Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013933.1 Corchorus capsularis cultivar CVL-1 contig13954, 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: 52428
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1877 original size:45 final size:45
Alignment explanation
Indices: 1826--1915 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
1816 AATTACTTCT
1826 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAATAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAATAATTCCAC
*
1871 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAATAATTCCAC
1916 TACTCTATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGGGATCTTTTAATAATTCCAC
Found at i:6018 original size:19 final size:19
Alignment explanation
Indices: 5994--6034 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
5984 ACAATAATAA
5994 TAATCCTTTGAGAAAACCC
1 TAATCCTTTGAGAAAACCC
6013 TAATCCTTTGAGAAAACCC
1 TAATCCTTTGAGAAAACCC
6032 TAA
1 TAA
6035 ACCTCCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (19 bp):
TAATCCTTTGAGAAAACCC
Found at i:7953 original size:6 final size:6
Alignment explanation
Indices: 7942--7981 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
7932 CGCATCACCC
7942 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
7982 AAGAATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:17758 original size:17 final size:18
Alignment explanation
Indices: 17727--17763 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
17717 TTTCTTCACC
17727 CAAGAACCATCCAAAACA
1 CAAGAACCATCCAAAACA
*
17745 CAAG-ACCATTCAAAACA
1 CAAGAACCATCCAAAACA
17762 CA
1 CA
17764 GGGAAATCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.54, C:0.32, G:0.05, T:0.08
Consensus pattern (18 bp):
CAAGAACCATCCAAAACA
Found at i:24150 original size:49 final size:48
Alignment explanation
Indices: 24087--24414 Score: 394
Period size: 49 Copynumber: 6.7 Consensus size: 48
24077 TCTTTACTTA
24087 CATTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATG
1 CATTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATG
24135 CAATTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATG
1 C-ATTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATG
* * * *
24184 CAATTTTCCCAAAATGCCCTTCCCGGATGGAAGACACTTATTGTACTTG
1 C-ATTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATG
* * *
24233 C-TTCTTCCCAAAATGCCCTTCCCGGACAGAAGGCACTTCTTTTTACTTG
1 CATT-TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT-ATTTTACATG
* *
24282 C-TCTTTCCCAAAACGCCCTTCCCGGACGGAAGTCACTCCT-TTTTACATG
1 CAT-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACT--TATTTTACATG
* * * *
24331 C-TATTTCCCAAAACGCCCTTCTCGGACGGAAGGCACTTCTTTTTACCTG
1 CAT-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT-ATTTTACATG
* * *
24380 CTTTTTCCAAAAAACGCCCTTCCCGGACGGAAGGC
1 CATTTTCC-CAAAATGCCCTTCCCGGACGGAAGGC
24415 GTTAATGTTT
Statistics
Matches: 251, Mismatches: 19, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
47 3 0.01
48 32 0.13
49 189 0.75
50 26 0.10
51 1 0.00
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.29
Consensus pattern (48 bp):
CATTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATG
Found at i:24349 original size:146 final size:146
Alignment explanation
Indices: 24091--24414 Score: 422
Period size: 146 Copynumber: 2.2 Consensus size: 146
24081 TACTTACATT
*
24091 TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATGCAATTTTCCCAAAATGCCCTT
1 TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATGC-ATTTTCCCAAAACGCCCTT
* *
24156 CCCGGACGGAAGGCACTTATTTTACATGCAATTTTCCCAAAATGCCCTTCCCGGATGGAAGACAC
65 CCCGGACGGAAGGCACTTATTTTACATGCAATTTTCCCAAAACGCCCTTCCCGGACGGAAGACAC
*
24221 TT-ATTGTACTTGCTTC
130 TTCATTGTACCTGCTTC
* * *
24237 TTCCCAAAATGCCCTTCCCGGACAGAAGGCACTTCTTTTTACTTGC-TCTTTCCCAAAACGCCCT
1 TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTT-ATTTTACATGCAT-TTTCCCAAAACGCCCT
* * * *
24301 TCCCGGACGGAAGTCACTCCT-TTTTACATGCTA-TTTCCCAAAACGCCCTTCTCGGACGGAAGG
64 TCCCGGACGGAAGGCACT--TATTTTACATGCAATTTTCCCAAAACGCCCTTCCCGGACGGAAGA
* * *
24364 CACTTCTTTTTACCTGCTTT
127 CACTTCATTGTACCTGCTTC
* *
24384 TTCCAAAAAACGCCCTTCCCGGACGGAAGGC
1 TTCC-CAAAATGCCCTTCCCGGACGGAAGGC
24415 GTTAATGTTT
Statistics
Matches: 155, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
145 1 0.01
146 96 0.62
147 34 0.22
148 24 0.15
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.29
Consensus pattern (146 bp):
TTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACATGCATTTTCCCAAAACGCCCTTC
CCGGACGGAAGGCACTTATTTTACATGCAATTTTCCCAAAACGCCCTTCCCGGACGGAAGACACT
TCATTGTACCTGCTTC
Found at i:25524 original size:13 final size:13
Alignment explanation
Indices: 25506--25530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25496 ACATGTACTT
25506 TAATTACAATTGC
1 TAATTACAATTGC
25519 TAATTACAATTG
1 TAATTACAATTG
25531 AGTTTGTTGG
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:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
TAATTACAATTGC
Found at i:26439 original size:30 final size:30
Alignment explanation
Indices: 26403--26468 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
26393 CCATCGCATG
*
26403 GGCCATCGGATGGAG-CAACCGGCCACAACC
1 GGCCATCGCATGG-GCCAACCGGCCACAACC
* *
26433 GGCCATCGCATGGGCCATCCGGGCACAACC
1 GGCCATCGCATGGGCCAACCGGCCACAACC
26463 GGCCAT
1 GGCCAT
26469 TTGACCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.09
Consensus pattern (30 bp):
GGCCATCGCATGGGCCAACCGGCCACAACC
Found at i:40058 original size:19 final size:18
Alignment explanation
Indices: 40034--40073 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40024 TTGAAGATTT
*
40034 ATTGAAGATAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
*
40053 ATTGAAGACCATTGAAGA
1 ATTGAAGACAATTGAAGA
40071 ATT
1 ATT
40074 ATCTCAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:43250 original size:58 final size:58
Alignment explanation
Indices: 43179--43354 Score: 300
Period size: 58 Copynumber: 3.1 Consensus size: 58
43169 AATTACTTAC
* *
43179 AAAGCTCGATAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACGA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
* *
43237 AAAGCTCGCTAAGTTGAAAATCCTG-AAAGGACGGCTCAGGCAAAAGTTAGAGTACAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
*
43294 AAAGCTCGCTAAGTTGAAAATCCTACAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
43352 AAA
1 AAA
43355 AAAACACCCC
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
57 53 0.48
58 57 0.52
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (58 bp):
AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
Found at i:48672 original size:13 final size:13
Alignment explanation
Indices: 48627--48673 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
48617 ATCATTTTTA
48627 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
48640 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
48653 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
48667 CTCTTTT
1 CTCTTTT
48674 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:48688 original size:29 final size:28
Alignment explanation
Indices: 48624--48701 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
48614 TTTATCATTT
*
48624 TTACTCTTTTCTTACTCT-TTTTACTAA
1 TTACACTTTTCTTACTCTCTTTTACTAA
* * *
48651 TTACTCTTTTCTTACTCTCTTTTATTTA
1 TTACACTTTTCTTACTCTCTTTTACTAA
48679 TTACCAC-TTT-TTACTCTTCTTTT
1 TTA-CACTTTTCTTACTC-TCTTTT
48702 TTCTTATACT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 24 0.53
28 19 0.42
29 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
TTACACTTTTCTTACTCTCTTTTACTAA
Found at i:48779 original size:21 final size:21
Alignment explanation
Indices: 48746--49004 Score: 172
Period size: 21 Copynumber: 12.7 Consensus size: 21
48736 AGTGATCACC
48746 TTTTACTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* *
48768 TTTTACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
* * *
48789 CTTTGCTCTTACTGATTACTG
1 TTTTACTCTTACTGATTACTA
*
48810 TTTTACTCTTACTGGTTAC--
1 TTTTACTCTTACTGATTACTA
*
48829 -----CTTTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
*
48845 TTTTTCTCTTTACTGATTAC--
1 TTTTACTC-TTACTGATTACTA
*
48865 -CTT--T-TT-CTGATTACTA
1 TTTTACTCTTACTGATTACTA
*
48881 TTTTACTATTTACTGATTACCT-
1 TTTTACT-CTTACTGATTA-CTA
* *
48903 TCTTACTTTTTACTGATTACTA
1 TTTTAC-TCTTACTGATTACTA
48925 TTTTACTCTTTACTGATTA-TCA
1 TTTTACTC-TTACTGATTACT-A
* * *
48947 TTTTACTCTCATTGATTACCA
1 TTTTACTCTTACTGATTACTA
* *
48968 TTTTGCTCTTATTGATTACTA
1 TTTTACTCTTACTGATTACTA
*
48989 TTTTACCTTTTACTGA
1 TTTTA-CTCTTACTGA
49005 CTATCATTAC
Statistics
Matches: 187, Mismatches: 27, Indels: 46
0.72 0.10 0.18
Matches are distributed among these distances:
14 20 0.11
15 2 0.01
17 3 0.02
19 3 0.02
21 82 0.44
22 74 0.40
23 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:48865 original size:36 final size:36
Alignment explanation
Indices: 48797--48953 Score: 172
Period size: 36 Copynumber: 4.1 Consensus size: 36
48787 CACTTTGCTC
* *
48797 TTACTGATTACTGTTTTACTC-TTACTGGTTACCTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
*
48832 TTACTGATTACTATTTTTCTCTTTACTGATTACCTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCTT
* *
48868 TTTCTGATTACTATTTTACTATTTACTGATTACCTTCTTACTTT
1 TTACTGATTACTATTTTACTCTTTACTGATTA----C---C-TT
*
48912 TTACTGATTACTATTTTACTCTTTACTGATTATCATT
1 TTACTGATTACTATTTTACTCTTTACTGATTA-CCTT
48949 TTACT
1 TTACT
48954 CTCATTGATT
Statistics
Matches: 104, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
35 19 0.18
36 42 0.40
37 7 0.07
40 1 0.01
41 2 0.02
43 1 0.01
44 32 0.31
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.55
Consensus pattern (36 bp):
TTACTGATTACTATTTTACTCTTTACTGATTACCTT
Found at i:48888 original size:44 final size:44
Alignment explanation
Indices: 48839--48943 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
48829 CTTTTACTGA
* *
48839 TTACTATTTTTCTCTTTA-CTGATTACCTTTTT-CTGATTACTATT
1 TTACTA-TTTACTCATTACCTGATTA-CTTTTTACTGATTACTATT
* **
48883 TTACTATTTACTGATTACCTTCTTACTTTTTACTGATTACTATT
1 TTACTATTTACTCATTACCTGATTACTTTTTACTGATTACTATT
* *
48927 TTACTCTTTACTGATTA
1 TTACTATTTACTCATTA
48944 TCATTTTACT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 14 0.26
44 39 0.74
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (44 bp):
TTACTATTTACTCATTACCTGATTACTTTTTACTGATTACTATT
Found at i:48953 original size:44 final size:43
Alignment explanation
Indices: 48865--49004 Score: 151
Period size: 44 Copynumber: 3.3 Consensus size: 43
48855 TACTGATTAC
* *
48865 CTTTTT-CTGATTACTATTTTACTATTTACTGATTACCTTCTTA
1 CTTTTTACTGATTACTATTTTACTCTTTACTGATTACATT-TTA
48908 CTTTTTACTGATTACTATTTTACTCTTTACTGATTATCATTTTA
1 CTTTTTACTGATTACTATTTTACTCTTTACTGATTA-CATTTTA
* * * * * *
48952 C-TCTCATTGATTACCATTTTGCTC-TTATTGATTACTATTTTA
1 CTTTTTACTGATTACTATTTTACTCTTTACTGATTAC-ATTTTA
*
48994 CCTTTTACTGA
1 CTTTTTACTGA
49005 CTATCATTAC
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 16 0.20
43 30 0.37
44 32 0.39
45 3 0.04
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (43 bp):
CTTTTTACTGATTACTATTTTACTCTTTACTGATTACATTTTA
Found at i:49115 original size:35 final size:35
Alignment explanation
Indices: 49074--49170 Score: 133
Period size: 35 Copynumber: 2.8 Consensus size: 35
49064 TTTACTTTTT
*
49074 ACTGATTACCCTTTACTCTTTACCATTCTTCCTTG
1 ACTGATTACTCTTTACTCTTTACCATTCTTCCTTG
* *
49109 ACTGATTACTCTTTAC-CTTTTACCATTCTTCTTTT
1 ACTGATTACTCTTTACTC-TTTACCATTCTTCCTTG
* *
49144 ACTGATTACTCTTTACTTTTTATCATT
1 ACTGATTACTCTTTACTCTTTACCATT
49171 GTACTCTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 1 0.02
35 54 0.98
ACGTcount: A:0.19, C:0.26, G:0.04, T:0.52
Consensus pattern (35 bp):
ACTGATTACTCTTTACTCTTTACCATTCTTCCTTG
Found at i:49326 original size:40 final size:38
Alignment explanation
Indices: 49282--49395 Score: 112
Period size: 40 Copynumber: 3.0 Consensus size: 38
49272 GATTAATCCA
*
49282 TTGACTTTTAATTACTGATTTGCTGATTACTATTTTTACC
1 TTGAC-TTTAATTACTGATTTACTGATTACTATTTTTA-C
* *
49322 TTGACTCTTAATTA-TCGGTTTACTGATTACTATCTTT--
1 TTGACT-TTAATTACT-GATTTACTGATTACTATTTTTAC
* *
49359 TT-AC-TTAATTGCTGATTTACTGATTACTACTTTTAC
1 TTGACTTTAATTACTGATTTACTGATTACTATTTTTAC
49395 T
1 T
49396 CCCTTAATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
34 24 0.39
35 1 0.02
36 3 0.05
37 2 0.03
39 2 0.03
40 30 0.48
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.52
Consensus pattern (38 bp):
TTGACTTTAATTACTGATTTACTGATTACTATTTTTAC
Found at i:49366 original size:34 final size:35
Alignment explanation
Indices: 49328--49457 Score: 112
Period size: 34 Copynumber: 3.8 Consensus size: 35
49318 TACCTTGACT
*
49328 CTTAATTATC-GGTTTACTGATTACTATCTTTTTA
1 CTTAATTATCTGATTTACTGATTACTATCTTTTTA
* *
49362 CTTAATT-GCTGATTTACTGATTACTA-CTTTTACTCC
1 CTTAATTATCTGATTTACTGATTACTATCTTTT--T-A
* *
49398 CTTAATTATC-AATTTACTTAATTA--ATCTTTTTA
1 CTTAATTATCTGATTTAC-TGATTACTATCTTTTTA
* *
49431 CTTTATTA-CTGATTTACCGATTACTAT
1 CTTAATTATCTGATTTACTGATTACTAT
49458 TACCTTGACT
Statistics
Matches: 75, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
32 5 0.07
33 19 0.25
34 25 0.33
35 2 0.03
36 18 0.24
37 6 0.08
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (35 bp):
CTTAATTATCTGATTTACTGATTACTATCTTTTTA
Found at i:49367 original size:74 final size:69
Alignment explanation
Indices: 49226--49458 Score: 200
Period size: 74 Copynumber: 3.2 Consensus size: 69
49216 CCATTTTCCC
* * ** ** *
49226 TTTACTGATTACTAATTTTACTTTCTCCCTTAAGTATCAATTTAC-CGATTAATCCATTGACTTT
1 TTTACTGATTACT-A-TTT--TTACTCCCTTAATTATCAATTTACTTAATTAATCTTTTTAC--T
49290 TAATTACTGA
60 TAATTACTGA
* * ** *
49300 TTTGCTGATTACTATTTTTACCTTGACTCTTAATTATCGGTTTAC-TGATTACTATCTTTTTACT
1 TTTACTGATTACTATTTTTA-C-T--CCCTTAATTATCAATTTACTTAATTA--ATCTTTTTACT
*
49364 TAATTGCTGA
60 TAATTACTGA
* *
49374 TTTACTGATTACTACTTTTACTCCCTTAATTATCAATTTACTTAATTAATCTTTTTACTTTATTA
1 TTTACTGATTACTATTTTTACTCCCTTAATTATCAATTTACTTAATTAATCTTTTTACTTAATTA
49439 CTGA
66 CTGA
*
49443 TTTACCGATTACTATT
1 TTTACTGATTACTATT
49459 ACCTTGACTT
Statistics
Matches: 131, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
69 33 0.25
70 18 0.14
71 6 0.05
72 5 0.04
73 2 0.02
74 60 0.46
76 7 0.05
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (69 bp):
TTTACTGATTACTATTTTTACTCCCTTAATTATCAATTTACTTAATTAATCTTTTTACTTAATTA
CTGA
Found at i:49486 original size:54 final size:54
Alignment explanation
Indices: 49418--49631 Score: 376
Period size: 54 Copynumber: 4.0 Consensus size: 54
49408 AATTTACTTA
* * * *
49418 ATTAATCT-TTTTACTTTATTACTGATTTACCGATTACTATTACCTTGACTTTG
1 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
*
49471 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATAACCTTGACTCTG
1 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
49525 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
1 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
49579 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
1 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
49632 TAACTATCAA
Statistics
Matches: 154, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
53 8 0.05
54 146 0.95
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (54 bp):
ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
Found at i:49553 original size:108 final size:108
Alignment explanation
Indices: 49418--49868 Score: 510
Period size: 108 Copynumber: 4.0 Consensus size: 108
49408 AATTTACTTA
* *
49418 ATTAATCT-TTTTACTTTATTACTGATTTACCGATTACTATTACCTTGACTTTGATTAATCTCTT
1 ATTAATCTCTTTTACTTAATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTCTT
*
49482 TTACTTAATTACCGATTTACTGATTACTATAACCTTGACTCTG
66 TTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
* *
49525 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTT
1 ATTAATCTCTTTTACTTAATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTCTT
*
49590 TTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTA
66 TTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC-TG
* * ** * *
49634 ACTATCAATTTACTAATTAATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGA
1 A-T-T-AATCT-CT--TTTA-CT-TAATTACTGATTTACCG----A-T---TACTATTACCTTGA
* * * ** *
49699 CTCTTAACT-ATCTCTTTTTACTTACTTACTAATTTTCTGATTACTATTACCTTGACTCTG
50 CTC-TGATTAATCTC-TTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
* *
49759 ATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCTGATTAATCTCT
1 ATTAATCTC-TTTTACTTAATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTCT
49824 TAATTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
65 T--TTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCT
49869 TAATTTATTG
Statistics
Matches: 285, Mismatches: 35, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
107 8 0.03
108 92 0.32
109 7 0.02
110 22 0.08
111 39 0.14
112 4 0.01
113 3 0.01
114 1 0.00
115 3 0.01
116 2 0.01
117 11 0.04
118 12 0.04
119 2 0.01
120 3 0.01
121 2 0.01
122 6 0.02
123 1 0.00
124 1 0.00
125 24 0.08
126 42 0.15
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.47
Consensus pattern (108 bp):
ATTAATCTCTTTTACTTAATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTCTT
TTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTG
Found at i:49677 original size:71 final size:70
Alignment explanation
Indices: 49579--49710 Score: 246
Period size: 71 Copynumber: 1.9 Consensus size: 70
49569 CTTGACTCTG
*
49579 ATTAATCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAATT
1 ATTAATCTCTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCAATT
49644 TACTA
66 TACTA
49649 ATTAATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATC
1 ATTAATCTC-TTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATC
49711 TCTTTTTACT
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
70 9 0.15
71 51 0.85
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (70 bp):
ATTAATCTCTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACTATCAATT
TACTA
Found at i:49680 original size:125 final size:119
Alignment explanation
Indices: 49520--49873 Score: 410
Period size: 110 Copynumber: 3.0 Consensus size: 119
49510 ATAACCTTGA
49520 CTCTGATTAATCTC-TTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAA
1 CTCT-ATTAATCTCTTTTTACTTAATTACCGATTTACTGA-TACTATTACCTTGACTCTGATTAA
49584 TCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAAT
64 TCTCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAA-T-T-AAT
* * *
49643 TTACTAATTAATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACTCTTAACT
1 CT-CT-ATTAATCTCTTTTTACTTAATTACCGATTTACTGA-TACTATTACCTTGACTC-TGATT
* ** *
49708 -ATCTCTTTTTACTTACTTACTAATTTTCTGATTACTATTACCTTGA--C--------T
62 AATCTC-TTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAATTAAT
* * *
49756 CT-GATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACTCTGATTAAT
1 CTCTATTAATCTCTTTTTACTTAATTACCGATTTACTGA-TACTATTACCTTGACTCTGATTAAT
49820 CTCTTAATTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAATT
65 CTCTT--TTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAATT
49874 TATTGGAGTA
Statistics
Matches: 196, Mismatches: 20, Indels: 34
0.78 0.08 0.14
Matches are distributed among these distances:
109 5 0.03
110 55 0.28
111 34 0.17
113 3 0.02
123 1 0.01
124 12 0.06
125 47 0.24
126 39 0.20
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.47
Consensus pattern (119 bp):
CTCTATTAATCTCTTTTTACTTAATTACCGATTTACTGATACTATTACCTTGACTCTGATTAATC
TCTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAATTAAT
Found at i:49712 original size:55 final size:55
Alignment explanation
Indices: 49646--49873 Score: 323
Period size: 55 Copynumber: 4.1 Consensus size: 55
49636 TATCAATTTA
*
49646 CTAATTAATCTCTTTTTACTTAATTACCGATTTACTGACTACTATTACCTTGACT
1 CTAATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACT
* * ** *
49701 CTTAACT-ATCTCTTTTTACTTACTTACTAATTTTCTGATTACTATTACCTTGACT
1 C-TAATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACT
* * *
49756 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTTCCTTGACT
1 CTAATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACT
* *
49811 CTGATTAATCTCTTAATTACTTAATTACCGATTTACTGATTACTATTACCTTGACT
1 CTAATTAATCTCTT-TTTACTTAATTACCGATTTACTGATTACTATTACCTTGACT
49867 CTTAATT
1 C-TAATT
49874 TATTGGAGTA
Statistics
Matches: 153, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
54 3 0.02
55 103 0.67
56 43 0.28
57 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (55 bp):
CTAATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACT
Done.