Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017529.1 Corchorus olitorius cultivar O-4 contig17562, 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: 20385
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1707 original size:14 final size:12
Alignment explanation
Indices: 1669--1713 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 12
1659 ATTTTATTAC
1669 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
1682 TGTTTTATAAAT
1 TGTTTTATAAAT
1694 TGTTTTAAATAAAT
1 TGTTTT--ATAAAT
1708 TGTTTT
1 TGTTTT
1714 GGGTGCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.37
13 7 0.23
14 12 0.40
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:6579 original size:7 final size:8
Alignment explanation
Indices: 6555--6602 Score: 60
Period size: 8 Copynumber: 5.5 Consensus size: 8
6545 AATGATGATG
6555 AAATGAAA
1 AAATGAAA
6563 AAATGAAA
1 AAATGAAA
6571 AAATGAAAAA
1 AAATG--AAA
6581 AAATGAAAAA
1 AAATG--AAA
6591 AAATGAAA
1 AAATGAAA
6599 AAAT
1 AAAT
6603 TAAGGCACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 20 0.53
10 18 0.47
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:6581 original size:10 final size:10
Alignment explanation
Indices: 6560--6601 Score: 70
Period size: 10 Copynumber: 4.4 Consensus size: 10
6550 TGATGAAATG
6560 AAAAAATG--
1 AAAAAATGAA
6568 AAAAAATGAA
1 AAAAAATGAA
6578 AAAAAATGAA
1 AAAAAATGAA
6588 AAAAAATGAA
1 AAAAAATGAA
6598 AAAA
1 AAAA
6602 TTAAGGCACT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.25
10 24 0.75
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:6978 original size:9 final size:9
Alignment explanation
Indices: 6966--7012 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
6956 GAAATTCAAT
6966 AAAAAAATC
1 AAAAAAATC
6975 AAAAAAATC
1 AAAAAAATC
*
6984 AAAAAGA--
1 AAAAAAATC
6991 AAAAAAAT-
1 AAAAAAATC
6999 AAAAAAATC
1 AAAAAAATC
7008 AAAAA
1 AAAAA
7013 TCCAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 6 0.18
8 8 0.24
9 20 0.59
ACGTcount: A:0.83, C:0.06, G:0.02, T:0.09
Consensus pattern (9 bp):
AAAAAAATC
Found at i:6980 original size:8 final size:8
Alignment explanation
Indices: 6967--7062 Score: 62
Period size: 8 Copynumber: 12.4 Consensus size: 8
6957 AAATTCAATA
6967 AAAAAATC
1 AAAAAATC
6975 AAAAAAATC
1 -AAAAAATC
*
6984 AAAAAGA-A
1 AAAAA-ATC
*
6992 AAAAAATA
1 AAAAAATC
7000 AAAAAATC
1 AAAAAATC
7008 -AAAAATCC
1 AAAAAAT-C
*
7016 AAAAAA-A
1 AAAAAATC
7023 ATAAAAAT-
1 A-AAAAATC
*
7031 AAAAAATA
1 AAAAAATC
7039 AAAAAAT-
1 AAAAAATC
*
7046 AATAAA--
1 AAAAAATC
7052 AAAAAATC
1 AAAAAATC
7060 AAA
1 AAA
7063 TCAAAATAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
6 5 0.07
7 19 0.26
8 35 0.48
9 14 0.19
ACGTcount: A:0.81, C:0.06, G:0.01, T:0.11
Consensus pattern (8 bp):
AAAAAATC
Found at i:7020 original size:9 final size:8
Alignment explanation
Indices: 6963--7057 Score: 83
Period size: 7 Copynumber: 11.9 Consensus size: 8
6953 CAAGAAATTC
6963 AATAAAAA
1 AATAAAAA
6971 AATCAAAAA
1 AAT-AAAAA
6980 AATCAAAAA
1 AAT-AAAAA
*
6989 GA-AAAAA
1 AATAAAAA
6996 AATAAAAA
1 AATAAAAA
*
7004 AAT-CAAA
1 AATAAAAA
7011 AATCCAAAAA
1 AAT--AAAAA
*
7021 AA-ATAAA
1 AATAAAAA
7028 AAT-AAAA
1 AATAAAAA
7035 AATAAAAA
1 AATAAAAA
7043 AATAATAAA
1 AATAA-AAA
7052 AA-AAAA
1 AATAAAA
7058 TCAAATCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
7 26 0.36
8 22 0.30
9 20 0.27
10 5 0.07
ACGTcount: A:0.82, C:0.05, G:0.01, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:7021 original size:33 final size:31
Alignment explanation
Indices: 6963--7057 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 31
6953 CAAGAAATTC
6963 AATAAAAAAATCAAAAAAATCAAAAAGAAAAAA
1 AATAAAAAAATC-AAAAAATCAAAAA-AAAAAA
6996 AATAAAAAAATC-AAAAATCCAAAAAAAATAAA
1 AATAAAAAAATCAAAAAAT-CAAAAAAAA-AAA
* *
7028 AAT-AAAAAATAAAAAAAT-AATAAAAAAAA
1 AATAAAAAAATCAAAAAATCAAAAAAAAAAA
7057 A
1 A
7058 TCAAATCAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
29 4 0.07
30 7 0.12
31 16 0.28
32 18 0.32
33 12 0.21
ACGTcount: A:0.82, C:0.05, G:0.01, T:0.12
Consensus pattern (31 bp):
AATAAAAAAATCAAAAAATCAAAAAAAAAAA
Found at i:7034 original size:11 final size:10
Alignment explanation
Indices: 6966--7073 Score: 60
Period size: 11 Copynumber: 10.2 Consensus size: 10
6956 GAAATTCAAT
*
6966 AAAAAAAT-C
1 AAAAAAATAA
6975 AAAAAAATCAA
1 AAAAAAAT-AA
6986 AAAGAAAA-AA
1 AAA-AAAATAA
6996 AATAAAAA-AA
1 AA-AAAAATAA
**
7006 TCAAAAATCCAA
1 AAAAAAAT--AA
*
7018 AAAAAATAAAA
1 AAAAAA-ATAA
7029 ATAAAAAATAA
1 A-AAAAAATAA
7040 AAAAATAATAA
1 AAAAA-AATAA
7051 AAAAAAATCAA
1 AAAAAAAT-AA
**
7062 ATCAAAATAA
1 AAAAAAATAA
7072 AA
1 AA
7074 GAGAATTGAT
Statistics
Matches: 78, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
9 13 0.17
10 20 0.26
11 29 0.37
12 15 0.19
13 1 0.01
ACGTcount: A:0.81, C:0.06, G:0.01, T:0.12
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:7063 original size:18 final size:17
Alignment explanation
Indices: 6966--7062 Score: 76
Period size: 18 Copynumber: 5.7 Consensus size: 17
6956 GAAATTCAAT
6966 AAAAAAATCAAAAA-AA
1 AAAAAAATCAAAAATAA
** * *
6982 TCAAAAA-GAAAAAAAA
1 AAAAAAATCAAAAATAA
*
6998 TAAAAAAATCAAAAATCCA
1 -AAAAAAATCAAAAAT-AA
7017 AAAAAAAT-AAAAATAA
1 AAAAAAATCAAAAATAA
*
7033 AAAATAAA-AAAATAATAA
1 AAAA-AAATCAAA-AATAA
7051 AAAAAAATCAAA
1 AAAAAAATCAAA
7063 TCAAAATAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
15 5 0.08
16 12 0.19
17 20 0.32
18 25 0.40
19 1 0.02
ACGTcount: A:0.81, C:0.06, G:0.01, T:0.11
Consensus pattern (17 bp):
AAAAAAATCAAAAATAA
Found at i:7068 original size:24 final size:21
Alignment explanation
Indices: 6991--7073 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 21
6981 ATCAAAAAGA
6991 AAAAAAATAAAAAAATCAAAAATC
1 AAAAAAAT-AAAAAA--AAAAATC
*
7015 CAAAAAAAATAAAAATAAAAAAT-
1 AAAAA--AATAAAAA-AAAAAATC
7038 AAAAAAATAATAAAAAAAAATC
1 AAAAAAATAA-AAAAAAAAATC
7060 AAATCAAAATAAAA
1 AAA--AAAATAAAA
7074 GAGAATTGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
21 12 0.24
22 6 0.12
23 6 0.12
24 17 0.34
25 5 0.10
26 4 0.08
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAAAATC
Found at i:7069 original size:39 final size:38
Alignment explanation
Indices: 6975--7073 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 38
6965 TAAAAAAATC
6975 AAAAAAATCAAA-AAGAA-AAAAAATAAAAAAATCAAAA
1 AAAAAAATCAAATAA-AATAAAAAATAAAAAAATCAAAA
*
7012 ATCCAAAAA--AAATAAAAATAAAAAATAAAAAAAT-AATAA
1 A--AAAAAATCAAAT-AAAATAAAAAATAAAAAAATCAA-AA
7051 AAAAAAATCAAATCAAAATAAAA
1 AAAAAAATCAAAT-AAAATAAAA
7074 GAGAATTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
37 9 0.18
38 4 0.08
39 38 0.75
ACGTcount: A:0.81, C:0.06, G:0.01, T:0.12
Consensus pattern (38 bp):
AAAAAAATCAAATAAAATAAAAAATAAAAAAATCAAAA
Found at i:9397 original size:15 final size:16
Alignment explanation
Indices: 9367--9400 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
9357 TTACTTTGCT
9367 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
9383 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
9398 TTG
1 TTG
9401 CTTTATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:12952 original size:24 final size:21
Alignment explanation
Indices: 12897--12951 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
12887 CGGCCATTCA
*
12897 CCGTGACACCACCGGTTAAGC
1 CCGTGCCACCACCGGTTAAGC
*
12918 CCGTGCCACCACCGGTTATGC
1 CCGTGCCACCACCGGTTAAGC
*
12939 CCGTGCCATCACC
1 CCGTGCCACCACC
12952 ATTCCAAGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.44, G:0.22, T:0.16
Consensus pattern (21 bp):
CCGTGCCACCACCGGTTAAGC
Found at i:15449 original size:11 final size:11
Alignment explanation
Indices: 15433--15458 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
15423 AGATAATTTC
15433 TTTTCTTCTAG
1 TTTTCTTCTAG
15444 TTTTCTTCTAG
1 TTTTCTTCTAG
15455 TTTT
1 TTTT
15459 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:16248 original size:15 final size:15
Alignment explanation
Indices: 16218--16259 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
16208 TTACTTTGCT
16218 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
16234 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
16249 TTGCTTTCTGT
1 TTGTTTTCTGT
16260 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:17786 original size:169 final size:169
Alignment explanation
Indices: 17507--17965 Score: 713
Period size: 169 Copynumber: 2.7 Consensus size: 169
17497 TTATTTCCAT
* *
17507 TTGATAAAACCTCCGGGTACCATTTCGTTTCATCAAGTTTGTCATTAAAAGTTCATGTTTAAGTT
1 TTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTGTCATTAAAAATTCATGTTTAAGTT
*
17572 TAAAATCCTTGTTCAAGGTCTC-TATTCAGAGTTTACATTGGTAAGTCCTCCGGGCACAAATTCA
66 TAAAATCCTTGTTCAAGGTCTCAT-TTCAAAGTTTACATTGGTAAGTCCTCCGGGCACAAATTCA
17636 GAAACCTCCGGGTAATAATTCTGATAAGTCCTCCGGGCAA
130 GAAACCTCCGGGTAATAATTCTGATAAGTCCTCCGGGCAA
* *
17676 TTGATAAAACCTCCGGGTATCATTTCATTTCATCGAGTTTGTCATTAAAAATTCATGTTTAAGTT
1 TTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTGTCATTAAAAATTCATGTTTAAGTT
* ** *
17741 TAAAATCCTTGTTTAAGGTCTCATTTCAAAGTTCGCATTGGTAAGTCCTCCGGACACAAATTCAG
66 TAAAATCCTTGTTCAAGGTCTCATTTCAAAGTTTACATTGGTAAGTCCTCCGGGCACAAATTCAG
**
17806 AAACCTCCGGGTGTTAATTCTGATAAGTCCTCCGGGCAA
131 AAACCTCCGGGTAATAATTCTGATAAGTCCTCCGGGCAA
* * * *
17845 TTGATAAAACCTCCGGGTACCATTTGATTTCATCAAGTTTTTCATCAAAAATCCATGTTTAAGTT
1 TTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTGTCATTAAAAATTCATGTTTAAGTT
* * * * * *
17910 TAAAATCCTTGGTCAAGGTTTCAATCCAAAGTTTACGTTGGTAAGTCCTCCAGGCA
66 TAAAATCCTTGTTCAAGGTCTCATTTCAAAGTTTACATTGGTAAGTCCTCCGGGCA
17966 ACTGATAAGT
Statistics
Matches: 262, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
169 261 1.00
170 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (169 bp):
TTGATAAAACCTCCGGGTACCATTTCATTTCATCAAGTTTGTCATTAAAAATTCATGTTTAAGTT
TAAAATCCTTGTTCAAGGTCTCATTTCAAAGTTTACATTGGTAAGTCCTCCGGGCACAAATTCAG
AAACCTCCGGGTAATAATTCTGATAAGTCCTCCGGGCAA
Found at i:18172 original size:39 final size:39
Alignment explanation
Indices: 18114--18238 Score: 144
Period size: 38 Copynumber: 3.2 Consensus size: 39
18104 GCTTTATCAG
*
18114 TTTATTTCAATTTACTTTCGATCCTAGTTTAGGATCATTGC
1 TTTATTT-AGTTTA-TTTCGATCCTAGTTTAGGATCATTGC
* * *
18155 TGTATTTAGTTTATTTCGATCCTAGTTAAGGATCATTCC
1 TTTATTTAGTTTATTTCGATCCTAGTTTAGGATCATTGC
* ** * *
18194 TTTA-TCAGTTTATTTTAATCCTGGTTTAGGATCATCGC
1 TTTATTTAGTTTATTTCGATCCTAGTTTAGGATCATTGC
18232 TTTATTT
1 TTTATTT
18239 TAGTCCTGGT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 31 0.44
39 28 0.40
40 5 0.07
41 6 0.09
ACGTcount: A:0.22, C:0.15, G:0.14, T:0.50
Consensus pattern (39 bp):
TTTATTTAGTTTATTTCGATCCTAGTTTAGGATCATTGC
Found at i:18236 original size:30 final size:30
Alignment explanation
Indices: 18202--19181 Score: 1323
Period size: 30 Copynumber: 32.6 Consensus size: 30
18192 CCTTTATCAG
* *
18202 TTTATTTTAATCCTGGTTTAGGATCATCGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
18232 TTTATTTTAGTCCTGGTTGAGGATCACTAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
18262 TTTATTCTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
18292 TTTATTTTAATCCCGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * * *
18322 TTTATTCTAGTCCTGGTTGAGGATCACTAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
18352 TTTATTCTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
18382 TTTATTTTAATCCTGGTTGAGGATCATAGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
18412 TTTATTCTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
18442 TTTATTATAGTCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * * *
18472 TTTAATTTAATCCTGGTTTAGGATTATCGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
18502 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
18532 TTTCTTCTAGTCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
18562 TTCATTTTAATCCTGTTTGAGGATTATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
18592 TTTGTTTTTAATCCTGGTTAAGGATCATCGC
1 TTT-ATTTTAATCCTGGTTGAGGATCATTGC
*
18623 TTTCATTTTAATCCTGGTTAAGGATCATTGC
1 TTT-ATTTTAATCCTGGTTGAGGATCATTGC
18654 TTTTATTTTAATCCTGGTTGAGGATCATTGC
1 -TTTATTTTAATCCTGGTTGAGGATCATTGC
* ** *
18685 TTTATTTTAATCCTGGTAGAGGATTGTTGT
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* ** *
18715 TTTATTTTAATCCTGGTCGAGGATCGCTGT
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
18745 TTTATTTTAATCCTGGTGGAGGAT-ATTCGC
1 TTTATTTTAATCCTGGTTGAGGATCATT-GC
* * * *
18775 ATCATTTTAATCCTGTTTGAGGATCATTAC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
**
18805 TTTATTTTAATCCTATTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
18835 TTTGTTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
18865 TTCATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
18895 GTCATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
18925 TTTATTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
18955 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
18985 TTAATTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
19015 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
19045 TTGATTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
19075 TTTATTTTAATCCTGGTTGAGGATAATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
19105 TTTACTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
19135 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
19165 TTCATTTTAATCCTGGT
1 TTTATTTTAATCCTGGT
19182 CATAAATTAA
Statistics
Matches: 835, Mismatches: 111, Indels: 8
0.88 0.12 0.01
Matches are distributed among these distances:
29 1 0.00
30 752 0.90
31 79 0.09
32 3 0.00
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:19288 original size:26 final size:28
Alignment explanation
Indices: 19221--19295 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
19211 TAAGGTCATT
* *
19221 CAGGGGCATTTTGGTTATTTTTCAATTA
1 CAGGGGCATTTTGGTCATTTTTCAACTA
19249 CAGGGGCATTTTGGTCATTTTT-ACACTA
1 CAGGGGCATTTTGGTCATTTTTCA-ACTA
19277 -A-GGGCATTTTGGTCATTTT
1 CAGGGGCATTTTGGTCATTTT
19296 AAGCTCACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.41
27 2 0.05
28 24 0.55
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (28 bp):
CAGGGGCATTTTGGTCATTTTTCAACTA
Done.