Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003124.1 Hibiscus syriacus cultivar Beakdansim tig00006541_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: 67810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3321 original size:40 final size:40
Alignment explanation
Indices: 3264--3404 Score: 153
Period size: 41 Copynumber: 3.5 Consensus size: 40
3254 GACTATATAT
* *
3264 TTAACA-TTTTGCAGCGTTTATACAAAAAATGCCA-TATTGA
1 TTAACACTATTGCGGCGTTT-T-CAAAAAATGCCACTATTGA
* * *
3304 TT-ACACTATTGTGGCGTTTGTTAAAAAACGCCACTATTGA
1 TTAACACTATTGCGGCGTTT-TCAAAAAATGCCACTATTGA
* *
3344 TTAAAACTATTGCGGCGTTTTTCTAAAAATGCCACTATTGA
1 TTAACACTATTGCGGCG-TTTTCAAAAAATGCCACTATTGA
*
3385 TTAACACTTTTGCGGCGTTT
1 TTAACACTATTGCGGCGTTT
3405 GTCTAAAACA
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
39 13 0.15
40 24 0.29
41 44 0.52
42 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (40 bp):
TTAACACTATTGCGGCGTTTTCAAAAAATGCCACTATTGA
Found at i:3363 original size:41 final size:41
Alignment explanation
Indices: 3287--3412 Score: 168
Period size: 41 Copynumber: 3.1 Consensus size: 41
3277 GCGTTTATAC
*
3287 AAAAAATGCCA-TATTGATT-ACACTATTGTGGCGTTTGTT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTT
* *
3326 AAAAAACGCCACTATTGATTAAAACTATTGCGGCGTTT-TT
1 AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTT
* *
3366 CTAAAAATGCCACTATTGATTAACACTTTTGCGGCGTTTGTCT
1 -AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGT-T
3409 AAAA
1 AAAA
3413 CACCATTTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
39 10 0.14
40 10 0.14
41 49 0.66
42 4 0.05
43 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (41 bp):
AAAAAATGCCACTATTGATTAACACTATTGCGGCGTTTGTT
Found at i:3541 original size:42 final size:42
Alignment explanation
Indices: 3468--3566 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
3458 ATGTGTAATA
* *
3468 TATTACGGTGTTTGTGGTATAAATACCGCTAATTTACCGA-TC
1 TATTACGGCGTTTGTGGTATAAACACCGCTAATTTACC-ACTC
* ***
3510 TATTACGGCATTTGTGGTATAAACGTTGCTAATTTACCACTC
1 TATTACGGCGTTTGTGGTATAAACACCGCTAATTTACCACTC
*
3552 TATTGCGGCGTTTGT
1 TATTACGGCGTTTGT
3567 TAAAAAATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (42 bp):
TATTACGGCGTTTGTGGTATAAACACCGCTAATTTACCACTC
Found at i:3601 original size:40 final size:41
Alignment explanation
Indices: 3545--3621 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
3535 TTGCTAATTT
* * *
3545 ACCACTCTATTGCGGCGTTTGTT-AAAAAATGCCGTAATAA
1 ACCACCCTATTACGGCGTTTGTTGAAAAAACGCCGTAATAA
*
3585 ACCACCCTATTACGGCGTTTGTTGTAAAAACGCCGTA
1 ACCACCCTATTACGGCGTTTGTTGAAAAAACGCCGTA
3622 TATGTCAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 21 0.66
41 11 0.34
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (41 bp):
ACCACCCTATTACGGCGTTTGTTGAAAAAACGCCGTAATAA
Found at i:4417 original size:43 final size:43
Alignment explanation
Indices: 4355--4481 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 43
4345 ACTAAGGCCG
* *
4355 CAACAAGTCGGGTTCTTTAGCGGCGTTTTTGTTACAAACGCCA
1 CAACAAGTCAGGTTATTTAGCGGCGTTTTTGTTACAAACGCCA
* * * * *
4398 CAACAAGTCAGGTTGTTTAGCGGCATATTT-TTACAAATGTCGA
1 CAACAAGTCAGGTTATTTAGCGGCGTTTTTGTTACAAACG-CCA
* **
4441 AAAC-AGTCAGGTTATTTAGAAGCGTTTTTGTTACAAACGCC
1 CAACAAGTCAGGTTATTTAGCGGCGTTTTTGTTACAAACGCC
4482 GTTAATAATG
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
42 29 0.43
43 39 0.57
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (43 bp):
CAACAAGTCAGGTTATTTAGCGGCGTTTTTGTTACAAACGCCA
Found at i:8431 original size:42 final size:41
Alignment explanation
Indices: 8382--8500 Score: 157
Period size: 42 Copynumber: 2.9 Consensus size: 41
8372 ATTTATAATA
* * *
8382 AAAACACCACTAATGTACTAATATATTGCGGCGTTTGTAAGG
1 AAAACACCACTAATGTACTAGTCTATTGCGGCGTTTGTAA-C
* *
8424 AAAACACCACTAATTTACTAGTCTATTGCGGCGCTTGTAAC
1 AAAACACCACTAATGTACTAGTCTATTGCGGCGTTTGTAAC
* * *
8465 AAAGCGCCACTAATGTACTAGTCTATGGCGGCGTTT
1 AAAACACCACTAATGTACTAGTCTATTGCGGCGTTT
8501 CTTAAAAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 31 0.46
42 36 0.54
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (41 bp):
AAAACACCACTAATGTACTAGTCTATTGCGGCGTTTGTAAC
Found at i:9113 original size:24 final size:24
Alignment explanation
Indices: 9080--9133 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
9070 AATAAATAAT
*
9080 ATATTGTTTATTATT-TACGTTATA
1 ATATTATTTATTATTATACGTTA-A
9104 ATATTATTTATTATTATACGTTAA
1 ATATTATTTATTATTATACGTTAA
9128 AT-TTAT
1 ATATTAT
9134 GTGTTGAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 4 0.14
24 17 0.61
25 7 0.25
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (24 bp):
ATATTATTTATTATTATACGTTAA
Found at i:12079 original size:92 final size:89
Alignment explanation
Indices: 11925--12119 Score: 318
Period size: 92 Copynumber: 2.2 Consensus size: 89
11915 TCTTCATGAA
* *
11925 CCAGAGTTCCTCTTCGTTACTTATTGTTATTTGTTGTTACAAATGATGTTAGGCTTGTGGTAGTT
1 CCAGAGTTCCTCTTCATTACTTATTGTTATTTGTTGTTACAAATGATGTTAGCCTTGTGGTAGTT
*
11990 TTGCTCGAGACTAAACACATTTTT
66 TTGCTAGAGACTAAACACATTTTT
12014 CCAGAGTTCCTCTTCATTACTTTTGATTGTTATTTGTTGTTACAAATGATGTTAGCCTTGTGGTA
1 CCAGAGTTCCTCTTCATTAC--TT-ATTGTTATTTGTTGTTACAAATGATGTTAGCCTTGTGGTA
*
12079 GTTTTGCTAGAGACTTAACACATTTTT
63 GTTTTGCTAGAGACTAAACACATTTTT
*
12106 CCAGAATTCCTCTT
1 CCAGAGTTCCTCTT
12120 TACTCTTTCT
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
89 19 0.19
91 2 0.02
92 77 0.79
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (89 bp):
CCAGAGTTCCTCTTCATTACTTATTGTTATTTGTTGTTACAAATGATGTTAGCCTTGTGGTAGTT
TTGCTAGAGACTAAACACATTTTT
Found at i:12613 original size:35 final size:35
Alignment explanation
Indices: 12574--12652 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
12564 CAGCGTAAAA
*
12574 AAACGCCGCAACTGTTAGTGACGTTTTTTAATAAT
1 AAACGCCGCAACTGTTAGTGACGTTTTCTAATAAT
* *
12609 AAACGCCGCAACTGTTAGTGGCGTTTTCTACTAAT
1 AAACGCCGCAACTGTTAGTGACGTTTTCTAATAAT
12644 AAACGCCGC
1 AAACGCCGC
12653 TAAAGTCAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (35 bp):
AAACGCCGCAACTGTTAGTGACGTTTTCTAATAAT
Found at i:17542 original size:21 final size:20
Alignment explanation
Indices: 17489--17542 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
17479 GTACCCATGT
17489 AAGTATCGATACCCAGTGGA
1 AAGTATCGATACCCAGTGGA
**
17509 AGAGTATTAATACCCAAGGTGG-
1 A-AGTATCGATACCC-A-GTGGA
17531 AAGTATCGATAC
1 AAGTATCGATAC
17543 TAGTGTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.04
21 20 0.74
22 2 0.07
23 4 0.15
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (20 bp):
AAGTATCGATACCCAGTGGA
Found at i:21175 original size:2 final size:2
Alignment explanation
Indices: 21164--21225 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
21154 TAATATTAAC
21164 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21205 TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
21226 ATTTGAATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23366 original size:30 final size:31
Alignment explanation
Indices: 23311--23370 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
23301 AATTTAAGGT
*
23311 AAAATGGTTTTTGAACTTGAATTGAATTTAC
1 AAAATAGTTTTTGAACTTGAATTGAATTTAC
* *
23342 AAAATAGTTTTTGGA-TTTAATTGAATTTA
1 AAAATAGTTTTTGAACTTGAATTGAATTTA
23371 TTCAAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (31 bp):
AAAATAGTTTTTGAACTTGAATTGAATTTAC
Found at i:23478 original size:22 final size:22
Alignment explanation
Indices: 23450--23512 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
23440 AGTGTGTCAA
*
23450 AGTGCATCCATGCACCCCCTGC
1 AGTGCATCCATGCACCCCATGC
*
23472 AGTGCATCCATGCA-CCCATGT
1 AGTGCATCCATGCACCCCATGC
*
23493 AGTGCATCCATGCACTCCAT
1 AGTGCATCCATGCACCCCAT
23513 TTCGAATGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.22
Consensus pattern (22 bp):
AGTGCATCCATGCACCCCATGC
Found at i:24874 original size:19 final size:20
Alignment explanation
Indices: 24850--24897 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
24840 AATTATTTTC
*
24850 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
24869 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
24889 TTTTGAAAA
1 TTTTGAAAA
24898 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:26114 original size:31 final size:30
Alignment explanation
Indices: 26076--26136 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 30
26066 CAATTTAAGG
26076 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTT-AATTGAATTTA
*
26107 CAAAATGGTTTTTGGACTTAATTTAATTTA
1 CAAAATGGTTTTTGGACTTAATTGAATTTA
26137 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (30 bp):
CAAAATGGTTTTTGGACTTAATTGAATTTA
Found at i:26242 original size:21 final size:21
Alignment explanation
Indices: 26216--26336 Score: 138
Period size: 21 Copynumber: 5.7 Consensus size: 21
26206 AGTGTGTCAA
*
26216 AGTGCATCAATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGT
* *
26237 AGTGCATTCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGT
26258 AGTGCA-CCTATGCACCCCTGT
1 AGTGCATCC-ATGCACCCCTGT
**
26279 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACC--CCTGT
* *
26302 AGTGCATCGATGCA-CCATGT
1 AGTGCATCCATGCACCCCTGT
26322 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
26337 TCCATTTCGA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
20 16 0.19
21 48 0.58
22 3 0.04
23 16 0.19
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGT
Found at i:26422 original size:20 final size:20
Alignment explanation
Indices: 26356--26421 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
26346 AATGCAATTA
*
26356 GTGCATCGATGCATCCTGCT
1 GTGCATCGACGCATCCTGCT
*
26376 GTGCATCGACGCATCCTGTT
1 GTGCATCGACGCATCCTGCT
*
26396 GTGCATTGACGCATCCTGCT
1 GTGCATCGACGCATCCTGCT
26416 GTGCAT
1 GTGCAT
26422 TCATGCACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.29, G:0.26, T:0.30
Consensus pattern (20 bp):
GTGCATCGACGCATCCTGCT
Found at i:31518 original size:2 final size:2
Alignment explanation
Indices: 31513--31541 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31503 ATTTGAAATG
31513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31542 ATGGGACTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47025 original size:21 final size:22
Alignment explanation
Indices: 47001--47050 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
46991 TTATTGTGCC
47001 AGTTACAGAGTTAATTACA-AG
1 AGTTACAGAGTTAATTACATAG
*
47022 AGTTACAGAGTTAATTACATGG
1 AGTTACAGAGTTAATTACATAG
47044 AGTTACA
1 AGTTACA
47051 AAAGACTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (22 bp):
AGTTACAGAGTTAATTACATAG
Found at i:58834 original size:19 final size:19
Alignment explanation
Indices: 58774--58834 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
58764 TTTGTGCAGA
* *
58774 GGGAATCGATACCCTCATG
1 GGGAATCGATACCCCCCTG
* *
58793 AGGGAACCGAT-TCCCCCTAG
1 -GGGAATCGATACCCCCCT-G
58813 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
58832 GGG
1 GGG
58835 TTCTGGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.23, C:0.31, G:0.30, T:0.16
Consensus pattern (19 bp):
GGGAATCGATACCCCCCTG
Found at i:63523 original size:39 final size:40
Alignment explanation
Indices: 63469--63547 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
63459 CCTTCATCTT
63469 ATGTGATAGAAATAAGTG-T-TTCTAAAAAAAAAAGGTAAA
1 ATGTGATAGAAATAAGTGTTATTCT-AAAAAAAAAGGTAAA
63508 ATGTGATAGAAATAAGTGTTATTCTAAAAAAAAAGGTAAA
1 ATGTGATAGAAATAAGTGTTATTCTAAAAAAAAAGGTAAA
63548 CTATTCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 18 0.47
40 16 0.42
41 4 0.11
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.27
Consensus pattern (40 bp):
ATGTGATAGAAATAAGTGTTATTCTAAAAAAAAAGGTAAA
Found at i:63926 original size:16 final size:15
Alignment explanation
Indices: 63905--63938 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
63895 TAAATTAAAT
63905 TTAAATAATTTATCAA
1 TTAAATAATTTAT-AA
*
63921 TTAAATTATTTATAA
1 TTAAATAATTTATAA
63936 TTA
1 TTA
63939 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAATAATTTATAA
Found at i:64376 original size:12 final size:12
Alignment explanation
Indices: 64351--64401 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
64341 TATTAGTGGA
64351 AAAAAATAAT-T
1 AAAAAATAATAT
*
64362 AAAAGATAATAT
1 AAAAAATAATAT
*
64374 AAATAATAATAT
1 AAAAAATAATAT
64386 AAAAAATTAATA-
1 AAAAAA-TAATAT
64398 AAAA
1 AAAA
64402 GTACATATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.26
12 20 0.59
13 5 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (12 bp):
AAAAAATAATAT
Found at i:65398 original size:42 final size:44
Alignment explanation
Indices: 65290--65388 Score: 166
Period size: 42 Copynumber: 2.3 Consensus size: 44
65280 GATAGACTTA
*
65290 TTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGATT
1 TTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGACT
*
65334 TTTTATTTATTTTGTTTCTTAATA-TTTTA-TTAATTATTGACT
1 TTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGACT
65376 TTTTATTTATTTT
1 TTTTATTTATTTT
65389 ATTATTTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
42 24 0.45
43 5 0.09
44 24 0.45
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (44 bp):
TTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGGACT
Found at i:65444 original size:22 final size:23
Alignment explanation
Indices: 65414--65472 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
65404 GAATTGTAAC
* * *
65414 TTTTGTATTTAATTTTTTTTAT-
1 TTTTTTATTTAATTTTTGTAATG
*
65436 TTTTTTATTT-A-GTTTGTAATG
1 TTTTTTATTTAATTTTTGTAATG
65457 TTTTTTATTTAATTTT
1 TTTTTTATTTAATTTT
65473 CACTTGAGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 6 0.21
21 11 0.38
22 10 0.34
23 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.75
Consensus pattern (23 bp):
TTTTTTATTTAATTTTTGTAATG
Found at i:65493 original size:15 final size:16
Alignment explanation
Indices: 65473--65502 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
65463 ATTTAATTTT
65473 CACTTGAGTA-AACAA
1 CACTTGAGTAGAACAA
65488 CACTTGAGTAGAACA
1 CACTTGAGTAGAACA
65503 TTAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (16 bp):
CACTTGAGTAGAACAA
Found at i:66174 original size:11 final size:12
Alignment explanation
Indices: 66160--66221 Score: 78
Period size: 11 Copynumber: 5.5 Consensus size: 12
66150 TCGTTAAGAA
66160 CTCGAG-TCGAG
1 CTCGAGATCGAG
66171 CTCGAGATCGAG
1 CTCGAGATCGAG
*
66183 -TCGAGCTCGAG
1 CTCGAGATCGAG
*
66194 ATCGAG-TCGAG
1 CTCGAGATCGAG
66205 CTCGAGATCGAG
1 CTCGAGATCGAG
66217 -TCGAG
1 CTCGAG
66222 TCCATTCGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
11 31 0.67
12 15 0.33
ACGTcount: A:0.23, C:0.24, G:0.35, T:0.18
Consensus pattern (12 bp):
CTCGAGATCGAG
Found at i:66183 original size:17 final size:17
Alignment explanation
Indices: 66161--66221 Score: 122
Period size: 17 Copynumber: 3.6 Consensus size: 17
66151 CGTTAAGAAC
66161 TCGAGTCGAGCTCGAGA
1 TCGAGTCGAGCTCGAGA
66178 TCGAGTCGAGCTCGAGA
1 TCGAGTCGAGCTCGAGA
66195 TCGAGTCGAGCTCGAGA
1 TCGAGTCGAGCTCGAGA
66212 TCGAGTCGAG
1 TCGAGTCGAG
66222 TCCATTCGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.36, T:0.18
Consensus pattern (17 bp):
TCGAGTCGAGCTCGAGA
Done.