Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 188 of 221
Found at i:55501618 original size:53 final size:53
Alignment explanation
Indices: 55501487--55501689 Score: 181
Period size: 53 Copynumber: 3.9 Consensus size: 53
55501477 TAGATTTTAG
* * *
55501487 TTAAGATAATTAGAGTTCTAATTTATTTAAGATAATTAACAATTTAAACTCATAGG
1 TTAAGATAATTAGAATTCTAATTTATTTAAGATAATTAATAATTTAAA-TCA-A-A
* *
55501543 TT-AGATAA-T--AATTCAAATTTTAGTTAAGATAATTAATAATTTAAATCAAA
1 TTAAGATAATTAGAATTCTAA-TTTATTTAAGATAATTAATAATTTAAATCAAA
* * *
55501593 TTAAGATAATTAGAATTCT-A---ATTT-AGATAATTAAGAGTTTAAATTAAA
1 TTAAGATAATTAGAATTCTAATTTATTTAAGATAATTAATAATTTAAATCAAA
* * * * * *
55501641 TTAGGATAACTAGAGTTTTAATTTATTTAAAATAATTAATAAATTAAAT
1 TTAAGATAATTAGAATTCTAATTTATTTAAGATAATTAATAATTTAAAT
55501690 TAATAGGTTA
Statistics
Matches: 119, Mismatches: 18, Indels: 23
0.74 0.11 0.14
Matches are distributed among these distances:
48 36 0.30
49 4 0.03
50 2 0.02
51 7 0.06
52 14 0.12
53 42 0.35
54 6 0.05
55 6 0.05
56 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (53 bp):
TTAAGATAATTAGAATTCTAATTTATTTAAGATAATTAATAATTTAAATCAAA
Found at i:55501624 original size:48 final size:48
Alignment explanation
Indices: 55501569--55501665 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
55501559 ATTTTAGTTA
* *
55501569 AGATAATTAATAATTTAAATCAAATTAAGATAATTAGAATTCTAATTT
1 AGATAATTAAGAATTTAAATCAAATTAAGATAACTAGAATTCTAATTT
* * * * *
55501617 AGATAATTAAGAGTTTAAATTAAATTAGGATAACTAGAGTTTTAATTT
1 AGATAATTAAGAATTTAAATCAAATTAAGATAACTAGAATTCTAATTT
55501665 A
1 A
55501666 TTTAAAATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.39
Consensus pattern (48 bp):
AGATAATTAAGAATTTAAATCAAATTAAGATAACTAGAATTCTAATTT
Found at i:55508763 original size:15 final size:16
Alignment explanation
Indices: 55508746--55508812 Score: 77
Period size: 15 Copynumber: 4.3 Consensus size: 16
55508736 GAAAACTTAA
*
55508746 AATAAATGATAATAA-
1 AATAAATAATAATAAT
**
55508761 AATAGTCTAATAATAAT
1 AATA-AATAATAATAAT
55508778 AAT-AATAATAATAAT
1 AATAAATAATAATAAT
55508793 AAT-AATAATAATAAT
1 AATAAATAATAATAAT
55508808 AATAA
1 AATAA
55508813 TAGGATATGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
15 32 0.73
16 9 0.20
17 3 0.07
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:55508774 original size:3 final size:3
Alignment explanation
Indices: 55508768--55508814 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
55508758 TAAAATAGTC
55508768 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55508815 GGATATGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55508870 original size:25 final size:25
Alignment explanation
Indices: 55508817--55508864 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
55508807 TAATAATAGG
**
55508817 ATATGAAACATTTTAAAGAATATAT
1 ATATGAAACATTCGAAAGAATATAT
55508842 ATATGAAA-ATTCGAAAGACATAT
1 ATATGAAACATTCGAAAGA-ATAT
55508865 TCATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.31
Consensus pattern (25 bp):
ATATGAAACATTCGAAAGAATATAT
Found at i:55509799 original size:4 final size:4
Alignment explanation
Indices: 55509792--55509817 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
55509782 TATAAAAAAT
55509792 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
55509818 CGAATAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:55515716 original size:15 final size:16
Alignment explanation
Indices: 55515677--55515718 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
55515667 ATTATGTCTT
55515677 CATATATTTTAATAAA
1 CATATATTTTAATAAA
* *
55515693 CAT-TTTTTTATTAAA
1 CATATATTTTAATAAA
55515708 -ATATATTTTAA
1 CATATATTTTAA
55515719 ATCTTCCTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
CATATATTTTAATAAA
Found at i:55515741 original size:28 final size:28
Alignment explanation
Indices: 55515708--55515767 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
55515698 TTTTATTAAA
55515708 ATATATTTTAAATCTTCCTACTATTCGT
1 ATATATTTTAAATCTTCCTACTATTCGT
*
55515736 ATATATTTTAAATCTTCCTGCTATTCGT
1 ATATATTTTAAATCTTCCTACTATTCGT
55515764 ATAT
1 ATAT
55515768 GACCTTATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (28 bp):
ATATATTTTAAATCTTCCTACTATTCGT
Found at i:55517191 original size:26 final size:28
Alignment explanation
Indices: 55517162--55517217 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
55517152 TAAGATTATT
*
55517162 TAAAAT-AATAGATAAA-AAGTTCAAAA
1 TAAAATAAATAGAAAAAGAAGTTCAAAA
*
55517188 T-AAATAAATAGAAAAAGAAGTTTAAAA
1 TAAAATAAATAGAAAAAGAAGTTCAAAA
55517215 TAA
1 TAA
55517218 TACACAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 10 0.40
28 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (28 bp):
TAAAATAAATAGAAAAAGAAGTTCAAAA
Found at i:55517219 original size:26 final size:26
Alignment explanation
Indices: 55517164--55517217 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
55517154 AGATTATTTA
*
55517164 AAAT-AATAGATAAAAAGTTCAAAAT
1 AAATAAATAGAAAAAAAGTTCAAAAT
*
55517189 AAATAAATAGAAAAAGAAGTTTAAAAT
1 AAATAAATAGAAAAA-AAGTTCAAAAT
55517216 AA
1 AA
55517218 TACACAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 9 0.36
27 12 0.48
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (26 bp):
AAATAAATAGAAAAAAAGTTCAAAAT
Found at i:55517327 original size:17 final size:17
Alignment explanation
Indices: 55517305--55517341 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
55517295 ATTTATACAG
**
55517305 TAATTTAAATTAAATAA
1 TAATTTAAAACAAATAA
55517322 TAATTTAAAACAAATAA
1 TAATTTAAAACAAATAA
55517339 TAA
1 TAA
55517342 AATGGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATTTAAAACAAATAA
Found at i:55519170 original size:44 final size:44
Alignment explanation
Indices: 55519110--55519421 Score: 232
Period size: 44 Copynumber: 6.8 Consensus size: 44
55519100 AATTTGCTAC
* * *
55519110 CTTCAGTCTACTCCACTGCAACTTCAGGGATATAAGACTTGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGG
* * * **
55519154 CTTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTTGTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGG
* *
55519198 CTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGC-TGTTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TGG
** *
55519242 CTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCTGCCATAATTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-----C-----TTGTGG
* * ** * * **
55519296 ATTTAATCTATTCCACTGCAATCTTCAGTGAGACAAGA-TTCGCTAT
1 CTTCAATCTGCTCCACTGCAA-CTTCAGGGAGATAAGACTT-G-TGG
* * * * *
55519342 CTTCAGTCTGCTCCGCTGCAACTTCAGGAAGATAAGGCTGGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGG
* *
55519386 CTTCAATCTGCACCACTGCAACTTCAGGAAGATAAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
55519422 GTCCACCATA
Statistics
Matches: 208, Mismatches: 44, Indels: 32
0.73 0.15 0.11
Matches are distributed among these distances:
43 2 0.01
44 139 0.67
45 14 0.07
46 18 0.09
49 1 0.00
54 19 0.09
55 15 0.07
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGG
Found at i:55519455 original size:144 final size:144
Alignment explanation
Indices: 55519166--55519569 Score: 569
Period size: 144 Copynumber: 2.8 Consensus size: 144
55519156 TCAATCTGCC
* * * ** * *
55519166 CCACTGCAA-CTTCAGGGGGATAAGATTTG-TATCTTCAACCTGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAATCTTCAGGGAGACAAGATTCGCTATCTTCAGTCTGCTCCGCTGCAACTTCAGGAAG
* **
55519229 ATAAGGCTGTTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCTGCCATAATTTGT
66 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCACCATAATTTGT
55519294 AGATTTAATCTATT
131 AGATTTAATCTATT
*
55519308 CCACTGCAATCTTCAGTGAGACAAGATTCGCTATCTTCAGTCTGCTCCGCTGCAACTTCAGGAAG
1 CCACTGCAATCTTCAGGGAGACAAGATTCGCTATCTTCAGTCTGCTCCGCTGCAACTTCAGGAAG
* * *
55519373 ATAAGGCTGGTGGCTTCAATCTGCACCACTGCAACTTCAGGAAGATAAGGTCCACCATAATTTGT
66 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCACCATAATTTGT
* * *
55519438 AGCTTTAATTTGTT
131 AGATTTAATCTATT
* * * * * *
55519452 CCACTGCAATCTTCGGGGAAACAAGATTCACTGTCTTCAGTCTGCTCCGCTGTAACTTCAGGTAG
1 CCACTGCAATCTTCAGGGAGACAAGATTCGCTATCTTCAGTCTGCTCCGCTGCAACTTCAGGAAG
* *
55519517 ATAAGGTTGGTGGCTTCAATCTGCTCCACTGTAACTTCAGAAAGATAAGATCC
66 ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCC
55519570 GCGATAATGA
Statistics
Matches: 231, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
142 9 0.04
143 16 0.07
144 206 0.89
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (144 bp):
CCACTGCAATCTTCAGGGAGACAAGATTCGCTATCTTCAGTCTGCTCCGCTGCAACTTCAGGAAG
ATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCACCATAATTTGT
AGATTTAATCTATT
Found at i:55531513 original size:45 final size:45
Alignment explanation
Indices: 55531413--55531664 Score: 427
Period size: 45 Copynumber: 5.6 Consensus size: 45
55531403 TTTGAGTATT
*
55531413 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAAGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTA-GCTACACTTA
55531459 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
55531504 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
55531549 TCTGATTAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
55531595 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
55531640 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
55531665 ATCATACGTA
Statistics
Matches: 198, Mismatches: 7, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 104 0.53
46 77 0.39
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:55531586 original size:91 final size:90
Alignment explanation
Indices: 55531413--55531664 Score: 429
Period size: 91 Copynumber: 2.8 Consensus size: 90
55531403 TTTGAGTATT
*
55531413 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTAAGGCTACACTTATCTGATCAAGTGACAAAG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCT-A-GCTACACTTATCTGATTAAGTGACAAAG
55531477 TGATAAGTGGTAGCTTAGCTACACTTA
64 TGATAAGTGGTAGCTTAGCTACACTTA
55531504 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATTAAGTGACAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATTAAGTGACAAAGTG
55531569 ATAAGTGGTAGCTTTAGCTACACTTA
66 ATAAGTGGTAGC-TTAGCTACACTTA
* *
55531595 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGA-TCAGGGAC-AAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATTAAGTGACAAAGTG
55531658 ATAAGTG
66 ATAAGTG
55531665 ATCATACGTA
Statistics
Matches: 156, Mismatches: 3, Indels: 6
0.95 0.02 0.04
Matches are distributed among these distances:
89 12 0.08
90 47 0.30
91 95 0.61
92 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (90 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATTAAGTGACAAAGTG
ATAAGTGGTAGCTTAGCTACACTTA
Found at i:55531614 original size:136 final size:134
Alignment explanation
Indices: 55531413--55531664 Score: 434
Period size: 136 Copynumber: 1.9 Consensus size: 134
55531403 TTTGAGTATT
55531413 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAAGGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAAGGCTACACTTATCTGATCAAGTGACAAAGT
* *
55531478 GATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTA
66 GATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTGGTAGCCTAGCTA
55531543 CACTTA
129 CACTTA
* *
55531549 TCTGATTAAGTGACAAAGTGATAAGTGGTAGCTTTA-GCTACACTTATCTGATCAAGTGACAAAG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TAAGGCTACACTTATCTGATCAAGTGACAAAG
55531613 TGATAAGTGGTAGCCTAGCTACACTTATCTGATCAGGGACAAGTGATAAGTG
65 TGATAAGTGGTAGCCTAGCTACACTTATCTGATCAGGGACAAGTGATAAGTG
55531665 ATCATACGTA
Statistics
Matches: 111, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
134 12 0.11
135 5 0.05
136 92 0.83
137 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (134 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAAGGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGGTAGCCTAGCTACACTTATCTGATCAGGGACAAGTGATAAGTGGTAGCCTAGCTACA
CTTA
Found at i:55532902 original size:17 final size:17
Alignment explanation
Indices: 55532880--55532918 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
55532870 GAGTTTATAC
**
55532880 AATAATTTAAATTAAAT
1 AATAATTTAAAACAAAT
55532897 AATAATTTAAAACAAAT
1 AATAATTTAAAACAAAT
55532914 AATAA
1 AATAA
55532919 AATGGAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATTTAAAACAAAT
Found at i:55533022 original size:22 final size:22
Alignment explanation
Indices: 55532997--55533090 Score: 57
Period size: 22 Copynumber: 4.2 Consensus size: 22
55532987 TGTATTGGGG
55532997 AAATTTAAAATAAATAATATTA
1 AAATTTAAAATAAATAATATTA
* *
55533019 AAATGGTTTAAAACAAATAATATATG
1 AAA---TTTAAAATAAATAATAT-TA
* * * *
55533045 TAACTT-AAATAAATAATAATG
1 AAATTTAAAATAAATAATATTA
***
55533066 CGGTTTAAAATAAATAATA-TA
1 AAATTTAAAATAAATAATATTA
55533087 AAAT
1 AAAT
55533091 GAATAACAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
21 6 0.11
22 26 0.49
23 2 0.04
25 16 0.30
26 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (22 bp):
AAATTTAAAATAAATAATATTA
Found at i:55534322 original size:14 final size:15
Alignment explanation
Indices: 55534293--55534325 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
55534283 ACTTGAACTC
*
55534293 TTTTATTTGTTTTGG
1 TTTTATTTGATTTGG
55534308 TTTTATTT-ATTTGG
1 TTTTATTTGATTTGG
55534322 TTTT
1 TTTT
55534326 GGGCCCGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (15 bp):
TTTTATTTGATTTGG
Found at i:55535935 original size:24 final size:24
Alignment explanation
Indices: 55535889--55535935 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
55535879 GACAGCCATG
*
55535889 GAAGAAAGGGAAAAGAGAGAAAAA
1 GAAGAAAGGGAAAAGAAAGAAAAA
* * *
55535913 GAAGAGAGGGTAAAGAAATAAAA
1 GAAGAAAGGGAAAAGAAAGAAAA
55535936 TAAAAAGAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (24 bp):
GAAGAAAGGGAAAAGAAAGAAAAA
Found at i:55536617 original size:22 final size:22
Alignment explanation
Indices: 55536588--55536634 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
55536578 AAAAGTTATC
55536588 TACAAATCAAATC-TCTAATAT
1 TACAAATCAAATCTTCTAATAT
* *
55536609 TACAGAATCATATCTTTTAATAT
1 TACA-AATCAAATCTTCTAATAT
55536632 TAC
1 TAC
55536635 GTTCCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (22 bp):
TACAAATCAAATCTTCTAATAT
Found at i:55539571 original size:41 final size:41
Alignment explanation
Indices: 55539514--55539736 Score: 338
Period size: 41 Copynumber: 5.4 Consensus size: 41
55539504 AGTTTTAAAA
* *
55539514 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
55539555 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
55539596 CCTAGCAGGTTAAGTGCCGGTGATCTGAATCAGGCTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* * *
55539637 CCTAGCAGGCTAAGTGCCGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
55539678 CCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
55539719 CCTAACAAGCTAAGTGCC
1 CCTAGCAGGCTAAGTGCC
55539737 AGCGAATCTG
Statistics
Matches: 163, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 163 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
Found at i:55548676 original size:22 final size:22
Alignment explanation
Indices: 55548611--55548679 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
55548601 TATGCACTAT
* *
55548611 TAAACAGAGAGCACTAAAGTGA
1 TAAACAGAGAGCACTAATGTGC
* *
55548633 TATACAGAGAGCACAAATGTGC
1 TAAACAGAGAGCACTAATGTGC
*
55548655 TAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAATGTGC
55548677 TAA
1 TAA
55548680 TAATCGGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (22 bp):
TAAACAGAGAGCACTAATGTGC
Found at i:55551756 original size:14 final size:16
Alignment explanation
Indices: 55551721--55551759 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
55551711 AAAGTATACA
55551721 TATATATACATACTTT
1 TATATATACATACTTT
**
55551737 TATATATACATGTTTT
1 TATATATACATACTTT
55551753 TATATAT
1 TATATAT
55551760 TTCCATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:55552999 original size:25 final size:25
Alignment explanation
Indices: 55552951--55553001 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
55552941 AAAATTTATG
55552951 TATAAAACAACTAAAAATAGAATCA
1 TATAAAACAACTAAAAATAGAATCA
* *
55552976 TATATAAATAACTTAAAATA-AATCA
1 TATA-AAACAACTAAAAATAGAATCA
55553001 T
1 T
55553002 TAGCAAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (25 bp):
TATAAAACAACTAAAAATAGAATCA
Found at i:55553165 original size:40 final size:40
Alignment explanation
Indices: 55553103--55553192 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 40
55553093 TTGAAATAAC
*
55553103 ATATAAAAAAATAATTTCAACTAAATAA-TATATATACAT
1 ATATAAAAAAATAATTTAAACTAAATAATTATATATACAT
*
55553142 ATATAAAAAAA-ACCATTTAAACTAAATAATTTGTATATACAT
1 ATATAAAAAAATA--ATTTAAACTAAATAA-TTATATATACAT
*
55553184 ATATTAAAA
1 ATATAAAAA
55553193 TAGGTGCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 11 0.25
40 14 0.32
42 18 0.41
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (40 bp):
ATATAAAAAAATAATTTAAACTAAATAATTATATATACAT
Found at i:55560189 original size:30 final size:30
Alignment explanation
Indices: 55560145--55560207 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
55560135 ATTTAACAAG
55560145 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
55560175 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
55560205 CAA
1 CAA
55560208 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:55560306 original size:12 final size:13
Alignment explanation
Indices: 55560289--55560317 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55560279 AAATAGGGAG
55560289 AAAATAATAA-AA
1 AAAATAATAATAA
55560301 AAAATAATAATAA
1 AAAATAATAATAA
55560314 AAAA
1 AAAA
55560318 ATATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:55564692 original size:24 final size:24
Alignment explanation
Indices: 55564664--55564717 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
55564654 TAATGTTTAT
*
55564664 ATTTTTTGTT-AATTTGATTCTTA
1 ATTTTTAGTTAAATTTGATTCTTA
* *
55564687 TTTTTTAGTTAAATTTGATTTTTA
1 ATTTTTAGTTAAATTTGATTCTTA
*
55564711 ACTTTTA
1 ATTTTTA
55564718 AAAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (24 bp):
ATTTTTAGTTAAATTTGATTCTTA
Found at i:55564697 original size:23 final size:23
Alignment explanation
Indices: 55564663--55564706 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
55564653 TTAATGTTTA
55564663 TATTTTTTGTT-AATTTGATTCT
1 TATTTTTTGTTAAATTTGATTCT
55564685 TATTTTTTAGTTAAATTTGATT
1 TATTTTTT-GTTAAATTTGATT
55564707 TTTAACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (23 bp):
TATTTTTTGTTAAATTTGATTCT
Found at i:55572070 original size:19 final size:18
Alignment explanation
Indices: 55572037--55572096 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
55572027 CGAATATAAA
55572037 TTTAAAAAT-TAAAATTTT
1 TTTAAAAATAT-AAATTTT
*
55572055 TTTAAGAAATATAAATTAAT
1 TTTAA-AAATATAAATT-TT
55572075 TTTAAAAATAT-AATTTAT
1 TTTAAAAATATAAATTT-T
55572093 TTTA
1 TTTA
55572097 CAAGTTCAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 14 0.39
19 15 0.42
20 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTAAAAATATAAATTTT
Found at i:55572094 original size:18 final size:18
Alignment explanation
Indices: 55572037--55572096 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
55572027 CGAATATAAA
*
55572037 TTTAAAAATTAAAATTT-T
1 TTTAAAAA-TATAATTTAT
*
55572055 TTTAAGAAATATAAATTAAT
1 TTTAA-AAATAT-AATTTAT
55572075 TTTAAAAATATAATTTAT
1 TTTAAAAATATAATTTAT
55572093 TTTA
1 TTTA
55572097 CAAGTTCAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 17 0.47
19 13 0.36
20 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTAAAAATATAATTTAT
Found at i:55573218 original size:17 final size:17
Alignment explanation
Indices: 55573196--55573237 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
55573186 GTTTGTATGA
55573196 TTATTTTTCAAAT-TTAT
1 TTATTTTT-AAATATTAT
*
55573213 TTATTTTTAAATATTTT
1 TTATTTTTAAATATTAT
55573230 TTATTTTT
1 TTATTTTT
55573238 TTGAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTTAAATATTAT
Found at i:55576153 original size:17 final size:17
Alignment explanation
Indices: 55576117--55576165 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
55576107 TATAAAATAA
*
55576117 AAAATAGTAGAAATTGT
1 AAAATAGTAAAAATTGT
* * *
55576134 AAATTATTAAAAATTTT
1 AAAATAGTAAAAATTGT
55576151 AAAATAGTAAAAATT
1 AAAATAGTAAAAATT
55576166 ATCGTTTCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (17 bp):
AAAATAGTAAAAATTGT
Found at i:55577434 original size:40 final size:40
Alignment explanation
Indices: 55577379--55577456 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
55577369 TTTTATATTC
* *
55577379 TTTTTTTAATTTTTTAATTTATGCT-TTTCTATTTTTAATA
1 TTTTTTTAATTTTTTAATATAT-ATATTTCTATTTTTAATA
55577419 TTTTTGTT-ATTTTTTAATATATATATTTCTATTTTTAA
1 TTTTT-TTAATTTTTTAATATATATATTTCTATTTTTAA
55577457 AAATTTTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 1 0.03
40 31 0.91
41 2 0.06
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (40 bp):
TTTTTTTAATTTTTTAATATATATATTTCTATTTTTAATA
Found at i:55578186 original size:25 final size:25
Alignment explanation
Indices: 55578153--55578205 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
55578143 ATTAAAAATA
* *
55578153 AAAAAAATTAAATTTTAATAATTTT
1 AAAAAAATTAAATATAAATAATTTT
*
55578178 AAAATAATTAAATATAAATAATTTT
1 AAAAAAATTAAATATAAATAATTTT
55578203 AAA
1 AAA
55578206 TTGAAGCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAAAATTAAATATAAATAATTTT
Found at i:55578695 original size:18 final size:19
Alignment explanation
Indices: 55578672--55578711 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
55578662 CATTTTGAAC
*
55578672 TTTAAAATAATAT-TAAAA
1 TTTAAAACAATATATAAAA
55578690 TTTAAAACAATATATAAAA
1 TTTAAAACAATATATAAAA
55578709 TTT
1 TTT
55578712 TAGCATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTAAAACAATATATAAAA
Found at i:55578856 original size:11 final size:11
Alignment explanation
Indices: 55578813--55578858 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
55578803 TCAAACAAAG
55578813 TTAAAATTTTA
1 TTAAAATTTTA
* *
55578824 TTTAAATTATAA
1 TTAAAATT-TTA
55578836 TTAAATATTTTA
1 TTAAA-ATTTTA
55578848 TTAAAATTTTA
1 TTAAAATTTTA
55578859 CTTTCAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 13 0.45
12 13 0.45
13 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAAAATTTTA
Found at i:55580957 original size:16 final size:16
Alignment explanation
Indices: 55580936--55580966 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55580926 GAGAGAAATA
55580936 AAAAATAATAATAAAG
1 AAAAATAATAATAAAG
55580952 AAAAATAATAATAAA
1 AAAAATAATAATAAA
55580967 AAGATGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATAATAATAAAG
Found at i:55586693 original size:44 final size:44
Alignment explanation
Indices: 55586599--55586711 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 44
55586589 GTTTTAATCC
* * * *
55586599 ACTCCATTGCAACTTCAAGGAGATAGGATTGGTTTTTTCTATCT
1 ACTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTCTATCA
* * *
55586643 GCTCCACTGCAACTTTAGGGAGATAGGATT-ATTTTCTTCTGTCA
1 ACTCCACTGCAACTTCAGGGAGATAGGATTGATTTT-TTCTATCA
* *
55586687 ATTCCACTGCAACTTCAGGAAGATA
1 ACTCCACTGCAACTTCAGGGAGATA
55586712 AGACTTGTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 4 0.07
44 53 0.93
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (44 bp):
ACTCCACTGCAACTTCAGGGAGATAGGATTGATTTTTTCTATCA
Found at i:55587318 original size:399 final size:400
Alignment explanation
Indices: 55586721--55587712 Score: 1250
Period size: 399 Copynumber: 2.5 Consensus size: 400
55586711 AAGACTTGTA
* * * *
55586721 TCTTCAATCTACTTCATTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTTCGCCA-
1 TCTTCGATCTACTTCA-CGCCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCAC
* * * * * *
55586785 CTGATATGGGAATACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATC
65 CAG-TATGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATC
* *
55586850 TGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTC
129 TACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTC
*
55586915 ACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAA
194 ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAA
* * *
55586980 GATCTGTTGTCTTTGATCTACCTCACGCC-AGTACATGAAGACAAGATCTACTTTTTTCGATCTA
259 GATCTGTTGTCTTTAATCTACCTCACGCCTA-TACATGAAGACAAGATCTACTATCTTCGATCTA
* * *
55587044 CTTCACCACCAGTATGGGGAGACAAGATCTG-TATATTCGATCCACTTCACTACCAATATAGGAA
323 CTTCACCACCAATATGGGAAGACAAGATCTGCTATATTCGATCCACTTCA-TACCAATACAGGAA
*
55587108 GACATGATCTG-CT
387 GACAAGATCTGTCT
* *
55587121 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
1 TCTTCGATCTACTTCACGCCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
*
55587186 AGTATGGGAAGACAAGATCTACTTTCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATCTA
66 AGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATCTA
* * * *
55587251 CTTT-TTCCGATCTACTTCACCACCAGTATTGGAAGATAATATCTGCTATCTTTTATCTACTTCA
131 CTTTCTT-CGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCA
55587315 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAG
195 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAG
* *
55587380 ATCTGTTGTCTTTAATCTACTTCACGCCTATACATGAAGACAAGATCTGCTATCTTCGATCTACT
260 ATCTGTTGTCTTTAATCTACCTCACGCCTATACATGAAGACAAGATCTACTATCTTCGATCTACT
* * * * ** * * *
55587445 TCGCCACCAATATGGGAAGATAAGATCTGCTATCTTTGATTTACTTCATGCCAGTACATGAAGAC
325 TCACCACCAATATGGGAAGACAAGATCTGCTATATTCGATCCACTTCATACCAATACAGGAAGAC
*
55587510 AAGATCTGTTT
390 AAGATCTGTCT
* * ** * *
55587521 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATTT-TT-AATCTACTTC-AC
1 TCTTCGATCTACTTC-ACGCCAGTACAGGAAGACAAGATCT-GT-TTTCTTCGATCTACTTCGCC
* *** * *
55587583 GCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTT--CGCCACTAGTATGGGAAGACAA
63 ACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTA-TAT--GAAGACAA
** * * * *** * * *
55587646 GATCTGGTATCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTA
125 GATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTA
55587710 CTT
190 CTT
55587713 TGCCACCAGT
Statistics
Matches: 512, Mismatches: 68, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
398 9 0.02
399 325 0.63
400 114 0.22
401 55 0.11
402 6 0.01
403 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (400 bp):
TCTTCGATCTACTTCACGCCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACC
AGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATCTA
CTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCAC
GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGA
TCTGTTGTCTTTAATCTACCTCACGCCTATACATGAAGACAAGATCTACTATCTTCGATCTACTT
CACCACCAATATGGGAAGACAAGATCTGCTATATTCGATCCACTTCATACCAATACAGGAAGACA
AGATCTGTCT
Found at i:55587848 original size:89 final size:89
Alignment explanation
Indices: 55586748--55587881 Score: 1244
Period size: 89 Copynumber: 12.8 Consensus size: 89
55586738 TGCCAATACA
* * * * * * *
55586748 GGAAGACAAGATCTGTTATCTTCGATCTACTT--CGCCACTGATATGGGAATACAAGATCTGGTA
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGT-ACAT--GAAGACAAGATCTGTTT
* * * **
55586811 TCTTTGATCTACTTC-ACGCCAGTACA
63 TCTTCGATCTACTTCGCCACCAGTATG
* * * * * *** * *
55586837 TGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATC
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTTTC
* * * **
55586902 TTTGATCTACTTC-ACGCCAGTACA
65 TTCGATCTACTTCGCCACCAGTATG
* * * * * *** * *
55586926 TGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTGTC
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTTTTC
* * * * **
55586991 TTTGATCTACCTC-ACGCCAGTACA
65 TTCGATCTACTTCGCCACCAGTATG
* * * * *** * *
55587015 TGAAGACAAGATCTACT-TTTTTCGATCTACTTCACCACCAGTATGGGGAGACAAGATCTG-TAT
1 GGAAGACAAGATCTGCTATCTTT-GATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTTTT
* * * * * *
55587078 ATTCGATCCACTTCACTACCAATATA
64 CTTCGATCTACTTCGCCACCAGTATG
*
55587104 GGAAGACATGATCTGCT-TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
55587168 TCGATCTACTTCGCCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* * * * *
55587192 GGAAGACAAGATCTACTTTCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATCTACTTTT-
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-GTTTTC
* * *
55587256 TCCGATCTACTTCACCACCAGTATT
65 TTCGATCTACTTCGCCACCAGTATG
* * * * *
55587281 GGAAGATAATATCTGCTATCTTTTATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
* *
55587346 TCGATCTACTCCACCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* * * * * *
55587370 GGGAGACAAGATCTGTTGTCTTTAATCTACTTCACGCCTA-TACATGAAGACAAGATCTGCTATC
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC-AGTACATGAAGACAAGATCTGTTTTC
*
55587434 TTCGATCTACTTCGCCACCAATATG
65 TTCGATCTACTTCGCCACCAGTATG
* * *
55587459 GGAAGATAAGATCTGCTATCTTTGATTTACTTCATGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
55587524 TCGATCTACTTCGCCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* * *
55587548 GGAAGACAAGATCTGGTATTTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
*
55587613 TCGATCTACTTCGCCACTAGTATG
66 TCGATCTACTTCGCCACCAGTATG
*
55587637 GGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
*
55587702 TCGATCTACTTTGCCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* *
55587726 GGAAGACAAGATCTGGTATCTTTGATCTACTTCACGTCAGTACATGAAGACAAGATCTGTTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
*
55587791 TCGATCTGCTTCGCCACCAGTATG
66 TCGATCTACTTCGCCACCAGTATG
* * * *
55587815 GGAAGACAAGATCTGGTATCTTTAATCTACTTCACGCCAGTACATGAAGATAAGATCTATTTTCT
1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
55587880 TC
66 TC
55587882 CTAGCCTACT
Statistics
Matches: 929, Mismatches: 104, Indels: 24
0.88 0.10 0.02
Matches are distributed among these distances:
87 20 0.02
88 67 0.07
89 830 0.89
90 5 0.01
91 2 0.00
92 5 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (89 bp):
GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
TCGATCTACTTCGCCACCAGTATG
Found at i:55589178 original size:14 final size:13
Alignment explanation
Indices: 55589145--55589184 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
55589135 TTAGCCTCTC
55589145 CATTTTT-ACTTTT
1 CATTTTTCA-TTTT
55589158 CATTTTTCATTTT
1 CATTTTTCATTTT
55589171 CATCTTTTCATTTT
1 CAT-TTTTCATTTT
55589185 TTCACATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:55589179 original size:21 final size:20
Alignment explanation
Indices: 55589145--55589185 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
55589135 TTAGCCTCTC
*
55589145 CATTTTTACTTTTCATTTTT
1 CATTTTCACTTTTCATTTTT
55589165 CATTTTCATCTTTTCATTTTT
1 CATTTTCA-CTTTTCATTTTT
55589186 TCACATCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (20 bp):
CATTTTCACTTTTCATTTTT
Found at i:55589188 original size:8 final size:7
Alignment explanation
Indices: 55589145--55589185 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
55589135 TTAGCCTCTC
55589145 CATTTTT
1 CATTTTT
*
55589152 -ACTTTT
1 CATTTTT
55589158 CATTTTT
1 CATTTTT
55589165 CA-TTTT
1 CATTTTT
55589171 CATCTTTT
1 CAT-TTTT
55589179 CATTTTT
1 CATTTTT
55589186 TCACATCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 11 0.38
7 11 0.38
8 7 0.24
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:55590459 original size:9 final size:9
Alignment explanation
Indices: 55590443--55590479 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55590433 TATAGTTTGA
55590443 TATTCGAAT
1 TATTCGAAT
*
55590452 TGTTCGAAT
1 TATTCGAAT
*
55590461 TATTCGAGT
1 TATTCGAAT
55590470 TATTCGAAT
1 TATTCGAAT
55590479 T
1 T
55590480 CAAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55593329 original size:19 final size:19
Alignment explanation
Indices: 55593289--55593333 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
55593279 ACCGCTTTTT
* *
55593289 ATGCATATGATGTAATGTA
1 ATGCAAATGATGAAATGTA
55593308 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGTA
55593327 ATGCAAA
1 ATGCAAA
55593334 AAGAGACGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (19 bp):
ATGCAAATGATGAAATGTA
Found at i:55595568 original size:4 final size:4
Alignment explanation
Indices: 55595559--55595596 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
55595549 ACGTATCTTG
55595559 AAAT AAAT AAAT AAGAT AAAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AA-AT -AAAT AAAT AAAT AAAT AAAT
55595597 TGATTGGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 26 0.81
5 4 0.12
6 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:55595582 original size:18 final size:17
Alignment explanation
Indices: 55595559--55595595 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
55595549 ACGTATCTTG
55595559 AAATAAATAAATAAGATA
1 AAATAAATAAATAA-ATA
55595577 AAATAAATAAATAAATA
1 AAATAAATAAATAAATA
55595594 AA
1 AA
55595596 TTGATTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAATAAATAAATAAATA
Found at i:55606641 original size:25 final size:26
Alignment explanation
Indices: 55606593--55606641 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
55606583 AGATTAAAAA
55606593 GATAAAAATGAATAAATAATAATAGT
1 GATAAAAATGAATAAATAATAATAGT
* *
55606619 GATAATAAT-AATCAATAATAATA
1 GATAAAAATGAATAAATAATAATA
55606642 CAAGATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (26 bp):
GATAAAAATGAATAAATAATAATAGT
Found at i:55615277 original size:35 final size:34
Alignment explanation
Indices: 55615214--55615286 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 34
55615204 AACAATTAAT
*
55615214 ACAATTAATAATTAATAATTTGATAATTTTACTA
1 ACAATTAATAATTAACAATTTGATAATTTTACTA
55615248 ACAATTAATATAATTAACAA-TTGATAATTTTACTA
1 ACAATT-A-ATAATTAACAATTTGATAATTTTACTA
55615283 ACAA
1 ACAA
55615287 AATGTTAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
34 6 0.17
35 20 0.56
36 10 0.28
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (34 bp):
ACAATTAATAATTAACAATTTGATAATTTTACTA
Found at i:55615284 original size:19 final size:19
Alignment explanation
Indices: 55615233--55615286 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 19
55615223 AATTAATAAT
55615233 TTGATAATTTTACTAACAA
1 TTGATAATTTTACTAACAA
* * *
55615252 -T--TAATATAATTAACAA
1 TTGATAATTTTACTAACAA
55615268 TTGATAATTTTACTAACAA
1 TTGATAATTTTACTAACAA
55615287 AATGTTAGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 1 0.04
19 12 0.46
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (19 bp):
TTGATAATTTTACTAACAA
Found at i:55615333 original size:93 final size:91
Alignment explanation
Indices: 55615198--55615387 Score: 294
Period size: 93 Copynumber: 2.1 Consensus size: 91
55615188 TGTTAGATTT
*
55615198 TGTTA-TAACAATTAATACAATTAATAATTAATAATTTGATAATTTTACTAACAATTAATATAAT
1 TGTTAGTAACAATTAATA-AATTAATAATTAATAATTTGATAATTTTACTAACAATTAATACAAT
*
55615262 TAACAATTGATAATTTTACTAACAAAA
65 TAACAATTAATAATTTTACTAACAAAA
* *
55615289 TGTTAGTAACAATTAAT-AATTAATAATTTGATATAATTTTATAATTTTAGTAACAATTAATACA
1 TGTTAGTAACAATTAATAAATTAATAA-TT-A-ATAATTTGATAATTTTACTAACAATTAATACA
55615353 ATTAACAATTAATAATTTTACTAACAAAA
63 ATTAACAATTAATAATTTTACTAACAAAA
55615382 TGTTAG
1 TGTTAG
55615388 ATTTTACAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
90 9 0.10
91 7 0.08
92 12 0.13
93 63 0.69
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (91 bp):
TGTTAGTAACAATTAATAAATTAATAATTAATAATTTGATAATTTTACTAACAATTAATACAATT
AACAATTAATAATTTTACTAACAAAA
Found at i:55615453 original size:16 final size:16
Alignment explanation
Indices: 55615432--55615472 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
55615422 AATTTGATAC
*
55615432 AATTTTGATAACAATT
1 AATTTTAATAACAATT
55615448 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
55615464 AGTTTTAAT
1 AATTTTAAT
55615473 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:55615474 original size:22 final size:23
Alignment explanation
Indices: 55615446--55615507 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
55615436 TTGATAACAA
* *
55615446 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
55615468 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
*
55615491 TTTATTTTAAATAAAAA
1 TTAATTTT-AATAAAAA
55615508 ACAGGCTGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 16 0.46
23 11 0.31
24 8 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:55615972 original size:3 final size:3
Alignment explanation
Indices: 55615964--55616033 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
55615954 AGTCATTCTG
55615964 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
55616012 TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
55616034 CATCATCATC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:55616140 original size:28 final size:26
Alignment explanation
Indices: 55616097--55616168 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
55616087 CATTTTTGCA
* *
55616097 ATATATATAC-ATATTTTTTATAATTT
1 ATATATATACTACATTTTTT-TAAATT
55616123 ATATATATACGTACATTTTTTTAAATT
1 ATATATATAC-TACATTTTTTTAAATT
*
55616150 AT-TATA-AATACATTTTTTT
1 ATATATATACTACATTTTTTT
55616169 GCATATTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 11 0.27
25 1 0.02
26 14 0.34
27 7 0.17
28 8 0.20
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.56
Consensus pattern (26 bp):
ATATATATACTACATTTTTTTAAATT
Found at i:55616155 original size:30 final size:28
Alignment explanation
Indices: 55616097--55616168 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 28
55616087 CATTTTTGCA
55616097 ATATATATACATATTTTTTATAATTTAT
1 ATATATATACATATTTTTTATAATTTAT
55616125 ATATATACGTACAT-TTTTTTA-AA-TTAT
1 ATATATA--TACATATTTTTTATAATTTAT
*
55616152 -TATAAATACAT-TTTTTT
1 ATATATATACATATTTTTT
55616169 GCATATTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 11 0.27
26 5 0.12
27 4 0.10
28 9 0.22
29 7 0.17
30 5 0.12
ACGTcount: A:0.38, C:0.06, G:0.01, T:0.56
Consensus pattern (28 bp):
ATATATATACATATTTTTTATAATTTAT
Found at i:55619818 original size:25 final size:24
Alignment explanation
Indices: 55619774--55619861 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 24
55619764 CGAGCATGTA
*
55619774 AACGAGAAGCTC-TTTCGAGCCATAT
1 AACGAGAAGCTCATGT-GAGCCA-AT
*
55619799 AACGAGAAGCTCATGTGAGCTAAGT
1 AACGAGAAGCTCATGTGAGCCAA-T
* * *
55619824 AACGGGAAGCTCTTGCGAGCCAAAT
1 AACGAGAAGCTCATGTGAGCC-AAT
* *
55619849 ATCAAGAAGCTCA
1 AACGAGAAGCTCA
55619862 AGAGAGTTGT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
24 1 0.02
25 45 0.90
26 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (24 bp):
AACGAGAAGCTCATGTGAGCCAAT
Found at i:55622194 original size:11 final size:10
Alignment explanation
Indices: 55622177--55622214 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
55622167 AGAAATCCAA
55622177 AAAGAAACAG
1 AAAGAAACAG
55622187 AAACGAAACAG
1 AAA-GAAACAG
55622198 AAAGAAA-AGG
1 AAAGAAACA-G
55622208 AAAGAAA
1 AAAGAAA
55622215 AATATCTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 15 0.58
11 10 0.38
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAGAAACAG
Found at i:55627591 original size:72 final size:72
Alignment explanation
Indices: 55627473--55627716 Score: 337
Period size: 72 Copynumber: 3.4 Consensus size: 72
55627463 AAAATAAGCA
* * * * * *
55627473 TTAGCGGCGTTTTTGAGAAAGCGCTGCAAAAAACCTAAGCCTAACGACTTC-GTTTCCCGAGCTT
1 TTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGAC-ACGGTTTTCTGAGCTT
55627537 TCGGGGAT
65 TCGGGGAT
* * * * * *
55627545 TTAGCGGCGTTTCTGAGAAAGTGCCACAAAAAACATAAGCCCAACGACGCTGTTTTGTGAGCTTT
1 TTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACACGGTTTTCTGAGCTTT
55627610 CGGGGAT
66 CGGGGAT
55627617 TTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACGGTTTTCTGAGCTT
1 TTAGCGGCGTTTCTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACACGGTTTTCTGAGCTT
55627682 TCGGGGAT
65 TCGGGGAT
* *
55627690 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCGTTTCTGAGAAAGCGCCGC
55627717 TAATGCTCAG
Statistics
Matches: 152, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
71 1 0.01
72 85 0.56
73 66 0.43
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (72 bp):
TTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACACGGTTTTCTGAGCTTT
CGGGGAT
Found at i:55627792 original size:119 final size:114
Alignment explanation
Indices: 55627616--55627987 Score: 539
Period size: 119 Copynumber: 3.2 Consensus size: 114
55627606 CTTTCGGGGA
* * * * *
55627616 TTTAGCGGCGTTTCTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACGGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
*
55627681 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
66 TTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
55627730 TTTCGCGGCGTTTTTGGGAAAGCGCCACAAAAAAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCAC-----AAAAAAACCTAAGCCCAACGACGCCGTTTTCT
55627795 GAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
61 GAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
* * * **
55627849 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAGAAAAACCTAAGCCCAACAACGCCGTTTTCTGAATT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
55627914 TTCGAGGATTTAGCAG-TTTTTTAAGAAAGCGCCGCTAATGCTCAGCGC
66 TTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
55627962 TTTAACGGCGTTTTTGGGAAAGCGCC
1 TTTAGCGGCGTTTTTGGGAAAGCGCC
55627988 GCTAAAAATA
Statistics
Matches: 235, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
113 55 0.23
114 71 0.30
119 109 0.46
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:55628257 original size:15 final size:15
Alignment explanation
Indices: 55628237--55628266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55628227 ATATTTTAAT
55628237 GTTTAGGGAGTATGG
1 GTTTAGGGAGTATGG
*
55628252 GTTTAGGGATTATGG
1 GTTTAGGGAGTATGG
55628267 ATTAGGGGTT
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:0.20, C:0.00, G:0.43, T:0.37
Consensus pattern (15 bp):
GTTTAGGGAGTATGG
Found at i:55628589 original size:21 final size:20
Alignment explanation
Indices: 55628555--55628595 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
55628545 TTATGAATTA
*
55628555 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
55628575 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
55628596 AGGGGGTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:55628595 original size:29 final size:29
Alignment explanation
Indices: 55628566--55628648 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
55628556 GGATTATGGT
55628566 TTAAGGGTT-GGGATTTAAGGTTTAGGGG
1 TTAAGGGTTAGGGATTTAAGGTTTAGGGG
* * *
55628594 TTAGGGGGTTAGGG-TTT-AGATGTTAGTGG
1 TTA-AGGGTTAGGGATTTAAGGT-TTAGGGG
*
55628623 TTAAGAGTTAGGGATTTAAGGTTTAG
1 TTAAGGGTTAGGGATTTAAGGTTTAG
55628649 AGATTCAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 14 0.32
29 24 0.55
30 6 0.14
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (29 bp):
TTAAGGGTTAGGGATTTAAGGTTTAGGGG
Found at i:55629666 original size:254 final size:243
Alignment explanation
Indices: 55629209--55629780 Score: 797
Period size: 254 Copynumber: 2.3 Consensus size: 243
55629199 TTATTATAAA
* * **
55629209 AAATCAATTTAT-AAAAAACAAAATAAAAAAATTTTAGCATAGCAAAACATCGTCATTTTGTTCA
1 AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
*
55629273 AAATGAAATAGAGGCGTTTTTGATATAAACGCCGCAAAAAATAAATCAATTAATAAAAACCAAAA
66 AAATGAAATAGAGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCAAAA
* ** * *
55629338 TAGCAAAACGATGTCATTTTGTTCAAAATGAAAACTTTTTTGTGGAGTTTTTATTAAAAACGCCT
131 TAGCAAAACGACGTCATTTTGTTCAAAATGAAAAAATTTTTGTGGAGTTTTTATGAAAAACGCCA
* *
55629403 CCAAAGATAAGCAATAGTGGC-GTTTTTATAAAAAGCGCCGCAAAAAAT
196 CAAAAGATAAGCAATAGCGGCAGTTTTTATAAAAA-CGCCGCAAAAAAT
*
55629451 AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGTAAAACGGCGTCATTTTGTTCA
1 AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
* * *
55629516 AAATGAAATAGCGGCGTCTTTATCGCGCTTTTGATAAAAACGCCGCAAATAATAAATCAATTATT
66 AAATGAAATAGAGGCG------T-----TTTTGATAAAAACGCCGCAAAAAATAAATCAATTAAT
* *
55629581 AAAAACCAAAATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAAAATTTTTGTGGCGTTTTTAT
120 AAAAACCAAAATAGCAAAACGACGTCATTTTGTTCAAAATGAAAAAATTTTTGTGGAGTTTTTAT
* *
55629646 GGAAAACGCCACAAAAGATAAGCAATAGCGGCATTTTTTATAAAAACGCCGCAAAAAAT
185 GAAAAACGCCACAAAAGATAAGCAATAGCGGCAGTTTTTATAAAAACGCCGCAAAAAAT
* * * *
55629705 AAAACAATTTATAAAAAAATAAAATAAAAAATTTTTAACATAACAAAACGGTGTCATTTTGTTCA
1 AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
*
55629770 AAATGATATAG
66 AAATGAAATAG
55629781 GAATATAATT
Statistics
Matches: 291, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
242 12 0.04
243 62 0.21
249 1 0.00
254 204 0.70
255 12 0.04
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (243 bp):
AAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
AAATGAAATAGAGGCGTTTTTGATAAAAACGCCGCAAAAAATAAATCAATTAATAAAAACCAAAA
TAGCAAAACGACGTCATTTTGTTCAAAATGAAAAAATTTTTGTGGAGTTTTTATGAAAAACGCCA
CAAAAGATAAGCAATAGCGGCAGTTTTTATAAAAACGCCGCAAAAAAT
Found at i:55629752 original size:24 final size:25
Alignment explanation
Indices: 55629700--55629752 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
55629690 AACGCCGCAA
*
55629700 AAAATAAAACAATTTATAAAAAAAT
1 AAAATAAAACAATTTATAAAAAAAC
* * *
55629725 AAAATAAAA-AATTTTTAACATAAC
1 AAAATAAAACAATTTATAAAAAAAC
55629749 AAAA
1 AAAA
55629753 CGGTGTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAATAAAACAATTTATAAAAAAAC
Found at i:55632346 original size:95 final size:94
Alignment explanation
Indices: 55632177--55632365 Score: 297
Period size: 95 Copynumber: 2.0 Consensus size: 94
55632167 TTAGCCTGAG
55632177 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
* *
55632242 CCATTCTTGCAGTAGGTACCTTTTTCTCA
66 CCATTCTTGCAGCACGTACCTTTTTCTCA
** * **
55632271 TGCTTCCTCTTTCATTGCCTCTGTGCGCTTCCCTTTTTTGTTTTTGAAGTTCTAGAGTTGGTGAT
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCC-TTTTTGTTTTTGAAGTTCTAGAGCTGGCAAT
*
55632336 ACCATTCTTGCAGCACGTACTTTTTTCTCA
65 ACCATTCTTGCAGCACGTACCTTTTTCTCA
55632366 ATTATTATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 31 0.36
95 55 0.64
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.44
Consensus pattern (94 bp):
TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
CCATTCTTGCAGCACGTACCTTTTTCTCA
Found at i:55633827 original size:43 final size:43
Alignment explanation
Indices: 55633748--55633953 Score: 247
Period size: 43 Copynumber: 4.8 Consensus size: 43
55633738 TTTTTATGAT
* *
55633748 AAGCGTCGCTAAAGG-CTTGTTCTATAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* * * *
55633790 AATCGCCGCTAAAGGTCTTGAGCTATAGCGGCATTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* ** * *
55633833 AGGCGTTGCTAAAGGCCTTGATCTATAGCGGCGTTTGT-GCAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
* *
55633875 AAGCACCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGT-GGAAA
* *
55633919 AA-CGCCGCTAAAGGTCATGATTTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
55633954 ATTTCTAAAA
Statistics
Matches: 137, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
42 48 0.35
43 84 0.61
44 5 0.04
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGAAA
Found at i:55633901 original size:85 final size:85
Alignment explanation
Indices: 55633748--55633953 Score: 270
Period size: 85 Copynumber: 2.4 Consensus size: 85
55633738 TTTTTATGAT
* * * *
55633748 AAGCGTCGCTAAAGGCTTGTTCTATAGCGGCGTTTGTGGAAAAATCGCCGCTAAAGGTCTTGAGC
1 AAGCGTCGCTAAAGGCTTGATCTATAGCGGCGTTTGTGGAAAAAGCACCGCTAAAGGTCCTGAGC
55633813 TATAGCGGCATTTGTGGGAA
66 TATAGCGGCATTTGTGGGAA
* * * *
55633833 AGGCGTTGCTAAAGGCCTTGATCTATAGCGGCGTTTGT-GCAAAAGCACCGCTAAAGGTCCTGAT
1 AAGCGTCGCTAAAGG-CTTGATCTATAGCGGCGTTTGTGGAAAAAGCACCGCTAAAGGTCCTGAG
*
55633897 CTATAGCGGCGTTTGTGGGAA
65 CTATAGCGGCATTTGTGGGAA
* * * *
55633918 AAACGCCGCTAAAGGTCATGATTTATAGCGGCGTTT
1 AAGCGTCGCTAAAGG-CTTGATCTATAGCGGCGTTT
55633954 ATTTCTAAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 83 0.80
86 21 0.20
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (85 bp):
AAGCGTCGCTAAAGGCTTGATCTATAGCGGCGTTTGTGGAAAAAGCACCGCTAAAGGTCCTGAGC
TATAGCGGCATTTGTGGGAA
Found at i:55639772 original size:23 final size:23
Alignment explanation
Indices: 55639745--55639792 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
55639735 CACCAAAATC
55639745 TATTGGATTTGAATATTTAATAT
1 TATTGGATTTGAATATTTAATAT
55639768 TATTGGATTTGAATATTTAATAT
1 TATTGGATTTGAATATTTAATAT
55639791 TA
1 TA
55639793 AAGAGTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (23 bp):
TATTGGATTTGAATATTTAATAT
Found at i:55644826 original size:41 final size:41
Alignment explanation
Indices: 55644769--55644874 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
55644759 AATGAGATAA
* *
55644769 TTCAGACTTTACGTCTAGCAGACTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGACTTGACGCCGGTGAAATAT
*
55644810 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGACTTGACGCCGGTGAAATAT
*
55644851 TTCGGACTTTACGTCTAGCAGACT
1 TTCAGACTTTACGTCTAGCAGACT
55644875 AATTGCCAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGACTTGACGCCGGTGAAATAT
Found at i:55647287 original size:25 final size:25
Alignment explanation
Indices: 55647248--55647486 Score: 221
Period size: 25 Copynumber: 9.6 Consensus size: 25
55647238 ATAGTAAATA
*
55647248 CGAATTCTCTAGAAAGCCTTTGTGG
1 CGAATTCTCTGGAAAGCCTTTGTGG
* * *
55647273 CGAATTCTATGGAAAACCTTTGTGA
1 CGAATTCTCTGGAAAGCCTTTGTGG
** * * * * *
55647298 TAAATT-TTTTGAAGAACCTTTAT-A
1 CGAATTCTCTGGAA-AGCCTTTGTGG
* * *
55647322 AGAATTCTCTGAAAAGCCTTTGTGA
1 CGAATTCTCTGGAAAGCCTTTGTGG
55647347 CGAATTCTCTGGAAAGCCTTTGTGG
1 CGAATTCTCTGGAAAGCCTTTGTGG
* * * *
55647372 CAAATCCTCTGGAAATCCTTTATGG
1 CGAATTCTCTGGAAAGCCTTTGTGG
* *
55647397 CGAATTCTTTAGAAAGCCTTTGTGG
1 CGAATTCTCTGGAAAGCCTTTGTGG
* * *
55647422 TGAATTCTTTGGAAAGCTTTTGTGG
1 CGAATTCTCTGGAAAGCCTTTGTGG
* * *
55647447 TGAATTCTTTGGAAAGCTTTTGTGG
1 CGAATTCTCTGGAAAGCCTTTGTGG
55647472 CGAATTCTCTGGAAA
1 CGAATTCTCTGGAAA
55647487 ATGCGTAGAG
Statistics
Matches: 177, Mismatches: 34, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
24 17 0.10
25 160 0.90
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (25 bp):
CGAATTCTCTGGAAAGCCTTTGTGG
Found at i:55647392 original size:74 final size:75
Alignment explanation
Indices: 55647249--55647446 Score: 222
Period size: 74 Copynumber: 2.7 Consensus size: 75
55647239 TAGTAAATAC
* ** * * *
55647249 GAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAACCTTTGTGATAAATTTTTTGAAGAA
1 GAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGGCAAATCTCTGGAAGAA
55647314 CCTTTAT-AA
66 CCTTTATGAA
* *
55647323 GAATTCTCT-GAAAAGCCTTTGTGACGAATTCTCTGGAAAGCCTTTGTGGCAAATCCTCTGGAA-
1 GAATTCTCTAG-AAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGGCAAAT-CTCTGGAAG
* **
55647386 ATCCTTTATGGC
64 AACCTTTATGAA
* * * *
55647398 GAATTCTTTAGAAAGCCTTTGTGGTGAATTCTTTGGAAAGCTTTTGTGG
1 GAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGG
55647447 TGAATTCTTT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
73 1 0.01
74 55 0.53
75 47 0.45
76 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (75 bp):
GAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGGCAAATCTCTGGAAGAA
CCTTTATGAA
Found at i:55647428 original size:75 final size:74
Alignment explanation
Indices: 55647248--55647486 Score: 248
Period size: 75 Copynumber: 3.2 Consensus size: 74
55647238 ATAGTAAATA
* * * *
55647248 CGAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAACCTTTGTGATAAATTTTTTGAAGA
1 CGAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGGTAAATCTTTGGAA-A
*
55647313 ACCTTTAT-A
65 ACCTTTATGG
* * * * *
55647322 AGAATTCTCT-GAAAAGCCTTTGTGACGAATTCTCTGGAAAGCCTTTGTGGCAAATCCTCTGGAA
1 CGAATTCTCTAG-AAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGGTAAAT-CTTTGGAA
*
55647386 ATCCTTTATGG
64 AACCTTTATGG
* * * * *
55647397 CGAATTCTTTAGAAAGCCTTTGTGGTGAATTCTTTGGAAAGCTTTTGTGGTGAATTCTTTGGAAA
1 CGAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGGT-AAATCTTTGGAAA
* * *
55647462 GCTTTTGTGG
65 ACCTTTATGG
*
55647472 CGAATTCTCTGGAAA
1 CGAATTCTCTAGAAA
55647487 ATGCGTAGAG
Statistics
Matches: 135, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
73 1 0.01
74 55 0.41
75 75 0.56
76 4 0.03
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (74 bp):
CGAATTCTCTAGAAAGCCTTTGTGGCGAATTCTATGGAAAGCCTTTGTGGTAAATCTTTGGAAAA
CCTTTATGG
Found at i:55647500 original size:50 final size:49
Alignment explanation
Indices: 55647348--55647504 Score: 156
Period size: 50 Copynumber: 3.1 Consensus size: 49
55647338 CCTTTGTGAC
* * * * *
55647348 GAATTCTCTGGAAAGCCTTTGTGGCAAATCCTCTGGAAATCCTTTATGGC
1 GAATTCTTTGGAAAGCCTTTGTGGCGAATTCTCTGGAAATGCTTTA-GGT
* * * *
55647398 GAATTCTTTAGAAAGCCTTTGTGGTGAATTCTTTGGAAA-GCTTTTGTGGT
1 GAATTCTTTGGAAAGCCTTTGTGGCGAATTCTCTGGAAATGC-TTT-AGGT
* *
55647448 GAATTCTTTGGAAAGCTTTTGTGGCGAATTCTCTGGAAAATGC-GTAGAGT
1 GAATTCTTTGGAAAGCCTTTGTGGCGAATTCTCTGG-AAATGCTTTAG-GT
55647498 GAATTCT
1 GAATTCT
55647505 GTAATGACCA
Statistics
Matches: 87, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
49 2 0.02
50 80 0.92
51 3 0.03
52 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (49 bp):
GAATTCTTTGGAAAGCCTTTGTGGCGAATTCTCTGGAAATGCTTTAGGT
Found at i:55656085 original size:126 final size:126
Alignment explanation
Indices: 55655766--55656237 Score: 810
Period size: 125 Copynumber: 3.8 Consensus size: 126
55655756 TAATTTCGAG
* *
55655766 TTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAACAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
55655831 AAATCACGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTA-TTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
*
55655891 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAAGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * *
55655956 AAATCGCAG-CCTCATAGACGCGCTTTTGCTACAGTAGGTCACGGAATAAATAATTATTTTT
66 AAATCGC-GCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
55656017 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
55656082 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAAGTAAGAAAT-ATT-TTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
*
55656141 TTGACGTTTCTGAGCAAAAAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
55656206 AAATCGCGCCCTCGTGGACGCGC-TTTGCTACA
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACA
55656238 ATAGCATGTT
Statistics
Matches: 330, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
123 9 0.03
124 92 0.28
125 116 0.35
126 113 0.34
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (126 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
Found at i:55658793 original size:29 final size:29
Alignment explanation
Indices: 55658751--55659060 Score: 228
Period size: 29 Copynumber: 10.9 Consensus size: 29
55658741 ACAACATAGC
55658751 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
55658780 ATTAAATTAGGTTAGGGTTAGGGTTTTT-
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
*
55658808 A--AAATTA----AGGTTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
* *
55658831 AGTT-AA--AGTTTAGGGTT---TTTATTTAA
1 A-TTAAATTAGGTTAGGGTTAGGGTT-TTT-A
* *
55658857 ATT--A-G--GTTAGGGTTAAGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
55658881 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
55658910 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
* * *
55658939 ATTAAATTAGGTTAGGGTT--TGTATTAA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
** ** *
55658966 ATTAGGTTAGGGTTTTTAAAGTTAAGGTTTAGGGTTTTTA
1 ATTAAATTA-GG---TTAGGGTTAGGGTTT-------TTA
55659006 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
55659035 ATTAAATTAGGTTAGGGTTTAGGGTT
1 ATTAAATTAGGTTAGGG-TTAGGGTT
55659061 AAATTAGGTT
Statistics
Matches: 226, Mismatches: 22, Indels: 65
0.72 0.07 0.21
Matches are distributed among these distances:
22 14 0.06
23 10 0.04
24 7 0.03
25 10 0.04
26 11 0.05
27 17 0.08
28 3 0.01
29 114 0.50
30 8 0.04
31 6 0.03
33 3 0.01
36 12 0.05
39 2 0.01
40 9 0.04
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (29 bp):
ATTAAATTAGGTTAGGGTTAGGGTTTTTA
Found at i:55658823 original size:22 final size:22
Alignment explanation
Indices: 55658797--55658851 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
55658787 TAGGTTAGGG
*
55658797 TTAGGGTTTTTAAAATTAAGGT
1 TTAGGGTTTTTAAAATTAAAGT
*
55658819 TTAGGGTTTTT-AAGTTAAAGT
1 TTAGGGTTTTTAAAATTAAAGT
55658840 TTAGGGTTTTTA
1 TTAGGGTTTTTA
55658852 TTTAAATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (22 bp):
TTAGGGTTTTTAAAATTAAAGT
Found at i:55658883 original size:101 final size:104
Alignment explanation
Indices: 55658751--55659076 Score: 337
Period size: 96 Copynumber: 3.2 Consensus size: 104
55658741 ACAACATAGC
*
55658751 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT-A-AAATT
1 ATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATAAATT
* * *
55658814 A-AGGTTTAGGGTTTTTAAGTT-AA-AGTTTAGGGTTTTT
66 AGAGGGTTAGGGTTTTTAA-TTAAATAGGTTAGGGTTTGT
55658851 ATTTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAA
1 A-TTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TAAA
55658916 TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTGT
64 TTA-G--AGGGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTTTGT
* *
55658961 ATTAAATTAGGTTA--G----GGTTTTT-A--AAGTTA----AGGTTTAGGGTTTTTAATTAAAT
1 ATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAA-TAAAT
*
55659013 TAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
65 TA-G--AGGGTTAGGGTTTTTAATTAAA-TAGGTTAGGGTTT-GT
*
55659058 GTTAAATTAGGTTAGGGTT
1 ATTAAATTAGGTTAGGGTT
55659077 TTTATTACAT
Statistics
Matches: 202, Mismatches: 8, Indels: 31
0.84 0.03 0.13
Matches are distributed among these distances:
96 64 0.32
97 14 0.07
99 1 0.00
100 6 0.03
101 55 0.27
102 2 0.01
103 7 0.03
104 6 0.03
107 3 0.01
108 18 0.09
109 13 0.06
110 13 0.06
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (104 bp):
ATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATAAATT
AGAGGGTTAGGGTTTTTAATTAAATAGGTTAGGGTTTGT
Found at i:55658994 original size:130 final size:122
Alignment explanation
Indices: 55658751--55659060 Score: 412
Period size: 130 Copynumber: 2.4 Consensus size: 122
55658741 ACAACATAGC
55658751 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAAATTAA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAAATTAA
* *
55658816 GGTTTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTTATTTAAATTAGGTTAGGGTTAAGGTTTTTA
66 GGTTTAGGGTTTTTAAATT-AAGGTTAGGGTTTTTA--TAAATTAGG-T----TTAAGGTTTTTA
55658881 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAAT
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTT-A--AAAT
* *
55658946 T-AGG-TTAGGGTTTGTATTAAATT-AGGTTAGGGTTTTTA-AAGTTAAGGTTTAGGGTTTTTA
63 TAAGGTTTAGGG-TT-T-TTAAATTAAGGTTAGGGTTTTTATAAATT-AGGTTTAAGGTTTTTA
55659006 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTT
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT
55659061 AAATTAGGTT
Statistics
Matches: 168, Mismatches: 4, Indels: 20
0.88 0.02 0.10
Matches are distributed among these distances:
125 57 0.34
126 8 0.05
129 5 0.03
130 60 0.36
131 7 0.04
132 19 0.11
133 6 0.04
134 6 0.04
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (122 bp):
ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAAATTAA
GGTTTAGGGTTTTTAAATTAAGGTTAGGGTTTTTATAAATTAGGTTTAAGGTTTTTA
Found at i:55659012 original size:96 final size:97
Alignment explanation
Indices: 55658898--55659080 Score: 341
Period size: 96 Copynumber: 1.9 Consensus size: 97
55658888 TAGGTTAGGG
*
55658898 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT-GTA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGA
55658962 TTAAATTAGGTTAGGGTTTTTAAAGTTAAGGT
66 TTAAATTAGGTTAGGGTTTTTAAAGTTAAGGT
*
55658994 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGA
55659059 TTAAATTAGGTTAGGGTTTTTA
66 TTAAATTAGGTTAGGGTTTTTA
55659081 TTACATCAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 61 0.73
97 23 0.27
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (97 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGA
TTAAATTAGGTTAGGGTTTTTAAAGTTAAGGT
Found at i:55659035 original size:154 final size:159
Alignment explanation
Indices: 55658751--55659060 Score: 515
Period size: 154 Copynumber: 2.0 Consensus size: 159
55658741 ACAACATAGC
*
55658751 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAAAATTAA
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA-GGTTATTAAAATTAA
*
55658816 GGTTTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTTATTTAAATTAGGTTAGGGTTAAGGTTTTTA
65 GGTTTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTA
55658881 ATTAAATTAGGTTAGGG-TTAGGGTTTTTA
130 ATTAAATTAGGTTAGGGTTTAGGGTTTTTA
*
55658910 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTT-TG-TATT-AAATT-AG
1 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGTTATTAAAATTAAG
* *
55658971 G-TTAGGGTTTTTAAAGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTA
66 GTTTAGGGTTTTT-AAGTTAAAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTA
55659035 ATTAAATTAGGTTAGGGTTTAGGGTT
130 ATTAAATTAGGTTAGGGTTTAGGGTT
55659061 AAATTAGGTT
Statistics
Matches: 144, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
153 11 0.08
154 68 0.47
155 13 0.09
156 3 0.02
157 1 0.01
159 48 0.33
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (159 bp):
ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGTTATTAAAATTAAG
GTTTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAA
TTAAATTAGGTTAGGGTTTAGGGTTTTTA
Found at i:55659104 original size:25 final size:25
Alignment explanation
Indices: 55659076--55659213 Score: 164
Period size: 25 Copynumber: 5.7 Consensus size: 25
55659066 AGGTTAGGGT
55659076 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
55659101 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * *
55659124 --AAATAAC-TCGAAA-AAATTTCTA
1 TTTTATTACATC-AAATAAACTTCTA
55659146 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
55659171 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
55659196 TTTTATTCCATCAAATAA
1 TTTTATTACATCAAATAA
55659214 TATTAAAATA
Statistics
Matches: 96, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
20 2 0.02
21 11 0.11
22 2 0.02
23 2 0.02
24 11 0.11
25 68 0.71
ACGTcount: A:0.43, C:0.15, G:0.01, T:0.41
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:55659160 original size:45 final size:44
Alignment explanation
Indices: 55659086--55659267 Score: 195
Period size: 44 Copynumber: 4.0 Consensus size: 44
55659076 TTTTATTACA
*
55659086 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAA-AAATTTCTATTTTATTACATCAAATAATATCAAAATAAC
** *
55659131 TCGAAAAAATTTCTATTTTATTACATCAAATAA-ACTTCTATTTTATTAC
1 TC-AAAAAATTTCTATTTTATTACATCAAATAATA--TC-A--AAATAAC
* * *
55659180 ATCAAATAAACTTCTATTTTATTCCATCAAATAATATTAAAATAAC
1 -TCAAA-AAATTTCTATTTTATTACATCAAATAATATCAAAATAAC
* *
55659226 TCAAAAAATTTCTATTTTTTTACATAAAATAATATCAAAATA
1 TCAAAAAATTTCTATTTTATTACATCAAATAATATCAAAATA
55659268 TTCAAAATAT
Statistics
Matches: 113, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
44 33 0.29
45 33 0.29
46 9 0.08
47 1 0.01
48 1 0.01
49 8 0.07
50 27 0.24
51 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.40
Consensus pattern (44 bp):
TCAAAAAATTTCTATTTTATTACATCAAATAATATCAAAATAAC
Found at i:55660386 original size:7 final size:7
Alignment explanation
Indices: 55660376--55660400 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55660366 TTATATACAT
55660376 AATACTA
1 AATACTA
55660383 AATACTA
1 AATACTA
55660390 AATACTA
1 AATACTA
55660397 AATA
1 AATA
55660401 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:55661627 original size:12 final size:11
Alignment explanation
Indices: 55661592--55661629 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
55661582 GAATTTTGGA
55661592 AGGAAATTGAG
1 AGGAAATTGAG
55661603 AGGAAATTGAG
1 AGGAAATTGAG
55661614 AGGAAATATGAG
1 AGGAAAT-TGAG
55661626 AGGA
1 AGGA
55661630 TTTGTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.16
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:55665147 original size:9 final size:9
Alignment explanation
Indices: 55665133--55665307 Score: 88
Period size: 9 Copynumber: 18.7 Consensus size: 9
55665123 TTAAATCGAC
55665133 ATAAAAATT
1 ATAAAAATT
*
55665142 ATAAAAA-A
1 ATAAAAATT
*
55665150 ATAATAATTT
1 ATAA-AAATT
*
55665160 ATAAATATT
1 ATAAAAATT
* *
55665169 GTAGAAA-T
1 ATAAAAATT
*
55665177 ATAACAATT
1 ATAAAAATT
*
55665186 CTAATAAATT
1 ATAA-AAATT
55665196 AT-AAAATT
1 ATAAAAATT
55665204 AATAAAACATAT
1 -ATAAAA-AT-T
*
55665216 TTAAAATATT
1 ATAAAA-ATT
**
55665226 -TGAAATTTT
1 AT-AAAAATT
55665235 ATAAAAATT
1 ATAAAAATT
* *
55665244 CTTAAAAGCTT
1 -ATAAAA-ATT
55665255 ATAAAAATT
1 ATAAAAATT
*
55665264 ATAAAAAAT
1 ATAAAAATT
*
55665273 ATTAAAATT
1 ATAAAAATT
*
55665282 GATACAAATTT
1 -ATA-AAAATT
55665293 ATAAAAATT
1 ATAAAAATT
55665302 ATAAAA
1 ATAAAA
55665308 GAACATAAAA
Statistics
Matches: 122, Mismatches: 30, Indels: 28
0.68 0.17 0.16
Matches are distributed among these distances:
8 14 0.11
9 59 0.48
10 32 0.26
11 16 0.13
12 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:55665265 original size:29 final size:29
Alignment explanation
Indices: 55665233--55665307 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
55665223 ATTTGAAATT
*
55665233 TTATAAAAATTCTTAAAAGCTT-ATA-AAAA
1 TTATAAAAATTATTAAAA--TTGATACAAAA
* *
55665262 TTATAAAAAATATTAAAATTGATACAAAT
1 TTATAAAAATTATTAAAATTGATACAAAA
55665291 TTATAAAAATTA-TAAAA
1 TTATAAAAATTATTAAAA
55665308 GAACATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.05
28 8 0.20
29 30 0.75
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (29 bp):
TTATAAAAATTATTAAAATTGATACAAAA
Found at i:55665913 original size:28 final size:29
Alignment explanation
Indices: 55665882--55665948 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 29
55665872 GGTTTAAATG
55665882 ATTTTTTTAA-TATTTTAT-ATTTTATTAT-
1 ATTTTTTTAACT-TTTTATGATTTT-TTATA
*
55665910 ATTTTTATAACTTTTTATGATTTTTTATA
1 ATTTTTTTAACTTTTTATGATTTTTTATA
55665939 ATTTTTTTAA
1 ATTTTTTTAA
55665949 GTTTATATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 19 0.56
29 15 0.44
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (29 bp):
ATTTTTTTAACTTTTTATGATTTTTTATA
Found at i:55665924 original size:10 final size:9
Alignment explanation
Indices: 55665882--55666197 Score: 137
Period size: 9 Copynumber: 33.9 Consensus size: 9
55665872 GGTTTAAATG
*
55665882 ATTTTTTTA
1 ATTTTTATA
55665891 ATATTTTATA
1 AT-TTTTATA
*
55665901 TTTTATTAT-
1 ATTT-TTATA
55665910 ATTTTTATA
1 ATTTTTATA
55665919 ACTTTTTATGA
1 A-TTTTTAT-A
*
55665930 TTTTTTATA
1 ATTTTTATA
*
55665939 ATTTTTTTA
1 ATTTTTATA
* *
55665948 AGTTTATATCT
1 A-TTTTTAT-A
*
55665959 ATTTTAAT-
1 ATTTTTATA
*
55665967 ATTCTTA-A
1 ATTTTTATA
*
55665975 ATATTTAT-
1 ATTTTTATA
*
55665983 ATTTTTATG
1 ATTTTTATA
55665992 ATTTTTATA
1 ATTTTTATA
* *
55666001 AGTTTTAAAGA
1 A-TTTT-TATA
* *
55666012 AATTTTATGT
1 ATTTTTAT-A
*
55666022 GTTTTTATAA
1 ATTTTTAT-A
* *
55666032 AATTTTAAA
1 ATTTTTATA
55666041 TATTTTTATA
1 -ATTTTTATA
55666051 ATTTATTATA
1 ATTT-TTATA
*
55666061 ATTTTTGT-
1 ATTTTTATA
55666069 -TTTTTATA
1 ATTTTTATA
*
55666077 ATATTTATTAA
1 ATTTTTA-T-A
*
55666088 ATTTTTTTA
1 ATTTTTATA
*
55666097 ATGTTTATA
1 ATTTTTATA
*
55666106 ATTTTATATCC
1 ATTTT-TAT-A
*
55666117 ATTTTAATA
1 ATTTTTATA
*
55666126 TTTTTTA-A
1 ATTTTTATA
55666134 ATATTTTATA
1 AT-TTTTATA
55666144 ATTTTTATA
1 ATTTTTATA
*
55666153 ATTTTCTCTA
1 ATTTT-TATA
* *
55666163 TGTTTTTATT
1 -ATTTTTATA
*
55666173 ATTTATA-A
1 ATTTTTATA
55666181 ATTTTTA-A
1 ATTTTTATA
55666189 GATTTTTAT
1 -ATTTTTAT
55666198 GGAAAAATAT
Statistics
Matches: 226, Mismatches: 54, Indels: 53
0.68 0.16 0.16
Matches are distributed among these distances:
7 6 0.03
8 30 0.13
9 86 0.38
10 84 0.37
11 20 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:55665934 original size:20 final size:20
Alignment explanation
Indices: 55665901--55665944 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
55665891 ATATTTTATA
*
55665901 TTTTATTATATTTTTATAACT
1 TTTTATGATATTTTTATAA-T
55665922 TTTTATGAT-TTTTTATAAT
1 TTTTATGATATTTTTATAAT
55665941 TTTT
1 TTTT
55665945 TTAAGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTATGATATTTTTATAAT
Found at i:55665997 original size:9 final size:8
Alignment explanation
Indices: 55665885--55666000 Score: 54
Period size: 8 Copynumber: 13.0 Consensus size: 8
55665875 TTAAATGATT
55665885 TTTTTA-A
1 TTTTTATA
55665892 TATTTTATA
1 T-TTTTATA
55665901 TTTTATTATA
1 -TTT-TTATA
55665911 TTTTTATAA
1 TTTTTAT-A
55665920 CTTTTTATGA
1 -TTTTTAT-A
55665930 TTTTTTATAA
1 -TTTTTAT-A
*
55665940 TTTTTTTAA
1 TTTTTAT-A
*
55665949 GTTTATATCTA
1 -TTT-T-TATA
*
55665960 TTTTAATA
1 TTTTTATA
* *
55665968 TTCTTAAA
1 TTTTTATA
*
55665976 TATTTATA
1 TTTTTATA
55665984 TTTTTATGA
1 TTTTTAT-A
55665993 TTTTTATA
1 TTTTTATA
55666001 AGTTTTAAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
7 1 0.01
8 28 0.33
9 24 0.28
10 28 0.33
11 2 0.02
12 2 0.02
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (8 bp):
TTTTTATA
Found at i:55666017 original size:30 final size:28
Alignment explanation
Indices: 55665983--55666066 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 28
55665973 AAATATTTAT
*
55665983 ATTTTTATGATTTTTATAAGTTTTAAAGA
1 ATTTTTATGATTTTTATAAATTTTAAA-A
* * *
55666012 AATTTTATGTGTTTTTATAAAATTTTAAAT
1 ATTTTTATG-ATTTTTAT-AAATTTTAAAA
* *
55666042 ATTTTTATAATTTATTATAATTTTT
1 ATTTTTATGATTT-TTATAAATTTT
55666067 GTTTTTTATA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 17 0.39
30 18 0.41
31 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (28 bp):
ATTTTTATGATTTTTATAAATTTTAAAA
Found at i:55666111 original size:28 final size:27
Alignment explanation
Indices: 55666043--55666112 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
55666033 ATTTTAAATA
55666043 TTTTTATAA-TTTATTATAATTTTTGT
1 TTTTTATAATTTTATTATAATTTTTGT
55666069 TTTTTATAATATTTATTA-AATTTTT-T
1 TTTTTATAAT-TTTATTATAATTTTTGT
55666095 TAATGTTTATAATTTTAT
1 T--T-TTTATAATTTTAT
55666113 ATCCATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 11 0.28
27 7 0.18
28 13 0.33
29 8 0.21
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTTTATAATTTTATTATAATTTTTGT
Found at i:55666111 original size:37 final size:38
Alignment explanation
Indices: 55666032--55666113 Score: 91
Period size: 37 Copynumber: 2.2 Consensus size: 38
55666022 GTTTTTATAA
* *
55666032 AATTTTA-AATATTTTTATAATTTATTATAATTTTTGT
1 AATTTTATAATATTTTTATAATTTATTATAATGTTTAT
* *
55666069 -TTTTTATAATATTTATTA-AATTT-TTTTAATGTTTAT
1 AATTTTATAATATTT-TTATAATTTATTATAATGTTTAT
55666105 AATTTTATA
1 AATTTTATA
55666114 TCCATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
36 15 0.41
37 19 0.51
38 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (38 bp):
AATTTTATAATATTTTTATAATTTATTATAATGTTTAT
Found at i:55667024 original size:16 final size:16
Alignment explanation
Indices: 55667003--55667054 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
55666993 TTTGGTTCGC
55667003 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
55667019 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
55667035 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
55667051 TGTA
1 TGTA
55667055 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:55667101 original size:45 final size:44
Alignment explanation
Indices: 55667035--55667129 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
55667025 GGATTAGAGG
* *
55667035 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
55667080 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
55667124 TGTAAT
1 TGTAAT
55667130 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:55667299 original size:25 final size:25
Alignment explanation
Indices: 55667267--55667321 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
55667257 TAATTTAATC
*
55667267 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
55667291 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
55667316 ATATAT
1 ATATAT
55667322 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:55675934 original size:3 final size:3
Alignment explanation
Indices: 55675926--55675969 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
55675916 TAGTCCCCAT
55675926 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55675970 CTACTACTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:55675955 original size:20 final size:20
Alignment explanation
Indices: 55675930--55675969 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55675920 CCCCATTTAT
55675930 TATTATTATTATTATTATTA
1 TATTATTATTATTATTATTA
55675950 TATTATTATTATTATTATTA
1 TATTATTATTATTATTATTA
55675970 CTACTACTAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATTATTATTATTATTA
Found at i:55677935 original size:17 final size:17
Alignment explanation
Indices: 55677909--55677944 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55677899 GTGTATTTTG
*
55677909 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
*
55677926 TTTTGACTGCATGGCAT
1 TTTTGACTGCATGACAT
55677943 TT
1 TT
55677945 CATCATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:55678429 original size:19 final size:20
Alignment explanation
Indices: 55678392--55678431 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
55678382 TCTTTTCGCA
* *
55678392 TTCATTTCATGCATTTGCAT
1 TTCATTGCATGCATATGCAT
55678412 TTCATTGCAT-CATATGCAT
1 TTCATTGCATGCATATGCAT
55678431 T
1 T
55678432 AAACACGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (20 bp):
TTCATTGCATGCATATGCAT
Found at i:55680320 original size:20 final size:20
Alignment explanation
Indices: 55680295--55680335 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
55680285 GCAAATGTTC
55680295 TTTCATTCTTT-ACGATTTTT
1 TTTCATTCTTTCA-GATTTTT
55680315 TTTCATTCTTTCAGATTTTT
1 TTTCATTCTTTCAGATTTTT
55680335 T
1 T
55680336 CTGCCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTCATTCTTTCAGATTTTT
Found at i:55682741 original size:132 final size:132
Alignment explanation
Indices: 55682504--55682845 Score: 490
Period size: 132 Copynumber: 2.6 Consensus size: 132
55682494 GGAGCAAGTT
* * * *
55682504 GATGGCGGATTTTACCTCCCTGAGGTTATAGAGGAGTATATTGAAGCCAGTAATTCTATCTCCAT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * * *
55682569 GGGCAACATTGGAATAGATTGAATATTACAGATCTTATCTCCCTAAAAAGTAGTGGAGCAAATC-
66 AGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAAAAGTAGTAGAGCAAATCG
55682633 AA
131 AA
*
55682635 GGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
1 -GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
* * ** *
55682700 TAGGTAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATC
65 TAGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAAAAGTAGTAGAGCAAATC
55682765 GAA
130 GAA
* * * *
55682768 GATGGCGGATTTTACCTCCTTGAGGTTACAATGAAGTACATTGAAGCTAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
55682833 -GAGCAACAGTGGA
66 AG-GCAACAGTGGA
55682846 GTAGCAGTAG
Statistics
Matches: 187, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
131 1 0.01
132 184 0.98
133 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (132 bp):
GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
AGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAAAAGTAGTAGAGCAAATCG
AA
Found at i:55682919 original size:44 final size:44
Alignment explanation
Indices: 55682854--55683288 Score: 254
Period size: 44 Copynumber: 9.8 Consensus size: 44
55682844 GAGTAGCAGT
* * *
55682854 AGATCTTGTCTTCATGTACTGGCATGAAGTAGATTAAAGATACC
1 AGATCTTGTCTTCATATACTGGCGTGAAGTAGATTAAAGATAAC
* * * *
55682898 ATATCTTGTCTTC-TCATACTGGTGGCGAAGTAGATTGAAA-AAAAC
1 AGATCTTGTCTTCAT-ATACTGG-CGTGAAGTAGATT-AAAGATAAC
* *
55682943 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAAC
1 AGATCTTGTCTTCATATACTGGCGTGAAGTAGATTAAAGATAAC
* ** * * ** *
55682987 AGATCTTGCCTTCCCATACTGGTG-GCAAAGCAGATCGAAGA-AAGT
1 AGATCTTGTCTTCATATACTGGCGTG--AAGTAGATTAAAGATAA-C
* * *
55683032 AGATCTTGTCATCATGTACTGGCGTGAAGTAGATCAAAGATAAC
1 AGATCTTGTCTTCATATACTGGCGTGAAGTAGATTAAAGATAAC
* * ** * * ** ** *
55683076 AGATATTGCCTTCCCATACTGGTGGCGAAACAGATCGAAGA-AAGT
1 AGATCTTGTCTTCATATACTGG-CGTGAAGTAGATTAAAGATAA-C
* * * *
55683121 AGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGAGAAC
1 AGATCTTGTCTTCATATACTGGCGTGAAGTAGATTAAAGATAAC
** * * ** *
55683165 AGATCTTGTCTTCCCATACTGGTGGCGAAGT-GCATCGAAGA-AAGT
1 AGATCTTGTCTTCATATACTGG-CGTGAAGTAG-ATTAAAGATAA-C
* * * * * *
55683210 AGATCTTATCTTCATGTACTGGTGTGAAGTAGATCAAAGAGAGC
1 AGATCTTGTCTTCATATACTGGCGTGAAGTAGATTAAAGATAAC
** *
55683254 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGAT
1 AGATCTTGTCTTCATATACTGG-CGTGAAGTAGAT
55683289 CGAAGATACA
Statistics
Matches: 298, Mismatches: 74, Indels: 37
0.73 0.18 0.09
Matches are distributed among these distances:
43 5 0.02
44 149 0.50
45 139 0.47
46 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (44 bp):
AGATCTTGTCTTCATATACTGGCGTGAAGTAGATTAAAGATAAC
Found at i:55683005 original size:89 final size:89
Alignment explanation
Indices: 55682851--55683294 Score: 656
Period size: 89 Copynumber: 5.0 Consensus size: 89
55682841 GTGGAGTAGC
* * * * *
55682851 AGTAGATCTTGTCTTCATGTACTGGCATGAAGTAGATTAAAGATACCATATCTTGTCTTCTCATA
1 AGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
* *
55682916 CTGGTGGCGAAGTAGATTGAAAAA
66 CTGGTGGCGAAGTAGATCGAAGAA
** *
55682940 AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATA
1 AGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
* *
55683005 CTGGTGGCAAAGCAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
* * *
55683029 AGTAGATCTTGTCATCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATATTGCCTTCCCATA
1 AGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
**
55683094 CTGGTGGCGAAACAGATCGAAGAA
66 CTGGTGGCGAAGTAGATCGAAGAA
* *
55683118 AGTAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGAGAACAGATCTTGTCTTCCCATA
1 AGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
55683183 CTGGTGGCGAAGT-GCATCGAAGAA
66 CTGGTGGCGAAGTAG-ATCGAAGAA
* * * *
55683207 AGTAGATCTTATCTTCATGTACTGGTGTGAAGTAGATCAAAGAGAGCAGATCTTGTCTTCCCATA
1 AGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
*
55683272 CTGGTGGTGAAGTAGATCGAAGA
66 CTGGTGGCGAAGTAGATCGAAGA
55683295 TACAAGTTTT
Statistics
Matches: 325, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
88 1 0.00
89 323 0.99
90 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (89 bp):
AGTAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATA
CTGGTGGCGAAGTAGATCGAAGAA
Found at i:55683486 original size:44 final size:44
Alignment explanation
Indices: 55683436--55683928 Score: 251
Period size: 44 Copynumber: 11.2 Consensus size: 44
55683426 CCAATAATTC
* *
55683436 TATCTCCCTAGGCAGCAGAGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * *
55683480 TATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGACAGATTT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * * *
55683524 TACCTCCCTGAGGTTA-CTGTGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCT-AGG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATCT
* * *
55683568 TATCTCCAT-GAGCAACAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAG-GCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * * * *
55683612 TATCTCCCTAAGCAGTAGTGGAGCAGA-TCAAGGATGACGGATTT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAA-GATTACAGATCT
* * * * * * * *
55683656 TACCTCCATGAGGTTA-CAGTAGAGTACATTAAAGCCAGTA-A-TTC-
1 TATCTCCCT-AGG-CAGCAGTGGAGTAGATTGAAG--ATTACAGATCT
* * *
55683700 TATCTCACTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * * ** * *
55683744 TATCTCCCTAAGCAGTAGTGGAGCAGA-TCAAGGATGGCAAATTT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAA-GATTACAGATCT
* * * * **
55683788 TACCTCCCTGAGGTTA-CAGTGGAGTACACTGAAG-CCAGCA-AT-T
1 TATCTCCCT-AGG-CAGCAGTGGAGTAGATTGAAGATTA-CAGATCT
* * *
55683831 CTATCTTCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 -TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
* * * *
55683876 TATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGACAGATTT
1 TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
*
55683920 TACCTCCCT
1 TATCTCCCT
55683929 GAGGTTATAG
Statistics
Matches: 322, Mismatches: 97, Indels: 60
0.67 0.20 0.13
Matches are distributed among these distances:
41 6 0.02
42 6 0.02
43 62 0.19
44 189 0.59
45 45 0.14
46 10 0.03
47 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATTACAGATCT
Found at i:55683508 original size:132 final size:131
Alignment explanation
Indices: 55683345--55683998 Score: 950
Period size: 132 Copynumber: 5.0 Consensus size: 131
55683335 AAACCACAAG
*** *
55683345 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCTCTGAGGTTATA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTATA
* *
55683410 GTGGAGTACATTGAAGCCAATAATTCTATCTCCCTAGGCAGCAGAGGAATAGATTGAAGATTACA
66 GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT-GGCAGCAGTGGAATAGATTGAAGATTACA
55683475 GA
130 GA
* * *
55683477 TCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGACAGATTTTACCTCCCTGAGGTTACT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTA-T
* *
55683542 -GTGGAGTACATTGAAGCCAGTAATTCTATCTCCATGAGCAACAGTGGAATAGATTGAAGATTAC
65 AGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTG-GCAGCAGTGGAATAGATTGAAGATTAC
55683606 AGA
129 AGA
* * * *
55683609 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGACGGATTTTACCTCCATGAGGTTACA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTATA
* * *
55683674 GTAGAGTACATTAAAGCCAGTAATTCTATCTCACTGGGCAGCAGTGGAATAGATTGAAGATTACA
66 GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT-GGCAGCAGTGGAATAGATTGAAGATTACA
55683739 GA
130 GA
* * * *
55683741 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGGCAAATTTTACCTCCCTGAGGTTACA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTATA
* * *
55683806 GTGGAGTACACTGAAGCCAGCAATTCTATCTTCCTGGGCAGCAGTGGAATAGATTGAAGATTACA
66 GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT-GGCAGCAGTGGAATAGATTGAAGATTACA
55683871 GA
130 GA
* * *
55683873 TCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGACAGATTTTACCTCCCTGAGGTTATA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTATA
* * * * *
55683938 GTGGACTATATTGAAGCCAGTAATTCTATCTCCCTGGTCGGCAGTGAAATAGATCGAAGAT
66 GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGG-CAGCAGTGGAATAGATTGAAGAT
55683999 AGCAGACCTT
Statistics
Matches: 469, Mismatches: 48, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
131 3 0.01
132 464 0.99
133 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (131 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACCTCCCTGAGGTTATA
GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGCAGCAGTGGAATAGATTGAAGATTACAG
A
Found at i:55684085 original size:45 final size:45
Alignment explanation
Indices: 55683981--55684175 Score: 223
Period size: 44 Copynumber: 4.4 Consensus size: 45
55683971 CTGGTCGGCA
* * * *** *
55683981 GTGAAATAGATCGAAGATAGCAGACCTTGTCTTCATGTATTGG-C
1 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTG
* * *
55684025 GTGAAGTAGATCGAAGAAAGTAGGTCTTGTCTTCCCATACTGGTG
1 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTG
*** *
55684070 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-C
1 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTG
* *
55684114 GTGAAGTAGATCAAAGACAGCAGATCTTGTCTTCCCATATTGGTG
1 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTG
*
55684159 GCGAAGTAGATCGAAGA
1 GTGAAGTAGATCGAAGA
55684176 TACAAGTCTT
Statistics
Matches: 124, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
44 72 0.58
45 52 0.42
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (45 bp):
GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATATTGGTG
Found at i:55684142 original size:89 final size:89
Alignment explanation
Indices: 55683981--55684175 Score: 309
Period size: 89 Copynumber: 2.2 Consensus size: 89
55683971 CTGGTCGGCA
* * * *
55683981 GTGAAATAGATCGAAGATAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAGT
1 GTGAAGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGC
*
55684046 AGGTCTTGTCTTCCCATACTGGTG
66 AGATCTTGTCTTCCCATACTGGTG
* *
55684070 GTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGACAGC
1 GTGAAGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGC
*
55684135 AGATCTTGTCTTCCCATATTGGTG
66 AGATCTTGTCTTCCCATACTGGTG
*
55684159 GCGAAGTAGATCGAAGA
1 GTGAAGTAGATCGAAGA
55684176 TACAAGTCTT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 97 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (89 bp):
GTGAAGTAGATCGAAGAAAGCAGACCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGAAAGC
AGATCTTGTCTTCCCATACTGGTG
Found at i:55688186 original size:14 final size:14
Alignment explanation
Indices: 55688167--55688205 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
55688157 TATTTAACCC
*
55688167 ACATATACAATGAT
1 ACATATAAAATGAT
55688181 ACATATAAAAATGAT
1 ACATAT-AAAATGAT
55688196 ACATATAAAA
1 ACATATAAAA
55688206 AGATGAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (14 bp):
ACATATAAAATGAT
Found at i:55688195 original size:15 final size:15
Alignment explanation
Indices: 55688175--55688206 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55688165 CCACATATAC
55688175 AATGATACATATAAA
1 AATGATACATATAAA
55688190 AATGATACATATAAA
1 AATGATACATATAAA
55688205 AA
1 AA
55688207 GATGAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (15 bp):
AATGATACATATAAA
Found at i:55688733 original size:3 final size:3
Alignment explanation
Indices: 55688725--55688763 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55688715 GAATATACGT
55688725 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55688764 CAGTAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:55698923 original size:43 final size:43
Alignment explanation
Indices: 55698860--55698975 Score: 178
Period size: 43 Copynumber: 2.7 Consensus size: 43
55698850 ATCCATCTTA
** **
55698860 TGGGAAAAGCGTTGCTAAAGGTCGTGGTCTATAGCGGTGTTTG
1 TGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCGGCATTTG
*
55698903 TTGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCGGCATTTG
1 TGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCGGCATTTG
*
55698946 TGGGAAAAGCGCCGCTAAAGGTCATGGTCT
1 TGGGAAAAGCGCCGCTAAAGGTCGTGGTCT
55698976 CACTACACCA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (43 bp):
TGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCGGCATTTG
Found at i:55699372 original size:41 final size:41
Alignment explanation
Indices: 55699327--55699421 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
55699317 TTTGGTCTTC
*
55699327 TAGCGGCGTTTTTAT-ATAAGCGAC-GCTAAAGTTAAGATTTT
1 TAGCGGCGTTTTTATGATAAGCG-CTGCTAAAGTT-AGAGTTT
* * * *
55699368 TAGCGGCGATTCTATGATAAGCGCTGCTAATGTTAGGGTTT
1 TAGCGGCGTTTTTATGATAAGCGCTGCTAAAGTTAGAGTTT
55699409 TAGCGGCGTTTTT
1 TAGCGGCGTTTTT
55699422 GTTGAAGCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
41 30 0.67
42 15 0.33
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (41 bp):
TAGCGGCGTTTTTATGATAAGCGCTGCTAAAGTTAGAGTTT
Found at i:55699413 original size:82 final size:80
Alignment explanation
Indices: 55699239--55699421 Score: 192
Period size: 82 Copynumber: 2.2 Consensus size: 80
55699229 TAATGGTCGG
* * * * *
55699239 GGGTTTTAGTGGCGTTTTTAATCAACCGCCGCTAAAGTTAAGGTATTTATCGGCGATTTCTTTGA
1 GGGTTTTAGCGGCGTTTTTAATCAACCGACGCTAAAGTTAAGATATTTAGCGGCGATTTCTATGA
55699304 AGCGCCGCGAAGATT
66 AGCGCCGCGAAGATT
* * *
55699319 TGGTCTTCTAGCGGCGTTTTTATAT-AAGCGACGCTAAAGTTAAGATTTTTAGCGGCGA-TTCTA
1 GGGT-TT-TAGCGGCGTTTTTA-ATCAACCGACGCTAAAGTTAAGATATTTAGCGGCGATTTCTA
* *
55699382 TGATAAGCGCTGCTAATG-TT
63 TG--AAGCGCCGCGAA-GATT
55699402 AGGGTTTTAGCGGCGTTTTT
1 -GGGTTTTAGCGGCGTTTTT
55699422 GTTGAAGCGC
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
80 3 0.04
81 8 0.09
82 54 0.64
83 16 0.19
84 4 0.05
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (80 bp):
GGGTTTTAGCGGCGTTTTTAATCAACCGACGCTAAAGTTAAGATATTTAGCGGCGATTTCTATGA
AGCGCCGCGAAGATT
Found at i:55700264 original size:7 final size:7
Alignment explanation
Indices: 55700252--55700299 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
55700242 GATATAAGGT
55700252 TTAGGGG
1 TTAGGGG
55700259 TTAGGGG
1 TTAGGGG
*
55700266 TTAGGGAT
1 TTAGGG-G
*
55700274 TTAGGTG
1 TTAGGGG
**
55700281 TTAGGAT
1 TTAGGGG
55700288 TTAGGGG
1 TTAGGGG
55700295 TTAGG
1 TTAGG
55700300 AATTTAGGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
7 28 0.85
8 5 0.15
ACGTcount: A:0.19, C:0.00, G:0.46, T:0.35
Consensus pattern (7 bp):
TTAGGGG
Found at i:55700269 original size:14 final size:14
Alignment explanation
Indices: 55700252--55700353 Score: 69
Period size: 15 Copynumber: 6.9 Consensus size: 14
55700242 GATATAAGGT
*
55700252 TTAGGGGTTAGGGG
1 TTAGGGTTTAGGGG
*
55700266 TTAGGGATTTAGGTG
1 TTAGGG-TTTAGGGG
*
55700281 TTAGGATTTAGGGG
1 TTAGGGTTTAGGGG
*
55700295 TTAGGAATTTAGGGG
1 TTAGG-GTTTAGGGG
* *
55700310 CTAGGAGATTTAAGGG
1 TTAGG-G-TTTAGGGG
* * *
55700326 TCAGGGGTTAGGGAT
1 TTAGGGTTTAGGG-G
*
55700341 TTAAGGTTTAGGG
1 TTAGGGTTTAGGG
55700354 TGTCAATTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
14 23 0.33
15 36 0.52
16 10 0.14
ACGTcount: A:0.23, C:0.02, G:0.43, T:0.32
Consensus pattern (14 bp):
TTAGGGTTTAGGGG
Found at i:55700272 original size:29 final size:29
Alignment explanation
Indices: 55700234--55700299 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
55700224 ATGATTATTA
* *
55700234 GGGTTTGGGATATAAGGT-TTAGGGGTTAG
1 GGGTTAGGGAT-TAAGGTGTTAGGAGTTAG
* *
55700263 GGGTTAGGGATTTAGGTGTTAGGATTTAG
1 GGGTTAGGGATTAAGGTGTTAGGAGTTAG
55700292 GGGTTAGG
1 GGGTTAGG
55700300 AATTTAGGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 5 0.16
29 27 0.84
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (29 bp):
GGGTTAGGGATTAAGGTGTTAGGAGTTAG
Done.