Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012698.1 Corchorus capsularis cultivar CVL-1 contig12719, 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: 74643
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3506 original size:40 final size:40
Alignment explanation
Indices: 3460--3539 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
3450 CCACTCCAAC
* *
3460 TTCCTGCTGTAAAAATCGACGCTCTTTTCAAGCAATGGGT
1 TTCCTGCTGTAAAAATCAACGCTCTTCTCAAGCAATGGGT
* * *
3500 TTCCTGCTGTAGAAGTCAACGCTCTTCTCAATCAATGGGT
1 TTCCTGCTGTAAAAATCAACGCTCTTCTCAAGCAATGGGT
3540 GGCAGAGAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (40 bp):
TTCCTGCTGTAAAAATCAACGCTCTTCTCAAGCAATGGGT
Found at i:4394 original size:26 final size:26
Alignment explanation
Indices: 4357--4576 Score: 141
Period size: 26 Copynumber: 7.8 Consensus size: 26
4347 TCTCTATCAA
4357 AAGTCCTCAAACACCAG-GGCATTCAT
1 AAGTCCTCAAACA-CAGAGGCATTCAT
*
4383 AAGTCC-CTAAACACAGAGGCACCTCTAT
1 AAGTCCTC-AAACACAGAGGCA-TTC-AT
4411 CAAAGTCCTCAAACACATG-GGCATTCAT
1 --AAGTCCTCAAACACA-GAGGCATTCAT
*
4439 AAGTCC-CTAAACACAGAGGCACCTCTATCAAA
1 AAGTCCTC-AAACACAGAGGCA----T-TC-AT
4471 AAGTCCTCAAACACCAG-GGCATTCAT
1 AAGTCCTCAAACA-CAGAGGCATTCAT
*
4497 AAGTCC-CTAAACACAGAGGCATCTATACTAAA
1 AAGTCCTC-AAACACAGAGGCA--T-T-C--AT
4529 AAGTCCTCAAACACA-AGGGCATTCAT
1 AAGTCCTCAAACACAGA-GGCATTCAT
4555 AAGTCC-CTAAACACAGAGGCAT
1 AAGTCCTC-AAACACAGAGGCAT
4577 CTATATCAAA
Statistics
Matches: 158, Mismatches: 6, Indels: 60
0.71 0.03 0.27
Matches are distributed among these distances:
25 11 0.07
26 67 0.42
27 5 0.03
28 7 0.04
29 4 0.03
30 20 0.13
31 5 0.03
32 34 0.22
33 5 0.03
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.18
Consensus pattern (26 bp):
AAGTCCTCAAACACAGAGGCATTCAT
Found at i:4502 original size:58 final size:57
Alignment explanation
Indices: 4348--4598 Score: 391
Period size: 58 Copynumber: 4.4 Consensus size: 57
4338 ATCTAATATT
4348 CTCTATCAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
1 CTCTATCAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
4405 CTCTATC-AAAGTCCTCAAACA-CATGGGCATTCATAAGTCCCTAAACACAGAGGCAC
1 CTCTATCAAAAGTCCTCAAACACCA-GGGCATTCATAAGTCCCTAAACACAGAGGCAC
*
4461 CTCTATCAAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCAT
1 CTCTATC-AAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
* * * *
4519 CTATACTAAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCAT
1 CTCTA-TCAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
* *
4577 CTATATC-AAAGTCCTTAAACAC
1 CTCTATCAAAAGTCCTCAAACAC
4599 ATGGGCAATC
Statistics
Matches: 183, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
55 2 0.01
56 67 0.37
57 8 0.04
58 103 0.56
59 3 0.02
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (57 bp):
CTCTATCAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
Found at i:4511 original size:114 final size:115
Alignment explanation
Indices: 4348--4598 Score: 409
Period size: 114 Copynumber: 2.2 Consensus size: 115
4338 ATCTAATATT
*
4348 CTCTATCAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCACCTCTA-T-
1 CTCTATCAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCACCTATACTA
* *
4411 CAAAGTCCTCAAACACATGGGCATTCATAAGTCCCTAAACACAGAGGCAC
66 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
*
4461 CTCTATCAAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACT
1 CTCTATC-AAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCACCTATACT
*
4526 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCAT
65 AAAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
* *
4577 CTATATC-AAAGTCCTTAAACAC
1 CTCTATCAAAAGTCCTCAAACAC
4599 ATGGGCAATC
Statistics
Matches: 128, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
113 7 0.05
114 67 0.52
115 1 0.01
116 53 0.41
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (115 bp):
CTCTATCAAAAGTCCTCAAACACCAGGGCATTCATAAGTCCCTAAACACAGAGGCACCTATACTA
AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCAC
Found at i:5309 original size:35 final size:34
Alignment explanation
Indices: 5270--5365 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 34
5260 ATTTCATCAG
*
5270 ATTCAACACTTGGGGACTCCAACAACCCCTTCATC
1 ATTCAACACTTGGGG-CTCCAACAACCCATTCATC
* ** * *
5305 ATTCAACAATTGGGTGCTCCAGGAACTCATTCTTC
1 ATTCAACACTTGGG-GCTCCAACAACCCATTCATC
* *
5340 ATTCAATACTTGGGGGCTTCAACAAC
1 ATTCAACACTT-GGGGCTCCAACAAC
5366 GAAAATTTCA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
35 44 0.92
36 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (34 bp):
ATTCAACACTTGGGGCTCCAACAACCCATTCATC
Found at i:5812 original size:72 final size:72
Alignment explanation
Indices: 5732--6134 Score: 562
Period size: 72 Copynumber: 5.6 Consensus size: 72
5722 TTCATTACGA
* * *
5732 TTGTAGCCGAGACGGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCAT
1 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCAT
5797 ATTGCGG
66 ATTGCGG
* *
5804 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATTCTTACATGATAATCTTCCGT
1 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCAT
5869 ATTGCGG
66 ATTGCGG
* * *** * *
5876 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCGCAACCCTTATGCGATTATATT-CAT
1 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCAT
*
5940 CATTGCGA
66 -ATTGCGG
* * *
5948 TTGTAGCAGAGGCAGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTTCAT
1 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCAT
6013 ATTGCGG
66 ATTGCGG
** *
6020 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTATCTTCC-T
1 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCAT
*
6084 CATTGCGA
66 -ATTGCGG
* *
6092 TTGTAGCCGAGGTAGTTCCCACA--TGCCAGTCCTTCGCACAATC
1 TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATC
6135 TTTGTTCTTC
Statistics
Matches: 294, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
70 19 0.06
71 3 0.01
72 269 0.91
73 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (72 bp):
TTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAATCTTCCAT
ATTGCGG
Found at i:6103 original size:216 final size:214
Alignment explanation
Indices: 5723--6128 Score: 670
Period size: 216 Copynumber: 1.9 Consensus size: 214
5713 TTCTTCTTCT
* *
5723 TCATTACGATTGTAGCCGAGACGGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTACGATTGTAGCAGAGACAGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATA
*
5788 ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATTCTTA
66 ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
* *
5853 CATGATAATCTTCCGTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCGCA
131 CATGATAATCTTCCGTATTGCGATTGTAGCCGAGGCAGTTCCCACA--TGCCAGTCCTTCGCGCA
5918 ACCCTTATGCGATTATATTCA
194 ACCCTTATGCGATTATATTCA
* *
5939 TCATTGCGATTGTAGCAGAGGCAGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATA
1 TCATTACGATTGTAGCAGAGACAGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATA
*
6004 ATCTTTCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
66 ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
** * *
6069 TGTGATTATCTTCC-TCATTGCGATTGTAGCCGAGGTAGTTCCCACATGCCAGTCCTTCGC
131 CATGATAATCTTCCGT-ATTGCGATTGTAGCCGAGGCAGTTCCCACATGCCAGTCCTTCGC
6129 ACAATCTTTG
Statistics
Matches: 177, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
214 13 0.07
215 1 0.01
216 163 0.92
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (214 bp):
TCATTACGATTGTAGCAGAGACAGTTCCCACATGTGGCAGTCCTTCGCACAATCCTTACATGATA
ATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
CATGATAATCTTCCGTATTGCGATTGTAGCCGAGGCAGTTCCCACATGCCAGTCCTTCGCGCAAC
CCTTATGCGATTATATTCA
Found at i:14252 original size:48 final size:48
Alignment explanation
Indices: 14120--14418 Score: 379
Period size: 48 Copynumber: 6.2 Consensus size: 48
14110 CTTATTTACA
* * *
14120 TTTCCTAAAAAGCCCTTCCCAGACGGAAGGCACTAATCTTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGGCATTAATCTTTACCTGTT
*
14168 TTTCCCAAAA-GCCCTTCCCAGACGGAAGGCACTAATCTTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGGCATTAATCTTTACCTGTT
* * *
14215 TTTCCCAAAACGCCCTTGCCAAACGGAAGGCATTAATCTTTACCTATT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGGCATTAATCTTTACCTGTT
* ** *
14263 TCTCCCAAAACGATCTTCCCAGACGGAAGGCATTAATCCTTACCTGTT
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGGCATTAATCTTTACCTGTT
* *
14311 TCTCCCAAAACGCCCTTCCCAGACAGAAGGCATTAATCTTTACCTG-T
1 TTTCCCAAAACGCCCTTCCCAGACGGAAGGCATTAATCTTTACCTGTT
* * * **
14358 TTTCCCTAAAATGCCCTTCCTAGATGGAAGGCACTTGCT-TTTACCTGCTT
1 TTTCCC-AAAACGCCCTTCCCAGACGGAAGGCA-TTAATCTTTACCTG-TT
14408 TTCTCCCAAAA
1 TT-TCCCAAAA
14419 TACCCTTTCG
Statistics
Matches: 222, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
47 53 0.24
48 155 0.70
49 3 0.01
50 7 0.03
51 4 0.02
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (48 bp):
TTTCCCAAAACGCCCTTCCCAGACGGAAGGCATTAATCTTTACCTGTT
Found at i:14489 original size:62 final size:62
Alignment explanation
Indices: 14411--14692 Score: 334
Period size: 62 Copynumber: 4.5 Consensus size: 62
14401 CCTGCTTTTC
* * * * * * *
14411 TCCCAAAATACCCTTTCGGACAAAGGGTCA-TTTTTGTTACATTCTTGCTCTTGGGTTCAAGT
1 TCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCT-TCACATTCCTGCACTTAGTTTCAATT
* * * * * *
14473 TCCCAAAATACCCTTTCGGAAAAAGGGTTAATTT-TGTCACACTCTTGCATTTAGTTTCAATT
1 TCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCT-TCACATTCCTGCACTTAGTTTCAATT
* * * * *
14535 TCCCAGAATACCCTTTCAGACAGAGGGTCAGTTTCTTCACATTCCTGCACTTAGATTCTATT
1 TCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCTTCACATTCCTGCACTTAGTTTCAATT
* * * *
14597 CCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCTTCACATTCCTACACTTAGTTTCTATT
1 TCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCTTCACATTCCTGCACTTAGTTTCAATT
14659 TCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT
1 TCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT
14693 AGGCATGTTT
Statistics
Matches: 191, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
62 187 0.98
63 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (62 bp):
TCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCTTCACATTCCTGCACTTAGTTTCAATT
Found at i:17596 original size:6 final size:6
Alignment explanation
Indices: 17585--17613 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17575 AAAGCAAAGC
17585 AATCTA AATCTA AATCTA AATCTA AATCT
1 AATCTA AATCTA AATCTA AATCTA AATCT
17614 GAAGCAGAAT
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:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
AATCTA
Found at i:18426 original size:6 final size:6
Alignment explanation
Indices: 18415--18448 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
18405 TATCTAATGT
*
18415 GTGTAA GTGTAA GTGTAA GTGTGA GTGTAA GTGT
1 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGT
18449 GTGATTTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (6 bp):
GTGTAA
Found at i:20732 original size:20 final size:20
Alignment explanation
Indices: 20703--20746 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
20693 CAAATTATGC
*
20703 ATATATTTTTAACTATTTTT
1 ATATACTTTTAACTATTTTT
**
20723 ATATACTTTTTGCTATTTTT
1 ATATACTTTTAACTATTTTT
20743 ATAT
1 ATAT
20747 GTGTTTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (20 bp):
ATATACTTTTAACTATTTTT
Found at i:21504 original size:6 final size:6
Alignment explanation
Indices: 21489--21522 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
21479 CACAAATCAC
*
21489 ACACTT ACACTC ACACTT ACACTT ACACTT ACAC
1 ACACTT ACACTT ACACTT ACACTT ACACTT ACAC
21523 ACATTAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.26
Consensus pattern (6 bp):
ACACTT
Found at i:25185 original size:12 final size:12
Alignment explanation
Indices: 25168--25194 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25158 CACAAAACTC
25168 ATACTTTTATAT
1 ATACTTTTATAT
25180 ATACTTTTATAT
1 ATACTTTTATAT
25192 ATA
1 ATA
25195 GTATAGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
ATACTTTTATAT
Found at i:25212 original size:6 final size:6
Alignment explanation
Indices: 25190--25273 Score: 88
Period size: 6 Copynumber: 14.5 Consensus size: 6
25180 ATACTTTTAT
* *
25190 ATATAG -TATAG --ATAG ATATAG --ATAG ATATAG ATAGATAG ATAGAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG AT--ATAG ATATAG
*
25235 AGATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
25274 GATAGATAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
4 8 0.12
5 5 0.08
6 47 0.71
8 6 0.09
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (6 bp):
ATATAG
Found at i:25230 original size:18 final size:18
Alignment explanation
Indices: 25192--25285 Score: 108
Period size: 18 Copynumber: 5.4 Consensus size: 18
25182 ACTTTTATAT
25192 ATAG-TATAGATAGATATAG
1 ATAGATATAGATAG--ATAG
25211 ATAGATATAGATAGATAG
1 ATAGATATAGATAGATAG
25229 ATAG--ATAGATAGAT--
1 ATAGATATAGATAGATAG
* * *
25243 ATAGATATAGATATAGAT
1 ATAGATATAGATAGATAG
25261 ATAGATATAGATAGATAG
1 ATAGATATAGATAGATAG
25279 ATAGATA
1 ATAGATA
25286 AATTTCTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
14 4 0.06
16 18 0.28
18 30 0.46
19 4 0.06
20 9 0.14
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (18 bp):
ATAGATATAGATAGATAG
Found at i:25234 original size:12 final size:12
Alignment explanation
Indices: 25192--25285 Score: 83
Period size: 12 Copynumber: 8.2 Consensus size: 12
25182 ACTTTTATAT
25192 ATAGTATAGATAG
1 ATAG-ATAGATAG
25205 AT--ATAGATAG
1 ATAGATAGATAG
25215 AT--ATAGATAG
1 ATAGATAGATAG
25225 ATAGATAGATAG
1 ATAGATAGATAG
25237 ATAGAT--ATAG
1 ATAGATAGATAG
* * *
25247 ATATAGATATAG
1 ATAGATAGATAG
* * *
25259 ATATAGATATAG
1 ATAGATAGATAG
25271 ATAGATAGATAG
1 ATAGATAGATAG
25283 ATA
1 ATA
25286 AATTTCTTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
10 28 0.39
12 42 0.58
13 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (12 bp):
ATAGATAGATAG
Found at i:35133 original size:430 final size:434
Alignment explanation
Indices: 34352--35335 Score: 1130
Period size: 430 Copynumber: 2.3 Consensus size: 434
34342 TTTCAAAAGT
* * * *
34352 ATTTTTTAGAATTGAAATATAAAATTTAGCTTTTGAGTCTTTCATGAAAGTTGTAGATCATAAAA
1 ATTTTTTAGAATTGAAACATAAAATTTAGCTTTTGAATCCTTCATGAAAGATGTAGATCATAAAA
* * * *
34417 TTACCTTTTAATAGACACCTGAATTACCTTAATTGGACAAATAGAACAAAGAAAATAAATAAAAA
66 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAG--AAT--ATAAAAA
*
34482 AATGAAGTGTTAAATCAAGTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAATAGAAAAGTA
127 AA-GAA--G-TAAAGCAAGTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAATAGAAAAGTA
* *
34547 TGAGGGTGATTTGATAACTATATCAAATAAGAAAATATATGTTAATAGAGATTTTGAAACATAAA
188 TGAGGGTCATTTGATAACTATATCAAATAAGAAAATATATGTTAATAGAGATCTTGAAACATAAA
* * * *
34612 AATTTCCTTTTGAACCCTTCATGAAACTCATAGATCAAATTAACTTTCGGGTTCTTCATGAAAGT
253 AATTCCCTTTTGAACCCTTAACGAAACTCATAGATCAAATTAACTTTCGGGTCCTTCATGAAAGT
* * * *
34677 CGTAGATTATACAGTAACCTTTTTAACCGACACTTGAATAACTTTAATTGCACATGTGGATCGAA
318 CGTAAATCATACAATAACCTTTTTAACCGACACTTCAATAACTTTAATTGCACATGTGGATCGAA
34742 AATTATATGGTATTAAATAGACCAACAATCGAAACGACCACATTTAGGAAGC
383 AATTATATGGTATTAAATAGACCAACAATCGAAACGACCACATTTAGGAAGC
* * *
34794 ATTTTTTCGAATTGAAACATAAAAATTT-GCTTTTGAATCCTTCATGAAAGATGTAGATTATGAA
1 ATTTTTTAGAATTGAAACAT-AAAATTTAGCTTTTGAATCCTTCATGAAAGATGTAGATCATAAA
34858 ATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAG-AT-TAAAAAAA-
65 ATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATATAAAAAAAG
* * * * *
34920 AA-TAAAGCGATTAAGATAGAATTTGTAAATGACTAAGTAGTATAAAGTATAAAAGTATGAGGGT
130 AAGTAAAGCAAGTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAATAGAAAAGTATGAGGGT
* * * * *
34984 CATTTGATCAGTA-ATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTCC
195 CATTTGATAACTATAT-CAAATAAGAAAATATATGTTAATAGAGATCTTGAAACATAAAAATTCC
* * * *
35048 CTTTTGAACCCTTAACGAAACTCGTAGATCAAATTTAGCTTTTGGGTCCTTCATGGAAGTCGTAA
259 CTTTTGAACCCTTAACGAAACTCATAGATCAAA-TTAACTTTCGGGTCCTTCATGAAAGTCGTAA
* * * * * * *
35113 ATCATGCAATAACC-TTTTAACCGACACTTCAATAACTTCAATCGGATATGTGGA-CAAAAAACT
323 ATCATACAATAACCTTTTTAACCGACACTTCAATAACTTTAATTGCACATGTGGATC-GAAAATT
*** ** * * * * *
35176 ATACAATATTAAATTA-ACCGGCAA-CTAAAACCACAAAATTTTGGAAGC
387 ATATGGTATTAAA-TAGACCAACAATC-GAAACGACCACATTTAGGAAGC
** * * * * * *
35224 ATTCTTTTAGAATCAAAATATTAAAATTGA-CTTTTGAGTTCTTAATGAAA-ATTGTAGGTCATA
1 ATT-TTTTAGAATTGAAACA-TAAAATTTAGCTTTTGAATCCTTCATGAAAGA-TGTAGATCATA
* * * *
35287 AAACTATCTTTTAATAGGCACTTGAAT-AACCTTAATCGGACAAATAGAA
63 AAATTACCTTTTAATAGACACATGAATCAA-CTTAATCGGACAAATAGAA
35336 AAAAAAAATA
Statistics
Matches: 463, Mismatches: 68, Indels: 33
0.82 0.12 0.06
Matches are distributed among these distances:
429 4 0.01
430 218 0.47
431 124 0.27
432 1 0.00
434 2 0.00
436 8 0.02
439 2 0.00
442 97 0.21
443 7 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (434 bp):
ATTTTTTAGAATTGAAACATAAAATTTAGCTTTTGAATCCTTCATGAAAGATGTAGATCATAAAA
TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATATAAAAAAAGA
AGTAAAGCAAGTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAATAGAAAAGTATGAGGGTC
ATTTGATAACTATATCAAATAAGAAAATATATGTTAATAGAGATCTTGAAACATAAAAATTCCCT
TTTGAACCCTTAACGAAACTCATAGATCAAATTAACTTTCGGGTCCTTCATGAAAGTCGTAAATC
ATACAATAACCTTTTTAACCGACACTTCAATAACTTTAATTGCACATGTGGATCGAAAATTATAT
GGTATTAAATAGACCAACAATCGAAACGACCACATTTAGGAAGC
Found at i:36495 original size:45 final size:45
Alignment explanation
Indices: 36444--36531 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
36434 TTACTTCTCA
*
36444 AGCTCATCATTAAGAC-GGGGTAGGGATCTTTTAGTAATCCCACCC
1 AGCTCATCATTAA-ACTAGGGTAGGGATCTTTTAGTAATCCCACCC
* *
36489 AGCTCATCATTAATCTAGGGTAGGGATCTTTTAGTAATTCCAC
1 AGCTCATCATTAAACTAGGGTAGGGATCTTTTAGTAATCCCAC
36532 TACTCTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
AGCTCATCATTAAACTAGGGTAGGGATCTTTTAGTAATCCCACCC
Found at i:36667 original size:211 final size:211
Alignment explanation
Indices: 36298--36692 Score: 542
Period size: 211 Copynumber: 1.9 Consensus size: 211
36288 CAAGCCTTGC
* * *
36298 TAGGGATCTTTTAGTAATTCCACTATTCTATTAAAGTCAAGTAAGAAATGACCAAAAAGTTTAGA
1 TAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTAAAGTAAGAAATGACCAAAAAGTCTAGA
* * * *
36363 TATTTAATCCCCTCAAGAATAAAAATTTAGGACATTTAAGTAATCTGCCAAGTAGGTAAAGACGA
66 TATTTAATCACCTCAAGAATAAAAAGTTAGGACATTTAAGTAATCGGCCAAGTAGGAAAAGACGA
** *
36428 AAATGATTACTTCTCAAGCTCATCATTAAGACGGGGTAGGGATCTTTTAGTAATCCCACCCAGCT
131 AAAAAATTACTTCTCAAGCTCATCATTAAGACGGGGTAGGAATCTTTTAGTAATCCCACCCAGCT
36493 CATCATTAATCTAGGG
196 CATCATTAATCTAGGG
* * *
36509 TAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTAAATTGAGAAATGACTAAAAAGTCTA-A
1 TAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTAAAGTAAGAAATGACCAAAAAGTCTAGA
* * *
36573 TTATTTAATCACCTCAAGAATCAAAAGTTAGGGCATTTAAGTAATCGGTCAAGT-GTGAAAAGAC
66 -TATTTAATCACCTCAAGAATAAAAAGTTAGGACATTTAAGTAATCGGCCAAGTAG-GAAAAGAC
* * ** * * **
36637 TAAAAAAATTAGTTCTCTCGTTCCTCATTAATCCGGGGTAGGAATCTTTTAGTAAT
129 GAAAAAAATTACTTCTCAAGCTCATCATTAAGACGGGGTAGGAATCTTTTAGTAAT
36693 TTTTATATGT
Statistics
Matches: 158, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
210 2 0.01
211 156 0.99
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (211 bp):
TAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTAAAGTAAGAAATGACCAAAAAGTCTAGA
TATTTAATCACCTCAAGAATAAAAAGTTAGGACATTTAAGTAATCGGCCAAGTAGGAAAAGACGA
AAAAAATTACTTCTCAAGCTCATCATTAAGACGGGGTAGGAATCTTTTAGTAATCCCACCCAGCT
CATCATTAATCTAGGG
Found at i:43369 original size:33 final size:33
Alignment explanation
Indices: 43332--43434 Score: 188
Period size: 33 Copynumber: 3.1 Consensus size: 33
43322 AACAAATCTA
43332 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
43365 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
* *
43398 TTTTGGTTGATCATAACATTGAAAATAATTCTG
1 TTTTGGTTGATCATAGCATTGCAAATAATTCTG
43431 TTTT
1 TTTT
43435 AGGTGAAAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (33 bp):
TTTTGGTTGATCATAGCATTGCAAATAATTCTG
Found at i:43369 original size:66 final size:66
Alignment explanation
Indices: 43295--43434 Score: 156
Period size: 66 Copynumber: 2.1 Consensus size: 66
43285 TGATACTAAA
* * * * *
43295 TCTGTTTTGGATGCTAATTGTGA-TAAAAACAAATCTATTTTGGTTGATCATAGCATTGCAAATA
1 TCTGTTTTGGATGATAATAG-CATTAAAAACAAATCTATTTTGGTTGATCATAACATTGAAAATA
43359 AT
65 AT
* * ** * * *
43361 TCTGTTTTGGTTGATCATAGCATTGCAAATAATTCTGTTTTGGTTGATCATAACATTGAAAATAA
1 TCTGTTTTGGATGATAATAGCATTAAAAACAAATCTATTTTGGTTGATCATAACATTGAAAATAA
43426 T
66 T
43427 TCTGTTTT
1 TCTGTTTT
43435 AGGTGAAAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 1 0.02
66 60 0.98
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (66 bp):
TCTGTTTTGGATGATAATAGCATTAAAAACAAATCTATTTTGGTTGATCATAACATTGAAAATAA
T
Found at i:43851 original size:30 final size:30
Alignment explanation
Indices: 43815--43873 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
43805 CAAGGGGGAG
*
43815 GGAATGATGTGCCCAA-GACTTATCATGGAA
1 GGAATGAAGTG-CCAAGGACTTATCATGGAA
43845 GGAATGAAGTGCCAAGGACTTATCATGGA
1 GGAATGAAGTGCCAAGGACTTATCATGGA
43874 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (30 bp):
GGAATGAAGTGCCAAGGACTTATCATGGAA
Found at i:48219 original size:156 final size:155
Alignment explanation
Indices: 47933--48292 Score: 410
Period size: 156 Copynumber: 2.3 Consensus size: 155
47923 TCATCTCAAA
* * * ** *
47933 CAGACTTAGGATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGGGGTGACAAACCAAC
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTCAGGGAGACAAACCAAC
* * * * * *
47998 TTCTCTATGTTAGAGAGTTTGGTTTTACTTAGATTTTTTCCTATAGATTTATGGAGATAATCTAA
66 TTCACCATGTAAGAGAGCTCGGTTTTACTTAGATTTTTTCCTATAGATTTATGGAGAGAATCTAA
48063 G--CCTACTGGTGGAAAA-TTAGCTTC-AT
131 GTCCCT--TGGT--AAAATTTAGC-TCGAT
** * * *
48089 TGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTCAGGGAGAGAAACCTAG
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTCAGGGAGACAAACCAAC
*
48154 TTCACCATG-AAGGAGAGCTCGGTTTTACTTAGAATTTTTTCC-ATAG-TCTTGTGGAGAGAATC
66 TTCACCATGTAA-GAGAGCTCGGTTTTACTTAG-ATTTTTTCCTATAGAT-TTATGGAGAGAATC
*
48216 TAAGTCCCTTGGTAAAATTTTATCTCGAT
128 TAAGTCCCTTGGTAAAA-TTTAGCTCGAT
*
48245 CAGATTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATT
1 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATT
48293 TGAGGTGTGA
Statistics
Matches: 174, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
154 4 0.02
155 4 0.02
156 154 0.89
157 9 0.05
158 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (155 bp):
CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTCAGGGAGACAAACCAAC
TTCACCATGTAAGAGAGCTCGGTTTTACTTAGATTTTTTCCTATAGATTTATGGAGAGAATCTAA
GTCCCTTGGTAAAATTTAGCTCGAT
Found at i:51046 original size:21 final size:21
Alignment explanation
Indices: 51020--51069 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
51010 GCACTGGAGT
* *
51020 ACATGGGTCGCGAGGCAAACC
1 ACATGGGTCGCCAAGCAAACC
*
51041 ACATGGGGCGCCAAGCAAACC
1 ACATGGGTCGCCAAGCAAACC
51062 ACATGGGT
1 ACATGGGT
51070 GCCCAACGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.32, T:0.10
Consensus pattern (21 bp):
ACATGGGTCGCCAAGCAAACC
Found at i:55299 original size:10 final size:10
Alignment explanation
Indices: 55284--55308 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55274 GAGGACTCTA
55284 GAATTTTCTG
1 GAATTTTCTG
55294 GAATTTTCTG
1 GAATTTTCTG
55304 GAATT
1 GAATT
55309 ATGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:66667 original size:6 final size:6
Alignment explanation
Indices: 66656--66686 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
66646 GATAACTGAT
66656 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG A
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG A
66687 ATTGAACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
ATTTGG
Found at i:66736 original size:12 final size:12
Alignment explanation
Indices: 66705--66738 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
66695 AATTTTTTAC
66705 AACATAAAAATT
1 AACATAAAAATT
66717 AA-ATAAAAATT
1 AACATAAAAATT
*
66728 AACAAAAAAAT
1 AACATAAAAAT
66739 ACAAATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (12 bp):
AACATAAAAATT
Found at i:72519 original size:13 final size:14
Alignment explanation
Indices: 72495--72526 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
72485 GAATTTTAAT
72495 TAAATCTAACTAAG
1 TAAATCTAACTAAG
72509 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
72522 -AAATC
1 TAAATC
72527 AATCAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (14 bp):
TAAATCTAACTAAG
Done.