Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010888.1 Corchorus capsularis cultivar CVL-1 contig10909, 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: 57421
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:69 original size:32 final size:31
Alignment explanation
Indices: 20--130 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 31
10 AATTTGCTCT
* *
20 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCAA
1 AGCCGCCCCA-TGGGGCGGCCTGCCGTGGCGA
*
52 AGCCGCCCCATGAGGGCGGCTTGCCTGCCTTGCGCGA
1 AGCCGCCCCATG-GGGC-G---GCCTGCCGTG-GCGA
** *
89 AGCCGCCCCAT-GGGCGGTTTGCCGTGACGA
1 AGCCGCCCCATGGGGCGGCCTGCCGTGGCGA
119 AGCCGCCCCATG
1 AGCCGCCCCATG
131 AAGCCGCCCC
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
30 14 0.22
31 8 0.12
32 14 0.22
33 1 0.02
34 1 0.02
35 4 0.06
36 9 0.14
37 14 0.22
ACGTcount: A:0.13, C:0.40, G:0.35, T:0.13
Consensus pattern (31 bp):
AGCCGCCCCATGGGGCGGCCTGCCGTGGCGA
Found at i:111 original size:35 final size:35
Alignment explanation
Indices: 38--111 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 35
28 CACCGGGGCG
38 GCCTGCCGTGGCAAAGCCGCCCCATGAGGGCGGCTT
1 GCCTGCCGTGGCAAAGCCGCCCCAT-AGGGCGGCTT
* * *
74 GCCTGCCTTGCGCGAAGCCGCCCCAT-GGGCGGTTT
1 GCCTGCCGTG-GCAAAGCCGCCCCATAGGGCGGCTT
109 GCC
1 GCC
112 GTGACGAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 11 0.32
36 9 0.26
37 14 0.41
ACGTcount: A:0.11, C:0.38, G:0.35, T:0.16
Consensus pattern (35 bp):
GCCTGCCGTGGCAAAGCCGCCCCATAGGGCGGCTT
Found at i:135 original size:13 final size:13
Alignment explanation
Indices: 117--141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107 TTGCCGTGAC
117 GAAGCCGCCCCAT
1 GAAGCCGCCCCAT
130 GAAGCCGCCCCA
1 GAAGCCGCCCCA
142 GTGGGGTGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.48, G:0.24, T:0.04
Consensus pattern (13 bp):
GAAGCCGCCCCAT
Found at i:221 original size:14 final size:15
Alignment explanation
Indices: 192--233 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
182 GACTCAATGT
*
192 AAAAGTGTAAAAAGGGT
1 AAAAGTGT--AAAGGGC
209 AAAAG-GTAAAGGGC
1 AAAAGTGTAAAGGGC
223 AAAAGTGTAAA
1 AAAAGTGTAAA
234 AAGTGGGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.48
15 5 0.22
16 2 0.09
17 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.29, T:0.14
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:5770 original size:24 final size:24
Alignment explanation
Indices: 5741--5787 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5731 GTTAAAGCCC
5741 CTCTGTCAAATGGGAAGGGAACCT
1 CTCTGTCAAATGGGAAGGGAACCT
*
5765 CTCTGTCTAATGGGAAGGGAACC
1 CTCTGTCAAATGGGAAGGGAACC
5788 ATGAAGCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (24 bp):
CTCTGTCAAATGGGAAGGGAACCT
Found at i:21747 original size:87 final size:82
Alignment explanation
Indices: 21591--21880 Score: 334
Period size: 87 Copynumber: 3.4 Consensus size: 82
21581 TCTAACAAAA
** * * *
21591 GGAGAGAAGACTTGTAAGAAAAGTGAGGAAAGCAAGGCCATTGCTTTGGAGATTAGTGAGATTTC
1 GGAGAGAAGACTTGTAA-AAAAGCCAGGATAGCAAGGCC--TGC-TTGGAGAGTAGTGAAATTT-
*
21656 TAACATTGACCAGGCACTTCAG
61 TAACATTGACCAGGCATTTCAG
* *
21678 GGAGAGAAGACTTCTAAGAAAAGCCAGGATAGCATGGCCGGTGCATTGGAGAGTAGTGAAATTCT
1 GGAGAGAAGACTTGTAA-AAAAGCCAGGATAGCAAGGCC--TGC-TTGGAGAGTAGTGAAATT-T
21743 TAACATTGACCAGGCATTTCAG
61 TAACATTGACCAGGCATTTCAG
* * *
21765 GAAGAGAAGACTTGTAAAAACAGCCAGGATAGCAAGG-CT--TTGGAGGGTAGTGAAATTTTTGA
1 GGAGAGAAGACTTGTAAAAA-AGCCAGGATAGCAAGGCCTGCTTGGAGAGTAGTGAAA-TTTTAA
21827 CATTGACCAGGCATTTCAG
64 CATTGACCAGGCATTTCAG
*
21846 GGAGAGAAGACTTGTAAAGAAAGCCAGGACAGCAA
1 GGAGAGAAGACTTGTAAA-AAAGCCAGGATAGCAA
21881 AGCTGTTGCT
Statistics
Matches: 181, Mismatches: 18, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
81 67 0.37
82 4 0.02
84 1 0.01
86 4 0.02
87 104 0.57
88 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (82 bp):
GGAGAGAAGACTTGTAAAAAAGCCAGGATAGCAAGGCCTGCTTGGAGAGTAGTGAAATTTTAACA
TTGACCAGGCATTTCAG
Found at i:21845 original size:81 final size:80
Alignment explanation
Indices: 21633--21880 Score: 316
Period size: 81 Copynumber: 3.0 Consensus size: 80
21623 CAAGGCCATT
* * * * *
21633 GCTTTGGAGATTAGTGAGATTTCTAACATTGACCAGGCACTTCAGGGAGAGAAGACTTCTAAGAA
1 GCTTTGGAGAGTAGTGAAATTTTTAACATTGACCAGGCATTTCAGGGAGAGAAGACTTGTAA-AA
*
21698 AAGCCAGGATAGCATG
65 AAGCCAGGATAGCAAG
* *
21714 GCCGGTGCATTGGAGAGTAGTGAAATTCTTAACATTGACCAGGCATTTCAGGAAGAGAAGACTTG
1 G-C--T---TTGGAGAGTAGTGAAATTTTTAACATTGACCAGGCATTTCAGGGAGAGAAGACTTG
21779 TAAAAACAGCCAGGATAGCAAG
60 TAAAAA-AGCCAGGATAGCAAG
* *
21801 GCTTTGGAGGGTAGTGAAATTTTTGACATTGACCAGGCATTTCAGGGAGAGAAGACTTGTAAAGA
1 GCTTTGGAGAGTAGTGAAATTTTTAACATTGACCAGGCATTTCAGGGAGAGAAGACTTGTAAA-A
*
21866 AAGCCAGGACAGCAA
65 AAGCCAGGATAGCAA
21881 AGCTGTTGCT
Statistics
Matches: 146, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
81 70 0.48
82 3 0.02
84 2 0.01
86 4 0.03
87 67 0.46
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.22
Consensus pattern (80 bp):
GCTTTGGAGAGTAGTGAAATTTTTAACATTGACCAGGCATTTCAGGGAGAGAAGACTTGTAAAAA
AGCCAGGATAGCAAG
Found at i:29583 original size:32 final size:31
Alignment explanation
Indices: 29500--29583 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
29490 ACATTTCGCA
* *
29500 TGCCACGTGTCACTTTTTGGTACATGTGGCG
1 TGCCACATGTCACTTTTTGGTACAGGTGGCG
* * *
29531 TGACATATGTCA-TTTTTGGTACAGGTGGTG
1 TGCCACATGTCACTTTTTGGTACAGGTGGCG
29561 TGCCACATGTCACTTATTTGGTA
1 TGCCACATGTCACTT-TTTGGTA
29584 TACGTGGCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 26 0.59
31 11 0.25
32 7 0.16
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (31 bp):
TGCCACATGTCACTTTTTGGTACAGGTGGCG
Found at i:35894 original size:16 final size:16
Alignment explanation
Indices: 35858--35931 Score: 114
Period size: 16 Copynumber: 4.7 Consensus size: 16
35848 CCCGAACCCG
*
35858 ACCCGAACCCG-AAAT
1 ACCCGAACCCGAAAAA
35873 ACCCGAACCCGAAAAA
1 ACCCGAACCCGAAAAA
35889 ACCCGAACCCGAAAAA
1 ACCCGAACCCGAAAAA
* *
35905 TCCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAA
35921 ACCCGAACCCG
1 ACCCGAACCCG
35932 CCCAATTGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
15 11 0.20
16 43 0.80
ACGTcount: A:0.42, C:0.41, G:0.14, T:0.04
Consensus pattern (16 bp):
ACCCGAACCCGAAAAA
Found at i:35901 original size:6 final size:6
Alignment explanation
Indices: 35844--35885 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
35834 ATATCGAAAG
35844 CGAACC CGAACC CG-ACC CGAACC CGAAATACC CGAACC CGAA
1 CGAACC CGAACC CGAACC CGAACC CG--A-ACC CGAACC CGAA
35886 AAAACCCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.16
6 20 0.62
7 1 0.03
8 1 0.03
9 5 0.16
ACGTcount: A:0.36, C:0.45, G:0.17, T:0.02
Consensus pattern (6 bp):
CGAACC
Found at i:52713 original size:6 final size:6
Alignment explanation
Indices: 52695--52738 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
52685 TGGAGGCCGG
* * * *
52695 GGCAGA GGTAGA GGCAGA GGCGGA GGAAGA GGCAGA GGCGGA GG
1 GGCAGA GGCAGA GGCAGA GGCAGA GGCAGA GGCAGA GGCAGA GG
52739 TGGCGGCAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.30, C:0.11, G:0.57, T:0.02
Consensus pattern (6 bp):
GGCAGA
Found at i:52720 original size:18 final size:18
Alignment explanation
Indices: 52699--52750 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
52689 GGCCGGGGCA
52699 GAGGTAGAGGCAGAGGCG
1 GAGGTAGAGGCAGAGGCG
*
52717 GAGGAAGAGGCAGAGGCG
1 GAGGTAGAGGCAGAGGCG
* *
52735 GAGGTGGCGGCAGAGG
1 GAGGTAGAGGCAGAGG
52751 ACGTGGCGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.12, G:0.58, T:0.04
Consensus pattern (18 bp):
GAGGTAGAGGCAGAGGCG
Found at i:55255 original size:330 final size:329
Alignment explanation
Indices: 54561--56267 Score: 2402
Period size: 330 Copynumber: 5.2 Consensus size: 329
54551 ATGAATTTCA
* * * * * * *
54561 GGGCACCGGCTCAGTTTTCCATGAATTTTGTCGTCGAAACTCCTTG-AATATCTATATTTATCTA
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
* * * *
54625 ATC-AATC-CTACGACACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCTTGTTTCGA
66 ATCAAATCTC-A-GCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTG-TTCGA
* * * * *
54688 TTTAATCAGAAATTAATTT-TAAAAAA-AGGAAAAAAC-TATTTGAAGCATGATAGGCCCATAAA
128 TTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCCCATAAA
* * * * * *
54750 TCTTTAAGACGTTGAATTATATATTTTTTATGAGTATTTTAGTCAAGAATTGAGAAAAAACATTT
193 TTTTTAA-A-GTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATATTT
* * * *
54815 CGGATCAATTTTTTGCAAAATTTTAGCCGAAATTGTGTACAAACCATCACAGTTTCTGGCTAAAA
256 CGGTTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACAAACCATCACGGTTTCTGGCTGAAA
*
54880 ACGAGTTCCG
320 ACGAGATCCG
* *
54890 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCTATATTCATCTT
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
* *
54955 ATCAAATCTCAGCCCCATTGGATTTAAGGATTTGCTTTTATGAGCATCTGAATCCTGTTCGATTT
66 ATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTCGATTT
55020 AATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCCCATAAATTT
131 AATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCCCATAAA--T
55085 TTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATATTTCGG
194 TTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATATTTCGG
*
55150 TTCAATTTTTGCAAAATTTTAGCCGAAATCGTCTACAAACCATCACGGTTTCTGGCTGAAAACGA
259 TTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACAAACCATCACGGTTTCTGGCTGAAAACGA
55215 GATCCG
324 GATCCG
*
55221 GGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCTTTGAAATATATATATTCATCTA
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
* * * * * *
55285 ATCAAATCTCAGTCCCATGGGATTTAAGGATTTATTTTTGTGAGCATTTGAATCTTGTTCAATTT
66 ATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTCGATTT
* *
55350 AATCAGAAATTAATTTGGAAAAAATAGGAAAAACTATATTTTAAGCATGGA-AAGCCCATAAATA
131 AATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCAT-GACAAGCCCATAAATT
* * * ** * *
55414 TTTAAGACGTTGGATTATATATTTTTCATGAGTATTTTATTCAAGAATTTAGGAAAAATATTTCG
195 TTTAA-A-GTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATATTTCG
* **
55479 GTTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTACGTTA-CATCACGGTTTCTGGCTGAAAAC
258 GTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-AAACCATCACGGTTTCTGGCTGAAAAC
55543 GAGATCCG
322 GAGATCCG
* * *
55551 GGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGTTGATACTCCTTGAAATATATATATATATTCG
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTG--A-A-ATATATATATTCA
* * * *
55615 TCTAATCAAATCTCAGTCCCATGGGATTTAAGAATTTGTTTTTATGAGCATCTGAATCTTATTCG
62 TCTAATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTCG
* *
55680 ATTTAATCAGAAAATAATTTGGAAAAAATAGGAAAACCCATATTTTAAGCATGACAAGCCCATAA
127 ATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCCCATAA
* * *
55745 A-TTTTGAAGTTGAATTATATA-TTTTTATGAGTATTGTGGCCAAAATTTGAGGAAAAATATTTC
192 ATTTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATATTTC
* *
55808 GGTTCAATTTTTGCATAATTTTAGCCGAAATCGAGTA-ATAACCATCACGGTTTCTGGCTGAAAA
257 GGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACA-AACCATCACGGTTTCTGGCTGAAAA
55872 CGAGATCCG
321 CGAGATCCG
* * *
55881 GGGCCCCGGCTCAATTTTGCATGATTTTTGGCGTCGTGACTCCTTGAAATATTTATATTCATCTA
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
* * *
55946 ATCAAATCTCAGCCCCATTGGATATAAGGATTTGTTTTTATGAGAATCTTAATCTTGTTCGATTT
66 ATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTCGATTT
* * *
56011 AATTAGAAATTAATTTGGAAAAAATAGGAAAAACCATACTTTAAGCATGAAAAGCCCATAAATTT
131 AATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCCCATAAA--T
*
56076 TTTTGAAGTTGAATTATATA-TTTTTATGAGTATTCG--GCCAAAAATTGAGGAAAAATATTTCG
194 TTTTAAAGTTGAATTATATATTTTTTATGAGTATT-GTAGCCAAAAATTGAGGAAAAATATTTCG
* *
56138 GTTCAATTTTTGCAAAATTTTAGCCGAAATCGAGTACTAACCATCACGGTTTCTGGCTGAAAACG
258 GTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACAAACCATCACGGTTTCTGGCTGAAAACG
*
56203 AGATTCG
323 AGATCCG
* *
56210 GGGTCCCGGCTCAGTTTTGCATGATTTTTGTCGTCGAGACTCCTTGAAATATATATAT
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATAT
56268 AAATATATAT
Statistics
Matches: 1243, Mismatches: 110, Indels: 50
0.89 0.08 0.04
Matches are distributed among these distances:
327 130 0.10
328 7 0.01
329 214 0.17
330 532 0.43
331 132 0.11
332 83 0.07
333 8 0.01
334 137 0.11
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (329 bp):
GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
ATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTCGATTT
AATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCCCATAAATTT
TTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATATTTCGGTT
CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACAAACCATCACGGTTTCTGGCTGAAAACGAGA
TCCG
Found at i:56021 original size:661 final size:659
Alignment explanation
Indices: 54561--57408 Score: 2806
Period size: 661 Copynumber: 4.2 Consensus size: 659
54551 ATGAATTTCA
* * * * * * *
54561 GGGCACCGGCTCAGTTTTCCATGAATTTTGTCGTCGAAACTCCTTG-AATATCTATATTTATCTA
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
* * * *
54625 ATC-AATC-CTACGACACATTGGATTTAAGGATTTGTTTTTACGACCATCTGAATCTTGTTTCGA
66 ATCAAATCTC-A-GACCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTTAATCTTG-TTCGA
* * *
54688 TTTAATCAGAAATTAATTT-TAAAAAA-AGGAAAAA-ACTATTTGAAGCAT-GATAGGCCCATAA
128 TTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACA-TATTTTAAGCATGGA-AAGCCCATAA
* * *
54749 ATCTTTAAGACGTTGAATTATATATTTTTTATGAGTATTTTAGTCAAGAATTGAGAAAAAACATT
191 ATATTTAAGACGTTGAATTATATA-TTTTTATGAGTATTTTAGTCAAGAATTGAGGAAAAATATT
* * * * *
54814 TCGGATCAATTTTTTGCAAAATTTTAGCCGAAATTGTGTACAAACCATCACAGTTTCTGGCTAAA
255 TCGGTTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTGAA
* *
54879 AACGAGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATCT
319 AACGAGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATAT
* *
54944 ATAT-TCATCTTATCAAATCTCAGCCCCATTGGATTTAAGGATTTGCTTTTATGAGCATCTGAAT
384 ATATATCATCTTATCAAATCTCAGCCCCATGGGATTTAAGAATTTGCTTTTATGAGCATCTGAAT
* *
55008 CCTGTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAA
449 CCTATTCGATTTAATCAGAAAATAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAA
55073 GCCCATAAATTTTTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGA
514 GCCCATAAA--TTTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGA
*
55138 AAAATATTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTCTACAAACCATCACGGTTTCT
577 AAAATATTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGACTACAAACCATCACGGTTTCT
55203 GGCTGAAAACGAGATCCG
642 GGCTGAAAACGAGATCCG
*
55221 GGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCTTTGAAATATATATATTCATCTA
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
* * * * *
55285 ATCAAATCTCAGTCCCATGGGATTTAAGGATTTATTTTTGTGAGCAT-TTGAATCTTGTTCAATT
66 ATCAAATCTCAGACCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTT-AATCTTGTTCGATT
55349 TAATCAGAAATTAATTTGGAAAAAATAGGAAAAACTATATTTTAAGCATGGAAAGCCCATAAATA
130 TAATCAGAAATTAATTTGGAAAAAATAGGAAAAAC-ATATTTTAAGCATGGAAAGCCCATAAATA
* * *
55414 TTTAAGACGTTGGATTATATATTTTTCATGAGTATTTTATTCAAGAATTTAGGAAAAATATTTCG
194 TTTAAGACGTTGAATTATATATTTTT-ATGAGTATTTTAGTCAAGAATTGAGGAAAAATATTTCG
* *
55479 GTTCAATTTTTGAAAAATTTTAGCCGAAATCGTGTACGTTA-CATCACGGTTTCTGGCTGAAAAC
258 GTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTCTGGCTGAAAAC
* *
55543 GAGATCCGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCGTTGATACTCCTTGAAATATATATA
322 GAGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATA
* *
55607 TAT-ATTCGTCTAATCAAATCTCAGTCCCATGGGATTTAAGAATTTGTTTTTATGAGCATCTGAA
387 TATCA-TC-T-T-ATCAAATCTCAGCCCCATGGGATTTAAGAATTTGCTTTTATGAGCATCTGAA
* *
55671 TCTTATTCGATTTAATCAGAAAATAATTTGGAAAAAATAGGAAAACCCATATTTTAAGCATGACA
448 TCCTATTCGATTTAATCAGAAAATAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACA
* * *
55736 AGCCCATAAA-TTTTGAAGTTGAATTATATA-TTTTTATGAGTATTGTGGCCAAAATTTGAGGAA
513 AGCCCATAAATTTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAA
* *
55799 AAATATTTCGGTTCAATTTTTGCATAATTTTAGCCGAAATCGAGTA-ATAACCATCACGGTTTCT
578 AAATATTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGACTACA-AACCATCACGGTTTCT
55863 GGCTGAAAACGAGATCCG
642 GGCTGAAAACGAGATCCG
* * *
55881 GGGCCCCGGCTCAATTTTGCATGATTTTTGGCGTCGTGACTCCTTGAAATATTTATATTCATCTA
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
* * *
55946 ATCAAATCTCAGCCCCATTGGATATAAGGATTTGTTTTTATGAGAATCTTAATCTTGTTCGATTT
66 ATCAAATCTCAGACCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTTAATCTTGTTCGATTT
* * * *
56011 AATTAGAAATTAATTTGGAAAAAATAGGAAAAACCATACTTTAAGCATGAAAAGCCCATAAATTT
131 AATCAGAAATTAATTTGGAAAAAATAGGAAAAA-CATATTTTAAGCATGGAAAGCCCATAAATAT
** * ** * *
56076 TTTTGAAGTTGAATTATATATTTTTATGAGTA-TTCGGCCAAAAATTGAGGAAAAATATTTCGGT
195 TTAAGACGTTGAATTATATATTTTTATGAGTATTTTAGTCAAGAATTGAGGAAAAATATTTCGGT
*
56140 TCAATTTTTGCAAAATTTTAGCCGAAATCGAGTACTAACCATCACGGTTTCTGGCTGAAAACGAG
260 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTGAAAACGAG
* * *
56205 ATTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGTCGTCGAGACTCCTTGAAATATATATATA-
325 ATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATAT
* * * * ** **** * * ** * *
56269 AATATATAT-ATATGTGTG-TGTGTGTGTATATATATATATATATATATATTCATCTAATCA-AA
390 CATCT-TATCAAATCTCAGCCCCATG-GGAT-T-TA-AGA-AT-T-T-GCTT--T-T-ATGAGCA
* * * * ** ***
56331 TCTCAGTTCC-ATTAGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTCGATTTAATCA
442 TCTGA-ATCCTATTCGATTT-A--A-------TCA-GA--AAAT-AAT-TTG---GAAAAAAT-A
* ** ** ** * * *
56395 -GAAATTA--AT-TTGGAAAAAATAGGA-AAAACCAT--A-TTTT-AAGCATGAA-AAGCCCATA
487 GGAAA-AACCATATT-TTAAGCAT--GACAAGCCCATAAATTTTTAAAG-TTGAATTA---TAT-
* * * * *** ** *
56450 AATATTTAAGACGTTGAAATACATATTTTTCATGAGTATTTTAGTCAAGAATTGAGGAAAAACAT
543 ATTTTTTATGA-G-T---AT---T-GTAGCCA--A--AAATT-G---AG-------GAAAAATAT
** ** *
56515 TTCAGG-TCAATTTTTTGCAAAATTTTAGCAAAAATCGTGTACAAACCATCACGGTTTATGGCTG
584 TTC-GGTTCAA-TTTTTGCAAAATTTTAGCCGAAATCGACTACAAACCATCACGGTTTCTGGCTG
*
56579 AAAACGAGTTCCG
647 AAAACGAGATCCG
* * * * *
56592 GGGCCTCGGCTCAGTTTTGCTTGATTTTTGGCGTCGTGTCTCCTTGAATTA-ACTATATTCATCT
1 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATA-TATATTCATCT
* * *
56656 AATCAAATCTCAGCCCCATTGGATTTAAGGTTTTGTTTTTATGAGCATCTGAATCTTGTTCGATT
65 AATCAAATCTCAGACCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTTAATCTTGTTCGATT
* * * *
56721 TAATCAGGAATTAATTTGGAAAAAATAGGAAAAACAATATTTTAAGCATTGAAAGCCCATAATTT
130 TAATCAGAAATTAATTTGGAAAAAATAGGAAAAAC-ATATTTTAAGCATGGAAAGCCCATAAATA
** * * * * * * * **
56786 TTTTTGATGTTGAATTATATATTCTTTATGAATATTGTGGCCAAAAATTGTGGAAAAATATTTTT
194 TTTAAGACGTTGAATTATATATT-TTTATGAGTATTTTAGTCAAGAATTGAGGAAAAATATTTCG
* * *
56851 GTTCAATTTTTGCACAAA-TTTAGCAGAAATCGTGTACAAACCATCACAGTTTCTGGCTGAAAAC
258 GTTCAATTTTTGCA-AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTGAAAAC
* * *
56915 AAGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGTCGAGACTCCTTGAAATATATTTA
322 GAGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATA
* * * *
56980 T-TCATCTAATCAAATCTCAGCCCCATGGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTT
387 TATCATCTTATCAAATCTCAGCCCCATGGGATTTAAGAATTTGCTTTTATGAGCATCTGAATCCT
* * * * * * * *
57044 GTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACCATA-ATGAAGCATTAAAAACC
452 ATTCGATTTAATCAGAAAATAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCC
* * * * *
57108 CATAAATTTTTTTGAAGTTTAATTATATATTTTTTATGAGTATTGTGGTCAAAAATTGAGAAAAA
517 CATAAA--TTTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAA
* * ** * *
57173 ATATTTCGGTTCAATTTTTGCAAAATTTTAGTCGAAATC-ATGTATTAACCATCACAGTTTTTGG
580 ATATTTCGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGA-CTACAAACCATCACGGTTTCTGG
* *
57237 CTGAAAAC-ACATTTCG
644 CTGAAAACGAGA-TCCG
* * * * * *
57253 GGGCACTGGCTCAGTTTT-CAATGAATTTTGTCGTCGAAACTCCTTGAAATATCTATATTCATCT
1 GGGCCCCGGCTCAGTTTTGC-ATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCT
* ** * * * *
57317 AATCAAATCTCAGGCATATTGGATTTAAGGATTTGCTTTTTACGAGAATCTGAATCTTATTTCGA
65 AATCAAATCTCAGACCCATTGGATTTAAGGATTTG-TTTTTATGAGCATCTTAATCTT-GTTCGA
* *
57382 TTTTATCAGAAATTAATTTGAAAAAAA
128 TTTAATCAGAAATTAATTTGGAAAAAA
57409 AAATACTCCC
Statistics
Matches: 1818, Mismatches: 249, Indels: 239
0.79 0.11 0.10
Matches are distributed among these distances:
655 2 0.00
656 8 0.00
657 3 0.00
658 6 0.00
659 156 0.09
660 291 0.16
661 428 0.24
662 122 0.07
663 35 0.02
664 119 0.07
665 1 0.00
666 14 0.01
667 6 0.00
669 3 0.00
672 1 0.00
673 3 0.00
675 1 0.00
676 2 0.00
677 6 0.00
678 1 0.00
679 2 0.00
680 3 0.00
681 9 0.00
682 11 0.01
683 7 0.00
684 27 0.01
685 18 0.01
686 18 0.01
687 3 0.00
688 4 0.00
689 10 0.01
690 6 0.00
691 2 0.00
692 2 0.00
693 3 0.00
694 1 0.00
695 3 0.00
697 1 0.00
699 4 0.00
700 2 0.00
702 6 0.00
703 15 0.01
704 1 0.00
706 2 0.00
707 1 0.00
708 1 0.00
709 2 0.00
710 17 0.01
711 259 0.14
712 13 0.01
713 152 0.08
714 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (659 bp):
GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATTCATCTA
ATCAAATCTCAGACCCATTGGATTTAAGGATTTGTTTTTATGAGCATCTTAATCTTGTTCGATTT
AATCAGAAATTAATTTGGAAAAAATAGGAAAAACATATTTTAAGCATGGAAAGCCCATAAATATT
TAAGACGTTGAATTATATATTTTTATGAGTATTTTAGTCAAGAATTGAGGAAAAATATTTCGGTT
CAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTCTGGCTGAAAACGAGA
TCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATATATATATC
ATCTTATCAAATCTCAGCCCCATGGGATTTAAGAATTTGCTTTTATGAGCATCTGAATCCTATTC
GATTTAATCAGAAAATAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCATGACAAGCCCATA
AATTTTTAAAGTTGAATTATATATTTTTTATGAGTATTGTAGCCAAAAATTGAGGAAAAATATTT
CGGTTCAATTTTTGCAAAATTTTAGCCGAAATCGACTACAAACCATCACGGTTTCTGGCTGAAAA
CGAGATCCG
Found at i:56273 original size:12 final size:12
Alignment explanation
Indices: 56256--56280 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56246 AGACTCCTTG
56256 AAATATATATAT
1 AAATATATATAT
56268 AAATATATATAT
1 AAATATATATAT
56280 A
1 A
56281 TGTGTGTGTG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATATAT
Found at i:57005 original size:331 final size:330
Alignment explanation
Indices: 56308--57408 Score: 1462
Period size: 331 Copynumber: 3.3 Consensus size: 330
56298 ATATATATAT
** *
56308 ATATATATATTCATCTAATCAAATCTCAGTTCCATTAGATTTAAGGATTTGTTTTTATGAGCATC
1 ATATATATATTCATCTAATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATC
56373 TGAATCTTGTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCA-
66 TGAATCTTGTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCAT
* ** * * * * * *
56437 TGAAAAGCCCATAAATATTTAAGACGTTGAAATACATATTTTTCATGAGTATTTTAGTCAAGAAT
131 TG-AAAGCCCATAAATTTTTTTGAAGTTGAATTATATATTTTT-ATGAGTATTGTGGTCAAAAAT
* * *
56502 TGAGGAAAAACATTTCAGGTCAATTTTTTGCAAAATTTTAGCAAAAATCGTGTACAAACCATCAC
194 TGAGGAAAAATATTTCAGTTCAA-TTTTTGCAAAATTTTAGCAGAAATCGTGTACAAACCATCAC
* * * * * * *
56567 GGTTTATGGCTGAAAACGAGTTCCGGGGCCTCGGCTCAGTTTTGCTTGATTTTTGGCGTCGTGTC
258 AGTTTATGGCTGAAAACAAGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGTCGAGAC
56632 TCCTTGAA
323 TCCTTGAA
* *
56640 TTA-ACTATATTCATCTAATCAAATCTCAGCCCCATTGGATTTAAGGTTTTGTTTTTATGAGCAT
1 ATATA-TATATTCATCTAATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCAT
* *
56704 CTGAATCTTGTTCGATTTAATCAGGAATTAATTTGGAAAAAATAGGAAAAACAATATTTTAAGCA
65 CTGAATCTTGTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCA
* * * *
56769 TTGAAAGCCCATAATTTTTTTTGATGTTGAATTATATATTCTTTATGAATATTGTGGCCAAAAAT
130 TTGAAAGCCCATAAATTTTTTTGAAGTTGAATTATATATT-TTTATGAGTATTGTGGTCAAAAAT
* **
56834 TGTGGAAAAATATTTTTGTTCAATTTTTGCACAAA-TTTAGCAGAAATCGTGTACAAACCATCAC
194 TGAGGAAAAATATTTCAGTTCAATTTTTGCA-AAATTTTAGCAGAAATCGTGTACAAACCATCAC
* *
56898 AGTTTCTGGCTGAAAACAAGATCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGTCGAGAC
258 AGTTTATGGCTGAAAACAAGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGTCGAGAC
56963 TCCTTGAA
323 TCCTTGAA
* *
56971 ATATATTTATTCATCTAATCAAATCTCAGCCCCATGGGATTTAAGGATTTGTTTTTATGAGCATC
1 ATATATATATTCATCTAATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATC
* * *
57036 TGAATCTTGTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACCATA-ATGAAGCAT
66 TGAATCTTGTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCAT
* * *
57100 TAAAAACCCATAAATTTTTTTGAAGTTTAATTATATATTTTTTATGAGTATTGTGGTCAAAAATT
131 TGAAAGCCCATAAATTTTTTTGAAGTTGAATTATATA-TTTTTATGAGTATTGTGGTCAAAAATT
* * * **
57165 GAGAAAAAATATTTCGGTTCAATTTTTGCAAAATTTTAGTC-GAAATCATGTATTAACCATCACA
195 GAGGAAAAATATTTCAGTTCAATTTTTGCAAAATTTTAG-CAGAAATCGTGTACAAACCATCACA
* * * * * *
57229 GTTTTTGGCTGAAAACACA-TTTCGGGGCACTGGCTCAGTTTT-CAATGAATTTT-GTCGTCGAA
259 GTTTATGGCTGAAAACA-AGTTCCGGGGCCCCGGCTCAGTTTTGC-ATGATTTTTGGT-GTCGAG
57291 ACTCCTTGAA
321 ACTCCTTGAA
* * ** * *
57301 ATATCTATATTCATCTAATCAAATCTCAGGCATATTGGATTTAAGGATTTGCTTTTTACGAGAAT
1 ATATATATATTCATCTAATCAAATCTCAGCCCCATTGGATTTAAGGATTTG-TTTTTATGAGCAT
* * *
57366 CTGAATCTTATTTCGATTTTATCAGAAATTAATTTGAAAAAAA
65 CTGAATCTT-GTTCGATTTAATCAGAAATTAATTTGGAAAAAA
57409 AAATACTCCC
Statistics
Matches: 680, Mismatches: 76, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
329 6 0.01
330 216 0.32
331 236 0.35
332 217 0.32
333 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (330 bp):
ATATATATATTCATCTAATCAAATCTCAGCCCCATTGGATTTAAGGATTTGTTTTTATGAGCATC
TGAATCTTGTTCGATTTAATCAGAAATTAATTTGGAAAAAATAGGAAAAACCATATTTTAAGCAT
TGAAAGCCCATAAATTTTTTTGAAGTTGAATTATATATTTTTATGAGTATTGTGGTCAAAAATTG
AGGAAAAATATTTCAGTTCAATTTTTGCAAAATTTTAGCAGAAATCGTGTACAAACCATCACAGT
TTATGGCTGAAAACAAGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGTCGAGACTCC
TTGAA
Done.