Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001686.1 Hibiscus syriacus cultivar Beakdansim tig00003365_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: 80468
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:4451 original size:27 final size:28
Alignment explanation
Indices: 4420--4472 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
4410 ATTTCAAACA
*
4420 TATATTATCTT-ATAATATTT-TATAATT
1 TATATTATATTAAT-ATATTTATATAATT
4447 TATATTATATTAATATATTTATATAA
1 TATATTATATTAATATATTTATATAA
4473 AATAAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TATATTATATTAATATATTTATATAATT
Found at i:6147 original size:20 final size:21
Alignment explanation
Indices: 6122--6173 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
6112 AACCAACAAA
6122 TTCGCAACGCGA-ATTCCAAT
1 TTCGCAACGCGAGATTCCAAT
* *
6142 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAGATTCCAAT
6162 TTCGCAACGCGA
1 TTCGCAACGCGA
6174 TAGTCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAGATTCCAAT
Found at i:6185 original size:20 final size:20
Alignment explanation
Indices: 6162--6283 Score: 90
Period size: 20 Copynumber: 6.0 Consensus size: 20
6152 AGTTTCCAAT
6162 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* **
6182 TTCGC-GCTGCGATTTTTCAAA
1 TTCGCAAC-GCGA-TAGTCAAA
* *
6203 TTCGCAACGGGAATTTGT-AAA
1 TTCGCAACGCG-A-TAGTCAAA
*
6224 -TCGCAACACAGA-AGTCAAA
1 TTCGCAACGC-GATAGTCAAA
*
6243 TTCGCAACGCGATAGTGAAA
1 TTCGCAACGCGATAGTCAAA
* *
6263 TTTGCAACGCGAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
6283 T
1 T
6284 GTTTTTACGC
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 49 0.61
21 17 0.21
22 6 0.08
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:6429 original size:22 final size:22
Alignment explanation
Indices: 6404--6457 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
6394 TCACTCTCTA
*
6404 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
* *
6426 CGACGAAATTCGTCCCCATTTC
1 CGACGAAATCCGTCCCCATCTC
6448 CGACGAAATC
1 CGACGAAATC
6458 TGTCTATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:6759 original size:19 final size:20
Alignment explanation
Indices: 6719--6761 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6709 CACACCAAAT
*
6719 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
6739 TCGCAACACGAAACT-AAAA
1 TCGCAACACGAAAATGAAAA
6758 TCGC
1 TCGC
6762 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:6799 original size:20 final size:20
Alignment explanation
Indices: 6758--6799 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6748 GAAACTAAAA
* * *
6758 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
6778 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
6798 TC
1 TC
6800 AGAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:10024 original size:24 final size:24
Alignment explanation
Indices: 9973--10024 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
9963 ATCTGAGTAT
** *
9973 TGACCAAGATCAAATTCCGGGTAT
1 TGACCAAGATCAAATTCCGAATAC
**
9997 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAATTCCGAATAC
10021 TGAC
1 TGAC
10025 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAATTCCGAATAC
Found at i:10927 original size:19 final size:19
Alignment explanation
Indices: 10903--10953 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
10893 ACTAAAACCG
10903 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
10922 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
10941 GTTGCGAATTTGA
1 GTTGCGAATTTGA
10954 CTTTCGCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:10967 original size:20 final size:20
Alignment explanation
Indices: 10942--10992 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
10932 TGAAATTCAG
*
10942 TTGCGAATTTGACTTTCGCA
1 TTGCGAATTTGACTATCGCA
*
10962 TTGCGAATTTGACTATCGCT
1 TTGCGAATTTGACTATCGCA
10982 TTGCGAATTTG
1 TTGCGAATTTG
10993 GAAAATCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCA
Found at i:11065 original size:20 final size:21
Alignment explanation
Indices: 11016--11069 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
11006 TGATTTACAT
*
11016 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTAGAA
*
11037 ATT-GGGTTGCGAAATTAG-A
1 ATTCGCGTTGCGAAATTAGAA
11056 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
11070 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 22 0.76
21 3 0.10
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTAGAA
Found at i:12158 original size:13 final size:13
Alignment explanation
Indices: 12131--12172 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
12121 AGGGTCTATT
12131 TGTTTTACTGAAAA
1 TGTTTT-CTGAAAA
12145 TGTTTT-TGGAAAA
1 TGTTTTCT-GAAAA
12158 TGTTTTCTGAAAA
1 TGTTTTCTGAAAA
12171 TG
1 TG
12173 AATTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.04
13 18 0.69
14 7 0.27
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (13 bp):
TGTTTTCTGAAAA
Found at i:12283 original size:14 final size:13
Alignment explanation
Indices: 12266--12312 Score: 62
Period size: 12 Copynumber: 3.7 Consensus size: 13
12256 GCAAATTTTC
12266 TATAAATTATTTAT
1 TATAAA-TATTTAT
12280 TATAAATATTT-T
1 TATAAATATTTAT
*
12292 TATTAA-ATTTAT
1 TATAAATATTTAT
12304 TATAAATAT
1 TATAAATAT
12313 CAAATACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 4 0.14
12 12 0.41
13 7 0.24
14 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATAAATATTTAT
Found at i:12298 original size:27 final size:24
Alignment explanation
Indices: 12260--12312 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
12250 CAAATGGCAA
12260 ATTTTCTATAAATTATTTATTATAAAT
1 ATTTTCTAT-AA--ATTTATTATAAAT
12287 ATTTT-TATTAAATTTATTATAAAT
1 ATTTTCTA-TAAATTTATTATAAAT
12311 AT
1 AT
12313 CAAATACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 15 0.60
26 4 0.16
27 6 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTCTATAAATTTATTATAAAT
Found at i:17099 original size:15 final size:15
Alignment explanation
Indices: 17079--17107 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17069 ATATCCTACG
17079 ATATTTCATTGACAT
1 ATATTTCATTGACAT
17094 ATATTTCATTGACA
1 ATATTTCATTGACA
17108 CTCTTGTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (15 bp):
ATATTTCATTGACAT
Found at i:18646 original size:18 final size:18
Alignment explanation
Indices: 18623--18694 Score: 108
Period size: 18 Copynumber: 4.0 Consensus size: 18
18613 ACTGAATATT
*
18623 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
18641 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
*
18659 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
18677 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
18695 ATAATCCCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:22546 original size:15 final size:16
Alignment explanation
Indices: 22528--22557 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22518 ATATTAATCA
22528 AAATA-ACAAAAATTT
1 AAATATACAAAAATTT
22543 AAATATACAAAAATT
1 AAATATACAAAAATT
22558 AAAAATTAAA
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:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATACAAAAATTT
Found at i:24827 original size:3 final size:3
Alignment explanation
Indices: 24819--24882 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
24809 AATTTTTCGT
** * *
24819 TTA TTA TTA TTA AAA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
24867 TTA TTAA ATA TTA TTA
1 TTA TT-A TTA TTA TTA
24883 CAAGCCCAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 48 0.96
4 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:24839 original size:15 final size:15
Alignment explanation
Indices: 24819--24882 Score: 82
Period size: 15 Copynumber: 4.4 Consensus size: 15
24809 AATTTTTCGT
24819 TTATTATTATTAAAA
1 TTATTATTATTAAAA
24834 TTATTATTATTATAAA
1 TTATTATTATTA-AAA
24850 -TATTATTATT---A
1 TTATTATTATTAAAA
24861 TTATTATTATTAAATA
1 TTATTATTATTAAA-A
24877 TTATTA
1 TTATTA
24883 CAAGCCCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
11 1 0.02
12 10 0.23
15 22 0.51
16 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTATTATTAAAA
Found at i:26174 original size:3 final size:3
Alignment explanation
Indices: 26161--26218 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
26151 TTATTTGCAA
*
26161 TAT TAT T-T TAT TAT TAT TAT T-T T-T TAAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
*
26203 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
26219 TATATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 7 0.15
3 38 0.81
4 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:26180 original size:14 final size:14
Alignment explanation
Indices: 26161--26218 Score: 82
Period size: 14 Copynumber: 4.1 Consensus size: 14
26151 TTATTTGCAA
26161 TATTATTTTATTAT
1 TATTATTTTATTAT
26175 TATTATTTT-TTAAT
1 TATTATTTTATT-AT
*
26189 TATTATTTCATTAT
1 TATTATTTTATTAT
26203 TATTATTTTTATTAT
1 TATTA-TTTTATTAT
26218 T
1 T
26219 TATATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.05
14 26 0.67
15 11 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:26490 original size:105 final size:104
Alignment explanation
Indices: 26295--26493 Score: 253
Period size: 105 Copynumber: 1.9 Consensus size: 104
26285 TTAATAGTCA
* *
26295 TATTTTAATATATATTTATTATATTAAGAAAAGGCCTGTCTTAAAGCACCTAGAAGTCTGTTTTC
1 TATTTTAATATATATTTATTATATAAAGAAAAGGCCTGTCTTAAAGCACCTAGAAGTCTCTTTTC
* * **
26360 TGATATTTTTATTAAATATCCTATTTTATAAATTATAAT
66 TGATATTTTAAATAAATATAATATTTTATAAATTATAAT
* *
26399 TATTTTAATTATTTATTTATTAATATCAAAGAAAAGAG-CTGT-TTAAGGCACCTAGAAGTC-CT
1 TATTTTAA-TATATATTTATT-ATAT-AAAGAAAAG-GCCTGTCTTAAAGCACCTAGAAGTCTCT
26461 TTTCTGATATTTCTAAATAAATA-AATATTTTAT
62 TTTCTGATATTT-TAAATAAATATAATATTTTAT
26494 TTATAAATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
104 8 0.10
105 32 0.39
106 29 0.35
107 12 0.15
108 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.45
Consensus pattern (104 bp):
TATTTTAATATATATTTATTATATAAAGAAAAGGCCTGTCTTAAAGCACCTAGAAGTCTCTTTTC
TGATATTTTAAATAAATATAATATTTTATAAATTATAAT
Found at i:26526 original size:27 final size:29
Alignment explanation
Indices: 26477--26531 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
26467 ATATTTCTAA
*
26477 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTATTCATAAATATAT
* *
26506 ATAAATTAAT-TTTT-TTCATAATTATA
1 ATAAATAAATATTTTATTCATAAATATA
26532 ATTTTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 4 0.17
29 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTATTCATAAATATAT
Found at i:29155 original size:14 final size:15
Alignment explanation
Indices: 29138--29175 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
29128 CATTACACAG
29138 TTTGCATTCTT-ATT
1 TTTGCATTCTTCATT
*
29152 TTTGCATTTTTGCATT
1 TTTGCATTCTT-CATT
29168 TTTGCATT
1 TTTGCATT
29176 TACATTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
16 11 0.52
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (15 bp):
TTTGCATTCTTCATT
Found at i:29169 original size:7 final size:8
Alignment explanation
Indices: 29149--29176 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
29139 TTGCATTCTT
29149 ATTTTTGC
1 ATTTTTGC
29157 ATTTTTGC
1 ATTTTTGC
29165 ATTTTTGC
1 ATTTTTGC
29173 ATTT
1 ATTT
29177 ACATTACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (8 bp):
ATTTTTGC
Found at i:33499 original size:114 final size:114
Alignment explanation
Indices: 33299--33636 Score: 577
Period size: 114 Copynumber: 3.0 Consensus size: 114
33289 GTGTCATGTT
33299 CTCGTAGTAGAAATAAGGAGGCCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGGCCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
33364 GTTCGGTAGGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
66 GTTCGGTAGGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
* *
33413 CTCGTAGTAGAAATAATGAGGCCCAATAGCATTTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGGCCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
33478 GTTCGGTAGGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTG
66 GTTCGGTAGGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
* * * * * *
33527 CCCATAGCAGAAATAAGGAGTCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGGCCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
33592 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTAAAAGATGAA
66 GTTCGGTAGGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
33637 CTGCATGATC
Statistics
Matches: 210, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 210 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (114 bp):
CTCGTAGTAGAAATAAGGAGGCCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTCGGTAGGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTG
Found at i:35745 original size:54 final size:54
Alignment explanation
Indices: 35683--35840 Score: 182
Period size: 54 Copynumber: 3.0 Consensus size: 54
35673 TAATTGAGAA
*
35683 ATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * * * *
35737 ATCTGAGCATAAGCTACAAGAAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
35790 -T-TGA-CAGAAACCACAGGAAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACA-AAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
35841 CAGTGATTAT
Statistics
Matches: 86, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
50 31 0.36
51 8 0.09
52 1 0.01
53 2 0.02
54 44 0.51
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:36235 original size:22 final size:22
Alignment explanation
Indices: 36202--36261 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
36192 TCTACATCTA
*
36202 CACTCTTCAAAGATGATAGATT
1 CACTTTTCAAAGATGATAGATT
*
36224 CACTTTTTAAAGATGATAGATT
1 CACTTTTCAAAGATGATAGATT
*
36246 CTCTTTTCAAAGATGA
1 CACTTTTCAAAGATGA
36262 AAGCTTTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (22 bp):
CACTTTTCAAAGATGATAGATT
Found at i:37077 original size:165 final size:167
Alignment explanation
Indices: 36776--37101 Score: 496
Period size: 165 Copynumber: 2.0 Consensus size: 167
36766 AAAATGAGCA
*
36776 TTATCTTCAGATTGGGTCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACA
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACA
* ** * *
36841 ATTTTCATAGTTTCTCATTTTATTTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
*
36906 CTTAG-TTTTTTACTTAGTAAACTATTTCCAACAGCC
131 CTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
* * ** * *
36942 TTATCTTGAGATTGGGGCATGTTACCCAATCAAGATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACA
37005 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
37070 CCTTAGTTTTTTTTACTTAATAAACTATTTCC
130 CCTTAG-TTTTTTTACTTAATAAACTATTTCC
37102 CACATCTGTA
Statistics
Matches: 144, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
164 38 0.26
165 43 0.30
166 40 0.28
167 23 0.16
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (167 bp):
TTATCTTCAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACA
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAGTTTTTTTACTTAATAAACTATTTCCAACAGCC
Found at i:37191 original size:76 final size:76
Alignment explanation
Indices: 37104--37321 Score: 409
Period size: 76 Copynumber: 2.9 Consensus size: 76
37094 CTATTTCCCA
*
37104 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37169 AACCTTAGGGT
66 AACCTTAGGGT
*
37180 CATTTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37245 AACCTTAGGGT
66 AACCTTAGGGT
*
37256 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37321 A
66 A
37322 GCCCTTCAGT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 138 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTAGGGT
Found at i:37498 original size:3 final size:3
Alignment explanation
Indices: 37490--37550 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
37480 AATTTTTCGT
** * *
37490 TTA TTA TTA TTA AAA TTA TTA TTA TTA TAA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
37538 TTAA ATA TTA TTA
1 TT-A TTA TTA TTA
37551 CAAGCCCAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:37539 original size:15 final size:15
Alignment explanation
Indices: 37490--37540 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
37480 AATTTTTCGT
*
37490 TTATTATTATTAAAA
1 TTATTATTATTATAA
37505 TTATTATTATTATAA
1 TTATTATTATTATAA
* *
37520 ATATTATTATTATTA
1 TTATTATTATTATAA
37535 TTATTA
1 TTATTA
37541 AATATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTATTATAA
Found at i:38842 original size:3 final size:3
Alignment explanation
Indices: 38829--38886 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
38819 TTATTTACAA
*
38829 TAT TAT T-T TAT TAT TAT TAT T-T T-T TAAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
*
38871 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
38887 TATATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 7 0.15
3 38 0.81
4 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:38848 original size:14 final size:14
Alignment explanation
Indices: 38829--38886 Score: 82
Period size: 14 Copynumber: 4.1 Consensus size: 14
38819 TTATTTACAA
38829 TATTATTTTATTAT
1 TATTATTTTATTAT
38843 TATTATTTT-TTAAT
1 TATTATTTTATT-AT
*
38857 TATTATTTCATTAT
1 TATTATTTTATTAT
38871 TATTATTTTTATTAT
1 TATTA-TTTTATTAT
38886 T
1 T
38887 TATATAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.05
14 26 0.67
15 11 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:39195 original size:27 final size:29
Alignment explanation
Indices: 39146--39200 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 29
39136 ATATTTCTAA
*
39146 ATAAATAAATATTTTATTTATAAATATAT
1 ATAAATAAATATTTTATTCATAAATATAT
* *
39175 ATAAATTAAT-TTTT-TTCATAATTATA
1 ATAAATAAATATTTTATTCATAAATATA
39201 ATTTTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 4 0.17
29 9 0.39
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTATTCATAAATATAT
Found at i:41016 original size:15 final size:15
Alignment explanation
Indices: 40996--41050 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
40986 ATTTTCTAAA
40996 ATATTTATATCAAAT
1 ATATTTATATCAAAT
***
41011 ATATTTATATGGGAT
1 ATATTTATATCAAAT
41026 ATATTTATATCAAAT
1 ATATTTATATCAAAT
*
41041 ATATTCATAT
1 ATATTTATAT
41051 GGGAGGGACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (15 bp):
ATATTTATATCAAAT
Found at i:41032 original size:30 final size:30
Alignment explanation
Indices: 40996--41054 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
40986 ATTTTCTAAA
*
40996 ATATTTATATCAAATATATTTATATGGGAT
1 ATATTTATATCAAATATATTCATATGGGAT
41026 ATATTTATATCAAATATATTCATATGGGA
1 ATATTTATATCAAATATATTCATATGGGA
41055 GGGACAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (30 bp):
ATATTTATATCAAATATATTCATATGGGAT
Found at i:42758 original size:14 final size:14
Alignment explanation
Indices: 42737--42792 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
42727 CGTTTCTTTC
*
42737 TATATGCAGAGATT
1 TATATGCAGGGATT
*
42751 TGTATGCAGGGATT
1 TATATGCAGGGATT
*
42765 TATTTGCAGGGATT
1 TATATGCAGGGATT
*
42779 TATTTGCAGGGATT
1 TATATGCAGGGATT
42793 ACTCCCCGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.25, C:0.07, G:0.29, T:0.39
Consensus pattern (14 bp):
TATATGCAGGGATT
Found at i:46345 original size:81 final size:80
Alignment explanation
Indices: 46205--46452 Score: 361
Period size: 81 Copynumber: 3.1 Consensus size: 80
46195 ACTTTTCATA
* *
46205 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGGCATAATTGACATCTTTCTACCAATTGCAC
1 TTTTACTCAGC-GTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
46270 AGTTAGGCCATTATTC
65 AGTTAGGCCATTATTC
* * *
46286 TTTTACTCAACAGTCTTTAACCGTTCATCTAATTGGCATAATTGACCCCTTTCTGCCAATTGCAC
1 TTTTACTCAGC-GTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
*
46351 AGTTAAGCCATTATTC
65 AGTTAGGCCATTATTC
* * * * *
46367 TTTTATTCAGCGATCTTTAATCGTTTATCTAACTGGCATAATTGACACATTTCTGTCAATTGCAC
1 TTTTACTCAGCG-TCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCAC
*
46432 AGTTAGACCATTATTC
65 AGTTAGGCCATTATTC
46448 TTTTA
1 TTTTA
46453 TTTTGGACTA
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
80 1 0.01
81 148 0.99
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (80 bp):
TTTTACTCAGCGTCTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCACA
GTTAGGCCATTATTC
Found at i:48929 original size:54 final size:54
Alignment explanation
Indices: 46593--48927 Score: 3242
Period size: 54 Copynumber: 43.2 Consensus size: 54
46583 TATTAAGACT
* * * **
46593 CACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCCGTGGATTTG
1 CACACTTAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTCCGT-GAAATG
* *
46648 CACACATAGTGTC-TGTACGGTTATTCATCAACTCATGATGAATTCTGTGAAATG
1 CACACTTAGTG-CATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
46702 CACACTTAGTGCATATACGGTTATTCATCAACTCATGATTAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * *
46756 CACACTTAATGCATATACGGTTATTCATCAACTAATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
46810 CACACTTAGTTCATGTACGGTTATTCATCAACTCATGATGAATTCCATGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
46864 CACACTTAGTGCCTGTACGATTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
46918 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * * **
46972 CACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTTCATGGAACA
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
47026 CACACTTAGTGTATGTACGGTTATTCATCAACTCATGATGAATTCCGTTG-AATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCG-TGAAATG
* * * ** * *
47080 TACACTTAGTGCCTTTACAATTATTCATCAACTCATGATGAATTTCGTGAAATA
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
47134 CACACTTAGTGCATGTACGGTGATTCATCAACTCATGACGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * * *
47188 TACACTTAATGCATTTACGGTTATTCATCAACTCATGACGAATTCTGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
47242 CACACTTAGTGTATGTACGGTTATTCATCAACTCATGATGAATTTCGGGGAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * *
47296 CACACTTAGTGCCTTTACGGTTATTCATCAACTCATGATGAATTTCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * * *
47350 CACACTTAGTTCATGTATGGTTATTCATCAACTCATGATAAATTCCCTGAAATA
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
47404 CACACTTAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
47458 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * * *
47512 CACACTTAGTGCTTGTATGGTTATTCATCAACTCATGATGAATTTCGTGGAACG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
47566 CACCCTTAGTACTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * *
47620 CACACTTAGTGTC-TTTACGATTATTCATCAACTCATGATGAATTTCGTGAAATG
1 CACACTTAGTG-CATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
47674 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGACGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * **
47728 TACACTTAATGCATGTACTATTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * ** *
47782 AACACTTAGTGCATGTACGGTTATTCATCAACTCATGACGAATTATGTTAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * * *
47836 TACACTTAGTGCCTGTACGGTTATTTATCAACTCATGACGAATTCCATGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
** * *
47890 CACACTTAGTGTTTGTACGGTTATTCATCAACTCATGATGAATTCCATAAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
47944 CACACTTAATGCATGTACGATTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
47998 CACACTTAGTGCAAGTACGGTGATTCATCAACTCATGATAAATTCCCTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* ** * *
48052 CACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTTTGTGGAACG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
48106 CAAACTTAGTG-ATTGTACGGTTATTCATCAACTTAGGATGAATTCCGTGGAATG
1 CACACTTAGTGCA-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * * * * *
48160 CTCACTTAGTGCCTTTATGATTATTCATCAACTCATGATGAATTTCGTGAAATA
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
48214 CACACTTAGTGTATGTACGGTTATTCATCAACTCATGACGAATTCTGTTAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
48268 TACACTTAGTGCCTGTACGGTTATTTATCAACTCATGACGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
48322 CACACTTAGTGTC-TGTACGGTTATTCATCAACTCATGATGAATTTCGTGGAATG
1 CACACTTAGTG-CATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
48376 CACACTTAGTGCCTTTACAGTTATTCATCAACTCATGATGAATTCTGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
48430 CACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * *
48484 CACACTTAGTGTATGTACGGTTACTCAACAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
48538 CACACTTAGTGTATGTACGGTTATTCATCAACTCATGATGAATTCCATGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
** * * *
48592 CACACTTAGTGTTTGTACGATTATTCATCAACTCATGATGAATTCCATGGAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
48646 CACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
48700 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * *
48754 CACACTTAGTGCCTTTACGGTTATTCATCAACTCATGATGAATTCTGTGAAGTG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * *
48808 CATACTTAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * * * * *
48862 CACATTTAGTGCCTGTACGGTTATTCATTAACTCACGGTGAATTTCGTGAAATG
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
48916 CACACTTAGTGC
1 CACACTTAGTGC
48928 CTATTTGGTA
Statistics
Matches: 2035, Mismatches: 234, Indels: 23
0.89 0.10 0.01
Matches are distributed among these distances:
53 5 0.00
54 1983 0.97
55 44 0.02
56 3 0.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (54 bp):
CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
Found at i:52579 original size:2 final size:2
Alignment explanation
Indices: 52572--52602 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52562 TATTGTACAT
52572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52603 CACTCATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52919 original size:81 final size:81
Alignment explanation
Indices: 52775--53021 Score: 370
Period size: 81 Copynumber: 3.1 Consensus size: 81
52765 ACTTTTCATA
* * * * *
52775 TTTTACTCAGCGGTCTTTAACTGTTCATCTAACTGGCATAATTGACACATTTCTTCCAGTTGCAC
1 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAATTGCAC
52840 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
* * * *
52856 TTTTACTCAACGGTCTTTAACCGTTCATCTAATTGACATAATTGACCCCTTTCTGCCAATTGCAA
1 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAATTGCAC
*
52921 AGTTAGACCATTATTC
66 AGTTAGGCCATTATTC
* * *
52937 TTTTATTCAGCGGTATTTAACCGTTCATCTAACTGACATAATTGACACCTTT-TGTCAATTGCAC
1 TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAATTGCAC
53001 AGTTAGGCCATTATTC
66 AGTTAGGCCATTATTC
53017 TTTTA
1 TTTTA
53022 TTTTGGACTA
Statistics
Matches: 148, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
80 30 0.20
81 118 0.80
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (81 bp):
TTTTACTCAGCGGTCTTTAACCGTTCATCTAACTGACATAATTGACACCTTTCTGCCAATTGCAC
AGTTAGGCCATTATTC
Found at i:53297 original size:54 final size:53
Alignment explanation
Indices: 53162--53652 Score: 680
Period size: 54 Copynumber: 9.1 Consensus size: 53
53152 TATTAAGACT
* * **
53162 CACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCCGTGGATTTG
1 CACACTTAGTG-CTGTACGGTTA-TTCATCAACTCATGATGAATTCCGT-GAAATG
*
53217 CACACATAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTG-CTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
53271 CACACTTAGTGCATATACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGC-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* *
53325 CACACTGAGTGTCTGTACGGTTATTCATCAACTAATGATGAATTCCGTGAAATG
1 CACACTTAGTG-CTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * *
53379 CGCACTTAGTTCATGTACGGTTATTCATCAACTCATGATGAATTCCATGAAATG
1 CACACTTAGTGC-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
53433 CACACTTAGTGTCTGTACGGTTATTCATCAACTCATGATGAATTCCGT-AGAATG
1 CACACTTAGTG-CTGTACGGTTATTCATCAACTCATGATGAATTCCGTGA-AATG
*
53487 CACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGAATG
1 CACACTTAGTG-CTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
* * ** * * *
53541 CACACTTAGTTCCTTTATAGTTATTCATCAACTCAGGATGAATTTCATGAAATG
1 CACACTTAG-TGCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
*
53595 CACACTTAGTGCATGTATGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
1 CACACTTAGTGC-TGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
53649 CACA
1 CACA
53653 GTTAATGCCT
Statistics
Matches: 393, Mismatches: 34, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
53 5 0.01
54 341 0.87
55 45 0.11
56 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (53 bp):
CACACTTAGTGCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAAATG
Found at i:54964 original size:15 final size:16
Alignment explanation
Indices: 54924--54964 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
54914 TCACCCCATA
54924 AAAT-TATAAATGATT
1 AAATATATAAATGATT
54939 -AATATATTAAAT-ATT
1 AAATATA-TAAATGATT
54954 AAATATATAAA
1 AAATATATAAA
54965 AAAATTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.13
15 9 0.39
16 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATATATAAATGATT
Found at i:55488 original size:19 final size:19
Alignment explanation
Indices: 55448--55489 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
55438 TCTAATATTT
* *
55448 TATAAAATAATACAATACA
1 TATAAAATAATAAAATAAA
55467 TATAAAAT-ATAAAATAAAA
1 TATAAAATAATAAAAT-AAA
55486 TATA
1 TATA
55490 TATCAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
TATAAAATAATAAAATAAA
Found at i:56758 original size:21 final size:21
Alignment explanation
Indices: 56742--56795 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
56732 GCGTTGCATT
56742 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
56763 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
56784 TCGCGTTGCGAT
1 TCGCGTTGCGAT
56796 GGTCTACAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGGAAA
Found at i:56894 original size:20 final size:20
Alignment explanation
Indices: 56874--56979 Score: 115
Period size: 20 Copynumber: 5.2 Consensus size: 20
56864 AAATCGTAAT
*
56874 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
*
56894 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* *
56914 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
56935 GAGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
56955 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
56975 GCGAT
1 GCGAT
56980 TTACATAGCG
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.03
20 57 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:57571 original size:19 final size:19
Alignment explanation
Indices: 57532--57572 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
57522 GCAACGAGAG
*
57532 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
57551 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
57570 AAT
1 AAT
57573 TGCATTGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:57599 original size:19 final size:19
Alignment explanation
Indices: 57577--57717 Score: 104
Period size: 19 Copynumber: 7.8 Consensus size: 19
57567 CAAAATTGCA
57577 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
57596 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
57615 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
* **
57629 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
57648 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
** *
57662 TTGCGATAGTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCG
* *
57682 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
57702 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
57718 AACCAAAAGA
Statistics
Matches: 95, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
14 19 0.20
16 4 0.04
17 5 0.05
19 37 0.39
20 29 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:57642 original size:33 final size:33
Alignment explanation
Indices: 57605--57692 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
57595 GTTGCGATTT
57605 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
57638 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
57671 TCATTTCCGCATTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
57693 ATTATCTCGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 38 0.73
34 14 0.27
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:57694 original size:20 final size:19
Alignment explanation
Indices: 57657--57717 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
57647 GTTGCGATTC
**
57657 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATTCTCATT
57676 TC-CGCATTGCGATTCTCATT
1 TCTCG--TTGCGATTCTCATT
*
57696 ATCTCGTTGCGATTTTCATT
1 -TCTCGTTGCGATTCTCATT
57716 TC
1 TC
57718 AACCAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 25 0.71
21 2 0.06
22 2 0.06
ACGTcount: A:0.15, C:0.25, G:0.16, T:0.44
Consensus pattern (19 bp):
TCTCGTTGCGATTCTCATT
Found at i:59483 original size:13 final size:13
Alignment explanation
Indices: 59465--59491 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59455 GAAGTTAGTA
59465 TTTGTCTTTTTGT
1 TTTGTCTTTTTGT
59478 TTTGTCTTTTTGT
1 TTTGTCTTTTTGT
59491 T
1 T
59492 GAAGTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.15, T:0.78
Consensus pattern (13 bp):
TTTGTCTTTTTGT
Found at i:59897 original size:42 final size:41
Alignment explanation
Indices: 59790--59959 Score: 175
Period size: 42 Copynumber: 4.1 Consensus size: 41
59780 CCCACTATCG
*
59790 AAGAGGCCCCTATAATTCC-CGAGAGTCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCTCCCACCGTTC
* * * * * *
59830 AAGAGGCCACTGTCA-TCCTCAAGAGTCCACTCCTATCGTTG
1 AAGAGGCCCCTATCATTCCTCGAGAGTCC-CTCCCACCGTTC
59871 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGT-CCCTCCCACCGTTC
* * * * *
59913 AAGAGGCCACTGTCA-TCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCTCCCACCGTTC
59955 AAGAG
1 AAGAG
59960 CTCGATTCAC
Statistics
Matches: 106, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
39 3 0.03
40 20 0.19
41 26 0.25
42 53 0.50
43 4 0.04
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (41 bp):
AAGAGGCCCCTATCATTCCTCGAGAGTCCCTCCCACCGTTC
Found at i:59917 original size:21 final size:21
Alignment explanation
Indices: 59893--59959 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
59883 TCATTCCTCG
59893 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
59914 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
59935 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
59956 AGAG
1 AGAG
59960 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:61336 original size:14 final size:14
Alignment explanation
Indices: 61317--61352 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
61307 ATTGTTTAAT
61317 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
61331 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
61345 TGATTTGT
1 TGATTTGT
61353 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:61496 original size:14 final size:14
Alignment explanation
Indices: 61477--61533 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
61467 GCGAAATGAA
61477 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
61491 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
61510 AATCGCAACGAGAG
1 AATCGCAACGAGAG
61524 AATCGCAACG
1 AATCGCAACG
61534 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:61509 original size:33 final size:33
Alignment explanation
Indices: 61467--61548 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
61457 CTATCGAAAT
61467 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
61500 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
* *
61533 GCGAAATTAAATTCGC
1 GCGAAATGAAAATCGC
61549 GTTGCGATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
Found at i:61515 original size:19 final size:19
Alignment explanation
Indices: 61467--61519 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
61457 CTATCGAAAT
61467 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
*
61485 -CG--A-GAGAATCGCAAC
1 GCGAAATGAAAATCGCAAC
61500 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
61519 G
1 G
61520 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 10 0.36
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 12 0.43
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.09
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:61584 original size:33 final size:33
Alignment explanation
Indices: 61541--61640 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 33
61531 ACGCGAAATT
61541 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
61574 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
61607 -ATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATTGCG
61640 A
1 A
61641 TAGTAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 2 0.03
33 59 0.97
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (33 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:61607 original size:19 final size:19
Alignment explanation
Indices: 61544--61660 Score: 83
Period size: 19 Copynumber: 6.7 Consensus size: 19
61534 CGAAATTAAA
*
61544 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
61563 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
61577 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
61596 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
61612 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
61629 TTCGCATTGCGATAGTAAT
1 TTCGCATTGCGATTTTCAT
*
61648 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
61661 AGACATTAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
14 17 0.23
16 7 0.09
17 7 0.09
19 44 0.59
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:63945 original size:12 final size:12
Alignment explanation
Indices: 63928--63952 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63918 TCTTCGGGGA
63928 CTTTTTCTTCTT
1 CTTTTTCTTCTT
63940 CTTTTTCTTCTT
1 CTTTTTCTTCTT
63952 C
1 C
63953 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:64161 original size:24 final size:24
Alignment explanation
Indices: 64127--64180 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
64117 CTGCAACATC
*
64127 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
64151 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
64175 ATCAAA
1 ATCAAA
64181 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:64194 original size:24 final size:24
Alignment explanation
Indices: 64127--64194 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
64117 CTGCAACATC
* * * *
64127 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAGTCCGAATACTGACCAAG
* *
64151 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
64175 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
64195 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:64981 original size:20 final size:21
Alignment explanation
Indices: 64956--65007 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
64946 TTTTCCTAAT
*
64956 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
64976 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
64997 TCGCAATGCGA
1 TCGCAATGCGA
65008 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:65081 original size:20 final size:20
Alignment explanation
Indices: 64973--65084 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
64963 GCGAATAAGT
*
64973 AAATCGCAATGCGAATT-TGGA
1 AAATCGCAATGAG-ATTCT-GA
* *
64994 AAATCGCAATGCGATACTGA
1 AAATCGCAATGAGATTCTGA
** * ** *
65014 CTATCGCAACGAGATAATACA
1 AAATCGCAATGAGATTCT-GA
*
65035 AAATCGCAACGAGATTCTGA
1 AAATCGCAATGAGATTCTGA
***
65055 CTTTCGCAATGAGATTCTGA
1 AAATCGCAATGAGATTCTGA
65075 AAATCGCAAT
1 AAATCGCAAT
65085 CATCTTCAAA
Statistics
Matches: 70, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
20 41 0.59
21 29 0.41
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGAGATTCTGA
Found at i:65322 original size:20 final size:20
Alignment explanation
Indices: 65297--65384 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
65287 CAACGGGGAA
65297 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
65317 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
65337 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
65357 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
65377 ATCACAAC
1 ATCGCAAC
65385 TAGAAAATCG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 5 0.09
20 45 0.82
21 5 0.09
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:65478 original size:19 final size:19
Alignment explanation
Indices: 65411--65478 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
65401 GAAATGAAAA
65411 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
65427 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
65444 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
65463 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
65479 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.22
16 3 0.07
17 3 0.07
19 29 0.64
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:65632 original size:14 final size:14
Alignment explanation
Indices: 65613--65649 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
65603 CATCAATTAA
65613 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
65627 ACAAATCATCTTTT
1 ACAAATCAACATTT
65641 ACAAATCAA
1 ACAAATCAA
65650 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:67535 original size:20 final size:20
Alignment explanation
Indices: 67512--67565 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
67502 GAAACTTAAA
67512 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* * * *
67532 ATCGCAACGAGGAAATGGCT
1 ATCGCAATGCGAAAATGACT
67552 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
67566 TGAAAATCGC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:67620 original size:14 final size:14
Alignment explanation
Indices: 67568--67658 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
67558 ATGCGAAATG
67568 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
67582 AAAATTGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
67601 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
67615 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
67631 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
67647 AAAATCGCAACG
1 AAAATCGCAACG
67659 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 9 0.15
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:67673 original size:32 final size:33
Alignment explanation
Indices: 67552--67663 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
67542 GGAAATGGCT
67552 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
67585 ATTGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
67618 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
67650 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
67664 CACAATCGCA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 29 0.38
33 47 0.62
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:67696 original size:19 final size:18
Alignment explanation
Indices: 67669--67746 Score: 83
Period size: 19 Copynumber: 4.4 Consensus size: 18
67659 CGAAACACAA
*
67669 TCGCATTGCGATTTTTATT
1 TCGCATTGCGA-TTTCATT
* *
67688 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
67704 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
67720 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
67739 TCGCATTG
1 TCGCATTG
67747 TGATAGCCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 9 0.18
16 8 0.16
18 9 0.18
19 25 0.49
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:67757 original size:19 final size:19
Alignment explanation
Indices: 67715--67778 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
67705 CGTTGCGATT
**
67715 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
*
67734 TCATTTCGCATTGTGATAG
1 TCATTTCGCATTGCGATAG
* *
67753 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
67773 TCATTT
1 TCATTT
67779 TCGTGTTGCG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:67777 original size:20 final size:19
Alignment explanation
Indices: 67705--67789 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 19
67695 GCGATTTTGT
*
67705 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATAGTCATTTCG
* **
67723 CATTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
67742 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
67762 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
67782 TGTTGCGA
1 CGTTGCGA
67790 AAGTAAACTA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
18 8 0.15
19 22 0.40
20 22 0.40
21 3 0.05
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.41
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:68297 original size:18 final size:18
Alignment explanation
Indices: 68271--68315 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
68261 GTTGATCAGA
*
68271 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
68289 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
68307 TGATGGCTC
1 TGATGGCTC
68316 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:69676 original size:20 final size:20
Alignment explanation
Indices: 69628--69686 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
69618 AATAGTTTCT
** *
69628 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
69648 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
69668 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
69687 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:69963 original size:20 final size:22
Alignment explanation
Indices: 69938--69986 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
69928 TCTGAGAGAT
69938 GGAGAT-AGG-CGGATTTCGCC
1 GGAGATGAGGACGGATTTCGCC
* *
69958 GGAGATGGGGACGGATTTCGTC
1 GGAGATGAGGACGGATTTCGCC
69980 GGAGATG
1 GGAGATG
69987 GGTGAGAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.24
21 2 0.08
22 17 0.68
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.20
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGCC
Found at i:69974 original size:22 final size:22
Alignment explanation
Indices: 69947--69988 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
69937 TGGAGATAGG
69947 CGGATTTCGCCGGAGATGGGGA
1 CGGATTTCGCCGGAGATGGGGA
*
69969 CGGATTTCGTCGGAGATGGG
1 CGGATTTCGCCGGAGATGGG
69989 TGAGAGAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
CGGATTTCGCCGGAGATGGGGA
Found at i:70256 original size:20 final size:20
Alignment explanation
Indices: 70153--70304 Score: 126
Period size: 20 Copynumber: 7.5 Consensus size: 20
70143 CGCTTTGAAA
*
70153 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
70174 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
70194 ATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATAGTAAGT
* * *
70214 ATCTCGTTGCGATTTTGTAAGT
1 ATCGCATTGCGA--TAGTAAGT
*
70236 ATCGCATTGCGATATTAAGT
1 ATCGCATTGCGATAGTAAGT
*
70256 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
*
70276 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
*
70296 ATCGTATTG
1 ATCGCATTG
70305 TGATTTTCCC
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.02
20 83 0.75
21 11 0.10
22 15 0.14
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:70260 original size:62 final size:61
Alignment explanation
Indices: 70153--70304 Score: 155
Period size: 62 Copynumber: 2.5 Consensus size: 61
70143 CGCTTTGAAA
* * * * *
70153 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * * *
70214 ATCTCGTTGCGATTTTGTAAGTATCGCATTGCGATATTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
*
70276 ATCGCATTGCGA-TA-GTCAGTATCGTATTG
1 ATCGCATTGCGATTATGT-AGTATCGCATTG
70305 TGATTTTCCC
Statistics
Matches: 73, Mismatches: 17, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
60 13 0.18
61 16 0.22
62 44 0.60
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:70310 original size:82 final size:83
Alignment explanation
Indices: 70153--70311 Score: 198
Period size: 82 Copynumber: 1.9 Consensus size: 83
70143 CGCTTTGAAA
* * * *
70153 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGTATCT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCT
*
70218 CGTTGCGATTTTGTAAGT
66 CATTGCGATTTTGTAAGT
* * *
70236 ATCGCATTGCGA-TAT-TAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATC
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATC
*
70299 GT-ATTGTGATTTT
65 -TCATTGCGATTTT
70312 CCCCAATTCG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
81 1 0.02
82 51 0.78
83 13 0.20
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.36
Consensus pattern (83 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCT
CATTGCGATTTTGTAAGT
Found at i:70823 original size:2 final size:2
Alignment explanation
Indices: 70816--70845 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
70806 CTGCCACTAC
*
70816 CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
70846 ACTTCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:77270 original size:17 final size:18
Alignment explanation
Indices: 77248--77281 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
77238 TCTTACCTAT
77248 ATCTTAGTTTTT-GTTTC
1 ATCTTAGTTTTTCGTTTC
77265 ATCTTAGTTTTTCGTTT
1 ATCTTAGTTTTTCGTTT
77282 AAAATTTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (18 bp):
ATCTTAGTTTTTCGTTTC
Done.