Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015263.1 Corchorus olitorius cultivar O-4 contig15296, 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: 44743
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:862 original size:2 final size:2
Alignment explanation
Indices: 855--882 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
845 CTGCTAGCCC
855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
883 TTTGGGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3267 original size:217 final size:216
Alignment explanation
Indices: 2984--3967 Score: 1151
Period size: 218 Copynumber: 4.6 Consensus size: 216
2974 ATTATTATCT
* * * * *
2984 TATACTAAAACGACGTTTTCGAAAAAATATTGTTATAAATATCGTAAAAGTTTATCTTAAAGCGA
1 TATATTAAAACGACGTTTCCG-AAAAATATTGTTATAAATGTCGAAAAAGTCTATCTTAAAGCGA
* * * * * *
3049 CGTTTG-TAAAAAATGTCGTATGATTGAACGAAGTTCGAGGAAAACGTCTTTACAACCGTCGTAA
65 CGTTTGTTAAAAAATGTCGCATGATTGAACGAAGTTTGAGAAAAACGTCTCTACAAACGTCGCAA
* * * * *
3113 AAGCGTAAGCAAAAGCGACGTTATTAAAAAAACGTCACTCAATTTTGAAAAAGAGTTGTAAGGTA
130 AAGCATAAACAAGAGCGACGTTATT-AAAAAACGTCACTCAATTTTGAAAAAGAGTCGCAAGGTA
* * *
3178 CTGCGACGTTTATTAAAACGCCA
194 CTACGACGTTTATTAAAATGTCA
* *
3201 TATATTAAAACGACGTTTTCGAAAAATATTGTTATAAATGTCGCAAAAAGTCTATTTTAAAGCGA
1 TATATTAAAACGACGTTTCCGAAAAATATTGTTATAAATGTCG-AAAAAGTCTATCTTAAAGCGA
* * *
3266 CGTTCGTTAACAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGTCTCTACAAACGTCGCAA
65 CGTTTGTTAAAAAATGTCGCATGATTGAACGAAGTTTGAGAAAAACGTCTCTACAAACGTCGCAA
* * * * ** * *
3331 AAGCATAAACAATAGTGACGTTATTAAAAAATGTCACTTAATTAAGAAAGAGTACTCGCAAGGTA
130 AAGCATAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTGAAAAAG-AGTCGCAAGGTA
3396 CTACGACGTTTATTAAAATGTCA
194 CTACGACGTTTATTAAAATGTCA
* * *
3419 TATATTAAAACGACATTTCCGAAAAATATTGTAATAAATGTCGGAAAAGTCTATCTTAAAGCGAC
1 TATATTAAAACGACGTTTCCGAAAAATATTGTTATAAATGTCGAAAAAGTCTATCTTAAAGCGAC
* * * *
3484 ATTTGTTAAAAAATGTCGCATGAATGAAC-AACGTTTGAAAAAAAGCGTCTCTACAAATGTCGCA
66 GTTTGTTAAAAAATGTCGCATGATTGAACGAA-GTTTGAGAAAAA-CGTCTCTACAAACGTCGCA
* * * *
3548 AAAGCATAAATAAGAGCGACGTTATAAAAAAACGTCACTCAA-TTTAAAAAAGAGTCGTAAGGTA
129 AAAGCATAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTGAAAAAGAGTCGCAAGGTA
* * *
3612 CAACGACATTCATTAAAATGTCA
194 CTACGACGTTTATTAAAATGTCA
* * *
3635 TATATTAAAACGACGTTTCCG-AAAATCGTTGTTATAAATGTCGGAAAAGTCTATCTTATAGCGA
1 TATATTAAAACGACGTTTCCGAAAAAT-ATTGTTATAAATGTCGAAAAAGTCTATCTTAAAGCGA
* * *
3699 CGTTTGTTAAAAAATGTCGCGTGATTGAATGACGTTTGAG-AAAACGTCTCTACAAACGTCGCAA
65 CGTTTGTTAAAAAATGTCGCATGATTGAACGAAGTTTGAGAAAAACGTCTCTACAAACGTCGCAA
* * * * * *
3763 AAGCATAAACAAGAGCGACATTATTAAAAAACGTCATTCAATTTT-AGAAAAGGGTTGCAAGATT
130 AAGCATAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTGA-AAAAGAGTCGCAAGGTA
* * * *
3827 TTGCAACTTTTATTAAAATGTCA
194 CTACGACGTTTATTAAAATGTCA
* * ** ** * *
3850 TTTATT-AAACGACATTTCCCTAAAACGTTGTTATAAATGTCGAAAAAGCCTATCTTAAAGCGAT
1 TATATTAAAACGACGTTTCCGAAAAATATTGTTATAAATGTCGAAAAAGTCTATCTTAAAGCGAC
* * * *
3914 GTTT-TT-ACAAATGTCGCATGATTGAACGACGTTAG-GCAAAAATGTCTCTACAAA
66 GTTTGTTAAAAAATGTCGCATGATTGAACGAAGTTTGAG-AAAAACGTCTCTACAAA
3968 TATCGTAAAA
Statistics
Matches: 660, Mismatches: 95, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
211 1 0.00
212 25 0.04
213 17 0.03
214 107 0.16
215 50 0.08
216 138 0.21
217 128 0.19
218 194 0.29
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (216 bp):
TATATTAAAACGACGTTTCCGAAAAATATTGTTATAAATGTCGAAAAAGTCTATCTTAAAGCGAC
GTTTGTTAAAAAATGTCGCATGATTGAACGAAGTTTGAGAAAAACGTCTCTACAAACGTCGCAAA
AGCATAAACAAGAGCGACGTTATTAAAAAACGTCACTCAATTTTGAAAAAGAGTCGCAAGGTACT
ACGACGTTTATTAAAATGTCA
Found at i:13573 original size:13 final size:13
Alignment explanation
Indices: 13555--13580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13545 GGAATAAGGT
13555 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
13568 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
13581 GATTAAACAT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:15524 original size:7 final size:7
Alignment explanation
Indices: 15512--15538 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
15502 GTTAAAATAA
15512 TAAAAGT
1 TAAAAGT
15519 TAAAAGT
1 TAAAAGT
15526 TAAAAGT
1 TAAAAGT
15533 TAAAAG
1 TAAAAG
15539 AAATGGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (7 bp):
TAAAAGT
Found at i:15949 original size:12 final size:12
Alignment explanation
Indices: 15932--15956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15922 GAGCTCGATT
15932 ACAAACTAAGAA
1 ACAAACTAAGAA
15944 ACAAACTAAGAA
1 ACAAACTAAGAA
15956 A
1 A
15957 TTTTAGCTCG
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:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (12 bp):
ACAAACTAAGAA
Found at i:17237 original size:2 final size:2
Alignment explanation
Indices: 17230--17256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17220 ATATAAATGA
17230 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 A
17257 ACGTCATCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18947 original size:30 final size:30
Alignment explanation
Indices: 18911--18973 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
18901 CATCCTCAAG
*
18911 TCCATGATAAGTCCTT-GGCGCATCATTCCC
1 TCCATGATAAG-CCTTGGGCACATCATTCCC
18941 TCCATGATAAGCCTTGGGCACATCATTCCC
1 TCCATGATAAGCCTTGGGCACATCATTCCC
18971 TCC
1 TCC
18974 CCCTTGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCACATCATTCCC
Found at i:23543 original size:42 final size:42
Alignment explanation
Indices: 23478--23557 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
23468 AGGGAAAGGC
* *
23478 TTTATGGGAAGTTTTCTGAGAAGAAAAATGATTAGGATAGGG
1 TTTATGAGAAGTTTACTGAGAAGAAAAATGATTAGGATAGGG
* *
23520 TTTATGAGAAGTTTACT-AGGAAGAAAAGTGATTCGGAT
1 TTTATGAGAAGTTTACTGA-GAAGAAAAATGATTAGGAT
23558 GAAAGATGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 32 0.97
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (42 bp):
TTTATGAGAAGTTTACTGAGAAGAAAAATGATTAGGATAGGG
Found at i:24111 original size:65 final size:65
Alignment explanation
Indices: 24024--24245 Score: 365
Period size: 65 Copynumber: 3.4 Consensus size: 65
24014 AAAGCTCGCC
* * * *
24024 CTTTGACCGAAAGGGCATTTTTGGAAAGTAGAATAAACTGAAATGCAAGAATGATGAAACTGACT
1 CTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCAAAAATGATGAAATTGACT
*
24089 CTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACCGAAATGCAAAAATGATGAAATTGAAC
1 CTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCAAAAATGATGAAATTG-AC
24154 T
65 T
*
24155 -TTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCAAAAATGATGAAATTGACC
1 CTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCAAAAATGATGAAATTGACT
*
24219 CTTTCACGGAAAGGGTATTTTTGGAAA
1 CTTTCACCGAAAGGGTATTTTTGGAAA
24246 ATCAAACGTG
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
64 2 0.01
65 142 0.97
66 3 0.02
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (65 bp):
CTTTCACCGAAAGGGTATTTTTGGAAAGTAGAATAAACTGAAATGCAAAAATGATGAAATTGACT
Found at i:24298 original size:67 final size:68
Alignment explanation
Indices: 24211--24380 Score: 290
Period size: 67 Copynumber: 2.5 Consensus size: 68
24201 AAAATGATGA
* * *
24211 AATTGACCCTTTCACGGAAAGGGTATT-TTTGGAAAATCAAACGTGAACTCAAACTCAAGAATGA
1 AATTGACCCTTTGACCGAAAGGGTATTCTTTGGAAAATCAAAAGTGAACTCAAACTCAAGAATGA
24275 CAG
66 CAG
24278 AATTGACCCTTTGACCGAAAGGGTATTCTTTGG-AAATCAAAAGTGAACTCAAACTCAAGAATGA
1 AATTGACCCTTTGACCGAAAGGGTATTCTTTGGAAAATCAAAAGTGAACTCAAACTCAAGAATGA
24342 CAG
66 CAG
*
24345 AATTGACCCTTTGACCGAAAAGGTATTCTTTGGAAA
1 AATTGACCCTTTGACCGAAAGGGTATTCTTTGGAAA
24381 GAAAGACTAG
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
67 90 0.93
68 7 0.07
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (68 bp):
AATTGACCCTTTGACCGAAAGGGTATTCTTTGGAAAATCAAAAGTGAACTCAAACTCAAGAATGA
CAG
Found at i:24741 original size:132 final size:131
Alignment explanation
Indices: 24409--24839 Score: 451
Period size: 132 Copynumber: 3.3 Consensus size: 131
24399 GCAACCTGAT
* * *
24409 GAAATTGACCCTTCGATCGGAAGGGTATTTTCGG--AGAAGAAAAT-TAAACTT-AGATGCGAAA
1 GAAA-TGACCCTTCGACCGAAAGGGTATTTT-GGAAAAAAGAAAATATAAACTTGA-ATGC-AAA
* * * * * **
24470 AGGCAAAAATGA-CCTTTGACCGAAAAGGCATTCTTGG--AAAAGAAAA-T--AC-TAAAT-TTA
62 AGACGAAAATGACCCTTCGACCGAAAGGGTATT-TTGGAAAAAAGAAAATTAAACTTAAATGCAA
24527 AAG--G
126 AAGACG
* * * *
24531 CAAATGACCCTTCGACCGAAAGGGTGTTTTTGAAAAAAGAAAATACTAAACTTTAATGCAAAAGA
1 GAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATA-TAAACTTGAATGCAAAAGA
* * ***
24596 CGAAAATGACCCTTCGGCCGAAAGGGTGTTTTGGAAATTTGAAAATGCTAAACTTAAATGCAAAA
65 CGAAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAAT--TAAACTTAAATGCAAAA
*
24661 GATG
128 GACG
***
24665 GAAATGACCCTTCGACCGAAAGGGTATTTTGGAAATTTGAAAAT-TAAACTTGAATGCAAAAGAC
1 GAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATATAAACTTGAATGCAAAAGAC
* *
24729 GGAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATTAAACTTGAATGCAAAAGAC
66 GAAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATTAAACTTAAATGCAAAAGAC
24794 G
131 G
*
24795 GAAATGACCCTTCGACCGAAAGGATATTTTGGAAAAAAGAAAATA
1 GAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATA
24840 CTAATGACCT
Statistics
Matches: 254, Mismatches: 37, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
120 1 0.00
121 23 0.09
122 12 0.05
123 17 0.07
124 26 0.10
125 7 0.03
128 1 0.00
130 61 0.24
131 5 0.02
132 62 0.24
134 39 0.15
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (131 bp):
GAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATATAAACTTGAATGCAAAAGAC
GAAAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATTAAACTTAAATGCAAAAGAC
G
Found at i:24745 original size:65 final size:66
Alignment explanation
Indices: 24532--24843 Score: 448
Period size: 65 Copynumber: 4.7 Consensus size: 66
24522 ATTTAAAGGC
* * *
24532 AAATGACCCTTCGACCGAAAGGGTGTTTTTGAAAAAAGAAAATACTAAACTTTAATGCAAAAGAC
1 AAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAAT-CTAAACTTGAATGCAAAAGAC
*
24597 GA
65 GG
* * *** * *
24599 AAATGACCCTTCGGCCGAAAGGGTGTTTTGGAAATTTGAAAATGCTAAACTTAAATGCAAAAGAT
1 AAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAAT-CTAAACTTGAATGCAAAAGAC
24664 GG
65 GG
***
24666 AAATGACCCTTCGACCGAAAGGGTATTTTGGAAATTTGAAAAT-TAAACTTGAATGCAAAAGACG
1 AAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATCTAAACTTGAATGCAAAAGACG
24730 G
66 G
24731 AAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAAT-TAAACTTGAATGCAAAAGACG
1 AAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATCTAAACTTGAATGCAAAAGACG
24795 G
66 G
*
24796 AAATGACCCTTCGACCGAAAGGATATTTTGGAAAAAAGAAAATACTAA
1 AAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAAT-CTAA
24844 TGACCTTTGG
Statistics
Matches: 226, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
65 124 0.55
67 102 0.45
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.23
Consensus pattern (66 bp):
AAATGACCCTTCGACCGAAAGGGTATTTTGGAAAAAAGAAAATCTAAACTTGAATGCAAAAGACG
G
Found at i:27499 original size:19 final size:18
Alignment explanation
Indices: 27466--27501 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
27456 TGGAAATAAT
27466 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
27484 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
27502 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:31277 original size:22 final size:22
Alignment explanation
Indices: 31251--31324 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 22
31241 GTAAAAAATG
31251 AATCTTTAGATTTAAAAGATTA
1 AATCTTTAGATTTAAAAGATTA
*
31273 AATCTTGGTAAGATTGGAATAAAA-ATTG
1 AATCTT--T-AGATT----TAAAAGATTA
*
31301 AATCTTTAGGTTTAAAAGATTA
1 AATCTTTAGATTTAAAAGATTA
31323 AA
1 AA
31325 CCTTGGTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 16
0.68 0.05 0.27
Matches are distributed among these distances:
21 5 0.12
22 11 0.27
24 1 0.02
25 9 0.22
26 1 0.02
28 9 0.22
29 5 0.12
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (22 bp):
AATCTTTAGATTTAAAAGATTA
Found at i:31359 original size:101 final size:101
Alignment explanation
Indices: 31242--31627 Score: 555
Period size: 101 Copynumber: 3.8 Consensus size: 101
31232 AGAACATGGG
* * *
31242 TAAAAAATGAATCTTTAGATTTAAAAGATTAAATCTTGGTAAG-ATTGGAATAAAAATTGAATCT
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTATTGGAATAAAAATTGAATCT
31306 TTAGGTTTAAAAGATTAAACCTTGGTAAGTTTTAGG-A
66 TTAGGTTTAAAAGATTAAACCTTGGTAAG-TTT-GGAA
* * * *
31343 TAAAAATTGAATCTTTAGGTTTAAAATATTAAACCTTGGTAAGTTTTGGGATAAAAGTTGAATCT
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTATTGGAATAAAAATTGAATCT
* *
31408 TTAGGTTTAAAAGATTAAATCTTGGTAAGATTGGAA
66 TTAGGTTTAAAAGATTAAACCTTGGTAAGTTTGGAA
* * * * *
31444 TAAAAATTAAATCATTAGGTTTAAAAGATTAATCCTTGGTAAGTTTTGGGATAAAAATTGAATCT
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTATTGGAATAAAAATTGAATCT
*
31509 TTAGGTTTAAAAGATTAAACCTTGGTAAAATTTGGAA
66 TTAGGTTTAAAAGATTAAACCTTGGT-AAGTTTGGAA
* *
31546 TAAAAATTGAAACTTTAGGTTTAAAAGATTAAACCTTAGTAAG-ATTGGAATAAAAATCT-AATC
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTATTGGAATAAAAAT-TGAATC
31609 TTTAGGTTTAAAAGATTAA
65 TTTAGGTTTAAAAGATTAA
31628 GGCTTCCTTT
Statistics
Matches: 257, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
100 2 0.01
101 162 0.63
102 93 0.36
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (101 bp):
TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTATTGGAATAAAAATTGAATCT
TTAGGTTTAAAAGATTAAACCTTGGTAAGTTTGGAA
Found at i:31364 original size:51 final size:50
Alignment explanation
Indices: 31242--31627 Score: 551
Period size: 51 Copynumber: 7.6 Consensus size: 50
31232 AGAACATGGG
* * * *
31242 TAAAAAATGAATCTTTAGATTTAAAAGATTAAATCTTGGTAAGATTGGAA
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTTTGGAA
31292 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTTTTAGG-A
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAG-TTT-GGAA
* *
31343 TAAAAATTGAATCTTTAGGTTTAAAATATTAAACCTTGGTAAGTTTTGGGA
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAG-TTTGGAA
* * *
31394 TAAAAGTTGAATCTTTAGGTTTAAAAGATTAAATCTTGGTAAGATTGGAA
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTTTGGAA
* * * *
31444 TAAAAATTAAATCATTAGGTTTAAAAGATTAATCCTTGGTAAGTTTTGGGA
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAG-TTTGGAA
*
31495 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAAATTTGGAA
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGT-AAGTTTGGAA
* * *
31546 TAAAAATTGAAACTTTAGGTTTAAAAGATTAAACCTTAGTAAGATTGGAA
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTTTGGAA
31596 TAAAAATCT-AATCTTTAGGTTTAAAAGATTAA
1 TAAAAAT-TGAATCTTTAGGTTTAAAAGATTAA
31628 GGCTTCCTTT
Statistics
Matches: 303, Mismatches: 27, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
50 122 0.40
51 177 0.58
52 4 0.01
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (50 bp):
TAAAAATTGAATCTTTAGGTTTAAAAGATTAAACCTTGGTAAGTTTGGAA
Found at i:31430 original size:22 final size:22
Alignment explanation
Indices: 31394--31475 Score: 60
Period size: 22 Copynumber: 3.5 Consensus size: 22
31384 AGTTTTGGGA
*
31394 TAAAAG-TTGAATCTTTAGGTT
1 TAAAAGATTAAATCTTTAGGTT
*
31415 TAAAAGATTAAATCTTGGTAAGATT
1 TAAAAGATTAAATCTT--T-AGGTT
*
31440 GGAATAAAA-ATTAAATCATTAGGTT
1 ----TAAAAGATTAAATCTTTAGGTT
31465 TAAAAGATTAA
1 TAAAAGATTAA
31476 TCCTTGGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 17
0.70 0.06 0.25
Matches are distributed among these distances:
21 11 0.23
22 13 0.27
24 1 0.02
25 8 0.17
26 1 0.02
28 9 0.19
29 5 0.10
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (22 bp):
TAAAAGATTAAATCTTTAGGTT
Found at i:31449 original size:152 final size:151
Alignment explanation
Indices: 31242--31627 Score: 628
Period size: 152 Copynumber: 2.5 Consensus size: 151
31232 AGAACATGGG
* *
31242 TAAAAAATGAATCTTTAGATTTAAAAGATTAAATCTTGGTAAGATTGGAATAAAAATTGAATCTT
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAATCTTGGTAAGATTGGAATAAAAATT-AATCTT
*
31307 TAGGTTTAAAAGATTAAACCTTGGTAAGTTTTAGGATAAAAATTGAATCTTTAGGTTTAAAATAT
65 TAGGTTTAAAAGATTAAACCTTGGTAAGTTTTAGGATAAAAATTGAATCTTTAGGTTTAAAAGAT
** *
31372 TAAACCTTGGTAAGTTTTGGGA
130 TAAACCTTGGTAAAATTTGGAA
* *
31394 TAAAAGTTGAATCTTTAGGTTTAAAAGATTAAATCTTGGTAAGATTGGAATAAAAATTAAATCAT
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAATCTTGGTAAGATTGGAATAAAAATT-AATCTT
* *
31459 TAGGTTTAAAAGATTAATCCTTGGTAAGTTTTGGGATAAAAATTGAATCTTTAGGTTTAAAAGAT
65 TAGGTTTAAAAGATTAAACCTTGGTAAGTTTTAGGATAAAAATTGAATCTTTAGGTTTAAAAGAT
31524 TAAACCTTGGTAAAATTTGGAA
130 TAAACCTTGGTAAAATTTGGAA
* * *
31546 TAAAAATTGAAACTTTAGGTTTAAAAGATTAAACCTTAGTAAGATTGGAATAAAAATCTAATCTT
1 TAAAAATTGAATCTTTAGGTTTAAAAGATTAAATCTTGGTAAGATTGGAATAAAAAT-TAATCTT
31611 TAGGTTTAAAAGATTAA
65 TAGGTTTAAAAGATTAA
31628 GGCTTCCTTT
Statistics
Matches: 217, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
152 216 1.00
153 1 0.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (151 bp):
TAAAAATTGAATCTTTAGGTTTAAAAGATTAAATCTTGGTAAGATTGGAATAAAAATTAATCTTT
AGGTTTAAAAGATTAAACCTTGGTAAGTTTTAGGATAAAAATTGAATCTTTAGGTTTAAAAGATT
AAACCTTGGTAAAATTTGGAA
Found at i:35611 original size:15 final size:15
Alignment explanation
Indices: 35591--35624 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35581 CTGGCGACCT
*
35591 AGCACTGACTTCCCC
1 AGCACTGACTTCCCA
*
35606 AGCACTGATTTCCCA
1 AGCACTGACTTCCCA
35621 AGCA
1 AGCA
35625 GCCATCGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (15 bp):
AGCACTGACTTCCCA
Found at i:40581 original size:26 final size:26
Alignment explanation
Indices: 40532--40584 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40522 TAATAATAAT
40532 AACAGCATTGAGCAGCATTTAATTTC
1 AACAGCATTGAGCAGCATTTAATTTC
40558 AACAGCATTGAGCAGCATTTAATTTC
1 AACAGCATTGAGCAGCATTTAATTTC
40584 A
1 A
40585 CTGCAATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (26 bp):
AACAGCATTGAGCAGCATTTAATTTC
Found at i:42259 original size:21 final size:21
Alignment explanation
Indices: 42233--42283 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
42223 TAATATGGAT
42233 TGTTTGTGGATTTATCTTGAA
1 TGTTTGTGGATTTATCTTGAA
* * *
42254 TGTTTGTGCATTTTTTTTGAA
1 TGTTTGTGGATTTATCTTGAA
*
42275 TGTATGTGG
1 TGTTTGTGG
42284 GTTTTGTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.04, G:0.25, T:0.55
Consensus pattern (21 bp):
TGTTTGTGGATTTATCTTGAA
Done.