Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000653.1 Hibiscus syriacus cultivar Beakdansim tig00001262_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: 127697
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8735 original size:42 final size:42
Alignment explanation
Indices: 8672--8758 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
8662 AGGTGTGATG
* * *
8672 TTTAGCGGCGTTTTCCCTACAAACGCCGTAGTAGTTTTGAGA
1 TTTAGCGGCGTTTTACCTACAAACGCCGTAGAAGGTTTGAGA
* *
8714 TTTAGCGGCGTTTTACTTACAAACGCCGTAGAAGGTTTGATA
1 TTTAGCGGCGTTTTACCTACAAACGCCGTAGAAGGTTTGAGA
8756 TTT
1 TTT
8759 GTAGCATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (42 bp):
TTTAGCGGCGTTTTACCTACAAACGCCGTAGAAGGTTTGAGA
Found at i:9334 original size:21 final size:21
Alignment explanation
Indices: 9309--9419 Score: 77
Period size: 21 Copynumber: 5.3 Consensus size: 21
9299 CTGTTGATAT
9309 GCTGCTTCTCTTTGTGCTTCC
1 GCTGCTTCTCTTTGTGCTTCC
*
9330 GCTGCTTCTCTTTGAGCTAT-C
1 GCTGCTTCTCTTTGTGCT-TCC
* *
9351 GATGCTTCTCTCTGTG-TTGCC
1 GCTGCTTCTCTTTGTGCTT-CC
** *
9372 ATTGCTTCT-TTCTCTGCTTCC
1 GCTGCTTCTCTT-TGTGCTTCC
* * *
9393 GCTACTGCTC-TGGCTGCTTCC
1 GCTGCTTCTCTTTG-TGCTTCC
9414 GCTGCT
1 GCTGCT
9420 GCTGGCTGCT
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
19 1 0.01
20 2 0.03
21 62 0.91
22 3 0.04
ACGTcount: A:0.05, C:0.32, G:0.20, T:0.43
Consensus pattern (21 bp):
GCTGCTTCTCTTTGTGCTTCC
Found at i:9421 original size:21 final size:21
Alignment explanation
Indices: 9385--9453 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
9375 GCTTCTTTCT
9385 CTGCTTCCGCTACTGCTCTGG
1 CTGCTTCCGCTACTGCTCTGG
*
9406 CTGCTTCCGCTGCTG--CTGG
1 CTGCTTCCGCTACTGCTCTGG
**
9425 CTGCTTCCGCTACTGCTCTCT
1 CTGCTTCCGCTACTGCTCTGG
9446 CTGCTTCC
1 CTGCTTCC
9454 CTTGCTTCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.43
21 24 0.57
ACGTcount: A:0.03, C:0.41, G:0.22, T:0.35
Consensus pattern (21 bp):
CTGCTTCCGCTACTGCTCTGG
Found at i:9426 original size:19 final size:19
Alignment explanation
Indices: 9385--9441 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
9375 GCTTCTTTCT
9385 CTGCTTCCGCTACTGCTCTGG
1 CTGCTTCCGCTACTG--CTGG
*
9406 CTGCTTCCGCTGCTGCTGG
1 CTGCTTCCGCTACTGCTGG
9425 CTGCTTCCGCTACTGCT
1 CTGCTTCCGCTACTGCT
9442 CTCTCTGCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 20 0.59
21 14 0.41
ACGTcount: A:0.04, C:0.39, G:0.25, T:0.33
Consensus pattern (19 bp):
CTGCTTCCGCTACTGCTGG
Found at i:15241 original size:27 final size:25
Alignment explanation
Indices: 15199--15275 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 25
15189 TCATAATAAG
*
15199 TTTGTCTCT-TAAAACAATACTTCA
1 TTTGTCTCTAAAAAACAATACTTCA
* *
15223 TTTGTCTCTCAAAATAACACTTCATT-A
1 TTTGTCTCT-AAAA-AACAATAC-TTCA
* *
15250 TTTGTCTCTTAAAAACAACACTTCA
1 TTTGTCTCTAAAAAACAATACTTCA
15275 T
1 T
15276 GCATCCTAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
24 11 0.27
25 7 0.17
26 5 0.12
27 16 0.39
28 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (25 bp):
TTTGTCTCTAAAAAACAATACTTCA
Found at i:15273 original size:28 final size:26
Alignment explanation
Indices: 15199--15275 Score: 95
Period size: 24 Copynumber: 3.0 Consensus size: 26
15189 TCATAATAAG
*
15199 TTTGTCTCTTAAAACAATACTTC--A
1 TTTGTCTCTTAAAACAACACTTCATA
* *
15223 TTTGTCTCTCAAAATAACACTTCATTA
1 TTTGTCTCTTAAAACAACACTTCA-TA
15250 TTTGTCTCTTAAAAACAACACTTCAT
1 TTTGTCTCTT-AAAACAACACTTCAT
15276 GCATCCTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 20 0.45
27 11 0.25
28 13 0.30
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (26 bp):
TTTGTCTCTTAAAACAACACTTCATA
Found at i:17391 original size:12 final size:12
Alignment explanation
Indices: 17374--17415 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
17364 TAGGGCCATT
17374 AGTTTTACATCA
1 AGTTTTACATCA
17386 AGTTTTACATCA
1 AGTTTTACATCA
*
17398 AGTTTTACATTA
1 AGTTTTACATCA
17410 AGTTTT
1 AGTTTT
17416 CTTTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:21360 original size:42 final size:42
Alignment explanation
Indices: 21301--21385 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
21291 TCAACACCAC
21301 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
1 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
21343 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
1 TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
21385 T
1 T
21386 AAATATGCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.36
Consensus pattern (42 bp):
TTCTGGTTTAGGAAACAAGATTCAAAGAAATTTTTTAAAATA
Found at i:23458 original size:12 final size:12
Alignment explanation
Indices: 23441--23482 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
23431 TAGGGCCATT
23441 AGTTTTACATCA
1 AGTTTTACATCA
23453 AGTTTTACATCA
1 AGTTTTACATCA
*
23465 AGTTTTACATTA
1 AGTTTTACATCA
23477 AGTTTT
1 AGTTTT
23483 CTTTATTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:26925 original size:22 final size:22
Alignment explanation
Indices: 26898--26946 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
26888 CACGTTTTGA
26898 AAAGCTATTATTATAATATTCG
1 AAAGCTATTATTATAATATTCG
* **
26920 AAAGCTATTATTTTTGTATTCG
1 AAAGCTATTATTATAATATTCG
26942 AAAGC
1 AAAGC
26947 AGTAAACCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTATAATATTCG
Found at i:27387 original size:25 final size:25
Alignment explanation
Indices: 27356--27412 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
27346 CACCATTATA
*
27356 AACAAACATATGGTAGCGTTTGTAT
1 AACAAACATATGGCAGCGTTTGTAT
27381 AACAAACATATGGCAGCGTTTGTAT
1 AACAAACATATGGCAGCGTTTGTAT
27406 AACAAAC
1 AACAAAC
27413 GCCACTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (25 bp):
AACAAACATATGGCAGCGTTTGTAT
Found at i:31403 original size:21 final size:21
Alignment explanation
Indices: 31370--31412 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31360 GAATGTCATA
* *
31370 TCAGTACTATTGATTGACATG
1 TCAGTACCATTGACTGACATG
* *
31391 TCAGTACCGTTGACTGTCATG
1 TCAGTACCATTGACTGACATG
31412 T
1 T
31413 TAATACTGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (21 bp):
TCAGTACCATTGACTGACATG
Found at i:33074 original size:3 final size:3
Alignment explanation
Indices: 33059--33128 Score: 90
Period size: 3 Copynumber: 23.0 Consensus size: 3
33049 CTATTTTAAT
*
33059 TTA TTA CTA TTA TTA TT- TGT- TTA TTA TTA TTAA TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A TTA TTA TT-A TTA
33105 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
33129 CAAATGGACA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.03
3 53 0.87
4 6 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:33083 original size:20 final size:20
Alignment explanation
Indices: 33057--33128 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
33047 TTCTATTTTA
*
33057 ATTTATTACTATTATTATTT
1 ATTTATTATTATTATTATTT
*
33077 GTTTATTATTATTAATTA-TT
1 ATTTATTATTATT-ATTATTT
*
33097 ATTAATTATTATTATTA-TT
1 ATTTATTATTATTATTATTT
33116 A-TTATTATTATTA
1 ATTTATTATTATTA
33129 CAAATGGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 11 0.24
19 7 0.15
20 24 0.52
21 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (20 bp):
ATTTATTATTATTATTATTT
Found at i:33096 original size:10 final size:10
Alignment explanation
Indices: 33081--33128 Score: 82
Period size: 10 Copynumber: 5.0 Consensus size: 10
33071 TTATTTGTTT
33081 ATTATTATTA
1 ATTATTATTA
33091 ATTATTATTA
1 ATTATTATTA
33101 ATTATTATT-
1 ATTATTATTA
33110 ATTATTATT-
1 ATTATTATTA
33119 ATTATTATTA
1 ATTATTATTA
33129 CAAATGGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 18 0.49
10 19 0.51
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATTATTA
Found at i:38924 original size:30 final size:30
Alignment explanation
Indices: 38867--38934 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
38857 ATGCATAAGT
* **
38867 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
38897 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
38927 ATATGCAT
1 AAATGCAT
38935 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:47305 original size:133 final size:133
Alignment explanation
Indices: 47030--47468 Score: 575
Period size: 133 Copynumber: 3.3 Consensus size: 133
47020 AACATCAGTT
* ** * ** *
47030 GACCAGATCTCCTCATCATGTAGGAGCAACGTCAACATTAGATAACCAGCCGTCCTCATTACGTA
1 GACCAGATCTCCTCATCACGTAGGAGCAGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTA
** *
47095 GGAACTATGTTATCG--C-T-ATAAA-ATGGCCCAGAACTCTTCATCACGTATGAGCCGTGTCAT
66 GGAACCGTGTTATCGCCCTTCCTAAAGATGG-CCAGAACTCTTCATCACGTATGAGCCGTGTCAT
47155 CCCC
130 CCCC
** * * *
47159 GATTAGATCTCCTCATCACGTAGGAGTC-GTGTCACCCCTAGATAACCAGACATCCTCATCAAGT
1 GACCAGATCTCCTCATCACGTAGGAG-CAGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGT
47223 AGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT
65 AGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCAT
47288 CCCC
130 CCCC
* * *
47292 GACCAGATCTCCTCATCGCGTAGGAGCTGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTA
1 GACCAGATCTCCTCATCACGTAGGAGCAGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTA
* * *
47357 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
66 GGAACCGTGTTATCGCCCTTCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTCAT
47422 CCCTC
130 CCC-C
* * * *
47427 GACCAGATTTCCTCATCACGTAGGAACCGTGTCACCCTTAGA
1 GACCAGATCTCCTCATCACGTAGGAGCAGTGTCACCCCTAGA
47469 CGACCCGAAC
Statistics
Matches: 271, Mismatches: 30, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
129 64 0.24
130 1 0.00
131 1 0.00
132 2 0.01
133 128 0.47
134 37 0.14
135 38 0.14
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (133 bp):
GACCAGATCTCCTCATCACGTAGGAGCAGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTA
GGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATC
CCC
Found at i:47324 original size:39 final size:38
Alignment explanation
Indices: 47255--47329 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
47245 CTAAAGATGG
* *
47255 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCGA
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCA-CCCCGA
* * *
47294 CCAGATCTCCTCATCGCGTAGGAGCTGTGTCACCCC
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCC
47330 TAGATAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 4 0.13
39 27 0.87
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (38 bp):
CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCGA
Found at i:47502 original size:43 final size:40
Alignment explanation
Indices: 47391--47507 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 40
47381 AAGATGGCCA
47391 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
** * * * *
47431 AGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC-T---CGACC
* *
47474 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
47508 CAACAACTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
39 3 0.05
40 25 0.43
43 27 0.47
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
Found at i:47679 original size:3 final size:3
Alignment explanation
Indices: 47664--47743 Score: 128
Period size: 3 Copynumber: 27.0 Consensus size: 3
47654 CTATTTTAAT
*
47664 TTA TTA CTA TTA TTA TT- TGT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
47708 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47744 CAAATGGACA
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:52250 original size:15 final size:16
Alignment explanation
Indices: 52222--52251 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52212 TAAAATACTT
52222 AAAATTATTGAAAATA
1 AAAATTATTGAAAATA
52238 AAAATTATT-AAAAT
1 AAAATTATTGAAAAT
52252 TTTAGAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAATTATTGAAAATA
Found at i:53882 original size:51 final size:48
Alignment explanation
Indices: 53822--53922 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 48
53812 CAAATGATAG
53822 TTGATAATATAATCTAATAATATTAAAAAAAAATCTTCTTCTTTTTTTACT
1 TTGATAATATAATCTAATAATATT--AAAAAAATCTTCTTC-TTTTTTACT
53873 TTGATAATATAATCTAATAATATTAAAAAAATCTTCTTCTTTTTTACT
1 TTGATAATATAATCTAATAATATTAAAAAAATCTTCTTCTTTTTTACT
53921 TT
1 TT
53923 TTGAGAGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
48 11 0.22
49 15 0.30
51 24 0.48
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.49
Consensus pattern (48 bp):
TTGATAATATAATCTAATAATATTAAAAAAATCTTCTTCTTTTTTACT
Found at i:62758 original size:23 final size:24
Alignment explanation
Indices: 62731--62776 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
62721 CGATTCCCAG
*
62731 CCCAATACC-GTCCCAATACCCGA
1 CCCAATACCTGGCCCAATACCCGA
62754 CCCAATACCTGGCCCAATACCCG
1 CCCAATACCTGGCCCAATACCCG
62777 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.28, C:0.48, G:0.11, T:0.13
Consensus pattern (24 bp):
CCCAATACCTGGCCCAATACCCGA
Found at i:62759 original size:12 final size:12
Alignment explanation
Indices: 62731--62776 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
62721 CGATTCCCAG
*
62731 CCCAATA-CCGT
1 CCCAATACCCGA
62742 CCCAATACCCGA
1 CCCAATACCCGA
* *
62754 CCCAATACCTGG
1 CCCAATACCCGA
62766 CCCAATACCCG
1 CCCAATACCCG
62777 TTTAAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 7 0.23
12 23 0.77
ACGTcount: A:0.28, C:0.48, G:0.11, T:0.13
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:74289 original size:14 final size:15
Alignment explanation
Indices: 74270--74302 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
74260 ATAATATAAA
74270 ATTATAAAAATA-TT
1 ATTATAAAAATATTT
74284 ATTATAAAAATATTT
1 ATTATAAAAATATTT
74299 ATTA
1 ATTA
74303 ATGGGTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATAAAAATATTT
Found at i:74620 original size:27 final size:27
Alignment explanation
Indices: 74580--74631 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
74570 CGTTGCCTTC
* * *
74580 AAACACCGATTCAACGATATAATATTT
1 AAACACCAACTCAACGACATAATATTT
*
74607 AAACACCAACTCAATGACATAATAT
1 AAACACCAACTCAACGACATAATAT
74632 AAATAGAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.25
Consensus pattern (27 bp):
AAACACCAACTCAACGACATAATATTT
Found at i:80950 original size:14 final size:13
Alignment explanation
Indices: 80922--80958 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
80912 AATGGGAAGT
80922 AATCCCTGCAAAA
1 AATCCCTGCAAAA
80935 AATCCCTGCGAAAA
1 AATCCCTGC-AAAA
*
80949 AATCTCTGCA
1 AATCCCTGCA
80959 TATAGACAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (13 bp):
AATCCCTGCAAAA
Found at i:86209 original size:16 final size:15
Alignment explanation
Indices: 86183--86222 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
86173 GCAATGTGAC
86183 TATAAGTATATGTGCT
1 TATAAGTATATG-GCT
86199 T-TAAGTGATATGGCT
1 TATAAGT-ATATGGCT
86214 TATAAGTAT
1 TATAAGTAT
86223 TTCTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (15 bp):
TATAAGTATATGGCT
Found at i:86787 original size:22 final size:22
Alignment explanation
Indices: 86759--86824 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
86749 TATGGACATC
*
86759 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
86781 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
*
86803 ATTCTATGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
86825 TTTATACGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:89946 original size:21 final size:21
Alignment explanation
Indices: 89920--89964 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
89910 GATTTCTGGG
* *
89920 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
89941 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
89962 CAA
1 CAA
89965 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:91683 original size:22 final size:22
Alignment explanation
Indices: 91610--91675 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
91600 TATGGACATC
*
91610 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
91632 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
*
91654 ATTCTACGGGCACTTTGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
91676 TTTATACGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:96749 original size:20 final size:20
Alignment explanation
Indices: 96712--96749 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
96702 TCTCAGTCAT
*
96712 TCCTTCCTCCAAGGTCTGTA
1 TCCTTCCTCCAAGCTCTGTA
96732 TCCTTCCCTCC-AGCTCTG
1 TCCTT-CCTCCAAGCTCTG
96750 CTTTCTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.11, C:0.42, G:0.13, T:0.34
Consensus pattern (20 bp):
TCCTTCCTCCAAGCTCTGTA
Found at i:116816 original size:30 final size:30
Alignment explanation
Indices: 116782--116839 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
116772 GTCATATCAT
* *
116782 ACATACACAAGTGATGACGTGACACATACC
1 ACATACACAAATGATGACGTAACACATACC
* *
116812 ACATATATAAATGATGACGTAACACATA
1 ACATACACAAATGATGACGTAACACATA
116840 TCACGTGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21
Consensus pattern (30 bp):
ACATACACAAATGATGACGTAACACATACC
Found at i:118513 original size:21 final size:21
Alignment explanation
Indices: 118487--118530 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
118477 TTTCTCTAGA
118487 TTTCATGAGTTCAAGCCGTTG
1 TTTCATGAGTTCAAGCCGTTG
118508 TTTCATGAGTTCAAGCCGTTG
1 TTTCATGAGTTCAAGCCGTTG
118529 TT
1 TT
118531 CCTGGGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (21 bp):
TTTCATGAGTTCAAGCCGTTG
Done.