Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold241
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1040028
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 103832 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:440693 original size:47 final size:47
Alignment explanation
Indices: 440634--440760 Score: 182
Period size: 47 Copynumber: 2.7 Consensus size: 47
440624 ACCATCATTC
*
440634 GCCGTGAACAGGGTCCAAATTATGTACTGAAATAGTGCATCATGTTA
1 GCCGTGAACAGGGTCCAAATGATGTACTGAAATAGTGCATCATGTTA
440681 GCCGTGAACAGGGTCCAAATGATGTACTGAAATAGTGCATCATGTTGTA
1 GCCGTGAACAGGGTCCAAATGATGTACTGAAATAGTGCATCATG-T-TA
* * * * *
440730 ACCATGAAAAGGGTCCAAACGGTGTACTGAA
1 GCCGTGAACAGGGTCCAAATGATGTACTGAA
440761 CTAGAAGAGA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
47 43 0.60
48 1 0.01
49 28 0.39
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (47 bp):
GCCGTGAACAGGGTCCAAATGATGTACTGAAATAGTGCATCATGTTA
Found at i:445458 original size:2 final size:2
Alignment explanation
Indices: 445451--445496 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
445441 GTTTAAAATT
445451 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
445493 GA GA
1 GA GA
445497 TGACCACATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:465696 original size:16 final size:16
Alignment explanation
Indices: 465675--465706 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
465665 GATTATGATG
*
465675 AAAATGCATCTGATTA
1 AAAATGCACCTGATTA
465691 AAAATGCACCTGATTA
1 AAAATGCACCTGATTA
465707 CCAGTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (16 bp):
AAAATGCACCTGATTA
Found at i:483545 original size:2 final size:2
Alignment explanation
Indices: 483538--483590 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
483528 AGTTTTGATA
483538 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
483580 TC TC TC TC TC T
1 TC TC TC TC TC T
483591 GTTTTAGAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:497733 original size:102 final size:102
Alignment explanation
Indices: 497614--497798 Score: 370
Period size: 102 Copynumber: 1.8 Consensus size: 102
497604 AAGACCAGAG
497614 GTATATATTTTATTTAGGCTATTAACAGCTACATATGTTAATTTATACCACGGCGACAAAACTGA
1 GTATATATTTTATTTAGGCTATTAACAGCTACATATGTTAATTTATACCACGGCGACAAAACTGA
497679 TGTCTTCATTTAAAATGCTTCAAGACCAGAGGTACAT
66 TGTCTTCATTTAAAATGCTTCAAGACCAGAGGTACAT
497716 GTATATATTTTATTTAGGCTATTAACAGCTACATATGTTAATTTATACCACGGCGACAAAACTGA
1 GTATATATTTTATTTAGGCTATTAACAGCTACATATGTTAATTTATACCACGGCGACAAAACTGA
497781 TGTCTTCATTTAAAATGC
66 TGTCTTCATTTAAAATGC
497799 CTTTTCCTTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 83 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (102 bp):
GTATATATTTTATTTAGGCTATTAACAGCTACATATGTTAATTTATACCACGGCGACAAAACTGA
TGTCTTCATTTAAAATGCTTCAAGACCAGAGGTACAT
Found at i:506484 original size:31 final size:31
Alignment explanation
Indices: 506385--506502 Score: 172
Period size: 29 Copynumber: 3.9 Consensus size: 31
506375 CTTGCAAGTC
*
506385 CTGTTACCTGACTACGTCATATCCT-C-CTA
1 CTGTTAACTGACTACGTCATATCCTCCTCTA
506414 CTGTTAACTGACTACGTCATATCCTCCT-T-
1 CTGTTAACTGACTACGTCATATCCTCCTCTA
*
506443 CTGTTAACTGAATACGTCATATCCTCCTCTA
1 CTGTTAACTGACTACGTCATATCCTCCTCTA
* *
506474 CTGTTTACTGACTACGTCATTTCCTCCTC
1 CTGTTAACTGACTACGTCATATCCTCCTC
506503 CTCTTCCACA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
29 51 0.64
30 3 0.04
31 26 0.32
ACGTcount: A:0.20, C:0.32, G:0.10, T:0.37
Consensus pattern (31 bp):
CTGTTAACTGACTACGTCATATCCTCCTCTA
Found at i:506493 original size:60 final size:58
Alignment explanation
Indices: 506385--506501 Score: 180
Period size: 60 Copynumber: 2.0 Consensus size: 58
506375 CTTGCAAGTC
* *
506385 CTGTTACCTGACTACGTCATATCCTCCTACTGTTAACTGACTACGTCATATCCTCCTT
1 CTGTTAACTGAATACGTCATATCCTCCTACTGTTAACTGACTACGTCATATCCTCCTT
* *
506443 CTGTTAACTGAATACGTCATATCCTCCTCTACTGTTTACTGACTACGTCATTTCCTCCT
1 CTGTTAACTGAATACGTCATATCCT-C-CTACTGTTAACTGACTACGTCATATCCTCCT
506502 CCTCTTCCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 23 0.43
59 1 0.02
60 29 0.55
ACGTcount: A:0.21, C:0.32, G:0.10, T:0.38
Consensus pattern (58 bp):
CTGTTAACTGAATACGTCATATCCTCCTACTGTTAACTGACTACGTCATATCCTCCTT
Found at i:507687 original size:29 final size:31
Alignment explanation
Indices: 507643--507731 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
507633 CTTTCAAGTC
*
507643 CTGTAAACTGACTACGTCATATCCTCC-C-A
1 CTGTTAACTGACTACGTCATATCCTCCTCTA
*
507672 CTGTTAACTGAATACGTCATATCCTCCTCTA
1 CTGTTAACTGACTACGTCATATCCTCCTCTA
* *
507703 CTGTTTACTGACTACGTCATTTCCTCCTC
1 CTGTTAACTGACTACGTCATATCCTCCTC
507732 CTCTTCCACA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
29 25 0.47
30 1 0.02
31 27 0.51
ACGTcount: A:0.22, C:0.33, G:0.10, T:0.35
Consensus pattern (31 bp):
CTGTTAACTGACTACGTCATATCCTCCTCTA
Found at i:513514 original size:27 final size:27
Alignment explanation
Indices: 513484--513566 Score: 157
Period size: 27 Copynumber: 3.1 Consensus size: 27
513474 AACAAAAAAG
513484 CCTACCCCAAGACCGACAACAAAGGCC
1 CCTACCCCAAGACCGACAACAAAGGCC
513511 CCTACCCCAAGACCGACAACAAAGGCC
1 CCTACCCCAAGACCGACAACAAAGGCC
*
513538 CCTACCCCAAGACCGACAACGAAGGCC
1 CCTACCCCAAGACCGACAACAAAGGCC
513565 CC
1 CC
513567 CACTGAGAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.35, C:0.46, G:0.16, T:0.04
Consensus pattern (27 bp):
CCTACCCCAAGACCGACAACAAAGGCC
Found at i:513577 original size:27 final size:26
Alignment explanation
Indices: 513492--513650 Score: 122
Period size: 27 Copynumber: 5.9 Consensus size: 26
513482 AGCCTACCCC
**
513492 AAGACCGACAACAAAGGCCCCTACCCC
1 AAGACCGACAACAAAGGCCCCTA-CTG
**
513519 AAGACCGACAACAAAGGCCCCTACCCC
1 AAGACCGACAACAAAGGCCCCTA-CTG
* *
513546 AAGACCGACAACGAAGGCCCCCACTG
1 AAGACCGACAACAAAGGCCCCTACTG
* * *
513572 AGAGACCAACAACGAGGGCCCCTACTG
1 A-AGACCGACAACAAAGGCCCCTACTG
* * *
513599 AAAAACC-AGCGACAAAGGCCCCCACTG
1 -AAGACCGA-CAACAAAGGCCCCTACTG
* * *
513626 AAGGACCAACAACCATGGCCCCTAC
1 AA-GACCGACAACAAAGGCCCCTAC
513651 AGAAAAACCA
Statistics
Matches: 110, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
26 5 0.05
27 103 0.94
28 2 0.02
ACGTcount: A:0.36, C:0.40, G:0.19, T:0.05
Consensus pattern (26 bp):
AAGACCGACAACAAAGGCCCCTACTG
Found at i:513578 original size:54 final size:54
Alignment explanation
Indices: 513484--513596 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
513474 AACAAAAAAG
* *
513484 CCTACCCCAAGACCGACAACAAAGGCCCCTACCCCAAGACCGACAACAAAGGCC
1 CCTACCCCAAGACCGACAACAAAGGCCCCCACCCCAAGACCAACAACAAAGGCC
* ** * *
513538 CCTACCCCAAGACCGACAACGAAGGCCCCCA-CTGAGAGACCAACAACGAGGGCC
1 CCTACCCCAAGACCGACAACAAAGGCCCCCACCCCA-AGACCAACAACAAAGGCC
513592 CCTAC
1 CCTAC
513597 TGAAAAACCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 2 0.04
54 49 0.96
ACGTcount: A:0.35, C:0.43, G:0.18, T:0.04
Consensus pattern (54 bp):
CCTACCCCAAGACCGACAACAAAGGCCCCCACCCCAAGACCAACAACAAAGGCC
Found at i:513660 original size:27 final size:27
Alignment explanation
Indices: 513553--513665 Score: 93
Period size: 27 Copynumber: 4.2 Consensus size: 27
513543 CCCAAGACCG
* * * *
513553 ACAACGAAGGCCCCCACTGAGAGACCA
1 ACAACCAAGGCCCCTACTGAAAAACCA
* *
513580 ACAACGAGGGCCCCTACTGAAAAACCA
1 ACAACCAAGGCCCCTACTGAAAAACCA
* * * * **
513607 GCGACAAAGGCCCCCACTGAAGGACCA
1 ACAACCAAGGCCCCTACTGAAAAACCA
* *
513634 ACAACCATGGCCCCTACAGAAAAACCA
1 ACAACCAAGGCCCCTACTGAAAAACCA
513661 A-AACC
1 ACAACC
513666 TAACAACCCT
Statistics
Matches: 67, Mismatches: 19, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
26 4 0.06
27 63 0.94
ACGTcount: A:0.40, C:0.36, G:0.19, T:0.05
Consensus pattern (27 bp):
ACAACCAAGGCCCCTACTGAAAAACCA
Found at i:514627 original size:89 final size:90
Alignment explanation
Indices: 514464--514645 Score: 267
Period size: 89 Copynumber: 2.0 Consensus size: 90
514454 ACACATTCAT
* * *
514464 TGGGATTTTTGATATGAGCCTTGTTTATAAATACTTATGTTAACTAACAGAAAATTAAATTACTG
1 TGGGATTTTTGATATGAGCCATGTTTATAAATACATATGTTAAATAACAGAAAATTAAATTACTG
*
514529 ATTCCTTTTTAAATACATTGTGTTA
66 ATTCCTTTTTAAATAAATTGTGTTA
* * * **
514554 TGGGATTTTT-CTATGAGTCATGTTTATTAATACATATGTTAAATAGTAGAAAATTAAATTACTG
1 TGGGATTTTTGATATGAGCCATGTTTATAAATACATATGTTAAATAACAGAAAATTAAATTACTG
*
514618 ATTCTTTTTTAAATAAATTGTGTTA
66 ATTCCTTTTTAAATAAATTGTGTTA
514643 TGG
1 TGG
514646 AAAAAACAAC
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
89 72 0.88
90 10 0.12
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.45
Consensus pattern (90 bp):
TGGGATTTTTGATATGAGCCATGTTTATAAATACATATGTTAAATAACAGAAAATTAAATTACTG
ATTCCTTTTTAAATAAATTGTGTTA
Found at i:522856 original size:16 final size:16
Alignment explanation
Indices: 522835--522866 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
522825 TTTAATGACA
522835 TTCAGGTCTTTAGTAT
1 TTCAGGTCTTTAGTAT
522851 TTCAGGTCTTTAGTAT
1 TTCAGGTCTTTAGTAT
522867 GTCCCGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (16 bp):
TTCAGGTCTTTAGTAT
Found at i:524761 original size:16 final size:15
Alignment explanation
Indices: 524736--524765 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
524726 TTGAGACCGC
524736 TCTACTGATCCTTTT
1 TCTACTGATCCTTTT
524751 TCTAGCTGATCCTTT
1 TCTA-CTGATCCTTT
524766 CTTTGAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.27, G:0.10, T:0.50
Consensus pattern (15 bp):
TCTACTGATCCTTTT
Found at i:532138 original size:9 final size:9
Alignment explanation
Indices: 532126--532157 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
532116 ATTGTTATCA
532126 TCTTCATCT
1 TCTTCATCT
*
532135 TCTTCATCA
1 TCTTCATCT
532144 TCTTCATCT
1 TCTTCATCT
532153 TCTTC
1 TCTTC
532158 CTTTTTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.34, G:0.00, T:0.53
Consensus pattern (9 bp):
TCTTCATCT
Found at i:532143 original size:18 final size:18
Alignment explanation
Indices: 532122--532157 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
532112 AATCATTGTT
532122 ATCATCTTCATCTTCTTC
1 ATCATCTTCATCTTCTTC
532140 ATCATCTTCATCTTCTTC
1 ATCATCTTCATCTTCTTC
532158 CTTTTTACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (18 bp):
ATCATCTTCATCTTCTTC
Found at i:533212 original size:2 final size:2
Alignment explanation
Indices: 533205--533310 Score: 185
Period size: 2 Copynumber: 53.0 Consensus size: 2
533195 GTCTTTAGAC
533205 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
533247 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA CA GA CA GA CA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
533289 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
533311 AAGACTGAAA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:533323 original size:16 final size:16
Alignment explanation
Indices: 533208--533324 Score: 72
Period size: 16 Copynumber: 7.3 Consensus size: 16
533198 TTTAGACGAG
* * *
533208 AGAGAGAGAGAGAGAG
1 AGAGAGAAAGACAGAA
* * *
533224 AGAGAGAGAGAGAGAG
1 AGAGAGAAAGACAGAA
* * *
533240 AGAGAGAGAGAGAGAG
1 AGAGAGAAAGACAGAA
* * *
533256 AGAGAGAGAGAGAGAG
1 AGAGAGAAAGACAGAA
* *
533272 AGAGAGACAGACAGAC
1 AGAGAGAAAGACAGAA
* * *
533288 AGAGAGAGAGAGAGAG
1 AGAGAGAAAGACAGAA
*
533304 AGAGAGAAAGACTGAA
1 AGAGAGAAAGACAGAA
533320 AGAGA
1 AGAGA
533325 CGGACAGACA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 91 1.00
ACGTcount: A:0.51, C:0.03, G:0.44, T:0.01
Consensus pattern (16 bp):
AGAGAGAAAGACAGAA
Found at i:533336 original size:4 final size:4
Alignment explanation
Indices: 533322--533366 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
533312 AGACTGAAAG
*
533322 AGAC GGAC AGAC AGAC --AC AGAC AGAC AGAC --AC AGAC AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC
533366 A
1 A
533367 AACACTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
2 4 0.11
4 31 0.89
ACGTcount: A:0.49, C:0.27, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:533343 original size:18 final size:18
Alignment explanation
Indices: 533322--533371 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
533312 AGACTGAAAG
* *
533322 AGACGGACAGACAGACAC
1 AGACAGACAGACACACAC
*
533340 AGACAGACAGACACAGAC
1 AGACAGACAGACACACAC
*
533358 AGACAGACAAACAC
1 AGACAGACAGACAC
533372 TTTTAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.50, C:0.28, G:0.22, T:0.00
Consensus pattern (18 bp):
AGACAGACAGACACACAC
Found at i:533346 original size:14 final size:14
Alignment explanation
Indices: 533327--533366 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
533317 GAAAGAGACG
533327 GACAGACAGACACA
1 GACAGACAGACACA
533341 GACAGACAGACACA
1 GACAGACAGACACA
533355 GACAGACAGACA
1 GACAGACAGACA
533367 AACACTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.28, G:0.23, T:0.00
Consensus pattern (14 bp):
GACAGACAGACACA
Found at i:533366 original size:8 final size:8
Alignment explanation
Indices: 533276--533366 Score: 59
Period size: 8 Copynumber: 12.1 Consensus size: 8
533266 AGAGAGAGAG
533276 AGACAGAC
1 AGACAGAC
*
533284 AGACAGAG
1 AGACAGAC
* *
533292 AGAGAGAG
1 AGACAGAC
* *
533300 AGAGAGAG
1 AGACAGAC
*
533308 AGAAAGAC
1 AGACAGAC
* *
533316 TGA-A-AG
1 AGACAGAC
*
533322 AGACGGAC
1 AGACAGAC
533330 AGACAGAC
1 AGACAGAC
533338 --ACAGAC
1 AGACAGAC
533344 AGACAGAC
1 AGACAGAC
533352 --ACAGAC
1 AGACAGAC
533358 AGACAGAC
1 AGACAGAC
533366 A
1 A
533367 AACACTTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
6 15 0.22
7 1 0.01
8 51 0.76
ACGTcount: A:0.51, C:0.18, G:0.31, T:0.01
Consensus pattern (8 bp):
AGACAGAC
Found at i:535188 original size:15 final size:18
Alignment explanation
Indices: 535178--535811 Score: 337
Period size: 18 Copynumber: 33.6 Consensus size: 18
535168 GTTGTGGTTT
535178 TAGGAGTTGTGGTTGTTG
1 TAGGAGTTGTGGTTGTTG
* * *
535196 TAGGAGTTGTAGTGGTGG
1 TAGGAGTTGTGGTTGTTG
* *
535214 TAGAAGTTGTTGTGGTTTTTG
1 TAG--G-AGTTGTGGTTGTTG
* * *
535235 TAGGAGTTGTTGTGGTGG
1 TAGGAGTTGTGGTTGTTG
*
535253 TGGGAGTTGTGGTTGTTG
1 TAGGAGTTGTGGTTGTTG
535271 TAGGAGTTGTGGTTGTTG
1 TAGGAGTTGTGGTTGTTG
* * *
535289 TAGGAGTTGTAGTGGTGG
1 TAGGAGTTGTGGTTGTTG
*
535307 TTGGAGTTGTTGTTGTTGTTG
1 TAGGAGTTG-TG--GTTGTTG
* ** * * *
535328 TTTTTGTTGTTGTAGTGGTGG
1 ---TAGGAGTTGTGGTTGTTG
* *
535349 TTGGAGTTGTTGTTGTTG
1 TAGGAGTTGTGGTTGTTG
* * *
535367 TAGGAGTTGTAGTGGTGG
1 TAGGAGTTGTGGTTGTTG
535385 TAGGAGTTGTTGTTGTTGTTGTTG
1 TAGGA---GTTG-TG--GTTGTTG
* * *
535409 TAGGAGTTGTTGTGGTGG
1 TAGGAGTTGTGGTTGTTG
* *
535427 TAGGAGTGGTGGTGGTGGTGG
1 TAGGAGT--T-GTGGTTGTTG
*
535448 TAGAAGTTGTGG-TG--G
1 TAGGAGTTGTGGTTGTTG
* *
535463 TAGGAGTTGTGGTGGTGG
1 TAGGAGTTGTGGTTGTTG
* *
535481 TAGGAGTGGTGGTGGTGGTGG
1 TAGGAGT--T-GTGGTTGTTG
*
535502 TAGGAGTTGTGGTGGTAGTCG
1 TAGGAGTTGTGGT--T-GTTG
* *
535523 TTGGTGTTGTGGTTGTTG
1 TAGGAGTTGTGGTTGTTG
*
535541 TAGGAGTTGTGGTTGTGG
1 TAGGAGTTGTGGTTGTTG
* *
535559 TGGGAGTTGTGGTTGTGG
1 TAGGAGTTGTGGTTGTTG
535577 TAGGAGTTGTGGTTGTTG
1 TAGGAGTTGTGGTTGTTG
*
535595 TAGTG-GTGGTAGGAGTTGTTG
1 TAG-GAGTTGT--G-GTTGTTG
* ** *
535616 TTGTTGTTGTTGTTGTTG
1 TAGGAGTTGTGGTTGTTG
*
535634 TAGGAGTTGTTGTTGTTG
1 TAGGAGTTGTGGTTGTTG
*
535652 TAGGAGTGGTTGTGGTGGTGGTGG
1 TAGGA---GTTGTGGT--T-GTTG
* *
535676 TAGGAGTGGTGGTGGTGGTGG
1 TAGGAGT--T-GTGGTTGTTG
* * *
535697 TAGGGGTTGTGGTGGTGG
1 TAGGAGTTGTGGTTGTTG
* * *
535715 TAGGGGTTGTGGTGGTGG
1 TAGGAGTTGTGGTTGTTG
* *
535733 TAGGGGTTGTGGTGGTTG
1 TAGGAGTTGTGGTTGTTG
*
535751 TAGGAG-T-T-GTTGTGG
1 TAGGAGTTGTGGTTGTTG
* * *
535766 TTGCAGTTGTAGTTGTTG
1 TAGGAGTTGTGGTTGTTG
535784 TAGGAGTTGTGGTTGTTG
1 TAGGAGTTGTGGTTGTTG
535802 TAGGAGTTGT
1 TAGGAGTTGT
535812 CCTAGTATAG
Statistics
Matches: 489, Mismatches: 83, Indels: 88
0.74 0.13 0.13
Matches are distributed among these distances:
15 21 0.04
16 3 0.01
17 3 0.01
18 308 0.63
19 7 0.01
20 5 0.01
21 108 0.22
22 1 0.00
23 3 0.01
24 30 0.06
ACGTcount: A:0.10, C:0.00, G:0.48, T:0.42
Consensus pattern (18 bp):
TAGGAGTTGTGGTTGTTG
Found at i:535212 original size:75 final size:73
Alignment explanation
Indices: 535135--535811 Score: 216
Period size: 75 Copynumber: 9.2 Consensus size: 73
535125 TGTTGTCGTG
* **
535135 GTGGTGGTTAGAA-TTGTAGTGG-TAGTTGGAGTGGTTGTGGTTTTAGGAGTTGTGGTTGTTGTA
1 GTGGTGG-TAGAAGTTGTAGTGGTTAGTAGGAGTGGTTGTGGTGGTAGGAGTTGTGGTTGTTGTA
535198 GGAGTTGTA
65 GGAGTTGTA
* * * *
535207 GTGGTGGTAGAAGTTGTTGTGGTTTTTGTAGGAGTTGTTGTGGTGGTGGGAGTTGTGGTTGTTGT
1 GTGGTGGTAGAAGTTGTAGTGG--TTAGTAGGAGTGGTTGTGGTGGTAGGAGTTGTGGTTGTTGT
*
535272 AGGAGTTGTG
64 AGGAGTTGTA
* * * * * ** * ** * *
535282 GTTGTTGTAGGAGTTGTAGTGG-TGGTTGGAGTTGTTGTTGTTGTTGTTTTTGTTGTTGTAGTGG
1 GTGGTGGTAGAAGTTGTAGTGGTTAGTAGGAG-TG--GTTG-TG--GTGGTAGGAGTTGTGGTTG
* * *
535346 TGGTTGGAGTTGTT
60 TTGTAGGAGTTGTA
* * * * * * *
535360 GTTGTTGTAGGAGTTGTAGTGG-TGGTAGGAGTTGTTGTTGTTGTTGTTGTAGGAGTTGTTGTGG
1 GTGGTGGTAGAAGTTGTAGTGGTTAGTAGGAG-TG--GTTG-TG--GTGGTAGGAGTTGTGGTTG
* *
535424 TGGTAGGAGTGGTGGTG
60 TTGTAGGAGT--T-GTA
* * * * *
535441 GTGGTGGTAGAAG-T-T-GTGG-TGGTAGGAGTTGTGGTGGTGGTAGGAGTGGTGGTGGTGGTGG
1 GTGGTGGTAGAAGTTGTAGTGGTTAGTAGGAGTGGTTGTGGTGGTAGGAGT--T-GTGGTTGTTG
*
535502 TAGGAGTTGTG
63 TAGGAGTTGTA
* ** * * * * * * *
535513 GTGGTAGTCGTTGGTGTTGTGGTTGTT-GTAGGAGTTGTGGTTGTGGTGGGAGTTGTGGTTGTGG
1 GTGGT-G--GTAGAAGTTGTAGTGGTTAGTAGGAGTGGTTGTGGTGGTAGGAGTTGTGGTTGTTG
*
535577 TAGGAGTTGTG
63 TAGGAGTTGTA
* * ** * * * * * * *
535588 GTTGTTGTAGTGGTGGTAG-GAGTT-GTTGTTGTTGTTGTTGTTGTTGTAGGAGTTGTTGTTGTT
1 GTGGTGGTAGAAGTTGTAGTG-GTTAGTAG--G-AGTGGTTGTGGTGGTAGGAGTTGTGGTTGTT
* *
535651 GTAGGAGTGGTT
62 GTAGGAGTTGTA
* * * * *
535663 GTGGTGGT-G--GTGGTA--GG--AGT--G-GTGGTGGTGGTGGTAGGGGTTGTGGTGGTGGTAG
1 GTGGTGGTAGAAGTTGTAGTGGTTAGTAGGAGTGGTTGTGGTGGTAGGAGTTGTGGTTGTTGTAG
* *
535718 GGGTTGTG
66 GAGTTGTA
** * * * *
535726 GTGGTGGTAGGGGTTGTGGTGGTT-GTAGGAGTTGTTGTGGT--T-GCAGTTGTAGTTGTTGTAG
1 GTGGTGGTAGAAGTTGTAGTGGTTAGTAGGAGTGGTTGTGGTGGTAGGAGTTGTGGTTGTTGTAG
*
535787 GAGTTGTG
66 GAGTTGTA
* * *
535795 GTTGTTGTAGGAGTTGT
1 GTGGTGGTAGAAGTTGT
535812 CCTAGTATAG
Statistics
Matches: 477, Mismatches: 90, Indels: 79
0.74 0.14 0.12
Matches are distributed among these distances:
63 39 0.08
64 1 0.00
65 1 0.00
66 4 0.01
68 2 0.00
69 39 0.08
70 2 0.00
71 7 0.01
72 69 0.14
73 3 0.01
74 5 0.01
75 153 0.32
76 4 0.01
77 2 0.00
78 130 0.27
79 2 0.00
80 2 0.00
81 12 0.03
ACGTcount: A:0.10, C:0.00, G:0.48, T:0.42
Consensus pattern (73 bp):
GTGGTGGTAGAAGTTGTAGTGGTTAGTAGGAGTGGTTGTGGTGGTAGGAGTTGTGGTTGTTGTAG
GAGTTGTA
Found at i:535421 original size:3 final size:3
Alignment explanation
Indices: 535312--535409 Score: 61
Period size: 3 Copynumber: 32.7 Consensus size: 3
535302 GGTGGTTGGA
* * * * **
535312 GTT GTT GTT GTT GTT GTT TTT GTT GTT GTA GTG GTG GTT GGA GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
* ** * * * * **
535360 GTT GTT GTA GGA GTT GTA GTG GTG GTA GGA GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT
535408 GT
1 GT
535410 AGGAGTTGTT
Statistics
Matches: 76, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.07, C:0.00, G:0.40, T:0.53
Consensus pattern (3 bp):
GTT
Found at i:535588 original size:27 final size:27
Alignment explanation
Indices: 535558--535613 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
535548 TGTGGTTGTG
* *
535558 GTGGGAGTTGTGGTTGTGGTAGGAGTT
1 GTGGGAGTTGTAGTGGTGGTAGGAGTT
**
535585 GTGGTTGTTGTAGTGGTGGTAGGAGTT
1 GTGGGAGTTGTAGTGGTGGTAGGAGTT
535612 GT
1 GT
535614 TGTTGTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.11, C:0.00, G:0.50, T:0.39
Consensus pattern (27 bp):
GTGGGAGTTGTAGTGGTGGTAGGAGTT
Found at i:535615 original size:3 final size:3
Alignment explanation
Indices: 535609--535652 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
535599 GGTGGTAGGA
* **
535609 GTT GTT GTT GTT GTT GTT GTT GTT GTA GGA GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
535653 AGGAGTGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.05, C:0.00, G:0.36, T:0.59
Consensus pattern (3 bp):
GTT
Found at i:535618 original size:27 final size:29
Alignment explanation
Indices: 535572--535654 Score: 116
Period size: 27 Copynumber: 2.9 Consensus size: 29
535562 GAGTTGTGGT
*
535572 TGTGGTAGGAGTTGTGGTTGTTGTAG-TG
1 TGTGGTAGGAGTTGTTGTTGTTGTAGTTG
*
535600 -GTGGTAGGAGTTGTTGTTGTTGTTGTTG
1 TGTGGTAGGAGTTGTTGTTGTTGTAGTTG
*
535628 TTGTTGTAGGAGTTGTTGTTGTTGTAG
1 -TGTGGTAGGAGTTGTTGTTGTTGTAG
535655 GAGTGGTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.48
28 2 0.04
30 23 0.48
ACGTcount: A:0.10, C:0.00, G:0.42, T:0.48
Consensus pattern (29 bp):
TGTGGTAGGAGTTGTTGTTGTTGTAGTTG
Found at i:535664 original size:30 final size:28
Alignment explanation
Indices: 535576--535664 Score: 99
Period size: 30 Copynumber: 3.1 Consensus size: 28
535566 TGTGGTTGTG
* *
535576 GTAGGAGTTGTGGTTGTTGT-AGTGGTG
1 GTAGGAGTTGTTGTTGTTGTGAGTGGTT
* *
535603 GTAGGAGTTGTTGTTGTTGTTGTTGTTGTT
1 GTAGGAGTTGTTGTTGTTG-TG-AGTGGTT
535633 GTAGGAGTTGTTGTTGTTGTAGGAGTGGTT
1 GTAGGAGTTGTTGTTGTTGT--GAGTGGTT
535663 GT
1 GT
535665 GGTGGTGGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 18 0.35
28 1 0.02
29 1 0.02
30 30 0.59
31 1 0.02
ACGTcount: A:0.10, C:0.00, G:0.43, T:0.47
Consensus pattern (28 bp):
GTAGGAGTTGTTGTTGTTGTGAGTGGTT
Found at i:535669 original size:3 final size:3
Alignment explanation
Indices: 535657--535748 Score: 75
Period size: 3 Copynumber: 30.7 Consensus size: 3
535647 TGTTGTAGGA
* *
535657 GTG GTT GTG GTG GTG GTG GTAG G-A GTG GTG GTG GTG GTG GTAG G-G
1 GTG GTG GTG GTG GTG GTG GT-G GTG GTG GTG GTG GTG GTG GT-G GTG
* * *
535702 GTT GTG GTG GTG GTAG G-G GTT GTG GTG GTG GTAG G-G GTT GTG GTG
1 GTG GTG GTG GTG GT-G GTG GTG GTG GTG GTG GT-G GTG GTG GTG GTG
535747 GT
1 GT
535749 TGTAGGAGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
2 7 0.10
3 56 0.79
4 8 0.11
ACGTcount: A:0.05, C:0.00, G:0.61, T:0.34
Consensus pattern (3 bp):
GTG
Found at i:547515 original size:138 final size:136
Alignment explanation
Indices: 547267--547541 Score: 496
Period size: 138 Copynumber: 2.0 Consensus size: 136
547257 AAATATGAAA
547267 TTATTCCTCGTCGGTGTAGAAATTCATTTGCCATTTTTTATTGGAGTTTCTTTCATAATTTATTT
1 TTATTCCTCGTCGGTGTAGAAATTCATTTGCCATTTTTTATTGGAGTTTCTTTCATAATTTATTT
* *
547332 ATTATTTAAATTTTAATTTAAATATTAAATATAAATATTTATTATTATTTAAATATTATTTAGCA
66 ATTATTTAAATTTTAATTTAAATATCAAATATAAATATTAATTA-T-TTTAAATATTATTTAGCA
547397 TCCTGATT
129 TCCTGATT
547405 TTATTCCTCGTCGGTGTAGAAATTCATTTGCCATTTTTTATTGGAGTTTCTTTCATAATTTATTT
1 TTATTCCTCGTCGGTGTAGAAATTCATTTGCCATTTTTTATTGGAGTTTCTTTCATAATTTATTT
* *
547470 ATTATTTTAATTTTAATTTAAATATCAAATATAAATATTAATTATTTTGAATATTATTTAGCATC
66 ATTATTTAAATTTTAATTTAAATATCAAATATAAATATTAATTATTTTAAATATTATTTAGCATC
547535 CTGATT
131 CTGATT
547541 T
1 T
547542 ATATCGTCTA
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
136 26 0.20
137 1 0.01
138 106 0.80
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (136 bp):
TTATTCCTCGTCGGTGTAGAAATTCATTTGCCATTTTTTATTGGAGTTTCTTTCATAATTTATTT
ATTATTTAAATTTTAATTTAAATATCAAATATAAATATTAATTATTTTAAATATTATTTAGCATC
CTGATT
Found at i:552130 original size:18 final size:19
Alignment explanation
Indices: 552102--552137 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
552092 ATGTAATTTC
*
552102 TAAATACTTAGTGAAAGAA
1 TAAATACTTAGTAAAAGAA
552121 TAAA-ACTTAGTAAAAGA
1 TAAATACTTAGTAAAAGA
552138 TCCGTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.25
Consensus pattern (19 bp):
TAAATACTTAGTAAAAGAA
Found at i:554250 original size:2 final size:2
Alignment explanation
Indices: 554228--554364 Score: 223
Period size: 2 Copynumber: 71.5 Consensus size: 2
554218 AAAAAACTAA
*
554228 CT CT CA CT CT C- CT CT CT -T CT CT CT CT CT CT -T CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
554267 CT CT C- CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
554306 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
554348 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
554365 CTGGTTTGGA
Statistics
Matches: 127, Mismatches: 2, Indels: 12
0.90 0.01 0.09
Matches are distributed among these distances:
1 6 0.05
2 121 0.95
ACGTcount: A:0.01, C:0.51, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:555435 original size:28 final size:28
Alignment explanation
Indices: 555404--555492 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
555394 CAAATTGATG
555404 TTAAAAGCACCATGCTTTAATGTAGAAT
1 TTAAAAGCACCATGCTTTAATGTAGAAT
* * **
555432 TTAAAA-TATTCTCACG-TCAAAT-T-G-AT
1 TTAAAAGCA--C-CATGCTTTAATGTAGAAT
555458 GTTAAAAGCACCATGCTTTAATGTAGAAT
1 -TTAAAAGCACCATGCTTTAATGTAGAAT
555487 TTAAAA
1 TTAAAA
555493 TATTCTCAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 18
0.63 0.11 0.26
Matches are distributed among these distances:
25 3 0.07
26 7 0.16
27 9 0.20
28 15 0.34
29 7 0.16
30 3 0.07
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (28 bp):
TTAAAAGCACCATGCTTTAATGTAGAAT
Found at i:555458 original size:55 final size:55
Alignment explanation
Indices: 555392--555500 Score: 218
Period size: 55 Copynumber: 2.0 Consensus size: 55
555382 CAACCAGATT
555392 GTCAAATTGATGTTAAAAGCACCATGCTTTAATGTAGAATTTAAAATATTCTCAC
1 GTCAAATTGATGTTAAAAGCACCATGCTTTAATGTAGAATTTAAAATATTCTCAC
555447 GTCAAATTGATGTTAAAAGCACCATGCTTTAATGTAGAATTTAAAATATTCTCA
1 GTCAAATTGATGTTAAAAGCACCATGCTTTAATGTAGAATTTAAAATATTCTCA
555501 ATCACAATGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (55 bp):
GTCAAATTGATGTTAAAAGCACCATGCTTTAATGTAGAATTTAAAATATTCTCAC
Found at i:557094 original size:26 final size:26
Alignment explanation
Indices: 557065--557297 Score: 385
Period size: 26 Copynumber: 9.0 Consensus size: 26
557055 AGTTTTCCTG
*
557065 AAACTGTCCAGTAGACAGCAGGCCTC
1 AAACTGTCCAGTAGACAACAGGCCTC
* * *
557091 AAACTGTCCTGTAGACAGCAGGCCCC
1 AAACTGTCCAGTAGACAACAGGCCTC
*
557117 AAACTGTCCAGTAGACAGCAGGCCTC
1 AAACTGTCCAGTAGACAACAGGCCTC
*
557143 AAACTGTCCAGTAGACAACAGACCTC
1 AAACTGTCCAGTAGACAACAGGCCTC
*
557169 AAATTGTCCAGTAGACAACAGGCCTC
1 AAACTGTCCAGTAGACAACAGGCCTC
*
557195 AAACTGTCCAGTAGACAACAGACCTC
1 AAACTGTCCAGTAGACAACAGGCCTC
*
557221 AAACTGTCCAGTAGACAACAGCCCTC
1 AAACTGTCCAGTAGACAACAGGCCTC
557247 AAACTGTCCAGTAGACAACAGGCCTC
1 AAACTGTCCAGTAGACAACAGGCCTC
557273 AAACTGTCCAGTAGACAACAGGCCT
1 AAACTGTCCAGTAGACAACAGGCCT
557298 GTCCATTCTT
Statistics
Matches: 195, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 195 1.00
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (26 bp):
AAACTGTCCAGTAGACAACAGGCCTC
Found at i:558747 original size:2 final size:2
Alignment explanation
Indices: 558740--558779 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
558730 TTAAAAGCAT
558740 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
558780 TTTTCAGTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:560232 original size:30 final size:29
Alignment explanation
Indices: 560169--560250 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
560159 AATGATATAT
* *
560169 TACAATATCATATAAAAAAATATCACGTGA
1 TACAATAT-ATATAATAAAATATCACATGA
* *
560199 TACAATAATATATAATAAAATATCATATTA
1 TACAAT-ATATATAATAAAATATCACATGA
* * *
560229 TACAGTTTTGTATAATAAAATA
1 TACA-ATATATATAATAAAATA
560251 CAATAAGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 40 0.93
31 3 0.07
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (29 bp):
TACAATATATATAATAAAATATCACATGA
Found at i:565701 original size:70 final size:70
Alignment explanation
Indices: 565588--565727 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
565578 TAAAAATTAT
* *
565588 GTTTGGAATGTCTACAGCTATAGTAGCGTTCGTGCGTGCTTGTGTGCATGCGTATGCGAATGTAT
1 GTTTGGAATGTCTACAGCGAGAGTAGCGTTCGTGCGTGCTTGTGTGCATGCGTATGCGAATGTAT
565653 TTGTG
66 TTGTG
565658 GTTTGGAATGTCTACAGCGAGAGTAGCGTTCGTGCGTGCTTGTGTGCATGCGTATGCGAATGTAT
1 GTTTGGAATGTCTACAGCGAGAGTAGCGTTCGTGCGTGCTTGTGTGCATGCGTATGCGAATGTAT
565723 TTGTG
66 TTGTG
565728 TCACATAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.36
Consensus pattern (70 bp):
GTTTGGAATGTCTACAGCGAGAGTAGCGTTCGTGCGTGCTTGTGTGCATGCGTATGCGAATGTAT
TTGTG
Found at i:570766 original size:43 final size:43
Alignment explanation
Indices: 570712--571005 Score: 516
Period size: 43 Copynumber: 6.8 Consensus size: 43
570702 AATATTTTAA
570712 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
1 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
570755 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
1 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
* * *
570798 TCTCGTAATTACGAGAACAGATCTCGTTATTACGACTTAATTA
1 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
* *
570841 TCTCGTTATAACGAGAAAAGATCTCGTTATTACGAGTTAATTT
1 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
570884 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
1 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
*
570927 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTA
1 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
* *
570970 TCTCGTAATTACAAGAGAAGATCTCGTTATTACGAG
1 TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAG
571006 AAAAGATCTT
Statistics
Matches: 238, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 238 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (43 bp):
TCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGTTAATTT
Found at i:571654 original size:21 final size:21
Alignment explanation
Indices: 571628--571896 Score: 270
Period size: 21 Copynumber: 12.7 Consensus size: 21
571618 AATCTTTTTT
571628 CGAGATCTTTTCTCGTAATAA
1 CGAGATCTTTTCTCGTAATAA
571649 CGAGATCTTTTCTCGTAATAA
1 CGAGATCTTTTCTCGTAATAA
571670 CGAGATCTTTTCTCGTAATAA
1 CGAGATCTTTTCTCGTAATAA
* *** *
571691 CGAGATAATTAAATCGTTATAA
1 CGAGAT-CTTTTCTCGTAATAA
*
571713 CGAGATCTTTTCTCGTTATAA
1 CGAGATCTTTTCTCGTAATAA
* **
571734 CGAGATAATTAACTCGTAATAA
1 CGAGAT-CTTTTCTCGTAATAA
* *
571756 CGAGATCTTTTCTCTTTATAA
1 CGAGATCTTTTCTCGTAATAA
* ***
571777 CGAGATAATTAAATCGTAATAA
1 CGAGAT-CTTTTCTCGTAATAA
**
571799 CGAGAT-TTAACTCGTAATAA
1 CGAGATCTTTTCTCGTAATAA
* *
571819 CGAGATCTTTTCTCGTTATTA
1 CGAGATCTTTTCTCGTAATAA
*
571840 CGAGATCTTTTCTCGTAATTA
1 CGAGATCTTTTCTCGTAATAA
** **
571861 CGAGATAAATAACTCGTAATAA
1 CGAGAT-CTTTTCTCGTAATAA
*
571883 CGAGATCTCTTCTC
1 CGAGATCTTTTCTC
571897 ATTATTAACA
Statistics
Matches: 203, Mismatches: 40, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
20 19 0.09
21 120 0.59
22 64 0.32
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
CGAGATCTTTTCTCGTAATAA
Found at i:571727 original size:43 final size:43
Alignment explanation
Indices: 571628--571896 Score: 346
Period size: 43 Copynumber: 6.3 Consensus size: 43
571618 AATCTTTTTT
* **
571628 CGAGATCTTTTCTCGTAATAACGAGAT-CTTTTCTCGTAATAA
1 CGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAA
* *
571670 CGAGATCTTTTCTCGTAATAACGAGATAATTAAATCGTTATAA
1 CGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAA
*
571713 CGAGATCTTTTCTCGTTATAACGAGATAATTAACTCGTAATAA
1 CGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAA
* * *
571756 CGAGATCTTTTCTCTTTATAACGAGATAATTAAATCGTAATAA
1 CGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAA
** * ** * *
571799 CGAGAT-TTAACTCGTAATAACGAGAT-CTTTTCTCGTTATTA
1 CGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAA
* *
571840 CGAGATCTTTTCTCGTAATTACGAGATAAATAACTCGTAATAA
1 CGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAA
*
571883 CGAGATCTCTTCTC
1 CGAGATCTTTTCTC
571897 ATTATTAACA
Statistics
Matches: 194, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
41 15 0.08
42 60 0.31
43 119 0.61
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (43 bp):
CGAGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAA
Found at i:571995 original size:54 final size:54
Alignment explanation
Indices: 571936--572046 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
571926 TGATATTAAT
571936 TTAGATTTTAAAAAATGACGTTGAATTAATTTAAATAATGATAATATTTTGCTA
1 TTAGATTTTAAAAAATGACGTTGAATTAATTTAAATAATGATAATATTTTGCTA
571990 TTAGATTTTAAAAAATGACGTTGAATTAATTTAAATAATGATAATATTTTGCTA
1 TTAGATTTTAAAAAATGACGTTGAATTAATTTAAATAATGATAATATTTTGCTA
572044 TTA
1 TTA
572047 AAAGTTGTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (54 bp):
TTAGATTTTAAAAAATGACGTTGAATTAATTTAAATAATGATAATATTTTGCTA
Found at i:572374 original size:16 final size:15
Alignment explanation
Indices: 572355--572397 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
572345 CCGAGACGAG
572355 GCATCACCTTTATGAA
1 GCATCACCTTTATG-A
*
572371 GCATCACTTTTATGA
1 GCATCACCTTTATGA
*
572386 G-ACCACCTTTAT
1 GCATCACCTTTAT
572398 CATGTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 9 0.38
15 2 0.08
16 13 0.54
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (15 bp):
GCATCACCTTTATGA
Found at i:575994 original size:2 final size:2
Alignment explanation
Indices: 575987--576030 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
575977 TTAAAAGCAT
575987 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
576029 GA
1 GA
576031 TTGTCAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:579557 original size:2 final size:2
Alignment explanation
Indices: 579552--579614 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
579542 AAAAATACAT
*
579552 TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
579594 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
579615 GTACCTTCTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:588554 original size:2 final size:2
Alignment explanation
Indices: 588547--588584 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
588537 AATCTTAATA
588547 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
588585 AACTGTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:589497 original size:15 final size:15
Alignment explanation
Indices: 589477--589510 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
589467 AAATAATCTT
589477 ATATTATTAATATAA
1 ATATTATTAATATAA
*
589492 ATATTATTAATATTA
1 ATATTATTAATATAA
589507 ATAT
1 ATAT
589511 ATACAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTATTAATATAA
Found at i:591450 original size:16 final size:16
Alignment explanation
Indices: 591431--591474 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
591421 TGAATAACAG
* **
591431 ACTGGTTGACTGACTC
1 ACTGATTGACTGACAA
591447 ACTGATTGACTGACAA
1 ACTGATTGACTGACAA
591463 ACTGATTGACTG
1 ACTGATTGACTG
591475 GTTGACTAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (16 bp):
ACTGATTGACTGACAA
Found at i:591460 original size:4 final size:4
Alignment explanation
Indices: 591437--591975 Score: 228
Period size: 4 Copynumber: 134.2 Consensus size: 4
591427 ACAGACTGGT
* * ** * **
591437 TGAC TGAC TCAC TGAT TGAC TGAC AAAC TGAT TGAC TGGT TGAC T-AGC
1 TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGA-C
* * * * ** *
591485 TCAC TAAC AT-AC TGAC TGAC TGAC TCAC TAAC AAAC TGAC TGAC TAAC
1 TGAC TGAC -TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC
* * * * ** * *
591533 TGAC TAAC TGAC TAAC AGAC TGAC TGAC TAAC TGAC CCAC TAAC AGAC
1 TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC
* * * * * ** *
591581 CGAC TGAC TGAC TCAC TAAC AGAC TGAC TGAC TCAC CCAC TCAC T-ACC
1 TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGA-C
* * * * * ** *
591629 TGAC TGAC TCAC TAAC AGAC TGAC TGAC TGAC TCAC TAAC AAAC TGAT
1 TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC
* * * * * * *
591677 TGAC TCAC TAAC TGAC TGGC TGAC TCAC TAAC AGAC TGAC TGAC TCAC
1 TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC
* * * * * * * * *
591725 TAAC AGAC TGAC TGAC TCAC ATAAC AT-AC TCAC TCAC TCAC TCAC TAAC
1 TGAC TGAC TGAC TGAC TGAC -TGAC -TGAC TGAC TGAC TGAC TGAC TGAC
* * * * * *
591774 AGAC TGAC TGACC TGAC TAAC TCAC TTAC TGAC TGAC AGAC AGAC TGAC
1 TGAC TGAC TGA-C TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC
* * * * * * *
591823 TGAC TCAC TTAC TGAC TGAC TCAC TCAC T-AA TAGTC TGAC TGAC TCAC
1 TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC T-GAC TGAC TGAC TGAC
* * * * * *
591871 TCAC T-ACC TGAC TGAC TGAC TCAC TTAC TAAA TGAC TGAC TGAC TCAC
1 TGAC TGA-C TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC
* * * * * *
591919 TCAC TAGA- TGAC TGAC TGAC TCAC TTAC TGAC TGAC TCAC TAAC AGAC
1 TGAC T-GAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC TGAC
*
591967 TGAC AGAC T
1 TGAC TGAC T
591976 CACTCACCAA
Statistics
Matches: 408, Mismatches: 112, Indels: 30
0.74 0.20 0.05
Matches are distributed among these distances:
3 9 0.02
4 384 0.94
5 15 0.04
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (4 bp):
TGAC
Found at i:591524 original size:20 final size:20
Alignment explanation
Indices: 591498--591979 Score: 340
Period size: 20 Copynumber: 22.8 Consensus size: 20
591488 CTAACATACT
591498 GACTGACTGACTCACTAACA
1 GACTGACTGACTCACTAACA
* * *
591518 AACTGACTGACTAACTGACTA
1 GACTGACTGACTCACTAAC-A
* ** * *
591539 -ACTGACTAACAGACTGACT
1 GACTGACTGACTCACTAACA
* *
591558 GACTAACTGACCCACTAACAGA
1 GACTGACTGACTCACTAAC--A
591580 CCGACTGACTGACTCACTAACA
1 --GACTGACTGACTCACTAACA
* *
591602 GACTGACTGACTCACCCACTCA
1 GACTGACTGACTCA-CTA-ACA
*
591624 CTACCTGACTGACTCACTAACAGA
1 -GA-CTGACTGACTCACTAAC--A
591648 CTGACTGACTGACTCACTAACA
1 --GACTGACTGACTCACTAACA
* * *
591670 AACTGATTGACTCACTAACT
1 GACTGACTGACTCACTAACA
*
591690 GACTGGCTGACTCACTAACA
1 GACTGACTGACTCACTAACA
591710 GACTGACTGACTCACTAACA
1 GACTGACTGACTCACTAACA
591730 GACTGACTGACTCACATAACATA
1 GACTGACTGACTCAC-TAAC--A
* * *
591753 CTCACTCACTCACTCACTAACA
1 --GACTGACTGACTCACTAACA
* *
591775 GACTGACTGACCTGACTAACT
1 GACTGACTGA-CTCACTAACA
* * *
591796 CACTTACTGACTGAC-AGACA
1 GACTGACTGACTCACTA-ACA
* *
591816 GACTGACTGACTCACTTACT
1 GACTGACTGACTCACTAACA
* *
591836 GACTGACTCACTCACTAATA
1 GACTGACTGACTCACTAACA
* *
591856 GTCTGACTGACTCACTCACTACCT
1 GACTGACTGACTCACT-A--A-CA
*
591880 GACTGACTGACTCACTTACTAAA
1 GACTGACTGACTCAC-TA--ACA
*
591903 TGACTGACTGACTCACTCACTA
1 -GACTGACTGACTCACTAAC-A
* * *
591925 GA-TGACTGACTGACTCACT
1 GACTGACTGACTCACTAACA
*
591944 TACTGACTGACTCACTAACA
1 GACTGACTGACTCACTAACA
*
591964 GACTGACAGACTCACT
1 GACTGACTGACTCACT
591980 CACCAACATA
Statistics
Matches: 366, Mismatches: 67, Indels: 58
0.75 0.14 0.12
Matches are distributed among these distances:
19 2 0.01
20 226 0.62
21 27 0.07
22 7 0.02
23 6 0.02
24 84 0.23
25 14 0.04
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.23
Consensus pattern (20 bp):
GACTGACTGACTCACTAACA
Found at i:591797 original size:37 final size:36
Alignment explanation
Indices: 591756--591827 Score: 99
Period size: 37 Copynumber: 2.0 Consensus size: 36
591746 TAACATACTC
*
591756 ACTCACTCACTCACTAACAGACTGACTGACCTGACTA
1 ACTCACTCACTCACTAACAGACAGACTGA-CTGACTA
* * *
591793 ACTCACTTACTGACTGACAGACAGACTGACTGACT
1 ACTCACTCACTCACTAACAGACAGACTGACTGACT
591828 CACTTACTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 6 0.19
37 25 0.81
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (36 bp):
ACTCACTCACTCACTAACAGACAGACTGACTGACTA
Found at i:591999 original size:24 final size:24
Alignment explanation
Indices: 591945--591999 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
591935 TGACTCACTT
* *
591945 ACTGACTGACTCACTAACAGACTG
1 ACTGACTCACTCACCAACAGACTG
* *
591969 ACAGACTCACTCACCAACATACTG
1 ACTGACTCACTCACCAACAGACTG
*
591993 ATTGACT
1 ACTGACT
592000 AATGGATAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.22
Consensus pattern (24 bp):
ACTGACTCACTCACCAACAGACTG
Found at i:601563 original size:2 final size:2
Alignment explanation
Indices: 601558--601595 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
601548 AACAAAAAAA
601558 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
601596 AAATTTATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:603160 original size:16 final size:16
Alignment explanation
Indices: 603135--603181 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
603125 ACTTCACGAG
*
603135 TTACTAGTGACTGAAA
1 TTACTGGTGACTGAAA
*
603151 TTACTGGTGACGGAAA
1 TTACTGGTGACTGAAA
603167 TTAAC-GGTGACTGAA
1 TT-ACTGGTGACTGAA
603182 CATACTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 25 0.93
17 2 0.07
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (16 bp):
TTACTGGTGACTGAAA
Found at i:611752 original size:2 final size:2
Alignment explanation
Indices: 611745--611790 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
611735 TCTTAAACTC
611745 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
611787 AG AG
1 AG AG
611791 TATAAATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:615240 original size:1 final size:1
Alignment explanation
Indices: 615234--615261 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
615224 GTCTGAAATA
615234 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
615262 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:627940 original size:12 final size:12
Alignment explanation
Indices: 627923--627957 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
627913 AAACATGGAT
627923 ATTAATAGATGC
1 ATTAATAGATGC
*
627935 ATTAATAGATGT
1 ATTAATAGATGC
627947 ATTATATAGAT
1 ATTA-ATAGAT
627958 TCCATATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (12 bp):
ATTAATAGATGC
Found at i:640318 original size:2 final size:2
Alignment explanation
Indices: 640313--640345 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
640303 AAAAAATAAA
640313 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
640346 TCTTCTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:640351 original size:3 final size:3
Alignment explanation
Indices: 640343--640375 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
640333 TCTCTCTCTC
*
640343 TCT TCT TCT TCT TCT TCT TCT TCT TGT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
640376 CTTGTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:643831 original size:17 final size:17
Alignment explanation
Indices: 643811--643849 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
643801 GACAGGCATA
643811 GCCTGCATGTAGGCTAT
1 GCCTGCATGTAGGCTAT
*
643828 GCCTGGATGTAGGCTAT
1 GCCTGCATGTAGGCTAT
643845 GCCTG
1 GCCTG
643850 TCCACTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.28
Consensus pattern (17 bp):
GCCTGCATGTAGGCTAT
Found at i:648461 original size:2 final size:2
Alignment explanation
Indices: 648456--648480 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
648446 ACACATGCTG
648456 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
648481 AACATGATTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:653395 original size:21 final size:21
Alignment explanation
Indices: 653369--653435 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
653359 CTATCGTAGT
653369 GTGCGTGTATACTGTTCTATC
1 GTGCGTGTATACTGTTCTATC
* * *
653390 GTGCGT-TAATTCTATCCTATC
1 GTGCGTGT-ATACTGTTCTATC
653411 GTGCGTGTATACTGTTCTATC
1 GTGCGTGTATACTGTTCTATC
653432 GTGC
1 GTGC
653436 ATTAATCCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.42
Consensus pattern (21 bp):
GTGCGTGTATACTGTTCTATC
Found at i:653405 original size:42 final size:42
Alignment explanation
Indices: 653344--653458 Score: 169
Period size: 42 Copynumber: 2.7 Consensus size: 42
653334 TATCCTATCG
* * *
653344 TATCGTGTATCAATCCTATCGTAGT-GTGCGTGTATACTGTTC
1 TATCGTGCATTAATCCTATCCTA-TCGTGCGTGTATACTGTTC
* *
653386 TATCGTGCGTTAATTCTATCCTATCGTGCGTGTATACTGTTC
1 TATCGTGCATTAATCCTATCCTATCGTGCGTGTATACTGTTC
653428 TATCGTGCATTAATCCTATCCTATCGTGCGT
1 TATCGTGCATTAATCCTATCCTATCGTGCGT
653459 TAATCCTATC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.02
42 64 0.98
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (42 bp):
TATCGTGCATTAATCCTATCCTATCGTGCGTGTATACTGTTC
Found at i:653451 original size:21 final size:21
Alignment explanation
Indices: 653385--653468 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
653375 GTATACTGTT
*
653385 CTATCGTGCGTTAATTCTATC
1 CTATCGTGCGTTAATCCTATC
* * *
653406 CTATCGTGCGTGT-ATACTGTT
1 CTATCGTGCGT-TAATCCTATC
*
653427 CTATCGTGCATTAATCCTATC
1 CTATCGTGCGTTAATCCTATC
653448 CTATCGTGCGTTAATCCTATC
1 CTATCGTGCGTTAATCCTATC
653469 AGGTTTATCG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.40
Consensus pattern (21 bp):
CTATCGTGCGTTAATCCTATC
Found at i:654519 original size:21 final size:22
Alignment explanation
Indices: 654489--654605 Score: 118
Period size: 21 Copynumber: 5.5 Consensus size: 22
654479 TGTATCAATC
*
654489 CTATCATATCGTGCGTGT-ATA
1 CTATCCTATCGTGCGTGTAATA
* * *
654510 CTGTTCTATCGTGCGT-TAATC
1 CTATCCTATCGTGCGTGTAATA
*
654531 CTATCCTTTCGTGCGTGT-ATA
1 CTATCCTATCGTGCGTGTAATA
* * *
654552 CTGTTCTATCGTGCGT-TAATG
1 CTATCCTATCGTGCGTGTAATA
*
654573 CTATCCTATCGTGCGTG-AATC
1 CTATCCTATCGTGCGTGTAATA
654594 CTATCCTATCGT
1 CTATCCTATCGT
654606 TTATCTTGTA
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.03
21 74 0.96
22 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (22 bp):
CTATCCTATCGTGCGTGTAATA
Found at i:654519 original size:42 final size:42
Alignment explanation
Indices: 654485--654589 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
654475 ATCGTGTATC
*
654485 AATCCTATCATATCGTGCGTGTATACTGTTCTATCGTGCGTT
1 AATCCTATCCTATCGTGCGTGTATACTGTTCTATCGTGCGTT
*
654527 AATCCTATCCTTTCGTGCGTGTATACTGTTCTATCGTGCGTT
1 AATCCTATCCTATCGTGCGTGTATACTGTTCTATCGTGCGTT
*
654569 AATGCTATCCTATCGTGCGTG
1 AATCCTATCCTATCGTGCGTG
654590 AATCCTATCC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (42 bp):
AATCCTATCCTATCGTGCGTGTATACTGTTCTATCGTGCGTT
Found at i:654603 original size:42 final size:42
Alignment explanation
Indices: 654471--654605 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 42
654461 GTTTATCCTT
** * *
654471 TCCTATCGTGTATCAATCCTATCATATCGTGCGTGTATACTG
1 TCCTATCGTGCGTTAATCCTATCCTATCGTGCGTGTATACTG
* *
654513 TTCTATCGTGCGTTAATCCTATCCTTTCGTGCGTGTATACTG
1 TCCTATCGTGCGTTAATCCTATCCTATCGTGCGTGTATACTG
* * * * *
654555 TTCTATCGTGCGTTAATGCTATCCTATCGTGCGTGAATCCTA
1 TCCTATCGTGCGTTAATCCTATCCTATCGTGCGTGTATACTG
654597 TCCTATCGT
1 TCCTATCGT
654606 TTATCTTGTA
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (42 bp):
TCCTATCGTGCGTTAATCCTATCCTATCGTGCGTGTATACTG
Found at i:658640 original size:29 final size:28
Alignment explanation
Indices: 658583--658642 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
658573 TAGCATCAAA
*
658583 ATTAATTTTTTTATTTCTTTCTTATAAT
1 ATTAATTTTTTTATTTCTTTCTCATAAT
658611 ATTACATTTTTTT-TTTCATTT-TCATGAAT
1 ATTA-ATTTTTTTATTTC-TTTCTCAT-AAT
658640 ATT
1 ATT
658643 TCTTTCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (28 bp):
ATTAATTTTTTTATTTCTTTCTCATAAT
Found at i:659731 original size:86 final size:87
Alignment explanation
Indices: 659614--659786 Score: 312
Period size: 86 Copynumber: 2.0 Consensus size: 87
659604 AAAATAATTT
659614 TGACCAAAATCGTGACCATGCCCCTTTAAGTTAATTGAATATTTTTCATAATAAATGGATATTAT
1 TGACCAAAATCGTGACCATGCCCCTTTAAGTTAATTGAATATTTTTCATAATAAATGGATATTAT
659679 CTTACAAAAAATTTT-CACTTA
66 CTTACAAAAAATTTTACACTTA
*
659700 TGACCAAAATCGTGACCATGCCCCTTTAAGTTAATTGAATATTTTTCATAATCAATGGATATTAT
1 TGACCAAAATCGTGACCATGCCCCTTTAAGTTAATTGAATATTTTTCATAATAAATGGATATTAT
* *
659765 CTTATAAAAATTTTTACACTTA
66 CTTACAAAAAATTTTACACTTA
659787 AATAAACTTA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
86 77 0.93
87 6 0.07
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (87 bp):
TGACCAAAATCGTGACCATGCCCCTTTAAGTTAATTGAATATTTTTCATAATAAATGGATATTAT
CTTACAAAAAATTTTACACTTA
Found at i:663574 original size:413 final size:410
Alignment explanation
Indices: 662792--663615 Score: 1531
Period size: 413 Copynumber: 2.0 Consensus size: 410
662782 TTTTTGTTGG
662792 AGTGTAATTTACAGGACTGTATATATGTAATGGGAAAAATATTTTTTTTTTTTAGAAAAGAACTT
1 AGTGTAATTTACAGGACTGTATATATGTAATGGGAAAAATATTTTTTTTTTTTAGAAAAGAACTT
662857 CTACTTTCATATTATATATATTATTCCAACAATGTAAACAAATTTGTTGCATGAATGCTCATATA
66 CTACTTTCATATTATATATATTATTCCAACAATGTAAACAAATTTGTTGCATGAATGCTCATATA
662922 TTTTTAATTCATGGACAAACACATAATATTCACGAAAAACATCCAAATAGATATTCAGTCGATTC
131 TTTTTAATTCATGGACAAACACATAATATTCACGAAAAACATCCAAATAGATATTCAGTCGATTC
*** * **
662987 TAGCATGCTACGGTTTAATGCTTGCTTCTTGACAGATGCAGATATTTGCTTACAAAAATTATACA
196 TAGCATGCTACGGTTTAATGCTTGCAGATTGACAGATGCAGATATTAGCACACAAAAATTATACA
663052 AAACCTATTGTTTGTAGCAATATTTCATATGTCTTCCAATTAATAGATACAGGCTGGCATATGAA
261 AAACCTATTGTTTGTAGCAATATTTCATATGTCTTCCAATTAATAGATACAGGCTGGCATATGAA
663117 GGAATACAATTAGAAAGGTATTTGGTACTGGATTCTATTGAGTGAGAGGGTATTTTAATTATGGT
326 GGAATACAATTAGAAAGGTATTTGGTACTGGATTCTATTGAGTGAGAGGGTATTTTAATTATGGT
663182 GCTTTAAACTGTTCTTGTAC
391 GCTTTAAACTGTTCTTGTAC
*
663202 ANGTGTAATTTACAGGACTGTATATGTGTAATGGGAAAAATATTTTTTTTTTTTAGAAAAGAACT
1 A-GTGTAATTTACAGGACTGTATATATGTAATGGGAAAAATATTTTTTTTTTTTAGAAAAGAACT
* *
663267 TCTACTTTCATATTGTATATATTATTCCAACAATGTAAACAAATTTGTTGCATGAATGCTTATAT
65 TCTACTTTCATATTATATATATTATTCCAACAATGTAAACAAATTTGTTGCATGAATGCTCATAT
*
663332 ATTTTTAATTCATGGACAAACACATAATATTCACTGAAAAACATCCAAATAGATATTCAGTTGAT
130 ATTTTTAATTCATGGACAAACACATAATATTCAC-GAAAAACATCCAAATAGATATTCAGTCGAT
663397 TCTAGCATGCTACGGTTTAATGCTTGACAGATTGACAGATGCAGATATTAGCACACAAAAATTAT
194 TCTAGCATGCTACGGTTTAATGCTTG-CAGATTGACAGATGCAGATATTAGCACACAAAAATTAT
663462 ACAAAACCTATTGTTTGTAGCAATATTTCATATGTCTTCCAATTAATAGATACAGGCTGGCATAT
258 ACAAAACCTATTGTTTGTAGCAATATTTCATATGTCTTCCAATTAATAGATACAGGCTGGCATAT
663527 GAAGGAATACAATTAGAAAGGTATTTGGTACTGGATTCTATTGAGTGAGAGGGTATTTTAATTAT
323 GAAGGAATACAATTAGAAAGGTATTTGGTACTGGATTCTATTGAGTGAGAGGGTATTTTAATTAT
663592 GGTGCTTTAAACTGTTCTTGTAC
388 GGTGCTTTAAACTGTTCTTGTAC
663615 A
1 A
663616 TCAGATGAAA
Statistics
Matches: 401, Mismatches: 10, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
410 1 0.00
411 159 0.40
412 55 0.14
413 186 0.46
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (410 bp):
AGTGTAATTTACAGGACTGTATATATGTAATGGGAAAAATATTTTTTTTTTTTAGAAAAGAACTT
CTACTTTCATATTATATATATTATTCCAACAATGTAAACAAATTTGTTGCATGAATGCTCATATA
TTTTTAATTCATGGACAAACACATAATATTCACGAAAAACATCCAAATAGATATTCAGTCGATTC
TAGCATGCTACGGTTTAATGCTTGCAGATTGACAGATGCAGATATTAGCACACAAAAATTATACA
AAACCTATTGTTTGTAGCAATATTTCATATGTCTTCCAATTAATAGATACAGGCTGGCATATGAA
GGAATACAATTAGAAAGGTATTTGGTACTGGATTCTATTGAGTGAGAGGGTATTTTAATTATGGT
GCTTTAAACTGTTCTTGTAC
Found at i:668230 original size:2 final size:2
Alignment explanation
Indices: 668225--668262 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
668215 ATGAATGAAA
* *
668225 CT CT CT CT CT CT CC CT CT CT CG CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
668263 GACGTTGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.03, T:0.45
Consensus pattern (2 bp):
CT
Found at i:669960 original size:2 final size:2
Alignment explanation
Indices: 669955--669994 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
669945 TTACACACAC
669955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
669995 TTTAGCACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:676271 original size:23 final size:23
Alignment explanation
Indices: 676136--676263 Score: 141
Period size: 23 Copynumber: 5.6 Consensus size: 23
676126 TTTCTAAGAG
* *
676136 TTCTCGGTATTCTATGAGTTTAA
1 TTCTCGGTATTCTACGAGTTTTA
* *
676159 TTCAT-GGTATTCAATGAGTTTTA
1 TTC-TCGGTATTCTACGAGTTTTA
* * *
676182 TTCTTGTTATTCTGCGAGTTTTA
1 TTCTCGGTATTCTACGAGTTTTA
* *
676205 TTCTCAGTATTCTACGATTTTTA
1 TTCTCGGTATTCTACGAGTTTTA
* *
676228 TTCTCAGTATTCTACGAGTTTGA
1 TTCTCGGTATTCTACGAGTTTTA
676251 TTCTCGGTATTCT
1 TTCTCGGTATTCT
676264 GTGAGTTTAG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 1 0.01
23 87 0.98
24 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.50
Consensus pattern (23 bp):
TTCTCGGTATTCTACGAGTTTTA
Found at i:679760 original size:29 final size:29
Alignment explanation
Indices: 679718--679875 Score: 226
Period size: 29 Copynumber: 5.1 Consensus size: 29
679708 ATGGTATCAG
679718 TGGTGCAAAGACACAGCATGAAGATGGTA
1 TGGTGCAAAGACACAGCATGAAGATGGTA
679747 TGGTGCAAAGACACAGCATGAAGATGGTA
1 TGGTGCAAAGACACAGCATGAAGATGGTA
679776 TGGTGCAAAGACACAGCATGAAGATGGTA
1 TGGTGCAAAGACACAGCATGAAGATGGTA
679805 TGGTGCAAAGACACAGCATGAAAATGGGATGGTATCA
1 TGGTGCAAAGACACAGCATG--AA---GATGG--T-A
*
679842 GTGGTGCAAAGAAACAGCATGAAGATGGTA
1 -TGGTGCAAAGACACAGCATGAAGATGGTA
679872 TGGT
1 TGGT
679876 ATAGATGGTG
Statistics
Matches: 119, Mismatches: 1, Indels: 18
0.86 0.01 0.13
Matches are distributed among these distances:
29 82 0.69
30 1 0.01
31 3 0.03
33 5 0.04
34 5 0.04
36 3 0.03
37 1 0.01
38 19 0.16
ACGTcount: A:0.37, C:0.13, G:0.32, T:0.18
Consensus pattern (29 bp):
TGGTGCAAAGACACAGCATGAAGATGGTA
Found at i:679788 original size:58 final size:63
Alignment explanation
Indices: 679679--679875 Score: 269
Period size: 67 Copynumber: 3.1 Consensus size: 63
679669 GATTGCATAA
*
679679 ATGGTGCAAAAACACAGCATGAAGATGGGATGGTATCAGTGGTGCAAAGACACAGCATGAAGATG
1 ATGGTGCAAAGACACAGCATGAA-A--GGATGG-ATCAGTGGTGCAAAGACACAGCATGAAGATG
679744 GT
62 GT
679746 ATGGTGCAAAGACACAGCATG-AA-GATGG-T-A-TGGTGCAAAGACACAGCATGAAGATGGT
1 ATGGTGCAAAGACACAGCATGAAAGGATGGATCAGTGGTGCAAAGACACAGCATGAAGATGGT
*
679804 ATGGTGCAAAGACACAGCATGAAAATGGGATGGTATCAGTGGTGCAAAGAAACAGCATGAAGATG
1 ATGGTGCAAAGACACAGCATG-AAA--GGATGG-ATCAGTGGTGCAAAGACACAGCATGAAGATG
679869 GT
62 GT
679871 ATGGT
1 ATGGT
679876 ATAGATGGTG
Statistics
Matches: 119, Mismatches: 2, Indels: 18
0.86 0.01 0.13
Matches are distributed among these distances:
58 49 0.41
59 1 0.01
60 3 0.03
62 5 0.04
63 5 0.04
65 2 0.02
66 2 0.02
67 52 0.44
ACGTcount: A:0.38, C:0.13, G:0.31, T:0.18
Consensus pattern (63 bp):
ATGGTGCAAAGACACAGCATGAAAGGATGGATCAGTGGTGCAAAGACACAGCATGAAGATGGT
Found at i:679876 original size:38 final size:38
Alignment explanation
Indices: 679804--679891 Score: 133
Period size: 38 Copynumber: 2.3 Consensus size: 38
679794 TGAAGATGGT
*
679804 ATGGTGCAAAGACACAGCATGAAAATGGGATGGTATCAG
1 ATGGTGCAAAGAAACAGCATGAAAATGGGATGGTAT-AG
* *
679843 -TGGTGCAAAGAAACAGCATGAAGATGGTATGGTATAG
1 ATGGTGCAAAGAAACAGCATGAAAATGGGATGGTATAG
679880 ATGGTGCAAAGA
1 ATGGTGCAAAGA
679892 CATATAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 2 0.04
38 43 0.96
ACGTcount: A:0.39, C:0.10, G:0.32, T:0.19
Consensus pattern (38 bp):
ATGGTGCAAAGAAACAGCATGAAAATGGGATGGTATAG
Found at i:682537 original size:31 final size:31
Alignment explanation
Indices: 682499--682629 Score: 262
Period size: 31 Copynumber: 4.2 Consensus size: 31
682489 AGAGTGCTTG
682499 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
1 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
682530 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
1 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
682561 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
1 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
682592 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
1 TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
682623 TGATCCC
1 TGATCCC
682630 AAAACTCCTG
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (31 bp):
TGATCCCTGAACAGGTCTCTGGTGAGCTAAA
Found at i:682791 original size:16 final size:16
Alignment explanation
Indices: 682770--682800 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
682760 TCACCGAGAC
682770 GAGGCATCAACTTTAT
1 GAGGCATCAACTTTAT
*
682786 GAGGCATCACCTTTA
1 GAGGCATCAACTTTA
682801 AAACCACCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (16 bp):
GAGGCATCAACTTTAT
Found at i:683285 original size:22 final size:23
Alignment explanation
Indices: 683242--683285 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
683232 GTATTGTATG
683242 ATATTGTATCATATTTGATACACA
1 ATATTGTATCATA-TTGATACACA
683266 ATATTGTATCATA-TGATACA
1 ATATTGTATCATATTGATACA
683286 ATATAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (23 bp):
ATATTGTATCATATTGATACACA
Found at i:683331 original size:15 final size:15
Alignment explanation
Indices: 683272--683340 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
683262 CACAATATTG
683272 TATCATATGATACAA
1 TATCATATGATACAA
* *
683287 TATAATTTGATA-AA
1 TATCATATGATACAA
* *
683301 -A-CAT-TGTTTC-A
1 TATCATATGATACAA
683312 TATCATATGATACAA
1 TATCATATGATACAA
*
683327 TATCATCTGATACA
1 TATCATATGATACA
683341 GTACGATATT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
11 4 0.10
12 3 0.07
13 4 0.10
14 6 0.15
15 24 0.59
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (15 bp):
TATCATATGATACAA
Found at i:687770 original size:18 final size:18
Alignment explanation
Indices: 687747--687782 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
687737 AGCATGTCTC
687747 AGAATTATCAGATTGCTT
1 AGAATTATCAGATTGCTT
687765 AGAATTATCAGATTGCTT
1 AGAATTATCAGATTGCTT
687783 TGCTGCAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
AGAATTATCAGATTGCTT
Found at i:691502 original size:39 final size:39
Alignment explanation
Indices: 691448--691525 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
691438 TAATTACTAA
691448 CTGGGTCAGCTAGTAACCTGTTACTTTCCCTTTAACAAT
1 CTGGGTCAGCTAGTAACCTGTTACTTTCCCTTTAACAAT
* *
691487 CTGGGTCCGCTAGTAACCTGTTACTTTCCTTTTAACAAT
1 CTGGGTCAGCTAGTAACCTGTTACTTTCCCTTTAACAAT
691526 TTTACGCCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (39 bp):
CTGGGTCAGCTAGTAACCTGTTACTTTCCCTTTAACAAT
Found at i:694596 original size:2 final size:2
Alignment explanation
Indices: 694589--694624 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
694579 AAATTTTTCA
694589 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
694625 GTCACACATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:703751 original size:2 final size:2
Alignment explanation
Indices: 703744--703792 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
703734 TAAACTGACC
703744 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
703786 CT CT CT C
1 CT CT CT C
703793 AAATCATGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:708857 original size:26 final size:26
Alignment explanation
Indices: 708828--708880 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
708818 TTTTTCTATC
708828 TAATAAAATTGATTTTCAAGTAAGAT
1 TAATAAAATTGATTTTCAAGTAAGAT
708854 TAATAAAATTGATTTTCAAGTAAGAT
1 TAATAAAATTGATTTTCAAGTAAGAT
708880 T
1 T
708881 TGAATGTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (26 bp):
TAATAAAATTGATTTTCAAGTAAGAT
Found at i:710591 original size:17 final size:16
Alignment explanation
Indices: 710566--710600 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
710556 CTGGCGTGTG
710566 ACCAGTTCTCGCCGAGT
1 ACCAGTTCTCGCC-AGT
*
710583 ACCATTTCTCGCCAGT
1 ACCAGTTCTCGCCAGT
710599 AC
1 AC
710601 ATTGTGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (16 bp):
ACCAGTTCTCGCCAGT
Found at i:710684 original size:17 final size:16
Alignment explanation
Indices: 710657--710691 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
710647 ACGTCACAAT
710657 GTACTGGCGAGAAATG
1 GTACTGGCGAGAAATG
*
710673 GTACTCGGCGAGAACTG
1 GTACT-GGCGAGAAATG
710690 GT
1 GT
710692 CGCATGCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.26, C:0.17, G:0.37, T:0.20
Consensus pattern (16 bp):
GTACTGGCGAGAAATG
Found at i:716702 original size:2 final size:2
Alignment explanation
Indices: 716695--716720 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
716685 TAGTAGAAGT
716695 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
716721 CAGTTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:725393 original size:17 final size:17
Alignment explanation
Indices: 725345--725393 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
725335 GTAGGGACAT
725345 GTAGCCACACTCACATACA
1 GTAGCCACACTCA-A-ACA
725364 -TA-CCAC-C-CAAACA
1 GTAGCCACACTCAAACA
725377 GTAGCCACACTCAAACA
1 GTAGCCACACTCAAACA
725394 AAATAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
13 3 0.12
14 3 0.12
15 6 0.23
16 2 0.08
17 10 0.38
18 2 0.08
ACGTcount: A:0.41, C:0.39, G:0.08, T:0.12
Consensus pattern (17 bp):
GTAGCCACACTCAAACA
Found at i:743763 original size:4 final size:4
Alignment explanation
Indices: 743754--743788 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
743744 AATGCTTTCA
743754 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
743789 TCACATACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:744834 original size:31 final size:31
Alignment explanation
Indices: 744799--744862 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
744789 AACGATTTAA
*
744799 AAACTATCAACATTTTAATTTGATTTGAACT
1 AAACTATCAACATTTTAATTTGATTTAAACT
744830 AAACTATCAACATTTTAATTTGATTTAAACT
1 AAACTATCAACATTTTAATTTGATTTAAACT
744861 AA
1 AA
744863 CAATAAATCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (31 bp):
AAACTATCAACATTTTAATTTGATTTAAACT
Found at i:744861 original size:26 final size:28
Alignment explanation
Indices: 744792--744856 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 28
744782 TAATGTCAAC
*
744792 GATTTAAAAACTATCAACATTTTAATTT
1 GATTTATAAACTATCAACATTTTAATTT
744820 GATTTGAACTAAACTATCAACATTTTAATTT
1 GATTT--A-TAAACTATCAACATTTTAATTT
744851 GATTTA
1 GATTTA
744857 AACTAACAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 5 0.15
29 1 0.03
30 1 0.03
31 26 0.79
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (28 bp):
GATTTATAAACTATCAACATTTTAATTT
Found at i:750409 original size:15 final size:14
Alignment explanation
Indices: 750380--750408 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
750370 CATAGGGGCA
750380 TGTCTTTTTTTTTT
1 TGTCTTTTTTTTTT
750394 TGTCTTTTTTTTTT
1 TGTCTTTTTTTTTT
750408 T
1 T
750409 TTTATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (14 bp):
TGTCTTTTTTTTTT
Found at i:758305 original size:2 final size:2
Alignment explanation
Indices: 758298--758350 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
758288 ATTTGCATTG
758298 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
758340 GA GA GA GA GA G
1 GA GA GA GA GA G
758351 NGAACTGAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:761205 original size:121 final size:121
Alignment explanation
Indices: 760991--761238 Score: 487
Period size: 121 Copynumber: 2.0 Consensus size: 121
760981 TATTAACACA
760991 ACAGAAAACATGTAAACGTTAAAATGATCAAAAGTTTAAAGCGGAAATTAGGTTACCAAAAGCAT
1 ACAGAAAACATGTAAACGTTAAAATGATCAAAAGTTTAAAGCGGAAATTAGGTTACCAAAAGCAT
*
761056 GCAGTTTATACAAATATTGGATTGTGTTAGAAATAATTCCAATAGAGGCATCACTT
66 GCAGTTTATACAAATATTAGATTGTGTTAGAAATAATTCCAATAGAGGCATCACTT
761112 ACAGAAAACATGTAAACGTTAAAATGATCAAAAGTTTAAAGCGGAAATTAGGTTACCAAAAGCAT
1 ACAGAAAACATGTAAACGTTAAAATGATCAAAAGTTTAAAGCGGAAATTAGGTTACCAAAAGCAT
761177 GCAGTTTATACAAATATTAGATTGTGTTAGAAATAATTCCAATAGAGGCATCACTT
66 GCAGTTTATACAAATATTAGATTGTGTTAGAAATAATTCCAATAGAGGCATCACTT
761233 ACAGAA
1 ACAGAA
761239 TTTTCATGAT
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
121 126 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (121 bp):
ACAGAAAACATGTAAACGTTAAAATGATCAAAAGTTTAAAGCGGAAATTAGGTTACCAAAAGCAT
GCAGTTTATACAAATATTAGATTGTGTTAGAAATAATTCCAATAGAGGCATCACTT
Found at i:765561 original size:4 final size:4
Alignment explanation
Indices: 765552--765611 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
765542 TACCCTTGTG
* * * * *
765552 TGTC TGTC TGTC CGTC CGTC TGTC CGTC CGTC TGTC TGTC CGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
*
765600 CGTC TGTC TGTC
1 TGTC TGTC TGTC
765612 CGTCCGTAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.00, C:0.35, G:0.25, T:0.40
Consensus pattern (4 bp):
TGTC
Found at i:765574 original size:12 final size:12
Alignment explanation
Indices: 765557--765618 Score: 106
Period size: 12 Copynumber: 5.2 Consensus size: 12
765547 TTGTGTGTCT
765557 GTCTGTCCGTCC
1 GTCTGTCCGTCC
765569 GTCTGTCCGTCC
1 GTCTGTCCGTCC
*
765581 GTCTGTCTGTCC
1 GTCTGTCCGTCC
*
765593 GTCTGTCCGTCT
1 GTCTGTCCGTCC
765605 GTCTGTCCGTCC
1 GTCTGTCCGTCC
765617 GT
1 GT
765619 AACAAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:765574 original size:16 final size:16
Alignment explanation
Indices: 765553--765618 Score: 96
Period size: 16 Copynumber: 4.1 Consensus size: 16
765543 ACCCTTGTGT
*
765553 GTCTGTCTGTCCGTCC
1 GTCTGTCCGTCCGTCC
*
765569 GTCTGTCCGTCCGTCT
1 GTCTGTCCGTCCGTCC
*
765585 GTCTGTCCGTCTGTCC
1 GTCTGTCCGTCCGTCC
*
765601 GTCTGTCTGTCCGTCC
1 GTCTGTCCGTCCGTCC
765617 GT
1 GT
765619 AACAAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.00, C:0.36, G:0.26, T:0.38
Consensus pattern (16 bp):
GTCTGTCCGTCCGTCC
Found at i:765616 original size:4 final size:4
Alignment explanation
Indices: 765561--765618 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
765551 GTGTCTGTCT
* * * * * *
765561 GTCC GTCC GTCT GTCC GTCC GTCT GTCT GTCC GTCT GTCC GTCT GTCT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC
765609 GTCC GTCC GT
1 GTCC GTCC GT
765619 AACAAAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (4 bp):
GTCC
Found at i:765916 original size:166 final size:166
Alignment explanation
Indices: 765642--765971 Score: 511
Period size: 166 Copynumber: 2.0 Consensus size: 166
765632 GTCGCATTTA
* *
765642 TCTCAGCAACTATTTATTGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT
** *
765707 CGGGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGGGGGATATATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGACTTCGCTTATTTT
*
765772 TTAACC-AAATTTTCAAACAAATTTTCGTCAAAGATT
131 TT-ACCAAAATTTTCAAACAAATTTCCGTCAAAGATT
* * *
765808 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCTATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTA-AGGCATGCCATA
* * *
765872 TCGTGGGATGTATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGACTTCGTTTATTT
65 TCGGGGGATATATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGACTTCGCTTATTT
*
765937 TTTGCCAAAATTTTCAAACAAATTTCCGTCAAAGA
130 TTTACCAAAATTTTCAAACAAATTTCCGTCAAAGA
765972 NNNNNNNNNN
Statistics
Matches: 149, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
165 4 0.03
166 145 0.97
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT
CGGGGGATATATTTTTGTACCAATCAAACGTCAACTTCCTGTTAAATGACGACTTCGCTTATTTT
TTACCAAAATTTTCAAACAAATTTCCGTCAAAGATT
Found at i:771208 original size:30 final size:30
Alignment explanation
Indices: 771107--771210 Score: 163
Period size: 30 Copynumber: 3.5 Consensus size: 30
771097 ATTTGAAAGT
* *
771107 GATCTATTGAACTGCCGGTCAATAGACTGC
1 GATCTATTGGACCGCCGGTCAATAGACTGC
* *
771137 GATCTATTAGACCGCCGGTCAATAGACTGT
1 GATCTATTGGACCGCCGGTCAATAGACTGC
771167 GATCTATTGGACCGCCGGTCAATAGACTGC
1 GATCTATTGGACCGCCGGTCAATAGACTGC
*
771197 GATCTACTGGACCG
1 GATCTATTGGACCG
771211 GTAACGTGTT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (30 bp):
GATCTATTGGACCGCCGGTCAATAGACTGC
Found at i:779730 original size:17 final size:17
Alignment explanation
Indices: 779708--779742 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
779698 ATTGAAATAA
779708 TTTATTTCAAAAGTGGT
1 TTTATTTCAAAAGTGGT
*
779725 TTTATTTCAATAGTGGT
1 TTTATTTCAAAAGTGGT
779742 T
1 T
779743 GCAAGATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (17 bp):
TTTATTTCAAAAGTGGT
Found at i:779778 original size:84 final size:84
Alignment explanation
Indices: 779637--779830 Score: 327
Period size: 84 Copynumber: 2.3 Consensus size: 84
779627 AATCATTACT
* *
779637 TGGTTGTATTTCAATAGTGGTTGCAAAGTGATTTTTCTAATGAAAAACGTCCCCAACCACTATTG
1 TGGTTTTATTTCAATAGTGGTTGCAAAGTGATTTTTCTAATGAAAAACATCCCCAACCACTATTG
779702 AAATAATTTATTTCAAAAG
66 AAATAATTTATTTCAAAAG
* *
779721 TGGTTTTATTTCAATAGTGGTTGC-AAGATGATTTTTCTAATGAAATACATTCCCAACCACTATT
1 TGGTTTTATTTCAATAGTGGTTGCAAAG-TGATTTTTCTAATGAAAAACATCCCCAACCACTATT
*
779785 GAAATAATTTATTTCAATAG
65 GAAATAATTTATTTCAAAAG
779805 TGGTTTTATTTCAATAGTGGTTGCAA
1 TGGTTTTATTTCAATAGTGGTTGCAA
779831 CAATCCTGCT
Statistics
Matches: 103, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
83 3 0.03
84 99 0.96
85 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.39
Consensus pattern (84 bp):
TGGTTTTATTTCAATAGTGGTTGCAAAGTGATTTTTCTAATGAAAAACATCCCCAACCACTATTG
AAATAATTTATTTCAAAAG
Found at i:779814 original size:17 final size:17
Alignment explanation
Indices: 779792--779826 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
779782 ATTGAAATAA
779792 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
779809 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
779826 T
1 T
779827 GCAACAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTATTTCAATAGTGGT
Found at i:783276 original size:15 final size:15
Alignment explanation
Indices: 783256--783287 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
783246 GTTTCATAAA
*
783256 TCTTCATCTTCATCC
1 TCTTCATCATCATCC
783271 TCTTCATCATCATCC
1 TCTTCATCATCATCC
783286 TC
1 TC
783288 AACATCATTT
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:0.16, C:0.41, G:0.00, T:0.44
Consensus pattern (15 bp):
TCTTCATCATCATCC
Found at i:787735 original size:33 final size:33
Alignment explanation
Indices: 787689--787769 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
787679 GCCCTCTAAG
* *
787689 GGGACACATGTAGACTTTACCTGTATATACTTT
1 GGGACACAGGTAGACTTTACCGGTATATACTTT
787722 GGGACACAGGTAGACTTTACCGGTATATACTTT
1 GGGACACAGGTAGACTTTACCGGTATATACTTT
*
787755 GGGACACAGTTAGAC
1 GGGACACAGGTAGAC
787770 GACATTGTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (33 bp):
GGGACACAGGTAGACTTTACCGGTATATACTTT
Found at i:789367 original size:15 final size:15
Alignment explanation
Indices: 789347--789376 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
789337 GACAAGTGGC
789347 AAGAAAATGAACTAT
1 AAGAAAATGAACTAT
789362 AAGAAAATGAACTAT
1 AAGAAAATGAACTAT
789377 GTTTGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (15 bp):
AAGAAAATGAACTAT
Found at i:799278 original size:2 final size:2
Alignment explanation
Indices: 799271--799307 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
799261 NNNNNNNNNN
799271 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
799308 CTGTTCTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:800800 original size:2 final size:2
Alignment explanation
Indices: 800795--800834 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
800785 AAAAACTTAC
*
800795 GT GT GT GT GT GT GT GT GT GT GT GG GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
800835 ATATATNNNN
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
GT
Found at i:804204 original size:29 final size:30
Alignment explanation
Indices: 804172--804238 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
804162 CTAATGGGAT
804172 GGGGGGGGGGG-AGGTTTTAGTGGAGGGGG
1 GGGGGGGGGGGTAGGTTTTAGTGGAGGGGG
*
804201 GGGGGGGGGGGTAGGTTTTAGTGGAGGTGG
1 GGGGGGGGGGGTAGGTTTTAGTGGAGGGGG
*
804231 GGAGGGGG
1 GGGGGGGG
804239 TCCGACTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.10, C:0.00, G:0.72, T:0.18
Consensus pattern (30 bp):
GGGGGGGGGGGTAGGTTTTAGTGGAGGGGG
Found at i:812190 original size:16 final size:16
Alignment explanation
Indices: 812169--812202 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
812159 ATTGACAAAC
*
812169 TGTCTGTAACATAGAT
1 TGTCTGTAACAAAGAT
812185 TGTCTGTAACAAAGAT
1 TGTCTGTAACAAAGAT
812201 TG
1 TG
812203 AATGGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (16 bp):
TGTCTGTAACAAAGAT
Found at i:814500 original size:2 final size:2
Alignment explanation
Indices: 814493--814525 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
814483 TAATAAAATC
814493 CT CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
814526 GTGGGTGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:814509 original size:15 final size:15
Alignment explanation
Indices: 814491--814522 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
814481 AGTAATAAAA
814491 TCCTCTCTCTCTCTC
1 TCCTCTCTCTCTCTC
814506 TCCTCTCTCTCTCTC
1 TCCTCTCTCTCTCTC
814521 TC
1 TC
814523 TCTGTGGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (15 bp):
TCCTCTCTCTCTCTC
Found at i:817831 original size:13 final size:13
Alignment explanation
Indices: 817815--817843 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
817805 CATTACATTC
817815 TAATCTTAAAGTA
1 TAATCTTAAAGTA
817828 TAATCTTAAAGTA
1 TAATCTTAAAGTA
817841 TAA
1 TAA
817844 AGATAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (13 bp):
TAATCTTAAAGTA
Found at i:819534 original size:2 final size:2
Alignment explanation
Indices: 819527--819593 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
819517 TGGATTGTGT
819527 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
819569 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
819594 ATATATATAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:826832 original size:177 final size:178
Alignment explanation
Indices: 826609--826933 Score: 519
Period size: 177 Copynumber: 1.8 Consensus size: 178
826599 GGCTGCCAAA
*
826609 AGGGTACCCTCATTGTATGGAAAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
1 AGGGTACCCTCATTGTACGGAAAACT-CTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCA
* * **
826674 GATCAATTGAACATATATCAGAGGTGTGCATATTGTTAGAATTTTAATTTCTGATAATTTCTGAA
65 GATCAATTGAACAAATATCAGAGGTGTGCATATTGCTAGAATTTTAATTTCTGATAATTAATG-A
826739 AAAAATACCAGCTTTTGAACTTTGTCATTTTTTGGCAAAATATTGCATAT
129 AAAAATACCAGCTTTTGAACTTTGTCATTTTTTGGCAAAATATTGCATAT
*
826789 AGGGTACCCTCATTGTACGGATAACT-T-CTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAG
1 AGGGTACCCTCATTGTACGGAAAACTCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAG
* * * * *
826852 ATCAGTTGTACAAATATCTGAGGTGTGCATATTGCTAGGATTTTTATTTCTGATAATTAATGAAA
66 ATCAATTGAACAAATATCAGAGGTGTGCATATTGCTAGAATTTTAATTTCTGATAATTAATGAAA
826917 AAATACCAGCTTTTGAA
131 AAATACCAGCTTTTGAA
826934 ATATTGCATA
Statistics
Matches: 134, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
176 20 0.15
177 89 0.66
178 1 0.01
180 24 0.18
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (178 bp):
AGGGTACCCTCATTGTACGGAAAACTCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAG
ATCAATTGAACAAATATCAGAGGTGTGCATATTGCTAGAATTTTAATTTCTGATAATTAATGAAA
AAATACCAGCTTTTGAACTTTGTCATTTTTTGGCAAAATATTGCATAT
Found at i:830516 original size:177 final size:176
Alignment explanation
Indices: 830298--831044 Score: 937
Period size: 177 Copynumber: 4.2 Consensus size: 176
830288 ACTTGAAAGA
* * * ** * * *
830298 CTTGGATGCTGAATCTGAGTTCTAAATTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGACCAGGT
1 CTTGAATGCTGAATCTGAGCTATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGT
* *
830363 TAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCA-ATATCTAAGTTACTGCAGGTCCGT-ACTTCA
66 TAAAGTTTTTGTTGCAGGTGCCCTCTGAT-G-ATATATCTAAGTTACTGCTGGTCC-TAACTTCA
* * * *
830426 CCAAACTTGCATGGATGATGTGTCTTATGATACTGATGGACCAGACAGG
128 CCAAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGG
* * *
830475 CTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGT
1 CTTGAATGCTGAATCTGAGCTATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGT
*
830540 TAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCA-ATATCTAAGTTACTGCTGGTCCGT-ACTTCA
66 TAAAGTTTTTGTTGCAGGTGCCCTCTGAT-G-ATATATCTAAGTTACTGCTGGTCC-TAACTTCA
* * * *
830603 CCAAACTTGCATTGATGGTGTGTCTTATGATACTGATGCACCAGGCAGG
128 CCAAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGG
* * * * *
830652 CTTGGATGCTGAATCTGAGCTATAGGCTACAGATGCT-GAGTAGGTTAAGGTTTTTAGAGCTGGT
1 CTTGAATGCTGAATCTGAGCTATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGT
* * *
830716 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTTCTTGTCCTAACTTCACC
66 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGA-TATATCTAAGTTACTGCTGGTCCTAACTTCACC
* * *
830781 AGACTTCCATTGATGGTGCGTCTAATGATACTGATGCACCAGACAGG
130 AAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGG
* * * *
830828 CTTGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTATAGCTGGT
1 CTTGAATGCTGAATCTGAGCTATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGT
*** * * * * *
830893 TAAAGTTTTTGAAACAGGTGCCCTCTGATGATTATATCTTAGTTATTACTTGTCCTAACTACACC
66 TAAAGTTTTTGTTGCAGGTGCCCTCTGATGA-TATATCTAAGTTACTGCTGGTCCTAACTTCACC
* * *
830958 AGACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACTGG
130 AAACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGG
* *
831005 CTTGAATGCTGAGTCTGAGCCATAGGTTTCAGATGCTGGA
1 CTTGAATGCTGAATCTGAGCTATAGGTTTCAGATGCTGGA
831045 TATGTTTAAG
Statistics
Matches: 516, Mismatches: 50, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
174 1 0.00
175 2 0.00
176 153 0.30
177 360 0.70
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (176 bp):
CTTGAATGCTGAATCTGAGCTATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGGT
TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATATATCTAAGTTACTGCTGGTCCTAACTTCACCA
AACTTCCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGG
Found at i:830558 original size:19 final size:19
Alignment explanation
Indices: 830511--830550 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
830501 TTTCGGATGC
* *
830511 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
830530 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
830549 TG
1 TG
830551 TTGCAGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Done.