Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold499
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: 498087
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 3 of 4
Found at i:285968 original size:5 final size:5
Alignment explanation
Indices: 285958--285988 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
285948 ATTTAAACGA
285958 ATTAT ATTAT ATTAT ATTAT ATTAT -TTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
285989 ATTTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:285991 original size:8 final size:9
Alignment explanation
Indices: 285958--285995 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
285948 ATTTAAACGA
285958 ATTATATTAT
1 ATTAT-TTAT
285968 ATTATATTAT
1 ATTAT-TTAT
285978 ATTATTTAT
1 ATTATTTAT
285987 A-TATTTAT
1 ATTATTTAT
285995 A
1 A
285996 AATAATGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.29
9 5 0.18
10 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTATTTAT
Found at i:286258 original size:18 final size:18
Alignment explanation
Indices: 286235--286277 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
286225 AATTTTAAAT
*
286235 TAATTTTATATATTTTTA
1 TAATTTTATATATTATTA
*
286253 TAATTTTTTATATTATTA
1 TAATTTTATATATTATTA
286271 -AATTTTA
1 TAATTTTA
286278 ATAAATTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTATATATTATTA
Found at i:286355 original size:22 final size:24
Alignment explanation
Indices: 286330--286381 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
286320 TTTATATATA
*
286330 TTTTAATAGTTAA-AATTAAATT-T
1 TTTTAATA-TAAATAATTAAATTAT
286353 TTTTAA-ATAAATAATTAAA-TAT
1 TTTTAATATAAATAATTAAATTAT
286375 TTTTAAT
1 TTTTAAT
286382 TTACTCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.16
22 15 0.60
23 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTAATATAAATAATTAAATTAT
Found at i:291966 original size:2 final size:2
Alignment explanation
Indices: 291959--291991 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
291949 AATTTCTATT
291959 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
291992 AAACAAACAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:294083 original size:29 final size:29
Alignment explanation
Indices: 294044--294102 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
294034 AAAGATAAAT
* *
294044 TTCTAGAATGAAACATGATTAACAACCTA
1 TTCTAGAATGAAACATGATAAACAAACTA
*
294073 TTCTAGTATGAAACATGATAAACAAACTA
1 TTCTAGAATGAAACATGATAAACAAACTA
294102 T
1 T
294103 AAAAAAGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TTCTAGAATGAAACATGATAAACAAACTA
Found at i:299022 original size:2 final size:2
Alignment explanation
Indices: 299015--299090 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
299005 GAGGCAAAAT
* *
299015 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
299057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
299091 ACAGAAAAGG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:299790 original size:25 final size:26
Alignment explanation
Indices: 299750--299804 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
299740 AACTTACTTA
299750 TTATTAAAAAATTAAATAATATTA-AT
1 TTATTAAAAAATTAAATAAT-TTATAT
*
299776 TTATT-AAAAATTAAATTATTTATAT
1 TTATTAAAAAATTAAATAATTTATAT
299801 TTAT
1 TTAT
299805 ATTATTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.11
25 19 0.70
26 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATTAAAAAATTAAATAATTTATAT
Found at i:299887 original size:28 final size:28
Alignment explanation
Indices: 299830--299887 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
299820 AATCATCACT
*
299830 AATTAAAATATATATATATAAAAAATTA
1 AATTAAAATATATATATATAAAAAAATA
*
299858 AATT-AAATATCTA-ATATAAAATACAATA
1 AATTAAAATATATATATATAAAA-A-AATA
299886 AA
1 AA
299888 AGATATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 8 0.31
27 9 0.35
28 9 0.35
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (28 bp):
AATTAAAATATATATATATAAAAAAATA
Found at i:300300 original size:349 final size:346
Alignment explanation
Indices: 299886--300585 Score: 1088
Period size: 351 Copynumber: 2.0 Consensus size: 346
299876 AAATACAATA
* *
299886 AAAGATATTCATGTAATTTACTTTAAAAAAGTCTATTTCTTATGTAATATTTTAACTTGATTATT
1 AAAGATATTCATATAATTTACTTAAAAAAAGTCTATTTCTTATGTAATATTTTAACTTGATTATT
* * *
299951 TTATTGAAAAAATTTTATTTTAA-TTTATTTT-ATA-TTTTTTAAAAGAATTTTGATCATTAGAT
66 TTATT-AAAAAA-ATTATTTTAATTTTATTTTCATATTTTTTTAAAAAAATCTTGATCATTAGAT
* * * *
300013 TATTTATTTTAAATGGTTTATTAAATTAATTATTTTTAAT-TTTTTTCATTGTAAATGTAATATT
129 TATTTATTTTAAATGATTTATTAAATTAATTATTTTTAATCTTCTCTCATCGTAAATGTAATATT
* * * *
300077 TAGTATATTTTTAAAATTCTTTTAATAAAATATTATAATCTAATTTATTAATTGTATATCAATAC
194 TAATATATTTTTAAAATTCTTTTAATAAAATATTATAATCTAATATATTAATCGTATATCAACAC
*
300142 ATTAAATATAA-TTTTTTT-CGTAAACCAACCATATCAAAGAAACTTCTTTTCTTTTCTTTTATT
259 ATTAAATATAATTTTTTTTCCGCAAACCAACCATATCAAAGAAA---C--TTCTTTTCTTTTATT
*
300205 TTTGGATTAATGCTTGATTTTATTATCC
319 TTTGGATAAATGCTTGATTTTATTATCC
*
300233 AAAGATATTCATATAATTTACTTAAAAAAAAAGTCTATTTCTTATGTAATATTTTAACTTTATTA
1 AAAGATATTCATATAATTTACTT--AAAAAAAGTCTATTTCTTATGTAATATTTTAACTTGATTA
* **
300298 TTTTATTAAAAAAATTATTTTAATTTTTTTTTCATATTTTTTTAAAAAAATCTTGATGGTTAGAT
64 TTTTATTAAAAAAATTATTTTAATTTTATTTTCATATTTTTTTAAAAAAATCTTGATCATTAGAT
300363 TATTTATTTTAAATGATTTATTAAATTAATTATTTTTAATCTTCTCTCATCGTAAATGTAATATT
129 TATTTATTTTAAATGATTTATTAAATTAATTATTTTTAATCTTCTCTCATCGTAAATGTAATATT
* *
300428 TAATTTATTTTTAAAATTCTTTTAATAAAATATTGTAATCTAATATATTAATCGTATATCAACAC
194 TAATATATTTTTAAAATTCTTTTAATAAAATATTATAATCTAATATATTAATCGTATATCAACAC
300493 ATTAAATATAATTTTTTTTCCGCAAACCAACCATATCAAAGAAACTTCTTTTCTTTTATTTTTGG
259 ATTAAATATAATTTTTTTTCCGCAAACCAACCATATCAAAGAAACTTCTTTTCTTTTATTTTTGG
300558 ATAAATGCTTGATTTTATTATCC
324 ATAAATGCTTGATTTTATTATCC
300581 AAAGA
1 AAAGA
300586 AGAAACTTCT
Statistics
Matches: 324, Mismatches: 21, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
347 31 0.10
348 60 0.19
349 48 0.15
350 64 0.20
351 91 0.28
352 7 0.02
353 23 0.07
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (346 bp):
AAAGATATTCATATAATTTACTTAAAAAAAGTCTATTTCTTATGTAATATTTTAACTTGATTATT
TTATTAAAAAAATTATTTTAATTTTATTTTCATATTTTTTTAAAAAAATCTTGATCATTAGATTA
TTTATTTTAAATGATTTATTAAATTAATTATTTTTAATCTTCTCTCATCGTAAATGTAATATTTA
ATATATTTTTAAAATTCTTTTAATAAAATATTATAATCTAATATATTAATCGTATATCAACACAT
TAAATATAATTTTTTTTCCGCAAACCAACCATATCAAAGAAACTTCTTTTCTTTTATTTTTGGAT
AAATGCTTGATTTTATTATCC
Found at i:301274 original size:2 final size:2
Alignment explanation
Indices: 301267--301297 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
301257 CTGAATTCTA
301267 TC 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 TC T
301298 GACTCATTCT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:303177 original size:11 final size:12
Alignment explanation
Indices: 303138--303180 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
303128 TAAAATTTAA
303138 AATTATGAAATAT
1 AATTAT-AAATAT
*
303151 ATTTATAAAT-T
1 AATTATAAATAT
303162 AATTA-AAATAT
1 AATTATAAATAT
303173 AATTATAA
1 AATTATAA
303181 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 11 0.42
12 6 0.23
13 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
AATTATAAATAT
Found at i:313836 original size:15 final size:15
Alignment explanation
Indices: 313813--313842 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
313803 ATTTTTATTT
*
313813 AAATTTAATTATTAA
1 AAATATAATTATTAA
313828 AAATATAATTATTAA
1 AAATATAATTATTAA
313843 TATAATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATATAATTATTAA
Found at i:316662 original size:18 final size:20
Alignment explanation
Indices: 316635--316675 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
316625 CATTTAAAAA
316635 TTAAATTATTTATCTAA-AT
1 TTAAATTATTTATCTAATAT
*
316654 TTAAA-TATTTATTTAATAT
1 TTAAATTATTTATCTAATAT
316673 TTA
1 TTA
316676 GAGAGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAAATTATTTATCTAATAT
Found at i:317233 original size:16 final size:15
Alignment explanation
Indices: 317207--317248 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
317197 CCCGAATCTG
317207 ATTTGATTTATAAATAA
1 ATTT-ATTTATAAAT-A
*
317224 ATTTATTTATACATA
1 ATTTATTTATAAATA
317239 ATTT-TTTATA
1 ATTTATTTATA
317249 TCTTTTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 5 0.21
16 9 0.38
17 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
ATTTATTTATAAATA
Found at i:317365 original size:21 final size:20
Alignment explanation
Indices: 317314--317366 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
317304 CAACGGTAAC
317314 AGTGAAATTAATTATTATAA
1 AGTGAAATTAATTATTATAA
*
317334 AGAT-AAGATTAATTATTATAGT
1 AG-TGAA-ATTAATTATTATA-A
317356 AGTGAAATTAA
1 AGTGAAATTAA
317367 AATTAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 20 0.71
22 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (20 bp):
AGTGAAATTAATTATTATAA
Found at i:317579 original size:17 final size:17
Alignment explanation
Indices: 317557--317618 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
317547 TGATTAAATT
317557 TATATTAAAAAATTATA
1 TATATTAAAAAATTATA
**
317574 TATATTAAATAATAAAATA
1 TATATTAAA-AA-ATTATA
* *
317593 TATAATAAAATAATT-TT
1 TATATTAAAA-AATTATA
317610 TATATTAAA
1 TATATTAAA
317619 TAATGATGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
17 18 0.51
18 4 0.11
19 13 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATTAAAAAATTATA
Found at i:317602 original size:36 final size:36
Alignment explanation
Indices: 317552--317622 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
317542 AATATTGATT
* *
317552 AAATTTATATTAAAA-AATTATATATATTAAATAATA
1 AAATATATAATAAAATAATT-TATATATTAAATAATA
*
317588 AAATATATAATAAAATAATTTTTATATTAAATAAT
1 AAATATATAATAAAATAATTTATATATTAAATAAT
317623 GATGCAGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
AAATATATAATAAAATAATTTATATATTAAATAATA
Found at i:318201 original size:19 final size:19
Alignment explanation
Indices: 318177--318214 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
318167 ATGTATTTTG
* *
318177 TTTATTTTACTTGTTATAT
1 TTTATTTTAATTATTATAT
318196 TTTATTTTAATTATTATAT
1 TTTATTTTAATTATTATAT
318215 AAATTTTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTATTTTAATTATTATAT
Found at i:318834 original size:10 final size:8
Alignment explanation
Indices: 318801--318829 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
318791 AATTATATTT
318801 ATATATAA
1 ATATATAA
318809 ATATATAA
1 ATATATAA
318817 ATATATAA
1 ATATATAA
318825 ATATA
1 ATATA
318830 CATAATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAA
Found at i:318908 original size:16 final size:17
Alignment explanation
Indices: 318887--318918 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
318877 TGAAAATGAT
318887 AAATTAA-AATTTAAAA
1 AAATTAATAATTTAAAA
318903 AAATTAATAATTTAAA
1 AAATTAATAATTTAAA
318919 TTTATATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTAATAATTTAAAA
Found at i:319172 original size:14 final size:14
Alignment explanation
Indices: 319155--319196 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
319145 TATTTATTTT
319155 TTTAATTTATAAAA
1 TTTAATTTATAAAA
*
319169 TTTAAATT-TAAAA
1 TTTAATTTATAAAA
* *
319182 TTTTATTTAAAAAA
1 TTTAATTTATAAAA
319196 T
1 T
319197 AAGTATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTTATAAAA
Found at i:319761 original size:31 final size:32
Alignment explanation
Indices: 319703--319777 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
319693 ATAAATTAAA
* *
319703 TTAAATTATGATTTAAATTTTTATATTTTTGT
1 TTAAATTATAATTTAAATTTATATATTTTTGT
*
319735 TTAAATT-TAATTTAAATATTAT-TATTTTTAT
1 TTAAATTATAATTTAAAT-TTATATATTTTTGT
319766 ATTAATATTATA
1 -TTAA-ATTATA
319778 TTTTTTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 17 0.47
32 14 0.39
33 3 0.08
34 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (32 bp):
TTAAATTATAATTTAAATTTATATATTTTTGT
Found at i:319774 original size:20 final size:18
Alignment explanation
Indices: 319749--319790 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 18
319739 ATTTAATTTA
319749 AATATTATTATTTTTATATT
1 AATATTA-TATTTTT-TATT
319769 AATATTATATTTTTTATT
1 AATATTATATTTTTTATT
319787 AATA
1 AATA
319791 AACAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATATTATATTTTTTATT
Found at i:320889 original size:30 final size:28
Alignment explanation
Indices: 320855--320928 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 28
320845 CTTTAAAAGT
*
320855 TAAATATATTTTAATTAAATTTTAAAAAAA
1 TAAATATATTTT--TTAAATATTAAAAAAA
*
320885 TAAATATATATTTTTTAATATTAAAAAAA
1 TAAATATAT-TTTTTAAATATTAAAAAAA
*
320914 TAATTATATTTTTTA
1 TAAATATATTTTTTA
320929 TAAAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 5 0.13
29 22 0.56
30 9 0.23
31 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAAATATATTTTTTAAATATTAAAAAAA
Found at i:320941 original size:15 final size:16
Alignment explanation
Indices: 320918--320951 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
320908 AAAAAATAAT
*
320918 TATATTTTTTATAAAA
1 TATATTTTTTAAAAAA
320934 TATA-TTTTTAAAAAA
1 TATATTTTTTAAAAAA
320949 TAT
1 TAT
320952 CTTTCACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTTTTTAAAAAA
Found at i:321327 original size:14 final size:14
Alignment explanation
Indices: 321276--321329 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
321266 AATAAATTTA
*
321276 ATAA-ATATTTAAA
1 ATAATATATTTAAT
*
321289 ATAATATTTTTAA-
1 ATAATATATTTAAT
321302 A-AAT-TA-TTAAT
1 ATAATATATTTAAT
321313 ATAATATATTTAAT
1 ATAATATATTTAAT
321327 ATA
1 ATA
321330 TTTATAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 4 0.12
11 2 0.06
12 6 0.18
13 7 0.21
14 15 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATAATATATTTAAT
Found at i:321404 original size:15 final size:16
Alignment explanation
Indices: 321386--321420 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
321376 AATAAATTAA
321386 TTAT-AAAAATATTTT
1 TTATAAAAAATATTTT
321401 TTATAAAAAAATATTTT
1 TTAT-AAAAAATATTTT
321418 TTA
1 TTA
321421 ATTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
17 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAAAAAATATTTT
Found at i:321695 original size:2 final size:2
Alignment explanation
Indices: 321688--321712 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
321678 TTTTATTATT
321688 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
321713 GAAGTTGAAA
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:322573 original size:14 final size:15
Alignment explanation
Indices: 322547--322575 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
322537 ATAAATTTAA
322547 TTTAATGATATAATT
1 TTTAATGATATAATT
322562 TTTAAT-ATATAATT
1 TTTAATGATATAATT
322576 ATATATAAAA
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:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTAATGATATAATT
Found at i:324461 original size:3 final size:3
Alignment explanation
Indices: 324444--324493 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
324434 TCAATGGATG
* * * *
324444 TTA TTA -TA TTG TTA TTA TCA TTA TCA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
324491 TTA
1 TTA
324494 GCATTAACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:324475 original size:9 final size:9
Alignment explanation
Indices: 324444--324499 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
324434 TCAATGGATG
324444 TTATTAT-A
1 TTATTATCA
* *
324452 TTGTTATTA
1 TTATTATCA
*
324461 TCATTATCA
1 TTATTATCA
*
324470 TTATTATTA
1 TTATTATCA
324479 TTATTATCA
1 TTATTATCA
*
324488 TTATTAGCA
1 TTATTATCA
324497 TTA
1 TTA
324500 ACTTCCTCTG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
8 6 0.15
9 33 0.85
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (9 bp):
TTATTATCA
Found at i:325579 original size:2 final size:2
Alignment explanation
Indices: 325572--325597 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
325562 TTAATAATTA
325572 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
325598 TTTGTTCCTT
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:329533 original size:10 final size:10
Alignment explanation
Indices: 329494--329530 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
329484 AGGTATTTAG
329494 ATATATAACT
1 ATATATAACT
329504 ATATATAACT
1 ATATATAACT
329514 ATATATATA-T
1 ATATATA-ACT
329524 ATATATA
1 ATATATA
329531 TATGTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 25 0.96
11 1 0.04
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATAACT
Found at i:330347 original size:21 final size:21
Alignment explanation
Indices: 330321--330360 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
330311 TCTACGACAG
330321 TGAAAGTACTCGCTCTCTCGA
1 TGAAAGTACTCGCTCTCTCGA
*
330342 TGAAAGTACTTGCTCTCTC
1 TGAAAGTACTCGCTCTCTC
330361 AGTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.33
Consensus pattern (21 bp):
TGAAAGTACTCGCTCTCTCGA
Found at i:331097 original size:24 final size:23
Alignment explanation
Indices: 331045--331099 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
331035 TTATGATATC
*
331045 AAATTTAATTAATAAGTTTAATA
1 AAATTTAATTAATAAGTGTAATA
*
331068 ATAATTTAGATATAATAAGTGT-ATT
1 A-AATTTA-AT-TAATAAGTGTAATA
331093 AAATTTA
1 AAATTTA
331100 TTGAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 12 0.44
25 5 0.19
26 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (23 bp):
AAATTTAATTAATAAGTGTAATA
Found at i:331687 original size:27 final size:28
Alignment explanation
Indices: 331657--331710 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
331647 ATTATACTTA
* *
331657 TTATAAAATATTATTTA-TTTTAAAAAT
1 TTATAAAATATTAATAATTTTTAAAAAT
*
331684 TTATAAATTATTAATAATTTTTAAAAA
1 TTATAAAATATTAATAATTTTTAAAAA
331711 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATAAAATATTAATAATTTTTAAAAAT
Found at i:331755 original size:42 final size:39
Alignment explanation
Indices: 331676--331763 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 39
331666 ATTATTTATT
331676 TTAAAAATTTATAAATTATTAATAATTTTTAAAAAAAAA
1 TTAAAAATTTATAAATTATTAATAATTTTTAAAAAAAAA
*
331715 TTAAAAATTTTATATTAATTAATTAA-AA-TTTTAAATAAAAA
1 TTAAAAA-TTTATA--AATT-ATTAATAATTTTTAAAAAAAAA
*
331756 TTTAAAAT
1 TTAAAAAT
331764 AATTATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
39 7 0.16
40 7 0.16
41 18 0.42
42 6 0.14
43 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (39 bp):
TTAAAAATTTATAAATTATTAATAATTTTTAAAAAAAAA
Found at i:336771 original size:4 final size:4
Alignment explanation
Indices: 336750--336798 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
336740 AGCTGGCAGA
* * * * *
336750 ATAT ACAT ATAC ATAT ATAT ATAT ATAT ATGT ATAT GTAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
336798 A
1 A
336799 GTAAATTTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (4 bp):
ATAT
Found at i:336775 original size:10 final size:10
Alignment explanation
Indices: 336750--336798 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
336740 AGCTGGCAGA
*
336750 ATATACATAT
1 ATATATATAT
*
336760 ACATATATAT
1 ATATATATAT
336770 ATATATATAT
1 ATATATATAT
* *
336780 GTATATGTAT
1 ATATATATAT
*
336790 GTATATATA
1 ATATATATA
336799 GTAAATTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (10 bp):
ATATATATAT
Found at i:336779 original size:6 final size:6
Alignment explanation
Indices: 336750--336798 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
336740 AGCTGGCAGA
* * * * *
336750 ATATAC ATATAC ATATAT ATATAT ATATAT GTATAT GTATGT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
336798 A
1 A
336799 GTAAATTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:344116 original size:78 final size:79
Alignment explanation
Indices: 343993--344137 Score: 283
Period size: 78 Copynumber: 1.8 Consensus size: 79
343983 AAACATGTAA
343993 ATGTGATACATTAAAGAACACTGTGATTTATGAAAAAGAAAAGGAGGAGAAA-GGGGGGTGATAT
1 ATGTGATACATTAAAGAACACTGTGATTTATGAAAAAGAAAAGGAGGAGAAAGGGGGGGTGATAT
344057 AAAGGAGGAGTTAC
66 AAAGGAGGAGTTAC
344071 ATGTGATACATTAAAGAACACTGTGATTTATGAAAAAGAAAAGGAGGAGAAAGGGGGGGTGATAT
1 ATGTGATACATTAAAGAACACTGTGATTTATGAAAAAGAAAAGGAGGAGAAAGGGGGGGTGATAT
344136 AA
66 AA
344138 GATAAACAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 52 0.79
79 14 0.21
ACGTcount: A:0.44, C:0.05, G:0.30, T:0.21
Consensus pattern (79 bp):
ATGTGATACATTAAAGAACACTGTGATTTATGAAAAAGAAAAGGAGGAGAAAGGGGGGGTGATAT
AAAGGAGGAGTTAC
Found at i:345202 original size:2 final size:2
Alignment explanation
Indices: 345195--345227 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
345185 CAATGAGATC
345195 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
345228 ACAAAAGACA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:353960 original size:12 final size:11
Alignment explanation
Indices: 353942--353972 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
353932 AGCAATAATT
353942 ATTTTTTTTGA
1 ATTTTTTTTGA
*
353953 ATTTTTTTTGG
1 ATTTTTTTTGA
353964 ATTTTTTTT
1 ATTTTTTTT
353973 AATGTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:353983 original size:21 final size:22
Alignment explanation
Indices: 353942--353984 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
353932 AGCAATAATT
* *
353942 ATTTTTTTTGAATTTTTTTTGG
1 ATTTTTTTTGAATGTTGTTTGG
353964 ATTTTTTTT-AATGTTGTTTGG
1 ATTTTTTTTGAATGTTGTTTGG
353985 TGGGATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (22 bp):
ATTTTTTTTGAATGTTGTTTGG
Found at i:354264 original size:15 final size:16
Alignment explanation
Indices: 354233--354271 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
354223 AAATGATAAG
*
354233 TATT-ATATATTTGAT
1 TATTGATATAATTGAT
354248 TATTGATATAATT-AT
1 TATTGATATAATTGAT
354263 TATTGATAT
1 TATTGATAT
354272 GTCATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (16 bp):
TATTGATATAATTGAT
Found at i:355167 original size:6 final size:6
Alignment explanation
Indices: 355158--355183 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
355148 TTAAAAATAT
355158 TTAAAA TTAAAA TTAAAA TTAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TT
355184 TATTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:355209 original size:20 final size:21
Alignment explanation
Indices: 355176--355235 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
355166 AAAATTAAAA
355176 TTAAAA-T-TTATTTAATTAT
1 TTAAAATTATTATTTAATTAT
* *
355195 TTAAATTTA-TATTTAAAATAT
1 TTAAAATTATTATTT-AATTAT
*
355216 TTAAAATTATTTTTTAATTA
1 TTAAAATTATTATTTAATTA
355236 AAATTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 17 0.53
22 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAATTATTATTTAATTAT
Found at i:355232 original size:22 final size:21
Alignment explanation
Indices: 355139--355225 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
355129 AAATTAAATC
*
355139 AAATTAAATTTAAAAATATTTA
1 AAATTATATTT-AAAATATTTA
* *
355161 AAATTAAAATT-AAA-A-TTA
1 AAATTATATTTAAAATATTTA
*
355179 AAATT-TATTT-AATTATTTA
1 AAATTATATTTAAAATATTTA
*
355198 AATTTATATTTAAAATATTTA
1 AAATTATATTTAAAATATTTA
355219 AAATTAT
1 AAATTAT
355226 TTTTTAATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.09
18 9 0.17
19 8 0.15
20 8 0.15
21 14 0.26
22 10 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTATATTTAAAATATTTA
Found at i:355238 original size:17 final size:18
Alignment explanation
Indices: 355216--355249 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
355206 TTTAAAATAT
355216 TTAAAA-TTATTTTTTAA
1 TTAAAATTTATTTTTTAA
355233 TTAAAATTTATTTTTTA
1 TTAAAATTTATTTTTTA
355250 TAATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAAAATTTATTTTTTAA
Found at i:355256 original size:24 final size:23
Alignment explanation
Indices: 355221--355282 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 23
355211 AATATTTAAA
*
355221 ATTATTTT--TTAAT-TAAAATTT
1 ATTATTTTAATTAATATAAAA-AT
*
355242 ATTTTTTATAATTAAATATAAAAAT
1 ATTATTT-TAATT-AATATAAAAAT
355267 ATTATTTTAATTAATA
1 ATTATTTTAATTAATA
355283 AATTATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
23 4 0.12
24 7 0.21
25 10 0.30
26 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTATTTTAATTAATATAAAAAT
Found at i:355289 original size:20 final size:20
Alignment explanation
Indices: 355219--355290 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
355209 AAAATATTTA
355219 AAATTATT-TTTTAATTAA-
1 AAATTATTATTTTAATTAAT
* *
355237 AATTTATTTTTTATAATTAAATAT
1 AAATTATTATTT-TAATT--A-AT
*
355261 AAAAATATTATTTTAATTAAT
1 -AAATTATTATTTTAATTAAT
355282 AAATTATTA
1 AAATTATTA
355291 ATCATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
18 7 0.17
19 3 0.07
20 13 0.31
21 2 0.05
22 2 0.05
23 1 0.02
24 5 0.12
25 9 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTATTATTTTAATTAAT
Found at i:355300 original size:44 final size:43
Alignment explanation
Indices: 355217--355302 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
355207 TTAAAATATT
* * ** *
355217 TAAAATTATTTTTTAATTAAAATTTATTTTTTATAATTAAATA
1 TAAAAATATTTTTTAATTAAAAATTATTAATCATAATTAAATA
355260 TAAAAATATTATTTTAATTAATAAATTATTAATCAT-ATTAAAT
1 TAAAAATATT-TTTTAATTAA-AAATTATTAATCATAATTAAAT
355303 CGATGAACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 9 0.25
44 17 0.47
45 10 0.28
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (43 bp):
TAAAAATATTTTTTAATTAAAAATTATTAATCATAATTAAATA
Found at i:356111 original size:16 final size:14
Alignment explanation
Indices: 356089--356154 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 14
356079 TTAACTTATC
356089 AAAATTAATATAAAT
1 AAAA-TAATATAAAT
* *
356104 ATAAATTATTTTAAAT
1 A-AAA-TAATATAAAT
356120 AAAATAATAATATAAT
1 AAAATAAT-ATA-AAT
356136 AAAAT-ATATAAAT
1 AAAATAATATAAAT
*
356149 ATAATA
1 AAAATA
356155 TAAATTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 7 0.17
14 6 0.14
15 8 0.19
16 21 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATAATATAAAT
Found at i:356134 original size:8 final size:8
Alignment explanation
Indices: 356117--356159 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
356107 AATTATTTTA
356117 AATAAAAT
1 AATAAAAT
*
356125 AATAATAT
1 AATAAAAT
356133 AATAAAAT
1 AATAAAAT
356141 ATATAAATAT
1 A-ATAAA-AT
356151 AATATAAAT
1 AATA-AAAT
356160 TATTAAACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 15 0.50
9 10 0.33
10 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAAAAT
Found at i:357579 original size:15 final size:15
Alignment explanation
Indices: 357559--357632 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
357549 GATATAATTT
357559 TTTAAATATT-TATTA
1 TTTAAAT-TTATATTA
357574 TTTAAATTTATATTA
1 TTTAAATTTATATTA
357589 -TT---TTTATA-TA
1 TTTAAATTTATATTA
* *
357599 TAATAAATTTAAATT-
1 T-TTAAATTTATATTA
*
357614 TTTAAATTTATTTTA
1 TTTAAATTTATATTA
357629 TTTA
1 TTTA
357633 CTAGATAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
10 2 0.04
11 6 0.13
12 1 0.02
14 14 0.30
15 22 0.48
16 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAAATTTATATTA
Found at i:358592 original size:17 final size:17
Alignment explanation
Indices: 358570--358622 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
358560 GATAAATTAT
358570 ATAAAATATATGATAAA
1 ATAAAATATATGATAAA
358587 AT-AAA-ATATGATATAA
1 ATAAAATATATGATA-AA
* *
358603 ATATAATATAT-AAAAA
1 ATAAAATATATGATAAA
358619 ATAA
1 ATAA
358623 TTTAAATACG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 8 0.27
16 12 0.40
17 6 0.20
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
ATAAAATATATGATAAA
Found at i:358597 original size:15 final size:15
Alignment explanation
Indices: 358577--358617 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
358567 TATATAAAAT
358577 ATATGATAAAATAAA
1 ATATGATAAAATAAA
*
358592 ATATGATATAAATATA
1 ATATGATA-AAATAAA
358608 ATAT-ATAAAA
1 ATATGATAAAA
358618 AATAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
ATATGATAAAATAAA
Found at i:358628 original size:25 final size:23
Alignment explanation
Indices: 358600--358646 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
358590 AAATATGATA
358600 TAAATATAATATATAAAAAATAATT
1 TAAATA-AAT-TATAAAAAATAATT
**
358625 TAAATACGTTATAAAAAATAAT
1 TAAATAAATTATAAAAAATAAT
358647 ACGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
TAAATAAATTATAAAAAATAATT
Found at i:358630 original size:20 final size:20
Alignment explanation
Indices: 358607--358663 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 20
358597 ATATAAATAT
**
358607 AATATATAAAAAATAATTTA
1 AATATATAAAAAATAATACA
*
358627 AATACGTTATAAAAAATAATACG
1 AATA---TATAAAAAATAATACA
358650 AATATATAAAAAAT
1 AATATATAAAAAAT
358664 TTTCTCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 14 0.45
23 17 0.55
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (20 bp):
AATATATAAAAAATAATACA
Found at i:358685 original size:17 final size:17
Alignment explanation
Indices: 358663--358704 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
358653 ATATAAAAAA
358663 TTTTCTCTTTTCTTTTT-
1 TTTTCT-TTTTCTTTTTC
358680 TTTTCTTTTTCTTTTTC
1 TTTTCTTTTTCTTTTTC
358697 TTTTCTTT
1 TTTTCTTT
358705 CCTTCTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTTC
Found at i:358688 original size:6 final size:6
Alignment explanation
Indices: 358663--358704 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
358653 ATATAAAAAA
358663 TTTTCT CTTTTC- TTTT-T TTTTCT TTTTCT TTTTC- TTTTCT TT
1 TTTTCT -TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
358705 CCTTCTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
5 13 0.41
6 14 0.44
7 5 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:358850 original size:3 final size:3
Alignment explanation
Indices: 358842--358879 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
358832 TGATTGTCTG
358842 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
358880 GTTTATGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:359191 original size:13 final size:13
Alignment explanation
Indices: 359161--359192 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
359151 GGCTAGATTT
359161 AATA-AATTTTAA
1 AATATAATTTTAA
359173 AA-ATAATTTTAA
1 AATATAATTTTAA
359185 AATATAAT
1 AATATAAT
359193 ATATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 12 0.67
13 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATAATTTTAA
Found at i:359960 original size:23 final size:23
Alignment explanation
Indices: 359944--360007 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
359934 AATAATATGT
359944 ATATAATAATTTTAATAAATATA
1 ATATAATAATTTTAATAAATATA
*
359967 ATATAATATTTTTATATATAAT-TA
1 ATATAATAATTTTA-ATA-AATATA
359991 ATATAAT-ATATTTAATA
1 ATATAATAAT-TTTAATA
360008 CATGTATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 17 0.47
24 16 0.44
25 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATAATAATTTTAATAAATATA
Found at i:359997 original size:24 final size:23
Alignment explanation
Indices: 359944--360007 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 23
359934 AATAATATGT
*
359944 ATATAATAATTTTAATAAATATA
1 ATATAATATTTTTAATAAATATA
359967 ATATAATATTTTTATATATAAT-TA
1 ATATAATATTTTTA-ATA-AATATA
*
359991 ATATAATATATTTAATA
1 ATATAATATTTTTAATA
360008 CATGTATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.43
24 18 0.49
25 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATAATATTTTTAATAAATATA
Found at i:360110 original size:20 final size:19
Alignment explanation
Indices: 360063--360111 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
360053 ATATTATATT
*
360063 TATATTTATAAAATTGATA
1 TATATATATAAAATTGATA
* *
360082 TAAAAATATAAAATATGATA
1 TATATATATAAAAT-TGATA
360102 TATATATATA
1 TATATATATA
360112 TATAAATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
TATATATATAAAATTGATA
Found at i:361454 original size:3 final size:3
Alignment explanation
Indices: 361446--361475 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
361436 TTCAAATTAA
361446 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
361476 TTATTTTAAA
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):
AAT
Found at i:361821 original size:11 final size:10
Alignment explanation
Indices: 361801--361858 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
361791 GTGGTATTGG
*
361801 TTTAATTTTA
1 TTTAAATTTA
361811 TATTAAATTTA
1 T-TTAAATTTA
361822 TTT-AATTATA
1 TTTAAATT-TA
* *
361832 TTTTAATTGA
1 TTTAAATTTA
361842 -TT-AATTTA
1 TTTAAATTTA
361850 TTTAAATTT
1 TTTAAATTT
361859 TAATATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 5 0.12
9 8 0.20
10 14 0.35
11 13 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:362593 original size:16 final size:16
Alignment explanation
Indices: 362568--362601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
362558 TTTAAATTTG
* *
362568 ATAATTTTATATTTAT
1 ATAATATTATAATTAT
362584 ATAATATTATAATTAT
1 ATAATATTATAATTAT
362600 AT
1 AT
362602 TTAAAATATT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATAATATTATAATTAT
Found at i:362601 original size:22 final size:21
Alignment explanation
Indices: 362574--362622 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
362564 TTTGATAATT
362574 TTATATTTATATAATATTATA-A
1 TTATATTTA-A-AATATTATATA
*
362596 TTATATTTAAAATATTTTATA
1 TTATATTTAAAATATTATATA
362617 TTATAT
1 TTATAT
362623 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 8 0.32
21 8 0.32
22 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATATTTAAAATATTATATA
Found at i:362671 original size:13 final size:14
Alignment explanation
Indices: 362634--362681 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
362624 AAATTTAAAA
* *
362634 ATTTATTTATTTTT
1 ATTTATTTAATTAT
362648 ATTATATTTTAATTAT
1 ATT-TA-TTTAATTAT
362664 -TTTATTTAATTAT
1 ATTTATTTAATTAT
362677 ATTTA
1 ATTTA
362682 ATATTATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 9 0.31
14 9 0.31
15 4 0.14
16 7 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTATTTAATTAT
Found at i:364122 original size:38 final size:37
Alignment explanation
Indices: 364027--364122 Score: 92
Period size: 38 Copynumber: 2.6 Consensus size: 37
364017 TATATACATA
364027 TTAATATAA-AAATATA-TTTTAATAATTTAATAAAAT
1 TTAA-ATAATAAATATATTTTTAATAATTTAATAAAAT
* **
364063 TTAAATAATAAA-ATAACTTTTTAA-AATTTGATTAACTT
1 TTAAATAATAAATAT-A-TTTTTAATAATTT-AATAAAAT
364101 TTAAATAAATAAATATATTTTT
1 TTAAAT-AATAAATATATTTTT
364123 TAATGTTTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
35 6 0.12
36 8 0.16
37 5 0.10
38 22 0.44
39 7 0.14
40 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (37 bp):
TTAAATAATAAATATATTTTTAATAATTTAATAAAAT
Found at i:365477 original size:17 final size:17
Alignment explanation
Indices: 365445--365490 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
365435 AAAAGTTTTT
*
365445 TGATTT-TAATTAATAA
1 TGATTTATAAATAATAA
365461 TGATTTATAAATAATAA
1 TGATTTATAAATAATAA
*
365478 -AATTTAATAAATA
1 TGATTT-ATAAATA
365491 TATATTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TGATTTATAAATAATAA
Found at i:365502 original size:92 final size:89
Alignment explanation
Indices: 365295--365536 Score: 344
Period size: 92 Copynumber: 2.7 Consensus size: 89
365285 TGATTAAATT
* * *
365295 AAAACATAATAAATATATATTTGAAAATTATTTAATTATTC-AAGTTTCTGAAAGAG-TTTTTAT
1 AAAACTTAATAAATATATATTTGAAAATTATTTAATTATTCAAAATTT-T-AAAAAGTTTTTTAT
365358 TTTAATTAATAATGATTATAAATAAC
64 TTTAATTAATAATGATTATAAATAAC
* *
365384 AAAACTCAATAAATATATATGTGAAAATTATTTAATTATTCAAAAATTTTAAAAAGTTTTTTGAT
1 AAAACTTAATAAATATATATTTGAAAATTATTTAATTATTC-AAAATTTTAAAAAGTTTTTT-AT
*
365449 TTTAATTAATAATGATTTATAAATAAT
64 TTTAATTAATAATGA-TTATAAATAAC
* * *
365476 AAAATTTAATAAATATATATTTGAAAATTATTTAATTATTTAAATTTTTAAAAAGTTTTTT
1 AAAACTTAATAAATATATATTTGAAAATTATTTAATTATTCAAAATTTTAAAAAGTTTTTT
365537 TAAAAGAGAT
Statistics
Matches: 137, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
89 43 0.31
90 6 0.04
91 41 0.30
92 47 0.34
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (89 bp):
AAAACTTAATAAATATATATTTGAAAATTATTTAATTATTCAAAATTTTAAAAAGTTTTTTATTT
TAATTAATAATGATTATAAATAAC
Found at i:366791 original size:29 final size:27
Alignment explanation
Indices: 366759--366891 Score: 72
Period size: 27 Copynumber: 5.1 Consensus size: 27
366749 GTTTTTATCT
* *
366759 TTATAGTAATATATTTATATATATATATA
1 TTATAATAATAT-TTTAAATAT-TATATA
*
366788 TTATAATTATATTTTAAATATTATATA
1 TTATAATAATATTTTAAATATTATATA
*
366815 --ATAATATAAATTTTAATATATTA-ATAA
1 TTATAATA-ATATTTTAA-ATATTATAT-A
* *
366842 TT-T-ATATTA-TATAAATATTA-ATA
1 TTATAATAATATTTTAAATATTATATA
* *
366865 TTTTTAT-ATATTTT--ATATT-TATA
1 TTATAATAATATTTTAAATATTATATA
366888 TTAT
1 TTAT
366892 TTTTATACTT
Statistics
Matches: 84, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
23 14 0.17
24 11 0.13
25 13 0.15
26 11 0.13
27 16 0.19
28 9 0.11
29 10 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TTATAATAATATTTTAAATATTATATA
Found at i:366854 original size:40 final size:40
Alignment explanation
Indices: 366805--366891 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
366795 TATATTTTAA
366805 ATATTATAT-AATAATATAA-ATTTTAATATATTA-ATAATTT
1 ATATTATATAAAT-AT-TAATATTTTAATATATTATAT-ATTT
* *
366845 ATATTATATAAATATTAATATTTTTATATATTTTATATTT
1 ATATTATATAAATATTAATATTTTAATATATTATATATTT
366885 ATATTAT
1 ATATTAT
366892 TTTTATACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
39 3 0.07
40 34 0.81
41 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (40 bp):
ATATTATATAAATATTAATATTTTAATATATTATATATTT
Found at i:366857 original size:32 final size:35
Alignment explanation
Indices: 366818--366888 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 35
366808 TTATATAATA
*
366818 ATATAAATTTTAATA-TATTA-ATAATTTATA-TT
1 ATATAAATATTAATATTATTATATAATTTATATTT
* *
366850 ATATAAATATTAATATTTTTATATATTTTATATTT
1 ATATAAATATTAATATTATTATATAATTTATATTT
366885 ATAT
1 ATAT
366889 TATTTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 14 0.42
33 4 0.12
34 9 0.27
35 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
ATATAAATATTAATATTATTATATAATTTATATTT
Found at i:366882 original size:17 final size:16
Alignment explanation
Indices: 366867--366904 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
366857 TATTAATATT
366867 TTTATA-TATTTTATA
1 TTTATATTATTTTATA
366882 TTTATATTATTTTTATA
1 TTTATATTA-TTTTATA
366899 CTTTAT
1 -TTTAT
366905 TTTTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 2 0.10
17 7 0.35
18 5 0.25
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATATTATTTTATA
Found at i:366885 original size:6 final size:6
Alignment explanation
Indices: 366831--366913 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
366821 TAAATTTTAA
* * * * * *
366831 TATATT AATAATT TATA-T TATATA AATATT AATATT TTTATA TAT-TT
1 TATATT TAT-ATT TATATT TATATT TATATT TATATT TATATT TATATT
*
366878 TATATT TATA-T TATTTT TATACTT TAT-TT T-TATT TA
1 TATATT TATATT TATATT TATA-TT TATATT TATATT TA
366914 AAATTAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
4 1 0.02
5 19 0.33
6 28 0.48
7 10 0.17
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:366903 original size:24 final size:23
Alignment explanation
Indices: 366856--366910 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
366846 TATTATATAA
* *
366856 ATATTAATATTTTTATATATTTT
1 ATATTTATATTTTTATATACTTT
*
366879 ATATTTATATTATTTTTATACTTT
1 ATATTTATATT-TTTATATACTTT
*
366903 ATTTTTAT
1 ATATTTAT
366911 TTAAAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATTTATATTTTTATATACTTT
Found at i:367977 original size:23 final size:22
Alignment explanation
Indices: 367900--367980 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 22
367890 TATATTGATG
*
367900 AATTTTAAAATTTA-ATTTATAT
1 AATTTTAAAATATATATTTA-AT
*
367922 AATTATTAATAAAATATATTAATAATT
1 AATT-TTAA-AATATATATT--TAA-T
*
367949 ATTTTTAAAATATAATATTTAAT
1 AATTTTAAAATAT-ATATTTAAT
367972 AATTTTAAA
1 AATTTTAAA
367981 TTTTAAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
22 4 0.09
23 13 0.28
24 7 0.15
25 7 0.15
26 10 0.21
27 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTTAAAATATATATTTAAT
Found at i:368542 original size:21 final size:22
Alignment explanation
Indices: 368511--368564 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
368501 AAAAATTTAA
368511 AAATAATTTT-TATATTAATATTT
1 AAATAATTTTATA-ATTAA-ATTT
*
368534 ATAT-ATTTTATAATTAAATTT
1 AAATAATTTTATAATTAAATTT
368555 AAATAATTTT
1 AAATAATTTT
368565 TTAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.26
22 15 0.56
23 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATAATTTTATAATTAAATTT
Found at i:368542 original size:22 final size:23
Alignment explanation
Indices: 368511--368565 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
368501 AAAAATTTAA
368511 AAATAATTTTTAT-ATTAATATTT
1 AAATAATTTTTATAATTAA-ATTT
*
368534 ATAT-A-TTTTATAATTAAATTT
1 AAATAATTTTTATAATTAAATTT
368555 AAATAATTTTT
1 AAATAATTTTT
368566 TAAAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 13 0.48
22 7 0.26
23 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATAATTTTTATAATTAAATTT
Found at i:370518 original size:14 final size:14
Alignment explanation
Indices: 370495--370537 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
370485 ATATCAAATG
*
370495 ATATAAATAAATTA
1 ATATATATAAATTA
*
370509 ATATATATAATTTA
1 ATATATATAAATTA
*
370523 TTATAATATAAATTA
1 ATAT-ATATAAATTA
370538 TTAATATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATATAAATTA
Found at i:370532 original size:33 final size:32
Alignment explanation
Indices: 370495--370599 Score: 94
Period size: 32 Copynumber: 3.3 Consensus size: 32
370485 ATATCAAATG
370495 ATATAAATAAATTAATATATATAATTTATTATA
1 ATATAAA-AAATTAATATATATAATTTATTATA
** * *
370528 ATATAAATTATTAATATATTAAAAGTTA-TATA
1 ATATAAAAAATTAATATA-TATAATTTATTATA
* *
370560 A-AT-AAAAA-TAATTTAAAT-ATTTAATTATA
1 ATATAAAAAATTAATATATATAATTT-ATTATA
370589 ATATAAAAAAT
1 ATATAAAAAAT
370600 ATACAAATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
27 3 0.05
28 2 0.04
29 11 0.20
30 5 0.09
31 7 0.12
32 14 0.25
33 14 0.25
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
ATATAAAAAATTAATATATATAATTTATTATA
Found at i:373385 original size:17 final size:17
Alignment explanation
Indices: 373360--373393 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
373350 ATTATTTATT
*
373360 AAATAATTTTAATAATA
1 AAATAATTTTAAAAATA
*
373377 AAATTATTTTAAAAATA
1 AAATAATTTTAAAAATA
373394 TTTAAAATTT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAATTTTAAAAATA
Found at i:375726 original size:16 final size:16
Alignment explanation
Indices: 375705--375755 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
375695 AGTTTAGAGC
375705 TTAAATTATTTTAAAT
1 TTAAATTATTTTAAAT
375721 TTAAATTATTTTAAAT
1 TTAAATTATTTTAAAT
* *
375737 TT-AATTTTTTTAATT
1 TTAAATTATTTTAAAT
375752 TTAA
1 TTAA
375756 CTTTATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAAATTATTTTAAAT
Found at i:375747 original size:15 final size:15
Alignment explanation
Indices: 375708--375755 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
375698 TTAGAGCTTA
375708 AATTATTTTAAATTT
1 AATTATTTTAAATTT
375723 AAATTATTTTAAATTT
1 -AATTATTTTAAATTT
* *
375739 AATTTTTTTAATTTT
1 AATTATTTTAAATTT
375754 AA
1 AA
375756 CTTTATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 15 0.50
16 15 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTATTTTAAATTT
Found at i:376417 original size:3 final size:3
Alignment explanation
Indices: 376399--376440 Score: 57
Period size: 3 Copynumber: 13.0 Consensus size: 3
376389 TGTTATAAAC
376399 TAT TAAT TACT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT
1 TAT T-AT TA-T TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
376441 CTTCTTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:382900 original size:2 final size:2
Alignment explanation
Indices: 382895--382943 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
382885 TCTCTCTTTC
*
382895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
382936 TA TA TA TA
1 TA TA TA TA
382944 AACTTAGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:389437 original size:17 final size:17
Alignment explanation
Indices: 389415--389449 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
389405 TCATACACAT
389415 AAAGATGATTTTGTTGC
1 AAAGATGATTTTGTTGC
389432 AAAGATGATTTTGTTGC
1 AAAGATGATTTTGTTGC
389449 A
1 A
389450 TACATGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (17 bp):
AAAGATGATTTTGTTGC
Found at i:394868 original size:30 final size:30
Alignment explanation
Indices: 394832--394893 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
394822 GCCCCAGTTG
394832 CAAAATTAAATACAGTAAGAGTATTTTTGT
1 CAAAATTAAATACAGTAAGAGTATTTTTGT
394862 CAAAATTAAATACAGTAAGAGTATTTTTGT
1 CAAAATTAAATACAGTAAGAGTATTTTTGT
394892 CA
1 CA
394894 TTAGCAGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (30 bp):
CAAAATTAAATACAGTAAGAGTATTTTTGT
Found at i:396202 original size:23 final size:23
Alignment explanation
Indices: 396172--396218 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
396162 GAAAGAAGAG
*
396172 ATATTTTCTGTTTTAATAGCTGT
1 ATATTTTCTGCTTTAATAGCTGT
396195 ATATTTTCTGCTTTAATAGCTGT
1 ATATTTTCTGCTTTAATAGCTGT
396218 A
1 A
396219 AATATTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (23 bp):
ATATTTTCTGCTTTAATAGCTGT
Found at i:397484 original size:12 final size:12
Alignment explanation
Indices: 397464--397497 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
397454 TATAGATGCT
*
397464 GCTGCTGCTGCG
1 GCTGTTGCTGCG
*
397476 GCTGTTGCTGCT
1 GCTGTTGCTGCG
397488 GCTGTTGCTG
1 GCTGTTGCTG
397498 TTGCAGAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.38, T:0.35
Consensus pattern (12 bp):
GCTGTTGCTGCG
Found at i:397672 original size:72 final size:72
Alignment explanation
Indices: 397555--397842 Score: 540
Period size: 72 Copynumber: 4.0 Consensus size: 72
397545 CAAAAATATT
397555 GGAAGGCATTCCTTGCCCCATTGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
1 GGAAGGCATTCCTTGCCCCATTGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
397620 GGCCAAC
66 GGCCAAC
397627 GGAAGGCATTCCTTGCCCCATTGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
1 GGAAGGCATTCCTTGCCCCATTGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
397692 GGCCAAC
66 GGCCAAC
* * *
397699 GGAAGGCATCCCTTGCCCCAGTGAGTTCTGTGAAATTCCAGACATGTTCTGCACGTTGGAATTCT
1 GGAAGGCATTCCTTGCCCCATTGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
397764 GGCCAAC
66 GGCCAAC
*
397771 GGAAGGCATTCCTTGCCCCAATGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
1 GGAAGGCATTCCTTGCCCCATTGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
397836 GGCCAAC
66 GGCCAAC
397843 AACATTAGGA
Statistics
Matches: 210, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 210 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (72 bp):
GGAAGGCATTCCTTGCCCCATTGAGTTCTGTGAAATTCCAGACATGTTCTGCATGTTGGAATTCT
GGCCAAC
Found at i:401682 original size:19 final size:19
Alignment explanation
Indices: 401654--401695 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
401644 TCAAATATTT
*
401654 TATAATATAAAAATATAAA
1 TATAACATAAAAATATAAA
401673 TATAACATAAAAATATAAA
1 TATAACATAAAAATATAAA
401692 TATA
1 TATA
401696 TTCATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TATAACATAAAAATATAAA
Found at i:401683 original size:47 final size:46
Alignment explanation
Indices: 401599--401690 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 46
401589 ATGATTTAAG
* *
401599 CAAAAATTTTAAAATTAATAACATAAAAATAATATAAAAAAATAAT
1 CAAAAATTTTAAAATTAAAAACATAAAAATAACATAAAAAAATAAT
* * * * *
401645 CAAATATTTTATAATATAAAAATATAAATATAACATAAAAATATAA
1 CAAAAATTTTAAAAT-TAAAAACATAAAAATAACATAAAAAAATAA
401691 ATATATTCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 13 0.34
47 25 0.66
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (46 bp):
CAAAAATTTTAAAATTAAAAACATAAAAATAACATAAAAAAATAAT
Found at i:401753 original size:22 final size:23
Alignment explanation
Indices: 401685--401761 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 23
401675 TAACATAAAA
* *
401685 ATATAAATATATTCATT-ATATATT
1 ATATAAA-AAATT-ATTAATATTTT
* * *
401709 ATATTAATAATTATTAA-AATTT
1 ATATAAAAAATTATTAATATTTT
401731 ATATAAAAAATTA-TAATATTTT
1 ATATAAAAAATTATTAATATTTT
*
401753 AAATAAAAA
1 ATATAAAAA
401762 TAATTATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
21 3 0.07
22 29 0.69
23 4 0.10
24 6 0.14
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATAAAAAATTATTAATATTTT
Found at i:401915 original size:3 final size:3
Alignment explanation
Indices: 401907--401957 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
401897 AAATTTTACT
* *
401907 TAA TAA TAA TAA TATA TAA -AA TAA TTA TTA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
401951 -AA TAA TA
1 TAA TAA TA
401958 TAAATACAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 6 0.14
3 33 0.79
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:402448 original size:27 final size:28
Alignment explanation
Indices: 402394--402448 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
402384 TGATGATTTG
* *
402394 AATTTTTTTAAACATTTAAATTTGTAAT
1 AATTATTTTAAACATTTAAATTTATAAT
402422 AATTATTTTAAA-ATTTAAATTTATAAT
1 AATTATTTTAAACATTTAAATTTATAAT
402449 TCGTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
AATTATTTTAAACATTTAAATTTATAAT
Found at i:403651 original size:19 final size:18
Alignment explanation
Indices: 403629--403680 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
403619 ATATTATATG
403629 ATATAAATATAATTAAAAA
1 ATATAAATATAA-TAAAAA
403648 ATAT--ATATAATAAAAA
1 ATATAAATATAATAAAAA
* *
403664 AGATAAAAATAAATAAA
1 ATATAAATAT-AATAAA
403681 TATATCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 9 0.32
17 6 0.21
18 3 0.11
19 10 0.36
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
ATATAAATATAATAAAAA
Found at i:403690 original size:18 final size:16
Alignment explanation
Indices: 403642--403691 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
403632 TAAATATAAT
*
403642 TAAAAAATATATATAA
1 TAAAAAATATATAAAA
*
403658 TAAAAAAGATA-AAAA
1 TAAAAAATATATAAAA
403673 TAAATAAATATATCAAAA
1 TAAA-AAATATAT-AAAA
403691 T
1 T
403692 TTATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.25
16 16 0.57
18 5 0.18
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
TAAAAAATATATAAAA
Found at i:403830 original size:15 final size:14
Alignment explanation
Indices: 403807--403888 Score: 59
Period size: 15 Copynumber: 6.1 Consensus size: 14
403797 TAAAATCAAA
403807 ATTTATTTAAATATT
1 ATTTATTTAAA-ATT
*
403822 ATTTTTTTAAAATT
1 ATTTATTTAAAATT
* *
403836 A-TTATAT-AAATC
1 ATTTATTTAAAATT
403848 A---A-TTAAAATT
1 ATTTATTTAAAATT
403858 ATTATATTTAAAATT
1 ATT-TATTTAAAATT
*
403873 ATTTTTTTAAATATT
1 ATTTATTTAAA-ATT
403888 A
1 A
403889 AGATAGATCG
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
9 1 0.02
10 6 0.11
12 5 0.09
13 4 0.08
14 12 0.23
15 25 0.47
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTATTTAAAATT
Found at i:405383 original size:35 final size:35
Alignment explanation
Indices: 405337--405404 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
405327 GTGTCGGTAT
405337 TCAGTAGTCATTGATAAAGGAGAGAAATCCATTAC
1 TCAGTAGTCATTGATAAAGGAGAGAAATCCATTAC
405372 TCAGTAGTCATTGATAAAGGAGAGAAATCCATT
1 TCAGTAGTCATTGATAAAGGAGAGAAATCCATT
405405 CTATAAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (35 bp):
TCAGTAGTCATTGATAAAGGAGAGAAATCCATTAC
Found at i:405591 original size:17 final size:17
Alignment explanation
Indices: 405569--405603 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
405559 TCATACACAT
405569 AAAGATCATTTTGTTGC
1 AAAGATCATTTTGTTGC
*
405586 AAAGATGATTTTGTTGC
1 AAAGATCATTTTGTTGC
405603 A
1 A
405604 TACATGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (17 bp):
AAAGATCATTTTGTTGC
Found at i:408371 original size:63 final size:63
Alignment explanation
Indices: 408287--408414 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
408277 AAATGATTGA
*
408287 TACATTTACGCGACCACGAGAAGGGAGACCTAAAAAGTTAACTATTTTCTGCTACAGACCTGT
1 TACATTTAAGCGACCACGAGAAGGGAGACCTAAAAAGTTAACTATTTTCTGCTACAGACCTGT
*
408350 TACATTTAAGCGATCACGAGAAGGGAGACCTAAAAAGTTAACTATTTTCTGCTACAGACCTGT
1 TACATTTAAGCGACCACGAGAAGGGAGACCTAAAAAGTTAACTATTTTCTGCTACAGACCTGT
408413 TA
1 TA
408415 ATCATCGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (63 bp):
TACATTTAAGCGACCACGAGAAGGGAGACCTAAAAAGTTAACTATTTTCTGCTACAGACCTGT
Found at i:410939 original size:21 final size:20
Alignment explanation
Indices: 410914--410966 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
410904 TATTTTTTCT
*
410914 AAATTTTATTTAATAAAATAA
1 AAATTTT-TTTAAGAAAATAA
*
410935 AAATTTTGTTAAGAAAATAA
1 AAATTTTTTTAAGAAAATAA
410955 AAATATTTTTTA
1 AAAT-TTTTTTA
410967 TTTACTTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
AAATTTTTTTAAGAAAATAA
Found at i:411113 original size:18 final size:17
Alignment explanation
Indices: 411092--411128 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
411082 ATATTAAAAT
411092 ATTTAAAAAATAATATAA
1 ATTTAAAAAAT-ATATAA
411110 ATTTAAAAAATATATAA
1 ATTTAAAAAATATATAA
411127 AT
1 AT
411129 ATATTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAAAATATATAA
Found at i:411138 original size:18 final size:17
Alignment explanation
Indices: 411095--411131 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
411085 TTAAAATATT
*
411095 TAAAAAATAATATAAATT
1 TAAAAAAT-ATATAAATA
411113 TAAAAAATATATAAATA
1 TAAAAAATATATAAATA
411130 TA
1 TA
411132 TTAAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAAATATATAAATA
Found at i:411435 original size:25 final size:26
Alignment explanation
Indices: 411401--411464 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
411391 AAATAATATA
*
411401 AATATAATATATTTTATA-AATATTTT
1 AATAT-ATATATTATATATAATATTTT
*
411427 AATATATATA-AATATATAATATTTT
1 AATATATATATTATATATAATATTTT
411452 AA-ATA-ATATTATA
1 AATATATATATTATA
411465 ATTCGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 3 0.09
24 10 0.30
25 15 0.45
26 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATATATTATATATAATATTTT
Found at i:411449 original size:36 final size:36
Alignment explanation
Indices: 411392--411466 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
411382 TTATATAAAA
* *
411392 AATAATATAAATATAATATATTTTATA-AATATTTT
1 AATAATATAAATATAATATATTTTAAATAATATTAT
411427 AATATATATAAATAT-ATAATATTTTAAATAATATTAT
1 AATA-ATATAAATATAAT-ATATTTTAAATAATATTAT
411464 AAT
1 AAT
411467 TCGTAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 6 0.17
36 19 0.54
37 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
AATAATATAAATATAATATATTTTAAATAATATTAT
Found at i:412480 original size:21 final size:22
Alignment explanation
Indices: 412454--412506 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
412444 TATAGAAAAG
*
412454 TAAAATATATTTTAATATA-TT
1 TAAAATATAATTTAATATATTT
412475 TAAAATATAATTTAATATATTT
1 TAAAATATAATTTAATATATTT
*
412497 TTAAATATAA
1 TAAAATATAA
412507 AATATTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAAAATATAATTTAATATATTT
Found at i:412504 original size:10 final size:11
Alignment explanation
Indices: 412456--412505 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
412446 TAGAAAAGTA
412456 AAATATATTTT
1 AAATATATTTT
*
412467 -AATATATTTA
1 AAATATATTTT
*
412477 AAATATAATTT
1 AAATATATTTT
412488 -AATATATTTTT
1 AAATATA-TTTT
412499 AAATATA
1 AAATATA
412506 AAATATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 15 0.47
11 11 0.34
12 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATATTTT
Found at i:412610 original size:13 final size:12
Alignment explanation
Indices: 412583--412656 Score: 69
Period size: 12 Copynumber: 6.0 Consensus size: 12
412573 TTGATGTCTA
* *
412583 AAATATAATTAT
1 AAATATTATTTT
412595 AAATATTAGTTTT
1 AAATATTA-TTTT
412608 AAAT-TATATTTT
1 AAATAT-TATTTT
*
412620 AAAATACTATTTT
1 -AAATATTATTTT
* *
412633 TAATATAATTTT
1 AAATATTATTTT
412645 AAATATTATTTT
1 AAATATTATTTT
412657 TAAGCGTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
12 31 0.62
13 19 0.38
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (12 bp):
AAATATTATTTT
Found at i:412659 original size:13 final size:13
Alignment explanation
Indices: 412594--412659 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
412584 AATATAATTA
*
412594 TAAATATTAGTTT
1 TAAATATTATTTT
412607 TAAAT-TATATTTT
1 TAAATAT-TATTTT
* *
412620 AAAATACTATTTT
1 TAAATATTATTTT
*
412633 T-AATA-TAATTT
1 TAAATATTATTTT
412644 TAAATATTATTTT
1 TAAATATTATTTT
412657 TAA
1 TAA
412660 GCGTAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
11 6 0.14
12 9 0.21
13 28 0.65
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTATTTT
Found at i:412668 original size:25 final size:24
Alignment explanation
Indices: 412587--412659 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
412577 TGTCTAAAAT
* *
412587 ATAATTATAAATATTAGTTTTAAA
1 ATAATTTTAAATATTATTTTTAAA
* * *
412611 TTATATTTTAAAATACTATTTTTAAT
1 ATA-ATTTT-AAATATTATTTTTAAA
412637 ATAATTTTAAATATTATTTTTAA
1 ATAATTTTAAATATTATTTTTAA
412660 GCGTAATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 16 0.40
25 9 0.22
26 15 0.38
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (24 bp):
ATAATTTTAAATATTATTTTTAAA
Found at i:420422 original size:23 final size:23
Alignment explanation
Indices: 420374--420422 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
420364 AAATTTTATT
* * *
420374 TATTTTTTAGTATTTAAATAATA
1 TATTTTTTAGAATTTAAAAAAAA
420397 TATTTTTTA-AATTTAATAAAAAA
1 TATTTTTTAGAATTTAA-AAAAAA
420420 TAT
1 TAT
420423 ATTGATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTTTTTAGAATTTAAAAAAAA
Found at i:420570 original size:11 final size:11
Alignment explanation
Indices: 420556--420589 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
420546 TTTAATTATT
420556 ATAAAATTAAA
1 ATAAAATTAAA
420567 ATAAAATTAAA
1 ATAAAATTAAA
*
420578 ATATAATTAAA
1 ATAAAATTAAA
420589 A
1 A
420590 ATATAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAAAATTAAA
Found at i:420838 original size:15 final size:16
Alignment explanation
Indices: 420820--420858 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
420810 GTCATTATTT
420820 TAAAAAATT-TAAAAA
1 TAAAAAATTATAAAAA
*
420835 TAAAAAATTGATTAAAA
1 TAAAAAATT-ATAAAAA
420852 TAAAAAA
1 TAAAAAA
420859 AATTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAAAATTATAAAAA
Done.