Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:296224 original size:23 final size:24
Alignment explanation
Indices: 296193--296238 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
296183 TTACGGGTAT
296193 ATTTCTATTCGAATTATCAATTAG
1 ATTTCTATTCGAATTATCAATTAG
** *
296217 ATTT-TATTTTAATTATTAATTA
1 ATTTCTATTCGAATTATCAATTA
296239 AAAAATAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTCTATTCGAATTATCAATTAG
Found at i:301429 original size:3 final size:3
Alignment explanation
Indices: 301421--301473 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
301411 TTTCTTTCCA
301421 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
301469 ATT AT
1 ATT AT
301474 CATATTTGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:306994 original size:2 final size:2
Alignment explanation
Indices: 306987--307018 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
306977 CCTGTCTTCT
306987 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
307019 TGAGTGAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:309402 original size:3 final size:3
Alignment explanation
Indices: 309394--309421 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
309384 AACCAGTTTT
309394 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
309422 TATCTGGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:310636 original size:14 final size:15
Alignment explanation
Indices: 310617--310645 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
310607 GAAAATTAAA
310617 GGGT-GGGGGTGGGG
1 GGGTGGGGGGTGGGG
310631 GGGTGGGGGGTGGGG
1 GGGTGGGGGGTGGGG
310646 CAAATTTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.00, C:0.00, G:0.86, T:0.14
Consensus pattern (15 bp):
GGGTGGGGGGTGGGG
Found at i:320762 original size:3 final size:3
Alignment explanation
Indices: 320756--320799 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
320746 ATCATCATCT
* * * *
320756 TCC TCC TCC TCC TCT TCT TCA TCT TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
320800 ATAATCTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.57, G:0.00, T:0.41
Consensus pattern (3 bp):
TCC
Found at i:320801 original size:24 final size:24
Alignment explanation
Indices: 320741--320793 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
320731 AGGAGTGAAT
320741 TCCTCATCATCATCTTCCTCCTCC
1 TCCTCATCATCATCTTCCTCCTCC
* *
320765 TCCTCTTCTTCATCTTCCTCCTCC
1 TCCTCATCATCATCTTCCTCCTCC
320789 TCCTC
1 TCCTC
320794 CTCCTCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.51, G:0.00, T:0.42
Consensus pattern (24 bp):
TCCTCATCATCATCTTCCTCCTCC
Found at i:320972 original size:159 final size:161
Alignment explanation
Indices: 320777--321294 Score: 452
Period size: 159 Copynumber: 3.1 Consensus size: 161
320767 CTCTTCTTCA
* * *
320777 TCTTCCTCCTCCTCCTCCTCCTCATAATCTGCATCTTCCTCTTCTTCATCGGATACAG-TTTTCT
1 TCTTCCTCCTCCTCCTCCTCCTCATAA----CATCTTCCCCTTCTTCATCAGATAC-GCTTTTCC
* * *
320841 GCTTTAGCAGTTTTCTATCAACAATATTCCTCTCCCTTG-CTGAAGACATCTGTTCCGCTTTCAA
61 ACTTTAGCAATTTTCTATCAACAATATTCCTCTCCCTTGTC-AAAGACATCTGTTCCGCTTTCAA
* * **
320905 CCTAACAGA-CTTTCTCATCTCTCTCCCTTCCTTGTCC
125 CCTAACA-ACCCTCCTCATCTCTCTCCCTTCCTCCTCC
*
320942 TCTTCATCCTCCTCCTCCTCCTCAT-A-ATCTTCCCCTTCTTCATCAGATACGCTTTTCCACTTT
1 TCTTCCTCCTCCTCCTCCTCCTCATAACATCTTCCCCTTCTTCATCAGATACGCTTTTCCACTTT
* *
321005 AGCAATTTTCTATCAACAATCTTCCTCTCCCTTGTCAAAGACATCTGTTCTGCTTTCAACCTAAC
66 AGCAATTTTCTATCAACAATATTCCTCTCCCTTGTCAAAGACATCTGTTCCGCTTTCAACCTAAC
* *
321070 AACCCTCCTCATCTCTTTCTCTTCCTCCTCC
131 AACCCTCCTCATCTCTCTCCCTTCCTCCTCC
* * * *
321101 TCCTCCTCCTCCTCCTCATCATCATCATCATCATAATCCGCATCTTCCTCGTCTTCATCTGATAC
1 T-CT--TCCTCCTCCTC--C-TC--C-TCCTCATAA----CATCTTCCCCTTCTTCATCAGATAC
* ** * * * * * * * * * **
321166 ACTTTTCGGCTTCAGCAATTTCCTATCCACAATCTTCCTATCCCTTGCCGAAGACTTCTGCTCTA
53 GCTTTTCCACTTTAGCAATTTTCTATCAACAATATTCCTCTCCCTTGTCAAAGACATCTGTTCCG
* * * *
321231 CTTTCAACCTAACAACCTTCCTCATCTCTTTGTCTTTCTCTTCCTCC
118 CTTTCAACCTAACAACCCTCCTCATCTCTCT-CCCTTC-C-TCCTCC
*
321278 TCTTCCTCATCCTCCTC
1 TCTTCCTCCTCCTCCTC
321295 ATTTAAAAAA
Statistics
Matches: 295, Mismatches: 37, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
158 2 0.01
159 114 0.39
160 3 0.01
162 10 0.03
164 2 0.01
165 26 0.09
167 1 0.00
168 6 0.02
169 1 0.00
171 2 0.01
172 1 0.00
174 114 0.39
175 3 0.01
176 3 0.01
177 7 0.02
ACGTcount: A:0.17, C:0.38, G:0.06, T:0.38
Consensus pattern (161 bp):
TCTTCCTCCTCCTCCTCCTCCTCATAACATCTTCCCCTTCTTCATCAGATACGCTTTTCCACTTT
AGCAATTTTCTATCAACAATATTCCTCTCCCTTGTCAAAGACATCTGTTCCGCTTTCAACCTAAC
AACCCTCCTCATCTCTCTCCCTTCCTCCTCC
Found at i:321098 original size:3 final size:3
Alignment explanation
Indices: 321092--321117 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
321082 CTCTTTCTCT
321092 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
321118 ATCATCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:321258 original size:174 final size:174
Alignment explanation
Indices: 320968--321296 Score: 460
Period size: 174 Copynumber: 1.9 Consensus size: 174
320958 CCTCCTCATA
* * * * *
320968 ATCTTCCCCTTCTTCATCAGATACGCTTTTCCACTTTAGCAATTTTCTATCAACAATCTTCCTCT
1 ATCTTCCCCGTCTTCATCAGATACACTTTTCCACTTCAGCAATTTCCTATCAACAATCTTCCTAT
* * *
321033 CCCTTGTCAAAGACATCTGTTCTGCTTTCAACCTAACAACCCTCCTCATCTCTTTCTCTTCCTCC
66 CCCTTGCCAAAGACATCTGCTCTACTTTCAACCTAACAACCCTCCTCATCTCTTTCTCTTCCTCC
*
321098 TCCTCCTCCTCCTCCTCCTCATCATCATCATCATCATAATCCGC
131 TCCTCCTCCTCCTCATCCTCATCATCATCATCATCATAATCCGC
* * ** *
321142 ATCTTCCTCGTCTTCATCTGATACACTTTTCGGCTTCAGCAATTTCCTATCCACAATCTTCCTAT
1 ATCTTCCCCGTCTTCATCAGATACACTTTTCCACTTCAGCAATTTCCTATCAACAATCTTCCTAT
* * * * * *
321207 CCCTTGCCGAAGACTTCTGCTCTACTTTCAACCTAACAACCTTCCTCATCTCTTTGTCTTTCTCT
66 CCCTTGCCAAAGACATCTGCTCTACTTTCAACCTAACAACCCTCCTCATCTCTTTCTCTTCCTCC
* *
321272 TCCTCCTCTTCCTCATCCTCCTCAT
131 TCCTCCTCCTCCTCATCCTCATCAT
321297 TTAAAAAACT
Statistics
Matches: 133, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
174 133 1.00
ACGTcount: A:0.18, C:0.38, G:0.05, T:0.38
Consensus pattern (174 bp):
ATCTTCCCCGTCTTCATCAGATACACTTTTCCACTTCAGCAATTTCCTATCAACAATCTTCCTAT
CCCTTGCCAAAGACATCTGCTCTACTTTCAACCTAACAACCCTCCTCATCTCTTTCTCTTCCTCC
TCCTCCTCCTCCTCATCCTCATCATCATCATCATCATAATCCGC
Found at i:322123 original size:2 final size:2
Alignment explanation
Indices: 322116--322145 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
322106 TGTCCGAGGA
322116 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
322146 AATTTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:323075 original size:19 final size:19
Alignment explanation
Indices: 323051--323090 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
323041 ATCTAAATAA
323051 TAAATATAAATATTATATT
1 TAAATATAAATATTATATT
* * *
323070 TAAATATTATTTTTATATT
1 TAAATATAAATATTATATT
323089 TA
1 TA
323091 TTAAATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAAATATAAATATTATATT
Found at i:323122 original size:27 final size:27
Alignment explanation
Indices: 323078--323131 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
323068 TTTAAATATT
*
323078 ATTTTTATATTTATT-AAATATATTAAA
1 ATTTTTATATATATTAAAAT-TATTAAA
323105 ATTTTTAT-TATATATAAAATTATTAAA
1 ATTTTTATATATAT-TAAAATTATTAAA
323132 TCTATATCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTTTATATATATTAAAATTATTAAA
Found at i:323187 original size:2 final size:2
Alignment explanation
Indices: 323182--323209 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
323172 TTTTTGAGGC
323182 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
323210 CCTTTCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323791 original size:3 final size:3
Alignment explanation
Indices: 323785--323829 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
323775 CCATATTATT
323785 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
323830 TACATAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:324909 original size:2 final size:2
Alignment explanation
Indices: 324902--324946 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
324892 AGCCAGCGTT
324902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
324944 TA T
1 TA T
324947 TTAAAAGCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:327779 original size:2 final size:2
Alignment explanation
Indices: 327774--327806 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
327764 ACACACACAC
327774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
327807 ACTAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:328026 original size:26 final size:27
Alignment explanation
Indices: 327973--328044 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
327963 TTATATTATT
*
327973 TTATATA-TTATAAGTATATTTAAAATA
1 TTATATATTTAT-ATTATATTTAAAATA
*
328000 TTATATATTTATATTA-ATTTAATATA
1 TTATATATTTATATTATATTTAAAATA
*
328026 TTA-ATAATTTGTATTATAT
1 TTATAT-ATTTATATTATAT
328045 ATATTTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.05
26 21 0.54
27 12 0.31
28 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
TTATATATTTATATTATATTTAAAATA
Found at i:329060 original size:29 final size:28
Alignment explanation
Indices: 329027--329081 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
329017 TTTTTTTAAA
*
329027 AAAATTTATAAAAATAATGTATTAAATAT
1 AAAATTTATAAAAATAAT-AATTAAATAT
* *
329056 AAAATTTTTTAAAATAATAATTAAAT
1 AAAATTTATAAAAATAATAATTAAAT
329082 TCTCATTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
AAAATTTATAAAAATAATAATTAAATAT
Found at i:331314 original size:12 final size:13
Alignment explanation
Indices: 331286--331316 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
331276 ACAAAATTAG
331286 AAAATAGAAAAGA
1 AAAATAGAAAAGA
331299 AAAATAG-AAAGA
1 AAAATAGAAAAGA
331311 AAAATA
1 AAAATA
331317 AAACAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAATAGAAAAGA
Found at i:339315 original size:15 final size:14
Alignment explanation
Indices: 339270--339313 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
339260 ATAATAGTTT
339270 AATAATTTATTTAA
1 AATAATTTATTTAA
339284 AATAATATTATTT-A
1 AATAAT-TTATTTAA
339298 AATAATTTATTTAA
1 AATAATTTATTTAA
339312 AA
1 AA
339314 ATCACCGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.21
14 16 0.57
15 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAATTTATTTAA
Found at i:342416 original size:2 final size:2
Alignment explanation
Indices: 342409--342440 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
342399 TGCCCTTTTA
342409 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
342441 TATTTTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344159 original size:33 final size:33
Alignment explanation
Indices: 344086--344160 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
344076 AGCAGTCCGA
* *
344086 CTTTCAGGTTCTGAAGTTGCAGGCTTGACCCAG
1 CTTTCAGGTTCTGAAGGTGCAGGCTGGACCCAG
** * *
344119 CGATCAGGTTCTGAAGGTGGA-GCTGGACCAGAG
1 CTTTCAGGTTCTGAAGGTGCAGGCTGGACC-CAG
344152 CTTTCAGGT
1 CTTTCAGGT
344161 CTTTCACGCC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.27
Consensus pattern (33 bp):
CTTTCAGGTTCTGAAGGTGCAGGCTGGACCCAG
Found at i:360282 original size:17 final size:17
Alignment explanation
Indices: 360214--360282 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
360204 CCTTCTAGTT
*
360214 TTTTAATAAATTTATAA
1 TTTTAATAAATTAATAA
*
360231 TTTATATTAAATT-AT-A
1 TTT-TAATAAATTAATAA
360247 -TTTAA-AATATTAA-ATA
1 TTTTAATAA-ATTAATA-A
360263 TTTTAATAAATTAATAA
1 TTTTAATAAATTAATAA
360280 TTT
1 TTT
360283 ATATTAAGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 3 0.07
16 2 0.05
17 19 0.45
18 11 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATAAATTAATAA
Found at i:360623 original size:16 final size:17
Alignment explanation
Indices: 360584--360638 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
360574 TGGATTAATT
* *
360584 ATATTAAAAATAATGTTA
1 ATATTAAATA-AATATTA
360602 ATATTAAATAAATATTA
1 ATATTAAATAAATATTA
*
360619 A-ATTATATAAATATTTA
1 ATATTAAATAAATA-TTA
360636 ATA
1 ATA
360639 AAAATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 11 0.34
17 11 0.34
18 10 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATATTAAATAAATATTA
Found at i:361156 original size:16 final size:16
Alignment explanation
Indices: 361135--361168 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
361125 ATATAACTTT
* *
361135 AATTTTAATTTTAATA
1 AATTTTAAATATAATA
361151 AATTTTAAATATAATA
1 AATTTTAAATATAATA
361167 AA
1 AA
361169 AATTTAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTTAAATATAATA
Found at i:363918 original size:16 final size:17
Alignment explanation
Indices: 363889--363920 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
363879 TTTAATTTTT
363889 TTTAAAAAATTTATATA
1 TTTAAAAAATTTATATA
363906 TTTAAAAAA-TTATAT
1 TTTAAAAAATTTATAT
363921 CTCTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAAAAATTTATATA
Found at i:365749 original size:27 final size:27
Alignment explanation
Indices: 365719--365772 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
365709 CTTAACCTTA
365719 GCTGAAACACTTTCTGAAAGTACAGTT
1 GCTGAAACACTTTCTGAAAGTACAGTT
*
365746 GCTGAAATACTTTCTGAAAGTACAGTT
1 GCTGAAACACTTTCTGAAAGTACAGTT
365773 TAATTCAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (27 bp):
GCTGAAACACTTTCTGAAAGTACAGTT
Found at i:365752 original size:15 final size:15
Alignment explanation
Indices: 365732--365772 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
365722 GAAACACTTT
365732 CTGAAAGTACAGTTG
1 CTGAAAGTACAGTTG
*
365747 CTGAAA-TAC--TTT
1 CTGAAAGTACAGTTG
365759 CTGAAAGTACAGTT
1 CTGAAAGTACAGTT
365773 TAATTCAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 8 0.36
13 3 0.14
14 3 0.14
15 8 0.36
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (15 bp):
CTGAAAGTACAGTTG
Found at i:366402 original size:15 final size:15
Alignment explanation
Indices: 366382--366410 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
366372 GATCTTTTTC
366382 ATTATTTTTTAATTG
1 ATTATTTTTTAATTG
366397 ATTATTTTTTAATT
1 ATTATTTTTTAATT
366411 TTTTTAATTA
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATTATTTTTTAATTG
Found at i:366537 original size:16 final size:16
Alignment explanation
Indices: 366516--366547 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
366506 AGACTAATCC
*
366516 CATAAATTGAATTATT
1 CATAAATTGAACTATT
366532 CATAAATTGAACTATT
1 CATAAATTGAACTATT
366548 TATTTAACTC
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:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
CATAAATTGAACTATT
Found at i:368603 original size:16 final size:14
Alignment explanation
Indices: 368582--368629 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 14
368572 TTGTATTTCC
368582 TTAATTATTATATAAA
1 TTAATTA-TAT-TAAA
368598 TTAATTATATTAAA
1 TTAATTATATTAAA
368612 TTTTAATTATATTAAA
1 --TTAATTATATTAAA
368628 TT
1 TT
368630 TTAAAATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.20
15 3 0.10
16 21 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAATTATATTAAA
Found at i:368630 original size:16 final size:16
Alignment explanation
Indices: 368598--368633 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
368588 ATTATATAAA
368598 TTAATTATATTAAATT
1 TTAATTATATTAAATT
368614 TTAATTATATTAAATT
1 TTAATTATATTAAATT
368630 TTAA
1 TTAA
368634 AATGTTCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTATATTAAATT
Found at i:369043 original size:3 final size:3
Alignment explanation
Indices: 369037--369066 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
369027 GATGATGATG
369037 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
369067 CTGAGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:370458 original size:62 final size:60
Alignment explanation
Indices: 370319--370459 Score: 148
Period size: 62 Copynumber: 2.3 Consensus size: 60
370309 CATAAAAATT
* *
370319 ATTAAATA-T-ATATTT-TTTTAAAAAATAATTTTATAAATTAATTAAATTAAATTTAAA
1 ATTAAATATTAATATTTATTTTAAAAAATAATTTTAAAAATAAATTAAATTAAATTTAAA
* * *
370376 AATAAAAATTAATCATTTTATTTT-AAAAATAATTATTAAAACATAATATTTAA-TAAATTTAAA
1 ATTAAATATTAAT-A-TTTATTTTAAAAAATAATT-TTAAAA-ATAA-ATTAAATTAAATTTAAA
370439 ATTTAAATATTAATATTTATT
1 A-TTAAATATTAATATTTATT
370460 ATATATTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
57 6 0.09
58 1 0.01
59 2 0.03
60 1 0.01
61 13 0.19
62 15 0.22
63 15 0.22
64 15 0.22
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (60 bp):
ATTAAATATTAATATTTATTTTAAAAAATAATTTTAAAAATAAATTAAATTAAATTTAAA
Found at i:377396 original size:2 final size:2
Alignment explanation
Indices: 377389--377414 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
377379 AGTATTTTTA
377389 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
377415 TATTTGGTTG
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:381168 original size:22 final size:19
Alignment explanation
Indices: 381137--381178 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
381127 TATTTTTATT
381137 TAAATTTAATTATAAAATATA
1 TAAATTTAA-TATAAAA-ATA
381158 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
381178 T
1 T
381179 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:381194 original size:49 final size:49
Alignment explanation
Indices: 381117--381216 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 49
381107 GAGTTTATAA
381117 AATAAAATAATATTTTTATTTAAATTTAAT-TA-TAAAATATATAAATATT
1 AATAAAATAATATTTTTATTTAAATTTAATATATTAAAATA-ATAAAT-TT
*
381166 AATATAAA-AATA-TTTT-TTTAATATTTTAATATATTTAAATAATAAATTT
1 AATA-AAATAATATTTTTATTTAA-A-TTTAATATATTAAAATAATAAATTT
381215 AA
1 AA
381217 GCTGTCAAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
47 5 0.11
48 5 0.11
49 18 0.40
50 11 0.24
51 6 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (49 bp):
AATAAAATAATATTTTTATTTAAATTTAATATATTAAAATAATAAATTT
Found at i:383752 original size:20 final size:20
Alignment explanation
Indices: 383727--383769 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
383717 CGGTTTGATT
383727 TATTCAAATTATTAATTAAA
1 TATTCAAATTATTAATTAAA
383747 TATTCAAATTATTAATTAAA
1 TATTCAAATTATTAATTAAA
383767 TAT
1 TAT
383770 GTTATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCAAATTATTAATTAAA
Found at i:384637 original size:21 final size:21
Alignment explanation
Indices: 384611--384666 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
384601 TAATAAATAA
384611 ATAAATAAATTTT-AATAATTT
1 ATAAATAAATTTTAAAT-ATTT
* *
384632 ATAAATACATATTAAATATTT
1 ATAAATAAATTTTAAATATTT
384653 A-AAATAATATTTTA
1 ATAAATAA-ATTTTA
384667 TTTATTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.17
21 21 0.72
22 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAATAAATTTTAAATATTT
Found at i:384707 original size:23 final size:23
Alignment explanation
Indices: 384647--384708 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
384637 TACATATTAA
384647 ATATT-TAA-AATAATATTTTATT
1 ATATTATAATAAT-ATATTTTATT
* **
384669 -TATTAATATTTTTATATTTTATT
1 ATATT-ATAATAATATATTTTATT
384692 ATATTATAATAATATAT
1 ATATTATAATAATATAT
384709 AAAAATTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
21 4 0.13
23 21 0.70
24 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTATAATAATATATTTTATT
Found at i:384719 original size:26 final size:24
Alignment explanation
Indices: 384688--384767 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
384678 TTTTATATTT
384688 TATTATATTATAATAATATATAAAAA
1 TATTATATT-TAATAA-ATATAAAAA
* * *
384714 TTTTATATTTATATAAATATTAATA
1 TATTATATTTA-ATAAATATAAAAA
* *
384739 TATTATATTTTATAAATTTAAAAA
1 TATTATATTTAATAAATATAAAAA
384763 TATTA
1 TATTA
384768 ATATATTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 15 0.33
25 18 0.40
26 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTATATTTAATAAATATAAAAA
Found at i:384744 original size:19 final size:19
Alignment explanation
Indices: 384704--384746 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
384694 ATTATAATAA
*
384704 TATATAAAAATTTTATATT
1 TATATAAAAATTATATATT
*
384723 TATATAAATATTA-ATATAT
1 TATATAAAAATTATATAT-T
384742 TATAT
1 TATAT
384747 TTTATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATAAAAATTATATATT
Found at i:384749 original size:32 final size:32
Alignment explanation
Indices: 384713--384814 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
384703 ATATATAAAA
384713 ATTTTATATTTATATAAATATTAATATATTAT
1 ATTTTATATTTATATAAATATTAATATATTAT
384745 ATTTTATAAATTTA-A-AAATATTAATATATT-T
1 ATTTTAT--ATTTATATAAATATTAATATATTAT
* * * *
384776 ATATCATATTTATAT-TATATTTATATATTAT
1 ATTTTATATTTATATAAATATTAATATATTAT
384807 -TTTTATAT
1 ATTTTATAT
384815 AATATTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
29 5 0.08
30 19 0.32
31 7 0.12
32 22 0.37
33 1 0.02
34 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTTTATATTTATATAAATATTAATATATTAT
Found at i:384795 original size:16 final size:16
Alignment explanation
Indices: 384769--384849 Score: 74
Period size: 16 Copynumber: 4.9 Consensus size: 16
384759 AAAATATTAA
*
384769 TATATTTATATCATATT
1 TATATTTATATTATA-T
*
384786 TATATTATATTTATATAT
1 TATATT-TATAT-TATAT
* *
384804 TATTTTTATATAATAT
1 TATATTTATATTATAT
384820 TAT-TTTATATTATAT
1 TATATTTATATTATAT
* *
384835 AATATTTATTTTATA
1 TATATTTATATTATA
384850 AAGGATTAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
15 13 0.25
16 17 0.32
17 10 0.19
18 10 0.19
19 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTTATATTATAT
Found at i:384802 original size:24 final size:24
Alignment explanation
Indices: 384766--384843 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
384756 TTAAAAATAT
*
384766 TAATATATT-TATATCATATTTATA
1 TAATAT-TTATATATTATATTTATA
* *
384790 TTATATTTATATATTATTTTTATA
1 TAATATTTATATATTATATTTATA
384814 TAATA-TTAT-T-TTATA-TTATA
1 TAATATTTATATATTATATTTATA
384834 TAATATTTAT
1 TAATATTTAT
384844 TTTATAAAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 10 0.21
21 8 0.17
22 1 0.02
23 6 0.13
24 22 0.47
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATATTTATATATTATATTTATA
Found at i:384807 original size:11 final size:11
Alignment explanation
Indices: 384771--384843 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 11
384761 AATATTAATA
384771 TATTTATATCA-
1 TATTTATAT-AT
384782 TATTTATAT-T
1 TATTTATATAT
384792 ATATTTATATAT
1 -TATTTATATAT
*
384804 TATTTTTATAT
1 TATTTATATAT
*
384815 AATATTAT-T-T
1 TAT-TTATATAT
*
384825 TATATTATATAA
1 TAT-TTATATAT
384837 TATTTAT
1 TATTTAT
384844 TTTATAAAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.16
11 36 0.71
12 7 0.14
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTATATAT
Found at i:392606 original size:28 final size:30
Alignment explanation
Indices: 392569--392635 Score: 111
Period size: 28 Copynumber: 2.3 Consensus size: 30
392559 CATTTCGTTC
*
392569 AAATTTTTATATTTTTA-TTATATTTAAAT
1 AAATTTTTATATTTTTATTTATATTAAAAT
392598 -AATTTTTATATTTTTATTTATATTAAAAT
1 AAATTTTTATATTTTTATTTATATTAAAAT
392627 AAATTTTTA
1 AAATTTTTA
392636 ATTCAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 16 0.46
29 11 0.31
30 8 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
AAATTTTTATATTTTTATTTATATTAAAAT
Found at i:392699 original size:30 final size:31
Alignment explanation
Indices: 392660--392771 Score: 113
Period size: 30 Copynumber: 3.7 Consensus size: 31
392650 TTGAATTATA
*
392660 TTAAAATTTTATTTAAATATAAATTAAA-AT
1 TTAAGATTTTATTTAAATATAAATTAAAGAT
*
392690 TTAAGATTTTATTTAAATACAAATTAAAGA-
1 TTAAGATTTTATTTAAATATAAATTAAAGAT
* * * * * *
392720 TTAATATTTTATATGAGTGTAAATTAAATAT
1 TTAAGATTTTATTTAAATATAAATTAAAGAT
* *
392751 TAAAGA-TTCATTTAAATATAA
1 TTAAGATTTTATTTAAATATAA
392772 TAAAAATAGA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
30 59 0.92
31 5 0.08
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (31 bp):
TTAAGATTTTATTTAAATATAAATTAAAGAT
Found at i:393811 original size:2 final size:2
Alignment explanation
Indices: 393806--393842 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
393796 TCTCTCCCAT
393806 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 T
393843 TGAAAATGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:395648 original size:14 final size:14
Alignment explanation
Indices: 395623--395667 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
395613 GAGAATCTTA
395623 AATTTATTAAATAT
1 AATTTATTAAATAT
395637 CAATTT-TTAAATAT
1 -AATTTATTAAATAT
395651 AATTGTA-TAAAT-T
1 AATT-TATTAAATAT
395664 AATT
1 AATT
395668 AGATTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.32
14 14 0.50
15 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (14 bp):
AATTTATTAAATAT
Found at i:395892 original size:36 final size:37
Alignment explanation
Indices: 395821--395894 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 37
395811 ATTTAAGTCG
*
395821 ATTTGAATTATAATTTATATAATAAAAAATAATTTTT
1 ATTTAAATTATAATTTATATAATAAAAAATAATTTTT
*
395858 ATTTAAATT-TAA-TTATATAAATATATAAAT-ATTTTT
1 ATTTAAATTATAATTTATAT-AATA-AAAAATAATTTTT
395894 A
1 A
395895 AAATAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (37 bp):
ATTTAAATTATAATTTATATAATAAAAAATAATTTTT
Found at i:400866 original size:3 final size:3
Alignment explanation
Indices: 400858--400886 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
400848 TGAAGGACTT
400858 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
400887 TTACAAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:403702 original size:81 final size:80
Alignment explanation
Indices: 403568--403729 Score: 279
Period size: 81 Copynumber: 2.0 Consensus size: 80
403558 AAGTAGCAGA
* *
403568 GCTACAATTAAAAAAAAAATGAAGAGAAAAGATACAATGATGAAAAACTTACATTGGTGAAGGAG
1 GCTACAATTAAAAAAAAAAAGAAGAGAAAAGATACAATGATAAAAAACTTACATTGGTGAAGGAG
*
403633 TCGGAGGGTATGCAT
66 TCGGAGGGTAGGCAT
*
403648 GCTACAATTAAAAGAAAAAAAGAAGGGAAAAGATACAATGATAAAAAACTTACATTGGTGAAGGA
1 GCTACAATTAAAA-AAAAAAAGAAGAGAAAAGATACAATGATAAAAAACTTACATTGGTGAAGGA
403713 GTCGGAGGGTAGGCAT
65 GTCGGAGGGTAGGCAT
403729 G
1 G
403730 TATGGTCCAT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 13 0.17
81 64 0.83
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.19
Consensus pattern (80 bp):
GCTACAATTAAAAAAAAAAAGAAGAGAAAAGATACAATGATAAAAAACTTACATTGGTGAAGGAG
TCGGAGGGTAGGCAT
Found at i:405993 original size:19 final size:19
Alignment explanation
Indices: 405971--406032 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
405961 TTTTTAAATA
405971 TAAATATAATATAAATTAT
1 TAAATATAATATAAATTAT
*
405990 TAAATATATTA-AAATT-T
1 TAAATATAATATAAATTAT
*
406007 TAAATATGAATGTAATATATAT
1 TAAATAT-AATATAA-AT-TAT
406029 TAAA
1 TAAA
406033 AATATGATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 8 0.23
18 7 0.20
19 12 0.34
20 2 0.06
21 1 0.03
22 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAATATAATATAAATTAT
Found at i:406002 original size:17 final size:19
Alignment explanation
Indices: 405971--406013 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
405961 TTTTTAAATA
405971 TAAATATAATAT-AAATTAT
1 TAAATATAATATAAAATT-T
405990 TAAATAT-AT-TAAAATTT
1 TAAATATAATATAAAATTT
406007 TAAATAT
1 TAAATAT
406014 GAATGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.39
18 7 0.30
19 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATAATATAAAATTT
Found at i:406954 original size:21 final size:21
Alignment explanation
Indices: 406921--406962 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
406911 TTGTGACATG
*
406921 TCATTTTTGTATTAT-TTTTA
1 TCATTTTTATATTATATTTTA
406941 TCATATTTTATATTATATTTTA
1 TCAT-TTTTATATTATATTTTA
406963 ATTTGTATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (21 bp):
TCATTTTTATATTATATTTTA
Found at i:408574 original size:2 final size:2
Alignment explanation
Indices: 408567--408598 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
408557 CTGCCGCAGC
408567 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
408599 TTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:408605 original size:2 final size:2
Alignment explanation
Indices: 408600--408624 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
408590 TATATATATT
408600 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
408625 TTAAATGCTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:410416 original size:24 final size:24
Alignment explanation
Indices: 410389--410441 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
410379 TAAAAAATTA
*
410389 TAAATATTAAATAT-TAAATTTTAT
1 TAAATATTAAATATATAAA-TTAAT
*
410413 TAAATATTAATTATATAAATTAAT
1 TAAATATTAAATATATAAATTAAT
410437 TAAAT
1 TAAAT
410442 TAAACTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATATTAAATATATAAATTAAT
Found at i:412051 original size:2 final size:2
Alignment explanation
Indices: 412044--412114 Score: 97
Period size: 2 Copynumber: 35.5 Consensus size: 2
412034 GTATACATAC
* * * * *
412044 AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT AT AT GT GT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
412086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
412115 AACCAGCTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
AT
Found at i:412066 original size:18 final size:18
Alignment explanation
Indices: 412045--412113 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
412035 TATACATACA
412045 TATATATATATATATGTG
1 TATATATATATATATGTG
412063 TATATATATATATATGTG
1 TATATATATATATATGTG
* * *
412081 TGTATATATATATATATA
1 TATATATATATATATGTG
412099 TATATATATATATAT
1 TATATATATATATAT
412114 AAACCAGCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
TATATATATATATATGTG
Found at i:418959 original size:6 final size:6
Alignment explanation
Indices: 418950--418983 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
418940 GTTTATATCG
*
418950 ATATTT ATATTT ATATTCT ATGTTT ATATTT ATA
1 ATATTT ATATTT ATATT-T ATATTT ATATTT ATA
418984 ACTGATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:418977 original size:13 final size:12
Alignment explanation
Indices: 418950--418983 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
418940 GTTTATATCG
418950 ATATTTATATTT
1 ATATTTATATTT
*
418962 ATATTCTATGTTT
1 ATATT-TATATTT
418975 ATATTTATA
1 ATATTTATA
418984 ACTGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (12 bp):
ATATTTATATTT
Found at i:419569 original size:2 final size:2
Alignment explanation
Indices: 419562--419589 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
419552 CAATCACCAT
419562 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
419590 TGAGGAACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:424912 original size:2 final size:2
Alignment explanation
Indices: 424905--424949 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
424895 CCTAAAACAA
424905 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
424947 AT A
1 AT A
424950 ATACTTAAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:427115 original size:2 final size:2
Alignment explanation
Indices: 427108--427150 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
427098 TGTCTTCAAA
427108 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
427150 A
1 A
427151 GACTGGTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:428013 original size:12 final size:12
Alignment explanation
Indices: 427998--428023 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
427988 TAGAAGCCCT
427998 AGTCGTAGTCGC
1 AGTCGTAGTCGC
428010 AGTCGTAGTCGC
1 AGTCGTAGTCGC
428022 AG
1 AG
428024 CTATAGTAGC
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:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (12 bp):
AGTCGTAGTCGC
Found at i:430230 original size:15 final size:15
Alignment explanation
Indices: 430210--430242 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
430200 TCCCATTCTC
430210 GTTCACCATCAGTAT
1 GTTCACCATCAGTAT
430225 GTTCACCATCAGTAT
1 GTTCACCATCAGTAT
430240 GTT
1 GTT
430243 ACATATACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (15 bp):
GTTCACCATCAGTAT
Found at i:436978 original size:41 final size:41
Alignment explanation
Indices: 436891--436971 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
436881 CCCATTAAGC
436891 TTATATT-ATGATTTAAAATATATTTTAAAATAAAAATATTT
1 TTATATTAAT-ATTTAAAATATATTTTAAAATAAAAATATTT
*
436932 TTATATTAATATTTATAAT-TATATTT-AAAT-AAAATATTT
1 TTATATTAATATTTAAAATATAT-TTTAAAATAAAAATATTT
436971 T
1 T
436972 ATTATATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
39 10 0.27
40 7 0.19
41 18 0.49
42 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (41 bp):
TTATATTAATATTTAAAATATATTTTAAAATAAAAATATTT
Found at i:441314 original size:22 final size:21
Alignment explanation
Indices: 441263--441315 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
441253 TGTTAATAAA
*
441263 TTATTTTTAAAATATTATCTT
1 TTATTATTAAAATATTATCTT
*
441284 TAATATATTAAAAT-TTATCTTAT
1 TTAT-TATTAAAATATTATC-T-T
441307 TTATTATTA
1 TTATTATTA
441316 TATTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 14 0.54
23 4 0.15
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATTATTAAAATATTATCTT
Found at i:442117 original size:4 final size:4
Alignment explanation
Indices: 442108--442132 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
442098 ACAGAGAGGG
442108 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
442133 TCCAGCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:447709 original size:2 final size:2
Alignment explanation
Indices: 447702--447757 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
447692 TTTCACAAAA
*
447702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
447742 AA AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT
447758 TCGACATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:451940 original size:2 final size:2
Alignment explanation
Indices: 451933--451973 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
451923 TTTCCCAGTT
*
451933 TA TA TA TA TG TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
451974 GTTCTTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:455564 original size:22 final size:22
Alignment explanation
Indices: 455513--455564 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
455503 TTCAATTCAA
* *
455513 AAAATTT-TTATATTTTTATTT
1 AAAATTTAATATATTTTAATTT
*
455534 -AAGTGTTAATATATTTTAATTT
1 AAAAT-TTAATATATTTTAATTT
455556 AAAATTTAA
1 AAAATTTAA
455565 AATTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 3 0.12
21 2 0.08
22 16 0.67
23 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
AAAATTTAATATATTTTAATTT
Found at i:456836 original size:27 final size:28
Alignment explanation
Indices: 456789--456927 Score: 101
Period size: 29 Copynumber: 4.9 Consensus size: 28
456779 AATAATTAAA
* *
456789 ATATAATAT-TAAAAA-AATAAATA-TG
1 ATATAATATATAAAAATATTAAATATTT
456814 ATATAATATATAAAAATATTAAA-ATTT
1 ATATAATATATAAAAATATTAAATATTT
*
456841 ATATAATATAAATTATTAATATATTAAA-ATTT
1 ATATAATAT--A-TA--AAAATATTAAATATTT
* * *
456873 ATATAAATATATATAATATTTTAAATA-TA
1 ATAT-AATATATA-AAAATATTAAATATTT
456902 ATTATAATATATAAAAATATATAAAT
1 A-TATAATATATAAAAATAT-TAAAT
456928 TATTAAATTT
Statistics
Matches: 95, Mismatches: 7, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
25 9 0.09
26 7 0.07
27 15 0.16
28 5 0.05
29 27 0.28
30 8 0.08
31 1 0.01
32 18 0.19
33 5 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATAATATATAAAAATATTAAATATTT
Found at i:456838 original size:32 final size:32
Alignment explanation
Indices: 456802--456926 Score: 88
Period size: 32 Copynumber: 4.1 Consensus size: 32
456792 TAATATTAAA
*
456802 AAAATAAATATGATATAATATATAAAAATATT
1 AAAATAAATATAATATAATATATAAAAATATT
** * *
456834 AAAATTTATATAATATAA-ATTATTAATATATT
1 AAAATAAATATAATATAATA-TATAAAAATATT
* *
456866 AAAAT--TTAT-ATA-AATATAT-ATAATATT
1 AAAATAAATATAATATAATATATAAAAATATT
*
456893 ---TTAAATATAATTATAATATATAAAAATATAT
1 AAAATAAATATAA-TATAATATATAAAAATAT-T
456924 AAA
1 AAA
456927 TTATTAAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 22
0.68 0.11 0.21
Matches are distributed among these distances:
24 1 0.01
26 3 0.04
27 7 0.10
28 7 0.10
29 11 0.16
30 9 0.13
31 2 0.03
32 30 0.43
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (32 bp):
AAAATAAATATAATATAATATATAAAAATATT
Found at i:456843 original size:20 final size:19
Alignment explanation
Indices: 456820--456884 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
456810 TATGATATAA
456820 TATATAAAAATATTAAAATT
1 TATAT-AAAATATTAAAATT
456840 TATAT--AATA-T-AAA-T
1 TATATAAAATATTAAAATT
*
456854 TAT-TAATATATTAAAATT
1 TATATAAAATATTAAAATT
456872 TATATAAATATAT
1 TATATAAA-ATAT
456885 ATAATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 6 0.17
16 2 0.06
17 7 0.19
18 4 0.11
19 3 0.08
20 9 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATAAAATATTAAAATT
Found at i:456843 original size:25 final size:24
Alignment explanation
Indices: 456767--456852 Score: 65
Period size: 25 Copynumber: 3.5 Consensus size: 24
456757 TAATTTTAAA
*
456767 TATAAAATAT-AAAATAATTAAAA-
1 TATAATATATAAAAAT-ATTAAAAT
*
456790 TATAATAT-TAAAAA-AATAAATAT
1 TATAATATATAAAAATATTAAA-AT
456813 GATATAATATATAAAAATATTAAAAT
1 --TATAATATATAAAAATATTAAAAT
456839 T-TATATAATATAAA
1 TATA-AT-ATATAAA
456853 TTATTAATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
21 5 0.10
22 2 0.04
23 13 0.25
24 3 0.06
25 15 0.29
26 8 0.16
27 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (24 bp):
TATAATATATAAAAATATTAAAAT
Found at i:456909 original size:20 final size:18
Alignment explanation
Indices: 456806--456935 Score: 62
Period size: 18 Copynumber: 7.3 Consensus size: 18
456796 ATTAAAAAAA
*
456806 TAAATATGATATAATA-TA
1 TAAATAT-ATATAATATTT
* *
456824 TAAAAATAT-TAA-AATT
1 TAAATATATATAATATTT
*
456840 TATATA-ATATAA-ATTAT
1 TAAATATATATAATATT-T
*
456857 T-AATATAT-TAAAATTTAT
1 TAAATATATATAATA-TT-T
456875 ATAAATATATATAATATTT
1 -TAAATATATATAATATTT
*
456894 TAAATATAATTATAATA-TA
1 TAAATAT-A-TATAATATTT
*
456913 TAAAAATATATAA-ATTAT
1 TAAATATATATAATATT-T
456931 TAAAT
1 TAAAT
456936 TTAAATATTA
Statistics
Matches: 88, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
15 3 0.03
16 20 0.23
17 13 0.15
18 22 0.25
19 10 0.11
20 16 0.18
21 4 0.05
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
TAAATATATATAATATTT
Found at i:456932 original size:27 final size:26
Alignment explanation
Indices: 456790--456916 Score: 54
Period size: 27 Copynumber: 4.9 Consensus size: 26
456780 ATAATTAAAA
*
456790 TATAATAT-TAAAAA-A-ATAAATATGA
1 TATAATATATAAAAATATATAAAT-T-T
*
456815 TATAATATATAAAAATAT-TAAAATT
1 TATAATATATAAAAATATATAAATTT
* *
456840 TAT-ATA-ATATAAAT-TATTAATATAT
1 TATAATATATAAAAATATA-TAA-ATTT
* *
456865 TAAAATTTATATAAATATATATAATATTT
1 TATAA--TATATAAAAATATATAA-ATTT
* *
456894 TA-AATATAATTATAATATATAAA
1 TATAATAT-ATAAAAATATATAAA
456917 AATATATAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
22 1 0.01
23 7 0.09
24 6 0.08
25 15 0.19
26 12 0.15
27 16 0.21
28 4 0.05
29 15 0.19
30 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
TATAATATATAAAAATATATAAATTT
Found at i:457576 original size:19 final size:20
Alignment explanation
Indices: 457554--457599 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
457544 TTAATTTTGA
*
457554 AAAAAATGTGTCA-AAATAT
1 AAAAAATATGTCATAAATAT
*
457573 AAAATATATGTCATAAATAT
1 AAAAAATATGTCATAAATAT
457593 AATAAAA
1 AA-AAAA
457600 ATAATTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 11 0.50
20 8 0.36
21 3 0.14
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAAAATATGTCATAAATAT
Found at i:457608 original size:15 final size:16
Alignment explanation
Indices: 457585--457625 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
457575 AATATATGTC
457585 ATAAATATAATA-AAA
1 ATAAATATAATATAAA
*
457600 ATAATTATAATATAAA
1 ATAAATATAATATAAA
457616 ATAAGATATA
1 ATAA-ATATA
457626 TAAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 11 0.50
16 7 0.32
17 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAAATATAATATAAA
Found at i:459191 original size:21 final size:22
Alignment explanation
Indices: 459147--459203 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
459137 AAATAAAAAA
*
459147 TAAATTAAATTTATAAATTATT
1 TAAATTAAATTTATAAAATATT
459169 TAAATTAAATATTA-AAAAT-TT
1 TAAATTAAAT-TTATAAAATATT
*
459190 TAAATTTAATTTAT
1 TAAATTAAATTTAT
459204 TCAATAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.10
21 11 0.35
22 14 0.45
23 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAATTAAATTTATAAAATATT
Found at i:461682 original size:53 final size:53
Alignment explanation
Indices: 461604--461717 Score: 129
Period size: 53 Copynumber: 2.2 Consensus size: 53
461594 TTTATTATCT
* ** * * *
461604 AAATTCGCATTACATATGTAGATAATAAACTTGGATATCTGAATTTGTTATTC
1 AAATTTGCATTACATATACAAATAATAAACTTAGATATCTGAATTCGTTATTC
* * * * *
461657 GAATTTGCATTACATATACAAATAATAGATTTAGATATTTGAATTCGTTATTT
1 AAATTTGCATTACATATACAAATAATAAACTTAGATATCTGAATTCGTTATTC
461710 AAATTTGC
1 AAATTTGC
461718 TTTTATAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (53 bp):
AAATTTGCATTACATATACAAATAATAAACTTAGATATCTGAATTCGTTATTC
Found at i:462274 original size:10 final size:11
Alignment explanation
Indices: 462257--462282 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
462247 AGCTGTAAGT
462257 GAAAAAAAAAA
1 GAAAAAAAAAA
462268 GAAAAAAAAAA
1 GAAAAAAAAAA
462279 GAAA
1 GAAA
462283 GGCATTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:463072 original size:5 final size:5
Alignment explanation
Indices: 463059--463129 Score: 51
Period size: 5 Copynumber: 14.8 Consensus size: 5
463049 CCCCCTTTTT
* * *
463059 TTTCC -TTCC TTTCC TTTCC TTTCCC TTCCC TTTCA TTTTC TTT-- TTT-C
1 TTTCC TTTCC TTTCC TTTCC TTT-CC TTTCC TTTCC TTTCC TTTCC TTTCC
* * *
463106 TTTTC TTTTC TTTTC TTTCC TTTC
1 TTTCC TTTCC TTTCC TTTCC TTTC
463130 TTCCATTTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
3 3 0.05
4 7 0.12
5 42 0.75
6 4 0.07
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (5 bp):
TTTCC
Found at i:463092 original size:21 final size:20
Alignment explanation
Indices: 463062--463101 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
463052 CCTTTTTTTT
*
463062 CCTTCCTTTCCTTTCCTTTC
1 CCTTCCTTTCATTTCCTTTC
*
463082 CCTTCCCTTTCATTTTCTTT
1 CCTT-CCTTTCATTTCCTTT
463102 TTTCTTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (20 bp):
CCTTCCTTTCATTTCCTTTC
Found at i:463504 original size:19 final size:21
Alignment explanation
Indices: 463480--463519 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
463470 TTCATTATAT
463480 TATTAA-AATAT-TATTTTTA
1 TATTAATAATATATATTTTTA
*
463499 TATTAATATTATATATTTTTA
1 TATTAATAATATATATTTTTA
463520 ATTTAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTAATAATATATATTTTTA
Found at i:464454 original size:2 final size:2
Alignment explanation
Indices: 464447--464472 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
464437 ATTTGAACCT
464447 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
464473 AAAGAAAAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:465648 original size:6 final size:6
Alignment explanation
Indices: 465639--465670 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
465629 TCCAGTTCCA
465639 GCTCCT GCTCCT GCTCCT GCTCCT GCTCCT GC
1 GCTCCT GCTCCT GCTCCT GCTCCT GCTCCT GC
465671 CTCTGCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.19, T:0.31
Consensus pattern (6 bp):
GCTCCT
Found at i:469045 original size:22 final size:23
Alignment explanation
Indices: 469020--469063 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
469010 ATGAAAAAAA
*
469020 TAAATATTAATGTAA-ATTTTTT
1 TAAATAATAATGTAAGATTTTTT
*
469042 TAAATAATAATTTAAGATTTTT
1 TAAATAATAATGTAAGATTTTT
469064 AAATCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
TAAATAATAATGTAAGATTTTTT
Found at i:477432 original size:2 final size:2
Alignment explanation
Indices: 477427--477457 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
477417 TGTGCATATA
477427 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
477458 ATGTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:478620 original size:21 final size:21
Alignment explanation
Indices: 478590--478642 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
478580 GTAACCATAT
* * *
478590 GGTGGTGGATATGATCCAGCA
1 GGTGGAGGATATGAACCACCA
*
478611 GGTGGCGGATATGAACCACCA
1 GGTGGAGGATATGAACCACCA
478632 GGTGGAGGATA
1 GGTGGAGGATA
478643 AGGATAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.40, T:0.19
Consensus pattern (21 bp):
GGTGGAGGATATGAACCACCA
Found at i:479889 original size:30 final size:31
Alignment explanation
Indices: 479824--479899 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
479814 TATCATACCT
* ** * **
479824 AAATAAATTTTTAATTTTTTAATTTATATTT
1 AAATAAATTTCTAAAATTTTAATTTACATCC
479855 AAAT-AATTTCTAAAATTTTAATTTACATCC
1 AAATAAATTTCTAAAATTTTAATTTACATCC
*
479885 AAATAAATTTTTAAA
1 AAATAAATTTCTAAA
479900 CTTTACTCTC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 24 0.65
31 13 0.35
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (31 bp):
AAATAAATTTCTAAAATTTTAATTTACATCC
Found at i:480548 original size:2 final size:2
Alignment explanation
Indices: 480541--480570 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
480531 TATGGTAAAC
480541 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
480571 GCACACACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:487639 original size:2 final size:2
Alignment explanation
Indices: 487632--487657 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
487622 CAATGACATG
487632 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
487658 AGTGAGAATG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:488098 original size:24 final size:23
Alignment explanation
Indices: 488070--488124 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
488060 AATGAGTAAA
488070 ATAATAAATATAAAATA-TAAAAT
1 ATAATAAATA-AAAATATTAAAAT
488093 ATTAATATAATAAAAATATTAAAAT
1 A-TAATA-AATAAAAATATTAAAAT
488118 ATAATAA
1 ATAATAA
488125 TAGTATACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.07
24 16 0.55
25 11 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAATAAATAAAAATATTAAAAT
Found at i:488110 original size:17 final size:18
Alignment explanation
Indices: 488045--488124 Score: 67
Period size: 17 Copynumber: 4.3 Consensus size: 18
488035 ATATAGATAT
488045 TAATAAAAATTATTAAAT-
1 TAATAAAAA-TATTAAATA
* * *
488063 GAGT-AAAATAATAAATA
1 TAATAAAAATATTAAATA
488080 TAAAATATAAAATATT-AATA
1 T--AATA-AAAATATTAAATA
488100 TAATAAAAATATTAAAATA
1 TAATAAAAATATT-AAATA
488119 TAATAA
1 TAATAA
488125 TAGTATACAC
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
16 7 0.14
17 12 0.24
18 6 0.12
19 12 0.24
20 5 0.10
21 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TAATAAAAATATTAAATA
Found at i:488119 original size:8 final size:8
Alignment explanation
Indices: 488066--488119 Score: 51
Period size: 7 Copynumber: 7.0 Consensus size: 8
488056 ATTAAATGAG
*
488066 TAAAATAA
1 TAAAATAT
488074 T-AAATA-
1 TAAAATAT
488080 TAAAATA-
1 TAAAATAT
488087 TAAAATAT
1 TAAAATAT
*
488095 TAATATAAT
1 TAAAAT-AT
*
488104 AAAAATAT
1 TAAAATAT
488112 TAAAATAT
1 TAAAATAT
488120 AATAATAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 1 0.03
7 17 0.44
8 15 0.38
9 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATAT
Found at i:488688 original size:27 final size:26
Alignment explanation
Indices: 488638--488700 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
488628 TATCGATTAG
*
488638 TTAATTTATTTAAATTAAAAATTAAT
1 TTAATTAATTTAAATTAAAAATTAAT
488664 TTAATTAATTATAATATT-AAAATTAAT
1 TTAATTAATT-TAA-ATTAAAAATTAAT
*
488691 TAAATTAATT
1 TTAATTAATT
488701 GATATTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 9 0.27
27 21 0.64
28 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTAATTAATTTAAATTAAAAATTAAT
Found at i:488699 original size:31 final size:31
Alignment explanation
Indices: 488657--488743 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
488647 TTAAATTAAA
*
488657 AATTAATTTAATTAAT-TATAATATTAAAATT
1 AATTAAATTAATTAATAT-TAATATTAAAATT
* *
488688 AATTAAATTAATTGATATTAATTTTAAAATT
1 AATTAAATTAATTAATATTAATATTAAAATT
* *
488719 AA-AATAATTAAATTAAAATTAATAT
1 AATTA-AATT-AATTAATATTAATAT
488744 CAATCAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 1 0.02
31 32 0.70
32 13 0.28
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
AATTAAATTAATTAATATTAATATTAAAATT
Found at i:488752 original size:20 final size:20
Alignment explanation
Indices: 488647--488740 Score: 65
Period size: 20 Copynumber: 4.8 Consensus size: 20
488637 GTTAATTTAT
**
488647 TTAAATTAAAAATTAATTTAA
1 TTAAATT-AAAATTAAAATAA
488668 TT-AATTATAATATTAAAATTAA
1 TTAAATTA-AA-ATTAAAA-TAA
*
488690 TTAAATT--AATT--GAT-A
1 TTAAATTAAAATTAAAATAA
*
488705 TTAATTTTAAAATTAAAATAA
1 TTAA-ATTAAAATTAAAATAA
488726 TTAAATTAAAATTAA
1 TTAAATTAAAATTAA
488741 TATCAATCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 21
0.68 0.07 0.25
Matches are distributed among these distances:
15 5 0.09
16 3 0.05
17 1 0.02
18 4 0.07
19 4 0.07
20 19 0.33
21 12 0.21
22 5 0.09
23 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (20 bp):
TTAAATTAAAATTAAAATAA
Found at i:488756 original size:57 final size:57
Alignment explanation
Indices: 488638--488762 Score: 128
Period size: 57 Copynumber: 2.2 Consensus size: 57
488628 TATCGATTAG
* ** * *
488638 TTAATTTATTTAAATTAAAAATTAATTTAATTAATTATAATATTAAAATTAATTAAA
1 TTAATTGATTTAAATTAAAAATTAAAATAATTAATTATAATATTAAAATCAATCAAA
* * * *
488695 TTAATTGATATTAATTTTAAAATTAAAATAATTAAATTA-AA-ATTAATATCAATCAAT
1 TTAATTGAT-TTAAATTAAAAATTAAAATAATT-AATTATAATATTAAAATCAATCAAA
*
488752 TTAATTAATTT
1 TTAATTGATTT
488763 TTTAAATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
56 2 0.04
57 28 0.50
58 21 0.38
59 5 0.09
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (57 bp):
TTAATTGATTTAAATTAAAAATTAAAATAATTAATTATAATATTAAAATCAATCAAA
Found at i:488790 original size:14 final size:14
Alignment explanation
Indices: 488771--488798 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
488761 TTTTTAAATT
488771 TTAAATATATTTTA
1 TTAAATATATTTTA
488785 TTAAATATATTTTA
1 TTAAATATATTTTA
488799 AATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:488790 original size:21 final size:19
Alignment explanation
Indices: 488751--488790 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
488741 TATCAATCAA
*
488751 TTTAATTAATTTTTTAAAT
1 TTTAAATAATTTTTTAAAT
488770 TTTAAATATATTTTATTAAAT
1 TTTAAATA-ATTTT-TTAAAT
488791 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAAATAATTTTTTAAAT
Found at i:488883 original size:5 final size:5
Alignment explanation
Indices: 488875--488916 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
488865 AGATCAAGAT
* *
488875 TTAAA TTAAA TT-AA TTAAA TT-AA TTAAA TAAAA TTTAA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
488917 TTCTTTCGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:488892 original size:9 final size:9
Alignment explanation
Indices: 488878--488918 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
488868 TCAAGATTTA
488878 AATTAAATT
1 AATTAAATT
488887 AATTAAATT
1 AATTAAATT
*
488896 AATTAAATAA
1 AATTAAAT-T
*
488906 AATTTAATT
1 AATTAAATT
488915 AATT
1 AATT
488919 CTTTCGATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAAATT
Found at i:500296 original size:12 final size:12
Alignment explanation
Indices: 500279--500304 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
500269 ACATTGAAAA
500279 AACAACAATAAT
1 AACAACAATAAT
500291 AACAACAATAAT
1 AACAACAATAAT
500303 AA
1 AA
500305 TTAAAAAAAC
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:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AACAACAATAAT
Found at i:500799 original size:2 final size:2
Alignment explanation
Indices: 500792--500824 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
500782 TCATGTAATG
*
500792 TA TA TA TA TA TA CA 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 T
500825 TAGTTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:503446 original size:13 final size:13
Alignment explanation
Indices: 503428--503452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
503418 CATAAAGTGT
503428 TGTATCGATACAA
1 TGTATCGATACAA
503441 TGTATCGATACA
1 TGTATCGATACA
503453 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:503464 original size:33 final size:33
Alignment explanation
Indices: 503408--503474 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
503398 TTCAACAATT
*
503408 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
*** *
503441 TGTATCGATACATATTTTTTTGTATCAATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
503474 T
1 T
503475 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCAATACAA
Found at i:503533 original size:13 final size:13
Alignment explanation
Indices: 503515--503539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
503505 ATTACTCAAA
503515 TGTATCGATACAT
1 TGTATCGATACAT
503528 TGTATCGATACA
1 TGTATCGATACA
503540 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:506360 original size:238 final size:238
Alignment explanation
Indices: 505942--506417 Score: 916
Period size: 238 Copynumber: 2.0 Consensus size: 238
505932 GATAATTGAT
*
505942 GGCAATTACGAGATACATCACGATCACCATTTTCTTTTTTCTTCCTTGTTCGGCATAATTAATTT
1 GGCAATTACGAGAAACATCACGATCACCATTTTCTTTTTTCTTCCTTGTTCGGCATAATTAATTT
506007 ATTTGCATGAAATATCATATGCCTCTATTGCTTTGTCAGCATGCTTCCTCCTTATTAATCTTGAT
66 ATTTGCATGAAATATCATATGCCTCTATTGCTTTGTCAGCATGCTTCCTCCTTATTAATCTTGAT
506072 AGCATTCATATTTTAAAAATGATTTACAAAAATCATAAGGCAATGTTCCGTGTCGGTATCTCTCT
131 AGCATTCATATTTTAAAAATGATTTACAAAAATCATAAGGCAATGTTCCGTGTCGGTATCTCTCT
506137 AGTGCTTGACACGGAATATCCTGTTTTCAAAATAAAATCCAAA
196 AGTGCTTGACACGGAATATCCTGTTTTCAAAATAAAATCCAAA
*
506180 GGCAATTACGAGAAACATCACGATTACCATTTTCTTTTTTCTTCCTTGTTCGGCATAATTAATTT
1 GGCAATTACGAGAAACATCACGATCACCATTTTCTTTTTTCTTCCTTGTTCGGCATAATTAATTT
*
506245 ATTTGCATGAAATATCATATGCCTCTATTGCTTTGTTAGCATGCTTCCTCCTTATTAATCTTGAT
66 ATTTGCATGAAATATCATATGCCTCTATTGCTTTGTCAGCATGCTTCCTCCTTATTAATCTTGAT
506310 AGCATTCATATTTTAAAAATGATTTACAAAAATCATAAGGCAATGTTCCGTGTCGGTATCTCTCT
131 AGCATTCATATTTTAAAAATGATTTACAAAAATCATAAGGCAATGTTCCGTGTCGGTATCTCTCT
*
506375 AGTGCTTGACACGGAATATCCTTTTTTCAAAATAAAATCCAAA
196 AGTGCTTGACACGGAATATCCTGTTTTCAAAATAAAATCCAAA
506418 AAGCTTTTAT
Statistics
Matches: 234, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
238 234 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (238 bp):
GGCAATTACGAGAAACATCACGATCACCATTTTCTTTTTTCTTCCTTGTTCGGCATAATTAATTT
ATTTGCATGAAATATCATATGCCTCTATTGCTTTGTCAGCATGCTTCCTCCTTATTAATCTTGAT
AGCATTCATATTTTAAAAATGATTTACAAAAATCATAAGGCAATGTTCCGTGTCGGTATCTCTCT
AGTGCTTGACACGGAATATCCTGTTTTCAAAATAAAATCCAAA
Found at i:507334 original size:18 final size:18
Alignment explanation
Indices: 507311--507348 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
507301 TTTAAAACGT
507311 ATTTAAATTAA-AAATTTA
1 ATTT-AATTAATAAATTTA
*
507329 ATTTAATTAATTAATTTA
1 ATTTAATTAATAAATTTA
507347 AT
1 AT
507349 AATCTTTAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAATTAATAAATTTA
Found at i:507815 original size:31 final size:29
Alignment explanation
Indices: 507777--507859 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
507767 ATATATACTC
507777 ATATATAAATATAAAAATATAATTTTT-TTAA
1 ATATATAAA-AT-AAAATAT-ATTTTTATTAA
*
507808 ATATATAAAATTAAATATATTTTTATTAA
1 ATATATAAAATAAAATATATTTTTATTAA
* **
507837 ATATAGACAAATATCATATATTT
1 ATATATA-AAATAAAATATATTT
507860 ATAAAAATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.13
29 16 0.36
30 14 0.31
31 9 0.20
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (29 bp):
ATATATAAAATAAAATATATTTTTATTAA
Found at i:507837 original size:15 final size:15
Alignment explanation
Indices: 507791--507841 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
507781 ATAAATATAA
507791 AAATATAATTTTT-TT
1 AAATAT-ATTTTTATT
***
507806 AAATATA-TAAAATT
1 AAATATATTTTTATT
507820 AAATATATTTTTATT
1 AAATATATTTTTATT
507835 AAATATA
1 AAATATA
507842 GACAAATATC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
13 1 0.04
14 10 0.36
15 17 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATATTTTTATT
Found at i:507876 original size:2 final size:2
Alignment explanation
Indices: 507871--507906 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
507861 TAAAAATTCG
507871 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
507907 CATAATGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:508901 original size:22 final size:22
Alignment explanation
Indices: 508870--508912 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
508860 TATTTAAAAA
508870 ATATTATTAT-ATTAATATTTAT
1 ATATTATTATAATTAA-ATTTAT
*
508892 ATATTTTTATAATTAAATTTA
1 ATATTATTATAATTAAATTTA
508913 AACATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTATTATAATTAAATTTAT
Found at i:509060 original size:2 final size:2
Alignment explanation
Indices: 509053--509081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
509043 AAATATAAAT
509053 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 T
509082 GTAACTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.