Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009307.1 Hibiscus syriacus cultivar Beakdansim tig00113043_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: 116140
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4315 original size:14 final size:13
Alignment explanation
Indices: 4296--4329 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
4286 TGTGTTAGGG
4296 TTTAGGGTTTATAA
1 TTTAGGGTTT-TAA
4310 TTTAGGGTTTTAA
1 TTTAGGGTTTTAA
*
4323 ATTAGGG
1 TTTAGGG
4330 GTAAGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (13 bp):
TTTAGGGTTTTAA
Found at i:4331 original size:14 final size:14
Alignment explanation
Indices: 4297--4329 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4287 GTGTTAGGGT
*
4297 TTAGGGTTTATAAT
1 TTAGGGTTTATAAA
4311 TTAGGGTTT-TAAA
1 TTAGGGTTTATAAA
4324 TTAGGG
1 TTAGGG
4330 GTAAGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTATAAA
Found at i:8160 original size:20 final size:20
Alignment explanation
Indices: 8116--8263 Score: 151
Period size: 20 Copynumber: 7.4 Consensus size: 20
8106 AGTTTCTAAT
*
8116 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACACG-ATA-GTCAAA
8137 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACAC-GATAGTCAAA
* *
8156 TTCGCAACGCGATAGTTAAA
1 TTCGCAACACGATAGTCAAA
8176 TTCGCAACACGATAGTCAAA
1 TTCGCAACACGATAGTCAAA
*
8196 TTCGCAACAC-ATAAGTTAAA
1 TTCGCAACACGAT-AGTCAAA
* *
8216 TTCGAAACGCGATAGTCAAA
1 TTCGCAACACGATAGTCAAA
* * *
8236 TTCGCAACACAAAATTCAAA
1 TTCGCAACACGATAGTCAAA
8256 TTCGCAAC
1 TTCGCAAC
8264 GCGAACTCCA
Statistics
Matches: 107, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.02
19 8 0.07
20 94 0.88
21 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (20 bp):
TTCGCAACACGATAGTCAAA
Found at i:8180 original size:60 final size:60
Alignment explanation
Indices: 8116--8263 Score: 192
Period size: 60 Copynumber: 2.5 Consensus size: 60
8106 AGTTTCTAAT
* * *
8116 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTTAAA
1 TTCGCAACACG-ATA-GTCAAATTCGCAACACAGAAGTCAAATTCGAAACGCGATAGTCAAA
* *
8176 TTCGCAACACGATAGTCAAATTCGCAACACATAAGTTAAATTCGAAACGCGATAGTCAAA
1 TTCGCAACACGATAGTCAAATTCGCAACACAGAAGTCAAATTCGAAACGCGATAGTCAAA
* * *
8236 TTCGCAACACAAAATTCAAATTCGCAAC
1 TTCGCAACACGATAGTCAAATTCGCAAC
8264 GCGAACTCCA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.03
59 6 0.08
60 70 0.90
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (60 bp):
TTCGCAACACGATAGTCAAATTCGCAACACAGAAGTCAAATTCGAAACGCGATAGTCAAA
Found at i:8244 original size:40 final size:40
Alignment explanation
Indices: 8133--8267 Score: 170
Period size: 40 Copynumber: 3.4 Consensus size: 40
8123 CGCGAATATG
* *
8133 TAAA-TCGCAACACAGA-AGTCAAATTCGCAACGCGAT-AGT
1 TAAATTCGCAACGC-GATAGTCAAATTCGCAACAC-ATAAGT
*
8172 TAAATTCGCAACACGATAGTCAAATTCGCAACACATAAGT
1 TAAATTCGCAACGCGATAGTCAAATTCGCAACACATAAGT
* *
8212 TAAATTCGAAACGCGATAGTCAAATTCGCAACACA-AAAT
1 TAAATTCGCAACGCGATAGTCAAATTCGCAACACATAAGT
8251 TCAAATTCGCAACGCGA
1 T-AAATTCGCAACGCGA
8268 ACTCCAATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
39 12 0.14
40 75 0.86
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (40 bp):
TAAATTCGCAACGCGATAGTCAAATTCGCAACACATAAGT
Found at i:8691 original size:20 final size:21
Alignment explanation
Indices: 8653--8703 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
8643 CAACGCGATT
8653 TTGCGATTTTCTAAATTCGCG
1 TTGCGATTTTCTAAATTCGCG
*
8674 TTGCGATTTTC-CAATTCGCG
1 TTGCGATTTTCTAAATTCGCG
*
8694 TTACGATTTT
1 TTGCGATTTT
8704 TACTATTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.45
Consensus pattern (21 bp):
TTGCGATTTTCTAAATTCGCG
Found at i:10356 original size:13 final size:15
Alignment explanation
Indices: 10327--10358 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
10317 ACATTAGATC
10327 TAAACATAAATTTCA
1 TAAACATAAATTTCA
10342 TAAACAT-AA-TTCA
1 TAAACATAAATTTCA
10355 TAAA
1 TAAA
10359 AAAAAGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAACATAAATTTCA
Found at i:10513 original size:2 final size:2
Alignment explanation
Indices: 10506--10556 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
10496 CTTATTTTTA
10506 AT AT AT AT AT 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 AT AT AT AT AT
10548 AT AT AT AT A
1 AT AT AT AT A
10557 GAAAAAATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14814 original size:14 final size:14
Alignment explanation
Indices: 14795--14831 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
14785 TACCTTGTGT
*
14795 CAGAAATCAAAAAC
1 CAGAAACCAAAAAC
*
14809 CAGAAACCAAAAAT
1 CAGAAACCAAAAAC
14823 CAGAAACCA
1 CAGAAACCA
14832 TACTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.24, G:0.08, T:0.05
Consensus pattern (14 bp):
CAGAAACCAAAAAC
Found at i:18693 original size:17 final size:17
Alignment explanation
Indices: 18662--18704 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
18652 AGAAGCAACC
*
18662 CGAACC-AAAATTAACA
1 CGAACCGAAAAGTAACA
18678 CGAACCGAAAAGTAACA
1 CGAACCGAAAAGTAACA
*
18695 CGAACTGAAA
1 CGAACCGAAA
18705 TCAACCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.53, C:0.23, G:0.14, T:0.09
Consensus pattern (17 bp):
CGAACCGAAAAGTAACA
Found at i:18801 original size:16 final size:16
Alignment explanation
Indices: 18771--18818 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
18761 GAACCGAATT
* *
18771 TAACCCGACTTGAAAG
1 TAACCCGAATCGAAAG
* * *
18787 TAATCCGAATGGAAAT
1 TAACCCGAATCGAAAG
18803 TAACCCGAATCGAAAG
1 TAACCCGAATCGAAAG
18819 GAAGAATCTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (16 bp):
TAACCCGAATCGAAAG
Found at i:27370 original size:13 final size:13
Alignment explanation
Indices: 27352--27403 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
27342 ATTTTTTCTA
27352 ATTTCAAAACTTG
1 ATTTCAAAACTTG
* *
27365 ATTTCAAAATTTTTCTA
1 ATTTCAAAA---CT-TG
27382 ATTTCAAAACTTG
1 ATTTCAAAACTTG
27395 ATTTCAAAA
1 ATTTCAAAA
27404 ATCTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
13 19 0.61
14 1 0.03
16 1 0.03
17 10 0.32
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:27379 original size:30 final size:30
Alignment explanation
Indices: 27344--27403 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
27334 CTAATTTCAT
27344 TTTTTCTAATTTCAAAACTTGATTTCAAAA
1 TTTTTCTAATTTCAAAACTTGATTTCAAAA
27374 TTTTTCTAATTTCAAAACTTGATTTCAAAA
1 TTTTTCTAATTTCAAAACTTGATTTCAAAA
27404 ATCTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTTCTAATTTCAAAACTTGATTTCAAAA
Found at i:28746 original size:132 final size:132
Alignment explanation
Indices: 28509--28829 Score: 531
Period size: 132 Copynumber: 2.5 Consensus size: 132
28499 TAACTCAACA
*
28509 AAATAAAGTTTACTTATCTTACTTGTAATAAAAATATTAGATTTATAAT-A-AA-AATAATAGAA
1 AAATAAAGTTTACTTATCTTACTTGTAATAAAAATATTATATTTATAATAATAATAATAATAGAA
* * * * *
28571 AGTTTACTTATGTTACCTAAGAGGGATATAAAAATAAGAATCTTATTGTAAGATTTAAAACATTA
66 AGTTTACTTAGGTTACCTAAGAGGAATATAAAAATAAGAATCTTATTGAAAGATTGAAAACAATA
28636 AC
131 AC
*
28638 AATTAAAGTTTACTTATCTTACTTGTAATAAAAATATTATATTTATAATAATAATAATAATAGAA
1 AAATAAAGTTTACTTATCTTACTTGTAATAAAAATATTATATTTATAATAATAATAATAATAGAA
*
28703 AGTTTACTTAGGTTATCTAAGAGGAATATAAAAATAAGAATCTTATTGAAAGATTGAAAACAATA
66 AGTTTACTTAGGTTACCTAAGAGGAATATAAAAATAAGAATCTTATTGAAAGATTGAAAACAATA
28768 AC
131 AC
* *
28770 AAATAAAGTTTAATTATGTTACTTGTAATAAAAATATTATATTTATAATAATAATAATAA
1 AAATAAAGTTTACTTATCTTACTTGTAATAAAAATATTATATTTATAATAATAATAATAA
28830 ACAACATATT
Statistics
Matches: 178, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
129 47 0.26
130 1 0.01
131 2 0.01
132 128 0.72
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (132 bp):
AAATAAAGTTTACTTATCTTACTTGTAATAAAAATATTATATTTATAATAATAATAATAATAGAA
AGTTTACTTAGGTTACCTAAGAGGAATATAAAAATAAGAATCTTATTGAAAGATTGAAAACAATA
AC
Found at i:28844 original size:32 final size:32
Alignment explanation
Indices: 28803--28865 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
28793 TGTAATAAAA
28803 ATATTATATTTATAATAATAATAATAAACAAC
1 ATATTATATTTATAATAATAATAATAAACAAC
28835 ATATTATATTTATAATAATAATAATAAACAA
1 ATATTATATTTATAATAATAATAATAAACAA
28866 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (32 bp):
ATATTATATTTATAATAATAATAATAAACAAC
Found at i:29006 original size:20 final size:18
Alignment explanation
Indices: 28963--29006 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28953 TATATTATTT
28963 TTTAAAATTTAATAAAAA
1 TTTAAAATTTAATAAAAA
*
28981 TATTAAATTTATAATTAAAAA
1 T-TTAAAATT-TAA-TAAAAA
29002 TTTAA
1 TTTAA
29007 TAAAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 7 0.32
20 7 0.32
21 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAAATTTAATAAAAA
Found at i:41884 original size:24 final size:24
Alignment explanation
Indices: 41857--41902 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41847 CTTTTCTTAT
41857 TTTTATAATACT-TTCTTTATTTAC
1 TTTTATAATA-TATTCTTTATTTAC
*
41881 TTTTATAGTATATTCTTTATTT
1 TTTTATAATATATTCTTTATTT
41903 TTAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTATAATATATTCTTTATTTAC
Found at i:47434 original size:24 final size:25
Alignment explanation
Indices: 47397--47460 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
47387 TTGCAATATT
47397 TTTTATATATTAACTT-TAAAAAATA
1 TTTT-TATATTAACTTATAAAAAATA
* *
47422 TTTTTATATTAACTTATTAAATATA
1 TTTTTATATTAACTTATAAAAAATA
47447 -TTTT-TATTAACTTA
1 TTTTTATATTAACTTA
47461 ATTTTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 10 0.28
24 15 0.42
25 11 0.31
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTTATATTAACTTATAAAAAATA
Found at i:47454 original size:23 final size:23
Alignment explanation
Indices: 47397--47460 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
47387 TTGCAATATT
**
47397 TTTTATATATTAACTTTAAAAAATA
1 TTTT-TATATTAAC-TTATTAAATA
47422 TTTTTATATTAACTTATTAAATA
1 TTTTTATATTAACTTATTAAATA
47445 TATTTT-TATTAACTTA
1 T-TTTTATATTAACTTA
47461 ATTTTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 19 0.53
24 13 0.36
25 4 0.11
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTTATATTAACTTATTAAATA
Found at i:47472 original size:25 final size:25
Alignment explanation
Indices: 47402--47477 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
47392 ATATTTTTTA
*
47402 TATATTAAC-T-TTAAAAAATATTTT
1 TATATTAACTTATTAAATAATA-TTT
47426 TATATTAACTTATTAAAT-ATATTT
1 TATATTAACTTATTAAATAATATTT
**
47450 T-TATTAACTTAATTTTATAATATTT
1 TATATTAACTT-ATTAAATAATATTT
47475 TAT
1 TAT
47478 TTTTTATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
23 9 0.20
24 18 0.41
25 11 0.25
26 6 0.14
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATTAACTTATTAAATAATATTT
Found at i:47760 original size:31 final size:31
Alignment explanation
Indices: 47715--47785 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
47705 TTAACATGTG
* * * *
47715 GTGACTATATCTTAATTAAATAAAGACGGAA
1 GTGACCATAGCTTAATTAAATAAAAACGAAA
*
47746 GTGATCATAGCTTAATTAAATAAAAACGAAA
1 GTGACCATAGCTTAATTAAATAAAAACGAAA
47777 GTGACCATA
1 GTGACCATA
47786 TATTATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.27
Consensus pattern (31 bp):
GTGACCATAGCTTAATTAAATAAAAACGAAA
Found at i:47990 original size:4 final size:4
Alignment explanation
Indices: 47981--48010 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
47971 CAAGCAGAGT
47981 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
48011 AGTTTGTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:49229 original size:65 final size:66
Alignment explanation
Indices: 49123--49255 Score: 250
Period size: 65 Copynumber: 2.0 Consensus size: 66
49113 AATATATGAC
49123 ACTATGCCTGAATTTCCATGTTTGTGTTAGCAAAATCATTGTCATTGGAATTTAAACGTCTCTTC
1 ACTATGCCTGAATTTCCATGTTTGTGTTAGCAAAATCATTGTCATTGGAATTTAAACGTCTCTTC
49188 T
66 T
*
49189 ACTATGCTTGAATTTCCATG-TTGTGTTAGCAAAATCATTGTCATTGGAATTTAAACGTCTCTTC
1 ACTATGCCTGAATTTCCATGTTTGTGTTAGCAAAATCATTGTCATTGGAATTTAAACGTCTCTTC
49253 T
66 T
49254 AC
1 AC
49256 ATATATTTGA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 47 0.71
66 19 0.29
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (66 bp):
ACTATGCCTGAATTTCCATGTTTGTGTTAGCAAAATCATTGTCATTGGAATTTAAACGTCTCTTC
T
Found at i:56649 original size:32 final size:32
Alignment explanation
Indices: 56608--56668 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
56598 CTTTTTTGTT
* *
56608 TGAAGGTTGAAGGCCATAAATTCCATCAATGG
1 TGAAGGTTGAAGGCAACAAATTCCATCAATGG
56640 TGAAGGTTGAAGGCAACAAATTCCATCAA
1 TGAAGGTTGAAGGCAACAAATTCCATCAA
56669 CAACTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (32 bp):
TGAAGGTTGAAGGCAACAAATTCCATCAATGG
Found at i:58546 original size:3 final size:3
Alignment explanation
Indices: 58538--58571 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
58528 ATATTAACCC
58538 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
58572 TTGAGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:60420 original size:20 final size:20
Alignment explanation
Indices: 60395--60434 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
60385 AGGGGTGGTT
60395 TGCCCTAGTTTTTGTAGACC
1 TGCCCTAGTTTTTGTAGACC
*
60415 TGCCCTTGTTTTTGTAGACC
1 TGCCCTAGTTTTTGTAGACC
60435 GGGACAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.42
Consensus pattern (20 bp):
TGCCCTAGTTTTTGTAGACC
Found at i:60828 original size:26 final size:26
Alignment explanation
Indices: 60799--60862 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
60789 ATCGGAATGT
60799 CTAAGGAAAGACAACCTAATATAAGA
1 CTAAGGAAAGACAACCTAATATAAGA
* * *
60825 CTAAGTAAAGATAACCTAATATAAGG
1 CTAAGGAAAGACAACCTAATATAAGA
*
60851 TTAAGGAAAGAC
1 CTAAGGAAAGAC
60863 GCTACCAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (26 bp):
CTAAGGAAAGACAACCTAATATAAGA
Found at i:62115 original size:26 final size:26
Alignment explanation
Indices: 62086--62137 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
62076 GACGATACCG
62086 ATAAACATCATTAAAATACGATTTTA
1 ATAAACATCATTAAAATACGATTTTA
62112 ATAAACATCATTAAAATACGATTTTA
1 ATAAACATCATTAAAATACGATTTTA
62138 TCATATCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (26 bp):
ATAAACATCATTAAAATACGATTTTA
Found at i:66735 original size:35 final size:35
Alignment explanation
Indices: 66689--66764 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
66679 AAAACAGTCA
* *
66689 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
66724 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
66759 TCAATT
1 TCAATT
66765 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:67314 original size:130 final size:130
Alignment explanation
Indices: 67161--67408 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
67151 TATTTATATA
* * * ** *
67161 ATCATTTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTG
* *
67226 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
67291 ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTG
* * *
67356 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
67409 GAAGAAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:67439 original size:130 final size:129
Alignment explanation
Indices: 67175--67439 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
67165 TTTTGGTCCT
* * ** * *
67175 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCA
* *** * * **** *
67240 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
67305 AAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCA
* * * *
67370 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
67434 -A
128 CA
67435 AAATT
1 AAATT
67440 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTAAATAAATTAATCATTTAACCAGGACCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:67762 original size:28 final size:27
Alignment explanation
Indices: 67731--67793 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
67721 AGTTGATACA
*
67731 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
67759 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
67787 ATATTTT
1 ATATTTT
67794 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:67894 original size:16 final size:18
Alignment explanation
Indices: 67873--67906 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
67863 ATTTCTTATT
67873 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
67889 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
67907 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:73679 original size:29 final size:28
Alignment explanation
Indices: 73625--73686 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
73615 GGCCCCCAAT
* * ** *
73625 TTTTTTGTGTTTATAATTAGGGCCCTGA
1 TTTTTTATATTTATAATTAGACCCCTAA
73653 TTTTTTATATTTATAATTAGTACCCCTAA
1 TTTTTTATATTTATAATTAG-ACCCCTAA
73682 TTTTT
1 TTTTT
73687 ATAATTTCGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (28 bp):
TTTTTTATATTTATAATTAGACCCCTAA
Found at i:76921 original size:21 final size:21
Alignment explanation
Indices: 76895--76934 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
76885 ACCCCAATTT
76895 CAAATCTTAAA-CTCTAAACCC
1 CAAATCTTAAAGCT-TAAACCC
76916 CAAATCTTAAAGCTTAAAC
1 CAAATCTTAAAGCTTAAAC
76935 TATAACCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.25
Consensus pattern (21 bp):
CAAATCTTAAAGCTTAAACCC
Found at i:77167 original size:12 final size:13
Alignment explanation
Indices: 77144--77186 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
77134 CGTTCTGGTA
77144 ATTTTAAAATTTT
1 ATTTTAAAATTTT
77157 ATTTT-AAATTTT
1 ATTTTAAAATTTT
*
77169 AAATTTTAAAATATT
1 --ATTTTAAAATTTT
77184 ATT
1 ATT
77187 ATATTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.27
13 8 0.31
14 5 0.19
15 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTTTAAAATTTT
Found at i:80367 original size:7 final size:7
Alignment explanation
Indices: 80357--80383 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
80347 TAAAAATACT
80357 TTATTTA
1 TTATTTA
80364 TTATTTA
1 TTATTTA
80371 TTATTTA
1 TTATTTA
80378 TTATTT
1 TTATTT
80384 TCCTTTTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:82143 original size:49 final size:49
Alignment explanation
Indices: 82071--82195 Score: 206
Period size: 49 Copynumber: 2.7 Consensus size: 49
82061 GCGATTGTGA
*
82071 GAGTTGCATTACTTCTGTTTGATTGTTGGTTTCAACATGTCTGAATATG
1 GAGTTGCATTACTTCTGTTTGATTGTTGGTTTCAACATGTCTGAACATG
82120 GAGTTGCATTACTTCTGTTTGATTGTTGGTTTCAACATGTCTGAACATG
1 GAGTTGCATTACTTCTGTTTGATTGTTGGTTTCAACATGTCTGAACATG
82169 GA-----ATTACTTCTGTTTGATTGTTGGTTT
1 GAGTTGCATTACTTCTGTTTGATTGTTGGTTT
82196 TATTGAGTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
44 25 0.33
49 50 0.67
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.46
Consensus pattern (49 bp):
GAGTTGCATTACTTCTGTTTGATTGTTGGTTTCAACATGTCTGAACATG
Found at i:83337 original size:14 final size:14
Alignment explanation
Indices: 83292--83348 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
83282 TAAACTGACA
* *
83292 AATAAGATAAAATT
1 AATAAAATAATATT
* *
83306 AGTAAATATAATAAT
1 AATAAA-ATAATATT
83321 AATAATAAT-ATATT
1 AATAA-AATAATATT
83335 AATAAAATAATATT
1 AATAAAATAATATT
83349 TTTGGTAGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 3 0.09
14 18 0.53
15 12 0.35
16 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (14 bp):
AATAAAATAATATT
Found at i:85217 original size:29 final size:29
Alignment explanation
Indices: 85174--85256 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
85164 CTCACCTAAC
85174 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
85204 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
85233 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
85257 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:89984 original size:29 final size:29
Alignment explanation
Indices: 89941--90023 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
89931 CTCACCTAAC
89941 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
89971 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
90000 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
90024 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:92638 original size:31 final size:31
Alignment explanation
Indices: 92603--92663 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
92593 ATTCGTAATC
* *
92603 ACTTTTGTTTCGTTTTAATTAATATGTGGTA
1 ACTTTCGTTTCGTTTTAATTAAGATGTGGTA
92634 ACTTTCGTTTCGTTTTAATTAAGATGTGGT
1 ACTTTCGTTTCGTTTTAATTAAGATGTGGT
92664 CACGATGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
ACTTTCGTTTCGTTTTAATTAAGATGTGGTA
Found at i:98700 original size:82 final size:81
Alignment explanation
Indices: 98583--98845 Score: 364
Period size: 81 Copynumber: 3.2 Consensus size: 81
98573 TCGGGTGGTA
* ** *
98583 TTTCACCAGCAAACGGACTATCGCGTTGAATGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
1 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
*
98648 TCGTCACTAGGTGATTT
66 TCATCACTAGGTGA-TT
* * * * *
98665 TTTTACCAGCGAACGGACCATCTTGTTGGACGTCATCTCCCATTGATATTTCCGGCTCCCCTGCC
1 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
* *
98730 TCATCACTAGTTGATA
66 TCATCACTAGGTGATT
* * *
98746 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCTTCTTCCATCGATATTTCCGGCTCTCCTACC
1 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
*
98811 TCATCACCAGGTGATT
66 TCATCACTAGGTGATT
*
98827 TTTCACCGGCGAACGGACT
1 TTTCACCAGCGAACGGACT
98846 CGCTGCTTGA
Statistics
Matches: 157, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 89 0.57
82 68 0.43
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.31
Consensus pattern (81 bp):
TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
TCATCACTAGGTGATT
Found at i:100425 original size:14 final size:14
Alignment explanation
Indices: 100406--100435 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
100396 CTCTTTTGCC
100406 TGCCTTTATCTTCT
1 TGCCTTTATCTTCT
*
100420 TGCCTTTCTCTTCT
1 TGCCTTTATCTTCT
100434 TG
1 TG
100436 TTGTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.30, G:0.10, T:0.57
Consensus pattern (14 bp):
TGCCTTTATCTTCT
Found at i:109497 original size:8 final size:8
Alignment explanation
Indices: 109484--109524 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
109474 CTCATTTTCA
109484 GAGAATTT
1 GAGAATTT
109492 GAGAATTT
1 GAGAATTT
*
109500 -AGAGTTT
1 GAGAATTT
*
109507 GGGAATTT
1 GAGAATTT
109515 GAGAATTT
1 GAGAATTT
109523 GA
1 GA
109525 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:109915 original size:128 final size:128
Alignment explanation
Indices: 109592--110341 Score: 1336
Period size: 128 Copynumber: 5.9 Consensus size: 128
109582 TAATCGGAGT
*
109592 ACTATTCATATGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTTGTCA-AGAATATG-TAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* * * *
109653 AATTACCCTATTA--TCACTCATGTCCCTCGGGAACACTA-ATATATCAGTAACTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
109713 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTTGTCAGAAAATATGTTA
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTTTGTCAGAGAATATGTTA
109778 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
109842 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* * *
109907 CATTGCCCTATTATATCACTGATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
109970 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGC-CCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
110034 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
110097 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
110162 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
110225 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
110290 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
110342 AATCAGGTAA
Statistics
Matches: 605, Mismatches: 15, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
121 23 0.04
122 4 0.01
123 13 0.02
124 8 0.01
125 7 0.01
126 14 0.02
127 124 0.20
128 347 0.57
129 65 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:110063 original size:255 final size:255
Alignment explanation
Indices: 109592--110341 Score: 1325
Period size: 255 Copynumber: 3.0 Consensus size: 255
109582 TAATCGGAGT
* * *
109592 ACTATTCATATGAAGGCGCGTTCCCGGGG-GCGCCTTCCATTATTTTGTCA-AGAATATG-TATA
1 ACTATTCACATGAAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATC
* * *
109654 ATTACCCTA-T-TATCACTCATGTCCCTCGGGAACACTA-ATATATCAGTAACTATTATTTCACT
66 ATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
* *
109716 ATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTTGTCAGAAAATATGTTATCA
131 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTA-TTTTGTCAGAGAATATGTTATCA
109781 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
195 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
109842 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTC-CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
109907 CATTGCCCTATTATATCACTGATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCAC
65 CATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
109972 TATTCACATGAAGGCGCGTTCCCGGGGGCGC-CCTTCCATTATTTTGTCAGAGAATATGTTATCA
130 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
110036 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
195 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
110097 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
110162 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
65 CATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
110227 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
130 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
110292 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
195 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
110342 AATCAGGTAA
Statistics
Matches: 478, Mismatches: 13, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
250 22 0.05
251 5 0.01
252 21 0.04
253 8 0.02
254 11 0.02
255 240 0.50
256 119 0.25
257 52 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (255 bp):
ACTATTCACATGAAGGCGCGTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATC
ATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:110616 original size:14 final size:14
Alignment explanation
Indices: 110597--110626 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
110587 CATAAGTTAA
*
110597 TTTTAATGTATATG
1 TTTTAATATATATG
110611 TTTTAATATATATG
1 TTTTAATATATATG
110625 TT
1 TT
110627 AATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:110802 original size:33 final size:34
Alignment explanation
Indices: 110741--110840 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
110731 AAATTTAATG
*
110741 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
110775 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
110808 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
110841 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:111384 original size:21 final size:21
Alignment explanation
Indices: 111354--111441 Score: 124
Period size: 21 Copynumber: 4.2 Consensus size: 21
111344 TATGGTATAA
*
111354 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
111375 AA-CCTAGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
111396 AATCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
111417 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
111438 AACC
1 AACC
111442 TGTGGAGATG
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.05
21 56 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:113236 original size:14 final size:14
Alignment explanation
Indices: 113219--113254 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
113209 TTTTAATAAA
*
113219 AAATATATTTACAT
1 AAATATATTAACAT
*
113233 AAATATATTAATAT
1 AAATATATTAACAT
113247 AAATATAT
1 AAATATAT
113255 AACTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATATTAACAT
Done.