Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014851.1 Corchorus capsularis cultivar CVL-1 contig14872, 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: 28198
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:316 original size:172 final size:174
Alignment explanation
Indices: 22--362 Score: 535
Period size: 172 Copynumber: 2.0 Consensus size: 174
12 AAGAAAAATT
* *
22 ATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGGGTGGGGTTTAAGGGTTGACATGTGTC
1 ATACAATACAACGTCAGTGGAGTTTAGCAGACTGCACAGGTGGGGTTTAAGGGTTGACATGTGTC
** *
87 GTCTTAGGGAATATTGTATTAATATTAAATATTTAATTAATTTTGAAATGAGTATGTGTCAACCT
66 CCCTTAGGGAATATTGTATTAATATTAAATATTTAATTAATTATGAAATGAGTATGTGTCAACCT
*
152 CTTATCCCGCTTAT-AGAGTCCAAAATTTACACTGACAGTATACA
131 CTTAACCCGCTTATGA-AGTCCAAAATTTACACTGACAGTATACA
* *
196 ATACAATACAACGTCATTGGAGTTTAGCAGACTGCACATGTGGGG-TTAAGGGTTGACATGTGTC
1 ATACAATACAACGTCAGTGGAGTTTAGCAGACTGCACAGGTGGGGTTTAAGGGTTGACATGTGTC
* * *
260 CCCTTAGGGAATA-TGTATTAATATTAAATATTTAATTACTTATGAAATGGGTATGTGTCAACTT
66 CCCTTAGGGAATATTGTATTAATATTAAATATTTAATTAATTATGAAATGAGTATGTGTCAACCT
* *
324 CTTAACCCTCTTATGAAGTCCAAAATTTACACTTACAGT
131 CTTAACCCGCTTATGAAGTCCAAAATTTACACTGACAGT
363 GTATTGTATA
Statistics
Matches: 153, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
172 81 0.53
173 31 0.20
174 41 0.27
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (174 bp):
ATACAATACAACGTCAGTGGAGTTTAGCAGACTGCACAGGTGGGGTTTAAGGGTTGACATGTGTC
CCCTTAGGGAATATTGTATTAATATTAAATATTTAATTAATTATGAAATGAGTATGTGTCAACCT
CTTAACCCGCTTATGAAGTCCAAAATTTACACTGACAGTATACA
Found at i:1344 original size:2 final size:2
Alignment explanation
Indices: 1337--1369 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1327 TACTCCTATC
1337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1370 CTACATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9439 original size:22 final size:22
Alignment explanation
Indices: 9417--9780 Score: 225
Period size: 22 Copynumber: 16.5 Consensus size: 22
9407 ATTAGGATGA
*
9417 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGG
*
9439 TTATCAAAATGTT-ATTAG-GAT-A
1 TTATCAAAAT-TTCA-TAGTG-TGG
*
9461 TTA-CTACAATTTCATAGTGTGG
1 TTATC-AAAATTTCATAGTGTGG
* * *
9483 TTATCAAAATTTTATAGAGAGAGG
1 TTATCAAAATTTCAT--AGTGTGG
** * *
9507 TTATC-AAATAACATAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
9528 TTATCAAAATTTCATAG-GTAGG
1 TTATCAAAATTTCATAGTGT-GG
*
9550 TTATCAAAATTTTCATAGTATGG
1 TTATCAAAA-TTTCATAGTGTGG
* * *
9573 TTACCGAAAA-TTCATTG-GAAGG
1 TTATC-AAAATTTCATAGTG-TGG
9595 TTATCAAAATTTC--AGTGTGG
1 TTATCAAAATTTCATAGTGTGG
*
9615 TTATCAAAATTTCATAG-GCAT-A
1 TTATCAAAATTTCATAGTG--TGG
* * *
9637 TTATTAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
*
9659 TTATCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAGTGTGG
*
9681 TTATCAAATTTTCATA-TGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
9702 ATTATCGAAATTTTATGGTGTGG
1 -TTATCAAAATTTCATAGTGTGG
** * ** *
9725 TTATTGAAATTTCATATTAAGA
1 TTATCAAAATTTCATAGTGTGG
* *
9747 CTATCAAAATTTCATAGTCAT-G
1 TTATCAAAATTTCATAGT-GTGG
9769 TTATCAAAATTT
1 TTATCAAAATTT
9781 TTGAAATTTC
Statistics
Matches: 267, Mismatches: 48, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
20 16 0.06
21 30 0.11
22 171 0.64
23 35 0.13
24 15 0.06
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:9552 original size:67 final size:65
Alignment explanation
Indices: 9468--9692 Score: 235
Period size: 67 Copynumber: 3.4 Consensus size: 65
9458 ATATTACTAC
*
9468 AATTTCATAGTGTGGTTATCAAAATTTTATAGAGAGAGGTTATCAAATAACATAGGGAGGTTATC
1 AATTTCATAGTGTGGTTATCAAAATTTTATAG-GA-AGGTTATCAAATATCATAGGGAGGTTATC
9533 AA
64 AA
* * * * *
9535 AATTTCATAG-GTAGGTTATCAAAATTTTCATAGTATGGTTACCGAAA-ATTCATTGGAAGGTTA
1 AATTTCATAGTGT-GGTTATCAAAATTTT-ATAGGAAGGTTATC-AAATA-TCATAGGGAGGTTA
9598 TCAA
62 TCAA
* * ** * *
9602 AATTTC--AGTGTGGTTATCAAAATTTCATAGGCATATTATTAAAATTTCATAGGGAGGTTATCA
1 AATTTCATAGTGTGGTTATCAAAATTTTATAGGAAGGTTA-TCAAATATCATAGGGAGGTTATCA
9665 A
65 A
*
9666 AATTTCATAATGTGGTTATC-AAATTTT
1 AATTTCATAGTGTGGTTATCAAAATTTT
9693 CATATGTGGA
Statistics
Matches: 130, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
64 32 0.25
65 22 0.17
66 22 0.17
67 50 0.38
68 4 0.03
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (65 bp):
AATTTCATAGTGTGGTTATCAAAATTTTATAGGAAGGTTATCAAATATCATAGGGAGGTTATCAA
Found at i:16721 original size:16 final size:16
Alignment explanation
Indices: 16700--16816 Score: 125
Period size: 16 Copynumber: 7.4 Consensus size: 16
16690 CCCGAGACCA
16700 AACCCGAAAATACCCG
1 AACCCGAAAATACCCG
*
16716 AACCCG-ACATAACCCG
1 AACCCGAAAAT-ACCCG
*
16732 AATCCGAAAATACCCG
1 AACCCGAAAATACCCG
**
16748 AACCCG-ACTTAACCCG
1 AACCCGAAAAT-ACCCG
16764 AACCCGAAAATACCCG
1 AACCCGAAAATACCCG
16780 AACCCGAAAA-AGCCCG
1 AACCCGAAAATA-CCCG
* *
16796 AGCCCG-AAGTACCCG
1 AACCCGAAAATACCCG
16811 AACCCG
1 AACCCG
16817 CCCGAGCCCG
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
15 17 0.20
16 62 0.74
17 5 0.06
ACGTcount: A:0.38, C:0.39, G:0.15, T:0.07
Consensus pattern (16 bp):
AACCCGAAAATACCCG
Found at i:16740 original size:32 final size:32
Alignment explanation
Indices: 16700--16816 Score: 166
Period size: 32 Copynumber: 3.7 Consensus size: 32
16690 CCCGAGACCA
16700 AACCCGAAAATACCCGAACCCGACATAACCCG
1 AACCCGAAAATACCCGAACCCGACATAACCCG
* *
16732 AATCCGAAAATACCCGAACCCGACTTAACCCG
1 AACCCGAAAATACCCGAACCCGACATAACCCG
*
16764 AACCCGAAAATACCCGAACCCGA-AAAAGCCCG
1 AACCCGAAAATACCCGAACCCGACATAA-CCCG
* *
16796 AGCCCG-AAGTACCCGAACCCG
1 AACCCGAAAATACCCGAACCCG
16817 CCCGAGCCCG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
31 16 0.21
32 61 0.79
ACGTcount: A:0.38, C:0.39, G:0.15, T:0.07
Consensus pattern (32 bp):
AACCCGAAAATACCCGAACCCGACATAACCCG
Found at i:20340 original size:30 final size:30
Alignment explanation
Indices: 20304--20362 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
20294 TGTCTTCAAG
*
20304 TCCATGATAAATCCTT-GACGCATCATTCCC
1 TCCATGAT-AAGCCTTGGACGCATCATTCCC
*
20334 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATGATAAGCCTTGGACGCATCATTCC
20363 GCCCCATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGACGCATCATTCCC
Found at i:21262 original size:25 final size:23
Alignment explanation
Indices: 21203--21263 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
21193 GATTAGAAAT
* *
21203 AACTAATGAAAAACAATTAGATA
1 AACTAATTAAAAACAATTACATA
* *
21226 AACTAAACTAAAGAACAATTACTTAA
1 AACT-AATTAAA-AACAATTACAT-A
21252 AACTAATTAAAA
1 AACTAATTAAAA
21264 CTAGAAAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 4 0.13
24 6 0.20
25 15 0.50
26 5 0.17
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (23 bp):
AACTAATTAAAAACAATTACATA
Found at i:23424 original size:29 final size:30
Alignment explanation
Indices: 23364--23432 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 30
23354 GCTAAATACC
* *
23364 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA
23395 CAAAATAATCCCTTATGTTTT-TTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTCGGGA
*
23424 CAAATTAAT
1 CAAAATAAT
23433 ACATTACGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 15 0.43
31 20 0.57
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTCGGGA
Found at i:23443 original size:29 final size:28
Alignment explanation
Indices: 23387--23443 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
23377 TATGTTTTGC
* * *
23387 TTTTGGGACAAAATAATCCCTTATGTTT
1 TTTTGGGACAAAATAATACATTACGTTT
*
23415 TTTTCGGGACAAATTAATACATTACGTTT
1 TTTT-GGGACAAAATAATACATTACGTTT
23444 CAAAAATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (28 bp):
TTTTGGGACAAAATAATACATTACGTTT
Found at i:24063 original size:177 final size:178
Alignment explanation
Indices: 23857--24212 Score: 518
Period size: 177 Copynumber: 2.0 Consensus size: 178
23847 TAATGTCATT
* *
23857 TAAGAAATATATTTTAAAAATTCTAATATATCTAATTTTTTAATTAAAATAGTAAAATGGTAAAA
1 TAAGAAATATATTTTAAAAATTATAATATATCTAAGTTTTTAATTAAAATAGTAAAATGGTAAAA
* ** * * *
23922 ATAAAATAGTTATAAATATATTATATTTGATTAAATAAAAATATATTTTTTAATTGAGTAAAATT
66 ATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACT
* ** * *
23987 GTAAAAGTTTAAACAATTGCATTTAAGAAATATATTTGAAAAA-AAGGG
131 ATAAAA-TTTAAACAACGGCATTTAAGAAATATAATCGAAAAATAAGGG
* * * *
24035 TAAGCAATATA-TTTAAAAATTATAATATATTTTAGTTTTTAATTAAAATATTAAAATGGTAAAA
1 TAAGAAATATATTTTAAAAATTATAATATATCTAAGTTTTTAATTAAAATAGTAAAATGGTAAAA
* *
24099 ATAAAATATTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTATTTGAGTAAAACT
66 ATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACT
24164 ATAAAATTTAAACAACGGCATTTAAGAAATATAATCGAAAAATAAGGG
131 ATAAAATTTAAACAACGGCATTTAAGAAATATAATCGAAAAATAAGGG
24212 T
1 T
24213 GTAATCGTCA
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
176 32 0.20
177 116 0.73
178 10 0.06
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (178 bp):
TAAGAAATATATTTTAAAAATTATAATATATCTAAGTTTTTAATTAAAATAGTAAAATGGTAAAA
ATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTTTTTAATTGAGTAAAACT
ATAAAATTTAAACAACGGCATTTAAGAAATATAATCGAAAAATAAGGG
Found at i:24682 original size:31 final size:31
Alignment explanation
Indices: 24639--24713 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
24629 TAAATATAAA
*
24639 AAAAAAATCCCTTATGTTTTTCTTT-TGGGAC
1 AAAATAATCCCTTATGTTTTT-TTTATGGGAC
24670 AAAATAATCCCTTATGTTTTTTTTATGGGAC
1 AAAATAATCCCTTATGTTTTTTTTATGGGAC
*
24701 AAATTAATCCCTT
1 AAAATAATCCCTT
24714 GTTGATATGG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.43
Consensus pattern (31 bp):
AAAATAATCCCTTATGTTTTTTTTATGGGAC
Found at i:24914 original size:31 final size:29
Alignment explanation
Indices: 24846--24926 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
24836 CTCATTTTTG
* *
24846 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCGAAAA
24875 AAACATAAGGGATTATTTTGTCCC-AAAA
1 AAACATAAGGGATTATTTTGTCCCGAAAA
*
24903 GCAGAACATAAGGGACTTTTTTTG
1 --A-AACATAAGGGA-TTATTTTG
24927 GGAATTTAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.09
29 22 0.49
30 1 0.02
31 11 0.24
32 7 0.16
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCGAAAA
Found at i:25896 original size:13 final size:13
Alignment explanation
Indices: 25878--25903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25868 ATGGATGAAT
25878 CCAATCTTTGTTC
1 CCAATCTTTGTTC
25891 CCAATCTTTGTTC
1 CCAATCTTTGTTC
25904 AATACTCGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
CCAATCTTTGTTC
Found at i:27668 original size:31 final size:31
Alignment explanation
Indices: 27633--27734 Score: 120
Period size: 31 Copynumber: 3.3 Consensus size: 31
27623 AAAATATTGC
*
27633 GGCGTCT-AGTCCAAAGACGCCGCTAAGTGGA
1 GGCGTCTGAGTCC-AAGACGCCGCTAAATGGA
27664 GGCGTCTGAGGAT-CAAGACGCCGCTAAATGGA
1 GGCGTCTGA-G-TCCAAGACGCCGCTAAATGGA
* *
27696 GGCGTCTTGACTCC-AGACGCCGCTAAATGGT
1 GGCGTC-TGAGTCCAAGACGCCGCTAAATGGA
27727 GGCGTCTG
1 GGCGTCTG
27735 TGGTTAAAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
30 2 0.03
31 30 0.48
32 25 0.40
33 5 0.08
34 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (31 bp):
GGCGTCTGAGTCCAAGACGCCGCTAAATGGA
Found at i:27684 original size:32 final size:32
Alignment explanation
Indices: 27646--27750 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
27636 GTCTAGTCCA
*
27646 AAGACGCCGCTAAGTGGAGGCGTCTGAGGATC
1 AAGACGCCGCTAAATGGAGGCGTCTGAGGATC
*
27678 AAGACGCCGCTAAATGGAGGCGTCTTGA--CTC
1 AAGACGCCGCTAAATGGAGGCGTC-TGAGGATC
* * * * *
27709 CAGACGCCGCTAAATGGTGGCGTCTGTGGTTA
1 AAGACGCCGCTAAATGGAGGCGTCTGAGGATC
27741 AAGACGCCGC
1 AAGACGCCGC
27751 CATATTTAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
30 2 0.03
31 24 0.39
32 33 0.53
33 3 0.05
ACGTcount: A:0.24, C:0.25, G:0.33, T:0.18
Consensus pattern (32 bp):
AAGACGCCGCTAAATGGAGGCGTCTGAGGATC
Found at i:27851 original size:32 final size:32
Alignment explanation
Indices: 27810--27926 Score: 157
Period size: 32 Copynumber: 3.7 Consensus size: 32
27800 AAATATAGCG
*
27810 GGCGTCTGTGGTTCAAGACGCTGCTAAATGAA
1 GGCGTCTGTGGTTCAAGACGCTGCTAAATGGA
*
27842 GGCGTCTGTGTTTCAAGACGCTGCTAAATGGA
1 GGCGTCTGTGGTTCAAGACGCTGCTAAATGGA
* *
27874 GGCGTTTGTGTTTCAAGACGAC-GCTAAATGGA
1 GGCGTCTGTGGTTCAAGACG-CTGCTAAATGGA
*
27906 GGCGTCTGAT-GTTCATGACGC
1 GGCGTCTG-TGGTTCAAGACGC
27927 CGCCATATTC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
31 1 0.01
32 74 0.96
33 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (32 bp):
GGCGTCTGTGGTTCAAGACGCTGCTAAATGGA
Found at i:28025 original size:178 final size:175
Alignment explanation
Indices: 27521--28045 Score: 633
Period size: 178 Copynumber: 3.0 Consensus size: 175
27511 GATAAATAGC
* * * *
27521 GGCGTCTTGAGTAAAGAC-ACCGCTAAATGGAGACGTCTGAGGTTAAAGACGCCGCCATATTTAA
1 GGCGTCTTGACTCAAGACGA-CGCTAAATGGAGGCGTCTGATGTTAAAGACGCCGCCATATTTAA
* * * * * * *
27585 TTTTTTCCGGGAAAGGCAAATTGGGTAACGC-CAAGGCTAAAATATTGCGGCGTCTAGTCCAAAG
65 TTTTTTCCGGGAAAGGCAAATTGGGTAAAGCTGAAGGATAAAATATAGCGGCGTCTTGGCCCAAG
* *
27649 ACGCCGCTAAGTGGAGGCGTCTGAGGATCAAGACGCCGCTAAATGGA
130 ACGCCGCTAAATGGAGGCGTCTGA-GTTCAAGACGCCGCTAAATGGA
* * *
27696 GGCGTCTTGACTCCAGACGCCGCTAAATGGTGGCGTCTG-TGGTTAAAGACGCCGCCATATTTAA
1 GGCGTCTTGACTCAAGACGACGCTAAATGGAGGCGTCTGAT-GTTAAAGACGCCGCCATATTTAA
* **
27760 TTTTTTCCGGGAAAGGCAAATTGGATAAAGCTGAAGGATAAAATATAGCGGGCGTCTGTGGTTCA
65 TTTTTTCCGGGAAAGGCAAATTGGGTAAAGCTGAAGGATAAAATATAGC-GGCGTCT-TGGCCCA
* * * *
27825 AGACGCTGCTAAATGAAGGCGTCTGTGTTTCAAGACGCTGCTAAATGGA
128 AGACGCCGCTAAATGGAGGCGTCTGAG-TTCAAGACGCCGCTAAATGGA
* ** * * *
27874 GGCGTTTGTGTTTCAAGACGACGCTAAATGGAGGCGTCTGATGTTCATGACGCCGCCATATTCAA
1 GGCGTCT-TGACTCAAGACGACGCTAAATGGAGGCGTCTGATGTTAAAGACGCCGCCATATTTAA
* * * * * *
27939 TTTTTTTTCGAGAAATGCAAATTGGGTAAAGCTGAATGTTAAAATATAGCGGCGTCTTGGCCCTA
65 -TTTTTTCCGGGAAAGGCAAATTGGGTAAAGCTGAAGGATAAAATATAGCGGCGTCTTGGCCCAA
28004 GACGCCGCTAAATGGAGGCGTCTGAAGTTCAAGACGCCGCTA
129 GACGCCGCTAAATGGAGGCGTCTG-AGTTCAAGACGCCGCTA
28046 TATTTAATTG
Statistics
Matches: 295, Mismatches: 45, Indels: 17
0.83 0.13 0.05
Matches are distributed among these distances:
175 84 0.28
176 14 0.05
177 8 0.03
178 90 0.31
179 55 0.19
180 44 0.15
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (175 bp):
GGCGTCTTGACTCAAGACGACGCTAAATGGAGGCGTCTGATGTTAAAGACGCCGCCATATTTAAT
TTTTTCCGGGAAAGGCAAATTGGGTAAAGCTGAAGGATAAAATATAGCGGCGTCTTGGCCCAAGA
CGCCGCTAAATGGAGGCGTCTGAGTTCAAGACGCCGCTAAATGGA
Found at i:28140 original size:32 final size:32
Alignment explanation
Indices: 28099--28188 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
28089 ATTAAATATG
28099 GCGGCGTCCTAAACCTCAGACGCCTCCATTTA
1 GCGGCGTCCTAAACCTCAGACGCCTCCATTTA
*
28131 GCGGCGTCCTTAACCTCAGACGCCTCCATTTA
1 GCGGCGTCCTAAACCTCAGACGCCTCCATTTA
*
28163 GCGGCGTCCCGAAA-CTCAGACGCCTC
1 GCGGCGT-CCTAAACCTCAGACGCCTC
28189 TCAAGACGCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 50 0.93
33 4 0.07
ACGTcount: A:0.20, C:0.39, G:0.21, T:0.20
Consensus pattern (32 bp):
GCGGCGTCCTAAACCTCAGACGCCTCCATTTA
Done.