTTCATACCC
*
5249363 TAATGGAAGCCGAAAAGGATACGGAATG-
121 TAATGGAAGCCGAAAAGGATACAGAATGT
5249391 TTTTTGAAACC
1 TTTTTGAAACC
5249402 CTAATGGAAG
Statistics
Matches: 140, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
147 5 0.04
148 11 0.08
149 29 0.21
157 6 0.04
158 7 0.05
159 82 0.59
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.36
Consensus pattern (149 bp):
TTTTTGAAACCTTTTATCCCCTAACAGATGCCCATAAGAATATAAAAAATTATAAAATTTATCTC
GAAAATATTAATTCAACTTAATTTTATTTATTTTTGAAAACACCATTTCATACCCTAATGGAAGC
CGAAAAGGATACAGAATGT
Found at i:5249420 original size:40 final size:40
Alignment explanation
Indices: 5249359--5249439 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
5249349 ATCATTTCGT
*
5249359 ACCCTAATGGAAGCCGAAAAGGATACGGAATGTTTTTGAA
1 ACCCTAATGGAAGCCGAAAAGGATACGAAATGTTTTTGAA
* *
5249399 ACCCTAATGGAAGCTTG-AAAGGATATGAAATGTTTTTGAA
1 ACCCTAATGGAAGC-CGAAAAGGATACGAAATGTTTTTGAA
5249439 A
1 A
5249440 TCTTTTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (40 bp):
ACCCTAATGGAAGCCGAAAAGGATACGAAATGTTTTTGAA
Found at i:5249557 original size:195 final size:199
Alignment explanation
Indices: 5249200--5249594 Score: 554
Period size: 195 Copynumber: 2.0 Consensus size: 199
5249190 ACCATTTCAT
*
5249200 ACCCTAATGGAAGCCTGAAAGGATACAGAATGTTTTTTGGAAACCTTTTATACCCCTAATGGATG
1 ACCCTAATGGAAGCCTGAAAGGATACAGAATGTTTTTTGGAAACCTTTTATACCCCTAACGGATG
* *
5249265 CCCATAAGAATATAAAAGATTAGAAAAAAATAAAATTTATCTCGAAAGTATTAATTCAATTTAAT
66 CCCATAAGAATATAAAAGATTAGAAAAAAATAAAATTTATCCCAAAAGTATTAATTCAATTTAAT
* ** * * * **
5249330 TTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAGC-CGAAAAGGATACGGAATGTTT
131 TTCATTTATTTTCAAAAATACCATTTCGTACCCTAATAGAAGCTCGAAAA-GATACGAAACATTT
5249394 TTGAA
195 TTGAA
* * *
5249399 ACCCTAATGGAAGCTTGAAAGGATA-TGAAATG-TTTTT-GAAATCTTTTATACCCCT-ACGGAT
1 ACCCTAATGGAAGCCTGAAAGGATACAG-AATGTTTTTTGGAAACCTTTTATACCCCTAACGGAT
* *
5249460 GCCCAT-AGAAATATAAAAGATTTA-AAAAAATTAAAATTTATCCCAAAAGTA-TACTTCAATTT
65 GCCCATAAG-AATATAAAAGA-TTAGAAAAAAATAAAATTTATCCCAAAAGTATTAATTCAATTT
5249522 AATTTCATTTATTTTCAAAAATACCATTTCGTACCCTAATAGAAGCTCGAAAAGATACGAAACAT
128 AATTTCATTTATTTTCAAAAATACCATTTCGTACCCTAATAGAAGCTCGAAAAGATACGAAACAT
5249587 TTTTGAA
193 TTTTGAA
5249594 A
1 A
5249595 TCTTTTATAC
Statistics
Matches: 176, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
195 70 0.40
196 52 0.30
197 20 0.11
198 6 0.03
199 28 0.16
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (199 bp):
ACCCTAATGGAAGCCTGAAAGGATACAGAATGTTTTTTGGAAACCTTTTATACCCCTAACGGATG
CCCATAAGAATATAAAAGATTAGAAAAAAATAAAATTTATCCCAAAAGTATTAATTCAATTTAAT
TTCATTTATTTTCAAAAATACCATTTCGTACCCTAATAGAAGCTCGAAAAGATACGAAACATTTT
TGAA
Found at i:5250420 original size:14 final size:13
Alignment explanation
Indices: 5250395--5250430 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
5250385 ATGCTCGGAA
5250395 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
5250408 TTTTCTCTTTTTTC
1 TTTTCT-TTTTTTC
5250422 TTTT-TTTTT
1 TTTTCTTTTT
5250431 CACTTGCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 11 0.50
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:5251266 original size:166 final size:163
Alignment explanation
Indices: 5251063--5251443 Score: 518
Period size: 166 Copynumber: 2.3 Consensus size: 163
5251053 GTTTTTTGGA
* *
5251063 AAAAAAGAA-AATTTTAAGGCAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTGA-AAATG
1 AAAAAAGAAGAA-TTCAAGG-AAAAATTCAAAAACTCATGAAAATGAAATAATTTTTGAGAAAT-
* * * * * *
5251126 GATTTAATATAAAATAAATGATGATA-TTGATGAATTTTAATAATTAAAAACTAAGAAAAATCTC
63 AATTTAATATAAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACAAAGAAAAATCTC
5251190 TCC-AAAAAAATTACAAAGTAGAAAATAACGTATTTCG
128 -CCTAAAAAAATTACAAAGTAGAAAA-AACGTATTTCG
*
5251227 AAAAAAGAAGAATATCAAGGAAACAAATTCAAAAACTCATGAAAATGAAATAATTTTTGAGAACT
1 AAAAAAGAAGAAT-TCAAGG-AA-AAATTCAAAAACTCATGAAAATGAAATAATTTTTGAGAAAT
5251292 AATTTAATATAAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACAAAGAAAAATCTC
63 AATTTAATATAAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACAAAGAAAAATCTC
* * *
5251357 CCTAAAAAAATTACGAAGTAGAAAAAATGTATTTTG
128 CCTAAAAAAATTACAAAGTAGAAAAAACGTATTTCG
* * *
5251393 GAAAAAGGAGAATTAGAAGGAAAAATTCAAAAACTCATGAAAATGAAATAA
1 AAAAAAGAAGAATT-CAAGGAAAAATTCAAAAACTCATGAAAATGAAATAA
5251444 ATAATAATAT
Statistics
Matches: 194, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
164 39 0.20
165 12 0.06
166 84 0.43
167 59 0.30
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.27
Consensus pattern (163 bp):
AAAAAAGAAGAATTCAAGGAAAAATTCAAAAACTCATGAAAATGAAATAATTTTTGAGAAATAAT
TTAATATAAAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACAAAGAAAAATCTCCCT
AAAAAAATTACAAAGTAGAAAAAACGTATTTCG
Found at i:5251448 original size:135 final size:139
Alignment explanation
Indices: 5251303--5251578 Score: 384
Period size: 135 Copynumber: 2.0 Consensus size: 139
5251293 ATTTAATATA
* * * *
5251303 AAATAAATAATAATATTTGATAAATTTTAAAAATTAAAAACAAAGA-AAAATCTCCCTAAAAAAA
1 AAATAAATAATAATATATGATAAATTTTAAAAATTAAAAACAAAGATAAAACCCCCCGAAAAAAA
* ** *
5251367 TTACGAAGTAGAAAA-AATGTATTTTG-GAAAAA-GGAGAA-TT-AGAAGGAAAAATTCAAAAAC
66 TTACAAAGTAGAAAATAACATATTTTGAGAAAAAGGGA-AATTTCA-AAGAAAAAATTCAAAAAC
5251427 TCATGAAAATG
129 TCATGAAAATG
* *
5251438 AAATAAATAATAATATATGATGAATTTTAAAAATTAAAAACCAAGATAAAACCCCCCGAAAAAAA
1 AAATAAATAATAATATATGATAAATTTTAAAAATTAAAAACAAAGATAAAACCCCCCGAAAAAAA
* *
5251503 TTACAAAGTAGAAAATAACATTTTTTGAGAAAAAGGGAAATTTCAAAGAAAAAATTCAAAAATTC
66 TTACAAAGTAGAAAATAACATATTTTGAGAAAAAGGGAAATTTCAAAGAAAAAATTCAAAAACTC
5251568 ATGAAAATG
131 ATGAAAATG
5251577 AA
1 AA
5251579 TTAATTTTTG
Statistics
Matches: 123, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
135 43 0.35
136 29 0.24
137 8 0.07
138 8 0.07
139 34 0.28
140 1 0.01
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (139 bp):
AAATAAATAATAATATATGATAAATTTTAAAAATTAAAAACAAAGATAAAACCCCCCGAAAAAAA
TTACAAAGTAGAAAATAACATATTTTGAGAAAAAGGGAAATTTCAAAGAAAAAATTCAAAAACTC
ATGAAAATG
Found at i:5262102 original size:27 final size:25
Alignment explanation
Indices: 5262066--5262117 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
5262056 ACCATTAATT
5262066 TTATTATAATTATGAATATAATAAATA
1 TTATTATAATTA--AATATAATAAATA
*
5262093 TTATTATAATTAATTATAATAAATA
1 TTATTATAATTAAATATAATAAATA
5262118 ACAATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.50
27 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TTATTATAATTAAATATAATAAATA
Found at i:5263407 original size:13 final size:14
Alignment explanation
Indices: 5263365--5263538 Score: 59
Period size: 13 Copynumber: 12.4 Consensus size: 14
5263355 ATCATAATTA
5263365 TAATATATTTTATA-
1 TAATAT-TTTTATAT
5263379 TAATATTTTTACATAT
1 TAATATTTTT--ATAT
5263395 TAAT-TTTTTATAT
1 TAATATTTTTATAT
*
5263408 TATATAAATTTTA-A-
1 TA-AT-ATTTTTATAT
**
5263422 T-ATATTCATATAT
1 TAATATTTTTATAT
5263435 TAATATTATTT-T-T
1 TAATATT-TTTATAT
*
5263448 TTATATTGTATTATAT
1 TAATATT-T-TTATAT
** * *
5263464 TTTTA-TTATATTT
1 TAATATTTTTATAT
5263477 TAATTATTTTTATAT
1 TAA-TATTTTTATAT
*
5263492 TATATTATATTTTATGT
1 TA-A-TAT-TTTTATAT
5263509 T-ATA-TTTTA-AT
1 TAATATTTTTATAT
5263520 T-AT-TTTTTATAT
1 TAATATTTTTATAT
5263532 ATAATAT
1 -TAATAT
5263539 AATCATATTA
Statistics
Matches: 121, Mismatches: 17, Indels: 43
0.67 0.09 0.24
Matches are distributed among these distances:
11 13 0.11
12 10 0.08
13 25 0.21
14 24 0.20
15 22 0.18
16 19 0.16
17 8 0.07
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (14 bp):
TAATATTTTTATAT
Found at i:5263412 original size:5 final size:5
Alignment explanation
Indices: 5263402--5263561 Score: 62
Period size: 5 Copynumber: 31.4 Consensus size: 5
5263392 TATTAATTTT
* * * * *
5263402 TTATA TTATA -TAAA TTTTA ATATA TTCATA -TAT- TAATA TTAT- TT-TT
1 TTATA TTATA TTATA TTATA TTATA TT-ATA TTATA TTATA TTATA TTATA
* * * *
5263448 TTATA TTGTA TTATA TTTTTA TTATA TTTTAA TTATTT TTATA TTATA
1 TTATA TTATA TTATA -TTATA TTATA TTAT-A TTA-TA TTATA TTATA
* * * * * *
5263496 TTATA TTTTATG TTATA TTTTAA TTATT TTTTA TATATA ATATAA TCATA
1 TTATA --TTATA TTATA TTAT-A TTATA TTATA T-TATA TTAT-A TTATA
5263546 TTATA TTA-A TTATA TT
1 TTATA TTATA TTATA TT
5263562 TAAAATTATA
Statistics
Matches: 111, Mismatches: 29, Indels: 30
0.65 0.17 0.18
Matches are distributed among these distances:
3 1 0.01
4 15 0.14
5 67 0.60
6 23 0.21
7 5 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:5263417 original size:18 final size:20
Alignment explanation
Indices: 5263390--5263433 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
5263380 AATATTTTTA
* *
5263390 CATATTAATTTT-TTATATT
1 CATATAAATTTTAATATATT
5263409 -ATATAAATTTTAATATATT
1 CATATAAATTTTAATATATT
5263428 CATATA
1 CATATA
5263434 TTAATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
CATATAAATTTTAATATATT
Found at i:5263472 original size:11 final size:11
Alignment explanation
Indices: 5263441--5263497 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
5263431 ATATTAATAT
5263441 TATTTTT-TTA
1 TATTTTTATTA
*
5263451 TA-TTGTATTA
1 TATTTTTATTA
5263461 TATTTTTATTA
1 TATTTTTATTA
*
5263472 TATTTTAATTA
1 TATTTTTATTA
5263483 T-TTTTATATTA
1 TATTTT-TATTA
5263494 TATT
1 TATT
5263498 ATATTTTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 3 0.08
10 11 0.28
11 23 0.59
12 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:5263474 original size:40 final size:39
Alignment explanation
Indices: 5263438--5263561 Score: 119
Period size: 38 Copynumber: 3.1 Consensus size: 39
5263428 CATATATTAA
*
5263438 TATTATTTTTTTATATTGTATTATATTTT-TATTATATT
1 TATTATTTTTTTATATTATATTATATTTTATATTATATT
* *
5263476 T-TAATTATTTTTATATTATATTATATTTTATGTTATATTT
1 TATTATT-TTTTTATATTATATTATATTTTATATTATA-TT
* * *
5263516 TAATTATTTTTTATATATAATATAATCATATTATATTA-ATT
1 T-ATTATTTTTT-TATATTATATTAT-ATTTTATATTATATT
5263557 ATATT
1 -TATT
5263562 TAAAATTATA
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
37 4 0.06
38 22 0.31
39 6 0.09
40 3 0.04
41 9 0.13
42 17 0.24
43 9 0.13
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (39 bp):
TATTATTTTTTTATATTATATTATATTTTATATTATATT
Found at i:5263491 original size:17 final size:17
Alignment explanation
Indices: 5263469--5263531 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 17
5263459 TATATTTTTA
5263469 TTATATTTTAATTATTT
1 TTATATTTTAATTATTT
5263486 TTATATTATATTATATT-TTAT
1 TTATA-T-T-TTA-ATTATT-T
5263507 GTTATATTTTAATTATTTT
1 -TTATATTTTAATTA-TTT
5263526 TTATAT
1 TTATAT
5263532 ATAATATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
17 5 0.13
18 10 0.26
19 5 0.13
20 8 0.21
21 5 0.13
22 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTATATTTTAATTATTT
Found at i:5263492 original size:22 final size:23
Alignment explanation
Indices: 5263422--5263571 Score: 83
Period size: 22 Copynumber: 6.9 Consensus size: 23
5263412 TAAATTTTAA
*
5263422 TATATTCATATATTAA-TATTATTT
1 TATATT-ATATTTTAATTA-TATTT
*
5263446 T-T-TTATATTGT-ATTATATTT
1 TATATTATATTTTAATTATATTT
5263466 T-TATTATATTTTAATTAT-TTT
1 TATATTATATTTTAATTATATTT
5263487 TATA-T-TA---T-ATTATATTT
1 TATATTATATTTTAATTATATTT
* *
5263504 TATGTTATATTTTAATTATTTTT
1 TATATTATATTTTAATTATATTT
* * * *
5263527 TATA-TATAATATAATCATATTA
1 TATATTATATTTTAATTATATTT
*
5263549 TATTAATTATATTTAAAATTATA
1 TA-T-ATTATATTT-TAATTATA
5263572 AAATCTAATA
Statistics
Matches: 96, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
16 5 0.05
17 7 0.07
18 1 0.01
19 2 0.02
20 10 0.10
21 20 0.21
22 25 0.26
23 13 0.14
24 2 0.02
25 5 0.05
26 6 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (23 bp):
TATATTATATTTTAATTATATTT
Found at i:5263505 original size:27 final size:27
Alignment explanation
Indices: 5263399--5263522 Score: 101
Period size: 29 Copynumber: 4.4 Consensus size: 27
5263389 ACATATTAAT
*
5263399 TTTTTATATTATA-TAAATTTTAATATA
1 TTTTTATATTATATTATATTTTAAT-TA
** * *
5263426 TTCATATATTAATATTATTTTTTTA-TA
1 TTTTTATATT-ATATTATATTTTAATTA
*
5263453 TTGTATTATATTTTTATTATATTTTAATTA
1 TT-T-TTATA-TTATATTATATTTTAATTA
*
5263483 TTTTTATATTATATTATATTTTATGTTA
1 TTTTTATATTATATTATATTTTA-ATTA
5263511 TATTTTA-ATTAT
1 T-TTTTATATTAT
5263523 TTTTTATATA
Statistics
Matches: 77, Mismatches: 12, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
27 26 0.34
28 17 0.22
29 28 0.36
30 6 0.08
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTATATTATATTATATTTTAATTA
Found at i:5263511 original size:12 final size:12
Alignment explanation
Indices: 5263362--5263531 Score: 80
Period size: 12 Copynumber: 13.5 Consensus size: 12
5263352 TTTATCATAA
*
5263362 TTATAATATATT
1 TTATATTATATT
*
5263374 TTATATAATATTT
1 TTATATTATA-TT
*
5263387 TTACATATTAATTTT
1 TT--ATATT-ATATT
5263402 TTATATTATATAAAT
1 TTATATTATAT---T
*
5263417 TT-TAATATATT
1 TTATATTATATT
*
5263428 CATATATTAATATT
1 -TTATATT-ATATT
* *
5263442 ATT-T-TTTTATA
1 -TTATATTATATT
*
5263453 TTGTATTATATT
1 TTATATTATATT
5263465 TT-TATTATATT
1 TTATATTATATT
* *
5263476 TTAATTATTTTTATA
1 TT-A-TA-TTATATT
5263491 TTATATTATATT
1 TTATATTATATT
*
5263503 TTATGTTATATT
1 TTATATTATATT
*
5263515 TTA-ATTATTTT
1 TTATATTATATT
5263526 TTATAT
1 TTATAT
5263532 ATAATATAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
10 2 0.02
11 25 0.21
12 42 0.35
13 15 0.12
14 16 0.13
15 18 0.15
16 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (12 bp):
TTATATTATATT
Found at i:5263512 original size:39 final size:38
Alignment explanation
Indices: 5263445--5263539 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 38
5263435 TAATATTATT
*
5263445 TTTTTATATTGTATTATATTTTTATTATATTTTAATTA
1 TTTTTATATTATATTATATTTTTATTATATTTTAATTA
*
5263483 TTTTTATATTATATTATATTTTATGTTATATTTTAATTA
1 TTTTTATATTATATTATATTTT-TATTATATTTTAATTA
*
5263522 TTTTT-TATATATAATATA
1 TTTTTATAT-TATATTATA
5263540 ATCATATTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
38 24 0.46
39 28 0.54
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (38 bp):
TTTTTATATTATATTATATTTTTATTATATTTTAATTA
Found at i:5264432 original size:17 final size:16
Alignment explanation
Indices: 5264389--5264455 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
5264379 TTTTTTAATT
*
5264389 TTATATTAAAAATTATA
1 TTATATTAAATATT-TA
5264406 TTATAAATTAAATATTTA
1 TTAT--ATTAAATATTTA
* *
5264424 TTTTTATTAATTATTTA
1 -TTATATTAAATATTTA
*
5264441 TTATATTTAATATTT
1 TTATATTAAATATTT
5264456 TTAATTTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
16 12 0.29
17 15 0.37
18 2 0.05
19 12 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATATTAAATATTTA
Found at i:5264897 original size:24 final size:26
Alignment explanation
Indices: 5264865--5264917 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
5264855 AAAAAAAATA
5264865 TATATAAATAATTT-T-TTTATACAT
1 TATATAAATAATTTATATTTATACAT
* *
5264889 TATATAAATATTTTATATTTATATAT
1 TATATAAATAATTTATATTTATACAT
5264915 TAT
1 TAT
5264918 TAATTATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.52
25 1 0.04
26 11 0.44
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TATATAAATAATTTATATTTATACAT
Found at i:5265028 original size:17 final size:17
Alignment explanation
Indices: 5264971--5265031 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
5264961 TATTTTTTAC
*
5264971 AATATAA-TTATTGCTTA
1 AATATAATTTATT-ATTA
5264988 AATATATATTTATTTATT-
1 AATATA-ATTTA-TTATTA
**
5265006 TTTATAATTTATTATTA
1 AATATAATTTATTATTA
5265023 AATATAATT
1 AATATAATT
5265032 ATTTAAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
16 5 0.14
17 18 0.51
18 5 0.14
19 5 0.14
20 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
AATATAATTTATTATTA
Found at i:5265751 original size:24 final size:24
Alignment explanation
Indices: 5265706--5265770 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
5265696 AATTATTATG
*
5265706 TATTAATAATTTATTTTATTTAAA
1 TATTAATAATTTATATTATTTAAA
*
5265730 TATTAGTAGATTTATATT-TTT--A
1 TATTAATA-ATTTATATTATTTAAA
5265752 TATT-AT-ATTTATATTATTT
1 TATTAATAATTTATATTATTT
5265771 TTTATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.25
20 3 0.08
21 1 0.03
22 5 0.14
24 10 0.28
25 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (24 bp):
TATTAATAATTTATATTATTTAAA
Found at i:5265787 original size:11 final size:10
Alignment explanation
Indices: 5265742--5265801 Score: 50
Period size: 11 Copynumber: 5.6 Consensus size: 10
5265732 TTAGTAGATT
5265742 TATATTTTTA
1 TATATTTTTA
*
5265752 TATTATATTTA
1 TA-TATTTTTA
5265763 TATTATTTTT-
1 TA-TATTTTTA
5265773 TATATTATTTA
1 TATATT-TTTA
*
5265784 TATAACTTTTA
1 TAT-ATTTTTA
5265795 TCATATT
1 T-ATATT
5265802 AATAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.10
10 7 0.17
11 26 0.63
12 4 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TATATTTTTA
Found at i:5265793 original size:21 final size:21
Alignment explanation
Indices: 5265746--5265802 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
5265736 TAGATTTATA
* *
5265746 TTTTTATATTATATTTATATTAT
1 TTTTTATA-T-TATTTATATAAC
5265769 TTTTTATATTATTTATATAAC
1 TTTTTATATTATTTATATAAC
5265790 TTTTATCATATTA
1 TTTT-T-ATATTA
5265803 ATAATTAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.47
22 2 0.07
23 14 0.47
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATATTATTTATATAAC
Found at i:5265863 original size:17 final size:18
Alignment explanation
Indices: 5265837--5265885 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
5265827 CATGTTCATA
*
5265837 TATT-TATTTTATGTTTA-
1 TATTATATTTTA-ATTTAT
5265854 TATTAT-TTTTAATTTAT
1 TATTATATTTTAATTTAT
5265871 TATTATATTTTAATT
1 TATTATATTTTAATT
5265886 ATTTCTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.14
17 15 0.54
18 9 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TATTATATTTTAATTTAT
Found at i:5265888 original size:17 final size:17
Alignment explanation
Indices: 5265850--5265885 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
5265840 TTATTTTATG
5265850 TTTA-TATTATTTTTAA
1 TTTATTATTATTTTTAA
5265866 TTTATTATTATATTTTAA
1 TTTATTATTAT-TTTTAA
5265884 TT
1 TT
5265886 ATTTCTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATTATTATTTTTAA
Found at i:5266295 original size:2 final size:2
Alignment explanation
Indices: 5266290--5266325 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5266280 TTTCAATTTC
* *
5266290 AT AT AT GT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5266326 CATAAAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5268262 original size:20 final size:19
Alignment explanation
Indices: 5268233--5268282 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
5268223 TGATATTCAA
5268233 AATAACTTAAAACTAAAAT
1 AATAACTTAAAACTAAAAT
*
5268252 AATATACTTAAAA-TTAAAT
1 AATA-ACTTAAAACTAAAAT
5268271 CAA-AACTTAAAA
1 -AATAACTTAAAA
5268283 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.29
19 10 0.36
20 10 0.36
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAACTTAAAACTAAAAT
Found at i:5268282 original size:32 final size:33
Alignment explanation
Indices: 5268208--5268282 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
5268198 CAAAAGTAAA
* *
5268208 AAAACTTAAAATAATTGATATTCAAAATAACTT
1 AAAACTTAAAATAATTGATATTCAAAATAAATC
5268241 AAAAC-TAAAATAA-T-ATACTT-AAAATTAAATC
1 AAAACTTAAAATAATTGATA-TTCAAAA-TAAATC
5268272 AAAACTTAAAA
1 AAAACTTAAAA
5268283 ATTTAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
30 7 0.19
31 12 0.32
32 13 0.35
33 5 0.14
ACGTcount: A:0.60, C:0.09, G:0.01, T:0.29
Consensus pattern (33 bp):
AAAACTTAAAATAATTGATATTCAAAATAAATC
Found at i:5268855 original size:23 final size:23
Alignment explanation
Indices: 5268829--5268880 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
5268819 AAGGATCTGT
5268829 ATGTAAAGGAAAAGGGGCATATG
1 ATGTAAAGGAAAAGGGGCATATG
5268852 ATGTAAAGGAAAAGGGGCATATG
1 ATGTAAAGGAAAAGGGGCATATG
5268875 ATGTAA
1 ATGTAA
5268881 CAAAAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.19
Consensus pattern (23 bp):
ATGTAAAGGAAAAGGGGCATATG
Found at i:5268887 original size:23 final size:23
Alignment explanation
Indices: 5268829--5268888 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
5268819 AAGGATCTGT
*
5268829 ATGTAAAGGAAAAGGGGCATATG
1 ATGTAAAGAAAAAGGGGCATATG
*
5268852 ATGTAAAGGAAAAGGGGCATATG
1 ATGTAAAGAAAAAGGGGCATATG
5268875 ATGTAACA-AAAAAG
1 ATGTAA-AGAAAAAG
5268889 ATAAATGGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.30, T:0.17
Consensus pattern (23 bp):
ATGTAAAGAAAAAGGGGCATATG
Found at i:5275217 original size:2 final size:2
Alignment explanation
Indices: 5275210--5275244 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5275200 GTTTTTGAGT
5275210 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5275245 AATAAGAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5275526 original size:20 final size:20
Alignment explanation
Indices: 5275494--5275545 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
5275484 GCCGCAAAAT
5275494 AAAAATATAAAAAG-AAGAA
1 AAAAATATAAAAAGAAAGAA
*
5275513 AAAAATTATTAAAAGAAAGAA
1 AAAAA-TATAAAAAGAAAGAA
5275534 AATAAA-ATAAAA
1 AA-AAATATAAAA
5275546 CTGGATTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 5 0.18
20 13 0.46
21 7 0.25
22 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAATATAAAAAGAAAGAA
Found at i:5277783 original size:24 final size:24
Alignment explanation
Indices: 5277751--5277798 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5277741 ACATATATTA
*
5277751 TCAAATTTGAATACGGTTCAAAAG
1 TCAAATTTGAATACGATTCAAAAG
*
5277775 TCAAATTTGAATATGATTCAAAAG
1 TCAAATTTGAATACGATTCAAAAG
5277799 AAAACAACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (24 bp):
TCAAATTTGAATACGATTCAAAAG
Found at i:5280573 original size:17 final size:18
Alignment explanation
Indices: 5280494--5280598 Score: 74
Period size: 20 Copynumber: 5.6 Consensus size: 18
5280484 AATGTCTTAT
5280494 AATATTATTTATTATTAA
1 AATATTATTTATTATTAA
*
5280512 AACATTAATTATATAAATATTTTAA
1 AATATT-ATT-TAT---TA--TTAA
5280537 AATATTATAATTATTATTAA
1 AATATTAT--TTATTATTAA
5280557 AATATTATTTA-TATT--
1 AATATTATTTATTATTAA
* *
5280572 AATA-TAATCATTATTAA
1 AATATTATTTATTATTAA
5280589 AATATTATTT
1 AATATTATTT
5280599 TATAATTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
14 4 0.06
15 8 0.12
17 8 0.12
18 11 0.16
19 3 0.04
20 15 0.22
22 2 0.03
23 2 0.03
24 2 0.03
25 12 0.18
26 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTATTTATTATTAA
Found at i:5281022 original size:19 final size:20
Alignment explanation
Indices: 5280986--5281031 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
5280976 ATAATGTTAC
5280986 AATTTGTTATTAAAATAATA
1 AATTTGTTATTAAAATAATA
5281006 ATATTT-TTATT-AAATAATA
1 A-ATTTGTTATTAAAATAATA
5281025 AATTTGT
1 AATTTGT
5281032 ATGTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 6 0.25
21 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
AATTTGTTATTAAAATAATA
Found at i:5281081 original size:14 final size:15
Alignment explanation
Indices: 5281039--5281080 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5281029 TGTATGTTTA
*
5281039 ATATTATTCAAAA-T
1 ATATTATTAAAAATT
*
5281053 ATAAATATTAAAAATT
1 AT-ATTATTAAAAATT
5281069 ATATTATTAAAA
1 ATATTATTAAAA
5281081 TAATTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 18 0.78
16 3 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATTATTAAAAATT
Found at i:5281498 original size:20 final size:20
Alignment explanation
Indices: 5281463--5281500 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5281453 AATAATTATG
5281463 TTAATAAAAATAATTTAATT
1 TTAATAAAAATAATTTAATT
5281483 TTAATTAAAAAT-ATTTAA
1 TTAA-TAAAAATAATTTAA
5281501 ATATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATAAAAATAATTTAATT
Found at i:5281656 original size:20 final size:18
Alignment explanation
Indices: 5281614--5281666 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
5281604 GTTGCTGTTT
*
5281614 CAATTATAAATATTAATA
1 CAATAATAAATATTAATA
*
5281632 CAATAAATAAATTATTAATT
1 CAAT-AATAAA-TATTAATA
*
5281652 TAATAATAAATATTA
1 CAATAATAAATATTA
5281667 TTTCTATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 9 0.30
19 11 0.37
20 10 0.33
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
CAATAATAAATATTAATA
Found at i:5284114 original size:2 final size:2
Alignment explanation
Indices: 5284107--5284163 Score: 96
Period size: 2 Copynumber: 28.0 Consensus size: 2
5284097 ATGAGAGTAG
5284107 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5284149 TA TA TGA CA TA TA TA
1 TA TA T-A TA TA TA TA
5284164 ATTATATGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 51 0.98
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5286275 original size:17 final size:17
Alignment explanation
Indices: 5286253--5286292 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
5286243 TTAAAAATTT
5286253 ATATAAAATATAATA-AA
1 ATATAAAA-ATAATATAA
5286270 ATATAAAAATAATATAA
1 ATATAAAAATAATATAA
5286287 ATATAA
1 ATATAA
5286293 CTCAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATAAAAATAATATAA
Found at i:5287543 original size:21 final size:20
Alignment explanation
Indices: 5287504--5287563 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 20
5287494 CTGTTGATCA
*
5287504 TTGACTTTGACAATTGATTG
1 TTGACCTTGACAATTGATTG
*
5287524 TTGACCTTGATAAGTTGATTTTG
1 TTGACCTTGACAA-TTGA--TTG
* *
5287547 TTGACATTGACTATTGA
1 TTGACCTTGACAATTGA
5287564 CTTTGATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 11 0.34
21 4 0.12
22 4 0.12
23 13 0.41
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (20 bp):
TTGACCTTGACAATTGATTG
Found at i:5292950 original size:28 final size:28
Alignment explanation
Indices: 5292836--5293614 Score: 758
Period size: 28 Copynumber: 26.5 Consensus size: 28
5292826 CATTAACTTG
* * *
5292836 TGTGGGTTTTGAAAAGAGTCGCCACCGACT
1 TGTGGGCTTTGAAAGGA-T-GCCACTGACT
* *
5292866 CGTGTGGGCTTTGAAAAGAGTTACCACT-AGCT
1 --TGTGGGCTTTG-AAAG-GATGCCACTGA-CT
*
5292898 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
5292927 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
5292955 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5292983 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
5293011 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
5293039 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
5293068 TGTGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
5293097 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
5293125 TGTGGGCTTTGAAAGGGTGCTACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
5293153 TGTGGGCTTTAAAAAGATGCAACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5293181 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
5293209 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
5293238 CGTGGGCTTTGAAAAGAGTTGCCA-TCGACT
1 TGTGGGCTTTG-AAAG-GATGCCACT-GACT
* *
5293268 CGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
5293296 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* **
5293324 TGTATGGGCTTTGAAATGGGTTGCCACCAACTT
1 TG--TGGGCTTTGAAA--GGATGCCACTGAC-T
* * **
5293357 GTGTGGGCTTTGAAATGGGTTGCCCCCAACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * *
5293389 GTGTGGGCTTTGAAATAGGTTACCACCGACTT
1 -TGTGGGCTTTG-AA-AGGATGCCACTGAC-T
*
5293421 ATGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
5293450 TGTGTGAGCTTTCAAATGAGTTGCCACCGACTT
1 TGTG-G-GCTTTGAAA-G-GATGCCACTGAC-T
*
5293483 GTGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
5293512 TGTGTAGGCTTTTAAATGAGTTGCCACCGACTT
1 TGTG--GGCTTTGAAA-G-GATGCCACTGAC-T
*
5293545 GTGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
*
5293574 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
5293602 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
5293615 GAGATGAATG
Statistics
Matches: 644, Mismatches: 66, Indels: 78
0.82 0.08 0.10
Matches are distributed among these distances:
27 10 0.02
28 272 0.42
29 112 0.17
30 99 0.15
31 4 0.01
32 124 0.19
33 11 0.02
34 12 0.02
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:5293154 original size:170 final size:173
Alignment explanation
Indices: 5292831--5293614 Score: 899
Period size: 170 Copynumber: 4.4 Consensus size: 173
5292821 AGTGCCATTA
* * *
5292831 ACTTGTGTGGGTTTTGAAAAGAGTCGCCACCGACTCGTGTGGGCTTTGAAAAGAGTTACCACT-A
1 ACTTGTGTGGGCTTTGAAAAG-GT-GCCACTGACT--TGTGGGCTTTGAAAAGAG-TGCCACTGA
5292895 GCTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTG
61 -CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGG-TGCCACTGACTTGTG
* *
5292959 GGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAA-AGATGCCACTG
124 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGATGCCACCG
5293008 AC-T-TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
1 ACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
* *
5293071 GGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTAACTTGTGGGCTTTG
66 GGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
* * * *
5293136 AAAGGGTGCTACTGACTTGTGGGCTTT-AAAAAGATGCAACTG
131 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGATGCCACCG
* *
5293178 AC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTCGT
1 ACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
* *
5293241 GGGCTTTGAAAAGAGTTGCCA-TCGACTCGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
66 GGGCTTTGAAAAGAG-TGCCACT-GACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
* * * *
5293305 TGAAAGAGTGCCACTGACTTGTATGGGCTTTGAAATGGGTTGCCACCA
129 TGAAAGGGTGCCACTGACTTG--TGGGCTTTGAAA-GAGATGCCACCG
* * ** * *
5293353 ACTTGTGTGGGCTTTGAAATGGGTTGCCCCCAACTTGTGTGGGCTTTGAAATAG-GTTACCACCG
1 ACTTGTGTGGGCTTTGAAA-AGG-TGCCACTGAC-T-TGTGGGCTTTGAAA-AGAG-TGCCACTG
* * * *
5293417 ACTTATGTGGGCTTTGAAATGA-TGCCACTGACTTGTGTGAGCTTTCAAATGAGTTGCCACCGAC
60 AC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG-G-GCTTTGAAA--AGGTGCCACTGAC
* * * *
5293481 TTGTGTGGGCTTTGAAATGATGCCACTGACTTGTGTAGGCTTTTAAATGAGTTGCCACCG
119 -T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTG--GGCTTTGAAA-GAGATGCCACCG
* * *
5293541 ACTTGTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGT
1 ACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
5293605 GGGCTTTGAA
66 GGGCTTTGAA
5293615 GAGATGAATG
Statistics
Matches: 531, Mismatches: 47, Indels: 55
0.84 0.07 0.09
Matches are distributed among these distances:
169 3 0.01
170 179 0.34
171 86 0.16
173 17 0.03
174 5 0.01
175 23 0.04
176 2 0.00
177 16 0.03
178 3 0.01
179 7 0.01
180 14 0.03
181 16 0.03
182 32 0.06
183 6 0.01
184 34 0.06
185 1 0.00
186 19 0.04
187 2 0.00
188 66 0.12
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (173 bp):
ACTTGTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGT
GGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTG
AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGATGCCACCG
Found at i:5294846 original size:21 final size:19
Alignment explanation
Indices: 5294820--5294892 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 19
5294810 ATCTGGACCC
5294820 TTTTCTTGTTTTTTTGCTATT
1 TTTTCTTGTTTTTTTG-T-TT
5294841 TTTTCTTGGTTTTTTT-TTGT
1 TTTTCTT-GTTTTTTTGTT-T
5294861 TTTT-TTG-TTTTTTGTTT
1 TTTTCTTGTTTTTTTGTTT
*
5294878 TTTTTTTGTTTTTTT
1 TTTTCTTGTTTTTTT
5294893 TTTGGTATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
17 11 0.23
18 6 0.13
19 9 0.19
20 6 0.13
21 7 0.15
22 8 0.17
ACGTcount: A:0.01, C:0.04, G:0.11, T:0.84
Consensus pattern (19 bp):
TTTTCTTGTTTTTTTGTTT
Found at i:5294854 original size:1 final size:1
Alignment explanation
Indices: 5294850--5294895 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
5294840 TTTTTCTTGG
* * * *
5294850 TTTTTTTTTGTTTTTTTGTTTTTTGTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5294896 GGTATAAAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:5294871 original size:15 final size:15
Alignment explanation
Indices: 5294853--5294896 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
5294843 TTCTTGGTTT
5294853 TTTTTTGTTTTTTTG
1 TTTTTTGTTTTTTTG
5294868 TTTTTTGTTTTTTT-
1 TTTTTTGTTTTTTTG
5294882 TTTGTTT-TTTTTTTG
1 TTT-TTTGTTTTTTTG
5294897 GTATAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
TTTTTTGTTTTTTTG
Found at i:5294872 original size:18 final size:17
Alignment explanation
Indices: 5294820--5294895 Score: 80
Period size: 18 Copynumber: 4.1 Consensus size: 17
5294810 ATCTGGACCC
*
5294820 TTTTCTTGTTTTTTTGCTAT
1 TTTTTTTGTTTTTTT--T-T
5294840 TTTTTCTTGGTTTTTTTTT
1 TTTTT-TT-GTTTTTTTTT
5294859 GTTTTTTTGTTTTTTGTTT
1 -TTTTTTTGTTTTTT-TTT
5294878 TTTTTTTGTTTTTTTTT
1 TTTTTTTGTTTTTTTTT
5294895 T
1 T
5294896 GGTATAAAGG
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
17 4 0.08
18 21 0.41
19 6 0.12
20 10 0.20
21 2 0.04
22 8 0.16
ACGTcount: A:0.01, C:0.04, G:0.11, T:0.84
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTTT
Found at i:5294879 original size:26 final size:27
Alignment explanation
Indices: 5294841--5294892 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
5294831 TTTTGCTATT
5294841 TTTTCTTGGTTTTTTTTTGTTTTTTTG
1 TTTTCTTGGTTTTTTTTTGTTTTTTTG
*
5294868 TTTT-TTGTTTTTTTTTTGTTTTTTT
1 TTTTCTTGGTTTTTTTTTGTTTTTTT
5294893 TTTGGTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.87
Consensus pattern (27 bp):
TTTTCTTGGTTTTTTTTTGTTTTTTTG
Found at i:5294894 original size:11 final size:11
Alignment explanation
Indices: 5294828--5294896 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 11
5294818 CCTTTTCTTG
5294828 TTTTTTTGCTATT
1 TTTTTTTG-T-TT
*
5294841 TTTTCTTGGTTTT
1 TTTT-TTTG-TTT
*
5294854 TTTTTGTTTTTT
1 TTTTT-TTGTTT
5294866 TGTTTTTTGTTT
1 T-TTTTTTGTTT
5294878 TTTTTTTGTTT
1 TTTTTTTGTTT
5294889 TTTTTTTG
1 TTTTTTTG
5294897 GTATAAAGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
11 18 0.38
12 11 0.23
13 15 0.31
14 4 0.08
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:5297582 original size:28 final size:28
Alignment explanation
Indices: 5297549--5297622 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
5297539 ATAAAGCCAG
* *
5297549 GGTTGGAGTATCCCC-TTGGAAGTAACGA
1 GGTTGGAGTATCCCCGAT-GAAATAACGA
5297577 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGATGAAATAACGA
* *
5297605 GGTTGGAGTGTCCTCGAT
1 GGTTGGAGTATCCCCGAT
5297623 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGA
Found at i:5297756 original size:236 final size:237
Alignment explanation
Indices: 5297333--5297955 Score: 600
Period size: 236 Copynumber: 2.6 Consensus size: 237
5297323 TTTTGGAGAT
* * * *
5297333 AATAACGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGAATCCCCGATTGTGAAAAA-
1 AATAACGAGGTTGGAGTAT-CCC-CGATGAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAAT
* * * * * ** * *
5297396 TCGATGATTTAG-AAATAAGA-CAAGGGTTGAAGTGTCCCCGATTAT-AGAAAA-TAGATGTTTC
64 TAG-TG-TTTCGAAAATAAAATC-AGAGTTGGAGAATCCCCGATTGTGA-AAAATTAG-TGTTTT
** * * * * * * ***
5297457 AAAAATAAAGTCGGGATTGGAGTATCCCGT-GAAAATAATAGG-GTTGAAGTATCCCCAATTATG
124 AAAAATAAAACCGGGGTTCGAGTATCCCCTCAAAAATAA-CGGAGTTGGAGTATCCTTGATTATG
* * ***
5297520 AGAAATCAATATTTTGGAAATA-AAGCCAGGGTTGGAGTATCCCCTTGGA
188 AAAAATCAATATTTTAGAAATATAAGCCAGGGTTGGAGTATCCCCTCAAA
* * *
5297569 AGTAACGAGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTGTCCTCGATTGTGAAAAATT
1 AATAACGAGGTTGGAGTATCCCCGATG-AATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATT
* * * * * * *
5297634 AGTGTTTTGGAAATAAAATCGGAGTTGGA-AATCCCCGATTGTGGAGAATTGGTGTTTTAGAAAT
65 AGTGTTTCGAAAATAAAATCAGAGTTGGAGAATCCCCGATTGTGAAAAATTAGTGTTTTAAAAAT
* * *
5297698 AAAGCTGGGGTTCGAGTATCCCCTCAAAAATAACGGAGTTGGAGTATCCTTGATTATGAAAAATT
130 AAAACCGGGGTTCGAGTATCCCCTCAAAAATAACGGAGTTGGAGTATCCTTGATTATGAAAAATC
* * * **
5297763 GATGTTTTAGAAATATAATCGGGGGTTGGAGTATCCCCTCAAA
195 AATATTTTAGAAATATAAGCCAGGGTTGGAGTATCCCCTCAAA
* * * * *
5297806 AATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTG
1 AATAACGAGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTA
* *
5297871 GTGTTTCGAAAATAAAATCAGAGTTGGAGTATCTCCGATTGTGAAAAATTAGTGTTTTAAAAATA
66 GTGTTTCGAAAATAAAATCAGAGTTGGAGAATCCCCGATTGTGAAAAATTAGTGTTTTAAAAATA
*
5297936 AAACCGGGGTTGGAGTATCC
131 AAACCGGGGTTCGAGTATCC
5297956 TCGATTATGA
Statistics
Matches: 313, Mismatches: 63, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
234 3 0.01
235 51 0.16
236 163 0.52
237 96 0.31
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (237 bp):
AATAACGAGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTA
GTGTTTCGAAAATAAAATCAGAGTTGGAGAATCCCCGATTGTGAAAAATTAGTGTTTTAAAAATA
AAACCGGGGTTCGAGTATCCCCTCAAAAATAACGGAGTTGGAGTATCCTTGATTATGAAAAATCA
ATATTTTAGAAATATAAGCCAGGGTTGGAGTATCCCCTCAAA
Found at i:5297776 original size:79 final size:80
Alignment explanation
Indices: 5297680--5297826 Score: 242
Period size: 80 Copynumber: 1.9 Consensus size: 80
5297670 GATTGTGGAG
* *
5297680 AATTGGTGTTTTAGAAATA-AAGCTGGGGTTCGAGTATCCCCTCAAAAATAACGGAGTTGGAGTA
1 AATTGATGTTTTAGAAATATAAGCGGGGGTTCGAGTATCCCCTCAAAAATAACGGAGTTGGAGTA
5297744 TCCTTGATTATGAAA
66 TCCTTGATTATGAAA
* * *
5297759 AATTGATGTTTTAGAAATATAATCGGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTA
1 AATTGATGTTTTAGAAATATAAGCGGGGGTTCGAGTATCCCCTCAAAAATAACGGAGTTGGAGTA
5297824 TCC
66 TCC
5297827 CCGATGATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
79 18 0.29
80 44 0.71
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (80 bp):
AATTGATGTTTTAGAAATATAAGCGGGGGTTCGAGTATCCCCTCAAAAATAACGGAGTTGGAGTA
TCCTTGATTATGAAA
Found at i:5297846 original size:27 final size:27
Alignment explanation
Indices: 5297784--5297858 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
5297774 AATATAATCG
* *
5297784 GGGGTTGGAGTATCCCCTCAAAAATAAC
1 GGGGTTGGAGTATCCCC-GATAAATAAC
* *
5297812 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATAAATAAC
5297839 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
5297859 TGTGGAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 26 0.60
28 17 0.40
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATAAATAAC
Found at i:5297919 original size:51 final size:50
Alignment explanation
Indices: 5297842--5297972 Score: 163
Period size: 51 Copynumber: 2.6 Consensus size: 50
5297832 GATTAACGGG
* * *
5297842 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTCGAAAATAAAATCAGA
1 GTTGGAGTAT-CCCGATTGTGAAAAATTGGTGTTTCAAAAATAAAACCAGA
* * * *
5297893 GTTGGAGTATCTCCGATTGTGAAAAATTAGTGTTTTAAAAATAAAACCGGG
1 GTTGGAGTATC-CCGATTGTGAAAAATTGGTGTTTCAAAAATAAAACCAGA
*
5297944 GTTGGAGTATCCTCGATTATGAAAAATTG
1 GTTGGAGTATCC-CGATTGTGAAAAATTG
5297973 AGAAACTTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 2 0.03
51 67 0.97
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (50 bp):
GTTGGAGTATCCCGATTGTGAAAAATTGGTGTTTCAAAAATAAAACCAGA
Found at i:5301776 original size:20 final size:20
Alignment explanation
Indices: 5301751--5301907 Score: 98
Period size: 20 Copynumber: 7.8 Consensus size: 20
5301741 ATTTCACAAT
5301751 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
5301771 TTGTATCGATACATTTTGGGTTTACCCA
1 TTGTATCGATACA--TT--G-TT---CA
* *
5301799 GATGTATCGATATATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
* *
5301820 TTGTATCGATACATTGCTCC
1 TTGTATCGATACATTGTTCA
5301840 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
*
5301853 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
5301873 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
5301893 ATGTATCGATACATT
1 TTGTATCGATACATT
5301908 CAAGCATTTT
Statistics
Matches: 109, Mismatches: 10, Indels: 36
0.70 0.06 0.23
Matches are distributed among these distances:
13 11 0.10
15 1 0.01
18 1 0.01
19 1 0.01
20 70 0.64
21 3 0.03
22 2 0.02
23 2 0.02
24 1 0.01
25 2 0.02
27 2 0.02
28 2 0.02
29 11 0.10
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:5301860 original size:33 final size:33
Alignment explanation
Indices: 5301818--5301887 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
5301808 ATATATTTTG
*
5301818 CATTGTATCGATACATTGCTCCTTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
5301851 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
5301884 CATT
1 CATT
5301888 TTACAATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCGATA
Found at i:5301887 original size:13 final size:13
Alignment explanation
Indices: 5301840--5301868 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5301830 ACATTGCTCC
5301840 TTGTATCGATACA
1 TTGTATCGATACA
5301853 TTGTATCGATACA
1 TTGTATCGATACA
5301866 TTG
1 TTG
5301869 CTCATTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5304249 original size:51 final size:51
Alignment explanation
Indices: 5304189--5304303 Score: 203
Period size: 51 Copynumber: 2.3 Consensus size: 51
5304179 TATTTTCGAA
* * *
5304189 GGGATACTCCAACTCCGGTTTTATTTCTAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATAG
5304240 GGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATAG
1 GGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATAG
5304291 GGGATACTCCAAC
1 GGGATACTCCAAC
5304304 CCCGTTATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATAG
Found at i:5304322 original size:79 final size:79
Alignment explanation
Indices: 5304239--5304545 Score: 368
Period size: 79 Copynumber: 3.9 Consensus size: 79
5304229 TTTCACAATC
*
5304239 GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
*
5304304 CCCGTTATTTCCAA
66 CCCGTTATTTTCAA
* ** * * * *
5304318 GGGGATACTTCAACCCCGACCTTATTTCTAAATCATCAATTTTTCACAATTGGGGATACTTCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
* *
5304383 CTCGTTATTTTTAA
66 CCCGTTATTTTCAA
* * *
5304397 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCGATTTTT-ATAATCA-GGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTTCACAAT-AGGGGATACTCCA
* * *
5304459 ACCCTGTAATTTTCGA
64 ACCCCGTTATTTTCAA
* * * * * *
5304475 GGGGATACTCCAACCCCAATTTTATTTCTAGAACACCAATTTTCCATAATCGGGGATACTCCAGC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
5304540 CCCGTT
66 CCCGTT
5304546 TTAATCTCCA
Statistics
Matches: 188, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
78 63 0.34
79 125 0.66
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
CCCGTTATTTTCAA
Found at i:5304343 original size:130 final size:128
Alignment explanation
Indices: 5304110--5304382 Score: 320
Period size: 130 Copynumber: 2.1 Consensus size: 128
5304100 ATTTCTCATC
* * * *
5304110 TCGGGGATACTTCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCATCGGGGATACTCTAAC
1 TCGGGGATACTTCAACTCCCGATTTCATTTCCAAAACACCAATTTTTCATAGGGGATACTCCAAC
* * * * ***
5304174 TCTGTTATTTTCGAAGGGATACTCCAACTCCGGTTTTATTTCTAAAAT-ACCAATTTTTCACAA
66 CCCGTTATTTTCCAAGGGATACTCCAACCCCGACCTTATTTCT-AAATCACCAATTTTTCACAA
* * *
5304237 TCGGGGATACTCCAACT-CCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCC
1 TCGGGGATACTTCAACTCCCGATTTCATTTCCAAAACACCAATTTTT--C-ATAGGGGATACTCC
* *
5304301 AACCCCGTTA-TTTCCAAGGGGATACTTCAACCCCGACCTTATTTCTAAATCATCAATTTTTCAC
63 AACCCCGTTATTTTCCAA-GGGATACTCCAACCCCGACCTTATTTCTAAATCACCAATTTTTCAC
5304365 AA
127 AA
*
5304367 TTGGGGATACTTCAAC
1 TCGGGGATACTTCAAC
5304383 CTCGTTATTT
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
127 39 0.32
128 1 0.01
129 11 0.09
130 71 0.58
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (128 bp):
TCGGGGATACTTCAACTCCCGATTTCATTTCCAAAACACCAATTTTTCATAGGGGATACTCCAAC
CCCGTTATTTTCCAAGGGATACTCCAACCCCGACCTTATTTCTAAATCACCAATTTTTCACAA
Found at i:5304530 original size:157 final size:158
Alignment explanation
Indices: 5304239--5304534 Score: 393
Period size: 157 Copynumber: 1.9 Consensus size: 158
5304229 TTTCACAATC
*
5304239 GGGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
* * * * * *
5304304 CCCGTTATTTCCAAGGGGATACTTCAACCCCGACCTTATTTCTAAATCATCAATTTTTCACAATT
66 CCCGTAATTTCCAAGGGGATACTCCAACCCCAACCTTATTTCTAAATCACCAATTTTCCACAATC
5304369 GGGGATACTTCAACCTCGTTATTTTTAA
131 GGGGATACTTCAACCTCGTTATTTTTAA
* * *
5304397 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCGATTTTT-ATAATCA-GGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTTCACAAT-AGGGGATACTCCA
* * * ** *
5304459 ACCCTGTAATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCTAGAA-CACCAATTTTCCATA
64 ACCCCGTAATTTCCAAGGGGATACTCCAACCCCAACCTTATTTCTA-AATCACCAATTTTCCACA
5304523 ATCGGGGATACT
128 ATCGGGGATACT
5304535 CCAGCCCCGT
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
157 77 0.65
158 42 0.35
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (158 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAATAGGGGATACTCCAAC
CCCGTAATTTCCAAGGGGATACTCCAACCCCAACCTTATTTCTAAATCACCAATTTTCCACAATC
GGGGATACTTCAACCTCGTTATTTTTAA
Found at i:5307521 original size:19 final size:19
Alignment explanation
Indices: 5307497--5307535 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5307487 AAATAATGGG
*
5307497 AATGAATAGCAAGAAAAAA
1 AATGAACAGCAAGAAAAAA
* *
5307516 AATGAACATCAATAAAAAA
1 AATGAACAGCAAGAAAAAA
5307535 A
1 A
5307536 GAGTGGCCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (19 bp):
AATGAACAGCAAGAAAAAA
Found at i:5315163 original size:15 final size:15
Alignment explanation
Indices: 5315138--5315180 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
5315128 TTCAACCAAA
5315138 AATATATATATATACT
1 AATA-ATATATATACT
5315154 AATAATATATATACT
1 AATAATATATATACT
**
5315169 TTTAATATATAT
1 AATAATATATAT
5315181 TTAATCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAATATATATACT
Found at i:5315768 original size:15 final size:16
Alignment explanation
Indices: 5315744--5315776 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5315734 TTGATTTCTG
*
5315744 TATATTTTTATAA-AA
1 TATATATTTATAATAA
5315759 TATATATTTATAATAA
1 TATATATTTATAATAA
5315775 TA
1 TA
5315777 AAAAATGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATTTATAATAA
Found at i:5319491 original size:33 final size:34
Alignment explanation
Indices: 5319452--5319528 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 34
5319442 ATTCAAATGT
5319452 ATCGATACATTGGTCCAAAGGT-CAAAA-TTTAA
1 ATCGATACATTGGTCCAAAGGTACAAAAGTTTAA
*
5319484 ATTCGATACATTGGTCCAACGGTACAAAAGTTTTAA
1 A-TCGATACATTGGTCCAAAGGTACAAAAG-TTTAA
5319520 ATCGATACA
1 ATCGATACA
5319529 ATTGTATCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 1 0.03
33 20 0.50
34 5 0.12
35 8 0.20
36 6 0.15
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (34 bp):
ATCGATACATTGGTCCAAAGGTACAAAAGTTTAA
Found at i:5319622 original size:13 final size:13
Alignment explanation
Indices: 5319604--5319630 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5319594 CTATTTTTCT
5319604 TTGTATCGATACA
1 TTGTATCGATACA
5319617 TTGTATCGATACA
1 TTGTATCGATACA
5319630 T
1 T
5319631 GGATCTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5322202 original size:51 final size:51
Alignment explanation
Indices: 5322139--5322361 Score: 241
Period size: 51 Copynumber: 4.3 Consensus size: 51
5322129 TTATTTCCAA
* * * *** *
5322139 GGGGATACTCCAACCCCAACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
* * * *
5322190 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA--TTTTTCACAATC
* * * **
5322243 GGGGATACTCCAACCCCGGTTTTATTTTCAACACACCAATTTTTCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTC-ACAATC
*
5322295 GGGGATACTCCAACTCCGATTTTATTTCCAAAA-ACACAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACAC-CAATTTTTCACAATC
*
5322346 GAGGATACTCCAACCC
1 GGGGATACTCCAACCC
5322362 TCGTTACTTC
Statistics
Matches: 144, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
51 57 0.40
52 42 0.29
53 45 0.31
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:5322257 original size:53 final size:51
Alignment explanation
Indices: 5322178--5322361 Score: 205
Period size: 53 Copynumber: 3.5 Consensus size: 51
5322168 AAAATATTGA
*
5322178 TTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
1 TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATT-CTAAAACAC-AATT
* *
5322231 TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAACACACCAATT
1 TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTCT-AAAACA-CAATT
* * * *
5322284 TTTCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACAA--
1 TTT-TTCACAATCGGGGATACTCCAACCCCGGTTTTA-TT-CTAAAACACAATT
*
5322334 TTTTTCACAATCGAGGATACTCCAACCC
1 TTTTTCACAATCGGGGATACTCCAACCC
5322362 TCGTTACTTC
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
49 2 0.02
50 3 0.03
51 18 0.16
52 30 0.27
53 56 0.50
54 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (51 bp):
TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTCTAAAACACAATT
Found at i:5322495 original size:79 final size:79
Alignment explanation
Indices: 5322295--5322550 Score: 239
Period size: 79 Copynumber: 3.2 Consensus size: 79
5322285 TTCTTTAATC
* * * * * * * *
5322295 GGGGATACTCCAACTCCGATTTTATTTCCAAAA-ACACAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAATA-TCGATTTCTCACAACCGGGGATACTCCAA
* *
5322359 CCCTCGTTACTTCCGA
65 CCC-CGTTATTTTCGA
* * * **
5322375 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATTTCTCACAACCGGGGATACTCCAAC
5322440 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * * ** * *
5322454 GGGGATACTCCAATCCCGATTTTTTTTTC-TAATCATCGATTTCTCACAACCGGGGATACTCCAG
1 GGGGATACTCCAACCCCGACTTTATTCCCAAAAT-ATCGATTTCTCACAACCGGGGATACTCCAA
5322518 CCCCGTTATTTT-GAA
65 CCCCGTTATTTTCG-A
* *
5322533 GGGAACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
5322551 TTATTATCTC
Statistics
Matches: 145, Mismatches: 28, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
78 4 0.03
79 86 0.59
80 54 0.37
81 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.30
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATTTCTCACAACCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:5328427 original size:118 final size:116
Alignment explanation
Indices: 5328309--5328522 Score: 270
Period size: 118 Copynumber: 1.8 Consensus size: 116
5328299 ATTTAAAAAT
* *
5328309 TTAATAAATAATAATATATTAATTATTATTTT-T-AATAAAAAATAATATTTAATTAATTTTAAA
1 TTAA-AAAGAATAATATATT-ATTATT-TTTTATAAATAAAAAATAATATTTAATTAAGTTTAAA
* * *
5328372 AAAATTACATTCATAAATTAAAATATTCATTATTTTTAAAATAAAAAAATTAAA
63 AAAATTACATTAACAAATTAAAATATTAATTATTTTTAAAATAAAAAAATTAAA
* ** * * *
5328426 TTAAAAAGGATTTTTTATTATTATTTTTTAATAAAATTAAAAATCATATTTAATTAAGTTTAAAA
1 TTAAAAAGAATAATATATTATTATTTTTT-AT-AAATAAAAAATAATATTTAATTAAGTTTAAAA
5328491 AAATTACATTAACAAATTAAAATATTAATTAT
64 AAATTACATTAACAAATTAAAATATTAATTAT
5328523 ATATTTTATA
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
114 4 0.05
115 6 0.07
116 11 0.13
117 4 0.05
118 57 0.70
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (116 bp):
TTAAAAAGAATAATATATTATTATTTTTTATAAATAAAAAATAATATTTAATTAAGTTTAAAAAA
ATTACATTAACAAATTAAAATATTAATTATTTTTAAAATAAAAAAATTAAA
Found at i:5328549 original size:110 final size:112
Alignment explanation
Indices: 5328346--5328622 Score: 357
Period size: 110 Copynumber: 2.4 Consensus size: 112
5328336 ATTTTTAATA
* * *
5328346 AAAAATAATATTTAATTAATTTTAAAAAAATTACATTCATAAATTAAAATATTCATTATTTTTAA
1 AAAAATAATATTTAATTAATTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTT--
5328411 AATAAAAAAATTAAATTAAAAAGGATTTTTTATTATTATTTTTTAATAAAATT
64 -AT--AAAAA-TAAATTAAAAAGGATTTTTTATTATTATTTTTTAATAAAATT
* *
5328464 AAAAATCATATTTAATTAAGTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATATATTT
1 AAAAATAATATTTAATTAATTTTAAAAAAATTACATTAACAAATTAAAATATTAATTAT-T-TTT
* *
5328529 -T-ATAA-AAA-TAAAAAGTATTTTTTATTATTATTTTTTAATAAAATT
64 ATAAAAATAAATTAAAAAGGATTTTTTATTATTATTTTTTAATAAAATT
* *
5328574 AAAAATAATATTTAATTAAATTTTAAAAAATTTATATTAAC-AATTAAAA
1 AAAAATAATATTTAATT-AATTTTAAAAAAATTACATTAACAAATTAAAA
5328623 AATAACATTT
Statistics
Matches: 145, Mismatches: 11, Indels: 14
0.85 0.06 0.08
Matches are distributed among these distances:
110 60 0.41
111 23 0.16
113 3 0.02
116 1 0.01
118 54 0.37
119 1 0.01
120 3 0.02
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (112 bp):
AAAAATAATATTTAATTAATTTTAAAAAAATTACATTAACAAATTAAAATATTAATTATTTTTAT
AAAAATAAATTAAAAAGGATTTTTTATTATTATTTTTTAATAAAATT
Found at i:5328588 original size:22 final size:22
Alignment explanation
Indices: 5328562--5328634 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
5328552 ATTATTATTT
5328562 TTTAATAAAATTAAAAATAATA
1 TTTAATAAAATTAAAAATAATA
* *
5328584 TTTAATTAAATTTTAAAA-AAT-
1 TTTAA-TAAAATTAAAAATAATA
* *
5328605 TTATATTAACAATTAAAAAATAACA
1 TT-TAATAA-AATT-AAAAATAATA
5328630 TTTAA
1 TTTAA
5328635 GGAATTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
21 5 0.13
22 13 0.34
23 14 0.37
24 4 0.11
25 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAATAAAATTAAAAATAATA
Found at i:5329060 original size:124 final size:126
Alignment explanation
Indices: 5328927--5329264 Score: 439
Period size: 124 Copynumber: 2.7 Consensus size: 126
5328917 ATTTTTTTAA
5328927 TTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTTA
1 TTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTTA
* *
5328992 AACTTAATTAAACTGA-TATTTTTTATTTTATT-AAAAT-T-ATAATAAAAAGCCATTTCTA-T
66 AACTTAATTAAA-T-ATTATTTTTAATTTTATTAAAAATATAATAATAAAAACCCATTT-TATT
*
5329051 TTTAAAATTTCTTATTTTTATAAAAACATAATAATTAA-ATTTTAATTTGTTAATGT-AATTTTT
1 TTTAAAATTTTTTA-TTTT-TAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTT
5329114 TAAACTTAATTAAATATTATTTTTAATTTTATTAAAAATAATAATAATAAAAACCCATTTTATT
64 TAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAT-ATAATAATAAAAACCCATTTTATT
* * *
5329178 TTTATTTAATTTTTT-TATTTT--AAA-A-AATACTTAATATTTTAATTTGTTAATATAAATTTC
1 TTTA--AAATTTTTTAT-TTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTT-
*
5329238 TTTAAAGTTAATTAAATATTATTTTTA
62 TTTAAACTTAATTAAATATTATTTTTA
5329265 TTAAAAATAA
Statistics
Matches: 192, Mismatches: 8, Indels: 26
0.85 0.04 0.12
Matches are distributed among these distances:
122 1 0.01
123 24 0.12
124 57 0.30
125 30 0.16
126 47 0.24
127 23 0.12
128 3 0.02
129 7 0.04
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (126 bp):
TTTAAAATTTTTTATTTTTAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTTTA
AACTTAATTAAATATTATTTTTAATTTTATTAAAAATATAATAATAAAAACCCATTTTATT
Found at i:5329517 original size:17 final size:18
Alignment explanation
Indices: 5329495--5329528 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5329485 GCGACATAGT
*
5329495 TTAAAAT-TTAAAGATAA
1 TTAAAATCTAAAAGATAA
5329512 TTAAAATCTAAAAGATA
1 TTAAAATCTAAAAGATA
5329529 TGAGTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (18 bp):
TTAAAATCTAAAAGATAA
Found at i:5329760 original size:11 final size:11
Alignment explanation
Indices: 5329744--5329824 Score: 108
Period size: 11 Copynumber: 7.4 Consensus size: 11
5329734 TTATTACTTT
5329744 TTATTTATAAA
1 TTATTTATAAA
* *
5329755 TTATTTTTAAT
1 TTATTTATAAA
5329766 TTATTTATAAA
1 TTATTTATAAA
* *
5329777 TTATTTTTAAT
1 TTATTTATAAA
5329788 TTATTTATAAA
1 TTATTTATAAA
* *
5329799 TTATTTTTAAT
1 TTATTTATAAA
5329810 TTATTTATAAA
1 TTATTTATAAA
5329821 TTAT
1 TTAT
5329825 ACAAATTTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 58 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:5329771 original size:22 final size:22
Alignment explanation
Indices: 5329743--5329824 Score: 164
Period size: 22 Copynumber: 3.7 Consensus size: 22
5329733 ATTATTACTT
5329743 TTTATTTATAAATTATTTTTAA
1 TTTATTTATAAATTATTTTTAA
5329765 TTTATTTATAAATTATTTTTAA
1 TTTATTTATAAATTATTTTTAA
5329787 TTTATTTATAAATTATTTTTAA
1 TTTATTTATAAATTATTTTTAA
5329809 TTTATTTATAAATTAT
1 TTTATTTATAAATTAT
5329825 ACAAATTTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTTATAAATTATTTTTAA
Found at i:5333949 original size:90 final size:90
Alignment explanation
Indices: 5333809--5334254 Score: 526
Period size: 90 Copynumber: 5.0 Consensus size: 90
5333799 TTAATCCTTG
* *
5333809 CAGTCTTTCTTTTTTCCTATAAAAAAATCCGATTCTTAGATATAATTCATGCATTAGTCTAATCC
1 CAGTCTTTCTTTTTTTCTATAAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCC
* *
5333874 TTGCAGTCTGACATTTATAATCAAT
66 TTGCAATCTGACATTTACAATCAAT
* * *
5333899 TAGTCTTTCTTTTTTTTTATAAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTGTAATCC
1 CAGTCTTTCTTTTTTTCTATAAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCC
5333964 TTGCAATCTGACATTTACAATCAAT
66 TTGCAATCTGACATTTACAATCAAT
* ** * *
5333989 CAGTTTTTCTTTTTTTTCTATAAAAAAAATCTTATTCTCAAATATAATTCATACATTAGTCTAAT
1 CAGTCTTTC-TTTTTTTCTAT-AAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTCTAAT
* *
5334054 TCTTGCAGTCTGACATTT---A-CAAT
64 CCTTGCAATCTGACATTTACAATCAAT
** * * * *
5334077 CAGTC-AACTTTTTTTATAAAAAAAATATTCAATTCTCAGATATAATTCATGCATTAGTCTAATC
1 CAGTCTTTCTTTTTTTCTATAAAAAA-ATCCGATTCTCAGATATAATTCATGCATTAGTCTAATC
* * * *
5334141 TTTACAATCTGATATTTACAATCAGT
65 CTTGCAATCTGACATTTACAATCAAT
* * * * * *
5334167 CA-ACTTTTCTTTTTTTCTATAAAAAAAATCTGATTCTTAAATAAAATTCATACATTAGTCTAAT
1 CAGTC-TTTCTTTTTTTCTAT-AAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTCTAAT
*
5334231 CCTTGCAATCTGATATTTACAATC
64 CCTTGCAATCTGACATTTACAATC
5334255 GATTCTCAGA
Statistics
Matches: 299, Mismatches: 47, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
85 6 0.02
86 54 0.18
87 1 0.00
88 8 0.03
89 3 0.01
90 95 0.32
91 72 0.24
92 60 0.20
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (90 bp):
CAGTCTTTCTTTTTTTCTATAAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCC
TTGCAATCTGACATTTACAATCAAT
Found at i:5334132 original size:86 final size:85
Alignment explanation
Indices: 5333829--5334254 Score: 397
Period size: 86 Copynumber: 4.8 Consensus size: 85
5333819 TTTTTCCTAT
* * *
5333829 AAAAAAATCCGATTCTTAGATATAATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTATAA
1 AAAAAAATTCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAATCTGACA-TT-T-A
* ** * *
5333894 TCAATTAGTCTTTCTTTTTTTTTAT
63 -CAATCAGTC-AACTTTTTTTATAA
* *
5333919 AAAAAAATCCGATTCTCAGATATAATTCATGCATTAGTGTAATCCTTGCAATCTGACATTTACAA
1 AAAAAAATTCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAATCTGACATTTACAA
* * *
5333984 TCAATCAGTTTTTCTTTTTTTTCTATA
66 TCAGTCA-----AC-TTTTTTTATA-A
* * * * *
5334011 AAAAAAA-TCTTATTCTCAAATATAATTCATACATTAGTCTAATTCTTGCAGTCTGACATTTACA
1 AAAAAAATTC-GATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAATCTGACATTTACA
5334075 ATCAGTCAACTTTTTTTATAA
65 ATCAGTCAACTTTTTTTATAA
* * * *
5334096 AAAAAATATTCAATTCTCAGATATAATTCATGCATTAGTCTAATCTTTACAATCTGATATTTACA
1 AAAAAA-ATTCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAATCTGACATTTACA
*
5334161 ATCAGTCAACTTTTCTTTTTTTCTATA
65 ATCAGTCAA-----CTTTTTTTATA-A
* * * * *
5334188 AAAAAAA-TCTGATTCTTAAATAAAATTCATACATTAGTCTAATCCTTGCAATCTGATATTTACA
1 AAAAAAATTC-GATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAATCTGACATTTACA
5334252 ATC
65 ATC
5334255 GATTCTCAGA
Statistics
Matches: 285, Mismatches: 34, Indels: 33
0.81 0.10 0.09
Matches are distributed among these distances:
85 7 0.02
86 72 0.25
87 4 0.01
88 1 0.00
89 2 0.01
90 59 0.21
91 71 0.25
92 69 0.24
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (85 bp):
AAAAAAATTCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAATCTGACATTTACAA
TCAGTCAACTTTTTTTATAA
Found at i:5334229 original size:177 final size:177
Alignment explanation
Indices: 5333814--5334254 Score: 598
Period size: 177 Copynumber: 2.5 Consensus size: 177
5333804 CCTTGCAGTC
* * * *
5333814 TTTCTTTTTTCCTAT-AAAAAAATCCGATTCTTAGATATAATTCATGCATTAGTCTAATCCTTGC
1 TTTCTTTTTTTCTATAAAAAAAATCTGATTCTTAAATATAATTCATACATTAGTCTAATCCTTGC
* ** * * *
5333878 AGTCTGACATTTATAATCAATTAGTCTTTCTTTTTTTTTATAAAAAAATCCGATTCTCAGATATA
66 AGTCTGACA-TT-T-A-CAATCAGTCTAACTTTTTTTATAAAAAAAAATCCAATTCTCAGATATA
* * **
5333943 ATTCATGCATTAGTGTAATCCTTGCAATCTGACATTTACAATCAATCAGTT
127 ATTCATGCATTAGTCTAATCCTTACAATCTGACATTTACAATCAATCAACT
* * *
5333994 TTTCTTTTTTTTCTATAAAAAAAATCTTATTCTCAAATATAATTCATACATTAGTCTAATTCTTG
1 TTTC-TTTTTTTCTATAAAAAAAATCTGATTCTTAAATATAATTCATACATTAGTCTAATCCTTG
*
5334059 CAGTCTGACATTTACAATCAGTC-AACTTTTTTTATAAAAAAAATATTCAATTCTCAGATATAAT
65 CAGTCTGACATTTACAATCAGTCTAACTTTTTTTATAAAAAAAA-ATCCAATTCTCAGATATAAT
* * *
5334123 TCATGCATTAGTCTAATCTTTACAATCTGATATTTACAATCAGTCAACT
129 TCATGCATTAGTCTAATCCTTACAATCTGACATTTACAATCAATCAACT
*
5334172 TTTCTTTTTTTCTATAAAAAAAATCTGATTCTTAAATAAAATTCATACATTAGTCTAATCCTTGC
1 TTTCTTTTTTTCTATAAAAAAAATCTGATTCTTAAATATAATTCATACATTAGTCTAATCCTTGC
* *
5334237 AATCTGATATTTACAATC
66 AGTCTGACATTTACAATC
5334255 GATTCTCAGA
Statistics
Matches: 231, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
177 89 0.39
178 72 0.31
179 1 0.00
180 5 0.02
181 12 0.05
182 52 0.23
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (177 bp):
TTTCTTTTTTTCTATAAAAAAAATCTGATTCTTAAATATAATTCATACATTAGTCTAATCCTTGC
AGTCTGACATTTACAATCAGTCTAACTTTTTTTATAAAAAAAAATCCAATTCTCAGATATAATTC
ATGCATTAGTCTAATCCTTACAATCTGACATTTACAATCAATCAACT
Found at i:5334286 original size:57 final size:58
Alignment explanation
Indices: 5334193--5334311 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 58
5334183 CTATAAAAAA
* * * *
5334193 AATCTGATTCTTAAATAAAATTCATACATTAGTCTAATCCTTGCAATCTGATATTTAC
1 AATCTGATTCTCAAATAAAATTCATACAGTAGTCTAATCCTTACAATCTGACATTTAC
* * * * * *
5334251 AATC-GATTCTCAGATATAATTCATTCAGTAGTCTAATCTTTACAGTTTGACATTTAC
1 AATCTGATTCTCAAATAAAATTCATACAGTAGTCTAATCCTTACAATCTGACATTTAC
5334308 AATC
1 AATC
5334312 AATCAACTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
57 47 0.92
58 4 0.08
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (58 bp):
AATCTGATTCTCAAATAAAATTCATACAGTAGTCTAATCCTTACAATCTGACATTTAC
Found at i:5335168 original size:22 final size:22
Alignment explanation
Indices: 5335142--5335200 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
5335132 TATTATTATT
5335142 TTTAATAAAATTAAAAATAATA
1 TTTAATAAAATTAAAAATAATA
** *
5335164 TTTAATTAAGTTTAAAAATTATA
1 TTTAA-TAAAATTAAAAATAATA
*
5335187 -TTAA-CAAATTAAAA
1 TTTAATAAAATTAAAA
5335201 TTTAATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 7 0.23
22 9 0.30
23 14 0.47
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTAATAAAATTAAAAATAATA
Found at i:5335292 original size:116 final size:120
Alignment explanation
Indices: 5335028--5335293 Score: 377
Period size: 116 Copynumber: 2.2 Consensus size: 120
5335018 TATTATTTTT
*
5335028 AATAAAAAATAATATTTAATTAACTTTAAAGAATTTATATTAACAAATTAAAATTAATTATTTTT
1 AATAAAAAATAATATTTAATTAAGTTTAAAGAATTTATATTAACAAATTAAAATTAATTATTTTT
*
5335093 TTAAAATAAAAAATTTAAATAAAAATAAAAAAGGTTTATTATTATTATTTTTAATAA
66 TTAAAAAAAAAAATTT--ATAAAAATAAAAAAGGTTTATTATTATTATTTTTAATAA
*
5335150 AATTAAAAATAATATTTAATTAAGTTTAAA-AA-TTATATTAACAAATTAAAATTTAATTATTAT
1 AATAAAAAATAATATTTAATTAAGTTTAAAGAATTTATATTAACAAATTAAAA-TTAATTATT-T
*
5335213 TTTTATAAAAAAAAAATTT-T-AAAATAAAACTA-GTTT-TT-TTA-TATTTTTAATAA
64 TTTTA-AAAAAAAAAATTTATAAAAATAAAA-AAGGTTTATTATTATTATTTTTAATAA
*
5335266 AATAAAAAATAATATTTAGTTAAGTTTA
1 AATAAAAAATAATATTTAATTAAGTTTA
5335294 CATTTCTAAC
Statistics
Matches: 134, Mismatches: 6, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
116 38 0.28
117 3 0.02
118 2 0.01
119 13 0.10
120 21 0.16
121 11 0.08
122 34 0.25
123 12 0.09
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.43
Consensus pattern (120 bp):
AATAAAAAATAATATTTAATTAAGTTTAAAGAATTTATATTAACAAATTAAAATTAATTATTTTT
TTAAAAAAAAAAATTTATAAAAATAAAAAAGGTTTATTATTATTATTTTTAATAA
Found at i:5335715 original size:23 final size:22
Alignment explanation
Indices: 5335650--5335711 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5335640 TTTATTTAAA
5335650 TAATGATAA-TTTTTTAATTTCT
1 TAATG-TAATTTTTTTAATTTCT
* * *
5335672 TAAATATTATTTTTTTAATTTGT
1 T-AATGTAATTTTTTTAATTTCT
5335695 TAATGTAATTTTTTTAA
1 TAATGTAATTTTTTTAA
5335712 ATTTAATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (22 bp):
TAATGTAATTTTTTTAATTTCT
Found at i:5335898 original size:24 final size:25
Alignment explanation
Indices: 5335871--5335935 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 25
5335861 AAACCCATTT
*
5335871 TAATTTATTTTTTATTTTA-AAAAA
1 TAATTTATTTTTTAATTTATAAAAA
* * * *
5335895 TAATTAATATTTTAATTTATTAATA
1 TAATTTATTTTTTAATTTATAAAAA
*
5335920 TAATTT-TTTTTAAATT
1 TAATTTATTTTTTAATT
5335936 AATTAAATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TAATTTATTTTTTAATTTATAAAAA
Found at i:5335956 original size:21 final size:23
Alignment explanation
Indices: 5335894--5335958 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
5335884 ATTTTAAAAA
*
5335894 ATAATTAATATTTTAATTTATTAAT
1 ATAATT-AT-TTTTAATTAATTAAT
*
5335919 ATAATTTTTTTTAAATTAATTAA-
1 ATAATTATTTTT-AATTAATTAAT
5335942 AT-ATTATTTTTAATTAA
1 ATAATTATTTTTAATTAA
5335959 AAATAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.17
22 8 0.22
23 6 0.17
24 10 0.28
25 6 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAATTATTTTTAATTAATTAAT
Found at i:5336005 original size:67 final size:69
Alignment explanation
Indices: 5335879--5336008 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 69
5335869 TTTAATTTAT
* * * *
5335879 TTTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATATAATTTTTTTTAAATTAATTAAAT
1 TTTTTAATTAAAAAAATAATTAATATATTAATTTATTAATATAATATTTTTTAAATTAATTAAAT
5335944 ATTA
66 ATTA
*
5335948 TTTTTAATTAAAAATAATAATTAATATATT-A-TTATTTAT-TAA-ATTTTTTAAATTTAATTAA
1 TTTTTAATTAAAAA-AATAATTAATATATTAATTTATTAATATAATATTTTTTAAA-TTAATTAA
5336009 TTTATAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
66 9 0.17
67 11 0.20
68 7 0.13
69 13 0.24
70 14 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (69 bp):
TTTTTAATTAAAAAAATAATTAATATATTAATTTATTAATATAATATTTTTTAAATTAATTAAAT
ATTA
Found at i:5336098 original size:28 final size:28
Alignment explanation
Indices: 5336068--5336123 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
5336058 TCTCAACAAA
5336068 TTTATAAAAAAACTTATTTTA-AAAAATAT
1 TTTAT-AAAAAACTTA-TTTACAAAAATAT
*
5336097 TTTATAAAAAATTTATTTACAAAAATA
1 TTTATAAAAAACTTATTTACAAAAATA
5336124 AAAAAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.16
28 16 0.64
29 5 0.20
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (28 bp):
TTTATAAAAAACTTATTTACAAAAATAT
Found at i:5336415 original size:20 final size:20
Alignment explanation
Indices: 5336390--5336429 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5336380 TAATTTGAAT
**
5336390 TTTAAATTTTGATTAATTTA
1 TTTAAATTTAAATTAATTTA
5336410 TTTAAATTTAAATTAATTTA
1 TTTAAATTTAAATTAATTTA
5336430 ATTTGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTAAATTTAAATTAATTTA
Found at i:5338837 original size:2 final size:2
Alignment explanation
Indices: 5338830--5338858 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5338820 CATGAAAATC
5338830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5338859 GAATTCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5343396 original size:2 final size:2
Alignment explanation
Indices: 5343389--5343413 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5343379 ATGTATCTTT
5343389 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5343414 TGTATATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.