Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016470.1 Corchorus capsularis cultivar CVL-1 contig16491, 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: 11231
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Found at i:613 original size:21 final size:21
Alignment explanation
Indices: 581--978 Score: 150
Period size: 21 Copynumber: 18.9 Consensus size: 21
571 CTGATCACCC
581 TTTACTCTTTACTGATTACTAT
1 TTTACTC-TTACTGATTACTAT
* * *
603 TTGACTCTTACTAATTA-TCAC
1 TTTACTCTTACTGATTACT-AT
* * * *
624 TTTGCTCTTATTGGTTACTGT
1 TTTACTCTTACTGATTACTAT
*
645 TTTACTCTTACTGATTA-TCT
1 TTTACTCTTACTGATTACTAT
* *
665 TTTACTGATT-CT--TTACAGAT
1 TTTACT-CTTACTGATTAC-TAT
685 TTTACTCTTTACTGATTACCT-T
1 TTTACTC-TTACTGATTA-CTAT
* * *
707 CTTACTTTTACTGATTACCAT
1 TTTACTCTTACTGATTACTAT
728 TTTACTCTTTTACTGATTACTAT
1 TTTACTC--TTACTGATTACTAT
* *
751 TTT-CTGCTCT-CT-CTCT-CT-C
1 TTTACT-CT-TACTGAT-TACTAT
*
770 TTT--T-TTACTGATTACTCT
1 TTTACTCTTACTGATTACTAT
* * *
788 TTTACTTTTTACTGATTGC-CT
1 TTTAC-TCTTACTGATTACTAT
* *
809 TTTGCTTTTTACTGATTACCT-T
1 TTTAC-TCTTACTGATTA-CTAT
* *
831 TTTATTTCTTGCTGATTAGCT-T
1 TTTA-CTCTTACTGATTA-CTAT
*
853 TTTACTCTTTACTGATCACCT-T
1 TTTACTC-TTACTGATTA-CTAT
* * * *
875 TTTACACTAACTGATTTC-CT
1 TTTACTCTTACTGATTACTAT
* *
895 TTTACTTCTTACTTATTACTTTT
1 TTTAC-TCTTACTGATTAC-TAT
918 TTTACTCTTACTGATTACTAT
1 TTTACTCTTACTGATTACTAT
* * *
939 TTTACTTTTTACTGCTTATTAT
1 TTTAC-TCTTACTGATTACTAT
* **
961 GTTACTCTTGTTGATTAC
1 TTTACTCTTACTGATTAC
979 CTTCTTGCTT
Statistics
Matches: 282, Mismatches: 61, Indels: 67
0.69 0.15 0.16
Matches are distributed among these distances:
15 1 0.00
16 4 0.01
17 3 0.01
18 7 0.02
19 3 0.01
20 31 0.11
21 112 0.40
22 94 0.33
23 26 0.09
24 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTACTCTTACTGATTACTAT
Found at i:735 original size:43 final size:42
Alignment explanation
Indices: 684--1000 Score: 172
Period size: 43 Copynumber: 7.5 Consensus size: 42
674 TCTTTACAGA
*
684 TTTTACTCTTTACTGATTACCTTCTTACTTTTACTGATTACC
1 TTTTACTCTTTACTGATTACCTTTTTACTTTTACTGATTACC
** *
726 ATTTTACTCTTTTACTGATTA-CTATTTT-CTGCT-CT-CTCT-CTC
1 -TTTTACTC-TTTACTGATTACCT-TTTTACTTTTACTGAT-TAC-C
* *
768 TCTT--T-TTTACTGATTA-CTCTTTTACTTTTTACTGATTGCC
1 TTTTACTCTTTACTGATTACCT-TTTTAC-TTTTACTGATTACC
* * * * *
808 TTTTGCTTTTTACTGATTACCTTTTTATTTCTTGCTGATTAGCT
1 TTTTACTCTTTACTGATTACCTTTTTACTT-TTACTGATTA-CC
* ** * *
852 TTTTACTCTTTACTGATCACCTTTTTACACTAACTGATTTCC
1 TTTTACTCTTTACTGATTACCTTTTTACTTTTACTGATTACC
* * * *
894 TTTTACT-TCTTACTTATTACTTTTTTTACTCTTACTGATTACTA
1 TTTTACTCT-TTACTGATTAC-CTTTTTACTTTTACTGATTAC-C
* * * **
938 TTTTACTTTTTACTGCTTA--TTATGTTACTCTTGTTGATTACC
1 TTTTACTCTTTACTGATTACCTT-T-TTACTTTTACTGATTACC
* *
980 TTCTTGCTTTTTACTGATTAC
1 TT-TTACTCTTTACTGATTAC
1001 TAATTACCGT
Statistics
Matches: 213, Mismatches: 38, Indels: 45
0.72 0.13 0.15
Matches are distributed among these distances:
37 17 0.08
38 1 0.00
39 3 0.01
40 7 0.03
41 10 0.05
42 27 0.13
43 91 0.43
44 56 0.26
45 1 0.00
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.56
Consensus pattern (42 bp):
TTTTACTCTTTACTGATTACCTTTTTACTTTTACTGATTACC
Found at i:741 original size:23 final size:23
Alignment explanation
Indices: 683--753 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
673 TTCTTTACAG
683 ATTTTACTC-TTTACTGATTACC
1 ATTTTACTCTTTTACTGATTACC
705 -TTCTTA--CTTTTACTGATTACC
1 ATT-TTACTCTTTTACTGATTACC
*
726 ATTTTACTCTTTTACTGATTACT
1 ATTTTACTCTTTTACTGATTACC
749 ATTTT
1 ATTTT
754 CTGCTCTCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
20 1 0.02
21 18 0.42
22 5 0.12
23 19 0.44
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.55
Consensus pattern (23 bp):
ATTTTACTCTTTTACTGATTACC
Found at i:796 original size:22 final size:22
Alignment explanation
Indices: 771--1001 Score: 142
Period size: 22 Copynumber: 10.7 Consensus size: 22
761 CTCTCTCTCT
771 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTACTCTTTTAC
* *
793 TTTTTACTGATTGC-CTTTTGC
1 TTTTTACTGATTACTCTTTTAC
814 TTTTTACTGATTAC-CTTTTTA-
1 TTTTTACTGATTACTC-TTTTAC
*
835 TTTCTTGCTGATTAGCT-TTTTAC
1 TTT-TTACTGATTA-CTCTTTTAC
* *
858 TCTTTACTGATCAC-CTTTTTAC
1 TTTTTACTGATTACTC-TTTTAC
** * *
880 -ACTAACTGATTTC-CTTTTAC
1 TTTTTACTGATTACTCTTTTAC
* * *
900 TTCTTACTTATTACTTTTTTTAC
1 TTTTTACTGATTAC-TCTTTTAC
* *
923 -TCTTACTGATTACTATTTTAC
1 TTTTTACTGATTACTCTTTTAC
* * * *
944 TTTTTACTGCTTATTATGTTAC
1 TTTTTACTGATTACTCTTTTAC
* *
966 TCTTGT--TGATTAC-CTTCTTGC
1 T-TTTTACTGATTACTCTT-TTAC
987 TTTTTACTGATTACT
1 TTTTTACTGATTACT
1002 AATTACCGTT
Statistics
Matches: 162, Mismatches: 31, Indels: 31
0.72 0.14 0.14
Matches are distributed among these distances:
20 10 0.06
21 58 0.36
22 82 0.51
23 12 0.07
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.56
Consensus pattern (22 bp):
TTTTTACTGATTACTCTTTTAC
Found at i:1293 original size:55 final size:55
Alignment explanation
Indices: 1232--1841 Score: 631
Period size: 55 Copynumber: 11.3 Consensus size: 55
1222 CATTTTAACT
* * *
1232 CTTAATTATTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
1287 CTTAATTACTGA-TTACT-ATTAC-----C-TTGCCTTTGATTAATCTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
** * *
1334 CTTAATTACTGATTTACTGATTACTGCTACTTTGACTCTGATTTACCTC-TTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
1388 CTTAACTATTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * * *
1443 CTTAATTAATAATTTACTGATTACTATTGCTTTGACTCTGATTAATCTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
1498 CTTAACTACTGATTTACTGATTTCTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
1553 C-------C-GATTTACTGATTACTATTACTTTAACTCTGATTAATCTC----T-
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
1595 -TT--TTACTGATTTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * * *
1647 CTGATTTACTGATTTACTGATTACTATTACTTTGACTTTGATTAATCTCTTTTCA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
1702 CTTAATTACTGATTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTA
1 CTTAATTACTG----A-T--TT-ACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* *
1765 CTTAATTACTGATTTATTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTA
1 CTTAATTACTG----A-T--TT-ACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1828 CTTAATTACTGATT
1 CTTAATTACTGATT
1842 GCCCCCTTTT
Statistics
Matches: 482, Mismatches: 42, Indels: 61
0.82 0.07 0.10
Matches are distributed among these distances:
43 1 0.00
46 1 0.00
47 107 0.22
48 7 0.01
49 5 0.01
51 1 0.00
53 6 0.01
54 53 0.11
55 185 0.38
56 1 0.00
58 1 0.00
59 2 0.00
60 1 0.00
62 2 0.00
63 109 0.23
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:1299 original size:47 final size:47
Alignment explanation
Indices: 1245--1715 Score: 384
Period size: 47 Copynumber: 9.2 Consensus size: 47
1235 AATTATTGAT
* *
1245 TTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTTACTTAA
1 TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAA
* * * *
1292 TTACTGATTACTATTACCTTGCCTTTGATTAATCTCTTTTCACTTAA
1 TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAA
* * *
1339 TTACTGATTTACTGATTACTGCTACTTTGACTCTGATTTACCTCTTTTACTTAACTATTGAT
1 TTACTGA-TTAC----TA-T--TACTTTGACTCTGATTAATCTC-TTT--TT-AC--TT-AA
*
1401 TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTAATTAATAA
1 TTACTGATTACTATTACTTTGACTCTGATTAATCTC-TTT---TT-ACT--TAA
* *
1455 TTTACTGATTACTATTGCTTTGACTCTGATTAATCTCTTTTCACTTAACTACTGAT
1 -TTACTGATTACTATTACTTTGACTCTGATTAATCTC-TTT---TT-ACT--T-AA
* * ** *
1511 TTACTGATTTCTATTACCTTGACTCTGATTAATCTCTTTTTACCGAT
1 TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAA
* * *
1558 TTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTTACTGAT
1 TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAA
*
1605 TTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTTACTGATTTACTGA
1 TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTAC----TTA---A
* *
1659 TTTACTGATTACTATTACTTTGACTTTGATTAATCTCTTTTCACTTAA
1 -TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAA
1707 TTACTGATT
1 TTACTGATT
1716 TACTGATTGA
Statistics
Matches: 363, Mismatches: 33, Indels: 56
0.80 0.07 0.12
Matches are distributed among these distances:
47 147 0.40
48 5 0.01
50 2 0.01
51 7 0.02
52 2 0.01
53 2 0.01
54 28 0.08
55 146 0.40
56 5 0.01
57 2 0.01
58 1 0.00
59 2 0.01
61 6 0.02
62 8 0.02
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (47 bp):
TTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTAA
Found at i:1348 original size:102 final size:102
Alignment explanation
Indices: 1232--1715 Score: 543
Period size: 102 Copynumber: 4.7 Consensus size: 102
1222 CATTTTAACT
* * * *
1232 CTTAATTATTGATTTACTGATTACTATTACCTTGACTCTGATTAATTTCTTTTTACTTAATTACT
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTATTTACT
* *
1297 GATTACTATTACCTTGCCTTTGATTAATCTCTTTTCA
66 GATTACTATTACCTTGACTCTGATTAATCTCTTTTCA
** * *
1334 CTTAATTACTGATTTACTGATTACTGCTACTTTGACTCTGATTTACCTCTTTTACTTAACTATTG
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTC-TTT--TT-AC--TT-
*
1399 ATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCA
59 ATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCA
* * *
1443 CTTAATTAATAATTTACTGATTACTATTGCTTTGACTCTGATTAATCTCTTTTCACTTAACTACT
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTC-TTT---TT-ACT--T
*
1508 GATTTACTGATTTCTATTACCTTGACTCTGATTAATCTC---T--
59 -ATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTCA
* * *
1548 -TT--TTACCGATTTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTTACTGATTTACT
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTATTTACT
* * *
1610 GATTACTATTACTTTAACTCTGATTAATCTCTTTTTA
66 GATTACTATTACCTTGACTCTGATTAATCTCTTTTCA
* * * * *
1647 CTGATTTACTGATTTACTGATTACTATTACTTTGACTTTGATTAATCTCTTTTCACTTAATTACT
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTATTTACT
1712 GATT
66 GATT
1716 TACTGATTGA
Statistics
Matches: 328, Mismatches: 36, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
94 35 0.11
97 4 0.01
98 2 0.01
100 1 0.00
101 3 0.01
102 139 0.42
103 3 0.01
104 2 0.01
105 2 0.01
106 2 0.01
107 1 0.00
108 3 0.01
109 86 0.26
110 45 0.14
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (102 bp):
CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTATTTACT
GATTACTATTACCTTGACTCTGATTAATCTCTTTTCA
Found at i:1564 original size:26 final size:25
Alignment explanation
Indices: 1535--1660 Score: 69
Period size: 26 Copynumber: 5.2 Consensus size: 25
1525 TACCTTGACT
1535 CTGATTAATCTCTTTTTACCGATTTA
1 CTGATTAATCTCTTTTTA-CGATTTA
* *
1561 CTGATT-A-CTATTACTTTA--A-CT-
1 CTGATTAATCTCTT--TTTACGATTTA
1582 CTGATTAATCTCTTTTTACTGATTTA
1 CTGATTAATCTCTTTTTAC-GATTTA
* *
1608 CTGATT-A-CTATTACTTTA--A-CT-
1 CTGATTAATCTCTT--TTTACGATTTA
1629 CTGATTAATCTCTTTTTACTGATTTA
1 CTGATTAATCTCTTTTTAC-GATTTA
1655 CTGATT
1 CTGATT
1661 TACTGATTAC
Statistics
Matches: 74, Mismatches: 8, Indels: 36
0.63 0.07 0.31
Matches are distributed among these distances:
21 20 0.27
22 4 0.05
23 10 0.14
24 10 0.14
25 4 0.05
26 26 0.35
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (25 bp):
CTGATTAATCTCTTTTTACGATTTA
Found at i:1656 original size:8 final size:8
Alignment explanation
Indices: 1643--1668 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1633 TTAATCTCTT
1643 TTTACTGA
1 TTTACTGA
1651 TTTACTGA
1 TTTACTGA
1659 TTTACTGA
1 TTTACTGA
1667 TT
1 TT
1669 ACTATTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (8 bp):
TTTACTGA
Found at i:1711 original size:63 final size:63
Alignment explanation
Indices: 1644--1841 Score: 342
Period size: 63 Copynumber: 3.1 Consensus size: 63
1634 TAATCTCTTT
* * * * *
1644 TTACTGATTTACTGATTTACTGATTACTATTACTTTGACTTTGATTAATCTCTTTTCACTTAA
1 TTACTGATTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAA
1707 TTACTGATTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAA
*
1770 TTACTGATTTATTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAA
1833 TTACTGATT
1 TTACTGATT
1842 GCCCCCTTTT
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 129 1.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (63 bp):
TTACTGATTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAA
Found at i:1733 original size:118 final size:121
Alignment explanation
Indices: 1596--1841 Score: 354
Period size: 126 Copynumber: 2.0 Consensus size: 121
1586 TTAATCTCTT
* *
1596 TTTACTGATTTACTGATTACTATTACTTTAACTCTGATTAATCTC-T-TT-TTACTGATTTACTG
1 TTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTATTATTACTGATTTACTG
* * * *
1658 ATTTACTGATTACTATTACTTTGACTTTGATTAATCTCTTTTCACTTAATTACTGA
66 ATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTCACTTAATTACTGA
1714 TTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAATTACTGATT
1 TTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTC---TTA-TT-ATTACTGATT
* *
1779 TATTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAATTACTGA
61 TACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTCACTTAATTACTGA
1840 TT
1 TT
1842 GCCCCCTTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
118 43 0.38
122 1 0.01
124 2 0.02
126 66 0.59
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (121 bp):
TTTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTATTATTACTGATTTACTG
ATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTCACTTAATTACTGA
Found at i:1842 original size:118 final size:117
Alignment explanation
Indices: 1597--1842 Score: 302
Period size: 118 Copynumber: 2.1 Consensus size: 117
1587 TAATCTCTTT
* * *
1597 TTACTGATTTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTTACTGATTTACTGATTT
1 TTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTGAATTACTGATTT
* ** *
1662 ACTGATTACTATTACTTTGACTTTGATTAATCTCTTTTCACTTAATTACTGAT
66 ACTGATTACTATTACTTTGACTTTAATTAA-CTCTAATCACTTAATTACTGAA
*
1715 TTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTTAATTACTGATTT
1 TTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTGAATTACTGATTT
* * * *
1780 ATTGATTGACTGATTACTATT-ACTTTAACTCTAA-T-TAATCTCTT-TTTACTTAA
66 ACTGATT-ACT-ATTACT-TTGACTTTAA-T-TAACTCTAATCACTTAATTACTGAA
1833 TTACTGATTG
1 TTACTGATTG
1843 CCCCCTTTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
118 83 0.75
119 9 0.08
120 13 0.12
121 3 0.03
122 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.50
Consensus pattern (117 bp):
TTACTGATTGACTGATTACTATTACTTTAACTCTAATTAATCTCTTTTTACTGAATTACTGATTT
ACTGATTACTATTACTTTGACTTTAATTAACTCTAATCACTTAATTACTGAA
Found at i:2663 original size:50 final size:51
Alignment explanation
Indices: 2609--2883 Score: 283
Period size: 50 Copynumber: 5.5 Consensus size: 51
2599 GGTCAAATCC
** * * * *
2609 TTATTTACTAGCTACTCT-AAAATTTAACCTTTCACCCAAAGATGACATTT
1 TTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGATGACATTT
* * * * * * *
2659 TTATTTACCAATTACT-TAAAAATTCAATTTTTTATTCAAA-AGTTAAATCT
1 TTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGA-TGACATTT
*
2709 TTATTTACTAATTACTCTAAAAATTCAATCTTTAACCCAAAGATGACATTT
1 TTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGATGACATTT
* * * * * * * *
2760 TTATTTACCAATTACT-TAAAAATT-AGTCTTTTATTCAAAGGTTAAATCT
1 TTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGATGACATTT
*
2809 TTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGAAGACATTT
1 TTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGATGACATTT
*
2860 TTATTTACCAATTACT-TAAAAATT
1 TTATTTACTAATTACTCTAAAAATT
2884 AGCCTTGTTA
Statistics
Matches: 180, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
49 34 0.19
50 73 0.41
51 72 0.40
52 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.42
Consensus pattern (51 bp):
TTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGATGACATTT
Found at i:2763 original size:51 final size:50
Alignment explanation
Indices: 2627--2883 Score: 284
Period size: 51 Copynumber: 5.1 Consensus size: 50
2617 TAGCTACTCT
* * * *
2627 AAAATTTAACCTTTCACCCAAAGATGACATTTTTATTTACCAATTACTTA
1 AAAATTCAATCTTTAACTCAAAGATGACATTTTTATTTACCAATTACTTA
* * * * * * *
2677 AAAATTCAATTTTTTATTCAAA-AGTTAAATCTTTATTTACTAATTACTCTA
1 AAAATTCAATCTTTAACTCAAAGA-TGACATTTTTATTTACCAATTACT-TA
*
2728 AAAATTCAATCTTTAACCCAAAGATGACATTTTTATTTACCAATTACTTA
1 AAAATTCAATCTTTAACTCAAAGATGACATTTTTATTTACCAATTACTTA
* * * * * * * *
2778 AAAATT-AGTCTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTA
1 AAAATTCAATCTTTAACTCAAAGATGACATTTTTATTTACCAATTACT-TA
*
2828 AAAATTCAATCTTTAACTCAAAGAAGACATTTTTATTTACCAATTACTTA
1 AAAATTCAATCTTTAACTCAAAGATGACATTTTTATTTACCAATTACTTA
2878 AAAATT
1 AAAATT
2884 AGCCTTGTTA
Statistics
Matches: 166, Mismatches: 36, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
49 33 0.20
50 60 0.36
51 72 0.43
52 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.41
Consensus pattern (50 bp):
AAAATTCAATCTTTAACTCAAAGATGACATTTTTATTTACCAATTACTTA
Found at i:2885 original size:100 final size:100
Alignment explanation
Indices: 2587--2903 Score: 474
Period size: 100 Copynumber: 3.1 Consensus size: 100
2577 AATCTTCAAA
* * ** * * *
2587 CTTTTATTCAAAGGTCAAATCCTTATTTACTAGCTACTCT-AAAATTTAACCTTTCACCCAAAGA
1 CTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAAATTCAATCTTTAACCCAAAGA
*
2651 TGACATTTTTATTTACCAATTACTTAAAAATTCAAT
66 TGACATTTTTATTTACCAATTACTTAAAAATT-AGT
* *
2687 TTTTTATTCAAAAGTTAAATCTTTATTTACTAATTACTCTAAAAATTCAATCTTTAACCCAAAGA
1 CTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAAATTCAATCTTTAACCCAAAGA
2752 TGACATTTTTATTTACCAATTACTTAAAAATTAGT
66 TGACATTTTTATTTACCAATTACTTAAAAATTAGT
*
2787 CTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAAATTCAATCTTTAACTCAAAGA
1 CTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAAATTCAATCTTTAACCCAAAGA
* *
2852 AGACATTTTTATTTACCAATTACTTAAAAATTAGC
66 TGACATTTTTATTTACCAATTACTTAAAAATTAGT
*
2887 CTTGTTATACCAAAGGT
1 CTT-TTAT-TCAAAGGT
2904 CGGATCTTTG
Statistics
Matches: 198, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
100 134 0.68
101 57 0.29
102 7 0.04
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (100 bp):
CTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAAATTCAATCTTTAACCCAAAGA
TGACATTTTTATTTACCAATTACTTAAAAATTAGT
Found at i:6642 original size:54 final size:53
Alignment explanation
Indices: 6562--6663 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 53
6552 CAGACTATGT
*
6562 CTTTTCATCTTCCACCTGAGTCGCCCTTTTCGGGTTTTCAACTCAAGTTCCTC
1 CTTTTCATCTTCCACCTGAGCCGCCCTTTTCGGGTTTTCAACTCAAGTTCCTC
*
6615 CTTTTCCATCCTT-CACTTGAGCCGCCCTTTTCGGGTTTTCAACTCAAGT
1 CTTTT-CAT-CTTCCACCTGAGCCGCCCTTTTCGGGTTTTCAACTCAAGT
6664 GACCCCCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
53 5 0.11
54 37 0.82
55 3 0.07
ACGTcount: A:0.14, C:0.33, G:0.14, T:0.39
Consensus pattern (53 bp):
CTTTTCATCTTCCACCTGAGCCGCCCTTTTCGGGTTTTCAACTCAAGTTCCTC
Done.