Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 2 of 373
Found at i:417267 original size:90 final size:92
Alignment explanation
Indices: 417155--417739 Score: 370
Period size: 104 Copynumber: 5.8 Consensus size: 92
417145 AGCTAAAACA
* * ** *
417155 ACCAGTTTTAAGCTATAAACCCATAAATTTCCTCCATAATTTAATCAACAATTACCCCATTTCAT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATCAACAATAACCCCATTTCAT
417220 T-ATCCACTAGCAAAAACTAAAAG-CC
66 TAATCCACTAGCAAAAACTAAAAGACC
* * *
417245 GCCAATTTTAAGCTGTAAACCCATAAATTTCTTCCATTGTTTAACAATCAACAATCACCCCATTT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTT---AATCAACAATAACCCCATTT
417310 CATTAATCCACTAG-AAAATACTAAAATCCAGCTAAAACC
63 CATTAATCCACTAGCAAAA-ACT-AAA---AG-----ACC
417349 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAA-CAATTACCAATAACCCCATT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATC-A--A-CAATAACCCCATT
**
417413 TCATTAATCCACTAGCAATTACTAAAATCCAGCTGAAACC
62 TCATTAATCCACTAGCAAAAACT-AAA---A---G--ACC
* * * *
417453 AACAATTTTTAAGCTGTAAACCCACAAATTTCCTACATAGTTTAACCATCAACAATAACCCCATT
1 ACCAA-TTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTT-A--ATCAACAATAACCCCATT
* * * **
417518 TCATTAACCCATTATCAATTACTAAAATCCAGCTAAAACC
62 TCATTAATCCACTAGCAAAAACT-AAA---AG-----ACC
* * * *
417558 ACCGATTTTAAGCTGTAAACTCATAAAATTCCTCCATGGTTTAA-CAATCAATGATCACCCCATT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATCAA-CAAT-A--ACCCCATT
* **
417622 TCATTGATCCACTAGCAATTACTAAAATCCAGCAAAACTC
62 TCATTAATCCACTAGCAAAAACT-AAA---AG----AC-C
* * *
417662 ACCAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAACAATCAACAATAACCCCATTT
1 ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTT---AATCAACAATAACCCCATTT
*
417727 CACTAATCCACTA
63 CATTAATCCACTA
417740 TCAATTACCA
Statistics
Matches: 418, Mismatches: 37, Indels: 66
0.80 0.07 0.13
Matches are distributed among these distances:
90 36 0.09
93 27 0.06
94 12 0.03
95 3 0.01
98 2 0.00
100 4 0.01
101 8 0.02
102 2 0.00
103 7 0.02
104 216 0.52
105 85 0.20
106 3 0.01
107 7 0.02
108 5 0.01
109 1 0.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.29
Consensus pattern (92 bp):
ACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAATCAACAATAACCCCATTTCAT
TAATCCACTAGCAAAAACTAAAAGACC
Found at i:417426 original size:104 final size:104
Alignment explanation
Indices: 417236--417798 Score: 770
Period size: 104 Copynumber: 5.4 Consensus size: 104
417226 CTAGCAAAAA
* * * *
417236 CTAAAAGCCGCCAATTTTAAGCTGTAAACCCATAAATTTCTTCCATTGTTTAACAATCAACAATC
1 CTAAAA-CCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATA
* *
417301 ACCCCATTTCATTAATCCACTAGAAAATACTAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* * *
417341 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATTGTTTAACAATTACCAATAA
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATAA
417406 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
66 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* * * * *
417445 CTGAAACCAACAATTTTTAAGCTGTAAACCCACAAATTTCCTACATAGTTTAACCATCAACAATA
1 CTAAAACCACCAA-TTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATA
* * *
417510 ACCCCATTTCATTAACCCATTATCAATTACTAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* * * * ** *
417550 CTAAAACCACCGATTTTAAGCTGTAAACTCATAAAATTCCTCCATGGTTTAACAATCAATGATCA
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATAA
*
417615 CCCCATTTCATTGATCCACTAGCAATTACTAAAATCCAG
66 CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* *
417654 C-AAAACTCACCAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAACAATCAACAATA
1 CTAAAAC-CACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATA
* * *
417718 ACCCCATTTCACTAATCCACTATCAATTACCAAAATCCAG
65 ACCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
* ** *
417758 CTTAAGTCATCAATTTTAAGCTGTAAACCCA-AAATTATCCT
1 CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATT-TCCT
417799 AAAAAAAAGG
Statistics
Matches: 404, Mismatches: 50, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
103 9 0.02
104 295 0.73
105 100 0.25
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (104 bp):
CTAAAACCACCAATTTTAAGCTGTAAACCCATAAATTTCCTCCATAGTTTAACAATCAACAATAA
CCCCATTTCATTAATCCACTAGCAATTACTAAAATCCAG
Found at i:417620 original size:209 final size:208
Alignment explanation
Indices: 417247--417788 Score: 789
Period size: 209 Copynumber: 2.6 Consensus size: 208
417237 TAAAAGCCGC
* * * *
417247 CAATTTTAAGCTGTAAACCCATAAATTTCTTCCATTGTTTAACAATCAACAATCACCCCATTTCA
1 CAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
** * *
417312 TTAATCCACTAGAAAATACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAAT
66 TTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAAA
* * *
417377 TTCCTCCATTGTTTAACAATTACCAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAATC
131 TTCCTCCATGGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAATC
*
417442 CAGCTGAAAC-CAA
196 CAGC-AAAACTCAA
* *
417455 CAATTTTTAAGCTGTAAACCCACAAATTTCCTACATAGTTTAACCATCAACAATAACCCCATTTC
1 CAA-TTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTC
* * * *
417520 ATTAACCCATTATCAATTACTAAAATCCAGCTAAAACCACCGATTTTAAGCTGTAAACTCATAAA
65 ATTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAA
** * *
417585 ATTCCTCCATGGTTTAACAATCAATGATCACCCCATTTCATTGATCCACTAGCAATTACTAAAAT
130 ATTCCTCCATGGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAAT
*
417650 CCAGCAAAACTCAC
195 CCAGCAAAACTCAA
*
417664 CAATTTTAAGCTGTAAACCCATAAAATTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
1 CAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
* * * ** *
417729 CTAATCCACTATCAATTACCAAAATCCAGCTTAAGTCATCAATTTTAAGCTGTAAACCCA
66 TTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCA
417789 AAATTATCCT
Statistics
Matches: 296, Mismatches: 36, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
208 116 0.39
209 180 0.61
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (208 bp):
CAATTTTAAGCTGTAAACCCATAAATTTCCTACATAGTTTAACAATCAACAATAACCCCATTTCA
TTAATCCACTATCAATTACTAAAATCCAGCTAAAACCACCAATTTTAAGCTGTAAACCCATAAAA
TTCCTCCATGGTTTAACAATCAACAATAACCCCATTTCATTAATCCACTAGCAATTACTAAAATC
CAGCAAAACTCAA
Found at i:422334 original size:15 final size:15
Alignment explanation
Indices: 422299--422350 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
422289 TTAAGAATTT
*
422299 TATTAAATTAT-ATA
1 TATTTAATTATAATA
422313 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
422327 TATTTAATAATAAT-
1 TATTTAATTATAATA
422341 TATGTTAATT
1 TAT-TTAATT
422351 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:422384 original size:120 final size:120
Alignment explanation
Indices: 422237--422466 Score: 460
Period size: 120 Copynumber: 1.9 Consensus size: 120
422227 TTTGAGTAAA
422237 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
422302 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
422357 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
422422 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
422467 TAAATATGAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (120 bp):
TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
Found at i:422432 original size:61 final size:61
Alignment explanation
Indices: 422247--422434 Score: 208
Period size: 61 Copynumber: 3.1 Consensus size: 61
422237 TTATAGTATC
422247 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
422308 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATT
422367 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
422428 ATATATT
1 ATATATT
422435 TTAATTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 26 0.27
61 36 0.37
62 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:422449 original size:16 final size:16
Alignment explanation
Indices: 422428--422469 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
422418 TTATTAAATT
*
422428 ATATATTTTAATTATA
1 ATATATTTTAATAATA
422444 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
422459 AT-TATGTTTAA
1 ATATAT-TTTAA
422470 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:422454 original size:15 final size:15
Alignment explanation
Indices: 422419--422460 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
422409 TTAAGAATTT
*
422419 TATTAAATTAT-ATA
1 TATTTAATTATAATA
422433 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
422447 TATTTAATAATAAT
1 TATTTAATTATAAT
422461 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:422695 original size:45 final size:43
Alignment explanation
Indices: 422595--422704 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
422585 TTTTCCATTA
422595 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
422634 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
422679 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
422705 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:422706 original size:16 final size:16
Alignment explanation
Indices: 422685--422752 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
422675 GATTTGCTAT
*
422685 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
422701 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
422717 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
422733 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
422749 TACA
1 TACA
422753 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:423858 original size:19 final size:18
Alignment explanation
Indices: 423810--423858 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
423800 TTTTATATAA
*
423810 TTTATAATTT-TTTTATAT
1 TTTA-AATTTATTTAATAT
*
423828 TTTAACTTTATTTAATAT
1 TTTAAATTTATTTAATAT
423846 TTGTAAATTTATT
1 TT-TAAATTTATT
423859 ATATTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 13 0.50
19 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTAAATTTATTTAATAT
Found at i:428512 original size:20 final size:20
Alignment explanation
Indices: 428487--428536 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
428477 TGGCTTAAAA
428487 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
428507 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
428524 GTGGTAGTGGATT
1 TTGGTAGTGGATT
428537 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:433151 original size:20 final size:20
Alignment explanation
Indices: 433126--433175 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
433116 TGGCTTAAAA
433126 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
433146 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
433163 GTGGTAGTGGATT
1 TTGGTAGTGGATT
433176 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:434490 original size:14 final size:15
Alignment explanation
Indices: 434471--434499 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
434461 GAGCTTACAG
434471 GTTTTTTT-TTCTTT
1 GTTTTTTTATTCTTT
434485 GTTTTTTTATTCTTT
1 GTTTTTTTATTCTTT
434500 CTTATGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (15 bp):
GTTTTTTTATTCTTT
Found at i:451036 original size:18 final size:18
Alignment explanation
Indices: 451015--451054 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
451005 ATTTATGTTT
451015 GTATATATACATATGTAG
1 GTATATATACATATGTAG
451033 GTATATATACATATGTAG
1 GTATATATACATATGTAG
451051 GTAT
1 GTAT
451055 GCATGCGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (18 bp):
GTATATATACATATGTAG
Found at i:451095 original size:18 final size:18
Alignment explanation
Indices: 451008--451096 Score: 70
Period size: 18 Copynumber: 4.6 Consensus size: 18
450998 TGTATGTATT
*
451008 TATGTTTGTATATATACA
1 TATGTATGTATATATACA
*
451026 TATGTAGGTATATATACA
1 TATGTATGTATATATACA
* * *
451044 TATGTAGGTATGCATGCGTGCA
1 TATGTATGTAT--AT--ATACA
*
451066 TTTATGTTTGTATATATACA
1 --TATGTATGTATATATACA
451086 TATGTATGTAT
1 TATGTATGTAT
451097 GCATATATGT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
18 37 0.66
20 5 0.09
22 5 0.09
24 9 0.16
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (18 bp):
TATGTATGTATATATACA
Found at i:451114 original size:42 final size:42
Alignment explanation
Indices: 451033--451120 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
451023 ACATATGTAG
* * *
451033 GTATATATACATATGTAGGTATGCATGCGTGCATTTATGTTT
1 GTATATATACATATGTAGGTATGCATACATGCATTTATGTGT
* * *
451075 GTATATATACATATGTATGTATGCATATATG-TTTGTATGTGT
1 GTATATATACATATGTAGGTATGCATACATGCATT-TATGTGT
451117 GTAT
1 GTAT
451121 TGGTATATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.45
Consensus pattern (42 bp):
GTATATATACATATGTAGGTATGCATACATGCATTTATGTGT
Found at i:452176 original size:21 final size:21
Alignment explanation
Indices: 452141--452227 Score: 56
Period size: 21 Copynumber: 4.2 Consensus size: 21
452131 GGTTTAAAAT
*
452141 TTTGA-GTTTAGGATTTGAGG
1 TTTGAGGTTTAAGATTTGAGG
*
452161 TTTGAGGTTTAAGATTCGA-G
1 TTTGAGGTTTAAGATTTGAGG
* * * *
452181 TTTG-GGATATAAGGTTTAAAG
1 TTTGAGG-TTTAAGATTTGAGG
* *
452202 TTT-AGGGTTCAAGATTTGAGA
1 TTTGA-GGTTTAAGATTTGAGG
452223 TTTGA
1 TTTGA
452228 AATTTGGGAT
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.04
20 18 0.37
21 26 0.53
22 3 0.06
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.41
Consensus pattern (21 bp):
TTTGAGGTTTAAGATTTGAGG
Found at i:453033 original size:64 final size:64
Alignment explanation
Indices: 452915--453055 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 64
452905 ATTTAACACA
* * ** * * **
452915 TATT-GACATATATCTCAACATTTGTGTAGAATTACAACTTTCACGTATTTAAAAAAATACTTG
1 TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATACTTG
*
452978 TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATATTTG
1 TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATACTTG
453042 TATTCGACACATAT
1 TATTCGACACATAT
453056 TAACATATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 4 0.06
64 64 0.94
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (64 bp):
TATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATACTTG
Found at i:453075 original size:138 final size:137
Alignment explanation
Indices: 452828--453277 Score: 465
Period size: 149 Copynumber: 3.2 Consensus size: 137
452818 CGCATATCCA
* * * *
452828 AAAAATAATACTTGTATTTGACACATAT-CTAACATTTATGTACAATTACAACTTCCACATAT-A
1 AAAAA-AATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCA
** ** * ** *
452891 TGGAAAATCGTTATATTTAACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTT
65 -AAAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTC
452956 CACGTATTT
129 CACGTATTT
452965 AAAAAAATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCA
1 AAAAAAATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATAT-CA
* * *
453030 AAAAAATATTTGTATTCGACACATATTAACATATATCTCAACATTTGTGTGGAATTACAACATCC
65 AAAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTCC
*
453095 ACATATTT
130 ACGTATTT
* * * *
453103 AAAAAAAAATACTTGTATTCGATACATATTAACACACATTCCATCATTCGTGTAGAATTATAAAT
1 --AAAAAAATACTTGTATTCGACACATA-T--C-C-CA----A-CATTCATGTAGAATTACAACT
* * * * * * *
453168 TACACATATCTAAAAAATATTTGTATTCGACATATATCGACACATATCCCAACATTCGTGTAGAA
54 TCCACATATCAAAAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAA
453233 TTACAACTTCCACGTATTT
119 TTACAACTTCCACGTATTT
* ** *
453252 -GAAAAATACTTCCATTCGCCACATAT
1 AAAAAAATACTTGTATTCGACACATAT
453278 GAATAATGTA
Statistics
Matches: 262, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
136 21 0.08
137 36 0.14
138 61 0.23
139 1 0.00
140 25 0.10
141 1 0.00
143 1 0.00
144 1 0.00
145 3 0.01
146 20 0.08
149 66 0.25
150 26 0.10
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (137 bp):
AAAAAAATACTTGTATTCGACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCAA
AAAAATATTTGTATTCGACACATATTGACATATATCTCAACATTTGTGTAGAATTACAACTTCCA
CGTATTT
Found at i:453257 original size:73 final size:73
Alignment explanation
Indices: 452984--453277 Score: 309
Period size: 73 Copynumber: 4.0 Consensus size: 73
452974 CTTGTATTCG
* *
452984 ACACATATCCCAACATTCATGTAGAATTACAACTTCCACATATCCAAAAAAATATTTGTATTCGA
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATAT-CTAAAAAATATTTGTATTCGA
*
453049 CACATATTA
65 CACATATCA
* * * * * * *
453058 ACATATATCTCAACATTTGTGTGGAATTACAACATCCACATATTTAAAAAAAAATACTTGTATTC
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCT---AAAAAATATTTGTATTC
* *
453123 GATACATATTA
63 GACACATATCA
* * * * * *
453134 ACACACATTCCATCATTCGTGTAGAATTATAAATTACACATATCTAAAAAATATTTGTATTCGAC
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCTAAAAAATATTTGTATTCGAC
* *
453199 ATATATCG
66 ACATATCA
* * * * ** *
453207 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACGTATTTGAAAAATACTTCCATTCGCC
1 ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCTAAAAAATATTTGTATTCGAC
453272 ACATAT
66 ACATAT
453278 GAATAATGTA
Statistics
Matches: 176, Mismatches: 41, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
73 80 0.45
74 37 0.21
76 59 0.34
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (73 bp):
ACACATATCCCAACATTCGTGTAGAATTACAACTTCCACATATCTAAAAAATATTTGTATTCGAC
ACATATCA
Found at i:456445 original size:18 final size:19
Alignment explanation
Indices: 456406--456447 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
456396 TAAACTATGA
456406 TTTAAATTTTAAATTGATT
1 TTTAAATTTTAAATTGATT
456425 TTTAAATTTTTAAA-T-ATT
1 TTTAAA-TTTTAAATTGATT
456443 TTTAA
1 TTTAA
456448 TTAAGTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAAATTTTAAATTGATT
Found at i:461175 original size:18 final size:18
Alignment explanation
Indices: 461146--461212 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
461136 TCCTCCTCCT
* *
461146 CCTCCTCCTCTTCTTCTT
1 CCTCCTCTTCTTCTTCTA
*
461164 CTTCCTCTTCTTCTTCTA
1 CCTCCTCTTCTTCTTCTA
* *
461182 CCTCCACTTCTTCATACT-
1 CCTCCTCTTCTTC-TTCTA
*
461200 CCACCTCTTCTTC
1 CCTCCTCTTCTTC
461213 CATAGTCTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 37 0.93
19 3 0.08
ACGTcount: A:0.07, C:0.46, G:0.00, T:0.46
Consensus pattern (18 bp):
CCTCCTCTTCTTCTTCTA
Found at i:461191 original size:15 final size:15
Alignment explanation
Indices: 461158--461210 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
461148 TCCTCCTCTT
* **
461158 CTTCTTCTTCCTCTT
1 CTTCTTCTACCTCCA
461173 CTTCTTCTACCTCCA
1 CTTCTTCTACCTCCA
461188 CTTCTTCATA-CTCCA
1 CTTCTTC-TACCTCCA
*
461203 CCTCTTCT
1 CTTCTTCT
461211 TCCATAGTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 1 0.03
15 30 0.91
16 2 0.06
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.47
Consensus pattern (15 bp):
CTTCTTCTACCTCCA
Found at i:463497 original size:18 final size:18
Alignment explanation
Indices: 463469--463503 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
463459 AATTTTTTTT
463469 ATTTTTAA-TTTTAAATA
1 ATTTTTAATTTTTAAATA
463486 ATTTTATAATTTTTAAAT
1 ATTTT-TAATTTTTAAAT
463504 TATTATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTAATTTTTAAATA
Found at i:463699 original size:24 final size:23
Alignment explanation
Indices: 463645--463700 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
463635 AAAGATTAAT
463645 AATTAAATTTAACTAAAAAATAAA
1 AATTAAA-TTAACTAAAAAATAAA
*
463669 AACTAAATTAAC-AAAATATATAAA
1 AATTAAATTAACTAAAA-A-ATAAA
*
463693 TATTAAAT
1 AATTAAAT
463701 ACATTTGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 6 0.22
24 17 0.63
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
AATTAAATTAACTAAAAAATAAA
Found at i:476420 original size:100 final size:100
Alignment explanation
Indices: 476247--476697 Score: 503
Period size: 100 Copynumber: 4.5 Consensus size: 100
476237 AAATATATGG
* * * * * * * *
476247 AAGTAATTATCCCGTATCACCGCCGTCACACGATATCTCTTGAGGCAAGGATCAAATGATCAAAT
1 AAGTAATAATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAAT
* *
476312 TAAGACTACGTATTACATAACCATGATTCATACAC
66 TAAGACTACATATTACATAACCATGATTCATATAC
* * * ** ** *
476347 AAGTAATAAGCCCTTATCAAGGCTGTCACACAATTTCTCTCGAGGCAAGGATTGAGTGAGCAAAT
1 AAGTAATAATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAAT
*
476412 TAAGACTACATATTACATAACCGTGATTCATATAC
66 TAAGACTACATATTACATAACCATGATTCATATAC
* * ** * *
476447 AAGTAA-ATATCCCATATCATCGCCATCACACAATTGCTCTTAAGGCGAGGATCAAATGATCAAA
1 AAGTAATA-ATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAA
* *
476511 TCAAGACTACATAGTACATAACCATGATTCATATAC
65 TTAAGACTACATATTACATAACCATGATTCATATAC
* * *
476547 AAGTAATAATCCCATATC-ACTGCCATCACACGATTTCTCTCGTGGCAAGTATCAAATGAGCAAA
1 AAGTAATAATCCCATATCAAC-GCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAA
* *
476611 TTAAGACTACATATTACATAACCATTATTCATATGC
65 TTAAGACTACATATTACATAACCATGATTCATATAC
* * * * * * *
476647 AAGTAA-ATATCCCGTATCATCGCCACCACGCGATTTCTCTCAAAGCAAGGA
1 AAGTAATA-ATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGA
476698 CCGATACAGT
Statistics
Matches: 292, Mismatches: 54, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
99 3 0.01
100 287 0.98
101 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (100 bp):
AAGTAATAATCCCATATCAACGCCATCACACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAAT
TAAGACTACATATTACATAACCATGATTCATATAC
Found at i:476643 original size:200 final size:200
Alignment explanation
Indices: 476247--476671 Score: 600
Period size: 200 Copynumber: 2.1 Consensus size: 200
476237 AAATATATGG
* * * * *
476247 AAGTAATTATCCCGTATCACCGCCGTCACACGATATCTCTTGAGGCAAGGATCAAATGATCAAAT
1 AAGTAAATATCCCGTATCATCGCCATCACACAATATCTCTTAAGGCAAGGATCAAATGATCAAAT
* * * * **
476312 TAAGACTACGTATTACATAACCATGATTCATACACAAGTAATAAGCCCTTATCAAGGCTGTCACA
66 CAAGACTACATAGTACATAACCATGATTCATACACAAGTAATAAGCCCATATCAAGGCCATCACA
** * *
476377 CAATTTCTCTCGAGGCAAGGATTGAGTGAGCAAATTAAGACTACATATTACATAACCGTGATTCA
131 CAATTTCTCTCGAGGCAAGGATCAAATGAGCAAATTAAGACTACATATTACATAACCATGATTCA
476442 TATAC
196 TATAC
* *
476447 AAGTAAATATCCCATATCATCGCCATCACACAAT-TGCTCTTAAGGCGAGGATCAAATGATCAAA
1 AAGTAAATATCCCGTATCATCGCCATCACACAATAT-CTCTTAAGGCAAGGATCAAATGATCAAA
* * **
476511 TCAAGACTACATAGTACATAACCATGATTCATATACAAGTAATAATCCCATATCACTGCCATCAC
65 TCAAGACTACATAGTACATAACCATGATTCATACACAAGTAATAAGCCCATATCAAGGCCATCAC
* * * *
476576 ACGATTTCTCTCGTGGCAAGTATCAAATGAGCAAATTAAGACTACATATTACATAACCATTATTC
130 ACAATTTCTCTCGAGGCAAGGATCAAATGAGCAAATTAAGACTACATATTACATAACCATGATTC
*
476641 ATATGC
195 ATATAC
476647 AAGTAAATATCCCGTATCATCGCCA
1 AAGTAAATATCCCGTATCATCGCCA
476672 CCACGCGATT
Statistics
Matches: 197, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
199 1 0.01
200 196 0.99
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (200 bp):
AAGTAAATATCCCGTATCATCGCCATCACACAATATCTCTTAAGGCAAGGATCAAATGATCAAAT
CAAGACTACATAGTACATAACCATGATTCATACACAAGTAATAAGCCCATATCAAGGCCATCACA
CAATTTCTCTCGAGGCAAGGATCAAATGAGCAAATTAAGACTACATATTACATAACCATGATTCA
TATAC
Found at i:477357 original size:24 final size:24
Alignment explanation
Indices: 477308--477365 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
477298 AAAATAACTC
* *
477308 TTAA-TATTTATATTTTATGTAAT
1 TTAACTATTTTTATTTTATATAAT
477331 TTAACTATTTTTATTTT-TATAAT
1 TTAACTATTTTTATTTTATATAAT
* *
477354 TTTACTTTTTTT
1 TTAACTATTTTT
477366 TGACATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (24 bp):
TTAACTATTTTTATTTTATATAAT
Found at i:477580 original size:25 final size:25
Alignment explanation
Indices: 477546--477593 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
477536 TACGAGTTAG
477546 ATTTTTAGAATCAAAGCTAATTTAA
1 ATTTTTAGAATCAAAGCTAATTTAA
477571 ATTTTTAGAATCAAAGCTAATTT
1 ATTTTTAGAATCAAAGCTAATTT
477594 GAGACAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTTTTAGAATCAAAGCTAATTTAA
Found at i:480522 original size:15 final size:16
Alignment explanation
Indices: 480493--480537 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
480483 AATGCGCTTC
*
480493 ATTTATTAT-TTATAT
1 ATTTATTATATAATAT
480508 AATTT-TTATA-AATAT
1 -ATTTATTATATAATAT
480523 ATTTATTATATAATA
1 ATTTATTATATAATA
480538 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.16
15 13 0.52
16 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTATTATATAATAT
Found at i:481691 original size:44 final size:44
Alignment explanation
Indices: 481639--481728 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
481629 AAAACTAAAA
481639 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
1 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
481683 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
1 TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
481727 TT
1 TT
481729 CCTGAGCAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (44 bp):
TTGTAAGGATAATTATTTAGTCCACTAACAATGGAGTAAAATTC
Found at i:485243 original size:43 final size:43
Alignment explanation
Indices: 485189--485279 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
485179 TTAAGCTAAC
* * *
485189 TTCTATGATTATAAAAATGGGTAATTAAAAG-ACAAATTTCAGA
1 TTCTTTGATTATAAAAATGGATAATTAAAAGCA-AAAATTCAGA
*
485232 TTCTTTGATTATTAAAATGGATAATTAAAAGCAAAAATTCAGA
1 TTCTTTGATTATAAAAATGGATAATTAAAAGCAAAAATTCAGA
485275 TTCTT
1 TTCTT
485280 GTAAATTGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (43 bp):
TTCTTTGATTATAAAAATGGATAATTAAAAGCAAAAATTCAGA
Found at i:485374 original size:16 final size:15
Alignment explanation
Indices: 485353--485399 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
485343 TTATGGAGAT
485353 TTTTAAAATATTAATA
1 TTTTAAAAT-TTAATA
485369 TTTTAAAATTT-ATCA
1 TTTTAAAATTTAAT-A
*
485384 ATTTAAAATGTTAATA
1 TTTTAAAAT-TTAATA
485400 AGTATAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 12 0.44
17 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TTTTAAAATTTAATA
Found at i:486085 original size:43 final size:43
Alignment explanation
Indices: 486019--486104 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
486009 TACAAATATG
*
486019 TAAGGCAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
1 TAAGACAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
**
486062 TAAGACAACCAATTTGATGTCTTTTCCAACTTTCTACCCAACC
1 TAAGACAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
486105 CATTCCTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (43 bp):
TAAGACAACCAATTTGATGTCTTTTCCAACTTAATACCCAACC
Found at i:486163 original size:32 final size:34
Alignment explanation
Indices: 486122--486264 Score: 132
Period size: 32 Copynumber: 4.0 Consensus size: 34
486112 GATTAAACCA
*
486122 ACCAATTTGATCAA-ATCCAAACATCCAT-ATGG
1 ACCAATTTGATCAAGATCAAAACATCCATGATGG
*
486154 ACCAATTTGATCAAGTTCAAAACATCCATGATGG
1 ACCAATTTGATCAAGATCAAAACATCCATGATGG
*
486188 AAACAAGAGTTTCAATTTGATCAA-ATCCAAACATCCATG-TGG
1 --AC--------CAATTTGATCAAGATCAAAACATCCATGATGG
*
486230 ACCAATTTGATCAAGTTCAAAACATCCATGATGG
1 ACCAATTTGATCAAGATCAAAACATCCATGATGG
486264 A
1 A
486265 AACAAGAGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 26
0.74 0.05 0.21
Matches are distributed among these distances:
32 26 0.29
33 25 0.27
34 8 0.09
36 2 0.02
40 2 0.02
42 3 0.03
43 13 0.14
44 12 0.13
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (34 bp):
ACCAATTTGATCAAGATCAAAACATCCATGATGG
Found at i:486206 original size:44 final size:44
Alignment explanation
Indices: 486156--486275 Score: 138
Period size: 33 Copynumber: 3.0 Consensus size: 44
486146 CCATATGGAC
486156 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
1 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
* *
486200 CAATTTGATCAA-ATCCAAACATCCATG-TGG--AC--------
1 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
486232 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
1 CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
486276 TGCAAGAATC
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
32 12 0.20
33 13 0.22
34 3 0.05
36 2 0.03
40 2 0.03
42 3 0.05
43 13 0.22
44 12 0.20
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (44 bp):
CAATTTGATCAAGTTCAAAACATCCATGATGGAAACAAGAGTTT
Found at i:486250 original size:76 final size:76
Alignment explanation
Indices: 486124--486275 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
486114 TTAAACCAAC
486124 CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
1 CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
486189 AACAAGAGTTT
66 AACAAGAGTTT
*
486200 CAATTTGATCAAATCCAAACATCCATGTGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
1 CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
486265 AACAAGAGTTT
66 AACAAGAGTTT
486276 TGCAAGAATC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (76 bp):
CAATTTGATCAAATCCAAACATCCATATGGACCAATTTGATCAAGTTCAAAACATCCATGATGGA
AACAAGAGTTT
Found at i:496786 original size:21 final size:21
Alignment explanation
Indices: 496762--496801 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
496752 TTTAATAGAT
*
496762 TAAAATTAAA-AAATGTTAAAA
1 TAAAATAAAATAAAT-TTAAAA
496783 TAAAATAAAATAAATTTAA
1 TAAAATAAAATAAATTTAA
496802 TTCTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
TAAAATAAAATAAATTTAAAA
Found at i:506220 original size:19 final size:18
Alignment explanation
Indices: 506170--506220 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
506160 TTTATGAATT
506170 TTTTATAATTATTTTTAAA
1 TTTTA-AATTATTTTTAAA
* *
506189 -TTTGATTTAATTTTATAAA
1 TTTTAAATT-ATTTT-TAAA
506208 TTTTAAATTATTT
1 TTTTAAATTATTT
506221 ATTGATGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 8 0.32
20 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTAAATTATTTTTAAA
Found at i:507601 original size:6 final size:6
Alignment explanation
Indices: 507590--507619 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
507580 CCAAAATTTA
507590 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
507620 CTTTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:511149 original size:24 final size:24
Alignment explanation
Indices: 511122--511167 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
511112 ATAACCTCTT
511122 TATAAAATT-TTAACAAATGAAAAA
1 TATAAAATTATTAA-AAATGAAAAA
* *
511146 TATATAATTATTAAATATGAAA
1 TATAAAATTATTAAAAATGAAA
511168 TTAAAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (24 bp):
TATAAAATTATTAAAAATGAAAAA
Found at i:514098 original size:22 final size:22
Alignment explanation
Indices: 514070--514134 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
514060 AATTTAAATT
514070 TTATATTTATCAAATAATTTAA
1 TTATATTTATCAAATAATTTAA
*
514092 TTATATTTCAT-AATTAATTTTAA
1 TTATATTT-ATCAAATAA-TTTAA
* *
514115 GTA-ATATATCAAATATATTT
1 TTATATTTATCAAATA-ATTT
514135 TTAACTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.06
22 23 0.66
23 10 0.29
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TTATATTTATCAAATAATTTAA
Found at i:518480 original size:29 final size:30
Alignment explanation
Indices: 518415--518482 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
518405 AATTTTAAAA
*
518415 TTATACATGAATTTTAGTTTAATGTATAATT
1 TTATACATGAATTTGAGTTT-ATGTATAATT
* *
518446 GTATACATGAACTTTGA-TTT-TGTGTAATT
1 TTATACATGAA-TTTGAGTTTATGTATAATT
518475 TTATACAT
1 TTATACAT
518483 AAAATTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 15 0.47
31 13 0.41
32 4 0.12
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (30 bp):
TTATACATGAATTTGAGTTTATGTATAATT
Found at i:521315 original size:3 final size:3
Alignment explanation
Indices: 521307--521335 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
521297 ATCCCTTGCT
521307 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
521336 TATAACTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:522975 original size:31 final size:27
Alignment explanation
Indices: 522931--522996 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
522921 AAAACAACTT
522931 TTAGTTCTTGAACTTAGCAATTTTTCCCAAC
1 TTAG-TCTTGAACTT--C-ATTTTTCCCAAC
* *
522962 TTAGTCTTAGAACTTCTTTTTTTCCAAC
1 TTAGTCTT-GAACTTCATTTTTCCCAAC
522990 TTAGTCT
1 TTAGTCT
522997 AAGTTCACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 17 0.53
29 1 0.03
30 4 0.12
31 10 0.31
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (27 bp):
TTAGTCTTGAACTTCATTTTTCCCAAC
Found at i:525152 original size:21 final size:23
Alignment explanation
Indices: 525126--525169 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
525116 AATTTCAAAA
525126 TAAATAT-AAA-TAAAAAAAATT
1 TAAATATCAAATTAAAAAAAATT
*
525147 TAAATATCAAATTAAGAAAAATT
1 TAAATATCAAATTAAAAAAAATT
525170 GACAAGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAATATCAAATTAAAAAAAATT
Found at i:525395 original size:15 final size:13
Alignment explanation
Indices: 525365--525394 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
525355 TTAACATTAA
525365 TTTTATTATAGAT
1 TTTTATTATAGAT
*
525378 TTTTATTATATAT
1 TTTTATTATAGAT
525391 TTTT
1 TTTT
525395 TATATAGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTATTATAGAT
Found at i:530806 original size:7 final size:7
Alignment explanation
Indices: 530796--530822 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
530786 TTTATTGTTT
530796 ATAAATA
1 ATAAATA
530803 ATAAATA
1 ATAAATA
530810 ATAAATA
1 ATAAATA
530817 ATAAAT
1 ATAAAT
530823 TATATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATAAATA
Found at i:530872 original size:15 final size:16
Alignment explanation
Indices: 530852--530883 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
530842 TTTTATAATT
530852 AATTTTAAA-AATAAA
1 AATTTTAAATAATAAA
530867 AATTTTAAATAATAAA
1 AATTTTAAATAATAAA
530883 A
1 A
530884 TGCGGATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTTTAAATAATAAA
Found at i:536254 original size:13 final size:13
Alignment explanation
Indices: 536236--536260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
536226 ATGAAATGTG
536236 ATTTCAATTTTAA
1 ATTTCAATTTTAA
536249 ATTTCAATTTTA
1 ATTTCAATTTTA
536261 TAGGGATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTCAATTTTAA
Found at i:536385 original size:19 final size:19
Alignment explanation
Indices: 536348--536385 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
536338 AGGACTCACT
536348 AAGCTCACTGTAAGTTTTTA
1 AAGCTCACTGT-AGTTTTTA
536368 AAGCTCACTTGT-GTTTTT
1 AAGCTCAC-TGTAGTTTTT
536386 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 8 0.47
21 3 0.18
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.45
Consensus pattern (19 bp):
AAGCTCACTGTAGTTTTTA
Found at i:536951 original size:150 final size:149
Alignment explanation
Indices: 536678--537188 Score: 543
Period size: 150 Copynumber: 3.5 Consensus size: 149
536668 AACACTCTTG
*
536678 GTATGAATTCGTAATCTTAAATGATCGTGTTTCAAAAGTTAACTTAGTTTGCATTTTGTGTTT-G
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTAGTTTGCA--TTGTGTTTCG
* * *
536742 AAATTGAAGTTTGAGATCAAAGTTGTTAAGAATATGGTCTGTATATTTGGGAGCCGAGTGTTGGG
64 AAATCGAAGTTTGATATCAAAGTTGTTAAGAATAAGGTCTGTATATTTGGGAGCCGAGTGTTGGG
*
536807 ATGGTAAGTACTTCCCGATTA
129 ATGGGAAGTACTTCCCGATTA
** ** *
536828 GTATGAATTCGTAATCTTAAACCATCACGATTCGAAAGTTAACTTAGTTTGCATTGTGTTTCGAA
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTAGTTTGCATTGTGTTTCGAA
* * * **
536893 ATCGAATTTTGATATCAAAGTTGTTAAGAATACAGTTCTGTTTATTTGGGAGTGGAGTGTTGGGA
66 ATCGAAGTTTGATATCAAAGTTGTTAAGAATA-AGGTCTGTATATTTGGGAGCCGAGTGTTGGGA
* * *
536958 TGGGAATTACTTCCTGATTG
130 TGGGAAGTACTTCCCGATTA
* * * *
536978 GTATGAATTTGTAATCATAAATGATCGTGTTTCGAATGTTAAC-TAGGTTTGCATTTTGTGTTCG
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTA-GTTTGCATTGTGT-TTCG
** **
537042 AAATCGAAGTTTGAGT-TTGAAGTTGTTAAG----A-------ATA-TTGGGAGTGGAGTGTTGG
64 AAATCGAAGTTTGA-TATCAAAGTTGTTAAGAATAAGGTCTGTATATTTGGGAGCCGAGTGTTGG
* *
537094 AATGGGAAGTACTTCCCGATTG
128 GATGGGAAGTACTTCCCGATTA
* * *
537116 GTATGAATTCGTAATCATAAATGATCGTGTTTC-AGATGTTAACTTGGTTTGCATTTTGTGTTT-
1 GTATGAATTCGTAATCTTAAATGATCGTGTTTCGA-AAGTTAACTTAGTTTGCA--TTGTGTTTC
537179 GAAATCGAAG
63 GAAATCGAAG
537189 ATAGAATCTG
Statistics
Matches: 315, Mismatches: 37, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
137 1 0.00
138 94 0.30
139 5 0.02
140 5 0.02
146 1 0.00
148 8 0.03
149 34 0.11
150 137 0.43
151 29 0.09
152 1 0.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.39
Consensus pattern (149 bp):
GTATGAATTCGTAATCTTAAATGATCGTGTTTCGAAAGTTAACTTAGTTTGCATTGTGTTTCGAA
ATCGAAGTTTGATATCAAAGTTGTTAAGAATAAGGTCTGTATATTTGGGAGCCGAGTGTTGGGAT
GGGAAGTACTTCCCGATTA
Found at i:537158 original size:138 final size:138
Alignment explanation
Indices: 536938--537188 Score: 432
Period size: 138 Copynumber: 1.8 Consensus size: 138
536928 TTCTGTTTAT
* * * *
536938 TTGGGAGTGGAGTGTTGGGATGGGAATTACTTCCTGATTGGTATGAATTTGTAATCATAAATGAT
1 TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
537003 CGTGTTTCGAATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGTTTGAAGTTGT
66 CGTGTTTCGAATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGTTTGAAGTTGT
537068 TAAGAATA
131 TAAGAATA
537076 TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
1 TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
* *
537141 CGTGTTTC-AGATGTTAACTTGGTTTGCATTTTGTGTTTGAAATCGAAG
66 CGTGTTTCGA-ATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAG
537189 ATAGAATCTG
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
137 1 0.01
138 105 0.99
ACGTcount: A:0.25, C:0.08, G:0.28, T:0.38
Consensus pattern (138 bp):
TTGGGAGTGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATCATAAATGAT
CGTGTTTCGAATGTTAACTAGGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGTTTGAAGTTGT
TAAGAATA
Found at i:541760 original size:26 final size:26
Alignment explanation
Indices: 541724--541807 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
541714 TGATACAAAT
* *
541724 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
541750 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
541776 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
541802 TGATAA
1 TGATAA
541808 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:544804 original size:14 final size:14
Alignment explanation
Indices: 544753--544807 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
544743 ATGTATAGGG
*
544753 GGTTTGCATGCATCAA
1 GGTTTGCA--CATAAA
*
544769 GGTTCGCACATAAA
1 GGTTTGCACATAAA
*
544783 GAGTTTGCACTTAAA
1 G-GTTTGCACATAAA
544798 GGTTTGCACA
1 GGTTTGCACA
544808 AGTAAGCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 14 0.42
15 12 0.36
16 7 0.21
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (14 bp):
GGTTTGCACATAAA
Found at i:544903 original size:22 final size:22
Alignment explanation
Indices: 544821--544907 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
544811 AAGCATGCGA
544821 GGTTCACATGGTAAACTAGGTAG
1 GGTTCACATGGTAAA-TAGGTAG
* * * * * *
544844 GGTTTACATGTTTAGACATGTAA
1 GGTTCACATG-GTAAATAGGTAG
** **
544867 GGTTTGCATATTAAATAGGTAG
1 GGTTCACATGGTAAATAGGTAG
544889 GGTTCACATGGTAAATAGG
1 GGTTCACATGGTAAATAGG
544908 GTTCGCATGT
Statistics
Matches: 47, Mismatches: 16, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
22 23 0.49
23 21 0.45
24 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (22 bp):
GGTTCACATGGTAAATAGGTAG
Found at i:544909 original size:18 final size:18
Alignment explanation
Indices: 544886--544921 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
544876 ATTAAATAGG
544886 TAGGGTTCACATGGTAAA
1 TAGGGTTCACATGGTAAA
* *
544904 TAGGGTTCGCATGTTAAA
1 TAGGGTTCACATGGTAAA
544922 CATGTAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (18 bp):
TAGGGTTCACATGGTAAA
Found at i:545044 original size:15 final size:15
Alignment explanation
Indices: 545024--545076 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
545014 ATCAACTACA
545024 GTTCGCCTAATAGGG
1 GTTCGCCTAATAGGG
*
545039 GTTCGCCT-ATAGGA
1 GTTCGCCTAATAGGG
* *
545053 GTTCACATAA-AGGGG
1 GTTCGCCTAATA-GGG
545068 GTTCGCCTA
1 GTTCGCCTA
545077 TTAATTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (15 bp):
GTTCGCCTAATAGGG
Found at i:545056 original size:14 final size:15
Alignment explanation
Indices: 545023--545056 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
545013 TATCAACTAC
545023 AGTTCGCCTAATAGG
1 AGTTCGCCTAATAGG
*
545038 GGTTCGCCT-ATAGG
1 AGTTCGCCTAATAGG
545052 AGTTC
1 AGTTC
545057 ACATAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (15 bp):
AGTTCGCCTAATAGG
Found at i:546007 original size:4 final size:5
Alignment explanation
Indices: 545980--546008 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
545970 GCGAAACAAT
545980 ATAAA ATAAA ATAAA ATAAA AT-AA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
546009 GCACTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:546447 original size:26 final size:25
Alignment explanation
Indices: 546418--546482 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
546408 AAAAATAAGT
546418 GTATATGTATATATATAGTACAAAAA
1 GTATATGTATATATATA-TACAAAAA
*
546444 GTATGCATGTA-A-ATATATAGAAAAA
1 GTAT--ATGTATATATATATACAAAAA
*
546469 -TATATTTATATATA
1 GTATATGTATATATA
546483 AAAGAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 6 0.18
25 7 0.21
26 9 0.27
27 1 0.03
28 5 0.15
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (25 bp):
GTATATGTATATATATATACAAAAA
Found at i:546492 original size:21 final size:21
Alignment explanation
Indices: 546456--546507 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
546446 ATGCATGTAA
* *
546456 ATATATAGAAAAATATA-TTT
1 ATATATAAAAAAATATACTGT
546476 ATATATAAAAGAAATATACGTGT
1 ATATATAAAA-AAATATAC-TGT
546499 ATATATAAA
1 ATATATAAA
546508 GCAACTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
23 11 0.41
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.35
Consensus pattern (21 bp):
ATATATAAAAAAATATACTGT
Found at i:548680 original size:41 final size:40
Alignment explanation
Indices: 548631--548749 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 40
548621 TTTGACTTTG
*
548631 AGTTGATGAGACACTGGGTATCAATTTATTACTTCGGATTA
1 AGTTGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTA
* * * *
548672 ATTTGATGAGGCACTGGGTGCCAA-T-TTACTTC-GATTT
1 AGTTGATGAGACACTGGGTGTCAATTATTACTTCGGATTA
* * *
548709 AGCTGATGAGACACTGGGTGTCAACTTATTGCTTCGAATTA
1 AGTTGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTA
548750 TCCGATGAGG
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
37 24 0.39
38 7 0.11
39 2 0.03
40 6 0.10
41 23 0.37
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (40 bp):
AGTTGATGAGACACTGGGTGTCAATTATTACTTCGGATTA
Found at i:551293 original size:18 final size:17
Alignment explanation
Indices: 551272--551330 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 17
551262 TTATTACTTA
551272 TATTATCATTATTATCAT
1 TATTAT-ATTATTATCAT
*
551290 TATTATTATTA-TATCAC
1 TATTA-TATTATTATCAT
*
551307 TATT-TATTATTGT-AT
1 TATTATATTATTATCAT
551322 TATTATATT
1 TATTATATT
551331 CATTTTCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 10 0.29
16 6 0.17
17 9 0.26
18 9 0.26
19 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTATATTATTATCAT
Found at i:554022 original size:12 final size:12
Alignment explanation
Indices: 553998--554038 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
553988 AGTATAACAA
*
553998 TAAATTTAA-AT
1 TAAAATTAATAT
554009 TAAAATTAATAT
1 TAAAATTAATAT
*
554021 TAATATTAATA-
1 TAAAATTAATAT
554032 TAAAATT
1 TAAAATT
554039 GTAAACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:555892 original size:50 final size:50
Alignment explanation
Indices: 555817--555916 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
555807 TGTCAACATG
* *
555817 CCATAATGTTCTATTAATACTGAGACTGGAGCATTTGTGTTGAAGGAGTT
1 CCATAATATTCTATTAATACTGAGACTGAAGCATTTGTGTTGAAGGAGTT
** *
555867 CCATAATATTCTATTAATGTTGAGACTGAAGCATTTGTGTTGATGGAGTT
1 CCATAATATTCTATTAATACTGAGACTGAAGCATTTGTGTTGAAGGAGTT
555917 TATCCTTCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (50 bp):
CCATAATATTCTATTAATACTGAGACTGAAGCATTTGTGTTGAAGGAGTT
Found at i:559681 original size:17 final size:17
Alignment explanation
Indices: 559656--559689 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
559646 ATTAACAAAT
*
559656 AATTCAAAATTTCATAA
1 AATTCAAAAATTCATAA
*
559673 AATTTAAAAATTCATAA
1 AATTCAAAAATTCATAA
559690 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTCAAAAATTCATAA
Found at i:560804 original size:19 final size:19
Alignment explanation
Indices: 560762--560804 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
560752 CTATATAATT
* *
560762 GATACTATTTAATAATTAA
1 GATAATATTTAATAATAAA
*
560781 GATAATATTTAATTATAAA
1 GATAATATTTAATAATAAA
*
560800 TATAA
1 GATAA
560805 ATAACATTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (19 bp):
GATAATATTTAATAATAAA
Found at i:561821 original size:75 final size:75
Alignment explanation
Indices: 561721--561982 Score: 395
Period size: 75 Copynumber: 3.5 Consensus size: 75
561711 TTTTCGAGGT
* *
561721 TTGGGTCATTGTCTCGAGGGTTAGAAATCTAGTTACCATAACTATGCAATAGGCAACTTGTTAAC
1 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAAC
561786 CAATTGGAGA
66 CAATTGGAGA
* *
561796 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCTTACCTATGCCATAGGCAACTTGTTAAC
1 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAAC
* * *
561861 CAATCGAAGC
66 CAATTGGAGA
* * *
561871 TT-GGTCCATTG--TCGAGGGTTAGAAATCTAGTTTCCATACCAATGCAATAGGCAACTTGTTAA
1 TTGGGT-CATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAA
561933 CCAATTGGAGA
65 CCAATTGGAGA
*
561944 TTGGGTCATTGTCTCGAGGGATAGAAATCTGGTTACCAT
1 TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCAT
561983 CGATTTTGAT
Statistics
Matches: 165, Mismatches: 18, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
73 61 0.37
74 6 0.04
75 98 0.59
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (75 bp):
TTGGGTCATTGTCTCGAGGGATAGAAATCTAGTTACCATACCTATGCAATAGGCAACTTGTTAAC
CAATTGGAGA
Found at i:570930 original size:45 final size:45
Alignment explanation
Indices: 570881--571040 Score: 241
Period size: 45 Copynumber: 3.6 Consensus size: 45
570871 GGTATTATGA
* * *
570881 CCTGCTAGGCTCGAAA-GCCTGAATAGTATCTCACCGGCATTATAG
1 CCTGCTAGGCTC-AAAGGCCCGAATAGTGTCTCACCGGCATAATAG
570926 CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
** *
570971 CCTGCTAGGCTCAAAGGCTTGAATAGTGTCTCACCAGCATAATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
*
571016 CTTGCTAGGCTCAAAGGCCCGAATA
1 CCTGCTAGGCTCAAAGGCCCGAATA
571041 TAATACCAGC
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
44 3 0.03
45 102 0.97
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (45 bp):
CCTGCTAGGCTCAAAGGCCCGAATAGTGTCTCACCGGCATAATAG
Found at i:571124 original size:38 final size:38
Alignment explanation
Indices: 571033--571171 Score: 183
Period size: 38 Copynumber: 3.7 Consensus size: 38
571023 GGCTCAAAGG
* * *
571033 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTT-A
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
571070 TCC-GATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
571107 CCCGGATATATTACCAGCACGAAGCCTGCGAGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* **
571145 CCCGGATATATTTTCAGCACGAAGCCT
1 CCCGGATATAATACCAGCACGAAGCCT
571172 ACAGGTCTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
36 29 0.32
37 5 0.05
38 57 0.63
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:572944 original size:20 final size:21
Alignment explanation
Indices: 572913--572953 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
572903 GTAGGAATGT
572913 TTTCTAAAAATTATGCATTGA
1 TTTCTAAAAATTATGCATTGA
*
572934 TTTCT-AAAATTTTGCATTGA
1 TTTCTAAAAATTATGCATTGA
572954 CATTATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTCTAAAAATTATGCATTGA
Found at i:575619 original size:20 final size:21
Alignment explanation
Indices: 575571--575622 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
575561 AAACCTTGGT
*
575571 AGGTATCGATA-CTTTTCTTA
1 AGGTATCGATATATTTTCTTA
*
575591 AGGTGTCGATATATTTTC-TA
1 AGGTATCGATATATTTTCTTA
*
575611 ATGTATCGATAT
1 AGGTATCGATAT
575623 TTCTGCTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (21 bp):
AGGTATCGATATATTTTCTTA
Found at i:576162 original size:2 final size:2
Alignment explanation
Indices: 576155--576187 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
576145 GAGTAAAAAT
576155 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
576188 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:579632 original size:21 final size:21
Alignment explanation
Indices: 579605--579653 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
579595 ATTGAAATAA
*
579605 AAAAAAATATTGGCT-TCTATT
1 AAAAAAATATTAGCTCT-TATT
*
579626 TAAAAAATATTAGCTCTTATT
1 AAAAAAATATTAGCTCTTATT
579647 AAAAAAA
1 AAAAAAA
579654 ATATAGCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (21 bp):
AAAAAAATATTAGCTCTTATT
Found at i:579986 original size:22 final size:22
Alignment explanation
Indices: 579961--580003 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
579951 TCTCCCTATT
579961 TTGCTACCATTTCATTATTATG
1 TTGCTACCATTTCATTATTATG
* **
579983 TTGCTACTATTTTGTTATTAT
1 TTGCTACCATTTCATTATTAT
580004 TGTTTAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGCTACCATTTCATTATTATG
Found at i:589435 original size:15 final size:15
Alignment explanation
Indices: 589415--589444 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
589405 AAAGCAAATA
589415 AACTAGGAAGATCAT
1 AACTAGGAAGATCAT
589430 AACTAGGAAGATCAT
1 AACTAGGAAGATCAT
589445 TTTATAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
AACTAGGAAGATCAT
Found at i:600495 original size:22 final size:23
Alignment explanation
Indices: 600469--600511 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
600459 TAAAATAAAA
**
600469 TTAGGGATTTAGGTT-ATTTTTG
1 TTAGGGAAATAGGTTGATTTTTG
600491 TTAGGGAAATAGGTTGATTTT
1 TTAGGGAAATAGGTTGATTTT
600512 GGAGAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (23 bp):
TTAGGGAAATAGGTTGATTTTTG
Found at i:613661 original size:77 final size:77
Alignment explanation
Indices: 613580--613743 Score: 256
Period size: 77 Copynumber: 2.1 Consensus size: 77
613570 TCTGCTTGGA
* *
613580 GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAATTTTCTGGGTTTCTTTTTGGTGTTTGTTT
1 GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAACTTTCTGGATTTCTTTTTGGTGTTTGTTT
*
613645 GGTGAAAAAATG
66 GATGAAAAAATG
* **
613657 GAGGTAAAGTAAATTCTGGGTGTTTCTTTGATTTTGCTTTCTGGATTTCTTTTTGGTGTTTGTTT
1 GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAACTTTCTGGATTTCTTTTTGGTGTTTGTTT
*
613722 GATGAGAAAATG
66 GATGAAAAAATG
*
613734 AAGGTAAAGT
1 GAGGTAAAGT
613744 TTAACAATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (77 bp):
GAGGTAAAGTAAATTCTGGGTATTTCTTTGATTTAACTTTCTGGATTTCTTTTTGGTGTTTGTTT
GATGAAAAAATG
Found at i:625168 original size:15 final size:14
Alignment explanation
Indices: 625148--625180 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
625138 GATTAAATCA
625148 ATTTTTAATAATATT
1 ATTTTTAATAAT-TT
625163 ATTTTTAATAATTT
1 ATTTTTAATAATTT
625177 ATTT
1 ATTT
625181 AATTAAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTTAATAATTT
Found at i:626515 original size:31 final size:29
Alignment explanation
Indices: 626454--626521 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
626444 ACAGTAATAG
* *
626454 ATTTTAGTTTATATACTTTGATTTGATCA
1 ATTTTAGTTTATAGACTTTGATTAGATCA
626483 ATTTTAGTTTATAGACTTTTTGAATTAG-TCA
1 ATTTTAGTTTATAGAC--TTTG-ATTAGATCA
626514 ATTTTAGT
1 ATTTTAGT
626522 ATTTGTCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 15 0.44
31 15 0.44
32 4 0.12
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (29 bp):
ATTTTAGTTTATAGACTTTGATTAGATCA
Found at i:629763 original size:70 final size:70
Alignment explanation
Indices: 629645--629780 Score: 254
Period size: 70 Copynumber: 1.9 Consensus size: 70
629635 AAATGTTCAG
629645 ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
1 ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
629710 TGAAC
66 TGAAC
* *
629715 ATTGGTATATAAGTACGGTTAGATCCAATCTCTTGATCCCCATTGAAAGGAAAAAGAATTACACA
1 ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
629780 T
66 T
629781 TCTTCTTTCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (70 bp):
ATTGGTATATAAGAACGGTTAGATCCAATCTCTTGATCCCCATGGAAAGGAAAAAGAATTACACA
TGAAC
Found at i:632886 original size:20 final size:20
Alignment explanation
Indices: 632861--632899 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
632851 ACAAAGAAAC
*
632861 TAAGTTTAAGTACTTAATTG
1 TAAGTTCAAGTACTTAATTG
632881 TAAGTTCAAGTACTTAATT
1 TAAGTTCAAGTACTTAATT
632900 AGATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (20 bp):
TAAGTTCAAGTACTTAATTG
Found at i:638205 original size:195 final size:195
Alignment explanation
Indices: 637890--638280 Score: 660
Period size: 195 Copynumber: 2.0 Consensus size: 195
637880 AGTAAAGTTC
* * *
637890 AATACATTTGGATGCATAATTTAGATTTTTTTTGATAATTAAGTTGATCTCAATGCTTATGTTAT
1 AATACATTTGGATACAGAATTTAGATTTTTTTTGATAATTAAGTTGATCTCAATGCTTATATTAT
* * *
637955 TGTTTCGCAACGAATTAAATGGTTTGAAAAGAGTAAGGTTAATGATTAGGAGGATTTAGTGTTTT
66 TGTTTCGCAAAGAATTAAATGGTTCGAAAAGAGTAAGGTTAATGATTAAGAGGATTTAGTGTTTT
*
638020 ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTTGTTTTGTTTTGTTCGAATT
131 ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
638085 AATACATTTGGATACAGAATTTAGATTTTTTTT-ATAAATTAAGTTGATCTCAATGCTTATATTA
1 AATACATTTGGATACAGAATTTAGATTTTTTTTGAT-AATTAAGTTGATCTCAATGCTTATATTA
* * *
638149 TTGTTTCGTAAAGAGTTAAATGGTTCG-AAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTT
65 TTGTTTCGCAAAGAATTAAATGGTTCGAAAAGAGTAAGGTTAAT-GATTAAGAGGATTTAGTGTT
638213 TTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAA
129 TTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAA
638278 TT
194 TT
638280 A
1 A
638281 GATGCTTGAA
Statistics
Matches: 184, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
194 17 0.09
195 167 0.91
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (195 bp):
AATACATTTGGATACAGAATTTAGATTTTTTTTGATAATTAAGTTGATCTCAATGCTTATATTAT
TGTTTCGCAAAGAATTAAATGGTTCGAAAAGAGTAAGGTTAATGATTAAGAGGATTTAGTGTTTT
ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
Found at i:638461 original size:217 final size:218
Alignment explanation
Indices: 638085--638476 Score: 671
Period size: 217 Copynumber: 1.8 Consensus size: 218
638075 TGTTCGAATT
* *
638085 AATACATTTGGATACAGAATTTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
1 AATACATTGGGATACAGAAATTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
638150 TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
66 TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
*
638215 ATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
131 ATGGTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
638280 AGATGCTTGAATTAGTAAAGTTC
196 AGATGCTTGAATTAGTAAAGTTC
* *
638303 AATACATTGGGATACAGAAATTGGATTTTTTTT-TTAATTAAGTTGATCTCAATGCTTATATTAT
1 AATACATTGGGATACAGAAATTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
* * * * *
638367 TGTTTCGTAACGAGTTAGATGGTTTGAAGGAGTAAGGTTAATTGATTAGGAGGATTTAGTGTTTT
66 TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
638432 ATGGTTGATAT-TAGATTTTGATTTTCAGGGAAAATTTGAATTTTT
131 ATGGTTGAT-TCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTT
638477 TTTTTGGTTG
Statistics
Matches: 163, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
217 132 0.81
218 31 0.19
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (218 bp):
AATACATTGGGATACAGAAATTAGATTTTTTTTATAAATTAAGTTGATCTCAATGCTTATATTAT
TGTTTCGTAAAGAGTTAAATGGTTCGAAGGAGTAAGGTTAATCGATTAAGAGGATTTAGTGTTTT
ATGGTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGAATTTTTGGTTTTGTTTTGTTCGAATT
AGATGCTTGAATTAGTAAAGTTC
Found at i:649629 original size:163 final size:165
Alignment explanation
Indices: 649320--650070 Score: 554
Period size: 163 Copynumber: 4.5 Consensus size: 165
649310 GGTATTAGAT
* * * * ** * * * *
649320 ACTTACTCGAGTTCGGCTAATGTAAGAAGTGTATAATGAATTCTCAAAATTATACTTACCTTATT
1 ACTTACTCGAGTTTGGCTAAAGTAAGAA-TGTGTCATGAATTCTCCGAACTATGCTTACTTTACT
* * * * * * * *
649385 CGAACTCTT-TTTTTACTCTAAAATACCAATGTTTGAAACTTGTTTTTGACACT-TATTC-AATC
65 -AAACTCTTCATTTT-CTCTAAAATACCCATGCTTGATATTTGTTTTTGACA-TGCATGCAAAT-
* * * *
649447 AT-AGATTTTAATTGTTTTTAGACATACATA-T-TA-AAC
126 GTGAGTTTTTGATTGTTTTTAGACATATATACTATATAAC
* * *
649483 ACTTACTCGAGTTTGGCTAATGCAA-AAAGTGTCATGAATTCTCCGAACTATGCTTACTTTACTT
1 ACTTACTCGAGTTTGGCTAAAGTAAGAATGTGTCATGAATTCTCCGAACTATGCTTACTTTAC-T
* * * * *
649547 AAACTTTTCATTTTCTCTAAAACACCCGTGCTCGATATTTGTTTTTGATATGCATGCCAACATG-
65 AAACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATG-CAA-ATGT
* * *
649611 G-GTTTTTGGTTAGTTTTTAGACATGTATACTTGTATAAC
128 GAGTTTTTGATT-GTTTTTAGACATATATAC-TATATAAC
* * ** *
649650 ACATTTATTTGAGTTCAGCTAAAGTAAGAGATGTGTCATGAATTCTCCGAATTATG------TT-
1 AC--TTACTCGAGTTTGGCTAAAGTAAGA-ATGTGTCATGAATTCTCCGAACTATGCTTACTTTA
*
649708 C-AAACTCTTCATTTTCTCTAAAATACGCATGCTTGATATTTGTTTTTGACATGCATGCAAATGT
63 CTAAACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAATGT
649772 GAGTTTTTGATTGTTTTTAGACATATGTATACTCATATCACAC
128 GAGTTTTTGATTGTTTTTAGACATA--TATACT-ATAT-A-AC
* * * *
649815 ATTTACTCGAGTTTGGCTAAAGTAAGAAGTGTGTCATGAATTATACAAACTATGCTTACTTTACT
1 ACTTACTCGAGTTTGGCTAAAGTAAGAA-TGTGTCATGAATTCTCCGAACTATGCTTACTTTACT
* *** * ***
649880 CAAACTCTTCATTTTCTCTAAAATACCAATGCTTGATATTTGTTTTTGACACATATACAAACACG
65 -AAACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTG
* ** * * * * *
649945 AG-TTTTGATTATCATTAAACATGTACACT-TGTATC
129 AGTTTTTGATTGTTTTTAGACATATATACTATATAAC
** * * *
649980 ACGAACTCAAGTTTGGCTAAAGTAAGAAGTGTGTCATGAATTCTTCGAA-TCATGCTTATTTTAC
1 ACTTACTCGAGTTTGGCTAAAGTAAGAA-TGTGTCATGAATTCTCCGAACT-ATGCTTACTTTA-
* *
650044 CCAAACCCTTCATTTTCTCTAAAATAC
63 CTAAACTCTTCATTTTCTCTAAAATAC
650071 TCATATTTGA
Statistics
Matches: 470, Mismatches: 83, Indels: 68
0.76 0.13 0.11
Matches are distributed among these distances:
160 4 0.01
161 78 0.17
162 76 0.16
163 89 0.19
164 5 0.01
165 84 0.18
166 4 0.01
167 7 0.01
169 24 0.05
170 2 0.00
171 40 0.09
172 57 0.12
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (165 bp):
ACTTACTCGAGTTTGGCTAAAGTAAGAATGTGTCATGAATTCTCCGAACTATGCTTACTTTACTA
AACTCTTCATTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGAG
TTTTTGATTGTTTTTAGACATATATACTATATAAC
Found at i:649748 original size:162 final size:166
Alignment explanation
Indices: 649547--649930 Score: 444
Period size: 162 Copynumber: 2.3 Consensus size: 166
649537 TACTTTACTT
* * * * *
649547 AAACTTTTCATTTTCTCTAAAACACCCGTGCTCGATATTTGTTTTTGATATGCATGCCAACATG-
1 AAACTCTTCATTTTCTCTAAAATA-CCATGCTTGATATTTGTTTTTGACATGCATG-CAA-ATGT
* ** * *
649611 G-GTTTTTGGTTAGTTTTTAGAC-ATGTATACTTGTATAACACATTTATTTGAGTTCAGCTAAAG
63 GAGTTTTTGATT-GTTTTTAGACAATGTATACTCATATAACACATTTACTCGAGTTCAGCTAAAG
*
649674 TAAG-AGATGTGTCATGAATTCT-C-CGA-ATTA-TGT-TC
127 TAAGAAG-TGTGTCATGAATTATACACGAGATTACTGTATC
649709 AAACTCTTCATTTTCTCTAAAATACGCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGA
1 AAACTCTTCATTTTCTCTAAAATAC-CATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGA
* **
649774 GTTTTTGATTGTTTTTAGACATATGTATACTCATATCACACATTTACTCGAGTTTGGCTAAAGTA
65 GTTTTTGATTGTTTTTAGACA-ATGTATACTCATATAACACATTTACTCGAGTTCAGCTAAAGTA
* * *
649839 AGAAGTGTGTCATGAATTATACAAACTATGCTTACTTTACTC
129 AGAAGTGTGTCATGAATTATAC--ACGA-GATTACTGTA-TC
649881 AAACTCTTCATTTTCTCTAAAATACCAATGCTTGATATTTGTTTTTGACA
1 AAACTCTTCATTTTCTCTAAAATACC-ATGCTTGATATTTGTTTTTGACA
649931 CATATACAAA
Statistics
Matches: 189, Mismatches: 17, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
160 3 0.02
161 15 0.08
162 58 0.31
163 52 0.28
164 3 0.02
167 2 0.01
169 3 0.02
170 2 0.01
171 1 0.01
172 50 0.26
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (166 bp):
AAACTCTTCATTTTCTCTAAAATACCATGCTTGATATTTGTTTTTGACATGCATGCAAATGTGAG
TTTTTGATTGTTTTTAGACAATGTATACTCATATAACACATTTACTCGAGTTCAGCTAAAGTAAG
AAGTGTGTCATGAATTATACACGAGATTACTGTATC
Found at i:653936 original size:22 final size:23
Alignment explanation
Indices: 653910--653954 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
653900 TTATGTATTT
*
653910 TATATTATATTAAAAT-TAAATA
1 TATATAATATTAAAATGTAAATA
*
653932 TATATAATATTATAATGTAAATA
1 TATATAATATTAAAATGTAAATA
653955 AAACTCTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TATATAATATTAAAATGTAAATA
Found at i:659969 original size:37 final size:38
Alignment explanation
Indices: 659913--659985 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
659903 GCTTAACTAT
*
659913 TTTAATATAGTTTACATTATGAAATTAT-TTTTTTATA
1 TTTAATATAGTTTAAATTATGAAATTATATTTTTTATA
*
659950 TTTAATATATTTTAAATTATGAAATTATATTTTTTA
1 TTTAATATAGTTTAAATTATGAAATTATATTTTTTA
659986 CTCAACTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (38 bp):
TTTAATATAGTTTAAATTATGAAATTATATTTTTTATA
Found at i:660052 original size:41 final size:41
Alignment explanation
Indices: 660003--660087 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
659993 TAATTACCAA
660003 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
1 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
660044 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
1 TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
660085 TAA
1 TAA
660088 TTAAGCTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (41 bp):
TAAACTTAATCGAATTCTAATGTCAACTTAAATACAAAAAT
Found at i:670611 original size:18 final size:18
Alignment explanation
Indices: 670590--670627 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
670580 TTTAAAAAAA
670590 TATAAA-TTTTGAAATTTT
1 TATAAAGTTTTG-AATTTT
670608 TATAAATGTTTTGAATTTT
1 TATAAA-GTTTTGAATTTT
670627 T
1 T
670628 TTGTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TATAAAGTTTTGAATTTT
Found at i:671392 original size:11 final size:11
Alignment explanation
Indices: 671363--671399 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
671353 TCATGTTAAC
*
671363 AAATAATT-TT
1 AAATAATTATA
671373 AAA-AATTATA
1 AAATAATTATA
671383 AAATAATTATA
1 AAATAATTATA
671394 AAATAA
1 AAATAA
671400 AAAATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
9 4 0.17
10 7 0.29
11 13 0.54
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAATTATA
Found at i:678557 original size:59 final size:59
Alignment explanation
Indices: 678460--678588 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
678450 ACCAAAAAAA
* *
678460 TATAAATTTACTAATAGTTTAGCGACTTTGAATGTAGTTTACCCATAATTAAAACAATC
1 TATAAAATTACTAATAGTTTAGCGACTTTGAATCTAGTTTACCCATAATTAAAACAATC
* * * * * *
678519 TATAAAATTACTACTAGTTTAGTGATTTTGAATCTAGTTTACCGATAATTAGAACGATC
1 TATAAAATTACTAATAGTTTAGCGACTTTGAATCTAGTTTACCCATAATTAAAACAATC
678578 TATAAATATTA
1 TATAAA-ATTA
678589 GATTATGTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
59 57 0.93
60 4 0.07
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (59 bp):
TATAAAATTACTAATAGTTTAGCGACTTTGAATCTAGTTTACCCATAATTAAAACAATC
Found at i:683793 original size:50 final size:50
Alignment explanation
Indices: 683647--683929 Score: 388
Period size: 50 Copynumber: 5.5 Consensus size: 50
683637 CCATGGAAAC
683647 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
683697 AAGTGATAAGTAATAGCTTCGGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATA------GCTTCGGCTACACTTATCTGATCAAGGACAAATGA
683753 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * **
683803 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGCGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
683853 AAGTGATAAGTGATAGCTTCGGCTACATTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
* * * *
683903 CAACTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
683930 CTGATCAGTG
Statistics
Matches: 208, Mismatches: 17, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
50 135 0.65
51 24 0.12
56 49 0.24
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:684053 original size:31 final size:31
Alignment explanation
Indices: 683907--684053 Score: 204
Period size: 31 Copynumber: 4.7 Consensus size: 31
683897 AAATGACAAC
*
683907 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* *
683938 TGAAAAGTGGTAGCTTCGTCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
*
683969 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* ** *
684000 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* *
684031 TGAATAGTGGTAGCTTTGGCTAC
1 TGAAAAGTGGTAGCTTCGGCTAC
684054 AAATGACAAG
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
Found at i:685223 original size:29 final size:30
Alignment explanation
Indices: 685191--685252 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
685181 ACTTAACAAG
*
685191 CAAATGCTTTTAAAATAATAA-AAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
685220 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
685250 CAA
1 CAA
685253 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAGAAAATTAA
Found at i:688639 original size:15 final size:13
Alignment explanation
Indices: 688612--688645 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
688602 CAATTTTTCA
688612 TATATTAATATAT
1 TATATTAATATAT
688625 TATATTATATCATAT
1 TATATTA-AT-ATAT
688640 TATATT
1 TATATT
688646 TGTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 2 0.11
15 10 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTAATATAT
Found at i:688790 original size:56 final size:56
Alignment explanation
Indices: 688720--688831 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
688710 CGATTGCATG
* *
688720 CTTTGATAAAAATATTTATTTGGAAGGACTTATGTCCTAGATTAAAATATGTAGGT
1 CTTTGACAAAAATATTTACTTGGAAGGACTTATGTCCTAGATTAAAATATGTAGGT
* *
688776 CTTTGACAGAAATATTTACTTGGAAGGACTTATGTCCTATATTAAAATATGTAGGT
1 CTTTGACAAAAATATTTACTTGGAAGGACTTATGTCCTAGATTAAAATATGTAGGT
688832 GTGTTAGACA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (56 bp):
CTTTGACAAAAATATTTACTTGGAAGGACTTATGTCCTAGATTAAAATATGTAGGT
Found at i:697688 original size:16 final size:17
Alignment explanation
Indices: 697667--697701 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
697657 AATTTAAATA
*
697667 AATT-AATAAATTTTTC
1 AATTAAATAAATTTCTC
697683 AATTAAATAAATTTCTC
1 AATTAAATAAATTTCTC
697700 AA
1 AA
697702 CTCGATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTAAATAAATTTCTC
Found at i:700822 original size:52 final size:49
Alignment explanation
Indices: 700766--700926 Score: 150
Period size: 52 Copynumber: 3.2 Consensus size: 49
700756 TGCTCCCATA
*
700766 TAAGACCATAGCTAGACTATGGCATCGGTGTGATAAGATATGTGCTTCTATG
1 TAAGACCATAGCTGGA-TATGGCATCGGTGTGAT--GATATGTGCTTCTATG
* * * *
700818 TAAGACCATAGCTGGGTTATGGCATCGGTGAGATTTGATTATGTGCTTCCATA
1 TAAGACCATAGCT-GGATATGGCATCGGTGTGA--TGA-TATGTGCTTCTATG
* * *
700871 TAAGACCAT-TCTGGGATATGGCGTC-G-GTGAT-ATATGTGCTTCTGTG
1 TAAGACCATAGCT-GGATATGGCATCGGTGTGATGATATGTGCTTCTATG
700917 TAAGACCATA
1 TAAGACCATA
700927 TCCATATCTA
Statistics
Matches: 92, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
46 20 0.22
47 1 0.01
48 1 0.01
50 3 0.03
51 1 0.01
52 43 0.47
53 22 0.24
54 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (49 bp):
TAAGACCATAGCTGGATATGGCATCGGTGTGATGATATGTGCTTCTATG
Found at i:703330 original size:2 final size:2
Alignment explanation
Indices: 703323--703348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
703313 ATTTGAAATA
703323 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
703349 TTGCTTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:703795 original size:31 final size:31
Alignment explanation
Indices: 703747--703825 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
703737 CAAAAAAAAA
*
703747 TTTAGGAAAA-TTCCATTTCCCCCTTGAAATT
1 TTTA-GAAAATTTTCATTTCCCCCTTGAAATT
* * * **
703778 TTTAGAATATTTTCATTTCTCTCTTGACGTT
1 TTTAGAAAATTTTCATTTCCCCCTTGAAATT
703809 TTTAGAAAATTTT-ATTT
1 TTTAGAAAATTTTCATTT
703826 AGGCCCCCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 8 0.20
31 32 0.80
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTAGAAAATTTTCATTTCCCCCTTGAAATT
Found at i:705693 original size:84 final size:85
Alignment explanation
Indices: 705545--705705 Score: 238
Period size: 84 Copynumber: 1.9 Consensus size: 85
705535 ATCCATGCAA
* * *
705545 CATCCATCCATTCATACATACACGTACATACATTATCTTAACCGTTTCACAATAGCTCGTCGTTA
1 CATCCATCCATTCATACATACACG-ACATACATTACCCTAACCGTTTCACAATAGCTCGCCGTTA
705610 CATAGTGTACATCCGTCCATC
65 CATAGTGTACATCCGTCCATC
*
705631 CATCCATCCATTTATACATACAC-ACATACATTACCCTAACCGTTTCACAAT-GACT-GACCGTT
1 CATCCATCCATTCATACATACACGACATACATTACCCTAACCGTTTCACAATAG-CTCG-CCGTT
705693 ACATAGTGTACAT
64 ACATAGTGTACAT
705706 AAATTGAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 2 0.03
84 45 0.65
86 22 0.32
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (85 bp):
CATCCATCCATTCATACATACACGACATACATTACCCTAACCGTTTCACAATAGCTCGCCGTTAC
ATAGTGTACATCCGTCCATC
Found at i:707918 original size:6 final size:7
Alignment explanation
Indices: 707903--707927 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
707893 TGATGTCATG
707903 TTTTATT
1 TTTTATT
707910 TTTTATT
1 TTTTATT
707917 TTTTATT
1 TTTTATT
707924 TTTT
1 TTTT
707928 TTATTTGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:712052 original size:21 final size:22
Alignment explanation
Indices: 712027--712076 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
712017 TTATCAATTT
712027 TTTAAATAAAATAAAATTT-AA
1 TTTAAATAAAATAAAATTTGAA
**
712048 TTTAAA-AAAATTCAATTTGAA
1 TTTAAATAAAATAAAATTTGAA
*
712069 ATTAAATA
1 TTTAAATA
712077 TTTGTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 13 0.54
22 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TTTAAATAAAATAAAATTTGAA
Found at i:712651 original size:28 final size:29
Alignment explanation
Indices: 712612--712666 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
712602 ATGGATATTA
*
712612 TTTTATGAATTTT-ATTTAATATTTAATT
1 TTTTATGAATTTTGATTTAAAATTTAATT
*
712640 TTTTA-GATATTTTGTTTTAAAATTTAA
1 TTTTATGA-ATTTTGATTTAAAATTTAA
712667 AATTTTACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 10 0.43
29 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (29 bp):
TTTTATGAATTTTGATTTAAAATTTAATT
Found at i:716703 original size:115 final size:115
Alignment explanation
Indices: 716501--716709 Score: 382
Period size: 115 Copynumber: 1.8 Consensus size: 115
716491 TGCAAAAGTT
*
716501 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATTAGTATGAACTCTCCATAAAAAAC
1 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATGAACTCTCCATAAAAAAC
*
716566 ACCTTGATCTTAGCAGGCACCAATGCATAATGGCATAATGGCCGTTGTAC
66 ACCTTGATCTTAGCAGGCACCAATACATAATGGCATAATGGCCGTTGTAC
*
716616 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATGAATTCTCCATAAAAAAC
1 TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATGAACTCTCCATAAAAAAC
*
716681 ACCTTGATTTTAGCAGGCACCAATACATA
66 ACCTTGATCTTAGCAGGCACCAATACATA
716710 TCCACTTCCA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 90 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (115 bp):
TAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATATTATAAGTATGAACTCTCCATAAAAAAC
ACCTTGATCTTAGCAGGCACCAATACATAATGGCATAATGGCCGTTGTAC
Found at i:720963 original size:2 final size:2
Alignment explanation
Indices: 720958--720985 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
720948 TATATATACT
720958 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
720986 AATTTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:722536 original size:25 final size:24
Alignment explanation
Indices: 722500--722574 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 24
722490 TTTGTCTCTT
722500 TTTTAAAACATTTAACACGTGGCA
1 TTTTAAAACATTTAACACGTGGCA
* **
722524 TTTTATAATCATTGT-GTAC-T---A
1 TTTTA-AAACATT-TAACACGTGGCA
722545 TCTTTAAAACATTTAACACGTGGCA
1 T-TTTAAAACATTTAACACGTGGCA
722570 TTTTA
1 TTTTA
722575 TAATCATTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 1 0.03
21 10 0.27
22 5 0.14
24 10 0.27
25 10 0.27
26 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (24 bp):
TTTTAAAACATTTAACACGTGGCA
Found at i:722551 original size:46 final size:46
Alignment explanation
Indices: 722501--722593 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
722491 TTGTCTCTTT
722501 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
1 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
722547 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
1 TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
722593 T
1 T
722594 CCTTAAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (46 bp):
TTTAAAACATTTAACACGTGGCATTTTATAATCATTGTGTACTATC
Found at i:722676 original size:19 final size:20
Alignment explanation
Indices: 722652--722689 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
722642 AGTCCGCGTA
722652 TTTTTA-TTTTCAAATTTTT
1 TTTTTACTTTTCAAATTTTT
*
722671 TTTTTACTTTTTAAATTTT
1 TTTTTACTTTTCAAATTTT
722690 AAAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTACTTTTCAAATTTTT
Found at i:723802 original size:31 final size:31
Alignment explanation
Indices: 723762--723829 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
723752 AAAAAAAGAC
723762 TAAA-TTACACAATGTGTAAACGTTGAGGGT
1 TAAATTTACACAATGTGTAAACGTTGAGGGT
723792 TAAATTTACACAATGTGTAAACGTTGAGGGT
1 TAAATTTACACAATGTGTAAACGTTGAGGGT
723823 TAAATTT
1 TAAATTT
723830 TTAAAAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.34
Consensus pattern (31 bp):
TAAATTTACACAATGTGTAAACGTTGAGGGT
Found at i:725216 original size:30 final size:30
Alignment explanation
Indices: 725180--725265 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
725170 TTTAAGTAAA
725180 ATTAAATTATATATTTATAATTTTTAAAAG
1 ATTAAATTATATATTTATAATTTTTAAAAG
* * *
725210 ATTAAATTA-ATTTTTTTATTATTTTAAAAG
1 ATTAAATTATATATTTATAAT-TTTTAAAAG
* * *
725240 -TAAAAGTATA-ATTTTATAATTATTAA
1 ATTAAATTATATA-TTTATAATTTTTAA
725266 TTTAAAATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
29 19 0.43
30 25 0.57
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTAAATTATATATTTATAATTTTTAAAAG
Found at i:725252 original size:31 final size:32
Alignment explanation
Indices: 725176--725272 Score: 83
Period size: 34 Copynumber: 2.9 Consensus size: 32
725166 TTTTTTTAAG
* *
725176 TAAAATTAAATTATATATTTATAATTTTTAAAAGA
1 TAAAATT-AATTTTATA-TTATTA-TTTTAAAAGA
*
725211 TTAAATTAATTTT-T-TTATTATTTTAAAAG-
1 TAAAATTAATTTTATATTATTATTTTAAAAGA
*
725240 TAAAAGTATAATTTTATAATTATTAATTTAAAA
1 TAAAA-T-TAATTTTAT-ATTATTATTTTAAAA
725273 TTTTATAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
29 4 0.08
30 10 0.19
31 12 0.23
32 1 0.02
33 1 0.02
34 18 0.35
35 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
TAAAATTAATTTTATATTATTATTTTAAAAGA
Found at i:729787 original size:120 final size:120
Alignment explanation
Indices: 729574--730327 Score: 1235
Period size: 120 Copynumber: 6.3 Consensus size: 120
729564 AGAAAAAAAT
* * * *
729574 ATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTA
* *
729639 GTAAATTCATATAAGAATATTGAA-TATTAAGAATTTTATTAAATCATATATTTTA
66 GTAAATTAATATAAGAATATT-AATTATTAAGAATTTTATTAAATTATATATTTTA
* *
729694 ATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTT
1 ATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTACAGTATCATATATTATGATTTT
* * * *
729758 AGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATCTTA
65 AGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
* *
729814 ATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTT
1 ATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTACAGTATCATATATTATGATTTT
* *
729878 AGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTA
65 AGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
* *
729934 ATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTA
* *
729999 GTAAATTAATATAATAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTA
66 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
* *
730054 ATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTA
730119 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
66 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
* *
730174 ATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCA
1 ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTA
730239 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
66 GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
730294 ATTAAAATATATTTAATAATAATTATGTTTAAAT
1 ATTAAAATATATTTAATAATAATTATG-TTAAAT
730328 ATGATTAAAT
Statistics
Matches: 611, Mismatches: 19, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
119 3 0.00
120 601 0.98
121 7 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
ATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATCATATATTATGATTTTA
GTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTA
Found at i:729939 original size:18 final size:17
Alignment explanation
Indices: 729911--729945 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
729901 ATTATTAAGA
*
729911 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
729928 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
729946 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:730179 original size:18 final size:17
Alignment explanation
Indices: 730151--730185 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
730141 ATTATTAAGA
*
730151 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
730168 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
730186 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:730299 original size:18 final size:17
Alignment explanation
Indices: 730271--730305 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
730261 ATTATTAAGA
*
730271 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
730288 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
730306 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:730519 original size:44 final size:45
Alignment explanation
Indices: 730470--730560 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
730460 ACCTCTATTC
* * *
730470 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
730514 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
730559 CA
1 CA
730561 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Done.