Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 4 of 199
Found at i:1313189 original size:4 final size:4
Alignment explanation
Indices: 1313172--1313205 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1313162 TGCTTGATTC
* *
1313172 ATTT ATTC ATTT ATTT ATTT ACTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
1313206 CCATTATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:1325259 original size:27 final size:30
Alignment explanation
Indices: 1325202--1325260 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
1325192 ACACGTGTTA
1325202 TTATTAATTTTAAATATTATATTTTATTAT
1 TTATTAATTTTAAATATTATATTTTATTAT
*
1325232 TTATTATTTTTAAATA-TAT-TTTTA-TAT
1 TTATTAATTTTAAATATTATATTTTATTAT
1325259 TT
1 TT
1325261 TAAATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.18
28 5 0.18
29 3 0.11
30 15 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
TTATTAATTTTAAATATTATATTTTATTAT
Found at i:1325261 original size:20 final size:21
Alignment explanation
Indices: 1325226--1325280 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
1325216 TATTATATTT
1325226 TATTATTTATTATTTTTAAAT-A
1 TATT-TTTA-TATTTTTAAATAA
1325248 TATTTTTATA-TTTTAAATAAA
1 TATTTTTATATTTTTAAAT-AA
1325269 TAATTTTTATAT
1 T-ATTTTTATAT
1325281 GTATACGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.28
20 2 0.07
21 6 0.21
22 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTATATTTTTAAATAA
Found at i:1333515 original size:26 final size:27
Alignment explanation
Indices: 1333486--1333538 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1333476 TCATTAGTTC
* *
1333486 AATTATCGGTTCAATCAATCT-ATATT
1 AATTATCAGATCAATCAATCTAATATT
*
1333512 AATTCTCAGATCAATCAATCTAATATT
1 AATTATCAGATCAATCAATCTAATATT
1333539 TCTCTCTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (27 bp):
AATTATCAGATCAATCAATCTAATATT
Found at i:1346772 original size:9 final size:9
Alignment explanation
Indices: 1346751--1346968 Score: 80
Period size: 9 Copynumber: 24.0 Consensus size: 9
1346741 TTAAAATCAT
1346751 AAAA-TATA
1 AAAATTATA
*
1346759 CAAATTATA
1 AAAATTATA
1346768 AAAATTATTA
1 AAAATTA-TA
* **
1346778 AAAACTGCA
1 AAAATTATA
*
1346787 AAAATTATT
1 AAAATTATA
1346796 AAAA-TA-A
1 AAAATTATA
*
1346803 CAAA-TATA
1 AAAATTATA
*
1346811 TAAATTA-A
1 AAAATTATA
*
1346819 AAAATTGTA
1 AAAATTATA
*
1346828 AAAATTATG
1 AAAATTATA
1346837 AAAATTATTTA
1 AAAATTA--TA
*
1346848 AAATATCATA
1 AAA-ATTATA
1346858 AAAA-TATA
1 AAAATTATA
*
1346866 GAAAAGTGCA-A
1 -AAAA-T-TATA
*
1346877 AAAATTAAA
1 AAAATTATA
1346886 ACAAATTA-A
1 A-AAATTATA
*
1346895 AGAATTATA
1 AAAATTATA
* *
1346904 TAAATCATAAA
1 AAAAT--TATA
1346915 AAAATTATA
1 AAAATTATA
**
1346924 TGAATTATGA
1 AAAATTAT-A
1346934 AAGAA--ATA
1 AA-AATTATA
1346942 AAAATT-TA
1 AAAATTATA
1346950 AAAATTATGA
1 AAAATTAT-A
*
1346960 AAAACTATA
1 AAAATTATA
1346969 GGTATTCATT
Statistics
Matches: 155, Mismatches: 32, Indels: 45
0.67 0.14 0.19
Matches are distributed among these distances:
7 7 0.05
8 35 0.23
9 64 0.41
10 31 0.20
11 14 0.09
12 4 0.03
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:1348120 original size:37 final size:40
Alignment explanation
Indices: 1348079--1348166 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
1348069 AAGAAAATGA
1348079 ATAAAATTAT-AAAAATGAAAAAGATATAT-A-TATATAT
1 ATAAAATTATGAAAAATGAAAAAGATATATAAGTATATAT
* * * *
1348116 ATAAAATAATGGAAATATGAAAAATATATGTAAGTATATAT
1 ATAAAATTAT-GAAAAATGAAAAAGATATATAAGTATATAT
*
1348157 TTAAAATTAT
1 ATAAAATTAT
1348167 TATATAGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
37 9 0.22
39 16 0.39
40 1 0.02
41 15 0.37
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (40 bp):
ATAAAATTATGAAAAATGAAAAAGATATATAAGTATATAT
Found at i:1348269 original size:44 final size:43
Alignment explanation
Indices: 1348219--1348302 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
1348209 ATTAAAATAT
* *
1348219 GTATATATACATAGATATATATAAAAATTATGAAATATGTGTAA
1 GTATATATACATAGAGATATATAAAAA-TAGGAAATATGTGTAA
* * *
1348263 GTATATATACATATAGGTTTATAAAAATAGGAAATATGTG
1 GTATATATACATAGAGATATATAAAAATAGGAAATATGTG
1348303 CGTGTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 12 0.34
44 23 0.66
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (43 bp):
GTATATATACATAGAGATATATAAAAATAGGAAATATGTGTAA
Found at i:1348321 original size:44 final size:44
Alignment explanation
Indices: 1348238--1348321 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 44
1348228 CATAGATATA
* * *
1348238 TATAAAAATTATGAAATATGTGTAAGTATATATACATATAGGTT
1 TATAAAAATTAGGAAATATGTGCAAGTATATAAACATATAGGTT
** *
1348282 TATAAAAA-TAGGAAATATGTGCGTGTATTATAAATATATA
1 TATAAAAATTAGGAAATATGTGCAAGTA-TATAAACATATA
1348322 CATGTATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
43 15 0.45
44 18 0.55
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.37
Consensus pattern (44 bp):
TATAAAAATTAGGAAATATGTGCAAGTATATAAACATATAGGTT
Found at i:1348348 original size:2 final size:2
Alignment explanation
Indices: 1348341--1348405 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
1348331 ATATTTTATA
*
1348341 GT GT GT GT GT GT GT TT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1348383 GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT G
1348406 CAAAAATGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
GT
Found at i:1348458 original size:3 final size:3
Alignment explanation
Indices: 1348450--1348481 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1348440 TATAACGATT
*
1348450 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1348482 GNNNNNNNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1350145 original size:129 final size:129
Alignment explanation
Indices: 1349981--1350279 Score: 490
Period size: 129 Copynumber: 2.3 Consensus size: 129
1349971 ATCTGAAATT
** * * * ** *
1349981 TTCAATCTATTCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTGCTGTAACTTC
1 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTC
*
1350046 AGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAAC
66 AGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAAGGAGATAGGATTACTAAC
1350110 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTC
1 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTC
* * *
1350175 AGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGC
66 AGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAAGGAGATAGGATTACTAAC
1350239 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
1 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
1350280 AATTCTTCGG
Statistics
Matches: 158, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 158 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (129 bp):
TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTC
AGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAAGGAGATAGGATTACTAAC
Found at i:1350309 original size:46 final size:45
Alignment explanation
Indices: 1349962--1350500 Score: 240
Period size: 44 Copynumber: 12.3 Consensus size: 45
1349952 CTCCACCTTA
* **
1349962 GGAGATAAGATCTGAAATT-TTCAATCTATTCCACTGTAATCTCAG
1 GGAGATAAGATCTGAAATTCTT-GATCTGCTCCACTGTAATCTCAG
* * * * **
1350007 GGAAATAAGACCTG--ATGC--GATCTACTCTGCTGTAA-CTTCAG
1 GGAGATAAGATCTGAAATTCTTGATCTGCTCCACTGTAATC-TCAG
* ** * **
1350048 AGAGATAAGATCCT-TCATT-TTAATCCACTCCACTGTAATCTCAG
1 GGAGATAAGAT-CTGAAATTCTTGATCTGCTCCACTGTAATCTCAG
* * * *
1350092 GGAGATAGGATTACT-AACTTC--AATCTGCTCCGCTGTAATCTCAG
1 GGAGATAAGA-T-CTGAAATTCTTGATCTGCTCCACTGTAATCTCAG
* * *
1350136 GGAGATAAGATCTGACA--C--GATCTACTCTACTGTAA-CTTCAG
1 GGAGATAAGATCTGAAATTCTTGATCTGCTCCACTGTAATC-TCAG
* ** * * *
1350177 AGAGATAAGATCCT-TTATT-TTAATCCGCTCCACTGTAATCTCAA
1 GGAGATAAGAT-CTGAAATTCTTGATCTGCTCCACTGTAATCTCAG
* * * * *
1350221 GGAGATAGGAT-T--ACTAGCTTCAATCTGCTCCGCTGTAATCTCAG
1 GGAGATAAGATCTGAAAT-TCTT-GATCTGCTCCACTGTAATCTCAG
* * *
1350265 GGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGCAATCTCAG
1 GGAGATAAGATCTGAAATTCTT-GATCTGCTCCACTGTAATCTCAG
* * * * *
1350311 GGAAATAAGACCTG--A-T-GTGATCTACTCTACTGTAA-CTTCAG
1 GGAGATAAGATCTGAAATTCTTGATCTGCTCCACTGTAATC-TCAG
* ** * *
1350352 AGAGATAAGATCAT-TTATT-TTAATCCGCTCCACTGTAATCTCAG
1 GGAGATAAGATC-TGAAATTCTTGATCTGCTCCACTGTAATCTCAG
* * * *
1350396 GGAGATAAGAT-T--ACTAGCTTAAATCTGCTCCGCTGTAATCTCAG
1 GGAGATAAGATCTGAAAT-TCTT-GATCTGCTCCACTGTAATCTCAG
* *
1350440 GGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAG
1 GGAGATAAGATCTGAAATTCTT-GATCTGCTCCACTGTAATCTCAG
* *
1350486 GGAAATAAGACCTGA
1 GGAGATAAGATCTGA
1350501 TGCGATCTAC
Statistics
Matches: 372, Mismatches: 86, Indels: 71
0.70 0.16 0.13
Matches are distributed among these distances:
40 3 0.01
41 81 0.22
42 10 0.03
43 12 0.03
44 171 0.46
45 22 0.06
46 69 0.19
47 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
GGAGATAAGATCTGAAATTCTTGATCTGCTCCACTGTAATCTCAG
Found at i:1350339 original size:175 final size:175
Alignment explanation
Indices: 1350128--1350596 Score: 812
Period size: 175 Copynumber: 2.7 Consensus size: 175
1350118 GCTCCGCTGT
* * ** *
1350128 AATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
1 AATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTT
*
1350193 ATTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTA
66 ATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTA
1350258 ATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGC
131 ATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGC
*
1350303 AATCTCAGGGAAATAAGACCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTT
1 AATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTT
* *
1350368 ATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTAAATCTGCTCCGCTGTA
66 ATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTA
*
1350433 ATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGT
131 ATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGC
* *
1350478 AATCTCAGGGAAATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCATTG
1 AATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTT
* *
1350543 GTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCT
66 ATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1350597 AATGCGATCT
Statistics
Matches: 277, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 277 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (175 bp):
AATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTT
ATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTA
ATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGC
Found at i:1350426 original size:44 final size:44
Alignment explanation
Indices: 1350075--1350596 Score: 272
Period size: 44 Copynumber: 12.0 Consensus size: 44
1350065 TTTTAATCCA
* *
1350075 CTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * *
1350119 CTCCGCTGTAATCTCAGGGAGATAAGA-T-CT-GAC-ACGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAG-CTTCAATCTG
* * * * * *
1350160 CTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCTG
* *
1350204 CTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * **
1350248 CTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTCAATCTG
* * * * * * *
1350294 TTCCACTGCAATCTCAGGGAAATAAGA--CCT-GATGT-GATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCT-TCAATCTG
* * * * * * *
1350335 CTCTACTGTAA-CTTCAGAGAGATAAGATCATTTA-TTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTA-CTAGCTTCAATCTG
*
1350379 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTAAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
* * * **
1350423 CTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-GCTTCAATCTG
* * * * * * *
1350469 TTCCACTGTAATCTCAGGGAAATAAGA--CCT-GATGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
** * * * * * * *
1350510 CTCTGCTGTAA-CTTCAGAGAGATAAGATCATTGGTTTTAATCCG
1 CTCCACTGTAATC-TCAGGGAGATAAGATTACTAGCTTCAATCTG
* *
1350554 CTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCT
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT
1350597 AATGCGATCT
Statistics
Matches: 347, Mismatches: 99, Indels: 64
0.68 0.19 0.13
Matches are distributed among these distances:
40 3 0.01
41 78 0.22
42 5 0.01
43 7 0.02
44 183 0.53
45 7 0.02
46 64 0.18
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTG
Found at i:1350669 original size:98 final size:98
Alignment explanation
Indices: 1350500--1350679 Score: 308
Period size: 98 Copynumber: 1.8 Consensus size: 98
1350490 ATAAGACCTG
* *
1350500 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCATTGGTTTTAATCCGCTCCACTGTAA
1 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCATTGATTTCAATCCGCTCCACTGTAA
1350565 TCTCAGGGAGATAGGATTACCAGCTTCAATCTA
66 TCTCAGGGAGATAGGATTACCAGCTTCAATCTA
* *
1350598 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTTCAATCCGCTCCACTGTAA
1 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCATTGATTTCAATCCGCTCCACTGTAA
1350663 -CTTCAGGGAGATAGGAT
66 TC-TCAGGGAGATAGGAT
1350680 AGTGTCTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 1 0.01
98 76 0.99
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (98 bp):
ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCATTGATTTCAATCCGCTCCACTGTAA
TCTCAGGGAGATAGGATTACCAGCTTCAATCTA
Found at i:1350704 original size:43 final size:44
Alignment explanation
Indices: 1350603--1350722 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 44
1350593 ATCTAATGCG
* * ** * *
1350603 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTTCA
1 ATCTACTCCGCTGTAACTTCAGGGAGATAAGATAGTGTACTTCA
** * *
1350647 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CTTCA
1 ATCTACTCCGCTGTAACTTCAGGGAGATAAGATAGTGTACTTCA
*
1350690 ATCTACTCCGCTGTAA-TCTGAGGGAGATAAGAT
1 ATCTACTCCGCTGTAACT-TCAGGGAGATAAGAT
1350723 CTGAAATTCT
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
42 1 0.02
43 30 0.50
44 29 0.48
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
ATCTACTCCGCTGTAACTTCAGGGAGATAAGATAGTGTACTTCA
Found at i:1350895 original size:88 final size:86
Alignment explanation
Indices: 1350730--1351504 Score: 840
Period size: 86 Copynumber: 9.0 Consensus size: 86
1350720 GATCTGAAAT
* * * * * *
1350730 TCTTCAACCAGCTCCACTATAACTGAGAGAGGTAAGGTTTGTCTTCGACCTGCTTCGCTGTCAAT
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTTAAT
* *
1350795 GCAAGAATGCAAGATCTCTTG
66 GCAGGAAGGCAAGATCTCTTG
* * *
1350816 TCTTCAACCAGCTCCA-TCACAACCGAGAGAGGCAAGGTTTGTATCTTCGACCTGTTTCGCTGTC
1 TCTTCAACCAGCTCCACT-ACAACCGAGAGAGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGTT
* *
1350880 AATGTAGGAAGGCAAGATCTGTTG
63 AATGCAGGAAGGCAAGATCTCTTG
* *
1350904 TCTTCAACCAGCTCCA-TCACAACCGATGA-AGGCAATGCTTGTTTTCGATCTGCTTCGCTGTTA
1 TCTTCAACCAGCTCCACT-ACAACCGA-GAGAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTTA
* *
1350967 ATGCAAGAAGGCAAGATCTTTTG
64 ATGCAGGAAGGCAAGATCTCTTG
*
1350990 TCTTCAACCAGCTCCA-TCACAACCGAGAGAGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTCAACCAGCTCCACT-ACAACCGAGAGAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTTAA
* * *
1351054 TGCAAGAAAGCAAGATCTTTTG
65 TGCAGGAAGGCAAGATCTCTTG
* * * * * *
1351076 TCTTCAATCAACTCCA-TCACAATCGAAAGAGGCAACGTTTGTGTCTTCGATCTGCTTCGCTGTC
1 TCTTCAACCAGCTCCACT-ACAACCGAGAGAGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGTT
*
1351140 AATGCAGGAAGGCAAGATCTTTTG
63 AATGCAGGAAGGCAAGATCTCTTG
* * *
1351164 TCTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCA
1 TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGTTA
1351229 ATGCAGGAAGGCAAGATCTGC-T-
64 ATGCAGGAAGGCAAGATCT-CTTG
* ** * * * *
1351251 TCTTTAACCAGCTCCACTGTAACCAATGA-AGGCAAGGCTTATTTTCGATCTGCTTCGTTGTTAA
1 TCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTTAA
* *
1351315 CGCAGGAAGGCAAGATCTAC--C
65 TGCAGGAAGGCAAGATCT-CTTG
* * * *
1351336 TCTTTAACCAGCTCCACTGCAACCAATGA-AGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTA
1 TCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTTTCGATCTGCTTCGCTGTTA
*
1351400 ACGCAGGAAGGCAAGATCTGC-T-
64 ATGCAGGAAGGCAAGATCT-CTTG
* * *
1351422 TCTTTAACCAGCTCCACTGCAACCAATGA-AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
1 TCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAAGG-TTTGTTTTCGATCTGCTTCGCTGTTA
*
1351486 ACGCAGGAAGGCAAGATCT
64 ATGCAGGAAGGCAAGATCT
1351505 AATTCTTTAA
Statistics
Matches: 623, Mismatches: 53, Indels: 26
0.89 0.08 0.04
Matches are distributed among these distances:
85 75 0.12
86 316 0.51
87 36 0.06
88 193 0.31
89 3 0.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (86 bp):
TCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTTAAT
GCAGGAAGGCAAGATCTCTTG
Found at i:1350935 original size:44 final size:43
Alignment explanation
Indices: 1350798--1351025 Score: 112
Period size: 44 Copynumber: 5.2 Consensus size: 43
1350788 TGTCAATGCA
* *
1350798 AGAATGCAAGATCTCTTGTCTTCAACCAGCTCCATCACAACCG
1 AGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCG
* * * * * * ** *
1350841 AGAGAGGCAAGGTTTG-TATCTTCGACCTGTTTCGC-TGTCAA-TG
1 AGA-AGGCAAGATCTGTTGTCTTCAACCAG-CTC-CATCACAACCG
1350884 TAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCG
1 -A-GAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCG
* * * * * * ** *
1350929 ATGAAGGC-A-A--TGCTTGTTTTCGATCTGCTTCGCTGTTA-ATGCA
1 A-GAAGGCAAGATCTG-TTGTCTTCAACCAGC-TC-C-ATCACAACCG
*
1350972 AGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCG
1 AGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCG
1351015 AGAGAGGCAAG
1 AGA-AGGCAAG
1351026 GCTTGTTTTC
Statistics
Matches: 127, Mismatches: 40, Indels: 35
0.63 0.20 0.17
Matches are distributed among these distances:
40 2 0.02
41 11 0.09
42 11 0.09
43 27 0.21
44 50 0.39
45 25 0.20
46 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (43 bp):
AGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCG
Found at i:1351241 original size:44 final size:44
Alignment explanation
Indices: 1351105--1351243 Score: 131
Period size: 44 Copynumber: 3.2 Consensus size: 44
1351095 CAATCGAAAG
* *
1351105 AGGCAACGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
* * ** * * * * *
1351149 AGGCAAGATCTTTTGTCTTTAACCAGCTCCACT-ACAA--CCGAGA
1 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGCTGTCAATGCAG-GA
1351192 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1351237 AGGCAAG
1 AGGCAAG
1351244 ATCTGCTTCT
Statistics
Matches: 69, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
42 2 0.03
43 19 0.28
44 28 0.41
45 18 0.26
46 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
Found at i:1351496 original size:43 final size:43
Alignment explanation
Indices: 1351363--1351500 Score: 138
Period size: 43 Copynumber: 3.2 Consensus size: 43
1351353 TGCAACCAAT
1351363 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAG
* * ** * * * * *
1351406 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CAAT
1 GAAGGCAAGGCTTTG-TT-TTCGATCTGCTTCACTGTTAACGC-AG
*
1351449 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAG
1351492 GAAGGCAAG
1 GAAGGCAAG
1351501 ATCTAATTCT
Statistics
Matches: 70, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
42 16 0.23
43 37 0.53
44 17 0.24
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (43 bp):
GAAGGCAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAG
Found at i:1352708 original size:7 final size:7
Alignment explanation
Indices: 1352689--1352740 Score: 61
Period size: 7 Copynumber: 7.0 Consensus size: 7
1352679 TTAGCCTCTC
1352689 CATTTTT
1 CATTTTT
1352696 -ACTTTTT
1 CA-TTTTT
1352703 CATTTTTTT
1 CA--TTTTT
1352712 CATTTTT
1 CATTTTT
1352719 CATTTTT
1 CATTTTT
1352726 CATTTTTT
1 CA-TTTTT
1352734 CATTTTT
1 CATTTTT
1352741 TTTGACTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 1 0.03
7 24 0.60
8 8 0.20
9 7 0.17
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:1352709 original size:8 final size:8
Alignment explanation
Indices: 1352698--1352741 Score: 65
Period size: 7 Copynumber: 5.6 Consensus size: 8
1352688 CCATTTTTAC
1352698 TTTTTCATT
1 TTTTTCA-T
1352707 TTTTTCA-
1 TTTTTCAT
1352714 TTTTTCA-
1 TTTTTCAT
1352721 TTTTTCAT
1 TTTTTCAT
1352729 TTTTTCAT
1 TTTTTCAT
1352737 TTTTT
1 TTTTT
1352742 TTGACTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 14 0.41
8 13 0.38
9 7 0.21
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:1352715 original size:23 final size:22
Alignment explanation
Indices: 1352689--1352740 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
1352679 TTAGCCTCTC
1352689 CATTTTT-ACTTTTTCATTTTTTT
1 CATTTTTCA-TTTTTCA-TTTTTT
1352712 CATTTTTCATTTTTCATTTTTT
1 CATTTTTCATTTTTCATTTTTT
1352734 CATTTTT
1 CATTTTT
1352741 TTTGACTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.46
23 14 0.50
24 1 0.04
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (22 bp):
CATTTTTCATTTTTCATTTTTT
Found at i:1353509 original size:6 final size:6
Alignment explanation
Indices: 1353498--1353537 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
1353488 TTGACCTCTC
1353498 CTTTTT CTTTTT CTTTTT CTTTTTT CTTCTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT C-TTTTT CTT-TTT CTTTTT CT
1353538 CCTATTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 20 0.62
7 12 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:1353515 original size:7 final size:7
Alignment explanation
Indices: 1353499--1353535 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
1353489 TGACCTCTCC
1353499 TTTTTC-
1 TTTTTCT
1353505 TTTTTC-
1 TTTTTCT
1353511 TTTTTCT
1 TTTTTCT
1353518 TTTTTCT
1 TTTTTCT
*
1353525 TCTTTCT
1 TTTTTCT
1353532 TTTT
1 TTTT
1353536 CTCCTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:1353521 original size:13 final size:13
Alignment explanation
Indices: 1353498--1353535 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
1353488 TTGACCTCTC
1353498 CTTTTTC-TTTTT
1 CTTTTTCTTTTTT
1353510 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
1353523 CTTCTTTCTTTTT
1 CTT-TTTCTTTTT
1353536 CTCCTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:1353536 original size:13 final size:12
Alignment explanation
Indices: 1353498--1353537 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
1353488 TTGACCTCTC
1353498 CTTTTTCTTTTT
1 CTTTTTCTTTTT
1353510 CTTTTTCTTTTTT
1 CTTTTTC-TTTTT
1353523 CTTCTTTCTTTTT
1 CTT-TTTCTTTTT
1353536 CT
1 CT
1353538 CCTATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.27
13 15 0.58
14 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTTCTTTTT
Found at i:1353574 original size:7 final size:7
Alignment explanation
Indices: 1353558--1353633 Score: 84
Period size: 7 Copynumber: 10.6 Consensus size: 7
1353548 ACTTTGATTT
*
1353558 TTTTTTA
1 TTTTTGA
1353565 TTTTTGA
1 TTTTTGA
1353572 TTTTTTGA
1 -TTTTTGA
1353580 -TTTTGA
1 TTTTTGA
*
1353586 TTTTTTA
1 TTTTTGA
1353593 TTTTTGA
1 TTTTTGA
1353600 TTTTTTGA
1 -TTTTTGA
1353608 TTTTTTTGA
1 --TTTTTGA
1353617 -TTTTGA
1 TTTTTGA
1353623 TTTTTGA
1 TTTTTGA
1353630 TTTT
1 TTTT
1353634 ATTTTTTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
6 12 0.20
7 27 0.44
8 14 0.23
9 8 0.13
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (7 bp):
TTTTTGA
Found at i:1353583 original size:22 final size:21
Alignment explanation
Indices: 1353558--1353650 Score: 75
Period size: 22 Copynumber: 4.3 Consensus size: 21
1353548 ACTTTGATTT
1353558 TTTTTTATTTTTGATTTTTTGA
1 TTTTTTATTTTT-ATTTTTTGA
*
1353580 -TTTTGATTTTT-TATTTTTGA
1 TTTTTTATTTTTAT-TTTTTGA
1353600 TTTTTTGATTTTT-TTGATTTTGA
1 TTTTTT-ATTTTTATT--TTTTGA
* * *
1353623 TTTTTGATTTTATTTTTTTTAA
1 TTTTTTATTTT-TATTTTTTGA
1353645 TTTTTT
1 TTTTTT
1353651 TGATTCTGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.02
20 7 0.12
21 15 0.25
22 22 0.37
23 12 0.20
24 2 0.03
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (21 bp):
TTTTTTATTTTTATTTTTTGA
Found at i:1353584 original size:37 final size:37
Alignment explanation
Indices: 1353543--1353655 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 37
1353533 TTTCTCCTAT
1353543 TTTTGACTTTGATTTTTTTTTATTTTTGA-TTTTTTGA
1 TTTTGA-TTTGATTTTTTTTTATTTTTGATTTTTTTGA
*
1353580 TTTTGATTT--TTTATTTTTGATTTTTTGATTTTTTTGA
1 TTTTGATTTGATTT-TTTTTTA-TTTTTGATTTTTTTGA
* *
1353617 TTTTGATTTTTGA-TTTTATTT-TTTTTAATTTTTTTGA
1 TTTTGA--TTTGATTTTTTTTTATTTTTGATTTTTTTGA
1353654 TT
1 TT
1353656 CTGAACTCAT
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
34 3 0.05
35 6 0.09
36 10 0.15
37 37 0.57
39 7 0.11
40 2 0.03
ACGTcount: A:0.14, C:0.01, G:0.10, T:0.75
Consensus pattern (37 bp):
TTTTGATTTGATTTTTTTTTATTTTTGATTTTTTTGA
Found at i:1353589 original size:28 final size:29
Alignment explanation
Indices: 1353558--1353650 Score: 111
Period size: 28 Copynumber: 3.2 Consensus size: 29
1353548 ACTTTGATTT
1353558 TTTTTTATTTTTGATTTTTTGA-TTTTGA
1 TTTTTTATTTTTGATTTTTTGATTTTTGA
1353586 TTTTTTATTTTTGATTTTTTGATTTTTTTGA
1 TTTTTTATTTTTGATTTTTTGA--TTTTTGA
* * *
1353617 -TTTTGATTTTTGATTTTATT-TTTTTTAA
1 TTTTTTATTTTTGATTTT-TTGATTTTTGA
1353645 TTTTTT
1 TTTTTT
1353651 TGATTCTGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
28 28 0.50
29 4 0.07
30 16 0.29
31 8 0.14
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (29 bp):
TTTTTTATTTTTGATTTTTTGATTTTTGA
Found at i:1355419 original size:46 final size:46
Alignment explanation
Indices: 1355367--1355459 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
1355357 ATATGTGTTT
1355367 GGTTGTGCTTGGATGTCGGTTGGAGTAAAATCTGAAAGATATGCAG
1 GGTTGTGCTTGGATGTCGGTTGGAGTAAAATCTGAAAGATATGCAG
*
1355413 GGTTGTGCTTGGATGTCGGTTGGAGTAAAATTTGAAAGATATGCAG
1 GGTTGTGCTTGGATGTCGGTTGGAGTAAAATCTGAAAGATATGCAG
1355459 G
1 G
1355460 ACCTTCATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.26, C:0.08, G:0.35, T:0.31
Consensus pattern (46 bp):
GGTTGTGCTTGGATGTCGGTTGGAGTAAAATCTGAAAGATATGCAG
Found at i:1355770 original size:19 final size:20
Alignment explanation
Indices: 1355741--1355789 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1355731 CACTTCGTGA
* *
1355741 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
1355760 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
1355780 AAATG-AATGC
1 AAATGTAATGC
1355790 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:1357882 original size:44 final size:43
Alignment explanation
Indices: 1357832--1357915 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
1357822 ATTAAAATAT
* *
1357832 GTATATATACATAGATATATATAAAAATTATGAAATATGTGTAA
1 GTATATATACATAGAGATATATAAAAA-TAGGAAATATGTGTAA
* * *
1357876 GTATATATACATATAGGTTTATAAAAATAGGAAATATGTG
1 GTATATATACATAGAGATATATAAAAATAGGAAATATGTG
1357916 CGTGTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 12 0.34
44 23 0.66
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (43 bp):
GTATATATACATAGAGATATATAAAAATAGGAAATATGTGTAA
Found at i:1357934 original size:44 final size:44
Alignment explanation
Indices: 1357851--1357934 Score: 98
Period size: 44 Copynumber: 1.9 Consensus size: 44
1357841 CATAGATATA
* * *
1357851 TATAAAAATTATGAAATATGTGTAAGTATATATACATATAGGTT
1 TATAAAAATTAGGAAATATGTGCAAGTATATAAACATATAGGTT
** *
1357895 TATAAAAA-TAGGAAATATGTGCGTGTATTATAAATATATA
1 TATAAAAATTAGGAAATATGTGCAAGTA-TATAAACATATA
1357935 CATGTATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
43 15 0.45
44 18 0.55
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.37
Consensus pattern (44 bp):
TATAAAAATTAGGAAATATGTGCAAGTATATAAACATATAGGTT
Found at i:1358013 original size:37 final size:35
Alignment explanation
Indices: 1357936--1358006 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
1357926 AAATATATAC
* * * * *
1357936 ATGTATAAATATTTTATAAAAATAGGTATGTTTAT
1 ATGTATAAATATATTACAAAAAAAAGTATGTGTAT
*
1357971 ATGTATATATATATTACAAAAAAAAGTATGTGTAT
1 ATGTATAAATATATTACAAAAAAAAGTATGTGTAT
1358006 A
1 A
1358007 AGTGTATGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.41
Consensus pattern (35 bp):
ATGTATAAATATATTACAAAAAAAAGTATGTGTAT
Found at i:1358069 original size:3 final size:3
Alignment explanation
Indices: 1358061--1358090 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1358051 TATAACGATT
*
1358061 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1358091 TGAAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1360889 original size:129 final size:129
Alignment explanation
Indices: 1360657--1360913 Score: 433
Period size: 129 Copynumber: 2.0 Consensus size: 129
1360647 ACAATTTTAC
*
1360657 CCTTAAATTTTTAACTTTCGATAATAAGAAACTGCCACTTGTTCAATCAAGTGTTAAAAAGCTTG
1 CCTTAAATTTTGAACTTTCGATAATAAGAAACTGCCACTTGTTCAATCAAGTGTTAAAAAGCTTG
* * *
1360722 ATGTCTATGAGTAAGGTCTCATATTTAAGTTTTGTAGATAAAAAATACAAGGGTGGAAAAGCTG
66 ATGTCAATGAGTAAGGTCTCAGATTTAAGTTTTATAGATAAAAAATACAAGGGTGGAAAAGCTG
** *
1360786 CCTTAAATTTTGAACTTTCGATCGTAAGAGACTGCCACTTGTTCAATCAAGTGTTAAAAAGCTTG
1 CCTTAAATTTTGAACTTTCGATAATAAGAAACTGCCACTTGTTCAATCAAGTGTTAAAAAGCTTG
* *
1360851 ATGTCAATGTGTAAGGTCTCAGATTTAAGTTTTATAGATAAAAAATACATGGGTGGAAAAGCT
66 ATGTCAATGAGTAAGGTCTCAGATTTAAGTTTTATAGATAAAAAATACAAGGGTGGAAAAGCT
1360914 TCCCTTCTTT
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (129 bp):
CCTTAAATTTTGAACTTTCGATAATAAGAAACTGCCACTTGTTCAATCAAGTGTTAAAAAGCTTG
ATGTCAATGAGTAAGGTCTCAGATTTAAGTTTTATAGATAAAAAATACAAGGGTGGAAAAGCTG
Found at i:1366394 original size:24 final size:25
Alignment explanation
Indices: 1366348--1366399 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1366338 TAGAAATGAA
* *
1366348 AAATAAATTAATTTAGATAATATTT
1 AAATAAATTAATATAGATAATATAT
* *
1366373 AAATAATTTAATATA-ATTATATAT
1 AAATAAATTAATATAGATAATATAT
1366397 AAA
1 AAA
1366400 ATATACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATAAATTAATATAGATAATATAT
Found at i:1372213 original size:7 final size:8
Alignment explanation
Indices: 1372196--1372251 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1372186 AAAATATTTT
1372196 AAAATTAA
1 AAAATTAA
1372204 AAAATTAA
1 AAAATTAA
1372212 AAAGTATTTTAA
1 AAA--A--TTAA
*
1372224 AAAATTTA
1 AAAATTAA
1372232 AAAATTAA
1 AAAATTAA
1372240 AAAATTAA
1 AAAATTAA
1372248 AAAA
1 AAAA
1372252 GTATTTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 33 0.79
10 2 0.05
12 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (8 bp):
AAAATTAA
Found at i:1372221 original size:37 final size:38
Alignment explanation
Indices: 1372158--1372264 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 38
1372148 ATTTTTAAAA
1372158 TTAAAATT--AAAATTAAAAAAGTATTTTAAAAATATT
1 TTAAAATTAAAAAATTAAAAAAGTATTTTAAAAATATT
1372194 TTAAAATTAAAAAATT-AAAAAGTATTTTAAAAA-ATT
1 TTAAAATTAAAAAATTAAAAAAGTATTTTAAAAATATT
*
1372230 TAAAAATTAAAAAATTAAAAAAGTA-TTTAAAAATA
1 TTAAAATTAAAAAATTAAAAAAGTATTTTAAAAATA
1372265 AAAAAATAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
36 34 0.52
37 26 0.39
38 6 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (38 bp):
TTAAAATTAAAAAATTAAAAAAGTATTTTAAAAATATT
Found at i:1372228 original size:28 final size:25
Alignment explanation
Indices: 1372183--1372242 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 25
1372173 AAAAAGTATT
1372183 TTAAAAATATTTTAAAATTAAAAAA
1 TTAAAAATATTTTAAAATTAAAAAA
*
1372208 TTAAAAAGTATTTTAAAAAATTTAAAAA
1 TTAAAAA-TATTTT--AAAATTAAAAAA
1372236 TTAAAAA
1 TTAAAAA
1372243 ATTAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 7 0.23
26 6 0.19
28 18 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
TTAAAAATATTTTAAAATTAAAAAA
Found at i:1375692 original size:19 final size:19
Alignment explanation
Indices: 1375665--1375701 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1375655 CATTTCCTTA
*
1375665 TTTTATTTATTTTATTTTC
1 TTTTATTTATTTCATTTTC
*
1375684 TTTTGTTTATTTCATTTT
1 TTTTATTTATTTCATTTT
1375702 ATTTAAAAAC
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:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTATTTATTTCATTTTC
Found at i:1383996 original size:17 final size:16
Alignment explanation
Indices: 1383969--1384004 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1383959 ATACATCAAT
1383969 AATAATAATTAATTGA
1 AATAATAATTAATTGA
*
1383985 AATAATATATTACTTGA
1 AATAATA-ATTAATTGA
1384002 AAT
1 AAT
1384005 TTATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
AATAATAATTAATTGA
Found at i:1384041 original size:22 final size:21
Alignment explanation
Indices: 1384007--1384049 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1383997 CTTGAAATTT
* *
1384007 ATAAATTTTATTTTACTTAAAA
1 ATAAAATTAATTTTAC-TAAAA
1384029 ATAAAATTAATTTTACTAAAA
1 ATAAAATTAATTTTACTAAAA
1384050 TTTGAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAAAATTAATTTTACTAAAA
Found at i:1391773 original size:13 final size:13
Alignment explanation
Indices: 1391755--1391781 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1391745 TGTGAGATTC
1391755 ATCTATAATTGTG
1 ATCTATAATTGTG
1391768 ATCTATAATTGTG
1 ATCTATAATTGTG
1391781 A
1 A
1391782 ACAATATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
ATCTATAATTGTG
Found at i:1397154 original size:37 final size:37
Alignment explanation
Indices: 1397104--1397179 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
1397094 ATCATTTGGT
1397104 CTTGGAATCAAATTCCAATCTAATAGGATC-AGTATTC
1 CTTGGAATCAAATTCCAATCTAATAGGATCGA-TATTC
* * *
1397141 CTTGGAATCAAATTCCAGTTTAATAGTATCGATATTC
1 CTTGGAATCAAATTCCAATCTAATAGGATCGATATTC
1397178 CT
1 CT
1397180 ACACCAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 34 0.97
38 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (37 bp):
CTTGGAATCAAATTCCAATCTAATAGGATCGATATTC
Found at i:1399087 original size:12 final size:13
Alignment explanation
Indices: 1399070--1399099 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1399060 TCGAGGAAGG
1399070 AAGGGTGATAT-T
1 AAGGGTGATATAT
1399082 AAGGGTGATATAT
1 AAGGGTGATATAT
1399095 AAGGG
1 AAGGG
1399100 GCTTCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (13 bp):
AAGGGTGATATAT
Found at i:1402325 original size:19 final size:21
Alignment explanation
Indices: 1402287--1402325 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1402277 CTGCTGTTCC
1402287 TTTGGAGATCTTTGTACGAGT
1 TTTGGAGATCTTTGTACGAGT
*
1402308 TTTGG-GATGTTT-TACGAG
1 TTTGGAGATCTTTGTACGAG
1402326 AAAGCATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.18, C:0.08, G:0.31, T:0.44
Consensus pattern (21 bp):
TTTGGAGATCTTTGTACGAGT
Found at i:1404948 original size:27 final size:27
Alignment explanation
Indices: 1404918--1404971 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1404908 TAGATTCTTC
**
1404918 CTAACATCTTCTACATGGAGTATATTG
1 CTAACATCTTCTACATAAAGTATATTG
* *
1404945 CTAATATCTTCTGCATAAAGTATATTG
1 CTAACATCTTCTACATAAAGTATATTG
1404972 TACAGGGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (27 bp):
CTAACATCTTCTACATAAAGTATATTG
Found at i:1409742 original size:24 final size:24
Alignment explanation
Indices: 1409714--1409766 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1409704 TTCGTACGTC
*
1409714 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATGCT
* *
1409738 AAATATATTTTACTAATAAATGCT
1 AAATAAATTATACTAATAAATGCT
1409762 AAATA
1 AAATA
1409767 TTTTAGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATGCT
Found at i:1416275 original size:5 final size:5
Alignment explanation
Indices: 1416256--1416303 Score: 82
Period size: 5 Copynumber: 10.0 Consensus size: 5
1416246 GCTTTAAATT
1416256 ATATA ATAT- AT-TA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1416304 TTACAAACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 1 0.02
4 4 0.10
5 36 0.88
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:1417440 original size:19 final size:21
Alignment explanation
Indices: 1417402--1417440 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1417392 AAAATAATTT
*
1417402 AAAAAATTCATATTTTTTATA
1 AAAAAATTCATATTTATTATA
1417423 AAAAAATT-AT-TTTATTAT
1 AAAAAATTCATATTTATTAT
1417441 TTGGAGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 2 0.12
21 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAAAATTCATATTTATTATA
Found at i:1422619 original size:2 final size:2
Alignment explanation
Indices: 1422612--1422657 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1422602 TGTACCACAA
1422612 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
1422654 AT AT
1 AT AT
1422658 TCTCATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1425577 original size:16 final size:16
Alignment explanation
Indices: 1425541--1425588 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1425531 TAAATAATTT
1425541 AAAAATT-AT-AAA-A
1 AAAAATTCATAAAATA
*
1425554 AAATATTCATAAAATA
1 AAAAATTCATAAAATA
*
1425570 AAAAATTCAAAAAATA
1 AAAAATTCATAAAATA
1425586 AAA
1 AAA
1425589 TAAAAAGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 6 0.21
14 2 0.07
15 3 0.10
16 18 0.62
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATTCATAAAATA
Found at i:1425586 original size:21 final size:22
Alignment explanation
Indices: 1425562--1425606 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
1425552 AAAAATATTC
1425562 ATAAAATAAAAAATTCA-AAAA
1 ATAAAATAAAAAATTCATAAAA
*
1425583 ATAAAATAAAAAGTTCATAAAA
1 ATAAAATAAAAAATTCATAAAA
1425605 AT
1 AT
1425607 TCAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
ATAAAATAAAAAATTCATAAAA
Found at i:1434911 original size:38 final size:39
Alignment explanation
Indices: 1434834--1434911 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
1434824 GCAGATGGTG
* *
1434834 ACTTCTTTGTAGGTATATATCATAGTTTCCCATAAAATT
1 ACTTCTTTGTAGGTATATATCATAGGTTCCCACAAAATT
* *
1434873 ACTTCTTTGTAGGTATATATCAT-GGTTCCCCCAGAATT
1 ACTTCTTTGTAGGTATATATCATAGGTTCCCACAAAATT
1434911 A
1 A
1434912 GATAAGTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 12 0.34
39 23 0.66
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (39 bp):
ACTTCTTTGTAGGTATATATCATAGGTTCCCACAAAATT
Found at i:1435654 original size:21 final size:21
Alignment explanation
Indices: 1435628--1435670 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1435618 TCAATGGTAT
1435628 AATCATTTCATTATGTAGTGG
1 AATCATTTCATTATGTAGTGG
1435649 AATCATTTCATTATGTAGTGG
1 AATCATTTCATTATGTAGTGG
1435670 A
1 A
1435671 CTTTGCTTTG
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:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (21 bp):
AATCATTTCATTATGTAGTGG
Found at i:1444885 original size:21 final size:22
Alignment explanation
Indices: 1444831--1444889 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1444821 TTTAAAATTG
* *
1444831 TTTATTATTTATTTTATAATAT
1 TTTATAATATATTTTATAATAT
1444853 TTT-TAATGTATATTTTA-AATAT
1 TTTATAA--TATATTTTATAATAT
1444875 TTTATAATATATTTT
1 TTTATAATATATTTT
1444890 TATTCAAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 10 0.31
22 11 0.34
23 11 0.34
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTATAATATATTTTATAATAT
Found at i:1444909 original size:63 final size:59
Alignment explanation
Indices: 1444837--1445018 Score: 151
Period size: 63 Copynumber: 3.0 Consensus size: 59
1444827 ATTGTTTATT
*
1444837 ATTTATTTTATAATATTTTTAATGTATATT-TTAAATATTTTATAATATATTTTTATTCAAAC
1 ATTTTTTTTAT-ATATTTTTAATGTATATTATT--ATATTTTATAATAT-TTTTTATTCAAAC
* * *
1444899 GCTTTTTTTTAT-T-TTTTAAAT-TAT-TTATTATTTGTTTTATAATATTTGTTTATTCAAAC
1 -ATTTTTTTTATATATTTTTAATGTATATTATTA--TATTTTATAATATTT-TTTATTCAAAC
* * *
1444958 ATTTTTTGAATATTTATTTTTTAATTGTTTATTATT-TATTTTATAATATTTTTTATTCAAA
1 ATTTTTT--TTATATA-TTTTTAA-TGTATATTATTATATTTTATAATATTTTTTATTCAAA
1445019 TGATTTTAAA
Statistics
Matches: 98, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
57 1 0.01
58 10 0.10
59 28 0.29
60 10 0.10
61 2 0.02
62 10 0.10
63 29 0.30
64 1 0.01
65 2 0.02
66 5 0.05
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (59 bp):
ATTTTTTTTATATATTTTTAATGTATATTATTATATTTTATAATATTTTTTATTCAAAC
Found at i:1444937 original size:59 final size:60
Alignment explanation
Indices: 1444872--1445018 Score: 192
Period size: 63 Copynumber: 2.4 Consensus size: 60
1444862 ATATTTTAAA
1444872 TATTTTATAATATATTTTTATTCAAAC-GCTTTT-T-TTTATTTTTTAAATTATTTATTATT
1 TATTTTATAATAT-TTTTTATTCAAACAGCTTTTATATTTATTTTTT-AATTATTTATTATT
* ** *
1444931 TGTTTTATAATATTTGTTTATTCAAACATTTTTTGAATATTTATTTTTTAATTGTTTATTATT
1 TATTTTATAATATTT-TTTATTCAAACAGCTTTT--ATATTTATTTTTTAATTATTTATTATT
1444994 TATTTTATAATATTTTTTATTCAAA
1 TATTTTATAATATTTTTTATTCAAA
1445019 TGATTTTAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
58 2 0.03
59 23 0.30
60 4 0.05
62 10 0.13
63 28 0.36
64 10 0.13
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.63
Consensus pattern (60 bp):
TATTTTATAATATTTTTTATTCAAACAGCTTTTATATTTATTTTTTAATTATTTATTATT
Found at i:1445760 original size:14 final size:14
Alignment explanation
Indices: 1445743--1445807 Score: 51
Period size: 16 Copynumber: 4.5 Consensus size: 14
1445733 ACATAATTAG
*
1445743 AATTAAATTTTAAA
1 AATTAAATATTAAA
* *
1445757 AATTAAAAGATAATAA
1 AATT-AAATATTA-AA
*
1445773 AATTAAAATTTTAAA
1 AATT-AAATATTAAA
1445788 AA-TAAATATTAAA
1 AATTAAATATTAAA
*
1445801 TATTAAA
1 AATTAAA
1445808 CTTATAACAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
13 10 0.25
14 9 0.22
15 9 0.22
16 12 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AATTAAATATTAAA
Found at i:1445761 original size:31 final size:31
Alignment explanation
Indices: 1445723--1445790 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1445713 AAATTTAATA
** *
1445723 AAAAATTATTACATAATTAGAATT-AAATTTT
1 AAAAATTAAAACATAA-TAAAATTAAAATTTT
*
1445754 AAAAATTAAAAGATAATAAAATTAAAATTTT
1 AAAAATTAAAACATAATAAAATTAAAATTTT
1445785 AAAAAT
1 AAAAAT
1445791 AAATATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (31 bp):
AAAAATTAAAACATAATAAAATTAAAATTTT
Found at i:1445801 original size:20 final size:20
Alignment explanation
Indices: 1445768--1445807 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1445758 ATTAAAAGAT
*
1445768 AATAAAATTAAAATTTTAAA
1 AATAAAATTAAAATATTAAA
1445788 AATAAATATT-AAATATTAAA
1 AATAAA-ATTAAAATATTAAA
1445808 CTTATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAAAATTAAAATATTAAA
Found at i:1447977 original size:10 final size:10
Alignment explanation
Indices: 1447964--1448012 Score: 55
Period size: 13 Copynumber: 4.6 Consensus size: 10
1447954 TTTAAATGTA
1447964 AAAAAATTAT
1 AAAAAATTAT
1447974 AAAAAAATT-T
1 -AAAAAATTAT
1447984 AAAAAATTATTTT
1 AAAAAATTA---T
1447997 AAAAAATTAT
1 AAAAAATTAT
1448007 AAAAAA
1 AAAAAA
1448013 AATTAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 8 0.24
13 10 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:1448017 original size:12 final size:11
Alignment explanation
Indices: 1447962--1448013 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
1447952 TTTTTAAATG
1447962 TAAAAAAATTA
1 TAAAAAAATTA
1447973 TAAAAAAATT-
1 TAAAAAAATTA
1447983 T-AAAAAATTA
1 TAAAAAAATTA
*
1447993 TTTTAAAAAATTA
1 --TAAAAAAATTA
1448006 TAAAAAAA
1 TAAAAAAA
1448014 ATTAAAATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 17 0.47
12 1 0.03
13 9 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAAAAATTA
Found at i:1449750 original size:2 final size:2
Alignment explanation
Indices: 1449743--1449768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1449733 TTTGTAATTC
1449743 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
1449769 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1449862 original size:9 final size:10
Alignment explanation
Indices: 1449833--1449870 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1449823 CTCATTTTTC
**
1449833 TTTTATATAG
1 TTTTATATTT
1449843 TTTTATATTT
1 TTTTATATTT
1449853 TTTTAT-TTT
1 TTTTATATTT
1449862 TTTTATATT
1 TTTTATATT
1449871 CATTGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTTATATTT
Found at i:1453810 original size:11 final size:12
Alignment explanation
Indices: 1453790--1453815 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1453780 GAGTTTCAGA
1453790 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1453802 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1453814 TT
1 TT
1453816 CTGCTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:1455154 original size:45 final size:46
Alignment explanation
Indices: 1455059--1455156 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
1455049 TGTGTATATC
* *
1455059 TATTTTCTTTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
1455105 TATTTTGTTTTAATTAGGAGATTAGATGCT-AAGTTTAAGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
1455150 TATTTTG
1 TATTTTG
1455157 GTTTCTATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 21 0.42
46 29 0.58
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (46 bp):
TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
Found at i:1459261 original size:45 final size:46
Alignment explanation
Indices: 1459166--1459263 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
1459156 TGTGTATATC
* *
1459166 TATTTTCTTTTAATTAGGAGATTAGATGCTAAAGTTTAGGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
1459212 TATTTTGTTTTAATTAGGAGATTAGATGCT-AAGTTTAAGAGATAA
1 TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
1459257 TATTTTG
1 TATTTTG
1459264 GTTTCTATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 21 0.42
46 29 0.58
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (46 bp):
TATTTTGTTTTAATTAGGAGATTAGATGCTAAAGTTTAAGAGATAA
Found at i:1460424 original size:4 final size:4
Alignment explanation
Indices: 1460417--1460449 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1460407 AAAGAGTAAG
*
1460417 TAAA TAAA TAAA TAAA TACA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1460450 TTCATGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:1461378 original size:45 final size:45
Alignment explanation
Indices: 1461329--1461429 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 45
1461319 AAAATCACCC
* *
1461329 TTGAAATTTTTAGTATTCTGGTTTTTGATTTCTTCTCTATGTGTT
1 TTGAAATTTTTAGTATTCTGGTTTCTGATTGCTTCTCTATGTGTT
* *
1461374 TTGAAATTTTTAGTATTTTGGTTTCTGATTGCTTCTCTGTGTGTT
1 TTGAAATTTTTAGTATTCTGGTTTCTGATTGCTTCTCTATGTGTT
1461419 TTGAAATTTTT
1 TTGAAATTTTT
1461430 TTGTATTTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.16, C:0.08, G:0.17, T:0.59
Consensus pattern (45 bp):
TTGAAATTTTTAGTATTCTGGTTTCTGATTGCTTCTCTATGTGTT
Found at i:1462473 original size:14 final size:14
Alignment explanation
Indices: 1462454--1462496 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1462444 AAAAAAAAAT
1462454 AAACAAATAAAGAC
1 AAACAAATAAAGAC
*
1462468 AAACAAATAAA-AA
1 AAACAAATAAAGAC
1462481 AAACTAGAATAAAGAC
1 AAAC-A-AATAAAGAC
1462497 TAAAGGTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 5 0.21
14 12 0.50
15 6 0.25
16 1 0.04
ACGTcount: A:0.72, C:0.12, G:0.07, T:0.09
Consensus pattern (14 bp):
AAACAAATAAAGAC
Found at i:1463143 original size:22 final size:22
Alignment explanation
Indices: 1463118--1463161 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1463108 CAATATTAAT
1463118 TTCCTTCAAAAATTCTCTCAAA
1 TTCCTTCAAAAATTCTCTCAAA
*
1463140 TTCCTTCCAAAATTCTCTCAAA
1 TTCCTTCAAAAATTCTCTCAAA
1463162 CTCTCAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (22 bp):
TTCCTTCAAAAATTCTCTCAAA
Found at i:1463168 original size:30 final size:30
Alignment explanation
Indices: 1463132--1463191 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1463122 TTCAAAAATT
*
1463132 CTCTCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
1463162 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
1463192 TTCCTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.32
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:1463180 original size:11 final size:12
Alignment explanation
Indices: 1463133--1463198 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 12
1463123 TCAAAAATTC
1463133 TCTCAAATTCCT
1 TCTCAAATTCCT
1463145 TC-CAAAATT-C-
1 TCTC-AAATTCCT
1463155 TCTCAAA---C-
1 TCTCAAATTCCT
1463163 TCTCAAATTCCT
1 TCTCAAATTCCT
*
1463175 TC-CAAAATCC-
1 TCTCAAATTCCT
1463185 TCTCAAATTCCT
1 TCTCAAATTCCT
1463197 TC
1 TC
1463199 AAAAAATCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
8 8 0.18
10 7 0.16
11 18 0.41
12 11 0.25
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (12 bp):
TCTCAAATTCCT
Found at i:1463189 original size:22 final size:22
Alignment explanation
Indices: 1463162--1463203 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1463152 TTCTCTCAAA
*
1463162 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCAAAAATC
1463184 CTCTCAAATTCCTTCAAAAA
1 CTCTCAAATTCCTTCAAAAA
1463204 ATCTCCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (22 bp):
CTCTCAAATTCCTTCAAAAATC
Found at i:1463309 original size:29 final size:29
Alignment explanation
Indices: 1463249--1463309 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1463239 AATTTCATTA
* * *
1463249 TTTTAAGAAAATTTTATAATTTTTTATTT
1 TTTTAAGAAAATTTTAAAATTTTTAATAT
1463278 TTTTAA-AATAATTTTAAAATTTTTAATAT
1 TTTTAAGAA-AATTTTAAAATTTTTAATAT
1463307 TTT
1 TTT
1463310 CAACAATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAAGAAAATTTTAAAATTTTTAATAT
Found at i:1463429 original size:14 final size:15
Alignment explanation
Indices: 1463400--1463433 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1463390 AAATTTTAAA
1463400 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
1463415 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
1463429 TTTTA
1 TTTTA
1463434 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:1465641 original size:28 final size:28
Alignment explanation
Indices: 1465583--1465885 Score: 316
Period size: 23 Copynumber: 11.7 Consensus size: 28
1465573 TTTTGACATT
* * *
1465583 ATTTGATTAAAAACCGTAACTCTAACCTA
1 ATTTAATTAAAAACCCTAAC-CTAACTTA
1465612 ATTTAATTAAAAA--C---CCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1465635 ACTTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1465663 ATTTAATTAAAAA--CT---CTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1465686 ACTTAA-TAAAAACCCTAACATAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1465713 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
* *
1465742 ATTTAATTAAAAATCGTAACCTAAC---
1 ATTTAATTAAAAACCCTAACCTAACTTA
1465767 --TTAATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1465793 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1465816 ATTTAATTAAAAACCCTAACCTAAC---
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1465841 --TTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1465867 ATTTAATTAAAAACCCTAA
1 ATTTAATTAAAAACCCTAA
1465886 TTTCATCTGG
Statistics
Matches: 233, Mismatches: 15, Indels: 53
0.77 0.05 0.18
Matches are distributed among these distances:
22 6 0.03
23 96 0.41
24 5 0.02
25 1 0.00
26 2 0.01
27 14 0.06
28 73 0.31
29 36 0.15
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:1465670 original size:51 final size:51
Alignment explanation
Indices: 1465588--1465885 Score: 337
Period size: 51 Copynumber: 5.8 Consensus size: 51
1465578 ACATTATTTG
* *
1465588 ATTAAAAACCGTAACTCTAACCTAATTTAATTAAAAACCCTAACTTAACTTA
1 ATTAAAAACCCTAAC-CTAACTTAATTTAATTAAAAACCCTAACTTAACTTA
*
1465640 ATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACTCTAACTTAACTTA
1 ATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACTTAACTTA
* *
1465691 A-TAAAAACCCTAACATAACTTAATTTAATTAAAAACCCTAACCCTAACCTAATTTA
1 ATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAA--CT----TAACTTA
* * *
1465747 ATTAAAAATCGTAACCTAACTTAA-TTAA--AAACCCTAA-CCTAACTTAATTTA
1 ATTAAAAACCCTAACCTAACTTAATTTAATTAAA----AACCCTAACTTAACTTA
*
1465798 ATTAAAAACCCTAA-C---C-TAATTTAATTAAAAACCCTAACCTAACTTA
1 ATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACTTAACTTA
*
1465844 ATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAA
1 ATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAA
1465886 TTTCATCTGG
Statistics
Matches: 212, Mismatches: 14, Indels: 41
0.79 0.05 0.15
Matches are distributed among these distances:
45 2 0.01
46 29 0.14
47 6 0.03
49 3 0.01
50 39 0.18
51 75 0.35
52 16 0.08
54 3 0.01
55 2 0.01
56 11 0.05
57 24 0.11
58 2 0.01
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.31
Consensus pattern (51 bp):
ATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACTTAACTTA
Found at i:1468269 original size:123 final size:125
Alignment explanation
Indices: 1468056--1468335 Score: 388
Period size: 123 Copynumber: 2.3 Consensus size: 125
1468046 CCACGAGGGC
*
1468056 GCGATTTGACACTATTTGCTCAGAAACGTCAAAACAAAATTATTTCCCACATGACCAATTGTAGC
1 GCGATTTGACACTATTTGCTCAGAAACGTCAAAACAAAATTATTTCCCACATGACCAACTGTAGC
* * * **
1468121 GAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * **
1468181 GCGATTTTATACTATTTGCTCAGAAAACGTC-AAA-AAAATTATTTCTTACATGACC-ACTGTAG
1 GCGATTTGACACTATTTGCTCAG-AAACGTCAAAACAAAATTATTTCCCACATGACCAACTGTAG
*
1468243 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCTTGGTAGAA
65 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
** *
1468304 GCGATTTCCCACTATTTGAC-CAGATACGTCAA
1 GCGATTTGACACTATTTG-CTCAGAAACGTCAA
1468336 CTCGAAAAAA
Statistics
Matches: 137, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
122 6 0.04
123 80 0.58
124 20 0.15
125 24 0.18
126 7 0.05
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (125 bp):
GCGATTTGACACTATTTGCTCAGAAACGTCAAAACAAAATTATTTCCCACATGACCAACTGTAGC
GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:1468683 original size:27 final size:27
Alignment explanation
Indices: 1468645--1468708 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1468635 GGATTGCCAC
*
1468645 AGGCGGCACCAATGGTGCCAGTGGCAG
1 AGGCGGCACCAATGGTACCAGTGGCAG
1468672 AGGCGGCACCAATGGTACCAGTGGCAG
1 AGGCGGCACCAATGGTACCAGTGGCAG
1468699 AGGCGGCACC
1 AGGCGGCACC
1468709 CCCCATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.23, C:0.28, G:0.39, T:0.09
Consensus pattern (27 bp):
AGGCGGCACCAATGGTACCAGTGGCAG
Found at i:1468816 original size:17 final size:16
Alignment explanation
Indices: 1468791--1468828 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
1468781 ATATGTTTAT
1468791 GAAAAAAATAAAATAC
1 GAAAAAAATAAAATAC
1468807 GAAAAGAAATAAAATAC
1 GAAAA-AAATAAAATAC
1468824 GAAAA
1 GAAAA
1468829 TAGTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.74, C:0.05, G:0.11, T:0.11
Consensus pattern (16 bp):
GAAAAAAATAAAATAC
Found at i:1468852 original size:51 final size:49
Alignment explanation
Indices: 1468763--1468880 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 49
1468753 ATAGTATTAA
*
1468763 AAATAAAATACCGAAAAAATATGTTTATGAAAAAAATAAAATAC-GAAAAG
1 AAATAAAATA-CGAAAAAATATATTTATGAAAAAAATAAAAT-CTGAAAAG
* ** *
1468813 AAATAAAATACGAAAATAGTATATTTACTGAAAGTAATAAAATCTGAAAAT
1 AAATAAAATACGAAAA-AATATATTTA-TGAAAAAAATAAAATCTGAAAAG
1468864 AAGA-AAAATACGAAAAA
1 AA-ATAAAATACGAAAAA
1468881 GGGCCAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
49 6 0.10
50 20 0.34
51 32 0.54
52 1 0.02
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.21
Consensus pattern (49 bp):
AAATAAAATACGAAAAAATATATTTATGAAAAAAATAAAATCTGAAAAG
Found at i:1469774 original size:16 final size:16
Alignment explanation
Indices: 1469749--1469802 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
1469739 TTGATACAAC
1469749 TTTAATAACAATTAAT
1 TTTAATAACAATTAAT
*
1469765 TTTGATAACAATTAAT
1 TTTAATAACAATTAAT
*
1469781 TTTAATAACAATTAGT
1 TTTAATAACAATTAAT
1469797 TTTAAT
1 TTTAAT
1469803 TTTAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (16 bp):
TTTAATAACAATTAAT
Found at i:1469785 original size:22 final size:23
Alignment explanation
Indices: 1469776--1469837 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
1469766 TTGATAACAA
* *
1469776 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
1469798 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
1469821 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
1469838 AGGGCCGGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:1472247 original size:11 final size:11
Alignment explanation
Indices: 1472231--1472287 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
1472221 TTTTAAATGG
1472231 AAAAAAATTAT
1 AAAAAAATTAT
1472242 AAAAAAATTA-
1 AAAAAAATTAT
*
1472252 AAAAATTATT-T
1 AAAAA-AATTAT
*
1472263 TAAAAAATTAT
1 AAAAAAATTAT
1472274 AAAAAAATT-T
1 AAAAAAATTAT
1472284 AAAA
1 AAAA
1472288 TAGGATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 13 0.33
11 26 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:1472265 original size:13 final size:13
Alignment explanation
Indices: 1472249--1472273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1472239 TATAAAAAAA
1472249 TTAAAAAATTATT
1 TTAAAAAATTATT
1472262 TTAAAAAATTAT
1 TTAAAAAATTAT
1472274 AAAAAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAAAATTATT
Found at i:1476020 original size:28 final size:27
Alignment explanation
Indices: 1475984--1476066 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
1475974 TTAAAGTATA
1475984 AGGATTAAATCTCAAATTTAAGCATATT
1 AGGATTAAAT-TCAAATTTAAGCATATT
* * * *
1476012 AGGACTAAAATTGAAATTAAAG--TATA
1 AGGA-TTAAATTCAAATTTAAGCATATT
*
1476038 AGAATTAAATTTCAAATTTAAGCATATT
1 AGGATTAAA-TTCAAATTTAAGCATATT
1476066 A
1 A
1476067 AAAGGACTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
25 4 0.10
26 16 0.38
28 17 0.40
29 5 0.12
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (27 bp):
AGGATTAAATTCAAATTTAAGCATATT
Found at i:1476033 original size:54 final size:55
Alignment explanation
Indices: 1475970--1476086 Score: 182
Period size: 54 Copynumber: 2.1 Consensus size: 55
1475960 AATGATGCTA
*
1475970 GAAATTAAAGTATAAGGATTAAATCTCAAATTTAAGCATATT-AGGACTAAAATT
1 GAAATTAAAGTATAAGAATTAAATCTCAAATTTAAGCATATTAAGGACTAAAATT
* *
1476024 GAAATTAAAGTATAAGAATTAAATTTCAAATTTAAGCATATTAAAAGGACTAAAGTT
1 GAAATTAAAGTATAAGAATTAAATCTCAAATTTAAGCATATT--AAGGACTAAAATT
1476081 GAAATT
1 GAAATT
1476087 TAACCAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 40 0.70
57 17 0.30
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.32
Consensus pattern (55 bp):
GAAATTAAAGTATAAGAATTAAATCTCAAATTTAAGCATATTAAGGACTAAAATT
Found at i:1476054 original size:26 final size:26
Alignment explanation
Indices: 1475971--1476055 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
1475961 ATGATGCTAG
*
1475971 AAATTAAAGTATAAGGATTAAATCTC
1 AAATTAAAGTATAAGGATTAAATTTC
* * * * *
1475997 AAATTTAAGCATATTAGGACTAAAATTG
1 AAATTAAAG--TATAAGGATTAAATTTC
*
1476025 AAATTAAAGTATAAGAATTAAATTTC
1 AAATTAAAGTATAAGGATTAAATTTC
1476051 AAATT
1 AAATT
1476056 TAAGCATATT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
26 25 0.56
28 20 0.44
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.33
Consensus pattern (26 bp):
AAATTAAAGTATAAGGATTAAATTTC
Found at i:1477200 original size:14 final size:14
Alignment explanation
Indices: 1477181--1477209 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1477171 ATAAAATACT
1477181 ATAAAATACTATAA
1 ATAAAATACTATAA
1477195 ATAAAATACTATAA
1 ATAAAATACTATAA
1477209 A
1 A
1477210 GTTTACTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAATACTATAA
Found at i:1477209 original size:10 final size:10
Alignment explanation
Indices: 1477171--1477195 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1477161 TTTAAATAAA
1477171 ATAAAATACT
1 ATAAAATACT
1477181 ATAAAATACT
1 ATAAAATACT
1477191 ATAAA
1 ATAAA
1477196 TAAAATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAAATACT
Found at i:1477219 original size:29 final size:28
Alignment explanation
Indices: 1477134--1477227 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 28
1477124 ACTATCAAAT
*
1477134 CTATATAAT-AAATACTATAAAGTTTATT
1 CTATA-AATAAAATACTATAAAGTTTATA
*
1477162 TTAAATAAAATAAAATACTATAAA----ATA
1 CT--AT-AAATAAAATACTATAAAGTTTATA
1477189 CTATAAATAAAATACTATAAAGTTTACTA
1 CTATAAATAAAATACTATAAAGTTTA-TA
1477218 CTATAAATAA
1 CTATAAATAA
1477228 GTGAAAACTT
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
24 17 0.31
25 2 0.04
27 3 0.06
28 2 0.04
29 12 0.22
30 5 0.09
31 13 0.24
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.35
Consensus pattern (28 bp):
CTATAAATAAAATACTATAAAGTTTATA
Found at i:1486459 original size:28 final size:27
Alignment explanation
Indices: 1486397--1486459 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
1486387 TATTCTTTAA
*
1486397 TTCTTTTATTTTTCTCTTTTTAAATTTT
1 TTCTTCTATTTTTCTCTTTTT-AATTTT
* *
1486425 TTTTTCTATTTTTCGTCTTTTT-CTTTCT
1 TTCTTCTATTTTTC-TCTTTTTAATTT-T
1486453 TTCTTCT
1 TTCTTCT
1486460 TCTAGCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 3 0.10
28 19 0.66
29 7 0.24
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.75
Consensus pattern (27 bp):
TTCTTCTATTTTTCTCTTTTTAATTTT
Found at i:1491937 original size:29 final size:29
Alignment explanation
Indices: 1491895--1491952 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1491885 TGTTTGGATG
1491895 TATGTGGGCAAGACAACCTATGAACTATC
1 TATGTGGGCAAGACAACCTATGAACTATC
1491924 TATGTGGGCAAGACAACCTATGAACTATC
1 TATGTGGGCAAGACAACCTATGAACTATC
1491953 CCTTGAGTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (29 bp):
TATGTGGGCAAGACAACCTATGAACTATC
Found at i:1512319 original size:12 final size:12
Alignment explanation
Indices: 1512284--1512324 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1512274 CAAATAATTT
1512284 AAAAATTATAAA
1 AAAAATTATAAA
*
1512296 ACAAA-TATTAAA
1 AAAAATTA-TAAA
1512308 AAAAATTATAAA
1 AAAAATTATAAA
1512320 AAAAA
1 AAAAA
1512325 ACATAAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:1512331 original size:24 final size:24
Alignment explanation
Indices: 1512284--1512331 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1512274 CAAATAATTT
* *
1512284 AAAAATTATAAAACAAATATTAAA
1 AAAAATTATAAAACAAAAAATAAA
1512308 AAAAATTATAAAA-AAAAACATAAA
1 AAAAATTATAAAACAAAAA-ATAAA
1512332 GTACACGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (24 bp):
AAAAATTATAAAACAAAAAATAAA
Found at i:1524847 original size:63 final size:63
Alignment explanation
Indices: 1524764--1524891 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
1524754 TCCTCCATCT
* * *
1524764 AAACCCATCCTTAACATATAATTCACCGTTAATCTAAACTCACCTTTTACCCAAATCTTGAAG
1 AAACACATCCTTAACATATAATTCACCGTCAATCTAAACTCACCCTTTACCCAAATCTTGAAG
*
1524827 AAACACATCCTTAACATATAATTCGCCGTCAATCTAAACTCACCCTTTACCCAAATCTTGAAG
1 AAACACATCCTTAACATATAATTCACCGTCAATCTAAACTCACCCTTTACCCAAATCTTGAAG
1524890 AA
1 AA
1524892 GTAACCCAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.38, C:0.29, G:0.05, T:0.28
Consensus pattern (63 bp):
AAACACATCCTTAACATATAATTCACCGTCAATCTAAACTCACCCTTTACCCAAATCTTGAAG
Found at i:1524900 original size:20 final size:20
Alignment explanation
Indices: 1524875--1524915 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1524865 CTCACCCTTT
1524875 ACCCAAATCTTGAAGAAGTA
1 ACCCAAATCTTGAAGAAGTA
*
1524895 ACCCAAATGTTGAAGAAGTA
1 ACCCAAATCTTGAAGAAGTA
1524915 A
1 A
1524916 AAGAGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (20 bp):
ACCCAAATCTTGAAGAAGTA
Found at i:1526842 original size:2 final size:2
Alignment explanation
Indices: 1526835--1526859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1526825 TATTAATGTT
1526835 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 T
1526860 TTTTTTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1527206 original size:31 final size:31
Alignment explanation
Indices: 1527171--1527232 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1527161 GGTTAAGAAT
*
1527171 AAAATTT-TACCAACTTTTAAGGGACCTAAAA
1 AAAATTTCT-CCAACTTTTAAGGAACCTAAAA
1527202 AAAATTTCTCCAACTTTTAAGGAACCTAAAA
1 AAAATTTCTCCAACTTTTAAGGAACCTAAAA
1527233 CCTCATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (31 bp):
AAAATTTCTCCAACTTTTAAGGAACCTAAAA
Found at i:1527518 original size:17 final size:20
Alignment explanation
Indices: 1527496--1527534 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
1527486 AATAAAAAAG
1527496 AAAAAAAT-T-AAT-TTAAA
1 AAAAAAATGTAAATGTTAAA
1527513 AAAAAAATGTAAATGTTAAA
1 AAAAAAATGTAAATGTTAAA
1527533 AA
1 AA
1527535 CTAAATTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 3 0.16
20 7 0.37
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAAAAAATGTAAATGTTAAA
Found at i:1528100 original size:11 final size:11
Alignment explanation
Indices: 1528081--1528114 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
1528071 GGTGAGATTA
*
1528081 GATATTGTAGC
1 GATACTGTAGC
1528092 GATACTGTAGC
1 GATACTGTAGC
1528103 GATACTGTAGC
1 GATACTGTAGC
1528114 G
1 G
1528115 TGAGACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (11 bp):
GATACTGTAGC
Found at i:1540222 original size:31 final size:33
Alignment explanation
Indices: 1540158--1540232 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 33
1540148 ATTTTAAATT
1540158 AATAA-AAATAAAATTATATATTAATCCCCTAAA
1 AATAATAAA-AAAATTATATATTAATCCCCTAAA
**
1540191 AATAATAAAAAAATTA-AT-TTAATCCTTTAAA
1 AATAATAAAAAAATTATATATTAATCCCCTAAA
*
1540222 AATTATAAAAA
1 AATAATAAAAA
1540233 TATAAGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 21 0.55
32 2 0.05
33 12 0.32
34 3 0.08
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (33 bp):
AATAATAAAAAAATTATATATTAATCCCCTAAA
Found at i:1541689 original size:23 final size:24
Alignment explanation
Indices: 1541663--1541709 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1541653 GCAAGGCTCG
1541663 ATTCTAAAT-GATCGCATAATCTT
1 ATTCTAAATGGATCGCATAATCTT
1541686 ATTCTAAATGGATCGCATAATCTT
1 ATTCTAAATGGATCGCATAATCTT
1541710 TTATATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (24 bp):
ATTCTAAATGGATCGCATAATCTT
Found at i:1542328 original size:30 final size:30
Alignment explanation
Indices: 1542228--1542347 Score: 89
Period size: 31 Copynumber: 3.9 Consensus size: 30
1542218 GGCATCAAGT
* * *
1542228 ATTCATATTTGCATTATCATACCCTATAATC
1 ATTCACATTTACA-TATCATACCCTGTAATC
* * * *
1542259 ATTCATATTCACATATTCATATCATGTAATC
1 ATTCACATTTACATA-TCATACCCTGTAATC
* *
1542290 ATTTACATTTACCTATCATACCCTGTAATC
1 ATTCACATTTACATATCATACCCTGTAATC
** *
1542320 GA-TCACATTTGTATTTTCATACCCTGTA
1 -ATTCACATTTACA-TATCATACCCTGTA
1542348 TACTGTACGA
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
30 22 0.31
31 48 0.69
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (30 bp):
ATTCACATTTACATATCATACCCTGTAATC
Found at i:1554154 original size:2 final size:2
Alignment explanation
Indices: 1554147--1554187 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1554137 ATTGTTACTC
1554147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1554188 TANNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1559515 original size:19 final size:21
Alignment explanation
Indices: 1559477--1559515 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1559467 GTAAATTACA
1559477 TTTAAGGTTATTATTAGAAAT
1 TTTAAGGTTATTATTAGAAAT
*
1559498 TTTAA-GTTA-TATTCGAAA
1 TTTAAGGTTATTATTAGAAA
1559516 ATTCTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTATTATTAGAAAT
Found at i:1566331 original size:15 final size:15
Alignment explanation
Indices: 1566294--1566325 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1566284 TCAAATTTTT
1566294 ACTGATTTTATTACC
1 ACTGATTTTATTACC
1566309 ACTGATTTTATTACC
1 ACTGATTTTATTACC
1566324 AC
1 AC
1566326 ATATTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (15 bp):
ACTGATTTTATTACC
Found at i:1570563 original size:25 final size:25
Alignment explanation
Indices: 1570535--1570592 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1570525 AAAATAATTT
*
1570535 TTTAAAATCTAAAAAT-ATATAAAAA
1 TTTAAAATCTAAAAATCACA-AAAAA
*
1570560 TTTAAAATTTAAAAATGCACAAAAAA
1 TTTAAAATCTAAAAAT-CACAAAAAA
1570586 TTTAAAA
1 TTTAAAA
1570593 AAGAAGTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.52
26 12 0.41
27 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (25 bp):
TTTAAAATCTAAAAATCACAAAAAA
Found at i:1571657 original size:15 final size:16
Alignment explanation
Indices: 1571637--1571673 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1571627 ACAAAATCAA
1571637 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
1571652 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
1571668 ATAAAA
1 ATAAAA
1571674 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:1571851 original size:60 final size:60
Alignment explanation
Indices: 1571787--1571906 Score: 179
Period size: 60 Copynumber: 2.0 Consensus size: 60
1571777 AATACTAAAC
* * * * *
1571787 TAAACACAACAATTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTA
1 TAAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTA
1571847 TAAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
1 TAAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
1571907 CAATATTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (60 bp):
TAAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
Found at i:1571931 original size:23 final size:23
Alignment explanation
Indices: 1571903--1572031 Score: 214
Period size: 23 Copynumber: 5.8 Consensus size: 23
1571893 TTATAAAATA
1571903 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
1571926 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
*
1571949 ATTACAATATCCATAC--A-AA-
1 ATTACAATATTCATACAAACAAT
1571968 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
1571991 ATTACAATATTCATACAAACAAT
1 ATTACAATATTCATACAAACAAT
1572014 ATTAC-ATATTCATACAAA
1 ATTACAATATTCATACAAA
1572032 ATTACAAAAT
Statistics
Matches: 100, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
19 15 0.15
20 2 0.02
21 2 0.02
22 15 0.15
23 66 0.66
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTACAATATTCATACAAACAAT
Found at i:1571978 original size:65 final size:64
Alignment explanation
Indices: 1571902--1572038 Score: 256
Period size: 65 Copynumber: 2.1 Consensus size: 64
1571892 ATTATAAAAT
1571902 AATTACAATATTCATACAAACAATATTACAATATTCATACAAACAATATTACAATATCCATACAA
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAACAATATTAC-ATATCCATACAA
*
1571967 AATTACAATATTCATACAAACAATATTACAATATTCATACAAACAATATTACATATTCATACAA
1 AATTACAATATTCATACAAACAATATTACAATATTCATACAAACAATATTACATATCCATACAA
1572031 AATTACAA
1 AATTACAA
1572039 AATTACAAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 19 0.27
65 52 0.73
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.30
Consensus pattern (64 bp):
AATTACAATATTCATACAAACAATATTACAATATTCATACAAACAATATTACATATCCATACAA
Found at i:1571985 original size:42 final size:41
Alignment explanation
Indices: 1571906--1572066 Score: 162
Period size: 42 Copynumber: 4.0 Consensus size: 41
1571896 TAAAATAATT
* *
1571906 ACAATATT-C-ATA-CAAACAATATTACAATATTCATACAA
1 ACAATATTACAATATCATACAAAATTACAATATTCATACAA
1571944 ACAATATTACAATATCCATACAAAATTACAATATTCATACAA
1 ACAATATTACAATAT-CATACAAAATTACAATATTCATACAA
1571986 ACAATATTACAATATTCATACAAACAATATTAC-ATATTCATAC--
1 ACAATATTACAATA-TCATAC--A-AA-ATTACAATATTCATACAA
* *
1572029 A-AA-ATTACAAAAT--TACAAAATTACAAAATTCATACAA
1 ACAATATTACAATATCATACAAAATTACAATATTCATACAA
1572066 A
1 A
1572067 ATACTAATCC
Statistics
Matches: 107, Mismatches: 4, Indels: 25
0.79 0.03 0.18
Matches are distributed among these distances:
34 5 0.05
35 11 0.10
36 1 0.01
37 1 0.01
38 11 0.10
39 1 0.01
40 4 0.04
41 8 0.07
42 45 0.42
43 2 0.02
44 1 0.01
45 12 0.11
46 5 0.05
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (41 bp):
ACAATATTACAATATCATACAAAATTACAATATTCATACAA
Found at i:1572055 original size:8 final size:8
Alignment explanation
Indices: 1572026--1572058 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
1572016 TACATATTCA
1572026 TACAAAAT
1 TACAAAAT
1572034 TACAAAAT
1 TACAAAAT
1572042 TACAAAAT
1 TACAAAAT
1572050 TACAAAAT
1 TACAAAAT
1572058 T
1 T
1572059 CATACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (8 bp):
TACAAAAT
Found at i:1572126 original size:80 final size:80
Alignment explanation
Indices: 1572042--1572464 Score: 571
Period size: 80 Copynumber: 5.1 Consensus size: 80
1572032 ATTACAAAAT
* *
1572042 TACAAAATTACAAAATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
1572107 TAATTACAATATTCA
66 TAATTACAATATTCA
* *
1572122 TACAACATTATAATATTCATACAAAATACTAATTC-AAAACTATAAATACAAAATTAATTATAAA
1 TACAAAATTACAATATTCATACAAAATACTAA-TCAAAAACTATAAATACAAAATTAATTATAAA
1572186 ATAATTACAATATTCA
65 ATAATTACAATATTCA
* * *
1572202 TACAACATTATAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAACTATAAATATTG
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAA-T-T--A-ATTA
* *
1572267 TAATTACA-AAATACAAAATTCA
61 TAA--A-ATAATTACAATATTCA
*
1572289 TACAAAATTACAAAATTACAATATTCATACAAAATACTAATCAAAAAATATAAATACAAAATTAA
1 T--------ACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAA
*
1572354 TTATAAAATAATTAAAATATTCA
58 TTATAAAATAATTACAATATTCA
*
1572377 TACAAAATTACAATATTCATACAAAATACTAATAAAAAACTATAAATACAAAATTAATTATAAAA
1 TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
1572442 TAATTACAATATTCA
66 TAATTACAATATTCA
1572457 TACAAAAT
1 TACAAAAT
1572465 ACTAATAAAA
Statistics
Matches: 308, Mismatches: 16, Indels: 38
0.85 0.04 0.10
Matches are distributed among these distances:
79 2 0.01
80 208 0.68
81 3 0.01
82 1 0.00
84 1 0.00
85 6 0.02
87 15 0.05
88 14 0.05
90 6 0.02
91 1 0.00
93 1 0.00
94 1 0.00
95 49 0.16
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (80 bp):
TACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAA
TAATTACAATATTCA
Done.