Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013271.1 Corchorus capsularis cultivar CVL-1 contig13292, 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: 34727
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Found at i:33 original size:16 final size:15
Alignment explanation
Indices: 9--47 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1 TTTTTTTA
*
9 TTCTTTAAAGGCATTT
1 TTCTTTAAAAG-ATTT
*
25 TTTTTTAAAAGATTT
1 TTCTTTAAAAGATTT
40 TTCTTTAA
1 TTCTTTAA
48 TTTCCTTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (15 bp):
TTCTTTAAAAGATTT
Found at i:4377 original size:22 final size:22
Alignment explanation
Indices: 4349--4552 Score: 98
Period size: 22 Copynumber: 9.3 Consensus size: 22
4339 TATCTCCATG
4349 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
4371 TGGTTATTATAATTT--TATGA
1 TGGTTATCAAAATTTCATAAGA
* *
4391 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
4412 TGGTTACCAAAA-TTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* *
4434 -AGTTATCAAAATTTCATATAGTC
1 TGGTTATCAAAATTTCATA-AG-A
*
4457 TGGTTACCAAAATTTCAT-AGTA
1 TGGTTATCAAAATTTCATAAG-A
* * *
4479 TGCTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * * * *
4501 TCAGATTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
4525 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
4547 TGGTTA
1 TGGTTA
4553 ATTATCACAT
Statistics
Matches: 140, Mismatches: 30, Indels: 24
0.72 0.15 0.12
Matches are distributed among these distances:
19 11 0.08
20 5 0.04
21 14 0.10
22 76 0.54
23 2 0.01
24 32 0.23
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:4492 original size:46 final size:45
Alignment explanation
Indices: 4406--4497 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 45
4396 TCAAAATTCC
* *
4406 ATAGTGTGGTTACCAAAATTCATATGGAAGTTATCAAAATTTCAT
1 ATAGTCTGGTTACCAAAATTCATATGGAAGTTACCAAAATTTCAT
* *
4451 ATAGTCTGGTTACCAAAATTTCATA-GTATGCTTACCAAAATTTCAT
1 ATAGTCTGGTTACCAAAA-TTCATATGGAAG-TTACCAAAATTTCAT
4497 A
1 A
4498 GGATCAGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
45 20 0.49
46 21 0.51
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (45 bp):
ATAGTCTGGTTACCAAAATTCATATGGAAGTTACCAAAATTTCAT
Found at i:4623 original size:22 final size:21
Alignment explanation
Indices: 4587--4726 Score: 104
Period size: 22 Copynumber: 6.4 Consensus size: 21
4577 ATCAAAGAGA
* *
4587 TTATCAAAATATCATAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
*
4609 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
* *
4631 TTAAAAAAATTTCATTA-AGAGG
1 TT-ATAAAATTTCA-TAGTGAGG
* * *
4653 TTACTAATATTTCATGGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
* *
4675 TTATCAAAATTTTATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
4697 TTATCAAAATTTCATA-TGAAGG
1 TTAT-AAAATTTCATAGTG-AGG
4719 TTATAAAA
1 TTATAAAA
4727 CTATCAATTT
Statistics
Matches: 94, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
21 11 0.12
22 78 0.83
23 5 0.05
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:4801 original size:22 final size:22
Alignment explanation
Indices: 4732--5002 Score: 125
Period size: 22 Copynumber: 12.4 Consensus size: 22
4722 TAAAACTATC
* *
4732 AATTTCAT-AAG-GAGTACCAA
1 AATTTCATAAAGTGATTATCAA
*
4752 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATA-AAGTGATTATCAA
* *
4772 AATCTCATAAAGTGATTATCGA
1 AATTTCATAAAGTGATTATCAA
*
4794 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATAAAG-T--GATTATCAA
**
4819 AATTTACAGGAA--GATTATCAA
1 AATTT-CATAAAGTGATTATCAA
**
4840 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAAAG-TGATTATCAA
*
4862 AATTTCAAAGCAAG-G-TTATCAA
1 AATTTCATA--AAGTGATTATCAA
* * *
4884 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGTGATTATCAA
* * * * *
4906 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGTGATTATCAA
* *
4928 AAGTTT-ATAAAGAGGTTATCAA
1 AA-TTTCATAAAGTGATTATCAA
* * *
4950 AATTTCATAAAGAGGTTATCGA
1 AATTTCATAAAGTGATTATCAA
* **
4972 ATTTTCA-AAATGTGATTAAAAA
1 AATTTCATAAA-GTGATTATCAA
4994 AATTTCATA
1 AATTTCATA
5003 GTGGTATTTT
Statistics
Matches: 189, Mismatches: 42, Indels: 37
0.71 0.16 0.14
Matches are distributed among these distances:
19 3 0.02
20 20 0.11
21 29 0.15
22 114 0.60
23 6 0.03
24 1 0.01
25 13 0.07
26 3 0.02
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (22 bp):
AATTTCATAAAGTGATTATCAA
Found at i:4929 original size:66 final size:66
Alignment explanation
Indices: 4831--4959 Score: 154
Period size: 66 Copynumber: 2.0 Consensus size: 66
4821 TTTACAGGAA
* ** * *
4831 GATTATCAAAATTTCATAGTGTTGTTATCAAAA-TTT-CAAAGCAAGGTTATCAAAATTACATAA
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAAGTTTACAAAG--AGGTTATCAAAATTACATAA
4894 TGT
64 TGT
* * *
4897 GATTATCAGAATTTCATAGAGGGGTCAACAAAAGTTTATAAAGAGGTTATCAAAATTTCATAA
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAAGTTTACAAAGAGGTTATCAAAATTACATAA
4960 AGAGGTTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
66 46 0.87
67 3 0.06
68 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAAGTTTACAAAGAGGTTATCAAAATTACATAATG
T
Found at i:5131 original size:22 final size:22
Alignment explanation
Indices: 5103--5644 Score: 99
Period size: 22 Copynumber: 24.7 Consensus size: 22
5093 TTAGGGAGGA
*
5103 TATCAAAATTTTATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
5125 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
5147 TTTCAAAATTTCATAAGAGGGG
1 TATCAAAATTTCATATGAAGGT
***
5169 TATCAAAATTTCATA-GTTTGT
1 TATCAAAATTTCATATGAAGGT
* * * *
5190 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
* *
5213 TAACAAAATTTCATAAT-TAGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
5235 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
5257 TATC-AAATTGT-AGTTATTAA-G-
1 TATCAAAATT-TCA--TATGAAGGT
* * *
5278 -AT--TAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* *
5297 TATCAAAATTTTATA-AAGAGGTT
1 TATCAAAATTTCATATGA-AGG-T
* *
5320 TATCAAAATTTGAT-TGGAAGATT
1 TATCAAAATTTCATAT-GAAG-GT
*
5343 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
5365 TATCACAATTTCAATAGTG-TGAT
1 TATCAAAATTTC-ATA-TGAAGGT
** * *
5388 TATCAAAATTTCAGGGTG-TGAT
1 TATCAAAATTTCA-TATGAAGGT
*
5410 TA-CTAACAA-TTCATATGTAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
5432 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
5454 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
5476 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
5499 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
5521 GT-TTAAAATTCCTTAGGGAA-GT
1 -TATCAAAATTTCATA-TGAAGGT
* *
5543 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** **
5565 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCATATGAAGGT
* * * ***
5587 TCTCGAAATTCCATA-GTATCAT
1 TATCAAAATTTCATATG-AAGGT
* *
5609 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
5631 TATC-AAATTTCATA
1 TATCAAAATTTCATA
5645 ATGGGATTAT
Statistics
Matches: 370, Mismatches: 106, Indels: 89
0.65 0.19 0.16
Matches are distributed among these distances:
17 4 0.01
18 2 0.01
19 5 0.01
20 10 0.03
21 33 0.09
22 215 0.58
23 95 0.26
24 5 0.01
25 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:5220 original size:44 final size:43
Alignment explanation
Indices: 5104--5263 Score: 137
Period size: 44 Copynumber: 3.6 Consensus size: 43
5094 TAGGGAGGAT
* * * *
5104 ATCAAAATTTTATATGAAGGTTATCAAAATTTCATAGTTTAGTT
1 ATCAAAATTTCATAGGGA-GTTATCAAAATTTCATAGTTTAGTG
* *
5148 TTCAAAATTTCATAAGAGG-GGTATCAAAATTTCATAGTTT-GTAG
1 ATCAAAATTTCAT-AG-GGAGTTATCAAAATTTCATAGTTTAGT-G
* * *
5192 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA-ATTAGGTT
1 ATCAAAATTTCATAGGGAG-TTATCAAAATTTCATAGTTTA-GTG
**
5236 ATCAAAAAATCATAGGGAGGTTATCAAA
1 ATCAAAATTTCATAGGGA-GTTATCAAA
5264 TTGTAGTTAT
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 7 0.07
44 80 0.85
45 4 0.04
46 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (43 bp):
ATCAAAATTTCATAGGGAGTTATCAAAATTTCATAGTTTAGTG
Found at i:5390 original size:23 final size:23
Alignment explanation
Indices: 5342--5400 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
5332 ATTGGAAGAT
*
5342 TTATCAAAATTTC-ATAGCGAGG
1 TTATCAAAATTTCAATAGCGAGA
* * *
5364 TTATCACAATTTCAATAGTGTGA
1 TTATCAAAATTTCAATAGCGAGA
5387 TTATCAAAATTTCA
1 TTATCAAAATTTCA
5401 GGGTGTGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCAATAGCGAGA
Found at i:7119 original size:14 final size:15
Alignment explanation
Indices: 7071--7124 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 15
7061 ACTGACTTAC
7071 TTAA-TTACCCTGAA
1 TTAAGTTACCCTGAA
* *
7085 TTAAGTTACTGACTTAA
1 TTAAGTTAC--CCTGAA
7102 TTAA-TTACCCTGAA
1 TTAAGTTACCCTGAA
7116 TTAAGTTAC
1 TTAAGTTAC
7125 TCATTGAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 12 0.38
15 8 0.25
16 4 0.12
17 8 0.25
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (15 bp):
TTAAGTTACCCTGAA
Found at i:7462 original size:35 final size:34
Alignment explanation
Indices: 6758--7462 Score: 744
Period size: 35 Copynumber: 20.7 Consensus size: 34
6748 TTCTTACTAA
* * *
6758 ACTTAATTACCCTGAATTAAGTCGATCAATGACTT
1 ACTTAATTACCCTGAATTAAGT-TATTACTGACTT
* *
6793 ACTTATTTACCCTGAATTAAGTTACTTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
*
6828 ACTTAATTACCCTGAATTAAGTTACTAACTGACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
* *
6863 ACTTAATTACCCTGAATTAAGCTATT--T-ACTG
1 ACTTAATTACCCTGAATTAAGTTATTACTGACTT
* * *
6894 ACTTAATTATCCTGAATTAAGTTGATTACTAAATT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTT
* * *
6929 ACTTAATTACCCTGAATTAAAGTAATAACTGAATT
1 ACTTAATTACCCTGAATT-AAGTTATTACTGACTT
* *
6964 ACTTAATCACCCTGAATTAAGTTAATTACTGACTG
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTT
* *
6999 ACTTAATTACCCTGAATTAAGTTGCTAACTGACTT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTT
*
7034 ACTTAATTACCCTGAATTAAGTTACTAACTGACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
7069 ACTTAATTACCCTGAATTAAG---TTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTATTACTGACTT
* * *
7100 AATTAATTACCCTGAATTAAGTTACTCATTGAAC-T
1 ACTTAATTACCCTGAATTAAGTTA-TTACTG-ACTT
*
7135 ACTTAATTACCCTGAATTAAGGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAA-GTT-ATTACTGACTT
* *
7171 ACCTAATTACCCTGAACTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTT
* * *
7206 GCTTAATCACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACTT
*
7241 ACTTAATTACCCTGAATTAAG---TTACTGCCTT
1 ACTTAATTACCCTGAATTAAGTTATTACTGACTT
* * * *
7272 ACTTAATTTCCCTGAACTAAGTTACTAACAGACTCT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACT-T
*
7308 ACTTAATTACCCTGAATTAAGCTACTTACT-A---
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
* *
7339 ACTTAATTACCCTGAATTAAGTTACCTA-TTACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
* *
7373 ACTTAACTACCCTGAATTAAG---TTGCTGACTT
1 ACTTAATTACCCTGAATTAAGTTATTACTGACTT
* *
7404 ACTTAATTACCCTGAATTCAGTTATTTACTAACTT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACTT
*
7439 ACTTAATTGCCCTGAATTAAGTTA
1 ACTTAATTACCCTGAATTAAGTTA
7463 CTTATTACTG
Statistics
Matches: 569, Mismatches: 71, Indels: 60
0.81 0.10 0.09
Matches are distributed among these distances:
30 2 0.00
31 131 0.23
32 4 0.01
34 27 0.05
35 347 0.61
36 57 0.10
37 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (34 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACTT
Found at i:10270 original size:3 final size:3
Alignment explanation
Indices: 10262--10302 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
10252 GCAAAAAGCG
* *
10262 AAT AAT AAT TAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10303 AAATTAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12070 original size:11 final size:11
Alignment explanation
Indices: 12054--12096 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
12044 TATACTATAT
12054 CTAATTAATAG
1 CTAATTAATAG
*
12065 CTAATTAATAT
1 CTAATTAATAG
12076 CTAATTAATAG
1 CTAATTAATAG
*
12087 TTAATTAATA
1 CTAATTAATA
12097 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:12075 original size:22 final size:22
Alignment explanation
Indices: 12050--12096 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
12040 CCATTATACT
12050 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
12072 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
12094 ATA
1 ATA
12097 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:12720 original size:30 final size:29
Alignment explanation
Indices: 12653--12724 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
12643 ACAATGAACC
* ****
12653 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCATGAACTATTAAAAAA
*
12682 GCCAAATAAGCCCATGAACTATTAAAAAAA
1 GTCAAATAAGCCCATGAACTATT-AAAAAA
12712 GTCAAATAAGCCC
1 GTCAAATAAGCCC
12725 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCATGAACTATTAAAAAA
Found at i:13645 original size:3 final size:3
Alignment explanation
Indices: 13637--13661 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13627 TACCCATCTC
13637 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
13662 CTCCCTCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:16974 original size:49 final size:49
Alignment explanation
Indices: 16913--17349 Score: 356
Period size: 49 Copynumber: 8.6 Consensus size: 49
16903 CTTGTGCAAT
* * * * * *
16913 GAAGGGCATTTTAAGAAAAAGCGAGTAAATATTAACGCTTTCCGTCCGG
1 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAATGCCTTCCGTCCGG
* *
16962 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAAAATAGTGCCTTCCGTCCGG
1 GAAGGGCGTTTTAGGAAAAAGCAAGT-AAAAATTAATGCCTTCCGTCCGG
* *
17012 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGA
1 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAATGCCTTCCGTCCGG
*
17061 GAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATTAAATAGCGCCTTCCGTCCGG
1 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATT-AAT---GCCTTCCGTCCGG
* * * * * * *
17114 GAATGGCATTTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGG
1 GAAGGGC-GTTTTAGGAAAAAGCAAGTAAAAATTAATGCCTTCCGTCCGG
* * * *
17164 AAAGGGCGTTTTGGGAAAAAACGAGTAAAAATTAAATAGCGCCTTCCGTCCGG
1 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATT-AAT---GCCTTCCGTCCGG
* * * * * * * * *
17217 AAAGTGCATTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATTCGG
1 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAATGCCTTCCGTCCGG
*** * * *
17266 GAATTACGTTTTGGGGAAAAA-CAAGTAAAAAGTAAATAGCGCCTTCCGCCCGG
1 GAAGGGCGTTTT-AGGAAAAAGCAAGTAAAAA-TTAAT---GCCTTCCGTCCGG
* * *
17319 GAAGGGCATTTT-GGGAAATGACAAGTAAAAA
1 GAAGGGCGTTTTAGGAAAAAG-CAAGTAAAAA
17350 CTGAAAAATG
Statistics
Matches: 317, Mismatches: 54, Indels: 30
0.79 0.13 0.07
Matches are distributed among these distances:
49 125 0.39
50 75 0.24
51 5 0.02
52 2 0.01
53 87 0.27
54 23 0.07
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (49 bp):
GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAATGCCTTCCGTCCGG
Found at i:17257 original size:152 final size:150
Alignment explanation
Indices: 16913--17349 Score: 402
Period size: 152 Copynumber: 2.9 Consensus size: 150
16903 CTTGTGCAAT
** * * * *
16913 GAAGGGCATTTTAAGAAAAAGCGAGTAAATATTA-A-CGCTTTCCGTCCGGGAAGGGCGTTTTAG
1 GAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTATAGCGCCTTCCGTCCGGGAATGGCGTTTTAG
* * *
16976 GAAAAAGCAAGTAAAAAAATAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAA
66 GAAAAAGCAAGTAAAAAAATAGTGCCTTCCATCCGGAAAGGGCGTTTTAGGAAAAAACAAGTAAA
*
17041 AATTAGTGCCTTCCGTCCGA
131 AATTAGCGCCTTCCGTCCGA
* *
17061 GAAGGGCGTTTTGGGAAAAAGCAAGTAAAAATTAAATAGCGCCTTCCGTCCGGGAATGGCATTTT
1 GAAGGGCATTTTGGGAAAAAGCAAGTAAAAATT--ATAGCGCCTTCCGTCCGGGAATGGC-GTTT
* * * * * *
17126 TGGGAAATAGCAAGT-AAAGATTAGTGCCTTCCATCCGGAAAGGGCGTTTTGGGAAAAAACGAGT
63 TAGGAAAAAGCAAGTAAAAAAATAGTGCCTTCCATCCGGAAAGGGCGTTTTAGGAAAAAACAAGT
17190 AAAAATTAAATAGCGCCTTCCGTCCG-
128 AAAAA-T---TAGCGCCTTCCGTCCGA
* * * * * * **
17216 GAAAGTGCATTTTGGGAAATAGCAAGTAAAGA-T-TAGTGCCTTCCATTCGGGAATTACGTTTTG
1 G-AAGGGCATTTTGGGAAAAAGCAAGTAAAAATTATAGCGCCTTCCGTCCGGGAATGGCGTTTT-
* * ** * * * **
17279 GGGAAAAA-CAAGTAAAAAGTAAATAGCGCCTTCCGCCCGGGAAGGGCATTTTGGGAAATGACAA
64 AGGAAAAAGCAAGT-AAAA--AAATAGTGCCTTCCATCCGGAAAGGGCGTTTTAGGAAAAAACAA
17343 GTAAAAA
126 GTAAAAA
17350 CTGAAAAATG
Statistics
Matches: 235, Mismatches: 39, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
148 28 0.12
150 1 0.00
151 10 0.04
152 92 0.39
153 20 0.09
155 43 0.18
156 41 0.17
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (150 bp):
GAAGGGCATTTTGGGAAAAAGCAAGTAAAAATTATAGCGCCTTCCGTCCGGGAATGGCGTTTTAG
GAAAAAGCAAGTAAAAAAATAGTGCCTTCCATCCGGAAAGGGCGTTTTAGGAAAAAACAAGTAAA
AATTAGCGCCTTCCGTCCGA
Found at i:17286 original size:102 final size:102
Alignment explanation
Indices: 16913--17347 Score: 531
Period size: 102 Copynumber: 4.3 Consensus size: 102
16903 CTTGTGCAAT
** * * * ** * * *
16913 GAAGGGCATTTTAAGAAAAAGCGAGTAAATATTAACGCTTTCCGTCCGGGAAGGGCGTTTT-AGG
1 GAAGGGCATTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTGGGG
*
16977 AAAAAGCAAGT-AAAA--AAATAGTGCCTTCCGTCCGG
66 AAAAA-CAAGTAAAAATTAAATAGCGCCTTCCGTCCGG
* * * * * *
17012 GAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAGTGCCTTCCGTCCGAGAAGGGCGTTTT-GGG
1 GAAGGGCATTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTGGGG
17076 AAAAAGCAAGTAAAAATTAAATAGCGCCTTCCGTCCGG
66 AAAAA-CAAGTAAAAATTAAATAGCGCCTTCCGTCCGG
* *
17114 GAATGGCATTTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGGAAAGGGCGTTTTGGG
1 GAAGGGCA-TTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTGGG
* *
17179 AAAAAACGAGTAAAAATTAAATAGCGCCTTCCGTCCGG
65 GAAAAACAAGTAAAAATTAAATAGCGCCTTCCGTCCGG
* * * ***
17217 AAAGTGCATTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATTCGGGAATTACGTTTTGGGG
1 GAAGGGCATTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTGGGG
* *
17282 AAAAACAAGTAAAAAGTAAATAGCGCCTTCCGCCCGG
66 AAAAACAAGTAAAAATTAAATAGCGCCTTCCGTCCGG
17319 GAAGGGCATTTTGGGAAAT-GACAAGTAAA
1 GAAGGGCATTTTGGGAAATAG-CAAGTAAA
17348 AACTGAAAAA
Statistics
Matches: 296, Mismatches: 34, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
99 66 0.22
100 4 0.01
101 1 0.00
102 135 0.46
103 83 0.28
104 7 0.02
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (102 bp):
GAAGGGCATTTTGGGAAATAGCAAGTAAAGATTAGTGCCTTCCATCCGGGAAGGGCGTTTTGGGG
AAAAACAAGTAAAAATTAAATAGCGCCTTCCGTCCGG
Found at i:17463 original size:23 final size:24
Alignment explanation
Indices: 17429--17497 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
17419 CCCCTTTTTC
17429 TTTTT-AAGTTTTTTTTTTTTA-CT
1 TTTTTGAA-TTTTTTTTTTTTACCT
**
17452 TTTTTGAATTTTTATTTTTCCACCT
1 TTTTTGAATTTTT-TTTTTTTACCT
* **
17477 TTTCTGAATTAATTTTTTTTA
1 TTTTTGAATTTTTTTTTTTTA
17498 TGCTTAATCA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
23 10 0.28
24 14 0.39
25 12 0.33
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTTTGAATTTTTTTTTTTTACCT
Found at i:20171 original size:25 final size:25
Alignment explanation
Indices: 20138--20187 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20128 ACAAAATGCC
20138 CCAAATAAAAGGCATAAGACAAGAA
1 CCAAATAAAAGGCATAAGACAAGAA
*
20163 CCAAATAAAAGGCATAGGACAAGAA
1 CCAAATAAAAGGCATAAGACAAGAA
20188 AGGAAATCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.16, G:0.18, T:0.08
Consensus pattern (25 bp):
CCAAATAAAAGGCATAAGACAAGAA
Found at i:20781 original size:33 final size:32
Alignment explanation
Indices: 20685--20781 Score: 80
Period size: 33 Copynumber: 3.1 Consensus size: 32
20675 ACTGATGTTA
*
20685 AAACTGAAAGTGACCAGTCCGTGGTCGACATTG
1 AAACTGAAAGAGACCAGTCCGTGGTCGAC-TTG
* * *
20718 AAAACTGAGAA-A-ACCTGTCTGAGGT---C-TG
1 -AAACTGA-AAGAGACCAGTCCGTGGTCGACTTG
20746 AAACTGAAAGAGACCAGTCCGTGGTCGACTTTG
1 AAACTGAAAGAGACCAGTCCGTGGTCGAC-TTG
20779 AAA
1 AAA
20782 ATCAAGAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 17
0.67 0.10 0.24
Matches are distributed among these distances:
26 2 0.04
27 8 0.17
28 12 0.25
30 1 0.02
31 1 0.02
33 15 0.31
34 7 0.15
35 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (32 bp):
AAACTGAAAGAGACCAGTCCGTGGTCGACTTG
Found at i:20832 original size:62 final size:63
Alignment explanation
Indices: 20696--20959 Score: 333
Period size: 62 Copynumber: 4.3 Consensus size: 63
20686 AACTGAAAGT
* * * *
20696 GACCAGTCCGTGGTCGACATTGAAAA-CTGAGAAA-ACCTGTCTGAGGTCTGAAACTGAA-AG
1 GACCAGTCTGTGGTCGACTTTGAAAATCTAAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAG
* *
20756 AGACCAGTCCGTGGTCGACTTTGAAAATC-AAGAAAGACCTGTCTGAGGTTTGAAATTGAAGAG
1 -GACCAGTCTGTGGTCGACTTTGAAAATCTAAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAG
** * *
20819 GACCAAACTGTGGTCGACTTTGAAAAT-TAAGAAAGACCTGTCTGAGGTCTGAAATTAAAGAA
1 GACCAGTCTGTGGTCGACTTTGAAAATCTAAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAG
* * * * *
20881 GACCGGTCTGTGGTCGAC-TTGAAAAACTAAGAAAGACCTGTCTGAGGTCTGAAGTTGAAAAA
1 GACCAGTCTGTGGTCGACTTTGAAAATCTAAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAG
*
20943 GACCAGTCTATGGTCGA
1 GACCAGTCTGTGGTCGA
20960 TATTGAGAAA
Statistics
Matches: 179, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
61 37 0.21
62 140 0.78
63 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (63 bp):
GACCAGTCTGTGGTCGACTTTGAAAATCTAAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAG
Found at i:20882 original size:28 final size:28
Alignment explanation
Indices: 20842--20973 Score: 83
Period size: 28 Copynumber: 4.5 Consensus size: 28
20832 TCGACTTTGA
*
20842 AAATTAAGAAAGACCTGTCTGAGGTCTG
1 AAATTAAGAAAGACCGGTCTGAGGTCTG
*
20870 AAATTAA-AGAAGACCGGTCTGTGGTCGACTTG
1 AAATTAAGA-AAGACCGGTCTGAGGT---C-TG
* *
20902 AAAAACTAAGAAAGACCTGTCTGAGGTCTG
1 --AAATTAAGAAAGACCGGTCTGAGGTCTG
* *
20932 AAGTTGAA-AAAGACCAGTCT-ATGGTC-G
1 AAATT-AAGAAAGACCGGTCTGA-GGTCTG
* *
20959 ATATTGAGAAAGACC
1 AAATTAAGAAAGACC
20974 TATCCGAGGT
Statistics
Matches: 82, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
26 1 0.01
27 13 0.16
28 39 0.48
29 2 0.02
30 2 0.02
31 2 0.02
32 2 0.02
34 20 0.24
35 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (28 bp):
AAATTAAGAAAGACCGGTCTGAGGTCTG
Found at i:21039 original size:28 final size:29
Alignment explanation
Indices: 20997--21306 Score: 185
Period size: 28 Copynumber: 10.3 Consensus size: 29
20987 CTTTGATAAT
*
20997 TGAAATTG-AGAAAGA-CATGTCTGAGGTC
1 TGAAATTGAAGAAAGACCA-GTCTGTGGTC
21025 TGAAATTGAAG-AAGACCAGTCTGTGGTC
1 TGAAATTGAAGAAAGACCAGTCTGTGGTC
* * ** *
21053 GATATTGAAATTG-GGAAAGACCTGTCTAAGGTT
1 -----TGAAATTGAAGAAAGACCAGTCTGTGGTC
* *
21086 TGAAATTGAA-TAGGACCAGTCTGTGGTC
1 TGAAATTGAAGAAAGACCAGTCTGTGGTC
* * *
21114 GATATTGAAATTG-GGAAAGACCTGTCTGAGGTC
1 -----TGAAATTGAAGAAAGACCAGTCTGTGGTC
21147 TGAAATTGAAG-AAGACCAGTCTGTGGTC
1 TGAAATTGAAGAAAGACCAGTCTGTGGTC
* *
21175 GATATTGAAATTG-AGAAAGACCTGTCTGAGGTC
1 -----TGAAATTGAAGAAAGACCAGTCTGTGGTC
*
21208 TGAAATTG-AGGAAGACCAGTCTGTGGTTGACTC
1 TGAAATTGAAGAAAGACCAGTCTGT-G--G--TC
* *
21241 TAGAAACTG-AGAAAGACCTGTCTGTGGTC
1 T-GAAATTGAAGAAAGACCAGTCTGTGGTC
21270 TGAAATTGAAG-AAGACCAGTCTGTGGTC
1 TGAAATTGAAGAAAGACCAGTCTGTGGTC
*
21298 -GATATTGAA
1 TGAAATTGAA
21307 ATTGAGAAAG
Statistics
Matches: 221, Mismatches: 32, Indels: 59
0.71 0.10 0.19
Matches are distributed among these distances:
27 8 0.04
28 107 0.48
29 11 0.05
31 2 0.01
32 3 0.01
33 70 0.32
34 20 0.09
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (29 bp):
TGAAATTGAAGAAAGACCAGTCTGTGGTC
Found at i:21090 original size:61 final size:61
Alignment explanation
Indices: 20995--21342 Score: 536
Period size: 61 Copynumber: 5.7 Consensus size: 61
20985 AACTTTGATA
*
20995 ATTGAAATTGAGAAAGACATGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
1 ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
* * * * *
21056 ATTGAAATTGGGAAAGACCTGTCTAAGGTTTGAAATTGAATAGGACCAGTCTGTGGTCGAT
1 ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
*
21117 ATTGAAATTGGGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
1 ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
* *
21178 ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAGGAAGACCAGTCTGTGGTTGACT
1 ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGA-T
* * * *
21240 CTAGAAACTGAGAAAGACCTGTCTGTGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
1 ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
* *
21301 ATTGAAATTGAGAAAGACCTATCTGAAGTC-GAGAATTGAAGA
1 ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGA-AATTGAAGA
21343 TTTGAGAGAG
Statistics
Matches: 260, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
60 2 0.01
61 203 0.78
62 55 0.21
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (61 bp):
ATTGAAATTGAGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTCTGTGGTCGAT
Found at i:30353 original size:28 final size:28
Alignment explanation
Indices: 30321--30388 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
30311 AGGTTTAAAA
*
30321 CACCACATCATTCAAACTTTAATTACAT
1 CACCAAATCATTCAAACTTTAATTACAT
*
30349 CACCAAATCGTTCAAACTTTAATTACAAT
1 CACCAAATCATTCAAACTTTAATTAC-AT
*
30378 CTCCAAA-CATT
1 CACCAAATCATT
30389 TTAACAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 27 0.77
29 8 0.23
ACGTcount: A:0.40, C:0.28, G:0.01, T:0.31
Consensus pattern (28 bp):
CACCAAATCATTCAAACTTTAATTACAT
Found at i:30929 original size:18 final size:18
Alignment explanation
Indices: 30906--30940 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30896 AAGTTCGTGA
*
30906 TTGAAGATATTTGAAGAT
1 TTGAAGATAATTGAAGAT
30924 TTGAAGATAATTGAAGA
1 TTGAAGATAATTGAAGA
30941 ATTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:32318 original size:18 final size:18
Alignment explanation
Indices: 32295--32329 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32285 AAGTTCGTGA
*
32295 TTGAAGATATTTGAAGAT
1 TTGAAGATAATTGAAGAT
32313 TTGAAGATAATTGAAGA
1 TTGAAGATAATTGAAGA
32330 ATTAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:33701 original size:18 final size:18
Alignment explanation
Indices: 33678--33712 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33668 AAGTTCGTGA
*
33678 TTGAAGATATTTGAAGAT
1 TTGAAGATAATTGAAGAT
33696 TTGAAGATAATTGAAGA
1 TTGAAGATAATTGAAGA
33713 ATTCAAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:33720 original size:18 final size:18
Alignment explanation
Indices: 33681--33720 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33671 TTCGTGATTG
* * *
33681 AAGATATTTGAAGATTTG
1 AAGATAATTGAAGAATTC
33699 AAGATAATTGAAGAATTC
1 AAGATAATTGAAGAATTC
33717 AAGA
1 AAGA
33721 AGTAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (18 bp):
AAGATAATTGAAGAATTC
Done.