Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold283
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: 2945114
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 15
Found at i:488515 original size:20 final size:20
Alignment explanation
Indices: 488492--488531 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
488482 TAATATAAAT
* *
488492 TATTTATATATTATATTTTA
1 TATTAATATATAATATTTTA
488512 TATTAATATATAATATTTTA
1 TATTAATATATAATATTTTA
488532 AATATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTAATATATAATATTTTA
Found at i:488536 original size:22 final size:22
Alignment explanation
Indices: 488452--488536 Score: 61
Period size: 22 Copynumber: 4.0 Consensus size: 22
488442 ATATGAATAG
* *
488452 AATATA-AATATATTAAAATATC
1 AATATATAATAT-TTTAAATATT
* * *
488474 AAAATAT-ATAATATAAATTATT
1 AATATATAATATTTTAAA-TATT
* *
488496 TATATATTATATTTT--ATATT
1 AATATATAATATTTTAAATATT
488516 AATATATAATATTTTAAATAT
1 AATATATAATATTTTAAATAT
488537 AATTATGACA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
20 17 0.36
21 5 0.11
22 20 0.43
23 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATATAATATTTTAAATATT
Found at i:488551 original size:22 final size:20
Alignment explanation
Indices: 488497--488539 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
488487 TAAATTATTT
* *
488497 ATATATTATATTTTATATTA
1 ATATATAATATTTTAAATTA
488517 ATATATAATATTTTAAATATA
1 ATATATAATATTTTAAAT-TA
488538 AT
1 AT
488540 TATGACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATAATATTTTAAATTA
Found at i:488591 original size:19 final size:20
Alignment explanation
Indices: 488567--488608 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
488557 ATATAATGAA
488567 TAAATTATAAAAATTA-TAT
1 TAAATTATAAAAATTAGTAT
* *
488586 TAAATTATTAAATTTAGTAT
1 TAAATTATAAAAATTAGTAT
488606 TAA
1 TAA
488609 TTGATAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAATTATAAAAATTAGTAT
Found at i:493852 original size:28 final size:29
Alignment explanation
Indices: 493814--493869 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
493804 CTATCGTATC
493814 ATAATTAT-AAATTATATTATTAT-TTAAA
1 ATAATTATAAAATTATATT-TTATATTAAA
* *
493842 ATAATTTTAAAATTTTATTTTATATTAA
1 ATAATTATAAAATTATATTTTATATTAA
493870 TATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
ATAATTATAAAATTATATTTTATATTAAA
Found at i:493951 original size:18 final size:19
Alignment explanation
Indices: 493892--493957 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 19
493882 AATTTAAACA
*
493892 AAAATATTTT--ATTAAATA
1 AAAATATTTTAAATT-AATT
*
493910 AATAATAATTTAAATTAAATT
1 AA-AATATTTTAAATT-AATT
*
493931 AAATTATTTTAAATT-ATT
1 AAAATATTTTAAATTAATT
493949 AAAATATTT
1 AAAATATTT
493958 ACTCAAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.32
19 7 0.17
20 11 0.28
21 9 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATATTTTAAATTAATT
Found at i:494189 original size:2 final size:2
Alignment explanation
Indices: 494182--494210 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
494172 TACACTTTAA
494182 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 A
494211 ACATGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:496376 original size:2 final size:2
Alignment explanation
Indices: 496369--496418 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
496359 AATTTATTTT
* *
496369 TA TA TA TA CA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
496411 TA TA TA TA
1 TA TA TA TA
496419 CATGGAGAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:496506 original size:28 final size:28
Alignment explanation
Indices: 496475--496528 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
496465 TTATTTTCAA
* *
496475 GACTATTTTGTTATTTTCGTGTGTGATT
1 GACTATTTTGTCATTTTCGTATGTGATT
496503 GACTATTTTGTCATTTTCGTATGTGA
1 GACTATTTTGTCATTTTCGTATGTGA
496529 AGAAAGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.17, C:0.09, G:0.20, T:0.54
Consensus pattern (28 bp):
GACTATTTTGTCATTTTCGTATGTGATT
Found at i:502765 original size:2 final size:2
Alignment explanation
Indices: 502748--502784 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
502738 CCACAAAATG
* *
502748 TA TA TA AA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
502785 TTATCAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:504223 original size:9 final size:9
Alignment explanation
Indices: 504209--504243 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
504199 GCTAGTTCAC
504209 CAACATCAT
1 CAACATCAT
504218 CAACATCAT
1 CAACATCAT
*
504227 CATCATCAT
1 CAACATCAT
*
504236 CACCATCA
1 CAACATCA
504244 CAAATTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (9 bp):
CAACATCAT
Found at i:504935 original size:24 final size:24
Alignment explanation
Indices: 504907--504956 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
504897 ATTATAACAA
504907 TTTGTAAGGTAAAGTCAAGAATTT
1 TTTGTAAGGTAAAGTCAAGAATTT
* *
504931 TTTGTAGGGTAAAGTTAAGAATTT
1 TTTGTAAGGTAAAGTCAAGAATTT
504955 TT
1 TT
504957 ATTGAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (24 bp):
TTTGTAAGGTAAAGTCAAGAATTT
Found at i:505905 original size:21 final size:21
Alignment explanation
Indices: 505863--505904 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
505853 TCTAACTTAA
505863 AATAATATTTTTAAATTAAAAT
1 AATAATATTTTT-AATTAAAAT
*
505885 AATATATATTTTTATTTAAA
1 AATA-ATATTTTTAATTAAA
505905 TTTAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATATTTTTAATTAAAAT
Found at i:506002 original size:11 final size:11
Alignment explanation
Indices: 505986--506015 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
505976 TCAAATTTAT
505986 AATTTAAATTA
1 AATTTAAATTA
*
505997 AATTTAATTTA
1 AATTTAAATTA
506008 AATTTAAA
1 AATTTAAA
506016 AATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:506003 original size:6 final size:6
Alignment explanation
Indices: 505978--506015 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
505968 TAATATATTC
505978 AAATTT ATAATTT AAA-TT AAATTT -AATTT AAATTT AAA
1 AAATTT A-AATTT AAATTT AAATTT AAATTT AAATTT AAA
506016 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 10 0.34
6 13 0.45
7 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:507165 original size:25 final size:27
Alignment explanation
Indices: 507136--507185 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
507126 ACTCGGATTA
*
507136 TTATTTA-TTTAATTA-AATAATATTT
1 TTATTTATTTTAATTATAAAAATATTT
507161 TTATTTATTTTAATTATAAAAATAT
1 TTATTTATTTTAATTATAAAAATAT
507186 ATAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 8 0.36
27 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATTTATTTTAATTATAAAAATATTT
Found at i:507753 original size:28 final size:28
Alignment explanation
Indices: 507694--507754 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
507684 TTATTAAAAT
*
507694 ATAAATTAAAAAATAAAAAATTATTTAG
1 ATAAATTAAAAAATAAAAAATTATTTAA
* *
507722 ATAAATTAAAAATATAAGAACTTA-TTAA
1 ATAAATTAAAAA-ATAAAAAATTATTTAA
507750 ATAAA
1 ATAAA
507755 GATATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (28 bp):
ATAAATTAAAAAATAAAAAATTATTTAA
Found at i:510676 original size:2 final size:2
Alignment explanation
Indices: 510669--510698 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
510659 TTCATAGGTT
*
510669 TA TA TA TA TA CA 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
510699 AACAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:514928 original size:21 final size:21
Alignment explanation
Indices: 514902--514952 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
514892 ATGATTCGGG
*
514902 TTCTTCTTCGTCATCGTCGTT-
1 TTCTTCTTCATCATCGTC-TTC
* *
514923 TTCTTCATCATCATCTTCTTC
1 TTCTTCTTCATCATCGTCTTC
514944 TTCTTCTTC
1 TTCTTCTTC
514953 TTCTTCTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.08, C:0.31, G:0.06, T:0.55
Consensus pattern (21 bp):
TTCTTCTTCATCATCGTCTTC
Found at i:514942 original size:3 final size:3
Alignment explanation
Indices: 514936--514961 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
514926 TTCATCATCA
514936 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
514962 ATCACCGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:519906 original size:3 final size:3
Alignment explanation
Indices: 519898--519923 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
519888 ATCCCAAGTA
519898 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
519924 CTTGAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:520901 original size:28 final size:28
Alignment explanation
Indices: 520871--520926 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
520861 TGGTAATCAT
520871 TTTTTTAT-ATTTTT-TT-ATTTAAGAA
1 TTTTTTATAATTTTTATTGATTTAAGAA
*
520896 TTTTTTATAATTTTTATTGATTTAAGTA
1 TTTTTTATAATTTTTATTGATTTAAGAA
520924 TTT
1 TTT
520927 AAATATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.30
26 6 0.22
27 2 0.07
28 11 0.41
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (28 bp):
TTTTTTATAATTTTTATTGATTTAAGAA
Found at i:520936 original size:28 final size:25
Alignment explanation
Indices: 520876--520937 Score: 61
Period size: 28 Copynumber: 2.3 Consensus size: 25
520866 ATCATTTTTT
**
520876 TATATTTTTTTATTTAAGAATTTTT
1 TATATTTTTTTATTTAAGAATTTAA
*
520901 TATAATTTTTATTGATTTAAGTATTTAAA
1 TAT-ATTTTT-TT-ATTTAAGAATTT-AA
520930 TATATTTT
1 TATATTTT
520938 GGGATCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 3 0.10
26 6 0.20
27 2 0.07
28 16 0.53
29 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (25 bp):
TATATTTTTTTATTTAAGAATTTAA
Found at i:525535 original size:19 final size:18
Alignment explanation
Indices: 525508--525546 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
525498 ACACCCTCGA
525508 TTTTTCTTTTTCT-TATTT
1 TTTTTCTTTTT-TATATTT
525526 TTTTTACTTTTTTATATTT
1 TTTTT-CTTTTTTATATTT
525545 TT
1 TT
525547 ACATTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTTATATTT
Found at i:526160 original size:24 final size:24
Alignment explanation
Indices: 526126--526173 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
526116 AACATATTTA
* * *
526126 ACGGCCTCGACCTCGTCCACGTCC
1 ACGGCCACGACCCCGACCACGTCC
526150 ACGGCCACGACCCCGACCACGTCC
1 ACGGCCACGACCCCGACCACGTCC
526174 CAGAGGCTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.52, G:0.21, T:0.10
Consensus pattern (24 bp):
ACGGCCACGACCCCGACCACGTCC
Found at i:526839 original size:105 final size:106
Alignment explanation
Indices: 526621--526885 Score: 401
Period size: 105 Copynumber: 2.5 Consensus size: 106
526611 TAAGCCGTTG
**
526621 AAATTTCATTGCATACAAATAAACCTATAATCTTTTATTTTGCAGTAAATACAAAAAAAAAAAAA
1 AAATTTCATTGCATACAAATAAACCTATAATCTTTTATTCCGCAGTAAATACAAAAAAAAAAAAA
*
526686 AGCTTAATACCCAAATCTACCCTCAACCTTTAATACAGTTG
66 AGCTTAATACCCAAATCTACCCTCAACCTTTAATACAGTTA
* * * **
526727 ACATTTCATTGCATACAAATAAAGCTATAATCTTTTATTCCGCAGTAAAT-TATTAAAAAAAAAA
1 AAATTTCATTGCATACAAATAAACCTATAATCTTTTATTCCGCAGTAAATACAAAAAAAAAAAAA
526791 AGCTTAATACCCAAATCTACCCTCAACCTTTAATACAGTTA
66 AGCTTAATACCCAAATCTACCCTCAACCTTTAATACAGTTA
* *
526832 AAATTTCATTGCATACAAATAAACCTATAGTCATTTATATTGCGC--TAAATACAA
1 AAATTTCATTGCATACAAATAAACCTATAATC-TTT-TATTCCGCAGTAAATACAA
526886 CCACAAACTT
Statistics
Matches: 142, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
105 85 0.60
106 50 0.35
107 7 0.05
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (106 bp):
AAATTTCATTGCATACAAATAAACCTATAATCTTTTATTCCGCAGTAAATACAAAAAAAAAAAAA
AGCTTAATACCCAAATCTACCCTCAACCTTTAATACAGTTA
Found at i:529081 original size:32 final size:32
Alignment explanation
Indices: 529026--529109 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
529016 GATATTGTTC
* *
529026 AGATCATTTTGAGTTC-AGATCATTTTAGGTTT
1 AGATCATTTCGAGTTCAAG-TCATTTGAGGTTT
* *
529058 AGGTCATTTCG-GATTCAAGTCATTTGGGGTTT
1 AGATCATTTCGAG-TTCAAGTCATTTGAGGTTT
529090 AGATCATTTCGAGTTCAAGT
1 AGATCATTTCGAGTTCAAGT
529110 TGTTTCGGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 1 0.02
32 40 0.91
33 3 0.07
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.42
Consensus pattern (32 bp):
AGATCATTTCGAGTTCAAGTCATTTGAGGTTT
Found at i:529096 original size:16 final size:16
Alignment explanation
Indices: 529022--529098 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 16
529012 TTTAGATATT
*
529022 GTTCAGATCATTTTGA
1 GTTCAGATCATTTTGG
*
529038 GTTCAGATCATTTTAG
1 GTTCAGATCATTTTGG
* * *
529054 GTTTAGGTCATTTCGG
1 GTTCAGATCATTTTGG
* *
529070 ATTCA-AGTCATTTGGG
1 GTTCAGA-TCATTTTGG
*
529086 GTTTAGATCATTT
1 GTTCAGATCATTT
529099 CGAGTTCAAG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
16 46 0.98
17 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (16 bp):
GTTCAGATCATTTTGG
Found at i:529120 original size:32 final size:32
Alignment explanation
Indices: 529053--529120 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
529043 GATCATTTTA
* *
529053 GGTTTAGGTCATTTCGGATTCAAGTCATTTGG
1 GGTTTAGATCATTTCGGATTCAAGTCATTTCG
**
529085 GGTTTAGATCATTTC-GAGTTCAAGTTGTTTCG
1 GGTTTAGATCATTTCGGA-TTCAAGTCATTTCG
529117 GGTT
1 GGTT
529121 CATGTCAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.43
Consensus pattern (32 bp):
GGTTTAGATCATTTCGGATTCAAGTCATTTCG
Found at i:530267 original size:15 final size:13
Alignment explanation
Indices: 530232--530286 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
530222 TATAAATAAT
530232 TAAATAATTTTTA
1 TAAATAATTTTTA
530245 -AAATAATTTTTAA
1 TAAATAATTTTT-A
* *
530258 TAAATAAATTATA
1 TAAATAATTTTTA
*
530271 AAAAT-ATTTATTA
1 TAAATAATTT-TTA
530284 TAA
1 TAA
530287 TTTAATTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 14 0.42
13 10 0.30
14 9 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATAATTTTTA
Found at i:530287 original size:36 final size:35
Alignment explanation
Indices: 530216--530289 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
530206 TTTTATAACT
* *
530216 TTTTTATATAAATAATTAAATAATTTTTAAAATAA
1 TTTTTATATAAATAATTAAAAAATATTTAAAATAA
**
530251 TTTTTA-ATAAATAAATTATAAAAATATTTATTATAA
1 TTTTTATATAAAT-AATTA-AAAAATATTTAAAATAA
530287 TTT
1 TTT
530290 AATTGGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 6 0.18
35 11 0.33
36 16 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
TTTTTATATAAATAATTAAAAAATATTTAAAATAA
Found at i:532054 original size:14 final size:16
Alignment explanation
Indices: 532024--532055 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
532014 TAATATTTAA
532024 TTTGAGTTTATATTAT
1 TTTGAGTTTATATTAT
532040 TTTGAG-TTA-ATTAT
1 TTTGAGTTTATATTAT
532054 TT
1 TT
532056 AGGTCATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTGAGTTTATATTAT
Found at i:532108 original size:16 final size:16
Alignment explanation
Indices: 532089--532137 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
532079 TTTAGGTTCA
*
532089 AGTTATTTCGGATTCG
1 AGTTATTTCAGATTCG
532105 AGTTATTTCAGATTC-
1 AGTTATTTCAGATTCG
* *
532120 AGATCATTTCAAATTCG
1 AG-TTATTTCAGATTCG
532137 A
1 A
532138 ATCATTCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 25 0.89
17 1 0.04
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (16 bp):
AGTTATTTCAGATTCG
Found at i:532214 original size:15 final size:15
Alignment explanation
Indices: 532186--532253 Score: 58
Period size: 15 Copynumber: 4.8 Consensus size: 15
532176 TTTAGGTTTG
532186 AATTAATTAATTTTA
1 AATTAATTAATTTTA
532201 AATT-ATTAACTTTT-
1 AATTAATTAA-TTTTA
*
532215 --TT-ATTAA-ATTA
1 AATTAATTAATTTTA
*
532226 AATTAATTAAAATTTA
1 AATTAATT-AATTTTA
532242 AATTAATTAATT
1 AATTAATTAATT
532254 AAATTTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.05
12 7 0.16
13 2 0.05
14 8 0.19
15 13 0.30
16 11 0.26
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTAATTAATTTTA
Found at i:532251 original size:20 final size:21
Alignment explanation
Indices: 532218--532256 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
532208 AACTTTTTTA
532218 TTAAATTAAATTAATTAAAAT
1 TTAAATTAAATTAATTAAAAT
532239 TTAAATT-AATTAATTAAA
1 TTAAATTAAATTAATTAAA
532257 TTTTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAATTAAATTAATTAAAAT
Found at i:532610 original size:3 final size:3
Alignment explanation
Indices: 532595--532627 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
532585 CTTTCCATTC
*
532595 CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
532628 TTTACTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:535235 original size:2 final size:2
Alignment explanation
Indices: 535230--535274 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
535220 TGAACTCAGG
535230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
535272 AT A
1 AT A
535275 AGCGTGCACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:535472 original size:2 final size:2
Alignment explanation
Indices: 535465--535495 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
535455 CAATCCTCGA
535465 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
535496 AGCGTGCACG
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:536581 original size:34 final size:34
Alignment explanation
Indices: 536517--536699 Score: 251
Period size: 34 Copynumber: 5.4 Consensus size: 34
536507 TTCAACAAAC
* *
536517 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
536550 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
536584 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
536618 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
536652 TGTTGACTAAATGGGAGATTTGGTAGGTTGCAAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
536686 TGTTGATTAAATGG
1 TGTTGATTAAATGG
536700 TGGTTTTTAC
Statistics
Matches: 131, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 11 0.08
34 120 0.92
ACGTcount: A:0.26, C:0.07, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:541176 original size:34 final size:34
Alignment explanation
Indices: 541110--541294 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
541100 AAGTGGGAGA
* *
541110 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
541143 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
541177 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
541211 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
541245 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
541279 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
541295 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:543944 original size:2 final size:2
Alignment explanation
Indices: 543937--543979 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
543927 GCTCTGATCC
543937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
543979 T
1 T
543980 CATTTACGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:544263 original size:12 final size:13
Alignment explanation
Indices: 544239--544268 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
544229 AGGCTGTAAT
544239 AAGAAACAAAAAA
1 AAGAAACAAAAAA
544252 AAGAAA-AAAAAA
1 AAGAAACAAAAAA
544264 AAGAA
1 AAGAA
544269 GCTTAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (13 bp):
AAGAAACAAAAAA
Found at i:547096 original size:50 final size:50
Alignment explanation
Indices: 547021--547120 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
547011 AAGATTTGTT
*
547021 TGTTGTGAAATTAAAAACTTTAATGAAAATTCATCAAAAATTAGCTCATA
1 TGTTGTGAAATTAAAAACTTCAATGAAAATTCATCAAAAATTAGCTCATA
*
547071 TGTTGTGAGATTAAAAACTTCAATGAAAATTCATCAAAAATTAGCTCATA
1 TGTTGTGAAATTAAAAACTTCAATGAAAATTCATCAAAAATTAGCTCATA
547121 CATTATATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (50 bp):
TGTTGTGAAATTAAAAACTTCAATGAAAATTCATCAAAAATTAGCTCATA
Found at i:548094 original size:16 final size:16
Alignment explanation
Indices: 548046--548096 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
548036 AATTTAAATG
*
548046 TAAAGTTTTTAT-ATT
1 TAAAATTTTTATAATT
* *
548061 TTAAA-TTTTAAAATTT
1 TAAAATTTTTATAA-TT
548077 TAAAATTTTTATAATT
1 TAAAATTTTTATAATT
548093 TAAA
1 TAAA
548097 TAAATATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 5 0.18
15 4 0.14
16 12 0.43
17 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TAAAATTTTTATAATT
Found at i:548135 original size:31 final size:30
Alignment explanation
Indices: 548097--548178 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
548087 ATAATTTAAA
548097 TAAATATAATTATTTAATTA-ATTTTAAATAT
1 TAAATATAATTATTTAATTATATTTT--ATAT
* **
548128 TAAATATAAATA-AAAATTATATTTTATAT
1 TAAATATAATTATTTAATTATATTTTATAT
* *
548157 TAAATA-AATTTTTTAATAATAT
1 TAAATATAATTATTTAATTATAT
548179 AAAATTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
28 3 0.07
29 17 0.41
30 5 0.12
31 16 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAATATAATTATTTAATTATATTTTATAT
Found at i:548148 original size:59 final size:58
Alignment explanation
Indices: 548085--548204 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 58
548075 TTTAAAATTT
*
548085 TTATAATTTA-AATAAATATAATTATTTAATTAATTTTAAATATT-AAATA-TAAATAAAAA
1 TTATAATTTATAATAAATA-AATTATTTAA-TAA-TATAAA-ATTAAAATATTAAATAAAAA
* * * *
548144 TTATATTTTATATTAAATAAATTTTTTAATAATATAAAATTAAAATATTTAATAAAAA
1 TTATAATTTATAATAAATAAATTATTTAATAATATAAAATTAAAATATTAAATAAAAA
548202 TTA
1 TTA
548205 AAAATATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
56 3 0.06
57 10 0.19
58 15 0.28
59 18 0.34
60 7 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (58 bp):
TTATAATTTATAATAAATAAATTATTTAATAATATAAAATTAAAATATTAAATAAAAA
Found at i:548203 original size:19 final size:21
Alignment explanation
Indices: 548173--548212 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
548163 AATTTTTTAA
548173 TAATATAAAATT-AAAATATT
1 TAATATAAAATTAAAAATATT
548193 TAATA-AAAATTAAAAATATT
1 TAATATAAAATTAAAAATATT
548213 ATATTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATAAAATTAAAAATATT
Found at i:548736 original size:23 final size:22
Alignment explanation
Indices: 548684--548736 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
548674 AATAATAAAA
548684 AATATTTTTTATTATTTTTATT
1 AATATTTTTTATTATTTTTATT
*
548706 TATAATTTTTT-TTAATTTTTTATT
1 AAT-ATTTTTTATT-A-TTTTTATT
548730 AATATTT
1 AATATTT
548737 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 12 0.46
24 10 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
AATATTTTTTATTATTTTTATT
Found at i:548779 original size:44 final size:44
Alignment explanation
Indices: 548702--548785 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
548692 TTATTATTTT
* *
548702 TATTTATAATTTTTTTTAATTTTTTATTAATATTTAAATAAAAA
1 TATTAATAATTTTTTTTAAATTTTTATTAATATTTAAATAAAAA
548746 TATTAATAATTTATTTTATAAATTTTTA-T-ATATTTAAATA
1 TATTAATAATTT-TTTT-TAAATTTTTATTAATATTTAAATA
548786 TTTCTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
44 22 0.61
45 5 0.14
46 9 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (44 bp):
TATTAATAATTTTTTTTAAATTTTTATTAATATTTAAATAAAAA
Found at i:548794 original size:44 final size:44
Alignment explanation
Indices: 548696--548794 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 44
548686 TATTTTTTAT
* * *
548696 TATTTTTATTTATAATTTTTTTTAATTTTTTATTAATATTTAAA
1 TATTTATATTAATAATTTTTTTTAAATTTTTATTAATATTTAAA
***
548740 TAAAAATATTAATAATTTATTTTATAAATTTTTA-T-ATATTTAAA
1 TATTTATATTAATAATTT-TTTT-TAAATTTTTATTAATATTTAAA
*
548784 TATTTCTATTA
1 TATTTATATTA
548795 TATTATAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
44 29 0.67
45 5 0.12
46 9 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (44 bp):
TATTTATATTAATAATTTTTTTTAAATTTTTATTAATATTTAAA
Found at i:548815 original size:19 final size:18
Alignment explanation
Indices: 548767--548815 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
548757 TATTTTATAA
548767 ATTTTTATATATTTAAAT
1 ATTTTTATATATTTAAAT
* *
548785 ATTTCTATTATATTATAATT
1 ATTTTTA-TATATT-TAAAT
548805 ATTTTTATATA
1 ATTTTTATATA
548816 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 6 0.23
19 10 0.38
20 10 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTATATATTTAAAT
Found at i:548820 original size:22 final size:19
Alignment explanation
Indices: 548767--548820 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
548757 TATTTTATAA
548767 ATTTTTATATAT-TTAAAT
1 ATTTTTATATATATTAAAT
*
548785 ATTTCTAT-TATATTATAATT
1 ATTTTTATATATATTA-AA-T
548805 ATTTTTATATAATATT
1 ATTTTTATAT-ATATT
548821 TTTATCGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 3 0.10
18 10 0.34
19 2 0.07
20 8 0.28
21 1 0.03
22 5 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTATATATATTAAAT
Found at i:557900 original size:27 final size:27
Alignment explanation
Indices: 557856--557931 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
557846 CATATATCAT
557856 ATATAATATATATATATAAAATAAAAT-A
1 ATATAA-ATATA-ATATAAAATAAAATAA
* *
557884 ATAATTAAA-ATAATATAAATTATAATAA
1 AT-A-TAAATATAATATAAAATAAAATAA
557912 ATATAAATATAA-ATAAAATA
1 ATATAAATATAATATAAAATA
557932 TTATTATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
26 11 0.27
27 17 0.41
28 8 0.20
29 2 0.05
30 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATAAATATAATATAAAATAAAATAA
Found at i:557916 original size:16 final size:16
Alignment explanation
Indices: 557886--557928 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
557876 ATAAAATAAT
*
557886 AATTAAAAT-AATATA
1 AATTATAATAAATATA
557901 AATTATAATAAATATA
1 AATTATAATAAATATA
557917 AA-TATAAATAAA
1 AATTAT-AATAAA
557929 ATATTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTATAATAAATATA
Found at i:557919 original size:6 final size:6
Alignment explanation
Indices: 557856--557932 Score: 53
Period size: 6 Copynumber: 13.7 Consensus size: 6
557846 CATATATCAT
*
557856 ATATAA TATATAT ATATAA A-ATAA A-AT-A ATAATTAA A-AT-A ATATAA
1 ATATAA -ATATAA ATATAA ATATAA ATATAA AT-A-TAA ATATAA ATATAA
*
557902 AT-TAT A-ATAA ATATAA ATATAA ATA-AA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
557933 TATTATATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
4 4 0.07
5 21 0.37
6 24 0.42
7 6 0.11
8 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:557942 original size:21 final size:21
Alignment explanation
Indices: 557918--557986 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
557908 ATAAATATAA
557918 ATATAAATAAAATATTATTAT
1 ATATAAATAAAATATTATTAT
* *
557939 ATATAAA-AAATACAATATT-T
1 ATATAAATAAA-ATATTATTAT
*
557959 ATAT-AAT-TAATATTAATTTAT
1 ATATAAATAAAATATT-A-TTAT
557980 ATATAAA
1 ATATAAA
557987 ATATTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 10 0.27
21 18 0.49
22 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAAATAAAATATTATTAT
Found at i:557944 original size:36 final size:37
Alignment explanation
Indices: 557858--557950 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 37
557848 TATATCATAT
*
557858 ATAATATATATAT-ATAAA-ATAAAATAATAATTAAA
1 ATAATATATATATAATAAATATAAAATAATAAATAAA
*
557893 ATAATATAAATTATAATAAATAT-AAAT-ATAAATAAA
1 ATAATATATA-TATAATAAATATAAAATAATAAATAAA
* *
557929 ATATTATTATATATAAAAAATA
1 ATAATA-TATATATAATAAATA
557951 CAATATTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
35 9 0.18
36 26 0.53
37 12 0.24
38 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (37 bp):
ATAATATATATATAATAAATATAAAATAATAAATAAA
Found at i:557956 original size:41 final size:40
Alignment explanation
Indices: 557907--557987 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 40
557897 TATAAATTAT
557907 AATAAATATAAATATAAATAAAATATT-A-TTATATATAAAA
1 AATAAATATAAATAT-AAT-AAATATTAATTTATATATAAAA
** *
557947 AATACAATATTTATATAATTAATATTAATTTATATATAAAA
1 AATA-AATATAAATATAATAAATATTAATTTATATATAAAA
557988 TATTTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 6 0.17
40 8 0.23
41 21 0.60
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (40 bp):
AATAAATATAAATATAATAAATATTAATTTATATATAAAA
Found at i:557989 original size:19 final size:19
Alignment explanation
Indices: 557919--557991 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 19
557909 TAAATATAAA
*
557919 TATAAATAAAATATT-A-T
1 TATATATAAAATATTAATT
* *
557936 TATATATAAAAAATACAATAT
1 TATATATAAAATAT-TAAT-T
557957 T-TATATAATTAATATTAATT
1 TATATATAA--AATATTAATT
557977 TATATATAAAATATT
1 TATATATAAAATATT
557992 TTAAAAACCA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
17 12 0.27
19 7 0.16
20 9 0.20
21 12 0.27
22 4 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATATAAAATATTAATT
Found at i:571088 original size:19 final size:19
Alignment explanation
Indices: 571036--571095 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
571026 TTAATAATAT
*
571036 TATTATATTATT-TTTTAA
1 TATTAAATTATTATTTTAA
571054 TATTATAATT-TATATTTT-A
1 TATTA-AATTAT-TATTTTAA
571073 TAATTAAATTATTATTTTAA
1 T-ATTAAATTATTATTTTAA
571093 TAT
1 TAT
571096 CAATTTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
18 6 0.17
19 18 0.51
20 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTAAATTATTATTTTAA
Found at i:572004 original size:20 final size:20
Alignment explanation
Indices: 571981--572025 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
571971 AAACTAAATT
571981 AAATAAATTTAAATTATATA-
1 AAATAAATTT-AATTATATAC
* *
572001 AAATTAATTTAATTTTATAC
1 AAATAAATTTAATTATATAC
572021 AAATA
1 AAATA
572026 TAAATAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATAAATTTAATTATATAC
Found at i:573109 original size:20 final size:20
Alignment explanation
Indices: 573073--573111 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
573063 TATTTATATT
*
573073 TTTTAATTATATTTAAAATA
1 TTTTAATTATATATAAAATA
573093 TTTTATATT-TATATAAAAT
1 TTTTA-ATTATATATAAAAT
573112 TAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTAATTATATATAAAATA
Found at i:573127 original size:29 final size:27
Alignment explanation
Indices: 573061--573140 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
573051 CAATAAATAT
* * *
573061 AATATTTATATTTT-TTAATTATATTTAA
1 AATATTT-TATTTTATT-ATAAAATTAAA
573089 AATATTTTATATTTA-TATAAAATTAAA
1 AATATTTTAT-TTTATTATAAAATTAAA
573116 AATATTAATTATTTTATTATAAAAT
1 AATATT--TTATTTTATTATAAAAT
573141 ATTTTAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 17 0.39
28 15 0.34
29 12 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AATATTTTATTTTATTATAAAATTAAA
Found at i:573314 original size:5 final size:5
Alignment explanation
Indices: 573304--573332 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
573294 TTGAAAATAT
573304 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
573333 CATTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:573419 original size:15 final size:15
Alignment explanation
Indices: 573388--573434 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
573378 TGATGTTATC
*
573388 TATATAAAAATTAAAA
1 TATA-AAAAATTTAAA
573404 TA-AAATAAATTTAAA
1 TATAAA-AAATTTAAA
*
573419 TATTAAAAATTTAAA
1 TATAAAAAATTTAAA
573434 T
1 T
573435 TTATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.07
15 21 0.78
16 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAAAAATTTAAA
Found at i:580261 original size:11 final size:11
Alignment explanation
Indices: 580242--580276 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
580232 AAAAATACAT
*
580242 AAATATATATA
1 AAATTTATATA
580253 AAATTTATATAA
1 AAATTTATAT-A
580265 AAATTTATATA
1 AAATTTATATA
580276 A
1 A
580277 TTTTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATTTATATA
Found at i:580264 original size:21 final size:21
Alignment explanation
Indices: 580240--580279 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
580230 AAAAAAATAC
*
580240 ATAAATATATATAAAATTTAT
1 ATAAAAATATATAAAATTTAT
* *
580261 ATAAAAATTTATATAATTT
1 ATAAAAATATATAAAATTT
580280 TTTAATATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAAAATATATAAAATTTAT
Found at i:580269 original size:12 final size:12
Alignment explanation
Indices: 580245--580276 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
580235 AATACATAAA
580245 TATATATAAAATT
1 TATATA-AAAATT
580258 TATATAAAAATT
1 TATATAAAAATT
580270 TATATAA
1 TATATAA
580277 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATAAAAATT
Found at i:580410 original size:13 final size:14
Alignment explanation
Indices: 580373--580422 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
580363 CTTTCTTTTA
*
580373 TTCTCTTTCTTTTCT
1 TTCTCTTT-TTCTCT
*
580388 TT-TTTTTTTC-CT
1 TTCTCTTTTTCTCT
580400 TTCTCTTTTTCTTCT
1 TTCTCTTTTTC-TCT
580415 TTCTCTTT
1 TTCTCTTT
580423 CTTGTGCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 9 0.31
14 4 0.14
15 12 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTCTTTTTCTCT
Found at i:580536 original size:15 final size:16
Alignment explanation
Indices: 580511--580541 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
580501 TAGATAGATA
580511 AATTGTTAATTTTTAT
1 AATTGTTAATTTTTAT
580527 AATT-TTAATTTTTAT
1 AATTGTTAATTTTTAT
580542 TTAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
AATTGTTAATTTTTAT
Found at i:580640 original size:14 final size:16
Alignment explanation
Indices: 580606--580643 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
580596 ATTATTTTTT
*
580606 AAAATAAATATTTATA
1 AAAATAAATATATATA
580622 AAAATAAAT-TATA-A
1 AAAATAAATATATATA
580636 AAAATAAA
1 AAAATAAA
580644 AAAATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 3 0.14
16 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAATATATATA
Found at i:581504 original size:63 final size:64
Alignment explanation
Indices: 581390--581585 Score: 304
Period size: 63 Copynumber: 3.0 Consensus size: 64
581380 TTTAAGCTTG
*
581390 AATTTTTATTTAAATTTGATAATTTATATATATGATTTTATTTTATATATTTTTTAAAATTTTAA
1 AATTTTTATTTAAATTTGATAA-TT-TATATATGATCTTATTTTATATATTTTTTAAAATTTTAA
581455 T
64 T
*
581456 AATTTTTATTTGAATTTGATAATTTATATAT-ATCTTATTTTATATATTTTTTAAAATTTTAAT
1 AATTTTTATTTAAATTTGATAATTTATATATGATCTTATTTTATATATTTTTTAAAATTTTAAT
* * *
581519 AATTTTTATTTAAATTTGATAATTTATATATACGATCGTATTTTATATATTTTTTTAAATTTCAA
1 AATTTTTATTTAAATTTGATAATTTATATAT--GATCTTATTTTATATATTTTTTAAAATTTTAA
581584 T
64 T
581585 A
1 A
581586 GCGGTAAGCT
Statistics
Matches: 121, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
63 61 0.50
64 7 0.06
65 2 0.02
66 51 0.42
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (64 bp):
AATTTTTATTTAAATTTGATAATTTATATATGATCTTATTTTATATATTTTTTAAAATTTTAAT
Found at i:589426 original size:28 final size:27
Alignment explanation
Indices: 589390--589453 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
589380 AAAACTTTAA
*
589390 TTTGATTTTGTTAA-TGCTTGATAAAATT
1 TTTGATTTTGGTAAGT-CTTGATAAAA-T
* *
589418 TTTGATTTTGGTAAGTTTTGATATAAT
1 TTTGATTTTGGTAAGTCTTGATAAAAT
589445 TTTGATTTT
1 TTTGATTTT
589454 TTTATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 21 0.66
29 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.58
Consensus pattern (27 bp):
TTTGATTTTGGTAAGTCTTGATAAAAT
Found at i:589486 original size:22 final size:21
Alignment explanation
Indices: 589461--589516 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
589451 TTTTTTATAA
*
589461 TTTTTAATATAATTATGATGAC
1 TTTTTAATATAATTATAAT-AC
* * *
589483 TTTTTGATATAATTTTAATAT
1 TTTTTAATATAATTATAATAC
589504 TTTTTAATATAAT
1 TTTTTAATATAAT
589517 AAAAAATTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTTTAATATAATTATAATAC
Found at i:589723 original size:23 final size:22
Alignment explanation
Indices: 589697--589750 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
589687 TTAGTTACTG
*
589697 TTTTAAATATAATTATGATAAAA
1 TTTT-AATATAATTATAATAAAA
*
589720 TTTTAA-ATAATTGTAATAAAA
1 TTTTAATATAATTATAATAAAA
589741 TTTTTAATAT
1 -TTTTAATAT
589751 TTAATATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 13 0.48
22 8 0.30
23 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTTAATATAATTATAATAAAA
Found at i:589731 original size:21 final size:21
Alignment explanation
Indices: 589705--589756 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
589695 TGTTTTAAAT
*
589705 ATAATTATGATAAAATTTTAA
1 ATAATTATAATAAAATTTTAA
* *
589726 ATAATTGTAATAAAATTTTTA
1 ATAATTATAATAAAATTTTAA
589747 AT-ATT-TAATA
1 ATAATTATAATA
589757 TACATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 5 0.18
20 3 0.11
21 20 0.71
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
ATAATTATAATAAAATTTTAA
Found at i:589801 original size:21 final size:21
Alignment explanation
Indices: 589771--589830 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
589761 TTAATAACTT
589771 TTTATAA-TTTTAAATATAAA
1 TTTATAATTTTTAAATATAAA
*
589791 TTTATTAATTTTTAAA-ATAAT
1 TTTA-TAATTTTTAAATATAAA
589812 TTTAATAATTTTTAAATAT
1 TTT-ATAATTTTTAAATAT
589831 TTAATATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 4 0.11
21 21 0.60
22 10 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTATAATTTTTAAATATAAA
Found at i:589839 original size:42 final size:42
Alignment explanation
Indices: 589763--589843 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
589753 AATATACATT
*
589763 AATAACTTTTTATAATTTTAAATATAAATTTATTAATTTTTAA
1 AATAACTTTTAATAATTTTAAATATAAA-TTATTAATTTTTAA
*
589806 AATAA-TTTTAATAATTTTTAAATATTTAA-TATTAATTT
1 AATAACTTTTAATAA-TTTTAAATA-TAAATTATTAATTT
589844 AATATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 17 0.50
43 14 0.41
44 3 0.09
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (42 bp):
AATAACTTTTAATAATTTTAAATATAAATTATTAATTTTTAA
Found at i:589841 original size:21 final size:21
Alignment explanation
Indices: 589793--589864 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
589783 AATATAAATT
589793 TATTAATTTTTAAAATAATTT--
1 TATTAATTTTT-AAAT-ATTTAA
*
589814 TAATAATTTTTAAATATTTAA
1 TATTAATTTTTAAATATTTAA
589835 TATTAA--TTTAATATATTTTAA
1 TATTAATTTTTAA-ATA-TTTAA
589856 TA-TAATTTT
1 TATTAATTTT
589865 GATACCTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
19 9 0.21
20 10 0.23
21 22 0.51
22 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATTTTTAAATATTTAA
Found at i:589846 original size:81 final size:81
Alignment explanation
Indices: 589697--589864 Score: 195
Period size: 81 Copynumber: 2.0 Consensus size: 81
589687 TTAGTTACTG
589697 TTTTAAATATAATTATGATAAAATTTTAAATAATTGTAATAAAATTTTTAATATTTAATATACAT
1 TTTTAAATATAATTATGATAAAATTTTAAATAATTGTAAT-AAATTTTTAATATTTAATATACAT
589762 TAATA-ACTTTT-TATAA
65 TAATATA-TTTTATATAA
* * *
589778 TTTTAAATATAAATT-T-ATTAATTTTTAAAATAATTTTAAT-AATTTTTAAATATTTAATATTA
1 TTTTAAATAT-AATTATGATAAAATTTT-AAATAATTGTAATAAATTTTT-AATATTTAATA-TA
589840 -ATTTAATATATTTTAATATAA
62 CA-TTAATATATTTT-ATATAA
589861 TTTT
1 TTTT
589865 GATACCTAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
79 7 0.09
80 20 0.26
81 35 0.46
82 5 0.07
83 9 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (81 bp):
TTTTAAATATAATTATGATAAAATTTTAAATAATTGTAATAAATTTTTAATATTTAATATACATT
AATATATTTTATATAA
Found at i:589852 original size:20 final size:19
Alignment explanation
Indices: 589822--589863 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
589812 TTTAATAATT
589822 TTTAAATA-TTTAATATTAA
1 TTTAAATATTTTAATA-TAA
589841 TTTAATATATTTTAATATAA
1 TTTAA-ATATTTTAATATAA
589861 TTT
1 TTT
589864 TGATACCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAAATATTTTAATATAA
Found at i:589861 original size:50 final size:52
Alignment explanation
Indices: 589761--589887 Score: 136
Period size: 50 Copynumber: 2.5 Consensus size: 52
589751 TTAATATACA
*
589761 TTAATAACTTTTTATAATTTTAAATATAAATTTATTAATTTTTAAAATAATT
1 TTAATAACTTTTTATAATTTTAAATATAAATTTAATAATTTTTAAAATAATT
* *
589813 TTAATAA-TTTTTA-AATATTT-AATATTAATTTAAT-ATATTTTAATATAATT
1 TTAATAACTTTTTATAAT-TTTAAATATAAATTTAATAAT-TTTTAAAATAATT
* * * *
589863 TTGATACCTAATATATAATTTTAAA
1 TTAATAACT-TTTTATAATTTTAAA
589888 ATTTTTTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
49 2 0.03
50 32 0.52
51 10 0.16
52 13 0.21
53 5 0.08
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (52 bp):
TTAATAACTTTTTATAATTTTAAATATAAATTTAATAATTTTTAAAATAATT
Found at i:602664 original size:3 final size:3
Alignment explanation
Indices: 602656--602696 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
602646 AGAGTTTCTT
602656 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 TT
602697 TATCTTTGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:610589 original size:3 final size:3
Alignment explanation
Indices: 610583--610610 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
610573 TCAGTCTTCT
610583 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
610611 CATTCCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:610980 original size:27 final size:26
Alignment explanation
Indices: 610920--610983 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
610910 TATTTGTATT
*
610920 ATTTAATATATTTAAATATAAATATA
1 ATTTAAAATATTTAAATATAAATATA
610946 ATTATAAAATATTTTAAATGCATAAA-A-A
1 ATT-TAAAATA-TTTAAAT--ATAAATATA
610974 ATTTAAAATA
1 ATTTAAAATA
610984 AATTAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
26 3 0.09
27 13 0.39
28 11 0.33
29 1 0.03
30 5 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTTAAAATATTTAAATATAAATATA
Found at i:611534 original size:2 final size:2
Alignment explanation
Indices: 611527--611551 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
611517 ATCATAAGTT
611527 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
611552 TTTATCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:614203 original size:17 final size:16
Alignment explanation
Indices: 614181--614233 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
614171 AAATTTAATT
614181 ATAAATATTAATATAAA
1 ATAAATATT-ATATAAA
* *
614198 ATAAATTTTATATTATA
1 ATAAATATTATA-TAAA
*
614215 TTAAATAATTATATAAA
1 ATAAAT-ATTATATAAA
614232 AT
1 AT
614234 TTTAAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 3 0.11
17 20 0.71
18 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATATTATATAAA
Found at i:614531 original size:16 final size:16
Alignment explanation
Indices: 614512--614566 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
614502 CATTAAATTT
614512 AATAATATAATTTTAA
1 AATAATATAATTTTAA
*
614528 AATATATAAAATTTTAA
1 AATA-ATATAATTTTAA
*
614545 ATTAATTTAATAATTTTAA
1 AATAA--T-ATAATTTTAA
614564 AAT
1 AAT
614567 TTAATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 5 0.16
17 14 0.45
18 1 0.03
19 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAATATAATTTTAA
Found at i:614569 original size:16 final size:16
Alignment explanation
Indices: 614518--614572 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
614508 ATTTAATAAT
614518 ATAATTTTAAAATATATA
1 ATAATTTTAAAAT-T-TA
614536 A-AATTTTAAATTAATTTA
1 ATAATTTT-AA--AATTTA
614554 ATAATTTTAAAATTTA
1 ATAATTTTAAAATTTA
614570 ATA
1 ATA
614573 TATTAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.27
17 6 0.18
18 8 0.24
19 7 0.21
20 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTTTAAAATTTA
Found at i:619958 original size:18 final size:19
Alignment explanation
Indices: 619901--619962 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 19
619891 TTTATAATTT
*
619901 TTTTATATAAATTAAATTAA
1 TTTTA-ATAAATTATATTAA
*
619921 -TTAAATAAATTGATACTTAA
1 TTTTAATAAATT-ATA-TTAA
619941 TTTTAA-AAATTATATTAA
1 TTTTAATAAATTATATTAA
619959 TTTT
1 TTTT
619963 TATTTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 15 0.42
19 8 0.22
20 9 0.25
21 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTAATAAATTATATTAA
Found at i:621610 original size:2 final size:2
Alignment explanation
Indices: 621603--621640 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
621593 CTTGCTTCCA
621603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
621641 GAATATAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:622032 original size:3 final size:3
Alignment explanation
Indices: 622024--622069 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
622014 TAACTCAAAT
622024 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA T-A TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA
622070 GTTATTGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 34 0.85
4 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:623816 original size:19 final size:19
Alignment explanation
Indices: 623779--623821 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
623769 TTATAATATA
*
623779 AAAATAAATAATTTATTTT
1 AAAATAAATAAATTATTTT
*
623798 TAAATAAATAAAATT-TTTT
1 AAAATAAAT-AAATTATTTT
623817 AAAAT
1 AAAAT
623822 TATTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATAAATAAATTATTTT
Found at i:627515 original size:11 final size:11
Alignment explanation
Indices: 627499--627523 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
627489 TATTTAAAAA
627499 ATTATATTTAT
1 ATTATATTTAT
627510 ATTATATTTAT
1 ATTATATTTAT
627521 ATT
1 ATT
627524 TAAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:630548 original size:17 final size:17
Alignment explanation
Indices: 630514--630552 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
630504 GTATAAGTGT
* *
630514 TATATATTTACATTTAA
1 TATATATTTAAATATAA
630531 TATATATTTAAATATAA
1 TATATATTTAAATATAA
630548 T-TATA
1 TATATA
630553 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATATTTAAATATAA
Found at i:630724 original size:20 final size:20
Alignment explanation
Indices: 630701--630740 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
630691 AAATTTCATA
630701 TAAATATAATAAAAAATAAT
1 TAAATATAATAAAAAATAAT
630721 TAAATATAATAAAAAATAAT
1 TAAATATAATAAAAAATAAT
630741 ACAAGTGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAATATAATAAAAAATAAT
Found at i:630729 original size:10 final size:10
Alignment explanation
Indices: 630706--630741 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
630696 TCATATAAAT
630706 ATAATAAAAA
1 ATAATAAAAA
* *
630716 ATAATTAAAT
1 ATAATAAAAA
630726 ATAATAAAAA
1 ATAATAAAAA
630736 ATAATA
1 ATAATA
630742 CAAGTGAGCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:634369 original size:9 final size:9
Alignment explanation
Indices: 634350--634423 Score: 64
Period size: 8 Copynumber: 8.1 Consensus size: 9
634340 AAATAATATT
634350 TTAAAAA-A
1 TTAAAAATA
634358 TTAAAAATA
1 TTAAAAATA
634367 TTAAACATATATA
1 TT-AA-A-A-ATA
*
634380 TTTAAAATA
1 TTAAAAATA
*
634389 ATAAAAAT-
1 TTAAAAATA
634397 TTAAAAATA
1 TTAAAAATA
634406 -TAAAAATA
1 TTAAAAATA
*
634414 ATAAAAATA
1 TTAAAAATA
634423 T
1 T
634424 GATAATACTT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 22 0.41
9 20 0.37
10 3 0.06
11 2 0.04
12 2 0.04
13 5 0.09
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (9 bp):
TTAAAAATA
Found at i:634407 original size:30 final size:32
Alignment explanation
Indices: 634339--634407 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
634329 ACATCACGAT
634339 AAAATA-ATATTTTAAAAAATTAAAAATATTA
1 AAAATATATATTTTAAAAAATTAAAAATATTA
*
634370 AACATATATA-TTTAAAATAA-TAAAAAT-TTA
1 AAAATATATATTTTAAAA-AATTAAAAATATTA
634400 AAAATATA
1 AAAATATA
634408 AAAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 10 0.29
31 19 0.56
32 5 0.15
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAATATATATTTTAAAAAATTAAAAATATTA
Found at i:634430 original size:17 final size:17
Alignment explanation
Indices: 634383--634423 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
634373 ATATATATTT
*
634383 AAAATAATAAAAAT-TTA
1 AAAAT-ATAAAAATAATA
634400 AAAATATAAAAATAATA
1 AAAATATAAAAATAATA
634417 AAAATAT
1 AAAATAT
634424 GATAATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATATAAAAATAATA
Found at i:634534 original size:18 final size:18
Alignment explanation
Indices: 634493--634537 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
634483 AGTTAATCTA
*
634493 ATTTAAAATGATATTTTT
1 ATTTAAAATAATATTTTT
*
634511 AATTAAAATAATATCTTTT
1 ATTTAAAATAATAT-TTTT
634530 -TTTAAAAT
1 ATTTAAAAT
634538 TAAAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTTAAAATAATATTTTT
Found at i:634550 original size:7 final size:7
Alignment explanation
Indices: 634532--634571 Score: 50
Period size: 6 Copynumber: 6.1 Consensus size: 7
634522 TATCTTTTTT
634532 TAAAAT-
1 TAAAATA
634538 TAAAATA
1 TAAAATA
634545 TAAAATA
1 TAAAATA
634552 T-AAATA
1 TAAAATA
*
634558 T-TAATA
1 TAAAATA
634564 TAAAATA
1 TAAAATA
634571 T
1 T
634572 TTTAAGTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
TAAAATA
Found at i:634563 original size:6 final size:6
Alignment explanation
Indices: 634540--634624 Score: 52
Period size: 6 Copynumber: 14.5 Consensus size: 6
634530 TTTAAAATTA
* * * * *
634540 AAATAT AAAATAT AAATAT TAATAT AAA-AT -ATTTT AAGT-T -AACAT
1 AAATAT -AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
* * *
634585 AAATAT TAATAT AAATAT TAATAT AAAATAT TAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT -AAATAT AAATAT AAA
634625 AAATAATAAT
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
4 2 0.03
5 5 0.08
6 41 0.69
7 11 0.19
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (6 bp):
AAATAT
Found at i:634565 original size:12 final size:12
Alignment explanation
Indices: 634548--634624 Score: 83
Period size: 12 Copynumber: 6.7 Consensus size: 12
634538 TAAAATATAA
634548 AATATAAATATT
1 AATATAAATATT
634560 AATATAAAATATT
1 AATAT-AAATATT
*
634573 --T-T-AA-GTT
1 AATATAAATATT
*
634580 AACATAAATATT
1 AATATAAATATT
634592 AATATAAATATT
1 AATATAAATATT
634604 AATATAAAATATT
1 AATAT-AAATATT
634617 AATATAAA
1 AATATAAA
634625 AAATAATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
10 2 0.04
11 3 0.06
12 26 0.48
13 19 0.35
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (12 bp):
AATATAAATATT
Found at i:634631 original size:25 final size:24
Alignment explanation
Indices: 634585--634640 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
634575 AAGTTAACAT
* *
634585 AAATATTAATATAAATATTAATATA
1 AAATATTAATATAAAAAATAATA-A
634610 AAATATTAATATAAAAAATAATAA
1 AAATATTAATATAAAAAATAATAA
*
634634 TAATATT
1 AAATATT
634641 TTAAGTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATATTAATATAAAAAATAATAA
Found at i:635189 original size:19 final size:20
Alignment explanation
Indices: 635165--635233 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 20
635155 TCAAATTTAC
635165 TATTTATATATGATA-TATT
1 TATTTATATATGATATTATT
*
635184 TATTTA-ATAATTATATTATT
1 TATTTATAT-ATGATATTATT
*
635204 T-TTTATAATATGTTTATGTA-T
1 TATTTAT-ATATG-ATAT-TATT
635225 TATTTATAT
1 TATTTATAT
635234 TATATGTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
18 2 0.05
19 15 0.38
20 7 0.17
21 9 0.22
22 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TATTTATATATGATATTATT
Found at i:639611 original size:2 final size:2
Alignment explanation
Indices: 639604--639648 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
639594 TAAAATATAC
* * *
639604 AG AG AG AG AG AG AG AG AG AG AG AG GG AG CG AG AG AG AG TG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
639646 AG A
1 AG A
639649 ATGGAAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.02, G:0.51, T:0.02
Consensus pattern (2 bp):
AG
Found at i:639798 original size:23 final size:23
Alignment explanation
Indices: 639762--639908 Score: 63
Period size: 23 Copynumber: 6.3 Consensus size: 23
639752 GTTAAAAAAT
*
639762 TAAA-ATATAATATAATATAATA
1 TAAATATATATTATAATATAATA
* *
639784 TAAATATATATTATAAAAT-TTA
1 TAAATATATATTATAATATAATA
* * *
639806 TATAATAAAAATTATTAAT-TTAT-
1 TA-AATATATATTA-TAATATAATA
* *
639829 TAAA-ATTTATTTTAATATAATA
1 TAAATATATATTATAATATAATA
* * *
639851 AAAATATTTTATT-TAAATTTAATTA
1 TAAATA-TATATTAT-AATATAA-TA
* *
639876 TAAAATATATAAATATTAATATAAAA
1 T-AAATATAT-ATTA-TAATATAATA
639902 TAAATAT
1 TAAATAT
639909 TTTATTATTT
Statistics
Matches: 92, Mismatches: 19, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
20 4 0.04
21 7 0.08
22 13 0.14
23 26 0.28
24 16 0.17
25 10 0.11
26 9 0.10
27 6 0.07
28 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATATATATTATAATATAATA
Found at i:639807 original size:14 final size:14
Alignment explanation
Indices: 639776--639824 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
639766 ATATAATATA
*
639776 ATATAATATAAATAT
1 ATATAATA-AAATTT
*
639791 ATATTATAAAATTT
1 ATATAATAAAATTT
*
639805 ATATAATAAAAATT
1 ATATAATAAAATTT
639819 AT-TAAT
1 ATATAAT
639825 TTATTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 4 0.13
14 19 0.63
15 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAATAAAATTT
Found at i:639810 original size:34 final size:36
Alignment explanation
Indices: 639760--639891 Score: 118
Period size: 34 Copynumber: 3.9 Consensus size: 36
639750 TGGTTAAAAA
* *
639760 ATTAAAATATAATATAATATAATATAAATATATATT
1 ATTAAAATTTATTATAATATAATATAAATATATATT
* * *
639796 A-TAAAATTTA-TATAATA-AAAATTATTA-AT-TT
1 ATTAAAATTTATTATAATATAATATAAATATATATT
* *
639827 ATTAAAATTTATTTTAATATAATA-AAA-ATATTTT
1 ATTAAAATTTATTATAATATAATATAAATATATATT
* *
639861 ATTTAAATTTAATTATAAAAT-ATATAAATAT
1 ATTAAAATTT-ATTATAATATAATATAAATAT
639892 TAATATAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
31 3 0.04
32 12 0.16
33 16 0.21
34 24 0.31
35 19 0.25
36 3 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTAAAATTTATTATAATATAATATAAATATATATT
Found at i:639852 original size:20 final size:18
Alignment explanation
Indices: 639805--639855 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
639795 TATAAAATTT
639805 ATATAATAAAAATTATTA
1 ATATAATAAAAATTATTA
* * *
639823 ATTTATTAAAATTTATTTTA
1 ATATAATAAAAATTA--TTA
639843 ATATAATAAAAAT
1 ATATAATAAAAAT
639856 ATTTTATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 12 0.48
20 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAATAAAAATTATTA
Found at i:639888 original size:21 final size:21
Alignment explanation
Indices: 639864--639903 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
639854 ATATTTTATT
639864 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
639885 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
639904 AATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:639985 original size:18 final size:19
Alignment explanation
Indices: 639962--639998 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
639952 TTTATAAATT
639962 AAAAATTACATT-AATTTA
1 AAAAATTACATTAAATTTA
*
639980 AAAAATTATATTAAATTTA
1 AAAAATTACATTAAATTTA
639999 TTTTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATTACATTAAATTTA
Found at i:640224 original size:3 final size:3
Alignment explanation
Indices: 640216--640241 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
640206 TTTGGTGATT
640216 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
640242 TTACTAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:640822 original size:17 final size:17
Alignment explanation
Indices: 640750--640824 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
640740 TTAAAAATAA
*
640750 TAAAAATATAATATAATAT
1 TAAAATTATAA-AT-ATAT
* *
640769 T-AATTTATAAATATTT
1 TAAAATTATAAATATAT
640785 TAAAATT-TAAAT-TA-
1 TAAAATTATAAATATAT
*
640799 TATAAATTATTAATATAT
1 TA-AAATTATAAATATAT
640817 TAAAATTA
1 TAAAATTA
640825 AAAGAATGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.04
15 6 0.13
16 13 0.29
17 14 0.31
18 9 0.20
19 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAATTATAAATATAT
Found at i:642209 original size:30 final size:28
Alignment explanation
Indices: 642178--642231 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
642168 AATTAAAATT
*
642178 TATTTAAT-TATTA-TTTTAATATTTTA
1 TATTTAATAAATTATTTTTAATATTTTA
*
642204 TATTTAATAAATTATTTTTATTATTTTA
1 TATTTAATAAATTATTTTTAATATTTTA
642232 AAAACAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 4 0.17
28 12 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTTAATAAATTATTTTTAATATTTTA
Found at i:642211 original size:14 final size:14
Alignment explanation
Indices: 642178--642223 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
642168 AATTAAAATT
642178 TATTTAAT-TATTA
1 TATTTAATATATTA
*
642191 T-TTTAATATTTTA
1 TATTTAATATATTA
*
642204 TATTTAATAAATTA
1 TATTTAATATATTA
*
642218 TTTTTA
1 TATTTA
642224 TTATTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 6 0.22
13 6 0.22
14 15 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTAATATATTA
Found at i:642736 original size:21 final size:22
Alignment explanation
Indices: 642710--642764 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
642700 TTTATAATAA
*
642710 TAAAATATTAGTATAA-ATTTT
1 TAAAATATTAGTATAATATATT
642731 TAAAATATATA-TATAATATATT
1 TAAAATAT-TAGTATAATATATT
* *
642753 AAAAAAATTAGT
1 TAAAATATTAGT
642765 TTATAAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAATATTAGTATAATATATT
Found at i:643258 original size:13 final size:13
Alignment explanation
Indices: 643218--643265 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
643208 TATATTTATA
*
643218 ATAAATTAATATT
1 ATAAATTTATATT
*
643231 -TAAATATTATTTT
1 ATAAAT-TTATATT
*
643244 ATACATTTATATT
1 ATAAATTTATATT
643257 ATAAATTTA
1 ATAAATTTA
643266 ACATATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 5 0.18
13 19 0.68
14 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAATTTATATT
Found at i:643274 original size:34 final size:34
Alignment explanation
Indices: 643228--643293 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
643218 ATAAATTAAT
643228 ATTTAAATATTATT-T-TATACATTTATATTATAA
1 ATTTAAATATTATTATGTATACATTTAT-TTATAA
*
643261 ATTTAACATATTATTATGTATACTTTTATTTAT
1 ATTTAA-ATATTATTATGTATACATTTATTTAT
643294 TGTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.21
34 8 0.28
35 5 0.17
36 10 0.34
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (34 bp):
ATTTAAATATTATTATGTATACATTTATTTATAA
Done.