Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009608.1 Hibiscus syriacus cultivar Beakdansim tig00116994_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: 1053610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:487517 original size:34 final size:37
Alignment explanation
Indices: 487437--487526 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 37
487427 CGCAACGGGG
*
487437 AAATCGCAACGCGAAAATGGCTATCGCAATGCGAAATGAA
1 AAATCGCAACGCGAAAATGGCTATC-C-A-GCGAAATAAA
487477 AAATCGCAACGCGAAAATGGCTAT-C-GC-AAATAAA
1 AAATCGCAACGCGAAAATGGCTATCCAGCGAAATAAA
*
487511 AAATCGCAATGCGAAA
1 AAATCGCAACGCGAAA
487527 TGAAAATCGC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
34 21 0.44
35 2 0.04
38 1 0.02
40 24 0.50
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (37 bp):
AAATCGCAACGCGAAAATGGCTATCCAGCGAAATAAA
Found at i:487527 original size:20 final size:19
Alignment explanation
Indices: 487504--487543 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
487494 TGGCTATCGC
487504 AAATAAAAAATCGCAATGCG
1 AAAT-AAAAATCGCAATGCG
* *
487524 AAATGAAAATCGCATTGCG
1 AAATAAAAATCGCAATGCG
487543 A
1 A
487544 TTTTCTCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
AAATAAAAATCGCAATGCG
Found at i:487557 original size:14 final size:14
Alignment explanation
Indices: 487538--487591 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
487528 GAAAATCGCA
487538 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
487552 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
487569 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
487585 TTGCGAT
1 TTGCGAT
487592 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:487557 original size:33 final size:33
Alignment explanation
Indices: 487520--487590 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
487510 AAAATCGCAA
487520 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
487553 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
487586 TGCGA
1 TGCGA
487591 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:489219 original size:41 final size:42
Alignment explanation
Indices: 489165--489256 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
489155 CCTCTTCAAC
* *
489165 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* * *
489206 GATGATAGGGGCCTCTTGAACGATTGGAGGGGAGTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
489248 AATGACAGG
1 GATGACAGG
489257 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 20 0.47
42 23 0.53
ACGTcount: A:0.22, C:0.14, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:489643 original size:20 final size:20
Alignment explanation
Indices: 489620--489687 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
489610 AAACTTACTT
*
489620 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
489640 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
**
489660 TCGCAACGCGGAAATGAAAA
1 TCGCAACGCGGAAATGACTA
489680 TCGCAACG
1 TCGCAACG
489688 ACAAAATCGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:489695 original size:14 final size:14
Alignment explanation
Indices: 489676--489733 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
489666 CGCGGAAATG
*
489676 AAAATCGCAACGAC
1 AAAATCGCAACGAA
489690 AAAATCGCAATGCGAAA
1 AAAATCGCAA--CG-AA
489707 TGAAAATCGCAACGAA
1 --AAAATCGCAACGAA
489723 AAAATCGCAAC
1 AAAATCGCAAC
489734 CCGAAACACA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 21 0.55
16 4 0.11
17 3 0.08
19 10 0.26
ACGTcount: A:0.52, C:0.22, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:489709 original size:33 final size:34
Alignment explanation
Indices: 489659--489733 Score: 125
Period size: 33 Copynumber: 2.2 Consensus size: 34
489649 GGAAATGGCT
*
489659 ATCGCAACGCGGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAAAAA
*
489693 ATCGCAATGC-GAAATGAAAATCGCAACGAAAAA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAAAAA
489726 ATCGCAAC
1 ATCGCAAC
489734 CCGAAACACA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (34 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAAAAA
Found at i:489747 original size:33 final size:33
Alignment explanation
Indices: 489659--489750 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
489649 GGAAATGGCT
* * *
489659 ATCGCAACGCGGAAATGAAAATCGCAACGACAAA
1 ATCGCAAC-CCGAAATCAAAATCGCAACGAAAAA
** *
489693 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAACCCGAAATCAAAATCGCAACGAAAAA
489726 ATCGCAACCCGAAA-CACAAATCGCA
1 ATCGCAACCCGAAATCA-AAATCGCA
489751 TTTCGATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.02
33 42 0.84
34 7 0.14
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (33 bp):
ATCGCAACCCGAAATCAAAATCGCAACGAAAAA
Found at i:489796 original size:33 final size:33
Alignment explanation
Indices: 489749--489842 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
489739 ACACAAATCG
* *
489749 CATTTCGATTTTCATTTCGCGTTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
**
489782 CATTGCGATTTTCATTGGGCATTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
* *
489815 CGTTGCGATTTTCATTTCGTATTGCGAT
1 CATTGCGATTTTCATTTCGCATTGCGAT
489843 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:489798 original size:12 final size:14
Alignment explanation
Indices: 489770--489826 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
489760 TCATTTCGCG
489770 TTGCGATTTTGTCA
1 TTGCGATTTTGTCA
*
489784 TTGCGATTTTCATTGGGCA
1 TTGCGA--TT--TT-GTCA
*
489803 TTGCGATTTTGTCG
1 TTGCGATTTTGTCA
489817 TTGCGATTTT
1 TTGCGATTTT
489827 CATTTCGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.26
ACGTcount: A:0.12, C:0.14, G:0.25, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTGTCA
Found at i:489861 original size:20 final size:20
Alignment explanation
Indices: 489836--489881 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
489826 TCATTTCGTA
489836 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
489856 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
489876 TTGCGA
1 TTGCGA
489882 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:490439 original size:18 final size:18
Alignment explanation
Indices: 490416--490463 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
490406 CGGGTCGATC
490416 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
490434 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
490452 AGGTGATGGCTC
1 AGGTGATGGCTC
490464 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:491825 original size:20 final size:20
Alignment explanation
Indices: 491777--491835 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
491767 AATAGTTTCT
* *
491777 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
491797 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
491817 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
491836 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:492427 original size:41 final size:41
Alignment explanation
Indices: 492314--492445 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 41
492304 GAAAATTGCA
* * * *
492314 TTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATTGAG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
** * * *
492355 TTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGTATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
*
492395 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
492436 TTGCGATTTT
1 TTGCGATTTT
492446 CCAAATTCGC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 32 0.43
41 43 0.57
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
Found at i:492442 original size:20 final size:20
Alignment explanation
Indices: 492328--492441 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
492318 GATTATGTAT
*
492328 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
492348 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
492368 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
492388 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
492409 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
492429 TATCGCGTTGCGA
1 TATCGCGTTGCGA
492442 TTTTCCAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:492461 original size:41 final size:41
Alignment explanation
Indices: 492335--492463 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 41
492325 TATTATCTCG
* * * ** *
492335 TTGCGAAAGTCAGTATTGAGTTGCGAAATT-AAGTATCG-A
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
* ** * *
492374 GTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 -TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
492416 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAATATCGCA
492457 TTGCGAT
1 TTGCGAT
492464 TTTCCAAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
40 26 0.35
41 46 0.62
42 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAATATCGCA
Found at i:492496 original size:20 final size:21
Alignment explanation
Indices: 492431--492503 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
492421 ATAGTCAGTA
*
492431 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
492452 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
**
492473 TCGCATTGCGATTTT-CTTAT
1 TCGCATTGCGATTTTCCAAAT
492493 TCGCATTGCGA
1 TCGCATTGCGA
492504 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 14 0.29
21 35 0.71
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:492518 original size:41 final size:42
Alignment explanation
Indices: 492430--492518 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
492420 GATAGTCAGT
* * *
492430 ATCGCGTTGCGATTTTCCAAATTCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTCCAAATTCGCATTGCGAATTACCAAA
* ** **
492472 TTCGCATTGCGATTTT-CTTATTCGCATTGCGAATTAGGAAA
1 ATCGCATTGCGATTTTCCAAATTCGCATTGCGAATTACCAAA
492513 ATCGCA
1 ATCGCA
492519 ACGCGAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 24 0.63
42 14 0.37
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (42 bp):
ATCGCATTGCGATTTTCCAAATTCGCATTGCGAATTACCAAA
Found at i:492545 original size:21 final size:22
Alignment explanation
Indices: 492493--492545 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
492483 ATTTTCTTAT
492493 TCGCATTGCG-AATTAGGAAAA
1 TCGCATTGCGAAATTAGGAAAA
**
492514 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTAGGAAAA
492535 TCGCATTGCGA
1 TCGCATTGCGA
492546 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTAGGAAAA
Found at i:494665 original size:29 final size:26
Alignment explanation
Indices: 494593--494675 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
494583 AATTGTGTTA
494593 AAAATTCATTTTCATTCTCTAAATTAT
1 AAAATTCATTTTCATTCTCT-AATTAT
*
494620 AAAATT--TTAT-ATT-TCTAATTGAT
1 AAAATTCATTTTCATTCTCTAATT-AT
*
494643 AATTAATTCATTTTCATTCTCTAAATTTT
1 AA--AATTCATTTTCATTCTCT-AATTAT
494672 AAAA
1 AAAA
494676 ATTTATCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
22 4 0.09
23 7 0.16
24 3 0.07
25 7 0.16
27 11 0.24
28 3 0.07
29 6 0.13
30 4 0.09
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (26 bp):
AAAATTCATTTTCATTCTCTAATTAT
Found at i:494701 original size:32 final size:32
Alignment explanation
Indices: 494665--494731 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
494655 TTCATTCTCT
*
494665 AAATTTTAAAAATTTATCCTTTAAAACTTATA
1 AAATTTTAAAAATTCATCCTTTAAAACTTATA
* *
494697 AAATTTTAAAAATTCATCTTTTAAAACTTGTA
1 AAATTTTAAAAATTCATCCTTTAAAACTTATA
494729 AAA
1 AAA
494732 GTTAGCTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (32 bp):
AAATTTTAAAAATTCATCCTTTAAAACTTATA
Found at i:507029 original size:16 final size:17
Alignment explanation
Indices: 506998--507030 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
506988 ATAACAGTGA
506998 TCTGAATTTCTTTTTTG
1 TCTGAATTTCTTTTTTG
*
507015 TCTGTATTT-TTTTTTG
1 TCTGAATTTCTTTTTTG
507031 GTACGGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.09, G:0.12, T:0.70
Consensus pattern (17 bp):
TCTGAATTTCTTTTTTG
Found at i:513300 original size:45 final size:44
Alignment explanation
Indices: 513232--513320 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
513222 TTTTGATAGA
513232 GCGCTACCTAAAATATTATTTTTTA-TCAAAAATATTAATATCGG
1 GCGCTACCTAAAATATTATTTTTTACT-AAAAATATTAATATCGG
* **
513276 GCGCTACCTAAAATTTTATTTTTTTACTGGAAATATTAATATCGG
1 GCGCTACCTAAAATATTA-TTTTTTACTAAAAATATTAATATCGG
513321 AAATATTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 17 0.43
45 22 0.55
46 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (44 bp):
GCGCTACCTAAAATATTATTTTTTACTAAAAATATTAATATCGG
Found at i:513352 original size:21 final size:21
Alignment explanation
Indices: 513328--513381 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
513318 CGGAAATATT
** *
513328 CATTTTAGGTAGCAAAATTAA
1 CATTTTAGGTAAAAAAAATAA
513349 CATTTCT-GGTAAAAAAAATAA
1 CATTT-TAGGTAAAAAAAATAA
*
513370 TATTTTAGGTAA
1 CATTTTAGGTAA
513382 TGTTATACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (21 bp):
CATTTTAGGTAAAAAAAATAA
Found at i:514342 original size:31 final size:31
Alignment explanation
Indices: 514279--514343 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
514269 TCTAAAATCA
* *
514279 TAATTTCTTAAATTTTGACACCATAACTTTC
1 TAATTTCTTAAATTATGACACCATAACGTTC
514310 TAATTTCTTAAATTAT-ATCA-CATTAACGTTC
1 TAATTTCTTAAATTATGA-CACCA-TAACGTTC
514341 TAA
1 TAA
514344 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (31 bp):
TAATTTCTTAAATTATGACACCATAACGTTC
Found at i:514635 original size:25 final size:26
Alignment explanation
Indices: 514602--514664 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
514592 ATATATTACC
514602 TTAAAATATTTTTA-TATCAACTT-A
1 TTAAAATATTTTTACTATCAACTTAA
*
514626 TT-AAATATATTTTACTATTAACTTAA
1 TTAAAATAT-TTTTACTATCAACTTAA
514652 TTATAAATATTTT
1 TTA-AAATATTTT
514665 ATTCTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 6 0.18
24 7 0.21
25 8 0.24
26 3 0.09
27 3 0.09
28 6 0.18
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAAATATTTTTACTATCAACTTAA
Found at i:515127 original size:39 final size:39
Alignment explanation
Indices: 515078--515194 Score: 125
Period size: 39 Copynumber: 3.0 Consensus size: 39
515068 TAAATATTTA
515078 AAAATAATTTAGAATGTTAATGTGAAATAATTTAAGAAAT
1 AAAA-AATTTAGAATGTTAATGTGAAATAATTTAAGAAAT
*
515118 AAAAAATTTAGAATGTT-ATGATAGCAA-AATTTAAGAAAT
1 AAAAAATTTAGAATGTTAATG-T-GAAATAATTTAAGAAAT
*** *
515157 TGGAAATTTAGAAGGTTAGA-GTGAAATAATTTAA-AAAT
1 AAAAAATTTAGAATGTTA-ATGTGAAATAATTTAAGAAAT
515195 TATAAATACA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
38 10 0.15
39 47 0.71
40 8 0.12
41 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.15, T:0.32
Consensus pattern (39 bp):
AAAAAATTTAGAATGTTAATGTGAAATAATTTAAGAAAT
Found at i:516067 original size:131 final size:132
Alignment explanation
Indices: 515833--516096 Score: 415
Period size: 131 Copynumber: 2.0 Consensus size: 132
515823 TAGTGAAATG
* * * *
515833 AGACACCAAATTCTTTAAACAATATCATAAATTTGAATTTTAATGCTATAAATTAAACAAATTGA
1 AGACACCAAATTCTTTAAACAATATCAAAAAATTGAAGTTTAATGCTATAAATAAAACAAATTGA
*
515898 GTTAGAAGGATCAACCCTTAATGAGCCTCTACAATACTCGA-TTAGATTAGTCAATCAATAGATC
66 GTTAGAAGGATCAACCCTTAATGAGCCTCTACAATACTCGATTTAGATTAATCAATCAATAGATC
515962 GA
131 GA
* *
515964 AGACACTAAATTCTTTAAACAATGTCAAAAAATTGAAGTTTAATGCTATAAATAAAACAAATTGA
1 AGACACCAAATTCTTTAAACAATATCAAAAAATTGAAGTTTAATGCTATAAATAAAACAAATTGA
* * *
516029 GTTAGAAGGATCAACCTTTAAT-AGACTTCTACAATACTCGATTTAGATTAATCGATCAATAGAT
66 GTTAGAAGGATCAACCCTTAATGAG-CCTCTACAATACTCGATTTAGATTAATCAATCAATAGAT
516093 CGA
130 CGA
516096 A
1 A
516097 TACTAACGAT
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
130 2 0.02
131 95 0.79
132 24 0.20
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (132 bp):
AGACACCAAATTCTTTAAACAATATCAAAAAATTGAAGTTTAATGCTATAAATAAAACAAATTGA
GTTAGAAGGATCAACCCTTAATGAGCCTCTACAATACTCGATTTAGATTAATCAATCAATAGATC
GA
Found at i:520306 original size:19 final size:19
Alignment explanation
Indices: 520269--520306 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
520259 CAAGCGATGC
*
520269 TCAAATAGGATGTTTGAGT
1 TCAAATAGGATGTTAGAGT
520288 TCAAATGAGGA-GTTAGAGT
1 TCAAAT-AGGATGTTAGAGT
520307 AAGATAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (19 bp):
TCAAATAGGATGTTAGAGT
Found at i:520793 original size:143 final size:143
Alignment explanation
Indices: 520631--520931 Score: 385
Period size: 143 Copynumber: 2.1 Consensus size: 143
520621 TTATTTACTA
520631 CTAACTACTAACTTTTATTTTATTGCACTT-TAATC-ATTG-TTATTTATTTATTTATGTATGTA
1 CTAACTACTAACTTTTATTTTATTGCA-TTCTAA-CAATTGTTTATTTATTTATTTATGTATGTA
* * * * *
520693 TGTATTTGTTTCTAATATTCGAATT-GGCCTTTTGGTGATCCGATCTGGGGTATGATCTACATTA
64 TGTA-TTATTTCTAATATTCG-ATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCACATTA
520757 TTATGGTTCGAACTCTG
127 TTATGGTTCGAACTCTG
* * * * * *
520774 CTAACTATTGACTTTTATTTTATTGCATTCTAACAATTGTTTATTTATTTATTTATTTGTTTATT
1 CTAACTACTAACTTTTATTTTATTGCATTCTAACAATTGTTTATTTATTTATTTATGTATGTATG
**
520839 TATTATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCGTATTATTAT
66 TATTATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCACATTATTAT
* *
520904 GGTTCGGACTTTG
131 GGTTCGAACTCTG
**
520917 CTAACCGCTAACTTT
1 CTAACTACTAACTTT
520932 CCCAACAACT
Statistics
Matches: 135, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
142 6 0.04
143 106 0.79
144 23 0.17
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (143 bp):
CTAACTACTAACTTTTATTTTATTGCATTCTAACAATTGTTTATTTATTTATTTATGTATGTATG
TATTATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCCGGGGTATGATCCACATTATTAT
GGTTCGAACTCTG
Found at i:520822 original size:4 final size:4
Alignment explanation
Indices: 520813--520846 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
520803 CTAACAATTG
*
520813 TTTA TTTA TTTA TTTA TTTG TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
520847 CTAATATTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:523680 original size:210 final size:210
Alignment explanation
Indices: 523305--523690 Score: 497
Period size: 210 Copynumber: 1.8 Consensus size: 210
523295 AATGAGGTCT
* * * * *
523305 GCTCGAAGATCATGCAACATTCGAGACTGAAATGATGATCCACTGATTCGATGAGTAATCCAACA
1 GCTCCAAGATCATGCAACATTCGAGAATGAAATGATAATCCACTAATTCGAGGAGTAATCCAACA
* * * *
523370 GTGGAATCTTATCTACAATCATGTCATCGCTAGTCATCAAGGAGCGACGCAATGGCTTCAGCACA
66 GTAGAATCTTATCTACAAGCATGTCATCGCTAATCATCAAGGAGCGACGCAATGACTTCAGCACA
** * * * * *
523435 GTTGAGGGATTAACGGAGTTAGTTTACAAAGCATTGAGGGGCATCAGTTCCAAATACAAAGATCC
131 CATGAGGCATCAACCGAGTTAGGTTACAAAGCATTGAGAGGCATCAGTTCCAAATACAAAGATCC
523500 GAGACGAAATAGTGA
196 GAGACGAAATAGTGA
* * * **
523515 GCTCCAAGATCGTGCAACATTTGAGAATGATATGATAATCCACTAATTCGAGGAGTAATCCAGTA
1 GCTCCAAGATCATGCAACATTCGAGAATGAAATGATAATCCACTAATTCGAGGAGTAATCCAACA
* * * * *
523580 GTAGATTCTTATCTACGAGCAT-TCCATCGCTAATCATTAAGGAGTGACGCATTGACTTCAGCAC
66 GTAGAATCTTATCTACAAGCATGT-CATCGCTAATCATCAAGGAGCGACGCAATGACTTCAGCA-
*
523644 CACATG-GGCATCAACCGAGTTAGGTTACAGAGCATTGAGAGGCATCA
129 CACATGAGGCATCAACCGAGTTAGGTTACAAAGCATTGAGAGGCATCA
523691 TTTTCGCGAA
Statistics
Matches: 147, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
209 1 0.01
210 142 0.97
211 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (210 bp):
GCTCCAAGATCATGCAACATTCGAGAATGAAATGATAATCCACTAATTCGAGGAGTAATCCAACA
GTAGAATCTTATCTACAAGCATGTCATCGCTAATCATCAAGGAGCGACGCAATGACTTCAGCACA
CATGAGGCATCAACCGAGTTAGGTTACAAAGCATTGAGAGGCATCAGTTCCAAATACAAAGATCC
GAGACGAAATAGTGA
Found at i:525210 original size:15 final size:14
Alignment explanation
Indices: 525192--525252 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
525182 AAACAAACAT
*
525192 AAAAGAAGCAAAGA
1 AAAAAAAGCAAAGA
*
525206 AAAAAAGTGCAAAG-
1 AAAAAA-AGCAAAGA
525220 AAAAAAA-CAAAGA
1 AAAAAAAGCAAAGA
525233 GAAAAGAAA-CAAAGA
1 -AAAA-AAAGCAAAGA
525248 AAAAA
1 AAAAA
525253 TTAAAGCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.12
13 1 0.03
14 19 0.47
15 15 0.38
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAAAAGCAAAGA
Found at i:525263 original size:26 final size:27
Alignment explanation
Indices: 525215--525267 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
525205 AAAAAAAGTG
*
525215 CAAAGAAAAAAACAAAGAGAAAAGAAA
1 CAAAGAAAAAAACAAAGACAAAAGAAA
**
525242 CAAAGAAAAAATTAAAG-CAAAAGAAA
1 CAAAGAAAAAAACAAAGACAAAAGAAA
525268 AAACAAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.75, C:0.08, G:0.13, T:0.04
Consensus pattern (27 bp):
CAAAGAAAAAAACAAAGACAAAAGAAA
Found at i:525288 original size:18 final size:19
Alignment explanation
Indices: 525243--525297 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 19
525233 GAAAAGAAAC
**
525243 AAAGAAAAAATTAA-AGCA
1 AAAGAAAAAACAAAGAGCA
525261 AAAGAAAAAACAAAGAGCA
1 AAAGAAAAAACAAAGAGCA
* *
525280 AAA-AGAAAACAAGGAGCA
1 AAAGAAAAAACAAAGAGCA
525298 TAGACAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 25 0.78
19 7 0.22
ACGTcount: A:0.71, C:0.09, G:0.16, T:0.04
Consensus pattern (19 bp):
AAAGAAAAAACAAAGAGCA
Found at i:526314 original size:15 final size:15
Alignment explanation
Indices: 526294--526342 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
526284 GCTCAAGATC
526294 GAAGCTGGGGCAAGA
1 GAAGCTGGGGCAAGA
526309 GAAGCT----CAAGA
1 GAAGCTGGGGCAAGA
526320 TCGAAGCTGGGGCAAGA
1 --GAAGCTGGGGCAAGA
526337 GAAGCT
1 GAAGCT
526343 AAATTTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
11 5 0.18
13 6 0.21
15 12 0.43
17 5 0.18
ACGTcount: A:0.35, C:0.16, G:0.39, T:0.10
Consensus pattern (15 bp):
GAAGCTGGGGCAAGA
Found at i:526321 original size:28 final size:28
Alignment explanation
Indices: 526281--526342 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
526271 ATATCTATCT
526281 GAAGCTCAAGATCGAAGCTGGGGCAAGA
1 GAAGCTCAAGATCGAAGCTGGGGCAAGA
526309 GAAGCTCAAGATCGAAGCTGGGGCAAGA
1 GAAGCTCAAGATCGAAGCTGGGGCAAGA
526337 GAAGCT
1 GAAGCT
526343 AAATTTTGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.35, T:0.11
Consensus pattern (28 bp):
GAAGCTCAAGATCGAAGCTGGGGCAAGA
Found at i:527003 original size:105 final size:105
Alignment explanation
Indices: 526871--527177 Score: 469
Period size: 105 Copynumber: 2.9 Consensus size: 105
526861 CTTAAGACAA
* *
526871 TTTCTCTT-AAAACAATATTT-GGCTCGCTTTAGACATTTTTCCTTTGAGATACAAATTTTGAAT
1 TTTCT-TTCAAAACAA-ATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAAT
526934 TTGCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
64 TTGCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
526976 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
1 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
* * *
527041 GCTTCACATAAAACAAAATTAATCTCACTTGAGATTGTTG
66 GCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
* * * * *
527081 TTTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTTCTCTGAGATACAAA-TTTAAATTA
1 TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
527145 G-TTGTACTTGAAACAAAATTAATCTCACTTGAG
66 GCTT-TACTTGAAACAAAATTAATCTCACTTGAG
527178 TTTTTCAAAA
Statistics
Matches: 186, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
103 2 0.01
104 40 0.22
105 144 0.77
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (105 bp):
TTTCTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTT
GCTTTACTTGAAACAAAATTAATCTCACTTGAGATTGTTG
Found at i:527388 original size:28 final size:29
Alignment explanation
Indices: 527324--527388 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
527314 AGTTTCTCTT
*
527324 GAAACAAATCTTTGAGTATGTTCCTTTTGA
1 GAAA-AAATCTTTGAGTATGTTCCTTGTGA
*
527354 -ATAAAAATCTTTGAGT-TGTTTCTTGTGA
1 GA-AAAAATCTTTGAGTATGTTCCTTGTGA
527382 GAAAAAA
1 GAAAAAA
527389 ATTTAGAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 15 0.48
29 14 0.45
30 2 0.06
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (29 bp):
GAAAAAATCTTTGAGTATGTTCCTTGTGA
Found at i:527388 original size:29 final size:30
Alignment explanation
Indices: 527324--527390 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
527314 AGTTTCTCTT
* *
527324 GAAACAAATCTTTGAGTATGTTCCTTTTGA
1 GAAAAAAATCTTTGAGTATGTTCCTTGTGA
* *
527354 -ATAAAAATCTTTGAGT-TGTTTCTTGTGA
1 GAAAAAAATCTTTGAGTATGTTCCTTGTGA
527382 GAAAAAAAT
1 GAAAAAAAT
527391 TTAGAGTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (30 bp):
GAAAAAAATCTTTGAGTATGTTCCTTGTGA
Found at i:527468 original size:63 final size:65
Alignment explanation
Indices: 527382--527534 Score: 206
Period size: 63 Copynumber: 2.4 Consensus size: 65
527372 TTTCTTGTGA
* * * *
527382 GAAAAAAAT-TTAGAGTCTATTTCTTTTG-AAACAAAGTTTTGTCTCTCTTGAGACAATTTC-AT
1 GAAAAAAATCTTTGAGTATGTTTCTTTTGAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAT
*
527444 GAAAAAAATCTTTGAGTATGTTTC-TTTGAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTT
1 GAAAAAAATCTTTGAGTATGTTTCTTTTGAAAACAAAATTTTGTCTCTCTTGAGACAATTTC-TA
527508 T
65 T
*
527509 GAGAAAAAATCTTTGAGTTTGTTTCT
1 GA-AAAAAATCTTTGAGTATGTTTCT
527535 ACTAACAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
62 13 0.16
63 42 0.53
65 3 0.04
66 21 0.27
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (65 bp):
GAAAAAAATCTTTGAGTATGTTTCTTTTGAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAT
Found at i:527627 original size:96 final size:96
Alignment explanation
Indices: 527451--527629 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
527441 CATGAAAAAA
* * * **
527451 ATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAA
1 ATCTTTGAGTATATTTATTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
* *
527516 AATCTTTGAGTTTGTTTCTACTAACAAAATC
66 AACCTTTGAGATTGTTTCTACTAACAAAATC
* *
527547 ATCTTTGAGTTTATTTATTTAAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTAATGA-AAAA
1 ATCTTTGAGTATATTTATTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
527610 CCAACCTTTGAGATTGTTTC
66 --AACCTTTGAGATTGTTTC
527630 CCTTGAAACG
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
94 4 0.06
95 30 0.42
96 38 0.53
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (96 bp):
ATCTTTGAGTATATTTATTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAGAAAA
AACCTTTGAGATTGTTTCTACTAACAAAATC
Found at i:527887 original size:36 final size:36
Alignment explanation
Indices: 527751--527887 Score: 161
Period size: 36 Copynumber: 3.8 Consensus size: 36
527741 TTGAAACATT
527751 TATCTTTGAGTCTGTTTCACTTGAAA-AAAACAAAGA
1 TATCTTTGAGTCTGTTTCACTTGAAACAAAACAAA-A
* *
527787 AATCTTTGAGTCTGTTTCACTTGCAACAAAACAAAAA
1 TATCTTTGAGTCTGTTTCACTTGAAACAAAAC-AAAA
* * *
527824 TCATATTTGAGTTTGTTTCCCTTGAAACAAAAC-AAA
1 T-ATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAA
* *
527860 TATCTTTGAGATTTGTTTCCCTTGAAAC
1 TATCTTTGAG-TCTGTTTCACTTGAAAC
527888 GAATTTTGTC
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
35 8 0.09
36 45 0.51
37 6 0.07
38 30 0.34
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (36 bp):
TATCTTTGAGTCTGTTTCACTTGAAACAAAACAAAA
Found at i:528360 original size:134 final size:133
Alignment explanation
Indices: 528032--528349 Score: 417
Period size: 134 Copynumber: 2.4 Consensus size: 133
528022 CGTAGGAACC
528032 GTGTCATCCCCTGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCTTAGATAACC-GATCG
1 GTGTCATCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTC-ACCTTAGATAACCAGATCG
* * * **
528096 TCCTCATCACGTAGGAATCGAGTTATCACCCTTCCTAAAAATGGCCAGAACTCTTCACCGCGTAT
64 TCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAAATGACCAGAACTCTTCACCAAGTAT
528161 GATCA
129 GATCA
* * * * * * *
528166 GTGTCATCCCTCAACCAAACCACCTCATCACGTAGGAGCCGTGTCACCCATAGATAACCAGCT-G
1 GTGTCATCCC-CGACCAGATCTCTTCATCACGTAGGAGCCGTGTCA-CCTTAGATAACCAGATCG
* * *
528230 TCCTCATCACGTAGGAACCGAGTTATCATCATTCCTAAAGATGACCAGAACTCTTCATCAAGTAT
64 TCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAAATGACCAGAACTCTTCACCAAGTAT
*
528295 GAGT-T
129 GA-TCA
528300 GTGTCATCCACCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCTT
1 GTGTCATCC-CCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCTT
528350 TAGACGACCA
Statistics
Matches: 157, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
133 4 0.03
134 148 0.94
135 5 0.03
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (133 bp):
GTGTCATCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCTTAGATAACCAGATCGTC
CTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAAATGACCAGAACTCTTCACCAAGTATGA
TCA
Found at i:529698 original size:139 final size:140
Alignment explanation
Indices: 529466--529751 Score: 425
Period size: 139 Copynumber: 2.0 Consensus size: 140
529456 TTATTTACTA
* *
529466 CTAACTACTAACTTTTATTTTATTACACTTTAATCATTGTTATTTATTTATTTATTTATGTATTT
1 CTAACTACTAACTTTTATTTTATTACACTTTAACCATTG-T-TTTATTTATATATTTATGTATTT
* *
529531 ATTCTTTCTAATATTCGATTCGGCCTTGTGGTGATCCGAT-TCGGGGTATGATCCACATTATTAT
64 ATTATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCT-GGGGTATGATCCACATTATTAT
529595 GGTTCGGACTCTG
128 GGTTCGGACTCTG
* * * * *
529608 CTAACTACTGACTTTTATTTTATTGCA-TTCTAACCATTG-TTTATTTATATGTTTGTTTATTTA
1 CTAACTACTAACTTTTATTTTATTACACTT-TAACCATTGTTTTATTTATATATTTATGTATTTA
*
529671 TTATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCTGGGGTATGATCCGCATTATTATGG
65 TTATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCTGGGGTATGATCCACATTATTATGG
529736 TTCGGACTCTG
130 TTCGGACTCTG
529747 CTAAC
1 CTAAC
529752 CGCTAATTAT
Statistics
Matches: 132, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
139 96 0.73
140 1 0.01
141 2 0.02
142 33 0.25
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.47
Consensus pattern (140 bp):
CTAACTACTAACTTTTATTTTATTACACTTTAACCATTGTTTTATTTATATATTTATGTATTTAT
TATTTCTAATATTCGATTCGGCCTTGTGGTGACCCGATCTGGGGTATGATCCACATTATTATGGT
TCGGACTCTG
Found at i:531122 original size:5 final size:5
Alignment explanation
Indices: 531114--531143 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
531104 TTTTGCTTTG
*
531114 TTAAA TTAAA TTAAA TTAAA TTAAA ATAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
531144 GTTATTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
TTAAA
Found at i:537931 original size:41 final size:43
Alignment explanation
Indices: 537862--537944 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 43
537852 AATCAATTCT
*
537862 AAAGTAACAATCCACACATACATAAAACT-A-ATATTACAACC
1 AAAGTAACAATCCACAAATACATAAAACTAACATATTACAACC
* *
537903 AAAGTAACAATCCACAAATATATTAAACTAACATATTACAAC
1 AAAGTAACAATCCACAAATACATAAAACTAACATATTACAAC
537945 TATTCTTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 26 0.70
42 1 0.03
43 10 0.27
ACGTcount: A:0.54, C:0.22, G:0.02, T:0.22
Consensus pattern (43 bp):
AAAGTAACAATCCACAAATACATAAAACTAACATATTACAACC
Found at i:539976 original size:5 final size:5
Alignment explanation
Indices: 539966--540004 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
539956 TTAAAAGGGA
* *
539966 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAC CAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
540005 AATTTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:540425 original size:21 final size:21
Alignment explanation
Indices: 540399--540534 Score: 161
Period size: 21 Copynumber: 6.5 Consensus size: 21
540389 GTTTCCAGAT
*
540399 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
540420 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
540441 TCGCAATGCGAACTT-GTA-AA
1 TCGCAATGCGAACTTCG-ACTA
* *
540461 TCGCAATGCGATA-GTCAACTA
1 TCGCAATGCGA-ACTTCGACTA
*
540482 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
540503 TCGCAATGCGAACTTCTACTA
1 TCGCAATGCGAACTTCGACTA
*
540524 TCGCATTGCGA
1 TCGCAATGCGA
540535 TTTACATATT
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.16
21 82 0.84
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:540446 original size:62 final size:63
Alignment explanation
Indices: 540399--540518 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 63
540389 GTTTCCAGAT
* * **
540399 TCGCAACGCGA-ACTTCGACTATCGCAATGCGAACTTGGACTATCGC-AATGCGAACTTGTAAA
1 TCGCAACGCGATA-GTCAACTATCGCAATGCGAACTTGGACTATCGCAAATGCGAACTTCCAAA
*
540461 TCGCAATGCGATAGTCAACTATCGCAATGCGAACTTGGACTATCGC-AATGCGAACTTC
1 TCGCAACGCGATAGTCAACTATCGCAATGCGAACTTGGACTATCGCAAATGCGAACTTC
540519 TACTATCGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 52 0.98
63 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (63 bp):
TCGCAACGCGATAGTCAACTATCGCAATGCGAACTTGGACTATCGCAAATGCGAACTTCCAAA
Found at i:540554 original size:62 final size:62
Alignment explanation
Indices: 540416--540535 Score: 204
Period size: 62 Copynumber: 1.9 Consensus size: 62
540406 GCGAACTTCG
*
540416 ACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGTAAATCGCAATGCGATAGTCA
1 ACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCTAAATCGCAATGCGATAGTCA
* *
540478 ACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCTACTATCGCATTGCGAT
1 ACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCTA-AATCGCAATGCGAT
540536 TTACATATTC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 42 0.78
63 12 0.22
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (62 bp):
ACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCTAAATCGCAATGCGATAGTCA
Found at i:540569 original size:21 final size:21
Alignment explanation
Indices: 540543--540827 Score: 389
Period size: 21 Copynumber: 13.6 Consensus size: 21
540533 GATTTACATA
540543 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
540564 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
540585 TTCGCATTGTGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
540605 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCCAAG
540627 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
540648 TTCGCATCGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
540669 TTCGC-TTCACGATAGTCCAAG
1 TTCGCATT-GCGATAGTCCAAG
* *
540690 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* * *
540710 TATCGTATTGCGATAGT-CGAC
1 T-TCGCATTGCGATAGTCCAAG
*
540731 TATCGTATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCCAAG
540753 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
540774 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
540795 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
540816 TTCGCATTGCGA
1 TTCGCATTGCGA
540828 CTGGTGGTAA
Statistics
Matches: 238, Mismatches: 20, Indels: 12
0.88 0.07 0.04
Matches are distributed among these distances:
20 6 0.03
21 224 0.94
22 8 0.03
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:540569 original size:83 final size:82
Alignment explanation
Indices: 540398--540653 Score: 243
Period size: 83 Copynumber: 3.1 Consensus size: 82
540388 AGTTTCCAGA
* * * *
540398 TTCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGTA-AA-
1 TTCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCG-A-TT-TACAAT
* *
540461 TCGCAATGCGATAGT-CAAC
63 TCGCATTGCGATAGTCCAAG
*
540480 TATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCTACTATCGCATTGCGATTTACATATT
1 T-TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGATTTACA-ATT
540545 CGCATTGCGATAGTCCAAG
64 CGCATTGCGATAGTCCAAG
* * * * * * * * * *
540564 TTCGCATTGCGATAGTCGAAGT-TCGCATTGTGATA-GTCGACTATCGCATTGCGATAGTCCAAG
1 TTCGCAATGCGA-ACTTGGACTATCGCAATGCGA-ACTTCGACTATCGCATTGCGAT-TTACAA-
540627 TTCGCATTGCGATAGTCCAAG
62 TTCGCATTGCGATAGTCCAAG
540648 TTCGCA
1 TTCGCA
540654 TCGCGATAGT
Statistics
Matches: 147, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
80 2 0.01
81 3 0.02
82 3 0.02
83 99 0.67
84 40 0.27
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (82 bp):
TTCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCATTGCGATTTACAATTCG
CATTGCGATAGTCCAAG
Found at i:541188 original size:23 final size:23
Alignment explanation
Indices: 541107--541231 Score: 117
Period size: 21 Copynumber: 5.8 Consensus size: 23
541097 ATTTTGGACT
541107 ATCGCAA--CGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
* * * *
541128 ATCACAACGCGAATTTTCGACT--
1 ATCGCAACGCGAA-CTTGGAATAA
*
541150 ATCGCAA--CGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
*
541171 ATCGGAACGCGAACTTGGAAT--
1 ATCGCAACGCGAACTTGGAATAA
541192 ATCGCAA--CGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
541213 ATCGCAACGCGAACTTGGA
1 ATCGCAACGCGAACTTGGA
541232 CTATCGCAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
19 18 0.22
20 4 0.05
21 25 0.30
22 6 0.07
23 25 0.30
24 5 0.06
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (23 bp):
ATCGCAACGCGAACTTGGAATAA
Found at i:541208 original size:42 final size:42
Alignment explanation
Indices: 541100--541240 Score: 219
Period size: 42 Copynumber: 3.3 Consensus size: 42
541090 CGTTGCGATT
* *
541100 TTGGACTATCGCAACGAACTTGGAATAAATCACAACGCGAATT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA-C
* * *
541143 TTCGACTATCGCAACGAATTTGGAATAAATCGGAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
541185 TTGGAATATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
541227 TTGGACTATCGCAA
1 TTGGACTATCGCAA
541241 TGCGAATATG
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 51 0.58
43 37 0.42
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:542495 original size:4 final size:4
Alignment explanation
Indices: 542464--542531 Score: 63
Period size: 4 Copynumber: 17.0 Consensus size: 4
542454 GATTTGGACC
542464 TAAA -AAA TAAA -AAA -AAA TGAAA TAAAA TAAA TAAA TAAA TAATA TAAA
1 TAAA TAAA TAAA TAAA TAAA T-AAA T-AAA TAAA TAAA TAAA TAA-A TAAA
*
542512 TAAC TAAA TATAA T-AA TAAA
1 TAAA TAAA TA-AA TAAA TAAA
542532 AACTATATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
3 12 0.22
4 28 0.51
5 15 0.27
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:542499 original size:13 final size:13
Alignment explanation
Indices: 542464--542527 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
542454 GATTTGGACC
542464 TAAA-AAATAAAAA
1 TAAATAAAT-AAAA
*
542477 AAAATGAAATAAAA
1 TAAAT-AAATAAAA
542491 TAAATAAAT-AAA
1 TAAATAAATAAAA
*
542503 TAATATAAAT-AAC
1 TAA-ATAAATAAAA
542516 TAAATATAATAA
1 TAAATA-AATAA
542528 TAAAAACTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
12 9 0.21
13 21 0.49
14 9 0.21
15 4 0.09
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:542505 original size:17 final size:17
Alignment explanation
Indices: 542478--542531 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
542468 AAATAAAAAA
542478 AAATGAAATAAAATAAAT
1 AAAT-AAATAAAATAAAT
*
542496 AAATAAATAATATAAAT
1 AAATAAATAAAATAAAT
* *
542513 AACTAAATATAAT-AAT
1 AAATAAATAAAATAAAT
542529 AAA
1 AAA
542532 AACTATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 5 0.16
17 22 0.71
18 4 0.13
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:542586 original size:22 final size:22
Alignment explanation
Indices: 542558--542618 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
542548 ATTTTCATAA
*
542558 ATATGTTTTCAAAAATTATTTT
1 ATATGTTCTCAAAAATTATTTT
542580 ATATGTTCTCAAAAATTATTTT
1 ATATGTTCTCAAAAATTATTTT
542602 ATATGTTCTCAAAAATT
1 ATATGTTCTCAAAAATT
542619 CGTTTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (22 bp):
ATATGTTCTCAAAAATTATTTT
Found at i:542673 original size:35 final size:35
Alignment explanation
Indices: 542622--542888 Score: 333
Period size: 35 Copynumber: 7.5 Consensus size: 35
542612 AAAAATTCGT
*
542622 TTTTAAAAAAATATATATTATATGTTTTCAAAATTA
1 TTTT-AAAAACTATATATTATATGTTTTCAAAATTA
** ***
542658 TTTTAAAAACTATATACCATATGTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAATTA
542693 TTTTAAAAACTATATATTATATG-TTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAATTA
**
542727 TTTTAAAAAC--TATATTATACATTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAATTA
* * *
542760 TTTTTAAAAAAACTATATACTATATTTTTTCAAAACTA
1 -TTTT--AAAAACTATATATTATATGTTTTCAAAATTA
542798 TTTTTAAAAACCTATATATTATATGTTTTCAAAATTA
1 -TTTTAAAAA-CTATATATTATATGTTTTCAAAATTA
***
542835 TTTTAAAAACTATATATTATATGTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAATTA
542870 TTTTAAAAACTATATATTA
1 TTTTAAAAACTATATATTA
542889 AAAAATAAGT
Statistics
Matches: 201, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
32 9 0.04
33 11 0.05
34 22 0.11
35 88 0.44
36 24 0.12
37 23 0.11
38 24 0.12
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAATTA
Found at i:542846 original size:142 final size:140
Alignment explanation
Indices: 542621--542884 Score: 395
Period size: 142 Copynumber: 1.9 Consensus size: 140
542611 CAAAAATTCG
* *
542621 TTTTTAAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTC
1 TTTTTAAAAAAATATATACTATATGTTTTCAAAACTATTTTAAAAACTATATACCATATGTTTTC
* **
542686 AAAACCGTTTTAAAAACTATATATTATATG-TTTCAAAATTATTTTAAAAACTATATTATACATT
66 AAAACCATTTTAAAAACTATATATTATATGTTTTCAAAACCATTTTAAAAACTATATTATACATT
542750 TTCAAAATTA
131 TTCAAAATTA
* **
542760 TTTTTAAAAAAACTATATACTATATTTTTTCAAAACTATTTTTAAAAACCTATATATTATATGTT
1 TTTTTAAAAAAA-TATATACTATATGTTTTCAAAACTA-TTTTAAAAA-CTATATACCATATGTT
** *
542825 TTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAAAACCGTTTTAAAAACTATAT
63 TTCAAAACCATTTTAAAAACTATATATTATATGTTTTCAAAACCATTTTAAAAACTATAT
542885 ATTAAAAAAT
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
139 12 0.11
140 22 0.20
141 9 0.08
142 44 0.40
143 23 0.21
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (140 bp):
TTTTTAAAAAAATATATACTATATGTTTTCAAAACTATTTTAAAAACTATATACCATATGTTTTC
AAAACCATTTTAAAAACTATATATTATATGTTTTCAAAACCATTTTAAAAACTATATTATACATT
TTCAAAATTA
Found at i:542959 original size:177 final size:172
Alignment explanation
Indices: 542621--542943 Score: 452
Period size: 177 Copynumber: 1.8 Consensus size: 172
542611 CAAAAATTCG
542621 TTTTTAAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTC
1 TTTTTAAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTC
* *
542686 AAAACCGTTTTAAAAACTATATATTATATGTTTCAAAATTATTTTAAAAACTATATTATACATTT
66 AAAACCGTTTTAAAAACTATATATTATA----T-AAAATAATTTCAAAAACTATATTATACATTT
* *
542751 TCAAAATTATTTTTAAAAAAACTATATACTATATTTTTTCAAAACTA
126 TCAAAACTATTTTGAAAAAAACTATATACTATATTTTTTCAAAACTA
** **
542798 TTTTTAAAAACCTATATATTATATGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTC
1 TTTTTAAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTC
*
542863 AAAACCGTTTTAAAAACTATATATTA-A-AAAATAAGTTTCCAAAAACTATATATTATATATTTT
66 AAAACCGTTTTAAAAACTATATATTATATAAAATAA-TTT-CAAAAAC--TATATTATACATTTT
542926 CAAAAACTATATTTGAAA
127 C-AAAACTAT-TTTGAAA
542944 TTATTTTATA
Statistics
Matches: 131, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
170 6 0.05
171 3 0.02
172 6 0.05
174 15 0.11
175 7 0.05
176 7 0.05
177 87 0.66
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (172 bp):
TTTTTAAAAAAATATATATTATATGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTC
AAAACCGTTTTAAAAACTATATATTATATAAAATAATTTCAAAAACTATATTATACATTTTCAAA
ACTATTTTGAAAAAAACTATATACTATATTTTTTCAAAACTA
Found at i:554600 original size:8 final size:8
Alignment explanation
Indices: 554589--554640 Score: 81
Period size: 8 Copynumber: 6.6 Consensus size: 8
554579 GTTAAAAGAG
554589 AAAATAAT
1 AAAATAAT
554597 AAAATAAT
1 AAAATAAT
554605 AAAATAAT
1 AAAATAAT
554613 AAAAT-A-
1 AAAATAAT
554619 AAAATAAT
1 AAAATAAT
554627 AATAATAAT
1 AA-AATAAT
554636 AAAAT
1 AAAAT
554641 GATTTTTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 5 0.12
7 2 0.05
8 26 0.63
9 8 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:554601 original size:30 final size:30
Alignment explanation
Indices: 554567--554639 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
554557 ATTTTCAAAG
**
554567 AAAATAA-AAAAGGTTAAAAGAGAAAATAAT
1 AAAATAATAAAAGAATAAAAGA-AAAATAAT
* *
554597 AAAATAATAAAATAATAAAATAAAAATAAT
1 AAAATAATAAAAGAATAAAAGAAAAATAAT
554627 AATAATAATAAAA
1 AA-AATAATAAAA
554640 TGATTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.46
31 20 0.54
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (30 bp):
AAAATAATAAAAGAATAAAAGAAAAATAAT
Found at i:554605 original size:3 final size:3
Alignment explanation
Indices: 554591--554637 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
554581 TAAAAGAGAA
*
554591 AAT AAT AA- AAT AAT AA- AAT AAT AA- AAT AAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
554636 AA
1 AA
554638 AATGATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:555870 original size:18 final size:18
Alignment explanation
Indices: 555847--555883 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
555837 CTAAAAATTG
555847 AAATAAATAAATAAAATA
1 AAATAAATAAATAAAATA
* *
555865 AAATAACTAAATATAATA
1 AAATAAATAAATAAAATA
555883 A
1 A
555884 TAAAAACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAATAAATAAAATA
Found at i:556005 original size:35 final size:35
Alignment explanation
Indices: 555956--556383 Score: 416
Period size: 35 Copynumber: 12.0 Consensus size: 35
555946 AAAAAAACAT
* * *
555956 TTTTAAAAAATATATATTATAAGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
** **
555991 TTTTAAAAACTATATACCATATGTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* *
556026 TTTTAAAAACTATATATTATAAG-TTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* *
556060 -TTTAAAAA--ATATATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* **
556092 GTTTTAAAAAACTATATACTATATGTTTTCAAAACCG
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
* * **
556129 TTTTAAAAACTATATACTATATTTTTTCAAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
*
556164 TTTTAAAAACTATATATTATACGTTTTCAAAACTA
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
**
556199 TTTTTAAAAAACTATATATTATACATTTTCAAAACTA
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACTA
* *
556236 TTTTTAAAAAACTATATATTATATGCTTTCAAAATTAA
1 -TTTT-AAAAACTATATATTATATGTTTTCAAAACT-A
* * **
556274 TTTTAAAAATTATATATTATATGTTTT-TAAACCG
1 TTTTAAAAACTATATATTATATGTTTTCAAAACTA
* * *
556308 TTTTAAAAACTATATATTATAAGTTTTTAAAAAATAA
1 TTTTAAAAACTATATATTATATG-TTTTCAAAACT-A
* * *
556345 GTTTACAAAAACTATATATTATATATTTTTAAAAACTA
1 -TTT-TAAAAACTATATATTATAT-GTTTTCAAAACTA
556383 T
1 T
556384 ATTTGAAATT
Statistics
Matches: 332, Mismatches: 46, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
31 11 0.03
32 11 0.03
33 8 0.02
34 32 0.10
35 120 0.36
36 32 0.10
37 86 0.26
38 5 0.02
39 27 0.08
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATGTTTTCAAAACTA
Found at i:556040 original size:70 final size:70
Alignment explanation
Indices: 555956--556378 Score: 460
Period size: 70 Copynumber: 6.0 Consensus size: 70
555946 AAAAAAACAT
* **
555956 TTTTAAAAAATATATATTATAAGTTTTCAAAATTATTTTAAAAACTATATACCATATGTTTTCAA
1 TTTTAAAAACTATATATTATAAGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAA
556021 AACCG
66 AACCG
*
556026 TTTTAAAAACTATATATTATAAG-TTTCAAAATTA-TTTAAAAA--ATATATTATACGTTTTCAA
1 TTTTAAAAACTATATATTATAAGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAA
**
556087 AATTAG
66 AA-CCG
* * *** * *
556093 TTTTAAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAAACTATATACTATATTTTTTCA
1 TTTT-AAAAACTATATATTATAAGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCA
556158 AAACCG
65 AAACCG
* * **
556164 TTTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAAAAAACTATATATTATACATTTTC
1 TTTTAAAAACTATATATTATAAGTTTTCAAAATTA-TTTT-AAAAACTATATATTATATGTTTTC
**
556229 AAAACTAT
64 AAAAC-CG
* * *
556237 TTTTAAAAAACTATATATTATATGCTTTCAAAATTAATTTTAAAAATTATATATTATATGTTTT-
1 TTTT-AAAAACTATATATTATAAGTTTTCAAAATT-ATTTTAAAAACTATATATTATATGTTTTC
*
556301 TAAACCG
64 AAAACCG
* * * *
556308 TTTTAAAAACTATATATTATAAGTTTTTAAAAAATAAGTTTACAAAAACTATATATTATATATTT
1 TTTTAAAAACTATATATTATAAG-TTTT-CAAAATTA-TTT-TAAAAACTATATATTATATGTTT
*
556373 TTAAAA
62 TCAAAA
556379 ACTATATTTG
Statistics
Matches: 295, Mismatches: 42, Indels: 28
0.81 0.12 0.08
Matches are distributed among these distances:
66 18 0.06
67 5 0.02
68 25 0.08
69 19 0.06
70 75 0.25
71 17 0.06
72 56 0.19
73 45 0.15
74 34 0.12
75 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (70 bp):
TTTTAAAAACTATATATTATAAGTTTTCAAAATTATTTTAAAAACTATATATTATATGTTTTCAA
AACCG
Found at i:556042 original size:37 final size:35
Alignment explanation
Indices: 555884--556378 Score: 405
Period size: 35 Copynumber: 13.8 Consensus size: 35
555874 AATATAATAA
* * *
555884 TAAAAACTATATAATACTATATTTTCAGAAATATGTTT
1 TAAAAACTATATATTA-TATGTTTTCA-AAACA-GTTT
* * *
555922 TCAAAAA-T-TATTTTATATGTTCTCAAAAAAACATTTT
1 T-AAAAACTATATATTATATGTTTTC---AAAACAGTTT
* * *
555959 TAAAAAATATATATTATAAGTTTTCAAAATTA-TTT
1 TAAAAACTATATATTATATGTTTTCAAAA-CAGTTT
** *
555994 TAAAAACTATATACCATATGTTTTCAAAACCGTTT
1 TAAAAACTATATATTATATGTTTTCAAAACAGTTT
* *
556029 TAAAAACTATATATTATAAG-TTTC-AAA-ATTATT
1 TAAAAACTATATATTATATGTTTTCAAAACAGT-TT
* *
556062 TAAAAA--ATATATTATACGTTTTCAAAATTAGTTT
1 TAAAAACTATATATTATATGTTTTCAAAA-CAGTTT
* *
556096 TAAAAAACTATATACTATATGTTTTCAAAACCGTTT
1 T-AAAAACTATATATTATATGTTTTCAAAACAGTTT
* * *
556132 TAAAAACTATATACTATATTTTTTCAAAACCGTTT
1 TAAAAACTATATATTATATGTTTTCAAAACAGTTT
* *
556167 TAAAAACTATATATTATACGTTTTCAAAACTATTTT
1 TAAAAACTATATATTATATGTTTTCAAAAC-AGTTT
** *
556203 TAAAAAACTATATATTATACATTTTCAAAACTATTTT
1 T-AAAAACTATATATTATATGTTTTCAAAAC-AGTTT
* * *
556240 TAAAAAACTATATATTATATGCTTTCAAAATTAATTT
1 T-AAAAACTATATATTATATGTTTTCAAAA-CAGTTT
* * *
556277 TAAAAATTATATATTATATGTTTT-TAAACCGTTT
1 TAAAAACTATATATTATATGTTTTCAAAACAGTTT
* * *
556311 TAAAAACTATATATTATAAGTTTTTAAAAAATAAGTTT
1 TAAAAACTATATATTATATG-TTTT-CAAAA-CAGTTT
* * *
556349 ACAAAAACTATATATTATATATTTTTAAAA
1 -TAAAAACTATATATTATATGTTTTCAAAA
556379 ACTATATTTG
Statistics
Matches: 379, Mismatches: 54, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
31 11 0.03
32 5 0.01
33 14 0.04
34 28 0.07
35 126 0.33
36 43 0.11
37 102 0.27
38 27 0.07
39 23 0.06
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (35 bp):
TAAAAACTATATATTATATGTTTTCAAAACAGTTT
Found at i:556393 original size:109 final size:110
Alignment explanation
Indices: 555949--556402 Score: 368
Period size: 107 Copynumber: 4.2 Consensus size: 110
555939 TGTTCTCAAA
* * * * **
555949 AAAAC-ATTTTTAAAAAATATATATTATAAGTTTTCAAAATTA-TTTT-AAAAACTATATACCAT
1 AAAACTATATTTAAAAATTATATATTATACGTTTTCAAAACTAGTTTTAAAAAACTATATATTAT
** * ** * **
556011 ATGTTTT-CAAAA-CCGTTTTAAAAACTATATATTATA-AGTTTC
66 ACATTTTAAAAAATAAGTTTAAAAAACTATATATTATATTTTTTC
* *
556053 AAAA-T-TATTTAAAAA--ATATATTATACGTTTTCAAAATTAGTTTTAAAAAACTATATACTAT
1 AAAACTATATTTAAAAATTATATATTATACGTTTTCAAAACTAGTTTTAAAAAACTATATATTAT
** * ** * *
556114 ATGTTTT-CAAAA-CCGTTTTAAAAACTATATACTATATTTTTTC
66 ACATTTTAAAAAATAAGTTTAAAAAACTATATATTATATTTTTTC
** * *
556157 AAAACCGT-TTTAAAAACTATATATTATACGTTTTCAAAACTATTTTTAAAAAACTATATATTAT
1 AAAACTATATTTAAAAATTATATATTATACGTTTTCAAAACTAGTTTTAAAAAACTATATATTAT
* * ** **
556221 ACATTTTCAAAACTATTTTTAAAAAACTATATATTATATGCTTTC
66 ACATTTTAAAAAATAAGTTTAAAAAACTATATATTATATTTTTTC
* * * *
556266 AAAATTA-ATTTTAAAAATTATATATTATATGTTTT-TAAAC-CGTTTT-AAAAACTATATATTA
1 AAAACTATA-TTTAAAAATTATATATTATACGTTTTCAAAACTAGTTTTAAAAAACTATATATTA
*
556327 TA-AGTTTTTAAAAAATAAGTTTACAAAAACTATATATTATATATTTTTA
65 TACA--TTTTAAAAAATAAGTTTA-AAAAACTATATATTATAT-TTTTTC
*
556376 AAAACTATATTTGAAATTATTATATAT
1 AAAACTATATTT-AAA-AATTATATAT
556403 ACTATGCTAT
Statistics
Matches: 293, Mismatches: 38, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
101 23 0.08
102 4 0.01
103 59 0.20
104 12 0.04
105 8 0.03
106 2 0.01
107 65 0.22
108 21 0.07
109 50 0.17
110 36 0.12
111 4 0.01
112 9 0.03
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (110 bp):
AAAACTATATTTAAAAATTATATATTATACGTTTTCAAAACTAGTTTTAAAAAACTATATATTAT
ACATTTTAAAAAATAAGTTTAAAAAACTATATATTATATTTTTTC
Found at i:558286 original size:3 final size:3
Alignment explanation
Indices: 558278--558315 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
558268 ATATATATAT
558278 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
558316 TGACATGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:568099 original size:22 final size:22
Alignment explanation
Indices: 568054--568116 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
568044 ATGTGAAATT
*
568054 TGTCCCGAAGTACCTCA--TATA
1 TGTCCCGAAGGACCT-ATGTATA
* *
568075 TGTCCTGAATGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
568097 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
568117 ACCCTCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 22 0.63
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:568253 original size:16 final size:16
Alignment explanation
Indices: 568232--568291 Score: 65
Period size: 15 Copynumber: 3.9 Consensus size: 16
568222 ATAAGCTTAT
568232 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
568248 GTCACATAGCTC--AT-
1 GTCACAT-TCTCATATG
568262 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
568278 GTCAC-TTATCATAT
1 GTCACATTCTCATAT
568292 CATTTATCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.08
14 7 0.19
15 12 0.32
16 12 0.32
17 3 0.08
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (16 bp):
GTCACATTCTCATATG
Found at i:568264 original size:30 final size:30
Alignment explanation
Indices: 568225--568282 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
568215 TAGTCATATA
*
568225 AGCTTATGTCACATTCTCATATGGTCACAT
1 AGCTCATGTCACATTCTCATATGGTCACAT
568255 AGCTCATGTCACATTCTCATATGGTCAC
1 AGCTCATGTCACATTCTCATATGGTCAC
568283 TTATCATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (30 bp):
AGCTCATGTCACATTCTCATATGGTCACAT
Found at i:572259 original size:22 final size:22
Alignment explanation
Indices: 572214--572274 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
572204 GTGAAATTTA
*
572214 TCCCGAATGACCTCATG--TATG
1 TCCCGAAAGACCT-ATGTATATG
572235 TCCCGAAAGACCTATGTATATG
1 TCCCGAAAGACCTATGTATATG
*
572257 TCCCGAAGGACCTATGTA
1 TCCCGAAAGACCTATGTA
572275 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 3 0.08
21 12 0.33
22 21 0.58
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (22 bp):
TCCCGAAAGACCTATGTATATG
Found at i:572430 original size:30 final size:30
Alignment explanation
Indices: 572389--572471 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
572379 ATATAAGCTT
* *
572389 ATGTCATATTCTCATATGGTCACATAGATC
1 ATGTCACATTCTCATATGGTCACACAGATC
* *
572419 ACT-TCACATTCTCATATGGTCACACAGCTT
1 A-TGTCACATTCTCATATGGTCACACAGATC
572449 ATGTCACATTCTCATATGGTCAC
1 ATGTCACATTCTCATATGGTCAC
572472 TTATCATATC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.96
31 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (30 bp):
ATGTCACATTCTCATATGGTCACACAGATC
Found at i:572466 original size:15 final size:16
Alignment explanation
Indices: 572422--572480 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
572412 ATAGATCACT
572422 TCACATTCTCATATGG
1 TCACATTCTCATATGG
* *
572438 TCACA--CAGCTTAT-G
1 TCACATTC-TCATATGG
572452 TCACATTCTCATATGG
1 TCACATTCTCATATGG
*
572468 TCAC-TTATCATAT
1 TCACATTCTCATAT
572481 CATGTATCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
14 7 0.21
15 16 0.47
16 11 0.32
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (16 bp):
TCACATTCTCATATGG
Found at i:573039 original size:65 final size:64
Alignment explanation
Indices: 572911--573046 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 64
572901 ACACCCTAAT
* * *
572911 TCGAATGCATTTTGTGTATCGATGCACAGCCATGCATCGATGAACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTTATGTATCGATGCACAGCCATGCATCGATGAACTCCTGATCTTATTAAAACA
* * * *
572975 TCGAATGCGTTTTATGTATCGATGCACAGACTATGCATCGATGCACTCCTGGCTCTT-TTAAAAC
1 TCGAATGCATTTTATGTATCGATGCACAG-CCATGCATCGATGAACTCCT-GATCTTATTAAAAC
573039 A
64 A
573040 TCGAATG
1 TCGAATG
573047 TAATCAGTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
64 27 0.43
65 32 0.51
66 4 0.06
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGTATCGATGCACAGCCATGCATCGATGAACTCCTGATCTTATTAAAACA
Found at i:573058 original size:65 final size:64
Alignment explanation
Indices: 572924--573063 Score: 160
Period size: 65 Copynumber: 2.2 Consensus size: 64
572914 AATGCATTTT
* * * *
572924 GTGTATCGATGCACAGCCATGCATCGATGAACTCCTGATTTTATTGAAACATCGAATGCGTTTTA
1 GTGTATCGATGCACAGCCATGCATCGATGAACTCCTGATCTTATTAAAACATCGAAT-CGTATCA
* * *
572989 -TGTATCGATGCACAGACTATGCATCGATGCACTCCTGGCTCTT-TTAAAACATCGAAT-GTAAT
1 GTGTATCGATGCACAG-CCATGCATCGATGAACTCCT-GATCTTATTAAAACATCGAATCGT-AT
573051 CA
63 CA
573053 GTGTATCGATG
1 GTGTATCGATG
573064 TACCCCAAGT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
63 2 0.03
64 17 0.27
65 41 0.64
66 4 0.06
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (64 bp):
GTGTATCGATGCACAGCCATGCATCGATGAACTCCTGATCTTATTAAAACATCGAATCGTATCA
Found at i:578882 original size:44 final size:44
Alignment explanation
Indices: 578819--578922 Score: 154
Period size: 44 Copynumber: 2.4 Consensus size: 44
578809 TTTTGTGCAC
* * *
578819 TATGCATCGATACACTATGAAAGTGTACCGATGCATCCCTTGAA
1 TATGCATCGATACACTATGAAAGTGCACCAATGCATCACTTGAA
* * *
578863 TATGCATCGATACACTATGAAGGTGCACCAATGCATTATTTGAA
1 TATGCATCGATACACTATGAAAGTGCACCAATGCATCACTTGAA
578907 TATGCATCGATACACT
1 TATGCATCGATACACT
578923 CGTCGTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (44 bp):
TATGCATCGATACACTATGAAAGTGCACCAATGCATCACTTGAA
Found at i:578889 original size:21 final size:21
Alignment explanation
Indices: 578821--578889 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
578811 TTGTGCACTA
578821 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
578842 TGTACCGATGCATCCCT-TGAATA-
1 TGCATCGAT--A-CACTATGAA-AG
*
578865 TGCATCGATACACTATGAAGG
1 TGCATCGATACACTATGAAAG
578886 TGCA
1 TGCA
578890 CCAATGCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 3 0.09
21 16 0.46
23 12 0.34
24 4 0.11
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:579402 original size:13 final size:13
Alignment explanation
Indices: 579379--579421 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
579369 AAAACTCCAT
579379 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
579393 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
* *
579406 ATAGGTTTCAAA-
1 ATTGTTTTCAAAC
579418 ATTG
1 ATTG
579422 CCCATTAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 3 0.12
13 19 0.73
14 4 0.15
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:580690 original size:25 final size:26
Alignment explanation
Indices: 580636--580691 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
580626 TGTTTAAACA
580636 TTTTGAATATTTAGTTTGGATTGTTTG
1 TTTTGAATA-TTAGTTTGGATTGTTTG
*
580663 TTTTGAATA-TATTTTGGA-TGTTTG
1 TTTTGAATATTAGTTTGGATTGTTTG
*
580687 GTTTG
1 TTTTG
580692 TTTGAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 10 0.37
25 8 0.30
27 9 0.33
ACGTcount: A:0.18, C:0.00, G:0.23, T:0.59
Consensus pattern (26 bp):
TTTTGAATATTAGTTTGGATTGTTTG
Found at i:580996 original size:12 final size:14
Alignment explanation
Indices: 580969--581003 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
580959 AGTGGGAGTA
580969 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
580983 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
580995 ATTTTCAAA
1 ATTTTCAAA
581004 TAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:581479 original size:65 final size:64
Alignment explanation
Indices: 581345--581500 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 64
581335 GCACCATAAT
* * * *
581345 TCGAATACATTTTGTGTACCGATGCACAGCCATGCATTAATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCAATGCACTCCTGATCTTATTGAAACA
* * ** *
581409 ACGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTTTTGGCTCTT-TTGAAAC
1 TCGAATGCATTTTATGTACCGATGCACAG-CCATGCATCAATGCACTCCT-GATCTTATTGAAAC
581473 A
64 A
* *
581474 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATTTTA-TGTACCGATGCAC
581501 CACAAGTGTA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 29 0.38
65 44 0.57
66 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAGCCATGCATCAATGCACTCCTGATCTTATTGAAACA
Found at i:582895 original size:60 final size:60
Alignment explanation
Indices: 582824--582941 Score: 186
Period size: 60 Copynumber: 2.0 Consensus size: 60
582814 CCCAAGCACC
582824 AATTATCACTCATTTTCTCTTTGA-AGTATCGATACTTGATGAACAA-TATCAATACCCCCT
1 AATTATCACTCATTTTCTCTTTGACA-TATCGATACTTGATGAA-AAGTATCAATACCCCCT
* *
582884 AATTATCACTCATTTTCTCTTTGACATATCGGTACTTGATGAAAAGTATCGATACCCC
1 AATTATCACTCATTTTCTCTTTGACATATCGATACTTGATGAAAAGTATCAATACCCC
582942 TACCCATAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
59 2 0.04
60 51 0.94
61 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (60 bp):
AATTATCACTCATTTTCTCTTTGACATATCGATACTTGATGAAAAGTATCAATACCCCCT
Found at i:585230 original size:23 final size:24
Alignment explanation
Indices: 585195--585246 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
585185 AGATGGTGAA
*
585195 GGTTTATGGTTTGGGTTAG-CTAG
1 GGTTTATGGTTTGGCTTAGACTAG
*
585218 GGTTTA-GGTTTTGGCTTCGACTAG
1 GGTTTATGG-TTTGGCTTAGACTAG
585242 GGTTT
1 GGTTT
585247 GATGTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 14 0.56
24 9 0.36
ACGTcount: A:0.12, C:0.08, G:0.37, T:0.44
Consensus pattern (24 bp):
GGTTTATGGTTTGGCTTAGACTAG
Found at i:590824 original size:22 final size:22
Alignment explanation
Indices: 590799--590840 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
590789 GTCAGAGGGG
**
590799 AACCGATTCCCCTGCTACAGGA
1 AACCGATAACCCTGCTACAGGA
590821 AACCGATAACCCTGCTACAG
1 AACCGATAACCCTGCTACAG
590841 TACTTCCGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (22 bp):
AACCGATAACCCTGCTACAGGA
Found at i:592681 original size:25 final size:26
Alignment explanation
Indices: 592643--592691 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
592633 AAAAGTCAAA
*
592643 TTCATCATTCAAA-TTCATTTAAACC
1 TTCATCATTCAAATTTCACTTAAACC
592668 TTCAT-ATTCAAAATTTCACTTAAA
1 TTCATCATTC-AAATTTCACTTAAA
592692 ACCCCATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 9 0.43
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (26 bp):
TTCATCATTCAAATTTCACTTAAACC
Found at i:610569 original size:24 final size:24
Alignment explanation
Indices: 610533--610595 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
610523 GATTACTATT
610533 TTAA-AAAAA-TCAATTAAATT-AA
1 TTAATAAAAATTCAATT-AATTCAA
610555 -TAATTAAAAATTCAATTAATTCAA
1 TTAA-TAAAAATTCAATTAATTCAA
*
610579 TTAATAATAATTCAATT
1 TTAATAAAAATTCAATT
610596 TGATACAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 3 0.09
23 9 0.26
24 20 0.57
25 3 0.09
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAATAAAAATTCAATTAATTCAA
Found at i:613270 original size:26 final size:26
Alignment explanation
Indices: 613231--613285 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
613221 TTTTATAATA
**
613231 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTAAAAAATT
613257 ATAAATTTCATATATTTTGAAAAAATT
1 ATAAATTTCATATATTTT-AAAAAATT
613284 AT
1 AT
613286 TTTCTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 11 0.44
27 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
ATAAATTTCATATATTTTAAAAAATT
Found at i:613538 original size:17 final size:17
Alignment explanation
Indices: 613486--613539 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
613476 AAACAGTTAA
613486 ATACTGCTATGTGTAAT
1 ATACTGCTATGTGTAAT
*
613503 ATA-T-CT-TGTCTAGTCAT
1 ATACTGCTATG--T-GTAAT
613520 ATACTGCTATGTGTAAT
1 ATACTGCTATGTGTAAT
613537 ATA
1 ATA
613540 TATAACAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
14 2 0.07
15 2 0.07
16 2 0.07
17 17 0.59
18 2 0.07
19 2 0.07
20 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (17 bp):
ATACTGCTATGTGTAAT
Found at i:615793 original size:18 final size:18
Alignment explanation
Indices: 615770--615809 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
615760 AATATATATT
*
615770 TTTTAAAGTAATAAAATA
1 TTTTAAAGTAAAAAAATA
**
615788 TTTTAACTTAAAAAAATA
1 TTTTAAAGTAAAAAAATA
615806 TTTT
1 TTTT
615810 TTTATTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTTAAAGTAAAAAAATA
Found at i:616017 original size:23 final size:24
Alignment explanation
Indices: 615987--616041 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
615977 AATATATGTA
*
615987 TTTTTATTTAAAAT-AAAATTTAT
1 TTTTTATTTAAAATAAAAATATAT
*
616010 TTTTTATTTTAAATAAAAATATAT
1 TTTTTATTTAAAATAAAAATATAT
*
616034 ATTTTATT
1 TTTTTATT
616042 CTTTTATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTTATTTAAAATAAAAATATAT
Found at i:616238 original size:25 final size:23
Alignment explanation
Indices: 616209--616276 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 23
616199 TAAAATATTT
*
616209 TTTAAGTTAAAATATATTATTAC
1 TTTAAGATAAAATATATTATTAC
*
616232 TGCTTAACCGAAAAAATATATTATTAC
1 T--TTAA--GATAAAATATATTATTAC
*
616259 TTTAAAATAAAATATATT
1 TTTAAGATAAAATATATT
616277 TTTAAGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 12 0.32
25 8 0.22
27 17 0.46
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (23 bp):
TTTAAGATAAAATATATTATTAC
Found at i:622197 original size:23 final size:23
Alignment explanation
Indices: 622167--622220 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
622157 ATGTTGAATT
* *
622167 ATTCAGCAGTGTTTTACTGTTTC
1 ATTCAGCAATATTTTACTGTTTC
622190 ATTCAGCAATATTTTACTGTTTC
1 ATTCAGCAATATTTTACTGTTTC
622213 ATTCAGCA
1 ATTCAGCA
622221 TGGTTTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (23 bp):
ATTCAGCAATATTTTACTGTTTC
Found at i:622227 original size:23 final size:23
Alignment explanation
Indices: 622167--622227 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
622157 ATGTTGAATT
622167 ATTCAGCA-GTGTTTTACTGTTTC
1 ATTCAGCATG-GTTTTACTGTTTC
*
622190 ATTCAGCAAT-ATTTTACTGTTTC
1 ATTCAGC-ATGGTTTTACTGTTTC
622213 ATTCAGCATGGTTTT
1 ATTCAGCATGGTTTT
622228 CATTCATAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 30 0.91
24 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (23 bp):
ATTCAGCATGGTTTTACTGTTTC
Found at i:636187 original size:31 final size:31
Alignment explanation
Indices: 636149--636301 Score: 206
Period size: 30 Copynumber: 5.0 Consensus size: 31
636139 CCCGAAGGAC
* *
636149 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
*
636180 CAGTCCATATG-TCCGAAGGACA-AGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
636209 CAGTCCGTATGTTCCGAAGAACATAGGT-AA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
636239 CAGTCCGTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
636270 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
636301 C
1 C
636302 CCTCGACCCT
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
29 16 0.14
30 48 0.43
31 46 0.41
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:636504 original size:23 final size:24
Alignment explanation
Indices: 636478--636524 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
636468 ATATACCTGT
*
636478 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
636501 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
636525 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:639966 original size:8 final size:8
Alignment explanation
Indices: 639953--639993 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
639943 CTCATTTTCA
639953 GAGAATTT
1 GAGAATTT
639961 GAGAATTT
1 GAGAATTT
*
639969 -AGAGTTT
1 GAGAATTT
*
639976 GGGAATTT
1 GAGAATTT
639984 GAGAATTT
1 GAGAATTT
639992 GA
1 GA
639994 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:640248 original size:93 final size:91
Alignment explanation
Indices: 640092--640276 Score: 300
Period size: 93 Copynumber: 2.0 Consensus size: 91
640082 TTCCCAGGGG
*
640092 CGCGCCTTCCATTATTTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAAGGCCCTCGGG
1 CGCGCCTTCCATTATTTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCAAGGCCCTCGGG
640157 GACACTAG-ATATCAGTACCTATTAT
66 GACACTAGAATATCAGTACCTATTAT
* *
640182 CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCATGTCCCTC
1 CGCGCCTTCCATTA--TT-TCAGAGAATATGTTATCATTGCCCTATTATGTCAATCAAGGCCCTC
640247 GGGGACACTAGATATATCAGTACCTATTAT
63 GGGGACACTAGA-ATATCAGTACCTATTAT
640277 TTATTCACAT
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
90 14 0.16
92 2 0.02
93 54 0.62
95 17 0.20
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (91 bp):
CGCGCCTTCCATTATTTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCAAGGCCCTCGGG
GACACTAGAATATCAGTACCTATTAT
Found at i:640396 original size:121 final size:124
Alignment explanation
Indices: 640182--640641 Score: 707
Period size: 121 Copynumber: 3.7 Consensus size: 124
640172 TACCTATTAT
* *
640182 CGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCATGTCCCTC
1 CGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
640247 GGGGACACTAGATATATCAGTACCTATTATT-TATTCACATGAA-G-GCGTTCCCGGGG
66 GGGGACACTAGATATATCAGTACCTATTATTCTATTCACATGAAGGCGCGTTCCCGGGG
640303 CGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
1 CGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
*
640368 GGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCTCGGGGG
66 GGGGACACTAGATATATCAGTACCTATTA-TT--CTATTCACATGAAGGCGCGTTC-CCGGGG
*
640431 CGCACCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
1 CGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
* * * *** *
640496 GGGGACATTA-TTCTATCAGTACCTATTATTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGG
66 GGGGACACTAGATATATCAGTACCTATTATTCT-A-TTCACATGAAGGCGCGTTCCC-GGGG
*
640557 CGCGCCTTCCATTA-TTT-TCATAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTC
1 CGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
640620 GGGGACACTAGATATATCAGTA
66 GGGGACACTAGATATATCAGTA
640642 AATCAGGTAA
Statistics
Matches: 311, Mismatches: 17, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
121 92 0.30
122 2 0.01
124 56 0.18
125 26 0.08
126 35 0.11
127 22 0.07
128 78 0.25
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (124 bp):
CGCGCCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
GGGGACACTAGATATATCAGTACCTATTATTCTATTCACATGAAGGCGCGTTCCCGGGG
Found at i:640640 original size:252 final size:249
Alignment explanation
Indices: 640186--640641 Score: 747
Period size: 249 Copynumber: 1.8 Consensus size: 249
640176 TATTATCGCG
640186 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCATGTCCCTCGGGG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCATGTCCCTCGGGG
**
640251 ACACTAGATATATCAGTACCTATTATTTATTCACATGAAGGCGTTCCCGGGGCGCGCCTTCCATT
66 ACACTAGATATATCAGTACCTATTATTTAGGCACATGAAGGCGTTCCCGGGGCGCGCCTTCCATT
*
640316 ATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAT
131 ATTTTGTCATAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGAT
640381 ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCTCGGGGGCGCA
196 ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCTCGGGGGCGCA
* *
640435 CCTTCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCATGTCCCTCGGGG
* * * * *
640500 ACATTA-TTCTATCAGTACCTATTATTCTCAGGGGACTTGAAGGCGCGTTCCCGGGGGCGCGCCT
66 ACACTAGATATATCAGTACCTATTATT-T-A-GGCACATGAA-G-GCGTTCCC-GGGGCGCGCCT
640564 TCCATTA-TTT-TCATAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACA
125 TCCATTATTTTGTCATAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACA
640627 CTAGATATATCAGTA
190 CTAGATATATCAGTA
640642 AATCAGGTAA
Statistics
Matches: 191, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
248 18 0.09
249 69 0.36
250 1 0.01
251 6 0.03
252 68 0.36
253 11 0.06
254 18 0.09
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (249 bp):
CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAATCATGTCCCTCGGGG
ACACTAGATATATCAGTACCTATTATTTAGGCACATGAAGGCGTTCCCGGGGCGCGCCTTCCATT
ATTTTGTCATAGAATATGTTATCATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGAT
ATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCTCGGGGGCGCA
Found at i:641071 original size:34 final size:34
Alignment explanation
Indices: 641033--641133 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
641023 AAATTTAATG
*
641033 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
641067 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
641101 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
641134 AACATTTATC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:641683 original size:21 final size:21
Alignment explanation
Indices: 641653--641725 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
641643 TATGGTATAA
*
641653 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
641674 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
641695 AACCCTGCGGGCTCGGAATAT
1 AACCCTGCGGGCTAGGAATGT
641716 AACCCTGCGG
1 AACCCTGCGG
641726 AGATGGCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 3 0.06
21 41 0.87
22 3 0.06
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:641736 original size:21 final size:21
Alignment explanation
Indices: 641653--641738 Score: 59
Period size: 21 Copynumber: 4.1 Consensus size: 21
641643 TATGGTATAA
* * * *
641653 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGATCGGAATAT
* * *
641674 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGATCGGAATAT
*
641695 AACCCTGCGGGCTCGGAATAT
1 AACCCTGCGGGATCGGAATAT
*
641716 AACCCTGCGGAGAT-GGCATAT
1 AACCCTGCGG-GATCGGAATAT
641737 AA
1 AA
641739 ACTGGTGGGC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
20 3 0.05
21 49 0.86
22 5 0.09
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGATCGGAATAT
Found at i:641753 original size:21 final size:21
Alignment explanation
Indices: 641729--641776 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
641719 CCTGCGGAGA
*
641729 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
641750 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
641771 GGGCAT
1 TGGCAT
641777 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:641820 original size:27 final size:27
Alignment explanation
Indices: 641790--641844 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
641780 CCCCTGCGGC
641790 ATCGACGAATAAGGATGTTGTGGTGGG
1 ATCGACGAATAAGGATGTTGTGGTGGG
641817 ATCGACGAATAAGGATGTTGTGGTGGG
1 ATCGACGAATAAGGATGTTGTGGTGGG
641844 A
1 A
641845 CTGATGCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.40, T:0.25
Consensus pattern (27 bp):
ATCGACGAATAAGGATGTTGTGGTGGG
Found at i:643335 original size:15 final size:17
Alignment explanation
Indices: 643307--643339 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
643297 TCAGTATCCT
643307 AAATAAATACATTATAA
1 AAATAAATACATTATAA
643324 AAATAAA-A-ATTATAA
1 AAATAAATACATTATAA
643339 A
1 A
643340 TTCATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAATACATTATAA
Found at i:643545 original size:31 final size:31
Alignment explanation
Indices: 643507--643585 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 31
643497 TAATAATTCT
*
643507 AAATAATAATTATATAAATTATTTTAATA-AA
1 AAATAATAATTATATAAA-TATATTAATATAA
* *
643538 AAATAATATTTACAT-AATATATTAATATAA
1 AAATAATAATTATATAAATATATTAATATAA
* *
643568 AAATAATAACTATTTAAA
1 AAATAATAATTATATAAA
643586 AAATACTAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 9 0.23
30 15 0.38
31 15 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATAATAATTATATAAATATATTAATATAA
Found at i:643572 original size:30 final size:31
Alignment explanation
Indices: 643507--643576 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
643497 TAATAATTCT
* *
643507 AAATAATAATTATATAAATTATTTTAATAAA
1 AAATAATAATTACATAAATTATATTAATAAA
*
643538 AAATAATATTTACAT-AA-TATATTAATATAA
1 AAATAATAATTACATAAATTATATTAATA-AA
643568 AAATAATAA
1 AAATAATAA
643577 CTATTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.26
30 12 0.35
31 13 0.38
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATAATAATTACATAAATTATATTAATAAA
Found at i:644842 original size:34 final size:36
Alignment explanation
Indices: 644689--645164 Score: 452
Period size: 36 Copynumber: 13.4 Consensus size: 36
644679 TTTAAAATAC
* ** *
644689 ATATAATATATAGTTTTGAAAATGGTTTTTGGAAA--T
1 ATATAATATATAGTTTTTAAAA--CATTTTGAAAACTT
*
644725 ATATAACATATAGTTTTTAAAAACATTTTGAAAAAC-T
1 ATATAATATATAGTTTTT-AAAACATTTTG-AAAACTT
* *
644762 -TATAATATACAGTTTTAAAAACATTTTTTGAAAA--T
1 ATATAATATATAGTTTTTAAAACA--TTTTGAAAACTT
*
644797 ATATAATATATAATTTTTAAAACATTTTGAAAACTT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
* *
644833 ATATAATATATAGTTTTGAAATCATTTTGAAAA-TAT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACT-T
644869 ATATAATATATAGTTTTTTAAAACATTTTGAAAAACTT
1 ATATAATATATAG-TTTTTAAAACATTTTG-AAAACTT
* *
644907 ATAT-A-ATATAGTTTTGAAATCATTTTGAAAA--T
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
* *
644939 ATATAATATATAGTTTTTAAAAAAATTTGAAAACTT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
* *
644975 ATATAGTATATAGTTTTAAAAACATTTTTTG-AAACTT
1 ATATAATATATAGTTTTTAAAACA--TTTTGAAAACTT
* *
645012 ATATAATATATAGTTTTAAAAACATTTGGAAAACTT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
*
645048 ATATAATAT-T--TTTTTAAATCATTTTGAAAAC-T
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
* * * **
645080 ATATAATATATAGTTTTGAAAACTTTTTAAAAAAAT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
* * *
645116 ATATAATTTATAG-TTTAAAAATATTTTTG-AAA--T
1 ATATAATATATAGTTTTTAAAACA-TTTTGAAAACTT
*
645149 ATATATTATATAGTTT
1 ATATAATATATAGTTT
645165 ATTTTATAAT
Statistics
Matches: 372, Mismatches: 43, Indels: 52
0.80 0.09 0.11
Matches are distributed among these distances:
32 15 0.04
33 32 0.09
34 37 0.10
35 58 0.16
36 162 0.44
37 54 0.15
38 13 0.03
39 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAACTT
Found at i:646380 original size:29 final size:29
Alignment explanation
Indices: 646285--646392 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 29
646275 GTTATTTTAT
* *
646285 TTTTATTTATTTATTTCTCTTTT-ATATTGT
1 TTTTATTTATTTATTTTTCTTTTAATA-T-C
*
646315 TTTTATTTTATTTAACATTTTTCTTTTAATATT
1 TTTTA-TTTATTT---ATTTTTCTTTTAATATC
*
646348 TTTTA-TTATTATATTTTTCTTTT-TTATCC
1 TTTTATTTATT-TATTTTTCTTTTAATAT-C
646377 TTTTATTTATTTATTT
1 TTTTATTTATTTATTT
646393 ATTTATTTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
28 3 0.04
29 21 0.31
30 10 0.15
31 12 0.18
32 1 0.01
33 6 0.09
34 11 0.16
35 3 0.04
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.73
Consensus pattern (29 bp):
TTTTATTTATTTATTTTTCTTTTAATATC
Found at i:646386 original size:33 final size:31
Alignment explanation
Indices: 646375--646437 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 31
646365 TCTTTTTTAT
*
646375 CCTTTTATTTATTTATTTATTTATTTATTTTTC
1 CCTTTGATTTA-TTATTTATTT-TTTATTTTTC
646408 CCTTTGATTTATTATTTTATTTTATTATTT
1 CCTTTGATTTATTA-TTTATTTT-TTATTT
646438 ATTTATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (31 bp):
CCTTTGATTTATTATTTATTTTTTATTTTTC
Found at i:646387 original size:4 final size:4
Alignment explanation
Indices: 646378--646518 Score: 66
Period size: 4 Copynumber: 35.0 Consensus size: 4
646368 TTTTTATCCT
**
646378 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTCCC TTTGA TTTA -TTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTT-A TTTA TTTA -TTTA
* *
646427 TTT- TATTA TTTA TTTA TTTA --TA TTTA TATTT TTTCC TTCT- TTTGA
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT-A TT-TA TTT-A
* * *
646472 TTTA -TTA TTTTA GTTTT TTTA GTT- TTTA TTTA TTTA -ATA TTTA TTTA
1 TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
646519 ATGTGTTTTA
Statistics
Matches: 107, Mismatches: 12, Indels: 36
0.69 0.08 0.23
Matches are distributed among these distances:
2 2 0.02
3 14 0.13
4 67 0.63
5 23 0.21
6 1 0.01
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:646394 original size:41 final size:42
Alignment explanation
Indices: 646344--646460 Score: 116
Period size: 45 Copynumber: 2.7 Consensus size: 42
646334 TTTCTTTTAA
*
646344 TATTT-TTTA-TTATTATATTTTTCTTTTTTATCCTTTTATT
1 TATTTATTTATTTATTATATTTTTCTTTTTTATCATTTTATT
*
646384 TATTTATTTATTTATT-TATTTTTCCCTTTGATTTATTATTTTATT
1 TATTTATTTATTTATTATATTTTT--CTTT--TTTATCATTTTATT
* *
646429 T-TATTATTTATTTATTTATATTTATATTTTTT
1 TAT-TTATTTATTTA-TTATATTTTTCTTTTTT
646461 CCTTCTTTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
40 5 0.08
41 11 0.17
42 5 0.08
43 7 0.11
44 1 0.02
45 27 0.42
46 2 0.03
47 6 0.09
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.74
Consensus pattern (42 bp):
TATTTATTTATTTATTATATTTTTCTTTTTTATCATTTTATT
Found at i:646439 original size:57 final size:60
Alignment explanation
Indices: 646378--646517 Score: 179
Period size: 57 Copynumber: 2.5 Consensus size: 60
646368 TTTTTATCCT
646378 TTTATTTATTTATTTATTTATTTATTTTTCC-C-TTTGATTTATTATTTTA-TTTTATTA
1 TTTATTTATTTATTTATTTATTTATTTTTCCTCTTTTGATTTATTATTTTAGTTTTATTA
* *
646435 TTTATTTATTTA--TATTTATAT-TTTTTCCTTCTTTTGATTTATTATTTTAGTTTTTTTA
1 TTTATTTATTTATTTATTTATTTATTTTTCC-TCTTTTGATTTATTATTTTAGTTTTATTA
* *
646493 GTT-TTTATTTATTTA-ATATTTATTT
1 TTTATTTATTTATTTATTTATTTATTT
646518 AATGTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
54 7 0.10
55 8 0.11
56 1 0.01
57 37 0.52
58 13 0.18
59 5 0.07
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (60 bp):
TTTATTTATTTATTTATTTATTTATTTTTCCTCTTTTGATTTATTATTTTAGTTTTATTA
Found at i:647192 original size:14 final size:14
Alignment explanation
Indices: 647173--647204 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
647163 ATAAAAATTT
647173 GAATAACTCAACTC
1 GAATAACTCAACTC
647187 GAATAACTCAACTC
1 GAATAACTCAACTC
647201 GAAT
1 GAAT
647205 TTCTTAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (14 bp):
GAATAACTCAACTC
Found at i:651930 original size:14 final size:14
Alignment explanation
Indices: 651911--651938 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
651901 CGTTCTTCTC
651911 CACATCTATTAGAT
1 CACATCTATTAGAT
651925 CACATCTATTAGAT
1 CACATCTATTAGAT
651939 ACACGAACAC
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:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CACATCTATTAGAT
Done.