Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 20 of 202
Found at i:5962685 original size:2 final size:2
Alignment explanation
Indices: 5962680--5962710 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5962670 TGTATAGAAG
5962680 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5962711 AACGTGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5969216 original size:23 final size:23
Alignment explanation
Indices: 5969190--5969235 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5969180 CATTTATATA
5969190 TTTAA-GATAGAATTTGAACAATT
1 TTTAAGGA-AGAATTTGAACAATT
* *
5969213 TTTAAGGAAGAGTTTGAAGAATT
1 TTTAAGGAAGAATTTGAACAATT
5969236 CTGATTGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (23 bp):
TTTAAGGAAGAATTTGAACAATT
Found at i:5979342 original size:8 final size:8
Alignment explanation
Indices: 5979329--5979362 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
5979319 TATGAATTAA
5979329 ATATTATT
1 ATATTATT
5979337 ATATTATT
1 ATATTATT
* *
5979345 ATAATAAT
1 ATATTATT
5979353 ATATTATT
1 ATATTATT
5979361 AT
1 AT
5979363 TGTTAACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
ATATTATT
Found at i:5979859 original size:17 final size:18
Alignment explanation
Indices: 5979837--5979870 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5979827 CAAATGAGTT
5979837 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
5979854 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
5979871 AAATGAAAAT
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:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:5980230 original size:36 final size:36
Alignment explanation
Indices: 5980150--5980241 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 36
5980140 ATATGTGTGG
* *
5980150 AATTGAAATGAATAT-TGACTTGAAAATGAAAAAGTA
1 AATTGAATTGAAT-TGTGACTTGAAAATAAAAAAGTA
*
5980186 AATTTTGAATTGAATTGTGA-TTGAAAGTAAAAAAGTGA
1 AA--TTGAATTGAATTGTGACTTGAAAATAAAAAAGT-A
*
5980224 AATTGAATTGAAATGTGA
1 AATTGAATTGAATTGTGA
5980242 ATTTGGAGAC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
36 17 0.35
37 15 0.31
38 16 0.33
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.32
Consensus pattern (36 bp):
AATTGAATTGAATTGTGACTTGAAAATAAAAAAGTA
Found at i:5981803 original size:20 final size:18
Alignment explanation
Indices: 5981778--5981814 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
5981768 CCGGCCCGAT
5981778 TTTTAATAAATACAAAAAAA
1 TTTTAA-AAATA-AAAAAAA
5981798 TTTTAAAAATAAAAAAA
1 TTTTAAAAATAAAAAAA
5981815 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TTTTAAAAATAAAAAAAA
Found at i:5984827 original size:6 final size:6
Alignment explanation
Indices: 5984816--5984840 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5984806 AAACAAAAAG
5984816 TATTAA TATTAA TATTAA TATTAA T
1 TATTAA TATTAA TATTAA TATTAA T
5984841 TATAAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:5990927 original size:89 final size:89
Alignment explanation
Indices: 5990763--5990930 Score: 198
Period size: 89 Copynumber: 1.9 Consensus size: 89
5990753 AGTTAGGCCC
* * * *
5990763 TGACTTGGCAACTTTTCCCACATTGGGCCTGAACATTTTGTTGTCCGAATTAGGTCCTAAACGTG
1 TGACTTCGCAACTTTTCCAACATTGGGCCTGAACATTTTGTTGTCCGAATTAAGCCCTAAACGTG
* **
5990828 GCAATTGTTCTCACGTTGGGACTT
66 ACAACAGTTCTCACGTTGGGACTT
* *
5990852 TGACTTCGCAAC-TTTCTCAACATTAGGGCCTGAAC-TTTTTTTGTCC-AAGTTAAGCCCTGAAC
1 TGACTTCGCAACTTTTC-CAACATT-GGGCCTGAACATTTTGTTGTCCGAA-TTAAGCCCTAAAC
*
5990914 TTGACAACAGTTCTCAC
63 GTGACAACAGTTCTCAC
5990931 ATTGAACCCT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
88 6 0.09
89 50 0.76
90 10 0.15
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (89 bp):
TGACTTCGCAACTTTTCCAACATTGGGCCTGAACATTTTGTTGTCCGAATTAAGCCCTAAACGTG
ACAACAGTTCTCACGTTGGGACTT
Found at i:5990942 original size:148 final size:148
Alignment explanation
Indices: 5990667--5990943 Score: 319
Period size: 148 Copynumber: 1.9 Consensus size: 148
5990657 TTTTAAGTTT
** * *
5990667 GGTCCTAAATTTGCCAATTGTTCTCACATTGGGACTTGGACTTGAAAATTTTTCCCACATTGGGA
1 GGTCCTAAACGTGCCAATTGTTCTCACATTGGGACTTGGACTTGAAAATTTCTCCAACATTGGGA
* * * * ** **
5990732 TATGAACTTCTTTTTAGTTCAAGTTAGGCCCTGACTTGGCAACTTTTCCCACATTGGGCCTGAAC
66 CATGAACTTCTTTTTAGTCCAAGTTAAGCCCTGACTTGACAACAGTTCCCACATTGACCCTGAAC
5990797 ATTTTGTTGTCCGAATTA
131 ATTTTGTTGTCCGAATTA
* * * * *
5990815 GGTCCTAAACGTGGCAATTGTTCTCACGTTGGGACTTTGACTTCGCAACTTTCT-CAACATTAGG
1 GGTCCTAAACGTGCCAATTGTTCTCACATTGGGACTTGGACTT-GAAAATTTCTCCAACATT-GG
* *
5990879 G-CCTGAACTT-TTTTT-GTCCAAGTTAAGCCCTGAACTTGACAACAGTTCTCACATTGAACCCT
64 GACATGAACTTCTTTTTAGTCCAAGTTAAGCCCTG-ACTTGACAACAGTTCCCACATTG-ACCCT
5990941 GAA
127 GAA
5990944 TTTAATAATT
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
146 15 0.14
147 24 0.23
148 57 0.54
149 10 0.09
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (148 bp):
GGTCCTAAACGTGCCAATTGTTCTCACATTGGGACTTGGACTTGAAAATTTCTCCAACATTGGGA
CATGAACTTCTTTTTAGTCCAAGTTAAGCCCTGACTTGACAACAGTTCCCACATTGACCCTGAAC
ATTTTGTTGTCCGAATTA
Found at i:5993498 original size:17 final size:17
Alignment explanation
Indices: 5993461--5993499 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5993451 TTATTTATTT
*
5993461 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
5993478 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
5993495 TATTG
1 TATTG
5993500 AATTGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:5995431 original size:40 final size:39
Alignment explanation
Indices: 5995371--5995511 Score: 135
Period size: 40 Copynumber: 3.6 Consensus size: 39
5995361 AACACATTAG
* *
5995371 TTTGGCACCCAGTGCCTCATCGAAAAATTCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGAAAAATCCAAAGT-ATAA
* **
5995411 TTTGACACCCAGTGTCTCATCGGTTAAA-CCAAAGTA-AA
1 TTTGACACCCAGTGCCTCATC-GAAAAATCCAAAGTATAA
* * *
5995449 -TTGGCACCTAGTGCCTCATCGAATAAATCCGAAGTGATAA
1 TTTGACACCCAGTGCCTCATCGAA-AAATCCAAAGT-ATAA
* *
5995489 ATTGACACCCAGTGTCTCATCGA
1 TTTGACACCCAGTGCCTCATCGA
5995512 CTCAAAGTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
36 1 0.01
37 20 0.25
38 8 0.10
39 2 0.02
40 27 0.33
41 23 0.28
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGAAAAATCCAAAGTATAA
Found at i:5998018 original size:3 final size:3
Alignment explanation
Indices: 5998010--5998037 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5998000 GGATCTATCC
5998010 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5998038 TTCGAAGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:5998419 original size:9 final size:9
Alignment explanation
Indices: 5998405--5998434 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5998395 ATACGTACAT
5998405 ATATATATA
1 ATATATATA
5998414 ATATATATA
1 ATATATATA
5998423 ATATATAATA
1 ATATAT-ATA
5998433 AT
1 AT
5998435 GTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.75
10 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATATATA
Found at i:5998623 original size:2 final size:2
Alignment explanation
Indices: 5998616--5998641 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5998606 CCTAAGTCAC
5998616 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
5998642 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6001263 original size:3 final size:3
Alignment explanation
Indices: 6001255--6001298 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
6001245 ATAATTTCTC
6001255 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6001299 ATCAGTTCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6007792 original size:24 final size:25
Alignment explanation
Indices: 6007756--6007820 Score: 62
Period size: 29 Copynumber: 2.5 Consensus size: 25
6007746 AATTAAAATT
6007756 ATTTAATTA-TTTTAT-AAAAATAAA
1 ATTTAA-TACTTTTATAAAAAATAAA
6007780 ATTTAATACTTTTTTTATACAAAAATAAA
1 ATTTAATAC---TTTTATA-AAAAATAAA
*
6007809 ATTCAATACTTT
1 ATTTAATACTTT
6007821 GTTTTTGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 2 0.06
24 6 0.18
26 3 0.09
27 6 0.18
29 17 0.50
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTAATACTTTTATAAAAAATAAA
Found at i:6009841 original size:4 final size:4
Alignment explanation
Indices: 6009832--6009870 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
6009822 TACTCCTCAG
6009832 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
6009871 CAATAATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:6014951 original size:43 final size:43
Alignment explanation
Indices: 6014897--6014985 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
6014887 AAATGTTTTC
6014897 CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
1 CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
*
6014940 CATTTTTTAATCCAAGATTGTGACTTTATCCGGCATTGATAAA
1 CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
6014983 CAT
1 CAT
6014986 ATTCTTCTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (43 bp):
CATTTTTTAATCCAAGATTGTGACTTTATCCGGAATTGATAAA
Found at i:6015218 original size:17 final size:18
Alignment explanation
Indices: 6015181--6015218 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6015171 GAAAATTTTT
* *
6015181 AATTAAACCGATTACATC
1 AATTAAACAGATGACATC
6015199 AATTAAACAGATGA-ATC
1 AATTAAACAGATGACATC
6015216 AAT
1 AAT
6015219 AACTTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTAAACAGATGACATC
Found at i:6015401 original size:55 final size:51
Alignment explanation
Indices: 6015298--6015406 Score: 164
Period size: 55 Copynumber: 2.1 Consensus size: 51
6015288 ATAAGAATCA
* *
6015298 GATTTTATATAATATTAAAAATAATACATTTTTTAATATGTGATGTGATGT
1 GATTTTATATAATACTAAAAATAATACATTTTTTAACATGTGATGTGATGT
6015349 GATTTTATATAATACTAAAAATAAAAATAACATTTTTTAACATGTGATGTGATGT
1 GATTTTATATAATACTAAAAAT---AAT-ACATTTTTTAACATGTGATGTGATGT
6015404 GAT
1 GAT
6015407 GTGATTTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
51 21 0.40
54 3 0.06
55 28 0.54
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (51 bp):
GATTTTATATAATACTAAAAATAATACATTTTTTAACATGTGATGTGATGT
Found at i:6023301 original size:21 final size:21
Alignment explanation
Indices: 6023277--6023317 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6023267 TCACCCATGT
*
6023277 TATTTTTAAATTTTTTTTAAA
1 TATTTATAAATTTTTTTTAAA
*
6023298 TATTTATATATTTTTTTTAA
1 TATTTATAAATTTTTTTTAA
6023318 TTCAATACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATAAATTTTTTTTAAA
Found at i:6029258 original size:1 final size:1
Alignment explanation
Indices: 6029252--6029278 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6029242 GATACTTTCA
6029252 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
6029279 GCAGACTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6030997 original size:20 final size:20
Alignment explanation
Indices: 6030951--6031001 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
6030941 ATATTTTCAA
* * **
6030951 TTATTTTTACTTTATTTTTT
1 TTATTTTTATTTTAATTGAT
*
6030971 TTCTTTTTATTTTAATTGAT
1 TTATTTTTATTTTAATTGAT
6030991 TTATTTTTATT
1 TTATTTTTATT
6031002 AAAACTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (20 bp):
TTATTTTTATTTTAATTGAT
Found at i:6033525 original size:31 final size:31
Alignment explanation
Indices: 6033490--6033548 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
6033480 AGTGATTTAA
6033490 TATAA-ATATAAAT-ATATATATAATTATTATT
1 TATAATATATAAATAATATA-AT-ATTATTATT
*
6033521 TATAATATATAACTAATATAATATTATT
1 TATAATATATAAATAATATAATATTATT
6033549 TTATAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 11 0.44
32 9 0.36
33 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
TATAATATATAAATAATATAATATTATTATT
Found at i:6033547 original size:24 final size:25
Alignment explanation
Indices: 6033487--6033547 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
6033477 ATTAGTGATT
6033487 TAATATAA-A-TATAAATATATATA
1 TAATATAATATTATAAATATATATA
*
6033510 TAAT-TATTATT-TATAATATATA-A
1 TAATATAATATTATA-AATATATATA
6033533 CTAATATAATATTAT
1 -TAATATAATATTAT
6033548 TTTATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 2 0.07
23 8 0.27
24 13 0.43
25 6 0.20
26 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATATAATATTATAAATATATATA
Found at i:6035083 original size:18 final size:19
Alignment explanation
Indices: 6035046--6035084 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6035036 ATTACAAAAT
* *
6035046 AATTTAAAATAATTTTTAA
1 AATTCAAAATAATTTATAA
6035065 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTTATAA
6035083 AA
1 AA
6035085 ATTTTAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTCAAAATAATTTATAA
Found at i:6037110 original size:23 final size:23
Alignment explanation
Indices: 6037075--6037119 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
6037065 TTAATCTCGA
6037075 TTTTTTTATTTTTAAGAATTTAGT
1 TTTTTTTATTTTTAA-AATTTAGT
6037099 TTTTTTTATTTTTAAAATTTA
1 TTTTTTTATTTTTAAAATTTA
6037120 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTTTTATTTTTAAAATTTAGT
Found at i:6044023 original size:31 final size:30
Alignment explanation
Indices: 6043980--6044040 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
6043970 ATTCATTATA
*
6043980 GGAAAATTAAATAA-AGAAA-ATGACTAAATT
1 GGAAAATGAAATAATA-AAAGATGA-TAAATT
6044010 GGAAAGATGAAATAATAAAAGATGATAAATT
1 GGAAA-ATGAAATAATAAAAGATGATAAATT
6044041 AATTAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 5 0.19
31 17 0.63
32 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.23
Consensus pattern (30 bp):
GGAAAATGAAATAATAAAAGATGATAAATT
Found at i:6044516 original size:24 final size:25
Alignment explanation
Indices: 6044464--6044510 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6044454 TAGCTCTCAT
* *
6044464 GAGCTTCCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGC
6044489 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
6044511 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGC
Found at i:6044725 original size:24 final size:25
Alignment explanation
Indices: 6044693--6044781 Score: 121
Period size: 24 Copynumber: 3.6 Consensus size: 25
6044683 TATTGGCTCG
6044693 TATGAGCTTCCCATTAATGGCTCTC
1 TATGAGCTTCCCATTAATGGCTCTC
6044718 TATG-GCTTCCCATTAATGGCTCTC
1 TATGAGCTTCCCATTAATGGCTCTC
* * *
6044742 T-GGAGCTTCCCGTTACATGGCTCAC
1 TATGAGCTTCCCATTA-ATGGCTCTC
6044767 -ATGAGCTTCCCATTA
1 TATGAGCTTCCCATTA
6044782 TGTGCTCGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
23 1 0.02
24 31 0.55
25 24 0.43
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (25 bp):
TATGAGCTTCCCATTAATGGCTCTC
Found at i:6044772 original size:25 final size:24
Alignment explanation
Indices: 6044594--6044781 Score: 118
Period size: 24 Copynumber: 7.5 Consensus size: 24
6044584 TGGCTCTTCG
*
6044594 GAGCTTCCCGATTAAAGGCTCTGTCAT
1 GAGCTTCCC-ATTAATGGCTC--TCAT
* **
6044621 GAGCTTCTCGATTAATTGGCTCTCCG
1 GAGCTTC-CCATTAA-TGGCTCTCAT
* *
6044647 GAGCTTCCCGA-TATTGGCT-TCCTT
1 GAGCTTCCC-ATTAATGGCTCT-CAT
* * *
6044671 GAACTTTCTCGA-TATTGGCTCGT-AT
1 GAGC-TTC-CCATTAATGGCTC-TCAT
6044696 GAGCTTCCCATTAATGGCTCTCTAT
1 GAGCTTCCCATTAATGGCTCTC-AT
6044721 G-GCTTCCCATTAATGGCTCTC-T
1 GAGCTTCCCATTAATGGCTCTCAT
* *
6044743 GGAGCTTCCCGTTACATGGCTCACAT
1 -GAGCTTCCCATTA-ATGGCTCTCAT
6044769 GAGCTTCCCATTA
1 GAGCTTCCCATTA
6044782 TGTGCTCGTA
Statistics
Matches: 129, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
22 1 0.01
23 5 0.04
24 50 0.39
25 42 0.33
26 12 0.09
27 13 0.10
28 6 0.05
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCATTAATGGCTCTCAT
Found at i:6044794 original size:24 final size:24
Alignment explanation
Indices: 6044686--6044796 Score: 120
Period size: 24 Copynumber: 4.6 Consensus size: 24
6044676 TTCTCGATAT
6044686 TGGCTCGTATGAGCTTCCCATTAA
1 TGGCTCGTATGAGCTTCCCATTAA
*
6044710 TGGCTCTCTATG-GCTTCCCATTAA
1 TGGCTC-GTATGAGCTTCCCATTAA
* *
6044734 TGGCTC-TCTGGAGCTTCCCGTTACA
1 TGGCTCGTAT-GAGCTTCCCATTA-A
**
6044759 TGGCTCACATGAGCTTCCCATT-A
1 TGGCTCGTATGAGCTTCCCATTAA
6044782 TGTGCTCGTATGAGC
1 TG-GCTCGTATGAGC
6044797 ATTCTCGAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.03
23 4 0.05
24 44 0.60
25 22 0.30
26 1 0.01
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (24 bp):
TGGCTCGTATGAGCTTCCCATTAA
Found at i:6046255 original size:27 final size:27
Alignment explanation
Indices: 6046225--6046298 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
6046215 GCTTCAAAGA
** *
6046225 GCCACAATCACTATGTTGCACTGAAGT
1 GCCACAATCACTATGTTGCACCAAAAT
* * *
6046252 GCCACGATCATTAAGTTGCACCAAAAT
1 GCCACAATCACTATGTTGCACCAAAAT
*
6046279 GCCACTATCACTGAT-TTGCA
1 GCCACAATCACT-ATGTTGCA
6046299 TCGAACTGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (27 bp):
GCCACAATCACTATGTTGCACCAAAAT
Found at i:6054743 original size:31 final size:35
Alignment explanation
Indices: 6054675--6054748 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
6054665 ATTCTATAAT
*
6054675 AATTTACAATAAATTCTTATTTATTGGCAAATAAAA
1 AATTTACAATAAATTCTTATTTATT-GCAAAGAAAA
6054711 AATTT-CAATAAATTCTTA-TT-TT-CAAAGGAAAA
1 AATTTACAATAAATTCTTATTTATTGCAAA-GAAAA
6054743 AATTTA
1 AATTTA
6054749 TAAATCCTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 4 0.11
32 9 0.26
33 2 0.06
34 2 0.06
35 13 0.37
36 5 0.14
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (35 bp):
AATTTACAATAAATTCTTATTTATTGCAAAGAAAA
Found at i:6059771 original size:129 final size:129
Alignment explanation
Indices: 6059634--6059892 Score: 518
Period size: 129 Copynumber: 2.0 Consensus size: 129
6059624 GGGCAAATTT
6059634 CAAAAAAAAACCTTTTTTTTTAATTTACTGAAATGGGTTCGATATATAATTATTTACCAGAATGG
1 CAAAAAAAAACCTTTTTTTTTAATTTACTGAAATGGGTTCGATATATAATTATTTACCAGAATGG
6059699 CCCAATTCCTCTAAAGCGCGTCCACGTCAGCGCGATGTCAGGGGACGTAGCAGAAAAACGCGTC
66 CCCAATTCCTCTAAAGCGCGTCCACGTCAGCGCGATGTCAGGGGACGTAGCAGAAAAACGCGTC
6059763 CAAAAAAAAACCTTTTTTTTTAATTTACTGAAATGGGTTCGATATATAATTATTTACCAGAATGG
1 CAAAAAAAAACCTTTTTTTTTAATTTACTGAAATGGGTTCGATATATAATTATTTACCAGAATGG
6059828 CCCAATTCCTCTAAAGCGCGTCCACGTCAGCGCGATGTCAGGGGACGTAGCAGAAAAACGCGTC
66 CCCAATTCCTCTAAAGCGCGTCCACGTCAGCGCGATGTCAGGGGACGTAGCAGAAAAACGCGTC
6059892 C
1 C
6059893 TCAAGGACGC
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (129 bp):
CAAAAAAAAACCTTTTTTTTTAATTTACTGAAATGGGTTCGATATATAATTATTTACCAGAATGG
CCCAATTCCTCTAAAGCGCGTCCACGTCAGCGCGATGTCAGGGGACGTAGCAGAAAAACGCGTC
Found at i:6060134 original size:11 final size:11
Alignment explanation
Indices: 6060096--6060149 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
6060086 TAAATCCTTT
*
6060096 CTCTC-AATTT
1 CTCTCAAATTC
6060106 CTCTCTAATATT-
1 CTCTC-AA-ATTC
6060118 CTCTCAAATTC
1 CTCTCAAATTC
6060129 CTCTCAAATTC
1 CTCTCAAATTC
6060140 CTCTCAAATT
1 CTCTCAAATT
6060150 TCTATTTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.20
11 23 0.57
12 6 0.15
13 3 0.08
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:6060215 original size:13 final size:12
Alignment explanation
Indices: 6060193--6060223 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
6060183 TTTAAAAAAG
6060193 TTTTAATTTTTT
1 TTTTAATTTTTT
6060205 TTTTGAATTTTTT
1 TTTT-AATTTTTT
6060218 TTTTAA
1 TTTTAA
6060224 ATCGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:6065425 original size:14 final size:15
Alignment explanation
Indices: 6065398--6065428 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6065388 TGTCTTGGTG
6065398 TCGAAAATTAAAAAA
1 TCGAAAATTAAAAAA
*
6065413 TCGAAAATAAAAAAA
1 TCGAAAATTAAAAAA
6065428 T
1 T
6065429 ACGATACCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
TCGAAAATTAAAAAA
Found at i:6066385 original size:2 final size:2
Alignment explanation
Indices: 6066326--6066366 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6066316 TTTTTTAAAG
6066326 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
6066367 ACAATTGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6068454 original size:30 final size:30
Alignment explanation
Indices: 6068420--6068477 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6068410 GTAGTCAAAG
*
6068420 CCGTGTGTCTCACACGACCAAGAGACACGT
1 CCGTGTATCTCACACGACCAAGAGACACGT
*
6068450 CCGTGTATCTCACACGGCCAAGAGACAC
1 CCGTGTATCTCACACGACCAAGAGACAC
6068478 CCTCATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (30 bp):
CCGTGTATCTCACACGACCAAGAGACACGT
Found at i:6068491 original size:30 final size:30
Alignment explanation
Indices: 6068425--6068493 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
6068415 CAAAGCCGTG
* * *
6068425 TGTCTCACACGACCAAGAGACACGTCCGTG
1 TGTCTCACACGACCAAGAGACACCTCCATA
* *
6068455 TATCTCACACGGCCAAGAGACACC-CTCATA
1 TGTCTCACACGACCAAGAGACACCTC-CATA
6068485 TGTCTCACA
1 TGTCTCACA
6068494 TAGCCGTGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (30 bp):
TGTCTCACACGACCAAGAGACACCTCCATA
Found at i:6078779 original size:25 final size:24
Alignment explanation
Indices: 6078736--6078788 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
6078726 AAGTTGAAGC
6078736 GAGCCATATCAGGAAGCTCATAAA
1 GAGCCATATCAGGAAGCTCATAAA
* *
6078760 GAGCCTATATCGGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
6078785 GAGC
1 GAGC
6078789 TGCAGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:6079342 original size:45 final size:45
Alignment explanation
Indices: 6079292--6079382 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
6079282 AATTCATATT
6079292 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
6079337 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
1 CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
6079382 C
1 C
6079383 TATACTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (45 bp):
CAATTAAATCAAATTCACATTTTAGGCAAAAGTATCATTTTGCCC
Found at i:6080599 original size:11 final size:11
Alignment explanation
Indices: 6080574--6080607 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6080564 ATAATTTAAT
6080574 AAATAAAAATAA
1 AAATAAAAAT-A
6080586 AAATAAAAATA
1 AAATAAAAATA
*
6080597 AAATATAAATA
1 AAATAAAAATA
6080608 GACACATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:6080607 original size:6 final size:6
Alignment explanation
Indices: 6080574--6080605 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
6080564 ATAATTTAAT
6080574 AAATAA AAATAA AAATAA AAATAA AATATAA A
1 AAATAA AAATAA AAATAA AAATAA AA-ATAA A
6080606 TAGACACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:6080747 original size:56 final size:56
Alignment explanation
Indices: 6080661--6080772 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
6080651 TTGGAGAGAA
6080661 GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
1 GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
*
6080717 GAAATGGATACAAATGGAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
1 GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
6080773 CAAGACTTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (56 bp):
GAAATGGATACAAATGAAGAATATTAAAGACTTATATTTCAATTATGTGTTAATTT
Found at i:6080815 original size:37 final size:37
Alignment explanation
Indices: 6080774--6080848 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
6080764 TGTTAATTTC
*
6080774 AAGACTTATGTTATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
6080811 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
6080848 A
1 A
6080849 TTTGGATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:6080838 original size:17 final size:17
Alignment explanation
Indices: 6080779--6080839 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
6080769 ATTTCAAGAC
*
6080779 TTATGTTATGTTTTTAA
1 TTATGTAATGTTTTTAA
* ***
6080796 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
6080815 CTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
6080833 TTATGTA
1 TTATGTA
6080840 GTGATTCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 4 0.12
20 9 0.28
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:6080867 original size:9 final size:9
Alignment explanation
Indices: 6080855--6080887 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
6080845 TCAATTTGGA
6080855 TAATTCGGT
1 TAATTCGGT
6080864 TAATTCAGG-
1 TAATTC-GGT
6080873 TAATTCGGT
1 TAATTCGGT
6080882 TAATTC
1 TAATTC
6080888 TTAACCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:6082011 original size:20 final size:20
Alignment explanation
Indices: 6081972--6082012 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6081962 AATAAGAACA
* **
6081972 ATATTTTAATTTTAGGATAT
1 ATATATTAATTTTAAAATAT
6081992 ATATATTAATTTTAAAATAT
1 ATATATTAATTTTAAAATAT
6082012 A
1 A
6082013 ATTATATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATATTAATTTTAAAATAT
Found at i:6085312 original size:3 final size:3
Alignment explanation
Indices: 6085306--6085433 Score: 157
Period size: 3 Copynumber: 42.7 Consensus size: 3
6085296 TCAGCAACAA
* * * * *
6085306 CAG CAG CAG CAA CAA CAG CAG CAG CAA CAA CAG CAG CAG CAG CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
6085354 CAG CAG CAG CAG CAG CAA CAA CAG CAG CAG CAG CAA CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
6085402 CAG CAG CAA CAA CAG CAA CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
6085434 ACAACAACAA
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.42, C:0.34, G:0.24, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:6085317 original size:15 final size:15
Alignment explanation
Indices: 6085297--6085471 Score: 191
Period size: 15 Copynumber: 12.1 Consensus size: 15
6085287 GAGGCATGCT
6085297 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
6085312 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
6085327 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
*
6085342 CAGCAGCAACAGCAG
1 CAGCAACAACAGCAG
6085357 CAG------CAGCAG
1 CAGCAACAACAGCAG
6085366 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
*
6085381 CAGCAGCAACAGCAG
1 CAGCAACAACAGCAG
* * *
6085396 CAGCAGCAGCAGCAA
1 CAGCAACAACAGCAG
* *
6085411 CAACAGCAACAGCAG
1 CAGCAACAACAGCAG
* * *
6085426 CAGCAGCAACAACAA
1 CAGCAACAACAGCAG
* * *
6085441 CAACAACAACAACAA
1 CAGCAACAACAGCAG
6085456 CAGCAACAACAGCAG
1 CAGCAACAACAGCAG
6085471 C
1 C
6085472 CGCAGCAGCA
Statistics
Matches: 139, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
9 9 0.06
15 130 0.94
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (15 bp):
CAGCAACAACAGCAG
Found at i:6085327 original size:18 final size:18
Alignment explanation
Indices: 6085300--6085478 Score: 187
Period size: 18 Copynumber: 9.9 Consensus size: 18
6085290 GCATGCTCAG
*
6085300 CAACAACAGCAGCAGCAA
1 CAACAGCAGCAGCAGCAA
*
6085318 CAACAGCAGCAGCAACAA
1 CAACAGCAGCAGCAGCAA
* * *
6085336 CAGCAGCAGCAGCAACAG
1 CAACAGCAGCAGCAGCAA
*
6085354 CAGCAGCAGCAGCAGCAA
1 CAACAGCAGCAGCAGCAA
6085372 CAACAGCAGCAGCAGCAA
1 CAACAGCAGCAGCAGCAA
* *
6085390 CAGCAGCAGCAGCAGCAG
1 CAACAGCAGCAGCAGCAA
* * *
6085408 CAACAACAGCAACAGCAG
1 CAACAGCAGCAGCAGCAA
* * * *
6085426 CAGCAGCAACAACAACAA
1 CAACAGCAGCAGCAGCAA
* * *
6085444 CAACAACAACAACAGCAA
1 CAACAGCAGCAGCAGCAA
*
6085462 CAACAGCAGCCGCAGCA
1 CAACAGCAGCAGCAGCA
6085479 GCAGTCGCCC
Statistics
Matches: 137, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 137 1.00
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (18 bp):
CAACAGCAGCAGCAGCAA
Found at i:6085438 original size:3 final size:3
Alignment explanation
Indices: 6085408--6085466 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
6085398 GCAGCAGCAG
* * * * *
6085408 CAA CAA CAG CAA CAG CAG CAG CAG CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
*
6085456 CAG CAA CAA CA
1 CAA CAA CAA CA
6085467 GCAGCCGCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.56, C:0.34, G:0.10, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:6086274 original size:13 final size:14
Alignment explanation
Indices: 6086241--6086287 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
6086231 GGTAGGTTTG
6086241 TTTGATCTCTTTCA
1 TTTGATCTCTTTCA
6086255 TTTGATCTC-TT-A
1 TTTGATCTCTTTCA
6086267 TATTGATCTCTTTCA
1 T-TTGATCTCTTTCA
6086282 TTTGAT
1 TTTGAT
6086288 GCTTCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.07
13 10 0.33
14 16 0.53
15 2 0.07
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (14 bp):
TTTGATCTCTTTCA
Found at i:6087252 original size:6 final size:6
Alignment explanation
Indices: 6087241--6087270 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6087231 TGGCTCAGTT
6087241 GCAACA GCAACA GCAACA GCAACA G-AACA G
1 GCAACA GCAACA GCAACA GCAACA GCAACA G
6087271 TAGCTCACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.50, C:0.30, G:0.20, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:6096393 original size:40 final size:40
Alignment explanation
Indices: 6096330--6096410 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
6096320 TTTTATGCTT
6096330 GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
1 GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
* *
6096370 GTTTTGCTATATGCAGCTTTGTAATTATCAAAGAACAAAG
1 GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
6096410 G
1 G
6096411 GTTGTCTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (40 bp):
GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
Found at i:6103132 original size:363 final size:363
Alignment explanation
Indices: 6102467--6103165 Score: 1157
Period size: 363 Copynumber: 1.9 Consensus size: 363
6102457 CACATATATG
*
6102467 CATATTTTACCAAATATGTTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
1 CATATTTTACCAAATATGCTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
*
6102532 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAATATACCAAACATAGCCCTTTAAAT
66 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
* *
6102597 GGCTATTTACAACCAAAATATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
131 AGCTATTTACAACCAAAACATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
* ** * *
6102662 ACCAAAATTAGTTTCATGCCTGTACCGAAAATGGGTCGGTGGGTAGTGTGAGTGATCTCTACCAA
196 ACCAAAATTAGTTTCATACCTGTACAAAAAATGGGCCGGTGGATAGTGTGAGTGATCTCTACCAA
*
6102727 GCTTCCAACCCGATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTT-A
261 GCTTCCAACCCAATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTTGA
6102791 GTGCTTAGTAAGTTCATATAAAACAGAGGATCAAGATAA
326 -TGCTTAGTAAGTTCATATAAAACAGAGGATCAAGATAA
*
6102830 CATATTTTACCAAATATGCTATCTTGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
1 CATATTTTACCAAATATGCTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
6102895 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
66 AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
* * * *
6102960 AGCTATTTACAACCAAAACATGTATGTGTCATCAATGGCTAAGTTAACCTATACATGTCATTATA
131 AGCTATTTACAACCAAAACATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
** * * * *
6103025 ACCAAAATTAGTTTCATATTTGTATAAAAAATGGGCCGGTGGATCGTGTGAGTGATCTTTGCCAA
196 ACCAAAATTAGTTTCATACCTGTACAAAAAATGGGCCGGTGGATAGTGTGAGTGATCTCTACCAA
** * *
6103090 GCTTCCAACCCAATGAGCCTCCGAGATTTATAAAATAGAGGAAATACAACTGAATAAGCACTTGA
261 GCTTCCAACCCAATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTTGA
6103155 TGCTTAGTAAG
326 TGCTTAGTAAG
6103166 CCCGTATAAT
Statistics
Matches: 310, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
363 309 1.00
364 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (363 bp):
CATATTTTACCAAATATGCTATCTAGATCCATTCATCCATGTACTTACCATCATTTGACCATTTC
AAACACACATAAAGTATATTAAGACTATTTACACATCAAAACATACCAAACATAGCCCTTTAAAT
AGCTATTTACAACCAAAACATGTATATGTCATCAATGACCAAGTTAACCTATACATGCCATTATA
ACCAAAATTAGTTTCATACCTGTACAAAAAATGGGCCGGTGGATAGTGTGAGTGATCTCTACCAA
GCTTCCAACCCAATGAGCCTCCGAGAACTATAAAACAGAGGAAATACAACTGAATAAACACTTGA
TGCTTAGTAAGTTCATATAAAACAGAGGATCAAGATAA
Found at i:6103650 original size:24 final size:24
Alignment explanation
Indices: 6103623--6103712 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 24
6103613 TATTTAGAAT
*
6103623 GCTCATGCGAGCA-TATAACGGGTA
1 GCTCATGAGAGCACT-TAACGGGTA
*
6103647 GCTC-TGAAGAGCACTTAACGAGTA
1 GCTCATG-AGAGCACTTAACGGGTA
6103671 GCTCA-GAGTAGCACTTAACGGGTA
1 GCTCATGAG-AGCACTTAACGGGTA
*
6103695 GCTC-CGAAGAGCACTTAA
1 GCTCATG-AGAGCACTTAA
6103713 TTAGGAAGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
23 4 0.07
24 50 0.88
25 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (24 bp):
GCTCATGAGAGCACTTAACGGGTA
Found at i:6104438 original size:46 final size:46
Alignment explanation
Indices: 6104371--6104620 Score: 419
Period size: 46 Copynumber: 5.4 Consensus size: 46
6104361 NNNNNNNNNN
*
6104371 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATC
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
* * *
6104417 ACTTAGCACTTTGTTACTTGATCAGATAAGTGTAGTTAAAGCTACC
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
*
6104463 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATC
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
* *
6104509 ACTTATCACTTTGTTACTTGATCAGATAAGTGTAGTTAAAGCTACC
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
6104555 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
* *
6104601 ACTTATCAATTTGCCACTTG
1 ACTTATCACTTTGTCACTTG
6104621 TCACTGATCA
Statistics
Matches: 189, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 189 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (46 bp):
ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACC
Found at i:6108101 original size:46 final size:41
Alignment explanation
Indices: 6108049--6108518 Score: 424
Period size: 46 Copynumber: 11.6 Consensus size: 41
6108039 TTTGAGTACT
6108049 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAG---T-GCTACACTTA
6108095 TCTGATCAAGTGACAAAGTGATAAGTG--GT--TACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGTGCTACACTTA
*
6108132 TCTGATCAAGTGACAAAGTGAT-A----AGTGCTAAACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGTGCTACACTTA
*
6108168 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAG---T-GCTACACTTA
*
6108214 TCTGATCAAGTGACAAAGTG---A----AGTGCTAAACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGTGCTACACTTA
*
6108248 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAG---T-GCTACACTTA
*
6108294 TCTGATCAAGAGACAAAGTGATAA--GT-G-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGTGCTACACTTA
**
6108331 TCTGATCAAGAAACAAAGTGATAAGTG--GT--TACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGTGCTACACTTA
*
6108368 TCTGATCAAGAGACAAAGTGATAA--GT-G-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGTGCTACACTTA
*
6108405 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAG--T--GCTACACTTA
*
6108451 TCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAG--T-GCTACACTTA
6108496 TCTGATCAAG-GAC-AAGTGATAAG
1 TCTGATCAAGTGACAAAGTGATAAG
6108519 AGGTCATATG
Statistics
Matches: 369, Mismatches: 15, Indels: 83
0.79 0.03 0.18
Matches are distributed among these distances:
34 30 0.08
35 2 0.01
36 30 0.08
37 126 0.34
38 3 0.01
39 1 0.00
40 3 0.01
41 1 0.00
42 5 0.01
43 14 0.04
44 2 0.01
45 24 0.07
46 128 0.35
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (41 bp):
TCTGATCAAGTGACAAAGTGATAAGTGTAGTGCTACACTTA
Found at i:6108129 original size:37 final size:37
Alignment explanation
Indices: 6108087--6108433 Score: 396
Period size: 37 Copynumber: 9.0 Consensus size: 37
6108077 TAGTTTTAGC
*
6108087 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
* *
6108124 TACACTTATCTGATCAAGTGACAAAGTGATAAGT-GC
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
*
6108160 TAAACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGT-G--G---T
* *
6108203 AGCTACACTTATCTGATCAAGTGACAAAGTG--AAGT-GC
1 ---TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
*
6108240 TAAACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGT-G--G---T
*
6108283 AGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGC
1 ---TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
*
6108323 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
*
6108360 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
* *
6108397 TACACTTATCTGATCAAGTGATAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
6108434 AGCTTCAGCT
Statistics
Matches: 269, Mismatches: 19, Indels: 44
0.81 0.06 0.13
Matches are distributed among these distances:
34 26 0.10
36 37 0.14
37 138 0.51
40 3 0.01
43 1 0.00
44 4 0.01
45 1 0.00
46 59 0.22
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
Found at i:6114724 original size:32 final size:31
Alignment explanation
Indices: 6114676--6114753 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 31
6114666 AGTTATTCAT
6114676 AAAATTAAT-T-AT-ATAAAAAATATTTTAA
1 AAAATTAATATAATGATAAAAAATATTTTAA
* * **
6114704 AAACTTAAATATGATGATAAATTATATTTTAA
1 AAAATT-AATATAATGATAAAAAATATTTTAA
6114736 AAAATTAATATAATGATA
1 AAAATTAATATAATGATA
6114754 CATGATATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 1 0.02
31 13 0.32
32 19 0.46
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (31 bp):
AAAATTAATATAATGATAAAAAATATTTTAA
Found at i:6114752 original size:31 final size:31
Alignment explanation
Indices: 6114695--6114776 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
6114685 TATATAAAAA
* * *
6114695 ATATTTTAAAAACTTAAATATGATGATAAATT
1 ATATTTTAAAAAATT-AATATAATGATAAATG
*
6114727 ATATTTTAAAAAATTAATATAATGATACATG
1 ATATTTTAAAAAATTAATATAATGATAAATG
*
6114758 ATA-TTTAAATAATCTAATA
1 ATATTTTAAAAAAT-TAATA
6114777 AATTAGTACA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 9 0.20
31 21 0.48
32 14 0.32
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (31 bp):
ATATTTTAAAAAATTAATATAATGATAAATG
Found at i:6114787 original size:31 final size:31
Alignment explanation
Indices: 6114731--6114807 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
6114721 TAAATTATAT
* *
6114731 TTTAAAAAAT-TAATATAATGATACATGATA
1 TTTAAATAATCTAATATAATGATACATGAAA
* *
6114761 TTTAAATAATCTAATA-AATTAGTACATTAAA
1 TTTAAATAATCTAATATAATGA-TACATGAAA
*
6114792 TATAAATTAATCTAAT
1 TTTAAA-TAATCTAAT
6114808 TTTTTATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 13 0.33
31 17 0.44
32 9 0.23
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (31 bp):
TTTAAATAATCTAATATAATGATACATGAAA
Found at i:6117327 original size:31 final size:31
Alignment explanation
Indices: 6117292--6117370 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
6117282 TTAATATACT
* *
6117292 ATTTGGTATCTTACTTTGG-TTTCAAAGTTCA
1 ATTTGGTATCTAAATTTGGATTT-AAAGTTCA
*
6117323 ATTTGGTATCTAAATTTGGATTTAAGGTTCA
1 ATTTGGTATCTAAATTTGGATTTAAAGTTCA
* *
6117354 CTTTGGTACCTAAATTT
1 ATTTGGTATCTAAATTT
6117371 TTTTAATTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 39 0.93
32 3 0.07
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.47
Consensus pattern (31 bp):
ATTTGGTATCTAAATTTGGATTTAAAGTTCA
Found at i:6122966 original size:6 final size:6
Alignment explanation
Indices: 6122957--6122991 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
6122947 TTTTTTCTTT
*
6122957 TAAAAA TAAAAA TAAGAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
6122992 TCTTGGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:6131209 original size:25 final size:25
Alignment explanation
Indices: 6131164--6131307 Score: 93
Period size: 25 Copynumber: 5.8 Consensus size: 25
6131154 TGGTTTTTAC
* *
6131164 GAGCTTCCCGA-TAACTAGCTCTTAT
1 GAGCTTCCTGATTAA-TGGCTCTTAT
* ***
6131189 GAGTTTCCTGATTAATGGCTCTCCG
1 GAGCTTCCTGATTAATGGCTCTTAT
* * *
6131214 GAGCTTCCCGA-TATTGGCTCGTAT
1 GAGCTTCCTGATTAATGGCTCTTAT
*
6131238 GAGCTTCCTG-TTAATGGCTCTCCA-
1 GAGCTTCCTGATTAATGGCTCT-TAT
** *
6131262 GAGCTTCCTG-TTACATGGCTCACAA
1 GAGCTTCCTGATTA-ATGGCTCTTAT
6131287 GAGCTTCCTG-TTATATGGCTC
1 GAGCTTCCTGATTA-ATGGCTC
6131308 GAAAGAACTT
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
24 40 0.42
25 52 0.55
26 3 0.03
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTTAT
Found at i:6131255 original size:24 final size:23
Alignment explanation
Indices: 6131181--6131307 Score: 94
Period size: 25 Copynumber: 5.2 Consensus size: 23
6131171 CCGATAACTA
*
6131181 GCTCTTATGAGTTTCCTGATTAATG
1 GCTC-TATGAGCTTCCTG-TTAATG
** * * *
6131206 GCTCTCCGGAGCTTCCCGATATTG
1 GCTCT-ATGAGCTTCCTGTTAATG
6131230 GCTCGTATGAGCTTCCTGTTAATG
1 GCTC-TATGAGCTTCCTGTTAATG
6131254 GCTCTCCA-GAGCTTCCTGTTACATG
1 GCTCT--ATGAGCTTCCTGTTA-ATG
* *
6131279 GCTCACAAGAGCTTCCTGTTATATG
1 GCTC-TATGAGCTTCCTGTTA-ATG
6131304 GCTC
1 GCTC
6131308 GAAAGAACTT
Statistics
Matches: 82, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
23 1 0.01
24 40 0.49
25 41 0.50
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (23 bp):
GCTCTATGAGCTTCCTGTTAATG
Found at i:6131281 original size:49 final size:48
Alignment explanation
Indices: 6131164--6131307 Score: 162
Period size: 49 Copynumber: 2.9 Consensus size: 48
6131154 TGGTTTTTAC
* * * *
6131164 GAGCTTCCCGATAACTAGCTCTTATGAGTTTCCTGATTAATGGCTCTCCG
1 GAGCTTCCCGATAA-TGGCTCATATGAGCTTCCTG-TTAATGGCTCTCCA
* *
6131214 GAGCTTCCCGATATTGGCTCGTATGAGCTTCCTGTTAATGGCTCTCCA
1 GAGCTTCCCGATAATGGCTCATATGAGCTTCCTGTTAATGGCTCTCCA
* * * *
6131262 GAGCTTCCTGTTACATGGCTCACAAGAGCTTCCTGTTATATGGCTC
1 GAGCTTCCCGATA-ATGGCTCATATGAGCTTCCTGTTA-ATGGCTC
6131308 GAAAGAACTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
48 24 0.30
49 37 0.46
50 20 0.25
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (48 bp):
GAGCTTCCCGATAATGGCTCATATGAGCTTCCTGTTAATGGCTCTCCA
Found at i:6131313 original size:25 final size:25
Alignment explanation
Indices: 6131214--6131313 Score: 98
Period size: 25 Copynumber: 4.1 Consensus size: 25
6131204 TGGCTCTCCG
* * * *
6131214 GAGCTTCCCGATAT-TGGCTCGTAT
1 GAGCTTCCTGTTATATGGCTCGAAA
***
6131238 GAGCTTCCTGTTA-ATGGCTCTCCA
1 GAGCTTCCTGTTATATGGCTCGAAA
*
6131262 GAGCTTCCTGTTACATGGCTC-ACAA
1 GAGCTTCCTGTTATATGGCTCGA-AA
6131287 GAGCTTCCTGTTATATGGCTCGAAA
1 GAGCTTCCTGTTATATGGCTCGAAA
6131312 GA
1 GA
6131314 ACTTTCCATT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
24 30 0.48
25 32 0.51
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCGAAA
Found at i:6138525 original size:13 final size:13
Alignment explanation
Indices: 6138504--6138736 Score: 185
Period size: 13 Copynumber: 18.1 Consensus size: 13
6138494 CTAATTTTAT
6138504 AACAGTATATTAA
1 AACAGTATATTAA
* *
6138517 AATAGTATATTAC
1 AACAGTATATTAA
*
6138530 AA-A-T-T-TTAT
1 AACAGTATATTAA
6138539 AACAGTATATTAA
1 AACAGTATATTAA
*
6138552 ACCAGTATATT--
1 AACAGTATATTAA
6138563 -ACAGTAATAATT-A
1 AACAGT-AT-ATTAA
*** *
6138576 AGGTGTAGTATTTAT
1 AACAGTA-TA-TTAA
*
6138591 AACAGTATACTAA
1 AACAGTATATTAA
*
6138604 AACATTATATTAA
1 AACAGTATATTAA
6138617 AACAGTATATTAA
1 AACAGTATATTAA
*
6138630 AACAGTATATTTAT
1 AACAGTATA-TTAA
*
6138644 AACAATATATTAA
1 AACAGTATATTAA
*
6138657 AACATTATATTAA
1 AACAGTATATTAA
* *
6138670 AACAATATATTTAT
1 AACAGTATA-TTAA
*
6138684 AACAGTATACTAA
1 AACAGTATATTAA
*
6138697 AACAATATATTAA
1 AACAGTATATTAA
*
6138710 AACAATATATTAA
1 AACAGTATATTAA
*
6138723 AACAGTATAATAA
1 AACAGTATATTAA
6138736 A
1 A
6138737 CTAGTTATTT
Statistics
Matches: 176, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
9 5 0.03
10 6 0.03
11 4 0.02
12 5 0.03
13 123 0.70
14 29 0.16
15 4 0.02
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (13 bp):
AACAGTATATTAA
Found at i:6138542 original size:35 final size:35
Alignment explanation
Indices: 6138496--6138565 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
6138486 AACATTGACT
*
6138496 AATTTTATAACAGTATATTAAAATAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAGTATATTACA
*
6138531 AATTTTATAACAGTATATTAAACCAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAGTATATTACA
6138566 GTAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.39
Consensus pattern (35 bp):
AATTTTATAACAGTATATTAAAACAGTATATTACA
Found at i:6138653 original size:40 final size:40
Alignment explanation
Indices: 6138604--6138720 Score: 180
Period size: 40 Copynumber: 2.9 Consensus size: 40
6138594 AGTATACTAA
* *
6138604 AACATTATATTAAAACAGTATATTAAAACAGTATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
*
6138644 AACAATATATTAAAACATTATATTAAAACAATATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
* * *
6138684 AACAGTATACTAAAACAATATATTAAAACAATATATT
1 AACAATATATTAAAACAGTATATTAAAACAATATATT
6138721 AAAACAGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.35
Consensus pattern (40 bp):
AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
Found at i:6138658 original size:53 final size:53
Alignment explanation
Indices: 6138584--6138736 Score: 218
Period size: 53 Copynumber: 2.9 Consensus size: 53
6138574 TAAGGTGTAG
* *
6138584 TATTTATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
* *
6138637 TATTTATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATA-TTAAAACAGTA
* * * *
6138691 TA-CTAAAACAATATATTAAAACAATATATTAAAACAGTATAATAAA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAA
6138737 CTAGTTATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 3 0.03
53 74 0.83
54 12 0.13
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (53 bp):
TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
Found at i:6138755 original size:53 final size:52
Alignment explanation
Indices: 6138584--6138756 Score: 201
Period size: 53 Copynumber: 3.3 Consensus size: 52
6138574 TAAGGTGTAG
* *
6138584 TATTT-ATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGT
1 TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATT-AAACAGT
*
6138636 ATATTT-ATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAG-
1 -TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATA-TTA-AACAGT
* * *
6138689 TATACTAA-AACAATATATTAAAACAATATATTAAAACAGTATAATAAACTAGT
1 TAT-TTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAC-AGT
*
6138742 TATTTAATTACAATA
1 TATTTAATAACAATA
6138757 GATCAAACTT
Statistics
Matches: 104, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
51 3 0.03
52 10 0.10
53 83 0.80
54 8 0.08
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (52 bp):
TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAACAGT
Found at i:6139471 original size:35 final size:35
Alignment explanation
Indices: 6139406--6139475 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
6139396 AACATTGACT
* *
6139406 AATTTTATAATAGTATATTAAAATAATATATTACA
1 AATTTTATAACAGTATATTAAAACAATATATTACA
* *
6139441 AATTTTATAACAGTATATTAAACCAGTATATTACA
1 AATTTTATAACAGTATATTAAAACAATATATTACA
6139476 TTAATAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (35 bp):
AATTTTATAACAGTATATTAAAACAATATATTACA
Found at i:6140173 original size:36 final size:36
Alignment explanation
Indices: 6140126--6140280 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
6140116 GCTAGGCTAC
*
6140126 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
6140162 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
6140204 CTACCACTTATCACTTTATCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
6140244 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
6140280 C
1 C
6140281 TAATGCTACC
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 64 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 28 0.27
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:6140213 original size:46 final size:46
Alignment explanation
Indices: 6140162--6140316 Score: 204
Period size: 46 Copynumber: 3.6 Consensus size: 46
6140152 ATAAGTATAG
6140162 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
6140208 CACTTATCACTTTATCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
6140244 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
6140290 CACTTATCACTTTCTCACTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
6140317 AGTACTCAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
36 28 0.30
38 2 0.02
39 1 0.01
40 3 0.03
42 2 0.02
43 1 0.01
44 2 0.02
46 54 0.58
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:6140229 original size:82 final size:82
Alignment explanation
Indices: 6140083--6140316 Score: 375
Period size: 82 Copynumber: 2.9 Consensus size: 82
6140073 TACATATGAT
* * * *
6140083 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
6140145 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
*
6140162 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
*
6140227 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
* *
6140244 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
6140309 TGATCAGA
66 TGATCAGA
6140317 AGTACTCAAA
Statistics
Matches: 143, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
79 10 0.07
80 4 0.03
81 20 0.14
82 109 0.76
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
TGATCAGATAAGTATAG
Found at i:6142366 original size:13 final size:13
Alignment explanation
Indices: 6142336--6142490 Score: 177
Period size: 13 Copynumber: 11.8 Consensus size: 13
6142326 ATTAAGGTGT
*
6142336 AGTAT-TTATAAC
1 AGTATATTAAAAC
*
6142348 AGTATACTAAAAC
1 AGTATATTAAAAC
*
6142361 ATTATATTAAAAC
1 AGTATATTAAAAC
6142374 AGTATATTAAAAC
1 AGTATATTAAAAC
*
6142387 AGTATATTTATAAC
1 AGTATA-TTAAAAC
*
6142401 AATATATTAAAAC
1 AGTATATTAAAAC
*
6142414 ATTATATTAAAAC
1 AGTATATTAAAAC
* *
6142427 AATATATTTATAAC
1 AGTATA-TTAAAAC
*
6142441 AGTATACTAAAAC
1 AGTATATTAAAAC
*
6142454 AATATATTAAAAC
1 AGTATATTAAAAC
*
6142467 AATATATTAAAAC
1 AGTATATTAAAAC
*
6142480 AGTATAATAAA
1 AGTATATTAAA
6142491 CTAGTTATTT
Statistics
Matches: 122, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
12 5 0.04
13 95 0.78
14 22 0.18
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (13 bp):
AGTATATTAAAAC
Found at i:6142396 original size:53 final size:53
Alignment explanation
Indices: 6142338--6142490 Score: 218
Period size: 53 Copynumber: 2.9 Consensus size: 53
6142328 TAAGGTGTAG
* *
6142338 TATTTATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
* *
6142391 TATTTATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAGTA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATA-TTAAAACAGTA
* * * *
6142445 TA-CTAAAACAATATATTAAAACAATATATTAAAACAGTATAATAAA
1 TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAA
6142491 CTAGTTATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 3 0.03
53 74 0.83
54 12 0.13
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (53 bp):
TATTTATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAACAGTA
Found at i:6142407 original size:40 final size:40
Alignment explanation
Indices: 6142358--6142474 Score: 180
Period size: 40 Copynumber: 2.9 Consensus size: 40
6142348 AGTATACTAA
* *
6142358 AACATTATATTAAAACAGTATATTAAAACAGTATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
*
6142398 AACAATATATTAAAACATTATATTAAAACAATATATTTAT
1 AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
* * *
6142438 AACAGTATACTAAAACAATATATTAAAACAATATATT
1 AACAATATATTAAAACAGTATATTAAAACAATATATT
6142475 AAAACAGTAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.35
Consensus pattern (40 bp):
AACAATATATTAAAACAGTATATTAAAACAATATATTTAT
Found at i:6142509 original size:53 final size:52
Alignment explanation
Indices: 6142338--6142510 Score: 201
Period size: 53 Copynumber: 3.3 Consensus size: 52
6142328 TAAGGTGTAG
* *
6142338 TATTT-ATAACAGTATACTAAAACATTATATTAAAACAGTATATTAAAACAGT
1 TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATT-AAACAGT
*
6142390 ATATTT-ATAACAATATATTAAAACATTATATTAAAACAATATATTTATAACAG-
1 -TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATA-TTA-AACAGT
* * *
6142443 TATACTAA-AACAATATATTAAAACAATATATTAAAACAGTATAATAAACTAGT
1 TAT-TTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAAC-AGT
*
6142496 TATTTAATTACAATA
1 TATTTAATAACAATA
6142511 GATCAAACTT
Statistics
Matches: 104, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
51 3 0.03
52 10 0.10
53 83 0.80
54 8 0.08
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (52 bp):
TATTTAATAACAATATATTAAAACATTATATTAAAACAGTATATTAAACAGT
Found at i:6156563 original size:17 final size:16
Alignment explanation
Indices: 6156536--6156570 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6156526 TAACATAAAG
*
6156536 ACCAATTTTTTATTTA
1 ACCAATTTTTTATCTA
6156552 ACCAATTTTTTTATCTA
1 ACCAA-TTTTTTATCTA
6156569 AC
1 AC
6156571 ATGTAAATAT
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:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (16 bp):
ACCAATTTTTTATCTA
Found at i:6156992 original size:79 final size:79
Alignment explanation
Indices: 6156861--6157019 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
6156851 CTACACTAAT
*
6156861 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAGTTTTTATACACTAAAAA
1 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
*
6156926 TATAATTTATCCTG
66 AATAATTTATCCTG
6156940 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
1 ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
6157005 AATAATTTATCCTG
66 AATAATTTATCCTG
6157019 A
1 A
6157020 CTTGACTCGT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (79 bp):
ATGTAAAGTTTATTTTAATCTTTTTTATTAAAAATTGCTTTAAATTAATTTTTATACACTAAAAA
AATAATTTATCCTG
Found at i:6164461 original size:80 final size:79
Alignment explanation
Indices: 6164327--6164483 Score: 287
Period size: 80 Copynumber: 2.0 Consensus size: 79
6164317 GTGGTAATGT
*
6164327 GGCTAAACATGGACATGACACGTGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
1 GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
6164392 TAAAAAAATTTTACC
66 T-AAAAAATTTTACC
*
6164407 GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCTTAGCTTCAATTATTC
1 GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
6164472 TAAAAAATTTTA
66 TAAAAAATTTTA
6164484 AAAAGTTGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
79 11 0.15
80 64 0.85
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (79 bp):
GGCTAAACATGGACATGACACATGGGCAAACAAGGGAATGACATGTATCCTAGCTTCAATTATTC
TAAAAAATTTTACC
Found at i:6164550 original size:12 final size:12
Alignment explanation
Indices: 6164513--6164560 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
6164503 ACATTTATAT
*
6164513 AAATTTAAAAAA
1 AAATTTATAAAA
* *
6164525 ATAATTTTTTAAA
1 A-AATTTATAAAA
6164538 AAATTTATAAAA
1 AAATTTATAAAA
6164550 AAATTTA-AAAA
1 AAATTTATAAAA
6164561 TAAGAAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 4 0.13
12 17 0.57
13 9 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATTTATAAAA
Found at i:6164602 original size:26 final size:27
Alignment explanation
Indices: 6164547--6164615 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 27
6164537 AAAATTTATA
* *
6164547 AAAAAATTTAAAAATA-AGAAACTTAT
1 AAAAAATTAAAAAATATAGAAACTTAC
*
6164573 AAAAAATTGAAAAATATAGACAA-TT-C
1 AAAAAATTAAAAAATATAGA-AACTTAC
6164599 AAAAAA-TAAAAAATATA
1 AAAAAATTAAAAAATATA
6164616 TAATTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 10 0.26
26 21 0.55
27 5 0.13
28 2 0.05
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAAAATTAAAAAATATAGAAACTTAC
Found at i:6167596 original size:3 final size:3
Alignment explanation
Indices: 6167588--6167622 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
6167578 GAGATTTTGA
6167588 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6167623 ATTCACTAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6168702 original size:47 final size:47
Alignment explanation
Indices: 6168633--6168726 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
6168623 AGATCTAAGA
6168633 TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
1 TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
*
6168680 TTTTAGGAACCAGTTACCAAAATATTTTATGCGCATAACTTATCTGC
1 TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
6168727 CAATATTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (47 bp):
TTTTAGGAACCAGTTAACAAAATATTTTATGCGCATAACTTATCTGC
Found at i:6172959 original size:82 final size:82
Alignment explanation
Indices: 6172859--6173031 Score: 328
Period size: 82 Copynumber: 2.1 Consensus size: 82
6172849 TACTGAAATT
6172859 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
1 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
6172924 GAAAAAAAGAAAAAGGC
66 GAAAAAAAGAAAAAGGC
6172941 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
1 TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
6173006 GAAAAAAAGAAAAAGGC
66 GAAAAAAAGAAAAAGGC
* *
6173023 ATCAGAATT
1 TTCAAAATT
6173032 GAAAACATCG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 89 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (82 bp):
TTCAAAATTCTAAAACCATATAAAAGAGTAGTCTTGATTTCTATTGCTGTATTCGGTGACTGCTA
GAAAAAAAGAAAAAGGC
Found at i:6192084 original size:29 final size:30
Alignment explanation
Indices: 6192020--6192084 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
6192010 AGTCTTGAAA
**
6192020 TTATATATAAATTTTGATTTTGTGTAATT-
1 TTATATATAAATTTTGATTTAATGTAATTC
*
6192049 TTATATATAAAATTTTGATTTAATTTAATTC
1 TTATATAT-AAATTTTGATTTAATGTAATTC
6192080 TTATA
1 TTATA
6192085 AATTAACATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 8 0.26
30 18 0.58
31 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (30 bp):
TTATATATAAATTTTGATTTAATGTAATTC
Found at i:6193098 original size:3 final size:3
Alignment explanation
Indices: 6193090--6193121 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6193080 CGGATTGTAA
6193090 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6193122 AGAAATATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6193321 original size:20 final size:19
Alignment explanation
Indices: 6193296--6193338 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
6193286 ATTAGTTACT
* *
6193296 TATTTACTATTTTGATTTTC
1 TATTTAATATATTG-TTTTC
6193316 TATTTAATATATTGTTTTC
1 TATTTAATATATTGTTTTC
6193335 TATT
1 TATT
6193339 GTTTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (19 bp):
TATTTAATATATTGTTTTC
Found at i:6201238 original size:25 final size:25
Alignment explanation
Indices: 6201168--6201248 Score: 110
Period size: 25 Copynumber: 3.2 Consensus size: 25
6201158 GACACACCAC
* *
6201168 AGCTCGCATGAGCTT-TCTGATACTT
1 AGCTCGCATGAGCTTCTC-GTTATTT
*
6201193 AGCTCGCATGAGCTTCCCGTTATTT
1 AGCTCGCATGAGCTTCTCGTTATTT
*
6201218 AGCTCGCATGAGCTTCTCGTTATTC
1 AGCTCGCATGAGCTTCTCGTTATTT
6201243 AGCTCG
1 AGCTCG
6201249 AAAGAACTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
25 49 0.98
26 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCTCGTTATTT
Found at i:6202128 original size:38 final size:39
Alignment explanation
Indices: 6202070--6202146 Score: 138
Period size: 38 Copynumber: 2.0 Consensus size: 39
6202060 ATCCAACCAA
*
6202070 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
6202109 ACCCAATTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
6202147 TACTCTTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 28 0.76
39 9 0.24
ACGTcount: A:0.51, C:0.29, G:0.03, T:0.18
Consensus pattern (39 bp):
ACCCAATTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:6202301 original size:17 final size:17
Alignment explanation
Indices: 6202281--6202346 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
6202271 TAATTTCAAG
6202281 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
6202298 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
6202316 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
6202335 AATTATGTAATG
1 AATTATGTAATG
6202347 ATTCAATTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 20 0.56
18 4 0.11
19 4 0.11
20 8 0.22
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:6202305 original size:37 final size:37
Alignment explanation
Indices: 6202278--6202352 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
6202268 TGCTAATTTC
* *
6202278 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
* * *
6202315 AAGACTTATGTAATATTTTTAATTATGTAATGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
6202352 A
1 A
6202353 TTTGGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
Found at i:6202371 original size:9 final size:9
Alignment explanation
Indices: 6202359--6202399 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
6202349 TCAATTTGGG
6202359 TAATTCGGT
1 TAATTCGGT
6202368 TAATTCGGT
1 TAATTCGGT
*
6202377 TAATTAGGT
1 TAATTCGGT
*
6202386 TAATTCAGT
1 TAATTCGGT
6202395 TAATT
1 TAATT
6202400 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:6204756 original size:24 final size:24
Alignment explanation
Indices: 6204698--6204777 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
6204688 GCTTATCCGG
* *
6204698 GCAATATAACAGGAAGCTCACAAAGA
1 GCAAT-TAATAGGTAGCTC-CAAAGA
* * *
6204724 GC-CTATAATGGGTAGCTCTAAAGA
1 GCAAT-TAATAGGTAGCTCCAAAGA
*
6204748 GCAATTAATAGGTAGCTCCGAAGA
1 GCAATTAATAGGTAGCTCCAAAGA
6204772 GCAATT
1 GCAATT
6204778 TAACGGGAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 29 0.66
25 13 0.30
26 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (24 bp):
GCAATTAATAGGTAGCTCCAAAGA
Found at i:6210473 original size:2 final size:2
Alignment explanation
Indices: 6210466--6210506 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6210456 TGATGTTTTA
*
6210466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6210507 AAATTTGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6219529 original size:31 final size:31
Alignment explanation
Indices: 6219488--6219556 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6219478 AAGGTAACTT
*
6219488 AATAACTTAGTAACTTAAATAAAAACTCTCG
1 AATAATTTAGTAACTTAAATAAAAACTCTCG
* * * *
6219519 AATAATTTAGTTACTTAAATGAAAACTTTTG
1 AATAATTTAGTAACTTAAATAAAAACTCTCG
6219550 AATAATT
1 AATAATT
6219557 CAGTGATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (31 bp):
AATAATTTAGTAACTTAAATAAAAACTCTCG
Found at i:6220273 original size:13 final size:13
Alignment explanation
Indices: 6220255--6220289 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
6220245 GGGCTGGACC
6220255 CAGGCCTAACAAA
1 CAGGCCTAACAAA
6220268 CAGGCCTAACAAA
1 CAGGCCTAACAAA
*
6220281 TAGGCCTAA
1 CAGGCCTAA
6220290 ATTTTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.17, T:0.11
Consensus pattern (13 bp):
CAGGCCTAACAAA
Found at i:6221840 original size:37 final size:40
Alignment explanation
Indices: 6221749--6221884 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 40
6221739 ACTAGTTTGG
* *
6221749 CACCCAGTACCTCATCGAATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGAATAAATCGAAGTAATAAGTTGA
** * **
6221789 CATACAGTGTCTCATCGGCTAAATCGAAGT-A-AA-TTGA
1 CACCCAGTGCCTCATCGAATAAATCGAAGTAATAAGTTGA
* * * *
6221826 CACCCAGTGCCTCATCGAATTAATTTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAAATCGAAGTAATAAGTTGA
**
6221867 CACCCAGTGTATCATCGA
1 CACCCAGTGCCTCATCGA
6221885 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 18 0.24
38 11 0.15
39 1 0.01
40 25 0.33
41 20 0.27
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAAATCGAAGTAATAAGTTGA
Found at i:6221868 original size:41 final size:40
Alignment explanation
Indices: 6221749--6221884 Score: 134
Period size: 41 Copynumber: 3.5 Consensus size: 40
6221739 ACTAGTTTGG
* * *
6221749 CACCCAGTACCTCATCGAATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
** * ** *
6221789 CATACAGTGTCTCATCGGCTAAATCG-A--AGTAAATTGA
1 CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
*
6221826 CACCCAGTGCCTCATCGAATTAATTTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATTCGAAGTAGTAAATTGA
**
6221867 CACCCAGTGTATCATCGA
1 CACCCAGTGCCTCATCGA
6221885 CTCGAAGTCG
Statistics
Matches: 74, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 22 0.30
38 5 0.07
39 2 0.03
40 19 0.26
41 26 0.35
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGA
Found at i:6225487 original size:18 final size:19
Alignment explanation
Indices: 6225461--6225496 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6225451 TAGACTAGAT
*
6225461 TTAACTCCCT-AATTTTAC
1 TTAAATCCCTAAATTTTAC
6225479 TTAAATCCCTAAATTTTA
1 TTAAATCCCTAAATTTTA
6225497 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAATCCCTAAATTTTAC
Found at i:6226214 original size:6 final size:6
Alignment explanation
Indices: 6226203--6226236 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
6226193 GAGTCGTTAC
6226203 AATTAT AATTAT AATTAT AATTAT AATTAT AATT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATT
6226237 CTGTGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:6226329 original size:18 final size:18
Alignment explanation
Indices: 6226306--6226340 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6226296 ATTTAATATA
6226306 TTATATAAAATAAATTTT
1 TTATATAAAATAAATTTT
* *
6226324 TTATATATAATTAATTT
1 TTATATAAAATAAATTT
6226341 GTATTCTCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATATAAAATAAATTTT
Found at i:6227306 original size:23 final size:22
Alignment explanation
Indices: 6227279--6227336 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
6227269 TAGTTCATGG
6227279 AAAAATTAAAAAATATCTTGA-AA
1 AAAAATTAAAAAATA-CTT-ATAA
* *
6227302 TAAAAA-TAAGAACTACTTATAA
1 -AAAAATTAAAAAATACTTATAA
6227324 AAAAATTAAAAAA
1 AAAAATTAAAAAA
6227337 AAAATAGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 6 0.21
22 10 0.36
23 7 0.25
24 5 0.18
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.24
Consensus pattern (22 bp):
AAAAATTAAAAAATACTTATAA
Found at i:6231471 original size:15 final size:15
Alignment explanation
Indices: 6231451--6231480 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6231441 AAACATAATA
6231451 AATTAAATATAAAAT
1 AATTAAATATAAAAT
6231466 AATTAAATATAAAAT
1 AATTAAATATAAAAT
6231481 TATATATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTAAATATAAAAT
Found at i:6235066 original size:42 final size:43
Alignment explanation
Indices: 6234990--6235073 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
6234980 ATTCTAAGAT
*
6234990 AAATAATAACTAACTAAAATAATAAGTATATATCAATTATTTA
1 AAATAATAACTAACTAAAATAATAAATATATATCAATTATTTA
* *
6235033 AAATAATAATTAATTAAAA-AATAAATATATATCAATTATTT
1 AAATAATAACTAACTAAAATAATAAATATATATCAATTATTT
6235074 TGAGAATTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 21 0.55
43 17 0.45
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (43 bp):
AAATAATAACTAACTAAAATAATAAATATATATCAATTATTTA
Found at i:6236433 original size:19 final size:20
Alignment explanation
Indices: 6236395--6236434 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
6236385 TTTATATAAA
*
6236395 ATAAATAAATATGCGTATAT
1 ATAAATAAATATGCGCATAT
*
6236415 ATAAA-AAATATGTGCATAT
1 ATAAATAAATATGCGCATAT
6236434 A
1 A
6236435 GGTGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (20 bp):
ATAAATAAATATGCGCATAT
Found at i:6236822 original size:3 final size:3
Alignment explanation
Indices: 6236814--6236869 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
6236804 AATAAATAGG
6236814 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6236862 TAA TAA TA
1 TAA TAA TA
6236870 GGACTAATTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6250452 original size:57 final size:57
Alignment explanation
Indices: 6250364--6250473 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
6250354 TTAAGTTTTT
* * * *
6250364 AATGTAATTTTCTCTAATTTAAGTTAATCCAACTCGACTCATGAACAACTCTATTTG
1 AATGTAATTTTCTCTAATTCAAGTCAATCCAACTCGACTCATAAAAAACTCTATTTG
** * *
6250421 AATGTAATTTTCTCTAATTCGGGTCGATCCAACTCTACTCATAAAAAACTCTA
1 AATGTAATTTTCTCTAATTCAAGTCAATCCAACTCGACTCATAAAAAACTCTA
6250474 ATTACTGATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (57 bp):
AATGTAATTTTCTCTAATTCAAGTCAATCCAACTCGACTCATAAAAAACTCTATTTG
Found at i:6256157 original size:13 final size:13
Alignment explanation
Indices: 6256141--6256178 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
6256131 CCGGGCGGCC
6256141 CGGCCCGGCCCGA
1 CGGCCCGGCCCGA
* *
6256154 CGGCCTGCCCCGA
1 CGGCCCGGCCCGA
6256167 CGGCCC-GCCCGA
1 CGGCCCGGCCCGA
6256179 AATATGGGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.08, C:0.55, G:0.34, T:0.03
Consensus pattern (13 bp):
CGGCCCGGCCCGA
Found at i:6256338 original size:22 final size:24
Alignment explanation
Indices: 6256312--6256355 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6256302 GAAAAATATT
6256312 AAATAT-ATA-TATTTTATTTTTA
1 AAATATAATAGTATTTTATTTTTA
*
6256334 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTATTTTATTTT
6256356 AAGTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AAATATAATAGTATTTTATTTTTA
Found at i:6256564 original size:16 final size:16
Alignment explanation
Indices: 6256543--6256584 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
6256533 AATAATTTGA
*
6256543 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
6256559 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
6256575 TAGTTTTAAT
1 TAATTTTAAT
6256585 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:6256568 original size:22 final size:23
Alignment explanation
Indices: 6256558--6256619 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
6256548 TTACTAACAA
* * *
6256558 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
6256580 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
6256603 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
6256620 CAGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:6271169 original size:13 final size:13
Alignment explanation
Indices: 6271151--6271175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6271141 TGTTTATATG
6271151 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
6271164 TTTTTCTTTTTT
1 TTTTTCTTTTTT
6271176 AAATTTCTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Done.