Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013103.1 Corchorus olitorius cultivar O-4 contig13136, 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: 26955
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:1729 original size:20 final size:21
Alignment explanation
Indices: 1691--1735 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1681 TTTAGCTAAG
1691 CAATAAAGAAAAAGAAAAGAC
1 CAATAAAGAAAAAGAAAAGAC
*
1712 CAATAAAGAAAAA-CAAAGAC
1 CAATAAAGAAAAAGAAAAGAC
1732 CAAT
1 CAAT
1736 CAAGTAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.69, C:0.13, G:0.11, T:0.07
Consensus pattern (21 bp):
CAATAAAGAAAAAGAAAAGAC
Found at i:5861 original size:27 final size:27
Alignment explanation
Indices: 5823--5886 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
5813 AGCAAGAGCT
* *
5823 AAAATGCCCCTGAATGTAAAAATGACC
1 AAAATGCCCCTGAACGTAAAAATGACA
* **
5850 AAAATGCCCCTGGACGTGCAAATGACA
1 AAAATGCCCCTGAACGTAAAAATGACA
5877 AAAATGCCCC
1 AAAATGCCCC
5887 ATAGATGACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.16
Consensus pattern (27 bp):
AAAATGCCCCTGAACGTAAAAATGACA
Found at i:6321 original size:232 final size:232
Alignment explanation
Indices: 5915--6347 Score: 866
Period size: 232 Copynumber: 1.9 Consensus size: 232
5905 GATTAAGAAA
5915 TAAAGTGCTTTAATTTAAAAGGATATGGACAAAAATGGGTGTCTACACCATGTGGGACCTCTCCA
1 TAAAGTGCTTTAATTTAAAAGGATATGGACAAAAATGGGTGTCTACACCATGTGGGACCTCTCCA
5980 CCTTTAAAATCAAGCTAAACCCTAAGCCTCCAAGGCCCAATAAGAACAAAGCCCAAATAGAATAT
66 CCTTTAAAATCAAGCTAAACCCTAAGCCTCCAAGGCCCAATAAGAACAAAGCCCAAATAGAATAT
6045 CTCCTCCACATTGCGCCACTTGTCAGCATTTGGTGAGAAGGGACCCTTGTACCTTGCTTTTATAT
131 CTCCTCCACATTGCGCCACTTGTCAGCATTTGGTGAGAAGGGACCCTTGTACCTTGCTTTTATAT
6110 GTAGTTATGGATATGTAGTTATAGATTATTATTATTG
196 GTAGTTATGGATATGTAGTTATAGATTATTATTATTG
6147 TAAAGTGCTTTAATTTAAAAGGATATGGACAAAAATGGGTGTCTACACCATGTGGGACCTCTCCA
1 TAAAGTGCTTTAATTTAAAAGGATATGGACAAAAATGGGTGTCTACACCATGTGGGACCTCTCCA
6212 CCTTTAAAATCAAGCTAAACCCTAAGCCTCCAAGGCCCAATAAGAACAAAGCCCAAATAGAATAT
66 CCTTTAAAATCAAGCTAAACCCTAAGCCTCCAAGGCCCAATAAGAACAAAGCCCAAATAGAATAT
6277 CTCCTCCACATTGCGCCACTTGTCAGCATTTGGTGAGAAGGGACCCTTGTACCTTGCTTTTATAT
131 CTCCTCCACATTGCGCCACTTGTCAGCATTTGGTGAGAAGGGACCCTTGTACCTTGCTTTTATAT
6342 GTAGTT
196 GTAGTT
6348 GTCCCGTGCT
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 201 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (232 bp):
TAAAGTGCTTTAATTTAAAAGGATATGGACAAAAATGGGTGTCTACACCATGTGGGACCTCTCCA
CCTTTAAAATCAAGCTAAACCCTAAGCCTCCAAGGCCCAATAAGAACAAAGCCCAAATAGAATAT
CTCCTCCACATTGCGCCACTTGTCAGCATTTGGTGAGAAGGGACCCTTGTACCTTGCTTTTATAT
GTAGTTATGGATATGTAGTTATAGATTATTATTATTG
Found at i:7346 original size:222 final size:222
Alignment explanation
Indices: 6960--7362 Score: 693
Period size: 222 Copynumber: 1.8 Consensus size: 222
6950 TAAAAGTCTT
* *
6960 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGGGTAATTACAAAAAAGGGTAGCATGAAAAG
1 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGGGTAGCAGGAAAAG
**
7025 GAAGGGGGGAAACTCATAGAGAGGCTTCTTAGTCATTTGAAAAGTGAGAAAAGACCAAAAAAAGC
66 GAAGGGGGGAAACTCATAGAGAGGCTTCTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAAAAGC
*
7090 CAAAAGGTGGCACCATATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTGGGTAATGAGTTGG
131 CAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTGGGTAATGAGTTGG
7155 TGAGAGGAAAAAATAAAAAGGGGGAAG
196 TGAGAGGAAAAAATAAAAAGGGGGAAG
* *
7182 AAACATTAATTAAAAGCAATTAAGGAAGTGAAATGAGTAATTACAAAAAAGGGTAGCAGGAAAAG
1 AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGGGTAGCAGGAAAAG
*
7247 GAAGGGAGGG-AACTCATAGA-AGGGCTTTTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAAAA
66 GAAGGG-GGGAAACTCATAGAGA-GGCTTCTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAAAA
*
7310 GCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTTCCCT
129 GCCAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCT
7363 AGTAACTAAA
Statistics
Matches: 170, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
221 1 0.01
222 166 0.98
223 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (222 bp):
AAACATTAATTAAAAACAATTAAGGAAGGGAAATGAGTAATTACAAAAAAGGGTAGCAGGAAAAG
GAAGGGGGGAAACTCATAGAGAGGCTTCTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAAAAGC
CAAAAGGTGGCACCACATTAATCCTCAATTTGGCCTTTTAGTAATTACCCTGGGTAATGAGTTGG
TGAGAGGAAAAAATAAAAAGGGGGAAG
Found at i:14005 original size:43 final size:41
Alignment explanation
Indices: 13946--14273 Score: 430
Period size: 43 Copynumber: 7.8 Consensus size: 41
13936 CCAATAACCA
13946 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACA-GGGCATCTCTATT-C
* *
13989 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATATT-
1 AAAGTCCCCAAACACATATATAACACAG-GGCATCTCTATTC
* *
14030 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACA-GGGCATCTCTATT-C
* *
14073 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-TC
1 AAAGTCCCCAAACACATATATAACACAG-GGCATCTCTATTC
* *
14114 AAAGTCCCCAAACACATATATAACACATGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGGGCATCTCTATT-C
*
14156 AAAGTCCTCAAACACATATATAACACAGAGGCAT-T-TATATC
1 AAAGTCCCCAAACACATATATAACACAG-GGCATCTCTAT-TC
14197 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACA-GGGCATCTCTATT-C
*
14240 AAAGTCCTCAAACACATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAG-GGCAT
14274 TTCTCCTTAT
Statistics
Matches: 254, Mismatches: 17, Indels: 28
0.85 0.06 0.09
Matches are distributed among these distances:
40 8 0.03
41 99 0.39
42 37 0.15
43 110 0.43
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGGGCATCTCTATTC
Found at i:14223 original size:167 final size:168
Alignment explanation
Indices: 13946--14273 Score: 595
Period size: 167 Copynumber: 2.0 Consensus size: 168
13936 CCAATAACCA
* *
13946 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACATGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
* *
14011 ACACAGAGGCATCTATATTAAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACAAA
66 ACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAA
14076 GTCCTCAAACACATATATAACACAGAGGCATCTATATC
131 GTCCTCAAACACATATATAACACAGAGGCATCTATATC
14114 AAAGTCCCCAAACACATATATAACACAT-GGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACATGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
* *
14178 ACACAGAGGCATTTATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAA
66 ACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAA
14243 GTCCTCAAACACATATATAACACAGAGGCAT
131 GTCCTCAAACACATATATAACACAGAGGCAT
14274 TTCTCCTTAT
Statistics
Matches: 154, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
167 126 0.82
168 28 0.18
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (168 bp):
AAAGTCCCCAAACACATATATAACACATGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATCAAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAA
GTCCTCAAACACATATATAACACAGAGGCATCTATATC
Found at i:14275 original size:84 final size:84
Alignment explanation
Indices: 13946--14273 Score: 577
Period size: 84 Copynumber: 3.9 Consensus size: 84
13936 CCAATAACCA
* *
13946 AAAGTCCCCAAACACATATATAACACATGGGCATCTCTATTCCAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
*
14011 ACACAGAGGCATCTATATT
66 ACACAGAGGCATCTATATC
* *
14030 AAAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
14095 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
* *
14114 AAAGTCCCCAAACACATATATAACACA-TGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
*
14178 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
14197 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
14262 ACACAGAGGCAT
66 ACACAGAGGCAT
14274 TTCTCCTTAT
Statistics
Matches: 232, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
83 79 0.34
84 153 0.66
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:14394 original size:2 final size:2
Alignment explanation
Indices: 14382--14415 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
14372 ACCAAATTCC
*
14382 TA TA T- TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14416 GTGACAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16882 original size:2 final size:2
Alignment explanation
Indices: 16875--16907 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16865 AAGTCATCAG
16875 TA TA TA TA 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 TA TA TA TA T
16908 TGTAAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20678 original size:408 final size:407
Alignment explanation
Indices: 19911--20725 Score: 1506
Period size: 408 Copynumber: 2.0 Consensus size: 407
19901 TGTGTCAAGG
*
19911 ACATTATGTTTCATAAGTTTCAAATCGCGATAATTTGTCGCTTAAATTTTCAAATTCAAAACAAT
1 ACATTATGTTTCATAAGTTTCAAATCGCGATAATTTGTCGCTTAAATTTCCAAATTCAAAACAAT
19976 TAGCCTCTAAACTTCCCAAATTCAATACAATTTACCCCTAGACGTGGGCAAATTGTCCTTGTTGC
66 TAGCCTCTAAACTTCCCAAATTCAATACAATTTACCCCTAGACGTGGGCAAATTGTCCTTGTTGC
20041 GCCAAATTTCTCTTTGACAGTTTTCGCGAGTAAAACTAAATGATAGTGCAGGGCGTGCCAGTCAA
131 GCCAAATTTCTCTTTGACAGTTTTCGCGAGTAAAACTAAATGATAGTGCAGGGCGTGCCAGTCAA
*
20106 TTTGCTGAAATTGACAAAATGTTGAAGGAACGTAAAGCTGGTGCGCATAACAGCAGATAAAAGAT
196 TTTGCTGAAATTGACAAAATGTTGAAGGAACGTAAAGCTGGTGCGCATAACAACAGATAAAAGAT
20171 CAGAGCGAGTGAATTGCGGGAACTGGATCAAAGTTAACCAGAGCATTTAAATCATCGATCCAGAT
261 CAGAGCGAGTGAATTGCGGGAACTGGATCAAAGTTAACCAGAGCATTTAAATCATCGATCCAGAT
20236 TTGTTTCTCAAAAATAAAGTTTCAAAGATTGTTCTTGATTGAAAAGAGAAAGAGAAATAACAAGC
326 TTGTTTCTCAAAAATAAAGTTTCAAAGATTGTTCTTGATTGAAAAGAGAAAGAGAAATAACAAGC
20301 TGATTGTTATTCATGAA
391 TGATTGTTATTCATGAA
*
20318 ACATTGTGTTTCATAAGTTTCAAATCGCG-TCAATTTGTCGCTTAAATTTCCAAATTCAAAACAA
1 ACATTATGTTTCATAAGTTTCAAATCGCGAT-AATTTGTCGCTTAAATTTCCAAATTCAAAACAA
20382 TTAGCCTCTAAACTTCCCAAATTCAATACAATTTACCCCTAGACGTGGGGCAAATTGTCCTTGTT
65 TTAGCCTCTAAACTTCCCAAATTCAATACAATTTACCCCTAGACGT-GGGCAAATTGTCCTTGTT
**
20447 GCGCCAAATTTCTCTTTGGGAGTTTTCGCGAGTAAAACTAAATGATAGTGCAGGGCGTGCCAGTC
129 GCGCCAAATTTCTCTTTGACAGTTTTCGCGAGTAAAACTAAATGATAGTGCAGGGCGTGCCAGTC
* * *
20512 AATTTGCTGAAATTGACAAAGTGTTGAAGGAACGTAAAGCTGTTGGGCATAACAACAGATAAAAG
194 AATTTGCTGAAATTGACAAAATGTTGAAGGAACGTAAAGCTGGTGCGCATAACAACAGATAAAAG
* *
20577 ATCAGAGCTAGTGAATTGCGGGAACTGGATCAAAGTTAACCGGAGCATTTAAATCATCGATCCAG
259 ATCAGAGCGAGTGAATTGCGGGAACTGGATCAAAGTTAACCAGAGCATTTAAATCATCGATCCAG
*
20642 ATTTGTTTCTCAAAAATAAAGTTTCAAAGGTTGTTCTTGATTGAAAAGAGAAAGAGAAATAACAA
324 ATTTGTTTCTCAAAAATAAAGTTTCAAAGATTGTTCTTGATTGAAAAGAGAAAGAGAAATAACAA
20707 GCTGATTGTTATTCATGAA
389 GCTGATTGTTATTCATGAA
20726 CTTATAACGA
Statistics
Matches: 395, Mismatches: 11, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
406 1 0.00
407 106 0.27
408 288 0.73
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (407 bp):
ACATTATGTTTCATAAGTTTCAAATCGCGATAATTTGTCGCTTAAATTTCCAAATTCAAAACAAT
TAGCCTCTAAACTTCCCAAATTCAATACAATTTACCCCTAGACGTGGGCAAATTGTCCTTGTTGC
GCCAAATTTCTCTTTGACAGTTTTCGCGAGTAAAACTAAATGATAGTGCAGGGCGTGCCAGTCAA
TTTGCTGAAATTGACAAAATGTTGAAGGAACGTAAAGCTGGTGCGCATAACAACAGATAAAAGAT
CAGAGCGAGTGAATTGCGGGAACTGGATCAAAGTTAACCAGAGCATTTAAATCATCGATCCAGAT
TTGTTTCTCAAAAATAAAGTTTCAAAGATTGTTCTTGATTGAAAAGAGAAAGAGAAATAACAAGC
TGATTGTTATTCATGAA
Found at i:22247 original size:15 final size:15
Alignment explanation
Indices: 22229--22348 Score: 71
Period size: 15 Copynumber: 8.5 Consensus size: 15
22219 ATATCATCAT
22229 AATATATCCTTCAAA
1 AATATATCCTTCAAA
* *
22244 AATAAATCCTTTAAA
1 AATATATCCTTCAAA
*
22259 AACTATATTCTT---A
1 AA-TATATCCTTCAAA
22272 AA-A-ATCCTTCAAA
1 AATATATCCTTCAAA
* *
22285 AATAAATCCTTTAAA
1 AATATATCCTTCAAA
*
22300 AACTATATTCTT---A
1 AA-TATATCCTTCAAA
22313 AA-A-ATCCTTCAAA
1 AATATATCCTTCAAA
* *
22326 AATAAATCCTTTAAAA
1 AATATATCC-TTCAAA
22342 AATATAT
1 AATATAT
22349 AATTAAATAT
Statistics
Matches: 81, Mismatches: 11, Indels: 25
0.69 0.09 0.21
Matches are distributed among these distances:
10 10 0.12
11 2 0.02
13 12 0.15
14 2 0.02
15 30 0.37
16 25 0.31
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (15 bp):
AATATATCCTTCAAA
Found at i:22279 original size:41 final size:41
Alignment explanation
Indices: 22234--22365 Score: 228
Period size: 41 Copynumber: 3.2 Consensus size: 41
22224 ATCATAATAT
22234 ATCCTTCAAAAATAAATCCTTTAAAAACTATATTCTTAAAA
1 ATCCTTCAAAAATAAATCCTTTAAAAACTATATTCTTAAAA
22275 ATCCTTCAAAAATAAATCCTTTAAAAACTATATTCTTAAAA
1 ATCCTTCAAAAATAAATCCTTTAAAAACTATATTCTTAAAA
* ** *
22316 ATCCTTCAAAAATAAATCCTTTAAAAAATATATAATTAAAT
1 ATCCTTCAAAAATAAATCCTTTAAAAACTATATTCTTAAAA
22357 ATCCTTCAA
1 ATCCTTCAA
22366 CAATGAAGGA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (41 bp):
ATCCTTCAAAAATAAATCCTTTAAAAACTATATTCTTAAAA
Found at i:22298 original size:26 final size:26
Alignment explanation
Indices: 22247--22301 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
22237 CTTCAAAAAT
* * *
22247 AAATCCTTTAAAAACTATATTCTTAA
1 AAATCCTTCAAAAACTAAATCCTTAA
22273 AAATCCTTCAAAAA-TAAATCCTTTAA
1 AAATCCTTCAAAAACTAAATCC-TTAA
22299 AAA
1 AAA
22302 CTATATTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATCCTTCAAAAACTAAATCCTTAA
Found at i:22339 original size:26 final size:26
Alignment explanation
Indices: 22288--22342 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
22278 CTTCAAAAAT
* * *
22288 AAATCCTTTAAAAACTATATTCTTAA
1 AAATCCTTCAAAAACTAAATCCTTAA
22314 AAATCCTTCAAAAA-TAAATCCTTTAA
1 AAATCCTTCAAAAACTAAATCC-TTAA
22340 AAA
1 AAA
22343 ATATATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATCCTTCAAAAACTAAATCCTTAA
Found at i:22956 original size:21 final size:21
Alignment explanation
Indices: 22930--22971 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
22920 GCACAAAGAA
22930 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
22951 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
22972 CCTAAGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:25500 original size:33 final size:33
Alignment explanation
Indices: 25455--25535 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
25445 GTGTTTTAGA
*
25455 TGTTGTTAGTGATGA-TACTAAACCTAATTTAAG
1 TGTTGTTTGTGATGACT-CTAAACCTAATTTAAG
* * *
25488 TGTTGTTTGTGATGACTCTAAATCTATTTTAGG
1 TGTTGTTTGTGATGACTCTAAACCTAATTTAAG
25521 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
25536 AACAAATTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 42 0.98
34 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (33 bp):
TGTTGTTTGTGATGACTCTAAACCTAATTTAAG
Done.