Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014215.1 Corchorus capsularis cultivar CVL-1 contig14236, 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: 29221
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1667 original size:22 final size:22
Alignment explanation
Indices: 1642--1844 Score: 93
Period size: 22 Copynumber: 9.5 Consensus size: 22
1632 CTGCTTATTC
* *
1642 TTTACTCTTTACTAATTACCAT
1 TTTACTCTTTACTGATTACCTT
* * *
1664 TTTACCCTTT-C-AAATACCTT
1 TTTACTCTTTACTGATTACCTT
*
1684 TTTACTTTTTTACTGATTACCTT
1 TTTAC-TCTTTACTGATTACCTT
* *
1707 TTTACCTTTTTACTGTTTA-C-T
1 TTTA-CTCTTTACTGATTACCTT
* *
1728 ATTACT-TCTTACTGATT-TC-T
1 TTTACTCT-TTACTGATTACCTT
* * * * **
1748 ATTACTCTTCATTGATTATCAC
1 TTTACTCTTTACTGATTACCTT
* ** *
1770 TTTACTCTTTACTAATTGTCAT
1 TTTACTCTTTACTGATTACCTT
1792 TTTAC-CTTTTACTGATT-CCTT
1 TTTACTC-TTTACTGATTACCTT
* *
1813 TTTACTTTTTTACTCATTACCTT
1 TTTAC-TCTTTACTGATTACCTT
1836 TTTAC-CTTT
1 TTTACTCTTT
1845 TTGCTGTTTA
Statistics
Matches: 143, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
19 1 0.01
20 37 0.26
21 22 0.15
22 50 0.35
23 32 0.22
24 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTACTCTTTACTGATTACCTT
Found at i:1695 original size:8 final size:8
Alignment explanation
Indices: 1678--1719 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1668 CCCTTTCAAA
1678 TACCTTTT
1 TACCTTTT
*
1686 TACTTTTT
1 TACCTTTT
**
1694 TA-CTGAT
1 TACCTTTT
1701 TACCTTTT
1 TACCTTTT
1709 TACCTTTT
1 TACCTTTT
1717 TAC
1 TAC
1720 TGTTTACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (8 bp):
TACCTTTT
Found at i:1743 original size:128 final size:129
Alignment explanation
Indices: 1608--1885 Score: 364
Period size: 129 Copynumber: 2.2 Consensus size: 129
1598 TTTTACTGAA
* * *
1608 TTACTGATTACCATTACAAT-TTTACTGCTTAT-TCTTTACTCTTTACTAATTACCATTTTACCC
1 TTACTGATTACCATTAC--TCTTCACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCC
* *
1671 TTT-CAAATACCTTTTTACTTTTTTACTGATTACCTTTTTACCTTTTTACTGTTTACTATTACTT
64 TTTACAAATACCTTTTTACTTTTTTACTCATTACCTTTTTACCTTTTTACTGTTTACTATTAATT
1735 C
129 C
* * * ** *
1736 TTACTGATTTCTATTACTCTTCATTGATTATCACTTTACTCTTTACTAATTGTCATTTTACCTTT
1 TTACTGATTACCATTACTCTTCACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTT
** * *
1801 TACTGATTCCTTTTTACTTTTTTACTCATTACCTTTTTACCTTTTTGCTGTTTACTATTAATTC
66 TACAAATACCTTTTTACTTTTTTACTCATTACCTTTTTACCTTTTTACTGTTTACTATTAATTC
* *
1865 TTACTGATTTCTATTACTCTT
1 TTACTGATTACCATTACTCTT
1886 TACTAATTGC
Statistics
Matches: 132, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
126 1 0.01
127 9 0.07
128 45 0.34
129 77 0.58
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (129 bp):
TTACTGATTACCATTACTCTTCACTGATTATCACTTTACTCTTTACTAATTACCATTTTACCCTT
TACAAATACCTTTTTACTTTTTTACTCATTACCTTTTTACCTTTTTACTGTTTACTATTAATTC
Found at i:1764 original size:20 final size:20
Alignment explanation
Indices: 1716--1753 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1706 TTTTACCTTT
1716 TTACTG-TTTACTATTACTTC
1 TTACTGATTT-CTATTACTTC
1736 TTACTGATTTCTATTACT
1 TTACTGATTTCTATTACT
1754 CTTCATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (20 bp):
TTACTGATTTCTATTACTTC
Found at i:1823 original size:106 final size:107
Alignment explanation
Indices: 1691--1915 Score: 266
Period size: 106 Copynumber: 2.1 Consensus size: 107
1681 CTTTTTACTT
**
1691 TTTTACTGATTACCTTTTTACCTTTTTACTGTTTA-C-TATTA-CTTCTTACTGATTT-CTATT-
1 TTTTACTGATTACCTTTTTACCTTTTTACTCATTACCTTATTACCTTCTTACTG-TTTACTATTA
* *
1751 ACTCTTCATTGATTATC-ACTTTACTCTTTACTAATTGTCATTTTACC
65 ACTCTT-ACTGATT-TCTA--TTACTCTTTACTAATTGCCA-TTTACC
* * * *
1798 TTTTACTGATT-CCTTTTTACTTTTTTACTCATTACCTTTTTACCTTTTTGCTGTTTACTATTAA
1 TTTTACTGATTACCTTTTTACCTTTTTACTCATTACCTTATTACCTTCTTACTGTTTACTATTAA
*
1862 TTCTTACTGATTTCTATTACTCTTTACTAATTGCCATTTACC
66 CTCTTACTGATTTCTATTACTCTTTACTAATTGCCATTTACC
1904 TTTTACTGATTA
1 TTTTACTGATTA
1916 TATCTTTCTT
Statistics
Matches: 102, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
106 37 0.36
107 31 0.30
108 9 0.09
109 20 0.20
110 5 0.05
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (107 bp):
TTTTACTGATTACCTTTTTACCTTTTTACTCATTACCTTATTACCTTCTTACTGTTTACTATTAA
CTCTTACTGATTTCTATTACTCTTTACTAATTGCCATTTACC
Found at i:1852 original size:129 final size:128
Alignment explanation
Indices: 1641--1885 Score: 400
Period size: 129 Copynumber: 1.9 Consensus size: 128
1631 ACTGCTTATT
*
1641 CTTTACTCTTTACTAATTACCATTTTACCCTTTCAAATACCTTTTTACTTTTTTACTGATTACCT
1 CTTTACTCTTTACTAATTACCATTTTACCCTTTCAAATACCTTTTTACTTTTTTACTCATTACCT
*
1706 TTTTACCTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTCATTGATTATCA
66 TTTTACCTTTTTACTGTTTACTATTAATTCTTACTGATTTCTATTACTCTTCATTGATTATCA
** * ** *
1769 CTTTACTCTTTACTAATTGTCATTTTACCTTTTACTGATTCCTTTTTACTTTTTTACTCATTACC
1 CTTTACTCTTTACTAATTACCATTTTACCCTTT-CAAATACCTTTTTACTTTTTTACTCATTACC
*
1834 TTTTTACCTTTTTGCTGTTTACTATTAATTCTTACTGATTTCTATTACTCTT
65 TTTTTACCTTTTTACTGTTTACTATTAATTCTTACTGATTTCTATTACTCTT
1886 TACTAATTGC
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
128 30 0.28
129 77 0.72
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (128 bp):
CTTTACTCTTTACTAATTACCATTTTACCCTTTCAAATACCTTTTTACTTTTTTACTCATTACCT
TTTTACCTTTTTACTGTTTACTATTAATTCTTACTGATTTCTATTACTCTTCATTGATTATCA
Found at i:1952 original size:129 final size:128
Alignment explanation
Indices: 1641--1953 Score: 332
Period size: 129 Copynumber: 2.4 Consensus size: 128
1631 ACTGCTTATT
* * * ** *
1641 CTTTACTCTTTACTAATTACCATTTTACCCTTT-C-AAATACCTTTTTACTTTTTTACTGATTAC
1 CTTTACTCTTTACTAATTATCATTTTA-CTTTTACTGAAT-CCTGATTACTTTTTTACTCATTAC
* * * *
1704 CTTTTTACCTTTTTACTGTTTACTATTACTTCTTACTGATTTCTATTACTCTTCATTGATTATCA
64 CTTTTTACCTTTTTACTGTTTACTATTAATTCTTACTGATTTCTATTACTCTTCACTAATTACCA
* * **
1769 CTTTACTCTTTACTAATTGTCATTTTACCTTTTACTGATTCCTTTTTACTTTTTTACTCATTACC
1 CTTTACTCTTTACTAATTATCATTTTA-CTTTTACTGAATCCTGATTACTTTTTTACTCATTACC
* * *
1834 TTTTTACCTTTTTGCTGTTTACTATTAATTCTTACTGATTTCTATTACTCTTTACTAATTGCCA
65 TTTTTACCTTTTTACTGTTTACTATTAATTCTTACTGATTTCTATTACTCTTCACTAATTACCA
* *
1898 -TTTAC-CTTTTACTGATTAT-ATCTTT-CTTATTGAACTTAATCACTGATTACTTTTTT
1 CTTTACTC-TTTACTAATTATCAT-TTTACTT-TT--ACTGAATC-CTGATTACTTTTTT
1954 TTATTGAACT
Statistics
Matches: 158, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
126 3 0.02
127 5 0.03
128 48 0.30
129 88 0.56
130 14 0.09
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.54
Consensus pattern (128 bp):
CTTTACTCTTTACTAATTATCATTTTACTTTTACTGAATCCTGATTACTTTTTTACTCATTACCT
TTTTACCTTTTTACTGTTTACTATTAATTCTTACTGATTTCTATTACTCTTCACTAATTACCA
Found at i:1960 original size:30 final size:32
Alignment explanation
Indices: 1924--2005 Score: 105
Period size: 30 Copynumber: 2.6 Consensus size: 32
1914 TATATCTTTC
1924 TTATTGAACTTAATCACTGATT-ACTTTTTT-
1 TTATTGAACTTAATCACTGATTGACTTTTTTA
* *
1954 TTATTGAACTTAATTACTGATTGCCTTTTTTA
1 TTATTGAACTTAATCACTGATTGACTTTTTTA
*
1986 CTTTTTGGAACTTAATCACT
1 -TTATT-GAACTTAATCACT
2006 CTAATCACCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 21 0.48
31 7 0.16
33 4 0.09
34 12 0.27
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (32 bp):
TTATTGAACTTAATCACTGATTGACTTTTTTA
Found at i:5527 original size:27 final size:27
Alignment explanation
Indices: 5489--5558 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
5479 GGTAAGGAAC
5489 CAAATGACCAAAATGCCCCTGAATGCA
1 CAAATGACCAAAATGCCCCTGAATGCA
* * *
5516 CAAATGACCAAAAT-ACCCTTAGTGCA
1 CAAATGACCAAAATGCCCCTGAATGCA
*
5542 AAAATGACCAAAATGCC
1 CAAATGACCAAAATGCC
5559 AATTAAGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 22 0.59
27 15 0.41
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.16
Consensus pattern (27 bp):
CAAATGACCAAAATGCCCCTGAATGCA
Found at i:5753 original size:9 final size:9
Alignment explanation
Indices: 5741--5775 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5731 CTTTTCTCCC
5741 TTTTTTTCTT
1 TTTTTTTC-T
5751 TTTTTTTCT
1 TTTTTTTCT
*
5760 TTTTCTTCT
1 TTTTTTTCT
5769 TTTTTTT
1 TTTTTTT
5776 ATAAAAGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:5754 original size:10 final size:10
Alignment explanation
Indices: 5741--5775 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5731 CTTTTCTCCC
5741 TTTTTTTCTT
1 TTTTTTTCTT
5751 TTTTTTTC-T
1 TTTTTTTCTT
*
5760 TTTTCTTCTT
1 TTTTTTTCTT
5770 TTTTTT
1 TTTTTT
5776 ATAAAAGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:5754 original size:19 final size:19
Alignment explanation
Indices: 5732--5774 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5722 TGCTTTTTGC
*
5732 TTTTCTCCCTTTTT-TTCT
1 TTTTTTCCCTTTTTCTTCT
**
5750 TTTTTTTTCTTTTTCTTCT
1 TTTTTTCCCTTTTTCTTCT
5769 TTTTTT
1 TTTTTT
5775 TATAAAAGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTCCCTTTTTCTTCT
Found at i:5762 original size:16 final size:17
Alignment explanation
Indices: 5743--5774 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5733 TTTCTCCCTT
5743 TTTTTCTT-TTTTTTTC
1 TTTTTCTTCTTTTTTTC
5759 TTTTTCTTCTTTTTTT
1 TTTTTCTTCTTTTTTT
5775 TATAAAAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTTC
Found at i:5775 original size:19 final size:18
Alignment explanation
Indices: 5740--5775 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5730 GCTTTTCTCC
5740 CTTTTTTTCTTTTTTTTT
1 CTTTTTTTCTTTTTTTTT
5758 CTTTTTCTTCTTTTTTTT
1 CTTTTT-TTCTTTTTTTT
5776 ATAAAAGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
CTTTTTTTCTTTTTTTTT
Found at i:6100 original size:70 final size:69
Alignment explanation
Indices: 5999--6682 Score: 847
Period size: 70 Copynumber: 9.9 Consensus size: 69
5989 GGAAATGAAC
* * * * * *
5999 TTGGCTTATGGAAAAGCCC---CTGCTTGAATGGAACCAAGGC-TAAACTAACTCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCCTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
6060 GAGT
66 GAGT
* *
6064 TTGCCTTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAA
1 TTGGC-TTGTGGAAAAGC-CCTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAA
6129 ACGAGT
64 ACGAGT
* *
6135 TTGGCTTGTGGAAAAGCCGCT-ACTGCTTGGATAGAACCAAGGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCC-CTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
6199 CGAGT
65 CGAGT
* * * * *
6204 TTGGCTTGTGGAAAAGCCTCTAAATGTTTGGATGGAACCAAAGCTTGAACTGACTCGTACGTAAA
1 TTGGCTTGTGGAAAAGCC-CTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
*
6269 CAAGT
65 CGAGT
*
6274 TTGGCTTGTGGAAAAGCCCTTG-CTGCTTGGATGG-A--AAGGCTTGAACT-ATCTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCC-TGAATGCTTGGATGGAACCAAGGCTTGAACTGA-CTCGTATGGAA
6334 ACGAGT
64 ACGAGT
* * *
6340 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAAGTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAG-CCCTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
6405 CGAGT
65 CGAGT
* * *
6410 TTGGCTTTTGGAAAAGCCGTTG-CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAGCC-CTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
6474 CGAGT
65 CGAGT
* * * * * *
6479 TTGGCTTGTGAAAAAGCCCCTAAATGTTTGAATGGAACCAAAGCTTGAACTGTCTCGTATGGAAA
1 TTGGCTTGTGGAAAAG-CCCTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAA
*
6544 CAAGT
65 CGAGT
* *
6549 TTGGCTTGTGGAAAAGCTCTTG-CTGCTTGGATGGAACCAAGGCTTGAACT-ATCTCGTATGGAA
1 TTGGCTTGTGGAAAAGC-CCTGAATGCTTGGATGGAACCAAGGCTTGAACTGA-CTCGTATGGAA
6612 ACGAGT
64 ACGAGT
* *
6618 TTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCACA-GCTTGAACTGACTCGTGTGGAA
1 TTGGCTTGTGGAAAAG-CCCTGAATGCTTGGATGGAACCA-AGGCTTGAACTGACTCGTATGGAA
6682 A
64 A
6683 AGTCAAAGCA
Statistics
Matches: 537, Mismatches: 57, Indels: 45
0.84 0.09 0.07
Matches are distributed among these distances:
65 5 0.01
66 54 0.10
67 16 0.03
68 2 0.00
69 198 0.37
70 233 0.43
71 29 0.05
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCCTGAATGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
GAGT
Found at i:6235 original size:139 final size:137
Alignment explanation
Indices: 5999--6682 Score: 984
Period size: 139 Copynumber: 5.0 Consensus size: 137
5989 GGAAATGAAC
* * * *
5999 TTGGCTTATGGAAAAGCCC--CTGCTTGAATGGAACCAAGGC-TAAACTAACTCATATGGAAACG
1 TTGGCTTGTGGAAAAGCCCTGCTGCTTGGATGGAACCAAGGCTTGAACT-ACTCGTATGGAAACG
* *
6061 AGTTTGCCTTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATG
65 AGTTTGGC-TTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATG
*
6126 GAAACGAGT
129 GAAACAAGT
* *
6135 TTGGCTTGTGGAAAAGCCGCTACTGCTTGGATAGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCC-CTGCTGCTTGGATGGAACCAAGGCTTGAACT-ACTCGTATGGAAAC
* * * *
6200 GAGTTTGGCTTGTGGAAAAGCCTCTAAATGTTTGGATGGAACCAAAGCTTGAACTGACTCGTACG
64 GAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATG
*
6265 TAAACAAGT
129 GAAACAAGT
6274 TTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGG-A--AAGGCTTGAACTATCTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCC-TGCTGCTTGGATGGAACCAAGGCTTGAACTA-CTCGTATGGAAAC
* *
6336 GAGTTTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAAGTGACTCGTATG
64 GAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATG
*
6401 GAAACGAGT
129 GAAACAAGT
* *
6410 TTGGCTTTTGGAAAAGCCGTTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCC-CTGCTGCTTGGATGGAACCAAGGCTTGAACT-ACTCGTATGGAAAC
* * * * *
6475 GAGTTTGGCTTGTGAAAAAGCCCCTAAATGTTTGAATGGAACCAAAGCTTGAACTGTCTCGTATG
64 GAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATG
6540 GAAACAAGT
129 GAAACAAGT
*
6549 TTGGCTTGTGGAAAAGCTCTTGCTGCTTGGATGGAACCAAGGCTTGAACTATCTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGC-CCTGCTGCTTGGATGGAACCAAGGCTTGAACTA-CTCGTATGGAAAC
* * *
6614 GAGTTTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCACAGCTTGAACTGACTCGTGTG
64 GAGTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATG
6679 GAAA
129 GAAA
6683 AGTCAAAGCA
Statistics
Matches: 492, Mismatches: 43, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
135 1 0.00
136 139 0.28
137 2 0.00
138 3 0.01
139 319 0.65
140 28 0.06
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (137 bp):
TTGGCTTGTGGAAAAGCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTACTCGTATGGAAACGA
GTTTGGCTTGTGGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGA
AACAAGT
Found at i:6496 original size:275 final size:277
Alignment explanation
Indices: 5999--6682 Score: 1101
Period size: 275 Copynumber: 2.5 Consensus size: 277
5989 GGAAATGAAC
* * * * *
5999 TTGGCTTATGGAAAAGCCC---CTGCTTGAATGGAACCAAGGC-TAAACTAACTCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAA-CAAGGCTTGAACTATCTCGTATGGAAAC
* * *
6060 GAGTTTGCCTTTGTGGAAAAGCTCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTAT
65 GAGTTTGGC-TTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTAT
6125 GGAAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATAGAACCAAGGCTTGAACTGACTC
129 GGAAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATAGAACCAAGGCTTGAACTGACTC
* * *
6190 GTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTCTAAATGTTTGGATGGAACCAAAGCTTGAACT
194 GTATGGAAACGAGTTTGGCTTGTGAAAAAGCCCCTAAATGTTTGAATGGAACCAAAGCTTGAACT
*
6255 GACTCGTACGTAAACAAGT
259 GACTCGTACGGAAACAAGT
6274 TTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGG-A-AAGGCTTGAACTATCTCGTATGGAAACG
1 TTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAACAAGGCTTGAACTATCTCGTATGGAAACG
*
6337 AGTTTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAAGTGACTCGTATGG
66 AGTTTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGG
* * * *
6402 AAACGAGTTTGGCTTTTGGAAAAGCCGTTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGT
131 AAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATAGAACCAAGGCTTGAACTGACTCGT
*
6467 ATGGAAACGAGTTTGGCTTGTGAAAAAGCCCCTAAATGTTTGAATGGAACCAAAGCTTGAACTGT
196 ATGGAAACGAGTTTGGCTTGTGAAAAAGCCCCTAAATGTTTGAATGGAACCAAAGCTTGAACTGA
*
6532 CTCGTATGGAAACAAGT
261 CTCGTACGGAAACAAGT
*
6549 TTGGCTTGTGGAAAAGCTCTTGCTGCTTGGATGGAACCAAGGCTTGAACTATCTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAA-CAAGGCTTGAACTATCTCGTATGGAAAC
* *
6614 GAGTTTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCACAGCTTGAACTGACTCGTGTG
65 GAGTTTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATG
6679 GAAA
130 GAAA
6683 AGTCAAAGCA
Statistics
Matches: 379, Mismatches: 23, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
275 247 0.65
276 27 0.07
277 1 0.00
278 104 0.27
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (277 bp):
TTGGCTTGTGGAAAAGCCCTTGCTGCTTGGATGGAACAAGGCTTGAACTATCTCGTATGGAAACG
AGTTTGGCTTGTGGAAAAGCCCCTGCATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGG
AAACGAGTTTGGCTTGTGGAAAAGCCGCTACTGCTTGGATAGAACCAAGGCTTGAACTGACTCGT
ATGGAAACGAGTTTGGCTTGTGAAAAAGCCCCTAAATGTTTGAATGGAACCAAAGCTTGAACTGA
CTCGTACGGAAACAAGT
Found at i:7221 original size:50 final size:50
Alignment explanation
Indices: 7157--7255 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
7147 AAAATGCCCT
*
7157 TTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATC
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC
* * *
7207 TTGAAAATCGAATTTTGATATTGGACTTACAAATGGAATGCAATCTTAT
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTAT
7256 TATAAAACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (50 bp):
TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAATGCAATCTTATC
Found at i:8222 original size:21 final size:21
Alignment explanation
Indices: 8169--8230 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
8159 TTAGGCCAAG
*
8169 GTTTTTCTT-TTCTTTTCTTTTT
1 GTTTTTCTTCTT-TTTT-TCTTT
*
8191 CTTTTTCCTTCTTTTTTTCTTT
1 GTTTTT-CTTCTTTTTTTCTTT
8213 GTTTTTCTTCTTTATTTT
1 GTTTTTCTTCTTT-TTTT
8231 GAATGTGAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 7 0.21
22 18 0.53
23 7 0.21
24 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (21 bp):
GTTTTTCTTCTTTTTTTCTTT
Found at i:8876 original size:44 final size:44
Alignment explanation
Indices: 8765--8949 Score: 280
Period size: 44 Copynumber: 4.2 Consensus size: 44
8755 ACAACTTTGG
* *
8765 AAAACCATTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTGA
1 AAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTT-T
* *
8810 AAAACCGTTTTATCAAAACCTTTTGAAAACCATGACTCTTTTTT
1 AAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTTT
* *
8854 AAAACCATTTTATCAAATCCTTTTAAAAACCATGGCTCTTTTTT
1 AAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTTT
* * *
8898 AAAACCATTTTATCAAATCCTTTTAAAAACCATGGCTCTTTTTG
1 AAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTTT
8942 AAAACCAT
1 AAAACCAT
8950 CATTGCTTTT
Statistics
Matches: 133, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
44 91 0.68
45 42 0.32
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (44 bp):
AAAACCATTTTATCAAAACCTTTTAAAAACCATGACTCTTTTTT
Found at i:8882 original size:25 final size:25
Alignment explanation
Indices: 8849--8930 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
8839 CCATGACTCT
*
8849 TTTTTAAAACCATTTTATCAAATCC
1 TTTTAAAAACCATTTTATCAAATCC
** *
8874 TTTTAAAAACCA---TGGC---TCT
1 TTTTAAAAACCATTTTATCAAATCC
*
8893 TTTTTAAAACCATTTTATCAAATCC
1 TTTTAAAAACCATTTTATCAAATCC
8918 TTTTAAAAACCAT
1 TTTTAAAAACCAT
8931 GGCTCTTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
19 13 0.31
22 4 0.10
25 25 0.60
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (25 bp):
TTTTAAAAACCATTTTATCAAATCC
Found at i:8969 original size:9 final size:9
Alignment explanation
Indices: 8955--8996 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
8945 ACCATCATTG
8955 CTTTTTTCT
1 CTTTTTTCT
8964 CTTTTTTCT
1 CTTTTTTCT
8973 -TTCTTTTCCT
1 CTT-TTTT-CT
8983 CTTTTTTCT
1 CTTTTTTCT
8992 CTTTT
1 CTTTT
8997 CATTATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.07
9 20 0.67
10 6 0.20
11 2 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
CTTTTTTCT
Found at i:8973 original size:7 final size:7
Alignment explanation
Indices: 8955--9031 Score: 50
Period size: 7 Copynumber: 11.0 Consensus size: 7
8945 ACCATCATTG
8955 CTTTTTT
1 CTTTTTT
*
8962 CTCTTTT
1 CTTTTTT
*
8969 -TTCTTT
1 CTTTTTT
*
8975 CTTTTCCT
1 CTTTT-TT
8983 CTTTTTT
1 CTTTTTT
*
8990 CTCTTTT
1 CTTTTTT
* *
8997 CATTATT
1 CTTTTTT
*
9004 CATTTTT
1 CTTTTTT
9011 CTTTCTTT
1 CTTT-TTT
*
9019 -TTCTTT
1 CTTTTTT
9025 CTTTTTT
1 CTTTTTT
9032 TGGGAAATTG
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
6 7 0.13
7 36 0.69
8 9 0.17
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (7 bp):
CTTTTTT
Found at i:9513 original size:75 final size:75
Alignment explanation
Indices: 9407--9558 Score: 216
Period size: 75 Copynumber: 2.0 Consensus size: 75
9397 TGGATTCAAT
* * *
9407 CACCTTGAAATCATTGCTTTGACTAAAACTGATTTTGAAA-CATCTTTTGATTAAAACTCATCAT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAAGC-TCTTTTGAATAAAACTCATCAT
*
9471 TCTTTTGCTCA
65 TCCTTTGCTCA
* * * *
9482 CACCTCGAAACCATTTCTTTGATTGAAACTGATTTTGAAAGCTGTTTTGAATAAAACTCATCATT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAAGCTCTTTTGAATAAAACTCATCATT
9547 CCTTTGCTCA
66 CCTTTGCTCA
9557 CA
1 CA
9559 GTCTAGATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 67 0.99
76 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (75 bp):
CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAAGCTCTTTTGAATAAAACTCATCATT
CCTTTGCTCA
Found at i:16681 original size:2 final size:2
Alignment explanation
Indices: 16668--16706 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
16658 ACTAAAACTA
* *
16668 AT AT AT AGT AT AT AT AT AT AT AC AT AT AT AC AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16707 TTGCTATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:17404 original size:25 final size:25
Alignment explanation
Indices: 17369--17422 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
17359 TGAGGGGCCA
17369 GTTCGCGGTTGAATCGGTTCGACCG
1 GTTCGCGGTTGAATCGGTTCGACCG
*
17394 GTTCGCTGTTGAATCGGTTCGACCG
1 GTTCGCGGTTGAATCGGTTCGACCG
17419 GTTC
1 GTTC
17423 AACCGTCCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.11, C:0.24, G:0.33, T:0.31
Consensus pattern (25 bp):
GTTCGCGGTTGAATCGGTTCGACCG
Found at i:19972 original size:44 final size:44
Alignment explanation
Indices: 19913--20008 Score: 147
Period size: 44 Copynumber: 2.2 Consensus size: 44
19903 TTTTTTATTA
* * *
19913 TTATTATTTTGTTTGGTTAGAATATTTTGTCAAACATTAATATG
1 TTATGATTTGGTTTGGTTAGAATATTTTGTCAAACATTAAGATG
* *
19957 TTATGATTTGGTTTGGTTAGAATATTTTGTCTAACATTCAGATG
1 TTATGATTTGGTTTGGTTAGAATATTTTGTCAAACATTAAGATG
20001 TTATGATT
1 TTATGATT
20009 GTCATGTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.27, C:0.05, G:0.17, T:0.51
Consensus pattern (44 bp):
TTATGATTTGGTTTGGTTAGAATATTTTGTCAAACATTAAGATG
Found at i:23684 original size:89 final size:89
Alignment explanation
Indices: 23533--23711 Score: 331
Period size: 89 Copynumber: 2.0 Consensus size: 89
23523 ATCGTATGAG
23533 GCTTTGTTTCTTACAAACAGGTGTGAAAATAAGCGCTCATGTTGGAAAACAGAGGAACAACTTTT
1 GCTTTGTTTCTTACAAACAGGTGTGAAAATAAGCGCTCATGTTGGAAAACAGAGGAACAACTTTT
23598 TTTATAGTGAAGTTAACATTCCAT
66 TTTATAGTGAAGTTAACATTCCAT
* * *
23622 GCTTTGTTTCTTACAAAGAGGTGTGAAAATAAGTGCTCCTGTTGGAAAACAGAGGAACAACTTTT
1 GCTTTGTTTCTTACAAACAGGTGTGAAAATAAGCGCTCATGTTGGAAAACAGAGGAACAACTTTT
23687 TTTATAGTGAAGTTAACATTCCAT
66 TTTATAGTGAAGTTAACATTCCAT
23711 G
1 G
23712 ACACATTGTT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (89 bp):
GCTTTGTTTCTTACAAACAGGTGTGAAAATAAGCGCTCATGTTGGAAAACAGAGGAACAACTTTT
TTTATAGTGAAGTTAACATTCCAT
Found at i:26092 original size:37 final size:35
Alignment explanation
Indices: 26039--26110 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 35
26029 AATGAAACAT
26039 TCCATATTACCGTCAATCAATTGTTGCGATTATTACC
1 TCCATATTACCGTCAATCAATTGTTGC-A-TATTACC
*
26076 TCCATATTACCTTCAATCAATTGTTGCATATTACC
1 TCCATATTACCGTCAATCAATTGTTGCATATTACC
26111 CAAAATGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 7 0.21
36 1 0.03
37 26 0.76
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (35 bp):
TCCATATTACCGTCAATCAATTGTTGCATATTACC
Found at i:28083 original size:16 final size:16
Alignment explanation
Indices: 28062--28093 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28052 ATTTGATATG
28062 TTTTTTAATTTCCAAC
1 TTTTTTAATTTCCAAC
*
28078 TTTTTTTATTTCCAAC
1 TTTTTTAATTTCCAAC
28094 AAACTACATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTTAATTTCCAAC
Done.