Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 33 of 56
Found at i:5630417 original size:21 final size:21
Alignment explanation
Indices: 5630372--5630456 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
5630362 TATCAAAATC
** **
5630372 AAAATTATACCAAAAGTTAAC
1 AAAATTATATAAAAAGTTATT
5630393 AAAATTATATAAAAAGTTATT
1 AAAATTATATAAAAAGTTATT
* * *
5630414 AAAATTCTATTAAATA-TTGTT
1 AAAATTATA-TAAAAAGTTATT
* *
5630435 GAAATTATATTAAAAGTTATT
1 AAAATTATATAAAAAGTTATT
5630456 A
1 A
5630457 CTATAGTTAT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
20 4 0.08
21 40 0.82
22 5 0.10
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.38
Consensus pattern (21 bp):
AAAATTATATAAAAAGTTATT
Found at i:5630560 original size:20 final size:21
Alignment explanation
Indices: 5630475--5630606 Score: 96
Period size: 20 Copynumber: 6.4 Consensus size: 21
5630465 ATATGTCATT
*
5630475 AAAAGTTA-CAAAAATTGTATC
1 AAAAGTTATC-AAAATTATATC
* * *
5630496 AAATGTTAT--TAATCTATATT
1 AAAAGTTATCAAAAT-TATATC
** *
5630516 AAAAACTATC-AAATTATATT
1 AAAAGTTATCAAAATTATATC
5630536 AAAAGTTATCAAAATTATA-C
1 AAAAGTTATCAAAATTATATC
* * *
5630556 CAAAG-CATACTAAATTATATC
1 AAAAGTTAT-CAAAATTATATC
5630577 AAAAGTTATCAAAAATTATATC
1 AAAAGTTATC-AAAATTATATC
5630599 AAAAGTTA
1 AAAAGTTA
5630607 ATAAAAAGCT
Statistics
Matches: 86, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
19 5 0.06
20 37 0.43
21 24 0.28
22 20 0.23
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAGTTATCAAAATTATATC
Found at i:5630594 original size:22 final size:22
Alignment explanation
Indices: 5630526--5630606 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 22
5630516 AAAAACTATC
*
5630526 AAATTATATTAAAAGTTATC-A
1 AAATTATATCAAAAGTTATCAA
* * *
5630547 AAATTATA-CCAAAG-CAT-ACT
1 AAATTATATCAAAAGTTATCA-A
5630567 AAATTATATCAAAAGTTATCAA
1 AAATTATATCAAAAGTTATCAA
5630589 AAATTATATCAAAAGTTA
1 AAATTATATCAAAAGTTA
5630607 ATAAAAAGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.04
20 12 0.25
21 13 0.27
22 20 0.42
23 1 0.02
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (22 bp):
AAATTATATCAAAAGTTATCAA
Found at i:5630598 original size:12 final size:12
Alignment explanation
Indices: 5630567--5630639 Score: 50
Period size: 12 Copynumber: 6.6 Consensus size: 12
5630557 AAAGCATACT
5630567 AAATTATATC-A
1 AAATTATATCAA
*
5630578 AAAGT-TATCAA
1 AAATTATATCAA
5630589 AAATTATATCAA
1 AAATTATATCAA
*
5630601 AAGTTA-AT-AA
1 AAATTATATCAA
** *
5630611 AAA-GCTA-CCA
1 AAATTATATCAA
*
5630621 AAATTACATCAA
1 AAATTATATCAA
5630633 AAATTAT
1 AAATTAT
5630640 TGAAATTATA
Statistics
Matches: 44, Mismatches: 12, Indels: 11
0.66 0.18 0.16
Matches are distributed among these distances:
10 13 0.30
11 12 0.27
12 19 0.43
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (12 bp):
AAATTATATCAA
Found at i:5630695 original size:21 final size:19
Alignment explanation
Indices: 5630522--5630736 Score: 79
Period size: 21 Copynumber: 10.9 Consensus size: 19
5630512 TATTAAAAAC
5630522 TATCAAATTATATTAAAAGT
1 TATCAAATTATA-TAAAAGT
**
5630542 TATCAAAATTATACCAAAG-
1 TATC-AAATTATATAAAAGT
*
5630561 CATACTAAATTATATCAAAAGT
1 TAT-C-AAATTATAT-AAAAGT
5630583 TATCAAAAATTATATCAAAAG-
1 TATC--AAATTATAT-AAAAGT
*
5630604 T-T---A--ATA-AAAAGC
1 TATCAAATTATATAAAAGT
* * *
5630616 TACCAAAATTACATCAAAAAT
1 TATC-AAATTATAT-AAAAGT
* *
5630637 TATTGAAATTATATAAATGGT
1 TA-TCAAATTATATAAA-AGT
*
5630658 TATCAAATCCATATAAAACGT
1 TATCAAAT-TATATAAAA-GT
5630679 TATCAAATTATATTAAAAGT
1 TATCAAATTATA-TAAAAGT
* * *
5630699 TAACAAAAGTATATCAAATGT
1 TATC-AAATTATAT-AAAAGT
* *
5630720 TATTAAATAATATAAAA
1 TATCAAATTATATAAAA
5630737 AATTACCAAA
Statistics
Matches: 144, Mismatches: 29, Indels: 45
0.66 0.13 0.21
Matches are distributed among these distances:
11 5 0.03
12 1 0.01
13 3 0.02
15 1 0.01
17 1 0.01
19 7 0.05
20 42 0.29
21 67 0.47
22 17 0.12
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.32
Consensus pattern (19 bp):
TATCAAATTATATAAAAGT
Found at i:5630722 original size:41 final size:41
Alignment explanation
Indices: 5630668--5630746 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
5630658 TATCAAATCC
* * *
5630668 ATATAAAACGTTATCAAATTATATTAAAAGTTAACAAAAGT
1 ATATAAAACGTTATCAAATAATATAAAAAATTAACAAAAGT
* * * *
5630709 ATATCAAATGTTATTAAATAATATAAAAAATTACCAAA
1 ATATAAAACGTTATCAAATAATATAAAAAATTAACAAA
5630747 GATGATCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.32
Consensus pattern (41 bp):
ATATAAAACGTTATCAAATAATATAAAAAATTAACAAAAGT
Found at i:5630856 original size:45 final size:46
Alignment explanation
Indices: 5630785--5630876 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 46
5630775 AAAGAGTTAT
* * *
5630785 AAAAATTATATTAAAGGTGATGAAAATTATATGAAATGTTA-CAAA
1 AAAAATTATATTAAAGATGATCAAAATTATATGAAAAGTTATCAAA
* *
5630830 AAAAATTATATTAAAGATTATCAAAATTATATTAAAAGTTATCAAA
1 AAAAATTATATTAAAGATGATCAAAATTATATGAAAAGTTATCAAA
5630876 A
1 A
5630877 TTGTATCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 36 0.88
46 5 0.12
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (46 bp):
AAAAATTATATTAAAGATGATCAAAATTATATGAAAAGTTATCAAA
Found at i:5630887 original size:21 final size:21
Alignment explanation
Indices: 5630573--5631053 Score: 116
Period size: 21 Copynumber: 22.5 Consensus size: 21
5630563 TACTAAATTA
* *
5630573 TATCAAAAGT-TATCAAAAATT
1 TATCAAAATTATATC-AAAAGT
* *
5630594 ATATCAAAAGTTA-ATAAAAAGC
1 -TATCAAAA-TTATATCAAAAGT
* * *
5630616 TACCAAAATTACATCAAAAAT
1 TATCAAAATTATATCAAAAGT
** *
5630637 TATTGAAATTATAT-AAATGGT
1 TATCAAAATTATATCAAA-AGT
*
5630658 TATC-AAATCCATAT-AAAACGT
1 TATCAAAAT-TATATCAAAA-GT
*
5630679 TATC-AAATTATATTAAAAGT
1 TATCAAAATTATATCAAAAGT
* * *
5630699 TAACAAAAGTATATCAAATGT
1 TATCAAAATTATATCAAAAGT
* * * *
5630720 TAT-TAAATAATATAAAAAAT
1 TATCAAAATTATATCAAAAGT
* * *
5630740 TACCAAAGA-T-GATCAAAATT
1 TATCAAA-ATTATATCAAAAGT
**
5630760 ATATCAAGGGTTA-AT-AAAGAGT
1 -TATCAA-AATTATATCAAA-AGT
* * *
5630782 TATAAAAATTATATTAAAGGT
1 TATCAAAATTATATCAAAAGT
* * * *
5630803 GATGAAAATTATATGAAATGT
1 TATCAAAATTATATCAAAAGT
*
5630824 TA-CAAAAAAAATTATAT-TAAAGAT
1 TATC----AAAATTATATCAAAAG-T
*
5630848 TATCAAAATTATATTAAAAGT
1 TATCAAAATTATATCAAAAGT
*
5630869 TATCAAAATTGTATCAAAAGT
1 TATCAAAATTATATCAAAAGT
* * *
5630890 TACTAGCAAAAATTACATTAAAGGT
1 TA-T--C-AAAATTATATCAAAAGT
* * * * *
5630915 TAGCAAAATCATATTAAAGGG
1 TATCAAAATTATATCAAAAGT
** *
5630936 TATCAAAACTTATCCAATTTTAAAGG
1 TATCAAAA-TTAT---A-TCAAAAGT
* * *
5630962 TACCAAAACTACATC-AAA--
1 TATCAAAATTATATCAAAAGT
* *
5630980 TAACTAAAATTATATTAAAAGT
1 TATC-AAAATTATATCAAAAGT
* *
5631002 TA-CTAAAATTATGT-TAAAGT
1 TATC-AAAATTATATCAAAAGT
* *
5631022 TATCAAAATTAAATTAAAAGT
1 TATCAAAATTATATCAAAAGT
5631043 TATCAAAATTA
1 TATCAAAATTA
5631054 AATTAAAGAT
Statistics
Matches: 341, Mismatches: 79, Indels: 79
0.68 0.16 0.16
Matches are distributed among these distances:
18 3 0.01
19 8 0.02
20 63 0.18
21 182 0.53
22 33 0.10
23 6 0.02
24 14 0.04
25 19 0.06
26 13 0.04
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.32
Consensus pattern (21 bp):
TATCAAAATTATATCAAAAGT
Found at i:5630929 original size:67 final size:66
Alignment explanation
Indices: 5630786--5630948 Score: 191
Period size: 67 Copynumber: 2.4 Consensus size: 66
5630776 AAGAGTTATA
* * * * * *
5630786 AAAATTATATTAAAGGTGATGAAAATTATATGAAATGTTACAAAAAAAATTATATTAAAGATTAT
1 AAAATTATATTAAAGGTTATCAAAATTATATCAAAAGTTACAAAAAAAATTACATTAAAGATTAG
5630851 C
66 C
* * ** *
5630852 AAAATTATATTAAAAGTTATCAAAATTGTATCAAAAGTTACTAGCAAAAATTACATTAAAGGTTA
1 AAAATTATATTAAAGGTTATCAAAATTATATCAAAAGTTAC-AAAAAAAATTACATTAAAGATTA
5630917 GC
65 GC
* *
5630919 AAAATCATATTAAAGGGTATCAAAACTTAT
1 AAAATTATATTAAAGGTTATCAAAA-TTAT
5630949 CCAATTTTAA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
66 35 0.44
67 42 0.52
68 3 0.04
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (66 bp):
AAAATTATATTAAAGGTTATCAAAATTATATCAAAAGTTACAAAAAAAATTACATTAAAGATTAG
C
Found at i:5631070 original size:21 final size:21
Alignment explanation
Indices: 5630985--5631073 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 21
5630975 TCAAATAACT
* * *
5630985 AAAATTATATTAAAAGTTACT
1 AAAATTAAATTAAAAGTCACC
** * *
5631006 AAAATTATGTT-AAAGTTATC
1 AAAATTAAATTAAAAGTCACC
* *
5631026 AAAATTAAATTAAAAGTTATC
1 AAAATTAAATTAAAAGTCACC
5631047 AAAATTAAATT-AAAGATCACC
1 AAAATTAAATTAAAAG-TCACC
5631068 AAAATT
1 AAAATT
5631074 GTACTAAAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 20 0.34
21 39 0.66
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.34
Consensus pattern (21 bp):
AAAATTAAATTAAAAGTCACC
Found at i:5633985 original size:20 final size:20
Alignment explanation
Indices: 5633949--5633986 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5633939 TTTTAACTTT
*
5633949 AATTTTAATTGAGTTTTTAG
1 AATTTTAATTGAATTTTTAG
5633969 AATTTTAAATT-AATTTTT
1 AATTTT-AATTGAATTTTT
5633987 TACTTATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
AATTTTAATTGAATTTTTAG
Found at i:5633986 original size:21 final size:20
Alignment explanation
Indices: 5633949--5633988 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5633939 TTTTAACTTT
*
5633949 AATTTTAATTGAGTTTTTAG
1 AATTTTAATTAAGTTTTTAG
*
5633969 AATTTTAAATTAATTTTTTA
1 AATTTT-AATTAAGTTTTTA
5633989 CTTATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
AATTTTAATTAAGTTTTTAG
Found at i:5634672 original size:2 final size:2
Alignment explanation
Indices: 5634665--5634701 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5634655 TCTTGAGCAG
5634665 AT AT AT 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 AT AT AT A
5634702 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5634706 original size:2 final size:2
Alignment explanation
Indices: 5634701--5634736 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5634691 ATATATATAT
5634701 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5634737 TCTCCCGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5635582 original size:25 final size:28
Alignment explanation
Indices: 5635537--5635593 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 28
5635527 AAATTAAAAA
5635537 TTTATTATTATTTAATCTTTAAT-AATT
1 TTTATTATTATTTAATCTTTAATAAATT
*
5635564 TTTATATATT-TTT-AT-TTTATTAAATT
1 TTTAT-TATTATTTAATCTTTAATAAATT
5635590 TTTA
1 TTTA
5635594 AACATGAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 5 0.19
26 10 0.37
27 8 0.30
28 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATTATTATTTAATCTTTAATAAATT
Found at i:5636769 original size:133 final size:134
Alignment explanation
Indices: 5636556--5636822 Score: 353
Period size: 133 Copynumber: 2.0 Consensus size: 134
5636546 ACAATAAAAT
* **
5636556 ATTTAAATTAAATCCAAAAAAAATCAAATTAAACAGCTTCGTAATATTCAAAATGTTTTACATTT
1 ATTTAAATTAAATCCAAAAAAAATCAAATTAAACAACTTCAAAATATTCAAAATGTTTTACATTT
* **
5636621 ATTTTAATTCAAATTCATTTGATAACTTAAATTTAA-TTTTTTT-TTAAATTCCTTTAAATTGAA
66 ATTTTAATTCAAATTCATTTGATAACATAAATTTAACTTTTTTTAAAAAATTCCTTTAAATTGAA
5636684 TATA
131 TATA
* * * *
5636688 ATTTAAATTAAATTC-AAAAAAATCAAA-TAAATAACTTCAAAATATTCTCAAATTTTATTTACA
1 ATTTAAATTAAATCCAAAAAAAATCAAATTAAACAACTTCAAAATA-T-TCAAAATGT-TTTACA
* *
5636751 TTTATTTTAATTCTAATTCATTTGGTAACATAAATTTAACTTTTTTTAAAAAAATTCCTTTAAAT
63 TTTATTTTAATTCAAATTCATTTGATAACATAAATTTAACTTTTTTT-AAAAAATTCCTTTAAAT
*
5636816 TTAATAT
127 TGAATAT
5636823 TTAGAAATTA
Statistics
Matches: 116, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
130 13 0.11
131 13 0.11
132 21 0.18
133 42 0.36
134 7 0.06
136 20 0.17
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (134 bp):
ATTTAAATTAAATCCAAAAAAAATCAAATTAAACAACTTCAAAATATTCAAAATGTTTTACATTT
ATTTTAATTCAAATTCATTTGATAACATAAATTTAACTTTTTTTAAAAAATTCCTTTAAATTGAA
TATA
Found at i:5637153 original size:2 final size:2
Alignment explanation
Indices: 5637109--5637138 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5637099 TACTCGAAGC
5637109 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
5637139 GATGCTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5637333 original size:3 final size:3
Alignment explanation
Indices: 5637321--5637363 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
5637311 ATTATCTTTC
*
5637321 ATT A-T ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5637364 ATTTTAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5638107 original size:23 final size:21
Alignment explanation
Indices: 5638045--5638115 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
5638035 TTTAATTTTT
* *
5638045 AAATGTAACTATAAAAAATTAA
1 AAAT-TAAATATATAAAATTAA
* *
5638067 AAATTAACTTTATAAAAATTAA
1 AAATTAAATATAT-AAAATTAA
*
5638089 ATAATTAAAATATATAAAAATAA
1 A-AATT-AAATATATAAAATTAA
5638112 AAAT
1 AAAT
5638116 CTTATACCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 7 0.17
22 16 0.39
23 12 0.29
24 6 0.15
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (21 bp):
AAATTAAATATATAAAATTAA
Found at i:5641597 original size:13 final size:13
Alignment explanation
Indices: 5641579--5641603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5641569 TTTGTAAAGC
5641579 TTTCAATGTTTTG
1 TTTCAATGTTTTG
5641592 TTTCAATGTTTT
1 TTTCAATGTTTT
5641604 AATCCAATAA
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:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTCAATGTTTTG
Found at i:5645156 original size:1 final size:1
Alignment explanation
Indices: 5645150--5645174 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
5645140 TGTGTTTGTG
5645150 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
5645175 AGGAATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5646157 original size:16 final size:16
Alignment explanation
Indices: 5646136--5646180 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
5646126 CATCCTTGTT
5646136 TATATATATGTGTATA
1 TATATATATGTGTATA
* *
5646152 TATATAGATATGTATA
1 TATATATATGTGTATA
*
5646168 TATATATGTGTGT
1 TATATATATGTGT
5646181 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (16 bp):
TATATATATGTGTATA
Found at i:5646179 original size:2 final size:2
Alignment explanation
Indices: 5646174--5646201 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5646164 TATATATATA
5646174 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5646202 AAAAGAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:5648485 original size:21 final size:19
Alignment explanation
Indices: 5648450--5648501 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
5648440 ATCAAATTAT
* *
5648450 TTAATTAAAAATTTTAAATG
1 TTAAATAAAAATTTT-AATA
5648470 TTAAATAAATAATTTTAATA
1 TTAAATAAA-AATTTTAATA
5648490 TTAAATAAAAAT
1 TTAAATAAAAAT
5648502 ATATATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 20 0.69
21 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAAATAAAAATTTTAATA
Found at i:5648636 original size:19 final size:21
Alignment explanation
Indices: 5648609--5648654 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 21
5648599 ACTTAAATTT
*
5648609 ATTTTTTAATT-TTTTT-TCA
1 ATTTATTAATTATTTTTATCA
5648628 ATTTATTAATTAATTTTTATCA
1 ATTTATTAATT-ATTTTTATCA
5648650 ATTTA
1 ATTTA
5648655 ATCAGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
21 5 0.22
22 8 0.35
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTATTAATTATTTTTATCA
Found at i:5648650 original size:22 final size:23
Alignment explanation
Indices: 5648604--5648654 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
5648594 AAATAACTTA
** *
5648604 AATTTATTTTTTAATTTTTTTTC
1 AATTTATTAATTAATTTTTTATC
5648627 AATTTATTAATTAA-TTTTTATC
1 AATTTATTAATTAATTTTTTATC
5648649 AATTTA
1 AATTTA
5648655 ATCAGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
AATTTATTAATTAATTTTTTATC
Found at i:5651034 original size:16 final size:16
Alignment explanation
Indices: 5651013--5651045 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5651003 AAAAATAAAT
5651013 TTATGTTCAACAT-ACA
1 TTATGTT-AACATCACA
5651029 TTATGTTAACATCACA
1 TTATGTTAACATCACA
5651045 T
1 T
5651046 GCATCCATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (16 bp):
TTATGTTAACATCACA
Found at i:5652573 original size:20 final size:20
Alignment explanation
Indices: 5652545--5652583 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5652535 TAACAATTAT
**
5652545 TATTATAATTTTTTTAAAAA
1 TATTATAATAATTTTAAAAA
*
5652565 TATTTTAATAATTTTAAAA
1 TATTATAATAATTTTAAAA
5652584 GTGATTTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATAATAATTTTAAAAA
Found at i:5653067 original size:24 final size:24
Alignment explanation
Indices: 5652999--5653070 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
5652989 AATTATTTAA
*
5652999 ATTAAAATAATAAA-AAT-ATAAAT
1 ATTAAAATAA-AAATTATAATAAAT
*
5653022 ATTAAAATAAAAATTATTATAAA-
1 ATTAAAATAAAAATTATAATAAAT
* *
5653045 ATTTAAATATAAATTATAAATAAAT
1 ATTAAAATAAAAATTAT-AATAAAT
5653070 A
1 A
5653071 ACAACTCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 3 0.07
23 27 0.66
24 10 0.24
25 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATTAAAATAAAAATTATAATAAAT
Found at i:5653128 original size:16 final size:17
Alignment explanation
Indices: 5653097--5653130 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5653087 TAAAGTAATT
5653097 ATATAATTATAAAAATA
1 ATATAATTATAAAAATA
*
5653114 ATATATTTA-AAAAATA
1 ATATAATTATAAAAATA
5653130 A
1 A
5653131 AAATTAATTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATAATTATAAAAATA
Found at i:5654167 original size:28 final size:29
Alignment explanation
Indices: 5654106--5654168 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
5654096 AAATTCATGA
*
5654106 TTTTT-AAATAAATTATTAAAATAATATT
1 TTTTTAAAATAAATTATTAAAAAAATATT
**
5654134 AATTTAAAATAAATTA-TAAAAAAATATT
1 TTTTTAAAATAAATTATTAAAAAAATATT
5654162 TTTTTAA
1 TTTTTAA
5654169 TGTGTGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTTAAAATAAATTATTAAAAAAATATT
Found at i:5654704 original size:13 final size:13
Alignment explanation
Indices: 5654686--5654714 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5654676 AATTTTTAAG
5654686 AAAAAAACAAT-T
1 AAAAAAACAATGT
5654698 AAAAAAACAATGT
1 AAAAAAACAATGT
5654711 AAAA
1 AAAA
5654715 TATATTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAAAACAATGT
Found at i:5654923 original size:2 final size:2
Alignment explanation
Indices: 5654916--5654949 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5654906 CCGCGTCAAG
5654916 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
5654950 GAAAGAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5659644 original size:57 final size:57
Alignment explanation
Indices: 5659556--5659669 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
5659546 GTCTTTGGGC
5659556 ATATAAATGGGTGCGCTACATATCTTATCATGTATGTTTTTTGGATGAGAGTAATGG
1 ATATAAATGGGTGCGCTACATATCTTATCATGTATGTTTTTTGGATGAGAGTAATGG
5659613 ATATAAATGGGTGCGCTACATATCTTATCATGTATGTTTTTTGGATGAGAGTAATGG
1 ATATAAATGGGTGCGCTACATATCTTATCATGTATGTTTTTTGGATGAGAGTAATGG
5659670 TTCAGTAACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.39
Consensus pattern (57 bp):
ATATAAATGGGTGCGCTACATATCTTATCATGTATGTTTTTTGGATGAGAGTAATGG
Found at i:5663688 original size:2 final size:2
Alignment explanation
Indices: 5663681--5663711 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5663671 TCGTTAAATG
5663681 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
5663712 ATGAGGTTTT
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:5672971 original size:32 final size:33
Alignment explanation
Indices: 5672916--5672987 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
5672906 TTCAACGATT
5672916 TGTATCGATACATAAAGTGTTGTATCGATAAAA
1 TGTATCGATACATAAAGTGTTGTATCGATAAAA
*
5672949 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATAAAA
5672981 TGTATCG
1 TGTATCG
5672988 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 25 0.66
33 13 0.34
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATAAAA
Found at i:5676951 original size:32 final size:32
Alignment explanation
Indices: 5676915--5676975 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
5676905 CTCGATTGAC
*
5676915 CCGAATCCAAAATGATATGAACCTGAAACAAT
1 CCGAATCCAAAATGATATGAACCCGAAACAAT
* *
5676947 CCGAATCCGAAATGATCTGAACCCGAAAC
1 CCGAATCCAAAATGATATGAACCCGAAAC
5676976 GACTCGAACC
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:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (32 bp):
CCGAATCCAAAATGATATGAACCCGAAACAAT
Found at i:5678665 original size:3 final size:3
Alignment explanation
Indices: 5678657--5678693 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5678647 TAATTCATAA
5678657 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5678694 CTACTGCTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5679487 original size:17 final size:18
Alignment explanation
Indices: 5679451--5679493 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5679441 AAAAAAAATG
*
5679451 TTTTAAAAAATTAAATTT
1 TTTTAAAAAATTAAAGTT
*
5679469 TTTTAAAAAA-TAGAGTT
1 TTTTAAAAAATTAAAGTT
5679486 TTCTTAAA
1 TT-TTAAA
5679494 GTAGGTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (18 bp):
TTTTAAAAAATTAAAGTT
Found at i:5681355 original size:26 final size:25
Alignment explanation
Indices: 5681309--5681357 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
5681299 ATTACATTTA
*
5681309 TAATTTTATTTATATATTTATTCCT
1 TAATTTTATTTATACATTTATTCCT
5681334 TAATTTTAATTTATGACA-TTATTC
1 TAATTTT-ATTTAT-ACATTTATTC
5681358 AATTCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 12 0.57
27 2 0.10
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (25 bp):
TAATTTTATTTATACATTTATTCCT
Found at i:5682345 original size:14 final size:13
Alignment explanation
Indices: 5682315--5682348 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5682305 ATCTTTAATT
5682315 TTATTAAATTATA
1 TTATTAAATTATA
*
5682328 TTATTAAACTTTTA
1 TTATTAAA-TTATA
5682342 TTATTAA
1 TTATTAA
5682349 CAAAATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTAAATTATA
Found at i:5683506 original size:41 final size:42
Alignment explanation
Indices: 5683456--5683557 Score: 109
Period size: 41 Copynumber: 2.4 Consensus size: 42
5683446 CGTTTTTACG
5683456 TTTATATTAGTGGCATTTAAATTTAAAAATACCACTATAT-TT
1 TTTA-ATTAGTGGCATTTAAATTTAAAAATACCACTATATGTT
* * ** *
5683498 TTTAATTAGTAGCACTTT-TATTTAAAAATACCGTTTTATGTT
1 TTTAATTAGTGGCA-TTTAAATTTAAAAATACCACTATATGTT
**
5683540 TTTAATTAACGGCATTTA
1 TTTAATTAGTGGCATTTA
5683558 GAAACAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
41 29 0.59
42 20 0.41
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (42 bp):
TTTAATTAGTGGCATTTAAATTTAAAAATACCACTATATGTT
Found at i:5684663 original size:2 final size:2
Alignment explanation
Indices: 5684656--5684686 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5684646 GATATGTATG
5684656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5684687 GAGTTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5685569 original size:34 final size:36
Alignment explanation
Indices: 5685531--5685606 Score: 86
Period size: 34 Copynumber: 2.2 Consensus size: 36
5685521 ATAGCTTGAT
*
5685531 ATATATAGTAATATACAGCTT-TAT-TATACT-ATAA
1 ATATATAGTAATATAAAG-TTATATATATACTAATAA
* * *
5685565 ATATATATTAGTATAAAGTTATATATATACTAATAT
1 ATATATAGTAATATAAAGTTATATATATACTAATAA
5685601 ATATAT
1 ATATAT
5685607 TCTATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 2 0.06
34 18 0.51
35 6 0.17
36 9 0.26
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (36 bp):
ATATATAGTAATATAAAGTTATATATATACTAATAA
Found at i:5686245 original size:15 final size:15
Alignment explanation
Indices: 5686221--5686250 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5686211 AGTATTTAAT
*
5686221 ATTTTTTATAATATA
1 ATTTTCTATAATATA
5686236 ATTTTCTATAATATA
1 ATTTTCTATAATATA
5686251 TATAATTATT
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:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTCTATAATATA
Found at i:5693378 original size:19 final size:18
Alignment explanation
Indices: 5693354--5693389 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5693344 TTCATTAAAA
5693354 TTTTTTT-AAAATTGTTAT
1 TTTTTTTCAAAATT-TTAT
5693372 TTTTTTTCAAAATTTTAT
1 TTTTTTTCAAAATTTTAT
5693390 GAATGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTTTCAAAATTTTAT
Found at i:5693673 original size:3 final size:3
Alignment explanation
Indices: 5693665--5693695 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5693655 GCAATTTGAC
5693665 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5693696 GAAAAGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5698648 original size:2 final size:2
Alignment explanation
Indices: 5698641--5698674 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5698631 ATGTATATTT
*
5698641 AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5698675 GTACTTGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:5703182 original size:2 final size:2
Alignment explanation
Indices: 5703171--5703199 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5703161 TGTATCAAAA
5703171 AT AT -T 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
5703200 TCATTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5704263 original size:17 final size:17
Alignment explanation
Indices: 5704238--5704276 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5704228 TAAATATGAG
* * *
5704238 TAAACAAAATGCATAGA
1 TAAATAAAATACATAAA
5704255 TAAATAAAATACATAAA
1 TAAATAAAATACATAAA
5704272 TAAAT
1 TAAAT
5704277 GATTAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (17 bp):
TAAATAAAATACATAAA
Found at i:5704388 original size:40 final size:39
Alignment explanation
Indices: 5704327--5704417 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
5704317 AATATGGACT
*
5704327 AATTAAAATAATTAACTAAAAA-TAATTCAAGAAAATAGAA
1 AATTAAAATAATTAAC-AAAAAGAAATTCAAGAAAAT-GAA
* *
5704367 AATTAAAATATATTTAA-AAAAAGAAATTTAAGAAAATTAA
1 AATTAAAATA-A-TTAACAAAAAGAAATTCAAGAAAATGAA
5704407 AATTAAAATAA
1 AATTAAAATAA
5704418 AAATTAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
39 1 0.02
40 27 0.60
41 13 0.29
42 4 0.09
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.27
Consensus pattern (39 bp):
AATTAAAATAATTAACAAAAAGAAATTCAAGAAAATGAA
Found at i:5704392 original size:25 final size:26
Alignment explanation
Indices: 5704345--5704397 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5704335 TAATTAACTA
5704345 AAAATAATTCAAGAAAATAGAAAATT
1 AAAATAATTCAAGAAAATAGAAAATT
* *
5704371 AAAATATATTTAA-AAAA-AGAAATTT
1 AAAATA-ATTCAAGAAAATAGAAAATT
5704396 AA
1 AA
5704398 GAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 10 0.42
27 5 0.21
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (26 bp):
AAAATAATTCAAGAAAATAGAAAATT
Found at i:5704585 original size:40 final size:39
Alignment explanation
Indices: 5704461--5704585 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 39
5704451 GTCGAAAGAA
*
5704461 TTGACTAAGACAAAACTTACAAGTTAATGAATAGAGAAAG
1 TTGACTAAGACAAAACTTACAAGTCAATGAATAG-GAAAG
* * * ** *
5704501 TTGACCAGGACAGAACTTGTAAGTCAACGAATGAGGAGAA-
1 TTGACTAAGACAAAACTTACAAGTCAATGAAT-AGGA-AAG
* * *
5704541 TTGACTAAGATAAAACCTACAAGCCAATGAATAAGGAAAG
1 TTGACTAAGACAAAACTTACAAGTCAATGAAT-AGGAAAG
5704581 TTGAC
1 TTGAC
5704586 CAGGCATAAA
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
39 2 0.03
40 59 0.91
41 4 0.06
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.20
Consensus pattern (39 bp):
TTGACTAAGACAAAACTTACAAGTCAATGAATAGGAAAG
Found at i:5705555 original size:120 final size:120
Alignment explanation
Indices: 5705391--5705665 Score: 319
Period size: 120 Copynumber: 2.3 Consensus size: 120
5705381 ATTTAATGAA
* * *
5705391 AAATGGCCTAGATAAAA-TCAAAAACCTAAACAATGACTTGGGTGAACCCAAGAC-TCAACTAAA
1 AAATGGCCTAGATAAAACT-AGAAACCTAAACAATGACTTGGGTGAAACCAAGACTTAAACTAAA
* * * * ** *
5705454 TGGTC-TAGACAATACTA-AAAGCCTTG-ACAATAACTTGAGTGAAATTAAGACTTAACT
65 T-GACAT-GACAAAACTAGAAA-CC-TGAACAATAACTTAAGTAAAACCAAGACTCAACT
* * *
5705511 AAATGGTCT-GAATAAAACTAGAAACCTAAACAATTACTTGGGTGAAACTAAGACTTAAACTAAA
1 AAATGGCCTAG-ATAAAACTAGAAACCTAAACAATGACTTGGGTGAAACCAAGACTTAAACTAAA
*
5705575 TGACATGACAAAACTAGAAACCTGAACAATGACTTAAGTAAAACCAAGACTCAACT
65 TGACATGACAAAACTAGAAACCTGAACAATAACTTAAGTAAAACCAAGACTCAACT
*
5705631 AAATTGCCTAGATAAAACTAGAAACCTAAACAATG
1 AAATGGCCTAGATAAAACTAGAAACCTAAACAATG
5705666 GTTATATATA
Statistics
Matches: 131, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
119 3 0.02
120 113 0.86
121 15 0.11
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (120 bp):
AAATGGCCTAGATAAAACTAGAAACCTAAACAATGACTTGGGTGAAACCAAGACTTAAACTAAAT
GACATGACAAAACTAGAAACCTGAACAATAACTTAAGTAAAACCAAGACTCAACT
Found at i:5705665 original size:60 final size:60
Alignment explanation
Indices: 5705300--5705665 Score: 278
Period size: 60 Copynumber: 6.1 Consensus size: 60
5705290 GAATCTACAA
* * * * * *
5705300 AATGACTTGGGT-AGAACCAAGACTCAA-TAGAATGGCTTGGACAACACTAGAAACCTGAAC
1 AATGACTTGAGTGA-AACCAAGACTCAACTA-AATGGCCTAGATAAAACTAGAAACCTAAAC
** * * * * *
5705360 AATGGTTTGGGTGAAATCAAGATTTAA-TGAAAAATGGCCTAGATAAAA-TCAAAAACCTAAAC
1 AATGACTTGAGTGAAACCAAGACTCAACT---AAATGGCCTAGATAAAACT-AGAAACCTAAAC
* * * * * **
5705422 AATGACTTGGGTGAACCCAAGACTCAACTAAATGGTCTAGACAATACTA-AAAGCCTTGAC
1 AATGACTTGAGTGAAACCAAGACTCAACTAAATGGCCTAGATAAAACTAGAAA-CCTAAAC
* ** * *
5705482 AATAACTTGAGTGAAATTAAGACTTAACTAAATGGTCT-GAATAAAACTAGAAACCTAAAC
1 AATGACTTGAGTGAAACCAAGACTCAACTAAATGGCCTAG-ATAAAACTAGAAACCTAAAC
* * * * * * * *
5705542 AATTACTTGGGTGAAACTAAGACTTAAACTAAATGACAT-GACAAAACTAGAAACCTGAAC
1 AATGACTTGAGTGAAACCAAGAC-TCAACTAAATGGCCTAGATAAAACTAGAAACCTAAAC
* * *
5705602 AATGACTTAAGTAAAACCAAGACTCAACTAAATTGCCTAGATAAAACTAGAAACCTAAAC
1 AATGACTTGAGTGAAACCAAGACTCAACTAAATGGCCTAGATAAAACTAGAAACCTAAAC
5705662 AATG
1 AATG
5705666 GTTATATATA
Statistics
Matches: 242, Mismatches: 52, Indels: 24
0.76 0.16 0.08
Matches are distributed among these distances:
59 15 0.06
60 164 0.68
61 18 0.07
62 43 0.18
63 2 0.01
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (60 bp):
AATGACTTGAGTGAAACCAAGACTCAACTAAATGGCCTAGATAAAACTAGAAACCTAAAC
Found at i:5706629 original size:108 final size:109
Alignment explanation
Indices: 5706505--5706721 Score: 276
Period size: 108 Copynumber: 2.0 Consensus size: 109
5706495 AACTTTAATG
* * * * *
5706505 GGCTCAAAATTTTCAAAACTAATAAGATATATACCTCATTTTCCTAAGCATGAATGGATTAAG-T
1 GGCTCAAAAGTTTCAAAACTAATAAGATACATACATCATTTTCCTAAGCATGAATAGA-TAAGAA
*
5706569 TGTAAAAAACATGAATTTCTTTGAAAAT-AAAAAAATTTGATGTT
65 TGTAAAAAACATGAATTTATTTGAAAATCAAAAAAATTTGATGTT
* * * * * *
5706613 GGCTTAAAAGTTTCAAAATTGATAAGATACATGCATCATTTTCCTAGGCATGAATAGATCAGAAT
1 GGCTCAAAAGTTTCAAAACTAATAAGATACATACATCATTTTCCTAAGCATGAATAGATAAGAAT
* * *
5706678 GTATAAAATATGAATTTATTTGAAAATCAAACAAATTTGATGTT
66 GTAAAAAACATGAATTTATTTGAAAATCAAAAAAATTTGATGTT
5706722 TTTTAAGTCC
Statistics
Matches: 92, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
107 3 0.03
108 74 0.80
109 15 0.16
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (109 bp):
GGCTCAAAAGTTTCAAAACTAATAAGATACATACATCATTTTCCTAAGCATGAATAGATAAGAAT
GTAAAAAACATGAATTTATTTGAAAATCAAAAAAATTTGATGTT
Found at i:5707542 original size:2 final size:2
Alignment explanation
Indices: 5707535--5707560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5707525 AGAGAAAATT
5707535 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
5707561 AAGATGACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5712348 original size:20 final size:20
Alignment explanation
Indices: 5712319--5712360 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5712309 TTTTTCCTTG
* * *
5712319 TTTTTTTTTTTATTTTTTTC
1 TTTTTCTTTTAATTATTTTC
5712339 TTTTTCTTTTAATTATTTTC
1 TTTTTCTTTTAATTATTTTC
5712359 TT
1 TT
5712361 AATAAAAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTCTTTTAATTATTTTC
Found at i:5712348 original size:23 final size:23
Alignment explanation
Indices: 5712309--5712357 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
5712299 TTCTAGGCCC
**
5712309 TTTTTCCTTGTTTTTTTTTTTAT
1 TTTTTCCTTGTTTTTTTAATTAT
*
5712332 TTTTTTCTT-TTTCTTTTAATTAT
1 TTTTTCCTTGTTT-TTTTAATTAT
5712355 TTT
1 TTT
5712358 CTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (23 bp):
TTTTTCCTTGTTTTTTTAATTAT
Found at i:5712547 original size:18 final size:19
Alignment explanation
Indices: 5712517--5712553 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
5712507 AAAAAAATAA
5712517 AAAAATTATAAATTAGAAT
1 AAAAATTATAAATTAGAAT
5712536 AAAAATTA-AAATTAGAAT
1 AAAAATTATAAATTAGAAT
5712554 TAATAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATTATAAATTAGAAT
Found at i:5719662 original size:2 final size:2
Alignment explanation
Indices: 5719655--5719696 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
5719645 ATTCTTCTCA
* *
5719655 AT AT AT AT AT AT AT AT AT AT GT AT GT 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
5719697 TCAAATATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5721316 original size:24 final size:24
Alignment explanation
Indices: 5721290--5721334 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5721280 TTTTTTATAA
* *
5721290 AAAAATTTATA-ATTTTAAAATAG
1 AAAAAGTTATATATATTAAAATAG
5721313 AAAAAGTTATATATATTAAAAT
1 AAAAAGTTATATATATTAAAAT
5721335 TTAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
AAAAAGTTATATATATTAAAATAG
Found at i:5724324 original size:16 final size:16
Alignment explanation
Indices: 5724279--5724340 Score: 76
Period size: 16 Copynumber: 4.1 Consensus size: 16
5724269 GTTAACTTTA
5724279 AATTTAAATTTAAAAT
1 AATTTAAATTTAAAAT
* *
5724295 AA-TT-CATATAAAAT
1 AATTTAAATTTAAAAT
*
5724309 AATTAAAATTTAAAAT
1 AATTTAAATTTAAAAT
5724325 AATTTAAA-TTAAAAT
1 AATTTAAATTTAAAAT
5724340 A
1 A
5724341 TACTTATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.26
15 11 0.29
16 17 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:5728381 original size:19 final size:18
Alignment explanation
Indices: 5728345--5728382 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5728335 CATGCATTTT
5728345 GACATGAAAAACATGATG
1 GACATGAAAAACATGATG
5728363 GACATGCAAGAAA-ATGATG
1 GACATG-AA-AAACATGATG
5728382 G
1 G
5728383 GTGACATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.16
Consensus pattern (18 bp):
GACATGAAAAACATGATG
Found at i:5733866 original size:27 final size:27
Alignment explanation
Indices: 5733836--5733887 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5733826 TGACAAGTTA
* *
5733836 AAAAAAATGGGGTTAGAGTATCCTCTC
1 AAAAAAATGAGGTTAGAATATCCTCTC
* *
5733863 AAAAGAATGAGGTTGGAATATCCTC
1 AAAAAAATGAGGTTAGAATATCCTC
5733888 GATAAGTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (27 bp):
AAAAAAATGAGGTTAGAATATCCTCTC
Found at i:5736386 original size:51 final size:51
Alignment explanation
Indices: 5736321--5736434 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
5736311 AATAAAAATG
*
5736321 TATCGATACATTTTCCTTCTAAAATGCAAAATTTACCTCGAAAATATCCAA
1 TATCGATACATTTTCCTTCTAAAATGCAAAATTTACCTCGAAAAGATCCAA
* * *
5736372 TATCGATACATTTTCCTTCTAAAATGCAAAATTTACTTCGACAAGATTCAA
1 TATCGATACATTTTCCTTCTAAAATGCAAAATTTACCTCGAAAAGATCCAA
5736423 TATCGATACATT
1 TATCGATACATT
5736435 CATTAATGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.35
Consensus pattern (51 bp):
TATCGATACATTTTCCTTCTAAAATGCAAAATTTACCTCGAAAAGATCCAA
Found at i:5738554 original size:14 final size:15
Alignment explanation
Indices: 5738537--5738565 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5738527 CCCAAAAAGC
5738537 AAGAAA-AAAAATAA
1 AAGAAAGAAAAATAA
5738551 AAGAAAGAAAAATAA
1 AAGAAAGAAAAATAA
5738566 GAAAGCTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAGAAAGAAAAATAA
Found at i:5743187 original size:2 final size:2
Alignment explanation
Indices: 5743180--5743222 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5743170 ACAAGAAACG
*
5743180 TA TA TA TA TA CA 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
5743222 T
1 T
5743223 TCATTCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5744319 original size:22 final size:23
Alignment explanation
Indices: 5744284--5744326 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5744274 AGTTTTATAT
* *
5744284 TTTTTTTTATAATTTTTAATTAA
1 TTTTATTTATAATTTTAAATTAA
5744307 TTTTATTTA-AATTTTAAATT
1 TTTTATTTATAATTTTAAATT
5744327 TGAAGTCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTTATAATTTTAAATTAA
Found at i:5745043 original size:21 final size:22
Alignment explanation
Indices: 5744995--5745043 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5744985 GATCAATCTC
* *
5744995 TTAATAAAAATATAAAATTTAA
1 TTAATAAAAAAATAAAATGTAA
*
5745017 AT-ATAAAAAAATAAAA-GTAA
1 TTAATAAAAAAATAAAATGTAA
5745037 TTAATAA
1 TTAATAA
5745044 TTTTATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.18
21 17 0.77
22 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAATAAAAAAATAAAATGTAA
Found at i:5746186 original size:20 final size:20
Alignment explanation
Indices: 5746163--5746206 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
5746153 TTTATAAATA
5746163 AATAAGTTTTTT-TTAATATT
1 AATAAGTTTTTTATT-ATATT
5746183 AAT-A-TTTTTTATTATATT
1 AATAAGTTTTTTATTATATT
5746201 -ATAAGT
1 AATAAGT
5746207 AGTAATAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
17 2 0.10
18 12 0.57
19 4 0.19
20 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
AATAAGTTTTTTATTATATT
Found at i:5746648 original size:22 final size:22
Alignment explanation
Indices: 5746606--5746648 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5746596 TTTTATAAAA
* *
5746606 TATTTTTTATAATTAGTATATT
1 TATTTTTTATAAGTAGAATATT
5746628 TATTTTTATATAAGTA-AATAT
1 TATTTTT-TATAAGTAGAATAT
5746649 AACAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TATTTTTTATAAGTAGAATATT
Found at i:5747141 original size:26 final size:27
Alignment explanation
Indices: 5747083--5747141 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
5747073 ATGTTAGAAT
*
5747083 AATATAATAAAATATAAATAAAGTAAG
1 AATATAACAAAATATAAATAAAGTAAG
*
5747110 ATATATAACAACATA-AAATAAA-TAAAG
1 A-ATATAACAAAATATAAATAAAGT-AAG
5747137 AATAT
1 AATAT
5747142 CAAGTACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 5 0.18
27 12 0.43
28 11 0.39
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.25
Consensus pattern (27 bp):
AATATAACAAAATATAAATAAAGTAAG
Found at i:5747180 original size:19 final size:19
Alignment explanation
Indices: 5747156--5747195 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5747146 TACATGTAAT
*
5747156 AATGAATATAAAGTAA-ATA
1 AATGAA-ATAAAATAACATA
5747175 AATGAAATAAAATAACATA
1 AATGAAATAAAATAACATA
5747194 AA
1 AA
5747196 ATAAAGTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (19 bp):
AATGAAATAAAATAACATA
Found at i:5749819 original size:98 final size:98
Alignment explanation
Indices: 5749711--5749906 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
5749701 ACCTTTTTAA
*
5749711 TGATGTCTTGTTTGTCCCTAGATCAGTCCAGACTAGGTAGTTATGATTTTTTGAGTCTAAGCTAT
1 TGATGTCTTGTTTGTCCCTAGATCAGTCCAGACTAGGTAGTTACGATTTTTTGAGTCTAAGCTAT
5749776 TCAAAGACCCTAGAATCAGTAAAATACATTCTG
66 TCAAAGACCCTAGAATCAGTAAAATACATTCTG
*
5749809 TGATGTCTTGTTTGTCCCTAGATCAGTCCAGACTAGGTAGTTACGATTTTTTGAGTCTAAGCTGT
1 TGATGTCTTGTTTGTCCCTAGATCAGTCCAGACTAGGTAGTTACGATTTTTTGAGTCTAAGCTAT
5749874 TCAAAGACCCTAGAATCAGTAAAATACATTCTG
66 TCAAAGACCCTAGAATCAGTAAAATACATTCTG
5749907 GTTGGGCCAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (98 bp):
TGATGTCTTGTTTGTCCCTAGATCAGTCCAGACTAGGTAGTTACGATTTTTTGAGTCTAAGCTAT
TCAAAGACCCTAGAATCAGTAAAATACATTCTG
Found at i:5750590 original size:79 final size:80
Alignment explanation
Indices: 5750409--5750929 Score: 436
Period size: 79 Copynumber: 6.6 Consensus size: 80
5750399 TCATTGATTT
* * * * *
5750409 TTTTATTTCCAAAACA-CTGATTTTCCACCATCGGGGATACCCCAACCCCATTATTTTTCGAGGG
1 TTTTATTTTCAAAACATC-GATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGAGGG
* **
5750473 GATATTTAAACCTCGG
65 GATACTCCAACCTCGG
* * * * *
5750489 CTGTA-TTTCTAAAACATCGATTTTTCATAATTGGGGATACTCCAACCCCGTTATTTCT-GAGGG
1 TTTTATTTTC-AAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGAGGG
5750552 GATACTCCAACCTCGG
65 GATACTCCAACCTCGG
* * * ** *
5750568 TTTTATTTTCAAAACA-CTGATTTTCCACCATCGGGGATACTCTAA-CCTATTA-TTTTCGAGAG
1 TTTTATTTTCAAAACATC-GATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGAGGG
* *
5750630 GATATTCCAAGCC-CAG
65 GATACTCCAA-CCTCGG
* * *
5750646 CTTTA-TTTCTAAAACATCGATTTTTCACAACCGTGGATACTCCAACCCCGTTATTTTT-GAGGG
1 TTTTATTTTC-AAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGAGGG
* *
5750709 GATACTCTAA-CTCCGA
65 GATACTCCAACCT-CGG
* * * *** * * * *
5750725 TTTTATTTCCAAAATATCGATTTTTCACCATCGAAAATATTCCAACCCTGTTA-TTTTCCAGGAG
1 TTTTATTTTCAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGAGGGG
*
5750789 ATACTCCAACCCCGG
66 ATACTCCAACCTCGG
* * * * * * *
5750804 CTTTATTTTTAAAACATCGATTTTCCACAATCGAGGATACTCTAACCCCGTTATTTTT-TAAGGG
1 TTTTATTTTCAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGAGGGG
* *
5750868 ATACTCCAACCCCAG
66 ATACTCCAACCTCGG
* * * ** *
5750883 TTTTATTTTCAAAACACCAATTTTTCACCATCAAGGATACTCAAACC
1 TTTTATTTTCAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
5750930 TGGTTTTATT
Statistics
Matches: 348, Mismatches: 77, Indels: 33
0.76 0.17 0.07
Matches are distributed among these distances:
77 8 0.02
78 57 0.16
79 224 0.64
80 58 0.17
81 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (80 bp):
TTTTATTTTCAAAACATCGATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGAGGGG
ATACTCCAACCTCGG
Found at i:5750697 original size:157 final size:157
Alignment explanation
Indices: 5750409--5750929 Score: 591
Period size: 158 Copynumber: 3.3 Consensus size: 157
5750399 TCATTGATTT
* * *
5750409 TTTTATTTCCAAAACACTGATTTTCCACCATCGGGGATACCCCAACCCCATTATTTTTCGAGGGG
1 TTTTATTTCCAAAACACTGATTTTCCACCATCGAGGATACTCCAACCCTATTA-TTTTCGA-GGG
* * * * *
5750474 ATATT-TAAACCTCGGCTGTATTTCTAAAACATCGATTTTTCATAATTGGGGATACTCCAACCCC
64 ATATTCCAAACC-CGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCC
*
5750538 GTTATTTCTGAGGGGATACTCCAACCTCGG
128 GTTATTTTTGAGGGGATACTCCAACCTCGG
* * *
5750568 TTTTATTTTCAAAACACTGATTTTCCACCATCGGGGATACTCTAA-CCTATTATTTTCGAGAGGA
1 TTTTATTTCCAAAACACTGATTTTCCACCATCGAGGATACTCCAACCCTATTATTTTCGAG-GGA
* * * *
5750632 TATTCCAAGCCCAGCTTTATTTCTAAAACATCGATTTTTCACAACCGTGGATACTCCAACCCCGT
65 TATTCCAAACCCGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCGT
* *
5750697 TATTTTTGAGGGGATACTCTAA-CTCCGA
130 TATTTTTGAGGGGATACTCCAACCT-CGG
* * ** * * *
5750725 TTTTATTTCCAAAATA-TCGATTTTTCACCATCGAAAATATTCCAACCCTGTTATTTTCCAGGAG
1 TTTTATTTCCAAAACACT-GATTTTCCACCATCGAGGATACTCCAACCCTATTATTTTCGAGG-G
* * * * *
5750789 ATACTCCAACCCCGGCTTTATTTTTAAAACATCGATTTTCCACAATCGAGGATACTCTAACCCCG
64 ATATTCCAAACCCGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCG
* * * *
5750854 TTATTTTTTAAGGGATACTCCAACCCCAG
129 TTATTTTTGAGGGGATACTCCAACCTCGG
* ** * * *
5750883 TTTTATTTTCAAAACACCAATTTTTCACCATCAAGGATACTCAAACC
1 TTTTATTTCCAAAACACTGATTTTCCACCATCGAGGATACTCCAACC
5750930 TGGTTTTATT
Statistics
Matches: 306, Mismatches: 48, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
156 4 0.01
157 120 0.39
158 139 0.45
159 43 0.14
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (157 bp):
TTTTATTTCCAAAACACTGATTTTCCACCATCGAGGATACTCCAACCCTATTATTTTCGAGGGAT
ATTCCAAACCCGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCGTT
ATTTTTGAGGGGATACTCCAACCTCGG
Found at i:5750828 original size:236 final size:237
Alignment explanation
Indices: 5750410--5750899 Score: 544
Period size: 236 Copynumber: 2.1 Consensus size: 237
5750400 CATTGATTTT
* *
5750410 TTTATTTCCAAAACACTGATTTTCCACCATCGGGGATACCCCAACCCCATTATTTTTCGAGGGGA
1 TTTATTTCCAAAACACTGATTTTCCACAACCGGGGATACCCCAACCCCATTATTTTTCGAGGGGA
* * * * * ***
5750475 TATTTAAACCTCGGCTGTATTTCTAAAACATCGATTTTTCATAATTGGGGATACTCCAACCCCGT
66 TATCTAAACCTCGACTGTATTTCCAAAACATCGATTTTTCACAATCGAAAATACTCCAACCCCGT
* * * * * *
5750540 TATTTCTGAGGGGATACTCCAACCTCGGTTTTATTTTCAAAACACTGATTTTCCACCATCGGGGA
131 TATTTCTCAGGAGATACTCCAACCCCGGCTTTATTTTCAAAACACTGATTTTCCACAATCGAGGA
5750605 TACTCTAACCTATTATTTTCGAGAGGATATTCCAAGCCCAGC
196 TACTCTAACCTATTATTTTCGAGAGGATATTCCAAGCCCAGC
* * * * *
5750647 TTTATTTCTAAAACA-TCGATTTTTCACAACCGTGGATACTCCAACCCCGTTATTTTT-GAGGGG
1 TTTATTTCCAAAACACT-GATTTTCCACAACCGGGGATACCCCAACCCCATTATTTTTCGAGGGG
* * * * *
5750710 ATACTCT-AA-CTCCGATTTTATTTCCAAAATATCGATTTTTCACCATCGAAAATATTCCAACCC
65 ATA-TCTAAACCT-CGACTGTATTTCCAAAACATCGATTTTTCACAATCGAAAATACTCCAACCC
* *
5750773 TGTTATTT-TCCAGGAGATACTCCAACCCCGGCTTTATTTTTAAAACA-TCGATTTTCCACAATC
128 CGTTATTTCT-CAGGAGATACTCCAACCCCGGCTTTATTTTCAAAACACT-GATTTTCCACAATC
** ** * * *
5750836 GAGGATACTCTAACCCCGTTATTTTTTA-AGGGATACTCCAACCCCAGT
191 GAGGATACTCTAA-CCTATTATTTTCGAGA-GGATATTCCAAGCCCAGC
*
5750884 TTTATTTTCAAAACAC
1 TTTATTTCCAAAACAC
5750900 CAATTTTTCA
Statistics
Matches: 208, Mismatches: 37, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
235 4 0.02
236 116 0.56
237 88 0.42
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (237 bp):
TTTATTTCCAAAACACTGATTTTCCACAACCGGGGATACCCCAACCCCATTATTTTTCGAGGGGA
TATCTAAACCTCGACTGTATTTCCAAAACATCGATTTTTCACAATCGAAAATACTCCAACCCCGT
TATTTCTCAGGAGATACTCCAACCCCGGCTTTATTTTCAAAACACTGATTTTCCACAATCGAGGA
TACTCTAACCTATTATTTTCGAGAGGATATTCCAAGCCCAGC
Found at i:5750858 original size:158 final size:155
Alignment explanation
Indices: 5750409--5750914 Score: 528
Period size: 157 Copynumber: 3.2 Consensus size: 155
5750399 TCATTGATTT
* * *** * * * *
5750409 TTTTATTTCCAAAACACTGATTTTCCACCATCGGGGATACCCCAACCCCATTATTTTTCGAGGGG
1 TTTTATTTTCAAAACAC-GATTTTTCACCATCGAAAATACTCCAA-CCTATTA-TTTTCCAGAGG
* ** * * * * *
5750474 ATATTTAAACCTCGGCTGTATTTCTAAAACATCGATTTTTCATAATTGGGGATACTCCAACCCCG
63 ATACTCCAACCCCGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCG
* *
5750539 TTATTTCTGAGGGGATACTCCAACCTCGG
128 TTATTTTTGAGGGGATACTCCAACC-CGA
* *** * *
5750568 TTTTATTTTCAAAACACTGATTTTCCACCATCGGGGATACTCTAACCTATTATTTTCGAGAGGAT
1 TTTTATTTTCAAAACAC-GATTTTTCACCATCGAAAATACTCCAACCTATTATTTTCCAGAGGAT
* * * * *
5750633 ATTCCAAGCCCAGCTTTATTTCTAAAACATCGATTTTTCACAACCGTGGATACTCCAACCCCGTT
65 ACTCCAACCCCGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCGTT
*
5750698 ATTTTTGAGGGGATACTCTAACTCCGA
130 ATTTTTGAGGGGATACTCCAAC-CCGA
* * * *
5750725 TTTTATTTCCAAAATATCGATTTTTCACCATCGAAAATATTCCAACCCTGTTATTTTCCAG-GAG
1 TTTTATTTTCAAAACA-CGATTTTTCACCATCGAAAATACTCCAA-CCTATTATTTTCCAGAG-G
* * *
5750789 ATACTCCAACCCCGGCTTTATTTTTAAAACATCGATTTTCCACAATCGAGGATACTCTAACCCCG
63 ATACTCCAACCCCGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCG
* * *
5750854 TTATTTTTTAAGGGATACTCCAACCCCA
128 TTATTTTTGAGGGGATACTCCAACCCGA
*
5750882 GTTTTATTTTCAAAACACCAATTTTTCACCATC
1 -TTTTATTTTCAAAACA-CGATTTTTCACCATC
5750915 AAGGATACTC
Statistics
Matches: 298, Mismatches: 44, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
157 128 0.43
158 128 0.43
159 42 0.14
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (155 bp):
TTTTATTTTCAAAACACGATTTTTCACCATCGAAAATACTCCAACCTATTATTTTCCAGAGGATA
CTCCAACCCCGGCTTTATTTCTAAAACATCGATTTTTCACAATCGAGGATACTCCAACCCCGTTA
TTTTTGAGGGGATACTCCAACCCGA
Found at i:5761268 original size:13 final size:13
Alignment explanation
Indices: 5761250--5761274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5761240 TTTTCCAGAT
5761250 TGTATCGATACAA
1 TGTATCGATACAA
5761263 TGTATCGATACA
1 TGTATCGATACA
5761275 TTGCTTCAGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5763362 original size:20 final size:20
Alignment explanation
Indices: 5763317--5763368 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
5763307 GTAGCCAAAC
**
5763317 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
5763337 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
5763356 TTGTATCGATACA
1 TTGTATCGATACA
5763369 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:5764235 original size:62 final size:62
Alignment explanation
Indices: 5764131--5764807 Score: 701
Period size: 62 Copynumber: 11.0 Consensus size: 62
5764121 GCTCACACAT
* ** * * *
5764131 CTTTTTCTTTTCAAAGTCCACATAAGTTAGCGGCACCTTTTAGTCCTCAAAGAGTAGGACAC
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACAC
* * * **
5764193 CTTTTTCTTTTCAAAGCTCACACAAGTTGGTAGCA-CTCTTTAGTCCTCAAAGAGCAGGATGC
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT-TTTAGTCCTCAAAGAGCAGGACAC
* * * * *
5764255 CTTTTTCATTTCAAAGCTCACACAAGTTGATGGAACCTTTTAGTCCTCAAAGAGCAGG--AC
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACAC
* * * * * *
5764315 GTCTTTCATTTCAAAGCCCACACGAGTTGGTGGCACCATTTAGTCCTCAAAGAGCAAGATAC
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACAC
* * * **
5764377 TTTTTTTCTTTTCAAAGCCCACATGAG-TGTGTGGCACTCTTTTAGTCCTCAAAGAGCAAGACGT
1 -CTTTTTCTTTTCAAAGCCCACACGAGTTG-GTGGCAC-CTTTTAGTCCTCAAAGAGCAGGACAC
* ** * * * **
5764441 CTTTTTCTTTTC-AAGCCCACATGAGTTGGTGGCATATTTTGGTCCTTAAAGAGTAGGATGC
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACAC
* * **
5764502 CTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGTT
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGAC-AC
* * * * * **
5764565 TTTTTTCTTTTCAAAGCCCACACTAGTTGATGACACCCTTTAGTCCTCAAAGAGCAGGATGC
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACAC
* * * *
5764627 CTTTTCCATTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGG--AC
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACAC
* * * **
5764687 GTTTTT-TTTTCAAAGCCCACATGAGTTGGTGGCACAC-TTTAGTCTTCAAAGAGCAGGACGT
1 CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CTTTTAGTCCTCAAAGAGCAGGACAC
* *
5764748 CTTTTT-TTGTTCAAA-CCTACACGAGTTGGTGGTACCTTTTAGTCCTCAAAGAGCAGGACA
1 CTTTTTCTT-TTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACA
5764808 TTTTCCTCAT
Statistics
Matches: 518, Mismatches: 82, Indels: 31
0.82 0.13 0.05
Matches are distributed among these distances:
59 44 0.08
60 58 0.11
61 78 0.15
62 220 0.42
63 96 0.19
64 22 0.04
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (62 bp):
CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACAC
Found at i:5764511 original size:124 final size:124
Alignment explanation
Indices: 5764131--5764806 Score: 807
Period size: 125 Copynumber: 5.5 Consensus size: 124
5764121 GCTCACACAT
* * * * * **
5764131 CTTTTTCTTTTCAAAGTCCACATAAGTTAGCGGCACCTTTTAGTCCTCAAAGAGTAGGACACCTT
1 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGTCTT
* ** * *
5764196 TTTCTTTTCAAAGCTCACACAAGTTGGTAGCACTCTTTAGTCCTCAAAGAGCAGGATGC
66 TTTCTTTTCAAAGCCCACATGAGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGATGC
* * * *
5764255 CTTTTTCATTTCAAAGCTCACACAAGTTGATGGAACCTTTTAGTCCTCAAAGAGCAGGACGTC--
1 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGTCTT
* * * *
5764318 TTTCATTTCAAAGCCCACACGAGTTGGTGGCAC-CATTTAGTCCTCAAAGAGCAAGATAC
66 TTTCTTTTCAAAGCCCACATGAGTTGGTGGCACAC-TTTAGTCCTCAAAGAGCAGGATGC
* ** *
5764377 TTTTTTTCTTTTCAAAGCCCACATGAG-TGTGTGGCACTCTTTTAGTCCTCAAAGAGCAAGACGT
1 -CTTTTTCTTTTCAAAGCCCACACAAGTTG-GTGGCAC-CTTTTAGTCCTCAAAGAGCAGGACGT
* * * * *
5764441 CTTTTTCTTTTC-AAGCCCACATGAGTTGGTGGCATATTTTGGTCCTTAAAGAGTAGGATGC
63 CTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGATGC
** * *
5764502 CTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGTTTT
1 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG-TCT
* * *
5764567 TTTTCTTTTCAAAGCCCACACT-AGTTGATGACACCCTTTAGTCCTCAAAGAGCAGGATGC
65 TTTTCTTTTCAAAGCCCACA-TGAGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGATGC
* * *
5764627 CTTTTCCATTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACG--TT
1 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGTCTT
* * *
5764690 TTT-TTTTCAAAGCCCACATGAGTTGGTGGCACACTTTAGTCTTCAAAGAGCAGGACGT
66 TTTCTTTTCAAAGCCCACATGAGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGATGC
* * *
5764748 CTTTTT-TTGTTCAAA-CCTACACGAGTTGGTGGTACCTTTTAGTCCTCAAAGAGCAGGAC
1 CTTTTTCTT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGAC
5764807 ATTTTCCTCA
Statistics
Matches: 477, Mismatches: 62, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
120 42 0.09
121 59 0.12
122 58 0.12
123 51 0.11
124 122 0.26
125 136 0.29
126 9 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (124 bp):
CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGTCTT
TTTCTTTTCAAAGCCCACATGAGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGATGC
Found at i:5764886 original size:45 final size:44
Alignment explanation
Indices: 5764816--5765657 Score: 425
Period size: 44 Copynumber: 19.8 Consensus size: 44
5764806 CATTTTCCTC
*
5764816 ATTTCCTTTTCTT--CTTTGTCCTCAAAGAGCAGGATGCACTTT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCACTTT
* *
5764858 ATTTCCTTTTTTTCCCTTTTGTCCTCAAAGAGTAGGATGTACTTT
1 ATTTCCTTTTTTTCCC-TTTGTCCTCAAAGAGCAGGATGCACTTT
*
5764903 ATTTCC--TTTTT-CCTTTGTCCTCAAAGAGCATGG-TGCACCTT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCA-GGATGCACTTT
* * * *
5764944 ATTT-CTTTCTTTTCCCTTAGTCTTTGAAA-AGCATGATGCA---T
1 ATTTCCTTT-TTTTCCCTTTGTC-CTCAAAGAGCAGGATGCACTTT
*
5764985 -TTT-CTTTTTTT-CCTTTGTCCTCAAAGAGTAGGA--CACATTT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCAC-TTT
* *
5765025 CATTTCCTTCATTTCCTTCATTTCCTTTTTGTCCTCAAAGAGTATGATGCACTTT
1 -ATTTCCTT--TTT--TTC----CC--TTTGTCCTCAAAGAGCAGGATGCACTTT
* * * * *
5765080 ATTTCC---TTTTCCCTTTATCCTCAAAGAACAGGGTGCACCTC
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCACTTT
* *
5765121 ATTTTCTTTTTTT-CCTTTAGTCCTCAAAGAGTAGGATGCA--TT
1 ATTTCCTTTTTTTCCCTTT-GTCCTCAAAGAGCAGGATGCACTTT
* * *
5765163 -TTT-C-TTTTCT-CCTTTATCCTCAAAGAGTAGGA--CACATTT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCAC-TTT
* *
5765202 CATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTT
1 -ATTTCCTTTTTTTCCC-TTTGTCCTCAAAGAGCAGGATGCACTTT
* * *
5765248 ATTTCC--TTTTT-CCTTTGTCCTCAAAAAGCA-GA-GCACACCTC
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATG--CACTTT
* * *
5765289 ATTTCCTTCTTTTCCCTTAGTCCTCAAAGAGC---ATG-ACGTCT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCAC-TTT
* * * *
5765330 -TTT-CTTTTTCT-CCTTTGTCCCCAAAGAGCATGA--CATATTT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCA-CTTT
* * **
5765370 CCTTTCC-TTTTTTCCCTTTTGTCCTCCAAGAGCAGGACACACTTT
1 -ATTTCCTTTTTTTCCC-TTTGTCCTCAAAGAGCAGGATGCACTTT
* * ** *
5765415 -TTTCC--TTTTT-CTTTTGTCCTCAAAAAGCAGGGCGCACCTT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCACTTT
* * * * *
5765455 ATTTTCTTATTTTCCCTTAGTCCTCAAAGAGCAAGACGC-C--T
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCACTTT
* * *
5765496 -TTTCC-TTTTCT-CCTTTATCCTCAAAGAGCAGGA--CATATTT
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCA-CTTT
* * * * ***
5765536 GATTCCCTTCTTTTCCTTTTTGTCCTCAAAGAGCAAGACATACTTT
1 -ATTTCCTTTTTTTCC-CTTTGTCCTCAAAGAGCAGGATGCACTTT
* *** * *
5765582 -TTTCC-TTTTTT--CTTTGTCCTCAAAGAGTAGGGCACACCTC
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCACTTT
* *
5765622 ATTTCCTTATTTTCCCTTTGTCCTCAAAGAGTAGGA
1 ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGA
5765658 CGCCTTTTTC
Statistics
Matches: 621, Mismatches: 95, Indels: 166
0.70 0.11 0.19
Matches are distributed among these distances:
36 5 0.01
37 4 0.01
38 63 0.10
39 27 0.04
40 70 0.11
41 97 0.16
42 47 0.08
43 55 0.09
44 117 0.19
45 84 0.14
46 8 0.01
47 9 0.01
49 2 0.00
52 2 0.00
54 25 0.04
55 3 0.00
56 3 0.00
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (44 bp):
ATTTCCTTTTTTTCCCTTTGTCCTCAAAGAGCAGGATGCACTTT
Found at i:5765032 original size:168 final size:168
Alignment explanation
Indices: 5764817--5765713 Score: 963
Period size: 167 Copynumber: 5.3 Consensus size: 168
5764807 ATTTTCCTCA
* *
5764817 TTTCCTTTTCTTCTTTGTCCTCAAAGAGCAGGATGCAC-TTT-ATTTCCTTTTTTTCCCTTTTGT
1 TTTCTTTTTCTCCTTTGTCCTCAAAGAGCAGGA--CACATTTCATTTCCTTTTTTTCCCTTTTGT
* * * * * *
5764880 CCTCAAAGAGTAGGATGTACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCATGGTGCACCTTA
64 CCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGGCGCACCTCA
* * *
5764945 TTTCTTTCTTTTCCCTTAGTCTTTGAAA-AGCATGATGCAT
129 TTTCTTTCTTTTCCCTTAGTC-CTCAAAGAGCATGACGCAT
* *
5764985 TTTCTTTTTTTCCTTTGTCCTCAAAGAGTAGGACACATTTCATTTCCTTCATTTCCTTCATTTCC
1 TTTCTTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTT--TTT--TTC----CC
* * * * * * *
5765050 TTTTTGTCCTCAAAGAGTATGATGCACTTTATTTCCTTTTCCCTTTATCCTCAAAGAACAGGGTG
58 -TTTTGTCCTCAAAGAGCAGGACGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGGCG
* * * *
5765115 CACCTCATTTTCTTT-TTTTCCTTTAGTCCTCAAAGAGTAGGATGCAT
122 CACCTCA-TTTCTTTCTTTTCCCTTAGTCCTCAAAGAGCATGACGCAT
* * *
5765162 TTT-TCTTTTCTCCTTTATCCTCAAAGAGTAGGACACATTTCATTTCCTTCTTTTCCCTTTTGTC
1 TTTCT-TTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTTTTGTC
* * *
5765226 CTCAAAGAGCAGGACGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAAAGCAGAGCACACCTCAT
65 CTCAAAGAGCAGGACGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGGCGCACCTCAT
*
5765291 TTCCTTCTTTTCCCTTAGTCCTCAAAGAGCATGACGTC-T
130 TTCTTTCTTTTCCCTTAGTCCTCAAAGAGCATGACG-CAT
* * * *
5765330 TTTCTTTTTCTCCTTTGTCCCCAAAGAGCATGACATATTTCCTTTCC-TTTTTTCCCTTTTGTCC
1 TTTCTTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTTTTGTCC
* * * * *
5765394 TCCAAGAGCAGGACACACTTT-TTTCCTTTTTCTTTTGTCCTCAAAAAGCAGGGCGCACCTTATT
66 TCAAAGAGCAGGACGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGGCGCACCTCATT
* * *
5765458 T-TCTTATTTTCCCTTAGTCCTCAAAGAGCAAGACGCCT
131 TCT-TTCTTTTCCCTTAGTCCTCAAAGAGCATGACGCAT
* * * * * * *
5765496 TTTCCTTTTCTCCTTTATCCTCAAAGAGCAGGACATATTTGATTCCCTTCTTTTCCTTTTTGTCC
1 TTTCTTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTTTTGTCC
* ** * * *
5765561 TCAAAGAGCAAGACATACTTT-TTTCCTTTTTTCTTTGTCCTCAAAGAGTAGGGCACACCTCATT
66 TCAAAGAGCAGGACGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGGCGCACCTCATT
* * * * * *
5765625 TCCTTATTTTCCCTTTGTCCTCAAAGAGTAGGACGCCT
131 TCTTTCTTTTCCCTTAGTCCTCAAAGAGCATGACGCAT
* * *
5765663 TTT-TCTTTTCTCTTTTGTCCTC-AAGAAGCAGGACCCATTTCATTTTCTTTT
1 TTTCT-TTTTCTCCTTTGTCCTCAAAG-AGCAGGACACATTTCATTTCCTTTT
5765714 CCTTCATCCT
Statistics
Matches: 625, Mismatches: 81, Indels: 47
0.83 0.11 0.06
Matches are distributed among these distances:
165 1 0.00
166 117 0.19
167 184 0.29
168 163 0.26
169 4 0.01
170 3 0.00
172 3 0.00
173 3 0.00
175 2 0.00
176 7 0.01
177 131 0.21
178 7 0.01
ACGTcount: A:0.20, C:0.26, G:0.12, T:0.42
Consensus pattern (168 bp):
TTTCTTTTTCTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTTTTTTCCCTTTTGTCC
TCAAAGAGCAGGACGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGGCGCACCTCATT
TCTTTCTTTTCCCTTAGTCCTCAAAGAGCATGACGCAT
Found at i:5765037 original size:9 final size:9
Alignment explanation
Indices: 5765023--5765051 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5765013 TAGGACACAT
5765023 TTCATTTCC
1 TTCATTTCC
5765032 TTCATTTCC
1 TTCATTTCC
5765041 TTCATTTCC
1 TTCATTTCC
5765050 TT
1 TT
5765052 TTTGTCCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.59
Consensus pattern (9 bp):
TTCATTTCC
Found at i:5769843 original size:27 final size:27
Alignment explanation
Indices: 5769795--5769866 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
5769785 TTACTCACGG
* * *
5769795 GGATACTTCAACCCTATCCTTCCAAAA
1 GGATACTCCAACCCCATTCTTCCAAAA
* * **
5769822 TGATACTCCAACCCCATTCTTCTAAGG
1 GGATACTCCAACCCCATTCTTCCAAAA
5769849 GGATACTCCAACCCCATT
1 GGATACTCCAACCCCATT
5769867 TTTAAACTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.35, G:0.10, T:0.26
Consensus pattern (27 bp):
GGATACTCCAACCCCATTCTTCCAAAA
Found at i:5770020 original size:97 final size:96
Alignment explanation
Indices: 5769823--5770029 Score: 272
Period size: 97 Copynumber: 2.1 Consensus size: 96
5769813 CTTCCAAAAT
5769823 GATACTCCAACCCCATTCTTCTAAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGTTTAAA
1 GATACTCCAACCCCATTCTTCTAAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGTTTAAA
* *
5769888 TCTTATTTTTGCTTAAATTATCATCTTTAGA
66 TCTTATTTTTGCTAAAATTATCATCATTAGA
* * * ** ** *
5769919 GATACTCCAATCTCATTCTTCCTAA-GGGATATTTTAACCCTGTTTTTAAACTTGTCACGATTTA
1 GATACTCCAACCCCATTCTT-CTAAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAG-TTTA
* * *
5769983 AATTTTATTTTTGCTAAAATTATCATCATTGGG
64 AATCTTATTTTTGCTAAAATTATCATCATTAGA
5770016 GATACTCCAACCCC
1 GATACTCCAACCCC
5770030 CTTTCTCCGA
Statistics
Matches: 94, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
96 46 0.49
97 48 0.51
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (96 bp):
GATACTCCAACCCCATTCTTCTAAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGTTTAAA
TCTTATTTTTGCTAAAATTATCATCATTAGA
Found at i:5770061 original size:97 final size:95
Alignment explanation
Indices: 5769823--5770066 Score: 258
Period size: 97 Copynumber: 2.5 Consensus size: 95
5769813 CTTCCAAAAT
* * *
5769823 GATACTCCAACCCCATTCTTCTAAGGGGATACTCCAACCCCATTTTTAAACTTGTCAAGTTTAAA
1 GATACTCCAACCCCATTCTTCCAAGAGGATACTCCAA-CCCGTTTTTAAACTTGTCAAGTTTAAA
* *
5769888 TCTTATTTTTGCTTAAATTATCATCTTTAGA
65 TCTTATTTTTGCTAAAATTATCATCATTAGA
* * * ** *
5769919 GATACTCCAATCTCATTCTTCCTAAG-GGATATTTTAACCCTGTTTTTAAACTTGTCACGATTTA
1 GATACTCCAACCCCATTCTTCC-AAGAGGATACTCCAACCC-GTTTTTAAACTTGTCAAG-TTTA
* * *
5769983 AATTTTATTTTTGCTAAAATTATCATCATTGGG
63 AATCTTATTTTTGCTAAAATTATCATCATTAGA
* * * *
5770016 GATACTCCAACCCCCTT-TCTCCGAGAGGATACTCGAACCTCGTTTTGAAAC
1 GATACTCCAACCCCATTCT-TCCAAGAGGATACTCCAACC-CGTTTTTAAAC
5770067 CAAAACTTAA
Statistics
Matches: 121, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
95 3 0.02
96 46 0.38
97 71 0.59
98 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (95 bp):
GATACTCCAACCCCATTCTTCCAAGAGGATACTCCAACCCGTTTTTAAACTTGTCAAGTTTAAAT
CTTATTTTTGCTAAAATTATCATCATTAGA
Found at i:5771031 original size:13 final size:13
Alignment explanation
Indices: 5771013--5771038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5771003 CATTTTTTGG
5771013 TGTATCGATACAT
1 TGTATCGATACAT
5771026 TGTATCGATACAT
1 TGTATCGATACAT
5771039 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5771053 original size:32 final size:33
Alignment explanation
Indices: 5770993--5771056 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5770983 TACAAGCTAA
**
5770993 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
5771026 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
5771057 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:5772731 original size:19 final size:19
Alignment explanation
Indices: 5772707--5772778 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
5772697 TTGAAATAGC
5772707 TTAAAATAATAATTTTAAA
1 TTAAAATAATAATTTTAAA
*
5772726 TTAAAATAATATATTTT-TA
1 TTAAAATAATA-ATTTTAAA
*
5772745 TTTAAAT-ATAATTATTAAA
1 TTAAAATAATAATT-TTAAA
*
5772764 TATATAAATATTAAT
1 T-TA-AAATAATAAT
5772779 ATAAAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 20 0.48
20 6 0.14
21 4 0.10
22 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAATAATAATTTTAAA
Found at i:5772749 original size:20 final size:20
Alignment explanation
Indices: 5772707--5772760 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5772697 TTGAAATAGC
5772707 TTAAAATAATA-ATTTTAAA
1 TTAAAATAATATATTTTAAA
* *
5772726 TTAAAATAATATATTTTTAT
1 TTAAAATAATATATTTTAAA
5772746 TTAAATATAAT-TATT
1 TTAAA-ATAATATATT
5772761 AAATATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 11 0.35
20 15 0.48
21 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAATAATATATTTTAAA
Found at i:5772770 original size:15 final size:14
Alignment explanation
Indices: 5772746--5772787 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5772736 ATATTTTTAT
*
5772746 TTAA-ATATAATTA
1 TTAATATATAAATA
5772759 TTAAATATATAAATA
1 TT-AATATATAAATA
*
5772774 TTAATATAAAAATA
1 TTAATATATAAATA
5772788 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 13 0.52
15 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAATATATAAATA
Found at i:5773894 original size:27 final size:27
Alignment explanation
Indices: 5773864--5773921 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
5773854 ATAAATGATG
*
5773864 ATTTAATAAT-GAATAATATTTTTAAAT
1 ATTTAATAATAGAATAAAATTTTT-AAT
* * *
5773891 ATTTGATATTAGTATAAAATTTTTAAT
1 ATTTAATAATAGAATAAAATTTTTAAT
5773918 ATTT
1 ATTT
5773922 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
ATTTAATAATAGAATAAAATTTTTAAT
Found at i:5784237 original size:44 final size:39
Alignment explanation
Indices: 5784153--5784227 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
5784143 TTGTAATCTA
**
5784153 AATAAATTAAATTTTTATATCTATTTTAATTATATATAT
1 AATAAATTAAATTCATATATCTATTTTAATTATATATAT
5784192 AATAAATTAAATTCATATAT-TATTTTATATT-TATAT
1 AATAAATTAAATTCATATATCTATTTTA-ATTATATAT
5784228 TTTACTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 12 0.36
39 21 0.64
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (39 bp):
AATAAATTAAATTCATATATCTATTTTAATTATATATAT
Found at i:5784553 original size:2 final size:2
Alignment explanation
Indices: 5784548--5784581 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5784538 TGTGTGTGTA
5784548 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
5784582 TTCTTTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5786728 original size:32 final size:32
Alignment explanation
Indices: 5786691--5786755 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
5786681 TAATTAAATA
5786691 AATGAATTGTTGAATTGTGATATTTAAATGGT
1 AATGAATTGTTGAATTGTGATATTTAAATGGT
*
5786723 AATGAATTGTTGAATTGTGATGTTTAAATGGT
1 AATGAATTGTTGAATTGTGATATTTAAATGGT
5786755 A
1 A
5786756 TGAGGTATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (32 bp):
AATGAATTGTTGAATTGTGATATTTAAATGGT
Found at i:5788703 original size:14 final size:14
Alignment explanation
Indices: 5788661--5788703 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5788651 CCACCCATAT
*
5788661 TATATTTTTTATAA
1 TATATTTTTTAAAA
*
5788675 TTTATTTTTTAAAAA
1 TATATTTTTT-AAAA
*
5788690 TATATATTTTAAAA
1 TATATTTTTTAAAA
5788704 ATTTTAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTTTTTAAAA
Found at i:5788741 original size:22 final size:24
Alignment explanation
Indices: 5788694--5788741 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
5788684 TAAAAATATA
5788694 TATTTTAAAAATTTTAATCTTTAT
1 TATTTTAAAAATTTTAATCTTTAT
* *
5788718 TATTTT-AATATTTT-ATTTTTAT
1 TATTTTAAAAATTTTAATCTTTAT
5788740 TA
1 TA
5788742 AATTTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 7 0.32
24 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTTAAAAATTTTAATCTTTAT
Found at i:5792594 original size:3 final size:3
Alignment explanation
Indices: 5792588--5792615 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5792578 AGAATAATAT
5792588 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5792616 CACGTATATG
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:5793247 original size:32 final size:31
Alignment explanation
Indices: 5793211--5793279 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 31
5793201 TGAATATATA
5793211 AATATATCAAAATTTATATAAA-ATAAATTATT
1 AATATATCAAAATTTATATAAATAT-AATTA-T
*
5793243 AATATATTAAAATTTATATAAATATAATTAT
1 AATATATCAAAATTTATATAAATATAATTAT
5793274 AATATA
1 AATATA
5793280 AAAATACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 7 0.20
32 26 0.74
33 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
AATATATCAAAATTTATATAAATATAATTAT
Found at i:5793268 original size:20 final size:19
Alignment explanation
Indices: 5793205--5793267 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 19
5793195 ATAACATGAA
*
5793205 TATATAAATATATCAAAATT
1 TATAT-AATATATTAAAATT
5793225 TATATAA-A-A-T-AAA-T
1 TATATAATATATTAAAATT
5793239 TAT-TAATATATTAAAATT
1 TATATAATATATTAAAATT
5793257 TATATAA-ATAT
1 TATATAATATAT
5793268 AATTATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.08
14 5 0.14
15 4 0.11
16 1 0.03
17 4 0.11
18 9 0.25
19 5 0.14
20 5 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TATATAATATATTAAAATT
Found at i:5793284 original size:19 final size:19
Alignment explanation
Indices: 5793257--5793300 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5793247 TATTAAAATT
* * *
5793257 TATATAAATATAATTATAA
1 TATAAAAATACAAATATAA
5793276 TATAAAAATACAAATATAA
1 TATAAAAATACAAATATAA
5793295 TATAAA
1 TATAAA
5793301 TATTTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TATAAAAATACAAATATAA
Found at i:5793776 original size:19 final size:19
Alignment explanation
Indices: 5793752--5793788 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5793742 TAAAAATATT
5793752 TATAAT-AATAATTTAAAAA
1 TATAATAAAT-ATTTAAAAA
5793771 TATAATAAATATTTAAAA
1 TATAATAAATATTTAAAA
5793789 TTAATTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAATAAATATTTAAAAA
Found at i:5795040 original size:29 final size:30
Alignment explanation
Indices: 5794984--5795040 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
5794974 ATTATATATT
*
5794984 ATTATTTGTTAAATTTTATAATTGTTTAAA
1 ATTATTTGTTAAATTTTATAATTATTTAAA
5795014 ATTATTT-TTAAATTTTAT-ATTAATTTA
1 ATTATTTGTTAAATTTTATAATT-ATTTA
5795041 TTAATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (30 bp):
ATTATTTGTTAAATTTTATAATTATTTAAA
Found at i:5795047 original size:30 final size:31
Alignment explanation
Indices: 5794973--5795047 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
5794963 ATTGATATTA
*
5794973 AATTATATATT-ATTATTTGTTAAATTTTAT
1 AATTATTTATTAATTATTTGTTAAATTTTAT
* *
5795003 AATTGTTTA-AAATTATTT-TTAAATTTTAT
1 AATTATTTATTAATTATTTGTTAAATTTTAT
5795032 -ATTAATTTATTAATTA
1 AATT-ATTTATTAATTA
5795048 ATATTATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 3 0.08
29 15 0.41
30 19 0.51
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
AATTATTTATTAATTATTTGTTAAATTTTAT
Found at i:5795070 original size:18 final size:18
Alignment explanation
Indices: 5795014--5795071 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
5795004 ATTGTTTAAA
*
5795014 ATTATT-TTTAAAT-TTT
1 ATTATTATTTTAATATTT
* * *
5795030 A-TATTAATTTATTAATT
1 ATTATTATTTTAATATTT
*
5795047 AATATTATTTTAATATTT
1 ATTATTATTTTAATATTT
5795065 ATTATTA
1 ATTATTA
5795072 ATACATAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 4 0.13
16 5 0.16
17 3 0.10
18 19 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATTATTTTAATATTT
Found at i:5796076 original size:5 final size:5
Alignment explanation
Indices: 5796066--5796136 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
5796056 TATAATTTTA
* * * *
5796066 AATAT AATAT AAT-T -ATAT GAATTT AAAAT AATTAA AATAT AATAT AAAAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT AA-TAT AATAT AATAT AATAT
5796116 AAATAT AATAT AA-AT -ATAT AA
1 -AATAT AATAT AATAT AATAT AA
5796137 ATTAGTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
3 3 0.06
4 6 0.12
5 32 0.63
6 10 0.20
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:5796120 original size:11 final size:11
Alignment explanation
Indices: 5796089--5796138 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
5796079 TATATGAATT
5796089 TAAAAT-AAT-
1 TAAAATAAATA
5796098 TAAAATATAATA
1 TAAAATA-AATA
5796110 TAAAATAAATA
1 TAAAATAAATA
*
5796121 TAATATAAATA
1 TAAAATAAATA
5796132 TATAAAT
1 TA-AAAT
5796139 TAGTTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 6 0.17
11 19 0.54
12 10 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAATAAATA
Found at i:5796443 original size:5 final size:5
Alignment explanation
Indices: 5796429--5796478 Score: 75
Period size: 5 Copynumber: 9.8 Consensus size: 5
5796419 TTTAAAATAT
5796429 TTAT- TTATA TTATA TTTATA TTATA TTATA TTTATA TTATA TTATA TTAT
1 TTATA TTATA TTATA -TTATA TTATA TTATA -TTATA TTATA TTATA TTAT
5796479 TTTTAATTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.09
5 29 0.67
6 10 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:5796454 original size:16 final size:16
Alignment explanation
Indices: 5796425--5796476 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
5796415 AAAATTTAAA
5796425 ATATTTAT-TTATATT
1 ATATTTATATTATATT
5796440 ATATTTATATTATATT
1 ATATTTATATTATATT
5796456 ATATTTATATTATATT
1 ATATTTATATTATATT
5796472 ATATT
1 ATATT
5796477 ATTTTTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 8 0.22
16 28 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTTATATTATATT
Found at i:5796457 original size:21 final size:21
Alignment explanation
Indices: 5796433--5796488 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
5796423 AAATATTTAT
5796433 TTATA-TTATATTTATATTATA
1 TTATATTTATA-TTATATTATA
5796454 TTATATTTATATTATATTATA
1 TTATATTTATATTATATTATA
*
5796475 TTATTTTTA-ATTAT
1 TTATATTTATATTAT
5796489 TTTTTTGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 5 0.15
21 23 0.70
22 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATATTTATATTATATTATA
Found at i:5796510 original size:11 final size:10
Alignment explanation
Indices: 5796428--5796510 Score: 64
Period size: 11 Copynumber: 8.0 Consensus size: 10
5796418 ATTTAAAATA
5796428 TTTATTTATAT
1 TTTA-TTATAT
*
5796439 TATATTTATAT
1 TTTA-TTATAT
*
5796450 TATATTATAT
1 TTTATTATAT
5796460 TTATATTATAT
1 TT-TATTATAT
*
5796471 TATATTAT-T
1 TTTATTATAT
5796480 TTTAATTAT-T
1 TTT-ATTATAT
5796490 TTT-TTGATAT
1 TTTATT-ATAT
5796500 TTTATTCATAT
1 TTTATT-ATAT
5796511 CATATATCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
8 2 0.03
9 5 0.08
10 26 0.42
11 29 0.47
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTATTATAT
Found at i:5798194 original size:19 final size:20
Alignment explanation
Indices: 5798161--5798204 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5798151 TTAATTGATA
*
5798161 AAAATTATAAAAATAGAT-T
1 AAAATTATAAAAATAAATAT
* *
5798180 AAAATTATTATAATAAATAT
1 AAAATTATAAAAATAAATAT
5798200 AAAAT
1 AAAAT
5798205 CAAAGATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAATTATAAAAATAAATAT
Found at i:5799398 original size:2 final size:2
Alignment explanation
Indices: 5799391--5799427 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5799381 AATTACAGTA
5799391 AT AT AT 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 AT AT AT A
5799428 CACATACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5799615 original size:2 final size:2
Alignment explanation
Indices: 5799608--5799642 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5799598 GAATTTTAAT
5799608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5799643 GTATGATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5802611 original size:16 final size:15
Alignment explanation
Indices: 5802592--5802631 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
5802582 AGCACTATCT
5802592 ACACCTTTAATTAAAG
1 ACACC-TTAATTAAAG
5802608 ACACC-TAATTAAAG
1 ACACCTTAATTAAAG
5802622 ACACCATTAA
1 ACACC-TTAA
5802632 ATAATTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 14 0.64
16 8 0.36
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (15 bp):
ACACCTTAATTAAAG
Found at i:5802618 original size:14 final size:14
Alignment explanation
Indices: 5802599--5802626 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5802589 TCTACACCTT
5802599 TAATTAAAGACACC
1 TAATTAAAGACACC
5802613 TAATTAAAGACACC
1 TAATTAAAGACACC
5802627 ATTAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
TAATTAAAGACACC
Found at i:5808185 original size:44 final size:44
Alignment explanation
Indices: 5808096--5808177 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
5808086 ATTTAATTAA
* *
5808096 TTAAAATATTTAAATAAATATATAAAATAATATATTTTAAAATT
1 TTAAAATATTAAAATAAATATATAAAATAATATATATTAAAATT
5808140 TTAAAATTATTAAAATATAA-ATA-AAAATAAT-T-TATTAA
1 TTAAAA-TATTAAAATA-AATATATAAAATAATATATATTAA
5808178 TATATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 5 0.15
43 1 0.03
44 14 0.41
45 12 0.35
46 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (44 bp):
TTAAAATATTAAAATAAATATATAAAATAATATATATTAAAATT
Done.