Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006736.1 Corchorus capsularis cultivar CVL-1 contig06757, 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: 86307
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1527 original size:26 final size:26
Alignment explanation
Indices: 1498--1602 Score: 108
Period size: 26 Copynumber: 4.0 Consensus size: 26
1488 AATTGGTAAT
1498 CAGTAATCAGTAAAAAGAGTAAGAAA
1 CAGTAATCAGTAAAAAGAGTAAGAAA
*
1524 CAGTATTCAGTAAAAAGAGTAAGAAA
1 CAGTAATCAGTAAAAAGAGTAAGAAA
* * * *
1550 -AGAATCATCAGTAAAAAGTGTAGGAAG
1 CAG--TAATCAGTAAAAAGAGTAAGAAA
1577 C--TATATCCAGTAAAAAGAGTAAGAAA
1 CAGTA-AT-CAGTAAAAAGAGTAAGAAA
1603 AAAAGCAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.02
25 4 0.06
26 41 0.64
27 18 0.28
ACGTcount: A:0.53, C:0.09, G:0.20, T:0.18
Consensus pattern (26 bp):
CAGTAATCAGTAAAAAGAGTAAGAAA
Found at i:1565 original size:53 final size:53
Alignment explanation
Indices: 1503--1603 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
1493 GTAATCAGTA
*
1503 ATCAGTAAAAAGAGTAAGAAAC-AGTATTCAGTAAAAAGAGTAAGAAAAGAATC
1 ATCAGTAAAAAGAGTAAGAAACTA-TATCCAGTAAAAAGAGTAAGAAAAGAATC
* * *
1556 ATCAGTAAAAAGTGTAGGAAGCTATATCCAGTAAAAAGAGTAAGAAAA
1 ATCAGTAAAAAGAGTAAGAAACTATATCCAGTAAAAAGAGTAAGAAAA
1604 AAAGCAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 42 0.98
54 1 0.02
ACGTcount: A:0.54, C:0.08, G:0.20, T:0.18
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAAGAAACTATATCCAGTAAAAAGAGTAAGAAAAGAATC
Found at i:1739 original size:22 final size:22
Alignment explanation
Indices: 1713--1804 Score: 91
Period size: 22 Copynumber: 4.2 Consensus size: 22
1703 AATGGTAGGG
*
1713 AGTAATCCGTAAAAGGTAAAAT
1 AGTAATCAGTAAAAGGTAAAAT
* * *
1735 GGTAATCAGTAAGA-GCAAAAT
1 AGTAATCAGTAAAAGGTAAAAT
*
1756 AGTAATCAGTAAAAAGTAAGAA-
1 AGTAATCAGTAAAAGGTAA-AAT
*
1778 GGTAATCAGT-AAAGAGTAAAAT
1 AGTAATCAGTAAAAG-GTAAAAT
1800 AGTAA
1 AGTAA
1805 AAAAGTGATG
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
21 23 0.41
22 31 0.55
23 2 0.04
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (22 bp):
AGTAATCAGTAAAAGGTAAAAT
Found at i:1745 original size:29 final size:29
Alignment explanation
Indices: 1655--1746 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
1645 AGGTCAAATT
* *
1655 GTAATCAGTAAAATGTGAAAA-GGCAATCA
1 GTAATCAGTAAAAGGT-AAAATGGTAATCA
** ***
1684 GTAAAGAGTAAAATGGTAAAATGGTAGGGA
1 GTAATCAGTAAAA-GGTAAAATGGTAATCA
*
1714 GTAATCCGTAAAAGGTAAAATGGTAATCA
1 GTAATCAGTAAAAGGTAAAATGGTAATCA
1743 GTAA
1 GTAA
1747 GAGCAAAATA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 32 0.67
30 16 0.33
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.22
Consensus pattern (29 bp):
GTAATCAGTAAAAGGTAAAATGGTAATCA
Found at i:1761 original size:43 final size:43
Alignment explanation
Indices: 1713--1970 Score: 236
Period size: 43 Copynumber: 6.1 Consensus size: 43
1703 AATGGTAGGG
* *
1713 AGTAATCCGTAAAAGGTAAAATGGTAATCAGT-AAGAGCAAAAT
1 AGTAATCAGTAAAA-GTAAAATGGTAATCAGTAAAGAGTAAAAT
1756 AGTAATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAAT
1 AGTAATCAGT-AAAAGTAA-AATGGTAATCAGTAAAGAGTAAAAT
* **
1800 AGT-A--A--AAAAGT--GATGACAATCAGTAAA-AGGTAAAAT
1 AGTAATCAGTAAAAGTAAAATGGTAATCAGTAAAGA-GTAAAAT
* * ** * *
1836 GGTAATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAA-
1 AGTAATCAGTAAAAGTAAAATGGTAATCAGTAAAGAGTAAAAT
*
1878 AGGTAATCAGTAAGAA-CAAAATGGTAATCAGTAAAGAGTAAAAT
1 A-GTAATCAGTAA-AAGTAAAATGGTAATCAGTAAAGAGTAAAAT
*
1922 AGTAATCAGTAAAAAGTAAGAA-GATAATCAGTAAAGAGTAAAAT
1 AGTAATCAGT-AAAAGTAA-AATGGTAATCAGTAAAGAGTAAAAT
1966 AGTAA
1 AGTAA
1971 AAAAGTAATC
Statistics
Matches: 176, Mismatches: 20, Indels: 37
0.76 0.09 0.16
Matches are distributed among these distances:
35 2 0.01
36 20 0.11
37 1 0.01
38 6 0.03
39 1 0.01
41 5 0.03
43 87 0.49
44 52 0.30
45 2 0.01
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.20
Consensus pattern (43 bp):
AGTAATCAGTAAAAGTAAAATGGTAATCAGTAAAGAGTAAAAT
Found at i:1790 original size:65 final size:66
Alignment explanation
Indices: 1714--2017 Score: 221
Period size: 65 Copynumber: 4.7 Consensus size: 66
1704 ATGGTAGGGA
* *
1714 GTAATCCGTAAAAG-GTAAAATGGTAATCAGT-AAGAGCAAAATAGTAATCAGTAAAAAGTAAGA
1 GTAATCAGTAAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATAGTAATCAGTAAAAAGTAA-A
1777 AG
65 AG
* * *
1779 GTAATCAGT-AAAGAGTAAAATAGTAA--A--AAAGTG----AT-GACAATCAGTAAAAGGTAAA
1 GTAATCAGTAAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATAG-TAATCAGTAAAAAGTAAA
1834 ATG
65 A-G
** * *
1837 GTAATCAGT--AAGAGCGAAATAGTAATCAGTAAAGAGCAAAA-AGGTAATCAGTAAGAA-CAAA
1 GTAATCAGTAAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATA-GTAATCAGTAAAAAGTAAA
1898 ATG
65 A-G
* **
1901 GTAATCAGT-AAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGATAATCAGTAAAGAGTAAAA
1 GTAATCAGTAAAAGAGTAAAATAGTAATCAGT--AAAG--AGCA-A-AAT-AGTAATCAGTAAAA
*
1965 TAGTAAAAAA
59 -AGT-AAAAG
* *
1975 GTAATCAATAAAAG-GTAAAATAGTAGTCAGTAAAGAGCAAAAT
1 GTAATCAGTAAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAAT
2018 GGTTATTAGA
Statistics
Matches: 189, Mismatches: 23, Indels: 51
0.72 0.09 0.19
Matches are distributed among these distances:
57 17 0.09
58 27 0.14
59 1 0.01
61 5 0.03
62 4 0.02
63 1 0.01
64 19 0.10
65 49 0.26
66 1 0.01
67 4 0.02
68 3 0.02
69 4 0.02
70 4 0.02
71 2 0.01
72 14 0.07
73 2 0.01
74 24 0.13
75 8 0.04
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.20
Consensus pattern (66 bp):
GTAATCAGTAAAAGAGTAAAATAGTAATCAGTAAAGAGCAAAATAGTAATCAGTAAAAAGTAAAA
G
Found at i:1845 original size:22 final size:23
Alignment explanation
Indices: 1817--1970 Score: 139
Period size: 22 Copynumber: 7.1 Consensus size: 23
1807 AAGTGATGAC
1817 AATCAGTAAAAG-GTAAAATGGT
1 AATCAGTAAAAGAGTAAAATGGT
** *
1839 AATCAGT--AAGAGCGAAATAGT
1 AATCAGTAAAAGAGTAAAATGGT
* *
1860 AATCAGT-AAAGAGCAAAAAGGT
1 AATCAGTAAAAGAGTAAAATGGT
**
1882 AATCAGT--AAGAACAAAATGGT
1 AATCAGTAAAAGAGTAAAATGGT
*
1903 AATCAGT-AAAGAGTAAAATAGT
1 AATCAGTAAAAGAGTAAAATGGT
*
1925 AATCAGTAAAA-AGTAAGAA-GAT
1 AATCAGTAAAAGAGTAA-AATGGT
*
1947 AATCAGT-AAAGAGTAAAATAGT
1 AATCAGTAAAAGAGTAAAATGGT
1969 AA
1 AA
1971 AAAAGTAATC
Statistics
Matches: 110, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
20 3 0.03
21 38 0.35
22 64 0.58
23 5 0.05
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.19
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAATGGT
Found at i:1860 original size:101 final size:101
Alignment explanation
Indices: 1635--1890 Score: 329
Period size: 101 Copynumber: 2.5 Consensus size: 101
1625 GAGTAATTGA
* * * *
1635 AATCAGTAAGAG-GTCAAATTGTAATCAGTAAAATGTGAAAAGGCAATCAGTAAAGAGTAAAATG
1 AATCAGTAAGAGCG--AAATAGTAATCAGTAAAAAGT-AAAAGGTAATCAGTAAAGAGTAAAATA
** * *
1699 GTAAAATGGTAGGGAGTAATCCGTAAAAGGTAAAATGGT
63 GTAAAAAAGTAGGGAGCAATCAGTAAAAGGTAAAATGGT
*
1738 AATCAGTAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAGAGCGAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAGTAAAGAGTAAAATAGT
*
1803 AAAAAAGT-GATGA-CAATCAGTAAAAGGTAAAATGGT
65 AAAAAAGTAG-GGAGCAATCAGTAAAAGGTAAAATGGT
* *
1839 AATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAAAGGTAATCAGTAA
1 AATCAGTAAGAGCGAAATAGTAATCAGTAAAAAG-TAAAAGGTAATCAGTAA
1891 GAACAAAATG
Statistics
Matches: 136, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
101 70 0.51
102 54 0.40
103 12 0.09
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (101 bp):
AATCAGTAAGAGCGAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAGTAAAGAGTAAAATAGTA
AAAAAGTAGGGAGCAATCAGTAAAAGGTAAAATGGT
Found at i:1980 original size:30 final size:30
Alignment explanation
Indices: 1929--1999 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
1919 AATAGTAATC
* *
1929 AGTAAAA-AGT-AAGAAGATAATCAGTAAA
1 AGTAAAATAGTAAAAAAGATAATCAATAAA
1957 GAGTAAAATAGTAAAAAAG-TAATCAATAAA
1 -AGTAAAATAGTAAAAAAGATAATCAATAAA
1987 AGGTAAAATAGTA
1 A-GTAAAATAGTA
2000 GTCAGTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.22
30 24 0.65
31 5 0.14
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.20
Consensus pattern (30 bp):
AGTAAAATAGTAAAAAAGATAATCAATAAA
Found at i:1987 original size:52 final size:52
Alignment explanation
Indices: 1914--2017 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 52
1904 ATCAGTAAAG
* * *
1914 AGTAAAATAGTAATCAGTAAAAAGTAAGAAGA-TAATCAGTAAAGAGTAAAAT
1 AGTAAAAAAGTAATCAATAAAAAGTAA-AAGAGTAATCAGTAAAGAGCAAAAT
* * *
1966 AGTAAAAAAGTAATCAATAAAAGGTAAAATAGTAGTCAGTAAAGAGCAAAAT
1 AGTAAAAAAGTAATCAATAAAAAGTAAAAGAGTAATCAGTAAAGAGCAAAAT
2018 GGTTATTAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
51 3 0.07
52 42 0.93
ACGTcount: A:0.58, C:0.05, G:0.17, T:0.20
Consensus pattern (52 bp):
AGTAAAAAAGTAATCAATAAAAAGTAAAAGAGTAATCAGTAAAGAGCAAAAT
Found at i:1999 original size:22 final size:22
Alignment explanation
Indices: 1967--2008 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1957 GAGTAAAATA
1967 GTAAAAAAGTAATCAATAAAAG
1 GTAAAAAAGTAATCAATAAAAG
* * *
1989 GTAAAATAGTAGTCAGTAAA
1 GTAAAAAAGTAATCAATAAA
2009 GAGCAAAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.21
Consensus pattern (22 bp):
GTAAAAAAGTAATCAATAAAAG
Found at i:6281 original size:3 final size:3
Alignment explanation
Indices: 6269--6297 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6259 CAAAAGCCGG
6269 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
6298 TCCCATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:20235 original size:24 final size:25
Alignment explanation
Indices: 20184--20237 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
20174 GAGTTGTGGC
* *
20184 AAAAATGAGCAAAATTTGCCAACCA
1 AAAAAAGAGCAAAATTTGCCAACAA
20209 AAAAAAGAGCAAAATTT-CC-ACAA
1 AAAAAAGAGCAAAATTTGCCAACAA
20232 AAAAAA
1 AAAAAA
20238 AAATACAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 9 0.33
24 2 0.07
25 16 0.59
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (25 bp):
AAAAAAGAGCAAAATTTGCCAACAA
Found at i:32854 original size:2 final size:2
Alignment explanation
Indices: 32847--32873 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32837 TGTTTCGTTC
32847 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
32874 TATTTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40068 original size:19 final size:19
Alignment explanation
Indices: 40040--40076 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40030 GACAATGACA
40040 AGTTCGTCGGT-CTCGGTC
1 AGTTCGTCGGTGCTCGGTC
40058 AGTTCCGTCGGTGCTCGGT
1 AGTT-CGTCGGTGCTCGGT
40077 GGATTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 7 0.41
20 6 0.35
ACGTcount: A:0.05, C:0.27, G:0.35, T:0.32
Consensus pattern (19 bp):
AGTTCGTCGGTGCTCGGTC
Found at i:49592 original size:20 final size:20
Alignment explanation
Indices: 49567--49609 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
49557 TTCGTGTTGG
* *
49567 TTATAAGTAGATTACATGTT
1 TTATAAGCAGATTAAATGTT
49587 TTATAAGCAGATTAAATGTT
1 TTATAAGCAGATTAAATGTT
49607 TTA
1 TTA
49610 AAATATCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (20 bp):
TTATAAGCAGATTAAATGTT
Found at i:50755 original size:2 final size:2
Alignment explanation
Indices: 50748--50789 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
50738 GCGACTTTTA
* * *
50748 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AA AA AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50789 A
1 A
50790 AAAAAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:50784 original size:15 final size:14
Alignment explanation
Indices: 50752--50795 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
50742 CTTTTAATAT
* * *
50752 ATATATATATATAT
1 ATATATATAAAAAA
50766 ATATATTATAAAAAA
1 ATATA-TATAAAAAA
50781 ATATATATAAAAAA
1 ATATATATAAAAAA
50795 A
1 A
50796 ATTATCTAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATATATAAAAAA
Found at i:50796 original size:15 final size:17
Alignment explanation
Indices: 50764--50797 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
50754 ATATATATAT
50764 ATATATATTATAAAAAA
1 ATATATATTATAAAAAA
50781 ATATATA-TA-AAAAAA
1 ATATATATTATAAAAAA
50796 AT
1 AT
50798 TATCTAGCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATATTATAAAAAA
Found at i:50814 original size:65 final size:67
Alignment explanation
Indices: 50710--50845 Score: 224
Period size: 65 Copynumber: 2.1 Consensus size: 67
50700 ATATATAAAA
50710 AAAAAAATTATAAAAAAAAAAGTATCTAGCGACTTTTAATATATATATATATATATATA-TAT-T
1 AAAAAAATTATAAAAAAAAAAGTATCTAGCGACTTTTAATATATATATATATATATATATTATAT
50773 AT
66 AT
* *
50775 AAAAAAATATATATAAAAAAAATTATCTAGCG-CTTTTAATATATATATATATATATATATTATA
1 AAAAAAAT-TATAAAAAAAAAAGTATCTAGCGACTTTTAATATATATATATATATATATATTATA
50839 TAT
65 TAT
50842 AAAA
1 AAAA
50846 GTACGAATAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
65 35 0.53
66 24 0.36
67 7 0.11
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (67 bp):
AAAAAAATTATAAAAAAAAAAGTATCTAGCGACTTTTAATATATATATATATATATATATTATAT
AT
Found at i:50820 original size:2 final size:2
Alignment explanation
Indices: 50813--50842 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
50803 AGCGCTTTTA
50813 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50843 AAAGTACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51266 original size:6 final size:6
Alignment explanation
Indices: 51255--51288 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
51245 TCTCTCTTTC
*
51255 TTTCTT TTTCTT TTTCTT TTTCTA TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
51289 CAGCTGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:51847 original size:2 final size:2
Alignment explanation
Indices: 51838--51885 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
51828 ATTTTTTTTT
*
51838 TA TA -A TA TA TA TA TA TA TA TT TA -A TA -A 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
51877 TA TA TA TA T
1 TA TA TA TA T
51886 GTTAATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51869 original size:14 final size:15
Alignment explanation
Indices: 51846--51893 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
51836 TTTATAATAT
51846 ATATATATATATTTA
1 ATATATATATATTTA
*
51861 ATA-ATATATATAT-
1 ATATATATATATTTA
51874 ATATATATATATGTTA
1 ATATATATATAT-TTA
51890 ATAT
1 ATAT
51894 TTAAATTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 3 0.11
14 17 0.61
15 4 0.14
16 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATATATATATATTTA
Found at i:57727 original size:19 final size:19
Alignment explanation
Indices: 57703--57740 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
57693 TTTTTGGTCC
57703 TATATCCTTAAATTTAAAT
1 TATATCCTTAAATTTAAAT
57722 TATATCCTTAAATTTAAAT
1 TATATCCTTAAATTTAAAT
57741 CAATTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATCCTTAAATTTAAAT
Found at i:62730 original size:10 final size:10
Alignment explanation
Indices: 62709--62760 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
62699 TGGATGGCTT
62709 GGCATAGGCCG
1 GGCAT-GGCCG
62720 GGCATGGCCG
1 GGCATGGCCG
62730 GGCATAGTGCGCG
1 GGCAT-G-GC-CG
* *
62743 GACAAGGCCG
1 GGCATGGCCG
62753 GGCATGGC
1 GGCATGGC
62761 ACGGTGATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 18 0.53
11 8 0.24
12 3 0.09
13 5 0.15
ACGTcount: A:0.17, C:0.27, G:0.46, T:0.10
Consensus pattern (10 bp):
GGCATGGCCG
Found at i:62754 original size:23 final size:21
Alignment explanation
Indices: 62709--62757 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
62699 TGGATGGCTT
* *
62709 GGCATAGGCCGGGCATGGCCG
1 GGCATAGGCCGGACAAGGCCG
62730 GGCATAGTGCGCGGACAAGGCCG
1 GGCATAG-GC-CGGACAAGGCCG
62753 GGCAT
1 GGCAT
62758 GGCACGGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 2 0.08
23 15 0.62
ACGTcount: A:0.18, C:0.27, G:0.45, T:0.10
Consensus pattern (21 bp):
GGCATAGGCCGGACAAGGCCG
Found at i:62973 original size:23 final size:23
Alignment explanation
Indices: 62945--63000 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
62935 AGGGCCGAGC
62945 ATGGCCTGGCAGGAGGCGCGGTG
1 ATGGCCTGGCAGGAGGCGCGGTG
62968 ATGGCCTGGCAGGAGGCGCGGTG
1 ATGGCCTGGCAGGAGGCGCGGTG
62991 ATGGCCTGGC
1 ATGGCCTGGC
63001 TCATCCGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.50, T:0.14
Consensus pattern (23 bp):
ATGGCCTGGCAGGAGGCGCGGTG
Found at i:67065 original size:33 final size:32
Alignment explanation
Indices: 67022--67121 Score: 119
Period size: 33 Copynumber: 3.1 Consensus size: 32
67012 CAAGTGTCCG
* * *
67022 GGTGTAGCCGGGCATGGCCATGTCGCGTGGCC
1 GGTGTGGCCGGGCATCGCCATGTCGCATGGCC
* *
67054 GGTGATGGCCGGGCATCTCCATGTTGCATGGCC
1 GGTG-TGGCCGGGCATCGCCATGTCGCATGGCC
* *
67087 GGTGTTGCGCGGGCATCTCCATGTCGCATGGCC
1 GGTGTGGC-CGGGCATCGCCATGTCGCATGGCC
67120 GG
1 GG
67122 ATCTCTAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
32 7 0.12
33 52 0.88
ACGTcount: A:0.10, C:0.28, G:0.40, T:0.22
Consensus pattern (32 bp):
GGTGTGGCCGGGCATCGCCATGTCGCATGGCC
Found at i:68154 original size:36 final size:36
Alignment explanation
Indices: 68086--68154 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
68076 AAATCGCAAA
**
68086 TTTTTTTTTTAGAAAAATCAGAAAAAGGAAAAAACT
1 TTTTTTTTTTAGAAAAATCAGAAAAAACAAAAAACT
68122 TTTTTTTTTTAGAAAAAAT-AGAAAAAACAAAAA
1 TTTTTTTTTTAG-AAAAATCAGAAAAAACAAAAA
68155 CTCATTCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 24 0.80
37 6 0.20
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (36 bp):
TTTTTTTTTTAGAAAAATCAGAAAAAACAAAAAACT
Found at i:71251 original size:21 final size:21
Alignment explanation
Indices: 71227--71269 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
71217 TTGCATAAAG
71227 TTTGGATATTTGG-TGACAAAA
1 TTTGG-TATTTGGTTGACAAAA
* *
71248 TTTGGTCTTTGGTTGATAAAA
1 TTTGGTATTTGGTTGACAAAA
71269 T
1 T
71270 ATATTGGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (21 bp):
TTTGGTATTTGGTTGACAAAA
Found at i:72334 original size:13 final size:14
Alignment explanation
Indices: 72316--72344 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
72306 ATAATTGGAC
72316 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
72329 TTTGCATTCATGCA
1 TTTGCATTCATGCA
72343 TT
1 TT
72345 GAGTGGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:74140 original size:52 final size:53
Alignment explanation
Indices: 74079--74191 Score: 149
Period size: 52 Copynumber: 2.2 Consensus size: 53
74069 AATTAATAAT
* * *
74079 TGACAAAATGTCCC-TGAATATGCAAATGACCAAAATACCCCTGAATGC-AAAA
1 TGACCAAATG-CCCATGAATATGAAAATGACCAAAATACCCCTAAATGCAAAAA
* *
74131 TGACCAAATGCCCATGAGTGTGAAAATGACCAAAATACCCCTAAATGCAAAAA
1 TGACCAAATGCCCATGAATATGAAAATGACCAAAATACCCCTAAATGCAAAAA
*
74184 AGACCAAA
1 TGACCAAA
74192 ATGCTAATTC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
51 3 0.06
52 39 0.74
53 11 0.21
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (53 bp):
TGACCAAATGCCCATGAATATGAAAATGACCAAAATACCCCTAAATGCAAAAA
Found at i:74183 original size:27 final size:26
Alignment explanation
Indices: 74098--74193 Score: 106
Period size: 27 Copynumber: 3.7 Consensus size: 26
74088 GTCCCTGAAT
74098 ATGC-AAATGACCAAAATACCCCTGA
1 ATGCAAAATGACCAAAATACCCCTGA
* *
74123 ATGCAAAATGACC-AAATGCCCATGA
1 ATGCAAAATGACCAAAATACCCCTGA
* * *
74148 GTGTGAAAATGACCAAAATACCCCTAA
1 ATG-CAAAATGACCAAAATACCCCTGA
*
74175 ATGCAAAAAAGACCAAAAT
1 ATGC-AAAATGACCAAAAT
74194 GCTAATTCGA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
25 16 0.28
26 17 0.30
27 24 0.42
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.16
Consensus pattern (26 bp):
ATGCAAAATGACCAAAATACCCCTGA
Found at i:74476 original size:43 final size:44
Alignment explanation
Indices: 74428--74516 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
74418 GTGGTAGACT
*
74428 TTGATAACCGCTG-AAACTGAAAAAAACCTGTTCTGAGGTCAAC
1 TTGATAACCGCTGAAAACTGAAAAAAACCTGTTCTGAGGACAAC
* *** *
74471 TTGATAACTGCTGAAAACTGAGGGAGACCTGTTCTGAGGACAAC
1 TTGATAACCGCTGAAAACTGAAAAAAACCTGTTCTGAGGACAAC
74515 TT
1 TT
74517 TGCTAACGGC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 12 0.31
44 27 0.69
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (44 bp):
TTGATAACCGCTGAAAACTGAAAAAAACCTGTTCTGAGGACAAC
Found at i:74583 original size:50 final size:50
Alignment explanation
Indices: 74525--74661 Score: 256
Period size: 50 Copynumber: 2.7 Consensus size: 50
74515 TTTGCTAACG
* *
74525 GCTAAAAATTGAGAGACCTTTTCTAACTTCTGAAGTTGATTTTGAAAACT
1 GCTAAAAATTGAGAGATCTGTTCTAACTTCTGAAGTTGATTTTGAAAACT
74575 GCTAAAAATTGAGAGATCTGTTCTAACTTCTGAAGTTGATTTTGAAAACT
1 GCTAAAAATTGAGAGATCTGTTCTAACTTCTGAAGTTGATTTTGAAAACT
74625 GCTAAAAATTGAGAGATCTGTTCTAACTTCTGAAGTT
1 GCTAAAAATTGAGAGATCTGTTCTAACTTCTGAAGTT
74662 TATGTTCTAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (50 bp):
GCTAAAAATTGAGAGATCTGTTCTAACTTCTGAAGTTGATTTTGAAAACT
Found at i:75115 original size:38 final size:32
Alignment explanation
Indices: 75071--75143 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
75061 CGGGCTTGAG
* * *
75071 TCGGGTTTGGATTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
75103 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
75135 TCGGGTTCG
1 TCGGGTTCG
75144 AGTTCTGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
Found at i:75131 original size:16 final size:15
Alignment explanation
Indices: 75090--75140 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
75080 GATTGGATTT
75090 GGGTCAGGTTAATTC
1 GGGTCAGGTTAATTC
* *
75105 GGGTTCGGGTTGAATTT
1 GGG-TCAGGTT-AATTC
75122 GGGTCAGGTTAATTC
1 GGGTCAGGTTAATTC
75137 GGGT
1 GGGT
75141 TCGAGTTCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.37
16 12 0.40
17 7 0.23
ACGTcount: A:0.16, C:0.10, G:0.39, T:0.35
Consensus pattern (15 bp):
GGGTCAGGTTAATTC
Found at i:75155 original size:32 final size:32
Alignment explanation
Indices: 75086--75157 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
75076 TTTGGATTGG
* *
75086 ATTTGGGTCAGGTTAATTCGGGTTCGGGTTGA
1 ATTTGGGTCAGGTTAATTCGGGTTCGAGTTCA
*
75118 ATTTGGGTCAGGTTAATTCGGGTTCGAGTTCT
1 ATTTGGGTCAGGTTAATTCGGGTTCGAGTTCA
*
75150 GTTTGGGT
1 ATTTGGGT
75158 TTTGGCCAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (32 bp):
ATTTGGGTCAGGTTAATTCGGGTTCGAGTTCA
Found at i:75324 original size:16 final size:16
Alignment explanation
Indices: 75303--75406 Score: 127
Period size: 16 Copynumber: 6.5 Consensus size: 16
75293 AATTTTTGGA
75303 TTCGGGTTTGAGTTTT
1 TTCGGGTTTGAGTTTT
* *
75319 TTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGTTTT
* *
75335 TTTGGGTTTGAGCTTT
1 TTCGGGTTTGAGTTTT
* * *
75351 TTCGGATTCGTGTTTT
1 TTCGGGTTTGAGTTTT
*
75367 TTCGGGTTTGAGCTTT
1 TTCGGGTTTGAGTTTT
*
75383 TTCGGGTTTGGGTTTT
1 TTCGGGTTTGAGTTTT
75399 TTCGGGTT
1 TTCGGGTT
75407 CAGGTTTAGG
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 71 1.00
ACGTcount: A:0.04, C:0.10, G:0.33, T:0.54
Consensus pattern (16 bp):
TTCGGGTTTGAGTTTT
Found at i:75342 original size:32 final size:32
Alignment explanation
Indices: 75303--75406 Score: 163
Period size: 32 Copynumber: 3.2 Consensus size: 32
75293 AATTTTTGGA
*
75303 TTCGGGTTTGAGTTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
* * *
75335 TTTGGGTTTGAGCTTTTTCGGATTCGTGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
*
75367 TTCGGGTTTGAGCTTTTTCGGGTTTGGGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
75399 TTCGGGTT
1 TTCGGGTT
75407 CAGGTTTAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.04, C:0.10, G:0.33, T:0.54
Consensus pattern (32 bp):
TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
Found at i:77984 original size:14 final size:14
Alignment explanation
Indices: 77961--78005 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
77951 TAAAAACATG
77961 AAAC-CTTTTTTGA
1 AAACTCTTTTTTGA
77974 AAACTCTTTTTTGA
1 AAACTCTTTTTTGA
77988 AAA-TCTTTTCTTGA
1 AAACTCTTTT-TTGA
78002 AAAC
1 AAAC
78006 AATTTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (14 bp):
AAACTCTTTTTTGA
Found at i:78014 original size:13 final size:12
Alignment explanation
Indices: 77959--78017 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 12
77949 TTTAAAAACA
*
77959 TGAAACCTTTTT
1 TGAAAACTTTTT
77971 TGAAAACTCTTTTT
1 TGAAAA--CTTTTT
77985 TGAAAATCTTTTCT
1 TGAAAA-CTTTT-T
*
77999 TGAAAACAATTTT
1 TGAAAAC-TTTTT
78012 TGAAAA
1 TGAAAA
78018 ACGTTTCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.12
13 14 0.34
14 22 0.54
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (12 bp):
TGAAAACTTTTT
Found at i:80967 original size:27 final size:28
Alignment explanation
Indices: 80937--80993 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 28
80927 TTTTTACTCT
80937 TTACTCTTTACCATTTTT-CTTTACTGA
1 TTACTCTTTACCATTTTTCCTTTACTGA
80964 TTACTCTTTACCATTTTTCCTTTACTGA
1 TTACTCTTTACCATTTTTCCTTTACTGA
80992 TT
1 TT
80994 GCCATTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.18, C:0.23, G:0.04, T:0.56
Consensus pattern (28 bp):
TTACTCTTTACCATTTTTCCTTTACTGA
Found at i:80974 original size:41 final size:41
Alignment explanation
Indices: 80892--81089 Score: 148
Period size: 41 Copynumber: 4.6 Consensus size: 41
80882 TTACTGATTC
* * * * *
80892 CTCTTCACTCTGTACCATTCTTCTTTACTGATTAGTTTTTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTA
80933 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTA
* * * *
80974 C-CATTT-TTCCTTTACTGATTGCCATTTCCTTTGCTGGTTACTCTTTA
1 CTC-TTTACT-CTTTAC-CATT----TTT-CTTTACTGATTACTCTTTA
* * *
81021 CTCTTTTCTCTTTACTCTTTTTTCTTTACTAATTACTCTTTTA
1 CTCTTTACTCTTTAC-CATTTTTCTTTACTGATTACTC-TTTA
* ** *
81064 CTTTTTACTGATTACCATTTTACTTT
1 CTCTTTACTCTTTACCATTTTTCTTT
81090 TTTCTAATTA
Statistics
Matches: 125, Mismatches: 21, Indels: 21
0.75 0.13 0.13
Matches are distributed among these distances:
40 2 0.02
41 46 0.37
42 24 0.19
43 18 0.14
46 3 0.02
47 30 0.24
48 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.56
Consensus pattern (41 bp):
CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTA
Found at i:80986 original size:14 final size:13
Alignment explanation
Indices: 80941--80988 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
80931 TACTCTTTAC
80941 TCTTTACCATTTT
1 TCTTTACCATTTT
* **
80954 TCTTTACTGATTAC
1 TCTTTAC-CATTTT
80968 TCTTTACCATTTT
1 TCTTTACCATTTT
80981 TCCTTTAC
1 T-CTTTAC
80989 TGATTGCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.17, C:0.25, G:0.02, T:0.56
Consensus pattern (13 bp):
TCTTTACCATTTT
Found at i:81023 original size:7 final size:7
Alignment explanation
Indices: 81011--81072 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
81001 CCTTTGCTGG
81011 TTACTCT
1 TTACTCT
81018 TTACTCT
1 TTACTCT
*
81025 TTTCTCT
1 TTACTCT
81032 TTACTCT
1 TTACTCT
**
81039 TTTTTCT
1 TTACTCT
**
81046 TTACTAA
1 TTACTCT
81053 TTACTCTT
1 TTACTC-T
*
81061 TTACTTT
1 TTACTCT
81068 TTACT
1 TTACT
81073 GATTACCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
7 38 0.88
8 5 0.12
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.63
Consensus pattern (7 bp):
TTACTCT
Found at i:81046 original size:21 final size:21
Alignment explanation
Indices: 81011--81106 Score: 68
Period size: 22 Copynumber: 4.5 Consensus size: 21
81001 CCTTTGCTGG
* * **
81011 TTACTCTTTACTCTTTTCTCT
1 TTACTCTTTTCTCTTTACTAA
*
81032 TTACTCTTTTTTCTTTACTAA
1 TTACTCTTTTCTCTTTACTAA
* *
81053 TTACTCTTTTACTTTTTACTGA
1 TTACTCTTTT-CTCTTTACTAA
* *
81075 TTAC-CATTTTACTTTTTTCTAA
1 TTACTC-TTTT-CTCTTTACTAA
*
81097 TTACTATTTT
1 TTACTCTTTT
81107 ACATTTACTG
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
21 27 0.44
22 34 0.56
ACGTcount: A:0.18, C:0.20, G:0.01, T:0.61
Consensus pattern (21 bp):
TTACTCTTTTCTCTTTACTAA
Found at i:81077 original size:22 final size:21
Alignment explanation
Indices: 81045--81263 Score: 228
Period size: 22 Copynumber: 10.2 Consensus size: 21
81035 CTCTTTTTTC
*
81045 TTTACTAATTACTCTTTTACTT
1 TTTACTGATTAC-CTTTTACTT
81067 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACC-TTTTACTT
* * * *
81089 TTTTCTAATTACTATTTTAC-A
1 TTTACTGATTAC-CTTTTACTT
81110 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACC-TTTTACTT
* *
81132 TTTACTGATTACC-ATTGCTT
1 TTTACTGATTACCTTTTACTT
* *
81152 CTTACTGATTA-CTATTACTT
1 TTTACTGATTACCTTTTACTT
* *
81172 TCTACTGATTACTCTTTTAATT
1 TTTACTGATTAC-CTTTTACTT
81194 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACC-TTTTACTT
* **
81216 TTTACTAATTACCATTTTACCC
1 TTTACTGATTACC-TTTTACTT
81238 TTTACTGATTACCTTTTACTT
1 TTTACTGATTACCTTTTACTT
81259 TTTAC
1 TTTAC
81264 CATTTTACCT
Statistics
Matches: 164, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.01
20 30 0.18
21 29 0.18
22 104 0.63
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTT
Found at i:81329 original size:15 final size:15
Alignment explanation
Indices: 81281--81329 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
81271 CCTTTTTACT
*
81281 CTTAATATCATTTTTA
1 CTTAATACCA-TTTTA
*
81297 C-TAAGTGCCATTTTA
1 CTTAA-TACCATTTTA
81312 CTTAATACCATTTTA
1 CTTAATACCATTTTA
81327 CTT
1 CTT
81330 TCTATCTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 21 0.75
16 7 0.25
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (15 bp):
CTTAATACCATTTTA
Found at i:81771 original size:34 final size:34
Alignment explanation
Indices: 81724--81844 Score: 122
Period size: 34 Copynumber: 3.5 Consensus size: 34
81714 TTAGTTATCA
81724 ATTTACTGATTACTATCTTTTTACATGATTACTG
1 ATTTACTGATTACTATCTTTTTACATGATTACTG
* * * *
81758 ATTCACTGATTACTAT-TATCTGGATT-CTTAATTA-TAA
1 ATTTACTGATTACTATCT-T-T---TTACATGATTACT-G
*
81795 ATTTACTGATTACTATCTTTTTACCTGATTACTG
1 ATTTACTGATTACTATCTTTTTACATGATTACTG
81829 ATTTACTGATTACTAT
1 ATTTACTGATTACTAT
81845 TACCTTGACT
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
33 3 0.04
34 38 0.54
35 2 0.03
36 2 0.03
37 22 0.31
38 3 0.04
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (34 bp):
ATTTACTGATTACTATCTTTTTACATGATTACTG
Found at i:81804 original size:71 final size:71
Alignment explanation
Indices: 81712--81846 Score: 234
Period size: 71 Copynumber: 1.9 Consensus size: 71
81702 TAACCTTGAC
* *
81712 TCTTAGTTATCAATTTACTGATTACTATCTTTTTACATGATTACTGATTCACTGATTACTATTAT
1 TCTTAATTATAAATTTACTGATTACTATCTTTTTACATGATTACTGATTCACTGATTACTATTAT
81777 CTGGAT
66 CTGGAT
* *
81783 TCTTAATTATAAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTA
1 TCTTAATTATAAATTTACTGATTACTATCTTTTTACATGATTACTGATTCACTGATTACTATTA
81847 CCTTGACTCT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (71 bp):
TCTTAATTATAAATTTACTGATTACTATCTTTTTACATGATTACTGATTCACTGATTACTATTAT
CTGGAT
Found at i:81869 original size:55 final size:55
Alignment explanation
Indices: 81822--82074 Score: 425
Period size: 55 Copynumber: 4.6 Consensus size: 55
81812 TTTTTACCTG
* *
81822 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATCTCTTTTCACTTA
*
81877 ATTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATTTCTTTTCACTTA
1 ATTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATCTCTTTTCACTTA
81932 ATTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATCTCTTTTCACTTA
1 ATTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATCTCTTTTCACTTA
* * * * *
81987 ATTACTGATTTACTGATTTCAATTACCTTGACTATGATTAATTTCTTTTCAGTTA
1 ATTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATCTCTTTTCACTTA
*
82042 ATTATTGATTTACTGATTACCATTACCTTGACT
1 ATTACTGATTTACTGATTACCATTACCTTGACT
82075 GTGTGATCGT
Statistics
Matches: 186, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 186 1.00
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (55 bp):
ATTACTGATTTACTGATTACCATTACCTTGACTCTGATTAATCTCTTTTCACTTA
Found at i:83583 original size:19 final size:18
Alignment explanation
Indices: 83550--83585 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
83540 TTGAAATAAT
83550 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
83568 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
83586 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.