Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 245 of 292
Found at i:71210073 original size:20 final size:20
Alignment explanation
Indices: 71210027--71210075 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
71210017 AACTTGTAAA
*
71210027 ATTATAAAAAATTGTAAAAAT
1 ATTA-AAAAAATTATAAAAAT
** *
71210048 GGTAAAAAAATTATTAAAAT
1 ATTAAAAAAATTATAAAAAT
71210068 ATTAAAAA
1 ATTAAAAA
71210076 TATGTAAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (20 bp):
ATTAAAAAAATTATAAAAAT
Found at i:71210096 original size:24 final size:23
Alignment explanation
Indices: 71210063--71210109 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
71210053 AAAAATTATT
71210063 AAAATATTAAAAATATGTAAAAA
1 AAAATATTAAAAATATGTAAAAA
* *
71210086 AAAAGTATTAAAAATTTTTAAAAA
1 AAAA-TATTAAAAATATGTAAAAA
71210110 TTTTGTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATATTAAAAATATGTAAAAA
Found at i:71213912 original size:4 final size:4
Alignment explanation
Indices: 71213903--71213946 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
71213893 GTCAATGTAA
* * *
71213903 CACT CACT CACT CACT CACT CACT CACT CGCT CGCT CGCT CACT
1 CACT CACT CACT CACT CACT CACT CACT CACT CACT CACT CACT
71213947 TTTTATCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.18, C:0.50, G:0.07, T:0.25
Consensus pattern (4 bp):
CACT
Found at i:71215799 original size:19 final size:19
Alignment explanation
Indices: 71215735--71215799 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 19
71215725 AATTATAATT
71215735 TTTTTAAAATATAACTTTTGGAA
1 TTTTTAAAA-AT-A-TTTT-GAA
*
71215758 TTTTTATAAATATTTTGAA
1 TTTTTAAAAATATTTTGAA
*
71215777 -TTTTAAAAAT-TGTTTTAA
1 TTTTTAAAAATAT-TTTGAA
71215795 TTTTT
1 TTTTT
71215800 TTAATTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 14 0.38
19 7 0.19
20 4 0.11
21 1 0.03
22 2 0.05
23 8 0.22
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (19 bp):
TTTTTAAAAATATTTTGAA
Found at i:71216467 original size:194 final size:192
Alignment explanation
Indices: 71216131--71216506 Score: 513
Period size: 194 Copynumber: 1.9 Consensus size: 192
71216121 TCAATTGTAA
* * *
71216131 ATATTGGTAATGTTGTTGATTGAGTTGGTGTCACAAGCCAACTCAACACTAACTTAAGGTTGATG
1 ATATTGATAATGTTGTTGATTGAGTTGGTGTCACAAGCCAACTCAACACTAACTCAAGATTGATG
* **
71216196 ACAACATCATGATAAACAATTGTAGTACATTAAGTATTCTTAATATGATGTATTTATGTGGTTAA
66 ACAACATCATGATAAACAATTGTAGTACATTAAGTATTATTAATATGATGTATTTACATGGTTAA
* * *
71216261 ATTTCATTTTACTCATAATTTAATC-AATTTTAATCATTTTAATATCGTACATATCTATTGTGTT
131 ATTTCATTTTACTCACAATTTAATCGAATTTT--T-ATTTTAAAATCATACATATCTATTGTGTT
** *
71216325 ATATTGATAATGTTGTTGATTGAGTTGGTGTCACAAGTGAACAT-AACATTAACTCAAGATTGAT
1 ATATTGATAATGTTGTTGATTGAGTTGGTGTCACAAGCCAAC-TCAACACTAACTCAAGATTGAT
* * * * * * * *
71216389 GCCAACGTCATGATAGACAATTTTAGTGCATTTAGTATTATTAATGTGATGTATTTACATGTTTA
65 GACAACATCATGATAAACAATTGTAGTACATTAAGTATTATTAATATGATGTATTTACATGGTTA
*
71216454 AATTTTATTTTACTCACAATTTAATCGAATTTTTATTTTAAAATCATACATAT
130 AATTTCATTTTACTCACAATTTAATCGAATTTTTATTTTAAAATCATACATAT
71216507 TTCATATGTT
Statistics
Matches: 159, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
192 17 0.11
193 1 0.01
194 134 0.84
195 7 0.04
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (192 bp):
ATATTGATAATGTTGTTGATTGAGTTGGTGTCACAAGCCAACTCAACACTAACTCAAGATTGATG
ACAACATCATGATAAACAATTGTAGTACATTAAGTATTATTAATATGATGTATTTACATGGTTAA
ATTTCATTTTACTCACAATTTAATCGAATTTTTATTTTAAAATCATACATATCTATTGTGTT
Found at i:71222227 original size:20 final size:19
Alignment explanation
Indices: 71222190--71222241 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
71222180 ACATGCCACG
*
71222190 TCAACAAAAAAAGATTTTT
1 TCAAAAAAAAAAGATTTTT
*
71222209 TCAAAAAATAAAAGCTTTTT
1 TCAAAAAA-AAAAGATTTTT
*
71222229 TTAAAAAAAAAAG
1 TCAAAAAAAAAAG
71222242 GTAAAATGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.29
Consensus pattern (19 bp):
TCAAAAAAAAAAGATTTTT
Found at i:71222335 original size:18 final size:20
Alignment explanation
Indices: 71222314--71222358 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
71222304 CAAAACTAAA
71222314 AAAAATTCAAAAAT-TAT-T
1 AAAAATTCAAAAATGTATAT
*
71222332 AAAAATTCTAAAATGTATAT
1 AAAAATTCAAAAATGTATAT
71222352 AAAAATT
1 AAAAATT
71222359 TTAAATGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
20 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAATTCAAAAATGTATAT
Found at i:71226524 original size:18 final size:19
Alignment explanation
Indices: 71226503--71226556 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
71226493 TATTAACTTT
71226503 AATATTGTTATACTTTA-G
1 AATATTGTTATACTTTATG
71226521 AATATT-TTAATTACTTTATG
1 AATATTGTT-A-TACTTTATG
*
71226541 AAT-TTGTTATATTTTA
1 AATATTGTTATACTTTA
71226557 ATATTTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.06
18 13 0.42
19 10 0.32
20 6 0.19
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (19 bp):
AATATTGTTATACTTTATG
Found at i:71228656 original size:20 final size:21
Alignment explanation
Indices: 71228617--71228668 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
71228607 GAAAATTAAA
* *
71228617 AATAAAATGGAAATGGG-AAAG
1 AATAAAA-GAAAAAGGGAAAAG
71228638 AATAAAAGAAAAAGGGAAAAG
1 AATAAAAGAAAAAGGGAAAAG
71228659 AA-AAAAGAAA
1 AATAAAAGAAA
71228669 GAGTGAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (21 bp):
AATAAAAGAAAAAGGGAAAAG
Found at i:71228686 original size:20 final size:20
Alignment explanation
Indices: 71228634--71228684 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
71228624 TGGAAATGGG
71228634 AAAGAATAAAAGAAAAAGGGA
1 AAAGAA-AAAAGAAAAAGGGA
* *
71228655 AAAGAAAAAAGAAAGAGTGA
1 AAAGAAAAAAGAAAAAGGGA
71228675 AATAGAAAAA
1 AA-AGAAAAA
71228685 GAGATTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.06
Consensus pattern (20 bp):
AAAGAAAAAAGAAAAAGGGA
Found at i:71230025 original size:29 final size:30
Alignment explanation
Indices: 71229983--71230039 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
71229973 ACAAAACGAT
* *
71229983 AATATAAGTGATTAAAACATAAC-ATTTCA
1 AATATAAATAATTAAAACATAACTATTTCA
*
71230012 AATATAAATAATTAAAATATAACTATTT
1 AATATAAATAATTAAAACATAACTATTT
71230040 AATAGTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (30 bp):
AATATAAATAATTAAAACATAACTATTTCA
Found at i:71230041 original size:15 final size:15
Alignment explanation
Indices: 71229994--71230041 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
71229984 ATATAAGTGA
*
71229994 TTAAAACATAAC-AT
1 TTAAAATATAACTAT
* * *
71230008 TTCAAATATAAATAA
1 TTAAAATATAACTAT
71230023 TTAAAATATAACTAT
1 TTAAAATATAACTAT
71230038 TTAA
1 TTAA
71230042 TAGTTTATTC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (15 bp):
TTAAAATATAACTAT
Found at i:71230907 original size:18 final size:19
Alignment explanation
Indices: 71230879--71230918 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
71230869 ATGAAAGTAA
*
71230879 GATTGTATTTGAAATGGAT
1 GATTGTATTTGAAATGAAT
*
71230898 GATTGT-TTTGATATGAAT
1 GATTGTATTTGAAATGAAT
71230916 GAT
1 GAT
71230919 ATTTATGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (19 bp):
GATTGTATTTGAAATGAAT
Found at i:71232442 original size:38 final size:38
Alignment explanation
Indices: 71232389--71232511 Score: 194
Period size: 38 Copynumber: 3.2 Consensus size: 38
71232379 GGTCCTTAAC
* *
71232389 CCGGATATTTTTCCAGCACT-TAGCTTGCGGACTTTAAGT
1 CCGGAT-TTATTCCAGCA-TATAGCCTGCGGACTTTAAGT
71232428 CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
1 CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
71232466 CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
1 CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
*
71232504 CTGGATTT
1 CCGGATTT
71232512 CTTCTTTTAC
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
37 1 0.01
38 73 0.91
39 6 0.08
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (38 bp):
CCGGATTTATTCCAGCATATAGCCTGCGGACTTTAAGT
Found at i:71241835 original size:17 final size:18
Alignment explanation
Indices: 71241804--71241837 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
71241794 AATTCACGCT
71241804 TTTTGCCCTTAAATTTAC
1 TTTTGCCCTTAAATTTAC
*
71241822 TTTTG-CCTTCAATTTA
1 TTTTGCCCTTAAATTTA
71241838 ATCCCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTTGCCCTTAAATTTAC
Found at i:71242456 original size:99 final size:99
Alignment explanation
Indices: 71242279--71242468 Score: 274
Period size: 99 Copynumber: 1.9 Consensus size: 99
71242269 AAATTAATTT
* *
71242279 ATTTATTTATTTTTGCTTAAGAATATATTGAACATTTTGAAACGAAAAGAGATGATAGCCAAGCA
1 ATTTATTTATTTTTGCTTAAGAATATATCGAACATTTTGAAACGAAAAGAGATGACAGCCAAGCA
* *
71242344 CCTTACCCTGGTTACTCAGCCCAATATACTCCTA
66 CCTCACCCCGGTTACTCAGCCCAATATACTCCTA
* * ** *
71242378 ATTTATTATATTTTT-CTTAATAATATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGC
1 ATTTATT-TATTTTTGCTTAAGAATATATCGAACATTTTGAAACGAAAAGAGATGACAGCCAAGC
*
71242442 ATCTCACCCCGGTTACTCAGCCCAATA
65 ACCTCACCCCGGTTACTCAGCCCAATA
71242469 CATTTTTAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 73 0.91
100 7 0.09
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (99 bp):
ATTTATTTATTTTTGCTTAAGAATATATCGAACATTTTGAAACGAAAAGAGATGACAGCCAAGCA
CCTCACCCCGGTTACTCAGCCCAATATACTCCTA
Found at i:71243595 original size:21 final size:21
Alignment explanation
Indices: 71243569--71243625 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
71243559 ATTAATATCC
*
71243569 AAAAAAATAATAAATAATAAA
1 AAAAAAAAAATAAATAATAAA
* *
71243590 AGAAAAAGAAA-GAATAATAAA
1 A-AAAAAAAAATAAATAATAAA
71243611 AAATAAAAAAATAAA
1 AAA-AAAAAAATAAA
71243626 AATTGGGTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.07
21 17 0.61
22 9 0.32
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAAAAAAAATAAATAATAAA
Found at i:71248764 original size:19 final size:19
Alignment explanation
Indices: 71248728--71248764 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
71248718 TAATTAGGCT
* *
71248728 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
71248747 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
71248765 GAAAAAGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:71249089 original size:19 final size:20
Alignment explanation
Indices: 71249039--71249091 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
71249029 CAATTGTAAA
* *
71249039 AAATATATATGTACATTTGT
1 AAATATATATTTACATTAGT
*
71249059 AATATTTATATTTA-ATTAGT
1 AA-ATATATATTTACATTAGT
71249079 AAATATATATTTA
1 AAATATATATTTA
71249092 TTTTTATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 10 0.36
20 9 0.32
21 9 0.32
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (20 bp):
AAATATATATTTACATTAGT
Found at i:71249361 original size:12 final size:12
Alignment explanation
Indices: 71249330--71249385 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
71249320 TAAATATGTG
*
71249330 TTATTAAAATATA
1 TTATTATAAT-TA
71249343 TTTATTATAATTA
1 -TTATTATAATTA
71249356 TTATTATAATTA
1 TTATTATAATTA
* * *
71249368 TTATCATTATCA
1 TTATTATAATTA
71249380 TTATTA
1 TTATTA
71249386 ACTAATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 26 0.70
13 2 0.05
14 9 0.24
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATTATAATTA
Found at i:71249397 original size:2 final size:2
Alignment explanation
Indices: 71249390--71249420 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
71249380 TTATTAACTA
71249390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71249421 AGATATAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71249458 original size:14 final size:15
Alignment explanation
Indices: 71249441--71249471 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
71249431 AAAATGAAAT
71249441 AAAGAAAGAA-AGCA
1 AAAGAAAGAATAGCA
71249455 AAAGAAAGAATAGCA
1 AAAGAAAGAATAGCA
71249470 AA
1 AA
71249472 GCCATTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.71, C:0.06, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAGAAAGAATAGCA
Found at i:71253627 original size:13 final size:14
Alignment explanation
Indices: 71253606--71253645 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
71253596 ATTTGATTGG
71253606 AAAATGAATTAAA-
1 AAAATGAATTAAAT
*
71253619 AATATGAATTAAAT
1 AAAATGAATTAAAT
71253633 AAAAGTGAATTAA
1 AAAA-TGAATTAA
71253646 TTTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 3 0.13
15 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
AAAATGAATTAAAT
Found at i:71254462 original size:13 final size:14
Alignment explanation
Indices: 71254427--71254465 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
71254417 GAAGATATTT
71254427 ATATATTATATATAA
1 ATATATTAT-TATAA
*
71254442 ATAAATTATTAT-A
1 ATATATTATTATAA
71254455 ATATATTATTA
1 ATATATTATTA
71254466 GTAACTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTATTATAA
Found at i:71254524 original size:26 final size:28
Alignment explanation
Indices: 71254472--71254528 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
71254462 ATTAGTAACT
*
71254472 AAAGCAAATAAAAGAAATAGAATAAAGA
1 AAAGCAAACAAAAGAAATAGAATAAAGA
71254500 AAAG-AAACAAAAG-AATAGAGA-AAAGA
1 AAAGCAAACAAAAGAAATAGA-ATAAAGA
71254526 AAA
1 AAA
71254529 CAGAAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 14 0.52
27 9 0.33
28 4 0.15
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.07
Consensus pattern (28 bp):
AAAGCAAACAAAAGAAATAGAATAAAGA
Found at i:71256630 original size:23 final size:23
Alignment explanation
Indices: 71256600--71256689 Score: 132
Period size: 23 Copynumber: 4.0 Consensus size: 23
71256590 GGCTTTGCCG
71256600 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
71256623 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
* * *
71256646 TTCAGGCACCTTGTGTGTCG--T
1 ATCAGGCACTTTATGTGTCGTAT
71256667 ATCAGGCAC-TTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAT
71256689 A
1 A
71256690 CTGATCATGT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.15
21 9 0.15
22 2 0.03
23 40 0.67
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAT
Found at i:71259034 original size:10 final size:10
Alignment explanation
Indices: 71259017--71259065 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
71259007 TTAAATTCTA
71259017 AAAGATAAAT
1 AAAGATAAAT
*
71259027 ATAGATAAAT
1 AAAGATAAAT
* *
71259037 AAATATAATT
1 AAAGATAAAT
71259047 AAAGATAAAT
1 AAAGATAAAT
71259057 AAAGATAAA
1 AAAGATAAA
71259066 AGCTAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:71261494 original size:14 final size:14
Alignment explanation
Indices: 71261477--71261504 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
71261467 AGTATAACAG
71261477 TGCGAATATAGCTA
1 TGCGAATATAGCTA
71261491 TGCGAATATAGCTA
1 TGCGAATATAGCTA
71261505 AACCTAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
TGCGAATATAGCTA
Found at i:71261708 original size:23 final size:23
Alignment explanation
Indices: 71261678--71261725 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
71261668 TAAGAATGTG
71261678 AAACATGACTCATCTACTTTACT
1 AAACATGACTCATCTACTTTACT
71261701 AAACATGACTCATCTACTTTACT
1 AAACATGACTCATCTACTTTACT
71261724 AA
1 AA
71261726 GGCAAGTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (23 bp):
AAACATGACTCATCTACTTTACT
Found at i:71262086 original size:46 final size:47
Alignment explanation
Indices: 71262033--71262125 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
71262023 AAAATTAATT
71262033 TTTAAATTA-TTTTTTATCTAAATTAATATCAAATTAACTTTTATAC
1 TTTAAATTATTTTTTTATCTAAATTAATATCAAATTAACTTTTATAC
71262079 TTTAAATTATTTTTTTATCTAAATTAATATCAAATTAACTTTTATAC
1 TTTAAATTATTTTTTTATCTAAATTAATATCAAATTAACTTTTATAC
71262126 ACAGGGATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 9 0.20
47 37 0.80
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (47 bp):
TTTAAATTATTTTTTTATCTAAATTAATATCAAATTAACTTTTATAC
Found at i:71265393 original size:12 final size:12
Alignment explanation
Indices: 71265376--71265407 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
71265366 ATTTGCTCTT
71265376 ATCATCATCACC
1 ATCATCATCACC
71265388 ATCATCATCACC
1 ATCATCATCACC
*
71265400 ACCATCAT
1 ATCATCAT
71265408 GACTCTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (12 bp):
ATCATCATCACC
Found at i:71265396 original size:15 final size:15
Alignment explanation
Indices: 71265376--71265407 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
71265366 ATTTGCTCTT
*
71265376 ATCATCATCACCATC
1 ATCATCACCACCATC
71265391 ATCATCACCACCATC
1 ATCATCACCACCATC
71265406 AT
1 AT
71265408 GACTCTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (15 bp):
ATCATCACCACCATC
Found at i:71265985 original size:2 final size:2
Alignment explanation
Indices: 71265978--71266003 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71265968 TTCTCATTTG
71265978 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
71266004 GTGTATGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:71274034 original size:70 final size:70
Alignment explanation
Indices: 71273921--71274063 Score: 268
Period size: 70 Copynumber: 2.0 Consensus size: 70
71273911 GAGCTATGAT
71273921 GAGTTTGATTTGAATACTGTCTTTTATACAATGTTTAAACTATCCAAATCTCTCCCCAATCCCTA
1 GAGTTTGATTTGAATACTGTCTTTTATACAATGTTTAAACTATCCAAATCTCTCCCCAATCCCTA
71273986 AAGTG
66 AAGTG
* *
71273991 GAGTTTGATTTGAATACTGTCTTTTATACAATGTTTAAACTATCCAAATCTCTCTCCACTCCCTA
1 GAGTTTGATTTGAATACTGTCTTTTATACAATGTTTAAACTATCCAAATCTCTCCCCAATCCCTA
71274056 AAGTG
66 AAGTG
71274061 GAG
1 GAG
71274064 GATATTACGC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (70 bp):
GAGTTTGATTTGAATACTGTCTTTTATACAATGTTTAAACTATCCAAATCTCTCCCCAATCCCTA
AAGTG
Found at i:71279828 original size:12 final size:12
Alignment explanation
Indices: 71279792--71279858 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
71279782 CAAAAGTAAA
*
71279792 TAAAAGAAAAAT
1 TAAAATAAAAAT
71279804 TAGAAAATAAAAAT
1 T--AAAATAAAAAT
*
71279818 TAAACTAAAAA-
1 TAAAATAAAAAT
*
71279829 CAAAATAAAAAT
1 TAAAATAAAAAT
* *
71279841 TATAATAGAAAT
1 TAAAATAAAAAT
*
71279853 AAAAAT
1 TAAAAT
71279859 GGCTAAATTA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
11 9 0.21
12 23 0.53
14 11 0.26
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (12 bp):
TAAAATAAAAAT
Found at i:71281236 original size:2 final size:2
Alignment explanation
Indices: 71281231--71281267 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
71281221 TAAACAAAAA
*
71281231 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71281268 ATAGAACGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:71281498 original size:25 final size:25
Alignment explanation
Indices: 71281470--71281530 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
71281460 GTTTGGTCAG
71281470 ACTCTCTTCGACCGTTCCGAAGTGT
1 ACTCTCTTCGACCGTTCCGAAGTGT
*
71281495 ACTCTCTTCGACCGTTCCGTAGTGT
1 ACTCTCTTCGACCGTTCCGAAGTGT
*
71281520 ACT-TGTTCGAC
1 ACTCTCTTCGAC
71281531 GTTGTGTGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (25 bp):
ACTCTCTTCGACCGTTCCGAAGTGT
Found at i:71283877 original size:30 final size:30
Alignment explanation
Indices: 71283841--71283920 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
71283831 TAGGCACTTC
* *
71283841 CACACGGGTAAACCACAC-TCCCGTATGAGG
1 CACACGGGCAAACCACACGT-CCGTATAAGG
*
71283871 CACACGGGCAAACCACACGTCCGTGTAAGG
1 CACACGGGCAAACCACACGTCCGTATAAGG
* *
71283901 CACACAGGCAGACCACACGT
1 CACACGGGCAAACCACACGT
71283921 TCGTGTGTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 43 0.98
31 1 0.02
ACGTcount: A:0.31, C:0.35, G:0.24, T:0.10
Consensus pattern (30 bp):
CACACGGGCAAACCACACGTCCGTATAAGG
Found at i:71295783 original size:15 final size:15
Alignment explanation
Indices: 71295760--71295793 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
71295750 AGTCCATTTC
*
71295760 TTTTATTTTTTTTAT
1 TTTTATTTTATTTAT
*
71295775 TTTTGTTTTATTTAT
1 TTTTATTTTATTTAT
71295790 TTTT
1 TTTT
71295794 TGAAGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (15 bp):
TTTTATTTTATTTAT
Found at i:71297441 original size:12 final size:12
Alignment explanation
Indices: 71297424--71297452 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
71297414 ATTTTTGGAT
71297424 GATTTATCATAA
1 GATTTATCATAA
71297436 GATTTATCATAA
1 GATTTATCATAA
71297448 GATTT
1 GATTT
71297453 GATAAACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (12 bp):
GATTTATCATAA
Found at i:71298919 original size:19 final size:19
Alignment explanation
Indices: 71298895--71298968 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
71298885 ATAATCTTCA
71298895 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
71298914 ATGATATGAAATCTTAGAT
1 ATGATATGCAATCTTAGAT
71298933 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
71298951 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
71298969 AGATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.33
19 35 0.67
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:71298943 original size:37 final size:38
Alignment explanation
Indices: 71298895--71298975 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 38
71298885 ATAATCTTCA
71298895 ATGATATGCAATCTTAGATATGATATGAAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATATGAAATCTTAGAT
*
71298933 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATATGAAATCTTAGAT
71298969 A-GATATG
1 ATGATATG
71298976 ATTTTGTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 3 0.07
36 3 0.07
37 30 0.73
38 5 0.12
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (38 bp):
ATGATATGCAATCTTAGATATGATATGAAATCTTAGAT
Found at i:71298994 original size:22 final size:22
Alignment explanation
Indices: 71298895--71298991 Score: 88
Period size: 19 Copynumber: 4.8 Consensus size: 22
71298885 ATAATCTTCA
71298895 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
71298914 ATGATATGAAATCTTAG---AT
1 ATGATATGCAATCTTAGAAGAT
71298933 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
71298951 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
71298973 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
71298992 GATTTAATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
18 15 0.23
19 30 0.46
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:71299281 original size:17 final size:17
Alignment explanation
Indices: 71299257--71299291 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
71299247 TGTTTCCCTG
*
71299257 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
71299275 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
71299292 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:71307872 original size:219 final size:220
Alignment explanation
Indices: 71307490--71308078 Score: 982
Period size: 219 Copynumber: 2.7 Consensus size: 220
71307480 CAGGCTAAAG
* * * * *
71307490 CATAGCAGATTTGACCTTCAGGTGTTTACGCTGAAGCGGATCCAAGATGATTTAACATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCTCTGTA
* *
71307555 TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCAATGGAGAGCAGATCGAAG
66 TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
* *
71307620 ACATAGCAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTTCCATCCTT
131 ACATAGCAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGCCATCCTT
71307685 GCGTTGACAAGGAGCA-ATCGAAGA
196 GCGTTGACAAGGAGCAGATCGAAGA
71307709 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCTCTGTA
*
71307774 TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCTATATTCGACGGAGAGCAGATCGAAG
66 TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
*
71307839 ACATAGCAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
131 ACATAGCAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGCCATCCTT
*
71307904 GCGTTGATAAGGAGCAGATCGAAGA
196 GCGTTGACAAGGAGCAGATCGAAGA
* * * **
71307929 CATAGTAGATTTGGCTTTCACGTGTTTATGCTGAAGTAGATCTAAGATGATTTGGCATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCTCTGTA
* *
71307994 CTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGAAGAGCAGATCGAAG
66 TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
* *
71308059 ACATAGCAGATTTGACCTTC
131 ACATAGCAGATCTAACCTTC
71308079 ATTGAAGCAG
Statistics
Matches: 347, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
219 199 0.57
220 148 0.43
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (220 bp):
CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTAACATCTCTGTA
TTGTCAGAGAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
ACATAGCAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGCCATCCTT
GCGTTGACAAGGAGCAGATCGAAGA
Found at i:71308153 original size:78 final size:78
Alignment explanation
Indices: 71308020--71308314 Score: 439
Period size: 78 Copynumber: 3.8 Consensus size: 78
71308010 CGAAGAAACA
* * ** *
71308020 GATTTGGCATCTCCATATTCGACGAAGAGCAGATCGAAGACATAGCAGATTTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
71308085 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
71308098 GATTTGGCATCTCTATATTAGACGGGGAACAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
71308163 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * *
71308176 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAAACATAACAGAT-TGGATCTTCATTGA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
*
71308240 AGTAGATCCAAGAT
65 AGCAGATCCAAGAT
* * *
71308254 GATTTGGCATCTTTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGTTCTGACCTTCAT
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
71308315 GTGTTTACAT
Statistics
Matches: 196, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
77 1 0.01
78 194 0.99
79 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (78 bp):
GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:71308513 original size:45 final size:45
Alignment explanation
Indices: 71308413--71308541 Score: 170
Period size: 45 Copynumber: 2.9 Consensus size: 45
71308403 TCTATCTAAT
* * *
71308413 ATCTCTGTATTAGATGGGGAGCAGATTGAAGAT-GCAGATTTGGC
1 ATCTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATTAGAC
* * *
71308457 ATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAGATTAGAT
1 ATCTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATTAGAC
* * *
71308502 GTCTCTATATTAGATGGGGAGCAGATCAAAGATAGCAGAT
1 ATCTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGAT
71308542 ATCGCCTTCC
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
44 31 0.42
45 42 0.58
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (45 bp):
ATCTCTGTATTAGATGGGGAGCAGATCGAAGATAGCAGATTAGAC
Found at i:71308911 original size:19 final size:19
Alignment explanation
Indices: 71308887--71308958 Score: 96
Period size: 17 Copynumber: 3.9 Consensus size: 19
71308877 ATAATCTTCA
71308887 ATGATATACAATCTTAGAT
1 ATGATATACAATCTTAGAT
*
71308906 ATG--ATACAATATTAGAT
1 ATGATATACAATCTTAGAT
*
71308923 ATGAT-TGCAATCTTAGAT
1 ATGATATACAATCTTAGAT
*
71308941 ATGATATGCAATCTTAGA
1 ATGATATACAATCTTAGA
71308959 AGATATGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
17 16 0.34
18 16 0.34
19 15 0.32
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATACAATCTTAGAT
Found at i:71308938 original size:18 final size:18
Alignment explanation
Indices: 71308895--71308958 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
71308885 CAATGATATA
*
71308895 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTG
*
71308912 CAATATTAGATATGATTG
1 CAATCTTAGATATGATTG
71308930 CAATCTTAGATATGATATG
1 CAATCTTAGATATGAT-TG
71308949 CAATCTTAGA
1 CAATCTTAGA
71308959 AGATATGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
17 14 0.33
18 16 0.38
19 12 0.29
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (18 bp):
CAATCTTAGATATGATTG
Found at i:71308946 original size:23 final size:23
Alignment explanation
Indices: 71308920--71308984 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 23
71308910 TACAATATTA
71308920 GATATGATTGCAATCTTAGATAT
1 GATATGATTGCAATCTTAGATAT
71308943 G--AT-A-TGCAATCTTAGA-A-
1 GATATGATTGCAATCTTAGATAT
*
71308960 GATATGATTTTGTAATCTTAGATAT
1 GATATGA--TTGCAATCTTAGATAT
71308985 TTAATTTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 14 0.42
20 2 0.06
21 2 0.06
23 12 0.36
24 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (23 bp):
GATATGATTGCAATCTTAGATAT
Found at i:71308965 original size:17 final size:19
Alignment explanation
Indices: 71308887--71308958 Score: 105
Period size: 19 Copynumber: 3.9 Consensus size: 19
71308877 ATAATCTTCA
*
71308887 ATGATATACAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
71308906 ATGATA--CAATATTAGAT
1 ATGATATGCAATCTTAGAT
71308923 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
71308941 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
71308959 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
17 15 0.31
18 15 0.31
19 18 0.38
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:71309272 original size:17 final size:17
Alignment explanation
Indices: 71309248--71309282 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
71309238 TGTTTCCCTG
*
71309248 ATTTTTTTATATATTTTA
1 ATTTTTTAATA-ATTTTA
71309266 ATTTTTTAATAATTTTA
1 ATTTTTTAATAATTTTA
71309283 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTAATAATTTTA
Found at i:71310408 original size:2 final size:2
Alignment explanation
Indices: 71310403--71310447 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
71310393 CCCAGCTGCA
*
71310403 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
71310445 TC T
1 TC T
71310448 TTGTCCCCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:71312989 original size:1 final size:1
Alignment explanation
Indices: 71312983--71313024 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
71312973 TTAGTACTTA
* *
71312983 TTTTTTTCTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
71313025 AAATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:71313305 original size:117 final size:118
Alignment explanation
Indices: 71313150--71313379 Score: 381
Period size: 117 Copynumber: 2.0 Consensus size: 118
71313140 TATTTCCGGT
71313150 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* *
71313215 CCTA-CCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
****
71313267 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
**
71313332 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCTGTACTCATAACC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACC
71313380 ATGGAAAACA
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 65 0.62
118 39 0.38
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:71314127 original size:41 final size:43
Alignment explanation
Indices: 71314041--71314130 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 43
71314031 CTGAAAAGGG
* * *
71314041 TGTTTGGCTGCAGGTTTTGGGGATTCTAAGGCTGGAATAGGAC
1 TGTTTGGCTGCAGGATATGGGGATTCTAAGGCTGGAATAGAAC
* *
71314084 TGTTTGGCTGCAGGATAT-GGTATTCT-GGGCTGGAATAGAAC
1 TGTTTGGCTGCAGGATATGGGGATTCTAAGGCTGGAATAGAAC
71314125 TGTTTG
1 TGTTTG
71314131 ATAGCATGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 19 0.45
42 7 0.17
43 16 0.38
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (43 bp):
TGTTTGGCTGCAGGATATGGGGATTCTAAGGCTGGAATAGAAC
Found at i:71314236 original size:6 final size:6
Alignment explanation
Indices: 71314219--71314269 Score: 57
Period size: 6 Copynumber: 8.0 Consensus size: 6
71314209 GGAAGAAGAG
* *
71314219 AAATATA AAATAA AAATAA AAATAA TAATAA ATAATAA AAGAAAA AAATAA
1 AAATA-A AAATAA AAATAA AAATAA AAATAA A-AATAA AA-ATAA AAATAA
71314270 TAAAAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 22 0.58
7 16 0.42
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:71314267 original size:16 final size:17
Alignment explanation
Indices: 71314233--71314279 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
71314223 ATAAAATAAA
*
71314233 AATAAAAATAATAATAAAT
1 AATAAAAAGAA-AA-AAAT
71314252 AAT-AAAAGAAAAAAAT
1 AATAAAAAGAAAAAAAT
71314268 AATAAAAAGAAA
1 AATAAAAAGAAA
71314280 GACTGGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 6 0.23
19 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (17 bp):
AATAAAAAGAAAAAAAT
Found at i:71324592 original size:2 final size:2
Alignment explanation
Indices: 71324579--71324625 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
71324569 CTCATCTCCA
*
71324579 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
71324621 TC TC T
1 TC TC T
71324626 TCCACCATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:71326031 original size:21 final size:23
Alignment explanation
Indices: 71326007--71326048 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
71325997 ATTTATTTAT
71326007 TTAATG-TAAAAAAAT-TCAACC
1 TTAATGATAAAAAAATATCAACC
71326028 TTAATGATAAAAAAATATCAA
1 TTAATGATAAAAAAATATCAA
71326049 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (23 bp):
TTAATGATAAAAAAATATCAACC
Found at i:71329446 original size:16 final size:15
Alignment explanation
Indices: 71329425--71329457 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
71329415 AAATAGATAA
71329425 ATATAAATAAATATTT
1 ATATAAATAAA-ATTT
71329441 ATATAAATAAAATTT
1 ATATAAATAAAATTT
71329456 AT
1 AT
71329458 GTAACACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAAATAAAATTT
Found at i:71330898 original size:25 final size:25
Alignment explanation
Indices: 71330870--71330917 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
71330860 TCTTTTCAAA
* *
71330870 TGCTCAAATTATATTTATATATAAG
1 TGCTAAAATTATACTTATATATAAG
71330895 TGCTAAAATTATACTTATATATA
1 TGCTAAAATTATACTTATATATA
71330918 TTTTCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (25 bp):
TGCTAAAATTATACTTATATATAAG
Found at i:71331300 original size:124 final size:118
Alignment explanation
Indices: 71331084--71331321 Score: 314
Period size: 124 Copynumber: 2.0 Consensus size: 118
71331074 CTTCATATAA
* *
71331084 TCTCTCTCTCTCTCTCCATATATATTAACACTTTAATTTTTTATCAGAAAAAATCCAGCTACAAC
1 TCTCTCTCTCTCTCTCCATATATATTAACACTTTAATTTTTTATCAGAAAAAACCCAACTACAAC
*
71331149 AATGGCGCAAAGAGAAGTAAACAAGAAGGGCAAAGGGAAAGCCATTGTGACTC
66 AATGGCGCAAAGAGAAGTAAACAAGAAGGGCAAAAGGAAAGCCATTGTGACTC
* ** *
71331202 TCTCTTTCTCTCTCTCCATATATATTAACACTTTCCCTTTTCTTTTTTATTAGAAAAAACCCAAC
1 TCTCTCTCTCTCTCTCCATATATATTAACA------CTTTAATTTTTTATCAGAAAAAACCCAAC
* * * * *
71331267 TACCACAATGGTGCAAGGAGAAGTAGACTAGAAGGGCAAAAGGAAAGCCATTGTG
60 TACAACAATGGCGCAAAGAGAAGTAAACAAGAAGGGCAAAAGGAAAGCCATTGTG
71331322 CCATGAAAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
118 29 0.28
124 73 0.72
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (118 bp):
TCTCTCTCTCTCTCTCCATATATATTAACACTTTAATTTTTTATCAGAAAAAACCCAACTACAAC
AATGGCGCAAAGAGAAGTAAACAAGAAGGGCAAAAGGAAAGCCATTGTGACTC
Found at i:71333844 original size:35 final size:35
Alignment explanation
Indices: 71333794--71333865 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
71333784 TAGTCATATA
* *
71333794 ATATATTTAATTATTAAATATACATAGATAAGCTC
1 ATATATTTAAATATTAAATAGACATAGATAAGCTC
71333829 ATATATTTAAATATTAAATAGACATAGATAAGCTC
1 ATATATTTAAATATTAAATAGACATAGATAAGCTC
71333864 AT
1 AT
71333866 CATTTATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (35 bp):
ATATATTTAAATATTAAATAGACATAGATAAGCTC
Found at i:71336170 original size:24 final size:24
Alignment explanation
Indices: 71336143--71336349 Score: 333
Period size: 24 Copynumber: 8.6 Consensus size: 24
71336133 CTTATTATGT
* * *
71336143 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
71336167 TCGCACACGTAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
71336191 TCGCACACTTAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
71336215 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
71336239 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
71336263 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
71336287 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
71336311 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
71336335 TCGCACACATAGTGC
1 TCGCACACATAGTGC
71336350 ATTTGAGATA
Statistics
Matches: 173, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 173 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:71339024 original size:3 final size:3
Alignment explanation
Indices: 71339016--71339062 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
71339006 TCTTTTTCAT
71339016 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
71339063 TATTCTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71339071 original size:7 final size:7
Alignment explanation
Indices: 71339019--71339071 Score: 55
Period size: 6 Copynumber: 8.4 Consensus size: 7
71339009 TTTTCATTTA
71339019 TTATTA-
1 TTATTAT
71339025 TTATTA-
1 TTATTAT
71339031 TTATTA-
1 TTATTAT
71339037 TTATTA-
1 TTATTAT
71339043 TTATTA-
1 TTATTAT
71339049 TTATTA-
1 TTATTAT
71339055 TTATTAT
1 TTATTAT
*
71339062 TTATTCT
1 TTATTAT
71339069 TTA
1 TTA
71339072 ACAGTTAGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 36 0.80
7 9 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATTAT
Found at i:71340543 original size:36 final size:36
Alignment explanation
Indices: 71340502--71340570 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
71340492 AATGCCATAG
*
71340502 TTGCTGAAAAATAAGCTCATGCCAAAATTCGAATAA
1 TTGCTGAAAAACAAGCTCATGCCAAAATTCGAATAA
71340538 TTGCTGAAAAACAAGCTCATGCCAAAATTCGAA
1 TTGCTGAAAAACAAGCTCATGCCAAAATTCGAA
71340571 CTCTATACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (36 bp):
TTGCTGAAAAACAAGCTCATGCCAAAATTCGAATAA
Found at i:71343361 original size:15 final size:16
Alignment explanation
Indices: 71343341--71343373 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
71343331 ATATATTTTT
71343341 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
71343356 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
71343373 T
1 T
71343374 ATAACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:71343457 original size:22 final size:21
Alignment explanation
Indices: 71343431--71343486 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
71343421 TGTTTTAGCA
71343431 TTATTTTTATTTATTTTAATAT
1 TTATTTTTATTTATTTTAA-AT
*
71343453 TTATTTTTATGT-TTTTAAAT
1 TTATTTTTATTTATTTTAAAT
* *
71343473 ATA-TTTGATTTATT
1 TTATTTTTATTTATT
71343487 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 6 0.21
20 6 0.21
21 6 0.21
22 11 0.38
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTATTTTTATTTATTTTAAAT
Found at i:71343488 original size:26 final size:24
Alignment explanation
Indices: 71343449--71343507 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
71343439 ATTTATTTTA
*
71343449 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
71343473 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
*
71343499 -TTTTTATTT
1 ATATTTATTT
71343508 AATGAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 10 0.32
25 8 0.26
26 13 0.42
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:71362579 original size:47 final size:47
Alignment explanation
Indices: 71362510--71363047 Score: 788
Period size: 47 Copynumber: 11.3 Consensus size: 47
71362500 CCCTTCGGGA
* * * * *
71362510 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
71362557 CTTATCACACATATGCACTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
71362604 TTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
71362651 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
71362698 CTTATAACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
71362745 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
71362792 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
71362839 CTTATCACACATATGCATTTTCACATTCATCACATGGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
71362886 TTTATCACATATATACACACTTTCACATTCATCACATCGGCCACTCGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
71362935 CTTATCACATATATACATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATAC--ACTTTCACATTCATCACATCGGCCATTAGGC
71362984 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
71363033 CTTATCACATATATA
1 CTTATCACATATATA
71363048 TATATCTCAT
Statistics
Matches: 441, Mismatches: 44, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
47 310 0.70
49 129 0.29
51 2 0.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:71362779 original size:25 final size:25
Alignment explanation
Indices: 71362607--71362685 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
71362597 ATTAGGCTTT
71362607 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
*** * *
71362632 ATCACAT-TGGCCAC--TCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
71362654 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
71362679 ATCACAT
1 ATCACAT
71362686 CGACCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 9 0.23
23 7 0.18
24 7 0.18
25 16 0.41
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:71362976 original size:41 final size:41
Alignment explanation
Indices: 71362930--71363025 Score: 111
Period size: 49 Copynumber: 2.1 Consensus size: 41
71362920 CATCGGCCAC
*
71362930 TCGGCCTTATCACATATATACATACTTTCACATTCATCACA
1 TCGGCCTTATCACATATATACACACTTTCACATTCATCACA
71362971 TCGGCCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACA
1 T----C----GGCCTTATCACATATATACACACTTTCACATTCATCACA
71363020 TCGGCC
1 TCGGCC
71363026 ATTAGGCCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
41 5 0.11
45 2 0.04
49 39 0.85
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.31
Consensus pattern (41 bp):
TCGGCCTTATCACATATATACACACTTTCACATTCATCACA
Found at i:71366795 original size:17 final size:18
Alignment explanation
Indices: 71366757--71366795 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
71366747 GAAATTAATA
*
71366757 TAAAAATAAAAACAAAAG
1 TAAAAACAAAAACAAAAG
71366775 -AAAAACAAAAAC-AAAG
1 TAAAAACAAAAACAAAAG
71366791 TAAAA
1 TAAAA
71366796 TAAATGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (18 bp):
TAAAAACAAAAACAAAAG
Found at i:71383149 original size:22 final size:22
Alignment explanation
Indices: 71383117--71383162 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
71383107 GACACCTATA
71383117 TTTTCGAGATAAAATGCTCAAC
1 TTTTCGAGATAAAATGCTCAAC
*
71383139 TTTTCGGGATAAAATGCTCAAC
1 TTTTCGAGATAAAATGCTCAAC
71383161 TT
1 TT
71383163 GGAATGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (22 bp):
TTTTCGAGATAAAATGCTCAAC
Found at i:71386605 original size:13 final size:13
Alignment explanation
Indices: 71386587--71386612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71386577 GGGATTTGTT
71386587 TTAACTAAACTAA
1 TTAACTAAACTAA
71386600 TTAACTAAACTAA
1 TTAACTAAACTAA
71386613 AAATGTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:71390455 original size:24 final size:25
Alignment explanation
Indices: 71390428--71390479 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
71390418 GCCTAGCCTC
71390428 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
**
71390452 TTTTGGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
71390477 TTT
1 TTT
71390480 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:71390714 original size:27 final size:27
Alignment explanation
Indices: 71390684--71390790 Score: 133
Period size: 27 Copynumber: 4.0 Consensus size: 27
71390674 GGGGCAAAAT
* * * *
71390684 GGTAATTTTACCCCACAAAGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
71390711 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
71390738 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
71390765 AGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
71390791 AAGTAATTTC
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:71390750 original size:54 final size:54
Alignment explanation
Indices: 71390683--71390799 Score: 164
Period size: 54 Copynumber: 2.2 Consensus size: 54
71390673 AGGGGCAAAA
*
71390683 TGGTAATTTTACCCCACAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTTTACCCCACAAAGGTATCTCAGTAATTCTACCCTACAGGGGTATTT
* * *
71390737 TGGT-ATTTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTT-TACCCCACAAAGGTATCTCAGTAATTCTACCCTACAGGGGTATTT
**
71390791 AAGTAATTT
1 TGGTAATTT
71390800 CACAAATTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
53 4 0.07
54 47 0.85
55 4 0.07
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (54 bp):
TGGTAATTTTACCCCACAAAGGTATCTCAGTAATTCTACCCTACAGGGGTATTT
Found at i:71390811 original size:27 final size:27
Alignment explanation
Indices: 71390780--71390991 Score: 255
Period size: 27 Copynumber: 7.9 Consensus size: 27
71390770 TTCTACCCTA
** * *
71390780 CAGGGGTATTTAAGTAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAC
* **
71390807 TAGGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* **
71390834 CAAGGGTATTTTGGTAATTTTACAAGT
1 CAGGGGTATTTTGGTAATTTTACAAAC
** * *
71390861 C-GAGGGTATTTCAGTAATTTCACAAAT
1 CAG-GGGTATTTTGGTAATTTTACAAAC
*
71390888 CAGGGGTATTTTGGTAATTTCACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
71390915 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
71390942 CAGGGTTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
71390969 CAGGGGTATTTTGGTAATTTTAC
1 CAGGGGTATTTTGGTAATTTTAC
71390992 TAATCGAGGG
Statistics
Matches: 157, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
27 156 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAC
Found at i:71390824 original size:54 final size:54
Alignment explanation
Indices: 71390711--71390987 Score: 208
Period size: 54 Copynumber: 5.1 Consensus size: 54
71390701 AAGGTATCTC
* ** * *
71390711 GGTAATTCTACCCTACAGGGGTATTTTGGT-ATTTCTACCCTAC-AAGGGTATTTC
1 GGTAATTCTACCCAACAGGGGTATTTTGGTAATTTC-A-CAAACTAGGGGTATTTT
* * ** *
71390765 AGTAATTCTACCCTACAGGGGTATTTAAGTAATTTCACAAATTAGGGGTATTTT
1 GGTAATTCTACCCAACAGGGGTATTTTGGTAATTTCACAAACTAGGGGTATTTT
**** * * * * *
71390819 GGTAATT-TTGTAAACCAAGGGTATTTTGGTAATTTTAC-AAGTCGAGGGTATTTC
1 GGTAATTCTACCCAA-CAGGGGTATTTTGGTAATTTCACAAACTAG-GGGTATTTT
* *
71390873 AGTAATT-T-CACAAATCAGGGGTATTTTGGTAATTTCACAAACTAGGGGTATTTT
1 GGTAATTCTAC-CCAA-CAGGGGTATTTTGGTAATTTCACAAACTAGGGGTATTTT
* * * * *
71390927 GGTAATTTTA-CAAACCAGGGTTATTTTGGTAATTTTACAAACCAGGGGTATTTT
1 GGTAATTCTACCCAA-CAGGGGTATTTTGGTAATTTCACAAACTAGGGGTATTTT
71390981 GGTAATT
1 GGTAATT
71390988 TTACTAATCG
Statistics
Matches: 180, Mismatches: 35, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
53 8 0.04
54 162 0.90
55 10 0.06
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (54 bp):
GGTAATTCTACCCAACAGGGGTATTTTGGTAATTTCACAAACTAGGGGTATTTT
Found at i:71391011 original size:54 final size:53
Alignment explanation
Indices: 71390783--71391042 Score: 229
Period size: 54 Copynumber: 4.8 Consensus size: 53
71390773 TACCCTACAG
** * * * *
71390783 GGGTATTTAAGTAATTTCACAAATTAGGGGTATTTTGGTAATTTT-GTAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACT-AATC-A
* ** * *
71390837 GGGTATTTTGGTAATTTTACAAGTC-GAGGGTATTTCAGTAATTTCACAAATCA
1 GGGTATTTTGGTAATTTTACAAATCAG-GGGTATTTTGGTAATTTTACTAATCA
* * *
71390890 GGGGTATTTTGGTAATTTCACAAA-CTAGGGGTATTTTGGTAATTTTACAAACCA
1 -GGGTATTTTGGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACTAATCA
*
71390944 GGGTTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACTAATCGA
1 GGG-TATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACTAATC-A
*** * * ** *
71390999 GGGTAAAATGGTAACTCTGTAAATCAGGGGTACTTTGGTAATTT
1 GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTT
71391043 GGTAAACTAA
Statistics
Matches: 169, Mismatches: 29, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
53 6 0.04
54 157 0.93
55 6 0.04
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACTAATCA
Found at i:71391012 original size:81 final size:81
Alignment explanation
Indices: 71390726--71391003 Score: 278
Period size: 81 Copynumber: 3.4 Consensus size: 81
71390716 TTCTACCCTA
*** ** * ***
71390726 CAGGGGTATTTTGGT-ATTTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTA-CAGGGGTAT
1 CAGGGGTATTTTGGTAATTT-TACTAAACAAGGGTATTTTGGTAATTTTACAAGACCA-GGGTAT
*
71390789 TTAAGTAATTTCACAAAT
64 TTCAGTAATTTCACAAAT
* * * *
71390807 TAGGGGTATTTTGGTAATTTT-GTAAACCAAGGGTATTTTGGTAATTTTACAAGTCGAGGGTATT
1 CAGGGGTATTTTGGTAATTTTACTAAA-CAAGGGTATTTTGGTAATTTTACAAGACCAGGGTATT
71390871 TCAGTAATTTCACAAAT
65 TCAGTAATTTCACAAAT
* *
71390888 CAGGGGTATTTTGGTAATTTCAC-AAACTAGGGGTATTTTGGTAATTTTACAA-ACCAGGGTTAT
1 CAGGGGTATTTTGGTAATTTTACTAAAC-AAGGGTATTTTGGTAATTTTACAAGACCAGGG-TAT
** * *
71390951 TTTGGTAATTTTACAAAC
64 TTCAGTAATTTCACAAAT
* *
71390969 CAGGGGTATTTTGGTAATTTTACTAATCGAGGGTA
1 CAGGGGTATTTTGGTAATTTTACTAAACAAGGGTA
71391004 AAATGGTAAC
Statistics
Matches: 162, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
80 7 0.04
81 147 0.91
82 8 0.05
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (81 bp):
CAGGGGTATTTTGGTAATTTTACTAAACAAGGGTATTTTGGTAATTTTACAAGACCAGGGTATTT
CAGTAATTTCACAAAT
Found at i:71391027 original size:81 final size:81
Alignment explanation
Indices: 71390874--71391042 Score: 187
Period size: 81 Copynumber: 2.1 Consensus size: 81
71390864 GGGTATTTCA
* * *** * *
71390874 GTAATTTCACAAATCAGGGGTATTTTGGTAATTTCACAAACTAGGGGTATTTTGGTAATTTTACA
1 GTAATTTCACAAACCAGGGGTATTTTGGTAATTTCACAAACGAGGGGTAAAATGGTAACTCTACA
* *
71390939 AACCAGGGTTATTTTG
66 AACCAGGGGTACTTTG
* * * **
71390955 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACTAATCGA-GGGTAAAATGGTAACTCTGT
1 GTAATTTCACAAACCAGGGGTATTTTGGTAATTTCAC-AAACGAGGGGTAAAATGGTAACTCTAC
*
71391019 AAATCAGGGGTACTTTG
65 AAACCAGGGGTACTTTG
71391036 GTAATTT
1 GTAATTT
71391043 GGTAAACTAA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
81 68 0.94
82 4 0.06
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (81 bp):
GTAATTTCACAAACCAGGGGTATTTTGGTAATTTCACAAACGAGGGGTAAAATGGTAACTCTACA
AACCAGGGGTACTTTG
Found at i:71391048 original size:27 final size:26
Alignment explanation
Indices: 71390780--71391042 Score: 167
Period size: 27 Copynumber: 9.8 Consensus size: 26
71390770 TTCTACCCTA
** *
71390780 CAGGGGTATTTAAGTAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTT-ATAAAT
* * *
71390807 TAGGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAA-TTTATAAAT
*
71390834 CAAGGGTATTTTGGTAATTT-TACAAGT
1 CAGGGGTATTTTGGTAATTTATA-AA-T
** *
71390861 C-GAGGGTATTTCAGTAATTTCACAAAT
1 CAG-GGGTATTTTGGTAATTT-ATAAAT
*
71390888 CAGGGGTATTTTGGTAATTTCACAAA-
1 CAGGGGTATTTTGGTAATTT-ATAAAT
* *
71390914 CTAGGGGTATTTTGGTAATTTTACAAAC
1 C-AGGGGTATTTTGGTAA-TTTATAAAT
* * *
71390942 CAGGGTTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAA-TTTATAAAT
71390969 CAGGGGTATTTTGGTAATTT-TACTAAT
1 CAGGGGTATTTTGGTAATTTATA--AAT
*** * *
71390996 C-GAGGGTAAAATGGTAACTCTGTAAAT
1 CAG-GGGTATTTTGGTAA-TTTATAAAT
*
71391023 CAGGGGTACTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
71391043 GGTAAACTAA
Statistics
Matches: 193, Mismatches: 27, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.02
26 12 0.06
27 162 0.84
28 13 0.07
29 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (26 bp):
CAGGGGTATTTTGGTAATTTATAAAT
Found at i:71393182 original size:20 final size:21
Alignment explanation
Indices: 71393154--71393205 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
71393144 AAAGAAAAAG
*
71393154 TAAATTAAAAAAATAAAGGTAA
1 TAAA-TAAAAAAATAAAGATAA
* *
71393176 -AAGTAAAAACATAAAGATAA
1 TAAATAAAAAAATAAAGATAA
71393196 TAAATAAAAA
1 TAAATAAAAA
71393206 TCTTCAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (21 bp):
TAAATAAAAAAATAAAGATAA
Found at i:71398546 original size:13 final size:13
Alignment explanation
Indices: 71398528--71398553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71398518 GGGATTTGTT
71398528 TTAACTAAACTAA
1 TTAACTAAACTAA
71398541 TTAACTAAACTAA
1 TTAACTAAACTAA
71398554 GAAAGCACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACTAAACTAA
Found at i:71403418 original size:55 final size:54
Alignment explanation
Indices: 71403335--71403442 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 54
71403325 AACAAATCGA
*
71403335 GCGTGCAACACGCCCTTGCCTTAAAACCGTGGCCAAACCTATCAAATTAACACAG
1 GCGTGCAACACGCCCGTGCC-TAAAACCGTGGCCAAACCTATCAAATTAACACAG
* * * *
71403390 GCGTGCAACACGCCCGTGCC-AAGCAACCGTGGTCGAACCTATTAGATTAACAC
1 GCGTGCAACACGCCCGTGCCTAA--AACCGTGGCCAAACCTATCAAATTAACAC
71403443 GGGTGTGAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 2 0.04
55 44 0.96
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (54 bp):
GCGTGCAACACGCCCGTGCCTAAAACCGTGGCCAAACCTATCAAATTAACACAG
Found at i:71421347 original size:6 final size:6
Alignment explanation
Indices: 71421336--71421404 Score: 93
Period size: 6 Copynumber: 11.5 Consensus size: 6
71421326 GTGCTGAAAT
* * *
71421336 TATATA TATATA TATATA TATATA TATATA TATATG TATATG TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
71421384 TATATG TATATG TATATA TAT
1 TATATA TATATA TATATA TAT
71421405 TCTATTTCTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:71425755 original size:2 final size:2
Alignment explanation
Indices: 71425748--71425781 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
71425738 AATTGCTAAA
71425748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71425782 TTGTTTTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71438147 original size:21 final size:23
Alignment explanation
Indices: 71438123--71438164 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
71438113 ATTTATTTAT
71438123 TTAATG-TAAAAAAAT-TCAACC
1 TTAATGATAAAAAAATATCAACC
71438144 TTAATGATAAAAAAATATCAA
1 TTAATGATAAAAAAATATCAA
71438165 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (23 bp):
TTAATGATAAAAAAATATCAACC
Found at i:71441561 original size:16 final size:15
Alignment explanation
Indices: 71441540--71441572 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
71441530 AAATAGATAA
71441540 ATATAAATAAATATTT
1 ATATAAATAAA-ATTT
71441556 ATATAAATAAAATTT
1 ATATAAATAAAATTT
71441571 AT
1 AT
71441573 GTAACACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAAATAAAATTT
Found at i:71443013 original size:25 final size:25
Alignment explanation
Indices: 71442985--71443032 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
71442975 TCTTTTCAAA
* *
71442985 TGCTCAAATTATATTTATATATAAG
1 TGCTAAAATTATACTTATATATAAG
71443010 TGCTAAAATTATACTTATATATA
1 TGCTAAAATTATACTTATATATA
71443033 TTTTCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (25 bp):
TGCTAAAATTATACTTATATATAAG
Found at i:71443415 original size:124 final size:118
Alignment explanation
Indices: 71443205--71443436 Score: 320
Period size: 124 Copynumber: 1.9 Consensus size: 118
71443195 ATAATCTCTC
* *
71443205 TCTCTCTCTCCATATATATTAACACTTTAATTTTTTATCAGAAAAAATCCAGCTACAACAATGGC
1 TCTCTCTCTCCATATATATTAACACTTTAATTTTTTATCAGAAAAAACCCAACTACAACAATGGC
71443270 GCAAAGAGAAGTAAACAAGAAGGGCAAAGGGAAAGCCATTGTGACTCTCTTTT
66 GCAAAGAGAAGTAAACAAGAAGGGCAAAGGGAAAGCCATTGTGACTCTCTTTT
** * *
71443323 TCTCTCTCTCCATATATATTAACACTTTCCCTTTTCTTTTTTATTAGAAAAAACCCAACTACCAC
1 TCTCTCTCTCCATATATATTAACA------CTTTAATTTTTTATCAGAAAAAACCCAACTACAAC
* * * *
71443388 AATGGTGCAAGGAGAAGTAGACTAGAAGGGCAAAGGGAAAGCCATTGTG
60 AATGGCGCAAAGAGAAGTAAACAAGAAGGGCAAAGGGAAAGCCATTGTG
71443437 CCATGAAAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
118 24 0.24
124 74 0.76
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (118 bp):
TCTCTCTCTCCATATATATTAACACTTTAATTTTTTATCAGAAAAAACCCAACTACAACAATGGC
GCAAAGAGAAGTAAACAAGAAGGGCAAAGGGAAAGCCATTGTGACTCTCTTTT
Found at i:71445925 original size:35 final size:35
Alignment explanation
Indices: 71445879--71445950 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
71445869 TAGTCATATA
*
71445879 ATATATTTAAATATTAAATATACATAGATAAGCTC
1 ATATATTTAAATATTAAATAGACATAGATAAGCTC
71445914 ATATATTTAAATATTAAATAGACATAGATAAGCTC
1 ATATATTTAAATATTAAATAGACATAGATAAGCTC
71445949 AT
1 AT
71445951 CATTTATTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (35 bp):
ATATATTTAAATATTAAATAGACATAGATAAGCTC
Found at i:71452972 original size:3 final size:3
Alignment explanation
Indices: 71452964--71452988 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
71452954 TCAATCCTAG
71452964 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
71452989 AAAATGGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:71457804 original size:6 final size:6
Alignment explanation
Indices: 71457793--71457826 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
71457783 ATTGTGACCG
71457793 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTC
71457827 CCTCCCCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTC
Found at i:71463150 original size:44 final size:43
Alignment explanation
Indices: 71463100--71463182 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
71463090 CATGTTGATA
71463100 TCTTCGATCTGCTCTCCGCCGAACACAGAGATGCCAAATCTGCT
1 TCTTCGATCTGCTCTCCGCC-AACACAGAGATGCCAAATCTGCT
* * * * * *
71463144 TCTTCGATTTGTTCTCTGGCAATATAGAGATGCCAAATC
1 TCTTCGATCTGCTCTCCGCCAACACAGAGATGCCAAATC
71463183 ATCTTAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 17 0.52
44 16 0.48
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (43 bp):
TCTTCGATCTGCTCTCCGCCAACACAGAGATGCCAAATCTGCT
Found at i:71463648 original size:204 final size:203
Alignment explanation
Indices: 71463145--71463726 Score: 819
Period size: 204 Copynumber: 2.8 Consensus size: 203
71463135 AAATCTGCTT
** * *
71463145 CTTCGATTTGTTCTCTGGCAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGAAAATACAAAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
*
71463210 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCTAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAG-ATGCCAAATCATCTT
* * *
71463275 GGATCTTCTTCAGTATAATCATCTGAAGGTGAGATCTGCAATGTATCTACTCCCCGTCGAAGTGG
130 GGATCTTCTTCAGTATAAACATCTGAAGGTG-GATCTGCTATGTATCTACTCCCCGTCGAAATGG
71463340 AGATGCCAGA
194 AGATGCCAGA
* * * *
71463350 CTTCGATTTGTTCTCT-AACAATACAGAA-ATGCCAAATCATCGTACATTTGCTTTATCGTAAAC
1 CTTCGATTTGTTCTCTGAA-AATACA-AAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGC
* * * * *
71463413 ATGTGAAAGCCAAATCAGCTATGTTTTCGATTCGCTCCTTGTAAGCACAATGATGCCAAATCATC
64 ACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAA-GATGCCAAATCATC
* * * *
71463478 TTGGATCTTCTTCGGTATAAACATCTGAAAGT-GATCTGCTATGTATCTGCTCTCCGTCGAATAT
128 TTGGATCTTCTTCAGTATAAACATCTGAAGGTGGATCTGCTATGTATCTACTCCCCGTCGAA-AT
71463542 GGAGATGCCAGA
192 GGAGATGCCAGA
*
71463554 CTTCGATTTGTTCTCTGAAAATACAAAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
1 CTTCGATTTGTTCTCTGAAAATACAAAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* * * *
71463619 GTGAAAACGAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAA-GATGCCAAATCATCTT
* *
71463684 GGATCTACGTCAGTATAAACATCTGAAGGTTGGATCTGCTATG
130 GGATCTTCTTCAGTATAAACATCTGAAGG-TGGATCTGCTATG
71463727 CTGCGGCCTA
Statistics
Matches: 329, Mismatches: 40, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
203 28 0.09
204 147 0.45
205 141 0.43
206 13 0.04
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (203 bp):
CTTCGATTTGTTCTCTGAAAATACAAAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGATGCCAAATCATCTTG
GATCTTCTTCAGTATAAACATCTGAAGGTGGATCTGCTATGTATCTACTCCCCGTCGAAATGGAG
ATGCCAGA
Found at i:71475864 original size:14 final size:14
Alignment explanation
Indices: 71475809--71475864 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
71475799 AAATAAAAAT
71475809 ATATAATGATATA-A
1 ATATAAT-ATATATA
*
71475823 ATTATGAAAATATATA
1 A-TAT-AATATATATA
* *
71475839 ATACAATGTATATA
1 ATATAATATATATA
71475853 ATATAATATATA
1 ATATAATATATA
71475865 AAAAAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 19 0.58
15 10 0.30
16 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:71477684 original size:2 final size:2
Alignment explanation
Indices: 71477677--71477707 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
71477667 TTGGTTAATG
71477677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71477708 ACTTGATATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71478530 original size:29 final size:29
Alignment explanation
Indices: 71478497--71478555 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
71478487 TCTCTCTCTC
71478497 TCTCCCTCTCTCCATATATATTAACACTT
1 TCTCCCTCTCTCCATATATATTAACACTT
71478526 TCTCCCTCTCTCCATATATATTAACACTT
1 TCTCCCTCTCTCCATATATATTAACACTT
71478555 T
1 T
71478556 GCTTTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (29 bp):
TCTCCCTCTCTCCATATATATTAACACTT
Found at i:71480017 original size:27 final size:29
Alignment explanation
Indices: 71479986--71480053 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 29
71479976 TGCTTTAGTT
71479986 ATCATAA-TC-TAACTAATTTTAGATATA
1 ATCATAACTCATAACTAATTTTAGATATA
71480013 ATCATAACTCAAGTAACTAATTTTAGATATA
1 ATCATAACTC-A-TAACTAATTTTAGATATA
71480044 ATCATAACTC
1 ATCATAACTC
71480054 TTTGACTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 7 0.19
28 2 0.05
31 28 0.76
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (29 bp):
ATCATAACTCATAACTAATTTTAGATATA
Found at i:71480070 original size:30 final size:31
Alignment explanation
Indices: 71479995--71480053 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
71479985 TATCATAATC
71479995 TAACTAATTTTAGATATAATCATAACTCAAG
1 TAACTAATTTTAGATATAATCATAACTCAAG
71480026 TAACTAATTTTAGATATAATCATAACTC
1 TAACTAATTTTAGATATAATCATAACTC
71480054 TTTGACTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (31 bp):
TAACTAATTTTAGATATAATCATAACTCAAG
Found at i:71480959 original size:2 final size:2
Alignment explanation
Indices: 71480952--71480988 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
71480942 AAACGTGAAT
71480952 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
71480989 TGTATATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:71488585 original size:361 final size:362
Alignment explanation
Indices: 71487888--71488613 Score: 1224
Period size: 361 Copynumber: 2.0 Consensus size: 362
71487878 CACAGAAGCA
71487888 TGAGTTTATCCATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAA
1 TGAGTTTATCCATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAA
71487953 CCAACATCTCAGCAAGCATATTTTGGAAGAAGAAATTTAAAATCAAACCATACATTATACTAGTT
66 CCAACATCTCAGCAAGCATATTTTGGAAGAAGAAATTTAAAATCAAACCATAC--TATA-TAGTT
71488018 TCAGACAACAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACA
128 TCAGACAACAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACA
71488083 ATATTTTGAGAAAGAAAAAGATAACAGGCATGACAAAAAATATTAAATAGGAAGTTTGTTCGATG
193 ATATTTTGAGAAAGAAAAAGATAACAGGCATGACAAAAAATATTAAATAGGAAGTTTGTTCGATG
71488148 TTACTCTGCTCTGTAATTGCATAAATTCTCTCCAAATACTTTGTTAAAGTTACCATATAGTTAAA
258 TTACTCTGCTCTGTAATTGCATAAATTCTCTCCAAATACTTTGTTAAAGTTACCATATAGTTAAA
71488213 TAACCTAACTGTATACACAGACAGTCAGAGGCAAATCTAG
323 TAACCTAACTGTATACACAGACAGTCAGAGGCAAATCTAG
* *
71488253 TGAGTTTATCCATGATGCGTTTGAAAATTGTGCTTCTTACAAACTTGTTTTAACAATTTAAGAAA
1 TGAGTTTATCCATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAA
* *
71488318 CCAACATCTCAGCAAGTATATTTTGGCAA-AAGAAATTTAAAATCATACCATAC-AT-TAGTTTC
66 CCAACATCTCAGCAAGCATATTTTGG-AAGAAGAAATTTAAAATCAAACCATACTATATAGTTTC
* * *
71488380 AGTCAACAGCTACACTATTAACATAATAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAAT
130 AGACAACAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAAT
* * *
71488445 ATTTTGAGCAGGAAAAAGATTAACAGGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGT
195 ATTTTGAGAAAGAAAAAGA-TAACAGGCATGACAAAAAATATTAAATAGGAAGTTTGTTCGATGT
* * * *
71488510 TACTCTGCTTTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTATCATATAGTTAAAT
259 TACTCTGCTCTGTAATTGCATAAATTCTCTCCAAATACTTTGTTAAAGTTACCATATAGTTAAAT
* * **
71488575 AACTTAACTGTATTCACAGACAGTCAGAGGTGAATCTAG
324 AACCTAACTGTATACACAGACAGTCAGAGGCAAATCTAG
71488614 GGGGCAGGCA
Statistics
Matches: 341, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
360 86 0.25
361 140 0.41
362 2 0.01
365 111 0.33
366 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (362 bp):
TGAGTTTATCCATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAA
CCAACATCTCAGCAAGCATATTTTGGAAGAAGAAATTTAAAATCAAACCATACTATATAGTTTCA
GACAACAGCTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATA
TTTTGAGAAAGAAAAAGATAACAGGCATGACAAAAAATATTAAATAGGAAGTTTGTTCGATGTTA
CTCTGCTCTGTAATTGCATAAATTCTCTCCAAATACTTTGTTAAAGTTACCATATAGTTAAATAA
CCTAACTGTATACACAGACAGTCAGAGGCAAATCTAG
Found at i:71499293 original size:23 final size:24
Alignment explanation
Indices: 71499249--71499300 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
71499239 ACTTAAGTTA
**
71499249 ATTAA-TTAAATTTATATTTATTT
1 ATTAATTTAAATTTATAACTATTT
71499272 ATTAATTTAAATTT-TAACTATTT
1 ATTAATTTAAATTTATAACTATTT
*
71499295 AATAAT
1 ATTAAT
71499301 CATCATCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTAATTTAAATTTATAACTATTT
Found at i:71508588 original size:91 final size:92
Alignment explanation
Indices: 71508317--71508594 Score: 371
Period size: 92 Copynumber: 3.0 Consensus size: 92
71508307 ATCAACCCAA
* *
71508317 AACAAGTTTCAAAAAATCAAAATAACTTAAAATAGTGCAATGCTAAAAATAAGTGCGACTTCTCG
1 AACAAGTTTCAAAAAATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCAACTTCTCG
* *
71508382 CCAAGATTTGTTAAGTAGTGAAATCGC
66 ACAAGATTTATTAAGTAGTGAAATCGC
* * * *
71508409 AACAAGTTTCAAGAAATCAAAACAACTTAAAATAGTACAAGGCTAAAAATAAGTGCAACTTCTTG
1 AACAAGTTTCAAAAAATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCAACTTCTCG
71508474 ACAAGATTTATTAAGTAGTGAAATCGC
66 ACAAGATTTATTAAGTAGTGAAATCGC
* * * * * ** *
71508501 AATAAGTTTCAAAAAACCAAAGCAACTT-AGACAGTGCAATGCTAAAAATAAAAGCCACTT-TCC
1 AACAAGTTTCAAAAAATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCAACTTCT-C
* *
71508564 GACAAAATTTATTAAGTAGTGAAATTGC
65 GACAAGATTTATTAAGTAGTGAAATCGC
71508592 AAC
1 AAC
71508595 GTGAATTATG
Statistics
Matches: 162, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
90 1 0.01
91 53 0.33
92 108 0.67
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (92 bp):
AACAAGTTTCAAAAAATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCAACTTCTCG
ACAAGATTTATTAAGTAGTGAAATCGC
Found at i:71511239 original size:10 final size:10
Alignment explanation
Indices: 71511223--71511270 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
71511213 AATATAACTA
71511223 TTAATTATTT
1 TTAATTATTT
* *
71511233 GTAATTAGTAT
1 TTAATTA-TTT
*
71511244 TTAATTTTTT
1 TTAATTATTT
*
71511254 TTATTTATTT
1 TTAATTATTT
71511264 TTAATTA
1 TTAATTA
71511271 ATAATTTTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (10 bp):
TTAATTATTT
Found at i:71532336 original size:2 final size:2
Alignment explanation
Indices: 71532329--71532360 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
71532319 AGCTCAACGC
71532329 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
71532361 TCAACAAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:71538093 original size:9 final size:9
Alignment explanation
Indices: 71538062--71538104 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
71538052 GTTCAAGGTG
71538062 TAATTAATT
1 TAATTAATT
71538071 TAA-TAATTT
1 TAATTAA-TT
71538080 TAATTAATT
1 TAATTAATT
* *
71538089 AAATTTATT
1 TAATTAATT
71538098 TAATTAA
1 TAATTAA
71538105 AAATCTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 3 0.11
9 22 0.79
10 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTAATT
Found at i:71538102 original size:14 final size:14
Alignment explanation
Indices: 71538063--71538105 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
71538053 TTCAAGGTGT
*
71538063 AATTAATTTAA-TA
1 AATTTATTTAATTA
* *
71538076 ATTTTAATTAATTA
1 AATTTATTTAATTA
71538090 AATTTATTTAATTA
1 AATTTATTTAATTA
71538104 AA
1 AA
71538106 AATCTATTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTATTTAATTA
Found at i:71545099 original size:19 final size:19
Alignment explanation
Indices: 71545035--71545099 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
71545025 AAATCCATCA
* *
71545035 ATTTTTTATTTATGAAATAT
1 ATTTTTAATTT-TTAAATAT
* * *
71545055 ATTTATAA-TTAT-AATAA
1 ATTTTTAATTTTTAAATAT
71545072 ATGTTTTAATTTTTAAATAT
1 AT-TTTTAATTTTTAAATAT
71545092 ATTTTTAA
1 ATTTTTAA
71545100 ATATTTTAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 11 0.32
20 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTTAATTTTTAAATAT
Found at i:71545917 original size:76 final size:76
Alignment explanation
Indices: 71545794--71545953 Score: 275
Period size: 76 Copynumber: 2.1 Consensus size: 76
71545784 ATATTTTTAA
** *
71545794 AATTATTATTAGAAGAATAGTAATGATTTGTTTCTTAATTAACAATATTTTAAAAATTTTATTTT
1 AATT-TTATTAGAAGAATAGTAATGATTTGTTTAATAATTAACAATATTTTAAAAATTATATTTT
*
71545859 TAATAGTATTTT
65 GAATAGTATTTT
71545871 AATTTTATTAGAAGAATAGTAATGATTTGTTTAATAATTAACAATATTTTAAAAATTATATTTTG
1 AATTTTATTAGAAGAATAGTAATGATTTGTTTAATAATTAACAATATTTTAAAAATTATATTTTG
71545936 AATAGTATTTT
66 AATAGTATTTT
71545947 AATTTTA
1 AATTTTA
71545954 AAACTACTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 75 0.95
77 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (76 bp):
AATTTTATTAGAAGAATAGTAATGATTTGTTTAATAATTAACAATATTTTAAAAATTATATTTTG
AATAGTATTTT
Found at i:71556953 original size:16 final size:15
Alignment explanation
Indices: 71556913--71556953 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
71556903 TCAAAACTTC
71556913 TATTTAGAATAATAT
1 TATTTAGAATAATAT
71556928 TATTTAAGAATAATTAT
1 TATTT-AGAATAA-TAT
*
71556945 TGTTTAGAA
1 TATTTAGAA
71556954 CAAAAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 11 0.48
17 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (15 bp):
TATTTAGAATAATAT
Found at i:71559849 original size:41 final size:40
Alignment explanation
Indices: 71559804--71559951 Score: 118
Period size: 41 Copynumber: 3.4 Consensus size: 40
71559794 CAAAAAGTTG
71559804 AGCAATAGTGGCGCTTTT-CTACCAAACGCCGCTAAAAGCTA
1 AGCAATAGTGGCG-TTTTACT-CCAAACGCCGCTAAAAGCTA
* *
71559845 AGCAATAGTGGCGTTTTAGGTCCAAACGCCGCTAAAAGTTGAGCAATTG
1 AGCAATAGTGGCGTTTTA-CTCCAAACGCCGCT-AAA----AGC---TA
* * * *
71559894 AGCAATAGTGGCATTTTAGGTCCAGACGCCGCTAAAAGCTG
1 AGCAATAGTGGCGTTTTA-CTCCAAACGCCGCTAAAAGCTA
*
71559935 ATCAATAGTGGCGTTTT
1 AGCAATAGTGGCGTTTT
71559952 TTGTCAAAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
40 4 0.04
41 42 0.46
42 4 0.04
44 3 0.03
46 3 0.03
48 3 0.03
49 32 0.35
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (40 bp):
AGCAATAGTGGCGTTTTACTCCAAACGCCGCTAAAAGCTA
Found at i:71559917 original size:49 final size:49
Alignment explanation
Indices: 71559845--71559940 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
71559835 CTAAAAGCTA
* *
71559845 AGCAATAGTGGCGTTTTAGGTCCAAACGCCGCTAAAAGTTGAGCAATTG
1 AGCAATAGTGGCATTTTAGGTCCAAACGCCGCTAAAAGCTGAGCAATTG
* *
71559894 AGCAATAGTGGCATTTTAGGTCCAGACGCCGCTAAAAGCTGATCAAT
1 AGCAATAGTGGCATTTTAGGTCCAAACGCCGCTAAAAGCTGAGCAAT
71559941 AGTGGCGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (49 bp):
AGCAATAGTGGCATTTTAGGTCCAAACGCCGCTAAAAGCTGAGCAATTG
Found at i:71560555 original size:7 final size:7
Alignment explanation
Indices: 71560545--71560631 Score: 61
Period size: 7 Copynumber: 12.6 Consensus size: 7
71560535 CACTAAACTT
71560545 TAAACCA
1 TAAACCA
*
71560552 TAAATTC-
1 TAAA-CCA
*
71560559 TAAACCC
1 TAAACCA
71560566 TAAACCA
1 TAAACCA
*
71560573 TAAACTA
1 TAAACCA
* *
71560580 TATACAA
1 TAAACCA
71560587 TAAACC-
1 TAAACCA
71560593 TAAACCA
1 TAAACCA
*
71560600 TAAACCC
1 TAAACCA
* *
71560607 TAATCCC
1 TAAACCA
*
71560614 TAAACCT
1 TAAACCA
*
71560621 TAAACCT
1 TAAACCA
71560628 TAAA
1 TAAA
71560632 TGATGCAAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
6 7 0.11
7 57 0.88
8 1 0.02
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCA
Found at i:71560555 original size:21 final size:21
Alignment explanation
Indices: 71560531--71560577 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
71560521 TGTTTATCCC
**
71560531 TAAACACTAAACTTTAAACCA
1 TAAACACTAAACCCTAAACCA
**
71560552 TAAATTCTAAACCCTAAACCA
1 TAAACACTAAACCCTAAACCA
71560573 TAAAC
1 TAAAC
71560578 TATATACAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACACTAAACCCTAAACCA
Done.