Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 161 of 163
Found at i:46086272 original size:15 final size:17
Alignment explanation
Indices: 46086252--46086284 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
46086242 ATCTTTTAAT
46086252 AATTA-TAAAAA-TATA
1 AATTATTAAAAATTATA
46086267 AATTATTAAAAATTATA
1 AATTATTAAAAATTATA
46086284 A
1 A
46086285 TTTAATTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATTAAAAATTATA
Found at i:46086649 original size:28 final size:26
Alignment explanation
Indices: 46086584--46086649 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
46086574 GATCCAAGTC
46086584 TTTATATTTTTT-TTTCTATTTCAAAT
1 TTTAT-TTTTTTATTTCTATTTCAAAT
* ** *
46086610 TTAATTACTTTATTTTTATTTCAAAAAT
1 TTTATTTTTTTATTTCTATTTC--AAAT
46086638 TTTATTTTTTTA
1 TTTATTTTTTTA
46086650 CAAATTATTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
25 4 0.13
26 13 0.43
28 13 0.43
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTATTTTTTTATTTCTATTTCAAAT
Found at i:46087474 original size:18 final size:18
Alignment explanation
Indices: 46087453--46087487 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46087443 ATTTAATAAC
46087453 AAATTACATAT-TAAATTA
1 AAATT-CATATATAAATTA
46087471 AAATTCATATATAAATT
1 AAATTCATATATAAATT
46087488 CGATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTCATATATAAATTA
Found at i:46089267 original size:31 final size:31
Alignment explanation
Indices: 46089232--46089298 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
46089222 TTTGCGAAGA
46089232 TTAATAAAAATTTTCAAAAAATTTAGAGGAT
1 TTAATAAAAATTTTCAAAAAATTTAGAGGAT
* * * *
46089263 TTAATTAAAATTTTCAAAATATTTTGAGGGT
1 TTAATAAAAATTTTCAAAAAATTTAGAGGAT
46089294 TTAAT
1 TTAAT
46089299 GAGGATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (31 bp):
TTAATAAAAATTTTCAAAAAATTTAGAGGAT
Found at i:46089307 original size:31 final size:31
Alignment explanation
Indices: 46089232--46089316 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
46089222 TTTGCGAAGA
* * *
46089232 TTAATAAAAATTTTCAAAAAATTTAGAGGAT
1 TTAATGAAAATTTTCAAAATATTTTGAGGAT
* *
46089263 TTAATTAAAATTTTCAAAATATTTTGAGGGT
1 TTAATGAAAATTTTCAAAATATTTTGAGGAT
**
46089294 TTAATGAGGATTTT-AAAAT-TTTT
1 TTAATGAAAATTTTCAAAATATTTT
46089317 AAAGGGATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 38 0.81
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (31 bp):
TTAATGAAAATTTTCAAAATATTTTGAGGAT
Found at i:46092077 original size:2 final size:2
Alignment explanation
Indices: 46092072--46092097 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46092062 TCATATATTC
46092072 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
46092098 GTGTGTGTGT
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:46105014 original size:18 final size:16
Alignment explanation
Indices: 46104973--46105016 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
46104963 TTTTATATTC
46104973 AGTTTTTATTTTCTTT
1 AGTTTTTATTTTCTTT
*
46104989 AATATTTTGATTTTCTTCT
1 AGT-TTTT-ATTTTCTT-T
46105008 AGTTTTTAT
1 AGTTTTTAT
46105017 CTGCTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 6 0.26
18 12 0.52
19 3 0.13
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (16 bp):
AGTTTTTATTTTCTTT
Found at i:46106388 original size:9 final size:9
Alignment explanation
Indices: 46106374--46106406 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
46106364 TTAATGTTTA
46106374 AAATAATAT
1 AAATAATAT
46106383 AAATAATAT
1 AAATAATAT
46106392 AAATAAT-T
1 AAATAATAT
46106400 AAATAAT
1 AAATAAT
46106407 TGCGAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATAATAT
Found at i:46113206 original size:35 final size:35
Alignment explanation
Indices: 46113179--46113247 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
46113169 TTACCTTAGG
*
46113179 CACATATACAGTAGTGTGGTTTTGTTTACATTAAC
1 CACATATACAGTAATGTGGTTTTGTTTACATTAAC
** *
46113214 CATTTATAGAGTAATGTGGTTTTGTTTACATTAA
1 CACATATACAGTAATGTGGTTTTGTTTACATTAA
46113248 AAACACATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (35 bp):
CACATATACAGTAATGTGGTTTTGTTTACATTAAC
Found at i:46113265 original size:35 final size:35
Alignment explanation
Indices: 46113193--46113266 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
46113183 TATACAGTAG
** *** *
46113193 TGTGGTTTTGTTTACATTAACCATTTATAGAGTAA
1 TGTGGTTTTGTTTACATTAAAAACACATAGAGGAA
*
46113228 TGTGGTTTTGTTTACATTAAAAACACATTGAGGAA
1 TGTGGTTTTGTTTACATTAAAAACACATAGAGGAA
46113263 TGTG
1 TGTG
46113267 CACATGCCGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (35 bp):
TGTGGTTTTGTTTACATTAAAAACACATAGAGGAA
Found at i:46123363 original size:26 final size:22
Alignment explanation
Indices: 46123307--46123350 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
46123297 TAGATTAATC
46123307 CAAAATATATGTATTTATTTCT
1 CAAAATATATGTATTTATTTCT
46123329 CAAAATATATGTATTTATTTCT
1 CAAAATATATGTATTTATTTCT
46123351 TTAAATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (22 bp):
CAAAATATATGTATTTATTTCT
Found at i:46124572 original size:228 final size:228
Alignment explanation
Indices: 46124175--46125062 Score: 1019
Period size: 228 Copynumber: 3.9 Consensus size: 228
46124165 TAAGACTCTA
*
46124175 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAGGCCAAAAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
* * * * * *
46124240 CCAGGATAAGGAAGGCATCCCTCCAGACCAGCAGCGTCTGATATTCGCCGGAAAACAACTCGAAG
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCTGGAAAACAACTCGAAG
46124305 ACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTCCGT-TT
131 ACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTCCGTCTT
*
46124369 GCGTGGTGGGATGCAAATCTTCGTGAAAACCTTG
196 -CGTGGTGGGATGCAAATCTTCGTGAAGACCTTG
* * * * *
46124403 ACCGGCAAGACAATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTTAAGGCGAAGAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
*
46124468 CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCTGGAAAACAACTTGAAG
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCTGGAAAACAACTCGAAG
* * *
46124533 ACGGCCGTACCTTGGCCGACTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTTCGT-TT
131 ACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTCCGTCTT
* *
46124597 GCGCGGCGGGATGCAAATCTTCGTGAAGACGCTT-
196 -CGTGGTGGGATGCAAATCTTCGTGAAGAC-CTTG
* * * *
46124631 ACCGGCAAGACGATCACTCTCGAGGTTGAGAGCTCTGATACGATTGACAACGTGAAAGCCAAAAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
* * *
46124696 CCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTCATCTTCGCTGGAAAGCAACTCGAGG
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCTGGAAAACAACTCGAAG
* * * * * * * * * * *
46124761 ACGGGCGGACTTTAGCCGATTACAATATCCAGAAGGAATCGACTCTTCATCTGGTTCTACGTCTT
131 ACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTCCGTCTT
* * * *
46124826 CGAGGTGGGATGCAGATCTTCGTCAAGACTTTG
196 CGTGGTGGGATGCAAATCTTCGTGAAGACCTTG
* * * * * * * * * * * *
46124859 ACCGGTAAGACGATTACTTTGGAAGTGGAGAGCTCGGATACGATTGATAACGTGAAAGCGAAGAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
* * * * * * * * * * * * *
46124924 TCAGGACAAAGAAGGAATTCCACCAGATCAGCAAAGGT-TGATTTTTGCTGGGAAACAACTGGAA
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGC-AACGTCTCATCTTCGCTGGAAAACAACTCGAA
* ** * * * * * * * *
46124988 GATGGAAGGACTTTGGCTGATTACAATATTCAAAAGGAGTCCACTCTTCACCTTGTTCTCCGTCT
130 GACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTCCGTCT
46125053 TCGTGGTGGG
195 TCGTGGTGGG
46125063 TTCTAAGCCT
Statistics
Matches: 570, Mismatches: 86, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
227 2 0.00
228 559 0.98
229 9 0.02
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (228 bp):
ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCTGGAAAACAACTCGAAG
ACGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTCCGTCTT
CGTGGTGGGATGCAAATCTTCGTGAAGACCTTG
Found at i:46127384 original size:2 final size:2
Alignment explanation
Indices: 46127377--46127429 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
46127367 ACCAATGGAG
46127377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46127419 AT CAT A- AT AT A
1 AT -AT AT AT AT A
46127430 AAAAATCATC
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:46129736 original size:20 final size:20
Alignment explanation
Indices: 46129695--46129736 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
46129685 TTACTTCTTA
* *
46129695 TATTTTTTATTTTCTGACTT
1 TATTTTTTATTTTCTAAATT
46129715 TATTTTTTATTTT-TAATATT
1 TATTTTTTATTTTCTAA-ATT
46129735 TA
1 TA
46129737 AATTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTTTTTATTTTCTAAATT
Found at i:46130045 original size:25 final size:25
Alignment explanation
Indices: 46130012--46130063 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
46130002 ATGATGGCTA
* *
46130012 AATTAGTCATATATGTCATTTTTTT
1 AATTAGTCAAATAAGTCATTTTTTT
* *
46130037 AATTGGTCAAATAAGTTATTTTTTT
1 AATTAGTCAAATAAGTCATTTTTTT
46130062 AA
1 AA
46130064 AGATTTAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.52
Consensus pattern (25 bp):
AATTAGTCAAATAAGTCATTTTTTT
Found at i:46131562 original size:31 final size:30
Alignment explanation
Indices: 46131516--46131574 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
46131506 TAATTGTACA
46131516 TAAAATATTTTAAAAATTTAAATATAATAT
1 TAAAATATTTTAAAAATTTAAATATAATAT
* * *
46131546 TAAATTATATTTAAAAATTTTACTATAAT
1 TAAAATAT-TTTAAAAATTTAAATATAAT
46131575 GATACATAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAAATATTTTAAAAATTTAAATATAATAT
Found at i:46143461 original size:12 final size:12
Alignment explanation
Indices: 46143444--46143490 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
46143434 TAGGAGAGTA
46143444 TGGTGGTCCTGG
1 TGGTGGTCCTGG
46143456 TGGTGGTCCT-G
1 TGGTGGTCCTGG
46143467 T--TGGTCCTGG
1 TGGTGGTCCTGG
* *
46143477 TGGTCGTCTTGG
1 TGGTGGTCCTGG
46143489 TG
1 TG
46143491 AGGTTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 7 0.23
10 2 0.07
11 2 0.07
12 19 0.63
ACGTcount: A:0.00, C:0.17, G:0.45, T:0.38
Consensus pattern (12 bp):
TGGTGGTCCTGG
Found at i:46154925 original size:44 final size:44
Alignment explanation
Indices: 46154877--46154967 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
46154867 TATCAATACA
* * * *
46154877 ATCAAAATCTAATTAATAAATTTATTTTA-TTTATTTATTATTTT
1 ATCAAAATATAATTAATAAAATTA-TTTAGGTTATTTATTACTTT
46154921 ATCAAAATATAATTAATAAAATTATTTAGGTTATTTATTACTTT
1 ATCAAAATATAATTAATAAAATTATTTAGGTTATTTATTACTTT
46154965 ATC
1 ATC
46154968 GATAATTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 4 0.10
44 38 0.90
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (44 bp):
ATCAAAATATAATTAATAAAATTATTTAGGTTATTTATTACTTT
Found at i:46159620 original size:16 final size:17
Alignment explanation
Indices: 46159580--46159624 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
46159570 TTAAAATTAA
*
46159580 AATTTATTTTTTAATTT
1 AATTTATTATTTAATTT
*
46159597 AATGTATTATTT-ATTT
1 AATTTATTATTTAATTT
*
46159613 ATTTTATTATTT
1 AATTTATTATTT
46159625 CCACGTGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
AATTTATTATTTAATTT
Found at i:46161319 original size:4 final size:4
Alignment explanation
Indices: 46161310--46161346 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
46161300 TTATGACCTA
* *
46161310 TCTG TCTG TCTG TCTG TCTG TCGG TCTG TATG TCTG T
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG T
46161347 ATGTAATTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.03, C:0.22, G:0.27, T:0.49
Consensus pattern (4 bp):
TCTG
Found at i:46163672 original size:14 final size:14
Alignment explanation
Indices: 46163653--46163680 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46163643 AAAATATGGA
46163653 ACTAACCTTACTTT
1 ACTAACCTTACTTT
46163667 ACTAACCTTACTTT
1 ACTAACCTTACTTT
46163681 GAGTACTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
ACTAACCTTACTTT
Found at i:46164106 original size:12 final size:12
Alignment explanation
Indices: 46164089--46164137 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
46164079 AAATATGAAT
46164089 AATTTTAAATAA
1 AATTTTAAATAA
*
46164101 AATTTTAAATTTA
1 AATTTTAAA-TAA
* *
46164114 TATTTTAAATTA
1 AATTTTAAATAA
46164126 AA-TTTAAATAA
1 AATTTTAAATAA
46164137 A
1 A
46164138 TATAAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 9 0.28
12 13 0.41
13 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATTTTAAATAA
Found at i:46164140 original size:24 final size:25
Alignment explanation
Indices: 46164090--46164140 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
46164080 AATATGAATA
**
46164090 ATTTTAAATAAAATTTTAAATTTAT
1 ATTTTAAATAAAATTTTAAATAAAT
*
46164115 ATTTTAAATTAAA-TTTAAATAAAT
1 ATTTTAAATAAAATTTTAAATAAAT
46164139 AT
1 AT
46164141 AAAATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTTAAATAAAATTTTAAATAAAT
Found at i:46165807 original size:18 final size:18
Alignment explanation
Indices: 46165772--46165813 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
46165762 AGTTATAAGG
*
46165772 AGGAAAATATGGGTTAGA
1 AGGAAAATATGGGCTAGA
46165790 AGGAAAA-ATGGGGCTAGA
1 AGGAAAATAT-GGGCTAGA
*
46165808 ACGAAA
1 AGGAAA
46165814 TTTTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.48, C:0.05, G:0.33, T:0.14
Consensus pattern (18 bp):
AGGAAAATATGGGCTAGA
Found at i:46166594 original size:158 final size:158
Alignment explanation
Indices: 46166306--46166594 Score: 506
Period size: 158 Copynumber: 1.8 Consensus size: 158
46166296 ATTTTTGGGA
46166306 ATTACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGC
1 ATTACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGC
* *
46166371 GGATACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACATCTCGACCCACAGTTAGTGTGA
66 GGATACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACACCTCGACCCACAGCTAGTGTGA
46166436 GTAGACCCACTTCACAGCTCGTGTGAGC
131 GTAGACCCACTTCACAGCTCGTGTGAGC
*
46166464 ATTACATGTTAGATGGGTGTTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGC
1 ATTACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGC
* * * * *
46166529 GGATTCTCCACAGCTCGTGTGAGTAGCATCGTATAGTTTAACACCTCGACCCACAGCTCGTGTGA
66 GGATACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACACCTCGACCCACAGCTAGTGTGA
46166594 G
131 G
46166595 CAAACCTATT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
158 123 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (158 bp):
ATTACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGC
GGATACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACACCTCGACCCACAGCTAGTGTGA
GTAGACCCACTTCACAGCTCGTGTGAGC
Found at i:46166629 original size:158 final size:158
Alignment explanation
Indices: 46166309--46166629 Score: 484
Period size: 158 Copynumber: 2.0 Consensus size: 158
46166299 TTTGGGAATT
46166309 ACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGCGGA
1 ACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGCGGA
* * *
46166374 TACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACATCTCGACCCACAGTTAGTGTGAGTA
66 TACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACACCTCGACCCACAGCTAGTGTGAGCA
* **
46166439 GACCCACTTCACAGCTCGTGTGAGCATT
131 AACCCACTTCACAGCTCGTGTGAGCACC
*
46166467 ACATGTTAGATGGGTGTTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGCGGA
1 ACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGCGGA
* * * * *
46166532 TTCTCCACAGCTCGTGTGAGTAGCATCGTATAGTTTAACACCTCGACCCACAGCTCGTGTGAGCA
66 TACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACACCTCGACCCACAGCTAGTGTGAGCA
* *
46166597 AACCTA-TTC-CGTAGCTTGTGTGAGCACC
131 AACCCACTTCAC--AGCTCGTGTGAGCACC
46166625 ACATG
1 ACATG
46166630 ATACAGAGAT
Statistics
Matches: 147, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
156 1 0.01
157 3 0.02
158 143 0.97
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (158 bp):
ACATGTTAGATGGGTGCTGGTCTTAGATGTACTATCGATGACTGAGATCTAGCATATGTTGCGGA
TACTCCACAACTCCTGTGAGCAGCATCGTATAGTTTAACACCTCGACCCACAGCTAGTGTGAGCA
AACCCACTTCACAGCTCGTGTGAGCACC
Found at i:46168669 original size:20 final size:20
Alignment explanation
Indices: 46168644--46168683 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46168634 ATATTTATAC
*
46168644 GTTCATGACATGACTTTACT
1 GTTCATGACATGACTCTACT
*
46168664 GTTCATGACTTGACTCTACT
1 GTTCATGACATGACTCTACT
46168684 ATTCTTAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (20 bp):
GTTCATGACATGACTCTACT
Found at i:46173147 original size:16 final size:16
Alignment explanation
Indices: 46173126--46173176 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 16
46173116 GATCATTTCA
46173126 ATTTAAATTGTTTTAG
1 ATTTAAATTGTTTTAG
* *
46173142 ATTTAAGTCGATTTTAG
1 ATTTAAATTG-TTTTAG
*
46173159 ATTTAAATTATTTT-G
1 ATTTAAATTGTTTTAG
46173174 ATT
1 ATT
46173177 CGAGTTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 4 0.14
16 12 0.41
17 13 0.45
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (16 bp):
ATTTAAATTGTTTTAG
Found at i:46189602 original size:2 final size:2
Alignment explanation
Indices: 46189595--46189636 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
46189585 CCTTTCTGTT
46189595 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46189637 AAGTTTTGAG
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:46194909 original size:10 final size:10
Alignment explanation
Indices: 46194894--46194925 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
46194884 TCAATTAAAT
46194894 AAATTATTAA
1 AAATTATTAA
46194904 AAATTA-TAA
1 AAATTATTAA
46194913 AAA-TATTAA
1 AAATTATTAA
46194922 AAAT
1 AAAT
46194926 ATAAAATCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.10
9 12 0.60
10 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATTATTAA
Found at i:46194921 original size:18 final size:17
Alignment explanation
Indices: 46194898--46194931 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
46194888 TTAAATAAAT
46194898 TATTAAAAATTATAAAAA
1 TATTAAAAA-TATAAAAA
46194916 TATTAAAAATATAAAA
1 TATTAAAAATATAAAA
46194932 TCCGGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TATTAAAAATATAAAAA
Found at i:46203298 original size:13 final size:13
Alignment explanation
Indices: 46203280--46203340 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
46203270 CTTAACCCAA
46203280 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
46203293 ACTTTTC-AAA-T
1 ACTTTTCAAAAGT
* *
46203304 CATTTTTC-CAAGT
1 -ACTTTTCAAAAGT
* *
46203317 ACTTTTTAAAAGC
1 ACTTTTCAAAAGT
46203330 ACTTTTCAAAA
1 ACTTTTCAAAA
46203341 ACAATGCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
11 1 0.03
12 16 0.42
13 21 0.55
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:46203309 original size:24 final size:26
Alignment explanation
Indices: 46203280--46203340 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
46203270 CTTAACCCAA
* *
46203280 ACTTTTCAAAAGTAC-TTTTCAAATC
1 ACTTTTCAAAAGTACTTTTTAAAAGC
* *
46203305 ATTTTTC-CAAGTACTTTTTAAAAGC
1 ACTTTTCAAAAGTACTTTTTAAAAGC
46203330 ACTTTTCAAAA
1 ACTTTTCAAAA
46203341 ACAATGCTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 6 0.21
25 20 0.71
26 2 0.07
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (26 bp):
ACTTTTCAAAAGTACTTTTTAAAAGC
Found at i:46205921 original size:22 final size:20
Alignment explanation
Indices: 46205874--46205914 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
46205864 AAATTGTCTT
46205874 ATCATT-TTTTTTAATATTA
1 ATCATTATTTTTTAATATTA
46205893 ATC-TTATTTTTTAATATTA
1 ATCATTATTTTTTAATATTA
46205912 ATC
1 ATC
46205915 TCATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (20 bp):
ATCATTATTTTTTAATATTA
Found at i:46208900 original size:55 final size:52
Alignment explanation
Indices: 46208834--46208973 Score: 185
Period size: 51 Copynumber: 2.7 Consensus size: 52
46208824 AATAAATTTA
* *
46208834 AAATAAATAATAAAAAATTTTAATTTTAAAATATGTTTTAAAATTATTGTGTTAC
1 AAATAAATAATAAAAAA--TTAAATTTAAAATATATTTTAAAATTATT-TGTTAC
*
46208889 AAATAAATAAT-AAAAATTAAATTTAAAATATATTTTAAAATTATTTTTTAC
1 AAATAAATAATAAAAAATTAAATTTAAAATATATTTTAAAATTATTTGTTAC
* * *
46208940 AAATAAATAA-ATAAATTTAAATTTAAAATGTATT
1 AAATAAATAATAAAAAATTAAATTTAAAATATATT
46208974 ACAATCGATA
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 35 0.45
52 27 0.35
54 5 0.06
55 11 0.14
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (52 bp):
AAATAAATAATAAAAAATTAAATTTAAAATATATTTTAAAATTATTTGTTAC
Found at i:46227576 original size:75 final size:75
Alignment explanation
Indices: 46227442--46228339 Score: 844
Period size: 75 Copynumber: 12.0 Consensus size: 75
46227432 TTGCCTAGAT
* * * * *
46227442 GAAGCCTGTTTACTGAATATGTTGAGTT-CAGTAGGTTCACAAGGTATGCCTTG-GTGTTCAGGT
1 GAAGCCTGTTTCCCGAACATGTTGA-TTCCAGTAGGTTCACAAGGCATGGCTTGAG-GTTCAGGT
* *
46227505 TCAAGAAACTTA
64 TCAGGAAATTTA
* * * * * * *
46227517 GCAGCTTGTTTCCCGAACATGTTGAGTCCAGTGGGTTCACAAGGTATGGTTTGAGGTTCAGATTC
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
46227582 AGGAAATTTA
66 AGGAAATTTA
* * * * * * *
46227592 GAAGCTTGTTTCCCGAAAATGTTTATTCCGGTGGGTTCACAAGACATGG-TTCGAAGTTCAGGTT
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTT-GAGGTTCAGGTT
*
46227656 CGGGAAATTTA
65 CAGGAAATTTA
*
46227667 GAAGCCTGCTTCCCGAA-ATTGTTGATTCCAGT-GGATTCACAAGGCATGGCTTGA-G----GG-
1 GAAGCCTGTTTCCCGAACA-TGTTGATTCCAGTAGG-TTCACAAGGCATGGCTTGAGGTTCAGGT
46227724 TCAGGAAATTTA
64 TCAGGAAATTTA
* * * *
46227736 GATGCCTGCTTT-CCGAACATGTTGATTCCTGTCA-TTTCACAAGGCATGGCTTGAGGTTCGGGT
1 GAAGCCTG-TTTCCCGAACATGTTGATTCCAGT-AGGTTCACAAGGCATGGCTTGAGGTTCAGGT
*
46227799 TCAGGAAATTTC
64 TCAGGAAATTTA
* * * * * *
46227811 GTAGCCTGTTTCCCGAAAATGTTGATTCCAGTTGGTTCAC-GGTGCATGGATTGAGTTTCAGGTT
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAG-GCATGGCTTGAGGTTCAGGTT
46227875 CAGGAAATTTA
65 CAGGAAATTTA
* * *
46227886 GAAGCCTGCTTT-CCAAACATGTTGATTCCAGCAGGTTCACAAGGCATGGCTAGAGGTTCAGGTT
1 GAAGCCTG-TTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTT
*
46227950 CGGGAAATTTA
65 CAGGAAATTTA
* * * * * * * * *
46227961 GAAGCCTGTTTTCCAAACACGTCGATTCCAATCGGTTCACAAGGTATGCCTCGAGGTTCAGGTTC
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
*
46228026 AGCAAATTTA
66 AGGAAATTTA
* * * * * *
46228036 GAAGCGTGCTTCCCGAACATGTGGATTCCAGCAGGTTCACATGGCATGCCTTGAGGTTCAGGTTC
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
46228101 AGGAAATTTA
66 AGGAAATTTA
*
46228111 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGTCAGCATCGG-TTGAGTTTCAG
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAG---GCAT-GGCTTGAGGTTCAG
46228175 GTTCAGGAAATTTA
62 GTTCAGGAAATTTA
* ** ** * *
46228189 GAAGGCC-GCTTT-CCAAACATGTTGATTCCACCAGGTTCACAAGGCATCACTTGAGGTTCAAGC
1 GAA-GCCTG-TTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGT
*
46228252 TCGGGAAATTTA
64 TCAGGAAATTTA
* * * * ** * * * * * *
46228264 GAAGCCTGTTTACCAAAAACGTCAATTCCAGTGGGTTCACAAGGTATAGCTCGGGGTTGAGGTTC
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
46228329 -GGTAAATTTA
66 AGG-AAATTTA
46228339 G
1 G
46228340 GTGTTTGGTT
Statistics
Matches: 683, Mismatches: 108, Indels: 64
0.80 0.13 0.07
Matches are distributed among these distances:
69 54 0.08
70 6 0.01
74 24 0.04
75 525 0.77
76 7 0.01
78 60 0.09
79 7 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (75 bp):
GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
AGGAAATTTA
Found at i:46227990 original size:294 final size:295
Alignment explanation
Indices: 46227474--46228307 Score: 961
Period size: 294 Copynumber: 2.8 Consensus size: 295
46227464 TGAGTTCAGT
* * * * *
46227474 AGGTTCACAAGGTATGCCTTG-GTGTTCAGGTTCAAGAAACTTAGCAGCTTGTTTCCCGAACATG
1 AGGTTCACAAGGCATGCCTTGAG-GTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAACATG
* * * * *
46227538 TTGAGTCCAGTGGGTTCACAAGGT--ATGGTTTGAGGTTCAGATTCAGGAAATTTAGAAGCTTG-
65 TTGATTCCAGTAGGTTCAC-AGGTGCATGG-TTGAGTTTCAGGTTCAGGAAATTTAGAAGCCTGC
* * ** * * * *
46227600 TTTCCCGAAA-ATGTTTATTCCGGTGGGTTCACAAGACATGGTTCGAAGTTCAGGTTCGGGAAAT
128 TTT-CC-AAACATGTTGATTCCAGCAGGTTCACAAGGCATGGCTAGAGGTTCAGGTTCGGGAAAT
* * ** * * *
46227664 TTAGAAGCCTGCTTCCCGAAATTGTTGATTCCAGTGGATTCACAAGGCATGGCTTGA-G-GG-TC
191 TTAGAAGCCTGTTTACC-AAAACGTCGATTCCAGTGG-TTCACAAGGCATGCCTCGAGGTGGTTC
* * * * *
46227726 AGGAAATTTAGATGCCTGCTTTCCGAACATGTTGATTCCTGTC
254 AGCAAATTTAGAAGCCTGCTTCCCGAACATGTGGATTCCAG-C
* * * * * *
46227769 A-TTTCACAAGGCATGGCTTGAGGTTCGGGTTCAGGAAATTTCGTAGCCTGTTTCCCGAAAATGT
1 AGGTTCACAAGGCATGCCTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAACATGT
*
46227833 TGATTCCAGTTGGTTCAC-GGTGCATGGATTGAGTTTCAGGTTCAGGAAATTTAGAAGCCTGCTT
66 TGATTCCAGTAGGTTCACAGGTGCATGG-TTGAGTTTCAGGTTCAGGAAATTTAGAAGCCTGCTT
46227897 TCCAAACATGTTGATTCCAGCAGGTTCACAAGGCATGGCTAGAGGTTCAGGTTCGGGAAATTTAG
130 TCCAAACATGTTGATTCCAGCAGGTTCACAAGGCATGGCTAGAGGTTCAGGTTCGGGAAATTTAG
* * *
46227962 AAGCCTGTTTTCCAAACACGTCGATTCCAATCGGTTCACAAGGTATGCCTCGAGGTTCAGGTTCA
195 AAGCCTGTTTACCAAA-ACGTCGATTCCAGT-GGTTCACAAGGCATGCCTCGAGG-T--GGTTCA
*
46228027 GCAAATTTAGAAGCGTGCTTCCCGAACATGTGGATTCCAGC
255 GCAAATTTAGAAGCCTGCTTCCCGAACATGTGGATTCCAGC
*
46228068 AGGTTCACATGGCATGCCTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAACATGT
1 AGGTTCACAAGGCATGCCTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAACATGT
*
46228133 TGATTCCAGTAGGTTCACAAGTCAGCATCGGTTGAGTTTCAGGTTCAGGAAATTTAGAAGGCC-G
66 TGATTCCAGTAGGTTCACAGGT--GCAT-GGTTGAGTTTCAGGTTCAGGAAATTTAGAA-GCCTG
* ** * * *
46228197 CTTTCCAAACATGTTGATTCCACCAGGTTCACAAGGCATCACTTGAGGTTCAAGCTCGGGAAATT
127 CTTTCCAAACATGTTGATTCCAGCAGGTTCACAAGGCATGGCTAGAGGTTCAGGTTCGGGAAATT
*
46228262 TAGAAGCCTGTTTACCAAAAACGTCAATTCCAGTGGGTTCACAAGG
192 TAGAAGCCTGTTTACC-AAAACGTCGATTCCAGT-GGTTCACAAGG
46228308 TATAGCTCGG
Statistics
Matches: 461, Mismatches: 58, Indels: 32
0.84 0.11 0.06
Matches are distributed among these distances:
292 3 0.01
293 6 0.01
294 190 0.41
295 8 0.02
299 4 0.01
300 110 0.24
301 2 0.00
303 130 0.28
304 8 0.02
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (295 bp):
AGGTTCACAAGGCATGCCTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAACATGT
TGATTCCAGTAGGTTCACAGGTGCATGGTTGAGTTTCAGGTTCAGGAAATTTAGAAGCCTGCTTT
CCAAACATGTTGATTCCAGCAGGTTCACAAGGCATGGCTAGAGGTTCAGGTTCGGGAAATTTAGA
AGCCTGTTTACCAAAACGTCGATTCCAGTGGTTCACAAGGCATGCCTCGAGGTGGTTCAGCAAAT
TTAGAAGCCTGCTTCCCGAACATGTGGATTCCAGC
Found at i:46233586 original size:28 final size:28
Alignment explanation
Indices: 46233533--46233588 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
46233523 TTAAATTAAT
* *
46233533 AATGGTAAAATTATATTTTATCTTTTAG
1 AATGATAAAATTATATTTAATCTTTTAG
* *
46233561 AATGATAAAATTTTAATTTAATTTTTTA
1 AATGATAAAATTAT-ATTTAATCTTTTA
46233589 AAAATTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (28 bp):
AATGATAAAATTATATTTAATCTTTTAG
Found at i:46234884 original size:7 final size:7
Alignment explanation
Indices: 46234872--46234900 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
46234862 TATATAATTT
46234872 TATTATA
1 TATTATA
46234879 TATTATA
1 TATTATA
46234886 TATTATA
1 TATTATA
46234893 TATTATA
1 TATTATA
46234900 T
1 T
46234901 TTCGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTATA
Found at i:46236465 original size:22 final size:22
Alignment explanation
Indices: 46236437--46236478 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
46236427 GAGATCAAAC
46236437 AAACTCAAGTA-TCAAATTAAAA
1 AAACTCAAGTACT-AAATTAAAA
*
46236459 AAACTCATGTACTAAATTAA
1 AAACTCAAGTACTAAATTAA
46236479 GATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (22 bp):
AAACTCAAGTACTAAATTAAAA
Found at i:46245814 original size:59 final size:58
Alignment explanation
Indices: 46245716--46245855 Score: 154
Period size: 59 Copynumber: 2.4 Consensus size: 58
46245706 AAAATATGAG
* * * *
46245716 AGACTAACATGGATCAGAAAAAAGTTCAGGTCTCAATGTGAGAACAATTGCCAAATTCAG
1 AGACTAACTTGGA-CA-AAAAAAGTACAAGTCTCAATGTGAGAACAATTGCCAAATTCAA
* * * * **
46245776 GGACTAACTTGGACAAATAAAAGTACAAGTCTTAATGTGGGAACAATTGTCAGGTTCAA
1 AGACTAACTTGGACAAA-AAAAGTACAAGTCTCAATGTGAGAACAATTGCCAAATTCAA
*
46245835 AGACGAACTTGGACAAAAAAA
1 AGACTAACTTGGACAAAAAAA
46245856 AATTAAGGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 6 0.09
59 50 0.75
60 11 0.16
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (58 bp):
AGACTAACTTGGACAAAAAAAGTACAAGTCTCAATGTGAGAACAATTGCCAAATTCAA
Found at i:46250562 original size:9 final size:9
Alignment explanation
Indices: 46250537--46250618 Score: 62
Period size: 10 Copynumber: 9.0 Consensus size: 9
46250527 ATTAATTATT
*
46250537 TTTTTAAAA
1 TTTTAAAAA
46250546 TTTT-AAAA
1 TTTTAAAAA
46250554 TTTTAAAAAA
1 TTTT-AAAAA
46250564 TTATTAAAAA
1 TT-TTAAAAA
*
46250574 TATATAAAAA
1 T-TTTAAAAA
*
46250584 ATTTAAAATA
1 TTTTAAAA-A
* *
46250594 TTTTTAATA
1 TTTTAAAAA
46250603 TTTT-AAAA
1 TTTTAAAAA
46250611 -TTTAAAAA
1 TTTTAAAAA
46250619 CTAATTAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
7 3 0.05
8 15 0.25
9 15 0.25
10 24 0.40
11 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:46251486 original size:21 final size:23
Alignment explanation
Indices: 46251444--46251488 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
46251434 TTTATCACAT
* *
46251444 TAATATTTATATTAAAATTTATA
1 TAATATATATATTAAAACTTATA
46251467 TAATATATA-ATT-AAACTTATA
1 TAATATATATATTAAAACTTATA
46251488 T
1 T
46251489 TTATATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 8 0.40
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATATATATTAAAACTTATA
Found at i:46260641 original size:30 final size:30
Alignment explanation
Indices: 46260601--46260668 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
46260591 TTAAATTAAT
* *
46260601 AATGAT-AAAATTATATTTTAA-TCTCTCAA
1 AATGATAAAAATT-TAGTTTAATTCTCTAAA
*
46260630 AATGATAAAAATTTGGTTTAATTCTCTAAA
1 AATGATAAAAATTTAGTTTAATTCTCTAAA
*
46260660 AATTATAAA
1 AATGATAAA
46260669 GATATATACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (30 bp):
AATGATAAAAATTTAGTTTAATTCTCTAAA
Found at i:46262275 original size:43 final size:44
Alignment explanation
Indices: 46262179--46262402 Score: 215
Period size: 43 Copynumber: 5.1 Consensus size: 44
46262169 GAAAAATGCT
* * * * *
46262179 GCTATAGAACATGGTCTTTA-ATGACGCTT-TTCCATAAACGTC
1 GCTAAAGAACATGGTCTTTAGCTGACGCTTCTCCCACAAACGCC
*
46262221 ACTAAAGAACATGGTCTTTAGCTG-CGCTTCTCCCACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCTGACGCTTCTCCCACAAACGCC
* * *
46262264 GCTAAAGAACATGGTCTTTAGTTAGCGACGCTTCTCCCTCAAACACC
1 GCTAAAGAACATGGTCTTTAGCT---GACGCTTCTCCCACAAACGCC
* * * *
46262311 GCTAAAGAACATGGTTTTTAGC-GGCGCTTTTCTCACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCTGACGCTTCTCCCACAAACGCC
* * * * * *
46262354 ACTAAAGAATATGGTCTTTAGC-GACGCTTTTCTCACAGATGCC
1 GCTAAAGAACATGGTCTTTAGCTGACGCTTCTCCCACAAACGCC
46262397 GCTAAA
1 GCTAAA
46262403 AATAAAAAAT
Statistics
Matches: 152, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
42 23 0.15
43 91 0.60
46 1 0.01
47 37 0.24
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
GCTAAAGAACATGGTCTTTAGCTGACGCTTCTCCCACAAACGCC
Found at i:46262747 original size:21 final size:21
Alignment explanation
Indices: 46262723--46262762 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
46262713 ATTCACTTTT
46262723 CTCGCTGCTGCCTCAGCTTCC
1 CTCGCTGCTGCCTCAGCTTCC
* * *
46262744 CTCGTTGTTGCCTCCGCTT
1 CTCGCTGCTGCCTCAGCTT
46262763 TAAGTTGTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.42, G:0.20, T:0.35
Consensus pattern (21 bp):
CTCGCTGCTGCCTCAGCTTCC
Found at i:46263593 original size:41 final size:40
Alignment explanation
Indices: 46263548--46263807 Score: 292
Period size: 41 Copynumber: 6.3 Consensus size: 40
46263538 TGGAGGCTCT
46263548 GACCTTTAGCGGCGTTTCTTCATAAACGCCGCTAATGCTTC
1 GACCTTTAGCGGCGTTT-TTCATAAACGCCGCTAATGCTTC
*
46263589 GACCTTTAGCGGCGTTTCTTCATAATCGCCGCTAATGCTTC
1 GACCTTTAGCGGCGTTT-TTCATAAACGCCGCTAATGCTTC
* * * *
46263630 GACCTTTAGCGGTGTTTTATCATAAACGCAGCTACTGCTTT
1 GACCTTTAGCGGCGTTTT-TCATAAACGCCGCTAATGCTTC
* * *
46263671 GACCTTTAGCGGCGCTTTTCTATAAACGCCGCTAATACTTT
1 GACCTTTAGCGGCGTTTTTC-ATAAACGCCGCTAATGCTTC
* *
46263712 GACCTTTA-CTGGCGCTTTATCATAAACGCCACTAATGC-TC
1 GACCTTTAGC-GGCG-TTTTTCATAAACGCCGCTAATGCTTC
* * **
46263752 TGACCTTTTGCGGCGATTCCCAATAAACGCCGCTAATGC-TC
1 -GACCTTTAGCGGCGTTTTTC-ATAAACGCCGCTAATGCTTC
46263793 AGACCTTTAGCGGCG
1 -GACCTTTAGCGGCG
46263808 CTTAGCCCTA
Statistics
Matches: 189, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
40 8 0.04
41 176 0.93
42 5 0.03
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (40 bp):
GACCTTTAGCGGCGTTTTTCATAAACGCCGCTAATGCTTC
Found at i:46263922 original size:40 final size:40
Alignment explanation
Indices: 46263817--46263931 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 40
46263807 GCTTAGCCCT
* * ***
46263817 AAACGCCGCTATTGGTTTACCTTTTACGGTATTTTTGGTT
1 AAACGCCGCTATTGGTTTACCTTTTGCGGTGTTTTTGAAA
* * * *
46263857 AAACACCGCTAATGGTTTACTTTTTGTGGTGTTTTTGAAA
1 AAACGCCGCTATTGGTTTACCTTTTGCGGTGTTTTTGAAA
** *
46263897 AAACGCCGCTATTACTTTACCTTTTGCGGCGTTTT
1 AAACGCCGCTATTGGTTTACCTTTTGCGGTGTTTT
46263932 ATTTTCAAAC
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (40 bp):
AAACGCCGCTATTGGTTTACCTTTTGCGGTGTTTTTGAAA
Found at i:46268846 original size:17 final size:17
Alignment explanation
Indices: 46268826--46268867 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
46268816 CTCCCTTGAC
*
46268826 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
46268843 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
46268860 CTTGTAAC
1 CTT-TAAC
46268868 TACTTTTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:46268851 original size:24 final size:24
Alignment explanation
Indices: 46268806--46268853 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
46268796 ATGGATGTTC
* *
46268806 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
* *
46268830 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
46268854 CATATTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.02, T:0.44
Consensus pattern (24 bp):
AACCTTCCATCTCCCTTAACCTTT
Found at i:46270227 original size:97 final size:97
Alignment explanation
Indices: 46270061--46270254 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
46270051 AACCTTGAAA
* * *
46270061 AAGGGTATTCAATTATCCCGGTTTGAAGAAAAGTCACGCCTAGCAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCAATTATCCCGATTTGAAGAAAAATCACACCTAGCAAGTTAAGGCACAAATTTTCA
*
46270126 AAACCCGAGATAAAGGAATATTGCCTCGATTT
66 AAACCCGAAATAAAGGAATATTGCCTCGATTT
* * * *
46270158 AAGGGTATTCGATTATCCCGATTTGAGGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCAATTATCCCGATTTGAAGAAAAATCACACCTAGCAAGTTAAGGCACAAATTTTCA
46270223 AAACCCGAAATAAAGGAATATTGCCTCGATTT
66 AAACCCGAAATAAAGGAATATTGCCTCGATTT
46270255 TAAAAATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (97 bp):
AAGGGTATTCAATTATCCCGATTTGAAGAAAAATCACACCTAGCAAGTTAAGGCACAAATTTTCA
AAACCCGAAATAAAGGAATATTGCCTCGATTT
Found at i:46270633 original size:29 final size:29
Alignment explanation
Indices: 46270530--46270760 Score: 191
Period size: 30 Copynumber: 7.9 Consensus size: 29
46270520 AGTTTAAGAG
* *
46270530 AGTTT-GGGGTTAAAATGTAA-TTTTAAA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAA
* * *
46270557 AGGTTTTAGGAGTAAAAATGTTATTTTCGGAA
1 A-G-TTTAGGGGTAAAAATGTAATTTT-TGAA
* * * * *
46270589 A-ATTCGAGGTAAAAAACGTGATTTTTGAA
1 AGTTTAGGGGT-AAAAATGTAATTTTTGAA
* *
46270618 AGTTTGGGGGTAAAAATGTAATTTTTGGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAA
* *
46270647 AGTTTAAGGGCAAAAATGTAATTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGA-A
*
46270677 AGTTTAGGGGTAAAAATGTGATTTTTGGAA
1 AGTTTAGGGGTAAAAATGTAATTTTT-GAA
* * * *
46270707 A-TTTAAGGGCATAAATGTAGTTTTTGAAA
1 AGTTTAGGGGTAAAAATGTAATTTTTG-AA
*
46270736 AGTTTAGGGGTAAACATGTAATTTT
1 AGTTTAGGGGTAAAAATGTAATTTT
46270761 AAACAAAATA
Statistics
Matches: 158, Mismatches: 35, Indels: 19
0.75 0.17 0.09
Matches are distributed among these distances:
27 1 0.01
28 2 0.01
29 73 0.46
30 74 0.47
31 5 0.03
32 3 0.02
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AGTTTAGGGGTAAAAATGTAATTTTTGAA
Found at i:46270635 original size:59 final size:60
Alignment explanation
Indices: 46270561--46270760 Score: 208
Period size: 59 Copynumber: 3.4 Consensus size: 60
46270551 TTTAAAAGGT
* * * * * *
46270561 TTTAGGAGTAAAAATGTTATTTTCGGAAAATTCGAGGTAAAAAACGTGATTTTTGA-AAG
1 TTTAGGGGTAAAAATGTAATTTTTGGAAAATTCAAGGGAAAAAACGTAATTTTTGAGAAG
* * * * *
46270620 TTTGGGGGTAAAAATGTAATTTTTGG-AAGTTTAAGGGCAAAAATGTAATTTTTGAGAAG
1 TTTAGGGGTAAAAATGTAATTTTTGGAAAATTCAAGGGAAAAAACGTAATTTTTGAGAAG
* * * * * * *
46270679 TTTAGGGGTAAAAATGTGATTTTTGG-AAATTTAAGGGCATAAATGTAGTTTTTGAAAAG
1 TTTAGGGGTAAAAATGTAATTTTTGGAAAATTCAAGGGAAAAAACGTAATTTTTGAGAAG
*
46270738 TTTAGGGGTAAACATGTAATTTT
1 TTTAGGGGTAAAAATGTAATTTT
46270761 AAACAAAATA
Statistics
Matches: 121, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
58 22 0.18
59 99 0.82
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (60 bp):
TTTAGGGGTAAAAATGTAATTTTTGGAAAATTCAAGGGAAAAAACGTAATTTTTGAGAAG
Found at i:46271880 original size:13 final size:12
Alignment explanation
Indices: 46271856--46271889 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
46271846 TCTTCCTTTT
46271856 TTATTATTAATA
1 TTATTATTAATA
46271868 TTATTATTTAATA
1 TTATTA-TTAATA
*
46271881 TTATAATTA
1 TTATTATTA
46271890 TGTATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:46271907 original size:19 final size:19
Alignment explanation
Indices: 46271855--46271907 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
46271845 ATCTTCCTTT
*
46271855 TTTATTATTAATATTATTA
1 TTTATTATTAAAATTATTA
* *
46271874 TTTAATATTATAATTATGTA
1 TTTATTATTAAAATTAT-TA
46271894 TTTATTA-TAAAATT
1 TTTATTATTAAAATT
46271908 TTCTCGCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATTATTAAAATTATTA
Found at i:46272596 original size:18 final size:17
Alignment explanation
Indices: 46272555--46272598 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
46272545 GGGATATTAT
*
46272555 TAAA-TTAAATTTAGAA
1 TAAATTTAAATTTAAAA
*
46272571 TAATTTTAAATTTAAAGA
1 TAAATTTAAATTTAAA-A
46272589 TAAATTTAAA
1 TAAATTTAAA
46272599 AAAATGAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 3 0.13
17 10 0.43
18 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:46287775 original size:31 final size:31
Alignment explanation
Indices: 46287711--46287779 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
46287701 TTATAAAATG
* *
46287711 GTCATTTAACTATTTAAAAATTTTCATTTAA
1 GTCATTGAACTATTTAAAAATTTTCATTCAA
* * **
46287742 GTCATTGAAGTATTTGAAAATTTTTGTTCAA
1 GTCATTGAACTATTTAAAAATTTTCATTCAA
46287773 GTCATTG
1 GTCATTG
46287780 GATTGTTAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (31 bp):
GTCATTGAACTATTTAAAAATTTTCATTCAA
Found at i:46298068 original size:52 final size:52
Alignment explanation
Indices: 46297972--46298078 Score: 128
Period size: 52 Copynumber: 2.0 Consensus size: 52
46297962 ACGCAAATAA
**
46297972 TTATTCAATTATAAAAAATTATAAAATTGTTAATTAATTATTAA-TATATTTT
1 TTATTCAATTATAAAAAATTATAAAATTCCT-ATTAATTATTAATTATATTTT
* * *
46298024 TTATTTAATTATGAAAAATTATAAAATATCCT-TTAATTATTTAATTTTATTTT
1 TTATTCAATTATAAAAAATTATAAAAT-TCCTATTAATTA-TTAATTATATTTT
46298077 TT
1 TT
46298079 TTAATCATCC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 7 0.15
52 29 0.62
53 11 0.23
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (52 bp):
TTATTCAATTATAAAAAATTATAAAATTCCTATTAATTATTAATTATATTTT
Found at i:46298599 original size:45 final size:48
Alignment explanation
Indices: 46298548--46298650 Score: 113
Period size: 51 Copynumber: 2.1 Consensus size: 48
46298538 GATCCTCCTC
* *
46298548 CAATGCC-AACAA-CAGAACCAA-AACAAGTTCAAACTCAGGAAGTAT
1 CAATGCCAAACAAGCAGAACCAACAACAAGTTCAAACCCAGAAAGTAT
** *
46298593 CAATGCCTCAAACAAGGCAGCCCCAACAAGAAGTTCAAACCCAGAAAGTAT
1 CAATG-C-CAAACAA-GCAGAACCAACAACAAGTTCAAACCCAGAAAGTAT
46298644 CAATGCC
1 CAATGCC
46298651 TGAAGCTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
45 5 0.11
46 1 0.02
47 1 0.02
48 5 0.11
49 1 0.02
50 8 0.17
51 26 0.55
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.13
Consensus pattern (48 bp):
CAATGCCAAACAAGCAGAACCAACAACAAGTTCAAACCCAGAAAGTAT
Found at i:46324593 original size:20 final size:21
Alignment explanation
Indices: 46324554--46324593 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
46324544 ATATAGGTGG
46324554 AAATTAAATTATAAAATTTTTA
1 AAATTAAA-TATAAAATTTTTA
*
46324576 AAATTAAA-ATATAATTTT
1 AAATTAAATATAAAATTTT
46324594 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATTAAATATAAAATTTTTA
Found at i:46324644 original size:31 final size:28
Alignment explanation
Indices: 46324569--46324652 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 28
46324559 AAATTATAAA
**
46324569 ATTTTTAAAATTA-AAATATAATTTTAT
1 ATTTTTAAAAAGATAAATATAATTTTAT
* *
46324596 ATTTTTAAAACGATAAATATAATATTTTT
1 ATTTTTAAAAAGATAAATATAAT-TTTAT
*
46324625 TTATTTTAAAAAGATTAAATAGTAATTT
1 AT-TTTTAAAAAGA-TAAATA-TAATTT
46324653 GATCATAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
27 11 0.23
28 9 0.19
29 5 0.11
30 10 0.21
31 8 0.17
32 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (28 bp):
ATTTTTAAAAAGATAAATATAATTTTAT
Found at i:46328905 original size:19 final size:19
Alignment explanation
Indices: 46328860--46328905 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
46328850 AATTATAAAT
46328860 AATTT-TAAATATAATATA
1 AATTTATAAATATAATATA
* *
46328878 AAATAATAAATATAAT-TA
1 AATTTATAAATATAATATA
46328896 GAATTTATAA
1 -AATTTATAA
46328906 TAAAATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AATTTATAAATATAATATA
Found at i:46336940 original size:4 final size:4
Alignment explanation
Indices: 46336926--46336963 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
46336916 ATTGTTTTGT
*
46336926 ATCC TTCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATCC AT
46336964 AAATACATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (4 bp):
ATCC
Found at i:46340803 original size:30 final size:30
Alignment explanation
Indices: 46340738--46340811 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
46340728 AAAATTTAAA
**
46340738 TTAAAAATGATAAAATTGTACTTTTTTCCT
1 TTAAAAATGATAAAATTGTACTTTAATCCT
* * *
46340768 CTAAAAATGATAAAATTTTGA-TTTAATCTT
1 TTAAAAATGATAAAATTGT-ACTTTAATCCT
*
46340798 TTAAAAATTATAAA
1 TTAAAAATGATAAA
46340812 TATAAAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (30 bp):
TTAAAAATGATAAAATTGTACTTTAATCCT
Found at i:46343323 original size:12 final size:12
Alignment explanation
Indices: 46343306--46343330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46343296 GGACTTAATA
46343306 TTTTTTTAAATT
1 TTTTTTTAAATT
46343318 TTTTTTTAAATT
1 TTTTTTTAAATT
46343330 T
1 T
46343331 CGAACGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTAAATT
Found at i:46346779 original size:23 final size:24
Alignment explanation
Indices: 46346753--46346837 Score: 97
Period size: 23 Copynumber: 3.7 Consensus size: 24
46346743 TAATGTTCAT
**
46346753 GAACATGTTCATTTAAC-TTAATC
1 GAACATGTTCATCGAACATTAATC
46346776 GAACATGTTCA-CGAACATTAATC
1 GAACATGTTCATCGAACATTAATC
*
46346799 GAACATGTTCAT-GAACATATAATT
1 GAACATGTTCATCGAACAT-TAATC
*
46346823 GAACACGTTCA-CGAA
1 GAACATGTTCATCGAA
46346838 TGATGTTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.06
23 34 0.63
24 17 0.31
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (24 bp):
GAACATGTTCATCGAACATTAATC
Found at i:46349144 original size:17 final size:16
Alignment explanation
Indices: 46349122--46349157 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
46349112 ATCCATTTTC
*
46349122 ATTCAAGTTTGAAATCG
1 ATTCAAGTATGAAAT-G
46349139 ATTCAAGTATGAAATG
1 ATTCAAGTATGAAATG
46349155 ATT
1 ATT
46349158 GAGCTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (16 bp):
ATTCAAGTATGAAATG
Found at i:46351515 original size:5 final size:5
Alignment explanation
Indices: 46351484--46351514 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
46351474 AGCCCGTAAC
*
46351484 ACACA ACACA ACACA ACACA ACACA AAACA A
1 ACACA ACACA ACACA ACACA ACACA ACACA A
46351515 ATTTTTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (5 bp):
ACACA
Found at i:46363197 original size:37 final size:32
Alignment explanation
Indices: 46363121--46363188 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
46363111 GAATTTTTAA
46363121 AATCAAATTATATCATACACAATAAGTTAAAC
1 AATCAAATTATATCATACACAATAAGTTAAAC
*
46363153 AATCAAATTATATCATATACAATAAGTTAAAC
1 AATCAAATTATATCATACACAATAAGTTAAAC
46363185 AATC
1 AATC
46363189 CAATCAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (32 bp):
AATCAAATTATATCATACACAATAAGTTAAAC
Found at i:46369219 original size:21 final size:20
Alignment explanation
Indices: 46369188--46369226 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
46369178 AACTACAAAG
46369188 AAGCATGCATCGGTAACAAGCA
1 AAGCATGCATC--TAACAAGCA
46369210 AAGCAT-CATCTAACAAG
1 AAGCATGCATCTAACAAG
46369227 ATCAAAACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
AAGCATGCATCTAACAAGCA
Found at i:46372649 original size:2 final size:2
Alignment explanation
Indices: 46372644--46372672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46372634 TATATATATA
46372644 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
46372673 AAAATAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:46374414 original size:16 final size:18
Alignment explanation
Indices: 46374382--46374421 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
46374372 TGGTGAGATG
46374382 CTGTTTTGGACTTGTGTA
1 CTGTTTTGGACTTGTGTA
*
46374400 -TGTTTT-GATTTGTGTA
1 CTGTTTTGGACTTGTGTA
46374416 CTGTTT
1 CTGTTT
46374422 GCTGTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.10, C:0.07, G:0.25, T:0.57
Consensus pattern (18 bp):
CTGTTTTGGACTTGTGTA
Found at i:46378484 original size:58 final size:57
Alignment explanation
Indices: 46378379--46378531 Score: 179
Period size: 54 Copynumber: 2.6 Consensus size: 57
46378369 TATTATTTTT
*
46378379 TTAATATTATATATTATAATTT-TTACTAATTCATATTTTAATAATAATTATATTAAAAACATTA
1 TTAA-ATTATATATTAT--TTTATTA--AATT-ATA-TTTAATAATAATTATATT-AAAACATAA
* *
46378443 TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATAA
1 TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAACATAA
46378500 TTAAATTA-AT-TT-TTTTATTAAATTATATTTAA
1 TTAAATTATATATTATTTTATTAAATTATATTTAA
46378532 CGATAATCTT
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
54 20 0.24
55 2 0.02
56 2 0.02
57 15 0.18
58 17 0.20
59 3 0.04
60 4 0.05
61 3 0.04
62 3 0.04
63 12 0.14
64 4 0.05
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (57 bp):
TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAACATAA
Found at i:46379054 original size:14 final size:14
Alignment explanation
Indices: 46379017--46379058 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
46379007 CTATATTTTA
46379017 AATATTTAAATA-T
1 AATATTTAAATATT
46379030 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
46379044 TATATTTAAATATT
1 AATATTTAAATATT
46379058 A
1 A
46379059 GCACAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:46384021 original size:25 final size:26
Alignment explanation
Indices: 46383981--46384029 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
46383971 TCAAAGAGTA
*
46383981 ATTTATTTTTTTCTGTTAAAAATTTC
1 ATTTATTTTTTACTGTTAAAAATTTC
46384007 ATTTA-TTTTTACTGTTAAAAATT
1 ATTTATTTTTTACTGTTAAAAATT
46384030 AGTATAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (26 bp):
ATTTATTTTTTACTGTTAAAAATTTC
Found at i:46388047 original size:18 final size:19
Alignment explanation
Indices: 46388010--46388049 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
46388000 AACCTTGAAT
*
46388010 CCTAAACTCTAAACTTAAC
1 CCTAAACTCCAAACTTAAC
*
46388029 CCTAAAC-CCAAATTTAAC
1 CCTAAACTCCAAACTTAAC
46388047 CCT
1 CCT
46388050 TAAATTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (19 bp):
CCTAAACTCCAAACTTAAC
Found at i:46388204 original size:33 final size:33
Alignment explanation
Indices: 46388144--46388212 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
46388134 ATTCATGATG
46388144 AAAAATTATCAAAATGATACATTAATAACATAAA
1 AAAAATTATCAAAATGATACATTAATAA-ATAAA
** *
46388178 AAAAATTATTGAAAT-AT-CATTAAATAATTAAA
1 AAAAATTATCAAAATGATACATT-AATAAATAAA
46388210 AAA
1 AAA
46388213 CCATAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 11 0.35
33 7 0.23
34 13 0.42
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (33 bp):
AAAAATTATCAAAATGATACATTAATAAATAAA
Found at i:46388755 original size:18 final size:17
Alignment explanation
Indices: 46388707--46388756 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
46388697 TGGATATTTC
46388707 ATTTTTCTTTCTTTCGTT
1 ATTTTTCTTT-TTTCGTT
* *
46388725 ATTTTTTTCTTTTTCTTT
1 ATTTTTCT-TTTTTCGTT
46388743 ATGTTTTCTTTTTT
1 AT-TTTTCTTTTTT
46388757 TGAATCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (17 bp):
ATTTTTCTTTTTTCGTT
Found at i:46396175 original size:16 final size:16
Alignment explanation
Indices: 46396156--46396196 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
46396146 TAATCTTTTA
46396156 AAAATTATAAAAGT-AT
1 AAAATTATAAAA-TAAT
46396172 AAAA-TATTAAAATAAT
1 AAAATTA-TAAAATAAT
46396188 AAAATTATA
1 AAAATTATA
46396197 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 17 0.77
17 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
AAAATTATAAAATAAT
Found at i:46410773 original size:21 final size:21
Alignment explanation
Indices: 46410732--46410773 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46410722 CTTTTCAAAT
**
46410732 GTGAGGATGATGAGACTGAAG
1 GTGAGGATGATGAGAAAGAAG
*
46410753 GTGATGATGATGAGAAAGAAG
1 GTGAGGATGATGAGAAAGAAG
46410774 AGCACAATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.40, T:0.19
Consensus pattern (21 bp):
GTGAGGATGATGAGAAAGAAG
Found at i:46411023 original size:96 final size:96
Alignment explanation
Indices: 46410802--46411047 Score: 294
Period size: 96 Copynumber: 2.6 Consensus size: 96
46410792 TACAATCATT
* * *
46410802 GTTTTTCTTCTTAGTCTCCTGTGGGCTTCTTTCAGTCATTGCACTGTCCAAATTTCTGCCTTTGC
1 GTTTTTCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATAGCACTGTCCAAATTTCTACCTTTGC
* *
46410867 CCCGCCCTTTAATGTTTATAGAAAGATCACA
66 CCCGCCCTTTAATGTTCATAAAAAGATCACA
* * ** * ** * * * *
46410898 GTTTTTCTCCCTAGTCTCCCAAGGACTTCTTTTGGTTAAAGCACTGTCCAGATTTCTACGTTTGC
1 GTTTTTCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATAGCACTGTCCAAATTTCTACCTTTGC
* * ** *
46410963 TCTGTGCTTTAATGTTCATAAAAAGATCGCA
66 CCCGCCCTTTAATGTTCATAAAAAGATCACA
*
46410994 GTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATAGCACTGTCCAAATT
1 GTTTTTCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATAGCACTGTCCAAATT
46411048 CGCTTTAATG
Statistics
Matches: 118, Mismatches: 32, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
96 118 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (96 bp):
GTTTTTCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATAGCACTGTCCAAATTTCTACCTTTGC
CCCGCCCTTTAATGTTCATAAAAAGATCACA
Found at i:46411295 original size:135 final size:131
Alignment explanation
Indices: 46411047--46411539 Score: 505
Period size: 135 Copynumber: 3.8 Consensus size: 131
46411037 CTGTCCAAAT
* * * * * * *
46411047 TCGCTTTAATGTTCATAAAAAGATTGCAATTTTCCTTTTTAGACTCCGGAGGGCATCTTTC-GAT
1 TCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAG-T
*
46411111 CATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATCGCACTGTCCAAATTTTTGAGTT
65 CATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCAT-GAACTGTCCAAA-TTTTGAG-T
46411176 TTGTC
127 TTGTC
* * * *
46411181 TCAGCTTTAACGTTCATAAAAATATCAC-GTTTTTCCTTCTTAGTCTCTTGAGGGCTTCTTTCGG
1 TC-GCTTTAACGTTCATAAAAAGATCGCAG-TTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAG
*
46411245 TCATTGCATTCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCACTGAACTGTCCAAATTTCTGCA-
64 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCA-TGAACTGTCCAAATTT-TG-AG
46411309 TTTGT-
126 TTTGTC
* * *
46411314 TCCGTGCTTTATCGTTCAAAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCA
1 T-C--GCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCA
* * * *
46411379 GTCATTGCATTCC-TCTCACTCTCCTGAGGGCTTCTTTCGGTCATCACACTGTCC--A-----AG
63 GTCATTGCA-TCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATGA-ACTGTCCAAATTTTGAG
46411436 -TT-TC
126 TTTGTC
* * *
46411440 T-GCTTTTGACGTTCATGAAAAGACCGCAGTTTTCCTTCTTAGTCT-CTCGAGGGCTTCTTTCAG
1 TCGC-TTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCT-GAGGGCTTCTTTCAG
* *
46411503 TCATTGCATCCTTCTTATTCTCCTGAGGGATTCTTTC
64 TCATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTC
46411540 GGTAATCGCA
Statistics
Matches: 309, Mismatches: 34, Indels: 43
0.80 0.09 0.11
Matches are distributed among these distances:
122 7 0.02
123 80 0.26
125 1 0.00
126 4 0.01
133 2 0.01
134 13 0.04
135 196 0.63
136 6 0.02
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (131 bp):
TCGCTTTAACGTTCATAAAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTC
ATTGCATCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCATGAACTGTCCAAATTTTGAGTTTGT
C
Found at i:46411556 original size:123 final size:123
Alignment explanation
Indices: 46411334--46411563 Score: 347
Period size: 123 Copynumber: 1.9 Consensus size: 123
46411324 ATCGTTCAAA
*
46411334 AAAAGATCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATTCCTCTCACT
1 AAAAGACCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATTCCTCTCACT
* * * *
46411399 CTCCTGAGGGCTTCTTTCGGTCATCACACTGTCCAAGTTTCTGCTTTTGACGTTCATG
66 CTCCTGAGGGATTCTTTCGGTAATCACACCGTCCAAATTTCTGCTTTTGACGTTCATG
* *
46411457 AAAAGACCGCAGTTTTCCTTCTTAGTCT-CTCGAGGGCTTCTTTCAGTCATTGCA-TCCTTCTTA
1 AAAAGACCGCAGTTTTCCTTCTTAGTCTCCT-GAGGGCTACTTTCAGTCATTGCATTCC-TCTCA
* *
46411520 TTCTCCTGAGGGATTCTTTCGGTAATCGCACCGTCCAAATTTCT
64 CTCTCCTGAGGGATTCTTTCGGTAATCACACCGTCCAAATTTCT
46411564 ACGTTTGCTC
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
122 5 0.05
123 91 0.95
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.37
Consensus pattern (123 bp):
AAAAGACCGCAGTTTTCCTTCTTAGTCTCCTGAGGGCTACTTTCAGTCATTGCATTCCTCTCACT
CTCCTGAGGGATTCTTTCGGTAATCACACCGTCCAAATTTCTGCTTTTGACGTTCATG
Found at i:46412780 original size:3 final size:3
Alignment explanation
Indices: 46412772--46412802 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
46412762 TCAATAAATA
46412772 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46412803 CAATTAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:46413112 original size:54 final size:53
Alignment explanation
Indices: 46412992--46413108 Score: 155
Period size: 53 Copynumber: 2.2 Consensus size: 53
46412982 ACTAACAATT
* * * * * *
46412992 ACTCAATTATTAGTATTTTTTATTATTTAATTATAAAAAGTTATAAAATATTC
1 ACTCAATTATTAATATTTTTTATCATTTAATTATAAAAAGATAAAAAATAATA
46413045 ACTCAATTATTAATATTTTTTTATCATTTAATTAT-AAAAGATAAAAAATAATA
1 ACTCAATTATTAATA-TTTTTTATCATTTAATTATAAAAAGATAAAAAATAATA
*
46413098 ATTCAATTATT
1 ACTCAATTATT
46413109 TAATTTTATC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 38 0.68
54 18 0.32
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (53 bp):
ACTCAATTATTAATATTTTTTATCATTTAATTATAAAAAGATAAAAAATAATA
Found at i:46413892 original size:43 final size:43
Alignment explanation
Indices: 46413819--46414107 Score: 406
Period size: 43 Copynumber: 6.8 Consensus size: 43
46413809 AGAACATGGC
*
46413819 CTTTAGTGGCGC-TTC-CCACAAGCGCCGCTAAAGGCCATGTT
1 CTTTAGCGGCGCTTTCTCCACAAGCGCCGCTAAAGGCCATGTT
* * *
46413860 CTTTAACGGCGCTTT-TCCCACAAACGCCGCTAAAAGCCATGTT
1 CTTTAGCGGCGCTTTCT-CCACAAGCGCCGCTAAAGGCCATGTT
46413903 CTTTAGCGGCGCTTTCTCCACAAGCGCCGCTAAAGGCCATGTT
1 CTTTAGCGGCGCTTTCTCCACAAGCGCCGCTAAAGGCCATGTT
*
46413946 CTTTAGCGGCGCTTTATCCACAAGCGCCGCTAAAGG-CATGTT
1 CTTTAGCGGCGCTTTCTCCACAAGCGCCGCTAAAGGCCATGTT
* * * * *
46413988 TTTTAGCGGCACTTTCTCCACAAGTGCCTCTAAAGCCCATGTT
1 CTTTAGCGGCGCTTTCTCCACAAGCGCCGCTAAAGGCCATGTT
* * *
46414031 CTTTAGCGACGCTTTTCTCCACAAGCGCCGCTAAAGCCCTTGTT
1 CTTTAGCGGCGC-TTTCTCCACAAGCGCCGCTAAAGGCCATGTT
*
46414075 CTTTAGCGGCGCTTTCTCCAAAAGCGCCGCTAA
1 CTTTAGCGGCGCTTTCTCCACAAGCGCCGCTAA
46414108 TATAACAGAT
Statistics
Matches: 220, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
41 10 0.05
42 38 0.17
43 132 0.60
44 40 0.18
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTCTCCACAAGCGCCGCTAAAGGCCATGTT
Found at i:46414425 original size:21 final size:21
Alignment explanation
Indices: 46414400--46414442 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
46414390 CTACTTCCTT
46414400 CGCTTGCCTCGCTGCTGCCTC
1 CGCTTGCCTCGCTGCTGCCTC
* *
46414421 CGCTTGCCTCGTTGTTGCCTC
1 CGCTTGCCTCGCTGCTGCCTC
46414442 C
1 C
46414443 ACTTTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.44, G:0.23, T:0.33
Consensus pattern (21 bp):
CGCTTGCCTCGCTGCTGCCTC
Found at i:46414514 original size:66 final size:66
Alignment explanation
Indices: 46414437--46414585 Score: 253
Period size: 66 Copynumber: 2.3 Consensus size: 66
46414427 CCTCGTTGTT
* *
46414437 GCCTCCACTTTAAGTTGTAGATGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
46414502 A
66 A
* * *
46414503 GCCTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTGAGCCTCTGCTTCTCTCGCTGC
1 GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
46414568 A
66 A
46414569 GCCTCCTCTTTAAGTTG
1 GCCTCCTCTTTAAGTTG
46414586 AGCAATTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (66 bp):
GCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTCTCTCACTGC
A
Found at i:46421270 original size:15 final size:17
Alignment explanation
Indices: 46421238--46421270 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
46421228 TTATTTGTTT
46421238 TTTTCTTTTAAATCTAA
1 TTTTCTTTTAAATCTAA
46421255 TTTT-TTTTAAAT-TAA
1 TTTTCTTTTAAATCTAA
46421270 T
1 T
46421271 CAAACTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCTTTTAAATCTAA
Found at i:46422511 original size:41 final size:40
Alignment explanation
Indices: 46422354--46422692 Score: 423
Period size: 41 Copynumber: 8.3 Consensus size: 40
46422344 GTTAAATAAA
* * * *
46422354 TTAGCGGCGCTTATGTGA-AAGCGCCGCTAAT-TCACACCT
1 TTAGCGGCGCTTTTCT-ATAAGCGCCGCTAATGACAGACCT
* * * **
46422393 TTAGTGGCGCTTTTCTAATAAGCGCCGCTAAAGGTCAGGTCT
1 TTAGCGGCGCTTTTCT-ATAAGCGCCGCT-AATGACAGACCT
* * *
46422435 TTAGCGGCGCTTATTATAAAAGCGCCGCTACTGACAAGACCT
1 TTAGCGGCGCTT-TTCTATAAGCGCCGCTAATGAC-AGACCT
46422477 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACAAGACCT
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGAC-AGACCT
*
46422518 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACCCGACCT
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGA-CAGACCT
*
46422559 TTAGCGGCGC-TTTCTATAAGCGCCGCTAATGACCCGACCT
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGA-CAGACCT
*
46422599 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACCCGACCT
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGA-CAGACCT
* *
46422640 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACCGACTT
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACAGACCT
46422680 TTAGCGGCGCTTT
1 TTAGCGGCGCTTT
46422693 GTGGAAAGCG
Statistics
Matches: 272, Mismatches: 21, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
39 14 0.05
40 69 0.25
41 142 0.52
42 44 0.16
43 3 0.01
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACAGACCT
Found at i:46422599 original size:81 final size:82
Alignment explanation
Indices: 46422354--46422692 Score: 454
Period size: 81 Copynumber: 4.2 Consensus size: 82
46422344 GTTAAATAAA
* * * *
46422354 TTAGCGGCGCTTATGTGA-AAGCGCCGCTAAT-TCAC-ACCTTTAGTGGCGCTTTTCTAATAAGC
1 TTAGCGGCGCTTTTCT-ATAAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTTCT-ATAAGC
* ** **
46422416 GCCGCTAAAGGTCAGGTCT
64 GCCGCTAATGACCAGACCT
* * * *
46422435 TTAGCGGCGCTTATTATAAAAGCGCCGCTACTGACAAGACCTTTAGCGGCGCTTTTCTATAAGCG
1 TTAGCGGCGCTT-TTCTATAAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTTCTATAAGCG
*
46422500 CCGCTAATGACAAGACCT
65 CCGCTAATGACCAGACCT
*
46422518 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACCCGACCTTTAGCGGCGC-TTTCTATAAGCGC
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTTCTATAAGCGC
*
46422582 CGCTAATGACCCGACCT
66 CGCTAATGACCAGACCT
*
46422599 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTTTCTATAAGCGC
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTTCTATAAGCGC
*
46422664 CGCTAATGACC-GACTT
66 CGCTAATGACCAGACCT
46422680 TTAGCGGCGCTTT
1 TTAGCGGCGCTTT
46422693 GTGGAAAGCG
Statistics
Matches: 233, Mismatches: 20, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
81 109 0.47
82 72 0.31
83 33 0.14
84 19 0.08
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (82 bp):
TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACACGACCTTTAGCGGCGCTTTTCTATAAGCGC
CGCTAATGACCAGACCT
Found at i:46422615 original size:122 final size:120
Alignment explanation
Indices: 46422354--46422711 Score: 443
Period size: 122 Copynumber: 2.9 Consensus size: 120
46422344 GTTAAATAAA
* * * * *
46422354 TTAGCGGCGCTTATGTGA-AAGCGCCGCTAAT-TCACACCTTTAGTGGCGCTTTTCTAATAAGCG
1 TTAGCGGCGCTTTTCT-ATAAGCGCCGCTAATGACAGACCTTTAGCGGCGCTTTTCT-ATAAGCG
* * * ** *
46422417 CCGCTAAAGGTCAGGTCTTTAGCGGCGCTTATTATAAAAGCGCCGCTACTGACAAGACCT
64 CCGCT-AATGACCGACCTTTAGCGGCGCTT-TTAT-AAAGCGCCGCTAATGACAAGACCT
46422477 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACAAGACCTTTAGCGGCGCTTTTCTATAAGCGC
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGAC-AGACCTTTAGCGGCGCTTTTCTATAAGCGC
**
46422542 CGCTAATGACCCGACCTTTAGCGGCGCTTTCTAT-AAGCGCCGCTAATGACCCGACCT
65 CGCTAATGA-CCGACCTTTAGCGGCGCTTT-TATAAAGCGCCGCTAATGACAAGACCT
*
46422599 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACCCGACCTTTAGCGGCGCTTTTCTATAAGCGC
1 TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGA-CAGACCTTTAGCGGCGCTTTTCTATAAGCGC
* ** *
46422664 CGCTAATGACCGACTTTTAGCGGCGCTTTGTGGAAAGCGCCGCGAATG
65 CGCTAATGACCGACCTTTAGCGGCGCTTT-TATAAAGCGCCGCTAATG
46422712 CTTTACCTTT
Statistics
Matches: 209, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
121 20 0.10
122 105 0.50
123 32 0.15
124 32 0.15
125 20 0.10
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (120 bp):
TTAGCGGCGCTTTTCTATAAGCGCCGCTAATGACAGACCTTTAGCGGCGCTTTTCTATAAGCGCC
GCTAATGACCGACCTTTAGCGGCGCTTTTATAAAGCGCCGCTAATGACAAGACCT
Found at i:46425574 original size:29 final size:30
Alignment explanation
Indices: 46425542--46425680 Score: 101
Period size: 29 Copynumber: 4.7 Consensus size: 30
46425532 AATTGGGATC
* *
46425542 AAAAACGGAATTTTTGGATATCTGGGGGT-
1 AAAAATGGAATTTTTGGATATTTGGGGGTA
* ***
46425571 AAAAA-GGTAATTTTT-GAAAGTTTCACGGTA
1 AAAAATGG-AATTTTTGGATA-TTTGGGGGTA
*
46425601 AAAAATGGAATTTTTGGATATTTGAGGGT-
1 AAAAATGGAATTTTTGGATATTTGGGGGTA
* * * *
46425630 -AAAAGGGTAATTTTT-GAAAGTTTCGGGGTC
1 AAAAATGG-AATTTTTGGATA-TTTGGGGGTA
46425660 AAAAATGGAATTTTTGGATAT
1 AAAAATGGAATTTTTGGATAT
46425681 CCGGGGCAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
28 14 0.16
29 31 0.36
30 27 0.31
31 14 0.16
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGATATTTGGGGGTA
Found at i:46425614 original size:59 final size:59
Alignment explanation
Indices: 46425542--46425770 Score: 311
Period size: 59 Copynumber: 3.9 Consensus size: 59
46425532 AATTGGGATC
* * * *
46425542 AAAAACGGAATTTTTGGATATCTGGGGGTAAAAAGGTAATTTTTGAAAGTTTCACGGTA
1 AAAAATGGAATTTTTGGATATCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTA
* * ** *
46425601 AAAAATGGAATTTTTGGATATTTGAGGGTAAAAGGGTAATTTTTGAAAGTTTCGGGGTC
1 AAAAATGGAATTTTTGGATATCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTA
* * *
46425660 AAAAATGGAATTTTTGGATATCCG-GGGCAAAATGGTAATTTTTGAAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGATATCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTA
46425718 AAAAATGGAATTTTTGGA-AGT-TCGAGGGTAAAATGGTAATTTTTGAAAGTTTC
1 AAAAATGGAATTTTTGGATA-TCT-GAGGGTAAAATGGTAATTTTTGAAAGTTTC
46425771 GGGGACCTTC
Statistics
Matches: 151, Mismatches: 16, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
57 1 0.01
58 49 0.32
59 101 0.67
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGATATCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTA
Found at i:46425685 original size:29 final size:30
Alignment explanation
Indices: 46425540--46425703 Score: 91
Period size: 29 Copynumber: 5.6 Consensus size: 30
46425530 AAAATTGGGA
* *
46425540 TCAAAAACGG-AATTTTTGGATATCTGGGGG
1 TCAAAAATGGTAATTTTTGGATATC-CGGGG
* *
46425570 T-AAAAA-GGTAATTTTTGAAAGTTTCAC--GG
1 TCAAAAATGGTAATTTTTG-GA-TATC-CGGGG
* **
46425599 TAAAAAATGG-AATTTTTGGATATTTGAGGG
1 TCAAAAATGGTAATTTTTGGATATCCG-GGG
* * *
46425629 T--AAAAGGGTAATTTTT-GAAAGTTTCGGGG
1 TCAAAAATGGTAATTTTTGGATA--TCCGGGG
46425658 TCAAAAATGG-AATTTTTGGATATCCGGGG
1 TCAAAAATGGTAATTTTTGGATATCCGGGG
46425687 -C-AAAATGGTAATTTTTG
1 TCAAAAATGGTAATTTTTG
46425704 AAAGTTTCAA
Statistics
Matches: 105, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
27 7 0.07
28 22 0.21
29 34 0.32
30 28 0.27
31 14 0.13
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (30 bp):
TCAAAAATGGTAATTTTTGGATATCCGGGG
Found at i:46425699 original size:28 final size:27
Alignment explanation
Indices: 46425602--46425703 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 27
46425592 TTCACGGTAA
* *
46425602 AAAATGGAATTTTTGGATATTTGAGGGT
1 AAAATGGAATTTTTGGATATTCG-GGGC
* *
46425630 AAAAGGGTAATTTTT-GAAAGTTTCGGGGTC
1 AAAATGG-AATTTTTGGATA--TTCGGGG-C
*
46425660 AAAAATGGAATTTTTGGATATCCGGGGC
1 -AAAATGGAATTTTTGGATATTCGGGGC
46425688 AAAATGGTAATTTTTG
1 AAAATGG-AATTTTTG
46425704 AAAGTTTCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
27 7 0.12
28 18 0.30
29 16 0.27
30 10 0.17
31 9 0.15
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTTGGATATTCGGGGC
Found at i:46425728 original size:117 final size:117
Alignment explanation
Indices: 46425451--46425774 Score: 384
Period size: 117 Copynumber: 2.7 Consensus size: 117
46425441 TCGAGAGGGT
* *** * * *
46425451 AAAATGGTAATTTTGGGAAAGTTTGGGGGTTAAAAAATGGAA-CTTTAGACATTTAAGGGTAAAA
1 AAAATGGTAATTTT-TGAAAGTTTCAAGGTT-AAAAATGGAATTTTTGGA-ATTTGAGGGTAAAA
* ** * * *
46425515 CGGTAACTTTTAGAAAAAATT-GGGATCAAAAACGGAATTTTTGGATATCTGGGGGT
63 CGGTAA-TTTTTG-AAAGTTTCGGGGTCAAAAACGGAATTTTTGGATATCTCGGGGC
* * * *
46425571 AAAAAGGTAATTTTTGAAAGTTTCACGGTAAAAAATGGAATTTTTGGATATTTGAGGGTAAAAGG
1 AAAATGGTAATTTTTGAAAGTTTCAAGGTTAAAAATGGAATTTTTGGA-ATTTGAGGGTAAAACG
*
46425636 GTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGATATC-CGGGGC
65 GTAATTTTTGAAAGTTTCGGGGTCAAAAACGGAATTTTTGGATATCTCGGGGC
* *
46425688 AAAATGGTAATTTTTGAAAGTTTCAAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGAAAGTTTCAAGGTTAAAAATGGAATTTTTGGAA-TTTGAGGGTAAAACG
46425753 GTAATTTTTGAAAGTTTCGGGG
65 GTAATTTTTGAAAGTTTCGGGG
46425775 ACCTTCAAGG
Statistics
Matches: 178, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 89 0.50
118 41 0.23
119 34 0.19
120 13 0.07
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (117 bp):
AAAATGGTAATTTTTGAAAGTTTCAAGGTTAAAAATGGAATTTTTGGAATTTGAGGGTAAAACGG
TAATTTTTGAAAGTTTCGGGGTCAAAAACGGAATTTTTGGATATCTCGGGGC
Found at i:46426795 original size:3 final size:3
Alignment explanation
Indices: 46426787--46426851 Score: 78
Period size: 3 Copynumber: 21.0 Consensus size: 3
46426777 GGTTTCTTTT
* *
46426787 TTA TTA TTA TTA TTA TTAA TTA ATA TTA TTA TTAA TTA TTA -TA CCTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A TTA TTA TTA -TTA
46426834 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
46426852 AAAATCAATG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
2 2 0.04
3 45 0.82
4 8 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:46427573 original size:6 final size:6
Alignment explanation
Indices: 46427562--46427632 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
46427552 ATTATTCAAA
*
46427562 TAAATT TAAATT TAAATT TAAGA-- TAAATT TAAATTT TCAATT TAAATT
1 TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAA-TT TAAATT TAAATT
* * *
46427610 TAAA-A TAAACT TAAATT CAAATT
1 TAAATT TAAATT TAAATT TAAATT
46427633 CTGTTGGGCC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
4 1 0.02
5 7 0.13
6 40 0.74
7 6 0.11
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:46427587 original size:23 final size:24
Alignment explanation
Indices: 46427561--46427606 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
46427551 CATTATTCAA
46427561 ATAAATTTAAA-TTTAAATTTAAG
1 ATAAATTTAAATTTTAAATTTAAG
*
46427584 ATAAATTTAAATTTTCAATTTAA
1 ATAAATTTAAATTTTAAATTTAA
46427607 ATTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (24 bp):
ATAAATTTAAATTTTAAATTTAAG
Found at i:46427590 original size:17 final size:16
Alignment explanation
Indices: 46427568--46427631 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 16
46427558 CAAATAAATT
46427568 TAAATTTAAATTTAAGA
1 TAAATTTAAATTTAA-A
46427585 TAAATTTAAATTT---
1 TAAATTTAAATTTAAA
*
46427598 TCAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
* *
46427615 TAAACTTAAATTCAAA
1 TAAATTTAAATTTAAA
46427631 T
1 T
46427632 TCTGTTGGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 12 0.31
16 4 0.10
17 23 0.59
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:46427606 original size:30 final size:30
Alignment explanation
Indices: 46427562--46427626 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
46427552 ATTATTCAAA
* *
46427562 TAAA-TTTAAATTTAAATTTAAGATAAATT
1 TAAATTTTAAATTTAAATTTAAAATAAACT
*
46427591 TAAATTTTCAATTTAAATTTAAAATAAACT
1 TAAATTTTAAATTTAAATTTAAAATAAACT
46427621 TAAATT
1 TAAATT
46427627 CAAATTCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAATTTTAAATTTAAATTTAAAATAAACT
Found at i:46427625 original size:36 final size:36
Alignment explanation
Indices: 46427564--46427632 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
46427554 TATTCAAATA
* * * *
46427564 AATTTAAATTTAAATTTAAGATAAATTTAAATTTTC
1 AATTTAAATTTAAAATAAACATAAATTCAAATTTTC
*
46427600 AATTTAAATTTAAAATAAACTTAAATTCAAATT
1 AATTTAAATTTAAAATAAACATAAATTCAAATT
46427633 CTGTTGGGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (36 bp):
AATTTAAATTTAAAATAAACATAAATTCAAATTTTC
Found at i:46428465 original size:22 final size:23
Alignment explanation
Indices: 46428440--46428496 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
46428430 CGGCGTTAAA
*
46428440 TTTA-ATTTAATATTTATACATT
1 TTTATATTTAATATTTAAACATT
* *
46428462 TTTATAATTAA-ATTTAAATATT
1 TTTATATTTAATATTTAAACATT
46428484 TTTATTATTTAAT
1 TTTA-TATTTAAT
46428497 TTGAATTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTATATTTAATATTTAAACATT
Found at i:46435018 original size:135 final size:135
Alignment explanation
Indices: 46434769--46435178 Score: 452
Period size: 135 Copynumber: 3.1 Consensus size: 135
46434759 GTCCAAATTC
* ** * *
46434769 GCTTTAATGTTCATAAAAAGATTGCAATTTTCCTTTTTAGTCTC-CGGAGGGCTTCTTTC-GATC
1 GCTTTAACGTTCATAAAAAGATCACAGTTTTCCTTCTTAGTCTCTC-GAGGGCTTCTTTCAG-TC
* * * *
46434832 ATTGCCTCCTTCTTAGTCTCCTGAGGGCTTCTTTCAGTCACCGCACTGTCCAAATTTCTGCGTTT
64 ATTGCATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACCGTCCAAATTTCTGCGTTT
46434897 GTTCCGT
129 GTTCCGT
* *
46434904 GCTTTAACGTTCATAAAAAGATCACAGCTTTCCTTCTTAGTCTCTTGAGGGCTTCTTTCAGTCAT
1 GCTTTAACGTTCATAAAAAGATCACAGTTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTCAT
* * * * * *
46434969 TGCATTCTTCTCACTCTCCTGGGGGCTTCTTTCGGTCATCACACCGTCCAAGTTTCTGC---T-T
66 TGCATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACCGTCCAAATTTCTGCGTTTGT
46435030 T---T
131 TCCGT
* *
46435032 G-----ACGTTCATGAAAAGATCACAGTTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTAAT
1 GCTTTAACGTTCATAAAAAGATCACAGTTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTCAT
* * * * * *
46435092 TGCATCCTTCTTATTCTCCTGAGGGATTCTTTCAGTCATTGCACCATCCAAATTTCTACGTTTGC
66 TGCATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACCGTCCAAATTTCTGCGTTTGT
*
46435157 TCCGC
131 TCCGT
* *
46435162 GTTTTAATGTTCATAAA
1 GCTTTAACGTTCATAAA
46435179 CACAATAGCC
Statistics
Matches: 225, Mismatches: 36, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
123 103 0.46
126 1 0.00
127 1 0.00
128 2 0.01
130 1 0.00
131 2 0.01
132 1 0.00
135 113 0.50
136 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (135 bp):
GCTTTAACGTTCATAAAAAGATCACAGTTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTCAT
TGCATCCTTCTTACTCTCCTGAGGGCTTCTTTCAGTCATCGCACCGTCCAAATTTCTGCGTTTGT
TCCGT
Found at i:46435116 original size:39 final size:39
Alignment explanation
Indices: 46435057--46435134 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
46435047 ATCACAGTTT
*
46435057 TCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTAATTGCA
1 TCCTTCTTAGTCTCTCGAGGGATTCTTTCAGTAATTGCA
* *
46435096 TCCTTCTTATTCTC-CTGAGGGATTCTTTCAGTCATTGCA
1 TCCTTCTTAGTCTCTC-GAGGGATTCTTTCAGTAATTGCA
46435135 CCATCCAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.15, C:0.26, G:0.17, T:0.42
Consensus pattern (39 bp):
TCCTTCTTAGTCTCTCGAGGGATTCTTTCAGTAATTGCA
Found at i:46435130 original size:123 final size:123
Alignment explanation
Indices: 46434910--46435148 Score: 352
Period size: 123 Copynumber: 1.9 Consensus size: 123
46434900 CCGTGCTTTA
* * *
46434910 ACGTTCATAAAAAGATCACAGCTTTCCTTCTTAGTCTCTTGAGGGCTTCTTTCAGTCATTGCATT
1 ACGTTCATAAAAAGATCACAGCTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTAATTGCATC
* * * * *
46434975 CTTCTCACTCTCCTGGGGGCTTCTTTCGGTCATCACACCGTCCAAGTTTCTGCTTTTG
66 CTTCTCACTCTCCTGAGGGATTCTTTCAGTCATCACACCATCCAAATTTCTGCTTTTG
* *
46435033 ACGTTCATGAAAAGATCACAGTTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTAATTGCATC
1 ACGTTCATAAAAAGATCACAGCTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTAATTGCATC
* * **
46435098 CTTCTTATTCTCCTGAGGGATTCTTTCAGTCATTGCACCATCCAAATTTCT
66 CTTCTCACTCTCCTGAGGGATTCTTTCAGTCATCACACCATCCAAATTTCT
46435149 ACGTTTGCTC
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
123 102 1.00
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.38
Consensus pattern (123 bp):
ACGTTCATAAAAAGATCACAGCTTTCCTTCTTAGTCTCTCGAGGGCTTCTTTCAGTAATTGCATC
CTTCTCACTCTCCTGAGGGATTCTTTCAGTCATCACACCATCCAAATTTCTGCTTTTG
Found at i:46436587 original size:52 final size:55
Alignment explanation
Indices: 46436530--46436650 Score: 149
Period size: 56 Copynumber: 2.2 Consensus size: 55
46436520 CTACTCTCAA
* *
46436530 TCACTCAATTATTAATA-TTTTTAT-T-ATTTAATTATAAAAAATTATAAAATAG
1 TCACTCAATTATTAATATTTTTTATGTCATTCAATTATAAAAAATTACAAAATAG
* * *
46436582 TCACTCAATTATTAGTATTTTTTTTGGTCATTCAATTATAAAAAATTACAAAATGG
1 TCACTCAATTATTAATATTTTTTAT-GTCATTCAATTATAAAAAATTACAAAATAG
* *
46436638 TAATTCAATTATT
1 TCACTCAATTATT
46436651 CAATTTTATC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
52 16 0.28
53 6 0.10
55 1 0.02
56 35 0.60
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.45
Consensus pattern (55 bp):
TCACTCAATTATTAATATTTTTTATGTCATTCAATTATAAAAAATTACAAAATAG
Found at i:46436796 original size:29 final size:30
Alignment explanation
Indices: 46436773--46436837 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
46436763 GAAATTTTCC
* *
46436773 ATAGTTTGATGATCAAAAAAAAATTTACTA
1 ATAGTTTAATGACCAAAAAAAAATTTACTA
* *
46436803 ATAGTTTAATGACC-AAAAAATATTTAATA
1 ATAGTTTAATGACCAAAAAAAAATTTACTA
46436832 ATAGTT
1 ATAGTT
46436838 ATAGTTAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.35
Consensus pattern (30 bp):
ATAGTTTAATGACCAAAAAAAAATTTACTA
Found at i:46453397 original size:22 final size:22
Alignment explanation
Indices: 46453372--46453419 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
46453362 TAAATTTAAG
*
46453372 ATTTGATCTCTTTATTTTCATA
1 ATTTGATCTCTCTATTTTCATA
* * *
46453394 ATTTTATTTCTCTATTTTTATA
1 ATTTGATCTCTCTATTTTCATA
46453416 ATTT
1 ATTT
46453420 TATTAAACGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTGATCTCTCTATTTTCATA
Found at i:46465408 original size:32 final size:32
Alignment explanation
Indices: 46465346--46465408 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
46465336 AAATCCTGGA
* * * *
46465346 CCCCCTAATTTTTTTGAGAATTTATCATTAAG
1 CCCCCAAATTTTTTTAAAAATTTATAATTAAG
46465378 CCCCCAAATATTTTTTAAAAATTT-TAATTAA
1 CCCCCAAAT-TTTTTTAAAAATTTATAATTAA
46465409 ACCCTCAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (32 bp):
CCCCCAAATTTTTTTAAAAATTTATAATTAAG
Found at i:46467603 original size:16 final size:18
Alignment explanation
Indices: 46467570--46467604 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
46467560 TTTTTTTATT
46467570 TAAATATTTTATAATTAA
1 TAAATATTTTATAATTAA
46467588 TAAA-ATTTTA-AATTAA
1 TAAATATTTTATAATTAA
46467604 T
1 T
46467605 GATAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 6 0.35
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATATTTTATAATTAA
Found at i:46471096 original size:2 final size:2
Alignment explanation
Indices: 46471089--46471128 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
46471079 AACAAAATTC
46471089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T 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
46471129 CAAAAACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46471566 original size:20 final size:20
Alignment explanation
Indices: 46471543--46471589 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
46471533 TACCAAATAT
*
46471543 TCAAATTTAACTTAAAATC-A
1 TCAAATTAAACTT-AAATCGA
*
46471563 TC-AATTAAACTTTAATCGA
1 TCAAATTAAACTTAAATCGA
46471582 TCAAATTA
1 TCAAATTA
46471590 TTGGAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 7 0.30
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (20 bp):
TCAAATTAAACTTAAATCGA
Found at i:46484325 original size:2 final size:2
Alignment explanation
Indices: 46484318--46484349 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46484308 ATTTCAATAA
46484318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46484350 TATTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46487038 original size:2 final size:2
Alignment explanation
Indices: 46487027--46487069 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
46487017 TCAACTTTAT
46487027 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46487068 TA
1 TA
46487070 ATGGGATTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:46493125 original size:16 final size:15
Alignment explanation
Indices: 46493106--46493136 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
46493096 GTTTAGATCA
46493106 TTTTTAATTTAGATTT
1 TTTTTAATTTA-ATTT
46493122 TTTTTAATTTAATTT
1 TTTTTAATTTAATTT
46493137 ATTGATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTTAATTTAATTT
Found at i:46493856 original size:30 final size:31
Alignment explanation
Indices: 46493820--46493891 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
46493810 ATTACGTTTA
* * *
46493820 ACAAAACAGTCACTCAACTT-TGGAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
*
46493850 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
*
46493881 ACAAAATAGTC
1 ACAAAACAGTC
46493892 CTCTTGTTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:46496006 original size:23 final size:23
Alignment explanation
Indices: 46495931--46496044 Score: 126
Period size: 23 Copynumber: 5.0 Consensus size: 23
46495921 AAGTGCTGGG
*
46495931 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACACAGTGC
* * * *
46495954 -AATCAGTAGGCGCACATAGCGC
1 GAAACAGTAGGCACACACAGTGC
46495976 -AAATCAGTAGGCACACGA-AGTGC
1 GAAA-CAGTAGGCACAC-ACAGTGC
*
46495999 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACACAGTGC
*
46496022 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACACAGTGC
46496045 TGAACGGTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
22 20 0.26
23 53 0.69
24 4 0.05
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.11
Consensus pattern (23 bp):
GAAACAGTAGGCACACACAGTGC
Found at i:46496030 original size:46 final size:45
Alignment explanation
Indices: 46495931--46496044 Score: 142
Period size: 46 Copynumber: 2.5 Consensus size: 45
46495921 AAGTGCTGGG
* * *
46495931 GAAACAGTAAGCACACACAGTGCAATCAGTAGGCGCACATAGCGC
1 GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
* *
46495976 -AAATCAGTAGGCACACGA-AGTGCGAAACAGTAGGCACACAAAGTGC
1 GAAA-CAGTAAGCACAC-ACAGTGC-AAACAGTAGGCACACAAAGCGC
46496022 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGC
46496045 TGAACGGTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
44 3 0.05
45 17 0.29
46 35 0.60
47 3 0.05
ACGTcount: A:0.40, C:0.25, G:0.25, T:0.11
Consensus pattern (45 bp):
GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
Done.