Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013836.1 Corchorus capsularis cultivar CVL-1 contig13857, 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: 71704
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:135 original size:21 final size:21
Alignment explanation
Indices: 111--154 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
101 TAAAAGTGTA
*
111 AAAAATGGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
*
132 AAAACTAGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
153 AA
1 AA
155 CATCCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCGGTATTTAGC
Found at i:5371 original size:22 final size:22
Alignment explanation
Indices: 5327--5372 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5317 CACTGTCACA
* * *
5327 TGCAATACACGTGCATCGTACG
1 TGCAATACACGTCCAACGCACG
*
5349 TGCAATGCACGTCCAACGCACG
1 TGCAATACACGTCCAACGCACG
5371 TG
1 TG
5373 GAAGTGAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (22 bp):
TGCAATACACGTCCAACGCACG
Found at i:5707 original size:42 final size:43
Alignment explanation
Indices: 5637--5723 Score: 133
Period size: 42 Copynumber: 2.0 Consensus size: 43
5627 ATTAATTCCT
5637 ATGTAATATATATAGTAATAAATAAAATACTTACATTAATTAA
1 ATGTAATATATATAGTAATAAATAAAATACTTACATTAATTAA
* *
5680 ATGTAATA-ATACTA-TAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATA-TAGTAATAAATAAAATACTTACATTAATTAA
5722 AT
1 AT
5724 TCTTAGGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 31 0.76
43 10 0.24
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.37
Consensus pattern (43 bp):
ATGTAATATATATAGTAATAAATAAAATACTTACATTAATTAA
Found at i:6583 original size:36 final size:36
Alignment explanation
Indices: 6536--6606 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
6526 TGAGATTTTG
6536 AAGAAATATGATAA-TCAAAATTACAAAAAATGTAAT
1 AAGAAATATGATAACT-AAAATTACAAAAAATGTAAT
6572 AAGAAATATGATAACTAAAATTACAAAAAATGTAA
1 AAGAAATATGATAACTAAAATTACAAAAAATGTAA
6607 GGTTATTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.24
Consensus pattern (36 bp):
AAGAAATATGATAACTAAAATTACAAAAAATGTAAT
Found at i:7369 original size:186 final size:181
Alignment explanation
Indices: 7060--7410 Score: 522
Period size: 186 Copynumber: 1.9 Consensus size: 181
7050 TACAAATGTT
**
7060 ATTAAGAATGTAAGGATTGATAAATACAATTTTAAAAACTTTTATAATTTTTTTAGTAGATTACT
1 ATTAAGAATGTAAGGATTGATAAATACAATTTTAAAAACTTTTATAATTTTAGTAGTAGATTACT
* *
7125 CAAGTTATTAAATTGGTAACTTTCATTATTGATCATAAAAAGTTACTAAAATTAATAAGGATGTA
66 CAAGTAATTAAATTGGTAACTTTCATTATTGATCATAAAAAATTACTAAAATTAATAAGGATGTA
* *
7190 GGATTACTTGAATCTAGATAGTACTATAATATTTTTCGGCAAAAAAAAAAA
131 AGATTACTTGAATCTAGATAGTAATATAATATTTTTCGGCAAAAAAAAAAA
* * * * * *
7241 ATTAAGAATGTGAGGATTGGTAAATACAATTTTAATAACTTTTTTAGCCTATTTAGTAGATTATA
1 ATTAAGAATGTAAGGATTGATAAATACAATTTTAAAAACTTTTATA--AT-TTTAGTAG--TAGA
*
7306 TTACTTAAGTAATTAAATTGGTAACTTTCATTATTGATCATAAAAAATTACTAAAATTAATAAGG
61 TTACTCAAGTAATTAAATTGGTAACTTTCATTATTGATCATAAAAAATTACTAAAATTAATAAGG
* *
7371 ATGTAAGATTATTTGAATCTAGATAGTAATATAATGTTTT
126 ATGTAAGATTACTTGAATCTAGATAGTAATATAATATTTT
7411 CATAACTTTT
Statistics
Matches: 150, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
181 42 0.28
183 1 0.01
184 6 0.04
186 101 0.67
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.39
Consensus pattern (181 bp):
ATTAAGAATGTAAGGATTGATAAATACAATTTTAAAAACTTTTATAATTTTAGTAGTAGATTACT
CAAGTAATTAAATTGGTAACTTTCATTATTGATCATAAAAAATTACTAAAATTAATAAGGATGTA
AGATTACTTGAATCTAGATAGTAATATAATATTTTTCGGCAAAAAAAAAAA
Found at i:7861 original size:57 final size:57
Alignment explanation
Indices: 7773--7885 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
7763 ATAGCATCAT
* *
7773 GCCTCGATCCTAAAATGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
1 GCCTCAATCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
* *
7830 GCCTCAATCCTAAAACGTCTTTTTTATGCATCTAATAAAAAACATGTCACTTGATA
1 GCCTCAATCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
7886 TTTGATTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (57 bp):
GCCTCAATCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
Found at i:9366 original size:2 final size:2
Alignment explanation
Indices: 9359--9393 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9349 CTTTAACTAG
*
9359 TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9394 GTTTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13996 original size:3 final size:3
Alignment explanation
Indices: 13988--14030 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
13978 AAGTGAATAT
* * *
13988 GAA GAA GAA GAA GAA GAG GAA GAA GAA GAA GAG GAA GAG GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
14031 TCGAAGAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:14011 original size:15 final size:15
Alignment explanation
Indices: 13991--14030 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
13981 TGAATATGAA
13991 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
14006 GAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAG
*
14021 GAAGAGGAAG
1 GAAGAAGAAG
14031 TCGAAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAGAG
Found at i:19839 original size:138 final size:138
Alignment explanation
Indices: 19586--19861 Score: 534
Period size: 138 Copynumber: 2.0 Consensus size: 138
19576 TTTATGTTCG
19586 TTTCCAGTTAACAAAACAGACGACAGTTCAATCTACAGGAGTGGCCTCCAGTTTGGTTGAGATCA
1 TTTCCAGTTAACAAAACAGACGACAGTTCAATCTACAGGAGTGGCCTCCAGTTTGGTTGAGATCA
19651 TACAGGGTGCAGGATTCAAATTACAAACATTAAATTTGAGTTTTGATGATGAAGAGGAAATTCTT
66 TACAGGGTGCAGGATTCAAATTACAAACATTAAATTTGAGTTTTGATGATGAAGAGGAAATTCTT
19716 GTCTAGAA
131 GTCTAGAA
19724 TTTCCAGTTAACAAAACAGACGACAGTTCAATCTACAGGAGTGGCCTCCAGTTTGGTTGAGATCA
1 TTTCCAGTTAACAAAACAGACGACAGTTCAATCTACAGGAGTGGCCTCCAGTTTGGTTGAGATCA
* *
19789 TACAGGGTGCAGGATTCAAATTACAACCATTAAATTTGAGTTTTGGTGATGAAGAGGAAATTCTT
66 TACAGGGTGCAGGATTCAAATTACAAACATTAAATTTGAGTTTTGATGATGAAGAGGAAATTCTT
19854 GTCTAGAA
131 GTCTAGAA
19862 ATCATATTTA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 136 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (138 bp):
TTTCCAGTTAACAAAACAGACGACAGTTCAATCTACAGGAGTGGCCTCCAGTTTGGTTGAGATCA
TACAGGGTGCAGGATTCAAATTACAAACATTAAATTTGAGTTTTGATGATGAAGAGGAAATTCTT
GTCTAGAA
Found at i:22338 original size:15 final size:15
Alignment explanation
Indices: 22312--22348 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
22302 TATTTTGTTT
22312 TATAAT-TAATTATA
1 TATAATATAATTATA
22326 TATAATATAATTATA
1 TATAATATAATTATA
22341 -AT-ATATAA
1 TATAATATAA
22349 ATTTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATATAATTATA
Found at i:22347 original size:20 final size:19
Alignment explanation
Indices: 22312--22368 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
22302 TATTTTGTTT
*
22312 TATAATTA-ATTATATATAA
1 TATAATTATAATATATA-AA
22331 TATAATTATAATATATAAA
1 TATAATTATAATATATAAA
* *
22350 TTTAAAT-TAATATATAAA
1 TATAATTATAATATATAAA
22368 T
1 T
22369 CCATTCGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 12 0.35
19 15 0.44
20 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAATTATAATATATAAA
Found at i:22367 original size:18 final size:18
Alignment explanation
Indices: 22310--22368 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
22300 TATATTTTGT
22310 TTTATAATTAATTATATATAA
1 TTTA-AATTAA-TATATA-AA
* *
22331 TATAATTATAATATATAAA
1 TTTAAAT-TAATATATAAA
22350 TTTAAATTAATATATAAA
1 TTTAAATTAATATATAAA
22368 T
1 T
22369 CCATTCGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 12 0.36
19 7 0.21
20 8 0.24
21 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAATTAATATATAAA
Found at i:23030 original size:19 final size:21
Alignment explanation
Indices: 23006--23056 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 21
22996 GGTGGAGTTT
23006 ATAATTTT-T-TTTATATTTC
1 ATAATTTTATATTTATATTTC
23025 ATAATTTTATATTTATATTT-
1 ATAATTTTATATTTATATTTC
23045 AT-A-TTTATATTT
1 ATAATTTTATATTT
23057 GTTTTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.30
19 9 0.30
20 3 0.10
21 9 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
ATAATTTTATATTTATATTTC
Found at i:23041 original size:6 final size:6
Alignment explanation
Indices: 23015--23056 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
23005 TATAATTTTT
23015 TTTATA TTTCATAA TTTTATA TTTATA TTTATA TTTATA TTT
1 TTTATA TTT-AT-A -TTTATA TTTATA TTTATA TTTATA TTT
23057 GTTTTATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 24 0.73
7 3 0.09
8 3 0.09
9 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:33475 original size:13 final size:13
Alignment explanation
Indices: 33433--33477 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
33423 TCATGCACCC
*
33433 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
33447 AAAACCATTT-AT
1 AAAACAATTTAAT
33459 AAAACAATTTAAT
1 AAAACAATTTAAT
33472 AAAACA
1 AAAACA
33478 GTAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:34740 original size:2 final size:2
Alignment explanation
Indices: 34733--34757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34723 TATTTTATTT
34733 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
34758 TCCTTTCTTT
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:39623 original size:16 final size:17
Alignment explanation
Indices: 39571--39625 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
39561 AAATAATTAT
*
39571 TTTTTCCTTTTCCTTTC
1 TTTTTACTTTTCCTTTC
* *
39588 CTTTTACTTTT-ATTTCC
1 TTTTTACTTTTCCTTT-C
39605 TTTTTA-TTTTCCTTTC
1 TTTTTACTTTTCCTTTC
39621 TTTTT
1 TTTTT
39626 CCCTTTGCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTACTTTTCCTTTC
Found at i:40754 original size:21 final size:21
Alignment explanation
Indices: 40728--40772 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
40718 TTTAACGTGA
*
40728 TTTAACTATCAAACTTTGGGG
1 TTTAACTATCAAAATTTGGGG
40749 TTTAACTATCAAAATTTGGGG
1 TTTAACTATCAAAATTTGGGG
40770 TTT
1 TTT
40773 GACCATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (21 bp):
TTTAACTATCAAAATTTGGGG
Found at i:40874 original size:59 final size:55
Alignment explanation
Indices: 40748--40878 Score: 138
Period size: 55 Copynumber: 2.3 Consensus size: 55
40738 AAACTTTGGG
* * * * *
40748 GTTTAACTATCAAAATTTGGGGTTTGACCATATATATAATAAAATGTTTTTTGTA
1 GTTTCACTATCAAACTTTGGGATTTGACCATATATACAATAAAATGCTTTTTGTA
* *
40803 GTTTCACTATCAAACTTTGGGATTTGACCATGCATGTACAATATTTAATGCTTTTTGT-
1 GTTTCACTATCAAACTTTGGGATTTGACCAT--ATATACAATA--AAATGCTTTTTGTA
*
40861 GATTTGACTATCAAACTT
1 G-TTTCACTATCAAACTT
40879 CAGGGTTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 28 0.44
57 8 0.13
58 1 0.02
59 26 0.41
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (55 bp):
GTTTCACTATCAAACTTTGGGATTTGACCATATATACAATAAAATGCTTTTTGTA
Found at i:41019 original size:48 final size:50
Alignment explanation
Indices: 40941--41039 Score: 175
Period size: 49 Copynumber: 2.0 Consensus size: 50
40931 TTTGACTATA
*
40941 CATGTACAATGATATTTTTGTGGTTTGACTATCAAA-TTTGGGGTTTGAC
1 CATGTACAATGATATTTTTGTGGTTCGACTATCAAACTTTGGGGTTTGAC
40990 CATGTACAATGAT-TTTTTGTGGTTCGACTATCAAACTTTGGGGTTTGAC
1 CATGTACAATGATATTTTTGTGGTTCGACTATCAAACTTTGGGGTTTGAC
41039 C
1 C
41040 TTGCATATAC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 21 0.44
49 27 0.56
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.41
Consensus pattern (50 bp):
CATGTACAATGATATTTTTGTGGTTCGACTATCAAACTTTGGGGTTTGAC
Found at i:41164 original size:76 final size:76
Alignment explanation
Indices: 41018--41168 Score: 196
Period size: 76 Copynumber: 2.0 Consensus size: 76
41008 GTGGTTCGAC
* * * * *
41018 TATCAAACTTTGGGGTTTGACCTTGCATATACAATAAAATGTTTTTGTGGTTTGACTATTAAACT
1 TATCAAAATTCGGGGTTTGACCATGCATATAAAATAAAA-GTTTTTGTGGTTTGACTATCAAACT
*
41083 TTGAGGTTTGCT
65 CTGAGGTTTGCT
* * *
41095 TATCAAAATTCGGGGTTTTATCATGCATATAAAATGAAAA-TTTTTGTGGTTTGACTATCATACT
1 TATCAAAATTCGGGGTTTGACCATGCATATAAAAT-AAAAGTTTTTGTGGTTTGACTATCAAACT
41159 CTGAGGTTTG
65 CTGAGGTTTG
41169 ACCATGCTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
76 31 0.48
77 29 0.45
78 4 0.06
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (76 bp):
TATCAAAATTCGGGGTTTGACCATGCATATAAAATAAAAGTTTTTGTGGTTTGACTATCAAACTC
TGAGGTTTGCT
Found at i:41375 original size:33 final size:35
Alignment explanation
Indices: 41338--41412 Score: 109
Period size: 33 Copynumber: 2.2 Consensus size: 35
41328 TTATTTGGGT
*
41338 TTTGACCATGCATGTACAATG-AT-TTTTTTGAGG
1 TTTGACCATGCATATACAATGAATGTTTTTTGAGG
*
41371 TTTGACCATGCATATACAATGAAATGTTTTTTGTGG
1 TTTGACCATGCATATACAATG-AATGTTTTTTGAGG
41407 TTTGAC
1 TTTGAC
41413 TATCGAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 20 0.54
35 2 0.05
36 15 0.41
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (35 bp):
TTTGACCATGCATATACAATGAATGTTTTTTGAGG
Found at i:41432 original size:111 final size:111
Alignment explanation
Indices: 41254--41488 Score: 298
Period size: 111 Copynumber: 2.1 Consensus size: 111
41244 TACTGTCGAA
* * * *
41254 TTTGGGGTTTGACTATGCATGTACAATGATGTTTTTTTGTGGTTTGACTATTAAACTTTGGAGTT
1 TTTGAGGTTTGACCATGCATATACAATGATGTTTTTTTGTGGTTTGACTATCAAACTTTGGAGTT
* * * * *
41319 TGACCATCAT-TATTTGGGTTTTGACCATGCATGTACAATGAT-TTT
66 TGACCATCATCCA-ATGGGGTTTGACCATGCATGTACAACGATGCTT
*
41364 TTTGAGGTTTGACCATGCATATACAATGAAATG-TTTTTTGTGGTTTGACTATCGAACTTTGG-G
1 TTTGAGGTTTGACCATGCATATACAATG--ATGTTTTTTTGTGGTTTGACTATCAAACTTTGGAG
*
41427 CTTTGACCATCATCCAATGGGGTTTGACTATGCATGTACAACGATGCTT
64 -TTTGACCATCATCCAATGGGGTTTGACCATGCATGTACAACGATGCTT
*
41476 TTTGTGGTTTGAC
1 TTTGAGGTTTGAC
41489 TATTAAACTT
Statistics
Matches: 108, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
110 26 0.24
111 64 0.59
112 18 0.17
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (111 bp):
TTTGAGGTTTGACCATGCATATACAATGATGTTTTTTTGTGGTTTGACTATCAAACTTTGGAGTT
TGACCATCATCCAATGGGGTTTGACCATGCATGTACAACGATGCTT
Found at i:41498 original size:76 final size:77
Alignment explanation
Indices: 41369--41512 Score: 200
Period size: 76 Copynumber: 1.9 Consensus size: 77
41359 ATTTTTTTGA
* * * * *
41369 GGTTTGACCATGCATATACAATGAAATGTTTTTTGTGGTTTGACTATCGAACTTTGGGCTTTGAC
1 GGTTTGACCATGCATATACAACG-AATGCTTTTTGTGGTTTGACTATCAAACTTTGAGATTTGAC
41434 CATCATCCAATGG
65 CATCATCCAATGG
* * *
41447 GGTTTGACTATGCATGTACAACG-ATGCTTTTTGTGGTTTGACTATTAAACTTTGAGATTTGACC
1 GGTTTGACCATGCATATACAACGAATGCTTTTTGTGGTTTGACTATCAAACTTTGAGATTTGACC
41511 AT
66 AT
41513 GCATGTACAG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 38 0.66
78 20 0.34
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (77 bp):
GGTTTGACCATGCATATACAACGAATGCTTTTTGTGGTTTGACTATCAAACTTTGAGATTTGACC
ATCATCCAATGG
Found at i:46341 original size:50 final size:49
Alignment explanation
Indices: 46265--46360 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 49
46255 CACTTCGCTA
* * ** **
46265 TTTCCATTTGGTATTTTAGTTTTAGTGTGTTGGGTTAGTTTATTTAGCT
1 TTTCCATTAGATATTTTAGTTTTAGTGAATTGGACTAGTTTATTTAGCT
46314 TTTCCATTAGATATTTTTAGTTTTAGTGAATTGGACTAGTTTATTTA
1 TTTCCATTAGATA-TTTTAGTTTTAGTGAATTGGACTAGTTTATTTA
46361 ACTCTGGGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 11 0.28
50 29 0.73
ACGTcount: A:0.20, C:0.06, G:0.19, T:0.55
Consensus pattern (49 bp):
TTTCCATTAGATATTTTAGTTTTAGTGAATTGGACTAGTTTATTTAGCT
Found at i:47396 original size:21 final size:21
Alignment explanation
Indices: 47372--47414 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
47362 TTCCCTCAAG
47372 AATTTAAGACTTTTAAAGCTA
1 AATTTAAGACTTTTAAAGCTA
*
47393 AATTTAGGACTTTTAAAGCTA
1 AATTTAAGACTTTTAAAGCTA
47414 A
1 A
47415 CTTAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
AATTTAAGACTTTTAAAGCTA
Found at i:47559 original size:17 final size:15
Alignment explanation
Indices: 47527--47557 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
47517 AATGAATACA
47527 ATATAAATGGACTTT
1 ATATAAATGGACTTT
47542 ATATATAATGGACTTT
1 ATATA-AATGGACTTT
47558 TAGGCAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
ATATAAATGGACTTT
Found at i:49895 original size:22 final size:22
Alignment explanation
Indices: 49868--49914 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
49858 TCGTCACTTC
49868 TCTCTCATTCGTCCATTTTATT
1 TCTCTCATTCGTCCATTTTATT
** *
49890 TCTCTCATTTTTCCATTTTGTT
1 TCTCTCATTCGTCCATTTTATT
49912 TCT
1 TCT
49915 AGATGATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.26, G:0.04, T:0.60
Consensus pattern (22 bp):
TCTCTCATTCGTCCATTTTATT
Found at i:50512 original size:22 final size:22
Alignment explanation
Indices: 50485--50531 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
50475 TCGTCACTTC
50485 TCTCTCATTCGTCCATTTTATT
1 TCTCTCATTCGTCCATTTTATT
* *
50507 TCTCTCATTCTTCCATTTTGTT
1 TCTCTCATTCGTCCATTTTATT
50529 TCT
1 TCT
50532 AGATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.11, C:0.28, G:0.04, T:0.57
Consensus pattern (22 bp):
TCTCTCATTCGTCCATTTTATT
Found at i:53907 original size:22 final size:21
Alignment explanation
Indices: 53860--53907 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
53850 TGTTTCGAAA
53860 TGGTTTATTCGGTTGAGGTGT
1 TGGTTTATTCGGTTGAGGTGT
* *
53881 CGGTTTATTTGGGTT-AGCGTGT
1 TGGTTTA-TTCGGTTGAG-GTGT
53903 TGGTT
1 TGGTT
53908 GTGTGTATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.08, C:0.06, G:0.38, T:0.48
Consensus pattern (21 bp):
TGGTTTATTCGGTTGAGGTGT
Found at i:59832 original size:36 final size:35
Alignment explanation
Indices: 59792--60194 Score: 414
Period size: 36 Copynumber: 11.1 Consensus size: 35
59782 TTCATGCATA
59792 AAGTAAAATCAGTAAAGAACTTAATTCAAGGTAATT
1 AAGTAAAATCAGTAAAG-ACTTAATTCAAGGTAATT
* * *
59828 AAGTAAAATCCGTCAAAGACTTGATTCAAGGTAGTT
1 AAGTAAAATCAGT-AAAGACTTAATTCAAGGTAATT
* * *
59864 AAGTAAACTCAGTCAAAGACTTAGTTCAAGGAAATT
1 AAGTAAAATCAGT-AAAGACTTAATTCAAGGTAATT
* * *
59900 AAGTAAAATCAAGCAAAGGCTTAATTTCAAGGAAATT
1 AAGTAAAATC-AGTAAAGACTTAA-TTCAAGGTAATT
* * *
59937 AAG-AAAACTCAAGCAAATACTTAATTTCAAGGAAATT
1 AAGTAAAA-TC-AGTAAAGACTTAA-TTCAAGGTAATT
* *
59974 AAGTAAAATCAAGCAAAAACTTAATTCAAGGTAATT
1 AAGTAAAATC-AGTAAAGACTTAATTCAAGGTAATT
* *
60010 AAGTAAAATCAAGCAAAGACTTAATTTCAAGGAAATT
1 AAGTAAAATC-AGTAAAGACTTAA-TTCAAGGTAATT
*
60047 AAGTAAAATCAATCAAA-ACTTAATTCAAGGTAATT
1 AAGTAAAATCAGT-AAAGACTTAATTCAAGGTAATT
* * *
60082 GAGTAAGATCAATCAAAGACTTAATTCAAGGTAATT
1 AAGTAAAATCAGT-AAAGACTTAATTCAAGGTAATT
* * * *
60118 AAGTAGAGTCAATAAAGAACTTAATTCAAGGAAATT
1 AAGTAAAATCAGTAAAG-ACTTAATTCAAGGTAATT
* * *
60154 AAGTAAAACCAATAAAGGACTTAATTCAGGGTAATT
1 AAGTAAAATCAGTAAA-GACTTAATTCAAGGTAATT
60190 AAGTA
1 AAGTA
60195 GATTAGAAAA
Statistics
Matches: 323, Mismatches: 34, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
35 30 0.09
36 198 0.61
37 91 0.28
38 4 0.01
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (35 bp):
AAGTAAAATCAGTAAAGACTTAATTCAAGGTAATT
Found at i:63171 original size:21 final size:22
Alignment explanation
Indices: 63146--63190 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
63136 TTAAACTGAA
63146 TTGCTAAAT-ACCGCCCCA-TTT
1 TTGCT-AATCACCGCCCCACTTT
*
63167 TTGCTATTCACCGCCCCACTTT
1 TTGCTAATCACCGCCCCACTTT
63189 TT
1 TT
63191 ACACTTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 14 0.67
22 5 0.24
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAATCACCGCCCCACTTT
Found at i:64160 original size:27 final size:27
Alignment explanation
Indices: 64114--64250 Score: 134
Period size: 27 Copynumber: 5.1 Consensus size: 27
64104 CTTGATGAGT
* * * *
64114 TGAGCGTGCTCAGCCGGGTTACTATGA
1 TGAGGGTGCTGAGCCCGGTTATTATGA
* *
64141 TGAGGGTGTTGAGCACGGTTATTATGA
1 TGAGGGTGCTGAGCCCGGTTATTATGA
*
64168 TGCGGGTGCTGAGCCCGGTTATTATGA
1 TGAGGGTGCTGAGCCCGGTTATTATGA
* * * *
64195 TG-GGGCAGCTCAG-GCGAGTTACTATGA
1 TGAGGG-TGCTGAGCCCG-GTTATTATGA
*
64222 AGAGGGTGCTGAGCCCGGTTATTATGA
1 TGAGGGTGCTGAGCCCGGTTATTATGA
64249 TG
1 TG
64251 GGGCAACTCA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
26 5 0.06
27 77 0.89
28 5 0.06
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.28
Consensus pattern (27 bp):
TGAGGGTGCTGAGCCCGGTTATTATGA
Found at i:66688 original size:38 final size:39
Alignment explanation
Indices: 66646--66727 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
66636 GTTACCGATT
* * * *
66646 TTTTTTGAAAAAA-AAAAAATTTTCTTTTCCGTTTTTCC
1 TTTTTTAAAAAAATAAAAAAATTTATTTTCCGTTTCTCC
* *
66684 TTTTTTAAAAAAATAAAAAAATTTATTTTCTGTTTCTGC
1 TTTTTTAAAAAAATAAAAAAATTTATTTTCCGTTTCTCC
66723 TTTTT
1 TTTTT
66728 ATTTTATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 12 0.32
39 25 0.68
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (39 bp):
TTTTTTAAAAAAATAAAAAAATTTATTTTCCGTTTCTCC
Done.