Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015611.1 Corchorus olitorius cultivar O-4 contig15644, 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: 49602
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:1847 original size:2 final size:2
Alignment explanation
Indices: 1840--1951 Score: 215
Period size: 2 Copynumber: 56.0 Consensus size: 2
1830 ATTATACCTA
1840 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1882 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
*
1924 GT GT GT GT GT GT AT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1952 CTATATATAT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.01, C:0.00, G:0.49, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2453 original size:27 final size:25
Alignment explanation
Indices: 2417--2479 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
2407 GAAAAAAAAT
2417 AATAGTAAATA-AATAGAT-AATAGCTA
1 AATA-TAAATATAA-AGATAAATAG-TA
2443 AATTAATAAATATAAAGATAAATAGTA
1 AA-T-ATAAATATAAAGATAAATAGTA
2470 AATATAAATA
1 AATATAAATA
2480 GATAATAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
25 7 0.21
26 3 0.09
27 15 0.45
28 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
AATATAAATATAAAGATAAATAGTA
Found at i:2486 original size:13 final size:13
Alignment explanation
Indices: 2448--2480 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2438 AGCTAAATTA
*
2448 ATAAATA-TAAAG
1 ATAAATAGTAAAT
2460 ATAAATAGTAAAT
1 ATAAATAGTAAAT
2473 ATAAATAG
1 ATAAATAG
2481 ATAATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (13 bp):
ATAAATAGTAAAT
Found at i:6001 original size:22 final size:22
Alignment explanation
Indices: 5973--6105 Score: 112
Period size: 22 Copynumber: 6.0 Consensus size: 22
5963 TTACCTGATC
*
5973 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
5995 CTATGAAATTTTGTTAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
6018 -TATGAAATTTTGGTGACCACA
1 CTATGAAATTTTGATAACCACA
* *
6039 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
6060 CTCATAAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
6083 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
6105 C
1 C
6106 AGAAACAAGA
Statistics
Matches: 87, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.06
22 76 0.87
23 4 0.05
24 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:6070 original size:44 final size:44
Alignment explanation
Indices: 5978--6101 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 44
5968 TGATCCTATG
* * *
5978 AAATTTTGGTAACCACACTATGAAATTTTGTTAACTTCCATATG
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCATATA
* *
6022 AAATTTTGGTGACCACACTATGGAATTTTGATAACCTCC-TCATA
1 AAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCAT-ATA
* ** *
6066 AAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 AAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
6102 ACACAGAAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 65 0.97
45 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (44 bp):
AAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCATATA
Found at i:6593 original size:13 final size:13
Alignment explanation
Indices: 6557--6595 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
6547 TCTAAATTAA
6557 AATTTT-ATAATT
1 AATTTTAATAATT
6569 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
6584 AATTTTAATAAT
1 AATTTTAATAAT
6596 GTCAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 4 0.17
15 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:6603 original size:15 final size:14
Alignment explanation
Indices: 6563--6595 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
6553 TTAAAATTTT
6563 ATAATTAATTTTTAA
1 ATAATTAA-TTTTAA
6578 ATAATTAATTTT-A
1 ATAATTAATTTTAA
6591 ATAAT
1 ATAAT
6596 GTCAATTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTAATTTTAA
Found at i:12276 original size:37 final size:37
Alignment explanation
Indices: 12232--12307 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
12222 CAAAATAGCA
12232 TTTCACTCAACATAGGAAAAAGTATTACCAGAAATAG
1 TTTCACTCAACATAGGAAAAAGTATTACCAGAAATAG
12269 TTTCACTCAACATAGGAAAAAGTATTACCAGAAATAG
1 TTTCACTCAACATAGGAAAAAGTATTACCAGAAATAG
12306 TT
1 TT
12308 GCACCTTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (37 bp):
TTTCACTCAACATAGGAAAAAGTATTACCAGAAATAG
Found at i:13770 original size:465 final size:464
Alignment explanation
Indices: 12846--13781 Score: 1750
Period size: 465 Copynumber: 2.0 Consensus size: 464
12836 GATGAATAGG
12846 CAAATAAGTATGAACATTCAAAAAGATGTGTGGTACAAAATCAAGGCTGAAACATGGACACATAG
1 CAAATAAGTATGAACATTCAAAAAGATGTGTGGTACAAAATCAAGGCTGAAACATGGACACATAG
12911 TTGGTAACAGAACGTGATTCCTGAGGCTCAGAACAAAGACAATGAAGAATATAGAAAGTATGCTA
66 TTGGTAACAGAACGTGATTCCTGAGGCTCAGAACAAAGACAATGAAGAATATAGAAAGTATGCTA
*
12976 AGATGTCTTTGAGTTTAACACTGTTCGGGAGAAAACCAGAAAAAATGCACCAAGATCTTGTTAAT
131 AGATATCTTTGAGTTTAACACTGTTCGGGAGAAAACCAGAAAAAATGCACCAAGATCTTGTTAAT
* *
13041 GAAATCCATTACAACCACTTTAATCCTAGAGATGAAAACTGAAATGAAAAACAAAAAACACAATG
196 GAAATCCATTACAACCACTTTAATCCTAGAGATGAAAACTGAAATGAAAAAAAAAAAAAACAATG
13106 GTGATTTTGCCGATGTGACTGCGGTTGATGAAATGTATCCTGAATATTGTTACTATAATTATAAA
261 GTGATTTTGCCGATGTGACTGCGGTTGATGAAATGTATCCTGAATATTGTTACTATAATTATAAA
*
13171 CAAAGGAACTTGCCACATTGCTTCTATTATAAAAGGGTGGTTTAGGGTAGATATTTAGCATTAAA
326 CAAAGGAACTTGCCACATTGCTTCTATTATAAAAGGGTGGTTTAGGGTAGATATTAAGCATTAAA
*
13236 ACCTAGAAAGGGTGAAACTCGAGAAACCACAACAAGAAAGCAACAAAAGGCTAGTAGAGTTTATT
391 ACCTAGAAAGGGTGAAACTCGAGAAACCACAACAAGAAAGCAACAAAACGCTAGTAGAGTTTATT
13301 TCCACTGCC
456 TCCACTGCC
13310 CAAATAAGTATGAACATTCAAAAAGATGTGTGGTACAAAATCAAGGCTGAAACATGGACACATAG
1 CAAATAAGTATGAACATTCAAAAAGATGTGTGGTACAAAATCAAGGCTGAAACATGGACACATAG
13375 TTGGTAACAGAACGTGATTCCTGAGGCTCAGAACAAAGACAATGAAGAATATAGAAAGTATGCTA
66 TTGGTAACAGAACGTGATTCCTGAGGCTCAGAACAAAGACAATGAAGAATATAGAAAGTATGCTA
*
13440 AGATATCTTTGAGTTTAACACTGTTCGGAGGAGAAAACCAGAAAAAATGTACCAAGATCTTGTTA
131 AGATATCTTTGAGTTTAACACTGTTC-G-GGAGAAAACCAGAAAAAATGCACCAAGATCTTGTTA
*
13505 ATGAAATCCATTACAACCACTTTAATCCTAGAGATGAAAATTGAAAT-AAAAAAAAAAAAAACAA
194 ATGAAATCCATTACAACCACTTTAATCCTAGAGATGAAAACTGAAATGAAAAAAAAAAAAAACAA
*
13569 TGGTGATTTTGCCGATGTGACTGTGGTTGATGAAATGTATCCTGAATATTGTTACTATAAATTAT
259 TGGTGATTTTGCCGATGTGACTGCGGTTGATGAAATGTATCCTGAATATTGTTACTAT-AATTAT
13634 AAACAAAGGAACTTGCCACATTGCTTCTATTATAAAA-GGTGGTTTAGGGTAGATATTAAGCATT
323 AAACAAAGGAACTTGCCACATTGCTTCTATTATAAAAGGGTGGTTTAGGGTAGATATTAAGCATT
*
13698 AAAACCTAGAAAGGGTGAAACTCGAGAAACCACAACAAGAAAGCAACAAAACGCTGGTAGAGTTT
388 AAAACCTAGAAAGGGTGAAACTCGAGAAACCACAACAAGAAAGCAACAAAACGCTAGTAGAGTTT
13763 ATTTCCACTGCC
453 ATTTCCACTGCC
13775 CAAATAA
1 CAAATAA
13782 TGTCCATGAG
Statistics
Matches: 460, Mismatches: 9, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
464 155 0.34
465 181 0.39
466 124 0.27
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (464 bp):
CAAATAAGTATGAACATTCAAAAAGATGTGTGGTACAAAATCAAGGCTGAAACATGGACACATAG
TTGGTAACAGAACGTGATTCCTGAGGCTCAGAACAAAGACAATGAAGAATATAGAAAGTATGCTA
AGATATCTTTGAGTTTAACACTGTTCGGGAGAAAACCAGAAAAAATGCACCAAGATCTTGTTAAT
GAAATCCATTACAACCACTTTAATCCTAGAGATGAAAACTGAAATGAAAAAAAAAAAAAACAATG
GTGATTTTGCCGATGTGACTGCGGTTGATGAAATGTATCCTGAATATTGTTACTATAATTATAAA
CAAAGGAACTTGCCACATTGCTTCTATTATAAAAGGGTGGTTTAGGGTAGATATTAAGCATTAAA
ACCTAGAAAGGGTGAAACTCGAGAAACCACAACAAGAAAGCAACAAAACGCTAGTAGAGTTTATT
TCCACTGCC
Found at i:15058 original size:28 final size:27
Alignment explanation
Indices: 15026--15085 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
15016 AGAATTAGAC
* *
15026 AATAATTAGAAACCAAAGAAAAAAGAA
1 AATAATAAAAAACCAAAGAAAAAAGAA
15053 GAATAATAAAAAACCAAAGAAAAAAGAA
1 -AATAATAAAAAACCAAAGAAAAAAGAA
15081 AATAA
1 AATAA
15086 ATTCCCGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (27 bp):
AATAATAAAAAACCAAAGAAAAAAGAA
Found at i:26577 original size:170 final size:170
Alignment explanation
Indices: 26293--26613 Score: 446
Period size: 170 Copynumber: 1.9 Consensus size: 170
26283 CTCAGTTAGC
** * *
26293 TCACTTAAATTTAATTGACAACAGGGCAAAACATTACTTGGCTTAGTTCATTTACTGACCTAAAT
1 TCACTTAAATTTAATCAACAACAAGGCAAAACATAACTTGGCTTAGTTCATTTACTGACCTAAAT
* * * * * *
26358 ACTACATCTTAGCCATCATGGAAAGCTTTAGAAGAAAAAATCTATATGCAACCCC-CTGCCAAGT
66 ACTACATCTTAACCAGCAGGGAAAGCTTTAAAAGAAAAAATCAATATGCAACCCCTC-ACCAAGT
26422 TCAAAATAATTTCTTAAGCTCAGCTTGAGCTTGATTCAAGT
130 TCAAAATAATTTCTTAAGCTCAGCTTGAGCTTGATTCAAGT
*
26463 TCACTTAAATTTAATCAACAACAAGGCAAAACATAACTTGGCTTAGTTCATTTACTGCCCTAAAT
1 TCACTTAAATTTAATCAACAACAAGGCAAAACATAACTTGGCTTAGTTCATTTACTGACCTAAAT
** * ** *
26528 ACTGTATCTTAACCAGCAGGGAAAGCTTTAAAAGCAAGCATCAATATGCAACCCCTCACCAATTT
66 ACTACATCTTAACCAGCAGGGAAAGCTTTAAAAGAAAAAATCAATATGCAACCCCTCACCAAGTT
* * *
26593 CGAACTACTTTCTTAAGCTCA
131 CAAAATAATTTCTTAAGCTCA
26614 CTTAAGTTTA
Statistics
Matches: 130, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
170 129 0.99
171 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.29
Consensus pattern (170 bp):
TCACTTAAATTTAATCAACAACAAGGCAAAACATAACTTGGCTTAGTTCATTTACTGACCTAAAT
ACTACATCTTAACCAGCAGGGAAAGCTTTAAAAGAAAAAATCAATATGCAACCCCTCACCAAGTT
CAAAATAATTTCTTAAGCTCAGCTTGAGCTTGATTCAAGT
Found at i:27036 original size:88 final size:89
Alignment explanation
Indices: 26895--27075 Score: 301
Period size: 88 Copynumber: 2.0 Consensus size: 89
26885 CCAACTTATT
* *
26895 TGCATACAACAAAGACTGAGGTGGGTGGGTGTGTTTATATATTGCAACAGGCATAAAAATCATAC
1 TGCATACAACAAAGACTGAGGTGGGTGGGTGTGTGTATACATTGCAACAGGCATAAAAATCATAC
* *
26960 AGAACAAGGTAAATATATTTTTAA
66 AGAACAAGGTAAAAATATGTTTAA
* *
26984 TGCATACTACAAGGACTG-GGTGGGTGGGTGTGTGTATACATTGCAACAGGCATAAAAATCATAC
1 TGCATACAACAAAGACTGAGGTGGGTGGGTGTGTGTATACATTGCAACAGGCATAAAAATCATAC
27048 AGAACAAGGTAAAAATATGTTTAA
66 AGAACAAGGTAAAAATATGTTTAA
27072 TGCA
1 TGCA
27076 AAGAAGCAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
88 70 0.81
89 16 0.19
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (89 bp):
TGCATACAACAAAGACTGAGGTGGGTGGGTGTGTGTATACATTGCAACAGGCATAAAAATCATAC
AGAACAAGGTAAAAATATGTTTAA
Found at i:28087 original size:23 final size:23
Alignment explanation
Indices: 28057--28102 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
28047 CAATCATTTA
28057 TTCTTTATTTCACTCTTACACCC
1 TTCTTTATTTCACTCTTACACCC
28080 TTCTTTATTTCACTCTTACACCC
1 TTCTTTATTTCACTCTTACACCC
28103 ATTCACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.00, T:0.48
Consensus pattern (23 bp):
TTCTTTATTTCACTCTTACACCC
Found at i:39035 original size:26 final size:26
Alignment explanation
Indices: 38999--39050 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38989 CTCTTTAGGC
38999 CTTTCATGTCCATATGAAGAAGAGAG
1 CTTTCATGTCCATATGAAGAAGAGAG
39025 CTTTCATGTCCATATGAAGAAGAGAG
1 CTTTCATGTCCATATGAAGAAGAGAG
39051 TAAACTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (26 bp):
CTTTCATGTCCATATGAAGAAGAGAG
Found at i:41524 original size:24 final size:25
Alignment explanation
Indices: 41465--41524 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
41455 CGAAGACAAT
*
41465 GAAGATGAG-GATGAAGAAGGGAAGA
1 GAAGA-GAGAGATGAAGAAGAGAAGA
*
41490 G-AGAAAGGAGATG-AGAAGAGAAGA
1 GAAGAGA-GAGATGAAGAAGAGAAGA
41514 GAAGAGAGAGA
1 GAAGAGAGAGA
41525 AACGAAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
23 1 0.03
24 19 0.66
25 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.43, T:0.05
Consensus pattern (25 bp):
GAAGAGAGAGATGAAGAAGAGAAGA
Found at i:41868 original size:12 final size:12
Alignment explanation
Indices: 41851--41876 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41841 GTATTTTCAC
41851 TTCTCATTCTTA
1 TTCTCATTCTTA
41863 TTCTCATTCTTA
1 TTCTCATTCTTA
41875 TT
1 TT
41877 GTTTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTCATTCTTA
Found at i:42353 original size:31 final size:31
Alignment explanation
Indices: 42312--42476 Score: 121
Period size: 31 Copynumber: 5.5 Consensus size: 31
42302 AAGGGCTAAT
42312 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * * **
42343 TGTTCAAATAAGGGCCCGATC-TTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGTCAAAA
*
42372 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
42403 TGCTCAAATAAGGGCCCGATC-TTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGTCAAAA
* * *
42432 TGGC-CAAATAAGGACCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
42463 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
42477 TCTGGCATCA
Statistics
Matches: 99, Mismatches: 23, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
28 8 0.08
29 31 0.31
30 8 0.08
31 44 0.44
32 8 0.08
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:42410 original size:60 final size:60
Alignment explanation
Indices: 42316--42476 Score: 286
Period size: 60 Copynumber: 2.7 Consensus size: 60
42306 GCTAATTGCT
* *
42316 CAAATAAGGGCCTAACGTTTGTCAAAATGTTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
42376 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* *
42436 CAAATAAGGACCTAACATTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
42477 TCTGGCATCA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:42558 original size:31 final size:31
Alignment explanation
Indices: 42520--42622 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
42510 TCGATGCCAA
42520 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
** * **
42551 GCCCTTATTTG-GCCAAATT---AAAAGATCGG
1 GCCCTTATTTGAG-CATTTTGGCAAACG-TTAG
*
42580 GCTCTTATTTGAGCATTTTGGCAAACGTTAG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
42611 GCCCTTATTTGA
1 GCCCTTATTTGA
42623 CCAAATTAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
28 4 0.07
29 16 0.30
30 2 0.04
31 28 0.52
32 4 0.07
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAG
Found at i:42596 original size:60 final size:60
Alignment explanation
Indices: 42521--42680 Score: 248
Period size: 60 Copynumber: 2.7 Consensus size: 60
42511 CGATGCCAAG
* * *
42521 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
*
42581 CTCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
* * * *
42641 CCCTTATTTGGGCATTTTGACAAACATTAAGCCCTTATTT
1 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
42681 AAGCAATTAG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCAGA
Found at i:42679 original size:31 final size:31
Alignment explanation
Indices: 42518--42685 Score: 96
Period size: 31 Copynumber: 5.5 Consensus size: 31
42508 TTTCGATGCC
* *
42518 AAGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AAGCCCTTATTTGAGCATTTTGACAAACATT
* ** * *
42549 AGGCCCTTATTTG-GCCAAATT-A-AAAGATC
1 AAGCCCTTATTTGAG-CATTTTGACAAACATT
** * * *
42578 GGGCTCTTATTTGAGCATTTTGGCAAACGTT
1 AAGCCCTTATTTGAGCATTTTGACAAACATT
* * ** *
42609 AGGCCCTTATTTGACCAAATT-A-AAAGA-T
1 AAGCCCTTATTTGAGCATTTTGACAAACATT
* *
42637 CAGACCCTTATTTGGGCATTTTGACAAACATT
1 AAG-CCCTTATTTGAGCATTTTGACAAACATT
*
42669 AAGCCCTTATTTAAGCA
1 AAGCCCTTATTTGAGCA
42686 ATTAGCCAAA
Statistics
Matches: 96, Mismatches: 33, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
28 2 0.02
29 36 0.38
30 3 0.03
31 52 0.54
32 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (31 bp):
AAGCCCTTATTTGAGCATTTTGACAAACATT
Found at i:45079 original size:2 final size:2
Alignment explanation
Indices: 45061--45106 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
45051 AAGATGTATG
* * *
45061 TA TA TG TA TA CA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45102 TA TA T
1 TA TA T
45107 TTAAGTAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:46247 original size:14 final size:14
Alignment explanation
Indices: 46228--46254 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46218 GATAAGCAAA
46228 AGTGAGCCTATAAC
1 AGTGAGCCTATAAC
46242 AGTGAGCCTATAA
1 AGTGAGCCTATAA
46255 TTTTCTGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (14 bp):
AGTGAGCCTATAAC
Found at i:46626 original size:46 final size:46
Alignment explanation
Indices: 46558--46676 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
46548 GCTCTGCATA
* *
46558 AATTCAAAACCATTCATAAAGCACTTAGTTATGTATTGTAAATTCCT
1 AATTCAAAAAC-TTCATAAAGCACTTAGTTATGAATTGTAAATTCCT
46605 AATTCAAAAACTTCATAAAGCACTTAGTTATGAATTGTAAATTCCT
1 AATTCAAAAACTTCATAAAGCACTTAGTTATGAATTGTAAATTCCT
*
46651 AATTCAAAAACTTCATAAAACACTTA
1 AATTCAAAAACTTCATAAAGCACTTA
46677 CCATTTCATG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 59 0.86
47 10 0.14
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.34
Consensus pattern (46 bp):
AATTCAAAAACTTCATAAAGCACTTAGTTATGAATTGTAAATTCCT
Done.