Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 2 of 113
Found at i:338382 original size:3 final size:3
Alignment explanation
Indices: 338374--338422 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
338364 TAAACCCAAT
* * *
338374 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA CAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
338422 T
1 T
338423 CAATTACCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:338395 original size:15 final size:15
Alignment explanation
Indices: 338375--338418 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
338365 AAACCCAATT
338375 AATAATAATAATAAC
1 AATAATAATAATAAC
338390 AATAATAATAATAAC
1 AATAATAATAATAAC
*
338405 AACAATAATAATAA
1 AATAATAATAATAA
338419 TAATCAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:338397 original size:18 final size:18
Alignment explanation
Indices: 338374--338422 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
338364 TAAACCCAAT
338374 TAATAATAATAATAACAA
1 TAATAATAATAATAACAA
*
338392 TAATAATAATAACAACAA
1 TAATAATAATAATAACAA
338410 TAATAATAATAAT
1 TAATAATAATAAT
338423 CAATTACCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
TAATAATAATAATAACAA
Found at i:360618 original size:10 final size:10
Alignment explanation
Indices: 360603--360632 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
360593 ATCGAATATT
360603 TATATTTTAA
1 TATATTTTAA
360613 TATATTTTAA
1 TATATTTTAA
360623 T-TATTTTAA
1 TATATTTTAA
360632 T
1 T
360633 TGATATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:360841 original size:22 final size:23
Alignment explanation
Indices: 360798--360841 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
360788 TAAATTTCAA
* *
360798 ATATCAAATTTAAATTTAATATT
1 ATATCAAATTCAAATTCAATATT
*
360821 ATATC-AATTCAAATTCGATAT
1 ATATCAAATTCAAATTCAATAT
360842 CACGTTTCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATCAAATTCAAATTCAATATT
Found at i:363485 original size:13 final size:13
Alignment explanation
Indices: 363467--363491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363457 TATTGATCCA
363467 TTAATTTTAATTC
1 TTAATTTTAATTC
363480 TTAATTTTAATT
1 TTAATTTTAATT
363492 TTTATTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATTTTAATTC
Found at i:363559 original size:23 final size:23
Alignment explanation
Indices: 363514--363560 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
363504 TTTTTAATAA
**
363514 AAAAATTTCACAAATTTTATTTT
1 AAAAATTTCACAAAAATTATTTT
* *
363537 AAAAATTTCATAAAAATTCTTTT
1 AAAAATTTCACAAAAATTATTTT
363560 A
1 A
363561 TCTGATCCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAAATTTCACAAAAATTATTTT
Found at i:363721 original size:2 final size:2
Alignment explanation
Indices: 363714--363747 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
363704 ATGTAACTTA
* *
363714 AT AT AT AT AT AT GT GT 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
363748 TAGTAGTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:365661 original size:4 final size:4
Alignment explanation
Indices: 365654--365685 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
365644 TATTTATATA
*
365654 TATG TATG TATG TATG TATG AATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
365686 CTTATAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:366801 original size:218 final size:218
Alignment explanation
Indices: 366423--366817 Score: 781
Period size: 218 Copynumber: 1.8 Consensus size: 218
366413 GGGTAATGGG
366423 TACATATCAACCATAATCCTCCCCTTTTATTGGGACCGGGGGGGCTTAGGTTTGGCTAACAATTA
1 TACATATCAACCATAATCCTCCCCTTTTATTGGGACCGGGGGGGCTTAGGTTTGGCTAACAATTA
*
366488 ATGACTACATTGGCAAAGCTATGCATGTACATAACCTTAGGTTCAGCTACGCATATAACTATTCA
66 ATGACTACATTGGCAAAGCTATGCATATACATAACCTTAGGTTCAGCTACGCATATAACTATTCA
366553 GGAGATGTATCAAATGTTAATGTTGGTATATGCAGATATTTAATTAACCATAATTAAATATGGTT
131 GGAGATGTATCAAATGTTAATGTTGGTATATGCAGATATTTAATTAACCATAATTAAATATGGTT
366618 AAATATATTTAATTATATGCATA
196 AAATATATTTAATTATATGCATA
366641 TACATATCAACCATAATCCTCCCCTTTTATTGGGACCGGGGGGGCTTAGGTTTGGCTAACAATTA
1 TACATATCAACCATAATCCTCCCCTTTTATTGGGACCGGGGGGGCTTAGGTTTGGCTAACAATTA
366706 ATGACTACATTGGCAAAGCTATGCATATACATAACCTTAGGTTCAGCTACGCATATAACTATTCA
66 ATGACTACATTGGCAAAGCTATGCATATACATAACCTTAGGTTCAGCTACGCATATAACTATTCA
366771 GGAGATGTATCAAATGTTAATGTTGGTATATGCAGATATTTAATTAA
131 GGAGATGTATCAAATGTTAATGTTGGTATATGCAGATATTTAATTAA
366818 ATTTTTGTAT
Statistics
Matches: 176, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
218 176 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (218 bp):
TACATATCAACCATAATCCTCCCCTTTTATTGGGACCGGGGGGGCTTAGGTTTGGCTAACAATTA
ATGACTACATTGGCAAAGCTATGCATATACATAACCTTAGGTTCAGCTACGCATATAACTATTCA
GGAGATGTATCAAATGTTAATGTTGGTATATGCAGATATTTAATTAACCATAATTAAATATGGTT
AAATATATTTAATTATATGCATA
Found at i:377092 original size:89 final size:88
Alignment explanation
Indices: 376990--377156 Score: 210
Period size: 89 Copynumber: 1.9 Consensus size: 88
376980 TTTTGCATAT
* * * * *
376990 ATCAAACACAAAATAAAATGAGATTATATAATTAAATCTTATTTATGATATTATCTTATCCT-AT
1 ATCAAACACAAAATAAAATAAGATTATATAATCAAATCATATTCATAATATTATCTTA--CTAAT
377054 TCTATCATAATTTTATCATTATTTA
64 TCTATCATAATTTTATCATTATTTA
* ** * *
377079 ATCAAACATAAAATAGGATAATATTATTTAATCAAATCATATTCATAATATTATCTTACTAAATT
1 ATCAAACACAAAATAAAATAAGATTATATAATCAAATCATATTCATAATATTATCTTACT-AATT
377144 CTATCATAATTTT
65 CTATCATAATTTT
377157 GTATACCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
87 2 0.03
89 64 0.97
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (88 bp):
ATCAAACACAAAATAAAATAAGATTATATAATCAAATCATATTCATAATATTATCTTACTAATTC
TATCATAATTTTATCATTATTTA
Found at i:383243 original size:2 final size:2
Alignment explanation
Indices: 383230--383270 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
383220 GATGATATGG
* *
383230 AT AT AT AC AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
383271 GCTGATACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:383826 original size:21 final size:20
Alignment explanation
Indices: 383786--383849 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
383776 TATATATATA
* * *
383786 TATATTTTAACATTTAAAAT
1 TATATTTTTATATTTTAAAT
*
383806 TCTTATTTTTATATTTTAAAT
1 T-ATATTTTTATATTTTAAAT
*
383827 TATATTTTATAATTTTTTAAAT
1 TATATTTT-T-ATATTTTAAAT
383849 T
1 T
383850 TTTTGCCATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 7 0.20
21 17 0.49
22 11 0.31
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATTTTTATATTTTAAAT
Found at i:389018 original size:160 final size:157
Alignment explanation
Indices: 388719--389038 Score: 559
Period size: 160 Copynumber: 2.0 Consensus size: 157
388709 GCTATAAGAC
* *
388719 ATTAATTAAAATTTTAGTTAATATTTTCCTTGAAGAGATTGCAAACTGCGAGAGATGTTAGCACG
1 ATTAATTAAAATTTTAGTTAATATTTTCCTTGAAGAGATTACAAACGGCGAGAGATGTTAGCACG
* *
388784 GAATAGTTTCTCCTTCATGTTTATCTGATATTTTGCCACTGTCTTGGTGCTGTGAATTGATAGCA
66 GAATAGTTTCTCCTTCACGTTTATCTGATATTTTGCCACTGTCTTAGTGCTGTGAATTGATAGCA
388849 TTATAGGAACCAGTCACTATCTGTGCT
131 TTATAGGAACCAGTCACTATCTGTGCT
*
388876 ATTAATTAAAATTTTAGTTAATATTTTCCTTGCAGAGATTACAAACGGCGAGAGATATGTTAGCA
1 ATTAATTAAAATTTTAGTTAATATTTTCCTTGAAGAGATTACAAACGGCGAGAG--ATGTTAGCA
*
388941 CGGAATAGTTTCTCCTTTACGTTGTATCTGATATTTTGCCACTGTCTTAGTGCTGTGAATTGATA
64 CGGAATAGTTTCTCCTTCACGTT-TATCTGATATTTTGCCACTGTCTTAGTGCTGTGAATTGATA
389006 GCATTATAGGAACCAGTCACTATCTGTGCT
128 GCATTATAGGAACCAGTCACTATCTGTGCT
389036 ATT
1 ATT
389039 TGCTGTGTGT
Statistics
Matches: 154, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
157 51 0.33
159 30 0.19
160 73 0.47
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (157 bp):
ATTAATTAAAATTTTAGTTAATATTTTCCTTGAAGAGATTACAAACGGCGAGAGATGTTAGCACG
GAATAGTTTCTCCTTCACGTTTATCTGATATTTTGCCACTGTCTTAGTGCTGTGAATTGATAGCA
TTATAGGAACCAGTCACTATCTGTGCT
Found at i:393544 original size:26 final size:25
Alignment explanation
Indices: 393515--393563 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
393505 TAGAAAAAAA
*
393515 TTATCATCTAGATATTTCTAAGAAAT
1 TTATCAT-TAGAAATTTCTAAGAAAT
*
393541 TTATCATTTGAAATTTCTAAGAA
1 TTATCATTAGAAATTTCTAAGAA
393564 TCTCATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (25 bp):
TTATCATTAGAAATTTCTAAGAAAT
Found at i:393822 original size:197 final size:189
Alignment explanation
Indices: 393453--393933 Score: 562
Period size: 197 Copynumber: 2.5 Consensus size: 189
393443 AAAAGAATAC
* *
393453 AATTACTT-TTATTGAAATTTCATCTAAATTATTCCACAATTTGGGACAAATTTAGAAAAAAATT
1 AATTA-TTGTTATTGAAATTTTATCTAAATTATTCCACAATTTGGGACAAATTTAGAAAAAATTT
* * * *
393517 ATCA-TCT-AGATATTTCTA-AGAAATTTATCATTTGAAATTTCTAAGAATCTCATCATTGGGTA
65 CTCACT-TAAGA-ATTT-TATAAAAATTTATCATTTGAAATTTCTAAAAATCTCATCATTGGATA
* *
393579 ATTTGTATTTAATTCCAAAATTTTTATTAATATTTTTTATTTTTTTATTTTTTTGTTTGAAAATA
127 ATTTGTATTTAATTCCAAAATTATTATTAATATTTTTTATTTTTTTA--------TTTAAAAATA
393644 AATATT
184 AATATT
* * * * *
393650 AATTATTGTTATTGAAATTTTGTCTAAATTATTCCACCATTTGAGATAAATTTAGACAAAATTTC
1 AATTATTGTTATTGAAATTTTATCTAAATTATTCCACAATTTGGGACAAATTTAGAAAAAATTTC
*
393715 TCACTTAAGAATTTTATAAAAATTTACCATTTGAAATTTCTAAAAAAT-TCCATCATTGGATAAT
66 TCACTTAAGAATTTTATAAAAATTTATCATTTGAAATTTCT-AAAAATCT-CATCATTGGATAAT
* *
393779 TTGTATTTAATTCTAAAATTATTATTATTATTTTTTA-TTTTTTATTTAAAAATAAATATT
129 TTGTATTTAATTCCAAAATTATTATTAATATTTTTTATTTTTTTATTTAAAAATAAATATT
* * * * * * *
393839 AATTATTGTTA-TGAAACTTTATTTAAATTATTCCGCTATTTGGGACAAATGTAGATAAAATTCC
1 AATTATTGTTATTGAAATTTTATCTAAATTATTCCACAATTTGGGACAAATTTAGAAAAAATTTC
* *
393903 TTACCTAAGAATTTTATAAAAATTTATCATT
66 TCACTTAAGAATTTTATAAAAATTTATCATT
393934 AGATAATTAA
Statistics
Matches: 249, Mismatches: 29, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
188 71 0.29
189 26 0.10
196 4 0.02
197 92 0.37
198 56 0.22
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.46
Consensus pattern (189 bp):
AATTATTGTTATTGAAATTTTATCTAAATTATTCCACAATTTGGGACAAATTTAGAAAAAATTTC
TCACTTAAGAATTTTATAAAAATTTATCATTTGAAATTTCTAAAAATCTCATCATTGGATAATTT
GTATTTAATTCCAAAATTATTATTAATATTTTTTATTTTTTTATTTAAAAATAAATATT
Found at i:393979 original size:11 final size:12
Alignment explanation
Indices: 393961--393989 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
393951 TCTAAAAATA
393961 TATTTTATTTTT
1 TATTTTATTTTT
393973 T-TTTTATTTTT
1 TATTTTATTTTT
393984 TATTTT
1 TATTTT
393990 TTCAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:394050 original size:12 final size:10
Alignment explanation
Indices: 394007--394084 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 10
393997 TTAATCATGT
394007 AAAAATACTAA
1 AAAAATA-TAA
394018 AAAAATA-AA
1 AAAAATATAA
*
394027 CAAACATATAA
1 -AAAAATATAA
394038 ATAAAATACTAA
1 A-AAAATA-TAA
*
394050 ATAAAATAAACA
1 A-AAAATATA-A
*
394062 AAAAATACCAAA
1 AAAAATA--TAA
394074 AAAAATATAA
1 AAAAATATAA
394084 A
1 A
394085 CAGCTTAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
9 2 0.04
10 10 0.18
11 21 0.38
12 21 0.38
13 2 0.04
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAAATATAA
Found at i:394366 original size:13 final size:13
Alignment explanation
Indices: 394350--394376 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
394340 CATTTCCCTC
394350 TTTTTTTTCTCTT
1 TTTTTTTTCTCTT
394363 TTTTTTTTCTCTT
1 TTTTTTTTCTCTT
394376 T
1 T
394377 CTCTTTAGAA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:395049 original size:24 final size:24
Alignment explanation
Indices: 395021--395067 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
395011 CCAACACTTT
*
395021 TTTTTTGTTTTCTTTCTTTTTTATC
1 TTTTTT-TATTCTTTCTTTTTTATC
* *
395046 TTTTTTTATTTTTTGTTTTTTA
1 TTTTTTTATTCTTTCTTTTTTA
395068 ATAATCAGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.83
Consensus pattern (24 bp):
TTTTTTTATTCTTTCTTTTTTATC
Found at i:395217 original size:43 final size:43
Alignment explanation
Indices: 395133--395227 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
395123 ACAACTTTTA
*
395133 GAAAATTAAATAAGGCTCCTCTAAAAAAAAGTTCAACGACTTTG
1 GAAAA-TAAATAAGGCTCCTCTAAAAAAAAGCTCAACGACTTTG
* ** * * *
395177 GAAAATAAATAATGCTCCTCTAAGTAGAGGCTCAATGACTTTG
1 GAAAATAAATAAGGCTCCTCTAAAAAAAAGCTCAACGACTTTG
*
395220 AAAAATAA
1 GAAAATAA
395228 CTCTAATCGG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 38 0.88
44 5 0.12
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (43 bp):
GAAAATAAATAAGGCTCCTCTAAAAAAAAGCTCAACGACTTTG
Found at i:395398 original size:85 final size:85
Alignment explanation
Indices: 395238--395466 Score: 254
Period size: 85 Copynumber: 2.7 Consensus size: 85
395228 CTCTAATCGG
* * *
395238 AGGCTCAACAACTTT--AAAA-AAA-AATGCTCCTCTAAACAGA-GCTCAATAACTTTGAAAAAT
1 AGGCTCAACAAATTTGAAAAATAAATAATGATACTCTAAACAGAGGCTCAATAACTTTG-AAAAT
* *
395298 AAATAATACTCCTCTAAACAG
65 AAACAATACTCCTCTAAACAA
* * * *
395319 AGGAGT-AACAAATTTGAAAAATAAATAATGCTATTCTAAATAGAGGCTCAATAACTTTGAAAAT
1 AGG-CTCAACAAATTTGAAAAATAAATAATGATACTCTAAACAGAGGCTCAATAACTTTGAAAAT
* * *
395383 AAACAATGCTTCTCTAATCAA
65 AAACAATACTCCTCTAAACAA
* * * *
395404 AGGCTCTACAACTTTGAAAAATAAATAATGATCCTCTAAACAGAGGCTTAATAACTTTGAAAA
1 AGGCTCAACAAATTTGAAAAATAAATAATGATACTCTAAACAGAGGCTCAATAACTTTGAAAA
395467 ATACAACTTC
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
81 11 0.09
82 1 0.01
83 4 0.03
84 4 0.03
85 89 0.72
86 14 0.11
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (85 bp):
AGGCTCAACAAATTTGAAAAATAAATAATGATACTCTAAACAGAGGCTCAATAACTTTGAAAATA
AACAATACTCCTCTAAACAA
Found at i:395399 original size:42 final size:43
Alignment explanation
Indices: 395228--395469 Score: 264
Period size: 43 Copynumber: 5.8 Consensus size: 43
395218 TGAAAAATAA
* *
395228 CTCTAATCGGAGGCTCAACAACTTT--AAAA-AAA-AATGCTC
1 CTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAATGCTC
* *
395267 CTCTAAACAGA-GCTCAATAACTTTGAAAAATAAATAATACTC
1 CTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAATGCTC
* * *
395309 CTCTAAACAGAGGAGT-AACAAATTTGAAAAATAAATAATGCTA
1 CTCTAAACAGAGG-CTCAACAACTTTGAAAAATAAATAATGCTC
* * * * *
395352 TTCTAAATAGAGGCTCAATAACTTTG-AAAATAAACAATGCTT
1 CTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAATGCTC
* * * *
395394 CTCTAATCAAAGGCTCTACAACTTTGAAAAATAAATAATGATC
1 CTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAATGCTC
* *
395437 CTCTAAACAGAGGCTTAATAACTTTGAAAAATA
1 CTCTAAACAGAGGCTCAACAACTTTGAAAAATA
395470 CAACTTCTCG
Statistics
Matches: 165, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
38 12 0.07
39 9 0.05
40 4 0.02
41 3 0.02
42 52 0.32
43 84 0.51
44 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (43 bp):
CTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATAATGCTC
Found at i:396103 original size:21 final size:20
Alignment explanation
Indices: 396077--396157 Score: 72
Period size: 22 Copynumber: 3.8 Consensus size: 20
396067 TTCACATCTT
396077 AAAGATTATCATTTGAAACTC
1 AAAGATT-TCATTTGAAACTC
*
396098 AAAGATCTTTATTTGAAAACTC
1 AAAGAT-TTCATTTG-AAACTC
** *
396120 AAAGATTCTCATGCGAAATCTT
1 AAAGATT-TCATTTGAAA-CTC
396142 AAAGACTTTCATTTGA
1 AAAGA-TTTCATTTGA
396158 GGATTCATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 16 0.33
22 30 0.62
23 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (20 bp):
AAAGATTTCATTTGAAACTC
Found at i:397445 original size:18 final size:17
Alignment explanation
Indices: 397424--397471 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
397414 TTTTTTTAAA
397424 TTTTCTTTTTTTTTCTTC
1 TTTTCTTTTTTTTTC-TC
*
397442 TTTTC--TTTCTTTCTC
1 TTTTCTTTTTTTTTCTC
397457 TTTTCTTTTTATTTT
1 TTTTCTTTTT-TTTT
397472 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 3 0.12
18 8 0.32
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTTTTTTCTC
Found at i:397460 original size:15 final size:16
Alignment explanation
Indices: 397435--397464 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
397425 TTTCTTTTTT
397435 TTTCTTCTTTTCTTTC
1 TTTCTTCTTTTCTTTC
397451 TTTC-TCTTTTCTTT
1 TTTCTTCTTTTCTTT
397465 TTATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTCTTTTCTTTC
Found at i:401917 original size:190 final size:194
Alignment explanation
Indices: 401664--402178 Score: 607
Period size: 196 Copynumber: 2.7 Consensus size: 194
401654 AAAAGACTAC
* * * * * * *
401664 AATTACTT-TTATTGAAATTTCATCTAAATTATTCCGTCATTTGTGACAAGTTTAGAGAAAATTT
1 AATTA-TTGTTATTGAAATTTTATCTAAATTATTTCGCCATTTGAGATAAATTTAGACAAAATTT
* * * * *
401728 TTTACCT-AGAAATTTCT-TAGAAATTTACTATTTAAAATTT-TTAAGAATCTCATCATTGGGTA
65 CTCACCTAAG-AATTT-TATAGAAATTTACTATTTAAAATTTCTAAAAAATCTCATCATTGGATA
*
401790 ATTTGTATTTAATTCCAAAATTTTTATTAATA-TTT-TTTTAT-TTTTTTGTTTGAAAATAAATA
128 ATTTATATTTAATTCCAAAATTTTTATTAATATTTTATTTTATATTTTTTGTTTGAAAATAAATA
401852 TT
193 TT
*
401854 AATTATTGTTATTGAAATTTTATCTAAATTATTTCACCATTT-AGGATAAATTTAGACAAAATTT
1 AATTATTGTTATTGAAATTTTATCTAAATTATTTCGCCATTTGA-GATAAATTTAGACAAAATTT
* * *
401918 CTCACTTAAGAATTTTATAGAAATTTACTATTTGAAATTTCTAAAAAATTTCATCATTGGATAAT
65 CTCACCTAAGAATTTTATAGAAATTTACTATTTAAAATTTCTAAAAAATCTCATCATTGGATAAT
** *
401983 TTATATTTAATTCCAATTTTTTTATTAATATTTTTTATTTTTTATTTTTTGTTTGAAAATAAATA
130 TTATATTTAATTCCAAAATTTTTATTAATA--TTTTATTTTATATTTTTTGTTTGAAAATAAATA
402048 TT
193 TT
* * * *
402050 AATTATTGTTATTGACACTTTATCTAAATTATTTCGCTATTTGAGATAAATTTAGTCAAAATTTC
1 AATTATTGTTATTGAAATTTTATCTAAATTATTTCGCCATTTGAGATAAATTTAGACAAAATTTC
* * * ** * * * * *
402115 TCACCTAAAAAGTTTATAAAAATTTACCGTTTGAAATTTTTATAAATTC-CATCATTAGATAATT
66 TCACCTAAGAATTTTATAGAAATTTACTATTTAAAATTTCTAAAAAATCTCATCATTGGATAATT
402179 AATACTTATT
Statistics
Matches: 278, Mismatches: 36, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
189 3 0.01
190 83 0.30
191 49 0.18
194 3 0.01
195 19 0.07
196 120 0.43
197 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (194 bp):
AATTATTGTTATTGAAATTTTATCTAAATTATTTCGCCATTTGAGATAAATTTAGACAAAATTTC
TCACCTAAGAATTTTATAGAAATTTACTATTTAAAATTTCTAAAAAATCTCATCATTGGATAATT
TATATTTAATTCCAAAATTTTTATTAATATTTTATTTTATATTTTTTGTTTGAAAATAAATATT
Found at i:402299 original size:28 final size:28
Alignment explanation
Indices: 402244--402305 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
402234 TAATCAAGCA
*
402244 AAAATACTAAAAAAATAAACATATAAAT
1 AAAATACTAAAAAAATAAACATAAAAAT
402272 AAAATACTAAATAAAA-AATACA-AAAAAT
1 AAAATACTAAA-AAAATAA-ACATAAAAAT
402300 AGAAAT
1 A-AAAT
402306 GGCTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (28 bp):
AAAATACTAAAAAAATAAACATAAAAAT
Found at i:402777 original size:31 final size:31
Alignment explanation
Indices: 402724--402782 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
402714 AAACCTACCA
* *
402724 AAAAATTCAACCGACACTAAAAAGTTCACCG
1 AAAAATTCAACCGACACCAAAAAATTCACCG
*
402755 AAAAATTCAACC-AGCGCCAAAAAATTCA
1 AAAAATTCAACCGA-CACCAAAAAATTCA
402783 ACCTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.51, C:0.25, G:0.08, T:0.15
Consensus pattern (31 bp):
AAAAATTCAACCGACACCAAAAAATTCACCG
Found at i:412696 original size:4 final size:4
Alignment explanation
Indices: 412687--412714 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
412677 TTGAAAACAG
412687 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA
412715 GGATTGCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:417034 original size:2 final size:2
Alignment explanation
Indices: 417027--417065 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
417017 TAGCCACATT
417027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
417066 TAATAAAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:417873 original size:32 final size:34
Alignment explanation
Indices: 417795--417863 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
417785 TTCAAAAGAA
**
417795 AGAAATGAAGAGCAAAATGGTGACAGAGAGGGAG
1 AGAAATGAAGAGCAAAAAAGTGACAGAGAGGGAG
* *
417829 AGAAATGGAGAGCAAAAAAGTGAGAGAGAGGGAG
1 AGAAATGAAGAGCAAAAAAGTGACAGAGAGGGAG
417863 A
1 A
417864 TAAGAAGAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.49, C:0.04, G:0.39, T:0.07
Consensus pattern (34 bp):
AGAAATGAAGAGCAAAAAAGTGACAGAGAGGGAG
Found at i:421203 original size:33 final size:30
Alignment explanation
Indices: 421166--421241 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 30
421156 TATAATAATT
* *
421166 TAAATATATATAATATAATATATCCTTATTTTA
1 TAAATA-ATATAATATAAAATAT-ATT-TTTTA
421199 TAAATAATATAAATATAAAATATATTTTTTA
1 TAAATAATAT-AATATAAAATATATTTTTTA
*
421230 TATATAATATAA
1 TAAATAATATAA
421242 ATATTGTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.05
31 14 0.36
32 6 0.15
33 17 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAATAATATAATATAAAATATATTTTTTA
Found at i:421237 original size:31 final size:33
Alignment explanation
Indices: 421166--421245 Score: 103
Period size: 31 Copynumber: 2.5 Consensus size: 33
421156 TATAATAATT
* *
421166 TAAAT-ATATATAATATAATATATCCTTATTTTA
1 TAAATAATATA-AATATAAAATATCATTATTTTA
421199 TAAATAATATAAATATAAAATAT-ATT-TTTTA
1 TAAATAATATAAATATAAAATATCATTATTTTA
*
421230 TATATAATATAAATAT
1 TAAATAATATAAATAT
421246 TGTATTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 20 0.47
32 2 0.05
33 16 0.37
34 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (33 bp):
TAAATAATATAAATATAAAATATCATTATTTTA
Found at i:422325 original size:38 final size:37
Alignment explanation
Indices: 422257--422349 Score: 125
Period size: 38 Copynumber: 2.5 Consensus size: 37
422247 ATATGAAAAA
*
422257 TATATCATTTATAATTA-TTATATTACAATTAATCAAT
1 TATAT-ATTTAAAATTATTTATATTACAATTAATCAAT
* *
422294 TCTATAATTTAAAATTATTTATATTATAATTAATCAAT
1 TATAT-ATTTAAAATTATTTATATTACAATTAATCAAT
422332 TATATATTTCAAAATTAT
1 TATATATTT-AAAATTAT
422350 ATAAAATTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 18 0.37
38 31 0.63
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.49
Consensus pattern (37 bp):
TATATATTTAAAATTATTTATATTACAATTAATCAAT
Found at i:422336 original size:19 final size:19
Alignment explanation
Indices: 422273--422336 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
422263 ATTTATAATT
*
422273 ATTATATTACAATTAATCA
1 ATTATATTATAATTAATCA
*
422292 ATTCTATAATT-TAA--AATTA
1 A-T-TAT-ATTATAATTAATCA
*
422311 TTTATATTATAATTAATCA
1 ATTATATTATAATTAATCA
422330 ATTATAT
1 ATTATAT
422337 ATTTCAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
16 3 0.09
17 6 0.18
18 1 0.03
19 15 0.44
20 1 0.03
21 5 0.15
22 3 0.09
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTATATTATAATTAATCA
Found at i:429346 original size:13 final size:13
Alignment explanation
Indices: 429330--429355 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429320 TTTTATTGAT
429330 TAATTATATTTTA
1 TAATTATATTTTA
429343 TAATTATATTTTA
1 TAATTATATTTTA
429356 CGCTTTAAAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATTATATTTTA
Found at i:429431 original size:21 final size:21
Alignment explanation
Indices: 429407--429453 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
429397 ATGAAATAAA
429407 AATAATATAATT-TA-AAATTTT
1 AATAA-ATAATTATATAAA-TTT
429428 AATAAA-AATTATATAAATTT
1 AATAAATAATTATATAAATTT
429448 AATAAA
1 AATAAA
429454 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.17
20 12 0.50
21 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAAATAATTATATAAATTT
Found at i:444144 original size:35 final size:35
Alignment explanation
Indices: 444094--444161 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
444084 TATATGTCAA
*
444094 GTCAGTTGTAGATTTATACCTAAAAAATATTTGCT
1 GTCAGTTGTAGATTTATACCCAAAAAATATTTGCT
* * *
444129 GTCAGTTGTATATTTATGCCCAGAAAATATTTG
1 GTCAGTTGTAGATTTATACCCAAAAAATATTTG
444162 GTTTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (35 bp):
GTCAGTTGTAGATTTATACCCAAAAAATATTTGCT
Found at i:447494 original size:80 final size:78
Alignment explanation
Indices: 447359--447668 Score: 413
Period size: 80 Copynumber: 3.9 Consensus size: 78
447349 TTTAGCAAAT
* * * *
447359 GATTTAGCCCTCCAATATCATACAAAACCATTAAGCAAAACAATATCAGACAACAACGTTCAGCA
1 GATTCAGCCC-CCAATATCATACAATACCATTCAGCAAAATAATATCAGACAACAA-GTTCAGCA
*
447424 AACCATTCAGCATAT
64 AACCATTCAGCATAC
* *
447439 GATTCAGCCCCCTAATATCATACAATACCATTCAGCAAAATAATATTAGATAACAAGGTTCAGCA
1 GATTCAGCCCCC-AATATCATACAATACCATTCAGCAAAATAATATCAGACAACAA-GTTCAGCA
*
447504 AACTATTCAGCATAC
64 AACCATTCAGCATAC
* * * *
447519 GATTCAGCCCCGCAATATCATACAATACCATTCAGTAAAATAATATCAGATAATAAGTTCAGTAA
1 GATTCAGCCCC-CAATATCATACAATACCATTCAGCAAAATAATATCAGACAACAAGTTCAGCAA
447584 ACCATTCAGCATAC
65 ACCATTCAGCATAC
* * **
447598 GATTCAACCCCTTAATATCATACAATACCATTCAATAAAATAATATCAGACAACAAAGTTCAGCA
1 GATTCAGCCCC-CAATATCATACAATACCATTCAGCAAAATAATATCAGACAAC-AAGTTCAGCA
447663 AACCAT
64 AACCAT
447669 AATATTTAAG
Statistics
Matches: 206, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
79 71 0.34
80 134 0.65
81 1 0.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (78 bp):
GATTCAGCCCCCAATATCATACAATACCATTCAGCAAAATAATATCAGACAACAAGTTCAGCAAA
CCATTCAGCATAC
Found at i:458235 original size:2 final size:2
Alignment explanation
Indices: 458228--458266 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
458218 AACTTGAGTT
458228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
458267 TTGCATCCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:464639 original size:7 final size:7
Alignment explanation
Indices: 464627--464652 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
464617 AAAGCAGCAA
464627 AATATAT
1 AATATAT
464634 AATATAT
1 AATATAT
464641 AATATAT
1 AATATAT
464648 AATAT
1 AATAT
464653 GCTAATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATAT
Found at i:469956 original size:25 final size:24
Alignment explanation
Indices: 469928--469979 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
469918 ATTTAAGATT
469928 AATAATATCTAATAA-TTTTATTAAA
1 AATAATAT-TAATAACTTTTA-TAAA
* *
469953 AATATTATTTATAACTTTTATAAA
1 AATAATATTAATAACTTTTATAAA
469977 AAT
1 AAT
469980 TATTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
AATAATATTAATAACTTTTATAAA
Found at i:469983 original size:25 final size:25
Alignment explanation
Indices: 469939--469989 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 25
469929 ATAATATCTA
469939 ATAATTTTATTAAAAATA-TTATTT
1 ATAATTTTATTAAAAATATTTATTT
469963 ATAACTTTTA-TAAAAATTATTTATTT
1 ATAA-TTTTATTAAAAA-TATTTATTT
469989 A
1 A
469990 AAAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.42
25 7 0.29
26 7 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
ATAATTTTATTAAAAATATTTATTT
Found at i:470072 original size:35 final size:34
Alignment explanation
Indices: 469998--470072 Score: 82
Period size: 36 Copynumber: 2.2 Consensus size: 34
469988 TAAAAATATA
469998 TATTTATTAAAAAAATTTTAAATTTTATATATTT
1 TATTTATTAAAAAAATTTTAAATTTTATATATTT
* * *
470032 AATTTATATAATAAAATTTTTTAATTTTA-AT-TTAT
1 TATTTAT-TAA-AAAAATTTTAAATTTTATATATT-T
470067 TATTTA
1 TATTTA
470073 ATTATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
34 8 0.24
35 11 0.32
36 15 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATTTATTAAAAAAATTTTAAATTTTATATATTT
Found at i:470891 original size:15 final size:16
Alignment explanation
Indices: 470873--470905 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
470863 TCATTTTTTT
*
470873 TTAATTTTATTA-AAA
1 TTAATCTTATTATAAA
470888 TTAATCTTATTATAAA
1 TTAATCTTATTATAAA
470904 TT
1 TT
470906 TAAAAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATCTTATTATAAA
Found at i:471652 original size:11 final size:12
Alignment explanation
Indices: 471632--471656 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
471622 CCATTCTTTC
471632 TTTTCTTTTTTT
1 TTTTCTTTTTTT
471644 TTTTCTTTTTTT
1 TTTTCTTTTTTT
471656 T
1 T
471657 AAATTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:474187 original size:27 final size:26
Alignment explanation
Indices: 474135--474189 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
474125 TTTTTAATTT
*
474135 TAATTTTAATTTAAAAAATTATAAAA
1 TAATTTTAATTTAAAAAATTAAAAAA
*
474161 TAATTTATAATTTAATATAA-TAAAAAA
1 TAATTT-TAATTTAA-AAAATTAAAAAA
474188 TA
1 TA
474190 TAATATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 16 0.64
28 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
TAATTTTAATTTAAAAAATTAAAAAA
Found at i:480600 original size:13 final size:13
Alignment explanation
Indices: 480570--480605 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
480560 TGGTCACATT
480570 ATTTTAAAATAAA
1 ATTTTAAAATAAA
*
480583 A-TTTAAAGTAAA
1 ATTTTAAAATAAA
480595 ATTTTAAAATA
1 ATTTTAAAATA
480606 GCATGAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATTTTAAAATAAA
Found at i:483931 original size:10 final size:10
Alignment explanation
Indices: 483907--483947 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
483897 TTTTTTTATT
*
483907 TTTTTAATTAT
1 TTTTTAA-TAA
483918 TTTTTAATAA
1 TTTTTAATAA
483928 TTTTTAATAA
1 TTTTTAATAA
*
483938 TTTTAAATAA
1 TTTTTAATAA
483948 ATTAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:483961 original size:11 final size:11
Alignment explanation
Indices: 483907--483961 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 11
483897 TTTTTTTATT
*
483907 TTTTTAATTAT
1 TTTTTAATTAA
483918 TTTTTAA-TAA
1 TTTTTAATTAA
483928 TTTTTAA-TAA
1 TTTTTAATTAA
483938 TTTTAAATAAATTAA
1 TTTT---T-AATTAA
483953 TTTTTAATT
1 TTTTTAATT
483962 TTAATTAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 16 0.42
11 11 0.29
12 1 0.03
13 1 0.03
14 2 0.05
15 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTTAATTAA
Found at i:490348 original size:32 final size:32
Alignment explanation
Indices: 490303--490365 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
490293 TAAAAATTAA
*
490303 GGAAGAGTACGGTATATAAAAGTTCCTACAGT
1 GGAAGAGTACGGTACATAAAAGTTCCTACAGT
* *
490335 GGAAGAGTGCGGTACATAAAAGTTTCTACAG
1 GGAAGAGTACGGTACATAAAAGTTCCTACAG
490366 CATCCGCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.24
Consensus pattern (32 bp):
GGAAGAGTACGGTACATAAAAGTTCCTACAGT
Found at i:497824 original size:23 final size:24
Alignment explanation
Indices: 497791--497847 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
497781 TGTCACCATC
*
497791 ATTTTTCAACTT-TACAACCATTT
1 ATTTTTCAACTTGAACAACCATTT
* *
497814 ATTTTTTAACTTGAACAACTATTT
1 ATTTTTCAACTTGAACAACCATTT
497838 ATTTTTCAAC
1 ATTTTTCAAC
497848 GGTCTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTTTCAACTTGAACAACCATTT
Found at i:501040 original size:17 final size:17
Alignment explanation
Indices: 501018--501052 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
501008 TAACTCCACC
501018 TCTTTTTATTAAGTAGT
1 TCTTTTTATTAAGTAGT
501035 TCTTTTTATTAAGTAGT
1 TCTTTTTATTAAGTAGT
501052 T
1 T
501053 AGGGCTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (17 bp):
TCTTTTTATTAAGTAGT
Found at i:506206 original size:23 final size:25
Alignment explanation
Indices: 506180--506225 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
506170 TGTTGCGCCT
*
506180 GAAGCAATA-ATCACAAT-AATACA
1 GAAGCAATAGATAACAATCAATACA
506203 GAAGCAATAGATAACAATCAATA
1 GAAGCAATAGATAACAATCAATA
506226 ATCAAAGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (25 bp):
GAAGCAATAGATAACAATCAATACA
Found at i:506553 original size:23 final size:25
Alignment explanation
Indices: 506511--506556 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
506501 CGTCTTTGAT
*
506511 TATTGATTGTTATCTATTGCTTCTG
1 TATTGATTGTGATCTATTGCTTCTG
506536 TATTG-TTGTGAT-TATTGCTTC
1 TATTGATTGTGATCTATTGCTTC
506557 AGGCGCAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.15, C:0.11, G:0.17, T:0.57
Consensus pattern (25 bp):
TATTGATTGTGATCTATTGCTTCTG
Found at i:509104 original size:17 final size:18
Alignment explanation
Indices: 509063--509105 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
509053 TTGGATTTAT
*
509063 TAAAAAATTTTTTAGTAAG
1 TAAAAAAGTTTTTAG-AAG
*
509082 TCAAAAAGTTTTTA-AAG
1 TAAAAAAGTTTTTAGAAG
509099 TAAAAAA
1 TAAAAAA
509106 TTAGGTACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.35
Consensus pattern (18 bp):
TAAAAAAGTTTTTAGAAG
Found at i:509639 original size:23 final size:22
Alignment explanation
Indices: 509613--509669 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
509603 ATTTGAATAA
509613 AAATAATTATTTTATAATAAAAT
1 AAATAATTATTTTAT-ATAAAAT
* * *
509636 AAATAATTGTAATTATTTAAAAT
1 AAATAATTAT-TTTATATAAAAT
*
509659 AAATAACTATT
1 AAATAATTATT
509670 CAAATAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATAATTATTTTATATAAAAT
Found at i:509685 original size:34 final size:33
Alignment explanation
Indices: 509636--509700 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
509626 ATAATAAAAT
*
509636 AAATAATTGTAATTATTTAAAATAAATAACTATTC
1 AAATAATTATAATTATTT-AAATAAA-AACTATTC
*
509671 AAATAA-TATAATTATTTGAATAAAAACTAT
1 AAATAATTATAATTATTTAAATAAAAACTAT
509701 AATTATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 6 0.21
34 10 0.36
35 6 0.21
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
AAATAATTATAATTATTTAAATAAAAACTATTC
Found at i:512296 original size:59 final size:59
Alignment explanation
Indices: 512204--512321 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
512194 GAAGCACCAG
512204 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAA
1 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAA
512263 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAA
1 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAA
512322 ATTGAAGGGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (59 bp):
GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAA
Found at i:512460 original size:112 final size:112
Alignment explanation
Indices: 512263--512476 Score: 401
Period size: 112 Copynumber: 1.9 Consensus size: 112
512253 GTCTATACAA
512263 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAAATTGAA
1 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAAATTGAA
512328 GGGCTTCCTAATTTGCGATCTCTGTCCATGGGGCTCTGAAGCACCAG
66 GGGCTTCCTAATTTGCGATCTCTGTCCATGGGGCTCTGAAGCACCAG
* * *
512375 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTGTAGTGTTTATACATATTGAA
1 GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAAATTGAA
512440 GGGCTTCCTAATTTGCGATCTCTGTCCATGGGGCTCT
66 GGGCTTCCTAATTTGCGATCTCTGTCCATGGGGCTCT
512477 ATAATCTGAC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 99 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (112 bp):
GCATAGTTTCCTTTCCAGATGAAAAGTGTCTGCTCCCCACAACTCTAGTGTCTATACAAATTGAA
GGGCTTCCTAATTTGCGATCTCTGTCCATGGGGCTCTGAAGCACCAG
Found at i:516913 original size:81 final size:81
Alignment explanation
Indices: 516778--516944 Score: 334
Period size: 81 Copynumber: 2.1 Consensus size: 81
516768 TTTTTGTGGG
516778 ATGTGTCACTGATAATAGTCAAACCATGCAAAAAGCATCTTTTGTCGAAAAACCTATATTGGGTG
1 ATGTGTCACTGATAATAGTCAAACCATGCAAAAAGCATCTTTTGTCGAAAAACCTATATTGGGTG
516843 GCGGTTACATTGTAGA
66 GCGGTTACATTGTAGA
516859 ATGTGTCACTGATAATAGTCAAACCATGCAAAAAGCATCTTTTGTCGAAAAACCTATATTGGGTG
1 ATGTGTCACTGATAATAGTCAAACCATGCAAAAAGCATCTTTTGTCGAAAAACCTATATTGGGTG
516924 GCGGTTACATTGTAGA
66 GCGGTTACATTGTAGA
516940 ATGTG
1 ATGTG
516945 ATGTATTTTA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (81 bp):
ATGTGTCACTGATAATAGTCAAACCATGCAAAAAGCATCTTTTGTCGAAAAACCTATATTGGGTG
GCGGTTACATTGTAGA
Found at i:517696 original size:23 final size:23
Alignment explanation
Indices: 517681--517725 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
517671 AATAATTGTT
*
517681 TTATGATAAAATAAATAGTTATAA
1 TTAT-ATAAAATAAATAATTATAA
*
517705 TTATTTAAAATAAATAATTAT
1 TTATATAAAATAAATAATTAT
517726 TCAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TTATATAAAATAAATAATTATAA
Found at i:517723 original size:17 final size:18
Alignment explanation
Indices: 517700--517744 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
517690 AATAAATAGT
517700 TATAATTATTTAAAATAA
1 TATAATTATTTAAAATAA
*
517718 -ATAATTA-TTCAAATAA
1 TATAATTATTTAAAATAA
*
517734 TATTATTATTT
1 TATAATTATTT
517745 GAATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 8 0.35
17 13 0.57
18 2 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATTATTTAAAATAA
Found at i:524645 original size:31 final size:31
Alignment explanation
Indices: 524603--524678 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
524593 TTTTAAAATG
* *
524603 ACCATTTTGTTAGGGATCATCATAGCTCTGAT
1 ACCA-TTTGTTAGGGATCACCATAACTCTGAT
* *
524635 ACCATTTGTTAGAGATCACCATAATTCTGAT
1 ACCATTTGTTAGGGATCACCATAACTCTGAT
*
524666 ACCACTTGTTAGG
1 ACCATTTGTTAGG
524679 CTAAAAACCT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (31 bp):
ACCATTTGTTAGGGATCACCATAACTCTGAT
Found at i:546267 original size:15 final size:15
Alignment explanation
Indices: 546249--546288 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
546239 ATTTTTAGAA
*
546249 TTTTAGATTTTAAGG
1 TTTTAGATTTAAAGG
*
546264 TTTTGGATTTAAAGG
1 TTTTAGATTTAAAGG
*
546279 TTTAAGATTT
1 TTTTAGATTT
546289 GAGATTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (15 bp):
TTTTAGATTTAAAGG
Found at i:546362 original size:14 final size:14
Alignment explanation
Indices: 546343--546377 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
546333 GGGGGTTTAA
546343 GGATTTTAGGGTTT
1 GGATTTTAGGGTTT
546357 GGATTTTAGGGTTT
1 GGATTTTAGGGTTT
*
546371 AGATTTT
1 GGATTTT
546378 TTAATCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (14 bp):
GGATTTTAGGGTTT
Found at i:546526 original size:3 final size:3
Alignment explanation
Indices: 546502--546572 Score: 115
Period size: 3 Copynumber: 23.3 Consensus size: 3
546492 TTATGAAAAC
* *
546502 TTA TTG TTA TTA TTG TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
546548 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
546573 CCTTTTATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 61 0.97
4 2 0.03
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:546685 original size:3 final size:3
Alignment explanation
Indices: 546670--546730 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
546660 AACAAAAAAT
*
546670 TTA TTA TT- CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
546717 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
546731 TTAGCATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 54 0.98
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:548049 original size:22 final size:23
Alignment explanation
Indices: 548010--548058 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
548000 CACCCCAATC
548010 TTTTGTTTTTTCTATTTT-TATT
1 TTTTGTTTTTTCTATTTTGTATT
* *
548032 TTTTGTTGTTTT-TGTTTTGTTTT
1 TTTTGTT-TTTTCTATTTTGTATT
548055 TTTT
1 TTTT
548059 TAATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.84
Consensus pattern (23 bp):
TTTTGTTTTTTCTATTTTGTATT
Found at i:548834 original size:22 final size:22
Alignment explanation
Indices: 548800--548884 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
548790 GTGAATCGAA
548800 ATTATGCCCAGAGGTCTTAAAG
1 ATTATGCCCAGAGGTCTTAAAG
* *
548822 ATTATGTCTAGAGGTCTTAAAG
1 ATTATGCCCAGAGGTCTTAAAG
* *
548844 ATTATACCCGGAGGTCTTAGAA-
1 ATTATGCCCAGAGGTCTTA-AAG
* **
548866 ATCATATCCAGAGGTCTTA
1 ATTATGCCCAGAGGTCTTA
548885 CAAAATCGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 51 0.96
23 2 0.04
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (22 bp):
ATTATGCCCAGAGGTCTTAAAG
Found at i:548879 original size:44 final size:44
Alignment explanation
Indices: 548800--548884 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
548790 GTGAATCGAA
* * * *
548800 ATTATGCCCAGAGGTCTTAAAGATTATGTCTAGAGGTCTTAAAG
1 ATTATACCCAGAGGTCTTAAAGATCATATCCAGAGGTCTTAAAG
*
548844 ATTATACCCGGAGGTCTTAGAA-ATCATATCCAGAGGTCTTA
1 ATTATACCCAGAGGTCTTA-AAGATCATATCCAGAGGTCTTA
548885 CAAAATCGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 33 0.94
45 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (44 bp):
ATTATACCCAGAGGTCTTAAAGATCATATCCAGAGGTCTTAAAG
Found at i:548970 original size:154 final size:154
Alignment explanation
Indices: 548698--548983 Score: 376
Period size: 154 Copynumber: 1.9 Consensus size: 154
548688 AAATTATGTT
* * * * * *
548698 CGGAGGTTTTAAAAATCATGCCCTGAGGTCTTACAGAATCGACTGGGATAACACCGCAAGTCAAA
1 CGGAGGTCTTAAAAATCATACCCAGAGGTCTTACAAAATCGACTGAGACAACACCGCAAGTCAAA
*** * *
548763 AAATAAAGAATCGATCGAGATAACACTGTGAATCGAAATTATGCCCAGAGGTCTTAAAGATTATG
66 AAATAAAGAATCGATCGAGATAACACCACGAATCGAAATTATGCCCAGAGGTCTTAAAAATCATG
548828 TCTAGAGGTCTTAAAGATTATACC
131 TCTAGAGGTCTTAAAGATTATACC
* * *
548852 CGGAGGTCTTAGAAATCATATCCAGAGGTCTTACAAAATCGACTGAGACGACACCGCAAGTCAAA
1 CGGAGGTCTTAAAAATCATACCCAGAGGTCTTACAAAATCGACTGAGACAACACCGCAAGTCAAA
* * * ***
548917 AAATAAAGAAT-GAATTGGGATAACACCACGAATTGAAATTATGCTTGGAGGTCTTAAAAATCAT
66 AAATAAAGAATCG-ATCGAGATAACACCACGAATCGAAATTATGCCCAGAGGTCTTAAAAATCAT
548981 GTC
130 GTC
548984 CGAAGGTCTT
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
153 1 0.01
154 110 0.99
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (154 bp):
CGGAGGTCTTAAAAATCATACCCAGAGGTCTTACAAAATCGACTGAGACAACACCGCAAGTCAAA
AAATAAAGAATCGATCGAGATAACACCACGAATCGAAATTATGCCCAGAGGTCTTAAAAATCATG
TCTAGAGGTCTTAAAGATTATACC
Found at i:549202 original size:22 final size:22
Alignment explanation
Indices: 549174--549236 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
549164 GCGAATCAAA
549174 ATTATGCTTGAAGGTCTTAAAG
1 ATTATGCTTGAAGGTCTTAAAG
*
549196 ATTATGCTT-AGAGGTTTTAAAG
1 ATTATGCTTGA-AGGTCTTAAAG
*
549218 ATTATGCTCGAAGGTCTTA
1 ATTATGCTTGAAGGTCTTA
549237 CAGAATCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (22 bp):
ATTATGCTTGAAGGTCTTAAAG
Found at i:549210 original size:110 final size:108
Alignment explanation
Indices: 548853--549210 Score: 319
Period size: 110 Copynumber: 3.2 Consensus size: 108
548843 GATTATACCC
* * ** *
548853 GGAGGTCTTAGAAATCATATCCAGAGGTCTTACAAAATCGACT-GAGACGACACCGCAAGTCAAA
1 GGAGGTCTTA-AAATCATGT-TAGAGGTCTTACAAAATCGACTGGA-ATAACACCGCAAGTCATA
* * * **
548917 AAATAAAGAA-TGAATTGGGATAACACCACGAATTGAAATTATGCTT
63 AAATAAAGAATTG-ATCGGGATAACATCGCGAATCAAAATTATGCTT
** * * ** * * *
548963 GGAGGTCTTAAAAATCATGTCCGAAGGTCTTATAGAATTAACTGGGATAATACCGTAAGT--TGA
1 GGAGGTCTT-AAAATCATGTTAG-AGGTCTTACAAAATCGACTGGAATAACACCGCAAGTCAT-A
* * ** *
549026 AATATAAAGAATCGATCGGGACAACATCGTAAATCAAAATTATGCTC
63 AA-ATAAAGAATTGATCGGGATAACATCGCGAATCAAAATTATGCTT
*
549073 GGAGGTCTTTAAAATCATGTCTGGAGGTCTTACAAAATCGACTGGAATAACACCGCAAGTCATAA
1 GGAGGTC-TTAAAATCATGT-TAGAGGTCTTACAAAATCGACTGGAATAACACCGCAAGTCATAA
* *
549138 AATAAAGAATTGATCGAGATAATATCGCGAATCAAAATTATGCTT
64 AATAAAGAATTGATCGGGATAACATCGCGAATCAAAATTATGCTT
* *
549183 GAAGGTCTTAAAGATTATGCTTAGAGGT
1 GGAGGTCTTAAA-ATCATG-TTAGAGGT
549211 TTTAAAGATT
Statistics
Matches: 195, Mismatches: 41, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
109 10 0.05
110 174 0.89
111 10 0.05
112 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (108 bp):
GGAGGTCTTAAAATCATGTTAGAGGTCTTACAAAATCGACTGGAATAACACCGCAAGTCATAAAA
TAAAGAATTGATCGGGATAACATCGCGAATCAAAATTATGCTT
Found at i:549265 original size:132 final size:132
Alignment explanation
Indices: 549061--549471 Score: 391
Period size: 132 Copynumber: 3.1 Consensus size: 132
549051 ATCGTAAATC
** * *
549061 AAAATTATGCTCGGAGGTCTTTAAA-ATCATG-TCTGGAGGTCTTACAAAATCGACTGGAATAAC
1 AAAATTATGCTTAGAGGT-TTTAAAGATTATGCTC-GAAGGTCTTACAAAATCGACTGGAATAAC
* * * *
549124 ACCGCAAGTCATAAAATAAAGAATTGATC-GAGATAATATCGCGAATCAAAATTATGCTTGAAGG
64 ACCGCAAGTCAAAAAATAAAGAATCGATCAG-GATAATATCGCGAATCAAAATTATGCTCGAAGA
549188 TCTTA
128 TCTTA
* * *
549193 AAGATTATGCTTAGAGGTTTTAAAGATTATGCTCGAAGGTCTTACAGAATCGACTGGGATAACAC
1 AAAATTATGCTTAGAGGTTTTAAAGATTATGCTCGAAGGTCTTACAAAATCGACTGGAATAACAC
* * **
549258 TGTAAGTCAAAAAATAAAGAATCGATCAGGATAATATCGCGAATTGAAATTATGCTCGAAGATCT
66 CGCAAGTCAAAAAATAAAGAATCGATCAGGATAATATCGCGAATCAAAATTATGCTCGAAGATCT
549323 TA
131 TA
** * * ** * * * *
549325 AAAATTATGCTCGGAGGTCTTACAA-ATCATGCTTAAAGATTTTATAAAATTGACTAGG-ATAAC
1 AAAATTATGCTTAGAGGTTTTA-AAGATTATGCTCGAAGGTCTTACAAAATCGACT-GGAATAAC
* * * ** ** * * * * *
549388 ACCACAAGTTAAAAAATAAAAAATCGATTGGGATAGCACCACGAATCAAAATTATGCCCGGAGGT
64 ACCGCAAGTCAAAAAATAAAGAATCGATCAGGATAATATCGCGAATCAAAATTATGCTCGAAGAT
549453 CTTA
129 CTTA
* *
549457 AAAATCATGCCTAGA
1 AAAATTATGCTTAGA
549472 AGTCTTACAA
Statistics
Matches: 227, Mismatches: 47, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
131 6 0.03
132 214 0.94
133 7 0.03
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (132 bp):
AAAATTATGCTTAGAGGTTTTAAAGATTATGCTCGAAGGTCTTACAAAATCGACTGGAATAACAC
CGCAAGTCAAAAAATAAAGAATCGATCAGGATAATATCGCGAATCAAAATTATGCTCGAAGATCT
TA
Found at i:549332 original size:22 final size:22
Alignment explanation
Indices: 549304--549375 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
549294 TCGCGAATTG
549304 AAATTATGCTCGAAGATCTTAA
1 AAATTATGCTCGAAGATCTTAA
* * *
549326 AAATTATGCTCGGAGGTCTTAC
1 AAATTATGCTCGAAGATCTTAA
* ** *
549348 AAATCATGCTTAAAGATTTTATA
1 AAATTATGCTCGAAGATCTTA-A
549371 AAATT
1 AAATT
549376 GACTAGGATA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 34 0.89
23 4 0.11
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (22 bp):
AAATTATGCTCGAAGATCTTAA
Found at i:549466 original size:22 final size:23
Alignment explanation
Indices: 549434--549485 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
549424 CACCACGAAT
* * *
549434 CAAAATTATGCCCGGAGGTCTTA
1 CAAAATCATGCCCAGAAGTCTTA
*
549457 -AAAATCATGCCTAGAAGTCTTA
1 CAAAATCATGCCCAGAAGTCTTA
549479 CAAAATC
1 CAAAATC
549486 GACTGGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (23 bp):
CAAAATCATGCCCAGAAGTCTTA
Found at i:549528 original size:110 final size:110
Alignment explanation
Indices: 549325--549592 Score: 335
Period size: 110 Copynumber: 2.4 Consensus size: 110
549315 GAAGATCTTA
* * * * * *
549325 AAAATTATGCTCGGAGGTCTTACAAATCATGCTTA-AAGATTTTATAAAATTGACTAGGATAACA
1 AAAATTATGCCCGGAGGTCTTAAAAATCATGCCTAGAAG-TCTTACAAAATCGACTAGGATAACA
* *
549389 CCACAAGTTAAAAAATAAAAAATCGATTGGGATAGCACCACGAATC
65 CCACAAGTCAAAAAATAAAAAATCGATTGGGATAACACCACGAATC
549435 AAAATTATGCCCGGAGGTCTTAAAAATCATGCCTAGAAGTCTTACAAAATCGACT-GGAATAACA
1 AAAATTATGCCCGGAGGTCTTAAAAATCATGCCTAGAAGTCTTACAAAATCGACTAGG-ATAACA
* * * * *
549499 CCACAAGTCAAAAAATAAAGAATCTATTGGGATAATATCATGAATC
65 CCACAAGTCAAAAAATAAAAAATCGATTGGGATAACACCACGAATC
* * * *
549545 AAAATTATGCCTGGAGGTCTTAAAGATTATG-CTCGAAAGTCTTACAAA
1 AAAATTATGCCCGGAGGTCTTAAAAATCATGCCTAG-AAGTCTTACAAA
549593 TCTCAAAATT
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
109 5 0.04
110 130 0.94
111 3 0.02
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (110 bp):
AAAATTATGCCCGGAGGTCTTAAAAATCATGCCTAGAAGTCTTACAAAATCGACTAGGATAACAC
CACAAGTCAAAAAATAAAAAATCGATTGGGATAACACCACGAATC
Found at i:549689 original size:22 final size:23
Alignment explanation
Indices: 549658--549703 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
549648 AAAAATCTTT
*
549658 TGCCCAAAGGTCTT-GAAAGTTA
1 TGCCCAAAGGCCTTCGAAAGTTA
* *
549680 TGCCCGAAGGCCTTCGAAATTTA
1 TGCCCAAAGGCCTTCGAAAGTTA
549703 T
1 T
549704 AAATCTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
TGCCCAAAGGCCTTCGAAAGTTA
Found at i:552373 original size:8 final size:8
Alignment explanation
Indices: 552362--552389 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
552352 TCTTCTTTCT
552362 TTTTTTTA
1 TTTTTTTA
552370 TTTTTTTA
1 TTTTTTTA
552378 TTTTTTTA
1 TTTTTTTA
552386 TTTT
1 TTTT
552390 ATCCTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:552373 original size:21 final size:21
Alignment explanation
Indices: 552349--552391 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
552339 CAAAGAAAAC
*
552349 TTTTCTTCTTTCTTTT-TTTTA
1 TTTTCTTATTT-TTTTATTTTA
*
552370 TTTTTTTATTTTTTTATTTTA
1 TTTTCTTATTTTTTTATTTTA
552391 T
1 T
552392 CCTGAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTCTTATTTTTTTATTTTA
Found at i:556601 original size:14 final size:15
Alignment explanation
Indices: 556573--556603 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
556563 TTTGAAAATG
556573 TTTTTTTTTACCTTT
1 TTTTTTTTTACCTTT
556588 TTTTTTTTTA-CTTT
1 TTTTTTTTTACCTTT
556602 TT
1 TT
556604 GCTTGTTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTACCTTT
Found at i:557192 original size:26 final size:26
Alignment explanation
Indices: 557154--557204 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
557144 TATATTTTGA
*
557154 AAATTTAAAATAAAAGAAATTAAATT
1 AAATATAAAATAAAAGAAATTAAATT
* **
557180 AAATATAAGATAAAATCAATTAAAT
1 AAATATAAAATAAAAGAAATTAAAT
557205 CCAAGAACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (26 bp):
AAATATAAAATAAAAGAAATTAAATT
Found at i:558369 original size:15 final size:15
Alignment explanation
Indices: 558346--558386 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
558336 ATTTTCAGAA
*
558346 TTTTAGATTTTAAGG
1 TTTTGGATTTTAAGG
*
558361 TTTTGGATTTAAAGG
1 TTTTGGATTTTAAGG
558376 TTTTGGATTTT
1 TTTTGGATTTT
558387 GGATTTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
TTTTGGATTTTAAGG
Found at i:558370 original size:22 final size:21
Alignment explanation
Indices: 558345--558395 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
558335 GATTTTCAGA
558345 ATTTTAGATTTTAAGG-TTTTGG
1 ATTTTAGATTTT--GGATTTTGG
* *
558367 ATTTAAAGGTTTTGGATTTTGG
1 ATTT-TAGATTTTGGATTTTGG
558389 ATTTTAG
1 ATTTTAG
558396 GGTTCGAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (21 bp):
ATTTTAGATTTTGGATTTTGG
Found at i:558654 original size:3 final size:3
Alignment explanation
Indices: 558625--558676 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
558615 AAACTTTTTG
* *
558625 TTA TTA TTG TTAA TT- TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
558670 TTA TTA T
1 TTA TTA T
558677 CATTTTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:558994 original size:18 final size:18
Alignment explanation
Indices: 558973--559011 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
558963 ATAATAATAC
* *
558973 ATAAAAAATTCAAAAAAA
1 ATAAAAAAGTAAAAAAAA
558991 ATAAAAAAGTAAAAAAAA
1 ATAAAAAAGTAAAAAAAA
559009 ATA
1 ATA
559012 TACTTGAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
ATAAAAAAGTAAAAAAAA
Found at i:560098 original size:22 final size:20
Alignment explanation
Indices: 560068--560135 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 20
560058 GCCACCCCGG
*
560068 TTTTCTGTTTTTTCTATTTCTA
1 TTTTTTGTTTTTT-TATTT-TA
* *
560090 TTTTTTGTTGTTTTTGTTTTG
1 TTTTTTGTT-TTTTTATTTTA
** *
560111 TTTTTTGTTTAATTATTATA
1 TTTTTTGTTTTTTTATTTTA
560131 TTTTT
1 TTTTT
560136 ATAATAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 11 0.30
21 10 0.27
22 12 0.32
23 4 0.11
ACGTcount: A:0.10, C:0.04, G:0.09, T:0.76
Consensus pattern (20 bp):
TTTTTTGTTTTTTTATTTTA
Found at i:561211 original size:24 final size:24
Alignment explanation
Indices: 561179--561233 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
561169 TTTTTTATTA
*
561179 AATTTTTTTAATTATAATTATAGT
1 AATTTTTTTAATTATAATTATAAT
561203 AATTTTTTTAATTATAATTATAAT
1 AATTTTTTTAATTATAATTATAAT
561227 AATTTTT
1 AATTTTT
561234 ACGATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTTTTTTAATTATAATTATAAT
Found at i:561240 original size:24 final size:24
Alignment explanation
Indices: 561179--561241 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
561169 TTTTTTATTA
** *
561179 AATTTTTTTAATTATAATTATAGT
1 AATTTTTACAATTATAATTATAAT
**
561203 AATTTTTTTAATTATAATTATAAT
1 AATTTTTACAATTATAATTATAAT
*
561227 AATTTTTACGATTAT
1 AATTTTTACAATTAT
561242 TTTCAATCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (24 bp):
AATTTTTACAATTATAATTATAAT
Found at i:574483 original size:13 final size:13
Alignment explanation
Indices: 574465--574489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
574455 GAATTCTAGT
574465 TTTATATATGTAA
1 TTTATATATGTAA
574478 TTTATATATGTA
1 TTTATATATGTA
574490 GCTTGCCTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TTTATATATGTAA
Found at i:586889 original size:5 final size:5
Alignment explanation
Indices: 586881--586906 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
586871 GTGCAGTCGC
586881 CTTTT CTTTT CTTTT CTTTT CTTTT C
1 CTTTT CTTTT CTTTT CTTTT CTTTT C
586907 GTTCTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:597088 original size:8 final size:9
Alignment explanation
Indices: 597063--597097 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
597053 TATATTTGGC
597063 TTTCTAGTT
1 TTTCTAGTT
597072 TTTCTAGTT
1 TTTCTAGTT
597081 TTTC-AGTT
1 TTTCTAGTT
597089 TTT-TAGTT
1 TTTCTAGTT
597097 T
1 T
597098 CTAATGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 12 0.48
9 13 0.52
ACGTcount: A:0.11, C:0.09, G:0.11, T:0.69
Consensus pattern (9 bp):
TTTCTAGTT
Found at i:597095 original size:16 final size:18
Alignment explanation
Indices: 597063--597097 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
597053 TATATTTGGC
597063 TTTCTAGTTTTTCTAGTT
1 TTTCTAGTTTTTCTAGTT
597081 TTTC-AGTTTTT-TAGTT
1 TTTCTAGTTTTTCTAGTT
597097 T
1 T
597098 CTAATGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.11, C:0.09, G:0.11, T:0.69
Consensus pattern (18 bp):
TTTCTAGTTTTTCTAGTT
Found at i:598083 original size:2 final size:2
Alignment explanation
Indices: 598048--598073 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
598038 ATAGATGAAG
598048 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
598074 GCTGATATAT
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:611559 original size:37 final size:37
Alignment explanation
Indices: 611511--611604 Score: 179
Period size: 37 Copynumber: 2.5 Consensus size: 37
611501 ATCAAAGGAG
*
611511 GGAGACGAAGTTAAGTAAGAGCAATAAGAGATTTGAA
1 GGAGAAGAAGTTAAGTAAGAGCAATAAGAGATTTGAA
611548 GGAGAAGAAGTTAAGTAAGAGCAATAAGAGATTTGAA
1 GGAGAAGAAGTTAAGTAAGAGCAATAAGAGATTTGAA
611585 GGAGAAGAAGTTAAGTAAGA
1 GGAGAAGAAGTTAAGTAAGA
611605 AAGTGCAGCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.48, C:0.03, G:0.31, T:0.18
Consensus pattern (37 bp):
GGAGAAGAAGTTAAGTAAGAGCAATAAGAGATTTGAA
Found at i:613523 original size:21 final size:21
Alignment explanation
Indices: 613485--613524 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
613475 GGTTTAGCAC
*
613485 AAAATATGAAAGAAAAATAAA
1 AAAATATGAAACAAAAATAAA
* *
613506 AAAATATGAATCAGAAATA
1 AAAATATGAAACAAAAATA
613525 GCACTAGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATATGAAACAAAAATAAA
Found at i:614509 original size:11 final size:11
Alignment explanation
Indices: 614493--614529 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
614483 TTACGTTTAT
*
614493 ATTTTTAATCA
1 ATTTTTAATTA
614504 ATTTTTAATTA
1 ATTTTTAATTA
614515 ATTTTTAATTA
1 ATTTTTAATTA
614526 ATTT
1 ATTT
614530 AAAATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTAATTA
Found at i:614535 original size:22 final size:22
Alignment explanation
Indices: 614493--614536 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
614483 TTACGTTTAT
**
614493 ATTTTTAATCAATTTTTAATTA
1 ATTTTTAATCAATTTAAAATTA
*
614515 ATTTTTAATTAATTTAAAATTA
1 ATTTTTAATCAATTTAAAATTA
614537 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTAATCAATTTAAAATTA
Found at i:618612 original size:3 final size:3
Alignment explanation
Indices: 618604--618637 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
618594 CATATATAAT
618604 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
618638 ACAAACAAGA
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:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:619233 original size:4 final size:4
Alignment explanation
Indices: 619224--619256 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
619214 TCAGCCTACA
619224 AATT AATT AATT AATT AATT AATT AATT -ATT AA
1 AATT AATT AATT AATT AATT AATT AATT AATT AA
619257 ATTTGATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:619825 original size:15 final size:15
Alignment explanation
Indices: 619798--619834 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
619788 AATAATATGA
*
619798 TAATTATTTTATATT
1 TAATTAATTTATATT
*
619813 TATTTAATTTATATT
1 TAATTAATTTATATT
619828 TAATTAA
1 TAATTAA
619835 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATTAATTTATATT
Found at i:620956 original size:2 final size:2
Alignment explanation
Indices: 620951--620980 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
620941 TGTTTACTTC
*
620951 AT AT AT AT AA 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
620981 CTTCGGAAGA
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):
AT
Found at i:633087 original size:2 final size:2
Alignment explanation
Indices: 633080--633104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
633070 GGTTAAACAA
633080 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
633105 ATTAATTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:633555 original size:2 final size:2
Alignment explanation
Indices: 633548--633577 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
633538 TTACTTAAGC
633548 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
633578 CCTTGACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:638810 original size:21 final size:21
Alignment explanation
Indices: 638781--638825 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
638771 CAAAATCCAA
638781 CCTCATTAATACTTATTAATC
1 CCTCATTAATACTTATTAATC
*
638802 CCTCGTTAATACTTATTAATC
1 CCTCATTAATACTTATTAATC
638823 CCT
1 CCT
638826 TTGTTTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.42
Consensus pattern (21 bp):
CCTCATTAATACTTATTAATC
Found at i:652307 original size:18 final size:18
Alignment explanation
Indices: 652280--652318 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
652270 TACCCTCTTA
*
652280 TATTACTTTAGTTCATGC
1 TATTACTTTAGATCATGC
* *
652298 TATTATTTTAGATGATGC
1 TATTACTTTAGATCATGC
652316 TAT
1 TAT
652319 CAGACCAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (18 bp):
TATTACTTTAGATCATGC
Found at i:659511 original size:6 final size:6
Alignment explanation
Indices: 659500--659531 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
659490 AATCTCGTCT
*
659500 TGTTTG TGTTTG TGTCTG TGTTTG TGTTTG TG
1 TGTTTG TGTTTG TGTTTG TGTTTG TGTTTG TG
659532 GACATGTGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.34, T:0.62
Consensus pattern (6 bp):
TGTTTG
Found at i:659523 original size:18 final size:17
Alignment explanation
Indices: 659496--659531 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
659486 GAATAATCTC
659496 GTCTTGTTTGTGTTTGT
1 GTCTTGTTTGTGTTTGT
659513 GTCTGTGTTTGTGTTTGT
1 GTCT-TGTTTGTGTTTGT
659531 G
1 G
659532 GACATGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.00, C:0.06, G:0.33, T:0.61
Consensus pattern (17 bp):
GTCTTGTTTGTGTTTGT
Found at i:671051 original size:37 final size:38
Alignment explanation
Indices: 670997--671073 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 38
670987 TTGAAATCAC
*
670997 ATTATTGAAAAGGCAGGTTTATTGATTGCAGAACCTGA
1 ATTATTGAAAAGGCAGGTTTACTGATTGCAGAACCTGA
671035 ATTATTG-AAAGGCAGGTTTACTGATTGCAGAACCTGA
1 ATTATTGAAAAGGCAGGTTTACTGATTGCAGAACCTGA
671072 AT
1 AT
671074 CTTACTTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 31 0.82
38 7 0.18
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (38 bp):
ATTATTGAAAAGGCAGGTTTACTGATTGCAGAACCTGA
Found at i:672232 original size:10 final size:10
Alignment explanation
Indices: 672219--672255 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
672209 TATTACTTTA
672219 AATTATAATT
1 AATTATAATT
672229 AATTAT-ATT
1 AATTATAATT
672238 ATATTATAATT
1 A-ATTATAATT
672249 -ATTATAA
1 AATTATAA
672256 ATTATATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 11 0.44
10 11 0.44
11 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTATAATT
Found at i:672258 original size:26 final size:25
Alignment explanation
Indices: 672206--672262 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
672196 TTGATGATGT
*
672206 TTATATTACTTTAAATTATAATTAA
1 TTATATTACTTTAAATTATAATAAA
*
672231 TTATATTA-TATTATAATTATTATAAA
1 TTATATTACT-TTA-AATTATAATAAA
672257 TTATAT
1 TTATAT
672263 GTTCTTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 11 0.39
26 16 0.57
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATATTACTTTAAATTATAATAAA
Found at i:673907 original size:22 final size:21
Alignment explanation
Indices: 673882--673929 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
673872 AATAATTTTA
*
673882 AATTAAGTATAAAATCAAATAT
1 AATTAAGTAAAAAAT-AAATAT
*
673904 AATTTAATTAAAAAATAAATAT
1 AA-TTAAGTAAAAAATAAATAT
673926 AATT
1 AATT
673930 TAAACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 10 0.43
23 11 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AATTAAGTAAAAAATAAATAT
Found at i:674705 original size:103 final size:105
Alignment explanation
Indices: 674560--674765 Score: 344
Period size: 104 Copynumber: 2.0 Consensus size: 105
674550 GTAGGGGCCG
* * *
674560 CATCCTGAACCACTTTGGCTTACAACATATCCAATAAAATTATAACACCTGTCATTAAC-AATGG
1 CATCCTCAACCACTTTCGCTAACAACATATCCAATAAAATTATAACACCTGTCATTAACAAATGG
674624 GCTTTAGTATTATACAATAGGCCGTGTAGTACTTGATTCC
66 GCTTTAGTATTATACAATAGGCCGTGTAGTACTTGATTCC
*
674664 CATCCTCAACCAC-TTCGCTAACAACATGTCCAATAAAATTATAACACCTGTCATTAACAAATGG
1 CATCCTCAACCACTTTCGCTAACAACATATCCAATAAAATTATAACACCTGTCATTAACAAATGG
* *
674728 GTTTTAGTATTATACAATAGGTCGTGTAGTACTTGATT
66 GCTTTAGTATTATACAATAGGCCGTGTAGTACTTGATT
674766 GCCCCAAGTC
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 42 0.44
104 53 0.56
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (105 bp):
CATCCTCAACCACTTTCGCTAACAACATATCCAATAAAATTATAACACCTGTCATTAACAAATGG
GCTTTAGTATTATACAATAGGCCGTGTAGTACTTGATTCC
Found at i:683983 original size:16 final size:16
Alignment explanation
Indices: 683962--683992 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
683952 AATACTTTAT
683962 AAAACAAAGCTTTCTG
1 AAAACAAAGCTTTCTG
683978 AAAACAAAGCTTTCT
1 AAAACAAAGCTTTCT
683993 ACTTCCCAAC
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:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (16 bp):
AAAACAAAGCTTTCTG
Found at i:687700 original size:23 final size:23
Alignment explanation
Indices: 687674--687719 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
687664 TATATTAATG
687674 ATTTATTTAAATACAAATTAAAA
1 ATTTATTTAAATACAAATTAAAA
* **
687697 ATTTATTTAGATATGAATTAAAA
1 ATTTATTTAAATACAAATTAAAA
687720 GTTAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTTATTTAAATACAAATTAAAA
Found at i:687725 original size:30 final size:30
Alignment explanation
Indices: 687691--687823 Score: 169
Period size: 30 Copynumber: 4.4 Consensus size: 30
687681 TAAATACAAA
*
687691 TTAAAAATTTATTTAGATATGAATTAAAAG
1 TTAAAAATTTATTTAGATATAAATTAAAAG
* *
687721 TTAAAAATTTATTT-GCATGTAAATTAAAAT
1 TTAAAAATTTATTTAG-ATATAAATTAAAAG
* *
687751 TTAAAAATTTATTTAAATACAAATTAAAAG
1 TTAAAAATTTATTTAGATATAAATTAAAAG
* * *
687781 TTAAAAATTTATTTACATGTAAATTAAAAT
1 TTAAAAATTTATTTAGATATAAATTAAAAG
*
687811 TTAAAAGTTTATT
1 TTAAAAATTTATT
687824 CATAATATTA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.01
30 88 0.99
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (30 bp):
TTAAAAATTTATTTAGATATAAATTAAAAG
Found at i:687755 original size:60 final size:60
Alignment explanation
Indices: 687691--687823 Score: 221
Period size: 60 Copynumber: 2.2 Consensus size: 60
687681 TAAATACAAA
* ** *
687691 TTAAAAATTTATTTAGATATGAATTAAAAGTTAAAAATTTATTTGCATGTAAATTAAAAT
1 TTAAAAATTTATTTAAATACAAATTAAAAGTTAAAAATTTATTTACATGTAAATTAAAAT
687751 TTAAAAATTTATTTAAATACAAATTAAAAGTTAAAAATTTATTTACATGTAAATTAAAAT
1 TTAAAAATTTATTTAAATACAAATTAAAAGTTAAAAATTTATTTACATGTAAATTAAAAT
*
687811 TTAAAAGTTTATT
1 TTAAAAATTTATT
687824 CATAATATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (60 bp):
TTAAAAATTTATTTAAATACAAATTAAAAGTTAAAAATTTATTTACATGTAAATTAAAAT
Found at i:694961 original size:13 final size:13
Alignment explanation
Indices: 694943--694967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
694933 CACGTATACC
694943 TTGCATAAGGACT
1 TTGCATAAGGACT
694956 TTGCATAAGGAC
1 TTGCATAAGGAC
694968 GAATATGTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (13 bp):
TTGCATAAGGACT
Done.