Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020359.1 Corchorus olitorius cultivar O-4 contig20392, 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: 84826
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2801 original size:30 final size:30
Alignment explanation
Indices: 2765--2851 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
2755 TACATACCAC
2765 TAATAATTATTATTATCATAATAATAAGTT
1 TAATAATTATTATTATCATAATAATAAGTT
* *
2795 TAATAATTA-TAATACCACTAATAATAAGTT
1 TAATAATTATTATTATCA-TAATAATAAGTT
* *
2825 TAATAATTATTATAATAATAATAATAA
1 TAATAATTATTATTATCATAATAATAA
2852 CTCTAAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.12
30 39 0.80
31 4 0.08
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (30 bp):
TAATAATTATTATTATCATAATAATAAGTT
Found at i:3299 original size:22 final size:21
Alignment explanation
Indices: 3265--3322 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
3255 TGAAACTTTA
**
3265 ATAACCTAACTATGAAATATT
1 ATAACCTTCCTATGAAATATT
* *
3286 ATAAATCTTCCTATGAAATTTT
1 AT-AACCTTCCTATGAAATATT
*
3308 GTAACCTTCCTATGA
1 ATAACCTTCCTATGA
3323 TTTTTGATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (21 bp):
ATAACCTTCCTATGAAATATT
Found at i:3318 original size:21 final size:21
Alignment explanation
Indices: 3274--3335 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3264 AATAACCTAA
* * *
3274 CTATGAAATATTATAAATCTTC
1 CTATGAAATTTTGT-AACCTTC
3296 CTATGAAATTTTGTAACCTTC
1 CTATGAAATTTTGTAACCTTC
*
3317 CTATG-ATTTTTGATAACCT
1 CTATGAAATTTTG-TAACCT
3336 CCCTGTAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.17
21 17 0.49
22 12 0.34
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (21 bp):
CTATGAAATTTTGTAACCTTC
Found at i:4306 original size:35 final size:35
Alignment explanation
Indices: 4245--4316 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
4235 GATCTTAAGC
* **
4245 TCTCTAAACACCTTAAGACCCCACTAACTTCAATA
1 TCTCCAAACACCTTAAGACCCCACTAACCCCAATA
* * *
4280 TCTCCAAACACCTTAATATCCTACTAACCCCAATA
1 TCTCCAAACACCTTAAGACCCCACTAACCCCAATA
4315 TC
1 TC
4317 AAACAAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.36, G:0.01, T:0.26
Consensus pattern (35 bp):
TCTCCAAACACCTTAAGACCCCACTAACCCCAATA
Found at i:11186 original size:12 final size:13
Alignment explanation
Indices: 11169--11200 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
11159 AAAGATAGGG
11169 TTTATTTTG-TTT
1 TTTATTTTGATTT
11181 TTTATTTTGATTT
1 TTTATTTTGATTT
11194 TTT-TTTT
1 TTTATTTT
11201 TAAATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.84
Consensus pattern (13 bp):
TTTATTTTGATTT
Found at i:13768 original size:19 final size:19
Alignment explanation
Indices: 13728--13764 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13718 GATTTCTAAG
13728 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
13747 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
13765 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:14020 original size:31 final size:31
Alignment explanation
Indices: 13978--14053 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
13968 CTTTATTAAT
* * *
13978 TGGACTCAATTGATCCAATCCTATAAGTATA
1 TGGACTAAATTGATCCAATCATATAAGTACA
* *
14009 TGGACTAAATTGATCCAATCATGTGAGTACA
1 TGGACTAAATTGATCCAATCATATAAGTACA
14040 TGGACTAAATTGAT
1 TGGACTAAATTGAT
14054 TATTTTTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (31 bp):
TGGACTAAATTGATCCAATCATATAAGTACA
Found at i:18725 original size:6 final size:6
Alignment explanation
Indices: 18706--18739 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
18696 TTTTAAGCGC
*
18706 AGAAAA A-AAAA AGAAGA AGAAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA
18740 GATTGCTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:23020 original size:35 final size:35
Alignment explanation
Indices: 22975--23070 Score: 174
Period size: 35 Copynumber: 2.7 Consensus size: 35
22965 AGTTCGTTTA
22975 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
* *
23010 TGTTCACGAACAAGTTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
23045 TGTTCACGAACAGGCTCGTTTATTGT
1 TGTTCACGAACAGGCTCGTTTATTGT
23071 CGTTTATATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGGCTCGTTTATTGTTCATTTAAG
Found at i:23298 original size:18 final size:18
Alignment explanation
Indices: 23271--23305 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23261 AATTATTACA
23271 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
23289 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
23306 CAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:23618 original size:41 final size:43
Alignment explanation
Indices: 23566--23760 Score: 231
Period size: 41 Copynumber: 4.6 Consensus size: 43
23556 TCAATGCCTT
*
23566 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCC
1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAGTGCCCC
* * * * *
23609 TGTGTTATATATGTGTTTGGGGAC-TTG-AATATAGGTGTCTC
1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAGTGCCCC
*
23650 TGTGTTATATATGTGTTTGAGGACTTTGTAATA-AAGGTGCCCA
1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAA-GTGCCCC
* * * *
23693 TGTGTTATATATGTGTTTGGGGAC-TTGGATATAG--GTGTCTC
1 TGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAAGTGCCCC
23734 TGTGTTATATATGTGTTTGAGGACTTT
1 TGTGTTATATATGTGTTTGAGGACTTT
23761 TGGTTATTGG
Statistics
Matches: 129, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
41 59 0.46
42 13 0.10
43 57 0.44
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.44
Consensus pattern (43 bp):
TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAGTGCCCC
Found at i:23707 original size:84 final size:84
Alignment explanation
Indices: 23566--23760 Score: 347
Period size: 84 Copynumber: 2.3 Consensus size: 84
23556 TCAATGCCTT
* *
23566 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATGTGTTTGGGG
1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAGTGCCCATGTGTTATATATGTGTTTGGGG
23631 ACTTGAATATAGGTGTCTC
66 ACTTGAATATAGGTGTCTC
23650 TGTGTTATATATGTGTTTGAGGACTTTGTAATA-AAGGTGCCCATGTGTTATATATGTGTTTGGG
1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAA-GTGCCCATGTGTTATATATGTGTTTGGG
*
23714 GACTTGGATATAGGTGTCTC
65 GACTTGAATATAGGTGTCTC
23734 TGTGTTATATATGTGTTTGAGGACTTT
1 TGTGTTATATATGTGTTTGAGGACTTT
23761 TGGTTATTGG
Statistics
Matches: 107, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
83 2 0.02
84 105 0.98
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.44
Consensus pattern (84 bp):
TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAGTGCCCATGTGTTATATATGTGTTTGGGG
ACTTGAATATAGGTGTCTC
Found at i:24680 original size:16 final size:16
Alignment explanation
Indices: 24655--24689 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
24645 AAATTCGGTG
*
24655 GAATTAAGGGGGAATT
1 GAATTAAGGGGGAACT
*
24671 GAATTGAGGGGGAACT
1 GAATTAAGGGGGAACT
24687 GAA
1 GAA
24690 AATAGTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.40, T:0.20
Consensus pattern (16 bp):
GAATTAAGGGGGAACT
Found at i:26503 original size:31 final size:30
Alignment explanation
Indices: 26468--26544 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
26458 ATACCGTACA
26468 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT
* **
26499 GGTCCCCCTAC-TACAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGTCAATTT
*
26528 GGTCTCTCTACTTACAA
1 GGTCCCTCTACTTACAA
26545 TTTGGTGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 16 0.40
30 14 0.35
31 10 0.25
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAAGGTCAATTT
Found at i:26637 original size:12 final size:12
Alignment explanation
Indices: 26616--26653 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
26606 TTGCATAGGT
26616 TGCTTATGTTTC
1 TGCTTATGTTTC
*
26628 TGCTTCTGTTTC
1 TGCTTATGTTTC
26640 TG-TTGATGTTTC
1 TGCTT-ATGTTTC
26652 TG
1 TG
26654 TTGAGTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 2 0.09
12 21 0.91
ACGTcount: A:0.05, C:0.16, G:0.21, T:0.58
Consensus pattern (12 bp):
TGCTTATGTTTC
Found at i:26654 original size:12 final size:12
Alignment explanation
Indices: 26621--26661 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
26611 TAGGTTGCTT
26621 ATGTTTCTGCTT-
1 ATGTTTCTG-TTG
*
26633 CTGTTTCTGTTG
1 ATGTTTCTGTTG
26645 ATGTTTCTGTTG
1 ATGTTTCTGTTG
26657 A-GTTT
1 ATGTTT
26662 GTTGTGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.07, C:0.12, G:0.22, T:0.59
Consensus pattern (12 bp):
ATGTTTCTGTTG
Found at i:26909 original size:31 final size:30
Alignment explanation
Indices: 26841--26911 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
26831 ACCAAATTGC
*
26841 AAGTAGAGGGATCAAATTGACAGTTTTTAT
1 AAGTAGAGGGACCAAATTGACAGTTTTTAT
** *
26871 -AGTAGAGGGACCAAATTGATCCTTTTTTGT
1 AAGTAGAGGGACCAAATTGA-CAGTTTTTAT
26901 AAGTAGAGGGA
1 AAGTAGAGGGA
26912 TCTGTTCGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.51
30 7 0.20
31 10 0.29
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (30 bp):
AAGTAGAGGGACCAAATTGACAGTTTTTAT
Found at i:32205 original size:45 final size:45
Alignment explanation
Indices: 32154--32246 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
32144 CATTACCTAA
* *
32154 ATTCTACTCCTCCATCTCTAGGTAATTCATCAAAATAAAGTTAAT
1 ATTCTACCCCTCCATCTCTAGATAATTCATCAAAATAAAGTTAAT
*
32199 ATTCTACCCCTCCATCTCTATATAATTCATCAAAATAAAGTTAAT
1 ATTCTACCCCTCCATCTCTAGATAATTCATCAAAATAAAGTTAAT
32244 ATT
1 ATT
32247 AATTGTTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (45 bp):
ATTCTACCCCTCCATCTCTAGATAATTCATCAAAATAAAGTTAAT
Found at i:33502 original size:29 final size:29
Alignment explanation
Indices: 33467--33522 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
33457 AGTCTTTCCA
33467 AAAAGTT-GGGACCCTTATTTGACATTTTT
1 AAAAGTTCGGG-CCCTTATTTGACATTTTT
*
33496 AAAAGTTCGGGCCCTTATTTGAGATTT
1 AAAAGTTCGGGCCCTTATTTGACATTT
33523 AAGGCAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (29 bp):
AAAAGTTCGGGCCCTTATTTGACATTTTT
Found at i:37888 original size:26 final size:26
Alignment explanation
Indices: 37852--37903 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
37842 CATAGTATAT
37852 TTAGTGCATATGTGCAAGTGAATAGG
1 TTAGTGCATATGTGCAAGTGAATAGG
* *
37878 TTAGTGCATATGTGTAAGTGCATAGG
1 TTAGTGCATATGTGCAAGTGAATAGG
37904 AGGTGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.33
Consensus pattern (26 bp):
TTAGTGCATATGTGCAAGTGAATAGG
Found at i:37899 original size:14 final size:14
Alignment explanation
Indices: 37854--37901 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
37844 TAGTATATTT
*
37854 AGTGCATATGTGCA
1 AGTGCATATGTGTA
* *
37868 AGTGAATA-G-GTT
1 AGTGCATATGTGTA
37880 AGTGCATATGTGTA
1 AGTGCATATGTGTA
37894 AGTGCATA
1 AGTGCATA
37902 GGAGGTGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 17 0.63
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.31
Consensus pattern (14 bp):
AGTGCATATGTGTA
Found at i:45840 original size:22 final size:23
Alignment explanation
Indices: 45792--45842 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
45782 AGATGATACT
*
45792 ACTCG-TGAACTACTCGGGCTCG
1 ACTCGATGAACTACTCGAGCTCG
* *
45814 GCTCGATGAA-TACTCGAGTTCG
1 ACTCGATGAACTACTCGAGCTCG
45836 ACTCGAT
1 ACTCGAT
45843 TTTTCTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
ACTCGATGAACTACTCGAGCTCG
Found at i:48339 original size:14 final size:14
Alignment explanation
Indices: 48320--48347 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48310 CAATTAATAC
48320 TAATGATATAAATT
1 TAATGATATAAATT
48334 TAATGATATAAATT
1 TAATGATATAAATT
48348 GATTGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TAATGATATAAATT
Found at i:48354 original size:14 final size:14
Alignment explanation
Indices: 48321--48354 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
48311 AATTAATACT
*
48321 AATGATATAAATTT
1 AATGATATAAATTG
48335 AATGATATAAATTG
1 AATGATATAAATTG
*
48349 ATTGAT
1 AATGAT
48355 TGATTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (14 bp):
AATGATATAAATTG
Found at i:49427 original size:21 final size:21
Alignment explanation
Indices: 49398--49451 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
49388 AATACTATTT
*
49398 AATCTATTGATAGAGATTATA
1 AATCAATTGATAGAGATTATA
49419 AATCAATTGATAGAGATTATA
1 AATCAATTGATAGAGATTATA
49440 AATCAATTGATA
1 AATCAATTGATA
49452 TAATTAGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
AATCAATTGATAGAGATTATA
Found at i:51423 original size:29 final size:29
Alignment explanation
Indices: 51390--51455 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
51380 AATTATTATG
** *
51390 ATTTCATTTTAATCCCTAATGTTTGAATT
1 ATTTCATTTTAATCCCTAACATTTGAATC
*
51419 ATTTCATTTTAGTCCCTAACATTTGAATC
1 ATTTCATTTTAATCCCTAACATTTGAATC
*
51448 ATCTCATT
1 ATTTCATT
51456 AGCTCCCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (29 bp):
ATTTCATTTTAATCCCTAACATTTGAATC
Found at i:51978 original size:26 final size:26
Alignment explanation
Indices: 51898--52078 Score: 89
Period size: 26 Copynumber: 7.1 Consensus size: 26
51888 AGTAGTCTCG
51898 ATAATCACCATAATTATCTCTAATA-
1 ATAATCACCATAATTATCTCTAATAT
* ** *
51923 ATATATAAAGATAA-TATGGT-TAATAAAT
1 ATA-ATCACCATAATTAT-CTCTAAT--AT
*
51951 ATAATCACCATAATTATCTCTAGTAT
1 ATAATCACCATAATTATCTCTAATAT
** *
51977 AT-AT--GGATAA-TATGGT-TAATAAT
1 ATAATCACCATAATTAT-CTCTAAT-AT
52000 ATAATCACCATAATTATCTCTAATAT
1 ATAATCACCATAATTATCTCTAATAT
** *
52026 AT-AT-ATGGATAA-TATGGT-TAATAAT
1 ATAATCA-CCATAATTAT-CTCTAAT-AT
*
52051 TTAATCACCATAATTATCTCTAATAT
1 ATAATCACCATAATTATCTCTAATAT
52077 AT
1 AT
52079 TTATGGTTAA
Statistics
Matches: 111, Mismatches: 24, Indels: 41
0.63 0.14 0.23
Matches are distributed among these distances:
22 6 0.05
23 9 0.08
24 10 0.09
25 22 0.20
26 31 0.28
27 24 0.22
28 9 0.08
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (26 bp):
ATAATCACCATAATTATCTCTAATAT
Found at i:52024 original size:24 final size:24
Alignment explanation
Indices: 51996--52077 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
51986 ATATGGTTAA
51996 TAATATAATCACCATAATTATCTC
1 TAATATAATCACCATAATTATCTC
** *
52020 TAATATATAT-ATGGATAA-TATGGT-
1 TAATATA-ATCA-CCATAATTAT-CTC
52044 TAATAATTTAATCACCATAATTATCTC
1 TAAT-A--TAATCACCATAATTATCTC
52071 TAATATA
1 TAATATA
52078 TTTATGGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
24 17 0.40
25 8 0.19
26 8 0.19
27 10 0.23
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (24 bp):
TAATATAATCACCATAATTATCTC
Found at i:52050 original size:51 final size:51
Alignment explanation
Indices: 51898--52090 Score: 300
Period size: 51 Copynumber: 3.8 Consensus size: 51
51888 AGTAGTCTCG
**
51898 ATAATCACCATAATTATCTCTAATAATATATAAAGATAATATGGTTAATAAAT
1 ATAATCACCATAATTATCTCTAAT-ATATATATGGATAATATGGTTAAT-AAT
*
51951 ATAATCACCATAATTATCTCT-A-GTATATATGGATAATATGGTTAATAAT
1 ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
52000 ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
1 ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
* * *
52051 TTAATCACCATAATTATCTCTAATATATTTATGGTTAATA
1 ATAATCACCATAATTATCTCTAATATATATATGGATAATA
52091 AAGGTAATGG
Statistics
Matches: 131, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
49 24 0.18
50 22 0.17
51 63 0.48
52 1 0.01
53 21 0.16
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (51 bp):
ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
Found at i:54077 original size:3 final size:3
Alignment explanation
Indices: 54065--54108 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
54055 TAAATACAAG
* *
54065 GAA G-A GAA GAA GAA GAA GAG GAA GATG GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GA
54109 GCAATGAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:54098 original size:22 final size:20
Alignment explanation
Indices: 54063--54105 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
54053 TATAAATACA
54063 AGGAAGAGAAGAAGAAGAAG
1 AGGAAGAGAAGAAGAAGAAG
54083 AGGAAGATGGAAGAAGAAGAAG
1 AGGAAGA--GAAGAAGAAGAAG
54105 A
1 A
54106 AGAGCAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (20 bp):
AGGAAGAGAAGAAGAAGAAG
Found at i:66853 original size:28 final size:28
Alignment explanation
Indices: 66821--66877 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
66811 TCCGACATTT
66821 TGGTTTAATGTGACATTGTCACATGGCA
1 TGGTTTAATGTGACATTGTCACATGGCA
* *
66849 TGGTTTGATGTGGCATTGTCACATGGCA
1 TGGTTTAATGTGACATTGTCACATGGCA
66877 T
1 T
66878 TTTTGGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (28 bp):
TGGTTTAATGTGACATTGTCACATGGCA
Found at i:74306 original size:25 final size:24
Alignment explanation
Indices: 74255--74311 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
74245 GTCAGTCTTG
*
74255 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
74278 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
74303 AATTTATTT
1 AATTTATTT
74312 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:75452 original size:21 final size:21
Alignment explanation
Indices: 75428--75467 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
75418 GTGTTTCATG
*
75428 ACACAAATAACACGTTTAAAA
1 ACACAAATAACACGCTTAAAA
* *
75449 ACACGATTAACACGCTTAA
1 ACACAAATAACACGCTTAA
75468 GTAACTAGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (21 bp):
ACACAAATAACACGCTTAAAA
Found at i:76904 original size:124 final size:127
Alignment explanation
Indices: 76703--76958 Score: 378
Period size: 124 Copynumber: 2.0 Consensus size: 127
76693 CATTGTTTAA
*
76703 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
*
76768 TTTTACCATTTTACTATTTTA-A-TT-A-AAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TTTTA-CATTTTACCATTTTACATTTAATAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
76827 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATA-A
*
76892 TATTTTA-TTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 T-TTTTACATTTTACCATTTTAC-A-TTTAA-TAAAAAACTTATATATATTAGAATTTTTTAAAT
76956 AT
126 AT
76958 A
1 A
76959 TTTCTTAAAT
Statistics
Matches: 118, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
124 73 0.62
125 1 0.01
126 6 0.05
128 2 0.02
129 1 0.01
131 35 0.30
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
TTTTACATTTTACCATTTTACATTTAATAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:78483 original size:21 final size:19
Alignment explanation
Indices: 78459--78516 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
78449 GCTGTTCTAA
*
78459 TAATCTCATCTGTACAGTACT
1 TAATCTCATCTGTACAGT--G
* *
78480 TAATCTAATTTGTACAGTG
1 TAATCTCATCTGTACAGTG
78499 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
78517 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTG
Done.