Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005809.1 Corchorus capsularis cultivar CVL-1 contig05827, 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: 4870
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Found at i:1240 original size:111 final size:110
Alignment explanation
Indices: 1045--1298 Score: 391
Period size: 111 Copynumber: 2.3 Consensus size: 110
1035 TAAAAAGGGG
* *
1045 CAATCAGTAAATCAGTAGAAAGAGATTAATCAAAGTCAAGGCGATGGTAATCAGTCAATCAGTAA
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGCGATGGTAATCAGTCAATCAGTAA
* * * * * *
1110 ATCAGTAAATAGAGGTTAATCAATAGTCAAGGTGATCGTAATTAGT
66 ATCAGTAAAAAGAGATTAATC-AGAGTCAAGATAATCGTAATCAGT
* *
1156 CAATCAGTAAATCAGTAAAAAGAGGTTAATCAGAGTCAAGGTGATGGTAATCAGTCAATCAGTAA
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGCGATGGTAATCAGTCAATCAGTAA
*
1221 ATCAGTAAAAAGAGATTAATCAGAGTCAAGATAATGGTAATCAGT
66 ATCAGTAAAAAGAGATTAATCAGAGTCAAGATAATCGTAATCAGT
*
1266 AAATCAGTAAATCAGTAAAAAGAGATTAATCAG
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAG
1299 TAATTAAGAG
Statistics
Matches: 130, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 50 0.38
111 80 0.62
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (110 bp):
CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGCGATGGTAATCAGTCAATCAGTAA
ATCAGTAAAAAGAGATTAATCAGAGTCAAGATAATCGTAATCAGT
Found at i:1272 original size:8 final size:8
Alignment explanation
Indices: 1259--1284 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1249 AGATAATGGT
1259 AATCAGTA
1 AATCAGTA
1267 AATCAGTA
1 AATCAGTA
1275 AATCAGTA
1 AATCAGTA
1283 AA
1 AA
1285 AAGAGATTAA
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:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AATCAGTA
Found at i:1298 original size:55 final size:55
Alignment explanation
Indices: 1045--1298 Score: 391
Period size: 55 Copynumber: 4.6 Consensus size: 55
1035 TAAAAAGGGG
* * *
1045 CAATCAGTAAATCAGTAGAAAGAGATTAATCAAAGTCAAGGCGATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
* * * * *
1100 CAATCAGTAAATCAGTAAATAGAGGTTAATCAATAGTCAAGGTGATCGTAATTAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATC-AGAGTCAAGGTGATGGTAATCAGT
*
1156 CAATCAGTAAATCAGTAAAAAGAGGTTAATCAGAGTCAAGGTGATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
* *
1211 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGATAATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
*
1266 AAATCAGTAAATCAGTAAAAAGAGATTAATCAG
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAG
1299 TAATTAAGAG
Statistics
Matches: 183, Mismatches: 15, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
55 133 0.73
56 50 0.27
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (55 bp):
CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
Found at i:1478 original size:7 final size:7
Alignment explanation
Indices: 1466--1655 Score: 59
Period size: 7 Copynumber: 26.6 Consensus size: 7
1456 AGGAAAAATG
1466 GTAAAGA
1 GTAAAGA
1473 GTAAAGA
1 GTAAAGA
* **
1480 ATAATCA
1 GTAAAGA
*
1487 GTAAGGA
1 GTAAAGA
**
1494 GTAATTA
1 GTAAAGA
1501 GTAAAGA
1 GTAAAGA
1508 GTAAA-A
1 GTAAAGA
*
1514 TGATAAAAAA
1 -G-T-AAAGA
1524 GTAAAGA
1 GTAAAGA
**
1531 GTAATCA
1 GTAAAGA
1538 GTAAAG-
1 GTAAAGA
*
1544 G-AAAAA
1 GTAAAGA
1550 TGGTAAAGA
1 --GTAAAGA
1559 GTAAAGA
1 GTAAAGA
* **
1566 ATAATCA
1 GTAAAGA
*
1573 GTAAGGA
1 GTAAAGA
**
1580 GTAATTA
1 GTAAAGA
1587 GTAAAGA
1 GTAAAGA
1594 GTAAA-A
1 GTAAAGA
*
1600 TGATAAAAAA
1 -G-T-AAAGA
1610 GTAAAGA
1 GTAAAGA
**
1617 GTAATTA
1 GTAAAGA
1624 GTAAAAGAA
1 GT-AAAG-A
*
1633 G-AATG-
1 GTAAAGA
*
1638 GTAAAAA
1 GTAAAGA
1645 GTAAAGA
1 GTAAAGA
1652 GTAA
1 GTAA
1656 TCAGTAAAGG
Statistics
Matches: 131, Mismatches: 36, Indels: 32
0.66 0.18 0.16
Matches are distributed among these distances:
5 4 0.03
6 5 0.04
7 99 0.76
8 7 0.05
9 14 0.11
10 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (7 bp):
GTAAAGA
Found at i:1485 original size:35 final size:35
Alignment explanation
Indices: 1440--1512 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
1430 ATTAAATTCA
1440 AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGT
1 AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGT
* * * *
1475 AAAGAATAATCAGT-AAGGAGTAATTAGTAAAGAGT
1 AAAGAGTAATCAGTAAAGGA-AAAATGGTAAAGAGT
1510 AAA
1 AAA
1513 ATGATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 5 0.15
35 28 0.85
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.19
Consensus pattern (35 bp):
AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGT
Found at i:1537 original size:86 final size:86
Alignment explanation
Indices: 1440--1687 Score: 410
Period size: 86 Copynumber: 2.9 Consensus size: 86
1430 ATTAAATTCA
1440 AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAA
1 AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAA
1505 AGAGTAAAATGATAAAAAAGT
66 AGAGTAAAATGATAAAAAAGT
1526 AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAA
1 AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAA
1591 AGAGTAAAATGATAAAAAAGT
66 AGAGTAAAATGATAAAAAAGT
* * * * * *
1612 AAAGAGTAATTAGTAAAAGAAGAATGGTAAAAAGTAAAGAGTAATCAGTAAAGGAAG-AA-TGGT
1 AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGT-AAGG-AGTAATTAGT
1675 AAAGAGTAAAATG
64 AAAGAGTAAAATG
1688 GTAATCATTA
Statistics
Matches: 154, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
86 146 0.95
87 6 0.04
88 2 0.01
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (86 bp):
AAAGAGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAA
AGAGTAAAATGATAAAAAAGT
Found at i:1571 original size:35 final size:35
Alignment explanation
Indices: 1486--1598 Score: 111
Period size: 35 Copynumber: 3.2 Consensus size: 35
1476 AAGAATAATC
* * * * *
1486 AGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAA
1 AGTAAAGAGTAATCAGTAAAG-GAAAAATGGT-AAAG
1523 AGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAG
* * * *
1558 AGTAAAGAATAATCAGT-AAGGAGTAATTAGTAAAG
1 AGTAAAGAGTAATCAGTAAAGGA-AAAATGGTAAAG
1593 AGTAAA
1 AGTAAA
1599 ATGATAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
34 5 0.08
35 34 0.52
36 8 0.12
37 19 0.29
ACGTcount: A:0.55, C:0.02, G:0.23, T:0.20
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAGGAAAAATGGTAAAG
Found at i:1704 original size:22 final size:22
Alignment explanation
Indices: 1673--1729 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1663 AGGAAGAATG
*
1673 GTAAAGAGTAA-AATGGTAATCA
1 GTAAAGAGTAAGAA-GGTAACCA
* *
1695 TTAAAAAGTAAGAAGGTAACCA
1 GTAAAGAGTAAGAAGGTAACCA
1717 GTAAAGAGTAAGA
1 GTAAAGAGTAAGA
1730 TGATAAAGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.19
Consensus pattern (22 bp):
GTAAAGAGTAAGAAGGTAACCA
Found at i:1758 original size:22 final size:22
Alignment explanation
Indices: 1733--1966 Score: 115
Period size: 22 Copynumber: 11.2 Consensus size: 22
1723 AGTAAGATGA
1733 TAAAGAGTAAAATAGTAATCAG
1 TAAAGAGTAAAATAGTAATCAG
* ** *
1755 TAAA-AG-ATAATCAGTAAAGAA
1 TAAAGAGTAAAAT-AGTAATCAG
* * *
1776 TGAAATAGTAAAA-GGTAATCAA
1 T-AAAGAGTAAAATAGTAATCAG
* *
1798 TAAAAACT--AAT-GATAATCAG
1 TAAAGAGTAAAATAG-TAATCAG
1818 TAAA-AGGTAAAATAGTAATCAG
1 TAAAGA-GTAAAATAGTAATCAG
* * *
1840 T-AAGAGCAAAATGGTAATCAA
1 TAAAGAGTAAAATAGTAATCAG
* * *
1861 T-GAGAGCAAAATGGTAATCAG
1 TAAAGAGTAAAATAGTAATCAG
* *
1882 TAAAGAGTAAAATGGTAATCAT
1 TAAAGAGTAAAATAGTAATCAG
* * *
1904 TAAAAAGTAAGAA-GGTAACCAG
1 TAAAGAGTAA-AATAGTAATCAG
*
1926 TAAAGAGT---A-AG--ATGA-
1 TAAAGAGTAAAATAGTAATCAG
1941 TAAAGAGTAAAATAGTAATCAG
1 TAAAGAGTAAAATAGTAATCAG
1963 TAAA
1 TAAA
1967 AGATAATTAG
Statistics
Matches: 164, Mismatches: 28, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
15 8 0.05
16 2 0.01
18 3 0.02
19 6 0.04
20 15 0.09
21 52 0.32
22 70 0.43
23 5 0.03
24 3 0.02
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (22 bp):
TAAAGAGTAAAATAGTAATCAG
Found at i:1767 original size:14 final size:14
Alignment explanation
Indices: 1738--1802 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
1728 GATGATAAAG
*
1738 AGTAAAATAGTAATC
1 AGTAAAAGA-TAATC
1753 AGTAAAAGATAATC
1 AGTAAAAGATAATC
1767 AGT-AAAGAATGAAAT-
1 AGTAAAAG-AT--AATC
*
1782 AGTAAAAGGTAATC
1 AGTAAAAGATAATC
*
1796 AATAAAA
1 AGTAAAA
1803 ACTAATGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 7 0.17
14 16 0.38
15 12 0.29
16 7 0.17
ACGTcount: A:0.58, C:0.05, G:0.15, T:0.22
Consensus pattern (14 bp):
AGTAAAAGATAATC
Found at i:1856 original size:21 final size:21
Alignment explanation
Indices: 1806--1902 Score: 113
Period size: 21 Copynumber: 4.5 Consensus size: 21
1796 AATAAAAACT
* * *
1806 AATGATAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAGA-GCAA
*
1828 AATAGTAATCAGTAAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
* *
1849 AATGGTAATCAATGAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
*
1870 AATGGTAATCAGTAAAGAGTAA
1 AATGGTAATCAGT-AAGAGCAA
1892 AATGGTAATCA
1 AATGGTAATCA
1903 TTAAAAAGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 33 0.52
22 31 0.48
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.22
Consensus pattern (21 bp):
AATGGTAATCAGTAAGAGCAA
Found at i:1959 original size:59 final size:59
Alignment explanation
Indices: 1880--2078 Score: 227
Period size: 59 Copynumber: 3.5 Consensus size: 59
1870 AATGGTAATC
* * *
1880 AGTAAAGAGTAAAATGGTAATCATTAAAAAGTAAGAAGGTAACCAGTAAAGAGTAAGAT
1 AGTAAAGAGTAAAATAGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAAT
* *
1939 -GATAAAGAGTAAAATAGTAATC-------AGTAA-AAGATAATTAGTAAAGAGTAAAAT
1 AG-TAAAGAGTAAAATAGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAAT
** * *
1990 AGTAATCAGCAAAATGGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAAT
1 AGTAAAGAGTAAAATAGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAAT
*
2049 CAGTAAAGAGTAAAATAGTAATCAGTAAAA
1 -AGTAAAGAGTAAAATAGTAATCATTAAAA
2079 GATAATCAGT
Statistics
Matches: 113, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
51 36 0.32
52 6 0.05
58 6 0.05
59 41 0.36
60 24 0.21
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (59 bp):
AGTAAAGAGTAAAATAGTAATCATTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAAT
Found at i:1978 original size:14 final size:15
Alignment explanation
Indices: 1946--1986 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1936 GATGATAAAG
*
1946 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
*
1961 AGTAAAAGA-TAATT
1 AGTAAAAGAGTAATC
1975 AGT-AAAGAGTAA
1 AGTAAAAGAGTAA
1987 AATAGTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 5 0.22
14 10 0.43
15 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:2049 original size:16 final size:16
Alignment explanation
Indices: 2030--2069 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
2020 GTAAGAAGGT
2030 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
2046 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
2062 AAT-AGTAA
1 AATCAGTAA
2070 TCAGTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (16 bp):
AATCAGTAAAGAGTAA
Found at i:2075 original size:15 final size:15
Alignment explanation
Indices: 1982--2090 Score: 73
Period size: 15 Copynumber: 7.3 Consensus size: 15
1972 ATTAGTAAAG
1982 AGTAAAATAGTAATC
1 AGTAAAATAGTAATC
* *
1997 AGCAAAATGGTAATC
1 AGTAAAATAGTAATC
* **
2012 ATTAAAA-AGTAAGA
1 AGTAAAATAGTAATC
**
2026 AGGT--AATCAGTAAAG
1 A-GTAAAAT-AGTAATC
**
2041 AGTAAAATCAGTAAAG
1 AGTAAAAT-AGTAATC
2057 AGTAAAATAGTAATC
1 AGTAAAATAGTAATC
*
2072 AGTAAAAGA-TAATC
1 AGTAAAATAGTAATC
2086 AGTAA
1 AGTAA
2091 GAGTAAAACA
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
13 2 0.03
14 17 0.22
15 38 0.50
16 19 0.25
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.22
Consensus pattern (15 bp):
AGTAAAATAGTAATC
Found at i:2079 original size:59 final size:60
Alignment explanation
Indices: 1961--2078 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
1951 AATAGTAATC
* * ** * * *
1961 AGTAA-AAGATAATTAGTAAAGAGTAAAAT-AGTAATCAGCAAAATGGTAATCATTAAAA
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
2019 AGTAAGAAGGTAATCAGTAAAGAGTAAAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
1 AGTAAGAAGGTAATCAGTAAAGAGTAAAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
2079 GATAATCAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 5 0.10
59 22 0.43
60 24 0.47
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (60 bp):
AGTAAGAAGGTAATCAGTAAAGAGTAAAATCAGTAAAGAGTAAAATAGTAATCAGTAAAA
Found at i:2086 original size:14 final size:15
Alignment explanation
Indices: 2057--2090 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2047 ATCAGTAAAG
*
2057 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
2072 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
2086 AGTAA
1 AGTAA
2091 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:2109 original size:21 final size:20
Alignment explanation
Indices: 2072--2114 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
2062 AATAGTAATC
* *
2072 AGTAAAAGATAATCAGTAAG
1 AGTAAAACATAACCAGTAAG
2092 AGTAAAACAGTAACCAGTAAG
1 AGTAAAACA-TAACCAGTAAG
2113 AG
1 AG
2115 CAAAGTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.16
Consensus pattern (20 bp):
AGTAAAACATAACCAGTAAG
Found at i:2111 original size:42 final size:41
Alignment explanation
Indices: 2072--2174 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
2062 AATAGTAATC
2072 AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAG
1 AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAG
* * * * * *
2113 AGCAAAGTGATAATTAGTAAGAGTCAAATAGTAATCAGTAAAG
1 AGTAAA-AGATAATCAGTAAGAGTAAAACAGTAACCAGT-AAG
* *
2156 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGATAATCAGTAA
2175 TTCAAAGAGT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 5 0.10
42 36 0.73
43 8 0.16
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.20
Consensus pattern (41 bp):
AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAG
Found at i:2147 original size:21 final size:21
Alignment explanation
Indices: 2081--2174 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
2071 CAGTAAAAGA
* *
2081 TAATCAGTAAGAGTAAAACAG
1 TAATCAGTAAGAGTCAAATAG
*
2102 TAACCAGTAAGAG-CAAAGT-G
1 TAATCAGTAAGAGTCAAA-TAG
*
2122 ATAATTAGTAAGAGTCAAATAG
1 -TAATCAGTAAGAGTCAAATAG
2144 TAATCAGTAAAGAGT-AAA-AGG
1 TAATCAGT-AAGAGTCAAATA-G
*
2165 TGATCAGTAA
1 TAATCAGTAA
2175 TTCAAAGAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
20 7 0.12
21 42 0.70
22 11 0.18
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (21 bp):
TAATCAGTAAGAGTCAAATAG
Found at i:2254 original size:13 final size:13
Alignment explanation
Indices: 2236--2282 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2226 GGTAATAAAT
2236 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
2249 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
2263 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
2276 AAAAGAG
1 AAAAGAG
2283 TAAAAATGAT
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:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:2258 original size:28 final size:28
Alignment explanation
Indices: 2207--2289 Score: 100
Period size: 27 Copynumber: 3.0 Consensus size: 28
2197 AGTATAAGAA
*
2207 AAAAGAAGAGTAA-AAAAGTGGTAATAAAT
1 AAAAG-AGAGTAAGAAAAG-AGTAATAAAT
* *
2236 AAAAGAGAGTAAGAAAAGAGTAATTAGT
1 AAAAGAGAGTAAGAAAAGAGTAATAAAT
2264 AAAA-AGAGTAAGAAAAGAGTAA-AAAT
1 AAAAGAGAGTAAGAAAAGAGTAATAAAT
2290 GATAAAAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.04
27 18 0.38
28 18 0.38
29 10 0.21
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.16
Consensus pattern (28 bp):
AAAAGAGAGTAAGAAAAGAGTAATAAAT
Found at i:2279 original size:27 final size:27
Alignment explanation
Indices: 2212--2298 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 27
2202 AAGAAAAAAG
*
2212 AAGAGTAA-AAAAGTGGTAATAAATAAA
1 AAGAGTAAGAAAAG-AGTAATAAATAAA
* *
2239 AGAGAGTAAGAAAAGAGTAATTAGTAAA
1 A-AGAGTAAGAAAAGAGTAATAAATAAA
2267 AAGAGTAAGAAAAGAGTAA-AAATGATAA
1 AAGAGTAAGAAAAGAGTAATAAAT-A-AA
2295 AAGA
1 AAGA
2299 AGCAAAAGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.04
27 20 0.39
28 24 0.47
29 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (27 bp):
AAGAGTAAGAAAAGAGTAATAAATAAA
Found at i:4375 original size:27 final size:27
Alignment explanation
Indices: 4345--4421 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
4335 ATTAGGGTCG
*
4345 CCCAGGGGTATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
4372 CCCAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
* *
4399 CTCAGGGGCATTTTAGTCATTTT
1 CCCAGGGGCATTTTGGTCATTTT
4422 CAAGTTCACC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTTGCA
Found at i:4595 original size:21 final size:21
Alignment explanation
Indices: 4553--4596 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4543 CATTATGGTG
*
4553 TTTTCAATTAGTATTGTTGCA
1 TTTTCAATTAGTATTGTGGCA
*
4574 TTTTCATTTAGTAATT-TGGCA
1 TTTTCAATTAGT-ATTGTGGCA
4595 TT
1 TT
4597 GTTACACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTTCAATTAGTATTGTGGCA
Done.