Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 90 of 235
Found at i:31383648 original size:40 final size:40
Alignment explanation
Indices: 31383570--31383753 Score: 248
Period size: 40 Copynumber: 4.5 Consensus size: 40
31383560 ACCCAAGTAT
* *
31383570 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
* **
31383609 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
31383649 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
*
31383689 CTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATGC
31383732 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
31383754 CATCCGAATA
Statistics
Matches: 129, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 12 0.09
40 85 0.66
41 1 0.01
43 31 0.24
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
Found at i:31396301 original size:20 final size:20
Alignment explanation
Indices: 31396278--31396331 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
31396268 ATAACAGAGG
31396278 CACCGAAGTGCAAACAAAGA
1 CACCGAAGTGCAAACAAAGA
* * * *
31396298 CACCAAAGTGTATACAAAGG
1 CACCGAAGTGCAAACAAAGA
*
31396318 CACCGAAGGGCAAA
1 CACCGAAGTGCAAA
31396332 GATAGGCAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.24, G:0.22, T:0.07
Consensus pattern (20 bp):
CACCGAAGTGCAAACAAAGA
Found at i:31398982 original size:24 final size:25
Alignment explanation
Indices: 31398945--31398992 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
31398935 CCTGATAGGC
*
31398945 TCTTTATGAGCTTCCCGA-TATGGT
1 TCTTTATGAACTTCCCGATTATGGT
* *
31398969 TCTTTGTGAACTTCTCGATTATGG
1 TCTTTATGAACTTCCCGATTATGG
31398993 CTCATATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.44
Consensus pattern (25 bp):
TCTTTATGAACTTCCCGATTATGGT
Found at i:31403854 original size:12 final size:12
Alignment explanation
Indices: 31403839--31403877 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
31403829 TTCTTTTTTC
31403839 TTTTTT-TTTAT
1 TTTTTTATTTAT
*
31403850 TTTTTAATTTAT
1 TTTTTTATTTAT
*
31403862 TTATTTATTTAT
1 TTTTTTATTTAT
31403874 TTTT
1 TTTT
31403878 GGTTAAGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:31403993 original size:96 final size:97
Alignment explanation
Indices: 31403869--31404070 Score: 309
Period size: 96 Copynumber: 2.1 Consensus size: 97
31403859 TATTTATTTA
* *
31403869 TTTATTTTTGGTTAAGAATATACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTA-TTTTGCTTAAGAACATACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
*
31403934 CCCCGGTTACTCAGCCCAACATACTCTTAA-TT
65 CCCCGATTACTCAGCCCAACATACTCTTAAGTT
* *
31403966 TTTATTTTGCTTAAGAACATAAC-GAACCTTTTGACGTGAAGAGAGATGACAGCCAAGCACCTCA
1 TTTATTTTGCTTAAGAACAT-ACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCA
*
31404030 CCCCGATTACTCAGCCCAACATATTCTTAAGTTT
65 CCCCGATTACTCAGCCCAACATACTCTTAAG-TT
31404064 TTTATTT
1 TTTATTT
31404071 CCGATTAGTG
Statistics
Matches: 96, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
96 81 0.84
97 6 0.06
98 9 0.09
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (97 bp):
TTTATTTTGCTTAAGAACATACTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCAC
CCCGATTACTCAGCCCAACATACTCTTAAGTT
Found at i:31406098 original size:16 final size:16
Alignment explanation
Indices: 31406077--31406111 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31406067 CCGACAAATC
31406077 CTGAAATGCAGAAAAG
1 CTGAAATGCAGAAAAG
*
31406093 CTGAAATGCCGAAAAG
1 CTGAAATGCAGAAAAG
31406109 CTG
1 CTG
31406112 GAAGTTTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (16 bp):
CTGAAATGCAGAAAAG
Found at i:31406361 original size:28 final size:28
Alignment explanation
Indices: 31406328--31406430 Score: 161
Period size: 28 Copynumber: 3.7 Consensus size: 28
31406318 ATTTCATGAC
31406328 TATGAATGTGATTGGGCCTGATTGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
* *
31406356 TATGAAAGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
* *
31406384 TATGAATGTGATTGTGCCCGATTGGCCA
1 TATGAATGTGATTGGGCCTGATTGGCCA
*
31406412 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
31406431 AAAGGGGCCA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATTGGCCA
Found at i:31414032 original size:16 final size:16
Alignment explanation
Indices: 31414011--31414045 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31414001 GCAAATCCCA
* *
31414011 AAATGCCGAAAAGTCG
1 AAATGCCAAAAAGCCG
31414027 AAATGCCAAAAAGCCG
1 AAATGCCAAAAAGCCG
31414043 AAA
1 AAA
31414046 GTTAGGCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.09
Consensus pattern (16 bp):
AAATGCCAAAAAGCCG
Found at i:31415206 original size:16 final size:16
Alignment explanation
Indices: 31415185--31415215 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31415175 CGACAAATCC
31415185 TGAAATGCAGAAAAGT
1 TGAAATGCAGAAAAGT
*
31415201 TGAAATGCCGAAAAG
1 TGAAATGCAGAAAAG
31415216 CTGGAAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.26, T:0.16
Consensus pattern (16 bp):
TGAAATGCAGAAAAGT
Found at i:31415482 original size:28 final size:27
Alignment explanation
Indices: 31415435--31415537 Score: 134
Period size: 28 Copynumber: 3.7 Consensus size: 27
31415425 ATTTCATGAC
31415435 TATGAATGTGATTGGGCCTGACTGGCCA
1 TATGAATGTGATTGGGCCTGA-TGGCCA
* *
31415463 TACGAAAGTGATTGGGCCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGAT-GGCCA
* *
31415491 TATGAATGTGATTGTGCCCGATTGGCCA
1 TATGAATGTGATTGGGCCTGA-TGGCCA
*
31415519 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
31415538 AAAGGGGCCA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 1 0.02
28 62 0.97
29 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (27 bp):
TATGAATGTGATTGGGCCTGATGGCCA
Found at i:31416826 original size:17 final size:18
Alignment explanation
Indices: 31416793--31416826 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31416783 TTCAAAGAAG
31416793 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
31416811 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
31416827 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:31417271 original size:25 final size:28
Alignment explanation
Indices: 31417246--31417323 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 28
31417236 CCCAAACAAA
31417246 ATAAAGTAATAAAT-AAT-AA-AATAAA
1 ATAAAGTAATAAATAAATAAATAATAAA
*
31417271 ATAAAGTAATGAATAAATAAATAATAAA
1 ATAAAGTAATAAATAAATAAATAATAAA
*
31417299 ATAAAG--A-AAATAAAGAAA-AATAAA
1 ATAAAGTAATAAATAAATAAATAATAAA
31417323 A
1 A
31417324 ATTGGGTTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 7 0.15
25 22 0.47
26 4 0.09
27 2 0.04
28 12 0.26
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (28 bp):
ATAAAGTAATAAATAAATAAATAATAAA
Found at i:31417290 original size:16 final size:15
Alignment explanation
Indices: 31417253--31417322 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 15
31417243 AAAATAAAGT
*
31417253 AATAAATAATAAAATAA
1 AATAAATAAT-GAAT-A
31417270 AATAAAGTAATGAATA
1 AATAAA-TAATGAATA
*
31417286 AATAAATAATAAAATA
1 AATAAATAAT-GAATA
* *
31417302 AAGAAAATAAAGAA-A
1 AA-TAAATAATGAATA
31417317 AATAAA
1 AATAAA
31417323 AATTGGGTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 3 0.07
15 7 0.16
16 15 0.34
17 15 0.34
18 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (15 bp):
AATAAATAATGAATA
Found at i:31420992 original size:20 final size:20
Alignment explanation
Indices: 31420969--31421028 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
31420959 TTAAATTCTA
31420969 AAAGATAAATACAA-ATAAAT
1 AAAGATAAATA-AATATAAAT
* *
31420989 AAAGATAATTAAATATAATT
1 AAAGATAAATAAATATAAAT
31421009 AAAGATAAATGAAAT-TAAAT
1 AAAGATAAAT-AAATATAAAT
31421029 CTTAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 28 0.82
21 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAATATAAAT
Found at i:31420996 original size:10 final size:10
Alignment explanation
Indices: 31420969--31421018 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
31420959 TTAAATTCTA
31420969 AAAGATAAAT
1 AAAGATAAAT
31420979 ACAA-ATAAAT
1 A-AAGATAAAT
*
31420989 AAAGATAATT
1 AAAGATAAAT
* *
31420999 AAATATAATT
1 AAAGATAAAT
31421009 AAAGATAAAT
1 AAAGATAAAT
31421019 GAAATTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:31424380 original size:20 final size:19
Alignment explanation
Indices: 31424355--31424424 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
31424345 CTCTCAACAA
31424355 AAAAATACAAAATAATTTT
1 AAAAATACAAAATAATTTT
*
31424374 CAAAAATTCAAAATAAATTTT
1 -AAAAATACAAAAT-AATTTT
*
31424395 -AAAATTCAAAAT-ATTTAT
1 AAAAATACAAAATAATTT-T
31424413 AAAAATTACAAA
1 AAAAA-TACAAA
31424425 TATATATCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 16 0.36
20 17 0.39
21 6 0.14
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATACAAAATAATTTT
Found at i:31424400 original size:19 final size:20
Alignment explanation
Indices: 31424355--31424424 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 20
31424345 CTCTCAACAA
*
31424355 AAAAATACAAAAT-AATTTT
1 AAAAATTCAAAATAAATTTT
31424374 CAAAAATTCAAAATAAATTTT
1 -AAAAATTCAAAATAAATTTT
31424395 -AAAATTCAAAAT--ATTTAT
1 AAAAATTCAAAATAAATTT-T
31424413 AAAAATTACAAA
1 AAAAATT-CAAA
31424425 TATATATCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 18 0.40
20 16 0.36
21 6 0.13
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTCAAAATAAATTTT
Found at i:31424436 original size:21 final size:19
Alignment explanation
Indices: 31424375--31424438 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
31424365 AATAATTTTC
* *
31424375 AAAAATTCAAAATAAATTT
1 AAAAATTCAAAATATATAT
* *
31424394 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATATAT
*
31424413 AAAAATTACAAATATATATCT
1 AAAAATT-CAAA-ATATATAT
31424434 AAAAA
1 AAAAA
31424439 AATTATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 21 0.58
20 4 0.11
21 11 0.31
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATATATAT
Found at i:31424437 original size:39 final size:39
Alignment explanation
Indices: 31424356--31424437 Score: 89
Period size: 38 Copynumber: 2.1 Consensus size: 39
31424346 TCTCAACAAA
*
31424356 AAAATACAAAATAATTTTCAAAAATTCAAAATAAATTTT
1 AAAATACAAAATAATTTTCAAAAATTCAAAATAAATTCT
* *
31424395 AAAATTCAAAAT-ATTTAT-AAAAATT-ACAAATATATATCT
1 AAAATACAAAATAATTT-TCAAAAATTCA-AAATAAAT-TCT
31424434 AAAA
1 AAAA
31424438 AAATTATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
37 1 0.03
38 18 0.49
39 18 0.49
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (39 bp):
AAAATACAAAATAATTTTCAAAAATTCAAAATAAATTCT
Found at i:31429368 original size:29 final size:30
Alignment explanation
Indices: 31429309--31429369 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
31429299 AACTTCTGAC
* *
31429309 TTGCAATTTTTTCTTTTTATTAAATTATTT
1 TTGCAATTCTTTCTTTTTATTAAATCATTT
*
31429339 TTGCAAGTTCTTT-TTTTT-TTAAATCCTTT
1 TTGCAA-TTCTTTCTTTTTATTAAATCATTT
31429368 TT
1 TT
31429370 CCCTCCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.66
Consensus pattern (30 bp):
TTGCAATTCTTTCTTTTTATTAAATCATTT
Found at i:31431135 original size:16 final size:16
Alignment explanation
Indices: 31431114--31431149 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31431104 TAAGAGTTTC
31431114 TATTGGCTGGAATCTG
1 TATTGGCTGGAATCTG
31431130 TATTGGCTGGAATCTG
1 TATTGGCTGGAATCTG
31431146 TATT
1 TATT
31431150 TTCAAGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (16 bp):
TATTGGCTGGAATCTG
Found at i:31436340 original size:39 final size:39
Alignment explanation
Indices: 31436283--31436377 Score: 145
Period size: 39 Copynumber: 2.4 Consensus size: 39
31436273 CACGGCTCGA
* * *
31436283 AAGTGCTATCAGGAGTACCGAAGTACAATAGGGGCACGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
*
31436322 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCATGT
1 AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
*
31436361 AAGTGCGATTAGGGGTA
1 AAGTGCGATCAGGGGTA
31436378 TAATTATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.18
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTACCGAAGTACAACAGGGGCACGT
Found at i:31436345 original size:20 final size:20
Alignment explanation
Indices: 31436283--31436355 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
31436273 CACGGCTCGA
* *
31436283 AAGTGCTATCAGGAGTACCG
1 AAGTGCAATCAGGGGTACCG
* *
31436303 AAGTACAAT-AGGGGCA-CG
1 AAGTGCAATCAGGGGTACCG
*
31436321 TAAGTGCGATCAGGGGTACCG
1 -AAGTGCAATCAGGGGTACCG
*
31436342 AAGTACAA-CAGGGG
1 AAGTGCAATCAGGGG
31436356 CATGTAAGTG
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
18 2 0.05
19 18 0.44
20 19 0.46
21 2 0.05
ACGTcount: A:0.33, C:0.18, G:0.34, T:0.15
Consensus pattern (20 bp):
AAGTGCAATCAGGGGTACCG
Found at i:31436355 original size:19 final size:19
Alignment explanation
Indices: 31436292--31436355 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
31436282 AAAGTGCTAT
*
31436292 CAGGAGTACCGAAGTACAA
1 CAGGGGTACCGAAGTACAA
* * * *
31436311 TAGGGGCA-CGTAAGTGCGAT
1 CAGGGGTACCG-AAGTAC-AA
31436331 CAGGGGTACCGAAGTACAA
1 CAGGGGTACCGAAGTACAA
31436350 CAGGGG
1 CAGGGG
31436356 CATGTAAGTG
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 2 0.06
19 17 0.52
20 12 0.36
21 2 0.06
ACGTcount: A:0.33, C:0.19, G:0.36, T:0.12
Consensus pattern (19 bp):
CAGGGGTACCGAAGTACAA
Found at i:31440013 original size:23 final size:23
Alignment explanation
Indices: 31439970--31440071 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
31439960 GCTTACCTAA
*
31439970 GAGCTTACTATTCTCAGCTCGTAT
1 GAGCTTACTGTT-TCAGCTCGTAT
31439994 GAGCTTACTGTTTCAGCTCGTAT
1 GAGCTTACTGTTTCAGCTCGTAT
*
31440017 GAGCATACTGTTTCAGCTCGTCA-
1 GAGCTTACTGTTTCAGCTCGT-AT
* * * *
31440040 AAGTTTACCGTTTCAGCTC-AAT
1 GAGCTTACTGTTTCAGCTCGTAT
31440062 AGAGCTTACT
1 -GAGCTTACT
31440072 ATCCATCAGC
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
23 52 0.80
24 12 0.18
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (23 bp):
GAGCTTACTGTTTCAGCTCGTAT
Found at i:31447916 original size:43 final size:43
Alignment explanation
Indices: 31447855--31447998 Score: 207
Period size: 43 Copynumber: 3.3 Consensus size: 43
31447845 ATAAACTCGC
* *
31447855 ACACTTAGTGCTAATTAATTAACCGAAGCTATAATTGTATCGA
1 ACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGA
* * *
31447898 ACACTTAGTGCCAATTAATTAGCCGTAGATATAATTGTATCGC
1 ACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGA
* * * *
31447941 ACACTTAGTTCCAATTAATTAGCCGAAGCTATAGTTTTATCGT
1 ACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGA
31447984 ACACTTAGTGCCAAT
1 ACACTTAGTGCCAAT
31447999 AGTTTAAACC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (43 bp):
ACACTTAGTGCCAATTAATTAGCCGAAGCTATAATTGTATCGA
Found at i:31451239 original size:40 final size:40
Alignment explanation
Indices: 31451041--31451258 Score: 332
Period size: 40 Copynumber: 5.5 Consensus size: 40
31451031 NNNNNNNNNN
* *
31451041 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
31451081 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
31451121 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
31451161 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
31451201 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
31451241 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
31451259 TACTTGGTTT
Statistics
Matches: 170, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 16 0.09
40 154 0.91
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:31458208 original size:27 final size:27
Alignment explanation
Indices: 31458172--31458295 Score: 185
Period size: 27 Copynumber: 4.6 Consensus size: 27
31458162 GGGACAAAAT
31458172 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
31458199 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
31458226 AATGACCGAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * * * *
31458253 AATAACTGTAATACCCTCGTAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
31458280 AATGACTGTAATACCC
1 AATGACCGAAATACCC
31458296 ATGTAAGGTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 91 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (27 bp):
AATGACCGAAATACCCCCATAGGGTAA
Found at i:31458313 original size:27 final size:27
Alignment explanation
Indices: 31458194--31458313 Score: 82
Period size: 27 Copynumber: 4.4 Consensus size: 27
31458184 ACCCCCATAG
* * * * * *
31458194 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAAAGACTGTAATACCCTCGTAA
* * * * * *
31458221 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAAAGACTGTAATACCCTCGTAA
*
31458248 GGTAAAATA-ACTGTAATACCCTCGTAG
1 GGTAAAA-AGACTGTAATACCCTCGTAA
*
31458275 GGTAAAATGACTGTAATACCCAT-GTAA
1 GGTAAAAAGACTGTAATACCC-TCGTAA
31458302 GGTAAAAAGACT
1 GGTAAAAAGACT
31458314 ATTTTACCCT
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
27 81 0.99
28 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (27 bp):
GGTAAAAAGACTGTAATACCCTCGTAA
Found at i:31458334 original size:27 final size:27
Alignment explanation
Indices: 31458304--31458490 Score: 193
Period size: 27 Copynumber: 6.9 Consensus size: 27
31458294 CCATGTAAGG
* * *
31458304 TAAAAAGACTATTTTACCCTTATGTGT
1 TAAAATGACTATTTTGCCCTTATGTGA
*
31458331 TAAAATGA-TAATTTTTCCCTTATGTGA
1 TAAAATGACT-ATTTTGCCCTTATGTGA
* *
31458358 TAAAATGACAATTTTGCCCTTATATGGA
1 TAAAATGACTATTTTGCCCTTATGT-GA
*
31458386 -AAAATGACTGTTTTGCCCTTATGTGA
1 TAAAATGACTATTTTGCCCTTATGTGA
*
31458412 TAAAATGAC-AGTTTTGCCCTTATGTGG
1 TAAAATGACTA-TTTTGCCCTTATGTGA
* * *
31458439 TAAAATGA-TGGTTTTGCCCTTATGAGG
1 TAAAATGACT-ATTTTGCCCTTATGTGA
* *
31458466 TAAAATTATTATTTTGCCCTTATGT
1 TAAAATGACTATTTTGCCCTTATGT
31458491 AGTAGGATAA
Statistics
Matches: 136, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
26 3 0.02
27 130 0.96
28 3 0.02
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGA
Found at i:31458362 original size:54 final size:53
Alignment explanation
Indices: 31458304--31458520 Score: 229
Period size: 54 Copynumber: 4.0 Consensus size: 53
31458294 CCATGTAAGG
* * * * *
31458304 TAAAAAGACTATTTTACCCTTATGTGTTAAAATGATAATTTTTCCCTTATGTGA
1 TAAAATGACTATTTTGCCCTTATGTGGTAAAATGAT-GTTTTGCCCTTATGTGA
* * *
31458358 TAAAATGACAATTTTGCCCTTATATGGAAAAATGACTGTTTTGCCCTTATGTGA
1 TAAAATGACTATTTTGCCCTTATGTGGTAAAATGA-TGTTTTGCCCTTATGTGA
* *
31458412 TAAAATGAC-AGTTTTGCCCTTATGTGGTAAAATGATGGTTTTGCCCTTATGAGG
1 TAAAATGACTA-TTTTGCCCTTATGTGGTAAAATGAT-GTTTTGCCCTTATGTGA
* * * ** * *
31458466 TAAAATTATTATTTTGCCCTTATGTAGTAGGATAACTGTTTTGCCCCTATGTGA
1 TAAAATGACTATTTTGCCCTTATGTGGTAAAATGA-TGTTTTGCCCTTATGTGA
31458520 T
1 T
31458521 GCATGTGATG
Statistics
Matches: 137, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.01
54 132 0.96
55 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (53 bp):
TAAAATGACTATTTTGCCCTTATGTGGTAAAATGATGTTTTGCCCTTATGTGA
Found at i:31458362 original size:81 final size:81
Alignment explanation
Indices: 31458277--31458446 Score: 189
Period size: 81 Copynumber: 2.1 Consensus size: 81
31458267 CCTCGTAGGG
** * * *
31458277 TAAAATGACTGTAATACCCATGTAAGGTAAAAA-GACTATTTTACCCTTATGTGTTAAAATGATA
1 TAAAATGACAATAATACCCATATAAGG-AAAAATGACTATTTTACCCTTATGTGATAAAATGACA
*
31458341 ATTTTTCCCTTATGTGA
65 ATTTTGCCCTTATGTGA
** * * * * * *
31458358 TAAAATGACAATTTTGCCCTTATATGGAAAAATGACTGTTTTGCCCTTATGTGATAAAATGACAG
1 TAAAATGACAATAATACCCATATAAGGAAAAATGACTATTTTACCCTTATGTGATAAAATGACAA
*
31458423 TTTTGCCCTTATGTGG
66 TTTTGCCCTTATGTGA
31458439 TAAAATGA
1 TAAAATGA
31458447 TGGTTTTGCC
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
80 5 0.07
81 68 0.93
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (81 bp):
TAAAATGACAATAATACCCATATAAGGAAAAATGACTATTTTACCCTTATGTGATAAAATGACAA
TTTTGCCCTTATGTGA
Found at i:31458455 original size:81 final size:81
Alignment explanation
Indices: 31458305--31458490 Score: 232
Period size: 81 Copynumber: 2.3 Consensus size: 81
31458295 CATGTAAGGT
* * * *
31458305 AAAAA-GACTATTTTACCCTTATGTGTTAAAATGATAATTTTTCCCTTATGTGATAAAATGACAA
1 AAAAATGACTATTTTGCCCTTATGTGATAAAATGACAATTTTGCCCTTATGTGATAAAATGACAA
31458369 TTTTGCCCTTAT-ATGG
66 TTTTGCCCTTATGA-GG
* * * ***
31458385 AAAAATGACTGTTTTGCCCTTATGTGATAAAATGACAGTTTTGCCCTTATGTGGTAAAATGATGG
1 AAAAATGACTATTTTGCCCTTATGTGATAAAATGACAATTTTGCCCTTATGTGATAAAATGACAA
31458450 TTTTGCCCTTATGAGG
66 TTTTGCCCTTATGAGG
* * *
31458466 TAAAATTATTATTTTGCCCTTATGT
1 AAAAATGACTATTTTGCCCTTATGT
31458491 AGTAGGATAA
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 5 0.06
81 84 0.93
82 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (81 bp):
AAAAATGACTATTTTGCCCTTATGTGATAAAATGACAATTTTGCCCTTATGTGATAAAATGACAA
TTTTGCCCTTATGAGG
Found at i:31458507 original size:27 final size:27
Alignment explanation
Indices: 31458303--31458517 Score: 163
Period size: 27 Copynumber: 8.0 Consensus size: 27
31458293 CCCATGTAAG
* * *
31458303 GTAAAAAGACTATTTTACCCTTATGT-
1 GTAAAATGACTGTTTTGCCCTTATGTA
* *
31458329 GTTAAAATGA-TAATTTTTCCCTTATGT-
1 G-TAAAATGACT-GTTTTGCCCTTATGTA
** * *
31458356 GATAAAATGACAATTTTGCCCTTATATG
1 G-TAAAATGACTGTTTTGCCCTTATGTA
*
31458384 GAAAAATGACTGTTTTGCCCTTATGT-
1 GTAAAATGACTGTTTTGCCCTTATGTA
* *
31458410 GATAAAATGACAGTTTTGCCCTTATGTG
1 G-TAAAATGACTGTTTTGCCCTTATGTA
31458438 GTAAAATGA-TGGTTTTGCCCTTATG-A
1 GTAAAATGACT-GTTTTGCCCTTATGTA
* * *
31458464 GGTAAAATTATTATTTTGCCCTTATGTA
1 -GTAAAATGACTGTTTTGCCCTTATGTA
** * *
31458492 GTAGGATAACTGTTTTGCCCCTATGT
1 GTAAAATGACTGTTTTGCCCTTATGT
31458518 GATGCATGTG
Statistics
Matches: 157, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
26 3 0.02
27 150 0.96
28 4 0.03
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (27 bp):
GTAAAATGACTGTTTTGCCCTTATGTA
Found at i:31458507 original size:81 final size:81
Alignment explanation
Indices: 31458305--31458520 Score: 222
Period size: 81 Copynumber: 2.7 Consensus size: 81
31458295 CATGTAAGGT
* * * * * *
31458305 AAAAA-GACTATTTTACCCTTATGTGTTAAAATGATAATTTTTCCCTTATGTGATAAAATGACAA
1 AAAAATGACTATTTTGCCCTTATGTGATAAAATAACAGTTTTGCCCTTATGTGATAAAATGACAA
31458369 TTTTGCCCTTATATGG
66 TTTTGCCCTTATATGG
* * * ***
31458385 AAAAATGACTGTTTTGCCCTTATGTGATAAAATGACAGTTTTGCCCTTATGTGGTAAAATGATGG
1 AAAAATGACTATTTTGCCCTTATGTGATAAAATAACAGTTTTGCCCTTATGTGATAAAATGACAA
31458450 TTTTGCCCTTATGA-GG
66 TTTTGCCCTTAT-ATGG
* * * ** * *
31458466 TAAAATTATTATTTTGCCCTTATGT-AGTAGGATAACTGTTTTGCCCCTATGTGAT
1 AAAAATGACTATTTTGCCCTTATGTGA-TAAAATAACAGTTTTGCCCTTATGTGAT
31458521 GCATGTGATG
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
80 6 0.05
81 106 0.94
82 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (81 bp):
AAAAATGACTATTTTGCCCTTATGTGATAAAATAACAGTTTTGCCCTTATGTGATAAAATGACAA
TTTTGCCCTTATATGG
Found at i:31458896 original size:18 final size:18
Alignment explanation
Indices: 31458851--31458889 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31458841 GGACTGGCAT
* *
31458851 ACTGCTTACTGTTACTGC
1 ACTGATTACTGTTACTAC
31458869 ACTGATTACTGTTACTAC
1 ACTGATTACTGTTACTAC
31458887 ACT
1 ACT
31458890 ATTTACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (18 bp):
ACTGATTACTGTTACTAC
Found at i:31461026 original size:19 final size:18
Alignment explanation
Indices: 31460997--31461033 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
31460987 GTCTCTCGGG
31460997 CTTTTTTTTACTCATTTT
1 CTTTTTTTTACTCATTTT
*
31461015 CTTTTTTATTACTTATTTT
1 CTTTTTT-TTACTCATTTT
31461034 GATTTGCGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (18 bp):
CTTTTTTTTACTCATTTT
Found at i:31461940 original size:27 final size:27
Alignment explanation
Indices: 31461904--31462068 Score: 186
Period size: 27 Copynumber: 6.1 Consensus size: 27
31461894 TGGGAAAAAT
* *
31461904 AATGACCAAAATACCCCAATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* ** *
31461931 AATGACCAAAATATTCCCATTGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * * *
31461958 AATAACTGAAATACCCCTATAGGGCAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
31461985 AATGACTGAAATACCCCCATAAGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
31462012 AATGACCGAAATACCCCCATAAGGCAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
31462039 AATAACCTAAATACCCCCATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
31462066 AAT
1 AAT
31462069 AACTGTAATA
Statistics
Matches: 116, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 116 1.00
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (27 bp):
AATGACCGAAATACCCCCATAGGGTAA
Found at i:31462093 original size:81 final size:81
Alignment explanation
Indices: 31461912--31462080 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 81
31461902 ATAATGACCA
* * ** ** * *
31461912 AAATACCCCAATAGGGTAAAATGACCAAAATATTCCCATTGGGTAAAATAACTGAAATACCCCTA
1 AAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAAGGCAAAATAACTGAAATACCCCCA
*
31461977 TAGGGCAAAATGACTG
66 TAGGGCAAAATAACTG
*
31461993 AAATACCCCCATAAGGTAAAATGACCGAAATACCCCCATAAGGCAAAATAACCT-AAATACCCCC
1 AAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAAGGCAAAATAA-CTGAAATACCCCC
*
31462057 ATAGGGTAAAATAACTG
65 ATAGGGCAAAATAACTG
*
31462074 TAATACC
1 AAATACC
31462081 TTTGTAAGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
81 73 0.97
82 2 0.03
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (81 bp):
AAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATAAGGCAAAATAACTGAAATACCCCCA
TAGGGCAAAATAACTG
Found at i:31462102 original size:16 final size:16
Alignment explanation
Indices: 31462083--31462117 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31462073 GTAATACCTT
*
31462083 TGTAAGGTAAAGTGAC
1 TGTAAGGTAAAATGAC
31462099 TGTAAGGTAAAATGAC
1 TGTAAGGTAAAATGAC
31462115 TGT
1 TGT
31462118 TTTGCCCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
TGTAAGGTAAAATGAC
Found at i:31462281 original size:27 final size:27
Alignment explanation
Indices: 31462104--31462319 Score: 204
Period size: 27 Copynumber: 8.0 Consensus size: 27
31462094 GTGACTGTAA
*
31462104 GGTAAAATGACTGTTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
31462131 GGT-AAATGA-TAATTTTGCCCTTATGT
1 GGTAAAATGACT-ATTTTGCCCTTATGT
** ***
31462157 TATAAAATGACGGCTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* * *
31462184 GGAAAAATTACTACTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
** ** *
31462211 TTTAAAATGACGGTTTTTCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* *
31462238 GGTAAAATAAC-AGTTTTGCCCTTATGA
1 GGTAAAATGACTA-TTTTGCCCTTATGT
* *
31462265 GGTAAAATGACTATTTTACACTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* **
31462292 TGTAGGATGACTATTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
31462319 G
1 G
31462320 ATGTATGTTT
Statistics
Matches: 148, Mismatches: 36, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
25 1 0.01
26 21 0.14
27 125 0.84
28 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (27 bp):
GGTAAAATGACTATTTTGCCCTTATGT
Found at i:31463391 original size:154 final size:154
Alignment explanation
Indices: 31463111--31463419 Score: 519
Period size: 154 Copynumber: 2.0 Consensus size: 154
31463101 ATAAACAAGA
31463111 TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACACAAGGTTTAAAATTATTTT
1 TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACACAAGGTTTAAAATTATTTT
* *
31463176 CTAGATCATACAAAGAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTACGAAAAG
66 CTAGATCACACAAAGAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTACGAAAAA
*
31463241 CACTTCAATGTGAGATCGCTAGAT
131 CACTTCAATGTGAGATCGCCAGAT
** *
31463265 TTTTGAAATTAATAATGTTTTAAAGTAAATGCTTTTGATAGTGACGCAAGGTTTAAAATTATTTT
1 TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACACAAGGTTTAAAATTATTTT
* *
31463330 CTAGATCACACAAAGAGGCTAAATAAACATTGGGCTTTTCAAACGATATCATGCTTTACGAAAAA
66 CTAGATCACACAAAGAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTACGAAAAA
* * *
31463395 TACTTCAGTGTGATATCGCCAGAT
131 CACTTCAATGTGAGATCGCCAGAT
31463419 T
1 T
31463420 CGGCCATAGT
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 144 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (154 bp):
TTTTGAAATTAATAACATTTTAAAGTAAATGCTTTTGATAGTGACACAAGGTTTAAAATTATTTT
CTAGATCACACAAAGAGGCTAAATAAACATTCGGCTTTTCAAACAATATCATGCTTTACGAAAAA
CACTTCAATGTGAGATCGCCAGAT
Found at i:31464446 original size:20 final size:20
Alignment explanation
Indices: 31464382--31464447 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31464372 AAGAAAGAAG
*
31464382 GAGCTGAAAGTAAGCTCG-GTT
1 GAGCTCAAA-TAAGCT-GAGTT
** ***
31464403 GAGCTCAAACGAGCTGAAAC
1 GAGCTCAAATAAGCTGAGTT
31464423 GAGCTCAAATAAGCTGAGTT
1 GAGCTCAAATAAGCTGAGTT
31464443 GAGCT
1 GAGCT
31464448 GGACGGAGCT
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
19 1 0.03
20 24 0.73
21 8 0.24
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (20 bp):
GAGCTCAAATAAGCTGAGTT
Found at i:31466059 original size:18 final size:19
Alignment explanation
Indices: 31466036--31466074 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
31466026 TTTATCTCAA
*
31466036 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
31466054 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
31466073 TT
1 TT
31466075 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:31466090 original size:48 final size:49
Alignment explanation
Indices: 31466038--31466141 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 49
31466028 TATCTCAATT
* * *
31466038 TCTTTTTCCACTCT-TTTTTC-TTGTTCACATTCTTTTTCTCTCTCAAAC
1 TCTTTTTCCACTCTCTTTTTCAAT-CTCACATTCTTTTTCACTCTCAAAC
* ** *
31466086 TCTTTTT-CATTCTCTTTTTCAATCTCATTTTCTTTTTCACTCTCAATC
1 TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
31466134 TCTTTTTC
1 TCTTTTTC
31466142 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
47 5 0.11
48 40 0.87
49 1 0.02
ACGTcount: A:0.12, C:0.28, G:0.01, T:0.59
Consensus pattern (49 bp):
TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
Found at i:31466113 original size:18 final size:18
Alignment explanation
Indices: 31466092--31466141 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
31466082 AAACTCTTTT
31466092 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
31466110 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
31466128 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
31466142 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:31466131 original size:24 final size:24
Alignment explanation
Indices: 31466067--31466148 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
31466057 CTTGTTCACA
*
31466067 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
31466091 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
31466115 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
31466139 TTCTTTTTCT
1 TTCTTTTTCT
31466149 TTCATTTCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:31466200 original size:42 final size:42
Alignment explanation
Indices: 31466145--31466241 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
31466135 CTTTTTCTTT
* * *
31466145 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
31466186 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
31466228 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
31466242 CTCATAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:31466219 original size:21 final size:21
Alignment explanation
Indices: 31466152--31466219 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
31466142 TTTTTCTTTC
*
31466152 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
31466173 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
31466193 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
31466215 ATTTC
1 ATTTC
31466220 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:31468688 original size:20 final size:19
Alignment explanation
Indices: 31468636--31468689 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
31468626 GCTGAAAGTA
31468636 AGCTCGGTTGAGCTCAAACG
1 AGCT-GGTTGAGCTCAAACG
** *
31468656 AGCTGGAACGAGCTCAAATG
1 AGCTGG-TTGAGCTCAAACG
31468676 AGCTGAGTTGAGCT
1 AGCTG-GTTGAGCT
31468690 GGACGGAGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.20
Consensus pattern (19 bp):
AGCTGGTTGAGCTCAAACG
Found at i:31471194 original size:27 final size:27
Alignment explanation
Indices: 31471159--31471299 Score: 203
Period size: 27 Copynumber: 5.2 Consensus size: 27
31471149 GAGATAAAAT
31471159 AATGACCGAAATACCTCTATAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
31471186 AATGACCGAAATACCTCTATAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
* *
31471213 AATGACTGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
* *
31471240 AATGATCGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCTCTATAGGGTAA
* * *
31471267 AATGACTGTAATACCAT-TGTAGGGTAA
1 AATGACCGAAATACC-TCTATAGGGTAA
31471294 AATGAC
1 AATGAC
31471300 TGTGGGTAAG
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 104 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (27 bp):
AATGACCGAAATACCTCTATAGGGTAA
Found at i:31471352 original size:27 final size:27
Alignment explanation
Indices: 31471311--31471487 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
31471301 GTGGGTAAGG
31471311 TAAAATGACTGTTTTGCCCTTATGTGT
1 TAAAATGACTGTTTTGCCCTTATGTGT
** *
31471338 TAAAATGACAATTTTTCCCTTATGT-T
1 TAAAATGACTGTTTTGCCCTTATGTGT
* * *
31471364 ATAAAATGACGGCTTTGCCCTTATGTGGC
1 -TAAAATGACTGTTTTGCCCTTATGT-GT
* * *
31471393 AAAAAT-ACTATTTTGCCCTTATGTTT
1 TAAAATGACTGTTTTGCCCTTATGTGT
* *
31471419 TAAAATGACAGTTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCTTATGTGT
* *
31471446 TAAAATGA-TGGTTTTGCCCTTATGAGG
1 TAAAATGACT-GTTTTGCCCTTATGTGT
*
31471473 TAAAATGACTATTTT
1 TAAAATGACTGTTTT
31471488 ACAATTATGT
Statistics
Matches: 122, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
26 6 0.05
27 110 0.90
28 6 0.05
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATGTGT
Found at i:31471496 original size:81 final size:80
Alignment explanation
Indices: 31471308--31471527 Score: 262
Period size: 81 Copynumber: 2.7 Consensus size: 80
31471298 ACTGTGGGTA
* * *
31471308 AGGTAAAATGACTGTTTTGCCCTTATGTGTTAAAATGACAATTTTTCCCTTATGTTATAAAATGA
1 AGGTAAAATGACTATTTTGCCCTTATGTTTTAAAATGAC-ATTTTTCCCTTATGTGATAAAATGA
31471373 CGGCTTTGCCCTTATG
65 CGGCTTTGCCCTTATG
* * * *
31471389 TGGCAAAAAT-ACTATTTTGCCCTTATGTTTTAAAATGACAGTTTTGCCCTTATGTGGTAAAATG
1 AGG-TAAAATGACTATTTTGCCCTTATGTTTTAAAATGACA-TTTTTCCCTTATGTGATAAAATG
* *
31471453 ATGGTTTTGCCCTTATG
64 ACGGCTTTGCCCTTATG
* ** * **
31471470 AGGTAAAATGACTATTTTACAATTATGTTGTAGGATGACTATTTTTCCCTTATGTGAT
1 AGGTAAAATGACTATTTTGCCCTTATGTTTTAAAATGAC-ATTTTTCCCTTATGTGAT
31471528 GTATGTTTAT
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
80 6 0.05
81 104 0.90
82 6 0.05
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (80 bp):
AGGTAAAATGACTATTTTGCCCTTATGTTTTAAAATGACATTTTTCCCTTATGTGATAAAATGAC
GGCTTTGCCCTTATG
Found at i:31471873 original size:18 final size:18
Alignment explanation
Indices: 31471847--31471883 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31471837 GGACTTGCAT
*
31471847 ACTGCTTACTGTTACTGC
1 ACTGCTTACTATTACTGC
*
31471865 ACTGTTTACTATTACTGC
1 ACTGCTTACTATTACTGC
31471883 A
1 A
31471884 ATGGGCCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (18 bp):
ACTGCTTACTATTACTGC
Found at i:31474692 original size:24 final size:23
Alignment explanation
Indices: 31474624--31474739 Score: 121
Period size: 23 Copynumber: 4.9 Consensus size: 23
31474614 GACTCACCGT
*
31474624 AGCTCGTATGAGCTTACTGATATATT
1 AGCTCGTATGAGCTTACTG-T-T-TC
*
31474650 AGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCGTATGAGCTTACTGTT-TC
31474674 AGCTCGTATGAG-TTCACTGTTTC
1 AGCTCGTATGAGCTT-ACTGTTTC
*
31474697 AGCTCGTCA-GAGCTTACCGTTTC
1 AGCTCGT-ATGAGCTTACTGTTTC
31474720 AGCTC-TATAGAGCTTACTGT
1 AGCTCGTAT-GAGCTTACTGT
31474740 CCATCAACTC
Statistics
Matches: 79, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 36 0.46
24 22 0.28
25 1 0.01
26 18 0.23
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (23 bp):
AGCTCGTATGAGCTTACTGTTTC
Found at i:31474709 original size:47 final size:49
Alignment explanation
Indices: 31474624--31474738 Score: 141
Period size: 47 Copynumber: 2.4 Consensus size: 49
31474614 GACTCACCGT
* *
31474624 AGCTCGTATGAGCTTACTGATATATTAGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCGTATGAGCTTACTGATATATCAGCTCGTAAGAGCTTACCGTT-TC
*
31474674 AGCTCGTATGAG-TTCACTG-T-T-TCAGCTCGTCAGAGCTTACCGTTTC
1 AGCTCGTATGAGCTT-ACTGATATATCAGCTCGTAAGAGCTTACCGTTTC
31474720 AGCTC-TATAGAGCTTACTG
1 AGCTCGTAT-GAGCTTACTG
31474739 TCCATCAACT
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
45 3 0.05
46 14 0.24
47 22 0.37
48 1 0.02
49 3 0.05
50 16 0.27
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (49 bp):
AGCTCGTATGAGCTTACTGATATATCAGCTCGTAAGAGCTTACCGTTTC
Found at i:31483395 original size:24 final size:24
Alignment explanation
Indices: 31483363--31483415 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
31483353 AAGTCTGTCA
*
31483363 GGAGAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
*
31483387 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
31483411 GGAGA
1 GGAGA
31483416 ACAGTGTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.32, C:0.02, G:0.43, T:0.23
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:31484901 original size:54 final size:53
Alignment explanation
Indices: 31484809--31484919 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 53
31484799 AGGAAGCGTC
* *
31484809 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTATT
1 CTGGGGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACAT-TATCTATT
* * * *
31484863 CTGGGGGCTCTGCCACGATTATCTGTTCTGGTGACTCTGTCACATTATCTATT
1 CTGGGGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTATT
31484916 CTGG
1 CTGG
31484920 CAGCCATACT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 12 0.24
54 39 0.76
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (53 bp):
CTGGGGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTATT
Found at i:31484917 original size:26 final size:26
Alignment explanation
Indices: 31484809--31484919 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
31484799 AGGAAGCGTC
*
31484809 CTGGTGGCTATGCCACAATTATCTGA-T
1 CTGGTGGCTCTGCCAC-ATTATCT-ATT
31484836 CTGGTGGCTCTGCCACATATATCTATT
1 CTGGTGGCTCTGCCACAT-TATCTATT
* *
31484863 CTGGGGGCTCTGCCACGATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTATT
* *
31484890 CTGGTGACTCTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTATT
31484916 CTGG
1 CTGG
31484920 CAGCCATACT
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.22
27 56 0.76
28 2 0.03
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTATT
Found at i:31486968 original size:28 final size:29
Alignment explanation
Indices: 31486928--31487021 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 29
31486918 ATTGCATGAC
** *
31486928 TATGAATGTGATTGGGGTC-GATGGGCCA
1 TATGAATGTGATTGGGACCTAATGGGCCA
* *
31486956 TATGGATGTGATTTGGACCTAATGGGCCA
1 TATGAATGTGATTGGGACCTAATGGGCCA
* * *
31486985 TATGAATGAGATTGGG-CCTAGTGGCCCA
1 TATGAATGTGATTGGGACCTAATGGGCCA
*
31487013 TATGCATGT
1 TATGAATGT
31487022 ATGTAGACCT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 32 0.60
29 21 0.40
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (29 bp):
TATGAATGTGATTGGGACCTAATGGGCCA
Found at i:31490382 original size:24 final size:24
Alignment explanation
Indices: 31490350--31490398 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
31490340 GATAAATTCG
31490350 AACATGATAAATATATGTATTTTT
1 AACATGATAAATATATGTATTTTT
31490374 AACATGATAAATATATGTATTTTT
1 AACATGATAAATATATGTATTTTT
31490398 A
1 A
31490399 TGTTGCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (24 bp):
AACATGATAAATATATGTATTTTT
Found at i:31493656 original size:21 final size:21
Alignment explanation
Indices: 31493630--31493711 Score: 103
Period size: 21 Copynumber: 3.9 Consensus size: 21
31493620 TCATGCTAAT
*
31493630 AGAAGCTCATAAGAGTTGAAC
1 AGAAGCTCATAAGAGCTGAAC
*
31493651 AGAAGCTCGA-AAGAGCTGAAT
1 AGAAGCTC-ATAAGAGCTGAAC
* * *
31493672 AGAAGCTCGTGAGAGCTAAAC
1 AGAAGCTCATAAGAGCTGAAC
31493693 AGAAGCTCATAAGAGCTGA
1 AGAAGCTCATAAGAGCTGA
31493712 TCCACCAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
21 49 0.98
22 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.16
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:31493694 original size:42 final size:42
Alignment explanation
Indices: 31493627--31493711 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
31493617 AGATCATGCT
* *
31493627 AATAGAAGCTCATAAGAGTTGAACAGAAGCTCGA-AAGAGCTG
1 AATAGAAGCTCATAAGAGCTAAACAGAAGCTC-ATAAGAGCTG
* *
31493669 AATAGAAGCTCGTGAGAGCTAAACAGAAGCTCATAAGAGCTG
1 AATAGAAGCTCATAAGAGCTAAACAGAAGCTCATAAGAGCTG
31493711 A
1 A
31493712 TCCACCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.42, C:0.15, G:0.26, T:0.16
Consensus pattern (42 bp):
AATAGAAGCTCATAAGAGCTAAACAGAAGCTCATAAGAGCTG
Found at i:31496901 original size:13 final size:13
Alignment explanation
Indices: 31496883--31496909 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31496873 GCCCGACAGG
31496883 GACACGCCCGTGT
1 GACACGCCCGTGT
31496896 GACACGCCCGTGT
1 GACACGCCCGTGT
31496909 G
1 G
31496910 CGATTGCTTC
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:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:31501206 original size:49 final size:49
Alignment explanation
Indices: 31501134--31501358 Score: 265
Period size: 49 Copynumber: 4.5 Consensus size: 49
31501124 TGAGGTCACG
31501134 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * *
31501183 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACT--TCGATCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCG--CA
* * * ** * *
31501232 TGCGTGTAGTACTAAGTGTAGGCTACTACGTGCATCAGATGGTTAGGTCACG
1 T--GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCGCA
* *
31501284 TGTGTAGTACTAAGTGCAGTCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
31501333 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
31501359 TGCGTATCAG
Statistics
Matches: 142, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
47 3 0.02
49 70 0.49
50 34 0.24
51 31 0.22
52 2 0.01
54 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:31505870 original size:34 final size:34
Alignment explanation
Indices: 31505824--31505891 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
31505814 AGATTCATAG
31505824 CAGGAATAAGGAGTATAAACTCCTCGAACCACCA
1 CAGGAATAAGGAGTATAAACTCCTCGAACCACCA
*
31505858 CAGGAATGAGGAGTATAAACTCCTCGAACCACCA
1 CAGGAATAAGGAGTATAAACTCCTCGAACCACCA
31505892 TGACCATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (34 bp):
CAGGAATAAGGAGTATAAACTCCTCGAACCACCA
Found at i:31508731 original size:79 final size:80
Alignment explanation
Indices: 31508596--31508819 Score: 289
Period size: 79 Copynumber: 2.8 Consensus size: 80
31508586 TTGAATGATG
* * *
31508596 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGCTAAG-TCCCGAAGGCA
*
31508657 TTTGTGCGAGATACTAAT
63 TTTGTGCGAGATACTAAA
*
31508675 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
31508739 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* * *
31508754 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
31508818 TG
65 TG
31508820 AACGAGGAGC
Statistics
Matches: 129, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
78 10 0.08
79 61 0.47
80 56 0.43
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:31508833 original size:40 final size:40
Alignment explanation
Indices: 31508596--31508819 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
31508586 TTGAATGATG
* *
31508596 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
31508635 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
31508675 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31508714 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
31508754 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31508795 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31508820 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 53 0.32
40 103 0.62
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31508837 original size:80 final size:80
Alignment explanation
Indices: 31508596--31508852 Score: 244
Period size: 79 Copynumber: 3.2 Consensus size: 80
31508586 TTGAATGATG
* * * *
31508596 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAA-ATCCGGGCTAAG-TCCCGAAGGCA
** *
31508657 TTTGTGCGAGAT-ACTAAT
63 TTTGAACGAG-TGACTAAA
* * *
31508675 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
** *
31508739 GTGCGAGTTACTAAA
66 GAACGAGTGACTAAA
*
31508754 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
*
31508818 TGAACGAG-GAGCTATA
65 TGAACGAGTGA-CTAAA
* *
31508834 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
31508853 TACGTGATTT
Statistics
Matches: 154, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
78 11 0.07
79 73 0.47
80 68 0.44
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTGACTAAA
Found at i:31516683 original size:39 final size:40
Alignment explanation
Indices: 31516588--31516849 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
31516578 TTGAATGATG
*
31516588 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
31516626 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
31516667 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
31516706 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31516745 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
31516784 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
31516823 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
31516850 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31518139 original size:24 final size:26
Alignment explanation
Indices: 31518107--31518156 Score: 86
Period size: 24 Copynumber: 2.0 Consensus size: 26
31518097 TATTACGCAG
31518107 ATTGGCAGTGTCT-GGAAA-ATTTTT
1 ATTGGCAGTGTCTGGGAAATATTTTT
31518131 ATTGGCAGTGTCTGGGAAATATTTTT
1 ATTGGCAGTGTCTGGGAAATATTTTT
31518157 TATAAGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 13 0.54
25 5 0.21
26 6 0.25
ACGTcount: A:0.24, C:0.08, G:0.26, T:0.42
Consensus pattern (26 bp):
ATTGGCAGTGTCTGGGAAATATTTTT
Found at i:31526380 original size:22 final size:22
Alignment explanation
Indices: 31526352--31526394 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
31526342 CGTTGGGACG
31526352 AAATACAAGGCATTATCTAACA
1 AAATACAAGGCATTATCTAACA
31526374 AAATACAAGGCATTATCTAAC
1 AAATACAAGGCATTATCTAAC
31526395 CTTAAACTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (22 bp):
AAATACAAGGCATTATCTAACA
Found at i:31526595 original size:20 final size:21
Alignment explanation
Indices: 31526570--31526611 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31526560 TCTTTAAAAC
*
31526570 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCATGTGGA
31526590 AGGGCAACACGCCCATGTGGA
1 AGGGCAACACGCCCATGTGGA
31526611 A
1 A
31526612 TTAATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.26, C:0.29, G:0.36, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCATGTGGA
Found at i:31527856 original size:46 final size:45
Alignment explanation
Indices: 31527787--31527942 Score: 141
Period size: 46 Copynumber: 3.4 Consensus size: 45
31527777 ATGTCTCATG
* * * *
31527787 CATGTCTTACACTAGCTTACGTCTTGAGGCCGAAGCATGTCCTAGA
1 CATGTCTTACACTAGCCT-CGTCTTGACGTCGATGCATGTCCTAGA
** * *
31527833 CATGTCTTACACTAGCACTCGTCTCAATGTCGATGCCATGTCCCAGA
1 CATGTCTTACACTAGC-CTCGTCTTGACGTCGATG-CATGTCCTAGA
* **** *
31527880 CATGGTCTTATACTAGCTCTCAAAATGTCGTCGATGCATGTCCTAGA
1 CAT-GTCTTACACTAGC-CTCGTCTTGACGTCGATGCATGTCCTAGA
31527927 CATGTCTTACACTAGC
1 CATGTCTTACACTAGC
31527943 TCACACAAGT
Statistics
Matches: 88, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
46 39 0.44
47 27 0.31
48 22 0.25
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (45 bp):
CATGTCTTACACTAGCCTCGTCTTGACGTCGATGCATGTCCTAGA
Found at i:31534124 original size:40 final size:40
Alignment explanation
Indices: 31534064--31534252 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
31534054 TGACAACAAA
* * *
31534064 TCAGATATATGTGGCACTTAGTATGCGATTCGACATAGCT
1 TCAGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT
*
31534104 TCAGCTATATATGGCACTTAGTGTGCGATTTGACATAGCT
1 TCAGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT
* * * * *
31534144 TCGGCTATATATGGAACTTAGTGTGCGAGATCGAGATAGAT
1 TCAGCTATATATGGCACTTAGTGTGCGA-TTCGACATAGCT
* * * *
31534185 TCAGCTATATATGACACTTAGTGTGCAATTTGAGATAGCT
1 TCAGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT
* * *
31534225 TCAACTATGA-ATGGAACTTTGTGTGCGA
1 TCAGCTAT-ATATGGCACTTAGTGTGCGA
31534253 GATATCGAGT
Statistics
Matches: 125, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
40 92 0.74
41 33 0.26
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (40 bp):
TCAGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT
Found at i:31534208 original size:81 final size:81
Alignment explanation
Indices: 31534069--31534255 Score: 243
Period size: 81 Copynumber: 2.3 Consensus size: 81
31534059 ACAAATCAGA
* * * * * * *
31534069 TATATGTGGCACTTAGTATGCGA-TTCGACATAGCTTCAGCTATATATGGCACTTAGTGTGCGAT
1 TATATATGGAACTTAGTGTGCGAGATCGACATAGATTCAGCTATATATGACACTTAGTGTGCAAT
**
31534133 TTGACATAGCTTCGGC
66 TTGACATAGCTTCAAC
*
31534149 TATATATGGAACTTAGTGTGCGAGATCGAGATAGATTCAGCTATATATGACACTTAGTGTGCAAT
1 TATATATGGAACTTAGTGTGCGAGATCGACATAGATTCAGCTATATATGACACTTAGTGTGCAAT
*
31534214 TTGAGATAGCTTCAAC
66 TTGACATAGCTTCAAC
*
31534230 TATGA-ATGGAACTTTGTGTGCGAGAT
1 TAT-ATATGGAACTTAGTGTGCGAGAT
31534256 ATCGAGTATT
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
80 20 0.22
81 72 0.77
82 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (81 bp):
TATATATGGAACTTAGTGTGCGAGATCGACATAGATTCAGCTATATATGACACTTAGTGTGCAAT
TTGACATAGCTTCAAC
Found at i:31535112 original size:13 final size:13
Alignment explanation
Indices: 31535094--31535125 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
31535084 AAGTTGTGGG
31535094 TGGCAAATTGGCT
1 TGGCAAATTGGCT
31535107 TGGCAAATTGGCT
1 TGGCAAATTGGCT
31535120 TGGCAA
1 TGGCAA
31535126 TCCAAGAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (13 bp):
TGGCAAATTGGCT
Found at i:31536957 original size:18 final size:18
Alignment explanation
Indices: 31536927--31536975 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
31536917 ATTTTAAGTC
*
31536927 ATTTGTTTATTTTTC-TT
1 ATTTATTTATTTTTCATT
31536944 ATTTATTTATTTTTCATT
1 ATTTATTTATTTTTCATT
*
31536962 ATTAATTTATTTTT
1 ATTTATTTATTTTT
31536976 TTAACCCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTTCATT
Found at i:31538911 original size:43 final size:42
Alignment explanation
Indices: 31538795--31538911 Score: 103
Period size: 42 Copynumber: 2.8 Consensus size: 42
31538785 ATATGTGTTA
* **
31538795 TCGTGTAAAACCACATCTAGGAC-GTTGGCATCAACTTGAGAT
1 TCGTGTAAGACCATGTCTAGGACAG-TGGCATCAACTTGAGAT
* * * * * *
31538837 TCGTGTAAGACTATGTTTGGGGCACTAGCATCAA-TTAGAGAT
1 TCGTGTAAGACCATGTCTAGGACAGTGGCATCAACTT-GAGAT
*
31538879 TACGTGTAAGACCCTGTCTAGGACAGTGGCATC
1 T-CGTGTAAGACCATGTCTAGGACAGTGGCATC
31538912 GATATTTGAT
Statistics
Matches: 56, Mismatches: 16, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
41 2 0.04
42 30 0.54
43 24 0.43
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTAGGACAGTGGCATCAACTTGAGAT
Found at i:31546467 original size:22 final size:22
Alignment explanation
Indices: 31546442--31546491 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
31546432 TAATAAAGCC
31546442 ATAATAAATAAAACAAAACATG
1 ATAATAAATAAAACAAAACATG
31546464 ATAATAAATAAAACAAAACATG
1 ATAATAAATAAAACAAAACATG
31546486 ATAATA
1 ATAATA
31546492 TTGCCGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.68, C:0.08, G:0.04, T:0.20
Consensus pattern (22 bp):
ATAATAAATAAAACAAAACATG
Found at i:31547422 original size:43 final size:44
Alignment explanation
Indices: 31547343--31547443 Score: 102
Period size: 43 Copynumber: 2.3 Consensus size: 44
31547333 GTGATATGTG
31547343 TTATCGTGTAAGACCAAGTCTGGGACGATGGAATCAACTT-GAGA
1 TTATCGTGTAAGACCAAGTCTGGGACGATGGAATCAA-TTAGAGA
*** * *
31547387 -TATCGTGTAAGACTGTGTTTGGGAC-ACTGGCATCAATTAGAGA
1 TTATCGTGTAAGACCAAGTCTGGGACGA-TGGAATCAATTAGAGA
*
31547430 TTAT-GTGTATGACC
1 TTATCGTGTAAGACC
31547444 CTGTCTATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
42 3 0.06
43 41 0.87
44 3 0.06
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (44 bp):
TTATCGTGTAAGACCAAGTCTGGGACGATGGAATCAATTAGAGA
Found at i:31549533 original size:15 final size:17
Alignment explanation
Indices: 31549515--31549553 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
31549505 ATATTATTTT
31549515 TTTTTCA-TTTAT-TCC
1 TTTTTCATTTTATCTCC
*
31549530 TTTTTCATTTTCTCTCC
1 TTTTTCATTTTATCTCC
31549547 TTTTTCA
1 TTTTTCA
31549554 CAAACAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 10 0.48
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTCATTTTATCTCC
Found at i:31555329 original size:20 final size:20
Alignment explanation
Indices: 31555188--31555329 Score: 58
Period size: 20 Copynumber: 7.1 Consensus size: 20
31555178 ACTAGTTGAA
31555188 TGATTGCACATACGTGCCCC
1 TGATTGCACATACGTGCCCC
* * ** *
31555208 T-ATTTGTACTTTGGTACCCC
1 TGA-TTGCACATACGTGCCCC
* * *
31555228 TGGTTGCACATATGAGCCCC
1 TGATTGCACATACGTGCCCC
* * *
31555248 TG-TTAGTAC-TTCGGTACCCC
1 TGATT-GCACATAC-GTGCCCC
* *
31555268 TGATTGCACATACCTGCCCT
1 TGATTGCACATACGTGCCCC
* * ** *
31555288 TG-TTAGTACTTTGGTACCCC
1 TGATT-GCACATACGTGCCCC
31555308 TGATTGCACATACGTGCCCC
1 TGATTGCACATACGTGCCCC
31555328 TG
1 TG
31555330 TTAGTACTTT
Statistics
Matches: 80, Mismatches: 34, Indels: 16
0.62 0.26 0.12
Matches are distributed among these distances:
19 6 0.08
20 68 0.85
21 6 0.08
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.32
Consensus pattern (20 bp):
TGATTGCACATACGTGCCCC
Found at i:31555366 original size:40 final size:40
Alignment explanation
Indices: 31555188--31555350 Score: 245
Period size: 40 Copynumber: 4.1 Consensus size: 40
31555178 ACTAGTTGAA
* *
31555188 TGATTGCACATACGTGCCCCTATTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTAGTACTTTGGTACCCC
* * * *
31555228 TGGTTGCACATATGAGCCCCTGTTAGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTAGTACTTTGGTACCCC
* *
31555268 TGATTGCACATACCTGCCCTTGTTAGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTAGTACTTTGGTACCCC
*
31555308 TGATTGCACATACGTGCCCCTGTTAGTACTTTGGTACACC
1 TGATTGCACATACGTGCCCCTGTTAGTACTTTGGTACCCC
31555348 TGA
1 TGA
31555351 ACGTATTTAC
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 108 1.00
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTAGTACTTTGGTACCCC
Found at i:31555366 original size:80 final size:79
Alignment explanation
Indices: 31555193--31555376 Score: 233
Period size: 80 Copynumber: 2.3 Consensus size: 79
31555183 TTGAATGATT
* * *
31555193 GCACATACGTGCCCCTATTTGTACTTTGGTACCCCTGGTTGCACATATGAGCCCCTGTTAGTACT
1 GCACATACGTGCCCTTA-TTGTACTTTGGTACCCCTGATTGCACATACGAGCCCCTGTTAGTACT
* **
31555258 TCGGTACCCCTGATT
65 TCGGTACACCTGAAC
* * *
31555273 GCACATACCTGCCCTTGTTAGTACTTTGGTACCCCTGATTGCACATACGTGCCCCTGTTAGTACT
1 GCACATACGTGCCCTTATT-GTACTTTGGTACCCCTGATTGCACATACGAGCCCCTGTTAGTACT
*
31555338 TTGGTACACCTGAAC
65 TCGGTACACCTGAAC
* **
31555353 GTATTTACGTGCCCTTATTGTACT
1 GCACATACGTGCCCTTATTGTACT
31555377 CTAATAAATC
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 7 0.08
80 81 0.92
ACGTcount: A:0.18, C:0.29, G:0.19, T:0.34
Consensus pattern (79 bp):
GCACATACGTGCCCTTATTGTACTTTGGTACCCCTGATTGCACATACGAGCCCCTGTTAGTACTT
CGGTACACCTGAAC
Found at i:31558369 original size:110 final size:110
Alignment explanation
Indices: 31558171--31558392 Score: 399
Period size: 110 Copynumber: 2.0 Consensus size: 110
31558161 GGCTACTCTG
*
31558171 AATCCCCTCCGGCCCAAGTCCCCACATCAAGGCTCACTTGCAAGGTTAAGGAAAGGGGGTGAGTT
1 AATCCCCTCCGGCCCAAGTCCCCACATCAAGGCTCACCTGCAAGGTTAAGGAAAGGGGGTGAGTT
*
31558236 TGGAAACTCAATGTGCAATAAGGCCCTTTCAGAGCCCAAAACAAT
66 TGGAAACTCAATGTGCAACAAGGCCCTTTCAGAGCCCAAAACAAT
* *
31558281 AATCCTCTCCGGCCTAAGTCCCCACATCAAGGCTCACCTGCAAGGTTAAGGAAAGGGGGTGAGTT
1 AATCCCCTCCGGCCCAAGTCCCCACATCAAGGCTCACCTGCAAGGTTAAGGAAAGGGGGTGAGTT
*
31558346 TGGAAACTCAGTGTGCAACAAGGCCCTTTCAGAGCCCAAAACAAT
66 TGGAAACTCAATGTGCAACAAGGCCCTTTCAGAGCCCAAAACAAT
31558391 AA
1 AA
31558393 CAGCCTGTTG
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (110 bp):
AATCCCCTCCGGCCCAAGTCCCCACATCAAGGCTCACCTGCAAGGTTAAGGAAAGGGGGTGAGTT
TGGAAACTCAATGTGCAACAAGGCCCTTTCAGAGCCCAAAACAAT
Found at i:31558461 original size:7 final size:7
Alignment explanation
Indices: 31558449--31558476 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31558439 TCGTAGCCCT
31558449 TTTCATA
1 TTTCATA
31558456 TTTCATA
1 TTTCATA
31558463 TTTCATA
1 TTTCATA
31558470 TTTCATA
1 TTTCATA
31558477 ACACTGGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTCATA
Found at i:31558739 original size:24 final size:24
Alignment explanation
Indices: 31558703--31558760 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
31558693 ATGGAGGCCT
31558703 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCAAA
*
31558728 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCAAA
31558752 AGCCCTTTT
1 AGCCCTTTT
31558761 GCACTTCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCAAA
Found at i:31558830 original size:9 final size:9
Alignment explanation
Indices: 31558816--31558868 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
31558806 ACATCATGTG
31558816 CATATCATA
1 CATATCATA
*
31558825 CATATCATGTG
1 CATATCA--TA
31558836 CATATCATA
1 CATATCATA
*
31558845 CATGTCATGTA
1 CATATCA--TA
31558856 CATATCATA
1 CATATCATA
31558865 CATA
1 CATA
31558869 CCATGTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 20 0.56
11 16 0.44
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (9 bp):
CATATCATA
Found at i:31558833 original size:20 final size:20
Alignment explanation
Indices: 31558808--31558874 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
31558798 TTATGAATAC
31558808 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
31558828 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
31558848 GTCATGTACATATCATACAT
1 ATCATGTGCATATCATACAT
*
31558868 ACCATGT
1 ATCATGT
31558875 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31558857 original size:11 final size:11
Alignment explanation
Indices: 31558808--31558863 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
31558798 TTATGAATAC
*
31558808 ATCATGTGCAT
1 ATCATGTACAT
31558819 ATCA--TACAT
1 ATCATGTACAT
*
31558828 ATCATGTGCAT
1 ATCATGTACAT
31558839 ATCA--TACAT
1 ATCATGTACAT
*
31558848 GTCATGTACAT
1 ATCATGTACAT
31558859 ATCAT
1 ATCAT
31558864 ACATACCATG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 15 0.42
11 21 0.58
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (11 bp):
ATCATGTACAT
Found at i:31560725 original size:44 final size:44
Alignment explanation
Indices: 31560662--31560750 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
31560652 TCAATAATAT
*
31560662 ACCGTCACATTTTATCTTAAAGGTTCCCTACTGAAGTCCCGTTC
1 ACCGTCACATTTTATCTTAAAGGTTACCTACTGAAGTCCCGTTC
31560706 ACCGTCACATTTTATCTTAAAGGTTACCTACTGAAGTCCCGTTC
1 ACCGTCACATTTTATCTTAAAGGTTACCTACTGAAGTCCCGTTC
31560750 A
1 A
31560751 TTTTAAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (44 bp):
ACCGTCACATTTTATCTTAAAGGTTACCTACTGAAGTCCCGTTC
Found at i:31563105 original size:31 final size:31
Alignment explanation
Indices: 31563067--31563130 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
31563057 CCTTTTCATA
31563067 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
31563098 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
31563129 TT
1 TT
31563131 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:31563375 original size:24 final size:24
Alignment explanation
Indices: 31563338--31563395 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
31563328 CTGGAGGCTT
31563338 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCAAA
*
31563363 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCAAA
31563387 AGCCCTTTT
1 AGCCCTTTT
31563396 GCACTTCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCAAA
Found at i:31563465 original size:9 final size:9
Alignment explanation
Indices: 31563451--31563503 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
31563441 ACATCATGTG
31563451 CATATCATA
1 CATATCATA
*
31563460 CATATCATGTG
1 CATATCA--TA
31563471 CATATCATA
1 CATATCATA
*
31563480 CATGTCATGTA
1 CATATCA--TA
31563491 CATATCATA
1 CATATCATA
31563500 CATA
1 CATA
31563504 CCATGTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 20 0.56
11 16 0.44
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (9 bp):
CATATCATA
Found at i:31563468 original size:20 final size:20
Alignment explanation
Indices: 31563443--31563509 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
31563433 TTATGAATAC
31563443 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
31563463 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
31563483 GTCATGTACATATCATACAT
1 ATCATGTGCATATCATACAT
*
31563503 ACCATGT
1 ATCATGT
31563510 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31563492 original size:11 final size:11
Alignment explanation
Indices: 31563443--31563498 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
31563433 TTATGAATAC
*
31563443 ATCATGTGCAT
1 ATCATGTACAT
31563454 ATCA--TACAT
1 ATCATGTACAT
*
31563463 ATCATGTGCAT
1 ATCATGTACAT
31563474 ATCA--TACAT
1 ATCATGTACAT
*
31563483 GTCATGTACAT
1 ATCATGTACAT
31563494 ATCAT
1 ATCAT
31563499 ACATACCATG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 15 0.42
11 21 0.58
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (11 bp):
ATCATGTACAT
Found at i:31563588 original size:25 final size:25
Alignment explanation
Indices: 31563546--31563593 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31563536 ATATTTAAAC
* * *
31563546 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
31563571 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
31563594 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:31565793 original size:19 final size:18
Alignment explanation
Indices: 31565756--31565799 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
31565746 ATACTTACAG
31565756 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
31565773 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
31565792 TACTAATT
1 TAATAATT
31565800 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:31568097 original size:14 final size:14
Alignment explanation
Indices: 31568078--31568108 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31568068 TTATTATGAT
31568078 GATTGATATGTTGA
1 GATTGATATGTTGA
*
31568092 GATTGATATTTTGA
1 GATTGATATGTTGA
31568106 GAT
1 GAT
31568109 GTATGCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (14 bp):
GATTGATATGTTGA
Found at i:31568105 original size:22 final size:22
Alignment explanation
Indices: 31568080--31568129 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
31568070 ATTATGATGA
31568080 TTGATATGT-TGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
* *
31568102 TTGAGATGTATGCGATTATATT
1 TTGATATGTATGAGATTATATT
31568124 TGTGAT
1 T-TGAT
31568130 GATCTCACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:31586251 original size:18 final size:17
Alignment explanation
Indices: 31586228--31586270 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31586218 CACACTCCTC
*
31586228 AAACACTCAGTAATAGTA
1 AAACACTCAG-AATAATA
* *
31586246 AAACACGCAGCATAATA
1 AAACACTCAGAATAATA
31586263 AAACACTC
1 AAACACTC
31586271 CTTTACATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.51, C:0.23, G:0.09, T:0.16
Consensus pattern (17 bp):
AAACACTCAGAATAATA
Found at i:31592343 original size:47 final size:47
Alignment explanation
Indices: 31592272--31592366 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
31592262 ACAAGGAGGG
* * * *
31592272 TGTAATCGACCTTCATCAATGGTTTAAGTAGGCTAAACCACACTCTT
1 TGTAATCAACCTTCATCAACGGTTTAAGCAGGCTAAAACACACTCTT
* *
31592319 TGTAATCAACCTTCGTCAACGGTTTAAGCAGGCTAAAACACAGTCTT
1 TGTAATCAACCTTCATCAACGGTTTAAGCAGGCTAAAACACACTCTT
31592366 T
1 T
31592367 CAATCAAGAC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (47 bp):
TGTAATCAACCTTCATCAACGGTTTAAGCAGGCTAAAACACACTCTT
Found at i:31595765 original size:23 final size:24
Alignment explanation
Indices: 31595727--31595771 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
31595717 TTTGCTCTTC
*
31595727 TAGCATGAACTTGTCTTACCTTTT
1 TAGCATGAACTCGTCTTACCTTTT
31595751 TAGCAT-AACTCGTCTTACCTT
1 TAGCATGAACTCGTCTTACCTT
31595772 ACCTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (24 bp):
TAGCATGAACTCGTCTTACCTTTT
Found at i:31596037 original size:108 final size:110
Alignment explanation
Indices: 31595887--31596087 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
31595877 ATCCTTTTGA
* * *
31595887 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCATGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
31595950 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * * *
31595995 AACTTATCAATGCCATGTCATGACATGGTCTTTCATGATATCCTTTCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCATGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
31596060 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
31596088 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.57
109 7 0.08
110 28 0.34
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCATGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:31596045 original size:55 final size:54
Alignment explanation
Indices: 31595840--31596094 Score: 247
Period size: 55 Copynumber: 4.8 Consensus size: 54
31595830 ACACGGGTAC
* * * * * *
31595840 CTTACCATTTCCATGACTTGTCATGGTCTTACGTGGTATCC-TT--TT-GA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTTCCTTATAGAA
* * *
31595889 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTTCCTTATAGAA
* * *
31595942 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTT-CCTTATAG-AA
* * * * * *
31595997 CTTATCAATGCCATGTCATGACATGGTCTTTCATGATATCCTTTCCTTAGA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTTCCTTATAGAA
*
31596050 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
31596095 AAACCCTAAT
Statistics
Matches: 168, Mismatches: 27, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 6 0.04
53 43 0.26
54 8 0.05
55 68 0.40
56 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTTCCTTATAGAA
Found at i:31597952 original size:21 final size:21
Alignment explanation
Indices: 31597924--31597963 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
31597914 GCTTGAGAAA
*
31597924 TTTTAGAAT-ATTTTGGCTAC
1 TTTTAGAATAATTTCGGCTAC
31597944 TTTTGAGAATAATTTCGGCT
1 TTTT-AGAATAATTTCGGCT
31597964 GAATTGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTTAGAATAATTTCGGCTAC
Found at i:31599996 original size:47 final size:46
Alignment explanation
Indices: 31599927--31600147 Score: 157
Period size: 47 Copynumber: 4.7 Consensus size: 46
31599917 ATGTGAGAGA
*
31599927 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GATGATGGC
1 CAGTGTAAGA-CGTGTCTGGGACAT-GCATCGGCATTGACGATGA-GGC
* *
31599975 TAGTGTAAGACGTGTCTGGGACATGCATCAGCCACATT-ACGAT-A-GC
1 CAGTGTAAGACGTGTCTGGGACATGCATC-G--GCATTGACGATGAGGC
* * * ** * *
31600021 CATTGTAAGACCATGTCTAGGACATGGCATCAACGTAGA-GATGAGTGC
1 CAGTGTAAGA-CGTGTCTGGGACAT-GCATCGGCATTGACGATGAG-GC
* * * ** *
31600069 CAGTGTAAGACGTGTTTGGGACATACATCGGCCTCAATGATG-GTAGC
1 CAGTGTAAGACGTGTCTGGGACATGCATCGGCATTGACGATGAG--GC
31600116 CAGTGTAAGACGTGTCTGGGACATGCATCGGC
1 CAGTGTAAGACGTGTCTGGGACATGCATCGGC
31600148 TAAGCTTCGT
Statistics
Matches: 138, Mismatches: 23, Indels: 25
0.74 0.12 0.13
Matches are distributed among these distances:
45 6 0.04
46 25 0.18
47 73 0.53
48 27 0.20
49 7 0.05
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (46 bp):
CAGTGTAAGACGTGTCTGGGACATGCATCGGCATTGACGATGAGGC
Found at i:31600132 original size:94 final size:94
Alignment explanation
Indices: 31599927--31600144 Score: 262
Period size: 94 Copynumber: 2.3 Consensus size: 94
31599917 ATGTGAGAGA
** * *
31599927 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGATGGCTAGTGTAAGACGTGTCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAACATAGAGATGATGGCCAGTGTAAGACGTGTCT
* *
31599992 GGGACATGCATCAGCCACATTACGATAGC
66 GGGACATACATCAGCCACATGACGATAGC
* * * *
31600021 CATTGTAAGACCATGTCTAGGACATGGCATCAACGTAGAGATGA-GTGCCAGTGTAAGACGTGTT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCAACATAGAGATGATG-GCCAGTGTAAGACGTGTC
* * * *
31600085 TGGGACATACATCGGCCTCAATGATGGTAGC
65 TGGGACATACATCAGCCAC-ATGACGATAGC
*
31600116 CAGTGTAAGA-CGTGTCTGGGACAT-GCATC
1 CAGTGTAAGACCATGTCTGGGACATGGCATC
31600145 GGCTAAGCTT
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
93 6 0.06
94 82 0.78
95 17 0.16
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (94 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCAACATAGAGATGATGGCCAGTGTAAGACGTGTCT
GGGACATACATCAGCCACATGACGATAGC
Found at i:31601936 original size:27 final size:27
Alignment explanation
Indices: 31601920--31602033 Score: 156
Period size: 27 Copynumber: 4.2 Consensus size: 27
31601910 CAATTTGTAA
* *
31601920 AATTACCGTTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTACAG
* *
31601947 AATTACTATTTTAGCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTACAG
* *
31601974 AATTACCGTTTTACCCTCGATTTGCAG
1 AATTACCATTTTACCCTCGATTTACAG
* *
31602001 AATTGCCATTTTACCCTCGATTTACAA
1 AATTACCATTTTACCCTCGATTTACAG
31602028 AATTAC
1 AATTAC
31602034 TAAAATACCC
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (27 bp):
AATTACCATTTTACCCTCGATTTACAG
Found at i:31601982 original size:54 final size:54
Alignment explanation
Indices: 31601918--31602033 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
31601908 CTCAATTTGT
* * *
31601918 AAAATTACCGTTTTACCCTCGATTTATAGAATTACTATTTTAGCCTCGATTTAC
1 AAAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTAC
* * *
31601972 AGAATTACCGTTTTACCCTCGATTTGCAGAATTGCCATTTTACCCTCGATTTAC
1 AAAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTAC
31602026 AAAATTAC
1 AAAATTAC
31602034 TAAAATACCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (54 bp):
AAAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTAC
Found at i:31602042 original size:27 final size:27
Alignment explanation
Indices: 31602012--31602097 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
31602002 ATTGCCATTT
*
31602012 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACAAAAA
* * *
31602039 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACAAAAA
* * *
31602066 TACCGTCGA-TCAGTAAAATTACAAAAA
1 TACCCTCGATTTA-CAAAATTACAAAAA
31602093 TACCC
1 TACCC
31602098 CAGGTTTGTA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 2 0.04
27 46 0.96
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACAAAAA
Found at i:31602043 original size:54 final size:54
Alignment explanation
Indices: 31601931--31602062 Score: 138
Period size: 54 Copynumber: 2.4 Consensus size: 54
31601921 ATTACCGTTT
* * * * ****
31601931 TACCCTCGATTTATAGAATTACTATTTTAGCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
* * *
31601985 TACCCTCGATTTGCAGAATTGCCATTTTACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
* * *
31602039 TACCCTTGGTTTACAAAATTACCA
1 TACCCTCGATTTACAGAATTACCA
31602063 AAATACCGTC
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACCAAAA
Found at i:31602159 original size:53 final size:54
Alignment explanation
Indices: 31602026--31602191 Score: 181
Period size: 54 Copynumber: 3.1 Consensus size: 54
31602016 CTCGATTTAC
* * ** *
31602026 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCGTCGATCAGT
1 AAAATTACAAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTCGATCAGT
* * * * *
31602080 AAAATTACAAAAATACCCCAGGTTTGTAAAATAACCAAAATACCCTGGCT-TGT
1 AAAATTACAAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTCGATCAGT
* * * * * *
31602133 AAAATTACCAAAATACCCCTGATTTGTGAAATTATCAAAATACTCTCGATCTGT
1 AAAATTACAAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTCGATCAGT
31602187 AAAAT
1 AAAAT
31602192 ACCGATATAC
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
53 43 0.47
54 49 0.53
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (54 bp):
AAAATTACAAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTCGATCAGT
Found at i:31602173 original size:27 final size:27
Alignment explanation
Indices: 31602026--31602175 Score: 142
Period size: 27 Copynumber: 5.6 Consensus size: 27
31602016 CTCGATTTAC
* * **
31602026 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGGTTTGT
* * **
31602053 AAAATTACCAAAATA-CCGTCGATCAGT
1 AAAATTACCAAAATACCCCT-GGTTTGT
* *
31602080 AAAATTACAAAAATACCCCAGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
31602107 AAAATAACCAAAATA-CCCTGGCTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
31602133 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
31602160 GAAATTATCAAAATAC
1 AAAATTACCAAAATAC
31602176 TCTCGATCTG
Statistics
Matches: 98, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
26 26 0.27
27 70 0.71
28 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:31602191 original size:27 final size:26
Alignment explanation
Indices: 31602053--31602191 Score: 118
Period size: 27 Copynumber: 5.2 Consensus size: 26
31602043 CTTGGTTTAC
*
31602053 AAAATTACCAAAATACCGTCGATCAGT
1 AAAATTACCAAAATACC-TCGATCTGT
* * * *
31602080 AAAATTACAAAAATACCCCAGGTTTGT
1 AAAATTACCAAAATACCTC-GATCTGT
* * *
31602107 AAAATAACCAAAATACCCTGGCT-TGT
1 AAAATTACCAAAATA-CCTCGATCTGT
* *
31602133 AAAATTACCAAAATACCCCTGATTTGT
1 AAAATTACCAAAATACCTC-GATCTGT
* *
31602160 GAAATTATCAAAATACTCTCGATCTGT
1 AAAATTACCAAAATAC-CTCGATCTGT
31602187 AAAAT
1 AAAAT
31602192 ACCGATATAC
Statistics
Matches: 88, Mismatches: 19, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
25 2 0.02
26 20 0.23
27 62 0.70
28 4 0.05
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (26 bp):
AAAATTACCAAAATACCTCGATCTGT
Found at i:31602202 original size:53 final size:53
Alignment explanation
Indices: 31602026--31602231 Score: 175
Period size: 53 Copynumber: 3.9 Consensus size: 53
31602016 CTCGATTTAC
* * * ** *
31602026 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCGTCGATCAGT
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACC-TCGATCTGT
* * * * * *
31602080 AAAATTACAAAAATACCCCAGGTTTGTAAAATAACCAAAATACCCTGGCT-TGT
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATA-CCTCGATCTGT
* *
31602133 AAAATTACCAAAATACCCCTGATTTGTGAAATTATCAAAATACTCTCGATCTGT
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATAC-CTCGATCTGT
* * ** * *
31602187 AAAA-TACCGATATACCCCT-ATAGGGTAGAATTACCGAAATACCTC
1 AAAATTACCAAAATACCCCTGAT-TTGTAAAATTACCAAAATACCTC
31602232 TGTAGGGTAG
Statistics
Matches: 123, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
52 6 0.05
53 69 0.56
54 46 0.37
55 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (53 bp):
AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACCTCGATCTGT
Found at i:31602221 original size:27 final size:27
Alignment explanation
Indices: 31602191--31602410 Score: 271
Period size: 27 Copynumber: 8.1 Consensus size: 27
31602181 ATCTGTAAAA
* *
31602191 TACCGATATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* *
31602218 TACCGAAATACCTCTGTAGGGTAGAAC
1 TACCGAAATACCCCTGTAGGGTAGAAT
** * *
31602245 TATTGAAATAACCCTGTAAGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
31602272 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
** *
31602299 TACTAAAATACCCCTGTAAGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* * *
31602326 TACTGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAT
31602353 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* * *
31602380 TACC-AAGATACCCTTGTGGGGTAAAAT
1 TACCGAA-ATACCCCTGTAGGGTAGAAT
31602407 TACC
1 TACC
31602411 TTTTTGCCCC
Statistics
Matches: 165, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
26 2 0.01
27 163 0.99
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
TACCGAAATACCCCTGTAGGGTAGAAT
Found at i:31602697 original size:24 final size:25
Alignment explanation
Indices: 31602640--31602697 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
31602630 TAGTTTACCG
*
31602640 AAAA-AGGCTCTGCCCCAATTTATC
1 AAAAGAGGCTCTGCCCCAAGTTATC
* *
31602664 AGAAAG-GGCTTTGCCCC-AGTTATT
1 A-AAAGAGGCTCTGCCCCAAGTTATC
31602688 AAAAGAGGCT
1 AAAAGAGGCT
31602698 AGGTCTCCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 4 0.14
24 11 0.39
25 13 0.46
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGAGGCTCTGCCCCAAGTTATC
Found at i:31605295 original size:27 final size:27
Alignment explanation
Indices: 31605279--31605392 Score: 183
Period size: 27 Copynumber: 4.2 Consensus size: 27
31605269 CAATTTGTAA
* *
31605279 AATTACCGTTTTACCCTCGATTTATAG
1 AATTACCATTTTACCCTCGATTTACAG
*
31605306 AATTACCATTTTACCCTTGATTTACAG
1 AATTACCATTTTACCCTCGATTTACAG
31605333 AATTACCATTTTACCCTCGATTTACAG
1 AATTACCATTTTACCCTCGATTTACAG
* *
31605360 AATTACCGTTTTACCCTCGATTTACAA
1 AATTACCATTTTACCCTCGATTTACAG
31605387 AATTAC
1 AATTAC
31605393 TAAAATACCC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.39
Consensus pattern (27 bp):
AATTACCATTTTACCCTCGATTTACAG
Done.