Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 180 of 186
Found at i:59655768 original size:18 final size:18
Alignment explanation
Indices: 59655741--59655804 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
59655731 GAAAAATAAA
* *
59655741 AAAAGAAAAATTAAAA-A
1 AAAATAAAAATTAAAATT
*
59655758 AATAATTAAAATTAAAATT
1 AA-AATAAAAATTAAAATT
*
59655777 AAAATTAAAATTAAAATT
1 AAAATAAAAATTAAAATT
59655795 AAAATAAAAA
1 AAAATAAAAA
59655805 GGAGAGGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
17 2 0.05
18 37 0.90
19 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAATAAAAATTAAAATT
Found at i:59655804 original size:12 final size:12
Alignment explanation
Indices: 59655747--59655803 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
59655737 TAAAAAAAGA
*
59655747 AAAATTAAAA-A
1 AAAATTAAAATT
59655758 AATAATTAAAATT
1 AA-AATTAAAATT
59655771 AAAATTAAAATT
1 AAAATTAAAATT
59655783 AAAATTAAAATT
1 AAAATTAAAATT
59655795 AAAA-TAAAA
1 AAAATTAAAA
59655804 AGGAGAGGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
11 7 0.16
12 34 0.79
13 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAATTAAAATT
Found at i:59656968 original size:64 final size:64
Alignment explanation
Indices: 59656895--59657341 Score: 732
Period size: 64 Copynumber: 7.0 Consensus size: 64
59656885 CATTCATAAT
*
59656895 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATATCATCCTAATTATTTGACATGAGCATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCATC
* *
59656959 ACATCTAGTTAAGAGCATTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATGAGCATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCATC
* * *
59657023 ACATCTAGTTAGGAGCATTCGATTCATTTCTATCATAACATCCTAATTATTTGACATGAGCATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCATC
* *
59657087 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCTTAATTATTTGACATGAGTATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCATC
* *
59657151 ACATCTAGTTAGAAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATAAGCATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCATC
* * *
59657215 ACATCTAGTTAGAAGCATTTGATTTATTTCGATCATAGCATCCTAATTATTTGACATAAGCATC
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCATC
* * * * *
59657279 ATATTTAGTTAGGAGCATTTGATTCATTTTGATCATAGCATCCTAATTATTTGGCATAAGCAT
1 ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCAT
59657342 AGATACATGA
Statistics
Matches: 359, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 359 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (64 bp):
ACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATGAGCATC
Found at i:59657880 original size:44 final size:45
Alignment explanation
Indices: 59657809--59657905 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 45
59657799 GCCACTGACA
**
59657809 TTATC-TCTCTGAGGTAGCAAGAGAGCAGGTTGAAGA-TGATAG-TC
1 TTATCTTC-CTGAGGTAGCAAGAGAGCAGACTGAAGATTGA-AGATC
59657853 TTATCTTCCTGAGGTAGCAAG-GAAGCAGACTGAAGATTGAAGATC
1 TTATCTTCCTGAGGTAGCAAGAG-AGCAGACTGAAGATTGAAGATC
59657898 TTAT-TTCC
1 TTATCTTCC
59657906 CTGAAGTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
43 1 0.02
44 35 0.74
45 11 0.23
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (45 bp):
TTATCTTCCTGAGGTAGCAAGAGAGCAGACTGAAGATTGAAGATC
Found at i:59658030 original size:177 final size:175
Alignment explanation
Indices: 59657454--59658679 Score: 1226
Period size: 177 Copynumber: 7.0 Consensus size: 175
59657444 AGATTACAAA
* * ** * *
59657454 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGCTCAATAGACA-AGTCTTATCTCCCTGAGGTTA-
1 CCTTATCTCCCTGAAGTAGAAG-GGAGCAGG-TTGA-AGATATAGTCTTATCTTCCTGAGG-TAG
* * * * * * * * * *
59657517 CAGTGGAA-TAGACTGAGGATTGCAGGTCTTATTTCCCTAAACAGTAGTGGAACAGACCAAAGAC
62 CA-AGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
* * * *
59657581 GACGAATCTTATCTCCATGTACAGGCAATGGAGCAGATTTAAGTCACCAG
126 GGCGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCACTAG
* * * * * **
59657631 CCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTCAAGATATAGTCTTATCTTTCTGACATAGCAA
1 CCTTATCTCCCTGAAGTAGAAG-GGAGCAGGTTGAAGATATAGTCTTATCTTCCTGAGGTAGCAA
* * * *
59657696 GAAAGCAGACTGAAGATTGAAAGATCTTA-TCCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGT
65 GGAAGCAGACTGAAGATTG-AAGATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* *
59657760 GAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCACT-G
129 GAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCACTAG
* * * *
59657806 ACATTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATGATAGTCTTATCTTCCTGAGGTAGC
1 -CCTTATCTCCCTGAAGTAG-AAGGGAGCAGGTTGAAGAT-ATAGTCTTATCTTCCTGAGGTAGC
** * * *
59657871 AAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTGAAGTTGCAGTGGAGTAGGTCGAAG-TC
63 AAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCT-AAGCAGTAGTGGAGCAGATCGAAGAT-
* * * * *
59657935 GACAAATCTTATCTCTATGTACCGGTAATGGAGCAGATTTAAGTCACTAG
126 GGCGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCACTAG
* * *
59657985 CCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTCAAGATATAGTCTTATCTTCCTGAGGTAGCAA
1 CCTTATCTCCCTGAAGTAGAAG-GGAGCAGGTTGAAGATATAGTCTTATCTTCCTGAGGTAGCAA
* * * * *
59658050 GGAAGTAGATTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGTAGATCGAAGATGGCG
65 GGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCG
* * * *
59658115 AATCGTATCTCCATGTACAGGCAATGGAGCAGATTTTAGCCACTGG
130 AATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCACTAG
* * * * * *
59658161 CCTTATCTCTCTGAGGTAACAAGAGAGTAGGTTGAAGATGGTAGTCTTATCTTCCTGAGGTAGCA
1 CCTTATCTCCCTGAAGT-AGAAGGGAGCAGGTTGAAGAT-ATAGTCTTATCTTCCTGAGGTAGCA
* * * *
59658226 AGGAAGCAGACTGAAGATTGAATATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGC
64 AGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* * * * * *
59658291 GAATCTTATCTCCATGTATCGACAATGGAGTAGATTTGAGCTACCAG
129 GAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCACTAG
* * * ** *
59658338 CCTTATCT-CTTTAAGGTAGCAAGAGAGCAGGTTGGCGATTGTAGTCTTA---T-C----GTAGC
1 CCTTATCTCCCTGAA-GTAG-AAGGGAGCAGGTTGAAGA-TATAGTCTTATCTTCCTGAGGTAGC
* * * * * *
59658394 AAGAAAGCAGACTGAAGATTGAAGATCTTATCTCCTTAAGAAGTAGTGGAGCAGATCGAGGACGG
63 AAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
* * *
59658459 CGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGCCA-TCGG
128 CGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCACT-AG
* * * *
59658507 CCTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATGGTAGTCTTATCTTCCTGAGGTAGCA
1 CCTTATCTCCCTGAAGTAG-AAGGGAGCAGGTTGAAGAT-ATAGTCTTATCTTCCTGAGGTAGCA
* * * * * *
59658572 AAGAAGCAGACTGAAGATTGAAGATC-TATTTCCCTAAGCAGTGGAGGAGTACATCGAGGATGGC
64 AGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* *
59658636 GAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTGAGCCAC
129 GAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCAC
59658680 CAGTCCTATT
Statistics
Matches: 877, Mismatches: 142, Indels: 60
0.81 0.13 0.06
Matches are distributed among these distances:
168 1 0.00
169 141 0.16
170 2 0.00
172 1 0.00
173 2 0.00
174 1 0.00
175 10 0.01
176 296 0.34
177 334 0.38
178 88 0.10
179 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (175 bp):
CCTTATCTCCCTGAAGTAGAAGGGAGCAGGTTGAAGATATAGTCTTATCTTCCTGAGGTAGCAAG
GAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGA
ATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGCCACTAG
Found at i:59658066 original size:354 final size:352
Alignment explanation
Indices: 59657496--59658705 Score: 1513
Period size: 354 Copynumber: 3.5 Consensus size: 352
59657486 TCAATAGACA
* * * * * * *
59657496 AGTCTTATCTCCCTGAGGTTA-CAGTGGAA-TAGACTGAGGATTGCAGGTCTTATTTCCCTAAAC
1 AGTCTTATCTTCCTGAGG-TAGCA-AGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGC
* ** * *
59657559 AGTAGTGGAACAGACCAAAGA-CGACGAATCTTATCTCCATGTACAGGCAATGGAGCAGATTTAA
64 AGCAGTGGAGTAGATCAAAGATCGACGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAA
*
59657623 GTCACCAGCCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTCAAGATATAGTCTTATCTTTCTGA
129 GTCACCAGCCTTATCTCCCTAAAGTTGTAGTGGAGCAGGTTCAAGATATAGTCTTATC-TTCTGA
*
59657688 CATAGCAAGAAAGCAGACTGAAGATTGAAAGATCTTATC-CCCTAAGCAGTAGCGGAGCAGATCG
193 -GTAGCAAGAAAGCAGACTGAAGATTG-AAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCG
* * *
59657752 AAGATGGTGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCACTGACATTATCTCT
256 AAGATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCACTGGCCTTATCTCT
*
59657817 CTGAGGTAGCAAGAGAGCAGGTTGAAGATGAT
321 CTGAGGTAGCAAGAGAGCAGGTTGAAGATGGT
**
59657849 AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTGAAGTT
1 AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCT-AAGCA
* * * * *
59657914 GCAGTGGAGTAGGTCGAAG-TCGACAAATCTTATCTCTATGTACCGGTAATGGAGCAGATTTAAG
65 GCAGTGGAGTAGATCAAAGATCGACGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAG
* *
59657978 TCACTAGCCTTATCTCCCTGAAGTTGTAGTGGAGCAGGTTCAAGATATAGTCTTATCTTCCTGAG
130 TCACCAGCCTTATCTCCCTAAAGTTGTAGTGGAGCAGGTTCAAGATATAGTCTTATCTT-CTGA-
* * * *
59658043 GTAGCAAGGAAGTAGATTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGTAGATCGAA
193 GTAGCAAGAAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAA
*
59658108 GATGGCGAATCGTATCTCCATGTA-CAGGCAATGGAGCAGATTTTAGCCACTGGCCTTATCTCTC
258 GATGGCGAATCTTATCTCCATGTATC-GGCAATGGAGCAGATTTTAGCCACTGGCCTTATCTCTC
* *
59658172 TGAGGTAACAAGAGAGTAGGTTGAAGATGGT
322 TGAGGTAGCAAGAGAGCAGGTTGAAGATGGT
* *
59658203 AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAATATCTTATCTCCCTAAGCAG
1 AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAG
* * * * * *
59658268 TAGTGGAGTAGATCAAAGAT-GGCGAATCTTATCTCCATGTATCGACAATGGAGTAGATTTGAG-
66 CAGTGGAGTAGATCAAAGATCGACGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGT
** * * * * *** *
59658331 CTACCAGCCTTATCTCTTTAAGGTAGCAAG-AGAGCAGGTTGGCGATTGTAGTCTTA---TC---
131 C-ACCAGCCTTATCTCCCTAAAGTTG-TAGTGGAGCAGGTTCAAGA-TATAGTCTTATCTTCTGA
* * * *
59658389 GTAGCAAGAAAGCAGACTGAAGATTGAAGATCTTATCTCCTTAAGAAGTAGTGGAGCAGATCGAG
193 GTAGCAAGAAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAA
* *
59658454 GACGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTCAGCCA-TCGGCCTTATCTCTC
258 GATGGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCACT-GGCCTTATCTCTC
59658518 TGAGGTAGCAAGAGAGCAGGTTGAAGATGGT
322 TGAGGTAGCAAGAGAGCAGGTTGAAGATGGT
*
59658549 AGTCTTATCTTCCTGAGGTAGCAAAGAAGCAGACTGAAGATTGAAGATC-TATTTCCCTAAGCAG
1 AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAG
** * * * * * * * *
59658613 TGGAGGAGTACATCGAGGAT-GGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTGAGC
66 CAGTGGAGTAGATCAAAGATCGACGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGT
* * *
59658677 CACCAGTCC-TATTTCCCAAAAGTTATAGT
131 CACCAG-CCTTATCTCCCTAAAGTTGTAGT
59658706 CAAGATTAAG
Statistics
Matches: 748, Mismatches: 93, Indels: 40
0.85 0.11 0.05
Matches are distributed among these distances:
344 2 0.00
345 85 0.11
346 193 0.26
347 1 0.00
350 1 0.00
351 1 0.00
352 7 0.01
353 142 0.19
354 316 0.42
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (352 bp):
AGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATTGAAGATCTTATTTCCCTAAGCAG
CAGTGGAGTAGATCAAAGATCGACGAATCTTATCTCCATGTACCGGCAATGGAGCAGATTTAAGT
CACCAGCCTTATCTCCCTAAAGTTGTAGTGGAGCAGGTTCAAGATATAGTCTTATCTTCTGAGTA
GCAAGAAAGCAGACTGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGAT
GGCGAATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCACTGGCCTTATCTCTCTGAG
GTAGCAAGAGAGCAGGTTGAAGATGGT
Found at i:59664768 original size:111 final size:111
Alignment explanation
Indices: 59664574--59664795 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
59664564 TTCTAAAAAA
*
59664574 TCGAAATAAACCAAAATTTCTCGTTCTTTTAATCGGATTATGACTAAATTTTACATTGAACTCTT
1 TCGAAATAAACCAAAATTTCTCGTTCTTTTAATCGGATTATGACTAAAGTTTACATTGAACTCTT
59664639 ATTTTTGAAAATTAAGACAACGCGTGTTTATGAGATACCAATTTTG
66 ATTTTTGAAAATTAAGACAACGCGTGTTTATGAGATACCAATTTTG
59664685 TCGAAATAAACCAAAATTTCTCGTTCTTTTAATCGGATTATGACTAAAGTTTACATTGAACTCTT
1 TCGAAATAAACCAAAATTTCTCGTTCTTTTAATCGGATTATGACTAAAGTTTACATTGAACTCTT
59664750 ATTTTTGAAAATTAAGACAACGCGTGTTTATGAGATACCAATTTTG
66 ATTTTTGAAAATTAAGACAACGCGTGTTTATGAGATACCAATTTTG
59664796 GGCGTCGCGA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (111 bp):
TCGAAATAAACCAAAATTTCTCGTTCTTTTAATCGGATTATGACTAAAGTTTACATTGAACTCTT
ATTTTTGAAAATTAAGACAACGCGTGTTTATGAGATACCAATTTTG
Found at i:59676507 original size:69 final size:69
Alignment explanation
Indices: 59676387--59676560 Score: 192
Period size: 69 Copynumber: 2.5 Consensus size: 69
59676377 CTTTCCAAGG
**
59676387 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATC-ACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
59676450 T-TTAAA
64 TGTT-AA
** * *
59676456 AAAATCATCTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCA-CTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
**
59676521 GTTTT
65 GTTAA
* * *
59676526 AAATTGACTCATATTGCGAGAAGTGAGTTAAGCCT
1 AAAATCACTCATATTGCGAGAAGTGAGTTGAGCCT
59676561 TTTAATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
68 1 0.01
69 79 0.88
70 8 0.09
71 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (69 bp):
AAAATCACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTATG
TTAA
Found at i:59676699 original size:74 final size:74
Alignment explanation
Indices: 59676578--59676716 Score: 251
Period size: 74 Copynumber: 1.9 Consensus size: 74
59676568 TTTGTTTTTC
* **
59676578 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
59676643 GTTGTCAAA
66 GTTGTCAAA
59676652 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
59676717 TTATTTTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTGTCAAA
Found at i:59677796 original size:22 final size:22
Alignment explanation
Indices: 59677771--59677815 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
59677761 TTATTAAAGT
59677771 ATATGTTTTTAATAATAAATTA
1 ATATGTTTTTAATAATAAATTA
59677793 ATATGTTTTTAATAATAAATTA
1 ATATGTTTTTAATAATAAATTA
59677815 A
1 A
59677816 CTTTTGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATGTTTTTAATAATAAATTA
Found at i:59679000 original size:13 final size:13
Alignment explanation
Indices: 59678975--59679032 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
59678965 AATTAAATTC
59678975 TTAATAAAT-ATAT
1 TTAA-AAATAATAT
59678988 TTAAAAATAATAT
1 TTAAAAATAATAT
* * *
59679001 TTAAATACAATAA
1 TTAAAAATAATAT
59679014 TTAAAAATAA-AT
1 TTAAAAATAATAT
59679026 ATTAAAA
1 -TTAAAA
59679033 TAAAATCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
12 5 0.14
13 32 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATAATAT
Found at i:59679007 original size:27 final size:26
Alignment explanation
Indices: 59678977--59679036 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
59678967 TTAAATTCTT
*
59678977 AATAAATATATTTAAAAAT-AATATTTA
1 AATAAATA-A-TTAAAAATAAATATTAA
59679004 AATACAATAATTAAAAATAAATATTAA
1 AATA-AATAATTAAAAATAAATATTAA
59679031 AATAAA
1 AATAAA
59679037 ATCATCCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 10 0.33
27 16 0.53
28 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATAAATAATTAAAAATAAATATTAA
Found at i:59691201 original size:35 final size:35
Alignment explanation
Indices: 59691155--59691226 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
59691145 TCCGAGAAGT
59691155 TAGATTTTTGGGGCACATTGTTTCAGTGGAAGGTA
1 TAGATTTTTGGGGCACATTGTTTCAGTGGAAGGTA
*
59691190 TAGATTTTTGGGGCACATTGTTTCAGTGGAATGTA
1 TAGATTTTTGGGGCACATTGTTTCAGTGGAAGGTA
59691225 TA
1 TA
59691227 CAGGTTGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (35 bp):
TAGATTTTTGGGGCACATTGTTTCAGTGGAAGGTA
Found at i:59693242 original size:43 final size:43
Alignment explanation
Indices: 59693194--59693407 Score: 213
Period size: 43 Copynumber: 5.0 Consensus size: 43
59693184 GTTACCGAGA
*
59693194 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAT
59693237 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTTAT
1 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTG-TAT
* * *
59693281 TCG-G-TTTCGTGTAAGACCATGTATGGGACATTGGCATCGTTAT
1 T-GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTG-TAT
** * * * * *
59693324 T-CAATTTCGTGCAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * * * *
59693365 ATGTGATAACATGAAAGACCATATCTGGGATA-TGGCATTGTAT
1 -TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAT
59693408 GAGCTTTATG
Statistics
Matches: 145, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.01
42 8 0.06
43 129 0.89
44 5 0.03
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:59694693 original size:12 final size:12
Alignment explanation
Indices: 59694676--59694701 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59694666 GTTTCCCAAA
59694676 GTTTTTGAAAGT
1 GTTTTTGAAAGT
59694688 GTTTTTGAAAGT
1 GTTTTTGAAAGT
59694700 GT
1 GT
59694702 CTCCGTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (12 bp):
GTTTTTGAAAGT
Found at i:59699595 original size:56 final size:55
Alignment explanation
Indices: 59699152--59699566 Score: 552
Period size: 56 Copynumber: 7.4 Consensus size: 55
59699142 TCATGGAATT
* **
59699152 GATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGATTCC
1 GATATATGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATT-C
59699208 GATATATGTGTGCT-AGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
1 GATATATGTGTG-TGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
* * *
59699263 TGATATATGTGTGAGAGTAAGACCACATTTAATACGTTGGCATCGATATATGACTTC
1 -GATATATGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGA-TTC
* **
59699320 GATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGATTCC
1 GATATATGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATT-C
59699376 GATATATGTGTGCT-AGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTC
1 GATATATGTGTG-TGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGA-TTC
* * * * *
59699432 GATATATGTGTGCGAGTAAGAACC-TGTCTGAGA-AAG-TGGCATCGATTTGTGATTC
1 GATATATGTGTGTGAGTAAG-ACCACGT-TTA-ATACGTTGGCATCGATATGTGATTC
*
59699487 TGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTTC
1 -GATATATGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGA-TTC
59699544 GATATATGTGTGTGAGTAAGACC
1 GATATATGTGTGTGAGTAAGACC
59699567 CTGTTTGGGA
Statistics
Matches: 318, Mismatches: 25, Indels: 32
0.85 0.07 0.09
Matches are distributed among these distances:
54 1 0.00
55 13 0.04
56 286 0.90
57 17 0.05
58 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (55 bp):
GATATATGTGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
Found at i:59699597 original size:168 final size:169
Alignment explanation
Indices: 59699151--59699566 Score: 625
Period size: 168 Copynumber: 2.5 Consensus size: 169
59699141 ATCATGGAAT
59699151 TGATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGATTCCGATATATG
1 TGATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGATTCCGATATATG
59699216 TGTGCTAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGA-TTCTGATATATGTGTGAGAG
66 TGTGCTAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTCTGATATATGTGTGAGAG
*
59699280 TAAGACCACATTTAATACGTTGGCATCGATATATGACTTC
131 TAAGA-CACATTTAATAAGTTGGCATCGATATATGACTTC
59699320 -GATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGATTCCGATATATG
1 TGATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGATTCCGATATATG
*
59699384 TGTGCTAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTC-GATATATGTGTGCGAG
66 TGTGCTAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTCTGATATATGTGTGAGAG
* * *
59699448 TAAGA-ACCTGTCTGAGA-AAG-TGGCATCGATTTGTGA-TTC
131 TAAGACACAT-T-T-A-ATAAGTTGGCATCGATATATGACTTC
* * **
59699487 TGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGACTT-CGATATAT
1 TGATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGA-TTCCGATATAT
59699551 GTGTG-TGAGTAAGACC
65 GTGTGCT-AGTAAGACC
59699567 CTGTTTGGGA
Statistics
Matches: 230, Mismatches: 9, Indels: 17
0.90 0.04 0.07
Matches are distributed among these distances:
166 3 0.01
167 5 0.02
168 213 0.93
169 8 0.03
170 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (169 bp):
TGATATATGTGTGTGAGTAAGACCACGTTTACTAAATTGGCATCGATATGTGATTCCGATATATG
TGTGCTAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTTCTGATATATGTGTGAGAG
TAAGACACATTTAATAAGTTGGCATCGATATATGACTTC
Found at i:59704771 original size:13 final size:13
Alignment explanation
Indices: 59704753--59704778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59704743 ATATATTATA
59704753 CGTGTGAAAATTT
1 CGTGTGAAAATTT
59704766 CGTGTGAAAATTT
1 CGTGTGAAAATTT
59704779 TATTGTTTGT
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:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
CGTGTGAAAATTT
Found at i:59706010 original size:56 final size:56
Alignment explanation
Indices: 59705915--59706036 Score: 185
Period size: 56 Copynumber: 2.2 Consensus size: 56
59705905 TCATGGAATT
* *
59705915 GATATATGTGTGTGAGTAAGACCACGTTTACTACATTGGCATCGATATGTGA-TTCC
1 GATATATGTGTGTGAGTAAGACCACGTTTAATACATTGGCATCGACATGTGACTT-C
*
59705971 GATATATGTGTGCT-AGTAAGACCACGTTTAATACGTTGGCATCGACATGTGACTTC
1 GATATATGTGTG-TGAGTAAGACCACGTTTAATACATTGGCATCGACATGTGACTTC
59706027 GATATATGTG
1 GATATATGTG
59706037 ACTTCGATAC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 58 0.95
57 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (56 bp):
GATATATGTGTGTGAGTAAGACCACGTTTAATACATTGGCATCGACATGTGACTTC
Found at i:59706037 original size:15 final size:15
Alignment explanation
Indices: 59706015--59706050 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
59706005 GTTGGCATCG
59706015 ACATGTGACTTCGAT
1 ACATGTGACTTCGAT
*
59706030 ATATGTGACTTCGAT
1 ACATGTGACTTCGAT
59706045 ACATGT
1 ACATGT
59706051 AAGACCACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (15 bp):
ACATGTGACTTCGAT
Found at i:59706278 original size:15 final size:15
Alignment explanation
Indices: 59706256--59706291 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
59706246 GTTGGCATCG
59706256 ACATGTGACTTCGAT
1 ACATGTGACTTCGAT
*
59706271 ATATGTGACTTCGAT
1 ACATGTGACTTCGAT
59706286 ACATGT
1 ACATGT
59706292 AAGACCACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (15 bp):
ACATGTGACTTCGAT
Found at i:59706393 original size:241 final size:241
Alignment explanation
Indices: 59705970--59706451 Score: 955
Period size: 241 Copynumber: 2.0 Consensus size: 241
59705960 TATGTGATTC
*
59705970 CGATATATGTGTGCTAGTAAGACCACGTTTAATACGTTGGCATCGACATGTGACTTCGATATATG
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGACATGTGACTTCGATATATG
59706035 TGACTTCGATACATGTAAGACCACGTTTGGGACGTTGGCATTGTACGATATGTGAGATTAGCTAA
66 TGACTTCGATACATGTAAGACCACGTTTGGGACGTTGGCATTGTACGATATGTGAGATTAGCTAA
59706100 GTATCCTATTCAATTTCGAATGGTTCAACGGGCAATATCGAGTTAAGATGGAATGTGAAATTATG
131 GTATCCTATTCAATTTCGAATGGTTCAACGGGCAATATCGAGTTAAGATGGAATGTGAAATTATG
59706165 TTAAAATGTCAGGTATATGCTAGTTTAAATTATTTGAAAGATAAGG
196 TTAAAATGTCAGGTATATGCTAGTTTAAATTATTTGAAAGATAAGG
59706211 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGACATGTGACTTCGATATATG
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGACATGTGACTTCGATATATG
59706276 TGACTTCGATACATGTAAGACCACGTTTGGGACGTTGGCATTGTACGATATGTGAGATTAGCTAA
66 TGACTTCGATACATGTAAGACCACGTTTGGGACGTTGGCATTGTACGATATGTGAGATTAGCTAA
59706341 GTATCCTATTCAATTTCGAATGGTTCAACGGGCAATATCGAGTTAAGATGGAATGTGAAATTATG
131 GTATCCTATTCAATTTCGAATGGTTCAACGGGCAATATCGAGTTAAGATGGAATGTGAAATTATG
59706406 TTAAAATGTCAGGTATATGCTAGTTTAAATTATTTGAAAGATAAGG
196 TTAAAATGTCAGGTATATGCTAGTTTAAATTATTTGAAAGATAAGG
59706452 TAAGTATATA
Statistics
Matches: 240, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 240 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (241 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTAATACGTTGGCATCGACATGTGACTTCGATATATG
TGACTTCGATACATGTAAGACCACGTTTGGGACGTTGGCATTGTACGATATGTGAGATTAGCTAA
GTATCCTATTCAATTTCGAATGGTTCAACGGGCAATATCGAGTTAAGATGGAATGTGAAATTATG
TTAAAATGTCAGGTATATGCTAGTTTAAATTATTTGAAAGATAAGG
Found at i:59710368 original size:22 final size:22
Alignment explanation
Indices: 59710342--59710391 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
59710332 AAACATTGTT
59710342 TGTTGCGGAAGCTTTTAAAATA
1 TGTTGCGGAAGCTTTTAAAATA
* *
59710364 TGTTGCGTAAGCTTTTAAAGTA
1 TGTTGCGGAAGCTTTTAAAATA
59710386 TGTTGC
1 TGTTGC
59710392 ATGAACGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (22 bp):
TGTTGCGGAAGCTTTTAAAATA
Found at i:59715287 original size:64 final size:64
Alignment explanation
Indices: 59715186--59715313 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
59715176 GAACCGTATC
59715186 TTCCGAGCGTATTTGGATAAATTTGTTGTTGTTTTTATTAATGACATACTGATATATTCTCGCG
1 TTCCGAGCGTATTTGGATAAATTTGTTGTTGTTTTTATTAATGACATACTGATATATTCTCGCG
*
59715250 TTCCGATCGTATTTGGATAAATTTGTTGTTGTTTTTATTAATGACATACTGATATATTCTCGCG
1 TTCCGAGCGTATTTGGATAAATTTGTTGTTGTTTTTATTAATGACATACTGATATATTCTCGCG
59715314 AAGAATCCGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.46
Consensus pattern (64 bp):
TTCCGAGCGTATTTGGATAAATTTGTTGTTGTTTTTATTAATGACATACTGATATATTCTCGCG
Found at i:59729314 original size:13 final size:13
Alignment explanation
Indices: 59729296--59729322 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59729286 TTGCAATAAC
59729296 TTCATCATCAACA
1 TTCATCATCAACA
59729309 TTCATCATCAACA
1 TTCATCATCAACA
59729322 T
1 T
59729323 AGCTATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (13 bp):
TTCATCATCAACA
Found at i:59733661 original size:15 final size:15
Alignment explanation
Indices: 59733641--59733671 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
59733631 CATGTTGTTT
59733641 ATGAAAGCAATAAGG
1 ATGAAAGCAATAAGG
59733656 ATGAAAGCAATAAGG
1 ATGAAAGCAATAAGG
59733671 A
1 A
59733672 GCTAATCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (15 bp):
ATGAAAGCAATAAGG
Found at i:59735387 original size:37 final size:37
Alignment explanation
Indices: 59735266--59735376 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
59735256 AGCTCAGATG
* * *
59735266 AAATCTCCACACGAAGTTAT-CGAGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCCG-GTCTTACCCGGACA
*
59735303 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCCGGTCTTACCCGGACA
59735340 AAATCTCCACACGTAGTCATCCGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCCGGTCTTACCCGGACA
59735377 TAGTCACCAC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
37 67 0.99
38 1 0.01
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCCGGTCTTACCCGGACA
Found at i:59735396 original size:37 final size:37
Alignment explanation
Indices: 59735289--59735404 Score: 133
Period size: 37 Copynumber: 3.1 Consensus size: 37
59735279 AAGTTATCGA
* * * *
59735289 GTCTTACCCGAACAAAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCACCACACATAGTCATCCG
* *
59735326 GTCTTACCCGGACAAAATCTCCACACGTAGTCATCCG
1 GTCTTACCCGGACAAAATCACCACACATAGTCATCCG
* * * * *
59735363 GTCTTACCCGGACATAGTCACCACATATGGTCATCTG
1 GTCTTACCCGGACAAAATCACCACACATAGTCATCCG
59735400 GTCTT
1 GTCTT
59735405 TAATCCCAGG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCACCACACATAGTCATCCG
Found at i:59735396 original size:74 final size:74
Alignment explanation
Indices: 59735266--59735404 Score: 172
Period size: 74 Copynumber: 1.9 Consensus size: 74
59735256 AGCTCAGATG
* * *
59735266 AAATCTCCACACGAAGTTATCGAGTCTTACCCGAACAAAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGAAGTCATCGAGTCTTACCCGAACAAAATCACCACACATAGTCATCGGGTCTT
59735331 ACCCGGACA
66 ACCCGGACA
* * * * * * *
59735340 AAATCTCCACACGTAGTCATCCG-GTCTTACCCGGACATAGTCACCACATATGGTCATCTGGTCT
1 AAATCTCCACACGAAGTCAT-CGAGTCTTACCCGAACAAAATCACCACACATAGTCATCGGGTCT
59735404 T
65 T
59735405 TAATCCCAGG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 52 0.96
75 2 0.04
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (74 bp):
AAATCTCCACACGAAGTCATCGAGTCTTACCCGAACAAAATCACCACACATAGTCATCGGGTCTT
ACCCGGACA
Found at i:59735612 original size:46 final size:46
Alignment explanation
Indices: 59735559--59735695 Score: 202
Period size: 46 Copynumber: 3.0 Consensus size: 46
59735549 TATATATACA
* * *
59735559 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCGCATTAGCCATTCGGCTTTACCACATATC
* *
59735605 CATCTCATACACGTCTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATCTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
59735651 TATCTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATCTCGCATTAGCCATTCGGCTTTACCACATAT
59735696 ATATATGTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:59736615 original size:47 final size:47
Alignment explanation
Indices: 59735701--59736586 Score: 1666
Period size: 47 Copynumber: 18.8 Consensus size: 47
59735691 CATATATATA
59735701 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59735748 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59735795 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59735842 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59735889 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59735936 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59735983 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736030 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736077 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736124 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736171 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736218 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736265 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736312 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736359 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
*
59736406 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCA
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
59736453 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
* **
59736500 TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCACATATATACAG
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATCA--CAC--ATACGC-G
* *
59736552 -GTTCACATTCATCACATTTGCCATTCGGCCTTATC
1 TGTTCACATTCATCACATTGGCCATTCGGCCATATC
59736587 TCATATATAC
Statistics
Matches: 828, Mismatches: 6, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
47 786 0.95
49 3 0.00
51 38 0.05
52 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.28
Consensus pattern (47 bp):
TGTTCACATTCATCACATTGGCCATTCGGCCATATCACACATACGCG
Found at i:59736616 original size:25 final size:25
Alignment explanation
Indices: 59736539--59736616 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
59736529 CCTTATCACG
**
59736539 CACATATATACAGGTTCACATTCAT
1 CACATATATACACATTCACATTCAT
* * *
59736564 CACAT-T-TGC-CATTCGGCCTT-AT
1 CACATATATACACATTC-ACATTCAT
*
59736586 CTCATATATACACATTCACATTCAT
1 CACATATATACACATTCACATTCAT
59736611 CACATA
1 CACATA
59736617 AAATCCTAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 9 0.24
23 6 0.16
24 6 0.16
25 17 0.45
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (25 bp):
CACATATATACACATTCACATTCAT
Found at i:59747521 original size:48 final size:47
Alignment explanation
Indices: 59747465--59747689 Score: 195
Period size: 48 Copynumber: 4.7 Consensus size: 47
59747455 TACGATGCCA
* *
59747465 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCAACTCGGCGCCG
1 ATGCCATATCCCAGATATGGTCTTATATGGGATCTC-ACTCGACGCCG
* * * * *
59747513 ATGCCATATCCCAGATGTAGTCTTATACGGGACCTCA-TACGACGTCG
1 ATGCCATATCCCAGATATGGTCTTATATGGGATCTCACT-CGACGCCG
** * * * * *
59747560 ATGCCAGGTCCCAGATGTGGTCTTATATAGGG-TTTCA-TAATGATGCTG
1 ATGCCATATCCCAGATATGGTCTTATAT-GGGATCTCACT--CGACGCCG
* * * *
59747608 ATGCCATGTCCCAGACATGGTCTTATATAGGATCTCACATCGATGCCG
1 ATGCCATATCCCAGATATGGTCTTATATGGGATCTCAC-TCGACGCCG
* *
59747656 ATGCCATATCCCAGATATGGTCCTATACGGGATC
1 ATGCCATATCCCAGATATGGTCTTATATGGGATC
59747690 GCAATAACCC
Statistics
Matches: 142, Mismatches: 29, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
46 1 0.01
47 37 0.26
48 103 0.73
50 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (47 bp):
ATGCCATATCCCAGATATGGTCTTATATGGGATCTCACTCGACGCCG
Found at i:59754788 original size:40 final size:41
Alignment explanation
Indices: 59754705--59754850 Score: 185
Period size: 40 Copynumber: 3.6 Consensus size: 41
59754695 TTGAATGATG
* * *
59754705 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
*
59754745 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT-TAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
59754785 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
59754826 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
59754851 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.02
40 80 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:59761180 original size:46 final size:46
Alignment explanation
Indices: 59759910--59761177 Score: 2182
Period size: 46 Copynumber: 27.6 Consensus size: 46
59759900 GATGCCATAA
* * * ***
59759910 TGTCTTTCAACTATGGTCTTACTCATTTT-TGTTAGGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
* *** * * * *
59759955 TATCTTTCAACCATGGTCTTGTTCATTTCATGTTAC-ATTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTAT-ATCCTGTTGCCATGG
* ** **** *
59760001 TATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
* * *
59760046 TATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760092 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760138 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760184 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760230 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760276 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760322 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760368 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760414 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760460 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760506 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760552 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760598 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760644 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760690 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760736 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760782 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760828 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760874 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
59760920 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
* *
59760966 TGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
* * *
59761012 TATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
* *
59761058 TGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
* * *
59761104 TGTCTTTCAACCATGGACTTACACATTTCATATCATGTTGCCATGG
1 TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
*
59761150 TATCTTTCAACCATGGTCTTACACATTT
1 TGTCTTTCAACCATGGTCTTACACATTT
59761178 CATTTCAGAA
Statistics
Matches: 1188, Mismatches: 31, Indels: 7
0.97 0.03 0.01
Matches are distributed among these distances:
44 1 0.00
45 59 0.05
46 1127 0.95
47 1 0.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
TGTCTTTCAACCATGGTCTTACACATTTTATATCCTGTTGCCATGG
Found at i:59769477 original size:46 final size:46
Alignment explanation
Indices: 59769422--59769597 Score: 162
Period size: 46 Copynumber: 3.8 Consensus size: 46
59769412 TATTTGGGCA
59769422 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * *
59769468 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* * * *
59769513 TATCCAAAGTAGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
59769561 CCCGAGCTCATTGAGTTGAGTCCAATTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
59769598 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
45 3 0.03
46 57 0.56
47 26 0.25
48 4 0.04
50 3 0.03
51 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:59772551 original size:15 final size:15
Alignment explanation
Indices: 59772531--59772595 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
59772521 GTATCTTGGG
59772531 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
59772546 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
* *
59772561 TTTC-TCAATCTTGGA
1 TTTCTTTATTC-TGGA
*
59772576 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
59772590 TTTCTT
1 TTTCTT
59772596 GTTATCTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
14 12 0.29
15 25 0.61
16 4 0.10
ACGTcount: A:0.11, C:0.15, G:0.14, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:59772563 original size:30 final size:31
Alignment explanation
Indices: 59772527--59772595 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
59772517 TATCGTATCT
* *
59772527 TGGGTTTCTTTATTC-TGGATTTCTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
59772557 TGGGTTTC-TCAATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
*
59772587 -GGTTTTCTT
1 TGGGTTTCTT
59772596 GTTATCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.10, C:0.14, G:0.17, T:0.58
Consensus pattern (31 bp):
TGGGTTTCTTCAATCTTGGATTTCTTTATTC
Found at i:59781604 original size:33 final size:33
Alignment explanation
Indices: 59781563--59781628 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
59781553 AGCCAAAGAG
* * *
59781563 CCCTCCCATGGCCTGCCGCACATTTGGCAAGTT
1 CCCTCCCATGGCCAGCCACACATGTGGCAAGTT
59781596 CCCTCCCATGGCCAGCCACACATGTGGCAAGTT
1 CCCTCCCATGGCCAGCCACACATGTGGCAAGTT
59781629 TGAAGTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.21
Consensus pattern (33 bp):
CCCTCCCATGGCCAGCCACACATGTGGCAAGTT
Found at i:59782084 original size:22 final size:22
Alignment explanation
Indices: 59782058--59782101 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
59782048 GAAAATGATC
*
59782058 AAAATTAATCAAAATTTATTAT
1 AAAATTAATCAAAATTCATTAT
* *
59782080 AAAATTATTTAAAATTCATTAT
1 AAAATTAATCAAAATTCATTAT
59782102 GTTAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATTAATCAAAATTCATTAT
Found at i:59785465 original size:21 final size:22
Alignment explanation
Indices: 59785441--59785485 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
59785431 CAAGTTATGT
* *
59785441 GTTTGAGTCATTTT-ATTTTAG
1 GTTTGAATCATTTTGAGTTTAG
*
59785462 GTTTTAATCATTTTGAGTTTAG
1 GTTTGAATCATTTTGAGTTTAG
59785484 GT
1 GT
59785486 CAATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.56
Consensus pattern (22 bp):
GTTTGAATCATTTTGAGTTTAG
Found at i:59787212 original size:23 final size:24
Alignment explanation
Indices: 59787185--59787234 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
59787175 TGATTTAGAG
59787185 GAAAACTATTTTA-ATATAAA-TTA
1 GAAAACTATTTTACAT-TAAATTTA
*
59787208 GAAAATTATTTTACATTAAATTTA
1 GAAAACTATTTTACATTAAATTTA
59787232 GAA
1 GAA
59787235 GAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (24 bp):
GAAAACTATTTTACATTAAATTTA
Found at i:59793897 original size:17 final size:17
Alignment explanation
Indices: 59793870--59793928 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
59793860 TTTAAATTTA
59793870 TTATT-TTATAATTGTT
1 TTATTATTATAATTGTT
*
59793886 TTGTTATTATAATT-TT
1 TTATTATTATAATTGTT
59793902 TATATTATTATAATTGTAT
1 T-TATTATTATAATTGT-T
*
59793921 TTTTTATT
1 TTATTATT
59793929 TATTAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 7 0.19
17 20 0.56
18 7 0.19
19 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTATTATTATAATTGTT
Found at i:59794291 original size:107 final size:107
Alignment explanation
Indices: 59794164--59794385 Score: 417
Period size: 107 Copynumber: 2.1 Consensus size: 107
59794154 CAATCGCAAC
*
59794164 TTTGCTTAGACTTAAAAAAATGAGCTTTTTTATGTTTTGTGTTCGGAAATAATGAGAATAGAGTA
1 TTTGTTTAGACTTAAAAAAATGAGCTTTTTTATGTTTTGTGTTCGGAAATAATGAGAATAGAGTA
59794229 AAAATTCTAAGGAAAGGCCCTTAATAGTTTATTTTCTCCAAT
66 AAAATTCTAAGGAAAGGCCCTTAATAGTTTATTTTCTCCAAT
59794271 TTTGTTTAGACTTAAAAAAATGAGCTTTTTTATGTTTTGTGTTCGGAAATAATGAGAATAGAGTA
1 TTTGTTTAGACTTAAAAAAATGAGCTTTTTTATGTTTTGTGTTCGGAAATAATGAGAATAGAGTA
* *
59794336 AAAATTTTAAGGAAAGGCCCTTAATAGTTTATTTTCTCTAAT
66 AAAATTCTAAGGAAAGGCCCTTAATAGTTTATTTTCTCCAAT
59794378 TTTGTTTA
1 TTTGTTTA
59794386 TTTGAATGTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 112 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.41
Consensus pattern (107 bp):
TTTGTTTAGACTTAAAAAAATGAGCTTTTTTATGTTTTGTGTTCGGAAATAATGAGAATAGAGTA
AAAATTCTAAGGAAAGGCCCTTAATAGTTTATTTTCTCCAAT
Found at i:59795728 original size:18 final size:18
Alignment explanation
Indices: 59795692--59795729 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
59795682 TGCTTCTAAG
*
59795692 AAGCACTTTTGGGACAAA
1 AAGCACTTTTGAGACAAA
*
59795710 AAGCACTTTTGAGATAAA
1 AAGCACTTTTGAGACAAA
59795728 AA
1 AA
59795730 CATTCCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (18 bp):
AAGCACTTTTGAGACAAA
Found at i:59799238 original size:21 final size:20
Alignment explanation
Indices: 59799214--59799276 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
59799204 TCTTCTTTCG
59799214 AATCGATTGTCTTTATGTTTA
1 AATCGATTGT-TTTATGTTTA
* * * *
59799235 AATCAATTGTTTTTCTATTTG
1 AATCGATTG-TTTTATGTTTA
59799256 AATCGATT-TTTTATTGTTTA
1 AATCGATTGTTTTA-TGTTTA
59799276 A
1 A
59799277 CCTGATTCAC
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
19 4 0.12
20 5 0.16
21 22 0.69
22 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (20 bp):
AATCGATTGTTTTATGTTTA
Found at i:59803600 original size:47 final size:47
Alignment explanation
Indices: 59803549--59804227 Score: 1009
Period size: 47 Copynumber: 14.3 Consensus size: 47
59803539 TACTTGATAG
* *
59803549 TATATGTGATAAGACCGAATGGCCAACGTGATGAATGTGAAAGTGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA--GTGTA
* *
59803598 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TA
* * *
59803647 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TA
* *
59803696 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG--TA
59803745 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
59803792 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
59803839 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
59803886 TATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
59803933 TATAAGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * *
59803980 TATCTGTGATAAGGCCGAATGGCCCATGTGATGAATGTGGAAGCGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
59804027 TATATGTGATAAGGCCGAATGGCCCATGTGATGAATGTGGAAGCGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
59804074 TATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
59804121 TATAAGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
59804168 TATATGTGATAGGGCCGAGTGGCCAACGTGATCG-ATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGAT-GAATGTGAAAGTGTA
*
59804215 TAAATGTGATAAG
1 TATATGTGATAAG
59804228 TCCCGAAGGG
Statistics
Matches: 588, Mismatches: 39, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
47 408 0.69
48 1 0.00
49 179 0.30
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:59812644 original size:43 final size:42
Alignment explanation
Indices: 59812555--59812670 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 42
59812545 TGTGATTACA
* * *
59812555 TGTAAGACCATGTCTAGGACATTGGCATTGTATTGAGATTATG
1 TGTAAGATCATGTCT-GGACATTGGCATCGTAATGAGATTATG
*
59812598 TGTAAGATCATGTCTGGAACATTGGCATCGTTAAT-CGATT-TCG
1 TGTAAGATCATGTCTGG-ACATTGGCATCG-TAATGAGATTAT-G
*
59812641 TGTAAGACTC-TGTCTGGGACAGTGGCATCG
1 TGTAAGA-TCATGTCT-GGACATTGGCATCG
59812671 ATATGGAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
42 3 0.05
43 53 0.84
44 7 0.11
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
TGTAAGATCATGTCTGGACATTGGCATCGTAATGAGATTATG
Found at i:59816313 original size:16 final size:17
Alignment explanation
Indices: 59816282--59816314 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
59816272 AATTTCTATC
59816282 CAATTTATACCCTAATT
1 CAATTTATACCCTAATT
*
59816299 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
59816315 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
CAATTTATACCCTAATT
Found at i:59816805 original size:3 final size:3
Alignment explanation
Indices: 59816790--59816834 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
59816780 ATATGTTAGT
* *
59816790 TAA TAA TAT TAA TAA TAA TAA TACA TTA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
59816835 ATATCTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:59817267 original size:11 final size:11
Alignment explanation
Indices: 59817245--59817295 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
59817235 TATTTATTTC
59817245 ATAATA-AA-T
1 ATAATATAATT
59817254 ATAATATAATT
1 ATAATATAATT
59817265 ATAATATAATT
1 ATAATATAATT
59817276 AT--TATAATT
1 ATAATATAATT
*
59817285 -TAACATAATT
1 ATAATATAATT
59817295 A
1 A
59817296 AATTTATAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
8 1 0.03
9 13 0.36
10 8 0.22
11 14 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAATATAATT
Found at i:59817279 original size:14 final size:16
Alignment explanation
Indices: 59817251--59817295 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
59817241 TTTCATAATA
59817251 AATATAATATAATTAT
1 AATATAATATAATTAT
59817267 AATATAAT-T-ATTAT
1 AATATAATATAATTAT
* *
59817281 AATTTAACATAATTA
1 AATATAATATAATTA
59817296 AATTTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 11 0.44
15 2 0.08
16 12 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATAATATAATTAT
Found at i:59823895 original size:22 final size:21
Alignment explanation
Indices: 59823870--59823920 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
59823860 TCTAGACTTA
*
59823870 AATTATTAACATAATGAATTTT
1 AATTATT-ACATAATAAATTTT
**
59823892 AATTAATTTTATAATAAATTTT
1 AATT-ATTACATAATAAATTTT
59823914 AATTATT
1 AATTATT
59823921 TTCAACAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTATTACATAATAAATTTT
Found at i:59827919 original size:23 final size:23
Alignment explanation
Indices: 59827893--59827938 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
59827883 AAGTTAAACA
*
59827893 AGGCCACCAGGAAAGGTTATTAT
1 AGGCCACCAGGAAAGGTCATTAT
*
59827916 AGGCCACTAGGAAAGGTCATTAT
1 AGGCCACCAGGAAAGGTCATTAT
59827939 GGGTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (23 bp):
AGGCCACCAGGAAAGGTCATTAT
Found at i:59831509 original size:43 final size:44
Alignment explanation
Indices: 59831462--59831617 Score: 194
Period size: 43 Copynumber: 3.6 Consensus size: 44
59831452 TACCGAGATA
* *
59831462 TGATTACATGTAAGACCATGTCTGAGACATTGGCTTTGTAT-TG
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCTTCGTATATG
* *
59831505 TGATTACGTGTAAGACCATGTCTGGGACATTGG-TATCGT-TATA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCT-TCGTATATG
* *
59831548 TGATTTCATGTAAGACCATGTCTGGGACATTGGCATCG-ATATG
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCTTCGTATATG
* * *
59831591 TGATAACATGTTAGACCATATCTGGGA
1 TGATTACATGTAAGACCATGTCTGGGA
59831618 TATGGCATTG
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.02
43 95 0.98
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (44 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCTTCGTATATG
Found at i:59831562 original size:86 final size:86
Alignment explanation
Indices: 59831459--59831617 Score: 230
Period size: 86 Copynumber: 1.8 Consensus size: 86
59831449 GATTACCGAG
* * * *
59831459 ATATGATTACATGTAAGACCATGTCTGAGACATTGGCTTTG-TATTGTGATTACGTGTAAGACCA
1 ATATGATTACATGTAAGACCATGTCTGAGACATTGGCATCGATA-TGTGATAACATGTAAGACCA
*
59831523 TGTCTGGGACATTGGTATCGTT
65 TATCTGGGACATTGGTATCGTT
* * *
59831545 ATATGATTTCATGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATAACATGTTAGACCAT
1 ATATGATTACATGTAAGACCATGTCTGAGACATTGGCATCGATATGTGATAACATGTAAGACCAT
59831610 ATCTGGGA
66 ATCTGGGA
59831618 TATGGCATTG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
86 62 0.97
87 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (86 bp):
ATATGATTACATGTAAGACCATGTCTGAGACATTGGCATCGATATGTGATAACATGTAAGACCAT
ATCTGGGACATTGGTATCGTT
Found at i:59835137 original size:10 final size:10
Alignment explanation
Indices: 59835122--59835146 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59835112 TAATAAGTTA
59835122 TTATATTTTT
1 TTATATTTTT
59835132 TTATATTTTT
1 TTATATTTTT
59835142 TTATA
1 TTATA
59835147 ATCTAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTATATTTTT
Found at i:59835633 original size:19 final size:20
Alignment explanation
Indices: 59835592--59835637 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
59835582 TTTAAATAAG
*
59835592 AATTTTATATAGTTTTTTTA
1 AATTTTATATAGTTTTTTAA
59835612 AATTTTAT-T-GTTTTTTAAA
1 AATTTTATATAGTTTTTT-AA
59835631 AATTTTA
1 AATTTTA
59835638 AAAATGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 9 0.38
20 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
AATTTTATATAGTTTTTTAA
Found at i:59837412 original size:22 final size:23
Alignment explanation
Indices: 59837384--59837482 Score: 105
Period size: 23 Copynumber: 4.3 Consensus size: 23
59837374 GCTAAAAACG
*
59837384 GTAAGCTCTATTGAGCTGAA-CA
1 GTAAGCTCTATCGAGCTGAATCA
*
59837406 GTAAGCTCTATCGAACTGAATCA
1 GTAAGCTCTATCGAGCTGAATCA
* * *
59837429 ATAAGCTCCAAT-GAGCTGAAACA
1 GTAAGCT-CTATCGAGCTGAATCA
*
59837452 GTAAGCTCT-TACGAGTTGAATCA
1 GTAAGCTCTAT-CGAGCTGAATCA
59837475 GTAAGCTC
1 GTAAGCTC
59837483 ATACAAGCTA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
22 19 0.30
23 40 0.63
24 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (23 bp):
GTAAGCTCTATCGAGCTGAATCA
Found at i:59837444 original size:45 final size:46
Alignment explanation
Indices: 59837385--59837482 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
59837375 CTAAAAACGG
* *
59837385 TAAGCTCTATTGAGCTG-AACAGTAAGCTC-TATCGAACTGAATCAA
1 TAAGCTCCAATGAGCTGAAACAGTAAGCTCTTA-CGAACTGAATCAA
** *
59837430 TAAGCTCCAATGAGCTGAAACAGTAAGCTCTTACGAGTTGAATCAG
1 TAAGCTCCAATGAGCTGAAACAGTAAGCTCTTACGAACTGAATCAA
59837476 TAAGCTC
1 TAAGCTC
59837483 ATACAAGCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 15 0.33
46 29 0.63
47 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (46 bp):
TAAGCTCCAATGAGCTGAAACAGTAAGCTCTTACGAACTGAATCAA
Found at i:59839480 original size:20 final size:20
Alignment explanation
Indices: 59839457--59839499 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
59839447 CACATTGTAA
59839457 CAATTCAAAAACAGAATTTC
1 CAATTCAAAAACAGAATTTC
*
59839477 CAATTTAAAAACAGAATTTC
1 CAATTCAAAAACAGAATTTC
59839497 CAA
1 CAA
59839500 CATTCTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.26
Consensus pattern (20 bp):
CAATTCAAAAACAGAATTTC
Found at i:59842479 original size:83 final size:82
Alignment explanation
Indices: 59842314--59842465 Score: 182
Period size: 82 Copynumber: 1.9 Consensus size: 82
59842304 TAATCCAACA
* ** * *
59842314 TATTTTATGTGATATGTATGAGGTATACAATTATTTTTCTGTTGAAATTCATTTTAAAATATATA
1 TATTTTATGTAATATGTATGAGGTATACAATTATTTCCCTATTAAAATTCATTTTAAAATATATA
* *
59842379 ATATTTATAACCTAATT
66 ACATTTATAACCAAATT
* * *
59842396 TATTTTATGTAATATTTAT-ATGGATATACAATTATTTCCCTATTAAAATTTA-TTTCAAATATA
1 TATTTTATGTAATATGTATGA-GG-TATACAATTATTTCCCTATTAAAATTCATTTTAAAATATA
59842459 TAACATT
64 TAACATT
59842466 ATATCTTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
81 1 0.02
82 35 0.59
83 23 0.39
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (82 bp):
TATTTTATGTAATATGTATGAGGTATACAATTATTTCCCTATTAAAATTCATTTTAAAATATATA
ACATTTATAACCAAATT
Found at i:59846542 original size:92 final size:91
Alignment explanation
Indices: 59846388--59846559 Score: 211
Period size: 92 Copynumber: 1.9 Consensus size: 91
59846378 TCCTCCTCTC
* * * * * *
59846388 TTTTTCACTCATTTGGGTATTTTAACTTTCAAAATACATCAAAAAAGCCCTCAAAGTTTTTCAAA
1 TTTTTCACTCAATTGGGTACTTAAACTTTCAAAATACATCAAAAAAACCCTCAAACTGTTTCAAA
* *
59846453 AAAAGTATTTAAGCCCTTACTCTTTT
66 AAAAGCAATTAAGCCCTTACTCTTTT
* * **
59846479 TTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCAT-AAAAAATACTCTCCCACTGTTTCA
1 TTTTT-CACTCAATTGGGTACTTAAACTTTCAAAATACATCAAAAAA-ACCCTCAAACTGTTTCA
59846543 AAAAAAGCAATTAAGCC
64 AAAAAAGCAATTAAGCC
59846560 ACTGCTTTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
91 11 0.16
92 56 0.84
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (91 bp):
TTTTTCACTCAATTGGGTACTTAAACTTTCAAAATACATCAAAAAAACCCTCAAACTGTTTCAAA
AAAAGCAATTAAGCCCTTACTCTTTT
Found at i:59846646 original size:19 final size:20
Alignment explanation
Indices: 59846618--59846672 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
59846608 AATAAAATCT
* *
59846618 ATAAATAATATTAAATTTTA
1 ATAAATAATATAAAATATTA
59846638 ATAAA-AATATAAAATATTA
1 ATAAATAATATAAAATATTA
*
59846657 A-AAATCATAATAAAAT
1 ATAAATAAT-ATAAAAT
59846673 TTGTAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 15 0.50
20 12 0.40
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATAATATAAAATATTA
Found at i:59846661 original size:46 final size:47
Alignment explanation
Indices: 59846590--59846692 Score: 115
Period size: 46 Copynumber: 2.2 Consensus size: 47
59846580 GAAAAAAAAC
* *
59846590 TTATAAAAATTTAAAATCAATAAAATCTATAA-ATAATAT-T-AAATT
1 TTATAAAAATATAAAATCAATAAAATC-ATAATAAAATATGTAAAATT
* *
59846635 TTAATAAAAATATAAAAT-ATTAAAAATCATAATAAAATTTGTAAAATT
1 TT-ATAAAAATATAAAATCAAT-AAAATCATAATAAAATATGTAAAATT
59846683 TTATAAAAAT
1 TTATAAAAAT
59846693 CGTAAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
45 8 0.16
46 25 0.51
47 9 0.18
48 7 0.14
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (47 bp):
TTATAAAAATATAAAATCAATAAAATCATAATAAAATATGTAAAATT
Found at i:59846719 original size:10 final size:9
Alignment explanation
Indices: 59846591--59846737 Score: 54
Period size: 9 Copynumber: 15.9 Consensus size: 9
59846581 AAAAAAAACT
59846591 TATAAAA-A
1 TATAAAATA
*
59846599 TTTAAAATCA
1 TATAAAAT-A
*
59846609 -ATAAAATC
1 TATAAAATA
59846617 TAT-AAATAA
1 TATAAAAT-A
* *
59846626 TATTAAATTT
1 TA-TAAAATA
59846636 TAATAAAA-A
1 T-ATAAAATA
59846645 TATAAAATA
1 TATAAAATA
59846654 T-TAAAAATCA
1 TAT-AAAAT-A
*
59846664 TAATAAAATT
1 T-ATAAAATA
* *
59846674 TGTAAAATTT
1 TATAAAA-TA
59846684 TATAAAA-A
1 TATAAAATA
* *
59846692 TCGTAAAAAA
1 T-ATAAAATA
59846702 TATAAAATA
1 TATAAAATA
59846711 TATAGAAATA
1 TATA-AAATA
* *
59846721 TAAAAAAAA
1 TATAAAATA
*
59846730 TAAAAAAT
1 TATAAAAT
59846738 GTAAAGAAAT
Statistics
Matches: 105, Mismatches: 18, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
8 18 0.17
9 49 0.47
10 28 0.27
11 9 0.09
12 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (9 bp):
TATAAAATA
Found at i:59846736 original size:28 final size:28
Alignment explanation
Indices: 59846696--59846752 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
59846686 TAAAAATCGT
* *
59846696 AAAAAATATAAAATATATAGAAATATAA
1 AAAAAATAAAAAATATAAAGAAATATAA
*
59846724 AAAAAATAAAAAATGTAAAGAAATATAA
1 AAAAAATAAAAAATATAAAGAAATATAA
59846752 A
1 A
59846753 TTTTGTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (28 bp):
AAAAAATAAAAAATATAAAGAAATATAA
Found at i:59846747 original size:10 final size:9
Alignment explanation
Indices: 59846695--59846752 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
59846685 ATAAAAATCG
59846695 TAAAAAATA
1 TAAAAAATA
*
59846704 TAAAATATA
1 TAAAAAATA
*
59846713 T-AGAAATA
1 TAAAAAATA
*
59846721 TAAAAAAAA
1 TAAAAAATA
*
59846730 TAAAAAATG
1 TAAAAAATA
59846739 TAAAGAAATA
1 TAAA-AAATA
59846749 TAAA
1 TAAA
59846753 TTTTGTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
8 6 0.15
9 25 0.64
10 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (9 bp):
TAAAAAATA
Found at i:59847962 original size:7 final size:7
Alignment explanation
Indices: 59847950--59847974 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59847940 TTTAAAAATA
59847950 AAATGTT
1 AAATGTT
59847957 AAATGTT
1 AAATGTT
59847964 AAATGTT
1 AAATGTT
59847971 AAAT
1 AAAT
59847975 ATAGTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (7 bp):
AAATGTT
Found at i:59853519 original size:18 final size:17
Alignment explanation
Indices: 59853496--59853534 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
59853486 TATGATTCAT
*
59853496 ATTTTAAATTTATTTAAA
1 ATTTTAAA-ATATTTAAA
*
59853514 ATTTTAAAATATTTTAA
1 ATTTTAAAATATTTAAA
59853531 ATTT
1 ATTT
59853535 AGTCCTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAAAATATTTAAA
Found at i:59855290 original size:8 final size:8
Alignment explanation
Indices: 59855277--59855306 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
59855267 GAAATGAAGG
59855277 AGAAAAAA
1 AGAAAAAA
59855285 AGAAAAAA
1 AGAAAAAA
*
59855293 AGAAAGAA
1 AGAAAAAA
59855301 AGAAAA
1 AGAAAA
59855307 GGAAGATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:59855742 original size:103 final size:103
Alignment explanation
Indices: 59855427--59855753 Score: 353
Period size: 106 Copynumber: 3.1 Consensus size: 103
59855417 TTGGTTTATA
*
59855427 ATTATATTATTTGTGTTTAGTTTAGTGTTTATTGTG-ATTTTAAATTTTATTTTATTTTTTAAAA
1 ATTA-ATTATTTGTGTTTAGTTTAGTATTTATTGTGAATTTT-AA-TTTATTTTATTTTTTAAAA
*
59855491 ATAATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTGTT
63 ATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTA--TGTT
* * * * * *
59855534 A--AACTGTTTGTGTTTAGTTTAGTGTGATTT-TTAAT-AAATTTAATTTTTTTTATTTTTT--T
1 ATTAATTATTTGTGTTTAGTTTA--GT-ATTTATT-GTGAATTTTAATTTATTTTATTTTTTAAA
*
59855593 AATTATTTTAAAGTTATTATTTTGTTAGTAATTTATGATTAGGTT
62 AATTATTTTAAAG---TTATTTTGTTAGTAATTTATGATTATGTT
* * ** * *
59855638 ATTAATTGTTTGTGTTTAGTTTAGTATTTATTGTGAATTTTTATGAATATAATTTTTTAAAAATT
1 ATTAATTATTTGTGTTTAGTTTAGTATTTATTGTGAATTTTAATTTATTTTATTTTTTAAAAATT
59855703 ATTTTAAAGTTATTTTGTTAGTAATTTATGATTATGTT
66 ATTTTAAAGTTATTTTGTTAGTAATTTATGATTATGTT
*
59855741 ATAAATTATTTGT
1 ATTAATTATTTGT
59855754 TTAGTTAAAT
Statistics
Matches: 184, Mismatches: 22, Indels: 32
0.77 0.09 0.13
Matches are distributed among these distances:
103 56 0.30
104 41 0.22
105 15 0.08
106 63 0.34
107 9 0.05
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (103 bp):
ATTAATTATTTGTGTTTAGTTTAGTATTTATTGTGAATTTTAATTTATTTTATTTTTTAAAAATT
ATTTTAAAGTTATTTTGTTAGTAATTTATGATTATGTT
Found at i:59855867 original size:19 final size:20
Alignment explanation
Indices: 59855831--59855869 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
59855821 AAAATAGACT
*
59855831 TTTAGCGGCATTTTTTAGCC
1 TTTAGCGGCATCTTTTAGCC
59855851 TTTAGCGGC-TCTTTTAGCC
1 TTTAGCGGCATCTTTTAGCC
59855870 ACAAAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (20 bp):
TTTAGCGGCATCTTTTAGCC
Found at i:59856833 original size:13 final size:14
Alignment explanation
Indices: 59856807--59856835 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
59856797 ACTAACGATG
59856807 AATTAAACCATTAT
1 AATTAAACCATTAT
59856821 AATTAAA-CATTAT
1 AATTAAACCATTAT
59856834 AA
1 AA
59856836 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:59864073 original size:16 final size:17
Alignment explanation
Indices: 59864052--59864086 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
59864042 ACTATTTAAT
59864052 ATATAAATT-AAAAACA
1 ATATAAATTAAAAAACA
59864068 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
59864085 AT
1 AT
59864087 CACTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:59864231 original size:26 final size:24
Alignment explanation
Indices: 59864197--59864252 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 24
59864187 AAGAATTAGA
59864197 TAAAA-TTTGAAATCATGAAAATTAT
1 TAAAATTTTGAAATCATGAAAA-T-T
* *
59864222 TAAAATTTTGAAATCTTTAAAATT
1 TAAAATTTTGAAATCATGAAAATT
59864246 TAAAATT
1 TAAAATT
59864253 ATTTAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 8 0.29
25 6 0.21
26 14 0.50
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (24 bp):
TAAAATTTTGAAATCATGAAAATT
Found at i:59864257 original size:17 final size:18
Alignment explanation
Indices: 59864214--59864258 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
59864204 TGAAATCATG
59864214 AAAATTA-TTAAAATTTT
1 AAAATTATTTAAAATTTT
* *
59864231 GAAA-TCTTTAAAA-TTT
1 AAAATTATTTAAAATTTT
59864247 AAAATTATTTAA
1 AAAATTATTTAA
59864259 TATATAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATTATTTAAAATTTT
Found at i:59865343 original size:14 final size:14
Alignment explanation
Indices: 59865324--59865355 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
59865314 TGGGATTTGG
59865324 GTGGATCGGTGGAA
1 GTGGATCGGTGGAA
*
59865338 GTGGATCGGTGGAG
1 GTGGATCGGTGGAA
59865352 GTGG
1 GTGG
59865356 TGGTGAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.56, T:0.22
Consensus pattern (14 bp):
GTGGATCGGTGGAA
Found at i:59865924 original size:7 final size:7
Alignment explanation
Indices: 59865877--59865938 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
59865867 CTAAATTTTA
59865877 AACCC-T
1 AACCCTT
*
59865883 AAACCTT
1 AACCCTT
59865890 ATACCCTT
1 A-ACCCTT
*
59865898 AACCTTT
1 AACCCTT
59865905 AACTCC-T
1 AAC-CCTT
59865912 AGACCCTT
1 A-ACCCTT
59865920 AACCCTT
1 AACCCTT
*
59865927 AACTCTT
1 AACCCTT
59865934 AACCC
1 AACCC
59865939 CTAAATTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
6 4 0.09
7 30 0.67
8 11 0.24
ACGTcount: A:0.31, C:0.39, G:0.02, T:0.29
Consensus pattern (7 bp):
AACCCTT
Found at i:59865940 original size:22 final size:22
Alignment explanation
Indices: 59865877--59865938 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
59865867 CTAAATTTTA
* *
59865877 AACCCTAAAC-CTTATACCCTT
1 AACCCTTAACTCTTAGACCCTT
* *
59865898 AACCTTTAACTCCTAGACCCTT
1 AACCCTTAACTCTTAGACCCTT
59865920 AACCCTTAACTCTTA-ACCC
1 AACCCTTAACTCTTAGACCC
59865939 CTAAATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.31, C:0.39, G:0.02, T:0.29
Consensus pattern (22 bp):
AACCCTTAACTCTTAGACCCTT
Found at i:59866008 original size:15 final size:14
Alignment explanation
Indices: 59865988--59866021 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
59865978 AACCATAAAT
*
59865988 CATAATCCCTAAGTC
1 CATAATCCATAA-TC
59866003 CATAATCCATAATC
1 CATAATCCATAATC
59866017 CATAA
1 CATAA
59866022 ACCTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.26
Consensus pattern (14 bp):
CATAATCCATAATC
Found at i:59866011 original size:7 final size:7
Alignment explanation
Indices: 59865988--59866021 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
59865978 AACCATAAAT
59865988 CATAATC
1 CATAATC
*
59865995 CCTAAGTC
1 CATAA-TC
59866003 CATAATC
1 CATAATC
59866010 CATAATC
1 CATAATC
59866017 CATAA
1 CATAA
59866022 ACCTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.26
Consensus pattern (7 bp):
CATAATC
Found at i:59866134 original size:14 final size:14
Alignment explanation
Indices: 59866107--59866146 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
59866097 TAACTTATCA
59866107 TAAACCATAAACCC
1 TAAACCATAAACCC
* *
59866121 TAAACTATATACCC
1 TAAACCATAAACCC
*
59866135 TAAACCTTAAAC
1 TAAACCATAAAC
59866147 ATTAAACTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:59870232 original size:23 final size:23
Alignment explanation
Indices: 59870206--59870303 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
59870196 ATAAGTGCCA
*
59870206 CACTGATATGTAGCGGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
59870229 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
59870252 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
59870274 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
59870297 CACTGAT
1 CACTGAT
59870304 CAATAACACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:59870271 original size:45 final size:45
Alignment explanation
Indices: 59870213--59870301 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
59870203 CCACACTGAT
** *
59870213 ATGTAGCGGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
59870258 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
59870302 ATCAATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:59875147 original size:48 final size:47
Alignment explanation
Indices: 59874976--59875188 Score: 213
Period size: 48 Copynumber: 4.5 Consensus size: 47
59874966 GCAAAATTAT
*
59874976 AAACTTTGTAATTTAAATTAGATTAATTGCAAC----AAACTTTAGAA
1 AAACTTTGTAATTTAAATTAGATTAATTGCAACATTAAAAC-TCAGAA
* * *
59875020 AAATTTTGT-ATTTATTTAATTGAGATTCATTGCAACATTAAAACGCAGAA
1 AAACTTTGTAATTTA---AATT-AGATTAATTGCAACATTAAAACTCAGAA
* * **
59875070 TAACTTTGTAATTT-AATTGAGATTCATTGCAACATTAAAACTTGGAA
1 AAACTTTGTAATTTAAATT-AGATTAATTGCAACATTAAAACTCAGAA
* *
59875117 CAAAATTTGTAATTTAAATTAGATTAATTGCAACATTAAAACACAGAA
1 -AAACTTTGTAATTTAAATTAGATTAATTGCAACATTAAAACTCAGAA
*
59875165 CAAACTTTGTAATATAAATTAGAT
1 -AAACTTTGTAATTTAAATTAGAT
59875189 ACATTGGAGT
Statistics
Matches: 141, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
43 5 0.04
44 8 0.06
46 4 0.03
47 43 0.30
48 58 0.41
49 4 0.03
50 11 0.08
51 8 0.06
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (47 bp):
AAACTTTGTAATTTAAATTAGATTAATTGCAACATTAAAACTCAGAA
Found at i:59878207 original size:7 final size:7
Alignment explanation
Indices: 59878195--59878230 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
59878185 TTTTCTATAT
59878195 TAAATTC
1 TAAATTC
59878202 TAAATTC
1 TAAATTC
59878209 TAAATTC
1 TAAATTC
59878216 TAAATTC
1 TAAATTC
59878223 TAAATTC
1 TAAATTC
59878230 T
1 T
59878231 TTTCAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (7 bp):
TAAATTC
Found at i:59878866 original size:26 final size:28
Alignment explanation
Indices: 59878814--59878866 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
59878804 TCTGGTGTCA
* *
59878814 TTACTAACTAACAATTAGTTTATAATAG
1 TTACTAACTAACAATAAGTTTAAAATAG
59878842 TTACTAAC-AA-AATAAGTTTAAAATA
1 TTACTAACTAACAATAAGTTTAAAATA
59878867 AATTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 2 0.09
28 8 0.35
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (28 bp):
TTACTAACTAACAATAAGTTTAAAATAG
Found at i:59880106 original size:8 final size:9
Alignment explanation
Indices: 59880079--59880105 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
59880069 ATAAAATAAA
59880079 TAATTTTTT
1 TAATTTTTT
59880088 TAATTTTTT
1 TAATTTTTT
59880097 TAATTTTTT
1 TAATTTTTT
59880106 ATAAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TAATTTTTT
Found at i:59881530 original size:22 final size:22
Alignment explanation
Indices: 59881495--59881539 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
59881485 CACATATTAT
* *
59881495 AATTTATTCAATTTTAGTCCTTA
1 AATTTATTAAATTTCA-TCCTTA
59881518 AATTT-TTAAATTTCATCCTTA
1 AATTTATTAAATTTCATCCTTA
59881539 A
1 A
59881540 TTCAATCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTATTAAATTTCATCCTTA
Found at i:59882169 original size:113 final size:113
Alignment explanation
Indices: 59881971--59882414 Score: 888
Period size: 113 Copynumber: 3.9 Consensus size: 113
59881961 ATAAATGAAG
59881971 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
1 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
59882036 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTCCTGTATCA
66 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTCCTGTATCA
59882084 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
1 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
59882149 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTCCTGTATCA
66 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTCCTGTATCA
59882197 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
1 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
59882262 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTCCTGTATCA
66 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTCCTGTATCA
59882310 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
1 TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
59882375 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTC
66 TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTC
59882415 ACCTCACCTC
Statistics
Matches: 331, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 331 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (113 bp):
TAAAGTACTAAATTATAAGGACTGATACCAAAATTTTACCATGAAACCCTCTTTTTTTTTCTATA
TATATTCAGCCCAGCGGAGGAGGAATTTGGACTTCACCTCCTGTATCA
Found at i:59889096 original size:27 final size:27
Alignment explanation
Indices: 59889005--59889100 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
59888995 CTATGCCATG
*
59889005 ATTATTTG-ATCTGGTGGCTCTACCAC
1 ATTATCTGTATCTGGTGGCTCTACCAC
*
59889031 ATATATTTGT-TCTGGTGGCTCTACCAC
1 AT-TATCTGTATCTGGTGGCTCTACCAC
* **
59889058 GATTATCTGTATCTGGTGACTCTGTCAC
1 -ATTATCTGTATCTGGTGGCTCTACCAC
59889086 ATTATCTGTATCTGG
1 ATTATCTGTATCTGG
59889101 CAGCCATGCT
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
26 2 0.03
27 44 0.71
28 16 0.26
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTATCTGTATCTGGTGGCTCTACCAC
Found at i:59892790 original size:30 final size:30
Alignment explanation
Indices: 59892756--59892818 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
59892746 ACTTATTTTA
59892756 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
59892786 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
59892816 TTG
1 TTG
59892819 CTTGTTCAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:59895796 original size:21 final size:20
Alignment explanation
Indices: 59895772--59895810 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
59895762 AATACCTGGT
59895772 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCG-TACTTTTTG
* *
59895793 AAAATGTATTGTACTTTT
1 AAAAGGTATCGTACTTTT
59895811 AGTATTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (20 bp):
AAAAGGTATCGTACTTTTTG
Found at i:59901599 original size:39 final size:37
Alignment explanation
Indices: 59901553--59901664 Score: 104
Period size: 39 Copynumber: 2.9 Consensus size: 37
59901543 TATCTAGATA
59901553 AACATTAAATTAAATTTAAAATATTAAGATAATCATTTT
1 AACATTAAATT-AATTTAAAATATTAAGATAATCA-TTT
**
59901592 AACATTAAATTAATAAAATAATATTAAGATAAGT-A-TT
1 AACATTAAATTAATTTAA-AATATTAAGATAA-TCATTT
* * *
59901629 AA-ATGAAATTTAATATTAAATTATTAAAATAATCAT
1 AACATTAAA-TTAAT-TTAAAATATTAAGATAATCAT
59901665 ATTTTTGGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
36 6 0.10
37 21 0.35
38 7 0.12
39 25 0.42
40 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (37 bp):
AACATTAAATTAATTTAAAATATTAAGATAATCATTT
Found at i:59902126 original size:14 final size:14
Alignment explanation
Indices: 59902107--59902133 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59902097 TACTTGATCA
59902107 AAATTAATTTTTCT
1 AAATTAATTTTTCT
59902121 AAATTAATTTTTC
1 AAATTAATTTTTC
59902134 AAGAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (14 bp):
AAATTAATTTTTCT
Found at i:59903269 original size:15 final size:15
Alignment explanation
Indices: 59903245--59903276 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
59903235 TATGCATACA
*
59903245 AAATATAAAAGACAT
1 AAATACAAAAGACAT
59903260 AAATACAAAAGACAT
1 AAATACAAAAGACAT
59903275 AA
1 AA
59903277 TAGTGAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:59916635 original size:348 final size:348
Alignment explanation
Indices: 59915998--59916694 Score: 1385
Period size: 348 Copynumber: 2.0 Consensus size: 348
59915988 AATAGCCCAA
59915998 GGTGAAAACCCACAAAGGGCGCTTTGAGACCAAACAAAAAATGAAAATAAAAAGATAAAAAGGAG
1 GGTGAAAACCCACAAAGGGCGCTTTGAGACCAAACAAAAAATGAAAATAAAAAGATAAAAAGGAG
59916063 ATTCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGACCAAAGGGGATTTGAGTTGAAGACCCGAA
66 ATTCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGACCAAAGGGGATTTGAGTTGAAGACCCGAA
59916128 AATGGCGTCTCAAATTTTGAACAAAAATGGGAAGGCGGCGATCTTACTATACCTGAATTAGCAAG
131 AATGGCGTCTCAAATTTTGAACAAAAATGGGAAGGCGGCGATCTTACTATACCTGAATTAGCAAG
59916193 GAAAAGGGTATGCTGCATCTTGGGGCATTGACAAAGTGCTTCTGATCTCCTCAACACATGTCAAG
196 GAAAAGGGTATGCTGCATCTTGGGGCATTGACAAAGTGCTTCTGATCTCCTCAACACATGTCAAG
59916258 TTTAAATTGGTCTTCAAGAAGTTCGTACAGCGAAACTCAGGTTGCGATATCAGGGGTACCTAGTC
261 TTTAAATTGGTCTTCAAGAAGTTCGTACAGCGAAACTCAGGTTGCGATATCAGGGGTACCTAGTC
*
59916323 TTCATCTTGTTCATAATAAATTG
326 TTCATCTTGTTCATAAAAAATTG
59916346 GGTGAAAACCCACAAAGGGCGCTTTGAGACCAAACAAAAAATGAAAATAAAAAGATAAAAAGGAG
1 GGTGAAAACCCACAAAGGGCGCTTTGAGACCAAACAAAAAATGAAAATAAAAAGATAAAAAGGAG
59916411 ATTCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGACCAAAGGGGATTTGAGTTGAAGACCCGAA
66 ATTCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGACCAAAGGGGATTTGAGTTGAAGACCCGAA
59916476 AATGGCGTCTCAAATTTTGAACAAAAATGGGAAGGCGGCGATCTTACTATACCTGAATTAGCAAG
131 AATGGCGTCTCAAATTTTGAACAAAAATGGGAAGGCGGCGATCTTACTATACCTGAATTAGCAAG
59916541 GAAAAGGGTATGCTGCATCTTGGGGCATTGACAAAGTGCTTCTGATCTCCTCAACACATGTCAAG
196 GAAAAGGGTATGCTGCATCTTGGGGCATTGACAAAGTGCTTCTGATCTCCTCAACACATGTCAAG
59916606 TTTAAATTGGTCTTCAAGAAGTTCGTACAGCGAAACTCAGGTTGCGATATCAGGGGTACCTAGTC
261 TTTAAATTGGTCTTCAAGAAGTTCGTACAGCGAAACTCAGGTTGCGATATCAGGGGTACCTAGTC
59916671 TTCATCTTGTTCATAAAAAATTG
326 TTCATCTTGTTCATAAAAAATTG
59916694 G
1 G
59916695 CTATCTTTGA
Statistics
Matches: 348, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
348 348 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (348 bp):
GGTGAAAACCCACAAAGGGCGCTTTGAGACCAAACAAAAAATGAAAATAAAAAGATAAAAAGGAG
ATTCCAAGGTGAAAACCCGCAAAGGGCGCCTTGAGACCAAAGGGGATTTGAGTTGAAGACCCGAA
AATGGCGTCTCAAATTTTGAACAAAAATGGGAAGGCGGCGATCTTACTATACCTGAATTAGCAAG
GAAAAGGGTATGCTGCATCTTGGGGCATTGACAAAGTGCTTCTGATCTCCTCAACACATGTCAAG
TTTAAATTGGTCTTCAAGAAGTTCGTACAGCGAAACTCAGGTTGCGATATCAGGGGTACCTAGTC
TTCATCTTGTTCATAAAAAATTG
Found at i:59917746 original size:44 final size:45
Alignment explanation
Indices: 59917708--59917970 Score: 200
Period size: 44 Copynumber: 5.9 Consensus size: 45
59917698 CTTATTTCTT
* *
59917708 TGAGGTAGCAA-GAGAGTAGGTTGAAGATTGTAG-TCTTATCTTCC
1 TGAGGTAGCAAGGA-AGCAGATTGAAGATTGTAGATCTTATCTTCC
* *
59917752 TGCGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTCCC
1 TGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTTCC
* * * ** *
59917797 TGAGCAGTAG--TGG-AGCAAATCGAAGAGGGTGGATCTTATCTTCC
1 TGAG--GTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTTCC
* * * ** **** **
59917841 CGAGGTAGCAGGGGAGCAGATTTTAG-CCACAGGCCTTATC-TCC
1 TGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTTCC
* *
59917884 TTGAGGTAGCAAGGGAGCAGGTTGAAGATTGTAG-TCTTATCTTCC
1 -TGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTTCC
* * *
59917929 TAAGGTAGCAAGGAAGCAGACTGAAGATGGTAGATCTTATCT
1 TGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCT
59917971 CTCTGAAGTT
Statistics
Matches: 168, Mismatches: 40, Indels: 21
0.73 0.17 0.09
Matches are distributed among these distances:
42 4 0.02
43 3 0.02
44 119 0.71
45 38 0.23
47 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.27
Consensus pattern (45 bp):
TGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTTCC
Found at i:59917926 original size:177 final size:177
Alignment explanation
Indices: 59917652--59917976 Score: 526
Period size: 177 Copynumber: 1.8 Consensus size: 177
59917642 AAAATGGAAA
* * * *
59917652 ATCTTATTTTCCCAAGGTAGTAGGGGAGCAGATTTTAGCCACCAGCCTTATTTCTTTGAGGTAGC
1 ATCTTATCTTCCCAAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCTTGAGGTAGC
* ** * *
59917717 AAGAGAGTAGGTTGAAGATTGTAGTCTTATCTTCCTGCGGTAGCAAGGAAGCAGATTGAAGATTG
66 AAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAGATGG
59917782 TAGATCTTATCTCCCTGAGCAGTAGTGGAGCAAATCGAAGAGGGTGG
131 TAGATCTTATCTCCCTGAGCAGTAGTGGAGCAAATCGAAGAGGGTGG
*
59917829 ATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCA-CAGGCCTTATCTCCTTGAGGTAG
1 ATCTTATCTTCCCAAGGTAGCAGGGGAGCAGATTTTAGCCACCA-GCCTTATCTCCTTGAGGTAG
*
59917893 CAAGGGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAGATG
65 CAAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAGATG
*
59917958 GTAGATCTTATCTCTCTGA
130 GTAGATCTTATCTCCCTGA
59917977 AGTTGCAGTG
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 2 0.01
177 133 0.99
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (177 bp):
ATCTTATCTTCCCAAGGTAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCCTTGAGGTAGC
AAGAGAGCAGGTTGAAGATTGTAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAGATGG
TAGATCTTATCTCCCTGAGCAGTAGTGGAGCAAATCGAAGAGGGTGG
Found at i:59917990 original size:133 final size:132
Alignment explanation
Indices: 59917742--59918187 Score: 294
Period size: 133 Copynumber: 3.4 Consensus size: 132
59917732 AGATTGTAGT
* *
59917742 CTTATCTTCCTGCGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTCCCTGAGCAGTAG
1 CTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTCCCTAAG-AGTAG
* * *
59917807 TGGAGCAAATCGAAGAGGGTGGATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACA
65 AGGAGCAAATCGAAGAGGGTAGATCTTATCTTCCCGAAGTAGCAGGGGAGCAGATTTTAGCCACA
59917872 GGC
130 GGC
* * *
59917875 CTTATC-TCCTTGAGGTAGCAAGGGAGCAGGTTGAAGATTGTAG-TCTTATCTTCCTAAG-GTAG
1 CTTATCTTCC-TGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTCCCTAAGAGTAG
* * * * * * ***
59917937 CAAGGAAGCAGA-CTGAAGATGGTAGATCTTATC-TCTCTGAAGTTGCAGTGGAGCATATCAAAG
65 --AGG-AGCAAATC-GAAGAGGGTAGATCTTATCTTC-CCGAAGTAGCAGGGGAGCAGATTTTAG
*
59918000 -CA-A-GT
125 CCACAGGC
* * * * * *
59918005 CTTATCTCCCTGAAGTTA-C-AGCAGAGCAGACTGAAGATTGAAAATCTTATCTCCCTAAGCAGT
1 CTTATCTTCCTG-AGGTAGCAAGGA-AGCAGATTGAAGATTGTAGATCTTATCTCCCTAAG-AGT
* * *** * * * * * * *
59918068 AGCGAAGTTGATCAAAGA-TGT-GAATCTTATGTTCCCGAGGTAGCAGGGGAGCATATATTAACC
63 AGAGGAGCAAATCGAAGAGGGTAG-ATCTTATCTTCCCGAAGTAGCAGGGGAGCAGATTTTAGCC
59918131 ACTA-GC
127 AC-AGGC
* * * *
59918137 CTTATC-TCTCTAAGGTAGCAA-GAGAGCCGGTTGAAGATTGTAG-TCCTATCT
1 CTTATCTTC-CTGAGGTAGCAAGGA-AGCAGATTGAAGATTGTAGATCTTATCT
59918188 TCTTGAGGAA
Statistics
Matches: 239, Mismatches: 53, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
128 1 0.00
129 30 0.13
130 41 0.17
131 35 0.15
132 50 0.21
133 82 0.34
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (132 bp):
CTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAAGATTGTAGATCTTATCTCCCTAAGAGTAGA
GGAGCAAATCGAAGAGGGTAGATCTTATCTTCCCGAAGTAGCAGGGGAGCAGATTTTAGCCACAG
GC
Found at i:59919031 original size:17 final size:17
Alignment explanation
Indices: 59919009--59919047 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
59918999 CTTATTCGAG
*
59919009 TATAAAAGAAAACTGAA
1 TATAAAAGAAAACCGAA
59919026 TATAAAAGAAAACCGAA
1 TATAAAAGAAAACCGAA
59919043 TATAA
1 TATAA
59919048 TTTTTAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (17 bp):
TATAAAAGAAAACCGAA
Found at i:59919917 original size:5 final size:5
Alignment explanation
Indices: 59919907--59919931 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
59919897 TACTTTGATA
59919907 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
59919932 TGTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:59922406 original size:28 final size:27
Alignment explanation
Indices: 59922354--59922406 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
59922344 CTATTCAGAA
* * *
59922354 ATCAGTGTTAACTGGGCCTTAGCCCAT
1 ATCAGTATTAACTAGGCCATAGCCCAT
59922381 ATCAGTATTAATCTAGGCCATAGCCC
1 ATCAGTATTAA-CTAGGCCATAGCCC
59922407 TATTACAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (27 bp):
ATCAGTATTAACTAGGCCATAGCCCAT
Found at i:59922537 original size:19 final size:20
Alignment explanation
Indices: 59922494--59922549 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
59922484 ATTGGGTCTT
59922494 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
59922514 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
* *
59922533 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
59922550 CTCATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:59930935 original size:55 final size:55
Alignment explanation
Indices: 59930867--59930970 Score: 120
Period size: 55 Copynumber: 1.9 Consensus size: 55
59930857 CAGTTGCTCG
* *
59930867 GCACGGGCGTGTCGCACGCCCGTGTTAATTTGACAGGTTCGGCC-ACGGTTTCCAA
1 GCACAGGCATGTCGCACGCCCGTGTTAATTTGACAGGTTC-GCCTACGGTTTCCAA
* * * ** *
59930922 GCACAGGCATGTCGTATGTCCGTGTTGTTTTGGCAGGTTCGCCTACGGT
1 GCACAGGCATGTCGCACGCCCGTGTTAATTTGACAGGTTCGCCTACGGT
59930971 CATGTCGCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 3 0.08
55 37 0.93
ACGTcount: A:0.14, C:0.26, G:0.32, T:0.28
Consensus pattern (55 bp):
GCACAGGCATGTCGCACGCCCGTGTTAATTTGACAGGTTCGCCTACGGTTTCCAA
Found at i:59937320 original size:25 final size:25
Alignment explanation
Indices: 59937258--59937314 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
59937248 TATTGCCTAG
*
59937258 CAGGCTTTATGTCGGTGTATTATAT
1 CAGGCTTTATGCCGGTGTATTATAT
59937283 CAGGCTTTATGCCGGTGTATTATAT
1 CAGGCTTTATGCCGGTGTATTATAT
59937308 CAGGCTT
1 CAGGCTT
59937315 ATTGCCTAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.40
Consensus pattern (25 bp):
CAGGCTTTATGCCGGTGTATTATAT
Found at i:59937340 original size:41 final size:41
Alignment explanation
Indices: 59937283--59937366 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 41
59937273 TGTATTATAT
*
59937283 CAGGCTTTATGCCGGTGTATTATATC-AGGC-TTATTGCCTAG
1 CAGGCTCTATGCCGGTGTATTAT-TCTAGGCTTTA-TGCCTAG
*
59937324 CAGGCTCTGTGCCGGTGTATTATTCTAGGCTTTATGCCTAG
1 CAGGCTCTATGCCGGTGTATTATTCTAGGCTTTATGCCTAG
59937365 CA
1 CA
59937367 AATTTTATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 2 0.05
41 34 0.87
42 3 0.08
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (41 bp):
CAGGCTCTATGCCGGTGTATTATTCTAGGCTTTATGCCTAG
Found at i:59939812 original size:12 final size:13
Alignment explanation
Indices: 59939785--59939825 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
59939775 ATATTTTTTA
*
59939785 AAAAATATTTATAT
1 AAAAA-ATTAATAT
59939799 AAAAAA-TAATAT
1 AAAAAATTAATAT
59939811 AAAAAATTAATAT
1 AAAAAATTAATAT
59939824 AA
1 AA
59939826 TCAGGTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 9 0.36
14 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATTAATAT
Found at i:59941286 original size:40 final size:40
Alignment explanation
Indices: 59941156--59941891 Score: 893
Period size: 40 Copynumber: 18.2 Consensus size: 40
59941146 ATACATTAGT
* * * * *
59941156 AAACGCCGCAAAAAACTGAACAATAACGGCATTTTTGGCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
* * *
59941196 AAAAAGCCACTAAAAACTGAACAATAGCGGCGTTTTTTGCC
1 -AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
* * * * *
59941237 AAAATGCCACTACAAGCTTATCAATAGCGGCATTTTTGGCC
1 -AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
* * **
59941278 AAACGCCACTAAAAGCTGATCAATAGTGGCGTTTTTATCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCC
* * *
59941319 AAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGACC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
**
59941359 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTATCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCC
59941400 AAACGCCACTAAAAACTGATCAATAGCGGC-TCTTTTGGCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGT-TTTTGGCC
59941440 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
* * * *
59941480 AAACGCCACTAAAAACTGATGAATAGCGCCATTTTTGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
59941520 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
* * * *
59941560 AAACGCCACTAAAAACTGATGAATAGCGCCATTTTTGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
*
59941600 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTTGCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCG-TTTTTGGCC
* * * * * **
59941641 AAGCGCCACTAAAAACTGATTAATAGTGTCATTTTTCTCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCC
* * *
59941682 AAACGCCACTAAAAACTTG-TGAATAGCAGCGTTTTTGGTC
1 AAACGCCACTAAAAAC-TGATCAATAGCGGCGTTTTTGGCC
* **
59941722 AAACGCCACTAAAAACTTATCAATAGCGGCGTTTTTATCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCC
* **
59941763 AAACGCCACTAAAAACTGATCAATAGTGGCGTTTTTATCTC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGC-C
* *
59941804 AAATGCCACTAAAAAATGATCAATAGCGGCGTTTTTGGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGG-CC
*
59941845 AAACGCCACT-AAAACTCATCAATAGCGGCGTTTTTGGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGG-CC
59941885 AAACGCC
1 AAACGCC
59941892 GCAAAAAGTT
Statistics
Matches: 603, Mismatches: 81, Indels: 23
0.85 0.11 0.03
Matches are distributed among these distances:
39 1 0.00
40 317 0.53
41 282 0.47
42 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
Found at i:59941312 original size:81 final size:80
Alignment explanation
Indices: 59941156--59941891 Score: 913
Period size: 81 Copynumber: 9.1 Consensus size: 80
59941146 ATACATTAGT
* * * * * *
59941156 AAACGCCGCAAAAAACTGAACAATAACGGCATTTTTGGCCAAAAAGCCACTAAAAACTGAACAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTGGCC-AAACGCCACTAAAAACTGATCAAT
59941221 AGCGGCGTTTTTTGCC
65 AGCGGCGTTTTTTGCC
* * * * *
59941237 AAAATGCCACTACAAGCTTATCAATAGCGGCATTTTTGGCCAAACGCCACTAAAAGCTGATCAAT
1 -AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTGGCCAAACGCCACTAAAAACTGATCAAT
* *
59941302 AGTGGCGTTTTTATCCC
65 AGCGGCGTTTTT-TGCC
* * * *
59941319 AAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGACCAAACGCCACTAAAAACTGATCAATA
1 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTGGCCAAACGCCACTAAAAACTGATCAATA
*
59941384 GCGGCGTTTTTATCCC
66 GCGGCGTTTTT-TGCC
59941400 AAACGCCACTAAAAACTGATCAATAGCGGC-TCTTTTGGCCAAACGCCACTAAAAACTGATCAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCAT-TTTTGGCCAAACGCCACTAAAAACTGATCAAT
*
59941464 AGCGGCGTTTTTGGCC
65 AGCGGCGTTTTTTGCC
* * *
59941480 AAACGCCACTAAAAACTGATGAATAGCGCCATTTTTGTCCAAACGCCACTAAAAACTGATCAATA
1 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTGGCCAAACGCCACTAAAAACTGATCAATA
*
59941545 GCGGCGTTTTTGGCC
66 GCGGCGTTTTTTGCC
* * *
59941560 AAACGCCACTAAAAACTGATGAATAGCGCCATTTTTGTCCAAACGCCACTAAAAACTGATCAATA
1 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTGGCCAAACGCCACTAAAAACTGATCAATA
59941625 GCGGCGTTTTTTGCCC
66 GCGGCGTTTTTTG-CC
* * * * ** *
59941641 AAGCGCCACTAAAAACTGATTAATAGTGTCATTTTTCTCCCAAACGCCACTAAAAACTTG-TGAA
1 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTT-GGCCAAACGCCACTAAAAAC-TGATCAA
* * *
59941705 TAGCAGCGTTTTTGGTC
64 TAGCGGCGTTTTTTGCC
* * **
59941722 AAACGCCACTAAAAACTTATCAATAGCGGCGTTTTTATCCCAAACGCCACTAAAAACTGATCAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTT-GGCCAAACGCCACTAAAAACTGATCAAT
*
59941787 AGTGGCGTTTTTAT-CTC
65 AGCGGCGTTTTT-TGC-C
* * * *
59941804 AAATGCCACTAAAAAATGATCAATAGCGGCGTTTTTGGTCCAAACGCCACT-AAAACTCATCAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTGG-CCAAACGCCACTAAAAACTGATCAAT
*
59941868 AGCGGCGTTTTTGGTCC
65 AGCGGCGTTTTTTG-CC
59941885 AAACGCC
1 AAACGCC
59941892 GCAAAAAGTT
Statistics
Matches: 580, Mismatches: 62, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
80 157 0.27
81 305 0.53
82 116 0.20
83 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (80 bp):
AAACGCCACTAAAAACTGATCAATAGCGGCATTTTTGGCCAAACGCCACTAAAAACTGATCAATA
GCGGCGTTTTTTGCC
Found at i:59942220 original size:21 final size:21
Alignment explanation
Indices: 59942181--59942243 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
59942171 TGGCTTTCTG
* *
59942181 TAAACCCTTAAATCTTAAACAT
1 TAAACCC-TAAACCATAAACAT
* **
59942203 TAAACCCTAAACCCTAAATTT
1 TAAACCCTAAACCATAAACAT
* *
59942224 TAAAACATAAACCATAAACA
1 TAAACCCTAAACCATAAACA
59942244 CTAATCTATA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACAT
Found at i:59942466 original size:38 final size:41
Alignment explanation
Indices: 59942418--59942504 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 41
59942408 GTTTAAGGCC
*
59942418 TATGGTTTA-G-GGTTCAATGG-TAGAATATATTTTAAGTT
1 TATGGTTTAGGCGGTTCAATGGATAGAATATATGTTAAGTT
*
59942456 TATGGTTTAGGCCGGTTCAATGGTATAGTATATATGTTAAGTT
1 TATGGTTTAGG-CGGTTCAATGG-ATAGAATATATGTTAAGTT
59942499 TATGGT
1 TATGGT
59942505 ATGGGTCGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
38 9 0.21
39 1 0.02
41 10 0.24
43 22 0.52
ACGTcount: A:0.26, C:0.05, G:0.25, T:0.44
Consensus pattern (41 bp):
TATGGTTTAGGCGGTTCAATGGATAGAATATATGTTAAGTT
Found at i:59943620 original size:40 final size:41
Alignment explanation
Indices: 59943565--59943675 Score: 147
Period size: 40 Copynumber: 2.8 Consensus size: 41
59943555 CTGCAGAGGC
*
59943565 ATTAGCGGCGTTTTTGTAAAAACGCCGCTAAAAA-TAGAGA
1 ATTAGCGGCGCTTTTGTAAAAACGCCGCTAAAAATTAGAGA
* *
59943605 ATTAGTGGCGCTTTTGTAAAAACGCCGC-AAAAATTTGAGA
1 ATTAGCGGCGCTTTTGTAAAAACGCCGCTAAAAATTAGAGA
* * *
59943645 TTTAGCGACGCTTTTGT-AAAACGCCACTAAA
1 ATTAGCGGCGCTTTTGTAAAAACGCCGCTAAA
59943676 TGTTTAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 14 0.23
40 48 0.77
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTGTAAAAACGCCGCTAAAAATTAGAGA
Found at i:59946504 original size:22 final size:22
Alignment explanation
Indices: 59946476--59946520 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
59946466 GCACTTTGAA
59946476 AAAACTATACTTTAAGAAAGAT
1 AAAACTATACTTTAAGAAAGAT
*
59946498 AAAACTATATTTTAAGAAAGAT
1 AAAACTATACTTTAAGAAAGAT
59946520 A
1 A
59946521 TAAGCCTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (22 bp):
AAAACTATACTTTAAGAAAGAT
Found at i:59951023 original size:20 final size:20
Alignment explanation
Indices: 59950993--59951037 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
59950983 CTGTTTTGTT
59950993 ATGGG-CCAACTGTATTGAA
1 ATGGGCCCAACTGTATTGAA
* *
59951012 ATGGGCCCAACTGTGTTGAT
1 ATGGGCCCAACTGTATTGAA
59951032 ATGGGC
1 ATGGGC
59951038 AAGGCCCAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTGAA
Found at i:59955089 original size:20 final size:20
Alignment explanation
Indices: 59955059--59955103 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
59955049 CTGTTTTATT
59955059 ATGGG-CCAACTGTATTGAA
1 ATGGGCCCAACTGTATTGAA
* *
59955078 ATGGGCCCAACTGTGTTGAT
1 ATGGGCCCAACTGTATTGAA
59955098 ATGGGC
1 ATGGGC
59955104 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (20 bp):
ATGGGCCCAACTGTATTGAA
Found at i:59955196 original size:60 final size:62
Alignment explanation
Indices: 59955094--59955244 Score: 179
Period size: 60 Copynumber: 2.5 Consensus size: 62
59955084 CCAACTGTGT
* * *
59955094 TGATATGGGCAAGGCCCAATATA-TCTCG--ACTTGTAATAGGGCTATGGCCAAGATTGATAC
1 TGATATGGGCTAGGCCCAGTATACTCT-GATACTTGTAATAGGGCTATGGCCAAGATTAATAC
* *
59955154 TGATATGGGCTAGGCCCAGTATACTCTGATAC-TGTAA-GGGGCTATGGCCCAGATTAATAC
1 TGATATGGGCTAGGCCCAGTATACTCTGATACTTGTAATAGGGCTATGGCCAAGATTAATAC
*
59955214 TGATATGGGCTAAGACCCAGT-TAACTCTGAT
1 TGATATGGGCT-AGGCCCAGTAT-ACTCTGAT
59955245 TTCTGAATAG
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
60 54 0.68
61 24 0.30
62 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (62 bp):
TGATATGGGCTAGGCCCAGTATACTCTGATACTTGTAATAGGGCTATGGCCAAGATTAATAC
Found at i:59955223 original size:28 final size:28
Alignment explanation
Indices: 59955132--59955225 Score: 93
Period size: 28 Copynumber: 3.2 Consensus size: 28
59955122 ACTTGTAATA
*
59955132 GGGCTATGGCCAAGATTGATACTGATAT
1 GGGCTATGGCCCAGATTGATACTGATAT
*
59955160 GGGCTA-GGCCCAGTATACTCTGATACTG-TAAG
1 GGGCTATGGCCCAG---A-T-TGATACTGAT-AT
*
59955192 GGGCTATGGCCCAGATTAATACTGATAT
1 GGGCTATGGCCCAGATTGATACTGATAT
59955220 GGGCTA
1 GGGCTA
59955226 AGACCCAGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
27 6 0.11
28 20 0.37
29 2 0.04
30 2 0.04
31 2 0.04
32 15 0.28
33 7 0.13
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (28 bp):
GGGCTATGGCCCAGATTGATACTGATAT
Found at i:59956517 original size:110 final size:112
Alignment explanation
Indices: 59956345--59957038 Score: 958
Period size: 110 Copynumber: 6.4 Consensus size: 112
59956335 ATTGTTTTTT
* * * **
59956345 TTTGTGTTTAGTTTAGTG-TT-TTGTGAT-TTATTATGAATGTAATTTTTTT-TATTTTTCTAAT
1 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTTTTGTGTTTTTAAAAT
59956406 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
66 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
59956453 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTT-TTATGAATGTAATTTTTTTGT-TTTTTAAAAT
1 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTTTTGTGTTTTTAAAAT
59956516 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
66 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
59956563 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTT-TTATGAATGTAATTTTTTTGT-TTTTTAAAAT
1 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTTTTGTGTTTTTAAAAT
59956626 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
66 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
59956673 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTT-TTATGAATGTAATTTTTTTGT-TTTTTAAAAT
1 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTTTTGTGTTTTTAAAAT
* * *
59956736 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGATTATAATTTT
66 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
* * * * *
59956783 TTTGTGTTTAGTTTAGTGTTTGTTGTGA-CTTGCTATAAATGTAA-ATTTTTGTGTTTTT-AAA-
1 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTTTTGTGTTTTTAAAAT
**
59956844 -A--TT--A--T-TTTT-TTAGTAATTTATGATTACATTATAAATTG
66 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
* * *
59956882 TTTGTGTTTAGTTTAGTGTTTATTGTGA-CTTGTTATAAATGTAATTTTTTTGTGTTTTTTAAAT
1 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTTTTGTGTTTTTAAAAT
* *
59956946 TATTTTAAAGTCATTTTGTTAGTAATTTATGATTAGGTTATCAATT-
66 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
* * * * * *
59956992 ATT-TGTTTAGTTTAATGTGTATTGTGAT-TTGTTA-AAATGTAAATTTT
1 TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTT
59957039 ATTTATGATT
Statistics
Matches: 542, Mismatches: 25, Indels: 38
0.90 0.04 0.06
Matches are distributed among these distances:
99 68 0.13
100 17 0.03
101 4 0.01
103 2 0.00
105 4 0.01
107 2 0.00
108 30 0.06
109 43 0.08
110 344 0.63
111 28 0.05
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (112 bp):
TTTGTGTTTAGTTTAGTGTTTATTGCGATCTTGTTATGAATGTAATTTTTTTGTGTTTTTAAAAT
TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTG
Done.