Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024682.1 Corchorus olitorius cultivar O-4 contig24715, 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: 56139
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:2861 original size:38 final size:38
Alignment explanation
Indices: 2799--2889 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
2789 GCCCAATAGA
*
2799 AAAAGAAAAGAAAAAGAAAGAAAGGAGGAAA-GGAAAAGG
1 AAAAGAAAA-AAAAAGAAAGAAAGGA-AAAAGGGAAAAGG
** *
2838 AAGAAGAAAAAAAAAGGGA-AAAGGAAAAAGGGAAAGGG
1 AA-AAGAAAAAAAAAGAAAGAAAGGAAAAAGGGAAAAGG
*
2876 AAAACAAAAAAAAA
1 AAAAGAAAAAAAAA
2890 TAAGAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
37 14 0.31
38 15 0.33
39 9 0.20
40 7 0.16
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.00
Consensus pattern (38 bp):
AAAAGAAAAAAAAAGAAAGAAAGGAAAAAGGGAAAAGG
Found at i:2865 original size:14 final size:14
Alignment explanation
Indices: 2848--2879 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2838 AAGAAGAAAA
2848 AAAAAGGGAAAAGG
1 AAAAAGGGAAAAGG
*
2862 AAAAAGGGAAAGGG
1 AAAAAGGGAAAAGG
2876 AAAA
1 AAAA
2880 CAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AAAAAGGGAAAAGG
Found at i:10554 original size:90 final size:90
Alignment explanation
Indices: 10372--10731 Score: 468
Period size: 90 Copynumber: 3.9 Consensus size: 90
10362 TTTGAAGGGT
* * * * *** * *
10372 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAATGTCTATTGGAAA
1 AAAATCATGACAACTTCTGGTGTCAATTG--CAAGATCATGACAACTTCTGGTGTCAATT-GCAA
*
10437 TTTATCATGACAACTTCTGGTGTCAATTGC
63 --GATCATGACAACTTCTGGTGTCAATTGC
* * * *
10467 AACATCATGACAACTTCTAGTGTCAATTGCAACATCATGACAACTTCTGGTGTCAATTGCAAAAT
1 AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
10532 CATGACAACTTCTGGTGTCAATTGC
66 CATGACAACTTCTGGTGTCAATTGC
* *
10557 AAAATCATGACAACTTCTGGTGTCAATTGCAAGATTATGACAACTTCTGGTGTCAATTGCAAGAG
1 AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
10622 CATGACAACTTCTGGTGTCAATTGC
66 CATGACAACTTCTGGTGTCAATTGC
* * * * * * *
10647 AAGATTATGACAACTTCTGGTGTCATTTGTAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
1 AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
10712 CATGACAACTTCTGGTGTCA
66 CATGACAACTTCTGGTGTCA
10732 TTTGTAAGTA
Statistics
Matches: 239, Mismatches: 26, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
90 188 0.79
92 3 0.01
93 21 0.09
95 27 0.11
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (90 bp):
AAAATCATGACAACTTCTGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAAGAT
CATGACAACTTCTGGTGTCAATTGC
Found at i:10739 original size:30 final size:30
Alignment explanation
Indices: 10440--10731 Score: 467
Period size: 30 Copynumber: 9.7 Consensus size: 30
10430 TTGGAAATTT
*
10440 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
10470 ATCATGACAACTTCTAGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
10500 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
10530 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
10560 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
10590 ATTATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
10620 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
10650 ATTATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
10680 ACCATGACAACTTCTGGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
10710 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
10732 TTTGTAAGTA
Statistics
Matches: 248, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 248 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:12396 original size:31 final size:29
Alignment explanation
Indices: 12310--12404 Score: 154
Period size: 29 Copynumber: 3.2 Consensus size: 29
12300 TGCAATTTGA
12310 GATATAACGTTACAAAACAAGCAATTAAG
1 GATATAACGTTACAAAACAAGCAATTAAG
*
12339 GGTATAACGTTACAAAACAAGCAATTAAG
1 GATATAACGTTACAAAACAAGCAATTAAG
*
12368 GATATAACGTTACGAAAAGCGAGCAATTAAG
1 GATATAACGTTAC-AAAA-CAAGCAATTAAG
12399 GATATA
1 GATATA
12405 GTCTGTTATG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 40 0.66
30 4 0.07
31 17 0.28
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (29 bp):
GATATAACGTTACAAAACAAGCAATTAAG
Found at i:12570 original size:31 final size:31
Alignment explanation
Indices: 12535--12613 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
12525 CTAACTGATT
*
12535 ATATCCTTAATTGCTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
12566 ATATCCTTAATTGCTTGAAATAGAAAACGTT
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
12597 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
12614 TTTTGTAACG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAGAAAACGTC
Found at i:12658 original size:60 final size:62
Alignment explanation
Indices: 12533--12669 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 62
12523 ACCTAACTGA
*
12533 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAATAGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAGAAAACG
** * * * ***
12595 TTATATCCTTAATTGCTTG-TTTTG-TAACGTTATATCCTTAATTGCTTGTGGCAGCAAAA-G
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAG-AAAACG
*
12655 TTATATCCTAAATTG
1 TTATATCCTTAATTG
12670 ATTATTTGAC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 39 0.61
61 6 0.09
62 19 0.30
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (62 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCTTAATTGCTTGAAACAGAAAACG
Found at i:12661 original size:31 final size:29
Alignment explanation
Indices: 12533--12669 Score: 121
Period size: 31 Copynumber: 4.5 Consensus size: 29
12523 ACCTAACTGA
* *
12533 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTG-TATAGAAAA-G
* *
12564 TCATATCCTTAATTGCTTGAAATAGAAAACG
1 TTATATCCTTAATTGCTTG-TATAGAAAA-G
* * * *
12595 TTATATCCTTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTTGTATAGAAAAG
**
12624 TTATATCCTTAATTGCTTGTGGCAGCAAAAG
1 TTATATCCTTAATTGCTTGT-ATAG-AAAAG
*
12655 TTATATCCTAAATTG
1 TTATATCCTTAATTG
12670 ATTATTTGAC
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.23
30 5 0.06
31 64 0.71
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (29 bp):
TTATATCCTTAATTGCTTGTATAGAAAAG
Found at i:13598 original size:15 final size:16
Alignment explanation
Indices: 13573--13605 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
13563 TAAAAAGTGA
13573 TTTAAATAAAATATTT
1 TTTAAATAAAATATTT
13589 TTTAAA-AAAATATTT
1 TTTAAATAAAATATTT
13604 TT
1 TT
13606 CTTTTGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATAAAATATTT
Found at i:13710 original size:60 final size:60
Alignment explanation
Indices: 13636--13749 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
13626 AGATGATAAG
* *
13636 CAAGCAATTTAGGATATAACGTTTTCTGCCGTAAGCAATTAAGGATATAACGTTACAAAA
1 CAAGCAATTAAGGATATAACGTTTTCTACCGTAAGCAATTAAGGATATAACGTTACAAAA
* *** *
13696 CAAGCAATTAAGGATATAACGTTTTTTATTTTAAGCAATTAAGGATATGACGTT
1 CAAGCAATTAAGGATATAACGTTTTCTACCGTAAGCAATTAAGGATATAACGTT
13750 TTTGATTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (60 bp):
CAAGCAATTAAGGATATAACGTTTTCTACCGTAAGCAATTAAGGATATAACGTTACAAAA
Found at i:13735 original size:31 final size:31
Alignment explanation
Indices: 13636--13776 Score: 135
Period size: 31 Copynumber: 4.6 Consensus size: 31
13626 AGATGATAAG
* ***
13636 CAAGCAATTTAGGATATAACGTTTTCTGCCGT
1 CAAGCAATTAAGGATATAACGTTTT-TGATTT
** ***
13668 -AAGCAATTAAGGATATAACG--TTACAAAA
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
*
13696 CAAGCAATTAAGGATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
* *
13727 TAAGCAATTAAGGATATGACGTTTTTGATTT
1 CAAGCAATTAAGGATATAACGTTTTTGATTT
*
13758 CAAGCAACTAAGGATATAA
1 CAAGCAATTAAGGATATAA
13777 TCAGTAAGGG
Statistics
Matches: 88, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
29 22 0.25
31 66 0.75
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTTGATTT
Found at i:13972 original size:29 final size:31
Alignment explanation
Indices: 13906--13972 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
13896 CCTAACGGAC
13906 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
* *
13937 TATATCCTTAATTGTTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
13966 TATATCC
1 TATATCC
13973 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Found at i:14786 original size:21 final size:24
Alignment explanation
Indices: 14730--14807 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 24
14720 AGTAATTAAG
* *
14730 TATATATTATTTATTTATTTTGAAC
1 TATATATTA-TTATTTATTTAGAAA
14755 TCAT-TA-T-TTA-TTATTTA-AAA
1 T-ATATATTATTATTTATTTAGAAA
*
14775 TATAT-TTATTATTTATTTAGTAA
1 TATATATTATTATTTATTTAGAAA
14798 TATATATTAT
1 TATATATTAT
14808 ATCTAAGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
19 2 0.05
20 5 0.12
21 9 0.21
22 10 0.23
23 7 0.16
24 5 0.12
25 3 0.07
26 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (24 bp):
TATATATTATTATTTATTTAGAAA
Found at i:14802 original size:25 final size:25
Alignment explanation
Indices: 14757--14805 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
14747 TTTTGAACTC
*
14757 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATGTAAAATATATTT
*
14782 ATTATTTATT-TAGTAATATATATT
1 ATTATTTATTAT-GTAAAATATATT
14806 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATGTAAAATATATTT
Found at i:15436 original size:2 final size:2
Alignment explanation
Indices: 15429--15495 Score: 51
Period size: 2 Copynumber: 37.5 Consensus size: 2
15419 CCGTTTAGTA
* *
15429 AT AT AT AT A- AT -T AA AT AT AT AT -T TT AT AT AT AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
15466 AT AT -T AG AT AT AT AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15496 ATTATTAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
1 8 0.15
2 44 0.85
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15469 original size:21 final size:22
Alignment explanation
Indices: 15429--15493 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
15419 CCGTTTAGTA
**
15429 ATATATATAATTAAATATATATTTT
1 ATATATATAA-T-AATATATA-GAT
15454 ATATATATAATAATAT-TAGAT
1 ATATATATAATAATATATAGAT
15475 ATATATATAATAATATATA
1 ATATATATAATAATATATA
15494 TAATTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 17 0.46
22 4 0.11
23 5 0.14
24 1 0.03
25 10 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATATATAATAATATATAGAT
Found at i:15479 original size:30 final size:31
Alignment explanation
Indices: 15429--15504 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
15419 CCGTTTAGTA
* * *
15429 ATATAT-ATAATTAAATATATATTTTAT-AT
1 ATATATAATTATTAAATATATATATAATAAT
*
15458 ATATAATAA-TATTAGATATATATATAATAAT
1 ATAT-ATAATTATTAAATATATATATAATAAT
15489 ATATATAATTATTAAA
1 ATATATAATTATTAAA
15505 CGGTCTAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 4 0.11
30 21 0.55
31 13 0.34
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
ATATATAATTATTAAATATATATATAATAAT
Found at i:16978 original size:52 final size:52
Alignment explanation
Indices: 16904--17002 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
16894 ATGGCTGGTC
* * *
16904 GTGAGCCGATCGCGACCAAGCCGTGGCTCGGTCGAGAGCCGTGGTCGCTCGT
1 GTGAGCCGAGCGCGACCAAGCCGCGGCTCGATCGAGAGCCGTGGTCGCTCGT
* * * * *
16956 GTGAGCCGCGCGCGACCGAGCCGCGGCTTGATCGTGAGCCTTGGTCG
1 GTGAGCCGAGCGCGACCAAGCCGCGGCTCGATCGAGAGCCGTGGTCG
17003 TGAGCCTGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.12, C:0.31, G:0.39, T:0.17
Consensus pattern (52 bp):
GTGAGCCGAGCGCGACCAAGCCGCGGCTCGATCGAGAGCCGTGGTCGCTCGT
Found at i:22516 original size:51 final size:50
Alignment explanation
Indices: 22415--22516 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
22405 GTTCATCAAC
* **
22415 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
22465 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
22516 T
1 T
22517 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 9 0.20
51 34 0.77
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:32929 original size:198 final size:196
Alignment explanation
Indices: 32703--33102 Score: 656
Period size: 198 Copynumber: 2.0 Consensus size: 196
32693 TAGGGTTTTT
* * * *
32703 AATTCTATCAAATTAGGTTGTACACGTGTGAAATTAAACCTAATTCCATGTGTATGGGGCCTGAT
1 AATTATATCAAATTAGGTAGTACACGTGTGAAATTAAACCTAATTCCATGTGTATAGGACCTGAT
* * *
32768 TTAGTGTTAATCATTGGCTAATTTTATCAATTGGGCCAAACTTAGCAAGAATTTCAACCTAAAAA
66 TTAGTGTTAATCATTGGCCAATTTCATCAATTGGGCCAAAATTAGCAAGAATTTCAACCTAAAAA
* *
32833 CCTAATACTATGCCGCACAATTTGCAATTTATGCAATTGGGGGGGCGTGCGGCATACTAAGGCTT
131 CCTAATACTATGCCGCACAAATTGCAATTCATGCAA-TGGGGGGGC-TGCGGCATACTAAGGCTT
32898 AAA
194 AAA
* * *
32901 AATTATATCAAATTGGGTAGTGCACGTGTGAAATTAAACCTAATTTCATGTGTATAGGACCTGAT
1 AATTATATCAAATTAGGTAGTACACGTGTGAAATTAAACCTAATTCCATGTGTATAGGACCTGAT
*
32966 TTAGTGTTAATTATTGGCCAATTTCATCAATTGGGCCAAAATTAGCAAGAATTTCAACCTAAAAA
66 TTAGTGTTAATCATTGGCCAATTTCATCAATTGGGCCAAAATTAGCAAGAATTTCAACCTAAAAA
*
33031 CCTAATACTATGCCGCACAAATTGTAATTCATGCAATGGGGGGGCTGCGGCATACTAAGGCTTAA
131 CCTAATACTATGCCGCACAAATTGCAATTCATGCAATGGGGGGGCTGCGGCATACTAAGGCTTAA
33096 A
196 A
33097 AATTAT
1 AATTAT
33103 GAAAATTAAG
Statistics
Matches: 188, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
196 27 0.14
197 9 0.05
198 152 0.81
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (196 bp):
AATTATATCAAATTAGGTAGTACACGTGTGAAATTAAACCTAATTCCATGTGTATAGGACCTGAT
TTAGTGTTAATCATTGGCCAATTTCATCAATTGGGCCAAAATTAGCAAGAATTTCAACCTAAAAA
CCTAATACTATGCCGCACAAATTGCAATTCATGCAATGGGGGGGCTGCGGCATACTAAGGCTTAA
A
Found at i:33961 original size:13 final size:13
Alignment explanation
Indices: 33943--33968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33933 CTTGGCATGA
33943 GTGATGATTTTTG
1 GTGATGATTTTTG
33956 GTGATGATTTTTG
1 GTGATGATTTTTG
33969 TTGTTACTTT
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:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:34315 original size:19 final size:19
Alignment explanation
Indices: 34293--34344 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
34283 GGGCTGAAAT
34293 TAATTAATTATTAAATAAA
1 TAATTAATTATTAAATAAA
* * *
34312 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAAATAAA
34331 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
34345 AATTCCACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATTAATTATTAAATAAA
Found at i:35792 original size:51 final size:50
Alignment explanation
Indices: 35691--35792 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
35681 GTTCGACAAC
* **
35691 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
35741 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
35792 T
1 T
35793 CTTCATTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 9 0.20
51 34 0.77
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:45335 original size:24 final size:23
Alignment explanation
Indices: 45308--45354 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
45298 ATTGATTTTC
* *
45308 TTAATTAATTTTCATAATTTAATA
1 TTAATAAATTATC-TAATTTAATA
*
45332 TTAATAAATTATCTTATTTAATA
1 TTAATAAATTATCTAATTTAATA
45355 GTTTATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAATAAATTATCTAATTTAATA
Found at i:46949 original size:50 final size:50
Alignment explanation
Indices: 46894--47022 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
46884 GAGAGAGCTA
46894 TCACATGTGAATGGGGGAGTTTGTTGGATTAGCCGTATCG-GGGAGAA-CTG
1 TCACATGTGAATGGGGGAGTTTGTTGGATTAGCCGTAT-GAGGGAGAATC-G
* *
46944 TCACATGTGAATGGAGGAGTTTGTTAGATTAGCCGTATGAGGGAGAATCG
1 TCACATGTGAATGGGGGAGTTTGTTGGATTAGCCGTATGAGGGAGAATCG
* *
46994 TCA-ATGTGAACGAGGGAGTTTGTTGGATT
1 TCACATGTGAATGGGGGAGTTTGTTGGATT
47023 TCACATGTGA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
49 23 0.32
50 47 0.66
51 1 0.01
ACGTcount: A:0.25, C:0.10, G:0.36, T:0.29
Consensus pattern (50 bp):
TCACATGTGAATGGGGGAGTTTGTTGGATTAGCCGTATGAGGGAGAATCG
Found at i:48498 original size:31 final size:31
Alignment explanation
Indices: 48417--48504 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
48407 GATTAGACCC
* **
48417 AATTGACTCAATCTTGTGAACACAAGGATTA
1 AATTGACCCAATCTTGTGAGTACAAGGATTA
*
48448 AATTGACCCAATCTTGTGAGTACATGGATTA
1 AATTGACCCAATCTTGTGAGTACAAGGATTA
*
48479 AATTGACCCAATCATGTGAGTACAAG
1 AATTGACCCAATCTTGTGAGTACAAG
48505 AACTACATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (31 bp):
AATTGACCCAATCTTGTGAGTACAAGGATTA
Found at i:51133 original size:20 final size:20
Alignment explanation
Indices: 51096--51135 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
51086 TGTGGGACTG
* * *
51096 TTTGGTATTGTTTTGTAATT
1 TTTGGGATTATTTAGTAATT
51116 TTTGGGATTATTTAGTAATT
1 TTTGGGATTATTTAGTAATT
51136 GTTAAGTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (20 bp):
TTTGGGATTATTTAGTAATT
Found at i:53477 original size:2 final size:2
Alignment explanation
Indices: 53470--53501 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53460 CTGTAAATTT
53470 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
53502 AAATAAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55282 original size:83 final size:85
Alignment explanation
Indices: 55155--55312 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 85
55145 CAAGTTGTGG
** *
55155 TGATTGTATGTTGGGCTTGGCTGCAAAGAATTTTACTTTTCATGCCACGTAAAA-G-ATAATGCG
1 TGATTGTATGTTGGGCTTGGCTGCAAAGAATTTTACTTGCCATGCAACGTAAAATGAATAATGCG
55218 AGTCTTCTAACAAGTCATCA
66 AGTCTTCTAACAAGTCATCA
* *
55238 TGATTGTATGTTGGGCTTGGCTGGC-AAGAATTTTAGTTGCCATGCAATGTAAAATGATATAATG
1 TGATTGTATGTTGGGCTTGGCT-GCAAAGAATTTTACTTGCCATGCAACGTAAAATGA-ATAATG
55302 CGAGTCTTCTA
64 CGAGTCTTCTA
55313 TTTCTTTTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
83 46 0.70
84 3 0.05
86 17 0.26
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (85 bp):
TGATTGTATGTTGGGCTTGGCTGCAAAGAATTTTACTTGCCATGCAACGTAAAATGAATAATGCG
AGTCTTCTAACAAGTCATCA
Done.