Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009023.1 Hibiscus syriacus cultivar Beakdansim tig00112416_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 540103
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 3
Found at i:242123 original size:18 final size:18
Alignment explanation
Indices: 242085--242123 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
242075 ACCAATTTAT
*
242085 ATATTATTTTTTAATTGA
1 ATATTATTTTTTAATTAA
242103 ATATCTATTTTTT-ATTAA
1 ATAT-TATTTTTTAATTAA
242121 ATA
1 ATA
242124 AAAGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
ATATTATTTTTTAATTAA
Found at i:244412 original size:13 final size:13
Alignment explanation
Indices: 244390--244493 Score: 56
Period size: 13 Copynumber: 7.9 Consensus size: 13
244380 ACGTATGAAT
*
244390 TAAATGAATATAA
1 TAAATAAATATAA
244403 TAAATAAATATAA
1 TAAATAAATATAA
244416 T-AAT-AAT-TAA
1 TAAATAAATATAA
* *
244426 TAATATTAAT-TAT
1 TAA-ATAAATATAA
244439 TAAATATAATA-AA
1 TAAATA-AATATAA
*
244452 TAATTAAAATATAACAA
1 TAAAT-AAATAT---AA
* *
244469 TATATAAATATAG
1 TAAATAAATATAA
*
244482 TAATTAAATATA
1 TAAATAAATATA
244494 TATTTTATAA
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
10 4 0.06
11 4 0.06
12 7 0.10
13 44 0.62
14 1 0.01
16 6 0.08
17 5 0.07
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.37
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:244420 original size:16 final size:16
Alignment explanation
Indices: 244399--244496 Score: 72
Period size: 16 Copynumber: 5.9 Consensus size: 16
244389 TTAAATGAAT
244399 ATAATAAATAAATATA
1 ATAATAAATAAATATA
*
244415 ATAAT-AATTAATAATA
1 ATAATAAATAAAT-ATA
* * *
244431 TTAATTATTAAATATA
1 ATAATAAATAAATATA
*
244447 ATAAATAATTAAAATATA
1 AT-AATAAAT-AAATATA
* *
244465 ACAATATATAAATATA
1 ATAATAAATAAATATA
* *
244481 GTAATTAAATATATAT
1 ATAA-TAAATAAATAT
244497 TTTATAAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 9
0.74 0.15 0.10
Matches are distributed among these distances:
15 6 0.09
16 25 0.39
17 25 0.39
18 8 0.12
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (16 bp):
ATAATAAATAAATATA
Found at i:246539 original size:18 final size:18
Alignment explanation
Indices: 246512--246602 Score: 110
Period size: 18 Copynumber: 4.8 Consensus size: 18
246502 GGATTATCAT
*
246512 TGGTCCTTCGGGATATAG
1 TGGTCCTTCGGGACATAG
*
246530 TGGTCTTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
246548 TGGTCCTTCGGGACATATACAG
1 TGGTCCTTCGGGAC--AT--AG
*
246570 TGGTCTTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
246588 TGGTCCTACGGGACA
1 TGGTCCTTCGGGACA
246603 AATTCTACGC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
18 44 0.70
20 4 0.06
22 15 0.24
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.30
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:246580 original size:40 final size:38
Alignment explanation
Indices: 246512--246602 Score: 141
Period size: 40 Copynumber: 2.4 Consensus size: 38
246502 GGATTATCAT
246512 TGGTCCTTCGGG--ATATAGTGGTCTTTCGGGACATAG
1 TGGTCCTTCGGGACATATAGTGGTCTTTCGGGACATAG
246548 TGGTCCTTCGGGACATATACAGTGGTCTTTCGGGACATAG
1 TGGTCCTTCGGGACATAT--AGTGGTCTTTCGGGACATAG
*
246588 TGGTCCTACGGGACA
1 TGGTCCTTCGGGACA
246603 AATTCTACGC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 12 0.24
38 4 0.08
40 34 0.68
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.30
Consensus pattern (38 bp):
TGGTCCTTCGGGACATATAGTGGTCTTTCGGGACATAG
Found at i:250638 original size:18 final size:18
Alignment explanation
Indices: 250615--250677 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 18
250605 GGATTATCAG
250615 TGGTCCTTCGGGACATAA
1 TGGTCCTTCGGGACATAA
250633 TGGTCCTTCGGGACATATACA
1 TGGTCCTTCGGGAC--ATA-A
*
250654 GTGGTCCTTCGGGACATAG
1 -TGGTCCTTCGGGACATAA
250673 TGGTC
1 TGGTC
250678 TTATGAGTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 19 0.47
20 6 0.15
21 1 0.03
22 14 0.35
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAA
Found at i:250661 original size:22 final size:22
Alignment explanation
Indices: 250612--250671 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
250602 AAGGGATTAT
250612 CAGTGGTCCTTCGGGAC--ATA
1 CAGTGGTCCTTCGGGACATATA
250632 -A-TGGTCCTTCGGGACATATA
1 CAGTGGTCCTTCGGGACATATA
250652 CAGTGGTCCTTCGGGACATA
1 CAGTGGTCCTTCGGGACATA
250672 GTGGTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.39
19 1 0.03
20 3 0.08
21 1 0.03
22 17 0.47
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (22 bp):
CAGTGGTCCTTCGGGACATATA
Found at i:252258 original size:29 final size:29
Alignment explanation
Indices: 252217--252279 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
252207 TCCTTCGACT
252217 TTTA-TCTTATAATTTTAGAATAATTTAA
1 TTTATTCTTATAATTTTAGAATAATTTAA
252245 TTTATTCTTATAATTTTAGAATAATTTAA
1 TTTATTCTTATAATTTTAGAATAATTTAA
252274 TTTATT
1 TTTATT
252280 TGAGGTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (29 bp):
TTTATTCTTATAATTTTAGAATAATTTAA
Found at i:266780 original size:21 final size:21
Alignment explanation
Indices: 266754--266803 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
266744 GAAATTAGAG
*
266754 TTTTTTATAAATATAATAATA
1 TTTTTTAAAAATATAATAATA
266775 TTTTTTAAAAATATAATAATA
1 TTTTTTAAAAATATAATAATA
266796 TTTTTTAA
1 TTTTTTAA
266804 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTTTAAAAATATAATAATA
Found at i:273214 original size:2 final size:2
Alignment explanation
Indices: 273207--273239 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
273197 GGAATTAAAA
273207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
273240 ATTAATTGAG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:273463 original size:3 final size:3
Alignment explanation
Indices: 273455--273479 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
273445 TGAGGAAGAA
273455 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
273480 CCAAGTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:275354 original size:30 final size:30
Alignment explanation
Indices: 275306--275363 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
275296 GAACATATGA
* *
275306 ATAGTTGCCGAGGATCTTTATGACCTCTGG
1 ATAGTTACCGAGGATCTTTATAACCTCTGG
* * *
275336 ATAGTTACCGGGGTTCTTTGTAACCTCT
1 ATAGTTACCGAGGATCTTTATAACCTCT
275364 TGACAGGTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (30 bp):
ATAGTTACCGAGGATCTTTATAACCTCTGG
Found at i:276960 original size:37 final size:36
Alignment explanation
Indices: 276902--277020 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
276892 TCTCATTATC
* *
276902 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
* *
276938 ATTTTTCAAAGAAACATTTACCAATCTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
276974 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
277009 ATTTTTTCAAAG
1 A-TTTTTCAAAG
277021 TTGGTTGCCA
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 33 0.45
36 13 0.18
37 28 0.38
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:281459 original size:35 final size:35
Alignment explanation
Indices: 281370--281485 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
281360 TTATTCCATT
* * *
281370 ATCATTTTTCAATAAATATCTACCAAATTTTGAAAA
1 ATCATTTTTAAATAAACATTTACCAAATTTTG-AAA
* * *
281406 ATTATTTTTTAAAGAAACATTTACCAAACTTTGAAA
1 ATCA-TTTTTAAATAAACATTTACCAAATTTTGAAA
281442 ATCATTTTTAAATAAACATTTACCAAATTTTGAAA
1 ATCATTTTTAAATAAACATTTACCAAATTTTGAAA
*
281477 ACCATTTTT
1 ATCATTTTT
281486 TCAAAGTTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 37 0.54
36 9 0.13
37 23 0.33
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.41
Consensus pattern (35 bp):
ATCATTTTTAAATAAACATTTACCAAATTTTGAAA
Found at i:283278 original size:29 final size:29
Alignment explanation
Indices: 283243--283324 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
283233 AAACTAAATT
*
283243 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
283272 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
283301 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
283325 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:288040 original size:29 final size:29
Alignment explanation
Indices: 288005--288086 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
287995 AAACTAAATT
288005 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTACTTACATCATTTAATTAAA
* *
288034 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTACTTACATCATTTAATTAAA
288063 GATGTCATTACTTACATCAATTTA
1 GATGTCATTACTTACATC-ATTTA
288087 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
GATGTCATTACTTACATCATTTAATTAAA
Found at i:292116 original size:338 final size:337
Alignment explanation
Indices: 291453--292172 Score: 1187
Period size: 338 Copynumber: 2.1 Consensus size: 337
291443 TTTATTTTTT
* * *
291453 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTCCATATATTTTTTAAAAATTTATTAC
1 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
* *
291518 CTTTTAAAATTAATTGTTTATAAATAGAAAAAAATATTAAAATAAACTTTTAATTGCAATTGAGG
66 CTTTTAAAATTAATTGTTTATAAATAGAAAAAAATATTAAAATAAACTTTTAAATACAATTGAGG
291583 GATCAAATGAATTATTATTCATTAATTTTTATTTTTTAACAACAATTAATAATGTTTATTCATTT
131 GATCAAATGAATTATTATTCATTAATTTTTATTTTTTAACAACAATTAATAATGTTTATTCATTT
* * *
291648 TTAATAAAATTATTTTAATTTTTGCATTAAAATTACATAATATGTATAACCTAGTATAGAAAAAC
196 TTAATAAAATTATTTAAATTTTTGCATTAAAATTACACAATACGTATAACCTAGTATAGAAAAAC
* *
291713 TTTGAGGGTAAATATTTTAAAATGTGAATAATTTTATAAAAGTTTTATAACTAGTATTTTTTTAC
261 TTTGAGGGTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTTTTTTAC
291778 AAAATAATGATGATG
326 --AA-AATGATGATG
*
291793 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTGC
1 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
* * *
291858 TTTTTAAAATTAATTGTTTA-AAA-ATATAAAAATATTAAAATAAACTTTTAAATACAATTGAGG
66 CTTTTAAAATTAATTGTTTATAAATAGAAAAAAATATTAAAATAAACTTTTAAATACAATTGAGG
* *
291921 GATTAAATGAATTATTATTCATTAATTTTTATTTTTTAACAACAGTTAATAATGTTTATTCATTT
131 GATCAAATGAATTATTATTCATTAATTTTTATTTTTTAACAACAATTAATAATGTTTATTCATTT
* * * *
291986 TTAATAAAATTATTTAAATTTTTGCA-TCAAATTACACAGTACGTATAATCTAGTATAGGAAAAC
196 TTAATAAAATTATTTAAATTTTTGCATTAAAATTACACAATACGTATAACCTAGTATAGAAAAAC
292050 TTTGAGGGTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTTCTTTTA
261 TTTGAGGGTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTT-TTTTA
292115 CAAAATGATGATG
325 CAAAATGATGATG
*
292128 ATGATAATAAATATTTTATAATTTAAAAAATTATAAATTT-ATATA
1 ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATA
292173 GAATATAATA
Statistics
Matches: 358, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
334 5 0.01
335 49 0.14
336 2 0.01
337 89 0.25
338 130 0.36
339 3 0.01
340 80 0.22
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (337 bp):
ATAATAATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTAC
CTTTTAAAATTAATTGTTTATAAATAGAAAAAAATATTAAAATAAACTTTTAAATACAATTGAGG
GATCAAATGAATTATTATTCATTAATTTTTATTTTTTAACAACAATTAATAATGTTTATTCATTT
TTAATAAAATTATTTAAATTTTTGCATTAAAATTACACAATACGTATAACCTAGTATAGAAAAAC
TTTGAGGGTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTTTTTTAC
AAAATGATGATG
Found at i:293522 original size:65 final size:64
Alignment explanation
Indices: 293361--293531 Score: 243
Period size: 65 Copynumber: 2.6 Consensus size: 64
293351 AATCGGAACC
* *
293361 TTTTAGGCATCGGCTTTCTAGTGGCCCTATTTTTTCCAAAGCAATGTTTCATGTGTGTGGGTACA
1 TTTTAGGCATCGGCTTCCT-GTGGCCCTATTTTTTCGAAAGCAATGTTTCATGTGTGTGGGTACA
* * * *
293426 TTTTATGCATCGACTGTCTTTTGGCCCTATTTTTTCGAAAGCAATGTTTCATGTGTGTGGGTACA
1 TTTTAGGCATCGGCT-TCCTGTGGCCCTATTTTTTCGAAAGCAATGTTTCATGTGTGTGGGTACA
* *
293491 TTTTAGGCATCGGCCTTCCTGTGGGCATATTTTTTCGAAAG
1 TTTTAGGCATCGG-CTTCCTGTGGCCCTATTTTTTCGAAAG
293532 GTTTATTGTT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 88 0.96
66 4 0.04
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (64 bp):
TTTTAGGCATCGGCTTCCTGTGGCCCTATTTTTTCGAAAGCAATGTTTCATGTGTGTGGGTACA
Found at i:294949 original size:15 final size:16
Alignment explanation
Indices: 294922--294951 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
294912 TTCTGTTTTA
294922 TATTTTATATTTATTT
1 TATTTTATATTTATTT
294938 TATTTT-TATTTATT
1 TATTTTATATTTATT
294952 AACCATTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTATATTTATTT
Found at i:298653 original size:19 final size:20
Alignment explanation
Indices: 298622--298660 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
298612 GAAGGAAATG
298622 AGAATGAAGAGAA-ATGAAA
1 AGAATGAAGAGAATATGAAA
298641 AGAAT-AAGAAGAATATGAAA
1 AGAATGAAG-AGAATATGAAA
298661 TGGGATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (20 bp):
AGAATGAAGAGAATATGAAA
Found at i:299338 original size:26 final size:26
Alignment explanation
Indices: 299303--299352 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
299293 GGAATAAAGT
299303 TTTTCAAAG-TTTGGGTTTTTTAAGA
1 TTTTCAAAGTTTTGGGTTTTTTAAGA
299328 TTTTCAAAAGTTTTGGGTTTTTTAA
1 TTTTC-AAAGTTTTGGGTTTTTTAA
299353 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.22
26 4 0.17
27 14 0.61
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.54
Consensus pattern (26 bp):
TTTTCAAAGTTTTGGGTTTTTTAAGA
Found at i:299578 original size:29 final size:29
Alignment explanation
Indices: 299514--299578 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
299504 ATGTTTAAAC
* * *
299514 AAAAAAAAATTTAGGTACCTATTTAGATT
1 AAAAAATAATTTAGGCACCTATTTAGACT
* * * *
299543 AAGAAATACTTTAGGCACTTATTTTGACT
1 AAAAAATAATTTAGGCACCTATTTAGACT
299572 AAAAAAT
1 AAAAAAT
299579 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (29 bp):
AAAAAATAATTTAGGCACCTATTTAGACT
Found at i:300268 original size:2 final size:2
Alignment explanation
Indices: 300263--300291 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
300253 AATTCTTTTT
300263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
300292 TTGTTGGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:300486 original size:3 final size:3
Alignment explanation
Indices: 300478--300547 Score: 131
Period size: 3 Copynumber: 23.0 Consensus size: 3
300468 AGTCAACCAA
300478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
300526 AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT
300548 CTTATCTTGA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:307299 original size:2 final size:2
Alignment explanation
Indices: 307288--307323 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
307278 ATTATTTAAC
307288 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
307324 TATCTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:307721 original size:15 final size:16
Alignment explanation
Indices: 307701--307730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
307691 GCGTAATGAG
307701 AATATATG-ATATTTA
1 AATATATGTATATTTA
307716 AATATATGTATATTT
1 AATATATGTATATTT
307731 TTAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
AATATATGTATATTTA
Found at i:310487 original size:16 final size:18
Alignment explanation
Indices: 310448--310488 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
310438 GTATTTATTT
*
310448 TATTTATTATATCTTAAA
1 TATTTATCATATCTTAAA
*
310466 TTTTTATCATAT-TT-AA
1 TATTTATCATATCTTAAA
310482 TATTTAT
1 TATTTAT
310489 AGGTAATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTATCATATCTTAAA
Found at i:319540 original size:19 final size:19
Alignment explanation
Indices: 319516--319562 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
319506 GATTCGCAAC
319516 GCGATAGTTAAAATGTGTT
1 GCGATAGTTAAAATGTGTT
319535 GCGATAGTTAAAATGTGTT
1 GCGATAGTTAAAATGTGTT
*
319554 GCGAGAGTT
1 GCGATAGTT
319563 TGAAAAACGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.34
Consensus pattern (19 bp):
GCGATAGTTAAAATGTGTT
Found at i:320002 original size:21 final size:20
Alignment explanation
Indices: 319976--320070 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
319966 TACCACCAGT
* *
319976 CGTTGCGATTTTAGAAAATCG
1 CGTTGCGATTTT-CATAATCG
* *
319997 CGTTGCGATTTTGTATTATCG
1 CGTTGCGATTTT-CATAATCG
**
320018 CGTTGCGATAGTCATAATCG
1 CGTTGCGATTTTCATAATCG
* *
320038 CGTTGCGATTTACATATTCG
1 CGTTGCGATTTTCATAATCG
*
320058 CATTGCGATTTTC
1 CGTTGCGATTTTC
320071 TAAAATCGCA
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCATAATCG
Found at i:321709 original size:24 final size:25
Alignment explanation
Indices: 321682--321728 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
321672 CTATTCTTTC
321682 ACTTCAATCAAAC-TCGAATTTTAG
1 ACTTCAATCAAACTTCGAATTTTAG
* *
321706 ACTTCAATCGAACTTCTAATTTT
1 ACTTCAATCAAACTTCGAATTTT
321729 TTTTTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAACTTCGAATTTTAG
Found at i:333592 original size:14 final size:14
Alignment explanation
Indices: 333573--333600 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
333563 TTTCCTTTTA
333573 AAAATATCATCCGT
1 AAAATATCATCCGT
333587 AAAATATCATCCGT
1 AAAATATCATCCGT
333601 TCCATGCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAATATCATCCGT
Found at i:336415 original size:17 final size:17
Alignment explanation
Indices: 336393--336429 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
336383 TTGACCGGTT
336393 CCGACCCGACCCATTGA
1 CCGACCCGACCCATTGA
* *
336410 CCGACCTGACCCGTTGA
1 CCGACCCGACCCATTGA
336427 CCG
1 CCG
336430 GGTGATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.14
Consensus pattern (17 bp):
CCGACCCGACCCATTGA
Found at i:336476 original size:29 final size:29
Alignment explanation
Indices: 336429--336511 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 29
336419 CCCGTTGACC
*
336429 GGGTGATATTTTG-GAAATTAATTCGAAAT
1 GGGTGCTATTTTGAG-AATTAATTCGAAAT
336458 GGGTGCTATTTTGAGAATTAATTCGAAAT
1 GGGTGCTATTTTGAGAATTAATTCGAAAT
*
336487 AGGTGCTATTTT-AGGAATTTAATTC
1 GGGTGCTATTTTGA-GAA-TTAATTC
336512 AAAAAGTGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
28 1 0.02
29 40 0.82
30 8 0.16
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (29 bp):
GGGTGCTATTTTGAGAATTAATTCGAAAT
Found at i:336581 original size:28 final size:28
Alignment explanation
Indices: 336435--336582 Score: 149
Period size: 28 Copynumber: 5.2 Consensus size: 28
336425 GACCGGGTGA
**
336435 TATTTTGGAAATTAATTCGAAATGGGTGC
1 TATTTTGGAAATTAATTCGAAA-AAGTGC
*
336464 TATTTT-GAGAATTAATTCGAAATAGGTGC
1 TATTTTGGA-AATTAATTCGAAA-AAGTGC
*
336493 TATTTTAGGAATTTAATTC-AAAAAGTGC
1 TATTTT-GGAAATTAATTCGAAAAAGTGC
** * *
336521 TATATAGGGAATTTAATTC-AAAAAGTGT
1 TAT-TTTGGAAATTAATTCGAAAAAGTGC
*
336549 TATTTTGGAAATTAAATCGAAAAAGTGC
1 TATTTTGGAAATTAATTCGAAAAAGTGC
336577 TATTTT
1 TATTTT
336583 AGTAATTATT
Statistics
Matches: 103, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.11
28 47 0.46
29 35 0.34
30 8 0.08
31 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (28 bp):
TATTTTGGAAATTAATTCGAAAAAGTGC
Found at i:336589 original size:28 final size:27
Alignment explanation
Indices: 336460--336600 Score: 126
Period size: 28 Copynumber: 5.0 Consensus size: 27
336450 TTCGAAATGG
*
336460 GTGCTATTTT-GAGAATTAATTCGAAATAG
1 GTGCTATTTTAG-GAATTAATTC-AAA-AA
336489 GTGCTATTTTAGGAATTTAATTCAAAAA
1 GTGCTATTTTAGGAA-TTAATTCAAAAA
*
336517 GTGCTA-TATAGGGAATTTAATTCAAAAA
1 GTGCTATTTTA-GGAA-TTAATTCAAAAA
* *
336545 GTGTTATTTT-GGAAATTAAATCGAAAAA
1 GTGCTATTTTAGG-AATTAATTC-AAAAA
* * *
336573 GTGCTATTTTAGTAATTATTTTAAAAA
1 GTGCTATTTTAGGAATTAATTCAAAAA
336600 G
1 G
336601 GGTATCATTT
Statistics
Matches: 95, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
27 17 0.18
28 51 0.54
29 19 0.20
30 8 0.08
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (27 bp):
GTGCTATTTTAGGAATTAATTCAAAAA
Found at i:337384 original size:15 final size:15
Alignment explanation
Indices: 337364--337396 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
337354 TGATACGTGA
337364 TTCCTGAATAT-TGAT
1 TTCCTG-ATATCTGAT
337379 TTCCTGATATCTGAT
1 TTCCTGATATCTGAT
337394 TTC
1 TTC
337397 TGTATTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (15 bp):
TTCCTGATATCTGAT
Found at i:343631 original size:17 final size:17
Alignment explanation
Indices: 343609--343641 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
343599 ACCGGTTCCG
343609 ACTCGACCCGTTGACCT
1 ACTCGACCCGTTGACCT
343626 ACTCGACCCGTTGACC
1 ACTCGACCCGTTGACC
343642 CGACCCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.42, G:0.18, T:0.21
Consensus pattern (17 bp):
ACTCGACCCGTTGACCT
Found at i:343647 original size:13 final size:13
Alignment explanation
Indices: 343629--343654 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343619 TTGACCTACT
343629 CGACCCGTTGACC
1 CGACCCGTTGACC
343642 CGACCCGTTGACC
1 CGACCCGTTGACC
343655 GTTGACCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.46, G:0.23, T:0.15
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:343718 original size:29 final size:28
Alignment explanation
Indices: 343676--343806 Score: 151
Period size: 29 Copynumber: 4.6 Consensus size: 28
343666 ACCGGATGAC
343676 ATTTTGGGAA-TTAATTTAAAATGGGTGCT
1 ATTTTGGGAATTTAATTTAAAA--GGTGCT
*
343705 ATTTTGGGAA-TTAATTTGAAATGGGTGCT
1 ATTTTGGGAATTTAATTT-AAA-AGGTGCT
*
343734 ATTTTGGGAATTTAATTCAAAA-GTGCT
1 ATTTTGGGAATTTAATTTAAAAGGTGCT
* * *
343761 ATATTGGGAATTTAATTCGAAAAAGTGCT
1 ATTTTGGGAATTTAATT-TAAAAGGTGCT
343790 ATTTTGGGAATTTAATT
1 ATTTTGGGAATTTAATT
343807 CGAAAAATGT
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
27 21 0.23
28 4 0.04
29 57 0.63
30 9 0.10
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (28 bp):
ATTTTGGGAATTTAATTTAAAAGGTGCT
Found at i:343768 original size:56 final size:57
Alignment explanation
Indices: 343676--343812 Score: 172
Period size: 56 Copynumber: 2.4 Consensus size: 57
343666 ACCGGATGAC
* * * **
343676 ATTTTGGGAA-TTAATTTAAAATGGGTGCTATTTTGGGAA-TTAATTTGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCAAAA--GGTGCTATATTGGGAATTTAATTCGAAA-AAGTGCT
343734 ATTTTGGGAATTTAATTCAAAA-GTGCTATATTGGGAATTTAATTCGAAAAAGTGCT
1 ATTTTGGGAATTTAATTCAAAAGGTGCTATATTGGGAATTTAATTCGAAAAAGTGCT
343790 ATTTTGGGAATTTAATTCGAAAA
1 ATTTTGGGAATTTAATTC-AAAA
343813 ATGTGTTATT
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
56 37 0.52
57 14 0.20
58 10 0.14
59 10 0.14
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (57 bp):
ATTTTGGGAATTTAATTCAAAAGGTGCTATATTGGGAATTTAATTCGAAAAAGTGCT
Found at i:343807 original size:29 final size:29
Alignment explanation
Indices: 343700--343824 Score: 166
Period size: 29 Copynumber: 4.3 Consensus size: 29
343690 TTTAAAATGG
* **
343700 GTGCTATTTTGGGAA-TTAATTTGAAATGG
1 GTGCTATTTTGGGAATTTAATTCGAAA-AA
343729 GTGCTATTTTGGGAATTTAATTC--AAAA
1 GTGCTATTTTGGGAATTTAATTCGAAAAA
*
343756 GTGCTATATTGGGAATTTAATTCGAAAAA
1 GTGCTATTTTGGGAATTTAATTCGAAAAA
343785 GTGCTATTTTGGGAATTTAATTCGAAAAA
1 GTGCTATTTTGGGAATTTAATTCGAAAAA
*
343814 TGTGTTATTTT
1 -GTGCTATTTT
343825 AGTAATTATT
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
27 22 0.26
28 2 0.02
29 47 0.55
30 15 0.17
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTTAATTCGAAAAA
Found at i:344616 original size:15 final size:15
Alignment explanation
Indices: 344596--344628 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
344586 TGATACATGA
344596 TTCCTGAATAT-TGAT
1 TTCCTG-ATATCTGAT
344611 TTCCTGATATCTGAT
1 TTCCTGATATCTGAT
344626 TTC
1 TTC
344629 TGTATTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (15 bp):
TTCCTGATATCTGAT
Found at i:348413 original size:20 final size:20
Alignment explanation
Indices: 348385--348425 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
348375 ATCTGTAGCC
* *
348385 GGGGTATCTGTACCCCCTGG
1 GGGGAATCTATACCCCCTGG
348405 GGGGAATCTATACCCCCTGG
1 GGGGAATCTATACCCCCTGG
348425 G
1 G
348426 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.34, T:0.22
Consensus pattern (20 bp):
GGGGAATCTATACCCCCTGG
Found at i:349425 original size:15 final size:15
Alignment explanation
Indices: 349405--349446 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
349395 CATTTTTTAT
*
349405 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
349420 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
349437 ATTTTGGATT
1 ATTTTGGATT
349447 TATGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:349431 original size:17 final size:17
Alignment explanation
Indices: 349409--349442 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
349399 TTTTATATTT
*
349409 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
349426 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
349443 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:352243 original size:29 final size:30
Alignment explanation
Indices: 352172--352231 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
352162 CAATTTAAGG
352172 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
352203 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
352232 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:352344 original size:20 final size:20
Alignment explanation
Indices: 352321--352396 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
352311 TTCAAGATTG
* *
352321 CCCAGGGGGTATAGATTCCC
1 CCCAGGGGGTACAGATACCC
352341 CCCAGGGGGTACAGATA--C
1 CCCAGGGGGTACAGATACCC
352359 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATA-CCC
352377 CCCAGGGGGTACAGATACCC
1 CCCAGGGGGTACAGATACCC
352397 TCCTGTAGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
15 11 0.23
18 8 0.17
20 18 0.38
21 11 0.23
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGTACAGATACCC
Found at i:352367 original size:15 final size:15
Alignment explanation
Indices: 352347--352376 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
352337 TCCCCCCAGG
352347 GGGTACAGATACCCC
1 GGGTACAGATACCCC
352362 GGGTACAGATACCCC
1 GGGTACAGATACCCC
352377 CCCAGGGGGT
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:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:352460 original size:21 final size:21
Alignment explanation
Indices: 352434--352474 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
352424 ACAGAATGTC
352434 CAGGGGGTACCGATTCCCCCA
1 CAGGGGGTACCGATTCCCCCA
352455 CAGGGGGTACCGATTCCCCC
1 CAGGGGGTACCGATTCCCCC
352475 CTGTTCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.39, G:0.29, T:0.15
Consensus pattern (21 bp):
CAGGGGGTACCGATTCCCCCA
Found at i:352537 original size:21 final size:21
Alignment explanation
Indices: 352511--352553 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
352501 ATTTGAATAT
*
352511 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
352532 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
352553 T
1 T
352554 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:359913 original size:15 final size:15
Alignment explanation
Indices: 359893--359942 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
359883 CCGTAGGACC
359893 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
359908 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
359923 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
359938 ACTAC
1 ACTAC
359943 AGAACCCTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.28, C:0.34, G:0.24, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:360151 original size:22 final size:20
Alignment explanation
Indices: 360109--360159 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
360099 TCACATTTTG
*
360109 TATATTCATATGTTATTTCA
1 TATATTCACATGTTATTTCA
360129 TATATTCACATAGTT-TTTC-
1 TATATTCACAT-GTTATTTCA
360148 TCAT-TTCACATG
1 T-ATATTCACATG
360160 GTCATGTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 8 0.29
20 16 0.57
21 3 0.11
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (20 bp):
TATATTCACATGTTATTTCA
Found at i:366785 original size:15 final size:15
Alignment explanation
Indices: 366765--366799 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
366755 CCGTAGGACC
366765 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
366780 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
366795 ACTAC
1 ACTAC
366800 AGAACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:370912 original size:20 final size:20
Alignment explanation
Indices: 370887--370927 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
370877 GAAAGCTTGA
370887 CAGAGTTCTTGTCAATCCTT
1 CAGAGTTCTTGTCAATCCTT
370907 CAGAGTTCTTGTCAATCCTT
1 CAGAGTTCTTGTCAATCCTT
370927 C
1 C
370928 TTGGGTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (20 bp):
CAGAGTTCTTGTCAATCCTT
Found at i:371882 original size:20 final size:19
Alignment explanation
Indices: 371857--371926 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
371847 GTTACAGCCA
*
371857 GGGGTTATCGATACCCCTG
1 GGGGGTATCGATACCCCTG
371876 GGGGGTTATCGATA--CCT-
1 GGGGG-TATCGATACCCCTG
*
371893 -GGGGTATGGATACCCCTG
1 GGGGGTATCGATACCCCTG
*
371911 GGGGGTATAGATACCC
1 GGGGGTATCGATACCC
371927 TCCGAGCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
15 7 0.16
16 4 0.09
17 3 0.07
18 3 0.07
19 18 0.42
20 8 0.19
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (19 bp):
GGGGGTATCGATACCCCTG
Found at i:371893 original size:18 final size:19
Alignment explanation
Indices: 371857--371927 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 19
371847 GTTACAGCCA
371857 GGGGTTATCGATACCCCTGG
1 GGGGTTATCGATA-CCCTGG
371877 GGGGTTATCGATA-CCT--
1 GGGGTTATCGATACCCTGG
*
371893 GGGG-TATGGATACCCCTGG
1 GGGGTTATCGATA-CCCTGG
*
371912 GGGG-TATAGATACCCT
1 GGGGTTATCGATACCCT
371928 CCGAGCAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
15 7 0.16
16 4 0.09
17 3 0.07
18 7 0.16
19 11 0.24
20 13 0.29
ACGTcount: A:0.18, C:0.21, G:0.35, T:0.25
Consensus pattern (19 bp):
GGGGTTATCGATACCCTGG
Found at i:371905 original size:35 final size:35
Alignment explanation
Indices: 371857--371925 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
371847 GTTACAGCCA
*
371857 GGGGTTATCGATACCCCTGGGGGGTTATCGATACCT
1 GGGGTTATCGATACCCCTGGGGGG-TATAGATACCT
*
371893 GGGG-TATGGATACCCCTGGGGGGTATAGATACC
1 GGGGTTATCGATACCCCTGGGGGGTATAGATACC
371926 CTCCGAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 9 0.29
35 18 0.58
36 4 0.13
ACGTcount: A:0.19, C:0.20, G:0.36, T:0.25
Consensus pattern (35 bp):
GGGGTTATCGATACCCCTGGGGGGTATAGATACCT
Found at i:372084 original size:29 final size:29
Alignment explanation
Indices: 372064--372120 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
372054 AACTTTGAAT
*
372064 AAATTCAATT-AAGTCTAAAAACATTTTGA
1 AAATTCAATTCAAGTCCAAAAACA-TTTGA
372093 AAATTCAATTCAAGTCCAAAAACCATTT
1 AAATTCAATTCAAGTCCAAAAA-CATTT
372121 TGCCTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATTCAATTCAAGTCCAAAAACATTTGA
Found at i:372092 original size:31 final size:31
Alignment explanation
Indices: 372064--372122 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
372054 AACTTTGAAT
*
372064 AAATTCAATT-AAGTCTAAAAA-CATTTTGA
1 AAATTCAATTCAAGTCCAAAAACCATTTTGA
372093 AAATTCAATTCAAGTCCAAAAACCATTTTG
1 AAATTCAATTCAAGTCCAAAAACCATTTTG
372123 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (31 bp):
AAATTCAATTCAAGTCCAAAAACCATTTTGA
Found at i:374585 original size:22 final size:23
Alignment explanation
Indices: 374560--374603 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
374550 AATTAAGTTT
374560 TAATCTTA-AAA-TAATTTCAAAA
1 TAATCTTACAAAGT-ATTTCAAAA
*
374582 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAGTATTTCAAA
374604 CAATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATCTTACAAAGTATTTCAAAA
Found at i:380393 original size:21 final size:21
Alignment explanation
Indices: 380323--380405 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 21
380313 TTAGTGCAGA
*
380323 GGGAATCGATACTCCCCTTGAAG
1 GGGAATCGAT--TCCCCCTGAAG
*
380346 GGGAA-CTGATTCCCTCTTTGAAG
1 GGGAATC-GATTCCC-C-CTGAAG
*
380369 GGGAATCGATTCCCCCTGTAG
1 GGGAATCGATTCCCCCTGAAG
*
380390 GGGAATCGATACCCCC
1 GGGAATCGATTCCCCC
380406 CTGAGGTTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
21 23 0.43
22 3 0.06
23 26 0.49
24 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.23
Consensus pattern (21 bp):
GGGAATCGATTCCCCCTGAAG
Found at i:382019 original size:18 final size:18
Alignment explanation
Indices: 381982--382022 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
381972 AGAACAGTAC
*
381982 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACGACCA
382000 GAGGAACAAGCAC-ATCCA
1 GAGGAACAAGCACGA-CCA
382018 GAGGA
1 GAGGA
382023 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.44, C:0.22, G:0.32, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACGACCA
Found at i:401514 original size:19 final size:20
Alignment explanation
Indices: 401490--401535 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
401480 TTCGACGTGC
401490 ACGCTC-TCCACATTGAGCT
1 ACGCTCATCCACATTGAGCT
401509 ACGCTCCATCCACATTGAGCT
1 ACGCT-CATCCACATTGAGCT
401530 ACGCTC
1 ACGCTC
401536 CATGTGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.20
20 2 0.08
21 18 0.72
ACGTcount: A:0.22, C:0.39, G:0.15, T:0.24
Consensus pattern (20 bp):
ACGCTCATCCACATTGAGCT
Found at i:401522 original size:21 final size:21
Alignment explanation
Indices: 401496--401538 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
401486 GTGCACGCTC
401496 TCCACATTGAGCTACGCTCCA
1 TCCACATTGAGCTACGCTCCA
401517 TCCACATTGAGCTACGCTCCA
1 TCCACATTGAGCTACGCTCCA
401538 T
1 T
401539 GTGGAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (21 bp):
TCCACATTGAGCTACGCTCCA
Found at i:404351 original size:25 final size:25
Alignment explanation
Indices: 404323--404374 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
404313 AATATGAGGA
404323 GGATTTGGAGGTGAATTTGGTTGAC
1 GGATTTGGAGGTGAATTTGGTTGAC
404348 GGATTTGGAGGTGAATTTGGTTGAC
1 GGATTTGGAGGTGAATTTGGTTGAC
404373 GG
1 GG
404375 TGTGAGCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.04, G:0.42, T:0.35
Consensus pattern (25 bp):
GGATTTGGAGGTGAATTTGGTTGAC
Found at i:404891 original size:20 final size:20
Alignment explanation
Indices: 404854--404892 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
404844 AGATTGAGTG
* * *
404854 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
404874 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
404893 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:405116 original size:20 final size:21
Alignment explanation
Indices: 405070--405130 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
405060 TCCCCTGTGG
405070 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
405093 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
405113 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
405131 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:407693 original size:24 final size:24
Alignment explanation
Indices: 407658--407712 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
407648 TAGAGTTACA
*
407658 AAATTCAGTAAATCCAAGATTTTC
1 AAATTCAATAAATCCAAGATTTTC
407682 AAATTCAATAAATCCAAGATTTTC
1 AAATTCAATAAATCCAAGATTTTC
407706 AAATTCA
1 AAATTCA
407713 GTTCCATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.33
Consensus pattern (24 bp):
AAATTCAATAAATCCAAGATTTTC
Found at i:409026 original size:22 final size:21
Alignment explanation
Indices: 408986--409025 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
408976 GAGTTTGTTT
408986 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
409007 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
409026 ATAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:411489 original size:38 final size:38
Alignment explanation
Indices: 411447--411524 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
411437 CAAAGAGTTA
411447 AGAAGTTTGGGATTTGAATTGCAAGTTCGTAAATTTAG
1 AGAAGTTTGGGATTTGAATTGCAAGTTCGTAAATTTAG
*
411485 AGAAGTTTGGGATTTGAATTGCAAGTTTGTAAATTTAG
1 AGAAGTTTGGGATTTGAATTGCAAGTTCGTAAATTTAG
411523 AG
1 AG
411525 GAATTAGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (38 bp):
AGAAGTTTGGGATTTGAATTGCAAGTTCGTAAATTTAG
Found at i:411512 original size:20 final size:20
Alignment explanation
Indices: 411449--411513 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
411439 AAGAGTTAAG
411449 AAGTTTGGGATTTGAATTGC
1 AAGTTTGGGATTTGAATTGC
* **
411469 AAGTTCGTAAATTT-AGA--G-
1 AAGTTTG-GGATTTGA-ATTGC
411487 AAGTTTGGGATTTGAATTGC
1 AAGTTTGGGATTTGAATTGC
411507 AAGTTTG
1 AAGTTTG
411514 TAAATTTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
17 5 0.15
18 7 0.21
19 2 0.06
20 14 0.42
21 5 0.15
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (20 bp):
AAGTTTGGGATTTGAATTGC
Found at i:412517 original size:17 final size:19
Alignment explanation
Indices: 412489--412537 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
412479 TATTTTGAAA
412489 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
412507 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
412526 CACCGATGCACT
1 CATCGATGCACT
412538 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:420853 original size:64 final size:65
Alignment explanation
Indices: 420736--420880 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 65
420726 TTTTTCAGAG
* * * * *
420736 TGATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTAAACATCGAATGCATT
1 TGATGCATCGATGCACCAAGCCATGCATCGATGCACCATGAACTAAATTAAACATCGAATACAGT
* **
420801 TGATGCATCGATGCACC-AGCCATGCATCGATGCACTC-TG-GCTATTTTGAAACATCGAATACA
1 TGATGCATCGATGCACCAAGCCATGCATCGATGCAC-CATGAACTAAATT-AAACATCGAATACA
420863 GT
64 GT
420865 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
420881 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 4 0.06
64 49 0.70
65 17 0.24
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (65 bp):
TGATGCATCGATGCACCAAGCCATGCATCGATGCACCATGAACTAAATTAAACATCGAATACAGT
Found at i:427734 original size:32 final size:33
Alignment explanation
Indices: 427664--427740 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
427654 CCTAAACCCG
427664 AACCCGACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAA
*
427697 AACCCGACCCGACCCGAATATCAGACTT-AAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAA
427729 AACCCGACCCGA
1 AACCCGACCCGA
427741 ACAAAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 16 0.37
33 27 0.63
ACGTcount: A:0.40, C:0.38, G:0.12, T:0.10
Consensus pattern (33 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAA
Found at i:427797 original size:258 final size:254
Alignment explanation
Indices: 427500--427967 Score: 780
Period size: 258 Copynumber: 1.8 Consensus size: 254
427490 TGAATTAGAA
* *
427500 ACCCGACCCGACACGAAATAAAAAAAATATTTTTATTCAATAAAAATATTGACTTAATTGAAAAA
1 ACCCGACCCGACACGAAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAA
*
427565 AATTATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTT
66 AATTATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
*
427630 TCGGGTTGGATCCGGT-TTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAA
131 TCGGG-TCGA----GTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAA
427694 AAAAA-C-CCGACCCGACCCGAATATCAGACTTAAAAAACCCGACCCGAACAAAATAAAGTTTC
191 AAAAATCACCGACCCGACCCGAATATCAGACTTAAAAAACCCGACCCGAACAAAATAAAGTTTC
*
427756 ACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAA
1 ACCCGACCCGACACGAAAT-A-AAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAA
*
427821 AAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATAT
64 AAAATTATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATAT
*
427886 TTTCGGGTCGAGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAA
129 TTTCGGGTCGAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAA
427951 AATCGACCGACCCGACC
194 AATC-ACCGACCCGACC
427968 AAAATAAAGT
Statistics
Matches: 199, Mismatches: 7, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
253 2 0.01
254 52 0.26
255 1 0.01
256 18 0.09
257 15 0.08
258 111 0.56
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (254 bp):
ACCCGACCCGACACGAAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAA
AATTATATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
TCGGGTCGAGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAA
TCACCGACCCGACCCGAATATCAGACTTAAAAAACCCGACCCGAACAAAATAAAGTTTC
Found at i:445114 original size:21 final size:21
Alignment explanation
Indices: 445090--445129 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
445080 TTTATTTTAT
445090 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
445111 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
445130 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:445177 original size:33 final size:33
Alignment explanation
Indices: 445124--445222 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
445114 TTTGTTTCAA
445124 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
445156 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
445189 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
445222 T
1 T
445223 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:445251 original size:13 final size:13
Alignment explanation
Indices: 445208--445262 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
445198 TTGGAAGTAT
445208 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
445221 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
445235 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
445248 TTAAGTATTTGAA
1 TTAAGTATTTCAA
445261 TT
1 TT
445263 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:445484 original size:21 final size:21
Alignment explanation
Indices: 445458--445514 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
445448 TGGAGCGTGG
*
445458 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
445479 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
445500 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
445515 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:445719 original size:17 final size:18
Alignment explanation
Indices: 445699--445732 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
445689 GTTTTTTTAT
445699 AACC-GGTTTTTTAAAAA
1 AACCAGGTTTTTTAAAAA
*
445716 AACCAGTTTTTTTAAAA
1 AACCAGGTTTTTTAAAA
445733 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCAGGTTTTTTAAAAA
Found at i:445852 original size:15 final size:17
Alignment explanation
Indices: 445826--445857 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
445816 TTCTATGAGA
445826 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
445842 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
445858 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:447677 original size:20 final size:20
Alignment explanation
Indices: 447652--447690 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
447642 AACAAAGAAA
447652 AGATAATTCCTAAAAATAAG
1 AGATAATTCCTAAAAATAAG
* *
447672 AGATAATTTCTAAAGATAA
1 AGATAATTCCTAAAAATAA
447691 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (20 bp):
AGATAATTCCTAAAAATAAG
Found at i:448910 original size:2 final size:2
Alignment explanation
Indices: 448903--448942 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
448893 CCAAAACATA
448903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
448943 TATGTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:450560 original size:4 final size:4
Alignment explanation
Indices: 450551--453254 Score: 5317
Period size: 4 Copynumber: 679.2 Consensus size: 4
450541 AAGGGGATGA
450551 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450599 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450647 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450695 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450743 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450791 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450839 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450887 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450935 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
450983 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451031 ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451077 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451125 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451171 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451219 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451267 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451315 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451363 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451411 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451459 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451507 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451555 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451603 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451651 ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451698 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451746 ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451792 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451840 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451888 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451934 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
451982 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452030 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452078 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452126 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452174 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452222 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452270 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452318 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452366 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452414 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452462 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452510 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452558 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452604 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452652 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452700 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452748 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452795 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452843 ATGT ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452890 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452938 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
452986 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
453034 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
453082 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
453130 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
453178 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
453226 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
453255 ATGGTTATAT
Statistics
Matches: 2687, Mismatches: 0, Indels: 26
0.99 0.00 0.01
Matches are distributed among these distances:
2 10 0.00
3 9 0.00
4 2668 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:453535 original size:30 final size:30
Alignment explanation
Indices: 453501--453633 Score: 221
Period size: 30 Copynumber: 4.4 Consensus size: 30
453491 GGTTCTTCGG
* * *
453501 GACCTATGGACAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
453531 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
453561 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
453591 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
453621 GACCTCTGGATAG
1 GACCTCTGGATAG
453634 GTCATTCAGA
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 99 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:453576 original size:60 final size:60
Alignment explanation
Indices: 453474--453633 Score: 221
Period size: 60 Copynumber: 2.6 Consensus size: 60
453464 CTAAGGAACA
* * *** * * *
453474 TATGGATAGTTTACCTAGGTTCTTCGGGACCTATGGACAGTTACCGATGATCTTTATGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTATGACC
453535 TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTATGACC
* *
453595 TCTGGATAGTTACTGAGGATCTTTATGACCTCTGGATAG
1 TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAG
453634 GTCATTCAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 80 0.90
61 9 0.10
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (60 bp):
TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTATGACC
Found at i:456108 original size:21 final size:22
Alignment explanation
Indices: 456065--456108 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
456055 TAGAGATGAT
*
456065 CAACAAGACCCACCTCATCCATA
1 CAACAAGA-CCACATCATCCATA
*
456088 CAACAAGA-CACATCATTCATA
1 CAACAAGACCACATCATCCATA
456109 TCAAGAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.43, C:0.36, G:0.05, T:0.16
Consensus pattern (22 bp):
CAACAAGACCACATCATCCATA
Found at i:461526 original size:14 final size:14
Alignment explanation
Indices: 461507--461540 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
461497 GATACAAGAG
461507 TGTAATTATAAAAC
1 TGTAATTATAAAAC
461521 TGTAATTATAAAAC
1 TGTAATTATAAAAC
*
461535 AGTAAT
1 TGTAAT
461541 AGTTCCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (14 bp):
TGTAATTATAAAAC
Found at i:464530 original size:19 final size:18
Alignment explanation
Indices: 464486--464531 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
464476 TTATATTTAC
*
464486 TAATAATTTAATTTTAAA
1 TAATTATTTAATTTTAAA
*
464504 TATTTTATTTAAATTTTAAA
1 TA-ATTATTT-AATTTTAAA
464524 TAATTATT
1 TAATTATT
464532 CTTAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 11 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTATTTAATTTTAAA
Found at i:464538 original size:21 final size:20
Alignment explanation
Indices: 464495--464538 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
464485 CTAATAATTT
*
464495 AATTTTAAATATTTTATTTA
1 AATTTTAAATATTTTACTTA
464515 AATTTTAAATAATTATT-CTTA
1 AATTTTAAAT-ATT-TTACTTA
464536 AAT
1 AAT
464539 AATTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 9 0.43
22 2 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTAAATATTTTACTTA
Found at i:465024 original size:16 final size:16
Alignment explanation
Indices: 464993--465034 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
464983 TATAATCTAA
*
464993 AAATAAATATTATAGAT
1 AAATAGATA-TATAGAT
*
465010 AGATAGATATATAGAT
1 AAATAGATATATAGAT
465026 AAATAGATA
1 AAATAGATA
465035 AAAAAAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (16 bp):
AAATAGATATATAGAT
Found at i:467553 original size:20 final size:21
Alignment explanation
Indices: 467522--467567 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
467512 ACTGGAAATA
*
467522 TTATTATTTCTACCGGTTTTG
1 TTATTATTTCTACCAGTTTTG
*
467543 TTATT-TTTCTATCAGTTTTG
1 TTATTATTTCTACCAGTTTTG
467563 TTATT
1 TTATT
467568 GTTAGATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.63
Consensus pattern (21 bp):
TTATTATTTCTACCAGTTTTG
Found at i:468193 original size:17 final size:16
Alignment explanation
Indices: 468173--468217 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
468163 AGTTTTTAAA
468173 AAAATAAAAATAAGAAT
1 AAAATAAAAATAA-AAT
*
468190 AAAATAATAAGTAAAAT
1 AAAATAA-AAATAAAAT
468207 -AAATAAAAATA
1 AAAATAAAAATA
468218 TATGTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 4 0.16
16 6 0.24
17 10 0.40
18 5 0.20
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:468224 original size:21 final size:22
Alignment explanation
Indices: 468190--468230 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
468180 AAATAAGAAT
468190 AAAATAATAAGTAAAATAAATA
1 AAAATAATAAGTAAAATAAATA
* *
468212 AAAAT-ATATGTAAACTAAA
1 AAAATAATAAGTAAAATAAA
468231 ACCGTGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAATAATAAGTAAAATAAATA
Found at i:468682 original size:3 final size:3
Alignment explanation
Indices: 468674--468708 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
468664 TTTTGTTTGT
468674 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
468709 TAAGACATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:469939 original size:84 final size:82
Alignment explanation
Indices: 469696--470860 Score: 985
Period size: 84 Copynumber: 14.2 Consensus size: 82
469686 TGCCTTGGGC
* ** * *
469696 TATGCTGTAAATGATGTGCCTAAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGT-GCAGATA
* * *
469761 ACCCTTAT-AACCTTGAGT
65 ACCCTTCTCGA-CTTAAGT
* * * * ** * *
469779 TATGTTTCAAATGATGTGCCCTCGAAATTGAGTGTAATCGAACTTGAAGGTCTTTGG-G-AGATA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGCAGATA
*
469842 ACCCTTCTCGACTTAAGC
65 ACCCTTCTCGACTTAAGT
* * * *
469860 TATGCTGCAAATAATGTGCCTTGGAGTTGAACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG-TG-CAGAT
469925 AACCCTTCTCGACTTAAGT
64 AACCCTTCTCGACTTAAGT
* ** * *
469944 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTGGTTGAACTCGAAGGTCTTTAGTGACAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTG-CAGATA
* * *
470009 ACCCTTCTAGCCTTGAGT
65 ACCCTTCTCGACTTAAGT
* * * * * * * * *
470027 TATGTTGTAAATAATATGCCCTTGAAGTTGAGTGTAATCGAACTCGAGGGTATTT-G-GCAGATA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGCAGATA
* * * *
470090 GCCCTTTTTGACTTAAGC
65 ACCCTTCTCGACTTAAGT
* *
470108 TATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG-T-GCAGAT
*
470173 AACCCTTCTCGATTTAAGT
64 AACCCTTCTCGACTTAAGT
* * * * * * * *
470192 TATGCTGCAAATGATATGCCATGGAGCTGAACGCAGTCGAACTTGAAGATCTTTGGTGATAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTG-CAGATA
* * *
470257 ACCCTTTTAGCCTTGAA-T
65 ACCCTTCTCGACTT-AAGT
* * * * * *
470275 TATGCTGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCGAGGGTCTTT-G-GCAGATA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGCAGATA
*
470338 GCCCTTCTCGACTTAAGT
65 ACCCTTCTCGACTTAAGT
*** * * * * ** *
470356 TATGCAAAAAATGATGTGCCCTCGAAGCTGAGTGTAATGGAACTCGGGGGTCTTT-G-GCAAATA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGCAGATA
*
470419 ACCCTTCTCGACTTAAGC
65 ACCCTTCTCGACTTAAGT
* * * *
470437 TATGCTGCAAATGGTGTGCCTTTGAGCTGAACGTAATCGAACTCGAAGGTCTTTTGGTGATAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTG-CAGAT
* * *
470502 AACCCTTCTAGCCTTGAGT
64 AACCCTTCTCGACTTAAGT
* * * * * * ** *
470521 TATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGCCTTTGGT--AGATA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGCAGATA
* *
470584 GCCCTTCTCGACTTAAGC
65 ACCCTTCTCGACTTAAGT
** * * *
470602 TATATTGCAAATGATGTGCCTTGGAGCTGAACGTAATCGAACTCAAAGGTCTTTTGGTGATAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTG-CAGAT
* * *
470667 AACCCTTCTAGCCTTGAGT
64 AACCCTTCTCGACTTAAGT
* * * * * * *
470686 TATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTT-G-GCAGATA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGCAGATA
*
470749 GCCCTTCTCGACTTAAGT
65 ACCCTTCTCGACTTAAGT
* * * * * *
470767 TATTCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGTTGGCA-AAA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGT-GCAGATA
* * *
470830 ACCCTTCTAGCCTTGAGT
65 ACCCTTCTCGACTTAAGT
470848 TATGCTGCAAATG
1 TATGCTGCAAATG
470861 TTGTCTTTTA
Statistics
Matches: 862, Mismatches: 192, Indels: 58
0.78 0.17 0.05
Matches are distributed among these distances:
79 2 0.00
80 138 0.16
81 270 0.31
82 11 0.01
83 91 0.11
84 300 0.35
85 50 0.06
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (82 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGCAGATAA
CCCTTCTCGACTTAAGT
Found at i:470145 original size:248 final size:247
Alignment explanation
Indices: 469696--470860 Score: 1268
Period size: 248 Copynumber: 4.7 Consensus size: 247
469686 TGCCTTGGGC
* ** * * *
469696 TATGCTGTAAATGATGTGCCTAAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
* * * ** *
469761 ACCCTTATAACCTTGAGTTATG-TTTCAAATGATGTGCCCTCGAAATTGAGTGTAATCGAACTTG
66 ACCCTTCTAGCCTTGAGTTATGCTGT-AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * * * *
469825 AAGGTCTTTGGGAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTGGAGTTGA
130 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
*
469890 ACGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGT
195 ACGTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTCGACTTAAGT
* * * * *
469944 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTGGTTGAACTCGAAGGTCTTTAGTGACAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
* * * * *
470009 ACCCTTCTAGCCTTGAGTTATGTTGTAAATAATATGCCCTTGAAGTTGAGTGTAATCGAACTCGA
66 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA
* * * * *
470074 GGGTATTTGGCAGATAGCCCTTTTTGACTTAAGCTATGCTGCAAATGATGCGCCTTGGAGCTGAG
131 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAA
* * *
470139 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGT
196 CGTAATCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTCGACTTAAGT
* * * * * *
470192 TATGCTGCAAATGATATGCCATGGAGCTGAACGCAGTCGAACTTGAAGATCTTTGGTGATAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
* * *
470257 ACCCTTTTAGCCTTGAATTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCGA
66 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA
* *** * *
470322 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCAAAAAATGATGTGCCCTCGAAGCTGA
131 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGA
** * ** * *
470387 GTGTAATGGAACTCGGGGGTCTTT-G-G-CAAATAACCCTTCTCGACTTAAGC
195 ACGTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGT
* * * *
470437 TATGCTGCAAATGGTGTGCCTTTGAGCTGAACGTAATCGAACTCGAAGGTCTTTTGGTGATAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTC-TTTGGTGACAGAT
* *
470502 AACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCG
65 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * * **
470567 GGGGCCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATGATGTGCCTTGGAGCTGA
130 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
* * * * *
470632 ACGTAATCGAACTCAAAGGTCTTTTGGTGATAGATAACCCTTCTAGCCTTGAGT
195 ACGTAATCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTCGACTTAAGT
* * * * ** * * *
470686 TATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTT-G-G-CAGAT
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
* * * * * * * * * * * *
470748 AGCCCTTCTCGACTTAAGTTATTCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCA
65 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * * * * * *
470812 AAGGTCTTGTTGGCA-AAAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
130 AGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
470861 TTGTCTTTTA
Statistics
Matches: 771, Mismatches: 136, Indels: 22
0.83 0.15 0.02
Matches are distributed among these distances:
245 113 0.15
246 182 0.24
247 7 0.01
248 376 0.49
249 67 0.09
250 26 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (247 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGA
GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAA
CGTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGT
Found at i:470535 original size:165 final size:164
Alignment explanation
Indices: 469669--470860 Score: 1055
Period size: 165 Copynumber: 7.2 Consensus size: 164
469659 ACAATTTTAT
* * * * * * * * *
469669 TGACATATAACTCTTATTGCCTTGGGCTATGCTGTAAATGATGTG-CCT-AAGAGCTGAGCGTAG
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA-AGCTGAGTGTAA
* * * * * * *
469732 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTAT-AACCTTGAGTTATGTTTCAAATGATGT
65 TCGAACTCGAGGGTC--T-TTGGCAGATAACCCTTCTCGA-CTTAAGCTATGCTGCAAATGATGT
* * ** ** *
469796 GCCCTCGAAATTGAGTGTAATCGAACTTGAAGGTCTTTGG
126 G-CCTTGGAGCTGAACGTAATCGAACTCGAAGGTCTTTGG
* * * * * * * * * ** *
469836 -G--AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGTG-CCTTGGAGTTGAACGTAGT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* * *
469897 CGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
66 CGAACTCGAGGGTCTTT-G--G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* ** * *
469962 CCTTGGAGCTGAGCGTGGTTGAACTCGAAGGTCTTTAG
127 CCTTGGAGCTGAACGTAATCGAACTCGAAGGTCTTTGG
* * * * *
470000 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATATGCCCTTGAAGTTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* * * * *
470065 CGAACTCGAGGGTATTTGGCAGATAGCCCTTTTTGACTTAAGCTATGCTGCAAATGATGCGCCTT
66 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
470130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
131 GGAGCTGAACGTAATCGAACTCGAAGGTCTTTGG
* * ** * * * * * ** * *
470164 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCAT-GGAGCTGAACGCAG
1 -TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * * * * * * * *
470228 TCGAACTTGAAGATCTTTGGTGATAGATAACCCTTTTAGCCTTGAA-TTATGCTGTAAATGATGT
65 TCGAACTCGAGGGTCTTT-G-G-CAGATAACCCTTCTCGACTT-AAGCTATGCTGCAAATGATGT
* * * *
470292 GCCCTCGAAGCT-AAGTGTAATCGAACTCGAGGGTCTTT-G
126 G-CCTTGGAGCTGAA-CGTAATCGAACTCGAAGGTCTTTGG
* * * * ***
470331 -G-CAGATAGCCCTTCTCGACTTAAGTTATGCAAAAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* * * *
470394 GGAACTCGGGGGTCTTTGGCAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGGTGTGCCTT
66 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
*
470459 TGAGCTGAACGTAATCGAACTCGAAGGTCTTTTGG
131 GGAGCTGAACGTAATCGAACTCGAAGGTC-TTTGG
* *
470494 TGATAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* * * * * **
470559 TGAACTCGGGGGCCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATATTGCAAATGATGTGCCTT
66 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
*
470624 GGAGCTGAACGTAATCGAACTCAAAGGTCTTTTGG
131 GGAGCTGAACGTAATCGAACTCGAAGGTC-TTTGG
* *
470659 TGATAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* * * * *
470724 CGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATTCTGCAAATGATATGCCTT
66 CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
* * * *
470789 GGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGT
131 GGAGCTGAACGTAATCGAACTCGAAGGTCTTTGG
* * *
470822 TGGCA-AAAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
470861 TTGTCTTTTA
Statistics
Matches: 850, Mismatches: 151, Indels: 53
0.81 0.14 0.05
Matches are distributed among these distances:
161 29 0.03
162 69 0.08
163 8 0.01
164 223 0.26
165 389 0.46
166 3 0.00
167 69 0.08
168 60 0.07
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (164 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
CGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
GGAGCTGAACGTAATCGAACTCGAAGGTCTTTGG
Found at i:474141 original size:279 final size:280
Alignment explanation
Indices: 473641--474202 Score: 1117
Period size: 279 Copynumber: 2.0 Consensus size: 280
473631 AACCCGGATT
473641 ATTCTCAGTGTTAAATACAGAGACCGAGGGCTTCGCTTTTGTAGTACATGTGTCCCCTCGAAGTT
1 ATTCTCAGTGTTAAATACAGAGACCGAGGGCTTCGCTTTTGTAGTACATGTGTCCCCTCGAAGTT
473706 CCGGTAAGATTTCAGGTGAGACAACTACTTGTGGGGTAGGTGGTATAGTTACCCCTTCCGGTAAA
66 CCGGTAAGATTTCAGGTGAGACAACTACTTGTGGGGTAGGTGGTATAGTTACCCCTTCCGGTAAA
473771 CCTACCCCAGGCGCACTAGTCTGTTGTAAGCCAACTAACTTGGCAACAATCTGATCAACCAAAGA
131 CCTACCCCAGGCGCACTAGTCTGTTGTAAGCCAACTAACTTGGCAACAATCTGATCAACCAAAGA
473836 CTCTTGGTTCTTCATGATTGTATTCAGAGTACTCTGGTTTAT-TTGTCTTCAAGTTCTTTCTGCA
196 CTCTTGGTTCTTCATGATTGTATTCAGAGTACTCTGGTTTATCTTGTCTTCAAGTTCTTTCTGCA
473900 ATTTTGCCATGTTCTCCTCG
261 ATTTTGCCATGTTCTCCTCG
473920 ATTCTCAGTGTTAAATACAGAGACCGAGGGCTTCGCTTTTGTAGTACATGTGTCCCCTCGAAGTT
1 ATTCTCAGTGTTAAATACAGAGACCGAGGGCTTCGCTTTTGTAGTACATGTGTCCCCTCGAAGTT
473985 CCGGTAAGATTTCAGGTGAGACAACTACTTGTGGGGTAGGTGGTATAGTTACCCCTTCCGGTAAA
66 CCGGTAAGATTTCAGGTGAGACAACTACTTGTGGGGTAGGTGGTATAGTTACCCCTTCCGGTAAA
474050 CCTACCCCAGGCGCACTAGTCTGTTGTAAGCCAACTAACTTGGCAACAATCTGATCAACCAAAGA
131 CCTACCCCAGGCGCACTAGTCTGTTGTAAGCCAACTAACTTGGCAACAATCTGATCAACCAAAGA
474115 CTCTTGGTTCTTCATGATTGTATTCAGAGTACTCTGGTTTATCTTGTCTTCAAGTTCTTTCTGCA
196 CTCTTGGTTCTTCATGATTGTATTCAGAGTACTCTGGTTTATCTTGTCTTCAAGTTCTTTCTGCA
474180 ATTTTGCCATGTTCTCCTCG
261 ATTTTGCCATGTTCTCCTCG
474200 ATT
1 ATT
474203 TCTCCATTCT
Statistics
Matches: 282, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
279 237 0.84
280 45 0.16
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (280 bp):
ATTCTCAGTGTTAAATACAGAGACCGAGGGCTTCGCTTTTGTAGTACATGTGTCCCCTCGAAGTT
CCGGTAAGATTTCAGGTGAGACAACTACTTGTGGGGTAGGTGGTATAGTTACCCCTTCCGGTAAA
CCTACCCCAGGCGCACTAGTCTGTTGTAAGCCAACTAACTTGGCAACAATCTGATCAACCAAAGA
CTCTTGGTTCTTCATGATTGTATTCAGAGTACTCTGGTTTATCTTGTCTTCAAGTTCTTTCTGCA
ATTTTGCCATGTTCTCCTCG
Found at i:474361 original size:20 final size:21
Alignment explanation
Indices: 474336--474378 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
474326 ATGTGAATGC
474336 AAAGAAAATAACAAAATG-AA
1 AAAGAAAATAACAAAATGCAA
474356 AAAGAAAATAACAAAATGCAA
1 AAAGAAAATAACAAAATGCAA
474377 AA
1 AA
474379 TGTCTAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAGAAAATAACAAAATGCAA
Found at i:476681 original size:3 final size:3
Alignment explanation
Indices: 476673--476697 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
476663 GTTTTGTTTA
476673 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
476698 TAAAACATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:477281 original size:15 final size:15
Alignment explanation
Indices: 477228--477289 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
477218 AAAATAAATG
*
477228 AAAATATATATTATGT
1 AAAATA-ATATTATAT
*
477244 AATATAATA--ATAT
1 AAAATAATATTATAT
*
477257 -AACT-ATATTATAT
1 AAAATAATATTATAT
*
477270 AAAATAATATTAGAT
1 AAAATAATATTATAT
477285 AAAAT
1 AAAAT
477290 TTAGTGTCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 3 0.08
12 2 0.06
13 7 0.19
14 3 0.08
15 16 0.44
16 5 0.14
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAATAATATTATAT
Found at i:478988 original size:227 final size:227
Alignment explanation
Indices: 478058--479368 Score: 1227
Period size: 227 Copynumber: 5.8 Consensus size: 227
478048 AACCTTCGTG
* * * * * * *
478058 AAGACCCTTACTGGCAAGACCATCACCCTT-GAGGTGGAAAGCTCCGACACCATTGATAATGTCA
1 AAGACACTCACTGGGAAGACCATCA-CATTGGAGGTTGAGAGCTCCGACACCATTGACAATGTCA
* * * * * * * * * *
478122 AGGCCAAGATCCAGGACAAGGAAGGAATCCCACCAGACCAACAGTGGCTTATCTTTGC-TGAAAA
65 AGGCTAAGATCCAGGATAAGGAAGGTATCCCCCCGGACCAGCAGAGGCTGATCTTTGCAGGGAAA
* * * * * * * *
478186 CAGCTGGAGG-GGGCCGTACCCTTGCCGACTACAACATTCAGAAGGAGTCCACCCTCCACTTGGT
130 CAGCTCGAGGATGGCAGGACCCTTGCTGACTACAACATCCAGAAAGAATCCACCCT-CACTTGGT
* * * ** * * * * *
478250 CCTTCGTTTGAGGGGTTGTATGCAAATCTTTGTT
194 GCTCCGTCTCCGTGGTGGTATGCAGATTTTTGTC
* * * * * * * * * * *
478284 AAGACCCTTACTGGCAAGACTATCA-ACCTCGAGGTGGAAAGCTCCGACACCATTAATAACGTCA
1 AAGACACTCACTGGGAAGACCATCACA-TTGGAGGTTGAGAGCTCCGACACCATTGACAATGTCA
* * * * * * * ** * *
478348 AGGCAAAGATTCAAGACAAGGAAGGGATTCCCCCAGACCAGCAGAGATTGATCTTTGCCGGTAAA
65 AGGCTAAGATCCAGGATAAGGAAGGTATCCCCCCGGACCAGCAGAGGCTGATCTTTGCAGGGAAA
* * * * * *
478413 CAACTCGAGGATGGC--CACACCTTGGCTGACTATAACATCCAGAAGGAATCTAACCTTCACTTG
130 CAGCTCGAGGATGGCAGGAC-CCTT-GCTGACTACAACATCCAGAAAGAATC-CACCCTCACTTG
*
478476 GTGCTCCGTCTCCGTGGGTGGTATGCAGATTTTTGTG
192 GTGCTCCGTCTCCGT-GGTGGTATGCAGATTTTTGTC
* * * *
478513 AAGACACTCACTGGGAAGACCATCACCTTGGAGGTTGAGAGCTCGGACA-TATTAACAATGTCAA
1 AAGACACTCACTGGGAAGACCATCACATTGGAGGTTGAGAGCTCCGACACCATTGACAATGTCAA
* * * ** * * * *
478577 GGCTAAGATTCA-GATAAGGAGGGTAT-CCACCATACCAGCAGAGGTTGATATTTGCCGGTAAAA
66 GGCTAAGATCCAGGATAAGGAAGGTATCCCCCCGGACCAGCAGAGGCTGATCTTTGCAGG-GAAA
* * * * * *
478640 CAACTCGAAGATGGC-CG-CACTTGGCTGACTACAACGTTCA-AAAGGAATCCACCCTTCACTTG
130 CAGCTCGAGGATGGCAGGACCCTT-GCTGACTACAACATCCAGAAA-GAATCCACCC-TCACTTG
* *
478702 GTGCT--G-C-CCGTGGTGGTATGCAG-GTTTTGTG
192 GTGCTCCGTCTCCGTGGTGGTATGCAGATTTTTGTC
*
478733 AAGACACTCACTGGGAAGACCATCACATTGGAGGTTGAGAGCTCGGACACCATTGACAATGTCAA
1 AAGACACTCACTGGGAAGACCATCACATTGGAGGTTGAGAGCTCCGACACCATTGACAATGTCAA
* * *
478798 GGCTAAGATCCAGGATAAGGAAGGTATCCCCCCGGTCCAGCAGAGGCTAATCTTTGCAGGGAAGC
66 GGCTAAGATCCAGGATAAGGAAGGTATCCCCCCGGACCAGCAGAGGCTGATCTTTGCAGGGAAAC
* * *
478863 AGCTGGAGGATGGCAGGACCCTTGCTGACTACAACATCCAGAAAGAATCTACCCTCATTTGGTGC
131 AGCTCGAGGATGGCAGGACCCTTGCTGACTACAACATCCAGAAAGAATCCACCCTCACTTGGTGC
* *
478928 TCCGTTTCCGTGGTGGTATGTAGATTTTTGTC
196 TCCGTCTCCGTGGTGGTATGCAGATTTTTGTC
* * *
478960 AAGACACTCACAGGGAAGACCTTCACATTGGAGGTTGAGAGCT-CGAACACCATTGATAATGTCA
1 AAGACACTCACTGGGAAGACCATCACATTGGAGGTTGAGAGCTCCG-ACACCATTGACAATGTCA
** * * * *
479024 AGGCTAAGATCCAGGATAAGGAAGGTATCCCTGCGGACCGGCAGAGGATAATCTTTGCAGGGAAG
65 AGGCTAAGATCCAGGATAAGGAAGGTATCCCCCCGGACCAGCAGAGGCTGATCTTTGCAGGGAAA
* * * *
479089 CAGCTCGAGGATGGCAGGACTCTTGCTGACTACAACATCCTGAAAGAGTCGACCCTTCACTTGGT
130 CAGCTCGAGGATGGCAGGACCCTTGCTGACTACAACATCCAGAAAGAATCCACCC-TCACTTGGT
479154 GCTCCGTCTCCGTGGTGGTATGCAGATTTTTGTC
194 GCTCCGTCTCCGTGGTGGTATGCAGATTTTTGTC
* * * * *
479188 AAGACACCCACAGGGAAGACCATCACCTTGGAGGTTGAGAGCTCCAACACCATTGACAATGTGAA
1 AAGACACTCACTGGGAAGACCATCACATTGGAGGTTGAGAGCTCCGACACCATTGACAATGTCAA
* *
479253 GGCTAAGATCCAGGATAACTGGATAAGGAAGGGATACCCCCGGACCAGCAGAGGCTGATCTTTGC
66 GGCTAAGATCC------A--GGATAAGGAAGGTATCCCCCCGGACCAGCAGAGGCTGATCTTTGC
* * * * * *
479318 AGGGAAGCAGCTGGAGGATGGCAGGACTCTTGCGGAGTACAATATCCAGAA
123 AGGGAAACAGCTCGAGGATGGCAGGACCCTTGCTGACTACAACATCCAGAA
479369 GGAACTCACT
Statistics
Matches: 917, Mismatches: 133, Indels: 60
0.83 0.12 0.05
Matches are distributed among these distances:
220 55 0.06
221 36 0.04
222 42 0.05
223 50 0.05
224 9 0.01
225 6 0.01
226 184 0.20
227 219 0.24
228 171 0.19
229 60 0.07
234 1 0.00
236 84 0.09
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (227 bp):
AAGACACTCACTGGGAAGACCATCACATTGGAGGTTGAGAGCTCCGACACCATTGACAATGTCAA
GGCTAAGATCCAGGATAAGGAAGGTATCCCCCCGGACCAGCAGAGGCTGATCTTTGCAGGGAAAC
AGCTCGAGGATGGCAGGACCCTTGCTGACTACAACATCCAGAAAGAATCCACCCTCACTTGGTGC
TCCGTCTCCGTGGTGGTATGCAGATTTTTGTC
Found at i:479845 original size:63 final size:66
Alignment explanation
Indices: 479769--479900 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 66
479759 GTTCACACTT
* *
479769 TTGAAGTTGGTAAGTACGAGTTGAAATAAAAAAT-TACAGTTCG-A-TTTGAGTTCG-ATTTTAA
1 TTGAAATTGGTAAGTACGAGTTGAAATAAAAAATATAC-GTTCGAATTTTAAGTTCGAATTTTAA
479830 AA
65 AA
* * * *
479832 TTGAAATTGGTAAGTATGATTTGAAATAAAAAATATGCGTTCGAATTTTAAGTTTGAATTTTAAA
1 TTGAAATTGGTAAGTACGAGTTGAAATAAAAAATATACGTTCGAATTTTAAGTTCGAATTTTAAA
479897 A
66 A
479898 TTG
1 TTG
479901 GTAAGTACGA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
63 36 0.61
64 3 0.05
65 8 0.14
66 12 0.20
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.38
Consensus pattern (66 bp):
TTGAAATTGGTAAGTACGAGTTGAAATAAAAAATATACGTTCGAATTTTAAGTTCGAATTTTAAA
A
Found at i:479969 original size:64 final size:60
Alignment explanation
Indices: 479832--479988 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 60
479822 GATTTTAAAA
* *
479832 TTGAAATTGGTAAGTATGATTTGAAATAAAAAATATGCGTTCGAATTTTAAGTTTGAATT
1 TTGAAATTGGTAAGTATGATTTGAAATAAAAAAAATGCGTTCGAATGTTAAGTTTGAATT
* *
479892 TTAAAATTGGTAAGTACGATTTGAAATAAAAAAAATTG-GAATTCGAAATGAGTT-AGTTCT-AA
1 TTGAAATTGGTAAGTATGATTTGAAATAAAAAAAA-TGCG--TTCG-AAT--GTTAAGTT-TGAA
479954 TT
59 TT
* *
479956 TTGAAATTAGTAAGTATGACTTGAAATAAAAAA
1 TTGAAATTGGTAAGTATGATTTGAAATAAAAAA
479989 CTAGAGTTGA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
60 33 0.40
61 2 0.02
62 4 0.05
63 3 0.04
64 37 0.45
65 3 0.04
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (60 bp):
TTGAAATTGGTAAGTATGATTTGAAATAAAAAAAATGCGTTCGAATGTTAAGTTTGAATT
Found at i:480029 original size:55 final size:56
Alignment explanation
Indices: 479946--480122 Score: 207
Period size: 55 Copynumber: 3.1 Consensus size: 56
479936 GAAATGAGTT
* * * *
479946 AGTTCTAATTTTGAAATTAGTAAGTATGACTTGAAATAAAAAACTAGAGTTGA-TTG
1 AGTTCAAATTTTGAAATTAGTAAGTATGACTCGAAAT-AAAAATTGGAGTTGATTTG
* ** *
480002 AGTTCAAATTTT-AAATTGGTTGGTATGACTCGAAAT-CAAATTGGAGTTTGATTTG
1 AGTTCAAATTTTGAAATTAGTAAGTATGACTCGAAATAAAAATTGGAG-TTGATTTG
*
480057 AGTTCGAATTTTGAAATTAGTAAGTATGACTCGAAATTAAAAATTGGAGTTCGATTTG
1 AGTTCAAATTTTGAAATTAGTAAGTATGACTCGAAA-TAAAAATTGGAGTT-GATTTG
*
480115 AATTCAAA
1 AGTTCAAA
480123 AAATTTGAAC
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
53 7 0.07
54 4 0.04
55 34 0.34
56 31 0.31
57 3 0.03
58 21 0.21
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (56 bp):
AGTTCAAATTTTGAAATTAGTAAGTATGACTCGAAATAAAAATTGGAGTTGATTTG
Found at i:484271 original size:32 final size:32
Alignment explanation
Indices: 484230--484326 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
484220 AAGAGTCGGG
484230 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
484262 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
484293 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
484325 TT
1 TT
484327 ACTGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:484316 original size:31 final size:31
Alignment explanation
Indices: 484232--484324 Score: 116
Period size: 31 Copynumber: 3.0 Consensus size: 31
484222 GAGTCGGGTT
* *
484232 TACCTATGTTCTACGGAACATATGGACAGTTT
1 TACCTATGTTCTAAGGAACATATGGACAG-TA
***
484264 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGGA-ACATATGGACAGTA
484295 TACCTATGTTCTAAGGAACATATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
484325 TTACTGAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 27 0.52
32 25 0.48
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:484366 original size:30 final size:30
Alignment explanation
Indices: 484317--484408 Score: 109
Period size: 29 Copynumber: 3.1 Consensus size: 30
484307 AAGGAACATA
*
484317 TGGACAGTTTACTGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
484348 TGGACAGTTACCGAGGATC-TTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
484377 TGGATAGTTA-CG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
484405 TGGA
1 TGGA
484409 TAGGTCCTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.07
28 14 0.25
29 19 0.35
30 11 0.20
31 7 0.13
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:490035 original size:45 final size:45
Alignment explanation
Indices: 489986--490085 Score: 164
Period size: 45 Copynumber: 2.2 Consensus size: 45
489976 CGAAATCTTT
*
489986 TATTTTCCTAAAATCTACCTCACACGTGGCCTCCTATCAATCGTA
1 TATTTTCCTAAAATCTACCTCACACGTGGCCTCATATCAATCGTA
* * *
490031 TATTTTCCTAAAATCTACCTCACACGTGGCTTCATATCGATCGTT
1 TATTTTCCTAAAATCTACCTCACACGTGGCCTCATATCAATCGTA
490076 TATTTTCCTA
1 TATTTTCCTA
490086 CTTTTCTTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (45 bp):
TATTTTCCTAAAATCTACCTCACACGTGGCCTCATATCAATCGTA
Found at i:490166 original size:6 final size:6
Alignment explanation
Indices: 490155--490195 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
490145 CTTCGCACCA
490155 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
490196 ACCCAAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:491432 original size:228 final size:226
Alignment explanation
Indices: 491033--491973 Score: 978
Period size: 228 Copynumber: 4.1 Consensus size: 226
491023 TAAAGGCCAA
* * *
491033 GAGGGTATCCCACCAGACCAGCAGAGGCTTATCTTTGCTGGAAAACAACTTGAGGATGGCCGCAC
1 GAGGGCATCCCACCAGACCAGCAGAGGCTTATCTTTGCCGG-AAACAACTTGAGGATGGCCGAAC
* * *
491098 TCTCGCTGACTACAATATCCA-AAAGGAGTCTACCCTCCACCTTGTCCTTCGGCTCAGGGGTGGC
65 TCTTGCTGACTACAACATCCAGAAA-GAGTCTACCCTCCACCTTGTCCTTCGTCTCAGGGGTGGC
* * *
491162 ATGCAGATCTTTGTAAAAACCCTTACTGGCAAGACAATCACCCTCGAGGTGGAGAACTCTGACAC
129 ATGCAGATCTTTGT-AAAACACTTACTGGCAAGACCATCACCCTCGAGGTGGAGAGCTCTGACAC
*
491227 TATTGACAATGTCAAGGCCAAGATCCAAGACAAG
193 TATTGACAATGTCAAGGCCAAGATCCAGGACAAG
* *
491261 GAGGGTATCCCACCAGACCAGCAGAGGCTTATCTTTGCCGGAAAGCAACTTGAGGATGGCCGTAC
1 GAGGGCATCCCACCAGACCAGCAGAGGCTTATCTTTGCCGGAAA-CAACTTGAGGATGGCCGAAC
* * * *
491326 TCTTGCTGACTACAACATCCAGAAAGAATCTACCTTGCACCTTGTCCTTCGTCTTAGGGGTGGCA
65 TCTTGCTGACTACAACATCCAGAAAGAGTCTACCCTCCACCTTGTCCTTCGTCTCAGGGGTGGCA
* *
491391 TGCAAATCTTTGTAAAGACTCTTACTGGCAAGACCATCACCCTCGAGGTGGAGAGCTCTGACACT
130 TGCAGATCTTTGTAAA-ACACTTACTGGCAAGACCATCACCCTCGAGGTGGAGAGCTCTGACACT
*
491456 ATTGACAATGTTAAGGCCAAGATCCAGGACAAG
194 ATTGACAATGTCAAGGCCAAGATCCAGGACAAG
* * * * *
491489 GAGGGCATTCCACCAGATCATCAGAGGCTTATCTTTGCGGGTAAACAACTTGAGGATGGCAGAAC
1 GAGGGCATCCCACCAGACCAGCAGAGGCTTATCTTTGCCGG-AAACAACTTGAGGATGGCCGAAC
* *
491554 CCTTGCTGACTACAACATCCAGAAAGAGTCTACCCTCCATCTTGTCCTTCGTCTCAGGGGTGGCA
65 TCTTGCTGACTACAACATCCAGAAAGAGTCTACCCTCCACCTTGTCCTTCGTCTCAGGGGTGGCA
* * * * ** * * * *
491619 TGCAGATCTTTGTGAAAACAGTCACTGGAAAAACCATCACTTTGGAGGTGGAGAGTTCTGATACA
130 TGCAGATCTTTGT-AAAACACTTACTGGCAAGACCATCACCCTCGAGGTGGAGAGCTCTGACACT
* * ** * *
491684 ATCGATAACCTGAAGGCCAAGATTCAGGACAAG
194 ATTGACAATGTCAAGGCCAAGATCCAGGACAAG
* * * * * * *
491717 GAGGGCATCCCA-CAGGACCAGCAGAGG-TTGATTTTTTCTGGGAAACAGCTTGAAGATGGCAGG
1 GAGGGCATCCCACCA-GACCAGCAGAGGCTT-ATCTTTGC-CGGAAACAACTTGAGGATGGCCGA
* * * * * * *
491780 ACTCTCGCAGACTATAACATTCA-AAAGGAGTCTACCCTCCA-CTTGGT-GTTGCGTCTCCGTGG
63 ACTCTTGCTGACTACAACATCCAGAAA-GAGTCTACCCTCCACCTT-GTCCTT-CGTCTCAGGGG
* * * * * * * * * * * * * * *
491842 TGGTATGCAAATATTTGTGAAGACTCTCACAGGGAAGACTATTACCTTGGAAGTAGAGAGTTCTG
125 TGGCATGCAGATCTTTGT-AAAACACTTACTGGCAAGACCATCACCCTCGAGGTGGAGAGCTCTG
* * ** *
491907 ACACAATTGACAATGTTAAAACTAAGATCCAGGACAAG
189 ACACTATTGACAATGTCAAGGCCAAGATCCAGGACAAG
* * * *
491945 GAAGGG-ATTCCACCTGATCAACAGAGGCT
1 G-AGGGCATCCCACCAGACCAGCAGAGGCT
491974 GATTTTCGCT
Statistics
Matches: 609, Mismatches: 90, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
227 18 0.03
228 573 0.94
229 18 0.03
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (226 bp):
GAGGGCATCCCACCAGACCAGCAGAGGCTTATCTTTGCCGGAAACAACTTGAGGATGGCCGAACT
CTTGCTGACTACAACATCCAGAAAGAGTCTACCCTCCACCTTGTCCTTCGTCTCAGGGGTGGCAT
GCAGATCTTTGTAAAACACTTACTGGCAAGACCATCACCCTCGAGGTGGAGAGCTCTGACACTAT
TGACAATGTCAAGGCCAAGATCCAGGACAAG
Found at i:492002 original size:456 final size:455
Alignment explanation
Indices: 491033--492003 Score: 1105
Period size: 456 Copynumber: 2.1 Consensus size: 455
491023 TAAAGGCCAA
* * * * * *
491033 GAGGGTATCCCACCAGACCAGCAGAGGCTTATCTTTGCTGGAAAACAACTTGAGGATGGCCGCAC
1 GAGGGCATTCCACCAGATCAACAGAGGCTTATCTTTGCTGG-AAACAACTTGAGGATGGCAGAAC
* *
491098 TCTCGCTGACTACAATATCCAAAAGGAGTCTACCCTCCACCTTGTCCTTCGGCTCAGGGGTGGCA
65 CCTCGCTGACTACAACATCCAAAAGGAGTCTACCCTCCACCTTGTCCTTCGGCTCAGGGGTGGCA
* * * * *
491163 TGCAGATCTTTGTAAAAACCCTTACTGGCAAGACAATCACCCTCGAGGTGGAGAACTCTGACACT
130 TGCAGATCTTTGTAAAAACACTCACTGGAAAAACAATCACCCTCGAGGTGGAGAACTCTGACACA
* ** *
491228 ATTGACAATGTCAAGGCCAAGATCCAAGACAAGGAGGGTATCCCACCAGACCAGCAGAGGCTTAT
195 ATCGACAACCTCAAGGCCAAGATCCAAGACAAGGAGGGCATCCCACCAGACCAGCAGAGGCTTAT
* * * * *
491293 CTTTGCCGGAAAGCAACTTGAGGATGGCCGTACTCTTGCTGACTACAACATCCAGAAAGAATCTA
260 CTTTGCCGGAAAGCAACTTGAAGATGGCAGGACTCTCGCAGACTACAACATCCAGAAAGAATCTA
* * * * * *
491358 CCTTGCACCTTGTCCTTCGTCTTAGGGGTGGCATGCAAATCTTTGTAAAGACTCTTACTGGCAAG
325 CCCTCCACCTTGTCCTTCGTCTCAGGGGTGGCATGCAAATATTTGTAAAGACTCTCACAGGCAAG
* * * **
491423 ACCATCACCCTCGAGGTGGAGAGCTCTGACACTATTGACAATGTTAAGGCCAAGATCCAGGACAA
390 ACCATCACCCTCGAAGTAGAGAGCTCTGACACAATTGACAATGTTAAAACCAAGATCCAGGACAA
491488 G
455 G
* *
491489 GAGGGCATTCCACCAGATCATCAGAGGCTTATCTTTGCGGGTAAACAACTTGAGGATGGCAGAAC
1 GAGGGCATTCCACCAGATCAACAGAGGCTTATCTTTGCTGG-AAACAACTTGAGGATGGCAGAAC
* * *
491554 CCTTGCTGACTACAACATCCAGAAA-GAGTCTACCCTCCATCTTGTCCTTCGTCTCAGGGGTGGC
65 CCTCGCTGACTACAACATCCA-AAAGGAGTCTACCCTCCACCTTGTCCTTCGGCTCAGGGGTGGC
* * * ** * ** *
491618 ATGCAGATCTTTGTGAAAACAGTCACTGGAAAAACCATCACTTTGGAGGTGGAGAGTTCTGATAC
129 ATGCAGATCTTTGTAAAAACACTCACTGGAAAAACAATCACCCTCGAGGTGGAGAACTCTGACAC
* * * *
491683 AATCGATAACCTGAAGGCCAAGATTCAGGACAAGGAGGGCATCCCA-CAGGACCAGCAGAGG-TT
194 AATCGACAACCTCAAGGCCAAGATCCAAGACAAGGAGGGCATCCCACCA-GACCAGCAGAGGCTT
* * * * * *
491746 GATTTTTTCTGGGAAA-CAGCTTGAAGATGGCAGGACTCTCGCAGACTATAACATTCA-AAAGGA
258 -ATCTTTGC-CGGAAAGCAACTTGAAGATGGCAGGACTCTCGCAGACTACAACATCCAGAAA-GA
* * * * * *
491809 GTCTACCCTCCA-CTTGGT-GTTGCGTCTCCGTGGTGGTATGCAAATATTTGTGAAGACTCTCAC
320 ATCTACCCTCCACCTT-GTCCTT-CGTCTCAGGGGTGGCATGCAAATATTTGTAAAGACTCTCAC
* * * * * * *
491872 AGGGAAGACTATTACCTTGGAAGTAGAGAGTTCTGACACAATTGACAATGTTAAAACTAAGATCC
383 AGGCAAGACCATCACCCTCGAAGTAGAGAGCTCTGACACAATTGACAATGTTAAAACCAAGATCC
491937 AGGACAAG
448 AGGACAAG
* * * *
491945 GAAGGG-ATTCCACCTGATCAACAGAGGCTGAT-TTTCGCTGGAAAGCAGCTGGAGGATGG
1 G-AGGGCATTCCACCAGATCAACAGAGGCTTATCTTT-GCTGGAAA-CAACTTGAGGATGG
492004 GAGGACACTA
Statistics
Matches: 429, Mismatches: 76, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
455 18 0.04
456 399 0.93
457 12 0.03
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (455 bp):
GAGGGCATTCCACCAGATCAACAGAGGCTTATCTTTGCTGGAAACAACTTGAGGATGGCAGAACC
CTCGCTGACTACAACATCCAAAAGGAGTCTACCCTCCACCTTGTCCTTCGGCTCAGGGGTGGCAT
GCAGATCTTTGTAAAAACACTCACTGGAAAAACAATCACCCTCGAGGTGGAGAACTCTGACACAA
TCGACAACCTCAAGGCCAAGATCCAAGACAAGGAGGGCATCCCACCAGACCAGCAGAGGCTTATC
TTTGCCGGAAAGCAACTTGAAGATGGCAGGACTCTCGCAGACTACAACATCCAGAAAGAATCTAC
CCTCCACCTTGTCCTTCGTCTCAGGGGTGGCATGCAAATATTTGTAAAGACTCTCACAGGCAAGA
CCATCACCCTCGAAGTAGAGAGCTCTGACACAATTGACAATGTTAAAACCAAGATCCAGGACAAG
Found at i:494566 original size:2 final size:2
Alignment explanation
Indices: 494559--494592 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
494549 ACAGACACGC
494559 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
494593 CTCGGACTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:505591 original size:64 final size:64
Alignment explanation
Indices: 505490--505617 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
505480 CGGGCTCTCT
505490 TGAGCCTACTAGCTCAGCAAGGACCCGTCCTAAGGTCACTATCATCGAACAATCTGTTAGCCCC
1 TGAGCCTACTAGCTCAGCAAGGACCCGTCCTAAGGTCACTATCATCGAACAATCTGTTAGCCCC
505554 TGAGCCTACTAGCTCAGCAAGGACCC-TCCGTAAGGTCACTATCATCGAACAATCTGTTAGCCCC
1 TGAGCCTACTAGCTCAGCAAGGACCCGTCC-TAAGGTCACTATCATCGAACAATCTGTTAGCCCC
505618 GGTGGCGGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 3 0.05
64 60 0.95
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.22
Consensus pattern (64 bp):
TGAGCCTACTAGCTCAGCAAGGACCCGTCCTAAGGTCACTATCATCGAACAATCTGTTAGCCCC
Found at i:506090 original size:89 final size:89
Alignment explanation
Indices: 505939--506117 Score: 326
Period size: 89 Copynumber: 2.0 Consensus size: 89
505929 CTAGAGAGAA
505939 TTCAGAGAGTTTCTTGAGAGTTGTTTTTCCTTTTTATCGAGGAGAGAATTATCTTGTTTTCTCCT
1 TTCAGAGAGTTTCTTGAGAGTTGTTTTTCCTTTTTATCGAGGAGAGAATTATCTTGTTTTCTCCT
506004 TGGTAGATCGAGAGAGGTTGTAAT
66 TGGTAGATCGAGAGAGGTTGTAAT
506028 TTCAGAGAGTTTCTTGAGAG-TGTTTTCTCCTTTTTATCGA-GAGAGAATTATCATTGTTTTCTC
1 TTCAGAGAGTTTCTTGAGAGTTGTTTT-TCCTTTTTATCGAGGAGAGAATTATC-TTGTTTTCTC
506091 CTTGGTAGATCGAGAGAGGTTGTAAT
64 CTTGGTAGATCGAGAGAGGTTGTAAT
506117 T
1 T
506118 CCTATTTTCT
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
88 18 0.20
89 70 0.80
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.42
Consensus pattern (89 bp):
TTCAGAGAGTTTCTTGAGAGTTGTTTTTCCTTTTTATCGAGGAGAGAATTATCTTGTTTTCTCCT
TGGTAGATCGAGAGAGGTTGTAAT
Found at i:510467 original size:12 final size:12
Alignment explanation
Indices: 510450--510474 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
510440 GTCAAATAAT
510450 TTAGGCACCAAA
1 TTAGGCACCAAA
510462 TTAGGCACCAAA
1 TTAGGCACCAAA
510474 T
1 T
510475 GGTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:514480 original size:63 final size:64
Alignment explanation
Indices: 514401--514534 Score: 155
Period size: 64 Copynumber: 2.1 Consensus size: 64
514391 TACAGAGTGT
* * * * *
514401 ATCGATGCACAGGGAGTGCATCGATGC-GCCCA-TATTAATGGAAACATTGAATGTAATTGGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCAGCCCATTA-AAATGAAAACATCGAAGGTAATTGGTGC
* * * * *
514464 ATCGATGCATAAGGAGTGCATCTATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCAGCCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
514528 ATCGATG
1 ATCGATG
514535 TACTGTTGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
63 24 0.41
64 33 0.56
65 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (64 bp):
ATCGATGCACAAGGAGTGCATCGATGCAGCCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
Found at i:516352 original size:24 final size:24
Alignment explanation
Indices: 516320--516400 Score: 153
Period size: 24 Copynumber: 3.4 Consensus size: 24
516310 CCAGTTTCCA
516320 TTACTACTTTCATCTTCATATCTT
1 TTACTACTTTCATCTTCATATCTT
516344 TTACTACTTTCATCTTCATATCTT
1 TTACTACTTTCATCTTCATATCTT
*
516368 TTACTACTTCCATCTTCATATCTT
1 TTACTACTTTCATCTTCATATCTT
516392 TTACTACTT
1 TTACTACTT
516401 CCCCACTGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53
Consensus pattern (24 bp):
TTACTACTTTCATCTTCATATCTT
Found at i:517678 original size:23 final size:21
Alignment explanation
Indices: 517652--517702 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
517642 TACAATTATA
*
517652 AAATTAGTTAAAAATTTAAAGAT
1 AAATTA-TTAAAAA-TAAAAGAT
*
517675 AAATTATTTAAAATAAAAGAT
1 AAATTATTAAAAATAAAAGAT
517696 AAATTAT
1 AAATTAT
517703 ACTAGTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.54
22 6 0.23
23 6 0.23
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (21 bp):
AAATTATTAAAAATAAAAGAT
Done.