Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001746.1 Hibiscus syriacus cultivar Beakdansim tig00003535_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: 81191
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1926 original size:59 final size:58
Alignment explanation
Indices: 1789--1954 Score: 169
Period size: 61 Copynumber: 2.8 Consensus size: 58
1779 TGGACAGTTC
** * *
1789 ATACCCAAAATCATCCATATCCATGTAGTAAATA-TCATATAAAATATATGGGTAATTA
1 ATACCCAAAATCATATAAATCCATTTAGTAAATACT-ATATAAAATATATGGGTAATTA
* * *
1847 AAACCCAAAATCATTGATAAAT-CATTTAGTAAATACTATATAAAACTATATTGGGTACTTC
1 ATACCCAAAATCA-T-ATAAATCCATTTAGTAAATACTATATAAAA-TATA-TGGGTAATTA
*
1908 TTACCCAAAATCATATAAATACCATTTTAG-AAATACTATA-AAAATAT
1 ATACCCAAAATCATATAAAT-CCA-TTTAGTAAATACTATATAAAATAT
1955 TTCATAATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
58 12 0.13
59 30 0.33
60 13 0.14
61 31 0.34
62 5 0.05
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (58 bp):
ATACCCAAAATCATATAAATCCATTTAGTAAATACTATATAAAATATATGGGTAATTA
Found at i:5291 original size:21 final size:21
Alignment explanation
Indices: 5267--5309 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5257 TCTATATAAT
5267 AATTCATTTATAACACCGTTA
1 AATTCATTTATAACACCGTTA
* *
5288 AATTTATTTATAACATCGTTA
1 AATTCATTTATAACACCGTTA
5309 A
1 A
5310 GTGAAAAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (21 bp):
AATTCATTTATAACACCGTTA
Found at i:9729 original size:3 final size:3
Alignment explanation
Indices: 9721--9760 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9711 CTTTTAGAAT
9721 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9761 ACAATTGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11934 original size:54 final size:54
Alignment explanation
Indices: 11654--11926 Score: 395
Period size: 54 Copynumber: 5.1 Consensus size: 54
11644 CTATGTGTAC
* * * *
11654 TATAGGCACTAAATGTGCAACCCACGGAACTCATCATATGTTTATGAACGGCCA
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTTATGAACGACCG
* * * *
11708 TATAGGCACTAAGTGTACAACCCACGGAACTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTTATGAACGACCG
* * * *
11762 TATAGGCACTAAGTGTGTAACCCACGGAATTCATAATGTGTTTATGAACGACTG
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTTATGAACGACCG
* *
11816 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGACCGACCG
1 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTTATGAACGACCG
*
11870 TATCA-GCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
1 TAT-AGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTTATGAACGACCG
11924 TAT
1 TAT
11927 CGACACTACG
Statistics
Matches: 197, Mismatches: 21, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
54 196 0.99
55 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTTATGAACGACCG
Found at i:12898 original size:11 final size:11
Alignment explanation
Indices: 12882--12906 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12872 TGAAATACTT
12882 AAAAAAAAATA
1 AAAAAAAAATA
12893 AAAAAAAAATA
1 AAAAAAAAATA
12904 AAA
1 AAA
12907 GACCAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATA
Found at i:17421 original size:18 final size:17
Alignment explanation
Indices: 17398--17431 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17388 TGTCAAAAGC
*
17398 ACAAAACCCAAACCAAAA
1 ACAAAAACC-AACCAAAA
17416 ACAAAAACCAACCAAA
1 ACAAAAACCAACCAAA
17432 CAGACGGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (17 bp):
ACAAAAACCAACCAAAA
Found at i:21107 original size:13 final size:14
Alignment explanation
Indices: 21063--21110 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
21053 ATTAATAGTA
*
21063 ATAATAATTAAATAT
1 ATAA-AATTAAACAT
*
21078 ATTAAAAATAAACAT
1 A-TAAAATTAAACAT
21093 ATAAAATTAAA-AT
1 ATAAAATTAAACAT
21106 ATAAA
1 ATAAA
21111 TAAACAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 7 0.24
14 9 0.31
15 10 0.34
16 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAATTAAACAT
Found at i:22519 original size:3 final size:3
Alignment explanation
Indices: 22513--22592 Score: 76
Period size: 3 Copynumber: 27.3 Consensus size: 3
22503 AATAATTATT
* *
22513 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
** **
22556 TAA TAA TAA TAA TTT TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
22593 TTAGTAAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 6 0.10
3 52 0.85
4 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:22558 original size:18 final size:18
Alignment explanation
Indices: 22502--22580 Score: 90
Period size: 18 Copynumber: 4.2 Consensus size: 18
22492 TCTTGGCTTG
22502 TAATAATTATTTAATAATAA
1 TAATAA-TATTT-ATAATAA
*
22522 T-ATAATATATATAATATAA
1 TAATAATATTTAT-A-ATAA
22541 TAATAATATTTATAATAA
1 TAATAATATTTATAATAA
22559 TAATAATAATTT-TAATAA
1 TAATAAT-ATTTATAATAA
22577 TAAT
1 TAAT
22581 TTTAATAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.04
18 26 0.49
19 14 0.26
20 11 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATATTTATAATAA
Found at i:22593 original size:12 final size:12
Alignment explanation
Indices: 22502--22594 Score: 81
Period size: 12 Copynumber: 8.0 Consensus size: 12
22492 TCTTGGCTTG
*
22502 TAATAATTA-TT
1 TAATAATAATTT
*
22513 TAATAATAA-TA
1 TAATAATAATTT
* *
22524 TAATATATATAATA
1 TAATA-ATA-ATTT
22538 TAATAATAATATT
1 TAATAATAAT-TT
22551 T-ATAATAA---
1 TAATAATAATTT
22559 TAATAATAATTT
1 TAATAATAATTT
22571 TAATAATAATTT
1 TAATAATAATTT
22583 TAATAATAATTT
1 TAATAATAATTT
22595 AGTAAAATTA
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
8 1 0.01
9 7 0.10
11 14 0.20
12 35 0.50
13 6 0.09
14 7 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:22873 original size:76 final size:76
Alignment explanation
Indices: 22747--23156 Score: 784
Period size: 76 Copynumber: 5.4 Consensus size: 76
22737 GAGGTCTTAA
* *
22747 AAACATCATGCACTGAAGGTCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
22812 AGGCTTTTTGG
66 AGGCTTTTTGG
22823 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
22888 AGGCTTTTTGG
66 AGGCTTTTTGG
*
22899 AAACATCATGCACTGTAGGAATTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
22964 AGGCTTTTTGG
66 AGGCTTTTTGG
22975 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23040 AGGCTTTTTGG
66 AGGCTTTTTGG
*
23051 AAACATCATGCACTGTAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
23116 AGGCTTTTTGG
66 AGGCTTTTTGG
23127 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
23157 TGGAAAATAG
Statistics
Matches: 328, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 328 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:23856 original size:22 final size:22
Alignment explanation
Indices: 23831--23907 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
23821 AATAAAGCTT
*
23831 TCATCTTTGAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
23853 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
23875 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
23897 TCATCTTTGAA
1 TCATCTTTGAA
23908 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:26641 original size:114 final size:114
Alignment explanation
Indices: 26441--26660 Score: 370
Period size: 114 Copynumber: 1.9 Consensus size: 114
26431 GATCATGCAG
* * * * *
26441 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAAATAACTCAAAGA
26506 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
26555 TTCATCTTTCAAATCCAATGATTGGGTT-TGGGGTTCATACCAAATCAAATCAAATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATT-GGTTCTGGGGTTCATACCAAACCAAATCAAATAACTCAAAG
26619 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
65 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
26661 CGAGAACGTG
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
114 95 0.96
115 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAAATCAAATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:33267 original size:21 final size:21
Alignment explanation
Indices: 33243--33287 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33233 TTAATATCTG
33243 AAAATAAAATAAAAAAT-ATAA
1 AAAATAAAAT-AAAAATCATAA
**
33264 AAAATATTATAAAAATCATAA
1 AAAATAAAATAAAAATCATAA
33285 AAA
1 AAA
33288 TTTGAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAATAAAATAAAAATCATAA
Found at i:34045 original size:13 final size:14
Alignment explanation
Indices: 34001--34048 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
33991 ATTAATAGTA
*
34001 ATAATAATTAAATAT
1 ATAA-AATTAAACAT
*
34016 ATTAAAAATAAACAT
1 A-TAAAATTAAACAT
34031 ATAAAATTAAA-AT
1 ATAAAATTAAACAT
34044 ATAAA
1 ATAAA
34049 TAAACAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 7 0.24
14 9 0.31
15 10 0.34
16 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAATTAAACAT
Found at i:35354 original size:15 final size:14
Alignment explanation
Indices: 35330--35359 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
35320 GCCAGATCCA
35330 ACGGTGGAGCTGAG
1 ACGGTGGAGCTGAG
35344 ACGGCTGGAGCTGAG
1 ACGG-TGGAGCTGAG
35359 A
1 A
35360 AGTGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.23, C:0.17, G:0.47, T:0.13
Consensus pattern (14 bp):
ACGGTGGAGCTGAG
Found at i:35460 original size:3 final size:3
Alignment explanation
Indices: 35454--35523 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
35444 AATAATTATT
* *
35454 TAA TAA TAA T-A TAA TATA TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
35499 TAA TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
35524 TAAGTAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 4 0.07
3 45 0.80
4 7 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:35488 original size:24 final size:26
Alignment explanation
Indices: 35454--35511 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 26
35444 AATAATTATT
35454 TAATAATAATATAATATATAT-ATAA
1 TAATAATAATATAATATATATAATAA
*
35479 T-ATAAT-A-ATAATATTTATAATAA
1 TAATAATAATATAATATATATAATAA
35502 TAATAATAAT
1 TAATAATAAT
35512 TTTAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 10 0.36
23 6 0.21
24 10 0.36
25 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAATAATAATATAATATATATAATAA
Found at i:35501 original size:18 final size:18
Alignment explanation
Indices: 35443--35523 Score: 85
Period size: 18 Copynumber: 4.2 Consensus size: 18
35433 TCTTGGCTTG
35443 TAATAATTATTTAATAATAA
1 TAATAA-TATTT-ATAATAA
35463 T-ATAATATATATATAATATAA
1 TAATAATAT-T-TAT-A-ATAA
35484 TAATAATATTTATAATAA
1 TAATAATATTTATAATAA
35502 TAATAATAATTT-TAATAA
1 TAATAAT-ATTTATAATAA
35520 TAAT
1 TAAT
35524 TAAGTAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
18 24 0.44
19 12 0.22
20 6 0.11
21 6 0.11
22 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATATTTATAATAA
Found at i:37018 original size:15 final size:15
Alignment explanation
Indices: 36998--37026 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36988 AAAAACTCCA
36998 TGGTTATGACATGGC
1 TGGTTATGACATGGC
37013 TGGTTATGACATGG
1 TGGTTATGACATGG
37027 AGGAGGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.34
Consensus pattern (15 bp):
TGGTTATGACATGGC
Found at i:43135 original size:2 final size:2
Alignment explanation
Indices: 43128--43159 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43118 AAATTAAATA
43128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43160 TATTTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44422 original size:6 final size:7
Alignment explanation
Indices: 44400--44424 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44390 ATTATTTGAT
44400 AAATTAA
1 AAATTAA
44407 AAATTAA
1 AAATTAA
44414 AAATTAA
1 AAATTAA
44421 AAAT
1 AAAT
44425 ATTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAA
Found at i:44909 original size:12 final size:12
Alignment explanation
Indices: 44892--44952 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
44882 TTCAAAGAGG
44892 TTTTATATTTAA
1 TTTTATATTTAA
44904 TTTTATA-TT-A
1 TTTTATATTTAA
*
44914 TATTATA-TTATA
1 TTTTATATTTA-A
*
44926 TTTGAT-TTTAA
1 TTTTATATTTAA
44937 TTTTA-ATATTAA
1 TTTTATAT-TTAA
44949 TTTT
1 TTTT
44953 TTAAATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 9 0.22
11 8 0.20
12 23 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:44974 original size:36 final size:36
Alignment explanation
Indices: 44933--45050 Score: 124
Period size: 36 Copynumber: 3.4 Consensus size: 36
44923 ATATTTGATT
44933 TTAATTTTAATATTAATTTTTTAAATAAATTAAATA
1 TTAATTTTAATATTAATTTTTTAAATAAATTAAATA
* * * *
44969 TTAATTTT--T-TTAA--TATTATAT-TA-TAGATA
1 TTAATTTTAATATTAATTTTTTAAATAAATTAAATA
*
44998 TTAATTTTCATATTAATTTTTTAAATAAATTAAATA
1 TTAATTTTAATATTAATTTTTTAAATAAATTAAATA
45034 TTAATTTTTTAATATTA
1 TTAA--TTTTAATATTA
45051 TATTATAGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
29 13 0.20
30 1 0.02
31 7 0.11
32 4 0.06
33 4 0.06
34 7 0.11
35 1 0.02
36 17 0.27
38 10 0.16
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (36 bp):
TTAATTTTAATATTAATTTTTTAAATAAATTAAATA
Found at i:45053 original size:64 final size:64
Alignment explanation
Indices: 44918--45074 Score: 257
Period size: 65 Copynumber: 2.5 Consensus size: 64
44908 ATATTATATT
*
44918 ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTTA
1 ATATTATATTATAGATATTAATTTT-ATATTAATTTTTTAAATAAATTAAATATTAATTTTTTTA
44981 ATATTATATTATAGATATTAATTTTCATATTAATTTTTTAAATAAATTAAATATTAA-TTTTTTA
1 ATATTATATTATAGATATTAATTTT-ATATTAATTTTTTAAATAAATTAAATATTAATTTTTTTA
45045 ATATTATATTATAGATATTTAATTTTATAT
1 ATATTATATTATAGATA-TTAATTTTATAT
45075 CATATAAATT
Statistics
Matches: 89, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
63 10 0.11
64 29 0.33
65 50 0.56
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.57
Consensus pattern (64 bp):
ATATTATATTATAGATATTAATTTTATATTAATTTTTTAAATAAATTAAATATTAATTTTTTTA
Found at i:45609 original size:31 final size:31
Alignment explanation
Indices: 45574--45633 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
45564 CAGTTGTATG
* * *
45574 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCACTATTGCAAAACTAA
45605 AATTATTTAAATCTCACTATTGCAAAACT
1 AATTATTTAAATCTCACTATTGCAAAACT
45634 TTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCACTATTGCAAAACTAA
Found at i:52751 original size:36 final size:36
Alignment explanation
Indices: 52704--52811 Score: 180
Period size: 36 Copynumber: 3.0 Consensus size: 36
52694 AGGAGCAACC
*
52704 CAATCAAGAAAGAGGCAAACGTGATCAGCATTTGCA
1 CAATCAAGAAAGAGGCAGACGTGATCAGCATTTGCA
*
52740 CAATCAAGAAAGAGGCAGACGTGACCAGCATTTGCA
1 CAATCAAGAAAGAGGCAGACGTGATCAGCATTTGCA
* *
52776 CAGTCAAGAAAGACGCAGACGTGATCAGCATTTGCA
1 CAATCAAGAAAGAGGCAGACGTGATCAGCATTTGCA
52812 GTCTCAATCA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (36 bp):
CAATCAAGAAAGAGGCAGACGTGATCAGCATTTGCA
Found at i:55859 original size:2 final size:2
Alignment explanation
Indices: 55852--55885 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
55842 ACCATGTGTA
55852 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CAT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT C
55886 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:66438 original size:13 final size:12
Alignment explanation
Indices: 66422--66462 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
66412 TGAATAAGTA
66422 AAATAGAAAAAAT
1 AAATA-AAAAAAT
66435 AAATAAAAAAAT
1 AAATAAAAAAAT
*
66447 -AA-AAAAATAT
1 AAATAAAAAAAT
66457 AAATAA
1 AAATAA
66463 CTAACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.28
11 4 0.16
12 9 0.36
13 5 0.20
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (12 bp):
AAATAAAAAAAT
Found at i:66439 original size:22 final size:21
Alignment explanation
Indices: 66397--66475 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 21
66387 AGCTAAAACC
*
66397 TAAAATAAAATAAAATGAATAA
1 TAAAATAAAA-AAAATAAATAA
*
66419 GTAAAATAGAAAAAATAAATAA
1 -TAAAATAAAAAAAATAAATAA
*
66441 AAAAATAAAAAAATATAAATAA
1 TAAAATAAAAAAA-ATAAATAA
*
66463 CT-AACTAAAAAAA
1 -TAAAATAAAAAAA
66476 CTATTATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
21 11 0.23
22 28 0.58
23 9 0.19
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.19
Consensus pattern (21 bp):
TAAAATAAAAAAAATAAATAA
Found at i:66442 original size:9 final size:9
Alignment explanation
Indices: 66399--66462 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
66389 CTAAAACCTA
66399 AAATAAAAT
1 AAATAAAAT
*
66408 AAA-ATGAAT
1 AAATA-AAAT
*
66417 AAGTAAAAT
1 AAATAAAAT
66426 AGAA-AAAAT
1 A-AATAAAAT
66435 AAATAAAA-
1 AAATAAAAT
66443 AAATAAAA-
1 AAATAAAAT
66451 AAATATAAAT
1 AAATA-AAAT
66461 AA
1 AA
66463 CTAACTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
8 16 0.36
9 25 0.56
10 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:66614 original size:38 final size:38
Alignment explanation
Indices: 66507--66906 Score: 321
Period size: 38 Copynumber: 10.3 Consensus size: 38
66497 TTTTCAAAGC
* *
66507 TATATAATATATATTTTTAAAAATTGTTTTC-AAAA-TAA
1 TATATTATATATATTTTCAAAAA-TGTTTTCAAAAACT-A
* *
66545 TATAATATATTTATTTTC-AAAATGTTTTCAAAAACTA
1 TATATTATATATATTTTCAAAAATGTTTTCAAAAACTA
66582 TATATTATATATATTTTCAAAAATGTTTTCAAAAACTA
1 TATATTATATATATTTTCAAAAATGTTTTCAAAAACTA
66620 TATATTATATATATTTTTTTC-AAAATGTTTTC-AAAACTATAA
1 TATATTATATATA---TTTTCAAAAATGTTTTCAAAAAC--T-A
*
66662 TATATATATATATATTTTCAAAAATGTTTTCAAAAATTA
1 TATAT-TATATATATTTTCAAAAATGTTTTCAAAAACTA
66701 TATATTATATATATGTTTTC--AAA--TTTTC-AAAACTA
1 TATATTATATATA--TTTTCAAAAATGTTTTCAAAAACTA
* * * * *
66736 TATAATATATATATTTTCGAAAATCATTTT-GAAAGCTA
1 TATATTATATATATTTTCAAAAAT-GTTTTCAAAAACTA
* *
66774 TATAATATATATATATATATTCAAAAATCG-ATT-AAAAAGTA
1 TAT-AT-TATATATAT-T-TTCAAAAAT-GTTTTCAAAAACTA
** *
66815 TATA-T-TATATGCTTTCAAAAACCGTTTTCTAAAAAACTA
1 TATATTATATATATTTTCAAAAA-TGTTTTC--AAAAACTA
*
66854 TATATTATAT-T-TTTTCAAAAATATTTTCAAAAACTCTA
1 TATATTATATATATTTTCAAAAATGTTTTCAAAAA--CTA
66892 CTATATTAATATATA
1 -TATATT-ATATATA
66907 CTAAATAAGC
Statistics
Matches: 300, Mismatches: 25, Indels: 70
0.76 0.06 0.18
Matches are distributed among these distances:
33 5 0.02
35 30 0.10
36 20 0.07
37 30 0.10
38 80 0.27
39 38 0.13
40 38 0.13
41 32 0.11
42 19 0.06
43 8 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATTATATATATTTTCAAAAATGTTTTCAAAAACTA
Found at i:66669 original size:77 final size:76
Alignment explanation
Indices: 66497--66863 Score: 337
Period size: 73 Copynumber: 4.8 Consensus size: 76
66487 TGTTTAATTT
* *
66497 TTTTCAAAGCTATATA-ATATATATTTTTAAAAATTGTTTTC-AAAA-TA-ATA-TA-ATATATT
1 TTTTCAAAACTATATATATATATATTTTCAAAAA-TGTTTTCAAAAACTATATATTATATATATT
66556 TATTTTCAAAATG
65 T-TTTTCAAAATG
66569 TTTTCAAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATAT
1 TTTTC-AAAACTATATA-TATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATAT
66634 TTTTTTCAAAATG
64 TTTTTTCAAAATG
*
66647 TTTTCAAAACTATAATATATATATATATATTTTCAAAAATGTTTTCAAAAATTATATATTATATA
1 TTTTCAAAAC-----TATATATATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATA
*
66712 TA-TGTTTTC-AAA--
61 TATTTTTTTCAAAATG
* * * * *
66724 TTTTCAAAACTATATAATATATATATTTTCGAAAATCATTTT-GAAAGCTATATAATATATATAT
1 TTTTCAAAACTATAT-ATATATATATTTTCAAAAAT-GTTTTCAAAAACTATATATTATATATAT
* *
66788 ATATATTCAAAAATCG
64 -TTTTTTC-AAAAT-G
* * * ** *
66804 -ATTAAAAAGTATATAT-TATATGCTTTCAAAAACCGTTTTCTAAAAAACTATATATTATAT
1 TTTTCAAAACTATATATATATATATTTTCAAAAA-TGTTTTC--AAAAACTATATATTATAT
66864 TTTTTCAAAA
Statistics
Matches: 246, Mismatches: 23, Indels: 44
0.79 0.07 0.14
Matches are distributed among these distances:
72 10 0.04
73 46 0.19
74 11 0.04
75 25 0.10
76 2 0.01
77 38 0.15
78 20 0.08
79 22 0.09
80 21 0.09
81 45 0.18
82 6 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (76 bp):
TTTTCAAAACTATATATATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATTT
TTTTCAAAATG
Found at i:66784 original size:40 final size:39
Alignment explanation
Indices: 66497--66799 Score: 291
Period size: 40 Copynumber: 7.9 Consensus size: 39
66487 TGTTTAATTT
* *
66497 TTTTC-AAAGCTATAT-A-ATATATAT-TTTTAAAAATTG
1 TTTTCAAAAACTATATAATATATATATATTTTCAAAA-TG
66533 TTTTC-AAAA-TAATATAATATAT-T-TATTTTCAAAATG
1 TTTTCAAAAACT-ATATAATATATATATATTTTCAAAATG
66569 TTTTCAAAAACTATAT-AT-TATATATATTTTCAAAAATG
1 TTTTCAAAAACTATATAATATATATATATTTTC-AAAATG
* *
66607 TTTTCAAAAACTATATATTATATATATTTTTTTCAAAATG
1 TTTTCAAAAACTATATAATATATATA-TATTTTCAAAATG
66647 TTTTC-AAAACTATAATATATATATATATATTTTCAAAAATG
1 TTTTCAAAAACTAT-ATA-ATATATATATATTTTC-AAAATG
* * *
66688 TTTTCAAAAATTATATATTATATATATGTTTTC-AAA--
1 TTTTCAAAAACTATATAATATATATATATTTTCAAAATG
*
66724 TTTTC-AAAACTATAT-A-ATATATATATTTTCGAAAATCA
1 TTTTCAAAAACTATATAATATATATATATTTTC-AAAAT-G
* *
66762 TTTT-GAAAGCTATATAATATATATATATATATTCAAAA
1 TTTTCAAAAACTATATAATATATATATAT-T-TTCAAAA
66800 ATCGATTAAA
Statistics
Matches: 228, Mismatches: 13, Indels: 47
0.79 0.05 0.16
Matches are distributed among these distances:
33 13 0.06
35 16 0.07
36 28 0.12
37 25 0.11
38 43 0.19
39 10 0.04
40 50 0.22
41 33 0.14
42 10 0.04
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (39 bp):
TTTTCAAAAACTATATAATATATATATATTTTCAAAATG
Found at i:67522 original size:85 final size:85
Alignment explanation
Indices: 67392--67563 Score: 236
Period size: 85 Copynumber: 2.0 Consensus size: 85
67382 ATATACCATC
* * *
67392 GAGCAGAATGGAATCGAACTCGAAAGTCTTTATTGACAGATAGCCCTTCTTACCTTGAGCTATGC
1 GAGCAGAATGGAATCAAACTCGAAAGTCTTTATTGACAGATAGCCCTTCTCACCTTGACCTATGC
*
67457 TATAAACTTGATATGCCCTT
66 TATAAACTTGATATGCACTT
* * * * * *
67477 GAGCTGAATGGAATCAAACTCGAAGGTTTTTGTTGACATATAGCCCTTCTCGCCTTGACCTATGC
1 GAGCAGAATGGAATCAAACTCGAAAGTCTTTATTGACAGATAGCCCTTCTCACCTTGACCTATGC
* *
67542 TGTAAATTTGATATGCACTT
66 TATAAACTTGATATGCACTT
67562 GA
1 GA
67564 AGGTTTTTGT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (85 bp):
GAGCAGAATGGAATCAAACTCGAAAGTCTTTATTGACAGATAGCCCTTCTCACCTTGACCTATGC
TATAAACTTGATATGCACTT
Found at i:67572 original size:64 final size:64
Alignment explanation
Indices: 67498--67627 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
67488 AATCAAACTC
* *
67498 GAAGGTTTTTGTTGACATATAGCCCTTCTCGCCTTGACCTATGCTGTAAATTTGATATGCACTT
1 GAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGACCTATGCTGTAAATTTGATATGCACTT
* * * *
67562 GAAGGTTTTTGTTGACAGATAGCTATTCTCTCCTTGAGCTATGCTGTAAATTTGATATGCCCTT
1 GAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGACCTATGCTGTAAATTTGATATGCACTT
67626 GA
1 GA
67628 GCTGAATGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (64 bp):
GAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGACCTATGCTGTAAATTTGATATGCACTT
Found at i:67801 original size:85 final size:85
Alignment explanation
Indices: 67562--67868 Score: 434
Period size: 85 Copynumber: 3.6 Consensus size: 85
67552 ATATGCACTT
* *
67562 GAAGGTTTTTGTTGACAGATAGCTATTCTCTCCTTGAGCTATGCTGTAAATTTGATATGCCCTTG
1 GAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTG
67627 AGCTGAATGTAATCGAACTC
66 AGCTGAATGTAATCGAACTC
* * *
67647 GAAGGTTTTTTTTGTTGACAGATAGCCCTTCTCGCGTTGAGTTATGCTGTAAATTTGATATGCCC
1 GAAGG---TTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCC
*
67712 TTGAGTTGAATGTAATCGAACTC
63 TTGAGCTGAATGTAATCGAACTC
* * * * * *
67735 GAAGGTTTTTGTTGATATATAGCCATTTTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTTG
1 GAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTG
*
67800 AGCTAAATGTAATCGAACTC
66 AGCTGAATGTAATCGAACTC
* * * *
67820 GAAGGTTTTTGTTGACATATAGCCCTTTTCGCCTTGAGCTATGTTGTAA
1 GAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGCTGTAA
67869 TTTTCCTCTA
Statistics
Matches: 199, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
85 120 0.60
88 79 0.40
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (85 bp):
GAAGGTTTTTGTTGACAGATAGCCATTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTG
AGCTGAATGTAATCGAACTC
Found at i:69279 original size:83 final size:84
Alignment explanation
Indices: 69140--69294 Score: 240
Period size: 83 Copynumber: 1.9 Consensus size: 84
69130 GTAATTTTGT
* * * *
69140 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGTGATTAACTAATTGCTCTAGAGGG-C
1 CTTTATCAAGCTAGCTGAATCTTATCCATAAAGCCAGGGCGATTAACCAATTGCTCTAGAGGGAC
*
69204 AGCTCAATATTATAATCAC
66 AACTCAATATTATAATCAC
* *
69223 CTTTATCAAGCTAGCTGAATCTTATCCATAAATCCAGGGCGTTTAACCAATTGCTCTAGAGGGAC
1 CTTTATCAAGCTAGCTGAATCTTATCCATAAAGCCAGGGCGATTAACCAATTGCTCTAGAGGGAC
69288 AACTCAA
66 AACTCAA
69295 GCTTTATTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 57 0.89
84 7 0.11
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (84 bp):
CTTTATCAAGCTAGCTGAATCTTATCCATAAAGCCAGGGCGATTAACCAATTGCTCTAGAGGGAC
AACTCAATATTATAATCAC
Found at i:74399 original size:40 final size:40
Alignment explanation
Indices: 74343--74463 Score: 172
Period size: 40 Copynumber: 3.0 Consensus size: 40
74333 ACAGGTTTAA
74343 AATACAATTCGGTGTATATGGTGGGCACGACCTTATGTGT
1 AATACAATTCGGTGTATATGGTGGGCACGACCTTATGTGT
* * * *
74383 AATACACTTCGATGTATATGGTGGGC-CAACCTCATGTGT
1 AATACAATTCGGTGTATATGGTGGGCACGACCTTATGTGT
* * *
74422 AATGCATTTCGGTGTATATGGTGGGCATGACCTTATGTGT
1 AATACAATTCGGTGTATATGGTGGGCACGACCTTATGTGT
74462 AA
1 AA
74464 CACTATGGTG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
39 34 0.49
40 36 0.51
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
AATACAATTCGGTGTATATGGTGGGCACGACCTTATGTGT
Done.