Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007982.1 Corchorus capsularis cultivar CVL-1 contig08003, 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: 9995
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:550 original size:24 final size:24
Alignment explanation
Indices: 505--551 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
495 AAACATTCTT
*
505 AAAAATTCAAAGCAATCATCAATC
1 AAAAATTCAAAGCAATAATCAATC
*
529 AAAAA-TCAAATCAATAACTCAAT
1 AAAAATTCAAAGCAATAA-TCAAT
552 ATAAGCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAAATTCAAAGCAATAATCAATC
Found at i:918 original size:17 final size:18
Alignment explanation
Indices: 890--926 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
880 TGGAAAATCC
890 TAAAAAAGAAAAGAAAAA
1 TAAAAAAGAAAAGAAAAA
908 TAAAAAA-AAAAGAAAAA
1 TAAAAAAGAAAAGAAAAA
925 TA
1 TA
927 TTATGGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (18 bp):
TAAAAAAGAAAAGAAAAA
Found at i:924 original size:11 final size:11
Alignment explanation
Indices: 891--924 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
881 GGAAAATCCT
891 AAAAAAGAAAA
1 AAAAAAGAAAA
* *
902 GAAAAATAAAA
1 AAAAAAGAAAA
913 AAAAAAGAAAA
1 AAAAAAGAAAA
924 A
1 A
925 TATTATGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:4379 original size:14 final size:15
Alignment explanation
Indices: 4347--4398 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
4337 CAAGAGACGT
4347 TTTTCAAAAAAATGG
1 TTTTCAAAAAAATGG
*
4362 TTTTCAAGAAAA-GG
1 TTTTCAAAAAAATGG
*
4376 TTTTC--GAAAATGAG
1 TTTTCAAAAAAATG-G
4390 TTTTCAAAA
1 TTTTCAAAA
4399 GGTTTTTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 1 0.03
14 13 0.42
15 11 0.35
16 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (15 bp):
TTTTCAAAAAAATGG
Found at i:5165 original size:94 final size:95
Alignment explanation
Indices: 4998--5170 Score: 278
Period size: 94 Copynumber: 1.8 Consensus size: 95
4988 CAAAATTGTC
* * *
4998 TTTGCAAAAGAAAAGTGTTTTTTCTCGAAAAAGGTTTTAGAGAAAATTTGTTTCAAAAGTTTTTC
1 TTTGCAAAAGAAAAGTGTTTTTTCTCGAAAAAGGTTTTAGAGAAAACTGGTTTCAAAACTTTTTC
5063 AAAGGCAAGCGCATAGTACAAGAAATAGTT
66 AAAGGCAAGCGCATAGTACAAGAAATAGTT
* *
5093 TTTGCAGAAGAAATGTGTTTTTTCTC-AAAAAGGTTTTAGAGAAAACTGGTTTCAAAACTTTTTC
1 TTTGCAAAAGAAAAGTGTTTTTTCTCGAAAAAGGTTTTAGAGAAAACTGGTTTCAAAACTTTTTC
5157 GAAA-GCAAGCGCAT
66 -AAAGGCAAGCGCAT
5171 GAAAAAGAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
94 45 0.62
95 27 0.38
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (95 bp):
TTTGCAAAAGAAAAGTGTTTTTTCTCGAAAAAGGTTTTAGAGAAAACTGGTTTCAAAACTTTTTC
AAAGGCAAGCGCATAGTACAAGAAATAGTT
Found at i:5186 original size:14 final size:15
Alignment explanation
Indices: 5169--5197 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5159 AAGCAAGCGC
5169 ATGAAAAAG-AGAAA
1 ATGAAAAAGAAGAAA
5183 ATGAAAAAGAAGAAA
1 ATGAAAAAGAAGAAA
5198 GAAGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (15 bp):
ATGAAAAAGAAGAAA
Found at i:6302 original size:38 final size:38
Alignment explanation
Indices: 6218--6354 Score: 152
Period size: 38 Copynumber: 3.6 Consensus size: 38
6208 TGGTCCCTTT
* * * * *
6218 CAGGTCACCTTTCGACAATTATCAAAAGTTGACTGGAAA
1 CAGGTCATCTTTCAACACTTATCAAGA-TCGACTGGAAA
*
6257 CAGGTCATCTTTTAACACTTATCAAGATCGACTGGAAA
1 CAGGTCATCTTTCAACACTTATCAAGATCGACTGGAAA
* * * *
6295 TATGTCATCTTTCAACAGTTGTCAAGATCGACTGGAAA
1 CAGGTCATCTTTCAACACTTATCAAGATCGACTGGAAA
*
6333 CAGGTCATTTTTCAA-A-TTATCA
1 CAGGTCATCTTTCAACACTTATCA
6355 TAGGTTATCT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
36 5 0.06
37 1 0.01
38 55 0.66
39 22 0.27
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (38 bp):
CAGGTCATCTTTCAACACTTATCAAGATCGACTGGAAA
Found at i:6359 original size:22 final size:24
Alignment explanation
Indices: 6334--6378 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
6324 GACTGGAAAC
*
6334 AGGTCATTTTTC-A-AATTATCAT
1 AGGTCATCTTTCAACAATTATCAT
*
6356 AGGTTATCTTTCAACAATTATCA
1 AGGTCATCTTTCAACAATTATCA
6379 AGATCGACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (24 bp):
AGGTCATCTTTCAACAATTATCAT
Found at i:6432 original size:98 final size:98
Alignment explanation
Indices: 6258--6435 Score: 284
Period size: 98 Copynumber: 1.8 Consensus size: 98
6248 GACTGGAAAC
* * * *
6258 AGGTCATCTTTTAACACTTATCAAGATCGACTGGAAATATGTCATCTTTCAACAGTTGTCAAGAT
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAATAGGTCATCTTTCAACACTTGTCAAGAT
6323 CGACTGGAAACAGGTCATTTTTCAAATTATCAT
66 CGACTGGAAACAGGTCATTTTTCAAATTATCAT
* * *
6356 AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAATAGGTCATCTTTCAGCACTTGTCAAGTT
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAATAGGTCATCTTTCAACACTTGTCAAGAT
*
6421 CGACTTGAAACAGGT
66 CGACTGGAAACAGGT
6436 TGTCTTTCAG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 72 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (98 bp):
AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAATAGGTCATCTTTCAACACTTGTCAAGAT
CGACTGGAAACAGGTCATTTTTCAAATTATCAT
Found at i:6445 original size:38 final size:38
Alignment explanation
Indices: 6356--6447 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
6346 AAATTATCAT
* *
6356 AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAAT
1 AGGTTATCTTTCAGCAATTATCAAGATCGACTGGAAAC
* * * * *
6394 AGGTCATCTTTCAGCACTTGTCAAGTTCGACTTGAAAC
1 AGGTTATCTTTCAGCAATTATCAAGATCGACTGGAAAC
*
6432 AGGTTGTCTTTCAGCA
1 AGGTTATCTTTCAGCA
6448 GTTTTCGGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (38 bp):
AGGTTATCTTTCAGCAATTATCAAGATCGACTGGAAAC
Found at i:6508 original size:8 final size:8
Alignment explanation
Indices: 6483--6700 Score: 65
Period size: 8 Copynumber: 26.4 Consensus size: 8
6473 GGGCACTCCA
6483 ACAACTTT
1 ACAACTTT
*
6491 TCAA-TTT
1 ACAACTTT
6498 ACAACTTT
1 ACAACTTT
*
6506 ACAGCATTT
1 ACAAC-TTT
6515 GAACAACTATT
1 --ACAACT-TT
*
6526 TCAA--TT
1 ACAACTTT
6532 ACAACTTT
1 ACAACTTT
* *
6540 GCAGCATTT
1 ACAAC-TTT
6549 CAACAACTTT
1 --ACAACTTT
* *
6559 TCAGCTTTT
1 ACAAC-TTT
*
6568 ACAAATTTT
1 AC-AACTTT
*
6577 TCAA-TTT
1 ACAACTTT
6584 ACAACTTT
1 ACAACTTT
* *
6592 TCAGCATTT
1 ACAAC-TTT
6601 -CAA-TTT
1 ACAACTTT
6607 ACAACTTT
1 ACAACTTT
* *
6615 TCGA-TTT
1 ACAACTTT
6622 ACAACTTT
1 ACAACTTT
*
6630 TCAGACTTT
1 ACA-ACTTT
6639 ACAACTTT
1 ACAACTTT
*
6647 ACAGCATTT
1 ACAAC-TTT
6656 CAACAACTTT
1 --ACAACTTT
* * *
6666 TCGA-TTG
1 ACAACTTT
6673 ACAACTTT
1 ACAACTTT
* *
6681 TCAGAATTT
1 ACA-ACTTT
6690 ACAACTTT
1 ACAACTTT
6698 ACA
1 ACA
6701 GCAATCTTCC
Statistics
Matches: 149, Mismatches: 38, Indels: 46
0.64 0.16 0.20
Matches are distributed among these distances:
6 8 0.05
7 24 0.16
8 60 0.40
9 36 0.24
10 8 0.05
11 13 0.09
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.40
Consensus pattern (8 bp):
ACAACTTT
Found at i:6522 original size:19 final size:18
Alignment explanation
Indices: 6482--6703 Score: 133
Period size: 17 Copynumber: 12.8 Consensus size: 18
6472 GGGGCACTCC
6482 AACAACTTTTCA--ATTT
1 AACAACTTTTCAGCATTT
*
6498 -ACAACTTTACAGCATTT
1 AACAACTTTTCAGCATTT
6515 GAACAACTATTTCA--A-TT
1 -AACAACT-TTTCAGCATTT
*
6532 -ACAACTTTGCAGCATTT
1 AACAACTTTTCAGCATTT
6549 CAACAACTTTTCAGC-TTT
1 -AACAACTTTTCAGCATTT
* *
6567 TACAAATTTTTCA--ATTT
1 AAC-AACTTTTCAGCATTT
6584 -ACAACTTTTCAGCATTT
1 AACAACTTTTCAGCATTT
6601 CAATTTACAACTTTTC-G-ATTT
1 --A---ACAACTTTTCAGCATTT
6622 -ACAACTTTTCAG-ACTTT
1 AACAACTTTTCAGCA-TTT
*
6639 -ACAACTTTACAGCATTT
1 AACAACTTTTCAGCATTT
6656 CAACAACTTTTC-G-A-TT
1 -AACAACTTTTCAGCATTT
* *
6672 GACAACTTTTCAGAATTT
1 AACAACTTTTCAGCATTT
*
6690 -ACAACTTTACAGCA
1 AACAACTTTTCAGCA
6704 ATCTTCCGAC
Statistics
Matches: 166, Mismatches: 12, Indels: 55
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.02
15 44 0.27
16 8 0.05
17 48 0.29
18 16 0.10
19 27 0.16
20 4 0.02
21 4 0.02
22 1 0.01
23 10 0.06
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
AACAACTTTTCAGCATTT
Found at i:6534 original size:34 final size:34
Alignment explanation
Indices: 6481--6697 Score: 164
Period size: 34 Copynumber: 6.3 Consensus size: 34
6471 GGGGGCACTC
6481 CAACAACTTTTCAATTTACAACTTTACAGCATTT
1 CAACAACTTTTCAATTTACAACTTTACAGCATTT
* *
6515 GAACAACTATTTCAA-TTACAACTTTGCAGCATTT
1 CAACAACT-TTTCAATTTACAACTTTACAGCATTT
* * *
6549 CAACAACTTTTCAGCTTTTACAAATTTTTCA--ATTT
1 CAACAACTTTTCA--ATTTAC-AACTTTACAGCATTT
* *
6584 --ACAACTTTTCAGCATTT-CAA-TTTACAACTTTT
1 CAACAACTTTTCA--ATTTACAACTTTACAGCATTT
6616 CGATTTACAACTTTTCAGACTTTACAACTTTACAGCATTT
1 C-A---ACAACTTTTCA-A-TTTACAACTTTACAGCATTT
* * * *
6656 CAACAACTTTTCGATTGACAACTTTTCAGAATTT
1 CAACAACTTTTCAATTTACAACTTTACAGCATTT
6690 --ACAACTTT
1 CAACAACTTT
6698 ACAGCAATCT
Statistics
Matches: 151, Mismatches: 16, Indels: 34
0.75 0.08 0.17
Matches are distributed among these distances:
30 5 0.03
31 2 0.01
32 12 0.08
33 21 0.14
34 49 0.32
35 11 0.07
36 14 0.09
37 8 0.05
38 14 0.09
39 4 0.03
40 11 0.07
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.40
Consensus pattern (34 bp):
CAACAACTTTTCAATTTACAACTTTACAGCATTT
Found at i:6680 original size:51 final size:50
Alignment explanation
Indices: 6517--6703 Score: 218
Period size: 51 Copynumber: 3.6 Consensus size: 50
6507 CAGCATTTGA
* *
6517 ACAACTATTTCA-A-TTACAACTTTGCAGCATTTCAACAACTTTTCAGCTTTT
1 ACAACT-TTTCAGATTTACAACTTTACAGCATTTCAACAACTTTTC-G-ATTT
* *
6568 ACAAATTTTTCA-ATTTACAACTTTTCAGCATTTCAATTTACAACTTTTCGATTT
1 AC-AACTTTTCAGATTTACAACTTTACAGCATTTC-A---ACAACTTTTCGATTT
*
6622 ACAACTTTTCAGACTTTACAACTTTACAGCATTTCAACAACTTTTCGATTG
1 ACAACTTTTCAGA-TTTACAACTTTACAGCATTTCAACAACTTTTCGATTT
6673 ACAACTTTTCAGAATTTACAACTTTACAGCA
1 ACAACTTTTCAG-ATTTACAACTTTACAGCA
6704 ATCTTCCGAC
Statistics
Matches: 121, Mismatches: 6, Indels: 18
0.83 0.04 0.12
Matches are distributed among these distances:
51 51 0.42
52 23 0.19
53 9 0.07
54 7 0.06
55 21 0.17
56 10 0.08
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.40
Consensus pattern (50 bp):
ACAACTTTTCAGATTTACAACTTTACAGCATTTCAACAACTTTTCGATTT
Found at i:6829 original size:47 final size:47
Alignment explanation
Indices: 6722--6973 Score: 369
Period size: 47 Copynumber: 5.3 Consensus size: 47
6712 ACTTAAGTCA
*
6722 GTCTTTCCTCACTTCCATGTGAGTCAGAAATCTTTTCGACCCAAGTTG
1 GTCTTTCCTCACTTCCATGTGAGTCAGAAATC-CTTCGACCCAAGTTG
* * *
6770 GTCTTTCCTCACTTCTATGTGAGTTAGAAATCCTTCAACCCAAGTTG
1 GTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTG
*
6817 GTCTTTCCTCACTTCCATGTGAGTCAGTAATCCTTCGACCCAAGTTG
1 GTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTG
*
6864 GTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCCACCCAAGTTG
1 GTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTT-CGACCCAAGTTG
* *** *
6912 GTGTTTCCTCACTTCCATGTGAGTCAGTGGTCCTTCGACCAAAGTTG
1 GTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTG
* *
6959 GTCTTTTCTAACTTC
1 GTCTTTCCTCACTTC
6974 TATGCAAAGT
Statistics
Matches: 184, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
47 112 0.61
48 72 0.39
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (47 bp):
GTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTG
Found at i:6910 original size:95 final size:94
Alignment explanation
Indices: 6722--6973 Score: 387
Period size: 95 Copynumber: 2.7 Consensus size: 94
6712 ACTTAAGTCA
* * *
6722 GTCTTTCCTCACTTCCATGTGAGTCAGAAATCTTTTCGACCCAAGTTGGTCTTTCCTCACTTCTA
1 GTCTTTCCTCACTTCCATGTGAGTCAGTAATC-CTTCGACCCAAGTTGGTCTTTCCTCACTTCCA
*
6787 TGTGAGTTAGAAATCCTTCAACCCAAGTTG
65 TGTGAGTCAGAAATCCTTCAACCCAAGTTG
6817 GTCTTTCCTCACTTCCATGTGAGTCAGTAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCCAT
1 GTCTTTCCTCACTTCCATGTGAGTCAGTAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCCAT
*
6882 GTGAGTCAGAAATCCTTCCCACCCAAGTTG
66 GTGAGTCAGAAATCCTT-CAACCCAAGTTG
* ** * * *
6912 GTGTTTCCTCACTTCCATGTGAGTCAGTGGTCCTTCGACCAAAGTTGGTCTTTTCTAACTTC
1 GTCTTTCCTCACTTCCATGTGAGTCAGTAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTC
6974 TATGCAAAGT
Statistics
Matches: 145, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
94 47 0.32
95 98 0.68
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (94 bp):
GTCTTTCCTCACTTCCATGTGAGTCAGTAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCCAT
GTGAGTCAGAAATCCTTCAACCCAAGTTG
Found at i:6999 original size:47 final size:47
Alignment explanation
Indices: 6948--7054 Score: 117
Period size: 47 Copynumber: 2.3 Consensus size: 47
6938 GTGGTCCTTC
* *
6948 GACCAAAGTTGGTCTTTTCTAACTTCTATGCAAAGT-TACAATTTAGT
1 GACCAAAGTTGGTCTTTCCTAACTTCCATGC-AAGTCTACAATTTAGT
* * ** * *
6995 GACCATAGTCGGTCTTTCCTCGCTTCCATGCGAGTCTACAATTTGGT
1 GACCAAAGTTGGTCTTTCCTAACTTCCATGCAAGTCTACAATTTAGT
*
7042 GACCACAGTTGGT
1 GACCAAAGTTGGT
7055 TTCCTTCCGC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
46 3 0.06
47 46 0.94
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (47 bp):
GACCAAAGTTGGTCTTTCCTAACTTCCATGCAAGTCTACAATTTAGT
Found at i:7009 original size:142 final size:141
Alignment explanation
Indices: 6699--7030 Score: 364
Period size: 142 Copynumber: 2.3 Consensus size: 141
6689 TACAACTTTA
** * * * *
6699 CAGCAATCTTCCGACTTAAGTCAGTCTTTCCTCACTTCCATGTGAGTCAGAAATCTTTTCGACCC
1 CAGCAATCTT-CGACCCAAGTCGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCCACCC
* * * *
6764 AAGTTGGTCTTTCCTCACTTCTATGTGAGTTAGAAATCCTTCAACCCAAGTTGGTCTTTCCTCAC
65 AAGTTGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCAACCAAAGTTGGTCTTTCCTAAC
**
6829 TTCCATGTGAGT
130 TTCCATGAAAGT
* *
6841 CAGTAATCCTTCGACCCAAGTTGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCCACCC
1 CAGCAAT-CTTCGACCCAAGTCGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCCACCC
* *** * *
6906 AAGTTGGTGTTTCCTCACTTCCATGTGAGTCAGTGGTCCTTCGACCAAAGTTGGTCTTTTCTAAC
65 AAGTTGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCAACCAAAGTTGGTCTTTCCTAAC
*
6971 TTCTATGCAAAGT
130 TTCCATG-AAAGT
* * * *
6984 TA-CAAT-TTAGTGA-CCATAGTCGGTCTTTCCTCGCTTCCATGCGAGTC
1 CAGCAATCTT--CGACCCA-AGTCGGTCTTTCCTCACTTCCATGTGAGTC
7031 TACAATTTGG
Statistics
Matches: 158, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
140 2 0.01
141 3 0.02
142 146 0.92
143 7 0.04
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (141 bp):
CAGCAATCTTCGACCCAAGTCGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCCACCCA
AGTTGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCAACCAAAGTTGGTCTTTCCTAACT
TCCATGAAAGT
Found at i:7333 original size:102 final size:102
Alignment explanation
Indices: 7193--7377 Score: 271
Period size: 102 Copynumber: 1.8 Consensus size: 102
7183 ACCACAGACT
* * * *
7193 CAGACTAGTCTTATTCAATTCCATACCTCAGACGGGTCTTTCTCAATGTCATTTATCAAAGTTGA
1 CAGACTAGTCTTATTCAATTCCAGACCTCAGACAGGTCTTTCTAAATGTCAATTATCAAAGTTGA
**
7258 CCTTGGACAGGTCCTTCTTAGTTTTTCATATCGACCA
66 CCTCAGACAGGTCCTTCTTAGTTTTTCATATCGACCA
* * * *
7295 CAGACTGGTCTTCTTCAATTCCAGACCTCATACAGGTCTTTCTAAATTTCAATTATCAAAGTTGA
1 CAGACTAGTCTTATTCAATTCCAGACCTCAGACAGGTCTTTCTAAATGTCAATTATCAAAGTTGA
*
7360 CCTCAGACAGGTCTTTCT
66 CCTCAGACAGGTCCTTCT
7378 CAATGTCAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 72 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (102 bp):
CAGACTAGTCTTATTCAATTCCAGACCTCAGACAGGTCTTTCTAAATGTCAATTATCAAAGTTGA
CCTCAGACAGGTCCTTCTTAGTTTTTCATATCGACCA
Found at i:7387 original size:33 final size:33
Alignment explanation
Indices: 7343--7457 Score: 90
Period size: 35 Copynumber: 3.3 Consensus size: 33
7333 TTTCTAAATT
7343 TCAATTATCAAAGTTGACCTCAGACAGGTCTTTC
1 TCAATT-TCAAAGTTGACCTCAGACAGGTCTTTC
* * * *
7377 TCAATGTCAAAAG-CGACCACAGACTGGTCTCTTTC
1 TCAATTTC-AAAGTTGACCTCAGACAGG--TCTTTC
* *
7412 TCAAATATTC-AATTTCAGACCTCAGACAAGTCTTTC
1 TC-AAT-TTCAAAGTT--GACCTCAGACAGGTCTTTC
7448 TCAATTTCAA
1 TCAATTTCAA
7458 TATTGGTCGC
Statistics
Matches: 62, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
33 13 0.21
34 12 0.19
35 14 0.23
36 11 0.18
37 2 0.03
38 10 0.16
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (33 bp):
TCAATTTCAAAGTTGACCTCAGACAGGTCTTTC
Found at i:7486 original size:61 final size:61
Alignment explanation
Indices: 7416--7578 Score: 245
Period size: 61 Copynumber: 2.7 Consensus size: 61
7406 TCTTTCTCAA
* * ** * *
7416 ATATTCAATTTCAGACCTCAGACAAGTCTTTCTCAATTTCAATATTGGTCGCAGATTGGTC
1 ATATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGAATGGTC
* *
7477 CTATTCAATTTCAGACCTTAGACAGGTCTTTCTCAATTTCAATATCGACCACAGAATGGTC
1 ATATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGAATGGTC
*
7538 ATATTCAATTTCAGACCTCAGACGGGTCTTTCTCAATTTCA
1 ATATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCA
7579 TTTATCAAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 91 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (61 bp):
ATATTCAATTTCAGACCTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGAATGGTC
Found at i:7513 original size:28 final size:28
Alignment explanation
Indices: 7481--7578 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 28
7471 TTGGTCCTAT
*
7481 TCAATTTCAGACCTTAGACAGGTCTTTC
1 TCAATTTCAGACCTCAGACAGGTCTTTC
* *
7509 TCAATTTCAATATCGACCACAGA-ATGGTCATAT-
1 TCAATTTC---A--GACCTCAGACA-GGTC-TTTC
*
7542 TCAATTTCAGACCTCAGACGGGTCTTTC
1 TCAATTTCAGACCTCAGACAGGTCTTTC
7570 TCAATTTCA
1 TCAATTTCA
7579 TTTATCAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
27 2 0.04
28 29 0.53
30 1 0.02
31 1 0.02
32 1 0.02
33 19 0.35
34 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (28 bp):
TCAATTTCAGACCTCAGACAGGTCTTTC
Found at i:7708 original size:61 final size:62
Alignment explanation
Indices: 7591--7711 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 62
7581 TATCAAAGTT
* * * * *
7591 GACCTCGGACAGGTCTTTCTTAGTTTTTCAAGTCGACCACGGAATGGTCTTCTTCAGTTTCA
1 GACCTCAGACAGGTCTTTCTCAGATTTTCAAGTCAACCACGGAATGGTCCTCTTCAGTTTCA
* *
7653 GACCTCAGACAGGTTTTTCTCA-ATTTT-AATGTCAACCACGGACTGGTCACT-TTCAGTTT
1 GACCTCAGACAGGTCTTTCTCAGATTTTCAA-GTCAACCACGGAATGGTC-CTCTTCAGTTT
7712 TAACATCACT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
60 2 0.04
61 28 0.56
62 20 0.40
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (62 bp):
GACCTCAGACAGGTCTTTCTCAGATTTTCAAGTCAACCACGGAATGGTCCTCTTCAGTTTCA
Found at i:8566 original size:21 final size:21
Alignment explanation
Indices: 8542--8583 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
8532 AAAGTTCTTG
* *
8542 CAAAATTGAGCTTGTCACCAA
1 CAAAATTGAACCTGTCACCAA
8563 CAAAATTGAACCTGTCACCAA
1 CAAAATTGAACCTGTCACCAA
8584 TATACATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (21 bp):
CAAAATTGAACCTGTCACCAA
Done.