Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 98 of 770
Found at i:28595322 original size:32 final size:34
Alignment explanation
Indices: 28595286--28595350 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
28595276 TAACAGTGGT
*
28595286 ACTGGACCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGACCAGAGTCCCTTATTCAGATAACAATAA
* **
28595318 ACTGGGCCTTAGTCCCTTATTCAGATAACAATA
1 ACTGGACCAGAGTCCCTTATTCAGATAACAATA
28595351 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (34 bp):
ACTGGACCAGAGTCCCTTATTCAGATAACAATAA
Found at i:28597221 original size:26 final size:26
Alignment explanation
Indices: 28597191--28597271 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
28597181 TGAAATTCCC
28597191 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
28597217 ATCAT-AAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28597242 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
28597268 ATCA
1 ATCA
28597272 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
25 24 0.46
26 28 0.54
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:28600252 original size:21 final size:22
Alignment explanation
Indices: 28600223--28600263 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
28600213 TATGTTAAAG
28600223 ATATATAATAA-AACATATATTA
1 ATATATAATAATAA-ATATATTA
28600245 ATAT-TAATAATAAATATAT
1 ATATATAATAATAAATATAT
28600264 AGGTAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATATAATAATAAATATATTA
Found at i:28601899 original size:48 final size:48
Alignment explanation
Indices: 28601839--28601935 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
28601829 AATAAGTTAG
28601839 CTTCTCCAGATGTTGAAGGGATGAAGGAAGCTCACGCAAGTTAGAACA
1 CTTCTCCAGATGTTGAAGGGATGAAGGAAGCTCACGCAAGTTAGAACA
28601887 CTTCTCCAGATGTTGAAGGGATGAAGGAAGCTCACGCAAGTTAGAACA
1 CTTCTCCAGATGTTGAAGGGATGAAGGAAGCTCACGCAAGTTAGAACA
28601935 C
1 C
28601936 CCCATAAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.21
Consensus pattern (48 bp):
CTTCTCCAGATGTTGAAGGGATGAAGGAAGCTCACGCAAGTTAGAACA
Found at i:28602482 original size:18 final size:17
Alignment explanation
Indices: 28602448--28602483 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
28602438 TGCACGTAAT
*
28602448 ATTATATAATTAAAATA
1 ATTATATAATAAAAATA
28602465 ATTATATAAATAAAAATA
1 ATTATAT-AATAAAAATA
28602483 A
1 A
28602484 AAATGATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTATATAATAAAAATA
Found at i:28602768 original size:16 final size:17
Alignment explanation
Indices: 28602729--28602767 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
28602719 GGTCTAAAAA
28602729 AATTTTGCATTTACTAAT
1 AATTTTGCATTTAC-AAT
28602747 AATTTTGCATTTA-AAT
1 AATTTTGCATTTACAAT
28602763 -ATTTT
1 AATTTT
28602768 TTTTCTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 3 0.14
18 13 0.62
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTTGCATTTACAAT
Found at i:28604957 original size:40 final size:40
Alignment explanation
Indices: 28604891--28605057 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
28604881 AAATTGAATG
* * *
28604891 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
28604930 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
28604970 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
28605010 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
28605050 ATATCCGG
1 ATATCCGG
28605058 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28612962 original size:40 final size:40
Alignment explanation
Indices: 28612896--28613062 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
28612886 AAATTGAATG
* * *
28612896 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
28612935 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
28612975 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
28613015 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
28613055 ATATCCGG
1 ATATCCGG
28613063 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:28618646 original size:18 final size:18
Alignment explanation
Indices: 28618625--28618711 Score: 120
Period size: 18 Copynumber: 4.8 Consensus size: 18
28618615 CGTTTACGAT
28618625 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
** *
28618643 ACTATTCATATATACGAC
1 ACTATTCACGTATACGGC
*
28618661 ACTATTCATGTATACGGC
1 ACTATTCACGTATACGGC
*
28618679 ACTATTTACGTATACGGC
1 ACTATTCACGTATACGGC
*
28618697 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
28618712 AGTAGTTGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:28621721 original size:15 final size:16
Alignment explanation
Indices: 28621703--28621732 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28621693 AAAAGATATC
28621703 TAAAAAAAAA-TTAAT
1 TAAAAAAAAAGTTAAT
28621718 TAAAAAAAAAGTTAA
1 TAAAAAAAAAGTTAA
28621733 AAGCTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAAAAAAAAGTTAAT
Found at i:28622588 original size:18 final size:18
Alignment explanation
Indices: 28622545--28622600 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
28622535 TCACGTCAAC
*
28622545 AATTAAATAATTTTTAAAA
1 AATTAAA-AATATTTAAAA
*
28622564 ATTTTAAAAATATTTAAAA
1 A-ATTAAAAATATTTAAAA
*
28622583 AATTAAAATTA-TTAAAA
1 AATTAAAAATATTTAAAA
28622600 A
1 A
28622601 GTATAAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.22
18 8 0.25
19 12 0.38
20 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTAAAAATATTTAAAA
Found at i:28622608 original size:18 final size:17
Alignment explanation
Indices: 28622553--28622600 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
28622543 ACAATTAAAT
* *
28622553 AATTTTTAAAAATTTTAA
1 AATTATTAAAAA-ATTAA
*
28622571 AAATATTTAAAAAATTAA
1 AATTA-TTAAAAAATTAA
28622589 AATTATTAAAAA
1 AATTATTAAAAA
28622601 GTATAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 7 0.28
18 11 0.44
19 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTATTAAAAAATTAA
Found at i:28624132 original size:50 final size:50
Alignment explanation
Indices: 28624078--28624178 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
28624068 AAATTGTATA
28624078 TATCTTAGTGTTATTTAAATATACATATTTTTTAAAATTTATTTTCAATT
1 TATCTTAGTGTTATTTAAATATACATATTTTTTAAAATTTATTTTCAATT
28624128 TATCTTAGTGTTATTTAAATATACATATTTTTTAAAATTTATTTTCAATT
1 TATCTTAGTGTTATTTAAATATACATATTTTTTAAAATTTATTTTCAATT
28624178 T
1 T
28624179 GTTGGGAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (50 bp):
TATCTTAGTGTTATTTAAATATACATATTTTTTAAAATTTATTTTCAATT
Found at i:28626779 original size:20 final size:21
Alignment explanation
Indices: 28626751--28626799 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
28626741 ATATATCATT
*
28626751 ATTTTATTTGATTCTAAT-AA
1 ATTTGATTTGATTCTAATCAA
*
28626771 ATTTGATTTGATTTTAATCAA
1 ATTTGATTTGATTCTAATCAA
28626792 A-TTGATTT
1 ATTTGATTT
28626800 AATTGTCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (21 bp):
ATTTGATTTGATTCTAATCAA
Found at i:28627816 original size:61 final size:61
Alignment explanation
Indices: 28627738--28627864 Score: 245
Period size: 61 Copynumber: 2.1 Consensus size: 61
28627728 AATTCACAAG
28627738 ATTTTTTCCTCAATTTTATGGTAAAAGTATCATAGAGGTTATTGTACTAGAAGTCAAATTA
1 ATTTTTTCCTCAATTTTATGGTAAAAGTATCATAGAGGTTATTGTACTAGAAGTCAAATTA
*
28627799 ATTTTTTCCTCAATTTTATGGTAAAAGTATTATAGAGGTTATTGTACTAGAAGTCAAATTA
1 ATTTTTTCCTCAATTTTATGGTAAAAGTATCATAGAGGTTATTGTACTAGAAGTCAAATTA
28627860 ATTTT
1 ATTTT
28627865 GTCCCTTCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (61 bp):
ATTTTTTCCTCAATTTTATGGTAAAAGTATCATAGAGGTTATTGTACTAGAAGTCAAATTA
Found at i:28633372 original size:23 final size:24
Alignment explanation
Indices: 28633328--28633373 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28633318 TTAAATCTTA
**
28633328 AAAATAAAAAATTTATGTTATCAT
1 AAAATAAAAAATTTATAATATCAT
*
28633352 AAAATAAAAAGTTTA-AATATCA
1 AAAATAAAAAATTTATAATATCA
28633374 ACAAACTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATAAAAAATTTATAATATCAT
Found at i:28640871 original size:17 final size:14
Alignment explanation
Indices: 28640820--28640894 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 14
28640810 AAATATGTAA
28640820 TAATATAAATCATATAG
1 TAATA-AAAT-ATAT-G
28640837 TAATAAAATATATG
1 TAATAAAATATATG
28640851 TAATAAAATATAGTGTG
1 TAATAAAATATA---TG
* **
28640868 TAATAAAAAATACA
1 TAATAAAATATATG
28640882 TAAATAAAATATA
1 T-AATAAAATATA
28640895 ATAAAATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 14 0.28
15 14 0.28
16 4 0.08
17 18 0.36
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.32
Consensus pattern (14 bp):
TAATAAAATATATG
Found at i:28640897 original size:25 final size:26
Alignment explanation
Indices: 28640868--28640944 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 26
28640858 ATATAGTGTG
28640868 TAATAAAAAATACAT-AAATAAAATA
1 TAATAAAAAATACATAAAATAAAATA
* * *
28640893 TAATAAAATATA-ATGAAATATAATA
1 TAATAAAAAATACATAAAATAAAATA
* *
28640918 TAATAAAGAATTCATAAAATAATAATA
1 TAATAAAAAATACATAAAATAA-AATA
28640945 ATATAATAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.05
25 29 0.69
26 7 0.17
27 4 0.10
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (26 bp):
TAATAAAAAATACATAAAATAAAATA
Found at i:28640899 original size:10 final size:10
Alignment explanation
Indices: 28640884--28640922 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
28640874 AAAATACATA
28640884 AATAAAATAT
1 AATAAAATAT
28640894 AATAAAATAT
1 AATAAAATAT
*
28640904 AATGAAATAT
1 AATAAAATAT
*
28640914 AATATAATA
1 AATAAAATA
28640923 AAGAATTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (10 bp):
AATAAAATAT
Found at i:28641143 original size:29 final size:29
Alignment explanation
Indices: 28641102--28641173 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
28641092 AAAATATGAA
* *
28641102 ATAAAATAATATATAATATATATTAAAAC
1 ATAAAATAATATATAACATATAATAAAAC
* * *
28641131 ATAAAATAGTATATAACATTTAATAAAAT
1 ATAAAATAATATATAACATATAATAAAAC
28641160 ATAAAATAATATAT
1 ATAAAATAATATAT
28641174 GTTAATATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (29 bp):
ATAAAATAATATATAACATATAATAAAAC
Found at i:28641185 original size:25 final size:25
Alignment explanation
Indices: 28641150--28641197 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
28641140 TATATAACAT
28641150 TTAATAAAATATAAAATAATATATG
1 TTAATAAAATATAAAATAATATATG
*
28641175 TTAATATAATATAAAATAATATA
1 TTAATAAAATATAAAATAATATA
28641198 ATTATACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
TTAATAAAATATAAAATAATATATG
Found at i:28644377 original size:12 final size:12
Alignment explanation
Indices: 28644362--28644396 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
28644352 AAATCTAAAT
28644362 AATAATCCTAAC
1 AATAATCCTAAC
28644374 AATAATCCTAAC
1 AATAATCCTAAC
28644386 AATAATCCTAA
1 AATAATCCTAA
28644397 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAATCCTAAC
Found at i:28645223 original size:63 final size:63
Alignment explanation
Indices: 28645156--28645275 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
28645146 CCTGGAAACG
* * * * * *
28645156 GTGTTAGTTCAGGAAATGATTGTGCATGCTGTGGTGCTTGTGTAAAATAAATTGGTGATTATT
1 GTGTTAGTGCAGGAAATGAATATGCATGCTATGGTGCTAGTGTAAAATAAACTGGTGATTATT
* * *
28645219 GTGTTGGTGCAGGGAATGAATATGTATGCTATGGTGCTAGTGTAAAATAAACTGGTG
1 GTGTTAGTGCAGGAAATGAATATGCATGCTATGGTGCTAGTGTAAAATAAACTGGTG
28645276 TGTGTTGTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.27, C:0.07, G:0.31, T:0.36
Consensus pattern (63 bp):
GTGTTAGTGCAGGAAATGAATATGCATGCTATGGTGCTAGTGTAAAATAAACTGGTGATTATT
Found at i:28650469 original size:25 final size:27
Alignment explanation
Indices: 28650432--28650484 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28650422 TCAAACATGC
28650432 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
28650458 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
28650484 A
1 A
28650485 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:28652018 original size:32 final size:32
Alignment explanation
Indices: 28651974--28652066 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
28651964 GTTATCATGT
*
28651974 CCATCATCCATTAACTATTAAAACGCTAATGC
1 CCATCATCCATTAACTATTAAAATGCTAATGC
*
28652006 CCATCATTCATTAACTATTAAAATGCTAATGC
1 CCATCATCCATTAACTATTAAAATGCTAATGC
28652038 CCATCATCCATTAACTATTAAAATGCTAA
1 CCATCATCCATTAACTATTAAAATGCTAA
28652067 AATGCATACA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (32 bp):
CCATCATCCATTAACTATTAAAATGCTAATGC
Found at i:28654460 original size:6 final size:6
Alignment explanation
Indices: 28654451--28654476 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28654441 CACCGTAAGG
28654451 GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GT
28654477 TGTGGTACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:28654561 original size:51 final size:53
Alignment explanation
Indices: 28654462--28654565 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 53
28654452 TAACAGTAAC
**
28654462 AGTAACAGTAACAGTTGTGGTACACAAAGTACCTTATCGGAACAAATCCGGAAT
1 AGTAACAGTAACAGTTCAGGTA-ACAAAGTACCTTATCGGAACAAATCCGGAAT
* *
28654516 AGTAACAGTAACAG-TCAGGT-ACAGAGTACCTCT-TCGGAACGAATCCGGAA
1 AGTAACAGTAACAGTTCAGGTAACAAAGTACCT-TATCGGAACAAATCCGGAA
28654566 CAGTCATAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 26 0.58
52 1 0.02
53 4 0.09
54 14 0.31
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (53 bp):
AGTAACAGTAACAGTTCAGGTAACAAAGTACCTTATCGGAACAAATCCGGAAT
Found at i:28654891 original size:21 final size:21
Alignment explanation
Indices: 28654867--28654909 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28654857 TTTTTCCTTT
28654867 TCTCCCATACTCTCTGTTTCG
1 TCTCCCATACTCTCTGTTTCG
28654888 TCTCCCATACTCTCTGTTTCG
1 TCTCCCATACTCTCTGTTTCG
28654909 T
1 T
28654910 TTCATTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.37, G:0.09, T:0.44
Consensus pattern (21 bp):
TCTCCCATACTCTCTGTTTCG
Found at i:28655076 original size:20 final size:20
Alignment explanation
Indices: 28655051--28655088 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28655041 TATTCAATTA
28655051 ATAAATATCTTTTATAATCT
1 ATAAATATCTTTTATAATCT
28655071 ATAAATATCTTTTATAAT
1 ATAAATATCTTTTATAAT
28655089 TAAATACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATATCTTTTATAATCT
Found at i:28655615 original size:13 final size:14
Alignment explanation
Indices: 28655597--28655625 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28655587 TATTAACTTC
28655597 ATAAATATTTT-TA
1 ATAAATATTTTCTA
28655610 ATAAATATTTTCTA
1 ATAAATATTTTCTA
28655624 AT
1 AT
28655626 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:28656011 original size:20 final size:19
Alignment explanation
Indices: 28655966--28656011 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
28655956 ATTTCCACCT
**
28655966 ATTCAAAACATATTCAAAC
1 ATTCAAAACATATAAAAAC
28655985 ATGTCAAAACATACTAAAAAC
1 AT-TCAAAACATA-TAAAAAC
28656006 ATTCAA
1 ATTCAA
28656012 CCTAAGTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 14 0.61
21 7 0.30
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (19 bp):
ATTCAAAACATATAAAAAC
Found at i:28656608 original size:36 final size:36
Alignment explanation
Indices: 28656561--28656634 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
28656551 TTTCTCCTCC
28656561 AAACAATAAGCTAGTTATAGTGACAAAGAACATCCT
1 AAACAATAAGCTAGTTATAGTGACAAAGAACATCCT
28656597 AAACAATAAGCTAGTTATAGTGACAAAGAACATCCT
1 AAACAATAAGCTAGTTATAGTGACAAAGAACATCCT
28656633 AA
1 AA
28656635 CTACCAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (36 bp):
AAACAATAAGCTAGTTATAGTGACAAAGAACATCCT
Found at i:28658304 original size:40 final size:41
Alignment explanation
Indices: 28658227--28658309 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 41
28658217 TCTGTTTTTG
* * * *
28658227 TATAACTAATTCATATAACCATTACATATATCTATTTC-TA
1 TATAACCAATTCATATAACCATTACACATAACCATTTCGTA
* * *
28658267 TATAACCAATTCTTATAATCATTTCACATAACCATTTCGTA
1 TATAACCAATTCATATAACCATTACACATAACCATTTCGTA
28658308 TA
1 TA
28658310 GCCATTTCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
40 31 0.89
41 4 0.11
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (41 bp):
TATAACCAATTCATATAACCATTACACATAACCATTTCGTA
Found at i:28658309 original size:26 final size:26
Alignment explanation
Indices: 28658236--28658318 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
28658226 GTATAACTAA
*
28658236 TTCATATAACCATTACATAT-ATCTAT
1 TTCATATAACCATTTCATATAATC-AT
* *
28658262 TTCTATATAACCAATTCTTATAATCAT
1 TTC-ATATAACCATTTCATATAATCAT
* * **
28658289 TTCACATAACCATTTCGTATAGCCAT
1 TTCATATAACCATTTCATATAATCAT
28658315 TTCA
1 TTCA
28658319 AAGTGTTAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
26 25 0.53
27 19 0.40
28 3 0.06
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (26 bp):
TTCATATAACCATTTCATATAATCAT
Found at i:28661048 original size:18 final size:17
Alignment explanation
Indices: 28661007--28661049 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28660997 ATATTAGGAT
*
28661007 AAAATAATAAGTATAATG
1 AAAAT-ATAAGGATAATG
28661025 ATAAATATAAGGATATATG
1 A-AAATATAAGGATA-ATG
28661044 AAAATA
1 AAAATA
28661050 ATACTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (17 bp):
AAAATATAAGGATAATG
Found at i:28664036 original size:26 final size:25
Alignment explanation
Indices: 28663969--28664099 Score: 196
Period size: 26 Copynumber: 5.2 Consensus size: 25
28663959 TGATACAAAT
28663969 TGATAATA-GTTA-GTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
28663992 TGATAATA-GTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
28664017 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
*
28664042 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
*
28664068 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
28664094 TGATAA
1 TGATAA
28664100 GAATTTCATG
Statistics
Matches: 103, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
23 12 0.12
24 9 0.09
25 32 0.31
26 50 0.49
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:28664070 original size:51 final size:50
Alignment explanation
Indices: 28663969--28664099 Score: 203
Period size: 51 Copynumber: 2.6 Consensus size: 50
28663959 TGATACAAAT
28663969 TGATAATA-GTTA-GTAAATGTTCATGATAATAGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGTTAGGTAAATGTTCCA
* *
28664017 TGATAATAGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAAT-AGTTAGGTAAATGTTCCA
*
28664068 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATG-TTCATGATAA
28664100 GAATTTCATG
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
48 8 0.11
49 4 0.05
50 18 0.24
51 36 0.47
52 10 0.13
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (50 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATAGTTAGGTAAATGTTCCA
Found at i:28665607 original size:25 final size:26
Alignment explanation
Indices: 28665579--28665630 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
28665569 TTTACAGTTT
28665579 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
28665604 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
28665630 T
1 T
28665631 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:28669836 original size:26 final size:26
Alignment explanation
Indices: 28669774--28669882 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28669764 TGATACAAAT
28669774 TGATAATAGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
28669799 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
28669825 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
28669851 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
28669877 TGATAA
1 TGATAA
28669883 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 21 0.26
26 59 0.74
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:28671391 original size:25 final size:26
Alignment explanation
Indices: 28671363--28671414 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
28671353 TTTACAGTTT
28671363 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
28671388 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
28671414 T
1 T
28671415 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:28672882 original size:17 final size:19
Alignment explanation
Indices: 28672850--28672884 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
28672840 ATCCTTTATG
28672850 TTAATTTAGATTTAATAAT
1 TTAATTTAGATTTAATAAT
28672869 TTAA-TTAG-TTTAATAA
1 TTAATTTAGATTTAATAA
28672885 ATCTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
TTAATTTAGATTTAATAAT
Found at i:28674430 original size:15 final size:17
Alignment explanation
Indices: 28674396--28674432 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
28674386 CTATCAAATA
*
28674396 TATAATTGATTGTTTTT
1 TATAATTGATTGTCTTT
28674413 TATAATT-ATT-TCTTT
1 TATAATTGATTGTCTTT
28674428 TATAA
1 TATAA
28674433 ATAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
TATAATTGATTGTCTTT
Found at i:28677162 original size:9 final size:9
Alignment explanation
Indices: 28677152--28677204 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
28677142 TTAAAAAGTA
28677152 TAAAATTTAT
1 TAAAATTT-T
*
28677162 AAAAATATTTT
1 TAAAAT-T-TT
28677173 TTAAAATTTT
1 T-AAAATTTT
28677183 TAAAATTTT
1 TAAAATTTT
*
28677192 TAAAATTGT
1 TAAAATTTT
28677201 TAAA
1 TAAA
28677205 TGTTGACATG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 20 0.54
10 8 0.22
11 3 0.08
12 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (9 bp):
TAAAATTTT
Found at i:28677193 original size:18 final size:18
Alignment explanation
Indices: 28677170--28677204 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28677160 ATAAAAATAT
*
28677170 TTTTTAAAATTTTTAAAA
1 TTTTTAAAATTGTTAAAA
28677188 TTTTTAAAATTGTTAAA
1 TTTTTAAAATTGTTAAA
28677205 TGTTGACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTTAAAATTGTTAAAA
Found at i:28678496 original size:9 final size:9
Alignment explanation
Indices: 28678482--28678513 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
28678472 ACATCAATCT
*
28678482 ATTATTCGA
1 ATTATTTGA
28678491 ATTATTTGA
1 ATTATTTGA
28678500 ATTATTTGA
1 ATTATTTGA
28678509 ATTAT
1 ATTAT
28678514 AAAATTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53
Consensus pattern (9 bp):
ATTATTTGA
Found at i:28679191 original size:18 final size:18
Alignment explanation
Indices: 28679168--28679205 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28679158 GATCTTTACT
*
28679168 GATTTTATATAAAA-AAAA
1 GATTTT-TAAAAAATAAAA
28679186 GATTTTTAAAAAATAAAA
1 GATTTTTAAAAAATAAAA
28679204 GA
1 GA
28679206 CTCTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (18 bp):
GATTTTTAAAAAATAAAA
Found at i:28681678 original size:213 final size:212
Alignment explanation
Indices: 28680625--28681639 Score: 1435
Period size: 213 Copynumber: 4.8 Consensus size: 212
28680615 AAGTCTCCTA
* * * ** * *
28680625 AGAGATTCCAGTTTATAAAAGCTGTAAGGAAGGCAAACAAGGTTTTCACAGTGGTCCAATATCAA
1 AGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCAA
* * *
28680690 TTTCTCAAGACCAATAAGATTGCCAAATGAGGATGATAATTCCTTCAAAGCTGTTCCGCTTAAAT
66 TTGCTCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
* *
28680755 CAAGATCCCTCAACATCTCCATGGTGTCCAAGACTTCTGGGAAAATCTCCAATCTCGAGCAACCT
131 CAAGAT-CCTCAACATCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTTGAGCAACCT
* * **
28680820 TGAACTG-T-GAATGTCTTA
195 TTAA--GATCGAATCTCTCG
* * *
28680838 AGAGATTTCAGTTTATAAAAGCTGTCAGGAAGGCAAACAAGCTTTTTACAGTTTTTCAATCTCAA
1 AGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCAA
*
28680903 TTGCCCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
66 TTGCTCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
* * * *
28680968 CAAGATCCCACAACATCTCCATGGTATCCATGACTTCTGGGAAAATCTCTAATCTCGAGCAACCT
131 CAAGAT-CCTCAACATCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTTGAGCAACCT
*
28681033 TTAAGA-CTGAATATCTCG
195 TTAAGATC-GAATCTCTCG
* * *
28681051 AGAGGTTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGCTTTTTACAGTTTTTCAATCTCAA
1 AGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCAA
28681116 TTGCTCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
66 TTGCTCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
*
28681181 CAAGATACCTCAACATCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATATTGAGCAACCT
131 CAAGAT-CCTCAACATCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTTGAGCAACCT
* *
28681246 TTAAGATTGAATCTCTTG
195 TTAAGATCGAATCTCTCG
* *
28681264 AGAGATTTCAATTTATAAAAACTGTCAGGAAGGCAAACAAAGTTTTCACAGTTTTTCAATCTCAA
1 AGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCAA
* * * ** * * * * *
28681329 TTGATTAAGATCAATAAGATTATCAATTGAGGATGGTAATTCTTTCAAACCCGTTCCACCTAAAT
66 TTGCTCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
* * * *
28681394 CAAGTTCTATCAACATCTCCATGATGTCCATGATTTCTGGGAAAATCTCCAATCTTGAGCAACCT
131 CAAGATC-CTCAACATCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTTGAGCAACCT
28681459 TTAAGATCGAATCTCTCG
195 TTAAGATCGAATCTCTCG
28681477 AGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCAA
1 AGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCAA
* * ** * *
28681542 TTGCTTAAGACCAATAAGGTTTTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAG
66 TTGCTCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
*
28681607 AAAGATGCCTCAA-ACTCTCCATGGTGTCCATGA
131 CAAGAT-CCTCAACA-TCTCCATGGTGTCCATGA
28681640 TTATTGGAAA
Statistics
Matches: 726, Mismatches: 69, Indels: 14
0.90 0.09 0.02
Matches are distributed among these distances:
211 1 0.00
212 2 0.00
213 722 0.99
214 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (212 bp):
AGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTTTTTCAATCTCAA
TTGCTCAAGACCAATAAGATTGCCAAATGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAAT
CAAGATCCTCAACATCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTTGAGCAACCTT
TAAGATCGAATCTCTCG
Found at i:28686001 original size:17 final size:19
Alignment explanation
Indices: 28685969--28686003 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
28685959 GTTCATTAGG
28685969 TTAATTTAGATTTAATAAT
1 TTAATTTAGATTTAATAAT
28685988 TTAA-TTAG-TTTAATAA
1 TTAATTTAGATTTAATAA
28686004 ATCTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
TTAATTTAGATTTAATAAT
Found at i:28688065 original size:12 final size:13
Alignment explanation
Indices: 28688043--28688071 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28688033 ATTTTAAATG
28688043 ATAAAATAAATAT
1 ATAAAATAAATAT
28688056 ATAAAA-AAATAT
1 ATAAAATAAATAT
28688068 ATAA
1 ATAA
28688072 TACAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAAAATAAATAT
Found at i:28690072 original size:30 final size:30
Alignment explanation
Indices: 28690038--28690099 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
28690028 ATTCTTTGAG
28690038 TAAACTTATGACCTGATGATTAAGGATATT
1 TAAACTTATGACCTGATGATTAAGGATATT
*
28690068 TAAACTTATGATCTGATGATTAAGGATATT
1 TAAACTTATGACCTGATGATTAAGGATATT
28690098 TA
1 TA
28690100 CCACTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (30 bp):
TAAACTTATGACCTGATGATTAAGGATATT
Found at i:28691093 original size:18 final size:18
Alignment explanation
Indices: 28691070--28691108 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28691060 AGGTTAGGGC
28691070 TTAGTGATTTAGGGTTTT
1 TTAGTGATTTAGGGTTTT
* *
28691088 TTAGTGTTTTAGTGTTTT
1 TTAGTGATTTAGGGTTTT
28691106 TTA
1 TTA
28691109 AGGAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (18 bp):
TTAGTGATTTAGGGTTTT
Found at i:28691286 original size:17 final size:16
Alignment explanation
Indices: 28691251--28691286 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28691241 CCTAAAACAA
*
28691251 TAAAAAACCCTAACTC
1 TAAAAAACCCTAACCC
28691267 TAAAAAACCCTAAACCC
1 TAAAAAACCCT-AACCC
28691284 TAA
1 TAA
28691287 TTTAATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.17
Consensus pattern (16 bp):
TAAAAAACCCTAACCC
Found at i:28691377 original size:8 final size:8
Alignment explanation
Indices: 28691364--28691405 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
28691354 TTTTCCTTAA
28691364 AAAACACT
1 AAAACACT
28691372 AAAACACT
1 AAAACACT
*
28691380 AAATC-CT
1 AAAACACT
*
28691387 AAAACCCT
1 AAAACACT
*
28691395 AAATCACT
1 AAAACACT
28691403 AAA
1 AAA
28691406 CCCTAACCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAACACT
Found at i:28691390 original size:23 final size:23
Alignment explanation
Indices: 28691364--28691411 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
28691354 TTTTCCTTAA
*
28691364 AAAACACTAAAACACTAAATCCT
1 AAAACACTAAAACACTAAACCCT
* *
28691387 AAAACCCTAAATCACTAAACCCT
1 AAAACACTAAAACACTAAACCCT
28691410 AA
1 AA
28691412 CCTTAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (23 bp):
AAAACACTAAAACACTAAACCCT
Found at i:28691406 original size:15 final size:16
Alignment explanation
Indices: 28691368--28691411 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
28691358 CCTTAAAAAA
*
28691368 CACTAAAACACTAAAT
1 CACTAAAACCCTAAAT
28691384 C-CTAAAACCCTAAAT
1 CACTAAAACCCTAAAT
28691399 CACT-AAACCCTAA
1 CACTAAAACCCTAA
28691412 CCTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (16 bp):
CACTAAAACCCTAAAT
Found at i:28693056 original size:8 final size:8
Alignment explanation
Indices: 28693028--28693087 Score: 59
Period size: 9 Copynumber: 7.1 Consensus size: 8
28693018 TAAATGATTT
28693028 TTTTATTAA
1 TTTT-TTAA
28693037 -TTTTTAA
1 TTTTTTAA
28693044 TTTTTTTAA
1 -TTTTTTAA
*
28693053 TTTTTTAT
1 TTTTTTAA
28693061 TTTGTTTAA
1 TTT-TTTAA
*
28693070 TATTTTAA
1 TTTTTTAA
28693078 TATTTTTAA
1 T-TTTTTAA
28693087 T
1 T
28693088 AATATTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 4 0.09
8 19 0.44
9 20 0.47
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTTTAA
Found at i:28693083 original size:20 final size:19
Alignment explanation
Indices: 28693024--28693103 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 19
28693014 CTTTTAAATG
* *
28693024 ATTTTTTTATTAATTTTTA-
1 ATTTTTTTAAT-ATTTTAAT
28693043 ATTTTTTTAAT-TTTT--T
1 ATTTTTTTAATATTTTAAT
28693059 ATTTTGTTTAATATTTTAAT
1 ATTTT-TTTAATATTTTAAT
*
28693079 ATTTTTAATAATATTTTATAT
1 ATTTTT-TTAATATTTTA-AT
28693100 ATTT
1 ATTT
28693104 ATAAATTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.10
17 10 0.19
18 4 0.08
19 11 0.21
20 16 0.31
21 6 0.12
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (19 bp):
ATTTTTTTAATATTTTAAT
Found at i:28693088 original size:9 final size:9
Alignment explanation
Indices: 28693036--28693112 Score: 63
Period size: 9 Copynumber: 8.6 Consensus size: 9
28693026 TTTTTTATTA
28693036 ATTTTTAAT
1 ATTTTTAAT
*
28693045 TTTTTTAAT
1 ATTTTTAAT
28693054 -TTTTT-AT
1 ATTTTTAAT
*
28693061 TTTGTTTAAT
1 ATT-TTTAAT
28693071 A-TTTTAAT
1 ATTTTTAAT
28693079 ATTTTTAAT
1 ATTTTTAAT
28693088 AATATTTTATAT
1 -AT-TTTTA-AT
*
28693100 ATTTATAA-
1 ATTTTTAAT
28693108 ATTTT
1 ATTTT
28693113 AAAAAAGTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
7 2 0.04
8 18 0.32
9 20 0.35
10 8 0.14
11 7 0.12
12 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:28693088 original size:17 final size:16
Alignment explanation
Indices: 28693027--28693087 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 16
28693017 TTAAATGATT
28693027 TTTTTATTAATTTTTAA
1 TTTTT-TTAATTTTTAA
*
28693044 TTTTTTTAATTTTTTA
1 TTTTTTTAATTTTTAA
28693060 TTTTGTTTAATATTTTAA
1 TTTT-TTTAAT-TTTTAA
*
28693078 TATTTTTAAT
1 TTTTTTTAAT
28693088 AATATTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
16 14 0.36
17 17 0.44
18 8 0.21
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTTTAATTTTTAA
Found at i:28695088 original size:213 final size:213
Alignment explanation
Indices: 28694720--28695254 Score: 948
Period size: 213 Copynumber: 2.5 Consensus size: 213
28694710 CTAAGACACA
28694720 AAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTCGTTCAAGCTC
1 AAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTCGTTCAAGCTC
* *
28694785 AAATACTCAAGACCAATAAGATTATCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCTGCTTAA
66 AAATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAA
*
28694850 ATCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCTAATCTCGAGCAAC
131 ATCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
28694915 CTTTAAGATT-GAATGTGCT
196 CTTTAAG-TTCGAATGT-CT
* *
28694934 -AAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAATTGTTCAAGCTC
1 AAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTCGTTCAAGCTC
*
28694998 AAATACACAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAA
66 AAATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAA
28695063 ATCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
131 ATCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
28695128 CTTTAAGTTCGAATGTCT
196 CTTTAAGTTCGAATGTCT
* * *
28695146 AAAGAGATTTCGATTTATAAAAGCTGTCAGGAAGGCAAACAAGGATTTCACAGTCGTGCAAGCTC
1 AAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTCGTTCAAGCTC
*
28695211 AAATACTCAAGACCAATAAGATTGTCAATTGAGAATGGTAATTC
66 AAATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTC
28695255 AAGTTTATAT
Statistics
Matches: 306, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
212 4 0.01
213 302 0.99
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (213 bp):
AAAGAGATTTCAATTTATAAAAGCTGTCAGGAAGGCAAACAAGGTTTTCACAGTCGTTCAAGCTC
AAATACTCAAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAA
ATCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAAC
CTTTAAGTTCGAATGTCT
Found at i:28695386 original size:189 final size:189
Alignment explanation
Indices: 28695064--28695443 Score: 555
Period size: 189 Copynumber: 2.0 Consensus size: 189
28695054 TCCGCTTAAA
*
28695064 TCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCGAGCAACC
1 TCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCAAGCAACC
* * * * *
28695129 TTTAAGTTCGAATGTCTAAAGAGATTTCGATTTATAAAAGCTGTCAGGAAGGCAAACAAGGATTT
66 TTGAAGATAGAATGTCTAAAGAGATTTCAATTTATAAAAGCTATCAGGAAGGCAAACAAGGATTT
* * *
28695194 CACAGTCGTGCAAGCTCAAATACTCAAGACCAATAAGATTGTCAATTGAGAATGGTAAT
131 CACAGTAGTGCAAGCTCAAACAATCAAGACCAATAAGATTGTCAATTGAGAATGGTAAT
* * *
28695253 TCAAGTTTATATAGTTCCTCCATGGTGTCCATGACTTTTGGGAAAATCTCCAATCTCAAGCAA-C
1 TCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCAAGCAACC
* * * *
28695317 TATGAAGATAGAATGTCTCAAGAGATTTCAATTTATAAAAGCTATCAGGAAGGCCAATAAGGTTT
66 T-TGAAGATAGAATGTCTAAAGAGATTTCAATTTATAAAAGCTATCAGGAAGGCAAACAAGGATT
* * * * *
28695382 TCACAGTAGTTCAAGCTCAAGCAATCAAGACTAATAAGATTTTCAATTGAGGATGGTAAT
130 TCACAGTAGTGCAAGCTCAAACAATCAAGACCAATAAGATTGTCAATTGAGAATGGTAAT
28695442 TC
1 TC
28695444 CTTCAAAGCC
Statistics
Matches: 169, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
188 2 0.01
189 167 0.99
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (189 bp):
TCAAGTTCATACAGTTCCTCCATGGTGTCCATGACTTCTGGGAAAATCTCCAATCTCAAGCAACC
TTGAAGATAGAATGTCTAAAGAGATTTCAATTTATAAAAGCTATCAGGAAGGCAAACAAGGATTT
CACAGTAGTGCAAGCTCAAACAATCAAGACCAATAAGATTGTCAATTGAGAATGGTAAT
Found at i:28699200 original size:26 final size:26
Alignment explanation
Indices: 28699164--28699216 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28699154 CACGAGTATC
28699164 CTTGCCTCTGAAGCTAAGGAAAACAT
1 CTTGCCTCTGAAGCTAAGGAAAACAT
28699190 CTTGCCTCTGAAGCTAAGGAAAACAT
1 CTTGCCTCTGAAGCTAAGGAAAACAT
28699216 C
1 C
28699217 GTATGTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (26 bp):
CTTGCCTCTGAAGCTAAGGAAAACAT
Found at i:28700448 original size:33 final size:33
Alignment explanation
Indices: 28700410--28700477 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
28700400 TTGTCATAAG
28700410 AAAGCTTAAATAAGCTAAAAATAATAATAAAAT
1 AAAGCTTAAATAAGCTAAAAATAATAATAAAAT
28700443 AAAGCTTAAATAAGCTAAAAATAATAATAAAAT
1 AAAGCTTAAATAAGCTAAAAATAATAATAAAAT
28700476 AA
1 AA
28700478 TTATAATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (33 bp):
AAAGCTTAAATAAGCTAAAAATAATAATAAAAT
Found at i:28703494 original size:29 final size:28
Alignment explanation
Indices: 28703447--28703513 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
28703437 TATATATATT
**
28703447 TTTA-TTTAAATTATTTTTTGTACAATA
1 TTTATTTTAAATTATTTTTTACACAATA
* *
28703474 TTTATTTTAAATT-TCTCTTTTACCCATTA
1 TTTATTTTAAATTAT-T-TTTTACACAATA
28703503 TTTATTTTAAA
1 TTTATTTTAAA
28703514 CTCTTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.15
28 9 0.27
29 19 0.58
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTATTTTAAATTATTTTTTACACAATA
Found at i:28703632 original size:27 final size:28
Alignment explanation
Indices: 28703578--28703641 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
28703568 GATTTATTTA
*
28703578 ACATATT-GTTTATTTGAAATTTGCTTT
1 ACATATTATTTTATTTGAAATTTGCTTT
* * *
28703605 ATATATTATTTTATTTTAAA-TTGTTTT
1 ACATATTATTTTATTTGAAATTTGCTTT
*
28703632 ACATTTTATT
1 ACATATTATT
28703642 CATGTTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 20 0.67
28 10 0.33
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.61
Consensus pattern (28 bp):
ACATATTATTTTATTTGAAATTTGCTTT
Found at i:28704411 original size:17 final size:17
Alignment explanation
Indices: 28704389--28704424 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28704379 TAATAAACTA
28704389 AAACGTTTTATTAAAGC
1 AAACGTTTTATTAAAGC
28704406 AAACGTTTTATTAAAGC
1 AAACGTTTTATTAAAGC
28704423 AA
1 AA
28704425 GGGTGATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
AAACGTTTTATTAAAGC
Found at i:28707715 original size:28 final size:28
Alignment explanation
Indices: 28707684--28707755 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
28707674 TAGATATTTT
*
28707684 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
28707712 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
28707740 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
28707756 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:28710767 original size:3 final size:3
Alignment explanation
Indices: 28710761--28710791 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28710751 GCACTACTAT
28710761 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28710792 AGTATAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28712305 original size:16 final size:16
Alignment explanation
Indices: 28712284--28712317 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28712274 TGTAATTGAG
28712284 TTAAGTTT-GTTGGGTT
1 TTAAGTTTAG-TGGGTT
28712300 TTAAGTTTAGTGGGTT
1 TTAAGTTTAGTGGGTT
28712316 TT
1 TT
28712318 TGAGTAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (16 bp):
TTAAGTTTAGTGGGTT
Found at i:28714089 original size:20 final size:21
Alignment explanation
Indices: 28714050--28714089 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
28714040 CATTTCAAGA
* *
28714050 CTTTCAATCTCTTTGAAAATG
1 CTTTCAATCACTTAGAAAATG
28714071 CTTTCAA-CACTTAGAAAAT
1 CTTTCAATCACTTAGAAAAT
28714090 TTTGACAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
CTTTCAATCACTTAGAAAATG
Found at i:28714270 original size:19 final size:19
Alignment explanation
Indices: 28714246--28714343 Score: 53
Period size: 19 Copynumber: 5.1 Consensus size: 19
28714236 TTTCGATATC
28714246 ATTTTTAATAATATTTTAA
1 ATTTTTAATAATATTTTAA
*
28714265 ATTTTT-TTGAACT-TTTTAA
1 ATTTTTAAT-AA-TATTTTAA
*
28714284 A-TTTTATTTAATACTTTTATA
1 ATTTTTA-ATAATA-TTTTA-A
**
28714305 AAATTTAATAATATTTTATA
1 ATTTTTAATAATATTTTA-A
*
28714325 TATTTATAA-AAT-TTTTAA
1 -ATTTTTAATAATATTTTAA
28714343 A
1 A
28714344 ATTTAAAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
17 1 0.02
18 7 0.11
19 22 0.34
20 18 0.28
21 12 0.19
22 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (19 bp):
ATTTTTAATAATATTTTAA
Found at i:28714333 original size:18 final size:20
Alignment explanation
Indices: 28714292--28714349 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 20
28714282 AAATTTTATT
28714292 TAATACTTTTATAAAATTTAA
1 TAATA-TTTTATAAAATTTAA
*
28714313 TAATATTTTAT-ATATTT-A
1 TAATATTTTATAAAATTTAA
*
28714331 TAAAATTTT-TAAAATTTAA
1 TAATATTTTATAAAATTTAA
28714350 AGTTTATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.44
19 6 0.19
20 6 0.19
21 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATATTTTATAAAATTTAA
Found at i:28714469 original size:17 final size:17
Alignment explanation
Indices: 28714447--28714482 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28714437 TAAGTATTCC
* *
28714447 TTTTAATTTTTTTATTT
1 TTTTAAATTTTATATTT
28714464 TTTTAAATTTTATATTT
1 TTTTAAATTTTATATTT
28714481 TT
1 TT
28714483 ATAACGTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTAAATTTTATATTT
Found at i:28720752 original size:31 final size:31
Alignment explanation
Indices: 28720714--28720783 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
28720704 TTTGGGTCAA
* ** *
28720714 AACTAAAATTTAAAAATTTTAAAAATATAGG
1 AACTAAAATTGAAAAATTAAAAAAATATAAG
**
28720745 AACTAAAATTGACCAATTAAAAAAATATAAG
1 AACTAAAATTGAAAAATTAAAAAAATATAAG
28720776 AACTAAAA
1 AACTAAAA
28720784 ATAATTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.26
Consensus pattern (31 bp):
AACTAAAATTGAAAAATTAAAAAAATATAAG
Found at i:28721434 original size:14 final size:14
Alignment explanation
Indices: 28721412--28721444 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28721402 TACATTTTAC
*
28721412 TATTATGTTGTTAT
1 TATTTTGTTGTTAT
28721426 TATTTTGTTGTTAT
1 TATTTTGTTGTTAT
28721440 TATTT
1 TATTT
28721445 AGATATTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (14 bp):
TATTTTGTTGTTAT
Found at i:28725284 original size:15 final size:15
Alignment explanation
Indices: 28725248--28725286 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
28725238 AACCTATGAT
*
28725248 AAATATATATTAACA
1 AAATATTTATTAACA
28725263 AAATATTTATTAACA
1 AAATATTTATTAACA
*
28725278 ACATATTTA
1 AAATATTTA
28725287 GGGTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATTTATTAACA
Found at i:28735985 original size:21 final size:20
Alignment explanation
Indices: 28735954--28735995 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
28735944 TATTATACCT
28735954 TTATCATTATTATCATTTTA
1 TTATCATTATTATCATTTTA
*
28735974 TTATCTATTATTATTATTTTA
1 TTATC-ATTATTATCATTTTA
28735995 T
1 T
28735996 CATTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATCATTATTATCATTTTA
Found at i:28736013 original size:18 final size:18
Alignment explanation
Indices: 28735961--28736002 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28735951 CCTTTATCAT
*
28735961 TATTATCATT-TTATTATC
1 TATTATTATTATT-TTATC
28735979 TATTATTATTATTTTATC
1 TATTATTATTATTTTATC
28735997 -ATTATT
1 TATTATT
28736003 TATTCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
19 2 0.09
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTATTATTATTTTATC
Found at i:28737326 original size:20 final size:20
Alignment explanation
Indices: 28737282--28737327 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
28737272 GCCAAGTATA
28737282 TATTTTTTTATTAATGAATT
1 TATTTTTTTATTAATGAATT
*
28737302 AATTTATTTTA-TAAT-AATTT
1 TATTT-TTTTATTAATGAA-TT
28737322 TATTTT
1 TATTTT
28737328 AATATCTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTTTTTTATTAATGAATT
Found at i:28739502 original size:50 final size:50
Alignment explanation
Indices: 28739427--28739603 Score: 275
Period size: 50 Copynumber: 3.5 Consensus size: 50
28739417 CCATGGCAAT
28739427 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
28739477 AAGTGATAAGT-AGTAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGA-TAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
28739527 AAGTGATAAGTGATAGCTTCTGCTACACCTATCTGATCAGGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
28739577 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
28739604 CTGATCAGTG
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.01
50 91 0.78
51 24 0.21
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:28739617 original size:31 final size:31
Alignment explanation
Indices: 28739579--28739728 Score: 221
Period size: 31 Copynumber: 4.8 Consensus size: 31
28739569 ACAAATGACA
28739579 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
28739610 AGTGAAAAGTGGTAGC-TCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
* * *
28739641 AGTGAAAAATTGGTAGCTCCGGCCACCTGATC
1 AGTG-AAAAGTGGTAGCTTCGGCTACCTGATC
* *
28739673 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28739704 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
28739729 AAGTGACAAG
Statistics
Matches: 108, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
30 2 0.02
31 79 0.73
32 26 0.24
33 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:28739677 original size:63 final size:63
Alignment explanation
Indices: 28739579--28739725 Score: 217
Period size: 63 Copynumber: 2.4 Consensus size: 63
28739569 ACAAATGACA
* * * *
28739579 AGTG-AAAAGTGGTAGCTTCGGCTACCTGATCAGTGAAAAGTGGTAGCTCTGGCTACCTGATC
1 AGTGAAAAAGTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
*
28739641 AGTGAAAAATTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAAGTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
* *
28739704 AGTG-AATAGTGGTAGCTTCGGC
1 AGTGAAAAAGTGGTAGCTCCGGC
28739726 TACAAGTGAC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
62 19 0.25
63 57 0.75
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (63 bp):
AGTGAAAAAGTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
Found at i:28739863 original size:46 final size:46
Alignment explanation
Indices: 28739750--28739910 Score: 147
Period size: 46 Copynumber: 3.6 Consensus size: 46
28739740 GATTTCCGTA
* * * * * * *
28739750 TAAGACCATATCTGAGATATGGCATCGGTGTGATATATGCTACTGTA
1 TAAGACCATAGCTGGGATATGGCATCAGTGAGATATATGATTC-GTG
* *
28739797 TAATACCATA-TTGGGATATGGCATCAGTGAGATATATGATTCGTG
1 TAAGACCATAGCTGGGATATGGCATCAGTGAGATATATGATTCGTG
*
28739842 TAAGACCATAGCTGGGCTATGGCATC----A-ATATATGAATAT-GTG
1 TAAGACCATAGCTGGGATATGGCATCAGTGAGATATATG-AT-TCGTG
*
28739884 TAAGACCATAGCTGGGCTATGGCATCA
1 TAAGACCATAGCTGGGATATGGCATCA
28739911 TTATGTGAAG
Statistics
Matches: 99, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
41 7 0.07
42 32 0.32
43 1 0.01
45 11 0.11
46 39 0.39
47 9 0.09
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (46 bp):
TAAGACCATAGCTGGGATATGGCATCAGTGAGATATATGATTCGTG
Found at i:28739890 original size:42 final size:42
Alignment explanation
Indices: 28739839--28739951 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
28739829 TATATGATTC
*
28739839 GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAAGAT
* *
28739881 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAAGAT
* **
28739923 GTGTAAGACCATAGTTGAACTATGGCATC
1 GTGTAAGACCATAGCTGGGCTATGGCATC
28739952 GAGAAAACGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAAGAT
Found at i:28744342 original size:50 final size:50
Alignment explanation
Indices: 28744267--28744443 Score: 275
Period size: 50 Copynumber: 3.5 Consensus size: 50
28744257 CCATGGCAAT
28744267 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
28744317 AAGTGATAAGT-AGTAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGA-TAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
28744367 AAGTGATAAGTGATAGCTTCTGCTACACCTATCTGATCAGGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
28744417 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
28744444 CTGATCAGTG
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.01
50 91 0.78
51 24 0.21
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:28744509 original size:32 final size:31
Alignment explanation
Indices: 28744419--28744537 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
28744409 ACAAATGACA
*
28744419 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
28744450 AGTGAAAAGTGGTAGCTCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
28744481 AGTGAAAAATTGGTAGCTCCGGCCACCTGATC
1 AGTG-AAAAGTGGTAGCTCCGGCTACCTGATC
*
28744513 AGTGAAAAATGGTAGCTCCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
28744538 AAGTGACAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 52 0.65
32 28 0.35
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:28744517 original size:63 final size:62
Alignment explanation
Indices: 28744419--28744537 Score: 184
Period size: 63 Copynumber: 1.9 Consensus size: 62
28744409 ACAAATGACA
* * * *
28744419 AGTGAAAAGTGGTAGCTTCGGCTACCTGATCAGTGAAAAGTGGTAGCTCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
*
28744481 AGTGAAAAATTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTAC
1 AGTG-AAAAGTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTAC
28744538 AAGTGACAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 4 0.08
63 47 0.92
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (62 bp):
AGTGAAAAGTGGTAGCTCCGGCCACCTGATCAGTGAAAAATGGTAGCTCCGGCTACCTGATC
Found at i:28744625 original size:47 final size:46
Alignment explanation
Indices: 28744555--28744720 Score: 162
Period size: 47 Copynumber: 3.7 Consensus size: 46
28744545 AAGTGATTTC
* * * *
28744555 CGTATAAGACCATATCTGAGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* *
28744601 CTGTATAAGACCATATTTGGGATATGGCATCAGTGAGATATATGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * *
28744648 CGTGTAAGACCATAGCTGGGCTATGGCATC----A-ATATATGAATA
1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATG-ATA
* * * *
28744690 TGTGTAAGACCATAGCTGGGCTATGGCATCA
1 CGTATAAGACCATATCTGGGATATGGCATCA
28744721 TTATGTGAAG
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
41 7 0.07
42 32 0.30
46 26 0.25
47 40 0.38
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:28744707 original size:42 final size:42
Alignment explanation
Indices: 28744649--28744761 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
28744639 TATATGATTC
*
28744649 GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAAGAT
* *
28744691 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAAGAT
* **
28744733 GTGTAAGACCATAGTTGAACTATGGCATC
1 GTGTAAGACCATAGCTGGGCTATGGCATC
28744762 GAGAAAACGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCAATATATGAAGAT
Found at i:28753456 original size:12 final size:12
Alignment explanation
Indices: 28753439--28753465 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28753429 AGACTTACAA
28753439 ATAAAAAAAATT
1 ATAAAAAAAATT
28753451 ATAAAAAAAATT
1 ATAAAAAAAATT
28753463 ATA
1 ATA
28753466 TAATATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAAAAAAATT
Found at i:28753474 original size:19 final size:18
Alignment explanation
Indices: 28753450--28753486 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28753440 TAAAAAAAAT
28753450 TATAAAAAAAATTATATAA
1 TATAAAAAAAA-TATATAA
*
28753469 TATAAAATAAATATATAA
1 TATAAAAAAAATATATAA
28753487 AAAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAAAAAAAATATATAA
Found at i:28753475 original size:16 final size:16
Alignment explanation
Indices: 28753456--28753505 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
28753446 AAATTATAAA
28753456 AAAAATTATATAATAT
1 AAAAATTATATAATAT
*
28753472 -AAAA-TAAAT-ATAT
1 AAAAATTATATAATAT
28753485 AAAAAATTATATAATAT
1 -AAAAATTATATAATAT
28753502 AAAA
1 AAAA
28753506 TAATTCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 8 0.29
16 8 0.29
17 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTATATAATAT
Found at i:28753491 original size:30 final size:31
Alignment explanation
Indices: 28753439--28753508 Score: 115
Period size: 30 Copynumber: 2.3 Consensus size: 31
28753429 AGACTTACAA
*
28753439 ATAAAAAAAATTATAAAAAAAATTATATAAT
1 ATAAAATAAATTATAAAAAAAATTATATAAT
*
28753470 ATAAAATAAA-TATATAAAAAATTATATAAT
1 ATAAAATAAATTATAAAAAAAATTATATAAT
28753500 ATAAAATAA
1 ATAAAATAA
28753509 TTCACAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
30 28 0.76
31 9 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (31 bp):
ATAAAATAAATTATAAAAAAAATTATATAAT
Found at i:28758810 original size:213 final size:214
Alignment explanation
Indices: 28758450--28759035 Score: 921
Period size: 213 Copynumber: 2.8 Consensus size: 214
28758440 TCAAGCTTCG
* **
28758450 AAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCTGTTCCGCTTAAATCAAGCT
1 AAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAA
* * *
28758515 CCCTCAACATCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTTGAGCAACCTTTAAGA
66 ACCTCAACCTCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTTGAGCAACCTTCAAGA
* * *
28758580 TCAAATCT-CTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTCACAGT
131 TTAAATATCCTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAAGCAAACAAGGTTTTCACAGT
28758644 TGTTCAATCTCAGATAATC
196 TGTTCAATCTCAGATAATC
28758663 AAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAA
1 AAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAA
28758728 ACCTCAACCTCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTTGAGCAACCTTCAAGA
66 ACCTCAACCTCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTTGAGCAACCTTCAAGA
28758793 TTAAATATCCT-AAGAGATTTCAATTTATAAAGGTTGTCAGGAAAGCAAACAAGGTTTTCACAGT
131 TTAAATATCCTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAAGCAAACAAGGTTTTCACAGT
28758857 TGTTCAATCTCAGATAATC
196 TGTTCAATCTCAGATAATC
28758876 AAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAA
1 AAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAA
* * * *
28758941 AGCTCAACCTCTCTATGG-C-C------TTC-GGAAAAATCTCCAATCTCGAGC-ACCTGCTAAG
66 ACCTCAACCTCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTTGAGCAACCTTC-AAG
* *
28758996 ATTAAA-A-CGCTCAAGAGATTTCAATTTAAAAAGATTGTCA
130 ATTAAATATC-CTCAAGAGATTTCAATTTATAAAGGTTGTCA
28759036 ATTGAGGATG
Statistics
Matches: 354, Mismatches: 15, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
202 1 0.00
203 8 0.02
204 56 0.16
205 3 0.01
211 1 0.00
212 1 0.00
213 282 0.80
214 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (214 bp):
AAGACCAATAAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAA
ACCTCAACCTCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTTGAGCAACCTTCAAGA
TTAAATATCCTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAAGCAAACAAGGTTTTCACAGT
TGTTCAATCTCAGATAATC
Found at i:28759393 original size:213 final size:213
Alignment explanation
Indices: 28759026--28760823 Score: 3100
Period size: 213 Copynumber: 8.4 Consensus size: 213
28759016 TCAATTTAAA
*
28759026 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAAGCTCAACC
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
28759091 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCTC
66 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCTC
* *
28759156 CCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGGAAACAAGGTTTTTACAGTTGTTCAATCT
131 TCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATCT
*
28759221 CAGATCATCAAGACCAAT
196 CAGATAATCAAGACCAAT
28759239 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
28759304 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACC-TTCAAGATCAAATCT
66 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTT-AAGATCAAATCT
*
28759368 CTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGGAAACAAGGTTTTTACAGTTGTTCAATC
130 CTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATC
28759433 TCAGATAATCAAGACCAAT
195 TCAGATAATCAAGACCAAT
*
28759452 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAAGCTCAACC
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
28759517 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCTC
66 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCTC
* *
28759582 CCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGGAAACAAGGTTTTTACAGTTGTTCAATCT
131 TCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATCT
*
28759647 CAGATCATCAAGACCAAT
196 CAGATAATCAAGACCAAT
28759665 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
* * *
28759730 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACC-TTCAAGATTAAAACA
66 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTT-AAGATCAAATCT
* * *
28759794 CGCAAGAGATTTCAATTTATAAAGGTTGTCAGCAAGGCAAACAAGGTTTTTACAGTTGGTCAATC
130 CTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATC
*
28759859 CCAGATAATCAAGACCAAT
195 TCAGATAATCAAGACCAAT
* *
28759878 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCTCTTAAATCAAGAACCCTCAACC
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
* *
28759943 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACC-TTCAAGATCAAAACG
66 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTT-AAGATCAAATCT
*
28760007 CTCAAGAGATTTCAATTTATAAAGGTTGTCAAGAAGGCAAACAAGGTTTTTACAGTTGTTCAATC
130 CTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATC
*
28760072 CCAGATAATCAAGACCAAT
195 TCAGATAATCAAGACCAAT
28760091 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
* * *
28760156 TCTCCATGGTCTCTAAGATTTCTGAAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAAACGC
66 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCTC
28760221 TCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATCT
131 TCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATCT
* *
28760286 CAGATCATCAAGACCAAC
196 CAGATAATCAAGACCAAT
* *
28760304 AAGATTGTCAATTGGGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAAGCTCAACC
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
*
28760369 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAACCTCGAGCAACCGTTAAGATCAAATCTC
66 TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCTC
*
28760434 TCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGGAAACAAGGTTTTTACAGTTGTTCAATCT
131 TCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATCT
*
28760499 CAGATCATCAAGACCAAT
196 CAGATAATCAAGACCAAT
* * *
28760517 AAGATTGTCAATT-AGGGATGGTAATTCCTTCAAAGCCGTTTCGCTTAAATAAAGAAACCCCAAC
1 AAGATTGTCAATTGA-GGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAAC
* *
28760581 CTCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTGAAGATCAAATCC
65 CTCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCT
* * * * *
28760646 CTTAAGAGATTTCAATTTATAAAGGCTGTCAGGAAGGCAAACAAGGTTTTCACAGCTGTTCAATA
130 CTCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATC
28760711 TCAGATAATCAAGACCAAT
195 TCAGATAATCAAGACCAAT
* * *** *
28760730 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCTGTTTCGCTTAAATCAAGCTCCCTCAACA
1 AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
28760795 TCTCCATGGTCTCTAAGATTTCTGGAAAA
66 TCTCCATGGTCTCTAAGATTTCTGGAAAA
28760824 CTACACAGAT
Statistics
Matches: 1518, Mismatches: 61, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
212 4 0.00
213 1509 0.99
214 5 0.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (213 bp):
AAGATTGTCAATTGAGGATGGTAATTCCTTCAAAGCCGTTCCGCTTAAATCAAGAAACCTCAACC
TCTCCATGGTCTCTAAGATTTCTGGAAAAATCTCCAATCTCGAGCAACCGTTAAGATCAAATCTC
TCAAGAGATTTCAATTTATAAAGGTTGTCAGGAAGGCAAACAAGGTTTTTACAGTTGTTCAATCT
CAGATAATCAAGACCAAT
Found at i:28763941 original size:15 final size:16
Alignment explanation
Indices: 28763921--28763955 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28763911 CCTCCACTTC
*
28763921 ATAAATG-CAATCTGG
1 ATAAATGTCAAACTGG
28763936 ATAAATGTCAAACTGG
1 ATAAATGTCAAACTGG
28763952 ATAA
1 ATAA
28763956 GCACTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (16 bp):
ATAAATGTCAAACTGG
Found at i:28765921 original size:12 final size:12
Alignment explanation
Indices: 28765904--28765928 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28765894 TAAATATTAA
28765904 TTAATATTTATT
1 TTAATATTTATT
28765916 TTAATATTTATT
1 TTAATATTTATT
28765928 T
1 T
28765929 GTTGCATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAATATTTATT
Found at i:28768348 original size:12 final size:12
Alignment explanation
Indices: 28768330--28768375 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
28768320 TATAATTATC
28768330 ATATTATATTTA
1 ATATTATATTTA
*
28768342 GTATTAT-TTTA
1 ATATTATATTTA
*
28768353 ACATTATA-TTA
1 ATATTATATTTA
28768364 ACTATTATATTT
1 A-TATTATATTT
28768376 TACTATTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 13 0.48
12 12 0.44
13 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:28768358 original size:11 final size:12
Alignment explanation
Indices: 28768331--28768374 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
28768321 ATAATTATCA
* *
28768331 TATTATATTTAG
1 TATTATATTAAC
*
28768343 TATTATTTTAAC
1 TATTATATTAAC
28768355 -ATTATATTAAC
1 TATTATATTAAC
28768366 TATTATATT
1 TATTATATT
28768375 TTACTATTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (12 bp):
TATTATATTAAC
Found at i:28768452 original size:25 final size:24
Alignment explanation
Indices: 28768420--28768478 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
28768410 GTACATTATT
** *
28768420 TTATTATTTTCTTTTATTGTAAATA
1 TTATTATTTTCTAATATTCT-AATA
28768445 TTATTATTATTCTAATATTCTAATA
1 TTATTATT-TTCTAATATTCTAATA
28768470 TTA-TATTTT
1 TTATTATTTT
28768479 AATATTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.07
24 4 0.13
25 15 0.50
26 9 0.30
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (24 bp):
TTATTATTTTCTAATATTCTAATA
Found at i:28768554 original size:13 final size:13
Alignment explanation
Indices: 28768534--28768570 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
28768524 TATATGTCAT
28768534 TTTA-TTTATTTA
1 TTTATTTTATTTA
*
28768546 TTTATTTTATTTC
1 TTTATTTTATTTA
28768559 TTTATTTTATTT
1 TTTATTTTATTT
28768571 TTCGTTATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:28768554 original size:17 final size:18
Alignment explanation
Indices: 28768532--28768571 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
28768522 TATATATGTC
28768532 ATTTTATTTATTTA-TTT
1 ATTTTATTTATTTATTTT
*
28768549 ATTTTATTTCTTTATTTT
1 ATTTTATTTATTTATTTT
28768567 ATTTT
1 ATTTT
28768572 TCGTTATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (18 bp):
ATTTTATTTATTTATTTT
Found at i:28776472 original size:22 final size:22
Alignment explanation
Indices: 28776447--28776488 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28776437 TTTGGATTTT
*
28776447 GGGTTT-AGAGTTTAGGGTTCAA
1 GGGTTTGAG-GTTAAGGGTTCAA
28776469 GGGTTTGAGGTTAAGGGTTC
1 GGGTTTGAGGTTAAGGGTTC
28776489 GAGTTCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.19, C:0.05, G:0.40, T:0.36
Consensus pattern (22 bp):
GGGTTTGAGGTTAAGGGTTCAA
Found at i:28777347 original size:2 final size:2
Alignment explanation
Indices: 28777332--28777365 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
28777322 TTTTGTATTT
*
28777332 TA TA TA TT TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
28777366 TTCCAGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.97
3 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28781761 original size:46 final size:44
Alignment explanation
Indices: 28781657--28781764 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
28781647 TGTCTTTGAC
** * * *
28781657 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
28781701 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
28781747 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
28781765 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:28789135 original size:46 final size:44
Alignment explanation
Indices: 28789031--28789138 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
28789021 TGTCTTTGAC
** * * *
28789031 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
28789075 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
28789121 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
28789139 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:28791558 original size:15 final size:15
Alignment explanation
Indices: 28791538--28791566 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28791528 TAATATTAAA
28791538 TTATTTTTAATTTTT
1 TTATTTTTAATTTTT
28791553 TTATTTTTAATTTT
1 TTATTTTTAATTTT
28791567 AAGTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTATTTTTAATTTTT
Found at i:28791816 original size:24 final size:24
Alignment explanation
Indices: 28791774--28791843 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
28791764 ATTTGTTTTT
* *
28791774 TATTTT-AA-TATTTATTTTAATG
1 TATTTTAAAGTATTTAATTTAATA
* *
28791796 T-TTTTAAATGTATTTGATTTATTA
1 TATTTTAAA-GTATTTAATTTAATA
*
28791820 TATTTTAAAGTTTTTAATTTAATA
1 TATTTTAAAGTATTTAATTTAATA
28791844 AAAAAGTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
21 4 0.11
22 3 0.08
24 23 0.62
25 7 0.19
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TATTTTAAAGTATTTAATTTAATA
Found at i:28795554 original size:27 final size:27
Alignment explanation
Indices: 28795516--28795592 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
28795506 AAGTCTTATG
*
28795516 AGGATTTGTTAGCTTGTTAGTAGAAGT
1 AGGAGTTGTTAGCTTGTTAGTAGAAGT
28795543 AGGAGTTGTTAGCTTGTTAGTAGAAGT
1 AGGAGTTGTTAGCTTGTTAGTAGAAGT
28795570 AGGAGTTGTTAGCTTGTTAGTAG
1 AGGAGTTGTTAGCTTGTTAGTAG
28795593 CAATTTGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.39
Consensus pattern (27 bp):
AGGAGTTGTTAGCTTGTTAGTAGAAGT
Found at i:28803267 original size:20 final size:21
Alignment explanation
Indices: 28803242--28803283 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
28803232 CTAAGGAAAA
28803242 AAATTTTATA-CAATTTTTTT
1 AAATTTTATATCAATTTTTTT
*
28803262 AAATTTTATATCATTTTTTTT
1 AAATTTTATATCAATTTTTTT
28803283 A
1 A
28803284 TTTCAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATTTTATATCAATTTTTTT
Found at i:28803316 original size:16 final size:16
Alignment explanation
Indices: 28803297--28803328 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28803287 CAAAAGATAT
28803297 TTAAAAATAAAATTAA
1 TTAAAAATAAAATTAA
*
28803313 TTAAAAATAAAGTTAA
1 TTAAAAATAAAATTAA
28803329 AAGTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
TTAAAAATAAAATTAA
Found at i:28804352 original size:9 final size:9
Alignment explanation
Indices: 28804340--28804403 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
28804330 TTTAATTAAT
28804340 TTTTTAAAA
1 TTTTTAAAA
28804349 TTTTTAAAA
1 TTTTTAAAA
*
28804358 ---TAAAAA
1 TTTTTAAAA
*
28804364 TATTATAATAA
1 T-TTTTAA-AA
28804375 TTTTTAAAA
1 TTTTTAAAA
*
28804384 TTATTAAAA
1 TTTTTAAAA
28804393 TTATTTAAAA
1 TT-TTTAAAA
28804403 T
1 T
28804404 ATATATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
6 5 0.12
9 21 0.49
10 14 0.33
11 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:28804388 original size:21 final size:21
Alignment explanation
Indices: 28804358--28804398 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28804348 ATTTTTAAAA
*
28804358 TAAAAATATTATAATAATTTT
1 TAAAAATATTAAAATAATTTT
* *
28804379 TAAAATTATTAAAATTATTT
1 TAAAAATATTAAAATAATTT
28804399 AAAATATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAAATATTAAAATAATTTT
Found at i:28804414 original size:21 final size:21
Alignment explanation
Indices: 28804360--28804422 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 21
28804350 TTTTAAAATA
28804360 AAAATAT-TATAATAATT-TTT
1 AAAATATATATAA-AATTATTT
28804380 AAAAT-TAT-TAAAATTATTT
1 AAAATATATATAAAATTATTT
* *
28804399 AAAATATATATTAAATTAATT
1 AAAATATATATAAAATTATTT
28804420 AAA
1 AAA
28804423 TATTGACATG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 9 0.24
21 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAATATATATAAAATTATTT
Found at i:28806721 original size:55 final size:54
Alignment explanation
Indices: 28806647--28807050 Score: 218
Period size: 55 Copynumber: 7.4 Consensus size: 54
28806637 TCGTATTCTG
*
28806647 GTGCCGGCCATTGATAGGCCAGCACTAAAAAAAAATTGAAATTTTTTT-AATACTA
1 GTGCCGGCCATTGACAGGCCAGCAC-AAAAAAAAATT-AAATTTTTTTAAATACTA
* * * * *
28806702 GTGTCGGCCATTGACAGGCCAGTACCAAAAAAAATTAATTTTTTTTAAATACTG
1 GTGCCGGCCATTGACAGGCCAGCACAAAAAAAAATTAAATTTTTTTAAATACTA
* ****** ***** *** * *
28806756 GTGCCGACCATTGACAGGCCAGCAC-AATTTTTTTTAAAAAAACTCGTATTCTT
1 GTGCCGGCCATTGACAGGCCAGCACAAAAAAAAATTAAATTTTTTTAAATACTA
* ****** ***** *** * *
28806809 GTGCCGGCCATTGATAGGCCAGCAACAAATTTTTTTTTAAAAAAACTCGTATTCTG
1 GTGCCGGCCATTGACAGGCCAGC-ACAAA-AAAAAATTAAATTTTTTTAAATACTA
* * * * *
28806865 GTGCCGGCTATTGACAGGCCAACACAAAAAAAATTTGAATTTTTTTTAAATACTG
1 GTGCCGGCCATTGACAGGCCAGCACAAAAAAAAATT-AAATTTTTTTAAATACTA
* * * *
28806920 GTGCCGGCCATTGACAGGTCAGCACCAAAAAAAATTTAAATTTTTTTTAATACTG
1 GTGCCGGCCATTGACAGGCCAGCA-CAAAAAAAAATTAAATTTTTTTAAATACTA
* * * *
28806975 GTGCCGGCCATTGATAGGCTAGCACAAAAGAAAAATTGAATTTTTTTTAAATACTG
1 GTGCCGGCCATTGACAGGCCAGCACAAAA-AAAAATT-AAATTTTTTTAAATACTA
* * *
28807031 GTGCTGGCAATTGACTGGCC
1 GTGCCGGCCATTGACAGGCC
28807051 TGCCAATGAC
Statistics
Matches: 278, Mismatches: 63, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
53 41 0.15
54 48 0.17
55 101 0.36
56 88 0.32
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (54 bp):
GTGCCGGCCATTGACAGGCCAGCACAAAAAAAAATTAAATTTTTTTAAATACTA
Found at i:28806828 original size:53 final size:54
Alignment explanation
Indices: 28806753--28806891 Score: 208
Period size: 56 Copynumber: 2.6 Consensus size: 54
28806743 TTTTTAAATA
*
28806753 CTGGTGCCGACCATTGACAGGCCAGCACAA-TTTTTTTTAAAAAAACTCGTATT
1 CTGGTGCCGGCCATTGACAGGCCAGCACAATTTTTTTTTAAAAAAACTCGTATT
* *
28806806 CTTGTGCCGGCCATTGATAGGCCAGCAACAAATTTTTTTTTAAAAAAACTCGTATT
1 CTGGTGCCGGCCATTGACAGGCCAGC-AC-AATTTTTTTTTAAAAAAACTCGTATT
* *
28806862 CTGGTGCCGGCTATTGACAGGCCAACACAA
1 CTGGTGCCGGCCATTGACAGGCCAGCACAA
28806892 AAAAAATTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
53 23 0.30
54 4 0.05
55 4 0.05
56 45 0.59
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (54 bp):
CTGGTGCCGGCCATTGACAGGCCAGCACAATTTTTTTTTAAAAAAACTCGTATT
Found at i:28806932 original size:218 final size:218
Alignment explanation
Indices: 28806566--28807001 Score: 630
Period size: 219 Copynumber: 2.0 Consensus size: 218
28806556 GCACCAAAAG
*
28806566 TTTTTTTTAAAAACTCGTATTTTGGTGCCAGCCATTAATAGGCCAGCATCAAAATTTTTTAAAAA
1 TTTTTTTTAAAAACTCGTATTTTGGTGCCAGCCATTAATAGGCCAGCAACAAAATTTTTTAAAAA
* *
28806631 AAAACCTCGTATTCTGGTGCCGGCCATTGATAGGCCAGCACTAAAAAAAAATTGAAATTTTTTTA
66 AAAACCTCGTATTCTGGTGCCGGCCATTGACAGGCCAACACTAAAAAAAAATTGAAATTTTTTTA
* *
28806696 ATACTAGTGTCGGCCATTGACAGGCCAGTACCAAAAAAAA-TT-AATTTTTTTTAAATACTGGTG
131 ATACTAGTGCCGGCCATTGACAGGCCAGCACCAAAAAAAATTTAAATTTTTTTT-AATACTGGTG
28806759 CCGACCATTGACAGGCCAGCACAA
195 CCGACCATTGACAGGCCAGCACAA
* * * **
28806783 TTTTTTTTAAAAAAACTCGTATTCTT-GTGCCGGCCATTGATAGGCCAGCAACAAATTTTTTTTT
1 TTTTTTTT--AAAAACTCGTATT-TTGGTGCCAGCCATTAATAGGCCAGCAACAAAATTTTTTAA
* * *
28806847 AAAAAAA-CTCGTATTCTGGTGCCGGCTATTGACAGGCCAACAC-AAAAAAAATTTGAATTTTTT
63 AAAAAAACCTCGTATTCTGGTGCCGGCCATTGACAGGCCAACACTAAAAAAAAATTGAAATTTTT
* *
28806910 TTAAATACTGGTGCCGGCCATTGACAGGTCAGCACCAAAAAAAATTTAAATTTTTTTTAATACTG
128 TT-AATACTAGTGCCGGCCATTGACAGGCCAGCACCAAAAAAAATTTAAATTTTTTTTAATACTG
* * *
28806975 GTGCCGGCCATTGATAGGCTAGCACAA
192 GTGCCGACCATTGACAGGCCAGCACAA
28807002 AAGAAAAATT
Statistics
Matches: 195, Mismatches: 18, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
217 28 0.14
218 70 0.36
219 85 0.44
220 12 0.06
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (218 bp):
TTTTTTTTAAAAACTCGTATTTTGGTGCCAGCCATTAATAGGCCAGCAACAAAATTTTTTAAAAA
AAAACCTCGTATTCTGGTGCCGGCCATTGACAGGCCAACACTAAAAAAAAATTGAAATTTTTTTA
ATACTAGTGCCGGCCATTGACAGGCCAGCACCAAAAAAAATTTAAATTTTTTTTAATACTGGTGC
CGACCATTGACAGGCCAGCACAA
Found at i:28806952 original size:56 final size:54
Alignment explanation
Indices: 28806862--28807045 Score: 253
Period size: 55 Copynumber: 3.3 Consensus size: 54
28806852 AACTCGTATT
* *
28806862 CTGGTGCCGGCTATTGACAGGCCAACACAAAAAAAATTTGAATTTTTTTTAAATA
1 CTGGTGCCGGCCATTGACAGG-CAGCACAAAAAAAATTTGAATTTTTTTTAAATA
*
28806917 CTGGTGCCGGCCATTGACAGGTCAGCACCAAAAAAAATTTAAATTTTTTTT-AATA
1 CTGGTGCCGGCCATTGACAGG-CAGCA-CAAAAAAAATTTGAATTTTTTTTAAATA
* *
28806972 CTGGTGCCGGCCATTGATAGGCTAGCACAAAAGAAAAATTGAATTTTTTTTAAATA
1 CTGGTGCCGGCCATTGACAGGC-AGCACAAAA-AAAATTTGAATTTTTTTTAAATA
* *
28807028 CTGGTGCTGGCAATTGAC
1 CTGGTGCCGGCCATTGAC
28807046 TGGCCTGCCA
Statistics
Matches: 115, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
54 6 0.05
55 68 0.59
56 41 0.36
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (54 bp):
CTGGTGCCGGCCATTGACAGGCAGCACAAAAAAAATTTGAATTTTTTTTAAATA
Found at i:28807219 original size:21 final size:21
Alignment explanation
Indices: 28807195--28807251 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
28807185 TTTTTTTAAA
**
28807195 AAAATGAAGTTGAAATGAAAT
1 AAAATGAAAATGAAATGAAAT
*
28807216 AAAATTAAAATGAAATGAAAAT
1 AAAATGAAAATGAAATG-AAAT
28807238 GAAAA-G-AAATGAAA
1 -AAAATGAAAATGAAA
28807252 AAAAAAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 22 0.73
22 4 0.13
23 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (21 bp):
AAAATGAAAATGAAATGAAAT
Found at i:28807226 original size:16 final size:17
Alignment explanation
Indices: 28807207--28807252 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
28807197 AATGAAGTTG
*
28807207 AAATGAAAT-AAAATTA
1 AAATGAAATGAAAATGA
28807223 AAATGAAATGAAAATGA
1 AAATGAAATGAAAATGA
28807240 AAA-GAAATGAAAA
1 AAATGAAATGAAAA
28807253 AAAAAGTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (17 bp):
AAATGAAATGAAAATGA
Done.