Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006734.1 Corchorus capsularis cultivar CVL-1 contig06755, 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: 68726
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:2268 original size:222 final size:222
Alignment explanation
Indices: 1882--2319 Score: 813
Period size: 222 Copynumber: 2.0 Consensus size: 222
1872 AATTTTTAGT
* *
1882 TTTGGTGATGATATATAGAATTTCAGATTTGTTCTTCAATTTCCACTTTTGGTCATTTATTTTCT
1 TTTGGTGATGATATATAGAATTTCAGATTTATTCTTCAATTTCCACTTTTGGTCATTTATTATCT
1947 GCCTCCCCAATACCCATTTCGAAGATAATGTGGAGTTTGGTAGTATTTGGTTTTAGGCAATGTGA
66 GCCTCCCCAATACCCATTTCGAAGATAATGTGGAGTTTGGTAGTATTTGGTTTTAGGCAATGTGA
*
2012 AAATTGAGAAATTCTGAAAATTAATGTTGTGTAGTTGGCATTGTTGTTCCTGATTTGGGTTTTGA
131 AAATTGAGAAATTCTAAAAATTAATGTTGTGTAGTTGGCATTGTTGTTCCTGATTTGGGTTTTGA
2077 TATGATAGGCCTGAAAATGACTTTCAG
196 TATGATAGGCCTGAAAATGACTTTCAG
*
2104 TTTGGTGATGATATATGGAATTTCAGATTTATTCTTCAATTTCCACTTTTGGTCATTTATTATCT
1 TTTGGTGATGATATATAGAATTTCAGATTTATTCTTCAATTTCCACTTTTGGTCATTTATTATCT
* *
2169 GCCTCCCCAATACCCATTTTGAAGGTAATGTGGAGTTTGGTAGTATTTGGTTTTAGGCAATGTGA
66 GCCTCCCCAATACCCATTTCGAAGATAATGTGGAGTTTGGTAGTATTTGGTTTTAGGCAATGTGA
*
2234 AAATTGAGAAATTCTAAAAATTAATGTTGTGTAGTTGGTATTGTTGTTCCTGATTTGGGTTTTGA
131 AAATTGAGAAATTCTAAAAATTAATGTTGTGTAGTTGGCATTGTTGTTCCTGATTTGGGTTTTGA
2299 TATGATAGGCCTGAAAATGAC
196 TATGATAGGCCTGAAAATGAC
2320 AATGAATTAG
Statistics
Matches: 209, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
222 209 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (222 bp):
TTTGGTGATGATATATAGAATTTCAGATTTATTCTTCAATTTCCACTTTTGGTCATTTATTATCT
GCCTCCCCAATACCCATTTCGAAGATAATGTGGAGTTTGGTAGTATTTGGTTTTAGGCAATGTGA
AAATTGAGAAATTCTAAAAATTAATGTTGTGTAGTTGGCATTGTTGTTCCTGATTTGGGTTTTGA
TATGATAGGCCTGAAAATGACTTTCAG
Found at i:6650 original size:11 final size:11
Alignment explanation
Indices: 6636--6673 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6626 ATTCATAACA
6636 AATTTATAATT
1 AATTTATAATT
6647 AATTTATAATT
1 AATTTATAATT
6658 -ATTTGATAATT
1 AATTT-ATAATT
*
6669 TATTT
1 AATTT
6674 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:9489 original size:14 final size:14
Alignment explanation
Indices: 9470--9503 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
9460 CTAGCCGCTC
9470 CCCTCTCCCCTTCT
1 CCCTCTCCCCTTCT
*
9484 CCCTCTCCTCTTCT
1 CCCTCTCCCCTTCT
*
9498 CTCTCT
1 CCCTCT
9504 AGTTCTCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (14 bp):
CCCTCTCCCCTTCT
Found at i:10298 original size:30 final size:30
Alignment explanation
Indices: 10262--10323 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
10252 GCTTAAGTTT
* *
10262 ATATAGGGGTTGAAATCTCTTGTATACTTG
1 ATATAGGGGTCGAAATCTCTTGTATACCTG
10292 ATATAGGGGTCGAAATCTCTTGTATACCTG
1 ATATAGGGGTCGAAATCTCTTGTATACCTG
10322 AT
1 AT
10324 GTATATTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (30 bp):
ATATAGGGGTCGAAATCTCTTGTATACCTG
Found at i:11984 original size:12 final size:12
Alignment explanation
Indices: 11967--11992 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11957 GCATGCATAG
11967 ATGAATTAGAAA
1 ATGAATTAGAAA
11979 ATGAATTAGAAA
1 ATGAATTAGAAA
11991 AT
1 AT
11993 AATAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (12 bp):
ATGAATTAGAAA
Found at i:13004 original size:31 final size:31
Alignment explanation
Indices: 12969--13034 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
12959 AATTTTATGT
* *
12969 TTTCCGATTGTACCCTTATT-TTTAAAATATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
13000 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
13031 TTTC
1 TTTC
13035 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:13198 original size:38 final size:35
Alignment explanation
Indices: 13134--13210 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 35
13124 AATTTGACTT
13134 TTTGTTTCCAACGTTCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTTCTATTTAATTTTG-C-TTTGTC
*
13171 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTC
1 TTTGTTTCCAA-CGTTCTATTTAATTTTGCTTTGTC
13207 TTTG
1 TTTG
13211 GTCTTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 10 0.26
37 12 0.32
38 16 0.42
ACGTcount: A:0.13, C:0.16, G:0.13, T:0.58
Consensus pattern (35 bp):
TTTGTTTCCAACGTTCTATTTAATTTTGCTTTGTC
Found at i:13374 original size:19 final size:20
Alignment explanation
Indices: 13347--13384 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
13337 TACTACTATT
13347 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
13367 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
13385 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:13416 original size:6 final size:6
Alignment explanation
Indices: 13405--13430 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
13395 AAAAGATTAA
13405 ACTAAC ACTAAC ACTAAC ACTAAC AC
1 ACTAAC ACTAAC ACTAAC ACTAAC AC
13431 GTACAATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
ACTAAC
Found at i:13721 original size:22 final size:22
Alignment explanation
Indices: 13561--13723 Score: 121
Period size: 22 Copynumber: 7.3 Consensus size: 22
13551 TTGTCTATAT
* **
13561 GTGGTTATCAAAATTTCATAAA
1 GTGGTTATTAAAATTTCATAGG
* *
13583 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * * *
13605 GAGGTTATCAAAATTCCATAGT
1 GTGGTTATTAAAATTTCATAGG
** *
13627 GTGGTTACCAAAATTTCATAGT
1 GTGGTTATTAAAATTTCATAGG
* *
13649 GTGGTTATCATAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
* * *
13671 ATCAGGTTATTAAAATCTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
13695 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
13717 GTGGTTA
1 GTGGTTA
13724 ATTATCACAA
Statistics
Matches: 110, Mismatches: 27, Indels: 8
0.76 0.19 0.06
Matches are distributed among these distances:
22 92 0.84
23 1 0.01
24 17 0.15
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:13784 original size:22 final size:22
Alignment explanation
Indices: 13759--13812 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
13749 ATCAAAGAGA
13759 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATGTCATAGCGAGG
* * *
13781 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATGTCATAGCGAGG
*
13803 TTAACAAAAT
1 TTATCAAAAT
13813 TTAATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (22 bp):
TTATCAAAATGTCATAGCGAGG
Found at i:13882 original size:22 final size:21
Alignment explanation
Indices: 13834--14139 Score: 113
Period size: 22 Copynumber: 13.8 Consensus size: 21
13824 TTTCATGGGG
* *
13834 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
13856 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
13878 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
13903 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
13925 AGGTTATC-AAATCTCATA-A
1 AGGTTATCAAAATTTCATAGA
*
13944 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
*
13967 GATCTGATTATC-AAATTT-ATAGAA
1 -A---GGTTATCAAAATTTCATAG-A
*
13991 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
14011 TGTTGTTATCAAAATTTCAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
* *
14035 AGGCTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* * *
14055 TGTGATTATCGAAATTTTATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
14078 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
14100 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
14122 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
14140 AAATGTGATT
Statistics
Matches: 217, Mismatches: 40, Indels: 54
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.01
20 18 0.08
21 19 0.09
22 135 0.62
23 11 0.05
24 10 0.05
25 11 0.05
26 5 0.02
27 5 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:13994 original size:25 final size:25
Alignment explanation
Indices: 13946--14010 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
13936 TCTCATAAAG
13946 TGATTATCGAAATTTCATAGAGATC
1 TGATTATCGAAATTTCATAGAGATC
13971 TGATTATC-AAATTT-ATAGA-A--
1 TGATTATCGAAATTTCATAGAGATC
* *
13991 AGATTATCAAAATTTCATAG
1 TGATTATCGAAATTTCATAG
14011 TGTTGTTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 7 0.19
21 6 0.16
22 5 0.14
23 5 0.14
24 6 0.16
25 8 0.22
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (25 bp):
TGATTATCGAAATTTCATAGAGATC
Found at i:14297 original size:22 final size:22
Alignment explanation
Indices: 14264--14820 Score: 115
Period size: 22 Copynumber: 25.7 Consensus size: 22
14254 TCAGGGAGGA
*
14264 TATCGAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
14286 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
14308 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
14330 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * **
14351 AGATCAAAATTTCATAGGGAGAA
1 -TATCAAAATTTCATATGAAGGT
*
14374 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
14396 TATCAAAAAATT-ATAGGGAGGT
1 TATC-AAAATTTCATATGAAGGT
* *
14418 AATCAAAA-TT--TGT-AA--T
1 TATCAAAATTTCATATGAAGGT
* * *
14434 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * * *
14456 TATCAAAATTTTATAGGGACGTT
1 TATCAAAATTTCATA-TGAAGGT
* * *
14479 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
14502 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* *
14524 TATCACAATTTCAT-TG-TGTGAT
1 TATCAAAATTTCATATGAAG-G-T
* * *
14546 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
14568 T-TCTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
14590 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
14612 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
14634 TATCAACATCTCATTGTGTTGGT
1 TATCAAAATTTCA-TATGAAGGT
*
14657 TATCAAAA-TTCAT-TGGAAAGT
1 TATCAAAATTTCATAT-GAAGGT
*
14678 TATCAAAATTCCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
14700 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
14722 TAACCAAATTT--TAT-AAGGT
1 TATCAAAATTTCATATGAAGGT
** **
14741 TAAAAAAAATTT-ATAAAAAGGT
1 T-ATCAAAATTTCATATGAAGGT
* * * **
14763 TCTCGAAA-TCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
14784 TATTAAAAATTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
14806 TATCAAAATTTCATA
1 TATCAAAATTTCATA
14821 ACGCGATCAT
Statistics
Matches: 388, Mismatches: 104, Indels: 86
0.67 0.18 0.15
Matches are distributed among these distances:
16 7 0.02
17 2 0.01
18 1 0.00
19 7 0.02
20 17 0.04
21 47 0.12
22 233 0.60
23 69 0.18
24 5 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:14483 original size:23 final size:22
Alignment explanation
Indices: 14455--14534 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
14445 CATAAGAAAG
14455 TTATCAAAATTTTATAGGGACGT
1 TTATCAAAATTTTATAGGGA-GT
*
14478 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAG-T
* * *
14501 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTTATAGGGAGT
*
14523 TTATCACAATTT
1 TTATCAAAATTT
14535 CATTGTGTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 12 0.24
23 38 0.76
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGT
Found at i:16107 original size:2 final size:2
Alignment explanation
Indices: 16100--16125 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16090 TTATTAGTAG
16100 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
16126 CTATGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16477 original size:21 final size:21
Alignment explanation
Indices: 16453--16492 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16443 AGAAATTTCG
16453 GTTATAAAATAAAAATCATCA
1 GTTATAAAATAAAAATCATCA
* * *
16474 GTTATGATATAAAGATCAT
1 GTTATAAAATAAAAATCAT
16493 AAAAGATGAT
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:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
GTTATAAAATAAAAATCATCA
Found at i:17745 original size:46 final size:47
Alignment explanation
Indices: 17688--17779 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 47
17678 AATTCTATTG
* *
17688 TTCCTTTAAATCT-GTTTCATTCTTCTCTTAG-GAGGATG-GGTTTGGA
1 TTCCTTCAAATCTGGTTT-ATCCTTCT-TTAGAGAGGATGTGGTTTGGA
*
17734 TTCCTTCAAATCTGGTTTATCCTTCTTTTGAGAGGATGTGGTTTGG
1 TTCCTTCAAATCTGGTTTATCCTTCTTTAGAGAGGATGTGGTTTGG
17780 TTAAAAGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
45 3 0.08
46 26 0.65
47 11 0.28
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.46
Consensus pattern (47 bp):
TTCCTTCAAATCTGGTTTATCCTTCTTTAGAGAGGATGTGGTTTGGA
Found at i:20988 original size:2 final size:2
Alignment explanation
Indices: 20981--21012 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20971 GCTTTCCTGC
20981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21013 GTAAACGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23168 original size:45 final size:45
Alignment explanation
Indices: 23118--23204 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
23108 TTACTTCTCT
23118 AGCTTATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCC
1 AGCTTATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCC
* *
23163 AGCTTATCATTAATTCGGGGTATGGATCTTTTAGTAATTCCA
1 AGCTTATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCA
23205 TCTATTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (45 bp):
AGCTTATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCC
Found at i:24201 original size:25 final size:27
Alignment explanation
Indices: 24149--24201 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
24139 TTACTCAACT
* **
24149 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTCATTTTAATGTAA
24176 AAAAACTCTATTTTCA-TTTAAT-TAA
1 AAAAACTCTATTTTCATTTTAATGTAA
24201 A
1 A
24202 TCTAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.65
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAAACTCTATTTTCATTTTAATGTAA
Found at i:25794 original size:21 final size:21
Alignment explanation
Indices: 25751--25794 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
25741 TTTTTATTCT
* **
25751 TTTCATTAAGTTTAGCCTTAA
1 TTTCACTAAGTTTAGCCCCAA
25772 TTTCACTAAGTTTAGCCCCAA
1 TTTCACTAAGTTTAGCCCCAA
25793 TT
1 TT
25795 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.43
Consensus pattern (21 bp):
TTTCACTAAGTTTAGCCCCAA
Found at i:25961 original size:102 final size:104
Alignment explanation
Indices: 25769--26026 Score: 335
Period size: 102 Copynumber: 2.5 Consensus size: 104
25759 AGTTTAGCCT
* * *
25769 TAATTTCACTAAGTTTAGCCCCAATTAAATTTTTATTTTTATTTTAAGGGTAAATTTCAAAATTA
1 TAATTTCACTAAGTTTAGCCCAAATT-AATTTTTATTTTTATTTTAAGGGTAAATTCCAAAACTA
*
25834 ATAATTTATTGTTATAGGGTTTTAGAAATAAGATACAAAAC
65 ATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
25875 TAATTTCACTAAGTTTAGTCCCAAATTAA-TTTT-TTTTTATTTTAAGGGTAAATTCCATAACTA
1 TAATTTCACTAAGTTTAG-CCCAAATTAATTTTTATTTTTATTTTAAGGGTAAATTCCAAAACTA
* * *
25938 ATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAAT
65 ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * ** *
25977 TAA-TTCACTAAGTTTAACCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATT-AATTTTTATTTTTATTTTAAGGGT
26027 TAGAAAAAAT
Statistics
Matches: 136, Mismatches: 12, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
100 8 0.06
101 15 0.11
102 36 0.26
103 15 0.11
104 31 0.23
105 4 0.03
106 20 0.15
107 7 0.05
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAATTTTTATTTTTATTTTAAGGGTAAATTCCAAAACTAA
TAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:26528 original size:13 final size:13
Alignment explanation
Indices: 26510--26534 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26500 GAATTTTGCT
26510 ATTTGATCCTCCA
1 ATTTGATCCTCCA
26523 ATTTGATCCTCC
1 ATTTGATCCTCC
26535 TGACATGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTTGATCCTCCA
Found at i:32147 original size:14 final size:14
Alignment explanation
Indices: 32128--32158 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32118 ACTGGAATCT
*
32128 TATGTGTGTGTATA
1 TATGTGTGTATATA
32142 TATGTGTGTATATA
1 TATGTGTGTATATA
32156 TAT
1 TAT
32159 ATATATACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (14 bp):
TATGTGTGTATATA
Found at i:32149 original size:12 final size:12
Alignment explanation
Indices: 32132--32156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32122 GAATCTTATG
32132 TGTGTGTATATA
1 TGTGTGTATATA
32144 TGTGTGTATATA
1 TGTGTGTATATA
32156 T
1 T
32157 ATATATATAC
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:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (12 bp):
TGTGTGTATATA
Found at i:32507 original size:2 final size:2
Alignment explanation
Indices: 32500--32529 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32490 ACCCGATGGC
32500 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
32530 CTAGACCCAT
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:49257 original size:36 final size:36
Alignment explanation
Indices: 49199--49292 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 36
49189 AATAGTGTAT
**
49199 ATGACAACTTCTTGTGTCAATTTGAAAGGTAAAATC
1 ATGACAACTTCAAGTGTCAATTTGAAAGGTAAAATC
* *
49235 ATGACAACTTCAAGTGTTAATTTTAAAGGTAAAATC
1 ATGACAACTTCAAGTGTCAATTTGAAAGGTAAAATC
*
49271 TTGACAACTTCAAAG-GTCAATT
1 ATGACAACTTC-AAGTGTCAATT
49293 GGAGATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
36 48 0.94
37 3 0.06
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (36 bp):
ATGACAACTTCAAGTGTCAATTTGAAAGGTAAAATC
Found at i:55301 original size:19 final size:19
Alignment explanation
Indices: 55290--55326 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55280 AATTTTTAAG
55290 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
55309 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
55327 ACAATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:63478 original size:127 final size:125
Alignment explanation
Indices: 63238--63490 Score: 452
Period size: 125 Copynumber: 2.0 Consensus size: 125
63228 CCATGAACAG
* *
63238 GTCTAGACACACACAGGCATATAAACATTTTGGCTTAAGAGGAGGTAGCTTAAGGTACATGATAC
1 GTCTAGACACACACAGGCATATAAACATTTTGCCTTAAGAGGACGTAGCTTAAGGTACATGATAC
*
63303 GCCCCTCCTATAACAAGTGCGTTGGTGGTCGAATTAATTGTACTCTCGCACTCTTGTTAA
66 CCCCCTCCTATAACAAGTGCGTTGGTGGTCGAATTAATTGTACTCTCGCACTCTTGTTAA
*
63363 GTCTAGACACACACATGCATATAAACATTTTGCCTTAAGAGGACGTAGCTTAAGGTACATGATAC
1 GTCTAGACACACACAGGCATATAAACATTTTGCCTTAAGAGGACGTAGCTTAAGGTACATGATAC
63428 ACCCCTCTCCTATAACAAGTGCGTTGGTGGTCGAATTAATTGTACTCTCGCACTCTTGTTAA
66 -CCCC-CTCCTATAACAAGTGCGTTGGTGGTCGAATTAATTGTACTCTCGCACTCTTGTTAA
63490 G
1 G
63491 GTAGAGACCA
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
125 62 0.51
126 3 0.02
127 57 0.47
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (125 bp):
GTCTAGACACACACAGGCATATAAACATTTTGCCTTAAGAGGACGTAGCTTAAGGTACATGATAC
CCCCCTCCTATAACAAGTGCGTTGGTGGTCGAATTAATTGTACTCTCGCACTCTTGTTAA
Found at i:64712 original size:3 final size:3
Alignment explanation
Indices: 64706--64738 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
64696 AAAAAGAAAG
64706 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
64739 ATTTACTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Done.