Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006527.1 Corchorus capsularis cultivar CVL-1 contig06548, 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: 9357
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1201 original size:13 final size:13
Alignment explanation
Indices: 1156--1202 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1146 ATCATTTTTA
1156 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
1169 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
1182 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
1196 CTCTTTT
1 CTCTTTT
1203 ATTGATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:1308 original size:21 final size:21
Alignment explanation
Indices: 1275--1479 Score: 156
Period size: 21 Copynumber: 9.9 Consensus size: 21
1265 ACTGATCACC
*
1275 TTTTAGTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* *
1297 TTTTACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
* *
1318 TTTTGCTCTTACTAATTAC--
1 TTTTACTCTTACTGATTACTA
*
1337 -----CTTTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
1353 TTTTACTCTTTACTGATTACCT-
1 TTTTACTC-TTACTGATTA-CTA
* *
1375 TCTTACTTTTTACTGATTACTA
1 TTTTAC-TCTTACTGATTACTA
* *
1397 TTTTAATCTTTACTGATTACCA
1 TTTTACTC-TTACTGATTACTA
* * * *
1419 TTTTGCCCTCACTGATTACCA
1 TTTTACTCTTACTGATTACTA
*
1440 TTTTGCTCTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
*
1461 TTTTACCTTTTACTGATTA
1 TTTTA-CTCTTACTGATTA
1480 TCATTATTTT
Statistics
Matches: 148, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
14 12 0.08
21 68 0.46
22 65 0.44
23 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:1330 original size:35 final size:35
Alignment explanation
Indices: 1302--1381 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
1292 TACTATTTTA
*
1302 CTCTTACTAATTACCATTTTGCTCTTACTAATTAC
1 CTCTTACTAATTACCATTTTACTCTTACTAATTAC
* * * *
1337 CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
1 CTCTTACTAATTACCATTTTACTC-TTACTAATTAC
1373 CTTCTTACT
1 C-TCTTACT
1382 TTTTACTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 20 0.54
36 11 0.30
37 6 0.16
ACGTcount: A:0.23, C:0.24, G:0.04, T:0.50
Consensus pattern (35 bp):
CTCTTACTAATTACCATTTTACTCTTACTAATTAC
Found at i:1358 original size:15 final size:15
Alignment explanation
Indices: 1338--1401 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
1328 ACTAATTACC
1338 TTTTACTGATTACTA
1 TTTTACTGATTACTA
**
1353 TTTTACTCTTTACTGA
1 TTTTACTGATTACT-A
**
1369 --TTACCTTCTTACT-
1 TTTTA-CTGATTACTA
1382 TTTTACTGATTACTA
1 TTTTACTGATTACTA
1397 TTTTA
1 TTTTA
1402 ATCTTTACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
14 10 0.26
15 27 0.71
16 1 0.03
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (15 bp):
TTTTACTGATTACTA
Found at i:1364 original size:22 final size:22
Alignment explanation
Indices: 1339--1560 Score: 158
Period size: 22 Copynumber: 10.2 Consensus size: 22
1329 CTAATTACCT
1339 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
1361 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
1383 TTTACTGATTACTATTTTAATC
1 TTTACTGATTACTATTTTACTC
* *
1405 TTTACTGATTACCATTTTGC-C
1 TTTACTGATTACTATTTTACTC
* * * *
1426 CTCACTGATTACCATTTTGCTC
1 TTTACTGATTACTATTTTACTC
1448 -TTACTGATTACTATTTTAC-C
1 TTTACTGATTACTATTTTACTC
1468 TTTTACTGATTATCATTATTTT--T-
1 -TTTACTGATTA-C--TATTTTACTC
* *
1491 TTTACTGATTAC-CTTTTACTAT
1 TTTACTGATTACTATTTTACT-C
** * *
1513 TTTACTCTTTACTGATTAT-CTT
1 TTTACTGATTACT-ATTTTACTC
**
1535 TTTACTGATTAC-CCTTTACTC
1 TTTACTGATTACTATTTTACTC
1556 TTTAC
1 TTTAC
1561 CATTCTTCCT
Statistics
Matches: 160, Mismatches: 24, Indels: 33
0.74 0.11 0.15
Matches are distributed among these distances:
18 4 0.03
20 4 0.03
21 45 0.28
22 93 0.58
23 5 0.03
24 3 0.02
25 6 0.04
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:1387 original size:44 final size:42
Alignment explanation
Indices: 1333--1560 Score: 194
Period size: 44 Copynumber: 5.3 Consensus size: 42
1323 CTCTTACTAA
*
1333 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCTT
1 TTACTTTTTACTGATTACTATTTT-CTCTTTACTGATTACCTT
*
1376 CTTACTTTTTACTGATTACTATTTTAATCTTTACTGATTACCATT
1 -TTACTTTTTACTGATTACTATTTT-CTCTTTACTGATTACC-TT
* ** * * *
1421 TTGC-CCTCACTGATTACCATTTTGCTC-TTACTGATTACTATT
1 TTACTTTTTACTGATTACTATTTT-CTCTTTACTGATTAC-CTT
*
1463 TTACCTTTTACTGATTATCATTATTTT-T-TTTACTGATTACCTT
1 TTACTTTTTACTGATTA-C--TATTTTCTCTTTACTGATTACCTT
** * * *
1506 TTACTATTTTACTCTTTACTGATTATCTTTTTACTGATTACCCT
1 TTACT-TTTTACTGATTACT-ATTTTCTCTTTACTGATTACCTT
*
1550 TTACTCTTTAC
1 TTACTTTTTAC
1561 CATTCTTCCT
Statistics
Matches: 151, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
41 1 0.01
42 20 0.13
43 39 0.26
44 84 0.56
45 2 0.01
46 5 0.03
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (42 bp):
TTACTTTTTACTGATTACTATTTTCTCTTTACTGATTACCTT
Found at i:1455 original size:86 final size:85
Alignment explanation
Indices: 1265--1507 Score: 215
Period size: 86 Copynumber: 2.9 Consensus size: 85
1255 TCTTGGAATT
* * * * * * * *
1265 ACTGATCACC-TTTTAGTCTTTACTGATTACTATTTTA-CTCTTACTAATTACCAT-TTTGCTCT
1 ACTGATTACCATTTTACTCTTTACTGATTACTATCTTACCTTTTACTGATTATCATATTT-TTTT
*
1327 TACTAATTACC-TTT----T-
65 TACTGATTACCTTTTGCCCTC
* *
1342 ACTGATTACTATTTTACTCTTTACTGATTACCT-TCTTACTTTTTACTGATTA-C-TATTTTAAT
1 ACTGATTACCATTTTACTCTTTACTGATTA-CTATCTTACCTTTTACTGATTATCATATTTT--T
1404 CTTTACTGATTACCATTTTGCCCTC
63 -TTTACTGATTACC-TTTTGCCCTC
* *
1429 ACTGATTACCATTTTGCTC-TTACTGATTACTATTTTACCTTTTACTGATTATCATTATTTTTTT
1 ACTGATTACCATTTTACTCTTTACTGATTACTATCTTACCTTTTACTGATTATCA-TATTTTTTT
1493 TACTGATTACCTTTT
65 TACTGATTACCTTTT
1508 ACTATTTTAC
Statistics
Matches: 134, Mismatches: 14, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
77 9 0.07
78 26 0.19
79 13 0.10
80 11 0.08
82 3 0.02
85 6 0.04
86 41 0.31
87 19 0.14
89 6 0.04
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (85 bp):
ACTGATTACCATTTTACTCTTTACTGATTACTATCTTACCTTTTACTGATTATCATATTTTTTTT
ACTGATTACCTTTTGCCCTC
Found at i:1493 original size:108 final size:100
Alignment explanation
Indices: 1283--1502 Score: 264
Period size: 108 Copynumber: 2.1 Consensus size: 100
1273 CCTTTTAGTC
* * *
1283 TTTACTGATTACTATTTTACTCTTACTAATTACCATTTTGCTCTTACTAATTACCTTTTACTGAT
1 TTTACTGATTACTATTTTAATCTTACTAATTACCATTTTGCCCTCACTAATTACCTTTTACTGAT
* *
1348 TACTATTTTACTCTTTACTGATTACCTTCTTACTT
66 TACTATTTTACTCTTTACTGATTACATTATTACTT
* *
1383 TTTACTGATTACTATTTTAATCTTTACTGATTACCATTTTGCCCTCACTGATTACCATTTTGCTC
1 TTTACTGATTACTATTTTAATC-TTACTAATTACCATTTTGCCCTCACTAATTACC----T--T-
*
1448 TTACTGATTACTATTTTAC-CTTTTACTGATTATCATTATT-TTT
58 TTACTGATTACTATTTTACTC-TTTACTGATTA-CATTATTACTT
1491 TTTACTGATTAC
1 TTTACTGATTAC
1503 CTTTTACTAT
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
100 21 0.21
101 29 0.28
105 1 0.01
107 2 0.02
108 44 0.43
109 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (100 bp):
TTTACTGATTACTATTTTAATCTTACTAATTACCATTTTGCCCTCACTAATTACCTTTTACTGAT
TACTATTTTACTCTTTACTGATTACATTATTACTT
Found at i:1538 original size:15 final size:15
Alignment explanation
Indices: 1489--1545 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
1479 ATCATTATTT
1489 TTTTTACTGATTA-C
1 TTTTTACTGATTATC
* *
1503 CTTTTACT-ATTTTAC
1 TTTTTACTGATTAT-C
*
1518 TCTTTACTGATTATC
1 TTTTTACTGATTATC
1533 TTTTTACTGATTA
1 TTTTTACTGATTA
1546 CCCTTTACTC
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
13 3 0.09
14 7 0.21
15 20 0.59
16 4 0.12
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (15 bp):
TTTTTACTGATTATC
Found at i:1546 original size:29 final size:28
Alignment explanation
Indices: 1491--1554 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
1481 CATTATTTTT
*
1491 TTTACTGATTACCTTTTACTATTTTACTC
1 TTTACTGATTACCTTTTACTA-TTTACCC
*
1520 TTTACTGATTATCTTTTTACTGA-TTACCC
1 TTTACTGATTA-CCTTTTACT-ATTTACCC
1549 TTTACT
1 TTTACT
1555 CTTTACCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 22 0.71
30 8 0.26
31 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTACTGATTACCTTTTACTATTTACCC
Found at i:1581 original size:35 final size:35
Alignment explanation
Indices: 1535--1622 Score: 149
Period size: 35 Copynumber: 2.5 Consensus size: 35
1525 TGATTATCTT
*
1535 TTTACTGATTACCCTTTACTCTTTACCATTCTTCC
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
* *
1570 TTTACTGATTACTCTTTACTTTTTACCATTCTTCT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
1605 TTTACTGATTACTCTTTA
1 TTTACTGATTACTCTTTA
1623 TTTCTTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.18, C:0.25, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
Found at i:1663 original size:88 final size:88
Alignment explanation
Indices: 1549--1710 Score: 247
Period size: 88 Copynumber: 1.8 Consensus size: 88
1539 CTGATTACCC
* * *
1549 TTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATTCTTCTTTTACTGAT
1 TTTACTCTTTACAATTCTTCCTTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGAT
1614 TACTCTTTATTTCTTTTTATCAT
66 TACTCTTTATTTCTTTTTATCAT
* *
1637 TTTACTCTTTACGAATTAC-TCC-TTACTGATTATTCTTTACTCTTTACCATTTTTCCTTTACTG
1 TTTACTCTTTAC-AATT-CTTCCTTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTG
1700 ATTACTCTTTA
64 ATTACTCTTTA
1711 CTCTTTACCA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 60 0.90
89 6 0.09
90 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.56
Consensus pattern (88 bp):
TTTACTCTTTACAATTCTTCCTTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGAT
TACTCTTTATTTCTTTTTATCAT
Found at i:1683 original size:35 final size:34
Alignment explanation
Indices: 1637--1780 Score: 182
Period size: 35 Copynumber: 4.1 Consensus size: 34
1627 TTTTTATCAT
* *
1637 TTTACTCTTTACGAATTACTCC-TTACTGATTATTC
1 TTTACTCTTTAC-CATT-CTCCTTTACTGATTACTC
*
1672 TTTACTCTTTACCATTTTTCCTTTACTGATTACTC
1 TTTACTCTTTACCA-TTCTCCTTTACTGATTACTC
1707 TTTACTCTTTACCATTCTTCCTTTACTGATTACTC
1 TTTACTCTTTACCATTC-TCCTTTACTGATTACTC
* * *
1742 TTTACTTTTTACCATTCTTCTTTTACTGATTACAC
1 TTTACTCTTTACCATTC-TCCTTTACTGATTACTC
1777 TTTA
1 TTTA
1781 TTTCTTTTTA
Statistics
Matches: 99, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
34 6 0.06
35 93 0.94
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTACTCTTTACCATTCTCCTTTACTGATTACTC
Found at i:1700 original size:158 final size:158
Alignment explanation
Indices: 1535--1903 Score: 686
Period size: 158 Copynumber: 2.3 Consensus size: 158
1525 TGATTATCTT
*
1535 TTTACTGATTACCCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
*
1600 CTTCTTTTACTGATTACTCTTTATTTCTTTTTATCATTTTACTCTTTACGAATTACTCCTTACTG
66 CTTCTTTTACTGATTACACTTTATTTCTTTTTATCATTTTACTCTTTACGAATTACTCCTTACTG
1665 ATTATTCTTTACTCTTTACCATTTTTCC
131 ATTATTCTTTACTCTTTACCATTTTTCC
1693 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
1758 CTTCTTTTACTGATTACACTTTATTTCTTTTTATCATTTTACTCTTTACGAATTACTCCTTACTG
66 CTTCTTTTACTGATTACACTTTATTTCTTTTTATCATTTTACTCTTTACGAATTACTCCTTACTG
1823 ATTATTCTTTACTCTTTACCATTTTTCC
131 ATTATTCTTTACTCTTTACCATTTTTCC
* * *
1851 TTTACTGATTACTCTTTACTCTTTACCATT-TTTCTTTAATAATTACTCTTTAC
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTAC
1904 CCTTTACTCT
Statistics
Matches: 206, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
157 20 0.10
158 186 0.90
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.54
Consensus pattern (158 bp):
TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
CTTCTTTTACTGATTACACTTTATTTCTTTTTATCATTTTACTCTTTACGAATTACTCCTTACTG
ATTATTCTTTACTCTTTACCATTTTTCC
Found at i:1825 original size:88 final size:88
Alignment explanation
Indices: 1707--1868 Score: 238
Period size: 88 Copynumber: 1.8 Consensus size: 88
1697 CTGATTACTC
* * *
1707 TTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATTCTTCTTTTACTGAT
1 TTTACTCTTTACAATTCTTCCTTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGAT
1772 TACACTTTATTTCTTTTTATCAT
66 TACACTTTATTTCTTTTTATCAT
* *
1795 TTTACTCTTTACGAATTAC-TCC-TTACTGATTATTCTTTACTCTTTACCATTTTTCCTTTACTG
1 TTTACTCTTTAC-AATT-CTTCCTTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTG
*
1858 ATTACTCTTTA
64 ATTACACTTTA
1869 CTCTTTACCA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 59 0.89
89 6 0.09
90 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (88 bp):
TTTACTCTTTACAATTCTTCCTTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGAT
TACACTTTATTTCTTTTTATCAT
Found at i:1838 original size:7 final size:7
Alignment explanation
Indices: 1795--2164 Score: 105
Period size: 7 Copynumber: 51.6 Consensus size: 7
1785 TTTTTATCAT
1795 TTTACTC
1 TTTACTC
**
1802 TTTACGA
1 TTTACTC
*
1809 ATTACTC
1 TTTACTC
* *
1816 CTTACTG
1 TTTACTC
* *
1823 ATTATTC
1 TTTACTC
1830 TTTACTC
1 TTTACTC
1837 TTTAC-C
1 TTTACTC
*
1843 ATTT-TTCC
1 -TTTACT-C
*
1851 TTTACTG
1 TTTACTC
*
1858 ATTACTC
1 TTTACTC
1865 TTTACTC
1 TTTACTC
1872 TTTAC-C
1 TTTACTC
*
1878 ATTT-TTC
1 -TTTACTC
* *
1885 TTTAATA
1 TTTACTC
*
1892 ATTACTC
1 TTTACTC
*
1899 TTTACCC
1 TTTACTC
1906 TTTACTC
1 TTTACTC
*
1913 TTTACTA
1 TTTACTC
*
1920 TTT-TTCC
1 TTTACT-C
*
1927 TTTACTG
1 TTTACTC
*
1934 ATTACTC
1 TTTACTC
*
1941 TTTACTT
1 TTTACTC
1948 TTTAC-C
1 TTTACTC
*
1954 ATTT-TTC
1 -TTTACTC
*
1961 -TTACTG
1 TTTACTC
*
1967 ATTACTC
1 TTTACTC
1974 TTTACTC
1 TTTACTC
1981 TTTACTC
1 TTTACTC
1988 TTTTACTC
1 -TTTACTC
*
1996 TTTACTA
1 TTTACTC
* *
2003 ATTACTAT
1 TTTACT-C
2011 TTTACTC
1 TTTACTC
* *
2018 TCTTGAATT
1 T-TT-ACTC
*
2027 TAATTACTAT
1 T--TTACT-C
2037 TTTAC-C
1 TTTACTC
*
2043 ATTTTTCTC
1 --TTTACTC
*
2052 TTTACTG
1 TTTACTC
*
2059 ATTACTC
1 TTTACTC
*
2066 TTTACTTT
1 TTTAC-TC
*
2074 TTTTCTC
1 TTTACTC
*
2081 TTTTCTC
1 TTTACTC
*
2088 TTTACTG
1 TTTACTC
*
2095 ATTACTC
1 TTTACTC
*
2102 TATACTC
1 TTTACTC
2109 TTTAC-C
1 TTTACTC
*
2115 ATTTTCCTC
1 --TTTACTC
*
2124 TTTACTG
1 TTTACTC
*
2131 ATTACTC
1 TTTACTC
2138 TTTTACTC
1 -TTTACTC
*
2146 CTTAC-C
1 TTTACTC
2152 ATTTTACTC
1 --TTTACTC
2161 TTTA
1 TTTA
2165 ATTACTAATT
Statistics
Matches: 257, Mismatches: 76, Indels: 60
0.65 0.19 0.15
Matches are distributed among these distances:
5 2 0.01
6 9 0.04
7 190 0.74
8 44 0.17
9 8 0.03
10 4 0.02
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.55
Consensus pattern (7 bp):
TTTACTC
Found at i:1970 original size:33 final size:35
Alignment explanation
Indices: 1795--2018 Score: 215
Period size: 35 Copynumber: 6.2 Consensus size: 35
1785 TTTTTATCAT
* ** *
1795 TTTACTCTTTACGAATTACTCC-TTACTGATTATTC
1 TTTACTCTTTAC-CATTTTTCCTTTACTGATTACTC
1830 TTTACTCTTTACCATTTTTCCTTTACTGATTACTC
1 TTTACTCTTTACCATTTTTCCTTTACTGATTACTC
* *
1865 TTTACTCTTTACCATTTTT-CTTTAATAATTACTCTTTACCC
1 TTTACTCTTTACCATTTTTCCTTTACTGATTA--C--T---C
*
1906 TTTACTCTTTACTATTTTTCCTTTACTGATTACTC
1 TTTACTCTTTACCATTTTTCCTTTACTGATTACTC
*
1941 TTTACTTTTTACCATTTTT-C-TTACTGATTACTC
1 TTTACTCTTTACCATTTTTCCTTTACTGATTACTC
* * *
1974 TTTACTCTTTACTC-TTTTACTCTTTACTAATTACTAT
1 TTTACTCTTTAC-CATTTTTC-CTTTACTGATTACT-C
2011 TTTACTCT
1 TTTACTCT
2019 CTTGAATTTA
Statistics
Matches: 160, Mismatches: 15, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
33 28 0.17
34 18 0.11
35 62 0.39
36 12 0.08
37 8 0.05
38 2 0.01
40 1 0.01
41 19 0.12
42 10 0.06
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (35 bp):
TTTACTCTTTACCATTTTTCCTTTACTGATTACTC
Found at i:1971 original size:158 final size:155
Alignment explanation
Indices: 1535--2000 Score: 645
Period size: 158 Copynumber: 2.9 Consensus size: 155
1525 TGATTATCTT
*
1535 TTTACTGATTACCCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
1600 CTTCTTTTACTGATTACTCTTTATTTCTTTTTATCATTTTACTCTTTACGAATTACTCCTTACTG
66 CTTCTTTTACTGATTACTCTTTA--TCTTTTTATCATTTTA-TCTTTACGAATTACTCCTTACTG
1665 ATTATTCTTTACTCTTTACCATTTTTCC
128 ATTATTCTTTACTCTTTACCATTTTTCC
1693 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
*
1758 CTTCTTTTACTGATTACACTTTATTTCTTTTTATCATTTTACTCTTTACGAATTACTCCTTACTG
66 CTTCTTTTACTGATTACTCTTTA--TCTTTTTATCATTTTA-TCTTTACGAATTACTCCTTACTG
1823 ATTATTCTTTACTCTTTACCATTTTTCC
128 ATTATTCTTTACTCTTTACCATTTTTCC
* * *
1851 TTTACTGATTACTCTTTACTCTTTACCATT-TTTCTTTAATAATTACTCTTTACCCTTTACTCTT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTA--C--T--T-TT
* * * * *
1915 TACTATTTTTCCTTTACTGATTACTCTTTA-CTTTTTACCATTTT-TC-TTACTG-ATTACTCTT
59 TACCATTCTTCTTTTACTGATTACTCTTTATCTTTTTATCATTTTATCTTTAC-GAATTACTCCT
** *
1976 TACTCTTTACTCTTTTACTCTTTAC
123 TACTGATTATTC-TTTACTCTTTAC
2001 TAATTACTAT
Statistics
Matches: 285, Mismatches: 14, Indels: 17
0.90 0.04 0.05
Matches are distributed among these distances:
157 19 0.07
158 207 0.73
159 16 0.06
161 14 0.05
163 1 0.00
164 28 0.10
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.55
Consensus pattern (155 bp):
TTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTACCATT
CTTCTTTTACTGATTACTCTTTATCTTTTTATCATTTTATCTTTACGAATTACTCCTTACTGATT
ATTCTTTACTCTTTACCATTTTTCC
Found at i:1994 original size:76 final size:76
Alignment explanation
Indices: 1828--1990 Score: 274
Period size: 76 Copynumber: 2.2 Consensus size: 76
1818 TACTGATTAT
*
1828 TCTTTACTCTTTACCATTTTTCCTTTACTGATTACTCTTTACTCTTTACCATTTTTCTTTAATAA
1 TCTTTACTCTTTACTATTTTTCCTTTACTGATTACTCTTTACTCTTTACCATTTTTCTTTAATAA
1893 TTACTCTTTAC
66 TTACTCTTTAC
* * * *
1904 CCTTTACTCTTTACTATTTTTCCTTTACTGATTACTCTTTACTTTTTACCATTTTTC-TTACTGA
1 TCTTTACTCTTTACTATTTTTCCTTTACTGATTACTCTTTACTCTTTACCATTTTTCTTTAATAA
1968 TTACTCTTTAC
66 TTACTCTTTAC
1979 TCTTTACTCTTT
1 TCTTTACTCTTT
1991 TACTCTTTAC
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 27 0.33
76 54 0.67
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (76 bp):
TCTTTACTCTTTACTATTTTTCCTTTACTGATTACTCTTTACTCTTTACCATTTTTCTTTAATAA
TTACTCTTTAC
Found at i:2085 original size:36 final size:35
Alignment explanation
Indices: 2037--2164 Score: 159
Period size: 36 Copynumber: 3.5 Consensus size: 35
2027 TAATTACTAT
*
2037 TTTACCATTTTTCTCTTTACTGATTACTCTTTACTTT
1 TTTACCA-TTTTCTCTTTACTGATTACTCTTTAC-TC
* *
2074 TTTTCTC-TTTTCTCTTTACTGATTACTCTATACTC
1 TTTAC-CATTTTCTCTTTACTGATTACTCTTTACTC
2109 TTTACCATTTTCCTCTTTACTGATTACTCTTTTACTC
1 TTTACCATTTT-CTCTTTACTGATTACTC-TTTACTC
*
2146 CTTACCATTTTACTCTTTA
1 TTTACCATTTT-CTCTTTA
2165 ATTACTAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
34 1 0.01
35 9 0.11
36 42 0.52
37 27 0.34
38 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.56
Consensus pattern (35 bp):
TTTACCATTTTCTCTTTACTGATTACTCTTTACTC
Found at i:2330 original size:32 final size:32
Alignment explanation
Indices: 2262--2352 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
2252 GATCAGTTCT
** **
2262 TTTTACTTCCTTTCTTAATTGCTAATTAACCC
1 TTTTACTTCCTTTCTTAATTATTAATTAACAA
*
2294 TTTTACTTCCTTTCTTAATTATTGATT-ACTAA
1 TTTTACTTCCTTTCTTAATTATTAATTAAC-AA
* * *
2326 TTTTACTTTCTCTCTTAATTATCAATT
1 TTTTACTTCCTTTCTTAATTATTAATT
2353 CACTGATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 2 0.04
32 47 0.96
ACGTcount: A:0.23, C:0.20, G:0.02, T:0.55
Consensus pattern (32 bp):
TTTTACTTCCTTTCTTAATTATTAATTAACAA
Found at i:2449 original size:80 final size:80
Alignment explanation
Indices: 2316--2497 Score: 265
Period size: 80 Copynumber: 2.3 Consensus size: 80
2306 TCTTAATTAT
* * * *
2316 TGATTACTAATTTTACTTTCTCTCTTAATTATCAATTCACTGATTTATCCCTTTACTTTGACTCT
1 TGATTACTACTTTTACTTCCTCTCTTAATTATCAATTCACTGATTAATCCCTTTACCTTGACTCT
2381 TAATTACTAATCTAC
66 TAATTACTAATCTAC
* * * *
2396 TGATTACTACTTTTGCTTCCTCTTTTAATTATGAATTTACTGATTAATCCCTTTACCTTGACTCT
1 TGATTACTACTTTTACTTCCTCTCTTAATTATCAATTCACTGATTAATCCCTTTACCTTGACTCT
* *
2461 TAATTACTGATTTAC
66 TAATTACTAATCTAC
2476 TGATTTACTACTTTTACTTCCT
1 TGA-TTACTACTTTTACTTCCT
2498 TACTCCTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 73 0.81
81 17 0.19
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.49
Consensus pattern (80 bp):
TGATTACTACTTTTACTTCCTCTCTTAATTATCAATTCACTGATTAATCCCTTTACCTTGACTCT
TAATTACTAATCTAC
Found at i:2474 original size:40 final size:39
Alignment explanation
Indices: 2337--2480 Score: 130
Period size: 40 Copynumber: 3.6 Consensus size: 39
2327 TTTACTTTCT
* * *
2337 CTCTTAATTATCAATTCACTGATTTATCCCTTTACTTTGA
1 CTCTTAATTAT-AATTTACTGATTAATCCCTTTACCTTGA
* * * ** *
2377 CTCTTAATTACTAATCTACTGATTACT-ACTTTTGCTT-C
1 CTCTTAATTA-TAATTTACTGATTAATCCCTTTACCTTGA
2415 CTCTTTTAATTATGAATTTACTGATTAATCCCTTTACCTTGA
1 CTC--TTAATTAT-AATTTACTGATTAATCCCTTTACCTTGA
*
2457 CTCTTAATTACTGATTTACTGATT
1 CTCTTAATTA-TAATTTACTGATT
2481 TACTACTTTT
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
38 3 0.04
39 7 0.09
40 59 0.73
41 9 0.11
42 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (39 bp):
CTCTTAATTATAATTTACTGATTAATCCCTTTACCTTGA
Found at i:6736 original size:25 final size:25
Alignment explanation
Indices: 6708--6777 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
6698 AAATGAACTA
* *
6708 AAAATGACTAAAGTGCCCCTAGTTC
1 AAAATGACCAAAATGCCCCTAGTTC
6733 AAAATGACCAAAATGCCCCTAGTTC
1 AAAATGACCAAAATGCCCCTAGTTC
6758 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
6778 CGGTGACTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (25 bp):
AAAATGACCAAAATGCCCCTAGTTC
Found at i:8155 original size:33 final size:33
Alignment explanation
Indices: 8118--8194 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
8108 TGTCCATGTT
*
8118 GCGTGGCCGGTGATGGCCGGGCATCTCCGAGTC
1 GCGTGGCCGGTGATGGCCGGGCATCTCCAAGTC
* *
8151 GCGTGGCCGGTGTTGGCCGGGCTTCTCCAAGTC
1 GCGTGGCCGGTGATGGCCGGGCATCTCCAAGTC
* *
8184 GCATGGTCGGT
1 GCGTGGCCGGT
8195 CACTCGCGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.08, C:0.29, G:0.42, T:0.22
Consensus pattern (33 bp):
GCGTGGCCGGTGATGGCCGGGCATCTCCAAGTC
Done.