Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003640.1 Hibiscus syriacus cultivar Beakdansim tig00007712_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: 96877
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1639 original size:64 final size:65
Alignment explanation
Indices: 1517--1777 Score: 393
Period size: 66 Copynumber: 4.0 Consensus size: 65
1507 GTCTTGGATA
* * *
1517 AAAGCTCTGAT-GTCAGGTGAAAAATAAGAGCTCAGATGAAGTTTT-CCATCTGGTGCTCAGTCT
1 AAAGCTCTGATGGTCAAGTG-AAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1580 G
65 G
* *
1581 -AAGTTCTGACGGTCAAGTGAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCTG
1 AAAGCTCTGATGGTCAAGTGAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCTG
* * *
1645 AAAACTCTGATGGTCAAGCGAAAGAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAATCT
1 AAAGCTCTGATGGTCAAGTGAAA-AGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1710 G
65 G
*
1711 AAAGCTCTGATAGTCAAGTGGAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1 AAAGCTCTGATGGTCAAGT-GAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCT
1776 G
65 G
1777 A
1 A
1778 GCTTTTGAAG
Statistics
Matches: 178, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
63 31 0.17
64 26 0.15
65 18 0.10
66 99 0.56
67 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (65 bp):
AAAGCTCTGATGGTCAAGTGAAAAGAAGAGCTCAAATGAAGTTTTCCCATCTGGTGCTCAGTCTG
Found at i:8742 original size:27 final size:27
Alignment explanation
Indices: 8707--8782 Score: 152
Period size: 27 Copynumber: 2.8 Consensus size: 27
8697 CATACCCATT
8707 CCTAGTTTATTTATCCAAATATATTTC
1 CCTAGTTTATTTATCCAAATATATTTC
8734 CCTAGTTTATTTATCCAAATATATTTC
1 CCTAGTTTATTTATCCAAATATATTTC
8761 CCTAGTTTATTTATCCAAATAT
1 CCTAGTTTATTTATCCAAATAT
8783 TAAAAAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.30, C:0.18, G:0.04, T:0.47
Consensus pattern (27 bp):
CCTAGTTTATTTATCCAAATATATTTC
Found at i:16060 original size:15 final size:17
Alignment explanation
Indices: 16040--16071 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16030 TTTAAAAATT
16040 ATATTAT-AA-TTATAA
1 ATATTATCAATTTATAA
16055 ATATTATCAATTTATAA
1 ATATTATCAATTTATAA
16072 TAAAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTATCAATTTATAA
Found at i:21275 original size:2 final size:2
Alignment explanation
Indices: 21270--21301 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21260 TGTATGTGTG
21270 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
21302 GAACATAAGT
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:21404 original size:20 final size:21
Alignment explanation
Indices: 21376--21415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21366 GATTATGAAA
21376 TCATATGAA-AAGTGAAATGT
1 TCATATGAATAAGTGAAATGT
* *
21396 TCATGTGAATATGTGAAATG
1 TCATATGAATAAGTGAAATG
21416 ATCTTTCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (21 bp):
TCATATGAATAAGTGAAATGT
Found at i:25036 original size:3 final size:3
Alignment explanation
Indices: 25028--25095 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
25018 AAAATAAAGA
25028 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25076 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
25096 AACAAAGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27179 original size:3 final size:3
Alignment explanation
Indices: 27171--27195 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27161 CTTACAATGG
27171 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
27196 ATGATGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:28529 original size:35 final size:36
Alignment explanation
Indices: 28443--28599 Score: 221
Period size: 35 Copynumber: 4.4 Consensus size: 36
28433 TTATCCCATT
* * *
28443 ATCATTTTTC-AACAAACATCTACCTAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
* *
28478 AACTATTTTTCAAAGAAATATTTACCAAACTTTGAAA
1 ATC-ATTTTTCAAAGAAACATTTACCAAACTTTGAAA
28515 ATCA-TTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
28550 ATCA-TTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
28585 ACCATCTTTTCAAAG
1 ATCAT-TTTTCAAAG
28600 TTGGTTACCA
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
35 70 0.64
36 8 0.07
37 32 0.29
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:28608 original size:70 final size:69
Alignment explanation
Indices: 28463--28626 Score: 188
Period size: 70 Copynumber: 2.3 Consensus size: 69
28453 AACAAACATC
* * *
28463 TACCTAACTTTGAAAAACTATTTTTCAAAGAAATATTTACCAAACTTTGAAAATCATTTTCAAAG
1 TACCAAACTTTGAAAAAC-A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAG
*
28528 AAACATT
64 -AACAGT
*
28535 TACCAAACTTTGAAAATCATTTTCAAAGAAACATTTACCAAACTTTGAAAACCATCTTTTCAAAG
1 TACCAAACTTTGAAAAACATTTTCAAAGAAACATTTACCAAACTTTGAAAACCA--TTTTCAAAG
***
28600 -TTGGT
64 AACAGT
*
28605 TACCAAAC-TTGAAAACCATTTT
1 TACCAAACTTTGAAAAACATTTT
28627 AATACTTTCA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
69 13 0.16
70 42 0.52
71 1 0.01
72 25 0.31
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (69 bp):
TACCAAACTTTGAAAAACATTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAGAA
CAGT
Found at i:32683 original size:16 final size:16
Alignment explanation
Indices: 32659--32690 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32649 TATCGCCGAC
*
32659 TGAATTTCACTATTCA
1 TGAAATTCACTATTCA
32675 TGAAATTCACTATTCA
1 TGAAATTCACTATTCA
32691 CGCGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (16 bp):
TGAAATTCACTATTCA
Found at i:33150 original size:37 final size:36
Alignment explanation
Indices: 33087--33205 Score: 161
Period size: 35 Copynumber: 3.3 Consensus size: 36
33077 ATCCCATTAT
*
33087 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTG-AAAAC
* * *
33123 TATTTTTCAAATAAATATTTACCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
*
33159 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
33194 CATTTTTTCAAA
1 CA-TTTTTCAAA
33206 GTTGGTTACC
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 33 0.45
36 13 0.18
37 27 0.37
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (36 bp):
CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
Found at i:33204 original size:72 final size:68
Alignment explanation
Indices: 33090--33233 Score: 175
Period size: 72 Copynumber: 2.1 Consensus size: 68
33080 CCATTATCAT
*
33090 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAA-TAAATATTTACCAAACTTTG
1 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGT---TAGTTACCAAA-TTTG
33154 AAAACCA
62 AAAACCA
* * * *
33161 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCATTTTTTCAAAGTTGGTTACCAAATTTGAA
1 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA-TTTTTCAAAGTTAGTTACCAAATTTGAA
33225 AACCA
64 AACCA
33230 TTTT
1 TTTT
33234 AATACTTTCA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
69 15 0.23
70 9 0.14
71 11 0.17
72 29 0.45
73 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.35
Consensus pattern (68 bp):
TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGTTAGTTACCAAATTTGAAAA
CCA
Found at i:33215 original size:35 final size:36
Alignment explanation
Indices: 33089--33233 Score: 124
Period size: 35 Copynumber: 4.1 Consensus size: 36
33079 CCCATTATCA
*
33089 TTTTTCAACA-AACA-TCTACCAAACTTTGAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
* * *
33124 ATTTTTCAAATAAATATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAA-GAACAGTTACCAAACTTTGAAAACCAT
*
33161 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
33197 TTTTTCAAAG-TTGGTTACCAAA-TTTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
33231 TTT
1 TTT
33234 AATACTTTCA
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
34 15 0.16
35 41 0.44
36 8 0.09
37 29 0.31
38 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:35178 original size:12 final size:11
Alignment explanation
Indices: 35159--35188 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
35149 CCCCAATCCC
35159 ATTTAATAATA
1 ATTTAATAATA
35170 ATATTAATAATA
1 AT-TTAATAATA
35182 ATTTAAT
1 ATTTAAT
35189 CTCAATCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:42983 original size:3 final size:3
Alignment explanation
Indices: 42977--43014 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
42967 ATTATTAAAT
*
42977 TTA TTA TAA ATTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43015 ATAATTTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:47880 original size:9 final size:9
Alignment explanation
Indices: 47866--47909 Score: 72
Period size: 9 Copynumber: 4.9 Consensus size: 9
47856 CGAATTAAAT
47866 TTTTAATAA
1 TTTTAATAA
47875 TTTTAA-AA
1 TTTTAATAA
47883 TTTTTAATAA
1 -TTTTAATAA
47893 TTTTAATAA
1 TTTTAATAA
47902 TTTTAATA
1 TTTTAATA
47910 TAAAATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 2 0.06
9 29 0.88
10 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:47885 original size:18 final size:18
Alignment explanation
Indices: 47862--47909 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
47852 AAAACGAATT
47862 AAATTTTTAATAATTTTA
1 AAATTTTTAATAATTTTA
47880 AAATTTTTAATAATTTTA
1 AAATTTTTAATAATTTTA
47898 ATAA-TTTTAATA
1 A-AATTTTTAATA
47910 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTTTTAATAATTTTA
Found at i:52425 original size:23 final size:22
Alignment explanation
Indices: 52395--52441 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
52385 TATAATGTAA
52395 GGGTGAATCTATAAAATTTTAG
1 GGGTGAATCTATAAAATTTTAG
**
52417 GGGTCGAATCTATATTATTTTAG
1 GGGT-GAATCTATAAAATTTTAG
52440 GG
1 GG
52442 AATCGAAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (22 bp):
GGGTGAATCTATAAAATTTTAG
Found at i:54314 original size:16 final size:17
Alignment explanation
Indices: 54293--54330 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
54283 TGTGCAAATC
*
54293 CGGGTACCAG-GATTTT
1 CGGGTACCAGAAATTTT
*
54309 CGGGTACCCGAAATTTT
1 CGGGTACCAGAAATTTT
54326 CGGGT
1 CGGGT
54331 CGACGATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (17 bp):
CGGGTACCAGAAATTTT
Found at i:54565 original size:16 final size:15
Alignment explanation
Indices: 54539--54574 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
54529 CAAAATACAA
54539 AATATAATAATTCAT
1 AATATAATAATTCAT
54554 AATATAAATAATTCAT
1 AATAT-AATAATTCAT
*
54570 TATAT
1 AATAT
54575 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATAATTCAT
Found at i:70079 original size:14 final size:14
Alignment explanation
Indices: 70062--70090 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
70052 ACTGCAAGGG
70062 TTCAGTTCAACCAA
1 TTCAGTTCAACCAA
70076 TTCAGTTCAACCAA
1 TTCAGTTCAACCAA
70090 T
1 T
70091 AGATGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.31
Consensus pattern (14 bp):
TTCAGTTCAACCAA
Found at i:75542 original size:25 final size:24
Alignment explanation
Indices: 75493--75542 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
75483 ATTTAATGAT
* *
75493 TTAATATTTTAACTAAATCTGAAA
1 TTAAAATTTTAACTAAATCTAAAA
75517 TTAAAATTTTATACT-AATACTAAAA
1 TTAAAATTTTA-ACTAAAT-CTAAAA
75542 T
1 T
75543 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (24 bp):
TTAAAATTTTAACTAAATCTAAAA
Found at i:78082 original size:18 final size:19
Alignment explanation
Indices: 78059--78098 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
78049 AGGTAATCTC
*
78059 ATTATAGAAAT-TTAGATT
1 ATTATAGAAATCTAAGATT
*
78077 ATTATAGTAATCTAAGATT
1 ATTATAGAAATCTAAGATT
78096 ATT
1 ATT
78099 TGAATTAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (19 bp):
ATTATAGAAATCTAAGATT
Found at i:79607 original size:50 final size:51
Alignment explanation
Indices: 79532--79633 Score: 197
Period size: 50 Copynumber: 2.0 Consensus size: 51
79522 CTCCAACTTT
79532 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGAT-ATATCTGACCATTGA
1 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATAATATCTGACCATTGA
79582 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATAATATCTGACCATTGA
1 TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATAATATCTGACCATTGA
79633 T
1 T
79634 ACAAATTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 35 0.69
51 16 0.31
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (51 bp):
TCCATCTGGGAAACAGAAGAATTTCAATTAAGGATAATATCTGACCATTGA
Found at i:81587 original size:21 final size:22
Alignment explanation
Indices: 81539--81594 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
81529 TTGATAAACA
*
81539 ATATTATCATTAGTATACTAAAT
1 ATATTATAATTA-TATACTAAAT
*
81562 A-ATTATAATTATATA-TATAT
1 ATATTATAATTATATACTAAAT
*
81582 ATATTATATTTAT
1 ATATTATAATTAT
81595 GAGTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 5 0.17
21 14 0.48
22 9 0.31
23 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
ATATTATAATTATATACTAAAT
Found at i:88556 original size:59 final size:58
Alignment explanation
Indices: 88492--88629 Score: 170
Period size: 59 Copynumber: 2.3 Consensus size: 58
88482 TTAGGATGTT
*
88492 TTTAAATTATAATTTTATTTTAAATCGA-TTCTTAAATTTTAAAATATTTTATATCAATC
1 TTTAAATTATAATTTTATTTT-AAT-GATTTCTTAAATTTTAAAACATTTTATATCAATC
* * **
88551 TTTAAATTATAATTTTCATTTTAATTATTTCTTAAATTTTAAAACGTTTTATATTGATC
1 TTTAAATTATAATTTT-ATTTTAATGATTTCTTAAATTTTAAAACATTTTATATCAATC
* *
88610 CTTAAATTATCAATATTATT
1 TTTAAATTAT-AATTTTATT
88630 CTATTTTGGT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 1 0.01
59 58 0.84
60 10 0.14
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (58 bp):
TTTAAATTATAATTTTATTTTAATGATTTCTTAAATTTTAAAACATTTTATATCAATC
Found at i:94830 original size:14 final size:15
Alignment explanation
Indices: 94811--94894 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 15
94801 TTATAAGGTT
94811 ATTATTTTAAAAT-A
1 ATTATTTTAAAATAA
*
94825 ATTATTATAAAATAA
1 ATTATTTTAAAATAA
* **
94840 ATTATTATAAATATGG
1 ATTATTTTAAA-ATAA
94856 ATTGATTTATTTAAAATAA
1 ATT-A--T-TTTAAAATAA
94875 ATTATTTT-AAATAA
1 ATTATTTTAAAATAA
*
94889 TTTATT
1 ATTATT
94895 AGTATGAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
14 23 0.40
15 15 0.26
16 6 0.11
17 1 0.02
18 1 0.02
19 6 0.11
20 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
ATTATTTTAAAATAA
Found at i:94869 original size:49 final size:46
Alignment explanation
Indices: 94812--94920 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 46
94802 TATAAGGTTA
*
94812 TTATTTTAAAATAATTATTATAAAATAAATTATTATAAATATGGATTGAT
1 TTATTTTAAAATAATTATT-TAAAAT-AA-T-TTATAAATATGAATTGAT
* * *
94862 TTA-TTTAAAATAAATTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAAT-AATTATTTAAAATAATTTATAAATATGAATTGAT
94908 TTATTTTAAAATA
1 TTATTTTAAAATA
94921 TGGATTGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 19 0.36
47 9 0.17
48 2 0.04
49 13 0.25
50 10 0.19
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (46 bp):
TTATTTTAAAATAATTATTTAAAATAATTTATAAATATGAATTGAT
Found at i:96786 original size:14 final size:14
Alignment explanation
Indices: 96756--96798 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
96746 TATATAATAC
96756 TGTTGGTTTATGTAA
1 TGTTGGTTTA-GTAA
96771 TGTTGGTTTAGTAA
1 TGTTGGTTTAGTAA
*
96785 TG-TGGGTTAGTAA
1 TGTTGGTTTAGTAA
96798 T
1 T
96799 ATGCATGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 11 0.41
14 6 0.22
15 10 0.37
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (14 bp):
TGTTGGTTTAGTAA
Done.