Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007383.1 Corchorus capsularis cultivar CVL-1 contig07404, 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: 52803
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2748 original size:2 final size:2
Alignment explanation
Indices: 2741--2769 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2731 AAAGTTATTC
2741 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 T
2770 GTCTAGGCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6344 original size:14 final size:14
Alignment explanation
Indices: 6305--6355 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
6295 ATTTATATTT
*
6305 ATTAATTTTTTTA-
1 ATTATTTTTTTTAC
*
6318 ATTA-TTTTATTAC
1 ATTATTTTTTTTAC
6331 ATTATTTTTTTTAC
1 ATTATTTTTTTTAC
*
6345 TTTATATTTTT
1 ATTAT-TTTTT
6356 ATTTTTGGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 7 0.22
13 8 0.25
14 12 0.38
15 5 0.16
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTATTTTTTTTAC
Found at i:20355 original size:2 final size:2
Alignment explanation
Indices: 20350--20380 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20340 AATATATATA
20350 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
20381 AACAAATATA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:23062 original size:11 final size:11
Alignment explanation
Indices: 23019--23056 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23009 TTCCTATGTA
*
23019 AAATAAATTAT
1 AAATTAATTAT
23030 CAAA-TAATTAT
1 -AAATTAATTAT
23041 AAATTAATTAT
1 AAATTAATTAT
23052 AAATT
1 AAATT
23057 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:23583 original size:5 final size:5
Alignment explanation
Indices: 23573--23598 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
23563 ATTAACTAAT
23573 ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA A
23599 CCTACTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:23800 original size:11 final size:11
Alignment explanation
Indices: 23757--23794 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23747 TTCCTATATA
*
23757 AAATAAATTAT
1 AAATTAATTAT
23768 CAAA-TAATTAT
1 -AAATTAATTAT
23779 AAATTAATTAT
1 AAATTAATTAT
23790 AAATT
1 AAATT
23795 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:24145 original size:27 final size:27
Alignment explanation
Indices: 24107--24158 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
24097 TTTCACAACA
24107 AAATTTCATTTCTTAACTGAATTTTCT
1 AAATTTCATTTCTTAACTGAATTTTCT
*
24134 AAATTTCATTTCTTAACTGATTTTT
1 AAATTTCATTTCTTAACTGAATTTT
24159 TTTAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (27 bp):
AAATTTCATTTCTTAACTGAATTTTCT
Found at i:28009 original size:2 final size:2
Alignment explanation
Indices: 28002--28031 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27992 GTAGGAGGCT
28002 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
28032 CATAGGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30813 original size:27 final size:27
Alignment explanation
Indices: 30779--30835 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
30769 TTTGGTCATT
*
30779 TTTGCACATTCAGGGGCATTCTGGTTA
1 TTTGCACATTCAGGGGCATTCTGGTCA
* *
30806 TTTGCACATTCAGGGGTATTTTGGTCA
1 TTTGCACATTCAGGGGCATTCTGGTCA
30833 TTT
1 TTT
30836 TAAGTCTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.42
Consensus pattern (27 bp):
TTTGCACATTCAGGGGCATTCTGGTCA
Found at i:31402 original size:161 final size:162
Alignment explanation
Indices: 31226--31539 Score: 438
Period size: 161 Copynumber: 1.9 Consensus size: 162
31216 TCATTTGTCA
* *
31226 ATTGAGAAATGACCAAAAAGTTTAGTTATTTAATC-CCTTCAAGAATAAAAAATTAGGACATTTA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCGCC-TCAAGAATAAAAAATTAGGACATTTA
* * * * ** *
31290 AATAATCTGCCAAGTAGGTAAAGAC-AAAAAATGTTAGTTCTCTAGCT-CATCATCAA-TCCTTG
65 AATAATCTGCCAAGTAGGAAAAGACGAAAAAA-ATAAGTTCTCTAACTCCAAAAGCAAGT-CTTG
* *
31352 ATGGGGATCATTTATTAATTCCACTATTCAAGTCC
128 ATAGGGATCATTTAGTAATTCCACTATTCAAGTCC
* *
31387 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCGCCTCAAGAATCAAAAGTTAGGACATTTAA
1 ATTGAGAAATGACCAAAAAGATTACTTATTTAATCGCCTCAAGAATAAAAAATTAGGACATTTAA
*
31452 GTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGTCTTGATA
66 ATAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGTCTTGATA
*
31517 GGGATCTTTTAGTAATTCCACTA
131 GGGATCATTTAGTAATTCCACTA
31540 CTCTATTGAA
Statistics
Matches: 134, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
161 92 0.69
162 41 0.31
163 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (162 bp):
ATTGAGAAATGACCAAAAAGATTACTTATTTAATCGCCTCAAGAATAAAAAATTAGGACATTTAA
ATAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGTCTTGATA
GGGATCATTTAGTAATTCCACTATTCAAGTCC
Found at i:31654 original size:45 final size:45
Alignment explanation
Indices: 31604--31693 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
31594 AGATTACTTC
31604 TCCAGCTCATCAATAATCCGGGGTAGGGATCTTTTAGTAATTCCA
1 TCCAGCTCATCAATAATCCGGGGTAGGGATCTTTTAGTAATTCCA
* * * *
31649 TCCAGCTTATCATTAATTCGGGGTAGTGATCTTTTAGTAATTCCA
1 TCCAGCTCATCAATAATCCGGGGTAGGGATCTTTTAGTAATTCCA
31694 CTACTCTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (45 bp):
TCCAGCTCATCAATAATCCGGGGTAGGGATCTTTTAGTAATTCCA
Found at i:33590 original size:1 final size:1
Alignment explanation
Indices: 33586--33616 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
33576 CAGTCTCATT
33586 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33617 CGAAGAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:34567 original size:39 final size:38
Alignment explanation
Indices: 34488--34568 Score: 92
Period size: 40 Copynumber: 2.1 Consensus size: 38
34478 GATCTTTAGT
* **
34488 TAAAAGATGAAACTTTTAATTGATTTATATAATCTTATG
1 TAAAAGATGAAACTTTTAATTGACTTATATAA-CAAATG
*
34527 TAAAATGATGAAATTTTTAATTGACTTATAATAA-AAATG
1 TAAAA-GATGAAACTTTTAATTGACTTAT-ATAACAAATG
34566 TAA
1 TAA
34569 TCATTGTGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 11 0.31
40 21 0.58
41 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.41
Consensus pattern (38 bp):
TAAAAGATGAAACTTTTAATTGACTTATATAACAAATG
Found at i:34614 original size:30 final size:30
Alignment explanation
Indices: 34580--34738 Score: 88
Period size: 31 Copynumber: 5.6 Consensus size: 30
34570 CATTGTGTCG
34580 AAAGA-TGAAGTCTTTAAGTAATTTGTAAAC
1 AAAGATTGAA-TCTTTAAGTAATTTGTAAAC
* * * *
34610 AAAGATTGGATTTTTAAGTAATTTGTATAT
1 AAAGATTGAATCTTTAAGTAATTTGTAAAC
* * *
34640 AGAGATTAAATGTTTAAG-----TG-----
1 AAAGATTGAATCTTTAAGTAATTTGTAAAC
* *
34660 AAAGATTGAATCTTTTAAGTAATTTGTGAAT
1 AAAGATTGAATC-TTTAAGTAATTTGTAAAC
* * *
34691 AAAGATTGAATCTTTTAAATAATTTGTGAAT
1 AAAGATTGAATC-TTTAAGTAATTTGTAAAC
* *
34722 AATGATTGAATTTTTAA
1 AAAGATTGAATCTTTAA
34739 TTAAAAGATT
Statistics
Matches: 103, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
20 9 0.09
21 6 0.06
25 2 0.02
26 2 0.02
30 41 0.40
31 43 0.42
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41
Consensus pattern (30 bp):
AAAGATTGAATCTTTAAGTAATTTGTAAAC
Found at i:34695 original size:31 final size:31
Alignment explanation
Indices: 34660--34738 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
34650 TGTTTAAGTG
*
34660 AAAGATTGAATCTTTTAAGTAATTTGTGAAT
1 AAAGATTGAATCTTTTAAATAATTTGTGAAT
34691 AAAGATTGAATCTTTTAAATAATTTGTGAAT
1 AAAGATTGAATCTTTTAAATAATTTGTGAAT
*
34722 AATGATTGAAT-TTTTAA
1 AAAGATTGAATCTTTTAA
34739 TTAAAAGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 6 0.13
31 40 0.87
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.43
Consensus pattern (31 bp):
AAAGATTGAATCTTTTAAATAATTTGTGAAT
Found at i:34696 original size:81 final size:81
Alignment explanation
Indices: 34579--34787 Score: 232
Period size: 81 Copynumber: 2.6 Consensus size: 81
34569 TCATTGTGTC
* *
34579 GAAAGA-TGAAGTC-TTTAAGTAATTTGTAAACAAAGATTGGATTTTTAAGTAATTTGT-ATATA
1 GAAAGATTGAA-TCTTTTAAGTAATTTGTAAATAAAGATTGGATTTTTAAATAATTTGTGA-ATA
34641 GA-GATTAAATGTTTAAGT
64 -ATGATTAAATGTTTAAGT
* *
34659 GAAAGATTGAATCTTTTAAGTAATTTGTGAATAAAGATTGAATCTTTTAAATAATTTGTGAATAA
1 GAAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATTGGAT-TTTTAAATAATTTGTGAATAA
* * *
34724 TGATTGAATTTTTAATT
65 TGATTAAATGTTTAAGT
* * *
34741 AAAAGATTGAA-CTTTTATGTAATTTTTGTAAATGAAGATT-GATTTTT
1 GAAAGATTGAATCTTTTAAGTAA--TTTGTAAATAAAGATTGGATTTTT
34788 TTTTGTAAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
80 8 0.07
81 45 0.41
82 42 0.38
83 15 0.14
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (81 bp):
GAAAGATTGAATCTTTTAAGTAATTTGTAAATAAAGATTGGATTTTTAAATAATTTGTGAATAAT
GATTAAATGTTTAAGT
Found at i:34786 original size:51 final size:51
Alignment explanation
Indices: 34691--34788 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 51
34681 ATTTGTGAAT
*
34691 AAAGATTGAATCTTTTAAATAATTTGTGAATAATGATTGAATTTTTAATTA
1 AAAGATTGAATCTTTTAAATAATTTGTAAATAATGATTGAATTTTTAATTA
** *
34742 AAAGATTGAA-CTTTTATGTAATTTTTGTAAATGAA-GATTGATTTTTT
1 AAAGATTGAATCTTTTAAATAA--TTTGTAAAT-AATGATTGAATTTTT
34789 TTTGTAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
50 9 0.22
51 10 0.25
52 19 0.47
53 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (51 bp):
AAAGATTGAATCTTTTAAATAATTTGTAAATAATGATTGAATTTTTAATTA
Found at i:34913 original size:50 final size:49
Alignment explanation
Indices: 34819--34917 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 49
34809 TGACTAATGA
* * *
34819 AAAATTAAAATGGGATCTTTGAATAAAAAGATTAATCTTTTGATTGAAAT
1 AAAATAAAAATGAGATCTTTGAATAAAAAGATTAATCTTGTGATT-AAAT
* *
34869 AAAATAAAAATGAGATCTTTGAATTAAATGATTGAA-CTTGTGATTAAAT
1 AAAATAAAAATGAGATCTTTGAATAAAAAGATT-AATCTTGTGATTAAAT
34918 GAGATGGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.09
50 37 0.86
51 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (49 bp):
AAAATAAAAATGAGATCTTTGAATAAAAAGATTAATCTTGTGATTAAAT
Found at i:35013 original size:49 final size:51
Alignment explanation
Indices: 34919--35026 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 51
34909 TGATTAAATG
* * * * *
34919 AGATGGAATCTTTAAGCTAAGAGGTGAAATTCTTGATTAATTGGTGA-TAA
1 AGATGAAACCTTTAAGCTAAAAGATGAAACTCTTGATTAATTGGTGATTAA
34969 AGATGAAACCTTTAAGCTAAAAGATG-AACTCTTGATTAATTGGTGATTAA
1 AGATGAAACCTTTAAGCTAAAAGATGAAACTCTTGATTAATTGGTGATTAA
*
35019 AAATGAAA
1 AGATGAAA
35027 TTTGTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 19 0.37
50 32 0.63
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (51 bp):
AGATGAAACCTTTAAGCTAAAAGATGAAACTCTTGATTAATTGGTGATTAA
Found at i:35676 original size:48 final size:48
Alignment explanation
Indices: 35620--35745 Score: 141
Period size: 48 Copynumber: 2.6 Consensus size: 48
35610 AATTTTCGGT
35620 TTTG-CCTTTCCCAGTCGGAAGGTGTTGTTTAGTTG-TCAAATTCCCAC
1 TTTGCCCTTTCCCA-TCGGAAGGTGTTGTTTAGTTGCTCAAATTCCCAC
* * * * * * * *
35667 TTTGCCCTTTCCTACCGGAAGGTGTTGTCTATTTGCTTAGATTCCTAG
1 TTTGCCCTTTCCCATCGGAAGGTGTTGTTTAGTTGCTCAAATTCCCAC
35715 TTTGCCC-TTCCCTATCGGAAGGTGTTGTTTA
1 TTTGCCCTTTCCC-ATCGGAAGGTGTTGTTTA
35746 CATTCCTATT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
47 26 0.40
48 39 0.60
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (48 bp):
TTTGCCCTTTCCCATCGGAAGGTGTTGTTTAGTTGCTCAAATTCCCAC
Found at i:35687 original size:47 final size:48
Alignment explanation
Indices: 35635--35745 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
35625 CTTTCCCAGT
*
35635 CGGAAGGTGTTGTTTAGTTG-TCAAATTCCCACTTTGCCCTTTCCTAC
1 CGGAAGGTGTTGTTTAGTTGCTCAAATTCCCACTTTGCCCTTCCCTAC
* * * * * * *
35682 CGGAAGGTGTTGTCTATTTGCTTAGATTCCTAGTTTGCCCTTCCCTAT
1 CGGAAGGTGTTGTTTAGTTGCTCAAATTCCCACTTTGCCCTTCCCTAC
35730 CGGAAGGTGTTGTTTA
1 CGGAAGGTGTTGTTTA
35746 CATTCCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 18 0.33
48 36 0.67
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.40
Consensus pattern (48 bp):
CGGAAGGTGTTGTTTAGTTGCTCAAATTCCCACTTTGCCCTTCCCTAC
Found at i:35766 original size:40 final size:40
Alignment explanation
Indices: 35707--36168 Score: 319
Period size: 40 Copynumber: 11.0 Consensus size: 40
35697 ATTTGCTTAG
*
35707 ATTCCTAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTAC
1 ATTCCTAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAC
* * **
35747 ATTCCTATTTTGCCATTCCCCGCCGGAAGGTGTTGTTTAAGTC
1 ATTCCTAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTT-A--C
* *
35790 TATATTTTCC-AGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTAC
1 ---A--TTCCTAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAC
*
35834 ATTCC-AGTTTGCCCTT-CCTCGCCGGAAGGTGTTGTTTAAGTC
1 ATTCCTAGTTTGCCCTTCCCT-ACCGGAAGGTGTTGTTT-A--C
* ** * * ** *
35876 TATATTTCCCAGTACGTCCTTCCCCACTAGAAGTTGTTGTTTAC
1 ---A-TTCCTAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAC
* * * *
35920 ATTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGT
1 A-TTCCTAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTA-C
*
35962 TTTCCTAGTTTGCCCTT-CCTCACCGGAAGGTGTTGTCTAAGTCTAC
1 ATTCCTAGTTTGCCCTTCCCT-ACCGGAAGGTGTTG--T---T-TAC
* * *
36008 ATTTCCTAGTTTGCCCGTTCCC-ATCAGAAGGTGTTGTTTAT
1 A-TTCCTAGTTTGCCC-TTCCCTACCGGAAGGTGTTGTTTAC
* *
36049 ATTCCTAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTAT
1 ATTCCTAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAC
* * *
36089 ATTCCT-GTTTTGCCCTTCCCCACCGAAAGGTGTTGTCTAC
1 ATTCCTAG-TTTGCCCTTCCCTACCGGAAGGTGTTGTTTAC
* *
36129 ATT-CTTGTCTTGCCCTT-CCTCACCGGAAGGTGTTCTTTAC
1 ATTCCTAGT-TTGCCCTTCCCT-ACCGGAAGGTGTTGTTTAC
36169 TTTTCTTGTT
Statistics
Matches: 341, Mismatches: 47, Indels: 68
0.75 0.10 0.15
Matches are distributed among these distances:
38 2 0.01
39 41 0.12
40 129 0.38
41 66 0.19
42 2 0.01
43 2 0.01
44 2 0.01
45 2 0.01
46 8 0.02
47 77 0.23
48 8 0.02
49 2 0.01
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCCTAGTTTGCCCTTCCCTACCGGAAGGTGTTGTTTAC
Found at i:35778 original size:88 final size:85
Alignment explanation
Indices: 35667--36124 Score: 368
Period size: 88 Copynumber: 5.3 Consensus size: 85
35657 AAATTCCCAC
* * ** *
35667 TTTGCCCTTTCCTACCGGAAGGTGTTGTCTATTTGCTTAGATTCCTAGTTTGCCCTTCCCTATCG
1 TTTGCCCTTCCCCACCGGAAGGTGTTGT-TAAGT-CTTA-ATTCCTAGTTTGCCCTTCCCTACCG
*
35732 GAAGGTGTTGTTTACATTCCTAT
63 GAAGGTGTTGTTTACATTCCTAG
* * * *
35755 TTTGCCATTCCCCGCCGGAAGGTGTTGTTTAAGTCTATATTTTCC-AGTTTGCCCTTCCCCACCG
1 TTTGCCCTTCCCCACCGGAAGGTGTTG-TTAAGTCT-TA-ATTCCTAGTTTGCCCTTCCCTACCG
*
35819 GAAAGTGTTGTTTACATTCC-AG
63 GAAGGTGTTGTTTACATTCCTAG
* * * * ** * * **
35841 TTTGCCCTTCCTCGCCGGAAGGTGTTGTTTAAGTCTATATTTCCCAGTACGTCCTTCCCCACTAG
1 TTTGCCCTTCCCCACCGGAAGGTGTTG-TTAAGTCT-TAATTCCTAGTTTGCCCTTCCCTACCGG
* *
35906 AAGTTGTTGTTTACATTTCCCAG
64 AAGGTGTTGTTTACA-TTCCTAG
* *
35929 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG--TT--TTCCTAGTTTGCCCTT-CCTCACCGGA
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTAAGTCTTAATTCCTAGTTTGCCCTTCCCT-ACCGGA
35989 AGGTGTTGTCTAAGTCTACATTTCCTAG
65 AGGTGTTG--T---T-TACA-TTCCTAG
* * * *
36017 TTTGCCCGTT-CCCATCAGAAGGTGTTGTT---T-AT-ATTCCTAGTTTGCCCTTCCCTATCGGA
1 TTTGCCC-TTCCCCACCGGAAGGTGTTGTTAAGTCTTAATTCCTAGTTTGCCCTTCCCTACCGGA
*
36076 AGGTGTTGTTTATATTCCT-G
65 AGGTGTTGTTTACATTCCTAG
*
36096 TTTTGCCCTTCCCCACCGAAAGGTGTTGT
1 -TTTGCCCTTCCCCACCGGAAGGTGTTGT
36125 CTACATTCTT
Statistics
Matches: 311, Mismatches: 41, Indels: 44
0.79 0.10 0.11
Matches are distributed among these distances:
79 3 0.01
80 27 0.09
81 5 0.02
82 24 0.08
84 2 0.01
85 7 0.02
86 67 0.22
87 76 0.24
88 97 0.31
89 3 0.01
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.39
Consensus pattern (85 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGTTAAGTCTTAATTCCTAGTTTGCCCTTCCCTACCGGAA
GGTGTTGTTTACATTCCTAG
Found at i:35881 original size:86 final size:87
Alignment explanation
Indices: 35708--36124 Score: 341
Period size: 87 Copynumber: 4.9 Consensus size: 87
35698 TTTGCTTAGA
* * * * *
35708 TTCCTAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTACATTCCTATTTTGCCATTCCCCGCCGG
1 TTCCTAGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTACATTCC-AGTTTGCCCTTCCCCGCCGG
35773 AAGGTGTTGTTTAAGTCTATATT
65 AAGGTGTTGTTTAAGTCTATATT
*
35796 TTCC-AGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTACATTCCAGTTTGCCCTTCCTCGCCGGA
1 TTCCTAGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTACATTCCAGTTTGCCCTTCCCCGCCGGA
35860 AGGTGTTGTTTAAGTCTATA-T
66 AGGTGTTGTTTAAGTCTATATT
* ** * ** **
35881 TTCCCAGTACGTCCTTCCCCACTAG-AAGTTGTTGTTTACATTTCCCAGTTTGCCCTTCCCCATC
1 TTCCTAGTTTGCCCTTCCCCACCGGAAAG-TGTTGTTTACA-TT-CCAGTTTGCCCTTCCCCGCC
35945 GGAAGGTGTTGTTT-AG------TT
63 GGAAGGTGTTGTTTAAGTCTATATT
* *
35963 TTCCTAGTTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAGTCTACATTTCCTAGTTTGCCCGTT-
1 TTCCTAGTTTGCCCTTCCCCACCGGAAAGTGTTG--T---T-TACA-TTCC-AGTTTGCCC-TTC
** *
36027 CCCATCAGAAGGTGTTG--T---T-TATA--
57 CCCGCCGGAAGGTGTTGTTTAAGTCTATATT
* * * * * * *
36050 TTCCTAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTATATTCCTGTTTTGCCCTTCCCCACCGA
1 TTCCTAGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTACATTCCAG-TTTGCCCTTCCCCGCCGG
36115 AAGGTGTTGT
65 AAGGTGTTGT
36125 CTACATTCTT
Statistics
Matches: 276, Mismatches: 31, Indels: 51
0.77 0.09 0.14
Matches are distributed among these distances:
79 3 0.01
80 25 0.09
81 3 0.01
82 25 0.09
83 2 0.01
84 1 0.00
85 9 0.03
86 65 0.24
87 74 0.27
88 67 0.24
89 2 0.01
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (87 bp):
TTCCTAGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTACATTCCAGTTTGCCCTTCCCCGCCGGA
AGGTGTTGTTTAAGTCTATATT
Found at i:36126 original size:127 final size:126
Alignment explanation
Indices: 35795--36127 Score: 429
Period size: 127 Copynumber: 2.6 Consensus size: 126
35785 AAGTCTATAT
* * * * *
35795 TTTCCAGTTTGCCCTTCCCCACCGGAAAGTGTTGTTTACATTCCAGTTTGCCCTTCCTCGCCGGA
1 TTTCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTATATTCCTGTTTGCCCTTCCTCACCGGA
* * * *
35860 AGGTGTTGTTTAAGTCTATATTTCCCAGTACGTCCTTCCCCACTAGAAGTTGTTGTTTACA
66 AGGTGTTGTCTAAGTCTACATTTCCCAGTACGCCCTTCCCCACTAGAAGGTGTTGTTTACA
*
35921 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTTCCTAGTTTGCCCTTCCTCACC
1 TTT-CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-TATTCCT-GTTTGCCCTTCCTCACC
* ** *
35986 GGAAGGTGTTGTCTAAGTCTACATTTCCTAGTTTGCCCGTT-CCCA-TCAGAAGGTGTTGTTTAT
63 GGAAGGTGTTGTCTAAGTCTACATTTCCCAGTACGCCC-TTCCCCACT-AGAAGGTGTTGTTTAC
36049 A
126 A
* *
36050 -TTCCTAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTATATTCCTGTTTTGCCCTTCCCCACCG
1 TTTCC-AGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTATATTCCTG-TTTGCCCTTCCTCACCG
*
36114 AAAGGTGTTGTCTA
64 GAAGGTGTTGTCTA
36128 CATTCTTGTC
Statistics
Matches: 182, Mismatches: 18, Indels: 13
0.85 0.08 0.06
Matches are distributed among these distances:
126 4 0.02
127 70 0.38
128 39 0.21
129 67 0.37
130 2 0.01
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (126 bp):
TTTCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTATATTCCTGTTTGCCCTTCCTCACCGGA
AGGTGTTGTCTAAGTCTACATTTCCCAGTACGCCCTTCCCCACTAGAAGGTGTTGTTTACA
Found at i:40833 original size:44 final size:44
Alignment explanation
Indices: 40770--40858 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
40760 AAGCAGTTTT
*
40770 CTAAATCGAATAAAACATATAGCGGTGTTTGTTTCCAAAAACGC
1 CTAAATCGAATAAAACATATAGCAGTGTTTGTTTCCAAAAACGC
40814 CTAAATCGAATAAAACATATAGCAGTGTTTGTTTCCAAAAACGC
1 CTAAATCGAATAAAACATATAGCAGTGTTTGTTTCCAAAAACGC
40858 C
1 C
40859 ACAAAATGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (44 bp):
CTAAATCGAATAAAACATATAGCAGTGTTTGTTTCCAAAAACGC
Found at i:51148 original size:22 final size:21
Alignment explanation
Indices: 51120--51174 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
51110 CGAAGTTCGT
51120 ATTTGAAGACTTATTGAAGATA
1 ATTTGAAGA-TTATTGAAGATA
*
51142 ATTTGAAGA-T-TTGAAGATC
1 ATTTGAAGATTATTGAAGATA
51161 A-TTGAAGAATTATT
1 ATTTGAAG-ATTATT
51175 TCAAGAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 2 0.07
21 2 0.07
22 9 0.31
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (21 bp):
ATTTGAAGATTATTGAAGATA
Found at i:52466 original size:16 final size:16
Alignment explanation
Indices: 52445--52476 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52435 GAACCTCGGG
*
52445 TTTTCGGGTTTGGGTC
1 TTTTCGGGTTCGGGTC
52461 TTTTCGGGTTCGGGTC
1 TTTTCGGGTTCGGGTC
52477 GTTAATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.38, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTC
Done.