Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016235.1 Corchorus capsularis cultivar CVL-1 contig16256, 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: 89541
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:599 original size:24 final size:27
Alignment explanation
Indices: 572--624 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
562 TTCTAGTGAT
*
572 GAGAAT-AAG-GAAGGAAAA-GAGGAG
1 GAGAATCAAGAGAAGGAAAATAAGGAG
596 GAGAATCAAGAGAAGGAAAATAAGGAG
1 GAGAATCAAGAGAAGGAAAATAAGGAG
623 GA
1 GA
625 ATTTCATCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 9 0.36
27 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.38, T:0.06
Consensus pattern (27 bp):
GAGAATCAAGAGAAGGAAAATAAGGAG
Found at i:2370 original size:21 final size:19
Alignment explanation
Indices: 2346--2392 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
2336 AAAGTTCGTG
2346 TTTGAAGATTTTTGAAGATAA
1 TTTGAAGA--TTTGAAGATAA
*
2367 TTTGAAGATTTGAAGATCA
1 TTTGAAGATTTGAAGATAA
2386 -TTGAAGA
1 TTTGAAGA
2393 ATTATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
21 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (19 bp):
TTTGAAGATTTGAAGATAA
Found at i:8902 original size:49 final size:49
Alignment explanation
Indices: 8843--9176 Score: 499
Period size: 49 Copynumber: 6.8 Consensus size: 49
8833 TTACCTACTT
* *
8843 TTTCCTAAAGCGCCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
*
8892 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTCTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
**
8941 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTCGCTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
* * *
8990 TTTCCCAAAACACCCTTCCCAGACGGAA-CCATTCATTTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
* * * * * *
9038 TCTCCCAAAACGCCCTTCCCGGACGCAAGCCGTTTATCTTTACTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
** *
9087 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTGCTTTTGCTTGCTA
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
*
9136 TTTCCCAAAACGCCCTTCCCAGACGGAAGCCATTTATTTTT
1 TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTT
9177 TCCTGCCATT
Statistics
Matches: 254, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
48 41 0.16
49 213 0.84
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (49 bp):
TTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTA
Found at i:9108 original size:146 final size:147
Alignment explanation
Indices: 8855--9176 Score: 533
Period size: 146 Copynumber: 2.2 Consensus size: 147
8845 TCCTAAAGCG
* * *
8855 CCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAA
1 CCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATCTCCCAAAACGCCCTTCCCAGACGCAA
8920 GCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTT-ATTTTCGC
66 GCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTGATTTT-GC
8984 TTGCTATTTCCCAAAACA
130 TTGCTATTTCCCAAAACA
*
9002 CCCTTCCCAGACGGAA-CCATTCATTTTTACTTGCTATCTCCCAAAACGCCCTTCCCGGACGCAA
1 CCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATCTCCCAAAACGCCCTTCCCAGACGCAA
* *
9066 GCCGTTTA-TCTTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTGCTTTTGC
66 GCCATTTATTC-TTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTGATTTTGC
*
9130 TTGCTATTTCCCAAAACG
130 TTGCTATTTCCCAAAACA
*
9148 CCCTTCCCAGACGGAAGCCATTTATTTTT
1 CCCTTCCCAGACGGAAGCCATTCATTTTT
9177 TCCTGCCATT
Statistics
Matches: 164, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
145 2 0.01
146 131 0.80
147 31 0.19
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (147 bp):
CCCTTCCCAGACGGAAGCCATTCATTTTTACTTGCTATCTCCCAAAACGCCCTTCCCAGACGCAA
GCCATTTATTCTTACTTGCTATTTCCCAAAGCGCCCTTCCCAGACGGAAGCCATTTGATTTTGCT
TGCTATTTCCCAAAACA
Found at i:11892 original size:15 final size:15
Alignment explanation
Indices: 11872--11903 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11862 TTGCACTTCT
11872 TCATTTCTGAATCTG
1 TCATTTCTGAATCTG
*
11887 TCATTTCTGTATCTG
1 TCATTTCTGAATCTG
11902 TC
1 TC
11904 TCGTCCATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (15 bp):
TCATTTCTGAATCTG
Found at i:19778 original size:7 final size:7
Alignment explanation
Indices: 19766--19791 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19756 GAATTTCGAA
19766 GGATTGG
1 GGATTGG
19773 GGATTGG
1 GGATTGG
19780 GGATTGG
1 GGATTGG
19787 GGATT
1 GGATT
19792 TTCGATTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (7 bp):
GGATTGG
Found at i:25131 original size:30 final size:30
Alignment explanation
Indices: 25095--25157 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
25085 TCTTTAAGGG
25095 GGAGGGAATGATGCGCCCAA-GGCTTATCAT
1 GGAGGGAATGATGCG-CCAAGGGCTTATCAT
25125 GGAGGGAATGATGCGCCAAGGGCTTATCAT
1 GGAGGGAATGATGCGCCAAGGGCTTATCAT
25155 GGA
1 GGA
25158 CTTGAAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.27, C:0.17, G:0.37, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGGCTTATCAT
Found at i:25246 original size:85 final size:85
Alignment explanation
Indices: 25103--25276 Score: 323
Period size: 85 Copynumber: 2.1 Consensus size: 85
25093 GGGGAGGGAA
*
25103 TGATGCGCCCAAGGCTTATCATGGAGGGAATGATGCGCCAAGGGCTTATCATGGACTTGAAGATG
1 TGATGCGCCCAAGGCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCATGGACTTGAAGATG
25168 ACAATGGAGAGCAAGGAAAG
66 ACAATGGAGAGCAAGGAAAG
*
25188 TGATGCGCCCGAGGCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCATGGACTTGAAGATG
1 TGATGCGCCCAAGGCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCATGGACTTGAAGATG
25253 ACAATGGAGAGCAAGGAAAG
66 ACAATGGAGAGCAAGGAAAG
25273 -GATG
1 TGATG
25277 TGCATGGGCT
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 4 0.05
85 83 0.95
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19
Consensus pattern (85 bp):
TGATGCGCCCAAGGCTTATCATGGAGGGAATGATGCGCCAAGGACTTATCATGGACTTGAAGATG
ACAATGGAGAGCAAGGAAAG
Found at i:27750 original size:41 final size:41
Alignment explanation
Indices: 27650--27750 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 41
27640 CCTTTGTTTG
* * *
27650 ATGCAACTTGGTCCCTGATCTAGGATTTTATTTTCTGATTT
1 ATGCAACTTGGTCCCTGATATAAGATTTTATTTACTGATTT
** *
27691 ATGCGGCTTAGTCCCTGATATAAGATTTTATTTACT-ATTT
1 ATGCAACTTGGTCCCTGATATAAGATTTTATTTACTGATTT
* *
27731 AATGCAATTTGGTCTCTGAT
1 -ATGCAACTTGGTCCCTGAT
27751 TTTAGAAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 4 0.08
41 44 0.92
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.45
Consensus pattern (41 bp):
ATGCAACTTGGTCCCTGATATAAGATTTTATTTACTGATTT
Found at i:28000 original size:18 final size:17
Alignment explanation
Indices: 27969--28002 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27959 TTAATCTAGG
*
27969 TTAGTTTAATAATAAGT
1 TTAGTTTAAAAATAAGT
27986 TTAGTTTAAAAAATAAG
1 TTAGTTT-AAAAATAAG
28003 CATATGCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
TTAGTTTAAAAATAAGT
Found at i:32363 original size:66 final size:63
Alignment explanation
Indices: 32273--32727 Score: 204
Period size: 66 Copynumber: 6.8 Consensus size: 63
32263 ATGACAAGTT
* * * * *
32273 TGACTCTTTGACCGAAAGGGCATTTTTGGAAATTGAAAGTAAACTTAAATTCGAAAATGAGGAAA
1 TGACCCTTTCACCG-AAGGGCATTTTTGGAAA-TGAAACTAAACTTAAATGC-AAAAAGAGGAAA
*
32338 C
63 A
* * *
32339 TGACCCTTTCACCGAAGGGGCATTTTTGTAAGATAAAACTAAACTTAGATGCAAAAAGAGGAAAA
1 TGACCCTTTCACCGAA-GGGCATTTTTGGAA-ATGAAACTAAACTTAAATGCAAAAAGAGGAAAA
* * *
32404 TGACCC-TTCGACTGGAAGGGTATTTTTGGAAATGAAAATACTAAACTTGAATGC-AAAAGA--A
1 TGACCCTTTC-AC-CGAAGGGCATTTTTGGAAATG--AA-ACTAAACTTAAATGCAAAAAGAGGA
32465 AACA
61 AA-A
* * ** * * *
32469 CTGACCCTTTGACCGAAAGGGTATTCCTGGAAATGGGAATGCTAAAACTTGAATGC-AAAAGA-C
1 -TGACCCTTTCACCG-AAGGGCATTTTTGGAAAT--GAA-ACT-AAACTTAAATGCAAAAAGAGG
*
32532 AATAT
60 AA-AA
* * ** * * * * * *
32537 TGAACCTTTGACCGAAAGGTTATTTATGGAAAAAAGATACTAAACTT-AATGCGAAAGGACGAAA
1 TGACCCTTTCACCG-AAGGGCATTTTTGG--AAATGAAACTAAACTTAAATGCAAAAAGAGGAAA
32601 A
63 A
* * * * * * *
32602 TGACCCTTCCACCGAAAGGGTACTTTTGGGAAAAGAAAATACTAAACTTAAATGCGAAAGGACGA
1 TGACCCTTTCACCG-AAGGGCA-TTTTTGGAAATG--AA-ACTAAACTTAAATGCAAAAAGAGGA
32667 AAA
61 AAA
* * * * *
32670 TGACCCTTCCACCGAAAGGGTACTTTTGGGAAAAGAAAATACTAAACTCAAATGCAAA
1 TGACCCTTTCACCG-AAGGGCA-TTTTTGGAAATG--AA-ACTAAACTTAAATGCAAA
32728 GGACGAAACT
Statistics
Matches: 324, Mismatches: 40, Indels: 48
0.79 0.10 0.12
Matches are distributed among these distances:
64 18 0.06
65 65 0.20
66 90 0.28
67 70 0.22
68 77 0.24
69 4 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (63 bp):
TGACCCTTTCACCGAAGGGCATTTTTGGAAATGAAACTAAACTTAAATGCAAAAAGAGGAAAA
Found at i:32527 original size:67 final size:66
Alignment explanation
Indices: 32404--32727 Score: 225
Period size: 68 Copynumber: 4.9 Consensus size: 66
32394 AAGAGGAAAA
* * * **
32404 TGACCCTTCGACTGGAAGGGTATTTTTGGAAATGAAAATACTAAACTTGAATGCAAAAGAAAACA
1 TGACCCTTTGACCGAAAGGGTATTCCTGGAAATGAAAATACTAAACTTGAATGCAAAAGAAAACA
32469 C
66 C
** * * *
32470 TGACCCTTTGACCGAAAGGGTATTCCTGGAAATGGGAATGCTAAAACTTGAATGCAAAAGACAAT
1 TGACCCTTTGACCGAAAGGGTATTCCTGGAAATGAAAATACT-AAACTTGAATGCAAAAGAAAAC
*
32535 AT
65 AC
* * ** *
32537 TGAACCTTTGACCGAAAGGTTATTTATGGAAA--AAAGATACTAAACTT-AATGCGAAAGGACGA
1 TGACCCTTTGACCGAAAGGGTATTCCTGGAAATGAAA-ATACTAAACTTGAATGC-AAAAGA--A
32599 AA-A-
62 AACAC
** * * * *
32602 TGACCCTTCCACCGAAAGGGTACTT-TTGGGAAAAGAAAATACTAAACTTAAATGCGAAAGGACG
1 TGACCCTTTGACCGAAAGGGTA-TTCCT-GGAAATGAAAATACTAAACTTGAATGC-AAAAGA--
32666 AAA-A-
61 AAACAC
** * * **
32670 TGACCCTTCCACCGAAAGGGTACTT-TTGGGAAAAGAAAATACTAAACTCAAATGCAAA
1 TGACCCTTTGACCGAAAGGGTA-TTCCT-GGAAATGAAAATACTAAACTTGAATGCAAA
32728 GGACGAAACT
Statistics
Matches: 222, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
64 5 0.02
65 31 0.14
66 46 0.21
67 65 0.29
68 75 0.34
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (66 bp):
TGACCCTTTGACCGAAAGGGTATTCCTGGAAATGAAAATACTAAACTTGAATGCAAAAGAAAACA
C
Found at i:32660 original size:68 final size:65
Alignment explanation
Indices: 32312--32735 Score: 349
Period size: 67 Copynumber: 6.4 Consensus size: 65
32302 AAATTGAAAG
* * * * * * * *
32312 TAAACTTAAATTCGAAAATGAGGAAACTGACCCTTTCACCGAAGGGGCATTTTTG-TAAGATAAA
1 TAAACTTAAATGC-AAAA-GACGAAAATGACCCTTCCACCGAAAGGGTATTTTGGAAAAGA-AAA
32376 -AC
63 TAC
* * * * * *
32378 TAAACTTAGATGCAAAAAGAGGAAAATGACCCTTCGACTGGAAGGGTATTTTTGGAAATGAAAAT
1 TAAACTTAAATGC-AAAAGACGAAAATGACCCTTCCACCGAAAGGGTA-TTTTGGAAAAGAAAAT
32443 AC
64 AC
* ** * * **
32445 TAAACTTGAATGCAAAAGA--AAACACTGACCCTTTGACCGAAAGGGTATTCCTGGAAATGGGAA
1 TAAACTTAAATGCAAAAGACGAAA-A-TGACCCTTCCACCGAAAGGGTATT-TTGGAAAAGAAAA
*
32508 TGC
63 TAC
* * * ** * *
32511 TAAAACTTGAATGCAAAAGAC-AATATTGAACCTTTGACCGAAAGGTTATTTATGGAAAA-AAGA
1 T-AAACTTAAATGCAAAAGACGAA-AATGACCCTTCCACCGAAAGGGTATTT-TGGAAAAGAAAA
32574 TAC
63 TAC
*
32577 TAAACTT-AATGCGAAAGGACGAAAATGACCCTTCCACCGAAAGGGTACTTTTGGGAAAAGAAAA
1 TAAACTTAAATGC-AAAAGACGAAAATGACCCTTCCACCGAAAGGGTA-TTTT-GGAAAAGAAAA
32641 TAC
63 TAC
*
32644 TAAACTTAAATGCGAAAGGACGAAAATGACCCTTCCACCGAAAGGGTACTTTTGGGAAAAGAAAA
1 TAAACTTAAATGC-AAAAGACGAAAATGACCCTTCCACCGAAAGGGTA-TTTT-GGAAAAGAAAA
32709 TAC
63 TAC
* *
32712 TAAACTCAAATGCAAAGGACGAAA
1 TAAACTTAAATGCAAAAGACGAAA
32736 CTAAAACCCT
Statistics
Matches: 303, Mismatches: 39, Indels: 31
0.81 0.10 0.08
Matches are distributed among these distances:
64 8 0.03
65 58 0.19
66 76 0.25
67 86 0.28
68 74 0.24
69 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (65 bp):
TAAACTTAAATGCAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTGGAAAAGAAAATAC
Found at i:41011 original size:12 final size:12
Alignment explanation
Indices: 40994--41018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40984 ACCTGGCAAT
40994 TCGTGTTTCGTG
1 TCGTGTTTCGTG
41006 TCGTGTTTCGTG
1 TCGTGTTTCGTG
41018 T
1 T
41019 TGTATAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:46523 original size:33 final size:32
Alignment explanation
Indices: 46471--46563 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 32
46461 AACTGAGTGC
** *
46471 CCAATAATCGTAGCGTCGATTTAAGTTAAGAG
1 CCAATAATTTTAGCGTCGATTTAAGCTAAGAG
* * * *
46503 TCCAATAATTTTAGCATCGATCTGAGCTGAGAG
1 -CCAATAATTTTAGCGTCGATTTAAGCTAAGAG
* *
46536 CATAATAATTTTAGCGTCGATTTGAGCT
1 C-CAATAATTTTAGCGTCGATTTAAGCT
46564 GGTCGTCTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
32 1 0.02
33 48 0.98
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (32 bp):
CCAATAATTTTAGCGTCGATTTAAGCTAAGAG
Found at i:47980 original size:24 final size:24
Alignment explanation
Indices: 47948--47994 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
47938 TGCCAGGGAA
*
47948 TGCAATGGTCCCCGAAGAGTGCAT
1 TGCAATGGTCCCCAAAGAGTGCAT
*
47972 TGCAATGGTTCCCAAAGAGTGCA
1 TGCAATGGTCCCCAAAGAGTGCA
47995 CCTTATCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (24 bp):
TGCAATGGTCCCCAAAGAGTGCAT
Found at i:49738 original size:8 final size:7
Alignment explanation
Indices: 49711--49757 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
49701 GATAGATAGG
49711 TTTTTTC
1 TTTTTTC
49718 TTTTTTC
1 TTTTTTC
49725 -TTTTTC
1 TTTTTTC
49731 TTTCTTTCC
1 TTT-TTT-C
*
49740 TTCTTTTA
1 TT-TTTTC
49748 TTTTTTC
1 TTTTTTC
49755 TTT
1 TTT
49758 AGCTTGGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.18
7 16 0.47
8 5 0.15
9 6 0.18
10 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:51364 original size:28 final size:28
Alignment explanation
Indices: 51331--51604 Score: 320
Period size: 28 Copynumber: 9.8 Consensus size: 28
51321 AAGATTTTCA
* *
51331 CTCGAGGAGTGTTGAGCAGGGTTTCTCG
1 CTCGAGGAGTGTTGAGCATGGATTCTCG
** *
51359 CTCGAGGAGCATTGAGCATAGATTCTCG
1 CTCGAGGAGTGTTGAGCATGGATTCTCG
* *
51387 CTCGAGGAGCGTTGAGCGTGGATTCTCG
1 CTCGAGGAGTGTTGAGCATGGATTCTCG
* *
51415 CTCGAGGAATGTTAAGCATGGATTCTCG
1 CTCGAGGAGTGTTGAGCATGGATTCTCG
* *
51443 CTCGAGGAGCGTTGAGCGTGGATTCTCG
1 CTCGAGGAGTGTTGAGCATGGATTCTCG
* * * *
51471 CTCGAGGAGTGGTAAGCATAGATCCTCG
1 CTCGAGGAGTGTTGAGCATGGATTCTCG
* *
51499 CTCGATGAGCT-TTGAGCATGAATTCTCAG
1 CTCGAGGAG-TGTTGAGCATGGATTCTC-G
51528 CTCGAGGAGCT-TTGAGCATGGATTCTCG
1 CTCGAGGAG-TGTTGAGCATGGATTCTCG
*
51556 CTCGAGGAGTGTTAAGCATGGA-TCTTCG
1 CTCGAGGAGTGTTGAGCATGGATTC-TCG
*
51584 CTCGAGGAGCGTTGAGCATGG
1 CTCGAGGAGTGTTGAGCATGG
51605 TGTAGTAGTC
Statistics
Matches: 209, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
27 3 0.01
28 179 0.86
29 27 0.13
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (28 bp):
CTCGAGGAGTGTTGAGCATGGATTCTCG
Found at i:52004 original size:149 final size:148
Alignment explanation
Indices: 51733--52182 Score: 603
Period size: 149 Copynumber: 3.0 Consensus size: 148
51723 CTCGTTAGAG
* * * *
51733 CAGCTCTGAGAGCGATTTAGGGGCTTCTTAGAGAGGGAGAATTTATATCGGAGCTCATCATTTTT
1 CAGCTCTGAGAGCGTTTTAGGGGCTTTTTAGAGAGGGAGGATTTAAATCGGAGCTCA-C-TTTTT
*
51798 GAGTCCATTCTTTAGGGCTGCTATGGCAGCATATTACTCTAAGTCTTTGACCTGGAGAGCTTTGG
64 GAGTCCATTCTTTAGGGCTGCTATGGCAGCATATTGCTCTAAGTCTTTGACCTGGAGAGCTTTGG
51863 TTGGTCTCGACCTCTCTCCC
129 TTGGTCTCGACCTCTCTCCC
* * *
51883 CAGCTCGGAGAGCGTTTTAGGGGCTTTTTAGAGAGGAAGGATTTAAATCGGAGCTCACTGCTTTG
1 CAGCTCTGAGAGCGTTTTAGGGGCTTTTTAGAGAGGGAGGATTTAAATCGGAGCTCACT-TTTTG
*
51948 AGTCCATTCTTTAGGGCTACTATGGCAGCATATTGCTCTAAGTCTTTGACCTGGAGAGCTTTGGT
65 AGTCCATTCTTTAGGGCTGCTATGGCAGCATATTGCTCTAAGTCTTTGACCTGGAGAGCTTTGGT
52013 TGGTCTCGACCTCTCTCCC
130 TGGTCTCGACCTCTCTCCC
* * * ** * *
52032 GAGCTTTGAGAGTGTTTTAGGGGAATTTTAGAGAGGGATGATTTAAATCGGAGCTCACAATTTTG
1 CAGCTCTGAGAGCGTTTTAGGGGCTTTTTAGAGAGGGAGGATTTAAATCGGAGCTCAC-TTTTTG
* *** *** * * * *
52097 AGTCCATTCTTTAGGGCCGCTACAACCTTAGATTGCCCTAAGTCTTTGACTTGGAGAGCTTTGAT
65 AGTCCATTCTTTAGGGCTGCTATGGCAGCATATTGCTCTAAGTCTTTGACCTGGAGAGCTTTGGT
*
52162 CGGTCTCGACCTCTCTACCC
130 TGGTCTCGACCTCTCT-CCC
52182 C
1 C
52183 TTTTTTTTGT
Statistics
Matches: 264, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
148 1 0.00
149 209 0.79
150 54 0.20
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (148 bp):
CAGCTCTGAGAGCGTTTTAGGGGCTTTTTAGAGAGGGAGGATTTAAATCGGAGCTCACTTTTTGA
GTCCATTCTTTAGGGCTGCTATGGCAGCATATTGCTCTAAGTCTTTGACCTGGAGAGCTTTGGTT
GGTCTCGACCTCTCTCCC
Found at i:54832 original size:131 final size:131
Alignment explanation
Indices: 54607--54870 Score: 372
Period size: 131 Copynumber: 2.0 Consensus size: 131
54597 CATTGTATAA
54607 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTCTAAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTCTAAC
* * *
54672 TATTTAATTTTTACCATTTTACTATTTTAATT-AAAAACTTATATACATTAGAATTTTTTA-AAT
66 TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATACATTAGAA-ATTTTACAAT
54735 AT
130 AT
* * * *
54737 ACTTTTATAGTTTTACTCAACTAAAAGCTCTATTTTTTTATTTAATT-TATCTAATATCCTTGTA
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTA--TTTTCATTTAATTAAATCTAATATCCTTCTA
* * * *
54801 CCTATTTTATTTTTATCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAAATTTTACA
64 ACTATTTAATTTTTACCATTTTACTAATTTAATT-AAAAAACTTAGATACATTAGAAATTTTACA
54866 ATAT
128 ATAT
54870 A
1 A
54871 TTTCTTGAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
130 31 0.26
131 45 0.38
132 17 0.14
133 25 0.21
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.49
Consensus pattern (131 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCCTTCTAAC
TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATACATTAGAAATTTTACAATA
T
Found at i:75476 original size:21 final size:21
Alignment explanation
Indices: 75450--75494 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
75440 AAGCTCAAGT
* *
75450 TCATGATAAGCCTTGGGTGCA
1 TCATGATAAACCTTGGGCGCA
75471 TCATGATAAACCTTGGGCGCA
1 TCATGATAAACCTTGGGCGCA
75492 TCA
1 TCA
75495 ATTACCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (21 bp):
TCATGATAAACCTTGGGCGCA
Done.