Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000380.1 Hibiscus syriacus cultivar Beakdansim tig00000696_pilon, 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: 69022
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:12220 original size:20 final size:20
Alignment explanation
Indices: 12195--12237 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12185 TCTAAAAGCT
12195 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
12215 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
12235 CAT
1 CAT
12238 GTGGTGGAAT
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:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:15958 original size:54 final size:54
Alignment explanation
Indices: 15890--16049 Score: 158
Period size: 54 Copynumber: 3.0 Consensus size: 54
15880 TGCAGTTAAA
* ** * * *
15890 AATGACTGAACACCTCTGTGCTTCAGTCTAGAATCTGGCACCCCCGTGTTTTGT
1 AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTTGG
* * * * *
15944 AATGATTGAGCACCTCTGTGCTTCAAACTAGGATTTGGCACCTATGTGCTTTGG
1 AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTTGG
* * * * * * *
15998 AATGATTGAACACCTCTGTGGTTTAATCTAAAATATGGCACCTATGTGCTTT
1 AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTT
16050 AAAATTGATA
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (54 bp):
AATGATTGAACACCTCTGTGCTTCAAACTAGAATCTGGCACCCACGTGCTTTGG
Found at i:17323 original size:29 final size:30
Alignment explanation
Indices: 17259--17315 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
17249 ATGCTTTCGC
*
17259 CCCTAGAATTTTGATAAGTTCAAATTCAGA
1 CCCTAAAATTTTGATAAGTTCAAATTCAGA
17289 CCCTAAAATTTT-ATAAGTTCAAATTCA
1 CCCTAAAATTTTGATAAGTTCAAATTCA
17316 CCTCCTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (30 bp):
CCCTAAAATTTTGATAAGTTCAAATTCAGA
Found at i:23132 original size:20 final size:20
Alignment explanation
Indices: 23096--23133 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23086 TGTTAATTTA
*
23096 TGTATAATTTTAGAGATTGT
1 TGTATAATCTTAGAGATTGT
23116 TGTATAAATCTTA-AGATT
1 TGTAT-AATCTTAGAGATT
23134 TTATAAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (20 bp):
TGTATAATCTTAGAGATTGT
Found at i:33631 original size:15 final size:14
Alignment explanation
Indices: 33599--33656 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 14
33589 ATGCTTAAAG
33599 AAAAAAAAA--AG-
1 AAAAAAAAAGGAGA
33610 AAAAAAAAAGGAGA
1 AAAAAAAAAGGAGA
**
33624 AAAGAAAAAAAAAG-
1 AAA-AAAAAAGGAGA
33638 AAAAAAAAAGGAAGA
1 AAAAAAAAAGG-AGA
33653 AAAA
1 AAAA
33657 GGAGGAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 9 0.24
13 8 0.22
14 8 0.22
15 12 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGGAGA
Found at i:33631 original size:28 final size:30
Alignment explanation
Indices: 33595--33655 Score: 108
Period size: 28 Copynumber: 2.1 Consensus size: 30
33585 TATTATGCTT
33595 AAAGAAAAAAAAAAGAAAAAAAAAGG-AGA
1 AAAGAAAAAAAAAAGAAAAAAAAAGGAAGA
33624 AAAG-AAAAAAAAAGAAAAAAAAAGGAAGA
1 AAAGAAAAAAAAAAGAAAAAAAAAGGAAGA
33653 AAA
1 AAA
33656 AGGAGGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 21 0.68
29 10 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (30 bp):
AAAGAAAAAAAAAAGAAAAAAAAAGGAAGA
Found at i:33659 original size:10 final size:10
Alignment explanation
Indices: 33595--33657 Score: 67
Period size: 10 Copynumber: 6.4 Consensus size: 10
33585 TATTATGCTT
33595 AAAGAAAAAAA
1 AAAG-AAAAAA
33606 AAAGAAAAAA
1 AAAGAAAAAA
* *
33616 AAAG--GAGA
1 AAAGAAAAAA
33624 AAAGAAAAAA
1 AAAGAAAAAA
33634 AAAGAAAAAA
1 AAAGAAAAAA
* *
33644 AAAGGAAGAA
1 AAAGAAAAAA
33654 AAAG
1 AAAG
33658 GAGGAAGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
8 6 0.14
10 34 0.77
11 4 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:34630 original size:20 final size:21
Alignment explanation
Indices: 34593--34633 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
34583 GATATTTTTA
**
34593 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
34614 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
34634 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:35653 original size:20 final size:21
Alignment explanation
Indices: 35630--35670 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
35620 TATTATATGT
**
35630 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
35650 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
35671 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:36576 original size:18 final size:19
Alignment explanation
Indices: 36538--36577 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
36528 GTTGTTGTTG
**
36538 TTTTTTTTTCTTTCTTTGT
1 TTTTTTTTTCTTTCTCCGT
36557 TTTTTTTTTC-TTCTCCGT
1 TTTTTTTTTCTTTCTCCGT
36575 TTT
1 TTT
36578 CTGTTTCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTCTTTCTCCGT
Found at i:37046 original size:2 final size:2
Alignment explanation
Indices: 37041--37096 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
37031 TTTTATTATT
* *
37041 TA TA TA TA TA TA TA TA TA TA TA TA TT TA -A TA -A TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
37081 TA TG TA TT TA -A TA TA T
1 TA TA TA TA TA TA TA TA T
37097 TTAATAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:37080 original size:22 final size:22
Alignment explanation
Indices: 37050--37114 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
37040 TTATATATAT
*
37050 ATATATATATATATATTTAATA
1 ATATTTATATATATATTTAATA
*
37072 ATATTTATATATGTATTTAAT-
1 ATATTTATATATATATTTAATA
*
37093 ATATTTA-ATA-ATA-ATAATA
1 ATATTTATATATATATTTAATA
37112 ATA
1 ATA
37115 ATGATAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 5 0.13
20 3 0.08
21 7 0.18
22 19 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTTATATATATATTTAATA
Found at i:37106 original size:3 final size:3
Alignment explanation
Indices: 37098--37203 Score: 176
Period size: 3 Copynumber: 35.3 Consensus size: 3
37088 TTAATATATT
* *
37098 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
37146 TAA TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37194 TAA TAA TAA T
1 TAA TAA TAA T
37204 GATGATATGG
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:37121 original size:18 final size:18
Alignment explanation
Indices: 37100--37210 Score: 204
Period size: 18 Copynumber: 6.2 Consensus size: 18
37090 AATATATTTA
37100 ATAATAATAATAATAATG
1 ATAATAATAATAATAATG
37118 ATAATAATAATAATAATG
1 ATAATAATAATAATAATG
37136 ATAATAATAATAATAATG
1 ATAATAATAATAATAATG
37154 ATAATAATAATAATAATG
1 ATAATAATAATAATAATG
*
37172 ATAATAATAATAATAATA
1 ATAATAATAATAATAATG
*
37190 ATAATAATAATAATGATG
1 ATAATAATAATAATAATG
37208 ATA
1 ATA
37211 TGGGTAAAAA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 90 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
ATAATAATAATAATAATG
Found at i:37775 original size:113 final size:113
Alignment explanation
Indices: 37530--38088 Score: 877
Period size: 113 Copynumber: 5.0 Consensus size: 113
37520 AGAATTATGC
* * * *
37530 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
37595 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
37642 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * **
37707 TATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
37755 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** *
37820 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
37868 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
37933 TATGAACTTTCTCTGGAAAAGATGATCCATCAATTGACGAATTCATGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
* *
37981 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
38046 TATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATT
38089 TGAATCTTTG
Statistics
Matches: 407, Mismatches: 39, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
112 68 0.17
113 339 0.83
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:38801 original size:84 final size:84
Alignment explanation
Indices: 38703--39052 Score: 632
Period size: 84 Copynumber: 4.2 Consensus size: 84
38693 TTCATCTTTT
* * *
38703 AATTCCAACGATTGGTTCTGTCC-AACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATT-CAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
38767 ATTGAGCAAATTCATCTTCCA
64 ATTGAGCAAATTCATCTTCCA
*
38788 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
38853 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
38872 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
38937 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
38956 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
39021 TG-GCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
39039 AATTCAATGATTGG
1 AATTCAATGATTGG
39053 ACTAAGATAT
Statistics
Matches: 259, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
83 32 0.12
84 223 0.86
85 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (84 bp):
AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGAGCAAATTCATCTTCCA
Found at i:40182 original size:1 final size:1
Alignment explanation
Indices: 40178--40237 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
40168 ACCCCCTTTC
* * * * ** *
40178 TTTTTTTTCTTCTTTTCTTTTTTTTTTTTTTTTTTTCTCCTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40238 CTTTAAGCAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:40197 original size:21 final size:20
Alignment explanation
Indices: 40173--40241 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
40163 CCTTGACCCC
40173 CTTTCTTTTTTTTCTTCTTTT
1 CTTTCTTTTTTTTCTT-TTTT
* *
40194 CTTTTTTTTTTTTTTTTTTT
1 CTTTCTTTTTTTTCTTTTTT
*
40214 C-TCCTTTTTTTTTCTTTTTT
1 CTTTC-TTTTTTTTCTTTTTT
*
40234 TTTTCTTT
1 CTTTCTTT
40242 AAGCATAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.03
20 22 0.56
21 16 0.41
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
CTTTCTTTTTTTTCTTTTTT
Found at i:40204 original size:11 final size:11
Alignment explanation
Indices: 40190--40241 Score: 79
Period size: 11 Copynumber: 4.7 Consensus size: 11
40180 TTTTTTCTTC
40190 TTTTCTTTTTT
1 TTTTCTTTTTT
40201 TTTT-TTTTTT
1 TTTTCTTTTTT
*
40211 TTTCTCCTTTTT
1 TTT-TCTTTTTT
40223 TTTTCTTTTTT
1 TTTTCTTTTTT
40234 TTTTCTTT
1 TTTTCTTT
40242 AAGCATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
10 9 0.24
11 20 0.54
12 8 0.22
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:40220 original size:28 final size:27
Alignment explanation
Indices: 40178--40237 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
40168 ACCCCCTTTC
* *
40178 TTTTTTTTCTTCTTTTCTTTTTTTTTTT
1 TTTTTTTTCTCCTTTT-TTTTTCTTTTT
40206 TTTTTTTTCTCCTTTTTTTTTCTTTTT
1 TTTTTTTTCTCCTTTTTTTTTCTTTTT
40233 TTTTT
1 TTTTT
40238 CTTTAAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (27 bp):
TTTTTTTTCTCCTTTTTTTTTCTTTTT
Found at i:50898 original size:18 final size:17
Alignment explanation
Indices: 50856--50903 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
50846 CTTGCAAAGA
50856 AAATAAAAACATATAAAT
1 AAATAAAAA-ATATAAAT
*
50874 ATTATAAAAAATAATAAAT
1 A-AATAAAAAAT-ATAAAT
50893 AAATAAAAAAT
1 AAATAAAAAAT
50904 TTGAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAAAAATATAAAT
Found at i:52567 original size:18 final size:19
Alignment explanation
Indices: 52529--52568 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
52519 GTTGTTGTTG
**
52529 TTTTTTTTTCTTTCTTTGT
1 TTTTTTTTTCTTTCTCCGT
52548 TTTTTTTTTC-TTCTCCGT
1 TTTTTTTTTCTTTCTCCGT
52566 TTT
1 TTT
52569 CTGTTTCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTCTTTCTCCGT
Found at i:53061 original size:22 final size:21
Alignment explanation
Indices: 53030--53080 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
53020 TTTTATTATT
* *
53030 TATATATATATATATTTTTAA
1 TATATTTATATATATATTTAA
*
53051 TAATATTTATATATGTATTTAA
1 T-ATATTTATATATATATTTAA
53073 TATATTTA
1 TATATTTA
53081 ATAATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATTTATATATATATTTAA
Found at i:53087 original size:3 final size:3
Alignment explanation
Indices: 53079--53179 Score: 184
Period size: 3 Copynumber: 33.7 Consensus size: 3
53069 TTAATATATT
* *
53079 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53127 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53175 TAA TA
1 TAA TA
53180 TGGGTAAAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:56587 original size:55 final size:55
Alignment explanation
Indices: 56478--56652 Score: 185
Period size: 55 Copynumber: 3.1 Consensus size: 55
56468 TCTATCAATG
* * ** *
56478 TATATAT-TATTATATAGCATATATATTAAGTTTAAAAATGTATATATAGTTTTAAAGTA
1 TATATATATATTATAT---ATATATATTATGTTTGAAAACATATATA-ATTTTTAAA-TA
56537 TATATATATATTATA-ATATATATTATGTTTGAAAACATATATAATTTTTAAA-A
1 TATATATATATTATATATATATATTATGTTTGAAAACATATATAATTTTTAAATA
* * * * *
56590 TATATGTATATTATATATAACATATTATATTTGAAAGCATATATAATTTTGAAATA
1 TATATATATATTATATAT-ATATATTATGTTTGAAAACATATATAATTTTTAAATA
56646 TATATAT
1 TATATAT
56653 TGAAACACAG
Statistics
Matches: 101, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
53 15 0.15
54 2 0.02
55 39 0.39
56 31 0.31
59 7 0.07
60 7 0.07
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (55 bp):
TATATATATATTATATATATATATTATGTTTGAAAACATATATAATTTTTAAATA
Found at i:56650 original size:19 final size:17
Alignment explanation
Indices: 56513--56652 Score: 72
Period size: 19 Copynumber: 7.7 Consensus size: 17
56503 TTAAGTTTAA
*
56513 AAATGTATATATAGTTTT
1 AAATATATATATA-TTTT
*
56531 AAAGTATATATATATATT
1 AAA-TATATATATATTTT
56549 ATAATATATAT-TATGTTT
1 A-AATATATATATAT-TTT
*
56567 GAAA-ACATATATAATTTTT
1 -AAATATATATAT-A-TTTT
*
56586 AAAATATATGTATATTATAT
1 -AAATATATATATATT-T-T
* *
56606 ATAACATAT-TATATTTG
1 A-AATATATATATATTTT
*
56623 AAAGCATATATA-ATTTT
1 AAA-TATATATATATTTT
56640 GAAATATATATAT
1 -AAATATATATAT
56653 TGAAACACAG
Statistics
Matches: 96, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
16 2 0.02
17 25 0.26
18 27 0.28
19 28 0.29
20 14 0.15
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (17 bp):
AAATATATATATATTTT
Found at i:56767 original size:2 final size:2
Alignment explanation
Indices: 56762--56796 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
56752 GGGGAAAATA
56762 AT AT AT AT AT -T AT AT AT AGT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A
56797 GTAGGTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57805 original size:41 final size:41
Alignment explanation
Indices: 57748--57828 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
57738 ATATATTTGG
57748 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGGC
1 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGGC
57789 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGG
1 CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGG
57829 ACTTTGGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (41 bp):
CTCACGAGGTCGAGAATGAACTTTTGAGTTAAGTTTTAGGC
Found at i:65545 original size:17 final size:17
Alignment explanation
Indices: 65458--65550 Score: 57
Period size: 17 Copynumber: 5.4 Consensus size: 17
65448 TAGTATGTAT
*
65458 ATATATTATGTTTAAAA
1 ATATATTATGTTTTAAA
*
65475 ATGTATATATAGTTTTAAA
1 ATATAT-TAT-GTTTTAAA
* *
65494 GTATATATTA--TATTATA
1 --ATATATTATGTTTTAAA
*
65511 TTATATTAT-TTTATAAA
1 ATATATTATGTTT-TAAA
*
65528 ATATATTATGTTTGAAA
1 ATATATTATGTTTTAAA
*
65545 ACATAT
1 ATATAT
65551 ACAATTGTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
15 7 0.12
16 2 0.03
17 29 0.50
18 6 0.10
19 7 0.12
20 2 0.03
21 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (17 bp):
ATATATTATGTTTTAAA
Found at i:65681 original size:51 final size:48
Alignment explanation
Indices: 65583--65713 Score: 124
Period size: 51 Copynumber: 2.7 Consensus size: 48
65573 TAATATTGCA
*
65583 TTTGAATATATA-TAT-ATATATATGT-TATATTTGAAAACATATAGTT
1 TTTGAAAATATATTATAATATATA-GTATATATTTGAAAACATATAGTT
* * *
65629 TTTGAAAATATATGTATAATATATAGTATATTTTTTAAAATATACATAGTT
1 TTTGAAAATATAT-TATAATATATAGTATATATTTGAAAACAT--ATAGTT
** * *
65680 TTAAAAAAATATATAATATTATATAGTATATATT
1 TT-TGAAAATATATTATAATATATAGTATATATT
65714 AGTATATATA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
46 11 0.16
48 5 0.07
49 19 0.28
51 25 0.36
52 9 0.13
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (48 bp):
TTTGAAAATATATTATAATATATAGTATATATTTGAAAACATATAGTT
Found at i:65710 original size:12 final size:11
Alignment explanation
Indices: 65688--65724 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
65678 TTTTAAAAAA
*
65688 ATATATAATAT
1 ATATATAGTAT
65699 -TATATAGTAT
1 ATATATAGTAT
65709 ATAT-TAGTAT
1 ATATATAGTAT
65719 ATATAT
1 ATATAT
65725 TTTAGGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (11 bp):
ATATATAGTAT
Found at i:65796 original size:3 final size:3
Alignment explanation
Indices: 65779--65848 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
65769 AGTAGGTATA
* * * * * *
65779 TAT T-T TAT ATAT TAT TAT TGT TAT TAT TAT TGT TGT TGT TGT TGT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
65824 TGT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
65849 TTCTTTATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (3 bp):
TAT
Done.