Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015087.1 Corchorus olitorius cultivar O-4 contig15120, 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: 120681
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1696 original size:16 final size:16
Alignment explanation
Indices: 1675--1707 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1665 TCTTGATCTT
*
1675 ATAATAAATATAATAA
1 ATAATAAATAAAATAA
1691 ATAATAAATAAAATAA
1 ATAATAAATAAAATAA
1707 A
1 A
1708 ATAAGAAGGA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAATAAATAAAATAA
Found at i:2285 original size:12 final size:12
Alignment explanation
Indices: 2268--2292 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2258 GCAGCTTATT
2268 TTCCTTAGGTGC
1 TTCCTTAGGTGC
2280 TTCCTTAGGTGC
1 TTCCTTAGGTGC
2292 T
1 T
2293 GAGTGCTTAT
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:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TTCCTTAGGTGC
Found at i:2384 original size:32 final size:32
Alignment explanation
Indices: 2348--2413 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
2338 TAGGTGCTTC
*
2348 TTTAGGTGCTGAATGCTTATAAGCAATTTATT
1 TTTAGGTGCTGAATGCTTATAAGCAACTTATT
* * *
2380 TTTAGGTGCTGAGTGTTTATAAGCAGCTTATT
1 TTTAGGTGCTGAATGCTTATAAGCAACTTATT
2412 TT
1 TT
2414 CCTTAGGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45
Consensus pattern (32 bp):
TTTAGGTGCTGAATGCTTATAAGCAACTTATT
Found at i:2730 original size:66 final size:66
Alignment explanation
Indices: 2658--2785 Score: 220
Period size: 66 Copynumber: 1.9 Consensus size: 66
2648 CAAAAACAAC
*
2658 TGAAAAAAGCACTTCTGAAAAACACTTCTGGATTTTCCGTTTGACCCAGCTTAAGTTTTTCTCAA
1 TGAAAAAAGCACTTCTGAAAAACACTTCTGGATTTTCCGTTTGACACAGCTTAAGTTTTTCTCAA
2723 T
66 T
* * *
2724 TGAAAAAAGTACTTCTGAAAAACACTTCTGGATTTTCTGTTTGGCACAGCTTAAGTTTTTCT
1 TGAAAAAAGCACTTCTGAAAAACACTTCTGGATTTTCCGTTTGACACAGCTTAAGTTTTTCT
2786 TAGTAGATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (66 bp):
TGAAAAAAGCACTTCTGAAAAACACTTCTGGATTTTCCGTTTGACACAGCTTAAGTTTTTCTCAA
T
Found at i:2849 original size:117 final size:118
Alignment explanation
Indices: 2707--2943 Score: 397
Period size: 117 Copynumber: 2.0 Consensus size: 118
2697 TTTGACCCAG
* * *
2707 CTTAAGTTTTTCTCAATTGAAAAAAGTACTTCTGAAAAACACTTCTGGATTTTCTGTTTGG-CAC
1 CTTAAGTTTTTCTCAACTGAAAAAAGCACTTCTGAAAAACACTTCTGGATTTTCCGTTTGGTC-C
2771 AGCTTAAGTTTTTCTTAGTAGATAAACTGTTAAATAAGCTGGG-CAAACAGACC
65 AGCTTAAGTTTTTCTTAGTAGATAAACTGTTAAATAAGCTGGGTCAAACAGACC
*
2824 CTTAAGTTTTTCTCAACTGAAAAAAGCACTTCTGAAAAGCACTTCTGGATTTTCCGTTTGGTCCA
1 CTTAAGTTTTTCTCAACTGAAAAAAGCACTTCTGAAAAACACTTCTGGATTTTCCGTTTGGTCCA
* *
2889 GCTTAAGTTTTTCTTAGTAGATAAATTGTTAAATAAGCTGGGTCAAACGGACC
66 GCTTAAGTTTTTCTTAGTAGATAAACTGTTAAATAAGCTGGGTCAAACAGACC
2942 CT
1 CT
2944 AAATGGTGTC
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
117 100 0.89
118 12 0.11
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (118 bp):
CTTAAGTTTTTCTCAACTGAAAAAAGCACTTCTGAAAAACACTTCTGGATTTTCCGTTTGGTCCA
GCTTAAGTTTTTCTTAGTAGATAAACTGTTAAATAAGCTGGGTCAAACAGACC
Found at i:2863 original size:13 final size:13
Alignment explanation
Indices: 2845--2870 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2835 CTCAACTGAA
2845 AAAAGCACTTCTG
1 AAAAGCACTTCTG
2858 AAAAGCACTTCTG
1 AAAAGCACTTCTG
2871 GATTTTCCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
AAAAGCACTTCTG
Found at i:7159 original size:22 final size:22
Alignment explanation
Indices: 7134--7366 Score: 118
Period size: 22 Copynumber: 10.5 Consensus size: 22
7124 TGTCTCTGTG
*
7134 TGGTTATAAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
7156 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
7179 -GGTTATCAAAATTCCAT-CGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
7200 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
7223 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
7244 AGGTTACCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
7266 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
7288 TCAGGTTATTAAAATTTCTTAAAA
1 T--GGTTATCAAAATTTCATAAGA
* **
7312 AGGTTATTGAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* *
7334 TGGTTATCACAATTTTAT-AGAA
1 TGGTTATCAAAATTTCATAAG-A
*
7356 AGGTTATCAAA
1 TGGTTATCAAA
7367 GAGATAATCA
Statistics
Matches: 160, Mismatches: 38, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.01
21 5 0.03
22 132 0.82
23 4 0.03
24 17 0.11
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:7237 original size:66 final size:66
Alignment explanation
Indices: 7131--7305 Score: 201
Period size: 66 Copynumber: 2.6 Consensus size: 66
7121 TCTTGTCTCT
** * * * *
7131 GTGTGGTTATAAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATG-GGAAGGTTACCAAAATTCCA
*
7195 TC
65 TA
* *
7197 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATGGGAAGGTTACCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGGGAAGGTTACCAAAATTCCA
7261 TA
65 TA
* *
7263 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC
1 GTGTGGTTACCAAAATTTCATAAGAT-A-GTTATCAAAATTTC
7306 TTAAAAAGGT
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
65 5 0.05
66 73 0.78
67 3 0.03
68 13 0.14
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGGAAGGTTACCAAAATTCCAT
A
Found at i:7438 original size:22 final size:22
Alignment explanation
Indices: 7413--7474 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
7403 TCCGTAGTGT
7413 GGTTAACAAAATTTCATAAGAA
1 GGTTAACAAAATTTCATAAGAA
* ** *
7435 GGTT-ACTAATATTTCATGGGGA
1 GGTTAAC-AAAATTTCATAAGAA
*
7457 GGTTATCAAAATTTCATA
1 GGTTAACAAAATTTCATA
7475 CTATGGTTAC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
GGTTAACAAAATTTCATAAGAA
Found at i:7569 original size:22 final size:22
Alignment explanation
Indices: 7513--7959 Score: 193
Period size: 22 Copynumber: 20.5 Consensus size: 22
7503 AAACTTTTAC
*
7513 TATGGA-GTGATCAAAATTTC-
1 TATGGAGGTTATCAAAATTTCA
* *
7533 -AGGGAGGATATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
7554 TATGAAGGTTATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
** * *
7576 TAGTTTA-GTTTTTAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
* * *
7598 TAGGGAGATTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
7620 TAAT-GAGGTTATCCAAAA-ATCA
1 T-ATGGAGGTTAT-CAAAATTTCA
7642 TA-GAGAGGTTATCAAAATTT--
1 TATG-GAGGTTATCAAAATTTCA
*
7662 T-T--A-GTTATCAAGATTTCA
1 TATGGAGGTTATCAAAATTTCA
* *
7680 TAAGGAGGTTATCAAAATTTTA
1 TATGGAGGTTATCAAAATTTCA
* *
7702 TAGGGAGGTTTATCAAAATTTTA
1 TATGGAGG-TTATCAAAATTTCA
* *
7725 TA-GCGAGATTATCACAATTTCA
1 TATG-GAGGTTATCAAAATTTCA
7747 TAGTGTGA--TTATCAAAATTTCA
1 TA-TG-GAGGTTATCAAAATTTCA
*
7769 GAGTGTGA--TTA-CTAACAA-TTCA
1 TA-TG-GAGGTTATC-AA-AATTTCA
* * *
7791 TATGGAGGTTTTTAAATTTTCA
1 TATGGAGGTTATCAAAATTTCA
** * * * *
7813 TAACGTGATTATCAATATATCA
1 TATGGAGGTTATCAAAATTTCA
* * *
7835 TATAGAGGTTATCAACATCTCA
1 TATGGAGGTTATCAAAATTTCA
*
7857 TAGTGTTGTTGGTTATCAAAATTTCA
1 TA-TG--G-AGGTTATCAAAATTTCA
*
7883 T-TCGGAAGTTATCAAAATTTCA
1 TAT-GGAGGTTATCAAAATTTCA
* *
7905 TA-GTGAGGTCT-TCAAAATTCCT
1 TATG-GAGGT-TATCAAAATTTCA
* * *
7927 TAAGGATGTTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
* *
7949 TAAGAAGGTTA
1 TATGGAGGTTA
7960 AAAAAAATTT
Statistics
Matches: 323, Mismatches: 67, Indels: 72
0.70 0.15 0.16
Matches are distributed among these distances:
16 12 0.04
17 1 0.00
18 1 0.00
19 4 0.01
20 15 0.05
21 14 0.04
22 222 0.69
23 33 0.10
24 4 0.01
25 2 0.01
26 15 0.05
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATGGAGGTTATCAAAATTTCA
Found at i:16212 original size:121 final size:127
Alignment explanation
Indices: 15971--16220 Score: 386
Period size: 121 Copynumber: 2.0 Consensus size: 127
15961 TAAGAAATAA
*
15971 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-
*
16036 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAAAAGTA
62 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTA
16101 T
127 T
16102 ATTTAAAAAATTC-TA-ATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-
1 ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
* *
16162 AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
66 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGT
16221 TTAAACAATG
Statistics
Matches: 115, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
121 54 0.47
122 2 0.02
123 2 0.02
125 2 0.02
129 40 0.35
130 2 0.02
131 13 0.11
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
ATTTAAAAAATTCTTATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAGTAT
Found at i:19654 original size:3 final size:3
Alignment explanation
Indices: 19646--19677 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19636 TTATAATTAT
19646 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
19678 GATCATTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:24665 original size:3 final size:3
Alignment explanation
Indices: 24657--24699 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
24647 AGATAAAAAG
24657 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
24700 AGAAGTAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32664 original size:131 final size:132
Alignment explanation
Indices: 32494--32737 Score: 382
Period size: 132 Copynumber: 1.9 Consensus size: 132
32484 ATATATATAT
* *
32494 ATATATAAGTTTTTTTAATTAAATTAATAAAATGAT-AAAATAAAATAGGTATAAGGATATTAGA
1 ATATATAAGTTTTTTAAATTAAAATAATAAAATGATAAAAATAAAATAGGTATAAGGATATTAGA
* * *
32558 TTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAAATTCTA
66 TTTAATTAAATAAAAAAAGAGTTTTAAATTGAGTAAAACTATAAAAGTATATTTAAAAAATTCTA
32623 AC
131 AC
* * * * *
32625 ATATATAAGTTTTTTAAATTAAAATAGTTAAATGGTAAAAATCAAATAGTTATAAGGATATTAGA
1 ATATATAAGTTTTTTAAATTAAAATAATAAAATGATAAAAATAAAATAGGTATAAGGATATTAGA
*
32690 TTTAGTTAAATAAAAAAAGAGTTTTAAATTGAGTAAAACTATAAAAGT
66 TTTAATTAAATAAAAAAAGAGTTTTAAATTGAGTAAAACTATAAAAGT
32738 CTAAACAATG
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
131 31 0.31
132 70 0.69
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (132 bp):
ATATATAAGTTTTTTAAATTAAAATAATAAAATGATAAAAATAAAATAGGTATAAGGATATTAGA
TTTAATTAAATAAAAAAAGAGTTTTAAATTGAGTAAAACTATAAAAGTATATTTAAAAAATTCTA
AC
Found at i:37262 original size:29 final size:29
Alignment explanation
Indices: 37229--37288 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
37219 GTTTAATCTT
37229 GAACATACGCTAAAATTAGTTAGAGAGAA
1 GAACATACGCTAAAATTAGTTAGAGAGAA
*
37258 GAACATGCGCTAAAATTAGTTAGAGAGAA
1 GAACATACGCTAAAATTAGTTAGAGAGAA
37287 GA
1 GA
37289 GGGTAGGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (29 bp):
GAACATACGCTAAAATTAGTTAGAGAGAA
Found at i:37575 original size:42 final size:42
Alignment explanation
Indices: 37511--37592 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
37501 CCAATGATGT
37511 TGTATTGAATAATTTTCCTTTAACCTTTCCTTTTCTTTAATG
1 TGTATTGAATAATTTTCCTTTAACCTTTCCTTTTCTTTAATG
*
37553 TGTATTGAATAATTTTCTTTTAACCTTTCCTTTTCTTTAA
1 TGTATTGAATAATTTTCCTTTAACCTTTCCTTTTCTTTAA
37593 CTCCACTGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (42 bp):
TGTATTGAATAATTTTCCTTTAACCTTTCCTTTTCTTTAATG
Found at i:37695 original size:39 final size:39
Alignment explanation
Indices: 37642--37725 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
37632 TTTTAGTTAT
** *
37642 TCACTTATGTATTAAGATAAGTATAATAGTAACCTTCAC
1 TCACTTATACATTAAGATAAGTATAATAGTAACCTTCAA
*
37681 TCACTTATACATTAAGATAAGTATATTAGTAACCTTCAA
1 TCACTTATACATTAAGATAAGTATAATAGTAACCTTCAA
37720 TCACTT
1 TCACTT
37726 TTTTGTAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (39 bp):
TCACTTATACATTAAGATAAGTATAATAGTAACCTTCAA
Found at i:59958 original size:16 final size:17
Alignment explanation
Indices: 59926--59958 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59916 CCCTGGTTCT
59926 TCCTTTGTCTGAGCAAC
1 TCCTTTGTCTGAGCAAC
*
59943 TCCTTTTTCT-AGCAAC
1 TCCTTTGTCTGAGCAAC
59959 ATTAGTCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.39
Consensus pattern (17 bp):
TCCTTTGTCTGAGCAAC
Found at i:69048 original size:16 final size:17
Alignment explanation
Indices: 69016--69048 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
69006 CTTTGGTTCT
69016 TCCTTTGTCTGAGCAAC
1 TCCTTTGTCTGAGCAAC
*
69033 TCCTTTTTCT-AGCAAC
1 TCCTTTGTCTGAGCAAC
69049 ATTAGTCGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.39
Consensus pattern (17 bp):
TCCTTTGTCTGAGCAAC
Found at i:71068 original size:16 final size:16
Alignment explanation
Indices: 71034--71068 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
71024 ACAATTCAAA
* *
71034 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAACTCAG
71050 AAGCAGAAAAACTCAG
1 AAGCAGAAAAACTCAG
71066 AAG
1 AAG
71069 TATTTTCAGA
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:0.51, C:0.17, G:0.23, T:0.09
Consensus pattern (16 bp):
AAGCAGAAAAACTCAG
Found at i:71209 original size:41 final size:41
Alignment explanation
Indices: 71164--71446 Score: 372
Period size: 41 Copynumber: 6.9 Consensus size: 41
71154 TTTTCGTTTG
71164 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
71205 TTCAAGATTGAGTTATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
71246 TTCAAGAACAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
71287 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
71328 TTCAAGAACAAGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * * *
71372 TTCAAGACCAAGTCGTCAAGACCTTTGAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
71413 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
71447 CAAATCAAAC
Statistics
Matches: 213, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
40 13 0.06
41 161 0.76
42 4 0.02
43 1 0.00
44 34 0.16
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:71883 original size:29 final size:29
Alignment explanation
Indices: 71840--71896 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
71830 ATCAATGGGT
*
71840 TCCAAATTGACAATTCATTGGAGAAAACG
1 TCCAAATTGACAATTCAATGGAGAAAACG
*
71869 TCCAAAGTTGA-AATTCAATGGATAAAAC
1 TCCAAA-TTGACAATTCAATGGAGAAAAC
71897 ATCCCAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (29 bp):
TCCAAATTGACAATTCAATGGAGAAAACG
Found at i:72833 original size:2 final size:2
Alignment explanation
Indices: 72783--72817 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
72773 ATAAATTAAT
72783 TA 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 TA T
72818 CAAGTTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73381 original size:27 final size:27
Alignment explanation
Indices: 73343--73394 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
73333 AATTTTCATA
73343 TCTTGATTTAAAAAGATTGGGATTATT
1 TCTTGATTTAAAAAGATTGGGATTATT
* *
73370 TCTTGGTTTAAAGAGATTGGGATTA
1 TCTTGATTTAAAAAGATTGGGATTA
73395 CAAACGCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (27 bp):
TCTTGATTTAAAAAGATTGGGATTATT
Found at i:73525 original size:13 final size:13
Alignment explanation
Indices: 73507--73534 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
73497 CACAGATGAG
73507 AATACCTACCTAC
1 AATACCTACCTAC
73520 AATACCTACCTAC
1 AATACCTACCTAC
73533 AA
1 AA
73535 ATAAACGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (13 bp):
AATACCTACCTAC
Found at i:73620 original size:48 final size:48
Alignment explanation
Indices: 73566--73667 Score: 177
Period size: 48 Copynumber: 2.1 Consensus size: 48
73556 GATTGGGATT
* **
73566 ACAAACGCACAGTAATCCCCGTACACAGATGAGAATACCTACCTACAA
1 ACAAACGCACAGGAAGACCCGTACACAGATGAGAATACCTACCTACAA
73614 ACAAACGCACAGGAAGACCCGTACACAGATGAGAATACCTACCTACAA
1 ACAAACGCACAGGAAGACCCGTACACAGATGAGAATACCTACCTACAA
73662 ACAAAC
1 ACAAAC
73668 AAATTACAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.44, C:0.30, G:0.14, T:0.12
Consensus pattern (48 bp):
ACAAACGCACAGGAAGACCCGTACACAGATGAGAATACCTACCTACAA
Found at i:87247 original size:16 final size:15
Alignment explanation
Indices: 87226--87255 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
87216 TTTTAAAGTG
87226 TGTATTGGTAGTGTAA
1 TGTATTGG-AGTGTAA
87242 TGTATTGGAGTGTA
1 TGTATTGGAGTGTA
87256 TAATAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
TGTATTGGAGTGTAA
Found at i:88872 original size:104 final size:104
Alignment explanation
Indices: 88687--88892 Score: 295
Period size: 104 Copynumber: 2.0 Consensus size: 104
88677 GGAATGATCA
* ** *
88687 GCACCGCTTCCCTCAATTTCCTATATAAGTTGTGAATCTTCATCTCTCTCGATAGTTTCCTCCGT
1 GCACCGCTTCCCTCAATTTCCTATATAAATCCTGAATCTTCATCTCTCTCGATAGTTTCCTACGT
* *
88752 TTTTTTCTCTCTCTTTTTGCTCCGCTTCTCCTTGATTCT
66 TTTTTTCTCTCTCTTTTTGCTCCGATTCTCCTAGATTCT
* * * * * *
88791 GCACTGCTTCCCTCAATTTCTTATATAAATCCTGTATCTTCATCTCTCTCGATGGTTTTCTATGT
1 GCACCGCTTCCCTCAATTTCCTATATAAATCCTGAATCTTCATCTCTCTCGATAGTTTCCTACGT
*
88856 TTTTTTCTCTCTCTTTTTGCTCTGATTCTCCTAGATT
66 TTTTTTCTCTCTCTTTTTGCTCCGATTCTCCTAGATT
88893 TTCTCTGTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 89 1.00
ACGTcount: A:0.14, C:0.28, G:0.10, T:0.48
Consensus pattern (104 bp):
GCACCGCTTCCCTCAATTTCCTATATAAATCCTGAATCTTCATCTCTCTCGATAGTTTCCTACGT
TTTTTTCTCTCTCTTTTTGCTCCGATTCTCCTAGATTCT
Found at i:89952 original size:117 final size:118
Alignment explanation
Indices: 89730--89965 Score: 431
Period size: 117 Copynumber: 2.0 Consensus size: 118
89720 CACCAAATTA
89730 ATGTTGAATTACTTAATTCAAGTATATTTTCCCCCATCTATGTAGTAGTATCTAACTACCCCAGG
1 ATGTTGAATTACTTAATTCAAGTATATTTTCCCCCATCTA-GTAGTAGTATCTAACTACCCCAGG
89795 TTATGATTTGTGTGATTCGTTTATCATAATCTTAAGAAGCTCCTCTTTTACATG
65 TTATGATTTGTGTGATTCGTTTATCATAATCTTAAGAAGCTCCTCTTTTACATG
89849 ATGTTGAATTACTTAATTCAAGTATATTTTCCCCCATCTA-T-GTAGTATCTAACTACCCCCAGG
1 ATGTTGAATTACTTAATTCAAGTATATTTTCCCCCATCTAGTAGTAGTATCTAACTA-CCCCAGG
*
89912 TTATGATTTGTGTGATTCGTTTATCATTATCTTAAGAAGCTCCTCTTTTACATG
65 TTATGATTTGTGTGATTCGTTTATCATAATCTTAAGAAGCTCCTCTTTTACATG
89966 CAAACAATCA
Statistics
Matches: 115, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
116 14 0.12
117 61 0.53
119 40 0.35
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (118 bp):
ATGTTGAATTACTTAATTCAAGTATATTTTCCCCCATCTAGTAGTAGTATCTAACTACCCCAGGT
TATGATTTGTGTGATTCGTTTATCATAATCTTAAGAAGCTCCTCTTTTACATG
Found at i:92427 original size:31 final size:29
Alignment explanation
Indices: 92388--92468 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
92378 GGCTAAATAA
*
92388 TCAATTCAGGATATAAAGTTTGACGAAAAA-
1 TCAATTCAGGATATAAAG-TT-ACAAAAAAG
* *
92418 TGCAATTCAGAATATAACGTTACAAAAAAG
1 T-CAATTCAGGATATAAAGTTACAAAAAAG
* *
92448 TTAATTCAGGATATAATGTTA
1 TCAATTCAGGATATAAAGTTA
92469 TCTAATCCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 24 0.56
30 4 0.09
31 15 0.35
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.30
Consensus pattern (29 bp):
TCAATTCAGGATATAAAGTTACAAAAAAG
Found at i:98046 original size:3 final size:3
Alignment explanation
Indices: 98040--98064 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
98030 GAGTATCTCC
98040 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
98065 TTTTTTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:104761 original size:41 final size:41
Alignment explanation
Indices: 104704--104785 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
104694 AATGGTATCA
104704 AACCTCAAATAATATGAAACTCTACCTATATTTATAATTTT
1 AACCTCAAATAATATGAAACTCTACCTATATTTATAATTTT
104745 AACCTCAAATAATATGAAACTCTACCTATATTTATAATTTT
1 AACCTCAAATAATATGAAACTCTACCTATATTTATAATTTT
104786 TTATTCACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (41 bp):
AACCTCAAATAATATGAAACTCTACCTATATTTATAATTTT
Found at i:104771 original size:22 final size:22
Alignment explanation
Indices: 104705--104771 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
104695 ATGGTATCAA
104705 ACCTCAAATAATATGAAACTCT
1 ACCTCAAATAATATGAAACTCT
* * * *
104727 ACCT-ATAT-TTAT--AATTTT
1 ACCTCAAATAATATGAAACTCT
104745 AACCTCAAATAATATGAAACTCT
1 -ACCTCAAATAATATGAAACTCT
104768 ACCT
1 ACCT
104772 ATATTTATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 6 0.19
21 6 0.19
22 8 0.25
23 4 0.12
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (22 bp):
ACCTCAAATAATATGAAACTCT
Found at i:108976 original size:11 final size:11
Alignment explanation
Indices: 108960--108994 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
108950 TTGACAACGC
*
108960 AACAAAAATAA
1 AACAAAAACAA
*
108971 AACAAAAACGA
1 AACAAAAACAA
108982 AACAAAAACAA
1 AACAAAAACAA
108993 AA
1 AA
108995 AACAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:115522 original size:30 final size:31
Alignment explanation
Indices: 115486--115545 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
115476 TTTGCAAATA
* *
115486 TTGACCCG-GAAAATGTATATGATTGGAATG
1 TTGACCCGAAAAAATGTATAAGATTGGAATG
*
115516 TTGACCCGAAAAAATGTATAAGATTTGAAT
1 TTGACCCGAAAAAATGTATAAGATTGGAAT
115546 CTTTCCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (31 bp):
TTGACCCGAAAAAATGTATAAGATTGGAATG
Found at i:118242 original size:2 final size:2
Alignment explanation
Indices: 118231--118274 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
118221 TGACTCTCCT
118231 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118272 TA T
1 TA T
118275 TCTCAAAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119841 original size:12 final size:12
Alignment explanation
Indices: 119820--119851 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
119810 TACCCTATGT
119820 AAACACGACACG
1 AAACACGACACG
*
119832 AAATACGACACG
1 AAACACGACACG
119844 AAACACGA
1 AAACACGA
119852 ATTGCCAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.28, G:0.16, T:0.03
Consensus pattern (12 bp):
AAACACGACACG
Found at i:120283 original size:39 final size:40
Alignment explanation
Indices: 120227--120305 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
120217 TTTAATTCCT
*
120227 ATGTAATATATATAATAACTAAAATATTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
120267 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
120306 GTTCTTAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.