Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold231
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: 1009718
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 7
Found at i:324983 original size:4 final size:4
Alignment explanation
Indices: 324974--325002 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
324964 TAGTAAAAGC
324974 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
325003 AAGTTTGCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:325250 original size:2 final size:2
Alignment explanation
Indices: 325243--325273 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
325233 TAATATGAGT
325243 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 T
325274 TCAGGATGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:340034 original size:3 final size:3
Alignment explanation
Indices: 340026--340053 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
340016 ACTCCTGCAT
340026 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
340054 CCACTTCCAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:340186 original size:22 final size:22
Alignment explanation
Indices: 340161--340202 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
340151 TTTTAGACAT
*
340161 TAAA-ATTGTTATTTACAATTGC
1 TAAATATTGTTAATTA-AATTGC
340183 TAAATATTGTTAATTAAATT
1 TAAATATTGTTAATTAAATT
340203 TAAAAACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (22 bp):
TAAATATTGTTAATTAAATTGC
Found at i:342812 original size:19 final size:19
Alignment explanation
Indices: 342774--342809 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
342764 TATTTAAATT
342774 TAAAATTATATAATTATTA
1 TAAAATTATATAATTATTA
*
342793 TAAAATT-TATATTTATT
1 TAAAATTATATAATTATT
342810 TATTATTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAAATTATATAATTATTA
Found at i:342840 original size:28 final size:28
Alignment explanation
Indices: 342769--342888 Score: 75
Period size: 28 Copynumber: 4.6 Consensus size: 28
342759 TTTAATATTT
342769 AAATTTAAA-ATTA-TATAATTATTATA
1 AAATTTAAATATTATTATAATTATTATA
* * *
342795 AAATTTATAT-TTATTTATTATT-TGTATC
1 AAATTTAAATATTA-TTATAATTAT-TATA
* *
342823 AAATTTAAATATTATTAT-ATAAATAT-
1 AAATTTAAATATTATTATAATTATTATA
*
342849 AAA-TTAAATAATATTAT--TT-TT-TA
1 AAATTTAAATATTATTATAATTATTATA
342872 AATATTTAAAT-TTATTA
1 AA-ATTTAAATATTATTA
342889 AATATTTAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
22 1 0.01
23 3 0.04
24 7 0.09
25 19 0.25
26 14 0.19
27 6 0.08
28 22 0.29
29 3 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
AAATTTAAATATTATTATAATTATTATA
Found at i:342902 original size:17 final size:17
Alignment explanation
Indices: 342851--342902 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
342841 ATAAATATAA
342851 ATTAAATAATATT-ATTTT
1 ATTAAAT-AT-TTAATTTT
*
342869 -TTAAATATTTAAATTT
1 ATTAAATATTTAATTTT
342885 ATTAAATATTTAATTTT
1 ATTAAATATTTAATTTT
342902 A
1 A
342903 ATAATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 6 0.20
17 22 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAAATATTTAATTTT
Found at i:342925 original size:15 final size:16
Alignment explanation
Indices: 342896--342929 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
342886 TTAAATATTT
342896 AATTTTAATAATAAAA
1 AATTTTAATAATAAAA
342912 AATTTTAA-AATAAAA
1 AATTTTAATAATAAAA
342927 AAT
1 AAT
342930 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTTTAATAATAAAA
Found at i:344227 original size:17 final size:16
Alignment explanation
Indices: 344200--344255 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 16
344190 TATTGAGAAT
344200 TATATATAATTCAAAATA
1 TATA-ATAATTCAAAA-A
*
344218 TTTAATAATT-AAAAA
1 TATAATAATTCAAAAA
344233 TATAATAATTACAAAAA
1 TATAATAATT-CAAAAA
344250 TTATAA
1 -TATAA
344256 ATATTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 10 0.30
16 4 0.12
17 11 0.33
18 8 0.24
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAATAATTCAAAAA
Found at i:344249 original size:18 final size:17
Alignment explanation
Indices: 344200--344307 Score: 57
Period size: 15 Copynumber: 6.2 Consensus size: 17
344190 TATTGAGAAT
*
344200 TATATATAATTCAAAATA
1 TATA-ATAATTCAAAAAA
*
344218 TTTAATAATT--AAAAA
1 TATAATAATTCAAAAAA
*
344233 TATAATAATTACAAAAAT
1 TATAATAATT-CAAAAAA
*
344251 TATAAATATTATTTAAAAAA
1 TAT-AATA--ATTCAAAAAA
*
344271 TA-AAT-ATACAAAATAA
1 TATAATAATTCAAAA-AA
344287 TA-AATAAATT-AAAAATA
1 TATAAT-AATTCAAAAA-A
344304 TATA
1 TATA
344308 TACTAAAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
15 19 0.27
16 8 0.11
17 13 0.19
18 16 0.23
19 4 0.06
20 7 0.10
21 3 0.04
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TATAATAATTCAAAAAA
Found at i:344340 original size:31 final size:31
Alignment explanation
Indices: 344211--344340 Score: 104
Period size: 31 Copynumber: 4.0 Consensus size: 31
344201 ATATATAATT
* *
344211 CAAAATATTTAATAA-TTAAAAATATAATAATTA
1 CAAAATAATAAATAATTTAAAAATA-AAT-A-TA
*
344244 CAAAAATTATAAATATTATTTAAAAAATAAATATA
1 C-AAAATAATAAATA--ATTT-AAAAATAAATATA
* *
344279 CAAAATAATAAATAAATTAAAAATATATATA
1 CAAAATAATAAATAATTTAAAAATAAATATA
*
344310 CTAAAATAA-AAA-ATTTTAAAACATAAATATA
1 C-AAAATAATAAATAATTTAAAA-ATAAATATA
344341 ATTTTATGTT
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
30 7 0.09
31 24 0.30
32 10 0.12
33 1 0.01
34 22 0.27
35 3 0.04
36 2 0.02
37 5 0.06
38 7 0.09
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (31 bp):
CAAAATAATAAATAATTTAAAAATAAATATA
Found at i:344948 original size:23 final size:22
Alignment explanation
Indices: 344905--344949 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
344895 ATTTTATTAA
* *
344905 AATTTTAATTATTTTTAATATT
1 AATTTTAATCATTGTTAATATT
*
344927 AATTCTTAATCATTGTTCATATT
1 AATT-TTAATCATTGTTAATATT
344950 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (22 bp):
AATTTTAATCATTGTTAATATT
Found at i:345553 original size:24 final size:24
Alignment explanation
Indices: 345526--345572 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
345516 GAAAACATAA
* *
345526 GAAAAGAATATTTATATATATTTT
1 GAAAAGAAAATTTACATATATTTT
* *
345550 GAAAATAAAATTTCCATATATTT
1 GAAAAGAAAATTTACATATATTT
345573 GTGTCCATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (24 bp):
GAAAAGAAAATTTACATATATTTT
Found at i:345879 original size:23 final size:24
Alignment explanation
Indices: 345853--345897 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
345843 TGATTCACCA
345853 AATTGATTGAA-TAAAAAATTAAT
1 AATTGATTGAATTAAAAAATTAAT
* * *
345876 AATTTATTTAATTCAAAAATTA
1 AATTGATTGAATTAAAAAATTA
345898 GTTAAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
AATTGATTGAATTAAAAAATTAAT
Found at i:352604 original size:13 final size:13
Alignment explanation
Indices: 352588--352612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
352578 TCTTTTGCAC
352588 TTTGATTTTTTTA
1 TTTGATTTTTTTA
352601 TTTGATTTTTTT
1 TTTGATTTTTTT
352613 CTCAGTTTCT
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:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTGATTTTTTTA
Found at i:353661 original size:16 final size:16
Alignment explanation
Indices: 353604--353676 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 16
353594 TAATTCAACT
353604 ATAAAAAAAT-TAAAA
1 ATAAAAAAATATAAAA
*
353619 AT-AATAAATATTAAATATA
1 ATAAAAAAATA-T-AA-A-A
*
353638 ATTAAAAAATTATAAAA
1 A-TAAAAAAATATAAAA
* *
353655 ATAAAAAAAAAGAAAA
1 ATAAAAAAATATAAAA
353671 ATAAAA
1 ATAAAA
353677 GAAGATCATA
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.13
15 2 0.04
16 19 0.42
17 4 0.09
18 2 0.04
19 4 0.09
20 2 0.04
21 6 0.13
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.23
Consensus pattern (16 bp):
ATAAAAAAATATAAAA
Found at i:358926 original size:216 final size:219
Alignment explanation
Indices: 358549--359034 Score: 825
Period size: 216 Copynumber: 2.2 Consensus size: 219
358539 ACGTTGCGAC
* *
358549 AATGATCTAAAAAATAAAAGTTCTTATTTCGTCTTAACTTTATGATCTAAAAAACAAAGTTTTCT
1 AATGATCTAAAAAACAAAAGTTCTTATTTCGTCTTAACTTTATGATCTAAAAAACAAAGTTCTCT
* * *
358614 AACTTTCCTTTTTTTCATTAAAACCAAGAAAAAAACTTATCTTTCTTTCTTCTTTGAATGAGAAA
66 AACTTT-CTTTTTTTCATTAAAACCAAGAAAAAAACTTACCTTTCTTTCTTCCTTGAATGACAAA
358679 GAAAGAAAACCAAAGTTCTTATATTTTCTTCTTCCTTCAATGACTG-AAAAAAAATAAAAGTTCA
130 GAAAGAAAACCAAAGTTCTTATATTTTCTTCTTCCTTCAATGACTGAAAAAAAAATAAAAGTTCA
358743 TTCATTTATCTTTCATTCTTCGTTT
195 TTCATTTATCTTTCATTCTTCGTTT
358768 AATGATCTAAAAAACAAAAGTTCTTATTTCGTCTTAACTTTATGATCTAAAAAACAAAGTTCTCT
1 AATGATCTAAAAAACAAAAGTTCTTATTTCGTCTTAACTTTATGATCTAAAAAACAAAGTTCTCT
*
358833 AAC-TT-TTTTTTTCATTAAAACCAAGGAAAAAACTTACCTTTCTTTCTTCCTTGAATGACAAAG
66 AACTTTCTTTTTTTCATTAAAACCAAGAAAAAAACTTACCTTTCTTTCTTCCTTGAATGACAAAG
* * * *
358896 AAAGAAAACCAAAGTTCTTCTATTTTCTTCTTCCTTCAATGATTGAAAAAAAAAATGAAAGTTCT
131 AAAGAAAACCAAAGTTCTTATATTTTCTTCTTCCTTCAATGACTG-AAAAAAAAATAAAAGTTCA
*
358961 TTCTTTTATCTTTCATTCTTCGTTT
195 TTCATTTATCTTTCATTCTTCGTTT
*
358986 AATGATCTAAAAAACAAAAGTTCTTATTTCTTCTTAACTTTATGATCTA
1 AATGATCTAAAAAACAAAAGTTCTTATTTCGTCTTAACTTTATGATCTA
359035 TCGGTCTTAT
Statistics
Matches: 253, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
216 97 0.38
218 90 0.36
219 66 0.26
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (219 bp):
AATGATCTAAAAAACAAAAGTTCTTATTTCGTCTTAACTTTATGATCTAAAAAACAAAGTTCTCT
AACTTTCTTTTTTTCATTAAAACCAAGAAAAAAACTTACCTTTCTTTCTTCCTTGAATGACAAAG
AAAGAAAACCAAAGTTCTTATATTTTCTTCTTCCTTCAATGACTGAAAAAAAAATAAAAGTTCAT
TCATTTATCTTTCATTCTTCGTTT
Found at i:360177 original size:2 final size:2
Alignment explanation
Indices: 360170--360203 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
360160 CTACTATTTA
360170 AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
360204 CAGCAAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360181 original size:26 final size:26
Alignment explanation
Indices: 360147--360203 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
360137 TTAATTCTTT
*
360147 TATATATAT-TACTCTACTATT-TAATA
1 TATATATATATA-TATA-TATTATAATA
360173 TATATATATATATATATATTATAATA
1 TATATATATATATATATATTATAATA
360199 TATAT
1 TATAT
360204 CAGCAAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 4 0.14
26 22 0.79
27 2 0.07
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATATATATATATATATTATAATA
Found at i:360273 original size:9 final size:9
Alignment explanation
Indices: 360259--360289 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
360249 TTTAGTTTTC
360259 GATTTGATT
1 GATTTGATT
360268 GATTTGATT
1 GATTTGATT
*
360277 GATTCGATT
1 GATTTGATT
360286 GATT
1 GATT
360290 CAATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.52
Consensus pattern (9 bp):
GATTTGATT
Found at i:360320 original size:16 final size:16
Alignment explanation
Indices: 360295--360359 Score: 71
Period size: 15 Copynumber: 4.1 Consensus size: 16
360285 TGATTCAATT
360295 ATAA-AAAAATTAAAA
1 ATAATAAAAATTAAAA
*
360310 ATAATAAAAATTAAAT
1 ATAATAAAAATTAAAA
*
360326 ATAATTTAAAAATTATAA
1 ATAA--TAAAAATTAAAA
*
360344 A-AATAAAAAATAAAA
1 ATAATAAAAATTAAAA
360359 A
1 A
360360 ATTGAAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
15 15 0.36
16 14 0.33
17 2 0.05
18 11 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAATAAAAATTAAAA
Found at i:360334 original size:27 final size:27
Alignment explanation
Indices: 360297--360356 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
360287 ATTCAATTAT
*
360297 AAAAA-AA-TTAAAAATAATAAAAATT
1 AAAAATAATTTAAAAATAATAAAAATA
* *
360322 AAATATAATTTAAAAATTATAAAAATA
1 AAAAATAATTTAAAAATAATAAAAATA
360349 AAAAATAA
1 AAAAATAA
360357 AAAATTGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 4 0.14
26 2 0.07
27 23 0.79
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAATAATTTAAAAATAATAAAAATA
Found at i:361179 original size:17 final size:17
Alignment explanation
Indices: 361157--361189 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
361147 AATATAATTC
*
361157 AAAAAATTATAAAAATA
1 AAAAAATAATAAAAATA
361174 AAAAAATAATAAAAAT
1 AAAAAATAATAAAAAT
361190 CAGAGAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAATAATAAAAATA
Found at i:362674 original size:13 final size:14
Alignment explanation
Indices: 362640--362704 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
362630 ATAATAATAT
362640 ATAAAATATACTAA
1 ATAAAATATACTAA
362654 ATAAAATATACT-A
1 ATAAAATATACTAA
*
362667 ATAGAATATA-TAA
1 ATAAAATATACTAA
** *
362680 CATTTAATATAATAA
1 -ATAAAATATACTAA
*
362695 ATAGAATATA
1 ATAAAATATA
362705 AAAGTATAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
12 1 0.02
13 11 0.26
14 28 0.65
15 3 0.07
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (14 bp):
ATAAAATATACTAA
Found at i:362705 original size:14 final size:14
Alignment explanation
Indices: 362633--362705 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
362623 AATCTTTATA
*
362633 ATAATATATAAAAT
1 ATAATAAATAAAAT
*
362647 ATACTAAATAAAAT
1 ATAATAAATAAAAT
* *
362661 ATACT-AATAGAAT
1 ATAATAAATAAAAT
**
362674 AT-ATAACATTTAAT
1 ATAATAA-ATAAAAT
*
362688 ATAATAAATAGAAT
1 ATAATAAATAAAAT
362702 ATAA
1 ATAA
362706 AAGTATAAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
12 1 0.02
13 10 0.21
14 33 0.69
15 4 0.08
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (14 bp):
ATAATAAATAAAAT
Found at i:364243 original size:2 final size:2
Alignment explanation
Indices: 364236--364269 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
364226 TTCGGACTTT
364236 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
364270 GATTCTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:366832 original size:20 final size:17
Alignment explanation
Indices: 366809--366851 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
366799 ATTATATTCA
366809 TATATTTTAAGAATTATTAT
1 TATATTTTAA-AA-TATT-T
366829 TATA-TTTAAAATATTT
1 TATATTTTAAAATATTT
366845 TATATTT
1 TATATTT
366852 ATATAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 2 0.09
19 5 0.23
20 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TATATTTTAAAATATTT
Found at i:366853 original size:28 final size:27
Alignment explanation
Indices: 366786--366853 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
366776 AATAAAATTT
* *
366786 TATTTT-TATTT-TTATTATATTCATA
1 TATTTTATATTTATTATTATATTAAAA
* *
366811 TATTTTAAGAATTATTATTATATTTAAAA
1 TATTTT-ATATTTATTATTATA-TTAAAA
366840 TATTTTATATTTAT
1 TATTTTATATTTAT
366854 ATAAACATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
25 6 0.18
27 3 0.09
28 14 0.42
29 10 0.30
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (27 bp):
TATTTTATATTTATTATTATATTAAAA
Found at i:373306 original size:26 final size:27
Alignment explanation
Indices: 373261--373312 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
373251 AAAATATATG
* *
373261 TATACAAAATAAAATGAAATTGAATAA
1 TATACAAAATAAAATAAAATTAAATAA
*
373288 TATA-AAAATAATATAAAATTAAATA
1 TATACAAAATAAAATAAAATTAAATA
373313 TGGATGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (27 bp):
TATACAAAATAAAATAAAATTAAATAA
Found at i:375740 original size:263 final size:263
Alignment explanation
Indices: 375201--375728 Score: 1020
Period size: 263 Copynumber: 2.0 Consensus size: 263
375191 TCACATGTAA
375201 ATACATATAATTTATATTATGTATATATTTATAAATATAATTATATGTACTAATAATAAAATCAG
1 ATACATATAATTTATATTATGTATATATTTATAAATATAATTATATGTACTAATAATAAAATCAG
375266 AATGTGCAAATGACTATATTTAAAGAATAAATAAGTGTATAAGACTAAGATTTAAAAGTTGGTAA
66 AATGTGCAAATGACTATATTTAAAGAATAAATAAGTGTATAAGACTAAGATTTAAAAGTTGGTAA
* *
375331 GACATATAAAAAATTACCACTAAATGTATAGTTATCGCTCGATTATTTGTCATGATGATTTAATT
131 GACATATAAAAAATTACCACTAAATGTATAGTTATCACTCGATTATTTGTCATAATGATTTAATT
375396 TTAATTTAAAATTAAATTTTTTAAAAAATAATAATTAAAAATTGCTTGATATATATTATATGTTT
196 TTAATTTAAAATTAAATTTTTTAAAAAATAATAATTAAAAATTGCTTGATATATATTATATGTTT
375461 AAT
261 AAT
375464 ATACATATAATTTATATTATGTATATATTTATAAATATAATTATATGTACTAATAATAAAATCAG
1 ATACATATAATTTATATTATGTATATATTTATAAATATAATTATATGTACTAATAATAAAATCAG
* *
375529 AATGTGTAAATGACTATATTTTAAGAATAAATAAGTGTATAAGACTAAGATTTAAAAGTTGGTAA
66 AATGTGCAAATGACTATATTTAAAGAATAAATAAGTGTATAAGACTAAGATTTAAAAGTTGGTAA
375594 GACATATAAAAAATTACCACTAAATGTATAGTTATCACTCGATTATTTGTCATAATGATTTAATT
131 GACATATAAAAAATTACCACTAAATGTATAGTTATCACTCGATTATTTGTCATAATGATTTAATT
375659 TTAATTTAAAATTAAATTTTTTAAAAAATAATAATTAAAAATTGCTTGATATATATTATATGTTT
196 TTAATTTAAAATTAAATTTTTTAAAAAATAATAATTAAAAATTGCTTGATATATATTATATGTTT
375724 AAT
261 AAT
375727 AT
1 AT
375729 TTTAATAATT
Statistics
Matches: 261, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
263 261 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.40
Consensus pattern (263 bp):
ATACATATAATTTATATTATGTATATATTTATAAATATAATTATATGTACTAATAATAAAATCAG
AATGTGCAAATGACTATATTTAAAGAATAAATAAGTGTATAAGACTAAGATTTAAAAGTTGGTAA
GACATATAAAAAATTACCACTAAATGTATAGTTATCACTCGATTATTTGTCATAATGATTTAATT
TTAATTTAAAATTAAATTTTTTAAAAAATAATAATTAAAAATTGCTTGATATATATTATATGTTT
AAT
Found at i:376877 original size:2 final size:2
Alignment explanation
Indices: 376870--376898 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
376860 ACCCATATTA
376870 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
376899 ATTATTATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:381066 original size:23 final size:23
Alignment explanation
Indices: 381036--381081 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
381026 AATTTAATCC
381036 ATAGTTATGCTAGCGCCAGAGAT
1 ATAGTTATGCTAGCGCCAGAGAT
381059 ATAGTTATGCTAGCGCCAGAGAT
1 ATAGTTATGCTAGCGCCAGAGAT
381082 CACATGACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (23 bp):
ATAGTTATGCTAGCGCCAGAGAT
Found at i:384450 original size:15 final size:15
Alignment explanation
Indices: 384427--384493 Score: 73
Period size: 16 Copynumber: 4.4 Consensus size: 15
384417 TTTAATATTT
*
384427 TTTTGAATTTAAATA
1 TTTTAAATTTAAATA
*
384442 TTTTAAATTTAAAACA
1 TTTTAAATTT-AAATA
*
384458 TTTTAAATTCGAAATA
1 TTTTAAATT-TAAATA
*
384474 ATTTAAATTTAAAT-
1 TTTTAAATTTAAATA
384488 TTTTAA
1 TTTTAA
384494 TTTTTATCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
14 5 0.12
15 13 0.30
16 25 0.58
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
TTTTAAATTTAAATA
Found at i:384534 original size:19 final size:20
Alignment explanation
Indices: 384510--384548 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
384500 TCAAATCAAT
384510 TTAATTAA-ATTTAAATTTA
1 TTAATTAATATTTAAATTTA
*
384529 TTAATTAATTTTTAAATTTA
1 TTAATTAATATTTAAATTTA
384549 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTAATATTTAAATTTA
Found at i:384566 original size:26 final size:25
Alignment explanation
Indices: 384514--384584 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
384504 ATCAATTTAA
*
384514 TTAAATTTAAATTTATTAATTAATTT
1 TTAAATTTAAATTTATTAATCAA-TT
* * *
384540 TTAAATTTAAATTTTTTTATCACTT
1 TTAAATTTAAATTTATTAATCAATT
*
384565 TTATATTT-AATTTAATTAAT
1 TTAAATTTAAATTT-ATTAAT
384585 TTTTATAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 5 0.14
25 13 0.35
26 19 0.51
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAAATTTAAATTTATTAATCAATT
Found at i:388587 original size:78 final size:80
Alignment explanation
Indices: 388505--388669 Score: 178
Period size: 80 Copynumber: 2.1 Consensus size: 80
388495 CAAGAAAGAG
* * *
388505 TAATTATAATTTTTTTTAAAATATTT-T-TTTGCTTTTTAT-TTTAATAC-CTATTT-AATATTA
1 TAATT-TAA-TTTTTTT-AAATATTTATAGTTGATATTTATATTTAATACGCTATTTGAATATTA
388565 AATATAAATATAAAAATA
63 AATATAAATATAAAAATA
* * * *
388583 TAATTTTATTTTTTTAAATATTTATAGTTGATATTTATATTTAATACGTTATTTGCATATTAGAT
1 TAATTTAATTTTTTTAAATATTTATAGTTGATATTTATATTTAATACGCTATTTGAATATTAAAT
* *
388648 ATAAGTATAAAAAAA
66 ATAAATATAAAAATA
388663 TATATTT
1 TA-ATTT
388670 CAAATGTATG
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
75 8 0.11
76 8 0.11
77 11 0.15
78 13 0.18
79 5 0.07
80 23 0.32
81 4 0.06
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (80 bp):
TAATTTAATTTTTTTAAATATTTATAGTTGATATTTATATTTAATACGCTATTTGAATATTAAAT
ATAAATATAAAAATA
Found at i:389964 original size:10 final size:10
Alignment explanation
Indices: 389946--389989 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
389936 CTTGCAGGTT
389946 TAAATATATA
1 TAAATATATA
389956 T--ATATATA
1 TAAATATATA
*
389964 TAAATATACA
1 TAAATATATA
389974 TAAATATATA
1 TAAATATATA
389984 TAAATA
1 TAAATA
389990 GTATTCGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 8 0.27
10 22 0.73
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAATATATA
Found at i:390567 original size:17 final size:18
Alignment explanation
Indices: 390546--390585 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
390536 TTAATTTGAC
390546 ATTAAAAAATAT-TTTTT
1 ATTAAAAAATATATTTTT
*
390563 TTTAAAAAATATATTTTT
1 ATTAAAAAATATATTTTT
390581 ATTAA
1 ATTAA
390586 TTATTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAAAAAATATATTTTT
Found at i:395303 original size:12 final size:12
Alignment explanation
Indices: 395286--395311 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
395276 CAAATCCATT
395286 ACAGTTATCAAA
1 ACAGTTATCAAA
395298 ACAGTTATCAAA
1 ACAGTTATCAAA
395310 AC
1 AC
395312 CTTGCCCTTT
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:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (12 bp):
ACAGTTATCAAA
Found at i:401476 original size:18 final size:15
Alignment explanation
Indices: 401437--401468 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
401427 TTGGAAGGGG
401437 TTCTT-CATTTTTTT
1 TTCTTCCATTTTTTT
401451 TTCTTCCATTTTTTT
1 TTCTTCCATTTTTTT
401466 TTC
1 TTC
401469 AGTCTCCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (15 bp):
TTCTTCCATTTTTTT
Found at i:401884 original size:12 final size:12
Alignment explanation
Indices: 401855--401888 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
401845 TTATTAACCT
401855 ATAATAAAA-TA
1 ATAATAAAATTA
401866 A-AATAAAATTA
1 ATAATAAAATTA
401877 ATAATAAAATTA
1 ATAATAAAATTA
401889 GTAGGATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.33
11 4 0.19
12 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATAAAATTA
Found at i:403754 original size:2 final size:2
Alignment explanation
Indices: 403749--403776 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
403739 CTCTTTGTAA
403749 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
403777 CATAGCAGGT
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:411411 original size:18 final size:18
Alignment explanation
Indices: 411390--411430 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
411380 TTTACATAGC
411390 ATAACAATGACAAGCATA
1 ATAACAATGACAAGCATA
411408 ATAACAATGACAAGCATA
1 ATAACAATGACAAGCATA
411426 ATAAC
1 ATAAC
411431 TTTTAGTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (18 bp):
ATAACAATGACAAGCATA
Found at i:414783 original size:20 final size:20
Alignment explanation
Indices: 414755--414800 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
414745 AGAGATACGT
*
414755 CAATCAGATCATTCAAGCAG
1 CAATAAGATCATTCAAGCAG
414775 CAATAAGATCATTCAAGCAG
1 CAATAAGATCATTCAAGCAG
414795 CAATAA
1 CAATAA
414801 CTAGAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.20
Consensus pattern (20 bp):
CAATAAGATCATTCAAGCAG
Found at i:415619 original size:40 final size:40
Alignment explanation
Indices: 415527--415639 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 40
415517 AGCAAAATCC
* *
415527 CACTAATTTTAATTATTTAGAGGCGTTTAATATAAAAAAG
1 CACTAATTTTAATTATTTAGTGGCGTTTCATATAAAAAAG
*
415567 TCACTAAATTTAATTATTTAGTGGCGTTTCATATAAAAACA-
1 -CACTAATTTTAATTATTTAGTGGCGTTTCATATAAAAA-AG
* *
415608 CACTAATTTTAACTATTTAGTGGCATTTCATA
1 CACTAATTTTAATTATTTAGTGGCGTTTCATA
415640 GCAAAACGCT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 29 0.45
41 35 0.54
42 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (40 bp):
CACTAATTTTAATTATTTAGTGGCGTTTCATATAAAAAAG
Found at i:415646 original size:40 final size:40
Alignment explanation
Indices: 415509--415646 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
415499 AAATTAGCCA
* *
415509 CATTTCATAGCAAAATCCCACTAATTTTAATTATTTAGAGG
1 CATTTCATAGCAAAA-CACACTAATTTTAATTATTTAGTGG
* * * * *
415550 CGTTTAATA-TAAAAAAGTCACTAAATTTAATTATTTAGTGG
1 CATTTCATAGCAAAACA--CACTAATTTTAATTATTTAGTGG
* ** *
415591 CGTTTCATATAAAAACACACTAATTTTAACTATTTAGTGG
1 CATTTCATAGCAAAACACACTAATTTTAATTATTTAGTGG
415631 CATTTCATAGCAAAAC
1 CATTTCATAGCAAAAC
415647 GCTGTAAAAC
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
40 38 0.48
41 36 0.46
42 5 0.06
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (40 bp):
CATTTCATAGCAAAACACACTAATTTTAATTATTTAGTGG
Found at i:416537 original size:19 final size:16
Alignment explanation
Indices: 416502--416540 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 16
416492 ATTCTTGTAC
416502 ATTAATTTTATTATTT
1 ATTAATTTTATTATTT
416518 ATTAATTGTTAATATATTT
1 ATTAATT-TT-AT-TATTT
416537 ATTA
1 ATTA
416541 TCATAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 2 0.10
19 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTAATTTTATTATTT
Found at i:418146 original size:77 final size:78
Alignment explanation
Indices: 418007--418159 Score: 263
Period size: 77 Copynumber: 2.0 Consensus size: 78
417997 AGTAACGAAG
* *
418007 GGGTTAGTTATTAAAATATGGTAGAGAAATGCACTGATGAATATGTTATGTTGAATGATTATGCT
1 GGGTTAGTTATTAAAATATGGTAGAGAAATGCACTGATGAATATGCTATATTGAATGATTATGCT
418072 AAGGAATTAAAAA
66 AAGGAATTAAAAA
*
418085 GGGTTAGTTATTAAAATATGGTAGA-AAATGTACTGATGAATATGCTATATTGAATGATTATGCT
1 GGGTTAGTTATTAAAATATGGTAGAGAAATGCACTGATGAATATGCTATATTGAATGATTATGCT
*
418149 ATGGAATTAAA
66 AAGGAATTAAA
418160 GGCGACAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
77 46 0.65
78 25 0.35
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (78 bp):
GGGTTAGTTATTAAAATATGGTAGAGAAATGCACTGATGAATATGCTATATTGAATGATTATGCT
AAGGAATTAAAAA
Found at i:419462 original size:271 final size:273
Alignment explanation
Indices: 418800--419463 Score: 672
Period size: 276 Copynumber: 2.4 Consensus size: 273
418790 TAGCTAATGG
* * * * * * *
418800 ACTTACTGCAAAAGAATTATTGTTAGAAAAATAATCAATTCA-AGGTTGATGTTAAGCTTTTTTT
1 ACTTAGTGCAAAAGAATCATTATTAG-AAAATAGT-GATTCAGA-GTTGATGTCAAGTTTTTTTT
* * * *
418864 AGTGAACTCATTAAGTGTGATGACAGCTTATAACT-ATATGTGTGAAATATTTACCTTTTGTCAA
63 AGTGAACTCATTAAGTATGATGTCAGCTTAT-AGTAATATGTGTGAAACATTTACCTTTTGTCAA
* * * * * *
418928 GCAAAAAATCTATGTTAGGTACATTTATGCTAGATGGGAAAAAACTTACAAGGATAAAAATTTGA
127 GCAAAAAATCTATGCTAGGCACATTTATGCTAGATAGGAAAAAACTCACAAAGATAAAAATTTAA
* * *
418993 AACTACAATTCTAAAATTGTGCAAGGCATCAAACCAGCCTCAATTGAATAAATAATTACAAAGTT
192 AACTACAATTCTAAAATTGTGCAAGGCACCAAACCAGCCTCAATTGAATAAAGAATTACAAAATT
**
419058 TACAAGTTTGACTATAT
257 TACAAGCATGACTATAT
* *
419075 ACTTAGTGCAAAAGAATCATTATTAGAAAATTGAGTGATTCAGGGTTAACT-TCAAGTTTTTTTT
1 ACTTAGTGCAAAAGAATCATTATTAGAAAA-T-AGTGATTCAGAGTTGA-TGTCAAG-TTTTTTT
* * *
419139 TAGTGCATTCATTAAGTATGATGTCAGCTTATAGCAATATGTGTGAAACATTTA-CTTTTAGTCA
62 TAGTGAACTCATTAAGTATGATGTCAGCTTATAGTAATATGTGTGAAACATTTACCTTTT-GTCA
* * *
419203 AGTAAAAAATCTATGCTAGGCACATTTATGTTAGATAAGG-AAAAACTCATAAAGATAAAGAA-T
126 AGCAAAAAATCTATGCTAGGCACATTTATGCTAGAT-AGGAAAAAACTCACAAAGATAAA-AATT
* * * * *
419266 TAAAATTACAGTTCTAAAATTGTGTAAGGTGC-CCAAACTAGCCT-AAGTTGAATAAAGAATTAG
189 TAAAACTACAATTCTAAAATTGTGCAA-G-GCACCAAACCAGCCTCAA-TTGAATAAAGAATTAC
* **
419329 AAAATTTGACATGCATGGTTAGTGA-
251 AAAATTT-ACAAGCATGACTA-T-AT
* * * * *
419354 ACTTATTGCAAAAGAGTTATTATTAGAAAA-A-TGA-TC-GATTTGATGTCAAG-TTTCTTTAGT
1 ACTTAGTGCAAAAGAATCATTATTAGAAAATAGTGATTCAGAGTTGATGTCAAGTTTTTTTTAGT
* *
419414 GAACTCATTAAGTATGATGTCAACTTATAGTAACATGTGTGAAACATTTA
66 GAACTCATTAAGTATGATGTCAGCTTATAGTAATATGTGTGAAACATTTA
419464 ATGGGGTGAT
Statistics
Matches: 323, Mismatches: 50, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
271 54 0.17
272 1 0.00
273 9 0.03
274 6 0.02
275 46 0.14
276 133 0.41
277 35 0.11
278 10 0.03
279 28 0.09
280 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (273 bp):
ACTTAGTGCAAAAGAATCATTATTAGAAAATAGTGATTCAGAGTTGATGTCAAGTTTTTTTTAGT
GAACTCATTAAGTATGATGTCAGCTTATAGTAATATGTGTGAAACATTTACCTTTTGTCAAGCAA
AAAATCTATGCTAGGCACATTTATGCTAGATAGGAAAAAACTCACAAAGATAAAAATTTAAAACT
ACAATTCTAAAATTGTGCAAGGCACCAAACCAGCCTCAATTGAATAAAGAATTACAAAATTTACA
AGCATGACTATAT
Found at i:434908 original size:2 final size:2
Alignment explanation
Indices: 434895--434949 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
434885 AGTGTTACCA
*
434895 AT AT AT AC 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
434937 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
434950 CAAGGCAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:440603 original size:2 final size:2
Alignment explanation
Indices: 440598--440628 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
440588 TGTGTAAATA
*
440598 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
440629 ATCAAGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:446234 original size:14 final size:15
Alignment explanation
Indices: 446215--446248 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
446205 TCCTTTTCTC
446215 TTTCTCTTTCT-CTT
1 TTTCTCTTTCTACTT
446229 TTTCTCTTTCTACTT
1 TTTCTCTTTCTACTT
446244 TTTCT
1 TTTCT
446249 AACTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTCTTTCTACTT
Found at i:446679 original size:28 final size:27
Alignment explanation
Indices: 446648--446709 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
446638 TTTTAAAAAA
* * * *
446648 TTTTAATTATTTTTTTATATTTTTTTAT
1 TTTTAATT-TTTTCTTAAATATTCTTAT
446676 TTTTAAATTTTTTCTTAAATATTCTTAT
1 TTTT-AATTTTTTCTTAAATATTCTTAT
446704 TTTTAA
1 TTTTAA
446710 ATCCCTTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.07
28 23 0.79
29 4 0.14
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTAATTTTTTCTTAAATATTCTTAT
Found at i:446900 original size:20 final size:21
Alignment explanation
Indices: 446862--446901 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
446852 GTTTATCATG
* *
446862 TATTTTATTTTTATTTTTAAT
1 TATTTTATTATTATATTTAAT
446883 TATTTT-TTATTATATTTAA
1 TATTTTATTATTATATTTAA
446902 GATACACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTTTATTATTATATTTAAT
Found at i:447566 original size:27 final size:30
Alignment explanation
Indices: 447535--447590 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
447525 AAAAGCTTTC
447535 TAAG-ACAAAATATAATA-TAA-AAATAAT
1 TAAGAACAAAATATAATATTAATAAATAAT
*
447562 TAAGATATAAAATATAATATTAATAAATA
1 TAAGA-ACAAAATATAATATTAATAAATA
447591 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.17
29 12 0.50
30 3 0.12
31 5 0.21
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (30 bp):
TAAGAACAAAATATAATATTAATAAATAAT
Found at i:447640 original size:27 final size:28
Alignment explanation
Indices: 447567--447641 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
447557 ATAATTAAGA
*
447567 TATAAAATAT-AATATTAATAAATATTT
1 TATAAAATATAAATATTATTAAATATTT
*
447594 TATTAATATATAAATA-TATTAAA-A-TT
1 TA-TAAAATATAAATATTATTAAATATTT
447620 TATAAAATATAAATTATTATTA
1 TATAAAATATAAA-TATTATTA
447642 TTATATCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 10 0.24
26 6 0.15
27 8 0.20
28 13 0.32
29 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TATAAAATATAAATATTATTAAATATTT
Found at i:447701 original size:17 final size:17
Alignment explanation
Indices: 447651--447703 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
447641 ATTATATCAA
*
447651 ATTTTATATAAAATATATA
1 ATTTTATA-AAAATA-ATT
*
447670 ATATTT-TAAATATAATT
1 AT-TTTATAAAAATAATT
447687 ATTTTATAAAAATAATT
1 ATTTTATAAAAATAATT
447704 TAAATAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.10
17 14 0.48
18 5 0.17
19 4 0.14
20 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTTATAAAAATAATT
Found at i:447819 original size:27 final size:26
Alignment explanation
Indices: 447789--447875 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 26
447779 ATTTTTATTT
447789 TATTTACATTATTTTATATTATAATAA
1 TATTTA-ATTATTTTATATTATAATAA
*
447816 TATTTAA-AATTTTATA-TATAAT-A
1 TATTTAATTATTTTATATTATAATAA
*
447839 TA-TTAATTATTAT-TATTAT-ATAA
1 TATTTAATTATTTTATATTATAATAA
447862 -ATTTTAATATATTT
1 TA-TTTAAT-TATTT
447876 ATTAAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
22 9 0.18
23 11 0.22
24 11 0.22
25 12 0.24
26 1 0.02
27 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTTAATTATTTTATATTATAATAA
Found at i:448133 original size:6 final size:6
Alignment explanation
Indices: 448122--448184 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
448112 CATTTAATAC
* * *
448122 TTATAT TTATAT TTATAT TTATAT TTATAC TTATAC ATATAT TTA-A-
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
448168 -TATAT TTATAAT TTATA
1 TTATAT TTAT-AT TTATA
448185 AATTTATATG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 39 0.80
7 6 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (6 bp):
TTATAT
Found at i:448264 original size:23 final size:24
Alignment explanation
Indices: 448238--448320 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 24
448228 AATTTTTAAA
448238 AATAAATATAAATAATTTATT-TT
1 AATAAATATAAATAATTTATTATT
*
448261 AATAAA-ATAATATAATTAATTTATT
1 AATAAATATAA-ATAATTTA-TTATT
*
448286 AAT-AATATATAAT-ATATATTATT
1 AATAAATATA-AATAATTTATTATT
448309 AATAAAT-TAAAT
1 AATAAATATAAAT
448321 TTAAATATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
22 7 0.14
23 23 0.45
24 10 0.20
25 10 0.20
26 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATAAATATAAATAATTTATTATT
Found at i:448272 original size:27 final size:25
Alignment explanation
Indices: 448236--448333 Score: 78
Period size: 27 Copynumber: 3.8 Consensus size: 25
448226 AAAATTTTTA
448236 AAAATAAATATAAATAATTTATTTTAAT
1 AAAAT-AATATAAATAATTTA--TTAAT
*
448264 AAAATAATATAATTAATTTATTAAT
1 AAAATAATATAAATAATTTATTAAT
448289 --AAT-ATAT-AATATATATTATTAAT
1 AAAATAATATAAATA-AT-TTATTAAT
* * *
448312 AAATTAAATTTAAATATTTTAT
1 AAAAT-AATATAAATAATTTAT
448334 ATTTATATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
21 3 0.05
22 6 0.10
23 11 0.19
25 7 0.12
26 4 0.07
27 18 0.31
28 9 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAATAATATAAATAATTTATTAAT
Found at i:448415 original size:21 final size:22
Alignment explanation
Indices: 448390--448431 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
448380 ATTGATTTTT
*
448390 AATTT-AATATATATTTTATCA
1 AATTTAAAAATATATTTTATCA
448411 AATTTAAAAAATATATTTTAT
1 AATTT-AAAAATATATTTTAT
448432 ATTTTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTAAAAATATATTTTATCA
Found at i:448992 original size:36 final size:36
Alignment explanation
Indices: 448952--449023 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
448942 CATACAAGAA
448952 AGTGATTTTCAAGCCTAAGGCCGCGCGGTTTGCTAG
1 AGTGATTTTCAAGCCTAAGGCCGCGCGGTTTGCTAG
448988 AGTGATTTTCAAGCCTAAGGCCGCGCGGTTTGCTAG
1 AGTGATTTTCAAGCCTAAGGCCGCGCGGTTTGCTAG
449024 GCTAAAGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (36 bp):
AGTGATTTTCAAGCCTAAGGCCGCGCGGTTTGCTAG
Found at i:449037 original size:36 final size:36
Alignment explanation
Indices: 448961--449037 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
448951 AAGTGATTTT
* ** *
448961 CAAGCCTAAGGCCGCGCGGTTTGCTAGAGTGATTTT
1 CAAGCCTAAGGCCGCGCGGTTTGCTAGAGTAAAGTC
448997 CAAGCCTAAGGCCGCGCGGTTTGCTAG-GCTAAAGTC
1 CAAGCCTAAGGCCGCGCGGTTTGCTAGAG-TAAAGTC
449033 CAAGC
1 CAAGC
449038 TCGTGACAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 1 0.03
36 35 0.97
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (36 bp):
CAAGCCTAAGGCCGCGCGGTTTGCTAGAGTAAAGTC
Found at i:449177 original size:55 final size:55
Alignment explanation
Indices: 449093--449202 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
449083 CGTAGAAATG
*
449093 GCGTCTCAAGCAGAAAACCAGACACAAGAGGTCCCGGAGACTCATGGGAGAGGAA
1 GCGTCTCAAGCAGAAAACCAGACACAAGAGGTCCCGGAGACGCATGGGAGAGGAA
*
449148 GCGTCTCAAGCAGAAAACCAGACACAAGAGGTCCTGGAGACGCATGGGAGAGGAA
1 GCGTCTCAAGCAGAAAACCAGACACAAGAGGTCCCGGAGACGCATGGGAGAGGAA
449203 AGAAGGCCAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.36, C:0.23, G:0.32, T:0.09
Consensus pattern (55 bp):
GCGTCTCAAGCAGAAAACCAGACACAAGAGGTCCCGGAGACGCATGGGAGAGGAA
Found at i:450430 original size:123 final size:123
Alignment explanation
Indices: 450211--450461 Score: 484
Period size: 123 Copynumber: 2.0 Consensus size: 123
450201 GGGTAGATCA
*
450211 GAAACGTAGGGATGTACAGTTTCAGGTTGGAGACTTAGTCCTTGTTAAATTGCACTTGGTGTTAT
1 GAAACGTAGGGATGTACAGTTTCAGGTTGGAGACTTAGTCCTTGTTAAATTGCACTTGGTGTTAC
*
450276 GCAACCCAGGCATGCACAAAGGGCTTGTGCGAAGATACGAAGGCCCTTTCAAAGTTCT
66 GCAACCCAGGCATGCACAAAAGGCTTGTGCGAAGATACGAAGGCCCTTTCAAAGTTCT
450334 GAAACGTAGGGATGTACAGTTTCAGGTTGGAGACTTAGTCCTTGTTAAATTGCACTTGGTGTTAC
1 GAAACGTAGGGATGTACAGTTTCAGGTTGGAGACTTAGTCCTTGTTAAATTGCACTTGGTGTTAC
450399 GCAACCCAGGCATGCACAAAAGGCTTGTGCGAAGATACGAAGGCCCTTTCAAAGTTCT
66 GCAACCCAGGCATGCACAAAAGGCTTGTGCGAAGATACGAAGGCCCTTTCAAAGTTCT
450457 GAAAC
1 GAAAC
450462 TGGTAGGTAA
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (123 bp):
GAAACGTAGGGATGTACAGTTTCAGGTTGGAGACTTAGTCCTTGTTAAATTGCACTTGGTGTTAC
GCAACCCAGGCATGCACAAAAGGCTTGTGCGAAGATACGAAGGCCCTTTCAAAGTTCT
Found at i:451633 original size:12 final size:12
Alignment explanation
Indices: 451618--451677 Score: 72
Period size: 11 Copynumber: 5.2 Consensus size: 12
451608 TGTTATGAAA
*
451618 ATTATTAAAAAT
1 ATTATTAAAATT
451630 ATTATTAAAATT
1 ATTATTAAAATT
451642 ATTA-TAAAATT
1 ATTATTAAAATT
*
451653 A-TATCAAAATT
1 ATTATTAAAATT
451664 A-TATTAAAAGTT
1 ATTATTAAAA-TT
451676 AT
1 AT
451678 CAAAATTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
10 2 0.05
11 22 0.52
12 18 0.43
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
ATTATTAAAATT
Found at i:451649 original size:11 final size:11
Alignment explanation
Indices: 451610--451665 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
451600 ATGTCTAATG
451610 TTATGAAAATTA
1 TTAT-AAAATTA
451622 TTA-AAAA-TA
1 TTATAAAATTA
451631 TTATTAAAATTA
1 TTA-TAAAATTA
451643 TTATAAAATTA
1 TTATAAAATTA
451654 -TATCAAAATTA
1 TTAT-AAAATTA
451665 T
1 T
451666 ATTAAAAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 19 0.49
12 8 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (11 bp):
TTATAAAATTA
Found at i:451666 original size:11 final size:10
Alignment explanation
Indices: 451615--451688 Score: 62
Period size: 11 Copynumber: 7.0 Consensus size: 10
451605 TAATGTTATG
451615 AAAATTAT-T
1 AAAATTATAT
*
451624 AAAAATATTATT
1 AAAATTA-TA-T
451636 AAAATTATTAT
1 AAAATTA-TAT
451647 AAAATTATAT
1 AAAATTATAT
451657 CAAAATTATATT
1 -AAAATTATA-T
*
451669 AAAAGTTAT-C
1 AAAA-TTATAT
451679 AAAATTATAT
1 AAAATTATAT
451689 TAATGATTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
9 10 0.19
10 8 0.15
11 21 0.39
12 15 0.28
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (10 bp):
AAAATTATAT
Found at i:451699 original size:21 final size:21
Alignment explanation
Indices: 451609--451691 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
451599 TATGTCTAAT
* *
451609 GTTATGAAAATTAT-TAAAAA
1 GTTATCAAAATTATATTAAAA
* *
451629 TATTATTAAAATTATTA-TAAAA
1 -GTTATCAAAATTA-TATTAAAA
*
451651 TTATATCAAAATTATATTAAAA
1 GT-TATCAAAATTATATTAAAA
451673 GTTATCAAAATTATATTAA
1 GTTATCAAAATTATATTAA
451692 TGATTATCTC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 31 0.60
22 21 0.40
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
GTTATCAAAATTATATTAAAA
Found at i:453028 original size:20 final size:20
Alignment explanation
Indices: 452999--453074 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
452989 TTTTTACCTT
452999 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
453019 AATATATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* * *
453039 AATGTATCGATATATTCTAC
1 AATGTATCGATACATTTTTC
*
453059 AATGTATTGATACATT
1 AATGTATCGATACATT
453075 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:453071 original size:40 final size:39
Alignment explanation
Indices: 452999--453077 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
452989 TTTTTACCTT
* *
452999 AATGTATCGATACATTTTTCAATATATCGATACATGTATG
1 AATGTATCGATACATTCTACAATATATCGATACAT-TATG
* * *
453039 AATGTATCGATATATTCTACAATGTATTGATACATTATG
1 AATGTATCGATACATTCTACAATATATCGATACATTATG
453078 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (39 bp):
AATGTATCGATACATTCTACAATATATCGATACATTATG
Found at i:459351 original size:13 final size:13
Alignment explanation
Indices: 459330--459364 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
459320 ATTCACATTA
*
459330 TATCGATACACTG
1 TATCAATACACTG
459343 TATCAATACACTG
1 TATCAATACACTG
459356 TATCAATAC
1 TATCAATAC
459365 TAAGTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (13 bp):
TATCAATACACTG
Found at i:461964 original size:15 final size:15
Alignment explanation
Indices: 461917--461975 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
461907 TATAAATTGA
*
461917 AATAA-AATAATAAT
1 AATAATAATAATAAC
461931 AATAATAATAATAAC
1 AATAATAATAATAAC
*
461946 AATAATAATAA-AGC
1 AATAATAATAATAAC
461960 AAATAATAAATAATAA
1 -AATAAT-AATAATAA
461976 AAGCATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
14 7 0.18
15 25 0.66
16 5 0.13
17 1 0.03
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:461975 original size:3 final size:3
Alignment explanation
Indices: 461917--461956 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
461907 TATAAATTGA
*
461917 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
461957 AGCAAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:462447 original size:19 final size:20
Alignment explanation
Indices: 462411--462448 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
462401 ATTGAGCTCT
*
462411 ATTACAATCTTAAAAAATAA
1 ATTACAATCATAAAAAATAA
*
462431 ATTA-AATCATAATAAATA
1 ATTACAATCATAAAAAATA
462449 TATAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTACAATCATAAAAAATAA
Found at i:464244 original size:23 final size:22
Alignment explanation
Indices: 464209--464252 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
464199 AGAATTAAAA
**
464209 TTTTAAATTTAATAAATATTAAT
1 TTTTAAAAATAAT-AATATTAAT
*
464232 TTTTAAAAATAATTATATTAA
1 TTTTAAAAATAATAATATTAA
464253 CTAATTGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAAATAATAATATTAAT
Found at i:468819 original size:29 final size:31
Alignment explanation
Indices: 468753--468835 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 31
468743 AATGTGAAAT
*
468753 AAAATTTATTT-GAGTGTAAATAAAAAATTA
1 AAAATTTATTTAGAGTATAAATAAAAAATTA
* *
468783 ATATTTTATTTAGA-TAT-AAT-AAAAATATA
1 AAAATTTATTTAGAGTATAAATAAAAAAT-TA
*
468812 AAAATTTATTTA-AG-AAAAATAAAA
1 AAAATTTATTTAGAGTATAAATAAAA
468836 GAGTGCGGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
28 8 0.19
29 18 0.43
30 14 0.33
31 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (31 bp):
AAAATTTATTTAGAGTATAAATAAAAAATTA
Found at i:469396 original size:18 final size:18
Alignment explanation
Indices: 469373--469413 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
469363 ACTTCATTTG
469373 TTTTTTTTCCTTTTGC-C
1 TTTTTTTTCCTTTTGCTC
*
469390 TTTTTTTTCCTTTTTCTC
1 TTTTTTTTCCTTTTGCTC
469408 TTTTTT
1 TTTTTT
469414 GCCTTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTTTCCTTTTGCTC
Found at i:469441 original size:3 final size:3
Alignment explanation
Indices: 469433--469462 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
469423 ACGATTTTTT
469433 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
469463 TTTTAATTTT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:469922 original size:14 final size:14
Alignment explanation
Indices: 469902--469936 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
469892 TAAATTTATA
469902 AAAAAATAATTTTT
1 AAAAAATAATTTTT
*
469916 TAAAAATAATTTTT
1 AAAAAATAATTTTT
469930 AAAAAAT
1 AAAAAAT
469937 TAAAAAGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAAATAATTTTT
Found at i:470608 original size:30 final size:30
Alignment explanation
Indices: 470574--470630 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
470564 TTTCTCTCTT
470574 TTTTTTTTTAGATTAACTTTAAGCTTTCTC
1 TTTTTTTTTAGATTAACTTTAAGCTTTCTC
*
470604 TTTTTTTTTAGATTAATTTTAAGCTTT
1 TTTTTTTTTAGATTAACTTTAAGCTTT
470631 TAGATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTTTTTTTAGATTAACTTTAAGCTTTCTC
Found at i:472568 original size:17 final size:17
Alignment explanation
Indices: 472546--472579 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
472536 CAAGCTATTG
*
472546 AAAAAATAAAGACAATA
1 AAAAAAGAAAGACAATA
*
472563 AAAAAAGAAAGAGAATA
1 AAAAAAGAAAGACAATA
472580 CCAAAGATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (17 bp):
AAAAAAGAAAGACAATA
Found at i:472686 original size:13 final size:13
Alignment explanation
Indices: 472668--472698 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
472658 GAGAATACAA
472668 GAGAGAGATGCTT
1 GAGAGAGATGCTT
472681 GAGAGAGATGCTT
1 GAGAGAGATGCTT
472694 GAGAG
1 GAGAG
472699 GGAGGAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.19
Consensus pattern (13 bp):
GAGAGAGATGCTT
Found at i:472816 original size:26 final size:24
Alignment explanation
Indices: 472764--472817 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
472754 TAGCCACAAA
* * *
472764 TTTTGACAAATAACATACCACTAT
1 TTTTGACAAATAAAAAACCACCAT
472788 TTTTGACAAATAAAAAAAACCACCAT
1 TTTTGACAAAT--AAAAAACCACCAT
472814 TTTT
1 TTTT
472818 TGCAAACACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
26 14 0.56
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (24 bp):
TTTTGACAAATAAAAAACCACCAT
Found at i:476627 original size:2 final size:2
Alignment explanation
Indices: 476620--476644 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
476610 CATCTTTATT
476620 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
476645 GATGTGGCGG
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:478118 original size:31 final size:31
Alignment explanation
Indices: 478080--478151 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
478070 TATTAGTTTC
*
478080 AAGTTTTTTCAGGTTAAAATTTTTTAAATTA
1 AAGTTTTTTCAGGTTAAAAATTTTTAAATTA
478111 AAGTTTTTTCAGGTTAAAAATTTTTAAATTA
1 AAGTTTTTTCAGGTTAAAAATTTTTAAATTA
*
478142 AAATTTTTTC
1 AAGTTTTTTC
478152 TGATTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.51
Consensus pattern (31 bp):
AAGTTTTTTCAGGTTAAAAATTTTTAAATTA
Found at i:478157 original size:16 final size:16
Alignment explanation
Indices: 478083--478159 Score: 77
Period size: 15 Copynumber: 4.9 Consensus size: 16
478073 TAGTTTCAAG
*
478083 TTTTTTCAGGTTAAAA
1 TTTTTTCAGATTAAAA
* *
478099 TTTTTT-AAATTAAAG
1 TTTTTTCAGATTAAAA
*
478114 TTTTTTCAGGTTAAAA
1 TTTTTTCAGATTAAAA
* *
478130 ATTTTT-AAATTAAAA
1 TTTTTTCAGATTAAAA
*
478145 TTTTTTCTGATTAAA
1 TTTTTTCAGATTAAA
478160 TTCACCTTGA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
15 24 0.51
16 23 0.49
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.52
Consensus pattern (16 bp):
TTTTTTCAGATTAAAA
Found at i:478767 original size:22 final size:21
Alignment explanation
Indices: 478715--478771 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
478705 ATTTATTCAA
478715 TTTATAAAATAAAATTTTAAT
1 TTTATAAAATAAAATTTTAAT
*
478736 TTTATTAAAATAAAATGATTTTAT
1 TTTA-TAAAATAAAAT--TTTAAT
478760 TTTA-AAAATAAA
1 TTTATAAAATAAA
478772 TAAAGTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 4 0.12
22 19 0.59
24 9 0.28
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTATAAAATAAAATTTTAAT
Found at i:485411 original size:14 final size:15
Alignment explanation
Indices: 485385--485413 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
485375 ATGTTTTAAC
485385 ATTTTATAAAATATA
1 ATTTTATAAAATATA
485400 ATTTTA-AAAATATA
1 ATTTTATAAAATATA
485414 TAGAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTATAAAATATA
Found at i:486404 original size:3 final size:3
Alignment explanation
Indices: 486396--486432 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
486386 TGTATTTTAT
486396 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
486433 GTTCTGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:486612 original size:2 final size:2
Alignment explanation
Indices: 486605--486648 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
486595 TTGCATTGCA
*
486605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486647 AT
1 AT
486649 TACACTTCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:486702 original size:2 final size:2
Alignment explanation
Indices: 486695--486721 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
486685 TTAGCAGCAA
486695 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 A
486722 AATAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:489904 original size:2 final size:2
Alignment explanation
Indices: 489893--489925 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
489883 GTAATGGTAA
489893 AT AT -T 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
489926 TGGTTTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:497855 original size:17 final size:15
Alignment explanation
Indices: 497811--497859 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
497801 CTGATGTTCG
497811 TTATAATTAATTAAT
1 TTATAATTAATTAAT
*
497826 TTCTAA-TATATTATCAT
1 TTATAATTA-ATTA--AT
497843 TTATAATTAATTAAT
1 TTATAATTAATTAAT
497858 TT
1 TT
497860 TCATTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.07
15 13 0.46
17 11 0.39
18 2 0.07
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATAATTAATTAAT
Found at i:498654 original size:14 final size:14
Alignment explanation
Indices: 498635--498665 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
498625 CTTCTTAAAG
498635 TTAAATTTTTTATT
1 TTAAATTTTTTATT
498649 TTAAATTTTTTATT
1 TTAAATTTTTTATT
498663 TTA
1 TTA
498666 CTGAGTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTAAATTTTTTATT
Found at i:499914 original size:2 final size:2
Alignment explanation
Indices: 499907--499942 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
499897 ATAAATACTA
* *
499907 AT AT AT AT AT AT AA AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
499943 TCCACCTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 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:502214 original size:18 final size:18
Alignment explanation
Indices: 502172--502216 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
502162 AACAAATGCC
* *
502172 TCTTTTCATTTGAATACA
1 TCTTTTTATCTGAATACA
502190 TCTTTTTATCTGAATACA
1 TCTTTTTATCTGAATACA
502208 TCTTTTTAT
1 TCTTTTTAT
502217 TAAAGATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (18 bp):
TCTTTTTATCTGAATACA
Found at i:505185 original size:30 final size:31
Alignment explanation
Indices: 505144--505205 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
505134 TTTATTATTA
505144 TTTAAAATATAT-A-AATATAATAAATAAATT
1 TTTAAAATATATAATAAT-TAATAAATAAATT
* *
505174 TTTATAATATATAATAATTAATTAATAAATT
1 TTTAAAATATATAATAATTAATAAATAAATT
505205 T
1 T
505206 AAATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.39
31 14 0.50
32 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTAAAATATATAATAATTAATAAATAAATT
Found at i:505349 original size:21 final size:21
Alignment explanation
Indices: 505320--505371 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
505310 TAATTTTTAT
* * *
505320 TTTATTTTTATTTTTATAATA
1 TTTAATTTTATTATTATAACA
505341 TTTAATTTTATTATTATAACA
1 TTTAATTTTATTATTATAACA
*
505362 ATTAATTTTA
1 TTTAATTTTA
505372 CTGTACTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAATTTTATTATTATAACA
Found at i:505357 original size:27 final size:30
Alignment explanation
Indices: 505293--505357 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 30
505283 TATTTTTACA
* *
505293 ATTAATATTTTTAATAATAATTTTTATTTT
1 ATTATTATTTTTAATAATAATTTTAATTTT
*
505323 ATTTTTATTTTT-ATAAT-A-TTTAATTTT
1 ATTATTATTTTTAATAATAATTTTAATTTT
505350 ATTATTAT
1 ATTATTAT
505358 AACAATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 15 0.48
28 1 0.03
29 5 0.16
30 10 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
ATTATTATTTTTAATAATAATTTTAATTTT
Found at i:507848 original size:46 final size:46
Alignment explanation
Indices: 507780--507877 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
507770 ATGTAGCCTT
* * * * *
507780 CAAGACTAGGAGTAGGATTAGGGCATTCAATAAGGTATACAGCTTG
1 CAAGACTAGGACTACGACTAGGGCATTCAATAAGGTATACACCTCG
*
507826 CAAGACTAGGACTACGACTAGGGCATTCAATTAGGTATACACCTCG
1 CAAGACTAGGACTACGACTAGGGCATTCAATAAGGTATACACCTCG
507872 CAAGAC
1 CAAGAC
507878 CGGAGCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (46 bp):
CAAGACTAGGACTACGACTAGGGCATTCAATAAGGTATACACCTCG
Found at i:508074 original size:16 final size:15
Alignment explanation
Indices: 508055--508121 Score: 55
Period size: 17 Copynumber: 4.2 Consensus size: 15
508045 TATATTATAA
508055 TTATATTTAAAATATT
1 TTATATTTAAAA-ATT
508071 TTATATTTATATAAATT
1 TTATATTTA-A-AAATT
*
508088 TTAATATATTAATAATT
1 TT-ATAT-TTAAAAATT
* *
508105 TTAT-TATAAAATTT
1 TTATATTTAAAAATT
508119 TTA
1 TTA
508122 AATATATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 9 0.21
15 1 0.02
16 11 0.26
17 12 0.28
18 7 0.16
19 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTTAAAAATT
Found at i:508076 original size:45 final size:45
Alignment explanation
Indices: 508026--508155 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 45
508016 ATAATTTATA
508026 TTATATTTATATATTTTATTATATTATAATTATATT-TAAAATATT
1 TTATATTTATATATTTTATTATATTATAATTATATTATAAAAT-TT
* *
508071 TTATATTTATATAAATTTTAATATATTAATAATTTTATTATAAAATTT
1 TTATATTTATAT--ATTTTATTATATT-ATAATTATATTATAAAATTT
* * * *
508119 TTA-A-ATATATATTAATATTATATTATATTTTTATTAT
1 TTATATTTATATATT-TTATTATATTATAATTATATTAT
508156 TTTATATATT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
44 15 0.20
45 20 0.27
46 5 0.07
47 13 0.18
48 15 0.20
49 6 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (45 bp):
TTATATTTATATATTTTATTATATTATAATTATATTATAAAATTT
Found at i:508076 original size:50 final size:52
Alignment explanation
Indices: 508015--508147 Score: 147
Period size: 50 Copynumber: 2.7 Consensus size: 52
508005 ATTTAAATTT
*
508015 AATAATTTATATTATATTTATATATTTTATTATATT-ATAATTATATT-TAA
1 AATATTTTATATTATATTTATATATTTTATTATATTAATAATTATATTATAA
* * *
508065 AATATTTTATATT-TA--TATAAATTTTAATATATTAATAATTTTATTATAA
1 AATATTTTATATTATATTTATATATTTTATTATATTAATAATTATATTATAA
* *
508114 AAT-TTTTA-AATATATATTA-ATATTATATTATATT
1 AATATTTTATATTATAT-TTATATATTTTATTATATT
508148 TTTATTATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
47 18 0.26
48 17 0.25
49 8 0.12
50 24 0.35
51 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (52 bp):
AATATTTTATATTATATTTATATATTTTATTATATTAATAATTATATTATAA
Found at i:508084 original size:30 final size:29
Alignment explanation
Indices: 508021--508168 Score: 89
Period size: 28 Copynumber: 5.2 Consensus size: 29
508011 ATTTAATAAT
*
508021 TTAT-ATTATATTTATATATTTTATTATA
1 TTATAATTATATTTAAATATTTTATTATA
508049 TTATAATTATATTTAAAATATTTTA-TAT-
1 TTATAATTATATTT-AAATATTTTATTATA
* * *
508077 TTAT-A-TAAATTTTAATATATTAATAATTTTA
1 TTATAATTATA-TTTAA-ATATT--TTATTATA
* * *
508108 TTATAA-AATTTTTAAATA-TATATTAATA
1 TTATAATTATATTTAAATATTTTATT-ATA
* *
508136 TTAT-ATTATATTTTTATTATTTTA-TATA
1 TTATAATTATA-TTTAAATATTTTATTATA
508164 TTATA
1 TTATA
508169 TTTAAATAAT
Statistics
Matches: 91, Mismatches: 15, Indels: 27
0.68 0.11 0.20
Matches are distributed among these distances:
26 5 0.05
27 13 0.14
28 23 0.25
29 22 0.24
30 17 0.19
31 9 0.10
32 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTATAATTATATTTAAATATTTTATTATA
Found at i:508098 original size:47 final size:46
Alignment explanation
Indices: 508026--508130 Score: 133
Period size: 48 Copynumber: 2.3 Consensus size: 46
508016 ATAATTTATA
*
508026 TTATATTTATATATTTTATTATATT-ATAATTATATT-TAAAATATT
1 TTATATTTATATATTTTAATATATTAATAATTATATTATAAAAT-TT
*
508071 TTATATTTATATAAATTTTAATATATTAATAATTTTATTATAAAATTT
1 TTATATTTATAT--ATTTTAATATATTAATAATTATATTATAAAATTT
* *
508119 TTAAATATATAT
1 TTATATTTATAT
508131 TAATATTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
45 12 0.23
47 12 0.23
48 22 0.42
49 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (46 bp):
TTATATTTATATATTTTAATATATTAATAATTATATTATAAAATTT
Found at i:508121 original size:31 final size:32
Alignment explanation
Indices: 508071--508146 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 32
508061 TTAAAATATT
508071 TTATATTTATATAAATTTT-A-ATATATTAATAA
1 TTATA-TTATATAAATTTTAATATATATTAAT-A
*
508103 TTTTATTATA-AAATTTTTAAATATATATTAATA
1 TTATATTATATAAA-TTTT-AATATATATTAATA
508136 TTATATTATAT
1 TTATATTATAT
508147 TTTTATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 3 0.08
31 9 0.24
32 4 0.11
33 11 0.30
34 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTATATTATATAAATTTTAATATATATTAATA
Found at i:508186 original size:14 final size:13
Alignment explanation
Indices: 508138--508193 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
508128 TATTAATATT
508138 ATATTATATTT--
1 ATATTATATTTAA
* *
508149 TTATTAT-TTTAT
1 ATATTATATTTAA
508161 ATATTATATTTAA
1 ATATTATATTTAA
508174 ATAATTATATTTAA
1 AT-ATTATATTTAA
508188 A-ATTAT
1 ATATTAT
508194 TATATATACT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.08
11 6 0.16
12 11 0.29
13 6 0.16
14 12 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTATATTTAA
Found at i:508195 original size:15 final size:14
Alignment explanation
Indices: 508149--508198 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
508139 TATTATATTT
*
508149 TTATTAT-TTTATA
1 TTATTATATTTAAA
508162 -TATTATATTTAAA
1 TTATTATATTTAAA
*
508175 TAATTATATTTAAAA
1 TTATTATATTT-AAA
508190 TTATTATAT
1 TTATTATAT
508199 ATACTCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 6 0.19
13 5 0.16
14 9 0.29
15 11 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATTATATTTAAA
Found at i:508409 original size:20 final size:20
Alignment explanation
Indices: 508384--508436 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
508374 TGATTAAATT
508384 AATTAAATT-ATTAATTTTTA
1 AATTAAATTAATT-ATTTTTA
*
508404 AATTAATTTAATTATTTTTA
1 AATTAAATTAATTATTTTTA
508424 ATATTAAA-TAATT
1 A-ATTAAATTAATT
508437 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTAAATTAATTATTTTTA
Found at i:508500 original size:24 final size:23
Alignment explanation
Indices: 508473--508535 Score: 90
Period size: 24 Copynumber: 2.7 Consensus size: 23
508463 TTTTTTTAAG
*
508473 AAAAATTCTAAAAATATAAAATTA
1 AAAAATTCTAAAAATA-AAAAATA
*
508497 AAAAATTTTAAAAATAAAAAATA
1 AAAAATTCTAAAAATAAAAAATA
508520 AATAAATTCTAAAAAT
1 AA-AAATTCTAAAAAT
508536 TTTTAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
23 8 0.23
24 27 0.77
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAATTCTAAAAATAAAAAATA
Found at i:508525 original size:33 final size:31
Alignment explanation
Indices: 508482--508565 Score: 98
Period size: 34 Copynumber: 2.6 Consensus size: 31
508472 GAAAAATTCT
*
508482 AAAAATATAAAATTAAAAAATTTTAAAAATAA
1 AAAAAAATAAAATTAAAAAATTTTAAAAA-AA
* *
508514 AAAATAAATAAATTCTAAAAATTTTTAAAAAAA
1 AAAA-AAATAAAAT-TAAAAAATTTTAAAAAAA
*
508547 TAAAAAATAAAA-TAAAAAA
1 AAAAAAATAAAATTAAAAAA
508566 CCTTTTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 6 0.14
32 11 0.25
33 12 0.27
34 15 0.34
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (31 bp):
AAAAAAATAAAATTAAAAAATTTTAAAAAAA
Found at i:509537 original size:2 final size:2
Alignment explanation
Indices: 509530--509568 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
509520 TTAATTAGAC
509530 AT AT AT 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 AT AT AT A
509569 CCCATGGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:510239 original size:16 final size:16
Alignment explanation
Indices: 510220--510259 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
510210 TTATATACAT
*
510220 ATTTTAATATCTTAAA
1 ATTTCAATATCTTAAA
* *
510236 ATTTCATTATCTTAAT
1 ATTTCAATATCTTAAA
510252 ATTTCAAT
1 ATTTCAAT
510260 TTTAACATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCAATATCTTAAA
Found at i:511429 original size:13 final size:13
Alignment explanation
Indices: 511393--511418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
511383 TTTTAGTTAC
511393 CTCTCTTCAAAAG
1 CTCTCTTCAAAAG
511406 CTCTCTTCAAAAG
1 CTCTCTTCAAAAG
511419 TGTGCTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
CTCTCTTCAAAAG
Found at i:512014 original size:27 final size:27
Alignment explanation
Indices: 511984--512125 Score: 93
Period size: 27 Copynumber: 5.2 Consensus size: 27
511974 TATAATGACG
511984 TTATATTTATATAATTTTATA-TTATAA
1 TTATATTTATATAATTTTATATTTAT-A
** *
512011 TTATATAAAAAT-ATTTTATATTTATA
1 TTATATTTATATAATTTTATATTTATA
512037 TTA-ATTT-TA-ATATATTTATAATTTATA
1 TTATATTTATATA-AT-TTTAT-ATTTATA
**
512064 TTATA-TTATATAAATTTTA-AAATATA
1 TTATATTTATAT-AATTTTATATTTATA
*
512090 TT-TATATTATAATTATTTTATATATTATA
1 TTATAT-TTAT-ATAATTTTATAT-TTATA
512119 TATATAT
1 T-TATAT
512126 AATTATATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
24 1 0.01
25 6 0.07
26 24 0.27
27 35 0.40
28 10 0.11
29 7 0.08
30 2 0.02
31 3 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATATTTATATAATTTTATATTTATA
Found at i:512123 original size:59 final size:60
Alignment explanation
Indices: 511984--512133 Score: 141
Period size: 64 Copynumber: 2.5 Consensus size: 60
511974 TATAATGACG
* *
511984 TTATAT-TTATATAATTTTATATTATA-ATTATATAAAAATATTTTATATTTATATTAATT
1 TTATATATTATAT-ATATTATATTATATATAATATAAAAATATTTTATATTTATATTAATT
* *
512043 TTAATATATTTATAATTTATATTATATTATATA-AATTTTAAAATATATTTATA-TTATAATT-A
1 TT-ATATA-TTAT-A--TATATTATATTATATATAATATAAAAATAT-TTTATATTTAT-ATTAA
512105 TT
59 TT
512107 TTATATATTATATATA-TATAATTATAT
1 TTATATATTATATATATTAT-ATTATAT
512134 TTGATATTAT
Statistics
Matches: 77, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
58 3 0.04
59 13 0.17
60 4 0.05
61 1 0.01
62 8 0.10
63 6 0.08
64 31 0.40
65 11 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (60 bp):
TTATATATTATATATATTATATTATATATAATATAAAAATATTTTATATTTATATTAATT
Found at i:512144 original size:29 final size:25
Alignment explanation
Indices: 512085--512145 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 25
512075 AAATTTTAAA
512085 ATATATT-TATATTATAATTATTTT
1 ATATATTATATATTATAATTATTTT
512109 ATATATTATATATATATAATTATATTT
1 ATATATTATATAT-TATAATTAT-TTT
512136 GATATTATTA
1 -ATA-TATTA
512146 AAATAACTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.22
25 5 0.16
26 9 0.28
27 3 0.09
28 3 0.09
29 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATATTATATATTATAATTATTTT
Found at i:519328 original size:153 final size:152
Alignment explanation
Indices: 518967--519335 Score: 361
Period size: 154 Copynumber: 2.4 Consensus size: 152
518957 ATTTAGACCT
* * * * * *
518967 GAGTCTTAGGTTGTCATTGAGTCGCTTTTATGTCAAAGGTGTGTATTTAGGCTAGGTTCACTCTT
1 GAGTC-TAGGTAGTCATCGAGTCACTTTTATGTCAAAGGTGTGTATTTAAGATAGATTCA-TCTT
* * * *
519032 CTAGTTTCACTTTTGTGTCCTTTAAGGTTATTGGAATGCTTTCACATTAAAGGTATACCCTAAGG
64 CTAGTTTCACTTTTGTGTCCTTTAAGGTTATAGGAATACTTTCACATCAAAGGTATACCCTAAAG
* * * *
519097 GCATTTTGATTTTTTTTTAGAATC
129 ACATTTTGATATTTTATTAAAATC
* ** * * * * * *
519121 AAGTCTCAATTAATCACCGAATCACTTTTATATCAAAGGTGTGTGTTTATGATAGATTCATCATT
1 GAGTCT-AGGTAGTCATCGAGTCACTTTTATGTCAAAGGTGTGTATTTAAGATAGATTCATC-TT
* * * *
519186 TTA-TGTTCA-TTTTCGTGTCTTTTAGGGTTATAGGAATAAC-TTCACGTCCAAA-GTATA-CCT
64 CTAGT-TTCACTTTT-GTGTCCTTTAAGGTTATAGGAAT-ACTTTCACAT-CAAAGGTATACCCT
*
519246 AAAGATATTTTGATAATTTTATTAAAATC
125 AAAGACATTTTGAT-ATTTTATTAAAATC
*
519275 GAGTCTAGGTAGTCATCGAGTCACTTTTATGTCAAAGGTGTGCATTTAAGATAGATTCATC
1 GAGTCTAGGTAGTCATCGAGTCACTTTTATGTCAAAGGTGTGTATTTAAGATAGATTCATC
519336 CTTATATTTT
Statistics
Matches: 171, Mismatches: 37, Indels: 15
0.77 0.17 0.07
Matches are distributed among these distances:
153 68 0.40
154 99 0.58
155 4 0.02
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (152 bp):
GAGTCTAGGTAGTCATCGAGTCACTTTTATGTCAAAGGTGTGTATTTAAGATAGATTCATCTTCT
AGTTTCACTTTTGTGTCCTTTAAGGTTATAGGAATACTTTCACATCAAAGGTATACCCTAAAGAC
ATTTTGATATTTTATTAAAATC
Done.