Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020577.1 Corchorus olitorius cultivar O-4 contig20610, 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: 169259
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:5820 original size:40 final size:40
Alignment explanation
Indices: 5765--5845 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
5755 AAACGCTAAT
5765 CAATCCCATGAATTCACCACAATACTAATTAAAGCGAACG
1 CAATCCCATGAATTCACCACAATACTAATTAAAGCGAACG
5805 CAATCCCATGAATTCACCACAATACTAATTAAAGCGAACG
1 CAATCCCATGAATTCACCACAATACTAATTAAAGCGAACG
5845 C
1 C
5846 TATTAAGTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (40 bp):
CAATCCCATGAATTCACCACAATACTAATTAAAGCGAACG
Found at i:6133 original size:27 final size:27
Alignment explanation
Indices: 6086--6138 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
6076 AAATCAATTA
6086 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACA-AAAGATAAATCT
*
6114 GAAATCATAAAATAC-CAAGATAAAT
1 GAAATCATAAAA-ACAAAAGATAAAT
6139 AATCAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.39
28 12 0.52
29 2 0.09
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (27 bp):
GAAATCATAAAAACAAAAGATAAATCT
Found at i:7239 original size:13 final size:12
Alignment explanation
Indices: 7220--7257 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
7210 ATATATTTTA
7220 TAAAAAAAAATG
1 TAAAAAAAAATG
*
7232 TAACAAAAAAATA
1 TAA-AAAAAAATG
7245 T-AAAAAAAATG
1 TAAAAAAAAATG
7256 TA
1 TA
7258 CTAGAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (12 bp):
TAAAAAAAAATG
Found at i:7254 original size:11 final size:12
Alignment explanation
Indices: 7218--7253 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
7208 ATATATATTT
7218 TATAAAAAAAAA
1 TATAAAAAAAAA
*
7230 TGTAACAAAAAAA
1 TATAA-AAAAAAA
7243 TATAAAAAAAA
1 TATAAAAAAAA
7254 TGTACTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (12 bp):
TATAAAAAAAAA
Found at i:9011 original size:31 final size:31
Alignment explanation
Indices: 8971--9134 Score: 143
Period size: 31 Copynumber: 5.4 Consensus size: 31
8961 ACACTGTCCG
* *
8971 ACGTGGCATGTCACGTGCACCAAAAAGAGAC
1 ACGTGGCATGTCACGTGTACCAAAAAGTGAC
* * * *
9002 ATGTGGCATGTCATGCGTACCAAAAAGCGAC
1 ACGTGGCATGTCACGTGTACCAAAAAGTGAC
* * *
9033 ACGTGGCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCATGTCACGTGTACCAAAAAGTGAC
* * * *
9064 ATGTGTCACGTCATGTGTACCAAAAAGTGAC
1 ACGTGGCATGTCACGTGTACCAAAAAGTGAC
* * * * *
9095 ACATGACATGCCTCGTGCA-CAAAAAG-GAC
1 ACGTGGCATGTCACGTGTACCAAAAAGTGAC
*
9124 ACGTGCCATGT
1 ACGTGGCATGT
9135 GTCATTTTTT
Statistics
Matches: 105, Mismatches: 28, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
29 11 0.10
30 7 0.07
31 87 0.83
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.18
Consensus pattern (31 bp):
ACGTGGCATGTCACGTGTACCAAAAAGTGAC
Found at i:9068 original size:62 final size:62
Alignment explanation
Indices: 8971--9096 Score: 171
Period size: 62 Copynumber: 2.0 Consensus size: 62
8961 ACACTGTCCG
* * * *
8971 ACGTGGCATGTCACGTGCACCAAAAAGAGACATGTGGCATGTCATGCGTACCAAAAAGCGAC
1 ACGTGGCACGCCACATGCACCAAAAAGAGACATGTGGCACGTCATGCGTACCAAAAAGCGAC
* * * * *
9033 ACGTGGCACGCCACATGTACCAAAAAGTGACATGTGTCACGTCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGCACCAAAAAGAGACATGTGGCACGTCATGCGTACCAAAAAGCGAC
9095 AC
1 AC
9097 ATGACATGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (62 bp):
ACGTGGCACGCCACATGCACCAAAAAGAGACATGTGGCACGTCATGCGTACCAAAAAGCGAC
Found at i:16074 original size:8 final size:8
Alignment explanation
Indices: 16061--16085 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16051 GTGTATGTAT
16061 ATATATCC
1 ATATATCC
16069 ATATATCC
1 ATATATCC
16077 ATATATCC
1 ATATATCC
16085 A
1 A
16086 GCCTCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATCC
Found at i:19080 original size:27 final size:27
Alignment explanation
Indices: 19040--19093 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
19030 TTAATAGGAG
19040 AAATTCTCTAAGTGTCTATTCTT-TTAA
1 AAATTCTCTAAGTGTCTA-TCTTCTTAA
*
19067 AAATTCTCTCAGTGTCTATCTTCTTAA
1 AAATTCTCTAAGTGTCTATCTTCTTAA
19094 TTAACAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (27 bp):
AAATTCTCTAAGTGTCTATCTTCTTAA
Found at i:25328 original size:42 final size:42
Alignment explanation
Indices: 25271--25362 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
25261 ACTGTTAGGC
25271 GATTCGT--AAGTTTGAAAAATTCAAAGGTGAAAGTCCAATT
1 GATTCGTAAAAGTTTGAAAAATTCAAAGGTGAAAGTCCAATT
* ***
25311 GATTCGTAAAAGTTTGAAAATTTTGCAGGTGAAAGTCCAATT
1 GATTCGTAAAAGTTTGAAAAATTCAAAGGTGAAAGTCCAATT
25353 GATTCGTAAA
1 GATTCGTAAA
25363 TCTCCAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 7 0.15
42 39 0.85
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (42 bp):
GATTCGTAAAAGTTTGAAAAATTCAAAGGTGAAAGTCCAATT
Found at i:26741 original size:10 final size:10
Alignment explanation
Indices: 26722--26767 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
26712 ATACCTCAAT
26722 ATATCCGTAA
1 ATATCCGTAA
*
26732 ATATCTGTAA
1 ATATCCGTAA
**
26742 ATATCTATAA
1 ATATCCGTAA
26752 ATATCCGTAA
1 ATATCCGTAA
26762 ATATCC
1 ATATCC
26768 ATATTAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:30174 original size:11 final size:11
Alignment explanation
Indices: 30158--30184 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
30148 TGATTTGATT
30158 TTTTTATTTTA
1 TTTTTATTTTA
30169 TTTTTATTTTA
1 TTTTTATTTTA
30180 TTTTT
1 TTTTT
30185 TTGTATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:30177 original size:24 final size:25
Alignment explanation
Indices: 30134--30186 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
30124 ATTCTTTTCC
30134 TTTTATTTTATAATTGATTTGATTT
1 TTTTATTTTATAATTGATTTGATTT
* * *
30159 TTTTATTTTAT-TTTTATTTTATTT
1 TTTTATTTTATAATTGATTTGATTT
30183 TTTT
1 TTTT
30187 GTATTTGTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (25 bp):
TTTTATTTTATAATTGATTTGATTT
Found at i:36802 original size:21 final size:21
Alignment explanation
Indices: 36778--36860 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
36768 TATTTTAGAT
36778 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
36799 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
36820 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
36842 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
36861 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:36811 original size:25 final size:25
Alignment explanation
Indices: 36780--36828 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
36770 TTTTAGATAT
*
36780 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
36805 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
36829 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:83230 original size:55 final size:54
Alignment explanation
Indices: 83161--83272 Score: 127
Period size: 55 Copynumber: 2.1 Consensus size: 54
83151 AAAGTGCAAC
* * * * * *
83161 ATCTGCAAATCAAACGGGGTGATCAGAGATTACC-ACCTAAAATCACCATAGGTG
1 ATCTGCAAACCAAACGAGCTGATCAGAAATTACCAACC-AAAATCACCAGAAGTG
* *
83215 ATCTGCAAAACCAAACGAGCTGATCTGAAATTACCAACCAAGATCACCAGAAGTG
1 ATCTGC-AAACCAAACGAGCTGATCAGAAATTACCAACCAAAATCACCAGAAGTG
83270 ATC
1 ATC
83273 AAAGATCACC
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
54 6 0.12
55 39 0.81
56 3 0.06
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (54 bp):
ATCTGCAAACCAAACGAGCTGATCAGAAATTACCAACCAAAATCACCAGAAGTG
Found at i:84724 original size:12 final size:12
Alignment explanation
Indices: 84707--84731 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84697 TACTAAATAA
84707 ATTATACAAAAC
1 ATTATACAAAAC
84719 ATTATACAAAAC
1 ATTATACAAAAC
84731 A
1 A
84732 AGGTCAAAGT
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:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTATACAAAAC
Found at i:87208 original size:438 final size:434
Alignment explanation
Indices: 86328--87240 Score: 1093
Period size: 438 Copynumber: 2.1 Consensus size: 434
86318 ACGCTTTAGG
* * **
86328 TTTTTT-TTATTATTTGTCGGATTAAGGTGATTCAGCTGTTTATTAAAAGGTAATTTCATGACTT
1 TTTTTTGTTA-TATTTATCCGATTAAGGTGATTCAGCTGTCGATTAAAAGGTAATTTCATGACTT
** * ** * *
86392 ACAACTTTCATGAAGGACTTAAAAGCCAATTTTCATGTTTCAATTCAAAAAATTACTTCCGAAAT
65 ACAACTTTCATGAAAAACTCAAAAGCCAATTTTCACATTTCAATTCAAAAAAATACTTCCCAAAT
* * * *
86457 TTGGTGATTTTGATTGTCGATCTATTTAATATATCATATAATTTTCGATCAACATGTCCGATTAA
130 TTAGTGATTTTGATTGCCGATCTATTTAATATACCATATAATTTTAGATCAACATGTCCGATTAA
* * * * *
86522 TGTTTCTCAAGTGTCGCTTAAAAGGTTATTGCATGATCTACGACTTTCATGGAGGACCCGAAAGC
195 AGTTTCTCAAATGTCGCTTAAAAGGTTATTACATGATCTACAACTTTCATGAAGGACCCGAAAGC
** ** *
86587 TAAATTTGATATACGGGTTTCATTGAGTGTTTAAAAGGGAATTTTTATGTTTCAAGATCTCAATC
260 TAAATTTGATATACAAGTTTCATTGAGAATTCAAAAGGGAATTTTTATGTTTCAAGATCTCAATC
* * * *
86652 AACAAACATTTTTTTTTATTTTGATTATTTATGAAATGACCTGATATTTTTCTACTTTATACTAC
325 AACAAACA-TTTTTCTTACTTGGATTATTTATCAAATGACCTGATATTTTTCTACTTTATACTAC
* *
86717 TTAGTCCTAACTAATTCTATCTTAAATGATTTAACGCATAAGTTTTATT
389 TTAGTCCTAACAAATTCTATCTTAAATGATTTAACACATAA---TTATT
* * * *
86766 TTTTTTGTTATATTTTTCCGATTAAGGTGATTCAGGTGTCGATTAAAAGGTAATTTCATGATTTC
1 TTTTTTGTTATATTTATCCGATTAAGGTGATTCAGCTGTCGATTAAAAGGTAATTTCATGACTTA
* * *
86831 CAACTTTCATGAAAAACTCAGAAGCCAATTTTTACATTTCAATTCAAAGAAAAATACTTCCCAAC
66 CAACTTTCATGAAAAACTCAAAAGCCAATTTTCACATTTCAATTC-AA-AAAAATACTTCCCAAA
* * * *
86896 TTTAGTGGTTTTGATTGCCGGTCTATTT-A-ATACCATATAATTTTAGATCCACATGTTCGATTA
129 TTTAGTGATTTTGATTGCCGATCTATTTAATATACCATATAATTTTAGATCAACATGTCCGATTA
* * * *
86959 AAGTTAT-TTAAATGTCGGTTAAAAGGTTATTACGTGATCTACAACTTTCATGAAGTACCCGAAA
194 AAGTT-TCTCAAATGTCGCTTAAAAGGTTATTACATGATCTACAACTTTCATGAAGGACCCGAAA
* * *
87023 GCTAAATTTGATCTACAAGTTTCA-TGAAGAATTCAAAAGGGAATTTTTATGTTTGAAGATCTCT
258 GCTAAATTTGATATACAAGTTTCATTG-AGAATTCAAAAGGGAATTTTTATGTTTCAAGATCTCA
*
87087 ATCAACAAACA-TTTTCTTACTTGGATTATTTATCAAATGACCCTCATATATACTTTTCTACTTT
322 ATCAACAAACATTTTTCTTACTTGGATTATTTATCAAATGA-CCT--GATAT--TTTTCTACTTT
* * * * *
87151 ATACTACTTAGTCCTTTACAAATTCTAT-TTTACTCGATTTAACACTTCAATTTTT
382 ATACTACTTAGTCC-TAACAAATTCTATCTTAAAT-GATTTAACACAT-AATTATT
* * *
87206 TTTCTTTGTTCTATTTATCCAATTAAGGTAATTCA
1 TTT-TTTGTTATATTTATCCGATTAAGGTGATTCA
87241 TGAAGCACTA
Statistics
Matches: 403, Mismatches: 58, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
436 25 0.06
437 5 0.01
438 239 0.59
439 11 0.03
440 44 0.11
441 56 0.14
442 21 0.05
443 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (434 bp):
TTTTTTGTTATATTTATCCGATTAAGGTGATTCAGCTGTCGATTAAAAGGTAATTTCATGACTTA
CAACTTTCATGAAAAACTCAAAAGCCAATTTTCACATTTCAATTCAAAAAAATACTTCCCAAATT
TAGTGATTTTGATTGCCGATCTATTTAATATACCATATAATTTTAGATCAACATGTCCGATTAAA
GTTTCTCAAATGTCGCTTAAAAGGTTATTACATGATCTACAACTTTCATGAAGGACCCGAAAGCT
AAATTTGATATACAAGTTTCATTGAGAATTCAAAAGGGAATTTTTATGTTTCAAGATCTCAATCA
ACAAACATTTTTCTTACTTGGATTATTTATCAAATGACCTGATATTTTTCTACTTTATACTACTT
AGTCCTAACAAATTCTATCTTAAATGATTTAACACATAATTATT
Found at i:94591 original size:76 final size:76
Alignment explanation
Indices: 94507--94750 Score: 364
Period size: 76 Copynumber: 3.2 Consensus size: 76
94497 CAGAATGGTG
* * *
94507 CCCCCGTTCGCCCACCAGTGAGACAGAGCGTCCACACAGACGCCGCTCACTAAACGGCTGAGTGC
1 CCCCCGTTCGTCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGGCTGAGTGC
94572 CTAGACTGGCA
66 CTAGACTGGCA
* * *
94583 CCCCCGTTCGTCTACCAGTGAGACGGAACGTCCACGCAGACGCCGCTCACTCAACGGCTGAGTGC
1 CCCCCGTTCGTCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGGCTGAGTGC
*
94648 CTAGACTGGCG
66 CTAGACTGGCA
* * * *
94659 CCCCCGTTCGTCTACTAGTGAGACAGAGCATCCACGCAGACGCCGCTCACTCAACGGCTAAGTGC
1 CCCCCGTTCGTCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGGCTGAGTGC
94724 CT-GAACTGGCA
66 CTAG-ACTGGCA
*
94735 CCTCCGTTCGTCCACC
1 CCCCCGTTCGTCCACC
94751 CATGTTGACG
Statistics
Matches: 151, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 1 0.01
76 150 0.99
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (76 bp):
CCCCCGTTCGTCCACCAGTGAGACAGAGCGTCCACGCAGACGCCGCTCACTCAACGGCTGAGTGC
CTAGACTGGCA
Found at i:94944 original size:4 final size:4
Alignment explanation
Indices: 94935--94971 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
94925 ACGGCGTATA
94935 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
94972 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:94976 original size:2 final size:2
Alignment explanation
Indices: 94969--94994 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
94959 AAATAAATAA
94969 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
94995 TGTTTGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98365 original size:41 final size:42
Alignment explanation
Indices: 98287--98368 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 42
98277 AAGACAAGAG
* * *
98287 CTGGAAAATTTGACGAGCGTACGAGAATAAAGCTTAGGAAAA
1 CTGGAAAACTTGACGAACGTACGAGAATAAAACTTAGGAAAA
* * *
98329 CTGGAGAACTTGACGAACG-ACGAGGATAAAATTTAGGAAA
1 CTGGAAAACTTGACGAACGTACGAGAATAAAACTTAGGAAA
98369 TTTCAGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 18 0.53
42 16 0.47
ACGTcount: A:0.43, C:0.12, G:0.27, T:0.18
Consensus pattern (42 bp):
CTGGAAAACTTGACGAACGTACGAGAATAAAACTTAGGAAAA
Found at i:98548 original size:21 final size:22
Alignment explanation
Indices: 98524--98565 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
98514 CCAACTTCCG
98524 AAATTCAAATTTTG-AATTTCA
1 AAATTCAAATTTTGAAATTTCA
*
98545 AAATTCGAATTTTGAAATTTC
1 AAATTCAAATTTTGAAATTTC
98566 GCGCGCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (22 bp):
AAATTCAAATTTTGAAATTTCA
Found at i:100404 original size:31 final size:29
Alignment explanation
Indices: 100353--100412 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 29
100343 ATTAATTAAT
*
100353 GCTTTAATTGGTTTATATATAAGTACAAA
1 GCTTTAATTGGTTTATATATAACTACAAA
100382 GCTTTAATTGGTTTATATATATAACTACAAA
1 GCTTTAATTGG-TT-TATATATAACTACAAA
100413 AGAAGTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 2 0.07
31 15 0.54
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (29 bp):
GCTTTAATTGGTTTATATATAACTACAAA
Found at i:108587 original size:16 final size:15
Alignment explanation
Indices: 108562--108591 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
108552 AGCACTTCAG
108562 GAGACAAATTGTCAT
1 GAGACAAATTGTCAT
108577 GAGAGCAAATTGTCA
1 GAGA-CAAATTGTCA
108592 CGATTTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (15 bp):
GAGACAAATTGTCAT
Found at i:109174 original size:17 final size:17
Alignment explanation
Indices: 109152--109186 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
109142 ACAAATAGTA
109152 GTAGATTGTAAAGAAGT
1 GTAGATTGTAAAGAAGT
109169 GTAGATTGTAAAGAAGT
1 GTAGATTGTAAAGAAGT
109186 G
1 G
109187 ATTTAAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (17 bp):
GTAGATTGTAAAGAAGT
Found at i:116454 original size:13 final size:13
Alignment explanation
Indices: 116436--116465 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
116426 TTGATTTCAC
116436 GTTTATGATTTTT
1 GTTTATGATTTTT
*
116449 GTTTATTATTTTT
1 GTTTATGATTTTT
116462 GTTT
1 GTTT
116466 TTTTTCCAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (13 bp):
GTTTATGATTTTT
Found at i:118987 original size:18 final size:16
Alignment explanation
Indices: 118965--118999 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
118955 CATATTTTTT
*
118965 ATATATTTTTTAAAAA
1 ATATATATTTTAAAAA
118981 ATATATATTTTAAAAA
1 ATATATATTTTAAAAA
118997 ATA
1 ATA
119000 ATTGGGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATATATTTTAAAAA
Found at i:119609 original size:40 final size:40
Alignment explanation
Indices: 119565--119644 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
119555 TTTCACATAA
* *
119565 ATGTTATAATAAATCCTATCCCCCTTACTTATCTAAAATT
1 ATGTTATAATAAATCATATCCCCCTTAATTATCTAAAATT
*
119605 ATGTTATAATAAATCATATCCCCCTTAATTATCTAGAATT
1 ATGTTATAATAAATCATATCCCCCTTAATTATCTAAAATT
119645 GTAACCGCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (40 bp):
ATGTTATAATAAATCATATCCCCCTTAATTATCTAAAATT
Found at i:120721 original size:31 final size:31
Alignment explanation
Indices: 120666--120744 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
120656 GTCCGGTTAT
* *
120666 CTCCACTTGAGGGACC-GAATGCTAGTTTCG
1 CTCCACTTGAGGGACCAAAATGCTAGTTTCA
120696 CTCCACTTGAGGGACCAAAATGCTAGTTTCA
1 CTCCACTTGAGGGACCAAAATGCTAGTTTCA
* *
120727 CTCCACTTAAGAGACCAA
1 CTCCACTTGAGGGACCAA
120745 TTCTGTACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 16 0.36
31 28 0.64
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (31 bp):
CTCCACTTGAGGGACCAAAATGCTAGTTTCA
Found at i:121969 original size:195 final size:196
Alignment explanation
Indices: 121559--122008 Score: 848
Period size: 195 Copynumber: 2.3 Consensus size: 196
121549 AATAAACCCA
* *
121559 TTGTTAACAATACCAAAACTCTGCTCTGCCCTAAGCCCTAAACCCAATTTCTTCTTCTTTTTGCT
1 TTGTTAACAATACCGAATCTCTGCTCTGCCCTAAGCCCTAAACCCAATTTCTTCTTCTTTTTGCT
121624 CTCTCCAATTTTCTGAATTCCCTTCCCTGCAATTCCATCATTATCCCAAAAAAACCCTAAACCCA
66 CTCTCCAATTTTCTGAATTCCCTTCCCTGCAATTCCATCATTATCCCAAAAAAACCCTAAACCCA
*
121689 CTGTTTTCCAGAAATTTTAACTTAGATTTTTTTGTTTCTGGAAAAATCAAAGAAAGCCCTCAAAC
131 CTGTTTTCCAGAAATTTTAACTTAGATTTTTTTGTTTCTAGAAAAATCAAAGAAAGCCCTCAAAC
121754 C
196 C
121755 TTGTTAACAATACCGAATCTCTGCTCTGCCCTAAGCCCTAAACCCAATTTCTTCTTCTTTTTGCT
1 TTGTTAACAATACCGAATCTCTGCTCTGCCCTAAGCCCTAAACCCAATTTCTTCTTCTTTTTGCT
*
121820 CTCTCCAATTTTCTGAATTCCCTTCCCTGCAATTCCATCATTATCCC-AGAAAACCCTAAACCCA
66 CTCTCCAATTTTCTGAATTCCCTTCCCTGCAATTCCATCATTATCCCAAAAAAACCCTAAACCCA
*
121884 CTGTTTTCCAGAAATTTTAACTTAGATTTTTTTGTTTCTAGAAAGATCAAAGAAAGCCCTCAAAC
131 CTGTTTTCCAGAAATTTTAACTTAGATTTTTTTGTTTCTAGAAAAATCAAAGAAAGCCCTCAAAC
121949 C
196 C
121950 TTGTTAACAATACCGAATCTCTGCTCTGCCCTAAGCCCTAAACCCAATTTCTTCTTCTT
1 TTGTTAACAATACCGAATCTCTGCTCTGCCCTAAGCCCTAAACCCAATTTCTTCTTCTT
122009 GTTTCTGACT
Statistics
Matches: 249, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
195 139 0.56
196 110 0.44
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.35
Consensus pattern (196 bp):
TTGTTAACAATACCGAATCTCTGCTCTGCCCTAAGCCCTAAACCCAATTTCTTCTTCTTTTTGCT
CTCTCCAATTTTCTGAATTCCCTTCCCTGCAATTCCATCATTATCCCAAAAAAACCCTAAACCCA
CTGTTTTCCAGAAATTTTAACTTAGATTTTTTTGTTTCTAGAAAAATCAAAGAAAGCCCTCAAAC
C
Found at i:135071 original size:6 final size:6
Alignment explanation
Indices: 135054--135109 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
135044 TAAACTCTTA
*
135054 ACTCCC -CTCCC ACTCCC ACTCCC ACTCCA ACTCCC ACTCCC ACTCCC
1 ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC
135101 ACTCCC ACT
1 ACTCCC ACT
135110 TTTATAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 5 0.11
6 42 0.89
ACGTcount: A:0.18, C:0.64, G:0.00, T:0.18
Consensus pattern (6 bp):
ACTCCC
Found at i:136223 original size:30 final size:30
Alignment explanation
Indices: 136187--136266 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
136177 AGGTTCCGAT
136187 TCCATGTCTGTGTCTATGTGCTCATCGTCC
1 TCCATGTCTGTGTCTATGTGCTCATCGTCC
* *
136217 TCCATGTCTGTGTCTATGAGGTCATCGTCC
1 TCCATGTCTGTGTCTATGTGCTCATCGTCC
136247 TCCATGTCTGTGTCTATGTG
1 TCCATGTCTGTGTCTATGTG
136267 GGCCCTATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (30 bp):
TCCATGTCTGTGTCTATGTGCTCATCGTCC
Found at i:146722 original size:4 final size:4
Alignment explanation
Indices: 146715--146788 Score: 148
Period size: 4 Copynumber: 18.5 Consensus size: 4
146705 TATATAAAAA
146715 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
146763 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
146789 CAAAGAAAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 70 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:162714 original size:15 final size:15
Alignment explanation
Indices: 162694--162724 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
162684 TTCAATAAAA
*
162694 TAATAATTATTTAAT
1 TAATAATTAATTAAT
162709 TAATAATTAATTAAT
1 TAATAATTAATTAAT
162724 T
1 T
162725 TCAGCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:162719 original size:19 final size:18
Alignment explanation
Indices: 162671--162721 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
162661 TGTAAGATTT
162671 TTAATAATAATTATTCAA
1 TTAATAATAATTATTCAA
* *
162689 TAAAATAATAATTATTTAA
1 T-TAATAATAATTATTCAA
162708 TTAATAATTAATTA
1 TTAATAA-TAATTA
162722 ATTTCAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATAATAATTATTCAA
Done.