Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015131.1 Kokia drynarioides strain JFW-HI SEQ_130175, 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: 745397
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 719 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:328260 original size:6 final size:6
Alignment explanation
Indices: 328249--328325 Score: 61
Period size: 6 Copynumber: 12.3 Consensus size: 6
328239 GGCAACCCAA
328249 TTATTT TTATTT TTATTTT CATTATTT TTATTT TTA--- TTATTT TTATTTT
1 TTATTT TTATTT TTA-TTT --TTATTT TTATTT TTATTT TTATTT TTA-TTT
* *
328298 TCTATTA TTATTA TTATTAT TTATTT TT
1 T-TATTT TTATTT TTATT-T TTATTT TT
328326 GTTTATTCAC
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.05
6 34 0.57
7 15 0.25
8 5 0.08
9 3 0.05
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (6 bp):
TTATTT
Found at i:328275 original size:15 final size:15
Alignment explanation
Indices: 328255--328325 Score: 81
Period size: 15 Copynumber: 4.5 Consensus size: 15
328245 CCAATTATTT
328255 TTATTTTTATTTTCA
1 TTATTTTTATTTTCA
*
328270 TTATTTTTATTTTTA
1 TTATTTTTATTTTCA
328285 TTATTTTTATTTTTCTA
1 TTATTTTTA-TTTTC-A
*
328302 TTATTATTATTATT-A
1 TTATTTTTATT-TTCA
328317 TTTATTTTT
1 -TTATTTTT
328326 GTTTATTCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
15 24 0.50
16 13 0.27
17 11 0.23
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTTATTTTCA
Found at i:328288 original size:9 final size:9
Alignment explanation
Indices: 328248--328332 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
328238 AGGCAACCCA
328248 ATTATTTTT
1 ATTATTTTT
328257 ATT-TTTATT
1 ATTATTT-TT
328266 -TTCATTATTT
1 ATT-ATT-TTT
328276 -TTATTTTT
1 ATTATTTTT
328284 ATTATTTTT
1 ATTATTTTT
*
328293 ATT-TTTCT
1 ATTATTTTT
*
328301 ATTATTATT
1 ATTATTTTT
328310 ATTATTATTT
1 ATTATT-TTT
*
328320 ATTTTTGTTT
1 ATTATT-TTT
328330 ATT
1 ATT
328333 CACTTTCTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
8 15 0.24
9 28 0.44
10 19 0.30
11 1 0.02
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.75
Consensus pattern (9 bp):
ATTATTTTT
Found at i:330720 original size:15 final size:16
Alignment explanation
Indices: 330702--330731 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
330692 CACTCCTATT
330702 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
330717 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
330732 TTTTTATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:330739 original size:16 final size:16
Alignment explanation
Indices: 330698--330739 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
330688 TCGACACTCC
330698 TATTTTCTA-TTTCTTT
1 TATTTT-TATTTTCTTT
* *
330714 TAATTCTATTTTCTTT
1 TATTTTTATTTTCTTT
330730 TATTTTTATT
1 TATTTTTATT
330740 GTTCCCCAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTATTTTCTTT
Found at i:340677 original size:15 final size:17
Alignment explanation
Indices: 340652--340683 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
340642 TAAATTCAAT
340652 TATTGAATTGT-TAAAA
1 TATTGAATTGTATAAAA
340668 TATT-AATTGTATAAAA
1 TATTGAATTGTATAAAA
340684 ACTTATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
TATTGAATTGTATAAAA
Found at i:342234 original size:30 final size:29
Alignment explanation
Indices: 342200--342262 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
342190 TATAAACTAT
*
342200 TAAAATA-ATAAAATTGTAATTTTACTATC
1 TAAAATATAT-AAATTGTAATTTTAATATC
* *
342229 GTAAAATATATAATTTTTAATTTTAATATC
1 -TAAAATATATAAATTGTAATTTTAATATC
342259 TAAA
1 TAAA
342263 CTTGATACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 4 0.14
30 23 0.79
31 2 0.07
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (29 bp):
TAAAATATATAAATTGTAATTTTAATATC
Found at i:342352 original size:59 final size:58
Alignment explanation
Indices: 342259--342418 Score: 212
Period size: 59 Copynumber: 2.7 Consensus size: 58
342249 TTTTAATATC
* * * *
342259 TAAACTTGATACTTTTTCCTAATTTGGTACCTAAATTTTTTTTATCTAATTTGATAAT
1 TAAACTTGACACTTTTTCTTAATTTGGTACCTAAATTTTTTTTACCCAATTTGATAAT
* * * *
342317 TGAACTTGACACTTTTTCTTAATTTTGGTACCTAAACTTTTTTTACCCAATTTGGTACT
1 TAAACTTGACACTTTTTCTTAA-TTTGGTACCTAAATTTTTTTTACCCAATTTGATAAT
* *
342376 TAAACTTGACATTTTTTCTTAATTTGGTACTTAAGATTTTTTT
1 TAAACTTGACACTTTTTCTTAATTTGGTACCTAA-ATTTTTTT
342419 AAGATTCAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
58 30 0.34
59 58 0.66
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (58 bp):
TAAACTTGACACTTTTTCTTAATTTGGTACCTAAATTTTTTTTACCCAATTTGATAAT
Found at i:355227 original size:34 final size:34
Alignment explanation
Indices: 355177--355264 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
355167 GTACACGATT
* *
355177 AACCATCCAACACACCAGATGCTTGTATAAGCCA
1 AACCAACCAACACACCAGATGCTCGTATAAGCCA
* * * *
355211 AATCAATCAACACACCAAATGCTCGTATGAGCCA
1 AACCAACCAACACACCAGATGCTCGTATAAGCCA
*
355245 AACCAACCAACACACTAGAT
1 AACCAACCAACACACCAGAT
355265 AACATTGTAC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.42, C:0.32, G:0.10, T:0.16
Consensus pattern (34 bp):
AACCAACCAACACACCAGATGCTCGTATAAGCCA
Found at i:360360 original size:19 final size:20
Alignment explanation
Indices: 360323--360360 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
360313 AAACCCTCAA
*
360323 AACTATTTATTTTCCCCCAG
1 AACTATTTATTCTCCCCCAG
*
360343 AACT-TTTATTCTCTCCCA
1 AACTATTTATTCTCCCCCA
360361 CTTTCCTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.24, C:0.32, G:0.03, T:0.42
Consensus pattern (20 bp):
AACTATTTATTCTCCCCCAG
Found at i:360551 original size:20 final size:20
Alignment explanation
Indices: 360508--360551 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
360498 CCCCAAAACC
* * *
360508 CCCTAAACTTTTTATTTTCT
1 CCCTAAAATTTTTATTCTCA
*
360528 CCCTAAAATTTTTCTTCTCA
1 CCCTAAAATTTTTATTCTCA
360548 CCCT
1 CCCT
360552 TTACCCCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (20 bp):
CCCTAAAATTTTTATTCTCA
Found at i:364865 original size:18 final size:18
Alignment explanation
Indices: 364850--364886 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
364840 GAATTTTAGG
364850 TTATT-TTATTAATTTAA
1 TTATTATTATTAATTTAA
*
364867 TTATTATTATTATTTTAA
1 TTATTATTATTAATTTAA
364885 TT
1 TT
364887 TTTTTTGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTATTAATTTAA
Found at i:388831 original size:22 final size:22
Alignment explanation
Indices: 388781--388846 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
388771 AATATCACAT
388781 AAATAAATAATAAATAATAATA
1 AAATAAATAATAAATAATAATA
* * *
388803 AAGTAAATAA-AATTAAATGATA
1 AAATAAATAATAAAT-AATAATA
388825 AAATAAATGAATGCAAATAATA
1 AAATAAAT-AAT--AAATAATA
388847 TGGAAAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
21 3 0.09
22 22 0.67
23 2 0.06
25 3 0.09
26 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (22 bp):
AAATAAATAATAAATAATAATA
Found at i:390561 original size:20 final size:20
Alignment explanation
Indices: 390536--390576 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
390526 TCATAGTGTA
*
390536 GCATACCTTAATCCTGAGTG
1 GCATACCTCAATCCTGAGTG
390556 GCATACCTCAATCCTGAGTG
1 GCATACCTCAATCCTGAGTG
390576 G
1 G
390577 ATGATGGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (20 bp):
GCATACCTCAATCCTGAGTG
Found at i:395057 original size:23 final size:23
Alignment explanation
Indices: 395031--395157 Score: 121
Period size: 23 Copynumber: 5.4 Consensus size: 23
395021 AGTGCTGGGC
* * *
395031 AACAGAGAGAATACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
395054 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
395077 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
395100 ATCAGAGAGCACACATAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* * *
395124 TAACAGAGAGCATGA-GACGTGCTA
1 -AACAGAGAGCA-CACAAAGTGCTA
395148 AACAGAGAGC
1 AACAGAGAGC
395158 GCTCTAGTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 70 0.80
24 2 0.02
25 15 0.17
26 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:395084 original size:46 final size:47
Alignment explanation
Indices: 395032--395157 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 47
395022 GTGCTGGGCA
* *
395032 ACAGAGAGAATACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCATACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
* * * * *
395079 -CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACATAGTGCTAAT
1 ACAGAGAGCATACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
*
395125 AACAGAGAGCATGAGAC-GTGCTAAACAGAGAGC
1 -ACAGAGAGCAT-ACACAGTGCTAAACAGAGAGC
395158 GCTCTAGTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
46 39 0.60
48 24 0.37
49 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (47 bp):
ACAGAGAGCATACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Found at i:395106 original size:69 final size:67
Alignment explanation
Indices: 394984--395133 Score: 160
Period size: 69 Copynumber: 2.1 Consensus size: 67
394974 TATACGGAAC
* * * *
394984 AAACAAAGAGTACCAAAGTACTAACGGAGAGCACATAAGTGCTGGGCAACAGAGAGAATACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGAACACACAG
395049 TGCT-
63 TGCTA
* *
395053 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACATA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGAACACACA
395117 GTGCTA
62 GTGCTA
395123 ATAACAGAGAG
1 A-AACAGAGAG
395134 CATGAGACGT
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
68 2 0.03
69 29 0.42
70 12 0.17
71 19 0.28
72 7 0.10
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGAACACACAGTGC
TA
Found at i:395114 original size:25 final size:23
Alignment explanation
Indices: 395033--395135 Score: 125
Period size: 23 Copynumber: 4.4 Consensus size: 23
395023 TGCTGGGCAA
* * * *
395033 CAGAGAGAATACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
* *
395056 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
395079 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
395102 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
395125 AACAGAGAGCA
1 --CAGAGAGCA
395136 TGAGACGTGC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
23 61 0.87
25 9 0.13
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:404413 original size:158 final size:158
Alignment explanation
Indices: 404116--404595 Score: 663
Period size: 158 Copynumber: 3.0 Consensus size: 158
404106 CATCATCGGG
* * * * * * *
404116 ATTATAGGTTATATGGGTGCCGGTCTTAAATGTCTTACTGATGGCTGAGATCCGACAATTATTGC
1 ATTACAGGTTATATGGGTGCTGGTATTAGATGTCCTATTGATGGTTGAGATCCGACAATTATTGC
* * * *
404181 GGATTCTTCACAGCTCGTGTGAGCAGTATCGTGTAGCTCAACATCTCGACCCATAATTCGTGTGA
66 GGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCGTGTGA
* *
404246 GCAGACCCATTTAACAGCTCGTGTGAGC
131 GCAGGCCCATTTCACAGCTCGTGTGAGC
* ** *
404274 ATTACAGGTTATATGGGTGCTGGTTTTAGATGTCCTATTGATGGTTGAGATTTGATAATTATTGC
1 ATTACAGGTTATATGGGTGCTGGTATTAGATGTCCTATTGATGGTTGAGATCCGACAATTATTGC
* * *
404339 AGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTCAACATCTCGACTCACAGCTCGTGTGA
66 GGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCGTGTGA
*
404404 GCAGGCCCATTTCACGGCTCGTGTGAGC
131 GCAGGCCCATTTCACAGCTCGTGTGAGC
* * * *
404432 ATTACATGTTATATGGGTGCTGGTATTAGATGTCCTATCGATGGTTGAGATCCGGCAATTATTGT
1 ATTACAGGTTATATGGGTGCTGGTATTAGATGTCCTATTGATGGTTGAGATCCGACAATTATTGC
* * * * * *
404497 GGATTCTCCATAGCTCGTGTGAGTATCATCATGTAGCTTAACATCTCGACCCACAACTCATGTGA
66 GGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCGTGTGA
* *
404562 GTAGGCCCATTTCACAGCTCGTGCGAGC
131 GCAGGCCCATTTCACAGCTCGTGTGAGC
404590 ATTACA
1 ATTACA
404596 TGATATGATA
Statistics
Matches: 282, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
158 282 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (158 bp):
ATTACAGGTTATATGGGTGCTGGTATTAGATGTCCTATTGATGGTTGAGATCCGACAATTATTGC
GGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCGTGTGA
GCAGGCCCATTTCACAGCTCGTGTGAGC
Found at i:410743 original size:257 final size:257
Alignment explanation
Indices: 410287--410802 Score: 1005
Period size: 257 Copynumber: 2.0 Consensus size: 257
410277 AACTGGCCCT
*
410287 ATGCCTAGAAATACCACAGAAGAGCTTTAAGATATCAGATAATAGGTAAGCTTGCACCATATCAG
1 ATGCCTAGAAATACCACAAAAGAGCTTTAAGATATCAGATAATAGGTAAGCTTGCACCATATCAG
410352 CTTTGCAAAATAACTCCAAGTCGTCTGCAAAAAAGAGATGAGAGATATCTGGTCCCATTCTTGCC
66 CTTTGCAAAATAACTCCAAGTCGTCTGCAAAAAAGAGATGAGAGATATCTGGTCCCATTCTTGCC
*
410417 AATCTAATAGGTTTCCACTAACCTTCACTAATCCTGGCTTGAATTATACGACCTAACCATTCCAT
131 AATCTAATAGGCTTCCACTAACCTTCACTAATCCTGGCTTGAATTATACGACCTAACCATTCCAT
410482 ACTCAGAACAAAGAGATAAGGTGAAAGTGGACAACTTTGTCTGATTCCCTTAGAAGGCTTGA
196 ACTCAGAACAAAGAGATAAGGTGAAAGTGGACAACTTTGTCTGATTCCCTTAGAAGGCTTGA
410544 ATGCCTAGAAATACCACAAAAGAGCTTTAAGATATCAGATAATAGGTAAGCTTGCACCATATCAG
1 ATGCCTAGAAATACCACAAAAGAGCTTTAAGATATCAGATAATAGGTAAGCTTGCACCATATCAG
410609 CTTTGCAAAATAACTCCAAGTCGTCTGCAAAAAAGAGATGAGAGATATCTGGTCCCATTCTTGCC
66 CTTTGCAAAATAACTCCAAGTCGTCTGCAAAAAAGAGATGAGAGATATCTGGTCCCATTCTTGCC
*
410674 AATCTAATAGGCTTCCACTAACCTTCACTAGTCCTGGCTTGAATTATACGACCTAACCATTCCAT
131 AATCTAATAGGCTTCCACTAACCTTCACTAATCCTGGCTTGAATTATACGACCTAACCATTCCAT
410739 ACTCAGAACAAAGAGATAAGGTGAAAGTGGACAACTTTGTCTGATTCCCTTAGAAGGCTTGA
196 ACTCAGAACAAAGAGATAAGGTGAAAGTGGACAACTTTGTCTGATTCCCTTAGAAGGCTTGA
410801 AT
1 AT
410803 TTTTGCGTTG
Statistics
Matches: 256, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
257 256 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (257 bp):
ATGCCTAGAAATACCACAAAAGAGCTTTAAGATATCAGATAATAGGTAAGCTTGCACCATATCAG
CTTTGCAAAATAACTCCAAGTCGTCTGCAAAAAAGAGATGAGAGATATCTGGTCCCATTCTTGCC
AATCTAATAGGCTTCCACTAACCTTCACTAATCCTGGCTTGAATTATACGACCTAACCATTCCAT
ACTCAGAACAAAGAGATAAGGTGAAAGTGGACAACTTTGTCTGATTCCCTTAGAAGGCTTGA
Found at i:414868 original size:15 final size:15
Alignment explanation
Indices: 414845--414874 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
414835 GTCAAATAAG
*
414845 TTATGCTAATAAATA
1 TTATACTAATAAATA
414860 TTATACTAATAAATA
1 TTATACTAATAAATA
414875 CTAAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (15 bp):
TTATACTAATAAATA
Found at i:418192 original size:20 final size:20
Alignment explanation
Indices: 418136--418198 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 20
418126 GTTTTATTTA
418136 TTTTTATTTTTATTTCTAGTTG
1 TTTTTA-TTTTATTT-TAGTTG
418158 TACTTTTA-TTT-TTTTAGTTG
1 T--TTTTATTTTATTTTAGTTG
*
418178 TTTTTATTTTATTTTATTTG
1 TTTTTATTTTATTTTAGTTG
418198 T
1 T
418199 GAGACTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 16 0.44
21 3 0.08
22 4 0.11
24 5 0.14
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTATTTTAGTTG
Found at i:420473 original size:17 final size:19
Alignment explanation
Indices: 420445--420481 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
420435 AAAATCAATT
420445 ATCAATCAGAAAAA-AAAA
1 ATCAATCAGAAAAAGAAAA
420463 ATCAA-CAGAAAAAGAAAA
1 ATCAATCAGAAAAAGAAAA
420481 A
1 A
420482 GTAAAGTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.73, C:0.11, G:0.08, T:0.08
Consensus pattern (19 bp):
ATCAATCAGAAAAAGAAAA
Found at i:421777 original size:16 final size:17
Alignment explanation
Indices: 421752--421793 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
421742 TTTATTGGAC
*
421752 ATGA-ATGAAGGTT-AA
1 ATGAGATGAAGATTAAA
421767 ATGAGATGAAGATTAAA
1 ATGAGATGAAGATTAAA
*
421784 ATTAGATGAA
1 ATGAGATGAA
421794 TAAATATAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (17 bp):
ATGAGATGAAGATTAAA
Found at i:423800 original size:17 final size:17
Alignment explanation
Indices: 423759--423792 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
423749 AATAAGTCAA
423759 AATAAAAGGAAATTTTT
1 AATAAAAGGAAATTTTT
*
423776 AATCAAAATGAAATTTT
1 AAT-AAAAGGAAATTTT
423793 ATATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 3 0.20
18 12 0.80
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (17 bp):
AATAAAAGGAAATTTTT
Found at i:423967 original size:29 final size:30
Alignment explanation
Indices: 423925--424130 Score: 161
Period size: 30 Copynumber: 6.9 Consensus size: 30
423915 AAAAGGGGTT
* * *
423925 AAATGTAATTTTTAGAAATTTTGAGGGTCA
1 AAATGAAATTTTTAGAAAGTTTAAGGGTCA
* * *
423955 AAATGCAA-TTTTAAAAAGTTT-AGGGTTA
1 AAATGAAATTTTTAGAAAGTTTAAGGGTCA
* *
423983 AAATGTAATTTTTAGAAAATTTAAGGGTCA
1 AAATGAAATTTTTAGAAAGTTTAAGGGTCA
* * * *
424013 AAATGAAATTTTCAAAAAGTTCAAAGGTCA
1 AAATGAAATTTTTAGAAAGTTTAAGGGTCA
* * *
424043 AAATGAAATTTTTAGAAAGATAAAGGGTTAA
1 AAATGAAATTTTTAGAAAGTTTAAGGG-TCA
* * *
424074 AAATGGAA-TTTTAAAAAGTTT-AGGGTTA
1 AAATGAAATTTTTAGAAAGTTTAAGGGTCA
* * *
424102 AATTTG-AATTTTTGGGAAAGTTTATGGGT
1 AA-ATGAAATTTTT-AGAAAGTTTAAGGGT
424131 TAAATATAAT
Statistics
Matches: 140, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
28 19 0.14
29 32 0.23
30 76 0.54
31 13 0.09
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (30 bp):
AAATGAAATTTTTAGAAAGTTTAAGGGTCA
Found at i:423997 original size:58 final size:58
Alignment explanation
Indices: 423920--424103 Score: 228
Period size: 58 Copynumber: 3.1 Consensus size: 58
423910 AGTAAAAAAG
* * *
423920 GGGTT-AAATGTAATTTTTAGAAATTTTGAGGGTCAAAATGCAATTTTAAAAAGTTTA
1 GGGTTAAAATGTAATTTTTAGAAAATTTAAGGGTCAAAATGAAATTTTAAAAAGTTTA
*
423977 GGGTTAAAATGTAATTTTTAGAAAATTTAAGGGTCAAAATGAAATTTTCAAAAAGTTCAA
1 GGGTTAAAATGTAATTTTTAGAAAATTTAAGGGTCAAAATGAAATTTT-AAAAAGTT-TA
* * * * * *
424037 AGGTCAAAATGAAATTTTTAGAAAGA-TAAAGGGTTAAAAATGGAATTTTAAAAAGTTTA
1 GGGTTAAAATGTAATTTTTAGAAA-ATTTAAGGG-TCAAAATGAAATTTTAAAAAGTTTA
424096 GGGTTAAA
1 GGGTTAAA
424104 TTTGAATTTT
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
57 5 0.05
58 39 0.36
59 15 0.14
60 36 0.33
61 14 0.13
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (58 bp):
GGGTTAAAATGTAATTTTTAGAAAATTTAAGGGTCAAAATGAAATTTTAAAAAGTTTA
Found at i:424131 original size:60 final size:59
Alignment explanation
Indices: 423920--424134 Score: 213
Period size: 60 Copynumber: 3.6 Consensus size: 59
423910 AGTAAAAAAG
* * * * *
423920 GGGTT-AAATGTAATTTTTAGAAATTTTGAGGG-TCAAAATGCAATTTTAAAAAGTTTA
1 GGGTTAAAATGAAATTTTTAGAAAGTTTAAGGGTTAAAAATGAAATTTTAAAAAGTTTA
* * * *
423977 GGGTTAAAATGTAATTTTTAGAAAATTTAAGGG-TCAAAATGAAATTTTCAAAAAGTTCAA
1 GGGTTAAAATGAAATTTTTAGAAAGTTTAAGGGTTAAAAATGAAATTTT-AAAAAGTT-TA
* * * * *
424037 AGGTCAAAATGAAATTTTTAGAAAGATAAAGGGTTAAAAATGGAATTTTAAAAAGTTTA
1 GGGTTAAAATGAAATTTTTAGAAAGTTTAAGGGTTAAAAATGAAATTTTAAAAAGTTTA
* * *
424096 GGGTTAAATTTG-AATTTTTGGGAAAGTTTATGGGTTAAA
1 GGGTTAAA-ATGAAATTTTT-AGAAAGTTTAAGGGTTAAA
424135 TATAATTTTT
Statistics
Matches: 132, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
57 5 0.04
58 39 0.30
59 22 0.17
60 53 0.40
61 13 0.10
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (59 bp):
GGGTTAAAATGAAATTTTTAGAAAGTTTAAGGGTTAAAAATGAAATTTTAAAAAGTTTA
Found at i:424145 original size:31 final size:30
Alignment explanation
Indices: 424088--424144 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
424078 GGAATTTTAA
*
424088 AAAGTTTAGGGTTAAATTTGAATTTTTGGG
1 AAAGTTTAGGGTTAAATATGAATTTTTGGG
424118 AAAGTTTATGGGTTAAATAT-AATTTTT
1 AAAGTTTA-GGGTTAAATATGAATTTTT
424145 TTAAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (30 bp):
AAAGTTTAGGGTTAAATATGAATTTTTGGG
Found at i:424905 original size:22 final size:22
Alignment explanation
Indices: 424862--424910 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
424852 AAAATAAGGA
*
424862 AAATAAATAAATAAATATATGC
1 AAATAAATAAATAAATAAATGC
* * *
424884 AAATATATATATATATAAATGC
1 AAATAAATAAATAAATAAATGC
*
424906 TAATA
1 AAATA
424911 CCTTGCACGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATAAATAAATAAATAAATGC
Found at i:427030 original size:19 final size:19
Alignment explanation
Indices: 426999--427041 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
426989 GGGTAAATAG
426999 TTAA-TTAAATTAT-TTACT
1 TTAATTTAAATTATATTA-T
*
427017 TTAATTTAATTTATATTAT
1 TTAATTTAAATTATATTAT
427036 TTAATT
1 TTAATT
427042 ATATTGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 15 0.68
20 3 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTAAATTATATTAT
Found at i:435056 original size:48 final size:48
Alignment explanation
Indices: 435001--435097 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
434991 CTATGAGTTT
* *
435001 TAATCCGTCCCTTTATAACTTTAGAGGTATAGGATTTGAGGTTGTAAC
1 TAATCCGTCCCTTTACAACTTTAGAGGTATAAGATTTGAGGTTGTAAC
435049 TAATCCGTCCCTTTACAACTTTAGAGGTATAAGATTTGAGGTTGTAAC
1 TAATCCGTCCCTTTACAACTTTAGAGGTATAAGATTTGAGGTTGTAAC
435097 T
1 T
435098 TCGCTCCATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (48 bp):
TAATCCGTCCCTTTACAACTTTAGAGGTATAAGATTTGAGGTTGTAAC
Found at i:436283 original size:14 final size:15
Alignment explanation
Indices: 436259--436289 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
436249 GGGTTGTTTG
436259 AAAGAATAAAAATAA
1 AAAGAATAAAAATAA
436274 AAAG-ATAAAAATAA
1 AAAGAATAAAAATAA
436288 AA
1 AA
436290 TAAAGTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAGAATAAAAATAA
Found at i:448419 original size:51 final size:51
Alignment explanation
Indices: 448209--448602 Score: 150
Period size: 51 Copynumber: 7.7 Consensus size: 51
448199 TATTTTAAAG
* * *
448209 AAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTTAATTATTTCAAAAT
1 AAAAA-TTTAAATTTTTAAACAAAGTATTGA--TTTTTTTAACTATTTCAAAAC
* * ** * * ** *
448263 AAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAA--A--AAAAAAG
1 AAAAATTTAAATTTTTAAACAAAGTATTGA-TTTTTTTAACTATTTCAAAAC
* * *** * * *
448311 AGAAAGTTTATATTTTTAAA-AAA-TAAAAATCTGTTTTTTAGTAATTTTAAAGA-
1 A-AAAATTTAAATTTTTAAACAAAGTATTGAT-T-TTTTTAACT-ATTTCAAA-AC
* *
448364 AAAAATTTAAAATTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAAC
1 AAAAATTTAAATTTTTAAACAAAGTATTGATTTTTTTAACTATTTCAAAAC
* ** * *** *
448415 AAAAATTTAGATTTTTAAGTAAAGTAGTGA-TTTTTTAA--A-AAAAAAAG
1 AAAAATTTAAATTTTTAAACAAAGTATTGATTTTTTTAACTATTTCAAAAC
* * *** * * *
448462 AGAAAGTTTATATTTTTAAA-AAA-TAAAAATCTGTTTTTTAGTAATTTTAAAGA-
1 A-AAAATTTAAATTTTTAAACAAAGTATTGAT-T-TTTTTAACT-ATTTCAAA-AC
* *
448515 AAAAATTTAAAATTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAAC
1 AAAAATTTAAATTTTTAAACAAAGTATTGATTTTTTTAACTATTTCAAAAC
* * ** * *
448566 AAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTT
1 AAAAATTTAAATTTTTAAACAAAGTATTGATTTTTTT
448603 TAAAAAAAAA
Statistics
Matches: 250, Mismatches: 66, Indels: 51
0.68 0.18 0.14
Matches are distributed among these distances:
46 4 0.02
47 12 0.05
48 31 0.12
49 22 0.09
50 11 0.04
51 68 0.27
52 55 0.22
53 35 0.14
54 12 0.05
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (51 bp):
AAAAATTTAAATTTTTAAACAAAGTATTGATTTTTTTAACTATTTCAAAAC
Found at i:448709 original size:52 final size:52
Alignment explanation
Indices: 448192--448709 Score: 244
Period size: 52 Copynumber: 10.1 Consensus size: 52
448182 AAAATATACC
* *
448192 TTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTT
1 TTTTAGTAATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTATTGA-TTTT
* * * * ** * *
448245 TTTTAATTATTTCAAA-ATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTT
1 TTTTAGTAATTTTAAAGA-AAAAGTTTAAATTTTTAAACAAAGTATTGATTTT
*** * * ***
448297 TTTTA--AA-AAAAAAGAGAAAGTTTATATTTTTAAA-AAA-TAAAAATCTGTT
1 TTTTAGTAATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTATTGAT-T-TT
* * *
448346 TTTTAGTAATTTTAAAGAAAAAATTTAAAATTTTAAACAAAGTTTTGATTTT
1 TTTTAGTAATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTATTGATTTT
* * * * * ** *
448398 TTTAACT-ATTTCAAA-ACAAAAATTTAGATTTTTAAGTAAAGTAGTGA--TT
1 TTTTAGTAATTTTAAAGA-AAAAGTTTAAATTTTTAAACAAAGTATTGATTTT
**** * * ***
448447 TTTTA--AAAAAAAAAGAGAAAGTTTATATTTTTAAA-AAA-TAAAAATCTGTT
1 TTTTAGTAATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTATTGAT-T-TT
* * *
448497 TTTTAGTAATTTTAAAGAAAAAATTTAAAATTTTAAACAAAGTTTTGATTTT
1 TTTTAGTAATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTATTGATTTT
* * * * ** * *
448549 TTTAACT-ATTTCAAA-ACAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTT
1 TTTTAGTAATTTTAAAGA-AAAAGTTTAAATTTTTAAACAAAGTATTGATTTT
** **** * *** **
448600 TTTTAAAAAAAAAAAAAGAGAAAGTTTAAATTTTTTAAA-AAA-TAAAAATCTGC
1 TTTT-AGTAATTTTAAAGAAAAAGTTTAAA-TTTTTAAACAAAGTATTGAT-TTT
* *
448653 TTTTAGTGATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTT
1 TTTTAGTAATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTATTGATTTT
448705 TTTTA
1 TTTTA
448710 ACTATTTCGT
Statistics
Matches: 335, Mismatches: 102, Indels: 57
0.68 0.21 0.12
Matches are distributed among these distances:
46 3 0.01
47 7 0.02
48 23 0.07
49 33 0.10
50 11 0.03
51 77 0.23
52 97 0.29
53 70 0.21
54 14 0.04
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (52 bp):
TTTTAGTAATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTATTGATTTT
Found at i:448776 original size:307 final size:304
Alignment explanation
Indices: 448175--448913 Score: 1074
Period size: 307 Copynumber: 2.4 Consensus size: 304
448165 AAGAAAAAGT
*** * *
448175 AAAAATAAAAATATACCTTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGA
1 AAAAATAAAAATATGTTTTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGA
*
448240 TTTTTTTTTAATTATTTCAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTT--AA
66 --TTTTTTTAACTATTTCAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAA
* *
448303 AAAAAAAGAGAAAGTTTATATTTTTAAAAAATAAAAATCTGTTTTTTAGTAATTTTAAAGAAAAA
129 AAAAAAAGAGAAAGTTTAAATTTTTAAAAAATAAAAATCTGTCTTTTAGTAATTTTAAAGAAAAA
448368 ATTTAAAATTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAACAAAAATTTAGATTTTTAA
194 ATTTAAAATTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAACAAAAATTTAGATTTTTAA
* * *
448433 GTAAAGTAGTGATTTTTTAAAAAAAAAAGAGAAAGTTTATATTTTTA
259 GTAAAATAGTGATTTTTT-AAAAAAAAAGAGAAAGTTTAGATTTTAA
* *
448480 AAAAATAAAAATCTGTTTTTTAGTAATTTTAAAGAAAAAATTTAAAATTTTAAACAAAGTTTTGA
1 AAAAATAAAAATATGTTTTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGA
*
448545 TTTTTTTAACTATTTCAAAACAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAAAA
66 TTTTTTTAACTATTTCAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTT--AAAA
*
448610 AAAAAAAGAGAAAGTTTAAATTTTTTAAAAAATAAAAATCTG-CTTTTAGTGATTTTAAAGAAAA
129 AAAAAAAGAGAAAGTTTAAA-TTTTTAAAAAATAAAAATCTGTCTTTTAGTAATTTTAAAGAAAA
* * ** * * *
448674 AGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTCGTAATAAAAGTTTGGATTTTT
193 AATTTAAAATTTTAAACAAAGTTTTGA-TTTTTTTAACTATTTCAAAACAAAAATTTAGATTTTT
* *
448739 AAGTAAAATAGTGATTTTCATT-AAAAAGAA-AGAAAGTTTCGATTTTAA
257 AAGTAAAATAGTGATTTT--TTAAAAAAAAAGAGAAAGTTTAGATTTTAA
* *
448787 AAAAATAAAAATATGTTTTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAATAAAATTTTGA
1 AAAAATAAAAATATGTTTTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGA
* * * * *
448852 TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAATGATTTTATTTTAA
66 TTTTTTTAACTATTTCAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTT-TTTTAA
448914 TCAAAAGAAA
Statistics
Matches: 391, Mismatches: 34, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
303 57 0.15
305 58 0.15
306 2 0.01
307 191 0.49
308 81 0.21
310 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (304 bp):
AAAAATAAAAATATGTTTTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGA
TTTTTTTAACTATTTCAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAAAA
AAAAAGAGAAAGTTTAAATTTTTAAAAAATAAAAATCTGTCTTTTAGTAATTTTAAAGAAAAAAT
TTAAAATTTTAAACAAAGTTTTGATTTTTTTAACTATTTCAAAACAAAAATTTAGATTTTTAAGT
AAAATAGTGATTTTTTAAAAAAAAAGAGAAAGTTTAGATTTTAA
Found at i:448948 original size:151 final size:151
Alignment explanation
Indices: 448192--448913 Score: 1034
Period size: 151 Copynumber: 4.7 Consensus size: 151
448182 AAAATATACC
* * *
448192 TTTTAGTTATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTTAATTATTT
1 TTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGA--TTTTTTTAACTATTT
*
448257 CAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAAAAAAAGAGAAAGTTTAT
64 CAAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTT-AAAAAAAAGAGAAAGTTTAG
448322 ATTTTTAAAAAATAAAAATCTGTT
128 ATTTTTAAAAAATAAAAATCTGTT
*
448346 TTTTAGTAATTTTAAAGAAAAAATTTAAAATTTTAAACAAAGTTTTGATTTTTTTAACTATTTCA
1 TTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCA
* * * ** *
448411 AAACAAAAATTTAGATTTTTAAGTAAAGTAGTGATTTTTTAAAAAAAAAAGAGAAAGTTTATATT
66 AAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAAAAAAGAGAAAGTTTAGATT
448476 TTTAAAAAATAAAAATCTGTT
131 TTTAAAAAATAAAAATCTGTT
*
448497 TTTTAGTAATTTTAAAGAAAAAATTTAAAATTTTAAACAAAGTTTTGATTTTTTTAACTATTTCA
1 TTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCA
*
448562 AAACAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAAAAAAAAAAAGAGAAAGTTT
66 AAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTT-----AAAAAAAAGAGAAAGTTT
* *
448627 AAATTTTTTAAAAAATAAAAATCTG-C
126 AGA-TTTTTAAAAAATAAAAATCTGTT
* *
448653 TTTTAGTGATTTTAAAGAAAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTAACTATTTC
1 TTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGA-TTTTTTTAACTATTTC
** * ** * *
448718 GTAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCATTAAAAAGAA-AGAAAGTTTCGAT
65 AAAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAAAAAAGAGAAAGTTTAGAT
* *
448782 TTTAAAAAAATAAAAATATGTT
130 TTTTAAAAAATAAAAATCTGTT
* * *
448804 TTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAATAAAATTTTGATTTTTTTAACTATTTCG
1 TTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCA
* * * *
448869 AAATAAAAGTTTTGATTTTGAAGTAAAGTAATGATTTTATTTTAA
66 AAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTT-TTTTAA
448914 TCAAAAGAAA
Statistics
Matches: 518, Mismatches: 41, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
150 69 0.13
151 205 0.40
152 60 0.12
154 45 0.09
156 65 0.13
157 74 0.14
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (151 bp):
TTTTAGTAATTTTAAAGAAAAAATTTAAATTTTTAAACAAAGTTTTGATTTTTTTAACTATTTCA
AAATAAAAGTTTAGATTTTTAAGTAAAATAGTGATTTTTTTTAAAAAAAAGAGAAAGTTTAGATT
TTTAAAAAATAAAAATCTGTT
Found at i:450641 original size:20 final size:22
Alignment explanation
Indices: 450600--450644 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
450590 TTTTTTTTAG
450600 TATTCGTGCATATTAGATTTATT
1 TATTCGTGCA-ATTAGATTTATT
450623 TATTCGTGC-ATTA-ATTTATT
1 TATTCGTGCAATTAGATTTATT
450643 TA
1 TA
450645 ATTCTCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
23 9 0.41
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (22 bp):
TATTCGTGCAATTAGATTTATT
Found at i:453463 original size:4 final size:4
Alignment explanation
Indices: 453454--453492 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
453444 AATTTCAATT
* * *
453454 ATTC ATTC ATTC ATCC ATTC ATTC ACTC ATTC ACTC ATT
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATT
453493 GGTTTATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (4 bp):
ATTC
Found at i:459793 original size:7 final size:7
Alignment explanation
Indices: 459783--459828 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
459773 AAAAAAACAC
459783 AAAAGAA
1 AAAAGAA
459790 AAAAGAA
1 AAAAGAA
459797 AAAAGAA
1 AAAAGAA
*
459804 AAAGGAA
1 AAAAGAA
459811 AAAA-AA
1 AAAAGAA
459817 AAGAAGAA
1 AA-AAGAA
459825 AAAA
1 AAAA
459829 TAGAGAGTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 4 0.11
7 27 0.77
8 4 0.11
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:459823 original size:21 final size:20
Alignment explanation
Indices: 459771--459828 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
459761 TTAAATCAAG
* *
459771 AAAAAAAAACACAAAAGAAA
1 AAAAAAAAAGAAAAAAGAAA
*
459791 AAAGAAAAAAGAAAAAGGAAA
1 AAA-AAAAAAGAAAAAAGAAA
459812 AAAAAAAGAAGAAAAAA
1 AAAAAAA-AAGAAAAAA
459829 TAGAGAGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAAGAAA
Found at i:460306 original size:42 final size:42
Alignment explanation
Indices: 460233--461272 Score: 810
Period size: 42 Copynumber: 23.9 Consensus size: 42
460223 AAGGAAAACA
* * * *
460233 TTCATTGCATTCAGAGGCCTAGGTATGGAGGCCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * *
460275 TTCATTGCATTTAGATGCCCAGATGTTGAGGCTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
460317 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
460359 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* ** * *
460401 TTCATTGCATTTAGAGACTTAGGTATGGAGGCTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
460443 TTCATTGCATTTAGAGGCCCAGGTGTGGTGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
460485 TTCATTGCATTTATAGGCTCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
460527 TTCATTGCATTTATAGGCTCAGGTGTAGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
460569 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* *
460611 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * *
460653 TTCATTGCATTTAGAGGCCCAAGTGTGAAGGCTCATTTACCT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * *
460695 TTCATTGCATTTAGAGACCTAAGTGTGAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* **** * * * * *
460737 TTCATTGCATTTATTTACTTTTCATTGCATTTAGAGGCCTAGGTGTGAAGGCTCAT
1 TTCATTGCATTTA--GA-GGCCCA--G-GTGTGGAGGCCCA--T-T-TA--CT--T
* * * * * *
460793 TTACTTTTCATTGCATTTAGCA-ACTCAAGTGTGGCA-GCCCAAGTGTGAAGGCCCATT
1 TT-CATTGC-----ATTTAG-AGGCCCAGGTGTGG-AGGCCC-A-T-T-TA----C-TT
* * * * ** *
460850 TACTTTTCATTGCATTTAAAGGCCCAAATATGGAGGCCCATTTACTT
1 TTCATTGC-----ATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
*
460897 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
** *
460939 TTCATTGCATTTAGAGGCTTAAGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * *
460981 TTCATTGCATTTTAGAGGCCTAGGTATAGAGGCCCATTTAC-T
1 TTCATTGCA-TTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * *
461023 TTCAATTGCATTTTAGAGGCCTAGGTATAGAGGTCCATTTACTT
1 TTC-ATTGCA-TTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
** * **
461067 TTCATCACATTTAGAGGCCTAGGTGTGGAGATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * **
461109 TTCATCGCATTTAGAGACCCAGGTGTGGAGGTGCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * * * * * **
461151 TCCATCGCATTTAAATGCCCAAGTATAGAGGTACATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * * *
461193 TTTATCGCA-TTAGAGGCCTAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
* * * * *
461234 TTCATTGCATTTATAGGCCTAGGCGTAGAGGTCCATTTA
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTA
461273 TTTATTTGTT
Statistics
Matches: 829, Mismatches: 137, Indels: 64
0.80 0.13 0.06
Matches are distributed among these distances:
41 31 0.04
42 634 0.76
43 68 0.08
44 5 0.01
45 1 0.00
47 7 0.01
48 9 0.01
50 1 0.00
51 1 0.00
52 2 0.00
53 1 0.00
54 3 0.00
55 3 0.00
56 44 0.05
57 8 0.01
58 1 0.00
59 4 0.00
61 1 0.00
62 5 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
Found at i:460458 original size:126 final size:126
Alignment explanation
Indices: 460233--461272 Score: 911
Period size: 126 Copynumber: 8.0 Consensus size: 126
460223 AAGGAAAACA
* * * * * * *
460233 TTCATTGCATTCAGAGGCCTAGGTATGGAGGCCCATTTATTTTTCATTGCATTTAGATGCCCAGA
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* *
460298 TGTTGAGGCTCATTTACTTTTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
66 TGTGGAGGCTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * **
460359 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGACTTAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
460424 TATGGAGGCTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGTGGTCCATTTATTT
66 TGTGGAGGCTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
460485 TTCATTGCATTTATAGGCTCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTTATAGGCTCAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
460550 TGTAGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCTATTTACTT
66 TGTGGAGGCTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
460611 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAAG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * * * * * *
460676 TGTGAAGGCTCATTTACCTTTCATTGCATTTAGAGACCTAAGTGTGAAGGCCCATTTACTT
66 TGTGGAGGCTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* **** * * * * * *
460737 TTCATTGCATTTATTTACTTTTCATTGCATTTAGAGG-CCTAGGTGTGAAGGCTCATTTACTTTT
1 TTCATTGCATTTA--GA-GGCCCA--G-GTGTGGAGGTCC-A--T-T-TA--CT--TTT-CATTG
* * *
460801 CATTGCATTTAGCAACTCAAGTGTGGCAGCCCAAGTGTGAAGGCCCATTTACTTTTCATTGCATT
50 CA-T----TTAG-------A----G---GCCCAGGTGTGGAGGCTCATTTACTTTTCATTGCATT
* ** * *
460866 TAAAGGCCCAAATATGGAGGCCCATTTACTT
96 TAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
460897 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCTTAAG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * * * *
460962 TGTGGAGGCCCATTTACTTTTCATTGCATTTTAGAGGCCTAGGTATAGAGGCCCATTTAC-T
66 TGTGGAGGCTCATTTACTTTTCATTGCA-TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * ** *
461023 TTCAATTGCATTTTAGAGGCCTAGGTATAGAGGTCCATTTACTTTTCATCACATTTAGAGGCCTA
1 TTC-ATTGCA-TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
* * * *
461088 GGTGTGGA-GATCCATTTACTTTTCATCGCATTTAGAGACCCAGGTGTGGAGGTGCATTTACTT
64 GGTGTGGAGGCT-CATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * * * * * * *
461151 TCCATCGCATTTAAATGCCCAAGTATAGAGGTACATTTACTTTTTATCGCA-TTAGAGGCCTAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * * * *
461215 TGTGGAGG-TCCATTCACTTTTCATTGCATTTATAGGCCTAGGCGTAGAGGTCCATTTA
66 TGTGGAGGCT-CATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTA
461273 TTTATTTGTT
Statistics
Matches: 758, Mismatches: 114, Indels: 85
0.79 0.12 0.09
Matches are distributed among these distances:
125 61 0.08
126 419 0.55
127 63 0.08
128 76 0.10
129 4 0.01
131 3 0.00
132 7 0.01
133 1 0.00
134 1 0.00
135 1 0.00
136 1 0.00
138 2 0.00
140 7 0.01
141 5 0.01
142 1 0.00
144 1 0.00
145 5 0.01
146 7 0.01
148 2 0.00
150 1 0.00
151 1 0.00
152 1 0.00
153 1 0.00
154 7 0.01
155 3 0.00
157 3 0.00
158 1 0.00
160 73 0.10
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (126 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
TGTGGAGGCTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:460754 original size:20 final size:20
Alignment explanation
Indices: 460729--460769 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
460719 GTGAAGGCCC
460729 ATTTACTTTTCATTGCATTT
1 ATTTACTTTTCATTGCATTT
460749 ATTTACTTTTCATTGCATTT
1 ATTTACTTTTCATTGCATTT
460769 A
1 A
460770 GAGGCCTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.15, G:0.05, T:0.59
Consensus pattern (20 bp):
ATTTACTTTTCATTGCATTT
Found at i:460761 original size:62 final size:62
Alignment explanation
Indices: 460687--460811 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
460677 GTGAAGGCTC
460687 ATTTACCTTTCATTGCATTTAGAGACCTAAGTGTGAAGGCCCATTTACTTTTCATTGCATTT
1 ATTTACCTTTCATTGCATTTAGAGACCTAAGTGTGAAGGCCCATTTACTTTTCATTGCATTT
* * * *
460749 ATTTACTTTTCATTGCATTTAGAGGCCTAGGTGTGAAGGCTCATTTACTTTTCATTGCATTT
1 ATTTACCTTTCATTGCATTTAGAGACCTAAGTGTGAAGGCCCATTTACTTTTCATTGCATTT
460811 A
1 A
460812 GCAACTCAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (62 bp):
ATTTACCTTTCATTGCATTTAGAGACCTAAGTGTGAAGGCCCATTTACTTTTCATTGCATTT
Found at i:460889 original size:56 final size:55
Alignment explanation
Indices: 460770--460889 Score: 136
Period size: 56 Copynumber: 2.1 Consensus size: 55
460760 ATTGCATTTA
* * * * * *
460770 GAGGCCTAGGTGTGAAGGCTCATTTACTTTTCATTGCATTTAGCAACTCAAGTGTG
1 GAGGCCCAAGTGTGAAGGCCCATTTACTTTTCATTGCATTTA-CAACCCAAATATG
460826 GCA-GCCCAAGTGTGAAGGCCCATTTACTTTTCATTGCATTTA-AAGGCCCAAATATG
1 G-AGGCCCAAGTGTGAAGGCCCATTTACTTTTCATTGCATTTACAA--CCCAAATATG
460882 GAGGCCCA
1 GAGGCCCA
460890 TTTACTTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
54 2 0.04
55 1 0.02
56 50 0.93
57 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (55 bp):
GAGGCCCAAGTGTGAAGGCCCATTTACTTTTCATTGCATTTACAACCCAAATATG
Found at i:461836 original size:149 final size:149
Alignment explanation
Indices: 461679--462294 Score: 679
Period size: 149 Copynumber: 4.0 Consensus size: 149
461669 AATTTTGGGA
* * *
461679 AAAGTTTTGGTTTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGAGATTT
1 AAAGTTTTGATTTTTTTAACT-ATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTT
* * *
461744 TCTTTAAAA-AGAGAAAGTTTATACTTTT-AAAAATAAAAATCTGTTTTTTTAGTTATTTTAAAG
65 TCTTTAAAAGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTG-TTTTTTAGTTATTTTAAAG
* *
461807 AAAAGGTTTAAAATTTTAAGC
129 AAAAAGTTTAAAATTTTAAAC
461828 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAT-ATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTT-TGATTTTTAAGTAAAATAGTGATT
* * *
461892 TTCTTTAAAAAAAAAAAAAAGAGAGAGAAAGTTTATATTTTT-AAAAATAAAATTATGTTTTTTA
64 TTCTTT----------AAAAGA-A-AGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTA
* *
461956 GTTATTTTAAAGAAAAATTTTAAATTTTTAAA-
117 GTTATTTTAAAGAAAAAGTTTAAAATTTTAAAC
*** * *
461988 ATTTTTTTGATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAATAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT
* * *
462053 CATTAAAAGGAAAGGAAGTTTAGATTTTTTAAAAAATAAAAATCTG-TTTTTAGTGATTTTAAAG
66 CTTTAAAA-GAAAGAAAGTTTAGA-TTTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAG
*
462117 AAAAAATTT-AAATTTTAAAC
129 AAAAAGTTTAAAATTTTAAAC
* * * * *
462137 AAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAACTATAGTAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT
* * * * *
462202 CATTAAAAAAATTAAGAAAGGTTAGATTTTTAAAAAATAAAAATCTGTTTTTTTAATAATTTTAA
66 C-TTTAAAAGA--AAGAAAGTTTAGATTTTTAAAAAATAAAAATCTG-TTTTTTAGTTATTTTAA
* *
462267 AGAAAAAGATTAAATTTTTAAAC
127 AGAAAAAGTTTAAAATTTTAAAC
462290 AAAGT
1 AAAGT
462295 AAGATAAATA
Statistics
Matches: 398, Mismatches: 43, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
148 19 0.05
149 148 0.37
150 52 0.13
151 11 0.03
152 23 0.06
153 14 0.04
159 59 0.15
160 8 0.02
161 35 0.09
162 29 0.07
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (149 bp):
AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT
CTTTAAAAGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAA
AAAGTTTAAAATTTTAAAC
Found at i:462284 original size:308 final size:304
Alignment explanation
Indices: 461683--462288 Score: 780
Period size: 308 Copynumber: 2.0 Consensus size: 304
461673 TTGGGAAAAG
* * * *
461683 TTTTGGTTTTTTTAAATAATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGAGATTTTCTT
1 TTTTGATTTTTTTAAATAATTTCGAAATAAAAATTTAGATTTTTAAGTAAAATAGAGATTTTCAT
* * * **
461748 TAAAAAGAGAAAGTTTATACTTTTAAAAATAAAAATCTGTTTTTTTAGTTATTTTAAAGAAAAGG
66 TAAAAAAAGAAAGTTTAGACTTTTAAAAATAAAAATCTG-TTTTTTAGTGATTTTAAAGAAAAAA
* * *
461813 TTTAAAATTTTAAGCAAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTATATTTTTAA
130 TTTAAAATTTTAAACAAAATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAA
* * *
461878 GTAAAATAGTGATTTTCTTTAAAAAAAAAAAAAAGAGAGAGAAAGTTTATATTTTTAAAAATAAA
195 CTAAAATAGTGATTTTCATT--AAAAAAAAAAAAGAGAGAG--AGTTTAGATTTTTAAAAATAAA
* * *
461943 ATTATGTTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAAAATTT
256 AATATGTTTTTTAATAATTTTAAAGAAAAATTTTAAATTTTTAAAATTT
* *
461992 TTTTGATTTTTTTAACT-ATTTCGAAATAAAAATTTAGATTTTTAAGTAAAATAGTGATTTTCAT
1 TTTTGATTTTTTTAAATAATTTCGAAATAAAAATTTAGATTTTTAAGTAAAATAGAGATTTTCAT
* *
462056 TAAAAGGAAAGGAAGTTTAGATTTTTTAAAAAATAAAAATCTG-TTTTTAGTGATTTTAAAGAAA
66 TAAAA--AAAGAAAGTTTAGA-CTTTT-AAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAA
*
462120 AAATTT-AAATTTTAAACAAAATTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTT
127 AAATTTAAAATTTTAAACAAAATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTT
* * **
462183 TAACTATAGTAGTGATTTTCATT-AAAAAAATTAAGA-A-AG-G-TTAGATTTTTAAAAAATAAA
192 TAACTAAAATAGTGATTTTCATTAAAAAAAAAAAAGAGAGAGAGTTTAGATTTTT-AAAAATAAA
* **
462243 AATCTGTTTTTTTAATAATTTTAAAGAAAAAGATTAAATTTTTAAA
256 AATATG-TTTTTTAATAATTTTAAAGAAAAATTTTAAATTTTTAAA
462289 CAAAGTAAGA
Statistics
Matches: 261, Mismatches: 30, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
299 9 0.03
300 14 0.05
301 35 0.13
303 2 0.01
304 1 0.00
305 11 0.04
308 101 0.39
309 34 0.13
310 35 0.13
311 4 0.02
312 15 0.06
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (304 bp):
TTTTGATTTTTTTAAATAATTTCGAAATAAAAATTTAGATTTTTAAGTAAAATAGAGATTTTCAT
TAAAAAAAGAAAGTTTAGACTTTTAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAAAAAAT
TTAAAATTTTAAACAAAATTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAC
TAAAATAGTGATTTTCATTAAAAAAAAAAAAGAGAGAGAGTTTAGATTTTTAAAAATAAAAATAT
GTTTTTTAATAATTTTAAAGAAAAATTTTAAATTTTTAAAATTT
Found at i:463642 original size:25 final size:23
Alignment explanation
Indices: 463591--463656 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
463581 TATTGTCTCG
* *
463591 ATTTTTTTAAAAATAAT-TTATGT
1 ATTTTTTTAAAAA-AATGTCACGT
463614 ATTTTTTTTAAAAAAATGTCACGT
1 A-TTTTTTTAAAAAAATGTCACGT
* *
463638 AATTTATTTAATAAAATGT
1 -ATTTTTTTAAAAAAATGT
463657 TATACAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 31 0.86
25 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (23 bp):
ATTTTTTTAAAAAAATGTCACGT
Found at i:463979 original size:13 final size:13
Alignment explanation
Indices: 463963--463988 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
463953 ATTTAAAACA
463963 AATAATAAATAAT
1 AATAATAAATAAT
463976 AATAATAAATAAT
1 AATAATAAATAAT
463989 GCAAATTAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:464057 original size:23 final size:23
Alignment explanation
Indices: 464031--464078 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
464021 AATTTGGCAT
*
464031 AAAATAACAAC-ATAAGTAAATAA
1 AAAAT-ACAACAATAAATAAATAA
*
464054 AAAATATAACAATAAATAAATAA
1 AAAATACAACAATAAATAAATAA
464077 AA
1 AA
464079 TTAAACACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (23 bp):
AAAATACAACAATAAATAAATAA
Found at i:464078 original size:44 final size:40
Alignment explanation
Indices: 464029--464146 Score: 98
Period size: 41 Copynumber: 2.9 Consensus size: 40
464019 AAAATTTGGC
*
464029 ATAAAATAACAACA-TAAGTAAATAAA-AAATATAACAATAAATAA
1 ATAAAATAACAACACT-A--AAATAAACAAATAT-A-AACAAAT-A
*
464073 ATAAAATTA-AACACTAAAATAAACAAATATAAACAAATA
1 ATAAAATAACAACACTAAAATAAACAAATATAAACAAATA
* * * *
464112 ATAAAATAACAATAACTAAATTAAATAAAAATAAA
1 ATAAAATAACAA-CACTAAAATAAACAAATATAAA
464147 ACAGTGAGGT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
39 9 0.14
40 8 0.13
41 26 0.41
42 6 0.10
43 5 0.08
44 9 0.14
ACGTcount: A:0.70, C:0.08, G:0.01, T:0.21
Consensus pattern (40 bp):
ATAAAATAACAACACTAAAATAAACAAATATAAACAAATA
Found at i:464105 original size:22 final size:20
Alignment explanation
Indices: 464047--464117 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 20
464037 ACAACATAAG
464047 TAAATAAAAAATAT-AACAA
1 TAAATAAAAAATATAAACAA
*
464066 TAAATAAATAAA-ATTAAACAC
1 TAAATAAA-AAATA-TAAACAA
464087 TAAAATAAACAAATATAAACAA
1 T-AAATAAA-AAATATAAACAA
464109 -ATAATAAAA
1 TA-AATAAAA
464118 TAACAATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
19 9 0.21
20 6 0.14
21 11 0.26
22 16 0.37
23 1 0.02
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAATAAAAAATATAAACAA
Found at i:465080 original size:21 final size:21
Alignment explanation
Indices: 465056--465108 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
465046 TTGTGCTAAC
465056 TCTACTGATACAAGT-ATG-A
1 TCTACTGATACAAGTCATGCA
*
465075 TTTCTACTAATACAAGTCATGCA
1 --TCTACTGATACAAGTCATGCA
465098 TCTACTGATAC
1 TCTACTGATAC
465109 CAAAAACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (21 bp):
TCTACTGATACAAGTCATGCA
Found at i:466372 original size:14 final size:14
Alignment explanation
Indices: 466353--466380 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
466343 AATTTTACCC
466353 CTAATAGTTTCCTT
1 CTAATAGTTTCCTT
466367 CTAATAGTTTCCTT
1 CTAATAGTTTCCTT
466381 TTATTAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
CTAATAGTTTCCTT
Found at i:467812 original size:3 final size:3
Alignment explanation
Indices: 467804--467836 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
467794 CCTGAACGAA
*
467804 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
467837 TACTTATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:468890 original size:18 final size:17
Alignment explanation
Indices: 468867--468901 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
468857 TTTATATTAC
*
468867 CAATTCATATCATCATTT
1 CAATTCAAAT-ATCATTT
468885 CAATTCAAATATCATTT
1 CAATTCAAATATCATTT
468902 ATCCAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (17 bp):
CAATTCAAATATCATTT
Found at i:470647 original size:2 final size:2
Alignment explanation
Indices: 470634--470690 Score: 105
Period size: 2 Copynumber: 28.0 Consensus size: 2
470624 TAATATCAAA
470634 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
470677 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
470691 TTACAACCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 52 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:470778 original size:81 final size:81
Alignment explanation
Indices: 470683--470845 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 81
470673 ATATATATAT
* *
470683 ATATATATTTACAACCAACATTACAAGCATATATATGTAACCTATACAACACTTAGTACATGGCA
1 ATATATATTTACAACCAACATTACAAGCATATACATATAACCTATACAACACTTAGTACATGGCA
470748 CTTTTACCAAAAGAGC
66 CTTTTACCAAAAGAGC
* *
470764 ATATATATTTACAACCAACATTACAAGCATATACATATAACCTATACGACACTTAGTACATGTCA
1 ATATATATTTACAACCAACATTACAAGCATATACATATAACCTATACAACACTTAGTACATGGCA
470829 CTTTTACCAAAAGAGC
66 CTTTTACCAAAAGAGC
470845 A
1 A
470846 AAATTACATC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.28
Consensus pattern (81 bp):
ATATATATTTACAACCAACATTACAAGCATATACATATAACCTATACAACACTTAGTACATGGCA
CTTTTACCAAAAGAGC
Found at i:471739 original size:17 final size:18
Alignment explanation
Indices: 471705--471740 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
471695 TGAATTTCTA
471705 TCCAATTTATAGCTTAAT
1 TCCAATTTATAGCTTAAT
*
471723 TCCAATTTA-ATCTTAAT
1 TCCAATTTATAGCTTAAT
471740 T
1 T
471741 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (18 bp):
TCCAATTTATAGCTTAAT
Found at i:483084 original size:20 final size:20
Alignment explanation
Indices: 483036--483095 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
483026 TTAGTAATTA
*
483036 TTATAAA-TTATTTGTTTAG
1 TTATAAATTTATGTGTTTAG
483055 TT-TAATATTTATGTGATTT-G
1 TTATAA-ATTTATGTG-TTTAG
* *
483075 TTATAAATTTTTTTGTTTAG
1 TTATAAATTTATGTGTTTAG
483095 T
1 T
483096 AAAGTAGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 3 0.09
19 6 0.18
20 18 0.55
21 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (20 bp):
TTATAAATTTATGTGTTTAG
Found at i:483194 original size:147 final size:147
Alignment explanation
Indices: 483003--483374 Score: 491
Period size: 147 Copynumber: 2.5 Consensus size: 147
482993 AAAATAATAA
*
483003 TAATTTAATTTAAATTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGTTTAATATTTATG
1 TAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGTTTAATATTTATG
* **
483068 TGATTTGTTATAAATTTTTTTGTTTAGTAAAGTAGATTAAA-GGGAAGAAAGCTAA-A-AGAATG
66 TGATTTGTTATAAATTTTTTTATTTAGTAAAGTAGATTAAACGCAAAGAAAGCTAAGATA-AATG
* *
483130 GTAAATTATTTTGTTGTTTT
130 GT--ATTATTGTCTTGTTTT
*
483150 TAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGTTTAATTTTTATG
1 TAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGTTTAATATTTATG
* * * * * ** * *
483215 TTATTTATTATAATTTTTTTTATTTGGTAGAGTATCTTAAACGCAAAGAAAGGTAAGATAAATTG
66 TGATTTGTTATAAATTTTTTTATTTAGTAAAGTAGATTAAACGCAAAGAAAGCTAAGATAAATGG
* *
483280 TTTTGTTGTCTTGTTTT
131 TATTATTGTCTTGTTTT
* * * *
483297 TAATTTAATTTAAAGTTA-TTTGTTAGTTATTCTTATAAATTATTTGTTTAGTTTAATGTTTATA
1 TAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGTTTAATATTTATG
483361 TGATTTGTTATAAA
66 TGATTTGTTATAAA
483375 AAAATTTTGT
Statistics
Matches: 197, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
146 53 0.27
147 126 0.64
148 11 0.06
149 6 0.03
150 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.53
Consensus pattern (147 bp):
TAATTTAATTTAAAGTTATTTTGTTAGTAATTATTATAAATTATTTGTTTAGTTTAATATTTATG
TGATTTGTTATAAATTTTTTTATTTAGTAAAGTAGATTAAACGCAAAGAAAGCTAAGATAAATGG
TATTATTGTCTTGTTTT
Found at i:483435 original size:5 final size:5
Alignment explanation
Indices: 483420--483449 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
483410 GTTTTACTGT
483420 TTTTAA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTT
483450 GTTAGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:483575 original size:25 final size:26
Alignment explanation
Indices: 483530--483583 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
483520 TTTTGTTGTT
*
483530 TTTTTAATTATTTTTAAATTATTTTG
1 TTTTTAATTATTTATAAATTATTTTG
*
483556 TTTTTAATTA-TTATATATTATTTTG
1 TTTTTAATTATTTATAAATTATTTTG
483581 TTT
1 TTT
483584 AGTTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTAATTATTTATAAATTATTTTG
Found at i:485901 original size:44 final size:43
Alignment explanation
Indices: 485831--486028 Score: 234
Period size: 44 Copynumber: 4.5 Consensus size: 43
485821 TATATCCCGG
* *
485831 CTTGGAACAAACATATTAATTCAAATTAGATGTATTAAAATAAA
1 CTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAAA-AAA
* ** * * *
485875 TTTTAAACAAACATAGTAATTTAAATTAGATATATTATAACAAT
1 CTTGGAACAAACATAGTAATTTAAATTAGATGTATTA-AAAAAA
* *
485919 CTTGGAACAAACATAGTAATTTAAATAAGACGTATTAAAACAAA
1 CTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAAA-AAA
* * *
485963 CTTGGAACAGACATAGTAATTTAAATGAGATGCATTAAAGAAAA
1 CTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAA-AAAA
*
486007 CATGGAACAAACATAGTAATTT
1 CTTGGAACAAACATAGTAATTT
486029 CACCATCAAG
Statistics
Matches: 129, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.02
44 124 0.96
45 3 0.02
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (43 bp):
CTTGGAACAAACATAGTAATTTAAATTAGATGTATTAAAAAAA
Found at i:495859 original size:28 final size:28
Alignment explanation
Indices: 495805--495862 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
495795 TTGAATTTGA
** * * *
495805 TTTTTTTTTTTTAATTTGGTTTTTAAAC
1 TTTTTTTGATTTAATTTGATATCTAAAC
495833 TTTTTTTGATTTAATTTGATATCTAAAC
1 TTTTTTTGATTTAATTTGATATCTAAAC
495861 TT
1 TT
495863 AACATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (28 bp):
TTTTTTTGATTTAATTTGATATCTAAAC
Found at i:495909 original size:60 final size:59
Alignment explanation
Indices: 495809--495980 Score: 168
Period size: 60 Copynumber: 2.9 Consensus size: 59
495799 ATTTGATTTT
** **
495809 TTTTTTTTAATTTGGTTTTTAAAC-TTTTTTTGATTTAATTT-GATATCTAAACTTAACA
1 TTTTTTTTAATTTGGTACTTAAACTTTTTTTTGATCCAATTTAG-TATCTAAACTTAACA
* * * *
495867 TTTTTTCTTAATTTAGTACTTAAACTTTTTTTTTATCCAATTTAGTATCTGAACTTGACA
1 TTTTTT-TTAATTTGGTACTTAAACTTTTTTTTGATCCAATTTAGTATCTAAACTTAACA
** * * * *
495927 TTTTTTTCTAATTTGGTACCCAAGCTTTTTTTTAGATTCAGTTTAGTACCTAAA
1 TTTTTTT-TAATTTGGTACTTAAACTTTTTTTT-GATCCAATTTAGTATCTAAA
495981 TTTATTAAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
58 6 0.07
59 16 0.17
60 54 0.59
61 16 0.17
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.54
Consensus pattern (59 bp):
TTTTTTTTAATTTGGTACTTAAACTTTTTTTTGATCCAATTTAGTATCTAAACTTAACA
Found at i:496283 original size:27 final size:25
Alignment explanation
Indices: 496248--496297 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
496238 AAATGTCAAG
496248 TTTAAGTACCAAATTGAACAAAAAAAA
1 TTTAAGTACCAAATT-AA-AAAAAAAA
*
496275 TTTAGGTACCAAATTAAAAAAAA
1 TTTAAGTACCAAATTAAAAAAAA
496298 TATCAAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 2 0.09
27 14 0.64
ACGTcount: A:0.58, C:0.10, G:0.08, T:0.24
Consensus pattern (25 bp):
TTTAAGTACCAAATTAAAAAAAAAA
Found at i:496316 original size:30 final size:30
Alignment explanation
Indices: 496184--496318 Score: 134
Period size: 30 Copynumber: 4.6 Consensus size: 30
496174 GGACACCAAA
* * *
496184 AAGTTTAAGAAGCAACTTAAAAAAAAGTATC
1 AAGTTTAAGTACCAAATTAAAAAAAA-TATC
* * ** *
496215 AAGTTTAGGTATCAAATTAGGAAAAATGTC
1 AAGTTTAAGTACCAAATTAAAAAAAATATC
*
496245 AAGTTTAAGTACCAAATTGAACAAAAA-A--
1 AAGTTTAAGTACCAAATT-AAAAAAAATATC
*
496273 AA-TTTAGGTACCAAATTAAAAAAAATATC
1 AAGTTTAAGTACCAAATTAAAAAAAATATC
496302 AAGTTTAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
496319 ATTATATTAA
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
26 7 0.08
27 15 0.18
28 2 0.02
29 2 0.02
30 32 0.38
31 26 0.31
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAAAAAAAATATC
Found at i:501543 original size:2 final size:2
Alignment explanation
Indices: 501536--501565 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
501526 AAATCAATAA
501536 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
501566 TATGGTATTT
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:502422 original size:20 final size:19
Alignment explanation
Indices: 502393--502431 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
502383 ATTTATTTAT
502393 TAAAATTATTTTTTATAAA
1 TAAAATTATTTTTTATAAA
*
502412 TAAAATATATTTTTTTTAAA
1 TAAAAT-TATTTTTTATAAA
502432 AACTCACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAAAATTATTTTTTATAAA
Found at i:504413 original size:30 final size:30
Alignment explanation
Indices: 504377--504466 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
504367 CAATTTACCG
504377 AATAAGTTCACTAGTAAGCTTTCATAGCTT
1 AATAAGTTCACTAGTAAGCTTTCATAGCTT
* *
504407 AATAAGTT--C--GCAAG-GTTCA-A-C--
1 AATAAGTTCACTAGTAAGCTTTCATAGCTT
* *
504428 AAAAAATTCACTAGTAAGCTTTCATAGCTT
1 AATAAGTTCACTAGTAAGCTTTCATAGCTT
504458 AATAAGTTC
1 AATAAGTTC
504467 GCAAGGTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
21 6 0.14
23 2 0.05
24 1 0.02
25 8 0.19
26 8 0.19
27 1 0.02
28 2 0.05
30 15 0.35
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (30 bp):
AATAAGTTCACTAGTAAGCTTTCATAGCTT
Found at i:505508 original size:59 final size:59
Alignment explanation
Indices: 505415--505528 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
505405 TTCAAAACTC
* * *
505415 ATCAATGGAAAAATCTATAACATTTGGCAGATTCACAAATTAGTCTCCGGGTTAGACTA
1 ATCAATGGAAAAATCTATAACATTTGGCAAATTCACAAATTAGTCCCCGAGTTAGACTA
*
505474 ATCAATGGCAAAATCTATAACATTTGGCAAATTCACAAATTAGTCCCCGAGTTAG
1 ATCAATGGAAAAATCTATAACATTTGGCAAATTCACAAATTAGTCCCCGAGTTAG
505529 CTAGATTAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (59 bp):
ATCAATGGAAAAATCTATAACATTTGGCAAATTCACAAATTAGTCCCCGAGTTAGACTA
Found at i:506547 original size:21 final size:21
Alignment explanation
Indices: 506523--506594 Score: 135
Period size: 21 Copynumber: 3.4 Consensus size: 21
506513 TCATTTTCAA
506523 AAACCACTTGACTTTTGAACC
1 AAACCACTTGACTTTTGAACC
*
506544 AAACCACTTGACTTTTGCACC
1 AAACCACTTGACTTTTGAACC
506565 AAACCACTTGACTTTTGAACC
1 AAACCACTTGACTTTTGAACC
506586 AAACCACTT
1 AAACCACTT
506595 ATACTAACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.28
Consensus pattern (21 bp):
AAACCACTTGACTTTTGAACC
Found at i:508552 original size:29 final size:30
Alignment explanation
Indices: 508454--508560 Score: 180
Period size: 30 Copynumber: 3.6 Consensus size: 30
508444 GCCTTACACT
*
508454 GAAGAAATTGATTATACACTTAGTGAACCA
1 GAAGAAATTGATGATACACTTAGTGAACCA
* *
508484 GAAGAAATTGATCATACACTCAGTGAACCA
1 GAAGAAATTGATGATACACTTAGTGAACCA
508514 GAAGAAATTGATGATACACTTAGTG-ACCA
1 GAAGAAATTGATGATACACTTAGTGAACCA
508543 GAAGAAATTGATGATACA
1 GAAGAAATTGATGATACA
508561 AATCATTCGA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 22 0.30
30 51 0.70
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (30 bp):
GAAGAAATTGATGATACACTTAGTGAACCA
Found at i:513712 original size:29 final size:29
Alignment explanation
Indices: 513425--513706 Score: 261
Period size: 30 Copynumber: 9.6 Consensus size: 29
513415 TTTTTCCTTC
*
513425 AAACTTTT-TAAAATCACATTTTGA-CCT
1 AAACTTTTCTAAAATTACATTTTGACCCT
* * *
513452 CAAACTTTTTTAAAATTATATTTTGACCTT
1 -AAACTTTTCTAAAATTACATTTTGACCCT
* * *
513482 AAAATTTTGTAAAATTACATTTTGATCCT
1 AAACTTTTCTAAAATTACATTTTGACCCT
* * *
513511 AAAC-TTCCCAAAATTACATTTTAACCCT
1 AAACTTTTCTAAAATTACATTTTGACCCT
* * *
513539 CCAAACTTTTCAAAAATTACATTCTAATCGCC-
1 --AAACTTTTCTAAAATTACATTTTGA-C-CCT
* * *
513571 AAAATTTTCTAAAATCACTTTTTGATCCCT
1 AAACTTTTCTAAAATTACATTTTGA-CCCT
* *
513601 AAACTTTTCCAAAATTACATTTTAACCCCT
1 AAACTTTTCTAAAATTACATTTTGA-CCCT
513631 AAACTTCTTC-AAAATTACATTTTGACTCCT
1 AAACTT-TTCTAAAATTACATTTTGAC-CCT
*
513661 AAACTTCTT-TAAAATCACATTTTGACCCT
1 AAACTT-TTCTAAAATTACATTTTGACCCT
513690 AAACTTTTCTAAAATTA
1 AAACTTTTCTAAAATTA
513707 TGTTTTAACC
Statistics
Matches: 210, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 29 0.14
29 60 0.29
30 98 0.47
31 20 0.10
32 1 0.00
33 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.40
Consensus pattern (29 bp):
AAACTTTTCTAAAATTACATTTTGACCCT
Found at i:515443 original size:17 final size:17
Alignment explanation
Indices: 515415--515449 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
515405 TTCAAAAAGC
515415 AGAAATATTTTGTGTGAA
1 AGAAATATTTTGT-TGAA
515433 AGAAA-ATTTTGTTGAA
1 AGAAATATTTTGTTGAA
515449 A
1 A
515450 ACACAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (17 bp):
AGAAATATTTTGTTGAA
Found at i:516883 original size:17 final size:17
Alignment explanation
Indices: 516861--516913 Score: 90
Period size: 17 Copynumber: 3.2 Consensus size: 17
516851 TTAAAACTTT
*
516861 AATTTATTTTAAGTTTA
1 AATTTATTTTAAATTTA
516878 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
516895 AATTTATTTTAAA-TTA
1 AATTTATTTTAAATTTA
516911 AAT
1 AAT
516914 AGAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 6 0.17
17 29 0.83
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:520939 original size:2 final size:2
Alignment explanation
Indices: 520932--520970 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
520922 TTCAGGATGC
520932 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
520971 AAAGAAATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:522353 original size:14 final size:14
Alignment explanation
Indices: 522334--522381 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
522324 GGATCAAATC
522334 AAAATTTTAAATAT
1 AAAATTTTAAATAT
*
522348 AAAATTATACAATAT
1 AAAATTTTA-AATAT
*
522363 CAAAA-TTTATATAT
1 -AAAATTTTAAATAT
522377 AAAAT
1 AAAAT
522382 CACATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 8 0.29
16 4 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATTTTAAATAT
Found at i:532586 original size:3 final size:3
Alignment explanation
Indices: 532578--532615 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
532568 TGATTTACAA
532578 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
532616 AGATTCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:533115 original size:1 final size:1
Alignment explanation
Indices: 533109--533134 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
533099 NNNNNNNNNN
533109 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
533135 CCCTAACGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:534503 original size:9 final size:9
Alignment explanation
Indices: 534349--534564 Score: 68
Period size: 10 Copynumber: 23.1 Consensus size: 9
534339 TTTAATATTT
534349 TTATAAAAA
1 TTATAAAAA
*
534358 ATATTAAAAA
1 TTA-TAAAAA
*
534368 TTATAGAAA
1 TTATAAAAA
534377 -TA-AAAGAA
1 TTATAAA-AA
534385 TTATCAAAACA
1 TTAT-AAAA-A
534396 -TATAAAAAA
1 TTAT-AAAAA
*
534405 TTAT-TAAA
1 TTATAAAAA
534413 -TATTAAAAA
1 TTA-TAAAAA
534422 -TATAAAAA
1 TTATAAAAA
*
534430 TTGATATAAA
1 TT-ATAAAAA
*
534440 CT-TAAAAA
1 TTATAAAAA
**
534448 GCATAAAATA
1 TTATAAAA-A
* *
534458 TTATGAATA
1 TTATAAAAA
534467 TTATAAAAA
1 TTATAAAAA
* *
534476 ATCTAATAAA
1 TTATAA-AAA
*
534486 TTCTAAAAAA
1 TTAT-AAAAA
*
534496 TTATAAAAG
1 TTATAAAAA
*
534505 TAATAAAACA
1 TTATAAAA-A
* *
534515 TATTTAAAATT
1 T-TATAAAA-A
*
534526 TTACAAAACA
1 TTATAAAA-A
* * *
534536 TTTTAAGAT
1 TTATAAAAA
534545 TCTATAAAAA
1 T-TATAAAAA
534555 TTATAAAAA
1 TTATAAAAA
534564 T
1 T
534565 ATTTCTAAAA
Statistics
Matches: 149, Mismatches: 40, Indels: 36
0.66 0.18 0.16
Matches are distributed among these distances:
7 4 0.03
8 19 0.13
9 54 0.36
10 60 0.40
11 12 0.08
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:535189 original size:27 final size:28
Alignment explanation
Indices: 535152--535232 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
535142 CTAATACATT
* *
535152 TTTTTTTATTTTTTATAATTTATTAGA-
1 TTTTTATATTTTTTATAATTTATTAAAG
* *
535179 TTTTTCTA-TTTTTATAATATT-TAAAAG
1 TTTTTATATTTTTTATAAT-TTATTAAAG
535206 TTTTTATATTTGTATTATAATTTATTA
1 TTTTTATATTT-T-TTATAATTTATTA
535233 TAATTTTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 13 0.30
27 16 0.37
28 2 0.05
29 3 0.07
30 9 0.21
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTTATATTTTTTATAATTTATTAAAG
Found at i:535191 original size:28 final size:27
Alignment explanation
Indices: 535152--535232 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 27
535142 CTAATACATT
*
535152 TTTTTTTA-TTTTTTATAATTTATTAG
1 TTTTTATATTTTTTTATAATTTATTAG
* * **
535178 ATTTTTCTATTTTTATA-ATATTTAAAAG
1 -TTTTTATATTTTTTTATA-ATTTATTAG
*
535206 TTTTTATATTTGTATTATAATTTATTA
1 TTTTTATATTT-TTTTATAATTTATTA
535233 TAATTTTATA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
27 18 0.44
28 22 0.54
29 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTTATATTTTTTTATAATTTATTAG
Found at i:535272 original size:12 final size:11
Alignment explanation
Indices: 535246--535278 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
535236 TTTTATATCA
535246 ATTTTAATATT
1 ATTTTAATATT
535257 -TTTTAATACTT
1 ATTTTAATA-TT
535268 ATTTTAATATT
1 ATTTTAATATT
535279 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.40
11 4 0.20
12 8 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTAATATT
Found at i:535883 original size:10 final size:10
Alignment explanation
Indices: 535870--535934 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
535860 ATATATATAG
535870 TTTTAATAAT
1 TTTTAATAAT
535880 TTTTAA-AAT
1 TTTTAATAAT
535889 TTTTAA-ATAT
1 TTTTAATA-AT
535899 TATTT-ATAAT
1 T-TTTAATAAT
535909 TTCTT-ATAAT
1 TT-TTAATAAT
* *
535919 TCTTAATATT
1 TTTTAATAAT
535929 TTTTAA
1 TTTTAA
535935 AATAATTTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 13 0.28
10 30 0.64
11 4 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:535894 original size:19 final size:19
Alignment explanation
Indices: 535870--535937 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
535860 ATATATATAG
535870 TTTTAATAATTTTTAA-AAT
1 TTTTAA-AATTTTTAATAAT
535889 TTTTAAATATTATTT-ATAAT
1 TTTTAAA-ATT-TTTAATAAT
* * *
535909 TTCTTATAATTCTTAATATT
1 TT-TTAAAATTTTTAATAAT
535929 TTTTAAAAT
1 TTTTAAAAT
535938 AATTTCCTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
18 1 0.03
19 18 0.45
20 17 0.43
21 4 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTTTTAATAAT
Found at i:542409 original size:2 final size:2
Alignment explanation
Indices: 542368--542392 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
542358 CAAGCTGCAA
542368 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
542393 GGCATTGTTC
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:544889 original size:86 final size:85
Alignment explanation
Indices: 544744--544916 Score: 337
Period size: 86 Copynumber: 2.0 Consensus size: 85
544734 GTAATCACAA
544744 ATATTAACCCACTAGTTCAAGATATCCCTTTTGGTACTATCGTTCACTCACATTGTTTGTATTTG
1 ATATTAACCCACTAGTTCAAGATATCCCTTTTGGTACTATCGTTCACTCACATTGTTTGTATTTG
544809 TGATTTTCGAAAAAAAATGGT
66 TGATTTTCG-AAAAAAATGGT
544830 ATATTAACCCACTAGTTCAAGATATCCCTTTTGGTACTATCGTTCACTCACATTGTTTGTATTTG
1 ATATTAACCCACTAGTTCAAGATATCCCTTTTGGTACTATCGTTCACTCACATTGTTTGTATTTG
544895 TGATTTTCGAAAAAAATGGT
66 TGATTTTCGAAAAAAATGGT
544915 AT
1 AT
544917 GAAATTATAA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 13 0.15
86 74 0.85
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (85 bp):
ATATTAACCCACTAGTTCAAGATATCCCTTTTGGTACTATCGTTCACTCACATTGTTTGTATTTG
TGATTTTCGAAAAAAATGGT
Found at i:545771 original size:2 final size:2
Alignment explanation
Indices: 545764--545788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
545754 ATTCCAACCG
545764 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
545789 GAGAGAGAGA
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:545926 original size:31 final size:30
Alignment explanation
Indices: 545869--545935 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
545859 ATATAAACCT
*
545869 TAATTTGGTACAATTATACACGTGAAACTC
1 TAATTTGGTACAAATATACACGTGAAACTC
* * * *
545899 TAATTGTGGTTCAAATATATACTTGAAACTT
1 TAATT-TGGTACAAATATACACGTGAAACTC
545930 TAATTT
1 TAATTT
545936 TGATTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (30 bp):
TAATTTGGTACAAATATACACGTGAAACTC
Found at i:546664 original size:3 final size:3
Alignment explanation
Indices: 546656--546688 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
546646 ATACTTCTCC
546656 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
546689 ATGTTGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:547825 original size:18 final size:19
Alignment explanation
Indices: 547810--547844 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
547800 CTAAAATAGT
547810 AACAA-AATTA-ACAATAA
1 AACAAGAATTATACAATAA
547827 AACAAGAATTATACAATA
1 AACAAGAATTATACAATA
547845 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAGAATTATACAATAA
Found at i:549839 original size:32 final size:32
Alignment explanation
Indices: 549802--549863 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
549792 AAATTTCAAT
* * *
549802 AAATTA-AAAATGTATGAATTATTATAATAAAA
1 AAATTATAAAAT-TATAAAATATTAAAATAAAA
549834 AAATTATAAAATTATAAAATATTAAAATAA
1 AAATTATAAAATTATAAAATATTAAAATAA
549864 TACAATACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (32 bp):
AAATTATAAAATTATAAAATATTAAAATAAAA
Found at i:551193 original size:2 final size:2
Alignment explanation
Indices: 551186--551218 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
551176 CTTCCAAGGG
*
551186 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
551219 TAGTAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:551990 original size:19 final size:18
Alignment explanation
Indices: 551968--552006 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
551958 TTAAATTAAT
551968 TAAATATTTAACTACAAAA
1 TAAATATTTAACTA-AAAA
*
551987 TAAATATTTAATTAAAAA
1 TAAATATTTAACTAAAAA
552005 TA
1 TA
552007 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATATTTAACTAAAAA
Found at i:555312 original size:3 final size:3
Alignment explanation
Indices: 555304--555333 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
555294 ATAATATTCA
555304 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
555334 GCAAAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:556799 original size:18 final size:20
Alignment explanation
Indices: 556776--556816 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
556766 ATGAAAATGA
556776 TTTTT-AAAAAA-TAATATT
1 TTTTTAAAAAAATTAATATT
556794 TTTTTAAAAAAATTAATATT
1 TTTTTAAAAAAATTAATATT
556814 TTT
1 TTT
556817 AGTGTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTAAAAAAATTAATATT
Found at i:556817 original size:18 final size:17
Alignment explanation
Indices: 556775--556817 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
556765 AATGAAAATG
556775 ATTTTT-AAAAAATAAT
1 ATTTTTAAAAAAATAAT
556791 ATTTTTTTAAAAAAATTAAT
1 A--TTTTTAAAAAAA-TAAT
556811 ATTTTTA
1 ATTTTTA
556818 GTGTTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
18 11 0.48
19 6 0.26
20 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTTAAAAAAATAAT
Found at i:558541 original size:31 final size:31
Alignment explanation
Indices: 558485--558567 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
558475 GACCATTGAA
* * *
558485 AAGTTTAAGTACCAACTTA-AGAAAAAGTGTC
1 AAGTTTGAGTACCAAATTAGA-AAAAAATGTC
* *
558516 AAGTTT-AGGTACTAAATTAGAAAAAAATGTT
1 AAGTTTGA-GTACCAAATTAGAAAAAAATGTC
558547 AAGTTTGAGTACCAAATTAGA
1 AAGTTTGAGTACCAAATTAGA
558568 TATAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 1 0.02
31 41 0.93
32 2 0.05
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (31 bp):
AAGTTTGAGTACCAAATTAGAAAAAAATGTC
Found at i:559295 original size:12 final size:12
Alignment explanation
Indices: 559278--559302 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
559268 TCGACGAGAT
559278 TTGAAAAGTTAA
1 TTGAAAAGTTAA
559290 TTGAAAAGTTAA
1 TTGAAAAGTTAA
559302 T
1 T
559303 ATTAGTTATT
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:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TTGAAAAGTTAA
Found at i:560336 original size:15 final size:15
Alignment explanation
Indices: 560316--560349 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
560306 GAGAAGGAGG
560316 AGGAGAAGATAG-AGA
1 AGGAGAAGA-AGAAGA
560331 AGGAGAAGAAGAAGA
1 AGGAGAAGAAGAAGA
560346 AGGA
1 AGGA
560350 AGAGGAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (15 bp):
AGGAGAAGAAGAAGA
Found at i:560357 original size:3 final size:3
Alignment explanation
Indices: 560346--560501 Score: 120
Period size: 3 Copynumber: 52.0 Consensus size: 3
560336 AAGAAGAAGA
* * * *
560346 AGG AAG AGG AGG AGG AGA AGG A-G AGG AAG AGG AAAG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG -AGG AGG AGG AGG
* * * * *
560391 AGG AGA AGA AGG AGG AGG AGG AGG AGA AGA AAG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
* * * * **
560439 -GG AAGG AGG AGG AAGG A-A AGG AGG AGA AGA AAG AGG AGG AAA AGG
1 AGG -AGG AGG AGG -AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
*
560484 AGG AGG AGA AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG
560502 TTGAAGATGA
Statistics
Matches: 121, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
2 5 0.04
3 109 0.90
4 7 0.06
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:560447 original size:21 final size:21
Alignment explanation
Indices: 560302--560501 Score: 155
Period size: 21 Copynumber: 9.5 Consensus size: 21
560292 CCACCATCTT
*
560302 GAAGGAGAAGGAGGAGGAGAA
1 GAAGGAGGAGGAGGAGGAGAA
*
560323 GATA-GA-GA--AGGAGAAGAA
1 GA-AGGAGGAGGAGGAGGAGAA
* * *
560341 GAAGAAGGAAGAGGAGGAGGA
1 GAAGGAGGAGGAGGAGGAGAA
*
560362 GAAGGA-GAGGAAGAGGA-AA
1 GAAGGAGGAGGAGGAGGAGAA
*
560381 G-AGGAGGAGGAGGAGAAGAA
1 GAAGGAGGAGGAGGAGGAGAA
* *
560401 GGAGGAGGAGGAGGAGAAGAA
1 GAAGGAGGAGGAGGAGGAGAA
*
560422 -AGAGGAGGAGGAGGAGGGGAA
1 GA-AGGAGGAGGAGGAGGAGAA
*
560443 GGAGGAGGAAGGAAAGGAGGAGAA
1 GAAGGAGG-AGG--AGGAGGAGAA
* *
560467 GAAAGAGGAGGAAAAGGAGGAGGA
1 GAAGGAGGAGG---AGGAGGAGAA
560491 GAAGGAGGAGG
1 GAAGGAGGAGG
560502 TTGAAGATGA
Statistics
Matches: 145, Mismatches: 20, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.01
18 16 0.11
19 13 0.09
20 13 0.09
21 59 0.41
22 4 0.03
23 3 0.02
24 36 0.25
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.01
Consensus pattern (21 bp):
GAAGGAGGAGGAGGAGGAGAA
Found at i:560501 original size:27 final size:27
Alignment explanation
Indices: 560304--560501 Score: 141
Period size: 24 Copynumber: 7.6 Consensus size: 27
560294 ACCATCTTGA
*
560304 AGGAGAAGGAGGAGGA-GAAGATA-GAGA
1 AGGAGAAGGAGGAGGAGGAA-A-AGGAGG
* * * *
560331 AGGAGAAGAAGAAGAAGGAAGAGGAGG
1 AGGAGAAGGAGGAGGAGGAAAAGGAGG
*
560358 AGGAGAAGGAGAGGAAGAGGAAAGAGGAGG
1 AGGAGAA-G-GAGGAGGAGGAAA-AGGAGG
* * *
560388 AGGAGGAGAAGAAGGAGG---AGGAGG
1 AGGAGAAGGAGGAGGAGGAAAAGGAGG
* *
560412 AGGAGAAGAAAGAGGAGG---AGGAGG
1 AGGAGAAGGAGGAGGAGGAAAAGGAGG
*
560436 AGGGGAAGGAGGAGGAAGG-AAAGGAGG
1 AGGAGAAGGAGGAGG-AGGAAAAGGAGG
*
560463 AGAAGAA--A-GAGGAGGAAAAGGAGG
1 AGGAGAAGGAGGAGGAGGAAAAGGAGG
560487 AGGAGAAGGAGGAGG
1 AGGAGAAGGAGGAGG
560502 TTGAAGATGA
Statistics
Matches: 136, Mismatches: 23, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
23 3 0.02
24 57 0.42
25 4 0.03
26 2 0.01
27 38 0.28
28 11 0.08
29 9 0.07
30 12 0.09
ACGTcount: A:0.46, C:0.00, G:0.53, T:0.01
Consensus pattern (27 bp):
AGGAGAAGGAGGAGGAGGAAAAGGAGG
Found at i:563250 original size:29 final size:30
Alignment explanation
Indices: 563213--563281 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
563203 TTAAATTATT
* * *
563213 TATATTTTTATA-ATTTTTAAAAGATTAAAC
1 TATAATTTTATATATTTTTAAAAG-TAAAAA
*
563243 TA-AATTTT-TATTTTTTTAAAAGTAAAAA
1 TATAATTTTATATATTTTTAAAAGTAAAAA
563271 TATAATTTTAT
1 TATAATTTTAT
563282 TTTTATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 8 0.25
29 21 0.66
30 3 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (30 bp):
TATAATTTTATATATTTTTAAAAGTAAAAA
Found at i:563285 original size:29 final size:29
Alignment explanation
Indices: 563216--563290 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
563206 AATTATTTAT
* * *
563216 ATTTTTATAATTTTTAAAAGATTAAACTAA
1 ATTTTTAT-TTTTTTAAAAGATAAAAATAA
563246 ATTTTTATTTTTTTAAAAG-TAAAAATATA
1 ATTTTTATTTTTTTAAAAGATAAAAATA-A
563275 A-TTTTATTTTTATTAA
1 ATTTTTATTTTT-TTAA
563291 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 16 0.40
29 16 0.40
30 8 0.20
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (29 bp):
ATTTTTATTTTTTTAAAAGATAAAAATAA
Found at i:563334 original size:20 final size:21
Alignment explanation
Indices: 563286--563339 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
563276 TTTTATTTTT
* * *
563286 ATTAATTTAAAATTTTTAAAT
1 ATTATTTTAATATTTTTAAAC
*
563307 ATTATTTTAATATTTTTATAC
1 ATTATTTTAATATTTTTAAAC
563328 ATT-TTTTAATAT
1 ATTATTTTAATAT
563340 GTATAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 9 0.31
21 20 0.69
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTTTAATATTTTTAAAC
Found at i:566873 original size:14 final size:14
Alignment explanation
Indices: 566850--566884 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
566840 GAAATTTGTT
*
566850 TTCTAGTAAAGTTG
1 TTCTAATAAAGTTG
566864 TTCTAATAAAGTTG
1 TTCTAATAAAGTTG
566878 TTCTAAT
1 TTCTAAT
566885 GGAATTGAAC
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:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (14 bp):
TTCTAATAAAGTTG
Found at i:568717 original size:7 final size:7
Alignment explanation
Indices: 568705--568777 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 7
568695 GAAATTTCAC
568705 AAAAAAG
1 AAAAAAG
568712 -AAAAA-
1 AAAAAAG
*
568717 ACAAAA-
1 AAAAAAG
568723 AAAAAAG
1 AAAAAAG
*
568730 GAAAAA-
1 AAAAAAG
568736 AAAAAAG
1 AAAAAAG
568743 AAAAAAG
1 AAAAAAG
568750 AGAAAAAG
1 A-AAAAAG
568758 AGAAAAAG
1 A-AAAAAG
*
568766 --GAAAG
1 AAAAAAG
568771 AAAAAAG
1 AAAAAAG
568778 GGGGAGGTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 4 0.07
6 19 0.35
7 17 0.31
8 14 0.26
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:568735 original size:20 final size:21
Alignment explanation
Indices: 568705--568765 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 21
568695 GAAATTTCAC
*
568705 AAAAA-AGAAAAAACAAAA-A
1 AAAAAGAGAAAAAAAAAAAGA
568724 AAAAAG-GAAAAAAAAAAAGA
1 AAAAAGAGAAAAAAAAAAAGA
568744 AAAAAGAGAAAAAGAGAAAAAG
1 AAAAAGAGAAAAA-A-AAAAAG
568766 GAAAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 16 0.44
20 7 0.19
21 6 0.17
22 1 0.03
23 6 0.17
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAAAAAAAAAAGA
Found at i:568755 original size:8 final size:8
Alignment explanation
Indices: 568724--568769 Score: 57
Period size: 7 Copynumber: 6.4 Consensus size: 8
568714 AAAACAAAAA
568724 AAAAAG-G
1 AAAAAGAG
568731 AAAAA-A-
1 AAAAAGAG
568737 AAAAAGA-
1 AAAAAGAG
568744 AAAAAGAG
1 AAAAAGAG
568752 AAAAAGAG
1 AAAAAGAG
568760 AAAAAG-G
1 AAAAAGAG
568767 AAA
1 AAA
568770 GAAAAAAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.14
7 17 0.47
8 14 0.39
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAGAG
Found at i:569897 original size:98 final size:98
Alignment explanation
Indices: 569655--569897 Score: 279
Period size: 98 Copynumber: 2.5 Consensus size: 98
569645 TATATTCTAC
* ** * *
569655 AGATTTGAAGGGAAAGATTGAAGTCGCAACGGCAAATCTAATACCCCAGAGATATGAAGAGAAAG
1 AGATGTGAAGGGAAAGATTGAAGTCGCAACGATAAATCTTATACCCTAGAGATATGAAGAGAAAG
*
569720 GTTGGAGCCGCAACGACGAACCTTGTACCTTAG
66 GTTGAAGCCGCAACGACGAACCTTGTACCTTAG
* * * * * * * * *
569753 GGACGTGATGGGAAAGACTAAAGTCGCGACGATAAATCTTGTACCCTAGAGTTATGAAGGGAAAG
1 AGATGTGAAGGGAAAGATTGAAGTCGCAACGATAAATCTTATACCCTAGAGATATGAAGAGAAAG
* **
569818 GTTGAAGCCGCAATGGTGAACCTTGTACCTTAG
66 GTTGAAGCCGCAACGACGAACCTTGTACCTTAG
* * * * *
569851 AGATGTGAAAGGAAAGATTGAGGTTGCAACGATGAATCTTACACCCT
1 AGATGTGAAGGGAAAGATTGAAGTCGCAACGATAAATCTTATACCCT
569898 GAAGAAGAGG
Statistics
Matches: 115, Mismatches: 30, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
98 115 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.21
Consensus pattern (98 bp):
AGATGTGAAGGGAAAGATTGAAGTCGCAACGATAAATCTTATACCCTAGAGATATGAAGAGAAAG
GTTGAAGCCGCAACGACGAACCTTGTACCTTAG
Found at i:570187 original size:39 final size:38
Alignment explanation
Indices: 570075--570220 Score: 100
Period size: 39 Copynumber: 3.7 Consensus size: 38
570065 AATTACAATA
* * * * *
570075 ATCCAATCTTTTACCCTGATTAGAGGGCAGATTCAAGTC
1 ATCCAATC-TTTACCCTAATCAGAGGGCAAATTGAAGAC
* ** * * *
570114 ATCCTATCTCTTACCCCGACCATGA-GACAGATTGAAG-C
1 ATCCAATCT-TTACCCTAATCA-GAGGGCAAATTGAAGAC
*
570152 ATTCCGATCTTTTACCCTAA-CTAGAGGGCAAATTGAAGACC
1 A-TCCAATC-TTTACCCTAATC-AGAGGGCAAATTGAAGA-C
570193 ATCCAATCTTTACCCTAATCAGAGGGCA
1 ATCCAATCTTTACCCTAATCAGAGGGCA
570221 GATCTTTTAC
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
38 6 0.07
39 68 0.79
40 10 0.12
41 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (38 bp):
ATCCAATCTTTACCCTAATCAGAGGGCAAATTGAAGAC
Found at i:570231 original size:25 final size:25
Alignment explanation
Indices: 570201--570248 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
570191 CCATCCAATC
570201 TTTACCCTAA-TCAGAGGGCAGATCT
1 TTTACCCTAAGT-AGAGGGCAGATCT
*
570226 TTTACCTTAAGTAGAGGGCAGAT
1 TTTACCCTAAGTAGAGGGCAGAT
570249 TGAAGACCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (25 bp):
TTTACCCTAAGTAGAGGGCAGATCT
Found at i:570258 original size:64 final size:65
Alignment explanation
Indices: 570157--570289 Score: 198
Period size: 64 Copynumber: 2.1 Consensus size: 65
570147 GAAGCATTCC
*
570157 GATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCCAATCT-TTACCCTAATCA-GAGGGC
1 GATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCCAATCATG-GGGC
570220 A
65 A
* * * *
570221 GATCTTTTACCTTAAGTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGGGGCA
1 GATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCCAATCATGGGGCA
570286 GATC
1 GATC
570290 GAAACAATCC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
64 42 0.68
65 19 0.31
66 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (65 bp):
GATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCCAATCTCTTACCCCAATCATGGGGCA
Found at i:570285 original size:40 final size:41
Alignment explanation
Indices: 570239--570806 Score: 376
Period size: 39 Copynumber: 14.4 Consensus size: 41
570229 ACCTTAAGTA
*
570239 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCAT
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* * *
570280 G-GGGCAGATCGAA-ACAATCCAATCTTTTACCCCGACCAT
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* * * ** *
570319 G-GGGCAAATTGAAGTA--ATTCAGATCTTTTACCCTAACTA-
1 GAGGGCAGATTGAAG-ACCATCCA-ATCTCTTACCCCGACCAT
* * * * * * * **
570358 GAGAGAAGATTGAATTA--ATCTAATATTTTACCCCAATTA-
1 GAGGGCAGATTGAA-GACCATCCAATCTCTTACCCCGACCAT
*
570397 GAGGGCAGATTGAAG-CCATCCAATCTCTTACCCTGACCAT
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* * * ** *
570437 G-GTGCAGATTGAAG-CAATCCAATCTTTTACCCTAACTA-
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* * * *
570475 GAGGGCAGATTAAAGATCATTCGATCTCTTACCCCGACCAT
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* * * * * ** *
570516 -AGGGCAAATTGAAG-CAACCCAATCTTTTACTCTAACTA-
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* ** ** *
570554 GAAGGCAGATTGAAG-TTATTTAATCTCTTACCTCGACCAT
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* *** *
570594 -AGGGCAGATTGAAGTA--ATCCAATCTTTTACCTTAACTA-
1 GAGGGCAGATTGAAG-ACCATCCAATCTCTTACCCCGACCAT
*
570632 GAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCA-
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* * * * *
570672 GAGGGTAGATTAAAGACCATCCGATCTCTTTCCCCAACCAT
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* *
570713 G-GGGCAGATTGAAGACCATCCAATCTTTTACCCCAACCA-
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
* * *
570752 GAGGGCAGATTGAAGACCATCCGATCTCTTACTCCAACCAT
1 GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
*
570793 G-GGGTAGATTGAAG
1 GAGGGCAGATTGAAG
570807 TAATTCAGAT
Statistics
Matches: 411, Mismatches: 95, Indels: 43
0.75 0.17 0.08
Matches are distributed among these distances:
38 2 0.00
39 206 0.50
40 199 0.48
41 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (41 bp):
GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCAT
Found at i:570345 original size:143 final size:142
Alignment explanation
Indices: 570080--570508 Score: 335
Period size: 157 Copynumber: 2.9 Consensus size: 142
570070 CAATAATCCA
* * * *
570080 ATCTTTTACCCTGATTAGAGGGCAGATTCAAGTCATCCTATCTCTTACCCCGACCATGAGACAGA
1 ATCTTTTACCCTAAGTAGAGGGCAGATTCAAGCCATCCAATCTCTTACCCCGACCATGAGACAGA
* * * * * *
570145 TTGAAGCATTCCGATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCCAATC-TTTACCCT
66 TCGAAACAATCCAATCTTTTACCCCAACCAGAGGGCAAATTGAAGA-CATCCAATCTTTTACCCT
570209 AATCAGAGGGCAG
130 AATCAGAGGGCAG
* * * * *
570222 ATCTTTTACCTTAAGTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGGGGCAG
1 ATCTTTTACCCTAAGTAGAGGGCAGATTCAAG-CCATCCAATCTCTTACCCCGACCATGAGACAG
* *
570287 ATCGAAACAATCCAATCTTTTACCCCGACCATG-GGGCAAATTGAAGTA-ATTCAGATCTTTTAC
65 ATCGAAACAATCCAATCTTTTACCCCAACCA-GAGGGCAAATTGAAG-ACATCCA-ATCTTTTAC
* * *
570350 CCTAACTAGAGAGAAGATTGAATTA
127 CCTAA-T-CAGAG--G---GCA--G
* * * *
570375 ATCTAATATTTTACCCCAATTAGAGGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATG-G
1 ATC-----TTTTACCCTAAGTAGAGGGCAGATTCAAGCCATCCAATCTCTTACCCCGACCATGAG
* * * * * * * * * *
570439 TGCAGATTGAAGCAATCCAATCTTTTACCCTAACTAGAGGGCAGATTAAAGATCATTCGATCTCT
61 -ACAGATCGAAACAATCCAATCTTTTACCCCAACCAGAGGGCAAATTGAAGA-CATCCAATCTTT
570504 TACCC
124 TACCC
570509 CGACCATAGG
Statistics
Matches: 230, Mismatches: 34, Indels: 31
0.78 0.12 0.11
Matches are distributed among these distances:
142 32 0.14
143 67 0.29
144 12 0.05
145 1 0.00
146 4 0.02
148 1 0.00
151 2 0.01
153 3 0.01
156 3 0.01
157 75 0.33
158 30 0.13
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (142 bp):
ATCTTTTACCCTAAGTAGAGGGCAGATTCAAGCCATCCAATCTCTTACCCCGACCATGAGACAGA
TCGAAACAATCCAATCTTTTACCCCAACCAGAGGGCAAATTGAAGACATCCAATCTTTTACCCTA
ATCAGAGGGCAG
Found at i:570527 original size:79 final size:79
Alignment explanation
Indices: 570222--570766 Score: 512
Period size: 79 Copynumber: 6.9 Consensus size: 79
570212 CAGAGGGCAG
* * * *
570222 ATCTTTTACCTTAAGTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGGGGCAG
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATAGGGCAG
* *
570287 ATCGAAACAATCCA
66 ATTGAAGCAATCCA
** * * * * ** * * *
570301 ATCTTTTACCCCGACCATG-GGGCAAATTGAAGTA--ATTCAGATCTTTTACCCTAACTAGAGAG
1 ATCTTTTACCCTAACTA-GAGGGCAGATTGAAG-ACCATCCA-ATCTCTTACCCCGACCATAGGG
* ** *
570363 AAGATTGAATTAATCTA
63 CAGATTGAAGCAATCCA
* * * *
570380 ATATTTTACCCCAATTAGAGGGCAGATTGAAG-CCATCCAATCTCTTACCCTGACCAT-GGTGCA
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATAGG-GCA
570443 GATTGAAGCAATCCA
65 GATTGAAGCAATCCA
* * * * *
570458 ATCTTTTACCCTAACTAGAGGGCAGATTAAAGATCATTCGATCTCTTACCCCGACCATAGGGCAA
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATAGGGCAG
*
570523 ATTGAAGCAACCCA
66 ATTGAAGCAATCCA
* * ** ** *
570537 ATCTTTTACTCTAACTAGAAGGCAGATTGAAG-TTATTTAATCTCTTACCTCGACCATAGGGCAG
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATAGGGCAG
*
570601 ATTGAAGTAATCCA
66 ATTGAAGCAATCCA
* * * *
570615 ATCTTTTACCTTAACTAGAGGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAGAGGGTAG
1 ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATAGGGCAG
* * *
570680 ATTAAAGACCATCCG
66 ATTGAAG-CAATCCA
* * * * *
570695 ATCTCTTT-CCCCAACCATG-GGGCAGATTGAAGACCATCCAATCTTTTACCCCAACCAGAGGGC
1 ATCT-TTTACCCTAACTA-GAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATAGGGC
570758 AGATTGAAG
64 AGATTGAAG
570767 ACCATCCGAT
Statistics
Matches: 375, Mismatches: 78, Indels: 25
0.78 0.16 0.05
Matches are distributed among these distances:
77 1 0.00
78 129 0.34
79 175 0.47
80 66 0.18
81 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (79 bp):
ATCTTTTACCCTAACTAGAGGGCAGATTGAAGACCATCCAATCTCTTACCCCGACCATAGGGCAG
ATTGAAGCAATCCA
Done.