Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 31 of 126
Found at i:9503088 original size:4 final size:4
Alignment explanation
Indices: 9503066--9503120 Score: 83
Period size: 4 Copynumber: 13.2 Consensus size: 4
9503056 TCTCCTTCTA
*
9503066 CTTT CTTT CCTTT CCTT CTTT CTTT CTTT CTTT CTTT CTTT CTTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT
9503116 CTTT C
1 CTTT C
9503121 ATGTTTATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
4 39 0.83
5 8 0.17
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:9504154 original size:24 final size:22
Alignment explanation
Indices: 9504127--9504177 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
9504117 AATAAAATTT
9504127 TAAAATATAAAAATATATATCAAA
1 TAAAATATAAAAA-ATATA-CAAA
9504151 TAAAAT-TAAAAAATATACAAA
1 TAAAATATAAAAAATATACAAA
9504172 -AAAATA
1 TAAAATA
9504178 GCCAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 5 0.19
23 6 0.23
24 6 0.23
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAAATATAAAAAATATACAAA
Found at i:9510813 original size:594 final size:594
Alignment explanation
Indices: 9509685--9510872 Score: 2358
Period size: 594 Copynumber: 2.0 Consensus size: 594
9509675 GTCATGACAG
9509685 ACGAGGGATTCATAAGTGTAAATGGGAGCAGCTTTGTGATTTAAAAGAAAATGGGGGTATGAGAT
1 ACGAGGGATTCATAAGTGTAAATGGGAGCAGCTTTGTGATTTAAAAGAAAATGGGGGTATGAGAT
9509750 TTAGAAATTTAGCAAAATTCAACATTACTCTACTAGCTAAACAAGGATGGCGACTCATTGAAAAT
66 TTAGAAATTTAGCAAAATTCAACATTACTCTACTAGCTAAACAAGGATGGCGACTCATTGAAAAT
9509815 CCTAACTCTTTATTAGCTCGTGTTTTGAAAGTAAAATATTACCCAAATTGTGATTTCCTTCATTC
131 CCTAACTCTTTATTAGCTCGTGTTTTGAAAGTAAAATATTACCCAAATTGTGATTTCCTTCATTC
9509880 AGTTCTAAAATTCGATGCCTCTTACACGTGAAAAAGCATTTGGTCAGCGAAAAAAGTAATTCAAG
196 AGTTCTAAAATTCGATGCCTCTTACACGTGAAAAAGCATTTGGTCAGCGAAAAAAGTAATTCAAG
9509945 ATGGTGTGTGTTGGCATGTCGGAACAGGTTTTAAAATATCCATTTTTAACTACGCTCGAATTTTA
261 ATGGTGTGTGTTGGCATGTCGGAACAGGTTTTAAAATATCCATTTTTAACTACGCTCGAATTTTA
9510010 GGTGCTCCTGATTTTAGATTATCTCATCCGGTTATTAGTGATGATTTGTTAACAGTTGATCAAAT
326 GGTGCTCCTGATTTTAGATTATCTCATCCGGTTATTAGTGATGATTTGTTAACAGTTGATCAAAT
9510075 TATAAATAGTGACAGCAAAAGTTGGAATAGTGAGTTAGTGAAGTATACCTTCCACCTGGTTGATG
391 TATAAATAGTGACAGCAAAAGTTGGAATAGTGAGTTAGTGAAGTATACCTTCCACCTGGTTGATG
9510140 CAAAGCGTATTTTAAGGATTCCCCTTGTAAATTTTCCACATGACGATGTGTTGGTCTGGAGTGGT
456 CAAAGCGTATTTTAAGGATTCCCCTTGTAAATTTTCCACATGACGATGTGTTGGTCTGGAGTGGT
9510205 GAACCATCAGGTGTCTTCTCTGTCCGAAGCGCCTATAAACTATTACAAGTGGGTTTACCTAATTT
521 GAACCATCAGGTGTCTTCTCTGTCCGAAGCGCCTATAAACTATTACAAGTGGGTTTACCTAATTT
9510270 AAATTTACA
586 AAATTTACA
*
9510279 ACGAGGGATTCATTAGTGTAAATGGGAGCAGCTTTGTGATTTAAAAGAAAATGGGGGTATGAGAT
1 ACGAGGGATTCATAAGTGTAAATGGGAGCAGCTTTGTGATTTAAAAGAAAATGGGGGTATGAGAT
9510344 TTAGAAATTTAGCAAAATTCAACATTACTCTACTAGCTAAACAAGGATGGCGACTCATTGAAAAT
66 TTAGAAATTTAGCAAAATTCAACATTACTCTACTAGCTAAACAAGGATGGCGACTCATTGAAAAT
9510409 CCTAACTCTTTATTAGCTCGTGTTTTGAAAGTAAAATATTACCCAAATTGTGATTTCCTTCATTC
131 CCTAACTCTTTATTAGCTCGTGTTTTGAAAGTAAAATATTACCCAAATTGTGATTTCCTTCATTC
9510474 AGTTCTAAAATTCGATGCCTCTTACACGTGAAAAAGCATTTGGTCAGCGAAAAAAGTAATTCAAG
196 AGTTCTAAAATTCGATGCCTCTTACACGTGAAAAAGCATTTGGTCAGCGAAAAAAGTAATTCAAG
9510539 ATGGTGTGTGTTGGCATGTCGGAACAGGTTTTAAAATATCCATTTTTAACTACGCTCGAATTTTA
261 ATGGTGTGTGTTGGCATGTCGGAACAGGTTTTAAAATATCCATTTTTAACTACGCTCGAATTTTA
9510604 GGTGCTCCTGATTTTAGATTATCTCATCCGGTTATTAGTGATGATTTGTTAACAGTTGATCAAAT
326 GGTGCTCCTGATTTTAGATTATCTCATCCGGTTATTAGTGATGATTTGTTAACAGTTGATCAAAT
9510669 TATAAATAGTGACAGCAAAAGTTGGAATAGTGAGTTAGTGAAGTATACCTTCCACCTGGTTGATG
391 TATAAATAGTGACAGCAAAAGTTGGAATAGTGAGTTAGTGAAGTATACCTTCCACCTGGTTGATG
9510734 CAAAGCGTATTTTAAGGATTCCCCTTGTAAATTTTCCACATGACGATGTGTTGGTCTGGAGTGGT
456 CAAAGCGTATTTTAAGGATTCCCCTTGTAAATTTTCCACATGACGATGTGTTGGTCTGGAGTGGT
*
9510799 GAACCATCAGGTGTCTTCTCTGTCCGGAGCGCCTATAAACTATTACAAGTGGGTTTACCTAATTT
521 GAACCATCAGGTGTCTTCTCTGTCCGAAGCGCCTATAAACTATTACAAGTGGGTTTACCTAATTT
9510864 AAATTTACA
586 AAATTTACA
9510873 GACCACTAAA
Statistics
Matches: 592, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
594 592 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (594 bp):
ACGAGGGATTCATAAGTGTAAATGGGAGCAGCTTTGTGATTTAAAAGAAAATGGGGGTATGAGAT
TTAGAAATTTAGCAAAATTCAACATTACTCTACTAGCTAAACAAGGATGGCGACTCATTGAAAAT
CCTAACTCTTTATTAGCTCGTGTTTTGAAAGTAAAATATTACCCAAATTGTGATTTCCTTCATTC
AGTTCTAAAATTCGATGCCTCTTACACGTGAAAAAGCATTTGGTCAGCGAAAAAAGTAATTCAAG
ATGGTGTGTGTTGGCATGTCGGAACAGGTTTTAAAATATCCATTTTTAACTACGCTCGAATTTTA
GGTGCTCCTGATTTTAGATTATCTCATCCGGTTATTAGTGATGATTTGTTAACAGTTGATCAAAT
TATAAATAGTGACAGCAAAAGTTGGAATAGTGAGTTAGTGAAGTATACCTTCCACCTGGTTGATG
CAAAGCGTATTTTAAGGATTCCCCTTGTAAATTTTCCACATGACGATGTGTTGGTCTGGAGTGGT
GAACCATCAGGTGTCTTCTCTGTCCGAAGCGCCTATAAACTATTACAAGTGGGTTTACCTAATTT
AAATTTACA
Found at i:9516545 original size:24 final size:24
Alignment explanation
Indices: 9516517--9516570 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
9516507 AAAAATTATA
*
9516517 TAAAATAT-TAAAAATCAATAATTT
1 TAAAATATATAAAAAT-AATAAATT
*
9516541 TAAAA-ATATAATAATAATAAATT
1 TAAAATATATAAAAATAATAAATT
9516564 TATAAAT
1 TA-AAAT
9516571 CACATTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAATATATAAAAATAATAAATT
Found at i:9516561 original size:17 final size:17
Alignment explanation
Indices: 9516514--9516561 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
9516504 AAAAAAAATT
9516514 ATATAA-AATATTAAAA
1 ATATAATAATATTAAAA
* *
9516530 AT-CAATAATTTTAAAA
1 ATATAATAATATTAAAA
*
9516546 ATATAATAATAATAAA
1 ATATAATAATATTAAA
9516562 TTTATAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.08
16 13 0.52
17 10 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAATAATATTAAAA
Found at i:9516926 original size:19 final size:20
Alignment explanation
Indices: 9516877--9516941 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
9516867 TTTTACAATC
** *
9516877 TTTTACAATTCCTAATAATTT
1 TTTTACAATTTGTAATAA-TA
*
9516898 TTTTATAATTTGT-ATAATA
1 TTTTACAATTTGTAATAATA
*
9516917 TTTTACAATTTTTAATAATA
1 TTTTACAATTTGTAATAATA
9516937 TTTTA
1 TTTTA
9516942 TAATGTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 12 0.32
20 15 0.41
21 10 0.27
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTACAATTTGTAATAATA
Found at i:9516950 original size:10 final size:9
Alignment explanation
Indices: 9516897--9516969 Score: 67
Period size: 9 Copynumber: 7.7 Consensus size: 9
9516887 CCTAATAATT
9516897 TTTTTATAA
1 TTTTTATAA
*
9516906 TTTGTATAA
1 TTTTTATAA
*
9516915 TATTTTACAA
1 T-TTTTATAA
9516925 TTTTTAATAA
1 TTTTT-ATAA
9516935 TATTTTATAA
1 T-TTTTATAA
9516945 TGTTTTGAT-A
1 T-TTTT-ATAA
*
9516955 TTTTTATTA
1 TTTTTATAA
9516964 TTTTTA
1 TTTTTA
9516970 CGTGTCGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
8 2 0.04
9 24 0.44
10 22 0.41
11 6 0.11
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:9531693 original size:28 final size:29
Alignment explanation
Indices: 9531641--9531695 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
9531631 TTTAACTCTT
* *
9531641 TTTAATTATATAAAAATTAAATTGATCTA
1 TTTAATAATATAAAAACTAAATTGATCTA
*
9531670 TTTAATAATA-AAAAACTAATTTGATC
1 TTTAATAATATAAAAACTAAATTGATC
9531696 AAGTCCGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTAATAATATAAAAACTAAATTGATCTA
Found at i:9533787 original size:16 final size:16
Alignment explanation
Indices: 9533766--9533803 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
9533756 ATAATACAAA
9533766 AAAATAATTATCTACC
1 AAAATAATTATCTACC
*
9533782 AAAATAATTATTTACC
1 AAAATAATTATCTACC
9533798 AAAATA
1 AAAATA
9533804 GTACACTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATAATTATCTACC
Found at i:9533952 original size:39 final size:40
Alignment explanation
Indices: 9533907--9533983 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
9533897 GGGTCTGGTA
9533907 TAAACCCGAT-AAAAATACGAGTATAATATAAAAGAGTAG
1 TAAACCCGATAAAAAATACGAGTATAATATAAAAGAGTAG
* * *
9533946 TAAACCCGATAAAAAATACGAGTGTAGTATAAAGGAGT
1 TAAACCCGATAAAAAATACGAGTATAATATAAAAGAGT
9533984 GGTGCCTACC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 10 0.29
40 24 0.71
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (40 bp):
TAAACCCGATAAAAAATACGAGTATAATATAAAAGAGTAG
Found at i:9534052 original size:26 final size:26
Alignment explanation
Indices: 9534016--9534109 Score: 116
Period size: 26 Copynumber: 3.4 Consensus size: 26
9534006 CCACAAAAAA
9534016 TATGTTTATGTTTGTATTTAATTAAT
1 TATGTTTATGTTTGTATTTAATTAAT
*
9534042 TATGTTTATGTTTAAATTTGTATTTAATCAAT
1 TATGTTTATG------TTTGTATTTAATTAAT
9534074 TATGTTTATGTTTGTATTTAATTAAT
1 TATGTTTATGTTTGTATTTAATTAAT
*
9534100 TATATTTATG
1 TATGTTTATG
9534110 CTTATGCTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
26 34 0.58
32 25 0.42
ACGTcount: A:0.29, C:0.01, G:0.11, T:0.60
Consensus pattern (26 bp):
TATGTTTATGTTTGTATTTAATTAAT
Found at i:9534062 original size:32 final size:32
Alignment explanation
Indices: 9534016--9534086 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
9534006 CCACAAAAAA
** *
9534016 TATGTTTATGTTTGTATTTAATTAATTATGTT
1 TATGTTTAAATTTGTATTTAATCAATTATGTT
9534048 TATGTTTAAATTTGTATTTAATCAATTATGTT
1 TATGTTTAAATTTGTATTTAATCAATTATGTT
9534080 TATGTTT
1 TATGTTT
9534087 GTATTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.61
Consensus pattern (32 bp):
TATGTTTAAATTTGTATTTAATCAATTATGTT
Found at i:9534109 original size:32 final size:32
Alignment explanation
Indices: 9534016--9534115 Score: 113
Period size: 32 Copynumber: 3.3 Consensus size: 32
9534006 CCACAAAAAA
*
9534016 TATGTTTATGTTTGTATTTAATTAATTATGTT
1 TATGTTTATGTTTGTATTTAATTAATTATATT
** *
9534048 TATGTTTAAATTTGTA--T--TTAATCA-A-T
1 TATGTTTATGTTTGTATTTAATTAATTATATT
9534074 TATGTTTATGTTTGTATTTAATTAATTATATT
1 TATGTTTATGTTTGTATTTAATTAATTATATT
*
9534106 TATGCTTATG
1 TATGTTTATG
9534116 CTTATGTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
26 15 0.28
28 7 0.13
30 7 0.13
31 1 0.02
32 24 0.44
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (32 bp):
TATGTTTATGTTTGTATTTAATTAATTATATT
Found at i:9534159 original size:21 final size:20
Alignment explanation
Indices: 9534135--9534196 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
9534125 GGGGTATCGA
9534135 ATTTAGGATTTAGGGTTTAAG
1 ATTT-GGATTTAGGGTTTAAG
*
9534156 ATTT-GAGTTTTGGGTTTTAAG
1 ATTTGGA-TTTAGGG-TTTAAG
*
9534177 -TTTGGGGTTTAGGGTTTAAG
1 ATTT-GGATTTAGGGTTTAAG
9534197 GTTTTGAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 16 0.47
22 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (20 bp):
ATTTGGATTTAGGGTTTAAG
Found at i:9534200 original size:21 final size:20
Alignment explanation
Indices: 9534143--9534206 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
9534133 GAATTTAGGA
*
9534143 TTTAGGGTTTAAGATTTGAG
1 TTTAGGGTTTAAGGTTTGAG
* *
9534163 TTTTGGGTTTTAA-GTTTGGGG
1 TTTAGGG-TTTAAGGTTT-GAG
9534184 TTTAGGGTTTAAGGTTTTGAG
1 TTTAGGGTTTAAGG-TTTGAG
9534205 TT
1 TT
9534207 ACTACATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 14 0.40
21 18 0.51
22 3 0.09
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (20 bp):
TTTAGGGTTTAAGGTTTGAG
Found at i:9534260 original size:14 final size:14
Alignment explanation
Indices: 9534238--9534279 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
9534228 GCCTATACCC
*
9534238 AAAACCTTAAA-CTT
1 AAAATCTTAAATC-T
9534252 AAAATCTTAAATCT
1 AAAATCTTAAATCT
*
9534266 CAAATCTTAAATCT
1 AAAATCTTAAATCT
9534280 CAAACTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 24 0.96
15 1 0.04
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATCTTAAATCT
Found at i:9534290 original size:14 final size:14
Alignment explanation
Indices: 9534253--9534283 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
9534243 CTTAAACTTA
9534253 AAATCTTAAATCTC
1 AAATCTTAAATCTC
9534267 AAATCTTAAATCTC
1 AAATCTTAAATCTC
9534281 AAA
1 AAA
9534284 CTCTAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATCTTAAATCTC
Found at i:9534387 original size:32 final size:32
Alignment explanation
Indices: 9534308--9534390 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 32
9534298 CTCCAAACAT
* *
9534308 AAACATAAGCATAAAAATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
*
9534340 AAACATAAATATAAACATAATTAATTAAATAC
1 AAACATAAACATAAACATAATTAATTAAATAC
9534372 AAACATAAACATAAACATA
1 AAACATAAACATAAACATA
9534391 TTTGTTTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.64, C:0.11, G:0.01, T:0.24
Consensus pattern (32 bp):
AAACATAAACATAAACATAATTAATTAAATAC
Found at i:9534441 original size:27 final size:27
Alignment explanation
Indices: 9534399--9534453 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
9534389 TATTTGTTTG
*
9534399 TGGTGATGCCTGTCAGGTAGGCACCAC
1 TGGTGATGCCTATCAGGTAGGCACCAC
9534426 TGGTGATGCCTATCAGGTAGGCACCAC
1 TGGTGATGCCTATCAGGTAGGCACCAC
9534453 T
1 T
9534454 TCTTTATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (27 bp):
TGGTGATGCCTATCAGGTAGGCACCAC
Found at i:9534524 original size:13 final size:13
Alignment explanation
Indices: 9534506--9534531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9534496 GACCTGTATT
9534506 TTTTTATTTTTTA
1 TTTTTATTTTTTA
9534519 TTTTTATTTTTTA
1 TTTTTATTTTTTA
9534532 ATATTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:9536002 original size:24 final size:24
Alignment explanation
Indices: 9535975--9536020 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9535965 GGAGATTCAA
9535975 TATTTATTAATATAATATATTTTG
1 TATTTATTAATATAATATATTTTG
* *
9535999 TATTTATTAGTATAATTTATTT
1 TATTTATTAATATAATATATTT
9536021 GACCTACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TATTTATTAATATAATATATTTTG
Found at i:9536135 original size:18 final size:17
Alignment explanation
Indices: 9536108--9536142 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9536098 AAATTTTGTA
9536108 TTTATATTTTGTGGGTTT
1 TTTATATTTTG-GGGTTT
*
9536126 TTTATTTTTTGGGGTTT
1 TTTATATTTTGGGGTTT
9536143 ATTTTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.09, C:0.00, G:0.23, T:0.69
Consensus pattern (17 bp):
TTTATATTTTGGGGTTT
Found at i:9536149 original size:16 final size:18
Alignment explanation
Indices: 9536109--9536149 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
9536099 AATTTTGTAT
* *
9536109 TTATATTTTGTGGGTTTT
1 TTATTTTTTGTGGGTTTA
9536127 TTATTTTTTG-GGGTTTA
1 TTATTTTTTGTGGGTTTA
9536144 TT-TTTT
1 TTATTTT
9536150 ATCTCCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 9 0.43
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.71
Consensus pattern (18 bp):
TTATTTTTTGTGGGTTTA
Found at i:9536235 original size:20 final size:21
Alignment explanation
Indices: 9536209--9536254 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
9536199 CTTTATCCGT
*
9536209 GATTTTTTATCATCTTCGAAA
1 GATTTTTTATCATATTCGAAA
9536230 GATTTTTTATCATATTCGAAA
1 GATTTTTTATCATATTCGAAA
9536251 GATT
1 GATT
9536255 AAATTTGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (21 bp):
GATTTTTTATCATATTCGAAA
Found at i:9538955 original size:43 final size:43
Alignment explanation
Indices: 9538891--9538974 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
9538881 ATGTTTAACG
* * * *
9538891 AAATTGGATCAAAATCTTTAAAATTGACTGCAATTGTCACAAA
1 AAATTGAATCAAAATCATTAAAATGGACTGAAATTGTCACAAA
9538934 AAATTGAATCAAAATCATTAAAATGGACTGAAATTGTCACA
1 AAATTGAATCAAAATCATTAAAATGGACTGAAATTGTCACA
9538975 GATTTCAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.29
Consensus pattern (43 bp):
AAATTGAATCAAAATCATTAAAATGGACTGAAATTGTCACAAA
Found at i:9542946 original size:3 final size:3
Alignment explanation
Indices: 9542940--9542990 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
9542930 AGAGGGGAGG
* *
9542940 AGA AGA AGA AGA AGA AGG AGA AGA AGGG AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA
9542986 AGA AG
1 AGA AG
9542991 TCCCAGTGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9542974 original size:22 final size:22
Alignment explanation
Indices: 9542946--9542987 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9542936 GAGGAGAAGA
*
9542946 AGAAGAAGAAGGAGAAGAAGGG
1 AGAAGAAGAAGAAGAAGAAGGG
9542968 AGAAGAAGAAGAAGAAGAAG
1 AGAAGAAGAAGAAGAAGAAG
9542988 AAGTCCCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (22 bp):
AGAAGAAGAAGAAGAAGAAGGG
Found at i:9544049 original size:28 final size:27
Alignment explanation
Indices: 9544015--9544076 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
9544005 GGACACTATA
* *
9544015 AAAATATATTAT-AACTTTGTATATAAT
1 AAAATATATAATAAACTTT-AATATAAT
9544042 AATAATATATAATAAACTTTAATATAA-
1 AA-AATATATAATAAACTTTAATATAAT
9544069 AAAATATA
1 AAAATATA
9544077 AATTGAGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 6 0.19
27 4 0.13
28 15 0.48
29 6 0.19
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
AAAATATATAATAAACTTTAATATAAT
Found at i:9545068 original size:14 final size:14
Alignment explanation
Indices: 9545049--9545087 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
9545039 TTGTTTGAGT
*
9545049 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
9545063 GAAAATGATTTCTG
1 GAAAATGATTTCTG
*
9545077 AAAAATGATTT
1 GAAAATGATTT
9545088 ACTTTTCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:9547623 original size:61 final size:59
Alignment explanation
Indices: 9547521--9547636 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 59
9547511 ATCATTTTAA
* *
9547521 TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATAT
1 TATTAAATTAATAGAATACTTATCAAAATAAATATTAAATTAAATTTAATATTAAATAT
9547580 TATTAAATTAATAGAATA-TTATCTACAAAATAAATATTAAATTAAATTTAATATTAA
1 TATTAAATTAATAGAATACTTA--T-CAAAATAAATATTAAATTAAATTTAATATTAA
9547637 GATAATCACC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
58 3 0.06
59 17 0.33
60 1 0.02
61 31 0.60
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAAATAAATATTAAATTAAATTTAATATTAAATAT
Found at i:9547636 original size:12 final size:12
Alignment explanation
Indices: 9547549--9547581 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9547539 CTTATCAAGA
9547549 TAAATATTAAAT
1 TAAATATTAAAT
9547561 TAAAT-TTAATAT
1 TAAATATTAA-AT
9547573 TAAATATTA
1 TAAATATTA
9547582 TTAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:9552309 original size:72 final size:72
Alignment explanation
Indices: 9552192--9552331 Score: 280
Period size: 72 Copynumber: 1.9 Consensus size: 72
9552182 AAAAAGAAGA
9552192 TGTTATTCATCTTAAGGGTCTCGAGTTCGAGCGCCTATATGTGCAAAGTATGTGTGCAAGGTGTG
1 TGTTATTCATCTTAAGGGTCTCGAGTTCGAGCGCCTATATGTGCAAAGTATGTGTGCAAGGTGTG
9552257 TGTGCCT
66 TGTGCCT
9552264 TGTTATTCATCTTAAGGGTCTCGAGTTCGAGCGCCTATATGTGCAAAGTATGTGTGCAAGGTGTG
1 TGTTATTCATCTTAAGGGTCTCGAGTTCGAGCGCCTATATGTGCAAAGTATGTGTGCAAGGTGTG
9552329 TGT
66 TGT
9552332 CTTGTCAAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (72 bp):
TGTTATTCATCTTAAGGGTCTCGAGTTCGAGCGCCTATATGTGCAAAGTATGTGTGCAAGGTGTG
TGTGCCT
Found at i:9552878 original size:96 final size:96
Alignment explanation
Indices: 9552706--9552898 Score: 323
Period size: 96 Copynumber: 2.0 Consensus size: 96
9552696 CTTTGATCTG
* *
9552706 TACGGTGTGGATGAAAAAGTCTTTCAACCCGGATAGCCTTCGAGCTCAAATGAGAAGTTTGTGGA
1 TACGGTGTGGACGAAAAAGTCTTTCAACCCGGATAGCCTTCGAGCTCAAATGAAAAGTTTGTGGA
*
9552771 AAACTCAAAAAAAGTTCGAGATTCGTTCGAT
66 AAAATCAAAAAAAGTTCGAGATTCGTTCGAT
* *
9552802 TACGGTGTGGACGAAAAAGTCTTTCAACCTGGATAGCCTTCGGGCTCAAATGAAAAGTTTGTGGA
1 TACGGTGTGGACGAAAAAGTCTTTCAACCCGGATAGCCTTCGAGCTCAAATGAAAAGTTTGTGGA
* *
9552867 AAAATCGAAAAAAGTTCGAGATTTGTTCGAT
66 AAAATCAAAAAAAGTTCGAGATTCGTTCGAT
9552898 T
1 T
9552899 GGTCCGAATT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 90 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (96 bp):
TACGGTGTGGACGAAAAAGTCTTTCAACCCGGATAGCCTTCGAGCTCAAATGAAAAGTTTGTGGA
AAAATCAAAAAAAGTTCGAGATTCGTTCGAT
Found at i:9558307 original size:16 final size:16
Alignment explanation
Indices: 9558284--9558355 Score: 94
Period size: 16 Copynumber: 4.5 Consensus size: 16
9558274 GGCACGTTTG
9558284 GCTGTAATGGAATAGAA
1 GCTGTAATGGAATAG-A
9558301 G-TGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
9558316 GTTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
9558332 GCTGTAATGGAATAG-
1 GCTGTAATGGAATAGA
9558347 GACTGTAAT
1 G-CTGTAAT
9558356 CAGTAATTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
15 3 0.06
16 46 0.92
17 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:9558595 original size:58 final size:59
Alignment explanation
Indices: 9558526--9558667 Score: 191
Period size: 58 Copynumber: 2.4 Consensus size: 59
9558516 AATTTTAATG
* *
9558526 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTAAT-TATATTTTAACGTA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTAATATATATTTTAACATA
* *
9558584 ATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATAATATTTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAAT-ATATATTTTAACATA
*
9558643 ATTATTATTAAAATATAAATTAATA
1 ATTATTATT-AAATATAATTTAATA
9558668 TATAATCTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
57 17 0.23
58 24 0.32
59 20 0.27
60 13 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.48
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATATATATTTTAACATA
Found at i:9558626 original size:12 final size:12
Alignment explanation
Indices: 9558591--9558678 Score: 51
Period size: 12 Copynumber: 7.4 Consensus size: 12
9558581 GTAATTATTA
9558591 TTAA-ATATAAT
1 TTAATATATAAT
9558602 TTAATA-A-AA-
1 TTAATATATAAT
9558611 -TAATATATAAT
1 TTAATATATAAT
**
9558622 TTAATAATATTTT
1 TTAAT-ATATAAT
*
9558635 TTAATATAATTATT
1 TTAATAT-A-TAAT
* *
9558649 ATTAAAATATAAA
1 -TTAATATATAAT
9558662 TTAATATATAAT
1 TTAATATATAAT
*
9558674 CTAAT
1 TTAAT
9558679 TTATTAGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
8 5 0.08
9 1 0.02
10 4 0.07
11 5 0.08
12 21 0.36
13 13 0.22
14 4 0.07
15 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAATATATAAT
Found at i:9563288 original size:3 final size:3
Alignment explanation
Indices: 9563280--9563316 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
9563270 GTCTATCCAC
9563280 TTA TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
9563317 CTACTACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:9569621 original size:45 final size:47
Alignment explanation
Indices: 9569569--9569660 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 47
9569559 TCCCTCTCCT
*
9569569 TCTTCCCCATCATCCCTCC-CCTACTCTGATTCTCTCCCTC-CCCCC
1 TCTTCCCCACCATCCCTCCTCCTACTCTGATTCTCTCCCTCTCCCCC
* *
9569614 TCTTCCCCACCATCCCTCCTCTTACTCTGATTCTTTCCCTCTCCCCC
1 TCTTCCCCACCATCCCTCCTCCTACTCTGATTCTCTCCCTCTCCCCC
9569661 ACCGTCCCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
45 18 0.43
46 19 0.45
47 5 0.12
ACGTcount: A:0.09, C:0.55, G:0.02, T:0.34
Consensus pattern (47 bp):
TCTTCCCCACCATCCCTCCTCCTACTCTGATTCTCTCCCTCTCCCCC
Found at i:9571213 original size:89 final size:90
Alignment explanation
Indices: 9571029--9571268 Score: 317
Period size: 89 Copynumber: 2.7 Consensus size: 90
9571019 AATAAGGGTG
* *
9571029 GTTCAAGTACCCAATT-AAGTGC--AAAAAATATCAGGAGCTTAATTGTTTTTTTTAAAAAAAGT
1 GTTCAAGTACCCAATTGAA-TGCAAAAAAAATATAAGG-GCTTAATTG-CTTTTTTAAAAAAAGT
*
9571091 TTTAGGGCCTTTTTGATGCATTTTGAAA
63 TTGAGGGCCTTTTTGATGCATTTTGAAA
* **
9571119 GTTCAAGTACCCAATTGAATGCAAAAAAAATGTAAGGGCTTAATTGCTTTTTTGGAAAAAGTTTG
1 GTTCAAGTACCCAATTGAATGCAAAAAAAATATAAGGGCTTAATTGCTTTTTTAAAAAAAGTTTG
*
9571184 AGGGCC-TTTTGATGCATTTTGATA
66 AGGGCCTTTTTGATGCATTTTGAAA
* * * *
9571208 GTTCAAGTACCCAATTGAGTACAAAAAAATTATAGGGGCTTAATTGCTCTTTTTAAAAAAA
1 GTTCAAGTACCCAATTGAATGCAAAAAAAATATAAGGGCTTAATTGCT-TTTTTAAAAAAA
9571269 TTTAAATTTT
Statistics
Matches: 132, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
89 60 0.45
90 50 0.38
91 11 0.08
92 11 0.08
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (90 bp):
GTTCAAGTACCCAATTGAATGCAAAAAAAATATAAGGGCTTAATTGCTTTTTTAAAAAAAGTTTG
AGGGCCTTTTTGATGCATTTTGAAA
Found at i:9572981 original size:25 final size:25
Alignment explanation
Indices: 9572947--9572995 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
9572937 ATTTGGTTTC
* *
9572947 AAATTTATTTCTAAGTTTAAATTTA
1 AAATTCATTTCTAAATTTAAATTTA
*
9572972 AAATTCATTTTTAAATTTAAATTT
1 AAATTCATTTCTAAATTTAAATTT
9572996 GTTCTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (25 bp):
AAATTCATTTCTAAATTTAAATTTA
Found at i:9573020 original size:17 final size:16
Alignment explanation
Indices: 9572982--9573021 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
9572972 AAATTCATTT
*
9572982 TTAAATTTAAATTTGT
1 TTAAATTTAAATTTGC
9572998 TCTAAATTTAAATTTAGC
1 T-TAAATTTAAATTT-GC
9573016 TTAAAT
1 TTAAAT
9573022 ATGAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.86
18 2 0.10
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (16 bp):
TTAAATTTAAATTTGC
Found at i:9573704 original size:24 final size:24
Alignment explanation
Indices: 9573672--9573722 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
9573662 TATTGATTGC
9573672 ATTGTTTTAAATGCATTAATAAGT
1 ATTGTTTTAAATGCATTAATAAGT
*
9573696 ATTGTTTTAAATGCATTAATGAGT
1 ATTGTTTTAAATGCATTAATAAGT
9573720 ATT
1 ATT
9573723 AATAACATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (24 bp):
ATTGTTTTAAATGCATTAATAAGT
Found at i:9574951 original size:30 final size:31
Alignment explanation
Indices: 9574917--9574999 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 31
9574907 AAAAATTGTA
9574917 TTTTAACCCCGAAAC-TTCTAAAAATTACAT
1 TTTTAACCCCGAAACTTTCTAAAAATTACAT
* * *
9574947 TTTTAACCTCG-AGCTTTTTAAAAATTACAT
1 TTTTAACCCCGAAACTTTCTAAAAATTACAT
* *
9574977 TTTTTACCCCG-AACTTTCCAAAA
1 TTTTAACCCCGAAACTTTCTAAAA
9575000 TCCCATTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 2 0.05
30 42 0.95
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (31 bp):
TTTTAACCCCGAAACTTTCTAAAAATTACAT
Found at i:9575000 original size:29 final size:29
Alignment explanation
Indices: 9574937--9575154 Score: 89
Period size: 29 Copynumber: 7.5 Consensus size: 29
9574927 GAAACTTCTA
* * * **
9574937 AAAATTACATTTTTAACCTCGAGCTTTTTA
1 AAAATTACATTTTTTACCCCGAAC-TTTCC
9574967 AAAATTACATTTTTTACCCCGAACTTTCC
1 AAAATTACATTTTTTACCCCGAACTTTCC
** * *
9574996 AAAATCCCATTTTTCACCTCG-A-TTTCACC
1 AAAATTACATTTTTTACCCCGAACTTT--CC
* *
9575025 AAAAATTACCATTTTAT-CCCTGAACTTTCC
1 -AAAATTA-CATTTTTTACCCCGAACTTTCC
9575055 AAAATT---TTGTTTTAACCCC-AA-TTTCACC
1 AAAATTACATT-TTTT-ACCCCGAACTTT--CC
*
9575083 AAAAATTACCA--TTTTACCCTCAAACTTTCC
1 -AAAATTA-CATTTTTTACCC-CGAACTTTCC
* * ** *
9575113 AAAATTCCA-TTTTAACCCAAAATTTTCC
1 AAAATTACATTTTTTACCCCGAACTTTCC
*
9575141 AAAATTTCATTTTT
1 AAAATTACATTTTT
9575155 ACCATCGAGA
Statistics
Matches: 145, Mismatches: 22, Indels: 43
0.69 0.10 0.20
Matches are distributed among these distances:
25 2 0.01
26 6 0.04
27 5 0.03
28 24 0.17
29 55 0.38
30 38 0.26
31 9 0.06
32 6 0.04
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATTACATTTTTTACCCCGAACTTTCC
Found at i:9575000 original size:59 final size:58
Alignment explanation
Indices: 9574937--9575129 Score: 173
Period size: 58 Copynumber: 3.3 Consensus size: 58
9574927 GAAACTTCTA
** *
9574937 AAAATTACATTTTTAACCTCGAGCTTT-TTAAAAATTA-CATTTTTTACCCCGAACTTTCC
1 AAAATTACATTTTTAACCTCGA--TTTACCAAAAATTACCATTTTAT-CCCCGAACTTTCC
** * *
9574996 AAAATCCCATTTTTCACCTCGATTTCACCAAAAATTACCATTTTATCCCTGAACTTTCC
1 AAAATTACATTTTTAACCTCGATTT-ACCAAAAATTACCATTTTATCCCCGAACTTTCC
* * * *
9575055 AAAATT--TTGTTTTAACCCCAATTTCACCAAAAATTACCATTTTA-CCCTCAAACTTTCC
1 AAAATTACAT-TTTTAACCTCGATTT-ACCAAAAATTACCATTTTATCCC-CGAACTTTCC
*
9575113 AAAATTCCA-TTTTAACC
1 AAAATTACATTTTTAACC
9575130 CAAAATTTTC
Statistics
Matches: 112, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
57 7 0.06
58 54 0.48
59 44 0.39
60 7 0.06
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAATTACATTTTTAACCTCGATTTACCAAAAATTACCATTTTATCCCCGAACTTTCC
Found at i:9575126 original size:58 final size:58
Alignment explanation
Indices: 9574978--9575130 Score: 202
Period size: 58 Copynumber: 2.6 Consensus size: 58
9574968 AAATTACATT
* * * *
9574978 TTTTACCC-CGAACTTTCCAAAATCCCATTTTTCACCTCGATTTCACCAAAAATTACCA
1 TTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCCCAATTTCACCAAAAATTACCA
***
9575036 TTTTATCCCT-GAACTTTCCAAAATTTTGTTTTAACCCCAATTTCACCAAAAATTACCA
1 TTTTA-CCCTCGAACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCA
*
9575094 TTTTACCCTCAAACTTTCCAAAATTCCATTTTAACCC
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCC
9575131 AAAATTTTCC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
57 4 0.05
58 60 0.74
59 17 0.21
ACGTcount: A:0.31, C:0.30, G:0.03, T:0.36
Consensus pattern (58 bp):
TTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCA
Found at i:9575139 original size:28 final size:27
Alignment explanation
Indices: 9575026--9575153 Score: 96
Period size: 28 Copynumber: 4.5 Consensus size: 27
9575016 GATTTCACCA
* *
9575026 AAAATTACCATTTTATCCCTGAACTTTCC
1 AAAATT-CCATTTTAACCC-AAACTTTCC
*** *
9575055 AAAATTTTGTTTTAACCCCAA-TTTCACC
1 AAAATTCCATTTTAACCCAAACTTT--CC
*
9575083 AAAAATTACCATTTTACCCTCAAACTTTCC
1 -AAAATT-CCATTTTAACC-CAAACTTTCC
*
9575113 AAAATTCCATTTTAACCCAAAATTTTCC
1 AAAATTCCATTTTAACCC-AAACTTTCC
*
9575141 AAAATTTCATTTT
1 AAAATTCCATTTT
9575154 TACCATCGAG
Statistics
Matches: 79, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
26 3 0.04
27 3 0.04
28 40 0.51
29 18 0.23
30 9 0.11
31 3 0.04
32 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAATTCCATTTTAACCCAAACTTTCC
Found at i:9587753 original size:200 final size:200
Alignment explanation
Indices: 9587203--9588042 Score: 1052
Period size: 200 Copynumber: 4.2 Consensus size: 200
9587193 ACAGGACAGC
* * * * *
9587203 GAGGCGATCATCTTCCTGATGAGATACAGAGAAAGAATACCAACTTAACATTCAACACGATCCAA
1 GAGGCGGTCATCTTCCTGATGAGATACAGAG-AAGAATACCAACTCAACACTCAACACGAGCAAA
* * * * * * *
9587268 TCTTCGTACCCAGCTTCCTGATGAGACCCCGAGAAGCAGATTGAAATAATAAAATGGTTAGCTTC
65 TCTTCGTACCCAGCCTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAAAGGTTAGCTTC
* * *
9587333 CTGATGAGATACAGAGAAGTAGACCAAATTCGTCTTCCTGAGGAGATCCAGAG-AAGGAATTAAA
130 CTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAACGAATTAAA
9587397 ACAAGC-
195 ACAA-CA
* *
9587403 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAG
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACACGAG-CAAA
* * * * *
9587468 T-TGCGGT---CAGCTTCCTGATGAGACACTGAGAAGTAAGTCGAAGCAATAAAAAGGTTAGCTT
65 TCTTC-GTACCCAGCCTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAAAGGTTAGCTT
* *
9587529 CCTGATGAGACACAAAGAAGTGGACCAAATTCGTCTTCTTGAGGAGATCCAGAGAAACGAATTAA
129 CCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAACGAATTAA
9587594 AACAACA
194 AACAACA
* * ** * *
9587601 GAGGTGGTCATCTTCCTGATGACACGCAGAGAAGAATACCAAATCAACGCTCAA-AGCGAGCAAA
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACA-CGAGCAAA
* *
9587665 TCTTCGTACCCAGCCTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGTTTAGCTTC
65 TCTTCGTACCCAGCCTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAAAGGTTAGCTTC
* * * * * *
9587730 CTGATGAGATATAGAGAAGTGGACCAAATTTGTCTTCCTGAAGAGATCTAGAGAAACAAATTAAA
130 CTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAACGAATTAAA
9587795 ACAACA
195 ACAACA
* * *
9587801 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACATTCAACCCGAGTAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACACGAGCAAAT
* * * *
9587866 CTTCGAACCCTA--CTCCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAAAGGTTAGCTT
66 CTTCGTACCC-AGCCT-CCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAAAGGTTAGCTT
* *
9587929 CCTGATGAGACACAGAGAAGTGGACCAAATTCGCCTTCCTGAGGAGATCCAGAGAAGCGAATTAA
129 CCTGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAACGAATTAA
*
9587994 AACAGA-T
194 AACA-ACA
** * * *
9588001 GATTACGGTCATGTTCCTGATGAGACACAGAGAAGAAGACCA
1 GA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
9588043 GGTCAATGAA
Statistics
Matches: 554, Mismatches: 72, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
197 103 0.19
198 69 0.12
199 29 0.05
200 317 0.57
201 36 0.06
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACACGAGCAAAT
CTTCGTACCCAGCCTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAAAGGTTAGCTTCC
TGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAACGAATTAAAA
CAACA
Found at i:9588439 original size:11 final size:12
Alignment explanation
Indices: 9588425--9588493 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 12
9588415 TATTTCTAAG
9588425 TTTAAATTT-AA
1 TTTAAATTTAAA
9588436 TTTAAATTTAAA
1 TTTAAATTTAAA
* **
9588448 TTTAAAATTCATT
1 TTT-AAATTTAAA
9588461 TTTAAATTTAAA
1 TTTAAATTTAAA
*
9588473 TTT--GTTCTAAA
1 TTTAAATT-TAAA
9588484 TTTAAATTTA
1 TTTAAATTTA
9588494 GCTTAAATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
10 2 0.04
11 16 0.36
12 16 0.36
13 11 0.24
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:9588447 original size:17 final size:17
Alignment explanation
Indices: 9588425--9588529 Score: 65
Period size: 17 Copynumber: 6.0 Consensus size: 17
9588415 TATTTCTAAG
9588425 TTTAAATTT-AATTTAAA
1 TTTAAATTTAAATTT-AA
* *
9588442 TTTAAATTTAAAATTCATT
1 TTTAAATTT-AAATTTA-A
*
9588461 TTTAAATTTAAATTT-G
1 TTTAAATTTAAATTTAA
*
9588477 TTCTAAATTTAAATTTAG
1 TT-TAAATTTAAATTTAA
* *
9588495 CTTAAATATGAAA--TAA
1 TTTAAAT-TTAAATTTAA
9588511 TTTTAAATTTTAAATTTAA
1 -TTTAAA-TTTAAATTTAA
9588530 AAAACTAAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
16 4 0.06
17 36 0.52
18 13 0.19
19 16 0.23
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:9588472 original size:42 final size:42
Alignment explanation
Indices: 9588410--9588493 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
9588400 ATTTGGTTTC
* *
9588410 AAATTTATTTCTAAGTTTAAATTTAATT-TAAATTTAAATTTA
1 AAATTCATTTCTAAATTTAAATTT-ATTCTAAATTTAAATTTA
* *
9588452 AAATTCATTTTTAAATTTAAATTTGTTCTAAATTTAAATTTA
1 AAATTCATTTCTAAATTTAAATTTATTCTAAATTTAAATTTA
9588494 GCTTAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.05
42 35 0.95
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (42 bp):
AAATTCATTTCTAAATTTAAATTTATTCTAAATTTAAATTTA
Found at i:9588530 original size:6 final size:6
Alignment explanation
Indices: 9588425--9588493 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
9588415 TATTTCTAAG
* **
9588425 TTTAAA TTT-AA TTTAAA TTTAAA TTTAAAA TTCATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
9588473 TTT--G TTCTAAA TTTAAA TTTA
1 TTTAAA TT-TAAA TTTAAA TTTA
9588494 GCTTAAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
4 2 0.04
5 6 0.12
6 35 0.70
7 7 0.14
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:9590427 original size:29 final size:30
Alignment explanation
Indices: 9590382--9590438 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
9590372 TTTAGTCCTT
9590382 AAACTTCCTAAAAATTATATTTTGACCCCA
1 AAACTTCCTAAAAATTATATTTTGACCCCA
*
9590412 AAACTTCC-AAAAATTATATTTTTACCC
1 AAACTTCCTAAAAATTATATTTTGACCC
9590439 TCGAGCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (30 bp):
AAACTTCCTAAAAATTATATTTTGACCCCA
Found at i:9590485 original size:30 final size:30
Alignment explanation
Indices: 9590392--9590494 Score: 77
Period size: 30 Copynumber: 3.5 Consensus size: 30
9590382 AAACTTCCTA
* * *
9590392 AAAATTATATTTTGA-CCCCAAAAC-TTCC
1 AAAATTACATTTTTACCCCCGAAACTTTCC
* * * *
9590420 AAAAATTATATTTTTACCCTCG-AGCTTTTCA
1 -AAAATTACATTTTTACCCCCGAAAC-TTTCC
*
9590451 AAAATTACGTTTTTACCCCCGAAACTTTCC
1 AAAATTACATTTTTACCCCCGAAACTTTCC
**
9590481 AAAATCCCATTTTT
1 AAAATTACATTTTT
9590495 GACCTCGATT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
29 16 0.28
30 36 0.63
31 5 0.09
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTTACCCCCGAAACTTTCC
Found at i:9590531 original size:30 final size:29
Alignment explanation
Indices: 9590481--9590583 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 29
9590471 GAAACTTTCC
* *
9590481 AAAATCCCATTTTTGACCTCGATTTCACCA
1 AAAATTCCA-TTTTAACCTCGATTTCACCA
*
9590511 AAAATTACCATTTTATCCTCGAACTTT--CC-
1 AAAATT-CCATTTTAACCTCG-A-TTTCACCA
**
9590540 AAAATTTTATTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTAACCTCGATTTCACCA
9590569 AAAATTGCCATTTTA
1 AAAATT-CCATTTTA
9590584 CCCCTAAACT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 13 0.22
29 12 0.21
30 22 0.38
31 4 0.07
32 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTCCATTTTAACCTCGATTTCACCA
Found at i:9590571 original size:58 final size:60
Alignment explanation
Indices: 9590449--9590613 Score: 201
Period size: 58 Copynumber: 2.8 Consensus size: 60
9590439 TCGAGCTTTT
** *
9590449 CAAAAATTACGTTTTTACCCCCGAAACTTTCCAAAATCCCATTTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC
* * ***
9590509 CAAAAATTACCATTTTATCCTCG-AACTTTCCAAAATTTTA-TTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC
* * * *
9590567 CAAAAATTGCCATTTTA-CCCCTAAACTTTCTAAAATTCCATTTTTAA
1 CAAAAATTACCATTTTACCCCCGAAACTTTCCAAAATCCCATTTTTAA
9590614 ACCTAAATTT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
57 3 0.03
58 47 0.53
59 20 0.22
60 19 0.21
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (60 bp):
CAAAAATTACCATTTTACCCCCGAAACTTTCCAAAATCCCATTTTTAACCTCGATTTCAC
Found at i:9590611 original size:29 final size:29
Alignment explanation
Indices: 9590569--9590640 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
9590559 GATTTCACCA
**
9590569 AAAATTGCCA-TTTTACCCCTAAACTTTCT-
1 AAAATT-CCATTTTTAAACCTAAA-TTTCTC
*
9590598 AAAATTCCATTTTTAAACCTAAATTTTTC
1 AAAATTCCATTTTTAAACCTAAATTTCTC
*
9590627 AAAATTTCATTTTT
1 AAAATTCCATTTTT
9590641 GCCATCGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.19
29 30 0.81
ACGTcount: A:0.35, C:0.19, G:0.01, T:0.44
Consensus pattern (29 bp):
AAAATTCCATTTTTAAACCTAAATTTCTC
Found at i:9600825 original size:21 final size:21
Alignment explanation
Indices: 9600801--9600844 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
9600791 GATATCATGG
9600801 TTGCAAGAAGACCATGTTTCA
1 TTGCAAGAAGACCATGTTTCA
9600822 TTGCAAGAAGACCATGTTTCA
1 TTGCAAGAAGACCATGTTTCA
9600843 TT
1 TT
9600845 TTTTACTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (21 bp):
TTGCAAGAAGACCATGTTTCA
Found at i:9601563 original size:61 final size:61
Alignment explanation
Indices: 9601458--9601575 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 61
9601448 TGAATCTGTT
* ** *
9601458 AAAATACTCAGTTACTTACATCTGTTTCTTTTTCCATAACAAAGATATAAAATCAAAGAAG
1 AAAATACTCAGTTACTTAAATCAATTTCTTTTTCCAAAACAAAGATATAAAATCAAAGAAG
* * *
9601519 AAAATACTTAGTTATTTAAATCAATTTCTTTTGT-CAAAATAAAGATATAAAATCAAA
1 AAAATACTCAGTTACTTAAATCAATTTCTTTT-TCCAAAACAAAGATATAAAATCAAA
9601576 CGGGAATTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 48 0.98
62 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (61 bp):
AAAATACTCAGTTACTTAAATCAATTTCTTTTTCCAAAACAAAGATATAAAATCAAAGAAG
Found at i:9604446 original size:45 final size:45
Alignment explanation
Indices: 9604379--9604501 Score: 210
Period size: 45 Copynumber: 2.7 Consensus size: 45
9604369 AAAAGATAAG
* * * *
9604379 GAAAACACGTTGATGCTCGCAAAACTGAGAAGATAATAAGAACAA
1 GAAAACACATAGATGTTTGCAAAACTGAGAAGATAATAAGAACAA
9604424 GAAAACACATAGATGTTTGCAAAACTGAGAAGATAATAAGAACAA
1 GAAAACACATAGATGTTTGCAAAACTGAGAAGATAATAAGAACAA
9604469 GAAAACACATAGATGTTTGCAAAACTGAGAAGA
1 GAAAACACATAGATGTTTGCAAAACTGAGAAGA
9604502 ACATATTGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (45 bp):
GAAAACACATAGATGTTTGCAAAACTGAGAAGATAATAAGAACAA
Found at i:9606090 original size:17 final size:18
Alignment explanation
Indices: 9606044--9606090 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
9606034 TTATGGTATC
* *
9606044 ATTAATAATTCAATTTTA
1 ATTAAAAATTCAATATTA
*
9606062 ATATAAATATTCAATATT-
1 AT-TAAAAATTCAATATTA
9606080 ATTAAAAATTC
1 ATTAAAAATTC
9606091 TATAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 8 0.33
18 4 0.17
19 12 0.50
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTAAAAATTCAATATTA
Found at i:9606290 original size:29 final size:30
Alignment explanation
Indices: 9606242--9606301 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
9606232 GGAAGTAAAA
* *
9606242 TTTTGAGGGAAAGTAAATAAAGAAATAAATT
1 TTTTGAGGGAAAG-AAATAAAAAAAAAAATT
*
9606273 TTTTGAGGGAAA-ATATAAAAAAAAAAATT
1 TTTTGAGGGAAAGAAATAAAAAAAAAAATT
9606302 GGAGGGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
31 12 0.46
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (30 bp):
TTTTGAGGGAAAGAAATAAAAAAAAAAATT
Found at i:9607366 original size:129 final size:129
Alignment explanation
Indices: 9607152--9607407 Score: 372
Period size: 129 Copynumber: 2.0 Consensus size: 129
9607142 GAGTCCATAG
*
9607152 TTCAAGTAAAATATAAGCAGTTAAATTAAAATAAAAACAAGAGTCTAAGTGCCTGTTCACTGAAT
1 TTCAAGTAAAATATAAACAGTTAAATTAAAATAAAAACAAGAGTCTAAGTGCCTGTTCACTGAAT
** * * *
9607217 GGCTTCAGTGTTTTGGGAATTCATTCTCTCCTCA-TTCTCCCAACACTAGAGTCATGCAACAAA
66 GGCTTCAGTGTACTGGGAATTCATTCTCACCTCATTTCCCCCAAAACTAGAGTCATGCAACAAA
* ** **
9607280 TTCAAGTCAAATATAAACAGTTAAATTAAAATAGAAAACAACG-GTCTAAGTTTCTGTTCTGTGA
1 TTCAAGTAAAATATAAACAGTTAAATTAAAATA-AAAACAA-GAGTCTAAGTGCCTGTTCACTGA
*
9607344 ATGGCTTCAGTGTACTGGGAATTCATTCTCACTTCATTTCCCCCAAAACTAGAGTCATGCAACA
64 ATGGCTTCAGTGTACTGGGAATTCATTCTCACCTCATTTCCCCCAAAACTAGAGTCATGCAACA
9607408 GATGAAGCCT
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
128 31 0.27
129 56 0.50
130 26 0.23
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (129 bp):
TTCAAGTAAAATATAAACAGTTAAATTAAAATAAAAACAAGAGTCTAAGTGCCTGTTCACTGAAT
GGCTTCAGTGTACTGGGAATTCATTCTCACCTCATTTCCCCCAAAACTAGAGTCATGCAACAAA
Found at i:9610771 original size:4 final size:4
Alignment explanation
Indices: 9610764--9610813 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
9610754 AAAAAAAAAG
* *
9610764 GAAA GAAA GGAA GAAA G-AA G-AA GGAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
9610810 -AAA G
1 GAAA G
9610814 GAAAACTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
3 9 0.22
4 32 0.78
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:9610793 original size:22 final size:23
Alignment explanation
Indices: 9610761--9610804 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
9610751 ACAAAAAAAA
*
9610761 AAGGAAAGAAAGGAAGAAAGAAG
1 AAGGAAAGAAAGAAAGAAAGAAG
9610784 AAGG-AAGAAAGAAAGAAAGAA
1 AAGGAAAGAAAGAAAGAAAGAA
9610805 AGAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAGGAAAGAAAGAAAGAAAGAAG
Found at i:9610817 original size:12 final size:11
Alignment explanation
Indices: 9610757--9610813 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 11
9610747 TGAGACAAAA
9610757 AAAAAAGGAAAG
1 AAAAAA-GAAAG
*
9610769 AAAGGAAGAAAG
1 AAA-AAAGAAAG
9610781 AAGAAGGAAGAAAG
1 AA-AA--AAGAAAG
9610795 AAAGAAAGAAAG
1 AAA-AAAGAAAG
9610807 AAAAAAG
1 AAAAAAG
9610814 GAAAACTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
11 4 0.11
12 20 0.53
13 4 0.11
14 10 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:9614765 original size:54 final size:54
Alignment explanation
Indices: 9614683--9614817 Score: 270
Period size: 54 Copynumber: 2.5 Consensus size: 54
9614673 ACTAATCATC
9614683 CTTCATTTTTCAAACCCTTGCCTTTACTTGGCATTTAAATGGAAAATGCATGAT
1 CTTCATTTTTCAAACCCTTGCCTTTACTTGGCATTTAAATGGAAAATGCATGAT
9614737 CTTCATTTTTCAAACCCTTGCCTTTACTTGGCATTTAAATGGAAAATGCATGAT
1 CTTCATTTTTCAAACCCTTGCCTTTACTTGGCATTTAAATGGAAAATGCATGAT
9614791 CTTCATTTTTCAAACCCTTGCCTTTAC
1 CTTCATTTTTCAAACCCTTGCCTTTAC
9614818 AATTGGGATC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (54 bp):
CTTCATTTTTCAAACCCTTGCCTTTACTTGGCATTTAAATGGAAAATGCATGAT
Found at i:9617402 original size:21 final size:20
Alignment explanation
Indices: 9617356--9617408 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
9617346 AATTAATACT
* * *
9617356 TTTAAAAAAATTTAGAAAAA
1 TTTAAATAAACTTAAAAAAA
*
9617376 TATAAATAAACTTAAAATAAA
1 TTTAAATAAACTTAAAA-AAA
9617397 TTTAAATAAACT
1 TTTAAATAAACT
9617409 ATTTATAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (20 bp):
TTTAAATAAACTTAAAAAAA
Found at i:9617403 original size:10 final size:10
Alignment explanation
Indices: 9617356--9617406 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
9617346 AATTAATACT
*
9617356 TTTAAAAAAA
1 TTTAAATAAA
9617366 TTTAGAA-AAA
1 TTTA-AATAAA
*
9617376 TATAAATAAA
1 TTTAAATAAA
*
9617386 CTTAAAATAAA
1 -TTTAAATAAA
9617397 TTTAAATAAA
1 TTTAAATAAA
9617407 CTATTTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 2 0.06
10 22 0.65
11 10 0.29
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:9622601 original size:9 final size:9
Alignment explanation
Indices: 9622583--9622635 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
9622573 GACAGTAAAT
9622583 AATT-TTAA
1 AATTATTAA
9622591 AATTATTAA
1 AATTATTAA
9622600 AATTATT--
1 AATTATTAA
9622607 -ATT-TT-A
1 AATTATTAA
9622613 AA-TA-TAA
1 AATTATTAA
9622620 AATTATTAA
1 AATTATTAA
9622629 AATTATT
1 AATTATT
9622636 TTTTTGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
5 2 0.05
6 5 0.13
7 4 0.11
8 6 0.16
9 21 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:9622630 original size:29 final size:31
Alignment explanation
Indices: 9622588--9622660 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
9622578 TAAATAATTT
9622588 TAAAATTATTAAAATTATTATTTT-AAAT-A
1 TAAAATTATTAAAATTATTATTTTGAAATAA
*
9622617 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTATTTTGAAATAA
9622648 TAAAATTATTAAA
1 TAAAATTATTAAA
9622661 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 23 0.56
30 4 0.10
31 14 0.34
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTATTTTGAAATAA
Found at i:9652768 original size:24 final size:24
Alignment explanation
Indices: 9652723--9652769 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
9652713 ACAACATGAC
9652723 AAAAATGTCATCCTTATCCAAAAG
1 AAAAATGTCATCCTTATCCAAAAG
*
9652747 AAAAGATGTCATCTTTAT-CAAAA
1 AAAA-ATGTCATCCTTATCCAAAA
9652770 TACTGTGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.28
Consensus pattern (24 bp):
AAAAATGTCATCCTTATCCAAAAG
Found at i:9673824 original size:48 final size:46
Alignment explanation
Indices: 9673772--9673862 Score: 114
Period size: 50 Copynumber: 1.9 Consensus size: 46
9673762 TGAAAATTCG
9673772 TTATCC-TTAATA-ACATCAATCGATTTGTTACTATGATATTAAAATAAT
1 TTATCCTTTAATATAC-TCAATCGATTTG-TA-TAT-ATATTAAAATAAT
*
9673820 TTATCCTTTTAATATTCTCAATCGATTTGTATATATATTAAAA
1 TTATCC-TTTAATATACTCAATCGATTTGTATATATATTAAAA
9673863 ATTGGATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
47 9 0.23
48 9 0.23
49 2 0.05
50 18 0.46
51 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.45
Consensus pattern (46 bp):
TTATCCTTTAATATACTCAATCGATTTGTATATATATTAAAATAAT
Found at i:9678456 original size:5 final size:5
Alignment explanation
Indices: 9678442--9678492 Score: 52
Period size: 5 Copynumber: 10.6 Consensus size: 5
9678432 TTTTCTAAGT
* * * *
9678442 TTATA ATATA TTATA TTAAA TTGTA TTATA TTATA TTAT- TTTTA -TATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
9678490 TTA
1 TTA
9678493 AGTAATTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
4 6 0.17
5 30 0.83
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:9683598 original size:24 final size:25
Alignment explanation
Indices: 9683566--9683616 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
9683556 AAAAGTCTTA
*
9683566 ATTTTAAGATTCAA-TAATTTTATT
1 ATTTTAAGATTCAATTAAATTTATT
*
9683590 ATTTTAAGATTTAATTAAATTTATT
1 ATTTTAAGATTCAATTAAATTTATT
9683615 AT
1 AT
9683617 ACAAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (25 bp):
ATTTTAAGATTCAATTAAATTTATT
Found at i:9687767 original size:3 final size:3
Alignment explanation
Indices: 9687761--9687786 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9687751 AATAGATACT
9687761 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
9687787 TGGTAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9688910 original size:18 final size:18
Alignment explanation
Indices: 9688889--9688932 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
9688879 TAAAAATTAT
9688889 AAAAATATATAAAATATA
1 AAAAATATATAAAATATA
* * *
9688907 AAAAATTTATAAAATTTC
1 AAAAATATATAAAATATA
9688925 AAAAATAT
1 AAAAATAT
9688933 TAGAATTGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATATATAAAATATA
Found at i:9692927 original size:2 final size:2
Alignment explanation
Indices: 9692920--9692985 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
9692910 ATTAAAAATA
9692920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9692962 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
9692986 TTAAAAAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9697192 original size:23 final size:23
Alignment explanation
Indices: 9697164--9697219 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
9697154 ACGCTTTGAC
* *
9697164 AATCAAAACACATCCATATCCAA
1 AATCAAAACACATCAACATCCAA
* *
9697187 AATCAAGATACATCAACATCCAA
1 AATCAAAACACATCAACATCCAA
* *
9697210 GATGAAAACA
1 AATCAAAACA
9697220 TGCTCAATTG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.25, G:0.05, T:0.16
Consensus pattern (23 bp):
AATCAAAACACATCAACATCCAA
Found at i:9700456 original size:33 final size:33
Alignment explanation
Indices: 9700364--9700463 Score: 128
Period size: 33 Copynumber: 3.0 Consensus size: 33
9700354 AGTCGAACAA
* * *
9700364 AATGATGAAGCTGCCCCTAGAGATGTTCCAATC
1 AATGATGAAGCTGCCGCGATAGATGTTCCAATC
*
9700397 AATGATGAAGCTGCCGCGATAAATGTTCCAATC
1 AATGATGAAGCTGCCGCGATAGATGTTCCAATC
* ***
9700430 ATTGATGAAGCTGCTTTGATAGATGTTCCAATC
1 AATGATGAAGCTGCCGCGATAGATGTTCCAATC
9700463 A
1 A
9700464 CTTATGTTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (33 bp):
AATGATGAAGCTGCCGCGATAGATGTTCCAATC
Found at i:9703185 original size:24 final size:24
Alignment explanation
Indices: 9703157--9703221 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
9703147 TAGAGTAATA
* *
9703157 AGAGTTTGACTCAAATAAATAAAT
1 AGAGTTTAACTCAAATAAATAAAC
* *
9703181 AGAGTTTAATTCAAACAAATAAAC
1 AGAGTTTAACTCAAATAAATAAAC
*
9703205 AGAGTTTAACTGAAATA
1 AGAGTTTAACTCAAATA
9703222 TTATTTCTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (24 bp):
AGAGTTTAACTCAAATAAATAAAC
Found at i:9710202 original size:33 final size:33
Alignment explanation
Indices: 9710165--9710242 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
9710155 GCCCCTAGAG
9710165 ATGTTCCAATCAATGATGAAGCTGCCGCGATAA
1 ATGTTCCAATCAATGATGAAGCTGCCGCGATAA
* *** *
9710198 ATGTTCCAATCATTGATGAAGCTGCTTTGATAG
1 ATGTTCCAATCAATGATGAAGCTGCCGCGATAA
9710231 ATGTTCCAATCA
1 ATGTTCCAATCA
9710243 CTTATGTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (33 bp):
ATGTTCCAATCAATGATGAAGCTGCCGCGATAA
Found at i:9714643 original size:97 final size:97
Alignment explanation
Indices: 9714468--9714657 Score: 254
Period size: 97 Copynumber: 2.0 Consensus size: 97
9714458 AACCTTGAAA
* *
9714468 AAGGGTATTCGATTATCCCGATTAGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
*
9714533 AAACCAGAGATAAAGAAACATTGCCTCGATTT
66 AAACCAGAAATAAAGAAACATTGCCTCGATTT
* * * * * * *
9714565 AAGGGTTTTTGATTATCCCGGTTTGAAGAAAAATTGCACCTAGTATGTTAAGGCACGAATTTTCA
1 AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
* * * *
9714630 AGACCTGAAATAAAGGAATATTGCCTCG
66 AAACCAGAAATAAAGAAACATTGCCTCG
9714658 GTTTTAAATA
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAGAAATAAAGAAACATTGCCTCGATTT
Found at i:9715023 original size:28 final size:28
Alignment explanation
Indices: 9714992--9715278 Score: 148
Period size: 29 Copynumber: 9.9 Consensus size: 28
9714982 AAAACGTGAT
*
9714992 TTTTGGAAGTTCGAAGGCAAAAATGGAA
1 TTTTGGAAGTTCGAGGGCAAAAATGGAA
* * *
9715020 TTTTTGGTAGTCCGAGGGCAAAAATGTGAT
1 -TTTTGGAAGTTCGAGGGCAAAAATG-GAA
* **
9715050 TTTTGGAAGTTCGAGGGCAAATATATAA
1 TTTTGGAAGTTCGAGGGCAAAAATGGAA
* * *
9715078 TTTTTGAAAAGTTCGGGGGTCAAAATAT-GAT
1 -TTTTG-GAAGTTCGAGGG-CAAAA-ATGGAA
* * *
9715109 TTTTGGAAATTCGACGG-TAAAATGGTAA
1 TTTTGGAAGTTCGAGGGCAAAAATGG-AA
** * *
9715137 TTTTTAAAGTTCGAGGGTAAAAATGTGAT
1 TTTTGGAAGTTCGAGGGCAAAAATG-GAA
* **
9715166 TTTTGGAAGTT-AAGGGGTAAAATGGTAA
1 TTTTGGAAGTTCGAGGGCAAAAATGG-AA
* * * *
9715194 TTTTTAGAAGTTTGAGGGTAAAAATGCAA
1 -TTTTGGAAGTTCGAGGGCAAAAATGGAA
* ** * *
9715223 TTTTTAGAAAGTTTAAGGGTAAAAATGTAA
1 -TTTT-GGAAGTTCGAGGGCAAAAATGGAA
* *
9715253 TTTTTGTGAAGTTTGGGGGCAAAAAT
1 -TTTTG-GAAGTTCGAGGGCAAAAAT
9715279 ATAATTTTTT
Statistics
Matches: 198, Mismatches: 46, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
26 2 0.01
27 5 0.03
28 26 0.13
29 90 0.45
30 68 0.34
31 5 0.03
32 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (28 bp):
TTTTGGAAGTTCGAGGGCAAAAATGGAA
Found at i:9715043 original size:58 final size:58
Alignment explanation
Indices: 9714981--9715298 Score: 227
Period size: 58 Copynumber: 5.4 Consensus size: 58
9714971 AATTCGGCTT
* ** *
9714981 AAAAACGTGATTTTTGGAAGTTCGAAGGCAAAAATGGAATTTTTGGTAGTCCGAGGGC
1 AAAAATGTGATTTTTGGAAGTTCGAAGGCAAAAATGGAATTTTTGAAAGTTCGAGGGC
* * ** *
9715039 AAAAATGTGATTTTTGGAAGTTCGAGGGCAAATATATAATTTTTGAAAAGTTCGGGGGTC
1 AAAAATGTGATTTTTGGAAGTTCGAAGGCAAAAATGGAATTTTTG-AAAGTTCGAGGG-C
* * * * *
9715099 -AAAATATGATTTTTGGAAATTCGACGG-TAAAATGGTAATTTTT-AAAGTTCGAGGGT
1 AAAAATGTGATTTTTGGAAGTTCGAAGGCAAAAATGG-AATTTTTGAAAGTTCGAGGGC
** * *
9715155 AAAAATGTGATTTTTGGAAGTT--AAGGGGTAAAATGGTAATTTTT-AGAAGTTTGAGGGT
1 AAAAATGTGATTTTTGGAAGTTCGAA-GGCAAAAATGG-AATTTTTGA-AAGTTCGAGGGC
** * * * * * * *
9715213 AAAAATGCAATTTTTAGAAAGTT-TAAGGGTAAAAATGTAATTTTTGTGAAGTTTGGGGGC
1 AAAAATGTGATTTTT-GGAAGTTCGAA-GGCAAAAATGGAATTTTTG-AAAGTTCGAGGGC
* * *
9715273 AAAAATATAATTTTTTTGAAGTTCGA
1 AAAAATGTGA-TTTTTGGAAGTTCGA
9715299 GAGTTAAAAT
Statistics
Matches: 211, Mismatches: 36, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
55 1 0.00
56 2 0.01
57 47 0.22
58 68 0.32
59 52 0.25
60 35 0.17
61 6 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (58 bp):
AAAAATGTGATTTTTGGAAGTTCGAAGGCAAAAATGGAATTTTTGAAAGTTCGAGGGC
Found at i:9715092 original size:30 final size:29
Alignment explanation
Indices: 9714990--9715376 Score: 231
Period size: 30 Copynumber: 13.2 Consensus size: 29
9714980 TAAAAACGTG
** *
9714990 ATTTTTG-GAAGTTCGAAGGCAAAAATGGA
1 ATTTTTGAGAAGTTCG-AGGGTAAAATGTA
* * * *
9715019 ATTTTTG-GTAGTCCGAGGGCAAAAATGTG
1 ATTTTTGAGAAGTTCGAGGG-TAAAATGTA
* *
9715048 ATTTTTG-GAAGTTCGAGGGCAAATATATA
1 ATTTTTGAGAAGTTCGAGGGTAAA-ATGTA
* * * *
9715077 ATTTTTGAAAAGTTCGGGGGTCAAAATATG
1 ATTTTTGAGAAGTTCGAGGGT-AAAATGTA
* *
9715107 ATTTTTG-GAAATTCGACGGTAAAATGGTA
1 ATTTTTGAGAAGTTCGAGGGTAAAAT-GTA
*
9715136 ATTTTT-A-AAGTTCGAGGGTAAAAATGTG
1 ATTTTTGAGAAGTTCGAGGGT-AAAATGTA
*
9715164 ATTTTTG-GAAGTT-AAGGGGTAAAATGGTA
1 ATTTTTGAGAAGTTCGA-GGGTAAAAT-GTA
* *
9715193 ATTTTT-AGAAGTTTGAGGGTAAAAATGCA
1 ATTTTTGAGAAGTTCGAGGGT-AAAATGTA
**
9715222 ATTTTT-AGAAAGTTTAAGGGTAAAAATGTA
1 ATTTTTGAG-AAGTTCGAGGGT-AAAATGTA
* * * * *
9715252 ATTTTTGTGAAGTTTGGGGGCAAAAATATA
1 ATTTTTGAGAAGTTCGAGGG-TAAAATGTA
** * *
9715282 ATTTTTTTGAAGTTCGAGAGTTAAAATATA
1 ATTTTTGAGAAGTTCGAG-GGTAAAATGTA
* *
9715312 ATTTTT-AGGAAGTTCGGGGGTTAAAATATA
1 ATTTTTGA-GAAGTTCGAGGG-TAAAATGTA
* *
9715342 ATTTTTGTA-AAGTTTGAGGGTTAAAATGTG
1 ATTTTTG-AGAAGTTCGAGGG-TAAAATGTA
9715372 ATTTT
1 ATTTT
9715377 GGAAAAGTGT
Statistics
Matches: 290, Mismatches: 46, Indels: 43
0.77 0.12 0.11
Matches are distributed among these distances:
28 35 0.12
29 106 0.37
30 143 0.49
31 5 0.02
32 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
ATTTTTGAGAAGTTCGAGGGTAAAATGTA
Found at i:9715173 original size:57 final size:58
Alignment explanation
Indices: 9714980--9715369 Score: 281
Period size: 60 Copynumber: 6.6 Consensus size: 58
9714970 AAATTCGGCT
* ** ** *
9714980 TAAAAACGTGATTTTTGGAAGTTCGAAGGCAAAAATGG-AATTTTTGGTAGTCCGAGGG
1 TAAAAATGTGATTTTTGGAAGTTCG-AGGGTAAAATGGTAATTTTTGAAAGTTCGAGGG
* * * *
9715038 CAAAAATGTGATTTTTGGAAGTTCGAGGGCAAATAT-ATAATTTTTGAAAAGTTCGGGGG
1 TAAAAATGTGATTTTTGGAAGTTCGAGGGTAAA-ATGGTAATTTTTG-AAAGTTCGAGGG
* * * *
9715097 TCAAAATATGATTTTTGGAAATTCGACGGTAAAATGGTAATTTTT-AAAGTTCGAGGG
1 TAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTCGAGGG
* *
9715154 TAAAAATGTGATTTTTGGAAGTT-AAGGGGTAAAATGGTAATTTTT-AGAAGTTTGAGGG
1 TAAAAATGTGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTGA-AAGTTCGAGGG
** * ** * * *
9715212 TAAAAATGCAATTTTTAGAAAGTTTAAGGGTAAAAAT-GTAATTTTTGTGAAGTTTGGGGG
1 TAAAAATGTGATTTTT-GGAAGTTCGAGGGT-AAAATGGTAATTTTTG-AAAGTTCGAGGG
* * * * * * * *
9715272 CAAAAATATAATTTTTTTGAAGTTCGAGAGTTAAAAT-ATAATTTTTAGGAAGTTCGGGGG
1 TAAAAATGTGA-TTTTTGGAAGTTCGAG-GGTAAAATGGTAATTTTT-GAAAGTTCGAGGG
* * * * *
9715332 TTAAAATATAATTTTTGTAAAGTTTGAGGGTTAAAATG
1 TAAAAATGTGATTTTTG-GAAGTTCGAGGG-TAAAATG
9715370 TGATTTTGGA
Statistics
Matches: 271, Mismatches: 44, Indels: 31
0.78 0.13 0.09
Matches are distributed among these distances:
56 1 0.00
57 56 0.21
58 59 0.22
59 68 0.25
60 79 0.29
61 8 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (58 bp):
TAAAAATGTGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTCGAGGG
Found at i:9715384 original size:30 final size:29
Alignment explanation
Indices: 9715329--9715406 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
9715319 GGAAGTTCGG
* * * *
9715329 GGGTTAAAATATAATTTTTGTAAAGTTTGA
1 GGGTTAAAATATGATTTTGGAAAAGTGT-A
*
9715359 GGGTTAAAATGTGATTTTGGAAAAGTGTA
1 GGGTTAAAATATGATTTTGGAAAAGTGTA
*
9715388 GTGGTCAAAATATGATTTT
1 G-GGTTAAAATATGATTTT
9715407 TGGGTAGTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.40
Consensus pattern (29 bp):
GGGTTAAAATATGATTTTGGAAAAGTGTA
Found at i:9717172 original size:18 final size:17
Alignment explanation
Indices: 9717135--9717229 Score: 73
Period size: 17 Copynumber: 5.5 Consensus size: 17
9717125 GGACTTTATT
* **
9717135 AATTTATATTTAGGATA
1 AATTTAAATTTAAAATA
*
9717152 AATTTAAATTTGATAATA
1 AATTTAAATTT-AAAATA
*
9717170 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
* *
9717187 AATTGAAATTTAAAAACA
1 AATTTAAATTT-AAAATA
* * *
9717205 AATTCAAACTTAAGATA
1 AATTTAAATTTAAAATA
*
9717222 AATCTAAA
1 AATTTAAA
9717230 ACAAAATAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
17 34 0.55
18 28 0.45
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:9717188 original size:35 final size:35
Alignment explanation
Indices: 9717149--9717229 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
9717139 TATATTTAGG
* * * *
9717149 ATAAATTTAAATTTGATAATAAATTTAAACTTAAA
1 ATAAATTTAAATTTAAAAACAAATTCAAACTTAAA
* *
9717184 ATAAATTGAAATTTAAAAACAAATTCAAACTTAAG
1 ATAAATTTAAATTTAAAAACAAATTCAAACTTAAA
*
9717219 ATAAATCTAAA
1 ATAAATTTAAA
9717230 ACAAAATAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (35 bp):
ATAAATTTAAATTTAAAAACAAATTCAAACTTAAA
Found at i:9718088 original size:210 final size:210
Alignment explanation
Indices: 9717726--9718189 Score: 696
Period size: 210 Copynumber: 2.2 Consensus size: 210
9717716 TTAATCGGAT
* * * *
9717726 TTGATTTGGTCTACTTCTCTGTACCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTT
* * * * *
9717791 CTCTGTGTCTAAACAGGAAGATAAATCTGGTTCACTTTTCTGTATCTCATCAGGAAGGTAACCGT
66 CTCTGTGTCTAAACAGGAAAACAAATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCGC
* *
9717856 TTTTATTGCTTCGAGCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCATT
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACT
* **
9717921 TTGAGCCTGGTTTTG
196 TTGAGCCTAGTTTCA
* * * *
9717936 TTGATTTGGTCTACTTCTCAGTATCTCA-CAAGGAAGATGATCGTATCACTTGTTTTGATTCACT
1 TTGATTTGGTCTACTTCTCAGTATCTCATC-AGGAAGATGACCGCATCACTTGTTTTAATCCACT
* * **
9718000 TCTCTGTGTCTCATCAGGAAAACGGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCG
65 TCTCTGTGTCTAAACAGGAAAACAAATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCG
9718065 CTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCAC
130 CTTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCAC
9718130 TTTGAGCCTAGTTTCA
195 TTTGAGCCTAGTTTCA
* *
9718146 TTGGTTTGGTCTACTTCGCAGTATCTCATCAGGAAGATGACCGC
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGC
9718190 CTCGTTATTT
Statistics
Matches: 226, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
209 1 0.00
210 224 0.99
211 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (210 bp):
TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTT
CTCTGTGTCTAAACAGGAAAACAAATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCGC
TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACT
TTGAGCCTAGTTTCA
Found at i:9729783 original size:97 final size:97
Alignment explanation
Indices: 9729590--9729783 Score: 246
Period size: 97 Copynumber: 2.0 Consensus size: 97
9729580 AGCCTTGGAA
* * * *
9729590 AAGGGTATTTGATTATCCCGATTAGCAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTTA
1 AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
* * *
9729655 AAACCAAAGATAAAGAAACGTTGCCTTGATTT
66 AAACCAAAGATAAAGAAACATTACCTCGATTT
* * * *
9729687 AAGGGTATTCGATTATCCTGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACGAATTTTCA
1 AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
* * *
9729752 AAACCCGAA-ATAAAGGAATATTACCTCGATTT
66 AAA-CCAAAGATAAAGAAACATTACCTCGATTT
9729784 TAAATATTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 78 0.95
98 4 0.05
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTAGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAAAGATAAAGAAACATTACCTCGATTT
Found at i:9730080 original size:30 final size:28
Alignment explanation
Indices: 9730035--9730530 Score: 322
Period size: 29 Copynumber: 17.0 Consensus size: 28
9730025 AGTTTTAAAG
*
9730035 AGTTTGGGGTTAAAATGTAATTTTTGAA
1 AGTTTGGGGTAAAAATGTAATTTTTGAA
*
9730063 AGCTTTAGGGGTAAAAATGTCATTTTTGGAA
1 AG-TTT-GGGGTAAAAATGTAATTTTT-GAA
* * *
9730094 AATTTGGGGTAAAAATGTGATTTTTGGA
1 AGTTTGGGGTAAAAATGTAATTTTTGAA
* * *
9730122 AGTTCGAGGGAAAAAATGGAATTTTTGAA
1 AGTTTG-GGGTAAAAATGTAATTTTTGAA
* * *** *
9730151 AGTTCGGGGGTGAAAATACGATTTTTGGA
1 AGTT-TGGGGTAAAAATGTAATTTTTGAA
* *
9730180 AGTTCGAGGG-AAAAATGGAATTTTT-AGA
1 AGTTTG-GGGTAAAAATGTAATTTTTGA-A
** * *
9730208 AGTTCAGAGCAAAAATGTAATTTTTTGAA
1 AGTTTGGGGTAAAAATGTAA-TTTTTGAA
* * *
9730237 AGTTCGGGGGTTAAAATGTGATTTTTGGAA
1 AGTT-TGGGGTAAAAATGTAATTTTT-GAA
*
9730267 A-TTTAGGGGT-AAAATGGTAATTTTTAAA
1 AGTTT-GGGGTAAAAAT-GTAATTTTTGAA
* *
9730295 AGTTTGAGGGTAAAAATGTGATTTTTGGA
1 AGTTTG-GGGTAAAAATGTAATTTTTGAA
* *
9730324 AGTTCAGGGGT-AAAATGATAATTTTTGGA
1 AGTT-TGGGGTAAAAATG-TAATTTTTGAA
*
9730353 AGTTTGAGGGTAAAAATGAAATTTTTGGAA
1 AGTTTG-GGGTAAAAATGTAATTTTT-GAA
*
9730383 AGTTCGAGGGTAAAAATGTAATTTTT-ATGA
1 AGTTTG-GGGTAAAAATGTAATTTTTGA--A
* * * *
9730413 TGCTCGAGGGTAAAAATGT-ATTTTTGTGA
1 AGTTTG-GGGTAAAAATGTAATTTTTG-AA
* * * *
9730442 AGTTCGGGGGTCAAAATATAATTTTTGGA
1 AGTT-TGGGGTAAAAATGTAATTTTTGAA
* *
9730471 AGTTTGAGGGTTAAAATATAATTTTTGTAA
1 AGTTTG-GGGTAAAAATGTAATTTTTG-AA
* * *
9730501 AGTTTGAGGGTCAAAATGTGATTTTAGAA
1 AGTTTG-GGGTAAAAATGTAATTTTTGAA
9730530 A
1 A
9730531 ATTGTAAGGG
Statistics
Matches: 377, Mismatches: 61, Indels: 59
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.01
28 53 0.14
29 193 0.51
30 125 0.33
31 4 0.01
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (28 bp):
AGTTTGGGGTAAAAATGTAATTTTTGAA
Found at i:9730107 original size:58 final size:57
Alignment explanation
Indices: 9730035--9730565 Score: 390
Period size: 58 Copynumber: 9.1 Consensus size: 57
9730025 AGTTTTAAAG
* *
9730035 AGTTTGGGGTTAAAATGTAATTTTTGAAAGCTTT-AGGGGTAAAAATGTCATTTTTGGAA
1 AGTTTGGGGTAAAAATGTAATTTTTGAAAG-TTTGA-GGGTAAAAATGTAATTTTTGG-A
* * * * * * *
9730094 AATTTGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGAAAAAATGGAATTTTTGAA
1 AGTTTGGGGTAAAAATGTAATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTGGA
* * *** * * * *
9730151 AGTTCGGGGGTGAAAATACGATTTTTGGAAGTTCGAGGG-AAAAATGGAATTTTTAGA
1 AGTT-TGGGGTAAAAATGTAATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTGGA
** * * * * * *
9730208 AGTTCAGAGCAAAAATGTAATTTTTTGAAAGTTCGGGGGTTAAAATGTGATTTTTGGA
1 AGTTTGGGGTAAAAATGTAA-TTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTGGA
* * *
9730266 AATTTAGGGGT-AAAATGGTAATTTTTAAAAGTTTGAGGGTAAAAATGTGATTTTTGGA
1 AGTTT-GGGGTAAAAAT-GTAATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTGGA
* * *
9730324 AGTTCAGGGGT-AAAATGATAATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTGGAA
1 AGTT-TGGGGTAAAAATG-TAATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTGG-A
* * * *
9730383 AGTTCGAGGGTAAAAATGTAATTTTT-ATGATGCTCGAGGGTAAAAATGT-ATTTTTGTGA
1 AGTTTG-GGGTAAAAATGTAATTTTTGA--AAGTTTGAGGGTAAAAATGTAATTTTTG-GA
* * * * * * *
9730442 AGTTCGGGGGTCAAAATATAATTTTTGGAAGTTTGAGGGTTAAAATATAATTTTTGTAA
1 AGTT-TGGGGTAAAAATGTAATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTG-GA
* * * * * * * *
9730501 AGTTTGAGGGTCAAAATGTGATTTTAGAAAATTGTAAGGGTCAAAATATGATTTTTGGA
1 AGTTTG-GGGTAAAAATGTAATTTTTGAAAGTT-TGAGGGTAAAAATGTAATTTTTGGA
9730560 CAGTTT
1 -AGTTT
9730566 TAGGGACCTT
Statistics
Matches: 381, Mismatches: 71, Indels: 39
0.78 0.14 0.08
Matches are distributed among these distances:
56 8 0.02
57 41 0.11
58 169 0.44
59 114 0.30
60 49 0.13
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
AGTTTGGGGTAAAAATGTAATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTGGA
Found at i:9732390 original size:6 final size:6
Alignment explanation
Indices: 9732381--9732413 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
9732371 ATATTTAGGA
*
9732381 TAAATT TAAACT TAAA-T TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
9732414 GACAAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:9732401 original size:17 final size:17
Alignment explanation
Indices: 9732381--9732413 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9732371 ATATTTAGGA
9732381 TAAATTTAAACTTAAAT
1 TAAATTTAAACTTAAAT
*
9732398 TAAATTTAAATTTAAA
1 TAAATTTAAACTTAAA
9732414 GACAAATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAACTTAAAT
Found at i:9732933 original size:23 final size:23
Alignment explanation
Indices: 9732907--9732962 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
9732897 AGGCTTTGAC
* *
9732907 AATCAAAACACATCCATATCCAA
1 AATCAAAACACATCAACATCCAA
*
9732930 AATCAAAATACATCAACATCCAA
1 AATCAAAACACATCAACATCCAA
* *
9732953 GATGAAAACA
1 AATCAAAACA
9732963 TGCTCTGTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.55, C:0.25, G:0.04, T:0.16
Consensus pattern (23 bp):
AATCAAAACACATCAACATCCAA
Found at i:9733038 original size:17 final size:17
Alignment explanation
Indices: 9733026--9733065 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
9733016 CAATTTGTAT
9733026 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
9733043 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
9733060 TTTAAA
1 TTTAAA
9733066 ATTTGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:9733099 original size:31 final size:31
Alignment explanation
Indices: 9733058--9733137 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
9733048 ATTTATTTTA
* *
9733058 AATTTAAAATTTGTAATATTATTCTAAACTT
1 AATTTCAAATTTGAAATATTATTCTAAACTT
*
9733089 AATTTCAAATTTGAAATATTGTTCTAAACTT
1 AATTTCAAATTTGAAATATTATTCTAAACTT
*
9733120 AATTTCAAATTTAAAATA
1 AATTTCAAATTTGAAATA
9733138 CAAAGTCTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (31 bp):
AATTTCAAATTTGAAATATTATTCTAAACTT
Found at i:9733484 original size:29 final size:29
Alignment explanation
Indices: 9733393--9733676 Score: 169
Period size: 30 Copynumber: 9.7 Consensus size: 29
9733383 TAAAATTCAT
9733393 AAAAATTACATTATT-ACCTCTAAAC-TTCAC
1 AAAAATTACATT-TTGACC-CTAAACTTTC-C
* *
9733423 AAAAATTACATTTTTACCCTCGAAC-TTCAC
1 AAAAATTACATTTTGACCCT-AAACTTTC-C
*
9733453 AAAAATTACATTTTGACCCTAAACATTCC
1 AAAAATTACATTTTGACCCTAAACTTTCC
*
9733482 AAAAATTACCATTTT-ACCCTCAAA-TTTCAA
1 AAAAATTA-CATTTTGACCCT-AAACTTTC-C
* * *
9733512 AAAAATATA-ATTTTTGACCTTGAACTTTCT
1 AAAAAT-TACA-TTTTGACCCTAAACTTTCC
* **
9733542 AAAAATTACCATTTTG-CCCTCGAA-TTTAT
1 AAAAATTA-CATTTTGACCCT-AAACTTTCC
* *
9733571 TAAAATT-CAATTTTAACCCTAAACTTTCC
1 AAAAATTAC-ATTTTGACCCTAAACTTTCC
*
9733600 AAAAATTACCATTTT-ACCCTCGAA-TTTCC
1 AAAAATTA-CATTTTGACCCT-AAACTTTCC
* * *** *
9733629 AAAAATTCCATTTTTACCCCCGAGTTTCC
1 AAAAATTACATTTTGACCCTAAACTTTCC
9733658 AAAAATTACCATTTT-ACCC
1 AAAAATTA-CATTTTGACCC
9733677 CTCGGGCATC
Statistics
Matches: 210, Mismatches: 22, Indels: 45
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.00
28 14 0.07
29 90 0.43
30 93 0.44
31 12 0.06
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCTAAACTTTCC
Found at i:9733620 original size:58 final size:57
Alignment explanation
Indices: 9733393--9733676 Score: 277
Period size: 58 Copynumber: 4.8 Consensus size: 57
9733383 TAAAATTCAT
*
9733393 AAAAATTACATTATT-ACCTCTAAAC-TTCACAAAAATTA-CATTTTTACCCTCGAACTTCAC
1 AAAAATTA-ATT-TTGACC-CTAAACTTTC-CAAAAATTACCA-TTTTACCCTCGAA-TTTAC
* * *
9733453 AAAAATTACATTTTGACCCTAAACATTCCAAAAATTACCATTTTACCCTCAAATTTCAA
1 AAAAATTA-ATTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATTT-AC
* * * * *
9733512 AAAAATATAATTTTTGACCTTGAACTTTCTAAAAATTACCATTTTGCCCTCGAATTTAT
1 AAAAAT-TAA-TTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATTTAC
* * *
9733571 TAAAATTCAATTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCC
1 AAAAATT-AATTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATTTAC
* * *** *
9733629 AAAAATTCCATTTTTACCCCCGAGTTTCCAAAAATTACCATTTTACCC
1 AAAAATT-AATTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCC
9733677 CTCGGGCATC
Statistics
Matches: 192, Mismatches: 25, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
58 85 0.44
59 45 0.23
60 62 0.32
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAAATTAATTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAATTTAC
Found at i:9733677 original size:29 final size:29
Alignment explanation
Indices: 9733422--9733677 Score: 164
Period size: 29 Copynumber: 8.7 Consensus size: 29
9733412 CTAAACTTCA
* *
9733422 CAAAAATTA-CATTTTTACCCTCGAACTTC
1 CAAAAATTACCA-TTTTACCCCCGAATTTC
** *
9733451 ACAAAAATTA-CATTTTGA-CCCTAAACATTC
1 -CAAAAATTACCATTTT-ACCCCCGAA-TTTC
* *
9733481 CAAAAATTACCATTTTACCCTCAAATTTC
1 CAAAAATTACCATTTTACCCCCGAATTTC
* * ** **
9733510 AAAAAAATATAATTTTTGA-CCTTGAACTTTC
1 CAAAAATTACCA-TTTT-ACCCCCGAA-TTTC
* * * *
9733541 TAAAAATTACCATTTTGCCCTCGAATTTA
1 CAAAAATTACCATTTTACCCCCGAATTTC
** * * **
9733570 TTAAAATT-CAATTTTAACCCTAAACTTTC
1 CAAAAATTACCATTTTACCCCCGAA-TTTC
*
9733599 CAAAAATTACCATTTTACCCTCGAATTTC
1 CAAAAATTACCATTTTACCCCCGAATTTC
*
9733628 CAAAAATT-CCATTTTTACCCCCGAGTTTC
1 CAAAAATTACCA-TTTTACCCCCGAATTTC
9733657 CAAAAATTACCATTTTACCCC
1 CAAAAATTACCATTTTACCCC
9733678 TCGGGCATCC
Statistics
Matches: 177, Mismatches: 37, Indels: 25
0.74 0.15 0.10
Matches are distributed among these distances:
28 13 0.07
29 92 0.52
30 59 0.33
31 13 0.07
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCGAATTTC
Found at i:9742057 original size:17 final size:15
Alignment explanation
Indices: 9742026--9742067 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
9742016 TCAGTCACTT
9742026 GAAAAAGAAAAATGA
1 GAAAAAGAAAAATGA
9742041 GAAAAAGGAAGAAAT--
1 GAAAAA-GAA-AAATGA
9742056 GAAAAAGAAAAA
1 GAAAAAGAAAAA
9742068 AAATTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 3 0.12
15 12 0.48
16 3 0.12
17 4 0.16
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (15 bp):
GAAAAAGAAAAATGA
Found at i:9748681 original size:16 final size:17
Alignment explanation
Indices: 9748660--9748695 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
9748650 AGAAGATTTT
*
9748660 ATAAAAAATTTA-AAAA
1 ATAAAAAATCTATAAAA
9748676 ATAAAAAATCTATAAAA
1 ATAAAAAATCTATAAAA
9748693 ATA
1 ATA
9748696 TTAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAAAATCTATAAAA
Found at i:9748706 original size:15 final size:16
Alignment explanation
Indices: 9748686--9748722 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
9748676 ATAAAAAATC
*
9748686 TATAAAAATATTA-AA
1 TATAAAAATAGTATAA
9748701 TATAAAAATAGTATAA
1 TATAAAAATAGTATAA
9748717 TATAAA
1 TATAAA
9748723 TATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TATAAAAATAGTATAA
Found at i:9752542 original size:20 final size:20
Alignment explanation
Indices: 9752519--9752570 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
9752509 AGATTAACTC
9752519 AATCTCTTACAAAATTAGTG
1 AATCTCTTACAAAATTAGTG
** * *
9752539 AATCTCTTGTAGAATTATTG
1 AATCTCTTACAAAATTAGTG
*
9752559 AATCTTTTACAA
1 AATCTCTTACAA
9752571 TATTGTAATA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (20 bp):
AATCTCTTACAAAATTAGTG
Found at i:9752704 original size:25 final size:24
Alignment explanation
Indices: 9752655--9752707 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
9752645 TTATTAAATC
* *
9752655 TCTTACAACATTGCAATTTTAGTT
1 TCTTAAAACATTGAAATTTTAGTT
9752679 TCTTAAAACATTGTAAATTATT-GTT
1 TCTTAAAACATTG-AAATT-TTAGTT
9752704 TCTT
1 TCTT
9752708 TTACAGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 11 0.44
26 2 0.08
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (24 bp):
TCTTAAAACATTGAAATTTTAGTT
Found at i:9753026 original size:20 final size:21
Alignment explanation
Indices: 9752944--9753025 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 21
9752934 ATAACTTTGT
* *
9752944 ATTACTTAATTTCTTACAACATA
1 ATTACTAAATTTCTTAC-A-AGA
9752967 ATTTACTAAA-TTCTTACAAGA
1 A-TTACTAAATTTCTTACAAGA
* * *
9752988 ATGT--TGAATCTCTTGCAA-A
1 AT-TACTAAATTTCTTACAAGA
9753007 ATTACTAAATTTCTTACAA
1 ATTACTAAATTTCTTACAA
9753026 ATTTATAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
18 1 0.02
19 6 0.13
20 19 0.41
21 4 0.09
22 1 0.02
23 8 0.17
24 7 0.15
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTACTAAATTTCTTACAAGA
Found at i:9754731 original size:14 final size:14
Alignment explanation
Indices: 9754695--9754736 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
9754685 TCCTTTTGTA
9754695 TCATACTTAGCA-T
1 TCATACTTAGCATT
**
9754708 TCATTTTTAGCATT
1 TCATACTTAGCATT
*
9754722 TCATACTTAGTATT
1 TCATACTTAGCATT
9754736 T
1 T
9754737 GTATTTTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (14 bp):
TCATACTTAGCATT
Found at i:9757123 original size:29 final size:29
Alignment explanation
Indices: 9757077--9757181 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 29
9757067 TAGAAATAAT
* *
9757077 ACAAATACGGTTACAGATTCAGTCATGCC
1 ACAAATACAGTTACAGATACAGTCATGCC
* * *
9757106 ACAGATACAGTTACAGATACATTCATGTC
1 ACAAATACAGTTACAGATACAGTCATGCC
* * ** **
9757135 ACAAATACAGTTACGGATGCAAACATGAT
1 ACAAATACAGTTACAGATACAGTCATGCC
*
9757164 ACAAATACAATTACAGAT
1 ACAAATACAGTTACAGAT
9757182 GTAGACGTGA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (29 bp):
ACAAATACAGTTACAGATACAGTCATGCC
Found at i:9759723 original size:21 final size:21
Alignment explanation
Indices: 9759697--9759750 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
9759687 GGAGTTTTTA
*
9759697 GTATCGATAGAAG-CATGACTT
1 GTATCGATAGAAGTC-TCACTT
* *
9759718 GTATCGGTAGATGTCTCACTT
1 GTATCGATAGAAGTCTCACTT
9759739 GTATCGATAGAA
1 GTATCGATAGAA
9759751 CTGTCATAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (21 bp):
GTATCGATAGAAGTCTCACTT
Found at i:9760367 original size:53 final size:52
Alignment explanation
Indices: 9760286--9760430 Score: 159
Period size: 53 Copynumber: 2.7 Consensus size: 52
9760276 TACCCAAACC
* *
9760286 CATGTGTCAGCCCATGTTTCC-CAAAACAGTATACACACACCCTGACACACGCT
1 CATGTGTCAGCCCGTG-TACCTC-AAACAGTATACACACACCCTGACACACGCT
* *
9760339 CATGTGTCAGCCCGTGTACCTCATAACAGTATACACACACCCTGACCCATGCT
1 CATGTGTCAGCCCGTGTACCTCA-AACAGTATACACACACCCTGACACACGCT
* * * *
9760392 CGTGTG-CTAGCCTGTGTGCCTCCAAACAATATACACACA
1 CATGTGTC-AGCCCGTGTACCT-CAAACAGTATACACACA
9760431 AACCCTAACA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
52 5 0.06
53 73 0.91
54 2 0.03
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.22
Consensus pattern (52 bp):
CATGTGTCAGCCCGTGTACCTCAAACAGTATACACACACCCTGACACACGCT
Found at i:9761852 original size:42 final size:42
Alignment explanation
Indices: 9761800--9761894 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
9761790 GTTTCATCAT
* * **
9761800 ATTGATGTTGAAAAAAATCGGAA-TTGATCTCCGCCTTGTGAC
1 ATTGGTGTTGAAAAAAATCGAAACTT-ATCTCCGCCTTGCCAC
* *
9761842 GTTGGTGTTGAAAAAAATTGAAACTTATCTCCGCCTTGCCAC
1 ATTGGTGTTGAAAAAAATCGAAACTTATCTCCGCCTTGCCAC
9761884 ATTGGTGTTGA
1 ATTGGTGTTGA
9761895 GATTATGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (42 bp):
ATTGGTGTTGAAAAAAATCGAAACTTATCTCCGCCTTGCCAC
Found at i:9766863 original size:41 final size:41
Alignment explanation
Indices: 9766692--9766870 Score: 189
Period size: 41 Copynumber: 4.4 Consensus size: 41
9766682 AAAAGGTAAA
** ** *
9766692 GCATTAGTAGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGG
1 GCATTAGCGGCGCTTATGAAAAAGCGCCGCTAAAGATCAGG
* * * * * *
9766733 GCATTAGTGGCACTTATGAAGAAGCACCGCCAAAAATCAGG
1 GCATTAGCGGCGCTTATGAAAAAGCGCCGCTAAAGATCAGG
* **
9766774 GCATTAGCGACGCTTAT-AAAGAAGCGCCGCTAAAGATCAAA
1 GCATTAGCGGCGCTTATGAAA-AAGCGCCGCTAAAGATCAGG
* *
9766815 GCATTAGCGGCGCTTATGAAAAAGTGCCGCTAAAGATCGGG
1 GCATTAGCGGCGCTTATGAAAAAGCGCCGCTAAAGATCAGG
*
9766856 GCATTAGCGGTGCTT
1 GCATTAGCGGCGCTT
9766871 TTCCATCAGC
Statistics
Matches: 112, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
40 2 0.02
41 107 0.96
42 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATGAAAAAGCGCCGCTAAAGATCAGG
Found at i:9770447 original size:43 final size:43
Alignment explanation
Indices: 9770358--9770439 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
9770348 AAAGTGTCGT
* * *
9770358 TAAAGATCATATTTTTTAGCAACGTTTGTGAGAAAAGTGCCAC
1 TAAAAATCATATTCTTTAGCAACGTTTGTGAGAAAAGCGCCAC
* * *
9770401 TAAAAATCATGTTCTTTAGTAACGTTTGTGTGAAAAGCG
1 TAAAAATCATATTCTTTAGCAACGTTTGTGAGAAAAGCG
9770440 TTGCTAAAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (43 bp):
TAAAAATCATATTCTTTAGCAACGTTTGTGAGAAAAGCGCCAC
Found at i:9774017 original size:31 final size:31
Alignment explanation
Indices: 9773979--9774038 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
9773969 AAATAAAAAA
* *
9773979 GAGAGAAAAAAGGCTAAGAAAGATGAAAAGG
1 GAGAGAAAAAAGACAAAGAAAGATGAAAAGG
9774010 GAGAGAAAAAAGACAAAGAAAGATGAAAA
1 GAGAGAAAAAAGACAAAGAAAGATGAAAA
9774039 AGAAGAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.63, C:0.03, G:0.28, T:0.05
Consensus pattern (31 bp):
GAGAGAAAAAAGACAAAGAAAGATGAAAAGG
Found at i:9774046 original size:31 final size:30
Alignment explanation
Indices: 9773974--9774046 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
9773964 GCTATAAATA
* *
9773974 AAAAAGAGAGAAAAAAGGCTAAGAAAGATG
1 AAAAAGAGAGAAAAAAGACAAAGAAAGATG
*
9774004 AAAAGGGAGAGAAAAAAGACAAAGAAAGATG
1 AAAA-AGAGAGAAAAAAGACAAAGAAAGATG
9774035 AAAAAGAAGAGA
1 AAAAAG-AGAGA
9774047 GTATAAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.66, C:0.03, G:0.27, T:0.04
Consensus pattern (30 bp):
AAAAAGAGAGAAAAAAGACAAAGAAAGATG
Found at i:9777959 original size:7 final size:7
Alignment explanation
Indices: 9777947--9778012 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
9777937 TTTCAAAAAA
9777947 AGTCAAC
1 AGTCAAC
9777954 AGTCAA-
1 AGTCAAC
*
9777960 AGTCAAT
1 AGTCAAC
*
9777967 GGTCAAC
1 AGTCAAC
*
9777974 AGTCAAT
1 AGTCAAC
9777981 AGTCAA-
1 AGTCAAC
*
9777987 AGTTAAC
1 AGTCAAC
9777994 AGTCAAC
1 AGTCAAC
*
9778001 GGTCAAC
1 AGTCAAC
*
9778008 GGTCA
1 AGTCA
9778013 GTCAACGGCC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 11 0.22
7 39 0.78
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (7 bp):
AGTCAAC
Found at i:9777973 original size:20 final size:20
Alignment explanation
Indices: 9777945--9777999 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
9777935 TTTTTCAAAA
9777945 AAAGTCAACAGTCAA-AGTC
1 AAAGTCAACAGTCAATAGTC
*
9777964 AATGGTCAACAGTCAATAGTC
1 AA-AGTCAACAGTCAATAGTC
*
9777985 AAAGTTAACAGTCAA
1 AAAGTCAACAGTCAA
9778000 CGGTCAACGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 23 0.74
21 6 0.19
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAGTCAACAGTCAATAGTC
Found at i:9777979 original size:14 final size:13
Alignment explanation
Indices: 9777945--9777999 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
9777935 TTTTTCAAAA
*
9777945 AAAGTCAACAGTC
1 AAAGTCAATAGTC
*
9777958 AAAGTCAATGGTC
1 AAAGTCAATAGTC
9777971 AACAGTCAATAGTC
1 AA-AGTCAATAGTC
* *
9777985 AAAGTTAACAGTC
1 AAAGTCAATAGTC
9777998 AA
1 AA
9778000 CGGTCAACGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
13 24 0.67
14 12 0.33
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (13 bp):
AAAGTCAATAGTC
Done.