Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008121.1 Hibiscus syriacus cultivar Beakdansim tig00110674_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: 1116347
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:263433 original size:14 final size:14
Alignment explanation
Indices: 263414--263454 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
263404 ATCATATTTT
263414 TATTTTTATAATTA
1 TATTTTTATAATTA
*
263428 TATTTTTA-AA-AA
1 TATTTTTATAATTA
263440 TATTTTATATAATTA
1 TATTTT-TATAATTA
263455 AGGCAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 10 0.45
15 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTATAATTA
Found at i:263594 original size:21 final size:21
Alignment explanation
Indices: 263568--263652 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
263558 ATATAAATAC
* *
263568 TAAATTTTATTCAATTGATAT
1 TAAATTTAACTCAATTGATAT
*
263589 TAAATTTAACTCGATTGATAT
1 TAAATTTAACTCAATTGATAT
* ** *
263610 T--A-TTAAATCCATATAAATAC
1 TAAATTTAACT-CA-ATTGATAT
263630 TAAATTTAACTCAATTGATAT
1 TAAATTTAACTCAATTGATAT
263651 TA
1 TA
263653 TCAAATTCAT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
18 5 0.11
19 2 0.04
20 6 0.13
21 26 0.55
22 3 0.06
23 5 0.11
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAATTTAACTCAATTGATAT
Found at i:268340 original size:12 final size:11
Alignment explanation
Indices: 268319--268345 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
268309 ACAGGCCTCC
268319 AAAAAGAAAAA
1 AAAAAGAAAAA
268330 AAAAAGAAAAA
1 AAAAAGAAAAA
268341 AAAAA
1 AAAAA
268346 CACAAGAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:271132 original size:18 final size:18
Alignment explanation
Indices: 271104--271148 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
271094 GGGAGAGTCG
*
271104 GAAACGGAAACGGTACG-
1 GAAAGGGAAACGGTACGT
271121 GAGAAGGGAAACGGTACGT
1 GA-AAGGGAAACGGTACGT
271140 GAAAGGGAA
1 GAAAGGGAA
271149 GAGAGAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 21 0.84
19 2 0.08
ACGTcount: A:0.42, C:0.11, G:0.40, T:0.07
Consensus pattern (18 bp):
GAAAGGGAAACGGTACGT
Found at i:272308 original size:29 final size:29
Alignment explanation
Indices: 272266--272500 Score: 452
Period size: 29 Copynumber: 8.1 Consensus size: 29
272256 AACCATTATT
*
272266 TTCATTCAACTTATCAATCTCATACTTGG
1 TTCATTCAACTTATCAATCTCATACTTAG
272295 TTCATTCAACTTATCAATCTCATACTTAG
1 TTCATTCAACTTATCAATCTCATACTTAG
272324 TTCATTCAACTTATCAATCTCATACTTAG
1 TTCATTCAACTTATCAATCTCATACTTAG
272353 TTCATTCAACTTATCAATCTCATACTTAG
1 TTCATTCAACTTATCAATCTCATACTTAG
272382 TTCATTCAACTTATCAATCTCATACTTAG
1 TTCATTCAACTTATCAATCTCATACTTAG
*
272411 TACATTCAACTTATCAATCTCATACTTAG
1 TTCATTCAACTTATCAATCTCATACTTAG
272440 TTCATTCAACTTATCAATCTCATACTTAG
1 TTCATTCAACTTATCAATCTCATACTTAG
272469 TTCATTCAACTTATCAATCTCATACTTAG
1 TTCATTCAACTTATCAATCTCATACTTAG
272498 TTC
1 TTC
272501 TATAAATATA
Statistics
Matches: 203, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 203 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (29 bp):
TTCATTCAACTTATCAATCTCATACTTAG
Found at i:303430 original size:28 final size:27
Alignment explanation
Indices: 303390--303451 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
303380 GCTGCTGGAA
303390 ACCGGTTGACCGGTTTTCAA-CGGTTCTG
1 ACCGGTTGACCGG-TTTCAACCGGTTC-G
303418 ACCGGTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTGACCGGTTTCAACCGGTTCG
*
303445 AACGGTT
1 ACCGGTT
303452 TAACCGGTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (27 bp):
ACCGGTTGACCGGTTTCAACCGGTTCG
Found at i:303439 original size:18 final size:18
Alignment explanation
Indices: 303408--303459 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
303398 ACCGGTTTTC
*
303408 AACGGTTCTGACCGGTT-G
1 AACGGTT-TAACCGGTTCG
*
303426 ACCGGTTTCAACCGGTTCG
1 AACGGTTT-AACCGGTTCG
303445 AACGGTTTAACCGGT
1 AACGGTTTAACCGGT
303460 CTGAATCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 20 0.69
19 8 0.28
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (18 bp):
AACGGTTTAACCGGTTCG
Found at i:303457 original size:28 final size:27
Alignment explanation
Indices: 303392--303459 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
303382 TGCTGGAAAC
* *
303392 CGGTTGACCGGTTTTCAACGGTTCTGAC
1 CGGTTAACCGG-TTTCAACGGTTCTGAA
*
303420 CGGTTGACCGGTTTCAACCGGTTC-GAA
1 CGGTTAACCGGTTTCAA-CGGTTCTGAA
303447 CGGTTTAACCGGT
1 CGG-TTAACCGGT
303460 CTGAATCGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 11 0.31
28 25 0.69
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (27 bp):
CGGTTAACCGGTTTCAACGGTTCTGAA
Found at i:303502 original size:22 final size:22
Alignment explanation
Indices: 303474--303525 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
303464 ATCGGTTTGA
303474 CGTTGACCCGA-CCGACCCCGAC
1 CGTTGACCCGACCCGA-CCCGAC
*
303496 CGTTGACCCGACCCGACCTGAC
1 CGTTGACCCGACCCGACCCGAC
303518 CGTTGACC
1 CGTTGACC
303526 GTTGACCGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.13
Consensus pattern (22 bp):
CGTTGACCCGACCCGACCCGAC
Found at i:304464 original size:31 final size:28
Alignment explanation
Indices: 304392--304464 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
304382 CTAATGTGAC
* *
304392 TCTTAGGTAGGCTCTGCGGCCTGAGATTT
1 TCTTA-GTAGGCCCTGCGGCCTAAGATTT
**
304421 TCTCGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGTAGGCCCTGCGG-CCTAAGAT-T-T
304452 TCTTAGTAGGCCC
1 TCTTAGTAGGCCC
304465 CACGGCCCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 12 0.34
29 10 0.29
30 1 0.03
31 12 0.34
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (28 bp):
TCTTAGTAGGCCCTGCGGCCTAAGATTT
Found at i:322684 original size:43 final size:45
Alignment explanation
Indices: 322637--322724 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
322627 GAATAATGAA
322637 AACCTCATTTAATAAAA-TTT-AAAAAAATACTAATTTTCAAAGG
1 AACCTCATTTAATAAAATTTTAAAAAAAATACTAATTTTCAAAGG
322680 AACCTCATTTAATAAAATTTTAAAAAAAATACTAATTTTCAAAGG
1 AACCTCATTTAATAAAATTTTAAAAAAAATACTAATTTTCAAAGG
322725 CTTGTCATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 17 0.40
44 3 0.07
45 23 0.53
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (45 bp):
AACCTCATTTAATAAAATTTTAAAAAAAATACTAATTTTCAAAGG
Found at i:326432 original size:45 final size:47
Alignment explanation
Indices: 326354--326443 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 47
326344 TTAAAGAGAG
*
326354 TAATTATTTTTTTATCATTTAGATCGTTTAATAAATTTAACATATTA
1 TAATTATTTTTTTATCATTTAGATCGTTTAATAAATGTAACATATTA
*
326401 TAATTA-TTTTTTATCATTTAGATCG-TTAATAAATGTAATATAT
1 TAATTATTTTTTTATCATTTAGATCGTTTAATAAATGTAACATAT
326444 AAATTTTGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 16 0.39
46 19 0.46
47 6 0.15
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (47 bp):
TAATTATTTTTTTATCATTTAGATCGTTTAATAAATGTAACATATTA
Found at i:340302 original size:2 final size:2
Alignment explanation
Indices: 340295--340360 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
340285 TCTTTTTAAA
340295 AT 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 AT
340337 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
340361 TTTTTTAATT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344074 original size:22 final size:21
Alignment explanation
Indices: 344043--344085 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
344033 TTTTTAATAG
344043 AAAATATATATAGAAATCTTTA
1 AAAATATATATAGAAAT-TTTA
* *
344065 AAAATGTATATAGTAATTTTA
1 AAAATATATATAGAAATTTTA
344086 GATTTTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAATATATATAGAAATTTTA
Found at i:344754 original size:2 final size:2
Alignment explanation
Indices: 344749--344780 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
344739 ACACACACAC
344749 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
344781 CATTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344930 original size:19 final size:18
Alignment explanation
Indices: 344888--344930 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
344878 AAATTATTTT
344888 ATAAAAACTTAAACTGAG
1 ATAAAAACTTAAACTGAG
344906 ATAAAAACTTAAACTGAG
1 ATAAAAACTTAAACTGAG
*
344924 TTAAAAA
1 ATAAAAA
344931 TATATAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (18 bp):
ATAAAAACTTAAACTGAG
Found at i:345979 original size:25 final size:26
Alignment explanation
Indices: 345931--346009 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 26
345921 TAAAAGATGT
*
345931 AAAATAATTTTATTTTAAGT-AATA-C
1 AAAATAATATTATTTTAA-TAAATATC
*
345956 AAAATAATATTATTTTAATAAATAAATG
1 AAAATAATATTATTTTAATAAAT--ATC
345984 ATAAATAATATTATTTTAATAAATAT
1 A-AAATAATATTATTTTAATAAATAT
346010 TTTTAATAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
24 1 0.02
25 20 0.43
27 3 0.06
28 1 0.02
29 22 0.47
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (26 bp):
AAAATAATATTATTTTAATAAATATC
Found at i:346008 original size:15 final size:15
Alignment explanation
Indices: 345961--346010 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
345951 AATACAAAAT
345961 AATATTATTTTAATA
1 AATATTATTTTAATA
* **
345976 AATA-AATGATAA-A
1 AATATTATTTTAATA
345989 TAATATTATTTTAATA
1 -AATATTATTTTAATA
346005 AATATT
1 AATATT
346011 TTTAATAGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.35
15 15 0.58
16 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATATTATTTTAATA
Found at i:346237 original size:20 final size:22
Alignment explanation
Indices: 346214--346266 Score: 83
Period size: 20 Copynumber: 2.5 Consensus size: 22
346204 TTGCAACGGG
346214 TGATTAAGAATTCATATC-G-A
1 TGATTAAGAATTCATATCGGTA
*
346234 TGATTAAGAATTCATATCGGTG
1 TGATTAAGAATTCATATCGGTA
346256 TGATTAAGAAT
1 TGATTAAGAAT
346267 CTCTCGCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 18 0.60
21 1 0.03
22 11 0.37
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (22 bp):
TGATTAAGAATTCATATCGGTA
Found at i:346373 original size:13 final size:13
Alignment explanation
Indices: 346352--346386 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
346342 TATTGATATA
346352 ATATAATAAAATT
1 ATATAATAAAATT
*
346365 ATATTATAAAATT
1 ATATAATAAAATT
*
346378 ATAAAATAA
1 ATATAATAA
346387 TATTCATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAATAAAATT
Found at i:346373 original size:21 final size:21
Alignment explanation
Indices: 346348--346398 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
346338 TGATTATTGA
*
346348 TATAATATAATAAAATTATAT
1 TATAATATAATAAAATAATAT
* *
346369 TATAAAATTATAAAATAATAT
1 TATAATATAATAAAATAATAT
346390 TCATAATAT
1 T-ATAATAT
346399 TTTATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAATATAATAAAATAATAT
Found at i:346410 original size:28 final size:28
Alignment explanation
Indices: 346348--346440 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
346338 TGATTATTGA
* * *
346348 TATAATATAAT-AAAATTATATTATAAAAT
1 TATAAAATAATAAAAATAATATT-T-TAAT
*** *
346377 TATAAAATAATATTCATAATATTTTATT
1 TATAAAATAATAAAAATAATATTTTAAT
*
346405 TATAAAATTATAAAAATAATATTTTAAT
1 TATAAAATAATAAAAATAATATTTTAAT
*
346433 AATAAAAT
1 TATAAAAT
346441 TGACGTAAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
28 32 0.64
29 11 0.22
30 7 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
TATAAAATAATAAAAATAATATTTTAAT
Found at i:351713 original size:83 final size:82
Alignment explanation
Indices: 351551--351917 Score: 257
Period size: 83 Copynumber: 4.5 Consensus size: 82
351541 ACTTTAAACA
* * * * *
351551 TATAGCGGCGTTTACATC-ACAAACGCCGCAAAATTGTA-ACTTTAACGGCGTTTTTATACAAAC
1 TATAGTGGCGTTT-TATCAACAAACGCCGCAACATAGTATACTTTAACGGCATTTTTATACAAAC
*
351614 ACCGCAGTAGGATTCATC
65 ACCGCAATAGGATTCATC
* * * *
351632 TATAGTGGCGTTTTTTTAACAAACGCCGCAACATAGTAGTACTTTAGCGGCATTTTTATACAAAT
1 TATAGTGGCGTTTTATCAACAAACGCCGCAACATAGTA-TACTTTAACGGCATTTTTATACAAAC
* *
351697 GCCGCAATAGGGTTCATC
65 ACCGCAATAGGATTCATC
* * * * * *
351715 TATAGTGGCGTTTTATCAACAAACGTCGTAACACAGTATTACTTTAATGGCGTTTTT-TAATAAA
1 TATAGTGGCGTTTTATCAACAAACGCCGCAACATAGTA-TACTTTAACGGCATTTTTAT-ACAAA
* * *
351779 CATCGTAATA-GAGT-AGTAC
64 CACCGCAATAGGATTCA-T-C
* * * * * * * * *
351798 TTTAGCGACGTTTTCA-AAGACAAACGCCGCAACAGAGTTTTACTTTAGCGGCGTTTTTATAAAA
1 TATAGTGGCGTTTT-ATCA-ACAAACGCCGCAACATAG-TATACTTTAACGGCATTTTTATACAA
*
351862 ACGCCGCAATA-GATTCCATC
63 ACACCGCAATAGGATT-CATC
* * * * *
351882 TTTAGTGGTGTTTT-T-AATAAACGCCACAACAGAGTA
1 TATAGTGGCGTTTTATCAACAAACGCCGCAACATAGTA
351918 GTAGTTTAGC
Statistics
Matches: 224, Mismatches: 49, Indels: 27
0.75 0.16 0.09
Matches are distributed among these distances:
80 2 0.01
81 47 0.21
82 5 0.02
83 108 0.48
84 58 0.26
85 3 0.01
86 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (82 bp):
TATAGTGGCGTTTTATCAACAAACGCCGCAACATAGTATACTTTAACGGCATTTTTATACAAACA
CCGCAATAGGATTCATC
Found at i:351799 original size:41 final size:42
Alignment explanation
Indices: 351720--351801 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 42
351710 TCATCTATAG
* *
351720 TGGCGTTTTATCAACAAACGTCGTAACACAGTATTACTTTAA
1 TGGCGTTTTATCAACAAACATCGTAACACAGTAGTACTTTAA
* * * *
351762 TGGCGTTTT-TTAATAAACATCGTAATAGAGTAGTACTTTA
1 TGGCGTTTTATCAACAAACATCGTAACACAGTAGTACTTTA
351802 GCGACGTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 25 0.74
42 9 0.26
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (42 bp):
TGGCGTTTTATCAACAAACATCGTAACACAGTAGTACTTTAA
Found at i:353296 original size:4 final size:4
Alignment explanation
Indices: 353289--353315 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
353279 AGTGTAGATA
353289 GATG GATG GATG GATG GATG GATG GAT
1 GATG GATG GATG GATG GATG GATG GAT
353316 AGATCATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
GATG
Found at i:355187 original size:23 final size:23
Alignment explanation
Indices: 355161--355205 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
355151 CACCACAGCT
*
355161 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
355184 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
355206 ATATATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:355459 original size:147 final size:146
Alignment explanation
Indices: 355173--355482 Score: 500
Period size: 147 Copynumber: 2.1 Consensus size: 146
355163 TATAATTGCA
355173 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATATAATGTCCATAAGGACCACATAGAAT
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATATAATGTCCATAAGGACCACATAGAAT
* **
355237 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
65 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATATGTCTCACAAGACTTCACACATGTTC
*
355302 CACAGAATATATATATC
130 CAAAGAATATATATATC
*
355319 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATAT-ATAATGTCCATAAGGACCACATAGAAT
*
355384 TCCTTAAGAATCATATACATATGCTAGGGATC-A-TATATGTCTCACCAGACTTCACACATGTTC
65 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATATGTCTCACAAGACTTCACACATGTTC
355447 CAAAGAATATATATATATC
130 CAAAG-A-ATATATATATC
*
355466 TCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
355483 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
145 31 0.20
146 37 0.24
147 85 0.56
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (146 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATATAATGTCCATAAGGACCACATAGAATT
CCTTAAGAATCATATACATATGCTAGGGATCAAGTATATGTCTCACAAGACTTCACACATGTTCC
AAAGAATATATATATC
Found at i:356833 original size:64 final size:63
Alignment explanation
Indices: 356735--356895 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
356725 TAATGAAGGT
* *
356735 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
356798 GG
62 GC
* *
356800 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCTTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
356864 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
356896 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:358662 original size:43 final size:43
Alignment explanation
Indices: 358614--358956 Score: 364
Period size: 43 Copynumber: 8.1 Consensus size: 43
358604 TACAAATGCA
* * * *
358614 CTAAATACACAGTTAATAGTGGCGTTTAT-AAAGATAAACGTCG
1 CTAAATACACAGTCAATAGCGGCGTTT-TCAAAGACAAACGCCG
*** * *
358657 CTAAATACACAGTCAATAGCGGCGTTTGTCTTTGA-AAATGCCA
1 CTAAATACACAGTCAATAGCGGCGTTT-TCAAAGACAAACGCCG
* *
358700 CTAAATACACAGTCAATAGTGGCGTTTTCAAAGACAAATGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAACGCCG
* * *
358743 CTAAATACACAGTCAATAACAGCGTTTAT-AAAGTCAAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTT-TCAAAGACAAACGCCG
* *
358786 CTAAATACACGGTCAATAGCGGCGTTTTCAAAGACGAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAACGCCG
* *
358829 CTAAATACACAGTCAATAACGGCGTTTAT-AAA-ATCAAACGCTG
1 CTAAATACACAGTCAATAGCGGCGTTT-TCAAAGA-CAAACGCCG
* *
358872 TTAAATACACTGTCAATAGCGGCGTTTTCAAAGACAAACGCCG
1 CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAACGCCG
* *
358915 CTAAAT----AGTCAATAGCGGCACTTGT-AAAGACAAACGCCG
1 CTAAATACACAGTCAATAGCGGC-GTTTTCAAAGACAAACGCCG
358954 CTA
1 CTA
358957 TATGTCTCGA
Statistics
Matches: 255, Mismatches: 36, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
39 29 0.11
40 3 0.01
42 7 0.03
43 211 0.83
44 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (43 bp):
CTAAATACACAGTCAATAGCGGCGTTTTCAAAGACAAACGCCG
Found at i:379330 original size:92 final size:93
Alignment explanation
Indices: 379174--379363 Score: 312
Period size: 92 Copynumber: 2.1 Consensus size: 93
379164 AATTAGGCGT
379174 GGCAGCCATGATACATTCTTTGATGGGTTATTTGAGAGCAGAGCAGGGTTCATTA-TTTCCTTTT
1 GGCAGCCATGATACATTCTTTGATGGGTTATTTGAGAGCAGAGCAGGGTTCATTATTTTCCTTTT
*
379238 TGTTTCTTTGTTAACAAGTTACAATGTA
66 TGTTTCTTTGTTAACAAGTTAAAATGTA
* *
379266 GGCAGCCATGATACATTCTTTGATGGGTTATTTGAGAGCATAGCAGGGTTTCATTATTTT-TTTT
1 GGCAGCCATGATACATTCTTTGATGGGTTATTTGAGAGCAGAGCAGGG-TTCATTATTTTCCTTT
**
379330 TTGTTTCTTTGTTTTCAAGTTAAAATGTA
65 TTGTTTCTTTGTTAACAAGTTAAAATGTA
379359 GGCAG
1 GGCAG
379364 AGGTGGCAAA
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
92 47 0.52
93 41 0.45
94 3 0.03
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (93 bp):
GGCAGCCATGATACATTCTTTGATGGGTTATTTGAGAGCAGAGCAGGGTTCATTATTTTCCTTTT
TGTTTCTTTGTTAACAAGTTAAAATGTA
Found at i:385024 original size:30 final size:29
Alignment explanation
Indices: 384959--385026 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
384949 TTTTTATGTA
384959 AGTACCTAAAGTAATTTTTAGTCAAAATG
1 AGTACCTAAAGTAATTTTTAGTCAAAATG
* * * *
384988 AATACCTAGAGTTATTTTTTTGTCAAAAT-
1 AGTACCTAAAG-TAATTTTTAGTCAAAATG
385017 AGGTACCTAA
1 A-GTACCTAA
385027 GAATATGTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (29 bp):
AGTACCTAAAGTAATTTTTAGTCAAAATG
Found at i:402129 original size:2 final size:2
Alignment explanation
Indices: 402122--402152 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
402112 ATAACAAGTA
402122 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 A
402153 GTTACACTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:402900 original size:53 final size:53
Alignment explanation
Indices: 402839--402944 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
402829 GAGAACCGAG
* **
402839 TAAACGAGTCAATAAACGAATTTTTAAACAAGTTTATTCGTGTACATAAATGA
1 TAAACGAGTCAATAAACGAACTTCCAAACAAGTTTATTCGTGTACATAAATGA
* * *
402892 TAAACGAGTTAATAAACGAACTTCCAAACAAGTTTGTTCGTGTATATAAATGA
1 TAAACGAGTCAATAAACGAACTTCCAAACAAGTTTATTCGTGTACATAAATGA
402945 ACCGAATACA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (53 bp):
TAAACGAGTCAATAAACGAACTTCCAAACAAGTTTATTCGTGTACATAAATGA
Found at i:410010 original size:27 final size:27
Alignment explanation
Indices: 409964--410033 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
409954 TTTTTTGTAC
*
409964 TAACTT-A-TTAAATATATTTTATTAT
1 TAACTTAATTTAAAAATATTTTATTAT
* *
409989 TAACTTAATTTAAAAATGTTTTATTTT
1 TAACTTAATTTAAAAATATTTTATTAT
**
410016 TATTTTAATTTAAAAATA
1 TAACTTAATTTAAAAATA
410034 GATGTTATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 6 0.16
26 1 0.03
27 30 0.81
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
TAACTTAATTTAAAAATATTTTATTAT
Found at i:414377 original size:40 final size:39
Alignment explanation
Indices: 414326--414434 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 39
414316 CTATAATCTG
414326 ATTCGAGATAAGATTTAAATTAAAAGAAAGTTTCATTCAA
1 ATTCGA-ATAAGATTTAAATTAAAAGAAAGTTTCATTCAA
*
414366 ATTCGATATAAGATTTAAATTAAAAGAAAGTTCCATTCAA
1 ATTCGA-ATAAGATTTAAATTAAAAGAAAGTTTCATTCAA
* *
414406 ATTCG---AAGTTTTAAATTAAAAGAGAGTTT
1 ATTCGAATAAGATTTAAATTAAAAGAAAGTTT
414435 TATAACATCT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 21 0.33
40 43 0.67
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (39 bp):
ATTCGAATAAGATTTAAATTAAAAGAAAGTTTCATTCAA
Found at i:424526 original size:76 final size:77
Alignment explanation
Indices: 424400--424557 Score: 282
Period size: 76 Copynumber: 2.0 Consensus size: 77
424390 GAGAACAACT
424400 TCTGATTTCTCCTTCAACTCTGCATTCTTTCTCTGCATGTGGGT-GGGGGGGGAAGATTCCTCGA
1 TCTGATTTCTCCTTCAACTCTGCATTCTTTCTCTGCATGTGGGTGGGGGGGGGAAGATTCCTCGA
424464 CGAGCTAAGATC
66 CGAGCTAAGATC
424476 TCTGATTTCTCCTTCAACTCTGCATTCTTTCTCTGCATGTGGGTGGGGGGGGGGGGAAGATTCCT
1 TCTGATTTCTCCTTCAACTCTGCATTCTTTCTCTGCATGTGGGT---GGGGGGGGGAAGATTCCT
424541 CGACGAGCTAAGATC
63 CGACGAGCTAAGATC
424556 TC
1 TC
424558 CATGATAAGG
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
76 44 0.56
80 34 0.44
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.32
Consensus pattern (77 bp):
TCTGATTTCTCCTTCAACTCTGCATTCTTTCTCTGCATGTGGGTGGGGGGGGGAAGATTCCTCGA
CGAGCTAAGATC
Found at i:436974 original size:49 final size:47
Alignment explanation
Indices: 436916--437040 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 47
436906 GATGAACACT
436916 AAAAAGTCCAAAACC-GGGAAAAAGAAGTCT-GAAAGAATCTGCAAGTATG
1 AAAAAGTCCAAAACCGGGGAAAAAGAAGTCTAGAAAGAATCT----GTATG
* *
436965 AAAAGGTCCAAACCCGGGGAAAAA-AAGTCTGAGAAAGAATCTGTATG
1 AAAAAGTCCAAAACCGGGGAAAAAGAAGTCT-AGAAAGAATCTGTATG
*
437012 AAAAAGTCC-AAACCTGGGAAAAAGAAGTC
1 AAAAAGTCCAAAACCGGGGAAAAAGAAGTC
437041 ATCTAAGTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
46 12 0.18
47 18 0.27
49 19 0.28
50 8 0.12
51 10 0.15
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.14
Consensus pattern (47 bp):
AAAAAGTCCAAAACCGGGGAAAAAGAAGTCTAGAAAGAATCTGTATG
Found at i:437025 original size:47 final size:45
Alignment explanation
Indices: 436916--437040 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 45
436906 GATGAACACT
436916 AAAAAGTCCAAAACCGGGAAAAAGAAGTCTGAAAGAATCTGCAAGTATG
1 AAAAAGTCC-AAACCGGGAAAAAGAAGTCTGAAAGAATCT---AGTATG
*
436965 AAAAGGTCCAAACCCGGGGAAAAA-AAGTCTGAGAAAGAATCT-GTATG
1 AAAAAGTCCAAA-CC-GGGAAAAAGAAGTCT--GAAAGAATCTAGTATG
437012 AAAAAGTCCAAACCTGGGAAAAAGAAGTC
1 AAAAAGTCCAAACC-GGGAAAAAGAAGTC
437041 ATCTAAGTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
46 10 0.15
47 21 0.31
48 3 0.04
49 16 0.24
50 8 0.12
51 10 0.15
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.14
Consensus pattern (45 bp):
AAAAAGTCCAAACCGGGAAAAAGAAGTCTGAAAGAATCTAGTATG
Found at i:440155 original size:35 final size:35
Alignment explanation
Indices: 440109--440184 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
440099 AAAACAATCC
* *
440109 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
440144 TCAATTTCATTCTAAATCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
440179 TCAATT
1 TCAATT
440185 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:440727 original size:130 final size:130
Alignment explanation
Indices: 440581--440828 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
440571 TATTTATATA
* *
440581 ATCAATTTGGTCCTAAATTAAATATAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
440646 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
440711 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
440776 TTAATACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
440829 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:440859 original size:130 final size:129
Alignment explanation
Indices: 440595--440859 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
440585 ATTTGGTCCT
* * *
440595 AAATTAAATATAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
440660 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
440725 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAATACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * *
440790 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
440854 -A
128 CA
440855 AAATT
1 AAATT
440860 TGGGTATTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:441186 original size:28 final size:27
Alignment explanation
Indices: 441151--441212 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
441141 AGTTGATACA
*
441151 ATATTTTAAAAGAATAAATTTAA-GATT
1 ATATTTTAAAA-AATAAATTTAATAATT
* *
441178 ATATATTTATAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAATAATT
441206 ATATTTT
1 ATATTTT
441213 TCATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAATAATT
Found at i:441313 original size:16 final size:18
Alignment explanation
Indices: 441292--441325 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
441282 ATTTTTTATT
441292 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
441308 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
441326 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:444022 original size:18 final size:17
Alignment explanation
Indices: 443999--444042 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
443989 TTATAAGGTG
443999 AAAATATTATTATTGTAA
1 AAAATATTATTATT-TAA
*
444017 AAAATATAATTATTTAA
1 AAAATATTATTATTTAA
444034 AATAATATT
1 AA-AATATT
444043 TAATTTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AAAATATTATTATTTAA
Found at i:444992 original size:15 final size:15
Alignment explanation
Indices: 444972--445004 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
444962 TAACTTAGTT
444972 TAATAAATA-AATTAA
1 TAATAAA-AGAATTAA
444987 TAATAAAAGAATTAA
1 TAATAAAAGAATTAA
445002 TAA
1 TAA
445005 AAGAATAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TAATAAAAGAATTAA
Found at i:454494 original size:20 final size:20
Alignment explanation
Indices: 454469--454509 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
454459 GTTACTTTGA
*
454469 GGTATTGTGAATGAAGTTTT
1 GGTATTGTGAATGAAATTTT
454489 GGTATTGTGAATGAAATTTT
1 GGTATTGTGAATGAAATTTT
454509 G
1 G
454510 CTGATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (20 bp):
GGTATTGTGAATGAAATTTT
Found at i:472543 original size:21 final size:22
Alignment explanation
Indices: 472506--472551 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
472496 CTAAAAATAT
*
472506 TAAAAATAATTAATATTTTAGA
1 TAAAAATAATTAATATTTTAAA
*
472528 TAAAAATAA-TACTATTTTAAA
1 TAAAAATAATTAATATTTTAAA
472549 TAA
1 TAA
472552 TTTTTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAAAATAATTAATATTTTAAA
Found at i:480137 original size:18 final size:20
Alignment explanation
Indices: 480110--480146 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
480100 AAGGTTACCC
480110 TTTTTGTCCCC-TTCTTTTG
1 TTTTTGTCCCCTTTCTTTTG
480129 TTTTT-TCCCCTTTCTTTT
1 TTTTTGTCCCCTTTCTTTT
480147 TTGTGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTGTCCCCTTTCTTTTG
Found at i:485623 original size:52 final size:52
Alignment explanation
Indices: 485555--485661 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 52
485545 TGGGTTTTTA
* * *
485555 AGTCATTTGGTGGGATTAAGAGTAGTTTTAGCTTAGGGTCATTTTGGGTTCG
1 AGTCATTTGGTGGGATTAAGAGTAGTTTTAGCTGAGGGCCATCTTGGGTTCG
* *
485607 AGTCATTTGGTTGGATTGAGAGTAGTTTTAGCTGAGGGCCATCTTGGGTTCG
1 AGTCATTTGGTGGGATTAAGAGTAGTTTTAGCTGAGGGCCATCTTGGGTTCG
485659 AGT
1 AGT
485662 TGGATGAGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.19, C:0.09, G:0.34, T:0.38
Consensus pattern (52 bp):
AGTCATTTGGTGGGATTAAGAGTAGTTTTAGCTGAGGGCCATCTTGGGTTCG
Found at i:488171 original size:2 final size:2
Alignment explanation
Indices: 488164--488225 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
488154 TGTAATCGGA
488164 AT 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 AT
488206 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
488226 GTGTGTGTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:490291 original size:18 final size:18
Alignment explanation
Indices: 490270--490306 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
490260 GAAATTGAGA
* *
490270 AAATAACAATAATTTAAT
1 AAATAAAAATAAATTAAT
490288 AAATAAAAATAAATTAAT
1 AAATAAAAATAAATTAAT
490306 A
1 A
490307 GTGGCCGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATAAAAATAAATTAAT
Found at i:492163 original size:2 final size:2
Alignment explanation
Indices: 492156--492186 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
492146 ATTAAATTGA
492156 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 A
492187 AGAAATGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:495564 original size:122 final size:121
Alignment explanation
Indices: 495368--495779 Score: 370
Period size: 121 Copynumber: 3.4 Consensus size: 121
495358 AAAAAGGGGA
* * * * *
495368 AAACGCATCCCCTGCAACGAGCCTTTCATTAAGTTTGTTTTATTTT-TATGT-ATTTCTTAGTCA
1 AAACGCGTCCCCTGCAATGAGCCTTTCATTAAGTTTGTCTGATTTTCT-T-TCATTTCTCAGTCA
* * * * * *
495431 ATCAATTGAAGTTTTGATTTTTTTTAATGAAATTATAGAGATTTTCTGGAAA-AAAT-GG
64 ATTAATTGAAG-TTTGATTTTTTAT-ATGAAATGACAAAGATTCTCTGGAAACAAATAGG
* * * * **
495489 AAAGTGTGTCCCCTGTAATGAGCCTTTCATTAAGTTTGTCTGGTTTTCTTTCATTTCTCAACCAA
1 AAA-CGCGTCCCCTGCAATGAGCCTTTCATTAAGTTTGTCTGATTTTCTTTCATTTCTCAGTCAA
* * *
495554 TTAATTGAAGTTTGA-TTTTTATATGACATGGCAAAGATTCTCTGTAAACAAATAGGG
65 TTAATTGAAGTTTGATTTTTTATATGAAATGACAAAGATTCTCTGGAAACAAATA-GG
* * *
495611 AAACGCGTCCCCTGCAATGAGCATTTCATTAAGTTTGTCTGATTTTCCTACATTTCTCAGTCAAT
1 AAACGCGTCCCCTGCAATGAGCCTTTCATTAAGTTTGTCTGATTTTCTTTCATTTCTCAGTCAAT
* * * * * * * *
495676 TAATTTAGGTTTGA-TTTTTACATGACATGGCAGAGATTCGCTGCAAGAAA-AAAAAGG
66 TAATTGAAGTTTGATTTTTTATATGAAATGACAAAGATTCTCTG---GAAACAAATAGG
* * * *
495733 AAAGCGTGTCCCCTTCAACGAGCCTTTCATTAAGTTTATCTGATTTT
1 AAA-CGCGTCCCCTGCAATGAGCCTTTCATTAAGTTTGTCTGATTTT
495780 TCAGCATTTC
Statistics
Matches: 240, Mismatches: 41, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
119 19 0.08
120 10 0.04
121 100 0.42
122 65 0.27
123 43 0.18
124 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (121 bp):
AAACGCGTCCCCTGCAATGAGCCTTTCATTAAGTTTGTCTGATTTTCTTTCATTTCTCAGTCAAT
TAATTGAAGTTTGATTTTTTATATGAAATGACAAAGATTCTCTGGAAACAAATAGG
Found at i:495798 original size:123 final size:122
Alignment explanation
Indices: 495480--495804 Score: 381
Period size: 121 Copynumber: 2.7 Consensus size: 122
495470 GATTTTCTGG
* * * *
495480 AAAAAATGGAAAGTGTGTCCCCTGT-AATGAGCCTTTCATTAAGTTTGTCTG-GTTTTCTTTCAT
1 AAAAAAAGGAAAGCGTGTCCCCT-TCAATGAGCCTTTCATTAAGTTTGTCTGATTTTTC-TACAT
* * * *
495543 TTCTCAACCAATTAATTGAAGTTTGATTTTTATATGACATGGCAAAGATTCTCTGTAAA
64 TTCTCAATCAATTAATTGAAGTTTGATTTTTACATGACATGGCAAAGATTCGCTGCAAA
* * * * * * *
495602 CAAATAGGGAAA-CGCGTCCCCTGCAATGAGCATTTCATTAAGTTTGTCTGATTTTCCTACATTT
1 AAAAAAAGGAAAGCGTGTCCCCTTCAATGAGCCTTTCATTAAGTTTGTCTGATTTTTCTACATTT
* * * *
495666 CTCAGTCAATTAATTTAGGTTTGATTTTTACATGACATGGCAGAGATTCGCTGCAAGA
66 CTCAATCAATTAATTGAAGTTTGATTTTTACATGACATGGCAAAGATTCGCTGCAA-A
* *
495724 AAAAAAAGGAAAGCGTGTCCCCTTCAACGAGCCTTTCATTAAGTTTATCTGATTTTTC-AGCATT
1 AAAAAAAGGAAAGCGTGTCCCCTTCAATGAGCCTTTCATTAAGTTTGTCTGATTTTTCTA-CATT
495788 TC-CTAATCAATTAATTG
65 TCTC-AATCAATTAATTG
495805 GGCAATTTTA
Statistics
Matches: 168, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
121 87 0.52
122 25 0.15
123 56 0.33
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (122 bp):
AAAAAAAGGAAAGCGTGTCCCCTTCAATGAGCCTTTCATTAAGTTTGTCTGATTTTTCTACATTT
CTCAATCAATTAATTGAAGTTTGATTTTTACATGACATGGCAAAGATTCGCTGCAAA
Found at i:502242 original size:122 final size:120
Alignment explanation
Indices: 501876--502248 Score: 394
Period size: 122 Copynumber: 3.1 Consensus size: 120
501866 AAATTTCCAA
** * * * *
501876 TTCTATGAAATGAAATAGATTCTCTGAAGAAAAAAAAGGG-ATGTGTGTCTCCTGCAATGAGCAT
1 TTCTATGAAATGGTATAGATTCTCT--ACAAAAAAAAGGGAAAGTGTGTC-CCTGCAACGAGCCT
* * * * *
501940 TTCATTAAGTTTGTCTTATTTTTTTGTATTTCTCAATCAATTAATTGAAGTTTTATTT
63 TTCATTAAGTTTGTCTGATTTTTCTGTATTTCTCAGTCAATTAATTGAAATTTTTTTT
* * * * ** * *
501998 TTCTATGAAATGGTAGAGATTCTCTGCAAAGAAAGGGGAAAGTACGCCCCCTGCAACGAGCCTGT
1 TTCTATGAAATGGTATAGATTCTCTACAAAAAAAAGGGAAAGTGTG-TCCCTGCAACGAGCCTTT
* * *
502063 CATTAAGTTTGTATGAGTTTTCTGTATTTCTCAGTCAATTAATTAAAAATTTATTTTT
65 CATTAAGTTTGTCTGATTTTTCTGTATTTCTCAGTCAATTAATT-GAAATTT-TTTTT
* *
502121 TAC-ATGACAT-GTCATAGATTCTCTACAAAAAAAAGGGAAAGTGTGTCCCTTGCAACGAGCCTT
1 TTCTATGAAATGGT-ATAGATTCTCTACAAAAAAAAGGGAAAGTGTGTCCC-TGCAACGAGCCTT
* *
502184 TCATTAAGTTTATCTGATTTTTCTGCATTTCTCAGTCAATTAATTG-AATTTTGTTTT
64 TCATTAAGTTTGTCTGATTTTTCTGTATTTCTCAGTCAATTAATTGAAATTTT-TTTT
*
502241 TTATATGA
1 TTCTATGA
502249 TGGCAGTCGA
Statistics
Matches: 204, Mismatches: 39, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
119 1 0.00
120 19 0.09
121 65 0.32
122 113 0.55
123 6 0.03
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (120 bp):
TTCTATGAAATGGTATAGATTCTCTACAAAAAAAAGGGAAAGTGTGTCCCTGCAACGAGCCTTTC
ATTAAGTTTGTCTGATTTTTCTGTATTTCTCAGTCAATTAATTGAAATTTTTTTT
Found at i:503324 original size:32 final size:32
Alignment explanation
Indices: 503254--503349 Score: 93
Period size: 32 Copynumber: 3.0 Consensus size: 32
503244 TTACATTAAA
* * * * *
503254 ATTAAACATGAACAGAAAAACATGGACAAACAC
1 ATTAAACA-GAAAATAAAATCATAGACATACAC
* * *
503287 TTTAAATAGAAAATAAAGTCATAGACATACAC
1 ATTAAACAGAAAATAAAATCATAGACATACAC
**
503319 ATTAAACAGTGAATAAAATCATAGACATACA
1 ATTAAACAGAAAATAAAATCATAGACATACA
503350 ACTTTTTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 44 0.88
33 6 0.12
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (32 bp):
ATTAAACAGAAAATAAAATCATAGACATACAC
Found at i:506572 original size:26 final size:26
Alignment explanation
Indices: 506534--506584 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
506524 AATAACAACG
* *
506534 AACCTTCATATACTGGAAAGTGGAAC
1 AACCTTAAAATACTGGAAAGTGGAAC
506560 AACCTTAAAATACTGGAAAGTGGAA
1 AACCTTAAAATACTGGAAAGTGGAA
506585 GATAGGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (26 bp):
AACCTTAAAATACTGGAAAGTGGAAC
Found at i:506654 original size:5 final size:5
Alignment explanation
Indices: 506644--506678 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
506634 TTATATAGGA
506644 GAGGG GAGGG GAGGG GAGGG GAGGG GAGGG G-GGG G
1 GAGGG GAGGG GAGGG GAGGG GAGGG GAGGG GAGGG G
506679 CAATTGGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (5 bp):
GAGGG
Found at i:507142 original size:2 final size:2
Alignment explanation
Indices: 507135--507160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
507125 TAAAATACCA
507135 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
507161 CATTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:516888 original size:36 final size:36
Alignment explanation
Indices: 516841--516912 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
516831 ATACCTAAAA
516841 CATCTTCAAACCCAAAGCTAAAGCTTGAAGTTAACC
1 CATCTTCAAACCCAAAGCTAAAGCTTGAAGTTAACC
516877 CATCTTCAAACCCAAAGCTAAAGCTTGAAGTTAACC
1 CATCTTCAAACCCAAAGCTAAAGCTTGAAGTTAACC
516913 TTTTCTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (36 bp):
CATCTTCAAACCCAAAGCTAAAGCTTGAAGTTAACC
Found at i:520231 original size:9 final size:9
Alignment explanation
Indices: 520217--520251 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
520207 AATATATTTC
520217 TTTTCTTTT
1 TTTTCTTTT
520226 TTTTCTTTT
1 TTTTCTTTT
520235 TCTTTCTTTT
1 T-TTTCTTTT
520245 TTTTCTT
1 TTTTCTT
520252 CTCCTTCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:520242 original size:19 final size:20
Alignment explanation
Indices: 520213--520251 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
520203 AAAAAATATA
520213 TTTCTTTTCTTTTTTTTCTT
1 TTTCTTTTCTTTTTTTTCTT
520233 TTTC-TTTCTTTTTTTTCTT
1 TTTCTTTTCTTTTTTTTCTT
520252 CTCCTTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTCTTTTCTTTTTTTTCTT
Found at i:522084 original size:189 final size:190
Alignment explanation
Indices: 521745--522101 Score: 576
Period size: 189 Copynumber: 1.9 Consensus size: 190
521735 TGTGTTCATT
* * * * * *
521745 TGTTTGTTTTGTTTACTGTTTATGAACATATTTAGTTCGTTTAGTGTTCTCGAACATATGCATTT
1 TGTTTGGTTTGTTTACCGTTTATGAACATATTTAGTTCGTTTAGAGTTCGCAAACATATACATTT
* * * *
521810 AATGGTCGTCAACTTGTTTGTTTAGCATTCACCACGTTAGTTAGATTTCGCGAGCATGCCTGTCA
66 AATGATCGTCAACATGTTTGTTTAGCATTCACCACGTTAGTTAGATTTCACGAACATGCCTGTCA
*
521875 AAATAGTAAAATTACTCTACATGTCCTTAAGTTCTTTATATTATTTTTTTAAGGTGTTTG
131 AAATAGTAAAATTACTCTACATGTCCTTAAATTCTTTATATTATTTTTTTAAGGTGTTTG
521935 TGTTTGGTTTGTTTACCG-TTATGAACATATTTAGTTCGTTTAGAGTTCGCAAACATATACATTT
1 TGTTTGGTTTGTTTACCGTTTATGAACATATTTAGTTCGTTTAGAGTTCGCAAACATATACATTT
521999 AATGATCGTCAACATGTTTGTTTAGCATTCACCACGTTAGTTAG-TGTTCACGAACATGTCC-GT
66 AATGATCGTCAACATGTTTGTTTAGCATTCACCACGTTAGTTAGAT-TTCACGAACATG-CCTGT
522062 CAAAATAGTAAAATTACTCTACATGTCCTTAAATTCTTTA
129 CAAAATAGTAAAATTACTCTACATGTCCTTAAATTCTTTA
522102 GACTTTACAG
Statistics
Matches: 154, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
188 1 0.01
189 135 0.88
190 18 0.12
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (190 bp):
TGTTTGGTTTGTTTACCGTTTATGAACATATTTAGTTCGTTTAGAGTTCGCAAACATATACATTT
AATGATCGTCAACATGTTTGTTTAGCATTCACCACGTTAGTTAGATTTCACGAACATGCCTGTCA
AAATAGTAAAATTACTCTACATGTCCTTAAATTCTTTATATTATTTTTTTAAGGTGTTTG
Found at i:539877 original size:94 final size:94
Alignment explanation
Indices: 539771--539960 Score: 353
Period size: 94 Copynumber: 2.0 Consensus size: 94
539761 TAAATACATT
539771 CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
1 CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
539836 AAGTGAAGCAATGACATACAAAAACTGAA
66 AAGTGAAGCAATGACATACAAAAACTGAA
* *
539865 CAAAATTATTGAAAATAAAATATAACAATTATCGTTTATAGATAGCATATAAACAAACCATTAAC
1 CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
*
539930 AAGTGAAGTAATGACATACAAAAACTGAA
66 AAGTGAAGCAATGACATACAAAAACTGAA
539959 CA
1 CA
539961 CACCAACCAA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (94 bp):
CAAAACTATTGAAAATAAAATATAACAATGATCGTTTATAGATAGCATATAAACAAACCATTAAC
AAGTGAAGCAATGACATACAAAAACTGAA
Found at i:550336 original size:19 final size:20
Alignment explanation
Indices: 550311--550357 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
550301 AAAATAACCA
* *
550311 ACAAATTCGCAATACGATCT
1 ACAAATTCGCAACACGAACT
550331 -CAAATTCGCAACACGAACT
1 ACAAATTCGCAACACGAACT
550350 ACAAATTC
1 ACAAATTC
550358 ATAACTCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.28, G:0.09, T:0.21
Consensus pattern (20 bp):
ACAAATTCGCAACACGAACT
Found at i:550390 original size:20 final size:20
Alignment explanation
Indices: 550367--550624 Score: 74
Period size: 20 Copynumber: 12.8 Consensus size: 20
550357 CATAACTCAG
*
550367 TTTTGAAATTCGCAACGCGA
1 TTTTCAAATTCGCAACGCGA
* * *
550387 TTTTCTAAATTCACAATGCGG
1 TTTTC-AAATTCGCAACGCGA
**
550408 TTTTCAAATTCGCAATACGA
1 TTTTCAAATTCGCAACGCGA
** * *
550428 -ACTCTAATTTCGTAACGC-A
1 TTTTC-AAATTCGCAACGCGA
* ***
550447 TTTTCCAAATTAGCGTTGCGA
1 TTTT-CAAATTCGCAACGCGA
* *** *
550468 ATTTGGTATTCGCAACACGAA
1 TTTTCAAATTCGCAACGCG-A
* **
550489 ATTTCAAATTCGCAATTCGA
1 TTTTCAAATTCGCAACGCGA
*
550509 -TTTCTGAATTCGCAACGCGA
1 TTTTC-AAATTCGCAACGCGA
*** *
550529 TTTTCTTTTTAGCAACGCGA
1 TTTTCAAATTCGCAACGCGA
* * **
550549 TTTTTAAACTCGCAACAAGA
1 TTTTCAAATTCGCAACGCGA
* * *
550569 TTTTCTAATTCACAACACGAA
1 TTTTCAAATTCGCAACGCG-A
*** *
550590 TTTT-GTTTTCGCAACTCGA
1 TTTTCAAATTCGCAACGCGA
* *
550609 TTTCCGAATTCGCAAC
1 TTTTCAAATTCGCAAC
550625 ACAAATTTTA
Statistics
Matches: 165, Mismatches: 63, Indels: 20
0.67 0.25 0.08
Matches are distributed among these distances:
19 11 0.07
20 108 0.65
21 46 0.28
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (20 bp):
TTTTCAAATTCGCAACGCGA
Found at i:550602 original size:40 final size:40
Alignment explanation
Indices: 550558--550645 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
550548 ATTTTTAAAC
* * * **
550558 TCGCAACAAGATTTTCTAATTCACAACACGAATTTTGTTT
1 TCGCAACAAGATTTCCGAATTCACAACACAAATTTTAATT
** *
550598 TCGCAACTCGATTTCCGAATTCGCAACACAAATTTTAATT
1 TCGCAACAAGATTTCCGAATTCACAACACAAATTTTAATT
550638 TCGCAACA
1 TCGCAACA
550646 GTTTTTATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (40 bp):
TCGCAACAAGATTTCCGAATTCACAACACAAATTTTAATT
Found at i:550640 original size:20 final size:20
Alignment explanation
Indices: 550617--550668 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
550607 GATTTCCGAA
550617 TTCGCAACACAAATTTTAAT
1 TTCGCAACACAAATTTTAAT
** *
550637 TTCGC-A-ACAGTTTTTATT
1 TTCGCAACACAAATTTTAAT
550655 TTCGCAACACAAAT
1 TTCGCAACACAAAT
550669 GTTTTGGGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 14 0.56
19 2 0.08
20 9 0.36
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (20 bp):
TTCGCAACACAAATTTTAAT
Found at i:551592 original size:24 final size:24
Alignment explanation
Indices: 551574--551620 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
551564 AGTCAGTATT
551574 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
551598 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
551621 TCAGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:551630 original size:24 final size:24
Alignment explanation
Indices: 551579--551632 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
551569 GTATTCGAAA
*
551579 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
551603 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
551627 TTTGAT
1 TTTGAT
551633 GTTGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:554320 original size:16 final size:15
Alignment explanation
Indices: 554299--554333 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
554289 TACAAATTGA
*
554299 AATTAAACAACAAATC
1 AATTAAACAA-AAAAC
554315 AATTAAACAAAAAAC
1 AATTAAACAAAAAAC
554330 AATT
1 AATT
554334 TTTATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTAAACAAAAAAC
Found at i:555740 original size:21 final size:21
Alignment explanation
Indices: 555718--555793 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
555708 TGACATGTGG
*
555718 ATCTTGAACGGTGGGAGGTGG-
1 ATCTTGAACGATGGGAGG-GGC
* *
555739 ATCCTGAATGATGGGAGGGGC
1 ATCTTGAACGATGGGAGGGGC
* *
555760 CTCTTGAATGATGGGAGGGGC
1 ATCTTGAACGATGGGAGGGGC
*
555781 CTCTTGAACGATG
1 ATCTTGAACGATG
555794 ACAGGTGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.21, C:0.14, G:0.41, T:0.24
Consensus pattern (21 bp):
ATCTTGAACGATGGGAGGGGC
Found at i:555858 original size:21 final size:21
Alignment explanation
Indices: 555803--555863 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
555793 GACAGGTGAT
* *
555803 TCCTGAACAATGGGAAGTGGA
1 TCCTGAACAATGGTAGGTGGA
*
555824 TCCTGAATAATGGTAGGTGGA
1 TCCTGAACAATGGTAGGTGGA
*
555845 TCCTGAACACTGGTAGGTG
1 TCCTGAACAATGGTAGGTG
555864 TATCGGGCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.33, T:0.25
Consensus pattern (21 bp):
TCCTGAACAATGGTAGGTGGA
Found at i:557872 original size:16 final size:16
Alignment explanation
Indices: 557853--557905 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
557843 CCATAACCCC
557853 TATCACACATATATCA
1 TATCACACATATATCA
** * *
557869 TATCATGCACACATCA
1 TATCACACATATATCA
557885 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
557903 TAT
1 TAT
557906 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:558302 original size:23 final size:23
Alignment explanation
Indices: 558237--558305 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
558227 CACCACAGCT
* *
558237 CGTATAATTGCACCGAAGTACCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
558260 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
558283 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
558306 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:558492 original size:103 final size:103
Alignment explanation
Indices: 558321--558533 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
558311 TAATGTCCAT
* *
558321 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
558386 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
*
558424 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
558489 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
558527 AAGGACC
1 AAGGACC
558534 GCGTAGACCC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAAAATACATATATGTCCCG
Found at i:561188 original size:20 final size:20
Alignment explanation
Indices: 561165--561202 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
561155 CTTGAAACTT
*
561165 AAATTCGCAACTCGAAAATG
1 AAATTCGCAACACGAAAATG
561185 AAATTCGCAACACGAAAA
1 AAATTCGCAACACGAAAA
561203 CTAAAATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:561212 original size:20 final size:20
Alignment explanation
Indices: 561159--561212 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
561149 TTTATTCTTG
*
561159 AAACTTAAATTCGCAACTCGA
1 AAAC-TAAATTCGCAACACGA
561180 AAA-TGAAATTCGCAACACGA
1 AAACT-AAATTCGCAACACGA
*
561200 AAACTAAAATCGC
1 AAACTAAATTCGC
561213 GTTGCGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 1 0.03
20 24 0.83
21 4 0.14
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.19
Consensus pattern (20 bp):
AAACTAAATTCGCAACACGA
Found at i:561864 original size:20 final size:20
Alignment explanation
Indices: 561798--561911 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
561788 ATTTGACCTC
**
561798 TGTGTTGCGAA-TTCCAAAT
1 TGTGTTGCGAATTTGGAAAT
* ** *
561817 TCGCGTTGCGAATTTCAAAAC
1 T-GTGTTGCGAATTTGGAAAT
*
561838 TGAGTTGCGAATTTGGAAAT
1 TGTGTTGCGAATTTGGAAAT
* *
561858 TGTGTTGCGAAATTGG-AGT
1 TGTGTTGCGAATTTGGAAAT
*
561877 TCGTGTTGCGAATTT-GAGAT
1 T-GTGTTGCGAATTTGGAAAT
561897 TGTGTTGCGAATTTG
1 TGTGTTGCGAATTTG
561912 TTGGTTATTT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 18 0.23
20 52 0.68
21 7 0.09
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (20 bp):
TGTGTTGCGAATTTGGAAAT
Found at i:569571 original size:20 final size:20
Alignment explanation
Indices: 569548--569590 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
569538 TTATTAATTT
*
569548 AATAAA-TTTAATTATTTGTA
1 AATAAATTTTAATT-TTTGAA
569568 AATAAATTTTAATTTTTGAA
1 AATAAATTTTAATTTTTGAA
569588 AAT
1 AAT
569591 TTTATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AATAAATTTTAATTTTTGAA
Found at i:570766 original size:186 final size:186
Alignment explanation
Indices: 570452--570827 Score: 716
Period size: 186 Copynumber: 2.0 Consensus size: 186
570442 GGAATACATT
570452 TTCAAGAAAAAATGTAATATTTATATAAATACTATTAAAAAGCTTAATGTAAAAGTAATTATCTA
1 TTCAAGAAAAAATGTAATATTTATATAAATACTATTAAAAAGCTTAATGTAAAAGTAATTATCTA
*
570517 AACTATATTTAAAATTAATTTTTCATGTTTAAATAAAATTTTGTTAAAAATAAATATTTTATATT
66 AACTATATTTAAAATTAACTTTTCATGTTTAAATAAAATTTTGTTAAAAATAAATATTTTATATT
*
570582 TTATATGTTATACTTTTAAGTATCTACAGTTAAAAGAAATCATAAAATATGCTATA
131 TTATATGTTATACTTTTAAATATCTACAGTTAAAAGAAATCATAAAATATGCTATA
570638 TTCAAGAAAAAATGTAATATTTATATAAATACTATTAAAAAGCTTAATGTAAAAGTAATTATCTA
1 TTCAAGAAAAAATGTAATATTTATATAAATACTATTAAAAAGCTTAATGTAAAAGTAATTATCTA
*
570703 AACTATATTTAAAATTAACTTTTCGTGTTTAAATAAAATTTTGTTAAAAATAAATATTTTATATT
66 AACTATATTTAAAATTAACTTTTCATGTTTAAATAAAATTTTGTTAAAAATAAATATTTTATATT
*
570768 TTATATGTTATACTTTTAAATATCTACAGTTAAAAGAAATCGTAAAATATGCTATA
131 TTATATGTTATACTTTTAAATATCTACAGTTAAAAGAAATCATAAAATATGCTATA
570824 TTCA
1 TTCA
570828 GATATAACTA
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
186 186 1.00
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (186 bp):
TTCAAGAAAAAATGTAATATTTATATAAATACTATTAAAAAGCTTAATGTAAAAGTAATTATCTA
AACTATATTTAAAATTAACTTTTCATGTTTAAATAAAATTTTGTTAAAAATAAATATTTTATATT
TTATATGTTATACTTTTAAATATCTACAGTTAAAAGAAATCATAAAATATGCTATA
Found at i:570967 original size:11 final size:12
Alignment explanation
Indices: 570943--570971 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
570933 TAAAAAATAA
570943 TTTTAAATATTT
1 TTTTAAATATTT
570955 TTTTAAATATTT
1 TTTTAAATATTT
570967 TTTTA
1 TTTTA
570972 TTAAACCCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTAAATATTT
Found at i:571230 original size:2 final size:2
Alignment explanation
Indices: 571225--571264 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
571215 CTCTCTTATT
571225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
571265 AAGGATTAAT
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):
TA
Found at i:572997 original size:40 final size:40
Alignment explanation
Indices: 572951--573055 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 40
572941 TATAGATGTC
* * *
572951 ATATTTATCGTGCATCTATATTTTTTATTCCAAATCTATT
1 ATATTTATTGTGTATCTATATTTTTTATTCCAAATCGATT
* *
572991 ATATTTATTGTGTATCTATATTTTTTATTTCATATCGATT
1 ATATTTATTGTGTATCTATATTTTTTATTCCAAATCGATT
573031 ATATTTATTGTGTATCTATATTTTT
1 ATATTTATTGTGTATCTATATTTTT
573056 ATTTTGAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.58
Consensus pattern (40 bp):
ATATTTATTGTGTATCTATATTTTTTATTCCAAATCGATT
Found at i:573007 original size:20 final size:19
Alignment explanation
Indices: 572984--573058 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
572974 TTTATTCCAA
572984 ATCTATTATATTTATTGTGT
1 ATCTA-TATATTTATTGTGT
* *
573004 ATCTATATTTTTTATT-TCAT
1 ATCTATA-TATTTATTGT-GT
*
573024 ATCGATTATATTTATTGTGT
1 ATCTA-TATATTTATTGTGT
*
573044 ATCTATATTTTTATT
1 ATCTATATATTTATT
573059 TTGAATAGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 12 0.27
20 29 0.66
21 3 0.07
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (19 bp):
ATCTATATATTTATTGTGT
Found at i:573074 original size:39 final size:39
Alignment explanation
Indices: 572991--573104 Score: 149
Period size: 39 Copynumber: 2.9 Consensus size: 39
572981 CAAATCTATT
* * **
572991 ATATTTATTGTGTATCTATATTTTT-TATTTCATATCGATT
1 ATATTTATTGTGTATCTATATTTTTAT-TTTGA-ATAGACA
573031 ATATTTATTGTGTATCTATATTTTTATTTTGAATAGACA
1 ATATTTATTGTGTATCTATATTTTTATTTTGAATAGACA
* *
573070 ATATTTATTATCTATCTATATTTTTATTTTGAATA
1 ATATTTATTGTGTATCTATATTTTTATTTTGAATA
573105 TATCGATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 37 0.55
40 29 0.43
41 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.58
Consensus pattern (39 bp):
ATATTTATTGTGTATCTATATTTTTATTTTGAATAGACA
Found at i:580543 original size:13 final size:13
Alignment explanation
Indices: 580525--580549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
580515 GGTCACTGTC
580525 GAAAATTTCAGCT
1 GAAAATTTCAGCT
580538 GAAAATTTCAGC
1 GAAAATTTCAGC
580550 CTGCCCTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GAAAATTTCAGCT
Found at i:583880 original size:15 final size:15
Alignment explanation
Indices: 583862--583897 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
583852 TTAAATAATG
583862 TAAATATTGTAGTAT
1 TAAATATTGTAGTAT
583877 TAAATATTGTAGTAT
1 TAAATATTGTAGTAT
583892 TAAATA
1 TAAATA
583898 ATAAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (15 bp):
TAAATATTGTAGTAT
Found at i:584838 original size:2 final size:2
Alignment explanation
Indices: 584833--584857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
584823 ATAATCTTCA
584833 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
584858 GGCTTAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:585171 original size:20 final size:19
Alignment explanation
Indices: 585146--585184 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
585136 ACCTATTTTT
585146 AACAAAAAAAAATTTCTAAG
1 AACAAAAAAAAATTT-TAAG
*
585166 AACAAAAAATAATTTTAAG
1 AACAAAAAAAAATTTTAAG
585185 TATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (19 bp):
AACAAAAAAAAATTTTAAG
Found at i:588256 original size:12 final size:12
Alignment explanation
Indices: 588241--588304 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
588231 TATTTAAACA
588241 GGTATTGGGCCG
1 GGTATTGGGCCG
* *
588253 GGTATTGAGTCG
1 GGTATTGGGCCG
*
588265 GGTATTGGGTC-
1 GGTATTGGGCCG
588276 GGTATTGGGCCG
1 GGTATTGGGCCG
* *
588288 GGAATCGGGCCG
1 GGTATTGGGCCG
588300 GGTAT
1 GGTAT
588305 ATATATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 10 0.23
12 34 0.77
ACGTcount: A:0.12, C:0.14, G:0.47, T:0.27
Consensus pattern (12 bp):
GGTATTGGGCCG
Found at i:588268 original size:24 final size:24
Alignment explanation
Indices: 588241--588304 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
588231 TATTTAAACA
*
588241 GGTATTGGGCCGGGTATTGAGTCG
1 GGTATTGGGCCGGGTATTGAGCCG
* *
588265 GGTATTGGGTC-GGTATTGGGCCG
1 GGTATTGGGCCGGGTATTGAGCCG
* *
588288 GGAATCGGGCCGGGTAT
1 GGTATTGGGCCGGGTAT
588305 ATATATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.12, C:0.14, G:0.47, T:0.27
Consensus pattern (24 bp):
GGTATTGGGCCGGGTATTGAGCCG
Found at i:588362 original size:24 final size:25
Alignment explanation
Indices: 588302--588362 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
588292 TCGGGCCGGG
588302 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
588325 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
588349 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
588363 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:588477 original size:6 final size:6
Alignment explanation
Indices: 588466--588490 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
588456 AAATGGGTTT
588466 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
588491 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:596564 original size:2 final size:2
Alignment explanation
Indices: 596559--596583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
596549 AAACACACAC
596559 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
596584 CCCCATCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:596770 original size:24 final size:24
Alignment explanation
Indices: 596742--596793 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
596732 AACAGATATA
*
596742 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
* * *
596766 TCAAATATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
596790 TCAA
1 TCAA
596794 GTAACAGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:596804 original size:24 final size:24
Alignment explanation
Indices: 596762--596880 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
596752 AAACATAAAT
*
596762 CAGGTCAAATATCATATCAGAAAT-
1 CAGGTCAAGTATCATATCAG-AATC
* *
596786 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
596810 CAAGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* *
596834 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCATATCAGAATC
*
596858 CATGTCAAGTATCATATCAGAAT
1 CAGGTCAAGTATCATATCAGAAT
596881 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.06
24 76 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:596850 original size:48 final size:47
Alignment explanation
Indices: 596765--596880 Score: 162
Period size: 48 Copynumber: 2.4 Consensus size: 47
596755 CATAAATCAG
*
596765 GTCAAATATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCATATCAG-AATCAGGTCAAGTAACAGATCAGAATCCAA
* * *
596813 GTCAAGTATCATATCAGAATCCATGTC-AGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAAT-CAGGTCAAG-TAACAGATCAGAATCCAA
596861 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
596881 TCAAATCGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
47 5 0.08
48 57 0.92
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (47 bp):
GTCAAGTATCATATCAGAATCAGGTCAAGTAACAGATCAGAATCCAA
Found at i:596896 original size:48 final size:48
Alignment explanation
Indices: 596798--596898 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
596788 GGTCAAGTAA
** *
596798 CAGATCAGAATCCAAGTCAAGTATCATATCAGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCATATCAGAATCCAAATCAGAAAT
* *
596846 CAGATCAGAATCCATGTCAAGTATCATATCAGAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCATATCAGAATCCAAATCAG-AAAT
596894 CAGAT
1 CAGAT
596899 AAAATATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCATATCAGAATCCAAATCAGAAAT
Found at i:599434 original size:18 final size:18
Alignment explanation
Indices: 599411--599456 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
599401 CAACGGTTAA
*
599411 CGGGTCTGGTCAATGGGT
1 CGGGTCGGGTCAATGGGT
599429 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAATGGGT
599447 CGGGTCGGGT
1 CGGGTCGGGT
599457 TGTGACCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.09, C:0.17, G:0.50, T:0.24
Consensus pattern (18 bp):
CGGGTCGGGTCAATGGGT
Found at i:600141 original size:144 final size:144
Alignment explanation
Indices: 599881--600169 Score: 524
Period size: 144 Copynumber: 2.0 Consensus size: 144
599871 CGAAAGGTTT
599881 TAGGGGTTTTGTTCCTCGGTTGACAACGAACACGATGGTGGTCTCGGCTTGTCGATCGAAGGTCG
1 TAGGGGTTTTGTTCCTCGGTTGACAACGAACACGATGGTGGTCTCGGCTTGTCGATCGAAGGTCG
* *
599946 GAAGGCGAGTAGATCGGAGTTGAAATTTGGTTGATCAGAGAGGGAAAATCTGGAAAATTTTCCAA
66 GAAGGCGAGTAGATCGGAGTTGAAAGTTGATTGATCAGAGAGGGAAAATCTGGAAAATTTTCCAA
600011 AAAACATACGGGAA
131 AAAACATACGGGAA
* *
600025 TAGGGGTTTTGTTCCTCGGTTGACAATGAACACGATGGTGGTTTCGGCTTGTCGATCGAAGGTCG
1 TAGGGGTTTTGTTCCTCGGTTGACAACGAACACGATGGTGGTCTCGGCTTGTCGATCGAAGGTCG
* *
600090 GAAGGCGAGTAGATCGGAGTTGAAAGTTGATTGATCGGAGAGGGAAAATCTGGAAAATTTTCCAG
66 GAAGGCGAGTAGATCGGAGTTGAAAGTTGATTGATCAGAGAGGGAAAATCTGGAAAATTTTCCAA
600155 AAAACATACGGGAA
131 AAAACATACGGGAA
600169 T
1 T
600170 GGAGGATTTA
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 139 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.26
Consensus pattern (144 bp):
TAGGGGTTTTGTTCCTCGGTTGACAACGAACACGATGGTGGTCTCGGCTTGTCGATCGAAGGTCG
GAAGGCGAGTAGATCGGAGTTGAAAGTTGATTGATCAGAGAGGGAAAATCTGGAAAATTTTCCAA
AAAACATACGGGAA
Found at i:612451 original size:22 final size:21
Alignment explanation
Indices: 612426--612466 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
612416 ATTCTACCTA
612426 AAAAATCAC-AAAATATATATAT
1 AAAAAT-ACTAAAATA-ATATAT
612448 AAAAATACTAAAATAATAT
1 AAAAATACTAAAATAATAT
612467 CATTTGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATACTAAAATAATATAT
Found at i:612907 original size:198 final size:198
Alignment explanation
Indices: 612583--613026 Score: 560
Period size: 198 Copynumber: 2.2 Consensus size: 198
612573 AAACTAGTAA
* * * * * *
612583 ATTTAAACCGGTTACATTATAAATTGACCTATTACATTAT-GTATATCGGTTTTGATGTTTTCGG
1 ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAAT-TATCGATTTCGATGTTTTCGG
* * * *
612647 GATCGATACAATTTTAAATGTATCGACACTTTATGTGTGCAACTCGTTTGTTCTTTATTTTGGAA
65 GATCGATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAA
* * * *
612712 AAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-TGCTAATTAA-CC
130 AAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CTAATGAACCC
612775 GGTAT
194 GGTAT
* *
612780 ATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGATG-TTTCGAG
1 ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTCG-G
* *
612844 GATCGATAC-TTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTG-CCATTCATTTTG
65 GATCGATACAATTTT--AAATGTATCGACACTTTATGCGTACAACTCGTTTGTCC-TTCATTTTG
* * * * *
612907 GAAAAATGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACCTATTCTCTCATGAAC
127 GAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGAAC
612972 CCGGTAT
192 CCGGTAT
*
612979 ATTTCT-ACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCG
1 ATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCG
613027 GTCTCTTTGA
Statistics
Matches: 213, Mismatches: 26, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
196 9 0.04
197 58 0.27
198 94 0.44
199 51 0.24
200 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (198 bp):
ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTCGGG
ATCGATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTTTGGAAA
AAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGAACCCGG
TAT
Found at i:616702 original size:201 final size:202
Alignment explanation
Indices: 616181--616817 Score: 711
Period size: 201 Copynumber: 3.2 Consensus size: 202
616171 AATTTTAAAA
* * * * *
616181 AAGTATCGACATAAATTTAA-AAAGTGTCGATGCATTATGTAGACCTATTTTCTCATGAAATC-A
1 AAGTATCGACACAAA-TGAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCTA
* *
616244 GAAAATTAAACCGGTTACATTTTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTTT
65 TAAATTTAAACCGGTTACATTTTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * * * **
616309 AGGATCGACACTTTTTCTAAACGTATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATTTATTA
130 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTGGAAAATACATTA
616372 TGGACATA-
195 TGGACA-AC
* * * * * * * ***
616380 AAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAAATGGT
1 AAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTAGACC--TATTTTCTCATAAAACCT
* * * * * *
616445 AT--ATTTAGACCGGTTACATTTTTATGTTACTTATTACATTATAATTATGTGTTTCGATGTTTT
64 ATAAATTTAAACCGGTTACATTTTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTT
*
616508 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGG-AAATACATT
129 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTGGAAAATACATT
*
616572 TTGGACAAC
194 ATGGACAAC
*
616581 ATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAAAACCTA
1 AAGTATCGACACAAATGAATAAAGTGTCGATACATTA-TGTAGACCTATTTTCTCATAAAACCTA
* * * * *
616645 TAAATTTAAACTGGTTACATTGTAAAGTGACCTATTATATTATAGTTACGGGTTTCGATGTTTTT
65 TAAATTTAAACCGGTTACATTTTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTTT
* * * * *
616710 GGGATCGATACTTGATATAAATGTGTCGACACTTATTT-GTGAACTTGTTTTGGTTGGAAAATAC
130 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTG----GTTTGGAAAATAC
616774 ATTATGGAC-AC
191 ATTATGGACAAC
* *
616785 AAAGTATCGACACAAATGTATAAAGTGTTGATA
1 -AAGTATCGACACAAATGAATAAAGTGTCGATA
616818 TTTGTGAACT
Statistics
Matches: 360, Mismatches: 62, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
198 2 0.01
199 49 0.14
200 94 0.26
201 158 0.44
202 7 0.02
204 7 0.02
205 43 0.12
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (202 bp):
AAGTATCGACACAAATGAATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCTAT
AAATTTAAACCGGTTACATTTTAAAGTGACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGAACTTGGTTTGGAAAATACATTAT
GGACAAC
Found at i:616833 original size:12 final size:12
Alignment explanation
Indices: 616816--616840 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
616806 AAAGTGTTGA
616816 TATTTGTGAACT
1 TATTTGTGAACT
616828 TATTTGTGAACT
1 TATTTGTGAACT
616840 T
1 T
616841 GTTTTGGTTG
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:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TATTTGTGAACT
Found at i:617325 original size:24 final size:24
Alignment explanation
Indices: 617274--617325 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
617264 ATTTACATTT
* *
617274 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAAATG
*
617298 AAATTCAAACTCTAATT-ATAAATG
1 AAATTCAAACTCAAATTGA-AAATG
617322 AAAT
1 AAAT
617326 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAAATG
Found at i:619696 original size:15 final size:15
Alignment explanation
Indices: 619684--619712 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
619674 TCAGAAGATC
619684 TGGGTTGAGAAGAGA
1 TGGGTTGAGAAGAGA
619699 TGGGTTGAGAAGAG
1 TGGGTTGAGAAGAG
619713 CCCTGATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.48, T:0.21
Consensus pattern (15 bp):
TGGGTTGAGAAGAGA
Found at i:620527 original size:203 final size:198
Alignment explanation
Indices: 620103--620614 Score: 832
Period size: 203 Copynumber: 2.6 Consensus size: 198
620093 TTGCAAAATG
*
620103 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTACAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
*
620168 CACATTGTGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGT-ATCGACACAAATTAAAAAA
66 CACATT-TAGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTAATCGACACAAATTAAAAAA
*
620232 GTGTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTTTATTTAGACCGGTTAGATTGATA
130 GTGTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATTGATA
620297 ATTT
195 ATTT
*
620301 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAAGGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
*
620366 CACATTATAGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTACGGGATCGGCACAAATTAA
66 CACATT-TAGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTA----ATCGACACAAATTAA
* * *
620431 ACAAGTGTCGATACTTTATGTACACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATT
126 AAAAGTGTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATT
620496 GATAATTT
191 GATAATTT
* *
620504 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGAATCGATACTTTTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
620569 CACATTTCCA-TG-CACTTGGTAAGGAAATCATTCTGGACACAAAGTA
66 CACATTT--AGTGAC-CTTGGTAAGGAAATCATTCTGGACACAAAGTA
620615 TACTTGGAAT
Statistics
Matches: 294, Mismatches: 12, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
198 106 0.36
202 2 0.01
203 185 0.63
204 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (198 bp):
ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
CACATTTAGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTAATCGACACAAATTAAAAAAG
TGTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATTGATAA
TTT
Found at i:620781 original size:19 final size:19
Alignment explanation
Indices: 620757--620806 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
620747 TTACATTCAC
* *
620757 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAAGCGT
*
620776 ATACAAAATTAAAAAGCTT
1 ATACAAAATTAAAAAGCGT
620795 ATACAAAATTAA
1 ATACAAAATTAA
620807 CCCTACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.28
Consensus pattern (19 bp):
ATACAAAATTAAAAAGCGT
Found at i:622783 original size:182 final size:181
Alignment explanation
Indices: 622476--622948 Score: 720
Period size: 182 Copynumber: 2.6 Consensus size: 181
622466 TTAACTCCAT
* *
622476 CAAAAGTGTCGATACTTATATTAATTTATTGACACTTTCAATATATCTGGTAGCT--TATTACCG
1 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAG-TGGT-TTACCG
* * * * * *
622539 GTTTTATCAT-TTCGAGACCTGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACA
64 GTTTTATCATAAT-GACACC-GTTTTATCATATTTTTACCTGTTATATTACTATAGATCGATACA
*
622603 TTTGTATAAAATATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTA
127 TTTGTATAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
*
622658 CAAAAGTGTCGATACTTATATTAATTTATCGACATTTTCAATATATCCGGTAGTGGTTTACCGGT
1 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGTGGTTTACCGGT
*
622723 TTTATCATAATGACACCGATTTTATCATATTTTTACCTGTTATATTACTATATATCGATACATTT
66 TTTATCATAATGACACCG-TTTTATCATATTTTTACCTGTTATATTACTATAGATCGATACATTT
*
622788 GTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
130 GTATAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
** *
622840 CAAAAGTGTTAATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGCGGTTTACC-GT
1 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGTGGTTTACCGGT
*
622904 TTTATTATAATGACACCGGTTTTATCATATTTTTACCTGTTATAT
66 TTTATCATAATGACACC-GTTTTATCATATTTTTACCTGTTATAT
622949 GGCTGTGATC
Statistics
Matches: 269, Mismatches: 17, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
181 46 0.17
182 221 0.82
183 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (181 bp):
CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGTGGTTTACCGGT
TTTATCATAATGACACCGTTTTATCATATTTTTACCTGTTATATTACTATAGATCGATACATTTG
TATAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
Found at i:623895 original size:44 final size:41
Alignment explanation
Indices: 623818--623899 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
623808 GCAACGCGAT
* *
623818 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
623859 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
623900 TAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 2 0.06
44 25 0.69
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:623909 original size:19 final size:20
Alignment explanation
Indices: 623820--623910 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
623810 AACGCGATTT
623820 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
623840 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
623859 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
623884 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
623903 TGAAAAAT
1 TGAAAAAT
623911 CCAAAATAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 34 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:624058 original size:65 final size:65
Alignment explanation
Indices: 623952--624130 Score: 295
Period size: 65 Copynumber: 2.8 Consensus size: 65
623942 ATTCACGTGG
* * *
623952 AGTTTGAAACAATAAAGAATGTGTTACAATAGTGTATAAGATTCTCAAGCCATTTGTAAGATCTT
1 AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGCCATTTGTAAGATCTT
* *
624017 AGTTTGAAACAATAAAGATTGTGTTGCGATAGTATAAAAGATTCTCAAGCCATTTGTAAGATCTT
1 AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGCCATTTGTAAGATCTT
* *
624082 AGTTTGAAACAATAAAGAATATGTTGCGATAGTGTAAAAGATTCCCAAG
1 AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAG
624131 TGTTGGCAAT
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 105 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (65 bp):
AGTTTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGCCATTTGTAAGATCTT
Found at i:624396 original size:21 final size:21
Alignment explanation
Indices: 624367--624537 Score: 172
Period size: 21 Copynumber: 8.3 Consensus size: 21
624357 CAATTCGCAA
* *
624367 CGAATTTGGAAAATCGCAACG
1 CGAACTTGGAATATCGCAACG
*
624388 CGAACTTGGACTATCGCAACG
1 CGAACTTGGAATATCGCAACG
*
624409 CGAACTT-CAACTATCGCAACG
1 CGAACTTGGAA-TATCGCAACG
*
624430 CGAACTTGGACTATCGCAA--
1 CGAACTTGGAATATCGCAACG
* *
624449 CGAATTTGGAAAATCGCAACG
1 CGAACTTGGAATATCGCAACG
* * *
624470 CGAACTTCGACTATCGCAATG
1 CGAACTTGGAATATCGCAACG
* *
624491 TGAACTTGGACTATCGCAA--
1 CGAACTTGGAATATCGCAACG
* *
624510 CGAATTTGGAAAATCGCAACG
1 CGAACTTGGAATATCGCAACG
624531 CGAACTT
1 CGAACTT
624538 CGAACGTGAA
Statistics
Matches: 122, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
19 31 0.25
20 1 0.01
21 89 0.73
22 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
CGAACTTGGAATATCGCAACG
Found at i:624405 original size:40 final size:40
Alignment explanation
Indices: 624361--624604 Score: 227
Period size: 40 Copynumber: 6.2 Consensus size: 40
624351 CAAATGCAAT
624361 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTA
* * *
624401 TCGCAACGCGAACTT-CAACTATCGCAACGCGAACTTGGACTA
1 TCGCAA--CGAATTTGGAA-AATCGCAACGCGAACTTGGACTA
*
624443 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTA
* * ** * **
624483 TCGCAATGTGAACTTGGACTATCGCAA--CGAATTTGGAAAA
1 TCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTGGACTA
* ** *
624523 TCGCAACG-----CGAACTTCG-AACGTGAACTTGGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTA
* *
624557 TCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTA
624597 TCGCAACG
1 TCGCAACG
624605 TGAACTTGGA
Statistics
Matches: 159, Mismatches: 31, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
32 2 0.01
33 5 0.03
34 16 0.10
38 1 0.01
39 6 0.04
40 76 0.48
41 4 0.03
42 49 0.31
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTA
Found at i:624465 original size:61 final size:61
Alignment explanation
Indices: 624400--624623 Score: 347
Period size: 61 Copynumber: 3.8 Consensus size: 61
624390 AACTTGGACT
*
624400 ATCGCAACGCGAACTTCAACTATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCAACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
* *
624461 ATCGCAACGCGAACTTCGACTATCGCAATGTGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCAACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
*
624522 ATCGCAACGCG------AACT-TCG-AACGTGAACTTGGACTATCGCAACAAATTTGGAAA
1 ATCGCAACGCGAACTTCAACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
*
624575 ATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTCAACTATCGCAACGTGAACTTGGACTATCGCAA
624624 AATCGCGTTG
Statistics
Matches: 148, Mismatches: 7, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
53 44 0.30
54 3 0.02
55 3 0.02
59 3 0.02
60 3 0.02
61 92 0.62
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGAACTTCAACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
Found at i:624504 original size:82 final size:82
Alignment explanation
Indices: 624361--624511 Score: 257
Period size: 82 Copynumber: 1.8 Consensus size: 82
624351 CAAATGCAAT
*
624361 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTCAACTATCGC
1 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCAACTATCGC
624426 AACGCGAACTTGGACTA
66 AACGCGAACTTGGACTA
* * **
624443 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAATGTGAACTTGGACTATCGC
1 TCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCAACTATCGC
624508 AACG
66 AACG
624512 AATTTGGAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (82 bp):
TCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCAACTATCGC
AACGCGAACTTGGACTA
Found at i:624570 original size:53 final size:53
Alignment explanation
Indices: 624490--624593 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
624480 CTATCGCAAT
*
624490 GTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGAAC
1 GTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGAAC
624543 GTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGA
1 GTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGA
624594 CTATCGCAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (53 bp):
GTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCGAAC
Found at i:624601 original size:21 final size:21
Alignment explanation
Indices: 624575--624623 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
624565 AATTTGGAAA
624575 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
624596 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
624617 ATCGCAA
1 ATCGCAA
624624 AATCGCGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:634496 original size:27 final size:27
Alignment explanation
Indices: 634465--634518 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
634455 TATGTGTGTA
*
634465 TGTTTGTATCTATCTAAATGTATCTCC
1 TGTTTGTATCTATCTAAATGTACCTCC
*
634492 TGTTTGTATCTATCTATATGTACCTCC
1 TGTTTGTATCTATCTAAATGTACCTCC
634519 GTAAGCTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.48
Consensus pattern (27 bp):
TGTTTGTATCTATCTAAATGTACCTCC
Done.