Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 25
Found at i:143487 original size:2 final size:2
Alignment explanation
Indices: 143475--143518 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
143465 AAGGAATACT
*
143475 GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
143517 GA
1 GA
143519 AGGCTGGGGT
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:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:151279 original size:6 final size:6
Alignment explanation
Indices: 151268--151293 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
151258 ACAAACAGGG
151268 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
151294 CAGAAGAAAG
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:152649 original size:1 final size:1
Alignment explanation
Indices: 152643--152673 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
152633 TCTCCTGCCT
*
152643 CCCCCCCCTCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
152674 TCTTCCTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:155102 original size:124 final size:124
Alignment explanation
Indices: 154882--155130 Score: 480
Period size: 124 Copynumber: 2.0 Consensus size: 124
154872 ACAACCATAT
154882 CTAATATCCACACATTTAACAAAATAGTTTGCAGCCGAAAAAAACAAACTAACCATTTTTGATAG
1 CTAATATCCACACATTTAACAAAATAGTTTGCAGCCGAAAAAAACAAACTAACCATTTTTGATAG
*
154947 ACAACAGTTTCTCAAACAAAATTCTAGAATAAAAATTTGAACTCAATTCAAGTGACTGA
66 ACAACAGTTTCTCAAACAAAATTCTAGAATAAAAATTTAAACTCAATTCAAGTGACTGA
*
155006 CTAATATCCACACATTTAACAAAATAGTTTGCAGCTGAAAAAAACAAACTAACCATTTTTGATAG
1 CTAATATCCACACATTTAACAAAATAGTTTGCAGCCGAAAAAAACAAACTAACCATTTTTGATAG
155071 ACAACAGTTTCTCAAACAAAATTCTAGAATAAAAATTTAAACTCAATTCAAGTGACTGA
66 ACAACAGTTTCTCAAACAAAATTCTAGAATAAAAATTTAAACTCAATTCAAGTGACTGA
155130 C
1 C
155131 AATGCATTTA
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (124 bp):
CTAATATCCACACATTTAACAAAATAGTTTGCAGCCGAAAAAAACAAACTAACCATTTTTGATAG
ACAACAGTTTCTCAAACAAAATTCTAGAATAAAAATTTAAACTCAATTCAAGTGACTGA
Found at i:164822 original size:2 final size:2
Alignment explanation
Indices: 164815--164847 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
164805 CTATCTATCC
164815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
164848 GCTTAGGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:172107 original size:2 final size:2
Alignment explanation
Indices: 172100--172141 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
172090 TTCATTTTTA
172100 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
172142 TCCAATGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:172596 original size:2 final size:2
Alignment explanation
Indices: 172589--172619 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
172579 AATAATGTTA
172589 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 A
172620 AAAGCAGAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:190282 original size:3 final size:3
Alignment explanation
Indices: 190274--190303 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
190264 TTGAGACATT
190274 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
190304 ATGGGGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:191130 original size:5 final size:5
Alignment explanation
Indices: 191109--191142 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
191099 TTGATTGATG
* *
191109 CTTCT CTCCT TTTCT CTTCT CTTCT CTTCT CTTC
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTC
191143 CTCACAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTTCT
Found at i:191425 original size:5 final size:5
Alignment explanation
Indices: 191404--191442 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
191394 TTGATTGATG
* *
191404 CTTCT CTCCT TTTCT CTTCT CTTCT CTTCT CTTCT CTTC
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CTTC
191443 CTCACAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTTCT
Found at i:191620 original size:300 final size:295
Alignment explanation
Indices: 191047--191643 Score: 1013
Period size: 300 Copynumber: 2.0 Consensus size: 295
191037 TTCTTTGACA
*
191047 TTTCCCACAATTTGGTAAAAACATTTACCATTTTACCTTTTCCACCATTGAATTGATTGATGCTT
1 TTTCCCACAATTTGGTAAAAACATTTACCATTTCACCTTTTCCACCATTGAATTGATTGATGCTT
191112 CTCTCCTTTTCTCTTCTCTTCTCTTCTCTTCCTCACAAACTCTCTCACACTACTTTTGTCTGTCT
66 CTCTCCTTTTCTCTTCTCTTCTCTTCTCTTCCTCACAAACTCTCTCACACTACTTTTGTCTGTCT
* *
191177 TACAATCGTCTTGATGCAACTATTAAATCTAGCTTTAAGGTCTAAGTCCAACGTCAAAATTCTCA
131 TACAATCGTCTCGATGCAACTATAAAATCTAGCTTTAAGGTCTAAGTCCAACGTCAAAATTCTCA
191242 TCTTTATTATTGCTTGCAAATGATTGAAGAAAATAAAACTATTTTAGAGACTTCAATACTTAGAT
196 TCTTTATTATTGCTTGCAAATGATTGAAGAAAATAAAACTATTTTAGAGACTTCAATACTTAGAT
191307 CAAAAATATCAAAACAA-CACATTATTTTACTAGTAG
261 CAAAAATATCAAAACAATC-CATTA-TTTACTAGTAG
191343 TTTCCCACAATTTGGTAAAAACATTTACCA-TTCACCTTTTCCACCATTGAATTGATTGATGCTT
1 TTTCCCACAATTTGGTAAAAACATTTACCATTTCACCTTTTCCACCATTGAATTGATTGATGCTT
*
191407 CTCTCCTTTTCTCTTCTCTTCTCTTCTCTTCTCTTCCTCACAAACTCTCTCACACTATTTTTGTC
66 CTCTCC---T-T-TTCTCTTCTCTTCTCTTCTCTTCCTCACAAACTCTCTCACACTACTTTTGTC
* * *
191472 TGTTTTACAATTGTCTCGATGCAACTATAAAAGT-TAGCTTTAAGGTCTATGTCCAACGTCAAAA
126 TGTCTTACAATCGTCTCGATGCAACTATAAAA-TCTAGCTTTAAGGTCTAAGTCCAACGTCAAAA
*
191536 TTCTCATCTTTATTATTGCTTGCAATTGATTGAAGAAAATAAAACTATTTTAGAGACTTCAATAC
190 TTCTCATCTTTATTATTGCTTGCAAATGATTGAAGAAAATAAAACTATTTTAGAGACTTCAATAC
191601 TTAGATCAAGAAA-ATCAAAACAATCCATTATTTACTAGTAG
255 TTAGATCAA-AAATATCAAAACAATCCATTATTTACTAGTAG
191642 TT
1 TT
191644 CCCCTTTTAA
Statistics
Matches: 285, Mismatches: 8, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
295 39 0.14
296 30 0.11
298 1 0.00
299 14 0.05
300 196 0.69
301 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (295 bp):
TTTCCCACAATTTGGTAAAAACATTTACCATTTCACCTTTTCCACCATTGAATTGATTGATGCTT
CTCTCCTTTTCTCTTCTCTTCTCTTCTCTTCCTCACAAACTCTCTCACACTACTTTTGTCTGTCT
TACAATCGTCTCGATGCAACTATAAAATCTAGCTTTAAGGTCTAAGTCCAACGTCAAAATTCTCA
TCTTTATTATTGCTTGCAAATGATTGAAGAAAATAAAACTATTTTAGAGACTTCAATACTTAGAT
CAAAAATATCAAAACAATCCATTATTTACTAGTAG
Found at i:192975 original size:2 final size:2
Alignment explanation
Indices: 192968--192996 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
192958 ATTATCCTAC
192968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
192997 ATAAGCTCCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:193561 original size:2 final size:2
Alignment explanation
Indices: 193554--193583 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
193544 ATAAAGAATC
193554 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
193584 CTTGCATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193859 original size:2 final size:2
Alignment explanation
Indices: 193817--193844 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
193807 TTTTACATAC
193817 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
193845 TAAATCAAGA
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:194277 original size:2 final size:2
Alignment explanation
Indices: 194270--194302 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
194260 TGTCAAATGT
194270 TC 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 TC T
194303 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:194924 original size:3 final size:3
Alignment explanation
Indices: 194916--194940 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
194906 AACACCATTT
194916 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
194941 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:197638 original size:12 final size:12
Alignment explanation
Indices: 197621--197652 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
197611 ACCATAATCT
197621 ATATATATTATA
1 ATATATATTATA
197633 ATATATATTATA
1 ATATATATTATA
*
197645 TTATATAT
1 ATATATAT
197653 AAATAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATATATTATA
Found at i:198916 original size:10 final size:10
Alignment explanation
Indices: 198898--198941 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
198888 TGAAAGGCAA
*
198898 TTTCATTTCT
1 TTTCCTTTCT
198908 TTTCCTTTCT
1 TTTCCTTTCT
* *
198918 TGTCCTTCCT
1 TTTCCTTTCT
*
198928 TTTCCTTTCC
1 TTTCCTTTCT
198938 TTTC
1 TTTC
198942 ACGGCCAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTCCTTTCT
Found at i:200965 original size:2 final size:2
Alignment explanation
Indices: 200958--200992 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
200948 TTGTGATTGA
200958 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 A
200993 AATTAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:201073 original size:3 final size:3
Alignment explanation
Indices: 201067--201107 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
201057 ATTTACAAAA
201067 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
201108 GGTTGTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:202320 original size:21 final size:18
Alignment explanation
Indices: 202284--202327 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
202274 TGAGATACTC
*
202284 TTTTTCTATTTTATTTTA
1 TTTTTCTATTTTATTTAA
202302 TTTTTCTATAATTTAATTTAA
1 TTTTTCTAT--TTT-ATTTAA
202323 TTTTT
1 TTTTT
202328 TTTAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
20 3 0.14
21 10 0.45
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTCTATTTTATTTAA
Found at i:204455 original size:26 final size:27
Alignment explanation
Indices: 204423--204501 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
204413 TATATTTTAA
204423 TTATATA-TAAATTTTATATAATTATAT
1 TTATATATTAAATTTT-TATAATTATAT
204450 TT-TATATTATAATTATTT-TAA-TATAT
1 TTATATATTA-AATT-TTTATAATTATAT
204476 TTATAATATTAAATTTTTAT-ATTATA
1 TTAT-ATATTAAATTTTTATAATTATA
204502 AACATGTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
26 15 0.33
27 17 0.38
28 11 0.24
29 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATATATTAAATTTTTATAATTATAT
Found at i:204462 original size:18 final size:18
Alignment explanation
Indices: 204439--204502 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 18
204429 ATAAATTTTA
204439 TATAATTATATTTTATAT
1 TATAATTATATTTTATAT
204457 TATAATTAT-TTTAATATATT
1 TATAATTATATTT--TATA-T
*
204477 TATAATATTAAATTTTTATAT
1 TAT-A-ATTATA-TTTTATAT
204498 TATAA
1 TATAA
204503 ACATGTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
17 3 0.08
18 9 0.24
19 5 0.13
20 5 0.13
21 5 0.13
22 8 0.21
24 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATAATTATATTTTATAT
Found at i:206469 original size:3 final size:3
Alignment explanation
Indices: 206461--206495 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
206451 TCCTGGAGCA
* *
206461 AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
206496 AATGAGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:208973 original size:2 final size:2
Alignment explanation
Indices: 208966--208993 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
208956 CAAGCACCAA
208966 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
208994 TTTTAAAGAG
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:212596 original size:3 final size:3
Alignment explanation
Indices: 212590--212617 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
212580 CATCATCATC
212590 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
212618 GATTAGGTAT
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:213595 original size:2 final size:2
Alignment explanation
Indices: 213588--213613 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
213578 AACAAAATCA
213588 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
213614 TTATGACTAA
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:221265 original size:16 final size:15
Alignment explanation
Indices: 221244--221299 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
221234 AGTAAATTTT
221244 TTTTATATTATGTATA
1 TTTTATATTAT-TATA
221260 TTTTATA-TATATATA
1 TTTTATATTAT-TATA
*
221275 TATATATATATATTATA
1 T-TTTATAT-TATTATA
*
221292 TATTATAT
1 TTTTATAT
221300 ATAAACAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 8 0.24
16 17 0.52
17 5 0.15
18 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TTTTATATTATTATA
Found at i:221270 original size:2 final size:2
Alignment explanation
Indices: 221263--221347 Score: 80
Period size: 2 Copynumber: 46.5 Consensus size: 2
221253 ATGTATATTT
221263 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
221303 AA CA -A CTA TA TA TA -A TA -A TA TA -A TA -A TA TA TA -A TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
221340 TA TA -A TA T
1 TA TA TA TA T
221348 TTTGTTTATT
Statistics
Matches: 71, Mismatches: 2, Indels: 20
0.76 0.02 0.22
Matches are distributed among these distances:
1 9 0.13
2 61 0.86
3 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:221292 original size:32 final size:31
Alignment explanation
Indices: 221247--221348 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 31
221237 AAATTTTTTT
*
221247 TATAT-TATGTATATTTTATATATATATATATA
1 TATATATAT-TATATATTATATATATA-ATATA
*
221279 TATATATATTATATATTATATATA-AACA-A
1 TATATATATTATATATTATATATATAATATA
* *
221308 CTATATATAATA-ATATAATAATATATAATATA
1 -TATATATATTATATATTAT-ATATATAATATA
221340 TATA-ATATT
1 TATATATATT
221349 TTGTTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
29 7 0.12
30 21 0.36
31 8 0.14
32 20 0.34
33 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (31 bp):
TATATATATTATATATTATATATATAATATA
Found at i:221460 original size:18 final size:18
Alignment explanation
Indices: 221419--221462 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
221409 TATATTGTAA
221419 TTTTTTTCAATTTTACTT
1 TTTTTTTCAATTTTACTT
221437 TATTTTTT-AATTTTA-TAT
1 T-TTTTTTCAATTTTACT-T
221455 TTTTTTTC
1 TTTTTTTC
221463 GTTAAATCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.30
18 10 0.43
19 6 0.26
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTTCAATTTTACTT
Found at i:221653 original size:7 final size:7
Alignment explanation
Indices: 221640--221718 Score: 63
Period size: 7 Copynumber: 10.7 Consensus size: 7
221630 AAATAAAAAA
221640 ATATTAT
1 ATATTAT
*
221647 ATGTTAT
1 ATATTAT
221654 ATATTAT
1 ATATTAT
221661 ATATTAT
1 ATATTAT
221668 -TATATATT
1 ATAT-TA-T
221676 ATATTAAAT
1 ATATT--AT
221685 ATATTAT
1 ATATTAT
*
221692 ATACTAT
1 ATATTAT
*
221699 GT-TATAT
1 ATAT-TAT
221706 ATATATAT
1 ATAT-TAT
221714 ATATT
1 ATATT
221719 TCATATAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
6 3 0.05
7 35 0.59
8 11 0.19
9 9 0.15
10 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (7 bp):
ATATTAT
Found at i:221656 original size:2 final size:2
Alignment explanation
Indices: 221651--221717 Score: 58
Period size: 2 Copynumber: 36.5 Consensus size: 2
221641 TATTATATGT
*
221651 TA TA TA T- TA TA TA T- TA T- TA TA TA T- TA TA T- TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
221688 T- TA TA TA CTA TG T- 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
221718 TTCATATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
1 7 0.13
2 45 0.83
3 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:221678 original size:31 final size:33
Alignment explanation
Indices: 221652--221713 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
221642 ATTATATGTT
221652 ATATATTATATA-T-TATTATATATTATATTAA
1 ATATATTATATACTATATTATATATTATATTAA
*
221683 ATATATTATATACTATGTTATATATATATAT
1 ATATATTATATACTATATTATATAT-TATAT
221714 ATATTTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 9 0.33
34 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (33 bp):
ATATATTATATACTATATTATATATTATATTAA
Found at i:222445 original size:16 final size:17
Alignment explanation
Indices: 222419--222452 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
222409 ATTTATCAAT
*
222419 ATTTAAAATTTAATTAA
1 ATTTAAAATTTAAATAA
222436 ATTT-AAATTTAAATAA
1 ATTTAAAATTTAAATAA
222452 A
1 A
222453 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAAATTTAAATAA
Found at i:222484 original size:17 final size:18
Alignment explanation
Indices: 222449--222492 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
222439 TAAATTTAAA
222449 TAAAATATT-TTTATTTTT
1 TAAAAT-TTATTTATTTTT
222467 TAAAATTTATTT-TTTTT
1 TAAAATTTATTTATTTTT
*
222484 TAAATTTTA
1 TAAAATTTA
222493 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAAAATTTATTTATTTTT
Found at i:227925 original size:29 final size:28
Alignment explanation
Indices: 227892--228007 Score: 84
Period size: 27 Copynumber: 4.2 Consensus size: 28
227882 GTTTACGATT
227892 TATTATATTTAAATATATTTATATATTAA
1 TATTATATTTAAATATATTTATATATT-A
* * *
227921 TATTATA-AT-AATATTATTTTTATATTT
1 TATTATATTTAAATA-TATTTATATATTA
* *
227948 TATTATATTTTTATATCATATTTATATATGA
1 TATTATA--TTTAAAT-ATATTTATATATTA
*
227979 TA-T-TATTTAAATA-ATTTTTA-ATT-
1 TATTATATTTAAATATATTTATATATTA
228002 TATTAT
1 TATTAT
228008 TATGTTTTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
23 2 0.03
24 3 0.04
25 7 0.10
26 1 0.01
27 17 0.25
28 12 0.18
29 9 0.13
30 2 0.03
31 14 0.21
32 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (28 bp):
TATTATATTTAAATATATTTATATATTA
Found at i:227945 original size:46 final size:48
Alignment explanation
Indices: 227889--227987 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 48
227879 GAAGTTTACG
227889 ATTTATTATATTTAAATATATTTATATATTAATA-TTATA-ATAATATT
1 ATTTATTATATTTAAATATATTTATATA-TAATATTTATATATAATATT
* * * * *
227936 ATTT-TTATATTTTATTATATTTTTATATCATATTTATATATGATATT
1 ATTTATTATATTTAAATATATTTATATATAATATTTATATATAATATT
227983 ATTTA
1 ATTTA
227988 AATAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
45 4 0.09
46 25 0.57
47 15 0.34
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (48 bp):
ATTTATTATATTTAAATATATTTATATATAATATTTATATATAATATT
Found at i:227969 original size:18 final size:19
Alignment explanation
Indices: 227935--227974 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
227925 ATAATAATAT
**
227935 TATTTTTATATTTTA-TTA
1 TATTTTTATATCATATTTA
227953 TATTTTTATATCATATTTA
1 TATTTTTATATCATATTTA
227972 TAT
1 TAT
227975 ATGATATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTATATCATATTTA
Found at i:228050 original size:156 final size:164
Alignment explanation
Indices: 227874--228182 Score: 456
Period size: 156 Copynumber: 1.9 Consensus size: 164
227864 AAAGTTTTTG
* *
227874 ATTTTGAAGTTTACGATTTATTATATTTAAATATATTTATATATTAATATTATAATAATATTATT
1 ATTTTGAAGTTTACGATTTATTATATTTAAATATATTTAGATATTAATATCATAATAATATTATT
*
227939 TTT-A-TA-T-T-TTAT-TA-TATTTTT-ATATCATATTTATATATGATATTATTTAAATAATTT
66 TTTGATTATTATATTATATATTATTTTTGATATCATATTTATATATGATACTATTTAAATAATTT
227996 TTAATTTATTATTATGTTTTATATAAAATTTTAA
131 TTAATTTATTATTATGTTTTATATAAAATTTTAA
* *
228030 ATTTTGAGGTTTACTG-TTTATTATATTTAAATATATTTAGATATTGATATCATAATAATATTAT
1 ATTTTGAAGTTTAC-GATTTATTATATTTAAATATATTTAGATATTAATATCATAATAATATTAT
*
228094 TTTTGATGTCTTATTATATTATATATTTTTTTTGATATCATATTTATATATGATACTATTTAAAT
65 TTTTGA----TTATTATATTATATATTATTTTTGATATCATATTTATATATGATACTATTTAAAT
228159 AATTTTTAATTTATTATTATGTTT
126 AATTTTTAATTTATTATTATGTTT
228183 CAATTGATTT
Statistics
Matches: 134, Mismatches: 6, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
156 62 0.46
157 2 0.01
162 2 0.01
163 1 0.01
164 1 0.01
165 4 0.03
166 2 0.01
167 6 0.04
168 54 0.40
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.57
Consensus pattern (164 bp):
ATTTTGAAGTTTACGATTTATTATATTTAAATATATTTAGATATTAATATCATAATAATATTATT
TTTGATTATTATATTATATATTATTTTTGATATCATATTTATATATGATACTATTTAAATAATTT
TTAATTTATTATTATGTTTTATATAAAATTTTAA
Found at i:234679 original size:21 final size:21
Alignment explanation
Indices: 234655--234696 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
234645 TGAATTCAAT
234655 TATAACA-AAAAAATATAAATA
1 TATAACATAAAAAATA-AAATA
*
234676 TATAATATAAAAAATAAAATA
1 TATAACATAAAAAATAAAATA
234697 AAAAAAGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
TATAACATAAAAAATAAAATA
Found at i:235215 original size:2 final size:2
Alignment explanation
Indices: 235210--235252 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
235200 GAGGCAAAAA
*
235210 AT AT AT AT AT AT AT AT AT GT AT AT -T 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
235251 AT
1 AT
235253 CAAATGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:239892 original size:23 final size:22
Alignment explanation
Indices: 239866--239937 Score: 87
Period size: 22 Copynumber: 3.2 Consensus size: 22
239856 ATAATTTTAC
239866 ATATAAATATAATATATAAAAAA
1 ATAT-AATATAATATATAAAAAA
239889 ATATAATA-ATATATAGTAAAAAA
1 ATATAATATA-ATATA-TAAAAAA
239912 A-ATAATATAA-ATATAATAAAA
1 ATATAATATAATATATAA-AAAA
239933 ATATA
1 ATATA
239938 TAAAATTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.07
21 9 0.20
22 19 0.43
23 13 0.30
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (22 bp):
ATATAATATAATATATAAAAAA
Found at i:239902 original size:22 final size:22
Alignment explanation
Indices: 239877--239951 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
239867 TATAAATATA
239877 ATATATAAAAAAATATAATAAT
1 ATATATAAAAAAATATAATAAT
239899 ATATAGTAAAAAAA-ATAAT-AT
1 ATATA-TAAAAAAATATAATAAT
* *
239920 AAATATAATAAAAATATATAAAAT
1 ATATATAA-AAAAATATA-ATAAT
*
239944 TTATATAA
1 ATATATAA
239952 TATAAATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 13 0.30
23 9 0.20
24 8 0.18
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (22 bp):
ATATATAAAAAAATATAATAAT
Found at i:239940 original size:24 final size:23
Alignment explanation
Indices: 239866--239990 Score: 84
Period size: 23 Copynumber: 5.5 Consensus size: 23
239856 ATAATTTTAC
239866 ATATA-AATATAATAT-ATAAAA
1 ATATATAATATAATATAATAAAA
* *
239887 AAATATAATA-ATATATAGTAAAA
1 ATATATAATATA-ATATAATAAAA
*
239910 A-AAATAATATAAATATAATAAAA
1 ATATATAATAT-AATATAATAAAA
* * *
239933 ATATATAAAATTTATATAATATAA
1 ATATATAATA-TAATATAATAAAA
*
239957 AT-TATTAACT-TAATAT-ATATATA
1 ATATA-TAA-TATAATATAATA-AAA
239980 ATATATAATAT
1 ATATATAATAT
239991 TTTAAATATA
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
21 5 0.06
22 19 0.24
23 31 0.39
24 24 0.30
25 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37
Consensus pattern (23 bp):
ATATATAATATAATATAATAAAA
Found at i:239985 original size:36 final size:33
Alignment explanation
Indices: 239866--240027 Score: 111
Period size: 35 Copynumber: 4.8 Consensus size: 33
239856 ATAATTTTAC
* * *
239866 ATATAAATATAATATATAA-AAAAATATAA-TA
1 ATATATATAAAATATATAATATAAATATAATTA
* * *
239897 ATATATAGTAAAAAAAATAATATAAATATAATAA
1 ATATATA-TAAAATATATAATATAAATATAATTA
*
239931 AAATATATAAAATTTATATAATATAAATTATTAACTTA
1 ATATATATAAAA--TATATAATATAAA-TA-TAA-TTA
*
239969 ATATATATATAATATATAATATTTTAAATAT-A-TA
1 ATATATATAAAATATATAATA---TAAATATAATTA
240003 ATTATATAGTAAAA-A-ATAATATAAA
1 A-TATATA-TAAAATATATAATATAAA
240028 CTTATGTAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
31 10 0.10
32 9 0.09
33 14 0.13
34 16 0.15
35 18 0.17
36 16 0.15
37 4 0.04
38 14 0.13
39 4 0.04
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
ATATATATAAAATATATAATATAAATATAATTA
Found at i:250662 original size:4 final size:4
Alignment explanation
Indices: 250653--250677 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
250643 GCAAGCTAGT
250653 TTTG TTTG TTTG TTTG TTTG TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG T
250678 AATGTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:252010 original size:3 final size:3
Alignment explanation
Indices: 251997--252026 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
251987 TTAAATTAAA
*
251997 ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
252027 TAATTTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:252413 original size:16 final size:16
Alignment explanation
Indices: 252392--252426 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
252382 TTGCTTTTGT
252392 TTAAAAAATATTAAAA
1 TTAAAAAATATTAAAA
* *
252408 TTAAAAATTATTTAAA
1 TTAAAAAATATTAAAA
252424 TTA
1 TTA
252427 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAAAATATTAAAA
Found at i:253141 original size:24 final size:24
Alignment explanation
Indices: 253102--253147 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
253092 ATTAATAAAT
** *
253102 ATTTATTTATTCATATTTATTTAA
1 ATTTATTTATAAATATATATTTAA
253126 ATTTATTTATAAATATATATTT
1 ATTTATTTATAAATATATATTT
253148 TAACTGTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTATTTATAAATATATATTTAA
Found at i:253273 original size:6 final size:6
Alignment explanation
Indices: 253262--253286 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
253252 TTCAAATAAA
253262 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
253287 TTAGTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:253316 original size:17 final size:18
Alignment explanation
Indices: 253296--253329 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
253286 TTTAGTGAAT
253296 ATAAAT-AAAATAAAAAA
1 ATAAATAAAAATAAAAAA
253313 ATAAATAAAAATAAAAA
1 ATAAATAAAAATAAAAA
253330 TTTATTTATT
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:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (18 bp):
ATAAATAAAAATAAAAAA
Found at i:257004 original size:3 final size:3
Alignment explanation
Indices: 256996--257028 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
256986 TGTAACTTGG
256996 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
257029 ATTTGTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:267096 original size:20 final size:20
Alignment explanation
Indices: 267049--267123 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
267039 AAAAAGACAT
*
267049 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
267068 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * * *
267089 CATGTATCAATATATTGAAA
1 AATGTATCGATACATTCATA
267109 AATGTATCGATACAT
1 AATGTATCGATACAT
267124 CAAGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:267117 original size:40 final size:39
Alignment explanation
Indices: 267046--267123 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
267036 GGTAAAAAGA
* * *
267046 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCAATACATTGAAAAATATATCGATACATT
* *
267085 CATACATGTATCAATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCAATACATTGAAAAATATATCGATACAT
267124 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCAATACATTGAAAAATATATCGATACATT
Found at i:270108 original size:10 final size:10
Alignment explanation
Indices: 270056--270146 Score: 69
Period size: 10 Copynumber: 9.1 Consensus size: 10
270046 TAATAAATAA
*
270056 TATATATTTT
1 TATATATATT
* *
270066 TATGTATAAT
1 TATATATATT
*
270076 AATTATATATT
1 TA-TATATATT
* *
270087 TA-AAAAATT
1 TATATATATT
270096 TATATATATT
1 TATATATATT
*
270106 TATATAAATT
1 TATATATATT
*
270116 TTTATATATT
1 TATATATATT
*
270126 TATAT-TTTT
1 TATATATATT
270135 TATACTATATT
1 TATA-TATATT
270146 T
1 T
270147 TTATTGTATA
Statistics
Matches: 60, Mismatches: 17, Indels: 7
0.71 0.20 0.08
Matches are distributed among these distances:
9 14 0.23
10 35 0.58
11 11 0.18
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
TATATATATT
Found at i:270116 original size:20 final size:20
Alignment explanation
Indices: 270079--270130 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
270069 GTATAATAAT
*
270079 TATATATTTA-AAAAATTTA
1 TATATATTTATATAAATTTA
*
270098 TATATATTTATATAAATTTT
1 TATATATTTATATAAATTTA
270118 TATATATTTATAT
1 TATATATTTATAT
270131 TTTTTATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATATTTATATAAATTTA
Found at i:270127 original size:30 final size:30
Alignment explanation
Indices: 270093--270150 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
270083 TATTTAAAAA
270093 ATTTATATATATTTATA-TAAATTTTTATAT
1 ATTTATAT-TATTTATACTAAATTTTTATAT
* *
270123 ATTTATATTTTTTATACTATATTTTTAT
1 ATTTATATTATTTATACTAAATTTTTAT
270151 TGTATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTATATTATTTATACTAAATTTTTATAT
Found at i:270158 original size:20 final size:20
Alignment explanation
Indices: 270120--270158 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
270110 TAAATTTTTA
* *
270120 TATATTTATATTTTTTATAC
1 TATATTTATATTGTATATAC
*
270140 TATATTTTTATTGTATATA
1 TATATTTATATTGTATATA
270159 ATTGTATCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (20 bp):
TATATTTATATTGTATATAC
Found at i:290082 original size:17 final size:17
Alignment explanation
Indices: 290060--290092 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
290050 TTTTTACTAC
290060 ATAATTATAATAAAAAA
1 ATAATTATAATAAAAAA
290077 ATAATTATAATAAAAA
1 ATAATTATAATAAAAA
290093 TATGTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATTATAATAAAAAA
Found at i:295771 original size:2 final size:2
Alignment explanation
Indices: 295764--295793 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
295754 TGAATGAAGC
295764 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
295794 TGGAGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:300653 original size:15 final size:14
Alignment explanation
Indices: 300623--300649 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
300613 ACAATTCTCA
300623 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
300637 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
300650 AGAATCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:304622 original size:21 final size:20
Alignment explanation
Indices: 304593--304631 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
304583 AGAATATGGT
*
304593 GGAGTGGATTCTGATGAGAA
1 GGAGTGGATCCTGATGAGAA
304613 GGAGTTGGATCCTGATGAG
1 GGAG-TGGATCCTGATGAG
304632 GTGGGAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.08, G:0.41, T:0.26
Consensus pattern (20 bp):
GGAGTGGATCCTGATGAGAA
Found at i:310167 original size:8 final size:8
Alignment explanation
Indices: 310152--310190 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
310142 ATATTTTAAA
310152 TTTTATTT
1 TTTTATTT
*
310160 TATTATTT
1 TTTTATTT
*
310168 TTTAATTT
1 TTTTATTT
310176 TTTTAATTT
1 TTTT-ATTT
310185 TTTTAT
1 TTTTAT
310191 AAAAAGAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATTT
Found at i:310177 original size:9 final size:9
Alignment explanation
Indices: 310165--310189 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
310155 TATTTTATTA
310165 TTTTTTAAT
1 TTTTTTAAT
310174 TTTTTTAAT
1 TTTTTTAAT
310183 TTTTTTA
1 TTTTTTA
310190 TAAAAAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:314241 original size:11 final size:11
Alignment explanation
Indices: 314225--314249 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
314215 GTCCCGTATG
314225 TTCCTTTCTTT
1 TTCCTTTCTTT
314236 TTCCTTTCTTT
1 TTCCTTTCTTT
314247 TTC
1 TTC
314250 AATGTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCCTTTCTTT
Found at i:317499 original size:20 final size:20
Alignment explanation
Indices: 317476--317515 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
317466 TCTAGAACAC
317476 TTTGAAATGTTTTAGAATAT
1 TTTGAAATGTTTTAGAATAT
317496 TTTGAAATGTTTTAGAATAT
1 TTTGAAATGTTTTAGAATAT
317516 CGTAAAAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTGAAATGTTTTAGAATAT
Found at i:317570 original size:40 final size:40
Alignment explanation
Indices: 317494--317608 Score: 113
Period size: 40 Copynumber: 2.9 Consensus size: 40
317484 GTTTTAGAAT
* * * * ** *
317494 ATTTTGAAATGTTTTAGAATATCGTAAAAGGCTCTGAAAG
1 ATTTTAAAATGTTCTAAAATATTGTGGAAGGTTCTGAAAG
*
317534 ATTTTAAAATGTTCTAAAATATTGTGGAAGGTTCTGAATG
1 ATTTTAAAATGTTCTAAAATATTGTGGAAGGTTCTGAAAG
* * * * *
317574 ATTCTAGAATATTCTAAAATAATGAGGAAGGTTCT
1 ATTTTAAAATGTTCTAAAATATTGTGGAAGGTTCT
317609 AGAACTTTAT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (40 bp):
ATTTTAAAATGTTCTAAAATATTGTGGAAGGTTCTGAAAG
Found at i:318559 original size:24 final size:24
Alignment explanation
Indices: 318521--318570 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
318511 CAACAAGACT
* *
318521 GTTTTTCTTAATAATTGGGAGATA
1 GTTTTTCCTAATAATTAGGAGATA
*
318545 GTTTTTCCTAGTAATTAGGAGATA
1 GTTTTTCCTAATAATTAGGAGATA
318569 GT
1 GT
318571 CGATGTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (24 bp):
GTTTTTCCTAATAATTAGGAGATA
Found at i:322715 original size:20 final size:20
Alignment explanation
Indices: 322692--322738 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
322682 TACAAAAGAA
322692 TCTAGAACACTT-TGGAATGT
1 TCTAGAA-ACTTCTGGAATGT
**
322712 TCTAGAATGTTCTGGAATGT
1 TCTAGAAACTTCTGGAATGT
322732 TCTAGAA
1 TCTAGAA
322739 TATCGTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
TCTAGAAACTTCTGGAATGT
Found at i:322721 original size:10 final size:10
Alignment explanation
Indices: 322706--322819 Score: 65
Period size: 10 Copynumber: 11.4 Consensus size: 10
322696 GAACACTTTG
322706 GAATGTTCTA
1 GAATGTTCTA
*
322716 GAATGTTCTG
1 GAATGTTCTA
322726 GAATGTTCTA
1 GAATGTTCTA
* *
322736 GAAT-ATCGTG
1 GAATGTTC-TA
* * *
322746 GAAGGCTCTG
1 GAATGTTCTA
322756 GAA-GATTCTA
1 GAATG-TTCTA
322766 GAATGTTCTA
1 GAATGTTCTA
* * *
322776 GAATATTGTG
1 GAATGTTCTA
* *
322786 GAAGGCTT-TG
1 GAATG-TTCTA
322796 GAA-GATTCTA
1 GAATG-TTCTA
322806 GAATGTTCTA
1 GAATGTTCTA
322816 GAAT
1 GAAT
322820 AATGGGGAAG
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
9 6 0.07
10 70 0.85
11 6 0.07
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (10 bp):
GAATGTTCTA
Found at i:322748 original size:40 final size:39
Alignment explanation
Indices: 322704--322838 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 39
322694 TAGAACACTT
* *
322704 TGGAATGTTCTAGAATG-TTCTGGAATGTTCTAGAATATCG
1 TGGAAGGTTCTAGAA-GATTCTAGAATGTTCTAGAATAT-G
* *
322744 TGGAAGGCTCTGGAAGATTCTAGAATGTTCTAGAATATTG
1 TGGAAGGTTCTAGAAGATTCTAGAATGTTCTAGAATA-TG
*
322784 TGGAAGGCTT-TGGAAGATTCTAGAATGTTCTAGAATAATG
1 TGGAAGG-TTCTAGAAGATTCTAGAATGTTCTAGAAT-ATG
*
322824 GGGAAGGTTCTAGAA
1 TGGAAGGTTCTAGAA
322839 CTTTATGGAG
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
39 3 0.04
40 77 0.93
41 3 0.04
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (39 bp):
TGGAAGGTTCTAGAAGATTCTAGAATGTTCTAGAATATG
Found at i:323783 original size:24 final size:24
Alignment explanation
Indices: 323748--323797 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
323738 CAACAAGACT
* *
323748 GTTTTTCTTAGTAATTGGGAGATA
1 GTTTTTCCTAGTAATTAGGAGATA
323772 GTTTTTCCTAGTAATTAGGAGATA
1 GTTTTTCCTAGTAATTAGGAGATA
323796 GT
1 GT
323798 CGATGTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (24 bp):
GTTTTTCCTAGTAATTAGGAGATA
Found at i:329985 original size:57 final size:57
Alignment explanation
Indices: 329911--330023 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
329901 TCCAAGTAAA
329911 ATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATC
1 ATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATC
*
329968 ATAGCTCTAGGAGACTAATCAAACCCAAACTTATCTTAGAAAATTTGTCTGGCTAT
1 ATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
330024 TTTCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (57 bp):
ATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATC
Found at i:330264 original size:57 final size:57
Alignment explanation
Indices: 330203--330316 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
330193 GTCCAAGTAA
330203 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
330260 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
330317 TTTCATTTCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (57 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:330327 original size:293 final size:293
Alignment explanation
Indices: 329800--330845 Score: 2020
Period size: 293 Copynumber: 3.6 Consensus size: 293
329790 TATATTTGTA
329800 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
1 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
*
329865 AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAAAATAGCTCTAGGAGACTAAT
66 AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
329930 CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCA
131 CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCA
* *
329995 AACTTATCTTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGGGCT
196 AACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCT
330060 GCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTG
261 GCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTG
*
330093 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTTATGATAAGCTAAAACATGAATACAAAAATAT
1 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
330158 AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
66 AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
330223 CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCA
131 CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCA
330288 AACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCT
196 AACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCT
* *
330353 GCAAAGAAAGAGTCAAGGACGCCATCTTGGCTA
261 GCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTG
330386 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
1 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
330451 AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
66 AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
*
330516 CAAACCCAAACTTATCCAAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCA
131 CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCA
330581 AACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCT
196 AACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCT
330646 GCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTG
261 GCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTG
330679 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
1 AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
*
330744 AATTTTTAAAAAATATAAAAATATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
66 AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
330809 CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
131 CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
330846 TTTCATTTCC
Statistics
Matches: 741, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
293 741 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (293 bp):
AATTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATAT
AATTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAAT
CAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCA
AACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCT
GCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTG
Found at i:330557 original size:57 final size:57
Alignment explanation
Indices: 330496--330609 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
330486 GTCCAAGTAA
330496 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCAAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCAAGAAAATTTGTCTGGCTAT
*
330553 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCAAGAAAATTTGTCTGGCTAT
330610 TTTCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (57 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCAAGAAAATTTGTCTGGCTAT
Found at i:330970 original size:236 final size:236
Alignment explanation
Indices: 330553--331081 Score: 1022
Period size: 236 Copynumber: 2.2 Consensus size: 236
330543 GTCTGGCTAT
330553 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
330618 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
330683 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTAGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
*
330748 TTTAAAAAATATAAAAATATATAAATTGTTTGTCCAAGTAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
330789 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
330854 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTTGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
330919 CTAGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTAGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
330984 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
331025 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331082 CATAGCTCTA
Statistics
Matches: 289, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 289 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (236 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
CTAGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
Found at i:330970 original size:529 final size:529
Alignment explanation
Indices: 330260--333019 Score: 3092
Period size: 529 Copynumber: 5.1 Consensus size: 529
330250 GTCTGGCTAT
330260 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
* *
330325 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCATCTTGGCTAAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
330390 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
330455 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
*
330520 CCCAAACTTATCCAAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
330585 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCAA
326 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCAA
330650 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
391 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
*
330715 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATATAAAAATATATAAATTGTTTG
456 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATATAAAAAAATATAAATTGTTTG
330780 TCCAAGTAA
521 TCCAAGTAA
330789 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
330854 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTTGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
330919 CTAGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
330984 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
331049 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
*
331114 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
326 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCAA
*
331179 AGAAAGAGTCAAGGACGCCGTCTTGGTTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
391 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
331244 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATATAAAAAAATATAAATTGTTTG
456 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATATAAAAAAATATAAATTGTTTG
331309 TCCAAGTAA
521 TCCAAGTAA
331318 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGATC
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT--T---T-
* * * * * * **** ***** ** * *
331383 TAGGAGACTAAT-CAAACCCAAACTTATCCTAGAAAATT-TGTCTGGCTATTTTCA-TTTCCA-T
60 T----CA-T-TTCCATA-CC---TTTCTCTTATTTTATTGTG-CT-GC-AAAGAAAGAGTCAAGG
** *** ** * * * ** *
331444 AC-CTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTG-GCTGAA-TTC
112 ACGCCGTCT-TGGCTGAATTCT--TG----G--AGA-T-TA-TA-G-C-T-TTGATTTAAAGTTC
* *** * * * * ** *** * * *
331506 TTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACA-A-AAATATAAT
161 AT---GA-TA-AGCTAAAATATGAA-TACA--AAAATAT-AATTTTTAAAAAATATAAA-A-A--
331569 TTTTAAAAAATAAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
213 -----------------AATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
** ** * * * ** ** ****
331634 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCA-TA-CCTTTCTCTTA-TTTTA
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCAT-AGCTCTAGGAGAC-TAATCAAACCCAAA
* * *** * **** ** * * ** *
331696 -TTGTGCT-GCAAAGAAAGAGTCAAGGAC-GCCGTC-TTGGC-TGA--ATTCT-TGGAGATTATA
324 CTTATCCTAG--AA-AATTTGTC-TGG-CTATTTTCATTTCCAT-ACCTTTCTCT-TATTTTATT
* *** * * * * *** ** * * * * *
331753 GCT-TTG-ATTTAAAG-TTCATGATAAG-C-TAAAGTATGAATAC---AAAAATATA-ATTT--T
382 G-TGCTGCAAAGAAAGAGTCAAG-GACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGAT
* ** * * ** * ** * * * ** * *
331807 TAAAAAAT-ATAAAAAAATATAAA-TTGTTTGTCCAAGTAACAT-AGCTCTAGGAGACTAATCA-
445 TTAAAGTTCATGATAAGCTA-AAACATG--AATACAA-AAATATAATTTTTA--A-A-AAAT-AT
* * ** ** *
331868 AACCCAAACTTATCCTAGAA-AATTTGT-CTGGCTAT
501 AA---AAA--AAT-ATA-AATTGTTTGTCCAAG-TAA
331903 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
331968 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
* *
332033 CTTGGAGATTATAGCTTTGATTTAAAGTTCTTGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
* *
332098 TTTAAAAAATAAAAAAAAAATATAATTTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAA
196 TTTAAAAAAT-ATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAA
*
332163 ACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGATCTAGGAGACTAATCAAACCCAAAC
260 ACCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAAC
332228 TTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCA
325 TTATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCA
332293 AAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCA
390 AAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCA
332358 TGATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATATAAAAAAATATAAATTGTTT
455 TGATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATATAAAAAAATATAAATTGTTT
332423 GTCCAAGTAA
520 GTCCAAGTAA
332433 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
332498 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
332563 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
*
332628 TTTAAAAAATATAAAAAAATATAATTTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
* *
332693 CCCAAACTTATCCTAGAAAATTTGTGTGGCTATCATAGCTCTAGGAGACTAATCAAACCTAAACT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
*
332758 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
326 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCAA
332823 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
391 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
*
332888 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAAATTGTTT
456 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAAT-ATAAAAAAATATAAATTGTTT
*
332953 ATCCAAGTAA
520 GTCCAAGTAA
* *
332963 CATAGCTCTAGGAGACTAATCGAACCCAAACTTATCCTAGAAAATTTGTTTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
333020 CATAGATCTA
Statistics
Matches: 1833, Mismatches: 266, Indels: 263
0.78 0.11 0.11
Matches are distributed among these distances:
528 1 0.00
529 875 0.48
530 391 0.21
531 11 0.01
532 17 0.01
533 12 0.01
534 6 0.00
535 10 0.01
536 5 0.00
537 1 0.00
538 7 0.00
539 8 0.00
540 12 0.01
541 12 0.01
542 9 0.00
543 6 0.00
544 20 0.01
545 5 0.00
546 3 0.00
548 7 0.00
549 5 0.00
550 3 0.00
551 6 0.00
552 11 0.01
553 3 0.00
554 3 0.00
555 4 0.00
556 5 0.00
557 11 0.01
558 5 0.00
559 4 0.00
560 3 0.00
561 3 0.00
562 12 0.01
563 3 0.00
564 4 0.00
565 6 0.00
566 8 0.00
568 4 0.00
569 5 0.00
570 18 0.01
571 6 0.00
573 12 0.01
574 13 0.01
575 9 0.00
576 7 0.00
577 7 0.00
578 1 0.00
579 6 0.00
580 10 0.01
581 5 0.00
582 12 0.01
583 18 0.01
584 10 0.01
585 162 0.09
586 10 0.01
587 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (529 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCAA
AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATATAAAAAAATATAAATTGTTTG
TCCAAGTAA
Found at i:331096 original size:293 final size:293
Alignment explanation
Indices: 330789--331666 Score: 1695
Period size: 293 Copynumber: 3.0 Consensus size: 293
330779 GTCCAAGTAA
330789 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
330854 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTTGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
* *
330919 CTAGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
330984 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
331049 CCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331082 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
* *
331147 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGTTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
331212 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
331277 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
331342 CCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
*
331375 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
331440 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
331505 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
331570 TTTAAAAAATA-AAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
331634 CCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331667 TTTCATTTCC
Statistics
Matches: 577, Mismatches: 8, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
292 86 0.15
293 491 0.85
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (293 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
CCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:331100 original size:57 final size:57
Alignment explanation
Indices: 331025--331138 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
331015 GTCCAAGTAA
331025 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331082 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331139 TTTCATTTCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (57 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:331379 original size:57 final size:57
Alignment explanation
Indices: 331318--331431 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
331308 GTCCAAGTAA
*
331318 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331375 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331432 TTTCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (57 bp):
CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:331550 original size:822 final size:823
Alignment explanation
Indices: 329967--333312 Score: 6428
Period size: 822 Copynumber: 4.1 Consensus size: 823
329957 GTCTGGCTAT
*
329967 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCTTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
330032 CCATACCTTTCTCTTATTTTATTGGGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
* *
330097 CTTGGAGATTATAGCTTTGATTTAAAGTTTATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
330162 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
330227 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
*
330292 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGCTGCAA
326 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
* *
330357 AGAAAGAGTCAAGGACGCCATCTTGGCTAAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
391 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
*
330422 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAAT-ATAAAAAAATATAAATTGTTT
456 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAAATTGTTT
*
330486 GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCAAGAAAATTTGTCTGGCT
521 GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCT
*
330551 ATCATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
586 ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
330616 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
651 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
330681 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
716 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
*
330746 TTTTTAAAAAATATAAAAATATATAAATTGTTTGTCCAAGTAA
781 TTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
330789 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
330854 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTTGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
330919 CTAGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
330984 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
331049 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
331114 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
326 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
*
331179 AGAAAGAGTCAAGGACGCCGTCTTGGTTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
391 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
*
331244 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAAT-ATAAAAAAATATAAATTGTTT
456 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAAATTGTTT
331308 GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCT
521 GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCT
331373 ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
586 ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
331438 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
651 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
331503 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
716 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
331568 TTTTTAAAAAATA-AAAAAAATATAAATTGTTTGTCCAAGTAA
781 TTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
331610 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
331675 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
331740 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAGTATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
331805 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
331870 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
331935 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
326 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
*
332000 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCTT
391 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
*
332065 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAATTTGTTT
456 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAAATTGTTT
332130 GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCT
521 GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCT
332195 ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
586 ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
332260 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
651 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
332325 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
716 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
332390 TTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
781 TTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
332433 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
332498 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
332563 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
*
332628 TTTAAAAAATATAAAAAAATATAATTTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
* *
332693 CCCAAACTTATCCTAGAAAATTTGTGTGGCTATCATAGCTCTAGGAGACTAATCAAACCTAAACT
261 CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
332758 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
326 TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
332823 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
391 AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
332888 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAAATTGTTT
456 GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAAATTGTTT
* * *
332953 ATCCAAGTAACATAGCTCTAGGAGACTAATCGAACCCAAACTTATCCTAGAAAATTTGTTTGGCT
521 GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCT
333018 ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
586 ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
333083 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
651 TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
333148 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
716 TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
*
333213 TTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCTAAGTAA
781 TTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
*
333256 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
333313 CATAGCTCTA
Statistics
Matches: 2490, Mismatches: 32, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
821 521 0.21
822 1072 0.43
823 897 0.36
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (823 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
CCCAAACTTATCCTAGAAAATTTGTCTGGCTATCATAGCTCTAGGAGACTAATCAAACCCAAACT
TATCCTAGAAAATTTGTCTGGCTATTTTCATTTCCATACCTTTCTCTTATTTTATTGTGGTGCAA
AGAAAGAGTCAAGGACGCCGTCTTGGCTGAATTCTTGGAGATTATAGCTTTGATTTAAAGTTCAT
GATAAGCTAAAACATGAATACAAAAATATAATTTTTAAAAAATAAAAAAAAAATATAAATTGTTT
GTCCAAGTAACATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCT
ATCATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCAT
TTCCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAA
TTCTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAA
TTTTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
Found at i:331792 original size:235 final size:236
Alignment explanation
Indices: 331375--331902 Score: 1022
Period size: 235 Copynumber: 2.2 Consensus size: 236
331365 GTCTGGCTAT
*
331375 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
331440 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
331505 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
331570 TTTAAAAAATA-AAAAAAATATAAATTGTTTGTCCAAGTAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
331610 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
331675 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
**
331740 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAGTATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
331805 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
331846 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331903 CATAGCTCTA
Statistics
Matches: 289, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
235 203 0.70
236 86 0.30
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (236 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
Found at i:331921 original size:57 final size:57
Alignment explanation
Indices: 331846--331959 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
331836 GTCCAAGTAA
331846 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331903 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
331960 TTTCATTTCC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (57 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:332213 original size:57 final size:57
Alignment explanation
Indices: 332140--332253 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
332130 GTCCAAGTAA
*
332140 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
332197 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
332254 TTTCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (57 bp):
CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:332616 original size:236 final size:236
Alignment explanation
Indices: 332197--332725 Score: 1013
Period size: 236 Copynumber: 2.2 Consensus size: 236
332187 GTCTGGCTAT
*
332197 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
332262 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
332327 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
332392 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
332433 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
332498 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
332563 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
*
332628 TTTAAAAAATATAAAAAAATATAATTTGTTTGTCCAAGTAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
*
332669 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
332726 CATAGCTCTA
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
236 288 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (236 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAA
Found at i:332742 original size:57 final size:57
Alignment explanation
Indices: 332669--332782 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
332659 GTCCAAGTAA
*
332669 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
*
332726 CATAGCTCTAGGAGACTAATCAAACCTAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
332783 TTTCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (57 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:333035 original size:57 final size:57
Alignment explanation
Indices: 332963--333076 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
332953 ATCCAAGTAA
* * *
332963 CATAGCTCTAGGAGACTAATCGAACCCAAACTTATCCTAGAAAATTTGTTTGGCTAT
1 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
333020 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
333077 TTTCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (57 bp):
CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:333131 original size:294 final size:293
Alignment explanation
Indices: 332433--333488 Score: 1977
Period size: 293 Copynumber: 3.6 Consensus size: 293
332423 GTCCAAGTAA
332433 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
332498 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
*
332563 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAATATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
*
332628 TTTAAAAAATATAAAAAAATATAATTTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
332693 CCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
261 CCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
*
332726 CATAGCTCTAGGAGACTAATCAAACCTAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
332791 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
332856 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
* * *
332921 TTTAAAAAATAAAAAAAAAATATAAATTGTTTATCCAAGTAACATAGCTCTAGGAGACTAATCGA
196 TTTAAAAAAT-ATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAA
*
332986 ACCCAAACTTATCCTAGAAAATTTGTTTGGCTAT
260 ACCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
*
333020 CATAGATCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
333085 CCATACCTTTCTCTTATTTTATTGTGCTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
333150 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
*
333215 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCTAAGTAACATAGCTCTAGGAGACTAATCAAA
196 TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
333280 CCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
261 CCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
333313 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
*
333378 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGTCGTCTTGGCTGAATT
66 CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
* * *
333443 CTTTGAGATTATAGTTTTGATTTAAAGTTCATGATAAGTTAAAACA
131 CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACA
333489 CTCTGTCAAT
Statistics
Matches: 741, Mismatches: 21, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
293 456 0.62
294 285 0.38
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (293 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTATTTTCATTT
CCATACCTTTCTCTTATTTTATTGTGGTGCAAAGAAAGAGTCAAGGACGCCGTCTTGGCTGAATT
CTTGGAGATTATAGCTTTGATTTAAAGTTCATGATAAGCTAAAACATGAATACAAAAATATAATT
TTTAAAAAATATAAAAAAATATAAATTGTTTGTCCAAGTAACATAGCTCTAGGAGACTAATCAAA
CCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
Found at i:333317 original size:57 final size:57
Alignment explanation
Indices: 333256--333369 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
333246 GTCTAAGTAA
*
333256 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTGTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
333313 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
1 CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
333370 TTTCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (57 bp):
CATAGCTCTAGGAGACTAATCAAACCCAAACTTATCCTAGAAAATTTGTCTGGCTAT
Found at i:334316 original size:14 final size:14
Alignment explanation
Indices: 334293--334390 Score: 71
Period size: 13 Copynumber: 6.9 Consensus size: 14
334283 TTGAATCAAG
334293 AATTTATATTATAT
1 AATTTATATTATAT
*
334307 AATTTTTATTTATTAAT
1 AATTTATA-TTA-T-AT
334324 AATTTATATTATAT
1 AATTTATATTATAT
*
334338 ATATTAAATATT-TAT
1 A-ATT-TATATTATAT
334353 -ATATTATATT-T-T
1 AAT-TTATATTATAT
*
334365 AATTATTTATTATAT
1 AATT-TATATTATAT
334380 AA-TTATATTAT
1 AATTTATATTAT
334391 GTTTAATATT
Statistics
Matches: 68, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
12 2 0.03
13 22 0.32
14 13 0.19
15 13 0.19
16 9 0.13
17 9 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTTATATTATAT
Found at i:334342 original size:22 final size:22
Alignment explanation
Indices: 334312--334389 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
334302 TATATAATTT
*
334312 TTATTTATTAATAATTTATAT-
1 TTATATATTAATAATTTATATA
334333 TATATATATTAA-ATATTTATATA
1 T-TATATATTAATA-ATTTATATA
* *
334356 TTATATTTTAATTATTTATTATA
1 TTATATATTAATAATTTA-TATA
*
334379 TAATTATATTA
1 TTA-TATATTA
334390 TGTTTAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.04
22 31 0.67
23 7 0.15
24 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATATTAATAATTTATATA
Found at i:334355 original size:15 final size:16
Alignment explanation
Indices: 334329--334358 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
334319 TTAATAATTT
334329 ATATTATATATATTAA
1 ATATTATATATATTAA
334345 ATATT-TATATATTA
1 ATATTATATATATTA
334359 TATTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTATATATATTAA
Found at i:339902 original size:16 final size:16
Alignment explanation
Indices: 339883--339972 Score: 62
Period size: 16 Copynumber: 5.6 Consensus size: 16
339873 TTTTGAGTTT
339883 AGATTATTTTAATTTC
1 AGATTATTTTAATTTC
*
339899 AGATTA-TTTCATGTTC
1 AGATTATTTTAAT-TTC
339915 -GAATTATTTTAATTTC
1 AG-ATTATTTTAATTTC
* * **
339931 AAACTATTTTAGGTTC
1 AGATTATTTTAATTTC
*
339947 A-AGTTATTTTGATTTC
1 AGA-TTATTTTAATTTC
339963 -GATATATTTT
1 AGAT-TATTTT
339973 GACATGGGTC
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
15 8 0.14
16 44 0.77
17 5 0.09
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (16 bp):
AGATTATTTTAATTTC
Found at i:339921 original size:32 final size:31
Alignment explanation
Indices: 339885--339971 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 31
339875 TTGAGTTTAG
*
339885 ATTATTTTAATTTCAGATTATTTCATGTTCGA
1 ATTATTTTAATTTCAGATTATTTCAGGTTC-A
* * *
339917 ATTATTTTAATTTCAAACTATTTTAGGTTCA
1 ATTATTTTAATTTCAGATTATTTCAGGTTCA
*
339948 AGTTATTTTGATTTC-GATATATTT
1 A-TTATTTTAATTTCAGAT-TATTT
339972 TGACATGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 3 0.07
32 43 0.93
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (31 bp):
ATTATTTTAATTTCAGATTATTTCAGGTTCA
Found at i:340367 original size:19 final size:19
Alignment explanation
Indices: 340330--340370 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
340320 GAAAGTTTAC
340330 TTTTTAATTGTATAAATATT
1 TTTTTAATTGTAT-AATATT
340350 TTTTTAATTGTGAT-ATATT
1 TTTTTAATTGT-ATAATATT
340369 TT
1 TT
340371 CTATGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 11 0.55
21 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTTTAATTGTATAATATT
Found at i:346993 original size:3 final size:3
Alignment explanation
Indices: 346985--347023 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
346975 GTTTCCTAAA
346985 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
347024 GTGTCACTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:350108 original size:2 final size:2
Alignment explanation
Indices: 350097--350144 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
350087 ATACACACAC
* *
350097 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T A- AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
350136 AT AT AT AT A
1 AT AT AT AT A
350145 GAGATATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:357085 original size:29 final size:29
Alignment explanation
Indices: 357052--357115 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
357042 AAAGACTTTT
* * *
357052 AAAATGATATTGTCACATAAGATGTCATG
1 AAAATGATATTGTCACATAAAATATCATA
*
357081 AAAATGATATTGTCATATAAAATATCATA
1 AAAATGATATTGTCACATAAAATATCATA
357110 AAAATG
1 AAAATG
357116 TAACTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (29 bp):
AAAATGATATTGTCACATAAAATATCATA
Found at i:361168 original size:7 final size:7
Alignment explanation
Indices: 361158--361182 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
361148 ATTATACTGT
361158 AATTTAA
1 AATTTAA
361165 AATTTAA
1 AATTTAA
361172 AATTTAA
1 AATTTAA
361179 AATT
1 AATT
361183 ATATTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:361308 original size:21 final size:20
Alignment explanation
Indices: 361284--361333 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
361274 TATAATTAAA
361284 TTTAAATAAAAAATATATTAT
1 TTTAAATAAAAAAT-TATTAT
*
361305 TTT-AATTAAAAATTATTAT
1 TTTAAATAAAAAATTATTAT
*
361324 TTTAGATAAA
1 TTTAAATAAA
361334 CCGGCTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 13 0.52
21 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TTTAAATAAAAAATTATTAT
Found at i:361755 original size:16 final size:15
Alignment explanation
Indices: 361733--361780 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
361723 CTTCATACAT
361733 AAATATAAATTTTTA
1 AAATATAAATTTTTA
**
361748 AAATTATAAAAATTTA
1 AAA-TATAAATTTTTA
*
361764 ATATATAAAATTTTTA
1 AAATAT-AAATTTTTA
361780 A
1 A
361781 CATCAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATAAATTTTTA
Found at i:361923 original size:24 final size:24
Alignment explanation
Indices: 361896--361956 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 24
361886 ATTAAGAGAG
361896 ATAAATATTAAAATTTTGTTAAA-A
1 ATAAATATTAAAATTTT-TTAAATA
**
361920 ATAAA-A-TAAAA-AATTTAAATA
1 ATAAATATTAAAATTTTTTAAATA
361941 A-AAATATTAAAATTTT
1 ATAAATATTAAAATTTT
361957 ATATCAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
20 8 0.28
21 4 0.14
22 10 0.34
23 2 0.07
24 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATAAATATTAAAATTTTTTAAATA
Found at i:361953 original size:14 final size:13
Alignment explanation
Indices: 361916--361953 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
361906 AAATTTTGTT
361916 AAAAA-TAAAATA
1 AAAAATTAAAATA
*
361928 AAAAATTTAAATA
1 AAAAATTAAAATA
361941 AAAATATTAAAAT
1 AAAA-ATTAAAAT
361954 TTTATATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 5 0.23
13 10 0.45
14 7 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:362182 original size:24 final size:23
Alignment explanation
Indices: 362135--362185 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
362125 TATTATATTT
* * *
362135 AAATAAATTTTTAATTTATATAA
1 AAATAAAATATTAATTTAAATAA
362158 AAATAAAATATTAATTTAAATTAA
1 AAATAAAATATTAATTTAAA-TAA
362182 AAAT
1 AAAT
362186 TTATTAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAAAATATTAATTTAAATAA
Found at i:362243 original size:31 final size:30
Alignment explanation
Indices: 362197--362256 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
362187 TATTAAGATT
* * *
362197 AAAAGTTTGTTTAAATGTAAAACAAAATTTA
1 AAAAATTTATTTAAATAT-AAACAAAATTTA
*
362228 AAAAATTTATTTAAATATAAATAAAATTT
1 AAAAATTTATTTAAATATAAACAAAATTT
362257 TGTTTAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (30 bp):
AAAAATTTATTTAAATATAAACAAAATTTA
Found at i:370746 original size:208 final size:210
Alignment explanation
Indices: 370378--370798 Score: 810
Period size: 208 Copynumber: 2.0 Consensus size: 210
370368 AATGCAATGC
370378 TTTACCAGCCTGTAAGAACACGTATAGGCTATAGCTGTAGAATCTGGTCAATTTTAGTACACAAA
1 TTTACCAGCCTGTAAGAACACGTATAGGCTATAGCTGTAGAATCTGGTCAATTTTAGTACACAAA
*
370443 GCTCAAGCTCAAGTCATATCATCATCAAAGAAGTCCATCCAGTTTCAGATATGATTTCAATTCAG
66 GCTCAAGCTCAAGTCACATCATCATCAAAGAAGTCCATCCAGTTTCAGATATGATTTCAATTCAG
370508 AGGTTCAATCTGTTCACCTGATCAGGTTCAGGAGCAGATTTTTCATCACTGACCCGTCCCCATTT
131 AGGTTCAATCTGTTCACCTGATCAGGTTCAGGAGCAGATTTTTCATCACTGACCCGTCCCCATTT
370573 CGTGTAAGGATGAAT
196 CGTGTAAGGATGAAT
370588 TTTACCAGCCTGTAAGAACACGTATAGGCTATAGCTGTAGAATCTGGTCAATTTTAGTACACAAA
1 TTTACCAGCCTGTAAGAACACGTATAGGCTATAGCTGTAGAATCTGGTCAATTTTAGTACACAAA
*
370653 GCTCAAGCTCAAG-C-CATCATCATCAAAGAAGTCCATCCAGTTTCATATATGATTTCAATTCAG
66 GCTCAAGCTCAAGTCACATCATCATCAAAGAAGTCCATCCAGTTTCAGATATGATTTCAATTCAG
370716 AGGTTCAATCTGTTCACCTGATCAGGTTCAGGAGCAGATTTTTCATCACTGACCCGTCCCCATTT
131 AGGTTCAATCTGTTCACCTGATCAGGTTCAGGAGCAGATTTTTCATCACTGACCCGTCCCCATTT
370781 CGTGTAAGGATGAAT
196 CGTGTAAGGATGAAT
370796 TTT
1 TTT
370799 TCCAAGTCAA
Statistics
Matches: 209, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
208 130 0.62
209 1 0.00
210 78 0.37
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (210 bp):
TTTACCAGCCTGTAAGAACACGTATAGGCTATAGCTGTAGAATCTGGTCAATTTTAGTACACAAA
GCTCAAGCTCAAGTCACATCATCATCAAAGAAGTCCATCCAGTTTCAGATATGATTTCAATTCAG
AGGTTCAATCTGTTCACCTGATCAGGTTCAGGAGCAGATTTTTCATCACTGACCCGTCCCCATTT
CGTGTAAGGATGAAT
Found at i:375147 original size:2 final size:2
Alignment explanation
Indices: 375140--375166 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
375130 AGCATATAGC
375140 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
375167 AAAATTATTC
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:380284 original size:8 final size:8
Alignment explanation
Indices: 380271--380330 Score: 70
Period size: 8 Copynumber: 7.8 Consensus size: 8
380261 ATGAAATCCT
380271 TATATATG
1 TATATATG
380279 TATATA--
1 TATATATG
*
380285 TATATATA
1 TATATATG
*
380293 TATGTATG
1 TATATATG
380301 TATATATG
1 TATATATG
*
380309 TATGTATG
1 TATATATG
*
380317 TATGTATG
1 TATATATG
380325 TATATA
1 TATATA
380331 AACACACATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
6 6 0.13
8 39 0.87
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:380288 original size:12 final size:12
Alignment explanation
Indices: 380275--380330 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
380265 AATCCTTATA
380275 TATGTATATA--
1 TATGTATATATG
*
380285 TATATATATATG
1 TATGTATATATG
380297 TATGTATATATG
1 TATGTATATATG
*
380309 TATGTATGTATG
1 TATGTATATATG
380321 TATGTATATA
1 TATGTATATA
380331 AACACACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.22
12 31 0.77
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (12 bp):
TATGTATATATG
Found at i:389819 original size:13 final size:13
Alignment explanation
Indices: 389784--389819 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
389774 CGTTTCTTCC
389784 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
* *
389797 CTTTTCTTCTTTT
1 TTTTTTTTCTTTT
389810 TTTTTTTTCT
1 TTTTTTTTCT
389820 GAAAAGATCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:390095 original size:32 final size:32
Alignment explanation
Indices: 390054--390117 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
390044 GTAATATCGG
390054 TAAGTCATTTTAGATTGAGATGGGGTTCAACT
1 TAAGTCATTTTAGATTGAGATGGGGTTCAACT
390086 TAAGTCATTTTAGATTGAGATGGGGTTCAACT
1 TAAGTCATTTTAGATTGAGATGGGGTTCAACT
390118 GTTCAAGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (32 bp):
TAAGTCATTTTAGATTGAGATGGGGTTCAACT
Found at i:393724 original size:14 final size:14
Alignment explanation
Indices: 393680--393727 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
393670 AAATTTTAGT
393680 TTTTACATTA-AATA
1 TTTTA-ATTATAATA
*
393694 TTTAAATTATAAT-
1 TTTTAATTATAATA
*
393707 TTTTATTTATAATA
1 TTTTAATTATAATA
393721 TTTTAAT
1 TTTTAAT
393728 AAATTATTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 15 0.54
14 13 0.46
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATTATAATA
Found at i:395159 original size:30 final size:30
Alignment explanation
Indices: 395082--395159 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
395072 TGTTTATTTT
* **
395082 TTAAAATATTTTTATATATTTTTATTAAATA
1 TTAAAA-AATTTTATATATTCATATTAAATA
*
395113 TATATAAAAA--TTATATATTCATATTATATA
1 T-TA-AAAAATTTTATATATTCATATTAAATA
395143 TTAAAAAATTTTATATA
1 TTAAAAAATTTTATATA
395160 CTAAATTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
28 5 0.13
29 2 0.05
30 25 0.64
31 1 0.03
32 3 0.08
33 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAAAAAATTTTATATATTCATATTAAATA
Found at i:395642 original size:3 final size:3
Alignment explanation
Indices: 395636--395664 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
395626 ATTGACCTCT
395636 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
395665 TTATTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:396103 original size:7 final size:7
Alignment explanation
Indices: 396091--396130 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
396081 TCGCTCTATC
*
396091 AAAAATG
1 AAAAATA
*
396098 AAAAATG
1 AAAAATA
396105 AAAAATA
1 AAAAATA
396112 AAAAATA
1 AAAAATA
396119 AAAAATA
1 AAAAATA
396126 AAAAA
1 AAAAA
396131 GCAAAAGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:396136 original size:14 final size:14
Alignment explanation
Indices: 396090--396136 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
396080 TTCGCTCTAT
*
396090 CAAAAATGAAAAATG
1 CAAAAAT-AAAAAAG
*
396105 -AAAAATAAAAAAT
1 CAAAAATAAAAAAG
*
396118 AAAAAATAAAAAAG
1 CAAAAATAAAAAAG
396132 CAAAA
1 CAAAA
396137 GCAAAAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (14 bp):
CAAAAATAAAAAAG
Found at i:396136 original size:21 final size:21
Alignment explanation
Indices: 396090--396136 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
396080 TTCGCTCTAT
* * *
396090 CAAAAATGAAAAATGAAAAAT
1 CAAAAATAAAAAATAAAAAAG
*
396111 AAAAAATAAAAAATAAAAAAG
1 CAAAAATAAAAAATAAAAAAG
396132 CAAAA
1 CAAAA
396137 GCAAAAGTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (21 bp):
CAAAAATAAAAAATAAAAAAG
Found at i:400607 original size:6 final size:6
Alignment explanation
Indices: 400593--400632 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
400583 AAAGAATGGT
* *
400593 AGGGCC AGGGAC AGGGAT AGGGAC AGGGAC AGGGAC -GGGA
1 AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC AGGGAC AGGGA
400633 ACAGACATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.30, C:0.15, G:0.53, T:0.03
Consensus pattern (6 bp):
AGGGAC
Done.