Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013938.1 Corchorus capsularis cultivar CVL-1 contig13959, 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: 53181
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:239 original size:42 final size:43
Alignment explanation
Indices: 174--256 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
164 CGTGTTTGGT
*
174 TTATCGTGTCTCGTATCTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTATCTGAATCGTGTCAAGACACGATTAAGA
* *
216 TTATCGTGTTTCGTGTC-GTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTATCTG-AATCGTGTCAAGACACGATTAA
257 CACGTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 24 0.67
43 11 0.31
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (43 bp):
TTATCGTGTCTCGTATCTGAATCGTGTCAAGACACGATTAAGA
Found at i:269 original size:20 final size:21
Alignment explanation
Indices: 244--286 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
234 TAATCGTGTC
*
244 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
264 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
285 AA
1 AA
287 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:442 original size:11 final size:11
Alignment explanation
Indices: 428--458 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
418 TATCTTTAAT
428 TATATATATAA
1 TATATATATAA
439 TATATATATAA
1 TATATATATAA
450 T-TATATATA
1 TATATATATA
459 TGATTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATATATATAA
Found at i:452 original size:33 final size:32
Alignment explanation
Indices: 392--453 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
382 TATACCCAAA
392 TAATTATTATAAAAAATATATTAAATTATCTT
1 TAATTATTATAAAAAATATATTAAATTATCTT
* *
424 TAATTA-TATATATAATATATATATAATTAT
1 TAATTATTATAAAAAATATAT-TA-AATTAT
454 ATATATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 12 0.46
32 8 0.31
33 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TAATTATTATAAAAAATATATTAAATTATCTT
Found at i:649 original size:12 final size:12
Alignment explanation
Indices: 628--659 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
618 TATCCTATGT
*
628 AAACATGACACG
1 AAACACGACACG
640 AAACACGACACG
1 AAACACGACACG
652 AAACACGA
1 AAACACGA
660 ATTGCCAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.28, G:0.16, T:0.03
Consensus pattern (12 bp):
AAACACGACACG
Found at i:2419 original size:89 final size:89
Alignment explanation
Indices: 2167--2402 Score: 436
Period size: 89 Copynumber: 2.7 Consensus size: 89
2157 AAAATAAAAC
* *
2167 TTGTAAATAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAT
1 TTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAAAT
2232 AAATAAAAATTATAAAGATTTAAT
66 AAATAAAAATTATAAAGATTTAAT
*
2256 TTGTAAAGAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAAAT
1 TTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAAAT
2321 AAATAAAAATTATAAAGATTTAAT
66 AAATAAAAATTATAAAGATTTAAT
*
2345 TTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTATGAGATATTTT
1 TTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTT
2403 TACAAATATT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 143 1.00
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.38
Consensus pattern (89 bp):
TTGTAAAAAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGAAAT
AAATAAAAATTATAAAGATTTAAT
Found at i:2563 original size:14 final size:13
Alignment explanation
Indices: 2527--2564 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2517 AAATTCAATT
2527 ATAAAAG-TAATA
1 ATAAAAGATAATA
*
2539 ATAAAAAATAATA
1 ATAAAAGATAATA
2552 ATTAAAAGATAAT
1 A-TAAAAGATAAT
2565 TTTAGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 6 0.27
13 6 0.27
14 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
ATAAAAGATAATA
Found at i:6388 original size:5 final size:5
Alignment explanation
Indices: 6366--6407 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
6356 GAAAAAAATG
**
6366 AAGAA AAGAA TTGAAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA AAGAA A
6408 GAAGTTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 29 0.91
6 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (5 bp):
AAGAA
Found at i:6684 original size:37 final size:37
Alignment explanation
Indices: 6606--6682 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
6596 ATGAAGAAGA
* ** *
6606 TTTTCTTCAAAGTGTGATCTTTTCACAAGAAAAAATG
1 TTTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAATG
6643 TTTTCCTCAAAGTGCAATCTTTTCAAAAG-AAAAATG
1 TTTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAATG
6679 TTTT
1 TTTT
6683 TCAAAAAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (37 bp):
TTTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAATG
Found at i:6691 original size:36 final size:37
Alignment explanation
Indices: 6622--6691 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
6612 TCAAAGTGTG
* **
6622 ATCTTTTCACAAGAAAAAATGTTTTCCTCAAAGTGCA
1 ATCTTTTCAAAAGAAAAAATGTTTTCCAAAAAGTGCA
*
6659 ATCTTTTCAAAAG-AAAAATGTTTTTCAAAAAGT
1 ATCTTTTCAAAAGAAAAAATGTTTTCCAAAAAGT
6692 TTTTAAGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 17 0.59
37 12 0.41
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (37 bp):
ATCTTTTCAAAAGAAAAAATGTTTTCCAAAAAGTGCA
Found at i:7168 original size:21 final size:21
Alignment explanation
Indices: 7129--7176 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
7119 AATTGACTTG
7129 GCGGGAAATTTTTTGGTTG-A
1 GCGGGAAATTTTTTGGTTGCA
* *
7149 GCGGGAACTTCTTTTTGTTGCA
1 GCGGGAAATT-TTTTGGTTGCA
7171 -CGGGAA
1 GCGGGAA
7177 GCTATGCGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 14 0.58
22 1 0.04
ACGTcount: A:0.19, C:0.12, G:0.33, T:0.35
Consensus pattern (21 bp):
GCGGGAAATTTTTTGGTTGCA
Found at i:11588 original size:22 final size:22
Alignment explanation
Indices: 11563--11609 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11553 GACAGTAGCT
*
11563 AAGAATGGGTA-AAGAAGAAGTC
1 AAGAAAGGGTAGAAGAAG-AGTC
*
11585 AAGAAAGGGTAGATGAAGAGTC
1 AAGAAAGGGTAGAAGAAGAGTC
11607 AAG
1 AAG
11610 TACAGGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.49, C:0.04, G:0.34, T:0.13
Consensus pattern (22 bp):
AAGAAAGGGTAGAAGAAGAGTC
Found at i:11839 original size:35 final size:34
Alignment explanation
Indices: 11778--12301 Score: 499
Period size: 35 Copynumber: 14.6 Consensus size: 34
11768 AGGTCAGAGT
* *
11778 TGACCTCTGAAAACTTCTTTAAAATGAGATCAACTC
1 TGACCTTTG-AAACTTC-TTGAAATGAGATCAACTC
* * *
11814 TGATCGTTTGAAATTTCTTGGAATGAGATCAACTC
1 TGA-CCTTTGAAACTTCTTGAAATGAGATCAACTC
* ** *
11849 TGACATCTAAAAACTTCTTGGAATGAGATCAACTC
1 TGACCT-TTGAAACTTCTTGAAATGAGATCAACTC
* * *
11884 TGAGCTCTGAAAACTTCTTGGAATGAGATCAACTC
1 TGACCTTTG-AAACTTCTTGAAATGAGATCAACTC
*
11919 TGACCTCTGAAAACTTCTTAATATGAAATGAGATCAACTC
1 TGACCTTTG-AAACTTC----T-TGAAATGAGATCAACTC
* *
11959 TGGCCTCTGGAAACTTCTTGAAATGAGATCAACTC
1 TGACCT-TTGAAACTTCTTGAAATGAGATCAACTC
*
11994 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
1 TGACCTTTG-AAACTTCTTGAAATGAGATCAACTC
*
12029 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
1 TGACCTTTG-AAACTTCTTGAAATGAGATCAACTC
* * * * *
12064 TGATCGTTGGAAACTTCTTGGAATCAGATCAACTT
1 TGA-CCTTTGAAACTTCTTGAAATGAGATCAACTC
** * *
12099 TGACCTCTAAAAACTTCTTTAAAATGAGACCAACTC
1 TGACCT-TTGAAACTTC-TTGAAATGAGATCAACTC
* *
12135 TGATCGTTTGAAACTTCTTGGAATGAGATCAACTC
1 TGA-CCTTTGAAACTTCTTGAAATGAGATCAACTC
* *
12170 TGACCTCTGAAAACTTCTTAATATGAAATGAGTTCAACTC
1 TGACCTTTG-AAACTTC----T-TGAAATGAGATCAACTC
* *
12210 TGGCCTCTGGAAACTTCTTGAAATGAGATCAACTC
1 TGACCT-TTGAAACTTCTTGAAATGAGATCAACTC
*
12245 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
1 TGACCTTTG-AAACTTCTTGAAATGAGATCAACTC
*
12280 TGACCTCTGAAAACTTCTTGAA
1 TGACCTTTG-AAACTTCTTGAA
12302 GCGTTTGACT
Statistics
Matches: 413, Mismatches: 53, Indels: 45
0.81 0.10 0.09
Matches are distributed among these distances:
34 10 0.02
35 300 0.73
36 38 0.09
37 6 0.01
39 2 0.00
40 55 0.13
41 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (34 bp):
TGACCTTTGAAACTTCTTGAAATGAGATCAACTC
Found at i:11879 original size:70 final size:70
Alignment explanation
Indices: 11778--12301 Score: 658
Period size: 70 Copynumber: 7.3 Consensus size: 70
11768 AGGTCAGAGT
* * * * *
11778 TGACCTCTGAAAACTTCTTTAAAATGAGATCAACTCTGATCGTTTG-AAATTTCTTGGAATGAGA
1 TGACCTCTGAAAACTTC-TTGAAATGAGATCAACTCTGA-CCTCTGAAAACTTCTTGAAATGAGA
11842 TCAACTC
64 TCAACTC
* * * * *
11849 TGACATCTAAAAACTTCTTGGAATGAGATCAACTCTGAGCTCTGAAAACTTCTTGGAATGAGATC
1 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATC
11914 AACTC
66 AACTC
* *
11919 TGACCTCTGAAAACTTCTTAATATGAAATGAGATCAACTCTGGCCTCTGGAAACTTCTTGAAATG
1 TGACCTCTGAAAACTTC----T-TGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATG
11984 AGATCAACTC
61 AGATCAACTC
11994 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATC
1 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATC
12059 AACTC
66 AACTC
* * * * * * *
12064 TGATCGT-TGGAAACTTCTTGGAATCAGATCAACTTTGACCTCTAAAAACTTCTTTAAAATGAGA
1 TGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTC-TTGAAATGAGA
*
12128 CCAACTC
64 TCAACTC
* * *
12135 TGATCGTTTG-AAACTTCTTGGAATGAGATCAACTCTGACCTCTGAAAACTTCTTAATATGAAAT
1 TGA-CCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTC----T-TGAAAT
*
12199 GAGTTCAACTC
60 GAGATCAACTC
* *
12210 TGGCCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATC
1 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATC
12275 AACTC
66 AACTC
12280 TGACCTCTGAAAACTTCTTGAA
1 TGACCTCTGAAAACTTCTTGAA
12302 GCGTTTGACT
Statistics
Matches: 400, Mismatches: 39, Indels: 29
0.85 0.08 0.06
Matches are distributed among these distances:
69 3 0.01
70 187 0.47
71 81 0.20
72 2 0.00
74 6 0.01
75 121 0.30
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (70 bp):
TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATC
AACTC
Found at i:12221 original size:251 final size:250
Alignment explanation
Indices: 11778--12301 Score: 906
Period size: 251 Copynumber: 2.1 Consensus size: 250
11768 AGGTCAGAGT
* * * *
11778 TGACCTCTGAAAACTTCTTTAAAATGAGATCAACTCTGATCGTTTGAAATTTCTTGGAATGAGAT
1 TGACCTCTGAAAACTTC-TTGAAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAATCAGAT
** *
11843 CAACTCTGACATCTAAAAACTTCTTGGAATGAGATCAACTCTGAGCTCTGAAAACTTCTTGGAAT
65 CAACTCTGACATCTAAAAACTTCTTAAAATGAGACCAACTCTGAGCTCTGAAAACTTCTTGGAAT
11908 GAGATCAACTCTGACCTCTGAAAACTTCTTAATATGAAATGAGATCAACTCTGGCCTCTGGAAAC
130 GAGATCAACTCTGACCTCTGAAAACTTCTTAATATGAAATGAGATCAACTCTGGCCTCTGGAAAC
11973 TTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
195 TTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
12029 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAATCAGATC
1 TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAATCAGATC
* * * *
12094 AACTTTGACCTCTAAAAACTTCTTTAAAATGAGACCAACTCTGATCGTTTG-AAACTTCTTGGAA
66 AACTCTGACATCTAAAAACTTC-TTAAAATGAGACCAACTCTGAGC-TCTGAAAACTTCTTGGAA
*
12158 TGAGATCAACTCTGACCTCTGAAAACTTCTTAATATGAAATGAGTTCAACTCTGGCCTCTGGAAA
129 TGAGATCAACTCTGACCTCTGAAAACTTCTTAATATGAAATGAGATCAACTCTGGCCTCTGGAAA
12223 CTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
194 CTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
12280 TGACCTCTGAAAACTTCTTGAA
1 TGACCTCTGAAAACTTCTTGAA
12302 GCGTTTGACT
Statistics
Matches: 259, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
250 64 0.25
251 192 0.74
252 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (250 bp):
TGACCTCTGAAAACTTCTTGAAATGAGATCAACTCTGATCGTTGGAAACTTCTTGGAATCAGATC
AACTCTGACATCTAAAAACTTCTTAAAATGAGACCAACTCTGAGCTCTGAAAACTTCTTGGAATG
AGATCAACTCTGACCTCTGAAAACTTCTTAATATGAAATGAGATCAACTCTGGCCTCTGGAAACT
TCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGAAATGAGATCAACTC
Found at i:12427 original size:16 final size:17
Alignment explanation
Indices: 12400--12448 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
12390 AAATTAAGAG
*
12400 TTAAGTAATTAAAAAAT
1 TTAAGCAATTAAAAAAT
*
12417 TTCAG-AATTAAAAAA-
1 TTAAGCAATTAAAAAAT
12432 TTAAGCAATTAAAAAAT
1 TTAAGCAATTAAAAAAT
12449 GAAAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.14
16 20 0.71
17 4 0.14
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (17 bp):
TTAAGCAATTAAAAAAT
Found at i:17186 original size:31 final size:31
Alignment explanation
Indices: 17147--17228 Score: 146
Period size: 31 Copynumber: 2.6 Consensus size: 31
17137 GTCACCTCAT
17147 CAAACGTTATATCCTGAATTAGATTTTCGGG
1 CAAACGTTATATCCTGAATTAGATTTTCGGG
* *
17178 GAAACGTTAAATCCTGAATTAGATTTTCGGG
1 CAAACGTTATATCCTGAATTAGATTTTCGGG
17209 CAAACGTTATATCCTGAATT
1 CAAACGTTATATCCTGAATT
17229 GATCATTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (31 bp):
CAAACGTTATATCCTGAATTAGATTTTCGGG
Found at i:17808 original size:21 final size:20
Alignment explanation
Indices: 17778--17816 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17768 TAAATTTTTT
17778 GTCGGAATAGCCATTTTTACC
1 GTCGGAATAGCC-TTTTTACC
* *
17799 GTCGGTATAGGCTTTTTA
1 GTCGGAATAGCCTTTTTA
17817 AGCCTATACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
GTCGGAATAGCCTTTTTACC
Found at i:19236 original size:31 final size:32
Alignment explanation
Indices: 19160--19242 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 32
19150 TCGGATTTGG
* *
19160 GATTGAGTT-AGG-TCGGGTTGAATTTGGGTCA
1 GATTGA-TTCAGGTTCGGGTTAAAATTGGGTCA
19191 GATTGATTCAGGTTCGGGTTAAAATTGGGTCA
1 GATTGATTCAGGTTCGGGTTAAAATTGGGTCA
* *
19223 G-TTGATTCGGGTTCAGGTTA
1 GATTGATTCAGGTTCGGGTTA
19243 TATTACAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
30 2 0.04
31 26 0.57
32 18 0.39
ACGTcount: A:0.20, C:0.08, G:0.35, T:0.36
Consensus pattern (32 bp):
GATTGATTCAGGTTCGGGTTAAAATTGGGTCA
Found at i:22875 original size:23 final size:24
Alignment explanation
Indices: 22849--22903 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
22839 CTAAAACCTC
*
22849 TATTTTTATTCA-ATTAAATCTAA
1 TATTTTTATTCATAGTAAATCTAA
*
22872 TATTTTT-TTGATAGTAAATCTAA
1 TATTTTTATTCATAGTAAATCTAA
*
22895 TATCTTTAT
1 TATTTTTAT
22904 AATTACTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 23 0.85
24 1 0.04
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.55
Consensus pattern (24 bp):
TATTTTTATTCATAGTAAATCTAA
Found at i:24567 original size:27 final size:27
Alignment explanation
Indices: 24537--24604 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
24527 GTCAGACTCT
* *
24537 CATTCCAAGTTAGTCAAGACAG-TTCTC
1 CATTCAAAGTTAGTCAAAACAGTTTC-C
**
24564 CATTCAAAACTAGTCAAAACAGTTTCC
1 CATTCAAAGTTAGTCAAAACAGTTTCC
24591 CATTCAAAGTTAGT
1 CATTCAAAGTTAGT
24605 TCCCTAGGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 31 0.91
28 3 0.09
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (27 bp):
CATTCAAAGTTAGTCAAAACAGTTTCC
Found at i:29088 original size:27 final size:27
Alignment explanation
Indices: 29021--29088 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
29011 GTCAAACCCT
* *
29021 CATTCCAAGTTAGTCAAGACAGTTCTC
1 CATTCAAAGTTAGTCAAAACAGTTCTC
**
29048 CATTCAAAACTAGTCAAAACAGTT-TCC
1 CATTCAAAGTTAGTCAAAACAGTTCT-C
29075 CATTCAAAGTTAGT
1 CATTCAAAGTTAGT
29089 TCCCTAGGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (27 bp):
CATTCAAAGTTAGTCAAAACAGTTCTC
Found at i:32925 original size:21 final size:20
Alignment explanation
Indices: 32886--32930 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
32876 AATTATCAAT
* *
32886 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
32906 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
32927 TAAA
1 TAAA
32931 TCTAGATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:43058 original size:48 final size:49
Alignment explanation
Indices: 43006--43099 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 49
42996 TGACAACACC
* * *
43006 GAGCTTAACCCAAGCTCTAGCAAGTGC-TCCCCGCACTGATTACAACAA
1 GAGCTTAACCCAAGCTCAAACAAGTGCTTCACCGCACTGATTACAACAA
**
43054 GAGCTTTCCCCAAGCTCAAACAAGTGCTTCACCGCACTGATTACAA
1 GAGCTTAACCCAAGCTCAAACAAGTGCTTCACCGCACTGATTACAA
43100 TCAAAGAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 23 0.57
49 17 0.43
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (49 bp):
GAGCTTAACCCAAGCTCAAACAAGTGCTTCACCGCACTGATTACAACAA
Found at i:43467 original size:76 final size:76
Alignment explanation
Indices: 43338--43487 Score: 203
Period size: 76 Copynumber: 2.0 Consensus size: 76
43328 TTCTCTTAGG
* * * *
43338 TCCTTATATACTCAGATCTGTCTCCAACGGTAATTCTCCTCATTAAATGCAAATCTCTCAAATCT
1 TCCTTAAATACTCAGATCTGCCTCCAACGGTAAATCTCCTCATCAAATGCAAATCTCTCAAATCT
43403 GTCAATTTGTT
66 GTCAATTTGTT
* * * *
43414 TCCTTAAATACTTAGATCTGCCTCCAACGGTCAAAT-TCCTCATCAATTTCAAATCTTTCAAATC
1 TCCTTAAATACTCAGATCTGCCTCCAACGGT-AAATCTCCTCATCAAATGCAAATCTCTCAAATC
*
43478 TGTCTATTTG
65 TGTCAATTTG
43488 AATTATAGCC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 61 0.95
77 3 0.05
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (76 bp):
TCCTTAAATACTCAGATCTGCCTCCAACGGTAAATCTCCTCATCAAATGCAAATCTCTCAAATCT
GTCAATTTGTT
Found at i:43726 original size:96 final size:96
Alignment explanation
Indices: 43556--43740 Score: 221
Period size: 96 Copynumber: 1.9 Consensus size: 96
43546 TTTCTGGTAG
* * * * *
43556 TCCCACTAAAGTGATGCTTCTCATTGTTGGCATTAATCCTTCCTTCAACTGAATACCTTATGACT
1 TCCCACTAAAGTCATGCTTCACATTGTTGGCACTAATACTTCCTTCAACTAAATACCTTATGACT
** ** *
43621 TGTGTCTTGTGGCTTCTACTTCTTACGTTAA
66 AATAACTTGTAGCTTCTACTTCTTACGTTAA
* *
43652 TCCCACTAAAGTCATG-TTCCACATTGTTGGCACTAATACTTGCTTCAACTAAATACCTTATCTA
1 TCCCACTAAAGTCATGCTT-CACATTGTTGGCACTAATACTTCCTTCAACTAAATACCTTAT-GA
*
43716 C-AATAACTTGTAGCTTCTGCTTCTT
64 CTAATAACTTGTAGCTTCTACTTCTT
43741 CCTTGATGTG
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
95 2 0.03
96 70 0.95
97 2 0.03
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (96 bp):
TCCCACTAAAGTCATGCTTCACATTGTTGGCACTAATACTTCCTTCAACTAAATACCTTATGACT
AATAACTTGTAGCTTCTACTTCTTACGTTAA
Done.