Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003806.1 Hibiscus syriacus cultivar Beakdansim tig00008146_pilon, whole genome shotgun sequence
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: 1419252
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:456296 original size:31 final size:31
Alignment explanation
Indices: 456258--456348 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 31
456248 GAAGGACATA
* *
456258 TCCATATGTTCCGAAGAACATAGATAACCTG
1 TCCATATGTTCCGAAGGACATAGGTAACCTG
* *
456289 TCCATATG-TCCTGAAGGGCATAGGTAAACTG
1 TCCATATGTTCC-GAAGGACATAGGTAACCTG
* *
456320 TCTATATGTCCCGAAGGACATAGGTAACC
1 TCCATATGTTCCGAAGGACATAGGTAACC
456349 CTCGACTCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 3 0.06
31 45 0.90
32 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (31 bp):
TCCATATGTTCCGAAGGACATAGGTAACCTG
Found at i:460514 original size:31 final size:29
Alignment explanation
Indices: 460476--460571 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 29
460466 GTCCCGAATG
460476 ACCTATCCATATGCTCCGAAGAACATAGGTA
1 ACCTATCCATATG-TCCGAAG-ACATAGGTA
460507 ACCTATCCATATGTCCCGAATGACATAGGTA
1 ACCTATCCATATGT-CCGAA-GACATAGGTA
* * * *
460538 AACTGTCCATTTATCACGAAGGACATAGGTA
1 ACCTATCCATATGTC-CGAA-GACATAGGTA
460569 ACC
1 ACC
460572 CTCGACTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.04
31 53 0.95
32 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (29 bp):
ACCTATCCATATGTCCGAAGACATAGGTA
Found at i:461441 original size:21 final size:22
Alignment explanation
Indices: 461392--461446 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
461382 CCCTCCACAT
461392 AGGTATCGATACTTCTTCCATA
1 AGGTATCGATACTTCTTCCATA
* *
461414 TGGTATCGATAC-TGTT-CATA
1 AGGTATCGATACTTCTTCCATA
461434 CAGGTATCGATAC
1 -AGGTATCGATAC
461447 CACATGCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 14 0.48
22 11 0.38
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (22 bp):
AGGTATCGATACTTCTTCCATA
Found at i:464766 original size:24 final size:24
Alignment explanation
Indices: 464739--464788 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
464729 ATAAAGAACC
464739 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
464763 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
464787 AA
1 AA
464789 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:465932 original size:10 final size:9
Alignment explanation
Indices: 465917--465943 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
465907 TTAGTACACA
465917 TTTTTTTTC
1 TTTTTTTTC
465926 TTTTTTTTC
1 TTTTTTTTC
465935 TTTTTTTTC
1 TTTTTTTTC
465944 ACTTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:465949 original size:18 final size:18
Alignment explanation
Indices: 465915--465959 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
465905 ATTTAGTACA
**
465915 CATTTTTTTTCTTTTTTTT
1 CATTTTTTTTC-ACTTTTT
465934 C-TTTTTTTTCACTTTTT
1 CATTTTTTTTCACTTTTT
465951 CATTTTTTT
1 CATTTTTTT
465960 ACGCTGCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 16 0.70
19 1 0.04
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (18 bp):
CATTTTTTTTCACTTTTT
Found at i:465959 original size:9 final size:9
Alignment explanation
Indices: 465918--465959 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
465908 TAGTACACAT
*
465918 TTTTTTTCT
1 TTTTTTTCA
*
465927 TTTTTTTCT
1 TTTTTTTCA
465936 TTTTTTTCA
1 TTTTTTTCA
*
465945 -CTTTTTCA
1 TTTTTTTCA
465953 TTTTTTT
1 TTTTTTT
465960 ACGCTGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:468879 original size:3 final size:3
Alignment explanation
Indices: 468871--468899 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
468861 CTTTTAATAT
468871 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
468900 GTTGTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:469517 original size:184 final size:185
Alignment explanation
Indices: 469207--469576 Score: 715
Period size: 184 Copynumber: 2.0 Consensus size: 185
469197 ACGAAAACGA
*
469207 AAAAAAAAATGGGATAAAAGACAGAGGGCTCGGTTTTTCAACAGGGGGAATTCACAGGGGAACGA
1 AAAAAAAAATGGGATAAAAGACAGAGGGCTCAGTTTTTCAACAGGGGGAATTCACAGGGGAACGA
469272 AAAGCTAAAAAAGATCATTTGTAATAGAGGATTGAGCCTCCATTGAAGAAAGACATAACCATTGT
66 AAAGCTAAAAAAGATCATTTGTAATAGAGGATTGAGCCTCCATTGAAGAAAGACATAACCATTGT
469337 AATCATTCAACTTCAATCAAGAATAGAATACTGAACGGAGTTTTTTTTAAGGTAT
131 AATCATTCAACTTCAATCAAGAATAGAATACTGAACGGAGTTTTTTTTAAGGTAT
469392 AAAAAAAAA-GGGATAAAAGACAGAGGGCTCAGTTTTTCAACAGGGGGAATTCACAGGGGAACGA
1 AAAAAAAAATGGGATAAAAGACAGAGGGCTCAGTTTTTCAACAGGGGGAATTCACAGGGGAACGA
469456 AAAGCTAAAAAAGATCATTTGTAATAGAGGATTGAGCCTCCATTGAAGAAAGACATAACCATTGT
66 AAAGCTAAAAAAGATCATTTGTAATAGAGGATTGAGCCTCCATTGAAGAAAGACATAACCATTGT
*
469521 AATCATTCAACTTCAATCAAGAATATAATACTGAACGGAGTTTTTTTTAAGGTAT
131 AATCATTCAACTTCAATCAAGAATAGAATACTGAACGGAGTTTTTTTTAAGGTAT
469576 A
1 A
469577 TATATCATTT
Statistics
Matches: 183, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
184 174 0.95
185 9 0.05
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (185 bp):
AAAAAAAAATGGGATAAAAGACAGAGGGCTCAGTTTTTCAACAGGGGGAATTCACAGGGGAACGA
AAAGCTAAAAAAGATCATTTGTAATAGAGGATTGAGCCTCCATTGAAGAAAGACATAACCATTGT
AATCATTCAACTTCAATCAAGAATAGAATACTGAACGGAGTTTTTTTTAAGGTAT
Found at i:470721 original size:14 final size:14
Alignment explanation
Indices: 470704--470739 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
470694 TTTTATTATC
470704 CATATTATGTAATA
1 CATATTATGTAATA
470718 CATATTATGTAATA
1 CATATTATGTAATA
470732 CATATTAT
1 CATATTAT
470740 AGCATATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (14 bp):
CATATTATGTAATA
Found at i:470862 original size:2 final size:2
Alignment explanation
Indices: 470855--470898 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
470845 CAATTTATTA
470855 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
470897 AT
1 AT
470899 TAGTTGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:473379 original size:24 final size:24
Alignment explanation
Indices: 473352--473401 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
473342 ATAAAGAACC
473352 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
473376 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
473400 AA
1 AA
473402 CCAACAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:483181 original size:108 final size:107
Alignment explanation
Indices: 483069--483299 Score: 277
Period size: 108 Copynumber: 2.1 Consensus size: 107
483059 ACCAAAGTGT
* * *
483069 AAAAATATGCTAAACTTAGAGGGACCAAATAGTGAATAACCCAAAAAATACAAATCATGCAA-AA
1 AAAAA-ATGCTAAACTTAGAGGGACCAAACAGTGAATAACCCAAAAAATACAAAGCACGCAAGAA
*
483133 AGAGAGAAAATAAC-ATTTTTAAACCCTACAAGTGACCAAAATAC
65 A-AGAGAAAATAACAATTTTT-AACCCTACAAGTAACCAAAATAC
* * * * *
483177 AAAAACACGCTAAAATTAGAGGGACTAAACAGTGAATAACCCAAATATTACAAAGCACGCAAGGA
1 AAAAA-ATGCTAAACTTAGAGGGACCAAACAGTGAATAACCCAAAAAATACAAAGCACGCAA-GA
* * * **
483242 AAAGGGAAAATAACAATTTTTGACCCTATAAGTAACCAAAATGT
64 AAAGAGAAAATAACAATTTTTAACCCTACAAGTAACCAAAATAC
483286 AAAAAATGCTAAAC
1 AAAAAATGCTAAAC
483300 CTAGTGGCCT
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
108 60 0.58
109 34 0.33
110 9 0.09
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.18
Consensus pattern (107 bp):
AAAAAATGCTAAACTTAGAGGGACCAAACAGTGAATAACCCAAAAAATACAAAGCACGCAAGAAA
AGAGAAAATAACAATTTTTAACCCTACAAGTAACCAAAATAC
Found at i:484242 original size:18 final size:18
Alignment explanation
Indices: 484219--484255 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
484209 GCCCCGGGTC
*
484219 GGGTATTTAGGTTGGTTT
1 GGGTATTTAGGTTAGTTT
484237 GGGTATTTAGGTTAGTTT
1 GGGTATTTAGGTTAGTTT
484255 G
1 G
484256 TGTTGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.49
Consensus pattern (18 bp):
GGGTATTTAGGTTAGTTT
Found at i:485520 original size:19 final size:19
Alignment explanation
Indices: 485496--485555 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
485486 AGAATAGACA
485496 ATAACAGAAATCAGAGATC
1 ATAACAGAAATCAGAGATC
* * *
485515 ATAACAGATATCAAAGTTC
1 ATAACAGAAATCAGAGATC
* * *
485534 AGAGCAGAAATCAGAGGTC
1 ATAACAGAAATCAGAGATC
485553 ATA
1 ATA
485556 CTTTATTTCC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (19 bp):
ATAACAGAAATCAGAGATC
Found at i:487213 original size:21 final size:21
Alignment explanation
Indices: 487170--487213 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
487160 ATCAAAGACA
* *
487170 AAGTCAACAGTCATACCGGTC
1 AAGTCAACAGTCAGACCGATC
* *
487191 AAGTCAACGGTCAGACTGATC
1 AAGTCAACAGTCAGACCGATC
487212 AA
1 AA
487214 ATTCAATCGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (21 bp):
AAGTCAACAGTCAGACCGATC
Found at i:488307 original size:135 final size:135
Alignment explanation
Indices: 488065--488650 Score: 804
Period size: 135 Copynumber: 4.4 Consensus size: 135
488055 CGTTTTCTCA
* *
488065 CTCTATCGGATGAGTTCTTCTCGTTATGAACTCTCTATTGGAAATGTTAATCCCTAAAGTGAGGC
1 CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGC
*
488130 ATCGATGATTCAAAATGTCATGAATCGAGCAAAGGTTGAACAAGTTCTT-TTCATTACAAACTTC
66 ATCGATGATTCAAAATGTCATGAATCGAGCAAAGGTTGAACAAGTTCTTCTT-ATTACGAACTTC
*
488194 TTGTCC
130 TTTTCC
* * * * * *
488200 CTCTATCAGATGAGTTCTTGTCATTATGATCTCTTTATTGGAAATATTAATCCCTCAAGTAAGGC
1 CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGC
* * * *
488265 ATTGATGATTCAAAATGTCATAAATCGAGCAAAGGTTGAACAAGTTATTCTCATTACGAACTTCT
66 ATCGATGATTCAAAATGTCATGAATCGAGCAAAGGTTGAACAAGTTCTTCTTATTACGAACTTCT
488330 TTTCC
131 TTTCC
* * *
488335 CTCTATCGGATGAGTGCTTCTCATTATGAA--CTCTACTGGAAATGTTAATCCCTCAATTGAGGC
1 CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGC
* * * * *
488398 ATCGATGATTCCAAATATTATGAATCGAGCAAAGTTTGAACAAGTTCTTCTTATTACGAACATCT
66 ATCGATGATTCAAAATGTCATGAATCGAGCAAAGGTTGAACAAGTTCTTCTTATTACGAACTTCT
488463 TTTCC
131 TTTCC
* * *
488468 CTTTATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGTGAGGC
1 CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGC
* * * * *
488533 ATC-AGTGATTCGAAATGTCGTGAATGGAGAAAAGGTTGAACAAGTTCTTCTTATTATGAACTT-
66 ATCGA-TGATTCAAAATGTCATGAATCGAGCAAAGGTTGAACAAGTTCTTCTTATTACGAACTTC
488596 TTTCTCC
130 TTT-TCC
* * * *
488603 CTCTATCGTATAAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTT
1 CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAATGTT
488651 GATTGGTTTA
Statistics
Matches: 394, Mismatches: 52, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
133 117 0.30
134 4 0.01
135 272 0.69
136 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (135 bp):
CTCTATCGGATGAGTTCTTCTCATTATGAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGC
ATCGATGATTCAAAATGTCATGAATCGAGCAAAGGTTGAACAAGTTCTTCTTATTACGAACTTCT
TTTCC
Found at i:488606 original size:268 final size:268
Alignment explanation
Indices: 488041--488636 Score: 811
Period size: 268 Copynumber: 2.2 Consensus size: 268
488031 AGATGTTATA
* * * * *
488041 CTTCCTATTATGAACGTTTTCTCACTCTATCGGATGAGTTCTTCTCGTTATGAACTCTCTATTGG
1 CTTCTTATTATGAACTTTTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAA--CTCTACTGG
*
488106 AAATGTTAATCCCTAAAGTGAGGCATCGATGATTCAAAATGTCATGAATCGAGCAAAGGTTGAAC
64 AAATGTTAATCCCTAAAGTGAGGCATCGATGATTCAAAATATCATGAATCGAGCAAAGGTTGAAC
* * * **
488171 AAGTTCTTTTCATTACAAACTTCTTGTCCCTCTATCAGATGAGTTCTTGTCATTATGATCTCTTT
129 AAGTTCTTTTCATTACAAACATCTTGTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCC
* * *
488236 ATTGGAAATATTAATCCCTCAAGTAAGGCATTGATGATTCAAAATGTCATAAATCGAGCAAAGGT
194 ATTGGAAATATCAATCCCTCAAGTAAGGCATAGATGATTCAAAATGTCATAAATCGAGAAAAGGT
488301 TGAACAAGTT
259 TGAACAAGTT
* * * *
488311 ATTCTCATTACGAACTTCTTT-TCCCTCTATCGGATGAGTGCTTCTCATTATGAACTCTACTGGA
1 CTTCTTATTATGAACTT-TTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTACTGGA
* * * * *
488375 AATGTTAATCCCTCAATTGAGGCATCGATGATTCCAAATATTATGAATCGAGCAAAGTTTGAACA
65 AATGTTAATCCCTAAAGTGAGGCATCGATGATTCAAAATATCATGAATCGAGCAAAGGTTGAACA
* * * *
488440 AGTTCTTCTT-ATTACGAACATCTTTTCCCTTTATCGGATGAGTTCTTCTCATTATGAACTCTCC
130 AGTTCTT-TTCATTACAAACATCTTGTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCC
* * * * * *
488504 ATTGGAAATGTCAATCCCTCAAGTGAGGCATCAG-TGATTCGAAATGTCGTGAATGGAGAAAAGG
194 ATTGGAAATATCAATCCCTCAAGTAAGGCAT-AGATGATTCAAAATGTCATAAATCGAGAAAAGG
488568 TTGAACAAGTT
258 TTGAACAAGTT
* *
488579 CTTCTTATTATGAACTTTTTCTCCCTCTATCGTATAAGTTCTTCTCATTATGAACTCT
1 CTTCTTATTATGAACTTTTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCT
488637 CCATTGAAAA
Statistics
Matches: 283, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
267 3 0.01
268 232 0.82
269 3 0.01
270 42 0.15
271 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (268 bp):
CTTCTTATTATGAACTTTTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTACTGGAA
ATGTTAATCCCTAAAGTGAGGCATCGATGATTCAAAATATCATGAATCGAGCAAAGGTTGAACAA
GTTCTTTTCATTACAAACATCTTGTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCAT
TGGAAATATCAATCCCTCAAGTAAGGCATAGATGATTCAAAATGTCATAAATCGAGAAAAGGTTG
AACAAGTT
Found at i:490053 original size:54 final size:54
Alignment explanation
Indices: 489995--490107 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
489985 ACTGGAAGTA
* *
489995 ATCAAGAAACCCT-TAAAAATCAGGCTTAGCTCCTTTCCAAATCCATTTGAAAAC
1 ATCAAGAAA-CATGTAAAAATCAGGCTTAGCTCCTTTCAAAATCCATTTGAAAAC
* * * * *
490049 ATCAAGAAACATGTTAAAATCAGGCTTAGTTTCTTTCAAAATTCATTTGAAGAC
1 ATCAAGAAACATGTAAAAATCAGGCTTAGCTCCTTTCAAAATCCATTTGAAAAC
490103 ATCAA
1 ATCAA
490108 CATGTTTGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (54 bp):
ATCAAGAAACATGTAAAAATCAGGCTTAGCTCCTTTCAAAATCCATTTGAAAAC
Found at i:493405 original size:21 final size:21
Alignment explanation
Indices: 493380--493419 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
493370 TGTTGAGATG
493380 CAATGTATACCATG-TAATGTA
1 CAATGTATA-CATGTTAATGTA
493401 CAATGTATACATGTTAATG
1 CAATGTATACATGTTAATG
493420 CAAAGATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
CAATGTATACATGTTAATGTA
Found at i:496062 original size:18 final size:19
Alignment explanation
Indices: 496009--496062 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
495999 TCTTCTTATT
*
496009 TTTACTTTAATTA-CTTTTA
1 TTTA-TTTAATCATCTTTTA
496028 TTTATTTAATCAT-TTTTA
1 TTTATTTAATCATCTTTTA
496046 -TTATTTTAAT-ATCTTTT
1 TTTA-TTTAATCATCTTTT
496063 TACAGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.16
18 22 0.71
19 4 0.13
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTAATCATCTTTTA
Found at i:498942 original size:11 final size:11
Alignment explanation
Indices: 498928--498954 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
498918 TTCCATTACA
498928 ATTTTATTTTT
1 ATTTTATTTTT
498939 ATTTTATTTTT
1 ATTTTATTTTT
498950 ATTTT
1 ATTTT
498955 TCATTTCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:501643 original size:18 final size:18
Alignment explanation
Indices: 501590--501632 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
501580 TCTTCTTATT
*
501590 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
501609 TTTATTTAATCACTTTTA
1 TTTATTTAATCACTTTTA
501627 -TTATTT
1 TTTATTT
501633 TAATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:504977 original size:18 final size:18
Alignment explanation
Indices: 504954--505011 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
504944 GCCCCAGGTC
504954 GGGTATTTAGTTTGGTTT
1 GGGTATTTAGTTTGGTTT
504972 GGGTATTTAGTTTGGTTT
1 GGGTATTTAGTTTGGTTT
*
504990 GGGTATTTAGGTTGGTTT
1 GGGTATTTAGTTTGGTTT
505008 GGGT
1 GGGT
505012 TGGGCTTGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.10, C:0.00, G:0.38, T:0.52
Consensus pattern (18 bp):
GGGTATTTAGTTTGGTTT
Found at i:505007 original size:23 final size:23
Alignment explanation
Indices: 504963--505031 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 23
504953 CGGGTATTTA
504963 GTTTGGTTTGGGTATTTA-----
1 GTTTGGTTTGGGTATTTAGGTTG
504981 GTTTGGTTTGGGTATTTAGGTTG
1 GTTTGGTTTGGGTATTTAGGTTG
* * *
505004 GTTTGGGTTGGG-CTTGAGGTTG
1 GTTTGGTTTGGGTATTTAGGTTG
505026 GTTTGG
1 GTTTGG
505032 GTATTTATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 18 0.42
22 14 0.33
23 11 0.26
ACGTcount: A:0.07, C:0.01, G:0.42, T:0.49
Consensus pattern (23 bp):
GTTTGGTTTGGGTATTTAGGTTG
Found at i:505035 original size:40 final size:40
Alignment explanation
Indices: 504960--505062 Score: 143
Period size: 40 Copynumber: 2.5 Consensus size: 40
504950 GGTCGGGTAT
* * * *
504960 TTAGTTTGGTTTGGGTATTTAGTTTGGTTTGGGTATTTAGG
1 TTAGTTTGGGTTGGG-CTTGAGGTTGGTTTGGGTATTTAGG
* *
505001 TTGGTTTGGGTTGGGCTTGAGGTTGGTTTGGGTATTTATG
1 TTAGTTTGGGTTGGGCTTGAGGTTGGTTTGGGTATTTAGG
505041 TTAGTTTGGGTTGGGCTTGAGG
1 TTAGTTTGGGTTGGGCTTGAGG
505063 CCCGTTTGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 42 0.76
41 13 0.24
ACGTcount: A:0.10, C:0.02, G:0.40, T:0.49
Consensus pattern (40 bp):
TTAGTTTGGGTTGGGCTTGAGGTTGGTTTGGGTATTTAGG
Found at i:511367 original size:2 final size:2
Alignment explanation
Indices: 511356--511388 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
511346 AAACATTATT
511356 TA TA -A 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
511389 ATTTTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:516486 original size:17 final size:17
Alignment explanation
Indices: 516464--516496 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
516454 TCTTACACTA
*
516464 AATTTCCTGAAGAGTAT
1 AATTTCCTGAACAGTAT
516481 AATTTCCTGAACAGTA
1 AATTTCCTGAACAGTA
516497 ACATGTTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (17 bp):
AATTTCCTGAACAGTAT
Found at i:521585 original size:24 final size:25
Alignment explanation
Indices: 521544--521613 Score: 63
Period size: 25 Copynumber: 2.7 Consensus size: 25
521534 TATGACTAAA
*
521544 ATAATAATAAAATTAATAAATT-AAAT
1 ATAATAA-AAAA-AAATAAATTGAAAT
*
521570 AT-ATAAAAATAAAATAAAATTGCAAT
1 ATAATAAAAA-AAAAT-AAATTGAAAT
*
521596 ATAATAAAAACAAATAAA
1 ATAATAAAAAAAAATAAA
521614 ATTATATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 6 0.16
25 13 0.35
26 11 0.30
27 7 0.19
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (25 bp):
ATAATAAAAAAAAATAAATTGAAAT
Found at i:521604 original size:26 final size:25
Alignment explanation
Indices: 521542--521617 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 25
521532 AATATGACTA
*
521542 AAATAATAATAAAAT-TAAT-AAATT
1 AAAT-ATAATAAAATAAAATAAAATT
521566 AAATAT-ATAAAAATAAAATAAAATT
1 AAATATAAT-AAAATAAAATAAAATT
*
521591 GCAATATAATAAAA-ACAAATAAAATT
1 -AAATATAATAAAATA-AAATAAAATT
521617 A
1 A
521618 TATGATCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
22 2 0.05
23 7 0.16
24 7 0.16
25 6 0.14
26 19 0.44
27 2 0.05
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (25 bp):
AAATATAATAAAATAAAATAAAATT
Found at i:523067 original size:3 final size:3
Alignment explanation
Indices: 523059--523169 Score: 98
Period size: 3 Copynumber: 37.0 Consensus size: 3
523049 CTGTAATATG
* * * * *
523059 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAG TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
523104 TAA TAA TAA TTA TAA CAA TTA TAA TAA TAA TTA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
523152 TAA AAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
523170 AACGGGTAAA
Statistics
Matches: 84, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.02
3 80 0.95
4 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:523109 original size:21 final size:21
Alignment explanation
Indices: 523061--523163 Score: 120
Period size: 21 Copynumber: 4.9 Consensus size: 21
523051 GTAATATGTA
* **
523061 ATAATAATATTTATTAATAAAA
1 ATAATAATAATTA-TAATAATT
523083 AT-ATAATAA-TAGTAATAATT
1 ATAATAATAATTA-TAATAATT
*
523103 ATAATAATAATTATAACAATT
1 ATAATAATAATTATAATAATT
523124 ATAATAATAATTATAATAATT
1 ATAATAATAATTATAATAATT
**
523145 ATAATAATAAAAATAATAA
1 ATAATAATAATTATAATAA
523164 AAATAAAACG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
20 10 0.14
21 57 0.80
22 4 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (21 bp):
ATAATAATAATTATAATAATT
Found at i:523464 original size:39 final size:39
Alignment explanation
Indices: 523410--523505 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
523400 GTTGAACAAA
* * * *
523410 TTCTTCTCATTATGAATTTCTTCTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTCCTTCTCATTATTCAGATGAG
523449 TTCTTCTCATTATGAACTCCTTCTCATTATTCAGATGAG
1 TTCTTCTCATTATGAACTCCTTCTCATTATTCAGATGAG
523488 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
523506 TCCTCTGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (39 bp):
TTCTTCTCATTATGAACTCCTTCTCATTATTCAGATGAG
Found at i:523493 original size:22 final size:22
Alignment explanation
Indices: 523427--523500 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
523417 CATTATGAAT
* *
523427 TTCTTCTCCTTCTTCAGATGAG
1 TTCTTCTCATTATTCAGATGAG
*
523449 TTCTTCTCATTA-T--GA--AC
1 TTCTTCTCATTATTCAGATGAG
*
523466 TCCTTCTCATTATTCAGATGAG
1 TTCTTCTCATTATTCAGATGAG
523488 TTCTTCTCATTAT
1 TTCTTCTCATTAT
523501 GAACTTCCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
17 12 0.29
18 1 0.02
19 2 0.05
20 2 0.05
21 1 0.02
22 23 0.56
ACGTcount: A:0.19, C:0.24, G:0.09, T:0.47
Consensus pattern (22 bp):
TTCTTCTCATTATTCAGATGAG
Found at i:523777 original size:123 final size:123
Alignment explanation
Indices: 523575--523856 Score: 415
Period size: 123 Copynumber: 2.3 Consensus size: 123
523565 GAATCAAGCT
* * **
523575 AAGGTCGAACAAGTTCTTCTCATTACAAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * *
523640 GAACTTTATCTGGAAATGTTGGTGATGATCTATCT-CTTTTGTGACAGAGTCATACAA
66 GAACTTTATATGGAAAAGTTGATGATGATCTATCTCCTTCTGTGACAGAGTCATACAA
* *
523697 AAGGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
* * * *
523762 TGAACTTTCTATGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
65 TGAACTTTATATGGAAAAGTTGATGATGATCTATCTCCTTCTGTGACAGAGTCATACAA
523821 AAGGTTGAACAAGCTCTTCTCATTATGAACTT-TTCT
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
523857 GGAAATGTCG
Statistics
Matches: 143, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
122 35 0.24
123 58 0.41
124 50 0.35
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTATATGGAAAAGTTGATGATGATCTATCTCCTTCTGTGACAGAGTCATACAA
Found at i:524083 original size:114 final size:114
Alignment explanation
Indices: 523835--524305 Score: 847
Period size: 114 Copynumber: 4.1 Consensus size: 114
523825 TTGAACAAGC
* *
523835 TCTTCTCATTATGAAC-TTTTCTGGAAATGTCGATCCATCGAATGATGAATTCAAACAAAAGGTT
1 TCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTT
* *
523899 TGAACAAATT-TTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGT
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
523947 TCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTT
1 TCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTT
*
524012 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGT
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
* * *
524061 TCTTCTCATTATTAACTTTTTCTGGAAACGTTGATCAATCGAATGATGAATTCAAACAAAAGGTT
1 TCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTT
*
524126 TGAACAAATTATTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
524175 TCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTT
1 TCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTT
524240 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
66 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
524289 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
524306 CTACCTGGCA
Statistics
Matches: 343, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
112 16 0.05
113 56 0.16
114 271 0.79
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (114 bp):
TCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTT
TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGT
Found at i:531419 original size:22 final size:22
Alignment explanation
Indices: 531380--531421 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
531370 GTTTGAAATA
** *
531380 AAATGTAATTATGCAAATATGC
1 AAATGTAAAAATGAAAATATGC
531402 AAATGTAAAAATGAAAATAT
1 AAATGTAAAAATGAAAATAT
531422 AAATATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (22 bp):
AAATGTAAAAATGAAAATATGC
Found at i:533057 original size:20 final size:20
Alignment explanation
Indices: 533019--533057 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
533009 ATAAATAATG
*
533019 AAAATAAAATACTTGAAAAT
1 AAAATAAAATACTTAAAAAT
533039 AAAATAAAAATA-TTAAAAA
1 AAAAT-AAAATACTTAAAAA
533058 ATAATACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATAAAATACTTAAAAAT
Found at i:533096 original size:26 final size:25
Alignment explanation
Indices: 533011--533097 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 25
533001 ACAAACAAAT
* *
533011 AAATAATGAAAATA-AAATACT-TGA
1 AAATAAT-AATATATAAATATTATGA
*
533035 AAATAA-AATA-A-AAATATTA-AA
1 AAATAATAATATATAAATATTATGA
*
533056 AAATAATACACATATAAATATTATGA
1 AAATAATA-ATATATAAATATTATGA
533082 AAATAATAAGTATATA
1 AAATAATAA-TATATA
533098 TAAAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
21 14 0.28
22 4 0.08
23 2 0.04
24 7 0.14
25 9 0.18
26 14 0.28
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (25 bp):
AAATAATAATATATAAATATTATGA
Found at i:533112 original size:28 final size:26
Alignment explanation
Indices: 533042--533112 Score: 61
Period size: 28 Copynumber: 2.6 Consensus size: 26
533032 TGAAAATAAA
*
533042 ATAAAAATATTAAAAAATAATACACAT
1 ATAAAAAT-TTTAAAAATAATACACAT
* * * * *
533069 ATAAATATTATGAAAATAATAAGTATAT
1 ATAAAAATTTTAAAAATAAT-A-CACAT
533097 ATAAAAATTTTAAAAA
1 ATAAAAATTTTAAAAA
533113 GAAAGAATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
26 9 0.27
27 8 0.24
28 16 0.48
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
ATAAAAATTTTAAAAATAATACACAT
Found at i:533751 original size:20 final size:19
Alignment explanation
Indices: 533726--533779 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
533716 TTAATAAAAC
*
533726 ATTTATTAAAAATATATAT
1 ATTTATTAAAAATATAAAT
533745 AATTTA-TAAAAAGTA-AAAT
1 -ATTTATTAAAAA-TATAAAT
533764 ATTTATTTAAAAATAT
1 ATTTA-TTAAAAATAT
533780 CAGAAAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 11 0.38
20 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTATTAAAAATATAAAT
Found at i:535561 original size:3 final size:3
Alignment explanation
Indices: 535553--535663 Score: 80
Period size: 3 Copynumber: 37.0 Consensus size: 3
535543 CTGTAATATG
* * * * *
535553 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAG TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
535598 TAA TAA TTA TTA TAA CAA TTA TAA TAA TAA TTA TAA CAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
535646 TAA AAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
535664 AACGGGCAAA
Statistics
Matches: 82, Mismatches: 24, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
2 2 0.02
3 78 0.95
4 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:535654 original size:21 final size:21
Alignment explanation
Indices: 535579--535654 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
535569 TAATAAAAAT
* *
535579 ATAATAATAGTAATAATTATA
1 ATAATAATAATAACAATTATA
* *
535600 ATAATTATTATAACAATTATA
1 ATAATAATAATAACAATTATA
*
535621 ATAATAATTATAACAATTATA
1 ATAATAATAATAACAATTATA
*
535642 ATAATAAAAATAA
1 ATAATAATAATAA
535655 TAAAAATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (21 bp):
ATAATAATAATAACAATTATA
Found at i:536665 original size:39 final size:39
Alignment explanation
Indices: 536585--536691 Score: 146
Period size: 39 Copynumber: 2.8 Consensus size: 39
536575 CTCATAAACA
* *
536585 AAAACTCTCTAACATCC-AAGA-ACTTTTAAGTTCACAAT
1 AAAACACTCTAAC-TCCTAAGAGACTCTTAAGTTCACAAT
*
536623 AAAACACTCTAACTCCTAAGAGACTCTTAATTTCACAAT
1 AAAACACTCTAACTCCTAAGAGACTCTTAAGTTCACAAT
**
536662 AAAACACTCTAACTTTTAAGAGACTCTTAA
1 AAAACACTCTAACTCCTAAGAGACTCTTAA
536692 ATTCCCCCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
37 3 0.05
38 16 0.26
39 43 0.69
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (39 bp):
AAAACACTCTAACTCCTAAGAGACTCTTAAGTTCACAAT
Found at i:537924 original size:32 final size:32
Alignment explanation
Indices: 537883--537990 Score: 91
Period size: 32 Copynumber: 3.4 Consensus size: 32
537873 CGGGGGAATG
*
537883 CTCGACGTCTTCAAGCATGGGAAAATGGATCT
1 CTCGGCGTCTTCAAGCATGGGAAAATGGATCT
* * **
537915 CTCAGCGTCTTCTATGCACGCTCGGGGGAAT-G----
1 CTCGGCGTCTTC-AAGCA---T-GGGAAAATGGATCT
537947 CTCGGCGTCTTCAAGCATGGGAAAATGGATCT
1 CTCGGCGTCTTCAAGCATGGGAAAATGGATCT
537979 CTCGGCGTCTTC
1 CTCGGCGTCTTC
537991 CATTCAAAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 20
0.66 0.10 0.23
Matches are distributed among these distances:
27 6 0.11
28 2 0.04
31 4 0.07
32 33 0.58
33 4 0.07
36 2 0.04
37 6 0.11
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (32 bp):
CTCGGCGTCTTCAAGCATGGGAAAATGGATCT
Found at i:537945 original size:64 final size:64
Alignment explanation
Indices: 537844--537993 Score: 264
Period size: 64 Copynumber: 2.3 Consensus size: 64
537834 CTTGCCAACT
*
537844 TGGATCTCTCGGCTTCTTCCATGCACGCTCGGGGGAATGCTCGACGTCTTCAAGCATGGGAAAA
1 TGGATCTCTCGGCGTCTTCCATGCACGCTCGGGGGAATGCTCGACGTCTTCAAGCATGGGAAAA
* * *
537908 TGGATCTCTCAGCGTCTTCTATGCACGCTCGGGGGAATGCTCGGCGTCTTCAAGCATGGGAAAA
1 TGGATCTCTCGGCGTCTTCCATGCACGCTCGGGGGAATGCTCGACGTCTTCAAGCATGGGAAAA
537972 TGGATCTCTCGGCGTCTTCCAT
1 TGGATCTCTCGGCGTCTTCCAT
537994 TCAAAGGGAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (64 bp):
TGGATCTCTCGGCGTCTTCCATGCACGCTCGGGGGAATGCTCGACGTCTTCAAGCATGGGAAAA
Found at i:541675 original size:19 final size:19
Alignment explanation
Indices: 541653--541702 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
541643 AATTTAAGTG
*
541653 TAATGATATGATTTATTAA
1 TAATGATATGATTTAATAA
*
541672 TAATGATTTAATGATTTAATAC
1 TAATGA--T-ATGATTTAATAA
541694 TAATGATAT
1 TAATGATAT
541703 AATAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 8 0.31
20 1 0.04
21 1 0.04
22 16 0.62
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (19 bp):
TAATGATATGATTTAATAA
Found at i:541685 original size:22 final size:21
Alignment explanation
Indices: 541660--541730 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 21
541650 GTGTAATGAT
541660 ATGATTTATTAATAATGATTTA
1 ATGATTTA-TAATAATGATTTA
*
541682 ATGATTTAATACTAATGATATAATA
1 ATGATTT-ATAATAATGAT-T--TA
*
541707 ATAATTTGATAATAATGATTTA
1 ATGATTT-ATAATAATGATTTA
541729 AT
1 AT
541731 AGTGATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 20 0.49
23 2 0.05
24 1 0.02
25 18 0.44
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.45
Consensus pattern (21 bp):
ATGATTTATAATAATGATTTA
Found at i:541697 original size:14 final size:14
Alignment explanation
Indices: 541680--541731 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
541670 AATAATGATT
*
541680 TAATGATTTAATAC
1 TAATGATTTAATAA
541694 TAATGA--T-ATAA
1 TAATGATTTAATAA
* *
541705 TAATAATTTGATAA
1 TAATGATTTAATAA
541719 TAATGATTTAATA
1 TAATGATTTAATA
541732 GTGATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 8 0.26
12 1 0.03
13 1 0.03
14 21 0.68
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:541730 original size:11 final size:11
Alignment explanation
Indices: 541668--541800 Score: 51
Period size: 11 Copynumber: 11.1 Consensus size: 11
541658 ATATGATTTA
541668 TTAATAATGA-
1 TTAATAATGAT
541678 TT--TAATGAT
1 TTAATAATGAT
541687 TTAATACTAATGAT
1 TT-A-A-TAATGAT
* *
541701 ATAATAATAATT
1 TTAATAATGA-T
541713 TGATAATAATGAT
1 T--TAATAATGAT
*
541726 TTAATAGTGAT
1 TTAATAATGAT
*
541737 TTAATCA-GTATT
1 TTAATAATG-A-T
541749 TGATAATAAT-AT
1 T--TAATAATGAT
541761 TACTAATAATGAT
1 T--TAATAATGAT
541774 TTGAACTTTAATGAT
1 TT-AA---TAATGAT
541789 TTAATAATGAT
1 TTAATAATGAT
541800 T
1 T
541801 ACTACTAATT
Statistics
Matches: 94, Mismatches: 10, Indels: 37
0.67 0.07 0.26
Matches are distributed among these distances:
8 6 0.06
9 2 0.02
10 3 0.03
11 29 0.31
12 15 0.16
13 7 0.07
14 23 0.24
15 9 0.10
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (11 bp):
TTAATAATGAT
Found at i:542064 original size:35 final size:35
Alignment explanation
Indices: 542024--542090 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
542014 TAATGATATG
*
542024 ATTTAATGATTT-ACTATTAATAATTTAATAATAAT
1 ATTTAATGATTTGA-TAGTAATAATTTAATAATAAT
*
542059 ATTTAATGATTTGATAGTAATGATTTAATAAT
1 ATTTAATGATTTGATAGTAATAATTTAATAAT
542091 GAGTTGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (35 bp):
ATTTAATGATTTGATAGTAATAATTTAATAATAAT
Found at i:542070 original size:21 final size:22
Alignment explanation
Indices: 542040--542090 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
542030 TGATTTACTA
542040 TTAATAATTTAATAATAAT-AT
1 TTAATAATTTAATAATAATGAT
* * *
542061 TTAATGATTTGATAGTAATGAT
1 TTAATAATTTAATAATAATGAT
542083 TTAATAAT
1 TTAATAAT
542091 GAGTTGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (22 bp):
TTAATAATTTAATAATAATGAT
Found at i:542081 original size:14 final size:14
Alignment explanation
Indices: 542062--542138 Score: 67
Period size: 14 Copynumber: 5.8 Consensus size: 14
542052 TAATAATATT
*
542062 TAATGATTTGATAG
1 TAATGATTTGATAA
542076 TAATGA-TT--TAA
1 TAATGATTTGATAA
*
542087 TAATGAGTTGATAA
1 TAATGATTTGATAA
*
542101 TAAT-AGTTGAATAA
1 TAATGATTTG-ATAA
542115 TAATGA-TT-ACTAA
1 TAATGATTTGA-TAA
542128 TAATGATTTGA
1 TAATGATTTGA
542139 ACTTTAATGA
Statistics
Matches: 54, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
11 8 0.15
12 3 0.06
13 16 0.30
14 25 0.46
15 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.16, T:0.40
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:542092 original size:11 final size:11
Alignment explanation
Indices: 542027--542161 Score: 51
Period size: 14 Copynumber: 10.7 Consensus size: 11
542017 TGATATGATT
542027 TAATGATTTACTA
1 TAATGATTTA--A
*
542040 TTAATAATTTAA
1 -TAATGATTTAA
*
542052 TAATAATATT--
1 TAATGAT-TTAA
542062 TAATGATTTGATA
1 TAATGATTT-A-A
542075 GTAATGATTTAA
1 -TAATGATTTAA
542087 TAATGAGTTGATAA
1 TAATGA-TT--TAA
542101 TAAT-AGTTGAATAA
1 TAATGA-TT---TAA
542115 TAATGATTACTAA
1 TAATGATT--TAA
542128 TAATGATTTGAA
1 TAATGATTT-AA
542140 CTTTAATGATTTAA
1 ---TAATGATTTAA
542154 TAATGATT
1 TAATGATT
542162 ACTACTAATT
Statistics
Matches: 102, Mismatches: 4, Indels: 33
0.73 0.03 0.24
Matches are distributed among these distances:
9 2 0.02
10 6 0.06
11 22 0.22
12 8 0.08
13 17 0.17
14 37 0.36
15 10 0.10
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:542113 original size:25 final size:25
Alignment explanation
Indices: 542062--542115 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
542052 TAATAATATT
* * *
542062 TAATGATTTGATAGTAATGATTTAA
1 TAATGAGTTGATAATAATGATTGAA
542087 TAATGAGTTGATAATAAT-AGTTGAA
1 TAATGAGTTGATAATAATGA-TTGAA
542112 TAAT
1 TAAT
542116 AATGATTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.41
Consensus pattern (25 bp):
TAATGAGTTGATAATAATGATTGAA
Found at i:542128 original size:13 final size:13
Alignment explanation
Indices: 542112--542170 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
542102 AATAGTTGAA
542112 TAATAATGATTAC
1 TAATAATGATTAC
542125 TAATAATGATTTGAAC
1 TAATAATGA-TT--AC
*
542141 T-TTAATGATT--
1 TAATAATGATTAC
542151 TAATAATGATTAC
1 TAATAATGATTAC
*
542164 TACTAAT
1 TAATAAT
542171 TTTATAACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
10 1 0.03
11 8 0.22
13 15 0.41
14 4 0.11
15 6 0.16
16 3 0.08
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (13 bp):
TAATAATGATTAC
Found at i:542138 original size:28 final size:28
Alignment explanation
Indices: 542084--542161 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
542074 AGTAATGATT
*
542084 TAATAATGAGTTGATAATAAT-AGTTGAA-
1 TAATAATGA-TT-ATAATAATGATTTGAAC
542112 TAATAATGATTACTAATAATGATTTGAAC
1 TAATAATGATTA-TAATAATGATTTGAAC
*
542141 T-TTAATGATT-TAATAATGATT
1 TAATAATGATTATAATAATGATT
542162 ACTACTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 12 0.27
27 9 0.20
28 23 0.51
29 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (28 bp):
TAATAATGATTATAATAATGATTTGAAC
Found at i:542217 original size:361 final size:360
Alignment explanation
Indices: 541548--542250 Score: 1085
Period size: 361 Copynumber: 1.9 Consensus size: 360
541538 ATTCGAATAT
* *
541548 ATATATATTACTTAAAGTTTAAAATGTCAATTTTAACTCCTTATTGAAATGAAATTTTTTTACTA
1 ATATATATTACTTAAAGTTTAAAATGTCAATTTTAACTCCTTAATGAAATGAAAATTTTTTACTA
* *
541613 AAGGTTTCGAACTTTAATAATAAAATACTCAATTTAAGTGTAATGATATGATTTATTAATAATGA
66 AAGGTTTCGAACTTTAATAATAAAATACTCAATTAAAGTGTAATGATATGATTTATGAATAATGA
* * *
541678 TTTAATGATTTAATACTAATGATATAATAATAATTTGATAATAATGATTTAATAGTGATTTAATC
131 TTTAATAATTTAATAATAATGATAT-ATAATAATTTGATAATAATGATTTAATAATGATTTAATC
* *
541743 AGTATTTGATAATAATATTACTAATAATGATTTGAACTTTAATGATTTAATAATGATTACTACTA
195 AATAGTTGATAATAATATTACTAATAATGATTTGAACTTTAATGATTTAATAATGATTACTACTA
* * * *
541808 ATTTTATAACATTTTTTATTTCTTAAATGTCAAAAAAATTTGTTAATTAATTTTTATAATTTTTT
260 ATTTTATAACATTTTTTATTTCTTAAATGCCAAAAAAATTTGTTAATTAATATTTATAAATTTGT
541873 AGATTATATTCGATTCAATTACTCAAATATATATAC
325 AGATTATATTCGATTCAATTACTCAAATATATATAC
*
541909 ATATTTATTACTTAAAGTTTAAAATGTCAATTTTAACTCCTTAATGAAATGAAAATTTTTTACTA
1 ATATATATTACTTAAAGTTTAAAATGTCAATTTTAACTCCTTAATGAAATGAAAATTTTTTACTA
* * * * *
541974 AAGGTTTCGAACTTTAATAGTAAAATCCTCGATTAAAGTGTAATGATATGATTTAATGATTTACT
66 AAGGTTTCGAACTTTAATAATAAAATACTCAATTAAAGTGTAATGATATGATTT-ATGA-ATAAT
* *
542039 -A-TTAATAATTTAATAATAAT-AT-T-TAATGATTTGATAGTAATGATTTAATAATGAGTTGAT
129 GATTTAATAATTTAATAATAATGATATATAATAATTTGATAATAATGATTTAATAATGA-TT--T
542099 AAT-AATAGTTGAATAATAATGATTACTAATAATGATTTGAACTTTAATGATTTAATAATGATTA
191 AATCAATAGTTG-ATAATAAT-ATTACTAATAATGATTTGAACTTTAATGATTTAATAATGATTA
* *
542163 CTACTAATTTTATAACCTTTTTTATTTCTTAAATGCCAAACAAATTTGTTAATTAATATTTATAA
254 CTACTAATTTTATAACATTTTTTATTTCTTAAATGCCAAAAAAATTTGTTAATTAATATTTATAA
542228 ATTTGTAGATTATATTCGATTCA
319 ATTTGTAGATTATATTCGATTCA
542251 TTTAAACAAT
Statistics
Matches: 312, Mismatches: 23, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
357 28 0.09
358 2 0.01
359 7 0.02
360 14 0.04
361 254 0.81
362 4 0.01
363 3 0.01
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (360 bp):
ATATATATTACTTAAAGTTTAAAATGTCAATTTTAACTCCTTAATGAAATGAAAATTTTTTACTA
AAGGTTTCGAACTTTAATAATAAAATACTCAATTAAAGTGTAATGATATGATTTATGAATAATGA
TTTAATAATTTAATAATAATGATATATAATAATTTGATAATAATGATTTAATAATGATTTAATCA
ATAGTTGATAATAATATTACTAATAATGATTTGAACTTTAATGATTTAATAATGATTACTACTAA
TTTTATAACATTTTTTATTTCTTAAATGCCAAAAAAATTTGTTAATTAATATTTATAAATTTGTA
GATTATATTCGATTCAATTACTCAAATATATATAC
Found at i:542304 original size:23 final size:22
Alignment explanation
Indices: 542269--542345 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
542259 ATTAATCCAT
* *
542269 TAATTTATTAATTTATACAAAAA
1 TAATATATGAATTTA-ACAAAAA
*
542292 TAATATATGAA-TTAAC--AAT
1 TAATATATGAATTTAACAAAAA
* * *
542311 TAATCTATTAATTTAAACAAGAA
1 TAATATATGAATTT-AACAAAAA
542334 TAATATATGAAT
1 TAATATATGAAT
542346 AAAATATTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 11 0.27
20 2 0.05
21 5 0.12
22 3 0.07
23 20 0.49
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (22 bp):
TAATATATGAATTTAACAAAAA
Found at i:542320 original size:42 final size:43
Alignment explanation
Indices: 542258--542345 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 43
542248 TCATTTAAAC
* * *
542258 AATTAATCCATTAATTTATTAATTTATACAAAAATAATATATG
1 AATTAATCAATTAATCTATTAATTTAAACAAAAATAATATATG
*
542301 AATTAA-CAATTAATCTATTAATTTAAACAAGAATAATATATG
1 AATTAATCAATTAATCTATTAATTTAAACAAAAATAATATATG
542343 AAT
1 AAT
542346 AAAATATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 35 0.85
43 6 0.15
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (43 bp):
AATTAATCAATTAATCTATTAATTTAAACAAAAATAATATATG
Found at i:542348 original size:21 final size:20
Alignment explanation
Indices: 542288--542348 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
542278 AATTTATACA
*
542288 AAAATAATATATGAATTAAC
1 AAAATAATATATGAATAAAC
* * *
542308 -AATTAATCTATTAATTTAAAC
1 AAAATAATATATGAA--TAAAC
542329 AAGAATAATATATGAATAAA
1 AA-AATAATATATGAATAAA
542349 ATATTAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 11 0.37
21 8 0.27
22 1 0.03
23 10 0.33
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATAATATATGAATAAAC
Found at i:542355 original size:42 final size:42
Alignment explanation
Indices: 542267--542355 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
542257 CAATTAATCC
* * *
542267 ATTAATTTATTAATTTATACAAAAATAATATATGAATTAACA
1 ATTAATCTATTAATTTAAACAAAAATAATATATGAATTAAAA
*
542309 ATTAATCTATTAATTTAAACAAGAATAATATATGAA-TAAAA
1 ATTAATCTATTAATTTAAACAAAAATAATATATGAATTAAAA
542350 TATTAA
1 -ATTAA
542356 AAACCAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (42 bp):
ATTAATCTATTAATTTAAACAAAAATAATATATGAATTAAAA
Found at i:545129 original size:20 final size:20
Alignment explanation
Indices: 545104--545141 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
545094 CAATTTATTC
545104 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
545124 ATTGGTGCATCGATGCAT
1 ATTGGTGCATCGATGCAT
545142 TCCTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:546438 original size:83 final size:79
Alignment explanation
Indices: 546289--546469 Score: 272
Period size: 82 Copynumber: 2.2 Consensus size: 79
546279 TCCCATACTG
* * *
546289 AAGAAGACGCCAAGAAATCCTACTTCAATCATGCATGATTCCACGCCTGCAAAATCTGCTCACGT
1 AAGAAGACGCCAAGAAATCCCACTTCAAGCATGCATGATTCCACGCCTACAAAATCTGCTCACGT
*
546354 CCAGGCCCTCCTCATGT
66 CCAGG-CC-CC-CATGC
* *
546371 AAGAAGACGCCGAGAAATCCCACTTCAAGCATGCATGATTCCCACGCCTACGAAATCTGCTCACG
1 AAGAAGACGCCAAGAAATCCCACTTCAAGCATGCATGATT-CCACGCCTACAAAATCTGCTCACG
546436 TCCAGGCCCCCATGC
65 TCCAGGCCCCCATGC
546451 AAGAAGACGCCAAGAAATC
1 AAGAAGACGCCAAGAAATC
546470 TATCCCCACA
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
80 22 0.24
81 2 0.02
82 39 0.43
83 28 0.31
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.18
Consensus pattern (79 bp):
AAGAAGACGCCAAGAAATCCCACTTCAAGCATGCATGATTCCACGCCTACAAAATCTGCTCACGT
CCAGGCCCCCATGC
Found at i:546506 original size:27 final size:29
Alignment explanation
Indices: 546446--546510 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 29
546436 TCCAGGCCCC
546446 CATGCAAGAAGACGCCAAGAAATCTATCCCCA
1 CATGCAAGAAGACGCCAAGAAA-CTA--CCCA
*
546478 CATGCAAGAAGACGCCGAGAAA-TA-CCA
1 CATGCAAGAAGACGCCAAGAAACTACCCA
546505 CATGCA
1 CATGCA
546511 TCATGACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 9 0.28
30 2 0.06
32 21 0.66
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (29 bp):
CATGCAAGAAGACGCCAAGAAACTACCCA
Found at i:547359 original size:28 final size:28
Alignment explanation
Indices: 547326--547381 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
547316 ACTTCCGTTG
547326 CTTTCAAG-AATTGACTCGACGATATAAT
1 CTTTCAAGTAA-TGACTCGACGATATAAT
* *
547354 CTTTCAAGTAATGACTTGATGATATAAT
1 CTTTCAAGTAATGACTCGACGATATAAT
547382 GTAAACGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (28 bp):
CTTTCAAGTAATGACTCGACGATATAAT
Found at i:547886 original size:18 final size:20
Alignment explanation
Indices: 547860--547896 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
547850 GTGTCGGGCT
547860 TATAAATTT-TTTT-AAAAA
1 TATAAATTTATTTTCAAAAA
*
547878 TATATATTTATTTTCAAAA
1 TATAAATTTATTTTCAAAA
547897 CTTTATATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 4 0.25
20 4 0.25
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATAAATTTATTTTCAAAAA
Found at i:548570 original size:23 final size:23
Alignment explanation
Indices: 548527--548571 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
548517 ACATATTAGA
**
548527 TAGCGCTTATATAATGTAATAGG
1 TAGCGCTTATATAATAAAATAGG
548550 TAGCGCTTATATAATAAAATAG
1 TAGCGCTTATATAATAAAATAG
548572 ACATTTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGCGCTTATATAATAAAATAGG
Found at i:548632 original size:87 final size:87
Alignment explanation
Indices: 548486--548648 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
548476 AATGTTATAT
548486 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATATAATGTAATAGGT
548551 AGCGCTTATATAATAAAATAGA
66 AGCGCTTATATAATAAAATAGA
* * *
548573 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATATAATGTAATAGGT
548638 AGCGCTTATAT
66 AGCGCTTATAT
548649 TGACCTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGA
Found at i:552319 original size:251 final size:252
Alignment explanation
Indices: 551875--552367 Score: 678
Period size: 251 Copynumber: 2.0 Consensus size: 252
551865 GGTTTCGATG
*
551875 CTTTTGGGATCGACACATTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCA
1 CTTTTGGGATCGACACATTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCA
* * * * *
551940 TTATGGACAAAAATTATCAACACTATATTAATAAGTGTCGATACATATTATAGACCTATTCTCTC
66 TTATGGACAAAAAGTATCAACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTC
*
552005 ATAAAACCAGTATATGTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTT
131 ATAAAACCAGTATATGTATACCGGTTATATTACAAAATTACCCATTACATTATAATTATGGGTTT
552070 CGAT-ATTTTTGGGATCGACACTTTTAATAAAT-GTATCGACACTTTATGCGTGCAACC
196 CGATGATTTTTGGG-TCGACACTTTTAATAAATAG-ATCGACACTTTATGCGTGCAACC
* *
552127 CTTTT-GGATCGACAC-TCTATGAAAATGTATCGACACTTTGTAG-GTTCCCCCCTTTTTGGCAT
1 CTTTTGGGATCGACACAT-TATGAAAATGTATCGACACTTTAT-GCGTT-CACCCTTTTTGGCAT
* * * * *
552189 CCATTTTGGACAAAACGTATCGACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATT-T
63 CCATTATGGACAAAAAGTATCAACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCT
* *
552253 TTCATAAAACC-GATATATTTATACCGGTTATATTGA-AAAATTACCCATTACATTATAATTATG
128 CTCATAAAACCAG-TATATGTATACCGGTTATATT-ACAAAATTACCCATTACATTATAATTATG
* ** * *
552316 GGTTTCGATGTTTTTTGGGTCGTTACTTTTTATATATAGATCGACACTTTAT
191 GGTTTCGATGATTTTTGGGTCGACACTTTTAATAAATAGATCGACACTTTAT
552368 AGGAAACTTT
Statistics
Matches: 213, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
250 2 0.01
251 128 0.60
252 83 0.39
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (252 bp):
CTTTTGGGATCGACACATTATGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCA
TTATGGACAAAAAGTATCAACACAATACTAATAAGTGTCGATAAATATTATAGACATATTCTCTC
ATAAAACCAGTATATGTATACCGGTTATATTACAAAATTACCCATTACATTATAATTATGGGTTT
CGATGATTTTTGGGTCGACACTTTTAATAAATAGATCGACACTTTATGCGTGCAACC
Found at i:555856 original size:33 final size:33
Alignment explanation
Indices: 555819--555884 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
555809 CATCTTAAGA
*
555819 TCACCCCAT-AACACCTCAATTTCTTTCACCACT
1 TCACCCC-TCAACACCTCAACTTCTTTCACCACT
*
555852 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
555885 CCATCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:555943 original size:21 final size:21
Alignment explanation
Indices: 555918--555961 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
555908 CCCCTTATGC
555918 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
555939 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
555960 CT
1 CT
555962 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:557966 original size:21 final size:21
Alignment explanation
Indices: 557937--558012 Score: 116
Period size: 21 Copynumber: 3.6 Consensus size: 21
557927 AACTACCAAA
*
557937 GTGTTGATACTTTTATGTCAG
1 GTGTCGATACTTTTATGTCAG
*
557958 GTGTCGATACTTTTATATCAG
1 GTGTCGATACTTTTATGTCAG
* *
557979 TTGTCGATACTTTTATGTTAG
1 GTGTCGATACTTTTATGTCAG
558000 GTGTCGATACTTT
1 GTGTCGATACTTT
558013 CGATAGGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.47
Consensus pattern (21 bp):
GTGTCGATACTTTTATGTCAG
Found at i:558150 original size:20 final size:19
Alignment explanation
Indices: 558105--558150 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
558095 CCGATAGCGC
*
558105 TTTACTGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
558124 TGATACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCAT-TT
558145 TTTACC
1 TTTACC
558151 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:558265 original size:123 final size:123
Alignment explanation
Indices: 558079--558304 Score: 330
Period size: 123 Copynumber: 1.8 Consensus size: 123
558069 TTAAAGTATC
* * *
558079 GACACTTTCAATATATCCGATAGCGCTTTACTGGTTTTATCATTTTGATACCGGTTTTATCATAT
1 GACACTTTAAATATATCCGATAGCGCTTTACCGGTATTATCATTTTGATACCGGTTTTATCATAT
* *
558144 TTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTATA
66 TTTTACCTGTTATATCGATATGGATCGATACATTTTTATAAAGTATCGACACTTTATA
* * * *
558202 GACACTTTAAATATATCCGGTAGGGCTTTACCGGTATTGTC-TTTTCG-TGACCGGTTTTGTCAT
1 GACACTTTAAATATATCCGATAGCGCTTTACCGGTATTATCATTTT-GAT-ACCGGTTTTATCAT
*
558265 ATTTTTACCTGTTATATTGATATGGATCGATACATTTTTA
64 ATTTTTACCTGTTATATCGATATGGATCGATACATTTTTA
558305 ATTTGGATCG
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
122 5 0.05
123 86 0.95
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (123 bp):
GACACTTTAAATATATCCGATAGCGCTTTACCGGTATTATCATTTTGATACCGGTTTTATCATAT
TTTTACCTGTTATATCGATATGGATCGATACATTTTTATAAAGTATCGACACTTTATA
Found at i:558582 original size:29 final size:29
Alignment explanation
Indices: 558540--558627 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
558530 TGGTTATTGA
558540 ACCTATCAAAGTTGAGTTTAACAACACTG
1 ACCTATCAAAGTTGAGTTTAACAACACTG
* *
558569 ACCTATTAAAGTTGAGTTTAACAACACCG
1 ACCTATCAAAGTTGAGTTTAACAACACTG
558598 ACCTATCAAAGTTGAGTTTAACAACACTG
1 ACCTATCAAAGTTGAGTTTAACAACACTG
558627 A
1 A
558628 TGTTAGAGAG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (29 bp):
ACCTATCAAAGTTGAGTTTAACAACACTG
Found at i:559174 original size:12 final size:12
Alignment explanation
Indices: 559159--559190 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
559149 CAAAAAAGTA
559159 AATATAAAAAAT
1 AATATAAAAAAT
559171 AATATAAAAAAT
1 AATATAAAAAAT
*
559183 AATTTAAA
1 AATATAAA
559191 TTGGTTAATC
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:561809 original size:116 final size:116
Alignment explanation
Indices: 561634--561928 Score: 446
Period size: 116 Copynumber: 2.5 Consensus size: 116
561624 TTAATTAAAA
* * * * *
561634 TATTTATTTTGATTGTACAAATTAAACTGTATTCGAGTGATTTGGTAAGTTTAATTTAAATTTTC
1 TATTTATTTTGATTTTACATATTAAA-TTTATTAGAGTGGTTTGGTAAGTTTAATTTAAATTTTC
561699 GTGTAATTTTTAATATAATTTTTGTTTTTAATTTAAATTATAATTATTAGAC
65 GTGTAATTTTTAATATAATTTTTGTTTTTAATTTAAATTATAATTATTAGAC
*
561751 TATTTATTTTGATTTTACATATTAAATTTATTAAAGTGGTTTGGTAAGTTTAATTTAAATTTTCG
1 TATTTATTTTGATTTTACATATTAAATTTATTAGAGTGGTTTGGTAAGTTTAATTTAAATTTTCG
* *
561816 TGTAATTTTTAGTATAATTTTTGTTTTTAATTTAAATTGTAATTATTAGAC
66 TGTAATTTTTAATATAATTTTTGTTTTTAATTTAAATTATAATTATTAGAC
* * * * * *
561867 TATATATTTTTATTTTACATATTAAGTTTTATTTGAGTAGTTTGGTAAGTTTAGTTTAAATT
1 TATTTATTTTGATTTTACATATTAA-ATTTATTAGAGTGGTTTGGTAAGTTTAATTTAAATT
561929 ATTTTTTATT
Statistics
Matches: 162, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
116 107 0.66
117 55 0.34
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (116 bp):
TATTTATTTTGATTTTACATATTAAATTTATTAGAGTGGTTTGGTAAGTTTAATTTAAATTTTCG
TGTAATTTTTAATATAATTTTTGTTTTTAATTTAAATTATAATTATTAGAC
Found at i:562055 original size:109 final size:111
Alignment explanation
Indices: 561938--562424 Score: 448
Period size: 109 Copynumber: 4.4 Consensus size: 111
561928 TATTTTTTAT
* * *
561938 TTTTTATTGAGTAATATAAATTATTAGACTAATTATTTTTATTTTATAGATTAAATCATATTTGA
1 TTTTTATTGAGTAATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATCATATTTGA
* * *
562003 GTGGTTTGGTAAGTTTATTTTAATTTTTATTG-TTTTGT-TTTTTG
66 GTAGTTTGGTAAGTTTAGTTTAAATTTTATTGATTTTGTATTTTTG
* *
562047 TTTCTATT--GTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAGATT-AAGCTATATT
1 TTTTTATTGAGT-AATATAAATT-ATTAGACTATTTATTTTGATTTTACAGATTAAATC-ATATT
* * * * * *
562109 CGAGTGGTTTGCTAAGCTTAATTTAAATTTTAGTGCAATTTTTAGTATAATTTTTG
63 TGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATTG--A-TTTT-G--T-ATTTTTG
* * * * **
562165 TTTTTATTTA--AAT-TATAATTATTAGATTATTTATTTTGATTTTACATATTAAGTTGTATTTG
1 TTTTTATTGAGTAATATA-AATTATTAGACTATTTATTTTGATTTTACAGATTAAATCATATTTG
* * * *
562227 AGTAGTTTGGTAAGTTTAGTTT--AGTTTA---A-ATTATATTTTTAT
65 AGTAGTTTGGTAAGTTTAGTTTAAATTTTATTGATTTTGTATTTTT-G
* * *
562269 TTTTTATTGAGTAATATAAATTATTAGACTAATTATTTTTATTTTATAGATTAAATCATATTTGA
1 TTTTTATTGAGTAATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATCATATTTGA
* * *
562334 GTAGTTTGGTAAGTTTAGTTTAAATTTTATTGTTTTATTTGTTTTTG
66 GTAGTTTGGTAAGTTTAGTTTAAATTTTATTGATTT-TGTATTTTTG
*
562381 TTTTTATTGCA--AATATAAATTAATTATACTATTTATTTTGATTT
1 TTTTTATTG-AGTAATATAAATT-ATTAGACTATTTATTTTGATTT
562425 AACAATTTTT
Statistics
Matches: 304, Mismatches: 45, Indels: 55
0.75 0.11 0.14
Matches are distributed among these distances:
103 6 0.02
104 10 0.03
106 63 0.21
107 6 0.02
108 18 0.06
109 69 0.23
111 10 0.03
112 29 0.10
113 12 0.04
114 6 0.02
116 54 0.18
117 8 0.03
118 13 0.04
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (111 bp):
TTTTTATTGAGTAATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATCATATTTGA
GTAGTTTGGTAAGTTTAGTTTAAATTTTATTGATTTTGTATTTTTG
Found at i:562213 original size:325 final size:331
Alignment explanation
Indices: 561717--562424 Score: 1103
Period size: 331 Copynumber: 2.2 Consensus size: 331
561707 TTTAATATAA
* *
561717 TTTTTGTTTTTAATT-TAAAT-TATAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATT
1 TTTTTGTTTTT-ATTGTAAATATA-AATTAATTAGACTATTTATTTTGATTTTACAGATTAAATA
* * * *
561779 TATTAAAGTGGTTTGGTAAGTTTAATTTAAATTTTCGTGTAATTTTTAGTATAATTTTTGTTTTT
64 TATTAAAGTGGTTTGCTAAGCTTAATTTAAATTTTAGTGCAATTTTTAGTATAATTTTTGTTTTT
* * *
561844 AATTTAAATTGTAATTATTAGACTATATATTTTTATTTTACATATTAAGTTTTATTTGAGTAGTT
129 AATTTAAATTATAATTATTAGACTATATATTTTGATTTTACATATTAAGTTGTATTTGAGTAGTT
561909 TGGT-A-AGTTTAGTTTAAATTAT-TTTTTATTTTTTATTGAGTAATATAAATTATTAGACTAAT
194 TGGTAATAGTTTAGTTTAAATTATATTTTTATTTTTTATTGAGTAATATAAATTATTAGACTAAT
* * *
561971 TATTTTTATTTTATAGATTAAATCATATTTGAGTGGTTTGGTAAGTTTATTTTAATTTTTATTG-
259 TATTTTTATTTTATAGATTAAATCATATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATTGT
562035 TTT-TGT-
324 TTTATGTG
* *
562041 TTTTTGTTTCTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAGATTAAGCTAT
1 TTTTTGTTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAGATTAA-ATAT
**
562106 ATTCGAGTGGTTTGCTAAGCTTAATTTAAATTTTAGTGCAATTTTTAGTATAATTTTTGTTTTT-
65 ATTAAAGTGGTTTGCTAAGCTTAATTTAAATTTTAGTGCAATTTTTAGTATAATTTTTGTTTTTA
* *
562170 ATTTAAATTATAATTATTAGATTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTT
130 ATTTAAATTATAATTATTAGACTATATATTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTT
562235 GGTAAGTTTAGTTTAGTTTAAATTATATTTTTATTTTTTATTGAGTAATATAAATTATTAGACTA
195 GGTAA---TAGTTTAGTTTAAATTATATTTTTATTTTTTATTGAGTAATATAAATTATTAGACTA
562300 ATTATTTTTATTTTATAGATTAAATCATATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATT
257 ATTATTTTTATTTTATAGATTAAATCATATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATT
*
562365 GTTTTATTTG
322 GTTTTATGTG
* *
562375 TTTTTGTTTTTATTGCAAATATAAATTAATTATACTATTTATTTTGATTT
1 TTTTTGTTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTT
562425 AACAATTTTT
Statistics
Matches: 349, Mismatches: 22, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
323 3 0.01
324 19 0.05
325 96 0.28
326 61 0.17
330 17 0.05
331 101 0.29
332 3 0.01
333 2 0.01
334 47 0.13
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (331 bp):
TTTTTGTTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAGATTAAATATA
TTAAAGTGGTTTGCTAAGCTTAATTTAAATTTTAGTGCAATTTTTAGTATAATTTTTGTTTTTAA
TTTAAATTATAATTATTAGACTATATATTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTG
GTAATAGTTTAGTTTAAATTATATTTTTATTTTTTATTGAGTAATATAAATTATTAGACTAATTA
TTTTTATTTTATAGATTAAATCATATTTGAGTAGTTTGGTAAGTTTAGTTTAAATTTTATTGTTT
TATGTG
Found at i:563579 original size:21 final size:21
Alignment explanation
Indices: 563555--563613 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
563545 ATATAATTAA
*
563555 TTTATTTAGTTT-ATTATATTT
1 TTTATTTA-TTTAATTAAATTT
563576 TTTATTTATTTAATTAAATTT
1 TTTATTTATTTAATTAAATTT
*
563597 TAGTA-TTATTTAATTAA
1 T-TTATTTATTTAATTAA
563614 TTAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 29 0.85
22 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTATTTATTTAATTAAATTT
Found at i:564529 original size:23 final size:23
Alignment explanation
Indices: 564495--564538 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
564485 ATATTAAATA
* *
564495 AAATATTGATATTATTCACATAG
1 AAATATTAATATTAATCACATAG
564518 AAATATTAATATTAATCACAT
1 AAATATTAATATTAATCACAT
564539 TTATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (23 bp):
AAATATTAATATTAATCACATAG
Found at i:564592 original size:27 final size:27
Alignment explanation
Indices: 564568--564640 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
564558 ACAAATATCC
*
564568 ATCACATTCATTCAAATATTGATATTA
1 ATCACATTCATTCAAATATTAATATTA
564595 ATCACATTCATTCAAATATTAATATTA
1 ATCACATTCATTCAAATATTAATATTA
564622 ATCACATTCATTCAAATAT
1 ATCACATTCATTCAAATAT
564641 AACATCACCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.01, T:0.40
Consensus pattern (27 bp):
ATCACATTCATTCAAATATTAATATTA
Found at i:564667 original size:90 final size:86
Alignment explanation
Indices: 564495--564655 Score: 232
Period size: 90 Copynumber: 1.8 Consensus size: 86
564485 ATATTAAATA
* * *
564495 AAATATTGATATTATTCACATAGAAATATTAATATTAATCACATTTATTCAAATATAACATCAAC
1 AAATATTGATATTAATCACATACAAATATTAATATTAATCACATTCATTCAAATATAACATCAAC
* *
564560 AAATATCCATCACATTCATTC
66 AAATAGCCATCAAATTCATTC
564581 AAATATTGATATTAATCACATTCATTCAAATATTAATATTAATCACATTCATTCAAATATAACAT
1 AAATATTGATATTAATCACA-T-A--CAAATATTAATATTAATCACATTCATTCAAATATAACAT
*
564646 CACCAAATAG
62 CAACAAATAG
564656 GCCAGAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
86 19 0.29
87 1 0.02
88 1 0.02
90 45 0.68
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.35
Consensus pattern (86 bp):
AAATATTGATATTAATCACATACAAATATTAATATTAATCACATTCATTCAAATATAACATCAAC
AAATAGCCATCAAATTCATTC
Found at i:566475 original size:20 final size:22
Alignment explanation
Indices: 566422--566476 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
566412 TATGATCTAA
* *
566422 ATTTCGATTATTTATTGCGGTT
1 ATTTGGATTATTTATTGCAGTT
566444 -TTTGG-TTGATTT-TTG-AGTT
1 ATTTGGATT-ATTTATTGCAGTT
566463 ATTTGGATTATTTA
1 ATTTGGATTATTTA
566477 GTGTTGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
19 3 0.11
20 14 0.52
21 10 0.37
ACGTcount: A:0.18, C:0.04, G:0.20, T:0.58
Consensus pattern (22 bp):
ATTTGGATTATTTATTGCAGTT
Found at i:570308 original size:11 final size:11
Alignment explanation
Indices: 570292--570319 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
570282 GTCACACCCC
570292 AAAATTTATTT
1 AAAATTTATTT
570303 AAAATTTATTT
1 AAAATTTATTT
570314 AAAATT
1 AAAATT
570320 AATTATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATTTATTT
Found at i:574544 original size:16 final size:16
Alignment explanation
Indices: 574523--574561 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
574513 AATTTGTGAC
574523 ATATTAGATTAAAATT
1 ATATTAGATTAAAATT
*
574539 ATATTAGATTAAAGTT
1 ATATTAGATTAAAATT
574555 ACTATTA
1 A-TATTA
574562 TTATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATATTAGATTAAAATT
Found at i:574700 original size:47 final size:47
Alignment explanation
Indices: 574590--574730 Score: 189
Period size: 47 Copynumber: 3.0 Consensus size: 47
574580 AAATAATTGT
* * * *
574590 TTTTAACATTTTTAGTAGAAATACTAAATC-AATATT-ATTTTAA-CA
1 TTTTAACATTTTTACTAGAAATACTAAATCAAATGTTGA-TCTAATTA
*
574635 TTTTTAAAATTTTTACTAGAAATACTAAATCAAATGTTGATCTAATTA
1 -TTTTAACATTTTTACTAGAAATACTAAATCAAATGTTGATCTAATTA
*
574683 TTTTAACATTTTTACTAGAAATACTAAATCAAATGTTGATCAAATTA
1 TTTTAACATTTTTACTAGAAATACTAAATCAAATGTTGATCTAATTA
574730 T
1 T
574731 ACTAATGATT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
46 28 0.33
47 55 0.65
48 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (47 bp):
TTTTAACATTTTTACTAGAAATACTAAATCAAATGTTGATCTAATTA
Found at i:574889 original size:16 final size:17
Alignment explanation
Indices: 574858--574889 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
574848 ATAACTACTT
574858 ATGATTAAATTATAATA
1 ATGATTAAATTATAATA
574875 ATGATTAAA-TATAAT
1 ATGATTAAATTATAAT
574890 TAAAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATGATTAAATTATAATA
Found at i:575346 original size:28 final size:28
Alignment explanation
Indices: 575313--575388 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
575303 AAATAGATAT
575313 ATTTTATTCGAATAATACTTCAAATAAA
1 ATTTTATTCGAATAATACTTCAAATAAA
* * *
575341 ATTTTATTTGAAGAATACTTTAAATAAA
1 ATTTTATTCGAATAATACTTCAAATAAA
* *
575369 GTCTTATTCGAATAATACTT
1 ATTTTATTCGAATAATACTT
575389 ACATATTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (28 bp):
ATTTTATTCGAATAATACTTCAAATAAA
Found at i:575731 original size:39 final size:39
Alignment explanation
Indices: 575677--575823 Score: 176
Period size: 39 Copynumber: 3.8 Consensus size: 39
575667 TTTCTGCATA
575677 GCCTGAAGACGCCGTGCACTCATGGAGTCTTATACATTG
1 GCCTGAAGACGCCGTGCACTCATGGAGTCTTATACATTG
*
575716 GCCTGAAGACGCCGTGCACTC-TGGAGTCTTATCCATTG
1 GCCTGAAGACGCCGTGCACTCATGGAGTCTTATACATTG
* * * *
575754 GCCTGAATACGCTGTACACTCTTGGAGTCTT-TA-AGTTTG
1 GCCTGAAGACGCCGTGCACTCATGGAGTCTTATACA--TTG
* *
575793 GCCTGAAGACGCCAG-GCAGTCATGTAGTCTT
1 GCCTGAAGACGCC-GTGCACTCATGGAGTCTT
575824 TATGTTGTTA
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.01
38 35 0.38
39 56 0.60
40 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (39 bp):
GCCTGAAGACGCCGTGCACTCATGGAGTCTTATACATTG
Found at i:576514 original size:22 final size:22
Alignment explanation
Indices: 576482--576541 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
576472 AAGGTTGAAG
*
576482 TTTT-AAATTTAAGATTTTCAA
1 TTTTAAAATTTAAGATTTTAAA
576503 TTTTAAAATTTAA-AGTTTTAAA
1 TTTTAAAATTTAAGA-TTTTAAA
* *
576525 TTTTAAGATTTATGATT
1 TTTTAAAATTTAAGATT
576542 AAAATAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 5 0.15
22 27 0.82
23 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (22 bp):
TTTTAAAATTTAAGATTTTAAA
Found at i:576528 original size:7 final size:7
Alignment explanation
Indices: 576482--576535 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
576472 AAGGTTGAAG
576482 TTTTAAA
1 TTTTAAA
576489 -TTTAAGA
1 TTTTAA-A
*
576496 TTTTCAA
1 TTTTAAA
576503 TTTTAAA
1 TTTTAAA
*
576510 ATTTAAA
1 TTTTAAA
576517 GTTTTAAA
1 -TTTTAAA
576525 TTTTAAGA
1 TTTTAA-A
576533 TTT
1 TTT
576536 ATGATTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
6 5 0.13
7 20 0.51
8 14 0.36
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.54
Consensus pattern (7 bp):
TTTTAAA
Found at i:579407 original size:109 final size:109
Alignment explanation
Indices: 579293--579541 Score: 265
Period size: 109 Copynumber: 2.3 Consensus size: 109
579283 TCCCCCTAGG
* * * *
579293 TTTAGCACGTTTTTACATTTTGGTCACCTGT-AGAGA-CCAAA-TATGTTATTTTCCCTTTTCCT
1 TTTAGCATGTTTTTACATTTTGGTCACATGTGAG-GATCCAAACCA--TTATTTTCCCTTTTACT
* *
579355 TGCATTTTATATAATTT-TTGG-TCTATTTATTGTTTAGTCCCTCTAAC
63 TGCATGTTATAT-ATTTATTGGAT-TATTTATTGTTTAGTCCCTATAAC
* * * * **
579402 TTTAGCGTGTTTTTGCATTCTGGTCATATGTGAGGATTGAAACCATTATTTTCCCTTTTACTTGC
1 TTTAGCATGTTTTTACATTTTGGTCACATGTGAGGATCCAAACCATTATTTTCCCTTTTACTTGC
* *
579467 ATGTTATGTATTTATTGGATTATTTATTGTTTAGTCCCTATAAG
66 ATGTTATATATTTATTGGATTATTTATTGTTTAGTCCCTATAAC
* * *
579511 TTTAGCTTGTTTTTACACTTTGGTCAGATGT
1 TTTAGCATGTTTTTACATTTTGGTCACATGT
579542 AGTGACTGTT
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
108 4 0.03
109 105 0.91
110 6 0.05
111 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.49
Consensus pattern (109 bp):
TTTAGCATGTTTTTACATTTTGGTCACATGTGAGGATCCAAACCATTATTTTCCCTTTTACTTGC
ATGTTATATATTTATTGGATTATTTATTGTTTAGTCCCTATAAC
Found at i:584032 original size:3 final size:3
Alignment explanation
Indices: 584024--584064 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
584014 TTAAACCAAA
584024 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
584065 ATAAATAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:584069 original size:4 final size:4
Alignment explanation
Indices: 584060--584085 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
584050 TAATAATAAT
584060 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
584086 GATGGGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:584333 original size:40 final size:41
Alignment explanation
Indices: 584281--584357 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
584271 TCCACTGTTT
**
584281 TTCAGGGAAGATTGAATTGGAATCGATTTGCTTCACTACTG
1 TTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTACTG
* *
584322 TTCA-GGAAGATTGAATCATAATTGATTTGCTTCACT
1 TTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACT
584358 TCATAAAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (41 bp):
TTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTACTG
Found at i:584561 original size:134 final size:134
Alignment explanation
Indices: 584311--585136 Score: 1013
Period size: 134 Copynumber: 6.2 Consensus size: 134
584301 AATCGATTTG
* * * * * *
584311 CTTCACTACTGTTCA-GGAAGATTGAATCATAATTGATTTGCTTCACT--TCAT-A--AAGATCA
1 CTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCA
* ** * *
584370 AATCTGAAAG-AGCAAAAACCTGCTCCACTACCCTTTAGGGGAGGTCAGACTCGAGAAAAGTTTG
66 AATCTGAAAGAAG-AAGAATATGCTCCACTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTG
*
584434 ACCCA
130 ATCCA
* * * * * * *
584439 TTTCTCTTCTCTTTAGGGAAGATTAAATCAGAATCGATTTGCTTCGCTGCTCTTCAGGAATACCA
1 CTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCA
* * *
584504 AATCTAAAAGAAGAAGAATATGCTCCAGTACACTTTAGGGGAGGTCAGACTCGAGAAAACTTTGA
66 AATCTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTGA
584569 TCCA
131 TCCA
* * * * * *
584573 CTTCACTGCTATTTAGGGAAGATTGAATCATAATCGATTTACTTTC-CTGCGCTTCAAGAAGACC
1 CTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGC-TTCACTGCTCTTCAGGAAGACC
* * * ** * *
584637 AAATCTGAAAGAAAAAGAATCTGCTCCACTACTCTTTAGGGGCGACCAGACTCGAGAAATCTTCG
65 AAATCTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTG
*
584702 TTCCA
130 ATCCA
* * * **
584707 CTTCACTGCTCTTCAGGGAAGATTGAATCAAAATCTATTTTCTTCGTTGCTCTTCAGGAAGACCA
1 CTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCA
* * * * *
584772 AATCTGAAAGAAAAAGAATATGCTCCACTACACTTTAGGGGAGATCAGACTTGAGAAATCTTTGA
66 AATCTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTGA
584837 TCCA
131 TCCA
*
584841 CTTCACTGGTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCA
1 CTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCA
* * * *
584906 AATTTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGAGGCCAGACTCGAGAAAACTTTAA
66 AATCTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTGA
584971 TCCA
131 TCCA
* * * *
584975 CTTCACTGCTCTTCAGGGAAGATTGAATC-GAAATTGATTTGCTTTACTTCTCTTGAGGAAGACC
1 CTTCACTGCTCTTCAGGGAAGATTGAATCAG-AATCGATTTGCTTCACTGCTCTTCAGGAAGACC
* * *
585039 AAATATGAAAGAAGAAGAATATGCTCCACTACTCTTTACGGGAGGTCAGACTCAAGAAAACTTTG
65 AAATCTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTG
585104 ATCCA
130 ATCCA
* * *
585109 CTTCACTACTCTTCAGGAAAAATTGAAT
1 CTTCACTGCTCTTCAGGGAAGATTGAAT
585137 ATGAAAATCA
Statistics
Matches: 603, Mismatches: 85, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
128 10 0.02
129 28 0.05
131 3 0.00
132 1 0.00
133 4 0.01
134 552 0.92
135 5 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (134 bp):
CTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCA
AATCTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGGGGAGGTCAGACTCGAGAAAACTTTGA
TCCA
Found at i:585765 original size:50 final size:51
Alignment explanation
Indices: 585640--585774 Score: 157
Period size: 50 Copynumber: 2.7 Consensus size: 51
585630 ATTTAAGACA
* * * * *
585640 ACATTACTAAAAGATTAACTTCTCTACATGAGAAAGTTACGTTGAGGAAAG
1 ACATTACTAAAAGATTGACTTCTCTTCATGAGAAAATTAAGCTGAGGAAAG
* * * *
585691 ATACTACTAAAA-ATTGACTCCTCTTCATGAGAAAATTAAGCTGA-GAATG
1 ACATTACTAAAAGATTGACTTCTCTTCATGAGAAAATTAAGCTGAGGAAAG
* *
585740 ACATTACTAAAAGATCGACTTCTCTTCACGAGAAA
1 ACATTACTAAAAGATTGACTTCTCTTCATGAGAAA
585775 GTCAAGGAAG
Statistics
Matches: 69, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
49 14 0.20
50 45 0.65
51 10 0.14
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (51 bp):
ACATTACTAAAAGATTGACTTCTCTTCATGAGAAAATTAAGCTGAGGAAAG
Found at i:585797 original size:45 final size:44
Alignment explanation
Indices: 585745--586258 Score: 552
Period size: 45 Copynumber: 11.5 Consensus size: 44
585735 GAATGACATT
* *
585745 ACTAAAAGATCGACTTCTCTTCACGAGAAAGTCAAGGAAGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAAGACAAC
* ** *
585790 ACTAAAAGATTGATTCCTCTTCACGAGAAAGTCAAGGAAGGGAAT
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAAGACAAC
585835 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGGAAGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAAGACAAC
* *
585880 ACCAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGGTCAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA-GACAAC
** * *
585925 ACTAAAAGATTGACTCCTCTTTGCGAGAAATTCAAGAATGAAAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA-GACAAC
* * * *
585970 ACTAAAATATTGACTCCTTTTCACGAGAAAGTCAAGATTGACAAT
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA-AGACAAC
* ** * *
586015 ACTGAAAGATTGACTCCTCTTCGTGAGAAAGTAAAGAATAACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA-GACAAC
* *
586060 A-TGAAAA-AATGACTCCTCTTCATGAGAAAGTCAAGGAAGACAAC
1 ACT-AAAAGATTGACTCCTCTTCACGAGAAAGTCAA-GAAGACAAC
* * * *
586104 ACTGAAAGGTTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAAT
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA-GACAAC
* * *
586149 ACT--GAGATTGACTTCTCTTCATGAGAAAGTCAAGAAGGACAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAA-GACAAC
* * * * *
586192 ATTAAAAGATTAACTCCTCTTAATGAGAAAGTCAAGAAAGAAAAC
1 ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAG-AAGACAAC
*
586237 ACGT-AAAGATCGACTCCTCTTC
1 AC-TAAAAGATTGACTCCTCTTC
586259 GCGATAATAT
Statistics
Matches: 394, Mismatches: 63, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
43 36 0.09
44 40 0.10
45 315 0.80
46 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (44 bp):
ACTAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAGACAAC
Found at i:586318 original size:38 final size:38
Alignment explanation
Indices: 586276--586600 Score: 397
Period size: 38 Copynumber: 8.6 Consensus size: 38
586266 TATAAAAAAA
* *
586276 AACAAAGATCGACTTCTCTTCACGAGGAAGTCACGAAT
1 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT
586314 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGAA-
1 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAA-GAAT
* * *
586352 CACAAAGATTGACTTCTCTTCATGAGGAAGTCAATAAT
1 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT
* * * *
586390 AACAAATATTTACTTCTCTTCATGAGGAAGTTAAGAAT
1 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT
* * * *
586428 -ACAAATATTGATTTTTCTTAACGAGGAAGTCAAGAAT
1 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT
* * * *
586465 AACAATGATTGACTTGTCGTCACGAGGAAGTAAAGAAT
1 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT
*
586503 AACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAAT
1 AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT
* * * *
586541 AACAAAGATCGAATTCTCTTCACGA-GAGAGTTAGGAGA-
1 AACAAAGATTGACTTCTCTTCACGAGGA-AGTCAAGA-AT
586579 AACAAAGATTGACTTCTCTTCA
1 AACAAAGATTGACTTCTCTTCA
586601 TGAAGGGGTC
Statistics
Matches: 247, Mismatches: 35, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
37 35 0.14
38 208 0.84
39 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (38 bp):
AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT
Found at i:586492 original size:113 final size:114
Alignment explanation
Indices: 586276--586596 Score: 382
Period size: 113 Copynumber: 2.8 Consensus size: 114
586266 TATAAAAAAA
* *
586276 AACAAAGA-TCGACTTCTCTTCACGAGGAAGTCACGAATAACAAAGATTGACTTCTCTTCACGAG
1 AACAAAGACT-GACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTAACGAG
* * * * *
586340 GAAGTCAAGGAACACAAAGATTGACTTCTCTTCATGAGGAAGTCAATAAT
65 GAAGTCAAGGAAAACAAAGATTGACTTCTCGTCACGAGGAAGTAAAGAAT
* * * * * * * *
586390 AACAAATATTTACTTCTCTTCATGAGGAAGTTAAGAAT-ACAAATATTGATTTTTCTTAACGAGG
1 AACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTAACGAGG
* *
586454 AAGTCAA-GAATAACAATGATTGACTTGTCGTCACGAGGAAGTAAAGAAT
66 AAGTCAAGGAA-AACAAAGATTGACTTCTCGTCACGAGGAAGTAAAGAAT
* * *
586503 AACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAATTCTCTTCACGA-G
1 AACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTAACGAGG
*
586567 AGAGT-TAGGAGAAACAAAGATTGACTTCTC
66 A-AGTCAAGGA-AAACAAAGATTGACTTCTC
586597 TTCATGAAGG
Statistics
Matches: 172, Mismatches: 29, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
112 3 0.02
113 96 0.56
114 71 0.41
115 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (114 bp):
AACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTAACGAGG
AAGTCAAGGAAAACAAAGATTGACTTCTCGTCACGAGGAAGTAAAGAAT
Found at i:586573 original size:151 final size:151
Alignment explanation
Indices: 586275--586590 Score: 404
Period size: 151 Copynumber: 2.1 Consensus size: 151
586265 ATATAAAAAA
* * * * * *
586275 AAACAAAGATCGACTTCTCTTCACGAGGAAGTCACGAATAACAAAGATTGACTTCTCTTCACGAG
1 AAACAAAGATTGATTTTTCTTAACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCGTCACGAG
* * * * * * ** *
586340 GAAGTCAAGGAACACAAAGATTGACTTCTCTTCATGAGGAAGTCAATAATAACAAATATTTACTT
66 GAAGTCAAAGAAAACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAATT
*
586405 CTCTTCATGAGGAAGTTA-AG
131 CTCTTCACGAGGAAGTTAGAG
* * *
586425 AATACAAATATTGATTTTTCTTAACGAGGAAGTCAAGAATAACAATGATTGACTTGTCGTCACGA
1 AA-ACAAAGATTGATTTTTCTTAACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCGTCACGA
586490 GGAAGT-AAAGAATAACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAA
65 GGAAGTCAAAGAA-AACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAA
586554 TTCTCTTCACGA-GAGAGTTAGGAG
129 TTCTCTTCACGAGGA-AGTTA-GAG
586578 AAACAAAGATTGA
1 AAACAAAGATTGA
586591 CTTCTCTTCA
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
150 9 0.06
151 118 0.84
152 10 0.07
153 4 0.03
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (151 bp):
AAACAAAGATTGATTTTTCTTAACGAGGAAGTCAAGAATAACAAAGATTGACTTCTCGTCACGAG
GAAGTCAAAGAAAACAAAGACTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATCGAATT
CTCTTCACGAGGAAGTTAGAG
Found at i:588116 original size:27 final size:27
Alignment explanation
Indices: 588085--588138 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
588075 TTTTCTCTCA
588085 TTTTTTTAT-TTTTTTTTATATATTTTC
1 TTTTTTT-TCTTTTTTTTATATATTTTC
*
588112 TTTTTTTTCTTTTTTTTCTATATTTTC
1 TTTTTTTTCTTTTTTTTATATATTTTC
588139 CCTTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTTTTCTTTTTTTTATATATTTTC
Found at i:588129 original size:9 final size:9
Alignment explanation
Indices: 588085--588189 Score: 68
Period size: 9 Copynumber: 11.2 Consensus size: 9
588075 TTTTCTCTCA
588085 TTTTTTTAT-
1 TTTTTTT-TC
*
588094 TTTTTTTTA
1 TTTTTTTTC
* *
588103 TATATTTTC
1 TTTTTTTTC
588112 TTTTTTTTC
1 TTTTTTTTC
588121 TTTTTTTTC
1 TTTTTTTTC
**
588130 TATATTTTCCC
1 T-T-TTTTTTC
588141 TTTTCTTTTGC
1 TTTT-TTTT-C
*
588152 TATTTTTTC
1 TTTTTTTTC
*
588161 TCTTTTTTC
1 TTTTTTTTC
* *
588170 CTTTTTCTC
1 TTTTTTTTC
*
588179 CTTTTTTTC
1 TTTTTTTTC
588188 TT
1 TT
588190 CTCTCTCCTC
Statistics
Matches: 75, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
8 1 0.01
9 56 0.75
10 8 0.11
11 10 0.13
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:588137 original size:20 final size:20
Alignment explanation
Indices: 588113--588168 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
588103 TATATTTTCT
588113 TTTTTTTCTTTTTTTT-CTA
1 TTTTTTTCTTTTTTTTGCTA
**
588132 TATTTTCCCTTTTCTTTTGCTA
1 T-TTTTTTCTTTT-TTTTGCTA
588154 TTTTTTCTCTTTTTT
1 TTTTTT-TCTTTTTT
588169 CCTTTTTCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 9 0.31
21 10 0.34
22 9 0.31
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTTGCTA
Found at i:588149 original size:22 final size:22
Alignment explanation
Indices: 588120--588166 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
588110 TCTTTTTTTT
588120 CTTTT-TTTT-CTATATTTTCC
1 CTTTTCTTTTGCTATATTTTCC
* *
588140 CTTTTCTTTTGCTATTTTTTCT
1 CTTTTCTTTTGCTATATTTTCC
588162 CTTTT
1 CTTTT
588167 TTCCTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 14 0.61
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.72
Consensus pattern (22 bp):
CTTTTCTTTTGCTATATTTTCC
Found at i:592569 original size:14 final size:14
Alignment explanation
Indices: 592552--592583 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
592542 TCTTTGCATC
*
592552 ATATTCTTTATTCT
1 ATATTCTTTATTAT
592566 ATATTCTTTATTAT
1 ATATTCTTTATTAT
592580 ATAT
1 ATAT
592584 ATTCTAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTCTTTATTAT
Found at i:596047 original size:11 final size:11
Alignment explanation
Indices: 596028--596090 Score: 69
Period size: 11 Copynumber: 5.8 Consensus size: 11
596018 GCCTAAGAAA
*
596028 AAAATAAAAAG
1 AAAAGAAAAAG
596039 AAAAGAAAAAG
1 AAAAGAAAAAG
596050 AAAAAGAAGAAA-
1 -AAAAGAA-AAAG
*
596062 AAAAGAAGAA-
1 AAAAGAAAAAG
596072 AAAAG-AAAAG
1 AAAAGAAAAAG
596082 AAAAGAAAA
1 AAAAGAAAA
596091 TGAGGGTTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
9 3 0.07
10 12 0.27
11 20 0.44
12 7 0.16
13 3 0.07
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:596053 original size:17 final size:17
Alignment explanation
Indices: 596027--596090 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
596017 CGCCTAAGAA
*
596027 AAAAATAAAAAGAAAAG
1 AAAAAGAAAAAGAAAAG
596044 AAAAAGAAAAAGAAGAA-
1 AAAAAGAAAAAGAA-AAG
*
596061 AAAAAGAAGAA-AAAAG
1 AAAAAGAAAAAGAAAAG
596077 -AAAAG-AAAAGAAAA
1 AAAAAGAAAAAGAAAA
596091 TGAGGGTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.07
15 11 0.27
16 2 0.05
17 23 0.56
18 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAG
Found at i:596071 original size:31 final size:32
Alignment explanation
Indices: 596022--596090 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
596012 TATTACGCCT
*
596022 AAGAAAAAAATAAAAAGAAAAGA-AAAAGAAA
1 AAGAAAAAAATAAAAAGAAAAAAGAAAAGAAA
*
596053 AAGAAGAAAAA-AAGAAGAAAAAAGAAAAG-AA
1 AAGAA-AAAAATAAAAAGAAAAAAGAAAAGAAA
596084 AAGAAAA
1 AAGAAAA
596091 TGAGGGTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 22 0.65
32 10 0.29
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (32 bp):
AAGAAAAAAATAAAAAGAAAAAAGAAAAGAAA
Found at i:597388 original size:140 final size:140
Alignment explanation
Indices: 597136--597720 Score: 739
Period size: 140 Copynumber: 4.3 Consensus size: 140
597126 TAGACCAATC
* * * *
597136 AACATTTCCAATGGAGAGTTCACAATGAGAATAACTTATTCGATAGAAGGAGAAGAAGTTCATAA
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAGAAGAAGTTCATAA
* * *
597201 TGAGAAGAACTTGTTCAACCTTAGCTCGATTTATCGTATATAGAGTTGAATCAGCGACGCCTCAC
66 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
597266 TCGAGGGATT
131 TCGAGGGATT
* * * * *
597276 AACATTTTCAGTGGAGATTTTATAATGATAAGAACTCATTCGATATAAGGAGAAGAAGTTCATAA
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAGAAGAAGTTCATAA
* * * *
597341 TGAGAAAAAATTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGGGACGCCTCAC
66 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
597406 TCGAGGGATT
131 TCGAGGGATT
* *
597416 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCA-TCTGATAG-AGAGAAAAGAAGTTCAT
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTC-GATAGAAG-GAGAAGAAGTTCAT
** * * * *
597479 AATGAGAAGAACTTGTTCAATATTTGCTCGATTCATCACATATGGAGTTGAATCAACGATGCCTC
64 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTC
597544 ACTCGAGGGATT
129 ACTCGAGGGATT
* * *
597556 AACA-TTCCAGT---GAGTTCATAAT--G-AGAA--CATCCGATAGAGGGA-AATAAGTTCATAA
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAGAAGAAGTTCATAA
* * * * * *
597611 TGAGAAGAACTTGTTCAACCTTAGCTTGATTCATTGCATATGGAGTTAAAACAGCGAAGCCTCAT
66 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
597676 TCGAGGGA-T
131 TCGAGGGATT
* *
597685 AA-ATTTCCAGTAGAGAGTTCAGAATGAGAAGAACTC
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTC
597721 GCAGCCTTAA
Statistics
Matches: 385, Mismatches: 47, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
128 1 0.00
129 10 0.03
130 74 0.19
131 9 0.02
132 12 0.03
133 4 0.01
134 2 0.01
135 4 0.01
136 11 0.03
137 1 0.00
139 10 0.03
140 247 0.64
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (140 bp):
AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
TCGAGGGATT
Found at i:598637 original size:140 final size:140
Alignment explanation
Indices: 598385--598981 Score: 813
Period size: 140 Copynumber: 4.3 Consensus size: 140
598375 TAGACCAATC
* * * * *
598385 AACATTTCCAATGGAGAGTTCACAATGAGAATAACTTATTCGATAGAAGGAGAAGAAGTTCATAA
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAAAAGAAGTTCATAA
* * *
598450 TGAGAAGAACTTGTTCAACCTTAGCTCGATTTATCGTATATAGAGTTGAATCAGCGACGCCTCAC
66 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
598515 TCGAGGGATT
131 TCGAGGGATT
* * * * * *
598525 AACATTTTCAGTGGAGATTTTATAATGATAAGAACTCATTCGATATAAGGAGAAGAAGTTCATAA
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAAAAGAAGTTCATAA
* * * *
598590 TGAGAAAAAATTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAGGGACGCCTCAC
66 TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
598655 TCGAGGGATT
131 TCGAGGGATT
*
598665 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCA-TCTGATAG-AGAGAAAAGAAGTTCAT
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTC-GATAGAAG-GAAAAGAAGTTCAT
** * * * *
598728 AATGAGAAGAACTTGTTCAATATTTGCTCGATTCATCACATATGGAGTTGAATCAACGATGCCTC
64 AATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTC
598793 ACTCGAGGGATT
129 ACTCGAGGGATT
* * * *
598805 AACATTTCCAAGT-GAGAGTTCATAATGAGAAGAAATCATCCGATAGAGGGAAAATAAGTTCATA
1 AACATTTCC-AGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAAAAGAAGTTCATA
* * * *
598869 ATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATTGCATATGGAGTTAAAACAGCGACGCCTCA
65 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCA
*
598934 TTCGAGGGATT
130 CTCGAGGGATT
* * *
598945 AATATTTCCAGTAGAGAGTTCAGAATGAGAAGAACTC
1 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTC
598982 GCAGCCTTAA
Statistics
Matches: 401, Mismatches: 50, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
139 7 0.02
140 390 0.97
141 4 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (140 bp):
AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATTCGATAGAAGGAAAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCGACGCCTCAC
TCGAGGGATT
Found at i:600471 original size:17 final size:16
Alignment explanation
Indices: 600447--600501 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
600437 AACCCTTGCA
600447 TTTA-TTTTTATTTCAT
1 TTTATTTTTTATTT-AT
*
600463 TTTATTTTTTATTTTT
1 TTTATTTTTTATTTAT
600479 TATTATTTTTTAATTT-T
1 T-TTATTTTTT-ATTTAT
600496 TTTATT
1 TTTATT
600502 GGGTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 11 0.31
17 20 0.57
18 4 0.11
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTTTTTATTTAT
Found at i:612549 original size:13 final size:13
Alignment explanation
Indices: 612531--612555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
612521 GGTCAAAGGA
612531 GGTCAACGGTCAC
1 GGTCAACGGTCAC
612544 GGTCAACGGTCA
1 GGTCAACGGTCA
612556 ACGGACGAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTCAACGGTCAC
Found at i:612552 original size:7 final size:7
Alignment explanation
Indices: 612531--612559 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
612521 GGTCAAAGGA
612531 GGTCAAC
1 GGTCAAC
612538 GGTC-AC
1 GGTCAAC
612544 GGTCAAC
1 GGTCAAC
612551 GGTCAAC
1 GGTCAAC
612558 GG
1 GG
612560 ACGAGGCCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (7 bp):
GGTCAAC
Found at i:612579 original size:24 final size:24
Alignment explanation
Indices: 612543--612598 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
612533 TCAACGGTCA
*
612543 CGGTCAACGGTCAACGGACGAGGC
1 CGGTCAACAGTCAACGGACGAGGC
612567 CGGTCAACAGTCAACGGACGAGGC
1 CGGTCAACAGTCAACGGACGAGGC
612591 CGGTCAAC
1 CGGTCAAC
612599 GGTCGGGTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.30, G:0.34, T:0.09
Consensus pattern (24 bp):
CGGTCAACAGTCAACGGACGAGGC
Found at i:616692 original size:65 final size:62
Alignment explanation
Indices: 616592--616722 Score: 183
Period size: 65 Copynumber: 2.1 Consensus size: 62
616582 AAACTCAAGT
*
616592 TTTAGGATAATATTTTAATCATTATATTTTATCTTTGTTTTA-GATATTTTAGTTTAAATAGA
1 TTTAGGATAATATTTTAATAATTATATTTTATCTTTGTTTTAGGA-ATTTTAGTTTAAATAGA
* * *
616654 TTTAGGATATTATTTTAAATAGAATTTTATTTTATCTTTGTTTTAGGAATTTTAGTTTAAATAGT
1 TTTAGGATAATATTTT-AAT--AATTATATTTTATCTTTGTTTTAGGAATTTTAGTTTAAATAGA
616719 TTTA
1 TTTA
616723 AGTGTTTTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
62 15 0.25
63 3 0.05
65 41 0.67
66 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (62 bp):
TTTAGGATAATATTTTAATAATTATATTTTATCTTTGTTTTAGGAATTTTAGTTTAAATAGA
Found at i:617424 original size:16 final size:15
Alignment explanation
Indices: 617397--617439 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
617387 TTAAAACCAC
*
617397 ATTTTTATATTTAAT
1 ATTTTAATATTTAAT
*
617412 ATTATTAATATTTATT
1 ATT-TTAATATTTAAT
*
617428 ATTTTATTATTT
1 ATTTTAATATTT
617440 TTCCTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTAATATTTAAT
Found at i:621085 original size:85 final size:85
Alignment explanation
Indices: 620983--621142 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 85
620973 TTAAACATTA
* *
620983 TATTTTATCTTTGTTTTA-GATATTTTAGTTTAAATAGATGTT-AGTATTTCAATTAGGATTTAT
1 TATTTTATCTTTGTTTTAGGA-ATTTTAATTTAAATAG-TGTTAAGTATTTCAATTAGGATTTAA
*
621046 GATATTATTTTAAATAGTATTT
64 GATATTAATTTAAATAGTATTT
* * * *
621068 TATTTTATTTTTGTTTTAGGAATTTTAATTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGA
1 TATTTTATCTTTGTTTTAGGAATTTTAATTTAAATAGTGTTAAGTATTTCAATTAGGATTTAAGA
621133 TATTAATTTA
66 TATTAATTTA
621143 GGAATTATCT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 3 0.05
85 61 0.92
86 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (85 bp):
TATTTTATCTTTGTTTTAGGAATTTTAATTTAAATAGTGTTAAGTATTTCAATTAGGATTTAAGA
TATTAATTTAAATAGTATTT
Done.