Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold301
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: 1013018
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 32220 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:293975 original size:66 final size:67
Alignment explanation
Indices: 293849--293983 Score: 166
Period size: 66 Copynumber: 2.0 Consensus size: 67
293839 TTACCGTAAA
* * ** *
293849 ATAAAAAATAGAAATCTTCATTTTTTTTAAAAAAAATTGATAAAATTATGTTGATTTGTTTTTCA
1 ATAAAAAATAGAAATATTCATTTTTTTT-AAAAAAAGTGATAAAATTATGTCCATGTGTTTTTCA
293914 TTC
65 TTC
** *
293917 ATAAAAAATAGAAATTATTC-TTTTTTTT-TTAAAAGTGATAGAATTATGTCCATGTGTTTTTCA
1 ATAAAAAATAGAAA-TATTCATTTTTTTTAAAAAAAGTGATAAAATTATGTCCATGTGTTTTTCA
293980 TTC
65 TTC
293983 A
1 A
293984 ATACGTTGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 32 0.55
68 22 0.38
69 4 0.07
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (67 bp):
ATAAAAAATAGAAATATTCATTTTTTTTAAAAAAAGTGATAAAATTATGTCCATGTGTTTTTCAT
TC
Found at i:294925 original size:2 final size:2
Alignment explanation
Indices: 294918--294943 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
294908 CCTCTTGCTA
294918 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
294944 TTGTTTTTTT
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:295837 original size:2 final size:2
Alignment explanation
Indices: 295830--295856 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
295820 TTTCTTTCTT
295830 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
295857 TAAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:318214 original size:20 final size:21
Alignment explanation
Indices: 318174--318214 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
318164 CCAAAAAAAA
* *
318174 TATAAAAAAGTTATCATTTAT
1 TATAAAAAAATTATCAATTAT
318195 TATAAAAAAATTAT-AATTAT
1 TATAAAAAAATTATCAATTAT
318215 GTGAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TATAAAAAAATTATCAATTAT
Found at i:325391 original size:51 final size:50
Alignment explanation
Indices: 325234--325428 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 50
325224 ATGATCAATG
* *
325234 CTATCCGGTGCACATAGTAGCCTACACTTAGTACTACACATGTGACCAATA
1 CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAA-A
* * * * *
325285 CCATCCGGTACACGTAGTAGCCTGCACATAGTACTACACAAGTAACCAAA
1 CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAA
*
325335 GCTATCCGGTACATATAGTAGCCTGCACTTAGTACTACACATGTGACCATAA
1 -CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-AA
*** * * * * *
325387 CTATCTTATACTCATAGTAGCATACGCATAGTACTACACATG
1 CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATG
325429 AGTTCTCATG
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.01
51 117 0.98
52 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (50 bp):
CTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAA
Found at i:325405 original size:102 final size:102
Alignment explanation
Indices: 325233--325426 Score: 264
Period size: 102 Copynumber: 1.9 Consensus size: 102
325223 TATGATCAAT
* *
325233 GCTATCCGGTGCACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGGTACAC
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGATACAC
* * *
325298 GTAGTAGCCTGCACATAGTACTACACAAGTAACCAAA
66 ATAGTAGCATACACATAGTACTACACAAGTAACCAAA
* * * ** *
325335 GCTATCCGGTACATATAGTAGCCTGCACTTAGTACTACACATGTGACC-ATAACTATCTTATACT
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAAT-ACCATCCGATACA
*
325399 CATAGTAGCATACGCATAGTACTACACA
65 CATAGTAGCATACACATAGTACTACACA
325427 TGAGTTCTCA
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 2 0.03
102 77 0.97
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (102 bp):
GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGATACAC
ATAGTAGCATACACATAGTACTACACAAGTAACCAAA
Found at i:344305 original size:56 final size:56
Alignment explanation
Indices: 344219--344333 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
344209 ATGCTTATGT
344219 TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
1 TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
* * *
344275 TATTTTTTGTTTTGAGTGTGTCAGTTATGCATGTCAAGACCACATTAATGATTTGA
1 TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
344331 TAT
1 TAT
344334 ATTGAGATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.43
Consensus pattern (56 bp):
TATTTTTTGTGTTAAGTGTGTCAGTTATGCATGTCAAGACCACATTAAGGATTTGA
Found at i:346041 original size:28 final size:28
Alignment explanation
Indices: 345988--346065 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
345978 ACACACACAG
* * *
345988 GGTTAGCACATAT-GGTTCGCACCTAGT
1 GGTTCGCACATATGGGTTTGCACCTAGA
**
346015 GGTTCTTACATATGGGTTTGCACCTAGA
1 GGTTCGCACATATGGGTTTGCACCTAGA
346043 GGTTCGCACATATAGGGTTTGCA
1 GGTTCGCACATAT-GGGTTTGCA
346066 TATACATATA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 10 0.24
28 23 0.55
29 9 0.21
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (28 bp):
GGTTCGCACATATGGGTTTGCACCTAGA
Found at i:346296 original size:14 final size:14
Alignment explanation
Indices: 346279--346341 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
346269 CACATACAGA
346279 GGTTCACTTATAGG
1 GGTTCACTTATAGG
* *
346293 GGTTC-GTATACAGG
1 GGTTCACT-TATAGG
* * * *
346307 CGCTCGCCTATAGG
1 GGTTCACTTATAGG
346321 GGTTCACTTATAGG
1 GGTTCACTTATAGG
346335 GGTTCAC
1 GGTTCAC
346342 ATACATGGGC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
13 1 0.03
14 35 0.97
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (14 bp):
GGTTCACTTATAGG
Found at i:350590 original size:9 final size:9
Alignment explanation
Indices: 350578--350602 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
350568 TTTTCATTTA
350578 TTATTATTG
1 TTATTATTG
350587 TTATTATTG
1 TTATTATTG
350596 TTATTAT
1 TTATTAT
350603 AACATATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:355757 original size:22 final size:23
Alignment explanation
Indices: 355732--355781 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
355722 ATCTCATGCA
*
355732 TATTTTATGTATA-TCTTTTCCT
1 TATTTTATGTATATTATTTTCCT
355754 TA-TTTATGTATATTATTTTCCT
1 TATTTTATGTATATTATTTTCCT
355776 TGATTT
1 T-ATTT
355782 ATGGGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.42
22 11 0.46
23 1 0.04
24 2 0.08
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.64
Consensus pattern (23 bp):
TATTTTATGTATATTATTTTCCT
Found at i:355761 original size:21 final size:23
Alignment explanation
Indices: 355735--355784 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
355725 TCATGCATAT
*
355735 TTTATGTATA-TCTTTTCCTT-A
1 TTTATGTATATTATTTTCCTTGA
355756 TTTATGTATATTATTTTCCTTGA
1 TTTATGTATATTATTTTCCTTGA
355779 TTTATG
1 TTTATG
355785 GGCTAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 7 0.27
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTATGTATATTATTTTCCTTGA
Found at i:361119 original size:3 final size:3
Alignment explanation
Indices: 361111--361162 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
361101 GCAGAAGAGG
361111 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
361159 AGA A
1 AGA A
361163 AGAAAGAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:361408 original size:53 final size:53
Alignment explanation
Indices: 361350--361457 Score: 180
Period size: 53 Copynumber: 2.0 Consensus size: 53
361340 TTTTTTATAA
* *
361350 TTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTATTGTG
1 TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAATTATTGTG
* *
361403 TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAGTTGTTGTG
1 TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAATTATTGTG
361456 TT
1 TT
361458 TAGTTTAGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (53 bp):
TTATTTTAAAATTAATATATTAGTAATTTAGGATTATGTTATAAATTATTGTG
Found at i:361809 original size:50 final size:50
Alignment explanation
Indices: 361755--361912 Score: 135
Period size: 50 Copynumber: 3.1 Consensus size: 50
361745 AATAATTTTA
*
361755 TAGTTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTT
1 TAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAAATTGTTAGTGTT
** * * * * * *
361805 TAGTTATGTGTT-TTATGATTTTTTAGTAATGTA--TTTTAAAAAAT-ATAATTTT
1 TAGTTAT-T-TTGTTA-G-TAATTTA-TGAT-TAGGTTATAAAAATTGTTAGTGTT
*
361857 ATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTT
1 -TAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAAATTGTTAGTGTT
361908 TAGTT
1 TAGTT
361913 TAGTATTTTG
Statistics
Matches: 79, Mismatches: 18, Indels: 22
0.66 0.15 0.18
Matches are distributed among these distances:
48 2 0.03
49 3 0.04
50 25 0.32
51 12 0.15
52 12 0.15
53 20 0.25
54 3 0.04
55 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.54
Consensus pattern (50 bp):
TAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAAAATTGTTAGTGTT
Found at i:361873 original size:103 final size:104
Alignment explanation
Indices: 361653--361968 Score: 391
Period size: 103 Copynumber: 3.1 Consensus size: 104
361643 TTATAGTTAT
*
361653 TTATTTTGTTAATAATTTATGGGATTAGG-T-TACAAATTGTTAGTGTTTAG-TATAG-GATTTT
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTG-TTTT
* * * *
361714 TTGATTTTTTTGTGATGTAATGTTTTTTTAAA-ATAATTTTATAG
63 ATGA-TTTTTTGTAATGTAA--TTTTATAAAATATAATTTTATAG
361758 TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTAT-GTGTTTTATG
1 TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTGTTTTATG
*
361822 ATTTTTTAGTAATGT-ATTTTAAAAAATATAATTTTATAG
66 ATTTTTT-GTAATGTAATTTTATAAAATATAATTTTATAG
* * *
361861 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTT-TAGTATTTTGTG
1 TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTGTTTTATG
* * *
361925 ATTTTTT-TAATGTAATTTTATATAATGTAATTTTAT-T
66 ATTTTTTGTAATGTAATTTTATAAAATATAATTTTATAG
361962 TTATTTT
1 TTATTTT
361969 TCTTTATTTG
Statistics
Matches: 190, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
101 13 0.07
102 27 0.14
103 85 0.45
104 8 0.04
105 53 0.28
106 4 0.02
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (104 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATACAAATTGTTAGTGTTTAGTTATAGTGTTTTATG
ATTTTTTGTAATGTAATTTTATAAAATATAATTTTATAG
Found at i:361952 original size:15 final size:15
Alignment explanation
Indices: 361932--361960 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
361922 GTGATTTTTT
361932 TAATGTAATTTTATA
1 TAATGTAATTTTATA
361947 TAATGTAATTTTAT
1 TAATGTAATTTTAT
361961 TTTATTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TAATGTAATTTTATA
Found at i:363972 original size:13 final size:13
Alignment explanation
Indices: 363950--363983 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
363940 GTATTCAATT
363950 CAATCCAATTACC
1 CAATCCAATTACC
*
363963 CAATCTAATTACC
1 CAATCCAATTACC
*
363976 CAACCCAA
1 CAATCCAA
363984 CCCAATCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (13 bp):
CAATCCAATTACC
Found at i:364212 original size:9 final size:9
Alignment explanation
Indices: 364091--364211 Score: 147
Period size: 9 Copynumber: 13.4 Consensus size: 9
364081 TGTATGATTC
*
364091 AATTAGGTT
1 AATTCGGTT
364100 AATTCAGG-T
1 AATTC-GGTT
*
364109 AATTCGGGT
1 AATTCGGTT
364118 AATTCGGTT
1 AATTCGGTT
364127 AATTCGGTT
1 AATTCGGTT
364136 AATTCGGTT
1 AATTCGGTT
*
364145 AATTCGGGT
1 AATTCGGTT
364154 AATTCGAG-T
1 AATTCG-GTT
*
364163 AATTTGGTT
1 AATTCGGTT
*
364172 AATTCGGGT
1 AATTCGGTT
364181 AATTCGGTT
1 AATTCGGTT
*
364190 AATTTGGTT
1 AATTCGGTT
*
364199 AATTTGGTT
1 AATTCGGTT
364208 AATT
1 AATT
364212 TTTAACCAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
8 3 0.03
9 94 0.94
10 3 0.03
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:364699 original size:33 final size:33
Alignment explanation
Indices: 364662--364725 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
364652 CGTTCCTTCT
*
364662 GGCCCGTATCAACCACCGTACTCCACTCCTCTA
1 GGCCCGCATCAACCACCGTACTCCACTCCTCTA
* ***
364695 GGCCCGCATCCATTGCCGTACTCCACTCCTC
1 GGCCCGCATCAACCACCGTACTCCACTCCTC
364726 CCGGCTCAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.17, C:0.47, G:0.14, T:0.22
Consensus pattern (33 bp):
GGCCCGCATCAACCACCGTACTCCACTCCTCTA
Found at i:365078 original size:79 final size:80
Alignment explanation
Indices: 364922--365100 Score: 281
Period size: 79 Copynumber: 2.2 Consensus size: 80
364912 AATAACTTCA
* * *
364922 TATTTATGTAATGAATTTTTTTCCATTTTATTTATCAATTTTATGTTTTTTTTTTTTTGCAATTT
1 TATTTATGTAATGACTTTTTTTCCATTTTATTTATCAATTTTATGTGTTTGTTTTTTTGCAATTT
* *
364987 AAATAGTCAACTTTG
66 AAATAATAAACTTTG
*
365002 TATTTATGTAATGACTTTTTTTGTCATTTTATTTATCAATTTTATG-GTTTGTTTTTTT-CAATT
1 TATTTATGTAATGACTTTTTTT-CCATTTTATTTATCAATTTTATGTGTTTGTTTTTTTGCAATT
365065 TAAATAATAAACTTTG
65 TAAATAATAAACTTTG
365081 TATTTATGTAATGACTTTTT
1 TATTTATGTAATGACTTTTT
365101 CGCTATTTCA
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
79 39 0.42
80 31 0.34
81 22 0.24
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (80 bp):
TATTTATGTAATGACTTTTTTTCCATTTTATTTATCAATTTTATGTGTTTGTTTTTTTGCAATTT
AAATAATAAACTTTG
Found at i:381213 original size:2 final size:2
Alignment explanation
Indices: 381208--381235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
381198 TANNNNNNNN
381208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
381236 AGTGTGTGCC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:384678 original size:29 final size:29
Alignment explanation
Indices: 384625--384681 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
384615 TTTTATGCTA
*
384625 ATTTTTTTAATTTCAAGTTATTTTATTAT
1 ATTTTTTTAATTTCAAATTATTTTATTAT
*
384654 ATTTTTTTAATTATTAAATTA-TTTATTA
1 ATTTTTTTAATT-TCAAATTATTTTATTA
384682 ACGTGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTTTTTAATTTCAAATTATTTTATTAT
Found at i:385188 original size:5 final size:5
Alignment explanation
Indices: 385178--385211 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
385168 GTTGATAGAG
385178 AAAAT AAAAT AAACA- AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAA
385212 ACAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:387216 original size:29 final size:29
Alignment explanation
Indices: 387163--387219 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
387153 TTTTATGCTA
*
387163 ATTTTTTTAATTTCAAGTTATTTTATTAT
1 ATTTTTTTAATTTCAAATTATTTTATTAT
*
387192 ATTTTTTTAATTATTAAATTA-TTTATTA
1 ATTTTTTTAATT-TCAAATTATTTTATTA
387220 ACGTGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
ATTTTTTTAATTTCAAATTATTTTATTAT
Found at i:387726 original size:5 final size:5
Alignment explanation
Indices: 387716--387749 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
387706 GTTGATAGAG
387716 AAAAT AAAAT AAACA- AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAA
387750 ACAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:389534 original size:21 final size:20
Alignment explanation
Indices: 389508--389547 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
389498 AGATCCCTAT
389508 AAAATAATTACAAAAATATTC
1 AAAATAATTA-AAAAATATTC
* *
389529 AAAATATTTATAAAATATT
1 AAAATAATTAAAAAATATT
389548 TTTCCCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATAATTAAAAAATATTC
Found at i:391350 original size:72 final size:73
Alignment explanation
Indices: 391200--391352 Score: 184
Period size: 72 Copynumber: 2.1 Consensus size: 73
391190 CAAACTTTAC
* * * *
391200 TTGATGCT-TCTCACACAAGCTTCAGAGAATTCATAACACGTGTCGAATCTCAAGCCATCGGTAA
1 TTGATGCTATCTCACACAAGCTTCAGAAAATCCACAACACGTGTCGAATCTCAAGCCATCGATAA
**
391264 AGGATAAT
66 ACAATAAT
* * * *
391272 TCGATGCTAT-TCACACAAGCTTTAGAAAATCCACAACACGTGTTGGATCTCAAGCCATCGATAA
1 TTGATGCTATCTCACACAAGCTTCAGAAAATCCACAACACGTGTCGAATCTCAAGCCATCGATAA
* *
391336 TCAATGAT
66 ACAATAAT
391344 TTGATGCTA
1 TTGATGCTA
391353 CTTACTGATA
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
72 66 0.99
73 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (73 bp):
TTGATGCTATCTCACACAAGCTTCAGAAAATCCACAACACGTGTCGAATCTCAAGCCATCGATAA
ACAATAAT
Found at i:397935 original size:5 final size:5
Alignment explanation
Indices: 397921--397949 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
397911 ATAATAGTTT
397921 ATTT- ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
397950 TACTAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:397945 original size:15 final size:14
Alignment explanation
Indices: 397918--397950 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
397908 ACTATAATAG
397918 TTTATTT-ATTTAA
1 TTTATTTAATTTAA
397931 TTTAATTTAATTTAA
1 TTT-ATTTAATTTAA
397946 TTTAT
1 TTTAT
397951 ACTAGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 6 0.33
15 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTAATTTAA
Found at i:398083 original size:5 final size:5
Alignment explanation
Indices: 398071--398099 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
398061 TATATAGTTT
398071 ATTT- ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
398100 TACTAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:398089 original size:150 final size:151
Alignment explanation
Indices: 397903--398203 Score: 595
Period size: 150 Copynumber: 2.0 Consensus size: 151
397893 TTAGTTAATT
397903 TGTATACTATAATAGTTTATTTATTTAATTTAATTTAATTTAATTTATACTAGAAAATTAATAAA
1 TGTATACTATAATAGTTTATTTATTTAATTTAATTTAATTTAATTTATACTAGAAAATTAATAAA
397968 ACATAATTTATTATGCATATCATAATTTAATTTAAAGGACGGATTTTTGCCCACCCCAATTCTAA
66 ACATAATTTATTATGCATATCATAATTTAATTTAAAGGACGGATTTTTGCCCACCCCAATTCTAA
398033 CTAGAACCTTGATGAATCCAA
131 CTAGAACCTTGATGAATCCAA
398054 TGTATACTAT-ATAGTTTATTTATTTAATTTAATTTAATTTAATTTATACTAGAAAATTAATAAA
1 TGTATACTATAATAGTTTATTTATTTAATTTAATTTAATTTAATTTATACTAGAAAATTAATAAA
398118 ACATAATTTATTATGCATATCATAATTTAATTTAAAGGACGGATTTTTGCCCACCCCAATTCTAA
66 ACATAATTTATTATGCATATCATAATTTAATTTAAAGGACGGATTTTTGCCCACCCCAATTCTAA
398183 CTAGAACCTTGATGAATCCAA
131 CTAGAACCTTGATGAATCCAA
398204 CCCGACACAA
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
150 140 0.93
151 10 0.07
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41
Consensus pattern (151 bp):
TGTATACTATAATAGTTTATTTATTTAATTTAATTTAATTTAATTTATACTAGAAAATTAATAAA
ACATAATTTATTATGCATATCATAATTTAATTTAAAGGACGGATTTTTGCCCACCCCAATTCTAA
CTAGAACCTTGATGAATCCAA
Found at i:398095 original size:15 final size:14
Alignment explanation
Indices: 398068--398100 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
398058 TACTATATAG
398068 TTTATTT-ATTTAA
1 TTTATTTAATTTAA
398081 TTTAATTTAATTTAA
1 TTT-ATTTAATTTAA
398096 TTTAT
1 TTTAT
398101 ACTAGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 6 0.33
15 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTAATTTAA
Found at i:414671 original size:18 final size:18
Alignment explanation
Indices: 414648--414686 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
414638 CTCTTTTTGC
414648 TCTTTTAC-ATTCTCTTTT
1 TCTTTTACGATT-TCTTTT
*
414666 TCTTTTTCGATTTCTTTT
1 TCTTTTACGATTTCTTTT
414684 TCT
1 TCT
414687 GTCTTCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.08, C:0.21, G:0.03, T:0.69
Consensus pattern (18 bp):
TCTTTTACGATTTCTTTT
Found at i:415514 original size:17 final size:17
Alignment explanation
Indices: 415494--415528 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
415484 ATAATTTTTT
415494 AAAAAA-TAAAACATATA
1 AAAAAATTAAAA-ATATA
415511 AAAAAATTAAAAATATA
1 AAAAAATTAAAAATATA
415528 A
1 A
415529 TTTTGTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAAATTAAAAATATA
Found at i:415618 original size:16 final size:16
Alignment explanation
Indices: 415586--415641 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
415576 ATATTGAATT
415586 ATTTATAAAAA-AT-AA
1 ATTT-TAAAAATATAAA
415601 ATTTTAAAAATATAAA
1 ATTTTAAAAATATAAA
*
415617 ATTTTAAAAAT-GAAA
1 ATTTTAAAAATATAAA
*
415632 ATTATAAAAA
1 ATTTTAAAAA
415642 AAAGTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.16
15 18 0.49
16 13 0.35
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTTTAAAAATATAAA
Found at i:416138 original size:3 final size:3
Alignment explanation
Indices: 416130--416162 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
416120 TTTTCCTTAT
416130 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
416163 AATTTCATGA
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:416824 original size:16 final size:16
Alignment explanation
Indices: 416805--416846 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
416795 GTTTATAATT
416805 TTTTGGATTTAGGGAG
1 TTTTGGATTTAGGGAG
* **
416821 TTTTGGGTTTAGGGTT
1 TTTTGGATTTAGGGAG
416837 TTTTGGATTT
1 TTTTGGATTT
416847 CTTTGTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (16 bp):
TTTTGGATTTAGGGAG
Found at i:418498 original size:42 final size:43
Alignment explanation
Indices: 418451--418599 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 43
418441 CGAGATTACA
*
418451 TGTAAGACCATATCTAGGATA-TGGCATCGATATGA-GACTTCG
1 TGTAAGACCATATCTGGGATATTGGCATCGATAT-ATGACTTCG
* * *
418493 TGTAAGACCATGTCTGGGACATTGGCATCGATATATGATTTCG
1 TGTAAGACCATATCTGGGATATTGGCATCGATATATGACTTCG
* * * *
418536 TGTAAGACCATAGCTGGGCTATTGGCATCGATA-AAGA-TTACA
1 TGTAAGACCATATCTGGGATATTGGCATCGATATATGACTT-CG
* *
418578 TGTAAGACTATATATGGGATAT
1 TGTAAGACCATATCTGGGATAT
418600 GACATTGTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.02
42 41 0.46
43 47 0.52
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGATATTGGCATCGATATATGACTTCG
Found at i:420472 original size:46 final size:46
Alignment explanation
Indices: 420422--420584 Score: 188
Period size: 46 Copynumber: 3.6 Consensus size: 46
420412 GATATTGTTT
420422 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
* ** * **
420468 TGGATTTCTTTGTATTTTATTGTCT-GCCATGTGT--ATGAAAAAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTAT-TGTACATGAAAAAAA
* * *
420512 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATTATAGAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
* * *
420558 TTGATTTATTTGTATTGAATTGTTTGG
1 TGGATTTGTTTGTATTAAATTGTTTGG
420585 CTATCTCTAT
Statistics
Matches: 95, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
44 34 0.36
45 6 0.06
46 55 0.58
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.49
Consensus pattern (46 bp):
TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
Found at i:420614 original size:29 final size:28
Alignment explanation
Indices: 420582--420811 Score: 129
Period size: 29 Copynumber: 7.9 Consensus size: 28
420572 TTGAATTGTT
*
420582 TGGCTATCTCTATTAAATGGAAGCCTTTG
1 TGGCGATCTCTATTAAA-GGAAGCCTTTG
* * *
420611 TGGCGAACTTTGTTAAAATGGAAGCCTTTG
1 TGGCGATCTCTATT-AAA-GGAAGCCTTTG
* *
420641 TGGCGATCTCTATTATAAGAAAGCCTTTA
1 TGGCGATCTCTATTA-AAGGAAGCCTTTG
* * * *
420670 TGGCGACCTCTGTTATAAGAAAACCTTTG
1 TGGCGATCTCTATTA-AAGGAAGCCTTTG
* ** *
420699 TGTCGATCTCTATTATAAATATA-TCTTTG
1 TGGCGATCTCTATTA-AAGGA-AGCCTTTG
* * * *
420728 TGGCTAACTCAATTGAAAGGATGCCTTTG
1 TGGCGATCTCTATT-AAAGGAAGCCTTTG
* * * * * **
420757 TAGCTATCTCTATCAGAATGATGAATTTG
1 TGGCGATCTCTATTA-AAGGAAGCCTTTG
* *
420786 TGGTGATCTCTATTAAAGGAATCCTT
1 TGGCGATCTCTATTAAAGGAAGCCTT
420812 GGTGACAAAC
Statistics
Matches: 152, Mismatches: 43, Indels: 13
0.73 0.21 0.06
Matches are distributed among these distances:
28 7 0.05
29 115 0.76
30 30 0.20
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (28 bp):
TGGCGATCTCTATTAAAGGAAGCCTTTG
Found at i:420684 original size:59 final size:59
Alignment explanation
Indices: 420582--420716 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
420572 TTGAATTGTT
* * * * * *
420582 TGGCTATCTCTATTA-AATGGAAGCCTTTGTGGCGAACTTTGTTAAAATGGAAGCCTTTG
1 TGGCGATCTCTATTATAATGAAAGCCTTTATGGCGAACTCTGTTAAAA-GAAAACCTTTG
* *
420641 TGGCGATCTCTATTATAA-GAAAGCCTTTATGGCGACCTCTGTTATAAGAAAACCTTTG
1 TGGCGATCTCTATTATAATGAAAGCCTTTATGGCGAACTCTGTTAAAAGAAAACCTTTG
*
420699 TGTCGATCTCTATTATAA
1 TGGCGATCTCTATTATAA
420717 ATATATCTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
58 26 0.39
59 38 0.58
60 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (59 bp):
TGGCGATCTCTATTATAATGAAAGCCTTTATGGCGAACTCTGTTAAAAGAAAACCTTTG
Found at i:423258 original size:20 final size:21
Alignment explanation
Indices: 423235--423284 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
423225 ATTATTTAAG
423235 ATTTTTTG-ATAAT-TTTCACA
1 ATTTTTTGAATAATGTTT-ACA
*
423255 A-TTTCTGAATAATGTTTACA
1 ATTTTTTGAATAATGTTTACA
423275 A-TTTTTGAAT
1 ATTTTTTGAAT
423285 TTTTTTGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTTTTTGAATAATGTTTACA
Found at i:423823 original size:271 final size:272
Alignment explanation
Indices: 423329--423871 Score: 1079
Period size: 271 Copynumber: 2.0 Consensus size: 272
423319 ATAATTATTT
423329 AATTATTTATAGTTTAAATAATTTTAATTTTTAAAAAAATAATAATCATGTAAAATTTTAATGCT
1 AATTATTTATAGTTTAAATAATTTTAATTTTTAAAAAAATAATAATCATGTAAAATTTTAATGCT
423394 ATTTTAAATTTTTTATTATTGAAAATCATTTAACTTTTTACAATTTTACATGATTTTTAAATTTT
66 ATTTTAAATTTTTTATTATTGAAAATCATTTAACTTTTTACAATTTTACATGATTTTTAAATTTT
423459 TATTTTTGTAATATCTAATAATTTTTAATAATATTTTTTTAAAAATTTTGCCTGATGCAGGTCAA
131 TATTTTTGTAATATCTAATAATTTTTAATAATATTTTTTTAAAAATTTTGCCTGATGCAGGTCAA
423524 TACGGTCAACAACCTCAATGGTAAATGAATAGACTTGGCTTGTTCTAATTGGTTGTTGTTTTTAG
196 TACGGTCAACAACCTCAATGGTAAATGAATAGACTTGGCTTGTTCTAATTGGTTGTTGTTTTTAG
423589 CACCATTAATGA
261 CACCATTAATGA
423601 AATTATTTAT-GTTTAAATAATTTTAATTTTTAAAAAAATAATAATCATGTAAAATTTTAATGCT
1 AATTATTTATAGTTTAAATAATTTTAATTTTTAAAAAAATAATAATCATGTAAAATTTTAATGCT
423665 ATTTTAAATTTTTTATTATTGAAAATCATTTAACTTTTTACAATTTTACATGATTTTTAAATTTT
66 ATTTTAAATTTTTTATTATTGAAAATCATTTAACTTTTTACAATTTTACATGATTTTTAAATTTT
423730 TATTTTTGTAATATCTAATAATTTTTAATAATATTTTTTTAAAAATTTTGCCTGATGCAGGTCAA
131 TATTTTTGTAATATCTAATAATTTTTAATAATATTTTTTTAAAAATTTTGCCTGATGCAGGTCAA
423795 TACGGTCAACAACCTCAATGGTAAATGAATAGACTTGGCTTGTTCTAATTGGTTGTTGTTTTTAG
196 TACGGTCAACAACCTCAATGGTAAATGAATAGACTTGGCTTGTTCTAATTGGTTGTTGTTTTTAG
423860 CACCATTAATGA
261 CACCATTAATGA
423872 CAAAAGCAAA
Statistics
Matches: 271, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
271 261 0.96
272 10 0.04
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (272 bp):
AATTATTTATAGTTTAAATAATTTTAATTTTTAAAAAAATAATAATCATGTAAAATTTTAATGCT
ATTTTAAATTTTTTATTATTGAAAATCATTTAACTTTTTACAATTTTACATGATTTTTAAATTTT
TATTTTTGTAATATCTAATAATTTTTAATAATATTTTTTTAAAAATTTTGCCTGATGCAGGTCAA
TACGGTCAACAACCTCAATGGTAAATGAATAGACTTGGCTTGTTCTAATTGGTTGTTGTTTTTAG
CACCATTAATGA
Found at i:428546 original size:22 final size:22
Alignment explanation
Indices: 428517--428584 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
428507 TGCACTAATG
428517 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
428539 TACAGAGAGCAC-ATATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
* *
428561 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
428583 AA
1 AA
428585 TATCAGGGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.97
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:429711 original size:13 final size:13
Alignment explanation
Indices: 429688--429788 Score: 75
Period size: 13 Copynumber: 7.7 Consensus size: 13
429678 TCTGTTGTTT
429688 TATATATATAATAA
1 TATA-ATATAATAA
*
429702 TACAATATAATATTA
1 TATAATATAATA--A
*
429717 TATAATATTAT-A
1 TATAATATAATAA
429729 -ATAATATAATAA
1 TATAATATAATAA
429741 TATAATATAATAA
1 TATAATATAATAA
* * *
429754 CATACT-TATTAA
1 TATAATATAATAA
*
429766 T-TAAGTAAATATAA
1 TATAA-TATA-ATAA
429780 TATAATATA
1 TATAATATA
429789 TATTTTAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
11 11 0.16
12 8 0.12
13 25 0.37
14 10 0.15
15 13 0.19
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (13 bp):
TATAATATAATAA
Found at i:429713 original size:5 final size:5
Alignment explanation
Indices: 429698--429788 Score: 68
Period size: 5 Copynumber: 18.6 Consensus size: 5
429688 TATATATATA
* * *
429698 ATAAT ACAAT ATAAT ATTAT ATAAT ATTAT AATAAT AT-A- ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
*
429747 ATAAT A-ACAT ACTTAT -TAAT -TAAGT A-AAT ATAAT ATAAT ATA
1 ATAAT ATA-AT A-TAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATA
429789 TATTTTAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
3 2 0.03
4 11 0.16
5 50 0.72
6 6 0.09
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:430093 original size:19 final size:19
Alignment explanation
Indices: 430065--430102 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
430055 CATTTTTTTA
*
430065 TTTAATCCATTTAAATCAAT
1 TTTAATCCATAT-AATCAAT
430085 TTTAA-CCATATAATCAAT
1 TTTAATCCATATAATCAAT
430103 AAAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATCCATATAATCAAT
Found at i:446884 original size:12 final size:13
Alignment explanation
Indices: 446861--446892 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
446851 AAAAATATTT
446861 TAATAA-AATAAA
1 TAATAATAATAAA
446873 TAA-AATAATAAA
1 TAATAATAATAAA
446885 TAATAATA
1 TAATAATA
446893 TTTTATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 12 0.67
13 4 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:448027 original size:17 final size:16
Alignment explanation
Indices: 448005--448041 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
447995 ATAGAAAGTC
*
448005 AAATATATGGGTATCA
1 AAATATATGGATATCA
448021 GAAATATATGGATATCA
1 -AAATATATGGATATCA
448038 AAAT
1 AAAT
448042 CTGGGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (16 bp):
AAATATATGGATATCA
Found at i:448194 original size:2 final size:2
Alignment explanation
Indices: 448187--448215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
448177 GGCATTATTT
448187 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
448216 GTAAATTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:451180 original size:17 final size:17
Alignment explanation
Indices: 451158--451190 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
451148 ATAGAAATTT
*
451158 AAAGATATGGGTATCAG
1 AAAGATATGAGTATCAG
451175 AAAGATATGAGTATCA
1 AAAGATATGAGTATCA
451191 AAATTTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAGATATGAGTATCAG
Found at i:452843 original size:29 final size:28
Alignment explanation
Indices: 452814--452919 Score: 106
Period size: 28 Copynumber: 3.8 Consensus size: 28
452804 AGCAAATGGA
*
452814 AAAAACTATAAAATATGAAAAATAAGGG
1 AAAAACTATAAAATTTGAAAAATAAGGG
* ** *
452842 AAAAA-TGTAAAATCTAAAAAAATAAAGG
1 AAAAACTATAAAAT-TTGAAAAATAAGGG
* *
452870 TAAAACTATAAAATTTGAAAAATATGGG
1 AAAAACTATAAAATTTGAAAAATAAGGG
* * *
452898 CAAAATTGTAAAATTTGAAAAA
1 AAAAACTATAAAATTTGAAAAA
452920 CAGGGGATAC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
27 7 0.11
28 48 0.77
29 7 0.11
ACGTcount: A:0.61, C:0.04, G:0.12, T:0.23
Consensus pattern (28 bp):
AAAAACTATAAAATTTGAAAAATAAGGG
Found at i:453978 original size:21 final size:21
Alignment explanation
Indices: 453937--453978 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
453927 ATTAATATAA
* *
453937 TAATACTTGATTATATTATTT
1 TAATACTTAATTATATCATTT
453958 TAATACTTCAATTATA-CATTT
1 TAATACTT-AATTATATCATTT
453979 ATGACCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATACTTAATTATATCATTT
Found at i:456872 original size:14 final size:15
Alignment explanation
Indices: 456853--456881 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
456843 TCTATATAAA
456853 TATTTTA-GATTTAT
1 TATTTTATGATTTAT
456867 TATTTTATGATTTAT
1 TATTTTATGATTTAT
456882 CATCCAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TATTTTATGATTTAT
Found at i:458199 original size:6 final size:6
Alignment explanation
Indices: 458188--458221 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
458178 TAATATTATG
458188 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
458222 GTTTACACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:459004 original size:28 final size:30
Alignment explanation
Indices: 458941--459005 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
458931 AAATATATTT
*
458941 ATTTTTTTATTTTAATATATTTTTAAAATAC
1 ATTTTTTTATTTT-ATATATTTTTAAAATAA
*
458972 TTTTTTTTATTTT-T-TATTTTTAAAATAA
1 ATTTTTTTATTTTATATATTTTTAAAATAA
459000 ATTTTT
1 ATTTTT
459006 GGTGTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
31 12 0.39
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (30 bp):
ATTTTTTTATTTTATATATTTTTAAAATAA
Found at i:463768 original size:35 final size:35
Alignment explanation
Indices: 463729--463829 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
463719 GGGAAAAATT
* *
463729 GTGGAAACAATTATTAGGTCATTCGGGGCGACACC
1 GTGGAAACGATTATTAGGTCCTTCGGGGCGACACC
* * * *
463764 GTGGAAATGATTATTAGGTCCTTCGGAGTGACATC
1 GTGGAAACGATTATTAGGTCCTTCGGGGCGACACC
* * *
463799 TTAGAAACGATTATTAGGTCCTTCAGGGCGA
1 GTGGAAACGATTATTAGGTCCTTCGGGGCGA
463830 AACCTTGAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (35 bp):
GTGGAAACGATTATTAGGTCCTTCGGGGCGACACC
Found at i:465539 original size:37 final size:36
Alignment explanation
Indices: 465493--465562 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
465483 CACTTTAATA
*
465493 TTAAATTAATA-AAATACTATTAAGATAAGTATTAAAT
1 TTAAATTAATATAAA-ACTATTAAAATAA-TATTAAAT
* *
465530 TTAATTTAATATTAAACTATTAAAATAATATTA
1 TTAAATTAATATAAAACTATTAAAATAATATTA
465563 TTTTTGGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.17
37 22 0.76
38 2 0.07
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (36 bp):
TTAAATTAATATAAAACTATTAAAATAATATTAAAT
Found at i:466479 original size:6 final size:6
Alignment explanation
Indices: 466468--466508 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
466458 TAGTTCATGT
* *
466468 TTTCCA TTTCCA TTGCCA TTTCCA TTTCCAA TTTCAA TTTC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCC-A TTTCCA TTTC
466509 AATTCACAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.20, C:0.29, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTCCA
Found at i:466732 original size:21 final size:21
Alignment explanation
Indices: 466708--466760 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
466698 CGACACATAA
* *
466708 GTGCTTGAAATGATACACGAG
1 GTGCCTGAAATGACACACGAG
* * *
466729 GTGCCTGATACGACCCACGAG
1 GTGCCTGAAATGACACACGAG
466750 GTGCCTGAAAT
1 GTGCCTGAAAT
466761 ACGACACATA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:466776 original size:23 final size:23
Alignment explanation
Indices: 466750--466799 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
466740 GACCCACGAG
466750 GTGCCTGAAATACGACACATAAA
1 GTGCCTGAAATACGACACATAAA
* *
466773 GTGCCTGATATACGACACATATA
1 GTGCCTGAAATACGACACATAAA
466796 GTGC
1 GTGC
466800 TTCATCGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
GTGCCTGAAATACGACACATAAA
Found at i:468013 original size:27 final size:26
Alignment explanation
Indices: 467955--468013 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
467945 TCTGCTGTTC
*
467955 GTTTT-GTTTCTTTTACTTCTTTTTT
1 GTTTTAGTTTCTTTTACTTCTTTATT
* *
467980 TTCTTTAGTTTCTTTTATTTACTTTATT
1 GT-TTTAGTTTCTTTTACTT-CTTTATT
468008 GTTTTA
1 GTTTTA
468014 ATTACTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 1 0.04
26 3 0.11
27 16 0.59
28 7 0.26
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.73
Consensus pattern (26 bp):
GTTTTAGTTTCTTTTACTTCTTTATT
Found at i:468518 original size:84 final size:84
Alignment explanation
Indices: 468417--468582 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
468407 TTATGAATTG
* * *
468417 GCTTAATTCCCATTTTGGCCCTTTATACTTTCTTTTAATATTTAATTCAACTTTTACACCTTATT
1 GCTTAATTCCCAGTTTGGCCATTTATACTTTCTTTTAATATATAATTCAACTTTTACACCTTATT
*
468482 CTATTTAGTTATTTTTCTT
66 CTATTTAGTCATTTTTCTT
* *
468501 GCTTAATTGCCAGTTTGGCCATTTATACTTTCTTTTAATCTATAATTCAACTTTTACACCTTATT
1 GCTTAATTCCCAGTTTGGCCATTTATACTTTCTTTTAATATATAATTCAACTTTTACACCTTATT
468566 CTATTTAGTCATTTTTC
66 CTATTTAGTCATTTTTC
468583 CTAATTTCTC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.52
Consensus pattern (84 bp):
GCTTAATTCCCAGTTTGGCCATTTATACTTTCTTTTAATATATAATTCAACTTTTACACCTTATT
CTATTTAGTCATTTTTCTT
Found at i:469368 original size:280 final size:271
Alignment explanation
Indices: 468874--469416 Score: 750
Period size: 280 Copynumber: 2.0 Consensus size: 271
468864 CTTACGGCAC
* *
468874 CCCGAGCCGGTTCGATTGTTACCAGTTCTGTCTGGGTCAATGACGACACGACAAGTCTGATCTAG
1 CCCGAGCCGGTTCGATTATTACCAGTTCTGTCTGGGTCAATGACGACACAACAAGTCTGATCTAG
* * *
468939 CCACCGGTTGGACTGTCGATTCGGTTTCACATAGTTTGACCAGTTTTTGGGCCTTGGTCTCGATT
66 CCACCGGTTGGACCGTCGATCCAGTTTCACATAGTTTGACCAGTTTTTGGGCCTTGGTCTCGATT
* *
469004 TTGGGCTCCCGTACCCAATTTACGATTTCAAGTCCAATTTTCAAGTTTAATTACCCATTGGGCCA
131 TTGGGCTCCCGTACCCAATTTACGATCTCAAGTCCAATTTTCAAGTTCAATTACCCATTGGGCCA
* ** *
469069 ATTGTCTGACTTAAAAATTAACTTTCAAATTTATCATATTAATTTTAATTGATTTGATTAATTTA
196 ATCGTCTGACTTAAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGATTTAATTAATTTA
469134 ATTTTACTTAA
261 ATTTTACTTAA
* * *
469145 CCCGAGCCGGTTCGGTTATTATC-GATTCTGTCTGGGTCAATGACGACACAACCAGTCTGATCTA
1 CCCGAGCCGGTTCGATTATTACCAG-TTCTGTCTGGGTCAATGACGACACAACAAGTCTGATCTA
* **
469209 GCCACCGGTTGGACCGTC-AGTCCAGTTTCACATACTGGGCCTAGTTCGATCAGTTTTTGGGTTT
65 GCCACCGGTTGGACCGTCGA-TCCAGTTTCACATA----G--T--TT-GACCAGTTTTTGGGCCT
* * *
469273 TGGTCTCGATTTTGGGCTCCCGTACCTAATTTACGATCTC-AGATTCAATTTTTAAGTTCAATTA
120 TGGTCTCGATTTTGGGCTCCCGTACCCAATTTACGATCTCAAG-TCCAATTTTCAAGTTCAATTA
* *
469337 CCCATTGGGCCAATCGTCTTACTTGAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGAT
184 CCCATTGGGCCAATCGTCTGACTTAAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGAT
*
469402 TTAATTGATTTAATT
249 TTAATTAATTTAATT
469417 AATTTAATTA
Statistics
Matches: 237, Mismatches: 23, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
270 2 0.01
271 86 0.36
275 1 0.00
277 1 0.00
279 4 0.02
280 143 0.60
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (271 bp):
CCCGAGCCGGTTCGATTATTACCAGTTCTGTCTGGGTCAATGACGACACAACAAGTCTGATCTAG
CCACCGGTTGGACCGTCGATCCAGTTTCACATAGTTTGACCAGTTTTTGGGCCTTGGTCTCGATT
TTGGGCTCCCGTACCCAATTTACGATCTCAAGTCCAATTTTCAAGTTCAATTACCCATTGGGCCA
ATCGTCTGACTTAAAAATTAACTTTCAAAAATATCATATTAATTTTAATTGATTTAATTAATTTA
ATTTTACTTAA
Found at i:469406 original size:9 final size:9
Alignment explanation
Indices: 469386--469434 Score: 71
Period size: 9 Copynumber: 5.3 Consensus size: 9
469376 AAAATATCAT
469386 ATTAATTTTA
1 ATTAA-TTTA
*
469396 ATTGATTTA
1 ATTAATTTA
*
469405 ATTGATTTA
1 ATTAATTTA
469414 ATTAATTTA
1 ATTAATTTA
469423 ATTAATTTA
1 ATTAATTTA
469432 ATT
1 ATT
469435 TTACTTGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
9 33 0.89
10 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (9 bp):
ATTAATTTA
Found at i:474883 original size:21 final size:21
Alignment explanation
Indices: 474858--474901 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
474848 TGTTATATGG
* *
474858 CCTAGCCACACGATCGTGTAA
1 CCTAGCCACACAACCGTGTAA
474879 CCTAGCCACACAACCGTGTAA
1 CCTAGCCACACAACCGTGTAA
474900 CC
1 CC
474902 CCTTCATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.39, G:0.16, T:0.16
Consensus pattern (21 bp):
CCTAGCCACACAACCGTGTAA
Found at i:475407 original size:4 final size:4
Alignment explanation
Indices: 475398--475535 Score: 91
Period size: 4 Copynumber: 34.2 Consensus size: 4
475388 TGTCTTAACT
* * *
475398 TGCA TGCA TGCA TGCA T--A TTCA TGCA TGCA TGTA TGATA TGCA TGCA
1 TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TG-CA TGCA TGCA
* * * * * * *
475445 TACA TGCA TGCA TGTA TGATA TGCA TGCA TGCA TGTA TGATA TGAA TACA
1 TGCA TGCA TGCA TGCA TG-CA TGCA TGCA TGCA TGCA TG-CA TGCA TGCA
* * * * * *
475495 TGCA TGTA TGCA TGTA TGTA TGTA TGCA TGTA GGCA TGCA T
1 TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA T
475536 ATATGCTTGT
Statistics
Matches: 109, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
2 2 0.02
4 95 0.87
5 12 0.11
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (4 bp):
TGCA
Found at i:475457 original size:29 final size:29
Alignment explanation
Indices: 475405--475524 Score: 133
Period size: 29 Copynumber: 4.2 Consensus size: 29
475395 ACTTGCATGC
475405 ATGCATGCATATTCATGCATGCATGTATGAT
1 ATGCATGCATA--CATGCATGCATGTATGAT
475436 ATGCATGCATACATGCATGCATGTATGAT
1 ATGCATGCATACATGCATGCATGTATGAT
* *
475465 ATGCATGCATGCATGTATG-A--TATGA-
1 ATGCATGCATACATGCATGCATGTATGAT
* ** *
475490 ATACATGCATGTATGCATGTATGTATG-T
1 ATGCATGCATACATGCATGCATGTATGAT
475518 ATGCATG
1 ATGCATG
475525 TAGGCATGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
25 16 0.20
26 6 0.08
28 11 0.14
29 35 0.44
31 11 0.14
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (29 bp):
ATGCATGCATACATGCATGCATGTATGAT
Found at i:475541 original size:8 final size:8
Alignment explanation
Indices: 475398--476738 Score: 536
Period size: 8 Copynumber: 169.8 Consensus size: 8
475388 TGTCTTAACT
*
475398 TGCATGCA
1 TGCATGTA
475406 TGCATGCATA
1 TGCATG--TA
* *
475416 TTCATGCA
1 TGCATGTA
475424 TGCATGTA
1 TGCATGTA
475432 TG-A--TA
1 TGCATGTA
*
475437 TGCATGCA
1 TGCATGTA
* *
475445 TACATGCA
1 TGCATGTA
475453 TGCATGTA
1 TGCATGTA
475461 TG-A--TA
1 TGCATGTA
*
475466 TGCATGCA
1 TGCATGTA
475474 TGCATGTA
1 TGCATGTA
475482 TG-A--TA
1 TGCATGTA
* **
475487 TGAATACA
1 TGCATGTA
475495 TGCATGTA
1 TGCATGTA
475503 TGCATGTA
1 TGCATGTA
*
475511 TGTATGTA
1 TGCATGTA
475519 TGCATGTAGGCA
1 TGCATGT----A
*
475531 TGCATATA
1 TGCATGTA
*
475539 TGCTTGTA
1 TGCATGTA
*
475547 TGTATGTA
1 TGCATGTA
*
475555 TGTATGTA
1 TGCATGTA
*
475563 TGTATGTA
1 TGCATGTA
*
475571 TGTATGTA
1 TGCATGTA
475579 TG--TGTA
1 TGCATGTA
*
475585 TGTATGTA
1 TGCATGTA
*
475593 TGTATGTA
1 TGCATGTA
*
475601 TGTATGTA
1 TGCATGTA
*
475609 TGTATGTA
1 TGCATGTA
* *
475617 TGTATGGA
1 TGCATGTA
*
475625 TGTATGTA
1 TGCATGTA
* * *
475633 TGTATCTT
1 TGCATGTA
*
475641 TGTATGTA
1 TGCATGTA
* *
475649 CGTATGTA
1 TGCATGTA
* *
475657 CGTATGTA
1 TGCATGTA
* * *
475665 CGTATATA
1 TGCATGTA
*
475673 TGTATGTA
1 TGCATGTA
* *
475681 CGTATGTA
1 TGCATGTA
* *
475689 CGTATGTA
1 TGCATGTA
* *
475697 CGTATGTA
1 TGCATGTA
* *
475705 CGTATGTA
1 TGCATGTA
* *
475713 CGTATGTA
1 TGCATGTA
* *
475721 TGTATATA
1 TGCATGTA
* *
475729 CGTATGTA
1 TGCATGTA
* *
475737 TGTATCTA
1 TGCATGTA
* *
475745 CGTATGTA
1 TGCATGTA
*
475753 TGTATGTA
1 TGCATGTA
* *
475761 TGTAGGTA
1 TGCATGTA
*
475769 TGTATGTA
1 TGCATGTA
*
475777 TGTATGTA
1 TGCATGTA
*
475785 TGTATGTA
1 TGCATGTA
475793 TGCATGTA
1 TGCATGTA
*
475801 TCCATGTA
1 TGCATGTA
475809 TGCATGTA
1 TGCATGTA
*
475817 TGGATGTA
1 TGCATGTA
475825 TGCATGTA
1 TGCATGTA
475833 TGCATGTA
1 TGCATGTA
475841 TGCATGTA
1 TGCATGTA
475849 TGCATGTA
1 TGCATGTA
475857 TG-A---A
1 TGCATGTA
*
475861 TGTATGTA
1 TGCATGTA
*
475869 TGTATGTA
1 TGCATGTA
475877 TGCATGTA
1 TGCATGTA
475885 TGCATGTA
1 TGCATGTA
475893 TGCATGTA
1 TGCATGTA
475901 TG-A---A
1 TGCATGTA
*
475905 TGTATGTA
1 TGCATGTA
*
475913 TGTATGTA
1 TGCATGTA
475921 TGCATGTA
1 TGCATGTA
475929 TGCATGTA
1 TGCATGTA
475937 TGCATGTA
1 TGCATGTA
*
475945 TGGATGTA
1 TGCATGTA
*
475953 TGTATGTA
1 TGCATGTA
*
475961 TGGATGTA
1 TGCATGTA
475969 TGCATGTA
1 TGCATGTA
*
475977 TGGATGTA
1 TGCATGTA
*
475985 TGTATGTA
1 TGCATGTA
* *
475993 CGTATGTA
1 TGCATGTA
* *
476001 CGTATGTA
1 TGCATGTA
* *
476009 CGTATGTA
1 TGCATGTA
* *
476017 CGTATGTA
1 TGCATGTA
*
476025 TGTATGTA
1 TGCATGTA
*
476033 TGTATGTA
1 TGCATGTA
*
476041 TGTATGTA
1 TGCATGTA
*
476049 TGTATGTA
1 TGCATGTA
*
476057 TGTATGTA
1 TGCATGTA
*
476065 TGTATGTA
1 TGCATGTA
*
476073 TGTATGTA
1 TGCATGTA
* *
476081 TTC-TCT-
1 TGCATGTA
* *
476087 TCCATGCA
1 TGCATGTA
**
476095 TGCATCCA
1 TGCATGTA
476103 TGCATGTA
1 TGCATGTA
**
476111 TTAACTG--
1 TGCA-TGTA
*
476118 -GCAATATA
1 TGC-ATGTA
* *
476126 TTAACTTGTA
1 -T-GCATGTA
*
476136 TGTATGATA
1 TGCATG-TA
476145 TGCATGTA
1 TGCATGTA
476153 TGCATGTA
1 TGCATGTA
* *
476161 TGTATGCA
1 TGCATGTA
*
476169 TGTATGTA
1 TGCATGTA
* *
476177 T-TATCT-
1 TGCATGTA
*
476183 GGCA-GCT-
1 TGCATG-TA
** *
476190 TTTATCTA
1 TGCATGTA
* *
476198 TACTTAAGT-
1 TGC--ATGTA
476207 TG--TGTA
1 TGCATGTA
* ** *
476213 CTCACAACCATC
1 -T-GC-A-TGTA
476225 TGGCAATGTA
1 T-GC-ATGTA
*
476235 TGTATGTA
1 TGCATGTA
*
476243 TGTATGTA
1 TGCATGTA
*
476251 TGTATGTA
1 TGCATGTA
*
476259 TGTATGTA
1 TGCATGTA
**
476267 TATATGTA
1 TGCATGTA
*
476275 TGTATGTA
1 TGCATGTA
*
476283 TGTATGTA
1 TGCATGTA
**
476291 TATATGTA
1 TGCATGTA
*
476299 TGTATGTA
1 TGCATGTA
*
476307 TGTATGTA
1 TGCATGTA
**
476315 TATATGTA
1 TGCATGTA
*
476323 TGTATGTA
1 TGCATGTA
*
476331 TGTATGTA
1 TGCATGTA
**
476339 TATATGTA
1 TGCATGTA
*
476347 TGTATGTA
1 TGCATGTA
*
476355 TGTATGTA
1 TGCATGTA
**
476363 TATATGTA
1 TGCATGTA
*
476371 TGTATGTA
1 TGCATGTA
*
476379 TGTATGTA
1 TGCATGTA
**
476387 TATATGTA
1 TGCATGTA
*
476395 TGTATGTA
1 TGCATGTA
* *
476403 TGTATGTG
1 TGCATGTA
*
476411 TG--TGTG
1 TGCATGTA
*
476417 TG--TGTG
1 TGCATGTA
476423 TG--TGTA
1 TGCATGTA
**
476429 TGTGTGTA
1 TGCATGTA
**
476437 TGTGTGTA
1 TGCATGTA
**
476445 TGTGTGTA
1 TGCATGTA
476453 TGTC-TGTA
1 TG-CATGTA
476461 TGTC-TGTA
1 TG-CATGTA
*
476469 TGTC-TGTC
1 TG-CATGTA
476477 TGTC-TGTA
1 TG-CATGTA
*
476485 TGTATGTA
1 TGCATGTA
*
476493 TGTATGTA
1 TGCATGTA
*
476501 TGTATGTA
1 TGCATGTA
*
476509 TGTATGTA
1 TGCATGTA
476517 TG--TGATCA
1 TGCATG-T-A
*
476525 TGTATGTA
1 TGCATGTA
476533 TGCATGTA
1 TGCATGTA
476541 TGCATGTA
1 TGCATGTA
* *
476549 TGTATGCA
1 TGCATGTA
*
476557 TGTATGTA
1 TGCATGTA
476565 TGCATGTA
1 TGCATGTA
* *
476573 TGTATGGA
1 TGCATGTA
*
476581 TGTATGTA
1 TGCATGTA
*
476589 TGTATGTA
1 TGCATGTA
* *
476597 TGGATGCA
1 TGCATGTA
* *
476605 TGTATGGA
1 TGCATGTA
*
476613 TGTATGTA
1 TGCATGTA
*
476621 TGTATGTA
1 TGCATGTA
*
476629 TGTATGTA
1 TGCATGTA
*
476637 TGTATGTA
1 TGCATGTA
*
476645 TGTATGTA
1 TGCATGTA
*
476653 TGTATGTA
1 TGCATGTA
*
476661 TGTATGTA
1 TGCATGTA
*
476669 TGTATGTA
1 TGCATGTA
*
476677 TGTATGTA
1 TGCATGTA
*
476685 TGTATGTA
1 TGCATGTA
*
476693 TGTATGTA
1 TGCATGTA
*
476701 TGTATGTA
1 TGCATGTA
476709 TGCATGTA
1 TGCATGTA
476717 TGCATGTA
1 TGCATGTA
476725 TGCATGTA
1 TGCATGTA
476733 TGCATG
1 TGCATG
476739 ATATTCCGAA
Statistics
Matches: 1137, Mismatches: 140, Indels: 112
0.82 0.10 0.08
Matches are distributed among these distances:
4 6 0.01
5 16 0.01
6 31 0.03
7 19 0.02
8 1024 0.90
9 13 0.01
10 15 0.01
11 5 0.00
12 8 0.01
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.43
Consensus pattern (8 bp):
TGCATGTA
Found at i:475550 original size:4 final size:4
Alignment explanation
Indices: 475543--476734 Score: 1226
Period size: 4 Copynumber: 298.5 Consensus size: 4
475533 CATATATGCT
475543 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
475589 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGGA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * * * *
475637 TCTT TGTA TGTA CGTA TGTA CGTA TGTA CGTA TATA TGTA TGTA CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * * *
475685 TGTA CGTA TGTA CGTA TGTA CGTA TGTA CGTA TGTA TGTA TATA CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
475733 TGTA TGTA TCTA CGTA TGTA TGTA TGTA TGTA GGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* ** * * *
475781 TGTA TGTA TGTA TGCA TGTA TCCA TGTA TGCA TGTA TGGA TGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * *
475829 TGTA TGCA TGTA TGCA TGTA TGCA TGTA TGAA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
475877 TGCA TGTA TGCA TGTA TGCA TGTA TGAA TGTA TGTA TGTA TGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
475925 TGTA TGCA TGTA TGCA TGTA TGGA TGTA TGTA TGTA TGGA TGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
475973 TGTA TGGA TGTA TGTA TGTA CGTA TGTA CGTA TGTA CGTA TGTA CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
476021 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * ** * * ** *
476069 TGTA TGTA TGTA T-TC TCT- TCCA TGCA TGCA TCCA TGCA TGTA T-TAA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT-A
* * ** * *
476115 CTGGCAA TATA T-TA ACT- TGTA TGTA TGATA TGCA TGTA TGCA TGTA
1 -T-G-TA TGTA TGTA TGTA TGTA TGTA TG-TA TGTA TGTA TGTA TGTA
* * * * * * * * *
476161 TGTA TGCA TGTA TGTA T-TA TCT- GGCA -GCT- TTTA TCTA TACTTA AGTTG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-TA TGTA TGTA T--GTA TG-TA
** *** * * *
476209 TGTA CTCACA ACCA TCT- GGCAA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA -T-GTA TGTA TGTA TG-TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
476259 TGTA TGTA TATA TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
476307 TGTA TGTA TATA TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* *
476355 TGTA TGTA TATA TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * * * *
476403 TGTA TG-- TGTG TGTG TGTG TGTG TGTA TGTG TGTA TGTG TGTA TGTG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * * * *
476449 TGTA TGTC TGTA TGTC TGTA TGTC TGTC TGTC TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
476497 TGTA TGTA TGTA TGTA TGTA TGTGA T-CA TGTA TGTA TGCA TGTA TGCA
1 TGTA TGTA TGTA TGTA TGTA TGT-A TGTA TGTA TGTA TGTA TGTA TGTA
* * *
476545 TGTA TGTA TGCA TGTA TGTA TGCA TGTA TGTA TGGA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
476593 TGTA TGGA TGCA TGTA TGGA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
476641 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
476689 TGTA TGTA TGTA TGTA TGTA TGCA TGTA TGCA TGTA TGCA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
476735 CATGATATTC
Statistics
Matches: 987, Mismatches: 173, Indels: 56
0.81 0.14 0.05
Matches are distributed among these distances:
2 4 0.00
3 15 0.02
4 952 0.96
5 11 0.01
6 4 0.00
7 1 0.00
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:476414 original size:2 final size:2
Alignment explanation
Indices: 476407--476451 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
476397 TATGTATGTA
* * *
476407 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TA TG TG TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
476449 TG T
1 TG T
476452 ATGTCTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.07, C:0.00, G:0.42, T:0.51
Consensus pattern (2 bp):
TG
Found at i:477184 original size:151 final size:152
Alignment explanation
Indices: 476898--477201 Score: 592
Period size: 151 Copynumber: 2.0 Consensus size: 152
476888 AATTTGGTTC
476898 GAAATTAGTCGGTTAACCGAATTAACCAAACTTAATAAATAATATTATAATATATAAGTATTTTG
1 GAAATTAGTC-GTTAACCGAATTAACCAAACTTAATAAATAATATTATAATATATAAGTATTTTG
476963 TCGGAGGTCAGTCGGTTCGGTTAATTTTTTGGAAGTATAAATTAATCGATCGATTAATTCGGTTA
65 TCGGAGGTCAGTCGGTTCGGTTAATTTTTTGGAAGTATAAATTAATCGATCGATTAATTCGGTTA
477028 ATTTTTTATGTGTTTTATACTTG
130 ATTTTTTATGTGTTTTATACTTG
477051 GAAATTAGTC-TTAACCGAATTAACCAAACTTAATAAATAATATTATAATATATAAGTATTTTGT
1 GAAATTAGTCGTTAACCGAATTAACCAAACTTAATAAATAATATTATAATATATAAGTATTTTGT
477115 CGGAGGTCAGTCGGTTCGGTTAATTTTTTGGAAGTATAAATTAATCGATCGATTAATTCGGTTAA
66 CGGAGGTCAGTCGGTTCGGTTAATTTTTTGGAAGTATAAATTAATCGATCGATTAATTCGGTTAA
477180 TTTTTTATGTGTTTTATACTTG
131 TTTTTTATGTGTTTTATACTTG
477202 TTTTAACCAA
Statistics
Matches: 151, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
151 141 0.93
153 10 0.07
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.41
Consensus pattern (152 bp):
GAAATTAGTCGTTAACCGAATTAACCAAACTTAATAAATAATATTATAATATATAAGTATTTTGT
CGGAGGTCAGTCGGTTCGGTTAATTTTTTGGAAGTATAAATTAATCGATCGATTAATTCGGTTAA
TTTTTTATGTGTTTTATACTTG
Found at i:478002 original size:36 final size:34
Alignment explanation
Indices: 477936--478003 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 34
477926 TTATATTTTT
* *
477936 ATTTTTTTTAATTTTAAAGAGTTCTTATTTTTGC
1 ATTTTTTTTAATTTTAAAGAGTTATAATTTTTGC
477970 ATTTTTTTTAATTTTTTAAA-AGATTATAATTTTT
1 ATTTTTTTTAA--TTTTAAAGAG-TTATAATTTTT
478004 TTAGTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 11 0.38
35 2 0.07
36 16 0.55
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (34 bp):
ATTTTTTTTAATTTTAAAGAGTTATAATTTTTGC
Found at i:496100 original size:22 final size:22
Alignment explanation
Indices: 496072--496115 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
496062 TGTATCAATG
496072 ATTAAATTTATCCTTCATGATT
1 ATTAAATTTATCCTTCATGATT
496094 ATTAAATTTATCCTTCATGATT
1 ATTAAATTTATCCTTCATGATT
496116 TTCAAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (22 bp):
ATTAAATTTATCCTTCATGATT
Found at i:496446 original size:16 final size:17
Alignment explanation
Indices: 496409--496449 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
496399 TATGACTATA
* *
496409 TATATATTAATTATAAT
1 TATATTTTAATTAAAAT
496426 T-TATTTTAA-TAAAAT
1 TATATTTTAATTAAAAT
496441 TATATTTTA
1 TATATTTTA
496450 TAATTGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 6 0.29
16 14 0.67
17 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTTTAATTAAAAT
Found at i:501763 original size:41 final size:41
Alignment explanation
Indices: 501710--502077 Score: 508
Period size: 41 Copynumber: 9.0 Consensus size: 41
501700 CTTTCGGGGC
*
501710 TTTAGCGGCGTTTTTTAGAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
*
501751 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCCCAGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
*
501792 TTTAGCGGCGTTTTGGAGAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
*
501833 TTTAGCGGCATTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
501874 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
* * *
501915 TTTAGCGGCGTTTTTCAAAAAGCACCGCTAATGCTCAGGGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA-GGCT
* * * *
501957 TTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTCGGAGC-
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAG-GCT
* * * * *
501998 TTTAGCGGCATTTTTCAAAAAGCGCCGCTAATGTTCGGGGC-
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC-AGGCT
* **
502039 TTTAGCGGCATTTTCCA-AGAAGCGCCGCTAATGCTCAGG
1 TTTAGCGGCGTTTTTGAGA-AAGCGCCGCTAATGCTCAGG
502078 ATTTAGTATT
Statistics
Matches: 302, Mismatches: 21, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
40 3 0.01
41 258 0.85
42 41 0.14
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAGGCT
Found at i:502107 original size:20 final size:20
Alignment explanation
Indices: 502078--502122 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
502068 AATGCTCAGG
* *
502078 ATTTAGTATTTTATCTGTCT
1 ATTTACTATTTAATCTGTCT
* *
502098 ATTTACTATTTAATTTGTTT
1 ATTTACTATTTAATCTGTCT
502118 ATTTA
1 ATTTA
502123 ATTATATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTTACTATTTAATCTGTCT
Found at i:502782 original size:28 final size:28
Alignment explanation
Indices: 502724--502783 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
502714 TAAATAAGGT
*
502724 TTAGGGGTTAGTAGTTAAAGATTAAGGG
1 TTAGGGGTTAGTAGTTAAAGATTAAGAG
* *
502752 TTAGGGGTTAG-AGGTTAGAGGTTAAGAG
1 TTAGGGGTTAGTA-GTTAAAGATTAAGAG
502780 TTAG
1 TTAG
502784 TGATTTAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (28 bp):
TTAGGGGTTAGTAGTTAAAGATTAAGAG
Found at i:503833 original size:19 final size:20
Alignment explanation
Indices: 503809--503848 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
503799 GCCATTTTAT
503809 CCCTAAA-TTCCCCCTAAAA
1 CCCTAAATTTCCCCCTAAAA
503828 CCCTAAATTTTCCCCCTAAAA
1 CCCTAAA-TTTCCCCCTAAAA
503849 ATAATCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (20 bp):
CCCTAAATTTCCCCCTAAAA
Found at i:504242 original size:3 final size:3
Alignment explanation
Indices: 504234--504285 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
504224 CATTGAGCTG
504234 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
504282 TTA T
1 TTA T
504286 GGTTAATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:508285 original size:43 final size:43
Alignment explanation
Indices: 508191--508421 Score: 284
Period size: 43 Copynumber: 5.4 Consensus size: 43
508181 GATATGTTTT
* * * * * *
508191 TAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAGGT-TTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * *
508233 TAGCGGCGTTTGTGGGAAAATCGCCACTAAAGGTCATGGCCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* * * * *
508276 TAGCGGCGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
508319 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTT
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
* *
508362 TAGCGGCGTTTGTGGGAAGAGCGCCGCTAAAGCTCATGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
*
508405 TAGCGGAGTTTGTGGGA
1 TAGCGGCGTTTGTGGGA
508422 TCTTGACTTT
Statistics
Matches: 162, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
42 28 0.17
43 134 0.83
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTA
Found at i:508418 original size:129 final size:128
Alignment explanation
Indices: 508189--508421 Score: 340
Period size: 129 Copynumber: 1.8 Consensus size: 128
508179 ATGATATGTT
* * * * * *
508189 TTTAGCGGCGTTTTTGCGAGAAGCGTCGCTAAAGGTTTGATCTATAGCGGCGTTTGTGGGAAAAT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTATGATCTATAGCGGCGTTTGTGGGAAAAG
* *
508254 CGCCACTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTC
66 CGCCACTAAAGCTCATGGCCTATAGCGGAGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTC
* * *
508317 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAGA
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGT-ATGATCTATAGCGGCGTTTGTGGGAAAA
* *
508382 GCGCCGCTAAAGCTCATGGTCTATAGCGGAGTTTGTGGGA
65 GCGCCACTAAAGCTCATGGCCTATAGCGGAGTTTGTGGGA
508422 TCTTGACTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
128 32 0.35
129 59 0.65
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (128 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTATGATCTATAGCGGCGTTTGTGGGAAAAG
CGCCACTAAAGCTCATGGCCTATAGCGGAGTTTGTGGGAAAAACGTCGCTAAAGATTATGGTC
Found at i:519689 original size:94 final size:93
Alignment explanation
Indices: 519551--519774 Score: 288
Period size: 94 Copynumber: 2.4 Consensus size: 93
519541 GAAGCTGCAA
* * *
519551 CTACAAATCCTATACCCCTGAAGTTGCAGTGGGTCAGGTCGAATCTACCATAGCGAATCTTATCT
1 CTACAAATCCTATATCCTTGAAGTTGCAGTGGATC-GGTCGAATCTACCATAGCGAATCTTATCT
** *
519616 CCTTAAAGTTGCAGTGGAGCAAAATGAAG
65 CCCCAAAGTTGCAGTAGAGCAAAATGAAG
* *
519645 TTACAAATCCTATATCCTTGAAGTTGCAGTGGATCGGATTGAATCTACCATAGCGAATCTTATCT
1 CTACAAATCCTATATCCTTGAAGTTGCAGTGGATCGG-TCGAATCTACCATAGCGAATCTTATCT
* * *
519710 CCCCGAAGTTGTAGTAGAGCAAGATGAAG
65 CCCCAAAGTTGCAGTAGAGCAAAATGAAG
* * *
519739 CTACAAATCTTATAT-CTCTAAAGTTGCAGTGTATCG
1 CTACAAATCCTATATCCT-TGAAGTTGCAGTGGATCG
519775 AATTAAAGCT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
93 4 0.04
94 109 0.96
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (93 bp):
CTACAAATCCTATATCCTTGAAGTTGCAGTGGATCGGTCGAATCTACCATAGCGAATCTTATCTC
CCCAAAGTTGCAGTAGAGCAAAATGAAG
Found at i:537037 original size:18 final size:17
Alignment explanation
Indices: 537009--537043 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
536999 NNNNNTAAGA
*
537009 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
537026 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
537044 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:537273 original size:44 final size:45
Alignment explanation
Indices: 537208--537293 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
537198 ACCTCTATTC
* *
537208 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
***
537252 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCA
537294 ATATACCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 19 0.53
45 17 0.47
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.28
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCATTA
Found at i:537303 original size:16 final size:16
Alignment explanation
Indices: 537282--537312 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
537272 TAGCTATTAC
537282 ACCTCTAATCCAATAT
1 ACCTCTAATCCAATAT
537298 ACCTCTAATCCAATA
1 ACCTCTAATCCAATA
537313 CAGCGAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
ACCTCTAATCCAATAT
Found at i:544929 original size:15 final size:15
Alignment explanation
Indices: 544909--544938 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
544899 AAGCCCTAAG
*
544909 AAAATAGAATTAGAA
1 AAAATAGAAATAGAA
544924 AAAATAGAAATAGAA
1 AAAATAGAAATAGAA
544939 TTTTTAGGAT
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:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (15 bp):
AAAATAGAAATAGAA
Found at i:545399 original size:47 final size:47
Alignment explanation
Indices: 545345--545440 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
545335 GTAACGATAC
545345 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
1 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
545392 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
1 TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
545439 TT
1 TT
545441 ACAATTTCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (47 bp):
TTGGAGAAATAATATCGTAGTATTCATTGTAAGTTTTTATATTTTAT
Found at i:546639 original size:21 final size:21
Alignment explanation
Indices: 546598--546640 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
546588 ACCCTAAACT
*
546598 CTCAAAACTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
546619 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
546640 C
1 C
546641 AGTTTCCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:546954 original size:17 final size:16
Alignment explanation
Indices: 546919--546950 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
546909 CCCTAATTAC
*
546919 ATTCCCTCAAACTTTT
1 ATTCCCTAAAACTTTT
546935 ATTCCCTAAAACTTTT
1 ATTCCCTAAAACTTTT
546951 TATTTTCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTCCCTAAAACTTTT
Found at i:546976 original size:20 final size:21
Alignment explanation
Indices: 546938--546982 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
546928 AACTTTTATT
*
546938 CCCTAAAACTTTTTATTTTCC
1 CCCTAAAACTTTTTATTTTCA
546959 CCCT-AAAC-TTTTACTTTTCA
1 CCCTAAAACTTTTTA-TTTTCA
546979 CCCT
1 CCCT
546983 TTACTCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (21 bp):
CCCTAAAACTTTTTATTTTCA
Found at i:568864 original size:19 final size:19
Alignment explanation
Indices: 568840--568876 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
568830 TGGCCAGTGC
568840 TGGTCCTAGCATTAGACAA
1 TGGTCCTAGCATTAGACAA
*
568859 TGGTCCTAGCATTGGACA
1 TGGTCCTAGCATTAGACA
568877 GGGCTCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (19 bp):
TGGTCCTAGCATTAGACAA
Found at i:576552 original size:9 final size:9
Alignment explanation
Indices: 576538--576565 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
576528 GTTTCTTTCA
576538 AAACTACAT
1 AAACTACAT
576547 AAACTACAT
1 AAACTACAT
576556 AAACTACAT
1 AAACTACAT
576565 A
1 A
576566 TTGCTACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (9 bp):
AAACTACAT
Found at i:577617 original size:23 final size:23
Alignment explanation
Indices: 577580--577630 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
577570 GTTGTTTCTT
577580 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
577603 TGTAATA-CCCTGAAAATTACTAC
1 TGTAATATCCC-GAAAATTACTAC
*
577626 AGTAA
1 TGTAA
577631 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:580549 original size:9 final size:9
Alignment explanation
Indices: 580528--580561 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
580518 CTGGTTAGTG
580528 TTTAAGTTGT
1 TTTAA-TTGT
*
580538 TTTAATTTT
1 TTTAATTGT
580547 TTTAATTGT
1 TTTAATTGT
580556 TTTAAT
1 TTTAAT
580562 GGTGGGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (9 bp):
TTTAATTGT
Found at i:580625 original size:18 final size:18
Alignment explanation
Indices: 580590--580630 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
580580 ATTTTCTAAA
*
580590 CATTTTTTAATTTTAATT
1 CATTTTTTAATTTAAATT
580608 -ATTTTTTAAGTTTAAATT
1 CATTTTTTAA-TTTAAATT
580626 CATTT
1 CATTT
580631 GCTGACGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 7 0.35
19 4 0.20
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
CATTTTTTAATTTAAATT
Found at i:580737 original size:30 final size:30
Alignment explanation
Indices: 580701--580759 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
580691 ACAAAAAAAT
*
580701 TCGGTTAACCGACCGCATTCGGTTAATCGG
1 TCGGTTAACCGACCGAATTCGGTTAATCGG
580731 TCGGTTAACCGACCGAATTCGGTTAATCG
1 TCGGTTAACCGACCGAATTCGGTTAATCG
580760 ATTGGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (30 bp):
TCGGTTAACCGACCGAATTCGGTTAATCGG
Found at i:580754 original size:18 final size:18
Alignment explanation
Indices: 580698--580756 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
580688 AAAACAAAAA
580698 AATTCGGTTAACCGACCG
1 AATTCGGTTAACCGACCG
* *
580716 CATTCGGTTAATCG---G
1 AATTCGGTTAACCGACCG
580731 ---TCGGTTAACCGACCG
1 AATTCGGTTAACCGACCG
580746 AATTCGGTTAA
1 AATTCGGTTAA
580757 TCGATTGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
12 10 0.31
15 2 0.06
18 20 0.62
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (18 bp):
AATTCGGTTAACCGACCG
Found at i:580872 original size:17 final size:18
Alignment explanation
Indices: 580844--580893 Score: 75
Period size: 17 Copynumber: 2.8 Consensus size: 18
580834 TAATAAATAA
*
580844 AATTATCCAACCCAACCC
1 AATTACCCAACCCAACCC
*
580862 AATTA-CCAACCTAACCC
1 AATTACCCAACCCAACCC
580879 AATTACCCAACCCAA
1 AATTACCCAACCCAA
580894 TAAAACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (18 bp):
AATTACCCAACCCAACCC
Found at i:580928 original size:38 final size:39
Alignment explanation
Indices: 580875--580952 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
580865 TACCAACCTA
* *
580875 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAAGTACCCAACCCAATAAAAATAAAACTAAAGTCT
580914 ACCCAAGTA-CCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAAGTACCCAACCCAATAAAAATAAAACTAAAGTCT
580952 A
1 A
580953 ACTCTTAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 29 0.78
39 8 0.22
ACGTcount: A:0.51, C:0.28, G:0.04, T:0.17
Consensus pattern (39 bp):
ACCCAAGTACCCAACCCAATAAAAATAAAACTAAAGTCT
Found at i:581122 original size:37 final size:37
Alignment explanation
Indices: 581076--581150 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
581066 TGTTAATTTC
*
581076 AAGAATTATGTAATGTTTTTAATTACGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTACGTAGTGATTCA
* *
581113 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTACGTAGTGATTCA
581150 A
1 A
581151 TTCAGGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTACGTAGTGATTCA
Found at i:581856 original size:76 final size:77
Alignment explanation
Indices: 581764--581917 Score: 301
Period size: 76 Copynumber: 2.0 Consensus size: 77
581754 TCTATATAAA
581764 ATAAATTATTAATATGTAATATTTGTTTTTACAATTTTATAATATTTTAATCACATAAAATATAA
1 ATAAATTATTAATATGTAATATTTGTTTTTACAATTTTATAATATTTTAATCACATAAAATATAA
581829 CACAAAAGGGGC
66 CACAAAAGGGGC
581841 ATAAATTATT-ATATGTAATATTTGTTTTTACAATTTTATAATATTTTAATCACATAAAATATAA
1 ATAAATTATTAATATGTAATATTTGTTTTTACAATTTTATAATATTTTAATCACATAAAATATAA
581905 CACAAAAGGGGC
66 CACAAAAGGGGC
581917 A
1 A
581918 AACTATAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 67 0.87
77 10 0.13
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (77 bp):
ATAAATTATTAATATGTAATATTTGTTTTTACAATTTTATAATATTTTAATCACATAAAATATAA
CACAAAAGGGGC
Found at i:588493 original size:15 final size:15
Alignment explanation
Indices: 588473--588503 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
588463 AAAACAACAT
588473 AACTCTTGACATTTC
1 AACTCTTGACATTTC
*
588488 AACTCTTGACCTTTC
1 AACTCTTGACATTTC
588503 A
1 A
588504 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACATTTC
Found at i:591115 original size:18 final size:19
Alignment explanation
Indices: 591079--591117 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
591069 TTATTTAATT
*
591079 TAATTTTTATATTTATAAA
1 TAATTTTTATATATATAAA
591098 TAATTTTTATATAT-TAAA
1 TAATTTTTATATATATAAA
591116 TA
1 TA
591118 TATTGAAAAC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTTTTATATATATAAA
Found at i:594804 original size:2 final size:2
Alignment explanation
Indices: 594797--594830 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
594787 GAAATGATGC
*
594797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
594831 GCACATTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:596770 original size:16 final size:16
Alignment explanation
Indices: 596723--596771 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
596713 TTAAAAATTA
596723 ATAAGAAATGAAAATA-
1 ATAAGAAAT-AAAATAT
* *
596739 AAAAGAATTAATAATAT
1 ATAAGAAATAA-AATAT
596756 ATAAGAAATAAAATAT
1 ATAAGAAATAAAATAT
596772 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 16 0.59
17 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (16 bp):
ATAAGAAATAAAATAT
Found at i:614486 original size:35 final size:35
Alignment explanation
Indices: 614435--614503 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
614425 CTTATACAAG
614435 AATATAGTTACAAGGAACACAAATATTATCAATGT
1 AATATAGTTACAAGGAACACAAATATTATCAATGT
*
614470 AATATAGTTACGAGGAACACAAATATTATCAATG
1 AATATAGTTACAAGGAACACAAATATTATCAATG
614504 AACTTATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (35 bp):
AATATAGTTACAAGGAACACAAATATTATCAATGT
Found at i:618604 original size:20 final size:20
Alignment explanation
Indices: 618579--618620 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
618569 ATGGTAAAAG
618579 AGAAGGTTGAGGAGTATCAA
1 AGAAGGTTGAGGAGTATCAA
*
618599 AGAAGGTTGAGGAGTATTAA
1 AGAAGGTTGAGGAGTATCAA
618619 AG
1 AG
618621 TGGTAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.21
Consensus pattern (20 bp):
AGAAGGTTGAGGAGTATCAA
Found at i:629897 original size:5 final size:5
Alignment explanation
Indices: 629887--629924 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
629877 CCATCACCAT
629887 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATA
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATA
629925 AATATCAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATC
Found at i:632939 original size:67 final size:67
Alignment explanation
Indices: 632818--633234 Score: 416
Period size: 67 Copynumber: 6.3 Consensus size: 67
632808 TGGGGGAATG
* * * * * *
632818 ATGTATAATACCATAGCTCGACTATGGCAACATAAAAAGTCTGTTAGGACATTAAACATGGGGTA
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
632883 TA
66 TA
* * *
632885 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGTATATTAAACATGAGGTA
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
632950 TA
66 TA
* * * * * * *
632952 ATGTGTAACACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAAGACATTAATCATGAGGTA
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
633017 TA
66 TA
* * * * * * *
633019 ATGTGTAAAACCCTAGCTCGGCTATGGCAACATAAAGAGTATAGT-AGGACATTTAATATGGGAT
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTAT-GTCAGGACATTAAACATGGGGT
*
633083 ATG
65 ATA
* * * * * *
633086 ATATGTAAGACCATAGCTCGACTATGGCAACGTA-A-A--AAGTCCATGACATTAAACGTGGGAT
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGT-CAGGACATTAAACATGGGGT
*
633147 ATG
65 ATA
* * * **
633150 ATATGTAAAACCATAGCTCGATTATGGCAACATAGAGA--ATCCACTAGGACATTAAACATGGGG
1 ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTAT-GTC-AGGACATTAAACATGGGG
*
633213 TATG
64 TATA
633217 ATGTGTAAGACCATAGCT
1 ATGTGTAAGACCATAGCT
633235 TGGCTATGAT
Statistics
Matches: 291, Mismatches: 52, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
62 2 0.01
63 1 0.00
64 49 0.17
65 2 0.01
66 4 0.01
67 232 0.80
68 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (67 bp):
ATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTATGTCAGGACATTAAACATGGGGTA
TA
Found at i:633093 original size:134 final size:132
Alignment explanation
Indices: 632815--633265 Score: 471
Period size: 134 Copynumber: 3.4 Consensus size: 132
632805 TAATGGGGGA
* * * ** *
632815 ATGATGTATAATACCATAGCTCGACTATGGCAACATAAAAAGTCTGTTAGGACATTAAACATGGG
1 ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACAT-GG
* * *
632880 GTATAATGTGTAAGACCATAGCTCGACTATGGCAACATAGAGAGTAT-GTCAGTATATTAAACAT
65 GTATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGT-AGGACATTAAACAT
632944 GAGGT
129 G-GGT
* * * * * *
632949 ATAATGTGTAACACCATAGCTCGACTATGGAAACATAGAGAGTTTGCCAAGACATTAATCATGAG
1 ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACATG-G
* * * * *
633014 GTATAATGTGTAAAACCCTAGCTCGGCTATGGCAACATAAAGAGTATAGTAGGACATTTAATATG
65 GTATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGTAGGACATTAAACATG
633079 GGAT
130 GG-T
* * * * *
633083 ATGATATGTAAGACCATAGCTCGACTATGGCAACGTAAAAAG--T-CCATGACATTAAACGTGGG
1 ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACATGGG
* * * * ** *
633145 ATATGATATGTAAAACCATAGCTCGATTATGGCAACATAGAGAATCCACTAGGACATTAAACATG
66 -TATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGTAGGACATTAAACAT-
633210 GGGT
129 GGGT
* * * *
633214 ATGATGTGTAAGACCATAGCTTGGCTAT-GATAACATATAGAGTCTGCCAAGA
1 ATGATGTGTAAGACCATAGCTCGACTATGGA-AACATAAAAAGTCTGCCAAGA
633266 AATAAATGCG
Statistics
Matches: 259, Mismatches: 49, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
130 3 0.01
131 99 0.38
132 4 0.02
133 4 0.02
134 147 0.57
135 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (132 bp):
ATGATGTGTAAGACCATAGCTCGACTATGGAAACATAAAAAGTCTGCCAAGACATTAAACATGGG
TATAATGTGTAAAACCATAGCTCGACTATGGCAACATAGAGAGTATAGTAGGACATTAAACATGG
GT
Found at i:642217 original size:13 final size:13
Alignment explanation
Indices: 642187--642222 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
642177 ACTTAAAAAG
642187 AAACTTAA-G-AA
1 AAACTTAATGAAA
642198 AAA-TTAATGAAA
1 AAACTTAATGAAA
642210 AAACTTAATGAAA
1 AAACTTAATGAAA
642223 TTAGTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 4 0.18
12 5 0.23
13 9 0.41
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (13 bp):
AAACTTAATGAAA
Found at i:647464 original size:25 final size:27
Alignment explanation
Indices: 647436--647497 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
647426 AATTTTAATG
*
647436 ATTTTACCCCT-GATAA-TTTTTGACA
1 ATTTTACCCCTCGATAAGATTTTGACA
**
647461 ATTTTA-CGTTCGATAAGATTTTGACA
1 ATTTTACCCCTCGATAAGATTTTGACA
647487 ATTTTACCCCT
1 ATTTTACCCCT
647498 AGAAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 2 0.07
25 11 0.38
26 14 0.48
27 2 0.07
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (27 bp):
ATTTTACCCCTCGATAAGATTTTGACA
Found at i:647507 original size:26 final size:26
Alignment explanation
Indices: 647409--647507 Score: 69
Period size: 25 Copynumber: 3.9 Consensus size: 26
647399 TTTTTCATCC
* * *
647409 CAATTTTACTCC-AGTAAAATTTTAA
1 CAATTTTACCCCTAGAAAAATTTTGA
** * *
647434 TGATTTTACCCCT-GATAATTTTTGA
1 CAATTTTACCCCTAGAAAAATTTTGA
** * *
647459 CAATTTTA-CGTTCGATAAGATTTTGA
1 CAATTTTACCCCTAGA-AAAATTTTGA
647485 CAATTTTACCCCTAGAAAAATTT
1 CAATTTTACCCCTAGAAAAATTT
647508 CAAGAAAAAT
Statistics
Matches: 52, Mismatches: 18, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
24 2 0.04
25 25 0.48
26 21 0.40
27 4 0.08
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.41
Consensus pattern (26 bp):
CAATTTTACCCCTAGAAAAATTTTGA
Found at i:671111 original size:40 final size:39
Alignment explanation
Indices: 671049--671264 Score: 121
Period size: 40 Copynumber: 5.6 Consensus size: 39
671039 TGGTGAACAA
* * * *
671049 ATCTTTGTCGATTTACGTGACTAGTGTTAGGCACATCATT
1 ATCTTCGTCGATTTAC-CGACTAGTGCTGGGCACATCATT
* *
671089 ATCTTCGTCGATTTATCCGACTAGCGCTGGGCGCA--A--
1 ATCTTCGTCGATTTA-CCGACTAGTGCTGGGCACATCATT
* * *
671125 ATCTTCGTCAATTTACCTTACTAGTACTGGGCACATCATT
1 ATCTTCGTCGATTTACC-GACTAGTGCTGGGCACATCATT
* * * * *
671165 ATCTTCATCGATTTATTCGACTAGCGCAGGGCGCA--A--
1 ATCTTCGTCGATTTA-CCGACTAGTGCTGGGCACATCATT
*
671201 ATCTTTGTC-AGTTTACCTGACTA-TAGCTGGGCACATCATT
1 ATCTTCGTCGA-TTTACC-GACTAGT-GCTGGGCACATCATT
* *
671241 ATATTCGACGGA-TTATCCGACTAG
1 ATCTTCGTC-GATTTA-CCGACTAG
671265 CGCTAGGCGC
Statistics
Matches: 130, Mismatches: 28, Indels: 35
0.67 0.15 0.18
Matches are distributed among these distances:
35 4 0.03
36 51 0.39
38 4 0.03
40 66 0.51
41 4 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (39 bp):
ATCTTCGTCGATTTACCGACTAGTGCTGGGCACATCATT
Found at i:671139 original size:36 final size:36
Alignment explanation
Indices: 671089--671300 Score: 115
Period size: 36 Copynumber: 5.7 Consensus size: 36
671079 GCACATCATT
*
671089 ATCTTCGTCGATTTATCCGACTAGCGCTGGGCGCAA
1 ATCTTCGTCAATTTATCCGACTAGCGCTGGGCGCAA
* ** *
671125 ATCTTCGTCAATTTA-CCTTACTAGTACTGGGCACATCA
1 ATCTTCGTCAATTTATCC-GACTAGCGCTGGGCGCA--A
* * * *
671163 TTATCTTCATCGATTTATTCGACTAGCGCAGGGCGCAA
1 --ATCTTCGTCAATTTATCCGACTAGCGCTGGGCGCAA
* * ** *
671201 ATCTTTGTCAGTTTA-CCTGACTATAGCTGGGCACATCA
1 ATCTTCGTCAATTTATCC-GACTAGCGCTGGGCGCA--A
* * * *
671239 TTATATTCGACGGA-TTATCCGACTAGCGCTAGGCGCAA
1 --ATCTTCGTC-AATTTATCCGACTAGCGCTGGGCGCAA
* * *
671277 ATCTTCGTTAGTTTATCTGACTAG
1 ATCTTCGTCAATTTATCCGACTAG
671301 TGCTAGGCAC
Statistics
Matches: 125, Mismatches: 37, Indels: 28
0.66 0.19 0.15
Matches are distributed among these distances:
35 3 0.02
36 68 0.54
38 4 0.03
40 47 0.38
41 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (36 bp):
ATCTTCGTCAATTTATCCGACTAGCGCTGGGCGCAA
Found at i:671176 original size:76 final size:76
Alignment explanation
Indices: 671046--671311 Score: 313
Period size: 76 Copynumber: 3.5 Consensus size: 76
671036 TTTTGGTGAA
* * * ** *
671046 CAAATCTTTGTCGATTTACGTGACTAGTGTTAGGCACATCATTATCTTCGTCGATTTATCCGACT
1 CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACATCATTATCTTCATCGATTTATCCGACT
671111 AGCGCTGGGCG
66 AGCGCTGGGCG
* * *
671122 CAAATCTTCGTCAATTTACCTTACTAGTACTGGGCACATCATTATCTTCATCGATTTATTCGACT
1 CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACATCATTATCTTCATCGATTTATCCGACT
*
671187 AGCGCAGGGCG
66 AGCGCTGGGCG
* * * *
671198 CAAATCTTTGTCAGTTTACCTGACTA-TAGCTGGGCACATCATTATATTCGA-CGGA-TTATCCG
1 CAAATCTTCGTCAATTTACCTGACTAGTA-CTAGGCACATCATTATCTTC-ATC-GATTTATCCG
*
671260 ACTAGCGCTAGGCG
63 ACTAGCGCTGGGCG
* * * *
671274 CAAATCTTCGTTAGTTTATCTGACTAGTGCTAGGCACA
1 CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACA
671312 ACCTCTATAT
Statistics
Matches: 164, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
75 2 0.01
76 158 0.96
77 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (76 bp):
CAAATCTTCGTCAATTTACCTGACTAGTACTAGGCACATCATTATCTTCATCGATTTATCCGACT
AGCGCTGGGCG
Found at i:674913 original size:41 final size:41
Alignment explanation
Indices: 674858--675209 Score: 342
Period size: 41 Copynumber: 8.6 Consensus size: 41
674848 CTTTCGGGGC
*
674858 TTTAGCGGCT-TTTTTGATAAAGCGCCGCTAATGCTCAGAGC-
1 TTTAGCGG-TGTTTTTGAAAAAGCGCCGCTAATGCTCAG-GCT
* *
674899 TTTAGCGGTGTTTTTTAAAAAGCGCCGCTAATACTC-GAGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAG-GCT
* ** * * *
674940 TTTAGTGGCATTTTTAAAAAAGCACCTCTAATGCTCAGGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
* * *
674981 TTTAGCAGCGTTTTTAAAAAAGCGCCGCTAATGCTCAGGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
* *
675022 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGAC-
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGG-CT
* * *
675063 TTTAGTGGTGTTTTTAAAAAAGCGCCGCTAATGATCAGGCT
1 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
* * * * *
675104 TTTAG-TGTCATTTTTGAAGAAGCACAGCTAATGCTCAGGCT
1 TTTAGCGGT-GTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
** *
675145 TTTAGCGGCT-TTTTT-AAAAAGCATCGCTAATGCTCGGGGC-
1 TTTAGCGG-TGTTTTTGAAAAAGCGCCGCTAATGCTC-AGGCT
* *
675185 TTTAGCAGCGTTTTTGAAAAAGCGC
1 TTTAGCGGTGTTTTTGAAAAAGCGC
675210 TGCAAAAACA
Statistics
Matches: 261, Mismatches: 39, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
40 37 0.14
41 220 0.84
42 3 0.01
43 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (41 bp):
TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCT
Found at i:674962 original size:82 final size:82
Alignment explanation
Indices: 674858--675207 Score: 381
Period size: 82 Copynumber: 4.3 Consensus size: 82
674848 CTTTCGGGGC
* * * *
674858 TTTAGCGGCTTTTTTGATAAAGCGCCGCTAATGCTCAGAGC-TTTAGCGGTGTTTTTTAAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAG-GCTTTTAGCGGTGTTTTTAAAAAAGC
674922 GCCGCTAATACTC-GAGCT
65 GCCGCTAATACTCAG-GCT
* * * * *
674940 TTTAGTGGCATTTTTAAAAAAGCACCTCTAATGCTCAGGCTTTTAGCAGCGTTTTTAAAAAAGCG
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGGCTTTTAGCGGTGTTTTTAAAAAAGCG
*
675005 CCGCTAATGCTCAGGCT
66 CCGCTAATACTCAGGCT
* * * *
675022 TTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTCAGGAC-TTTAGTGGTGTTTTTAAAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGG-CTTTTAGCGGTGTTTTTAAAAAAGC
675086 GCCGCTAATGA-TCAGGCT
65 GCCGCTAAT-ACTCAGGCT
* * * *
675104 TTTAGTGTCATTTTTGAAGAAGCACAGCTAATGCTCAGGCTTTTAGCGGCT-TTTTT-AAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGGCTTTTAGCGG-TGTTTTTAAAAAAGC
** * *
675167 ATCGCTAATGCTCGGGGC-
65 GCCGCTAATACTC-AGGCT
* *
675185 TTTAGCAGCGTTTTTGAAAAAGC
1 TTTAGCGGCATTTTTGAAAAAGC
675208 GCTGCAAAAA
Statistics
Matches: 224, Mismatches: 36, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
81 37 0.17
82 184 0.82
83 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (82 bp):
TTTAGCGGCATTTTTGAAAAAGCACCGCTAATGCTCAGGCTTTTAGCGGTGTTTTTAAAAAAGCG
CCGCTAATACTCAGGCT
Done.