Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 39 of 120
Found at i:10284157 original size:17 final size:18
Alignment explanation
Indices: 10284125--10284159 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10284115 AATGTAATTA
*
10284125 TTGCATATTCATGATATT
1 TTGCATAATCATGATATT
10284143 TTGCATAAT-ATGATATT
1 TTGCATAATCATGATATT
10284160 GAGGTGAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (18 bp):
TTGCATAATCATGATATT
Found at i:10289051 original size:18 final size:18
Alignment explanation
Indices: 10289028--10289062 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10289018 ATAGAGCAAG
*
10289028 TTTGGTATCGATTTTGAC
1 TTTGGTATCGATATTGAC
10289046 TTTGGTATCGATATTGA
1 TTTGGTATCGATATTGA
10289063 AGGCTAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.49
Consensus pattern (18 bp):
TTTGGTATCGATATTGAC
Found at i:10293897 original size:32 final size:32
Alignment explanation
Indices: 10293860--10293920 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
10293850 ACATGCGAAG
*
10293860 CAGAATCAGATTTATGGTATGCTTAACATAAA
1 CAGAATCAGATTTATGGCATGCTTAACATAAA
* *
10293892 CAGAATCAGATTTATTGCGTGCTTAACAT
1 CAGAATCAGATTTATGGCATGCTTAACAT
10293921 GCAAAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
CAGAATCAGATTTATGGCATGCTTAACATAAA
Found at i:10297502 original size:18 final size:18
Alignment explanation
Indices: 10297476--10297510 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10297466 TACCTGGCCT
* *
10297476 TCAATATCGATATCAAAG
1 TCAAAATCGATACCAAAG
10297494 TCAAAATCGATACCAAA
1 TCAAAATCGATACCAAA
10297511 CTTGCTCTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.23
Consensus pattern (18 bp):
TCAAAATCGATACCAAAG
Found at i:10298875 original size:79 final size:78
Alignment explanation
Indices: 10298750--10298906 Score: 269
Period size: 79 Copynumber: 2.0 Consensus size: 78
10298740 TGAAATGAAT
* *
10298750 GCTACCATGAGAAAGAGGTTTGACCTACTAACTATCATCGAGAGTTGCATCGGAGGCTACAAAAT
1 GCTACCATGAGAAAGAGGTTTGACCCACTAACTATCATCGAGAGTTGCATCAGAGGCTACAAAAT
10298815 CTCAATCAAGGAA
66 CTCAATCAAGGAA
* *
10298828 GCTATCATGAGAAAGAGGTTTGTACCCACTCACTATCATCGAGAGTTGCATCAGAGGCTACAAAA
1 GCTACCATGAGAAAGAGGTTTG-ACCCACTAACTATCATCGAGAGTTGCATCAGAGGCTACAAAA
10298893 TCTCAATCAAGGAA
65 TCTCAATCAAGGAA
10298907 ATCGTAGTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 21 0.28
79 53 0.72
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (78 bp):
GCTACCATGAGAAAGAGGTTTGACCCACTAACTATCATCGAGAGTTGCATCAGAGGCTACAAAAT
CTCAATCAAGGAA
Found at i:10304114 original size:19 final size:19
Alignment explanation
Indices: 10304090--10304128 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
10304080 GCATTACAAA
*
10304090 AATAAAAAAGAAAGAAATT
1 AATAAAAAAGAAAAAAATT
*
10304109 AATAAAAAATAAAAAAATT
1 AATAAAAAAGAAAAAAATT
10304128 A
1 A
10304129 CAGCATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (19 bp):
AATAAAAAAGAAAAAAATT
Found at i:10314417 original size:19 final size:19
Alignment explanation
Indices: 10314382--10314418 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10314372 TTATATCTAG
*
10314382 ATTAATTAATTAATTAAAA
1 ATTAATTAACTAATTAAAA
*
10314401 ATTAATTAACTACTTAAA
1 ATTAATTAACTAATTAAA
10314419 TACTTTCACA
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:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAATTAACTAATTAAAA
Found at i:10318074 original size:43 final size:43
Alignment explanation
Indices: 10318023--10318169 Score: 188
Period size: 43 Copynumber: 3.4 Consensus size: 43
10318013 TGGAGATTAT
*
10318023 TAAATGGAAGACTTATGTCTCGAGTAA-AGCATAAGATTATTTA
1 TAAATGGAAGACTTATGTCTCG-GAAAGAGCATAAGATTATTTA
** *
10318066 TAAATGGAAGACTTATAACTCGGAAAGAGCATAAGATTAGTTA
1 TAAATGGAAGACTTATGTCTCGGAAAGAGCATAAGATTATTTA
* * * * *
10318109 TAAATGGAAGACCTATGTTTCGGAAAGAGCATAGGATTATGTG
1 TAAATGGAAGACTTATGTCTCGGAAAGAGCATAAGATTATTTA
10318152 TAAATGGAAGAACTTATG
1 TAAATGGAAG-ACTTATG
10318170 ACACGGTTGG
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
42 3 0.03
43 80 0.90
44 6 0.07
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (43 bp):
TAAATGGAAGACTTATGTCTCGGAAAGAGCATAAGATTATTTA
Found at i:10325422 original size:25 final size:24
Alignment explanation
Indices: 10325373--10325438 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 24
10325363 CTAAACGGAA
***
10325373 AGCACACAAAGTGCT-AAATGGAG
1 AGCACACAAAGTGCTAAAACAAAG
10325396 AGCACACAAAGTGCTAATAACAAAG
1 AGCACACAAAGTGCTAA-AACAAAG
10325421 AGCACACAAAGTGCTAAA
1 AGCACACAAAGTGCTAAA
10325439 CGGAGAGCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.39
24 2 0.05
25 21 0.55
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (24 bp):
AGCACACAAAGTGCTAAAACAAAG
Found at i:10325445 original size:23 final size:23
Alignment explanation
Indices: 10325347--10325446 Score: 123
Period size: 23 Copynumber: 4.3 Consensus size: 23
10325337 ACAAATGAAT
10325347 GGAGAGCACA-AACA-TGCTAAAC
1 GGAGAGCACACAA-AGTGCTAAAC
* *
10325369 GGAAAGCACACAAAGTGCTAAAT
1 GGAGAGCACACAAAGTGCTAAAC
10325392 GGAGAGCACACAAAGTGCTAATAAC
1 GGAGAGCACACAAAGTGCT-A-AAC
**
10325417 AAAGAGCACACAAAGTGCTAAAC
1 GGAGAGCACACAAAGTGCTAAAC
10325440 GGAGAGC
1 GGAGAGC
10325447 GCGCTAAGGT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
22 10 0.15
23 35 0.53
24 2 0.03
25 19 0.29
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (23 bp):
GGAGAGCACACAAAGTGCTAAAC
Found at i:10331014 original size:23 final size:23
Alignment explanation
Indices: 10330970--10331044 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
10330960 AAAAATGAAT
*
10330970 GGAGAGCACA-AACGTGCTAAAC
1 GGAGAGCACACAAAGTGCTAAAC
*
10330992 GGAGAGCACACAAAGTGCAAAAC
1 GGAGAGCACACAAAGTGCTAAAC
10331015 GGAGAGCACACAAAGTGCTAAAC
1 GGAGAGCACACAAAGTGCTAAAC
10331038 GGAGAGC
1 GGAGAGC
10331045 GCGCTAAGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 10 0.20
23 39 0.80
ACGTcount: A:0.43, C:0.21, G:0.29, T:0.07
Consensus pattern (23 bp):
GGAGAGCACACAAAGTGCTAAAC
Found at i:10345576 original size:43 final size:43
Alignment explanation
Indices: 10345524--10345675 Score: 173
Period size: 43 Copynumber: 3.5 Consensus size: 43
10345514 CGGTGATTAT
* *
10345524 TAAATGGAAGACTTATGTCTCAGG-TAGAGCATAAGATTATTTA
1 TAAATGGAAGACTTATGACTC-GGCAAGAGCATAAGATTATTTA
* * *
10345567 TAAATGGAAGACTTATGACTCAGAAAGAGCATAAGACTA-TTA
1 TAAATGGAAGACTTATGACTCGGCAAGAGCATAAGATTATTTA
* *** * *
10345609 TAAATGGAAGACCTATTTTTCGGCAAGAGCATAAGATTATGTG
1 TAAATGGAAGACTTATGACTCGGCAAGAGCATAAGATTATTTA
10345652 TAAATGGAAGAACTTATGACTCGG
1 TAAATGGAAG-ACTTATGACTCGG
10345676 TTGGAGCATA
Statistics
Matches: 89, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 36 0.40
43 44 0.49
44 9 0.10
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (43 bp):
TAAATGGAAGACTTATGACTCGGCAAGAGCATAAGATTATTTA
Found at i:10376774 original size:12 final size:12
Alignment explanation
Indices: 10376757--10376788 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
10376747 GGATCAAGAC
10376757 GAAGAAGAGAAA
1 GAAGAAGAGAAA
10376769 GAAGAAGAGAAA
1 GAAGAAGAGAAA
10376781 GAAGAAGA
1 GAAGAAGA
10376789 AGAACCTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAAGAAGAGAAA
Found at i:10384425 original size:18 final size:17
Alignment explanation
Indices: 10384395--10384442 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
10384385 GTTAGTTACA
*
10384395 TGCA-TTTTTTTGTCAT
1 TGCATTTTTTTTGTCAC
*
10384411 TGCATTTTTTATTGTCCC
1 TGCATTTTTT-TTGTCAC
*
10384429 TGCATTTTATTTGT
1 TGCATTTTTTTTGT
10384443 TTTCTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 4 0.15
17 9 0.33
18 14 0.52
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.60
Consensus pattern (17 bp):
TGCATTTTTTTTGTCAC
Found at i:10386651 original size:24 final size:24
Alignment explanation
Indices: 10386617--10386671 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
10386607 ACAATCAATT
10386617 CATTTTATATTACAGTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
* *
10386641 CATTTTGTATTACATTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
10386665 CAATTTT
1 C-ATTTT
10386672 TACTCTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (24 bp):
CATTTTATATTACAGTTGCACTGA
Found at i:10389383 original size:23 final size:23
Alignment explanation
Indices: 10389350--10389497 Score: 197
Period size: 23 Copynumber: 6.4 Consensus size: 23
10389340 TTCTTATATA
* *
10389350 TATGATTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* * *
10389373 TGTGCTCAAATATTAATGTCATT
1 TATGCTTAAATATTAATGTGATT
* *
10389396 TATGTTTAAACATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
10389419 TATGCTTAAATATTAATGTAATT
1 TATGCTTAAATATTAATGTGATT
10389442 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
10389465 TATGCTTAAATATTAGTATGATT
1 TATGCTTAAATATTAATGTGATT
*
10389488 TGTGCTTAAA
1 TATGCTTAAA
10389498 GAATTAAGAT
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 108 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:10392029 original size:42 final size:42
Alignment explanation
Indices: 10391959--10392210 Score: 183
Period size: 42 Copynumber: 6.0 Consensus size: 42
10391949 CTGAATTAAC
* *
10391959 CTTATGCTCTAACCGAGTCATAAGTCTTCCCTTTTAGACA-AAT
1 CTTATGCTCTAACCGAGACATAAGTCTT-CC-TTTAAACATAAT
**
10392002 CTTATGCTCT-ATTGAGACATAAGTCTTCCTTTAAACATAAT
1 CTTATGCTCTAACCGAGACATAAGTCTTCCTTTAAACATAAT
* * * ** *
10392043 CTCATGCTC-ATCCTAAGACACGAGTCTTCCTTTAAACATAGT
1 CTTATGCTCTAACC-GAGACATAAGTCTTCCTTTAAACATAAT
* * **
10392085 CTCATGCTC-ATCCCGAGACACGAGTCTTCCTTTAAACATAAT
1 CTTATGCTCTA-ACCGAGACATAAGTCTTCCTTTAAACATAAT
* * * **
10392127 CTCATGCTC-ATCCCGAGTCACGAGTCTTCCTTTAAACATAAT
1 CTTATGCTCTA-ACCGAGACATAAGTCTTCCTTTAAACATAAT
* * * * * *
10392169 CTCATCCTC-ATCTCGAAACATTACTCTTCCTTTAAACATAAT
1 CTTATGCTCTAAC-CGAGACATAAGTCTTCCTTTAAACATAAT
10392211 ATCATATTCA
Statistics
Matches: 181, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
40 7 0.04
41 14 0.08
42 148 0.82
43 12 0.07
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (42 bp):
CTTATGCTCTAACCGAGACATAAGTCTTCCTTTAAACATAAT
Found at i:10392222 original size:42 final size:42
Alignment explanation
Indices: 10392023--10392238 Score: 297
Period size: 42 Copynumber: 5.1 Consensus size: 42
10392013 TTGAGACATA
**
10392023 AGTCTTCCTTTAAACATAATCTCATGCTCATCCTAAGACACG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACACG
*
10392065 AGTCTTCCTTTAAACATAGTCTCATGCTCATCCCGAGACACG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACACG
*
10392107 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACACG
* * * **
10392149 AGTCTTCCTTTAAACATAATCTCATCCTCATCTCGAAACATT
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACACG
* * ** * *
10392191 ACTCTTCCTTTAAACATAATATCATATTCATCTCGAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACACG
10392233 AGTCTT
1 AGTCTT
10392239 TCATTTATAC
Statistics
Matches: 156, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 156 1.00
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (42 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACACG
Found at i:10397213 original size:42 final size:42
Alignment explanation
Indices: 10397132--10397652 Score: 832
Period size: 42 Copynumber: 12.4 Consensus size: 42
10397122 AAGACATAAA
* *
10397132 TCTTCTTTTAAACATAAT-TCATGCTCATCCCGAGACACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
10397173 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
*
10397215 TCTTCCTTTAAACATAATCTCATGCTCATCCTGAGTCACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
10397257 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
*
10397299 ACTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
10397341 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
* *
10397383 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
* *
10397425 TCTTCCTTTATACATAATCTCATGCTCATCTCGAGTCACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
*
10397467 TCTTCCTTTAAACATAATCTCATGCTCATCTCGAGTCACGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
*
10397509 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGAT-ATGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAG-TCACGAG
* * * *
10397551 TCTTCCTTTAAACATAATCTTATGCCCATCTCGAGAC-CTGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCAC-GAG
* * *
10397593 TTTTCCTTTAAACATAATCTCATGCTCATCCCGAGACATGAG
1 TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
*
10397635 TCTTCCATTTATACATAA
1 TCTTCC-TTTAAACATAA
10397653 AGTGATTCAA
Statistics
Matches: 447, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
41 17 0.04
42 419 0.94
43 11 0.02
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (42 bp):
TCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCACGAG
Found at i:10400675 original size:18 final size:18
Alignment explanation
Indices: 10400624--10400675 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
10400614 GCATAACCTG
*
10400624 ATCAGATGCAATAACATA
1 ATCAGATGCAATCACATA
** *
10400642 CCCAGATGCAGTCACATA
1 ATCAGATGCAATCACATA
*
10400660 ATCAGATGCAACCACA
1 ATCAGATGCAATCACA
10400676 ACAGACTGTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.17
Consensus pattern (18 bp):
ATCAGATGCAATCACATA
Found at i:10421715 original size:21 final size:20
Alignment explanation
Indices: 10421672--10421744 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
10421662 GTTCAGACTA
**
10421672 CTACCGATACAAGTAACAATT
1 CTACCGATACAAGT-ACTCTT
10421693 CTACCGATACAAGTGACTCTT
1 CTACCGATACAAGT-ACTCTT
* *
10421714 CTATCGAAACAAGT-CTTACTT
1 CTACCGATACAAGTAC-T-CTT
10421735 CTACCGATAC
1 CTACCGATAC
10421745 TAAAAACTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 41 0.95
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (20 bp):
CTACCGATACAAGTACTCTT
Found at i:10422357 original size:52 final size:52
Alignment explanation
Indices: 10422275--10422409 Score: 207
Period size: 52 Copynumber: 2.6 Consensus size: 52
10422265 ATTTATTTTA
*
10422275 ATACTCACGATGACACATAGTCATCAGACCTCTTAATCCGTAAAGGAACCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGAACCAT
* * **
10422327 ATACTCACGATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGAACCAT
* *
10422379 ATACTCACGATGACATATAGTCATCAAACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
10422410 TTTTCATTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGAACCAT
Found at i:10435001 original size:21 final size:21
Alignment explanation
Indices: 10434972--10435025 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
10434962 GGAGTTTTTA
* *
10434972 GTATTGGTAGAAGCAT-GACTT
1 GTATCGGTAGAAG-ATACACTT
*
10434993 GTATCGGTAGAAGTTACACTT
1 GTATCGGTAGAAGATACACTT
10435014 GTATCGGTAGAA
1 GTATCGGTAGAA
10435026 CTAGCACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGATACACTT
Found at i:10465692 original size:42 final size:42
Alignment explanation
Indices: 10465632--10465807 Score: 289
Period size: 42 Copynumber: 4.2 Consensus size: 42
10465622 TATGCTCTAT
* * *
10465632 CGAGACATAAGTCATCCTTTAATCATATTCTCATTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
* *
10465674 CGAGACATTAGTCTTCCTTTAATCATAATCTCATTCTAATCC
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
*
10465716 TGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
*
10465758 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATTC
1 CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
10465800 CGAGACAT
1 CGAGACAT
10465808 TAACTCTGAT
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 125 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
Found at i:10469613 original size:21 final size:21
Alignment explanation
Indices: 10469540--10469613 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
10469530 TGTAGACTTT
* *
10469540 TACCGATACTTGTGATAG-TTC
1 TACCGATACTAGTTAT-GCTTC
* *
10469561 TACCGATACAAGTGTAT-CATC
1 TACCGATACTAGT-TATGCTTC
* * *
10469582 TACCAAAACTAGTTATGCTTT
1 TACCGATACTAGTTATGCTTC
10469603 TACCGATACTA
1 TACCGATACTA
10469614 AAAACTCCAG
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
20 3 0.08
21 34 0.87
22 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (21 bp):
TACCGATACTAGTTATGCTTC
Found at i:10470324 original size:42 final size:42
Alignment explanation
Indices: 10470277--10470462 Score: 291
Period size: 42 Copynumber: 4.4 Consensus size: 42
10470267 TTAAGTCATA
* * *
10470277 AGTCTTCCTTTAATCATATTCCCATTCTCATCCCGAGACATT
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATG
* *
10470319 AGTCTTCATTTAATCATAATCTCATTCTCATCCCCAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATG
*
10470361 AGTCTTCCTTTAATCATAATCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATG
* * *
10470403 AGTCTTTCTTTAATCATAATATCATTCTCATTCCGAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATG
10470445 AGTCTTCCTTTAATCATA
1 AGTCTTCCTTTAATCATA
10470463 TAAACTTTTC
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 131 1.00
ACGTcount: A:0.27, C:0.26, G:0.08, T:0.39
Consensus pattern (42 bp):
AGTCTTCCTTTAATCATAATCTCATTCTCATCCCGAGACATG
Found at i:10475671 original size:51 final size:52
Alignment explanation
Indices: 10475468--10475691 Score: 146
Period size: 51 Copynumber: 4.4 Consensus size: 52
10475458 AAAACATTAT
* * *
10475468 TTTACTTAAAAATCTAAAGTTTTATTTCGAAATAGTT--AAAAAATCAAAAC
1 TTTACTTAAAAATCTAAACTTTTATTTTGAAATATTTAAAAAAAATCAAAAC
* * * ** ***
10475518 TTTATTTAAAAATTTAAACTTTT-TCTTTAAAATAACTAAAAAATATATTTTAA-
1 TTTACTTAAAAATCTAAACTTTTAT-TTTGAAATATTTAAAAAA-A-ATCAAAAC
* * * ** **
10475571 TTT--TTAAAAATATAAACTTTCTCTTTT----TTTTTAATGAAAATCACTAC
1 TTTACTTAAAAATCTAAACTTT-TATTTTGAAATATTTAAAAAAAATCAAAAC
10475618 TTT-CTTAAAAATCTAAACTTTTATTTTGAAATATTTAAAAAAAATCAAAAC
1 TTTACTTAAAAATCTAAACTTTTATTTTGAAATATTTAAAAAAAATCAAAAC
** *
10475669 TTTGTTTAAAAATTTAAACTTTT
1 TTTACTTAAAAATCTAAACTTTT
10475692 CTAAAAAAAC
Statistics
Matches: 131, Mismatches: 29, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
46 3 0.02
47 9 0.07
48 22 0.17
49 1 0.01
50 28 0.21
51 34 0.26
52 25 0.19
53 5 0.04
54 4 0.03
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (52 bp):
TTTACTTAAAAATCTAAACTTTTATTTTGAAATATTTAAAAAAAATCAAAAC
Found at i:10475797 original size:138 final size:137
Alignment explanation
Indices: 10475555--10475808 Score: 343
Period size: 137 Copynumber: 1.8 Consensus size: 137
10475545 TAAAATAACT
* * * *
10475555 AAAAAATATATTTTAATTTTTAAAAATATAAACTTTCTCTTTTTTTTTAATGAAAATCACTACTT
1 AAAAAACAAATTTTAATTTTTAAAAATATAAACTTTCTC--TATTTTTAAAGAAAATCACTACTT
* *
10475620 TCTTAAAAATCTAAACTTTTATTTTGAAATATTTAAAAAAAATCAAAACTTTGTTTAAAAATTTA
64 TCTTAAAAATCTAAACTTTTATTTCGAAATATTT-AAAAAAACCAAAACTTTGTTTAAAAATTTA
10475685 AACTTTTCTA
128 AACTTTTCTA
* * *
10475695 AAAAAACAAATTTTTATTTTTAAAAATCTAAACTTTCTC-ATTTTTAAAGAAAATCACTATTTTA
1 AAAAAACAAATTTTAATTTTTAAAAATATAAACTTTCTCTATTTTTAAAGAAAATCACTACTTT-
*
10475759 CTTAAAAATC-AAAGCTTTTATTTCGAAAT-TGTTTAAAAAACCAAAACTTT
65 CTTAAAAATCTAAA-CTTTTATTTCGAAATAT-TTAAAAAAACCAAAACTTT
10475809 TCCCAAAATC
Statistics
Matches: 101, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
137 40 0.40
138 26 0.26
140 35 0.35
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.43
Consensus pattern (137 bp):
AAAAAACAAATTTTAATTTTTAAAAATATAAACTTTCTCTATTTTTAAAGAAAATCACTACTTTC
TTAAAAATCTAAACTTTTATTTCGAAATATTTAAAAAAACCAAAACTTTGTTTAAAAATTTAAAC
TTTTCTA
Found at i:10476228 original size:3 final size:3
Alignment explanation
Indices: 10476220--10476291 Score: 65
Period size: 3 Copynumber: 24.0 Consensus size: 3
10476210 AAACCCTAAA
** **
10476220 AAT AAT AAT AAT AAT AATT AAT AAT AAT AAT AGG AAT AGG AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
10476266 AAT GAT GAT GAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
10476292 TTGGGCCCTT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:10476710 original size:42 final size:42
Alignment explanation
Indices: 10476664--10477230 Score: 751
Period size: 42 Copynumber: 13.5 Consensus size: 42
10476654 CCTCTATGCT
* *
10476664 TAGGCCTCTAATTGCAATGAAAAGTAAATGAACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
** * *
10476706 TAGGCCTCCGAATGCAATGAAAAATAAATAGG-CCTCCACAGC
1 TAGGCCTCTAAATGCAATGAAAAGTAAAT-GGACCTCCACACC
*
10476748 TAGGCCTCTAAATGCAATGAAAAGCAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
*
10476790 TAGGCCTCTAAATGCAATGAAAGGTAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
10476832 TAGGCATCTTAATGCAATGAAAAGTAAATGTG-CCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATG-GACCTCCACACC
* * * * *
10476874 TAGACCTCTGACTGCGATGAAAAGTAAATGAACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
*
10476916 TGGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* ** * * * *
10476958 TAGGCCTCTAATTGTGATGAAAAGTAAATGGAACTTCATACT
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * * * *
10477000 TGGGTCTCTAAATGTAATGAAAGGTAAATGGACTTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
*
10477042 TAGGCCTCTAAATGCAATGAAAGGTAAATGGACCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * * *
10477084 TCGACCTTTAAATGCAATGAAAAGTAAATGGACCTCCATACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* *
10477126 TGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACC
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
* * *
10477168 TGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACT
1 TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
*
10477210 TGGGCCTCTAAATGCAATGAA
1 TAGGCCTCTAAATGCAATGAA
10477231 TGCTTTCCTT
Statistics
Matches: 457, Mismatches: 64, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
41 2 0.00
42 453 0.99
43 2 0.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
TAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACC
Found at i:10477683 original size:17 final size:16
Alignment explanation
Indices: 10477633--10477683 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
10477623 TTGCTCTCTC
10477633 TTTCTATTTTTTTTCTAT
1 TTTCT-TTTTTTTTCT-T
*
10477651 TTTCTTTTTTTCTCTT
1 TTTCTTTTTTTTTCTT
10477667 TTT-TTGTATTTTTTCTT
1 TTTCTT-T-TTTTTTCTT
10477684 GATTTAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 17 0.59
18 5 0.17
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTTTTTCTT
Found at i:10493384 original size:21 final size:21
Alignment explanation
Indices: 10493359--10493414 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
10493349 AATAGTGCAG
10493359 ACTTCTACCGATACAAGTGATT
1 ACTTCTACCGATACAAGT-ATT
* *
10493381 -CTTCTACCGAAACAAGTTTT
1 ACTTCTACCGATACAAGTATT
10493401 ACTTCTACCGATAC
1 ACTTCTACCGATAC
10493415 TAAAAACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTATT
Found at i:10494235 original size:52 final size:52
Alignment explanation
Indices: 10494124--10494294 Score: 218
Period size: 52 Copynumber: 3.3 Consensus size: 52
10494114 ATACTCAAGG
* * * *
10494124 TGACACATAGTCATCGGACCTCTTAATTTTTTAAAGGAA-TCATAAACTCACAA
1 TGACACATAGTCATCGGACCTCATAA-TCTGTAAA-GAATTCATATACTCACAA
* * **
10494177 TAACACATAGTCAACGGACCTCATAATCTGTAAAGAATTCATATACTCATGA
1 TGACACATAGTCATCGGACCTCATAATCTGTAAAGAATTCATATACTCACAA
** *
10494229 TGACACATAGTCATCAAACCTCATAATCTGTAAAGGATTCATATACTCACAA
1 TGACACATAGTCATCGGACCTCATAATCTGTAAAGAATTCATATACTCACAA
10494281 TGACACATAGTCAT
1 TGACACATAGTCAT
10494295 TAGACCTTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
51 3 0.03
52 76 0.75
53 23 0.23
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (52 bp):
TGACACATAGTCATCGGACCTCATAATCTGTAAAGAATTCATATACTCACAA
Found at i:10513536 original size:22 final size:22
Alignment explanation
Indices: 10513508--10513609 Score: 125
Period size: 22 Copynumber: 4.6 Consensus size: 22
10513498 AAAAAAATAT
10513508 TCAATTATATTGGCGCAATCAA
1 TCAATTATATTGGCGCAATCAA
* *
10513530 TCAATTATATTAGCGCAATCAG
1 TCAATTATATTGGCGCAATCAA
* * *
10513552 TCAATTATATTAAG-GTAATGAA
1 TCAATTATATT-GGCGCAATCAA
*
10513574 TCAATTATATTGGCACAATCAA
1 TCAATTATATTGGCGCAATCAA
*
10513596 TCAATTATACTGGC
1 TCAATTATATTGGC
10513610 ATAATACACC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
21 1 0.01
22 65 0.96
23 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
TCAATTATATTGGCGCAATCAA
Found at i:10518498 original size:16 final size:17
Alignment explanation
Indices: 10518467--10518499 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
10518457 TTCTTAACCA
*
10518467 ATATAGCATTTATTTTC
1 ATATAGCATATATTTTC
10518484 ATATA-CATATATTTTC
1 ATATAGCATATATTTTC
10518500 TTCTTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (17 bp):
ATATAGCATATATTTTC
Found at i:10519574 original size:15 final size:15
Alignment explanation
Indices: 10519554--10519599 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
10519544 CTTCTTCTTT
10519554 TTCTTTTTCCTTCTC
1 TTCTTTTTCCTTCTC
10519569 TTC-TTTTCCTTCCTC
1 TTCTTTTTCCTT-CTC
10519584 TTCTCTTTTCTCTTCT
1 TTCT-TTTTC-CTTCT
10519600 TCCTCTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.30
15 9 0.33
17 7 0.26
18 3 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTCTTTTTCCTTCTC
Found at i:10519581 original size:18 final size:19
Alignment explanation
Indices: 10519546--10519607 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
10519536 CACAAAATCT
*
10519546 TCTTCTTTTTCTTTTTCCTTC
1 TCTTC-TTTTC-TCTTCCTTC
10519567 TCTTCTTTTC-CTTCC-TC
1 TCTTCTTTTCTCTTCCTTC
10519584 T-TCTCTTTTCTCTT-CTTCC
1 TCT-TCTTTTCTCTTCCTT-C
10519603 TCTTC
1 TCTTC
10519608 AATATCCGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
16 1 0.03
17 11 0.31
18 8 0.23
19 4 0.11
20 6 0.17
21 5 0.14
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTTCTTTTCTCTTCCTTC
Found at i:10525544 original size:18 final size:18
Alignment explanation
Indices: 10525523--10525559 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
10525513 GCATCCGAAC
*
10525523 ATGTGGTTGCATCTGATT
1 ATGTGATTGCATCTGATT
10525541 ATGTGATTGCATCTGATT
1 ATGTGATTGCATCTGATT
10525559 A
1 A
10525560 GGCTACACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (18 bp):
ATGTGATTGCATCTGATT
Found at i:10530508 original size:422 final size:421
Alignment explanation
Indices: 10529704--10530548 Score: 1182
Period size: 422 Copynumber: 2.0 Consensus size: 421
10529694 ACTAACACTA
* * * *
10529704 AAATGCAATGACAATTACAATGCAATGACAATATGCACTAATAAACTAAAAATTACAGCTACATG
1 AAATACAATGAAAATTACAATGCAACGACAATATGCACTAACAAACTAAAAATTACAGCTACATG
* *
10529769 TAATGCATGAATATTACAGCTAAAAAAACTTAAAATAAACTAACTCATTTTTCCTCAGCCATCGA
66 CAATGCATGAATACTACAGCTAAAAAAACTTAAAATAAACTAACTCATTTTTCCTCAGCCATCGA
* * * *
10529834 TATTGCTGTATGGTGTTTCTTCTTCCTTTTCTTCTTCTCTTCCTTTCTGCGCTTTTTGTCCTTGG
131 TATGGCTGTATGGTGTTTCTTCTTCCTTCTCTTCTTCTCTTCCTTTCTACGCTTTTTATCCTTGG
* * * * *
10529899 AGCGCTTTGTCTTCCTTTCTTTGGGCTTCTCTTGGTCCTCAGATTGCTCCTCAGTAGCTAGCTTT
196 AGCACTTTCTCTTCCTTTCTTTGGGCTTCTCTTGATCCTCAGAATGCTCCTCAGTAGCCAGCTTT
* * * *
10529964 ACCCCGGCATCATCAACTGCTTCTTGTGTTAGATGGATCACCTCAAGTGGTTCGGTGTAGGCCAC
261 ACCCCGACATCATCAACTGCTTCTTGTGTCAGATGGATCACCTCAAGTGGTTCGGTATAGACCAC
* * * * *
10530029 TATTGTCCAATGATTGTGGTGTTTCTCATTAGTTTCCCCCACATCTTTCGTCTGACTCGCTCCAT
326 TATTGTCCAATGATTGTGGTGTTTCTCATTAGTTTCCACCACAGCTTCCGCCTGACTCACTCCAT
* * * *
10530094 CTTGCTCCAAGTCCTCAATTGTTGCACTCAC
391 CTTACTCCAAGGCCTCAATCGTTGCACCCAC
10530125 AAATACAATGAAAATTACAATGCAACGACAATATGCACTAACAAACTAAAAATTACAGCTACATG
1 AAATACAATGAAAATTACAATGCAACGACAATATGCACTAACAAACTAAAAATTACAGCTACATG
*
10530190 CAATGCATGAATACTACAGCTAAAAAAAACTTAAAATAAACTAACTCATTTTTCCTCAGCCATTG
66 CAATGCATGAATACTACAGCT-AAAAAAACTTAAAATAAACTAACTCATTTTTCCTCAGCCATCG
* *
10530255 ATGTGGTTGTATGGTGCTTT-TTCTTCCTTCTCTTCTTCTCTTCCTTTCTACGCTTTTTATCCTT
130 ATATGGCTGTATGGTG-TTTCTTCTTCCTTCTCTTCTTCTCTTCCTTTCTACGCTTTTTATCCTT
** *
10530319 GGAGCACTTTCTCTTCCTTTCTTTGGGCTATGC-C-TGAT-CTTTGAAATGCTCCTCAGTATCCA
194 GGAGCACTTTCTCTTCCTTTCTTTGGGCT-T-CTCTTGATCCTCAG-AATGCTCCTCAGTAGCCA
* *** *
10530381 GCTTTGCCCCGACATCATCGGTTG-TGTCTTGTGTCAGATGGATCACCTTAAGTGG-TCTGGTAT
256 GCTTTACCCCGACATCATCAACTGCT-TCTTGTGTCAGATGGATCACCTCAAGTGGTTC-GGTAT
* *
10530444 AGACCACTATTG-CCAAATGATTGTGGTGTTTCTCATTAGTTTCCACTATAGCTTCCGCCTGACT
319 AGACCACTATTGTCC-AATGATTGTGGTGTTTCTCATTAGTTTCCACCACAGCTTCCGCCTGACT
* *
10530508 CACTCCATCTTACTCTAAGGCCTCAGTCGTTGCACCCAC
383 CACTCCATCTTACTCCAAGGCCTCAATCGTTGCACCCAC
10530547 AA
1 AA
10530549 CTTCGGGTGC
Statistics
Matches: 373, Mismatches: 43, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
421 88 0.24
422 279 0.75
423 5 0.01
424 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (421 bp):
AAATACAATGAAAATTACAATGCAACGACAATATGCACTAACAAACTAAAAATTACAGCTACATG
CAATGCATGAATACTACAGCTAAAAAAACTTAAAATAAACTAACTCATTTTTCCTCAGCCATCGA
TATGGCTGTATGGTGTTTCTTCTTCCTTCTCTTCTTCTCTTCCTTTCTACGCTTTTTATCCTTGG
AGCACTTTCTCTTCCTTTCTTTGGGCTTCTCTTGATCCTCAGAATGCTCCTCAGTAGCCAGCTTT
ACCCCGACATCATCAACTGCTTCTTGTGTCAGATGGATCACCTCAAGTGGTTCGGTATAGACCAC
TATTGTCCAATGATTGTGGTGTTTCTCATTAGTTTCCACCACAGCTTCCGCCTGACTCACTCCAT
CTTACTCCAAGGCCTCAATCGTTGCACCCAC
Found at i:10544030 original size:150 final size:151
Alignment explanation
Indices: 10543754--10544056 Score: 590
Period size: 150 Copynumber: 2.0 Consensus size: 151
10543744 CAATCTAACC
10543754 AAGGATACGAGTAACTCCCTCGAACCAGAACTCAGCATGAGTAGGGTCTTCTCCCCTAACTCCAC
1 AAGGATACGAGTAACTCCCTCGAACCAGAACTCAGCATGAGTAGGGTCTTCTCCCCTAACTCCAC
*
10543819 AAAACTCCTTACCACTTAAAGCTCGTAGATGCTCTAGTGGTAATCCCTTACGAACAGGGGCAGCA
66 AAAACTCCTTACCACTTAAAGCTCGTAGATGCTCTAGTGGTAATCCCTTACGAACAAGGGCAGCA
10543884 TT-GCACCAATGATACGCTGT
131 TTGGCACCAATGATACGCTGT
10543904 AAGGATACGAGTAACTCCCTCGAACCAGAACTCAGCATGAGTAGGGTCTTCTCCCCTAACTCCAC
1 AAGGATACGAGTAACTCCCTCGAACCAGAACTCAGCATGAGTAGGGTCTTCTCCCCTAACTCCAC
10543969 AAAACTCCTTACCACTTAAAGCTCGTAGATGCTCTAGTGGTAATCCCTTACGAACAAGGGCAGCA
66 AAAACTCCTTACCACTTAAAGCTCGTAGATGCTCTAGTGGTAATCCCTTACGAACAAGGGCAGCA
10544034 TTGGCACCAATGATACGCTGT
131 TTGGCACCAATGATACGCTGT
10544055 AA
1 AA
10544057 TGCCCTGACC
Statistics
Matches: 151, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
150 131 0.87
151 20 0.13
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (151 bp):
AAGGATACGAGTAACTCCCTCGAACCAGAACTCAGCATGAGTAGGGTCTTCTCCCCTAACTCCAC
AAAACTCCTTACCACTTAAAGCTCGTAGATGCTCTAGTGGTAATCCCTTACGAACAAGGGCAGCA
TTGGCACCAATGATACGCTGT
Found at i:10545823 original size:22 final size:21
Alignment explanation
Indices: 10545798--10545878 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 21
10545788 AAAAAAATAT
10545798 TCAATTATATTGGCACAACAAA
1 TCAATTATATTGGCACAAC-AA
* *
10545820 TCAATTATATTAGTGCA-ATCAG
1 TCAATTATATT-G-GCACAACAA
* *
10545842 TCAATTATATTAGCGCAATCAA
1 TCAATTATATTGGCACAA-CAA
10545864 TCAATTATATTGGCA
1 TCAATTATATTGGCA
10545879 TAATACATTC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
20 2 0.04
21 1 0.02
22 38 0.81
23 3 0.06
24 3 0.06
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (21 bp):
TCAATTATATTGGCACAACAA
Found at i:10547666 original size:19 final size:19
Alignment explanation
Indices: 10547635--10547673 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
10547625 TTAAATTCCA
10547635 ATTTAACCCAAAA-TATTT
1 ATTTAACCCAAAATTATTT
*
10547653 ATTTTACCCAAAAATTATTT
1 ATTTAACCC-AAAATTATTT
10547673 A
1 A
10547674 AAACCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAACCCAAAATTATTT
Found at i:10555200 original size:6 final size:6
Alignment explanation
Indices: 10555191--10555221 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
10555181 AATGAAAAAG
10555191 AAATAA AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA A
10555222 TGTTCCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:10555595 original size:6 final size:6
Alignment explanation
Indices: 10555584--10555613 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
10555574 GATAATATAT
10555584 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
1 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
10555614 TGATAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
ATCTCA
Found at i:10568151 original size:20 final size:20
Alignment explanation
Indices: 10568112--10568151 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
10568102 AATTTATACG
*
10568112 TAATTTTGAATTGAAGAGTT
1 TAATTTTGAATTGAAAAGTT
10568132 TAATTATTGAATT-AAAAGTT
1 TAATT-TTGAATTGAAAAGTT
10568152 AGTATAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (20 bp):
TAATTTTGAATTGAAAAGTT
Found at i:10569813 original size:3 final size:3
Alignment explanation
Indices: 10569805--10569833 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10569795 AGTTACCGCT
10569805 ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC AC
10569834 TTCGAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:10570841 original size:29 final size:30
Alignment explanation
Indices: 10570800--10570877 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
10570790 GCTTTATTTT
* *
10570800 AAAATTGTTTTTTGACCC-CAAACCATCCA
1 AAAATTATGTTTTGACCCTCAAACCATCCA
* ** *
10570829 AAAATTATGTTTTAACCCTCAAACTTTCTA
1 AAAATTATGTTTTGACCCTCAAACCATCCA
*
10570859 AAAATTATGTATTGACCCT
1 AAAATTATGTTTTGACCCT
10570878 TGAACTTTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (30 bp):
AAAATTATGTTTTGACCCTCAAACCATCCA
Found at i:10570862 original size:30 final size:30
Alignment explanation
Indices: 10570828--10570920 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
10570818 CAAACCATCC
10570828 AAAAATTATGTTTTAACCCTCAAACTTTCT
1 AAAAATTATGTTTTAACCCTCAAACTTTCT
* * ** *
10570858 AAAAATTATGTATTGACCCTTGAACTTTCC
1 AAAAATTATGTTTTAACCCTCAAACTTTCT
* *
10570888 AAAAATTCA-ATTTTAACTCTCAAACTTTCT
1 AAAAATT-ATGTTTTAACCCTCAAACTTTCT
10570918 AAA
1 AAA
10570921 GATTTAAATT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 49 0.98
31 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (30 bp):
AAAAATTATGTTTTAACCCTCAAACTTTCT
Found at i:10570934 original size:60 final size:60
Alignment explanation
Indices: 10570825--10570966 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 60
10570815 CCCCAAACCA
* ** * * *
10570825 TCCAAAAATT-ATGTTTTAACCCTCAAACTTTCTAAAAATTATGTATTGACCCTTGAACTT
1 TCCAAAAATTCA-ATTTTAACCCTCAAACTTTCTAAAAATTAAATATTGACCCCTAAAATT
* *
10570885 TCCAAAAATTCAATTTTAACTCTCAAACTTTCTAAAGATTTAAAT-TTGACCCCTAAAATT
1 TCCAAAAATTCAATTTTAACCCTCAAACTTTCTAAA-AATTAAATATTGACCCCTAAAATT
* * *
10570945 TCTAAAAATTCAAATTTGACCC
1 TCCAAAAATTCAATTTTAACCC
10570967 GGGTTTAATG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 62 0.91
61 6 0.09
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (60 bp):
TCCAAAAATTCAATTTTAACCCTCAAACTTTCTAAAAATTAAATATTGACCCCTAAAATT
Found at i:10589450 original size:101 final size:101
Alignment explanation
Indices: 10589344--10589525 Score: 238
Period size: 101 Copynumber: 1.8 Consensus size: 101
10589334 AGCTACAAAG
* * * * *
10589344 GCAAATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGATGAAGCTACAAGAACAAATCATATACC
1 GCAAATCCTTATCTCCCTAAAGTTACAGTAGAGCAAGATGAAGCTACAACAACAAATCATATACC
*
10589409 CCTGAAGTTGCAGTGGGTCGAATTAAAGTCATGAAA
66 CCTGAAATTGCAGTGGGTCGAATTAAAGTCATGAAA
* * * * * * *
10589445 GCAAATCTTTATCTCCCTAAAGTTACAGTGGAGTAAGATGAAGCTACGACATCAAATCCTATATC
1 GCAAATCCTTATCTCCCTAAAGTTACAGTAGAGCAAGATGAAGCTACAACAACAAATCATATACC
*
10589510 CTTGAAATTGCAGTGG
66 CCTGAAATTGCAGTGG
10589526 ATTGGATTGA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
101 67 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (101 bp):
GCAAATCCTTATCTCCCTAAAGTTACAGTAGAGCAAGATGAAGCTACAACAACAAATCATATACC
CCTGAAATTGCAGTGGGTCGAATTAAAGTCATGAAA
Found at i:10589880 original size:4 final size:4
Alignment explanation
Indices: 10589871--10589896 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
10589861 AATTTTGTTA
10589871 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
10589897 TATTCTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:10591195 original size:29 final size:29
Alignment explanation
Indices: 10591155--10591334 Score: 134
Period size: 29 Copynumber: 6.2 Consensus size: 29
10591145 ACATTATTTT
*
10591155 AAAATTAT-TTTTTGCCCCAAACTATCTA
1 AAAATTATGTTTTTACCCCAAACTATCTA
* * *
10591183 AAAATTATG-TTTTAACCCTAACTATCCA
1 AAAATTATGTTTTTACCCCAAACTATCTA
* **
10591211 AAAATTCTGTTTAAACCCCAAACTAT-TCA
1 AAAATTATGTTTTTACCCCAAACTATCT-A
* **
10591240 AAAATTAT-TTTTTGACCCTCAAACTTTCCC
1 AAAATTATGTTTTT-ACCC-CAAACTATCTA
* * * *
10591270 AAAATTATATTTTAACCCCAAACTTTTTA
1 AAAATTATGTTTTTACCCCAAACTATCTA
* * * *
10591299 AAAATTATGTTTTGACCCTTAAACTTTCCA
1 AAAATTATGTTTTTACCC-CAAACTATCTA
10591329 AAAATT
1 AAAATT
10591335 TGAATTTGAC
Statistics
Matches: 119, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
28 34 0.29
29 48 0.40
30 33 0.28
31 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTATGTTTTTACCCCAAACTATCTA
Found at i:10591274 original size:30 final size:30
Alignment explanation
Indices: 10591155--10591424 Score: 205
Period size: 30 Copynumber: 9.2 Consensus size: 30
10591145 ACATTATTTT
* *
10591155 AAAATTATTTTTTG-CCC-CAAACTATCTA
1 AAAATTATTTTTTGACCCTCAAACTTTCCA
* * *
10591183 AAAATTATGTTTTAACCCT--AACTATCCA
1 AAAATTATTTTTTGACCCTCAAACTTTCCA
* * **
10591211 AAAATTCTGTTTAAACCC-CAAACTATT-CA
1 AAAATTATTTTTTGACCCTCAAACT-TTCCA
*
10591240 AAAATTATTTTTTGACCCTCAAACTTTCCC
1 AAAATTATTTTTTGACCCTCAAACTTTCCA
* * **
10591270 AAAATTATATTTTAACCC-CAAACTTTTTA
1 AAAATTATTTTTTGACCCTCAAACTTTCCA
* *
10591299 AAAATTATGTTTTGACCCTTAAACTTTCCA
1 AAAATTATTTTTTGACCCTCAAACTTTCCA
** * *
10591329 AAAATT-TGAATTTGACCCTCGAACTTTCTA
1 AAAATTAT-TTTTTGACCCTCAAACTTTCCA
* * **
10591359 AAAATTCTTATTTGACCCTTGAACTTTCCA
1 AAAATTATTTTTTGACCCTCAAACTTTCCA
* * ** *
10591389 AAAATTCTTATTTGACCCTTGAACATTCCA
1 AAAATTATTTTTTGACCCTCAAACTTTCCA
10591419 AAAATT
1 AAAATT
10591425 CAAATTTGAC
Statistics
Matches: 202, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
28 36 0.18
29 50 0.25
30 115 0.57
31 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (30 bp):
AAAATTATTTTTTGACCCTCAAACTTTCCA
Found at i:10591293 original size:59 final size:60
Alignment explanation
Indices: 10591155--10591394 Score: 246
Period size: 59 Copynumber: 4.1 Consensus size: 60
10591145 ACATTATTTT
** * *
10591155 AAAATTAT-TTTTTGCCCCAAACTA-TCTAAAAATTATGTTTTAACCC-T-AACTATCCA
1 AAAATTATATTTTAACCCCAAACTATTCTAAAAATTATGTTTTGACCCTTAAACTTTCCA
* * * * * *
10591211 AAAATTCTGTTTAAACCCCAAACTATTC-AAAAATTATTTTTTGACCCTCAAACTTTCCC
1 AAAATTATATTTTAACCCCAAACTATTCTAAAAATTATGTTTTGACCCTTAAACTTTCCA
*
10591270 AAAATTATATTTTAACCCCAAACT-TTTTAAAAATTATGTTTTGACCCTTAAACTTTCCA
1 AAAATTATATTTTAACCCCAAACTATTCTAAAAATTATGTTTTGACCCTTAAACTTTCCA
* * * * *
10591329 AAAATT-TGAATTTGACCCTCGAACT-TTCTAAAAATTCT-TATTTGACCCTTGAACTTTCCA
1 AAAATTAT-ATTTTAACCC-CAAACTATTCTAAAAATTATGT-TTTGACCCTTAAACTTTCCA
10591389 AAAATT
1 AAAATT
10591395 CTTATTTGAC
Statistics
Matches: 154, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
56 7 0.05
57 30 0.19
58 5 0.03
59 71 0.46
60 41 0.27
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (60 bp):
AAAATTATATTTTAACCCCAAACTATTCTAAAAATTATGTTTTGACCCTTAAACTTTCCA
Found at i:10608456 original size:2 final size:2
Alignment explanation
Indices: 10608449--10608480 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10608439 GAAAACAATT
10608449 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
10608481 AATAATTCAC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10615842 original size:10 final size:10
Alignment explanation
Indices: 10615827--10615851 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10615817 CAATTTTGTT
10615827 TTTATTTTTA
1 TTTATTTTTA
10615837 TTTATTTTTA
1 TTTATTTTTA
10615847 TTTAT
1 TTTAT
10615852 AAATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:10615863 original size:10 final size:10
Alignment explanation
Indices: 10615850--10615874 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10615840 ATTTTTATTT
10615850 ATAAATATAA
1 ATAAATATAA
10615860 ATAAATATAA
1 ATAAATATAA
10615870 ATAAA
1 ATAAA
10615875 ATTGAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAATATAA
Found at i:10617255 original size:30 final size:29
Alignment explanation
Indices: 10617217--10617444 Score: 140
Period size: 30 Copynumber: 7.7 Consensus size: 29
10617207 AATTTTTCCA
10617217 AAAAATTCAAATTTGACCATCGAACTTTCT
1 AAAAATTCAAATTTGACC-TCGAACTTTCT
* * *
10617247 AGAAATTCAAATTT-CCCTTGAACTTTC-
1 AAAAATTCAAATTTGACCTCGAACTTTCT
* *
10617274 AATAAATTCAAATTTGACCCCTGAATTTTCT
1 AA-AAATTCAAATTTGACCTC-GAACTTTCT
* **
10617305 AAAAATTCAAATTTAACCCTTAAACTTT-T
1 AAAAATTCAAATTTGA-CCTCGAACTTTCT
* * * *
10617334 CAAAAATTCAAATTTAACCCCTAAATTTTCT
1 -AAAAATTCAAATTTGACCTC-GAACTTTCT
* * * *
10617365 AAAAATTCCAATTTAACCCTCAAAAATTT-T
1 AAAAATTCAAATTTGA-CCTC-GAACTTTCT
*** * * *
10617395 CAAAAATTTTGATTTGACCCTTGAAGTTTCC
1 -AAAAATTCAAATTTGA-CCTCGAACTTTCT
10617426 AAAAATTCAAATTTGACCT
1 AAAAATTCAAATTTGACCT
10617445 GGTTTTAATG
Statistics
Matches: 156, Mismatches: 31, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.01
28 21 0.13
29 10 0.06
30 94 0.60
31 30 0.19
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATTCAAATTTGACCTCGAACTTTCT
Found at i:10617354 original size:60 final size:60
Alignment explanation
Indices: 10617217--10617439 Score: 256
Period size: 60 Copynumber: 3.7 Consensus size: 60
10617207 AATTTTTCCA
* * * *
10617217 AAAAATTCAAATTTGA-CCATCGAACTTTCTAGAAATTCAAATTT--CCCTTGAAC-TTTC
1 AAAAATTCAAATTTGACCCCT-GAATTTTCTAAAAATTCAAATTTAACCCTTAAACTTTTC
10617274 AATAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCTTAAACTTTTC
1 AA-AAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCTTAAACTTTTC
* * * * *
10617335 AAAAATTCAAATTTAACCCCTAAATTTTCTAAAAATTCCAATTTAACCCTCAAAAATTTTC
1 AAAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCT-TAAACTTTTC
*** * * *
10617396 AAAAATTTTGATTTGACCCTTGAAGTTTCCAAAAATTCAAATTT
1 AAAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTT
10617440 GACCTGGTTT
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
57 2 0.01
58 35 0.25
59 3 0.02
60 53 0.37
61 49 0.35
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCTTAAACTTTTC
Found at i:10617432 original size:61 final size:60
Alignment explanation
Indices: 10617217--10617439 Score: 238
Period size: 61 Copynumber: 3.7 Consensus size: 60
10617207 AATTTTTCCA
* * * ** *
10617217 AAAAATTCAAATTTGA-CCATCGAACTTTCTAGAAATTCAAATTT--CCCT-TGAACTTTC
1 AAAAATTCAAATTTGACCCCT-GAATTTTCTAAAAATTCAAATTTAACCCTAAAAATTTTC
* *
10617274 AATAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCTTAAACTTTTC
1 AA-AAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCTAAAAATTTTC
* * *
10617335 AAAAATTCAAATTTAACCCCTAAATTTTCTAAAAATTCCAATTTAACCCTCAAAAATTTTC
1 AAAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCT-AAAAATTTTC
*** * * *
10617396 AAAAATTTTGATTTGACCCTTGAAGTTTCCAAAAATTCAAATTT
1 AAAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTT
10617440 GACCTGGTTT
Statistics
Matches: 139, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.01
58 35 0.25
59 3 0.02
60 49 0.35
61 50 0.36
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (60 bp):
AAAAATTCAAATTTGACCCCTGAATTTTCTAAAAATTCAAATTTAACCCTAAAAATTTTC
Found at i:10629039 original size:39 final size:39
Alignment explanation
Indices: 10628995--10629123 Score: 154
Period size: 39 Copynumber: 3.3 Consensus size: 39
10628985 AAGACCATCT
*
10628995 AATCTTTTACCCTGACCATGGGGCAGATTAAAGCAATCC
1 AATCTTTTACCCTGACCATGGGGCAGATTGAAGCAATCC
* * *
10629034 AATCTTTTACCCTAACCA-GAGGGTAGA-TGAAGACCATCC
1 AATCTTTTACCCTGACCATG-GGGCAGATTGAAG-CAATCC
* * *
10629073 GATCTCTTACCCCGACCATGGGGCAGATTGAAGCAATCC
1 AATCTTTTACCCTGACCATGGGGCAGATTGAAGCAATCC
*
10629112 AATATTTTACCC
1 AATCTTTTACCC
10629124 CTAAAGCTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
38 5 0.07
39 62 0.85
40 6 0.08
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (39 bp):
AATCTTTTACCCTGACCATGGGGCAGATTGAAGCAATCC
Found at i:10631262 original size:30 final size:30
Alignment explanation
Indices: 10631225--10631582 Score: 276
Period size: 30 Copynumber: 12.1 Consensus size: 30
10631215 CCCAGAAGGC
* *
10631225 CCCT-GAACTTTCCAAAAATCATATTTTAA
1 CCCTCGAACTTTCCAAAAATTACATTTTAA
* * *
10631254 CCCTTGAACTCTT-TAAAAATTACATTTTGA
1 CCCTCGAACT-TTCCAAAAATTACATTTTAA
* * * *
10631284 CCCTCAAACTTTTCATAAATTACATTTTGA
1 CCCTCGAACTTTCCAAAAATTACATTTTAA
* * *
10631314 CCCTCAAACTTTTCAAAAATTATATTTTAA
1 CCCTCGAACTTTCCAAAAATTACATTTTAA
* *
10631344 CCCTCGAGCTTTCCAAAAATTACATTTTGA
1 CCCTCGAACTTTCCAAAAATTACATTTTAA
* * *
10631374 -CCTCCGAGC-TTCCAAAAAATACATTTTGA
1 CCCT-CGAACTTTCCAAAAATTACATTTTAA
* * *
10631403 CCCCCAAAC-TTCCAAAAATTCCATTTTTAA
1 CCCTCGAACTTTCCAAAAATTACA-TTTTAA
* *
10631433 CCC-CGAATTTTCTAAAAATTACCATTTT-A
1 CCCTCGAACTTTCCAAAAATTA-CATTTTAA
* *
10631462 CCCTCAAAC-TTCTAAAAATTACATTTTTAA
1 CCCTCGAACTTTCCAAAAATTACA-TTTTAA
*
10631492 -CCTCGAACATTCC-AAAATTACCATTTT-A
1 CCCTCGAACTTTCCAAAAATTA-CATTTTAA
* * *
10631520 CCCCCGAA-TATCCAAAAATTCCATTTTTAA
1 CCCTCGAACTTTCCAAAAATTACA-TTTTAA
* *
10631550 -CCTCAAACTTTCC-AAAATTACCATTTTAC
1 CCCTCGAACTTTCCAAAAATTA-CATTTTAA
10631579 CCCT
1 CCCT
10631583 AAATGTTCAA
Statistics
Matches: 269, Mismatches: 40, Indels: 39
0.77 0.11 0.11
Matches are distributed among these distances:
28 8 0.03
29 116 0.43
30 141 0.52
31 4 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (30 bp):
CCCTCGAACTTTCCAAAAATTACATTTTAA
Found at i:10631450 original size:58 final size:59
Alignment explanation
Indices: 10631234--10631605 Score: 284
Period size: 58 Copynumber: 6.3 Consensus size: 59
10631224 CCCCTGAACT
* * *
10631234 TTCCAAAAA-T-CATATTTTAACCCTTGAACTCTT-TAAAAATTA-CATTTTGACCCTCAAAC
1 TTCCAAAAATTACAT-TTTTAACCC-CGAACT-TTCCAAAAATTACCATTTT-ACCCCCAAAC
* * * * * * * * *
10631293 TTTTCATAAATTACA-TTTTGACCCTCAAACTTTTCAAAAATTA-TATTTTAACCCTCGAGC
1 -TTCCAAAAATTACATTTTTAACCC-CGAACTTTCCAAAAATTACCATTTT-ACCCCCAAAC
* * *
10631353 TTTCCAAAAATTACA-TTTTGACCTCCGAGC-TTCCAAAAAATA-CATTTTGACCCCCAAAC
1 -TTCCAAAAATTACATTTTTAACC-CCGAACTTTCCAAAAATTACCATTTT-ACCCCCAAAC
* * * *
10631412 TTCCAAAAATTCCATTTTTAACCCCGAATTTTCTAAAAATTACCATTTTACCCTCAAAC
1 TTCCAAAAATTACATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCCCAAAC
* * * *
10631471 TTCTAAAAATTACATTTTTAACCTCGAACATTCC-AAAATTACCATTTTACCCCCGAA-
1 TTCCAAAAATTACATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCCCAAAC
* * * *
10631528 TATCCAAAAATTCCATTTTTAACCTCAAACTTTCC-AAAATTACCATTTTACCCCTAAA-
1 T-TCCAAAAATTACATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCCCAAAC
*
10631586 TGTTCAAAAATTACCATTTT
1 T-TCCAAAAATTA-CATTTT
10631606 GCCCCCAAAG
Statistics
Matches: 258, Mismatches: 45, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
57 1 0.00
58 98 0.38
59 84 0.33
60 71 0.28
61 2 0.01
62 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (59 bp):
TTCCAAAAATTACATTTTTAACCCCGAACTTTCCAAAAATTACCATTTTACCCCCAAAC
Found at i:10631610 original size:29 final size:29
Alignment explanation
Indices: 10631386--10631634 Score: 163
Period size: 29 Copynumber: 8.6 Consensus size: 29
10631376 TCCGAGCTTC
* *
10631386 CAAAAAATA-CATTTTGACCCCCAAACT-TC
1 CAAAAATTACCATTTT-ACCCCCAAA-TGTT
* * *
10631415 CAAAAATT-CCATTTTTAACCCCGAATTTT
1 CAAAAATTACCA-TTTTACCCCCAAATGTT
* *
10631444 CTAAAAATTACCATTTTACCCTCAAA-CTT
1 C-AAAAATTACCATTTTACCCCCAAATGTT
* * * **
10631473 CTAAAAATTA-CATTTTTAACCTCGAACATT
1 C-AAAAATTACCA-TTTTACCCCCAAATGTT
* * * *
10631503 CCAAAATTACCATTTTACCCCCGAATATC
1 CAAAAATTACCATTTTACCCCCAAATGTT
* *
10631532 CAAAAATT-CCATTTTTAACCTCAAACT-TT
1 CAAAAATTACCA-TTTTACCCCCAAA-TGTT
* *
10631561 CCAAAATTACCATTTTACCCCTAAATGTT
1 CAAAAATTACCATTTTACCCCCAAATGTT
*
10631590 CAAAAATTACCATTTTGCCCCCAAA-GTAT
1 CAAAAATTACCATTTTACCCCCAAATGT-T
*
10631619 CCAAAATTACCATTTT
1 CAAAAATTACCATTTT
10631635 GCACTCGAGC
Statistics
Matches: 178, Mismatches: 29, Indels: 26
0.76 0.12 0.11
Matches are distributed among these distances:
28 9 0.05
29 136 0.76
30 30 0.17
31 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCAAATGTT
Found at i:10631622 original size:58 final size:58
Alignment explanation
Indices: 10631395--10631634 Score: 236
Period size: 58 Copynumber: 4.1 Consensus size: 58
10631385 CCAAAAAATA
* * * *
10631395 CATTTTGACCCCCAAACT-TCCAAAAATTCCATTTTTAACCCCGAATTTTCTAAAAATTAC
1 CATTTT-ACCCCCAAA-TATCCAAAAATTCCATTTTTAACCCCAAACTATC-CAAAATTAC
* * * * *
10631455 CATTTTACCCTCAAACT-TCTAAAAATTACATTTTTAACCTCGAAC-ATTCCAAAATTAC
1 CATTTTACCCCCAAA-TATCCAAAAATTCCATTTTTAACCCCAAACTA-TCCAAAATTAC
* * *
10631513 CATTTTACCCCCGAATATCCAAAAATTCCATTTTTAACCTCAAACTTTCCAAAATTAC
1 CATTTTACCCCCAAATATCCAAAAATTCCATTTTTAACCCCAAACTATCCAAAATTAC
* * * ** *
10631571 CATTTTACCCCTAAATGTTCAAAAATTACCA-TTTTGCCCCCAAAGTATCCAAAATTAC
1 CATTTTACCCCCAAATATCCAAAAATT-CCATTTTTAACCCCAAACTATCCAAAATTAC
10631629 CATTTT
1 CATTTT
10631635 GCACTCGAGC
Statistics
Matches: 154, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
57 1 0.01
58 108 0.70
59 39 0.25
60 6 0.04
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
CATTTTACCCCCAAATATCCAAAAATTCCATTTTTAACCCCAAACTATCCAAAATTAC
Found at i:10631653 original size:29 final size:30
Alignment explanation
Indices: 10631355--10631654 Score: 89
Period size: 29 Copynumber: 10.3 Consensus size: 30
10631345 CCTCGAGCTT
** *
10631355 TCCAAAAATTA-CATTTTG-ACCTCCGAGCT
1 TCCAAAAATTACCATTTTGCACC-CAAAGCA
* * *
10631384 TCCAAAAAATA-CATTTTGACCCCCAAA-CT
1 TCCAAAAATTACCATTTTG-CACCCAAAGCA
** * ***
10631413 TCCAAAAATT-CCATTTTTAACCCCGAATTT
1 TCCAAAAATTACCATTTTGCA-CCCAAAGCA
* * *
10631443 TCTAAAAATTACCATTTTAC-CCTCAAA-CT
1 TCCAAAAATTACCATTTTGCACC-CAAAGCA
* ** *
10631472 TCTAAAAATTA-CATTTTTAACCTCGAA-CA
1 TCCAAAAATTACCATTTTGCACC-CAAAGCA
* * * *
10631501 TTCC-AAAATTACCATTTTACCCCCGAA-TA
1 -TCCAAAAATTACCATTTTGCACCCAAAGCA
** *
10631530 TCCAAAAATT-CCATTTTTAACCTCAAA-CTT
1 TCCAAAAATTACCATTTTGCACC-CAAAGC-A
*
10631560 TCC-AAAATTACCATTTTAC-CCCTAAATG--
1 TCCAAAAATTACCATTTTGCACCC-AAA-GCA
* * *
10631588 TTCAAAAATTACCATTTTGCCCCCAAAGTA
1 TCCAAAAATTACCATTTTGCACCCAAAGCA
* *
10631618 TCC-AAAATTACCATTTTGCACTC-GAGCA
1 TCCAAAAATTACCATTTTGCACCCAAAGCA
10631646 TCCAAAAAT
1 TCCAAAAAT
10631655 CGTATTTTCG
Statistics
Matches: 210, Mismatches: 39, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
28 28 0.13
29 133 0.63
30 40 0.19
31 9 0.04
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.32
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTGCACCCAAAGCA
Found at i:10633006 original size:14 final size:14
Alignment explanation
Indices: 10632987--10633013 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10632977 ATTATTTTAT
10632987 AAATATAAATAAAC
1 AAATATAAATAAAC
10633001 AAATATAAATAAA
1 AAATATAAATAAA
10633014 ATTGAATACA
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:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATATAAATAAAC
Found at i:10633579 original size:16 final size:16
Alignment explanation
Indices: 10633558--10633600 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
10633548 CACGCATATA
10633558 TATATTATATTTACTT
1 TATATTATATTTACTT
* * *
10633574 TATATTTTACTTATTT
1 TATATTATATTTACTT
10633590 TATATTATATT
1 TATATTATATT
10633601 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TATATTATATTTACTT
Found at i:10633597 original size:21 final size:21
Alignment explanation
Indices: 10633560--10633615 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
10633550 CGCATATATA
10633560 TATTATATTTACT-TTATATT-T
1 TATTAT-TTTA-TATTATATTAT
10633581 TACTTATTTTATATTATATTAT
1 TA-TTATTTTATATTATATTAT
*
10633603 TATTTTTTTATAT
1 TATTATTTTATAT
10633616 CGAAACTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 1 0.03
21 23 0.74
22 7 0.23
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTATTTTATATTATATTAT
Found at i:10634487 original size:30 final size:29
Alignment explanation
Indices: 10634377--10634558 Score: 123
Period size: 30 Copynumber: 6.1 Consensus size: 29
10634367 ATGTTTTAAC
* *
10634377 CCCCAAATTTTCTAAAAAATTCAAATTTGG
1 CCCCAAATTTTC-CAAAAATTCAAATTTGA
* * **
10634407 CCACCAAACTTTCTAAAAATTTGAATTTGA
1 CC-CCAAATTTTCCAAAAATTCAAATTTGA
*** * *
10634437 CCCTTGATCTTTTCATAAATTCAAATTTGA
1 CCCCAAAT-TTTCCAAAAATTCAAATTTGA
* *
10634467 TCCCCAAATTTTCCAAAAATTCCAATTTAA
1 -CCCCAAATTTTCCAAAAATTCAAATTTGA
* **
10634497 CCCTCAAATTTTTCAAAAAATT-TTATTTGA
1 CCC-CAAA-TTTTCCAAAAATTCAAATTTGA
** *
10634527 CCCTTGAAGTTTCCAAAAATTCAAATTTGA
1 CCC-CAAATTTTCCAAAAATTCAAATTTGA
10634557 CC
1 CC
10634559 GATTTTAGTG
Statistics
Matches: 115, Mismatches: 31, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
29 16 0.14
30 73 0.63
31 26 0.23
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (29 bp):
CCCCAAATTTTCCAAAAATTCAAATTTGA
Found at i:10634510 original size:60 final size:60
Alignment explanation
Indices: 10634371--10634515 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
10634361 AAAATTATGT
* * * **
10634371 TTTAACCCCCAAATTTTCTAAAAAATTCAAATTTGGCCACCAAACTTTCTAAAAATTTGAA
1 TTTAACCCTCAAATTTT-TCAAAAATTCAAATTTGGCCACCAAACTTTCCAAAAATTCCAA
* ** * * *
10634432 TTTGACCCT-TGATCTTTTCATAAATTCAAATTTGATCC-CCAAATTTTCCAAAAATTCCAA
1 TTTAACCCTCAAAT-TTTTCAAAAATTCAAATTTG-GCCACCAAACTTTCCAAAAATTCCAA
10634492 TTTAACCCTCAAATTTTTCAAAAA
1 TTTAACCCTCAAATTTTTCAAAAA
10634516 ATTTTATTTG
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
60 52 0.79
61 14 0.21
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (60 bp):
TTTAACCCTCAAATTTTTCAAAAATTCAAATTTGGCCACCAAACTTTCCAAAAATTCCAA
Found at i:10634532 original size:90 final size:91
Alignment explanation
Indices: 10634377--10634556 Score: 222
Period size: 90 Copynumber: 2.0 Consensus size: 91
10634367 ATGTTTTAAC
** *
10634377 CCCCAAATTTTCTAAAAAATTCAAATTTGGCCACCAAACTTTCTAAAAATTTGAATTTGACCCTT
1 CCCCAAATTTTCTAAAAAATTCAAATTTAACCACCAAACTTTCAAAAAATTTGAATTTGACCCTT
* * *
10634442 GATCTTTTCATAAATTCAAATTTGAT
66 GAACTTTCCAAAAATTCAAATTTGAT
* * * *
10634468 CCCCAAATTTTC-CAAAAATTCCAATTTAACC-CTCAAATTTTTCAAAAAATTT-TATTTGACCC
1 CCCCAAATTTTCTAAAAAATTCAAATTTAACCAC-CAAA-CTTTCAAAAAATTTGAATTTGACCC
*
10634530 TTGAAGTTTCCAAAAATTCAAATTTGA
64 TTGAACTTTCCAAAAATTCAAATTTGA
10634557 CCGATTTTAG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
89 1 0.01
90 51 0.67
91 24 0.32
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (91 bp):
CCCCAAATTTTCTAAAAAATTCAAATTTAACCACCAAACTTTCAAAAAATTTGAATTTGACCCTT
GAACTTTCCAAAAATTCAAATTTGAT
Found at i:10635473 original size:19 final size:19
Alignment explanation
Indices: 10635449--10635643 Score: 221
Period size: 19 Copynumber: 10.3 Consensus size: 19
10635439 AAAAGGAATA
10635449 CAATACTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
*
10635468 CAATACTGGCTGGTAAGAG
1 CAATACTGGCTCGTAAGAG
* *** *
10635487 CAATATTGGCTCACGATAG
1 CAATACTGGCTCGTAAGAG
* *
10635506 AAATACTGGCTCATAAG-G
1 CAATACTGGCTCGTAAGAG
*
10635524 ACAATACTGGCTCGCAAGAG
1 -CAATACTGGCTCGTAAGAG
*
10635544 CAATATTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
* *
10635563 CAATAGTGGCTCGCAAGAG
1 CAATACTGGCTCGTAAGAG
* *
10635582 CAATACTAGCTCGTAATAG
1 CAATACTGGCTCGTAAGAG
*
10635601 CATTACTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
* *
10635620 CATTACTGGCTCGTGAGAG
1 CAATACTGGCTCGTAAGAG
10635639 CAATA
1 CAATA
10635644 TACTGTACTG
Statistics
Matches: 146, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
18 1 0.01
19 144 0.99
20 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (19 bp):
CAATACTGGCTCGTAAGAG
Found at i:10643271 original size:36 final size:36
Alignment explanation
Indices: 10643229--10643362 Score: 214
Period size: 36 Copynumber: 3.7 Consensus size: 36
10643219 CAGTAACAAG
*
10643229 CATGACCTTTGGGTCAACAAGGAATATAATGAGCAT
1 CATGACCTTTGGGTCAACAAGGAGTATAATGAGCAT
* * *
10643265 CATGACCTTTGGGACAACAGGGAGTATAATGAACAT
1 CATGACCTTTGGGTCAACAAGGAGTATAATGAGCAT
*
10643301 CATGACCTTTGGGTCAACAGGGAGTATAATGAGCAT
1 CATGACCTTTGGGTCAACAAGGAGTATAATGAGCAT
*
10643337 CATGACCTTTGGGTCAACAAGTAGTA
1 CATGACCTTTGGGTCAACAAGGAGTA
10643363 AAACAAATAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 90 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAAGGAGTATAATGAGCAT
Found at i:10648871 original size:87 final size:87
Alignment explanation
Indices: 10648685--10648858 Score: 285
Period size: 87 Copynumber: 2.0 Consensus size: 87
10648675 AAGAGGAAGG
* ** ** *
10648685 ATATAGAATTTACCGTCGGAGATAGAGTCTTTTTGAGAGTTTCACCTTGGAAGAAGGTGTTACGG
1 ATATAGAATTTATCGTCAAAGATCTAGTCCTTTTGAGAGTTTCACCTTGGAAGAAGGTGTTACGG
10648750 TTTGGTAAAAAGGGCAAGTTGA
66 TTTGGTAAAAAGGGCAAGTTGA
10648772 ATATAGAATTTATCGTCAAAGATCTAGTCCTTTTGAGAGTTTCACCTTGGAAGAAGGTGTTACGG
1 ATATAGAATTTATCGTCAAAGATCTAGTCCTTTTGAGAGTTTCACCTTGGAAGAAGGTGTTACGG
*
10648837 TTTGGTAGAAAGGGCAAGTTGA
66 TTTGGTAAAAAGGGCAAGTTGA
10648859 GTCCGTGGTT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (87 bp):
ATATAGAATTTATCGTCAAAGATCTAGTCCTTTTGAGAGTTTCACCTTGGAAGAAGGTGTTACGG
TTTGGTAAAAAGGGCAAGTTGA
Found at i:10650668 original size:36 final size:34
Alignment explanation
Indices: 10650626--10650711 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
10650616 CGGTAATAAG
*
10650626 CATGACCTTTGGGTCAACAGGGATTATAATTAGCAT
1 CATGACCTTTGGGTCAACAGGG--TATAATGAGCAT
*
10650662 CATGACCTTTGGGCCAACAGGGTATAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGTATAATGAGCAT
10650696 CATGACCTTTGGGTCA
1 CATGACCTTTGGGTCA
10650712 GTAGGGAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 26 0.55
36 21 0.45
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (34 bp):
CATGACCTTTGGGTCAACAGGGTATAATGAGCAT
Found at i:10654194 original size:53 final size:53
Alignment explanation
Indices: 10654113--10654362 Score: 349
Period size: 53 Copynumber: 4.7 Consensus size: 53
10654103 CTTGTGCCAA
** *
10654113 AGATTAAAGGTTTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATCAC
1 AGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCAC
*
10654166 GGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCAC
1 AGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCAC
* * * *
10654219 AGATTAAAGGTTCGATGACTATGTGTCATCGTGAGTTATATGAATTCTATTAC
1 AGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCAC
* * * * * * *
10654272 GGATTAAAGGTCCGATGACTTTGTGCCATCATGAGTTACACGAATCC-ATCAT
1 AGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCAC
*
10654324 AGATTAAAGGTCCGATGACTCTGTGGCATCGTGAGTTAT
1 AGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
10654363 CAAATGCGAA
Statistics
Matches: 173, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 37 0.21
53 136 0.79
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (53 bp):
AGATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCAC
Found at i:10662848 original size:53 final size:53
Alignment explanation
Indices: 10662768--10663016 Score: 338
Period size: 53 Copynumber: 4.7 Consensus size: 53
10662758 TTATGCCAAA
* *
10662768 GATTAAAGGTCTGATGACTTTGTGTCATCGTGAGTTATATGAATCCTATCACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
*
10662821 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * * * * * * *
10662874 GATTAAAGGTTCGATGGCTATGTGCCATCGTGAGTTTTATGAATTCAATTACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * * * *
10662927 GATTAAAGGTCCAATGACTTTGTGTCATCGTGAGTTACACGAATCC-ATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
*
10662979 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
10663017 CAAATACGAA
Statistics
Matches: 169, Mismatches: 27, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
52 38 0.22
53 131 0.78
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
Found at i:10664338 original size:46 final size:46
Alignment explanation
Indices: 10664271--10664362 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
10664261 ATTTGATAGT
10664271 TAAATATTAAACACATTATGTGTACAAACTTATTGTACACGAATAA
1 TAAATATTAAACACATTATGTGTACAAACTTATTGTACACGAATAA
10664317 TAAATATTAAACACATTATGTGTACAAACTTATTGTACACGAATAA
1 TAAATATTAAACACATTATGTGTACAAACTTATTGTACACGAATAA
10664363 AGAACATAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.33
Consensus pattern (46 bp):
TAAATATTAAACACATTATGTGTACAAACTTATTGTACACGAATAA
Found at i:10665476 original size:15 final size:15
Alignment explanation
Indices: 10665458--10665487 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10665448 CGAAAGCACG
10665458 CAAAAAGAAAAAGAA
1 CAAAAAGAAAAAGAA
*
10665473 CAAAAAGAGAAAGAA
1 CAAAAAGAAAAAGAA
10665488 TGGGGAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
CAAAAAGAAAAAGAA
Found at i:10666662 original size:23 final size:23
Alignment explanation
Indices: 10666634--10666687 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
10666624 AAAATTGAAT
* *
10666634 TTCGAGTTAA-TCGAATTGAGTTA
1 TTCGAGTTAACTCGAA-TAAGTAA
*
10666657 TTCGAGTCAACTCGAATAAGTAA
1 TTCGAGTTAACTCGAATAAGTAA
10666680 TTCGAGTT
1 TTCGAGTT
10666688 TCGAGTTCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (23 bp):
TTCGAGTTAACTCGAATAAGTAA
Found at i:10666839 original size:19 final size:20
Alignment explanation
Indices: 10666815--10666871 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
10666805 CAAAATAATC
10666815 AAAATAATTTTTAAAATT-T
1 AAAATAATTTTTAAAATTCT
*
10666834 AAAAT-ATTTATAAAAATTCT
1 AAAATAATTT-TTAAAATTCT
*
10666854 AAATTTATATTTTTAAAA
1 AAA-ATA-ATTTTTAAAA
10666872 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.13
19 12 0.40
20 4 0.13
21 1 0.03
22 5 0.17
23 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTCT
Found at i:10666897 original size:34 final size:34
Alignment explanation
Indices: 10666831--10666897 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
10666821 ATTTTTAAAA
* * **
10666831 TTTAAAATATTTATAAAAATTCTAAATTTATATT
1 TTTAAAAAATTTATAAAAAATCTAAAAATATATT
10666865 TTTAAAAAATTT-TAAAAAATCTAAAGAATATAT
1 TTTAAAAAATTTATAAAAAATCTAAA-AATATAT
10666898 AAAGAAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (34 bp):
TTTAAAAAATTTATAAAAAATCTAAAAATATATT
Found at i:10668196 original size:16 final size:16
Alignment explanation
Indices: 10668172--10668221 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
10668162 CACTCTACCA
*
10668172 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
**
10668188 TTATAAATTATAAAAAA
1 TTATAAATT-TAAAATT
10668205 TTA-AAA-TTAAAATT
1 TTATAAATTTAAAATT
10668219 TTA
1 TTA
10668222 GAGTGTCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 8 0.29
15 1 0.04
16 11 0.39
17 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:10669468 original size:27 final size:26
Alignment explanation
Indices: 10669438--10669520 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 26
10669428 AGTACGAAAT
10669438 TAAATAAAAATTAGTTTAAATTGTGAG
1 TAAA-AAAAATTAGTTTAAATTGTGAG
* * *
10669465 TAAAAGAAA--A-TTTAAATAG-AAG
1 TAAAAAAAATTAGTTTAAATTGTGAG
10669487 T---AAA-ATTAGTTTAAATTGTGAG
1 TAAAAAAAATTAGTTTAAATTGTGAG
10669509 TAAAAAGAAATT
1 TAAAAA-AAATT
10669521 TAAATAGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
18 1 0.02
19 2 0.05
20 1 0.02
21 8 0.20
22 6 0.15
23 8 0.20
24 1 0.02
25 2 0.05
26 5 0.12
27 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (26 bp):
TAAAAAAAATTAGTTTAAATTGTGAG
Found at i:10669469 original size:23 final size:23
Alignment explanation
Indices: 10669442--10669514 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
10669432 CGAAATTAAA
10669442 TAAAAATTAGTTTAAATTGTGAG
1 TAAAAATTAGTTTAAATTGTGAG
* * * *
10669465 TAAAAGA-AAATTTAAATAG-AAG
1 TAAAA-ATTAGTTTAAATTGTGAG
10669487 T-AAAATTAGTTTAAATTGTGAG
1 TAAAAATTAGTTTAAATTGTGAG
10669509 TAAAAA
1 TAAAAA
10669515 GAAATTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 6 0.16
23 18 0.47
24 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (23 bp):
TAAAAATTAGTTTAAATTGTGAG
Found at i:10669506 original size:44 final size:44
Alignment explanation
Indices: 10669444--10669538 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
10669434 AAATTAAATA
10669444 AAAATTAGTTTAAATTGTGAGT-AAAAGAAAATTTAAATAGAAGT
1 AAAATTAGTTTAAATTGTGAGTAAAAAG-AAATTTAAATAGAAGT
10669488 AAAATTAGTTTAAATTGTGAGTAAAAAGAAATTTAAATAGAAGT
1 AAAATTAGTTTAAATTGTGAGTAAAAAGAAATTTAAATAGAAGT
*
10669532 ATAATTA
1 AAAATTA
10669539 AATTAATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (44 bp):
AAAATTAGTTTAAATTGTGAGTAAAAAGAAATTTAAATAGAAGT
Found at i:10669522 original size:23 final size:22
Alignment explanation
Indices: 10669452--10669525 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
10669442 TAAAAATTAG
10669452 TTTAAATTGTGAGTAAAAGAAAA
1 TTTAAATTGTGAGTAAAAG-AAA
* * ** *
10669475 TTTAAATAG-AAGTAAAATTAG
1 TTTAAATTGTGAGTAAAAGAAA
10669496 TTTAAATTGTGAGTAAAAAGAAA
1 TTTAAATTGTGAGT-AAAAGAAA
10669519 TTTAAAT
1 TTTAAAT
10669526 AGAAGTATAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
21 9 0.23
22 10 0.26
23 20 0.51
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (22 bp):
TTTAAATTGTGAGTAAAAGAAA
Found at i:10669541 original size:22 final size:22
Alignment explanation
Indices: 10669463--10669542 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
10669453 TTAAATTGTG
**
10669463 AGTAAAAGAAAATTTAAATAGA
1 AGTAAAATTAAATTTAAATAGA
* * *
10669485 AGTAAAATT-AGTTTAAATTGTG
1 AGTAAAATTAAATTTAAATAG-A
**
10669507 AGTAAAAAGAAATTTAAATAGA
1 AGTAAAATTAAATTTAAATAGA
*
10669529 AGTATAATTAAATT
1 AGTAAAATTAAATT
10669543 AATAATATTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
21 9 0.21
22 25 0.58
23 9 0.21
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (22 bp):
AGTAAAATTAAATTTAAATAGA
Found at i:10676735 original size:30 final size:31
Alignment explanation
Indices: 10676699--10676756 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
10676689 TCTTCTATAG
*
10676699 TTTTTAAAAGATTAAATTA-AATTTTAATTA
1 TTTTTAAAAGATTAAAATACAATTTTAATTA
*
10676729 TTTTTAAGAGATTAAAATACAATTTTAA
1 TTTTTAAAAGATTAAAATACAATTTTAA
10676757 ACTTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTTTAAAAGATTAAAATACAATTTTAATTA
Found at i:10680877 original size:11 final size:10
Alignment explanation
Indices: 10680847--10680880 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
10680837 TTTAGGAAAA
10680847 ATATTTTTTT
1 ATATTTTTTT
*
10680857 GTATTTTTTT
1 ATATTTTTTT
10680867 ATATTTGTTTT
1 ATATTT-TTTT
10680878 ATA
1 ATA
10680881 AAAAATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (10 bp):
ATATTTTTTT
Found at i:10681262 original size:16 final size:15
Alignment explanation
Indices: 10681222--10681262 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
10681212 TTTCAATTTT
10681222 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
10681236 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
10681250 ATTTTAAATAATA
1 ATTTTAAATAATA
10681263 TTCTTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:10681315 original size:15 final size:15
Alignment explanation
Indices: 10681295--10681346 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
10681285 ATTCAATATT
10681295 AATATTTTAATAATA
1 AATATTTTAATAATA
*
10681310 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
*
10681329 AATATATTAATAATA
1 AATATTTTAATAATA
10681344 AAT
1 AAT
10681347 GCTTTGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 14 0.47
16 1 0.03
17 2 0.07
18 2 0.07
19 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:10681324 original size:19 final size:19
Alignment explanation
Indices: 10681297--10681333 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10681287 TCAATATTAA
*
10681297 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
10681316 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
10681334 ATTAATAATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:10684850 original size:17 final size:18
Alignment explanation
Indices: 10684822--10684856 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10684812 AATCCTAGTT
*
10684822 TTCCCTTTTTCTTTTTCC
1 TTCCCTTTTTCTTCTTCC
10684840 TTCCC-TTTTCTTCTTCC
1 TTCCCTTTTTCTTCTTCC
10684857 CCTATTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCCCTTTTTCTTCTTCC
Found at i:10684906 original size:15 final size:16
Alignment explanation
Indices: 10684886--10684922 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
10684876 TGTTTTGTTC
*
10684886 TTCTTTTGTTTCTTT-
1 TTCTTTTCTTTCTTTA
10684901 TTC-TTTCTTTCTTTA
1 TTCTTTTCTTTCTTTA
10684916 TTCTTTT
1 TTCTTTT
10684923 ATTTATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.53
15 6 0.32
16 3 0.16
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (16 bp):
TTCTTTTCTTTCTTTA
Found at i:10684973 original size:14 final size:14
Alignment explanation
Indices: 10684950--10684984 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
10684940 AGATATTAGT
10684950 TAATAATAATAAAA
1 TAATAATAATAAAA
* *
10684964 TAATACTAATTAAA
1 TAATAATAATAAAA
10684978 TAATAAT
1 TAATAAT
10684985 TTATATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:10685007 original size:13 final size:12
Alignment explanation
Indices: 10684963--10685018 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
10684953 TAATAATAAA
*
10684963 ATAATACTAATT
1 ATAATATTAATT
*
10684975 A-AATAATAATTT
1 ATAATATTAA-TT
*
10684987 ATATTATTATATT
1 ATAATATTA-ATT
10685000 ATAATATTAATT
1 ATAATATTAATT
10685012 AATAATA
1 -ATAATA
10685019 AATTAAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 7 0.19
12 7 0.19
13 21 0.58
14 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:10686249 original size:16 final size:17
Alignment explanation
Indices: 10686218--10686251 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10686208 TACATTCTTC
*
10686218 TTTAGTTTTCTTTGTTT
1 TTTAGTATTCTTTGTTT
10686235 TTTAGTATT-TTTGTTT
1 TTTAGTATTCTTTGTTT
10686251 T
1 T
10686252 ATTTTTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.03, G:0.12, T:0.76
Consensus pattern (17 bp):
TTTAGTATTCTTTGTTT
Found at i:10688609 original size:51 final size:51
Alignment explanation
Indices: 10688541--10688743 Score: 248
Period size: 51 Copynumber: 4.0 Consensus size: 51
10688531 AAATAAGAGA
* * * * *
10688541 TAAATAGCAAGCTTTGAGCCGATGACTTTTAGTAGACTTCGAGCCGGTTAT
1 TAAATAGCAGGCCTTGAGCCGATGACTTTTAGCAGGCTTCGAGCCGGTGAT
* *
10688592 TAAATAGTAGGCCTTGAGCC-AGTGACTTTTAACAGGCTTCGAGCCGGTGAT
1 TAAATAGCAGGCCTTGAGCCGA-TGACTTTTAGCAGGCTTCGAGCCGGTGAT
* * *
10688643 TAAATAGCAAGCCTTGAGCCGGTGACTTTTAGCAGGCTTCGAGCCTGTGAT
1 TAAATAGCAGGCCTTGAGCCGATGACTTTTAGCAGGCTTCGAGCCGGTGAT
* * * *
10688694 TAAATAGCAGGCCTTGAG-CTAGTGACTTTAAGCAGGCTTTGTGCCGGTGA
1 TAAATAGCAGGCCTTGAGCCGA-TGACTTTTAGCAGGCTTCGAGCCGGTGA
10688744 ACATTTATCA
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.02
51 128 0.98
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (51 bp):
TAAATAGCAGGCCTTGAGCCGATGACTTTTAGCAGGCTTCGAGCCGGTGAT
Found at i:10688635 original size:25 final size:25
Alignment explanation
Indices: 10688545--10688743 Score: 104
Period size: 25 Copynumber: 7.8 Consensus size: 25
10688535 AAGAGATAAA
* * *
10688545 TAGCAAGCTTTGAGCCGATGACTTT
1 TAGCAGGCTTCGAGCCGGTGACTTT
* * * *
10688570 TAGTAGACTTCGAGCCGGTTA-TTAAA
1 TAGCAGGCTTCGAGCCGGTGACTT--T
* *
10688596 TAGTAGGCCTT-GAGCCAGTGACTTT
1 TAGCAGG-CTTCGAGCCGGTGACTTT
* *
10688621 TAACAGGCTTCGAGCCGGTGA-TTAAA
1 TAGCAGGCTTCGAGCCGGTGACTT--T
*
10688647 TAGCAAGCCTT-GAGCCGGTGACTTT
1 TAGC-AGGCTTCGAGCCGGTGACTTT
* *
10688672 TAGCAGGCTTCGAGCCTGTGA-TTAAA
1 TAGCAGGCTTCGAGCCGGTGACTT--T
**
10688698 TAGCAGGCCTT-GAGCTAGTGACTTT
1 TAGCAGG-CTTCGAGCCGGTGACTTT
* * *
10688723 AAGCAGGCTTTGTGCCGGTGA
1 TAGCAGGCTTCGAGCCGGTGA
10688744 ACATTTATCA
Statistics
Matches: 131, Mismatches: 28, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
24 17 0.13
25 55 0.42
26 42 0.32
27 17 0.13
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (25 bp):
TAGCAGGCTTCGAGCCGGTGACTTT
Found at i:10688718 original size:26 final size:26
Alignment explanation
Indices: 10688581--10688718 Score: 99
Period size: 26 Copynumber: 5.4 Consensus size: 26
10688571 AGTAGACTTC
* * *
10688581 GAGCCGGTTATTAAATAGTAGGCCTT
1 GAGCCAGTGATTAAATAGCAGGCCTT
* *
10688607 GAGCCAGTGACTT--TTAACAGG-CTT
1 GAGCCAGTGA-TTAAATAGCAGGCCTT
* *
10688631 CGAGCCGGTGATTAAATAGCAAGCCTT
1 -GAGCCAGTGATTAAATAGCAGGCCTT
* *
10688658 GAGCCGGTGACTT--TTAGCAGG-CTT
1 GAGCCAGTGA-TTAAATAGCAGGCCTT
*
10688682 CGAGCCTGTGATTAAATAGCAGGCCTT
1 -GAGCCAGTGATTAAATAGCAGGCCTT
*
10688709 GAGCTAGTGA
1 GAGCCAGTGA
10688719 CTTTAAGCAG
Statistics
Matches: 87, Mismatches: 15, Indels: 20
0.71 0.12 0.16
Matches are distributed among these distances:
24 10 0.11
25 29 0.33
26 38 0.44
27 10 0.11
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (26 bp):
GAGCCAGTGATTAAATAGCAGGCCTT
Found at i:10688718 original size:102 final size:102
Alignment explanation
Indices: 10688541--10688743 Score: 300
Period size: 102 Copynumber: 2.0 Consensus size: 102
10688531 AAATAAGAGA
* * * *
10688541 TAAATAGCAAGCTTTGAGCCGATGACTTTTAGTAGACTTCGAGCCGGTTATTAAATAGTAGGCCT
1 TAAATAGCAAGCCTTGAGCCGATGACTTTTAGCAGACTTCGAGCCGGTGATTAAATAGCAGGCCT
10688606 TGAGCCAGTGACTTTTAA-CAGGCTTCGAGCCGGTGAT
66 TGAGCCAGTGAC-TTTAAGCAGGCTTCGAGCCGGTGAT
* * *
10688643 TAAATAGCAAGCCTTGAGCCGGTGACTTTTAGCAGGCTTCGAGCCTGTGATTAAATAGCAGGCCT
1 TAAATAGCAAGCCTTGAGCCGATGACTTTTAGCAGACTTCGAGCCGGTGATTAAATAGCAGGCCT
* * *
10688708 TGAGCTAGTGACTTTAAGCAGGCTTTGTGCCGGTGA
66 TGAGCCAGTGACTTTAAGCAGGCTTCGAGCCGGTGA
10688744 ACATTTATCA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 5 0.06
102 85 0.94
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (102 bp):
TAAATAGCAAGCCTTGAGCCGATGACTTTTAGCAGACTTCGAGCCGGTGATTAAATAGCAGGCCT
TGAGCCAGTGACTTTAAGCAGGCTTCGAGCCGGTGAT
Found at i:10699552 original size:5 final size:5
Alignment explanation
Indices: 10699542--10699584 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
10699532 TAATATATAC
10699542 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
10699585 CGAAAGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:10701697 original size:14 final size:14
Alignment explanation
Indices: 10701680--10701706 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10701670 ACAAAATGAG
10701680 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
10701694 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
10701707 TTTTTGATAA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:10713596 original size:122 final size:122
Alignment explanation
Indices: 10713373--10713597 Score: 308
Period size: 122 Copynumber: 1.8 Consensus size: 122
10713363 CTTTTGGCCT
* * * ** * *
10713373 ACTTCTTTGTATCTCATCAGAAAGATGGGGTTTGTTGTTTCACTCTCATTGAGCTCCACTTCATT
1 ACTTCTCTATATCTCATCAGAAAGATGGGGCTTGAAGTTTCACTCACATTGAACTCCACTTCATT
* * * *
10713438 TTTTTGGTCCACTTCTCTATATCTCATTAGGAAGATGACCACTTCGTTGTTTGATCC
66 ATCTTGATCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCGTTGTTTGATCC
* * *
10713495 ACTTCTCTATATCTCATCAGGAAGATGGGGCTTGAAGTTTCTCTCACATTGAACTTCACTTCATT
1 ACTTCTCTATATCTCATCAGAAAGATGGGGCTTGAAGTTTCACTCACATTGAACTCCACTTCATT
10713560 ATCTTGATCCACTTCTCTATATCTCATCA-GATAGATGA
66 ATCTTGATCCACTTCTCTATATCTCATCAGGA-AGATGA
10713598 GGTTTGAAGT
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
121 2 0.02
122 86 0.98
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (122 bp):
ACTTCTCTATATCTCATCAGAAAGATGGGGCTTGAAGTTTCACTCACATTGAACTCCACTTCATT
ATCTTGATCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCGTTGTTTGATCC
Found at i:10713621 original size:75 final size:74
Alignment explanation
Indices: 10713488--10713671 Score: 242
Period size: 75 Copynumber: 2.4 Consensus size: 74
10713478 ACTTCGTTGT
* *
10713488 TTGATCCACTTCTCTATATCTCATCAGGAAGATGGGGCTTGAAGTTTCTCTCACATTGAACTTCA
1 TTGATCCACTTCTCTATATCTCATCA-GAAGATGAGGCTTGAAGTTTCACTCACATTGAACTTCA
10713553 CTTCATTATC
65 CTTCATTATC
* * * **
10713563 TTGATCCACTTCTCTATATCTCATCAGATAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTG
1 TTGATCCACTTCTCTATATCTCATCAGA-AGATGAGGCTTGAAGTTTCACTCACATTGAACTTCA
* * *
10713628 CTTCTTTGTT
65 CTTCATTATC
*
10713638 TTGATCCACTTCTCTGTATCTCATCAAGAAGATG
1 TTGATCCACTTCTCTATATCTCATC-AGAAGATG
10713672 TCCGCTTCAT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
74 2 0.02
75 91 0.95
76 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (74 bp):
TTGATCCACTTCTCTATATCTCATCAGAAGATGAGGCTTGAAGTTTCACTCACATTGAACTTCAC
TTCATTATC
Found at i:10713688 original size:48 final size:48
Alignment explanation
Indices: 10713627--10713719 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
10713617 ATTGAGCTTT
* * *
10713627 GCTTCTTTGTTTTGATCCACTTCTCTGTATCTCATCAAGAAGATGTCC
1 GCTTCATTATTTTGATCCACTTCTCTATATCTCATCAAGAAGATGTCC
* * *
10713675 GCTTCATTATTTTGATGCACTTCTCTATATCTTATCAGGAAGATG
1 GCTTCATTATTTTGATCCACTTCTCTATATCTCATCAAGAAGATG
10713720 GGGTTTGAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (48 bp):
GCTTCATTATTTTGATCCACTTCTCTATATCTCATCAAGAAGATGTCC
Found at i:10723394 original size:4 final size:5
Alignment explanation
Indices: 10723366--10723398 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
10723356 TAATAAAAAC
10723366 ATAAA ATAAAA ATAAA ATAAA AT-AA ATAAA ATA
1 ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA ATA
10723399 CGAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:10727804 original size:33 final size:33
Alignment explanation
Indices: 10727762--10727824 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
10727752 TTGTGGTGAC
10727762 AAGTTTTATTTGTCTGATGTTAATAGCATCGAT
1 AAGTTTTATTTGTCTGATGTTAATAGCATCGAT
10727795 AAGTTTTATTTGTCTGATGTTAATAGCATC
1 AAGTTTTATTTGTCTGATGTTAATAGCATC
10727825 AACAATTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (33 bp):
AAGTTTTATTTGTCTGATGTTAATAGCATCGAT
Found at i:10730541 original size:18 final size:18
Alignment explanation
Indices: 10730513--10730555 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
10730503 AATGTACTAT
*
10730513 CAACT-AAAATGCAGTGA
1 CAACTAAAAATGCAATGA
* *
10730530 CAATTAAAAATGTAATGA
1 CAACTAAAAATGCAATGA
10730548 CAACTAAA
1 CAACTAAA
10730556 TGCTATGCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (18 bp):
CAACTAAAAATGCAATGA
Found at i:10732810 original size:15 final size:14
Alignment explanation
Indices: 10732770--10732814 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
10732760 GCATAGAATC
*
10732770 TAAAAAGAAATAGA
1 TAAAAAGAAATAAA
10732784 TAAAAGAAGAAATAAA
1 T-AAA-AAGAAATAAA
10732800 GTAAAAAGAAATAAA
1 -TAAAAAGAAATAAA
10732815 CATAAATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 1 0.04
15 13 0.48
16 12 0.44
17 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
TAAAAAGAAATAAA
Found at i:10736923 original size:17 final size:17
Alignment explanation
Indices: 10736901--10736940 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
10736891 TTAGTTTTCA
*
10736901 TGCATTTTTATTGTGC-T
1 TGCATTTTAATTGT-CAT
10736918 TGCATTTTAATTGTCAT
1 TGCATTTTAATTGTCAT
10736935 TGCATT
1 TGCATT
10736941 CATTTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.55
Consensus pattern (17 bp):
TGCATTTTAATTGTCAT
Found at i:10752679 original size:20 final size:21
Alignment explanation
Indices: 10752643--10752681 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10752633 ATTTTTGTTA
*
10752643 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
10752664 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
10752682 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:10759382 original size:13 final size:13
Alignment explanation
Indices: 10759366--10759404 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
10759356 TTGTGAGAGA
*
10759366 TATTAATCTAAAG
1 TATTAATCTAAAC
10759379 TATTAATCTAAAC
1 TATTAATCTAAAC
10759392 TAAATTAATCTAA
1 T--ATTAATCTAA
10759405 GTTTAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.57
15 10 0.43
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (13 bp):
TATTAATCTAAAC
Found at i:10761595 original size:18 final size:18
Alignment explanation
Indices: 10761572--10761607 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10761562 GATCCAAACT
*
10761572 CGACCCGTTGACTTTGAC
1 CGACCCGTTGACATTGAC
10761590 CGACCCGTTGACATTGAC
1 CGACCCGTTGACATTGAC
10761608 TTTTCGTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.22, T:0.25
Consensus pattern (18 bp):
CGACCCGTTGACATTGAC
Found at i:10767480 original size:13 final size:13
Alignment explanation
Indices: 10767464--10767488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10767454 AATAATAAGA
10767464 CATAATAAATATT
1 CATAATAAATATT
10767477 CATAATAAATAT
1 CATAATAAATAT
10767489 AATATTGAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
CATAATAAATATT
Found at i:10770434 original size:17 final size:17
Alignment explanation
Indices: 10770409--10770446 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
10770399 AAGATATGAT
*
10770409 TTTTAATTAATTATTTA
1 TTTTAATTAAGTATTTA
*
10770426 TTTTCATTAAGTATTTA
1 TTTTAATTAAGTATTTA
10770443 TTTT
1 TTTT
10770447 TGTTTAATTT
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:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTAATTAAGTATTTA
Found at i:10772960 original size:14 final size:13
Alignment explanation
Indices: 10772941--10772971 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
10772931 AACATAGAAA
10772941 TTTTTTCTTTGTTT
1 TTTTTTCTTT-TTT
10772955 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
10772968 TTTT
1 TTTT
10772972 GTGTTCTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.90
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:10775585 original size:31 final size:31
Alignment explanation
Indices: 10775547--10775610 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
10775537 ATTTTTGAAC
*
10775547 TTGAGTAC-TCATGCTCTTTTCTCGTTTTCTT
1 TTGAGTACAT-ATGCTCTATTCTCGTTTTCTT
* *
10775578 TTGAGTACATATGCTCTATTCTTGTTTTTTT
1 TTGAGTACATATGCTCTATTCTCGTTTTCTT
10775609 TT
1 TT
10775611 CTCTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.58
Consensus pattern (31 bp):
TTGAGTACATATGCTCTATTCTCGTTTTCTT
Done.