Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012099.1 Corchorus olitorius cultivar O-4 contig12132, 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: 43481
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2029 original size:33 final size:33
Alignment explanation
Indices: 1982--2062 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
1972 GTGTTTTAGA
* *
1982 TGTTGTTTGCGATGATACTAAA-ACTAATTTGA-G
1 TGTTGTTTGTGATGACACTAAATA-T-ATTTGAGG
* *
2015 TGTTGTTTGTGATGACACTAAATATGTTTTAGG
1 TGTTGTTTGTGATGACACTAAATATATTTGAGG
2048 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
2063 AACAAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 4 0.10
33 37 0.88
34 1 0.02
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAATATATTTGAGG
Found at i:2074 original size:33 final size:32
Alignment explanation
Indices: 2009--2113 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 32
1999 CTAAAACTAA
*
2009 TTTGAGTGTTGTTTGTGATGACACTAAA-TATGT
1 TTTG-GTGTTGTTTGTGATGAAAC-AAATTATGT
2042 TTTAGGTGTTGTTTGTGATGAAACAAATTATGT
1 TTT-GGTGTTGTTTGTGATGAAACAAATTATGT
* ** *
2075 TTTGGATGCTAATTGTGATGAAAACAAA-TCTGT
1 TTTGG-TGTTGTTTGTGATG-AAACAAATTATGT
2108 TTTGGT
1 TTTGGT
2114 TGATCATAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
32 6 0.10
33 49 0.78
34 8 0.13
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.44
Consensus pattern (32 bp):
TTTGGTGTTGTTTGTGATGAAACAAATTATGT
Found at i:4091 original size:21 final size:21
Alignment explanation
Indices: 4065--4156 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
4055 TGCTAGGAGT
4065 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
4086 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
4107 TTATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
4128 TTATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
4149 TCATTGGA
1 TCATTGGA
4157 ATTGCCTAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
20 2 0.03
21 66 0.97
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:6332 original size:23 final size:24
Alignment explanation
Indices: 6300--6346 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
6290 AAACTGGCCG
* *
6300 AAAGGCAAAGCAGAGAA-CATAAA
1 AAAGGCAAAGAACAGAACCATAAA
*
6323 AAAGGTAAAGAACAGAACCATAAA
1 AAAGGCAAAGAACAGAACCATAAA
6347 TAAAACATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.62, C:0.13, G:0.19, T:0.06
Consensus pattern (24 bp):
AAAGGCAAAGAACAGAACCATAAA
Found at i:7832 original size:12 final size:12
Alignment explanation
Indices: 7812--7844 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7802 AACAGGCCGC
7812 AACAAAAAAGAA
1 AACAAAAAAGAA
7824 GAA-AAAAAAGAA
1 -AACAAAAAAGAA
7836 AACAAAAAA
1 AACAAAAAA
7845 AACAGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (12 bp):
AACAAAAAAGAA
Found at i:8854 original size:18 final size:18
Alignment explanation
Indices: 8831--8865 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
8821 GAGTAGACAA
8831 ATTAGAGTAGTTGTTTAG
1 ATTAGAGTAGTTGTTTAG
8849 ATTAGAGTAGTTGTTTA
1 ATTAGAGTAGTTGTTTA
8866 AATGAGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (18 bp):
ATTAGAGTAGTTGTTTAG
Found at i:11092 original size:13 final size:13
Alignment explanation
Indices: 11074--11100 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11064 AAACGAATAA
11074 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
11087 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
11100 T
1 T
11101 TTAGTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:11947 original size:109 final size:109
Alignment explanation
Indices: 11751--11957 Score: 351
Period size: 109 Copynumber: 1.9 Consensus size: 109
11741 ATAATATTAG
*
11751 TATTATTAATTGTGTGGTTTATTTAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
1 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
11816 AATGCAATGAACTATTGAATTTAAAGAAAAATACAAGAACCTAT
66 AATGCAATGAACTATTGAATTTAAAGAAAAATACAAGAACCTAT
* * *
11860 TATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATATCAAACAATAGAA
1 TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
* * *
11925 AGTGCAATGAATTATTGGATTTAAAGAAAAATA
66 AATGCAATGAACTATTGAATTTAAAGAAAAATA
11958 TAAACACCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 91 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (109 bp):
TATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAA
AATGCAATGAACTATTGAATTTAAAGAAAAATACAAGAACCTAT
Found at i:13740 original size:13 final size:12
Alignment explanation
Indices: 13713--13745 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
13703 AAGTTTATTG
13713 ATAATAT-ATAT
1 ATAATATAATAT
13724 ATAATATAATAAT
1 ATAATATAAT-AT
13737 ATAATATAA
1 ATAATATAA
13746 CATTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 2 0.10
13 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:14042 original size:31 final size:31
Alignment explanation
Indices: 14007--14078 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
13997 TAAATTATTG
*
14007 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
14038 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
14069 CAAATTAAAA
1 CAAATTAAAA
14079 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:14556 original size:16 final size:16
Alignment explanation
Indices: 14531--14565 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
14521 GGGTCTGGGC
* *
14531 TCGGGTTCGGGTATTT
1 TCGGGCTCGGGTAATT
14547 TCGGGCTCGGGTAATT
1 TCGGGCTCGGGTAATT
14563 TCG
1 TCG
14566 AGTTCGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.17, G:0.37, T:0.37
Consensus pattern (16 bp):
TCGGGCTCGGGTAATT
Found at i:14572 original size:16 final size:16
Alignment explanation
Indices: 14535--14574 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
14525 CTGGGCTCGG
* *
14535 GTTCGGGTATTTTCGG
1 GTTCGGGTAATTTCGA
*
14551 GCTCGGGTAATTTCGA
1 GTTCGGGTAATTTCGA
14567 GTTCGGGT
1 GTTCGGGT
14575 TCGGGACGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.38, T:0.38
Consensus pattern (16 bp):
GTTCGGGTAATTTCGA
Found at i:19361 original size:41 final size:43
Alignment explanation
Indices: 19316--19599 Score: 230
Period size: 41 Copynumber: 6.6 Consensus size: 43
19306 CTCTCTCCCC
* * *
19316 AAAGTCCCCAAGCACATAATAACACAGGGGCAACTCT-TC-CT
1 AAAGTCCTCAAGCACATTATAACACAGGGGCATCTCTATCTCT
* * *
19357 AAAGTCCTCAAGCACATATAGAACACAGAGGCA--TCTATATC-
1 AAAGTCCTCAAGCACAT-TATAACACAGGGGCATCTCTATCTCT
* * *
19398 AAAATCCCCAAACACAATTATAACACAGGGGCAATC-C--TCTCT
1 AAAGTCCTCAAGCAC-ATTATAACACAGGGGC-ATCTCTATCTCT
* *
19440 AAAAGTCCTCAAGCACATTTATAACACAGAGGCATC-C-ATATC-
1 -AAAGTCCTCAAGCACA-TTATAACACAGGGGCATCTCTATCTCT
* * * * *
19482 AAAATCCCCAAGCACAATTATAACACAAGGACATCTCTCTCTCT
1 AAAGTCCTCAAGCAC-ATTATAACACAGGGGCATCTCTATCTCT
* * *
19526 CAAAAGTCCTCAAGCACATTTATAACACAGGGACATCTCTCTCTCA
1 --AAAGTCCTCAAGCACA-TTATAACACAGGGGCATCTCTATCTCT
19572 AAAGTCCTCAAGCACATTTATAACACAG
1 AAAGTCCTCAAGCACA-TTATAACACAG
19600 AGACACCTAT
Statistics
Matches: 198, Mismatches: 27, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
40 3 0.02
41 72 0.36
42 23 0.12
43 33 0.17
44 28 0.14
45 1 0.01
46 38 0.19
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (43 bp):
AAAGTCCTCAAGCACATTATAACACAGGGGCATCTCTATCTCT
Found at i:19466 original size:84 final size:84
Alignment explanation
Indices: 19315--19599 Score: 344
Period size: 84 Copynumber: 3.3 Consensus size: 84
19305 TCTCTCTCCC
* * * *
19315 CAAAGTCCCCAAGCAC-ATAATAACACAGGGGCAACTCTTC-CT-AAAGTCCTCAAGCACATATA
1 CAAAATCCCCAAGCACAATTATAACACAGGGGCAA-TCCTCTCTAAAAGTCCTCAAGCACATTTA
*
19377 GAACACAGAGGCATCTATAT
65 TAACACAGAGGCATCTATAT
*
19397 CAAAATCCCCAAACACAATTATAACACAGGGGCAATCCTCTCTAAAAGTCCTCAAGCACATTTAT
1 CAAAATCCCCAAGCACAATTATAACACAGGGGCAATCCTCTCTAAAAGTCCTCAAGCACATTTAT
*
19462 AACACAGAGGCATCCATAT
66 AACACAGAGGCATCTATAT
* * *
19481 CAAAATCCCCAAGCACAATTATAACACAAGGACATCTCTCTCTCTCAAAAGTCCTCAAGCACATT
1 CAAAATCCCCAAGCACAATTATAACACAGGGGCA-ATC-CTCTCT-AAAAGTCCTCAAGCACATT
* *
19546 TATAACACAG-GGACATCTCTCTCT
63 TATAACACAGAGG-CA--TCTATAT
* *
19570 CAAAAGTCCTCAAGCACATTTATAACACAG
1 CAAAA-TCCCCAAGCACAATTATAACACAG
19600 AGACACCTAT
Statistics
Matches: 176, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
82 18 0.10
83 19 0.11
84 68 0.39
85 2 0.01
86 8 0.05
87 31 0.18
89 9 0.05
90 21 0.12
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (84 bp):
CAAAATCCCCAAGCACAATTATAACACAGGGGCAATCCTCTCTAAAAGTCCTCAAGCACATTTAT
AACACAGAGGCATCTATAT
Found at i:21514 original size:18 final size:17
Alignment explanation
Indices: 21469--21516 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
21459 TCCCTGACCC
21469 AAATTTTTTTAAAAAAA
1 AAATTTTTTTAAAAAAA
* *
21486 AAACATATTTTAAAAAAA
1 AAA-TTTTTTTAAAAAAA
*
21504 ATTATTTTTTTAA
1 A-AATTTTTTTAA
21517 TCAAAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.83
19 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTTTTTAAAAAAA
Found at i:23239 original size:18 final size:18
Alignment explanation
Indices: 23216--23252 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23206 GAAATTTTTC
23216 ATTTTCAAT-GATTTGAAA
1 ATTTTCAATAG-TTTGAAA
23234 ATTTTCAATAGTTTGAAA
1 ATTTTCAATAGTTTGAAA
23252 A
1 A
23253 AAAATTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTTTCAATAGTTTGAAA
Found at i:23444 original size:12 final size:12
Alignment explanation
Indices: 23427--23460 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
23417 AACATTTCAA
23427 CAACTAAACCTT
1 CAACTAAACCTT
23439 CAACTAAACCTT
1 CAACTAAACCTT
23451 CAACTAAACC
1 CAACTAAACC
23461 CTTCGCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (12 bp):
CAACTAAACCTT
Found at i:34358 original size:8 final size:8
Alignment explanation
Indices: 34347--34414 Score: 81
Period size: 8 Copynumber: 8.8 Consensus size: 8
34337 CGAATAAAGC
34347 AATATAT-
1 AATATATA
34354 AA-ATATA
1 AATATATA
34361 AATATATA
1 AATATATA
34369 AATATATA
1 AATATATA
34377 AATATATA
1 AATATATA
34385 AATATA-A
1 AATATATA
*
34392 ATATAAATA
1 A-ATATATA
34401 TAA-ATATA
1 -AATATATA
34409 AATATA
1 AATATA
34415 AGCATTTTGT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
6 4 0.08
7 8 0.15
8 38 0.72
9 2 0.04
10 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATATATA
Found at i:34361 original size:6 final size:6
Alignment explanation
Indices: 34350--34415 Score: 91
Period size: 6 Copynumber: 11.0 Consensus size: 6
34340 ATAAAGCAAT
*
34350 ATATAA ATATAA ATATATA A-ATAT ATA-AA TATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATA-A ATATAA ATATAA -ATATAA ATATAA ATATAA
34398 ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA
34416 GCATTTTGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
5 2 0.04
6 48 0.89
7 4 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:34366 original size:14 final size:14
Alignment explanation
Indices: 34347--34408 Score: 92
Period size: 14 Copynumber: 4.4 Consensus size: 14
34337 CGAATAAAGC
34347 AATATATAAATATA
1 AATATATAAATATA
34361 AATATATAAATATATA
1 AATATAT-AA-ATATA
34377 AATATATAAATAT-
1 AATATATAAATATA
34390 AA-ATATAAATATA
1 AATATATAAATATA
34403 AATATA
1 AATATA
34409 AATATAAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.23
13 4 0.09
14 14 0.32
15 4 0.09
16 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATATAAATATA
Found at i:36673 original size:36 final size:35
Alignment explanation
Indices: 36633--37072 Score: 329
Period size: 36 Copynumber: 12.2 Consensus size: 35
36623 TAGTGTCCCC
36633 ACTTAATTACCCTGAATTAAGTTCTTTATTGAATTT
1 ACTTAATTACCCTGAATTAAG-TCTTTATTGAATTT
* * *
36669 ACTTAATTA-CCTAGAATGAAG--TTCATTGACTCTTT
1 ACTTAATTACCCT-GAATTAAGTCTTTATTGA--ATTT
** *
36704 ACTTAATTACCCTGAATTAAGTCTTTGCCTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTT-ATTGAATTT
*
36740 ACTTAATTTCCCTGAATTAAGTTCTTTATTGAATTT
1 ACTTAATTACCCTGAATTAAG-TCTTTATTGAATTT
* * *
36776 ACTTAATTACCCAGAATTAAG--TTCATTGACTCTTT
1 ACTTAATTACCCTGAATTAAGTCTTTATTGA--ATTT
* ** *
36811 ACTTAATTACCTTGAATTAAGTCTTTGCCTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTT-ATTGAATTT
*
36847 ACTTTAATTTCCCTGAATTAAGTTCTTTATTGAATTT
1 AC-TTAATTACCCTGAATTAAG-TCTTTATTGAATTT
*
36884 ACTTAATTACCCAGAATTAAG--TTTATTGACTATGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTATTGA--A--TTT
* * **
36921 ACTTAATTTCCCTGAATTAAGTCTTTGACTGCTTTT
1 ACTTAATTACCCTGAATTAAGTCTTT-ATTGAATTT
* * * *
36957 ACTTAATTTCCCTGAATTAAGTCTTGGACTG-CTTCT
1 ACTTAATTACCCTGAATTAAGTCTT-TATTGAATT-T
* * * **
36993 ACTTAATTTCCCTGAATTAAGCCTTTGACTGTGTTT
1 ACTTAATTACCCTGAATTAAGTCTTT-ATTGAATTT
** * * **
37029 ACTTAATTTTCTTGAATTAAGTCTTTGACTGCTTTT
1 ACTTAATTACCCTGAATTAAGTCTTT-ATTGAATTT
37065 ACTTAATT
1 ACTTAATT
37073 CATGGATGCA
Statistics
Matches: 334, Mismatches: 44, Indels: 52
0.78 0.10 0.12
Matches are distributed among these distances:
33 22 0.07
35 47 0.14
36 190 0.57
37 58 0.17
38 11 0.03
39 3 0.01
40 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTCTTTATTGAATTT
Found at i:36796 original size:72 final size:72
Alignment explanation
Indices: 36633--37072 Score: 384
Period size: 72 Copynumber: 6.1 Consensus size: 72
36623 TAGTGTCCCC
* * * *
36633 ACTTAATTACCCTGAATTAAGTTCTTT-ATTGAATTTACTTAA-TTACCTAGAATGAAGTTCATT
1 ACTTAATTACCCTGAATTAAGTTCTTTGACTGATTTTACTTAATTTCCCT-GAATTAAG-TC-TT
* *
36696 GACT--CTTT
63 TACTGAATTT
*
36704 ACTTAATTACCCTGAATTAAG-TCTTTGCCTGATTTTACTTAATTTCCCTGAATTAAGTTCTTTA
1 ACTTAATTACCCTGAATTAAGTTCTTTGACTGATTTTACTTAATTTCCCTGAATTAAG-TCTTTA
*
36768 TTGAATTT
65 CTGAATTT
* * * * * *
36776 ACTTAATTACCCAGAATTAAGTTCATTGACT--CTTTACTTAATTACCTTGAATTAAGTCTTTGC
1 ACTTAATTACCCTGAATTAAGTTCTTTGACTGATTTTACTTAATTTCCCTGAATTAAGTCTTT-A
*
36839 CTGATTTT
65 CTGAATTT
* * * * * *
36847 ACTTTAATTTCCCTGAATTAAGTTCTTT-ATTGAATTTACTTAATTACCCAGAATTAAGTTTATT
1 AC-TTAATTACCCTGAATTAAGTTCTTTGACTGATTTTACTTAATTTCCCTGAATTAAGTCT-TT
*
36911 GACT-ATGTTT
64 -ACTGA-ATTT
* * *
36921 ACTTAATTTCCCTGAATTAAG-TCTTTGACTGCTTTTACTTAATTTCCCTGAATTAAGTCTTGGA
1 ACTTAATTACCCTGAATTAAGTTCTTTGACTGATTTTACTTAATTTCCCTGAATTAAGTCTT-TA
*
36985 CTG-CTTCT
65 CTGAATT-T
* * * *
36993 ACTTAATTTCCCTGAATTAAG-CCTTTGACTG-TGTTTACTTAATTTTCTTGAATTAAGTCTTTG
1 ACTTAATTACCCTGAATTAAGTTCTTTGACTGAT-TTTACTTAATTTCCCTGAATTAAGTCTTT-
**
37056 ACTGCTTTT
64 ACTGAATTT
37065 ACTTAATT
1 ACTTAATT
37073 CATGGATGCA
Statistics
Matches: 311, Mismatches: 40, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
70 14 0.05
71 78 0.25
72 129 0.41
73 80 0.26
74 10 0.03
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (72 bp):
ACTTAATTACCCTGAATTAAGTTCTTTGACTGATTTTACTTAATTTCCCTGAATTAAGTCTTTAC
TGAATTT
Found at i:36905 original size:108 final size:108
Alignment explanation
Indices: 36633--37072 Score: 602
Period size: 108 Copynumber: 4.1 Consensus size: 108
36623 TAGTGTCCCC
* * *
36633 ACTTAATTACCCTGAATTAAGTTCTTTATTGAATTTACTTAATTACCTAGAATGAAGTTCATTGA
1 ACTTAATTTCCCTGAATTAAGTTCTTTATTGAATTTACTTAATTACCCAGAATTAAGTTCATTGA
*
36698 C-TCTTTACTTAATTACCCTGAATTAAGTCTTTGCCTGATTTT
66 CTTCTTTACTTAATTACCCTGAATTAAGTCTTTGACTGATTTT
36740 ACTTAATTTCCCTGAATTAAGTTCTTTATTGAATTTACTTAATTACCCAGAATTAAGTTCATTGA
1 ACTTAATTTCCCTGAATTAAGTTCTTTATTGAATTTACTTAATTACCCAGAATTAAGTTCATTGA
* *
36805 C-TCTTTACTTAATTACCTTGAATTAAGTCTTTGCCTGATTTT
66 CTTCTTTACTTAATTACCCTGAATTAAGTCTTTGACTGATTTT
*
36847 ACTTTAATTTCCCTGAATTAAGTTCTTTATTGAATTTACTTAATTACCCAGAATTAAGTTTATTG
1 AC-TTAATTTCCCTGAATTAAGTTCTTTATTGAATTTACTTAATTACCCAGAATTAAGTTCATTG
* * *
36912 ACTATGTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGCTTTT
65 ACT-TCTTTACTTAATTACCCTGAATTAAGTCTTTGACTGATTTT
* * * * * * *
36957 ACTTAATTTCCCTGAATTAAG-TCTTGGACTG-CTTCTACTTAATTTCCCTGAATTAAG-CCTTT
1 ACTTAATTTCCCTGAATTAAGTTCTT-TATTGAATT-TACTTAATTACCCAGAATTAAGTTCATT
* ** * *
37019 GACTGTGTTTACTTAATTTTCTTGAATTAAGTCTTTGACTGCTTTT
64 GACT-TCTTTACTTAATTACCCTGAATTAAGTCTTTGACTGATTTT
37065 ACTTAATT
1 ACTTAATT
37073 CATGGATGCA
Statistics
Matches: 307, Mismatches: 21, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
107 105 0.34
108 122 0.40
109 42 0.14
110 38 0.12
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (108 bp):
ACTTAATTTCCCTGAATTAAGTTCTTTATTGAATTTACTTAATTACCCAGAATTAAGTTCATTGA
CTTCTTTACTTAATTACCCTGAATTAAGTCTTTGACTGATTTT
Found at i:40569 original size:25 final size:25
Alignment explanation
Indices: 40535--40584 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40525 TTAGTTGATT
40535 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
40560 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
40585 CAAAATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:40708 original size:26 final size:26
Alignment explanation
Indices: 40679--40728 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
40669 ATCTAGATGA
* *
40679 CTAAAAATGAATTAGCTACTCTAACT
1 CTAAAAATAAATTAGCTAATCTAACT
*
40705 CTAAATATAAATTAGCTAATCTAA
1 CTAAAAATAAATTAGCTAATCTAA
40729 ACCAAAAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (26 bp):
CTAAAAATAAATTAGCTAATCTAACT
Done.