Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018466.1 Corchorus olitorius cultivar O-4 contig18499, 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: 80085
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1702 original size:69 final size:70
Alignment explanation
Indices: 1562--1722 Score: 229
Period size: 69 Copynumber: 2.3 Consensus size: 70
1552 CAGATCTTGG
* *
1562 CCAAGTCCTGTCCAGGACTTGGGTTGTTGAGGTATGCAGAAATACAGAACAAGACCGGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGTATGCAGAAATACAGAACAAGACCGGGGCAGGA
1627 GTTAC
66 GTTAC
* * *
1632 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGG-A-GC-GCAAATTACAGGACAAGACCTGGGCAG
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGTATGCAG-AAA-TACAGAACAAGACCGGGGCAG
1694 GAGTTAC
64 GAGTTAC
*
1701 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
1723 TGCGGGAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
67 1 0.01
68 5 0.06
69 47 0.57
70 29 0.35
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.21
Consensus pattern (70 bp):
CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGTATGCAGAAATACAGAACAAGACCGGGGCAGGA
GTTAC
Found at i:7112 original size:324 final size:325
Alignment explanation
Indices: 6484--7367 Score: 832
Period size: 324 Copynumber: 2.7 Consensus size: 325
6474 TACTAAAAAC
* * * *
6484 TTTTTAGCCAAAAACTATGATGGTTATTACACGATTTTGGCTAAAATTTTGTTAAAATTGACCGG
1 TTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCAG
*
6549 AAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACACCAAAAATA
66 AAAGTTATTTCCTCAA-TTTT---T--AATACTCATAAAAAATATATAATTCAACACCAAAAATA
* * ** * * * *
6614 TTGAAGGGATTTTTTACGCTTCTAATATCGTTTTTCCTACTTTTTCTGAATTCATCTATTTAAAT
125 TTAAAGGGACTTTCCACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATTAATCTAATTAAAT
* * ** *
6679 CGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATTTAATATAGCTGAGATTTGATTAG
190 CAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATATAGCTGAAATTTGATTAG
* * * * * * *
6744 ATGAATGTGGATATCTCAAAGAGTCTTGGTGGCAAAAATCATGCAAAACTTAGCCGGG-GCCGCG
255 ATGAATATAGACATCTCAAAGAGTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGGGTACC-CG
*
6808 GAACGCA
319 AAACGCA
* * *
6815 TTTTTAGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAGAATTTTG-CAAAATTGACTC-
1 TTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGAC-CA
* * * * *
6878 GAAAGTTATTTCCTCAATTTTT-ATAGTTATAAAAATTATATAATTCAGCGCCCAAAAA-ATTAA
65 GAAAGTTATTTCCTCAATTTTTAATACTCATAAAAAATATATAATTCAAC-ACCAAAAATATTAA
* * * *
6941 AGGG-CTTTCCATGCTTTTAGTATCATTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATC
129 AGGGACTTTCCACGCTTCTAATATCATTTTTCCTACT-TTTTCCGAATTAA--TCTAATTAAATC
* * *** * * * *
7005 AAAACATGATTCAGATGCTTGT-TTGACAAATCCTTAAATCAAATGTGGTTGAAATTTGGTTAGA
191 AAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATATAGCTGAAATTTGATTAGA
* * * *
7069 TGAATATAGACATTTTAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTGAGTCGGGTACCCGAA
256 TGAATATAGACATCTCAAAGAGTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGGGTACCCGAA
*
7134 ACGCG
321 ACGCA
* * * * *
7139 TTTTTAGCAAAAAACCGTGATGGTTAGTACATGATTTCGGTTAAAATTTTGTAAAAAGTT-ACCA
1 TTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAA-TTGACCA
* * * * * * * *
7203 GAAAATTTTTTCCTCAATTTTTGGCTAAAATACTCATTAAATATGTATAATTTAACGCCAAAAAG
65 GAAAGTTATTTCCTCAA-TTTT---T--AATACTCATAAAAAATATATAATTCAACACCAAAAAT
** * * * * * *
7268 ATTTGA-GGACTTTTCACGCTTTTCATATCATTTTTCATATTTTTTCCGACTTAATTTCTAATTA
124 ATTAAAGGGACTTTCCACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATTAA--TCTAATTA
* * *
7332 AATCGAAAGAAGATTCAGATACTCGTAAAAACAAAT
187 AATCAAAACAAGATTCAGATGCTCGTAAAAACAAAT
7368 TTTTTGCTCA
Statistics
Matches: 449, Mismatches: 85, Indels: 37
0.79 0.15 0.06
Matches are distributed among these distances:
322 24 0.05
323 42 0.09
324 137 0.31
325 53 0.12
326 7 0.02
329 5 0.01
330 25 0.06
331 100 0.22
332 56 0.12
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (325 bp):
TTTTTAGCCAAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCAG
AAAGTTATTTCCTCAATTTTTAATACTCATAAAAAATATATAATTCAACACCAAAAATATTAAAG
GGACTTTCCACGCTTCTAATATCATTTTTCCTACTTTTTCCGAATTAATCTAATTAAATCAAAAC
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATATAGCTGAAATTTGATTAGATGAAT
ATAGACATCTCAAAGAGTCTCGGTGCCAAAAATCATGCAAAACTGAGCCGGGTACCCGAAACGCA
Found at i:8102 original size:335 final size:333
Alignment explanation
Indices: 7471--8131 Score: 845
Period size: 335 Copynumber: 2.0 Consensus size: 333
7461 AAACAAATTT
* * * * *
7471 TTAAATCCAATGTGTCTGAGATTTGATTAGATGAATATGAATATCTCAAGGAGTCTTGGCGCCAA
1 TTAAATCCAATGCGGCTGAGATTTGATTAGATAAATATGAATATCTCAAGGAGTCTCGGAGCCAA
* * * * *
7536 AAGTCATGAAAAATTGTGCCGGAGCTCCAGAACGCTTTTTTTATCCAAAAACCGTGATGGTTATT
66 AAATCATGAAAAATTGAGCCGGAGCTCCAGAACGCTGTTTTTAGCCAAAAACCGTGATGGTTAGT
* * * *
7601 ACACGATTTCGGCTAAAATTTTGTAAAAATTAACCCGAAAGATATTTTCTCAAATTTTGGCTAAA
131 ACACGATTTCGACTAAAATTTTGTAAAAAATAACACGAAAGATATTTCCTCAAATTTTGGCTAAA
*
7666 CTACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATC
196 ATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATC
* *
7731 GTTTTTCCTATTTTTTCCAAATGAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
261 GTATTTCCTAATTTTTCCAAATGAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
7796 ACAAACCC
326 ACAAACCC
* * *
7804 TTAAATCCAATGCGGCTGAGATTTGATTAGATAAATAT-AGATATTTCAAGTAGTCTCGGAGTCA
1 TTAAATCCAATGCGGCTGAGATTTGATTAGATAAATATGA-ATATCTCAAGGAGTCTCGGAGCCA
* * *
7868 AAAATCATGCAAAATTGAGCTGG-G-TCCCTGGAACGC-GTTTTTAGCCAAAAACCGTGATGCTT
65 AAAATCATGAAAAATTGAGCCGGAGCT-CC-AGAACGCTGTTTTTAGCCAAAAACCGTGATG---
* * **
7930 TGTTAGTACACGATTTCGACTAAAATTTTGTAAAAAATGACATGAAATG-T-TTCTCCTCATGTT
125 -GTTAGTACACGATTTCGACTAAAATTTTGTAAAAAATAACACGAAA-GATATT-TCCTCAAATT
* * *
7993 TTGTCTAAAATACTCAT-AAAAATATATAATTCAACG-CAAAAAGTATTGTAGGGCTTTTTACGC
187 TTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAG-ATTGAAGGGCTTTTGACG-
* * * *
8056 TTT-TAATATTGTATTTCTTAATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
250 TTTCTAATATCGTATTTCCTAATTTTTCCAAATGAATTTCTAATTAAATCGAAACAAGATTCAGA
*
8120 TGCTCGTAAAAA
315 TACTCGTAAAAA
8132 TAAATTATTA
Statistics
Matches: 282, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
331 1 0.00
332 25 0.09
333 79 0.28
334 7 0.02
335 103 0.37
336 66 0.23
337 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (333 bp):
TTAAATCCAATGCGGCTGAGATTTGATTAGATAAATATGAATATCTCAAGGAGTCTCGGAGCCAA
AAATCATGAAAAATTGAGCCGGAGCTCCAGAACGCTGTTTTTAGCCAAAAACCGTGATGGTTAGT
ACACGATTTCGACTAAAATTTTGTAAAAAATAACACGAAAGATATTTCCTCAAATTTTGGCTAAA
ATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATC
GTATTTCCTAATTTTTCCAAATGAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
ACAAACCC
Found at i:8575 original size:15 final size:16
Alignment explanation
Indices: 8557--8586 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8547 ATAAATAATA
8557 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
8572 ATATTATAATCTAAA
1 ATATTATAATCTAAA
8587 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:10856 original size:7 final size:7
Alignment explanation
Indices: 10844--10875 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
10834 TTCATTACAT
10844 AATAGTA
1 AATAGTA
10851 AATAGTA
1 AATAGTA
10858 AATAGTA
1 AATAGTA
10865 AATAGTA
1 AATAGTA
10872 AATA
1 AATA
10876 ATATTTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
AATAGTA
Found at i:25450 original size:16 final size:16
Alignment explanation
Indices: 25429--25461 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25419 GTTGAGGCAT
25429 GTAGTGAAAGTGAAGG
1 GTAGTGAAAGTGAAGG
*
25445 GTAGTGGAAGTGAAGG
1 GTAGTGAAAGTGAAGG
25461 G
1 G
25462 CAAGAGGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.18
Consensus pattern (16 bp):
GTAGTGAAAGTGAAGG
Found at i:27218 original size:12 final size:12
Alignment explanation
Indices: 27201--27225 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27191 CATTATCTCA
27201 CGAAAGAAATAG
1 CGAAAGAAATAG
27213 CGAAAGAAATAG
1 CGAAAGAAATAG
27225 C
1 C
27226 AATAGTTGTT
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:0.56, C:0.12, G:0.24, T:0.08
Consensus pattern (12 bp):
CGAAAGAAATAG
Found at i:29671 original size:12 final size:12
Alignment explanation
Indices: 29654--29686 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
29644 ATAATATATA
29654 AAAATATAAAAT
1 AAAATATAAAAT
29666 AAAATATAAAAT
1 AAAATATAAAAT
29678 ATAAATATA
1 A-AAATATA
29687 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATATAAAAT
Found at i:30015 original size:17 final size:15
Alignment explanation
Indices: 29994--30023 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29984 GTGTGCATGT
*
29994 ATATATGAGATTTTC
1 ATATATAAGATTTTC
30009 ATATATAAGATTTTC
1 ATATATAAGATTTTC
30024 CTTTTTGGCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (15 bp):
ATATATAAGATTTTC
Found at i:31647 original size:95 final size:95
Alignment explanation
Indices: 31484--31712 Score: 422
Period size: 95 Copynumber: 2.4 Consensus size: 95
31474 TCAACCCGAG
*
31484 ATTCAATCCGAGGCTTTTTCGGCCTTCGAACATAGACGCCGCTACAGCTTCAACCCTATCAACTA
1 ATTCAACCCGAGGCTTTTTCGGCCTTCGAACATAGACGCCGCTACAGCTTCAACCCTATCAACTA
*
31549 CACCCGCATCAATTGCTGCACCAGCCGTAA
66 CACCCGCATCAATTGCTGCACCAGCCGCAA
31579 ATTCAACCCGAGGCTTTTTCGGCCTTCGAACATAGACGCCGCTACAGCTTCAACCCTATCAACTA
1 ATTCAACCCGAGGCTTTTTCGGCCTTCGAACATAGACGCCGCTACAGCTTCAACCCTATCAACTA
*
31644 CACCCGCATCAATTGCTGCACCAGCCGCAG
66 CACCCGCATCAATTGCTGCACCAGCCGCAA
*
31674 ATTCAACCCAAGGCTTTTTCGGCCTTCGAACATAGACGC
1 ATTCAACCCGAGGCTTTTTCGGCCTTCGAACATAGACGC
31713 TAGGAGGTTT
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 130 1.00
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.23
Consensus pattern (95 bp):
ATTCAACCCGAGGCTTTTTCGGCCTTCGAACATAGACGCCGCTACAGCTTCAACCCTATCAACTA
CACCCGCATCAATTGCTGCACCAGCCGCAA
Found at i:32246 original size:26 final size:27
Alignment explanation
Indices: 32210--32260 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
32200 TGAGTTATAT
32210 ATTTATCATGTTTTAG-CCATTCATTA
1 ATTTATCATGTTTTAGCCCATTCATTA
*
32236 ATTTATCATGTTTTGGCCCATTCAT
1 ATTTATCATGTTTTAGCCCATTCAT
32261 CCTCACCCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (27 bp):
ATTTATCATGTTTTAGCCCATTCATTA
Found at i:33204 original size:106 final size:106
Alignment explanation
Indices: 32958--33223 Score: 326
Period size: 106 Copynumber: 2.5 Consensus size: 106
32948 ATTTTTCTAA
* **
32958 CCCTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAGTTATATATTTTAT
1 CCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATATTTTAT
*
33021 TTCTAAAACCCTATAACAATATTATTAATTATAGAATTTAC
66 TTCTAAAACCCTATAACAATATTATAAATTATAGAATTTAC
* * * * *
33062 CCTTAAAATAAAAATAAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTGTAT
1 CCCT----T-AAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATAT
* *
33127 TTTATTTCTAAAACCCTATAATAATAAATTA-AAATTTTTA-AATTT-C
61 TTTATTTCTAAAACCCTATAACAAT--ATTATAAA-TTATAGAATTTAC
33173 CCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
1 CCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
33224 AAGCTAAACT
Statistics
Matches: 138, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
104 3 0.02
106 44 0.32
107 1 0.01
108 1 0.01
109 21 0.15
110 13 0.09
111 40 0.29
112 7 0.05
113 8 0.06
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (106 bp):
CCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATATTATAAATTATAGAATTTAC
Found at i:38894 original size:188 final size:187
Alignment explanation
Indices: 38550--38924 Score: 543
Period size: 188 Copynumber: 2.0 Consensus size: 187
38540 AATGTATTTT
* * * * * * *
38550 GGGTAATTATTTGATACATTGGGGTGTAAATTTTGAACTCTACAAGCGGGTTGTAGAGTTGATAC
1 GGGTAATTATTTGATACATCGCGATGCAAATTTTGAACTCCACAAGCGGGTTGTAGAGCTGACAC
* * *
38615 ATATCCATTTTCTGAATTAATTAAATTTTTAATATTTCAATTTAGTCCCTAGGGGACAAATGTCA
66 ATATCCATTTTCTGAATTAATTAAACTTTAAATATTTCAATCTAGTCCCTAGGGGACAAATGTCA
* * *
38680 CCTTTCAAAACCCGCTTGTGCAGTCTGCTAAATTCCACTGATGGTATATTATATATA
131 CCTTTCAAAACCCGCTTGCGCAGTCTGCTAAACTCCACTAATGGTATATTATATATA
* * *
38737 GGGTAATTATTTGATATATCGACGATGCAAATTTTGGACTCCACAAGCGGGTTGTGGAGCTGACA
1 GGGTAATTATTTGATACATCG-CGATGCAAATTTTGAACTCCACAAGCGGGTTGTAGAGCTGACA
* *
38802 CATGTCCATTTTCTGAATTAATTAAACTTTAAATATTTCAATCTAGTCCCTAGGGGACACATGTC
65 CATATCCATTTTCTGAATTAATTAAACTTTAAATATTTCAATCTAGTCCCTAGGGGACAAATGTC
* * * *
38867 ACCTTTTAAGACCCGTTTGCGCAGTCTGCTAAACTCCACTAATGGTGTATTATATATA
130 ACCTTTCAAAACCCGCTTGCGCAGTCTGCTAAACTCCACTAATGGTATATTATATATA
38925 AGGCAAATTA
Statistics
Matches: 165, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
187 19 0.12
188 146 0.88
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (187 bp):
GGGTAATTATTTGATACATCGCGATGCAAATTTTGAACTCCACAAGCGGGTTGTAGAGCTGACAC
ATATCCATTTTCTGAATTAATTAAACTTTAAATATTTCAATCTAGTCCCTAGGGGACAAATGTCA
CCTTTCAAAACCCGCTTGCGCAGTCTGCTAAACTCCACTAATGGTATATTATATATA
Found at i:53317 original size:6 final size:6
Alignment explanation
Indices: 53306--53336 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
53296 CTTTGAAATC
*
53306 CTTCAT CTTCAT CTTCAT CTCCAT CTTCAT C
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT C
53337 CTCAGAGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.39, G:0.00, T:0.45
Consensus pattern (6 bp):
CTTCAT
Found at i:55403 original size:48 final size:47
Alignment explanation
Indices: 55349--55441 Score: 177
Period size: 48 Copynumber: 2.0 Consensus size: 47
55339 AGTTTTTCTA
55349 ATAGGGAAAAGCAAGTTTAGGTTTTATCCTTTTAACCTCTAAAATAAT
1 ATAGGGAAAAGCAAGTTTAGGTTTTATCCTTTTAACCTC-AAAATAAT
55397 ATAGGGAAAAGCAAGTTTAGGTTTTATCCTTTTAACCTCAAAATA
1 ATAGGGAAAAGCAAGTTTAGGTTTTATCCTTTTAACCTCAAAATA
55442 TTATTTTAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 6 0.13
48 39 0.87
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (47 bp):
ATAGGGAAAAGCAAGTTTAGGTTTTATCCTTTTAACCTCAAAATAAT
Found at i:56350 original size:85 final size:85
Alignment explanation
Indices: 56207--56376 Score: 286
Period size: 85 Copynumber: 2.0 Consensus size: 85
56197 TGATGTCAAG
* *
56207 GACATACAGAGAACATAGACCACCATATTATCAATAAAGAAACTAAAAACTAATGAAAGGTATGA
1 GACATACAGAGAACATAGACCACCATAATATCAATAAAGAAACTAAAAACTAATGAAAGGAATGA
*
56272 CTCTGATCAAGGGAACCAAC
66 CTCTGATCAAGGAAACCAAC
* * *
56292 GACATATAGAGAACATAGACCACCATAATATCCATGAAGAAACTAAAAACTAATGAAAGGAATGA
1 GACATACAGAGAACATAGACCACCATAATATCAATAAAGAAACTAAAAACTAATGAAAGGAATGA
56357 CTCTGATCAAGGAAACCAAC
66 CTCTGATCAAGGAAACCAAC
56377 TTTGAAGAAG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (85 bp):
GACATACAGAGAACATAGACCACCATAATATCAATAAAGAAACTAAAAACTAATGAAAGGAATGA
CTCTGATCAAGGAAACCAAC
Found at i:66648 original size:18 final size:19
Alignment explanation
Indices: 66610--66652 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
66600 ACTGAGACTC
66610 AAACT-AACTGACTCAACA
1 AAACTGAACTGACTCAACA
66628 AAACTGAACTGACTCAA-A
1 AAACTGAACTGACTCAACA
66646 AAACTGA
1 AAACTGA
66653 CTAAACCCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.51, C:0.23, G:0.09, T:0.16
Consensus pattern (19 bp):
AAACTGAACTGACTCAACA
Found at i:68022 original size:126 final size:127
Alignment explanation
Indices: 67789--68047 Score: 373
Period size: 126 Copynumber: 2.0 Consensus size: 127
67779 ATTTAAGAAA
67789 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGT---AATAAAA
* *
67854 TAGGTATAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAA
63 T--GCATAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
67919 AG
126 AG
* *
67921 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTTTAATTAAAATAGTAAAATGGT-A-AAAA
1 TATATTTAAAAAATTCTAATATATATAAG---TTTTTAAAATAAAATAGTAAAATGGTAATAAAA
*
67984 T-CATAAA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
63 TGCATAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
68047 T
1 T
68048 TTAAACAATG
Statistics
Matches: 119, Mismatches: 5, Indels: 12
0.88 0.04 0.09
Matches are distributed among these distances:
126 55 0.46
127 5 0.04
130 5 0.04
131 1 0.01
132 29 0.24
135 24 0.20
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAAAATAAAATAGTAAAATGGTAATAAAATGC
ATAAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:71158 original size:32 final size:32
Alignment explanation
Indices: 71122--71186 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
71112 TACTTCTAAA
71122 TAGAATAGTTCAATTTGATAGTGATATGTAAT
1 TAGAATAGTTCAATTTGATAGTGATATGTAAT
71154 TAGAATAGTTCAATTTGATAGTGATATGTAAT
1 TAGAATAGTTCAATTTGATAGTGATATGTAAT
71186 T
1 T
71187 TCATATTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (32 bp):
TAGAATAGTTCAATTTGATAGTGATATGTAAT
Found at i:71354 original size:22 final size:22
Alignment explanation
Indices: 71329--71411 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 22
71319 TTCGGGGAGT
*
71329 TTATCACAATTTCATAAGGTAA
1 TTATCAAAATTTCATAAGGTAA
* * **
71351 TTATGAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAAGGTAA
* * *
71373 TTATCAAAATTTCATATGATGA
1 TTATCAAAATTTCATAAGGTAA
* *
71395 TAATCAAAATTTTATAA
1 TTATCAAAATTTCATAA
71412 AAATTATTAA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGTAA
Found at i:71609 original size:13 final size:13
Alignment explanation
Indices: 71593--71636 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
71583 AAATAATTTT
71593 AAAATTAAATTAA
1 AAAATTAAATTAA
71606 AAAA-T---TTAA
1 AAAATTAAATTAA
71615 AAAATTAAATTAA
1 AAAATTAAATTAA
*
71628 AAATTTAAA
1 AAAATTAAA
71637 GAATCAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
12 1 0.04
13 16 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTAAATTAA
Found at i:71631 original size:21 final size:22
Alignment explanation
Indices: 71593--71636 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
71583 AAATAATTTT
71593 AAAATTAAATTAAAAAATTTAA
1 AAAATTAAATTAAAAAATTTAA
71615 AAAATTAAATT-AAAAATTTAA
1 AAAATTAAATTAAAAAATTTAA
71636 A
1 A
71637 GAATCAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATTAAATTAAAAAATTTAA
Found at i:74973 original size:31 final size:31
Alignment explanation
Indices: 74935--74999 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
74925 CATGTTTACT
74935 AAGTGGTCATCTGAGTTCAAAATTCAATTCC
1 AAGTGGTCATCTGAGTTCAAAATTCAATTCC
74966 AAGTGGTCATCTGAGTTCAAAATTCAATTCC
1 AAGTGGTCATCTGAGTTCAAAATTCAATTCC
74997 AAG
1 AAG
75000 GGCTGGGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (31 bp):
AAGTGGTCATCTGAGTTCAAAATTCAATTCC
Found at i:77103 original size:29 final size:29
Alignment explanation
Indices: 77029--77108 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
77019 TAAGTTCTCT
77029 TCAAAATCCAAATTTAGATCA-T-TATGA
1 TCAAAATCCAAATTTAGATCATTATATGA
* *
77056 --ATTATTCCAAATTTAGATCATTATATGA
1 TCA-AAATCCAAATTTAGATCATTATATGA
77084 TCAAAATCCAAATTTAGATCATTAT
1 TCAAAATCCAAATTTAGATCATTAT
77109 TATTATGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 16 0.36
27 1 0.02
28 5 0.11
29 20 0.45
30 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (29 bp):
TCAAAATCCAAATTTAGATCATTATATGA
Found at i:77119 original size:29 final size:28
Alignment explanation
Indices: 77032--77119 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
77022 GTTCTCTTCA
*
77032 AAATCCAAATTTAGATCATTATGAATTAT
1 AAATCCAAATTTAGATCATTAT-TATTAT
*
77061 ---TCCAAATTTAGATCATTA-TATGAT
1 AAATCCAAATTTAGATCATTATTATTAT
77085 CAAAATCCAAATTTAGATCATTATTATTAT
1 --AAATCCAAATTTAGATCATTATTATTAT
77115 GAAAT
1 -AAAT
77120 ACTAAAAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
24 4 0.08
26 18 0.37
29 22 0.45
30 5 0.10
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (28 bp):
AAATCCAAATTTAGATCATTATTATTAT
Found at i:79350 original size:2 final size:2
Alignment explanation
Indices: 79345--79369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
79335 TGATGATTAC
79345 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
79370 CTAAACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79723 original size:104 final size:104
Alignment explanation
Indices: 79541--79744 Score: 302
Period size: 104 Copynumber: 2.0 Consensus size: 104
79531 AATGATCAGT
*
79541 ACCGCTTCCCTCAATTTCCTATATAAGTTGTGAATCTTCATCTCTCTCAATAGTTTCCTCTGTTT
1 ACCGCTTCCCTCAATTTCCTATATAAATTGTGAATCTTCATCTCTCTCAATAGTTTCCTCTGTTT
* * *
79606 TTTTCTCTTTCTTTTTGCTCCGCTTCTCCTTGATTCTGC
66 TTTTCTCTCTCTTTTTGCTCCGATTCTCCTAGATTCTGC
* * * * * *
79645 ACCGCTTCCCTCAATTTCTTATATAAATCT-TGTATCTTCATCTCTCTCGATGGTTTTCTTTGTT
1 ACCGCTTCCCTCAATTTCCTATATAAAT-TGTGAATCTTCATCTCTCTCAATAGTTTCCTCTGTT
79709 TTTTTCTCTCTCTTTTTGCTCCGATTCTCCTAGATT
65 TTTTTCTCTCTCTTTTTGCTCCGATTCTCCTAGATT
79745 TTCTCTGTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
104 88 0.99
105 1 0.01
ACGTcount: A:0.14, C:0.27, G:0.09, T:0.50
Consensus pattern (104 bp):
ACCGCTTCCCTCAATTTCCTATATAAATTGTGAATCTTCATCTCTCTCAATAGTTTCCTCTGTTT
TTTTCTCTCTCTTTTTGCTCCGATTCTCCTAGATTCTGC
Done.