Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 107 of 284
Found at i:35100950 original size:27 final size:27
Alignment explanation
Indices: 35100917--35101465 Score: 715
Period size: 27 Copynumber: 20.4 Consensus size: 27
35100907 GGGCATAATC
* * *
35100917 GTCATTTTACCATATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
35100944 GTTATTTTACCC-ACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
35100970 GTCATTTTACCTTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35100997 GTTATTTTACCCTACAGGGGCATAATC-
1 GTCATTTTACCCTACAGGGGCATTA-CG
* * *
35101024 ATCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35101051 GTCATTTTACCCTACAAGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
35101078 ATCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
35101105 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
35101132 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35101159 ATCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * * * *
35101186 ATCATTTTACCCTATAAGGGTATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
35101213 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35101240 GTCATTTTACCCTATAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35101267 GTCATTTTACCTTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
35101294 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35101321 ATCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35101348 GTCATTTTACCCTATAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
35101375 GTTATTTTACCCTATAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
35101402 GTCATTTTACCCTACAAGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
*
35101429 GTCATTTTACCCTAAAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
35101456 GTCATTTTAC
1 GTCATTTTAC
35101466 TTATTTGGGG
Statistics
Matches: 451, Mismatches: 68, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
26 23 0.05
27 427 0.95
28 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:35106258 original size:27 final size:27
Alignment explanation
Indices: 35106227--35106300 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
35106217 GCGTACTTGA
*
35106227 GCCCTCATGTGATAAAATGACGATTTT
1 GCCCTTATGTGATAAAATGACGATTTT
* * *
35106254 GCCCTTATATGTTAAAATGATGATTTT
1 GCCCTTATGTGATAAAATGACGATTTT
* *
35106281 GCCCTTATGTTATCAAATGA
1 GCCCTTATGTGATAAAATGA
35106301 TCGAAATACC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (27 bp):
GCCCTTATGTGATAAAATGACGATTTT
Found at i:35106333 original size:27 final size:27
Alignment explanation
Indices: 35106295--35106365 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
35106285 TTATGTTATC
35106295 AAATGA-TCGAAATACCCTCATAGGGTA
1 AAATGACT-GAAATACCCTCATAGGGTA
* * *
35106322 AATTGTCTGAAATACCCTTATAGGGTA
1 AAATGACTGAAATACCCTCATAGGGTA
*
35106349 AAATGACTGTAATACCC
1 AAATGACTGAAATACCC
35106366 CAGTGAAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (27 bp):
AAATGACTGAAATACCCTCATAGGGTA
Found at i:35109242 original size:47 final size:47
Alignment explanation
Indices: 35109173--35109265 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
35109163 TGGCATGGCT
35109173 GTGTACACAAGTCAGAAGTTACATGGGGTTGAACACAGCCTCTAGCC
1 GTGTACACAAGTCAGAAGTTACATGGGGTTGAACACAGCCTCTAGCC
35109220 GTGTACACAAGTCAGAAGTTACATGGGGTTGAACACAGCCTCTAGC
1 GTGTACACAAGTCAGAAGTTACATGGGGTTGAACACAGCCTCTAGC
35109266 ACGGGTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (47 bp):
GTGTACACAAGTCAGAAGTTACATGGGGTTGAACACAGCCTCTAGCC
Found at i:35109293 original size:21 final size:21
Alignment explanation
Indices: 35109269--35109318 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
35109259 CTCTAGCACG
35109269 GGTGTGTCCTAGGGTCACACA
1 GGTGTGTCCTAGGGTCACACA
*
35109290 GGTGTGTCCTAGGGTCACACG
1 GGTGTGTCCTAGGGTCACACA
35109311 GGTGTGTC
1 GGTGTGTC
35109319 TCTTGGACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.38, T:0.26
Consensus pattern (21 bp):
GGTGTGTCCTAGGGTCACACA
Found at i:35112030 original size:47 final size:47
Alignment explanation
Indices: 35111979--35112089 Score: 150
Period size: 47 Copynumber: 2.4 Consensus size: 47
35111969 ACTGTAGCCC
* ** *
35111979 GTAGCCAAATCAAGGTAACTTATCCCGGAGTACCTATACCATGGCCT
1 GTAGCCAAATCAAGGTAACTCATCCCAAAATACCTATACCATGGCCT
* * *
35112026 GTAGCCAAATCAAGGTAACTCCTCTCAAAATACCTATATCATGGCCT
1 GTAGCCAAATCAAGGTAACTCATCCCAAAATACCTATACCATGGCCT
*
35112073 ATAGCCAAATCAAGGTA
1 GTAGCCAAATCAAGGTA
35112090 TTATTCACAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (47 bp):
GTAGCCAAATCAAGGTAACTCATCCCAAAATACCTATACCATGGCCT
Found at i:35116219 original size:18 final size:20
Alignment explanation
Indices: 35116196--35116233 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
35116186 TAAATTTGAA
*
35116196 TAATTTTAA-ATT-TATTTT
1 TAATTTGAACATTGTATTTT
35116214 TAATTTGAACATTGTATTTT
1 TAATTTGAACATTGTATTTT
35116234 AGTTCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
TAATTTGAACATTGTATTTT
Found at i:35118231 original size:56 final size:56
Alignment explanation
Indices: 35118075--35118248 Score: 233
Period size: 56 Copynumber: 3.1 Consensus size: 56
35118065 ATTAAGATAC
* *
35118075 ATGAATATATGTAAGACCATGTGGTTAAGACCCATGGT-AAAATATGATATGACTAA
1 ATGAATATATGTAAGACCATGTGGTTAAGACCCAT-GTCAAGATATGATATGACTGA
* * * *
35118131 ATGAATATATGTAAGACCTTGAGGTTAAGACACATGGCAAGATATGATATGACTGA
1 ATGAATATATGTAAGACCATGTGGTTAAGACCCATGTCAAGATATGATATGACTGA
* * * * *
35118187 ATGAACATATGTAAGACCATGTGGTTAAGACCCATGTCATGATATGAAATGTCTGT
1 ATGAATATATGTAAGACCATGTGGTTAAGACCCATGTCAAGATATGATATGACTGA
35118243 ATGAAT
1 ATGAAT
35118249 GTTCATGGCG
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
55 1 0.01
56 100 0.99
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (56 bp):
ATGAATATATGTAAGACCATGTGGTTAAGACCCATGTCAAGATATGATATGACTGA
Found at i:35118795 original size:18 final size:18
Alignment explanation
Indices: 35118769--35118803 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35118759 CTATGAGTAT
35118769 GAATAGATGGCGTTTGGC
1 GAATAGATGGCGTTTGGC
* *
35118787 GAATGGATGGTGTTTGG
1 GAATAGATGGCGTTTGG
35118804 TTCTACGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.43, T:0.31
Consensus pattern (18 bp):
GAATAGATGGCGTTTGGC
Found at i:35121860 original size:27 final size:28
Alignment explanation
Indices: 35121830--35121891 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
35121820 TATTTCAATA
* * *
35121830 ATTTTACAC-TATAAGGGTATTCTGGTC
1 ATTTTACACTTACAAGGGCATTATGGTC
35121857 ATTTTAC-CTTACAAGGGCATTATGGTC
1 ATTTTACACTTACAAGGGCATTATGGTC
35121884 ATTTTACA
1 ATTTTACA
35121892 AACTAGGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (28 bp):
ATTTTACACTTACAAGGGCATTATGGTC
Found at i:35121914 original size:27 final size:26
Alignment explanation
Indices: 35121884--35121958 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 26
35121874 CATTATGGTC
35121884 ATTTTACAAACTAGGGGTATTTCGGA-A
1 ATTTTACAAA-TAGGGGTATTT-GGATA
* * *
35121911 ATTTTTCAAATCGGGGGTATTTTGATA
1 ATTTTACAAAT-AGGGGTATTTGGATA
*
35121938 A-TTTGCAAATTAGGGGTATTT
1 ATTTTACAAA-TAGGGGTATTT
35121959 ATGACCCATC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
26 19 0.47
27 21 0.52
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTTACAAATAGGGGTATTTGGATA
Found at i:35130766 original size:15 final size:15
Alignment explanation
Indices: 35130746--35130774 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35130736 ATATCGTATC
35130746 TTGGATTCCTCTATT
1 TTGGATTCCTCTATT
35130761 TTGGATTCCTCTAT
1 TTGGATTCCTCTAT
35130775 CTTAGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (15 bp):
TTGGATTCCTCTATT
Found at i:35134295 original size:50 final size:50
Alignment explanation
Indices: 35134216--35134407 Score: 246
Period size: 50 Copynumber: 3.9 Consensus size: 50
35134206 ATCCCATGTA
* *
35134216 TGAGATCCCATGTAAAACCATGTTTGGGACATGGCATTGGCATCGATATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * * * *
35134266 TGAGATCCCATGTAAGACCATGTCCGGGACCTGACAGTGGCATTGATATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
*
35134316 TGAGATCCCATGTAGGACCATGTCTGGGACATGGCATTGGCATC-AGTATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA-TATG
* * * *
35134366 T--GATCCCATGTAAGACCATATCTGGGATACGGCCTTGGCATC
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
35134408 TTATTATGTG
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
48 36 0.29
49 1 0.01
50 86 0.70
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (50 bp):
TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
Found at i:35135622 original size:21 final size:21
Alignment explanation
Indices: 35135585--35135624 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35135575 CTTAATTAAA
*
35135585 TTGATGTTATGATATGTGTCT
1 TTGATGTTATGAAATGTGTCT
35135606 TTGATGTGTAT-AAATGTGT
1 TTGATGT-TATGAAATGTGT
35135625 AAGGGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (21 bp):
TTGATGTTATGAAATGTGTCT
Found at i:35138253 original size:50 final size:49
Alignment explanation
Indices: 35138199--35138347 Score: 232
Period size: 50 Copynumber: 3.1 Consensus size: 49
35138189 TACATGAATT
35138199 ATTCCTGTCTCCAATGCCATATATATATCTAATATGGGCTTACATGGCTC
1 ATTCCTGTCTCCAATGCCA-ATATATATCTAATATGGGCTTACATGGCTC
35138249 ATTCCTGTCTCCAATGCCACATATATATCTAATATGGGCTTACATGGCTC
1 ATTCCTGTCTCCAATGCCA-ATATATATCTAATATGGGCTTACATGGCTC
* * *
35138299 ATTCCTGTCTCCAAAGCC---ATATATCTGATATGGACTTACATGGCTC
1 ATTCCTGTCTCCAATGCCAATATATATCTAATATGGGCTTACATGGCTC
35138345 ATT
1 ATT
35138348 TTTGTCCTGT
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
46 29 0.31
50 66 0.69
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (49 bp):
ATTCCTGTCTCCAATGCCAATATATATCTAATATGGGCTTACATGGCTC
Found at i:35138338 original size:46 final size:47
Alignment explanation
Indices: 35138182--35138347 Score: 208
Period size: 50 Copynumber: 3.4 Consensus size: 47
35138172 TGTCTTCGAC
** *
35138182 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAATGCC--A-ATATATCTAAT
*
35138232 ATGGGCTTACATGGCTCATTCCTGTCTCCAATGCCACATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAATG-C-CA-ATATATCTAAT
* * *
35138282 ATGGGCTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAATGCCAATATATCTAAT
35138328 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
35138348 TTTGTCCTGT
Statistics
Matches: 107, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
46 29 0.27
48 1 0.01
49 1 0.01
50 74 0.69
51 1 0.01
52 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAATGCCAATATATCTAAT
Found at i:35140520 original size:13 final size:13
Alignment explanation
Indices: 35140502--35140545 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
35140492 GATTTTGTTG
*
35140502 TTTGTTATTTTTT
1 TTTGTTATTTATT
35140515 TTTGTTTATTTATT
1 TTTG-TTATTTATT
*
35140529 TTAGTTATTTAATT
1 TTTGTTATTT-ATT
35140543 TTT
1 TTT
35140546 ATCATTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTGTTATTTATT
Found at i:35144607 original size:10 final size:10
Alignment explanation
Indices: 35144582--35144622 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
35144572 ATCAATAAAA
35144582 CATA-TATAT
1 CATATTATAT
35144591 C-TATTATAT
1 CATATTATAT
35144600 CATATTATAT
1 CATATTATAT
35144610 CATATTATAT
1 CATATTATAT
35144620 CAT
1 CAT
35144623 CAAACATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 2 0.07
9 7 0.23
10 21 0.70
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (10 bp):
CATATTATAT
Found at i:35148401 original size:44 final size:44
Alignment explanation
Indices: 35148338--35148421 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
35148328 CCAAAACATG
*
35148338 TGTCATATATATAATGAACTCAGACCACAACTCATGAGTTTAGA
1 TGTCAAATATATAATGAACTCAGACCACAACTCATGAGTTTAGA
* *
35148382 TGTCAAATATATCATGAACTCAGATCACAACTCATGAGTT
1 TGTCAAATATATAATGAACTCAGACCACAACTCATGAGTT
35148422 CAAATCACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (44 bp):
TGTCAAATATATAATGAACTCAGACCACAACTCATGAGTTTAGA
Found at i:35148628 original size:24 final size:24
Alignment explanation
Indices: 35148583--35148628 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
35148573 AAGCATAATT
**
35148583 CATGATACAATTTAACAATAAACA
1 CATGATACAACATAACAATAAACA
* *
35148607 CATGATACAACATCACATTAAA
1 CATGATACAACATAACAATAAA
35148629 TATGTATGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.24
Consensus pattern (24 bp):
CATGATACAACATAACAATAAACA
Found at i:35150088 original size:19 final size:19
Alignment explanation
Indices: 35150052--35150089 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35150042 CACAAGCATA
*
35150052 CAAACATATCATAGATAAT
1 CAAACATATCATAAATAAT
35150071 CAAACA-ATCATAAAATAAT
1 CAAACATATCAT-AAATAAT
35150090 TATTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.24
Consensus pattern (19 bp):
CAAACATATCATAAATAAT
Found at i:35153894 original size:30 final size:25
Alignment explanation
Indices: 35153840--35153888 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
35153830 AAACAAAAGT
35153840 AAGGTCAAAATAATCCTATTACATA
1 AAGGTCAAAATAATCCTATTACATA
35153865 AAGGTCAAAATAATCCTATTACAT
1 AAGGTCAAAATAATCCTATTACAT
35153889 GACATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (25 bp):
AAGGTCAAAATAATCCTATTACATA
Found at i:35154391 original size:37 final size:37
Alignment explanation
Indices: 35154331--35154413 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
35154321 AAAAACATGC
* * *
35154331 CAAATGTTCATAAGAGCTAATCCAATCG-TAAACACGA
1 CAAATGCTCATAACAACTAATCCAATCGAT-AACACGA
* * *
35154368 CAAATGCTCATAACAACTCATCCACTCGATAACACGC
1 CAAATGCTCATAACAACTAATCCAATCGATAACACGA
*
35154405 CAATTGCTC
1 CAAATGCTC
35154414 CGAAGAGCTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.22
Consensus pattern (37 bp):
CAAATGCTCATAACAACTAATCCAATCGATAACACGA
Found at i:35157417 original size:29 final size:29
Alignment explanation
Indices: 35157378--35157476 Score: 153
Period size: 29 Copynumber: 3.4 Consensus size: 29
35157368 GGCCCAATCT
35157378 CATTTATATGGCCCATCAGGCCCACACCA
1 CATTTATATGGCCCATCAGGCCCACACCA
35157407 CATTTATATGGCCCATCAGGCCCACACCA
1 CATTTATATGGCCCATCAGGCCCACACCA
** * *
35157436 CATTTATATGGCCCATTTGGCCCAAATCA
1 CATTTATATGGCCCATCAGGCCCACACCA
*
35157465 CCTTTATATGGC
1 CATTTATATGGC
35157477 ACGTTAGGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.26
Consensus pattern (29 bp):
CATTTATATGGCCCATCAGGCCCACACCA
Found at i:35157497 original size:29 final size:29
Alignment explanation
Indices: 35157378--35157490 Score: 145
Period size: 29 Copynumber: 3.9 Consensus size: 29
35157368 GGCCCAATCT
*
35157378 CATTTATATGGCCCATCAGGCCCACACCA
1 CATTTATATGGCCCATCAGGCCCAAACCA
*
35157407 CATTTATATGGCCCATCAGGCCCACACCA
1 CATTTATATGGCCCATCAGGCCCAAACCA
** *
35157436 CATTTATATGGCCCATTTGGCCCAAATCA
1 CATTTATATGGCCCATCAGGCCCAAACCA
* * * *
35157465 CCTTTATATGGCACGTTAGGCCCAAA
1 CATTTATATGGCCCATCAGGCCCAAA
35157491 TCACCTTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
CATTTATATGGCCCATCAGGCCCAAACCA
Found at i:35165183 original size:29 final size:29
Alignment explanation
Indices: 35165112--35165228 Score: 103
Period size: 29 Copynumber: 4.1 Consensus size: 29
35165102 ACCCCTACAT
*
35165112 ACATGTATATGGCCCACTT-GGCCC-AATC
1 ACATTTATATGGCCCA-TTAGGCCCAAATC
** * *
35165140 TTATTTATATAGCCCATTAGGCCCAATTC
1 ACATTTATATGGCCCATTAGGCCCAAATC
* * *
35165169 ACATTCATATGGCCCATCAGGTCCAAATC
1 ACATTTATATGGCCCATTAGGCCCAAATC
* * * *
35165198 ACCTTTATCTGGCCCGTTACGCCCAAATC
1 ACATTTATATGGCCCATTAGGCCCAAATC
35165227 AC
1 AC
35165229 CTTATATTCT
Statistics
Matches: 68, Mismatches: 19, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
27 2 0.03
28 17 0.25
29 49 0.72
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (29 bp):
ACATTTATATGGCCCATTAGGCCCAAATC
Found at i:35165588 original size:19 final size:19
Alignment explanation
Indices: 35165564--35165601 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35165554 ACAAACCTAC
35165564 AAATGATATCACCCTTCAA
1 AAATGATATCACCCTTCAA
35165583 AAATGATATCACCCTTCAA
1 AAATGATATCACCCTTCAA
35165602 TTAATCGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATGATATCACCCTTCAA
Found at i:35170398 original size:39 final size:39
Alignment explanation
Indices: 35170355--35170497 Score: 151
Period size: 40 Copynumber: 3.6 Consensus size: 39
35170345 TCCTCGTTCA
* * *
35170355 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACAC
* *
35170394 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACAC
* * * * * *
35170433 GAATGCCTTCGGAACTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCA-CAC
* *
35170474 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
35170498 CAGCATTCAA
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
39 34 0.40
40 48 0.56
41 3 0.04
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACAC
Found at i:35172866 original size:46 final size:46
Alignment explanation
Indices: 35172790--35172881 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
35172780 GACATAAAAC
35172790 TTAATTAATTAATTGCGACCGTGGACGAGTCATAAAGTTAAGGTGT
1 TTAATTAATTAATTGCGACCGTGGACGAGTCATAAAGTTAAGGTGT
* * * * *
35172836 TTAATTAATTAATTGTGATCGTTGATGAGTCATAAGGTTAAGGTGT
1 TTAATTAATTAATTGCGACCGTGGACGAGTCATAAAGTTAAGGTGT
35172882 GGCAATGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (46 bp):
TTAATTAATTAATTGCGACCGTGGACGAGTCATAAAGTTAAGGTGT
Found at i:35178558 original size:47 final size:47
Alignment explanation
Indices: 35178498--35178679 Score: 274
Period size: 47 Copynumber: 3.9 Consensus size: 47
35178488 AATTCTAAAT
* *
35178498 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
35178545 TGTAACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
35178592 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * *
35178639 TGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
1 TGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
35178680 CCGAGTGGCC
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 123 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
TGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:35178683 original size:31 final size:31
Alignment explanation
Indices: 35178638--35178711 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 31
35178628 AAGTGTATAT
* *
35178638 ATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGCCGAGTGGCCAACGTGATGG
35178669 ATGTGAAAGTGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGCCGAGTGGCCAACGTGATGG
35178700 ATGTGAAAGTGC
1 ATGTGAAAGTGC
35178712 ATAAATGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.26, C:0.16, G:0.39, T:0.19
Consensus pattern (31 bp):
ATGTGAAAGTGCCGAGTGGCCAACGTGATGG
Found at i:35178900 original size:37 final size:37
Alignment explanation
Indices: 35178844--35178922 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
35178834 CCGAGCTCTA
* *
35178844 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
35178881 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
35178918 AAGAC
1 AAGAC
35178923 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:35184123 original size:43 final size:43
Alignment explanation
Indices: 35184069--35184151 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
35184059 AATTTATAAG
* * *
35184069 GCATCCGAGCTCTTTGAGTTGGTCCGAGTTCATTATGGATCGA
1 GCATCCAAGCTCGTTGAATTGGTCCGAGTTCATTATGGATCGA
35184112 GCATCCAAGCTCGTTGAATTGGTCCGAGTTCATTATGGAT
1 GCATCCAAGCTCGTTGAATTGGTCCGAGTTCATTATGGAT
35184152 GCGATACATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (43 bp):
GCATCCAAGCTCGTTGAATTGGTCCGAGTTCATTATGGATCGA
Found at i:35189179 original size:26 final size:26
Alignment explanation
Indices: 35189141--35189191 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35189131 ATCCCTTCCG
*
35189141 TATTCTGCCACAAA-GTCTTTCTTTCA
1 TATTATGCCACAAAGGT-TTTCTTTCA
*
35189167 TATTATGCTACAAAGGTTTTCTTTC
1 TATTATGCCACAAAGGTTTTCTTTC
35189192 CTACTGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.45
Consensus pattern (26 bp):
TATTATGCCACAAAGGTTTTCTTTCA
Found at i:35213921 original size:48 final size:46
Alignment explanation
Indices: 35213799--35213965 Score: 129
Period size: 46 Copynumber: 3.6 Consensus size: 46
35213789 CGCGAGATTA
* * ** * ** * *
35213799 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAACGCTG
1 ATGCATGTCCCAGACATGTCTTACACTGGATCTAATATTGAGGCCG
* * * * *
35213845 ATGCATGTGCTAGAAATGTCTTATACTGGAT-TAAATATCTTGAGGTCG
1 ATGCATGTCCCAGACATGTCTTACACTGGATCT-AATA--TTGAGGCCG
* * * *
35213893 ATGCATGTCCCAGACATGTATTACACTGGCTCTCATATTGTGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGATCTAATATTGAGGCCG
*
35213939 ATGCGTGTCCCAGACATGTCTTACACT
1 ATGCATGTCCCAGACATGTCTTACACT
35213966 AGCACACATA
Statistics
Matches: 92, Mismatches: 25, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
45 1 0.01
46 58 0.63
48 32 0.35
49 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTGGATCTAATATTGAGGCCG
Found at i:35217074 original size:43 final size:43
Alignment explanation
Indices: 35216962--35217044 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
35216952 CTAAGATGTG
* * *
35216962 ATTACATGTAAGACCATGTCTGGGACATTGGTATTGTATTGAA
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATTGAA
*
35217005 ATTACGTGTAAGACCATGTCTAGGACATTGGCATCGTATT
1 ATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATT
35217045 ATGATTTGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (43 bp):
ATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATTGAA
Found at i:35218563 original size:17 final size:18
Alignment explanation
Indices: 35218541--35218574 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35218531 CATTGTGAAT
*
35218541 GTTAATGAAT-TTTATTC
1 GTTAATCAATATTTATTC
35218558 GTTAATCAATATTTATT
1 GTTAATCAATATTTATT
35218575 GAGTTTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (18 bp):
GTTAATCAATATTTATTC
Found at i:35219008 original size:14 final size:14
Alignment explanation
Indices: 35218989--35219026 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
35218979 ATTTGCAAGT
35218989 AAAATGATTTCTGG
1 AAAATGATTTCTGG
35219003 AAAATGATTTCTGG
1 AAAATGATTTCTGG
35219017 AAAATGATTT
1 AAAATGATTT
35219027 ACTTTTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:35219035 original size:20 final size:20
Alignment explanation
Indices: 35219010--35219055 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
35219000 TGGAAAATGA
35219010 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
35219030 TTTCT-GAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
35219049 TTTCTGG
1 TTTCTGG
35219056 TGTTTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:35230292 original size:21 final size:20
Alignment explanation
Indices: 35230258--35230300 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
35230248 AGTTTTTGTG
*
35230258 AAAAAAATAAAAAATAAAAT
1 AAAAAAAGAAAAAATAAAAT
35230278 AAAATAAAGAAAAAATAAAAT
1 AAAA-AAAGAAAAAATAAAAT
35230299 AA
1 AA
35230301 CACACAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAAAAGAAAAAATAAAAT
Found at i:35230294 original size:16 final size:17
Alignment explanation
Indices: 35230261--35230300 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
35230251 TTTTGTGAAA
35230261 AAAATAAAAAATAAAAT
1 AAAATAAAAAATAAAAT
*
35230278 AAAATAAAGAA-AAAAT
1 AAAATAAAAAATAAAAT
35230294 AAAATAA
1 AAAATAA
35230301 CACACAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:35235025 original size:47 final size:47
Alignment explanation
Indices: 35234973--35235238 Score: 370
Period size: 47 Copynumber: 5.7 Consensus size: 47
35234963 TTTCACACCA
* * * * * *
35234973 GCCATTCGGCTTTACCGCATATATGCATTTTCATATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
35235020 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
35235067 GCCATTCGGCCTTATCACATATATGCATGCTCACATTTATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * *
35235114 GCCATTCGGCCTCATCACATATACGCATGTTCACATTCATCACATAG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* ** *
35235161 GCCATTCGACCTTATCACATATATGCATGTTCGTATTCACCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
*
35235208 GCCATTCGGCCTTATCACACATATGCATGTT
1 GCCATTCGGCCTTATCACATATATGCATGTT
35235239 TTTGAAACTT
Statistics
Matches: 195, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 195 1.00
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.32
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:35235180 original size:22 final size:22
Alignment explanation
Indices: 35235103--35235181 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
35235093 ATGCTCACAT
* *
35235103 TTATCACATTGGCCATTCGGCC
1 TTATCACATAGGCCATTCGACC
* ** *
35235125 TCATCACATATACGCATGTTC-ACA
1 TTATCACATAGGC-CA--TTCGACC
35235149 TTCATCACATAGGCCATTCGACC
1 TT-ATCACATAGGCCATTCGACC
35235172 TTATCACATA
1 TTATCACATA
35235182 TATGCATGTT
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
22 20 0.48
23 6 0.14
24 4 0.10
25 12 0.29
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (22 bp):
TTATCACATAGGCCATTCGACC
Found at i:35235362 original size:47 final size:47
Alignment explanation
Indices: 35235290--35235463 Score: 276
Period size: 47 Copynumber: 3.7 Consensus size: 47
35235280 ATAAAACTTC
35235290 ATCACATATATGCATGTTCACATTCATCACATAGGCCATTCGGCCTT
1 ATCACATATATGCATGTTCACATTCATCACATAGGCCATTCGGCCTT
* * *
35235337 ATCACATATATGCATGTTCATATTCACCACATTGGCCATTCGGCCTT
1 ATCACATATATGCATGTTCACATTCATCACATAGGCCATTCGGCCTT
* * * * *
35235384 ATCACACATATGCATGCTCACATTCATCACATTGGCCATTTGGCCTC
1 ATCACATATATGCATGTTCACATTCATCACATAGGCCATTCGGCCTT
35235431 ATCACATATATGCATGTTCACATTCATCACATA
1 ATCACATATATGCATGTTCACATTCATCACATA
35235464 AAATCCTAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 115 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (47 bp):
ATCACATATATGCATGTTCACATTCATCACATAGGCCATTCGGCCTT
Found at i:35241921 original size:14 final size:14
Alignment explanation
Indices: 35241902--35241951 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
35241892 GCTACTAAAT
35241902 TCATTTCATACATC
1 TCATTTCATACATC
35241916 TCATTTCAT--AT-
1 TCATTTCATACATC
**
35241927 TCATTTCGCACATC
1 TCATTTCATACATC
35241941 TCATTTCATAC
1 TCATTTCATAC
35241952 TTTGTAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
11 7 0.24
12 2 0.07
13 2 0.07
14 18 0.62
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (14 bp):
TCATTTCATACATC
Found at i:35241928 original size:25 final size:25
Alignment explanation
Indices: 35241900--35241950 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
35241890 TTGCTACTAA
*
35241900 ATTCATTTCATACATCTCATTTCAT
1 ATTCATTTCACACATCTCATTTCAT
*
35241925 ATTCATTTCGCACATCTCATTTCAT
1 ATTCATTTCACACATCTCATTTCAT
35241950 A
1 A
35241951 CTTTGTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTCATTTCACACATCTCATTTCAT
Found at i:35242814 original size:22 final size:22
Alignment explanation
Indices: 35242786--35242835 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
35242776 CCCTATGTTA
**
35242786 TGACATCGAATCATTTGTGTCG
1 TGACATCGAATCATCCGTGTCG
*
35242808 TGACATCGAATCATCCGTGTTG
1 TGACATCGAATCATCCGTGTCG
35242830 TGACAT
1 TGACAT
35242836 AGCTTTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (22 bp):
TGACATCGAATCATCCGTGTCG
Found at i:35243933 original size:15 final size:15
Alignment explanation
Indices: 35243899--35243931 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35243889 GGGTTTAGAA
*
35243899 ATTTGTTTGATTATT
1 ATTTGTTTGATTATG
35243914 ATTTGTTT-ATTATG
1 ATTTGTTTGATTATG
35243928 ATTT
1 ATTT
35243932 TGAACTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (15 bp):
ATTTGTTTGATTATG
Found at i:35246758 original size:19 final size:19
Alignment explanation
Indices: 35246734--35246774 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
35246724 TGAATTAATT
* *
35246734 TAATCATATACGAGCTTAC
1 TAATCACATACAAGCTTAC
35246753 TAATCACATACAAGCTTAC
1 TAATCACATACAAGCTTAC
35246772 TAA
1 TAA
35246775 GCTATGAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (19 bp):
TAATCACATACAAGCTTAC
Found at i:35250901 original size:21 final size:21
Alignment explanation
Indices: 35250877--35250916 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35250867 AAAATCCATT
*
35250877 TCATCATCTCCTTCTTCTTTA
1 TCATCATCTCCTTCCTCTTTA
*
35250898 TCATCCTCTCCTTCCTCTT
1 TCATCATCTCCTTCCTCTT
35250917 CGCTTTCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.40, G:0.00, T:0.50
Consensus pattern (21 bp):
TCATCATCTCCTTCCTCTTTA
Found at i:35252236 original size:10 final size:10
Alignment explanation
Indices: 35252223--35252260 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
35252213 GTTTAAGATA
35252223 TTTTAAAAGG
1 TTTTAAAAGG
*
35252233 TTTTGAAAGG
1 TTTTAAAAGG
35252243 TTTT-AAAGG
1 TTTTAAAAGG
*
35252252 ATTTAAAAG
1 TTTTAAAAG
35252261 ATGTTTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (10 bp):
TTTTAAAAGG
Found at i:35252260 original size:19 final size:20
Alignment explanation
Indices: 35252223--35252260 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
35252213 GTTTAAGATA
* *
35252223 TTTTAAAAGGTTTTGAAAGG
1 TTTTAAAAGGATTTAAAAGG
35252243 TTTT-AAAGGATTTAAAAG
1 TTTTAAAAGGATTTAAAAG
35252261 ATGTTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (20 bp):
TTTTAAAAGGATTTAAAAGG
Found at i:35262655 original size:58 final size:57
Alignment explanation
Indices: 35262584--35262697 Score: 201
Period size: 58 Copynumber: 2.0 Consensus size: 57
35262574 TAACCCAATT
* *
35262584 TTTGTTGGATCAAAAATAATTTTTTAATGGGTCCAAGGATTTGATTTGGGGTGTCCNC
1 TTTGTTAGATCAAAAATAATTTTTCAATGGGTCCAAGGATTTGATTTGGGGTGTCC-C
35262642 TTTGTTAGATCAAAAATAATTTTTCAATGGGTCCAAGGATTTGATTTGGGGTGTCC
1 TTTGTTAGATCAAAAATAATTTTTCAATGGGTCCAAGGATTTGATTTGGGGTGTCC
35262698 ATGGCTGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.39
Consensus pattern (57 bp):
TTTGTTAGATCAAAAATAATTTTTCAATGGGTCCAAGGATTTGATTTGGGGTGTCCC
Found at i:35264342 original size:27 final size:28
Alignment explanation
Indices: 35264285--35264354 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
35264275 GTGACAGAGT
* * *
35264285 CACCAGATACTGATATGTTGTGGCAGTGC
1 CACCAGA-ACAGATATGATGTGGCAGGGC
*
35264314 CACCAGAACAGATAT-ATGTGGTAGGGC
1 CACCAGAACAGATATGATGTGGCAGGGC
35264341 CACCAGAACAGATA
1 CACCAGAACAGATA
35264355 ATTTGTGGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 23 0.62
28 7 0.19
29 7 0.19
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (28 bp):
CACCAGAACAGATATGATGTGGCAGGGC
Found at i:35264370 original size:28 final size:26
Alignment explanation
Indices: 35264285--35264374 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 26
35264275 GTGACAGAGT
*
35264285 CACCAGATACTGATATGTTGTGGCAGTGC
1 CACCAGA-ACAGATAT-TTGTGGCA-TGC
* * *
35264314 CACCAGAACAGATATATGTGGTAGGGC
1 CACCAGAACAGATATTTGTGGCA-TGC
35264341 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCAT-GC
35264369 CACCAG
1 CACCAG
35264375 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (26 bp):
CACCAGAACAGATATTTGTGGCATGC
Found at i:35264527 original size:28 final size:28
Alignment explanation
Indices: 35264480--35264544 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
35264470 AAATTAACCC
*
35264480 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
*
35264508 TAGGGGTATA-ATGGTAATTTTGTATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
35264536 TAGGGGTAT
1 TAGGGGTAT
35264545 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:35266682 original size:14 final size:14
Alignment explanation
Indices: 35266663--35266693 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35266653 AATTGGGTAT
35266663 TTATTCAAGGGAAC
1 TTATTCAAGGGAAC
*
35266677 TTATTCAAGGGTAC
1 TTATTCAAGGGAAC
35266691 TTA
1 TTA
35266694 GTATATTAGG
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:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (14 bp):
TTATTCAAGGGAAC
Found at i:35267560 original size:89 final size:89
Alignment explanation
Indices: 35267409--35267583 Score: 332
Period size: 89 Copynumber: 2.0 Consensus size: 89
35267399 GAACATGGCT
*
35267409 CTTTTTGGGTTGAAGAATGTTTATATAGGTAAATTGTAAAGCCTCTAACCCGAATCCATCACCGG
1 CTTTTTGGGTTGAAGAATGTTTATATAGGGAAATTGTAAAGCCTCTAACCCGAATCCATCACCGG
35267474 AATAGAGTTACGGAGCATTACGCA
66 AATAGAGTTACGGAGCATTACGCA
*
35267498 CTTTTTGTGTTGAAGAATGTTTATATAGGGAAATTGTAAAGCCTCTAACCCGAATCCATCACCGG
1 CTTTTTGGGTTGAAGAATGTTTATATAGGGAAATTGTAAAGCCTCTAACCCGAATCCATCACCGG
35267563 AATAGAGTTACGGAGCATTAC
66 AATAGAGTTACGGAGCATTAC
35267584 CGGAGTTGCC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (89 bp):
CTTTTTGGGTTGAAGAATGTTTATATAGGGAAATTGTAAAGCCTCTAACCCGAATCCATCACCGG
AATAGAGTTACGGAGCATTACGCA
Found at i:35267924 original size:16 final size:17
Alignment explanation
Indices: 35267903--35267943 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
35267893 GTTCATGTTT
35267903 ATAATTTCATTA-ATCG
1 ATAATTTCATTATATCG
35267919 ATAA-TTCATTATATCG
1 ATAATTTCATTATATCG
35267935 AT-ATTTCAT
1 ATAATTTCAT
35267944 GTATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (17 bp):
ATAATTTCATTATATCG
Found at i:35267959 original size:97 final size:98
Alignment explanation
Indices: 35267822--35268019 Score: 353
Period size: 97 Copynumber: 2.0 Consensus size: 98
35267812 CATAAATCAA
*
35267822 ATAATTCATTATATCGATATTTCATGCATTTAAAAATACAATTCAAGTTACACTAACTTACCTCA
1 ATAATTCATTATATCGATATTTCATGCATTTAAAAATACAACTCAAGTTACACTAACTTACCTCA
35267887 TTACTTGTTCATGTTTATAATTTCATTAAT-CG
66 TTACTTGTTCATGTTTATAATTTCATTAATCCG
* *
35267919 ATAATTCATTATATCGATATTTCATGTATTTAAAAATACAACTCAAGTTACACTAACTTACCTCG
1 ATAATTCATTATATCGATATTTCATGCATTTAAAAATACAACTCAAGTTACACTAACTTACCTCA
*
35267984 TTGCTTGTTCATGTTTATAATTTCATTAATCCG
66 TTACTTGTTCATGTTTATAATTTCATTAATCCG
35268017 ATA
1 ATA
35268020 TCTTTTCTTT
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 91 0.95
98 5 0.05
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (98 bp):
ATAATTCATTATATCGATATTTCATGCATTTAAAAATACAACTCAAGTTACACTAACTTACCTCA
TTACTTGTTCATGTTTATAATTTCATTAATCCG
Found at i:35271311 original size:24 final size:23
Alignment explanation
Indices: 35271284--35271334 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
35271274 TTAATGGTAC
35271284 ACAATACCTA-AACAGTAATCAGTA
1 ACAATACC-AGAACAGTAA-CAGTA
*
35271308 ACAATAGCAGTAACAGTAACAGTA
1 ACAATACCAG-AACAGTAACAGTA
35271332 ACA
1 ACA
35271335 GTATTCAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 1 0.04
24 15 0.62
25 8 0.33
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.18
Consensus pattern (23 bp):
ACAATACCAGAACAGTAACAGTA
Found at i:35271326 original size:6 final size:6
Alignment explanation
Indices: 35271294--35271337 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
35271284 ACAATACCTA
* *
35271294 AACAGT AATCAGT AACAAT AGCAGT AACAGT AACAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
35271338 TTCAACACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:35271415 original size:33 final size:34
Alignment explanation
Indices: 35271372--35271450 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 34
35271362 GTAATAGTAA
35271372 CGGTAACAG-TATTCAACACACAAAGTGTCGAAT
1 CGGTAACAGATATTCAACACACAAAGTGTCGAAT
*
35271405 TGGTAACAGTAACAATATTCAACACACAAAGTGTCGAAT
1 CGGTAACAG-----ATATTCAACACACAAAGTGTCGAAT
35271444 CGGTAAC
1 CGGTAAC
35271451 GGTAACAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
33 8 0.21
39 30 0.79
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (34 bp):
CGGTAACAGATATTCAACACACAAAGTGTCGAAT
Found at i:35271531 original size:87 final size:87
Alignment explanation
Indices: 35271326--35271637 Score: 387
Period size: 87 Copynumber: 3.6 Consensus size: 87
35271316 AGTAACAGTA
* * * ** * * *
35271326 ACAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAATAGTAACGGTAACAGTATTCAACAC
1 ACAGTAACAATATTCAACACACAAAGTGCCGAATCGGTAACGGTAACAGTAACAATATTCGACAC
* *
35271391 ACAAAGTGTCGAATTGGT-A--
66 ACAAAGTGCCGAATCGGTAACG
* *
35271410 ACAGTAACAATATTCAACACACAAAGTGTCGAATCGGTAACGGTAACAATAACAATATTCGACAC
1 ACAGTAACAATATTCAACACACAAAGTGCCGAATCGGTAACGGTAACAGTAACAATATTCGACAC
*
35271475 ACATAGTGCCGAATCGGTAACG
66 ACAAAGTGCCGAATCGGTAACG
* *
35271497 ACAGTAACAATATTCGACACACAAAGTGCCGAATCAGTAACGGTAACAGTAACAATATTCGACAC
1 ACAGTAACAATATTCAACACACAAAGTGCCGAATCGGTAACGGTAACAGTAACAATATTCGACAC
35271562 ACAAAGTGCCGAATCGGTAACG
66 ACAAAGTGCCGAATCGGTAACG
* * * * * *
35271584 ATAGCAGTAGCAATATTCGATACATAAAGTGCCGAATCGGTAACAGTAGCAGTA
1 --A-CAGTAACAATATTCAACACACAAAGTGCCGAATCGGTAACGGTAACAGTA
35271638 GCGGTAACAG
Statistics
Matches: 198, Mismatches: 24, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
84 70 0.35
85 1 0.01
87 82 0.41
89 1 0.01
90 44 0.22
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (87 bp):
ACAGTAACAATATTCAACACACAAAGTGCCGAATCGGTAACGGTAACAGTAACAATATTCGACAC
ACAAAGTGCCGAATCGGTAACG
Found at i:35271575 original size:132 final size:127
Alignment explanation
Indices: 35271317--35271627 Score: 372
Period size: 132 Copynumber: 2.4 Consensus size: 127
35271307 AACAATAGCA
* * * * * * * *
35271317 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAATAGTAACGGTAACAGT
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAA-CG-AACAGTAACAAT
* *
35271382 ATTCAACACACAAAGTGTCGAATTGGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCG
64 ATTCAACACACAAAGTGCCGAATTGGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCG
* *
35271446 GTAACGGTAACAATAACAATATTCGACACACATAGTGCCGAATCGGTAACG-ACAGTAACAATAT
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGAACAGTAACAATAT
* *
35271510 TCGACACACAAAGTGCCGAATCAGTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAA
66 TCAACACACAAAGTGCCGAAT---T---GGTAACAGTAACAATATTCAACACACAAAGTGCCGAA
35271575 TCG
125 TCG
* * * * *
35271578 GTAACGATAGCAGTAGCAATATTCGATACATAAAGTGCCGAATCGGTAAC
1 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAAC
35271628 AGTAGCAGTA
Statistics
Matches: 155, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
126 30 0.19
128 1 0.01
129 43 0.28
132 81 0.52
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (127 bp):
GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACGAACAGTAACAATAT
TCAACACACAAAGTGCCGAATTGGTAACAGTAACAATATTCAACACACAAAGTGCCGAATCG
Found at i:35271639 original size:45 final size:44
Alignment explanation
Indices: 35271317--35271637 Score: 359
Period size: 45 Copynumber: 7.3 Consensus size: 44
35271307 AACAATAGCA
* * * *
35271317 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCT
1 GTAAC-GTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * * * *
35271362 GTAATAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAAT--
1 GTAA-CGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * *
35271405 -T--GGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCG
1 GTAACGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
35271446 GTAACGGTAACAATAACAATATTCGACACACATAGTGCCGAATCG
1 GTAAC-GTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
*
35271491 GTAACG--ACAGTAACAATATTCGACACACAAAGTGCCGAATCA
1 GTAACGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
35271533 GTAACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
1 GTAAC-GTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * * *
35271578 GTAACGATAGCAGTAGCAATATTCGATACATAAAGTGCCGAATCG
1 GTAACG-TAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
*
35271623 GTAACAGTAGCAGTA
1 GTAAC-GTAACAGTA
35271638 GCGGTAACAG
Statistics
Matches: 244, Mismatches: 20, Indels: 24
0.85 0.07 0.08
Matches are distributed among these distances:
39 35 0.14
42 40 0.16
43 1 0.00
44 2 0.01
45 165 0.68
46 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (44 bp):
GTAACGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
Found at i:35281434 original size:49 final size:49
Alignment explanation
Indices: 35281261--35282210 Score: 1765
Period size: 49 Copynumber: 19.6 Consensus size: 49
35281251 CCCTTCGGGA
* * * * *
35281261 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
35281308 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGG-
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281354 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281401 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281450 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281499 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281548 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281597 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281646 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281695 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281744 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281793 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281842 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281891 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281940 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35281989 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35282038 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35282087 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35282136 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
35282185 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
35282211 CACAATTATC
Statistics
Matches: 887, Mismatches: 11, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
46 44 0.05
47 50 0.06
49 793 0.89
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:35288762 original size:107 final size:107
Alignment explanation
Indices: 35288576--35289004 Score: 822
Period size: 107 Copynumber: 4.0 Consensus size: 107
35288566 CATATAAAAC
* *
35288576 AAGACTAATGACATAATTTAACCAAACAGATTTAACTGTTATCATCGCGTTAGAACTAAATTTCA
1 AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
35288641 AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
66 AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
35288683 AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
1 AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
35288748 AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
66 AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
35288790 AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
1 AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
35288855 AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
66 AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
35288897 AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
1 AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
* *
35288962 AAACTCAAAAAACATAAAGACTAAAATTAATCAAATTAAAGT
66 AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
35289004 A
1 A
35289005 CATGTACGAA
Statistics
Matches: 318, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 318 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (107 bp):
AAGACTAATGACATAATTTAACCAAACAGATTTAACTATTACCATCGCGTTAGAACTAAATTTCA
AAACTCAAAAAGCATAAAGATTAAAATTAATCAAATTAAAGT
Found at i:35290802 original size:95 final size:95
Alignment explanation
Indices: 35290639--35291019 Score: 753
Period size: 95 Copynumber: 4.0 Consensus size: 95
35290629 AGTGGTGCCA
*
35290639 TGCATTGTATTCAAGCTTTTTCCCCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
1 TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
35290704 GATAATGAGTGCTGCCTCCATCATGCATCT
66 GATAATGAGTGCTGCCTCCATCATGCATCT
35290734 TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
1 TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
35290799 GATAATGAGTGCTGCCTCCATCATGCATCT
66 GATAATGAGTGCTGCCTCCATCATGCATCT
35290829 TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
1 TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
35290894 GATAATGAGTGCTGCCTCCATCATGCATCT
66 GATAATGAGTGCTGCCTCCATCATGCATCT
35290924 TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
1 TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
35290989 GATAATGAGTGCTGCCTCCATCATGCATCT
66 GATAATGAGTGCTGCCTCCATCATGCATCT
35291019 T
1 T
35291020 TCTCTTTCTC
Statistics
Matches: 285, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 285 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (95 bp):
TGCATTGTATTCAAGCTTTTTCACCCCCTGAATTTCCTTTATCGGAATCTGAAACTTTTGCTTGA
GATAATGAGTGCTGCCTCCATCATGCATCT
Found at i:35291768 original size:34 final size:35
Alignment explanation
Indices: 35291729--35291806 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
35291719 TTGAATAAGT
*
35291729 TAATACTTTTTAG-TGTTTAGATA-AATTTTTTGAAA
1 TAATACTTTTT-GCTATTT-GATAGAATTTTTTGAAA
*
35291764 -AATACGTTTTGCTATTTGATAGAATTTTTTGAAA
1 TAATACTTTTTGCTATTTGATAGAATTTTTTGAAA
35291798 TAATA-TTTT
1 TAATACTTTT
35291807 CAGGAACTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 5 0.14
34 28 0.76
35 4 0.11
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (35 bp):
TAATACTTTTTGCTATTTGATAGAATTTTTTGAAA
Found at i:35293305 original size:13 final size:13
Alignment explanation
Indices: 35293287--35293314 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35293277 TCTGTAGATT
35293287 AAAAAAAAAAACA
1 AAAAAAAAAAACA
35293300 AAAAAAAAAAACA
1 AAAAAAAAAAACA
35293313 AA
1 AA
35293315 GAGGGACCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:35293390 original size:10 final size:11
Alignment explanation
Indices: 35293370--35293394 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35293360 ATGATAAGGA
35293370 TTTCTTTTTTT
1 TTTCTTTTTTT
35293381 TTTCTTTTTTT
1 TTTCTTTTTTT
35293392 TTT
1 TTT
35293395 AATTTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:35295440 original size:52 final size:52
Alignment explanation
Indices: 35295383--35295481 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
35295373 TCTTGGGTGG
35295383 ACACATACATATGGTGGATACTTACATAGTTTTTCACACTATTGATTTGCGA
1 ACACATACATATGGTGGATACTTACATAGTTTTTCACACTATTGATTTGCGA
*
35295435 ACACATACATATGGTGGATACTTATATAGTTTTTCACACTATTGATT
1 ACACATACATATGGTGGATACTTACATAGTTTTTCACACTATTGATT
35295482 CTTACTCAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (52 bp):
ACACATACATATGGTGGATACTTACATAGTTTTTCACACTATTGATTTGCGA
Found at i:35296043 original size:27 final size:27
Alignment explanation
Indices: 35296002--35296071 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
35295992 ATGGAGTTTT
* * **
35296002 CCACAAAGACGTTCTTTTCAAATTCTG
1 CCACAAAGGCTTTCTTTTCAAATTCCA
* *
35296029 CCACAAAGGTTTTC-TTTCATATTCCA
1 CCACAAAGGCTTTCTTTTCAAATTCCA
35296055 CCACAAAGGCTTTCTTT
1 CCACAAAGGCTTTCTTT
35296072 CATATTACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
26 22 0.63
27 13 0.37
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (27 bp):
CCACAAAGGCTTTCTTTTCAAATTCCA
Found at i:35296058 original size:26 final size:26
Alignment explanation
Indices: 35296029--35296099 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
35296019 TCAAATTCTG
*
35296029 CCACAAAGGTTTTCTTTCATATTCCA
1 CCACAAAGGTTTTCTTTCATATTACA
*
35296055 CCACAAAGGCTTTCTTTCATATTACA
1 CCACAAAGGTTTTCTTTCATATTACA
* *
35296081 TCAAAAAGGTTTTTCTTTC
1 CCACAAAGG-TTTTCTTTC
35296100 CTAATGTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 31 0.79
27 8 0.21
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.39
Consensus pattern (26 bp):
CCACAAAGGTTTTCTTTCATATTACA
Found at i:35309682 original size:27 final size:26
Alignment explanation
Indices: 35309638--35309689 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
35309628 CTCGCTGCAA
*
35309638 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
35309665 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
35309690 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:35309822 original size:104 final size:104
Alignment explanation
Indices: 35309642--35309908 Score: 509
Period size: 104 Copynumber: 2.6 Consensus size: 104
35309632 CTGCAATCTG
*
35309642 GTGGCCTCGCCACATATATCTGT-TCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTACAAT
1 GTGGCCTAGCCACA-ATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTACAAT
35309706 CTGGTGGCTTCGCCACACACACATATATATATCTGTTCTA
65 CTGGTGGCTTCGCCACACACACATATATATATCTGTTCTA
35309746 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTACAATC
1 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTACAATC
35309811 TGGTGGCTTCGCCACACACACATATATATATCTGTTCTA
66 TGGTGGCTTCGCCACACACACATATATATATCTGTTCTA
35309850 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCT
1 GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCT
35309909 GTAATTTCTG
Statistics
Matches: 161, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
103 8 0.05
104 153 0.95
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30
Consensus pattern (104 bp):
GTGGCCTAGCCACAATATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTACAATC
TGGTGGCTTCGCCACACACACATATATATATCTGTTCTA
Found at i:35316967 original size:27 final size:26
Alignment explanation
Indices: 35316923--35316974 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
35316913 TTCGCTGCAA
*
35316923 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
35316950 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
35316975 GTAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:35317028 original size:31 final size:32
Alignment explanation
Indices: 35316990--35317051 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
35316980 CTCGCTGCAA
* *
35316990 TCTGGTGGCTTCGCCAC-ATATATGTATCTGT
1 TCTGGTGGCCTAGCCACAATATATGTATCTGT
*
35317021 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATGTATCTG
35317052 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATGTATCTGT
Found at i:35317043 original size:26 final size:27
Alignment explanation
Indices: 35317014--35317072 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
35317004 CACATATATG
*
35317014 TATCTGT-TCTGGTGGCCTAGCCACAA
1 TATCTGTATCTGGTGACCTAGCCACAA
* * *
35317040 TATCTGTATCTGGTGACTTCGTCACAA
1 TATCTGTATCTGGTGACCTAGCCACAA
35317067 TATCTG
1 TATCTG
35317073 GTAGCCTCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (27 bp):
TATCTGTATCTGGTGACCTAGCCACAA
Found at i:35319221 original size:15 final size:14
Alignment explanation
Indices: 35319179--35319221 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
35319169 TGTTATGTAT
35319179 ACATAATATAAAAG
1 ACATAATATAAAAG
*
35319193 ACATAAATACAAAAG
1 ACAT-AATATAAAAG
*
35319208 CCATAATAGTAAAA
1 ACATAATA-TAAAA
35319222 TTTGAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.19
Consensus pattern (14 bp):
ACATAATATAAAAG
Found at i:35324067 original size:46 final size:46
Alignment explanation
Indices: 35324017--35324285 Score: 295
Period size: 46 Copynumber: 5.8 Consensus size: 46
35324007 TGATTGAGCA
35324017 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
35324063 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
35324108 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
35324156 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
35324201 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
35324249 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
35324286 GCGGGTTACA
Statistics
Matches: 189, Mismatches: 15, Indels: 38
0.78 0.06 0.16
Matches are distributed among these distances:
42 4 0.02
43 10 0.05
45 8 0.04
46 90 0.48
47 58 0.31
48 6 0.03
50 9 0.05
51 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:35324173 original size:93 final size:93
Alignment explanation
Indices: 35324014--35324278 Score: 496
Period size: 93 Copynumber: 2.8 Consensus size: 93
35324004 GGATGATTGA
35324014 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
35324079 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
35324107 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
35324172 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
35324200 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
35324264 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
35324279 CTTATGGGCG
Statistics
Matches: 169, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 2 0.01
93 167 0.99
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:35332903 original size:20 final size:19
Alignment explanation
Indices: 35332876--35332935 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
35332866 AAATGGTCGG
*
35332876 AATTGAGCTCAAGTGAGCT
1 AATTGAGCTCAAATGAGCT
*
35332895 AATTGGAGCTGAAATGAGCT
1 AATT-GAGCTCAAATGAGCT
** *
35332915 AAGGGAGCTGAAATTGAGCT
1 AATTGAGCTCAAA-TGAGCT
35332935 A
1 A
35332936 CAGTCAGGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (19 bp):
AATTGAGCTCAAATGAGCT
Found at i:35332923 original size:19 final size:21
Alignment explanation
Indices: 35332889--35332935 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
35332879 TGAGCTCAAG
*
35332889 TGAGCTAATTGGAGCTGAAA-
1 TGAGCTAATGGGAGCTGAAAT
35332909 TGAGCTAA-GGGAGCTGAAAT
1 TGAGCTAATGGGAGCTGAAAT
35332929 TGAGCTA
1 TGAGCTA
35332936 CAGTCAGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.23
Consensus pattern (21 bp):
TGAGCTAATGGGAGCTGAAAT
Found at i:35335187 original size:20 final size:20
Alignment explanation
Indices: 35335164--35335210 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
35335154 GGGTTAAGAT
*
35335164 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
35335184 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
35335204 TGAGCTG
1 TGAGCTG
35335211 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:35336936 original size:48 final size:48
Alignment explanation
Indices: 35336881--35336986 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
35336871 TTGTCTTTTC
*
35336881 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
35336929 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
35336977 TTTCTTTTTC
1 TTTCTTTTTC
35336987 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:35338027 original size:13 final size:13
Alignment explanation
Indices: 35338011--35338035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35338001 AGACTTTTCA
35338011 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
35338024 CTTTTTTTTTTT
1 CTTTTTTTTTTT
35338036 AACTCGATTT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:35339620 original size:20 final size:20
Alignment explanation
Indices: 35339597--35339642 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
35339587 GGGTTAAGAT
*
35339597 TGAGCTAAATTGAGCTTGAG
1 TGAGCTAAATTGAGCTCGAG
* * *
35339617 TGAGTTGACTTGAGCTCGAG
1 TGAGCTAAATTGAGCTCGAG
35339637 TGAGCT
1 TGAGCT
35339643 GGAAATGAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGCTAAATTGAGCTCGAG
Found at i:35340991 original size:18 final size:18
Alignment explanation
Indices: 35340958--35341004 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
35340948 TTTTTCATCA
* *
35340958 TCTTTTTCATTTTCAATT
1 TCTTTTTCAATCTCAATT
35340976 T-TTTTCTCAATCTCAATT
1 TCTTTT-TCAATCTCAATT
35340994 TCTTTTTCAAT
1 TCTTTTTCAAT
35341005 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTTTTCAATCTCAATT
Found at i:35341968 original size:12 final size:12
Alignment explanation
Indices: 35341939--35342008 Score: 79
Period size: 12 Copynumber: 5.6 Consensus size: 12
35341929 TTTCAACTCA
35341939 TTTTTTTTG-CT
1 TTTTTTTTGACT
35341950 TGATTTTTTTGACT
1 T--TTTTTTTGACT
35341964 TTTTTTTTGACT
1 TTTTTTTTGACT
*
35341976 TTTTTTTTGAATT
1 TTTTTTTTG-ACT
*
35341989 TCTTTTTTTGAAT
1 T-TTTTTTTGACT
35342002 TTTTTTT
1 TTTTTTT
35342009 AAACTTCGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
11 1 0.02
12 26 0.50
13 14 0.27
14 11 0.21
ACGTcount: A:0.10, C:0.06, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGACT
Found at i:35342021 original size:26 final size:26
Alignment explanation
Indices: 35341966--35342023 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
35341956 TTTTGACTTT
* * * *
35341966 TTTTTTGACTTTTTTTTTGAATTTCT
1 TTTTTTGACATTTTTTTTAAACTTCA
35341992 TTTTTTGA-ATTTTTTTTAAACTTCGA
1 TTTTTTGACATTTTTTTTAAACTTC-A
35342018 TTTTTT
1 TTTTTT
35342024 AATACTCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (26 bp):
TTTTTTGACATTTTTTTTAAACTTCA
Found at i:35344333 original size:15 final size:15
Alignment explanation
Indices: 35344313--35344342 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35344303 TAGGCTAAGA
35344313 AAGGAAGTAATATGT
1 AAGGAAGTAATATGT
35344328 AAGGAAGTAATATGT
1 AAGGAAGTAATATGT
35344343 TGAAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (15 bp):
AAGGAAGTAATATGT
Found at i:35350899 original size:14 final size:14
Alignment explanation
Indices: 35350880--35350906 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35350870 TGCATCTCCC
35350880 CATGCATGAATCTA
1 CATGCATGAATCTA
35350894 CATGCATGAATCT
1 CATGCATGAATCT
35350907 GCCCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (14 bp):
CATGCATGAATCTA
Found at i:35353613 original size:18 final size:18
Alignment explanation
Indices: 35353590--35353629 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
35353580 TTAATTCATA
35353590 AAGTCTAAAAATTAAACT
1 AAGTCTAAAAATTAAACT
35353608 AAGTCTAAAAATTAAACT
1 AAGTCTAAAAATTAAACT
35353626 AAGT
1 AAGT
35353630 ATTTAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (18 bp):
AAGTCTAAAAATTAAACT
Found at i:35354567 original size:33 final size:34
Alignment explanation
Indices: 35354519--35354593 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
35354509 AGATTTAAAC
35354519 AAATTAATTACTAACAATTATTTAAGCTGAACTA
1 AAATTAATTACTAACAATTATTTAAGCTGAACTA
* * *
35354553 AAATT-ATTTCTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACAATTATTTAAGCTGAACTA
*
35354586 AATTTAAT
1 AAATTAAT
35354594 AAACTAACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 29 0.81
34 7 0.19
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACAATTATTTAAGCTGAACTA
Found at i:35364101 original size:27 final size:27
Alignment explanation
Indices: 35364071--35364248 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35364061 ATATTGAGTC
* * * *
35364071 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
35364098 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35364125 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
35364153 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
35364180 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
35364207 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35364234 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35364249 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:35364210 original size:82 final size:81
Alignment explanation
Indices: 35364092--35364247 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35364082 TGCTATATAA
* *
35364092 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
35364157 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
35364174 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
35364238 CACTTAGTGC
65 CACTTAGTGC
35364248 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:35364262 original size:82 final size:83
Alignment explanation
Indices: 35364071--35364262 Score: 216
Period size: 82 Copynumber: 2.3 Consensus size: 83
35364061 ATATTGAGTC
* * * * *
35364071 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
35364135 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
35364153 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
35364214 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
*
35364234 CGCACACTTAGTGCTGTACAATTTAATTC
1 CGCACACTTAGTGCTGTACAATTCAATTC
35364263 CCGCGCACTT
Statistics
Matches: 91, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 70 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:35372187 original size:27 final size:27
Alignment explanation
Indices: 35372157--35372334 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
35372147 ATATTGAGTC
* * * *
35372157 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
35372184 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35372211 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
35372239 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * **
35372266 CGCACACTTAGTGC-ATTATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
35372293 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35372320 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35372335 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:35388524 original size:26 final size:26
Alignment explanation
Indices: 35388495--35388544 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
35388485 TAGTCCAATT
*
35388495 CAGAGATGGCCAATTTTGAGGGCTCA
1 CAGAAATGGCCAATTTTGAGGGCTCA
35388521 CAGAAATGGCCAATTTTGAGGGCT
1 CAGAAATGGCCAATTTTGAGGGCT
35388545 TTTAGGCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (26 bp):
CAGAAATGGCCAATTTTGAGGGCTCA
Found at i:35390754 original size:19 final size:19
Alignment explanation
Indices: 35390730--35390768 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35390720 GATTGCACAC
35390730 ATAATTTTGGCTCTCTTGT
1 ATAATTTTGGCTCTCTTGT
35390749 ATAATTTTGGCTCTCTTGT
1 ATAATTTTGGCTCTCTTGT
35390768 A
1 A
35390769 CACATGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (19 bp):
ATAATTTTGGCTCTCTTGT
Found at i:35391497 original size:30 final size:30
Alignment explanation
Indices: 35391463--35391519 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
35391453 TCCTTAACTC
35391463 AAACTTTTGCAAAATTACAATTTTGCCTCT
1 AAACTTTTGCAAAATTACAATTTTGCCTCT
* * *
35391493 AAACTTTTGCATATTTACACTTTTGCC
1 AAACTTTTGCAAAATTACAATTTTGCC
35391520 CCTAGGCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCTCT
Found at i:35403731 original size:40 final size:41
Alignment explanation
Indices: 35403648--35403832 Score: 207
Period size: 43 Copynumber: 4.5 Consensus size: 41
35403638 AAACCAAGTA
* * * *
35403648 CCTTCGGGATTTAG-CCGG-ATATAGCT-ACTTGCTCAACTG
1 CCTTCGGGACTTAGCCCGGTATATAG-TAACTCGCACAAATG
* *
35403687 CCTTCGAGACTTAGCCCGG-ATATAGTAACTCGCACAAATT
1 CCTTCGGGACTTAGCCCGGTATATAGTAACTCGCACAAATG
* * *
35403727 CCTTCGGGACATAGCCCGGTTACCATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGG-TA-TATAGTAACTCGCACAAATG
*
35403770 CCTTTGGGACTTAGCCCGGTTATCATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGG-TAT-ATAGTAACTCGCACAAATG
35403813 CCTTCGGGACTTAGCCCGGT
1 CCTTCGGGACTTAGCCCGGT
35403833 TATCATCTGA
Statistics
Matches: 124, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 13 0.10
40 36 0.29
42 2 0.02
43 73 0.59
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGTATATAGTAACTCGCACAAATG
Found at i:35403835 original size:43 final size:43
Alignment explanation
Indices: 35403685--35403838 Score: 233
Period size: 43 Copynumber: 3.7 Consensus size: 43
35403675 CTTGCTCAAC
*
35403685 TGCCTTCGAGACTTAGCCCGG--AT-ATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATCATAGTAACTCGCACAAA
* * * *
35403725 TTCCTTCGGGACATAGCCCGGTTACCATAGTAACTCACACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATCATAGTAACTCGCACAAA
*
35403768 TGCCTTTGGGACTTAGCCCGGTTATCATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATCATAGTAACTCGCACAAA
35403811 TGCCTTCGGGACTTAGCCCGGTTATCAT
1 TGCCTTCGGGACTTAGCCCGGTTATCAT
35403839 CTGAATATTC
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
40 18 0.18
42 1 0.01
43 81 0.81
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (43 bp):
TGCCTTCGGGACTTAGCCCGGTTATCATAGTAACTCGCACAAA
Found at i:35412028 original size:24 final size:24
Alignment explanation
Indices: 35412000--35412054 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
35411990 GAGAAGAAGA
35412000 AGCCAAAAAAATCTTAGAGAAAAT
1 AGCCAAAAAAATCTTAGAGAAAAT
35412024 AGCCAAAAAAATCTTAGAGAAAAT
1 AGCCAAAAAAATCTTAGAGAAAAT
*
35412048 GGCCAAA
1 AGCCAAA
35412055 CAAGTTCAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (24 bp):
AGCCAAAAAAATCTTAGAGAAAAT
Found at i:35413978 original size:27 final size:26
Alignment explanation
Indices: 35413910--35414021 Score: 131
Period size: 26 Copynumber: 4.3 Consensus size: 26
35413900 CTGGAGGCCT
*
35413910 AGCCTCTTTT-AAT-AACTGGGGCAAA
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
35413935 AGCCC-TTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
35413960 AGCCCTTTTTCAATAAACTGGGGCATA
1 AGCCC-TTTTCAATAAACTGGGGCATA
** *
35413987 AGCCCTTTTCGGTAAACTGGAGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
35414013 AGCCCTTTT
1 AGCCCTTTT
35414022 GCACTTCCTC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
23 3 0.04
24 2 0.03
25 20 0.27
26 27 0.36
27 23 0.31
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:35414002 original size:26 final size:26
Alignment explanation
Indices: 35413923--35414021 Score: 146
Period size: 26 Copynumber: 3.8 Consensus size: 26
35413913 CTCTTTTAAT
*
35413923 AACTGGGGCAAAAGCCC-TTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
35413948 AACTGGGGCATAAGCCCTTTTTCAATA
1 AACTGGGGCATAAGCCC-TTTTCGGTA
35413975 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
35414001 AACTGGAGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
35414022 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.24
26 27 0.41
27 23 0.35
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:35414012 original size:53 final size:50
Alignment explanation
Indices: 35413916--35414021 Score: 167
Period size: 53 Copynumber: 2.1 Consensus size: 50
35413906 GCCTAGCCTC
*
35413916 TTTTAATAACTGGGGCAAAAGCCCTTTCGGTAAACTGGGGCATAAGCCCT
1 TTTTAATAACTGGGGCAAAAGCCCTTTCGGTAAACTGGAGCATAAGCCCT
*
35413966 TTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGAGCATAAGCCCT
1 TTTT-AAT-AACTGGGGCAAAAGCCC-TTTCGGTAAACTGGAGCATAAGCCCT
35414019 TTT
1 TTT
35414022 GCACTTCCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
50 4 0.08
51 3 0.06
52 16 0.31
53 28 0.55
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (50 bp):
TTTTAATAACTGGGGCAAAAGCCCTTTCGGTAAACTGGAGCATAAGCCCT
Found at i:35422107 original size:20 final size:20
Alignment explanation
Indices: 35422082--35422318 Score: 429
Period size: 20 Copynumber: 11.8 Consensus size: 20
35422072 TTATGAATAC
35422082 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35422102 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
35422122 ACCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35422142 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
35422162 ACCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35422182 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
35422202 ACCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35422222 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
35422242 ACCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35422262 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
35422282 ACCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
35422302 ATCATGTGCATATCATA
1 ATCATGTGCATATCATA
35422319 TCAATATTGT
Statistics
Matches: 207, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 207 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:35422147 original size:60 final size:60
Alignment explanation
Indices: 35422082--35422346 Score: 430
Period size: 60 Copynumber: 4.5 Consensus size: 60
35422072 TTATGAATAC
*
35422082 ATCATGTGCATATCATACATATCATGTGCATATCATACATACCATGTGCATATCATACAT
1 ATCATGTGCATATCATACATACCATGTGCATATCATACATACCATGTGCATATCATACAT
*
35422142 ATCATGTGCATATCATACATACCATGTGCATATCATACATATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACATACCATGTGCATATCATACATACCATGTGCATATCATACAT
* *
35422202 ACCATGTGCATATCATACATATCATGTGCATATCATACATACCATGTGCATATCATACAT
1 ATCATGTGCATATCATACATACCATGTGCATATCATACATACCATGTGCATATCATACAT
*
35422262 ATCATGTGCATATCATACATACCATGTGCATATCATACATATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATACATACCATGTGCATATCATACATACCATGTGCATATCATA-CAT
* *
35422322 AT-AT-TGTATATCA-AAATACCATGTG
1 ATCATGTGCATATCATACATACCATGTG
35422347 TCAAGTTCAT
Statistics
Matches: 194, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
57 11 0.06
58 8 0.04
59 2 0.01
60 171 0.88
61 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.33
Consensus pattern (60 bp):
ATCATGTGCATATCATACATACCATGTGCATATCATACATACCATGTGCATATCATACAT
Found at i:35422325 original size:11 final size:10
Alignment explanation
Indices: 35422090--35422321 Score: 144
Period size: 11 Copynumber: 23.2 Consensus size: 10
35422080 ACATCATGTG
35422090 CATATCATA-
1 CATATCATAT
*
35422099 CATATCATGT
1 CATATCATAT
35422109 GCATATCATA-
1 -CATATCATAT
* *
35422119 CATACCATGT
1 CATATCATAT
35422129 GCATATCATA-
1 -CATATCATAT
*
35422139 CATATCATGT
1 CATATCATAT
35422149 GCATATCATA-
1 -CATATCATAT
* *
35422159 CATACCATGT
1 CATATCATAT
35422169 GCATATCATA-
1 -CATATCATAT
*
35422179 CATATCATGT
1 CATATCATAT
35422189 GCATATCATA-
1 -CATATCATAT
* *
35422199 CATACCATGT
1 CATATCATAT
35422209 GCATATCATA-
1 -CATATCATAT
*
35422219 CATATCATGT
1 CATATCATAT
35422229 GCATATCATA-
1 -CATATCATAT
* *
35422239 CATACCATGT
1 CATATCATAT
35422249 GCATATCATA-
1 -CATATCATAT
*
35422259 CATATCATGT
1 CATATCATAT
35422269 GCATATCATA-
1 -CATATCATAT
* *
35422279 CATACCATGT
1 CATATCATAT
35422289 GCATATCATA-
1 -CATATCATAT
*
35422299 CATATCATGT
1 CATATCATAT
35422309 GCATATCATAT
1 -CATATCATAT
35422320 CA
1 CA
35422322 ATATTGTATA
Statistics
Matches: 169, Mismatches: 32, Indels: 43
0.69 0.13 0.18
Matches are distributed among these distances:
9 83 0.49
10 2 0.01
11 84 0.50
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.33
Consensus pattern (10 bp):
CATATCATAT
Found at i:35422393 original size:25 final size:25
Alignment explanation
Indices: 35422365--35422412 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35422355 ATAATTAAAC
* * *
35422365 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTTA
35422390 CCTAGGGGCAAAATAGTCATTTT
1 CCTAGGGGCAAAATAGTCATTTT
35422413 CATACTATAA
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:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTTA
Found at i:35425248 original size:21 final size:21
Alignment explanation
Indices: 35425222--35425261 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35425212 TATATATATG
35425222 TAATGCCCACTATTGGAAATT
1 TAATGCCCACTATTGGAAATT
*
35425243 TAATGCTCACTATTGGAAA
1 TAATGCCCACTATTGGAAA
35425262 CTTACTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (21 bp):
TAATGCCCACTATTGGAAATT
Found at i:35426367 original size:58 final size:55
Alignment explanation
Indices: 35426302--35426466 Score: 154
Period size: 57 Copynumber: 2.9 Consensus size: 55
35426292 TTTTTATAGT
*
35426302 ATTATATATTATGTTTTTTTAATTCATATAATAATAATTATATTAAGAATTTTATTAGA
1 ATTATATATTAT-TTTTTTTAATT-ATATAATAATAATTATATTAA-AATTTGATTA-A
* * * * *
35426361 A-TATATATTATTTTATTAAATTATATTTAGTAATAATTATGTTAAAATATGATTAA
1 ATTATATATTATTTTTTTTAATTATA--TAATAATAATTATATTAAAATTTGATTAA
* * * *
35426417 ATTATTTATTATTTTTATTAATTTTTTTAATAATAATCT-TATTAAAATTT
1 ATTATATATTATTTTTTTTAA-TTATATAATAATAAT-TATATTAAAATTT
35426467 AATAATAATA
Statistics
Matches: 86, Mismatches: 15, Indels: 13
0.75 0.13 0.11
Matches are distributed among these distances:
56 23 0.27
57 33 0.38
58 29 0.34
59 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (55 bp):
ATTATATATTATTTTTTTTAATTATATAATAATAATTATATTAAAATTTGATTAA
Found at i:35426373 original size:20 final size:18
Alignment explanation
Indices: 35426350--35426387 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
35426340 TATATTAAGA
35426350 ATTTTATTAGAATATATATT
1 ATTTTATTA-AAT-TATATT
35426370 ATTTTATTAAATTATATT
1 ATTTTATTAAATTATATT
35426388 TAGTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTTATTAAATTATATT
Found at i:35426462 original size:56 final size:57
Alignment explanation
Indices: 35426302--35426464 Score: 172
Period size: 58 Copynumber: 2.8 Consensus size: 57
35426292 TTTTTATAGT
* * * * *
35426302 ATTATATATTATGTTTTTTTAATTCATATAATAATAATTATATTAAGAATTTTATTAGA
1 ATTATATATTAT-TTTTATTAATTTATTTAATAATAATTATATTAA-AATATGATTAGA
* *
35426361 A-TATATATTA-TTTTATTAAATTATATTTAGTAATAATTATGTTAAAATATGATTA-A
1 ATTATATATTATTTTTATT-AATT-TATTTAATAATAATTATATTAAAATATGATTAGA
* *
35426417 ATTATTTATTATTTTTATTAATTTTTTTAATAATAATCT-TATTAAAAT
1 ATTATATATTATTTTTATTAATTTATTTAATAATAAT-TATATTAAAAT
35426465 TTAATAATAA
Statistics
Matches: 88, Mismatches: 11, Indels: 13
0.79 0.10 0.12
Matches are distributed among these distances:
56 28 0.32
57 25 0.28
58 34 0.39
59 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (57 bp):
ATTATATATTATTTTTATTAATTTATTTAATAATAATTATATTAAAATATGATTAGA
Found at i:35426651 original size:16 final size:16
Alignment explanation
Indices: 35426630--35426684 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
35426620 TGAATTACTG
*
35426630 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
*
35426646 ATTACATCTCTATTCA
1 ATTACAGCTCTATTCA
* * *
35426662 ATTATAACTCTATTCT
1 ATTACAGCTCTATTCA
35426678 ATTACAG
1 ATTACAG
35426685 TGAACCAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:35428811 original size:65 final size:65
Alignment explanation
Indices: 35428735--35428864 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
35428725 TCATAAGTAC
* * * *
35428735 ATGTTAGAGTGTGAATTTGATGTTTTCATAGAAGGGAAAAATGATCAGCGTGTCATAAAACATAG
1 ATGTTAAAGTGTGAATTTGATGTTCTCATAGAAGGGAAAAATGATCAACATGTCATAAAACATAG
*
35428800 ATGTTAAAGTGTGAATTTGATGTTCTCATATAAGGGAAAAATGATCAACATGTCATAAAACATAG
1 ATGTTAAAGTGTGAATTTGATGTTCTCATAGAAGGGAAAAATGATCAACATGTCATAAAACATAG
35428865 GAAAATAGGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (65 bp):
ATGTTAAAGTGTGAATTTGATGTTCTCATAGAAGGGAAAAATGATCAACATGTCATAAAACATAG
Found at i:35429362 original size:46 final size:48
Alignment explanation
Indices: 35429290--35429392 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
35429280 GACAGGACAG
* * * *
35429290 GACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
35429336 GACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
35429384 GACAGGAAT
1 GACAGGAAT
35429393 AATTCATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 27 0.54
47 1 0.02
48 22 0.44
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGA
Done.