Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012767.1 Corchorus capsularis cultivar CVL-1 contig12788, 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: 55859
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:962 original size:18 final size:19
Alignment explanation
Indices: 939--989 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
929 AAAATGTTAG
939 ATTTAGATTAATTT-AGA-A
1 ATTTAGATTAATTTGA-ACA
*
957 ATTTAGTTTAACTTTGAACA
1 ATTTAGATTAA-TTTGAACA
977 ATTTA-ATTAATTT
1 ATTTAGATTAATTT
990 TAGTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 13 0.46
19 8 0.29
20 7 0.25
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (19 bp):
ATTTAGATTAATTTGAACA
Found at i:1706 original size:49 final size:49
Alignment explanation
Indices: 1437--1810 Score: 366
Period size: 48 Copynumber: 7.7 Consensus size: 49
1427 TTTCACTCGC
* *
1437 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA-TTTATAC--CCAT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTT-TACTTGC-T
* * ** *
1485 TTTTCCCAAAACGCCCTTCCCAGACGGAAGGCGTTTACTTTTACCTG-T
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTTTACTTGCT
* * * * * *
1533 TTTTCCCAAAGTGTCTTTCCCGGACGGAAGGCACTGATTTTTACCTGC-
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTTTACTTGCT
*
1581 TTTTCCCAAAATGCCCTTCCCGGGCGGAAGGCACTTA-TTTTACTTGCTAT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTTTACTTGC--T
* * *
1631 TTCTTCCAAAAATGCTCTTCCCGGACGGAAGGCATTTA-TTTTACTTGCTT
1 TT-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTTTACTTGC-T
* * * * ***
1681 TTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACCCACT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTTTACTTGCT
* * * *
1730 TTTTCCCAAAGTGCCTTTCCCGGACGGAATGCACTAACTTTTACTTGCT
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTTTACTTGCT
** *
1779 TTTTCTTAAAACGCCCTTCCCGGACGGAAGGC
1 TTTTCCCAAAATGCCCTTCCCGGACGGAAGGC
1811 GTTAATTTTG
Statistics
Matches: 269, Mismatches: 48, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
47 9 0.03
48 108 0.40
49 99 0.37
50 12 0.04
51 41 0.15
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.33
Consensus pattern (49 bp):
TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTACTTTTACTTGCT
Found at i:1847 original size:98 final size:97
Alignment explanation
Indices: 1426--1831 Score: 380
Period size: 98 Copynumber: 4.2 Consensus size: 97
1416 CAATTTTCGG
* * * * *
1426 TTTTCACTCGC-TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTATAC--CCATTTT
1 TTTT-ACTCGCTTTTTCCCAAAGTGCCTTTCCCGGACGGAAGGCACTAATTT-TACTTGC-TTTT
* * * *
1488 TCCCAAAACGCCCTTCCCAGACGGAAGGCGTTTAC
63 TCCAAAAACGCCCTTCCCGGACGGAAGGCGCTTAA
* * *
1523 TTTTAC-CTG-TTTTTCCCAAAGTGTCTTTCCCGGACGGAAGGCACTGATTTTTACCTGC-TTTT
1 TTTTACTC-GCTTTTTCCCAAAGTGCCTTTCCCGGACGGAAGGCACT-AATTTTACTTGCTTTTT
* * * *
1585 CCCAAAATGCCCTTCCCGGGCGGAAGGCACTT-A
64 CCAAAAACGCCCTTCCCGGACGGAAGGCGCTTAA
* * * * *
1618 TTTTACTTGCTATTTCTTCCAAAAATG-CTCTTCCCGGACGGAAGGCATTTATTTTACTTGCTTT
1 TTTTACTCGC--TTT-TTCCCAAAGTGCCT-TTCCCGGACGGAAGGCACTAATTTTACTTGC-TT
* * *
1682 TTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTAT
61 TTTCCAAAAACGCCCTTCCCGGACGGAAGGCGCTTAA
* * *
1719 TTTTACCCACTTTTTCCCAAAGTGCCTTTCCCGGACGGAATGCACTAACTTTTACTTGCTTTTTC
1 TTTTACTCGCTTTTTCCCAAAGTGCCTTTCCCGGACGGAAGGCACTAA-TTTTACTTGCTTTTTC
**
1784 TTAAAACGCCCTTCCCGGACGGAAGGCG-TTAA
65 CAAAAACGCCCTTCCCGGACGGAAGGCGCTTAA
*
1816 TTTTGCTCGCTTTTTC
1 TTTTACTCGCTTTTTC
1832 TTCAAATACC
Statistics
Matches: 252, Mismatches: 41, Indels: 32
0.78 0.13 0.10
Matches are distributed among these distances:
95 8 0.03
96 68 0.27
97 23 0.09
98 72 0.29
99 42 0.17
100 32 0.13
101 7 0.03
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (97 bp):
TTTTACTCGCTTTTTCCCAAAGTGCCTTTCCCGGACGGAAGGCACTAATTTTACTTGCTTTTTCC
AAAAACGCCCTTCCCGGACGGAAGGCGCTTAA
Found at i:10959 original size:17 final size:18
Alignment explanation
Indices: 10937--10976 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
10927 TATAGATACG
*
10937 ATATATTA-ATATTATAT
1 ATATATTATATACTATAT
10954 ATATA-TATATACTATAT
1 ATATATTATATACTATAT
10971 AT-TATT
1 ATATATT
10977 TTTGTTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATTATATACTATAT
Found at i:11125 original size:11 final size:11
Alignment explanation
Indices: 11109--11144 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
11099 ATTATACTAT
11109 ATATCTAATTA
1 ATATCTAATTA
11120 ATATCTAATTA
1 ATATCTAATTA
*
11131 ATATTTAATTA
1 ATATCTAATTA
11142 ATA
1 ATA
11145 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATCTAATTA
Found at i:11338 original size:21 final size:21
Alignment explanation
Indices: 11313--11353 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11303 GAGAGACTTT
11313 TTTCTTTTGTTTTCATTCATC
1 TTTCTTTTGTTTTCATTCATC
11334 TTTCTTTTGTTTTCATTCAT
1 TTTCTTTTGTTTTCATTCAT
11354 AAAGGCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTCTTTTGTTTTCATTCATC
Found at i:14738 original size:70 final size:70
Alignment explanation
Indices: 14625--14765 Score: 221
Period size: 70 Copynumber: 2.0 Consensus size: 70
14615 TTGATTGAAA
* * *
14625 TGCATTGTCTTTATATGTACTTTTAGCATTTGGATGTAATTAATGATGTTCCTACCATTTTTTTT
1 TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGATGCTCCCACCATTTTTTTT
14690 CTTAG
66 CTTAG
* *
14695 TGCATTGTTTTTATATGTAATTTTAGCA-TTGAGATGTAATTAATGGTGCTCCCACCATTTTTTT
1 TGCATTGTCTTTATATGTAATTTTAGCATTTG-GATGTAATTAATGATGCTCCCACCATTTTTTT
14759 TCTTAG
65 TCTTAG
14765 T
1 T
14766 TGTTAGTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 3 0.05
70 62 0.95
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (70 bp):
TGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGATGCTCCCACCATTTTTTTT
CTTAG
Found at i:15919 original size:25 final size:27
Alignment explanation
Indices: 15867--15919 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
15857 TTACTCAACT
**
15867 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
15894 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
15919 A
1 A
15920 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:17252 original size:91 final size:91
Alignment explanation
Indices: 17092--17260 Score: 259
Period size: 91 Copynumber: 1.9 Consensus size: 91
17082 ACCGTCCGAC
* * *
17092 CCTACAAAATAGGTGCTTACTAATAGGCTTAGTTTCTATGTCATGCAAGATATTTTCGTGAGAAA
1 CCTACAAAATAGGTGCTTACTAATAGGCTTAGTTTCTATATCATGCAAGACATTTTCATGAGAAA
17157 GGACAATATTTGTTACACAACCCCTA
66 GGACAATATTTGTTACACAACCCCTA
* *
17183 CCTACAAAACT-GGTGCTTACTGATAGGCTTAGTTTCTATATCATGCAAGACATTTTTATGAGAA
1 CCTACAAAA-TAGGTGCTTACTAATAGGCTTAGTTTCTATATCATGCAAGACATTTTCATGAGAA
* *
17247 GGGACATTATTTGT
65 AGGACAATATTTGT
17261 GTCATGTCGT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
91 69 0.99
92 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (91 bp):
CCTACAAAATAGGTGCTTACTAATAGGCTTAGTTTCTATATCATGCAAGACATTTTCATGAGAAA
GGACAATATTTGTTACACAACCCCTA
Found at i:20390 original size:31 final size:31
Alignment explanation
Indices: 20354--20414 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
20344 ACAAATACTT
20354 GCAAAA-TAGGGTAAAAATA-CATATAAAAATG
1 GCAAAAGTA-GGTAAAAATAGC-TATAAAAATG
*
20385 GCAAAAGTATGTAAAAATAGCTATAAAAAT
1 GCAAAAGTAGGTAAAAATAGCTATAAAAAT
20415 ATGCATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.21
Consensus pattern (31 bp):
GCAAAAGTAGGTAAAAATAGCTATAAAAATG
Found at i:22573 original size:8 final size:8
Alignment explanation
Indices: 22542--22572 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
22532 AATTTTCAAA
22542 AAATAAAC
1 AAATAAAC
22550 AAATAAAC
1 AAATAAAC
*
22558 AAATAAAT
1 AAATAAAC
22566 AAATAAA
1 AAATAAA
22573 TTTTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (8 bp):
AAATAAAC
Found at i:25977 original size:22 final size:23
Alignment explanation
Indices: 25949--25995 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
25939 TCTCCTCCAA
25949 TTTTGCTGCAATTTTTCT-TTAG
1 TTTTGCTGCAATTTTTCTCTTAG
*
25971 TTTTGCTGCAATTTTTTTCTTAG
1 TTTTGCTGCAATTTTTCTCTTAG
25994 TT
1 TT
25996 GAACTGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (23 bp):
TTTTGCTGCAATTTTTCTCTTAG
Found at i:26009 original size:24 final size:25
Alignment explanation
Indices: 25982--26028 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
25972 TTTGCTGCAA
*
25982 TTTTTTTCTTAGTTGAA-CTGGTGG
1 TTTTTATCTTAGTTGAATCTGGTGG
*
26006 TTTTTATCTTGGTTGAATCTGGT
1 TTTTTATCTTAGTTGAATCTGGT
26029 ATTACAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.13, C:0.09, G:0.23, T:0.55
Consensus pattern (25 bp):
TTTTTATCTTAGTTGAATCTGGTGG
Found at i:29721 original size:59 final size:60
Alignment explanation
Indices: 29690--29804 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 60
29680 TTCCCTTTTA
*
29690 ACTTTTAATTTGAAACTTTCACCTTCTAAACTATCAAAATTGAGATAATTTTCCCCCTGT
1 ACTTTTAATTTGAAACTTTCACCCTCTAAACTATCAAAATTGAGATAATTTTCCCCCTGT
* * *
29750 ACTTTTAATTTGGAACTTTCACCCT-TAAACTATCAAAATTGGGATGA-TTTCCCCC
1 ACTTTTAATTTGAAACTTTCACCCTCTAAACTATCAAAATTGAGATAATTTTCCCCC
29805 GGCCATTAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 8 0.16
59 20 0.39
60 23 0.45
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (60 bp):
ACTTTTAATTTGAAACTTTCACCCTCTAAACTATCAAAATTGAGATAATTTTCCCCCTGT
Found at i:29832 original size:2 final size:2
Alignment explanation
Indices: 29825--29863 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
29815 GGTTCCGTTA
29825 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
29864 AATAAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30251 original size:2 final size:2
Alignment explanation
Indices: 30244--30294 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
30234 CATCGTTTTG
*
30244 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A- AT -T AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30283 AT AT AT A- AT AT A
1 AT AT AT AT AT AT A
30295 ATAATTTAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30392 original size:9 final size:9
Alignment explanation
Indices: 30378--30461 Score: 72
Period size: 9 Copynumber: 9.8 Consensus size: 9
30368 TAAATAATTA
30378 AATATATAT
1 AATATATAT
30387 AATATATAT
1 AATATATAT
30396 AA-ATA-ATT
1 AATATATA-T
30404 AA-ATATAT
1 AATATATAT
*
30412 AATATGTAT
1 AATATATAT
* *
30421 TATAAATAT
1 AATATATAT
30430 AA-ATA-ATT
1 AATATATA-T
30438 AA-ATATAT
1 AATATATAT
30446 AATATATAT
1 AATATATAT
*
30455 TATATAT
1 AATATAT
30462 GTAAACCGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
7 2 0.03
8 23 0.37
9 37 0.60
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (9 bp):
AATATATAT
Found at i:30393 original size:7 final size:7
Alignment explanation
Indices: 30381--30460 Score: 64
Period size: 7 Copynumber: 12.0 Consensus size: 7
30371 ATAATTAAAT
30381 ATATATA
1 ATATATA
30388 ATATAT-
1 ATATATA
*
30394 ATAAATA
1 ATATATA
30401 AT-TA-A
1 ATATATA
30406 ATATATA
1 ATATATA
*
30413 ATATGTA
1 ATATATA
*
30420 TTATA-A
1 ATATATA
30426 ATATA-A
1 ATATATA
30432 ATA-ATTAA
1 ATATA-T-A
30440 ATATATA
1 ATATATA
30447 ATATATA
1 ATATATA
*
30454 TTATATA
1 ATATATA
30461 TGTAAACCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
5 4 0.07
6 17 0.29
7 32 0.54
8 5 0.08
9 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:30400 original size:27 final size:27
Alignment explanation
Indices: 30368--30454 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 27
30358 GGAGTTTAAG
30368 TAAATAATTAAATATATATAATATATA
1 TAAATAATTAAATATATATAATATATA
30395 TAAATAATTAAATATATAATATGTATTATAAATA
1 TAAATAATTAAATATAT-ATA---A-TAT--ATA
30429 TAAATAATT-AA-ATATATAATATATA
1 TAAATAATTAAATATATATAATATATA
30454 T
1 T
30455 TATATATGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
25 4 0.08
27 20 0.38
28 4 0.08
31 4 0.08
32 7 0.13
33 2 0.04
34 12 0.23
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
TAAATAATTAAATATATATAATATATA
Found at i:30430 original size:34 final size:34
Alignment explanation
Indices: 30378--30458 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
30368 TAAATAATTA
* *
30378 AATATATATAATATATATAAATAATTAAATATAT
1 AATATATATTATAAATATAAATAATTAAATATAT
*
30412 AATATGTATTATAAATATAAATAATTAAATATAT
1 AATATATATTATAAATATAAATAATTAAATATAT
30446 AATATATATTATA
1 AATATATATTATA
30459 TATGTAAACC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (34 bp):
AATATATATTATAAATATAAATAATTAAATATAT
Found at i:32266 original size:14 final size:14
Alignment explanation
Indices: 32247--32278 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
32237 TTTTTAAATT
*
32247 ATAAAAATATAAAA
1 ATAAAAATAAAAAA
32261 ATAAAAATAAAAAA
1 ATAAAAATAAAAAA
32275 ATAA
1 ATAA
32279 TTGTAGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:34652 original size:178 final size:178
Alignment explanation
Indices: 34336--34661 Score: 395
Period size: 178 Copynumber: 1.8 Consensus size: 178
34326 ATTGGCGGTT
* * ** *
34336 CACTTAATATAACATTACTTTTGCTGCAGATGTCTTATTGAGCTGATTCAAGTATCTCATAAAAG
1 CACTTAATATAACATAACTTTTGCTCCAGATGTCCGATTGAGATGATTCAAGTATCTCATAAAAG
* * * * *
34401 GTTATTTTATGATCTACAACTTTCATGCAGGGCTCGAAAGCTAAATTTAATGTTTCAAGTATAAA
66 GCTATTTCATGATCTACAACTTTCATGCAGGACTCGAAAGCTAAATTTAATGTTTCAAATACAAA
34466 ACATGCTTCCAAAAAATTAATTTTTTCGGTTAGCGAGAATGAACGATC
131 ACATGCTTCCAAAAAATTAATTTTTTCGGTTAGCGAGAATGAACGATC
* **
34514 CACTTAATA-ATACATAATTTTTGCTCCAGATGTCCGATTGAGATGATTCAAGTATCTGTTAAAA
1 CACTTAATATA-ACATAACTTTTGCTCCAGATGTCCGATTGAGATGATTCAAGTATCTCATAAAA
* * * ** * * * * *
34578 GGCTGTTTCGTGATCTTCAACTTTCATTTAGGACTTGAAAGCTGAATTTGATTTTTTAAATACCA
65 GGCTATTTCATGATCTACAACTTTCATGCAGGACTCGAAAGCTAAATTTAATGTTTCAAATA-CA
**
34643 AAA-ATGCTTCTGAAAAATT
129 AAACATGCTTCCAAAAAATT
34662 TATATGTCGG
Statistics
Matches: 121, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
177 1 0.01
178 116 0.96
179 4 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (178 bp):
CACTTAATATAACATAACTTTTGCTCCAGATGTCCGATTGAGATGATTCAAGTATCTCATAAAAG
GCTATTTCATGATCTACAACTTTCATGCAGGACTCGAAAGCTAAATTTAATGTTTCAAATACAAA
ACATGCTTCCAAAAAATTAATTTTTTCGGTTAGCGAGAATGAACGATC
Found at i:35001 original size:10 final size:10
Alignment explanation
Indices: 34986--35023 Score: 76
Period size: 10 Copynumber: 3.8 Consensus size: 10
34976 TTTTCCTTAT
34986 TTCATTTTCA
1 TTCATTTTCA
34996 TTCATTTTCA
1 TTCATTTTCA
35006 TTCATTTTCA
1 TTCATTTTCA
35016 TTCATTTT
1 TTCATTTT
35024 TGTTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.63
Consensus pattern (10 bp):
TTCATTTTCA
Found at i:37110 original size:15 final size:16
Alignment explanation
Indices: 37090--37127 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
37080 TGATCAAATG
37090 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
37105 TCGGGTCAATTCTGGGT
1 TCGGGTCAATT-TGGGT
37122 T-GGGTC
1 TCGGGTC
37128 GTTTTTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:38454 original size:16 final size:16
Alignment explanation
Indices: 38422--38497 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
38412 GTCGGGTTGA
* *
38422 TCGGGTTCTGGTCATT
1 TCGGGTTCGGGTAATT
* *
38438 TTGGGTTTGGGTAATT
1 TCGGGTTCGGGTAATT
**
38454 TCGGGTTCGGGTTGTT
1 TCGGGTTCGGGTAATT
* * *
38470 T-GGATTTGGGTCATT
1 TCGGGTTCGGGTAATT
38485 TCGGGTTCGGGTA
1 TCGGGTTCGGGTA
38498 CCCAAAAATT
Statistics
Matches: 44, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
15 11 0.25
16 33 0.75
ACGTcount: A:0.08, C:0.11, G:0.38, T:0.43
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:38478 original size:31 final size:31
Alignment explanation
Indices: 38437--38496 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
38427 TTCTGGTCAT
*
38437 TTTGGGTTTGGGTAATTTCGGGTTCGGGTTG
1 TTTGGATTTGGGTAATTTCGGGTTCGGGTTG
*
38468 TTTGGATTTGGGTCATTTCGGGTTCGGGT
1 TTTGGATTTGGGTAATTTCGGGTTCGGGT
38497 ACCCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.07, C:0.08, G:0.40, T:0.45
Consensus pattern (31 bp):
TTTGGATTTGGGTAATTTCGGGTTCGGGTTG
Found at i:40619 original size:78 final size:78
Alignment explanation
Indices: 40459--40612 Score: 245
Period size: 78 Copynumber: 2.0 Consensus size: 78
40449 AATTTTTAAT
* * * *
40459 TAAAATAGTAAACTAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAG
1 TAAAATAGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTCTTAG
40524 TTAAGTAAAATAG
66 TTAAGTAAAATAG
* *
40537 TAAAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAATATAGAGTTCTTAG
1 TAAAATAGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTCTTAG
*
40602 TTGAGTAAAAT
66 TTAAGTAAAAT
40613 TATAAAAGTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.35
Consensus pattern (78 bp):
TAAAATAGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTCTTAG
TTAAGTAAAATAG
Found at i:41234 original size:33 final size:33
Alignment explanation
Indices: 41152--41239 Score: 108
Period size: 32 Copynumber: 2.7 Consensus size: 33
41142 TGTCCTTTGT
* * *
41152 CACGGCGGAGCCTCCCCACTACAACGGCTCTGC
1 CACGGCGGAGCCGCCCCACTAGAACGACTCTGC
* *
41185 CACGGC-TAGCCGCCCCACTAGGACGACT-TAGC
1 CACGGCGGAGCCGCCCCACTAGAACGACTCT-GC
41217 CACGGCGGAGCCGCCCCACTAGA
1 CACGGCGGAGCCGCCCCACTAGA
41240 GCGGCAAGGC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.02
32 25 0.54
33 20 0.43
ACGTcount: A:0.20, C:0.43, G:0.26, T:0.10
Consensus pattern (33 bp):
CACGGCGGAGCCGCCCCACTAGAACGACTCTGC
Found at i:45664 original size:24 final size:24
Alignment explanation
Indices: 45618--45673 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
45608 ATCTCTGCCC
* *
45618 TCATTGCCATTGGTGCAGCAGCTT
1 TCATTGTCATTGGTGCAGCAGCTG
* *
45642 TCATTGTCATTGGTGTAGTAGCTG
1 TCATTGTCATTGGTGCAGCAGCTG
*
45666 TCACTGTC
1 TCATTGTC
45674 CTTAATATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (24 bp):
TCATTGTCATTGGTGCAGCAGCTG
Found at i:47940 original size:80 final size:80
Alignment explanation
Indices: 47778--47932 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 80
47768 TATTATTGCA
*
47778 TTTATTTATTTACTTTTATAAAAGGAACATCATACTATACTATGTATTTTGTAAATATTTTAAAA
1 TTTATTTATTTACCTTTATAAAAGGAACATCATACTATACTATGTATTTTGTAAATATTTTAAAA
47843 CCCAATTTTCTTTTT
66 CCCAATTTTCTTTTT
47858 TTTATTTATTTACCTTTATAAAAGG-A-A-CAT-C-ATACTATGTATTTTGTAAATATTTTAAAA
1 TTTATTTATTTACCTTTATAAAAGGAACATCATACTATACTATGTATTTTGTAAATATTTTAAAA
47918 CCCAATTTTCTTTTT
66 CCCAATTTTCTTTTT
47933 CTTTTTTTCA
Statistics
Matches: 74, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
75 44 0.59
76 1 0.01
77 3 0.04
78 1 0.01
79 1 0.01
80 24 0.32
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.50
Consensus pattern (80 bp):
TTTATTTATTTACCTTTATAAAAGGAACATCATACTATACTATGTATTTTGTAAATATTTTAAAA
CCCAATTTTCTTTTT
Found at i:54082 original size:6 final size:6
Alignment explanation
Indices: 54073--54101 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54063 TTATTCGAAT
54073 TTGAAC TTGAAC TTGAAC TTGAAC TTGAA
1 TTGAAC TTGAAC TTGAAC TTGAAC TTGAA
54102 TTGCTTCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (6 bp):
TTGAAC
Done.