Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 11 of 24
Found at i:2213503 original size:230 final size:229
Alignment explanation
Indices: 2212845--2213538 Score: 1051
Period size: 228 Copynumber: 3.0 Consensus size: 229
2212835 AGGCATTAAC
* * * *
2212845 AACCAGTTCTAGAAAGGAAACTGGTGAGAGAGGTTTTTTGAATGATTTGTCCATTTTTCCAAGC-
1 AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCA--TTTCCAAGCA
*
2212909 TGTCTTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCCTTGGTGT
64 T-TC-TTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGT
*
2212974 TCTGGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTC
127 TCCGGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTC
*
2213039 TTGTAGTTTGTTCGATAGGCCAAGTGGAAGACAATGAAGCA
192 TTGTA---TGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
*
2213080 AACCAGTTCTAGAAAGGATAGTGGTGAAAGAGTTTTTTTGAATGATTCGTCCATTTCCAAGCTAT
1 AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCATTTCCAAGC-AT
*
2213145 TCTTTTTATGAGCCCAATTGATTT--A--AAGTAGGCAAGGTGCTGGA-TTGGCCTTGGTGTTCC
65 TCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTCC
* * *
2213205 CGATTTCGTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTGTAATGTATTCTGCTTGCCTTCTTG
130 GGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTG
*
2213270 TA-GTTAGATAGGCCAACTGGAAGACAATGAAGCA
195 TATGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
* * *
2213304 AACCAGTTCTAGAAAGGATACTGTTGAAAGAGTTTTTTTTTATTGATTCGTCCATTTCCAAGCAA
1 AACCAGTTCTAGAAAGGATACTGGTGAAAGAG-TTTTTTTGAATGATTCGTCCATTTCCAAGC-A
2213369 TTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTC
64 TTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTC
* *
2213434 CGGATTTCTTTTTTATTTTAATTTTAAGAGGTTTCTTTTTTATAATGCATTCTGCTTGCCTTCTT
129 CGGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTT
*
2213499 GTAGTTTGTTAGATAGGCCAAGTGGTAGACAATGAAGCA
194 GTA---TGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
2213538 A
1 A
2213539 TGGATTTTGC
Statistics
Matches: 421, Mismatches: 26, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
224 60 0.14
225 53 0.13
227 1 0.00
228 79 0.19
229 37 0.09
230 78 0.19
231 1 0.00
233 30 0.07
234 33 0.08
235 49 0.12
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (229 bp):
AACCAGTTCTAGAAAGGATACTGGTGAAAGAGTTTTTTTGAATGATTCGTCCATTTCCAAGCATT
CTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCCTTGGTGTTCCG
GATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGTATTCTGCTTGCCTTCTTGT
ATGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
Found at i:2214325 original size:18 final size:19
Alignment explanation
Indices: 2214295--2214336 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
2214285 AAAGTGCTTT
* *
2214295 ATTTTCTTTGGTTTACTTG
1 ATTTTCTTTGGTTCACTTA
2214314 ATTTTC-TTGGTTCACTTA
1 ATTTTCTTTGGTTCACTTA
2214332 ATTTT
1 ATTTT
2214337 TCTCAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (19 bp):
ATTTTCTTTGGTTCACTTA
Found at i:2221939 original size:24 final size:24
Alignment explanation
Indices: 2221908--2221956 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2221898 GTTAAAATTT
*
2221908 TTTTTTGATTATATGATATCCTTA
1 TTTTTTGATTATATGACATCCTTA
2221932 TTTTTTGATTATATGACATCCTTA
1 TTTTTTGATTATATGACATCCTTA
2221956 T
1 T
2221957 ACAGTTACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTTTTGATTATATGACATCCTTA
Found at i:2227337 original size:14 final size:15
Alignment explanation
Indices: 2227313--2227341 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2227303 ATTTTTTATT
2227313 ATTATAAAATATAAA
1 ATTATAAAATATAAA
2227328 ATTA-AAAATATAAA
1 ATTATAAAATATAAA
2227342 TATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTATAAAATATAAA
Found at i:2227367 original size:16 final size:17
Alignment explanation
Indices: 2227338--2227370 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2227328 ATTAAAAATA
2227338 TAAATATATTTTTATTAT
1 TAAATATA-TTTTATTAT
2227356 TAAATATA-TTTATTA
1 TAAATATATTTTATTA
2227371 AAAATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATATATTTTATTAT
Found at i:2228460 original size:12 final size:12
Alignment explanation
Indices: 2228443--2228467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2228433 AGCCTTATAC
2228443 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2228455 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2228467 T
1 T
2228468 GTTTATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:2229303 original size:9 final size:9
Alignment explanation
Indices: 2229289--2229323 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2229279 TGGAGAGGTG
2229289 ATTTATGAA
1 ATTTATGAA
2229298 ATTTATGAA
1 ATTTATGAA
**
2229307 ACATATGAA
1 ATTTATGAA
2229316 ATTTATGA
1 ATTTATGA
2229324 TAAATTTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (9 bp):
ATTTATGAA
Found at i:2238834 original size:233 final size:234
Alignment explanation
Indices: 2238414--2238882 Score: 708
Period size: 233 Copynumber: 2.0 Consensus size: 234
2238404 AGGCATTGAC
* * * * *
2238414 AACCAGTTCTTGAAAGGAAACTGGTGAAAGAGGTTTTCTGAATGATTTGTCCTTTTTTCCAAGCT
1 AACCAGATCTAGAAAGGAAACTGGTGAAAGAGGTTTTATGAATGATTCGTCC-TATTTCCAAGCT
*
2238479 GGTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCCTTGGTGTT
65 GGTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCATTGGTGTT
* *
2238544 CTGGATTTCTTTTTTATTTTAATTATAAAAAGTTACTTTTTAATAATGTATTCTGCTTGCCTTCT
130 CCGGATTTCTTTTTTATTTTAATTATAAAAAGTTACTTTTTAATAATGCATTCTGCTTGCCTTCT
* *
2238609 TGTAGTTTTTTCGATAGGCCAAGTGGAAGACAATGAAGCA
195 TGTAGTTTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
** *
2238649 AACCAGATCTAGAAAGGATGCTGGTGAAAGAGTTTTTATGAATGATTCGTCC-ATTTCCAAGC-G
1 AACCAGATCTAGAAAGGAAACTGGTGAAAGAGGTTTTATGAATGATTCGTCCTATTTCCAAGCTG
* ** *
2238712 ATTCTTTTTATGATGCCAATTGATTTAGAGTAAGTAGGCAAGGTGCTGGATTTGGCATTGGTGTT
66 -GTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCATTGGTGTT
* * * *
2238777 CCGGATTTCTTTTTTATTTTAATTTTAAAAGGTTTCTTTTTTATAATGCATTCTGCTTGCCTTCT
130 CCGGATTTCTTTTTTATTTTAATTATAAAAAGTTACTTTTTAATAATGCATTCTGCTTGCCTTCT
*
2238842 TGTAGTTTGTTAGATAGGCCAAGTGGTAGACAATGAAGCA
195 TGTAGTTTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
2238882 A
1 A
2238883 TGGATTTTGC
Statistics
Matches: 211, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
232 1 0.00
233 165 0.78
235 45 0.21
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (234 bp):
AACCAGATCTAGAAAGGAAACTGGTGAAAGAGGTTTTATGAATGATTCGTCCTATTTCCAAGCTG
GTCTTTTTATGAACCCAATTGATTTAGAGTAAGTAGGCAAGGTGATGGATTTGGCATTGGTGTTC
CGGATTTCTTTTTTATTTTAATTATAAAAAGTTACTTTTTAATAATGCATTCTGCTTGCCTTCTT
GTAGTTTGTTAGATAGGCCAAGTGGAAGACAATGAAGCA
Found at i:2239669 original size:18 final size:19
Alignment explanation
Indices: 2239639--2239680 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
2239629 AAAATGCTTT
* *
2239639 ATTTTCTTTGGTTTACTTG
1 ATTTTCTTTGGTTCACTTA
2239658 ATTTTC-TTGGTTCACTTA
1 ATTTTCTTTGGTTCACTTA
2239676 ATTTT
1 ATTTT
2239681 TCTCAAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (19 bp):
ATTTTCTTTGGTTCACTTA
Found at i:2244499 original size:2 final size:2
Alignment explanation
Indices: 2244494--2244525 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2244484 AACCGGACAA
2244494 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2244526 TTTTCTGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2255513 original size:24 final size:23
Alignment explanation
Indices: 2255486--2255530 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2255476 CAAGTTTTTT
*
2255486 TAAATAAAAAATTTTAAAATTTCA
1 TAAA-AAAAAAGTTTAAAATTTCA
* *
2255510 TAAAAAGAAAGTTTATAATTT
1 TAAAAAAAAAGTTTAAAATTT
2255531 ATCATTCTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
TAAAAAAAAAGTTTAAAATTTCA
Found at i:2256068 original size:22 final size:21
Alignment explanation
Indices: 2256043--2256093 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2256033 AAATTATGTA
*
2256043 ATATAAATATTATTCATAAAAT
1 ATATAAATATTATTAAT-AAAT
*
2256065 ATATAAAAATTATTAATAAAT
1 ATATAAATATTATTAATAAAT
2256086 ATA-AAATA
1 ATATAAATA
2256094 AAATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 4 0.15
21 7 0.27
22 15 0.58
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAAATATTATTAATAAAT
Found at i:2256458 original size:6 final size:7
Alignment explanation
Indices: 2256439--2256464 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2256429 TACTAAATAA
2256439 AATTTTT
1 AATTTTT
2256446 AATTTTT
1 AATTTTT
2256453 AATTTTT
1 AATTTTT
2256460 AATTT
1 AATTT
2256465 GTATCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:2256584 original size:18 final size:18
Alignment explanation
Indices: 2256561--2256603 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2256551 TTAATTTTTA
*
2256561 ATTTAATTATAAAAATAT
1 ATTTAAATATAAAAATAT
*
2256579 ATTTAAATATAATAATAT
1 ATTTAAATATAAAAATAT
*
2256597 AATTAAA
1 ATTTAAA
2256604 AATATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAATATAAAAATAT
Found at i:2256651 original size:16 final size:17
Alignment explanation
Indices: 2256626--2256663 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2256616 TTTTAAACAT
2256626 TAAAAA-TAAAAT-TTG
1 TAAAAACTAAAATCTTG
2256641 TAAAAACTAAAATCTTG
1 TAAAAACTAAAATCTTG
2256658 -AAAAAC
1 TAAAAAC
2256664 CATAATCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 12 0.57
17 3 0.14
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (17 bp):
TAAAAACTAAAATCTTG
Found at i:2257734 original size:12 final size:12
Alignment explanation
Indices: 2257717--2257741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2257707 AGCCTTATAC
2257717 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2257729 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2257741 T
1 T
2257742 GCTTATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:2262961 original size:21 final size:21
Alignment explanation
Indices: 2262935--2262976 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2262925 AAACTTTTTC
2262935 CTGTATTTGTATGCAATTATT
1 CTGTATTTGTATGCAATTATT
2262956 CTGTATTTGTATGCAATTATT
1 CTGTATTTGTATGCAATTATT
2262977 TCTCAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (21 bp):
CTGTATTTGTATGCAATTATT
Found at i:2264695 original size:6 final size:6
Alignment explanation
Indices: 2264684--2264709 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2264674 TTGTTTCCCA
2264684 GGGACT GGGACT GGGACT GGGACT GG
1 GGGACT GGGACT GGGACT GGGACT GG
2264710 TCTTCTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.54, T:0.15
Consensus pattern (6 bp):
GGGACT
Found at i:2271808 original size:32 final size:32
Alignment explanation
Indices: 2271767--2271830 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2271757 AAGTAAGGAT
2271767 TTGTGGACCTGTTTTGTTTTATCATGGTTCTG
1 TTGTGGACCTGTTTTGTTTTATCATGGTTCTG
2271799 TTGTGGACCTGTTTTGTTTTATCATGGTTCTG
1 TTGTGGACCTGTTTTGTTTTATCATGGTTCTG
2271831 CTAATTTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.53
Consensus pattern (32 bp):
TTGTGGACCTGTTTTGTTTTATCATGGTTCTG
Found at i:2273729 original size:220 final size:220
Alignment explanation
Indices: 2273343--2273771 Score: 795
Period size: 220 Copynumber: 1.9 Consensus size: 220
2273333 CTTATTATAT
2273343 ACACACACACACACACACGTGTTTGTGTATGTATGTATCTCATCTCCTGAATTTTTATTTGTGTG
1 ACACACACACACACACACGTGTTTGTGTATGTATGTATCTCATCTCCTGAATTTTTATTTGTGTG
*
2273408 ATGCGATTTGTCTTTCCATATTCAGTTCCCACCCTGCTACCCCCTTCTACTGAAAAAAGTAAAAA
66 ATGCGATTTGTCTTTCCATATTCAGTTCCCACCCTGCTACCCCCTTCTACCGAAAAAAGTAAAAA
* *
2273473 GAATAAATACTTTCAACATTTCCTTTGGCTTTAAATCCTACATAAAAGAGTAGAGAAACTCTATG
131 GAATAAATACTTTCAACAATTCCTTTGGCCTTAAATCCTACATAAAAGAGTAGAGAAACTCTATG
*
2273538 CCTTGTGTAGTTTACACACACACAG
196 CCTTGTCTAGTTTACACACACACAG
*
2273563 ACACACACACACACATACGTGTTTGTGTATGTATGTATCTCATCTCCTGAATTTTTATTTGTGTG
1 ACACACACACACACACACGTGTTTGTGTATGTATGTATCTCATCTCCTGAATTTTTATTTGTGTG
*
2273628 ATGCGATTTGTCTTTCCATGTTCAGTTCCCACCCTGCTACCCCCTTCTACCGAAAAAAGTAAAAA
66 ATGCGATTTGTCTTTCCATATTCAGTTCCCACCCTGCTACCCCCTTCTACCGAAAAAAGTAAAAA
*
2273693 GAATAAATACTTTCAACAATTCCTTTGGCCTTAAATCCTACATGAAAGAGTAGAGAAACTCTATG
131 GAATAAATACTTTCAACAATTCCTTTGGCCTTAAATCCTACATAAAAGAGTAGAGAAACTCTATG
2273758 CCTTGTCTAGTTTA
196 CCTTGTCTAGTTTA
2273772 TCTATCCCTT
Statistics
Matches: 202, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
220 202 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (220 bp):
ACACACACACACACACACGTGTTTGTGTATGTATGTATCTCATCTCCTGAATTTTTATTTGTGTG
ATGCGATTTGTCTTTCCATATTCAGTTCCCACCCTGCTACCCCCTTCTACCGAAAAAAGTAAAAA
GAATAAATACTTTCAACAATTCCTTTGGCCTTAAATCCTACATAAAAGAGTAGAGAAACTCTATG
CCTTGTCTAGTTTACACACACACAG
Found at i:2280861 original size:70 final size:70
Alignment explanation
Indices: 2280778--2280918 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
2280768 ATTTCTTACG
2280778 GTCAGATTATAATTTTATTGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
1 GTCAGATTATAATTTTATTGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
2280843 AATGT
66 AATGT
* *
2280848 GTCAGATTATAATTTTATTGTTTCATCTATTTTCCAATAATTTCTTGTTGATGCATTTTTTGTTG
1 GTCAGATTATAATTTTATTGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
2280913 AATGT
66 AATGT
2280918 G
1 G
2280919 AAGCAATCCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.23, C:0.10, G:0.14, T:0.52
Consensus pattern (70 bp):
GTCAGATTATAATTTTATTGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
AATGT
Found at i:2286875 original size:23 final size:23
Alignment explanation
Indices: 2286848--2286896 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2286838 TATGTAGTAT
* *
2286848 AAATATCATTCATAAAATACATA
1 AAATATCATTAATAAAATAAATA
* *
2286871 AAATATTATTAATAATATAAATA
1 AAATATCATTAATAAAATAAATA
2286894 AAA
1 AAA
2286897 CATTTATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATCATTAATAAAATAAATA
Found at i:2286908 original size:23 final size:23
Alignment explanation
Indices: 2286859--2286917 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
2286849 AATATCATTC
* * *
2286859 ATAAAATACATAAAATATTATTA
1 ATAATATAAATAAAACATTATTA
2286882 ATAATATAAATAAAACATTTATT-
1 ATAATATAAATAAAACA-TTATTA
2286905 ATAAT-TAAA-AAAA
1 ATAATATAAATAAAA
2286918 TCAAGAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 19 0.59
24 5 0.16
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAATATAAATAAAACATTATTA
Found at i:2287205 original size:32 final size:31
Alignment explanation
Indices: 2287159--2287219 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
2287149 GGATGATAGA
* *
2287159 AATTGTTTTAATTTTATTATTTTATTTAATT
1 AATTGTTTTAATTTTATGATTATATTTAATT
*
2287190 AATTTTTTTATATTTTATGATTATATTTAA
1 AATTGTTTTA-ATTTTATGATTATATTTAA
2287220 ATAAATTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (31 bp):
AATTGTTTTAATTTTATGATTATATTTAATT
Found at i:2287285 original size:29 final size:30
Alignment explanation
Indices: 2287245--2287345 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 30
2287235 TAATTTACAT
*
2287245 TAAATTAATTTTTAATTTTTAATTTTTATC
1 TAAATAAATTTTTAATTTTTAATTTTTATC
*
2287275 TAAAT--TTTTTTAAATTTTTAATTTTTATC
1 TAAATAAATTTTT-AATTTTTAATTTTTATC
* * *
2287304 AAAATAAATTTTTAATTTTT-ATTTATATT
1 TAAATAAATTTTTAATTTTTAATTTTTATC
*
2287333 TAAATATATTTTT
1 TAAATAAATTTTT
2287346 GATATAAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
28 5 0.08
29 39 0.64
30 12 0.20
31 5 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TAAATAAATTTTTAATTTTTAATTTTTATC
Found at i:2287353 original size:17 final size:17
Alignment explanation
Indices: 2287333--2287375 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2287323 TATTTATATT
* *
2287333 TAAATATATTTTTGATA
1 TAAATATAATTTTAATA
* *
2287350 TAAATAAAATTTTAATT
1 TAAATATAATTTTAATA
2287367 TAAATATAA
1 TAAATATAA
2287376 AAATATATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TAAATATAATTTTAATA
Found at i:2287387 original size:18 final size:18
Alignment explanation
Indices: 2287364--2287435 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
2287354 TAAAATTTTA
2287364 ATTTAAATATAAAAATAT
1 ATTTAAATATAAAAATAT
*
2287382 ATTTAAATA-AAATGATAT
1 ATTTAAATATAAA-AATAT
* ***
2287400 AATTAAAAATATTTTAATAT
1 -ATT-TAAATATAAAAATAT
2287420 -TTTAAATATAAAAATA
1 ATTTAAATATAAAAATA
2287436 AAATATTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
17 13 0.32
18 15 0.38
19 3 0.08
20 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
ATTTAAATATAAAAATAT
Found at i:2288552 original size:12 final size:12
Alignment explanation
Indices: 2288535--2288559 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2288525 AGCCTTATAC
2288535 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2288547 TTTAGTCAAAGA
1 TTTAGTCAAAGA
2288559 T
1 T
2288560 GTTTATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (12 bp):
TTTAGTCAAAGA
Found at i:2289395 original size:9 final size:9
Alignment explanation
Indices: 2289381--2289415 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2289371 TGGAGAGGTG
2289381 ATTTATGAA
1 ATTTATGAA
2289390 ATTTATGAA
1 ATTTATGAA
**
2289399 ACATATGAA
1 ATTTATGAA
2289408 ATTTATGA
1 ATTTATGA
2289416 TAAATTTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (9 bp):
ATTTATGAA
Found at i:2306283 original size:39 final size:39
Alignment explanation
Indices: 2306229--2306306 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2306219 AACATAAGAC
2306229 CAGATAGCAGTTTGGAATTTTAATCATGCTGTTTTTCAT
1 CAGATAGCAGTTTGGAATTTTAATCATGCTGTTTTTCAT
2306268 CAGATAGCAGTTTGGAATTTTAATCATGCTGTTTTTCAT
1 CAGATAGCAGTTTGGAATTTTAATCATGCTGTTTTTCAT
2306307 TGCTTCACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.44
Consensus pattern (39 bp):
CAGATAGCAGTTTGGAATTTTAATCATGCTGTTTTTCAT
Found at i:2306950 original size:183 final size:184
Alignment explanation
Indices: 2306622--2306979 Score: 504
Period size: 183 Copynumber: 2.0 Consensus size: 184
2306612 AATACAATTT
* * * * *
2306622 TTTTTCTCTTCAGTCTGACATATTCTTGAGGCAAAACTCATTTCAATCTTTGAACTTTGTATTTT
1 TTTTTCTCTTCACTCTGACATATACTTAAGGCAAAACTAATTTCAATCTTTGAACTTTGTAATTT
* *
2306687 TGAAGTTGGAGTTTGCCCATTATGACTGCAAATTGCCTAGTACAATAACAGCTAAAGATTTCACA
66 TGAAGTTGGAGTTTGCCCATTACGACTGCAAATTACCTAGTACAATAACAGCTAAAGATTTCACA
* *
2306752 CTGTCAATTGTGGCCTCTGCTGATATTGGCAGCATAAACAAGCTTTGCCAGAAG
131 CTGTCAATGGTGGCCTCTGCTGATATTAGCAGCATAAACAAGCTTTGCCAGAAG
* * *
2306806 TTTTT-TCTTCACTCTGACATGTACTTAAGGCAAAACTAATTTCTATC-TTGAATTTTGTAAATT
1 TTTTTCTCTTCACTCTGACATATACTTAAGGCAAAACTAATTTCAATCTTTGAACTTTGT-AATT
** * * * *
2306869 TTGAAGTTGTTGTTTGCCCATTACGACTGCAAATTACGTGGTACAATAGCAGCTAAAGATTTCGC
65 TTGAAGTTGGAGTTTGCCCATTACGACTGCAAATTACCTAGTACAATAACAGCTAAAGATTTCAC
* * *
2306934 ATTGTCAATGGTGGCCTCTGCTGATATTAGCCGCATAGACAAGCTT
130 ACTGTCAATGGTGGCCTCTGCTGATATTAGCAGCATAAACAAGCTT
2306980 CTTGATCGCA
Statistics
Matches: 152, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
182 10 0.07
183 137 0.90
184 5 0.03
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (184 bp):
TTTTTCTCTTCACTCTGACATATACTTAAGGCAAAACTAATTTCAATCTTTGAACTTTGTAATTT
TGAAGTTGGAGTTTGCCCATTACGACTGCAAATTACCTAGTACAATAACAGCTAAAGATTTCACA
CTGTCAATGGTGGCCTCTGCTGATATTAGCAGCATAAACAAGCTTTGCCAGAAG
Found at i:2309664 original size:102 final size:102
Alignment explanation
Indices: 2309488--2309674 Score: 286
Period size: 102 Copynumber: 1.8 Consensus size: 102
2309478 TGTCAGTATA
* * *
2309488 TTTTGGTTAAAATAGTCTACTGGCATCTTAGCTTATTCTATTTCCTCTAAGATAATGACTAGTGT
1 TTTTGATTAAAATAGTCTACTGGCATCTTAGCTTATTCTATTTCCTATAAGATAATGACTAATGT
*
2309553 CTCAAATATGTTTGGTTGCATTATATTTTTTCATACT
66 CTCAAATATGTCTGGTTGCATTATATTTTTTCATACT
* * * *
2309590 TTTTGATTAAAATAGTCT-GTCGGTATTTTAGCTTATTCTATTTCTTATAAGATAATGACTAATG
1 TTTTGATTAAAATAGTCTACT-GGCATCTTAGCTTATTCTATTTCCTATAAGATAATGACTAATG
2309654 TCTCAAATATGTCTGGTTGCA
65 TCTCAAATATGTCTGGTTGCA
2309675 GGATATTCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
101 1 0.01
102 75 0.99
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.45
Consensus pattern (102 bp):
TTTTGATTAAAATAGTCTACTGGCATCTTAGCTTATTCTATTTCCTATAAGATAATGACTAATGT
CTCAAATATGTCTGGTTGCATTATATTTTTTCATACT
Found at i:2310201 original size:70 final size:70
Alignment explanation
Indices: 2310118--2310258 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
2310108 ATTTCTTACG
*
2310118 GTCAGATTATAATTTTATTGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
1 GTCAGATTATAATTTTATCGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
2310183 AATGT
66 AATGT
*
2310188 GTCAGATTATAATTTTATCGTTTCATCTATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
1 GTCAGATTATAATTTTATCGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
2310253 AATGT
66 AATGT
2310258 G
1 G
2310259 AAGCAATCCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (70 bp):
GTCAGATTATAATTTTATCGTTTCATCAATTTTCCAAGAATTTCTTGTTGATGCATTTTTTGTTG
AATGT
Found at i:2312480 original size:18 final size:19
Alignment explanation
Indices: 2312440--2312483 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2312430 AGTCTCTAAA
*
2312440 AATTTGTCTTTTATTTATG
1 AATTTATCTTTTATTTATG
2312459 AATTTATCTTTT-TTTAAT-
1 AATTTATCTTTTATTT-ATG
2312477 AATTTAT
1 AATTTAT
2312484 TATATATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (19 bp):
AATTTATCTTTTATTTATG
Found at i:2312665 original size:47 final size:47
Alignment explanation
Indices: 2312596--2312692 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
2312586 GATTATTTCT
2312596 TTAGGCCTTGTATCTTGGATCTTGAGCTTTGACTTACTTTCAAAATA
1 TTAGGCCTTGTATCTTGGATCTTGAGCTTTGACTTACTTTCAAAATA
2312643 TTAGGCCTTGTATCTTGGATCTTGAGCTTTGACTTACTTTCAAAATA
1 TTAGGCCTTGTATCTTGGATCTTGAGCTTTGACTTACTTTCAAAATA
2312690 TTA
1 TTA
2312693 AAAATCTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (47 bp):
TTAGGCCTTGTATCTTGGATCTTGAGCTTTGACTTACTTTCAAAATA
Found at i:2312755 original size:29 final size:30
Alignment explanation
Indices: 2312723--2312782 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
2312713 AATTTTACGG
2312723 TGAACTTTGAA-A-TCTTAATATTTTTAAAA
1 TGAACTTTGAAGAGT-TTAATATTTTTAAAA
2312752 TGAACTTTGAAGAGTTTAATATTTTTAAAA
1 TGAACTTTGAAGAGTTTAATATTTTTAAAA
2312782 T
1 T
2312783 TTTGGTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 11 0.38
30 17 0.59
31 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (30 bp):
TGAACTTTGAAGAGTTTAATATTTTTAAAA
Found at i:2313717 original size:13 final size:13
Alignment explanation
Indices: 2313701--2313725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2313691 TCGGCCATTT
2313701 CATTTTTGGCCAG
1 CATTTTTGGCCAG
2313714 CATTTTTGGCCA
1 CATTTTTGGCCA
2313726 TATGCAAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (13 bp):
CATTTTTGGCCAG
Found at i:2318629 original size:27 final size:26
Alignment explanation
Indices: 2318597--2318686 Score: 92
Period size: 28 Copynumber: 3.4 Consensus size: 26
2318587 CACCCATTTG
2318597 TTTGTCAAAAATGGTGGTTATTTTGTA
1 TTTGTCAAAAATGGTGGTT-TTTTGTA
* *
2318624 TTTGTCAAAAATGATGGTTTCCTTTGGA
1 TTTGTCAAAAATGGTGGTTT--TTTGTA
* * * *
2318652 TTTGTCAAATATGGAGGCTTGTT-TA
1 TTTGTCAAAAATGGTGGTTTTTTGTA
2318677 TTTGTCAAAA
1 TTTGTCAAAA
2318687 TTTGTGGCTA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
25 10 0.19
26 3 0.06
27 18 0.35
28 21 0.40
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (26 bp):
TTTGTCAAAAATGGTGGTTTTTTGTA
Found at i:2318654 original size:28 final size:27
Alignment explanation
Indices: 2318597--2318660 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
2318587 CACCCATTTG
* *
2318597 TTTGTCAAAAATGGTGGTTATTTTGTA
1 TTTGTCAAAAATGATGGTTATTTTGGA
2318624 TTTGTCAAAAATGATGGTT-TCCTTTGGA
1 TTTGTCAAAAATGATGGTTAT--TTTGGA
2318652 TTTGTCAAA
1 TTTGTCAAA
2318661 TATGGAGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 18 0.55
28 14 0.42
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGATGGTTATTTTGGA
Found at i:2318985 original size:22 final size:22
Alignment explanation
Indices: 2318943--2319023 Score: 58
Period size: 22 Copynumber: 3.6 Consensus size: 22
2318933 ACCACACAAA
2318943 CAACAACAACAGCAAGCAAGAG
1 CAACAACAACAGCAAGCAAGAG
* * *
2318965 CAACGACAGCAGC-AGCTAAGAAA
1 CAACAACAACAGCAAGC-AAG-AG
* * *
2318988 AAAGAAAAAACAGC-AGCAAGAG
1 CAA-CAACAACAGCAAGCAAGAG
*
2319010 CAACAACAATAGCA
1 CAACAACAACAGCA
2319024 GCTGCTGTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
21 10 0.24
22 17 0.40
23 6 0.14
24 9 0.21
ACGTcount: A:0.56, C:0.23, G:0.19, T:0.02
Consensus pattern (22 bp):
CAACAACAACAGCAAGCAAGAG
Found at i:2319104 original size:14 final size:14
Alignment explanation
Indices: 2319085--2319132 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 14
2319075 AGCAAGTGTG
2319085 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
2319099 AAAAAGAAAGAAGAAA
1 AAAAAGAAA-AA-AAA
2319115 AATAAAGGAAAAAAAA
1 AA-AAA-GAAAAAAAA
2319131 AA
1 AA
2319133 TTCCAAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 10 0.33
17 5 0.17
18 4 0.13
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:2319293 original size:12 final size:12
Alignment explanation
Indices: 2319276--2319301 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2319266 GAAATTTCAC
2319276 TATTATTGTTAT
1 TATTATTGTTAT
2319288 TATTATTGTTAT
1 TATTATTGTTAT
2319300 TA
1 TA
2319302 AATTCTTAAC
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:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (12 bp):
TATTATTGTTAT
Found at i:2322901 original size:5 final size:5
Alignment explanation
Indices: 2322888--2322917 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2322878 TACTCTTTGC
*
2322888 ATATG ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
2322918 TAAATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:2325364 original size:2 final size:2
Alignment explanation
Indices: 2325357--2325436 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
2325347 TGCTTTTTCC
*
2325357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2325399 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2325437 CTCATTGCCT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2334342 original size:13 final size:13
Alignment explanation
Indices: 2334320--2334349 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2334310 TGATGTTTAT
2334320 AAGG-GAGTTCCA
1 AAGGTGAGTTCCA
2334332 AAGGTGAGTTCCA
1 AAGGTGAGTTCCA
2334345 AAGGT
1 AAGGT
2334350 CTGTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (13 bp):
AAGGTGAGTTCCA
Found at i:2337840 original size:85 final size:85
Alignment explanation
Indices: 2337679--2337840 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 85
2337669 ACTTTAGTGC
* * * * * *
2337679 CTTCCAATTTAGTGGTTCTTAAACAGTTGTCTGGCTGATAACTAAGCCATCCGTCAGACCACGGT
1 CTTCCAATTTAGTGGTTCATAAACAGTTGTCTGGCTGACAACTAAGCCATCCATAAGACCAAGAT
* *
2337744 AAGTGCTATTCAGTATAATG
66 AACTGCCATTCAGTATAATG
* * *
2337764 CTTCCAATTTAGTGGTTCATAAACAGTTGTAC-GGTTGACATCTAAGCCATCCATAAGATCAAGA
1 CTTCCAATTTAGTGGTTCATAAACAGTTGT-CTGGCTGACAACTAAGCCATCCATAAGACCAAGA
2337828 TAACTGCCATTCA
65 TAACTGCCATTCA
2337841 TTATTATGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
85 64 0.98
86 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (85 bp):
CTTCCAATTTAGTGGTTCATAAACAGTTGTCTGGCTGACAACTAAGCCATCCATAAGACCAAGAT
AACTGCCATTCAGTATAATG
Found at i:2337979 original size:24 final size:27
Alignment explanation
Indices: 2337934--2337999 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 27
2337924 TAATTTTTCA
*
2337934 TATAATTAAAATATTATATATT-TATATT
1 TATAATT-AAATA-TATATATTAGATATT
2337962 TATAATTAAATAT-T-TATTAGATATT
1 TATAATTAAATATATATATTAGATATT
*
2337987 TAT-ATTGAATATA
1 TATAATTAAATATA
2338000 AATTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 12 0.35
25 9 0.26
26 1 0.03
27 5 0.15
28 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
TATAATTAAATATATATATTAGATATT
Found at i:2337986 original size:31 final size:28
Alignment explanation
Indices: 2337934--2337992 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 28
2337924 TAATTTTTCA
*
2337934 TATAATTAAAATATTATATATTTATATT
1 TATAATTAAAATATTAGATATTTATATT
2337962 TATAATTAAATATTTATTAGATATTTATATT
1 TATAATTAAA-A--TATTAGATATTTATATT
2337993 GAATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 10 0.37
29 1 0.04
31 16 0.59
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TATAATTAAAATATTAGATATTTATATT
Found at i:2343720 original size:17 final size:17
Alignment explanation
Indices: 2343700--2343736 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2343690 GGAGAATGTT
2343700 AGATTTTCTTTTTCTAG
1 AGATTTTCTTTTTCTAG
2343717 AGATTTTCTTTTTCTAG
1 AGATTTTCTTTTTCTAG
2343734 AGA
1 AGA
2343737 CCTTCATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.54
Consensus pattern (17 bp):
AGATTTTCTTTTTCTAG
Found at i:2349985 original size:16 final size:16
Alignment explanation
Indices: 2349963--2350005 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
2349953 ATTCAACTAG
2349963 ATAAATTTTATTT-AA
1 ATAAATTTTATTTGAA
*
2349978 ACTAAATTATATTTGAA
1 A-TAAATTTTATTTGAA
2349995 ATAAAATTTTA
1 AT-AAATTTTA
2350006 ATAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 10 0.43
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
ATAAATTTTATTTGAA
Found at i:2350914 original size:17 final size:19
Alignment explanation
Indices: 2350876--2350916 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2350866 TATATATCTC
*
2350876 AAAATTTATATAATGTATT
1 AAAATTTATATAATATATT
2350895 AAAATTTATATAA-ATA-T
1 AAAATTTATATAATATATT
2350912 AAAAT
1 AAAAT
2350917 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATTTATATAATATATT
Found at i:2352616 original size:62 final size:62
Alignment explanation
Indices: 2352538--2352786 Score: 480
Period size: 62 Copynumber: 4.0 Consensus size: 62
2352528 ATATGCATAA
*
2352538 GATATGAGTACTTTAAGAAAAATGAAAAATCGAAGCAACATAGCATATGTTTATATGTGTGC
1 GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAGCAACATAGCATATGTTTATATGTGTGC
*
2352600 GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAACAACATAGCATATGTTTATATGTGTGC
1 GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAGCAACATAGCATATGTTTATATGTGTGC
2352662 GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAGCAACATAGCATATGTTTATATGTGTGC
1 GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAGCAACATAGCATATGTTTATATGTGTGC
2352724 GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAGCAACATAGCATATGTTTATATGTGTGC
1 GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAGCAACATAGCATATGTTTATATGTGTGC
2352786 G
1 G
2352787 CATGTATCCA
Statistics
Matches: 184, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 184 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (62 bp):
GATATGAGTACTTTAAGAAAAATGAAAAGTCGAAGCAACATAGCATATGTTTATATGTGTGC
Found at i:2356291 original size:3 final size:3
Alignment explanation
Indices: 2356283--2356315 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2356273 ATTCAACCAA
2356283 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2356316 TACCAACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2357958 original size:2 final size:2
Alignment explanation
Indices: 2357951--2357976 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2357941 AAGCATGGGG
2357951 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2357977 CTTGGTGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2358398 original size:17 final size:18
Alignment explanation
Indices: 2358363--2358404 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2358353 AAATAAAATT
* *
2358363 TTAAATTTTATTTAAAAA
1 TTAAATTTGAGTTAAAAA
*
2358381 -TAAATTTGAGTTATAAA
1 TTAAATTTGAGTTAAAAA
2358398 TTAAATT
1 TTAAATT
2358405 CTAATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
TTAAATTTGAGTTAAAAA
Found at i:2358501 original size:20 final size:19
Alignment explanation
Indices: 2358456--2358503 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2358446 TAAATTAAAA
*
2358456 ATTTATTAATATTTAAATG
1 ATTTTTTAATATTTAAATG
* *
2358475 ATATTTTTAATATTATTAATT
1 AT-TTTTTAATATT-TAAATG
2358496 ATTTTTTA
1 ATTTTTTA
2358504 TTTATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 16 0.67
21 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTTTAATATTTAAATG
Found at i:2360062 original size:39 final size:39
Alignment explanation
Indices: 2360008--2360084 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
2359998 GGTTACAGTT
* *
2360008 TCATTTCTCTTTTCTTTCATTTCTTTCTTTGAAGTGCTC
1 TCATTTCTCTTTTCTTTCATTTCTTGCTTTGAAATGCTC
* *
2360047 TCATTTGTCTTTTCTTTCTTTTCTTGCTTTGAAATGCT
1 TCATTTCTCTTTTCTTTCATTTCTTGCTTTGAAATGCT
2360085 TACGGCAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.10, C:0.21, G:0.09, T:0.60
Consensus pattern (39 bp):
TCATTTCTCTTTTCTTTCATTTCTTGCTTTGAAATGCTC
Found at i:2363343 original size:2 final size:2
Alignment explanation
Indices: 2363338--2363377 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2363328 TGTGTGTGTG
2363338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2363378 GAGAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2363382 original size:2 final size:2
Alignment explanation
Indices: 2363377--2363407 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2363367 ATATATATAT
2363377 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2363408 TCGGAACGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2363574 original size:15 final size:18
Alignment explanation
Indices: 2363554--2363593 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
2363544 CTCATGATTT
2363554 TATATTAAA-C-AATATA
1 TATATTAAATCAAATATA
2363570 T-TATTAAATCAAATATA
1 TATATTAAATCAAATATA
2363587 TATATTA
1 TATATTA
2363594 TTAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 2 0.10
17 7 0.33
18 5 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATTAAATCAAATATA
Found at i:2364826 original size:2 final size:2
Alignment explanation
Indices: 2364819--2364846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2364809 CAGCCGTTGG
2364819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2364847 GTGTAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2365329 original size:2 final size:2
Alignment explanation
Indices: 2365324--2365354 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2365314 CATACTCTTT
2365324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2365355 GTTTTCCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2365443 original size:1 final size:1
Alignment explanation
Indices: 2365437--2365461 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2365427 TGGGTGTTCC
2365437 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2365462 GCCCTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2367588 original size:3 final size:3
Alignment explanation
Indices: 2367580--2367614 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2367570 GTTAACACTT
2367580 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2367615 TTCTTGGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2371342 original size:20 final size:20
Alignment explanation
Indices: 2371319--2371356 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2371309 TTTTAATATT
2371319 AAATAAATAATAAATATAAC
1 AAATAAATAATAAATATAAC
*
2371339 AAATAATTAATAAATATA
1 AAATAAATAATAAATATA
2371357 TATTCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAATAATAAATATAAC
Found at i:2372578 original size:1 final size:1
Alignment explanation
Indices: 2372572--2372597 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2372562 GTAAAAGAAG
2372572 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2372598 GGGCAAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2373117 original size:19 final size:19
Alignment explanation
Indices: 2373090--2373127 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2373080 TAAAAAGTTT
2373090 AAATGAAATAAAATTTATA
1 AAATGAAATAAAATTTATA
* *
2373109 AAATTAAATGAAATTTATA
1 AAATGAAATAAAATTTATA
2373128 CTAATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAATGAAATAAAATTTATA
Found at i:2373651 original size:16 final size:18
Alignment explanation
Indices: 2373630--2373663 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2373620 GATTGGTTAA
2373630 ATTAAA-AAA-ATTAAAT
1 ATTAAATAAATATTAAAT
2373646 ATTAAATAAATATTAAAT
1 ATTAAATAAATATTAAAT
2373664 CTCATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTAAATAAATATTAAAT
Found at i:2374172 original size:26 final size:25
Alignment explanation
Indices: 2374124--2374205 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
2374114 CTAAAGAATA
*
2374124 ATATTAATTTAATAATTTATATATTT
1 ATATTATTTTAATAATTTATATA-TT
* * *
2374150 ATATTATTTTTATATTTTTTATATT
1 ATATTATTTTAATAATTTATATATT
*
2374175 ATAATTATTTTAAAAATATTATATATT
1 AT-ATTATTTTAATAAT-TTATATATT
2374202 -TATT
1 ATATT
2374206 TAAATATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 7 0.15
26 31 0.67
27 8 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATATTATTTTAATAATTTATATATT
Found at i:2376535 original size:19 final size:19
Alignment explanation
Indices: 2376513--2376549 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2376503 TATTTAAATT
2376513 TAAATTAAATAATTTAAAA
1 TAAATTAAATAATTTAAAA
**
2376532 TAAATTATTTAATTTAAA
1 TAAATTAAATAATTTAAA
2376550 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATTAAATAATTTAAAA
Found at i:2376538 original size:34 final size:34
Alignment explanation
Indices: 2376491--2376564 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
2376481 CTCGTGTAAC
* *
2376491 TTTAAGATTAATTATTTAAATTTAAA-TTAAATAA
1 TTTAAAATAAATTATTT-AATTTAAATTTAAATAA
2376525 TTTAAAATAAATTATTTAATTTAAATTTAAATAA
1 TTTAAAATAAATTATTTAATTTAAATTTAAATAA
*
2376559 TCTAAA
1 TTTAAA
2376565 TTGTTATCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 8 0.22
34 28 0.78
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTAAAATAAATTATTTAATTTAAATTTAAATAA
Found at i:2376551 original size:14 final size:14
Alignment explanation
Indices: 2376510--2376551 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2376500 AATTATTTAA
*
2376510 ATTTAAATTAAATA
1 ATTTAAATTAAATT
*
2376524 ATTTAAAATAAATT
1 ATTTAAATTAAATT
*
2376538 ATTTAATTTAAATT
1 ATTTAAATTAAATT
2376552 TAAATAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAAATTAAATT
Found at i:2376823 original size:16 final size:17
Alignment explanation
Indices: 2376790--2376834 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2376780 AATATGAAAA
2376790 AAATATTTT-AAATAAT
1 AAATATTTTAAAATAAT
2376806 AAATATTTTAAAAT-AT
1 AAATATTTTAAAATAAT
2376822 AAA-ATTTATAAAA
1 AAATATTT-TAAAA
2376835 ATTTTTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.15
16 19 0.70
17 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATTTTAAAATAAT
Found at i:2380501 original size:13 final size:14
Alignment explanation
Indices: 2380479--2380527 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
2380469 ATTAAATATA
2380479 TTTATATATTTAAT
1 TTTATATATTTAAT
2380493 TTTAT-TATTTAAT
1 TTTATATATTTAAT
* * *
2380506 ATCATAAATTTAAT
1 TTTATATATTTAAT
*
2380520 TTTTTATA
1 TTTATATA
2380528 AATTAATAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTATATATTTAAT
Found at i:2380545 original size:27 final size:30
Alignment explanation
Indices: 2380492--2380604 Score: 107
Period size: 29 Copynumber: 3.9 Consensus size: 30
2380482 ATATATTTAA
* *
2380492 TTTTATTATTTAATATCA-TAAATTTAAT-T
1 TTTTATAAATTAATAT-ATTAAATTTAATAT
2380521 TTTTATAAATTAATA-ATTAAA-TTAATAT
1 TTTTATAAATTAATATATTAAATTTAATAT
* *
2380549 TATT-TAATTTAATAATATTAAATTTAATAT
1 TTTTATAAATTAAT-ATATTAAATTTAATAT
2380579 TTTTA-AAA-TAATATA-TAAATATTAAT
1 TTTTATAAATTAATATATTAAAT-TTAAT
2380605 TAATAAATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
27 19 0.27
28 17 0.24
29 23 0.32
30 12 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTTATAAATTAATATATTAAATTTAATAT
Found at i:2380578 original size:12 final size:11
Alignment explanation
Indices: 2380526--2380579 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 11
2380516 TAATTTTTTA
2380526 TAAATTAATAAT
1 TAAATTAAT-AT
2380538 TAAATTAATAT
1 TAAATTAATAT
*
2380549 T-ATTTAAT-T
1 TAAATTAATAT
2380558 T-AA-TAATAT
1 TAAATTAATAT
2380567 TAAATTTAATAT
1 TAAA-TTAATAT
2380579 T
1 T
2380580 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 4 0.11
9 5 0.14
10 8 0.22
11 3 0.08
12 16 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAAATTAATAT
Found at i:2380585 original size:15 final size:15
Alignment explanation
Indices: 2380510--2380585 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
2380500 TTTAATATCA
2380510 TAAATTTAAT-TTTT
1 TAAATTTAATATTTT
* *
2380524 TATAAATTAATA--AT
1 TA-AATTTAATATTTT
2380538 TAAA-TTAATATTATT
1 TAAATTTAATATT-TT
* *
2380553 T-AATTTAATAATAT
1 TAAATTTAATATTTT
2380567 TAAATTTAATATTTT
1 TAAATTTAATATTTT
2380582 TAAA
1 TAAA
2380586 ATAATATATA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
12 6 0.12
13 2 0.04
14 9 0.19
15 31 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATTTAATATTTT
Found at i:2381040 original size:31 final size:31
Alignment explanation
Indices: 2381000--2381059 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
2380990 TGCTATGGTC
*
2381000 TAATATATTAT-AAATTAATGATTTATTTTATA
1 TAATATATTATCAAA-TAATAATTT-TTTTATA
2381032 TAAT-TATTATCAAATAATAATTTTTTTA
1 TAATATATTATCAAATAATAATTTTTTTA
2381060 AAATTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.19
31 14 0.54
32 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (31 bp):
TAATATATTATCAAATAATAATTTTTTTATA
Found at i:2381159 original size:8 final size:8
Alignment explanation
Indices: 2381125--2381162 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2381115 TTTTAATTTT
2381125 AATTATAA
1 AATTATAA
2381133 AATTA-AA
1 AATTATAA
*
2381140 AATTTTTAA
1 AA-TTATAA
2381149 AATTATAA
1 AATTATAA
2381157 AATTAT
1 AATTAT
2381163 CTTATTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 4 0.15
8 18 0.69
9 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
AATTATAA
Found at i:2385288 original size:4 final size:4
Alignment explanation
Indices: 2385279--2385321 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
2385269 CTGGCAGGAT
* * * *
2385279 ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2385322 TGAACATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (4 bp):
ATAC
Found at i:2385330 original size:28 final size:28
Alignment explanation
Indices: 2385277--2385330 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2385267 TGCTGGCAGG
*
2385277 ATATACATACATACATATATATATATAT
1 ATATACATACATACATATATACATATAT
2385305 ATATACATACATACATATGA-ACATAT
1 ATATACATACATACATAT-ATACATAT
2385331 CGTCAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (28 bp):
ATATACATACATACATATATACATATAT
Found at i:2407748 original size:18 final size:17
Alignment explanation
Indices: 2407734--2407767 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2407724 GTTTTTTATA
2407734 TTAAATAATTATTTTAAT
1 TTAAA-AATTATTTTAAT
*
2407752 TTAAAATTTATTTTAA
1 TTAAAAATTATTTTAA
2407768 AATTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAAATTATTTTAAT
Found at i:2407766 original size:12 final size:12
Alignment explanation
Indices: 2407746--2407780 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
2407736 AAATAATTAT
*
2407746 TTTAATTTAAAA
1 TTTATTTTAAAA
2407758 TTTATTTTAAAA
1 TTTATTTTAAAA
2407770 -TTATTTTAAAA
1 TTTATTTTAAAA
2407781 AATTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTATTTTAAAA
Found at i:2408060 original size:15 final size:15
Alignment explanation
Indices: 2408024--2408056 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2408014 TTACAGATCT
2408024 TTTGATTTTGTTTGA
1 TTTGATTTTGTTTGA
*
2408039 TTTGATTTT-TTTTA
1 TTTGATTTTGTTTGA
2408053 TTTG
1 TTTG
2408057 GATTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.73
Consensus pattern (15 bp):
TTTGATTTTGTTTGA
Found at i:2415237 original size:2 final size:2
Alignment explanation
Indices: 2415230--2415262 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2415220 ACAAAATTTA
2415230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2415263 ATAGAAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2416973 original size:29 final size:28
Alignment explanation
Indices: 2416940--2416998 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
2416930 AAAAGTAATC
*
2416940 TATTA-TATTTAAATAAATCTTTATATTTT
1 TATTATTA-TTAAATAAATCATTAT-TTTT
*
2416969 TATTATTATTAAATCAATCATTATTTTT
1 TATTATTATTAAATAAATCATTATTTTT
2416997 TA
1 TA
2416999 ATTAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 19 0.70
30 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTATTATTAAATAAATCATTATTTTT
Found at i:2417813 original size:20 final size:18
Alignment explanation
Indices: 2417778--2417814 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
2417768 TTTATATTTT
2417778 ATTTAAAAAATTTTAATA
1 ATTTAAAAAATTTTAATA
2417796 ATTTAAAATAACTTTTAAT
1 ATTTAAAA-AA-TTTTAAT
2417815 TGGATACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTAAAAAATTTTAATA
Found at i:2417921 original size:19 final size:19
Alignment explanation
Indices: 2417899--2417950 Score: 50
Period size: 23 Copynumber: 2.5 Consensus size: 19
2417889 AAAATAAAAT
2417899 AAAAAATTAATATAAATTA
1 AAAAAATTAATATAAATTA
* *
2417918 AAAATTTTAATAAATATTAATTA
1 AAAA----AATTAATATAAATTA
2417941 AAAAAATTAA
1 AAAAAATTAA
2417951 AATTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
19 9 0.35
23 17 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATTAATATAAATTA
Found at i:2417930 original size:17 final size:17
Alignment explanation
Indices: 2417890--2417932 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2417880 TATTTATTAA
*
2417890 AAATAAAATAAAAAATT
1 AAATAAATTAAAAAATT
*
2417907 AATATAAATTAAAAATTT
1 AA-ATAAATTAAAAAATT
*
2417925 TAATAAAT
1 AAATAAAT
2417933 ATTAATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAATTAAAAAATT
Found at i:2417950 original size:23 final size:23
Alignment explanation
Indices: 2417907--2417950 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2417897 ATAAAAAATT
**
2417907 AATATAAATTAAAAATTTTAATA
1 AATATAAATTAAAAAAATTAATA
*
2417930 AATATTAATTAAAAAAATTAA
1 AATATAAATTAAAAAAATTAA
2417951 AATTAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATATAAATTAAAAAAATTAATA
Found at i:2417955 original size:19 final size:22
Alignment explanation
Indices: 2417928--2417968 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
2417918 AAAATTTTAA
2417928 TAAATATTAA-TTAA-AAAAAT
1 TAAATATTAATTTAATAAAAAT
2417948 TAAA-ATTAATTTAATAAAAAT
1 TAAATATTAATTTAATAAAAAT
2417969 ACAAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATTAATTTAATAAAAAT
Found at i:2418780 original size:30 final size:30
Alignment explanation
Indices: 2418746--2418813 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
2418736 CACTAATAAT
* *
2418746 ATATAATAATTTTCTCATAAAGGAAACAAC
1 ATATAACAATTTTCTCATAAAAGAAACAAC
* * *
2418776 ATATAACAGTTTTTTCATAAAAGAAACAAT
1 ATATAACAATTTTCTCATAAAAGAAACAAC
2418806 ATATAACA
1 ATATAACA
2418814 TTTATATACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (30 bp):
ATATAACAATTTTCTCATAAAAGAAACAAC
Found at i:2418882 original size:25 final size:23
Alignment explanation
Indices: 2418853--2418898 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2418843 TTATCCCACT
*
2418853 TAGGTTATATATTTTATATTATAGA
1 TAGG-TATA-ATTTTAAATTATAGA
*
2418878 TAGGTCTAATTTTAAATTATA
1 TAGGTATAATTTTAAATTATA
2418899 TTTTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 3 0.16
25 4 0.21
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (23 bp):
TAGGTATAATTTTAAATTATAGA
Found at i:2420005 original size:14 final size:15
Alignment explanation
Indices: 2419983--2420076 Score: 68
Period size: 15 Copynumber: 6.1 Consensus size: 15
2419973 AAATGTTTAA
*
2419983 ATATAATATATAATT
1 ATATAATATATAAAT
2419998 AT-TAATATATAAAT
1 ATATAATATATAAAT
* *
2420012 ATATAATATTTTTAA-
1 ATATAATA-TATAAAT
*
2420027 ATATAAT-TATAATAC
1 ATATAATATATAA-AT
*
2420042 ATAAAATATATTAATAT
1 ATATAATATA-TAA-AT
2420059 AATATAAATATATAAAT
1 -ATAT-AATATATAAAT
2420076 A
1 A
2420077 ATTAAATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
13 3 0.05
14 14 0.22
15 20 0.32
16 7 0.11
17 7 0.11
18 6 0.10
19 6 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAATATATAAAT
Found at i:2420006 original size:45 final size:43
Alignment explanation
Indices: 2419956--2420039 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 43
2419946 AAATGATATA
*
2419956 AATATATAAATTTATCAAAATGTTTAAATATAATATATAATTATT
1 AATATATAAATATAT-AAAATGTTTAAATATAAT-TATAATTATT
* *
2420001 AATATATAAATATATAATATTTTTAAATATAATTATAAT
1 AATATATAAATATATAAAATGTTTAAATATAATTATAAT
2420040 ACATAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 6 0.17
44 16 0.44
45 14 0.39
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (43 bp):
AATATATAAATATATAAAATGTTTAAATATAATTATAATTATT
Found at i:2420014 original size:8 final size:8
Alignment explanation
Indices: 2419935--2420076 Score: 69
Period size: 8 Copynumber: 16.9 Consensus size: 8
2419925 CAAAATAAAA
*
2419935 ATAAATAA
1 ATAAATAT
2419943 ATAAAATGAT
1 AT-AAAT-AT
2419953 ATAAATAT
1 ATAAATAT
*
2419961 ATAAATTT
1 ATAAATAT
2419969 ATCAAA-AT
1 AT-AAATAT
* *
2419977 GTTTAA-AT
1 -ATAAATAT
2419985 AT-AATAT
1 ATAAATAT
2419992 AT-AAT-T
1 ATAAATAT
*
2419998 ATTAATAT
1 ATAAATAT
2420006 ATAAATAT
1 ATAAATAT
*
2420014 ATAATATTT
1 ATAA-ATAT
*
2420023 TTAAATAT
1 ATAAATAT
*
2420031 AATTATAATAC
1 -A-TA-AATAT
2420042 ATAAAATAT
1 AT-AAATAT
2420051 ATTAATATAAT
1 A-TAA-AT-AT
2420062 ATAAATAT
1 ATAAATAT
2420070 ATAAATA
1 ATAAATA
2420077 ATTAAATTTA
Statistics
Matches: 106, Mismatches: 13, Indels: 30
0.71 0.09 0.20
Matches are distributed among these distances:
6 5 0.05
7 11 0.10
8 42 0.40
9 28 0.26
10 13 0.12
11 7 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (8 bp):
ATAAATAT
Found at i:2420015 original size:22 final size:20
Alignment explanation
Indices: 2419979--2420080 Score: 77
Period size: 20 Copynumber: 5.0 Consensus size: 20
2419969 ATCAAAATGT
2419979 TTAAATATAATATATAATTA
1 TTAAATATAATATATAATTA
*
2419999 TTAATATATAAATATATAATATTT
1 TTAA-ATAT-AATATAT-A-ATTA
*
2420023 TTAAATATAAT-TATAATACA
1 TTAAATATAATATATAAT-TA
* *
2420043 TAAAATATATTAATATAA-TA
1 TTAAATATAAT-ATATAATTA
*
2420063 -TAAATAT-ATAAATAATTA
1 TTAAATATAATATATAATTA
2420081 AATTTATTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
17 5 0.08
18 3 0.05
19 8 0.12
20 15 0.23
21 7 0.11
22 15 0.23
23 5 0.08
24 7 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAATATAATATATAATTA
Found at i:2420050 original size:45 final size:45
Alignment explanation
Indices: 2419953--2420059 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
2419943 ATAAAATGAT
* *
2419953 ATAAATATATAAATTTATCAAAATGTTTAAATATAATATATAATT
1 ATAAATATATAAATATATCAAAATGTTTAAATATAATATATAATC
* * *
2419998 ATTAATATATAAATATAT-AATATTTTTAAATATAAT-TATAATAC
1 ATAAATATATAAATATATCAAAATGTTTAAATATAATATATAAT-C
*
2420042 ATAAAATATATTAATATA
1 AT-AAATATATAAATATA
2420060 ATATAAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 6 0.11
44 18 0.34
45 29 0.55
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (45 bp):
ATAAATATATAAATATATCAAAATGTTTAAATATAATATATAATC
Found at i:2420057 original size:28 final size:26
Alignment explanation
Indices: 2420026--2420081 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
2420016 AATATTTTTA
2420026 AATATAATTATAATACATA-AAATATATT
1 AATATAA-TATAA-ACATATAAATA-ATT
*
2420054 AATATAATATAAATATATAAATAATT
1 AATATAATATAAACATATAAATAATT
2420080 AA
1 AA
2420082 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.35
27 10 0.38
28 7 0.27
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATAATATAAACATATAAATAATT
Found at i:2423105 original size:19 final size:21
Alignment explanation
Indices: 2423057--2423105 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
2423047 AAATTATTTC
2423057 ATAATATATGTATTAAAACAT
1 ATAATATATGTATTAAAACAT
*
2423078 AGTATATATATTTATT-AAA-AT
1 A-TA-ATATATGTATTAAAACAT
2423099 ATAATAT
1 ATAATAT
2423106 CAATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 4 0.16
20 2 0.08
21 4 0.16
22 5 0.20
23 10 0.40
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
ATAATATATGTATTAAAACAT
Found at i:2423105 original size:21 final size:21
Alignment explanation
Indices: 2423060--2423205 Score: 56
Period size: 23 Copynumber: 6.9 Consensus size: 21
2423050 TTATTTCATA
* *
2423060 ATATATGTATTAAAACATAGTAT
1 ATATATTTATTAAAATATA--AT
2423083 ATATATTTATTAAAATATAAT
1 ATATATTTATTAAAATATAAT
* *
2423104 ATCA-ATTT-TATAAAAAATTAT
1 AT-ATATTTAT-TAAAATATAAT
* * *
2423125 ATAAAATATAATTAAAATAGAAT
1 AT-ATAT-TTATTAAAATATAAT
*
2423148 ATTTATTTAATATAAAA-ATAATT
1 ATATATTT-AT-TAAAATATAA-T
* *
2423171 AAAATATTTAATAAAAT-T-AT
1 -ATATATTTATTAAAATATAAT
2423191 A-A-A-TTATTAAAATAT
1 ATATATTTATTAAAATAT
2423206 TAAAATTTAT
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
16 9 0.09
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 22 0.23
22 16 0.17
23 35 0.37
24 7 0.07
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATATTTATTAAAATATAAT
Found at i:2423141 original size:44 final size:44
Alignment explanation
Indices: 2423091--2423177 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
2423081 ATATATATTT
* * *
2423091 ATTAAAATATAATATCAATTTTATA-AAAAATTATATAAAATATA
1 ATTAAAATAGAATATCAATTTAATATAAAAATAAT-TAAAATATA
**
2423135 ATTAAAATAGAATATTTATTTAATATAAAAATAATTAAAATAT
1 ATTAAAATAGAATATCAATTTAATATAAAAATAATTAAAATAT
2423178 TTAATAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 29 0.78
45 8 0.22
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (44 bp):
ATTAAAATAGAATATCAATTTAATATAAAAATAATTAAAATATA
Found at i:2423176 original size:9 final size:9
Alignment explanation
Indices: 2423162--2423211 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
2423152 ATTTAATATA
2423162 AAAATAATT
1 AAAATAATT
*
2423171 AAAATATTT
1 AAAATAATT
2423180 AATAA-AATT
1 AA-AATAATT
*
2423189 ATAAATTATT
1 A-AAATAATT
2423199 AAAAT-ATT
1 AAAATAATT
2423207 AAAAT
1 AAAAT
2423212 TTATATAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
8 8 0.23
9 20 0.57
10 7 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAATAATT
Found at i:2423310 original size:2 final size:2
Alignment explanation
Indices: 2423303--2423329 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2423293 CAAATCACGC
2423303 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
2423330 CCCCTCCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2424290 original size:42 final size:42
Alignment explanation
Indices: 2424243--2424327 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
2424233 CACGTGCTTG
*
2424243 ACACATATTCGAGTATAGATATTGAAGATACTATACTCGAAT
1 ACACATATTCGAGTATAGATATTGAAGATACTATACTCAAAT
* * * *
2424285 ACACATATTTGGGTATGGATATTGAAGATACTATCCTCAAAT
1 ACACATATTCGAGTATAGATATTGAAGATACTATACTCAAAT
2424327 A
1 A
2424328 TAAGGAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (42 bp):
ACACATATTCGAGTATAGATATTGAAGATACTATACTCAAAT
Found at i:2426020 original size:18 final size:18
Alignment explanation
Indices: 2425972--2426021 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
2425962 AATATATGGT
2425972 TTAAAATTTATAT-AATA
1 TTAAAATTTATATAAATA
2425989 -T-AAA-TTAT-TAAAATA
1 TTAAAATTTATAT-AAATA
2426004 TTAAAATTTATATAAATA
1 TTAAAATTTATATAAATA
2426022 GGAAATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
13 1 0.04
14 4 0.15
15 7 0.26
16 2 0.07
17 3 0.11
18 9 0.33
19 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATTTATATAAATA
Found at i:2433060 original size:22 final size:24
Alignment explanation
Indices: 2433032--2433079 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
2433022 AGAATTTTAA
2433032 TATATTTGT-ATTA-TT-TTTATAT
1 TATATTT-TAATTATTTATTTATAT
2433054 TATATTTTAATTATTTATTTATAT
1 TATATTTTAATTATTTATTTATAT
2433078 TA
1 TA
2433080 AATAATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.04
22 11 0.48
23 2 0.09
24 9 0.39
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATATTTTAATTATTTATTTATAT
Found at i:2433273 original size:22 final size:22
Alignment explanation
Indices: 2433248--2433290 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2433238 AAATGTTTGA
2433248 TTGA-AATATTAATAAATTTAAT
1 TTGAGAATA-TAATAAATTTAAT
* *
2433270 TTGAGCATATAATAACTTTAA
1 TTGAGAATATAATAAATTTAA
2433291 AAGCTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (22 bp):
TTGAGAATATAATAAATTTAAT
Found at i:2433584 original size:23 final size:23
Alignment explanation
Indices: 2433547--2433599 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2433537 ATGCATGATA
* *
2433547 AAATTTTATTTTATTTTATAA-T
1 AAATTTTATTATATTTAATAACT
2433569 AAATTTTATTGATATTTAATAACT
1 AAATTTTATT-ATATTTAATAACT
2433593 AATATTT
1 AA-ATTT
2433600 ATATCAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 9 0.35
24 3 0.12
25 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATTTTATTATATTTAATAACT
Found at i:2433879 original size:14 final size:14
Alignment explanation
Indices: 2433860--2433905 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2433850 ATTATAAAAA
2433860 TAAAAATATTAATT
1 TAAAAATATTAATT
2433874 TAAAAATAATT--TT
1 TAAAAAT-ATTAATT
*
2433887 T-AAAATTTTAATT
1 TAAAAATATTAATT
2433900 TAAAAA
1 TAAAAA
2433906 AATGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
11 2 0.07
12 5 0.19
13 6 0.22
14 11 0.41
15 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAAATATTAATT
Found at i:2433882 original size:26 final size:26
Alignment explanation
Indices: 2433853--2433905 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
2433843 AATTATAATT
2433853 ATAAAAATAAAAATATTAATTTAAAA
1 ATAAAAATAAAAATATTAATTTAAAA
*** * *
2433879 ATAATTTTTAAAATTTTAATTTAAAA
1 ATAAAAATAAAAATATTAATTTAAAA
2433905 A
1 A
2433906 AATGATAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATAAAAATAAAAATATTAATTTAAAA
Found at i:2440657 original size:28 final size:27
Alignment explanation
Indices: 2440624--2440678 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
2440614 TTTTATATTA
2440624 ATATTTATAATTAAATTTAAATAA-AATT
1 ATATTTATAATT--ATTTAAATAATAATT
*
2440652 ATATTTTTAATTATTTAAATAATAATT
1 ATATTTATAATTATTTAAATAATAATT
2440679 TGATTAGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 10 0.40
27 4 0.16
28 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
ATATTTATAATTATTTAAATAATAATT
Found at i:2444980 original size:35 final size:35
Alignment explanation
Indices: 2444912--2444988 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
2444902 AAATAACAAT
* *
2444912 AATAAAAAAATTTATGATGAAAATATCATAAAATTA
1 AATAAAAAAATTTATGATAAAAATATCA-AAAAATA
* * * *
2444948 ATTAAAAAAA-TTATGTTAAAAATTTTAAAAAATA
1 AATAAAAAAATTTATGATAAAAATATCAAAAAATA
2444982 AATAAAA
1 AATAAAA
2444989 TTTATTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
34 12 0.35
35 13 0.38
36 9 0.26
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (35 bp):
AATAAAAAAATTTATGATAAAAATATCAAAAAATA
Found at i:2445025 original size:8 final size:8
Alignment explanation
Indices: 2445000--2445037 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2444990 TTATTAATTT
2445000 TATATAAA
1 TATATAAA
*
2445008 -ATAAAAA
1 TATATAAA
2445015 TATATAAA
1 TATATAAA
2445023 TATATAAA
1 TATATAAA
*
2445031 TAAATAA
1 TATATAA
2445038 GTTATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
TATATAAA
Found at i:2445483 original size:13 final size:13
Alignment explanation
Indices: 2445465--2445491 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2445455 CAAATGTGTC
2445465 ATTATTTTTTTAT
1 ATTATTTTTTTAT
2445478 ATTATTTTTTTAT
1 ATTATTTTTTTAT
2445491 A
1 A
2445492 AAATTTATTT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTATTTTTTTAT
Found at i:2445582 original size:18 final size:17
Alignment explanation
Indices: 2445559--2445593 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2445549 ATTATTCAAT
2445559 ATATATTAAATGAAAATA
1 ATATATTAAAT-AAAATA
2445577 ATATATTAAATAAAATA
1 ATATATTAAATAAAATA
2445594 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
ATATATTAAATAAAATA
Found at i:2445603 original size:16 final size:16
Alignment explanation
Indices: 2445582--2445613 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2445572 AAATAATATA
2445582 TTAAATAAAATATTTT
1 TTAAATAAAATATTTT
*
2445598 TTAAATAATATATTTT
1 TTAAATAAAATATTTT
2445614 ATCGTAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATAAAATATTTT
Found at i:2446232 original size:32 final size:32
Alignment explanation
Indices: 2446196--2446256 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2446186 ATAGTATTAA
2446196 ATAAATATAAAAATAAAATATAAATATATTTC
1 ATAAATATAAAAATAAAATATAAATATATTTC
* * *
2446228 ATAAATATTAAAATAATATATATATATAT
1 ATAAATATAAAAATAAAATATAAATATAT
2446257 ATATATGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (32 bp):
ATAAATATAAAAATAAAATATAAATATATTTC
Found at i:2446405 original size:24 final size:23
Alignment explanation
Indices: 2446353--2446405 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
2446343 TTAATAATTT
*
2446353 TAAATAAAATAAATAAAATATAT
1 TAAATAAAATAAATAAAATATAA
* *
2446376 TTAATAAATTTAAA-AATAATATAA
1 TAAATAAA-ATAAATAA-AATATAA
2446400 TAAATA
1 TAAATA
2446406 TGATAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAATAAAATAAATAAAATATAA
Found at i:2448361 original size:18 final size:21
Alignment explanation
Indices: 2448319--2448360 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2448309 GGTTAAACTT
2448319 AAATTATTATTTATATAATAA
1 AAATTATTATTTATATAATAA
*
2448340 AAATTATT-TTTAT-TTATAA
1 AAATTATTATTTATATAATAA
2448359 AA
1 AA
2448361 TATAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATTATTATTTATATAATAA
Done.