Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022610.1 Corchorus olitorius cultivar O-4 contig22643, 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: 38311
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1079 original size:16 final size:16
Alignment explanation
Indices: 1058--1094 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1048 ATTAGGTTTA
1058 TGTAATTTGCCAAAAT
1 TGTAATTTGCCAAAAT
*
1074 TGTAATTTGGCAAAAT
1 TGTAATTTGCCAAAAT
*
1090 CGTAA
1 TGTAA
1095 AAGGCAGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (16 bp):
TGTAATTTGCCAAAAT
Found at i:8261 original size:18 final size:20
Alignment explanation
Indices: 8234--8281 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
8224 GAAACAGGAA
8234 AATTTACTT-CTTTG-CTCC
1 AATTTACTTCCTTTGTCTCC
*
8252 AATTTGCTTCCTTTGTCTCC
1 AATTTACTTCCTTTGTCTCC
8272 AATTCTACTT
1 AATT-TACTT
8282 TTAAGTACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 5 0.20
20 8 0.32
21 4 0.16
ACGTcount: A:0.17, C:0.27, G:0.06, T:0.50
Consensus pattern (20 bp):
AATTTACTTCCTTTGTCTCC
Found at i:11080 original size:2 final size:2
Alignment explanation
Indices: 11073--11117 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
11063 AACAGCATGG
*
11073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11115 TA T
1 TA T
11118 CCTAAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11652 original size:2 final size:2
Alignment explanation
Indices: 11645--11672 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11635 TAATTATGTG
11645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11673 TACAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19699 original size:19 final size:19
Alignment explanation
Indices: 19658--19699 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19648 AAAAAAACAT
* *
19658 ATTTGGGTTTCTATTTATT
1 ATTTGGGTTTCTATCTATG
19677 ATTTGGGTCTT-TATCTATG
1 ATTTGGGT-TTCTATCTATG
19696 ATTT
1 ATTT
19700 AAGTCTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.60
Consensus pattern (19 bp):
ATTTGGGTTTCTATCTATG
Found at i:20390 original size:26 final size:26
Alignment explanation
Indices: 20351--20690 Score: 191
Period size: 26 Copynumber: 11.8 Consensus size: 26
20341 ATTGGTAAAC
20351 TTGGTTAATTAAAGAGTAAAAGGAAAT
1 TTGG-TAATTAAAGAGTAAAAGGAAAT
20378 TTGGTAATTAAAGAGTAAAAGGAAATTGGTTAAT
1 TTGGTAATTAAAGAGTAAAAGG--A------AAT
* * *
20412 TTGGTAATTAAAAAGTAAAAATGTAAT
1 TTGGTAATTAAAGAGTAAA-AGGAAAT
*
20439 TTGCTAATTAAAGAGTAAAAGGAAATTGGTTAAT
1 TTGGTAATTAAAGAGTAAAAGG--A------AAT
*
20473 TTGCTAATTAAAGAGTAAAAGGAAATTGGTTAAT
1 TTGGTAATTAAAGAGTAAAAGG--A------AAT
*
20507 TTGGTAATTAAATAGTAAAATGAAATTGATTAAT
1 TTGGTAATTAAAGAGTAAAA-G-----GA--AAT
* *
20541 TTGATAATTAAAGAGTAAAATGAAAT
1 TTGGTAATTAAAGAGTAAAAGGAAAT
* * *
20567 TAGGTAATTGAAGAGTAAAAGGAAAG
1 TTGGTAATTAAAGAGTAAAAGGAAAT
*
20593 TTGTTAATTAAAGAGTAAAA-GACAAT
1 TTGGTAATTAAAGAGTAAAAGGA-AAT
*
20619 TTGGTAATTAAAGAGTAAAA-TAAAT
1 TTGGTAATTAAAGAGTAAAAGGAAAT
* *
20644 TTGGACAATTAAAGAGTAAGA-GAAAGT
1 TTGG-TAATTAAAGAGTAAAAGGAAA-T
20671 TTGGTAATTAAAGAGTAAAA
1 TTGGTAATTAAAGAGTAAAA
20691 TTTAGTAATG
Statistics
Matches: 259, Mismatches: 28, Indels: 53
0.76 0.08 0.16
Matches are distributed among these distances:
25 9 0.03
26 114 0.44
27 29 0.11
28 3 0.01
34 99 0.38
35 3 0.01
38 1 0.00
40 1 0.00
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.31
Consensus pattern (26 bp):
TTGGTAATTAAAGAGTAAAAGGAAAT
Found at i:20394 original size:61 final size:60
Alignment explanation
Indices: 20313--20638 Score: 330
Period size: 61 Copynumber: 5.4 Consensus size: 60
20303 GAAATTGGTT
*
20313 AATTTGGTTAATTAAAGAGTAAAAGGAAATTGGTAAACTTGGTTAATTAAAGAGTAAAAGGA
1 AATTTGG-TAATTAAAGAGTAAAAGGAAATTGGTTAA-TTGGTTAATTAAAGAGTAAAAGGA
* * *
20375 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGG-TAATTAAAAAGTAAAAATGT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTTAA-TTGGTTAATTAAAGAGT-AAAAGGA
* * *
20436 AATTTGCTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGCTAATTAAAGAGTAAAAGGAAA
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTTAATTGGTTAATTAAAGAGTAAAAGG--A
* * * * * *
20498 TTGGTTAATTTGGTAATTAAATAGTAAAATGAAATTGATTAATTTGATAATTAAAGAGTAAAATG
1 ------AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTTAATTGGTTAATTAAAGAGTAAAAGG
20563 A
60 A
* *
20564 AATTAGGTAATTGAAGAGTAAAAGGAAA---G----TT-GTTAATTAAAGAGTAAAA-GA
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTTAATTGGTTAATTAAAGAGTAAAAGGA
20615 CAATTTGGTAATTAAAGAGTAAAA
1 -AATTTGGTAATTAAAGAGTAAAA
20639 TAAATTTGGA
Statistics
Matches: 229, Mismatches: 24, Indels: 32
0.80 0.08 0.11
Matches are distributed among these distances:
51 2 0.01
52 38 0.17
53 2 0.01
60 43 0.19
61 83 0.36
62 7 0.03
66 1 0.00
68 53 0.23
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.31
Consensus pattern (60 bp):
AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTTAATTGGTTAATTAAAGAGTAAAAGGA
Found at i:20415 original size:34 final size:34
Alignment explanation
Indices: 20375--20575 Score: 265
Period size: 34 Copynumber: 6.1 Consensus size: 34
20365 AGTAAAAGGA
20375 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
*
20409 AATTTGGTAATTAAAAAGT--AA--AAA-T-G-T
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
*
20436 AATTTGCTAATTAAAGAGTAAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
*
20470 AATTTGCTAATTAAAGAGTAAAAGGAAATTGGTT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
* * *
20504 AATTTGGTAATTAAATAGTAAAATGAAATTGATT
1 AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
* *
20538 AATTTGATAATTAAAGAGTAAAATGAAATTAGG-T
1 AATTTGGTAATTAAAGAGTAAAAGGAAATT-GGTT
20572 AATT
1 AATT
20576 GAAGAGTAAA
Statistics
Matches: 149, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
27 18 0.12
28 1 0.01
29 3 0.02
30 3 0.02
31 3 0.02
32 3 0.02
33 1 0.01
34 116 0.78
35 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.18, T:0.34
Consensus pattern (34 bp):
AATTTGGTAATTAAAGAGTAAAAGGAAATTGGTT
Found at i:20489 original size:95 final size:99
Alignment explanation
Indices: 20287--20575 Score: 334
Period size: 95 Copynumber: 3.0 Consensus size: 99
20277 AAGAGAGAAA
* *
20287 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTTAATTAAAGAGTAAAAGGAAATTGGTAAACT
1 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGG-TAATTAAAAAGT-AAA-GAAATTGAT-AA-T
* * *
20352 TGGTTAATTAAAGAGTAAAAGG-----A---AATTTGGT
61 TTGATAATTAAAGAGTAAAAGGAAATTAGGTAATTTGCT
*
20383 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAAAGT-AA-AAA-TG-TAATTTGCT
1 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAAAGTAAAGAAATTGATAATTTGAT
20444 AATTAAAGAGTAAAAGGAAATT-GGTTAATTTGCT
66 AATTAAAGAGTAAAAGGAAATTAGG-TAATTTGCT
*
20478 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAATAGTAAAATGAAATTGATTAATTT
1 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAAAGT-AAA-GAAATTGA-TAATTT
*
20543 GATAATTAAAGAGTAAAATGAAATTAGGTAATT
63 GATAATTAAAGAGTAAAAGGAAATTAGGTAATT
20576 GAAGAGTAAA
Statistics
Matches: 169, Mismatches: 7, Indels: 28
0.83 0.03 0.14
Matches are distributed among these distances:
87 21 0.12
88 2 0.01
89 1 0.01
90 2 0.01
91 3 0.02
93 2 0.01
95 62 0.37
96 33 0.20
97 2 0.01
99 3 0.02
100 2 0.01
102 34 0.20
103 2 0.01
ACGTcount: A:0.47, C:0.01, G:0.20, T:0.32
Consensus pattern (99 bp):
AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAAAGTAAAGAAATTGATAATTTGAT
AATTAAAGAGTAAAAGGAAATTAGGTAATTTGCT
Found at i:20679 original size:78 final size:78
Alignment explanation
Indices: 20538--20690 Score: 220
Period size: 78 Copynumber: 2.0 Consensus size: 78
20528 GAAATTGATT
* * *
20538 AATTTGATAATTAAAGAGTAAAATGAAATTAGGTAATTGAAGAGTAAAAGGAAAGTTGTTAATTA
1 AATTTGATAATTAAAGAGTAAAATGAAATTAGGCAATTAAAGAGTAAAAGGAAAGTTGGTAATTA
20603 AAGAGTAAAAGAC
66 AAGAGTAAAAGAC
* * *
20616 AATTTGGTAATTAAAGAGTAAAAT-AAATTTGGACAATTAAAGAGTAAGA-GAAAGTTTGGTAAT
1 AATTTGATAATTAAAGAGTAAAATGAAATTAGG-CAATTAAAGAGTAAAAGGAAAG-TTGGTAAT
20679 TAAAGAGTAAAA
64 TAAAGAGTAAAA
20691 TTTAGTAATG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 12 0.18
78 55 0.82
ACGTcount: A:0.51, C:0.01, G:0.20, T:0.27
Consensus pattern (78 bp):
AATTTGATAATTAAAGAGTAAAATGAAATTAGGCAATTAAAGAGTAAAAGGAAAGTTGGTAATTA
AAGAGTAAAAGAC
Found at i:20699 original size:21 final size:20
Alignment explanation
Indices: 20661--20699 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
20651 ATTAAAGAGT
* *
20661 AAGAGAAAGTTTGGTAATTA
1 AAGAGAAAATTTAGTAATTA
20681 AAGAGTAAAATTTAGTAAT
1 AAGAG-AAAATTTAGTAAT
20700 GAAATTTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.31
Consensus pattern (20 bp):
AAGAGAAAATTTAGTAATTA
Found at i:27000 original size:49 final size:49
Alignment explanation
Indices: 26899--27039 Score: 123
Period size: 49 Copynumber: 2.9 Consensus size: 49
26889 TCTTTGACGC
* * **
26899 AAAACACAAAACAGAT-TTTTTTTTTCAAA-AAACGCAAACACA-AAAATTA
1 AAAACACAAAACAAATATTTTTTTTTCAAATAAA---AAACGCAGAAAAGAA
*
26948 AAAACACAAAACAAATATTTTTTTTTCAAATCAAAAACGCAGAAAAGAA
1 AAAACACAAAACAAATATTTTTTTTTCAAATAAAAAACGCAGAAAAGAA
* * * *
26997 AAAATA-AAAACGAAA-ATTTTTTTTT-AGATGAAAGACGCAGAAA
1 AAAACACAAAAC-AAATATTTTTTTTTCAAATAAAAAACGCAGAAA
27040 CGCAGAAACA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
47 15 0.19
48 21 0.27
49 28 0.35
50 13 0.16
51 2 0.03
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (49 bp):
AAAACACAAAACAAATATTTTTTTTTCAAATAAAAAACGCAGAAAAGAA
Found at i:29915 original size:40 final size:38
Alignment explanation
Indices: 29824--29915 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
29814 TGTATATATG
* * * *
29824 ATGCATCCATCATGCATTGTCCATTCCTTTATATGTTC
1 ATGCATCCGTCATGCATTATCCATTCATTTATATGCTC
*
29862 ATGCGT-CGATCATGCATTATCCATTCATTACTATATGCTC
1 ATGCATCCG-TCATGCATTATCCATTCATT--TATATGCTC
29902 ATGCATCCGTCATG
1 ATGCATCCGTCATG
29916 TATTCACTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
37 1 0.02
38 23 0.52
40 18 0.41
41 2 0.05
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (38 bp):
ATGCATCCGTCATGCATTATCCATTCATTTATATGCTC
Found at i:31533 original size:35 final size:34
Alignment explanation
Indices: 31487--31730 Score: 243
Period size: 34 Copynumber: 7.6 Consensus size: 34
31477 AAGAGAGAAA
31487 AATTAAAGAGTAAAAGAAAATTGGTAAATTTGGTT
1 AATTAAAGAGTAAAAGAAAATTGGTAAATTTGG-T
* *
31522 AATTAAAGAGTAAAAGGAAATTGGTAAACTTGGTT
1 AATTAAAGAGTAAAAGAAAATTGGTAAATTTGG-T
31557 AATTAAAGAGT-----AAAA--GG-AAATTT-GT
1 AATTAAAGAGTAAAAGAAAATTGGTAAATTTGGT
* *
31582 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGT
1 AATTAAAGAGTAAAAGAAAATTGGTAAATTTGGT
* *
31616 AATTAAAAAGT---A-AAAA-T-GT-AATTTTGT
1 AATTAAAGAGTAAAAGAAAATTGGTAAATTTGGT
* *
31643 AATTAAAGAGTAAAAGGAAATTGGTTAATTTGGT
1 AATTAAAGAGTAAAAGAAAATTGGTAAATTTGGT
* *
31677 AATTAAAGAGTAAAATG-AAATTGGTTAATTTGAT
1 AATTAAAGAGTAAAA-GAAAATTGGTAAATTTGGT
31711 AATTAAAGAGTAAAATGAAA
1 AATTAAAGAGTAAAA-GAAA
31731 TTAGGTGATT
Statistics
Matches: 178, Mismatches: 13, Indels: 36
0.78 0.06 0.16
Matches are distributed among these distances:
25 12 0.07
26 1 0.01
27 22 0.12
28 4 0.02
29 1 0.01
30 10 0.06
31 4 0.02
32 3 0.02
33 7 0.04
34 67 0.38
35 47 0.26
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (34 bp):
AATTAAAGAGTAAAAGAAAATTGGTAAATTTGGT
Found at i:31584 original size:25 final size:25
Alignment explanation
Indices: 31556--31603 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
31546 TAAACTTGGT
31556 TAATTAAAGAGTAAAAGGAAATTTG
1 TAATTAAAGAGTAAAAGGAAATTTG
31581 TAATTAAAGAGTAAAAGGAAATT
1 TAATTAAAGAGTAAAAGGAAATT
31604 GGTTAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (25 bp):
TAATTAAAGAGTAAAAGGAAATTTG
Found at i:31597 original size:60 final size:59
Alignment explanation
Indices: 31512--31698 Score: 275
Period size: 61 Copynumber: 3.1 Consensus size: 59
31502 GAAAATTGGT
* *
31512 AAATTTGGTTAATTAAAGAGTAAAAGGAAATTGGTAAACTTGGTTAATTAAAGAGTAAAAGG
1 AAATTT-G-TAATTAAAGAGTAAAAGGAAATTGGTTAATTTGG-TAATTAAAGAGTAAAAGG
* *
31574 AAATTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAAAGTAAAAATGT
1 AAATTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGT-AAAA-GG
* *
31635 AATTTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATG
1 AAATTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAAGG
31694 AAATT
1 AAATT
31699 GGTTAATTTG
Statistics
Matches: 114, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
59 15 0.13
60 40 0.35
61 53 0.46
62 6 0.05
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.32
Consensus pattern (59 bp):
AAATTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAAGG
Found at i:31664 original size:26 final size:25
Alignment explanation
Indices: 31608--31672 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 25
31598 GAAATTGGTT
* *
31608 AATTTGGTAATTAAAAAGTAAAAATGT
1 AATTTGGTAATTAAAGAGT-AAAA-GA
*
31635 AATTTTGTAATTAAAGAGTAAAAGGA
1 AATTTGGTAATTAAAGAGTAAAA-GA
31661 AA-TTGGTTAATT
1 AATTTGG-TAATT
31673 TGGTAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 3 0.09
26 12 0.38
27 17 0.53
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (25 bp):
AATTTGGTAATTAAAGAGTAAAAGA
Found at i:31679 original size:95 final size:93
Alignment explanation
Indices: 31575--31766 Score: 278
Period size: 95 Copynumber: 2.0 Consensus size: 93
31565 AGTAAAAGGA
* * *
31575 AATTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAAAGTAAAAATGTAATTT
1 AATTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGATAATTAAAAAGT-AAAATGAAATTA
*
31640 TGTAATTAAAGAGTAAAAGGAAA-TTGGTT
65 GGTAATTAAAGAGTAAAAGGAAAGTT-GTT
* *
31669 AATTTGGTAATTAAAGAGTAAAATGAAATTGGTTAATTTGATAATTAAAGAGTAAAATGAAATTA
1 AATTT-GTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGATAATTAAAAAGTAAAATGAAATTA
* *
31734 GGTGATTGAAGAGTAAAAGGAAAGTTGTT
65 GGTAATTAAAGAGTAAAAGGAAAGTTGTT
31763 AATT
1 AATT
31767 AAAGACTAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 42 0.48
95 46 0.52
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.33
Consensus pattern (93 bp):
AATTTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGATAATTAAAAAGTAAAATGAAATTAG
GTAATTAAAGAGTAAAAGGAAAGTTGTT
Found at i:31698 original size:26 final size:26
Alignment explanation
Indices: 31551--31856 Score: 179
Period size: 26 Copynumber: 10.8 Consensus size: 26
31541 ATTGGTAAAC
*
31551 TTGGTTAATTAAAGAGTAAAAGGAAAT
1 TTGG-TAATTAAAGAGTAAAATGAAAT
*
31578 TT-GTAATTAAAGAGTAAAAGGAAATTGGTTAAT
1 TTGGTAATTAAAGAGT---A--AAA-T-G-AAAT
* *
31611 TTGGTAATTAAAAAGTAAAAATGTAAT
1 TTGGTAATTAAAGAGTAAA-ATGAAAT
* *
31638 TTTGTAATTAAAGAGTAAAAGGAAATTGGTTAAT
1 TTGGTAATTAAAGAGT---A--AAA-T-G-AAAT
31672 TTGGTAATTAAAGAGTAAAATGAAATTGGTTAAT
1 TTGGTAATTAAAGAGTAAAATG--A------AAT
*
31706 TTGATAATTAAAGAGTAAAATGAAAT
1 TTGGTAATTAAAGAGTAAAATGAAAT
* * * * *
31732 TAGGTGATTGAAGAGTAAAAGGAAAG
1 TTGGTAATTAAAGAGTAAAATGAAAT
* *
31758 TTGTTAATTAAAGACTAAAA-GACAAT
1 TTGGTAATTAAAGAGTAAAATGA-AAT
31784 TTGGTAATTAAAGAGTAAAAT-AAAT
1 TTGGTAATTAAAGAGTAAAATGAAAT
* *
31809 TTGGACAATTAAAGAGTAAGA-GAAAGT
1 TTGG-TAATTAAAGAGTAAAATGAAA-T
31836 TTGGTAATTAAAGAGTAAAAT
1 TTGGTAATTAAAGAGTAAAAT
31857 TTAGTACGAT
Statistics
Matches: 221, Mismatches: 27, Indels: 62
0.71 0.09 0.20
Matches are distributed among these distances:
25 21 0.10
26 91 0.41
27 26 0.12
28 3 0.01
29 6 0.03
30 5 0.02
31 3 0.01
32 5 0.02
33 6 0.03
34 55 0.25
ACGTcount: A:0.48, C:0.01, G:0.20, T:0.31
Consensus pattern (26 bp):
TTGGTAATTAAAGAGTAAAATGAAAT
Found at i:31793 original size:60 final size:58
Alignment explanation
Indices: 31519--31793 Score: 245
Period size: 60 Copynumber: 4.6 Consensus size: 58
31509 GGTAAATTTG
31519 GTTAATTAAAGAGTAAAAGGAAATTGGTAAACTT-GGTTAATTAAAGAGTAAAAGGAAATT
1 GTTAATTAAAGAGTAAAAGGAAATTGGT-AA-TTAGG-TAATTAAAGAGTAAAAGGAAATT
* * * *
31579 -TGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAAAGTAAAAATGTAATT
1 GT-TAATTAAAGAGTAAAAGGAAATTGG-TAATTAGGTAATTAAAGAGT-AAAAGGAAATT
* * *
31639 TTGTAATTAAAGAGTAAAAGGAAATTGGTTAATTTGGTAATTAAAGAGTAAAATGAAATT
1 GT-TAATTAAAGAGTAAAAGGAAATTGG-TAATTAGGTAATTAAAGAGTAAAAGGAAATT
* * * * * * *
31699 GGTTAATTTGATA-ATTAAAGAGTAAAAT-GAAATTAGGTGATTGAAGAGTAAAAGGAAAGTT
1 -GTTAA-TT-AAAGAGTAAA-AGGAAATTGGTAATTAGGTAATTAAAGAGTAAAAGGAAA-TT
*
31760 GTTAATTAAAGACTAAAA-GACAATTTGGTAATTA
1 GTTAATTAAAGAGTAAAAGGA-AA-TTGGTAATTA
31794 AAGAGTAAAA
Statistics
Matches: 181, Mismatches: 20, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
57 1 0.01
58 5 0.03
59 22 0.12
60 86 0.48
61 59 0.33
62 8 0.04
ACGTcount: A:0.47, C:0.01, G:0.20, T:0.31
Consensus pattern (58 bp):
GTTAATTAAAGAGTAAAAGGAAATTGGTAATTAGGTAATTAAAGAGTAAAAGGAAATT
Found at i:31844 original size:78 final size:78
Alignment explanation
Indices: 31703--31855 Score: 202
Period size: 78 Copynumber: 2.0 Consensus size: 78
31693 GAAATTGGTT
** * *
31703 AATTTGATAATTAAAGAGTAAAATGAAATTAGGTGATTGAAGAGTAAAAGGAAAGTTGTTAATTA
1 AATTTGATAATTAAAGAGTAAAATGAAATTAGGCAATTAAAGAGTAAAAGGAAAGTTGGTAATTA
31768 AAGACTAAAAGAC
66 AAGACTAAAAGAC
* * *
31781 AATTTGGTAATTAAAGAGTAAAAT-AAATTTGGACAATTAAAGAGTAAGA-GAAAGTTTGGTAAT
1 AATTTGATAATTAAAGAGTAAAATGAAATTAGG-CAATTAAAGAGTAAAAGGAAAG-TTGGTAAT
*
31844 TAAAGAGTAAAA
64 TAAAGACTAAAA
31856 TTTAGTACGA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
77 12 0.18
78 53 0.82
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.27
Consensus pattern (78 bp):
AATTTGATAATTAAAGAGTAAAATGAAATTAGGCAATTAAAGAGTAAAAGGAAAGTTGGTAATTA
AAGACTAAAAGAC
Found at i:33474 original size:169 final size:169
Alignment explanation
Indices: 32891--33508 Score: 916
Period size: 169 Copynumber: 3.7 Consensus size: 169
32881 TTAGAAGTAA
* * * * * *
32891 TGCCCGGAGGCCTT-CAAATGCAAACTCTGAATAGGGATCTTGAACAAGGATTTTAAATTTAAAC
1 TGCCCGGAGGACTTACCAATGCAAACTTTAAATAGGGACCTTGAACAAGGATTTTAAACTTAAAC
* ** * * *
32955 ATGAATTTTTGATTTAAAACTTGATGAGATGAAAATGGTACTCAGAGGTTTTACCAATTGCCCGG
66 ATGAATCTTTGATGAAAAACTTGATGAAATG-AAATGGTACCCGGAGGTTTTACCAATTGCCCGG
* *
33020 AGGACTTATCAAAATTAATACCCGGAGGTTTTTGAATCTG
130 AGGACTTATCAGAATTAATACCCGGAGGTTTTTGAATTTG
* * * * **
33060 TGCCCCGAGGACTTACCAATGCAAGCTTTGAATAGAGAATTTGAACAAGGATTTTAAACTTAAAC
1 TGCCCGGAGGACTTACCAATGCAAACTTTAAATAGGGACCTTGAACAAGGATTTTAAACTTAAAC
* *
33125 ATGAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGGGGTTTTACCAATTGCACGGA
66 ATGAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGA
* * *
33190 GTACTTATCAGAATTAATACCCGAAGGTTTCT-AATTTG
131 GGACTTATCAGAATTAATACCCGGAGGTTTTTGAATTTG
* *
33228 TGCCCAGAGGACTTACCAATGCAAACTTTAAATAGGGACCTTGAACAAGGATTTTAAAATTAAAC
1 TGCCCGGAGGACTTACCAATGCAAACTTTAAATAGGGACCTTGAACAAGGATTTTAAACTTAAAC
33293 ATGAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGA
66 ATGAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGA
* *
33358 GGACTTATCAGAATTAGTATCCGGAGGTTTTTGAATTTG
131 GGACTTATCAGAATTAATACCCGGAGGTTTTTGAATTTG
* *
33397 TGCCCGGAGGACTTACTAATGCAAACTTTAAATATGGACCTTGAACAAGGATTTTAAACTTAAAC
1 TGCCCGGAGGACTTACCAATGCAAACTTTAAATAGGGACCTTGAACAAGGATTTTAAACTTAAAC
* *
33462 ATAAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCGGGAGG
66 ATGAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGG
33509 ACTTATCAGA
Statistics
Matches: 405, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
168 153 0.38
169 182 0.45
170 70 0.17
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (169 bp):
TGCCCGGAGGACTTACCAATGCAAACTTTAAATAGGGACCTTGAACAAGGATTTTAAACTTAAAC
ATGAATCTTTGATGAAAAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGA
GGACTTATCAGAATTAATACCCGGAGGTTTTTGAATTTG
Found at i:33620 original size:67 final size:67
Alignment explanation
Indices: 33504--33632 Score: 201
Period size: 67 Copynumber: 1.9 Consensus size: 67
33494 AATGGTACCG
33504 GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGTCCGGA-GATCTTACCAATTG
1 GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGTCCGGAGGA-CTTACCAATTG
33568 CCC
65 CCC
*
33571 GGAGGACTTATCAGAATTAATACCTAGAGGTTTCT-AAATT-TGTTCCCGGAGGACTTACCAAT
1 GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTG-T-CCGGAGGACTTACCAAT
33633 ACAAGCTTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
65 2 0.03
66 6 0.10
67 48 0.83
68 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (67 bp):
GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGTCCGGAGGACTTACCAATTGC
CC
Done.