Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010714.1 Corchorus capsularis cultivar CVL-1 contig10735, 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: 84509
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:946 original size:102 final size:102
Alignment explanation
Indices: 822--1126 Score: 386
Period size: 102 Copynumber: 3.0 Consensus size: 102
812 TTTGCTACAG
* * * *
822 ATTTTGCCACGAAATTAATTTTCGTGGCAAATTAAAATTTGAATTCCCGCTCGCTAAAGAATTTT
1 ATTTTGCAACGAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCGCTAAA-TATTTT
* *
887 GCGCCAAAATTAAA-TTTTGCAAC-GAAATTATTACGAA
65 GCGCCAAAA-TAAATTTTTGCAACGGAAATTACTACAAA
* * *
924 ATTTTGCAACGAATTTAGTTTTCGTAACAAATTAAATTTTGAATTCCCGCTC-CTTAAATATTTT
1 ATTTTGCAACGAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCGC-TAAATATTTT
988 GCGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
65 GCGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
* * * * *
1026 ATTTTGCAACG-ATTGTAACTTCCGTGACAAATTAAAATTCGAATTCCCGCTAGCCCAAATATTT
1 ATTTTGCAACGAATT-TAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCG-CTAAATATTT
*
1090 TGCGCCAAAA-AAATTTGTTCCAACGGAAATTACTACA
64 TGCGCCAAAATAAATTT-TTGCAACGGAAATTACTACA
1127 GAAAAAATCC
Statistics
Matches: 178, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
100 4 0.02
101 27 0.15
102 109 0.61
103 37 0.21
104 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (102 bp):
ATTTTGCAACGAATTTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCGCTAAATATTTTG
CGCCAAAATAAATTTTTGCAACGGAAATTACTACAAA
Found at i:8257 original size:1 final size:1
Alignment explanation
Indices: 8251--8294 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
8241 GTTGAGGGTG
8251 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8295 AATAATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11582 original size:28 final size:30
Alignment explanation
Indices: 11525--11583 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
11515 AAATCTAATC
11525 AAACTAGACATCCCACCGGCCAAAAGAAAAA
1 AAACTAGACAT-CCACCGGCCAAAAGAAAAA
*
11556 AAACTAGACAT-C-CCGGCCCAAA-AAAAA
1 AAACTAGACATCCACCGGCCAAAAGAAAAA
11583 A
1 A
11584 GAAGCTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 6 0.22
28 9 0.33
29 1 0.04
31 11 0.41
ACGTcount: A:0.53, C:0.29, G:0.12, T:0.07
Consensus pattern (30 bp):
AAACTAGACATCCACCGGCCAAAAGAAAAA
Found at i:11811 original size:2 final size:2
Alignment explanation
Indices: 11804--11852 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
11794 TTATTATTAT
* *
11804 TA TA TA TA TC TA TA TC 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 TA TA TA TA TA TA
11846 T- TA TA TA
1 TA TA TA TA
11853 AGTCTAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17455 original size:19 final size:19
Alignment explanation
Indices: 17433--17470 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17423 ACGTCTATAG
17433 TTTTTTTAGTAACCTAATT
1 TTTTTTTAGTAACCTAATT
17452 TTTTTTTAGTAACCTAATT
1 TTTTTTTAGTAACCTAATT
17471 AGATGTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTTTAGTAACCTAATT
Found at i:18296 original size:25 final size:24
Alignment explanation
Indices: 18268--18326 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
18258 TTCGAACCCT
*
18268 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
*
18293 AAACTTCATTTTTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
18317 AAA-TTCATTT
1 AAACTTCATTT
18327 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 8 0.25
25 17 0.53
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:18365 original size:26 final size:26
Alignment explanation
Indices: 18336--18403 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
18326 TTCCTTCATT
18336 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
18362 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
18388 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
18404 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:18567 original size:32 final size:33
Alignment explanation
Indices: 18514--18602 Score: 135
Period size: 32 Copynumber: 2.7 Consensus size: 33
18504 TTAAAAAAAA
* * *
18514 GCCTTGCCCTTGGTTAGCCGCCCAAGCTGGGCG
1 GCCTTGACCATGGCTAGCCGCCCAAGCTGGGCG
18547 GCCTTG-CCATGGCTAGCCGCCCAAGCTGGGCG
1 GCCTTGACCATGGCTAGCCGCCCAAGCTGGGCG
*
18579 GCCTTGACCATGGCTAGCCACCCA
1 GCCTTGACCATGGCTAGCCGCCCA
18603 GTTTAGGCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 30 0.58
33 22 0.42
ACGTcount: A:0.13, C:0.38, G:0.30, T:0.18
Consensus pattern (33 bp):
GCCTTGACCATGGCTAGCCGCCCAAGCTGGGCG
Found at i:18830 original size:21 final size:21
Alignment explanation
Indices: 18801--18845 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18791 CAAAAATTAT
**
18801 AAAAAGGGGGCGGTATTTAGC
1 AAAAAGGGGGCGGTAAATAGC
*
18822 AAAAGGGGGGCGGTAAATAGC
1 AAAAAGGGGGCGGTAAATAGC
18843 AAA
1 AAA
18846 CCCCATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.38, T:0.13
Consensus pattern (21 bp):
AAAAAGGGGGCGGTAAATAGC
Found at i:20020 original size:25 final size:25
Alignment explanation
Indices: 19971--20021 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
19961 TTAGTAGAAT
*
19971 AATTGTAAAAATTTATTTCTAAAAA
1 AATTGTAAAAATATATTTCTAAAAA
19996 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGT-AAA-AATATATTTCTAAAAA
20022 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 9 0.39
27 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAATATATTTCTAAAAA
Found at i:20733 original size:2 final size:2
Alignment explanation
Indices: 20726--20767 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
20716 CTCGTACTTT
20726 TA TA TA TA GTA TA 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 TA TA TA TA TA TA T
20768 TAGTAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21814 original size:22 final size:22
Alignment explanation
Indices: 21699--21905 Score: 82
Period size: 22 Copynumber: 9.4 Consensus size: 22
21689 ATAACCATAT
* *
21699 TATGAAATTTTGATAA-TTACCC
1 TATGAAATTTTGATAACCT-CCA
* ** * *
21721 TATGAAATTGTGATAAATTTCT
1 TATGAAATTTTGATAACCTCCA
* * *
21743 TATAAAACTTTGATAACCT-AA
1 TATGAAATTTTGATAACCTCCA
* * * *
21764 TTTTGAAATTTTAATAAAACTTCA
1 -TATGAAATTTTGAT-AACCTCCA
21788 TATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCA
** *
21810 TATGATTTTTTTATAACCTTCC-
1 TATGAAATTTTGATAACC-TCCA
* * *
21832 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCA
* * **
21854 TAT-ACATTTTTGATACCCTAGA
1 TATGA-AATTTTGATAACCTCCA
* * **
21876 -ATGAAATTTCGATAATCTCTT
1 TATGAAATTTTGATAACCTCCA
21897 TATGAAATT
1 TATGAAATT
21906 ATATATCATT
Statistics
Matches: 134, Mismatches: 42, Indels: 18
0.69 0.22 0.09
Matches are distributed among these distances:
21 16 0.12
22 96 0.72
23 21 0.16
24 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:24260 original size:27 final size:26
Alignment explanation
Indices: 24206--24266 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
24196 CTAAATTTCC
24206 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
24234 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
24261 -TTATTT
1 ATTATTT
24267 GAAAAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 9 0.29
27 15 0.48
28 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:37565 original size:35 final size:35
Alignment explanation
Indices: 37490--37565 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
37480 ATAGTGAGAT
* * **
37490 TAAAAAAAAAAAACCAAACCCATAAAGTCTGGCAA
1 TAAAAAAAAAAAAACAAACCCATAAACTCTAACAA
* *
37525 AAAAAAAAAAAAAACAAATCCATAAACT-TAACAA
1 TAAAAAAAAAAAAACAAACCCATAAACTCTAACAA
37559 CTAAAAA
1 -TAAAAA
37566 CTTATCATAC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 4 0.12
35 29 0.88
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.12
Consensus pattern (35 bp):
TAAAAAAAAAAAAACAAACCCATAAACTCTAACAA
Found at i:37565 original size:36 final size:35
Alignment explanation
Indices: 37491--37558 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
37481 TAGTGAGATT
* * **
37491 AAAAAAAAAAAACCAAACCCATAAAGTCTGGCAAA
1 AAAAAAAAAAAAACAAACCCATAAACTCTAACAAA
*
37526 AAAAAAAAAAAAACAAATCCATAAACT-TAACAA
1 AAAAAAAAAAAAACAAACCCATAAACTCTAACAA
37559 CTAAAAACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.68, C:0.18, G:0.04, T:0.10
Consensus pattern (35 bp):
AAAAAAAAAAAAACAAACCCATAAACTCTAACAAA
Found at i:53509 original size:1 final size:1
Alignment explanation
Indices: 53505--53539 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
53495 GGGGGTTTGC
53505 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53540 CAGAAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:61708 original size:12 final size:12
Alignment explanation
Indices: 61693--61729 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
61683 GCAAAGCCAC
61693 CGGCAACGGCAG
1 CGGCAACGGCAG
61705 CGGCAACGGCAG
1 CGGCAACGGCAG
*
61717 CGGCAACAGCAG
1 CGGCAACGGCAG
61729 C
1 C
61730 CCCTCTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (12 bp):
CGGCAACGGCAG
Found at i:68317 original size:101 final size:100
Alignment explanation
Indices: 68137--68327 Score: 226
Period size: 101 Copynumber: 1.9 Consensus size: 100
68127 GTAATGCCTA
* * * *
68137 AAAATGTTAGAATCAATCAACTTATACAATTTGTGATGCCTGAAATTGTTAGAATAGGCCAACAG
1 AAAATGTTAGAATCAATCAACTTATACAATTTGTAACGCCTGAAATTGTTAGAATAGACCAACAA
*
68202 TACACAATCCGTAACGCATGAAAAATAATTAGCATG
66 TACACAATACGTAACGCAT-AAAAATAATTAGCATG
* * * *
68238 AAAATGTTAGAATGAGTTAAC-TAGTACAATTTGTAACGCTTGAAATTGTTAGAATCA-ACCAAT
1 AAAATGTTAGAATCAATCAACTTA-TACAATTTGTAACGCCTGAAATTGTTAGAAT-AGACCAA-
* *
68301 CAATACA-AATATGTAACGTATAAAAAT
63 CAATACACAATACGTAACGCATAAAAAT
68328 TAGCTAACCA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
100 8 0.11
101 61 0.80
102 7 0.09
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (100 bp):
AAAATGTTAGAATCAATCAACTTATACAATTTGTAACGCCTGAAATTGTTAGAATAGACCAACAA
TACACAATACGTAACGCATAAAAATAATTAGCATG
Found at i:68425 original size:42 final size:41
Alignment explanation
Indices: 68325--68456 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 41
68315 AACGTATAAA
* * * *
68325 AATTAGCTAACCAGTACAAGTTGCAACACCTAAAACTGTTGG
1 AATTAGCCAACCAGTACAATTTGTAACACCTAAAA-TGTTAG
* * * * * *
68367 GATCAGTCAACAAGTACAATTTGTAACGCCTGAAAATGTTAC
1 AATTAGCCAACCAGTACAATTTGTAACACCT-AAAATGTTAG
*
68409 AATTAGCCAACCAGTACAATCTGTAACACCTATAAATGTTAG
1 AATTAGCCAACCAGTACAATTTGTAACACCTA-AAATGTTAG
68451 AATTAG
1 AATTAG
68457 GCAATTAGCC
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
41 1 0.01
42 66 0.93
43 4 0.06
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (41 bp):
AATTAGCCAACCAGTACAATTTGTAACACCTAAAATGTTAG
Found at i:68623 original size:42 final size:42
Alignment explanation
Indices: 68560--68639 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
68550 GAACCATTCC
* * *
68560 GTACAATCTGTAACGCCTGAAAATGTTAAAATTTGCCAACTA
1 GTACAATCTGTAACACATGAAAATGTTAAAATTAGCCAACTA
* * *
68602 GTACAATCTGTAACATATGAAATTGTTAGAATTAGCCA
1 GTACAATCTGTAACACATGAAAATGTTAAAATTAGCCA
68640 GTCAAAACAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (42 bp):
GTACAATCTGTAACACATGAAAATGTTAAAATTAGCCAACTA
Found at i:76635 original size:42 final size:43
Alignment explanation
Indices: 76554--76636 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 43
76544 ATCAACAAGA
* * *
76554 AGTACAATTTGGTAATGCCTGAAATTGTTAGAATTAGCCAATT
1 AGTACAATTTGGTAACGCCTGAAATTGTTAAAATCAGCCAATT
* * *
76597 AGTACAATTT-TTAACGCTTGAATTTGTTAAAATCAGCCAA
1 AGTACAATTTGGTAACGCCTGAAATTGTTAAAATCAGCCAA
76637 CCAAACAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 24 0.71
43 10 0.29
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (43 bp):
AGTACAATTTGGTAACGCCTGAAATTGTTAAAATCAGCCAATT
Found at i:77484 original size:42 final size:42
Alignment explanation
Indices: 77431--77571 Score: 176
Period size: 42 Copynumber: 3.4 Consensus size: 42
77421 ACCTAACCAC
*
77431 TACAATATGTAACGCCTAAAAATGTTAGAATTAGCCAAAT-G
1 TACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAATAG
77472 ATACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAATAG
1 -TACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAATAG
* * ** * * *
77515 TACAATTTGTAACGCTTGAAAATACTAGAATCAACCAACTAG
1 TACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAATAG
**
77557 TACAACCTGTAACGC
1 TACAATTTGTAACGC
77572 GTGAAAATCA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 87 0.99
43 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (42 bp):
TACAATTTGTAACGCCTAAAAATGTTAGAATTAGCCAAATAG
Found at i:77613 original size:34 final size:34
Alignment explanation
Indices: 77543--77615 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
77533 AAAATACTAG
* * * *
77543 AATCAACCAACTAGTACAACCTGTAACGCGTGAA
1 AATCAACCAACCAGTACAACCTGTAACACATAAA
* **
77577 AATCAACCAACCGGTACAATTTGTAACACATAAA
1 AATCAACCAACCAGTACAACCTGTAACACATAAA
77611 AATCA
1 AATCA
77616 GCAAAGCAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.19
Consensus pattern (34 bp):
AATCAACCAACCAGTACAACCTGTAACACATAAA
Found at i:77858 original size:71 final size:72
Alignment explanation
Indices: 77779--77958 Score: 238
Period size: 72 Copynumber: 2.5 Consensus size: 72
77769 TCTGACAAAT
* * * *
77779 AATACAATATGTAATGCCTG-AAATCAACTAACCAGTAAAATTTGTAATGCTTCAAAATGCATCA
1 AATACAATATGTAATGCATGAAAATCAACCAACCAATAAAATTTATAATGCTTCAAAATGCATCA
77843 CCCAACC
66 CCCAACC
* * * *
77850 ATTACAATATTTAATGCATGAAAATCAACCAACCAATAAAATTTATAATTCTTGAAAATGCATCA
1 AATACAATATGTAATGCATGAAAATCAACCAACCAATAAAATTTATAATGCTTCAAAATGCATCA
*
77915 CCCAACT
66 CCCAACC
* * *
77922 AATA-AATTTGTAATGCATAAAAATCAGCCAACCAATA
1 AATACAATATGTAATGCATGAAAATCAACCAACCAATA
77959 GTATGTAATG
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 46 0.49
72 48 0.51
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.27
Consensus pattern (72 bp):
AATACAATATGTAATGCATGAAAATCAACCAACCAATAAAATTTATAATGCTTCAAAATGCATCA
CCCAACC
Found at i:77865 original size:38 final size:38
Alignment explanation
Indices: 77808--77937 Score: 128
Period size: 38 Copynumber: 3.6 Consensus size: 38
77798 GAAATCAACT
* * *
77808 AACCAGTAAAATTTGTAATGCTTCAAAATGCATCACCC
1 AACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
* * *
77846 AACCATTACAATATT-TAATGCATGAAAAT-CA--A-CC
1 AACCAATAAAAT-TTATAATGCTTGAAAATGCATCACCC
*
77880 AACCAATAAAATTTATAATTCTTGAAAATGCATCACCC
1 AACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
* *
77918 AACTAAT-AAATTTGTAATGC
1 AACCAATAAAATTTATAATGC
77938 ATAAAAATCA
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
33 2 0.03
34 24 0.32
35 3 0.04
37 14 0.19
38 30 0.40
39 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (38 bp):
AACCAATAAAATTTATAATGCTTGAAAATGCATCACCC
Found at i:78259 original size:42 final size:43
Alignment explanation
Indices: 78181--78271 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 43
78171 ATTGCTCGCT
* * *
78181 TGAAAATGTATAAAATTAACCAACCACTACATTTTGTAACGCA
1 TGAAAATATATAAAATCAACCAACCACTACAATTTGTAACGCA
* * * *
78224 TGAAAATAT-TAAAATCAACTAACTAGTACAATTTGTAACGTA
1 TGAAAATATATAAAATCAACCAACCACTACAATTTGTAACGCA
78266 TGAAAA
1 TGAAAA
78272 ACAATCAACA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 33 0.80
43 8 0.20
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (43 bp):
TGAAAATATATAAAATCAACCAACCACTACAATTTGTAACGCA
Found at i:78386 original size:42 final size:42
Alignment explanation
Indices: 78324--78426 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
78314 TTGACCAATG
* * * *
78324 CAATATGTAACACCTAAAAATGTTAGAAATAACCAAACGGTA
1 CAATTTGTAACGCCTGAAAATATTAGAAATAACCAAACGGTA
* * **
78366 CACTTTGTAACGCCTGAAAATATTAGAATTAGTCAAACGGTA
1 CAATTTGTAACGCCTGAAAATATTAGAAATAACCAAACGGTA
*
78408 CAATTTGTAACGCTTGAAA
1 CAATTTGTAACGCCTGAAA
78427 TTGCTAGAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (42 bp):
CAATTTGTAACGCCTGAAAATATTAGAAATAACCAAACGGTA
Found at i:78757 original size:114 final size:116
Alignment explanation
Indices: 78556--78764 Score: 296
Period size: 114 Copynumber: 1.8 Consensus size: 116
78546 TCGGCTAGCC
* * * *
78556 AATACAATATGTGTAACGCATGAAAATCAGCCAACTAGTACAATCAATAACTGCCAGAATATGCA
1 AATACAATATATGTAACGCATGAAAATCAACCAACTAGTACAATCAATAACTACCAGAAAATGCA
*
78621 TCACCTAACCAATACAATATGTAACGCATGGAAGGTTAGAATATGACAAAT
66 TCACCCAACCAATACAATATGTAACGCATGGAAGGTTAGAATATGACAAAT
* * *** **
78672 AATACAATATATGTAATGCCTG-AAATCAACCAACTAGTACAATTTGTAAC-ACTTGAAAATGCA
1 AATACAATATATGTAACGCATGAAAATCAACCAACTAGTACAATCAATAACTACCAGAAAATGCA
78735 TCACCCAACCAATACAATATGTAACGCATG
66 TCACCCAACCAATACAATATGTAACGCATG
78765 AAAATCAACC
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
114 38 0.47
115 24 0.30
116 19 0.23
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (116 bp):
AATACAATATATGTAACGCATGAAAATCAACCAACTAGTACAATCAATAACTACCAGAAAATGCA
TCACCCAACCAATACAATATGTAACGCATGGAAGGTTAGAATATGACAAAT
Found at i:78772 original size:72 final size:72
Alignment explanation
Indices: 78680--78852 Score: 188
Period size: 72 Copynumber: 2.4 Consensus size: 72
78670 ATAATACAAT
* * ** * *
78680 ATATGTAATGCCTG-AAATCAACCAACTAGTACAATTTGTAACACTTGAAAATGCATCA-CCCAA
1 ATATGTAATGCATGAAAATCAACCAACCAACAAAATTTATAACACTTGAAAATGCAT-AGCCCAA
78743 CCAATACA
65 CCAATACA
* **
78751 ATATGTAACGCATGAAAATCAACCAACCAACAAAATTTATAATGCTTGAAAATGCATAGCCCAAC
1 ATATGTAATGCATGAAAATCAACCAACCAACAAAATTTATAACACTTGAAAATGCATAGCCCAAC
* *
78816 TAGTACA
66 CAATACA
* * * *
78823 ATTTGTAATGCATAAAAATCAGCCAGCCAA
1 ATATGTAATGCATGAAAATCAACCAACCAA
78853 TACAATATGT
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
71 13 0.15
72 71 0.85
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.23
Consensus pattern (72 bp):
ATATGTAATGCATGAAAATCAACCAACCAACAAAATTTATAACACTTGAAAATGCATAGCCCAAC
CAATACA
Found at i:78833 original size:38 final size:37
Alignment explanation
Indices: 78709--78830 Score: 124
Period size: 38 Copynumber: 3.3 Consensus size: 37
78699 AACCAACTAG
*
78709 TACAATTTGTAACACTTGAAAATGCATCACCCAACCAA
1 TACAATTTGTAACGCTTGAAAATGCAT-ACCCAACCAA
* *
78747 TACAATATGTAACGCATGAAAAT-CA-A-CCAACCAA
1 TACAATTTGTAACGCTTGAAAATGCATACCCAACCAA
* * * * * *
78781 CAAAATTTATAATGCTTGAAAATGCATAGCCCAACTAG
1 TACAATTTGTAACGCTTGAAAATGCATA-CCCAACCAA
78819 TACAATTTGTAA
1 TACAATTTGTAA
78831 TGCATAAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
34 25 0.38
35 3 0.05
36 1 0.02
37 2 0.03
38 35 0.53
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (37 bp):
TACAATTTGTAACGCTTGAAAATGCATACCCAACCAA
Found at i:78841 original size:38 final size:37
Alignment explanation
Indices: 78709--78867 Score: 123
Period size: 38 Copynumber: 4.4 Consensus size: 37
78699 AACCAACTAG
* *
78709 TACAATTTGTAACACTTGAAAATGCATCACCCAACCAA
1 TACAATTTGTAACGCATGAAAATGCAT-ACCCAACCAA
*
78747 TACAATATGTAACGCATGAAAAT-CA-A-CCAACCAA
1 TACAATTTGTAACGCATGAAAATGCATACCCAACCAA
* * * * * * *
78781 CAAAATTTATAATGCTTGAAAATGCATAGCCCAACTAG
1 TACAATTTGTAACGCATGAAAATGCATA-CCCAACCAA
* * * *
78819 TACAATTTGTAATGCATAAAAAT-C--AGCCAGCCAA
1 TACAATTTGTAACGCATGAAAATGCATACCCAACCAA
*
78853 TACAATATGTAACGC
1 TACAATTTGTAACGC
78868 CTAGGACTGC
Statistics
Matches: 95, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
34 43 0.45
35 4 0.04
36 1 0.01
37 3 0.03
38 44 0.46
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.23
Consensus pattern (37 bp):
TACAATTTGTAACGCATGAAAATGCATACCCAACCAA
Found at i:79657 original size:33 final size:34
Alignment explanation
Indices: 79601--79664 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
79591 CTTAAATACA
* **
79601 ATCCTAGAAAAAAAAATGTAAGCATAACCTTTCC
1 ATCCAAGAAAAAAAAATACAAGCATAACCTTTCC
*
79635 ATCCAAGAAAAAAAAA-ACAAGCATATCCTT
1 ATCCAAGAAAAAAAAATACAAGCATAACCTT
79665 AAATTCAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.42
34 15 0.58
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (34 bp):
ATCCAAGAAAAAAAAATACAAGCATAACCTTTCC
Found at i:83252 original size:35 final size:37
Alignment explanation
Indices: 83212--83297 Score: 133
Period size: 37 Copynumber: 2.4 Consensus size: 37
83202 ATAATATCGG
83212 TACAATTTGTAACGCCTATAA-C-A-ATAACCAATCAA
1 TACAATTTGTAACGCCTA-AAGCAATATAACCAATCAA
*
83247 TACAATTTGTAACGCCTAAAGCAATATAACCATTCAA
1 TACAATTTGTAACGCCTAAAGCAATATAACCAATCAA
83284 TACAATTTGTAACG
1 TACAATTTGTAACG
83298 TTTAGTTACA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
34 2 0.04
35 19 0.40
36 1 0.02
37 25 0.53
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (37 bp):
TACAATTTGTAACGCCTAAAGCAATATAACCAATCAA
Found at i:84448 original size:2 final size:2
Alignment explanation
Indices: 84441--84509 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
84431 ATATTTACAG
84441 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
84483 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.