Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012654.1 Corchorus capsularis cultivar CVL-1 contig12675, 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: 97057
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:640 original size:23 final size:22
Alignment explanation
Indices: 588--649 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 22
578 CTTTATCTAC
588 TTGGGCTTGGTCTTTTTATTAGTA
1 TTGGGCTT--TCTTTTTATTAGTA
612 TGTGGGCTTTCTTTTATATATA-TA
1 T-TGGGCTTTCTTTT-TAT-TAGTA
*
636 TTGGGTTTTACTTT
1 TTGGGCTTT-CTTT
650 GTTTGCTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 13 0.39
24 11 0.33
25 9 0.27
ACGTcount: A:0.15, C:0.08, G:0.21, T:0.56
Consensus pattern (22 bp):
TTGGGCTTTCTTTTTATTAGTA
Found at i:1274 original size:105 final size:104
Alignment explanation
Indices: 1130--1405 Score: 392
Period size: 105 Copynumber: 2.6 Consensus size: 104
1120 ATGAATCAGT
*
1130 AATAATTAACTTAATTCAGGGTAATTAAGTAGATCAGTAAATAACTTAATTCAGGGTAATTAAGT
1 AATAATCAACTTAATTCAGGGTAATTAAGTAGATCAGT-AATAACTTAATTCAGGGTAATTAAGT
*
1195 TAGCCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGCC
65 TAGCCAGTAATCAACTTAATTCAAGGTAATTAAGTAAGCC
* *
1235 AGTAATCAACTTAATTCAGGGTAATTAAGTA-AGCCAGTAATCAACTTAATTCAGGGTAATTAAG
1 AATAATCAACTTAATTCAGGGTAATTAAGTAGA-TCAGTAAT-AACTTAATTCAGGGTAATTAAG
* * **
1299 TGAGTCAGTAATCAACTTAATTCAAGGTAATTAAGTAATTC
64 TTAGCCAGTAATCAACTTAATTCAAGGTAATTAAGTAAGCC
* * * * *
1340 AATAATCAACTTAATTCAGGGTAATTAAGTAGTTCAATGAGTAACTTAATTCGGGGAAATTAAGT
1 AATAATCAACTTAATTCAGGGTAATTAAGTAGATCAGT-AATAACTTAATTCAGGGTAATTAAGT
1405 T
65 T
1406 TAGTAAGAAG
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
104 4 0.03
105 145 0.96
106 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (104 bp):
AATAATCAACTTAATTCAGGGTAATTAAGTAGATCAGTAATAACTTAATTCAGGGTAATTAAGTT
AGCCAGTAATCAACTTAATTCAAGGTAATTAAGTAAGCC
Found at i:1376 original size:35 final size:34
Alignment explanation
Indices: 1132--1404 Score: 352
Period size: 35 Copynumber: 7.8 Consensus size: 34
1122 GAATCAGTAA
*
1132 TAATTAACTTAATTCAGGGTAATTAAGTAGATCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAG-TCAG
*
1167 TAAAT-AACTTAATTCAGGGTAATTAAGTTAGCCAG
1 T-AATCAACTTAATTCAGGGTAATTAAG-TAGTCAG
*
1202 TAATCAACTTAATTCAGGGTAATTAAGTAAGCCAG
1 TAATCAACTTAATTCAGGGTAATTAAGT-AGTCAG
*
1237 TAATCAACTTAATTCAGGGTAATTAAGTAAGCCAG
1 TAATCAACTTAATTCAGGGTAATTAAGT-AGTCAG
1272 TAATCAACTTAATTCAGGGTAATTAAGTGAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGT-AGTCAG
* * *
1307 TAATCAACTTAATTCAAGGTAATTAAGTAATTCAA
1 TAATCAACTTAATTCAGGGTAATTAAGT-AGTCAG
*
1342 TAATCAACTTAATTCAGGGTAATTAAGTAGTTCAA
1 TAATCAACTTAATTCAGGGTAATTAAGTAG-TCAG
* * *
1377 TGAGT-AACTTAATTCGGGGAAATTAAGT
1 T-AATCAACTTAATTCAGGGTAATTAAGT
1405 TTAGTAAGAA
Statistics
Matches: 220, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
34 5 0.02
35 207 0.94
36 8 0.04
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (34 bp):
TAATCAACTTAATTCAGGGTAATTAAGTAGTCAG
Found at i:4590 original size:19 final size:19
Alignment explanation
Indices: 4553--4589 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4543 CCTATGAAAT
*
4553 TCCAAAAAATTTTTCAAAA
1 TCCAAAAAATTCTTCAAAA
4572 TCCAAAAAA-TCTTCAAAA
1 TCCAAAAAATTCTTCAAAA
4590 AACATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (19 bp):
TCCAAAAAATTCTTCAAAA
Found at i:9726 original size:21 final size:21
Alignment explanation
Indices: 9702--9746 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
9692 CCATAAAAAA
9702 AAAGGAAAAATAATGGTCTGC
1 AAAGGAAAAATAATGGTCTGC
*
9723 AAA-GAAAAATAATGGTCTGT
1 AAAGGAAAAATAATGGTCTGC
9743 AAAG
1 AAAG
9747 TTATCATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.51, C:0.07, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAGGAAAAATAATGGTCTGC
Found at i:9893 original size:92 final size:92
Alignment explanation
Indices: 9736--9974 Score: 460
Period size: 92 Copynumber: 2.6 Consensus size: 92
9726 GAAAAATAAT
* *
9736 GGTCTGTAAAGTTATCATGAAGAATCTCTGCAGATATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
9801 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
9828 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
9893 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
9920 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
9975 TAGTACAAAG
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 145 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.26
Consensus pattern (92 bp):
GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
TGGATGAAGAGAAAGCCAAATTATGAA
Found at i:14916 original size:47 final size:47
Alignment explanation
Indices: 14845--14940 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
14835 CCTTGGCGGG
*
14845 AAAAATCCCGCCCAAAATATAAAAAAAACGGAGAAAATAAAAAAGAA
1 AAAAATCCCGCCCAAAATAAAAAAAAAACGGAGAAAATAAAAAAGAA
* **
14892 AAAAATCCCGCCTAAAATAAAAAAAAAACTTAGAAAATAAAAAAGAA
1 AAAAATCCCGCCCAAAATAAAAAAAAAACGGAGAAAATAAAAAAGAA
14939 AA
1 AA
14941 TAGAAAAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.68, C:0.14, G:0.08, T:0.10
Consensus pattern (47 bp):
AAAAATCCCGCCCAAAATAAAAAAAAAACGGAGAAAATAAAAAAGAA
Found at i:14949 original size:20 final size:19
Alignment explanation
Indices: 14905--14947 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
14895 AATCCCGCCT
14905 AAAATAAAAAAAAAACTTAG
1 AAAATAAAAAAAAAAC-TAG
14925 AAAATAAAAAAGAAAA-TAG
1 AAAATAAAAAA-AAAACTAG
14944 AAAA
1 AAAA
14948 ATCGAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAATAAAAAAAAAACTAG
Found at i:15321 original size:6 final size:6
Alignment explanation
Indices: 15310--15347 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
15300 TTTTTCATAG
15310 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GG
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GG
15348 CTGTAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GGAGGT
Found at i:16573 original size:10 final size:10
Alignment explanation
Indices: 16558--16610 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
16548 TGGAGGACCT
16558 TTGCTTGAGC
1 TTGCTTGAGC
16568 TTGCTTGAGC
1 TTGCTTGAGC
* *
16578 -AG---GACC
1 TTGCTTGAGC
16584 TTTGCTTGAGC
1 T-TGCTTGAGC
16595 TTGCTTGAGC
1 TTGCTTGAGC
16605 TTGCTT
1 TTGCTT
16611 CTTTCGAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
6 3 0.09
8 1 0.03
9 1 0.03
10 25 0.74
11 4 0.12
ACGTcount: A:0.11, C:0.21, G:0.28, T:0.40
Consensus pattern (10 bp):
TTGCTTGAGC
Found at i:16584 original size:27 final size:27
Alignment explanation
Indices: 16551--16604 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
16541 TGCTTATTGG
16551 AGGACCTTTGCTTGAGCTTGCTTGAGC
1 AGGACCTTTGCTTGAGCTTGCTTGAGC
16578 AGGACCTTTGCTTGAGCTTGCTTGAGC
1 AGGACCTTTGCTTGAGCTTGCTTGAGC
16605 TTGCTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (27 bp):
AGGACCTTTGCTTGAGCTTGCTTGAGC
Found at i:19069 original size:21 final size:21
Alignment explanation
Indices: 19045--19087 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
19035 ACAGAAACAC
*
19045 CATTTACATTTTCAGCAGCCT
1 CATTTACATCTTCAGCAGCCT
19066 CATTTACATCTTCAGCAGCCT
1 CATTTACATCTTCAGCAGCCT
19087 C
1 C
19088 TACCCCCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.09, T:0.35
Consensus pattern (21 bp):
CATTTACATCTTCAGCAGCCT
Found at i:20383 original size:36 final size:37
Alignment explanation
Indices: 20337--20406 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
20327 CTCTCTTTTT
*
20337 CCCTCTCTTTTTAGCTTTAGCCCTAAATCGATTTCCC
1 CCCTCTCTTTTTAGCTTTAGACCTAAATCGATTTCCC
20374 CCCT-TCTTTTTAGCTTTAGACCTAAATCGATTT
1 CCCTCTCTTTTTAGCTTTAGACCTAAATCGATTT
20407 TGTCTTTCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.43
Consensus pattern (37 bp):
CCCTCTCTTTTTAGCTTTAGACCTAAATCGATTTCCC
Found at i:20498 original size:3 final size:3
Alignment explanation
Indices: 20490--20553 Score: 101
Period size: 3 Copynumber: 20.7 Consensus size: 3
20480 CGATTTACTT
20490 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA
*
20537 TTA GTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
20554 TTTCTTTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
3 51 0.89
4 6 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:22085 original size:27 final size:28
Alignment explanation
Indices: 22046--22109 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
22036 CTTTTTTAAA
*
22046 AAAAGTATATTTTTAAAT-TGTCATTATC
1 AAAA-TATATTTTTAAATATGCCATTATC
* *
22074 AAAATATA-TTTTAATTATGCCATTATT
1 AAAATATATTTTTAAATATGCCATTATC
22101 AAAATATAT
1 AAAATATAT
22110 AAAATTGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 7 0.23
27 20 0.65
28 4 0.13
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (28 bp):
AAAATATATTTTTAAATATGCCATTATC
Found at i:23508 original size:22 final size:22
Alignment explanation
Indices: 23460--23648 Score: 111
Period size: 22 Copynumber: 8.6 Consensus size: 22
23450 TTGACTCTTG
* * *
23460 TGTTGTCAAAATTTTATAATGA
1 TGTTATCAAAATTTCATAACGA
* * ** *
23482 GGTTATCGAAATTTCATAGTGT
1 TGTTATCAAAATTTCATAACGA
*
23504 TGTTATCAAAATTTCACAACGA
1 TGTTATCAAAATTTCATAACGA
23526 TGTTATCAAAATTTCATAA-GAA
1 TGTTATCAAAATTTCATAACG-A
* * * * **
23548 AGTTCTCACAATTTCACAGTG-
1 TGTTATCAAAATTTCATAACGA
23569 TGGTTATCAAAATTTCAT-A-GTA
1 T-GTTATCAAAATTTCATAACG-A
**
23591 TGATTA-CGAAAATTTCATAAAAA
1 TG-TTATC-AAAATTTCATAACGA
* *
23614 GGTTATCAAAATTTCATAA-TA
1 TGTTATCAAAATTTCATAACGA
23635 TGGTTATCAAAATT
1 T-GTTATCAAAATT
23649 CAAAATTTCA
Statistics
Matches: 129, Mismatches: 27, Indels: 22
0.72 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 4 0.03
22 119 0.92
23 5 0.04
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TGTTATCAAAATTTCATAACGA
Found at i:23531 original size:44 final size:44
Alignment explanation
Indices: 23460--23648 Score: 141
Period size: 44 Copynumber: 4.3 Consensus size: 44
23450 TTGACTCTTG
* * * * *
23460 TGTTGTCAAAATTTTATAATGAGGTTATCGAAATTTCATAGTGT
1 TGTTATCAAAATTTCACAACGAGGTTATCAAAATTTCATAGTGT
* **
23504 TGTTATCAAAATTTCACAACGATGTTATCAAAATTTCATAAG-AA
1 TGTTATCAAAATTTCACAACGAGGTTATCAAAATTTCAT-AGTGT
* * * ** * *
23548 AGTTCTCACAATTTCACAGTGTGGTTATCAAAATTTCATAGT-A
1 TGTTATCAAAATTTCACAACGAGGTTATCAAAATTTCATAGTGT
* ** * *
23591 TGATTA-CGAAAATTTCATAAAAAGGTTATCAAAATTTCATAATAT
1 TG-TTATC-AAAATTTCACAACGAGGTTATCAAAATTTCATAGTGT
*
23636 GGTTATCAAAATT
1 TGTTATCAAAATT
23649 CAAAATTTCA
Statistics
Matches: 113, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
43 5 0.04
44 104 0.92
45 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (44 bp):
TGTTATCAAAATTTCACAACGAGGTTATCAAAATTTCATAGTGT
Found at i:23575 original size:66 final size:66
Alignment explanation
Indices: 23467--23652 Score: 202
Period size: 66 Copynumber: 2.8 Consensus size: 66
23457 TTGTGTTGTC
* ** * *
23467 AAAATTTTATAATGAGGTTATCGAAATTTCATAGTGTTGTTATCAAAATTTCACAACG-ATG-TT
1 AAAATTTCATAAAAAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCA-AA-GTATGATT
23530 ATC-
64 A-CG
* * * *
23533 AAAATTTCATAAGAAA-GTTCTCACAATTTCACAGTGTGGTTATCAAAATTTCATAGTATGATTA
1 AAAATTTCATAA-AAAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAAAGTATGATTA
23597 CG
65 CG
* *
23599 AAAATTTCATAAAAAGGTTATCAAAATTTCATAATATGGTTATCAAAA-TTCAAA
1 AAAATTTCATAAAAAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAAA
23653 ATTTCATGTT
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
64 1 0.01
65 13 0.13
66 85 0.85
67 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (66 bp):
AAAATTTCATAAAAAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCAAAGTATGATTAC
G
Found at i:23674 original size:29 final size:29
Alignment explanation
Indices: 23619--23677 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
23609 AAAAAGGTTA
* * *
23619 TCAAAATTTCATAATATGGTTATCAAAAT
1 TCAAAATTTCATAATAAGATTACCAAAAT
**
23648 TCAAAATTTCATGTTAAGATTACCAAAAT
1 TCAAAATTTCATAATAAGATTACCAAAAT
23677 T
1 T
23678 TCATTGGGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (29 bp):
TCAAAATTTCATAATAAGATTACCAAAAT
Found at i:23806 original size:21 final size:22
Alignment explanation
Indices: 23781--23830 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
23771 GTGGTTAGCA
23781 AAATTTCATTAAG-AGACAA-TC
1 AAATTTCA-TAAGCAGACAATTC
*
23802 AAATTTCATAAGCAGACAATTG
1 AAATTTCATAAGCAGACAATTC
23824 AAATTTC
1 AAATTTC
23831 GTAACCCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (22 bp):
AAATTTCATAAGCAGACAATTC
Found at i:23904 original size:22 final size:22
Alignment explanation
Indices: 23862--23948 Score: 97
Period size: 22 Copynumber: 4.0 Consensus size: 22
23852 TAACCCTAAA
*
23862 AGAGGTTATCAAGA-TTCATAG
1 AGAGGTTATCAAAATTTCATAG
* *
23883 GGAGGTTATCAAGATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
* *
23905 TGTGGTT-TCCAAAATTTCATAG
1 AGAGGTTAT-CAAAATTTCATAG
*
23927 AGAGGTTATCAAAATTTTATAG
1 AGAGGTTATCAAAATTTCATAG
23949 TGTGGCTACC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
21 14 0.25
22 41 0.73
23 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:23949 original size:44 final size:44
Alignment explanation
Indices: 23876--23965 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
23866 GTTATCAAGA
* * * *
23876 TTCATAGGGAGGTTATCAAGATTTCATAGTGTGGTTTCCAAAAT
1 TTCATAGAGAGGTTATCAAAATTTCATAGTGTGGCTACCAAAAT
*
23920 TTCATAGAGAGGTTATCAAAATTTTATAGTGTGGCTACCAAAAT
1 TTCATAGAGAGGTTATCAAAATTTCATAGTGTGGCTACCAAAAT
23964 TT
1 TT
23966 TATAATCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (44 bp):
TTCATAGAGAGGTTATCAAAATTTCATAGTGTGGCTACCAAAAT
Found at i:23969 original size:22 final size:22
Alignment explanation
Indices: 23876--23965 Score: 90
Period size: 22 Copynumber: 4.1 Consensus size: 22
23866 GTTATCAAGA
* * * *
23876 TTCATAGGGAGGTTATCAAGAT
1 TTCATAGTGTGGTTACCAAAAT
*
23898 TTCATAGTGTGGTTTCCAAAAT
1 TTCATAGTGTGGTTACCAAAAT
* * *
23920 TTCATAGAGAGGTTATCAAAAT
1 TTCATAGTGTGGTTACCAAAAT
* *
23942 TTTATAGTGTGGCTACCAAAAT
1 TTCATAGTGTGGTTACCAAAAT
23964 TT
1 TT
23966 TATAATCAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (22 bp):
TTCATAGTGTGGTTACCAAAAT
Found at i:24038 original size:22 final size:22
Alignment explanation
Indices: 23989--24050 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
23979 GTATAGCGTG
* * *
23989 GTTATCAAAATTTCATGGGGAG
1 GTTATCAAAATTTCATAGGCAA
* *
24011 GCTATCAAAATTTCATATGCAA
1 GTTATCAAAATTTCATAGGCAA
* *
24033 GTTATCGAAATTTTATAG
1 GTTATCAAAATTTCATAG
24051 TGCGGTACTG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGCAA
Found at i:24189 original size:22 final size:22
Alignment explanation
Indices: 24138--24189 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
24128 CGCAGTATGA
*
24138 TTATAAAAATTTCATATGGAGG
1 TTATCAAAATTTCATATGGAGG
* * * *
24160 TTAACAAAATTTCATTTTGTGG
1 TTATCAAAATTTCATATGGAGG
24182 TTATCAAA
1 TTATCAAA
24190 GTTTTGTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGAGG
Found at i:24766 original size:21 final size:22
Alignment explanation
Indices: 24733--24777 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
24723 TTAAGGGGTA
24733 TTGCTAAACACCG-CCTTTTTT
1 TTGCTAAACACCGCCCTTTTTT
* *
24754 TTGCTCAATACCGCCCTTTTTT
1 TTGCTAAACACCGCCCTTTTTT
24776 TT
1 TT
24778 ACACGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.16, C:0.29, G:0.09, T:0.47
Consensus pattern (22 bp):
TTGCTAAACACCGCCCTTTTTT
Found at i:25004 original size:32 final size:32
Alignment explanation
Indices: 24968--25046 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
24958 CCGCCCCACG
* * *
24968 AGGACGGCCAGCCATTGTCGAGCCGCCTTGTT
1 AGGACGGCTAGCCATTGTCGAGCCGCCATGCT
*
25000 AGGACGGCTAGCCACTGTCGAGCCGCCATGCT
1 AGGACGGCTAGCCATTGTCGAGCCGCCATGCT
25032 AGGACGGCTAGCCAT
1 AGGACGGCTAGCCAT
25047 GGTTATGCCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.18
Consensus pattern (32 bp):
AGGACGGCTAGCCATTGTCGAGCCGCCATGCT
Found at i:42316 original size:14 final size:14
Alignment explanation
Indices: 42293--42322 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42283 TTAATGTAGT
*
42293 TTAATCAAGTCAAA
1 TTAATAAAGTCAAA
42307 TTAATAAAGTCAAA
1 TTAATAAAGTCAAA
42321 TT
1 TT
42323 GCATTTAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (14 bp):
TTAATAAAGTCAAA
Found at i:53780 original size:17 final size:17
Alignment explanation
Indices: 53731--53785 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
53721 ATACAGTTCT
*
53731 AAATTCAGTAACAATAT
1 AAATTCAGTAACAATAA
*
53748 TAA-TCA--AA-AA-AA
1 AAATTCAGTAACAATAA
53760 AAATTCAGTAACAATAA
1 AAATTCAGTAACAATAA
53777 AAATTCAGT
1 AAATTCAGT
53786 GCTTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
12 3 0.10
13 5 0.17
14 2 0.07
15 2 0.07
16 5 0.17
17 13 0.43
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.25
Consensus pattern (17 bp):
AAATTCAGTAACAATAA
Found at i:55259 original size:22 final size:22
Alignment explanation
Indices: 55234--55360 Score: 107
Period size: 22 Copynumber: 5.8 Consensus size: 22
55224 TTGAATATTT
55234 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* *
55256 TTATTAAATTTTGATAACCACC
1 TTATGAAATTTTGATAACTACC
* *
55278 CTATGAAATTTTTGATAATTACC
1 TTATGAAA-TTTTGATAACTACC
* *
55301 -TATAAAATTGTGATAGACT-CC
1 TTATGAAATTTTGATA-ACTACC
* * * *
55322 ATAAGAAACTTTGATAACCTA-A
1 TTATGAAATTTTGATAA-CTACC
*
55344 TTATGAAATTTTAATAA
1 TTATGAAATTTTGATAA
55361 ACTTTCCTAT
Statistics
Matches: 82, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 10 0.12
22 60 0.73
23 12 0.15
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:55389 original size:20 final size:21
Alignment explanation
Indices: 55345--55402 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
55335 ATAACCTAAT
*
55345 TATGAAATTTTAATAAACTTTCC
1 TATG-AATTTTAAT-AACCTTCC
55368 TATGAATTTT-ATAACCTTCC
1 TATGAATTTTAATAACCTTCC
* *
55388 TATGATTTTTGATAA
1 TATGAATTTTAATAA
55403 TCTCTCTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
21 6 0.19
22 6 0.19
23 4 0.12
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (21 bp):
TATGAATTTTAATAACCTTCC
Found at i:60079 original size:120 final size:120
Alignment explanation
Indices: 59866--60082 Score: 346
Period size: 120 Copynumber: 1.8 Consensus size: 120
59856 CTGGGCACCA
* *
59866 AGACCAACCTGAGCCATGACTTGTTGGTTGTTCATCTCATTGTTGACTTATTGAAGAGGCAGAGC
1 AGACCAACCTGAGCCATGACTTGTTGGTTGTTCATCTCATTGTTGACTTATTGAAGAAGAAGAGC
*
59931 ACCAGGTTGGGCACCAAGCAGTTATTGGTTTTTCCCCCCAAGTCTTTCTTTGATC
66 ACCAGGCTGGGCACCAAGCAGTTATTGGTTTTTCCCCCCAAGTCTTTCTTTGATC
* *
59986 AGACCAACCTGAGCCATGACTTGTTGGTTGTTCATTTCATTGTTGACTTGTTGAAGAAGAAGATG
1 AGACCAACCTGAGCCATGACTTGTTGGTTGTTCATCTCATTGTTGACTTATTGAAGAAGAAGA-G
* * *
60051 -GCCGGGCTGGGCACCAAGCAGTTGTTGGTTTT
65 CACCAGGCTGGGCACCAAGCAGTTATTGGTTTT
60083 GCCTCCCGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
120 87 0.99
121 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (120 bp):
AGACCAACCTGAGCCATGACTTGTTGGTTGTTCATCTCATTGTTGACTTATTGAAGAAGAAGAGC
ACCAGGCTGGGCACCAAGCAGTTATTGGTTTTTCCCCCCAAGTCTTTCTTTGATC
Found at i:60132 original size:135 final size:135
Alignment explanation
Indices: 59964--60275 Score: 493
Period size: 135 Copynumber: 2.3 Consensus size: 135
59954 ATTGGTTTTT
* *
59964 CCCCCCAAGTCTTTCTTTGATCAGACCAACCTGAGCCATGACTTGTTGGTTGTTCATTTCATTGT
1 CCCCCCAAGTCTTTCTTTGATCAAACCAACCTGAGCCATGACTTGTTGGTTGTTCATCTCATTGT
** *
60029 TGACTTGTTG-AAGAAGAAGATGGCCGGGCTGGGCACCAA-GCAGTTGTTGGTTTTGCCTCCCGA
66 TGACTTGTTGCAA-AAGAAGATCACCGGGCTGGGCACCAACGCAGTAGTTGGTTTTGCC-CCCGA
60092 GTCCTTG
129 GTCCTTG
*
60099 CCCCCCAAGTCTTTCTTTGATCAAACCAACCTGAGTCATGACTTGTTGGTTGTTCATCTCATTGT
1 CCCCCCAAGTCTTTCTTTGATCAAACCAACCTGAGCCATGACTTGTTGGTTGTTCATCTCATTGT
* *
60164 TGACTTGTTGCAAAGGCAGATCACCGGGCTGGGCACCAAGCGCAGTAGTTGGTTTTGCCCCCGAG
66 TGACTTGTTGCAAAAGAAGATCACCGGGCTGGGCACCAA-CGCAGTAGTTGGTTTTGCCCCCGAG
60229 TCCTTG
130 TCCTTG
* *
60235 CCCCCCAAGTCTTTCTTCGATCAAACCAATCTGAGCCATGA
1 CCCCCCAAGTCTTTCTTTGATCAAACCAACCTGAGCCATGA
60276 TGTTTTCTCT
Statistics
Matches: 163, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
135 94 0.58
136 52 0.32
137 17 0.10
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (135 bp):
CCCCCCAAGTCTTTCTTTGATCAAACCAACCTGAGCCATGACTTGTTGGTTGTTCATCTCATTGT
TGACTTGTTGCAAAAGAAGATCACCGGGCTGGGCACCAACGCAGTAGTTGGTTTTGCCCCCGAGT
CCTTG
Found at i:62179 original size:154 final size:155
Alignment explanation
Indices: 61826--62236 Score: 506
Period size: 154 Copynumber: 2.7 Consensus size: 155
61816 TTCGAGCCGT
* * *
61826 CCTTCATAGTGAACTAGGTTTCACACCTCAAA-TAGTCCTTAAATGAAAAACTTGCATAAGTTTT
1 CCTTCATAGTGAACTTGGTTTCACACCCCAAACT-GTCCTTAACTGAAAAACTTGCATAAGTTTT
* * * * * * * * *
61890 TCA-CCTTAACTCTGATTGAGCTGAAACTTTGCCAAGGGACTTAGATTCTCTCCACAAGACTATG
65 TCATAC-TAAGTCTGATTGAGATGAAACTTGGCCAAGAGACTGAGACTATCTCCACAAAACTATG
* * *
61954 AAAAAAATTCTATGTAAAACCGAGCTTC
129 -AAAAAATTCTAAGTAAAACCAAACTTC
* * * *
61982 TCTTGATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTTAAAAACTTGCATAAGTTTTT
1 CCTTCATAGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTT
** * * *
62047 CATACTAAGTCCAATTGAGATGAAACTTGGCCACGAGACTGAGACTATCTCCATAAAACTATG-G
66 CATACTAAGTCTGATTGAGATGAAACTTGGCCAAGAGACTGAGACTATCTCCACAAAACTATGAA
62111 AAAATTCTAAGTAAAACCAAAC-TC
131 AAAATTCTAAGTAAAACCAAACTTC
* *
62135 CCTATCATAGTGAAGTTGGTTTCTCACCCCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTT
1 CCT-TCATAGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTT
* *
62200 TCATTCTAAGTCTGTTTGAGATGAAACTTGGCCAAGA
65 TCATACTAAGTCTGATTGAGATGAAACTTGGCCAAGA
62237 TGACCTACAT
Statistics
Matches: 217, Mismatches: 35, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
153 4 0.02
154 107 0.49
156 104 0.48
157 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (155 bp):
CCTTCATAGTGAACTTGGTTTCACACCCCAAACTGTCCTTAACTGAAAAACTTGCATAAGTTTTT
CATACTAAGTCTGATTGAGATGAAACTTGGCCAAGAGACTGAGACTATCTCCACAAAACTATGAA
AAAATTCTAAGTAAAACCAAACTTC
Found at i:65409 original size:15 final size:15
Alignment explanation
Indices: 65389--65417 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
65379 TTCAGAAGAA
65389 TATGAAAAATGGAAT
1 TATGAAAAATGGAAT
65404 TATGAAAAATGGAA
1 TATGAAAAATGGAA
65418 GGCTTCAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (15 bp):
TATGAAAAATGGAAT
Found at i:67188 original size:2 final size:2
Alignment explanation
Indices: 67181--67223 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
67171 TCTATCTATC
67181 TA TA TA TA TA TA 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 TA TA TA TA TA TA
67223 T
1 T
67224 GGTACATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77941 original size:23 final size:24
Alignment explanation
Indices: 77899--77943 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
77889 TATGCATTGC
77899 CTCTTCTCCATACTCAGTATTTTA
1 CTCTTCTCCATACTCAGTATTTTA
*
77923 CTCTTCTCC-TGCTCAGTATTT
1 CTCTTCTCCATACTCAGTATTT
77944 GTACAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.16, C:0.31, G:0.07, T:0.47
Consensus pattern (24 bp):
CTCTTCTCCATACTCAGTATTTTA
Found at i:82495 original size:28 final size:27
Alignment explanation
Indices: 82440--82495 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
82430 TTATCTTATG
***
82440 AATTCATTTATGCTTTTTTTTTGTTAC
1 AATTCATTTATGCTTTTTTTGAATTAC
82467 AATTCATTTATGCTTTTTTTGAATATAC
1 AATTCATTTATGCTTTTTTTGAAT-TAC
82495 A
1 A
82496 CAAGATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (27 bp):
AATTCATTTATGCTTTTTTTGAATTAC
Found at i:82644 original size:23 final size:26
Alignment explanation
Indices: 82613--82680 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 26
82603 CTTGAATTTT
82613 AACACATTTATTCATTTTTTTA-A-G
1 AACACATTTATTCATTTTTTTAGATG
*
82637 -ATACATTTATTCATTTTTTTAGATG
1 AACACATTTATTCATTTTTTTAGATG
*
82662 AACACATTTGTTCATTTTT
1 AACACATTTATTCATTTTT
82681 CCATACTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 20 0.53
24 1 0.03
25 1 0.03
26 16 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (26 bp):
AACACATTTATTCATTTTTTTAGATG
Found at i:84629 original size:5 final size:5
Alignment explanation
Indices: 84621--84661 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
84611 CTTTTTTCCA
*
84621 TTATT TTATT TT-CT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
84662 TTAATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:95652 original size:2 final size:2
Alignment explanation
Indices: 95645--95669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
95635 TATTTACTAG
95645 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 T
95670 TAATAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.