Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008473.1 Corchorus capsularis cultivar CVL-1 contig08494, 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: 56576
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:47 original size:35 final size:35
Alignment explanation
Indices: 1--393 Score: 504
Period size: 35 Copynumber: 11.3 Consensus size: 35
*
1 AGAGTTGATCGCATTTTCAGTATTTTCCAACGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
* * *
36 AGAGTTGATCGCATTTTCAGTATTTTTC-ATGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
*
70 AGAGTTGATCGCATTTTCAGTAGTTTCCAATGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
* * *
105 GGAGTTAATCGCATTTTCAGTATTTTCCAACGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
* * * *
140 AGAGTTGATCGCATTTTAAGTATTTTTC-ATGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
*
174 AGAGTTGATCGCATTTTCAGTAGTTTCCAATGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
* * * *
209 GGAGTTAATCGCATTTTCAGTATTTTACAACGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
244 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
* *
279 AAAGTTGATCACATTTTCAGTAGTTTCCAACGATC
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
* * *
314 AGAGTTGATCACATTTTCAGTAGTTTCCAACAATT
1 AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
* * * * * *
349 AGAGGTGATCTCA-TTTCAAGAAATTTCCGATGATC
1 AGAGTTGATCGCATTTTC-AGTAGTTTCCAACGATC
384 AGAGTTGATC
1 AGAGTTGATC
394 CAGAGGAGTT
Statistics
Matches: 316, Mismatches: 39, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
34 65 0.21
35 251 0.79
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (35 bp):
AGAGTTGATCGCATTTTCAGTAGTTTCCAACGATC
Found at i:182 original size:104 final size:105
Alignment explanation
Indices: 2--393 Score: 563
Period size: 104 Copynumber: 3.8 Consensus size: 105
1 A
* * *
2 GAGTTGATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTCAGTATTTTTC-AT
1 GAGTTAATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTAAGTATTTTCCAAT
66 GATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCG
66 GATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCG
*
106 GAGTTAATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTAAGTATTTTTC-AT
1 GAGTTAATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTAAGTATTTTCCAAT
170 GATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCG
66 GATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCG
* * * *
210 GAGTTAATCGCATTTTCAGTATTTTACAACGATCAGAGTTGATCGCATTTTCAGTAGTTTCCAAC
1 GAGTTAATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTAAGTATTTTCCAAT
* * * *
275 GATCAAAGTTGATCACATTTTCAGTAGTTTCCAACGATCA
66 GATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCG
* * * * * * * * * * *
315 GAGTTGATCACATTTTCAGTAGTTTCCAACAATTAGAGGTGATCTCATTTCAAGAAATTTCCGAT
1 GAGTTAATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTAAGTATTTTCCAAT
380 GATCAGAGTTGATC
66 GATCAGAGTTGATC
394 CAGAGGAGTT
Statistics
Matches: 261, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
104 160 0.61
105 101 0.39
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (105 bp):
GAGTTAATCGCATTTTCAGTATTTTCCAACGATCAGAGTTGATCGCATTTTAAGTATTTTCCAAT
GATCAGAGTTGATCGCATTTTCAGTAGTTTCCAATGATCG
Found at i:1415 original size:44 final size:44
Alignment explanation
Indices: 1389--1478 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
1379 CTTTTTACTC
1389 TTAAC-ATTTCACTCTTTACTGATTACCTTCTTACTCTTACTGA
1 TTAACAATTTCACTCTTTACTGATTACCTTCTTACTCTTACTGA
* * *
1432 TTTACAATTTTACTCTTTACTGATTACCTTCTTACTTTTACTGA
1 TTAACAATTTCACTCTTTACTGATTACCTTCTTACTCTTACTGA
1476 TTA
1 TTA
1479 CCCTTTTACT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 4 0.10
44 38 0.90
ACGTcount: A:0.23, C:0.22, G:0.04, T:0.50
Consensus pattern (44 bp):
TTAACAATTTCACTCTTTACTGATTACCTTCTTACTCTTACTGA
Found at i:1426 original size:22 final size:21
Alignment explanation
Indices: 1399--1493 Score: 122
Period size: 22 Copynumber: 4.4 Consensus size: 21
1389 TTAACATTTC
1399 ACTCTTTACTGATTACCTTCTT
1 ACTCTTTACTGATTACCTT-TT
*
1421 ACTC-TTACTGATTTACAATTTT
1 ACTCTTTACTGA-TTAC-CTTTT
1443 ACTCTTTACTGATTACCTTCTT
1 ACTCTTTACTGATTACCTT-TT
1465 ACT-TTTACTGATTACCCTTTT
1 ACTCTTTACTGATTA-CCTTTT
1486 ACTCTTTA
1 ACTCTTTA
1494 TCATTCTTCC
Statistics
Matches: 65, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
21 25 0.38
22 31 0.48
23 9 0.14
ACGTcount: A:0.21, C:0.24, G:0.04, T:0.51
Consensus pattern (21 bp):
ACTCTTTACTGATTACCTTTT
Found at i:1487 original size:36 final size:34
Alignment explanation
Indices: 1441--1529 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 34
1431 ATTTACAATT
* * *
1441 TTACTCTTTACTGATTACCTTCTTACTTTTACTGA
1 TTACCCTTTACTGATTACATTCTT-CCTTTACTGA
**
1476 TTACCCTTTTACTCTTTATCATTCTTCCTTTACTGA
1 TTACCC-TTTACTGATTA-CATTCTTCCTTTACTGA
* *
1512 TTACTCTTTGCTGATTAC
1 TTACCCTTTACTGATTAC
1530 TTTTACCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
34 1 0.02
35 13 0.30
36 23 0.53
37 6 0.14
ACGTcount: A:0.18, C:0.25, G:0.06, T:0.52
Consensus pattern (34 bp):
TTACCCTTTACTGATTACATTCTTCCTTTACTGA
Found at i:1520 original size:14 final size:14
Alignment explanation
Indices: 1503--1586 Score: 73
Period size: 14 Copynumber: 6.0 Consensus size: 14
1493 ATCATTCTTC
1503 CTTTACTGATTACT
1 CTTTACTGATTACT
*
1517 CTTTGCTGATTACT
1 CTTTACTGATTACT
**
1531 -TTTACCATTTTTACT
1 CTTTA-C-TGATTACT
*
1546 -TTTACGGATTACT
1 CTTTACTGATTACT
** *
1559 CTTTACTTTTTCCT
1 CTTTACTGATTACT
1573 CTTTACTGATTACT
1 CTTTACTGATTACT
1587 ATTTTACTCT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
13 8 0.15
14 35 0.66
15 10 0.19
ACGTcount: A:0.18, C:0.21, G:0.07, T:0.54
Consensus pattern (14 bp):
CTTTACTGATTACT
Found at i:1569 original size:28 final size:28
Alignment explanation
Indices: 1512--1586 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
1502 CCTTTACTGA
* *
1512 TTACTCTTTGCTGATTACTTTTACCATTT
1 TTACTCTTTACGGATTACTTTTACC-TTT
1541 TTACT-TTTACGGATTACTCTTTA-CTTT
1 TTACTCTTTACGGATTACT-TTTACCTTT
* *
1568 TTCCTCTTTACTGATTACT
1 TTACTCTTTACGGATTACT
1587 ATTTTACTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 7 0.17
28 24 0.60
29 9 0.22
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (28 bp):
TTACTCTTTACGGATTACTTTTACCTTT
Found at i:1616 original size:26 final size:26
Alignment explanation
Indices: 1581--1679 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 26
1571 CTCTTTACTG
1581 ATTACTATTTTACTCTCTTGAATTTA
1 ATTACTATTTTACTCTCTTGAATTTA
*
1607 ATTACTATTTT-CGCTCTTTGAATTTA
1 ATTACTATTTTACTCTC-TTGAATTTA
*
1633 ATCACCATTTTGTCATTTTACTCT-TTGAATTTA
1 ATTA-C------T-ATTTTACTCTCTTGAATTTA
1666 ATTACTATTTTACT
1 ATTACTATTTTACT
1680 ATTTTACTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 21
0.70 0.05 0.25
Matches are distributed among these distances:
25 12 0.20
26 24 0.41
27 1 0.02
32 1 0.02
33 13 0.22
34 5 0.08
35 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54
Consensus pattern (26 bp):
ATTACTATTTTACTCTCTTGAATTTA
Found at i:1657 original size:33 final size:33
Alignment explanation
Indices: 1608--1691 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
1598 TTGAATTTAA
*
1608 TTACTATTTTCGCTCTTTGAATTTAATCACCATT
1 TTACTATTTT-ACTCTTTGAATTTAATCACCATT
* * *
1642 TT-GTCATTTTACTCTTTGAATTTAATTACTATT
1 TTACT-ATTTTACTCTTTGAATTTAATCACCATT
1675 TTACTATTTTACTCTTT
1 TTACTATTTTACTCTTT
1692 ACCGATTACT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 35 0.81
34 8 0.19
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.56
Consensus pattern (33 bp):
TTACTATTTTACTCTTTGAATTTAATCACCATT
Found at i:1728 original size:21 final size:21
Alignment explanation
Indices: 1697--1757 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1687 TCTTTACCGA
*
1697 TTACTCTTTACTAATTACCATT
1 TTACTC-TTACTGATTACCATT
* *
1719 TTGCTCTTACTGATTACTATT
1 TTACTCTTACTGATTACCATT
1740 TTACTCTTACTGATTACC
1 TTACTCTTACTGATTACC
1758 TTTCACTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 29 0.85
22 5 0.15
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.49
Consensus pattern (21 bp):
TTACTCTTACTGATTACCATT
Found at i:2020 original size:34 final size:34
Alignment explanation
Indices: 1964--2091 Score: 109
Period size: 34 Copynumber: 3.6 Consensus size: 34
1954 CTTTGACTTT
1964 TTAATTACTGACTTTACTGATTAATCTCTTTTTAC
1 TTAATTACTGA-TTTACTGATTAATCTCTTTTTAC
* * * *
1999 TTAATTATTGATTTGCTGATTACTAT-TAC-CTTGACTC
1 TTAATTACTGATTTACTGATTA--ATCT-CTTTTTA--C
* *
2036 TTAATT-GTCAATTTACTGATTAATCTCTTTTTAC
1 TTAATTACT-GATTTACTGATTAATCTCTTTTTAC
*
2070 ATAATTACTGATTTACTGATTA
1 TTAATTACTGATTTACTGATTA
2092 CCATTACTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
34 28 0.39
35 18 0.25
36 8 0.11
37 18 0.25
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (34 bp):
TTAATTACTGATTTACTGATTAATCTCTTTTTAC
Found at i:5848 original size:27 final size:27
Alignment explanation
Indices: 5785--5863 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 27
5775 AGATGAACTT
* * * *
5785 AAAAATGACTAAAATGCCCC-GAGTGT
1 AAAAATGACCAAAATGCCCCTGGGCGC
5811 AAAAATGACCAAAATGCCCCTGGGCGC
1 AAAAATGACCAAAATGCCCCTGGGCGC
* * *
5838 GAAAATGACCAAAATACCCTTGGGCG
1 AAAAATGACCAAAATGCCCCTGGGCG
5864 ACCCCCAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 19 0.42
27 26 0.58
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGCGC
Found at i:6756 original size:72 final size:72
Alignment explanation
Indices: 6678--6824 Score: 187
Period size: 73 Copynumber: 2.0 Consensus size: 72
6668 AATTGTGGAA
6678 GCTTTAGGAGATA-TTTTAAGAAA-ACAAATAAATTAA-AAATAGAATTAAT-AA-TGAGAATAT
1 GCTTTAGGAGATATTTTTAAGAAATA-AAAT-AA-TAACAAA-AGAA-TAATAAAGTGAGAATAT
6738 TTTCTAAATCTT
61 TTTCTAAATCTT
* *
6750 GCTTTAGGAGATATTTTTAAGAAATAAAATAATAACAAAATAATAATAAAGTTGGGAATATTTTC
1 GCTTTAGGAGATATTTTTAAGAAATAAAATAATAACAAAAGAATAATAAAG-TGAGAATATTTTC
6815 TAAATCTT
65 TAAATCTT
6823 GC
1 GC
6825 CAAATTGTGG
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
70 4 0.06
71 8 0.12
72 18 0.27
73 36 0.54
74 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (72 bp):
GCTTTAGGAGATATTTTTAAGAAATAAAATAATAACAAAAGAATAATAAAGTGAGAATATTTTCT
AAATCTT
Found at i:6853 original size:87 final size:87
Alignment explanation
Indices: 6752--6942 Score: 239
Period size: 86 Copynumber: 2.2 Consensus size: 87
6742 TAAATCTTGC
*
6752 TTTAGGAGATATTTTTAAGAAATAAAAT-AATAACAAAA-T-AATAATAAAGTTGGGAATATTT-
1 TTTAGGAGATATTTTTAAGAAA-AAAATAAATAACAAAATTGAATAAT-AA--TGAGAATATTTC
6813 TCTAAATCTTGCCAAATTGTGGAAGA
62 TCTAAATCTTGCCAAATTGTGGAAGA
* * * *
6839 TTTAGGAGATA-TTTTAAGAAACAAATAAATAATAAAATTGAATAGTAATGAGAATATTTCTTTA
1 TTTAGGAGATATTTTTAAGAAAAAAATAAATAACAAAATTGAATAATAATGAGAATATTTCTCTA
* *
6903 AATCTTGCCAGATTGTGGGAGA
66 AATCTTGCCAAATTGTGGAAGA
*
6925 TTTAGGAGATATATTTAA
1 TTTAGGAGATATTTTTAA
6943 TAATGATAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
85 14 0.15
86 53 0.58
87 19 0.21
88 5 0.05
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (87 bp):
TTTAGGAGATATTTTTAAGAAAAAAATAAATAACAAAATTGAATAATAATGAGAATATTTCTCTA
AATCTTGCCAAATTGTGGAAGA
Found at i:9285 original size:31 final size:31
Alignment explanation
Indices: 9237--9295 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
9227 AGTGTTGAGA
* * *
9237 AACTTTTGAAATGCCTATTGTACCCTTATTT
1 AACTTTTAAAATACCTATTATACCCTTATTT
*
9268 AACTTTTAAAATACCTATTATATCCTTA
1 AACTTTTAAAATACCTATTATACCCTTA
9296 CTTATCTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (31 bp):
AACTTTTAAAATACCTATTATACCCTTATTT
Found at i:10398 original size:2 final size:2
Alignment explanation
Indices: 10391--10424 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10381 TGAAAACTAG
10391 AT AT AT 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 AT AT AT
10425 GATGATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11106 original size:31 final size:31
Alignment explanation
Indices: 11036--11198 Score: 123
Period size: 31 Copynumber: 5.5 Consensus size: 31
11026 TCCTTTTGTG
* * * *
11036 CACGTGGCATGCCACGTGCCATTTTTTTG-A
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
11066 AACTTGTGGCATGCCACGTGTTACTTTTTGGTA
1 CAC--GTGGCGTGCCACGTGTCACTTTTTGGTA
* *
11099 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
11130 CA--T---GTGGCAC--G--ACTTTTT-GTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
11151 CATGTGGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
11182 CACGTGGCGTGCCACGT
1 CACGTGGCGTGCCACGT
11199 CAGACATCGT
Statistics
Matches: 105, Mismatches: 15, Indels: 25
0.72 0.10 0.17
Matches are distributed among these distances:
21 5 0.05
22 7 0.07
23 1 0.01
24 1 0.01
26 11 0.10
28 1 0.01
29 1 0.01
30 9 0.09
31 44 0.42
32 22 0.21
33 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:11171 original size:52 final size:53
Alignment explanation
Indices: 11088--11189 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
11078 GCCACGTGTT
** *
11088 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
11141 ACTTTTT-GTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
11190 GTGCCACGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 37 0.84
53 7 0.16
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:12918 original size:2 final size:2
Alignment explanation
Indices: 12911--12942 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12901 TATCTTATCT
12911 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
12943 GTGATAACCT
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:14977 original size:20 final size:20
Alignment explanation
Indices: 14952--14991 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14942 TCAACTTAAT
14952 AAACACTTTAACTCTTGAAC
1 AAACACTTTAACTCTTGAAC
14972 AAACACTTTAACTCTTGAAC
1 AAACACTTTAACTCTTGAAC
14992 TTGTATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (20 bp):
AAACACTTTAACTCTTGAAC
Found at i:27666 original size:19 final size:20
Alignment explanation
Indices: 27624--27669 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27614 AAATATTGTA
*
27624 TTTTT-TCTATAATGGGTAG
1 TTTTTATCTAAAATGGGTAG
*
27643 TTTTTATCTAAAATTGGTAG
1 TTTTTATCTAAAATGGGTAG
27663 TTTTTAT
1 TTTTTAT
27670 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.57
Consensus pattern (20 bp):
TTTTTATCTAAAATGGGTAG
Found at i:27776 original size:28 final size:28
Alignment explanation
Indices: 27736--27792 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
27726 ACTCAGGTTT
27736 TGACATTATAATTAATATAGATAGATAG
1 TGACATTATAATTAATATAGATAGATAG
*
27764 TGACATTATAATTAGTATAGATAGATAG
1 TGACATTATAATTAATATAGATAGATAG
27792 T
1 T
27793 ATAGATATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.37
Consensus pattern (28 bp):
TGACATTATAATTAATATAGATAGATAG
Found at i:27904 original size:14 final size:14
Alignment explanation
Indices: 27885--27919 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
27875 TACAATTTAC
27885 AAGGAAAGAAAAGA
1 AAGGAAAGAAAAGA
* *
27899 AAGGAAAGGAAAGG
1 AAGGAAAGAAAAGA
27913 AAGGAAA
1 AAGGAAA
27920 ACAAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AAGGAAAGAAAAGA
Found at i:40673 original size:10 final size:10
Alignment explanation
Indices: 40651--40689 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
40641 AAATCTCGAT
*
40651 ATATCCGTAA
1 ATATCCATAA
40661 ATATCCATAA
1 ATATCCATAA
*
40671 ATATCCGTAA
1 ATATCCATAA
40681 ATATCCATA
1 ATATCCATA
40690 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (10 bp):
ATATCCATAA
Found at i:40674 original size:20 final size:20
Alignment explanation
Indices: 40651--40689 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40641 AAATCTCGAT
40651 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
40671 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
40690 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:41534 original size:10 final size:9
Alignment explanation
Indices: 41514--41538 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41504 TTCGCAGTAC
41514 AAAAAATAA
1 AAAAAATAA
41523 AAAAAATAA
1 AAAAAATAA
41532 AAAAAAT
1 AAAAAAT
41539 GTCTACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:41713 original size:12 final size:12
Alignment explanation
Indices: 41696--41752 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
41686 TTCATCGATA
41696 CATCGATATATC
1 CATCGATATATC
41708 CATCGATATATC
1 CATCGATATATC
*
41720 CGTCGATATATC
1 CATCGATATATC
*
41732 CGCTCGATATATC
1 C-ATCGATATATC
*
41745 CGTCGATA
1 CATCGATA
41753 CCTGTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
12 30 0.73
13 11 0.27
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (12 bp):
CATCGATATATC
Found at i:41744 original size:25 final size:24
Alignment explanation
Indices: 41698--41752 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
41688 CATCGATACA
41698 TCGATATATCCATCGATATATCCG
1 TCGATATATCCATCGATATATCCG
*
41722 TCGATATATCCGCTCGATATATCCG
1 TCGATATATCC-ATCGATATATCCG
41747 TCGATA
1 TCGATA
41753 CCTGTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (24 bp):
TCGATATATCCATCGATATATCCG
Found at i:43415 original size:26 final size:28
Alignment explanation
Indices: 43359--43424 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
43349 AAAAAAAAAC
* ** *
43359 ATATATATATATATATATTGTTACGTAA
1 ATATATATATATATATAATAATACATAA
43387 ATATATATATATATATAATAATA-AT-A
1 ATATATATATATATATAATAATACATAA
43413 ATA-ATA-ATATAT
1 ATATATATATATAT
43425 GAGAGATCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.18
25 3 0.09
26 4 0.12
27 1 0.03
28 20 0.59
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (28 bp):
ATATATATATATATATAATAATACATAA
Found at i:44352 original size:12 final size:12
Alignment explanation
Indices: 44335--44359 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44325 TTTTAATAGA
44335 TACTAGAATTTC
1 TACTAGAATTTC
44347 TACTAGAATTTC
1 TACTAGAATTTC
44359 T
1 T
44360 TAAATTGGAC
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TACTAGAATTTC
Found at i:45089 original size:181 final size:178
Alignment explanation
Indices: 44773--45259 Score: 473
Period size: 181 Copynumber: 2.7 Consensus size: 178
44763 TGAAACATTA
* * * * * * *
44773 AAATTTATCTTTTGAATCCTTCATGAAAGTTGTAGATCATGAAA-AACTTTTTAATAGACACTTC
1 AAATTTAGCTTTCGAGTCCTTCATGAAAGTTCTATATCATGAAACAACATTTTAATAGACACTTG
* ** * * *
44837 AATCAGCTCAATCAGACATCTTGAG-TAAAATGTATGTGATATATTTAAGTAGACTGTCTATTTC
66 AATCACCTCAATC-GACATCTAAAGCAAAAAT-TATGT-A-ATATTTAAGTAGACTATCCA-TTC
** * * * *
44901 CCGCTAACCGAAATTACTAATTTTTGGGAAGCATTTTTTATTCCTGCAATA-TC-
126 CCGCTAACCGAAACAACTAATTTTTCGGAAACATTTTTTATGCCTG-AA-ACGCT
* * *
44954 AAATTTAGCTTTC-ATGTCCTAATCATAAAAGTTTTATATCATGAAACAACATTTTAATAGATAC
1 AAATTTAGCTTTCGA-GTCCT--TCATGAAAGTTCTATATCATGAAACAACATTTTAATAGACAC
* *
45018 TTGAATAACCTCAATCGGACATCTAAAGCAAAAAATTATGTAATATTT-AGTAGGCTATCCATTC
63 TTGAATCACCTCAATC-GACATCTAAAGC-AAAAATTATGTAATATTTAAGTAGACTATCCATTC
* *
45082 TCGCTAACCGAAACAACTAATTTTTCGGAAACATTTTTTATGCTTGAAACGCT
126 CCGCTAACCGAAACAACTAATTTTTCGGAAACATTTTTTATGCCTGAAACGCT
* *** * *
45135 AAATTTAGCTTTCGAGTCCTCCATGGTCGTTCTATATCATGAAACAACCTTTTAATAAACACTTG
1 AAATTTAGCTTTCGAGTCCTTCATGAAAGTTCTATATCATGAAACAACATTTTAATAGACACTTG
* ** * *
45200 AATCACCTAAATCGACTATCTGTAGCAAGAATTATGTAATATATTAAGTAGACCATCCAT
66 AATCACCTCAATCGAC-ATCTAAAGCAAAAATTATGTAATAT-TTAAGTAGACTATCCAT
45260 GTTCGACAAC
Statistics
Matches: 252, Mismatches: 42, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
178 18 0.07
179 57 0.23
180 16 0.06
181 75 0.30
182 11 0.04
183 27 0.11
184 38 0.15
185 5 0.02
186 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (178 bp):
AAATTTAGCTTTCGAGTCCTTCATGAAAGTTCTATATCATGAAACAACATTTTAATAGACACTTG
AATCACCTCAATCGACATCTAAAGCAAAAATTATGTAATATTTAAGTAGACTATCCATTCCCGCT
AACCGAAACAACTAATTTTTCGGAAACATTTTTTATGCCTGAAACGCT
Found at i:46087 original size:3 final size:3
Alignment explanation
Indices: 46074--46131 Score: 98
Period size: 3 Copynumber: 18.7 Consensus size: 3
46064 TTATATATAT
46074 TTA TATA TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
46121 TTA TTA TTA TT
1 TTA TTA TTA TT
46132 GAGCAACCCA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:47922 original size:2 final size:2
Alignment explanation
Indices: 47910--47956 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
47900 CTCAATTCGA
*
47910 AT AT GT AT AT AT AT 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 AT AT AT AT AT AT AT
47952 AT AT A
1 AT AT A
47957 CCATCAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48233 original size:23 final size:21
Alignment explanation
Indices: 48156--48233 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
48146 AGGGAGATTA
* * *
48156 ACAAAATCTCATAGGGAGGTT
1 ACAAAATTTCATAAGAAGGTT
* **
48177 ATAAAAAATCATAAGAAGGTT
1 ACAAAATTTCATAAGAAGGTT
*
48198 ACAAGATTTCATAAGAAGGTTT
1 ACAAAATTTCATAAGAAGG-TT
*
48220 ATTAAAATTTCATA
1 A-CAAAATTTCATA
48234 TTTAAGTTAT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 31 0.70
22 3 0.07
23 10 0.23
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.29
Consensus pattern (21 bp):
ACAAAATTTCATAAGAAGGTT
Found at i:48276 original size:22 final size:21
Alignment explanation
Indices: 48262--48315 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
48252 CATATGGAAT
*
48262 TTAGCACAATTTCATAGGTAA
1 TTAGCAAAATTTCATAGGTAA
* *
48283 TTATCAAAATTTCATAGTGTGA
1 TTAGCAAAATTTCATAG-GTAA
*
48305 TTATCAAAATT
1 TTAGCAAAATT
48316 CAATAGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (21 bp):
TTAGCAAAATTTCATAGGTAA
Found at i:54694 original size:25 final size:26
Alignment explanation
Indices: 54665--54713 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
54655 TTATCCACCA
54665 CTCCTTTTT-CTT-TTCTCCTTTTCAT
1 CTCCTTTTTCCTTCTTC-CCTTTTCAT
54690 CTCCTTTTTCCTTCTTCCCTTTTC
1 CTCCTTTTTCCTTCTTCCCTTTTC
54714 TTTTTCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 10 0.45
27 3 0.14
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (26 bp):
CTCCTTTTTCCTTCTTCCCTTTTCAT
Found at i:56456 original size:15 final size:17
Alignment explanation
Indices: 56436--56469 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
56426 TATAACCTTT
56436 TTTCTTAA-AAAAA-AA
1 TTTCTTAACAAAAACAA
56451 TTTCTTAACAAAAACAA
1 TTTCTTAACAAAAACAA
56468 TT
1 TT
56470 CTGTTACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 5 0.29
17 4 0.24
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTCTTAACAAAAACAA
Done.