Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006859.1 Corchorus capsularis cultivar CVL-1 contig06880, 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: 38766
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1463 original size:30 final size:31
Alignment explanation
Indices: 1419--1479 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
1409 AGAAGCAATC
1419 TTGGGCCTAACATAAAGATAAATAAAAGGGA
1 TTGGGCCTAACATAAAGATAAATAAAAGGGA
*
1450 TTGGGCC-AACATAAAGATAAATAAGAGGGA
1 TTGGGCCTAACATAAAGATAAATAAAAGGGA
1480 ATAGAGGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.18
Consensus pattern (31 bp):
TTGGGCCTAACATAAAGATAAATAAAAGGGA
Found at i:1768 original size:2 final size:2
Alignment explanation
Indices: 1761--1785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1751 GTGAAGCCAC
1761 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1786 AATTAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3711 original size:56 final size:56
Alignment explanation
Indices: 3635--3747 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
3625 CTCGAATAGC
3635 ATGTATATATGTTTTGTATGAGTCATCACGAGGTGAAGGGTGATCTACTCTAGATT
1 ATGTATATATGTTTTGTATGAGTCATCACGAGGTGAAGGGTGATCTACTCTAGATT
3691 ATGTATATATGTTTTGTATGAGTCATCACGAGGTGAAGGGTGATCTACTCTAGATT
1 ATGTATATATGTTTTGTATGAGTCATCACGAGGTGAAGGGTGATCTACTCTAGATT
3747 A
1 A
3748 AATTTATCCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (56 bp):
ATGTATATATGTTTTGTATGAGTCATCACGAGGTGAAGGGTGATCTACTCTAGATT
Found at i:4305 original size:136 final size:136
Alignment explanation
Indices: 4061--4333 Score: 528
Period size: 136 Copynumber: 2.0 Consensus size: 136
4051 TATGATACAC
*
4061 CGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTTTATTTTTTGAATT
1 CGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTTTATTTTTTGAATT
4126 ATTTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAGGACCCGCTTG
66 ATTTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAGGACCCGCTTG
4191 TGTAGT
131 TGTAGT
4197 CGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTTTATTTTTTGAATT
1 CGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTTTATTTTTTGAATT
*
4262 ATTTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGATACATGTCACCCTTCAGGACCCGCTTG
66 ATTTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAGGACCCGCTTG
4327 TGTAGT
131 TGTAGT
4333 C
1 C
4334 TGCTAAACTC
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (136 bp):
CGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGAAGTTGACACATGTTTATTTTTTGAATT
ATTTAAGTTTTAAATATTTCAATCTAGTCCCTAAGGGACACATGTCACCCTTCAGGACCCGCTTG
TGTAGT
Found at i:8426 original size:35 final size:35
Alignment explanation
Indices: 8382--9336 Score: 1008
Period size: 35 Copynumber: 27.6 Consensus size: 35
8372 TTCTTACTAA
* * *
8382 ACTTAATTACCCTGAATTAAGTCGATCAATGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * * *
8417 ACTTGATTACCCAGACTTTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGA-ATTAAGTTGATTACTGACTT
* *
8453 ACTTAATTACCCTGAATTAAGTT-ACTAACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
8488 ACTTAATTACCCTAAATTAAGTT-ACTAACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
8523 GCTTAATTACCCTGAATTAAGCT-ACTTACTG----
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
8554 ACTTAATTACCCTGAATTAAGTTGATTACTAAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * * *
8589 ACTTAATTACCCTGAATTAAATTAATAACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
8624 ACTTAATTACTCTGAATTAAGTTAATTACTGACTG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * * *
8659 ACTTAATTTCCTTGAATTAAGTT-ACTTATTGAATT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* * *
8694 ACTTAATTACCTTGAATTGAGTTGAATA-TCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACT-GACTT
*
8729 ACTTAATTACCCTGAATTAAGTTTATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
** * *
8764 ACTTAATTACCCTGAATTAAGTTGAAGACTGAATC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
** * *
8799 ACTTAATTACCCTGAATTAAGTTTTTTTAATGAGTT
1 ACTTAATTACCCTGAATTAAG-TTGATTACTGACTT
* * *
8835 ACTTAATTATCCTGAATTAAGTT-ACTAACTGACCT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
8870 GCTTAATTACCCTGAATTAAGCT-ACTTACTG----
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
8901 ACTTAATTACCCTGAATTAAGTTG----CGGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
8932 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
8967 ACTTAATTACCCTGAATTAAGTTGGTTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
9002 ACTTAATTACCCTGAACTAAGTTTATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
9037 ACTTAATTACCCTGAATTAAGTTTATTAC-CACTG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
9071 ACTTAATTACCCTGAATTAAGTTG----CGGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
9102 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
9137 ACTTAATTACCCTGAATTAAGTTGGTTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
9172 ACTTAATTACCCTGAACTAAGTTTATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
9207 ACTTAATTACCCTGAATTAAGTTTATTA-TCACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
9241 ACTTAATTACCCTGAATTAAGTTACTGGCTTACTAACTT
1 ACTTAATTACCCTGAATTAAG-T--T-GATTACTGACTT
* *
9280 ACTTAATTACCCAGAATTAAGTT-ATTCACTGACCT
1 ACTTAATTACCCTGAATTAAGTTGATT-ACTGACTT
9315 ACTTAATTACCCTGAATTAAGT
1 ACTTAATTACCCTGAATTAAGT
9337 CACTTATTAC
Statistics
Matches: 788, Mismatches: 99, Indels: 66
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.00
30 1 0.00
31 98 0.12
32 1 0.00
34 56 0.07
35 542 0.69
36 58 0.07
37 1 0.00
38 4 0.01
39 25 0.03
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
Found at i:8622 original size:17 final size:17
Alignment explanation
Indices: 8600--8655 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
8590 CTTAATTACC
8600 CTGAATTAAATTAATAA
1 CTGAATTAAATTAATAA
* *
8617 CTGAATT-ACTTAATTACT
1 CTGAATTAAATTAA-TA-A
* *
8635 CTGAATTAAGTTAATTA
1 CTGAATTAAATTAATAA
8652 CTGA
1 CTGA
8656 CTGACTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 5 0.16
17 13 0.42
18 8 0.26
19 5 0.16
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (17 bp):
CTGAATTAAATTAATAA
Found at i:8664 original size:21 final size:19
Alignment explanation
Indices: 8556--8786 Score: 92
Period size: 19 Copynumber: 13.1 Consensus size: 19
8546 ACTTACTGAC
*
8556 TTAATTACCCTGAATTAAG
1 TTAATTACTCTGAATTAAG
* * *
8575 TTGATTA--CTAAATT-AC
1 TTAATTACTCTGAATTAAG
* *
8591 TTAATTACCCTGAATTAAA
1 TTAATTACTCTGAATTAAG
* *
8610 TTAA-TA-ACTGAATT-AC
1 TTAATTACTCTGAATTAAG
8626 TTAATTACTCTGAATTAAG
1 TTAATTACTCTGAATTAAG
*
8645 TTAATTACTGACTGACTTAA-
1 TTAATTACT--CTGAATTAAG
*
8665 -T--TTCCT-TGAATTAAG
1 TTAATTACTCTGAATTAAG
* *
8680 TTACTTA-T-TGAATT-AC
1 TTAATTACTCTGAATTAAG
*
8696 TTAATTAC-CTTGAATTGAG
1 TTAATTACTC-TGAATTAAG
* *
8715 TTGAA-TA-TC-GACTT-AC
1 TT-AATTACTCTGAATTAAG
*
8731 TTAATTACCCTGAATTAAG
1 TTAATTACTCTGAATTAAG
* * *
8750 TTTATTA--CTGACTT-AC
1 TTAATTACTCTGAATTAAG
*
8766 TTAATTACCCTGAATTAAG
1 TTAATTACTCTGAATTAAG
8785 TT
1 TT
8787 GAAGACTGAA
Statistics
Matches: 159, Mismatches: 28, Indels: 50
0.67 0.12 0.21
Matches are distributed among these distances:
14 7 0.04
15 2 0.01
16 32 0.20
17 37 0.23
18 33 0.21
19 38 0.24
20 2 0.01
21 8 0.05
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (19 bp):
TTAATTACTCTGAATTAAG
Found at i:10090 original size:51 final size:49
Alignment explanation
Indices: 9985--10115 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 49
9975 TATATATCAC
* * *
9985 TTTTACTTACCGATTAATCACAAGTTCAATTTTTGATCCAAAAATTTCAT
1 TTTTA-TTACCAATTAATCACAAATTCCATTTTTGATCCAAAAATTTCAT
* *
10035 TTTTATTCACCAATTAATCACAAATTCCATTTTTTAGT-CAAAAGTTTTCAT
1 TTTTATT-ACCAATTAATCACAAATTCCATTTTTGA-TCCAAAA-ATTTCAT
*
10086 TTTTATTTCCAAGTTAATCACAAATTCCAT
1 TTTTATTACCAA-TTAATCACAAATTCCAT
10116 CTTTCACTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
49 2 0.03
50 38 0.54
51 31 0.44
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.44
Consensus pattern (49 bp):
TTTTATTACCAATTAATCACAAATTCCATTTTTGATCCAAAAATTTCAT
Found at i:10154 original size:51 final size:51
Alignment explanation
Indices: 10048--10170 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
10038 TATTCACCAA
* * * * * * * * * *
10048 TTAATCACAAATTCCATTTTTTAGTCAAAAGTTTTCATTTTTATTTCCAAG
1 TTAATCACAAATTCCATCTTTCACTCAAAAATATCCATTCTTAATTACAAC
*
10099 TTAATCACAAATTCCATCTTTCACTTAAAAATATCCATTCTTAATTACAAC
1 TTAATCACAAATTCCATCTTTCACTCAAAAATATCCATTCTTAATTACAAC
*
10150 TTAATCAAAAATTCCATCTTT
1 TTAATCACAAATTCCATCTTT
10171 TAGCTAAAGA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (51 bp):
TTAATCACAAATTCCATCTTTCACTCAAAAATATCCATTCTTAATTACAAC
Found at i:14360 original size:447 final size:447
Alignment explanation
Indices: 13526--14380 Score: 1602
Period size: 447 Copynumber: 1.9 Consensus size: 447
13516 TGAGGAAGGC
* * *
13526 CTAGTTCGAGATATTATGATAAAAGCTTATCATTAGTGGGACTAACGCCAGAAGCAGAAGCTGTA
1 CTAGTTCGAGATATCAAGAAAAAAGCTTATCATTAGTGGGACTAACGCCAGAAGCAGAAGCTGTA
*
13591 TGACATGAGTCAATAAAGCTAAGGCATTCAGTTGAAGCAAGTATTAGTGCCAGCAATGAAAAGCA
66 TGACATGAGTCAATAAAGCTAAGGCATTCAATTGAAGCAAGTATTAGTGCCAGCAATGAAAAGCA
13656 TAACTTTAGTGGGAGTACCGAAAATCATCAGCCAGTCAGATTTTGCCAGCGTCAGAAAAAGTCAA
131 TAACTTTAGTGGGAGTACCGAAAATCATCAGCCAGTCAGATTTTGCCAGCGTCAGAAAAAGTCAA
* *
13721 AATAACGGCTATAAATTCAAACGGCTCTTTCAACACCATAAATTGGCATACTTGCATTTAATGAG
196 AATAACAGCTATAAATTCAAACAGCTCTTTCAACACCATAAATTGGCATACTTGCATTTAATGAG
13786 AAAAATGACCGTTGGGAGGCAGAAGTGAGTATTTAAGGAGCCAAAAGAAAGGGTTAACGATAAGG
261 AAAAATGACCGTTGGGAGGCAGAAGTGAGTATTTAAGGAGCCAAAAGAAAGGGTTAACGATAAGG
13851 AATCACAACCAAGTTGTTCTACACTCAAATCTCTGATTTTAGCTTGGTTTTTGTAAGAATGCTCT
326 AATCACAACCAAGTTGTTCTACACTCAAATCTCTGATTTTAGCTTGGTTTTTGTAAGAATGCTCT
13916 TAACGCTTTTCTTTGTAAGATAAAAGCTTATCATTTTCTTTGTAAGACAATCTCTGA
391 TAACGCTTTTCTTTGTAAGATAAAAGCTTATCATTTTCTTTGTAAGACAATCTCTGA
13973 CTAGTTCGAGATATCAAGAAAAAAGCTTATCATTAGTGGGACTAACGCCAGAAGCAGAAGCTGTA
1 CTAGTTCGAGATATCAAGAAAAAAGCTTATCATTAGTGGGACTAACGCCAGAAGCAGAAGCTGTA
14038 TGACATGAGTCAATAAAGCTAAGGCATTCAATTGAAGCAAGTATTAGTGCCAGCAATGAAAAGCA
66 TGACATGAGTCAATAAAGCTAAGGCATTCAATTGAAGCAAGTATTAGTGCCAGCAATGAAAAGCA
* *
14103 TAACTTTAGTGGGAGTACCGGAAATCATCAGCCAGTCAGATTTTGTCAGCGTCAGAAAAAGTCAA
131 TAACTTTAGTGGGAGTACCGAAAATCATCAGCCAGTCAGATTTTGCCAGCGTCAGAAAAAGTCAA
*
14168 AATAACAGCTATAAATTCAAACAGCTCTTTCATCACCATAAATTGGCATACTTGCATTTAATGAG
196 AATAACAGCTATAAATTCAAACAGCTCTTTCAACACCATAAATTGGCATACTTGCATTTAATGAG
* * *
14233 AAAAATGATCGTTGGGAGGCAGATGTGAGTATTTAAGGAGCCAAAAGAAAGGGTTAACGCTAAGG
261 AAAAATGACCGTTGGGAGGCAGAAGTGAGTATTTAAGGAGCCAAAAGAAAGGGTTAACGATAAGG
14298 AATCACAACCAAGTTGTTCTACACTCAAATCTCTGATTTTAGCTTGGTTTTTGTAAGAATGCTCT
326 AATCACAACCAAGTTGTTCTACACTCAAATCTCTGATTTTAGCTTGGTTTTTGTAAGAATGCTCT
14363 TAACGCTTTTCTTTGTAA
391 TAACGCTTTTCTTTGTAA
14381 ATCTTGCGCA
Statistics
Matches: 396, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
447 396 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (447 bp):
CTAGTTCGAGATATCAAGAAAAAAGCTTATCATTAGTGGGACTAACGCCAGAAGCAGAAGCTGTA
TGACATGAGTCAATAAAGCTAAGGCATTCAATTGAAGCAAGTATTAGTGCCAGCAATGAAAAGCA
TAACTTTAGTGGGAGTACCGAAAATCATCAGCCAGTCAGATTTTGCCAGCGTCAGAAAAAGTCAA
AATAACAGCTATAAATTCAAACAGCTCTTTCAACACCATAAATTGGCATACTTGCATTTAATGAG
AAAAATGACCGTTGGGAGGCAGAAGTGAGTATTTAAGGAGCCAAAAGAAAGGGTTAACGATAAGG
AATCACAACCAAGTTGTTCTACACTCAAATCTCTGATTTTAGCTTGGTTTTTGTAAGAATGCTCT
TAACGCTTTTCTTTGTAAGATAAAAGCTTATCATTTTCTTTGTAAGACAATCTCTGA
Found at i:17575 original size:18 final size:19
Alignment explanation
Indices: 17540--17576 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17530 TTGAAGATTT
17540 CTTGAAGATAATTTAAAGA
1 CTTGAAGATAATTTAAAGA
*
17559 CTTGAAGATCA-TTAAAGA
1 CTTGAAGATAATTTAAAGA
17577 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (19 bp):
CTTGAAGATAATTTAAAGA
Found at i:26808 original size:23 final size:23
Alignment explanation
Indices: 26782--26871 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 23
26772 AACAATATTG
26782 GCTCTTCCGGAGCCTTAATACTA
1 GCTCTTCCGGAGCCTTAATACTA
* * *
26805 GCTCTTCTGGAGCGATAAAACAATACTA
1 GCTCTTCCGGAGC-CT----TAATACTA
*
26833 GCTCTTCCGAAGCCTTAATACTA
1 GCTCTTCCGGAGCCTTAATACTA
* *
26856 GCTCTTCTGGAACCTT
1 GCTCTTCCGGAGCCTT
26872 CAATCAAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
23 32 0.62
24 1 0.02
27 1 0.02
28 18 0.35
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (23 bp):
GCTCTTCCGGAGCCTTAATACTA
Found at i:26826 original size:51 final size:51
Alignment explanation
Indices: 26767--26866 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
26757 TGTTCCTCCA
* * *
26767 GATAAAACAATATTGGCTCTTCCGGAGCCTTAATACTAGCTCTTCTGGAGC
1 GATAAAACAATACTAGCTCTTCCGAAGCCTTAATACTAGCTCTTCTGGAGC
26818 GATAAAACAATACTAGCTCTTCCGAAGCCTTAATACTAGCTCTTCTGGA
1 GATAAAACAATACTAGCTCTTCCGAAGCCTTAATACTAGCTCTTCTGGA
26867 ACCTTCAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (51 bp):
GATAAAACAATACTAGCTCTTCCGAAGCCTTAATACTAGCTCTTCTGGAGC
Found at i:28084 original size:85 final size:85
Alignment explanation
Indices: 27982--28246 Score: 209
Period size: 86 Copynumber: 3.2 Consensus size: 85
27972 TTTGTCTCAA
*
27982 TTTTCGTTTCCCTTTTTTGAAGCGATTCACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATA
1 TTTTCTTTTCCCTTTTTTGAAGCGATTCACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATA
28047 TGCTTGTAATTTTGTCCACC
66 TGCTTGTAATTTTGTCCACC
** ** * *** * *
28067 TTTTCATTTTCCCTTTTTCCATTC-ATTTC-C-CT--TTTTCCATTCAAAATCGT-T---ATCTT
1 TTTTC-TTTTCCCTTTTTTGAAGCGA-TTCACGATAAAGGT-CAATCAAAGT-GTATAAAAT-TT
* * *
28123 CACA-A-GC---AAAATTTGTCTCA-A
61 CA-ATATGCTTGTAATTTTGTC-CACC
* *
28144 TTTTCGTTTCCCTTTTTTGAAGCGATTCACGATAAAGGTCAATCAATGTGTATAAAATTTCAATA
1 TTTTCTTTTCCCTTTTTTGAAGCGATTCACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATA
28209 TGCTTGTAATTTTGTCCACC
66 TGCTTGTAATTTTGTCCACC
28229 TTTTCCTTTTCCCTTTTT
1 TTTT-CTTTTCCCTTTTT
28247 CCATTCATTT
Statistics
Matches: 127, Mismatches: 30, Indels: 45
0.63 0.15 0.22
Matches are distributed among these distances:
76 16 0.13
77 15 0.12
78 5 0.04
79 8 0.06
80 6 0.05
81 10 0.08
82 6 0.05
83 9 0.07
84 5 0.04
85 19 0.15
86 28 0.22
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.45
Consensus pattern (85 bp):
TTTTCTTTTCCCTTTTTTGAAGCGATTCACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATA
TGCTTGTAATTTTGTCCACC
Found at i:28097 original size:18 final size:19
Alignment explanation
Indices: 28069--28109 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
28059 TGTCCACCTT
28069 TTCATTTTCCCTTTTTCCA
1 TTCATTTTCCCTTTTTCCA
28088 TTCA-TTTCCCTTTTTCCA
1 TTCATTTTCCCTTTTTCCA
28106 TTCA
1 TTCA
28110 AAATCGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (19 bp):
TTCATTTTCCCTTTTTCCA
Found at i:28211 original size:162 final size:162
Alignment explanation
Indices: 27944--28262 Score: 611
Period size: 162 Copynumber: 2.0 Consensus size: 162
27934 TATGGCCAAG
27944 TTCAAAATCGCTATCTTCACAAGCAAAATTTGTCTCAATTTTCGTTTCCCTTTTTTGAAGCGATT
1 TTCAAAATCGCTATCTTCACAAGCAAAATTTGTCTCAATTTTCGTTTCCCTTTTTTGAAGCGATT
28009 CACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATATGCTTGTAATTTTGTCCACCTTTTCAT
66 CACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATATGCTTGTAATTTTGTCCACCTTTTCAT
28074 TTTCCCTTTTTCCATTCATTTCCCTTTTTCCA
131 TTTCCCTTTTTCCATTCATTTCCCTTTTTCCA
*
28106 TTCAAAATCGTTATCTTCACAAGCAAAATTTGTCTCAATTTTCGTTTCCCTTTTTTGAAGCGATT
1 TTCAAAATCGCTATCTTCACAAGCAAAATTTGTCTCAATTTTCGTTTCCCTTTTTTGAAGCGATT
* *
28171 CACGATAAAGGTCAATCAATGTGTATAAAATTTCAATATGCTTGTAATTTTGTCCACCTTTTCCT
66 CACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATATGCTTGTAATTTTGTCCACCTTTTCAT
28236 TTTCCCTTTTTCCATTCATTTCCCTTT
131 TTTCCCTTTTTCCATTCATTTCCCTTT
28263 CACTTCGAGT
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 154 1.00
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.43
Consensus pattern (162 bp):
TTCAAAATCGCTATCTTCACAAGCAAAATTTGTCTCAATTTTCGTTTCCCTTTTTTGAAGCGATT
CACGATAAAGGTCAATCAAAGTGTATAAAATTTCAATATGCTTGTAATTTTGTCCACCTTTTCAT
TTTCCCTTTTTCCATTCATTTCCCTTTTTCCA
Found at i:28979 original size:29 final size:29
Alignment explanation
Indices: 28937--29022 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
28927 TCATCCTTAA
28937 TATGACAACTTCGGGTGTCAAAATGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
28966 TATGACAACTTCGGGTGTCAAAATGATAC
1 TATGACAACTTCGGGTGTCAAAATGATAC
*
28995 TATGACAACTTCGGGTGTCAAAGTGATA
1 TATGACAACTTCGGGTGTCAAAATGATA
29023 ATATATTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAATGATAC
Found at i:29161 original size:32 final size:33
Alignment explanation
Indices: 29096--29168 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
29086 TAATTTTTTA
* **
29096 ATGATAAAGAAAGATAGATGGAGTAGATTATGC
1 ATGATAAAGAAAGATAGATAGAACAGATTATGC
*
29129 ATGATAAAGAAAGGTAGA-AGAACAGATTATGC
1 ATGATAAAGAAAGATAGATAGAACAGATTATGC
*
29161 ATGTTAAA
1 ATGATAAA
29169 TAAACTTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 18 0.51
33 17 0.49
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.23
Consensus pattern (33 bp):
ATGATAAAGAAAGATAGATAGAACAGATTATGC
Found at i:31083 original size:27 final size:27
Alignment explanation
Indices: 31053--31123 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
31043 ATTAGGGTCG
31053 CCCAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
31080 CCCAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
*
31107 CCCAAGGGCATTTTGGT
1 CCCAGGGGCATTTTGGT
31124 AAATTGGTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTTGCA
Found at i:31589 original size:54 final size:54
Alignment explanation
Indices: 31530--31637 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
31520 TGGCCCAATT
*
31530 TCCTTAAAAAGTACACTATTGCATTTGTGTTTACAAAAATACCAATAATAAAAA
1 TCCTTAAAAAGTACACTATTGCATTTGTGTTTACAAAAACACCAATAATAAAAA
* *
31584 TCCTTAATAAGTACACTATTGCATTTGTGTTTACAAAAACACCAGTAATAAAAA
1 TCCTTAAAAAGTACACTATTGCATTTGTGTTTACAAAAACACCAATAATAAAAA
31638 GAGAAGAAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (54 bp):
TCCTTAAAAAGTACACTATTGCATTTGTGTTTACAAAAACACCAATAATAAAAA
Found at i:34339 original size:190 final size:188
Alignment explanation
Indices: 33962--34340 Score: 740
Period size: 190 Copynumber: 2.0 Consensus size: 188
33952 GAAGGGTGGA
33962 AACAAAGTAAAATTAACTAGAATAATACTAAAGAAAACTATCAAATTAAAAAGCATATTTCCTTT
1 AACAAAGTAAAATTAACTAGAATAATACTAAAGAAAACTATCAAATTAAAAAGCATATTTCCTTT
34027 CCATTGGTTGAAATCAATCAATAAAGATAGATCATCGACACAAAATATGAATTTGATATTAATAT
66 CCATTGGTTGAAATCAATCAATAAAGATAGATCATCGACACAAAATATGAATTTGATATTAATAT
34092 TGCCAAAATAAGCAAGCATCACATTTTACCCTAAATCAATCTATCCTAAGATTTAGAC
131 TGCCAAAATAAGCAAGCATCACATTTTACCCTAAATCAATCTATCCTAAGATTTAGAC
34150 AACAAAGTAAAATTAACTAGAATAATACTAAAGAAAACTATCAAATTAAAAAGCATATTTCCTTT
1 AACAAAGTAAAATTAACTAGAATAATACTAAAGAAAACTATCAAATTAAAAAGCATATTTCCTTT
34215 CCATTGGTTGAAATCAATCAATAAAGATATGGATCATCGACACAAAATATGAATTTGATATTAAT
66 CCATTGGTTGAAATCAATCAATAAAGATA--GATCATCGACACAAAATATGAATTTGATATTAAT
34280 ATTGCCAAAATAAGCAAGCATCACATTTTACCCTAAATCAATCTATCCTAAGATTTAGAC
129 ATTGCCAAAATAAGCAAGCATCACATTTTACCCTAAATCAATCTATCCTAAGATTTAGAC
34340 A
1 A
34341 TCAATTTTCA
Statistics
Matches: 189, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
188 94 0.50
190 95 0.50
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (188 bp):
AACAAAGTAAAATTAACTAGAATAATACTAAAGAAAACTATCAAATTAAAAAGCATATTTCCTTT
CCATTGGTTGAAATCAATCAATAAAGATAGATCATCGACACAAAATATGAATTTGATATTAATAT
TGCCAAAATAAGCAAGCATCACATTTTACCCTAAATCAATCTATCCTAAGATTTAGAC
Found at i:36198 original size:25 final size:25
Alignment explanation
Indices: 36132--36200 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
36122 AGATATATAA
*
36132 TATTTATTTATTT-T-TA-ACTCAT
1 TATTTATTTATTTATATATATTCAT
* * *
36154 TATTTA-TTATCTAAATTATATTTAT
1 TATTTATTTATTTATA-TATATTCAT
36179 TATTTATTTATTTATATATATT
1 TATTTATTTATTTATATATATT
36201 ATATATATCT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 5 0.14
22 6 0.17
24 2 0.06
25 16 0.44
26 7 0.19
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTTATTTATTTATATATATTCAT
Done.