Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 93 of 204
Found at i:28358159 original size:15 final size:15
Alignment explanation
Indices: 28358141--28358189 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
28358131 ATAGGTACCA
28358141 AAAAAATGAAAATAC-
1 AAAAAA-GAAAATACG
28358156 AAAAAA-AAAATACG
1 AAAAAAGAAAATACG
*
28358170 AAAAAAGAAAA-AAG
1 AAAAAAGAAAATACG
28358184 AAAAAA
1 AAAAAA
28358190 AATATTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 7 0.23
14 14 0.45
15 10 0.32
ACGTcount: A:0.82, C:0.04, G:0.08, T:0.06
Consensus pattern (15 bp):
AAAAAAGAAAATACG
Found at i:28359285 original size:21 final size:21
Alignment explanation
Indices: 28359239--28359286 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28359229 CTAATTGTCA
* *
28359239 CTTTCGTTTATCAATTCTTTT
1 CTTTTGTTCATCAATTCTTTT
28359260 CTTTTGTTCATCAATT-TTCTT
1 CTTTTGTTCATCAATTCTT-TT
28359281 CTTTTG
1 CTTTTG
28359287 CTCCATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.12, C:0.19, G:0.06, T:0.62
Consensus pattern (21 bp):
CTTTTGTTCATCAATTCTTTT
Found at i:28363383 original size:852 final size:851
Alignment explanation
Indices: 28361049--28363605 Score: 4443
Period size: 851 Copynumber: 3.0 Consensus size: 851
28361039 TCATTTTAGG
* * *
28361049 ATCACTTCAGTGGTCAATGTAACCTCTGAGATCC-AGCTAAAACTTCTAGGTTGGGTTTTGGGGT
1 ATCACTTTAGTGGTCAATGTAACCTTTGAGATCCGA-CTGAAACTTCTAGGTTGGGTTTTGGGGT
* *
28361113 GCTATAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
65 GTTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
28361178 GATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCC
130 GATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCC
*
28361243 ACCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATGGAAAATTGAACTTATGT
195 ACCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGT
* *
28361308 TTCGTTACTATAAATTTCAGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATTTTAGGATTAT
260 TTCGTTACTATAAATTTCGGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATTTTAAGATTAT
*
28361373 GCATTGAGTTGGTGGATTCAACTTGGAATTGATCGTCAAAGAAACCACGAAAGGGTAATTGAAAC
325 GCATTGAGTTGGTGGATTCAACTTGGAATTGATCGTCAAAGAAACCGCGAAAGGGTAATTGAAAC
*
28361438 ATGGGACAAGTTGAAGCAAGTGATATGAAAGCGTTACGTTCCTTCTCATTACTATAGAGAGGTCT
390 ATGGGACAAGTTGAAGCAAGTGATACGAAAGCGTTACGTTCCTTCTCATTACTATAGAGAGGTCT
* *
28361503 CAACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTCTTGATGAGTACCTTAAGGAGATAAAG
455 CAACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTATTGATGAGTACTTTAAGGAGATAAAG
* * * * * *
28361568 ATGCTTGTGAAAAGAGCAAATATACGAGAGGATGAAGAAACTACCATCGTGTAATTTATAGATGG
520 ATGCTTATGCAAAGAGCAAATATACGAGAGGATGAAGAAACTAGCATGGTGCAATTTGTAGATGG
* *
28361633 CTTGAATGTTTCGATAGCCAATGCTTTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTAC
585 CTTGAACGTTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTAC
* *
28361698 ACAAGACAATTGAGATTGAGCAACAATTTCAGCAACATTAATCTCGTCCATTTGGCGCATCACAC
650 ACAAGACAATTGAGATTGAGCAACAATTTCAGCAGCATCAATCTCGTCCATTTGGCGCATCACAC
* * *
28361763 TATTATCGAGGTACAAGTTCTAATTCTAATTTCAACAATTTGAAACCTTCTTATGCTATTAATAA
715 TATTTTCAAGGTACAAGTTCTAATTCTACTTTCAACAATTTGAAACCTTCTTATGCTATTAATAA
*
28361828 GTTATTTCCAAAACATGTTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACATT
780 GTTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACATT
28361893 CTTCTAC
845 CTTCTAC
28361900 ATCACTTTAGTGGTCAATGTAACCTTTGAGATCCGACTGAAACTTCTAGGTTGGGTTTTGGGGTG
1 ATCACTTTAGTGGTCAATGTAACCTTTGAGATCCGACTGAAACTTCTAGGTTGGGTTTTGGGGTG
* *
28361965 TTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAATGTGTGTCTCGAGCAAATG
66 TTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
* *
28362030 ATAAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAATAATCCA
131 ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCCA
*
28362095 CCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAAAAAATTGAACTTATGTT
196 CCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTT
* *
28362160 TTGTTACTATAAATTTCGGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATGTTAAGATTATG
261 TCGTTACTATAAATTTCGGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATTTTAAGATTATG
* * * * *
28362225 CATTGAGTTAGTGGATTCAACTTGGAATTGGTTGTAAAAGAAATCGCGAAAGGGTAATTGAAACA
326 CATTGAGTTGGTGGATTCAACTTGGAATTGATCGTCAAAGAAACCGCGAAAGGGTAATTGAAACA
* *
28362290 TGGGACAAGTTGAAGCAAGTGATACGAAAGTGTTACGTTCCTTCTTATTACTATAGAGAGGTCTC
391 TGGGACAAGTTGAAGCAAGTGATACGAAAGCGTTACGTTCCTTCTCATTACTATAGAGAGGTCTC
* * * * *
28362355 AATGAGACTGCACCACCTTGTTCAAGATAATCGATCTATTGATGAGTACTTTAAGGAGATAAAAA
456 AACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTATTGATGAGTACTTTAAGGAGATAAAGA
* *
28362420 TGCTTATGCAAAGAGCAAATATATGAGAGGATGAATAAACTAGCATGGTGCAATTTGTAGATGGC
521 TGCTTATGCAAAGAGCAAATATACGAGAGGATGAAGAAACTAGCATGGTGCAATTTGTAGATGGC
28362485 TTGAACGTTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACA
586 TTGAACGTTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACA
*
28362550 CAAGACAATTGAGATTGAGCAACAATTTCAGTAGCATCAATCTCGTCCATTTGGCGCATCACACT
651 CAAGACAATTGAGATTGAGCAACAATTTCAGCAGCATCAATCTCGTCCATTTGGCGCATCACACT
*
28362615 ATTTTCAAGGTACAAGTTCTAATTCTACTTTCAACAGTTTGAAACCTTCTTATGCTATTAATAAG
716 ATTTTCAAGGTACAAGTTCTAATTCTACTTTCAACAATTTGAAACCTTCTTATGCTATTAATAAG
28362680 TTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACATTC
781 TTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACATTC
28362745 TTCTAC
846 TTCTAC
*
28362751 ATCACTTTAGTGGTCAATGTAACCTTTAAGATCCGACTGAAACTTCTAGGTTGGGTTTTGGGGTG
1 ATCACTTTAGTGGTCAATGTAACCTTTGAGATCCGACTGAAACTTCTAGGTTGGGTTTTGGGGTG
28362816 TTACAATAAGGTTGATCAGCCGT-GTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
66 TTACAATAAGGTTGATCAGCC-TCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAAT
* * *
28362880 GATGAGACTTTGGTTATTAATGACTGTATACAATATTTTTTTAGCTAAACTAAAGTTCAACAATC
130 GATGAGACTTTGGTTATTAATGACTGTATGCAACA-TTTTTTAGCTAAACCAAAGTTCAACAATC
*
28362945 CACCATTTCGAGGAAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATG
194 CACCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATG
* * * *
28363010 TTTCATTACTATAAATTTTGGGAAGAGGAGAAAGTCCAATTGGCGACCCTTGGATTTTAAGATCA
259 TTTCGTTACTATAAATTTCGGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATTTTAAGATTA
* * * *
28363075 TGCATTGAGTTGGTGGGTTTAACTTGGAATTGATCATCAAAGAAACCGCTAAAGGGTAATTGAAA
324 TGCATTGAGTTGGTGGATTCAACTTGGAATTGATCGTCAAAGAAACCGCGAAAGGGTAATTGAAA
28363140 CATGGGACAAGTTGAAGCAAGTGATACGAAAGCGTTACGTTCCTTCTCATTACTATAGAGAGGTC
389 CATGGGACAAGTTGAAGCAAGTGATACGAAAGCGTTACGTTCCTTCTCATTACTATAGAGAGGTC
* * *
28363205 TCAACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTGTTGATGAGTACTTTAAAGACATAAA
454 TCAACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTATTGATGAGTACTTTAAGGAGATAAA
* * * * *
28363270 GATGCTTACGCAAAGGGCAAATATACGAGAGGGTGAAGAAACTAGCGTGGTACAATTTGTAGATG
519 GATGCTTATGCAAAGAGCAAATATACGAGAGGATGAAGAAACTAGCATGGTGCAATTTGTAGATG
28363335 GCTTGAACGTTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTA
584 GCTTGAACGTTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTA
28363400 CACAAGACAATTGAGATTGAGCAACAATTTCAGCAGCATCAATCTCGTCCATTTGGCGCATCACA
649 CACAAGACAATTGAGATTGAGCAACAATTTCAGCAGCATCAATCTCGTCCATTTGGCGCATCACA
28363465 CTATTTTCAAGGTACAAGTTCTAATTCTACTTTCAACAATTTGAAACCTTCTTATGCTATTAATA
714 CTATTTTCAAGGTACAAGTTCTAATTCTACTTTCAACAATTTGAAACCTTCTTATGCTATTAATA
28363530 AGTTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACAT
779 AGTTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACAT
28363595 TCTTCTAC
844 TCTTCTAC
28363603 ATC
1 ATC
28363606 TTTCAAGGAA
Statistics
Matches: 1610, Mismatches: 93, Indels: 5
0.94 0.05 0.00
Matches are distributed among these distances:
851 956 0.59
852 654 0.41
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (851 bp):
ATCACTTTAGTGGTCAATGTAACCTTTGAGATCCGACTGAAACTTCTAGGTTGGGTTTTGGGGTG
TTACAATAAGGTTGATCAGCCTCGTCTTCATGTAAATAATGCTCAACGTGTGTCTCGTGCAAATG
ATGAGACTTTGGTTATTAATGACTGTATGCAACATTTTTTAGCTAAACCAAAGTTCAACAATCCA
CCATTTCGAGGGAAGTATGATCCCAAAGCATATTGTGAGTGGGAATAGAAAATTGAACTTATGTT
TCGTTACTATAAATTTCGGGAAGAGGAAAAAGTCCAATTGGCGACCCTTGGATTTTAAGATTATG
CATTGAGTTGGTGGATTCAACTTGGAATTGATCGTCAAAGAAACCGCGAAAGGGTAATTGAAACA
TGGGACAAGTTGAAGCAAGTGATACGAAAGCGTTACGTTCCTTCTCATTACTATAGAGAGGTCTC
AACGAGACTTCAACACCTTGTTCAAGGTAATCGATCTATTGATGAGTACTTTAAGGAGATAAAGA
TGCTTATGCAAAGAGCAAATATACGAGAGGATGAAGAAACTAGCATGGTGCAATTTGTAGATGGC
TTGAACGTTTCGATAGCCAATGCTCTTAATCTTCAAACCTATATTGATCTTGAGGAGATGGTACA
CAAGACAATTGAGATTGAGCAACAATTTCAGCAGCATCAATCTCGTCCATTTGGCGCATCACACT
ATTTTCAAGGTACAAGTTCTAATTCTACTTTCAACAATTTGAAACCTTCTTATGCTATTAATAAG
TTATTTCCAAAACATGCTGAGACTAAACCTTTTGAGTGGAAAAGTGGAGCTCCTACAAAACATTC
TTCTAC
Found at i:28365591 original size:14 final size:13
Alignment explanation
Indices: 28365568--28365609 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
28365558 TAATATTTGA
28365568 TTTATTATTTTAT
1 TTTATTATTTTAT
28365581 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
*
28365594 TTTAATTTTTTTAT
1 TTT-ATTATTTTAT
28365608 TT
1 TT
28365610 AACTTGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:28365607 original size:18 final size:18
Alignment explanation
Indices: 28365561--28365610 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
28365551 ATTATTCTAA
*
28365561 TATTTGATTTA-TTATTT
1 TATTTTATTTATTTATTT
*
28365578 TATTTTAGTTATTTATTT
1 TATTTTATTTATTTATTT
28365596 TAATTTT-TTTATTTA
1 T-ATTTTATTTATTTA
28365611 ACTTGGATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 14 0.50
19 5 0.18
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:28369572 original size:19 final size:21
Alignment explanation
Indices: 28369531--28369572 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
28369521 AATGTGATAT
* *
28369531 TTAAAACTATACAAATTATCA
1 TTAAAACTATACAAATAAGCA
28369552 TTAAAA-TATA-AAATAAGCA
1 TTAAAACTATACAAATAAGCA
28369571 TT
1 TT
28369573 CACTACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 4 0.21
21 6 0.32
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAACTATACAAATAAGCA
Found at i:28371891 original size:3 final size:3
Alignment explanation
Indices: 28371885--28371926 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
28371875 CCCTTTTTTT
* * *
28371885 ATA ATA ATA TTT ATA AGA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28371927 TTCAAGAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:28372157 original size:2 final size:2
Alignment explanation
Indices: 28372150--28372198 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
28372140 ATTTAATAAA
28372150 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
28372192 AT AT AT A
1 AT AT AT A
28372199 CTTACAAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28372382 original size:19 final size:18
Alignment explanation
Indices: 28372355--28372390 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28372345 CTAAACTTAT
28372355 TCATAAATTTAAAATTTAA
1 TCATAAATTT-AAATTTAA
*
28372374 TCATGAATTTAAATTTA
1 TCATAAATTTAAATTTA
28372391 TATATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
TCATAAATTTAAATTTAA
Found at i:28374246 original size:31 final size:31
Alignment explanation
Indices: 28374211--28374271 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
28374201 TTTTAAACTT
*
28374211 TATATAT-TTTTTGAAT-TTTAAATTATATA
1 TATATATATATTTGAATGTTTAAATTATATA
*
28374240 TATATATATATTTGAATGTTTAAGTTATATA
1 TATATATATATTTGAATGTTTAAATTATATA
28374271 T
1 T
28374272 TTTCGGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.25
30 8 0.29
31 13 0.46
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (31 bp):
TATATATATATTTGAATGTTTAAATTATATA
Found at i:28377855 original size:40 final size:40
Alignment explanation
Indices: 28377769--28377927 Score: 176
Period size: 40 Copynumber: 4.0 Consensus size: 40
28377759 CACACCAGTT
* * * *
28377769 TGTGGACAAGCCACCAGTATTACATATAAACTG-TCAGTAA
1 TGTGGACAAGCCACCAGAATTGCAAACAAACTGCT-AGTAA
* * *
28377809 TATGGACAAGCCACCAGAATTGCAAACAAATTGCTAGTAT
1 TGTGGACAAGCCACCAGAATTGCAAACAAACTGCTAGTAA
* * ** *
28377849 TGTGGACAAGCCACTAAAATTGCAAACAAGTTGCCAGTAA
1 TGTGGACAAGCCACCAGAATTGCAAACAAACTGCTAGTAA
* *
28377889 TGTGGACAAGCCACCAGAATTGCAGACAACCTGCTAGTA
1 TGTGGACAAGCCACCAGAATTGCAAACAAACTGCTAGTA
28377928 CTTCCTCCTT
Statistics
Matches: 99, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 98 0.99
41 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (40 bp):
TGTGGACAAGCCACCAGAATTGCAAACAAACTGCTAGTAA
Found at i:28379893 original size:8 final size:8
Alignment explanation
Indices: 28379880--28379909 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
28379870 GTTAAAATAT
28379880 ATATTATA
1 ATATTATA
28379888 ATATTATA
1 ATATTATA
28379896 ATATTATA
1 ATATTATA
28379904 ATATTA
1 ATATTA
28379910 AAACTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTATA
Found at i:28379981 original size:25 final size:25
Alignment explanation
Indices: 28379927--28379978 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
28379917 AATGTTAAGT
28379927 AAATATATTATATTATTATATATAA
1 AAATATATTATATTATTATATATAA
* *
28379952 TAATATATTATGTTATTATA-ATAA
1 AAATATATTATATTATTATATATAA
28379976 AAA
1 AAA
28379979 ATAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AAATATATTATATTATTATATATAA
Found at i:28380949 original size:40 final size:37
Alignment explanation
Indices: 28380905--28381012 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 37
28380895 ACTTTTTGTT
**
28380905 GATGAGACACTGGTGTCAATTTAGTACTTCGGATTAATTC
1 GATGAGACACTGGTGTCAA-TTA-TACTTCGG-TTAAGCC
* *
28380945 GATGAGACACTGGATGTGAATT-TACTTCGGTTTAGCC
1 GATGAGACACTGG-TGTCAATTATACTTCGGTTAAGCC
28380982 GATGAGACACTGGGTGTCAAATTATTACTTC
1 GATGAGACACT-GGTGTC-AATTA-TACTTC
28381013 AAATTATCTG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
37 18 0.31
38 14 0.24
40 21 0.36
41 5 0.09
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (37 bp):
GATGAGACACTGGTGTCAATTATACTTCGGTTAAGCC
Found at i:28382446 original size:2 final size:2
Alignment explanation
Indices: 28382439--28382470 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28382429 TTGGATGCTG
28382439 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
28382471 TTGTTGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28385691 original size:49 final size:49
Alignment explanation
Indices: 28385619--28385717 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
28385609 GCGATGTTTG
28385619 CTCAGCTCAGTATTAATGACGATTGAAGCTTATTGGCTGAATTAAAAAT
1 CTCAGCTCAGTATTAATGACGATTGAAGCTTATTGGCTGAATTAAAAAT
28385668 CTCAGCTCAGTATTAATGACGATTGAAGCTTATTGGCTGAATTAAAAAT
1 CTCAGCTCAGTATTAATGACGATTGAAGCTTATTGGCTGAATTAAAAAT
28385717 C
1 C
28385718 AAACCGGTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (49 bp):
CTCAGCTCAGTATTAATGACGATTGAAGCTTATTGGCTGAATTAAAAAT
Found at i:28386376 original size:25 final size:24
Alignment explanation
Indices: 28386348--28386398 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
28386338 ATGTTAAGTA
28386348 AATATATTATATTATTATATATAAT
1 AATATATTATATTATTAT-TATAAT
28386373 AATATATTATATTATTATTATAAT
1 AATATATTATATTATTATTATAAT
28386397 AA
1 AA
28386399 AACAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATATTATATTATTATTATAAT
Found at i:28386445 original size:20 final size:19
Alignment explanation
Indices: 28386410--28386454 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
28386400 ACAAATAAAT
*
28386410 AAAAAGAAAAAGGAAATAG
1 AAAAAGAAAAAGGAAACAG
28386429 AAAAAGAAGGAAA-GAAACAG
1 AAAAAGAA--AAAGGAAACAG
28386449 AAAAAG
1 AAAAAG
28386455 CCAAACGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 12 0.52
21 3 0.13
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAAAGGAAACAG
Found at i:28390908 original size:24 final size:24
Alignment explanation
Indices: 28390879--28390935 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
28390869 GTTATTACTG
28390879 TTTTGATGAGAACTTTGTAGGTGT
1 TTTTGATGAGAACTTTGTAGGTGT
*
28390903 TTTTGATGAGACCTTTGTAGGTGT
1 TTTTGATGAGAACTTTGTAGGTGT
28390927 TTTTGATGA
1 TTTTGATGA
28390936 AAGTTCAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.28, T:0.47
Consensus pattern (24 bp):
TTTTGATGAGAACTTTGTAGGTGT
Found at i:28403927 original size:25 final size:25
Alignment explanation
Indices: 28403893--28403945 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
28403883 TCAGTACAGT
*
28403893 CTACCTATAGTAGTCTCAATATATA
1 CTACCTATAGTAGTCTCAAGATATA
* *
28403918 CTACCTATAGTAGTTTCAGGATATA
1 CTACCTATAGTAGTCTCAAGATATA
28403943 CTA
1 CTA
28403946 TCAAAAACAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (25 bp):
CTACCTATAGTAGTCTCAAGATATA
Found at i:28409698 original size:22 final size:22
Alignment explanation
Indices: 28409673--28409717 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28409663 ATGGTTTTGT
*
28409673 GGTTATGAGCATAGGGTTTAGG
1 GGTTATGAGCATAGGGTCTAGG
* *
28409695 GGTTATGGGCTTAGGGTCTAGG
1 GGTTATGAGCATAGGGTCTAGG
28409717 G
1 G
28409718 AGTAGTGGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.07, G:0.44, T:0.31
Consensus pattern (22 bp):
GGTTATGAGCATAGGGTCTAGG
Found at i:28409781 original size:17 final size:17
Alignment explanation
Indices: 28409759--28409791 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28409749 TTATAGGTTA
28409759 GGGGTTTAGGGGTTTAC
1 GGGGTTTAGGGGTTTAC
*
28409776 GGGGTTTAGTGGTTTA
1 GGGGTTTAGGGGTTTA
28409792 GAGTTTAGGG
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:0.12, C:0.03, G:0.45, T:0.39
Consensus pattern (17 bp):
GGGGTTTAGGGGTTTAC
Found at i:28409799 original size:7 final size:7
Alignment explanation
Indices: 28409684--28409819 Score: 85
Period size: 7 Copynumber: 18.3 Consensus size: 7
28409674 GTTATGAGCA
28409684 TAGGGTT
1 TAGGGTT
*
28409691 TAGGGGT
1 TAGGGTT
*
28409698 TATGGGCT
1 TA-GGGTT
*
28409706 TAGGGTC
1 TAGGGTT
**
28409713 TAGGGAG
1 TAGGGTT
*
28409720 TAGTGGCT
1 TAG-GGTT
28409728 TAGGGTT
1 TAGGGTT
* *
28409735 TTGAGTT
1 TAGGGTT
28409742 TAAGGGTT
1 T-AGGGTT
*
28409750 TATAGG-T
1 TA-GGGTT
28409757 TAGGGGTT
1 TA-GGGTT
28409765 TAGGGGTT
1 TA-GGGTT
28409773 TACGGGGTT
1 TA--GGGTT
28409782 TAGTGGTT
1 TAG-GGTT
*
28409790 TAGAGTT
1 TAGGGTT
28409797 TAGGGTT
1 TAGGGTT
*
28409804 TATGGTT
1 TAGGGTT
28409811 TAGGGTT
1 TAGGGTT
28409818 TA
1 TA
28409820 TAATTTATGA
Statistics
Matches: 102, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
7 58 0.57
8 36 0.35
9 8 0.08
ACGTcount: A:0.17, C:0.03, G:0.40, T:0.40
Consensus pattern (7 bp):
TAGGGTT
Found at i:28409805 original size:14 final size:14
Alignment explanation
Indices: 28409779--28409976 Score: 72
Period size: 14 Copynumber: 14.4 Consensus size: 14
28409769 GGTTTACGGG
28409779 GTTTAGTGGTTTAGA
1 GTTTAG-GGTTTAGA
28409794 GTTTAGGGTTTATG-
1 GTTTAGGGTTTA-GA
*
28409808 GTTTAGGGTTTATA
1 GTTTAGGGTTTAGA
* * *
28409822 ATTTATGATTTACG-
1 GTTTAGGGTTTA-GA
28409836 GTTTTAGGG-TTA-A
1 G-TTTAGGGTTTAGA
*
28409849 -TTTAGGGTTTATA
1 GTTTAGGGTTTAGA
* ** *
28409862 GCTTAGGGTGCA-T
1 GTTTAGGGTTTAGA
* *
28409875 GTTTAGGGTATAAA
1 GTTTAGGGTTTAGA
*
28409889 GTTTAAGGTTTATG-
1 GTTTAGGGTTTA-GA
* *
28409903 GTTTAGTGTTAAGA
1 GTTTAGGGTTTAGA
*
28409917 GTTTAGTGTTTACGA
1 GTTTAGGGTTTA-GA
* *
28409932 -TTTATGGTGTAG-
1 GTTTAGGGTTTAGA
* * *
28409944 GTTTATGGTCTAGT
1 GTTTAGGGTTTAGA
** *
28409958 GTTTATTGTTTAGG
1 GTTTAGGGTTTAGA
28409972 GTTTA
1 GTTTA
28409977 AGAGGTTAAA
Statistics
Matches: 139, Mismatches: 30, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
11 7 0.05
12 3 0.02
13 23 0.17
14 92 0.66
15 14 0.10
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTAGA
Found at i:28410095 original size:23 final size:21
Alignment explanation
Indices: 28410069--28410110 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
28410059 ATTTAAGGGT
28410069 TATGCTAAAAACATAGAAAAATA
1 TATG-TAAAAA-ATAGAAAAATA
*
28410092 TATGTTAAAAATAGAAAAA
1 TATGTAAAAAATAGAAAAA
28410111 AATAAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (21 bp):
TATGTAAAAAATAGAAAAATA
Found at i:28410577 original size:115 final size:116
Alignment explanation
Indices: 28410295--28410693 Score: 344
Period size: 115 Copynumber: 3.5 Consensus size: 116
28410285 CGTTTCTACG
* * ** * * * * *
28410295 AAAAACACCGCAATTATGTTTTTTGTCTTTGTTAAACGTTGTCATTTTTATCTACGTT-TTCAGT
1 AAAAACGCCGCAATTATGTTATAAGTGTTCGCTAAACGTTGTCGTTTTTATCTACATTATT-AGT
* * * * * * * * * *
28410359 GGCGTTTTTTCCAAAACGCCGCAAAATGATATGTGTTAGTGGCATTTTCAGGT
65 GGCATTTGTACAAAAATGCCGCTAAAGGATATGTGGTAGTGGCATTTTTA-TT
* * * *
28410412 ---AACGCCGCAATTATGTTATTAACCT-TTTG-TAAACATTGTTGTTTTTATCTACATTATTAG
1 AAAAACGCCGCAATTATGTTA-TAA-GTGTTCGCTAAACGTTGTCGTTTTTATCTACATTATTAG
* * * *
28410472 TGGCATTTTTACAAAAATGCTGCTAAAGGTTATGTGGTAGTGGCGTTTTTA-T
64 TGGCATTTGTACAAAAATGCCGCTAAAGGATATGTGGTAGTGGCATTTTTATT
* * * *
28410524 AAAAATGCCGCAATTATGTTATAAGTGTTCGCTAAACGTTTTCGTTTTTATCTACGTTTTTAGTG
1 AAAAACGCCGCAATTATGTTATAAGTGTTCGCTAAACGTTGTCGTTTTTATCTACATTATTAGTG
* * * **
28410589 GCGTTTGTACTAAAATGCCGGTAAAGGATATGTTTTAGTGGCATTTTTATT
66 GCATTTGTACAAAAATGCCGCTAAAGGATATGTGGTAGTGGCATTTTTATT
* * * *
28410640 ATAAACGCCGCTATTATGTTTTAAGTGTTTGCTAAACGTTGTCGTTTTCTATCT
1 AAAAACGCCGCAATTATGTTATAAGTGTTCGCTAAACGTTGTCGTTTT-TATCT
28410694 GGGATTTTTT
Statistics
Matches: 229, Mismatches: 43, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
112 1 0.00
113 1 0.00
114 86 0.38
115 92 0.40
116 44 0.19
117 5 0.02
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.42
Consensus pattern (116 bp):
AAAAACGCCGCAATTATGTTATAAGTGTTCGCTAAACGTTGTCGTTTTTATCTACATTATTAGTG
GCATTTGTACAAAAATGCCGCTAAAGGATATGTGGTAGTGGCATTTTTATT
Found at i:28410827 original size:14 final size:14
Alignment explanation
Indices: 28410808--28410835 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28410798 CTCCACTCTG
28410808 ATTTCCCCAATTTC
1 ATTTCCCCAATTTC
28410822 ATTTCCCCAATTTC
1 ATTTCCCCAATTTC
28410836 CCATTTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTCCCCAATTTC
Found at i:28410836 original size:23 final size:22
Alignment explanation
Indices: 28410808--28410875 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
28410798 CTCCACTCTG
28410808 ATTTCCCCAATTTCATTTCCCCA
1 ATTTCCCC-ATTTCATTTCCCCA
**
28410831 ATTT-CCCATTTCCTATGCCCCCA
1 ATTTCCCCATTT-C-ATTTCCCCA
*
28410854 ACTTCCCCGATTTCATTTCCCC
1 ATTTCCCC-ATTTCATTTCCCC
28410876 CCAAATCCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 4 0.11
22 4 0.11
23 20 0.56
24 4 0.11
25 4 0.11
ACGTcount: A:0.18, C:0.43, G:0.03, T:0.37
Consensus pattern (22 bp):
ATTTCCCCATTTCATTTCCCCA
Found at i:28412103 original size:2 final size:2
Alignment explanation
Indices: 28412096--28412144 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
28412086 TTAAAAATAC
* * *
28412096 AT AT AT AT -T AT AT AT -T TT TT AA 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
28412136 AT AT AT AT A
1 AT AT AT AT A
28412145 AGCATGAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:28412529 original size:12 final size:12
Alignment explanation
Indices: 28412512--28412537 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28412502 TTCTAAATAA
28412512 TTATATATAAGC
1 TTATATATAAGC
28412524 TTATATATAAGC
1 TTATATATAAGC
28412536 TT
1 TT
28412538 GCATAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTATATATAAGC
Found at i:28412564 original size:9 final size:9
Alignment explanation
Indices: 28412552--28413277 Score: 617
Period size: 9 Copynumber: 83.4 Consensus size: 9
28412542 AACTTACATA
28412552 ATAACTTAC
1 ATAACTTAC
28412561 ATAACTTAC
1 ATAACTTAC
28412570 ATAACTTAC
1 ATAACTTAC
28412579 ATAA--TAC
1 ATAACTTAC
**
28412586 ACCACTTAC
1 ATAACTTAC
28412595 ATAACTTAC
1 ATAACTTAC
*
28412604 ATAACTTAT
1 ATAACTTAC
28412613 AT-A--TA-
1 ATAACTTAC
*
28412618 ATAACATA-
1 ATAACTTAC
28412626 ATAACTTAC
1 ATAACTTAC
*
28412635 ATAACTTAT
1 ATAACTTAC
28412644 AT-A--TA-
1 ATAACTTAC
28412649 ATAA-TATA-
1 ATAACT-TAC
*
28412657 ATAAATTAC
1 ATAACTTAC
28412666 ATAA--TAC
1 ATAACTTAC
*
28412673 ATAACTTATAT
1 ATAAC-T-TAC
*
28412684 ATAAGCTTGC
1 ATAA-CTTAC
28412694 ATAACTTAC
1 ATAACTTAC
28412703 ATAATAACTTAC
1 ---ATAACTTAC
28412715 ATAACTTAC
1 ATAACTTAC
* *
28412724 ACAAGTTAC
1 ATAACTTAC
28412733 ATAA--TAC
1 ATAACTTAC
**
28412740 ACCACTTAC
1 ATAACTTAC
28412749 ATAACTTAC
1 ATAACTTAC
*
28412758 ATAGCTTAC
1 ATAACTTAC
*
28412767 AT-TC-TAC
1 ATAACTTAC
*
28412774 ACAACTTAC
1 ATAACTTAC
*
28412783 ATAACATAC
1 ATAACTTAC
*
28412792 ATAA--TAT
1 ATAACTTAC
*
28412799 AGAACTTAC
1 ATAACTTAC
**
28412808 ATAAAATAC
1 ATAACTTAC
28412817 --AACTTAC
1 ATAACTTAC
*
28412824 ATATCTTAC
1 ATAACTTAC
28412833 ATAA--TAC
1 ATAACTTAC
28412840 ATAACTTAC
1 ATAACTTAC
28412849 ATAA--TAC
1 ATAACTTAC
*
28412856 A-ACATTTAC
1 ATA-ACTTAC
** *
28412865 ACGACTTAA
1 ATAACTTAC
*
28412874 ATAACTTAT
1 ATAACTTAC
*
28412883 ATAACTTGC
1 ATAACTTAC
*
28412892 ATAACTTAT
1 ATAACTTAC
*
28412901 ATAA-TAAC
1 ATAACTTAC
*
28412909 ATAA-TAAC
1 ATAACTTAC
28412917 -TAACATAATAC
1 ATAAC-T--TAC
*
28412928 ATAACCTAC
1 ATAACTTAC
28412937 ATAACTTAC
1 ATAACTTAC
28412946 ATAACTTAC
1 ATAACTTAC
* *
28412955 ATAAATTAA
1 ATAACTTAC
28412964 ATAACTTAC
1 ATAACTTAC
* *
28412973 ATAAATTAA
1 ATAACTTAC
28412982 ATAACTTAC
1 ATAACTTAC
28412991 ATAACTTA-
1 ATAACTTAC
28412999 ATAACTTAC
1 ATAACTTAC
*
28413008 ATAACTTAT
1 ATAACTTAC
28413017 ATAACTTAC
1 ATAACTTAC
* *
28413026 ATAAATTAA
1 ATAACTTAC
28413035 ATAACTTAC
1 ATAACTTAC
28413044 ATAACTTAC
1 ATAACTTAC
*
28413053 ATAACTTAA
1 ATAACTTAC
28413062 ATAACTTAC
1 ATAACTTAC
28413071 ATAA--TAC
1 ATAACTTAC
28413078 ATAACCTT-C
1 ATAA-CTTAC
*
28413087 CTAACTTAC
1 ATAACTTAC
* *
28413096 ATAAATTAA
1 ATAACTTAC
28413105 ATAACTTAC
1 ATAACTTAC
28413114 ATAACTTAC
1 ATAACTTAC
*
28413123 ATAACTTAA
1 ATAACTTAC
28413132 ATAACTTAC
1 ATAACTTAC
28413141 ATAA--TAC
1 ATAACTTAC
*
28413148 AGAACTTAC
1 ATAACTTAC
*
28413157 ATAACTTAT
1 ATAACTTAC
* *
28413166 ATAAATTAA
1 ATAACTTAC
*
28413175 ATGACTTAC
1 ATAACTTAC
28413184 ATAACTTAC
1 ATAACTTAC
28413193 ATAACTTAC
1 ATAACTTAC
* *
28413202 ATAAATTAA
1 ATAACTTAC
28413211 ATAACTTAC
1 ATAACTTAC
28413220 ATAACTTAC
1 ATAACTTAC
* *
28413229 ATAAATTAA
1 ATAACTTAC
28413238 ATAACTTAC
1 ATAACTTAC
28413247 ATAACTTAC
1 ATAACTTAC
28413256 ATAACTTAC
1 ATAACTTAC
28413265 ATAACTTAC
1 ATAACTTAC
28413274 ATAA
1 ATAA
28413278 TACATAAAAA
Statistics
Matches: 582, Mismatches: 90, Indels: 90
0.76 0.12 0.12
Matches are distributed among these distances:
5 4 0.01
6 7 0.01
7 59 0.10
8 42 0.07
9 441 0.76
10 6 0.01
11 9 0.02
12 14 0.02
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:28412633 original size:31 final size:32
Alignment explanation
Indices: 28412549--28412669 Score: 147
Period size: 31 Copynumber: 3.8 Consensus size: 32
28412539 CATAACTTAC
* *
28412549 ATAATAACTTACATAACTTACATAACTTACAT
1 ATAATAACATACATAACTTACATAACTTATAT
** *
28412581 AATACACCACTTACATAACTTACATAACTTATAT
1 -ATA-ATAACATACATAACTTACATAACTTATAT
28412615 ATAATAACATA-ATAACTTACATAACTTATAT
1 ATAATAACATACATAACTTACATAACTTATAT
* *
28412646 ATAATAATATA-ATAAATTACATAA
1 ATAATAACATACATAACTTACATAA
28412670 TACATAACTT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 42 0.53
32 5 0.06
33 6 0.08
34 26 0.33
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (32 bp):
ATAATAACATACATAACTTACATAACTTATAT
Found at i:28412696 original size:21 final size:21
Alignment explanation
Indices: 28412670--28412724 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
28412660 AATTACATAA
*
28412670 TACATAACTTATAT-ATAAGCT
1 TACATAACTTACATAATAA-CT
*
28412691 TGCATAACTTACATAATAACT
1 TACATAACTTACATAATAACT
28412712 TACATAACTTACA
1 TACATAACTTACA
28412725 CAAGTTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.35
Consensus pattern (21 bp):
TACATAACTTACATAATAACT
Found at i:28412711 original size:12 final size:12
Alignment explanation
Indices: 28412694--28412718 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28412684 ATAAGCTTGC
28412694 ATAACTTACATA
1 ATAACTTACATA
28412706 ATAACTTACATA
1 ATAACTTACATA
28412718 A
1 A
28412719 CTTACACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:28412792 original size:25 final size:25
Alignment explanation
Indices: 28412746--28412817 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 25
28412736 ATACACCACT
* * * **
28412746 TACATAACTTACATAGCTTACATTC
1 TACACAACTTACATAACATACATAA
28412771 TACACAACTTACATAACATACATAA
1 TACACAACTTACATAACATACATAA
* * *
28412796 TATAGAACTTACATAAAATACA
1 TACACAACTTACATAACATACA
28412818 ACTTACATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (25 bp):
TACACAACTTACATAACATACATAA
Found at i:28412819 original size:41 final size:41
Alignment explanation
Indices: 28412774--28412852 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
28412764 TACATTCTAC
*
28412774 ACAACTTACATAACATACATAATATAGAACTTACATAAAAT
1 ACAACTTACATAACATACATAATACAGAACTTACATAAAAT
* * *
28412815 ACAACTTACATATCTTACATAATACATAACTTACATAA
1 ACAACTTACATAACATACATAATACAGAACTTACATAA
28412853 TACAACATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.29
Consensus pattern (41 bp):
ACAACTTACATAACATACATAATACAGAACTTACATAAAAT
Found at i:28412831 original size:25 final size:25
Alignment explanation
Indices: 28412803--28412851 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
28412793 TAATATAGAA
*
28412803 CTTACATAAAATACAACTTACATAT
1 CTTACATAAAACACAACTTACATAT
* *
28412828 CTTACATAATACATAACTTACATA
1 CTTACATAAAACACAACTTACATA
28412852 ATACAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (25 bp):
CTTACATAAAACACAACTTACATAT
Found at i:28418810 original size:21 final size:21
Alignment explanation
Indices: 28418785--28418852 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
28418775 AACTTAAAGA
* * *
28418785 AGAGGCGGCAGCGAGGGAATC
1 AGAGGCTGCAGCGAGAGAAGC
28418806 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGC
*
28418827 AGAGGCTGCAACGAGAGAAGC
1 AGAGGCTGCAGCGAGAGAAGC
28418848 AGAGG
1 AGAGG
28418853 TTCAAAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAAGC
Found at i:28419339 original size:42 final size:42
Alignment explanation
Indices: 28419284--28419489 Score: 277
Period size: 42 Copynumber: 4.9 Consensus size: 42
28419274 TTTGTGAAGA
28419284 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
* * *
28419326 AAGCGCCACTAAAGAACATGATCTTTAGTGGCGTTTTTCTCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
* * * *
28419368 ATGCGCCCCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
* * * *
28419410 AAACGCCGCTAAAGAACATGACCTTTAGCGGCTTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
* * * *
28419452 AAACACCGCTAAAGAACATGACCTTTAGCGGTGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
28419490 TCTGTAAACG
Statistics
Matches: 146, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 146 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCT
Found at i:28444514 original size:24 final size:25
Alignment explanation
Indices: 28444470--28444516 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28444460 AAATACTTTA
* *
28444470 AAAATATTTTTTTATTTTTTATTTT
1 AAAATATTTTTTTAGTGTTTATTTT
28444495 AAAATATTTTTTT-GTGTTTATT
1 AAAATATTTTTTTAGTGTTTATT
28444517 AAAAACCGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (25 bp):
AAAATATTTTTTTAGTGTTTATTTT
Found at i:28444572 original size:40 final size:40
Alignment explanation
Indices: 28444522--28444608 Score: 122
Period size: 40 Copynumber: 2.1 Consensus size: 40
28444512 TTATTAAAAA
* *
28444522 CCGGGCCGGGC-CGGGCTTATTATTTTTTTCCCGGGCTGGG
1 CCGGGCCGGGCTCGGGCTTATTA-TTTTTTCCAGGGCCGGG
*
28444562 CCGGGTCGGGCTCGGGCTTATTATTTTTTCCAGGGCCGGG
1 CCGGGCCGGGCTCGGGCTTATTATTTTTTCCAGGGCCGGG
28444602 CCTGGGC
1 CC-GGGC
28444609 AAAATTTCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
40 27 0.66
41 14 0.34
ACGTcount: A:0.06, C:0.28, G:0.38, T:0.29
Consensus pattern (40 bp):
CCGGGCCGGGCTCGGGCTTATTATTTTTTCCAGGGCCGGG
Found at i:28446587 original size:21 final size:21
Alignment explanation
Indices: 28446558--28446603 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
28446548 TACACGGGCA
* *
28446558 TGTGGGTTTTGGGCCAAGTCG
1 TGTGAGTTTTGGGCCAAGCCG
28446579 TGTGAGTTTTGGGCCAAGCCG
1 TGTGAGTTTTGGGCCAAGCCG
28446600 TGTG
1 TGTG
28446604 GGCCACACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.15, G:0.41, T:0.33
Consensus pattern (21 bp):
TGTGAGTTTTGGGCCAAGCCG
Found at i:28454924 original size:70 final size:70
Alignment explanation
Indices: 28454836--28454996 Score: 322
Period size: 70 Copynumber: 2.3 Consensus size: 70
28454826 ATTGATTTCT
28454836 GAGGTAGTTGGGAGGATTACTTGCCATTAGAAGAGTTTGCTTATAACAACAGCTATCAGTCTAGC
1 GAGGTAGTTGGGAGGATTACTTGCCATTAGAAGAGTTTGCTTATAACAACAGCTATCAGTCTAGC
28454901 ATTCC
66 ATTCC
28454906 GAGGTAGTTGGGAGGATTACTTGCCATTAGAAGAGTTTGCTTATAACAACAGCTATCAGTCTAGC
1 GAGGTAGTTGGGAGGATTACTTGCCATTAGAAGAGTTTGCTTATAACAACAGCTATCAGTCTAGC
28454971 ATTCC
66 ATTCC
28454976 GAGGTAGTTGGGAGGATTACT
1 GAGGTAGTTGGGAGGATTACT
28454997 ATTGGTTTTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 91 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (70 bp):
GAGGTAGTTGGGAGGATTACTTGCCATTAGAAGAGTTTGCTTATAACAACAGCTATCAGTCTAGC
ATTCC
Found at i:28465572 original size:19 final size:19
Alignment explanation
Indices: 28465548--28465589 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
28465538 ATAAAATGAT
28465548 GTTGGCAAATATAATAATA
1 GTTGGCAAATATAATAATA
28465567 GTTGGCAAATATAATAATA
1 GTTGGCAAATATAATAATA
28465586 GTTG
1 GTTG
28465590 AATAAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (19 bp):
GTTGGCAAATATAATAATA
Found at i:28465999 original size:2 final size:2
Alignment explanation
Indices: 28465992--28466020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28465982 AAGTATTTTA
28465992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28466021 AGTATACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28466931 original size:6 final size:6
Alignment explanation
Indices: 28466920--28466946 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28466910 TAATATAAAT
28466920 TTTATA TTTATA TTTATA TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTT
28466947 GTTCTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:28474828 original size:43 final size:43
Alignment explanation
Indices: 28474761--28474881 Score: 161
Period size: 43 Copynumber: 2.8 Consensus size: 43
28474751 ACGACCTACA
* * * * *
28474761 ACACGGCCGTGTGTCCATAATTCGAATATACACATGGTTTGGC
1 ACACGACCGTGTGGCCCTATTTCGAATATACACACGGTTTGGC
28474804 ACACGACCGTGTGGCCCTATTTCGAATATACACACGGTTTGGC
1 ACACGACCGTGTGGCCCTATTTCGAATATACACACGGTTTGGC
* * * *
28474847 ACATGACCATGTGGCCCTATTTCAAATATTCACAC
1 ACACGACCGTGTGGCCCTATTTCGAATATACACAC
28474882 AGGCGGACAC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (43 bp):
ACACGACCGTGTGGCCCTATTTCGAATATACACACGGTTTGGC
Found at i:28476938 original size:44 final size:43
Alignment explanation
Indices: 28476873--28477025 Score: 152
Period size: 44 Copynumber: 3.6 Consensus size: 43
28476863 TGATTTCATA
* *
28476873 TAAGACCATAGCTGGGCTATGGCATCGATATATGAGACTTTGTG
1 TAAGACCATATCTGGGATATGGCATCGATATATGAGA-TTTGTG
* * *
28476917 TAAGACCATATCTGGGATATGGCATTGATATAT--GATTCGTA
1 TAAGACCATATCTGGGATATGGCATCGATATATGAGATTTGTG
* * * * * *
28476958 TGAGACCAT-TGCTGGGCTATTGGCATCGATATGTGATA-ATATG
1 TAAGACCATAT-CTGGGATA-TGGCATCGATATATGAGATTTGTG
28477001 TAAGACCATATCTGGGATATGGCAT
1 TAAGACCATATCTGGGATATGGCAT
28477026 TGTATGTGAT
Statistics
Matches: 88, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
40 1 0.01
41 19 0.22
42 20 0.23
43 16 0.18
44 32 0.36
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (43 bp):
TAAGACCATATCTGGGATATGGCATCGATATATGAGATTTGTG
Found at i:28477011 original size:84 final size:83
Alignment explanation
Indices: 28476875--28477035 Score: 234
Period size: 84 Copynumber: 1.9 Consensus size: 83
28476865 ATTTCATATA
* *
28476875 AGACCATAGCTGGGCTATGGCATCGATATATGAGACTTTGTGTAAGACCATATCTGGGATATGGC
1 AGACCATAGCTGGGCTATGGCATCGATATATGAGAC-ATATGTAAGACCATATCTGGGATATGGC
28476940 ATTGATATATGATTCGTATG
65 ATTG-TATATGATTCGTATG
* * *
28476960 AGACCATTGCTGGGCTATTGGCATCGATATGTGATA-ATATGTAAGACCATATCTGGGATATGGC
1 AGACCATAGCTGGGCTA-TGGCATCGATATATGAGACATATGTAAGACCATATCTGGGATATGGC
*
28477024 ATTGTATGTGAT
65 ATTGTATATGAT
28477036 ATACGAGACT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 7 0.10
84 30 0.43
85 16 0.23
86 16 0.23
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (83 bp):
AGACCATAGCTGGGCTATGGCATCGATATATGAGACATATGTAAGACCATATCTGGGATATGGCA
TTGTATATGATTCGTATG
Found at i:28480622 original size:592 final size:588
Alignment explanation
Indices: 28479738--28480919 Score: 2193
Period size: 592 Copynumber: 2.0 Consensus size: 588
28479728 TCATTTTTTT
* *
28479738 ATATACTTTCATTTCGGTTTTGTGTGGTGTTTTCACTCTTTTTGCTTGAAGGTCGATGTGCTAAG
1 ATATACTTTCATTTCAGTTTTGTGTGGTGTTTTCACTCTTTTTGCTTGAAGGCCGATGTGCTAAG
28479803 GGGTTTTTACATATTCTTCTGTCTCGTTTTTTTTTTTGGTGTAGGCAACCTCTCTTTGGCCAAAT
66 GGGTTTTTACATATTCTTCTGTCTCGTTTTTTTTTTTGGTGTAGGCAACCTCTCTTTGGCCAAAT
*
28479868 ATTGTCTCTCTCAATTGTCTCTTTTTCTTTCTTTTCCAAGTAATTATACTGGTGGCTAATCTATC
131 ATTGTCTCTCTCAATTGTCTCTTTTTCTTTCTTTTCCAAGTAATTATACTAGTGGCTAATCTATC
28479933 TTCTCTCCTTTTTCATTCATTCTTTCTTTATCCTCTATCGAAACCTCTTCGTCCCCTAAACCATT
196 TTCTCTCCTTTTTCATTCATTCTTTCTTTATCCTCTATCGAAACCTCTTCGTCCCCTAAACCATT
* * *
28479998 CTCCTCCCTTCTTGCCAATTTGCTCTTCTTTTTCTACCCTCTTTGTGCCGACTTTTTCCTTGCTC
261 CTCCTCCCTTCTTGCCAATTTGCTCCTCTTTTTCTACCCTCTTTGTGCCAACTTTTTCCTTACTC
*
28480063 TCTGCCGATTTTGTATACTATTCTTATTTTACGGTTTTATACTTTCGATAAGTTGGTGTTCGTTT
326 TCTGCCGATTTTGTATACCATTCTTATTTTACGGTTTTATACTTTCGATAAGTTGGTGTTCGTTT
*
28480128 TGACTTAAATTGTTTTAATAGATAATTGATATTAAGGGGTTCAACTGGATTGTAGGTAATAACCC
391 TGACTTAAATTGTTTTAATAGAAAATTGATATTAAGGGGTTCAACTGGATTGTAGGTAATAACCC
*
28480193 CGAGATCTAGTGACCAACGTTGTTCCAGTGAGTGAAATGCTTAGGGATTCGGTTGTTCAATCAAG
456 CGAGATCTAGTGACCAACGTTGTTCCAGTGAGTGAAATGCTTAGGGATTCGATTGTTCAATCAAG
*
28480258 GTAAGTGACTGTCAATTAAGAAGTTATGTGTAATGAATAAGATTCTTTTTAAATTCAATTGATAT
521 GTAAGTGACTGTCAATTAAGAAGTTATGTGTAATAAATAAGATTCTTTTTAAATTCAATTGATAT
28480323 GTG
586 GTG
*
28480326 ATATACTTTCATTTCAGTTTTGTGTGGTGTTTTCACTCTTTTTGCTTGAAGGCCGATGTGGTAAG
1 ATATACTTTCATTTCAGTTTTGTGTGGTGTTTTCACTCTTTTTGCTTGAAGGCCGATGTGCTAAG
28480391 GGGTTTTTACATATTCTTCTGTCTCGTTTTTTTATTTTTTGGTGTAGGCAACCTCTCTTTGGCCA
66 GGGTTTTTACATATTCTTCTGTCTCG--TTTTT-TTTTTTGGTGTAGGCAACCTCTCTTTGGCCA
*
28480456 AATATTGTCTCTCTCAATTGTCTCTTTTTCTTTCTTTTTCCAAGTAATTCTACTAGTGGCTAATC
128 AATATTGTCTCTCTCAATTGTCTCTTTTTCTTTC-TTTTCCAAGTAATTATACTAGTGGCTAATC
28480521 TATCTTCTCTCCTTTTTCATTCATTCTTTCTTTATCCTCTATCGAAACCTCTTCGTCCCCTAAAC
192 TATCTTCTCTCCTTTTTCATTCATTCTTTCTTTATCCTCTATCGAAACCTCTTCGTCCCCTAAAC
*
28480586 CATTCTCCTCCCTTCTTGCCGATTTGCTCCTCTTTTTCTACCCTCTTTGTGCCAACTTTTTCCTT
257 CATTCTCCTCCCTTCTTGCCAATTTGCTCCTCTTTTTCTACCCTCTTTGTGCCAACTTTTTCCTT
*
28480651 ACTCTCTGCCGATTTTGTATACCATTCTTATTTTACGGTTTTATACTTTCGGTAAGTTGGTGTTC
322 ACTCTCTGCCGATTTTGTATACCATTCTTATTTTACGGTTTTATACTTTCGATAAGTTGGTGTTC
28480716 GTTTTGACTTAAATTGTTTTAATAGAAAATTGATATTAAGGGGTTCAACTGGATTGTAGGTAATA
387 GTTTTGACTTAAATTGTTTTAATAGAAAATTGATATTAAGGGGTTCAACTGGATTGTAGGTAATA
*
28480781 ACCCCGAGATTTAGTGACCAACGTTGTTCCAGTGAGTGAAATGCTTAGGGATTCGATTGTTCAAT
452 ACCCCGAGATCTAGTGACCAACGTTGTTCCAGTGAGTGAAATGCTTAGGGATTCGATTGTTCAAT
28480846 CAAGGTAAGTGACTGTCAATTAAGAAGTTATGTGTAATAAATAAGATTCTTTTTAAATTCAATTG
517 CAAGGTAAGTGACTGTCAATTAAGAAGTTATGTGTAATAAATAAGATTCTTTTTAAATTCAATTG
28480911 ATATGTG
582 ATATGTG
28480918 AT
1 AT
28480920 TAACCGAGTG
Statistics
Matches: 575, Mismatches: 15, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
588 88 0.15
590 5 0.01
591 65 0.11
592 417 0.73
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (588 bp):
ATATACTTTCATTTCAGTTTTGTGTGGTGTTTTCACTCTTTTTGCTTGAAGGCCGATGTGCTAAG
GGGTTTTTACATATTCTTCTGTCTCGTTTTTTTTTTTGGTGTAGGCAACCTCTCTTTGGCCAAAT
ATTGTCTCTCTCAATTGTCTCTTTTTCTTTCTTTTCCAAGTAATTATACTAGTGGCTAATCTATC
TTCTCTCCTTTTTCATTCATTCTTTCTTTATCCTCTATCGAAACCTCTTCGTCCCCTAAACCATT
CTCCTCCCTTCTTGCCAATTTGCTCCTCTTTTTCTACCCTCTTTGTGCCAACTTTTTCCTTACTC
TCTGCCGATTTTGTATACCATTCTTATTTTACGGTTTTATACTTTCGATAAGTTGGTGTTCGTTT
TGACTTAAATTGTTTTAATAGAAAATTGATATTAAGGGGTTCAACTGGATTGTAGGTAATAACCC
CGAGATCTAGTGACCAACGTTGTTCCAGTGAGTGAAATGCTTAGGGATTCGATTGTTCAATCAAG
GTAAGTGACTGTCAATTAAGAAGTTATGTGTAATAAATAAGATTCTTTTTAAATTCAATTGATAT
GTG
Found at i:28481454 original size:26 final size:27
Alignment explanation
Indices: 28481425--28481479 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
28481415 CGATATCTGC
28481425 ACTGAAATA-CCCCACAAGATAAAATG
1 ACTGAAATACCCCCACAAGATAAAATG
* *
28481451 ACTGAAATACCCCCACAGGGTAAAATG
1 ACTGAAATACCCCCACAAGATAAAATG
28481478 AC
1 AC
28481480 CGTGTAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (27 bp):
ACTGAAATACCCCCACAAGATAAAATG
Found at i:28484327 original size:53 final size:54
Alignment explanation
Indices: 28484244--28484364 Score: 165
Period size: 53 Copynumber: 2.3 Consensus size: 54
28484234 GTTATAGACC
**
28484244 GAAATACTTCATAGGGTAAAATGACCAAAATA-CCCCCATAGAGTAAAATAACT
1 GAAATACCCCATAGGGTAAAATGACCAAAATATCCCCCATAGAGTAAAATAACT
* * *
28484297 GAAATACCCCATAGGGTAAAATGACTAAAATATCCCCCATAGGGTAAAATGACT
1 GAAATACCCCATAGGGTAAAATGACCAAAATATCCCCCATAGAGTAAAATAACT
**
28484351 GTTATACCCC-TAGG
1 GAAATACCCCATAGG
28484365 AGATGAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 33 0.55
54 27 0.45
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (54 bp):
GAAATACCCCATAGGGTAAAATGACCAAAATATCCCCCATAGAGTAAAATAACT
Found at i:28484342 original size:28 final size:27
Alignment explanation
Indices: 28484253--28484350 Score: 144
Period size: 26 Copynumber: 3.6 Consensus size: 27
28484243 CGAAATACTT
*
28484253 CATAGGGTAAAATGACCAAAATACCCC
1 CATAGGGTAAAATGACTAAAATACCCC
* * *
28484280 CATAGAGTAAAATAACTGAAATA-CCC
1 CATAGGGTAAAATGACTAAAATACCCC
28484306 CATAGGGTAAAATGACTAAAATATCCCC
1 CATAGGGTAAAATGACTAAAATA-CCCC
28484334 CATAGGGTAAAATGACT
1 CATAGGGTAAAATGACT
28484351 GTTATACCCC
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.37
27 19 0.31
28 20 0.32
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.19
Consensus pattern (27 bp):
CATAGGGTAAAATGACTAAAATACCCC
Found at i:28487561 original size:9 final size:9
Alignment explanation
Indices: 28487547--28487577 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28487537 GTTAAACTAA
28487547 TCGAGTTAT
1 TCGAGTTAT
*
28487556 TCGAGTTAA
1 TCGAGTTAT
28487565 TCGAGTTAT
1 TCGAGTTAT
28487574 TCGA
1 TCGA
28487578 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28487650 original size:9 final size:9
Alignment explanation
Indices: 28487633--28487669 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28487623 TGAGTTTTCG
28487633 AATTCGAAT
1 AATTCGAAT
*
28487642 AACTCGAAT
1 AATTCGAAT
28487651 AATTCGAAT
1 AATTCGAAT
28487660 AATTCGAAT
1 AATTCGAAT
28487669 A
1 A
28487670 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28487746 original size:21 final size:21
Alignment explanation
Indices: 28487705--28487747 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28487695 ACCCCAAACT
* *
28487705 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
28487726 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
28487747 C
1 C
28487748 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:28488807 original size:5 final size:5
Alignment explanation
Indices: 28488797--28488822 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28488787 CTCGAAAATC
28488797 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
28488823 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:28489006 original size:4 final size:4
Alignment explanation
Indices: 28488997--28489025 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28488987 TCAATTATTC
28488997 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
28489026 ACAAGAGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:28489375 original size:2 final size:2
Alignment explanation
Indices: 28489368--28489396 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28489358 CATCGAAAAT
28489368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28489397 GCAAATGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28489557 original size:21 final size:21
Alignment explanation
Indices: 28489532--28489571 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28489522 CCATCACTCA
28489532 TTTTAACCAT-TTATTAATATT
1 TTTTAACCATATT-TTAATATT
*
28489553 TTTTAATCATATTTTAATA
1 TTTTAACCATATTTTAATA
28489572 CCGTGTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAACCATATTTTAATATT
Found at i:28489852 original size:21 final size:21
Alignment explanation
Indices: 28489809--28489853 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
28489799 TTAAATTCAT
28489809 ATTTAAAATAATTATAATAAAA
1 ATTTAAAATAATTAT-ATAAAA
*
28489831 ATTTAAAATTATTAGT-TAAAA
1 ATTTAAAATAATTA-TATAAAA
28489852 AT
1 AT
28489854 AAAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 13 0.62
23 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTAAAATAATTATATAAAA
Found at i:28489908 original size:44 final size:43
Alignment explanation
Indices: 28489853--28489949 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 43
28489843 TAGTTAAAAA
* *
28489853 TAAAATATAATAGAAGTTGTCATAATTATACATTTAAAAATGAT
1 TAAAATTTAATAGAAGTTGTCATAATTATACATTT-AAAATAAT
** * *
28489897 TAAAATTTAATAGATTTTGTGATAATTATATATTTAAAATAAT
1 TAAAATTTAATAGAAGTTGTCATAATTATACATTTAAAATAAT
28489940 TAAAATTTAA
1 TAAAATTTAA
28489950 AGTAAAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 17 0.36
44 30 0.64
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (43 bp):
TAAAATTTAATAGAAGTTGTCATAATTATACATTTAAAATAAT
Found at i:28489949 original size:16 final size:17
Alignment explanation
Indices: 28489918--28489950 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28489908 AGATTTTGTG
*
28489918 ATAATTATATATTTAAA
1 ATAATTATAAATTTAAA
28489935 ATAATTA-AAATTTAAA
1 ATAATTATAAATTTAAA
28489951 GTAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATTATAAATTTAAA
Found at i:28497959 original size:49 final size:49
Alignment explanation
Indices: 28497902--28498004 Score: 206
Period size: 49 Copynumber: 2.1 Consensus size: 49
28497892 GCGGAAGCCA
28497902 TGATAGACAAAATCCAGAATCAAATGGCGAATGATACCTTGAAAGAACT
1 TGATAGACAAAATCCAGAATCAAATGGCGAATGATACCTTGAAAGAACT
28497951 TGATAGACAAAATCCAGAATCAAATGGCGAATGATACCTTGAAAGAACT
1 TGATAGACAAAATCCAGAATCAAATGGCGAATGATACCTTGAAAGAACT
28498000 TGATA
1 TGATA
28498005 AAAGAGAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (49 bp):
TGATAGACAAAATCCAGAATCAAATGGCGAATGATACCTTGAAAGAACT
Found at i:28498505 original size:21 final size:22
Alignment explanation
Indices: 28498463--28498515 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
28498453 TTAGGAAGAA
**
28498463 TTAAATTTTTTTTATATGTTCT
1 TTAAATTTTTTAGATATGTTCT
*
28498485 TTAAATTTTTTAGA-ATTTTCT
1 TTAAATTTTTTAGATATGTTCT
*
28498506 TTTAATTTTT
1 TTAAATTTTT
28498516 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (22 bp):
TTAAATTTTTTAGATATGTTCT
Found at i:28500863 original size:19 final size:19
Alignment explanation
Indices: 28500810--28500865 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
28500800 TGTATTCCAA
*
28500810 GTAATCAAAATTTTCACAT
1 GTAATCAAAATTTTAACAT
* * *
28500829 ATAAATTATGAATTTTAACAT
1 GT-AATCA-AAATTTTAACAT
28500850 GTAATCAAAATTTTAA
1 GTAATCAAAATTTTAA
28500866 TGGTTTAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 11 0.39
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (19 bp):
GTAATCAAAATTTTAACAT
Found at i:28504336 original size:42 final size:42
Alignment explanation
Indices: 28504266--28504389 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
28504256 ACTGAGATGT
* *
28504266 GATTTGTGTAAGACCATGTCTAGAACATTGGCATCGATATGA
1 GATTCGTGTAAGACCATGTCTAGAACATTAGCATCGATATGA
* * *
28504308 GATTCGTGTAAGACCATGTTTGGGACATTAGCATCGATATGA
1 GATTCGTGTAAGACCATGTCTAGAACATTAGCATCGATATGA
*
28504350 GATTCGTGTAAGACCATAG-CTAG-GCTATTAGCATCGATAT
1 GATTCGTGTAAGACCAT-GTCTAGAAC-ATTAGCATCGATAT
28504390 ATGATAGCAT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 70 0.97
43 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (42 bp):
GATTCGTGTAAGACCATGTCTAGAACATTAGCATCGATATGA
Found at i:28507007 original size:128 final size:128
Alignment explanation
Indices: 28506862--28507117 Score: 467
Period size: 128 Copynumber: 2.0 Consensus size: 128
28506852 CTAACGAATG
* *
28506862 TTTTTCATATTTATATTTTCCAAACACTCACTGAAATCAGAAGTTTTCAAACGAGATCAAGTTAA
1 TTTTTCATATTTATATTTTCCAAACACTCACTGAAATCAAAAGTTTTCAAACAAGATCAAGTTAA
* *
28506927 GAGCTATTATGTAAAATAAATAAGCTCTATGCGTAATTTTTGAAATAACAAGTGTTCTGCTAA
66 GAACTATTATGTAAAATAAATAAGCTCTATGCGTAATTTCTGAAATAACAAGTGTTCTGCTAA
28506990 TTTTTCATATTTATATTTTCCAAACACTCACTGAAATCAAAAGTTTTCAAACAAGATCAAGTTAA
1 TTTTTCATATTTATATTTTCCAAACACTCACTGAAATCAAAAGTTTTCAAACAAGATCAAGTTAA
*
28507055 GAACTATTATGTAAAATAAATAAGCTCTGTGCGTAATTTCTGAAATAACAAGTGTTCTGCTAA
66 GAACTATTATGTAAAATAAATAAGCTCTATGCGTAATTTCTGAAATAACAAGTGTTCTGCTAA
28507118 AAATATTATT
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (128 bp):
TTTTTCATATTTATATTTTCCAAACACTCACTGAAATCAAAAGTTTTCAAACAAGATCAAGTTAA
GAACTATTATGTAAAATAAATAAGCTCTATGCGTAATTTCTGAAATAACAAGTGTTCTGCTAA
Found at i:28507660 original size:92 final size:92
Alignment explanation
Indices: 28507550--28507736 Score: 347
Period size: 92 Copynumber: 2.0 Consensus size: 92
28507540 TTTATTAGGC
28507550 TGTATTGGGCTTAGACCTATCCAAAAATCGGGTAGTCCGCTTGACCTGATACGCTCGACCCAACT
1 TGTATTGGGCTTAGACCTATCCAAAAATCGGGTAGTCCGCTTGACCTGATACGCTCGACCCAACT
28507615 TAGGTCGAGCTTGGATAAGGATTATTG
66 TAGGTCGAGCTTGGATAAGGATTATTG
* * *
28507642 TGTATTGGGCTTAGACCTATCCAAAAATCGGGTTGTTCGCTTGACCTGATAGGCTCGACCCAACT
1 TGTATTGGGCTTAGACCTATCCAAAAATCGGGTAGTCCGCTTGACCTGATACGCTCGACCCAACT
28507707 TAGGTCGAGCTTGGATAAGGATTATTG
66 TAGGTCGAGCTTGGATAAGGATTATTG
28507734 TGT
1 TGT
28507737 CTCAAGCTGA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (92 bp):
TGTATTGGGCTTAGACCTATCCAAAAATCGGGTAGTCCGCTTGACCTGATACGCTCGACCCAACT
TAGGTCGAGCTTGGATAAGGATTATTG
Found at i:28510022 original size:11 final size:11
Alignment explanation
Indices: 28510000--28510051 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
28509990 AACTAATCCT
28510000 CTCTCAAATTTC
1 CTCTC-AATTTC
28510012 CTCTCAATTTC
1 CTCTCAATTTC
*
28510023 CTCTAAATTTC
1 CTCTCAATTTC
*
28510034 CTCTCAATTTG
1 CTCTCAATTTC
28510045 CTCTCAA
1 CTCTCAA
28510052 ACTCCTTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
11 32 0.86
12 5 0.14
ACGTcount: A:0.23, C:0.33, G:0.02, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:28510057 original size:22 final size:23
Alignment explanation
Indices: 28510000--28510052 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
28509990 AACTAATCCT
28510000 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
28510023 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
28510045 CTCTCAAA
1 CTCTCAAA
28510053 CTCCTTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.42
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:28510065 original size:34 final size:34
Alignment explanation
Indices: 28510000--28510075 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
28509990 AACTAATCCT
** *
28510000 CTCTCAAATTTCCTCTCAATTTCCTCTAAATTTC
1 CTCTCAAATTTCCTCTCAAACTCCTCCAAATTTC
*
28510034 CTCTC-AATTTGCTCTCAAACTCCTTCCAAATTT-
1 CTCTCAAATTTCCTCTCAAACTCC-TCCAAATTTC
*
28510067 CTCTAAAAT
1 CTCTCAAAT
28510076 CCATATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 19 0.54
34 16 0.46
ACGTcount: A:0.26, C:0.32, G:0.01, T:0.41
Consensus pattern (34 bp):
CTCTCAAATTTCCTCTCAAACTCCTCCAAATTTC
Found at i:28511197 original size:7 final size:7
Alignment explanation
Indices: 28511185--28511210 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28511175 TAGTCGATTG
28511185 GTATTTA
1 GTATTTA
28511192 GTATTTA
1 GTATTTA
28511199 GTATTTA
1 GTATTTA
28511206 GTATT
1 GTATT
28511211 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:28512337 original size:45 final size:45
Alignment explanation
Indices: 28512288--28512453 Score: 208
Period size: 45 Copynumber: 3.6 Consensus size: 45
28512278 GTGTTTTGAA
*
28512288 TATTTTGATATTATTTTATGTAATAAAATAGAAATTTTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTTTTTGAGT
* *
28512333 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTTTTTGA-GT
** * *
28512379 AATAAAATAGA-AGTTTATTTGATGTAATAAAATAGAAATTTTTTTGTGT
1 --T-ATTTTGATA--TTATTTGATGTAATAAAATAGAAATTTTTTTGAGT
28512428 TATTTTGATATTATTTGATGTAATAA
1 TATTTTGATATTATTTGATGTAATAA
28512454 CATGAGATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
45 56 0.55
46 6 0.06
47 2 0.02
48 2 0.02
49 6 0.06
50 30 0.29
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTTTTTGAGT
Found at i:28512371 original size:25 final size:25
Alignment explanation
Indices: 28512343--28512424 Score: 146
Period size: 25 Copynumber: 3.3 Consensus size: 25
28512333 TATTTTGATA
28512343 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
28512368 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
28512393 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
*
28512418 TTTTTTG
1 TTATTTG
28512425 TGTTATTTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:28514496 original size:61 final size:61
Alignment explanation
Indices: 28514401--28514522 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
28514391 ATTCAGAAAT
28514401 CGTCAATATTGTACCTGCAGCACAAGTATGTGGACCTTTGTACTTTTTAATCTCCCACAAC
1 CGTCAATATTGTACCTGCAGCACAAGTATGTGGACCTTTGTACTTTTTAATCTCCCACAAC
28514462 CGTCAATATTGTACCTGCAGCACAAGTATGTGGACCTTTGTACTTTTTAATCTCCCACAAC
1 CGTCAATATTGTACCTGCAGCACAAGTATGTGGACCTTTGTACTTTTTAATCTCCCACAAC
28514523 TCTGTCATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (61 bp):
CGTCAATATTGTACCTGCAGCACAAGTATGTGGACCTTTGTACTTTTTAATCTCCCACAAC
Found at i:28514875 original size:18 final size:18
Alignment explanation
Indices: 28514852--28514892 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
28514842 TTTTCTTCTT
28514852 CATCTGAACTCCTTTCAG
1 CATCTGAACTCCTTTCAG
28514870 CATCTGAACTCCTTTCAG
1 CATCTGAACTCCTTTCAG
28514888 CATCT
1 CATCT
28514893 TCAGGTTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.34, G:0.10, T:0.34
Consensus pattern (18 bp):
CATCTGAACTCCTTTCAG
Found at i:28515977 original size:124 final size:124
Alignment explanation
Indices: 28515733--28516104 Score: 568
Period size: 124 Copynumber: 3.0 Consensus size: 124
28515723 CAAACATGCT
*
28515733 ACTGTAGCAAAAGCGTGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
* *
28515798 GAAG-GATTTTATACTATTTGCTCAGAAGCGTCAACTCGAAATTATTTCTTCCAGGACCA
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTTCAGGACCA
* * * *
28515857 ACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGGT
* * * * *
28515921 TGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATAATTTTTTCAGGACCT
65 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
*
28515981 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTAACAAATTCTTCTCATAAAGCATCCTGGTA
1 ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
* *
28516046 AAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCTAGGACC
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTC-AGGACC
28516105 TAAAAACCCT
Statistics
Matches: 221, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
123 2 0.01
124 172 0.78
125 47 0.21
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (124 bp):
ACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGGTA
GAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACCA
Found at i:28516475 original size:2 final size:2
Alignment explanation
Indices: 28516468--28516506 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28516458 TATAATTTTA
28516468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28516507 ATTTCACAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28520808 original size:21 final size:21
Alignment explanation
Indices: 28520784--28520941 Score: 57
Period size: 21 Copynumber: 7.5 Consensus size: 21
28520774 AAGCCCGAAG
*
28520784 GCTAAACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
* * *
28520805 GCTAAATAGAAACCCATAAGG
1 GCTAAACAGAAACACATAAGT
* * * * *** *
28520826 GTTGAATAGAAGCTTGTAAGA
1 GCTAAACAGAAACACATAAGT
* * *
28520847 GCTGAAC-GAAAACCCATAAGG
1 GCTAAACAG-AAACACATAAGT
* * * *
28520868 GTTAAACAGAAACTCAAAAGA
1 GCTAAACAGAAACACATAAGT
* *
28520889 GCTAAACAGAAACCCATAAGG
1 GCTAAACAGAAACACATAAGT
* * * * *
28520910 GTTAAACATAAACTCATATGA
1 GCTAAACAGAAACACATAAGT
*
28520931 GTTAAACAGAA
1 GCTAAACAGAA
28520942 GCTCGTGAGA
Statistics
Matches: 102, Mismatches: 33, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
20 1 0.01
21 100 0.98
22 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.17
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:28520860 original size:42 final size:42
Alignment explanation
Indices: 28520786--28520941 Score: 152
Period size: 42 Copynumber: 3.7 Consensus size: 42
28520776 GCCCGAAGGC
* * * * *
28520786 TAAACAGAAGCACATAAGTGCTAAATAGAAACCCATAAGGGT
1 TAAACAGAAACTCAAAAGAGCTAAACAGAAACCCATAAGGGT
* * * *** *
28520828 TGAATAGAAGCTTGTAAGAGCTGAAC-GAAAACCCATAAGGGT
1 TAAACAGAAACTCAAAAGAGCTAAACAG-AAACCCATAAGGGT
28520870 TAAACAGAAACTCAAAAGAGCTAAACAGAAACCCATAAGGGT
1 TAAACAGAAACTCAAAAGAGCTAAACAGAAACCCATAAGGGT
* * * *
28520912 TAAACATAAACTCATATGAGTTAAACAGAA
1 TAAACAGAAACTCAAAAGAGCTAAACAGAA
28520942 GCTCGTGAGA
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
41 1 0.01
42 91 0.98
43 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.17
Consensus pattern (42 bp):
TAAACAGAAACTCAAAAGAGCTAAACAGAAACCCATAAGGGT
Found at i:28522570 original size:19 final size:19
Alignment explanation
Indices: 28522542--28522588 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
28522532 GGCATAGTTA
28522542 TAAAAA-ATATGTATATAT
1 TAAAAATATATGTATATAT
28522560 TAAAAATATATGTATATAT
1 TAAAAATATATGTATATAT
28522579 TAAAAATATA
1 TAAAAATATA
28522589 CGTAAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
TAAAAATATATGTATATAT
Found at i:28522679 original size:7 final size:7
Alignment explanation
Indices: 28522639--28522670 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
28522629 ACAATAATAA
28522639 AAAAAT-
1 AAAAATG
28522645 AAAAATG
1 AAAAATG
28522652 AAAAATG
1 AAAAATG
28522659 AAAAATG
1 AAAAATG
28522666 AAAAA
1 AAAAA
28522671 AACGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:28532136 original size:21 final size:21
Alignment explanation
Indices: 28532095--28532136 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28532085 AAAATTTTAG
* *
28532095 AAATTTCTAAAATATATAAAT
1 AAATTTCAAAAATATAAAAAT
28532116 AAATATTCAAAAATA-AAAAAT
1 AAAT-TTCAAAAATATAAAAAT
28532137 TAGTTAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTTCAAAAATATAAAAAT
Found at i:28532313 original size:2 final size:2
Alignment explanation
Indices: 28532306--28532346 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
28532296 TCAAAATTCA
*
28532306 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28532347 AACTCTAGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:28536713 original size:79 final size:78
Alignment explanation
Indices: 28536572--28536726 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 78
28536562 TAAGAATGTT
* *
28536572 TAGAAGTTCCATTTTTAAGTTGTGAGTTACTAAAGAAAATAAAAGTTGACAGACACAAAAAAACT
1 TAGAAGTGCCATTTTTAAGTTGTGAGTTACTAAAAAAAATAAAAGTTGACAGACAC-AAAAAACT
28536637 CCTTGATTGAAGAC
65 CCTTGATTGAAGAC
28536651 TAGAAGTGCCATTTTTAAGTTGTGTAAGTTACTAAAAAAAATAAAAGTTGA-AGGACACAAAAAA
1 TAGAAGTGCCATTTTTAAGTTGTG--AGTTACTAAAAAAAATAAAAGTTGACA-GACACAAAAAA
*
28536715 CTTCTTGATTGA
63 CTCCTTGATTGA
28536727 TGAGCAAGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
79 23 0.33
80 18 0.26
81 29 0.41
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (78 bp):
TAGAAGTGCCATTTTTAAGTTGTGAGTTACTAAAAAAAATAAAAGTTGACAGACACAAAAAACTC
CTTGATTGAAGAC
Found at i:28542554 original size:17 final size:18
Alignment explanation
Indices: 28542532--28542566 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28542522 AGATTAAGCT
28542532 ATAAAAA-TATCAAAAAC
1 ATAAAAATTATCAAAAAC
*
28542549 ATAAAAATTATTAAAAAC
1 ATAAAAATTATCAAAAAC
28542567 GGTCTTAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAATTATCAAAAAC
Found at i:28546829 original size:11 final size:11
Alignment explanation
Indices: 28546813--28546844 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
28546803 ATAAAGTAGA
28546813 TTATATATTAT
1 TTATATATTAT
28546824 TTATATATTA-
1 TTATATATTAT
28546834 TTATATATTAT
1 TTATATATTAT
28546845 GATTTTAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATATATTAT
Found at i:28547172 original size:16 final size:16
Alignment explanation
Indices: 28547151--28547189 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
28547141 TTGAATTACT
28547151 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
28547167 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
28547183 ATTACAG
1 ATTACAG
28547190 TGAACCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:28548477 original size:21 final size:21
Alignment explanation
Indices: 28548453--28548492 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28548443 TTTAAAATTA
28548453 GATTGTTTTCTA-AATTTTAAG
1 GATT-TTTTCTAGAATTTTAAG
*
28548474 GATTTTTTTTAGAATTTTA
1 GATTTTTTCTAGAATTTTA
28548493 GATATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (21 bp):
GATTTTTTCTAGAATTTTAAG
Found at i:28549932 original size:3 final size:3
Alignment explanation
Indices: 28549924--28549957 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
28549914 ATTTTTACAC
*
28549924 TAT TAT TAT CAT TAT TAT TCAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
28549958 ACTTACGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:28550167 original size:30 final size:29
Alignment explanation
Indices: 28550133--28550338 Score: 85
Period size: 32 Copynumber: 6.5 Consensus size: 29
28550123 TCCATATTAC
28550133 ATAATCTATATATATGTTTATACATTTTTT
1 ATAAT-TATATATATGTTTATACATTTTTT
***
28550163 ATAATATGTATATATATACATATACATCTTTTATT
1 AT-A-AT-TATATATATGTTTATACA--TTTT-TT
* *
28550198 ATTATTATATTATTAT-TTTATTTTCATAGTTTTT
1 ATAATTATA-TA-TATGTTTA--TACAT--TTTTT
*
28550232 ATATATTTATATATATGTATATACATTTATATTTT
1 ATA-A-TTATATATATGTTTATACA--T-T-TTTT
* ** * *
28550267 ATAA-TATCTATACATTT-TCCATATTTT
1 ATAATTATATATATGTTTATACATTTTTT
*
28550294 ATAATCTATATATATGTTTATACATTCTTT
1 ATAAT-TATATATATGTTTATACATTTTTT
*
28550324 ATAATATGTATATAT
1 ATAAT-TATATATAT
28550339 ATATTCTTAC
Statistics
Matches: 130, Mismatches: 26, Indels: 40
0.66 0.13 0.20
Matches are distributed among these distances:
27 8 0.06
29 11 0.08
30 22 0.17
31 4 0.03
32 30 0.23
33 10 0.08
34 16 0.12
35 24 0.18
36 5 0.04
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (29 bp):
ATAATTATATATATGTTTATACATTTTTT
Found at i:28550195 original size:155 final size:159
Alignment explanation
Indices: 28550026--28550341 Score: 532
Period size: 161 Copynumber: 2.0 Consensus size: 159
28550016 TTTTTAAATG
28550026 CATATACATATTTTATTATTATCATATTATTATTTTATTTTCATAG-TT-T-T-TTTATATATAT
1 CATATACATATTTTATTATTATCATATTATTATTTTATTTTCATAGTTTATATATTTATATATAT
*
28550087 GTATATACATTTATATTTTATAATATTTATACATTTTCCATATTACATAATCTATATATATGTTT
66 GTATATACATTTATATTTTATAATATCTATACATTTTCCATATTACATAATCTATATATATGTTT
*
28550152 ATACATTTTTTATAATATGTATATATATA
131 ATACATTCTTTATAATATGTATATATATA
* *
28550181 CATATACATCTTTTATTATTATTATATTATTATTTTATTTTCATAGTTTTTATATATTTATATAT
1 CATATACATATTTTATTATTATCATATTATTATTTTATTTTCATAG--TTTATATATTTATATAT
**
28550246 ATGTATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAATCTATATATATGT
64 ATGTATATACATTTATATTTTATAATATCTATACATTTTCCATATTACATAATCTATATATATGT
28550311 TTATACATTCTTTATAATATGTATATATATA
129 TTATACATTCTTTATAATATGTATATATATA
28550342 TTCTTACACT
Statistics
Matches: 149, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
155 44 0.30
158 2 0.01
159 1 0.01
160 1 0.01
161 101 0.68
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (159 bp):
CATATACATATTTTATTATTATCATATTATTATTTTATTTTCATAGTTTATATATTTATATATAT
GTATATACATTTATATTTTATAATATCTATACATTTTCCATATTACATAATCTATATATATGTTT
ATACATTCTTTATAATATGTATATATATA
Found at i:28550305 original size:27 final size:24
Alignment explanation
Indices: 28550233--28550305 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 24
28550223 ATAGTTTTTA
*
28550233 TATATTTATATATATGTATATACATT
1 TATATTT-TATA-ATATATATACATT
*
28550259 TATATTTTATAATATCTATACATTT
1 TATATTTTATAATATATATACA-TT
*
28550284 TCCATATTTTATAATCTATATA
1 T--ATATTTTATAATATATATA
28550306 TATGTTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.22
25 7 0.17
26 7 0.17
27 17 0.43
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.53
Consensus pattern (24 bp):
TATATTTTATAATATATATACATT
Found at i:28552164 original size:16 final size:16
Alignment explanation
Indices: 28552143--28552177 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28552133 TTGTGTTTTG
28552143 TTTTGACTGCATGACA
1 TTTTGACTGCATGACA
28552159 TTTTGACTGCATGACA
1 TTTTGACTGCATGACA
28552175 TTT
1 TTT
28552178 CATTATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (16 bp):
TTTTGACTGCATGACA
Found at i:28557089 original size:127 final size:127
Alignment explanation
Indices: 28556863--28557108 Score: 429
Period size: 127 Copynumber: 1.9 Consensus size: 127
28556853 ACAAACCAGT
* * * *
28556863 GAAATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTCTCTGAA
1 GAAATCAATCCTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAATTAGATCTTATCTCTCTAAA
28556928 GTTGCAGAAGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACAAAA
66 GTTGCAGAAGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACAAAA
28556990 GAAATCAATCCTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAATTAGATCTTATCTCTCTAAA
1 GAAATCAATCCTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAATTAGATCTTATCTCTCTAAA
* * *
28557055 GTTGTAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
66 GTTGCAGAAGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGGAGC
28557109 GGATTAAAAT
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 112 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (127 bp):
GAAATCAATCCTATCTCCCTGAAGTTACAGTAGAGCAGATTAAAATTAGATCTTATCTCTCTAAA
GTTGCAGAAGAGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACAAAA
Found at i:28557124 original size:83 final size:83
Alignment explanation
Indices: 28557001--28557530 Score: 496
Period size: 83 Copynumber: 6.3 Consensus size: 83
28556991 AAATCAATCC
* * * * * *
28557001 TATCTCCCTGAAGTTACAGTAGAGCAGATTAAAATTAGATCTTATCTCTCTAAAGTTGTAGTAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGTAGA
28557066 GCAGATCGCATCCAGTCT
66 GCAGATCGCATCCAGTCT
* * *
28557084 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTTTCTAAAGTTGCAATAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGTAGA
*
28557149 GCAGATCGCATCCAATCT
66 GCAGATCGCATCCAGTCT
* ** * *
28557167 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCA-ATCCTATCTCCCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGC-G-GATTA-AAATCAGATCTTATCTCTCTGAAGTTGCAGT
* * *** *
28557231 GGAGCGGATTAAAAT-TAGATCT
63 AGAGCAGA-TCGCATCCAG-TCT
* ** * * * *
28557253 TATCTCTCTGAAGTTGCAGAAGAGCAGA-TCACATCCAG-TCTTATCTCCCTGAAGTTGCAGTGG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAT-CAGATCTTATCTCTCTGAAGTTGCAGT--
* * *
28557316 AGTAGACAGA-AGAAAT-CAATCT
63 AG-AG-CAGATCG-CATCCAGTCT
* * * *
28557338 TATCTCCTTGAAGTTGCAGTGAAGCGGATTAAAATCAGATTTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGTAGA
* *
28557403 GTAGATCGCATCTAGTCT
66 GCAGATCGCATCCAGTCT
* * * *
28557421 TATCTCCCTGAGGTTGCAGTGGGGTGGATTAAAAATTACAGATCTTATCTCTCTGAAGTTGCATT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAA-T-CAGATCTTATCTCTCTGAAGTTGCAGT
28557486 AGAGCAGATCGCATCCAGTCT
63 AGAGCAGATCGCATCCAGTCT
* * *
28557507 TATCTCTCTAAATTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
28557531 TAGACTAGAG
Statistics
Matches: 360, Mismatches: 68, Indels: 35
0.78 0.15 0.08
Matches are distributed among these distances:
82 8 0.02
83 156 0.43
84 8 0.02
85 59 0.16
86 126 0.35
87 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (83 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGTAGA
GCAGATCGCATCCAGTCT
Found at i:28557215 original size:127 final size:127
Alignment explanation
Indices: 28557084--28557442 Score: 585
Period size: 127 Copynumber: 2.8 Consensus size: 127
28557074 CATCCAGTCT
* *
28557084 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTTTCTAAAGTTGCA-ATAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGA-AG
*
28557148 AGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
65 AGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
*
28557211 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
* * *
28557276 GCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAATCAATCT
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
* * *
28557338 TATCTCCTTGAAGTTGCAGTGAAGCGGATTAAAATCAGATTTTATCTCTCTGAAGTTGCAGAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
* * *
28557403 GTAGATCGCATCTAGTCTTATCTCCCTGAGGTTGCAGTGG
66 GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGG
28557443 GGTGGATTAA
Statistics
Matches: 216, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
127 215 1.00
128 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCTGAAGTTGCAGAAGA
GCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCC
Found at i:28557243 original size:210 final size:210
Alignment explanation
Indices: 28556874--28557530 Score: 785
Period size: 210 Copynumber: 3.1 Consensus size: 210
28556864 AAATCAATCC
* *
28556874 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTCTCTGAAGTTGCAGA-AG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTTTCTGAAGTTGCA-ATAG
* * *
28556938 AGCAGATCGCATCCAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACAAAAGAAATCAATCCTA
65 AGCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTA
* * * * *
28557003 TCTCCCTGAAGTTACAGTAGAGCAGATTAAAATTAGATCTTATCTCTCTAAAGTTGTAGTAGAGC
130 TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
28557068 AGATCGCATCCAGTCT
195 AGATCGCATCCAGTCT
*
28557084 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTTTCTAAAGTTGCAATAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTTTCTGAAGTTGCAATAGA
28557149 GCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTAT
66 GCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTAT
*
28557214 CTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTCTCTGAAGTTGCAGAAGAGCA
131 CTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
*
28557279 GATCACATCCAGTCT
196 GATCGCATCCAGTCT
* * ** * *
28557294 TATCTCCCTGAAGTTGCAGTGGAGTAGACAGAAGAAATCA-ATCTTATC-TCCTTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAG-CG-GATTA-AAATCAGATCTTATCTTTC-TGAAGTTGCAA
* *** * * * * * *
28557357 T-GAAGCGGATTAAAAT-CAGATTTTATCTCTCTGAAGTTGCA--GAAG-AG-TAGATCG-CATC
62 TAG-AGCAGA-TCGCATCCA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGA-AGAAATC
* * * * *
28557415 TAGTCTTATCTCCCTGAGGTTGCAGTGGGGTGGATTAAAAATTACAGATCTTATCTCTCTGAAGT
123 -AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAATT--AGATCTTATCTCTCTGAAGT
*
28557480 TGCATTAGAGCAGATCGCATCCAGTCT
184 TGCAGTAGAGCAGATCGCATCCAGTCT
* * *
28557507 TATCTCTCTAAATTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
28557531 TAGACTAGAG
Statistics
Matches: 393, Mismatches: 41, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
209 7 0.02
210 252 0.64
211 13 0.03
212 27 0.07
213 94 0.24
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (210 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTTTCTGAAGTTGCAATAGA
GCAGATCGCATCCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTAT
CTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
GATCGCATCCAGTCT
Found at i:28558784 original size:2 final size:2
Alignment explanation
Indices: 28558777--28558894 Score: 50
Period size: 2 Copynumber: 62.0 Consensus size: 2
28558767 TTTCATAGTT
* * * *
28558777 TA TA TA TA TA TA TA TA TA TG TA TA TA CA TT TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
28558818 -A TA TT TA TA CA T- TT TC CA TA T- TA TA TA -A TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
28558856 TG TT TA TA TA TT TT TA TA -A TA TG TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28558895 CATCTTTTAT
Statistics
Matches: 84, Mismatches: 26, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
1 6 0.07
2 78 0.93
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28558838 original size:27 final size:28
Alignment explanation
Indices: 28558808--28558882 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 28
28558798 ATATACATTT
* *
28558808 ATATTTTATAATATTTATACAT-TTTCC
1 ATATTTTATAATATATATACATGTTTAC
* * * *
28558835 ATATTATATAATCTATATATATGTTTAT
1 ATATTTTATAATATATATACATGTTTAC
*
28558863 ATATTTTTATAATATGTATA
1 ATA-TTTTATAATATATATA
28558883 TATATACATA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 18 0.49
28 6 0.16
29 13 0.35
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (28 bp):
ATATTTTATAATATATATACATGTTTAC
Found at i:28558966 original size:24 final size:24
Alignment explanation
Indices: 28558935--28559002 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 24
28558925 TTCATATTTT
28558935 TTTATATATTTAT-ATATGCATATACA
1 TTTATAT-TTTATAATAT-C-TATACA
28558961 TTTATATTTTATAATATCTATACA
1 TTTATATTTTATAATATCTATACA
28558985 TTTTCCATATTTTATAAT
1 -TTT--ATATTTTATAAT
28559003 CTATATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.16
25 9 0.24
26 11 0.29
27 12 0.32
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.54
Consensus pattern (24 bp):
TTTATATTTTATAATATCTATACA
Found at i:28558988 original size:156 final size:160
Alignment explanation
Indices: 28558726--28559045 Score: 522
Period size: 156 Copynumber: 2.0 Consensus size: 160
28558716 TGTTTTTTAA
28558726 ATACATATACATATTTTATTATTATCATATTATTATTTTATTTTCATAGTTTATATATATATATA
1 ATACATATACATATTTTATTATTAT-ATATTATTATTTTATTTTCATAGTTTATATATATATATA
* *
28558791 TATATGTATATACATTTATATTTTATAATATTTATACATTTTCCATATTATATAATCTATATATA
65 TATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATA
* *
28558856 TGTTTATATATT-TTTATAATATGTATATAT
130 TGTTTATACATTCTTTATAATATGCATATAT
* * * *
28558886 ATACATATACATCTTTTATTATTAT-T-TTATTATTTTATTTTCATA-TTTTTTTATATATTTAT
1 ATACATATACATATTTTATTATTATATATTATTATTTTATTTTCATAGTTTATATATATATATAT
*
28558948 ATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAATCTATATATAT
66 ATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAT
28559013 GTTTATACATTCTTTATAATATGCATATAT
131 GTTTATACATTCTTTATAATATGCATATAT
28559043 ATA
1 ATA
28559046 TTCTTACACT
Statistics
Matches: 150, Mismatches: 9, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
156 86 0.57
157 39 0.26
158 1 0.01
160 24 0.16
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.55
Consensus pattern (160 bp):
ATACATATACATATTTTATTATTATATATTATTATTTTATTTTCATAGTTTATATATATATATAT
ATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAATCTATATATAT
GTTTATACATTCTTTATAATATGCATATAT
Found at i:28559090 original size:156 final size:155
Alignment explanation
Indices: 28558781--28559117 Score: 421
Period size: 156 Copynumber: 2.1 Consensus size: 155
28558771 ATAGTTTATA
* *
28558781 TATATATATATATATGTATATACATTTATATTTTATAATATTTATACATTTTCCATATTATATAA
1 TATATATATATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAA
* * ** *
28558846 TCTATATATATGTTTATATATTTTTATAATATGTATATATATACATATACATCTTTTATTATTAT
66 TCTATATATATGTTTATACATTTTTATAATATGTATATATATACATATACATCTTTCAAAACTA-
* * * *
28558911 TTTATTATTTTATTTTCATATTTTTT
130 TTTATAAATATATTTTCACATTTTTT
* *
28558937 TATATATTTATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTTTATAA
1 TATATATATATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAA
*
28559002 TCTATATATATGTTTATACATTCTTTATAATATGCATATATATATTC-T-TACA-CTATTCAAAA
66 TCTATATATATGTTTATACATT-TTTATAATATG--TATATATATACATATACATCT-TTCAAAA
28559064 CTA-TTATAAATATATTTTCCACATTTTTTT
127 CTATTTATAAATATATTTT-CACA-TTTTTT
*
28559094 TGATATATACGTATATATCCATAT
1 T-ATATATA--TATATATGCATAT
28559118 TTTCATAATT
Statistics
Matches: 156, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
155 12 0.08
156 87 0.56
157 28 0.18
158 7 0.04
159 10 0.06
160 12 0.08
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (155 bp):
TATATATATATATATGCATATACATTTATATTTTATAATATCTATACATTTTCCATATTATATAA
TCTATATATATGTTTATACATTTTTATAATATGTATATATATACATATACATCTTTCAAAACTAT
TTATAAATATATTTTCACATTTTTT
Found at i:28563237 original size:17 final size:17
Alignment explanation
Indices: 28563212--28563250 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
28563202 CAGAATTAAA
*
28563212 ATTTGATTGAGAAATTT
1 ATTTAATTGAGAAATTT
28563229 ATTTAATTGAGAAATTT
1 ATTTAATTGAGAAATTT
28563246 ATTTA
1 ATTTA
28563251 GTTAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
ATTTAATTGAGAAATTT
Found at i:28569843 original size:7 final size:7
Alignment explanation
Indices: 28569831--28569858 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28569821 ACGTCCGTAT
28569831 ATATTTA
1 ATATTTA
28569838 ATATTTA
1 ATATTTA
28569845 ATATTTA
1 ATATTTA
28569852 ATATTTA
1 ATATTTA
28569859 CGAGTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:28571361 original size:76 final size:76
Alignment explanation
Indices: 28571217--28571363 Score: 179
Period size: 76 Copynumber: 1.9 Consensus size: 76
28571207 GCGCTGGGCA
* * * * * * * *
28571217 CAACTCATTATTGGTACATCCAACTAGTGCTGGGCACACATTTGATATTGTCAATTTACTCGATT
1 CAACTCATTATTGGTACATCCAACTAATGCTCGACACACATATGACATCGTCAATTTACTCAACT
28571282 AGCACTAGGCG
66 AGCACTAGGCG
* * *
28571293 CAACTCATTGTTGGTACATCTAACTAATGCTCGACACACATATGACATCGTCGATTTA-TCTAAC
1 CAACTCATTATTGGTACATCCAACTAATGCTCGACACACATATGACATCGTCAATTTACTC-AAC
28571357 TAGCACT
65 TAGCACT
28571364 GGGGTCAAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 2 0.03
76 57 0.97
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (76 bp):
CAACTCATTATTGGTACATCCAACTAATGCTCGACACACATATGACATCGTCAATTTACTCAACT
AGCACTAGGCG
Found at i:28582261 original size:76 final size:76
Alignment explanation
Indices: 28582038--28582261 Score: 205
Period size: 76 Copynumber: 2.9 Consensus size: 76
28582028 GATTTATCCA
* * * * * * * *
28582038 ACTAGCGCTAGGCGCAACTCATTCTTGGTACATCAAACTAGTGTTGGGCACACATTTGGTATCAT
1 ACTAGCACTGGGCACAACTCATTATTGGTATATCCAACTAGTGCTGGGCACACATTTGATATCAT
28582103 CAGTTTACGCG
66 CAGTTTACGCG
** * * * * * *
28582114 ACTAGCGTTGGGCACAACTCATTATTGGTATATCCAACTAGTGCAGTGCATATATTTGATACCGT
1 ACTAGCACTGGGCACAACTCATTATTGGTATATCCAACTAGTGCTGGGCACACATTTGATATCAT
** *
28582179 TGGTTTACTCG
66 CAGTTTACGCG
** * ** * **
28582190 ACTAGCACTGGGTGCAACTTATTATTTTTTTATCTGACTAGTGCTGGGCACACATTTGATATCAT
1 ACTAGCACTGGGCACAACTCATTATTGGTATATCCAACTAGTGCTGGGCACACATTTGATATCAT
28582255 CAGTTTA
66 CAGTTTA
28582262 TCTGAGTAGC
Statistics
Matches: 113, Mismatches: 35, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
76 113 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (76 bp):
ACTAGCACTGGGCACAACTCATTATTGGTATATCCAACTAGTGCTGGGCACACATTTGATATCAT
CAGTTTACGCG
Found at i:28594790 original size:16 final size:17
Alignment explanation
Indices: 28594761--28594792 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28594751 TGCGACGTTC
28594761 AACAAACAATTTATGAA
1 AACAAACAATTTATGAA
28594778 AACAAAC-ATTTATGA
1 AACAAACAATTTATGA
28594793 GATTACAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.25
Consensus pattern (17 bp):
AACAAACAATTTATGAA
Found at i:28597514 original size:10 final size:10
Alignment explanation
Indices: 28597501--28597571 Score: 69
Period size: 10 Copynumber: 7.4 Consensus size: 10
28597491 AAAATCATTA
28597501 AAAAACTTAT
1 AAAAACTTAT
28597511 -AAAACTTAT
1 AAAAACTTAT
*
28597520 AAAAAATTAT
1 AAAAACTTAT
*
28597530 AAGAA-TATAT
1 AAAAACT-TAT
*
28597540 AAAAGCTTAT
1 AAAAACTTAT
28597550 -AAAA-TTAT
1 AAAAACTTAT
*
28597558 AAAAAATTAT
1 AAAAACTTAT
28597568 AAAA
1 AAAA
28597572 TTGTAATATA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
8 4 0.08
9 17 0.33
10 29 0.57
11 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAAACTTAT
Found at i:28597584 original size:18 final size:18
Alignment explanation
Indices: 28597499--28597573 Score: 96
Period size: 20 Copynumber: 3.9 Consensus size: 18
28597489 AAAAAATCAT
28597499 TAAAAAACTTATAAAACTTA
1 TAAAAAA-TTATAAAA-TTA
28597519 TAAAAAATTATAAGAATATA
1 TAAAAAATTATAA-AAT-TA
**
28597539 TAAAAGCTTATAAAATTA
1 TAAAAAATTATAAAATTA
28597557 TAAAAAATTATAAAATT
1 TAAAAAATTATAAAATT
28597574 GTAATATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 17 0.35
19 10 0.20
20 22 0.45
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAAAATTATAAAATTA
Found at i:28598291 original size:20 final size:19
Alignment explanation
Indices: 28598268--28598328 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
28598258 ATCTTTATAT
28598268 TTTTTTTACATTTTTATAGG
1 TTTTTTTA-ATTTTTATAGG
* *
28598288 TTTTTGTGAATTTTTATAAG
1 TTTTT-TTAATTTTTATAGG
* *
28598308 TTTTTATAAGTTTTATAGG
1 TTTTTTTAATTTTTATAGG
28598327 TT
1 TT
28598329 CATATATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 12 0.35
20 20 0.59
21 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.62
Consensus pattern (19 bp):
TTTTTTTAATTTTTATAGG
Found at i:28598324 original size:9 final size:10
Alignment explanation
Indices: 28598278--28598321 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
28598268 TTTTTTTACA
*
28598278 TTTTTATAGG
1 TTTTTATAAG
*
28598288 TTTTTGTGAA-
1 TTTTTAT-AAG
28598298 TTTTTATAAG
1 TTTTTATAAG
28598308 TTTTTATAAG
1 TTTTTATAAG
28598318 TTTT
1 TTTT
28598322 ATAGGTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.90
11 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.64
Consensus pattern (10 bp):
TTTTTATAAG
Found at i:28598372 original size:21 final size:20
Alignment explanation
Indices: 28598359--28598403 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
28598349 TTATGGTTTA
28598359 TTTATAAGCTTTTATGAATTT
1 TTTATAAG-TTTTATGAATTT
*
28598380 TTTATAAGTTTTAT-AATTA
1 TTTATAAGTTTTATGAATTT
28598399 TTTAT
1 TTTAT
28598404 TTATGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 6 0.26
21 8 0.35
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTATAAGTTTTATGAATTT
Found at i:28598402 original size:19 final size:21
Alignment explanation
Indices: 28598356--28598403 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
28598346 TATTTATGGT
28598356 TTATTTATAAGCTTTTATGAA
1 TTATTTATAAGCTTTTATGAA
*
28598377 TTTTTTATAAG-TTTTAT-AA
1 TTATTTATAAGCTTTTATGAA
28598396 TTATTTAT
1 TTATTTAT
28598404 TTATGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATTTATAAGCTTTTATGAA
Found at i:28598599 original size:56 final size:58
Alignment explanation
Indices: 28598529--28598663 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 58
28598519 TAATGGATAA
* * * *
28598529 GCTTAATTAAATTTTTTT-ATTAACAAC-AACTCAATTGAGTGTGAATTAAGTTGAGTG
1 GCTTAATT-GATTTTTTTAATTAACAACAAACTCAATTGAGAGTGAAGTAAGTTGAGGG
* * *
28598586 GTTTAATTGATTTTTTTAATTAACAACAAAAATTCAATTGGGAGTGAAGTAAGTTGAGGG
1 GCTTAATTGATTTTTTTAATTAACAAC--AAACTCAATTGAGAGTGAAGTAAGTTGAGGG
28598646 GCTTAATTGATTTATTTT
1 GCTTAATTGATTT-TTTT
28598664 TCTTAGGAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 8 0.12
57 16 0.25
60 37 0.57
61 4 0.06
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (58 bp):
GCTTAATTGATTTTTTTAATTAACAACAAACTCAATTGAGAGTGAAGTAAGTTGAGGG
Found at i:28600685 original size:26 final size:26
Alignment explanation
Indices: 28600649--28600703 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
28600639 TTTGAAATTT
* *
28600649 ATTCGAATTGAATCAAGTGGAATGAA
1 ATTCGAATTGAATCAAATCGAATGAA
* *
28600675 ATTCGAGTTGAGTCAAATCGAATGAA
1 ATTCGAATTGAATCAAATCGAATGAA
28600701 ATT
1 ATT
28600704 GTTAAAGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (26 bp):
ATTCGAATTGAATCAAATCGAATGAA
Found at i:28604135 original size:29 final size:29
Alignment explanation
Indices: 28604093--28604150 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28604083 TTCCGAACGG
28604093 TGGATTTAACGCTTAGACTGAGAAGAACA
1 TGGATTTAACGCTTAGACTGAGAAGAACA
28604122 TGGATTTAACGCTTAGACTGAGAAGAACA
1 TGGATTTAACGCTTAGACTGAGAAGAACA
28604151 ACATACCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (29 bp):
TGGATTTAACGCTTAGACTGAGAAGAACA
Found at i:28611951 original size:16 final size:18
Alignment explanation
Indices: 28611916--28611953 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28611906 ATCCTTATTT
28611916 AAATAAAATACAATAGTA
1 AAATAAAATACAATAGTA
28611934 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
28611950 AAAT
1 AAAT
28611954 CCCTATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:28614406 original size:2 final size:2
Alignment explanation
Indices: 28614399--28614429 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28614389 GGGTAGCCTG
28614399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28614430 CTCAGCTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.