Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008069.1 Corchorus capsularis cultivar CVL-1 contig08090, 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: 89283
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6724 original size:12 final size:12
Alignment explanation
Indices: 6707--6736 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6697 CTGTGTCATC
6707 AAATTTGTTACT
1 AAATTTGTTACT
6719 AAATTTGTTACT
1 AAATTTGTTACT
*
6731 TAATTT
1 AAATTT
6737 TTGTACCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (12 bp):
AAATTTGTTACT
Found at i:23400 original size:18 final size:18
Alignment explanation
Indices: 23369--23405 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
23359 GGTGAAATGG
*
23369 GTCGGTTGAGTCGGTTTT
1 GTCGGGTGAGTCGGTTTT
*
23387 GTCGGGTGATTCGGTTTT
1 GTCGGGTGAGTCGGTTTT
23405 G
1 G
23406 AAAGTCGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.05, C:0.11, G:0.41, T:0.43
Consensus pattern (18 bp):
GTCGGGTGAGTCGGTTTT
Found at i:23619 original size:22 final size:22
Alignment explanation
Indices: 23569--23619 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
23559 TATAATATCC
*
23569 GAAAATCATTTTTATTTTAATAT
1 GAAAAT-ATTTTTATTTTAATAA
*
23592 G-TAATATATTTTA-TTTAATAA
1 GAAAATAT-TTTTATTTTAATAA
23613 GAAAATA
1 GAAAATA
23620 ATACGTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
21 10 0.43
22 12 0.52
23 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (22 bp):
GAAAATATTTTTATTTTAATAA
Found at i:45338 original size:8 final size:8
Alignment explanation
Indices: 45325--45351 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
45315 CATAAAGCAA
45325 AAAAAAAC
1 AAAAAAAC
45333 AAAAAAAC
1 AAAAAAAC
45341 AAAAAAAC
1 AAAAAAAC
45349 AAA
1 AAA
45352 CATTCCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:52532 original size:124 final size:124
Alignment explanation
Indices: 52310--52786 Score: 837
Period size: 124 Copynumber: 3.8 Consensus size: 124
52300 CTTTAATCAA
* * *
52310 ATATTTACCTTGTCTTTAAAGTTATGCAAATATTGGTCTGTGGCTCTGTAGTTTTGTGTTTGTTG
1 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTC--T-G---TGTGTTTGTTA
* ** *
52375 TATCTGTTTGCAGCTGCTACACCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATATAT
60 TGTCTGACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATATAT
52440 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTCTGTGTGTTTGTTATGTCTG
1 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTCTGTGTGTTTGTTATGTCTG
52505 ACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATATAT
66 ACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATATAT
52564 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTCTGTGTGTTTGTTATGTCTG
1 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTCTGTGTGTTTGTTATGTCTG
52629 ACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATATAT
66 ACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATATAT
52688 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTCTGTGTGTTTGTTATGTCTG
1 ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTCTGTGTGTTTGTTATGTCTG
52753 ACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTT
66 ACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTT
52787 TATGCTTATA
Statistics
Matches: 340, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
124 294 0.86
127 1 0.00
128 1 0.00
130 44 0.13
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.44
Consensus pattern (124 bp):
ATATTTACCTTGTCTTTAGAGTTATGCCAATATTGGTCTGTGGCTCTGTGTGTTTGTTATGTCTG
ACTGCAGCTGCTACTCCCTGTTCTGCTTCGTTTTAATAAGCTCCTTTAATCAAATATAT
Found at i:67749 original size:15 final size:14
Alignment explanation
Indices: 67713--67759 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
67703 GGTAGTGTAT
67713 AAGAGTAGTGTGGC
1 AAGAGTAGTGTGGC
67727 AAGAGTAGTGTGGC
1 AAGAGTAGTGTGGC
* *
67741 TAGGAGTAGTGTGGA
1 -AAGAGTAGTGTGGC
67756 AAGA
1 AAGA
67760 ATTAACAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.32, C:0.04, G:0.43, T:0.21
Consensus pattern (14 bp):
AAGAGTAGTGTGGC
Found at i:69038 original size:60 final size:60
Alignment explanation
Indices: 68972--69124 Score: 191
Period size: 60 Copynumber: 2.5 Consensus size: 60
68962 CTAATTGTTC
* * *
68972 AAATAGGATCCTAAAC-TATTTGGAAATGCTCAATTTAGGCCTCACACTTTTAATTTGGTG
1 AAATAGGATCCT-AACGTATGTGAAAATGCTCAATTTAGGCCTCACACTTGTAATTTGGTG
* * * * ** *
69032 AAATAGGGTCCTAACGTATGCGAAAATGCTCAATTTATGTCTCATGCTTGTAATTTGGTT
1 AAATAGGATCCTAACGTATGTGAAAATGCTCAATTTAGGCCTCACACTTGTAATTTGGTG
*
69092 AAATAGGAACCTAACGTATGTGAAAATGCTCAA
1 AAATAGGATCCTAACGTATGTGAAAATGCTCAA
69125 ATAAGGTCCC
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 3 0.04
60 76 0.96
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (60 bp):
AAATAGGATCCTAACGTATGTGAAAATGCTCAATTTAGGCCTCACACTTGTAATTTGGTG
Found at i:70669 original size:20 final size:20
Alignment explanation
Indices: 70629--70669 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
70619 AAACCGACCG
* *
70629 AATTATATATATATTTTTAT
1 AATTATATATATATATATAT
70649 AATTATATATATATATATAT
1 AATTATATATATATATATAT
70669 A
1 A
70670 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTATATATATATATATAT
Found at i:71931 original size:14 final size:14
Alignment explanation
Indices: 71912--71940 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
71902 ACACATCGTA
71912 CTTAATTTCAGTAG
1 CTTAATTTCAGTAG
71926 CTTAATTTCAGTAG
1 CTTAATTTCAGTAG
71940 C
1 C
71941 AAGAGACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (14 bp):
CTTAATTTCAGTAG
Found at i:75994 original size:6 final size:6
Alignment explanation
Indices: 75983--76011 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
75973 AGATATTGGG
75983 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
76012 GGTAAAGATA
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:79943 original size:29 final size:29
Alignment explanation
Indices: 79891--79951 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
79881 AAAACATCTG
* * *
79891 AAAATTGAAGTTCAGGTGGTAAAATGTCC
1 AAAATTGAAATTCAGGTGGCAAAACGTCC
79920 AAAATTGAAATTCAGG-GGACAAAACGTCC
1 AAAATTGAAATTCAGGTGG-CAAAACGTCC
79949 AAA
1 AAA
79952 CGCTACAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21
Consensus pattern (29 bp):
AAAATTGAAATTCAGGTGGCAAAACGTCC
Found at i:82906 original size:29 final size:29
Alignment explanation
Indices: 82864--82922 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
82854 ATGTTATGCA
82864 CTAGTTATTAACCATGTAAAGCTTCATTT
1 CTAGTTATTAACCATGTAAAGCTTCATTT
*
82893 CTAGTTATTAACCATGTAAGGCTTCATTT
1 CTAGTTATTAACCATGTAAAGCTTCATTT
82922 C
1 C
82923 ATTTTGGTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (29 bp):
CTAGTTATTAACCATGTAAAGCTTCATTT
Found at i:83110 original size:28 final size:28
Alignment explanation
Indices: 83070--83126 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
83060 AACCATGTAA
83070 GGCTTAATTTCATTTTGGTACTAATCAT
1 GGCTTAATTTCATTTTGGTACTAATCAT
83098 GGCTTAATTTCATTTTGGTACTAATCAT
1 GGCTTAATTTCATTTTGGTACTAATCAT
83126 G
1 G
83127 TAAGGGTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.46
Consensus pattern (28 bp):
GGCTTAATTTCATTTTGGTACTAATCAT
Found at i:83433 original size:10 final size:10
Alignment explanation
Indices: 83418--83455 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
83408 TTCTTAATCC
83418 TGAATATAAG
1 TGAATATAAG
83428 TGAATATAA-
1 TGAATATAAG
83437 -GAATATAAG
1 TGAATATAAG
*
83446 TGAGTATAAG
1 TGAATATAAG
83456 AATACCGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 8 0.32
10 17 0.68
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (10 bp):
TGAATATAAG
Found at i:83442 original size:18 final size:18
Alignment explanation
Indices: 83419--83459 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
83409 TCTTAATCCT
83419 GAATATAAGTGAATATAA
1 GAATATAAGTGAATATAA
*
83437 GAATATAAGTGAGTATAA
1 GAATATAAGTGAATATAA
83455 GAATA
1 GAATA
83460 CCGGATTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (18 bp):
GAATATAAGTGAATATAA
Found at i:84535 original size:1 final size:1
Alignment explanation
Indices: 84529--84570 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
84519 AACTCGCTGC
84529 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
84571 TCCCACCCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:88140 original size:333 final size:333
Alignment explanation
Indices: 86566--88472 Score: 1606
Period size: 331 Copynumber: 5.8 Consensus size: 333
86556 AATGTTCATA
* * ** *
86566 TTTTTTT-CGAATTAGTTTTTAATTAAATC-AAAACAAGATTCAGATTTTCGA-AAAAATAAATC
1 TTTTTTTCCGAATTA-TTTCTAATTAAATCGAAAAAAAGATTCAGATGCTC-ATAAAAACAAATC
* * ** * * * * * * * *
86628 TTTAAATTCAATGCGGCTGAGATTTGGTAAGATGAATATCGATATTTCAAGAAGTCTTGCCACCA
64 CTTAAATCCAATGTAGCTGAGAATTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGCGCAA
* *
86693 AAAATCATGCAAAACTGAGA-TGGGGGCCTC-GAAACGCGTTTTTAGCCAAAAA-C----T-G-T
129 AAAATCATTCAAAACTGAGACT--GGGCCCCAG-AACGCGTTTTTAGCCAAAAACCGTGATAGTT
*** * **
86749 AGTACACGATTTCCATTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTTTCC
191 AGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAAGATTTTTCCTCAATTTTTGGCC
* * * * ** **
86814 CAAAATACTAATAAAACAAAATATAATTCAACGCCACAAA-ATTGATA-GTTTTTTCATGCTTCT
256 GAAAATACTAATAAAA-AATATATAATTCAATGCCAAAAAGATTGA-AGGGCTTTTCACACTTCT
*
86877 AATATAATTTTTCCT
319 AATATCATTTTTCCT
* * * * * *
86892 ATTTTTTCCAAATTTATTTCTAATTAAATCG-AAACAAGATTTAGATGCTCGTAAAAAAAAAAAA
1 TTTTTTTCCGAA-TTATTTCTAATTAAATCGAAAAAAAGATTCAGATGCTC----ATAAAAACAA
* * * * *
86956 ATCCTTAAATCCAATGT-GAATGAGATTTAGTTAGATGAATATAGATATTTCAAGGGGTCTTGGC
61 ATCCTTAAATCCAATGTAG-CTGAGAATTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGC
* * * * * *
87020 GCCAAAAATCATGT-AAAACTGATAC-GGG-CTCGGAACACGTTTTTAGCTAAAAACC-------
125 GCAAAAAATCAT-TCAAAACTGAGACTGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATAG
* ** * * *
87075 ---G--CACGATTTCGACTAAAATTTTGTAAAAATTGA-CAAGAAAAATTATTCCTCAATTTTTG
189 TTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCA-AAAGATTTTTCCTCAATTTTTG
* * *
87134 GCCG-AAATACTAATAAAAAATATATAATTAAATGCTAAAAAGATTGAAGGGCCTTTCACAACTT
253 GCCGAAAATACTAATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCAC-ACTT
* * * *
87198 CAAATGTCGTTTTCCCT
317 CTAATATCATTTTTCCT
* * * * * *
87215 ATATTTTCCGAATTAATTCTAAATATATC-AAAACAAGATTCAGATGCTCATAAAAACAAATCCT
1 TTTTTTTCCGAATTATTTCTAATTAAATCGAAAAAAAGATTCAGATGCTCATAAAAACAAATCCT
* * * *
87279 TAAATCCAATGTAGCTGAGACTTGGTTAGAATAAA-ATATATATTTCAAGGATTCTTGGCGCCAA
66 TAAATCCAATGTAGCTGAGAATTGGTTAG-ATAAATATAGATATTTCAAGGAGTCTTGGCGCAAA
* * * * * **
87343 AAATCATGT-AAAATTGATAC-GAGACCCAGAACGCGTTTTTAGTCAAAAA-C-TG-TA-ACA-T
130 AAATCAT-TCAAAACTGAGACTGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGT
*
87401 ACACGATTTCGGCTAAAATTTCACAAAAATTGACCCAAAAGATTTTTCCTCAATTTTTGGCC-AA
194 ACACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAAGATTTTTCCTCAATTTTTGGCCGAA
* * * *
87465 AATACTAATAAAAAATATATAATTCAACGTCAAAAA-ATTGAAGGGATTTTCACACTTTTAATAT
259 AATACTAATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACACTTCTAATAT
87529 CATTTTTCCTTT
324 CATTTTTCC--T
* * * *
87541 TTTTTTCTCCCCGAATTTATTTCT-ATTTAATCG-AAACAAGATTCAGATGCCCGTAAAAACAAA
1 TTTTTT-T--CCGAA-TTATTTCTAATTAAATCGAAAAAAAGATTCAGATGCTCATAAAAACAAA
* * * *
87604 TCCTTAAATCCAATGTGTATCTCAGAATTGGTTAGATAAATATAGATATTTCAAGGTGTCTTAGC
62 TCCTTAAATCCAA--TGTAGCTGAGAATTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGC
* * * * *
87669 ATC-AAAAACCATGCAAAACT-ATGCCGGGGCCCCAGAACGCGTTTTTAGCC-AAAACCGTGATG
125 -GCAAAAAATCATTCAAAACTGA-GACTGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGAT-
* * * * *
87731 GTGTTAGTACACGATTTTGCCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTT
187 -AGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAAGATTTTTCCTCAATTTT
* * * *
87796 TGGTC-AAAATACTAATAAAAAAATATATAATTCAATACCAAAAAGATTG-ATGGCTTTTCACGC
251 TGGCCGAAAATACTAAT-AAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACAC
* *
87859 TTCTAATATCAATTTTCTT
315 TTCTAATATCATTTTTCCT
* * * *
87878 TTTCTTTTTCAAATTTATTTCTAATTAAATCGAAAAAAAGATTCATATGCTCATAAAAACAAATT
1 TTT-TTTTCCGAA-TTATTTCTAATTAAATCGAAAAAAAGATTCAGATGCTCATAAAAACAAATC
* * * * ** *
87943 CTTTAATCCAACGTCGCTGATAATAAGTTAGATAAATATAGATATTTCAAGGAATCTAT-GCGCA
64 CTTAAATCCAATGTAGCTGAGAATTGGTTAGATAAATATAGATATTTCAAGGAGTCT-TGGCGCA
* * * *
88007 AAAAAT-ATTCAAAACTGAGCCTGGGCCCCGGATCGCGATTTTAGCCAAAAACCGTGATAGTTAG
128 AAAAATCATTCAAAACTGAGACTGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAG
* * * * *
88071 TACACTATTTCGGCTAAAATTTTTCAAAAATTGATCCAAAATATTTTTTCTCAATTTTTGG-CGA
193 TACACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAAGATTTTTCCTCAATTTTTGGCCGA
* * * * *
88135 AAATACTAATAAAAAATAAAAAATTCAATGCCAAAAAGATTGTAGGGTTTTTCACGCTTCTAATA
258 AAATACTAATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACACTTCTAATA
*
88200 ACATTTTTCCT
323 TCATTTTTCCT
* * * *
88211 ATTTTTTCCGAATTAGTTTCAAATTAAATCGATAAATCGAAACAAGATTTAGATTCTCATAAAAA
1 TTTTTTTCCGAATTA-TTTCTAATTAAATCG---AA---AAA-AAGATTCAGATGCTCAT---AA
* * * * *
88276 AAACAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTGGATGAATATAGATATTTCTATGAGTC
55 AAACAAATCCTTAAATCCAATGTAGCTGAGAATTGGTTAGATAAATATAGATATTTCAAGGAGTC
* * *
88341 TTGGCGTC-AAAACTCATTCAAAACTGAGACTGGGCCTC-GAAATGCGTTTTTAGCCAAAAACCG
120 TTGGCG-CAAAAAATCATTCAAAACTGAGACTGGGCCCCAG-AACGCGTTTTTAGCCAAAAACCG
* * * *
88404 CGACAGTTAGTACACGATTTCGGCTGAAATTTTACAAAAATTGACCCGAAAA-TTTTTCTCCTCA
183 TGATAGTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCC-AAAAGATTTT-TCCTCA
88468 ATTTT
246 ATTTT
88473 CAGCCAAAAT
Statistics
Matches: 1294, Mismatches: 207, Indels: 142
0.79 0.13 0.09
Matches are distributed among these distances:
318 85 0.07
319 25 0.02
321 19 0.01
322 58 0.04
323 74 0.06
324 15 0.01
325 16 0.01
326 95 0.07
327 35 0.03
328 24 0.02
329 56 0.04
330 15 0.01
331 137 0.11
332 74 0.06
333 101 0.08
334 35 0.03
335 70 0.05
336 9 0.01
337 43 0.03
338 74 0.06
339 64 0.05
340 4 0.00
341 1 0.00
342 64 0.05
343 87 0.07
344 14 0.01
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33
Consensus pattern (333 bp):
TTTTTTTCCGAATTATTTCTAATTAAATCGAAAAAAAGATTCAGATGCTCATAAAAACAAATCCT
TAAATCCAATGTAGCTGAGAATTGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGCGCAAAA
AATCATTCAAAACTGAGACTGGGCCCCAGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTAC
ACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAAGATTTTTCCTCAATTTTTGGCCGAAAA
TACTAATAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACACTTCTAATATCA
TTTTTCCT
Found at i:88639 original size:19 final size:19
Alignment explanation
Indices: 88615--88654 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
88605 TTGCCCCTCT
88615 TCTCTCTCCCCCCACTAAG
1 TCTCTCTCCCCCCACTAAG
* *
88634 TCTCTCTCCTCCCACTTAG
1 TCTCTCTCCCCCCACTAAG
88653 TC
1 TC
88655 AAGATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.50, G:0.05, T:0.33
Consensus pattern (19 bp):
TCTCTCTCCCCCCACTAAG
Done.