Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007608.1 Corchorus capsularis cultivar CVL-1 contig07629, whole genome shotgun sequence
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: 70473
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:13507 original size:2 final size:2
Alignment explanation
Indices: 13500--13534 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
13490 TATTGTTTGT
*
13500 TA TA TA TA TA TA TA TA TA T- TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13535 GACAAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13524 original size:17 final size:17
Alignment explanation
Indices: 13502--13534 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13492 TTGTTTGTTA
13502 TATATATATATATATAT
1 TATATATATATATATAT
*
13519 TATATATGTATATATA
1 TATATATATATATATA
13535 GACAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:14810 original size:18 final size:18
Alignment explanation
Indices: 14787--14822 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
14777 TAAAAATGTT
*
14787 TTTTGAAGATTTTTTGGA
1 TTTTGAAAATTTTTTGGA
14805 TTTTGAAAATTTTTTGGA
1 TTTTGAAAATTTTTTGGA
14823 ATTTCATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (18 bp):
TTTTGAAAATTTTTTGGA
Found at i:16901 original size:2 final size:2
Alignment explanation
Indices: 16890--16936 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
16880 TTTTATCATA
16890 AT AT -T AT AT AT AT AT -T AT AT AT -T AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16928 AT AT AT AT A
1 AT AT AT AT A
16937 GCCAAGATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:16920 original size:23 final size:24
Alignment explanation
Indices: 16890--16935 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
16880 TTTTATCATA
16890 ATATTATATATATAT-TATATATT
1 ATATTATATATATATATATATATT
16913 ATATTATATATATATATATATAT
1 ATATTATATATATATATATATAT
16936 AGCCAAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATTATATATATATATATATATT
Found at i:17892 original size:53 final size:54
Alignment explanation
Indices: 17827--17929 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 54
17817 GTATGGAAAT
* * * *
17827 CAAGAATGATCGAGCATCCCTCGGTCGCACTATCTGTTAGGCATCCCCCACAAG
1 CAAGAATGATCGAGCATCCCTCAGTCGCACTACCTATTAGGCACCCCCCACAAG
*
17881 CAAGAA-GATCGAGCATCCCTCAGTCGCACTACCTATTGGGCACCCCCCA
1 CAAGAATGATCGAGCATCCCTCAGTCGCACTACCTATTAGGCACCCCCCA
17930 TGATGGGCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 38 0.86
54 6 0.14
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.18
Consensus pattern (54 bp):
CAAGAATGATCGAGCATCCCTCAGTCGCACTACCTATTAGGCACCCCCCACAAG
Found at i:20515 original size:38 final size:37
Alignment explanation
Indices: 20425--20552 Score: 150
Period size: 38 Copynumber: 3.4 Consensus size: 37
20415 GCAGTGATTT
* * *
20425 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGTTGCTGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCA
* * *
20462 GCAAGGAGAGCTCTGCGGTGAAA-ATGGGAGCCACCGCA
1 GTAAGGAGAGCTCTGCGGT-AAAGA-GGGTGCTACCGCA
* *
20500 GTAAGGAGAGCTCTGCGGCAAAGAGGGTGCTACCCACA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTA-CCGCA
20538 GTAAGGAGAGCTCTG
1 GTAAGGAGAGCTCTG
20553 TGATGAAGAG
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 28 0.37
38 48 0.63
ACGTcount: A:0.27, C:0.20, G:0.38, T:0.16
Consensus pattern (37 bp):
GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCA
Found at i:22619 original size:49 final size:49
Alignment explanation
Indices: 22554--22704 Score: 241
Period size: 49 Copynumber: 3.1 Consensus size: 49
22544 CAATGCTATG
* *
22554 AATTCTTTGT-GAAAGCTACAGCCATGAAGATTATTGGATGAATGCAACA
1 AATTCTTTGTAG-AAGCTACAGCCATGAAGATGATTGGATGAATGCCACA
*
22603 AATTCTTTGTAGAAGCTACAACCATGAAGATGATTGGATGAATGCCACA
1 AATTCTTTGTAGAAGCTACAGCCATGAAGATGATTGGATGAATGCCACA
* *
22652 AATTCTTTGTAGAAGCTGCAGTCATGAAGATGATTGGATGAATGCCACA
1 AATTCTTTGTAGAAGCTACAGCCATGAAGATGATTGGATGAATGCCACA
22701 AATT
1 AATT
22705 TTTTTGCCTT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 94 0.99
50 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (49 bp):
AATTCTTTGTAGAAGCTACAGCCATGAAGATGATTGGATGAATGCCACA
Found at i:25587 original size:37 final size:37
Alignment explanation
Indices: 25464--25591 Score: 118
Period size: 37 Copynumber: 3.4 Consensus size: 37
25454 GCAGTGATTT
* * *
25464 GTAAGGAGAGCTCTGCCA-TAAAGAGGGTGCTACTGCA
1 GTAAGGAGAGCTCTG-CAGAAAAGAGGGTACTACCGCA
* * * **
25501 GCAAGGAGAGCTCTACGGTAAAA-ATGGG-AGCCGCCGCA
1 GTAAGGAGAGCTCTGCAG-AAAAGA-GGGTA-CTACCGCA
*
25539 GTAAGGAGAGCTCTGCAGAAAAGAGGGTACTACCGCG
1 GTAAGGAGAGCTCTGCAGAAAAGAGGGTACTACCGCA
25576 GTAAGGAGAGCTCTGC
1 GTAAGGAGAGCTCTGC
25592 GATGAAGGGT
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
36 1 0.01
37 42 0.59
38 28 0.39
ACGTcount: A:0.30, C:0.20, G:0.34, T:0.15
Consensus pattern (37 bp):
GTAAGGAGAGCTCTGCAGAAAAGAGGGTACTACCGCA
Found at i:32243 original size:31 final size:30
Alignment explanation
Indices: 32205--32307 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 30
32195 ACTGACGATG
32205 GGCCCTTATTTGAGCATTTTCGATAACGTT
1 GGCCCTTATTTGAGCATTTTCGATAACGTT
**
32235 AGGCCCTTATTTG-GCCAAATTAACAGAT--CG--
1 -GGCCCTTATTTGAG-C--ATTTTC-GATAACGTT
32265 GGCCCTTATTTGAGCATTTTCGATAACGTT
1 GGCCCTTATTTGAGCATTTTCGATAACGTT
32295 GGGCCCTTATTTG
1 -GGCCCTTATTTG
32308 GTCAAATTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
26 3 0.05
27 4 0.07
28 2 0.03
29 13 0.22
30 2 0.03
31 25 0.43
32 2 0.03
33 4 0.07
34 3 0.05
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (30 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTT
Found at i:32276 original size:29 final size:27
Alignment explanation
Indices: 32236--32336 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 27
32226 GATAACGTTA
32236 GGCCCTTATTTGGCCAAATTAACAGATCG
1 GGCCCTTATTTGG-CAAATTAA-AGATCG
** *
32265 GGCCCTTATTTGAGCATTTTCGATAACG-TTG
1 GGCCCTTATTTG-GCAAATT--A-AA-GATCG
32296 GGCCCTTATTTGGTCAAATTAAAAGATCG
1 GGCCCTTATTTGG-CAAATT-AAAGATCG
*
32325 AGCCCTTATTTG
1 GGCCCTTATTTG
32337 AGCATTTTGG
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
28 1 0.02
29 31 0.54
30 3 0.05
31 20 0.35
32 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
GGCCCTTATTTGGCAAATTAAAGATCG
Found at i:32300 original size:60 final size:60
Alignment explanation
Indices: 32204--32366 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
32194 AACTGACGAT
*
32204 GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAACAGATC
1 GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* *
32264 GGGCCCTTATTTGAGCATTTTCGATAACGTTGGGCCCTTATTTGGTCAAATTAAAAGATC
1 GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* * *
32324 GAGCCCTTATTTGAGCATTTTGGCA-AACGTTAGACCCTTATTT
1 GGGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTT
32367 AAGCAGTTAG
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (60 bp):
GGGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:32450 original size:36 final size:36
Alignment explanation
Indices: 32401--32648 Score: 358
Period size: 36 Copynumber: 6.9 Consensus size: 36
32391 TTTCTAAGAT
* *
32401 TGAATTAAATCTTTGACTGATTTTACCTAATTACCC
1 TGAATTAAGTCTTTGACTGATTTTACTTAATTACCC
*
32437 TGAATTAAGTCTTTGACTGATTTTACTTAATTATCC
1 TGAATTAAGTCTTTGACTGATTTTACTTAATTACCC
*
32473 TGAATTAAGTCTTTGACTGATTTTTCTTAA-TAGCCC
1 TGAATTAAGTCTTTGACTGATTTTACTTAATTA-CCC
32509 TGAATTAAGT-TTCT-ACTGATTTTACTTAATTACCC
1 TGAATTAAGTCTT-TGACTGATTTTACTTAATTACCC
* *
32544 TGAATTAAGCCTTTGACTGATTTTACTTAATTATCC
1 TGAATTAAGTCTTTGACTGATTTTACTTAATTACCC
*
32580 TGAATTAAGTCTTTGACTGATTTTACTTAATCACCC
1 TGAATTAAGTCTTTGACTGATTTTACTTAATTACCC
* * * *
32616 TTAATTAAGTCTTTTAGTGATTTTACTCAATTA
1 TGAATTAAGTCTTTGACTGATTTTACTTAATTA
32649 TGTGAGATTA
Statistics
Matches: 191, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
35 31 0.16
36 160 0.84
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (36 bp):
TGAATTAAGTCTTTGACTGATTTTACTTAATTACCC
Found at i:32602 original size:107 final size:108
Alignment explanation
Indices: 32401--32648 Score: 385
Period size: 107 Copynumber: 2.3 Consensus size: 108
32391 TTTCTAAGAT
* * *
32401 TGAATTAAATCTT-TGACTGATTTTACCTAATTACCCTGAATTAAGTCTTTGACTGATTTTACTT
1 TGAATTAAGTCTTCT-ACTGATTTTACTTAATTACCCTGAATTAAGCCTTTGACTGATTTTACTT
*
32465 AATTATCCTGAATTAAGTCTTTGACTGATTTTTCTTAAT-AGCCC
65 AATTATCCTGAATTAAGTCTTTGACTGATTTTACTTAATCA-CCC
32509 TGAATTAAGT-TTCTACTGATTTTACTTAATTACCCTGAATTAAGCCTTTGACTGATTTTACTTA
1 TGAATTAAGTCTTCTACTGATTTTACTTAATTACCCTGAATTAAGCCTTTGACTGATTTTACTTA
32573 ATTATCCTGAATTAAGTCTTTGACTGATTTTACTTAATCACCC
66 ATTATCCTGAATTAAGTCTTTGACTGATTTTACTTAATCACCC
* * * *
32616 TTAATTAAGTCTTTTAGTGATTTTACTCAATTA
1 TGAATTAAGTCTTCTACTGATTTTACTTAATTA
32649 TGTGAGATTA
Statistics
Matches: 129, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
107 99 0.77
108 30 0.23
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (108 bp):
TGAATTAAGTCTTCTACTGATTTTACTTAATTACCCTGAATTAAGCCTTTGACTGATTTTACTTA
ATTATCCTGAATTAAGTCTTTGACTGATTTTACTTAATCACCC
Found at i:33088 original size:2 final size:2
Alignment explanation
Indices: 33081--33111 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
33071 TCCGGTAGAC
33081 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
33112 TATTTTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42510 original size:3 final size:3
Alignment explanation
Indices: 42502--42545 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
42492 AACTTCTTTA
42502 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT T
42546 GATAGTTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43776 original size:446 final size:447
Alignment explanation
Indices: 42942--43858 Score: 1291
Period size: 446 Copynumber: 2.1 Consensus size: 447
42932 TAATTTCATG
* *
42942 AAGGTGATTCAAGTGTCTATTGAAAGGTAATTTCATGATCTACAATTTCTATGAAGGACTCAAAA
1 AAGGTGATTCAAGTGTCTATTGAAACGTAATTCCATGATCTACAATTTCTATGAAGGACTCAAAA
*
43007 GTCAATTTTAATATTTTGATTCAAAAAAATGCTTCTGAAATTTTGTGGTCTCGATTGTCGGTCTA
66 GTCAATTTTAATATTTTGATTCAAAAAAATGCTTCTAAAATTTTGTGGTCTCGATTGTCGGTCTA
* *
43072 TTTGATATCGTATAAATTTCGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGT
131 TCTAATATCGTATAAATTTCGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGT
* ** ** * *
43137 TATTGTGTGGTCTATTACTTTCGTTAAGGGCCTGAGAGCCGAATTTGATTAATGAGTTTCGTAGA
196 TATTGTGTGATCTACGACTTTCGCCAAGGGCCTAAAAGCCGAATTTGATTAATGAGTTTCGTAGA
* **
43202 GGATTCAAGAGAGAATTTTTATGTTTGGTCTCCATAAACAAATCATTTTTTTGTTGGATTATTTA
261 GGATTCAAGAGAGAATTTTTATGTTTGATCTCCATAAACAAATCATTTTTTTCCTGGATTATTTA
* * * *
43267 TTAAATTATCCTCATACTTTTATAATTTATGCTATTTAATCCTTTACAATTATGGGTTGGACGAT
326 TCAAATGACCCTCATACTTTTATAATTTATGCTATTTAATCCTTTACAATTACGGGTTGGACGAT
43332 TGAATGTTTCGGCTTTAATTCTTTTATCCTTTTTTTTTTTTTCTATTTTGACCGATC
391 TGAATGTTTCGGCTTTAATTCTTTTATCCTTTTTTTTTTTTTCTATTTTGACCGATC
* * *
43389 AAGGTGATTCAGGTGTCTATTTAAACGTAATTCCATGGTCTACAACTTTC-ATGAAGGACTCAAA
1 AAGGTGATTCAAGTGTCTATTGAAACGTAATTCCATGATCTACAA-TTTCTATGAAGGACTCAAA
* * *
43453 AGTCAATTTTGATGTTTTGATTC-TAAAAATGCTTCTAAAATTTTGTGGTCTCGATTGTCGGTCT
65 AGTCAATTTTAATATTTTGATTCAAAAAAATGCTTCTAAAATTTTGTGGTCTCGATTGTCGGTCT
* * * * *
43517 ATCTAATGTTGTATAATTTTTGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTGAAAGG
130 ATCTAATATCGTATAAATTTCGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGG
* * *
43582 TTATTGTGTTATCTACGACTTTCGCCAAGGGCCTAAAAGCTGAATTTGATTAATGAGTTTCGTGG
195 TTATTGTGTGATCTACGACTTTCGCCAAGGGCCTAAAAGCCGAATTTGATTAATGAGTTTCGTAG
* *
43647 A-GAGTTCAAGAGGGAATTTTTATGTTTGATCTTCATAAACAAAT-ATTTTTTTCCCTGGATTAT
260 AGGA-TTCAAGAGAGAATTTTTATGTTTGATCTCCATAAACAAATCATTTTTTT-CCTGGATTAT
**
43710 TTATCAAATGACCCTCATACTTTTATGCTTTATGCTATTTAATCCTTTACAATTACGGGTTGGAC
323 TTATCAAATGACCCTCATACTTTTATAATTTATGCTATTTAATCCTTTACAATTACGGGTTGGAC
* ** * * * * * *
43775 GATTTAACATGTCGGCTTTTA-T-TTTTA----TATTTTTTGTTT-TA-TTTGTCAGATC
388 GATTGAATGTTTCGGCTTTAATTCTTTTATCCTTTTTTTTTTTTTCTATTTTGACCGATC
* *
43827 AAAGTGATTCAAGTGTCTATTGAAAGGTAATT
1 AAGGTGATTCAAGTGTCTATTGAAACGTAATT
43859 TAATGTCAGG
Statistics
Matches: 417, Mismatches: 50, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
438 37 0.09
439 2 0.00
440 10 0.02
444 5 0.01
445 11 0.03
446 273 0.65
447 75 0.18
448 4 0.01
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (447 bp):
AAGGTGATTCAAGTGTCTATTGAAACGTAATTCCATGATCTACAATTTCTATGAAGGACTCAAAA
GTCAATTTTAATATTTTGATTCAAAAAAATGCTTCTAAAATTTTGTGGTCTCGATTGTCGGTCTA
TCTAATATCGTATAAATTTCGGTCCACTTGTCCGATTGAGGTTGTTCAAGTGTCGGTTAAAAGGT
TATTGTGTGATCTACGACTTTCGCCAAGGGCCTAAAAGCCGAATTTGATTAATGAGTTTCGTAGA
GGATTCAAGAGAGAATTTTTATGTTTGATCTCCATAAACAAATCATTTTTTTCCTGGATTATTTA
TCAAATGACCCTCATACTTTTATAATTTATGCTATTTAATCCTTTACAATTACGGGTTGGACGAT
TGAATGTTTCGGCTTTAATTCTTTTATCCTTTTTTTTTTTTTCTATTTTGACCGATC
Found at i:45736 original size:15 final size:14
Alignment explanation
Indices: 45701--45751 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
45691 CACTATTATC
45701 CTACTTTTATATAA
1 CTACTTTTATATAA
45715 CTACTTTTATATATTA
1 CTACTTTTATATA--A
45731 -TACTTTTATATAA
1 CTACTTTTATATAA
*
45744 CTAGTTTT
1 CTACTTTT
45752 GCACGATCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.03
14 19 0.58
15 12 0.36
16 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (14 bp):
CTACTTTTATATAA
Found at i:50107 original size:2 final size:2
Alignment explanation
Indices: 50102--50129 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50092 TTTTATAGGG
50102 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
50130 GCTTTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:54292 original size:66 final size:66
Alignment explanation
Indices: 54157--54410 Score: 198
Period size: 66 Copynumber: 3.9 Consensus size: 66
54147 AAGATGATAT
* * * * * * *
54157 GCCAAGTAGTAGGGATGATGCCCCAG-TACGCAGGCCAGGTAGTAGGGATGATGAGCC-AATTAT
1 GCCAAGGAGTAGGGATGATGCCCCTGTTAAGCAGGCCAAGTAGCAGGGATGATG-CCCGAA-TAG
*
54220 CTG
64 CAG
* * *
54223 GCCAAGGAGAAGGGATGATG-CCCTGTTAAGCAGGCCAAGTAGTAGGGGTGATGCTCCGAATAGC
1 GCCAAGGAGTAGGGATGATGCCCCTGTTAAGCAGGCCAAGTAGCAGGGATGATGC-CCGAATAGC
54287 AG
65 AG
* * * * * * * *
54289 GCC-AGGTAGTACGGATCATGCCCC-GATGAGCAGGCTAAGTTGCATGGATGAGGCCTCG-ATAA
1 GCCAAGG-AGTAGGGATGATGCCCCTGTTAAGCAGGCCAAGTAGCAGGGATGATGCC-CGAAT-A
54351 GCAG
63 GCAG
* * * *
54355 GCCAAGTAGCAGGGATGATGCCCCT-TTAAGCAGCCCAAGCAGCAGGGATGATGCCC
1 GCCAAGGAGTAGGGATGATGCCCCTGTTAAGCAGGCCAAGTAGCAGGGATGATGCCC
54411 CTTTAAGCAG
Statistics
Matches: 147, Mismatches: 32, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
65 11 0.07
66 129 0.88
67 7 0.05
ACGTcount: A:0.27, C:0.22, G:0.33, T:0.17
Consensus pattern (66 bp):
GCCAAGGAGTAGGGATGATGCCCCTGTTAAGCAGGCCAAGTAGCAGGGATGATGCCCGAATAGCA
G
Found at i:54462 original size:33 final size:33
Alignment explanation
Indices: 54158--54453 Score: 175
Period size: 33 Copynumber: 9.0 Consensus size: 33
54148 AGATGATATG
* * *
54158 CCAAGTAGTAGGGATGATGCCCC-AGTACGCAGG
1 CCAAGTAGCAGGGATGATGCCCCTA-TAAGCAGC
* * ** * * * * *
54191 CCAGGTAGTAGGGATGATGAGCCAATTATCTGG
1 CCAAGTAGCAGGGATGATGCCCCTATAAGCAGC
* * * *
54224 CCAAGGAGAAGGGATGATG-CCCTGTTAAGCAGG
1 CCAAGTAGCAGGGATGATGCCCCT-ATAAGCAGC
* * * * *
54257 CCAAGTAGTAGGGGTGATGCTCCGA-ATAGCAGG
1 CCAAGTAGCAGGGATGATGCCCCTATA-AGCAGC
* * * * * * *
54290 CCAGGTAGTACGGATCATGCCCCGATGAGCAGG
1 CCAAGTAGCAGGGATGATGCCCCTATAAGCAGC
* * * * * * *
54323 CTAAGTTGCATGGATGAGGCCTCGATAAGCAGG
1 CCAAGTAGCAGGGATGATGCCCCTATAAGCAGC
*
54356 CCAAGTAGCAGGGATGATGCCCCTTTAAGCAGC
1 CCAAGTAGCAGGGATGATGCCCCTATAAGCAGC
* *
54389 CCAAGCAGCAGGGATGATGCCCCTTTAAGCAGC
1 CCAAGTAGCAGGGATGATGCCCCTATAAGCAGC
* * *
54422 CCAAGTAGCAGGGAAGAAGCCACTATAAGCAG
1 CCAAGTAGCAGGGATGATGCCCCTATAAGCAG
54454 GTTAAGTAGT
Statistics
Matches: 207, Mismatches: 51, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
32 3 0.01
33 201 0.97
34 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.17
Consensus pattern (33 bp):
CCAAGTAGCAGGGATGATGCCCCTATAAGCAGC
Found at i:56482 original size:24 final size:23
Alignment explanation
Indices: 56436--56488 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
56426 CTAAGCCTTA
56436 TCAAATCTGTTACTAGTTCAAAT
1 TCAAATCTGTTACTAGTTCAAAT
* *
56459 TTAAATCTTGTTATTAGCTT-AAAT
1 TCAAATC-TGTTACTAG-TTCAAAT
56483 TCAAAT
1 TCAAAT
56489 ATAACCAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 6 0.24
24 17 0.68
25 2 0.08
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (23 bp):
TCAAATCTGTTACTAGTTCAAAT
Found at i:61927 original size:438 final size:434
Alignment explanation
Indices: 61094--62103 Score: 1210
Period size: 438 Copynumber: 2.3 Consensus size: 434
61084 AAAATTTCAA
* * *
61094 AAGCATTTTTTAGAATTGAAATATAAAAATTAGCTTCTGAGTCTTTCATGAAAATTGTAGATCAT
1 AAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTTGAGTC-TTCATGAAAATTGTAGATCAT
* * * * * *
61159 AAAATTACCTTTTAATAGACACCTGAATTATCTTAATTGGACAAATAAAACAAAGAAAATTTAAA
65 GAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAAC-AA-AAAA--TAAA
* * * *
61224 AAAATGAAGTGTTAAATCGAGTATGATAGAATTTGCAAAGGACTAAGTAGCATCAAATAGAAAAG
126 AAAATAAAGTCTTAAATCGAGTAAGATAGAATTTGCAAAGGAATAAGTAGCATCAAATAGAAAAG
* * * * * *
61289 TATGAGGGTGATTTGATAACTAATTCAAATAAGAAATTATTTGTTAATGGAGATCTTGAAACTTA
191 TATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGAAGATCTTGAAACATA
* * * * * * *
61354 AAAATTCCCTTTTGAACCTTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAA
256 AAAAATCCCTTTTGAACCCTTCACGAAACGCGTAGATCAAATTAACTTTCAGATCCTTCATGAAA
* * * * * * * * * *
61419 GTAGTAGATTATACAGTAACCTTTTAATCGATAGTTGAATAACTTTAATTGGACATGTGGATCGA
321 GTAGTAAATCATACAATAACCTTTTAATCGACACTTCAATAACTTCAATCGAACATGTGGATCAA
* * * * **
61484 AAATTATATGGTATTAAA-TAGACCAACAATCGAAACGACCAAATTTAGG
386 AAATTATACGATATTAAATTA-ACCAACAATCAAAACCAAAAAATTTAGG
* * *
61533 TAGCATTTTTT-GAATTGAAACATAAAAATTTGCTTTTGAGTCATCCATGAAAGTTGTAGATCAT
1 AAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTTGAGTC-TTCATGAAAATTGTAGATCAT
61597 GAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAAAATAAAAAAA
65 GAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAAAAT-AAAAAA
* *
61662 ATAAAG-CTTAAA-CGTTAGATTAAGATAGAATTTGTAAAGGAATAAGTAGTAT-AAAGTAGAAA
129 ATAAAGTCTTAAATCG--AG--TAAGATAGAATTTGCAAAGGAATAAGTAGCATCAAA-TAGAAA
*
61724 AGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGAAGATCTTGAAACA
189 AGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGAAGATCTTGAAACA
*
61789 TAAAAAATCCCTTTTGAACCCTTCACGAAACGCGTAGATCAAATTTAGCTTTCAGATCCTTCATG
254 TAAAAAATCCCTTTTGAACCCTTCACGAAACGCGTAGATCAAA-TTAACTTTCAGATCCTTCATG
* *
61854 AAAGTCGTAAATCATGCAATAACCTTTTAA-CAGACACTTCAATAACTTCAATCGAACATGTGGA
318 AAAGTAGTAAATCATACAATAACCTTTTAATC-GACACTTCAATAACTTCAATCGAACATGTGGA
* ** *
61918 -CAAAAAATTATACGATATTAAATTAATCGGCAATCAAAACCAAAAAATTTCGG
382 TC-AAAAATTATACGATATTAAATTAACCAACAATCAAAACCAAAAAATTTAGG
* ** * * *
61971 AAACATTTTTTAGAATCAAAACATTAAAA-TTGACTTTTGAGTTCTTAATGAAAATTGTAAATCA
1 AAGCATTTTTTAGAATTGAAACATAAAAATTTG-CTTTTGAG-TCTTCATGAAAATTGTAGATCA
* * * *
62035 TGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAAAAGAA-AAAAAATACAAAA
64 TGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAAAATAAAAAA
62099 ATAAA
129 ATAAA
62104 AGTCAATGCA
Statistics
Matches: 489, Mismatches: 69, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
433 2 0.00
434 6 0.01
435 13 0.03
436 7 0.01
437 145 0.30
438 216 0.44
439 98 0.20
440 2 0.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (434 bp):
AAGCATTTTTTAGAATTGAAACATAAAAATTTGCTTTTGAGTCTTCATGAAAATTGTAGATCATG
AAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAAAATAAAAAAAT
AAAGTCTTAAATCGAGTAAGATAGAATTTGCAAAGGAATAAGTAGCATCAAATAGAAAAGTATGA
GGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGAAGATCTTGAAACATAAAAAA
TCCCTTTTGAACCCTTCACGAAACGCGTAGATCAAATTAACTTTCAGATCCTTCATGAAAGTAGT
AAATCATACAATAACCTTTTAATCGACACTTCAATAACTTCAATCGAACATGTGGATCAAAAATT
ATACGATATTAAATTAACCAACAATCAAAACCAAAAAATTTAGG
Found at i:62427 original size:2 final size:2
Alignment explanation
Indices: 62420--62444 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62410 TTTTTATTAT
62420 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
62445 CCATAAAGAG
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:68422 original size:11 final size:11
Alignment explanation
Indices: 68391--68423 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
68381 AAGATTTCAA
68391 CTGAAGATTAT
1 CTGAAGATTAT
68402 CTGGAA-ATTAT
1 CT-GAAGATTAT
68413 CTGAAGATTAT
1 CTGAAGATTAT
68424 GTAATCTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.15
11 14 0.70
12 3 0.15
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (11 bp):
CTGAAGATTAT
Done.