Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:3129614 original size:15 final size:13
Alignment explanation
Indices: 3129572--3129625 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 13
3129562 ATCGATATTC
3129572 ATTATTATTATTATT
1 ATTATT-TTATT-TT
3129587 -TTATTTTATTTT
1 ATTATTTTATTTT
3129599 ATTATATTTATATTT
1 ATTAT-TTTAT-TTT
3129614 ATT-TTTTATTTT
1 ATTATTTTATTTT
3129626 TAATAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.14
13 14 0.39
14 11 0.31
15 6 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTATTTTATTTT
Found at i:3137813 original size:21 final size:21
Alignment explanation
Indices: 3137789--3137860 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
3137779 TTATATTATT
3137789 ATAAATAGGATTAATATAAAA
1 ATAAATAGGATTAATATAAAA
* **
3137810 ATAAAT--GCTTAAATTATATTATT
1 ATAAATAGGATT-AA-TATA--AAA
*
3137833 ATAAATAGGTTTAATATAAAA
1 ATAAATAGGATTAATATAAAA
3137854 ATAAATA
1 ATAAATA
3137861 TTCAAACTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 18 0.46
23 11 0.28
24 2 0.05
25 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (21 bp):
ATAAATAGGATTAATATAAAA
Found at i:3137831 original size:44 final size:44
Alignment explanation
Indices: 3137778--3137879 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
3137768 GTTTTCAAAT
*
3137778 ATTATATTATTATAAATAGGATTAATATAAAAATAAATGCTT-AA
1 ATTATATTATTATAAATAGGATTAATATAAAAATAAAT-ATTCAA
*
3137822 ATTATATTATTATAAATAGGTTTAATATAAAAATAAATATTCAA
1 ATTATATTATTATAAATAGGATTAATATAAAAATAAATATTCAA
*
3137866 ACTATATTATTATA
1 ATTATATTATTATA
3137880 TTATTATGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
43 2 0.04
44 52 0.96
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (44 bp):
ATTATATTATTATAAATAGGATTAATATAAAAATAAATATTCAA
Found at i:3137878 original size:52 final size:52
Alignment explanation
Indices: 3137822--3137923 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
3137812 AAATGCTTAA
*
3137822 ATTATATTATTATAAATAGGTTTAATATAAAAATAAATATTCAAACTATATT
1 ATTATATTATTATAAATAGGTTTAATATAAAAATAAATACTCAAACTATATT
* * *
3137874 ATTATATTATTATGAATATGTTTAATATAAAAATAAATGCTCAAACTATA
1 ATTATATTATTATAAATAGGTTTAATATAAAAATAAATACTCAAACTATA
3137924 CATAGAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (52 bp):
ATTATATTATTATAAATAGGTTTAATATAAAAATAAATACTCAAACTATATT
Found at i:3138167 original size:15 final size:15
Alignment explanation
Indices: 3138147--3138178 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3138137 TTTTAAAATC
3138147 TTAATTCTAATCCAT
1 TTAATTCTAATCCAT
*
3138162 TTAATTTTAATCCAT
1 TTAATTCTAATCCAT
3138177 TT
1 TT
3138179 GCCACCGGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTCTAATCCAT
Found at i:3138559 original size:17 final size:19
Alignment explanation
Indices: 3138524--3138563 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
3138514 GTTTTTAGGA
3138524 TTTT-AAAAAAATAAGTTT
1 TTTTAAAAAAAATAAGTTT
3138542 TTTTAAAAAAAAT-A-TTT
1 TTTTAAAAAAAATAAGTTT
3138559 TTTTA
1 TTTTA
3138564 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTAAAAAAAATAAGTTT
Found at i:3148422 original size:2 final size:2
Alignment explanation
Indices: 3148417--3148461 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3148407 GTGCATATAT
3148417 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3148459 GA G
1 GA G
3148462 TGAACCTGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3150464 original size:2 final size:2
Alignment explanation
Indices: 3150457--3150483 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3150447 ATTTATTTAT
3150457 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3150484 TTCTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3166975 original size:18 final size:18
Alignment explanation
Indices: 3166939--3166980 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3166929 TTGCCATATA
*
3166939 CTTTTCCCTGTATCTCTC
1 CTTTTCCCTGTATCCCTC
3166957 CTTTTCCCTAGT-TCCCTC
1 CTTTTCCCT-GTATCCCTC
*
3166975 CATTTC
1 CTTTTC
3166981 ACATTTTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.07, C:0.40, G:0.05, T:0.48
Consensus pattern (18 bp):
CTTTTCCCTGTATCCCTC
Found at i:3174639 original size:37 final size:36
Alignment explanation
Indices: 3174596--3174697 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
3174586 TTAGTAGAAC
3174596 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
3174633 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
3174667 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
3174698 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:3175534 original size:105 final size:106
Alignment explanation
Indices: 3175239--3175690 Score: 594
Period size: 105 Copynumber: 4.3 Consensus size: 106
3175229 CATTGTTCCA
* * **
3175239 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
* * * * *
3175304 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * *
3175345 AGTCCAATATACTTCGTTGTGAAGTTGAAATTGAAT-TTGAA-T--GAAA-T-TTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
3175404 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
3175445 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTG-TTGTTGACAAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
3175509 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3175550 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGG-AAATTGTTTGTTGACAA
*
3175615 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3175657 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
3175691 CGCGGATGGC
Statistics
Matches: 302, Mismatches: 33, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
100 79 0.26
101 4 0.01
102 5 0.02
104 3 0.01
105 99 0.33
106 36 0.12
107 52 0.17
108 3 0.01
110 21 0.07
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:3176386 original size:68 final size:65
Alignment explanation
Indices: 3176293--3176450 Score: 190
Period size: 68 Copynumber: 2.4 Consensus size: 65
3176283 AAGATATCTG
* * * * ** *
3176293 TTGTTTCATGAGAAACAGTTTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGGGAAACTGTCTCAAGGGAAACAAAATTAT-TTTTAAGGGAAATAAATTCAAAG-G
3176358 TT
64 TT
* * * *
3176360 TGTGTTTCAAGTGTAACTGTCTCAAGGGAGACAAAATTATTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGGGAAACTGTCTCAAGGGAAACAAAATTATTTTTAAGGGAAATAAATTCAAAGGT
3176425 T
65 T
3176426 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGGGAAACTGTCTCAAG
3176451 ATAGACGAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 21 0.27
68 32 0.41
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.34
Consensus pattern (65 bp):
TTGTTTCAAGGGAAACTGTCTCAAGGGAAACAAAATTATTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:3176477 original size:36 final size:35
Alignment explanation
Indices: 3176426--3176706 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
3176416 TTCAAAGGTT
* *
3176426 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
3176462 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
3176497 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
3176535 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
3176564 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
3176599 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
3176636 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
3176671 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
3176707 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 133 0.65
37 33 0.16
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:3176529 original size:138 final size:137
Alignment explanation
Indices: 3176374--3176680 Score: 411
Period size: 138 Copynumber: 2.2 Consensus size: 137
3176364 TTTCAAGTGT
* ** * * *
3176374 AACTGTCTCAAGGGAGACAAAATTAT-TTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGG
1 AACTGTCTCAAGGGAGACAAAATT-TGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGG
* *
3176438 AAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
65 AAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAG
3176502 TTCCAAAAGA
128 TTCCAAAAGA
* * *
3176512 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
3176577 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
3176642 CAAGAGA
131 CAAAAGA
*
3176649 AACTGTCTCAAGAGAGACAAAATTTGTTTCAA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAA
3176681 GGGAAACTGT
Statistics
Matches: 148, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
137 46 0.31
138 102 0.69
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:3176585 original size:102 final size:102
Alignment explanation
Indices: 3176462--3176650 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
3176452 TAGACGAAAA
*
3176462 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGA
3176527 GACGAAATTTGTTTCAA-AGAAAACATATTCAAATATT
65 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * ** *
3176564 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
3176629 ACGAAATTTGTTTCAAGAGAAA
66 ACGAAATTTGTTTCAAGAGAAA
3176651 CTGTCTCAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 37 0.47
102 42 0.53
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAG
ACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:3176770 original size:36 final size:36
Alignment explanation
Indices: 3176728--3176843 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
3176718 AAAACGGTCT
3176728 CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
1 CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
** * * * ** * * *
3176764 TGAGTGAAATAAATCTTCTTTCGAGTAAAACAGTCC
1 CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
* *
3176800 CAAGTGAGACAAAGTC-TGTTTTAA-AAAAGCAATCT
1 CAAGTGAGACAAA-TCTTGTTTTAAGAAAAACAATCA
3176835 CAAGTGAGA
1 CAAGTGAGA
3176844 TAATCATCTG
Statistics
Matches: 58, Mismatches: 21, Indels: 3
0.71 0.26 0.04
Matches are distributed among these distances:
35 16 0.28
36 40 0.69
37 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (36 bp):
CAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCA
Found at i:3177193 original size:18 final size:18
Alignment explanation
Indices: 3177166--3177201 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3177156 TGTTGAATCC
* *
3177166 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
3177184 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
3177202 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:3177676 original size:29 final size:29
Alignment explanation
Indices: 3177634--3177696 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
3177624 TTGGCATTTG
3177634 ATGCTCAAAGGATTGATGGGGTAGCTTGC
1 ATGCTCAAAGGATTGATGGGGTAGCTTGC
3177663 ATGCTCAAAGGATTGATGGGGTAGCTTGC
1 ATGCTCAAAGGATTGATGGGGTAGCTTGC
3177692 ATGCT
1 ATGCT
3177697 TCTCTACTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (29 bp):
ATGCTCAAAGGATTGATGGGGTAGCTTGC
Found at i:3178328 original size:12 final size:11
Alignment explanation
Indices: 3178311--3178345 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
3178301 TTTCTGTTCG
3178311 TTTTTTGCTCTT
1 TTTTTTGCT-TT
3178323 TTTTTTGCTTT
1 TTTTTTGCTTT
3178334 TTTTTT-CTTT
1 TTTTTTGCTTT
3178344 TT
1 TT
3178346 GCCCTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.26
11 8 0.35
12 9 0.39
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (11 bp):
TTTTTTGCTTT
Found at i:3181463 original size:37 final size:36
Alignment explanation
Indices: 3181420--3181521 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
3181410 TTAGTAGAAC
3181420 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
3181457 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
3181491 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
3181522 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:3190291 original size:29 final size:29
Alignment explanation
Indices: 3190249--3190337 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
3190239 TACCGGGGGT
*
3190249 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
3190278 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
3190307 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
3190336 AG
1 AG
3190338 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:3190615 original size:29 final size:29
Alignment explanation
Indices: 3190554--3190637 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
3190544 ATGAATCCTT
** * **
3190554 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
3190583 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
3190612 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
3190638 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:3192802 original size:64 final size:64
Alignment explanation
Indices: 3192690--3192844 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 64
3192680 GAAGGTGAAT
* * * *
3192690 CGATGCACAGGTAGTGCATCGATGCA--CTGTTTTAAAATAAAAAGATCGAATGCA-ATTAGTGC
1 CGATGCACAAGCAGTGCATCGATGCATCCCG--TTAAAATAAAAACATCGAATGCATATTA-TGC
*
3192752 AT
63 AC
* *
3192754 CGATGCATAAGGCA-TGCATCGATGCATCCCGTTAATAAT-AAAACATCGAATGCATTTTATGCA
1 CGATGCACAA-GCAGTGCATCGATGCATCCCGTTAA-AATAAAAACATCGAATGCATATTATGCA
3192817 C
64 C
*
3192818 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGCAGTGCATCGATGCAT
3192845 ACCTTCATTA
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
63 2 0.03
64 64 0.84
65 8 0.11
66 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (64 bp):
CGATGCACAAGCAGTGCATCGATGCATCCCGTTAAAATAAAAACATCGAATGCATATTATGCAC
Found at i:3193260 original size:29 final size:29
Alignment explanation
Indices: 3193221--3193301 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3193211 TATGTGATAT
3193221 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
3193251 GAGAAATGACATGAGCTACATGATCATAA
1 GAGAAATGACATGAGCTACATGATCACAA
3193280 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
3193302 ACATATGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:3200184 original size:29 final size:29
Alignment explanation
Indices: 3200142--3200222 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
3200132 TATGTGATAT
*
3200142 GAGAACATAACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
3200172 GAGAAATGACATGAGCTACATGATCATAA
1 GAGAAATGACATGAGCTACATGATCACAA
3200201 GAGAAATGACATGA-CTACATGA
1 GAGAAATGACATGAGCTACATGA
3200223 ACATATGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 8 0.16
29 36 0.73
30 5 0.10
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:3201500 original size:21 final size:21
Alignment explanation
Indices: 3201458--3201500 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3201448 TTTCTGGGCT
* *
3201458 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
3201479 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
3201500 A
1 A
3201501 ACGAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3202752 original size:24 final size:24
Alignment explanation
Indices: 3202703--3202755 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3202693 TAAGTGAACC
*
3202703 ATGTG-TTTATATGTACATGTGAT
1 ATGTGATTTATATGTACATGAGAT
*
3202726 ATGTGATTTATATG-ACGATGAGCT
1 ATGTGATTTATATGTAC-ATGAGAT
3202750 ATGTGA
1 ATGTGA
3202756 AAGAACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.42
Consensus pattern (24 bp):
ATGTGATTTATATGTACATGAGAT
Found at i:3203093 original size:103 final size:103
Alignment explanation
Indices: 3202868--3203085 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
3202858 GTCGAGGGTC
3202868 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTAAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTAAAGTCTGGTGAGACACATAC
* *
3202933 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* * *
3202971 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTAAAGTCTGGTGAGACACATAC
*
3203036 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3203074 TATGTGGTCCTT
1 TATGTGGTCCTT
3203086 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTAAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3203138 original size:23 final size:23
Alignment explanation
Indices: 3203102--3203169 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
3203092 ATTATTATAT
*
3203102 GGCACTACGATGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
3203125 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
3203148 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
3203170 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:3206732 original size:21 final size:21
Alignment explanation
Indices: 3206690--3206732 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3206680 ATTCTGGGCT
* *
3206690 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
3206711 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
3206732 A
1 A
3206733 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3207981 original size:24 final size:24
Alignment explanation
Indices: 3207932--3207984 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3207922 TAAGTGAACC
*
3207932 ATGTG-TTTATATGTACATGTGAT
1 ATGTGATTTATATGTACATGAGAT
*
3207955 ATGTGATTTATATG-ACGATGAGCT
1 ATGTGATTTATATGTAC-ATGAGAT
3207979 ATGTGA
1 ATGTGA
3207985 AAGAACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.42
Consensus pattern (24 bp):
ATGTGATTTATATGTACATGAGAT
Found at i:3208281 original size:103 final size:103
Alignment explanation
Indices: 3208101--3208314 Score: 356
Period size: 103 Copynumber: 2.1 Consensus size: 103
3208091 AGGGTCTATG
*
3208101 TGGTCCTTTGGGACATATATGTATTCTTTGAAACATATGTAAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGAAACATATGTAAAGTCTGGTGAGACACATACTTGA
* *
3208166 TCCTTGGCATATGTATATGATTCTTAAGGAATGATATA
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
* * *
3208204 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGAAACATATGTAAAGTCTGGTGAGACACATACTTGA
* *
3208269 TCCCTAGTATATGTATATGATTCTTAAGGAATGATATG
66 TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
3208307 TGGTCCTT
1 TGGTCCTT
3208315 ATGGACATTA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (103 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGAAACATATGTAAAGTCTGGTGAGACACATACTTGA
TCCCTAGCATATGTATATGATTCTTAAGGAATGATATA
Found at i:3208367 original size:23 final size:23
Alignment explanation
Indices: 3208330--3208375 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3208320 CATTATTATA
* *
3208330 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGATGCAATTATACG
*
3208353 TGGCACTTCGATGCAATTATACG
1 TGGCACTCCGATGCAATTATACG
3208376 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTCCGATGCAATTATACG
Found at i:3210292 original size:2 final size:2
Alignment explanation
Indices: 3210285--3210340 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
3210275 GTATTTGAAA
3210285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3210327 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3210341 TAATTTGTCC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3213279 original size:20 final size:20
Alignment explanation
Indices: 3213254--3213509 Score: 148
Period size: 20 Copynumber: 12.7 Consensus size: 20
3213244 GATTTTCCAG
*
3213254 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
3213274 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
3213294 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
3213314 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
3213335 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
3213356 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
3213376 AATCGCAACGAGAGTACGTA
1 AATCGCAACGCGAATACGAA
* *
3213396 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* * *
3213416 AATCGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
3213436 AATCGCAATGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
3213456 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* *
3213477 AATCGCAACGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
3213497 AATCGCAACGCGA
1 AATCGCAACGCGA
3213510 TCTCTGGTAT
Statistics
Matches: 184, Mismatches: 37, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.03
20 127 0.69
21 51 0.28
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:3213410 original size:40 final size:41
Alignment explanation
Indices: 3213315--3213506 Score: 280
Period size: 40 Copynumber: 4.7 Consensus size: 41
3213305 GATTCTGACT
*
3213315 ATCGCAACGAGTATCCGTAAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGACAATACGTAAA
* *
3213357 ATCGCAACGCGTATCCGTAAATCGCAACGAGAGTACGT-AA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
* * *
3213397 ATCGCAACGCGTATCTGTAAATCGCAATGAGAATACGT-AA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
* *
3213437 ATCGCAATGCGTATCCATAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
*
3213478 ATCGCAACGCGTATCCATAAATCGCAACG
1 ATCGCAACGCGTATCCGTAAATCGCAACG
3213507 CGATCTCTGG
Statistics
Matches: 137, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
40 72 0.53
41 48 0.35
42 17 0.12
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
Found at i:3213669 original size:20 final size:20
Alignment explanation
Indices: 3213592--3213706 Score: 126
Period size: 20 Copynumber: 5.8 Consensus size: 20
3213582 GCGTTGCGAT
*
3213592 AATCGCAACGCGATTACCTA
1 AATCGCAACGCGATTACGTA
* *
3213612 ATTCGCAACGCGATTACCTA
1 AATCGCAACGCGATTACGTA
* *
3213632 ATTTGCAACGCGATTACGTA
1 AATCGCAACGCGATTACGTA
3213652 AATCGCAACGCGGA-TACGTA
1 AATCGCAACGC-GATTACGTA
* *
3213672 AATCGCAATGCGA-AACTGTA
1 AATCGCAACGCGATTAC-GTA
*
3213692 AATCGCAACGAGATT
1 AATCGCAACGCGATT
3213707 CTGATTATCG
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.05
20 76 0.93
21 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTACGTA
Found at i:3214591 original size:24 final size:24
Alignment explanation
Indices: 3214564--3214617 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3214554 GTATTCGAAA
3214564 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3214588 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3214612 TTTGAT
1 TTTGAT
3214618 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3217042 original size:20 final size:20
Alignment explanation
Indices: 3217004--3217090 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
3216994 CAACGCGGAA
3217004 ATCGCAACAC--AATATGACT
1 ATCGCAACACGGAA-ATGACT
*
3217023 ATCGTAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
** *
3217043 ATCGCAATGCGGAATTGACT
1 ATCGCAACACGGAAATGACT
3217063 ATCGCAACACGGAAATGACT
1 ATCGCAACACGGAAATGACT
*
3217083 ATCACAAC
1 ATCGCAAC
3217091 GAGAGAATCG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.16
20 46 0.81
21 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACACGGAAATGACT
Found at i:3217120 original size:19 final size:19
Alignment explanation
Indices: 3217096--3217260 Score: 126
Period size: 19 Copynumber: 9.4 Consensus size: 19
3217086 ACAACGAGAG
3217096 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3217115 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* **
3217134 AATCTCAA--CG--A-GCG
1 AATCGCAATGCGAAATGAA
*
3217148 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
*
3217167 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
3217186 AATTGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
3217200 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
3217219 AATTGCAAT--G-AGTG--
1 AATCGCAATGCGAAATGAA
3217233 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
3217253 AATCGCAA
1 AATCGCAA
3217261 CGCAAAATTA
Statistics
Matches: 112, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
14 24 0.21
15 2 0.02
16 7 0.06
17 5 0.04
18 5 0.04
19 61 0.54
20 8 0.07
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3217143 original size:52 final size:52
Alignment explanation
Indices: 3217087--3217228 Score: 232
Period size: 52 Copynumber: 2.7 Consensus size: 52
3217077 ATGACTATCA
*
3217087 CAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCT-
1 CAACGAGAGAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAAAAT-TG
* *
3217139 CAACGAGCGAATCGCAATGCAAAATGAAAATTGCAATGCGAAATGAAAATTG
1 CAACGAGAGAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAAAATTG
*
3217191 CAACGAGAGAATCACAATGCGAAATGAAAATTGCAATG
1 CAACGAGAGAATCGCAATGCGAAATGAAAATTGCAATG
3217229 AGTGAATCGC
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 1 0.01
52 82 0.99
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (52 bp):
CAACGAGAGAATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAAAATTG
Found at i:3217193 original size:33 final size:33
Alignment explanation
Indices: 3217156--3217260 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 33
3217146 CGAATCGCAA
* *
3217156 TGCAAAATGAAAATTGCAATGCGAAATGAAAAT
1 TGCAAAATGAGAATCGCAATGCGAAATGAAAAT
* *
3217189 TGCAACGA-GAGAATCACAATGCGAAATGAAAAT
1 TGCAA-AATGAGAATCGCAATGCGAAATGAAAAT
3217222 TGC--AATGAGTGAATCGCAATGCGAAAATGAAAAT
1 TGCAAAATGA--GAATCGCAATGCG-AAATGAAAAT
*
3217256 CGCAA
1 TGCAA
3217261 CGCAAAATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
30 1 0.02
31 2 0.03
33 42 0.72
34 13 0.22
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (33 bp):
TGCAAAATGAGAATCGCAATGCGAAATGAAAAT
Found at i:3217339 original size:33 final size:33
Alignment explanation
Indices: 3217277--3217361 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
3217267 ATTAGTTTCG
*
3217277 CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
3217311 CGTTGCGATTTTCATTTCGCATTTCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
3217344 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
3217362 CACGTTGCGA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 33 0.72
34 13 0.28
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:3217493 original size:14 final size:14
Alignment explanation
Indices: 3217474--3217510 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3217464 CATCAATTAA
3217474 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3217488 ACAAATCATCTTTT
1 ACAAATCAACATTT
3217502 ACAAATCAA
1 ACAAATCAA
3217511 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3218922 original size:21 final size:21
Alignment explanation
Indices: 3218867--3218925 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3218857 TCTAGAATGT
*
3218867 TGGGA-GGGACCTCTTCAACGA
1 TGGGAGGGGA-CTCTTGAACGA
** * *
3218888 TGACAGTGGCCTCTTGAACGA
1 TGGGAGGGGACTCTTGAACGA
3218909 TGGGAGGGGACTCTTGA
1 TGGGAGGGGACTCTTGA
3218926 GGGATGATAG
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
TGGGAGGGGACTCTTGAACGA
Found at i:3218967 original size:42 final size:42
Alignment explanation
Indices: 3218886--3218978 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 42
3218876 CCTCTTCAAC
* * * *
3218886 GATGACAGTGGCCTCTTGAACGATGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCCTGAACGATGGGAGAGGACACTTGAGG
* * **
3218928 GATGATAGGGGCCTCCTGAACGATAGGG-GAGGTCACTTGAAC
1 GATGACAGGGGCCTCCTGAACGAT-GGGAGAGGACACTTGAGG
3218970 GATGACAGG
1 GATGACAGG
3218979 TGAGTCGGGC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
42 38 0.93
43 3 0.07
ACGTcount: A:0.25, C:0.17, G:0.39, T:0.19
Consensus pattern (42 bp):
GATGACAGGGGCCTCCTGAACGATGGGAGAGGACACTTGAGG
Found at i:3219483 original size:20 final size:20
Alignment explanation
Indices: 3219458--3219506 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3219448 AAAACTTAAA
3219458 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
3219478 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3219498 ATCGCAACG
1 ATCGCAACG
3219507 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3219591 original size:19 final size:19
Alignment explanation
Indices: 3219567--3219636 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 19
3219557 TGCGATTTTG
3219567 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
3219586 TCGTTGCGA--TTCATTTC
1 TCGTTGCGATTTTCATTTC
* **
3219603 GCGTTGCGATAGTCATTTTTC
1 TCGTTGCGATTTTCA--TTTC
*
3219624 ACGTTGCGATTTT
1 TCGTTGCGATTTT
3219637 AAGTTTCGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 16 0.38
19 12 0.29
21 14 0.33
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:3219867 original size:94 final size:94
Alignment explanation
Indices: 3219700--3220079 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
3219690 ATGGATTGCA
* *
3219700 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3219764 TTAGTAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3219793 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
3219858 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
3219887 TTACTTTCAACCAAAAGACAAAACAAAGAGAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3219952 TTAGCAGAATTAGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
3219981 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
3220045 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
3220075 TTACT
1 TTACT
3220080 AAGCAATCTA
Statistics
Matches: 274, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
93 23 0.08
94 251 0.92
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3221807 original size:20 final size:20
Alignment explanation
Indices: 3221784--3221839 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3221774 TGAAATGAAA
3221784 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
3221804 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
*
3221824 ATCGCAACAAGAGAAT
1 ATCGCAACGAGAGAAT
3221840 TGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:3221923 original size:20 final size:20
Alignment explanation
Indices: 3221875--3221950 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
3221865 GCGATTTTGG
3221875 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
**
3221894 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
*
3221914 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
**
3221934 TTTCATGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
3221951 AAGTTTAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 17 0.34
20 33 0.66
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:3222533 original size:20 final size:20
Alignment explanation
Indices: 3222508--3222721 Score: 243
Period size: 20 Copynumber: 10.6 Consensus size: 20
3222498 CTTTAAAAAT
3222508 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3222528 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
3222548 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
3222569 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
3222589 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
3222609 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
3222629 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3222649 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
3222669 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
3222690 CGCATTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
3222711 CTCGTTGCGAT
1 CGCGTTGCGAT
3222722 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
20 109 0.68
21 51 0.32
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3222716 original size:41 final size:41
Alignment explanation
Indices: 3222510--3222721 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
3222500 TTAAAAATCG
*
3222510 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
3222551 CGTTGTGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
3222591 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
3222631 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
3222672 CGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
3222713 CGTTGCGAT
1 CGTTGCGAT
3222722 AGTCAGAATC
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 76 0.47
41 84 0.52
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:3222775 original size:20 final size:20
Alignment explanation
Indices: 3222507--3222782 Score: 168
Period size: 20 Copynumber: 13.7 Consensus size: 20
3222497 GCTTTAAAAA
* *
3222507 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCGTAT
*
3222527 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CGTAT
* * *
3222548 T-GTCGTTGTGATTTACGGAT
1 TCG-CGTTGCGATTTTCGTAT
* *
3222568 ACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTTCGTAT
* *
3222588 TCTCGTTGCGATTTACAG-AT
1 TCGCGTTGCGATTTTC-GTAT
* *
3222608 ACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTTCGTAT
* * *
3222628 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCGTAT
*
3222648 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CGTAT
* *
3222669 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTTCGTAT
* * *
3222689 ACGCATTGCGATTTTACGGAT
1 TCGCGTTGCGATTTT-CGTAT
* * ** *
3222710 ACTCGTTGCGATAGTCAG-AA
1 TCGCGTTGCGATTTTC-GTAT
*
3222730 TCGCGTTGCGATTTATATGT-T
1 TCGCGTTGCGATTT-T-CGTAT
*
3222751 T-GCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCGTAT
*
3222770 TCGCGTTGTGATT
1 TCGCGTTGCGATT
3222783 CTTGAAAATC
Statistics
Matches: 200, Mismatches: 41, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 143 0.71
21 52 0.26
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCGTAT
Found at i:3222835 original size:21 final size:21
Alignment explanation
Indices: 3222755--3222847 Score: 68
Period size: 21 Copynumber: 4.5 Consensus size: 21
3222745 TATGTTTGCG
* *
3222755 TTGCGATT-TTCATATTCGCG
1 TTGCGATTCTTCATAATCGCA
* * *
3222775 TTGTGATTCTTGAAAATCGCA
1 TTGCGATTCTTCATAATCGCA
*
3222796 ATGCGAATT-TGT-ACT-ATCGCA
1 TTGCG-ATTCT-TCA-TAATCGCA
*
3222817 TTGCGATTCTTCATAATCGCG
1 TTGCGATTCTTCATAATCGCA
3222838 TTGCGATTCT
1 TTGCGATTCT
3222848 AGGAACTGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
20 12 0.21
21 40 0.71
22 4 0.07
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
TTGCGATTCTTCATAATCGCA
Found at i:3222885 original size:20 final size:20
Alignment explanation
Indices: 3222831--3222885 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
3222821 GATTCTTCAT
3222831 AATCGCGTTGCGATTCTAGG
1 AATCGCGTTGCGATTCTAGG
** *
3222851 AA-CTGATTTGTGATTCT-GG
1 AATC-GCGTTGCGATTCTAGG
3222870 AGATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
3222886 TTTATTTCGC
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
19 4 0.15
20 21 0.81
21 1 0.04
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTAGG
Found at i:3226810 original size:22 final size:22
Alignment explanation
Indices: 3226782--3226827 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3226772 TAATCTCTAT
3226782 CAGGTTATCTTGGCATTGTCTG
1 CAGGTTATCTTGGCATTGTCTG
3226804 CAGGTTATCTTGGCATTGTCTG
1 CAGGTTATCTTGGCATTGTCTG
3226826 CA
1 CA
3226828 AACATTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (22 bp):
CAGGTTATCTTGGCATTGTCTG
Found at i:3227683 original size:28 final size:30
Alignment explanation
Indices: 3227644--3227705 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 30
3227634 AATAAAGTTG
*
3227644 TTTTCATGTTTG-TTTATATT-TTTTAAAT
1 TTTTCATGTTTGATTTATATTCGTTTAAAT
*
3227672 TTTTTATGTTTGATTTATATTCGTTTAAAT
1 TTTTCATGTTTGATTTATATTCGTTTAAAT
3227702 TTTT
1 TTTT
3227706 AATATTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
29 8 0.27
30 11 0.37
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (30 bp):
TTTTCATGTTTGATTTATATTCGTTTAAAT
Found at i:3234498 original size:5 final size:5
Alignment explanation
Indices: 3234484--3234573 Score: 173
Period size: 5 Copynumber: 18.2 Consensus size: 5
3234474 ATATACTTAC
3234484 ATAT- ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
3234533 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
3234574 GAAAATTGAG
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.05
5 81 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:3237166 original size:60 final size:58
Alignment explanation
Indices: 3237039--3237225 Score: 189
Period size: 60 Copynumber: 3.1 Consensus size: 58
3237029 GCATAGACAT
* * * *
3237039 ATAGTTT-GGGATGAAATTGAAATGTTCAAAAAGTTTGATGACCAATCTAGAATGAAGGTC
1 ATAGTTTAGGGATGAAATTGAAATATTC-AAAAG-TTGAGGACCAATTTAGAATGAA-ATC
* *
3237099 GA-AGTTTAGGGATGAAACTGAAATATTCAAAAGCTTGAGGACTAATTTAGAATGATAATC
1 -ATAGTTTAGGGATGAAATTGAAATATTCAAAAG-TTGAGGACCAATTTAGAATGA-AATC
* * * * *
3237159 ATAGTTTAGGGATGAAATTGGAATATTTAAAAGTTTAGGAACCAATTAAGAATGAGGATC
1 ATAGTTTAGGGATGAAATTGAAATATTCAAAAGTTGAGG-ACCAATTTAGAATGA-AATC
3237219 ATAGTTT
1 ATAGTTT
3237226 GAGGAAATGT
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
59 6 0.06
60 81 0.76
61 20 0.19
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (58 bp):
ATAGTTTAGGGATGAAATTGAAATATTCAAAAGTTGAGGACCAATTTAGAATGAAATC
Found at i:3245776 original size:51 final size:51
Alignment explanation
Indices: 3245700--3245810 Score: 179
Period size: 51 Copynumber: 2.2 Consensus size: 51
3245690 GAGTAACATA
*
3245700 AATAAGAGATATAACTTATGAGAAAGCACGGATGATGGATCTGGATGAGAT
1 AATAAGAGATATAACTTATGAGAAAGCACGGATGATGAATCTGGATGAGAT
*
3245751 AATAAGAGATATTACTTACT-AGAAAGCACGGATGATGAATCTGGATGAGAT
1 AATAAGAGATATAACTTA-TGAGAAAGCACGGATGATGAATCTGGATGAGAT
*
3245802 AGTAAGAGA
1 AATAAGAGA
3245811 CGAGCATGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.23
Consensus pattern (51 bp):
AATAAGAGATATAACTTATGAGAAAGCACGGATGATGAATCTGGATGAGAT
Found at i:3251118 original size:20 final size:19
Alignment explanation
Indices: 3251074--3251130 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
3251064 CAGTTTCCAA
*
3251074 ATTCGCAACGCGGATATTCAG
1 ATTCGCAACGC-GAT-TTAAG
3251095 ATTCGCAACGCGATTGTAAG
1 ATTCGCAACGCGATT-TAAG
*
3251115 ATTCACAACGCGATTT
1 ATTCGCAACGCGATTT
3251131 TAAAAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 20 0.61
21 11 0.33
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (19 bp):
ATTCGCAACGCGATTTAAG
Found at i:3251212 original size:19 final size:19
Alignment explanation
Indices: 3251184--3251220 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3251174 AAAAACTTGT
*
3251184 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAATGAAAAAG
*
3251203 TGTTGTGATAATGAAAAA
1 TGTTGCGATAATGAAAAA
3251221 TTCAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.30
Consensus pattern (19 bp):
TGTTGCGATAATGAAAAAG
Found at i:3251662 original size:21 final size:21
Alignment explanation
Indices: 3251638--3251743 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 21
3251628 CGTTGCGATT
3251638 TTGGAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAACGCGAAC
** * * *
3251659 TTGGACTATTGCAA--CAAAT
1 TTGGAAAATCGCAACGCGAAC
* *
3251678 TTGAAAAATCACAACGCGAAC
1 TTGGAAAATCGCAACGCGAAC
* ** *
3251699 TTCGACTATCGCAA--CGAAT
1 TTGGAAAATCGCAACGCGAAC
* *
3251718 TTGAAAAATCGCAACGTGAAC
1 TTGGAAAATCGCAACGCGAAC
3251739 TTGGA
1 TTGGA
3251744 CCAACGCAAC
Statistics
Matches: 56, Mismatches: 25, Indels: 8
0.63 0.28 0.09
Matches are distributed among these distances:
19 26 0.46
21 30 0.54
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
TTGGAAAATCGCAACGCGAAC
Found at i:3251695 original size:40 final size:40
Alignment explanation
Indices: 3251637--3251760 Score: 167
Period size: 40 Copynumber: 3.1 Consensus size: 40
3251627 TCGTTGCGAT
* *
3251637 TTTGGAAAATCGCAACGCGAACTTGGACTATTGCAACAAA
1 TTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACAAA
* * *
3251677 TTTGAAAAATCACAACGCGAACTTCGACTATCGCAACGAA
1 TTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACAAA
* * * *
3251717 TTTGAAAAATCGCAACGTGAACTTGGACCAACGCAACGAA
1 TTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACAAA
3251757 TTTG
1 TTTG
3251761 GACTAACGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 74 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (40 bp):
TTTGAAAAATCGCAACGCGAACTTGGACTATCGCAACAAA
Found at i:3251763 original size:19 final size:19
Alignment explanation
Indices: 3251708--3251768 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
3251698 CTTCGACTAT
*
3251708 CGCAACGAATTT-GAAAAA
1 CGCAACGAATTTGGACAAA
* *
3251726 TCGCAACGTGAACTTGGACCAA
1 -CGCAAC--GAATTTGGACAAA
*
3251748 CGCAACGAATTTGGACTAA
1 CGCAACGAATTTGGACAAA
3251767 CG
1 CG
3251769 TAAATTTGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 19 0.56
21 11 0.32
22 4 0.12
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (19 bp):
CGCAACGAATTTGGACAAA
Found at i:3251856 original size:22 final size:21
Alignment explanation
Indices: 3251787--3251857 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
3251777 GAAAATCACA
3251787 TTGCGATTTTGTATTATCGAG
1 TTGCGATTTTGTATTATCGAG
3251808 TTGCGATTTTGTATTATCGCA-
1 TTGCGATTTTGTATTATCG-AG
** *
3251829 ACGCGATTCTTGTATTATCGTG
1 TTGCGATT-TTGTATTATCGAG
3251851 TTGCGAT
1 TTGCGAT
3251858 AGTCAGAATC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
21 25 0.60
22 17 0.40
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (21 bp):
TTGCGATTTTGTATTATCGAG
Found at i:3252563 original size:60 final size:59
Alignment explanation
Indices: 3252498--3252629 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 59
3252488 ACTCAGTTTC
*
3252498 CAAATTCACAACGCGAATCTGGAAATCGCAACAC-ATAAGTCAAATTCGCAACATAGAAGT
1 CAAATTCGCAACGCGAATCTGGAAATCGCAACACAATAAGT-AAA-TCGCAACATAGAAGT
* * **
3252558 CAAATTCGCAACGCGAATCTGTAAATCGCAACCCGAATTTGTAAATCGCAACATAGAAGT
1 CAAATTCGCAACGCGAATCTGGAAATCGCAACAC-AATAAGTAAATCGCAACATAGAAGT
3252618 CAAATTCGCAAC
1 CAAATTCGCAAC
3252630 ACATAAGTCA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
60 58 0.89
61 3 0.05
62 4 0.06
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (59 bp):
CAAATTCGCAACGCGAATCTGGAAATCGCAACACAATAAGTAAATCGCAACATAGAAGT
Found at i:3252647 original size:60 final size:60
Alignment explanation
Indices: 3252520--3252689 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 60
3252510 GCGAATCTGG
** * * **
3252520 AAATCGCAACACATAA-GTCAAATTCGCAACATAGAAGTCAAATTCGCAACGCGAATCTGT
1 AAATCGCAACACCGAATTTCAAATTCGCAACATAGAAGTCAAATTCGCAACAC-AATAAGT
*
3252580 AAATCGCAAC-CCGAATTTGTAAA-TCGCAACATAGAAGTCAAATTCGCAACAC-ATAAGT
1 AAATCGCAACACCGAATTT-CAAATTCGCAACATAGAAGTCAAATTCGCAACACAATAAGT
* *
3252638 CAAATTCGCAACACTGAATTTCAAATTCGCAAC-T-GAATTTCAAATTCGCAAC
1 -AAA-TCGCAACACCGAATTTCAAATTCGCAACATAGAA-GTCAAATTCGCAAC
3252690 TCGATTTTCG
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
58 4 0.04
59 9 0.10
60 63 0.68
61 17 0.18
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (60 bp):
AAATCGCAACACCGAATTTCAAATTCGCAACATAGAAGTCAAATTCGCAACACAATAAGT
Found at i:3252674 original size:19 final size:19
Alignment explanation
Indices: 3252637--3252728 Score: 105
Period size: 19 Copynumber: 4.7 Consensus size: 19
3252627 AACACATAAG
3252637 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
3252658 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
3252677 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
* *
3252697 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
3252717 T-AATTTCGCAAC
1 TCAAATTCGCAAC
3252729 AGGTTTTAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 31 0.49
20 22 0.35
21 10 0.16
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:3252677 original size:80 final size:80
Alignment explanation
Indices: 3252506--3252656 Score: 221
Period size: 80 Copynumber: 1.9 Consensus size: 80
3252496 TCCAAATTCA
* * * * * *
3252506 CAACGCGAATCTGGAAATCGCAACACATAAGTCAAATTCGCAACATAGAAGTCAAATTCGCAACG
1 CAACCCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACA
3252571 CGAATCTGTAAATCG
66 CGAATCTGTAAATCG
* *
3252586 CAACCCGAATTTGTAAATCGCAACATAGAAGTCAAATTCGCAACACATAAGTCAAATTCGCAACA
1 CAACCCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACA
3252651 CTGAAT
66 C-GAAT
3252657 TTCAAATTCG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
80 58 0.94
81 4 0.06
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (80 bp):
CAACCCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACA
CGAATCTGTAAATCG
Found at i:3252687 original size:80 final size:80
Alignment explanation
Indices: 3252506--3252689 Score: 214
Period size: 80 Copynumber: 2.3 Consensus size: 80
3252496 TCCAAATTCA
* * * * * *
3252506 CAACGCGAATCTGGAAATCGCAACACATAAGTCAAATTCGCAACATAGAAGTCAAATTCGCAACG
1 CAACCCGAATTTGCAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACA
3252571 CGAATCTGTAAATCG
66 CGAATCTGTAAATCG
* * *
3252586 CAACCCGAATTTGTAAATCGCAACATAGAAGTCAAATTCGCAACACATAAGTCAAATTCGCAACA
1 CAACCCGAATTTGCAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACA
3252651 CTGAAT-T-TCAAATTCG
66 C-GAATCTGT-AAA-TCG
*
3252667 CAA-CTGAATTT-CAAATTCGCAAC
1 CAACCCGAATTTGCAAA-TCGCAAC
3252690 TCGATTTTCG
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
79 4 0.04
80 76 0.84
81 10 0.11
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (80 bp):
CAACCCGAATTTGCAAATCGCAACACAGAAGTCAAATTCGCAACACAGAAGTCAAATTCGCAACA
CGAATCTGTAAATCG
Found at i:3252729 original size:19 final size:20
Alignment explanation
Indices: 3252537--3252729 Score: 141
Period size: 20 Copynumber: 9.7 Consensus size: 20
3252527 AACACATAAG
* *
3252537 TCAAATTCGCAACATAGAA-G
1 TCAAATTCGCAACA-CGAATT
*
3252557 TCAAATTCGCAACGCGAATCT
1 TCAAATTCGCAACACGAAT-T
*
3252578 GT-AAA-TCGCAACCCGAATT
1 -TCAAATTCGCAACACGAATT
* * *
3252597 TGTAAA-TCGCAACATAGAA-G
1 T-CAAATTCGCAACA-CGAATT
**
3252617 TCAAATTCGCAACAC-ATAAG
1 TCAAATTCGCAACACGA-ATT
3252637 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACAC-GAATT
*
3252658 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
* *
3252677 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGAATT
*
3252697 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATT
*
3252717 T-AATTTCGCAACA
1 TCAAATTCGCAACA
3252730 GGTTTTAGTT
Statistics
Matches: 142, Mismatches: 19, Indels: 25
0.76 0.10 0.13
Matches are distributed among these distances:
18 2 0.01
19 36 0.25
20 82 0.58
21 20 0.14
22 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:3253687 original size:24 final size:24
Alignment explanation
Indices: 3253660--3253713 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3253650 GTATTCAAAA
3253660 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3253684 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3253708 TTTGAT
1 TTTGAT
3253714 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3253896 original size:3 final size:3
Alignment explanation
Indices: 3253888--3253912 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3253878 ATATAACCCT
3253888 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
3253913 TCCCCGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3256277 original size:20 final size:20
Alignment explanation
Indices: 3256221--3256285 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
3256211 GAAATCGAAA
3256221 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* * *** *
3256241 TTTGCGTTGTG-ATTTGACT
1 ATCGCAACGCGAATTTGACT
3256260 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
3256280 TTCGCA
1 ATCGCA
3256286 TTGAATTTGT
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:3256434 original size:66 final size:64
Alignment explanation
Indices: 3256348--3256491 Score: 234
Period size: 66 Copynumber: 2.2 Consensus size: 64
3256338 AATTTAAAAC
*
3256348 AACAAATCAACTTGTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTACACATC-AATT
3256413 A
64 A
* * *
3256414 AATAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
3256478 AACAAATCAACTTT
1 AACAAATCAACTTT
3256492 CAATGTAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 18 0.25
65 23 0.32
66 32 0.44
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:3257905 original size:21 final size:21
Alignment explanation
Indices: 3257866--3257959 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
3257856 GAAGCACCCA
*
3257866 TTGAACGATGACA-GGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* *
3257886 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
*
3257907 TTGAACGATGAGAGGAGCCTC
1 TTGAACGATGAGAGGGGCCTC
* **
3257928 TTGAACGATAAGAGACGCCTC
1 TTGAACGATGAGAGGGGCCTC
*
3257949 TTAAACGATGA
1 TTGAACGATGA
3257960 CAGGTGAATC
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
20 10 0.16
21 52 0.84
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (21 bp):
TTGAACGATGAGAGGGGCCTC
Found at i:3257911 original size:41 final size:42
Alignment explanation
Indices: 3257842--3257963 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
3257832 GTGAATCGGG
* *
3257842 CTCTTGAACGGTGGGAAGCACC-CATTGAACGATGACAGG-GC
1 CTCTTGAACGGTGGGAGGCGCCTC-TTGAACGATGACAGGAGC
* *
3257883 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGGTGGGAGGCGCCTCTTGAACGATGACAGGAGC
* ** * *
3257925 CTCTTGAACGATAAGAGACGCCTCTTAAACGATGACAGG
1 CTCTTGAACGGTGGGAGGCGCCTCTTGAACGATGACAGG
3257964 TGAATCGGGC
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 33 0.49
42 35 0.51
ACGTcount: A:0.27, C:0.22, G:0.32, T:0.19
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGCGCCTCTTGAACGATGACAGGAGC
Found at i:3258264 original size:21 final size:21
Alignment explanation
Indices: 3258240--3258289 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3258230 TGAAACAATC
* *
3258240 TCACGTAGAGCGGTTACCTCA
1 TCACGTAGAGCAGATACCTCA
* *
3258261 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
3258282 TCACGTAG
1 TCACGTAG
3258290 CGCACCATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Found at i:3260192 original size:20 final size:20
Alignment explanation
Indices: 3260132--3260181 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3260122 GAACTAAAAC
3260132 CGCGTTGCGATTTTCATTTT
1 CGCGTTGCGATTTTCATTTT
3260152 CGCGTTGCGATTTTCATTTT
1 CGCGTTGCGATTTTCATTTT
*
3260172 CGTGTTGCGA
1 CGCGTTGCGA
3260182 ATTTAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATTTT
Found at i:3260563 original size:20 final size:20
Alignment explanation
Indices: 3260538--3260575 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3260528 ATTTCACCGG
3260538 AGATGGGGAC-GATTTCGCGC
1 AGAT-GGGACGGATTTCGCGC
3260558 AGATGGGACGGATTTCGC
1 AGATGGGACGGATTTCGC
3260576 CGTAAAGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (20 bp):
AGATGGGACGGATTTCGCGC
Found at i:3260855 original size:20 final size:19
Alignment explanation
Indices: 3260755--3260858 Score: 92
Period size: 19 Copynumber: 5.4 Consensus size: 19
3260745 TTGGAATTTA
*
3260755 CGAATTTGACTTC-TGTTG
1 CGAATTTGACTTCGCGTTG
3260773 CG-ATTT-ACAAATTCGCGTTG
1 CGAATTTGAC---TTCGCGTTG
3260793 CG-ATTT-ACAATTCGCGTTG
1 CGAATTTGAC--TTCGCGTTG
3260812 CGAATTTGACTTCGCGTTG
1 CGAATTTGACTTCGCGTTG
*
3260831 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTC-GCGTTG
*
3260851 TGAATTTG
1 CGAATTTG
3260859 TTGGTTATTT
Statistics
Matches: 76, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.03
17 4 0.05
18 2 0.03
19 38 0.50
20 28 0.37
21 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (19 bp):
CGAATTTGACTTCGCGTTG
Found at i:3271834 original size:20 final size:20
Alignment explanation
Indices: 3271805--3271880 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
3271795 CGTTTGTTTC
3271805 ACGA-AATGTAAGATTACCA
1 ACGAGAATGTAAGATTACCA
3271824 ACGAGAATGTAAGATTACCA
1 ACGAGAATGTAAGATTACCA
* *
3271844 ACGGGAATATAAGATTACCA
1 ACGAGAATGTAAGATTACCA
* *
3271864 GCGGGAATGTAAGATTA
1 ACGAGAATGTAAGATTA
3271881 TCAGAGAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 4 0.08
20 48 0.92
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.21
Consensus pattern (20 bp):
ACGAGAATGTAAGATTACCA
Found at i:3272114 original size:37 final size:37
Alignment explanation
Indices: 3272034--3272107 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
3272024 TAACAAGTTA
* *
3272034 AAAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAA-ATTTATATATTTTCTTTAAAAAATTAAAAATC
*
3272072 AAAAAATTTATATAATTTT-TTTACAAAATTAAAAAT
1 AAAAAATTTATAT-ATTTTCTTTAAAAAATTAAAAAT
3272108 ATAAAAAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 22 0.69
38 10 0.31
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAAATC
Found at i:3272253 original size:14 final size:14
Alignment explanation
Indices: 3272236--3272266 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3272226 ACCTTCGTAA
3272236 AATTTTTATTATTT
1 AATTTTTATTATTT
3272250 AATTTTTATTATTT
1 AATTTTTATTATTT
3272264 AAT
1 AAT
3272267 GATAGAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
AATTTTTATTATTT
Found at i:3277749 original size:18 final size:17
Alignment explanation
Indices: 3277722--3277765 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
3277712 GTCATATATG
*
3277722 TCCCGTAGGACCACTACA
1 TCCCGAAGGA-CACTACA
3277740 TCCCGAAGG--ACTACA
1 TCCCGAAGGACACTACA
3277755 TCCCGAAGGAC
1 TCCCGAAGGAC
3277766 TATTATACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
18 8 0.35
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (17 bp):
TCCCGAAGGACACTACA
Found at i:3277754 original size:15 final size:15
Alignment explanation
Indices: 3277734--3277767 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3277724 CCGTAGGACC
3277734 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
3277749 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
3277764 ACTA
1 ACTA
3277768 TTATACCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:3277894 original size:29 final size:29
Alignment explanation
Indices: 3277852--3278021 Score: 252
Period size: 29 Copynumber: 5.8 Consensus size: 29
3277842 TTTTATATGT
3277852 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
* *
3277880 TCATGTTGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
3277909 TCATGTAGCTCATGTTATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
3277938 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
**
3277967 TCATACACAGCTCATGTCATTTCTCTTGTGA
1 TCAT--GTAGCTCATGTCATTTCTCTTGTGA
*
3277998 TCATATAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
3278022 ATATCACATG
Statistics
Matches: 129, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
28 6 0.05
29 91 0.71
30 5 0.04
31 27 0.21
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:3278455 original size:64 final size:63
Alignment explanation
Indices: 3278386--3278542 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 63
3278376 TAATAGAGGT
* * * **
3278386 ATGCATTGATGCACTACTTGTGCATCGGTGTA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
3278449 G
63 G
* * * *
3278450 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
3278513 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
3278543 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 3 0.04
64 64 0.84
65 9 0.12
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:3279542 original size:23 final size:23
Alignment explanation
Indices: 3279516--3279572 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
3279506 AACTCATAAA
3279516 ATTTAAAACATTCATCAT-TATAC
1 ATTTAAAACATTCA-CATATATAC
* *
3279539 ATTT--ACCATTTACATATATAC
1 ATTTAAAACATTCACATATATAC
*
3279560 GTTTAAAACATTC
1 ATTTAAAACATTC
3279573 CAAAATTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
20 3 0.12
21 14 0.54
23 9 0.35
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTAAAACATTCACATATATAC
Found at i:3281091 original size:38 final size:39
Alignment explanation
Indices: 3281049--3281131 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 39
3281039 TATCACACAA
* * * *
3281049 CACATAGAACAACATATCAAC-TGTGCATATAATCATGT
1 CACATACAACAACATATAAACTTATACATATAATCATGT
* *
3281087 CACATACAATAACATATAAACTTATACATATATTCATGT
1 CACATACAACAACATATAAACTTATACATATAATCATGT
3281126 -ACATAC
1 CACATAC
3281132 TTTCATATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 24 0.63
39 14 0.37
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (39 bp):
CACATACAACAACATATAAACTTATACATATAATCATGT
Found at i:3283373 original size:23 final size:24
Alignment explanation
Indices: 3283346--3283407 Score: 76
Period size: 23 Copynumber: 2.6 Consensus size: 24
3283336 TATATATATC
*
3283346 CCGAAGGATCGCGT-AATATTGTT
1 CCGAAGGACCGCGTAAATATTGTT
3283369 CCGAAGGACCGCGTAGAATATTG-T
1 CCGAAGGACCGCGTA-AATATTGTT
3283393 CTCG-AGGACCGCGTA
1 C-CGAAGGACCGCGTA
3283408 GACCCTCTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 13 0.37
24 13 0.37
25 9 0.26
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (24 bp):
CCGAAGGACCGCGTAAATATTGTT
Found at i:3283404 original size:24 final size:25
Alignment explanation
Indices: 3283346--3283409 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
3283336 TATATATATC
*
3283346 CCGAAGGATCGCGT--AATATTGTT
1 CCGAAGGACCGCGTAGAATATTGTT
3283369 CCGAAGGACCGCGTAGAATATTG-T
1 CCGAAGGACCGCGTAGAATATTGTT
3283393 CTCG-AGGACCGCGTAGA
1 C-CGAAGGACCGCGTAGA
3283410 CCCTCTACTC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 13 0.35
24 15 0.41
25 9 0.24
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (25 bp):
CCGAAGGACCGCGTAGAATATTGTT
Found at i:3284225 original size:15 final size:15
Alignment explanation
Indices: 3284185--3284226 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3284175 ACATTCTCGT
3284185 ATGATTACTTATACC
1 ATGATTACTTATACC
3284200 ATAGA-TACTTATACC
1 AT-GATTACTTATACC
3284215 -TGATTATCTTAT
1 ATGATTA-CTTAT
3284227 TCTCTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 3 0.12
15 17 0.71
16 2 0.08
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (15 bp):
ATGATTACTTATACC
Found at i:3284767 original size:64 final size:64
Alignment explanation
Indices: 3284673--3284833 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 64
3284663 TAATGAAGGT
* * * * *
3284673 ATGCATCGATGTACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
3284736 GG
63 GC
* *
3284738 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
3284802 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTCCATATGCATCGATGCA
3284834 CCTTAAGCAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 57 0.69
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:3286078 original size:29 final size:28
Alignment explanation
Indices: 3286033--3286089 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
3286023 TTCCCTTTCA
3286033 TATTTAACTCAAATATC-CATACTTAAAC
1 TATTTAACTCAAATATCTCAT-CTTAAAC
**
3286061 TATTTATACTCATTTATCTCATCTTAAAC
1 TATTTA-ACTCAAATATCTCATCTTAAAC
3286090 CTCAAAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 16 0.64
30 3 0.12
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (28 bp):
TATTTAACTCAAATATCTCATCTTAAAC
Found at i:3289207 original size:35 final size:37
Alignment explanation
Indices: 3289131--3289230 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 37
3289121 CCAAAATGCT
* * * * * * *
3289131 TTTAAAAACTATATATTATACATGTTTTTAAAAACGT
1 TTTAAAAATTATATATAATATATATTTTCAGAAACGG
3289168 TTTAAAAATT-T-TATAATATATATTTTCAGAAACGG
1 TTTAAAAATTATATATAATATATATTTTCAGAAACGG
*
3289203 TTTAAAAATTATATATTATATATATTTT
1 TTTAAAAATTATATATAATATATATTTT
3289231 TAAAATGTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 28 0.53
36 2 0.04
37 23 0.43
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAAAAATTATATATAATATATATTTTCAGAAACGG
Found at i:3289248 original size:37 final size:36
Alignment explanation
Indices: 3289123--3289447 Score: 218
Period size: 37 Copynumber: 9.0 Consensus size: 36
3289113 ATAAATTTCC
* *
3289123 AAAATGCTTTTAAAAACTATATATTATACATGTTTTT
1 AAAATG-TTTTAAAAACTATATATTATATATATTTTT
* * * *
3289160 AAAAACGTTTTAAAAA-T-TTTATAATATATATTTTC
1 -AAAATGTTTTAAAAACTATATATTATATATATTTTT
* * *
3289195 AGAAACGGTTTAAAAATTATATATTATATATATTTTT
1 A-AAATGTTTTAAAAACTATATATTATATATATTTTT
* * * * *
3289232 AAAATGTTTTTCAAAATTATATAATATTTAAATGTTTT
1 AAAATG-TTTTAAAAACTATATATTATATATAT-TTTT
**** * *
3289270 AAAAAAAATTCAAAAC-A-ATATTATA-AT-TTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATATTTT-T
*
3289303 AAAATGATTTTAAAAACTATATATTATATATATTTCT
1 AAAATG-TTTTAAAAACTATATATTATATATATTTTT
***
3289340 AAAATGTTTTAAAAACTATATA-TATATAGT-TTCAA
1 AAAATGTTTTAAAAACTATATATTATATA-TATTTTT
* * * *
3289375 AAAATATTTTTAAAACTATATATTATATACATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATATTTTT
* *
3289411 AAAATGTTTTCAAAATTATGTATATTATA-AGTATTTT
1 AAAATGTTTTAAAAACTA--TATATTATATA-TATTTT
3289448 CAAAGACCGT
Statistics
Matches: 225, Mismatches: 45, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
32 3 0.01
33 5 0.02
34 9 0.04
35 61 0.27
36 55 0.24
37 62 0.28
38 30 0.13
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATATATTTTT
Found at i:3289275 original size:28 final size:30
Alignment explanation
Indices: 3289217--3289275 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
3289207 AAAATTATAT
* **
3289217 ATTATATATATTTTTAAAATGTTTTTCAAA
1 ATTATATATATATTTAAAATGTTTTAAAAA
3289247 ATTATATA-ATATTT-AAATGTTTTAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAA
3289275 A
1 A
3289276 AATTCAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 5 0.19
30 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (30 bp):
ATTATATATATATTTAAAATGTTTTAAAAA
Found at i:3289373 original size:71 final size:72
Alignment explanation
Indices: 3289099--3289435 Score: 233
Period size: 71 Copynumber: 4.7 Consensus size: 72
3289089 AATATTTTCG
* * * *
3289099 AAAA-TATGTAATATATAAATTTCCAAAATGCTTTTAAAAACTATATATTATACATGTTTTTAAA
1 AAAACTATATAATATATAAATTTCTAAAATG-TTTTAAAAACTATATA-TATATATG-TTTCAAA
*
3289163 AACG-TTTTA
63 AATGATTTTA
* * * * * * * **
3289172 AAAATTTTATAATATAT-ATTTTC-AGAAACGGTTTAAAAATTATATATTATATATATTTTTAAA
1 AAAACTATATAATATATAAATTTCTA-AAATGTTTTAAAAACTATATA-TATATATGTTTCAAAA
* *
3289235 ATGTTTTTC
64 ATGATTTTA
* * * **** * * *
3289244 AAAATTATATAATATTTAAATGTTTTAAAAAAAATTCAAAACAATAT-TATA-ATTTTTCAAAAA
1 AAAACTATATAATATATAAAT-TTCTAAAATGTTTTAAAAACTATATATATATATGTTTCAAAAA
3289307 TGATTTTA
65 TGATTTTA
* *
3289315 AAAACTATATATTATATATATTTCTAAAATGTTTTAAAAACTATATATATATA-GTTTCAAAAAA
1 AAAACTATATAATATATAAATTTCTAAAATGTTTTAAAAACTATATATATATATGTTTC-AAAAA
*
3289379 T-ATTTTT
65 TGATTTTA
* * * * *
3289386 AAAACTATATATTATATACATTT-TCAAAATGTTTTCAAAATTATGTATAT
1 AAAACTATATAATATATAAATTTCT-AAAATGTTTTAAAAACTATATATAT
3289436 TATAAGTATT
Statistics
Matches: 210, Mismatches: 44, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
70 19 0.09
71 98 0.47
72 52 0.25
73 15 0.07
74 25 0.12
75 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (72 bp):
AAAACTATATAATATATAAATTTCTAAAATGTTTTAAAAACTATATATATATATGTTTCAAAAAT
GATTTTA
Found at i:3289395 original size:33 final size:32
Alignment explanation
Indices: 3289281--3289403 Score: 95
Period size: 35 Copynumber: 3.5 Consensus size: 32
3289271 AAAAAAATTC
*
3289281 AAAACA-ATATTATAATTTTTCAAAAATGATTTTA
1 AAAACATATA-TAT-ATATTTCAAAAAT-ATTTTA
* *
3289315 AAAACTATATATTATATATATTTCTAAAATGTTTTA
1 AAAAC---ATA-TATATATATTTCAAAAATATTTTA
*
3289351 AAAACTATATATATATAGTTTCAAAAAATATTTTT
1 AAAAC-ATATATATATA-TTTC-AAAAATATTTTA
3289386 AAAACTATATATTATATA
1 AAAAC-ATATA-TATATA
3289404 CATTTTCAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
33 8 0.11
34 13 0.17
35 20 0.27
36 16 0.21
37 12 0.16
38 4 0.05
39 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (32 bp):
AAAACATATATATATATTTCAAAAATATTTTA
Found at i:3290219 original size:84 final size:83
Alignment explanation
Indices: 3290112--3290866 Score: 824
Period size: 84 Copynumber: 9.2 Consensus size: 83
3290102 CGGAGGTCTT
* * *
3290112 TGGCAGATAGCTCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
3290177 GAACTCAAAGGTCTTTTGG
66 GAACTCAAAGGTC-TTTGG
* * * **
3290196 TGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
3290261 GAACTCAAAGGTCTTTGG
66 GAACTCAAAGGTCTTTGG
* * * * *
3290279 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 -TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
**
3290344 TCGAACTC-GGGGTC-TT--
64 TCGAACTCAAAGGTCTTTGG
* * *
3290360 TGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGA---GAGCGTAGTC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
3290422 GAACTCAAAGGTCTTTTGG
66 GAACTCAAAGGTC-TTTGG
* * * * * **
3290441 TGGTAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
3290506 GAACTCAAAGGTCTTTGG
66 GAACTCAAAGGTCTTTGG
* * * * *
3290524 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 -TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
***
3290589 TCGAACTCGGGGGTC-TT--
64 TCGAACTCAAAGGTCTTTGG
* * *
3290606 TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
3290671 GAACTCAAAGGTCTTTGC
66 GAACTCAAAGGTCTTTGG
** * * * * * * * * *
3290689 TAACAGATAACCCTTCTAGCCTTGAGTTATGT-TGTAAATGTTATGCCCTTGAAGCTGAGTGTAA
1 TGGCAGATAACCCTTCTCGACTTAAGTTAT-TCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
* *
3290753 TCGAACTTAAGGGTC-TT--
64 TCGAACTCAAAGGTCTTTGG
* *
3290770 TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGA--TGCCTTGGAGCTGAGCGTAGTC
1 TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
3290833 GAACTCGAAGGTC-TTGG
66 GAACTCAAAGGTCTTTGG
* *
3290850 TGGCAGGTAGCCCTTCT
1 TGGCAGATAACCCTTCT
3290867 GGCCTTGAGC
Statistics
Matches: 559, Mismatches: 92, Indels: 44
0.80 0.13 0.06
Matches are distributed among these distances:
76 14 0.03
77 4 0.01
78 29 0.05
79 9 0.02
80 84 0.15
81 117 0.21
83 47 0.08
84 207 0.37
85 48 0.09
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (83 bp):
TGGCAGATAACCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTGG
Found at i:3290277 original size:164 final size:164
Alignment explanation
Indices: 3290066--3290866 Score: 899
Period size: 164 Copynumber: 4.9 Consensus size: 164
3290056 GCTATGTTGT
* * ** *
3290066 AAATGATATGACCC-CGAAGTTGAGTGTAATCGAACTCGGAGGTCTTTGGCAGATAGCTCTTCTC
1 AAATGATATG-CCCTTGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTC
3290130 GACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
65 GACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTG
*
3290195 GTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGC
129 GTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * * *
3290231 AAATGACATG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTCAAAGGTC--T--TTGGCAGATAGCCCTT
* * * * * * **
3290295 CTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-GGGGTC-
62 CTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
* * * *
3290358 TT--TGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGC
126 TTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * * * * *
3290395 AAATGATGTG-CCTTG--G-AGAGCGTAGTCGAACTCAAAGGTCTTTTGGTGGTAGACAACCCTT
1 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTCAAAGGTC--TT--TGGCAGATAGCCCTT
* * * * **
3290456 CTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
62 CTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
*
3290521 TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
127 TGG-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * ***
3290560 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCG
* *
3290625 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
66 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
** * * * *
3290690 AACAGATAACCCTTCTAGCCTTGAGTTATGTTGT
131 GGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * *
3290724 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCG
*
3290789 ACTTAAGCTATTCTGCAAATGA--TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGT
66 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* *
3290851 GGCAGGTAGCCCTTCT
131 GGCAGATAACCCTTCT
3290867 GGCCTTGAGC
Statistics
Matches: 539, Mismatches: 80, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
159 1 0.00
160 22 0.04
161 85 0.16
162 36 0.07
163 2 0.00
164 175 0.32
165 122 0.23
166 7 0.01
167 2 0.00
168 47 0.09
169 40 0.07
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (164 bp):
AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
GGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:3290476 original size:245 final size:246
Alignment explanation
Indices: 3290066--3290866 Score: 1154
Period size: 245 Copynumber: 3.3 Consensus size: 246
3290056 GCTATGTTGT
* * *
3290066 AAATGATATGACCC-CGAAGTTGAGTGTAATCGAACTCGGAGGTCTTTGGCAGATAGCTCTTCTC
1 AAATGATGTG-CCCTCGAAGCTGAGTGTAATCGAACTCGG-GGTCTTTGGCAGATAGCCCTTCTC
3290130 GACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
64 GACTTAAGCTATTCTGCAAATGATGTGCCTTGGA-C-GAGCGTAGTCGAACTCAAAGGTCTTTTG
3290195 GTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGT
127 GTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGT
3290260 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
192 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
*
3290315 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTTGA
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGA
3290380 CTTAAGCTATTCTGCAAATGATGTGCCTTGGA-GAGCGTAGTCGAACTCAAAGGTCTTTTGGTGG
66 CTTAAGCTATTCTGCAAATGATGTGCCTTGGACGAGCGTAGTCGAACTCAAAGGTCTTTTGGTGG
* *
3290444 TAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAA
131 CAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAA
3290509 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
196 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
3290560 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-GGGGTCTTTGGCAGATAGCCCTTCTCG
* *
3290625 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGC
65 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGA-C-GAGCGTAGTCGAACTCAAAGGTCTTTTGG
** * * * * * ** * * *
3290689 TAACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGTTATGCCCTTGAAGCTGAGTGTAAT
128 TGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGACATG-CCTTGGAGCTGAGCGTAGT
* * * * *
3290754 CGAACTTAAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGC
192 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * * * *
3290805 AAATGA--TG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-GGGTCTT--TGGCAGATAGCCCTTCT
3290867 GGCCTTGAGC
Statistics
Matches: 509, Mismatches: 34, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
241 1 0.00
242 28 0.06
243 2 0.00
244 16 0.03
245 222 0.44
246 58 0.11
247 1 0.00
248 97 0.19
249 84 0.17
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (246 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGA
CTTAAGCTATTCTGCAAATGATGTGCCTTGGACGAGCGTAGTCGAACTCAAAGGTCTTTTGGTGG
CAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
Found at i:3290705 original size:329 final size:324
Alignment explanation
Indices: 3290030--3290866 Score: 893
Period size: 329 Copynumber: 2.6 Consensus size: 324
3290020 GACAATTTTA
* * * * * * * ** *
3290030 TTGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCC-CGAAGTTGAGTGTA
1 TTGACAGATAACCCTTCTAGACTTAAGCTATGTTGCAAATGATATG-CCCTTG-AGCAGAGCGTA
** * * * *
3290094 ATCGAACTCGGAGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
64 ATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTCGACTTAAGCTATTCTGCAAATGA-ATGCC
*
3290159 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTGGCAGACAACCCTTCTAGACTTAAGTT
128 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTGGCAGATAACCCTTCTAGACTTAAGTT
* * *
3290224 ATGCTGCAAATGACATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATA
192 ATGCTGCAAATGACATGCCTCGAAGCTGAGCGTAATCGAACTCAAAGGTC-TT-GTTGGCAGATA
* * * **
3290289 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGG
255 ACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTAGAAGCTGAGCGTAATCGAACTCAA
3290354 GGTCT
320 GGTCT
* * * * *
3290359 TTGGCAGATAGCCCTTCTTGACTTAAGCTAT-TCTGCAAATGATGTG-CCTTG-G-AGAGCGTAG
1 TTGACAGATAACCCTTCTAGACTTAAGCTATGT-TGCAAATGATATGCCCTTGAGCAGAGCGTAA
* * * * *
3290420 TCGAACTCAAAGGTCTTTTGGTGGTAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGACAT
65 TCGAACTCAAAGGTC--TT--TGGCAGACAACCCTTCTCGACTTAAGCTATTCTGCAAATGA-AT
*
3290485 GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
125 GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG-TGGCAGATAACCCTTCTAGACTTAA
** * ***
3290550 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-T-TTGGCAGA
189 GTTATGCTGCAAATGACATG-CCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTGTTGGCAGA
* * * *
3290613 TAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTAGGAGCTGAGCGTAGTCGAACTC
253 TAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTAGAAGCTGAGCGTAATCGAACTC
3290677 AAAGGTCT
318 -AAGGTCT
* * * * * * *
3290685 TTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGTTATGCCCTTGAAGCTGAGTG
1 TTG---ACAGATAACCCTTCTAGACTTAAGCTATGTTGCAAATGATATGCCCTTG-AGCAGAGCG
* * * *
3290750 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATG-ATGC
62 TAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTCTCGACTTAAGCTATTCTGCAAATGAATGC
* * *
3290814 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTGGCAGGTAGCCCTTCT
127 CTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCT
3290867 GGCCTTGAGC
Statistics
Matches: 425, Mismatches: 66, Indels: 38
0.80 0.12 0.07
Matches are distributed among these distances:
325 56 0.13
326 56 0.13
327 39 0.09
328 8 0.02
329 212 0.50
330 32 0.08
331 2 0.00
332 1 0.00
333 19 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (324 bp):
TTGACAGATAACCCTTCTAGACTTAAGCTATGTTGCAAATGATATGCCCTTGAGCAGAGCGTAAT
CGAACTCAAAGGTCTTTGGCAGACAACCCTTCTCGACTTAAGCTATTCTGCAAATGAATGCCTTG
GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGC
TGCAAATGACATGCCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTGTTGGCAGATAACCCTT
CTCGACTTAAGCTATGCTGCAAATGATGTGCCCTAGAAGCTGAGCGTAATCGAACTCAAGGTCT
Found at i:3294235 original size:19 final size:19
Alignment explanation
Indices: 3294211--3294256 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3294201 AGTTAATGTG
3294211 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
3294230 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
3294249 AATGCAAA
1 AATGCAAA
3294257 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:3295967 original size:14 final size:14
Alignment explanation
Indices: 3295948--3295993 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
3295938 ATTCAATAAT
3295948 AAACAAATAAAAAA
1 AAACAAATAAAAAA
3295962 AAACAAATCAAAATAA
1 AAACAAAT-AAAA-AA
* *
3295978 ATACAAAGAAAAAA
1 AAACAAATAAAAAA
3295992 AA
1 AA
3295994 GAGGAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.80, C:0.09, G:0.02, T:0.09
Consensus pattern (14 bp):
AAACAAATAAAAAA
Found at i:3297509 original size:30 final size:31
Alignment explanation
Indices: 3297445--3297511 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3297435 AAATTTTATA
3297445 ATATATATTTTCAGAAATGGTTTAAAAATAT
1 ATATATATTTTCAGAAATGGTTTAAAAATAT
* * *
3297476 ATATATATTTTTA-AAATGTTTTTCAAAAT-T
1 ATATATATTTTCAGAAATG-GTTTAAAAATAT
3297506 ATATAT
1 ATATAT
3297512 TTTAAATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (31 bp):
ATATATATTTTCAGAAATGGTTTAAAAATAT
Found at i:3297529 original size:26 final size:29
Alignment explanation
Indices: 3297445--3297529 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 29
3297435 AAATTTTATA
* *
3297445 ATATATATTTTCAGAAATGGTTTAAAAATAT
1 ATATATATTTTTA-AAATGTTTTAAAAA-AT
**
3297476 ATATATATTTTTAAAATGTTTTTCAAAAT
1 ATATATATTTTTAAAATGTTTTAAAAAAT
3297505 -TATATA-TTTT-AAATGTTTTAAAAAA
1 ATATATATTTTTAAAATGTTTTAAAAAA
3297530 ATTCAAACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
26 13 0.27
27 4 0.08
28 6 0.12
29 2 0.04
30 11 0.23
31 12 0.25
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (29 bp):
ATATATATTTTTAAAATGTTTTAAAAAAT
Found at i:3297617 original size:73 final size:70
Alignment explanation
Indices: 3297374--3297694 Score: 248
Period size: 73 Copynumber: 4.5 Consensus size: 70
3297364 AAAATATGTA
* * * * * *
3297374 ATATAAATTTCCAAAATGCTTTAAAAACTATATATTATACATGTTTTTAAAAACG-TTTTAAAAA
1 ATATATATTTTCAAAATGTTTTAAAAA-TATATA-TAT--ATATTTTCAAAAATGATTTTAAAAA
* *
3297438 -T-TTTATA
62 CTATATATT
* * * *
3297445 ATATATATTTTCAGAAATGGTTTAAAAATATATATATAT-TTTT--AAAATGTTTTTCAAAATTA
1 ATATATATTTTCA-AAATGTTTTAAAAATATATATATATATTTTCAAAAATGATTTTAAAAACTA
3297507 TATATT
65 TATATT
* * * *** *
3297513 TTAAATGTTTT-AAAAAAATTCAAACAATATAT-TATATAATTTTTCAAAAATGATTTTAAAAAC
1 ATATATATTTTCAAAATGTTTTAAA-AATATATATATAT-A-TTTTCAAAAATGATTTTAAAAAC
3297576 TATATATT
63 TATATATT
* *
3297584 ATATATATTTTCTAAAATGTTTTAAAAACTATATAATATATAGTTTCAAAAAAT-ATTTTTAAAA
1 ATATATATTTTC-AAAATGTTTTAAAAA-TATAT-ATATATATTTTC-AAAAATGATTTTAAAAA
3297648 CTATATATT
62 CTATATATT
* *
3297657 ATATACATTTTCAAAATGTTTTCAAAAAT-TATGTATAT
1 ATATATATTTTCAAAATGTTTT-AAAAATATATATATAT
3297695 TATAAGTATT
Statistics
Matches: 205, Mismatches: 28, Indels: 35
0.76 0.10 0.13
Matches are distributed among these distances:
65 5 0.02
66 21 0.10
67 13 0.06
68 14 0.07
69 4 0.02
70 8 0.04
71 50 0.24
72 26 0.13
73 52 0.25
74 7 0.03
75 5 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (70 bp):
ATATATATTTTCAAAATGTTTTAAAAATATATATATATATTTTCAAAAATGATTTTAAAAACTAT
ATATT
Found at i:3297673 original size:36 final size:37
Alignment explanation
Indices: 3297393--3297710 Score: 204
Period size: 35 Copynumber: 8.9 Consensus size: 37
3297383 TCCAAAATGC
* * * **
3297393 TTTAAAAACTATATATTATACATGTTTTTAAAAACGT
1 TTTAAAAACTATATATTATATATATTTTCAAAAATAT
* * * **
3297430 TTTAAAAA-T-TTTATAATATATATTTTCAGAAATGG
1 TTTAAAAACTATATATTATATATATTTTCAAAAATAT
*
3297465 TTT-AAAA--ATATA-TATATAT-TTTT--AAAATGTT
1 TTTAAAAACTATATATTATATATATTTTCAAAAAT-AT
* * * * *
3297496 TTTCAAAATTATATATTTTAAATGTTTT-AAAAA-A-
1 TTTAAAAACTATATATTATATATATTTTCAAAAATAT
* * *
3297530 ATT-CAAACAATATATTATATA-ATTTTTCAAAAATGAT
1 TTTAAAAACTATATATTATATATA-TTTTCAAAAAT-AT
* *
3297567 TTTAAAAACTATATATTATATATATTTTCTAAAATGT
1 TTTAAAAACTATATATTATATATATTTTCAAAAATAT
*
3297604 TTTAAAAACTATATA--ATATATAGTTTCAAAAAATAT
1 TTTAAAAACTATATATTATATATATTTTC-AAAAATAT
* * *
3297640 TTTTAAAACTATATATTATATACATTTTC-AAAATGT
1 TTTAAAAACTATATATTATATATATTTTCAAAAATAT
*
3297676 TTTCAAAAATTATGTATATTATA-AGTATTTTCAAA
1 TTT-AAAAACTA--TATATTATATA-TATTTTCAAA
3297711 GACCGTTTGC
Statistics
Matches: 220, Mismatches: 38, Indels: 43
0.73 0.13 0.14
Matches are distributed among these distances:
30 4 0.02
31 3 0.01
32 8 0.04
33 23 0.10
34 19 0.09
35 37 0.17
36 35 0.16
37 36 0.16
38 37 0.17
39 16 0.07
40 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAAAAACTATATATTATATATATTTTCAAAAATAT
Found at i:3302252 original size:26 final size:26
Alignment explanation
Indices: 3302208--3302265 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
3302198 CGGATGTAAG
*
3302208 ATTTTATACAATGAACGGACTTTTAAA
1 ATTTTATACAATGAACGGACTTAT-AA
* *
3302235 ATTTTA-AGAATGATCGGACTTATAA
1 ATTTTATACAATGAACGGACTTATAA
3302260 ATTTTA
1 ATTTTA
3302266 GGGGACATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 8 0.29
26 14 0.50
27 6 0.21
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (26 bp):
ATTTTATACAATGAACGGACTTATAA
Found at i:3304090 original size:27 final size:27
Alignment explanation
Indices: 3304060--3304124 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
3304050 TCGACAATTT
*
3304060 GAGTACAAATATCCGATACTCTCATTC
1 GAGTCCAAATATCCGATACTCTCATTC
* *
3304087 GAGTCCAAATATCTGATATTCTCATTC
1 GAGTCCAAATATCCGATACTCTCATTC
3304114 GAGTCCAAATA
1 GAGTCCAAATA
3304125 ACATAGCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (27 bp):
GAGTCCAAATATCCGATACTCTCATTC
Found at i:3310521 original size:21 final size:21
Alignment explanation
Indices: 3310497--3310539 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3310487 TAGTAAAAAA
* *
3310497 TATTTAAAATATTATTATTTT
1 TATTTAAAATATCAATATTTT
3310518 TATTTAAAATATCAATATTTT
1 TATTTAAAATATCAATATTTT
3310539 T
1 T
3310540 TAATATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTAAAATATCAATATTTT
Found at i:3325215 original size:11 final size:12
Alignment explanation
Indices: 3325194--3325222 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3325184 TATGTATATC
3325194 AAATATGAAAAA
1 AAATATGAAAAA
3325206 AAAT-TGAAAAA
1 AAATATGAAAAA
3325217 AAATAT
1 AAATAT
3325223 ATGTATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (12 bp):
AAATATGAAAAA
Found at i:3332522 original size:114 final size:114
Alignment explanation
Indices: 3332322--3332549 Score: 375
Period size: 114 Copynumber: 2.0 Consensus size: 114
3332312 CATTATCAAA
* * * *
3332322 TGATTGAGAATATTTCGATTGTATACTACTTTGTAATCATCCCATATTAATTAATAAAACTATAA
1 TGATTGAGAATATTTCGATTATATACTACCTTGTAATCATCCCAAATTAATTAACAAAACTATAA
*
3332387 GGATTAAATTTATAAATTTAAGACTAAATTAAAATTAAATGTAAAATTT
66 GGATTAAATTTATAAATTTAAGACTAAATTAAAATAAAATGTAAAATTT
* *
3332436 TGATTGAGATTCTTTCGATTATATACTACCTTGTAATCATCCCAAATTAATTAACAAAACTATAA
1 TGATTGAGAATATTTCGATTATATACTACCTTGTAATCATCCCAAATTAATTAACAAAACTATAA
* *
3332501 GGATTAAATTTTTAAATTTAAGACTAAATTAAAGTAAAATGTAAAATTT
66 GGATTAAATTTATAAATTTAAGACTAAATTAAAATAAAATGTAAAATTT
3332550 GGAGGGTAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (114 bp):
TGATTGAGAATATTTCGATTATATACTACCTTGTAATCATCCCAAATTAATTAACAAAACTATAA
GGATTAAATTTATAAATTTAAGACTAAATTAAAATAAAATGTAAAATTT
Found at i:3332925 original size:31 final size:32
Alignment explanation
Indices: 3332887--3332946 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
3332877 ATCCCTAACG
*
3332887 TTATCGATTCATTCGATTTTAGTC-CTTAATA
1 TTATCGATTCATTCCATTTTAGTCTCTTAATA
3332918 TTATCGATTCATTCCATTTTAGTCTCTTA
1 TTATCGATTCATTCCATTTTAGTCTCTTA
3332947 TTCGTTAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.23, C:0.18, G:0.08, T:0.50
Consensus pattern (32 bp):
TTATCGATTCATTCCATTTTAGTCTCTTAATA
Found at i:3344091 original size:3 final size:3
Alignment explanation
Indices: 3344083--3344139 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
3344073 AGGAATTCAG
3344083 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3344131 AGA AGA AGA
1 AGA AGA AGA
3344140 GATTCGTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3346546 original size:43 final size:43
Alignment explanation
Indices: 3346491--3346757 Score: 401
Period size: 43 Copynumber: 6.2 Consensus size: 43
3346481 TGTGAATAAA
*
3346491 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* *
3346534 AAACGCCTCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * *
3346577 AAACGCCTCAATAGGTCGAGATCTAAAGCGGTGTTTTTGGAAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
*
3346620 AAACGCCGCAATAGGTCGAGATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
*
3346663 AAACGCCGCAATAGGTCGAGATTTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
3346706 AAACGCCACAAAATGT-TAGATCTATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGA-AC
3346749 AAACGCCGC
1 AAACGCCGC
3346758 TAATGACCGT
Statistics
Matches: 206, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
42 21 0.10
43 185 0.90
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
Done.