Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 64 of 121
Found at i:10976620 original size:31 final size:31
Alignment explanation
Indices: 10976585--10976657 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
10976575 TATACAAATT
*
10976585 ATCCATGTACTCATATGAAATTTGAAATTTA
1 ATCCATGTACTCATATGAAATTTAAAATTTA
**
10976616 ATCCATGTACTTGTATGAAATTTAAAATTTA
1 ATCCATGTACTCATATGAAATTTAAAATTTA
* *
10976647 TTCCTTGTACT
1 ATCCATGTACT
10976658 GGCACGAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (31 bp):
ATCCATGTACTCATATGAAATTTAAAATTTA
Found at i:10976675 original size:31 final size:31
Alignment explanation
Indices: 10976601--10976684 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
10976591 GTACTCATAT
* * * * *
10976601 GAAATTTGAAATTTAATCCATGTACTTGTAT
1 GAAATTTGAAATTTATTCCTTGTACTGGCAC
*
10976632 GAAATTTAAAATTTATTCCTTGTACTGGCAC
1 GAAATTTGAAATTTATTCCTTGTACTGGCAC
*
10976663 GAATTTTGAAATTTAGTTCCTT
1 GAAATTTGAAATTTA-TTCCTT
10976685 TAATACAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 38 0.86
32 6 0.14
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (31 bp):
GAAATTTGAAATTTATTCCTTGTACTGGCAC
Found at i:10976728 original size:19 final size:20
Alignment explanation
Indices: 10976692--10976734 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
10976682 CTTTAATACA
10976692 AAAAATGTTTCAAA-TTTTT
1 AAAAATGTTTCAAATTTTTT
* * *
10976711 AAAAATTTTTCCAGTTTTTT
1 AAAAATGTTTCAAATTTTTT
10976731 AAAA
1 AAAA
10976735 CAATAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAAATGTTTCAAATTTTTT
Found at i:10979170 original size:3 final size:3
Alignment explanation
Indices: 10979164--10979214 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
10979154 CTTGATGATT
10979164 TAA TAA TAA 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 TAA TAA TAA
10979212 TAA
1 TAA
10979215 AAGTAAATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:10982230 original size:17 final size:18
Alignment explanation
Indices: 10982208--10982241 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
10982198 TTAAATTTTT
10982208 AAAAAGCT-AAAAGACAA
1 AAAAAGCTCAAAAGACAA
10982225 AAAAAGCTCAAAAGACA
1 AAAAAGCTCAAAAGACA
10982242 CAATCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.68, C:0.15, G:0.12, T:0.06
Consensus pattern (18 bp):
AAAAAGCTCAAAAGACAA
Found at i:10982455 original size:67 final size:65
Alignment explanation
Indices: 10982256--10982456 Score: 188
Period size: 72 Copynumber: 2.9 Consensus size: 65
10982246 CAATTATCAT
* **
10982256 AATTAATAGATAAATATTATTTTTAAAGTTAAAGAAAATGAAAAGGTAACAAACAAAAAAAATAA
1 AATTAATAAATAAATATTATTTTTAAA-TT-AAGAAAATGAAAAGGT-A-AAA-AAACCAAA-AA
* *
10982321 GTTATAC
60 G-TACAA
* * * *
10982328 AAGTAATTAATAAATATTATTTTTAAAATCTAATAAAATGGAAAGGTAAAGAAAACCAAAAAG-A
1 AATTAATAAATAAATATTATTTTT-AAAT-TAAGAAAATGAAAAGGTAAA-AAAACCAAAAAGTA
10982392 CAA
63 CAA
*
10982395 AATTAATAAATAAATATTATTTTTAAATTGAAGAAAACGAAAAGGTAGAAAAAACTCAAAAA
1 AATTAATAAATAAATATTATTTTTAAATT-AAGAAAATGAAAAGGTA-AAAAAAC-CAAAAA
10982457 TCCAATTATC
Statistics
Matches: 109, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
65 1 0.01
66 23 0.21
67 32 0.29
69 3 0.03
70 8 0.07
71 2 0.02
72 36 0.33
73 4 0.04
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (65 bp):
AATTAATAAATAAATATTATTTTTAAATTAAGAAAATGAAAAGGTAAAAAAACCAAAAAGTACAA
Found at i:10982484 original size:13 final size:13
Alignment explanation
Indices: 10982468--10982494 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10982458 CCAATTATCA
10982468 AAATTTATTATAT
1 AAATTTATTATAT
10982481 AAATTTATTATAT
1 AAATTTATTATAT
10982494 A
1 A
10982495 TACTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTTATTATAT
Found at i:10983558 original size:22 final size:23
Alignment explanation
Indices: 10983528--10983573 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
10983518 AAATAAAACA
10983528 CATCGTTTA-TCATTGGGATTTTC
1 CATCGTTTACT-ATTGGGATTTTC
10983551 CATC-TTTACTATTGGGATTTTC
1 CATCGTTTACTATTGGGATTTTC
10983573 C
1 C
10983574 TGTTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (23 bp):
CATCGTTTACTATTGGGATTTTC
Found at i:10986026 original size:107 final size:106
Alignment explanation
Indices: 10985842--10986048 Score: 272
Period size: 107 Copynumber: 1.9 Consensus size: 106
10985832 GATAAAATTG
* * * *
10985842 TTTAGAACTATTCTACATGTAGTAATATAGATTGTCTACTTAAACATCCATGTACGTAAATCTTT
1 TTTAGAACTATTCTACATGTAGTAATATAGATTGTCCACATAAACATCCATGTAAGCAAATCTTT
* *
10985907 TCAGGTTTTTATGTGTGTTGTAATATAATATTATAAAGTCC
66 TCAGATTTTTATGTATGTTGTAATATAATATTATAAAGTCC
* * * *** *
10985948 TTTAGAGCTATTGTACATGTTGATAATATAGATTGTCCACATAAGTGTTCATGTAAGCAAAT-TT
1 TTTAGAACTATTCTACATGTAG-TAATATAGATTGTCCACATAAACATCCATGTAAGCAAATCTT
10986012 TATCAGATTTTTATGTATGTTGTAATATAATATTATA
65 T-TCAGATTTTTATGTATGTTGTAATATAATATTATA
10986049 TATGATTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
106 22 0.26
107 64 0.74
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (106 bp):
TTTAGAACTATTCTACATGTAGTAATATAGATTGTCCACATAAACATCCATGTAAGCAAATCTTT
TCAGATTTTTATGTATGTTGTAATATAATATTATAAAGTCC
Found at i:10986074 original size:30 final size:31
Alignment explanation
Indices: 10986040--10986103 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
10986030 GTTGTAATAT
*
10986040 AATAT-TATATATGATTTATTT-TTTATTTTA
1 AATATGTA-ATATGATCTATTTATTTATTTTA
* *
10986070 AATATGTAATTTTATCTATTTATTTATTTTA
1 AATATGTAATATGATCTATTTATTTATTTTA
10986101 AAT
1 AAT
10986104 CAAAATTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (31 bp):
AATATGTAATATGATCTATTTATTTATTTTA
Found at i:10986346 original size:2 final size:2
Alignment explanation
Indices: 10986339--10986364 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10986329 GTATGTTGTA
10986339 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10986365 GAAAAGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10997394 original size:144 final size:144
Alignment explanation
Indices: 10997055--10997458 Score: 476
Period size: 145 Copynumber: 2.8 Consensus size: 144
10997045 TAAAACTCCT
* * * * * * ** * *
10997055 AAAATCATGAAATATTATAAAATTGAGATATAAAAAGTTTCATGAAAATTTGAGCTCTAAAAGGT
1 AAAATTATGAAATATTATGAAATTAAAATCTAAAAAGTTTCATAAAAATTCAAGCTCAAAAAGGC
* * *
10997120 CAACTTACA-AAAATACCCCTTATAAGGGTATTTTGATAATTTCACACTTCTCGGTTACTGCTAT
66 CAAATTA-AGAAAATACCCCTTATAAGGGTATTTT-ATAATTTTACACTTCTCGGGTACTGCTAT
10997184 GATTTCAAATGCACCA
129 GATTTCAAATGCACCA
* * * * *
10997200 AAAATTATTAAATATTATGAAATTAATATCTGAAAATTTTCATAAAAATTCAAGCCCCAAAAAGG
1 AAAATTATGAAATATTATGAAATTAAAATCTAAAAAGTTTCATAAAAATTCAAG-CTCAAAAAGG
* * *
10997265 CCAAATTATGAAAATA-CCCTTATAAGGGTATTTTCATAATTTTACACTTTTTGAGGTACTGCTA
65 CCAAATTAAGAAAATACCCCTTATAAGGGTATTTT-ATAATTTTACACTTCTCG-GGTACTGCTA
10997329 TGATTTCAAATGCA-C-
128 TGATTTCAAATGCACCA
* * *
10997344 AAAATTATGAAATATTATGAAATTAAAATCCAAAAAGTTTCATAAAAATTCAAGCTCAGAAAGAC
1 AAAATTATGAAATATTATGAAATTAAAATCTAAAAAGTTTCATAAAAATTCAAGCTCAAAAAGGC
* * *
10997409 CAAATTAAGAAAATACCCCTTA-AAAGGCATTTTAGTAATTTTATACTTCT
66 CAAATTAAGAAAATACCCCTTATAAGGGTATTTTA-TAATTTTACACTTCT
10997459 TCTAATGCAA
Statistics
Matches: 220, Mismatches: 34, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
142 1 0.00
143 44 0.20
144 55 0.25
145 77 0.35
146 43 0.20
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.33
Consensus pattern (144 bp):
AAAATTATGAAATATTATGAAATTAAAATCTAAAAAGTTTCATAAAAATTCAAGCTCAAAAAGGC
CAAATTAAGAAAATACCCCTTATAAGGGTATTTTATAATTTTACACTTCTCGGGTACTGCTATGA
TTTCAAATGCACCA
Found at i:11007016 original size:17 final size:17
Alignment explanation
Indices: 11006994--11007035 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
11006984 TAGCCCTGTT
*
11006994 CAAATATTCATCTTAAA
1 CAAATATTCATCTAAAA
*
11007011 CAAATATTCATGTAAAA
1 CAAATATTCATCTAAAA
*
11007028 AAAATATT
1 CAAATATT
11007036 AATCACATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (17 bp):
CAAATATTCATCTAAAA
Found at i:11010730 original size:663 final size:664
Alignment explanation
Indices: 11008444--11011098 Score: 4955
Period size: 664 Copynumber: 4.0 Consensus size: 664
11008434 CCCATACTTA
*
11008444 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGG-TCAAGTATGTATAGTATAATCATGAAAATG
1 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGGAACAAGTATGTATAGTATAATCATGAAAATG
11008508 ACAAAAATTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
66 ACAAAAATTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
11008573 TCAAAACTTTAAATTTTTTTAATCAAAAA-TTTTTTTTTCTAAAATTTCATACCTATTTTGAGAG
131 TCAAAACTTTAAATTTTTTTAATCAAAAATTTTTTTTTTCTAAAATTTCATACCTATTTTGAGAG
*
11008637 GTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATTTTTTGCATTTATTCATTAGA
196 GTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTAGA
11008702 TTCAACTTTGAAACCATTTTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCA
261 TTCAACTTTGAAACCA--TTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCA
11008767 TTGTAAGCCTCTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTT
324 TTGTAAGCCTCTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTT
11008832 CGGTTCTTCAAAGGCCATAAGACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCT
389 CGGTTCTTCAAAGGCCATAAGACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCT
* *
11008897 TCAATTTCCTCTATATTTCATTTAAAGTGGAGTAATTTGAGACTATGTTGAAGTAGTAAGCATAA
454 CCAATTTCCTCTATATTTCATTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCATAA
*
11008962 AAAATTCCATAATGAATGCACTTAGCCTTTGCATCATCCATTATTTGCTTCATGTAGTTTGCATC
519 AAAATTCCATAAAGAATGCACTTAGCCTTTGCATCATCCATTATTTGCTTCATGTAGTTTGCATC
*
11009027 TTTGGAAAGAGTTTCTAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTATGA
584 TTTGGAAAGAGTTTCAAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTATGA
11009092 ACACCTTCATCCTTTG
649 ACACCTTCATCCTTTG
11009108 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGGAACAAGTATGTATAGTATAATCATGAAAATG
1 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGGAACAAGTATGTATAGTATAATCATGAAAATG
11009173 ACAAAAATTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
66 ACAAAAATTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
11009238 TCAAAACTTTAAATTTTTTTAATCAAAAAAATTTTTTTTTTCTAAAATTTCATACCTATTTTGAG
131 TCAAAACTTTAAATTTTTTTAATC--AAAAATTTTTTTTTTCTAAAATTTCATACCTATTTTGAG
11009303 AGGTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTA
194 AGGTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTA
11009368 GATTCAACTTTGAAACCATTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCA
259 GATTCAACTTTGAAACCATTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCA
*
11009433 TTGTAAGCCTTTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTT
324 TTGTAAGCCTCTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTT
*
11009498 CGGTTCTTCAAAGGCCATAAAACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCT
389 CGGTTCTTCAAAGGCCATAAGACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCT
*
11009563 CCAATTTCCTCTATATTTCATTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCATCA
454 CCAATTTCCTCTATATTTCATTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCATAA
*
11009628 AAAATTCCATAAAGAATGTACTTAGCCTTTGCATCATCCATTATTTGCTTCATGTAGTTTGCATC
519 AAAATTCCATAAAGAATGCACTTAGCCTTTGCATCATCCATTATTTGCTTCATGTAGTTTGCATC
* *
11009693 TTTGGAAAGAGTTTCAAACCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTAGGCCATTATGA
584 TTTGGAAAGAGTTTCAAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTATGA
*
11009758 ACACCTTCATCATTTG
649 ACACCTTCATCCTTTG
*
11009774 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGGAAAAAGTATGTATAGTATAATCATGAAAATG
1 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGGAACAAGTATGTATAGTATAATCATGAAAATG
* *
11009839 ACAAAATTTATATTTAATCATTTTAGTACTTGAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
66 ACAAAAATTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
* *
11009904 TCAAAACTTTAAATTTCTTTAATCAAAAATTTTTTTTTTCTAAAATTTTATACCTATTTTGAGAG
131 TCAAAACTTTAAATTTTTTTAATCAAAAATTTTTTTTTTCTAAAATTTCATACCTATTTTGAGAG
*
11009969 GTTTTTAAATCTATTTTCACTTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTAGA
196 GTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTAGA
11010034 TTCAACTTTGAAACCATTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCATT
261 TTCAACTTTGAAACCATTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCATT
11010099 GTAAGCCTCTTGCAATTTATCAAAAATA-ATAAATTTGAATCAATAGAATTAGAGGTTACTTTCG
326 GTAAGCCTCTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTTCG
** *
11010163 GTTCTTCAAAGGCCATAAGACATGATGCATTTCAATTAGAGGTTTGCCTTTCATATATTTGCTTC
391 GTTCTTCAAAGGCCATAAGACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCTCC
11010228 AATTTCCTCTATATTTCATTTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCAT-AA
456 AATTTCCTCTATATTTCA-TTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCATAAA
11010292 AAATTCCATAAAGAATGCACTTAGCCTTTTGCATCATCCATTATTTGCTTC-TGTTAGTTTTGCA
520 AAATTCCATAAAGAATGCACTTAGCC-TTTGCATCATCCATTATTTGCTTCATG-TAG-TTTGCA
11010356 TCTTTGGAAAGAGTTTCAAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTAT
582 TCTTTGGAAAGAGTTTCAAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTAT
11010421 GAACACCTTCATCCTTTG
647 GAACACCTTCATCCTTTG
11010439 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGG-ACAAGTATGTATAGTATAATCATGAAAATG
1 CCTAATTTTAAATAGAATTTCTCTCTTTTATAGGAACAAGTATGTATAGTATAATCATGAAAATG
*
11010503 ACAAAATTTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
66 ACAAAAATTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
11010568 TCAAAACTTTAAATTTTTTTAATCAAAAA-TTTTTTTTTCTAAAATTTCATACCTATTTTGAGAG
131 TCAAAACTTTAAATTTTTTTAATCAAAAATTTTTTTTTTCTAAAATTTCATACCTATTTTGAGAG
11010632 GTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTAGA
196 GTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTAGA
11010697 TTCAACTTTGAAACCATTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCATT
261 TTCAACTTTGAAACCATTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCATT
*
11010762 GTGAGCCTCTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTTCG
326 GTAAGCCTCTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTTCG
*
11010827 GTTCTTCAAATGCCATAAGACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCTCC
391 GTTCTTCAAAGGCCATAAGACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCTCC
11010892 AATTTCCTCTATATTTCATTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCATAAAA
456 AATTTCCTCTATATTTCATTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCATAAAA
*
11010957 AATTCCATAAAGAATGCACTTAGCCTTTGCATCATCCATTATTTGCTTCATGTAGTTTGTATCTT
521 AATTCCATAAAGAATGCACTTAGCCTTTGCATCATCCATTATTTGCTTCATGTAGTTTGCATCTT
11011022 TGGAAAGAGTTTCAAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTATGAAC
586 TGGAAAGAGTTTCAAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTATGAAC
11011087 ACCTTCATCCTT
651 ACCTTCATCCTT
11011099 ATTCTCTATT
Statistics
Matches: 1941, Mismatches: 39, Indels: 24
0.97 0.02 0.01
Matches are distributed among these distances:
662 86 0.04
663 404 0.21
664 566 0.29
665 238 0.12
666 527 0.27
667 5 0.00
668 115 0.06
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (664 bp):
CCTAATTTTAAATAGAATTTCTCTCTTTTATAGGAACAAGTATGTATAGTATAATCATGAAAATG
ACAAAAATTATATTTAATCATTTTAGTACTTAAACTCTTGTTTAAAAGCTCTTATTTTTCATTCA
TCAAAACTTTAAATTTTTTTAATCAAAAATTTTTTTTTTCTAAAATTTCATACCTATTTTGAGAG
GTTTTTAAATCTATTTTCACCTTTTCATTTTTGTTCTAAAATATATTTTGCATTTATTCATTAGA
TTCAACTTTGAAACCATTTTTTTATAATTCCTTATCATTGATTCACATTCATCATACAACTCATT
GTAAGCCTCTTGCAATTTATCAAAAATATATAAATTTGAATCAATAGAATTAGAGGTTACTTTCG
GTTCTTCAAAGGCCATAAGACATGATGCATTTCGGTTAGAGGTTTGCCTTTCATATATTTGCTCC
AATTTCCTCTATATTTCATTTAAAGTGGAGTAATTTGAGACTAAGTTGAAGTAGTAAGCATAAAA
AATTCCATAAAGAATGCACTTAGCCTTTGCATCATCCATTATTTGCTTCATGTAGTTTGCATCTT
TGGAAAGAGTTTCAAGCCCTTTTTCAACCACATTCCAAGCTTTAAAATCTTGGGCCATTATGAAC
ACCTTCATCCTTTG
Found at i:11017509 original size:10 final size:9
Alignment explanation
Indices: 11017490--11017518 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
11017480 TGAAACTGGG
11017490 TTTA-TTTT
1 TTTATTTTT
11017498 TTTATTTTT
1 TTTATTTTT
11017507 TTTATTTTT
1 TTTATTTTT
11017516 TTT
1 TTT
11017519 GAACTTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTATTTTT
Found at i:11019572 original size:26 final size:27
Alignment explanation
Indices: 11019529--11019582 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
11019519 AGTCTACAGA
11019529 AACCCATTTTTTTTTCTTTCTTTCAAT
1 AACCCATTTTTTTTTCTTTCTTTCAAT
11019556 AACCCA-TTTTTTTTCTTTCTTTCAAT
1 AACCCATTTTTTTTTCTTTCTTTCAAT
11019582 A
1 A
11019583 TCTCTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.57
Consensus pattern (27 bp):
AACCCATTTTTTTTTCTTTCTTTCAAT
Found at i:11026646 original size:18 final size:18
Alignment explanation
Indices: 11026623--11026670 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
11026613 TTGTTTCCTT
*
11026623 AAAAAATTGAAAAATTTGA
1 AAAAAAATGAAAAA-TTGA
*
11026642 AAAAAAATCAAAAATTG-
1 AAAAAAATGAAAAATTGA
11026659 AAAAAAATGAAA
1 AAAAAAATGAAA
11026671 TAAATAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 3 0.12
19 12 0.46
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (18 bp):
AAAAAAATGAAAAATTGA
Found at i:11027339 original size:18 final size:18
Alignment explanation
Indices: 11027299--11027347 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
11027289 TTTACCAAAA
* *
11027299 AAAAAAAAATAAAATAAT
1 AAAAAAAAAGAAAAGAAT
11027317 AAAAAAAAAGAAAAGAA-
1 AAAAAAAAAGAAAAGAAT
* *
11027334 AGAAAAAATGAAAA
1 AAAAAAAAAGAAAA
11027348 AGGTTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAAAAAAAGAAAAGAAT
Found at i:11027348 original size:18 final size:17
Alignment explanation
Indices: 11027295--11027349 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
11027285 ACTTTTTACC
*
11027295 AAAA-AAAAAAAAATAA
1 AAAAGAAAAAAAAATGA
*
11027311 AATAATAAAAAAAAA-G-
1 AA-AAGAAAAAAAAATGA
11027327 AAAAGAAAGAAAAAATGA
1 AAAAGAAA-AAAAAATGA
11027345 AAAAG
1 AAAAG
11027350 GTTTGAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 5 0.16
16 10 0.31
17 3 0.09
18 14 0.44
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAAAAATGA
Found at i:11033107 original size:8 final size:8
Alignment explanation
Indices: 11033094--11033138 Score: 67
Period size: 7 Copynumber: 5.8 Consensus size: 8
11033084 AAATAATATA
11033094 TAAAAAAT
1 TAAAAAAT
11033102 TAAAAAAT
1 TAAAAAAT
11033110 TAAAAAAAT
1 T-AAAAAAT
11033119 T-AAAAAT
1 TAAAAAAT
11033126 T-AAAAAT
1 TAAAAAAT
11033133 TAAAAA
1 TAAAAA
11033139 TCGATAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.40
8 13 0.37
9 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
TAAAAAAT
Found at i:11033115 original size:9 final size:9
Alignment explanation
Indices: 11033080--11033124 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
11033070 AAAATTTTAT
*
11033080 ATTAAAATA
1 ATTAAAAAA
11033089 ATATATAAAAA
1 AT-TA-AAAAA
11033100 ATT-AAAAA
1 ATTAAAAAA
11033108 ATTAAAAAA
1 ATTAAAAAA
11033117 ATTAAAAA
1 ATTAAAAA
11033125 TTAAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.25
9 15 0.47
10 3 0.09
11 6 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:11033115 original size:16 final size:16
Alignment explanation
Indices: 11033094--11033138 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
11033084 AAATAATATA
11033094 TAAAAAATTAAAAAAT
1 TAAAAAATTAAAAAAT
11033110 TAAAAAAATT-AAAAAT
1 T-AAAAAATTAAAAAAT
11033126 T-AAAAATTAAAAA
1 TAAAAAATTAAAAA
11033139 TCGATAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.26
15 4 0.15
16 8 0.30
17 8 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
TAAAAAATTAAAAAAT
Found at i:11040530 original size:3 final size:3
Alignment explanation
Indices: 11040524--11040570 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
11040514 CAAAATCATC
11040524 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11040571 GCATAACTTT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11042095 original size:24 final size:26
Alignment explanation
Indices: 11042060--11042109 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
11042050 TAAAACACAA
11042060 AAAATCATAAAA-TATTAT-AAAATT
1 AAAATCATAAAAGTATTATGAAAATT
*
11042084 AAAATC-TAAAAAGTTTTATGAAAATT
1 AAAATCAT-AAAAGTATTATGAAAATT
11042110 CGAGCTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 1 0.05
24 10 0.45
25 5 0.23
26 6 0.27
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (26 bp):
AAAATCATAAAAGTATTATGAAAATT
Found at i:11042448 original size:144 final size:143
Alignment explanation
Indices: 11042059--11042595 Score: 505
Period size: 143 Copynumber: 3.7 Consensus size: 143
11042049 TTAAAACACA
* * * * *
11042059 AAAAATCATAAAATATTATAAAATTAAAATCTAAAAAGTTTTATGAAAAT-TCGAGCTCT-AGAA
1 AAAAATCATGAAATATTATGAAATT-AAATCTGAAAAGTTTCATGAAAATCT-GAGCT-TGGGAA
* * * * * *
11042122 AGCCAAATTA-GAAAAATACCCTTAAGGGGTATTTTGGTAATTTCACACTTCTCAGGGCACTACT
63 TGCCAAATTATG-AAAATACCCTTAAGGGGTATTTTGATAATTTTACACATATCAGGGTACTACT
11042186 GTGATTTCAAATGCACC
127 GTGATTTCAAATGCACC
* *
11042203 -AAAATCATGAAATATTATGAAATTAATATTTGAAAAGTTTCATGAAAATCT-AGGCTTAGGAAT
1 AAAAATCATGAAATATTATGAAATTAA-ATCTGAAAAGTTTCATGAAAATCTGA-GCTTGGGAAT
* * ** * * *
11042266 ACAAAATTACAAAAATACCTTTAAGGGGTATTTTGATAATTTTACACCTATC-GAGGTACCACTG
64 GCCAAATTATGAAAATACCCTTAAGGGGTATTTTGATAATTTTACACATATCAG-GGTACTACTG
*
11042330 TGATTTTAAATGCACC
128 TGATTTCAAATGCACC
* * *
11042346 AAAAATTATGAAAATATTATGAAATTCAAATTTGAAAAGTTTCATGTAAATCTGAGCTTGGGAAT
1 AAAAATCATG-AAATATTATGAAATT-AAATCTGAAAAGTTTCATGAAAATCTGAGCTTGGGAAT
* * * * * * *
11042411 G-CAAATTATGAAAATACCCCTAAGGGGTATTTTGATAAGTTCACATATTTAAGGGTACTATTGT
64 GCCAAATTATGAAAATACCCTTAAGGGGTATTTTGATAATTTTACACATATCAGGGTACTACTGT
11042475 GA-TTCAAATGCACC
129 GATTTCAAATGCACC
* * * * * ** * * *
11042489 AAAAATCTTGAAATATTAGGAAATTGAGATCTGAAAATTTTCATAAAAATCAAAGCATGGAAAGG
1 AAAAATCATGAAATATTATGAAATT-AAATCTGAAAAGTTTCATGAAAATCTGAGCTTGGGAATG
* * ** * *
11042554 TCAAATTATGAAAATACCTTTAAAAGGTGTTTTGGTAATTTT
65 CCAAATTATGAAAATACCCTTAAGGGGTATTTTGATAATTTT
11042596 GTTTCTCCAA
Statistics
Matches: 323, Mismatches: 58, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
142 48 0.15
143 165 0.51
144 59 0.18
145 48 0.15
146 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (143 bp):
AAAAATCATGAAATATTATGAAATTAAATCTGAAAAGTTTCATGAAAATCTGAGCTTGGGAATGC
CAAATTATGAAAATACCCTTAAGGGGTATTTTGATAATTTTACACATATCAGGGTACTACTGTGA
TTTCAAATGCACC
Found at i:11043037 original size:50 final size:50
Alignment explanation
Indices: 11042977--11043098 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 50
11042967 TATAATAGCT
** * *
11042977 TTTTTCAAATTGAGATTTTTCAAAATTTGTTGCCTATCTTCATATGAGCC
1 TTTTTCAAATTGAGATTTTTCAAAATTCATTACCTATCTTCATAGGAGCC
* * * *
11043027 TTTTTCAAATTAAGATATTTT-AAAGTTCATTACTTATTTTCATAGGAGCC
1 TTTTTCAAATTGAGAT-TTTTCAAAATTCATTACCTATCTTCATAGGAGCC
* *
11043077 CTTTTCAATTTGAGATTTTTCA
1 TTTTTCAAATTGAGATTTTTCA
11043099 TAAGAGCCCT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
49 4 0.07
50 51 0.86
51 4 0.07
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.48
Consensus pattern (50 bp):
TTTTTCAAATTGAGATTTTTCAAAATTCATTACCTATCTTCATAGGAGCC
Found at i:11043122 original size:80 final size:80
Alignment explanation
Indices: 11043015--11043164 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
11043005 GTTGCCTATC
* * *
11043015 TTCATATGAGCCTTTTTCAAATTAAGATATTTTAAAGTTCATTACT-TAT-TTTCATAGGAGCCC
1 TTCATAAGAGCCCTTTTCAAATAAAGATATTTTAAAGTTCATT-CTCTATCTTT-ATAGGAGCCC
11043078 TTTTCAATTTGAGATTT
64 TTTTCAATTTGAGATTT
* * * *
11043095 TTCATAAGAGCCCTTTTCGAATAAAGATTTTTTAAGGTTCGTTCTCTATCTTTATAGGAGCCCTT
1 TTCATAAGAGCCCTTTTCAAATAAAGATATTTTAAAGTTCATTCTCTATCTTTATAGGAGCCCTT
11043160 TTCAA
66 TTCAA
11043165 ATAGAGGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 2 0.03
80 56 0.92
81 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (80 bp):
TTCATAAGAGCCCTTTTCAAATAAAGATATTTTAAAGTTCATTCTCTATCTTTATAGGAGCCCTT
TTCAATTTGAGATTT
Found at i:11043123 original size:30 final size:30
Alignment explanation
Indices: 11043063--11043126 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
11043053 TCATTACTTA
* **
11043063 TTTTCATAGGAGCCCTTTTCAATTTGAGAT
1 TTTTCATAAGAGCCCTTTTCAATTAAAGAT
11043093 TTTTCATAAGAGCCCTTTTCGAA-TAAAGAT
1 TTTTCATAAGAGCCCTTTTC-AATTAAAGAT
11043123 TTTT
1 TTTT
11043127 TAAGGTTCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (30 bp):
TTTTCATAAGAGCCCTTTTCAATTAAAGAT
Found at i:11043731 original size:19 final size:19
Alignment explanation
Indices: 11043701--11043746 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
11043691 TTAAATCTGG
* *
11043701 TCAAACTTAGTTAAACTTAA
1 TCAAA-TTAGTTAAAATCAA
11043721 TCAAATTAGTTAAAATCAA
1 TCAAATTAGTTAAAATCAA
11043740 TCAAATT
1 TCAAATT
11043747 GGATTGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (19 bp):
TCAAATTAGTTAAAATCAA
Found at i:11044476 original size:125 final size:125
Alignment explanation
Indices: 11044252--11044499 Score: 381
Period size: 125 Copynumber: 2.0 Consensus size: 125
11044242 ATATAATGAA
* * * *
11044252 TTTTGGTGCATTAAAAACCTTAGTAGCACCTCGAAATGGGTGAAATTATTGAAATACCCTTTAGG
1 TTTTGGTGCATTAAAAACCTTAGCAGCACCTCGAAAGGGGTGAAATTATTAAAATACCCTTTAGA
**
11044317 GGTAATTTTGTATTTAACCTTTCTAAGATCGAATTTTCACAAAAA-TTTTAGATCTTAATT
66 GGTAATTTTGTATTTAACCTACCTAAGATCGAATTTTCACAAAAATTTTTAGAT-TTAATT
* * *
11044377 TTTTGGTGCATTAAAAACTTTAGCAGCACCTTGAAAGGGGTTAAATTATTAAAATACCCTTTAGA
1 TTTTGGTGCATTAAAAACCTTAGCAGCACCTCGAAAGGGGTGAAATTATTAAAATACCCTTTAGA
* *
11044442 GGTTATTTTGTATTTAACCTACCTAAGATTGAATTTTCACAAAAATTTTTAGATTTAA
66 GGTAATTTTGTATTTAACCTACCTAAGATCGAATTTTCACAAAAATTTTTAGATTTAA
11044500 ATTTCATATT
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
125 103 0.93
126 8 0.07
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (125 bp):
TTTTGGTGCATTAAAAACCTTAGCAGCACCTCGAAAGGGGTGAAATTATTAAAATACCCTTTAGA
GGTAATTTTGTATTTAACCTACCTAAGATCGAATTTTCACAAAAATTTTTAGATTTAATT
Found at i:11045964 original size:7 final size:7
Alignment explanation
Indices: 11045954--11046014 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
11045944 TTTGAAATCT
11045954 TAAACCC
1 TAAACCC
11045961 TAAACCC
1 TAAACCC
*
11045968 CAAA-CC
1 TAAACCC
11045974 TCAAA-CC
1 T-AAACCC
11045981 TAAACCC
1 TAAACCC
*
11045988 T-AAGCC
1 TAAACCC
*
11045994 TCAAACCT
1 T-AAACCC
11046002 TAAACCC
1 TAAACCC
11046009 TAAACC
1 TAAACC
11046015 TTATCCTAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 10 0.23
7 30 0.68
8 4 0.09
ACGTcount: A:0.43, C:0.41, G:0.02, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:11045984 original size:20 final size:20
Alignment explanation
Indices: 11045959--11046015 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
11045949 AATCTTAAAC
*
11045959 CCTAAACCCCAAACCTCAAA
1 CCTAAACCCTAAACCTCAAA
*
11045979 CCTAAACCCTAAGCCTCAAA
1 CCTAAACCCTAAACCTCAAA
11045999 CCTTAAACCCTAAACCT
1 CC-TAAACCCTAAACCT
11046016 TATCCTAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.40, C:0.42, G:0.02, T:0.16
Consensus pattern (20 bp):
CCTAAACCCTAAACCTCAAA
Found at i:11045990 original size:27 final size:28
Alignment explanation
Indices: 11045954--11046014 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
11045944 TTTGAAATCT
11045954 TAAACCCTAAACCCCAAACCTCAAA-CC
1 TAAACCCTAAACCCCAAACCTCAAACCC
* * *
11045981 TAAACCCTAAGCCTCAAACCTTAAACCC
1 TAAACCCTAAACCCCAAACCTCAAACCC
11046009 TAAACC
1 TAAACC
11046015 TTATCCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.73
28 8 0.27
ACGTcount: A:0.43, C:0.41, G:0.02, T:0.15
Consensus pattern (28 bp):
TAAACCCTAAACCCCAAACCTCAAACCC
Found at i:11050960 original size:10 final size:11
Alignment explanation
Indices: 11050935--11050963 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
11050925 ACCTCAAGCA
11050935 AAAAGAAAGAG
1 AAAAGAAAGAG
11050946 AAAAGAAAG-G
1 AAAAGAAAGAG
11050956 AAAAGAAA
1 AAAAGAAA
11050964 TTAGAGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAG
Found at i:11052725 original size:11 final size:11
Alignment explanation
Indices: 11052709--11052735 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11052699 TTATTTAATA
11052709 AAAAATTATAT
1 AAAAATTATAT
11052720 AAAAATTATAT
1 AAAAATTATAT
11052731 AAAAA
1 AAAAA
11052736 GAGTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:11053630 original size:7 final size:8
Alignment explanation
Indices: 11053603--11053667 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
11053593 AATTTACTTC
11053603 TTTTAATA
1 TTTTAATA
11053611 TTTTAATA
1 TTTTAATA
11053619 TTTTAA-A
1 TTTTAATA
11053626 TTTT-AT-
1 TTTTAATA
11053632 TTTTGAA-A
1 TTTT-AATA
*
11053640 GTTTTGCAT-
1 -TTTT-AATA
*
11053649 TTTTAATT
1 TTTTAATA
11053657 TTTTAATA
1 TTTTAATA
11053665 TTT
1 TTT
11053668 AGAGATTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
6 5 0.11
7 7 0.15
8 29 0.62
9 6 0.13
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (8 bp):
TTTTAATA
Found at i:11053887 original size:16 final size:15
Alignment explanation
Indices: 11053861--11053908 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
11053851 TTTTATAAAC
11053861 TTTTCTATTTTTTAA
1 TTTTCTATTTTTTAA
*
11053876 TTGTTTTATTTTTTAA
1 TT-TTCTATTTTTTAA
11053892 TTTTCTATATTTTTAA
1 TTTTCTAT-TTTTTAA
11053908 T
1 T
11053909 ATTTAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 22 0.76
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTCTATTTTTTAA
Found at i:11054200 original size:12 final size:12
Alignment explanation
Indices: 11054176--11054206 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
11054166 AAAATTTTAT
11054176 AAAATTT-CCAA
1 AAAATTTACCAA
11054187 AAAATTTACCAA
1 AAAATTTACCAA
11054199 AAAATTTA
1 AAAATTTA
11054207 AAGTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATTTACCAA
Found at i:11054283 original size:25 final size:21
Alignment explanation
Indices: 11054255--11054305 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 21
11054245 TATATTTTGA
11054255 AAATTACAAAAACTTTCAAAAAAT
1 AAATTA-AAAAA--TTCAAAAAAT
*
11054279 GAAATTAAAAAATTGAAAAAAT
1 -AAATTAAAAAATTCAAAAAAT
11054301 AAATT
1 AAATT
11054306 TAATATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 5 0.20
22 9 0.36
24 5 0.20
25 6 0.24
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (21 bp):
AAATTAAAAAATTCAAAAAAT
Found at i:11063277 original size:51 final size:51
Alignment explanation
Indices: 11063201--11063302 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
11063191 TAAGTGAGGA
11063201 AAGGGTTAAGAAAGACTGGGTGATACCTATGTTGGTGATGGGAAAAACTGC
1 AAGGGTTAAGAAAGACTGGGTGATACCTATGTTGGTGATGGGAAAAACTGC
11063252 AAGGGTTAAGAAAGACTGGGTGATACCTATGTTGGTGATGGGAAAAACTGC
1 AAGGGTTAAGAAAGACTGGGTGATACCTATGTTGGTGATGGGAAAAACTGC
11063303 CTACTAGGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.24
Consensus pattern (51 bp):
AAGGGTTAAGAAAGACTGGGTGATACCTATGTTGGTGATGGGAAAAACTGC
Found at i:11068802 original size:15 final size:15
Alignment explanation
Indices: 11068762--11068795 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11068752 GTTATGAAAT
* *
11068762 TTTAAGGTTTTAGGG
1 TTTATGGTTTTAAGG
11068777 TTTATGGTTTTAAGG
1 TTTATGGTTTTAAGG
11068792 TTTA
1 TTTA
11068796 GGATTTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (15 bp):
TTTATGGTTTTAAGG
Found at i:11068859 original size:16 final size:16
Alignment explanation
Indices: 11068812--11068943 Score: 89
Period size: 15 Copynumber: 8.6 Consensus size: 16
11068802 TGAGTGCTTT
*
11068812 GGGTTTTG-GATTTTA
1 GGGTTTTGAAATTTTA
* *
11068827 GGATTTT-AAA-ATTA
1 GGGTTTTGAAATTTTA
11068841 GGGTTTTGAAATTTTA
1 GGGTTTTGAAATTTTA
* *
11068857 GGG-TTTCAAGAGTTTA
1 GGGTTTTGAA-ATTTTA
* * *
11068873 TGATTTTG-AGTTTTA
1 GGGTTTTGAAATTTTA
*
11068888 GCGTTTTG-AATTTTA
1 GGGTTTTGAAATTTTA
*
11068903 TGGTTTTGAAA-TTTA
1 GGGTTTTGAAATTTTA
* *
11068918 TGGTTTTAAAATTTTA
1 GGGTTTTGAAATTTTA
*
11068934 AGGTTTTGAA
1 GGGTTTTGAA
11068944 GGTTTATGGT
Statistics
Matches: 89, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
14 9 0.10
15 50 0.56
16 27 0.30
17 3 0.03
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.50
Consensus pattern (16 bp):
GGGTTTTGAAATTTTA
Found at i:11068894 original size:15 final size:15
Alignment explanation
Indices: 11068869--11068956 Score: 88
Period size: 15 Copynumber: 5.7 Consensus size: 15
11068859 GTTTCAAGAG
* *
11068869 TTTATGATTTTGAGT
1 TTTATGGTTTTGAAT
11068884 TTTA-GCGTTTTGAAT
1 TTTATG-GTTTTGAAT
*
11068899 TTTATGGTTTTGAAA
1 TTTATGGTTTTGAAT
*
11068914 TTTATGGTTTTAAAAT
1 TTTATGGTTTT-GAAT
* *
11068930 TTTAAGGTTTTGAAGG
1 TTTATGGTTTTGAA-T
11068946 TTTATGGTTTT
1 TTTATGGTTTT
11068957 AAGGTTTCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
14 1 0.02
15 36 0.60
16 23 0.38
ACGTcount: A:0.23, C:0.01, G:0.20, T:0.56
Consensus pattern (15 bp):
TTTATGGTTTTGAAT
Found at i:11068930 original size:77 final size:75
Alignment explanation
Indices: 11068777--11068956 Score: 193
Period size: 77 Copynumber: 2.3 Consensus size: 75
11068767 GGTTTTAGGG
* * * * *
11068777 TTTATGGTTTTAAGGTTTAGGATTTTGAGTGCTTTGGGTTTTGGATTTTAGGATTTTAAAATTAG
1 TTTAGGGTTTCAAGGTTTATGATTTTGAGT-CTTTGCGTTTTGAATTTTAGGATTTTAAAATTAG
*
11068842 GGTTTTGAAAT
65 GGTTTTAAAAT
*
11068853 TTTAGGGTTTCAAGAGTTTATGATTTTGAGT-TTTAGCGTTTTGAATTTTATGG-TTTTGAAATT
1 TTTAGGGTTTCAAG-GTTTATGATTTTGAGTCTTT-GCGTTTTGAATTTTA-GGATTTT-AAAAT
*
11068916 TATGGTTTTAAAAT
62 TAGGGTTTTAAAAT
* * *
11068930 TTTAAGGTTTTGAAGGTTTATGGTTTT
1 TTT-AGGGTTTCAAGGTTTATGATTTT
11068957 AAGGTTTCAA
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
75 3 0.03
76 29 0.33
77 47 0.53
78 9 0.10
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (75 bp):
TTTAGGGTTTCAAGGTTTATGATTTTGAGTCTTTGCGTTTTGAATTTTAGGATTTTAAAATTAGG
GTTTTAAAAT
Found at i:11068939 original size:31 final size:32
Alignment explanation
Indices: 11068896--11068958 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
11068886 TAGCGTTTTG
*
11068896 AATTTTATGGTTTTGAA-ATTTATGGTTTTAA
1 AATTTTAAGGTTTTGAAGATTTATGGTTTTAA
*
11068927 AATTTTAAGGTTTTGAAGGTTTATGGTTTTAA
1 AATTTTAAGGTTTTGAAGATTTATGGTTTTAA
11068959 GGTTTCAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (32 bp):
AATTTTAAGGTTTTGAAGATTTATGGTTTTAA
Found at i:11068947 original size:9 final size:8
Alignment explanation
Indices: 11068914--11068975 Score: 56
Period size: 8 Copynumber: 7.9 Consensus size: 8
11068904 GGTTTTGAAA
*
11068914 TTTATGGT
1 TTTAAGGT
**
11068922 TTTAAAAT
1 TTTAAGGT
11068930 TTTAAGGT
1 TTTAAGGT
11068938 TTTGAAGG-
1 TTT-AAGGT
*
11068946 TTTATGGT
1 TTTAAGGT
11068954 TTTAAGGT
1 TTTAAGGT
*
11068962 TTCAA-GT
1 TTTAAGGT
11068969 TTTAAGG
1 TTTAAGG
11068976 CTTAAAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
7 9 0.21
8 29 0.69
9 4 0.10
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.50
Consensus pattern (8 bp):
TTTAAGGT
Found at i:11069219 original size:3 final size:3
Alignment explanation
Indices: 11069211--11069255 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
11069201 TTCATAAATT
11069211 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTTA CTTA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
11069255 T
1 T
11069256 CTTATTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
2 6 0.16
3 27 0.71
4 5 0.13
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11069360 original size:3 final size:3
Alignment explanation
Indices: 11069352--11069385 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11069342 TTTTGTTTTC
11069352 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
11069386 AAAAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:11070152 original size:24 final size:24
Alignment explanation
Indices: 11070120--11070166 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11070110 CTTTGTGGGT
11070120 TTTTTTTTTGGAAG-ATTTTTTTAC
1 TTTTTTTTT-GAAGCATTTTTTTAC
*
11070144 TTTTTTTTTGTAGCATTTTTTTA
1 TTTTTTTTTGAAGCATTTTTTTA
11070167 GTTTGGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.15, C:0.04, G:0.11, T:0.70
Consensus pattern (24 bp):
TTTTTTTTTGAAGCATTTTTTTAC
Found at i:11070940 original size:81 final size:81
Alignment explanation
Indices: 11070781--11070948 Score: 230
Period size: 81 Copynumber: 2.1 Consensus size: 81
11070771 AGGTTTTAAA
* * * *
11070781 AATCTCAACATCTATAAATGCTACTCTAAAAAGAGGCCTTGAAACTTTAAGATTTCAAATATTTT
1 AATCTCAACATCTACAAATGCTACTCTAAAAAGAGGCCTTGAAACTTTAAAATTTAAAATATTCT
* ** *
11070846 GCTTAGAGAACTTATG
66 ACCCAGAGAACTTACG
*
11070862 AATCTCAACATCTACAAATGCT-TTCTAAAAAGAGGCCTTGAAACTTTAAAAATTTAAAATATTC
1 AATCTCAACATCTACAAATGCTACTCTAAAAAGAGGCCTTGAAACTTT-AAAATTTAAAATATTC
*
11070926 TACCCAGAGGACTTACG
65 TACCCAGAGAACTTACG
11070943 AATCTC
1 AATCTC
11070949 TTTCTATAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
80 24 0.32
81 52 0.68
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (81 bp):
AATCTCAACATCTACAAATGCTACTCTAAAAAGAGGCCTTGAAACTTTAAAATTTAAAATATTCT
ACCCAGAGAACTTACG
Found at i:11071497 original size:57 final size:56
Alignment explanation
Indices: 11071344--11071612 Score: 190
Period size: 57 Copynumber: 4.7 Consensus size: 56
11071334 TGTGTGACAG
* * **
11071344 CTAAACTAGGCTTAAA-TCTGA-GTGCCAGCT-AATTAGGCTTAAA-ATTTGTGGGCCAA
1 CTAAA-TAGGCTTAAAGTCT-ATGTGCCAGCTAAACTGGGCTTAAATATAAGT--GCCAA
*
11071400 CTAAATAGGACTTAAA-TCTATGTGCCAGCTAATCTGGGCTTAAATATGAA-TGCCAA
1 CTAAATAGG-CTTAAAGTCTATGTGCCAGCTAAACTGGGCTTAAATAT-AAGTGCCAA
* * * * ** *
11071456 CTAAATTAGGCCTAAAGTCTGTGTGCCAACTAAACTTGGCTTAAAATATAAGTGTTAG
1 CTAAA-TAGGCTTAAAGTCTATGTGCCAGCTAAACTGGGCTT-AAATATAAGTGCCAA
* * * * *
11071514 CTAAACTGGGCTTAAAGTCTAAGTGCCAGCTAAACTGGGCTTAAAATCTAAGTGCTAG
1 CTAAA-TAGGCTTAAAGTCTATGTGCCAGCTAAACTGGGCTT-AAATATAAGTGCCAA
* * * * * * *
11071572 CTAATTGGGCTTAAAATTTATGTGCTAGCTAATCTAGGCTT
1 CTAAATAGGCTTAAAGTCTATGTGCCAGCTAAACTGGGCTT
11071613 GGGTGCCAAC
Statistics
Matches: 175, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
55 5 0.03
56 38 0.22
57 67 0.38
58 65 0.37
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (56 bp):
CTAAATAGGCTTAAAGTCTATGTGCCAGCTAAACTGGGCTTAAATATAAGTGCCAA
Found at i:11071500 original size:29 final size:28
Alignment explanation
Indices: 11071314--11071586 Score: 178
Period size: 28 Copynumber: 9.6 Consensus size: 28
11071304 TCTGTATGCT
* * *
11071314 AGCTAAA-TAGGGCTTAAATTTGTGTGAC
1 AGCTAAACT-GGGCTTAAATCTGAGTGCC
*
11071342 AGCTAAACTAGGCTTAAATCTGAGTGCC
1 AGCTAAACTGGGCTTAAATCTGAGTGCC
* * * * *
11071370 AGCT-AATTAGGCTTAAAATTTGTGGGCC
1 AGCTAAACTGGGCTT-AAATCTGAGTGCC
* *
11071398 AACTAAA-TAGGACTTAAATCT-ATGTGCC
1 AGCTAAACT-GGGCTTAAATCTGA-GTGCC
* * *
11071426 AGCTAATCTGGGCTTAAATATGAATGCC
1 AGCTAAACTGGGCTTAAATCTGAGTGCC
* * * * *
11071454 AACTAAATTAGGCCTAAAGTCTGTGTGCC
1 AGCTAAACTGGGCTTAAA-TCTGAGTGCC
* * * * **
11071483 AACTAAACTTGGCTTAAAATATAAGTGTT
1 AGCTAAACTGGGCTT-AAATCTGAGTGCC
*
11071512 AGCTAAACTGGGCTTAAAGTCTAAGTGCC
1 AGCTAAACTGGGCTTAAA-TCTGAGTGCC
* *
11071541 AGCTAAACTGGGCTTAAAATCTAAGTGCT
1 AGCTAAACTGGGCTT-AAATCTGAGTGCC
*
11071570 AGCT-AATTGGGCTTAAA
1 AGCTAAACTGGGCTTAAA
11071587 ATTTATGTGC
Statistics
Matches: 192, Mismatches: 42, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
27 12 0.06
28 93 0.48
29 81 0.42
30 6 0.03
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (28 bp):
AGCTAAACTGGGCTTAAATCTGAGTGCC
Found at i:11071530 original size:58 final size:57
Alignment explanation
Indices: 11071410--11071586 Score: 171
Period size: 58 Copynumber: 3.1 Consensus size: 57
11071400 CTAAATAGGA
* * * * * * *
11071410 CTTAAA-TCTATGTGCCAGCTAATCTGGGCTT-AAATATGAA-TGCCAACTAAATTAGG
1 CTTAAAGTCTAAGTGCCAACTAAACTGGGCTTAAAATAT-AAGTGCTAGCT-AACTGGG
* ** * *
11071466 CCTAAAGTCTGTGTGCCAACTAAACTTGGCTTAAAATATAAGTGTTAGCTAAACTGGG
1 CTTAAAGTCTAAGTGCCAACTAAACTGGGCTTAAAATATAAGTGCTAGCT-AACTGGG
* * *
11071524 CTTAAAGTCTAAGTGCCAGCTAAACTGGGCTTAAAATCTAAGTGCTAGCTAATTGGG
1 CTTAAAGTCTAAGTGCCAACTAAACTGGGCTTAAAATATAAGTGCTAGCTAACTGGG
11071581 CTTAAA
1 CTTAAA
11071587 ATTTATGTGC
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
56 5 0.05
57 35 0.35
58 60 0.60
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (57 bp):
CTTAAAGTCTAAGTGCCAACTAAACTGGGCTTAAAATATAAGTGCTAGCTAACTGGG
Found at i:11071596 original size:28 final size:29
Alignment explanation
Indices: 11071485--11071612 Score: 159
Period size: 29 Copynumber: 4.4 Consensus size: 29
11071475 TGTGTGCCAA
* * *
11071485 CTAAACTTGGCTTAAAATATAAGTGTTAG
1 CTAAACTGGGCTTAAAATCTAAGTGCTAG
* *
11071514 CTAAACTGGGCTTAAAGTCTAAGTGCCAG
1 CTAAACTGGGCTTAAAATCTAAGTGCTAG
11071543 CTAAACTGGGCTTAAAATCTAAGTGCTAG
1 CTAAACTGGGCTTAAAATCTAAGTGCTAG
* * *
11071572 CT-AATTGGGCTTAAAATTTATGTGCTAG
1 CTAAACTGGGCTTAAAATCTAAGTGCTAG
* *
11071600 CTAATCTAGGCTT
1 CTAAACTGGGCTT
11071613 GGGTGCCAAC
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 25 0.29
29 60 0.71
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (29 bp):
CTAAACTGGGCTTAAAATCTAAGTGCTAG
Found at i:11071889 original size:28 final size:28
Alignment explanation
Indices: 11071849--11071903 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
11071839 TTCCTTTCTT
* *
11071849 TTTCTTTTCTTTTTTTTGACAAACTTTC
1 TTTCTTTTCTTTTTCTTAACAAACTTTC
11071877 TTTC-TTTCTTTTTTCTTAACAAACTTT
1 TTTCTTTTC-TTTTTCTTAACAAACTTT
11071904 TTCCTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.16, C:0.18, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTCTTTTCTTTTTCTTAACAAACTTTC
Found at i:11079345 original size:41 final size:42
Alignment explanation
Indices: 11079300--11079385 Score: 147
Period size: 41 Copynumber: 2.0 Consensus size: 42
11079290 GTGTCAATGG
11079300 TATTCTAGTAATATTCAAGTAATATTCTAGATTGA-TGATAT
1 TATTCTAGTAATATTCAAGTAATATTCTAGATTGATTGATAT
*
11079341 TATTCTAGTAATATTCTAGTAATATTCTAGATTGATTTGATAT
1 TATTCTAGTAATATTCAAGTAATATTCTAGATTGA-TTGATAT
11079384 TA
1 TA
11079386 ATTTAGAGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
41 34 0.81
43 8 0.19
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (42 bp):
TATTCTAGTAATATTCAAGTAATATTCTAGATTGATTGATAT
Found at i:11079357 original size:11 final size:11
Alignment explanation
Indices: 11079341--11079370 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
11079331 TTGATGATAT
11079341 TATTCTAGTAA
1 TATTCTAGTAA
11079352 TATTCTAGTAA
1 TATTCTAGTAA
11079363 TATTCTAG
1 TATTCTAG
11079371 ATTGATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (11 bp):
TATTCTAGTAA
Found at i:11083067 original size:11 final size:11
Alignment explanation
Indices: 11083051--11083123 Score: 55
Period size: 11 Copynumber: 7.0 Consensus size: 11
11083041 GGGGTGTCAA
11083051 TAATATTCTAG
1 TAATATTCTAG
* *
11083062 TAATATTTTGG
1 TAATATTCTAG
11083073 TAATATTCTAG
1 TAATATTCTAG
** *
11083084 --AT-TGATAA
1 TAATATTCTAG
*
11083092 TATTATT-TAG
1 TAATATTCTAG
*
11083102 TAATATTCCAG
1 TAATATTCTAG
11083113 TAATATTCTAG
1 TAATATTCTAG
11083124 ATTGATTTAA
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
8 3 0.07
9 2 0.04
10 9 0.20
11 31 0.69
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (11 bp):
TAATATTCTAG
Found at i:11083106 original size:40 final size:42
Alignment explanation
Indices: 11083049--11083138 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 42
11083039 AAGGGGTGTC
* ***
11083049 AATAATATTCTAGTAATATTTTGGTAATATTCTAGATTGA-T
1 AATATTATTCTAGTAATATTCCAGTAATATTCTAGATTGATT
11083090 AATATTATT-TAGTAATATTCCAGTAATATTCTAGATTGATTT
1 AATATTATTCTAGTAATATTCCAGTAATATTCTAGATTGA-TT
11083132 AATATTA
1 AATATTA
11083139 ATTTGGAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 27 0.63
41 8 0.19
42 8 0.19
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.47
Consensus pattern (42 bp):
AATATTATTCTAGTAATATTCCAGTAATATTCTAGATTGATT
Found at i:11084793 original size:2 final size:2
Alignment explanation
Indices: 11084786--11084815 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11084776 CTAGTTGGTG
*
11084786 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11084816 ACTTTAGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11085321 original size:16 final size:16
Alignment explanation
Indices: 11085297--11085330 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11085287 ATTAACTTTC
*
11085297 TTCAATTTATGTCATT
1 TTCAATTTATGTAATT
*
11085313 TTCATTTTATGTAATT
1 TTCAATTTATGTAATT
11085329 TT
1 TT
11085331 TTTATACACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (16 bp):
TTCAATTTATGTAATT
Found at i:11085729 original size:16 final size:16
Alignment explanation
Indices: 11085708--11085750 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
11085698 TTGCTTTTAA
11085708 AAAAAAATAATACTAT
1 AAAAAAATAATACTAT
*
11085724 AAAAAAATTAA-ATTAT
1 AAAAAAA-TAATACTAT
*
11085740 AAAAAATTAAT
1 AAAAAAATAAT
11085751 TTGAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAAATAATACTAT
Found at i:11086858 original size:19 final size:20
Alignment explanation
Indices: 11086828--11086865 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11086818 AAGGGATCAA
11086828 GTTGGTTTTAGGATTTGGGT
1 GTTGGTTTTAGGATTTGGGT
*
11086848 GTTGG-TTTAGGGTTTGGG
1 GTTGGTTTTAGGATTTGGG
11086866 ATTAGGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.08, C:0.00, G:0.45, T:0.47
Consensus pattern (20 bp):
GTTGGTTTTAGGATTTGGGT
Found at i:11086861 original size:7 final size:7
Alignment explanation
Indices: 11086851--11086945 Score: 54
Period size: 7 Copynumber: 14.1 Consensus size: 7
11086841 TTTGGGTGTT
11086851 GGTTTAG
1 GGTTTAG
11086858 GGTTT-G
1 GGTTTAG
*
11086864 GGATTAG
1 GGTTTAG
* *
11086871 GATTTTG
1 GGTTTAG
* *
11086878 GTTTTAA
1 GGTTTAG
11086885 GGTTTAG
1 GGTTTAG
11086892 GG-TTAG
1 GGTTTAG
*
11086898 GGTTTAA
1 GGTTTAG
* *
11086905 GATTT-T
1 GGTTTAG
*
11086911 GGCTTA-
1 GGTTTAG
11086917 GGTTTAG
1 GGTTTAG
*
11086924 GGTTTAA
1 GGTTTAG
*
11086931 TGTTTAG
1 GGTTTAG
*
11086938 GATTTAG
1 GGTTTAG
11086945 G
1 G
11086946 TTTGGATTTA
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
6 19 0.30
7 45 0.70
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:11086918 original size:26 final size:27
Alignment explanation
Indices: 11086888--11086965 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 27
11086878 GTTTTAAGGT
11086888 TTAGGGTTAGGGTTTAAGATTTTGG-C
1 TTAGGGTTAGGGTTTAAGATTTTGGAC
* * *
11086914 TTAGGTTTAGGGTTTAATG-TTTAGGAT
1 TTAGGGTTAGGGTTTAA-GATTTTGGAC
* *
11086941 TTA-GGTTTGGATTTAAGATTTTGGA
1 TTAGGGTTAGGGTTTAAGATTTTGGA
11086966 ATGCATGAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
25 1 0.02
26 37 0.88
27 4 0.10
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (27 bp):
TTAGGGTTAGGGTTTAAGATTTTGGAC
Found at i:11086954 original size:12 final size:13
Alignment explanation
Indices: 11086851--11086955 Score: 54
Period size: 13 Copynumber: 8.0 Consensus size: 13
11086841 TTTGGGTGTT
* *
11086851 GGTTTAGGGTTTG
1 GGTTTAGGATTTA
* *
11086864 GGATTAGGATTTT
1 GGTTTAGGATTTA
11086877 GGTTTTAAGG-TTTA
1 GG-TTT-AGGATTTA
* *
11086891 GGGTTAGGGTTTAA
1 GGTTTAGGATTT-A
* * *
11086905 GATTTTGG-CTTA
1 GGTTTAGGATTTA
*
11086917 GGTTTAGGGTTTAA
1 GGTTTAGGATTT-A
*
11086931 TGTTTAGGATTTA
1 GGTTTAGGATTTA
11086944 GGTTT-GGATTTA
1 GGTTTAGGATTTA
11086956 AGATTTTGGA
Statistics
Matches: 70, Mismatches: 16, Indels: 13
0.71 0.16 0.13
Matches are distributed among these distances:
12 17 0.24
13 26 0.37
14 24 0.34
15 3 0.04
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.47
Consensus pattern (13 bp):
GGTTTAGGATTTA
Found at i:11088829 original size:21 final size:22
Alignment explanation
Indices: 11088805--11088858 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
11088795 ATTTGAAAAT
11088805 TTTAAATTAAAAAAAT-ATATA
1 TTTAAATTAAAAAAATAATATA
* ***
11088826 TTTAGATT-ATTTAATAATATA
1 TTTAAATTAAAAAAATAATATA
11088847 TTTAAATTAAAA
1 TTTAAATTAAAA
11088859 TTTGTTGCCA
Statistics
Matches: 24, Mismatches: 7, Indels: 3
0.71 0.21 0.09
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTTAAATTAAAAAAATAATATA
Found at i:11090636 original size:34 final size:35
Alignment explanation
Indices: 11090585--11090660 Score: 113
Period size: 34 Copynumber: 2.2 Consensus size: 35
11090575 GGAAATTCCA
11090585 TTTTGG-AAACATATTCAATCTATT-GAAAATGCAG
1 TTTTGGAAAACATATTCAAT-TATTCGAAAATGCAG
*
11090619 TTTTGGAAAACAT-TTCAATTATTCGAAAATGCAT
1 TTTTGGAAAACATATTCAATTATTCGAAAATGCAG
11090653 TTTTGGAA
1 TTTTGGAA
11090661 TTTTTTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 4 0.10
34 29 0.74
35 6 0.15
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (35 bp):
TTTTGGAAAACATATTCAATTATTCGAAAATGCAG
Found at i:11093599 original size:23 final size:21
Alignment explanation
Indices: 11093569--11093610 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
11093559 AAACTGATTA
11093569 ATGACTTTTCATAGATATTTTGT
1 ATGACTTTTCAT-G-TATTTTGT
11093592 ATGACTTTTCATGTATTTT
1 ATGACTTTTCATGTATTTT
11093611 TGTTGGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.55
Consensus pattern (21 bp):
ATGACTTTTCATGTATTTTGT
Found at i:11093636 original size:14 final size:14
Alignment explanation
Indices: 11093617--11093644 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11093607 TTTTTGTTGG
11093617 ATATTTTGTATTTT
1 ATATTTTGTATTTT
11093631 ATATTTTGTATTTT
1 ATATTTTGTATTTT
11093645 GATGGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (14 bp):
ATATTTTGTATTTT
Found at i:11097334 original size:87 final size:87
Alignment explanation
Indices: 11097188--11097366 Score: 315
Period size: 87 Copynumber: 2.1 Consensus size: 87
11097178 TATTTGGACT
11097188 TGAAGATAAAGAAAACTAGAGTGGAATTGGTAGTTACATGGAGTGGAGAATAGTATGTGGAGTAC
1 TGAAGATAAAGAAAACTAGAGTGGAATTGGTAGTTACATGGAGTGGAGAATAGTATGTGGAGTAC
*
11097253 TTTTTACCCATTATCAAGCACC
66 TTTTTACCCATTATCAAGCACA
*
11097275 TGAAGATAAATAAAACT-GAAGTGGAATTGGTAGTTACATGGAGTGGAGAATAGTATGTGGAGTA
1 TGAAGATAAAGAAAACTAG-AGTGGAATTGGTAGTTACATGGAGTGGAGAATAGTATGTGGAGTA
*
11097339 GTTTTTACCCATTATCAAGCACA
65 CTTTTTACCCATTATCAAGCACA
11097362 TGAAG
1 TGAAG
11097367 GCTTGAAAGC
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
86 1 0.01
87 87 0.99
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (87 bp):
TGAAGATAAAGAAAACTAGAGTGGAATTGGTAGTTACATGGAGTGGAGAATAGTATGTGGAGTAC
TTTTTACCCATTATCAAGCACA
Found at i:11101468 original size:23 final size:22
Alignment explanation
Indices: 11101421--11101469 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
11101411 AGGCTAGAAG
* *
11101421 AAAAAAGGGAAAAACTTTTAAA
1 AAAAAAGGGAAAAAATTCTAAA
*
11101443 AAAAAAGGGAAAAAATTGCTAGA
1 AAAAAAGGGAAAAAATT-CTAAA
11101466 AAAA
1 AAAA
11101470 GAACAGCAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.65, C:0.04, G:0.16, T:0.14
Consensus pattern (22 bp):
AAAAAAGGGAAAAAATTCTAAA
Found at i:11107121 original size:15 final size:15
Alignment explanation
Indices: 11107101--11107129 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11107091 TACATACAAA
11107101 TGCCACTAAATTTAG
1 TGCCACTAAATTTAG
11107116 TGCCACTAAATTTA
1 TGCCACTAAATTTA
11107130 ATAACATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
TGCCACTAAATTTAG
Found at i:11108542 original size:48 final size:47
Alignment explanation
Indices: 11108479--11108578 Score: 121
Period size: 48 Copynumber: 2.1 Consensus size: 47
11108469 ATATTACAAG
* *
11108479 TTTTTATTTCTAAATTTTTCACC-CTTTGGACCATTTCAGAAAATTTC
1 TTTTTATTTCTAAATTTTCCACCACTTGGGACCATTT-AGAAAATTTC
* * * *
11108526 TTTTTAATTTTTAAATTTTCCACCACTTGGGTCTATTTAGAAAATTTT
1 TTTTT-ATTTCTAAATTTTCCACCACTTGGGACCATTTAGAAAATTTC
11108574 TTTTT
1 TTTTT
11108579 CTTATCTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 5 0.11
48 30 0.67
49 10 0.22
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (47 bp):
TTTTTATTTCTAAATTTTCCACCACTTGGGACCATTTAGAAAATTTC
Found at i:11108863 original size:27 final size:25
Alignment explanation
Indices: 11108833--11108888 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
11108823 ACAAATTTAG
*
11108833 AGAAATTTCTCACCTAAAGATTTCTCA
1 AGAAATTTATCACCTAAA-ATTTCT-A
* *
11108860 AGAAATTTATCACTTGAAATTTCTA
1 AGAAATTTATCACCTAAAATTTCTA
11108885 AGAA
1 AGAA
11108889 TCTCATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 5 0.19
26 6 0.23
27 15 0.58
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (25 bp):
AGAAATTTATCACCTAAAATTTCTA
Found at i:11110994 original size:15 final size:15
Alignment explanation
Indices: 11110974--11111004 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11110964 CAATTTCAAT
*
11110974 ATTCAAAGGTTTGCA
1 ATTCAAAGATTTGCA
11110989 ATTCAAAGATTTGCA
1 ATTCAAAGATTTGCA
11111004 A
1 A
11111005 GAATTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (15 bp):
ATTCAAAGATTTGCA
Found at i:11111024 original size:18 final size:18
Alignment explanation
Indices: 11111003--11111042 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11110993 AAAGATTTGC
**
11111003 AAGAATTTTTAGGTTCGT
1 AAGAATTTCCAGGTTCGT
*
11111021 AAGAATTTCCAGGTTTGT
1 AAGAATTTCCAGGTTCGT
11111039 AAGA
1 AAGA
11111043 TAGAAAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (18 bp):
AAGAATTTCCAGGTTCGT
Found at i:11111087 original size:18 final size:18
Alignment explanation
Indices: 11111064--11111098 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11111054 GCAAGAACTT
11111064 AAATTCACAAAAATTTTC
1 AAATTCACAAAAATTTTC
*
11111082 AAATTCACCAAAATTTT
1 AAATTCACAAAAATTTT
11111099 ATTCATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTCACAAAAATTTTC
Found at i:11111173 original size:32 final size:35
Alignment explanation
Indices: 11111100--11111173 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 35
11111090 CAAAATTTTA
*
11111100 TTCATAA-AATTTTAGATTCCCAAGGATTTTTGGC
1 TTCATAAGAATTTTAGATTCCCAAGGATTTTAGGC
* *
11111134 TT-GTAAGAA-TTT-GATTCTCAAGGATTTTAGG-
1 TTCATAAGAATTTTAGATTCCCAAGGATTTTAGGC
11111165 TTCATAAGA
1 TTCATAAGA
11111174 CCTTAGATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
31 2 0.06
32 22 0.65
33 6 0.18
34 4 0.12
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (35 bp):
TTCATAAGAATTTTAGATTCCCAAGGATTTTAGGC
Found at i:11111184 original size:16 final size:16
Alignment explanation
Indices: 11111160--11111200 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
11111150 CTCAAGGATT
* *
11111160 TTAGGTTCATAAGACC
1 TTAGATTCATAAGAAC
11111176 TTAGATTCATAAGAAC
1 TTAGATTCATAAGAAC
11111192 TTAGATTCA
1 TTAGATTCA
11111201 CAAAATTTTA
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:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (16 bp):
TTAGATTCATAAGAAC
Found at i:11111582 original size:107 final size:108
Alignment explanation
Indices: 11111443--11111644 Score: 273
Period size: 107 Copynumber: 1.9 Consensus size: 108
11111433 TTTAGGATTT
* * *
11111443 CATCCAAAATTTCAAAGCTTTTTATTCAAGTTCAAAGATTCACATTCGAT-GAATTTTAGAGTTT
1 CATCCAAAAGTTCAAAGCTTTTCATTCAAGTTCAAAGATTCACATTCAATAG-ATTTTAGAGTTT
*
11111507 CACGTCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGTTTCA
65 CACATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGTTTCA
** * * *
11111551 CATCC-AAAGTTCAAAGCTTTTCATTTGAGTTCAATGATTGACATTCAATAGATTTTAGATTTTC
1 CATCCAAAAGTTCAAAGCTTTTCATTCAAGTTCAAAGATTCACATTCAATAGATTTTAGAGTTTC
** *
11111615 TTATCTAAATTCAAAGGTTCTCATTTAAAA
66 ACATCTAAATTCAAAGGTTCTCATTCAAAA
11111645 CTCATAGTTT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
107 75 0.93
108 6 0.07
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (108 bp):
CATCCAAAAGTTCAAAGCTTTTCATTCAAGTTCAAAGATTCACATTCAATAGATTTTAGAGTTTC
ACATCTAAATTCAAAGGTTCTCATTCAAAAAATTTAAGTTTCA
Found at i:11111656 original size:21 final size:21
Alignment explanation
Indices: 11111627--11111688 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
11111617 ATCTAAATTC
* *
11111627 AAAGGTTCTCATTTAAAACTC
1 AAAGTTTCTCATTTAAAACTA
* *
11111648 ATAGTTTCTCATTTAAAATTA
1 AAAGTTTCTCATTTAAAACTA
11111669 AAAGTTTCTCATTTAAAACT
1 AAAGTTTCTCATTTAAAACT
11111689 TCTAAAAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (21 bp):
AAAGTTTCTCATTTAAAACTA
Found at i:11111704 original size:24 final size:21
Alignment explanation
Indices: 11111621--11111705 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
11111611 TTTCTTATCT
* *
11111621 AAATTCAAAGGTTCTCATTTA
1 AAATTAAAAGATTCTCATTTA
* * * *
11111642 AAACTCATAGTTTCTCATTTA
1 AAATTAAAAGATTCTCATTTA
*
11111663 AAATTAAAAGTTTCTCATTTA
1 AAATTAAAAGATTCTCATTTA
*
11111684 AAACTTCTAAAAGATTGTCATT
1 AAA--T-TAAAAGATTCTCATT
11111706 ATTTTTAACT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
21 39 0.74
23 1 0.02
24 13 0.25
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTAAAAGATTCTCATTTA
Found at i:11112873 original size:9 final size:8
Alignment explanation
Indices: 11112845--11112944 Score: 91
Period size: 9 Copynumber: 12.2 Consensus size: 8
11112835 TCAATTTGAG
*
11112845 TTTTCCTT
1 TTTTCATT
11112853 TTTTC-TT
1 TTTTCATT
11112860 GTTTTACATT
1 -TTTT-CATT
11112870 TTTTCCATT
1 TTTT-CATT
*
11112879 TTTTTA-T
1 TTTTCATT
11112886 TTTTCA-T
1 TTTTCATT
11112893 TTTTCATT
1 TTTTCATT
11112901 TTTTCATT
1 TTTTCATT
11112909 TGTTTCATT
1 T-TTTCATT
11112918 TGTTTCA-T
1 T-TTTCATT
11112926 TTTTCATT
1 TTTTCATT
*
11112934 CTTTCACTT
1 TTTTCA-TT
11112943 TT
1 TT
11112945 CATCTATTAT
Statistics
Matches: 80, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
7 20 0.25
8 28 0.35
9 30 0.38
10 2 0.03
ACGTcount: A:0.11, C:0.15, G:0.03, T:0.71
Consensus pattern (8 bp):
TTTTCATT
Found at i:11112888 original size:7 final size:8
Alignment explanation
Indices: 11112845--11112944 Score: 91
Period size: 8 Copynumber: 12.4 Consensus size: 8
11112835 TCAATTTGAG
*
11112845 TTTTCCTT
1 TTTTCATT
11112853 TTTTC-TT
1 TTTTCATT
11112860 GTTTTACATT
1 -TTTT-CATT
11112870 TTTTCCATT
1 TTTT-CATT
*
11112879 TTTTTA-T
1 TTTTCATT
11112886 TTTTCA-T
1 TTTTCATT
11112893 TTTTCATT
1 TTTTCATT
11112901 TTTTCATT
1 TTTTCATT
11112909 TGTTTCATT
1 T-TTTCATT
11112918 TGTTTCA-T
1 T-TTTCATT
11112926 TTTTCATT
1 TTTTCATT
* *
11112934 CTTTCACT
1 TTTTCATT
11112942 TTT
1 TTT
11112945 CATCTATTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
7 20 0.25
8 31 0.39
9 27 0.34
10 2 0.03
ACGTcount: A:0.11, C:0.15, G:0.03, T:0.71
Consensus pattern (8 bp):
TTTTCATT
Found at i:11112896 original size:40 final size:40
Alignment explanation
Indices: 11112852--11112944 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 40
11112842 GAGTTTTCCT
*
11112852 TTTTTC-TTGTTTTACATTT-TTTCCATTT-TTTTATTTTTCA
1 TTTTTCATT-TTTT-CATTTGTTT-CATTTGTTTCATTTTTCA
11112892 TTTTTCATTTTTTCATTTGTTTCATTTGTTTCATTTTTCA
1 TTTTTCATTTTTTCATTTGTTTCATTTGTTTCATTTTTCA
*
11112932 TTCTTTCACTTTT
1 TT-TTTCATTTTT
11112945 CATCTATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
39 10 0.21
40 26 0.55
41 11 0.23
ACGTcount: A:0.12, C:0.14, G:0.03, T:0.71
Consensus pattern (40 bp):
TTTTTCATTTTTTCATTTGTTTCATTTGTTTCATTTTTCA
Found at i:11112918 original size:48 final size:48
Alignment explanation
Indices: 11112845--11112947 Score: 115
Period size: 48 Copynumber: 2.1 Consensus size: 48
11112835 TCAATTTGAG
* * *
11112845 TTTTCCTTTTTTCTTGTTTTACATTT-TTTCCATTTTTTTATT-TTTCAT
1 TTTTCATTTTTTCTTGTTTTACATTTGTTT-CA-TTTTTCATTCTTTCAC
11112893 TTTTCATTTTTTCATT-TGTTT-CATTTGTTTCATTTTTCATTCTTTCAC
1 TTTTCATTTTTTC-TTGT-TTTACATTTGTTTCATTTTTCATTCTTTCAC
11112941 TTTTCAT
1 TTTTCAT
11112948 CTATTATTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
47 8 0.17
48 32 0.67
49 8 0.17
ACGTcount: A:0.12, C:0.16, G:0.03, T:0.70
Consensus pattern (48 bp):
TTTTCATTTTTTCTTGTTTTACATTTGTTTCATTTTTCATTCTTTCAC
Found at i:11112929 original size:33 final size:30
Alignment explanation
Indices: 11112861--11112944 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 30
11112851 TTTTTTCTTG
* *
11112861 TTTTACATTTTTTCCATTTTTTTATTTTTCA
1 TTTTTCATTTTTT-CATTTTTTCATTTTTCA
11112892 TTTTTCATTTTTTCATTTGTTTCATTTGTTTCA
1 TTTTTCATTTTTTCATTT-TTTCA-TT-TTTCA
* *
11112925 TTTTTCATTCTTTCACTTTT
1 TTTTTCATTTTTTCATTTTT
11112945 CATCTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 5 0.11
31 16 0.35
32 4 0.09
33 21 0.46
ACGTcount: A:0.13, C:0.14, G:0.02, T:0.70
Consensus pattern (30 bp):
TTTTTCATTTTTTCATTTTTTCATTTTTCA
Found at i:11112945 original size:7 final size:7
Alignment explanation
Indices: 11112878--11112947 Score: 68
Period size: 7 Copynumber: 9.1 Consensus size: 7
11112868 TTTTTTCCAT
*
11112878 TTTTTTA
1 TTTTTCA
11112885 TTTTTCA
1 TTTTTCA
11112892 TTTTTCA
1 TTTTTCA
11112899 TTTTTTCA
1 -TTTTTCA
11112907 TTTGTTTCA
1 -TT-TTTCA
11112916 TTTGTTTCA
1 -TT-TTTCA
11112925 TTTTTCA
1 TTTTTCA
11112932 TTCTTTCA
1 TT-TTTCA
*
11112940 CTTTTCA
1 TTTTTCA
11112947 T
1 T
11112948 CTATTATTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
7 25 0.44
8 18 0.32
9 14 0.25
ACGTcount: A:0.13, C:0.14, G:0.03, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Found at i:11113354 original size:29 final size:29
Alignment explanation
Indices: 11113303--11113368 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
11113293 ATGGCATTCA
* *
11113303 TTTTTTTTTTGTAAAGAGTTTTTCTTTCC
1 TTTTTTTTGTGTAAAGAGGTTTTCTTTCC
* * **
11113332 TTTTTTTTGTGTAAAGGGGTTTTTTTTTT
1 TTTTTTTTGTGTAAAGAGGTTTTCTTTCC
11113361 TTTTTTTT
1 TTTTTTTT
11113369 TTTACTCTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.11, C:0.05, G:0.14, T:0.71
Consensus pattern (29 bp):
TTTTTTTTGTGTAAAGAGGTTTTCTTTCC
Found at i:11116300 original size:2 final size:2
Alignment explanation
Indices: 11116293--11116323 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11116283 TCATGTGATA
11116293 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
11116324 AAAGAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:11117022 original size:47 final size:46
Alignment explanation
Indices: 11116970--11117067 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 46
11116960 ATTTTACAAG
*
11116970 TTTTT-ATTCCTAAATTTTCCACCCTTTGGGTAAATTTAAAAATTTT
1 TTTTTAATTCCT-AATTTTCCACCATTTGGGTAAATTTAAAAATTTT
* * ** *
11117016 CTTTTTAATTTCTAATTTTTCACCATTTGGGTCTATTTAGAAATTTT
1 -TTTTTAATTCCTAATTTTCCACCATTTGGGTAAATTTAAAAATTTT
11117063 TTTTT
1 TTTTT
11117068 GTTTTTTATC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 5 0.11
47 34 0.77
48 5 0.11
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.55
Consensus pattern (46 bp):
TTTTTAATTCCTAATTTTCCACCATTTGGGTAAATTTAAAAATTTT
Found at i:11117563 original size:24 final size:26
Alignment explanation
Indices: 11117508--11117564 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
11117498 CAACTTTAGA
*
11117508 AAAAATTTCTCTCTTTGGAATTTTAT
1 AAAAATTTCTCTCTTTGAAATTTTAT
*
11117534 AGAAATTTAC-CT-TTTGAAATTTT-T
1 AAAAATTT-CTCTCTTTGAAATTTTAT
11117558 AAAAATT
1 AAAAATT
11117565 CTATCATTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.26
25 10 0.37
26 9 0.33
27 1 0.04
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (26 bp):
AAAAATTTCTCTCTTTGAAATTTTAT
Found at i:11128140 original size:16 final size:16
Alignment explanation
Indices: 11128121--11128151 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11128111 ATATTTTGCT
11128121 TGAAAAAAGAAAAAAA
1 TGAAAAAAGAAAAAAA
11128137 TGAAAAAAGAAAAAA
1 TGAAAAAAGAAAAAA
11128152 GAAAAAAATA
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:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (16 bp):
TGAAAAAAGAAAAAAA
Found at i:11128149 original size:6 final size:7
Alignment explanation
Indices: 11128122--11128158 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
11128112 TATTTTGCTT
11128122 GAAAAAA
1 GAAAAAA
11128129 GAAAAAAA
1 G-AAAAAA
11128137 TGAAAAAA
1 -GAAAAAA
11128145 GAAAAAA
1 GAAAAAA
11128152 GAAAAAA
1 GAAAAAA
11128159 ATAAGACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 15 0.54
8 12 0.43
9 1 0.04
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (7 bp):
GAAAAAA
Found at i:11129265 original size:49 final size:48
Alignment explanation
Indices: 11129191--11129466 Score: 236
Period size: 49 Copynumber: 5.7 Consensus size: 48
11129181 TTTTAAGGCA
* * * *
11129191 AAAGC-TTTTGATTGTGAATTTTTAAAGTTGCAATGCCTTTGTTAAGG
1 AAAGCTTTTTAATTGTCAATTTTTAAAGTTTCAATGCCTTTATTAAGG
** *
11129238 AGAAGCTTTTTAATTG-CAATTTTTTAAAGTTTCAACACCTTTCTTAA-G
1 A-AAGCTTTTTAATTGTCAA-TTTTTAAAGTTTCAATGCCTTTATTAAGG
* * *
11129286 AAAGATTTTTTTATTGTCAATTTTTAAAGTTTCAATGCCTTTATTGAGG
1 AAAG-CTTTTTAATTGTCAATTTTTAAAGTTTCAATGCCTTTATTAAGG
* * * * * * *
11129335 AAGAGCTTTTCAATTTTGAATTTTTAACA-TTTCAAAGCCTCTATTGAGAA
1 AA-AGCTTTTTAATTGTCAATTTTTAA-AGTTTCAATGCCTTTATTAAG-G
* * * *
11129385 AAAGCTTTTTTATTTTGAATTTTTAAAGTTTTAATGCCTTTATTAAGG
1 AAAGCTTTTTAATTGTCAATTTTTAAAGTTTCAATGCCTTTATTAAGG
* * * *
11129433 AAGAGCTTTCTAATTTTGAATTTTTTAAGTTTCA
1 AA-AGCTTTTTAATTGTCAATTTTTAAAGTTTCA
11129467 GCACCTCTGT
Statistics
Matches: 187, Mismatches: 31, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
47 4 0.02
48 43 0.23
49 135 0.72
50 5 0.03
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (48 bp):
AAAGCTTTTTAATTGTCAATTTTTAAAGTTTCAATGCCTTTATTAAGG
Found at i:11129360 original size:97 final size:96
Alignment explanation
Indices: 11129196--11129539 Score: 346
Period size: 98 Copynumber: 3.6 Consensus size: 96
11129186 AGGCAAAAGC
* * * *
11129196 TTTTGATTGTGAATTTTTAAAGTTGCAATGCCTTTGTTAAGG-AGAAGCTTTTTAA--TTGCAAT
1 TTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAG-AGCTTTTCAATTTTG-AA-
* *
11129258 TTTTTAAAGTTTCAACACCTTTCTTAAGAAAGATT
63 TTTTTAAAGTTTCAACACCTCTATT-AGAAAGATT
* *
11129293 TTTTTATTGTCAATTTTTAAAGTTTCAATGCCTTTATTGAGGAAGAGCTTTTCAATTTTGAATTT
1 TTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTCAATTTTGAATTT
* *
11129358 TTAACA-TTTCAA-AGCCTCTATTGAGAAAAAGCT
66 TTAA-AGTTTCAACA-CCTCTATT-AGAAAGA-TT
* *
11129391 TTTTTATTTTGAATTTTTAAAGTTTTAATGCCTTTATTAAGGAAGAGC-TTTCTAATTTTGAATT
1 TTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTC-AATTTTGAATT
* * * * *
11129455 TTTTAAGTTTCAGCACCTCTGTT--CATGATT
65 TTTAAAGTTTCAACACCTCTATTAGAAAGATT
* * * * *
11129485 TTTTTATTTTGAATTTTT-AAGTTTCAAAGCCTCTATTAAGGAGGATCTTTTCAAT
1 TTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTCAAT
11129540 ATTGTTTCCT
Statistics
Matches: 210, Mismatches: 27, Indels: 24
0.80 0.10 0.09
Matches are distributed among these distances:
93 27 0.13
94 23 0.11
95 2 0.01
96 1 0.00
97 76 0.36
98 77 0.37
99 4 0.02
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (96 bp):
TTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTCAATTTTGAATTT
TTAAAGTTTCAACACCTCTATTAGAAAGATT
Found at i:11129424 original size:98 final size:98
Alignment explanation
Indices: 11129190--11129539 Score: 332
Period size: 97 Copynumber: 3.6 Consensus size: 98
11129180 CTTTTAAGGC
* * * *
11129190 AAAAGC-TTTTGATTGTGAATTTTTAAAGTTGCAATGCCTTTGTTAAGG-AGAAGCTTTTTAA--
1 AAAAGCTTTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAG-AGCTTTTCAATT
* *
11129251 TTGCAATTTTTTAAAGTTTCAACACCTTTCTTAAGA
65 TTG-AA-TTTTTAAAGTTTCAACACCTCTATTAAGA
* * * *
11129287 AAGA-TTTTTTTATTGTCAATTTTTAAAGTTTCAATGCCTTTATTGAGGAAGAGCTTTTCAATTT
1 AAAAGCTTTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTCAATTT
*
11129351 TGAATTTTTAACA-TTTCAA-AGCCTCTATTGAGA
66 TGAATTTTTAA-AGTTTCAACA-CCTCTATTAAGA
* *
11129384 AAAAGCTTTTTTATTTTGAATTTTTAAAGTTTTAATGCCTTTATTAAGGAAGAGC-TTTCTAATT
1 AAAAGCTTTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTC-AATT
* * * *
11129448 TTGAATTTTTTAAGTTTCAGCACCTCTGTTCATG-
65 TTGAATTTTTAAAGTTTCAACACCTCTATT-AAGA
* * * * * *
11129482 ---A-TTTTTTTATTTTGAATTTTT-AAGTTTCAAAGCCTCTATTAAGGAGGATCTTTTCAAT
1 AAAAGCTTTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTCAAT
11129540 ATTGTTTCCT
Statistics
Matches: 213, Mismatches: 28, Indels: 28
0.79 0.10 0.10
Matches are distributed among these distances:
93 27 0.13
94 23 0.11
95 1 0.00
96 1 0.00
97 79 0.37
98 77 0.36
99 5 0.02
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (98 bp):
AAAAGCTTTTTTATTGTGAATTTTTAAAGTTTCAATGCCTTTATTAAGGAAGAGCTTTTCAATTT
TGAATTTTTAAAGTTTCAACACCTCTATTAAGA
Found at i:11129812 original size:25 final size:24
Alignment explanation
Indices: 11129766--11129814 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
11129756 CCAAAAAAAG
*
11129766 TTTTATTTATTCTTTTTAATTTTA
1 TTTTATTTATTCTTTCTAATTTTA
*
11129790 TTTTACTTTATTTCTTTCTATTTTT
1 TTTTA-TTTA-TTCTTTCTAATTTT
11129815 CAAGTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 4 0.19
26 12 0.57
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTATTTATTCTTTCTAATTTTA
Found at i:11130834 original size:31 final size:35
Alignment explanation
Indices: 11130791--11130859 Score: 92
Period size: 36 Copynumber: 2.1 Consensus size: 35
11130781 GGTATATTTA
11130791 TTATCATTTTA-T-T-ATTTTG-CATGATTTTATT
1 TTATCATTTTATTATGATTTTGCCATGATTTTATT
*
11130822 TTATGATTTTATTTATGATTTTGCCATGATTTTATT
1 TTATCATTTTA-TTATGATTTTGCCATGATTTTATT
11130858 TT
1 TT
11130860 TTATGAGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 10 0.31
33 1 0.03
34 1 0.03
35 6 0.19
36 14 0.44
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.64
Consensus pattern (35 bp):
TTATCATTTTATTATGATTTTGCCATGATTTTATT
Found at i:11130838 original size:12 final size:13
Alignment explanation
Indices: 11130811--11130843 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
11130801 ATTATTTTGC
11130811 ATGATTTTATTTT
1 ATGATTTTATTTT
11130824 ATGATTTTA-TTT
1 ATGATTTTATTTT
11130836 ATGATTTT
1 ATGATTTT
11130844 GCCATGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (13 bp):
ATGATTTTATTTT
Found at i:11132556 original size:23 final size:23
Alignment explanation
Indices: 11132526--11132569 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11132516 TTATGGTTTA
* *
11132526 TTTATTATTCATGAGTATATTTG
1 TTTATTATTCATAAATATATTTG
11132549 TTTATTATTCATAAATATATT
1 TTTATTATTCATAAATATATT
11132570 CGTTCATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTATTATTCATAAATATATTTG
Found at i:11136567 original size:2 final size:2
Alignment explanation
Indices: 11136560--11136590 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11136550 ATACACAAAA
11136560 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11136591 GTAAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11136694 original size:23 final size:23
Alignment explanation
Indices: 11136664--11136710 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
11136654 AATAATGAAG
11136664 AAGGTAGGCCAAATGTGTAGACA
1 AAGGTAGGCCAAATGTGTAGACA
**
11136687 AAGGTAGGCCATGTGTGTAGACA
1 AAGGTAGGCCAAATGTGTAGACA
11136710 A
1 A
11136711 CAAATGACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (23 bp):
AAGGTAGGCCAAATGTGTAGACA
Found at i:11147310 original size:19 final size:19
Alignment explanation
Indices: 11147286--11147324 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
11147276 AGGGTTTTTA
11147286 TGTTTTCATTATT-TTTCAT
1 TGTTTTCATT-TTCTTTCAT
*
11147305 TGTTTTCCTTTTCTTTCAT
1 TGTTTTCATTTTCTTTCAT
11147324 T
1 T
11147325 CCTCTCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.69
Consensus pattern (19 bp):
TGTTTTCATTTTCTTTCAT
Found at i:11162061 original size:33 final size:33
Alignment explanation
Indices: 11162019--11162088 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
11162009 CTTTTTATTT
* *
11162019 TATAATAGAAACATTATTTTCTAATAGGAATAG
1 TATAATAGAAACAGTATTTTATAATAGGAATAG
*
11162052 TATAATAGAAATAGTATTTTATAATAGGAATAG
1 TATAATAGAAACAGTATTTTATAATAGGAATAG
11162085 TATA
1 TATA
11162089 GGAACTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (33 bp):
TATAATAGAAACAGTATTTTATAATAGGAATAG
Found at i:11162076 original size:19 final size:19
Alignment explanation
Indices: 11162014--11162087 Score: 68
Period size: 19 Copynumber: 4.2 Consensus size: 19
11162004 TCATACTTTT
* *
11162014 TATTTTATAATAGAAACAT
1 TATTTTATAATAGAAATAG
* *
11162033 TATTTTCTAATAGGAATAG
1 TATTTTATAATAGAAATAG
11162052 -----TATAATAGAAATAG
1 TATTTTATAATAGAAATAG
*
11162066 TATTTTATAATAGGAATAG
1 TATTTTATAATAGAAATAG
11162085 TAT
1 TAT
11162088 AGGAACTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
14 12 0.28
19 31 0.72
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.41
Consensus pattern (19 bp):
TATTTTATAATAGAAATAG
Found at i:11162182 original size:100 final size:101
Alignment explanation
Indices: 11162067--11162268 Score: 334
Period size: 101 Copynumber: 2.0 Consensus size: 101
11162057 TAGAAATAGT
* *
11162067 ATTTTATAATAGGAATAGTATAGGAACTTTTAACTAA-TTACAATTTTATCTTTATTGAACTTTG
1 ATTTTATAATAGGAATAGTATAGAAACTTTTAACTAATTTACAATTTTATCGTTATTGAACTTTG
* *
11162131 TAAAATTTTAAACGTGGAAAAAAATGTTTGTCAAAA
66 CAAAATTTTAAACATGGAAAAAAATGTTTGTCAAAA
** *
11162167 ATTTTATAATAGGAATAGTATAGAAACTTTTAACTAATTTACGGTTTTATCGTTATTGACCTTTG
1 ATTTTATAATAGGAATAGTATAGAAACTTTTAACTAATTTACAATTTTATCGTTATTGAACTTTG
11162232 CAAAATTTTAAACATGGAAAAAAATGTTTGTCAAAA
66 CAAAATTTTAAACATGGAAAAAAATGTTTGTCAAAA
11162268 A
1 A
11162269 AAAAAAAACT
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
100 36 0.38
101 58 0.62
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (101 bp):
ATTTTATAATAGGAATAGTATAGAAACTTTTAACTAATTTACAATTTTATCGTTATTGAACTTTG
CAAAATTTTAAACATGGAAAAAAATGTTTGTCAAAA
Found at i:11162976 original size:3 final size:3
Alignment explanation
Indices: 11162963--11162992 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
11162953 GTTTGCTTAT
11162963 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
11162993 TAGTTCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:11165086 original size:9 final size:9
Alignment explanation
Indices: 11165072--11165121 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
11165062 CTTCTTTATG
11165072 TTTTGTATT
1 TTTTGTATT
11165081 TTTTGT-TT
1 TTTTGTATT
*
11165089 TCTTGTATAT
1 TTTTGTAT-T
11165099 TTTTGTCA-T
1 TTTTGT-ATT
11165108 TTTTGTCATT
1 TTTTGT-ATT
11165118 TTTT
1 TTTT
11165122 AATTAATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 7 0.20
9 16 0.46
10 11 0.31
11 1 0.03
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (9 bp):
TTTTGTATT
Found at i:11165113 original size:19 final size:16
Alignment explanation
Indices: 11165072--11165121 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 16
11165062 CTTCTTTATG
11165072 TTTTGTATTTTTTGTT
1 TTTTGTATTTTTTGTT
11165088 TTCTTGTATATTTTTGTCAT
1 TT-TTGTAT-TTTTTGT--T
11165108 TTTTGTCATTTTTT
1 TTTTGT-ATTTTTT
11165122 AATTAATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 7 0.24
19 9 0.31
20 5 0.17
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TTTTGTATTTTTTGTT
Found at i:11165177 original size:18 final size:19
Alignment explanation
Indices: 11165142--11165183 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
11165132 ATAAATAAAG
11165142 AAAATAAGAACAATAACA-
1 AAAATAAGAACAATAACAT
*
11165160 AAAATAA-AGCAATAAACAT
1 AAAATAAGAACAAT-AACAT
11165179 AAAAT
1 AAAAT
11165184 TGGGCTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 11 0.52
19 5 0.24
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAATAAGAACAATAACAT
Found at i:11165463 original size:15 final size:14
Alignment explanation
Indices: 11165441--11165503 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
11165431 TTTATGTGTG
11165441 TTTTTTTTCTTGAT
1 TTTTTTTTCTTGAT
* *
11165455 TTTTATTTTGTTTGGT
1 TTTT-TTTT-CTTGAT
11165471 TTTTTTTTCTTGAT
1 TTTTTTTTCTTGAT
11165485 TTTTGTTTTCTT-AT
1 TTTT-TTTTCTTGAT
11165499 TTTTT
1 TTTTT
11165504 GATTTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.02
14 18 0.43
15 15 0.36
16 8 0.19
ACGTcount: A:0.06, C:0.05, G:0.10, T:0.79
Consensus pattern (14 bp):
TTTTTTTTCTTGAT
Found at i:11166116 original size:41 final size:40
Alignment explanation
Indices: 11166071--11166188 Score: 110
Period size: 41 Copynumber: 2.9 Consensus size: 40
11166061 TTTTGCCTAG
11166071 AGGTCTTGAAAATAATATAAAAAATATGAGGTTTTGCCCGA
1 AGGTCTTGAAAATAAT-TAAAAAATATGAGGTTTTGCCCGA
* * * * * * **
11166112 AGGTCTTTGGAAATTATTCAAAATTTTAAAATTTTGCCCGA
1 AGGTC-TTGAAAATAATTAAAAAATATGAGGTTTTGCCCGA
* * *
11166153 AGGTCTTAAAAATCATGTAAAAAATCTGAGGTTTTG
1 AGGTCTTGAAAATAAT-TAAAAAATATGAGGTTTTG
11166189 TTTGAAAGTT
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
40 8 0.14
41 41 0.71
42 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (40 bp):
AGGTCTTGAAAATAATTAAAAAATATGAGGTTTTGCCCGA
Found at i:11166149 original size:82 final size:81
Alignment explanation
Indices: 11165965--11166228 Score: 239
Period size: 82 Copynumber: 3.2 Consensus size: 81
11165955 GCATTGAAAC
* * * * ** **
11165965 TTTAAAATTTAAACATTATGCCCGGAA-GTCTTAAAAATCATGTAAAAAATACAAGAATTTGCCC
1 TTTAAAATTTAAA-ATTTTG-CCAGAAGGTCTTAAAAATAATATAAAAAATATGAGGTTTTGCCC
**
11166029 -AGAAGT-TTTCAAAATTA
64 GA-AAGTCTTTGGAAATTA
* *
11166046 TTTAAAGATTTAAGATTTTGCCTAG-AGGTCTTGAAAATAATATAAAAAATATGAGGTTTTGCCC
1 TTTAAA-ATTTAAAATTTTGCC-AGAAGGTCTTAAAAATAATATAAAAAATATGAGGTTTTGCCC
*
11166110 GAAGGTCTTTGGAAATTA
64 GAAAGTCTTTGGAAATTA
* * * * * ***
11166128 TTCAAAATTTTAAAATTTTGCCCGAAGGTCTTAAAAATCATGTAAAAAATCTGAGGTTTTGTTTG
1 TTTAAAA-TTTAAAATTTTGCCAGAAGGTCTTAAAAATAATATAAAAAATATGAGGTTTTGCCCG
* *
11166193 AAAGTTTTTGGAAATCA
65 AAAGTCTTTGGAAATTA
11166210 TTTAAAATTTAAAATTTTG
1 TTTAAAATTTAAAATTTTG
11166229 GCTTAGAAAT
Statistics
Matches: 149, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
80 3 0.02
81 59 0.40
82 87 0.58
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (81 bp):
TTTAAAATTTAAAATTTTGCCAGAAGGTCTTAAAAATAATATAAAAAATATGAGGTTTTGCCCGA
AAGTCTTTGGAAATTA
Found at i:11167761 original size:16 final size:16
Alignment explanation
Indices: 11167717--11167762 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
11167707 CATATTCATC
11167717 TTTTATTCATCTATTTTT
1 TTTTATT-AT-TATTTTT
11167735 TTTCT-TT-TTATTTTT
1 TTT-TATTATTATTTTT
11167750 TTTTATTATTATT
1 TTTTATTATTATT
11167763 CTATGCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.04
15 12 0.48
16 6 0.24
18 5 0.20
19 1 0.04
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTATTATTTTT
Found at i:11168152 original size:1 final size:1
Alignment explanation
Indices: 11168148--11168207 Score: 84
Period size: 1 Copynumber: 60.0 Consensus size: 1
11168138 CACTTTTTCC
* * * *
11168148 TTTTTCTTTTTTTTTTTCTTTTTTTTCTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11168208 GCTTTTCTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:11168160 original size:9 final size:9
Alignment explanation
Indices: 11168141--11168232 Score: 84
Period size: 9 Copynumber: 10.2 Consensus size: 9
11168131 CTTTTTCCAC
*
11168141 TTTTTCCTT
1 TTTTTTCTT
11168150 TTTCTTT-TT
1 TTT-TTTCTT
11168159 TTTTTTCTT
1 TTTTTTCTT
11168168 TTTTTTCTT
1 TTTTTTCTT
11168177 TTTTTT-TT
1 TTTTTTCTT
11168185 CTTTTTT-TT
1 -TTTTTTCTT
11168194 TTTTTT-TT
1 TTTTTTCTT
11168202 TTTTTTGCTT
1 TTTTTT-CTT
* *
11168212 TTCTGTTCTC
1 TT-TTTTCTT
*
11168222 TTTGTTCTT
1 TTTTTTCTT
11168231 TT
1 TT
11168233 CATTTTTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
8 19 0.26
9 41 0.56
10 10 0.14
11 3 0.04
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:11168169 original size:34 final size:34
Alignment explanation
Indices: 11168108--11168202 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 34
11168098 TCCCCTTTCA
* * ***
11168108 TTTTCCTTTTTCTTATTCTTCCCCTTTTTCCACT
1 TTTTCCTTTTTCTTTTTTTTTTTCTTTTTCCACT
***
11168142 TTTTCCTTTTTCTTTTTTTTTTTCTTTTTTTTCT
1 TTTTCCTTTTTCTTTTTTTTTTTCTTTTTCCACT
*
11168176 TTTT--TTTTTCTTTTTTTTTTTTTTTTT
1 TTTTCCTTTTTCTTTTTTTTTTTCTTTTT
11168203 TTTTTGCTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 22 0.42
34 30 0.58
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (34 bp):
TTTTCCTTTTTCTTTTTTTTTTTCTTTTTCCACT
Found at i:11168171 original size:7 final size:7
Alignment explanation
Indices: 11168141--11168278 Score: 74
Period size: 7 Copynumber: 19.9 Consensus size: 7
11168131 CTTTTTCCAC
*
11168141 TTTTTCC
1 TTTTTCT
11168148 TTTTTC-
1 TTTTTCT
11168154 TTTTT-T
1 TTTTTCT
11168160 TTTTTCT
1 TTTTTCT
11168167 TTTTT-T
1 TTTTTCT
11168173 TCTTTT-T
1 T-TTTTCT
11168180 TTTTTCT
1 TTTTTCT
11168187 TTTTT-T
1 TTTTTCT
*
11168193 TTTTTTT
1 TTTTTCT
*
11168200 TTTTTTT
1 TTTTTCT
11168207 TGCTTTTCT
1 T--TTTTCT
* *
11168216 GTTCTCT
1 TTTTTCT
*
11168223 TTGTTCT
1 TTTTTCT
11168230 TTTCATT-T
1 TTT--TTCT
*
11168238 TTTTTAAT
1 TTTTT-CT
*
11168246 TTTTTCC
1 TTTTTCT
*
11168253 CTTTTCT
1 TTTTTCT
*
11168260 TATTT-T
1 TTTTTCT
11168266 TTTTTCT
1 TTTTTCT
*
11168273 TCTTTC
1 TTTTTC
11168279 ACATTTCTTT
Statistics
Matches: 104, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
6 29 0.28
7 58 0.56
8 10 0.10
9 7 0.07
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Done.