Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024502.1 Corchorus olitorius cultivar O-4 contig24535, 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: 44420
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:474 original size:76 final size:76
Alignment explanation
Indices: 356--799 Score: 522
Period size: 76 Copynumber: 5.9 Consensus size: 76
346 GCCACTCGCT
*
356 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGTAGATGCC
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
421 ACTCACTCATC
66 ACTCACTCATC
* * * * *
432 CAACGGCTGAGTGCCTATACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCGTTCATGTAGATGCT
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
497 ACTCACTCATC
66 ACTCACTCATC
* * * * * * * *
508 CAACGGCTGAGTGCCTAAAGTGGCA-CCCCGTCCCCTGAATGGGGCTGAGCGTCCATGCAGACGC
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGT-CCCTCAGTGAGGCAGAGCATCCATGCAGATGC
572 CACT---T-ATC
65 CACTCACTCATC
* ** *
580 CCACGGCTGAGTGCCTAGACTGGCGGCCCCGTCCCTTAGTGAGGCAGAGCATCCATGCAGATGCC
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
*
645 ACTCATTCATC
66 ACTCACTCATC
* *
656 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAACATTCATGCAGATGCC
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
721 ACTCACTCATC
66 ACTCACTCATC
* * * * * * * *** * **
732 AAACGACTAAGTGTCTATA-TCGACGCCCCCGTCCAAGAATGAGGCAGAGCGCCCATGCAGATGC
1 CAACGGCTGAGTGCCTAGACT-GGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGC
796 CACT
65 CACT
800 TGCTCAACAG
Statistics
Matches: 315, Mismatches: 46, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
72 54 0.17
73 7 0.02
75 8 0.03
76 246 0.78
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (76 bp):
CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
ACTCACTCATC
Found at i:813 original size:148 final size:151
Alignment explanation
Indices: 356--816 Score: 519
Period size: 148 Copynumber: 3.1 Consensus size: 151
346 GCCACTCGCT
*
356 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGTAGATGCC
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
* *
421 ACTCACTCATCCAACGGCTGAGTGCCTATACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCGTTC
66 ACTCACTCATCCAACGGCTGAGTGCCTATACTGGCGCCCCCGTCCCTCAGTGAGGCAGAGCGTCC
* *
486 ATGTAGATGCTACTCACT-CATC
131 ATGCAGATGCCACT--CTGCATC
* * * * * * * *
508 CAACGGCTGAGTGCCTAAAGTGGCA-CCCCGTCCCCTGAATGGGGCTGAGCGTCCATGCAGACGC
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGT-CCCTCAGTGAGGCAGAGCATCCATGCAGATGC
* * * * *
572 CACT---T-ATCCCACGGCTGAGTGCCTAGACTGGCGGCCCCGTCCCTTAGTGAGGCAGAGCATC
65 CACTCACTCATCCAACGGCTGAGTGCCTATACTGGCGCCCCCGTCCCTCAGTGAGGCAGAGCGTC
*
633 CATGCAGATGCCACTCATTCATC
130 CATGCAGATGCCACTC-TGCATC
* *
656 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAACATTCATGCAGATGCC
1 CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
* * * * * *** * *
721 ACTCACTCATCAAACGACTAAGTGTCTATA-TCGACGCCCCCGTCCAAGAATGAGGCAGAGCGCC
66 ACTCACTCATCCAACGGCTGAGTGCCTATACT-GGCGCCCCCGTCCCTCAGTGAGGCAGAGCGTC
785 CATGCAGATGCCACT-TGC-T-
130 CATGCAGATGCCACTCTGCATC
*
804 CAACAGCTGAGTG
1 CAACGGCTGAGTG
817 TCCACGCAGA
Statistics
Matches: 256, Mismatches: 44, Indels: 22
0.80 0.14 0.07
Matches are distributed among these distances:
146 1 0.00
147 1 0.00
148 129 0.50
149 8 0.03
150 2 0.01
151 8 0.03
152 107 0.42
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (151 bp):
CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCATCCATGCAGATGCC
ACTCACTCATCCAACGGCTGAGTGCCTATACTGGCGCCCCCGTCCCTCAGTGAGGCAGAGCGTCC
ATGCAGATGCCACTCTGCATC
Found at i:815 original size:224 final size:224
Alignment explanation
Indices: 343--816 Score: 659
Period size: 224 Copynumber: 2.1 Consensus size: 224
333 TCGGTTAAGG
*
343 GACGCCACTCGCTCAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCAT
1 GACGCCACTTGCTCAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCAT
* *
408 CCATGTAGATGCCACTCACTCATCCAACGGCTGAGTGCCTATACTGGCACCCCCGTCCCTCAGTG
66 CCATGCAGATGCCACTCACTCATCCAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTG
* * * * * * *
473 AGGCAGAGCGTTCATGTAGATGCTACTCACTCATCCAACGGCTGAGTGCCTAAAGTGGCACCCCG
131 AGGCAGAACATTCATGCAGATGCCACTCACTCATCAAACGACTAAGTGCCTAAAGTGGCACCCCG
** * * *
538 TCCCCTGAATGGGGCTGAGCGTCCATGCA
196 TCCCAAGAATGAGGCAGAGCGCCCATGCA
* * ** *
567 GACGCCACTT-ATCCCACGGCTGAGTGCCTAGACTGGCGGCCCCGTCCCTTAGTGAGGCAGAGCA
1 GACGCCACTTGCT-CAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCA
*
631 TCCATGCAGATGCCACTCATTCATCCAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGT
65 TCCATGCAGATGCCACTCACTCATCCAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGT
* *
696 GAGGCAGAACATTCATGCAGATGCCACTCACTCATCAAACGACTAAGTGTCTATA-TCGACGC-C
130 GAGGCAGAACATTCATGCAGATGCCACTCACTCATCAAACGACTAAGTGCCTAAAGT-G--GCAC
759 CCCGT-CCAAGAATGAGGCAGAGCGCCCATGCA
192 CCCGTCCCAAGAATGAGGCAGAGCGCCCATGCA
* *
791 GATGCCACTTGCTCAACAGCTGAGTG
1 GACGCCACTTGCTCAACGGCTGAGTG
817 TCCACGCAGA
Statistics
Matches: 218, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
223 2 0.01
224 207 0.95
225 7 0.03
226 2 0.01
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (224 bp):
GACGCCACTTGCTCAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTGAGGCAGAGCAT
CCATGCAGATGCCACTCACTCATCCAACGGCTGAGTGCCTAGACTGGCACCCCCGTCCCTCAGTG
AGGCAGAACATTCATGCAGATGCCACTCACTCATCAAACGACTAAGTGCCTAAAGTGGCACCCCG
TCCCAAGAATGAGGCAGAGCGCCCATGCA
Found at i:5472 original size:30 final size:30
Alignment explanation
Indices: 5438--5505 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
5428 AGGTTCGGAT
5438 GCGGCCTCCTTGCTGACGTGCGGCTGGTGC
1 GCGGCCTCCTTGCTGACGTGCGGCTGGTGC
*
5468 GCGGCCTCCTTGCTGGCGTGCGGCTGGTGC
1 GCGGCCTCCTTGCTGACGTGCGGCTGGTGC
5498 GCGGCCTC
1 GCGGCCTC
5506 GGCATGCCCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.01, C:0.35, G:0.41, T:0.22
Consensus pattern (30 bp):
GCGGCCTCCTTGCTGACGTGCGGCTGGTGC
Found at i:5602 original size:54 final size:54
Alignment explanation
Indices: 5544--5650 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
5534 CCGAGCCAAA
* *
5544 GCCTGGTG-TGGCCGGGGCTCATCCTTGGCATGGCTCGGTACTGCCCGGGCCATT
1 GCCTGGTGCT-GCCGGGGCACAGCCTTGGCATGGCTCGGTACTGCCCGGGCCATT
* * * ** *
5598 GCCTGGTGCTGCTGGTGCACGGCCTTGGCATGGCTCGGTGTTGTCCGGGCCAT
1 GCCTGGTGCTGCCGGGGCACAGCCTTGGCATGGCTCGGTACTGCCCGGGCCAT
5651 GTCTTTGTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
54 43 0.98
55 1 0.02
ACGTcount: A:0.07, C:0.30, G:0.38, T:0.25
Consensus pattern (54 bp):
GCCTGGTGCTGCCGGGGCACAGCCTTGGCATGGCTCGGTACTGCCCGGGCCATT
Found at i:17646 original size:16 final size:16
Alignment explanation
Indices: 17622--17654 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17612 AAGTATGCTG
17622 ATCTATGTCTATCAGT
1 ATCTATGTCTATCAGT
*
17638 ATCTCTGTCTATCAGT
1 ATCTATGTCTATCAGT
17654 A
1 A
17655 GAATGCTACT
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:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (16 bp):
ATCTATGTCTATCAGT
Found at i:20189 original size:15 final size:16
Alignment explanation
Indices: 20149--20189 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
20139 TTTTCTCGGA
*
20149 TCATTCGGGTTTCGGC
1 TCATTCGGGTTTAGGC
20165 TCA-TCTGGGTTTAGG-
1 TCATTC-GGGTTTAGGC
20180 TCATTCGGGT
1 TCATTCGGGT
20190 CTGCAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.10, C:0.20, G:0.32, T:0.39
Consensus pattern (16 bp):
TCATTCGGGTTTAGGC
Found at i:21532 original size:55 final size:55
Alignment explanation
Indices: 21449--21565 Score: 155
Period size: 55 Copynumber: 2.1 Consensus size: 55
21439 GTATATATTG
* **** *
21449 TATAGTAAGAGTAGTAATCTAGTCAGGTAATAATTGTTCATCAAATTAGATTTTA
1 TATAGTAAGAGTAATAATCTAGTCAGGTAATAATTACGAATCAAATTAAATTTTA
* *
21504 TATAGTAAGAGTAATAGTCTAGTTAGGTAATAATTACGAATCAAATTAAATTTTA
1 TATAGTAAGAGTAATAATCTAGTCAGGTAATAATTACGAATCAAATTAAATTTTA
21559 T-TAGTAA
1 TATAGTAA
21566 TCATTCGGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
54 6 0.11
55 48 0.89
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (55 bp):
TATAGTAAGAGTAATAATCTAGTCAGGTAATAATTACGAATCAAATTAAATTTTA
Found at i:22531 original size:41 final size:41
Alignment explanation
Indices: 22486--22577 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
22476 CCTCCATTGT
22486 TGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTTG
1 TGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTTG
* *
22527 TGAAGGATATTTAAGAATGTATTTTTTAAAGGATTTATTTT
1 TGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTTG
*
22568 TTAAGGATAT
1 TGAAGGATAT
22578 ATTATGATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (41 bp):
TGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTTG
Found at i:22567 original size:16 final size:15
Alignment explanation
Indices: 22536--22580 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
22526 GTGAAGGATA
* *
22536 TTTAAGAATGTATTT
1 TTTAAGGATATATTT
*
22551 TTTAAAGGATTTATTT
1 TTT-AAGGATATATTT
22567 TTTAAGGATATATT
1 TTTAAGGATATATT
22581 ATGATGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTAAGGATATATTT
Found at i:22649 original size:16 final size:16
Alignment explanation
Indices: 22625--22659 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22615 CAAGTATACT
22625 CGAAAAACCCAAAACC
1 CGAAAAACCCAAAACC
* *
22641 CGAATAACCCAGAACC
1 CGAAAAACCCAAAACC
22657 CGA
1 CGA
22660 GGCCAAAATC
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:0.49, C:0.37, G:0.11, T:0.03
Consensus pattern (16 bp):
CGAAAAACCCAAAACC
Found at i:23151 original size:21 final size:20
Alignment explanation
Indices: 23118--23156 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
23108 AATAAAAAAT
*
23118 TTAAAAAATATTGAATTTAA
1 TTAAAAAAAATTGAATTTAA
23138 TTAAATAAAAATTGAATTT
1 TTAAA-AAAAATTGAATTT
23157 TTAGTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TTAAAAAAAATTGAATTTAA
Found at i:23392 original size:138 final size:138
Alignment explanation
Indices: 23225--23485 Score: 332
Period size: 138 Copynumber: 1.9 Consensus size: 138
23215 ATTTAAGAAA
** * * * *
23225 TATATTTTTAAAATTCTAATATGTCTAAGTTTTTTAATTGAATTAGTAAAA-TG-ATAAAATTAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATTGTA-AAAATT-A
* * *
23288 AACAGGTATAAGGATTTTATAA-TTA-AATAAAAAAATAGAGTTTTTCGTTGGGTAAAAGTGTAA
64 AACAGGTATAAGGATATTA-AATTTATAATAAAAAAATAGAGTTTTTAGTTGAGTAAAAGTGTAA
23351 AACTATAAAAG
128 AACTATAAAAG
23362 TATATTTAAAAAACTTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATTGTAAAAATTAA
1 TATATTTAAAAAA-TTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATTGTAAAAATTAA
* * *
23427 ATAGTTATAAGGATATTAAATTTATTTAATTAAAAAATAGAGTTTTTAGTTGAGTAAAA
65 ACAGGTATAAGGATATTAAATTTA--TAATAAAAAAATAGAGTTTTTAGTTGAGTAAAA
23486 CTATAAAAGT
Statistics
Matches: 105, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
137 13 0.12
138 54 0.51
139 8 0.08
140 1 0.01
141 29 0.28
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (138 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATTGTAAAAATTAAA
CAGGTATAAGGATATTAAATTTATAATAAAAAAATAGAGTTTTTAGTTGAGTAAAAGTGTAAAAC
TATAAAAG
Found at i:24647 original size:2 final size:2
Alignment explanation
Indices: 24636--24672 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
24626 TTTTGATTCT
*
24636 TA TA TA -A TA TA TG TA TA -A 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 TA TA T
24673 GTTTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25048 original size:22 final size:23
Alignment explanation
Indices: 25010--25052 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
25000 AATCCTAATC
25010 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
*
25033 CTGGTATGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
25053 ACTCCTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:32907 original size:30 final size:30
Alignment explanation
Indices: 32866--32928 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
32856 TCTTTAAGGG
*
32866 GGAGTGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGC-CCCAAGGACTTATCAT
**
32896 GGAGGGAATGATGCTTCAAGGACTTATCAT
1 GGAGGGAATGATGCCCCAAGGACTTATCAT
32926 GGA
1 GGA
32929 CTTGAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (30 bp):
GGAGGGAATGATGCCCCAAGGACTTATCAT
Found at i:33084 original size:21 final size:21
Alignment explanation
Indices: 33048--33089 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33038 AGATGCCAAA
* *
33048 GATGCCATTTGATCCATTGAC
1 GATGCCATTAGATCCAATGAC
*
33069 GATGCCATTAGGTCCAATGAC
1 GATGCCATTAGATCCAATGAC
33090 AAGAGCAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
GATGCCATTAGATCCAATGAC
Found at i:35244 original size:33 final size:33
Alignment explanation
Indices: 35207--35293 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
35197 AGAATTTGTT
*
35207 TCATCACAAACAACACCTAAAGCAGATTTAGTG
1 TCATCACAAACAACACCTAAAGCAGATTTAGTA
* ** *
35240 TCATCACAAACAACACTTAAATTAGGTTTAGTA
1 TCATCACAAACAACACCTAAAGCAGATTTAGTA
* *
35273 TCATCACTAACAACATCTAAA
1 TCATCACAAACAACACCTAAA
35294 ACACTCTTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (33 bp):
TCATCACAAACAACACCTAAAGCAGATTTAGTA
Found at i:35895 original size:15 final size:15
Alignment explanation
Indices: 35875--35905 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35865 AACTAAGTGA
35875 AGCTTGTTGATTTTG
1 AGCTTGTTGATTTTG
35890 AGCTTGTTGATTTTG
1 AGCTTGTTGATTTTG
35905 A
1 A
35906 ACCTCCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.26, T:0.52
Consensus pattern (15 bp):
AGCTTGTTGATTTTG
Found at i:37382 original size:11 final size:11
Alignment explanation
Indices: 37362--37391 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
37352 CCTAGGGTAA
37362 AGGAAAGAGCT
1 AGGAAAGAGCT
*
37373 AGGAAGGAGCT
1 AGGAAAGAGCT
37384 AGGAAAGA
1 AGGAAAGA
37392 TCCTACTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.40, T:0.07
Consensus pattern (11 bp):
AGGAAAGAGCT
Found at i:37804 original size:21 final size:21
Alignment explanation
Indices: 37780--37821 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
37770 CTTTGTGCAC
37780 ATCCCTAGCATCTTCAAGCTT
1 ATCCCTAGCATCTTCAAGCTT
37801 ATCCCTAGCATCTTCAAGCTT
1 ATCCCTAGCATCTTCAAGCTT
37822 CTCCAAGCCT
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:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (21 bp):
ATCCCTAGCATCTTCAAGCTT
Found at i:40817 original size:22 final size:23
Alignment explanation
Indices: 40778--40820 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
40768 AATCCTAATC
40778 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
40801 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
40821 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:42779 original size:79 final size:79
Alignment explanation
Indices: 42648--42796 Score: 228
Period size: 79 Copynumber: 1.9 Consensus size: 79
42638 ATATTATGGC
* * * *
42648 TAATTGCTCAAATTGGTGCCTAATGTTTGCAAAAATACTCAAGTAAGGGCCTAACCTTGTAATTT
1 TAATTGCTCAAATTAGTGCCTAACGTTTGCAAAAATACTCAAATAAGGGCCTAACCTTCTAATTT
42713 GGTTAGTTAAGGGG
66 GGTTAGTTAAGGGG
* *
42727 TAATTGCTCAAATTAGT-CTCTAACGTTTGCGAAAATACTCAAATAAGGGCCTAACTTTCTAATT
1 TAATTGCTCAAATTAGTGC-CTAACGTTTGCAAAAATACTCAAATAAGGGCCTAACCTTCTAATT
42791 TGGTTA
65 TGGTTA
42797 ATTCATTAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 1 0.02
79 62 0.98
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (79 bp):
TAATTGCTCAAATTAGTGCCTAACGTTTGCAAAAATACTCAAATAAGGGCCTAACCTTCTAATTT
GGTTAGTTAAGGGG
Found at i:42873 original size:31 final size:31
Alignment explanation
Indices: 42805--42876 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
42795 TAATTCATTA
* * *
42805 AGTCCCAAACGTTGCAAAATCGATTCAAATC
1 AGTCCCTAACGTTACAAAATCGACTCAAATC
*
42836 AGTCCCTAACGTTACAAAATCGGCTCAAATC
1 AGTCCCTAACGTTACAAAATCGACTCAAATC
42867 AGTCCCTAAC
1 AGTCCCTAAC
42877 ATTTTGGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.22
Consensus pattern (31 bp):
AGTCCCTAACGTTACAAAATCGACTCAAATC
Done.