Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 125 of 208
Found at i:38443192 original size:101 final size:100
Alignment explanation
Indices: 38442971--38443161 Score: 267
Period size: 102 Copynumber: 1.9 Consensus size: 100
38442961 AGTTATGGTC
38442971 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTA
* * *
38443036 TGTGCAGGCTATTATGCGTACCGGATAACTTTGATC
65 TGTGCAGGCTACTATGCGAACCGGATAACTTTGATA
* * *
38443072 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACTTGTGTAGTAC
1 ACGTGTGTA-TACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCACATGTGTAGTAC
* *
38443136 TATGTGTAGGCTACTATGTGAACCGG
63 TATGTGCAGGCTACTATGCGAACCGG
38443162 TATCATTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 38 0.47
102 39 0.48
103 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTAT
GTGCAGGCTACTATGCGAACCGGATAACTTTGATA
Found at i:38443229 original size:46 final size:43
Alignment explanation
Indices: 38443157--38443255 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 43
38443147 TACTATGTGA
*
38443157 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
*
38443200 ACCGGATATCATTGATTACAAAGGGTGGTTGCTATGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
38443246 ACCGTGTATC
1 ACCG-GTATC
38443256 TGTTATTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
43 5 0.10
44 11 0.22
45 2 0.04
46 28 0.57
47 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:38445425 original size:44 final size:44
Alignment explanation
Indices: 38445377--38445484 Score: 162
Period size: 44 Copynumber: 2.5 Consensus size: 44
38445367 GGTATACAGT
* * * * *
38445377 GTAAGACCATAGATGTAAGATGAAATGACAGCTAGGTATGATAA
1 GTAAGACCATGGATGAAAGATGAAAAGACAGCCAAGTATGATAA
*
38445421 GTAAGACCATGGATGAAAGATGAAAAGACAGCCAAGTATGATGA
1 GTAAGACCATGGATGAAAGATGAAAAGACAGCCAAGTATGATAA
38445465 GTAAGACCATGGATGAAAGA
1 GTAAGACCATGGATGAAAGA
38445485 CTCCATAGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (44 bp):
GTAAGACCATGGATGAAAGATGAAAAGACAGCCAAGTATGATAA
Found at i:38445548 original size:33 final size:33
Alignment explanation
Indices: 38445502--38445592 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
38445492 GCATCCACAA
*
38445502 AGATAG-CCTGCTGGGATAGTAAA-AGCAAAATAG
1 AGATAGTCC-GCTGGGATAGTAAACA-CAAAACAG
*
38445535 AGATAGTCCGCTGGGACAGTAAACACAAAACAG
1 AGATAGTCCGCTGGGATAGTAAACACAAAACAG
* * *
38445568 AGATAGTCCACTTGGATTGTAAACA
1 AGATAGTCCGCTGGGATAGTAAACA
38445593 TAGAACAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 47 0.94
34 3 0.06
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (33 bp):
AGATAGTCCGCTGGGATAGTAAACACAAAACAG
Found at i:38445605 original size:33 final size:33
Alignment explanation
Indices: 38445498--38445605 Score: 85
Period size: 33 Copynumber: 3.3 Consensus size: 33
38445488 CATAGCATCC
* *
38445498 ACAAAGATAG-CCTGCTGGGATAGTAAA-AGCAAA
1 ACAAAGATAGTCC-ACTGGGACAGTAAACA-CAAA
* * *
38445531 ATAGAGATAGTCCGCTGGGACAGTAAACACAAA
1 ACAAAGATAGTCCACTGGGACAGTAAACACAAA
* * ** * *
38445564 ACAGAGATAGTCCACTTGGATTGTAAACATAGA
1 ACAAAGATAGTCCACTGGGACAGTAAACACAAA
38445597 ACAAAGATA
1 ACAAAGATA
38445606 ATTTATCAGG
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 59 0.95
34 3 0.05
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (33 bp):
ACAAAGATAGTCCACTGGGACAGTAAACACAAA
Found at i:38445640 original size:27 final size:26
Alignment explanation
Indices: 38445604--38445677 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
38445594 AGAACAAAGA
*
38445604 TAATTTATCAGGATAGTAAATATGAG
1 TAATTTATCAGGATAATAAATATGAG
*
38445630 TAATTCTATCAGGATAATAAATATGGG
1 TAATT-TATCAGGATAATAAATATGAG
* * *
38445657 TAAATTAGTCGGGACAATAAA
1 TAATTTA-TCAGGATAATAAA
38445678 CAAGAGATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (26 bp):
TAATTTATCAGGATAATAAATATGAG
Found at i:38450966 original size:51 final size:50
Alignment explanation
Indices: 38450838--38451022 Score: 185
Period size: 51 Copynumber: 3.7 Consensus size: 50
38450828 TATCATTCAA
* * * **
38450838 TACACGTAGTAGCCTT-CACATAGTACTACACACGTGATCAAAATTTTTGG
1 TACACGTAGTAG-CTTGCACATAGTACTACACACATGACCAAAACTTCCGG
*
38450888 TTCACGTAGTAGCTTGCACATAGTACTACACACATGACCAAAACCTTCCGG
1 TACACGTAGTAGCTTGCACATAGTACTACACACATGACCAAAA-CTTCCGG
* ** * * *
38450939 TACACATAGTAGCTTGCACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCTTGCACATAGTACTACACACATGACCA-AAACT-TCCGG
* * *
38450990 TACACGTAGTAGCCTACACTTAGTACTACACAC
1 TACACGTAGTAGCTTGCACATAGTACTACACAC
38451023 GTGTTTATAG
Statistics
Matches: 113, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
49 3 0.03
50 36 0.32
51 72 0.64
52 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCTTGCACATAGTACTACACACATGACCAAAACTTCCGG
Found at i:38467540 original size:23 final size:23
Alignment explanation
Indices: 38467498--38467541 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
38467488 CTTTCTTACT
** *
38467498 GTAGTAATTTTTGGGGTATTATA
1 GTAGTAATTTTCAGGATATTATA
38467521 GTAGTAATTTTCAGGATATTA
1 GTAGTAATTTTCAGGATATTA
38467542 CAAGTACAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (23 bp):
GTAGTAATTTTCAGGATATTATA
Found at i:38467738 original size:42 final size:42
Alignment explanation
Indices: 38467668--38467806 Score: 181
Period size: 42 Copynumber: 3.3 Consensus size: 42
38467658 AGTTAACTCA
* * *
38467668 TATGAGTTTCAGTTTAACCCTAATGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
* * *
38467710 TTTGAGCTTCTGTTTAACCCTTATGGGTTTTCGTTCAGCTCT
1 TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
* *
38467752 TATGAGCTT-TCGTTTAACCCTTATGGGTTTCTGTTTAGCACT
1 TATGAGCTTCT-GTTTAACCCTTATGGGTTTCCGTTTAGCTCT
*
38467794 TATGTGCTTCTGT
1 TATGAGCTTCTGT
38467807 GCAACCTTCA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 81 0.98
43 1 0.01
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.46
Consensus pattern (42 bp):
TATGAGCTTCTGTTTAACCCTTATGGGTTTCCGTTTAGCTCT
Found at i:38467795 original size:21 final size:21
Alignment explanation
Indices: 38467668--38467806 Score: 93
Period size: 21 Copynumber: 6.6 Consensus size: 21
38467658 AGTTAACTCA
* * *
38467668 TATGAGTTTCAGTTTAACCCT
1 TATGGGTTTCTGTTTAGCCCT
* * *
38467689 AATGGGTTTCCGTTTAGCTCT
1 TATGGGTTTCTGTTTAGCCCT
* * * *
38467710 TTTGAGCTTCTGTTTAACCCT
1 TATGGGTTTCTGTTTAGCCCT
* *
38467731 TATGGGTTT-TCGTTCAGCTCT
1 TATGGGTTTCT-GTTTAGCCCT
* *
38467752 TATGAGCTTTC-GTTTAACCCT
1 TATG-GGTTTCTGTTTAGCCCT
*
38467773 TATGGGTTTCTGTTTAGCACT
1 TATGGGTTTCTGTTTAGCCCT
* *
38467794 TATGTGCTTCTGT
1 TATGGGTTTCTGT
38467807 GCAACCTTCA
Statistics
Matches: 87, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
20 6 0.07
21 77 0.89
22 4 0.05
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.46
Consensus pattern (21 bp):
TATGGGTTTCTGTTTAGCCCT
Found at i:38470068 original size:50 final size:50
Alignment explanation
Indices: 38469959--38470257 Score: 264
Period size: 50 Copynumber: 5.9 Consensus size: 50
38469949 ACATTAAGAG
* * *
38469959 GATGAGA--TCCCATGTAAGACCATGTTTGGGACATGGAATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
38470010 GATTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * *
38470063 GATGAGAGGTCCCATGTAAGACAATGTCTGGGACATGGCGTTGGCACCAA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
*** * * *
38470113 GATGAGAGGTCCCCCATATGACCATGTCTGGGACATGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * * * *
38470163 TATGAGAACTCTCATGTAAGACCATATCTGGGATATGGGATTGGCA--GTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A
* * * ** * * *
38470212 CAAGAAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
38470258 TGTTATATTC
Statistics
Matches: 203, Mismatches: 39, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
49 35 0.17
50 122 0.60
51 1 0.00
53 3 0.01
54 6 0.03
55 1 0.00
56 35 0.17
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:38470487 original size:16 final size:17
Alignment explanation
Indices: 38470436--38470493 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 17
38470426 GCAATGAAGG
* *
38470436 AGTAAGTTAAGCAAGCA
1 AGTAAGTAAAGCAAGAA
*
38470453 AGTAAGTAAACGAGTAAGAA
1 AGTAAGT-AA--AGCAAGAA
38470473 AGTAAGTAAAG-AAGAA
1 AGTAAGTAAAGCAAGAA
38470489 AGTAA
1 AGTAA
38470494 AGATCTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 10 0.29
17 9 0.26
18 1 0.03
19 2 0.06
20 13 0.37
ACGTcount: A:0.55, C:0.05, G:0.24, T:0.16
Consensus pattern (17 bp):
AGTAAGTAAAGCAAGAA
Found at i:38472456 original size:22 final size:22
Alignment explanation
Indices: 38472428--38472480 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
38472418 AGGCTTAATA
38472428 CTCGAGACATGAATCCCAATGT
1 CTCGAGACATGAATCCCAATGT
38472450 CTCGAGACATGAATCCCAATGT
1 CTCGAGACATGAATCCCAATGT
38472472 CTCGAGACA
1 CTCGAGACA
38472481 CCAAACATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (22 bp):
CTCGAGACATGAATCCCAATGT
Found at i:38473291 original size:33 final size:33
Alignment explanation
Indices: 38473247--38473340 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
38473237 GTTTGCATTT
*
38473247 AATTATATCTTGCATTAAATGTTTGCATCTTTA
1 AATTATGTCTTGCATTAAATGTTTGCATCTTTA
* *
38473280 AATTATGTCTTGCATTATATGTCTGCATCTTTA
1 AATTATGTCTTGCATTAAATGTTTGCATCTTTA
**
38473313 AAACATGTCTTGCATTAAGA-GTTTGCAT
1 AATTATGTCTTGCATTAA-ATGTTTGCAT
38473341 TTAACTAAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.45
Consensus pattern (33 bp):
AATTATGTCTTGCATTAAATGTTTGCATCTTTA
Found at i:38487645 original size:5 final size:5
Alignment explanation
Indices: 38487635--38487664 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
38487625 TTTACCTTGA
38487635 TATTC TATTC TATTC TATTC TATTC TATTC
1 TATTC TATTC TATTC TATTC TATTC TATTC
38487665 ACTGAAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTC
Found at i:38489862 original size:26 final size:25
Alignment explanation
Indices: 38489833--38489898 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
38489823 TAATAATGGC
38489833 ATAATATGCATAATAAAATATAAAAT
1 ATAATATGCATAATAAAAT-TAAAAT
**
38489859 ATAATA-GCAATAAT-AAATTATGAT
1 ATAATATGC-ATAATAAAATTAAAAT
38489883 ACTAATATGCATAATA
1 A-TAATATGCATAATA
38489899 GAACAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 5 0.15
25 16 0.47
26 13 0.38
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (25 bp):
ATAATATGCATAATAAAATTAAAAT
Found at i:38490032 original size:17 final size:17
Alignment explanation
Indices: 38490006--38490042 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
38489996 TAATAATAAC
*
38490006 AATAATA-AAAGATA-A
1 AATAATATAAAAATATA
38490021 AATAATATAAAAATATA
1 AATAATATAAAAATATA
38490038 AATAA
1 AATAA
38490043 AAGGAATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AATAATATAAAAATATA
Found at i:38491811 original size:44 final size:44
Alignment explanation
Indices: 38491763--38492251 Score: 340
Period size: 44 Copynumber: 10.9 Consensus size: 44
38491753 TTGCCACTTT
* *
38491763 AATCTGCTCCGCTGCAACTTCAAGGAGATAAGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTC
* * *
38491807 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGT
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTT-C
* * * * *** *
38491852 AGT-TGTTCCACTGCAACTTCAGGGAAATAAGAAAATTCACACCTTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAG---ATTTGTAGCTTC
* * *
38491898 AATCTGCTCCACTGCAACTT-AAGGGAAATAAGATTTGTACCTTT
1 AATCTGCTCCACTGCAACTTCAA-GGAGATAAGATTTGTAGCTTC
* * * * * * *
38491942 AGTTTTCCCCACTACAACTTCAGGGAGATAAGATCTGTGACTTGTAGCTTT
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGA----T---TTGTAGCTTC
** * * * **
38491993 AATCTATTCCACTACAACTTCAGAGGA-ATAAGATTCGCATATTC
1 AATCTGCTCCACTGCAACTTCA-AGGAGATAAGATTTGTAGCTTC
* * *
38492037 AATCTACTCCACTGCAAATTCAAGGAGATAAGATTTGTAACTTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTC
* * * * * *
38492081 AATCTACTCTACTACAACTTCAGGGAGATACA-ATTTGTGGCTTT
1 AATCTGCTCCACTGCAACTTCAAGGAGATA-AGATTTGTAGCTTC
* * * *
38492125 AATCTACTTCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTG-TAGCTTC
* * * * *
38492170 AATCTGCTCCATTGCAACTTC-AGGAAGGTTAGATTTGTGGCTTT
1 AATCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTGTAGCTTC
* * *
38492214 AATTTGCTCCACTGCAACTTCAAGGATATAATATTTGT
1 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGT
38492252 CACGATAACT
Statistics
Matches: 350, Mismatches: 74, Indels: 42
0.75 0.16 0.09
Matches are distributed among these distances:
43 5 0.01
44 235 0.67
45 39 0.11
46 3 0.01
47 32 0.09
48 1 0.00
51 32 0.09
52 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTC
Found at i:38491929 original size:91 final size:90
Alignment explanation
Indices: 38491803--38491974 Score: 265
Period size: 91 Copynumber: 1.9 Consensus size: 90
38491793 AGATTAGTAG
* * *
38491803 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTGTAGTTGTT-CCACTGCA
1 CTTCAATCTGCTCCACTGCAACTTAAGGGAAATAAGATTTGTAACTT-TAGTT-TTCCCACTACA
38491867 ACTTCAGGGAAATAAGAAAATTCACAC
64 ACTTCAGGGAAATAAGAAAATTCACAC
*
38491894 CTTCAATCTGCTCCACTGCAACTTAAGGGAAATAAGATTTGTACCTTTAGTTTTCCCCACTACAA
1 CTTCAATCTGCTCCACTGCAACTTAAGGGAAATAAGATTTGTAACTTTAGTTTT-CCCACTACAA
*
38491959 CTTCAGGGAGATAAGA
65 CTTCAGGGAAATAAGA
38491975 TCTGTGACTT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
89 2 0.03
90 5 0.07
91 67 0.91
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (90 bp):
CTTCAATCTGCTCCACTGCAACTTAAGGGAAATAAGATTTGTAACTTTAGTTTTCCCACTACAAC
TTCAGGGAAATAAGAAAATTCACAC
Found at i:38498693 original size:3 final size:3
Alignment explanation
Indices: 38498660--38498728 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
38498650 TAGAACAATG
* * * *
38498660 ATA ATA ATGA A-A ATT ATG ATA ATA GTA ATA ATA ATA TTA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
38498705 ACA ACA ACA ATA ATA ATAA ATA AT
1 ATA ATA ATA ATA ATA AT-A ATA AT
38498729 TTTTAAAGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.87
4 5 0.09
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:38498806 original size:7 final size:7
Alignment explanation
Indices: 38498794--38498825 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
38498784 AATAACAATA
38498794 ATAAATT
1 ATAAATT
38498801 ATAAATT
1 ATAAATT
38498808 ATAAA-T
1 ATAAATT
38498814 ATAAA-T
1 ATAAATT
38498820 ATAAAT
1 ATAAAT
38498826 AAAAAGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
ATAAATT
Found at i:38498912 original size:8 final size:8
Alignment explanation
Indices: 38498899--38498927 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38498889 TAAAGGAGAT
38498899 AATAAGTA
1 AATAAGTA
38498907 AATAAGTA
1 AATAAGTA
38498915 AATAAGTA
1 AATAAGTA
38498923 AATAA
1 AATAA
38498928 AAAGTGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (8 bp):
AATAAGTA
Found at i:38499772 original size:23 final size:22
Alignment explanation
Indices: 38499730--38499772 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
38499720 CGAAAAATTA
*
38499730 TACTGTTCTGCTTCTGTTCTAT
1 TACTGTTCTGCTTCTATTCTAT
38499752 TACTGTTTCTGCCTT-TATTCT
1 TACTG-TTCTG-CTTCTATTCT
38499773 TGCTGCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 10 0.56
24 3 0.17
ACGTcount: A:0.09, C:0.23, G:0.12, T:0.56
Consensus pattern (22 bp):
TACTGTTCTGCTTCTATTCTAT
Found at i:38509932 original size:83 final size:83
Alignment explanation
Indices: 38509793--38509964 Score: 308
Period size: 83 Copynumber: 2.1 Consensus size: 83
38509783 TTCCACATCA
38509793 AATATTCTTTCAAAACTTATTGGAGTTGGATACATATAACAATATACACAGTCTATAAACAAAAC
1 AATATTCTTTCAAAACTTATTGGAGTTGGATACATATAACAATATACACAGTCTATAAACAAAAC
38509858 ATCTATTCTAAATGGTGT
66 ATCTATTCTAAATGGTGT
* * *
38509876 AATATTCTTTCAAAACTTCTTGGAGTTGGATACATATAACAATATATACCGTCTATAAACAAAAC
1 AATATTCTTTCAAAACTTATTGGAGTTGGATACATATAACAATATACACAGTCTATAAACAAAAC
38509941 ATCTATTCTAAATGGTGT
66 ATCTATTCTAAATGGTGT
38509959 ATATAT
1 A-ATAT
38509965 ACGAGAATAA
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 81 0.95
84 4 0.05
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (83 bp):
AATATTCTTTCAAAACTTATTGGAGTTGGATACATATAACAATATACACAGTCTATAAACAAAAC
ATCTATTCTAAATGGTGT
Found at i:38518656 original size:34 final size:35
Alignment explanation
Indices: 38518612--38518678 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
38518602 CAGTAAAATA
* *
38518612 TTTTCCGTAAAATTATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
38518646 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
38518679 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:38519142 original size:27 final size:27
Alignment explanation
Indices: 38519088--38519142 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
38519078 TTCTGTTGCT
* *
38519088 AATAAATATTCATATTACTATAGTAAA
1 AATAAATATTCATATTAATATACTAAA
* *
38519115 AATAAATTTTCA-ATTAATATACTGAA
1 AATAAATATTCATATTAATATACTAAA
38519141 AA
1 AA
38519143 GAAAAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (27 bp):
AATAAATATTCATATTAATATACTAAA
Found at i:38519168 original size:21 final size:21
Alignment explanation
Indices: 38519138--38519177 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38519128 TTAATATACT
* *
38519138 GAAAAGAAAAGAAAAGAAAGA
1 GAAAAAAAAACAAAAGAAAGA
*
38519159 GAAAAAAAAACAATAGAAA
1 GAAAAAAAAACAAAAGAAA
38519178 AAAACCATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (21 bp):
GAAAAAAAAACAAAAGAAAGA
Found at i:38519794 original size:97 final size:97
Alignment explanation
Indices: 38519684--38519915 Score: 308
Period size: 96 Copynumber: 2.4 Consensus size: 97
38519674 TGTTTATTGT
* * * *
38519684 TTTTTAAGAAAAAAATTAATTAAATTAAGGTTTAGGGTTACTTGAGTAATTTAATTAAAAATTAT
1 TTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAATT-T
38519749 TTA-AAAATCAGATAAGGGTTTAGAG-TTAAGGG
65 TTATAAAATCAGATAAGGGTTTAGAGTTTAA-GG
* *
38519781 TTTTTAAG-GAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTT
1 TTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAATTTT
** * *
38519845 TATAAAATTTGATTAGGGTTTAGTGTTTAAGG
66 TATAAAATCAGATAAGGGTTTAGAGTTTAAGG
* * *
38519877 TTTTTAAGTAAAAACTCAAATAAATTAGGGTTTGGGGTT
1 TTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTT
38519916 TAGGGTTACT
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
95 4 0.03
96 76 0.64
97 39 0.33
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.39
Consensus pattern (97 bp):
TTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAAATTTT
TATAAAATCAGATAAGGGTTTAGAGTTTAAGG
Found at i:38520220 original size:126 final size:126
Alignment explanation
Indices: 38519948--38520363 Score: 728
Period size: 126 Copynumber: 3.3 Consensus size: 126
38519938 TTGTTAATTT
* *
38519948 AAAGAAGCTCCCACGTGGACACGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
38520013 GTTTCTGAGCAAATGGTGTCAAAAACA-CTTTAAGCAGG-TGCTTTGTCAGCAGAAGTATTG
66 GTTTCTGAGCAAATAGTGTCAAAAA-AGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
38520073 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
*
38520138 GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGCTTTGTCAACAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* *
38520199 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTACTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
*
38520264 GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGCTTTGTTAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
38520325 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
38520364 ACATGTTTGA
Statistics
Matches: 277, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
124 1 0.00
125 97 0.35
126 179 0.65
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:38524469 original size:11 final size:11
Alignment explanation
Indices: 38524455--38524548 Score: 100
Period size: 11 Copynumber: 8.5 Consensus size: 11
38524445 TCTTTTAAAT
38524455 AGAAATTTGAG
1 AGAAATTTGAG
*
38524466 AGAAAATTGAG
1 AGAAATTTGAG
* *
38524477 AGGAATTTAAG
1 AGAAATTTGAG
**
38524488 AGGGATTTGAG
1 AGAAATTTGAG
*
38524499 AGGAATTTGAG
1 AGAAATTTGAG
*
38524510 AGGAATTTGAG
1 AGAAATTTGAG
*
38524521 AGAATATTAGAG
1 AGAA-ATTTGAG
38524533 AGAAA-TTGAG
1 AGAAATTTGAG
38524543 AGAAAT
1 AGAAAT
38524549 GATTTAGTTG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
10 9 0.13
11 52 0.73
12 10 0.14
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (11 bp):
AGAAATTTGAG
Found at i:38524978 original size:6 final size:6
Alignment explanation
Indices: 38524967--38525000 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
38524957 TCAAACCATC
*
38524967 TTCTTT TTCTTT TTCTTT TTCTCT TTCTTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
38525001 CTCTTCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:38524984 original size:12 final size:12
Alignment explanation
Indices: 38524967--38525008 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
38524957 TCAAACCATC
*
38524967 TTCTTTTTCTTT
1 TTCTTTTTCTCT
38524979 TTCTTTTTCTCT
1 TTCTTTTTCTCT
38524991 TTCTTTTTCTCT
1 TTCTTTTTCTCT
38525003 CTTCTT
1 -TTCTT
38525009 CTTTAAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTTTTCTCT
Found at i:38527356 original size:2 final size:2
Alignment explanation
Indices: 38527349--38527375 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38527339 GGTGATTTGA
38527349 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38527376 GCAACTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38529833 original size:29 final size:29
Alignment explanation
Indices: 38529791--38529851 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
38529781 TTCATATTTA
*
38529791 ATTATCTATATTTAATCCTATAATAAATT
1 ATTATCTATATTTAATACTATAATAAATT
* * *
38529820 ATTA-CTATAATTTATTATTTTAATAAATT
1 ATTATCTAT-ATTTAATACTATAATAAATT
38529849 ATT
1 ATT
38529852 TAATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTATCTATATTTAATACTATAATAAATT
Found at i:38530693 original size:14 final size:14
Alignment explanation
Indices: 38530674--38530709 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
38530664 GAAAACTAAG
38530674 TCATTTTCCAAAAA
1 TCATTTTCCAAAAA
* *
38530688 TCATTTTTCGAAAA
1 TCATTTTCCAAAAA
38530702 TCATTTTC
1 TCATTTTC
38530710 AGTGAGACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (14 bp):
TCATTTTCCAAAAA
Found at i:38532144 original size:14 final size:14
Alignment explanation
Indices: 38532121--38532154 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
38532111 TGGTATGTGT
38532121 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
38532134 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
38532148 TTATAGG
1 TTATAGG
38532155 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:38543848 original size:4 final size:5
Alignment explanation
Indices: 38543810--38543835 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38543800 ATAAATATTA
38543810 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
38543836 AACTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:38545303 original size:45 final size:45
Alignment explanation
Indices: 38545252--38545340 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
38545242 TGTGAACTGA
* *
38545252 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
38545297 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
38545341 AGTATCTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:38550954 original size:51 final size:50
Alignment explanation
Indices: 38550826--38550957 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 50
38550816 AAAGTGATGG
* * *
38550826 TCACGTGTGTAGTACTATGTGCAGGCTACCAAGTGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAAGCGTACCGGAATGATAGA
* * * * * *
38550876 TCGCATGTGCAGTACTATGTGCAGGCTACTATGCGTACCGG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAAGCGTACCGGAAT-G-ATAGA
38550927 TCACGTGTGTAGTACTATGTGCAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
38550958 CGTGTATCGA
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.03
50 36 0.53
51 30 0.44
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTAAGCGTACCGGAATGATAGA
Found at i:38550987 original size:51 final size:50
Alignment explanation
Indices: 38550822--38550998 Score: 167
Period size: 51 Copynumber: 3.5 Consensus size: 50
38550812 AGTGAAAGTG
* * *
38550822 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACCAAGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTAAGTGTACC-GAATGGT
* * * * * *
38550873 A-GGTCGCATGTGCAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTAAGTGTACCGAATGGT
* * * * *
38550922 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTAAGTGTACCGAATGGT
* **
38550973 AATGGCCACATGTGTACAACTATGTG
1 -ATGGTCACATGTGTAGTACTATGTG
38550999 AACTGAACAT
Statistics
Matches: 98, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
49 4 0.04
50 35 0.36
51 58 0.59
52 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTAAGTGTACCGAATGGT
Found at i:38551073 original size:45 final size:45
Alignment explanation
Indices: 38551005--38551093 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
38550995 TGTGAACTGA
* * *
38551005 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGATGGTTGCTATGTGCTGAATCCACCGG
38551050 ACATCATTGATTAATAAGATGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGATGGTTGCTATGTGCTGAATCCACCG
38551094 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGATGGTTGCTATGTGCTGAATCCACCGG
Found at i:38551211 original size:38 final size:37
Alignment explanation
Indices: 38551169--38551241 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
38551159 AGGTGTGGAG
*
38551169 TTGAATTGAATAT-TGACTTAGAAA-TGGAAAAGTGAATT
1 TTGAATTGAAT-TGTGA-TT-GAAAGTGAAAAAGTGAATT
38551207 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
38551242 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAATT
Found at i:38552064 original size:13 final size:13
Alignment explanation
Indices: 38552046--38552093 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
38552036 AGGTCCAATC
38552046 AAAAAATATTTCAA
1 AAAAAATATTTC-A
**
38552060 AAAAAATCAAAATCA
1 AAAAAAT--ATTTCA
38552075 AAAAAATATTTCA
1 AAAAAATATTTCA
38552088 AAAAAA
1 AAAAAA
38552094 GAAGAAGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 10 0.36
14 7 0.25
15 8 0.29
16 3 0.11
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAATATTTCA
Found at i:38552121 original size:23 final size:22
Alignment explanation
Indices: 38552087--38552136 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
38552077 AAAATATTTC
* * *
38552087 AAAAAAAGAAGAAGATGAAAAA
1 AAAAAAAAAAGAAAAGGAAAAA
*
38552109 AAAAAGAAAAAGAAAAGGAAAAG
1 AAAAA-AAAAAGAAAAGGAAAAA
38552132 AAAAA
1 AAAAA
38552137 TGAGAGGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAGGAAAAA
Found at i:38552123 original size:17 final size:17
Alignment explanation
Indices: 38552087--38552136 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
38552077 AAAATATTTC
* * *
38552087 AAAAAAAGAAGAAGATG
1 AAAAAAAAAAGAAAAAG
38552104 AAAAAAAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
**
38552121 AAAAGGAAAAGAAAAA
1 AAAAAAAAAAGAAAAA
38552137 TGAGAGGCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:38553873 original size:21 final size:21
Alignment explanation
Indices: 38553847--38553890 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
38553837 CTGGCGTTGC
*
38553847 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
*
38553868 AGTGGAACGGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
38553889 AG
1 AG
38553891 GCAGCGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.32, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:38553883 original size:123 final size:123
Alignment explanation
Indices: 38553756--38553981 Score: 357
Period size: 123 Copynumber: 1.8 Consensus size: 123
38553746 CTCCCTGGTG
* *
38553756 TTAAAGCTGAAGACAACGAATCTTAT-TTCCTTGGCT-TTGCAGTGGAACAGATTAAAGCTAAAG
1 TTAAAGCTGAAGACAACGAATCCTATCTT-CTTGG-TGTTACAGTGGAACAGATTAAAGCTAAAG
*
38553819 GTAGCGAATCTTGTTTACCTGGCGTTGCAGTGGAATAGATTAAAGCTGAAGTGGAACGGA
64 GTAGCGAATCTTGTTTACCTAGCGTTGCAGTGGAATAGATTAAAGCTGAAGTGGAACGGA
* *
38553879 TTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGTGTTACAGTGGAACAGATTAAAGCTAAAGGT
1 TTAAAGCTGAAGACAACGAATCCTATCTTCTTGGTGTTACAGTGGAACAGATTAAAGCTAAAGGT
* *
38553944 AGCGAATCTTGTTTCCCTAGCGTTGCAGTGGAGTAGAT
66 AGCGAATCTTGTTTACCTAGCGTTGCAGTGGAATAGAT
38553982 CAAGACTGAA
Statistics
Matches: 94, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
122 1 0.01
123 91 0.97
124 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (123 bp):
TTAAAGCTGAAGACAACGAATCCTATCTTCTTGGTGTTACAGTGGAACAGATTAAAGCTAAAGGT
AGCGAATCTTGTTTACCTAGCGTTGCAGTGGAATAGATTAAAGCTGAAGTGGAACGGA
Found at i:38553922 original size:72 final size:72
Alignment explanation
Indices: 38553796--38553937 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 72
38553786 TTGGCTTTGC
* * * * *
38553796 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTACCTGGCGTTGCAGTGGAATAGATTA
1 AGTGGAACAGATTAAAGCTAAAGGCAGCGAATCCTATTTACCTGGCGTTACAGTGGAACAGATTA
38553861 AAGCTGA
66 AAGCTGA
* * * *
38553868 AGTGGAACGGATTAAAGCTGAAGGCAGCGAATCCTATCTT-CTTGGTGTTACAGTGGAACAGATT
1 AGTGGAACAGATTAAAGCTAAAGGCAGCGAATCCTAT-TTACCTGGCGTTACAGTGGAACAGATT
38553932 AAAGCT
65 AAAGCT
38553938 AAAGGTAGCG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
72 58 0.97
73 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.26
Consensus pattern (72 bp):
AGTGGAACAGATTAAAGCTAAAGGCAGCGAATCCTATTTACCTGGCGTTACAGTGGAACAGATTA
AAGCTGA
Found at i:38553948 original size:51 final size:51
Alignment explanation
Indices: 38553868--38554269 Score: 263
Period size: 51 Copynumber: 7.6 Consensus size: 51
38553858 TTAAAGCTGA
* * * *
38553868 AGTGGAACGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGTGTTAC
1 AGTGGAACAGATTAAAGCTGAAGGTAGCGAATCCTATCTTCTTAGCGTTAC
* * * * *
38553919 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGT-TTCCCTAGCGTTGC
1 AGTGGAACAGATTAAAGCTGAAGGTAGCGAATCCTATCTT-CTTAGCGTTAC
** * * * * * * *
38553970 AGTGGAGTAGA-TCAAGACTGAAGATAGTGAATCGTATCTCCCTAGCATTAAAGC
1 AGTGGAACAGATTAAAG-CTGAAGGTAGCGAATCCTATCTTCTTAGCGTT--A-C
* * *
38554024 TGAAGTGGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTAGCGTTAC
1 ---AGTGGAACAGATTAAAGCTGAAGGTAGCGAATCCTATCTTCTTAGCGTTAC
* * * * * *
38554078 AGTGGAATAGATTAAAGCTAAAGGTAGCGAATCTTGT-TTCCTTAGCATTGC
1 AGTGGAACAGATTAAAGCTGAAGGTAGCGAATCCTATCTT-CTTAGCGTTAC
* * * * * * * * *
38554129 AGCGGAGCAGA-TCAAGACTGAAGATAGCGAATCGTATCTCCTTGGCATTAA
1 AGTGGAACAGATTAAAG-CTGAAGGTAGCGAATCCTATCTTCTTAGCGTTAC
* * * *
38554180 AGTTGAAGTTGAGCGGATTAAAGCTGAAGGTAGCGAATCCTATCTCCTTGGCGTTAC
1 AG-T---G--GAACAGATTAAAGCTGAAGGTAGCGAATCCTATCTTCTTAGCGTTAC
*
38554237 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATC
1 AGTGGAACAGATTAAAGCTGAAGGTAGCGAATC
38554270 TTGTTTCCCT
Statistics
Matches: 270, Mismatches: 61, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
50 12 0.04
51 170 0.63
52 2 0.01
53 1 0.00
54 2 0.01
55 2 0.01
56 1 0.00
57 72 0.27
58 8 0.03
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (51 bp):
AGTGGAACAGATTAAAGCTGAAGGTAGCGAATCCTATCTTCTTAGCGTTAC
Found at i:38554146 original size:159 final size:159
Alignment explanation
Indices: 38553857--38554312 Score: 752
Period size: 159 Copynumber: 2.9 Consensus size: 159
38553847 AGTGGAATAG
* *
38553857 ATTAAAGCTGAAGTGGAACGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGTGTTACAGT
1 ATTAAAGCTGAAGTGGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGCGTTACAGT
* *
38553922 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCGTTGCAGTGGAGTAGATCAAGA
66 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGTAGATCAAGA
*
38553987 CTGAAGATAGTGAATCGTATCTCCCTAGC
131 CTGAAGATAGCGAATCGTATCTCCCTAGC
*
38554016 ATTAAAGCTGAAGTGGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTAGCGTTACAGT
1 ATTAAAGCTGAAGTGGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGCGTTACAGT
* * *
38554081 GGAATAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCTTAGCATTGCAGCGGAGCAGATCAAGA
66 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGTAGATCAAGA
* *
38554146 CTGAAGATAGCGAATCGTATCTCCTTGGC
131 CTGAAGATAGCGAATCGTATCTCCCTAGC
* * * *
38554175 ATTAAAGTTGAAGTTGAGCGGATTAAAGCTGAAGGTAGCGAATCCTATCTCCTTGGCGTTACAGT
1 ATTAAAGCTGAAGTGGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGCGTTACAGT
* *
38554240 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTACAGC-GAGTAGATCAAGA
66 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGTAGATCAAGA
38554304 CTGAAGATA
131 CTGAAGATA
38554313 ACAAACCTTA
Statistics
Matches: 276, Mismatches: 21, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
158 21 0.08
159 255 0.92
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (159 bp):
ATTAAAGCTGAAGTGGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGCGTTACAGT
GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGTAGATCAAGA
CTGAAGATAGCGAATCGTATCTCCCTAGC
Found at i:38554283 original size:108 final size:108
Alignment explanation
Indices: 38553857--38554286 Score: 278
Period size: 108 Copynumber: 4.0 Consensus size: 108
38553847 AGTGGAATAG
* * * * * **
38553857 ATTAAAGCTGAAGTGGAACGGATTAAAGCTGAAGGCAGCGAATCCTATCTTCTTGGTGTTACAGT
1 ATTAAAGTTGAAGTGGAGCGGATTAAAGCTGAAGGTAGCGAATCCTATCTCCTTAGCATTACAGT
*
38553922 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGC
66 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCCTAGC
* ** * * * * *
38553965 ------GTTGCAGTGGAGTAGA-TCAAGACTGAAGATAGTGAATCGTATCTCCCTAGCATTAAAG
1 ATTAAAGTTGAAGTGGAGCGGATTAAAG-CTGAAGGTAGCGAATCCTATCTCCTTAGCATT--A-
* * * * * *
38554023 CTGAAGTGGAGCGGATTAAAGCTGAAGGCAGCGAATCCTATCTT-CTTAGC
62 C---AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTAT-TTCCCTAGC
* * * * * * * * *
38554073 GTTACAGTGGAA-T--A---GATTAAAGCTAAAGGTAGCGAATCTTGTTTCCTTAGCATTGCAGC
1 ATTAAAGTTGAAGTGGAGCGGATTAAAGCTGAAGGTAGCGAATCCTATCTCCTTAGCATTACAGT
* * * * * * * *
38554132 GGAGCAGA-TCAAGACTGAAGATAGCGAATCGTATCTCCTTGGC
66 GGAACAGATTAAAG-CTAAAGGTAGCGAATCTTATTTCCCTAGC
* * *
38554175 ATTAAAGTTGAAGTTGAGCGGATTAAAGCTGAAGGTAGCGAATCCTATCTCCTTGGCGTTACAGT
1 ATTAAAGTTGAAGTGGAGCGGATTAAAGCTGAAGGTAGCGAATCCTATCTCCTTAGCATTACAGT
* *
38554240 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGC
66 GGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCCTAGC
38554283 ATTA
1 ATTA
38554287 CAGCGAGTAG
Statistics
Matches: 238, Mismatches: 60, Indels: 48
0.69 0.17 0.14
Matches are distributed among these distances:
101 9 0.04
102 74 0.31
103 1 0.00
104 1 0.00
105 3 0.01
108 134 0.56
109 10 0.04
111 1 0.00
113 1 0.00
114 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (108 bp):
ATTAAAGTTGAAGTGGAGCGGATTAAAGCTGAAGGTAGCGAATCCTATCTCCTTAGCATTACAGT
GGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCCTAGC
Found at i:38554369 original size:44 final size:44
Alignment explanation
Indices: 38554319--38554654 Score: 257
Period size: 44 Copynumber: 7.5 Consensus size: 44
38554309 GATAACAAAC
38554319 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
* ** * * * *
38554363 CTTATCTCCCTGAAGTTGCAGTGAAGTGGATTAAAACGATGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
* * * * * * *
38554407 CCTATAC-CTCTGAAGTTGCAGTAGG-TCGGATTAAATCTACCATAACAAGT
1 CTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGCT---AT--TAA-T
* * ** *
38554457 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATAACAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-ATTAAT
* * **
38554502 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
*
38554546 CTTTTCT-CCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
* * * * * * *
38554589 CCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAACGATTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
* *
38554633 CCTATAC-CTCTGAAGTTGCAGT
1 CTTAT-CTCCCTGAAGTTGCAGT
38554655 AGGTCGAATT
Statistics
Matches: 234, Mismatches: 46, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
43 37 0.16
44 122 0.52
45 39 0.17
46 2 0.01
47 2 0.01
48 1 0.00
49 5 0.02
50 26 0.11
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTATTAAT
Found at i:38554666 original size:44 final size:44
Alignment explanation
Indices: 38554557--38554667 Score: 111
Period size: 44 Copynumber: 2.5 Consensus size: 44
38554547 TTTTCTCCTG
* * * *
38554557 AAGTTGCAGTGGAGC-AGATTGAAGCTATTAATCCTATCTCCCTA
1 AAGTTGCAGTAGAGCGA-ATTAAAACGATTAATCCTATCTCCCTA
* * *
38554601 AAGTTGCAGTAGAGCGGATTAAAACGATTAATCCTATAC-CTCTG
1 AAGTTGCAGTAGAGCGAATTAAAACGATTAATCCTAT-CTCCCTA
38554645 AAGTTGCAGTAG-GTCGAATTAAA
1 AAGTTGCAGTAGAG-CGAATTAAA
38554668 TCTACCATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.02
44 54 0.96
45 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (44 bp):
AAGTTGCAGTAGAGCGAATTAAAACGATTAATCCTATCTCCCTA
Found at i:38554789 original size:44 final size:44
Alignment explanation
Indices: 38554739--38554860 Score: 147
Period size: 44 Copynumber: 2.8 Consensus size: 44
38554729 TTATCATATC
* * * *
38554739 AAACCTTATCTCTCTGAAGTTTCAGTAGAGCAGGTTGAAGTAAT
1 AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGAAAA
* *
38554783 AAACCTTATCT-TCATAAAGTTGCAGTGGAGTAGGTTGAAGAAAA
1 AAACCTTATCTCTC-TGAAGTTGCAGTGGAGCAGGTTGAAGAAAA
* *
38554827 AAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 AAA-CCTTATCTCTCTGAAGTTGCAGTGGAGCAG
38554861 ACTGAAGATA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
43 2 0.03
44 38 0.58
45 24 0.37
46 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (44 bp):
AAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGAAAA
Found at i:38554848 original size:45 final size:44
Alignment explanation
Indices: 38554743--38554911 Score: 149
Period size: 45 Copynumber: 3.8 Consensus size: 44
38554733 CATATCAAAC
* * * * * * * *
38554743 CTTATCTCTCTGAAGTTTCAGTAGAGCAGGTTGAAGTAATAAAC
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGAAAAAAAT
* * * *
38554787 CTTATCTTCATAAAGTTGCAGTGGAGTAGGTTGAAGAAAAAAAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGAAAAAAA-T
* * **
38554832 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGA-AAAAAAT
* * *
38554877 CTTATTTCCCTAAAGTTGTAGTGGAGTAGATTGAA
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAA
38554912 CCATTAATCC
Statistics
Matches: 100, Mismatches: 23, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
44 34 0.34
45 62 0.62
46 4 0.04
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGAAAAAAAT
Found at i:38554911 original size:90 final size:89
Alignment explanation
Indices: 38554743--38554945 Score: 214
Period size: 89 Copynumber: 2.3 Consensus size: 89
38554733 CATATCAAAC
* * ** *
38554743 CTTATCTCTCTGAAGTTTCAGTAGAGCAGGTTGAAGTAATAAACCTTATCTTCATAAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGTAACAAACCTTATCTTCATAAAGTTGCAG
*
38554808 TGGAGTAGGTTGAAGAAAAAAAGT
66 TGGAGTAGATTGAAGAAAAAAAGT
* * * * *
38554832 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTAT-TTCCCTAAAGTTGT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAG-TAACAAACCTTATCTT-CATAAAGTTGC
** **
38554896 AGTGGAGTAGATTGAA-CCATTAA-T
64 AGTGGAGTAGATTGAAGAAAAAAAGT
* *
38554920 CCTATCTCCCTGAAGTTGTAGTAGAG
1 CTTATCTCCCTGAAGTTGCAGTAGAG
38554946 AAGATTAAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
88 24 0.26
89 36 0.38
90 34 0.36
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (89 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAGTAACAAACCTTATCTTCATAAAGTTGCAG
TGGAGTAGATTGAAGAAAAAAAGT
Found at i:38554939 original size:43 final size:43
Alignment explanation
Indices: 38554834--38554951 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 43
38554824 AAAAAAGTCT
* * * * *
38554834 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCT
1 TATCTCCCTGAAGTTGTAGTGGAGAAGATTGAACATA--AAATCC
* * * *
38554879 TATTTCCCTAAAGTTGTAGTGGAGTAGATTGAACCAT-TAATCC
1 TATCTCCCTGAAGTTGTAGTGGAGAAGATTGAA-CATAAAATCC
*
38554922 TATCTCCCTGAAGTTGTAGTAGAGAAGATT
1 TATCTCCCTGAAGTTGTAGTGGAGAAGATT
38554952 AAAACGATGA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
43 30 0.50
45 28 0.47
46 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGTAGTGGAGAAGATTGAACATAAAATCC
Found at i:38554979 original size:44 final size:43
Alignment explanation
Indices: 38554874--38554987 Score: 113
Period size: 43 Copynumber: 2.6 Consensus size: 43
38554864 GAAGATAGCA
* * * * * * *
38554874 AATCTTATTTCCCTAAAGTTGTAGTGGAGTAGATTGAACCATT
1 AATCCTATCTCCCTGAAGTTGTAGTAGAGAAGATTAAACCATG
*
38554917 AATCCTATCTCCCTGAAGTTGTAGTAGAGAAGATTAAAACGATG
1 AATCCTATCTCCCTGAAGTTGTAGTAGAGAAGATT-AAACCATG
* *
38554961 AATCCTATAC-CTCTGAAGTTGCAGTAG
1 AATCCTAT-CTCCCTGAAGTTGTAGTAG
38554988 GTCTGATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 30 0.51
44 28 0.47
45 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (43 bp):
AATCCTATCTCCCTGAAGTTGTAGTAGAGAAGATTAAACCATG
Found at i:38560253 original size:17 final size:18
Alignment explanation
Indices: 38560227--38560260 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38560217 TTAATCATTT
38560227 TTTTTCTTT-CCCTTAGC
1 TTTTTCTTTCCCCTTAGC
*
38560244 TTTTTGTTTCCCCTTAG
1 TTTTTCTTTCCCCTTAG
38560261 AGGACAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.06, C:0.26, G:0.09, T:0.59
Consensus pattern (18 bp):
TTTTTCTTTCCCCTTAGC
Found at i:38571125 original size:21 final size:23
Alignment explanation
Indices: 38571099--38571141 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
38571089 AAATTGCTCA
38571099 ACTTT-ACTTTTAT-TCAAAAAC
1 ACTTTAACTTTTATATCAAAAAC
*
38571120 ACTTTAATTTTTATATCAAAAA
1 ACTTTAACTTTTATATCAAAAA
38571142 ATATTATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (23 bp):
ACTTTAACTTTTATATCAAAAAC
Found at i:38572711 original size:18 final size:18
Alignment explanation
Indices: 38572670--38572712 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
38572660 AAAAATATCA
38572670 TATTAATTTTAATTGATT
1 TATTAATTTTAATTGATT
*
38572688 TGATTAA-TTTAATTTACTT
1 T-ATTAATTTTAATTGA-TT
38572707 TATTAA
1 TATTAA
38572713 AATTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (18 bp):
TATTAATTTTAATTGATT
Found at i:38575194 original size:19 final size:20
Alignment explanation
Indices: 38575166--38575204 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38575156 TAATTAAATT
38575166 TTAATGAAG-TAAAACATAA
1 TTAATGAAGTTAAAACATAA
* *
38575185 TTAATTAAGTTAAATCATAA
1 TTAATGAAGTTAAAACATAA
38575205 ACTAATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (20 bp):
TTAATGAAGTTAAAACATAA
Found at i:38577708 original size:18 final size:18
Alignment explanation
Indices: 38577685--38577726 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
38577675 ACATATTGTA
38577685 GCTCGGACCCGACGATCG
1 GCTCGGACCCGACGATCG
**
38577703 GCTCGGGTCCGACGATCG
1 GCTCGGACCCGACGATCG
38577721 GCTCGG
1 GCTCGG
38577727 GTATATGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.36, G:0.38, T:0.14
Consensus pattern (18 bp):
GCTCGGACCCGACGATCG
Found at i:38577727 original size:18 final size:18
Alignment explanation
Indices: 38577693--38577728 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
38577683 TAGCTCGGAC
38577693 CCGACGATCGGCTCGGGT
1 CCGACGATCGGCTCGGGT
38577711 CCGACGATCGGCTCGGGT
1 CCGACGATCGGCTCGGGT
38577729 ATATGGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.39, T:0.17
Consensus pattern (18 bp):
CCGACGATCGGCTCGGGT
Found at i:38578660 original size:5 final size:5
Alignment explanation
Indices: 38578650--38578674 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38578640 TATCATTTGT
38578650 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
38578675 AGTAATATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:38580515 original size:20 final size:20
Alignment explanation
Indices: 38580459--38580531 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
38580449 AATGTGCAAG
* * *
38580459 CAGAGGCTCCGAGGTGTGAA
1 CAGAGGCACCGAAGTGCGAA
*
38580479 CAGAGGCACCAAAGTGCGAA
1 CAGAGGCACCGAAGTGCGAA
* * *
38580499 TAGAGGCACCGACGTGCAAA
1 CAGAGGCACCGAAGTGCGAA
*
38580519 CAGAGCCACCGAA
1 CAGAGGCACCGAA
38580532 ATACAGAAAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.26, G:0.32, T:0.08
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCGAA
Found at i:38582243 original size:18 final size:17
Alignment explanation
Indices: 38582220--38582262 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
38582210 TTTTGTGTAC
38582220 ATATATATGAATACTAAA
1 ATATATATGAATA-TAAA
* *
38582238 ATATATTTGCATATAAA
1 ATATATATGAATATAAA
*
38582255 TTATATAT
1 ATATATAT
38582263 ATATATATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (17 bp):
ATATATATGAATATAAA
Found at i:38584122 original size:131 final size:131
Alignment explanation
Indices: 38583875--38584149 Score: 369
Period size: 131 Copynumber: 2.1 Consensus size: 131
38583865 CCAAAACGTC
* * * *
38583875 GGGGAGATAGGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATT
1 GGGGAGATAAGATTCGCTGTCCTCGATCTGCTCCACTACTACTTAGAGAGATAAGATCTGAAATT
* **
38583940 TTCAACCTACTCCGCTGTTGCTCAGGGAGATAAGGCTTGTGACTTAAATCTGCTTCC-CTACT-C
66 TTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTTGTGACTTAAATCTGC-TCCACTACTGC
38584003 CT
130 CT
38584005 GGGGAAGATAAGATTCGCTGTCCTCGATCTGCTCCACTACTACTTAGAGAGATAAGATCT-ACAA
1 GGGG-AGATAAGATTCGCTGTCCTCGATCTGCTCCACTACTACTTAGAGAGATAAGATCTGA-AA
* * **
38584069 TTTTCAACCTACTCCACTACTGCTTAGGGAGATAAGG-TTGGTGTCTTCGATCTGCTCCACTACT
64 TTTTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTT-GTGACTTAAATCTGCTCCACTACT
*
38584133 GCTT
128 GCCT
*
38584137 AGGGAGATAAGAT
1 GGGGAGATAAGAT
38584150 CTGTAATTTT
Statistics
Matches: 127, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
130 10 0.08
131 112 0.88
132 5 0.04
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (131 bp):
GGGGAGATAAGATTCGCTGTCCTCGATCTGCTCCACTACTACTTAGAGAGATAAGATCTGAAATT
TTCAACCTACTCCACTACTGCTCAGGGAGATAAGGCTTGTGACTTAAATCTGCTCCACTACTGCC
T
Found at i:38584126 original size:87 final size:87
Alignment explanation
Indices: 38584023--38584281 Score: 419
Period size: 87 Copynumber: 3.0 Consensus size: 87
38584013 TAAGATTCGC
* * * *
38584023 TGTCCTCGATCTGCTCCACTACTACTTAGAGAGATAAGATCTACAATTTTCAACCTACTCCACTA
1 TGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTA
* *
38584088 CTGCTTAGGGAGATAAGGTTGG
66 CTGCTCAGGGAGATAAGGCTGG
* * *
38584110 TGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCGCTG
1 TGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTA
38584175 CTGCTCAGGGAGATAAGGCTGG
66 CTGCTCAGGGAGATAAGGCTGG
**
38584197 TGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCTTTA
1 TGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTA
38584262 CTGCTCAGGGAGATAAGGCT
66 CTGCTCAGGGAGATAAGGCT
38584282 TGTGACTAAA
Statistics
Matches: 159, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 159 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (87 bp):
TGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTA
CTGCTCAGGGAGATAAGGCTGG
Found at i:38584272 original size:44 final size:44
Alignment explanation
Indices: 38583905--38584278 Score: 240
Period size: 44 Copynumber: 8.6 Consensus size: 44
38583895 CTTCGATCTG
*
38583905 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
* ** * * ** * * * *
38583949 CTCCGCTGTTGCTCAGGGAGATAAG-GCTTGTGA-CTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATC-TGCAATTTTCAACCTA
* * ** ** * * *
38583992 CTTCC-CTACT-CCTGGGGAAGATAAGAT-TCGCTGTCCTCGATCTG
1 C-TCCACTACTGCTTAGGG-AGATAAGATCT-GCAATTTTCAACCTA
* * *
38584036 CTCCACTACTACTTAGAGAGATAAGATCTACAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
* *** * * * *
38584080 CTCCACTACTGCTTAGGGAGATAAGGT-TGGTGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
*
38584123 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
* * * * *** * * * *
38584167 CTCCGCTGCTGCTCAGGGAGATAAG-GCTGGTGTCTTCGATCTG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
38584210 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
** *
38584254 CTCCTTTACTGCTCAGGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAG
38584279 GCTTGTGACT
Statistics
Matches: 241, Mismatches: 78, Indels: 22
0.71 0.23 0.06
Matches are distributed among these distances:
42 5 0.02
43 88 0.37
44 143 0.59
45 5 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTA
Found at i:38584525 original size:44 final size:44
Alignment explanation
Indices: 38584398--38585360 Score: 402
Period size: 44 Copynumber: 22.4 Consensus size: 44
38584388 ATCTATTCCC
* * * * *
38584398 CTGTAATCTCAGGGAGATAAGA--CCT-GATGCAATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * ** * * *
38584439 CTGTAATTTCAGAGAGATAAGATCCCTTA-TTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTAC-TAGCTTCAATCTGCTCCA
* *
38584483 CTGTAATCTCAGGGAAATAGGATTACTAGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
** * *
38584527 CTGTAATCTTGGGGAGATAAGATTTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * * **
38584571 CTATAACCTCAGGGAGATAAGATTTGAAATTA--TTCAGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGA-TT---ACTAGCTTCAATCTGCTCCA
* * * * * ** *
38584617 CTGTAATCTCAAGGAGATAAGA--CCT-GATGCGATCTATTCTA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * ** * *
38584658 CTGTAATTTCAGAGAGATAAGATCTTTTA-TTTTAA-CTTGCTCCA
1 CTGTAATCTCAGGGAGATAAGAT-TACTAGCTTCAATC-TGCTCCA
* * * *
38584702 CTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * * **
38584746 CTATAACCTCAGGGAGATAAGATTTGAAATTA--TTCAGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGA-TT---ACTAGCTTCAATCTGCTCCA
* * * * * ** *
38584792 CTGTAATCTCAAGGAGATAAGA--CCT-GATGCGATCTATTCTA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * ** * *
38584833 CTGTAATTTCAGAGAGATAAGATCTTTTA-TTTTAA-CTTGCTCCA
1 CTGTAATCTCAGGGAGATAAGAT-TACTAGCTTCAATC-TGCTCCA
* * * * *
38584877 CTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTTCA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * *
38584921 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGTTCCG
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * ** **
38584965 CTATAACCTCAGGGAGATAAGA-T--T--CTTCGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * * * *
38585004 CTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * * *
38585045 CTGTAATTTCAGAGAGATAAGATT-CTTTA-TTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTAC--TAGCTTCAATCTGCTCCA
* * * * * *
38585089 CTGTAATCTTAGGGAAATAAGATTACTAGCTTTAATCCGCTTCG
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * *
38585133 TTGTAATCTCAGGAAGATAAGATTTCTAGCTTCAATCTGATCCA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * **
38585177 CTGTAACCTCAAGGAGATAAGA-T--T--CTTCAGTCTATTCC-
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * * * *
38585215 CTTGTAATCTCAGGGAGATAAGA--CCT-GATGCGATCTACTCTA
1 C-TGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
* * * * * *
38585257 CTGTAATTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGAT--TACTAGCTTCAATCTGCTCCA
* * * * *
38585301 TTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
*
38585345 TTGTAATCTCAGGGAG
1 CTGTAATCTCAGGGAG
38585361 GTAAAATCCG
Statistics
Matches: 684, Mismatches: 185, Indels: 103
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.00
39 61 0.09
40 4 0.01
41 137 0.20
42 3 0.00
43 15 0.02
44 394 0.58
45 7 0.01
46 59 0.09
48 3 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCCA
Found at i:38584623 original size:219 final size:219
Alignment explanation
Indices: 38584369--38584770 Score: 646
Period size: 219 Copynumber: 1.8 Consensus size: 219
38584359 GCCTGGGAAG
* * *
38584369 TAAGATTTGAAATTCTTCGATCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCAATCTA
1 TAAGATTTGAAATTATTCGATCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCAATCTA
38584434 CTCTACTGTAATTTCAGAGAGATAAGATCCCTTATTTTAA-TCCGCTCCACTGTAATCTCAGGGA
66 CTCTACTGTAATTTCAGAGAGATAAGATCCCTTATTTTAACT-CGCTCCACTGTAATCTCAGGGA
* * **
38584498 AATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTTGGGGAGATAAGATTTCTGGCTTCAAT
130 AATAGGATTACTAGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGATTTCTGGCTTCAAT
38584563 CTGCTCCACTATAACCTCAGGGAGA
195 CTGCTCCACTATAACCTCAGGGAGA
*
38584588 TAAGATTTGAAATTATTC-AGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGATCT
1 TAAGATTTGAAATTATTCGA-TCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCAATCT
* ** *
38584652 ATTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAACTTGCTCCACTGTAATCTCAGGGA
65 ACTCTACTGTAATTTCAGAGAGATAAGATCCCTTATTTTAACTCGCTCCACTGTAATCTCAGGGA
* *
38584717 AATAGGATTACTGGCTTTAATCTGCTCCACTATAACCTCAGGGAGATAAGATTT
130 AATAGGATTACTAGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGATTT
38584771 GAAATTATTC
Statistics
Matches: 167, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
218 1 0.01
219 165 0.99
220 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (219 bp):
TAAGATTTGAAATTATTCGATCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCAATCTA
CTCTACTGTAATTTCAGAGAGATAAGATCCCTTATTTTAACTCGCTCCACTGTAATCTCAGGGAA
ATAGGATTACTAGCTTCAATCTGCTCCACTATAACCTCAGGGAGATAAGATTTCTGGCTTCAATC
TGCTCCACTATAACCTCAGGGAGA
Found at i:38584663 original size:175 final size:175
Alignment explanation
Indices: 38584520--38584945 Score: 771
Period size: 175 Copynumber: 2.4 Consensus size: 175
38584510 AGCTTCAATC
** * * * *
38584520 TGCTCCACTGTAATCTTGGGGAGATAAGATTTCTGGCTTCAATCTGCTCCACTATAACCTCAGGG
1 TGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTCCACTATAACCTCAGGG
38584585 AGATAAGATTTGAAATTATTCAGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGAT
66 AGATAAGATTTGAAATTATTCAGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGAT
38584650 CTATTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAACT
131 CTATTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAACT
38584695 TGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTCCACTATAACCTCAGGG
1 TGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTCCACTATAACCTCAGGG
38584760 AGATAAGATTTGAAATTATTCAGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGAT
66 AGATAAGATTTGAAATTATTCAGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGAT
38584825 CTATTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAACT
131 CTATTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAACT
* * *
38584870 TGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTTCACTGTAATCTCAGGG
1 TGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTCCACTATAACCTCAGGG
38584935 AGATAAGATTT
66 AGATAAGATTT
38584946 CTGGCTTCAA
Statistics
Matches: 242, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
175 242 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (175 bp):
TGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTCCACTATAACCTCAGGG
AGATAAGATTTGAAATTATTCAGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGAT
CTATTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAACT
Found at i:38585051 original size:212 final size:212
Alignment explanation
Indices: 38584695--38585360 Score: 960
Period size: 212 Copynumber: 3.1 Consensus size: 212
38584685 TATTTTAACT
* * * * *
38584695 TGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTTAATCTGCTCCACTATAACCTCAGGG
1 TGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATCCACTATAACCTCAGGG
* *
38584760 AGATAAGATTTGAAATTATTCAGTCTATTCCACTGTAATCTCAAGGAGATAAGACCTGATGCGAT
66 AGAT-A-A---G--ATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGAT
* *
38584825 CTATTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAA-CTTGCTCCACTGTAATCTCAG
124 CTACTCTACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAATC-CGCTCCACTGTAATCTCAG
38584889 GGAAATAGGATTACTGGCTTTAATC
188 GGAAATAGGATTACTGGCTTTAATC
* * *
38584914 TGCTTCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGTTCCGCTATAACCTCAGGG
1 TGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATCCACTATAACCTCAGGG
*
38584979 AGATAAGATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCT
66 AGATAAGATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCT
*
38585044 ACTGTAATTTCAGAGAGATAAGAT-TCTTTATTTTAATCCGCTCCACTGTAATCTTAGGGAAATA
131 ACTGTAATTTCAGAGAGATAAGATCT-TTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATA
* *
38585108 AGATTACTAGCTTTAATC
195 GGATTACTGGCTTTAATC
* * ** * * * *
38585126 CGCTTCGTTGTAATCTCAGGAAGATAAGATTTCTAGCTTCAATCTGATCCACTGTAACCTCAAGG
1 TGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATCCACTATAACCTCAGGG
38585191 AGATAAGATTCTTCAGTCTATTCC-CTTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTC
66 AGATAAGATTCTTCAGTCTATTCCAC-TGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTC
* *
38585255 TACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCATTGTAATCTCAGGGAAATA
130 TACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATA
*
38585320 GGATTACTGGCTTCAATC
195 GGATTACTGGCTTTAATC
**
38585338 TGCTCCGTTGTAATCTCAGGGAG
1 TGCTCCACTGTAATCTCAGGGAG
38585361 GTAAAATCCG
Statistics
Matches: 409, Mismatches: 34, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
211 2 0.00
212 341 0.83
213 1 0.00
214 1 0.00
217 1 0.00
218 1 0.00
219 62 0.15
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (212 bp):
TGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATCCACTATAACCTCAGGG
AGATAAGATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCT
ACTGTAATTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAG
GATTACTGGCTTTAATC
Found at i:38586731 original size:23 final size:22
Alignment explanation
Indices: 38586684--38586727 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38586674 ATTTTTTGAA
* * *
38586684 TTTTTTTTGGACTCAAAGTGCC
1 TTTTTTTAGGAATCAAAGCGCC
38586706 TTTTTTTAGGAATCAAAGCGCC
1 TTTTTTTAGGAATCAAAGCGCC
38586728 CTTTGTGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (22 bp):
TTTTTTTAGGAATCAAAGCGCC
Found at i:38596386 original size:18 final size:18
Alignment explanation
Indices: 38596363--38596403 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
38596353 AGGTGAAAAC
38596363 CTCACGAAGGAGTAGCTT
1 CTCACGAAGGAGTAGCTT
38596381 CTCACGAAGGAGTAGCTT
1 CTCACGAAGGAGTAGCTT
38596399 CTCAC
1 CTCAC
38596404 TCCCACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (18 bp):
CTCACGAAGGAGTAGCTT
Found at i:38597033 original size:23 final size:23
Alignment explanation
Indices: 38597006--38597053 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
38596996 AAAACATGTG
38597006 TTTAAAGAAGGTTACTTGATTGT
1 TTTAAAGAAGGTTACTTGATTGT
38597029 TTTAAAGAAGGTTACTTGATTGT
1 TTTAAAGAAGGTTACTTGATTGT
38597052 TT
1 TT
38597054 AAGTCAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTAAAGAAGGTTACTTGATTGT
Found at i:38602396 original size:19 final size:20
Alignment explanation
Indices: 38602372--38602419 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
38602362 TGCAAACTAA
*
38602372 AGTGAGCTAA-AACGAGCTT
1 AGTGAGCTAAGAACGAGCTC
*
38602391 AGTGAGCTAAGAATGAGCTC
1 AGTGAGCTAAGAACGAGCTC
*
38602411 ATTGAGCTA
1 AGTGAGCTA
38602420 GAGTTGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (20 bp):
AGTGAGCTAAGAACGAGCTC
Found at i:38605404 original size:15 final size:15
Alignment explanation
Indices: 38605384--38605416 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
38605374 TCTCTTTTTC
*
38605384 TTCACTCATTTTGTT
1 TTCACTCACTTTGTT
38605399 TTCACTCACTTTGTT
1 TTCACTCACTTTGTT
38605414 TTC
1 TTC
38605417 TCCTCTCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.58
Consensus pattern (15 bp):
TTCACTCACTTTGTT
Found at i:38614640 original size:10 final size:9
Alignment explanation
Indices: 38614549--38614701 Score: 53
Period size: 9 Copynumber: 17.6 Consensus size: 9
38614539 TTTTGAAACT
*
38614549 TTTTTATGA
1 TTTTTATAA
38614558 TTTTTATAA
1 TTTTTATAA
*
38614567 TAATTTTACAA
1 T--TTTTATAA
*
38614578 -TTTTATTCA
1 TTTTTA-TAA
38614587 TTTTTATAA
1 TTTTTATAA
38614596 --TTTATAA
1 TTTTTATAA
**
38614603 TAATTAT-A
1 TTTTTATAA
*
38614611 TTGTT-T-A
1 TTTTTATAA
38614618 TTTTTATAA
1 TTTTTATAA
*
38614627 TTTTTATTAC
1 TTTTTA-TAA
*
38614637 TTTTCTACAAA
1 TTTT-TA-TAA
*
38614648 TTTTTAAAA
1 TTTTTATAA
38614657 GTTTTTA-AA
1 -TTTTTATAA
38614666 --TTT-T-A
1 TTTTTATAA
*
38614671 -TTTTACAA
1 TTTTTATAA
38614679 TTTTTAT-A
1 TTTTTATAA
38614687 TATTTTATAA
1 T-TTTTATAA
38614697 TTTTT
1 TTTTT
38614702 TAAATAATTA
Statistics
Matches: 111, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
5 1 0.01
6 6 0.05
7 13 0.12
8 13 0.12
9 43 0.39
10 21 0.19
11 14 0.13
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:38614691 original size:23 final size:22
Alignment explanation
Indices: 38614649--38614694 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
38614639 TTCTACAAAT
38614649 TTTTAAAAGTTTTTAAATTTTA
1 TTTTAAAAGTTTTTAAATTTTA
*
38614671 TTTTACAA-TTTTTATATATTTTA
1 TTTTAAAAGTTTTTA-A-ATTTTA
38614694 T
1 T
38614695 AATTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 8 0.38
23 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTAAAAGTTTTTAAATTTTA
Found at i:38617492 original size:41 final size:41
Alignment explanation
Indices: 38617435--38617539 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 41
38617425 GCTGGTGTGA
*
38617435 TATATCAGGCTAAAAGCCTAGCAGGCGTAGTGCCGGTGAATT
1 TATATCAGGCT-AAAGCCTAGCAGGCGTAGAGCCGGTGAATT
* *
38617477 TATATCAGACTAAAGCCTAGCAGGCGTAGAGCTGGTGAATT
1 TATATCAGGCTAAAGCCTAGCAGGCGTAGAGCCGGTGAATT
* * *
38617518 TTTATCAGGCTTATGCCTAGCA
1 TATATCAGGCTAAAGCCTAGCA
38617540 AGTTTTATAC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
41 46 0.82
42 10 0.18
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (41 bp):
TATATCAGGCTAAAGCCTAGCAGGCGTAGAGCCGGTGAATT
Found at i:38617711 original size:2 final size:2
Alignment explanation
Indices: 38617704--38617733 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38617694 TGTTAATGAA
*
38617704 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38617734 TTGATTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:38618623 original size:2 final size:2
Alignment explanation
Indices: 38618616--38618640 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38618606 ATATGTCATG
38618616 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
38618641 GTTATGTTTA
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
Found at i:38626059 original size:23 final size:23
Alignment explanation
Indices: 38626033--38626108 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
38626023 ATAAGTGCCA
38626033 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
38626056 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
38626079 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
38626102 CACTGAT
1 CACTGAT
38626109 CAATAACANN
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:38634178 original size:25 final size:25
Alignment explanation
Indices: 38634096--38634189 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
38634086 GTTACAAATT
38634096 TTAGCTCT-TATGAGCTTACTGATAC
1 TTAGCT-TGTATGAGCTTACTGATAC
* *
38634121 TTAGCTCGTATGAGCTTACCGATAC
1 TTAGCTTGTATGAGCTTACTGATAC
* *
38634146 TTATCTTGTATGAGCTTACTGCTA-
1 TTAGCTTGTATGAGCTTACTGATAC
* *
38634170 TTCAGCTTGGAGGAGCTTAC
1 TT-AGCTTGTATGAGCTTAC
38634190 CGTTTATAGC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
24 2 0.03
25 56 0.97
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (25 bp):
TTAGCTTGTATGAGCTTACTGATAC
Found at i:38636158 original size:16 final size:16
Alignment explanation
Indices: 38636123--38636163 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
38636113 CCCGCATAAA
38636123 CAAA-AAATATAAAAC
1 CAAATAAATATAAAAC
38636138 CAAATAAAT-TAAAAC
1 CAAATAAATATAAAAC
38636153 CAAAATAAATA
1 C-AAATAAATA
38636164 AAGTCCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (16 bp):
CAAATAAATATAAAAC
Found at i:38636165 original size:15 final size:14
Alignment explanation
Indices: 38636131--38636165 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
38636121 AACAAAAAAT
38636131 ATAAAACCAAATAA
1 ATAAAACCAAATAA
38636145 ATTAAAACCAAAATAA
1 A-TAAAACC-AAATAA
38636161 ATAAA
1 ATAAA
38636166 GTCCAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 11 0.58
16 7 0.37
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (14 bp):
ATAAAACCAAATAA
Found at i:38637508 original size:23 final size:24
Alignment explanation
Indices: 38637439--38637519 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
38637429 ATTAATATTG
** *
38637439 TTTAAATTTATCGCATATTATTAT
1 TTTAAATTTATCATACATTATTAT
* *
38637463 TTTAAATTTATCATATATAATTAT
1 TTTAAATTTATCATACATTATTAT
*
38637487 TTTAAGTTT-TCATACATTATTA-
1 TTTAAATTTATCATACATTATTAT
*
38637509 TTCAAATTTAT
1 TTTAAATTTAT
38637520 TATGTATTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 7 0.15
23 12 0.25
24 29 0.60
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTAAATTTATCATACATTATTAT
Found at i:38637858 original size:17 final size:16
Alignment explanation
Indices: 38637832--38637866 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
38637822 TCAACTTTTC
*
38637832 ATATATTATTATTATAT
1 ATATAATATTATT-TAT
38637849 ATATAATATTATTTAT
1 ATATAATATTATTTAT
38637865 AT
1 AT
38637867 TGAGTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATAATATTATTTAT
Found at i:38639847 original size:19 final size:19
Alignment explanation
Indices: 38639823--38639863 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
38639813 GTGTTACATT
*
38639823 ATCGCTATGTATTCCTACA
1 ATCGCTATGCATTCCTACA
38639842 ATCGCTATGCATTCCTACA
1 ATCGCTATGCATTCCTACA
38639861 ATC
1 ATC
38639864 ACCATGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (19 bp):
ATCGCTATGCATTCCTACA
Found at i:38639900 original size:3 final size:3
Alignment explanation
Indices: 38639892--38639943 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
38639882 CATTAGTTAA
38639892 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
38639940 AAG A
1 AAG A
38639944 CAACAACAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:38641271 original size:10 final size:10
Alignment explanation
Indices: 38641258--38641283 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38641248 AATAATAAAA
38641258 AAAGTTCTTT
1 AAAGTTCTTT
38641268 AAAGTTCTTT
1 AAAGTTCTTT
38641278 AAAGTT
1 AAAGTT
38641284 TTTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (10 bp):
AAAGTTCTTT
Found at i:38643552 original size:22 final size:22
Alignment explanation
Indices: 38643507--38643553 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38643497 TGACAAAGGT
* *
38643507 GATATCGCGATACCTAGAAGAG
1 GATATCGCAATACCTAGAACAG
* *
38643529 GATATCGCAATAGCTCGAACAG
1 GATATCGCAATACCTAGAACAG
38643551 GAT
1 GAT
38643554 TGAAACTTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (22 bp):
GATATCGCAATACCTAGAACAG
Found at i:38645969 original size:27 final size:27
Alignment explanation
Indices: 38645933--38645998 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
38645923 TTACGAAGTT
* * *
38645933 TGCCAAAAAGGCATTCCTTTCATATTT
1 TGCCATAAAGGCATTCCTTCCATATTG
* * *
38645960 TTCCATAAAGACGTTCCTTCCATATTG
1 TGCCATAAAGGCATTCCTTCCATATTG
38645987 TGCCATAAAGGC
1 TGCCATAAAGGC
38645999 GCTAATCAGG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (27 bp):
TGCCATAAAGGCATTCCTTCCATATTG
Found at i:38648514 original size:22 final size:21
Alignment explanation
Indices: 38648468--38648523 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
38648458 AAAAATAATA
* *
38648468 TTATTTTAATAGATTTAATAT
1 TTATTTTAATAGATTTAAAAC
38648489 TTATTTTAATTTA-ATTTAAAAC
1 TTATTTTAA--TAGATTTAAAAC
*
38648511 TTATCTT-ATAGAT
1 TTATTTTAATAGAT
38648524 AAATATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 10 0.34
22 13 0.45
23 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
TTATTTTAATAGATTTAAAAC
Found at i:38651789 original size:37 final size:37
Alignment explanation
Indices: 38651739--38651809 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
38651729 CATGACAATA
* *
38651739 GCTCATAAGAGCTAATCCACCCGATAACACGCCAGAT
1 GCTCATAAGAGCTAATCCAACCGAAAACACGCCAGAT
*
38651776 GCTCATAAGAGCTAATTCAACCGAAAACACGCCA
1 GCTCATAAGAGCTAATCCAACCGAAAACACGCCA
38651810 AAACAAGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (37 bp):
GCTCATAAGAGCTAATCCAACCGAAAACACGCCAGAT
Found at i:38661145 original size:14 final size:14
Alignment explanation
Indices: 38661107--38661146 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
38661097 TTTGTTTTTC
38661107 TTTT-ACTT-TAACA
1 TTTTAACTTATAA-A
38661120 TTTTAA-TTATAAA
1 TTTTAACTTATAAA
38661133 TTTTAACTTATAAA
1 TTTTAACTTATAAA
38661147 ATCACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAACTTATAAA
Found at i:38665685 original size:23 final size:22
Alignment explanation
Indices: 38665659--38665717 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 22
38665649 ATTATTTTTA
* *
38665659 ATTAAAAATTATTGAATATAAAT
1 ATTAAAAATAATT-AAAATAAAT
*
38665682 ATTAAAGATAATTAAAATAAAT
1 ATTAAAAATAATTAAAATAAAT
* *
38665704 A-GAATAATAATTAA
1 ATTAAAAATAATTAA
38665718 TAAAAGGCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 10 0.33
22 9 0.30
23 11 0.37
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
ATTAAAAATAATTAAAATAAAT
Found at i:38666550 original size:16 final size:17
Alignment explanation
Indices: 38666524--38666557 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38666514 AGAAATTTTT
*
38666524 TTATCAAAAATATAAAA
1 TTATCAAAAATAAAAAA
38666541 TTAT-AAAAATAAAAAA
1 TTATCAAAAATAAAAAA
38666557 T
1 T
38666558 ACTTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TTATCAAAAATAAAAAA
Found at i:38666765 original size:16 final size:18
Alignment explanation
Indices: 38666746--38666782 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
38666736 TTTGAGAAAA
38666746 AAATT-CTA-TCAATTAT
1 AAATTCCTATTCAATTAT
*
38666762 AAATTCCTATTGAATTAT
1 AAATTCCTATTCAATTAT
38666780 AAA
1 AAA
38666783 ACAATTATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 10 0.56
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATTCCTATTCAATTAT
Found at i:38666926 original size:18 final size:18
Alignment explanation
Indices: 38666905--38666948 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
38666895 TTTTTCTTAT
*
38666905 ATTTTTTAATATTATTTA
1 ATTTTTTAATAATATTTA
* *
38666923 ATTTTTT-ATAATCTTTT
1 ATTTTTTAATAATATTTA
38666940 ATTTTTTAA
1 ATTTTTTAA
38666949 GAATTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTTAATAATATTTA
Found at i:38666943 original size:17 final size:17
Alignment explanation
Indices: 38666899--38666947 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
38666889 ATTTTATTTT
* *
38666899 TCTTATATTTTTTAATAT
1 TCTTTTATTTTTT-ATAA
* *
38666917 TATTTAATTTTTTATAA
1 TCTTTTATTTTTTATAA
38666934 TCTTTTATTTTTTA
1 TCTTTTATTTTTTA
38666948 AGAATTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTTTATTTTTTATAA
Found at i:38666956 original size:17 final size:16
Alignment explanation
Indices: 38666904--38666957 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
38666894 ATTTTTCTTA
*
38666904 TATTTTTTAATATTATT
1 TATTTTTTAAAATT-TT
*
38666921 TAATTTTTTATAATCTTT
1 T-ATTTTTTAAAAT-TTT
38666939 TATTTTTTAAGAATTTT
1 TATTTTTTAA-AATTTT
38666956 TA
1 TA
38666958 GGGGTTTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 14 0.45
18 16 0.52
19 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (16 bp):
TATTTTTTAAAATTTT
Found at i:38670656 original size:28 final size:29
Alignment explanation
Indices: 38670604--38670658 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
38670594 TAAGGGGGTC
* *
38670604 AAAATTAAATTATATCTTTTATAATAGTA
1 AAAATAAAATTATATCATTTATAATAGTA
*
38670633 AAAATAAAATTTTATCATTT-TAATAG
1 AAAATAAAATTATATCATTTATAATAG
38670659 CCTATATCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (29 bp):
AAAATAAAATTATATCATTTATAATAGTA
Found at i:38674363 original size:14 final size:15
Alignment explanation
Indices: 38674335--38674367 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
38674325 CTATCTAAAC
38674335 TTTAGTTTAATTTAT
1 TTTAGTTTAATTTAT
38674350 TTTAGTTT-ATTTAT
1 TTTAGTTTAATTTAT
38674364 TTTA
1 TTTA
38674368 AATTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTAGTTTAATTTAT
Found at i:38680412 original size:44 final size:45
Alignment explanation
Indices: 38680329--38680419 Score: 148
Period size: 44 Copynumber: 2.0 Consensus size: 45
38680319 TAGCAGATAC
* * *
38680329 TCGGTGGATTCAGCACATAGCAACCACTTTATTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
38680374 TCGGTGGAATCAGCACATA-CAACCACCTTACTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
38680418 TC
1 TC
38680420 AGTTCACATA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
44 25 0.58
45 18 0.42
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (45 bp):
TCGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
Found at i:38680486 original size:51 final size:50
Alignment explanation
Indices: 38680428--38680603 Score: 228
Period size: 51 Copynumber: 3.5 Consensus size: 50
38680418 TCAGTTCACA
*
38680428 TAGTAGCCTGCACATAGTACTACACATGTGATCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGATCA-TACCATCCGGTACACG
* * * ** *
38680479 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGATC-ATACCATCCGGTACACG
* * *
38680530 TAGTAGCCTGCACATAGTACTACACATGCGA-CCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGATCATACCA-TCCGGTACACG
38680580 TAGTAGCCTGCACATAGTACTACA
1 TAGTAGCCTGCACATAGTACTACA
38680604 AACGTGACCA
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.02
50 33 0.31
51 71 0.66
52 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGATCATACCATCCGGTACACG
Found at i:38680603 original size:101 final size:102
Alignment explanation
Indices: 38680426--38680610 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
38680416 GTTCAGTTCA
* *
38680426 CATAGTAGCCTGCACATAGTACTACACATGTGATCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGATCACTACCATCCGATACACGTAGTAGCCTGCA
*
38680491 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
66 CATAGTACTACAAACGTGATCGAAACTATCCGGTATG
* *
38680528 CATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGATCACTACCA-TCCGATACACGTAGTAGCCTGC
38680591 ACATAGTACTACAAACGTGA
65 ACATAGTACTACAAACGTGA
38680611 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 32 0.42
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGATCACTACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACAAACGTGATCGAAACTATCCGGTATG
Found at i:38684911 original size:25 final size:25
Alignment explanation
Indices: 38684828--38684914 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 25
38684818 CTATATCTTC
* * *
38684828 TTCATCTTCACCTCGAGCC-CCGTA
1 TTCATCTTCATCTCCACCCTCCGTA
* *
38684852 TTCATCTTCA--TCGACCCT-CGTC
1 TTCATCTTCATCTCCACCCTCCGTA
*
38684874 TTCATCTTTATCTCCACCCTCCGTA
1 TTCATCTTCATCTCCACCCTCCGTA
*
38684899 TTCGTCTTCATCTCCA
1 TTCATCTTCATCTCCA
38684915 TCCCATCTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
22 18 0.35
24 17 0.33
25 17 0.33
ACGTcount: A:0.15, C:0.40, G:0.08, T:0.37
Consensus pattern (25 bp):
TTCATCTTCATCTCCACCCTCCGTA
Found at i:38692277 original size:61 final size:61
Alignment explanation
Indices: 38692182--38692365 Score: 323
Period size: 61 Copynumber: 3.0 Consensus size: 61
38692172 GGAAGTGTAC
*
38692182 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTCGAACCCTTATGTGCCTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
*
38692243 TGGTTAAGTGCTCCTTAACAATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
* * *
38692304 TGTTTAAGTGCTCTTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTCTGTGCCTATTAT
1 TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
38692365 T
1 T
38692366 TTTATTTAAT
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 117 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (61 bp):
TGGTTAAGTGCTCCTTAACTATCCTTTAAGTCTCTAGTTTGAACCCTTATGTGCCTATTAT
Found at i:38692981 original size:16 final size:16
Alignment explanation
Indices: 38692960--38692990 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38692950 ACCGATACTG
38692960 ATTTCTTCTTCTTTTT
1 ATTTCTTCTTCTTTTT
*
38692976 ATTTCTTTTTCTTTT
1 ATTTCTTCTTCTTTT
38692991 GCTGATTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTCTTCTTCTTTTT
Found at i:38694006 original size:21 final size:22
Alignment explanation
Indices: 38693960--38694007 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
38693950 AGGAGGAAGC
* *
38693960 TATGTGGCAGTTTAACTACGAT
1 TATGTGGCAGTTTAACGACAAT
*
38693982 TATGTGGCAG-TTATCGACAAT
1 TATGTGGCAGTTTAACGACAAT
38694003 TATGT
1 TATGT
38694008 AGTGGCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (22 bp):
TATGTGGCAGTTTAACGACAAT
Found at i:38698953 original size:23 final size:23
Alignment explanation
Indices: 38698917--38698967 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
38698907 CTATTGGTTG
* *
38698917 TGTAATATCTCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
38698940 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
38698963 AGTAA
1 TGTAA
38698968 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:38703067 original size:45 final size:45
Alignment explanation
Indices: 38702988--38703241 Score: 300
Period size: 45 Copynumber: 5.7 Consensus size: 45
38702978 TATCTTACAG
* * *
38702988 AGCATCTTACAGCTACAG-TCTTACTCATTTTTATCATGACGCCAT
1 AGCATCTTTCAGCTA-TGTTCTTACTCATTTTTATCATGACACCAT
* * * * *
38703033 AGCATATTTCAACTATGTTCTTGCTCACTTTTATCATGACGCCAT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
* * *
38703078 AGCATCTCTCAGCTATGGTCTTACTAATTTTTATCATGACACCAT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
* * * * *
38703123 AGCAT-ATTCAACTATGGTT-TTGCTCACTTTTATCATGACACCGT
1 AGCATCTTTCAGCTAT-GTTCTTACTCATTTTTATCATGACACCAT
*
38703167 AGCATCTTTCAGCTATGGTCTTACTCATTTTTATCATGACACCAT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
*
38703212 AGCATCTTTCAGCTATG-TCTTAATCATTTT
1 AGCATCTTTCAGCTATGTTCTTACTCATTTT
38703242 AGGCTTATAA
Statistics
Matches: 176, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
44 48 0.27
45 128 0.73
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.39
Consensus pattern (45 bp):
AGCATCTTTCAGCTATGTTCTTACTCATTTTTATCATGACACCAT
Found at i:38703179 original size:89 final size:90
Alignment explanation
Indices: 38702988--38703229 Score: 371
Period size: 89 Copynumber: 2.7 Consensus size: 90
38702978 TATCTTACAG
* ** *
38702988 AGCATCTTACAGCTACAGTCTTACTCATTTTTATCATGACGCCATAGCATATTTCAACTATGTTC
1 AGCATCTTTCAGCTATGGTCTTACTCATTTTTATCATGACACCATAGCATATTTCAACTATGTTC
*
38703053 TTGCTCACTTTTATCATGACGCCAT
66 TTGCTCACTTTTATCATGACACCAT
* *
38703078 AGCATCTCTCAGCTATGGTCTTACTAATTTTTATCATGACACCATAGCATA-TTCAACTATGGTT
1 AGCATCTTTCAGCTATGGTCTTACTCATTTTTATCATGACACCATAGCATATTTCAACTAT-GTT
*
38703142 -TTGCTCACTTTTATCATGACACCGT
65 CTTGCTCACTTTTATCATGACACCAT
* *
38703167 AGCATCTTTCAGCTATGGTCTTACTCATTTTTATCATGACACCATAGCATCTTTCAGCTATGT
1 AGCATCTTTCAGCTATGGTCTTACTCATTTTTATCATGACACCATAGCATATTTCAACTATGT
38703230 CTTAATCATT
Statistics
Matches: 138, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
89 82 0.59
90 56 0.41
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.38
Consensus pattern (90 bp):
AGCATCTTTCAGCTATGGTCTTACTCATTTTTATCATGACACCATAGCATATTTCAACTATGTTC
TTGCTCACTTTTATCATGACACCAT
Found at i:38709469 original size:17 final size:17
Alignment explanation
Indices: 38709443--38709816 Score: 91
Period size: 17 Copynumber: 21.3 Consensus size: 17
38709433 AATACAAATT
* *
38709443 TTTTTTAAACACGAAGA
1 TTTTTGAAACACGAATA
* *
38709460 TTTTTGAAACA--ATTT
1 TTTTTGAAACACGAATA
* * *
38709475 TTTTTGAAAATACGATTT
1 TTTTTG-AAACACGAATA
*
38709493 TTTTTAAAACACGAGA-A
1 TTTTTGAAACACGA-ATA
* * *
38709510 TTTTAGAGACACGAAAA
1 TTTTTGAAACACGAATA
**
38709527 TTCTTAAAAACACGAATA
1 TT-TTTGAAACACGAATA
38709545 TTTTTTGAAAACACGACA-A
1 -TTTTTG-AAACACGA-ATA
38709564 TTTTTTGAAA-AC-AATA
1 -TTTTTGAAACACGAATA
38709580 TTTTTTTGAAA-AGCGGAA-A
1 --TTTTTGAAACA-C-GAATA
*
38709599 TTTTTCAAACACGAGA-A
1 TTTTTGAAACACGA-ATA
* *
38709616 TTGTTGAAAAACACGAAAA
1 TTTTTG--AAACACGAATA
38709635 TTTTTGAAACACGGAAT-
1 TTTTTGAAACAC-GAATA
*
38709652 TTTTTAGAAAACACGAGAAAAAA
1 TTTTT-G-AAACAC--G--AATA
* *
38709675 ATTTTG-ATCATC-AGA-A
1 TTTTTGAAACA-CGA-ATA
*
38709691 TTTTTGAGAACACGAAAA
1 TTTTTGA-AACACGAATA
**
38709709 TTTTTGAAACACCG-GGA
1 TTTTTGAAACA-CGAATA
* **
38709726 TTTTTGAAAACACTAGGA
1 TTTTTG-AAACACGAATA
38709744 TTTTTGAAACACGAA-A
1 TTTTTGAAACACGAATA
* *
38709760 ATTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAATA
*
38709778 CTTTT-AAACACGGGAAT-
1 TTTTTGAAACAC--GAATA
*
38709795 TTTTCGAAAACACGAA-A
1 TTTTTG-AAACACGAATA
38709812 TTTTT
1 TTTTT
38709817 TGAATATTTA
Statistics
Matches: 276, Mismatches: 39, Indels: 84
0.69 0.10 0.21
Matches are distributed among these distances:
15 8 0.03
16 28 0.10
17 111 0.40
18 69 0.25
19 45 0.16
20 7 0.03
21 1 0.00
22 3 0.01
23 4 0.01
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAATA
Found at i:38709513 original size:18 final size:18
Alignment explanation
Indices: 38709492--38709817 Score: 103
Period size: 17 Copynumber: 18.3 Consensus size: 18
38709482 AAATACGATT
38709492 TTTTTTAAAACACGAGAA
1 TTTTTTAAAACACGAGAA
* *
38709510 --TTTTAGAGACACGAAAA
1 TTTTTTA-AAACACGAGAA
* *
38709527 TTCTTAAAAACACGA-ATA
1 TTTTTTAAAACACGAGA-A
*
38709545 TTTTTTGAAAACACGACAA
1 TTTTTT-AAAACACGAGAA
* *
38709564 TTTTTTGAAAACA--ATAT
1 TTTTTT-AAAACACGAGAA
*
38709581 TTTTTTGAAAA-GCG-GAA
1 TTTTTT-AAAACACGAGAA
* *
38709598 ATTTTTCAAACACGAGAA
1 TTTTTTAAAACACGAGAA
**
38709616 TTGTTGAAAAACACGA-AA
1 TT-TTTTAAAACACGAGAA
* *
38709634 ATTTTTGAAACACG-GAA
1 TTTTTTAAAACACGAGAA
38709651 TTTTTTAGAAAACACGAGAAAAA
1 TTTTTT--AAAACACGAG---AA
** * *
38709674 AATTTT-GATCATC-AGAA
1 TTTTTTAAAACA-CGAGAA
* *
38709691 TTTTTGAGAACACGA-AA
1 TTTTTTAAAACACGAGAA
* * *
38709708 ATTTTTGAAACACCG-GGA
1 TTTTTTAAAACA-CGAGAA
* * *
38709726 TTTTTGAAAACACTAGGA
1 TTTTTTAAAACACGAGAA
*
38709744 -TTTTTGAAACACGA-AA
1 TTTTTTAAAACACGAGAA
* *
38709760 ATTTTGAAAACACGA-AA
1 TTTTTTAAAACACGAGAA
** *
38709777 ACTTTT-AAACACGGGAA
1 TTTTTTAAAACACGAGAA
*
38709794 TTTTTCGAAAACACGA-AA
1 TTTTT-TAAAACACGAGAA
38709812 TTTTTT
1 TTTTTT
38709818 GAATATTTAC
Statistics
Matches: 224, Mismatches: 56, Indels: 57
0.66 0.17 0.17
Matches are distributed among these distances:
16 16 0.07
17 98 0.44
18 46 0.21
19 50 0.22
20 7 0.03
21 1 0.00
23 6 0.03
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (18 bp):
TTTTTTAAAACACGAGAA
Found at i:38709513 original size:19 final size:19
Alignment explanation
Indices: 38709491--38709670 Score: 73
Period size: 19 Copynumber: 10.0 Consensus size: 19
38709481 AAAATACGAT
38709491 TTTTTTTAAAACACGAGAA
1 TTTTTTTAAAACACGAGAA
*
38709510 ---TTTTAGAGACACGA-AA
1 TTTTTTTA-AAACACGAGAA
* * *
38709526 ATTCTTAAAAACACGA-ATA
1 TTTTTTTAAAACACGAGA-A
* *
38709545 TTTTTTGAAAACACGACAA
1 TTTTTTTAAAACACGAGAA
* *
38709564 TTTTTTGAAAACA--A-TA
1 TTTTTTTAAAACACGAGAA
*
38709580 TTTTTTTGAAAA-GCG-GAA
1 TTTTTTT-AAAACACGAGAA
* *
38709598 -ATTTTTCAAACACGAGAA
1 TTTTTTTAAAACACGAGAA
* **
38709616 TTGTTGAAAAACACGA-AA
1 TTTTTTTAAAACACGAGAA
* *
38709634 -ATTTTTGAAACACG-GAA
1 TTTTTTTAAAACACGAGAA
*
38709651 TTTTTTAGAAAACACGAGAA
1 TTTTTT-TAAAACACGAGAA
38709671 AAAAATTTTG
Statistics
Matches: 117, Mismatches: 27, Indels: 33
0.66 0.15 0.19
Matches are distributed among these distances:
16 17 0.15
17 30 0.26
18 18 0.15
19 48 0.41
20 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (19 bp):
TTTTTTTAAAACACGAGAA
Found at i:38709732 original size:35 final size:34
Alignment explanation
Indices: 38709546--38709820 Score: 180
Period size: 35 Copynumber: 7.8 Consensus size: 34
38709536 ACACGAATAT
* ***
38709546 TTTTTGAAAACACGACAATTTTTTGAAA-ACAATA
1 TTTTTGAAAACACGA-AAATTTTTGAAACACGGGA
* * * *
38709580 TTTTTTTGAAAA-GCGGAAATTTTTCAAACACGAGAA
1 --TTTTTGAAAACACGAAAATTTTTGAAACACG-GGA
* *
38709616 TTGTTGAAAAACACGAAAATTTTTGAAACACGGAA
1 TTTTTG-AAAACACGAAAATTTTTGAAACACGGGA
* * * *
38709651 TTTTTTAGAAAACACGAGAAAAAAATTTTG-ATCATCAGAA
1 -TTTTT-GAAAACAC--G--AAAATTTTTGAAACA-CGGGA
*
38709691 TTTTTGAGAACACGAAAATTTTTGAAACACCGGGA
1 TTTTTGAAAACACGAAAATTTTTGAAACA-CGGGA
* ** **
38709726 TTTTTGAAAACACTAGGATTTTTGAAACACGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGGGA
* *
38709760 ATTTTGAAAACACGAAAACTTTT-AAACACGGGAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGGG-A
*
38709794 TTTTTCGAAAACACGAAATTTTTTGAA
1 TTTTT-GAAAACACGAAAATTTTTGAA
38709821 TATTTACAAT
Statistics
Matches: 187, Mismatches: 37, Indels: 30
0.74 0.15 0.12
Matches are distributed among these distances:
33 7 0.04
34 50 0.27
35 58 0.31
36 42 0.22
37 1 0.01
38 8 0.04
39 8 0.04
40 13 0.07
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (34 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGGGA
Done.