Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009235.1 Hibiscus syriacus cultivar Beakdansim tig00112857_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1478786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:346889 original size:2 final size:2
Alignment explanation
Indices: 346882--346910 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
346872 ATTAAATTTG
346882 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
346911 TATGATTGTT
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:356577 original size:29 final size:29
Alignment explanation
Indices: 356542--356623 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
356532 AAACTAAATT
*
356542 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
356571 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
356600 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
356624 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:361345 original size:29 final size:29
Alignment explanation
Indices: 361310--361391 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
361300 AAACTAAATT
*
361310 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
361339 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
361368 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
361392 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:364995 original size:17 final size:17
Alignment explanation
Indices: 364969--365001 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
364959 GTTAAAACAT
364969 AAAATATGACTTTTTGA
1 AAAATATGACTTTTTGA
*
364986 AAAATTTGACTTTTTG
1 AAAATATGACTTTTTG
365002 GTCAAAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAATATGACTTTTTGA
Found at i:368694 original size:19 final size:21
Alignment explanation
Indices: 368670--368709 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
368660 CATGCCAGTC
368670 AAACAATAAAA-AATT-ATTT
1 AAACAATAAAAGAATTGATTT
368689 AAACAATAAAAGAATTGATTT
1 AAACAATAAAAGAATTGATTT
368710 TGTTGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 4 0.21
21 4 0.21
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (21 bp):
AAACAATAAAAGAATTGATTT
Found at i:380776 original size:21 final size:22
Alignment explanation
Indices: 380750--380792 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
380740 TATATTATTT
*
380750 CACATA-TTTTTATCACATAGG
1 CACATACTTCTTATCACATAGG
380771 CACATAGCTTCTTATCACATAG
1 CACATA-CTTCTTATCACATAG
380793 CTCCTTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (22 bp):
CACATACTTCTTATCACATAGG
Found at i:380791 original size:15 final size:15
Alignment explanation
Indices: 380771--380802 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
380761 ATCACATAGG
*
380771 CACATAGCTTCTTAT
1 CACATAGCTCCTTAT
380786 CACATAGCTCCTTAT
1 CACATAGCTCCTTAT
380801 CA
1 CA
380803 TATCATTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.34
Consensus pattern (15 bp):
CACATAGCTCCTTAT
Found at i:381034 original size:18 final size:18
Alignment explanation
Indices: 380998--381037 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
380988 TTGTGTTTAT
**
380998 ATATATATATATATTCTC
1 ATATATATATATAAACTC
381016 ATATATATATATAAACTC
1 ATATATATATATAAACTC
381034 ATAT
1 ATAT
381038 TTTCTCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATATATATATAAACTC
Found at i:383889 original size:2 final size:2
Alignment explanation
Indices: 383882--383949 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
383872 TGTATATCAC
383882 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
383924 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
383950 TTATTATCCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384528 original size:12 final size:12
Alignment explanation
Indices: 384511--384547 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
384501 ATGACGACTC
384511 TAAATTTCAAAT
1 TAAATTTCAAAT
384523 TAAATTTCAAAT
1 TAAATTTCAAAT
384535 TAAATTTCAAAT
1 TAAATTTCAAAT
384547 T
1 T
384548 TATTAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAATTTCAAAT
Found at i:392983 original size:36 final size:36
Alignment explanation
Indices: 392937--393005 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
392927 AAAGCAAATT
392937 TTTTATCTCGCATAG-GATAACTTCTTTTGAAACTAA
1 TTTTATCTCGC-TAGAGATAACTTCTTTTGAAACTAA
* *
392973 TTTTGTCTCGCTCGAGATAACTTCTTTTGAAAC
1 TTTTATCTCGCTAGAGATAACTTCTTTTGAAAC
393006 CCAAAGCATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTTATCTCGCTAGAGATAACTTCTTTTGAAACTAA
Found at i:393451 original size:19 final size:20
Alignment explanation
Indices: 393427--393501 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
393417 AAATGACCAA
393427 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACGCGATCTC
* * *
393446 CAAATTCGCAATGCAAACTC
1 CAAATTCGCAACGCGATCTC
* * *
393466 CAATTTCGCAAC-CCACTTTC
1 CAAATTCGCAACGCGA-TCTC
393486 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
393502 ACATGTAAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 18 0.42
20 23 0.53
21 2 0.05
ACGTcount: A:0.33, C:0.33, G:0.12, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGATCTC
Found at i:393535 original size:21 final size:21
Alignment explanation
Indices: 393511--393557 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
393501 AACATGTAAA
*
393511 TCGCATTGCAATTTTCCAAAT
1 TCGCATTACAATTTTCCAAAT
* **
393532 TCGCGTTACGGTTTTCCAAAT
1 TCGCATTACAATTTTCCAAAT
393553 TCGCA
1 TCGCA
393558 ACGCGAATCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTACAATTTTCCAAAT
Found at i:393578 original size:20 final size:20
Alignment explanation
Indices: 393553--393601 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
393543 TTTTCCAAAT
*
393553 TCGCAACGCGAATCTGTAAA
1 TCGCAACACGAATCTGTAAA
*
393573 TCGCAACACGAATTTGTAAA
1 TCGCAACACGAATCTGTAAA
*
393593 TAGCAACAC
1 TCGCAACAC
393602 ATAAGTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.20
Consensus pattern (20 bp):
TCGCAACACGAATCTGTAAA
Found at i:393617 original size:40 final size:39
Alignment explanation
Indices: 393573--393702 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
393563 AATCTGTAAA
* *
393573 TCGCAACACGAATTTGTAAATAGCAACACATAAGTCATAT
1 TCGCAACAC-AATTTGTAAATCGCAACACATAAGTCAAAT
* * *
393613 TCGCAACGCAA-TAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAATTTGT-AAA-TCGCAACACATAAGTCAAAT
* *
393653 TCGCAACGCAAATCTGTAAATCGCAACACATAAGTCAAAT
1 TCGCAACAC-AATTTGTAAATCGCAACACATAAGTCAAAT
393693 TCGCAACACA
1 TCGCAACACA
393703 GAAGTCAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.04
39 6 0.08
40 61 0.79
41 5 0.06
42 2 0.03
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (39 bp):
TCGCAACACAATTTGTAAATCGCAACACATAAGTCAAAT
Found at i:393618 original size:20 final size:19
Alignment explanation
Indices: 393595--393733 Score: 138
Period size: 20 Copynumber: 6.9 Consensus size: 19
393585 TTTGTAAATA
*
393595 GCAACACATAAGTCATATTC
1 GCAACACA-AAGTCAAATTC
*
393615 GCAACGCAATAGTCAAATTC
1 GCAACACAA-AGTCAAATTC
393635 GCAACACAAAAGTCAAATTC
1 GCAACAC-AAAGTCAAATTC
*
393655 GCAACGCAAA-TCTGTAAA-TC
1 GCAACACAAAGTC---AAATTC
393675 GCAACACATAAGTCAAATTC
1 GCAACACA-AAGTCAAATTC
393695 GCAACACAGAAGTCAAATTC
1 GCAACACA-AAGTCAAATTC
* *
393715 GCAACGCGATAGTCAAATT
1 GCAACAC-AAAGTCAAATT
393734 TGAAACACTG
Statistics
Matches: 102, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.02
19 7 0.07
20 83 0.81
21 8 0.08
22 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.19
Consensus pattern (19 bp):
GCAACACAAAGTCAAATTC
Found at i:393657 original size:80 final size:80
Alignment explanation
Indices: 393573--393748 Score: 228
Period size: 80 Copynumber: 2.2 Consensus size: 80
393563 AATCTGTAAA
* *
393573 TCGCAACACGAATTTGTAAATAGCAACACATAAGTCATATTCGCAACGCA-ATAGTCAAATTCGC
1 TCGCAACACGAATTTGTAAATAGCAACACATAAGTCAAATTCGCAACACAGA-AGTCAAATTCGC
393637 AACACAAAAGTCAAAT
65 AACACAAAAGTCAAAT
* * * *
393653 TCGCAACGCAAATCTGTAAATCGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAATTCGCA
1 TCGCAACACGAATTTGTAAATAGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAATTCGCA
* * *
393718 ACGCGATAGTCAAAT
66 ACACAAAAGTCAAAT
* *
393733 TTGAAACACTGAATTT
1 TCGCAACAC-GAATTT
393749 CAAATTCGCA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
80 75 0.94
81 5 0.06
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.22
Consensus pattern (80 bp):
TCGCAACACGAATTTGTAAATAGCAACACATAAGTCAAATTCGCAACACAGAAGTCAAATTCGCA
ACACAAAAGTCAAAT
Found at i:393717 original size:40 final size:39
Alignment explanation
Indices: 393595--393760 Score: 158
Period size: 40 Copynumber: 4.1 Consensus size: 39
393585 TTTGTAAATA
* *
393595 GCAACACATAAGTCATATTCGCAACGCAATAGTCAAATTC
1 GCAACACATAAGTCAAATTCGCAACACAA-AGTCAAATTC
* *
393635 GCAACACAAAAGTCAAATTCGCAACGCAAA-TCTGTAAA-TC
1 GCAACACATAAGTCAAATTCGCAACACAAAGTC---AAATTC
393675 GCAACACATAAGTCAAATTCGCAACACAGAAGTCAAATTC
1 GCAACACATAAGTCAAATTCGCAACACA-AAGTCAAATTC
* * * **
393715 GCAACGCGAT-AGTCAAATTTGAAACACTGAATTTCAAATTC
1 GCAACAC-ATAAGTCAAATTCGCAACAC--AAAGTCAAATTC
393756 GCAAC
1 GCAAC
393761 TCGATTTTCG
Statistics
Matches: 108, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
38 2 0.02
39 4 0.04
40 78 0.72
41 21 0.19
42 3 0.03
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.20
Consensus pattern (39 bp):
GCAACACATAAGTCAAATTCGCAACACAAAGTCAAATTC
Found at i:393741 original size:60 final size:60
Alignment explanation
Indices: 393625--393760 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 60
393615 GCAACGCAAT
* *
393625 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCAAATCTGTAAATCGCAACACAT-A
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCAAATCAGTAAATCGAAACAC-TGA
* * *
393685 AGTCAAATTCGCAACACAGAAGTCAAATTCGCAACGC-GAT-AGTCAAATTTGAAACACTGA
1 AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCAAATCAGT-AAA-TCGAAACACTGA
*
393745 ATTTCAAATTCGCAAC
1 A-GTCAAATTCGCAAC
393761 TCGATTTTCG
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
58 2 0.03
59 6 0.09
60 45 0.68
61 13 0.20
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.21
Consensus pattern (60 bp):
AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCAAATCAGTAAATCGAAACACTGA
Found at i:394609 original size:12 final size:12
Alignment explanation
Indices: 394588--394621 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
394578 ACCACATTTC
*
394588 CAATACCAAACA
1 CAATATCAAACA
394600 CAATATCAAACA
1 CAATATCAAACA
*
394612 CAATCTCAAA
1 CAATATCAAA
394622 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:394766 original size:24 final size:24
Alignment explanation
Indices: 394734--394801 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
394724 GTGAGTACTA
*
394734 GTCAGTATCCGGACTTTGATCTTG
1 GTCAATATCCGGACTTTGATCTTG
*
394758 GTCAATATCTGGACTTTGATCTTG
1 GTCAATATCCGGACTTTGATCTTG
*
394782 GTCAATA-CTCGGATTTTGAT
1 GTCAATATC-CGGACTTTGAT
394802 GATGTTTCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.03
24 38 0.97
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (24 bp):
GTCAATATCCGGACTTTGATCTTG
Found at i:397477 original size:66 final size:64
Alignment explanation
Indices: 397395--397538 Score: 243
Period size: 66 Copynumber: 2.2 Consensus size: 64
397385 AATTTAAAAC
397395 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAG-AAAAAAATAATTCTTATTTACACATC-AATT
397460 A
64 A
* * *
397461 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAGTAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
397525 AACAAATCAACTTT
1 AACAAATCAACTTT
397539 CAATTAAACA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
64 19 0.25
65 23 0.31
66 33 0.44
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:398933 original size:21 final size:21
Alignment explanation
Indices: 398909--399007 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
398899 GAGGGACCCA
* *
398909 TTGAATGATGACATGGGCCTC
1 TTGAACGATGACAGGGGCCTC
* **
398930 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGACAGGGGCCTC
* *
398951 TTGAACGATGAGAGGAGCCTC
1 TTGAACGATGACAGGGGCCTC
* * * *
398972 TTAAACGAT-AGGAGGCGCCTT
1 TTGAACGATGA-CAGGGGCCTC
*
398993 TTGAACGGTGACAGG
1 TTGAACGATGACAGG
399008 TGAATCAGGC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.22
Consensus pattern (21 bp):
TTGAACGATGACAGGGGCCTC
Found at i:398955 original size:42 final size:42
Alignment explanation
Indices: 398885--399007 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
398875 GTGAATCGGG
* * *
398885 CTCTTGAATGGTGGGAGGGACC-CATTGAATGATGACATGG-GC
1 CTCTTGAACGGTGGGAGGGGCCTC-TTGAACGATGACA-GGAGC
*
398927 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGAGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGAGC
* * * * * *
398969 CTCTTAAACGATAGGAGGCGCCTTTTGAACGGTGACAGG
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGG
399008 TGAATCAGGC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 65 0.96
43 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGACAGGAGC
Found at i:401532 original size:22 final size:22
Alignment explanation
Indices: 401505--401547 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
401495 GGAGATAGAC
*
401505 GGATTTCGCCGGAGATGGGGAT
1 GGATTTCGCCGGAGATAGGGAT
*
401527 GGATTTCGTCGGAGATAGGGA
1 GGATTTCGCCGGAGATAGGGA
401548 CAGATGTCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.44, T:0.23
Consensus pattern (22 bp):
GGATTTCGCCGGAGATAGGGAT
Found at i:401737 original size:20 final size:20
Alignment explanation
Indices: 401712--401947 Score: 264
Period size: 20 Copynumber: 11.8 Consensus size: 20
401702 TAAACGCGCT
*
401712 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGTG
*
401732 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
**
401752 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTGACTTTC-GTG
* * *
401773 TTGCGAATTTTACTATCGCG
1 TTGCGAATTTGACTTTCGTG
401793 TTGCGAATTTGAC-TTCTGTG
1 TTGCGAATTTGACTTTC-GTG
*
401813 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGTG
*
401833 TTGCG-ATTT-ACATATTTGTG
1 TTGCGAATTTGAC-T-TTCGTG
* *
401853 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
* *
401873 TTGCGAATTTGAATTTTGTG
1 TTGCGAATTTGACTTTCGTG
401893 TTGCGAATTTGAC-TTCAGTG
1 TTGCGAATTTGACTTTC-GTG
* *
401913 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTCGTG
401933 TTGCGAATTTGACTT
1 TTGCGAATTTGACTT
401948 CTGTGTTACG
Statistics
Matches: 181, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
18 2 0.01
19 9 0.05
20 143 0.79
21 25 0.14
22 2 0.01
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGTG
Found at i:401863 original size:60 final size:60
Alignment explanation
Indices: 401712--401982 Score: 286
Period size: 60 Copynumber: 4.5 Consensus size: 60
401702 TAAACGCGCT
* * * *
401712 TTGCGAATTTGACT-TTCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAAATTCAGTG
1 TTGCGAATTT-ACTATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTG-AATTCTGTG
* * *
401773 TTGCGAATTTTACTA-TCGCGTTGCGAATTTGACT-TCTGTGTTGCGAATTTGACTTTTGTG
1 TTGCGAA-TTTACTATTCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGAATTCTGTG
* * *
401833 TTGCG-ATTTACATATTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGAATTTTGTG
1 TTGCGAATTTAC-TATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGAATTCTGTG
* *
401893 TTGCGAATTTGAC--TTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTT-ACTATTC-GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGAATTCTGTG
* * *
401953 TTACG-ATTTACAAATTCACGTTGCGAATTT
1 TTGCGAATTTAC-TATTCGCGTTGCGAATTT
401983 TGAAACTGGG
Statistics
Matches: 184, Mismatches: 14, Indels: 25
0.83 0.06 0.11
Matches are distributed among these distances:
58 7 0.04
59 9 0.05
60 111 0.60
61 52 0.28
62 5 0.03
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (60 bp):
TTGCGAATTTACTATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGAATTCTGTG
Found at i:401975 original size:40 final size:41
Alignment explanation
Indices: 401726--401982 Score: 212
Period size: 40 Copynumber: 6.4 Consensus size: 41
401716 GAATTTGACT
* *
401726 TTCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTT-GAAA
1 TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTACAAA
* * *
401766 TTCAGTGTTGCGAATTTTACTATC-GCGTTGCGAATTTGAC---
1 TTC-GCGTTGCGAATTTGACT-TCTGTGTTGCGAATTT-ACAAA
* * *
401806 TTCTGTGTTGCGAATTTGACTTTTGTGTTGCG-ATTTACATA
1 TTC-GCGTTGCGAATTTGACTTCTGTGTTGCGAATTTACAAA
* * * * *
401847 TTTGTGTTGCGAATTTGACTATC-GCGTTGCGAATTT-GAAT
1 TTCGCGTTGCGAATTTGACT-TCTGTGTTGCGAATTTACAAA
* * * *
401887 TTTGTGTTGCGAATTTGACTTCAGTGTTGCGAATTTGAC-TA
1 TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTT-ACAAA
*
401928 -TCGCGTTGCGAATTTGACTTCTGTGTTACG-ATTTACAAA
1 TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTACAAA
*
401967 TTCACGTTGCGAATTT
1 TTCGCGTTGCGAATTT
401983 TGAAACTGGG
Statistics
Matches: 177, Mismatches: 25, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
38 4 0.02
39 12 0.07
40 126 0.71
41 34 0.19
42 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (41 bp):
TTCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTACAAA
Found at i:403839 original size:2 final size:2
Alignment explanation
Indices: 403834--403869 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
403824 ACACACACAC
403834 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
403870 TTCTTATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:406231 original size:21 final size:20
Alignment explanation
Indices: 406205--406302 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
406195 ATCAGTTTCC
406205 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
406226 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
**
406245 ACAAATTCGCATTGCGATTTT-
1 A-AAA-TCGCAACGCGATTTTG
* *
406266 ACAGAATCGCAACGCGAATATG
1 A-A-AATCGCAACGCGATTTTG
406288 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
406303 ACACATAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.27
21 42 0.67
22 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:406364 original size:20 final size:20
Alignment explanation
Indices: 406270--406498 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
406260 GATTTTACAG
* ** *
406270 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
406290 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
406310 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
406330 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
406350 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
406370 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
406390 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
406410 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
406430 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
406450 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
406470 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
406490 AATCACAAC
1 AATCGCAAC
406499 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:407230 original size:24 final size:24
Alignment explanation
Indices: 407191--407237 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
407181 AAATTTGGTC
407191 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
407215 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
407238 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:407429 original size:12 final size:12
Alignment explanation
Indices: 407412--407436 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
407402 ATATAATCCT
407412 GAAGAAGAAAAA
1 GAAGAAGAAAAA
407424 GAAGAAGAAAAA
1 GAAGAAGAAAAA
407436 G
1 G
407437 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:409803 original size:53 final size:52
Alignment explanation
Indices: 409735--409957 Score: 367
Period size: 53 Copynumber: 4.2 Consensus size: 52
409725 GCAACGAGAG
* *
409735 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
*
409788 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
409841 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
409893 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
409945 AATCGCATTGCGA
1 AATCGCAATGCGA
409958 TTCTCTCGTT
Statistics
Matches: 163, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
52 71 0.44
53 91 0.56
54 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:409804 original size:19 final size:19
Alignment explanation
Indices: 409735--409957 Score: 225
Period size: 19 Copynumber: 12.7 Consensus size: 19
409725 GCAACGAGAG
409735 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
409754 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
409768 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
409788 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
409807 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
409821 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
409841 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
409860 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
409874 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
409893 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
409912 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
409926 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
409945 AATCGCATTGCGA
1 AATCGCAATGCGA
409958 TTCTCTCGTT
Statistics
Matches: 170, Mismatches: 12, Indels: 44
0.75 0.05 0.19
Matches are distributed among these distances:
14 42 0.25
15 3 0.02
16 6 0.04
17 7 0.04
18 2 0.01
19 82 0.48
20 28 0.16
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:409878 original size:86 final size:84
Alignment explanation
Indices: 409721--409900 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
409711 CGGAAATTAC
409721 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
*
409786 AAAATCGCAATGTGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
409807 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
409870 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
409893 AATCGCAA
1 AATCGCAA
409901 TGCGAAATGA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:409897 original size:33 final size:33
Alignment explanation
Indices: 409721--409900 Score: 161
Period size: 33 Copynumber: 5.2 Consensus size: 33
409711 CGGAAATTAC
*
409721 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
409754 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
* * * * *
409788 AATCGCAATGTG-AAAT-GAAAAT-CGCAACGAGA
1 AATCGCAACGAGAAAATCG-CAATGCGAAATGA-A
409820 GAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAA
*
409860 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
409893 AATCGCAA
1 AATCGCAA
409901 TGCGAAATGA
Statistics
Matches: 118, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
31 5 0.04
32 4 0.03
33 65 0.55
34 17 0.14
36 2 0.02
37 1 0.01
39 9 0.08
40 8 0.07
41 7 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:409930 original size:33 final size:33
Alignment explanation
Indices: 409788--409951 Score: 154
Period size: 33 Copynumber: 4.8 Consensus size: 33
409778 CGGAAATGAA
*
409788 AATCGCAATGTGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
409821 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
409854 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
409893 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
409926 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
409952 TTGCGATTCT
Statistics
Matches: 106, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 51 0.48
34 20 0.19
35 1 0.01
36 2 0.02
38 10 0.09
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:410060 original size:52 final size:53
Alignment explanation
Indices: 409947--410063 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
409937 GAAATTAAAA
409947 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
410000 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
410052 TCGCATTGCGAT
1 TCGCATTGCGAT
410064 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:410071 original size:19 final size:19
Alignment explanation
Indices: 409966--410063 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
409956 GATTCTCTCG
409966 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
409986 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
410005 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
410019 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
410038 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
410057 TTGCGAT
1 TTGCGAT
410064 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:410189 original size:14 final size:14
Alignment explanation
Indices: 410170--410206 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
410160 CATCAATTAC
410170 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
410184 ACAAATCATCTTTT
1 ACAAATCAACTTTT
410198 ACAAATCAA
1 ACAAATCAA
410207 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:411276 original size:20 final size:20
Alignment explanation
Indices: 411245--411341 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
411235 TTTTGGTTGA
411245 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
411265 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
411285 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
411304 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
411319 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
411339 AAT
1 AAT
411342 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:411297 original size:21 final size:21
Alignment explanation
Indices: 411243--411307 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
411233 TCTTTTGGTT
411243 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
411264 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
411284 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
411305 GAA
1 GAA
411308 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:411311 original size:14 final size:14
Alignment explanation
Indices: 411292--411348 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
411282 GAGAAATGAA
411292 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
411306 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
411325 AATCGCAACGAGAG
1 AATCGCAACGAGAG
411339 AATCGCAACG
1 AATCGCAACG
411349 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:411324 original size:33 final size:33
Alignment explanation
Indices: 411243--411365 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
411233 TCTTTTGGTT
*
411243 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
411284 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
411317 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
411350 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
411366 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:411439 original size:21 final size:20
Alignment explanation
Indices: 411393--411485 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
411383 GTTGCGATTC
411393 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
411412 TCGCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCA-TTT
**
411433 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
411454 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
411474 ATCTCGTTGCGA
1 -TCTCGTTGCGA
411486 CTCTTCTGCA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
19 16 0.26
20 9 0.15
21 31 0.50
22 6 0.10
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:411461 original size:42 final size:40
Alignment explanation
Indices: 411393--411485 Score: 132
Period size: 42 Copynumber: 2.3 Consensus size: 40
411383 GTTGCGATTC
** * *
411393 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCATTTA
411433 TCTCGTTGCAGATAGTCATTTTCACGTTGCGATTTTCATTTA
1 TCTCGTTGC-GATAGTCA-TTTCACGTTGCGATTTTCATTTA
411475 TCTCGTTGCGA
1 TCTCGTTGCGA
411486 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
40 9 0.19
41 8 0.17
42 30 0.64
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTCACGTTGCGATTTTCATTTA
Found at i:411607 original size:33 final size:33
Alignment explanation
Indices: 411565--411635 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
411555 AATACTAACT
*
411565 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* *
411598 TGAAAATCGCAACAAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
411631 TGAAA
1 TGAAA
411636 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:412043 original size:20 final size:20
Alignment explanation
Indices: 412018--412207 Score: 231
Period size: 20 Copynumber: 9.4 Consensus size: 20
412008 TAAAAATCGT
412018 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
412038 GTTGCGATTTTACGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
*
412059 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATACGC
*
412079 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
412099 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
412119 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
412139 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
412159 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
412179 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
412199 GTTGCGATT
1 GTTGCGATT
412208 CTGTAAAATT
Statistics
Matches: 147, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 129 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:415215 original size:14 final size:14
Alignment explanation
Indices: 415186--415269 Score: 113
Period size: 14 Copynumber: 6.1 Consensus size: 14
415176 CGTTCGTGAA
415186 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
415202 CGTTCATTTATGTT
1 CGTTCATTTATGTT
415216 CGTTCATTTA---T
1 CGTTCATTTATGTT
415227 -GTTCATTTATGTT
1 CGTTCATTTATGTT
415240 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
415254 TGTTCATTTATGTT
1 CGTTCATTTATGTT
415268 CG
1 CG
415270 AGTAGAGGGC
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
10 9 0.15
11 1 0.02
13 1 0.02
14 43 0.69
15 3 0.05
16 5 0.08
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:415230 original size:10 final size:10
Alignment explanation
Indices: 415217--415268 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
415207 ATTTATGTTC
415217 GTTCATTTAT
1 GTTCATTTAT
415227 GTTCATTTAT
1 GTTCATTTAT
* *
415237 GTTCGTTCAT
1 GTTCATTTAT
415247 -TT-ATGTT-T
1 GTTCAT-TTAT
415255 GTTCATTTAT
1 GTTCATTTAT
415265 GTTC
1 GTTC
415269 GAGTAGAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
8 2 0.06
9 7 0.21
10 25 0.74
ACGTcount: A:0.15, C:0.12, G:0.13, T:0.60
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:415232 original size:24 final size:24
Alignment explanation
Indices: 415203--415253 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
415193 TTATATGTTC
415203 GTTCATTTATGTTCGTTCATTTAT
1 GTTCATTTATGTTCGTTCATTTAT
415227 GTTCATTTATGTTCGTTCATTTAT
1 GTTCATTTATGTTCGTTCATTTAT
415251 GTT
1 GTT
415254 TGTTCATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.59
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTCATTTAT
Found at i:415247 original size:38 final size:40
Alignment explanation
Indices: 415187--415270 Score: 145
Period size: 38 Copynumber: 2.1 Consensus size: 40
415177 GTTCGTGAAC
415187 GTTCGATTATATGTTCGTTCATTTATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTATGTTCGTTCATTTAT
*
415227 GTTC-ATT-TATGTTCGTTCATTTATGTTTGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTATGTTCGTTCATTTAT
415265 GTTCGA
1 GTTCGA
415271 GTAGAGGGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 34 0.81
39 4 0.10
40 4 0.10
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.56
Consensus pattern (40 bp):
GTTCGATTATATGTTCGTTCATTTATGTTCGTTCATTTAT
Found at i:415588 original size:24 final size:23
Alignment explanation
Indices: 415541--415602 Score: 97
Period size: 24 Copynumber: 2.7 Consensus size: 23
415531 TGTTCATTTA
415541 TTATGTTCGTTTATTGTATTCGT
1 TTATGTTCGTTTATTGTATTCGT
* *
415564 TTATATTCGTTTGTTCGTATTCGT
1 TTATGTTCGTTTATT-GTATTCGT
415588 TTATGTTCGTTTATT
1 TTATGTTCGTTTATT
415603 ATTTAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.38
24 21 0.62
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.61
Consensus pattern (23 bp):
TTATGTTCGTTTATTGTATTCGT
Found at i:424791 original size:56 final size:56
Alignment explanation
Indices: 424723--424834 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
424713 CCGATTGCTG
424723 AATTAAGAGCCACTAAAAACCAGACTCAAACTCGGATGTGATTAATCTTTAATATT
1 AATTAAGAGCCACTAAAAACCAGACTCAAACTCGGATGTGATTAATCTTTAATATT
* *
424779 AATTAAGTGCCACTAAAAACCAGACTCAAACTCGGGTGTGATTAATCTTTAATATT
1 AATTAAGAGCCACTAAAAACCAGACTCAAACTCGGATGTGATTAATCTTTAATATT
424835 TTTTCCATGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (56 bp):
AATTAAGAGCCACTAAAAACCAGACTCAAACTCGGATGTGATTAATCTTTAATATT
Found at i:439850 original size:30 final size:30
Alignment explanation
Indices: 439814--439874 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
439804 TCCCACCCAT
439814 TTACCATCCCTAATTCTAATACTATACAAC
1 TTACCATCCCTAATTCTAATACTATACAAC
439844 TTACCATCCCTAATTCTAATACTATACAAC
1 TTACCATCCCTAATTCTAATACTATACAAC
439874 T
1 T
439875 GTTGTGGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (30 bp):
TTACCATCCCTAATTCTAATACTATACAAC
Found at i:440116 original size:12 final size:12
Alignment explanation
Indices: 440101--440138 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
440091 GTTATTTAAA
440101 CGGGTATTGGGC
1 CGGGTATTGGGC
*
440113 CGGGTATTGGGT
1 CGGGTATTGGGC
440125 CGGGTATTGGGC
1 CGGGTATTGGGC
440137 CG
1 CG
440139 AGAATCGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:440154 original size:24 final size:24
Alignment explanation
Indices: 440103--440155 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
440093 TATTTAAACG
* * * * *
440103 GGTATTGGGCCGGGTATTGGGTCG
1 GGTATTGGGCCGAGAATCGGGCCA
440127 GGTATTGGGCCGAGAATCGGGCCA
1 GGTATTGGGCCGAGAATCGGGCCA
440151 GGTAT
1 GGTAT
440156 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.45, T:0.25
Consensus pattern (24 bp):
GGTATTGGGCCGAGAATCGGGCCA
Found at i:440213 original size:24 final size:25
Alignment explanation
Indices: 440153--440231 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 25
440143 TCGGGCCAGG
440153 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
440176 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
440200 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
440225 TATATAT
1 TATATAT
440232 AAATAATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.09
23 8 0.18
24 24 0.55
25 4 0.09
26 1 0.02
27 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:443512 original size:41 final size:41
Alignment explanation
Indices: 443444--443675 Score: 270
Period size: 41 Copynumber: 5.7 Consensus size: 41
443434 GTTTTAGAAT
* * *
443444 AAACGCCGCTAAATAATCGTACTTTAGTGTCGTTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCG-TTTTTATAC
* * *
443486 AAACGCCGCTAAAGACTCGTAC-TTAGTGGCATCTTCATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
443526 AAACGCCGCTAAAGACTTGTACTTTATTGGTGTTTTCT-TAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTT-TATAC
* * *
443567 GAACGCTGCTAAAGACTCGTGCTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* **
443608 AAACTCCGCTAAAGACTCGTGTTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
443649 AAACTCTGCTAAAGACTCGTGCTTTAG
1 AAACGCCGCTAAAGACTCGTACTTTAG
443676 CGACAATTTT
Statistics
Matches: 163, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
40 29 0.18
41 114 0.70
42 20 0.12
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:443602 original size:123 final size:123
Alignment explanation
Indices: 443445--443674 Score: 309
Period size: 123 Copynumber: 1.9 Consensus size: 123
443435 TTTTAGAATA
* *
443445 AACGCCGCTAAATAATCGTACTTTAGTGTCGTTTTTTATACAAACGCCGCTAAAGACTCGT-ACT
1 AACGCCGCTAAAGAATCGTACTTTAGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTGACT
*
443509 TAGTGGCATCTTCATACAAACGCCGCTAAAGACTTGTACTTTATTGGTGTTTTCTTACG
65 TAGTGGCATCTTCATACAAACGCCGCTAAAGACTCGTACTTTATTGGTGTTTTCTTACG
* * * * **
443568 AACGCTGCTAAAGACTCGTGCTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACTCGTGTTTT
1 AACGCCGCTAAAGAATCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTGACTT
* * * * * *
443633 AGTGGCGTTTTTATACAAACTCTGCTAAAGACTCGTGCTTTA
66 AGTGGCATCTTCATACAAACGCCGCTAAAGACTCGTACTTTA
443675 GCGACAATTT
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
122 28 0.31
123 63 0.69
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (123 bp):
AACGCCGCTAAAGAATCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTGACTT
AGTGGCATCTTCATACAAACGCCGCTAAAGACTCGTACTTTATTGGTGTTTTCTTACG
Found at i:447667 original size:14 final size:14
Alignment explanation
Indices: 447648--447677 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
447638 AACATATATA
*
447648 GTTAGTGGTTTAGG
1 GTTAGTGGTATAGG
447662 GTTAGTGGTATAGG
1 GTTAGTGGTATAGG
447676 GT
1 GT
447678 AAGAGATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (14 bp):
GTTAGTGGTATAGG
Found at i:448011 original size:28 final size:28
Alignment explanation
Indices: 447976--448033 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
447966 TTGAAGTCTA
*
447976 GGGTTAAGGTTTATGGT-TTGAGGTA-AG
1 GGGTTAAGGTCTATGGTATTG-GGTATAG
448003 GGGTATAAGGTCTATGGTATTGGGTATAG
1 GGGT-TAAGGTCTATGGTATTGGGTATAG
448032 GG
1 GG
448034 ATATGAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 16 0.59
29 7 0.26
ACGTcount: A:0.22, C:0.02, G:0.41, T:0.34
Consensus pattern (28 bp):
GGGTTAAGGTCTATGGTATTGGGTATAG
Found at i:448579 original size:14 final size:14
Alignment explanation
Indices: 448560--448586 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
448550 GTCAGTGTTT
448560 ATGGTTTAGGGTTA
1 ATGGTTTAGGGTTA
448574 ATGGTTTAGGGTT
1 ATGGTTTAGGGTT
448587 CAAAGTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (14 bp):
ATGGTTTAGGGTTA
Found at i:448759 original size:21 final size:21
Alignment explanation
Indices: 448735--448778 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
448725 CCAATGTCAG
*
448735 TGGTCATGGGTCTA-GGGTCTA
1 TGGTCATAGGTC-AGGGGTCTA
*
448756 TGGTCCTAGGTCAGGGGTCTA
1 TGGTCATAGGTCAGGGGTCTA
448777 TG
1 TG
448779 AGACTAGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.14, C:0.16, G:0.39, T:0.32
Consensus pattern (21 bp):
TGGTCATAGGTCAGGGGTCTA
Found at i:470088 original size:30 final size:30
Alignment explanation
Indices: 470052--470119 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
470042 AGATTTGGAA
470052 GAATTCAAGGATGTGTAAAGGAGGGAAAGG
1 GAATTCAAGGATGTGTAAAGGAGGGAAAGG
470082 GAATTCAAGGATGTGTAAAGGAGGGAAAGG
1 GAATTCAAGGATGTGTAAAGGAGGGAAAGG
470112 GAATTCAA
1 GAATTCAA
470120 TTGCGGTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.04, G:0.37, T:0.18
Consensus pattern (30 bp):
GAATTCAAGGATGTGTAAAGGAGGGAAAGG
Found at i:478977 original size:23 final size:23
Alignment explanation
Indices: 478947--478993 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
478937 TAATTATACA
478947 TGTGTTGCAAGTTTATCTATGTC
1 TGTGTTGCAAGTTTATCTATGTC
* *
478970 TGTGTTGCACGTTTATCTCTGTC
1 TGTGTTGCAAGTTTATCTATGTC
478993 T
1 T
478994 TTGTAGCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (23 bp):
TGTGTTGCAAGTTTATCTATGTC
Found at i:479002 original size:23 final size:23
Alignment explanation
Indices: 478947--479006 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
478937 TAATTATACA
* *
478947 TGTGTTGCAAGTTTATCTATGTC
1 TGTGTAGCACGTTTATCTATGTC
* *
478970 TGTGTTGCACGTTTATCTCTGTC
1 TGTGTAGCACGTTTATCTATGTC
*
478993 TTTGTAGCACGTTT
1 TGTGTAGCACGTTT
479007 TTTAGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (23 bp):
TGTGTAGCACGTTTATCTATGTC
Found at i:479975 original size:2 final size:2
Alignment explanation
Indices: 479968--479999 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
479958 AGTTAGAAGA
479968 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
480000 TCAAATTTGC
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:481564 original size:19 final size:19
Alignment explanation
Indices: 481540--481576 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
481530 ATGTATATCT
481540 CCCCCTCCCCTGTTGTCCC
1 CCCCCTCCCCTGTTGTCCC
* *
481559 CCCCCTTCCTTGTTGTCC
1 CCCCCTCCCCTGTTGTCC
481577 TTCCCCTGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.57, G:0.11, T:0.32
Consensus pattern (19 bp):
CCCCCTCCCCTGTTGTCCC
Found at i:482239 original size:29 final size:28
Alignment explanation
Indices: 482205--482353 Score: 77
Period size: 29 Copynumber: 5.0 Consensus size: 28
482195 TGAACTGTTA
482205 CAAAATGACCACTACACGTTATAAAATAG
1 CAAAATGACCACTACAC-TTATAAAATAG
** * * * *
482234 CAAAATCG-TTATTAAACTTATTGAACT-G
1 CAAAAT-GACCACTACACTTA-TAAAATAG
482262 CTACAAAATGACCACTACACGTTATAAAATAG
1 C-A--AAATGACCACTACAC-TTATAAAATAG
** * ** *
482294 CAAAATGATTACTAAACTTATTGAATTG
1 CAAAATGACCACTACACTTATAAAATAG
482322 TTACAAAATGACCACTACACATTATAAAATAG
1 ---CAAAATGACCACTACAC-TTATAAAATAG
482354 TCATTAATTT
Statistics
Matches: 84, Mismatches: 24, Indels: 21
0.65 0.19 0.16
Matches are distributed among these distances:
28 13 0.15
29 28 0.33
30 2 0.02
31 28 0.33
32 13 0.15
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (28 bp):
CAAAATGACCACTACACTTATAAAATAG
Found at i:482268 original size:60 final size:60
Alignment explanation
Indices: 482185--482353 Score: 286
Period size: 60 Copynumber: 2.8 Consensus size: 60
482175 AAAATGGTCG
482185 CTAAACTTATTGAACTGTTACAAAATGACCACTACACGTTATAAAATAGCAAAATCG-TTA
1 CTAAACTTATTGAACTGTTACAAAATGACCACTACACGTTATAAAATAGCAAAAT-GATTA
* *
482245 TTAAACTTATTGAACTGCTACAAAATGACCACTACACGTTATAAAATAGCAAAATGATTA
1 CTAAACTTATTGAACTGTTACAAAATGACCACTACACGTTATAAAATAGCAAAATGATTA
* *
482305 CTAAACTTATTGAATTGTTACAAAATGACCACTACACATTATAAAATAG
1 CTAAACTTATTGAACTGTTACAAAATGACCACTACACGTTATAAAATAG
482354 TCATTAATTT
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
59 1 0.01
60 101 0.99
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.29
Consensus pattern (60 bp):
CTAAACTTATTGAACTGTTACAAAATGACCACTACACGTTATAAAATAGCAAAATGATTA
Found at i:482431 original size:32 final size:32
Alignment explanation
Indices: 482390--482521 Score: 133
Period size: 32 Copynumber: 4.2 Consensus size: 32
482380 CATTTTATAA
* *
482390 CATTTTGTACTGATTTGATAAAATTTAATGTT
1 CATTTTGTACTAATTTGATAAAATTTAATGAT
* *
482422 CATTTTGTACTAGTTTGATAAAATCTAA-GAT
1 CATTTTGTACTAATTTGATAAAATTTAATGAT
* * * *
482453 CATTTTATAATAATATGAT-AAGTTTAATGAT
1 CATTTTGTACTAATTTGATAAAATTTAATGAT
* * * *
482484 CATTTTGAACTAAATTGATAAAAATTAATAAT
1 CATTTTGTACTAATTTGATAAAATTTAATGAT
*
482516 TATTTT
1 CATTTT
482522 TATAATAATT
Statistics
Matches: 79, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
30 6 0.08
31 34 0.43
32 39 0.49
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (32 bp):
CATTTTGTACTAATTTGATAAAATTTAATGAT
Found at i:482472 original size:31 final size:32
Alignment explanation
Indices: 482405--482557 Score: 84
Period size: 31 Copynumber: 4.8 Consensus size: 32
482395 TGTACTGATT
* * * * * *
482405 TGATAAAATTTAATGTTCATTTTGTACTAGTT
1 TGATAAAATCTAATGATCATTTTATAATAATA
482437 TGATAAAATCTAA-GATCATTTTATAATAATA
1 TGATAAAATCTAATGATCATTTTATAATAATA
* * *
482468 TGAT-AAGTTTAATGATCATTTTGA-ACTAA-A
1 TGATAAAATCTAATGATCATTTT-ATAATAATA
* * *
482498 TTGATAAAAAT-TAATAATTATTTTTATAATAATT
1 -TGAT-AAAATCTAATGATCA-TTTTATAATAATA
* * * *
482532 TTATAAATTC-AATAATTATTTTATAA
1 TGATAAAATCTAATGATCATTTTATAA
482558 CATCTGAAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
30 7 0.07
31 42 0.44
32 33 0.34
33 14 0.15
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (32 bp):
TGATAAAATCTAATGATCATTTTATAATAATA
Found at i:497185 original size:31 final size:31
Alignment explanation
Indices: 497147--497206 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
497137 TAAACTTTAT
* * *
497147 GCATTAGGGGATAGTTTCAATTATTCATCCA
1 GCATTAGGGGATAGTATAAATTATGCATCCA
497178 GCATTAGGGGATAGTATAAATTATGCATC
1 GCATTAGGGGATAGTATAAATTATGCATC
497207 TAGAACTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33
Consensus pattern (31 bp):
GCATTAGGGGATAGTATAAATTATGCATCCA
Found at i:498770 original size:28 final size:25
Alignment explanation
Indices: 498739--498795 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
498729 TTAAGTATAA
*
498739 ATATAAAAGATAATAAATAAATTATTGT
1 ATATAAAAGAT-AT-AATAAA-TATTAT
**
498767 ATATTGAAGATATAATAAATATTAT
1 ATATAAAAGATATAATAAATATTAT
498792 ATAT
1 ATAT
498796 TAGATAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 9 0.35
26 6 0.23
27 2 0.08
28 9 0.35
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (25 bp):
ATATAAAAGATATAATAAATATTAT
Found at i:498795 original size:25 final size:28
Alignment explanation
Indices: 498745--498796 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
498735 ATAAATATAA
*
498745 AAGATAATAAATAAATTATTGTATATTG
1 AAGATAATAAATAAATTATTATATATTG
498773 AAGAT-AT-AATAAA-TATTATATATT
1 AAGATAATAAATAAATTATTATATATT
498797 AGATAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 10 0.43
26 6 0.26
27 2 0.09
28 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (28 bp):
AAGATAATAAATAAATTATTATATATTG
Found at i:500091 original size:16 final size:17
Alignment explanation
Indices: 500061--500094 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
500051 AGGAAAAAAG
*
500061 AAATAAAGATTAAAATA
1 AAATAAAGATAAAAATA
500078 AAATAAA-ATAAAAATA
1 AAATAAAGATAAAAATA
500094 A
1 A
500095 TAGTAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAAAGATAAAAATA
Found at i:500126 original size:5 final size:5
Alignment explanation
Indices: 500118--500145 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
500108 CAAATCAAAG
500118 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
500146 AAAATTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:500163 original size:14 final size:15
Alignment explanation
Indices: 500118--500163 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
500108 CAAATCAAAG
*
500118 AAATTAAATTAAATT
1 AAATTAAATTAAATA
500133 AAATTAAATTAAA-A
1 AAATTAAATTAAATA
*
500147 AAATTAGA-TAAATA
1 AAATTAAATTAAATA
500161 AAA
1 AAA
500164 AAATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.14
14 11 0.39
15 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AAATTAAATTAAATA
Found at i:500261 original size:39 final size:39
Alignment explanation
Indices: 500179--500266 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 39
500169 TTTTAAAAGT
* * *
500179 AATAAAATTGAAAAATATGAAATAAAAATAAATAATACT
1 AATAAAATTAAAAAACATGAAATAAAAATAAATAATACA
500218 AATAATAATTAAAAAACATGATAATAAATAA-AAA-AATA-A
1 AATAA-AATTAAAAAACATGA-AATAAA-AATAAATAATACA
500257 AATAAGAATT
1 AATAA-AATT
500267 TAGGGATCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
39 14 0.33
40 17 0.40
41 9 0.21
42 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (39 bp):
AATAAAATTAAAAAACATGAAATAAAAATAAATAATACA
Found at i:501387 original size:15 final size:15
Alignment explanation
Indices: 501344--501379 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
501334 ATATTAGATT
*
501344 AATAAAATGAAATAA
1 AATAAAATAAAATAA
501359 AATAAAATAAAATAA
1 AATAAAATAAAATAA
501374 AATAAA
1 AATAAA
501380 TATTAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AATAAAATAAAATAA
Found at i:501466 original size:24 final size:23
Alignment explanation
Indices: 501439--501498 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
501429 AACTATATAT
*
501439 TATATTTAAAAACGTTTTCAAAAC
1 TATATTTAAAAA-GTTTTCAAAAA
* *
501463 TATATATTATATAGTTTTCAAAAA
1 TATAT-TTAAAAAGTTTTCAAAAA
501487 TGAT-TTTAAAAA
1 T-ATATTTAAAAA
501499 TATTATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 5 0.17
24 17 0.59
25 7 0.24
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (23 bp):
TATATTTAAAAAGTTTTCAAAAA
Found at i:501507 original size:32 final size:31
Alignment explanation
Indices: 501466--501677 Score: 103
Period size: 35 Copynumber: 6.3 Consensus size: 31
501456 TCAAAACTAT
501466 ATATTATATAGTTTTCAAAAATGATTTTAAAA
1 ATATTATATAGTTTTCAAAAATG-TTTTAAAA
* *
501498 ATATTATATAAGCTTTCCAAAATGTTTTTTTAAACTA
1 ATATTATAT-AGTTTTCAAAAATG---TTTTAAA--A
*
501535 TATATTATATAAATTTTCAAAAACTGTTTTTTTAAAA
1 -ATATTATAT-AGTTTTCAAAAA-TG---TTTTAAAA
*
501572 ACTATATATTATA-TTTTC-AAAATGATTTCAAAA
1 A-TAT-TA-TATAGTTTTCAAAAATG-TTTTAAAA
*
501605 CTATATACTATATAATTTTC-AAAATGTTTT-AAA
1 --ATAT--TATATAGTTTTCAAAAATGTTTTAAAA
* * *
501638 A-CTTACATAAGTTTTCAAAAAAGTTTTAAAA
1 ATATTATAT-AGTTTTCAAAAATGTTTTAAAA
*
501669 A-ACTATATA
1 ATATTATATA
501678 ATATATATTT
Statistics
Matches: 146, Mismatches: 17, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
28 4 0.03
29 6 0.04
30 11 0.08
31 9 0.06
32 9 0.06
33 22 0.15
34 10 0.07
35 23 0.16
36 5 0.03
37 10 0.07
38 22 0.15
39 15 0.10
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.43
Consensus pattern (31 bp):
ATATTATATAGTTTTCAAAAATGTTTTAAAA
Found at i:501578 original size:39 final size:38
Alignment explanation
Indices: 501459--501634 Score: 126
Period size: 38 Copynumber: 4.9 Consensus size: 38
501449 AACGTTTTCA
* * *
501459 AAACTATATATTATAT-AGTTTTCAAAAATG--ATTTT
1 AAACAATATATTATATAAATTTTCAAAAATGTTTTTTT
** *
501494 -AA-AA-ATATTATATAAGCTTTCCAAAATGTTTTTTT
1 AAACAATATATTATATAAATTTTCAAAAATGTTTTTTT
*
501529 AAACTATATATTATATAAATTTTCAAAAACTGTTTTTTT
1 AAACAATATATTATATAAATTTTCAAAAA-TGTTTTTTT
* * **
501568 AAA-AACTATA-TAT-TATATTTTC-AAAATG-ATTTCA
1 AAACAA-TATATTATATAAATTTTCAAAAATGTTTTTTT
* *
501602 AAACTATATACTATAT-AATTTTC-AAAATGTTTT
1 AAACAATATATTATATAAATTTTCAAAAATGTTTT
501635 AAAACTTACA
Statistics
Matches: 113, Mismatches: 16, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
32 9 0.08
33 13 0.12
34 12 0.11
35 22 0.19
36 9 0.08
37 9 0.08
38 23 0.20
39 16 0.14
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (38 bp):
AAACAATATATTATATAAATTTTCAAAAATGTTTTTTT
Found at i:501713 original size:37 final size:36
Alignment explanation
Indices: 501667--501736 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
501657 AAAGTTTTAA
501667 AAAACTATATAATATATATTTCAAAAAATATTTTTTG
1 AAAACTATATAATATAT-TTTCAAAAAATATTTTTTG
* *
501704 AAAACTATATATTATATTTTTAAAAAATATTTT
1 AAAACTATATAATATATTTTCAAAAAATATTTT
501737 CAAAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 15 0.48
37 16 0.52
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (36 bp):
AAAACTATATAATATATTTTCAAAAAATATTTTTTG
Found at i:501720 original size:35 final size:38
Alignment explanation
Indices: 501667--501736 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
501657 AAAGTTTTAA
501667 AAAACTATATAATATATA-TTTCAAAAAATATTTTTTG
1 AAAACTATATAATATATATTTTCAAAAAATATTTTTTG
*
501704 AAAACTATAT-AT-TATATTTTTAAAAAATATTTT
1 AAAACTATATAATATATATTTTCAAAAAATATTTT
501737 CAAAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 4 0.13
36 17 0.55
37 10 0.32
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (38 bp):
AAAACTATATAATATATATTTTCAAAAAATATTTTTTG
Found at i:501748 original size:35 final size:37
Alignment explanation
Indices: 501661--501742 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
501651 TTCAAAAAAG
501661 TTTTAAAAAACTATATAATATATATTTCAAAAAATAT
1 TTTTAAAAAACTATATAATATATATTTCAAAAAATAT
** * *
501698 TTTTTGAAAACTATATATTATAT-TTTTAAAAAATAT
1 TTTTAAAAAACTATATAATATATATTTCAAAAAATAT
*
501734 TTTCAAAAA
1 TTTTAAAAA
501743 TTATATTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 18 0.47
37 20 0.53
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (37 bp):
TTTTAAAAAACTATATAATATATATTTCAAAAAATAT
Found at i:501753 original size:33 final size:35
Alignment explanation
Indices: 501547--501754 Score: 104
Period size: 33 Copynumber: 6.1 Consensus size: 35
501537 TATTATATAA
* * *
501547 ATTTTCAAAAACTGTTTTTTTAAAAACTATATATTAT
1 ATTTTCAAAAAAT-ATTTTTCAAAAA-TATATATTAT
*
501584 ATTTTC--AAAATGA--TTTCAAAACTATATACTATAT
1 ATTTTCAAAAAAT-ATTTTTCAAAAATATATA-T-TAT
* * *
501618 AATTTTC--AAAAT-GTTTT-AAAACT-TACA-TA-
1 -ATTTTCAAAAAATATTTTTCAAAAATATATATTAT
* * *
501647 AGTTTTC-AAAAA-AGTTTTAAAAAACTATATAATAT
1 A-TTTTCAAAAAATATTTTTCAAAAA-TATATATTAT
* *
501682 ATATTTCAAAAAATATTTTTTGAAAACTATATATTAT
1 AT-TTTCAAAAAATA-TTTTTCAAAAATATATATTAT
*
501719 ATTTTTAAAAAATA-TTTTCAAAAAT-TATATTAT
1 ATTTTCAAAAAATATTTTTCAAAAATATATATTAT
501752 ATT
1 ATT
501755 ACTATAATAA
Statistics
Matches: 140, Mismatches: 14, Indels: 38
0.73 0.07 0.20
Matches are distributed among these distances:
28 1 0.01
29 5 0.04
30 11 0.08
31 4 0.03
32 7 0.05
33 25 0.18
34 21 0.15
35 24 0.17
36 16 0.11
37 18 0.13
38 8 0.06
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (35 bp):
ATTTTCAAAAAATATTTTTCAAAAATATATATTAT
Found at i:510533 original size:13 final size:12
Alignment explanation
Indices: 510503--510532 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
510493 TCATGTTCCG
510503 TTTTTTGTCTTT
1 TTTTTTGTCTTT
510515 TTTTTTGTCTTT
1 TTTTTTGTCTTT
510527 TTTTTT
1 TTTTTT
510533 TACCTTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (12 bp):
TTTTTTGTCTTT
Found at i:519096 original size:29 final size:29
Alignment explanation
Indices: 519059--519114 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
519049 GTTATTTAAT
519059 GAAAAGTGGTGGTGCTTTAATAATGGAAG
1 GAAAAGTGGTGGTGCTTTAATAATGGAAG
*
519088 GAAACGTGGTGGTGCTTTAATAATGGA
1 GAAAAGTGGTGGTGCTTTAATAATGGA
519115 TGAATCTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (29 bp):
GAAAAGTGGTGGTGCTTTAATAATGGAAG
Found at i:519421 original size:4 final size:4
Alignment explanation
Indices: 519414--519461 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
519404 TTCCTCTTTG
*
519414 ATTT ATTT ATTT A-TT ATGTT ATTT ATTT ATTT ATTCT -TTG ATTT ATTT
1 ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT
519462 TTTTTCTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 30 0.79
5 5 0.13
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:519439 original size:20 final size:20
Alignment explanation
Indices: 519410--519461 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
519400 TTTTTTCCTC
519410 TTTGATTTATTTATTTATTA
1 TTTGATTTATTTATTTATTA
*
519430 TGTT-ATTTATTTATTTATTC
1 T-TTGATTTATTTATTTATTA
519450 TTTGATTTATTT
1 TTTGATTTATTT
519462 TTTTTCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (20 bp):
TTTGATTTATTTATTTATTA
Found at i:519533 original size:23 final size:24
Alignment explanation
Indices: 519463--519543 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 24
519453 GATTTATTTT
519463 TTTTCTTTATC-TTTTTTCCTTTTAA
1 TTTT-TTTATCATTTTTT-CTTTTAA
** *
519488 TTTATTTTATCATTTTTAATTTTTA
1 TTT-TTTTATCATTTTTTCTTTTAA
*
519513 TTTTTTTA-CATTTTTTCTTTTGA
1 TTTTTTTATCATTTTTTCTTTTAA
*
519536 TTTATTTA
1 TTTTTTTA
519544 ATATATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 19 0.40
24 5 0.11
25 17 0.36
26 6 0.13
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.73
Consensus pattern (24 bp):
TTTTTTTATCATTTTTTCTTTTAA
Found at i:519558 original size:48 final size:48
Alignment explanation
Indices: 519456--519563 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
519446 ATTCTTTGAT
* *
519456 TTATTTTT-TTTCTTTATCTTTTTTCCTTTTAATTTATTTTATCATTT
1 TTATTTTTATTTTTTTATCTTTTTTCCTTTTAATTTATTTTATCATTA
*
519503 TTAATTTTTATTTTTTTA-CATTTTTT-CTTTTGATTTATTTAATAT-ATTA
1 TT-ATTTTTATTTTTTTATC-TTTTTTCCTTTTAATTTATTT--TATCATTA
519552 TTA-TTTTATTTT
1 TTATTTTTATTTT
519564 ATTTTCCCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
47 11 0.21
48 21 0.40
49 18 0.34
50 3 0.06
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.73
Consensus pattern (48 bp):
TTATTTTTATTTTTTTATCTTTTTTCCTTTTAATTTATTTTATCATTA
Found at i:519592 original size:12 final size:11
Alignment explanation
Indices: 519549--519640 Score: 58
Period size: 13 Copynumber: 7.6 Consensus size: 11
519539 ATTTAATATA
519549 TTATTATTTTATT
1 TTATT-TTTT-TT
*
519562 TTATTTTCCCTTT
1 TTATTTT--TTTT
*
519575 TGATTTTTTTCT
1 TTATTTTTTT-T
*
519587 TTATTTATTTGT
1 TTATTT-TTTTT
* *
519599 TTATTTATTAT
1 TTATTTTTTTT
*
519610 TTATTTTTGTT
1 TTATTTTTTTT
519621 TTATTATTATTTT
1 TTATT-TT-TTTT
519634 TTATTTT
1 TTATTTT
519641 CATTCTCAGG
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
11 18 0.29
12 19 0.31
13 24 0.39
14 1 0.02
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.76
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:519620 original size:21 final size:19
Alignment explanation
Indices: 519587--519632 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
519577 ATTTTTTTCT
519587 TTATTTATTTG-TTTATTTA
1 TTATTTATTTGTTTTA-TTA
519606 TTATTTATTTTTGTTTTATTA
1 TTATTTA--TTTGTTTTATTA
519627 TTATTT
1 TTATTT
519633 TTTATTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (19 bp):
TTATTTATTTGTTTTATTA
Found at i:519635 original size:18 final size:18
Alignment explanation
Indices: 519587--519640 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
519577 ATTTTTTTCT
519587 TTATTTATTTGTT-TATTTA
1 TTATTTATTT-TTAT-TTTA
*
519606 TTATTTATTTTTGTTTTA
1 TTATTTATTTTTATTTTA
519624 TTA-TTATTTTTTATTTT
1 TTATTTA-TTTTTATTTT
519641 CATTCTCAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.09
18 18 0.56
19 11 0.34
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.78
Consensus pattern (18 bp):
TTATTTATTTTTATTTTA
Found at i:524017 original size:43 final size:43
Alignment explanation
Indices: 523956--524111 Score: 141
Period size: 43 Copynumber: 3.4 Consensus size: 43
523946 CAGAGCCAAT
523956 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
523999 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
524050 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
524093 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
524112 GACCGCTGGT
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
43 38 0.45
44 3 0.04
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:524030 original size:106 final size:105
Alignment explanation
Indices: 523782--525302 Score: 2229
Period size: 106 Copynumber: 15.0 Consensus size: 105
523772 ATATCGTGCC
* *
523782 ACTCAAGACAACGCAAGTTCAACTTCACGACCAAGGGACCGCTGGTTGTCAAT--A-AA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
523840 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
523876 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-C
523941 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
523982 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
524040 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
524076 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-C
524141 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
524182 ACTCCAGACAACGCAAGTTCAACTTCACGACCAAGGGACCGCTGGTTGTCAAT--A-AA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
524240 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
524276 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-C
524341 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
524382 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
524440 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
524476 ACTCCAGACAACGCAAGTTCAACTTCACGACCAAGGGACCGCTGGTTGTCAAT--A-AA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
524534 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
524570 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-C
524635 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
524676 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
524734 ATTTC----CCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
524770 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGATCGCTGGTTGTCAATAACCAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-C
524835 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
524876 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-C
524941 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
524982 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT-CC
525047 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
525088 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT-CC
** **
525153 AAACTCAGAGCCAATTTCAACTTCACTGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
525194 ACTCGAGGCAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCC-
* * ** *
525259 AGTTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
525300 ACT
1 ACT
525303 TGGAACAATA
Statistics
Matches: 1326, Mismatches: 39, Indels: 112
0.90 0.03 0.08
Matches are distributed among these distances:
94 474 0.36
96 3 0.00
97 10 0.01
98 28 0.02
102 35 0.03
103 8 0.01
104 3 0.00
105 2 0.00
106 762 0.57
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:524130 original size:200 final size:200
Alignment explanation
Indices: 523782--525257 Score: 2253
Period size: 200 Copynumber: 7.3 Consensus size: 200
523772 ATATCGTGCC
* *
523782 ACTCAAGACAACGCAAGTTCAACTTCACGACCAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
523847 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
523912 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
523977 ATTGG
196 ATTGG
523982 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
524047 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
524112 GACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
524177 ATTGG
196 ATTGG
*
524182 ACTCCAGACAACGCAAGTTCAACTTCACGACCAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
524247 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
524312 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
524377 ATTGG
196 ATTGG
*
524382 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
524447 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACCAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
524512 GACCGCTGGTTGTCAAT--A-AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGAT
131 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
524565 ATTGG
196 ATTGG
524570 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----C
*
524635 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
524700 TCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----CAATTTC----CCAATTTCAACTTC
119 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
524753 ACAACGAAGGATATTGG
184 ACAACGAAGGATATTGG
* *
524770 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGATCGCTGGTTGTCAATAACCAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-A--AA-----C
*
524835 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACT
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
524900 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
119 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
524965 ACAACGAAGGATATTGG
184 ACAACGAAGGATATTGG
*
524982 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----C
525047 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * **
525112 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAACTCAGAGCCAATTTCAACTTC
119 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
**
525177 ACTGCGAAGGATATTGG
184 ACAACGAAGGATATTGG
* * * * * *
525194 ACTCGAGGCAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
525258 TAGTTCCAGA
Statistics
Matches: 1218, Mismatches: 32, Indels: 52
0.94 0.02 0.04
Matches are distributed among these distances:
188 83 0.07
190 1 0.00
191 2 0.00
192 7 0.01
196 7 0.01
197 2 0.00
198 1 0.00
199 2 0.00
200 815 0.67
202 1 0.00
203 2 0.00
204 7 0.01
208 7 0.01
209 2 0.00
210 1 0.00
212 276 0.23
213 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (200 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
ATTGG
Found at i:524311 original size:43 final size:43
Alignment explanation
Indices: 524156--524311 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
524146 CAGAGCCAAT
524156 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *** ** * * * *
524199 TTCAACTTCACGACCAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
524250 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
524293 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
524312 GACCGCTGGT
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
43 37 0.45
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 3 0.04
51 19 0.23
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:524316 original size:294 final size:287
Alignment explanation
Indices: 523782--525245 Score: 2004
Period size: 294 Copynumber: 4.8 Consensus size: 287
523772 ATATCGTGCC
* *
523782 ACTCAAGACAACGCAAGTTCAACTTCACGACCAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
523847 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACCAAGG
523912 GACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GACCGCTGGTTGTCAAT--A-AA-----CAATTTC--A-CCAATTTCAACTTCACAACGAAGGAT
523977 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-A-AA-C
185 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACAATC
524039 AATTTC-CCAATTTCAACTTCACAACGAAGGATATTGG
250 AATTTCACCAATTTCAACTTCACAACGAAGGATATTGG
524076 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-A--AA-----C
524141 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
524206 TCACGACCAAGGGACCGCTGGTTGTCAATAAACAATTTC-CCAATTTCAACTTCACAACGAAGGA
119 TCACGACCAAGGGACCGCTGGTTGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGA
524270 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA
184 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-AACAA
524335 CTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
248 ----TCAATTTC--A-CCAATTTCAACTTCACAACGAAGGATATTGG
*
524382 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
524447 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACCAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACCAAGG
524512 GACCGCTGGTTGTCAATAAACAATTTC-CCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
131 GACCGCTGGTTGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
524576 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
196 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-AACAA----TCAATTTC
524641 AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
256 --A-CCAATTTCAACTTCACAACGAAGGATATTGG
*
524676 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
524741 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACAAAGG
66 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACCAAGG
*
524806 GATCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
131 GACCGCTGGTTGTCAAT-A--AA-----CAATTTC--A-CCAATTTCAACTTCACAACGAAGGAT
*
524871 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAAC
185 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-AACAA-
524936 TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
248 ---TCAATTTC--A-CCAATTTCAACTTCACAACGAAGGATATTGG
*
524982 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----C
525047 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
58 AATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
525112 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAACTCAGAGCCAATTTCAACTTC
119 TCACGACCAAGGGACCGCTGGTTGTCAATAAACAA-TT-------TC--A-CCAATTTCAACTTC
** * * * * *
525177 ACTGCGAAGGATATTGGACTCGAGGCAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTG
173 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
525242 TCAA
238 TCAA
525246 CAAACAATTT
Statistics
Matches: 1095, Mismatches: 19, Indels: 88
0.91 0.02 0.07
Matches are distributed among these distances:
294 511 0.47
295 2 0.00
296 1 0.00
297 6 0.01
298 14 0.01
302 21 0.02
303 4 0.00
304 1 0.00
305 1 0.00
306 353 0.32
308 1 0.00
309 2 0.00
310 3 0.00
311 2 0.00
314 7 0.01
315 2 0.00
317 1 0.00
318 163 0.15
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (287 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACCAAGG
GACCGCTGGTTGTCAATAAACAATTTCACCAATTTCAACTTCACAACGAAGGATATTGGACTCCA
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACAATCAATTTCACCAA
TTTCAACTTCACAACGAAGGATATTGG
Found at i:524417 original size:43 final size:43
Alignment explanation
Indices: 524356--524605 Score: 140
Period size: 43 Copynumber: 5.4 Consensus size: 43
524346 CAGAGCCAAT
524356 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
* *** ** * * * *
524399 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA--T-GCAAG
*
524450 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
* * *** ** * * * *
524493 TTCAACTTCACGACCAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA--T-GCAAG
*
524544 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
*
524587 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
524606 GACCGCTGGT
Statistics
Matches: 145, Mismatches: 46, Indels: 32
0.65 0.21 0.14
Matches are distributed among these distances:
43 55 0.38
44 6 0.04
45 6 0.04
46 14 0.10
48 14 0.10
49 6 0.04
50 7 0.05
51 37 0.26
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
Found at i:524711 original size:43 final size:43
Alignment explanation
Indices: 524650--524797 Score: 125
Period size: 43 Copynumber: 3.3 Consensus size: 43
524640 CAGAGCCAAT
524650 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
* *** ** * * * *
524693 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA--T-GCAAG
*
524744 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
524787 TTCAACTTCAC
1 TTCAACTTCAC
524798 GACAAAGGGA
Statistics
Matches: 76, Mismatches: 21, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
43 30 0.39
44 3 0.04
45 3 0.04
46 7 0.09
48 7 0.09
49 3 0.04
50 4 0.05
51 19 0.25
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
Found at i:526707 original size:29 final size:29
Alignment explanation
Indices: 526670--526725 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
526660 GTTATTTAAT
526670 GAAAAGTGGTGGTGCTTTAATAATGGAAG
1 GAAAAGTGGTGGTGCTTTAATAATGGAAG
*
526699 GAAACGTGGTGGTGCTTTAATAATGGA
1 GAAAAGTGGTGGTGCTTTAATAATGGA
526726 TGAATCTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (29 bp):
GAAAAGTGGTGGTGCTTTAATAATGGAAG
Found at i:527139 original size:23 final size:24
Alignment explanation
Indices: 527069--527149 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 24
527059 GATTTATTTT
527069 TTTTCTTTATC-TTTTTTCCTTTTAA
1 TTTT-TTTATCATTTTTT-CTTTTAA
** *
527094 TTTATTTTATCATTTTTAATTTTTA
1 TTT-TTTTATCATTTTTTCTTTTAA
*
527119 TTTTTTTA-CATTTTTTCTTTTGA
1 TTTTTTTATCATTTTTTCTTTTAA
*
527142 TTTATTTA
1 TTTTTTTA
527150 ATATATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 19 0.40
24 5 0.11
25 17 0.36
26 6 0.13
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.73
Consensus pattern (24 bp):
TTTTTTTATCATTTTTTCTTTTAA
Found at i:527164 original size:48 final size:48
Alignment explanation
Indices: 527062--527169 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
527052 ATTCTTTGAT
* *
527062 TTATTTTT-TTTCTTTATCTTTTTTCCTTTTAATTTATTTTATCATTT
1 TTATTTTTATTTTTTTATCTTTTTTCCTTTTAATTTATTTTATCATTA
*
527109 TTAATTTTTATTTTTTTA-CATTTTTT-CTTTTGATTTATTTAATAT-ATTA
1 TT-ATTTTTATTTTTTTATC-TTTTTTCCTTTTAATTTATTT--TATCATTA
527158 TTA-TTTTATTTT
1 TTATTTTTATTTT
527170 ATTTTCCCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
47 11 0.21
48 21 0.40
49 18 0.34
50 3 0.06
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.73
Consensus pattern (48 bp):
TTATTTTTATTTTTTTATCTTTTTTCCTTTTAATTTATTTTATCATTA
Found at i:527209 original size:11 final size:11
Alignment explanation
Indices: 527193--527234 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
527183 ATTTTTTTTC
527193 TTTATTTATTT
1 TTTATTTATTT
527204 TTTATTT-TTGT
1 TTTATTTATT-T
527215 TTTATTATTATTT
1 TTTA-T-TTATTT
527228 TTTATTT
1 TTTATTT
527235 TCATTCTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.07
11 14 0.52
12 2 0.07
13 7 0.26
14 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:545640 original size:37 final size:36
Alignment explanation
Indices: 545565--545640 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
545555 TTTTTATATT
*
545565 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
545601 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
545638 TTT
1 TTT
545641 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:550995 original size:27 final size:25
Alignment explanation
Indices: 550947--550996 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
550937 GTATTATTGA
*
550947 TAATTTTTTAAATAATTATATATTT
1 TAATTTTTTAAATAAATATATATTT
*
550972 TAATTTTTTGAATAAAATAGTATAT
1 TAATTTTTTAAAT-AAATA-TATAT
550997 GTATTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 4 0.19
27 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
TAATTTTTTAAATAAATATATATTT
Found at i:558726 original size:20 final size:20
Alignment explanation
Indices: 558701--558748 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
558691 GTCAGAGTGT
*
558701 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
558721 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
558741 GGCAGCGG
1 GGCGGCGG
558749 CCAGCAGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:558738 original size:17 final size:16
Alignment explanation
Indices: 558718--558749 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
558708 GACGGCTGAC
558718 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
558735 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
558750 CAGCAGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:571933 original size:2 final size:2
Alignment explanation
Indices: 571928--571952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
571918 GTAGGGTCTT
571928 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
571953 ATCAATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:572275 original size:31 final size:31
Alignment explanation
Indices: 572240--572345 Score: 106
Period size: 31 Copynumber: 3.4 Consensus size: 31
572230 ATCAAAAAGT
* *
572240 TTTGATAAGTTTAACGATAATTCTATAATCG
1 TTTGATAAGTTTAAAGATAATTTTATAATCG
* *
572271 TTTGATAAGTTTAAATATGATTTTATAA-CGG
1 TTTGATAAGTTTAAAGATAATTTTATAATC-G
* * **
572302 TTTGATAAATTCTAATGATCGTTTTATAATCG
1 TTTGATAAGTT-TAAAGATAATTTTATAATCG
*
572334 TTTGAGAAGTTT
1 TTTGATAAGTTT
572346 TTTGACCATT
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 1 0.02
31 36 0.59
32 23 0.38
33 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (31 bp):
TTTGATAAGTTTAAAGATAATTTTATAATCG
Found at i:574665 original size:35 final size:36
Alignment explanation
Indices: 574617--574704 Score: 128
Period size: 35 Copynumber: 2.5 Consensus size: 36
574607 CCCGATTATA
*
574617 TATATATAAATAATTTTTTATA-TTTTTATATTAAT
1 TATATATAAATAATATTTTATATTTTTTATATTAAT
* *
574652 TATATATATATAATATTTTATATTTTTTATATTAGT
1 TATATATAAATAATATTTTATATTTTTTATATTAAT
574688 TATATAT-AA-AATATTTT
1 TATATATAAATAATATTTT
574705 CGGGTTCGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
34 8 0.17
35 21 0.44
36 19 0.40
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (36 bp):
TATATATAAATAATATTTTATATTTTTTATATTAAT
Found at i:585619 original size:27 final size:27
Alignment explanation
Indices: 585579--585648 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
585569 TGTTCGTTTA
585579 CGTTCGTTTATGTTCATTTATTATGTT
1 CGTTCGTTTATGTTCATTTATTATGTT
* * *
585606 CGTTTGTTTGTGTTCGTTTA-T-TG-T
1 CGTTCGTTTATGTTCATTTATTATGTT
*
585630 -GTTCATTTATGTTCATTTA
1 CGTTCGTTTATGTTCATTTA
585649 CATCCGTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 15 0.42
24 1 0.03
25 2 0.06
26 1 0.03
27 17 0.47
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (27 bp):
CGTTCGTTTATGTTCATTTATTATGTT
Found at i:585621 original size:14 final size:13
Alignment explanation
Indices: 585589--585639 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
585579 CGTTCGTTTA
* *
585589 TGTTCATTTATTA
1 TGTTCGTTTATTG
*
585602 TGTTCGTTTGTTTG
1 TGTTCGTTT-ATTG
585616 TGTTCGTTTATTG
1 TGTTCGTTTATTG
*
585629 TGTTCATTTAT
1 TGTTCGTTTAT
585640 GTTCATTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.63
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:587323 original size:15 final size:15
Alignment explanation
Indices: 587305--587359 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
587295 TAACCGGTTT
587305 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
**
587320 CGGTTTTTTTAAAAAC
1 CGG-TTTTAAAAAAAC
*
587336 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
587351 CGATTTTAA
1 CGGTTTTAA
587360 TATTTCAGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 19 0.59
16 13 0.41
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:587552 original size:21 final size:21
Alignment explanation
Indices: 587528--587580 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
587518 ACACTTAGGG
587528 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
587549 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
587570 TACCGATTCCC
1 AACCGATTCCC
587581 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Done.