Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013959.1 Corchorus capsularis cultivar CVL-1 contig13980, 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: 58642
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2893 original size:20 final size:22
Alignment explanation
Indices: 2860--2926 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 22
2850 GAGAATGTAT
*
2860 AACT-AATAAATTAT-TATTTA
1 AACTAAATTAATTATATATTTA
*
2880 AA-TAAATTAATTATATTTTTA
1 AACTAAATTAATTATATATTTA
2901 AATCCTAAATTAATTATAGT-TTTA
1 AA--CTAAATTAATTATA-TATTTA
2925 AA
1 AA
2927 ATCTTAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 1 0.03
20 11 0.28
21 7 0.18
24 19 0.49
25 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (22 bp):
AACTAAATTAATTATATATTTA
Found at i:2929 original size:25 final size:24
Alignment explanation
Indices: 2882--2947 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
2872 ATTATTTAAA
*
2882 TAAATTAATTATATTTTTAAATCC
1 TAAATTAATTATATTTTAAAATCC
*
2906 TAAATTAATTATAGTTTTAAAATCT
1 TAAATTAATTATA-TTTTAAAATCC
*
2931 TAAAATATATTA-ATTTT
1 TAAATTA-ATTATATTTT
2948 CATGTCATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 17 0.46
25 16 0.43
26 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAATTAATTATATTTTAAAATCC
Found at i:4848 original size:10 final size:10
Alignment explanation
Indices: 4835--4883 Score: 64
Period size: 10 Copynumber: 4.7 Consensus size: 10
4825 CTCTTTCTTC
4835 TCTCTTCTCT
1 TCTCTTCTCT
4845 TCTCTTCTCT
1 TCTCTTCTCT
4855 TCTCTTCT-T
1 TCTCTTCTCT
4864 TCTTCTTCTTCT
1 TC-TCTTC-TCT
4876 TCTTCTTC
1 TC-TCTTC
4884 ACCATAACGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 3 0.08
10 23 0.64
11 1 0.03
12 9 0.25
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (10 bp):
TCTCTTCTCT
Found at i:4869 original size:3 final size:3
Alignment explanation
Indices: 4829--4883 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
4819 CAGACTCTCT
4829 TTC TTC TCTC TTC -TC TTC -TC TTC -TC TTC -TC TTC TTTC TTC TTC
1 TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
4872 TTC TTC TTC TTC
1 TTC TTC TTC TTC
4884 ACCATAACGT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 8 0.17
3 32 0.70
4 6 0.13
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:10223 original size:58 final size:58
Alignment explanation
Indices: 10133--10410 Score: 296
Period size: 58 Copynumber: 5.0 Consensus size: 58
10123 TTTATTACCT
* * * * *
10133 TTTTACTTCTTAATTGACTCAATTAC-CCGAATTAAGCTAATTACTACTGTTTACTCC
1 TTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGTTTACTCC
* * * *
10190 TTTTACTTATTGATTAACTTAATTGCTCTGAATTAAGTTAATCACTACTGTTTATTCC
1 TTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGTTTACTCC
* * *
10248 TTTTGCTTCTTGAGTAACTTAATTGCTCTGAATTAAGCTAATTACTATTGTTTACTCC
1 TTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGTTTACTCC
* *
10306 TTTTACTTCTTGATTAA-TT--TT-CTCTG-----A---A-TTACTACTGATTACTCT
1 TTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGTTTACTCC
* * * *
10351 TTTTATTTCTTGATTAACTTAATTACTCTGGATTAAGCTAATTACTACCGTTTACTCC
1 TTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGTTTACTCC
10409 TT
1 TT
10411 CTTTTACTTC
Statistics
Matches: 182, Mismatches: 25, Indels: 27
0.78 0.11 0.12
Matches are distributed among these distances:
45 30 0.16
46 3 0.02
48 2 0.01
49 6 0.03
54 6 0.03
55 2 0.01
57 24 0.13
58 109 0.60
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (58 bp):
TTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGTTTACTCC
Found at i:10474 original size:56 final size:54
Alignment explanation
Indices: 10402--10520 Score: 184
Period size: 55 Copynumber: 2.2 Consensus size: 54
10392 TTACTACCGT
*
10402 TTACTCCTTCTTTTACTTCTTTAGCTTAACTACTCTGAATTAAACCAATTTTCTGA
1 TTACTCCTTCTTTTACTTC-TTAGCTTAACTACTCTGAATTAAACCAA-TTACTGA
* *
10458 TTACTCCTTCTTTTACTTCTTAGTTTAATTACTCTGAATTAAACCAATTACTGA
1 TTACTCCTTCTTTTACTTCTTAGCTTAACTACTCTGAATTAAACCAATTACTGA
*
10512 TGACTCCTT
1 TTACTCCTT
10521 TTACTTTTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 14 0.24
55 26 0.44
56 19 0.32
ACGTcount: A:0.25, C:0.23, G:0.06, T:0.46
Consensus pattern (54 bp):
TTACTCCTTCTTTTACTTCTTAGCTTAACTACTCTGAATTAAACCAATTACTGA
Found at i:10562 original size:40 final size:40
Alignment explanation
Indices: 10486--10720 Score: 226
Period size: 40 Copynumber: 6.2 Consensus size: 40
10476 CTTAGTTTAA
* * *
10486 TTACTCTGAATTAAACCAA-TTACTGATGACTCCTTTTACTT
1 TTACTCTTAATT--ACCAATTTACTGATTACTTCTTTTACTT
* *
10527 TTACTTTTAATTATCAATTTACTGATTACTTCTTTTACTT
1 TTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTT
* *
10567 TTACTCTTAATTACCAATTTACCGATTACTTCTTTTACCT
1 TTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTT
** * *
10607 TTACTCTTAATTACCAATTTTTTGACTATTTCTTTTACTT
1 TTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTT
*
10647 TTA--C-----T-CCATTTTACTG---A-TTCTTTTACTT
1 TTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTT
* * *
10675 TTACACTTAATTACCACTTTTCTGATTACTTCTTTTACTT
1 TTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTT
10715 TTACTC
1 TTACTC
10721 CATTTTATTG
Statistics
Matches: 160, Mismatches: 21, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
28 14 0.09
29 1 0.01
30 1 0.01
32 8 0.05
33 1 0.01
35 1 0.01
36 9 0.06
38 1 0.01
39 5 0.03
40 109 0.68
41 10 0.06
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.52
Consensus pattern (40 bp):
TTACTCTTAATTACCAATTTACTGATTACTTCTTTTACTT
Found at i:10670 original size:68 final size:68
Alignment explanation
Indices: 10596--10788 Score: 307
Period size: 68 Copynumber: 2.8 Consensus size: 68
10586 TACCGATTAC
* * * *
10596 TTCTTTTACCTTTACTCTTAATTACCAATTTTTTGACTATTTCTTTTACTTTTACTCCATTTTAC
1 TTCTTTTACTTTTACTCTTAATTACCACTTTTCTGATTATTTCTTTTACTTTTACTCCATTTTAC
10661 TGA
66 TGA
* * *
10664 TTCTTTTACTTTTACACTTAATTACCACTTTTCTGATTACTTCTTTTACTTTTACTCCATTTTAT
1 TTCTTTTACTTTTACTCTTAATTACCACTTTTCTGATTATTTCTTTTACTTTTACTCCATTTTAC
10729 TGA
66 TGA
10732 -TCATTTTACTTTTACTCTTAATTACCACTTTTCTGATTATTTCTTTTACTTTTACTC
1 TTC-TTTTACTTTTACTCTTAATTACCACTTTTCTGATTATTTCTTTTACTTTTACTC
10789 TTGATGACCA
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
67 2 0.02
68 113 0.98
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.56
Consensus pattern (68 bp):
TTCTTTTACTTTTACTCTTAATTACCACTTTTCTGATTATTTCTTTTACTTTTACTCCATTTTAC
TGA
Found at i:10776 original size:108 final size:105
Alignment explanation
Indices: 10518--10824 Score: 288
Period size: 108 Copynumber: 2.8 Consensus size: 105
10508 CTGATGACTC
* *
10518 CTTTTACTTTTACTTTTAATTATCAATTTACTGATTACTTCTTTTACTTTTACTCTTAATTACCA
1 CTTTTACTTTTAC-TTTAATTA-CCATTTTCTGATTA-TTCTTTTACTTTTACTCTTAATTACCA
* *
10583 ATTTACCGATTACTTCTTTTACCTTTACTCTTAATTACCAATTTTTTGA
63 ATTTACTGATTACTTCTTTTA-C--T--T-TTAACTACCAATTTTTTGA
* * * *
10632 CTATTT-CTTTTACTTTTACT-CCATTTTACTG---ATTCTTTTACTTTTACACTTAATTACCAC
1 CT-TTTACTTTTACTTTAATTACCATTTT-CTGATTATTCTTTTACTTTTACTCTTAATTACCAA
*
10692 TTTTCTGATTACTTCTTTTACTTTT-ACT-CC-ATTTTATTGA
64 TTTACTGATTACTTCTTTTACTTTTAACTACCAATTTT-TTGA
* *
10732 TCATTTTACTTTTACTCTTAATTACCACTTTTCTGATTATTTCTTTTACTTTTACTCTTGATGAC
1 -C-TTTTACTTTTACT-TTAATTACCA-TTTTCTGATTA-TTCTTTTACTTTTACTCTTAATTAC
* *
10797 CAATTTACTGCTTACTCCTTTTACTTTT
61 CAATTTACTGATTACTTCTTTTACTTTT
10825 GCTTACTCTA
Statistics
Matches: 162, Mismatches: 18, Indels: 32
0.76 0.08 0.15
Matches are distributed among these distances:
99 5 0.03
100 6 0.04
101 6 0.04
102 11 0.07
103 5 0.03
104 6 0.04
105 5 0.03
107 2 0.01
108 90 0.56
109 1 0.01
111 5 0.03
112 3 0.02
113 5 0.03
114 9 0.06
115 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (105 bp):
CTTTTACTTTTACTTTAATTACCATTTTCTGATTATTCTTTTACTTTTACTCTTAATTACCAATT
TACTGATTACTTCTTTTACTTTTAACTACCAATTTTTTGA
Found at i:10784 original size:40 final size:40
Alignment explanation
Indices: 10735--10824 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
10725 TTATTGATCA
* * * * *
10735 TTTTACTTTTACTCTTAATTACCACTTTTCTGATTATTTC
1 TTTTACTTTTACTCTTAATGACCAATTTACTGATTACTCC
* *
10775 TTTTACTTTTACTCTTGATGACCAATTTACTGCTTACTCC
1 TTTTACTTTTACTCTTAATGACCAATTTACTGATTACTCC
10815 TTTTACTTTT
1 TTTTACTTTT
10825 GCTTACTCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (40 bp):
TTTTACTTTTACTCTTAATGACCAATTTACTGATTACTCC
Found at i:11092 original size:51 final size:51
Alignment explanation
Indices: 10860--11111 Score: 170
Period size: 54 Copynumber: 4.9 Consensus size: 51
10850 TCCTTTTGCT
* * * * * * *
10860 CTTTCTAGTTTAATTACGCTGAATTAAACTAATTTAATGTTTACTCTTTCTTTTA
1 CTTTTTAGCTTAATTACTCTGAATTAAACTAA-CTACTGATTAC-C-AT-TTTTA
* * * * * *
10915 CTTTTTAGCTTAACTAGTCAGAATTAAATTATCTACTGATTACTATTTTCTCTA
1 CTTTTTAGCTTAATTACTCTGAATTAAACTAACTACTGATTACCA-TTT-T-TA
* * * **
10969 CTTTATAGCTTAATTGCTCTGAATTAAACTATCTGTTGATTA-C-TTTTT-
1 CTTTTTAGCTTAATTACTCTGAATTAAACTAACTACTGATTACCATTTTTA
* * *** *
11017 CTTCTTAGTTTAATT-CAGAGGAATTAAACTAACTACTGACTACCATTTTTA
1 CTTTTTAGCTTAATTAC-TCTGAATTAAACTAACTACTGATTACCATTTTTA
* *
11068 CTTTTTAGCTTAATTACTCTGAATTAAACTAATTACTAATTACC
1 CTTTTTAGCTTAATTACTCTGAATTAAACTAACTACTGATTACC
11112 TTCTCTTTAT
Statistics
Matches: 149, Mismatches: 40, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
47 1 0.01
48 30 0.20
49 2 0.01
50 6 0.04
51 37 0.25
52 3 0.02
53 2 0.01
54 44 0.30
55 24 0.16
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (51 bp):
CTTTTTAGCTTAATTACTCTGAATTAAACTAACTACTGATTACCATTTTTA
Found at i:12575 original size:31 final size:30
Alignment explanation
Indices: 12537--12619 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
12527 GCATCCGATG
* *
12537 TGGCATGCCACGTGTACCAAAAATTGCCACA
1 TGGCATGCCACGTGTA-CAAAAATGGACACA
*
12568 TGGCATGCCACGTGTACAAAAAAGGACACA
1 TGGCATGCCACGTGTACAAAAATGGACACA
12598 TGGCATGCCACGTGT-CAAAAAT
1 TGGCATGCCACGTGTACAAAAAT
12620 ACCACGTGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 6 0.12
30 26 0.54
31 16 0.33
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (30 bp):
TGGCATGCCACGTGTACAAAAATGGACACA
Found at i:13819 original size:30 final size:30
Alignment explanation
Indices: 13783--13847 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
13773 AAAGGGTCAA
13783 ATGGCCGGTTGTGCCCGGATGGCC-CATGCG
1 ATGGCCGGTTGTGCCCGGAT-GCCTCATGCG
* *
13813 ATGGCCGGTTGTGGCCGGATGCCTCATGTG
1 ATGGCCGGTTGTGCCCGGATGCCTCATGCG
13843 ATGGC
1 ATGGC
13848 GCATGCGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.11, C:0.26, G:0.40, T:0.23
Consensus pattern (30 bp):
ATGGCCGGTTGTGCCCGGATGCCTCATGCG
Found at i:20327 original size:14 final size:14
Alignment explanation
Indices: 20308--20335 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20298 GTGATGGTGC
20308 ATGCGATGGCCGGT
1 ATGCGATGGCCGGT
20322 ATGCGATGGCCGGT
1 ATGCGATGGCCGGT
20336 TGTGGCCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.43, T:0.21
Consensus pattern (14 bp):
ATGCGATGGCCGGT
Found at i:22168 original size:20 final size:20
Alignment explanation
Indices: 22143--22181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22133 ACCCCAAGTT
22143 CCAAATACAAGTCCAAATCC
1 CCAAATACAAGTCCAAATCC
* *
22163 CCAAATACCAGTGCAAATC
1 CCAAATACAAGTCCAAATC
22182 TAAAATACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.33, G:0.08, T:0.15
Consensus pattern (20 bp):
CCAAATACAAGTCCAAATCC
Found at i:25776 original size:32 final size:32
Alignment explanation
Indices: 25740--25811 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 32
25730 ATTTATCATA
25740 TAATCCTCACACTTTTTATGTTTTATGATATT
1 TAATCCTCACACTTTTTATGTTTTATGATATT
* * *
25772 TAATCCTTTACATTTTTTATGTTTTATGCTATT
1 TAATCC-TCACACTTTTTATGTTTTATGATATT
25805 TAATCCT
1 TAATCCT
25812 TTATAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 7 0.19
33 29 0.81
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.56
Consensus pattern (32 bp):
TAATCCTCACACTTTTTATGTTTTATGATATT
Found at i:25794 original size:33 final size:33
Alignment explanation
Indices: 25752--25814 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
25742 ATCCTCACAC
25752 TTTTTATGTTTTATGATATTTAATCCTTTACAT
1 TTTTTATGTTTTATGATATTTAATCCTTTACAT
*
25785 TTTTTATGTTTTATGCTATTTAATCCTTTA
1 TTTTTATGTTTTATGATATTTAATCCTTTA
25815 TAATTATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.62
Consensus pattern (33 bp):
TTTTTATGTTTTATGATATTTAATCCTTTACAT
Found at i:26295 original size:40 final size:40
Alignment explanation
Indices: 26250--26388 Score: 131
Period size: 41 Copynumber: 3.4 Consensus size: 40
26240 TTTAATCACC
26250 ATCTCTCTTAGGGTTTAGCTTGATTTTGAGGGTTTGTTTT
1 ATCTCTCTTAGGGTTTAGCTTGATTTTGAGGGTTTGTTTT
* * * *
26290 ATCTCTCCTACGGTTTAGCTTTG-TTTTAGGGGTGTTTGATTT
1 ATCTCTCTTAGGGTTTAGC-TTGATTTT-GAGG-GTTTGTTTT
* * *
26332 CTCTCTTTTAGAGTTTAGCTT-ATTTT-AGGGGCTTATGTTTT
1 ATCTCTCTTAGGGTTTAGCTTGATTTTGA-GGG-TT-TGTTTT
*
26373 ATCTTTCTTAGGGTTT
1 ATCTCTCTTAGGGTTT
26389 GGGCTTACTT
Statistics
Matches: 77, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
39 1 0.01
40 25 0.32
41 29 0.38
42 22 0.29
ACGTcount: A:0.13, C:0.12, G:0.22, T:0.53
Consensus pattern (40 bp):
ATCTCTCTTAGGGTTTAGCTTGATTTTGAGGGTTTGTTTT
Found at i:26326 original size:38 final size:40
Alignment explanation
Indices: 26250--26326 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
26240 TTTAATCACC
* * *
26250 ATCTCTCTTAGGGTTTAGCTTGATTTTGAGGGTTTGTTTT
1 ATCTCTCCTACGGTTTAGCTTGATTTTGAGGGTGTGTTTT
26290 ATCTCTCCTACGGTTTAGCTTTG-TTTT-AGGG-GTGTTT
1 ATCTCTCCTACGGTTTAGC-TTGATTTTGAGGGTGTGTTT
26327 GATTTCTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 5 0.15
39 4 0.12
40 21 0.64
41 3 0.09
ACGTcount: A:0.12, C:0.13, G:0.25, T:0.51
Consensus pattern (40 bp):
ATCTCTCCTACGGTTTAGCTTGATTTTGAGGGTGTGTTTT
Found at i:27198 original size:2 final size:2
Alignment explanation
Indices: 27191--27221 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27181 AGGTAAATCT
27191 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 T
27222 TGTTTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27520 original size:55 final size:55
Alignment explanation
Indices: 27411--27521 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
27401 TTTGTCTTTT
* *
27411 TAGCTCTTAGGATAATTGATATTATGTTGATATGGATATAATTGGTACCCGCAAG
1 TAGCTCTTAGGATAATTGATATTATGTTGATATGGATATAATTGATACCAGCAAG
* *
27466 TAGCTCTTAGGATAATTGATTTTATGTTGATATGGATATAATTGATATCAGCAAG
1 TAGCTCTTAGGATAATTGATATTATGTTGATATGGATATAATTGATACCAGCAAG
27521 T
1 T
27522 GAAAAGTCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (55 bp):
TAGCTCTTAGGATAATTGATATTATGTTGATATGGATATAATTGATACCAGCAAG
Found at i:31545 original size:25 final size:25
Alignment explanation
Indices: 31511--31561 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31501 TAGTATGGTA
31511 ACTTGCTTTTGGAATTGGGCATATT
1 ACTTGCTTTTGGAATTGGGCATATT
31536 ACTTGCTTTTGGAATTGGGCATATT
1 ACTTGCTTTTGGAATTGGGCATATT
31561 A
1 A
31562 ATTATGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.43
Consensus pattern (25 bp):
ACTTGCTTTTGGAATTGGGCATATT
Found at i:31571 original size:25 final size:25
Alignment explanation
Indices: 31517--31572 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
31507 GGTAACTTGC
* *
31517 TTTTGGAATTGGGCATATTACTTGC
1 TTTTGGAATTGGGCATATTAATTGA
31542 TTTTGGAATTGGGCATATTAATT-A
1 TTTTGGAATTGGGCATATTAATTGA
31566 TGTTTGG
1 T-TTTGG
31573 GTCTTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (25 bp):
TTTTGGAATTGGGCATATTAATTGA
Found at i:31973 original size:31 final size:31
Alignment explanation
Indices: 31905--32066 Score: 137
Period size: 31 Copynumber: 5.5 Consensus size: 31
31895 TCCTTTTGTG
* * **
31905 CACGTGGCATGCCACGTGCCA-TTTTTGAAA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
31935 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* *
31966 CACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
31997 CA--T---GTGGCAC--G--ACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
* * *
32019 CATGTGGCGTGTCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA
*
32050 CACGTGGCGTGTCACGT
1 CACGTGGCGTGCCACGT
32067 CGGACACCGT
Statistics
Matches: 109, Mismatches: 13, Indels: 19
0.77 0.09 0.13
Matches are distributed among these distances:
22 13 0.12
24 2 0.02
26 5 0.05
27 6 0.06
29 2 0.02
30 19 0.17
31 62 0.57
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.33
Consensus pattern (31 bp):
CACGTGGCGTGCCACGTGTCACTTTTTGGTA
Found at i:32017 original size:53 final size:53
Alignment explanation
Indices: 31955--32057 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
31945 GCCACGTGTC
** *
31955 ACTTTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
* *
32008 ACTTTTTGGTACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGC
1 ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGC
32058 GTGTCACGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGGCGTGACACATGTCACTTTTTGGTACACGTGGCACG
Found at i:32996 original size:8 final size:8
Alignment explanation
Indices: 32983--33029 Score: 57
Period size: 7 Copynumber: 6.2 Consensus size: 8
32973 TAAAAAGGTT
32983 TTCAAAAA
1 TTCAAAAA
32991 TTCAAAAAA
1 TTC-AAAAA
33000 TTC-AAAA
1 TTCAAAAA
33007 TTC-AAAA
1 TTCAAAAA
33014 -TCAAAAA
1 TTCAAAAA
33021 -TCAAAAA
1 TTCAAAAA
33028 TT
1 TT
33030 TCATTCAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.06
7 22 0.61
8 4 0.11
9 8 0.22
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (8 bp):
TTCAAAAA
Found at i:35348 original size:1 final size:1
Alignment explanation
Indices: 35337--35373 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
35327 TGACTCTCGT
*
35337 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35374 GAGCATCTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:37458 original size:25 final size:24
Alignment explanation
Indices: 37431--37479 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
37421 ATTGCTATAA
*
37431 TTTAGATTTAATTTGCTTTGTTTTATT
1 TTTAG-TTTAA-TTGCTTTCTTTTA-T
37458 TTTAGTTTAATTGCTTTCTTTT
1 TTTAGTTTAATTGCTTTCTTTT
37480 TAATTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.52
26 5 0.24
27 5 0.24
ACGTcount: A:0.16, C:0.06, G:0.10, T:0.67
Consensus pattern (24 bp):
TTTAGTTTAATTGCTTTCTTTTAT
Found at i:38108 original size:21 final size:21
Alignment explanation
Indices: 38079--38118 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38069 TATAGACCTA
38079 AAACACCTATACCAACGGTGG
1 AAACACCTATACCAACGGTGG
* * *
38100 AAACCCCTATTCCGACGGT
1 AAACACCTATACCAACGGT
38119 AAATTTGGCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (21 bp):
AAACACCTATACCAACGGTGG
Found at i:39837 original size:3 final size:3
Alignment explanation
Indices: 39829--39887 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
39819 CTAGTAAGGC
*
39829 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39877 AAT AAT AAT AA
1 AAT AAT AAT AA
39888 GCCGACTACC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45208 original size:12 final size:12
Alignment explanation
Indices: 45191--45215 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45181 GGCAGACACG
45191 TGCAAATGTATT
1 TGCAAATGTATT
45203 TGCAAATGTATT
1 TGCAAATGTATT
45215 T
1 T
45216 CAGTGGTATA
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:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGCAAATGTATT
Found at i:45505 original size:22 final size:23
Alignment explanation
Indices: 45464--45516 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
45454 CCAAAAACCG
45464 GGGTCCCGGGTTGGGGGTCAACT
1 GGGTCCCGGGTTGGGGGTCAACT
*
45487 GGGTCCCGGGTT-GGGGTCAAGT
1 GGGTCCCGGGTTGGGGGTCAACT
45509 GGGATCCC
1 GGG-TCCC
45517 AATTGAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.09, C:0.23, G:0.47, T:0.21
Consensus pattern (23 bp):
GGGTCCCGGGTTGGGGGTCAACT
Found at i:45628 original size:23 final size:23
Alignment explanation
Indices: 45584--45633 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
45574 CTAACCGGGG
*
45584 TCCCGGTTGGGGGTCAACTGGGC
1 TCCCGGTTGGGGGTCAACTGGGA
* * *
45607 TCCCGGTTTGGGGTGAAGTGGGA
1 TCCCGGTTGGGGGTCAACTGGGA
45630 TCCC
1 TCCC
45634 ACTTCGACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.10, C:0.24, G:0.42, T:0.24
Consensus pattern (23 bp):
TCCCGGTTGGGGGTCAACTGGGA
Found at i:48153 original size:27 final size:27
Alignment explanation
Indices: 48099--48168 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
48089 GCCTGAGCTG
*
48099 CCCCATCATAATAACCGAACCCAGCAC
1 CCCCATCATAATAACCGAACCCAACAC
** *
48126 CCCCATCATAATAACCGGGCTCAACAC
1 CCCCATCATAATAACCGAACCCAACAC
* *
48153 CCTCATCATAGTAACC
1 CCCCATCATAATAACC
48169 CGGTTGACCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.34, C:0.41, G:0.09, T:0.16
Consensus pattern (27 bp):
CCCCATCATAATAACCGAACCCAACAC
Found at i:48430 original size:13 final size:14
Alignment explanation
Indices: 48412--48529 Score: 66
Period size: 14 Copynumber: 8.4 Consensus size: 14
48402 TAAATAACTC
48412 TAATTAAAATTAA-
1 TAATTAAAATTAAT
48425 TAATTAAAATTAAT
1 TAATTAAAATTAAT
** *
48439 TAATT-TCAGTATAT
1 TAATTAAAATTA-AT
* *
48453 AAATTATAATTAA-
1 TAATTAAAATTAAT
*
48466 -AATTATAATTAAT
1 TAATTAAAATTAAT
**
48479 TAAACAGAAATATAAT
1 TAATTA-AAAT-TAAT
*
48495 TAATTGTAAA-TAACT
1 TAATT-AAAATTAA-T
48510 CTAATTAAAATTAAT
1 -TAATTAAAATTAAT
48525 TAATT
1 TAATT
48530 TCAATATTCA
Statistics
Matches: 81, Mismatches: 13, Indels: 21
0.70 0.11 0.18
Matches are distributed among these distances:
12 12 0.15
13 16 0.20
14 23 0.28
15 12 0.15
16 18 0.22
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (14 bp):
TAATTAAAATTAAT
Found at i:48516 original size:46 final size:46
Alignment explanation
Indices: 48367--48527 Score: 148
Period size: 46 Copynumber: 3.3 Consensus size: 46
48357 ACATATTAAC
* *
48367 AATTATAATTAATTAAACAGAAATATAATTAATCGTAAATAACTCT
1 AATTAAAATTAATTAAACAGAAATATAATTAATTGTAAATAACTCT
** * * *
48413 AATTAAAATTAA-TAATTA-AAAT-TAATTAATTTCAGTATATAAATTAT
1 AATTAAAATTAATTAAACAGAAATATAATTAA-TT--GTAAAT-AACTCT
48460 AATTAAAATTATAATTAATTAAACAGAAATATAATTAATTGTAAATAACTCT
1 AATT---A--A-AATTAATTAAACAGAAATATAATTAATTGTAAATAACTCT
48512 AATTAAAATTAATTAA
1 AATTAAAATTAATTAA
48528 TTTCAATATT
Statistics
Matches: 90, Mismatches: 12, Indels: 26
0.70 0.09 0.20
Matches are distributed among these distances:
43 7 0.08
44 5 0.06
45 4 0.04
46 26 0.29
47 9 0.10
49 1 0.01
50 1 0.01
52 9 0.10
53 11 0.12
54 4 0.04
55 6 0.07
56 7 0.08
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (46 bp):
AATTAAAATTAATTAAACAGAAATATAATTAATTGTAAATAACTCT
Found at i:48633 original size:14 final size:13
Alignment explanation
Indices: 48577--48632 Score: 85
Period size: 14 Copynumber: 4.2 Consensus size: 13
48567 TATTAAAACT
48577 AATAATTTAAAAA
1 AATAATTTAAAAA
48590 AATAATTTTAAAAA
1 AATAA-TTTAAAAA
*
48604 AATAACCTTAAAAA
1 AATAA-TTTAAAAA
48618 AATAATTTAAAAA
1 AATAATTTAAAAA
48631 AA
1 AA
48633 AAACAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
13 14 0.36
14 25 0.64
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATTTAAAAA
Found at i:48772 original size:32 final size:32
Alignment explanation
Indices: 48676--48781 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
48666 GGCTCAGCCT
**
48676 AGGGTGCGGCCTTTCGTGGCAAGGCCGACCCC
1 AGGGTGCGGCCTACCGTGGCAAGGCCGACCCC
* * *
48708 ATGGTGCGGCCTGCCGTGGCAAGGCCAACCCC
1 AGGGTGCGGCCTACCGTGGCAAGGCCGACCCC
* *
48740 AGGGTGCGGCCTACCGTGGCGCA-GCCGCCCCC
1 AGGGTGCGGCCTACCGTGGC-AAGGCCGACCCC
*
48772 AGAGTGCGGC
1 AGGGTGCGGC
48782 TTGCTTGCCA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 62 0.98
33 1 0.02
ACGTcount: A:0.13, C:0.37, G:0.38, T:0.12
Consensus pattern (32 bp):
AGGGTGCGGCCTACCGTGGCAAGGCCGACCCC
Found at i:49006 original size:20 final size:20
Alignment explanation
Indices: 48981--49020 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
48971 CGGCTCAGCC
*
48981 CCTAGATCTATTTTTTTACA
1 CCTAGATCTAATTTTTTACA
49001 CCTAGATCTAATTTTTTACA
1 CCTAGATCTAATTTTTTACA
49021 TCCATTCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (20 bp):
CCTAGATCTAATTTTTTACA
Found at i:53320 original size:2 final size:2
Alignment explanation
Indices: 53265--53300 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
53255 AATCTAGTAG
*
53265 AT AT TT 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
53301 TTTTTCGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:55728 original size:2 final size:2
Alignment explanation
Indices: 55721--55750 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
55711 AGATATTTGA
55721 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55751 AAAAACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.