Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002446.1 Hibiscus syriacus cultivar Beakdansim tig00005016_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: 93974
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:14555 original size:21 final size:21
Alignment explanation
Indices: 14529--14568 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14519 CAGAACCCCA
*
14529 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
14550 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
14569 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:14597 original size:20 final size:21
Alignment explanation
Indices: 14551--14611 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
14541 TTCCCCTGTG
14551 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
14574 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
14594 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
14612 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:21209 original size:14 final size:14
Alignment explanation
Indices: 21190--21216 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21180 ACATTAAGGA
21190 GTGTATCGATACCT
1 GTGTATCGATACCT
21204 GTGTATCGATACC
1 GTGTATCGATACC
21217 CACAGGCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (14 bp):
GTGTATCGATACCT
Found at i:21608 original size:20 final size:23
Alignment explanation
Indices: 21585--21635 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
21575 GATTAGAAGC
21585 ATGATTATG-TT-TT-GTATTAT
1 ATGATTATGCTTGTTCGTATTAT
*
21605 ATGAATATGCTTGGTTCGTATTAT
1 ATGATTATGCTT-GTTCGTATTAT
21629 ATG-TTAT
1 ATGATTAT
21636 ATGATGTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
23 5 0.20
24 10 0.40
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (23 bp):
ATGATTATGCTTGTTCGTATTAT
Found at i:22541 original size:23 final size:23
Alignment explanation
Indices: 22515--22627 Score: 95
Period size: 23 Copynumber: 5.0 Consensus size: 23
22505 CATTTTATAT
*
22515 GGCACTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
22538 GGCACTTCAGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
22561 GGCACTTTGGTGCA-ATCTTACGT
1 GGCACTTCGGTGCATTTC-TACGC
* * **
22584 GGCACTTC-GTGCAATCCTACAT
1 GGCACTTCGGTGCATTTCTACGC
* *
22606 TGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
22628 AGCTGTGGTG
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
22 18 0.26
23 52 0.74
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:22598 original size:22 final size:22
Alignment explanation
Indices: 22561--22619 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
22551 ATTTCTATGC
* * *
22561 GGCACTTTGGTGCAATCTTACGT
1 GGCAC-TTCGTGCAATCCTACAT
22584 GGCACTTCGTGCAATCCTACAT
1 GGCACTTCGTGCAATCCTACAT
*
22606 TGCACTTCGGTGCA
1 GGCACTTC-GTGCA
22620 TTTATACGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (22 bp):
GGCACTTCGTGCAATCCTACAT
Found at i:23972 original size:35 final size:35
Alignment explanation
Indices: 23933--24002 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
23923 TTGACTCTTC
*
23933 TATAATCTTCTCAAGAGGTGGTAAAACCTTTCAAT
1 TATAATCTTCTCAAGAGATGGTAAAACCTTTCAAT
23968 TATAATCTTCTCAAGAGATGGTAAAACCTTTCAAT
1 TATAATCTTCTCAAGAGATGGTAAAACCTTTCAAT
24003 GAGTCTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (35 bp):
TATAATCTTCTCAAGAGATGGTAAAACCTTTCAAT
Found at i:24060 original size:54 final size:54
Alignment explanation
Indices: 23992--24101 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
23982 GAGATGGTAA
23992 AACCTTTCAATGAGTCTATATTTGATACCAATTGTATAGTCAATTGGTTTATAG
1 AACCTTTCAATGAGTCTATATTTGATACCAATTGTATAGTCAATTGGTTTATAG
*
24046 AACCTTTCAGTGAGTCTATATTTGATACCAATTGTATAGTCAATTGGTTTATAG
1 AACCTTTCAATGAGTCTATATTTGATACCAATTGTATAGTCAATTGGTTTATAG
24100 AA
1 AA
24102 AATGGCCAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (54 bp):
AACCTTTCAATGAGTCTATATTTGATACCAATTGTATAGTCAATTGGTTTATAG
Found at i:28328 original size:17 final size:17
Alignment explanation
Indices: 28303--28340 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28293 GCCAATATTC
*
28303 CTTTTCTTCTTCTCCTT
1 CTTTCCTTCTTCTCCTT
*
28320 CTTTCCTTCTTCTTCTT
1 CTTTCCTTCTTCTCCTT
28337 CTTT
1 CTTT
28341 TCTTTGAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTCCTTCTTCTCCTT
Found at i:30550 original size:31 final size:26
Alignment explanation
Indices: 30473--30579 Score: 90
Period size: 31 Copynumber: 3.8 Consensus size: 26
30463 TAATATATAT
*
30473 TTTTTATTTTTGAA-TTATTTTATTTTA
1 TTTTTATTTTT-AATTTAATTT-TTTTA
*
30500 TTTTTTAATTATTATATTTAAGTTTTTGATTA
1 -TTTTT-ATTTTTA-ATTTAA-TTTTT--TTA
30532 TTTTTATATTTTGAATTTAATTTTTTTA
1 TTTTTAT-TTTT-AATTTAATTTTTTTA
*
30560 TTTTTATTTTTAATTAAATT
1 TTTTTATTTTTAATTTAATT
30580 AACCCTTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
26 8 0.12
27 4 0.06
28 16 0.24
29 6 0.09
30 12 0.18
31 17 0.25
32 4 0.06
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTATTTTTAATTTAATTTTTTTA
Found at i:30571 original size:21 final size:21
Alignment explanation
Indices: 30473--30575 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 21
30463 TAATATATAT
30473 TTTTTATTTTTGAATTATTTTA
1 TTTTTATTTTT-AATTATTTTA
*
30495 -TTTTATTTTTTAATTATTATA
1 TTTTTA-TTTTTAATTATTTTA
* *
30516 -TTTAAGTTTTTGATTATTTTTA
1 TTTTTA-TTTTTAATTA-TTTTA
* *
30538 TATTTTGA-ATTTAATTTTTTTA
1 T-TTTT-ATTTTTAATTATTTTA
30560 TTTTTATTTTTAATTA
1 TTTTTATTTTTAATTA
30576 AATTAACCCT
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.02
21 38 0.59
22 15 0.23
23 6 0.09
24 3 0.05
25 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTTATTTTTAATTATTTTA
Found at i:31019 original size:21 final size:22
Alignment explanation
Indices: 30995--31045 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
30985 AAACGATTAT
30995 TATTA-TTAAAAGAATTAAAAA
1 TATTACTTAAAAGAATTAAAAA
* *
31016 TATTACGTTAAATGCATTAAAAA
1 TATTAC-TTAAAAGAATTAAAAA
*
31039 TAATACT
1 TATTACT
31046 ATCTTAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 1 0.04
23 19 0.76
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (22 bp):
TATTACTTAAAAGAATTAAAAA
Found at i:38170 original size:17 final size:17
Alignment explanation
Indices: 38139--38172 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38129 TATTATCATC
**
38139 TTTTAATTTTTATATTT
1 TTTTAATTTGAATATTT
38156 TTTTAATTTGAATATTT
1 TTTTAATTTGAATATTT
38173 AGTTTTTCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTAATTTGAATATTT
Found at i:38183 original size:69 final size:68
Alignment explanation
Indices: 38066--38278 Score: 353
Period size: 69 Copynumber: 3.2 Consensus size: 68
38056 CATTGAATTG
38066 TCATCTTTTAATTTTTATATTTTTTAATTTGAATATTTAGTTTTTCATGAAATAAAATACTATTA
1 TCATCTTTTAATTTTTATATTTTTTAATTTGAATATTTAGTTTTTCATGAAATAAAATACTATTA
38131 TTA
66 TTA
38134 TCATCTTTTAATTTTTATATTTTTTTAATTTGAATATTTAGTTTTTCATGAAATAAAATACTATT
1 TCATCTTTTAATTTTTATA-TTTTTTAATTTGAATATTTAGTTTTTCATGAAATAAAATACTATT
38199 ATTA
65 ATTA
*
38203 TCGA-CTTTTAATTTTTATATTTTTTAATTTGAATATTTAG-TTTT-ATGAATTAAAATACTATT
1 TC-ATCTTTTAATTTTTATATTTTTTAATTTGAATATTTAGTTTTTCATGAAATAAAATACTATT
*
38265 A-AA
65 ATTA
*
38268 TCATTTTTTAA
1 TCATCTTTTAA
38279 ATATTCATTT
Statistics
Matches: 139, Mismatches: 3, Indels: 9
0.92 0.02 0.06
Matches are distributed among these distances:
64 1 0.01
65 9 0.06
66 18 0.13
67 4 0.03
68 40 0.29
69 66 0.47
70 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.56
Consensus pattern (68 bp):
TCATCTTTTAATTTTTATATTTTTTAATTTGAATATTTAGTTTTTCATGAAATAAAATACTATTA
TTA
Found at i:38343 original size:54 final size:51
Alignment explanation
Indices: 38243--38364 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 51
38233 GAATATTTAG
* * * *
38243 TTTT-ATGAATTAAAATACTATTAAATCATTTTTTAAATATTCATTTATATTTT
1 TTTTCATGAACTAAAATACTAATAAATCATTTTTTAAATAATCATTTATA---C
*
38296 TTTTCATGAACTAAAATACTAATAAATCA-TTTTTAATTTGAAT-ATTTATAC
1 TTTTCATGAACTAAAATACTAATAAATCATTTTTTAA-AT-AATCATTTATAC
38347 TTTTCATGAACTAAAATA
1 TTTTCATGAACTAAAATA
38365 TTATTAGATC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
51 18 0.30
53 11 0.18
54 30 0.49
55 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (51 bp):
TTTTCATGAACTAAAATACTAATAAATCATTTTTTAAATAATCATTTATAC
Found at i:38415 original size:54 final size:55
Alignment explanation
Indices: 38334--38437 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 55
38324 ATTTTTAATT
38334 TGAATATTTATACTTTTCATGAACTAAAATATTATTAGATCAAAATTATCAAATA
1 TGAATATTTATACTTTTCATGAACTAAAATATTATTAGATCAAAATTATCAAATA
* *
38389 TGAATATTTATA-TTTTCATTATCTAAAATATTATTAGATCAAAATTATC
1 TGAATATTTATACTTTTCATGAACTAAAATATTATTAGATCAAAATTATC
38438 GAGACCCCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 35 0.74
55 12 0.26
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (55 bp):
TGAATATTTATACTTTTCATGAACTAAAATATTATTAGATCAAAATTATCAAATA
Found at i:47721 original size:14 final size:13
Alignment explanation
Indices: 47698--47741 Score: 72
Period size: 14 Copynumber: 3.4 Consensus size: 13
47688 AATAAAATAG
47698 AAAAAAGATATAT
1 AAAAAAGATATAT
47711 AAAAAATGATATAT
1 AAAAAA-GATATAT
47725 AAAAAAGATA-AT
1 AAAAAAGATATAT
47737 AAAAA
1 AAAAA
47742 TGAAAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.23
13 10 0.33
14 13 0.43
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (13 bp):
AAAAAAGATATAT
Found at i:47784 original size:13 final size:13
Alignment explanation
Indices: 47762--47796 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
47752 TATTTAAATA
*
47762 AAATACAAATAAT
1 AAATAAAAATAAT
*
47775 AGATAAAAATAAT
1 AAATAAAAATAAT
47788 AAATAAAAA
1 AAATAAAAA
47797 ACGAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (13 bp):
AAATAAAAATAAT
Found at i:47794 original size:31 final size:31
Alignment explanation
Indices: 47756--47828 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
47746 AAAGAATATT
*
47756 TAAATAAAATAC-AAATAATAG-ATAAAAATAA
1 TAAATAAAAAACGAAATAA-AGTA-AAAAATAA
47787 TAAATAAAAAACGAAATAAAGTAAAAAATAA
1 TAAATAAAAAACGAAATAAAGTAAAAAATAA
47818 T-AATAACAAAA
1 TAAATAA-AAAA
47829 TGTTAGTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
30 5 0.13
31 26 0.68
32 7 0.18
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (31 bp):
TAAATAAAAAACGAAATAAAGTAAAAAATAA
Found at i:49185 original size:31 final size:32
Alignment explanation
Indices: 49127--49188 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
49117 CTATATAATA
* **
49127 TATATATTTCAAAAAATATTTTTAAACTATAT
1 TATATATTTCAAAAAAGATTTCAAAACTATAT
*
49159 TATAT-TTTTAAAAAAGATTTCAAAACTATA
1 TATATATTTCAAAAAAGATTTCAAAACTATA
49189 CATTGTATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (32 bp):
TATATATTTCAAAAAAGATTTCAAAACTATAT
Found at i:49187 original size:67 final size:68
Alignment explanation
Indices: 49116--49563 Score: 211
Period size: 75 Copynumber: 6.2 Consensus size: 68
49106 TAATAATAAT
* * *
49116 ACTATATAATATATATATTTCAAAAAATATTTTTAAACTATATTAT-A-TTTTTAAAAAAGA-TT
1 ACTATATATTATATAT-TTTC-AAAAATGTTTTTAAACTATATTATAAGTTTTCAAAAAAGATTT
49178 TCAAA
64 TCAAA
* * * * *
49183 ACTATACATTGTATAGTTTTC-AAAATGTTTTAAAAATATA-TATAAGTTTTCAAAAAATATTTT
1 ACTATATATTATATA-TTTTCAAAAATGTTTTTAAACTATATTATAAGTTTTCAAAAAAGATTTT
* *
49246 TATA
65 CAAA
**
49250 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATAAAAAAATTTC-AAAA
1 ACTATATATTATAT-A-TTTTCAAAAATGTTTTT-AAAC--TATATTAT---AAGTTTTCAAAAA
* *
49314 ATATTTTTAAA
58 AGATTTTCAAA
* *
49325 ACGATATATTATATAATTTCTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTC--AAAA
1 ACTATATATTATAT-ATTT-TCAAAAATGTTTT-TAAAC--TATA-T-TATAAGTTTTCAAAAAA
** *
49388 TTTCTTTAAAA
59 GAT-TTTCAAA
* * *
49399 ACTATATAATATATAAATGTTTTC-AAAATGTTTTCAAAACTATTATTATATATTTTTTC--AAA
1 ACTATAT-AT-TAT--ATATTTTCAAAAATGTTTT-TAAACTA-TATTATA-A-GTTTTCAAAAA
*
49461 ATATTTTCAAA
58 AGATTTTCAAA
* * * * *
49472 ACTATATAATATAAAATTTCGAAAATTGTTTTCTAAA-AATTATATATTATA-TTTCGTCAAAAA
1 ACTATATATTATATATTTTC-AAAAATGTTTT-TAAACTA-TAT-TA-TA-AGTTT--TCAAAAA
*
49535 ACATTTTCACAA
58 AGATTTTCA-AA
49547 ACTATATTATTATATAT
1 ACTATA-TATTATATAT
49564 ATATATATAA
Statistics
Matches: 305, Mismatches: 41, Indels: 61
0.75 0.10 0.15
Matches are distributed among these distances:
64 3 0.01
65 17 0.06
66 11 0.04
67 33 0.11
68 7 0.02
69 15 0.05
70 11 0.04
71 18 0.06
72 15 0.05
73 26 0.09
74 45 0.15
75 77 0.25
76 19 0.06
77 6 0.02
78 2 0.01
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (68 bp):
ACTATATATTATATATTTTCAAAAATGTTTTTAAACTATATTATAAGTTTTCAAAAAAGATTTTC
AAA
Found at i:49290 original size:37 final size:37
Alignment explanation
Indices: 49116--49523 Score: 304
Period size: 37 Copynumber: 11.4 Consensus size: 37
49106 TAATAATAAT
* * *
49116 ACTATATAATATAT-ATATTTCAAAAAATATTTTT-AA
1 ACTATATATTATATAATTTTTC-AAAAATGTTTTTAAA
* * *
49152 AC--TATA-T-TAT-ATTTTT-AAAAAAGATTTCAAA
1 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
* * *
49183 ACTATACATTGTAT-AGTTTTC-AAAATG-TTTT-AA
1 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
* * *
49216 A--A-ATA-TATATAAGTTTTCAAAAAATATTTTTATA
1 ACTATATATTATATAATTTTTC-AAAAATGTTTTTAAA
49250 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
1 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
* ** *
49287 ACTATATATTATAAAAAAATTTCAAAAATATTTTTAAA
1 ACTATATATTAT-ATAATTTTTCAAAAATGTTTTTAAA
* * *
49325 ACGATATATTATATAATTTCTCAAAAATGTTTTAAAA
1 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
*
49362 ACTATATATTATATAAGTTTTC-AAAAT-TTCTTTAAAA
1 ACTATATATTATATAATTTTTCAAAAATGTT-TTT-AAA
* *
49399 ACTATATAATATATAAATGTTTTC-AAAATGTTTTCAAA
1 ACTATATATTATAT-AAT-TTTTCAAAAATGTTTTTAAA
* * *
49437 ACTAT-TATTATATATTTTTTC-AAAATATTTTCAAA
1 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
** *
49472 ACTATATA--ATATAAAATTTCGAAAATTGTTTTCTAAAA
1 ACTATATATTATATAATTTTTC-AAAAATGTTTT-T-AAA
*
49510 ATTATATATTATAT
1 ACTATATATTATAT
49524 TTCGTCAAAA
Statistics
Matches: 300, Mismatches: 44, Indels: 52
0.76 0.11 0.13
Matches are distributed among these distances:
29 4 0.01
30 17 0.06
31 5 0.02
32 13 0.04
33 11 0.04
34 19 0.06
35 38 0.13
36 22 0.07
37 89 0.30
38 64 0.21
39 12 0.04
40 6 0.02
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
Found at i:49332 original size:75 final size:73
Alignment explanation
Indices: 49221--49523 Score: 319
Period size: 75 Copynumber: 4.1 Consensus size: 73
49211 TTTAAAAATA
* *
49221 TATATAAGTTTTCAAAAAATATTTTTATAACTATATATTATATAATTTTTCAAAAATGTTTTTAA
1 TATATAAATTTTC--AAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAA
49286 AACTATATAT
64 AACTATATAT
* * * * *
49296 TATAAAAAAATTTCAAAAATATTTTTAAAACGATATATTATATAATTTCTCAAAAATGTTTTAAA
1 TAT-ATAAATTTTC-AAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAA
49361 AACTATATAT
64 AACTATATAT
* * *
49371 TATATAAGTTTTCAAAAT-TTCTTTAAAAACTATATAATATATAAATGTTTTC-AAAATGTTTTC
1 TATATAAATTTTCAAAATATT-TTT-AAAACTATATATTATAT-AAT-TTTTCAAAAATGTTTTT
49434 AAAACTAT-TAT
62 AAAACTATATAT
** * ** *
49445 TATATATTTTTTCAAAATATTTTCAAAACTATATA--ATATAAAATTTCGAAAATTGTTTTCTAA
1 TATATAAATTTTCAAAATATTTTTAAAACTATATATTATATAATTTTTC-AAAAATGTTTT-T-A
*
49508 AAATTATATAT
63 AAACTATATAT
49519 TATAT
1 TATAT
49524 TTCGTCAAAA
Statistics
Matches: 195, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
69 4 0.02
70 2 0.01
71 13 0.07
72 2 0.01
73 26 0.13
74 51 0.26
75 86 0.44
76 11 0.06
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (73 bp):
TATATAAATTTTCAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAA
CTATATAT
Found at i:49469 original size:11 final size:11
Alignment explanation
Indices: 49413--49472 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
49403 TATAATATAT
*
49413 AAATGTTTTCA
1 AAATATTTTCA
*
49424 AAATGTTTTCA
1 AAATATTTTCA
49435 AAACTATTATT-A
1 AAA-TATT-TTCA
* *
49447 TATATTTTTTCA
1 -AAATATTTTCA
49459 AAATATTTTCA
1 AAATATTTTCA
49470 AAA
1 AAA
49473 CTATATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 28 0.70
12 8 0.20
13 4 0.10
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (11 bp):
AAATATTTTCA
Found at i:49582 original size:15 final size:15
Alignment explanation
Indices: 49549--49593 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
49539 TTTCACAAAC
* *
49549 TATAT-TATTATATA
1 TATATATATAATAAA
49563 TATATATATAATAAA
1 TATATATATAATAAA
49578 TATATATATAA-AAA
1 TATATATATAATAAA
49592 TA
1 TA
49594 ACTCCGGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATATATAATAAA
Found at i:50305 original size:164 final size:164
Alignment explanation
Indices: 50113--50703 Score: 876
Period size: 164 Copynumber: 3.6 Consensus size: 164
50103 AATTTATTGA
* * * *
50113 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
**
50178 CTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTACGCTGCAAATGATGTGCCCTC
66 CTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCCTC
50243 GAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
131 GAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* *
50277 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
* * ** ** *
50342 CTCGAAGGTCCTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATACTGTGAATGATATGCCCTC
66 CTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCCTC
* * *
50407 GAAGCTGAGTGTAATCAAACTCAGAGGTCTTTGG
131 GAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
*
50441 CAGATAGCCCTTCTCGACTTAAGCTATGCTCCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
* * * ** * * *
50506 CTCGAAGGTCTATTGTTGGCAAATAACCCTTCCCGACTTAAGTTATACTGCAAATGATGTTCCCT
66 CTCAAAGGTCT-TTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCCT
50571 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
130 CGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
* * ** *
50606 CAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTCAGAGCTGAGCATAGTCGAA
1 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
50671 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCT
66 CTCAAAGGTCTTTGG-TGGCAGATAACCCTTCT
50704 CGATTTAAGT
Statistics
Matches: 380, Mismatches: 45, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
164 223 0.59
165 157 0.41
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (164 bp):
CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGATGAGCATAGTCGAA
CTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCCTC
GAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
Found at i:56036 original size:14 final size:13
Alignment explanation
Indices: 56013--56056 Score: 72
Period size: 14 Copynumber: 3.4 Consensus size: 13
56003 AATAAAATAG
56013 AAAAAAGATATAT
1 AAAAAAGATATAT
56026 AAAAAAGGATATAT
1 AAAAAA-GATATAT
56040 AAAAAAGATA-AT
1 AAAAAAGATATAT
56052 AAAAA
1 AAAAA
56057 TGAAAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.23
13 10 0.33
14 13 0.43
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (13 bp):
AAAAAAGATATAT
Found at i:56099 original size:13 final size:13
Alignment explanation
Indices: 56077--56111 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
56067 TATTTTAAAA
*
56077 AAATACAAATAAT
1 AAATAAAAATAAT
*
56090 AGATAAAAATAAT
1 AAATAAAAATAAT
56103 AAATAAAAA
1 AAATAAAAA
56112 ACGAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (13 bp):
AAATAAAAATAAT
Found at i:57518 original size:31 final size:32
Alignment explanation
Indices: 57460--57521 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
57450 CTATATAATA
* **
57460 TATATATTTCAAAAAATATTTTTAAACTATAT
1 TATATATTTCAAAAAAGATTTCAAAACTATAT
*
57492 TATAT-TTTTAAAAAAGATTTCAAAACTATA
1 TATATATTTCAAAAAAGATTTCAAAACTATA
57522 CATTGTATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (32 bp):
TATATATTTCAAAAAAGATTTCAAAACTATAT
Found at i:57604 original size:38 final size:37
Alignment explanation
Indices: 57554--57938 Score: 359
Period size: 38 Copynumber: 10.2 Consensus size: 37
57544 TTTAAAAATA
*
57554 TATATAAGTTTTCAAAAAATATTTTTAAAACTATATAT
1 TATATAATTTTTC-AAAAATATTTTTAAAACTATATAT
*
57592 TATATAATTTTTCAAAAATGTTTTTTAAAACTATATAT
1 TATATAATTTTTCAAAAAT-ATTTTTAAAACTATATAT
*
57630 TATATAATTTTTCAAAAATGTTTTTAAAACTATATAT
1 TATATAATTTTTCAAAAATATTTTTAAAACTATATAT
* ** *
57667 TATAAAAAAATTTCAAAAATATTTTTAAAACGATATAT
1 TAT-ATAATTTTTCAAAAATATTTTTAAAACTATATAT
* * *
57705 TATATAATTTCTCAAAAATGTTTTAAAAAACTATATAT
1 TATATAATTTTTCAAAAATATTTT-TAAAACTATATAT
* *
57743 TATATAAGTTTTC-AAAAT-TTCTTTAAAAACTATATAA
1 TATATAATTTTTCAAAAATATT-TTT-AAAACTATATAT
* *
57780 TATATAAATGTTTTC-AAAATGTTTTCAAAACTATATAT
1 TATAT-AAT-TTTTCAAAAATATTTTTAAAACTATATAT
* * *
57818 TATATATTTTTTC-AAAATATTTTCAAAAACTATATAA
1 TATATAATTTTTCAAAAATATTTT-TAAAACTATATAT
** * * *
57855 TATATAAAATTTCGAAAATTGTTTTCTGAAAATTATATAT
1 TATATAATTTTTC-AAAAATATTTT-T-AAAACTATATAT
** * *
57895 TATAT--TTCGTCAAAAAACATTTTCACAAACTATATTAT
1 TATATAATTTTTC-AAAAATATTTTTA-AAACTATA-TAT
57933 TATATA
1 TATATA
57939 TATATATATA
Statistics
Matches: 288, Mismatches: 44, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
36 17 0.06
37 95 0.33
38 138 0.48
39 21 0.07
40 17 0.06
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATAATTTTTCAAAAATATTTTTAAAACTATATAT
Found at i:57660 original size:75 final size:73
Alignment explanation
Indices: 57553--57899 Score: 383
Period size: 75 Copynumber: 4.6 Consensus size: 73
57543 TTTTAAAAAT
* * *
57553 ATATATAAGTTTTCAAAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTT
1 ATATATAATTTTTC-AAAAATGTTTTTAAAACTATATATTATATAATTTTTC-AAAAT-TTTTTA
57618 AAAACTATATA
63 AAAACTATATA
* * **
57629 TTATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATAAAAAAATTTCAAAAATATTTTT-
1 ATATATAATTTTTCAAAAATGTTTTTAAAACTATATATTAT-ATAATTTTTC-AAAAT-TTTTTA
*
57693 AAAACGATATA
63 AAAACTATATA
* * * *
57704 TTATATAATTTCTCAAAAATGTTTTAAAAAACTATATATTATATAAGTTTTCAAAATTTCTTTAA
1 ATATATAATTTTTCAAAAATGTTTT-TAAAACTATATATTATATAATTTTTCAAAATTT-TTTAA
57769 AAACTATATA
64 AAACTATATA
* * *
57779 ATATATAAATGTTTTC-AAAATGTTTTCAAAACTATATATTATATATTTTTTCAAAATATTTTCA
1 ATATAT-AAT-TTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTCAAAAT-TTTTTA
57843 AAAACTATATA
63 AAAACTATATA
** * *
57854 ATATATAAAATTTCGAAAATTGTTTTCTGAAAATTATATATTATAT
1 ATATATAATTTTTC-AAAAATGTTTT-T-AAAACTATATATTATAT
57900 TTCGTCAAAA
Statistics
Matches: 235, Mismatches: 25, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
73 6 0.03
74 10 0.04
75 139 0.59
76 60 0.26
77 20 0.09
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (73 bp):
ATATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATATAATTTTTCAAAATTTTTTAAAA
ACTATATA
Found at i:57690 original size:113 final size:115
Alignment explanation
Indices: 57563--57899 Score: 416
Period size: 113 Copynumber: 2.9 Consensus size: 115
57553 ATATATAAGT
**
57563 TTTCAAAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTTAAAACTATAT
1 TTTC-AAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAAACTATAT
*
57628 ATTATATAATTTTTCAAAAATGTTTTT-AAAACTATATATTATA-AAAAAA
65 ATTATATAAATTTTCAAAAATGTTTTTAAAAACTATATATTATATAAAAAA
* *
57677 TTTCAAAAATATTTTTAAAACGATATATTATATAATTTCTCAAAAATGTTTTAAAAAACTATATA
1 TTTCAAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAAACTATATA
* * ***
57742 TTATATAAGTTTTC-AAAAT-TTCTTTAAAAACTATATAATATATAAATGT
66 TTATATAAATTTTCAAAAATGTT-TTTAAAAACTATATATTATATAAAAAA
* * * * *
57791 TTTC-AAAATGTTTTCAAAACTATATATTATATATTTTTTC-AAAATATTTTCAAAAACTATATA
1 TTTCAAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAAACTATATA
* * * * *
57854 ATATATAAAATTTCGAAAATTGTTTTCTGAAAATTATATATTATAT
66 TTATATAAATTTTC-AAAAATGTTTT-TAAAAACTATATATTATAT
57900 TTCGTCAAAA
Statistics
Matches: 193, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
111 2 0.01
112 40 0.21
113 116 0.60
114 17 0.09
115 18 0.09
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (115 bp):
TTTCAAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTAAAAAACTATATA
TTATATAAATTTTCAAAAATGTTTTTAAAAACTATATATTATATAAAAAA
Found at i:57801 original size:11 final size:11
Alignment explanation
Indices: 57785--57809 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57775 TATAATATAT
57785 AAATGTTTTCA
1 AAATGTTTTCA
57796 AAATGTTTTCA
1 AAATGTTTTCA
57807 AAA
1 AAA
57810 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:57900 original size:75 final size:73
Alignment explanation
Indices: 57553--57938 Score: 298
Period size: 75 Copynumber: 5.1 Consensus size: 73
57543 TTTTAAAAAT
** * * **
57553 ATATATAAGTTTTCAAAAAATATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTT
1 ATATATAAAATTTC-AAAAATGTTTTTAAAACTATATATTATAT--TTTTTCAAAAATATTTTCA
57618 AAAACTATATA
63 AAAACTATATA
* ** *** *
57629 TTATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATAAAAAAATTTCAAAAATATTTT-T
1 ATATATAAAATTTCAAAAATGTTTTTAAAACTATATATTAT---ATTTTTTCAAAAATATTTTCA
*
57693 AAAACGATATA
63 AAAACTATATA
* * * *
57704 TTATAT-AATTTCTCAAAAATGTTTTAAAAAACTATATATTATATAAGTTTTC-AAAAT-TTCTT
1 ATATATAAAATT-TCAAAAATGTTTT-TAAAACTATATATTATAT--TTTTTCAAAAATATT-TT
*
57766 TAAAAACTATATA
61 CAAAAACTATATA
* *
57779 ATATATAAATGTTTTC-AAAATGTTTTCAAAACTATATATTATATATTTTTTC-AAAATATTTTC
1 ATATATAAA--ATTTCAAAAATGTTTTTAAAACTATATA-T-TATATTTTTTCAAAAATATTTTC
57842 AAAAACTATATA
62 AAAAACTATATA
* * ** *
57854 ATATATAAAATTTCGAAAATTGTTTTCTGAAAATTATATATTATATTTCGTCAAAAAACATTTTC
1 ATATATAAAATTTC-AAAAATGTTTT-T-AAAACTATATATTATATTTTTTC-AAAAATATTTTC
*
57919 ACAAACTATATTA
62 AAAAACTATA-TA
*
57932 TTATATA
1 ATATATA
57939 TATATATATA
Statistics
Matches: 260, Mismatches: 28, Indels: 42
0.79 0.08 0.13
Matches are distributed among these distances:
73 7 0.03
74 11 0.04
75 137 0.53
76 57 0.22
77 36 0.14
78 12 0.05
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (73 bp):
ATATATAAAATTTCAAAAATGTTTTTAAAACTATATATTATATTTTTTCAAAAATATTTTCAAAA
ACTATATA
Found at i:57918 original size:113 final size:108
Alignment explanation
Indices: 57513--57938 Score: 382
Period size: 113 Copynumber: 3.8 Consensus size: 108
57503 AAAAGATTTC
* * * *
57513 AAAACTATACATTGTAT-AGTTTTCAAAA-TG-TTTTAAAAATATATA-TA-AGTTTTCAAAAAA
1 AAAACTATATATTATATAAATTTTCAAAATTGTTTTTAAAATTATATATTATA-TTTTC-AAAAA
* **
57573 TATTTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTT
64 TATTTTCAAAACTATATATTATATAATTTTTCAAAAATGTTTTAA
* * * *
57618 AAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAAACTATATATTATAAAAAAATTTCAA
1 AAAACTATATATTATATAAATTTTCAAAATTGTTTTTAAAATTATATATTAT-----ATTTTCAA
* * *
57683 AAATATTTTTAAAACGATATATTATATAATTTCTCAAAAATGTTTTAA
61 AAATATTTTCAAAACTATATATTATATAATTTTTCAAAAATGTTTTAA
* * *
57731 AAAACTATATATTATATAAGTTTTCAAAATT-TCTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAACTATATATTATATAAATTTTCAAAATTGT-TTTTAAAA-T-TAT-ATAT-T--ATATTTTC
* * * *
57795 -AAAATGTTTTCAAAACTATATATTATATATTTTTTC-AAAATATTTTCA
59 AAAAATATTTTCAAAACTATATATTATATAATTTTTCAAAAATGTTTTAA
* *
57843 AAAACTATATAATATATAAAATTTCGAAAATTGTTTTCTGAAAATTATATATTATATTTCGTCAA
1 AAAACTATATATTATATAAATTTTC-AAAATTGTTTT-T-AAAATTATATATTATATTT--TC-A
*
57908 AAAACATTTTCACAAACTATATTATTATATA
60 AAAATATTTTCA-AAACTATA-TATTATATA
57939 TATATATATA
Statistics
Matches: 265, Mismatches: 29, Indels: 44
0.78 0.09 0.13
Matches are distributed among these distances:
105 15 0.06
106 10 0.04
107 2 0.01
108 14 0.05
109 7 0.03
111 3 0.01
112 37 0.14
113 135 0.51
114 18 0.07
115 17 0.06
116 4 0.02
117 1 0.00
119 2 0.01
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (108 bp):
AAAACTATATATTATATAAATTTTCAAAATTGTTTTTAAAATTATATATTATATTTTCAAAAATA
TTTTCAAAACTATATATTATATAATTTTTCAAAAATGTTTTAA
Found at i:57958 original size:15 final size:15
Alignment explanation
Indices: 57925--57969 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
57915 TTTCACAAAC
* *
57925 TATAT-TATTATATA
1 TATATATATAATAAA
57939 TATATATATAATAAA
1 TATATATATAATAAA
57954 TATATATATAA-AAA
1 TATATATATAATAAA
57968 TA
1 TA
57970 ACTCCGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATATATAATAAA
Found at i:59486 original size:21 final size:22
Alignment explanation
Indices: 59457--59500 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
59447 ACATAAAAAT
59457 ATATAAATATAAAAAAATAAAG
1 ATATAAATATAAAAAAATAAAG
* *
59479 ATAT-AATATAATAAATTAAAG
1 ATATAAATATAAAAAAATAAAG
59500 A
1 A
59501 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (22 bp):
ATATAAATATAAAAAAATAAAG
Found at i:64289 original size:14 final size:14
Alignment explanation
Indices: 64270--64299 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
64260 TCTAAACACT
64270 AAAAATCAATTTTA
1 AAAAATCAATTTTA
64284 AAAAATCAATTTTA
1 AAAAATCAATTTTA
64298 AA
1 AA
64300 TACAATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATCAATTTTA
Found at i:64310 original size:25 final size:25
Alignment explanation
Indices: 64282--64339 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
64272 AAATCAATTT
64282 TAAAAAATCAATTTTAA-ATACAATC
1 TAAAAAATCAATTTTAATAT-CAATC
* * * *
64307 TAAACACTTAATTTTAATATTAATC
1 TAAAAAATCAATTTTAATATCAATC
64332 TAAAAAAT
1 TAAAAAAT
64340 TTGAAAGCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAAAATCAATTTTAATATCAATC
Found at i:64829 original size:2 final size:2
Alignment explanation
Indices: 64822--64849 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64812 CAAAACAGCA
64822 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
64850 TGAAAATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72263 original size:32 final size:32
Alignment explanation
Indices: 72188--72380 Score: 322
Period size: 32 Copynumber: 6.1 Consensus size: 32
72178 GCTCTTATAA
72188 TAATA-TGTCCATATGTCCCGAACA-ACATAGG
1 TAATACTGTCCATATGTCCCGAA-AGACATAGG
72219 TAA-ACTGTCCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
72250 TAATACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
72282 TAATACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
72314 TAATACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
72346 TAATGCTGTCCATATGTCCTGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
72378 TAA
1 TAA
72381 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 2, Indels: 9
0.93 0.01 0.05
Matches are distributed among these distances:
29 1 0.01
30 2 0.01
31 28 0.18
32 121 0.78
33 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCGAAAGACATAGG
Found at i:80081 original size:18 final size:18
Alignment explanation
Indices: 80058--80112 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
80048 ATATGTGATA
80058 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
**
80076 TGTGGTCCTTCTAGAC-T
1 TGTGGTCCTTCGGGACAT
*
80093 TAGTGGTCTTTCGGGACAT
1 T-GTGGTCCTTCGGGACAT
80112 T
1 T
80113 TCTACGCCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.13, C:0.20, G:0.29, T:0.38
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:81183 original size:30 final size:30
Alignment explanation
Indices: 81124--81226 Score: 136
Period size: 30 Copynumber: 3.4 Consensus size: 30
81114 CCCGAAGGAC
* *
81124 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
81153 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
81183 CTGTCTAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
81214 CTGTCCATAGGTC
1 CTATCCAGAGGTC
81227 CCGAAGAACC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 19 0.29
30 34 0.52
31 13 0.20
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:81226 original size:31 final size:30
Alignment explanation
Indices: 81127--81251 Score: 135
Period size: 30 Copynumber: 4.1 Consensus size: 30
81117 GAAGGACCTA
* *
81127 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
*
81156 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGATCCTCGGTAACTG
* *
81186 TCTAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCACAAAGATCCTCGGT-AACTG
* * * * *
81217 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGATCCTCGGT-AACTG
81248 TCCA
1 TCCA
81252 TATGTCTCGA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
29 16 0.19
30 34 0.41
31 33 0.40
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGATCCTCGGTAACTG
Found at i:81252 original size:31 final size:31
Alignment explanation
Indices: 81199--81276 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
81189 AGAGGTCATA
* *
81199 AAGATCCTCGGTAAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
* *
81230 AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCCG
*
81261 AA-AGACATAGGTAAAC
1 AAGA-ACCTAGGTAAAC
81277 CCTCGACTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATAGGTCCCG
Found at i:81932 original size:2 final size:2
Alignment explanation
Indices: 81925--81975 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
81915 ATACAATTCC
81925 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81967 TA TA TA TA T
1 TA TA TA TA T
81976 CTAACTCATG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:82561 original size:21 final size:21
Alignment explanation
Indices: 82531--82575 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
82521 ATTCTGTCAT
* *
82531 TTGAAGGGGTATCGTTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
82552 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
82573 TTG
1 TTG
82576 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:87866 original size:21 final size:21
Alignment explanation
Indices: 87840--87879 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
87830 CAGAACCCCA
*
87840 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
87861 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
87880 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:87914 original size:20 final size:21
Alignment explanation
Indices: 87860--87922 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
87850 GATTCCCCTG
87860 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
87884 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
87904 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
87923 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Done.