Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009618.1 Hibiscus syriacus cultivar Beakdansim tig00117007_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: 1135495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:388677 original size:13 final size:13
Alignment explanation
Indices: 388548--388677 Score: 84
Period size: 13 Copynumber: 9.2 Consensus size: 13
388538 TATGACTTTT
388548 TATAGTTTATACATA
1 TATAGTTTAT--ATA
*
388563 TGTAGTTTATATA
1 TATAGTTTATATA
*
388576 CATAGTTTATATA
1 TATAGTTTATATA
*
388589 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
388604 CATAATTTATATA
1 TATAGTTTATATA
388617 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
388635 TATAGTTTATAATA
1 TATAGTTTAT-ATA
388649 TAATA-TAGTT-TATA
1 T-ATAGT--TTATATA
388663 TATAGTTTATATA
1 TATAGTTTATATA
388676 TA
1 TA
388678 AACTTATATT
Statistics
Matches: 93, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
12 2 0.02
13 37 0.40
14 11 0.12
15 28 0.30
16 5 0.05
17 3 0.03
18 7 0.08
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:388715 original size:19 final size:20
Alignment explanation
Indices: 388662--388715 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
388652 TATAGTTTAT
* *
388662 ATATAGTTTATATATAAACTT
1 ATATATTTTA-ATATAAACTA
*
388683 ATATTATATTAATATAAA-TA
1 ATA-TATTTTAATATAAACTA
388703 ATATATTTTAATA
1 ATATATTTTAATA
388716 CTTTATGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.32
20 4 0.14
21 10 0.36
22 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATATTTTAATATAAACTA
Found at i:388893 original size:21 final size:21
Alignment explanation
Indices: 388864--388916 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
388854 ACATAAATCT
* *
388864 TATATATTATATA-TTTATATA
1 TATAAATTACATAGTTTAT-TA
388885 TATAAATTACATAGTTTATTA
1 TATAAATTACATAGTTTATTA
*
388906 -ATAAACTACAT
1 TATAAATTACAT
388917 GTAAACTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (21 bp):
TATAAATTACATAGTTTATTA
Found at i:388930 original size:2 final size:2
Alignment explanation
Indices: 388923--389023 Score: 75
Period size: 2 Copynumber: 52.0 Consensus size: 2
388913 ACATGTAAAC
* * * *
388923 TA TA TA TA T- TA TA TT TG TT TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
388964 TGA -A TG CA TT TA TA TA TA TA TA TA TA TA T- TA TA TT TG TT TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
389005 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
389024 ATTGGTTTCA
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
1 4 0.05
2 73 0.94
3 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:389642 original size:16 final size:15
Alignment explanation
Indices: 389621--389654 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
389611 TAGTTTTTAT
389621 CTGTTTCGGACCTGAA
1 CTGTTT-GGACCTGAA
*
389637 CTGTTTTGACCTGAA
1 CTGTTTGGACCTGAA
389652 CTG
1 CTG
389655 ACATCGATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (15 bp):
CTGTTTGGACCTGAA
Found at i:395545 original size:20 final size:20
Alignment explanation
Indices: 395520--395569 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
395510 CTTCCAATCT
*
395520 CTTTCACTTTGCTTTGAACA
1 CTTTCACTTTACTTTGAACA
395540 CTTTCACTTTACTTTGAACA
1 CTTTCACTTTACTTTGAACA
395560 CTTTCACTTT
1 CTTTCACTTT
395570 CACTCTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.26, G:0.06, T:0.48
Consensus pattern (20 bp):
CTTTCACTTTACTTTGAACA
Found at i:407396 original size:5 final size:5
Alignment explanation
Indices: 407386--407437 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
407376 AACGGTCAAC
* *
407386 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC- GGTCG GGTCG AGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
407437 G
1 G
407438 ATCAAACCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
7 4 0.10
ACGTcount: A:0.06, C:0.21, G:0.54, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:407401 original size:17 final size:17
Alignment explanation
Indices: 407379--407416 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
407369 AACGGTCAAC
407379 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
407396 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
407413 GGTC
1 GGTC
407417 GGGTCGGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:407406 original size:7 final size:7
Alignment explanation
Indices: 407352--407389 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
407342 GGTCAAAGGA
*
407352 GGTCAAT
1 GGTCAAC
*
407359 GGTC-AT
1 GGTCAAC
407365 GGTCAAC
1 GGTCAAC
407372 GGTCAAC
1 GGTCAAC
407379 GGTCAAC
1 GGTCAAC
407386 GGTC
1 GGTC
407390 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (7 bp):
GGTCAAC
Found at i:409718 original size:20 final size:20
Alignment explanation
Indices: 409690--409728 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
409680 AAGGCATAAT
*
409690 GGATTGATCCTTTTACAAAG
1 GGATCGATCCTTTTACAAAG
*
409710 GGATCGATCCTTTTTCAAA
1 GGATCGATCCTTTTACAAA
409729 TATTTCGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
GGATCGATCCTTTTACAAAG
Found at i:409848 original size:20 final size:21
Alignment explanation
Indices: 409798--409854 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
409788 AGAGTTATCC
409798 AAGGGATCGATCCTTTGGTCA
1 AAGGGATCGATCCTTTGGTCA
* *
409819 AAGGGATCGATCCTTTTG-CG
1 AAGGGATCGATCCTTTGGTCA
*
409839 AAGGGGTCGATCCTTT
1 AAGGGATCGATCCTTT
409855 AAGCCAGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (21 bp):
AAGGGATCGATCCTTTGGTCA
Found at i:412437 original size:21 final size:21
Alignment explanation
Indices: 412411--412469 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
412401 TTTAAGGCAC
412411 AAGGGATCGATCCTTTTACCA
1 AAGGGATCGATCCTTTTACCA
412432 AAGGGATCGATCCTTTTACCA
1 AAGGGATCGATCCTTTTACCA
* *
412453 AATGGATCGATCATTTT
1 AAGGGATCGATCCTTTT
412470 TCAAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTACCA
Found at i:412630 original size:21 final size:21
Alignment explanation
Indices: 412584--412641 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
412574 ACTCTTGTCC
*
412584 AAGGGATCGATCCTTT-TTCA
1 AAGGGATCGATCCTTTGGTCA
* *
412604 AGGGGATTGATCCTTTGGTCA
1 AAGGGATCGATCCTTTGGTCA
412625 AAGGGATCGATCCTTTG
1 AAGGGATCGATCCTTTG
412642 AGCCAGATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (21 bp):
AAGGGATCGATCCTTTGGTCA
Found at i:413717 original size:16 final size:16
Alignment explanation
Indices: 413698--413786 Score: 87
Period size: 16 Copynumber: 5.7 Consensus size: 16
413688 TAGTTGAATC
*
413698 GAAAGCAACTCGAACT
1 GAAATCAACTCGAACT
413714 GAAATCAACTCGAA-T
1 GAAATCAACTCGAACT
* *
413729 CGAAATCAACCCAAACT
1 -GAAATCAACTCGAACT
*
413746 GAAATCAA-TCCGAACC
1 GAAATCAACT-CGAACT
413762 GAAA-CAAC-CGAACT
1 GAAATCAACTCGAACT
*
413776 GAAAACAACTC
1 GAAATCAACTC
413787 AAAGCAAAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.15
15 8 0.13
16 42 0.70
17 1 0.02
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.12
Consensus pattern (16 bp):
GAAATCAACTCGAACT
Found at i:413729 original size:32 final size:31
Alignment explanation
Indices: 413693--413799 Score: 112
Period size: 32 Copynumber: 3.5 Consensus size: 31
413683 AATTTTAGTT
413693 GAATCGAAAGCAACTCGAACTGAAATCAACTC
1 GAATCGAAAGCAAC-CGAACTGAAATCAACTC
* *
413725 GAATCGAAATCAACCCAAACTGAAATCAA-TCC
1 GAATCGAAAGCAA-CCGAACTGAAATCAACT-C
* *
413757 GAACCGAAA-CAACCGAACTGAAAACAACTC
1 GAATCGAAAGCAACCGAACTGAAATCAACTC
* *
413787 AAAGC-AAAGCAAC
1 GAATCGAAAGCAAC
413800 ATGAATTTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
29 3 0.05
30 21 0.33
31 5 0.08
32 34 0.53
33 1 0.02
ACGTcount: A:0.49, C:0.27, G:0.13, T:0.11
Consensus pattern (31 bp):
GAATCGAAAGCAACCGAACTGAAATCAACTC
Found at i:415621 original size:77 final size:77
Alignment explanation
Indices: 415494--415668 Score: 350
Period size: 77 Copynumber: 2.3 Consensus size: 77
415484 AATAACTTTG
415494 AATAGATCTCAGTCATTTAACTATATCAGTATTATTTAACTAAAATTATTATTAATCTGAGATTA
1 AATAGATCTCAGTCATTTAACTATATCAGTATTATTTAACTAAAATTATTATTAATCTGAGATTA
415559 CTTAAGAAGTCT
66 CTTAAGAAGTCT
415571 AATAGATCTCAGTCATTTAACTATATCAGTATTATTTAACTAAAATTATTATTAATCTGAGATTA
1 AATAGATCTCAGTCATTTAACTATATCAGTATTATTTAACTAAAATTATTATTAATCTGAGATTA
415636 CTTAAGAAGTCT
66 CTTAAGAAGTCT
415648 AATAGATCTCAGTCATTTAAC
1 AATAGATCTCAGTCATTTAAC
415669 GAAAATTATT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 98 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (77 bp):
AATAGATCTCAGTCATTTAACTATATCAGTATTATTTAACTAAAATTATTATTAATCTGAGATTA
CTTAAGAAGTCT
Found at i:425156 original size:15 final size:15
Alignment explanation
Indices: 425136--425173 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
425126 TTGTTGGACT
425136 AAGAAG-AAGCAAGTA
1 AAGAAGCAA-CAAGTA
*
425151 AAGAAGCAACAAGTG
1 AAGAAGCAACAAGTA
425166 AAGAAGCA
1 AAGAAGCA
425174 GCCTCAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.58, C:0.11, G:0.26, T:0.05
Consensus pattern (15 bp):
AAGAAGCAACAAGTA
Found at i:432084 original size:76 final size:75
Alignment explanation
Indices: 431959--432100 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 75
431949 TATCCGAGAT
* * * * *
431959 TTATACAACTGAGATGAAGAATGAGGCAAGAAATTGATGTGGAAACTGCAGTGTTGAAGCACAAG
1 TTATACAACTGAGATGAAGAAAGAGGCAAGAAATTGATGCGGAAACTGCAATATTCAAGCACAAG
432024 AATCGACGAC
66 AATCGACGAC
*
432034 TTATACAACTGAGATGGATGATAAG-GGCAAGAAATTGATGCGGAAACTGCAATATTCAAGCACA
1 TTATACAACTGAGAT-GAAGA-AAGAGGCAAGAAATTGATGCGGAAACTGCAATATTCAAGCACA
432098 AGA
64 AGA
432101 TGTGTTTTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
75 15 0.25
76 42 0.71
77 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.20
Consensus pattern (75 bp):
TTATACAACTGAGATGAAGAAAGAGGCAAGAAATTGATGCGGAAACTGCAATATTCAAGCACAAG
AATCGACGAC
Found at i:433452 original size:2 final size:2
Alignment explanation
Indices: 433445--433481 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
433435 ACATAACTTG
433445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
433482 GTGTCATATC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:437158 original size:18 final size:18
Alignment explanation
Indices: 437135--437177 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
437125 CTTTAATTTG
*
437135 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
437153 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
437171 TTTATTT
1 TTTATTT
437178 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:437246 original size:18 final size:17
Alignment explanation
Indices: 437206--437282 Score: 50
Period size: 18 Copynumber: 4.2 Consensus size: 17
437196 AATCCCCCTT
437206 TTATATTTATTACTATTACTA
1 TTATATTTATTA--ATT--TA
437227 TTACTATTTATTAATTTA
1 TTA-TATTTATTAATTTA
*
437245 TTATTATTTTATTTA-TTA
1 TTA-TA-TTTATTAATTTA
*
437263 TTATATATT-TTAATTCA
1 TTATAT-TTATTAATTTA
437280 TTA
1 TTA
437283 AATCTTTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 4 0.08
17 9 0.19
18 13 0.27
19 7 0.15
20 3 0.06
21 3 0.06
22 9 0.19
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATTTATTAATTTA
Found at i:437257 original size:19 final size:19
Alignment explanation
Indices: 437233--437274 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
437223 ACTATTACTA
437233 TTTATTAATTTATTAT-TAT
1 TTTATTAA-TTATTATATAT
*
437252 TTTATTTATTATTATATAT
1 TTTATTAATTATTATATAT
437271 TTTA
1 TTTA
437275 ATTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTAATTATTATATAT
Found at i:437274 original size:15 final size:15
Alignment explanation
Indices: 437206--437272 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
437196 AATCCCCCTT
*
437206 TTATATTTATTACTA
1 TTATATTTATTATTA
*
437221 TTACTA-TTACTATTTA
1 TTA-TATTTATTA-TTA
437237 TTA-ATTTATTATTA
1 TTATATTTATTATTA
*
437251 TTTTATTTATTATTA
1 TTATATTTATTATTA
437266 -TATATTT
1 TTATATTT
437273 TAATTCATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 12 0.28
15 24 0.56
16 7 0.16
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATATTTATTATTA
Found at i:442738 original size:11 final size:12
Alignment explanation
Indices: 442715--442754 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 12
442705 CATTTCGTTA
*
442715 TATTTTTGTTTT
1 TATTTTCGTTTT
442727 TATTTTCG-TTT
1 TATTTTCGTTTT
442738 TA-TTT-GTTTT
1 TATTTTCGTTTT
442748 TATTTTC
1 TATTTTC
442755 AGTGAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
9 1 0.04
10 8 0.33
11 8 0.33
12 7 0.29
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (12 bp):
TATTTTCGTTTT
Found at i:442788 original size:9 final size:9
Alignment explanation
Indices: 442762--442807 Score: 56
Period size: 9 Copynumber: 4.8 Consensus size: 9
442752 TTCAGTGAAA
442762 TTTATTTCAT
1 TTTATTT-AT
*
442772 TCTATTTAT
1 TTTATTTAT
442781 TTTATTTAT
1 TTTATTTAT
442790 TTTATTTTTAT
1 TTTA--TTTAT
442801 TTTATTT
1 TTTATTT
442808 TTTCTCTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 17 0.53
10 6 0.19
11 9 0.28
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:442797 original size:14 final size:14
Alignment explanation
Indices: 442761--442807 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
442751 TTTCAGTGAA
* *
442761 ATTTATTTCATTCT
1 ATTTATTTTATTTT
442775 ATTTATTTTA-TTT
1 ATTTATTTTATTTT
442788 ATTTTATTTTTATTTT
1 A-TTTA-TTTTATTTT
442804 ATTT
1 ATTT
442808 TTTCTCTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 3 0.11
14 13 0.46
15 8 0.29
16 4 0.14
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:442801 original size:11 final size:11
Alignment explanation
Indices: 442776--442809 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
442766 TTTCATTCTA
442776 TTTATTTTA--
1 TTTATTTTATT
442785 TTTATTTTATT
1 TTTATTTTATT
442796 TTTATTTTATT
1 TTTATTTTATT
442807 TTT
1 TTT
442810 TCTCTGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:442809 original size:6 final size:5
Alignment explanation
Indices: 442762--442808 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
442752 TTCAGTGAAA
* *
442762 TTTAT TTCAT TCTA- TTTAT TTTA- TTTAT TTTATT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTT
442809 TTCTCTGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 7 0.20
5 23 0.66
6 5 0.14
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:443002 original size:17 final size:15
Alignment explanation
Indices: 442968--442996 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
442958 TCGAACAATG
442968 CAGTGCAGAAAAAAA
1 CAGTGCAGAAAAAAA
442983 CAGTGCAGAAAAAA
1 CAGTGCAGAAAAAA
442997 CAACAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.21, T:0.07
Consensus pattern (15 bp):
CAGTGCAGAAAAAAA
Found at i:444707 original size:75 final size:76
Alignment explanation
Indices: 444624--444771 Score: 203
Period size: 76 Copynumber: 2.0 Consensus size: 76
444614 TAAACTCAAG
**
444624 TTTAGGATAATA-TTTTAAACATTATATTT-TATCT-TTGTATTTTAGTTTAAATAGGTTTTAGT
1 TTTAGGATAATATTTTTAAACATTATATTTGT-T-TGAGGTATTTTAGTTTAAATAGGTTTTAGT
444686 ATTTTAATTAAGT
64 ATTTTAATTAAGT
* * **
444699 TTTAGGATATTATTTTTATATTTTATATTTGTTTGAGGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATAATATTTTTAAACATTATATTTGTTTGAGGTATTTTAGTTTAAATAGGTTTTAGTAT
444764 TTTAATTA
66 TTTAATTA
444772 GGATTTATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
75 12 0.19
76 51 0.80
77 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (76 bp):
TTTAGGATAATATTTTTAAACATTATATTTGTTTGAGGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAGT
Found at i:445048 original size:18 final size:18
Alignment explanation
Indices: 445025--445059 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
445015 AATTTGTTTA
*
445025 TTTAATTATTTTCTTTTC
1 TTTAATTATTATCTTTTC
*
445043 TTTAATTCTTATCTTTT
1 TTTAATTATTATCTTTT
445060 ATTTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTAATTATTATCTTTTC
Found at i:445126 original size:25 final size:26
Alignment explanation
Indices: 445093--445142 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
445083 AATCCCCCTT
445093 TTATATTTATTACTATTA-ATATTTA
1 TTATATTTATTACTATTATATATTTA
* *
445118 TTATTTTTATTATTATTATATATTT
1 TTATATTTATTACTATTATATATTT
445143 TAATTCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATATTTATTACTATTATATATTTA
Found at i:445128 original size:19 final size:19
Alignment explanation
Indices: 445106--445143 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
445096 TATTTATTAC
445106 TATTAATATT-TATTATTTT
1 TATTAATATTATA-TATTTT
*
445125 TATTATTATTATATATTTT
1 TATTAATATTATATATTTT
445144 AATTCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTAATATTATATATTTT
Found at i:454727 original size:21 final size:22
Alignment explanation
Indices: 454687--454728 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
454677 GTTATATTTT
454687 TTATTTTTTATAAATAAAAATA
1 TTATTTTTTATAAATAAAAATA
454709 TTATTTTTTA-AAAGTAAAAA
1 TTATTTTTTATAAA-TAAAAA
454729 GAAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTATTTTTTATAAATAAAAATA
Found at i:455570 original size:48 final size:48
Alignment explanation
Indices: 455517--455612 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
455507 GAAGGAGTAA
* * * **
455517 AATAATATTAGATTTGATTAGTGTCCATTAGACTCATGTTTATGATTT
1 AATAATAATAGATTCGATTACTGGACATTAGACTCATGTTTATGATTT
*
455565 AATAATAATAGATTCGATTACTGGACATTGGACTCATGTTTATGATTT
1 AATAATAATAGATTCGATTACTGGACATTAGACTCATGTTTATGATTT
455613 GTTTCAATTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (48 bp):
AATAATAATAGATTCGATTACTGGACATTAGACTCATGTTTATGATTT
Found at i:459084 original size:55 final size:55
Alignment explanation
Indices: 459018--459126 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
459008 AAGAGTTTAT
*
459018 TCTTCCTTTAGTTGCTCTTGTATTCTTCATTATTTCTCATCTTGGGTTGTATTTC
1 TCTTCCTTTAGTTCCTCTTGTATTCTTCATTATTTCTCATCTTGGGTTGTATTTC
*
459073 TCTTCCTTTAGTTCCTCTTGTATTCTTCATTATTTCTCTTCTTGGGTTGTATTT
1 TCTTCCTTTAGTTCCTCTTGTATTCTTCATTATTTCTCATCTTGGGTTGTATTT
459127 AAATGAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.10, C:0.20, G:0.12, T:0.58
Consensus pattern (55 bp):
TCTTCCTTTAGTTCCTCTTGTATTCTTCATTATTTCTCATCTTGGGTTGTATTTC
Found at i:467825 original size:20 final size:20
Alignment explanation
Indices: 467796--467853 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
467786 ATGTGAAATT
*
467796 TGTCCCGAAGGACCTATGTA
1 TGTCCTGAAGGACCTATGTA
* *
467816 TGTCCTGAAGGATCTCTGTA
1 TGTCCTGAAGGACCTATGTA
*
467836 TGT-CTCGAAGGACATATG
1 TGTCCT-GAAGGACCTATG
467854 AACCCTCGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
TGTCCTGAAGGACCTATGTA
Found at i:468247 original size:2 final size:2
Alignment explanation
Indices: 468240--468273 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
468230 TTATGTAAAC
468240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
468274 CACTTATACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:471989 original size:2 final size:2
Alignment explanation
Indices: 471976--472008 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
471966 ACTTATGTAA
*
471976 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
472009 TATATATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:472908 original size:17 final size:18
Alignment explanation
Indices: 472886--472920 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
472876 CATTCAAAAA
*
472886 CTCCTAA-TCTTTAATCT
1 CTCCTAACTCCTTAATCT
472903 CTCCTAACTCCTTAATCT
1 CTCCTAACTCCTTAATCT
472921 TTTGATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (18 bp):
CTCCTAACTCCTTAATCT
Found at i:475011 original size:2 final size:2
Alignment explanation
Indices: 475004--475029 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
474994 AGATGTATGT
475004 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
475030 AGGCAGACAT
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):
GA
Found at i:475776 original size:24 final size:23
Alignment explanation
Indices: 475748--475806 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
475738 ACAATTATGA
*
475748 GAATTATCTTTTGTAATTTAATAG
1 GAATTATCTTTGGTAATTT-ATAG
* * *
475772 GAATTATATTTGGTGATTTTTAG
1 GAATTATCTTTGGTAATTTATAG
475795 GAATTATCTTTG
1 GAATTATCTTTG
475807 CAATTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (23 bp):
GAATTATCTTTGGTAATTTATAG
Found at i:475814 original size:23 final size:23
Alignment explanation
Indices: 475748--475838 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 23
475738 ACAATTATGA
**
475748 GAATTATCTTTTGTAATTTAATAG
1 GAATTATC-TTTGTAATTTTTTAG
* *
475772 GAATTATATTTGGTGA-TTTTTAG
1 GAATTATCTTT-GTAATTTTTTAG
*
475795 GAATTATCTTTGCAATTTTTTAG
1 GAATTATCTTTGTAATTTTTTAG
** *
475818 GAACAATCTCTTATAATTTTT
1 GAATTATCT-TTGTAATTTTT
475839 AGGGTTTTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
22 2 0.04
23 32 0.60
24 19 0.36
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.51
Consensus pattern (23 bp):
GAATTATCTTTGTAATTTTTTAG
Found at i:489628 original size:2 final size:2
Alignment explanation
Indices: 489621--489691 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
489611 AGTTATTAAT
489621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
489662 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
489692 TAATGTGCAC
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 65 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:491179 original size:2 final size:2
Alignment explanation
Indices: 491172--491207 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
491162 ATCTACAATT
491172 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
491208 ATTTACGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:491350 original size:85 final size:84
Alignment explanation
Indices: 491220--491379 Score: 218
Period size: 85 Copynumber: 1.9 Consensus size: 84
491210 TTACGACACA
* * * *
491220 CAAATATGTGTCATCTTTTCTAATGACGTGTGCTTCAATGACACGCAATGTAA-GTCATAAATGC
1 CAAATATATGTCATCTTTTCTAATGACGGGGGCTTCAATGACACGCAA--TAACGTAATAAATGC
491284 GTGTCATAAATTTATGGCACG
64 GTGTCATAAATTTATGGCACG
491305 CAAATATATGTCATCTTCATT-T-ATGACGGGGGCTTCAATGACACGCAATAAGCGTAATAAATG
1 CAAATATATGTCATCTT--TTCTAATGACGGGGGCTTCAATGACACGCAATAA-CGTAATAAATG
491368 CGTGTCATAAAT
63 CGTGTCATAAAT
491380 GCGCGTCACA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
83 3 0.04
85 61 0.91
86 1 0.01
87 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (84 bp):
CAAATATATGTCATCTTTTCTAATGACGGGGGCTTCAATGACACGCAATAACGTAATAAATGCGT
GTCATAAATTTATGGCACG
Found at i:492084 original size:27 final size:25
Alignment explanation
Indices: 492034--492085 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
492024 GTTTATGATG
*
492034 TATTATATGTATGACATGATTAATT
1 TATTATATGTATGACATGAGTAATT
*
492059 TATTATATGATTATTACATGAGTAATT
1 TATTATATG--TATGACATGAGTAATT
492086 ATTTGCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (25 bp):
TATTATATGTATGACATGAGTAATT
Found at i:496183 original size:188 final size:188
Alignment explanation
Indices: 495866--496243 Score: 756
Period size: 188 Copynumber: 2.0 Consensus size: 188
495856 CATGTTAAGG
495866 AATGTACTGATGCACCACAGAGTGTATCGATGCATACCTTAAATAAAAGATGTAATTAGCCTTTC
1 AATGTACTGATGCACCACAGAGTGTATCGATGCATACCTTAAATAAAAGATGTAATTAGCCTTTC
495931 TTTTAGTTTAAGGAGTGAACAATTAGAGTATATCCATTAGAATACTGAAATGGATCCATGTATTA
66 TTTTAGTTTAAGGAGTGAACAATTAGAGTATATCCATTAGAATACTGAAATGGATCCATGTATTA
495996 TTGTGTAGATATAGAACGTAATCTCGTTCCGAAACAATCAAAGAAATAGGATTGAATC
131 TTGTGTAGATATAGAACGTAATCTCGTTCCGAAACAATCAAAGAAATAGGATTGAATC
496054 AATGTACTGATGCACCACAGAGTGTATCGATGCATACCTTAAATAAAAGATGTAATTAGCCTTTC
1 AATGTACTGATGCACCACAGAGTGTATCGATGCATACCTTAAATAAAAGATGTAATTAGCCTTTC
496119 TTTTAGTTTAAGGAGTGAACAATTAGAGTATATCCATTAGAATACTGAAATGGATCCATGTATTA
66 TTTTAGTTTAAGGAGTGAACAATTAGAGTATATCCATTAGAATACTGAAATGGATCCATGTATTA
496184 TTGTGTAGATATAGAACGTAATCTCGTTCCGAAACAATCAAAGAAATAGGATTGAATC
131 TTGTGTAGATATAGAACGTAATCTCGTTCCGAAACAATCAAAGAAATAGGATTGAATC
496242 AA
1 AA
496244 AGCAAACAAG
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
188 190 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (188 bp):
AATGTACTGATGCACCACAGAGTGTATCGATGCATACCTTAAATAAAAGATGTAATTAGCCTTTC
TTTTAGTTTAAGGAGTGAACAATTAGAGTATATCCATTAGAATACTGAAATGGATCCATGTATTA
TTGTGTAGATATAGAACGTAATCTCGTTCCGAAACAATCAAAGAAATAGGATTGAATC
Found at i:496894 original size:27 final size:25
Alignment explanation
Indices: 496844--496895 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
496834 GTTTATGATG
*
496844 TATTATATGTATGACATGATTAATT
1 TATTATATGTATGACATGAGTAATT
*
496869 TATTATATGATTATTACATGAGTAATT
1 TATTATATG--TATGACATGAGTAATT
496896 ATTTGCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (25 bp):
TATTATATGTATGACATGAGTAATT
Found at i:497944 original size:209 final size:209
Alignment explanation
Indices: 497584--498001 Score: 836
Period size: 209 Copynumber: 2.0 Consensus size: 209
497574 TCGCCTCCTC
497584 TATATGATCTAAGTATCTTTAGATATTGGCCAATTTGTTGTTTTACCATAGCTTTGAATTATTTC
1 TATATGATCTAAGTATCTTTAGATATTGGCCAATTTGTTGTTTTACCATAGCTTTGAATTATTTC
497649 ACTTTCTTCAGTGCTTATGATTTTTCTTTCAAAATATAAACCTAATTTTTATACTAAAATCATTA
66 ACTTTCTTCAGTGCTTATGATTTTTCTTTCAAAATATAAACCTAATTTTTATACTAAAATCATTA
497714 ATAAAAATTAGATAATTCATGTTTCTACCAAGTGATGGTATGTTAAAAGGACTAGTTATATCTCT
131 ATAAAAATTAGATAATTCATGTTTCTACCAAGTGATGGTATGTTAAAAGGACTAGTTATATCTCT
497779 ATGTACAATCTCCA
196 ATGTACAATCTCCA
497793 TATATGATCTAAGTATCTTTAGATATTGGCCAATTTGTTGTTTTACCATAGCTTTGAATTATTTC
1 TATATGATCTAAGTATCTTTAGATATTGGCCAATTTGTTGTTTTACCATAGCTTTGAATTATTTC
497858 ACTTTCTTCAGTGCTTATGATTTTTCTTTCAAAATATAAACCTAATTTTTATACTAAAATCATTA
66 ACTTTCTTCAGTGCTTATGATTTTTCTTTCAAAATATAAACCTAATTTTTATACTAAAATCATTA
497923 ATAAAAATTAGATAATTCATGTTTCTACCAAGTGATGGTATGTTAAAAGGACTAGTTATATCTCT
131 ATAAAAATTAGATAATTCATGTTTCTACCAAGTGATGGTATGTTAAAAGGACTAGTTATATCTCT
497988 ATGTACAATCTCCA
196 ATGTACAATCTCCA
498002 ACTACTTTTG
Statistics
Matches: 209, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 209 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (209 bp):
TATATGATCTAAGTATCTTTAGATATTGGCCAATTTGTTGTTTTACCATAGCTTTGAATTATTTC
ACTTTCTTCAGTGCTTATGATTTTTCTTTCAAAATATAAACCTAATTTTTATACTAAAATCATTA
ATAAAAATTAGATAATTCATGTTTCTACCAAGTGATGGTATGTTAAAAGGACTAGTTATATCTCT
ATGTACAATCTCCA
Found at i:499322 original size:33 final size:34
Alignment explanation
Indices: 499285--499355 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
499275 CCTTTACAAC
* *
499285 TCCCTAG-TTTTTCATGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACATGGGATAAACTAGAAACTT
* * *
499318 TCCCTAGCTTTTACATGGGCTAAGCTATAAACTT
1 TCCCTAGCTTTTACATGGGATAAACTAGAAACTT
499352 TCCC
1 TCCC
499356 GTTTACAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (34 bp):
TCCCTAGCTTTTACATGGGATAAACTAGAAACTT
Found at i:499731 original size:17 final size:17
Alignment explanation
Indices: 499709--499765 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
499699 GTTGTATCCA
499709 GGGGGTATGAATACCCT
1 GGGGGTATGAATACCCT
* *
499726 GGGGGTATCAGTA-CCT
1 GGGGGTATGAATACCCT
*
499742 --GGGTATGGATACCCCT
1 GGGGGTATGAATA-CCCT
499758 GGGGGTAT
1 GGGGGTAT
499766 TGGTACCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
14 8 0.26
16 6 0.19
17 11 0.35
18 6 0.19
ACGTcount: A:0.19, C:0.18, G:0.39, T:0.25
Consensus pattern (17 bp):
GGGGGTATGAATACCCT
Found at i:501278 original size:44 final size:44
Alignment explanation
Indices: 501210--501296 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
501200 CCACATTACG
* *
501210 ACTCTAATTCCGATTTCATGAAGAAGGATATCATTTCAAAACTA
1 ACTCCAATTCCAATTTCATGAAGAAGGATATCATTTCAAAACTA
*
501254 ACTCCAATTCCAATTTCATGAAGAATGATATCATTTCAAAACT
1 ACTCCAATTCCAATTTCATGAAGAAGGATATCATTTCAAAACT
501297 GACCCAACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (44 bp):
ACTCCAATTCCAATTTCATGAAGAAGGATATCATTTCAAAACTA
Found at i:502130 original size:18 final size:18
Alignment explanation
Indices: 502107--502149 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
502097 CTTTAGATTA
502107 TTTATTTAATTATTTTAT
1 TTTATTTAATTATTTTAT
502125 TTTATTTAATTATTTTAT
1 TTTATTTAATTATTTTAT
502143 TTTATTT
1 TTTATTT
502150 TAAAATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTTTAT
Found at i:502211 original size:17 final size:17
Alignment explanation
Indices: 502198--502249 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
502188 CTATTTTTTA
502198 TTATTTTATCTTTTATT
1 TTATTTTATCTTTTATT
**
502215 TTATTTTAT-TATACATT
1 TTATTTTATCT-TTTATT
502232 TTATTTTA-CTTTTATT
1 TTATTTTATCTTTTATT
502248 TT
1 TT
502250 TTCCTTTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTTATCTTTTATT
Found at i:502223 original size:22 final size:22
Alignment explanation
Indices: 502189--502249 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
502179 TCTTTATTAC
502189 TATTTT-TTATTATTTTATC-TTT
1 TATTTTATT-TTATTTTA-CATTT
*
502211 TATTTTATTTTATTATACATTT
1 TATTTTATTTTATTTTACATTT
502233 TATTTTACTTTTATTTT
1 TATTTTA-TTTTATTTT
502250 TTCCTTTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 23 0.68
23 10 0.29
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (22 bp):
TATTTTATTTTATTTTACATTT
Found at i:502226 original size:28 final size:28
Alignment explanation
Indices: 502174--502251 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
502164 AAAAATTCAT
* *
502174 TTTTATC-TTTATTACTATTTTTTAT-TA
1 TTTTATCTTTTATT-TTATTTTTTATACA
502201 TTTTATCTTTTATTTTATTTTATTATACA
1 TTTTATCTTTTATTTTATTTT-TTATACA
502230 TTTTA--TTTTACTTTTATTTTTT
1 TTTTATCTTTTA-TTTTATTTTTT
502252 CCTTTCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
27 20 0.44
28 19 0.42
29 6 0.13
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTTATCTTTTATTTTATTTTTTATACA
Found at i:502250 original size:12 final size:11
Alignment explanation
Indices: 502198--502249 Score: 70
Period size: 12 Copynumber: 4.6 Consensus size: 11
502188 CTATTTTTTA
502198 TTATTTTATCTT
1 TTATTTTA-CTT
502210 TTATTTTA-TT
1 TTATTTTACTT
*
502220 TTATTATACATT
1 TTATTTTAC-TT
502232 TTATTTTACTT
1 TTATTTTACTT
502243 TTATTTT
1 TTATTTT
502250 TTCCTTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 9 0.25
11 9 0.25
12 18 0.50
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTACTT
Found at i:502250 original size:17 final size:17
Alignment explanation
Indices: 502185--502250 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
502175 TTTATCTTTA
502185 TTACTATTT-TTTATTATT
1 TTACT-TTTATTT-TTATT
502203 TTATCTTTTA-TTTTATT
1 TTA-CTTTTATTTTTATT
* *
502220 TTA-TTATACATTTTATT
1 TTACTTTTA-TTTTTATT
502237 TTACTTTTATTTTT
1 TTACTTTTATTTTT
502251 TCCTTTCCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
15 4 0.10
17 22 0.55
18 12 0.30
19 2 0.05
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTACTTTTATTTTTATT
Found at i:502352 original size:16 final size:16
Alignment explanation
Indices: 502290--502357 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
502280 ACACTTCTTT
*
502290 TTTTAATTTTATTTTG
1 TTTTATTTTTATTTTG
* *
502306 TTTTATCTTTATTTTC
1 TTTTATTTTTATTTTG
*
502322 TCACTTCTTTATTTTATTTTG
1 T---TT-TAT-TTTTATTTTG
502343 TTTTATTTTTATTTT
1 TTTTATTTTTATTTT
502358 CTATTTTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
16 23 0.57
17 2 0.05
18 2 0.05
19 2 0.05
20 2 0.05
21 9 0.22
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTATTTTTATTTTG
Found at i:502383 original size:36 final size:35
Alignment explanation
Indices: 502333--502442 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 35
502323 CACTTCTTTA
502333 TTTTATTTTGTTTTATTTTTATTTTCTATTTTAACATT
1 TTTTA-TTT-TTTTA-TTTTATTTTCTATTTTAACATT
* *
502371 TTTTATTTTTTTATTTTATTTTCTGAATTTAATA-T
1 TTTTATTTTTTTATTTTATTTTCT-ATTTTAACATT
* ** *
502406 TTTTCTTCATTTATTTTATTTT-TCTTTTAACATT
1 TTTTATTTTTTTATTTTATTTTCTATTTTAACATT
502440 TTT
1 TTT
502443 CATATAACAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
33 6 0.10
34 5 0.08
35 31 0.50
36 12 0.19
37 3 0.05
38 5 0.08
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (35 bp):
TTTTATTTTTTTATTTTATTTTCTATTTTAACATT
Found at i:502440 original size:14 final size:14
Alignment explanation
Indices: 502423--502456 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
502413 CATTTATTTT
* *
502423 ATTTTTCTTTTAAC
1 ATTTTTCATATAAC
502437 ATTTTTCATATAAC
1 ATTTTTCATATAAC
502451 ATTTTT
1 ATTTTT
502457 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTTCATATAAC
Found at i:503522 original size:18 final size:19
Alignment explanation
Indices: 503489--503534 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
503479 AATTTTTATA
503489 ATTTTAAGAAAAATGAT-AT
1 ATTTTAA-AAAAATGATAAT
* *
503508 TTTTTAAAAATATGATAAT
1 ATTTTAAAAAAATGATAAT
503527 ATTTTAAA
1 ATTTTAAA
503535 GCTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTTTAAAAAAATGATAAT
Found at i:508718 original size:17 final size:18
Alignment explanation
Indices: 508676--508719 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
508666 CATGTTGTGA
508676 TGCTAGATTTTTTATTGT
1 TGCTAGATTTTTTATTGT
508694 TGCTAGATTTTTTATTGT
1 TGCTAGATTTTTTATTGT
508712 TGC-AGATT
1 TGCTAGATT
508720 ATCTTTGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.57
Consensus pattern (18 bp):
TGCTAGATTTTTTATTGT
Found at i:520027 original size:21 final size:19
Alignment explanation
Indices: 519990--520028 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
519980 ACGTACTTGG
*
519990 TTTTCTAGAATGTAATTCA
1 TTTTCTAGAATATAATTCA
520009 TTTTCCTAGTAATATAATTC
1 TTTT-CTAG-AATATAATTC
520029 CTTTGTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (19 bp):
TTTTCTAGAATATAATTCA
Found at i:520342 original size:59 final size:57
Alignment explanation
Indices: 520202--520360 Score: 141
Period size: 59 Copynumber: 2.7 Consensus size: 57
520192 ATTAATATTT
*
520202 ATAATAATATAATATTATA-ATTTTAATATTATATAA-AATAATCAATTATATTATAATA
1 ATAATAATATAAT-TTATATATTTTAATAATATATAATAA-AA-CAATTATATTATAATA
*
520260 AT-ATAAGATATTATATTT-T-TATTTTAATAATATATAATAAAA-AATTTATATATTTAATA
1 ATAAT-A-ATA-TA-ATTTATATATTTTAATAATATATAATAAAACAA-TTATAT-TATAATA
* *
520319 ATGAATAATATAATTTATATATTTAAATAATATTTTAATAAA
1 AT-AATAATATAATTTATATATTTTAATAATA-TATAATAAA
520361 GATATTTAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
57 8 0.10
58 12 0.14
59 45 0.54
60 15 0.18
61 4 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (57 bp):
ATAATAATATAATTTATATATTTTAATAATATATAATAAAACAATTATATTATAATA
Found at i:520549 original size:20 final size:20
Alignment explanation
Indices: 520520--520700 Score: 263
Period size: 20 Copynumber: 9.1 Consensus size: 20
520510 ATATTCGAAC
520520 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* *
520540 TTCACAACGCGAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
* *
520560 TTCGCAATGCAATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
520580 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
*
520600 CTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
*
520620 TTTGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
*** *
520640 TTCGCAACATAAAAGTCAAA
1 TTCGCAACGCGATAGTCAAA
*
520660 TTTGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
520680 TTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAA
520700 T
1 T
520701 GTTTTTACGC
Statistics
Matches: 139, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 139 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGATAGTCAAA
Found at i:520852 original size:22 final size:22
Alignment explanation
Indices: 520827--520873 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
520817 CTACGGCGAC
520827 ATCCGTCCCCATCTCCAACGAA
1 ATCCGTCCCCATCTCCAACGAA
* *
520849 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCAACGAA
520871 ATC
1 ATC
520874 TGTCTATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAACGAA
Found at i:524780 original size:14 final size:14
Alignment explanation
Indices: 524761--524800 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
524751 TTTTGATTAA
524761 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
524775 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
524789 TTGATTTGTAAA
1 TTGATTTGTAAA
524801 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:524793 original size:61 final size:66
Alignment explanation
Indices: 524710--524850 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
524700 TTTTACATTG
524710 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
524770 A
66 A
* ** * * *
524771 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
524835 TA
65 TA
524837 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
524851 GTTTCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
61 26 0.38
62 4 0.06
63 1 0.01
64 6 0.09
66 31 0.46
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
A
Found at i:524985 original size:20 final size:20
Alignment explanation
Indices: 524960--525005 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
524950 GCAACGCTTA
*
524960 TTTCACATTGCGAATTTGAC
1 TTTCACATTGCGAAATTGAC
*
524980 TTTCACGTTGCGAAATTGAC
1 TTTCACATTGCGAAATTGAC
525000 TTTCAC
1 TTTCAC
525006 TTTGATCGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (20 bp):
TTTCACATTGCGAAATTGAC
Found at i:525316 original size:18 final size:18
Alignment explanation
Indices: 525293--525328 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
525283 AAGCCGGTTG
*
525293 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
525311 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
525329 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:527630 original size:24 final size:24
Alignment explanation
Indices: 527596--527649 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
527586 CCATCACATC
527596 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
527620 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
527644 ATCAAA
1 ATCAAA
527650 TTTCGATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:527663 original size:24 final size:24
Alignment explanation
Indices: 527596--527663 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
527586 CCATCACATC
* *
527596 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAGTACTGACCAAG
* *
527620 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAGTACTGACCAAG
* * *
527644 ATCAAATTTCGATTACTGAC
1 ATCAAAGTCCGAGTACTGAC
527664 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAGTACTGACCAAG
Found at i:528620 original size:20 final size:20
Alignment explanation
Indices: 528569--528643 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
528559 GAAATTAAAT
*
528569 TCGCGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
*** *
528588 TTTAGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
*
528608 TCGCGTTGAGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
528628 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
528644 GAATATCGCA
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:528652 original size:21 final size:21
Alignment explanation
Indices: 528569--528787 Score: 80
Period size: 21 Copynumber: 10.8 Consensus size: 21
528559 GAAATTAAAT
528569 TCGCGTTGCGAATTT-GAA-A
1 TCGCGTTGCGAATTTGGAATA
*** * *
528588 TTTAGTTGCGAATTT-GACTT
1 TCGCGTTGCGAATTTGGAATA
* *
528608 TCGCGTTGAGAATTT-GACTA
1 TCGCGTTGCGAATTTGGAATA
528628 TCGCGTTGCGAATTTGGAATA
1 TCGCGTTGCGAATTTGGAATA
*** * *
528649 TCGCAACGTGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAATA
*** * *
528670 TCGCAACGCGAATTTAGAAAA
1 TCGCGTTGCGAATTTGGAATA
*** ** *
528691 TCGCAACGTTAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAATA
**
528712 TCGCAATGCG-ATTT--ACATA
1 TCGCGTTGCGAATTTGGA-ATA
* *
528731 TTCGTGTTGCGAAATTGGAA-A
1 -TCGCGTTGCGAATTTGGAATA
* *
528752 -CTGGGTTGCGAAATTGGAAT-
1 TC-GCGTTGCGAATTTGGAATA
528772 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
528788 AGATCGTGTT
Statistics
Matches: 157, Mismatches: 33, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
18 1 0.01
19 17 0.11
20 68 0.43
21 69 0.44
22 1 0.01
23 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAATA
Found at i:528683 original size:42 final size:42
Alignment explanation
Indices: 528635--528726 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
528625 CTATCGCGTT
* *
528635 GCGAATTTGGAATATCGCAACGTGAATTTGGAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAACGTGAATTTGGAAAATCGCAAC
* *
528677 GCGAATTTAGAAAATCGCAACGTTAATTTGGAAAATCGCAAT
1 GCGAATTTAGAAAATCGCAACGTGAATTTGGAAAATCGCAAC
528719 GCG-ATTTA
1 GCGAATTTA
528727 CATATTCGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 5 0.11
42 41 0.89
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (42 bp):
GCGAATTTAGAAAATCGCAACGTGAATTTGGAAAATCGCAAC
Found at i:528779 original size:20 final size:20
Alignment explanation
Indices: 528730--528783 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
528720 CGATTTACAT
*
528730 ATTCGTGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
528750 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
528770 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
528784 TTTGAGATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:529319 original size:36 final size:35
Alignment explanation
Indices: 529272--529339 Score: 127
Period size: 36 Copynumber: 1.9 Consensus size: 35
529262 GTAATTCATT
529272 TTTCAGAATTCAAATTTCAGTAATTCATTTTTTAG
1 TTTCAGAATTCAAATTTCAGTAATTCATTTTTTAG
529307 TTTCAGTAATTCAAATTTCAGTAATTCATTTTT
1 TTTCAG-AATTCAAATTTCAGTAATTCATTTTT
529340 CGAAAAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 6 0.19
36 26 0.81
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (35 bp):
TTTCAGAATTCAAATTTCAGTAATTCATTTTTTAG
Found at i:529340 original size:15 final size:15
Alignment explanation
Indices: 529262--529340 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 15
529252 TTTCAGAAAT
529262 GTAATTCATTTTTCA
1 GTAATTCATTTTTCA
**
529277 G-AATTCAAATTTCA
1 GTAATTCATTTTTCA
529291 GTAATTCATTTTTTAGTTTCA
1 GTAATTCA----TT--TTTCA
**
529312 GTAATTCAAATTTCA
1 GTAATTCATTTTTCA
529327 GTAATTCATTTTTC
1 GTAATTCATTTTTC
529341 GAAAAATCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
14 12 0.24
15 24 0.49
21 13 0.27
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (15 bp):
GTAATTCATTTTTCA
Found at i:531616 original size:33 final size:33
Alignment explanation
Indices: 531568--531633 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
531558 CAATGCAGAA
531568 GATTGCATCAAATATCAAGAACCCCACCAAGTT
1 GATTGCATCAAATATCAAGAACCCCACCAAGTT
* *
531601 GATTGTATCACATATCAAGAACCCCACCAAGTT
1 GATTGCATCAAATATCAAGAACCCCACCAAGTT
531634 TTCTAAGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (33 bp):
GATTGCATCAAATATCAAGAACCCCACCAAGTT
Found at i:532903 original size:3 final size:3
Alignment explanation
Indices: 532895--532949 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
532885 TCCCATTTTA
* * * *
532895 TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC TAC TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
532942 TAT TAT TA
1 TAT TAT TA
532950 CAAAACCTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:533487 original size:9 final size:11
Alignment explanation
Indices: 533455--533484 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
533445 AAATGAGAGA
533455 AAAGAGAAAAC
1 AAAGAGAAAAC
533466 AAAGAGAAAAC
1 AAAGAGAAAAC
533477 AAAG-GAAA
1 AAAGAGAAA
533485 CAACCAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAGAGAAAAC
Found at i:538663 original size:93 final size:92
Alignment explanation
Indices: 538485--538670 Score: 236
Period size: 93 Copynumber: 2.0 Consensus size: 92
538475 CGTATACCCA
* * * *
538485 TATTATATTATTATATATATAATAAAGCTTTAGTTGTCCCTCTAGTACAATTTGTTAATAGCCCC
1 TATTATATTACTATATATATAATAAAGATTGAGTTGTCCCTCTAGTACAATTGGTTAATAGCCCC
*
538550 GTCTTTATGGATAATATTCAACTAGCC
66 GACTTTATGGATAATATTCAACTAGCC
*
538577 TATTATATTACTAT-TATATGCAATAAAGATTGATTTGTCCCT-TCAG-AGCAATTGGTTAATAG
1 TATTATATTACTATATATAT--AATAAAGATTGAGTTGTCCCTCT-AGTA-CAATTGGTTAATAG
*
538639 CCCTGACTTTATGGATAAGT-TTCAACTAGCC
62 CCCCGACTTTATGGATAA-TATTCAACTAGCC
538670 T
1 T
538671 GATAAAGGTG
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
91 5 0.06
92 15 0.18
93 61 0.74
94 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (92 bp):
TATTATATTACTATATATATAATAAAGATTGAGTTGTCCCTCTAGTACAATTGGTTAATAGCCCC
GACTTTATGGATAATATTCAACTAGCC
Found at i:539847 original size:41 final size:42
Alignment explanation
Indices: 539802--539882 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
539792 CAGTTGGAAA
539802 AATATTGTA-ACA-TTTTGAA-AGCCCATTTCA-ACCAGAAATAG
1 AATATTG-AGACATTTTTGAATA-CCCATTTCAGA-CAGAAATAG
*
539843 AATATTGAGGCATTTTTGAATACCCATTTCAGACAGAAAT
1 AATATTGAGACATTTTTGAATACCCATTTCAGACAGAAAT
539883 GATCCATGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
40 1 0.03
41 9 0.26
42 23 0.66
43 2 0.06
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (42 bp):
AATATTGAGACATTTTTGAATACCCATTTCAGACAGAAATAG
Found at i:541294 original size:37 final size:37
Alignment explanation
Indices: 541240--541374 Score: 137
Period size: 37 Copynumber: 3.6 Consensus size: 37
541230 AAGAAAAGAT
**
541240 TTTATCTCACTTTAGATAGTTTCACTCGAAACAAAAA
1 TTTATCTCACTCGAGATAGTTTCACTCGAAACAAAAA
** **
541277 TTTATCTCACTCGAGATAGTTTTTCTTAAAAC-AAAA
1 TTTATCTCACTCGAGATAGTTTCACTCGAAACAAAAA
* * * * *
541313 TTTGTCTCACTTGAGACAATTGTTTCGCTCGAAACAAAAT
1 TTTATCTCACTCGAG---ATAGTTTCACTCGAAACAAAAA
541353 TTTATCTCACTCGAGATAGTTT
1 TTTATCTCACTCGAGATAGTTT
541375 TTCTTAAAAC
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
36 17 0.22
37 32 0.42
39 12 0.16
40 16 0.21
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (37 bp):
TTTATCTCACTCGAGATAGTTTCACTCGAAACAAAAA
Found at i:541321 original size:36 final size:36
Alignment explanation
Indices: 541240--541430 Score: 150
Period size: 36 Copynumber: 5.2 Consensus size: 36
541230 AAGAAAAGAT
** ** **
541240 TTTATCTCACTTTAGATAGTTTCACTCGAAACAAAAA
1 TTTATCTCACTCGAGATAGTTTTTCTTAAAAC-AAAA
541277 TTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAA
1 TTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAA
* * * * **
541313 TTTGTCTCACTTGAGACAATTGTTTCGCTCGAAACAAAA
1 TTTATCTCACTCGAGATAGTT-TTT--CTTAAAACAAAA
*
541352 TTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAC
1 -TTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAA
* * * * * *
541389 TTTGTCTCACTTGAGACAATTTTCCCTCAAAAC-AAA
1 TTTATCTCACTCGAGATAGTTTT-TCTTAAAACAAAA
541425 TTTATC
1 TTTATC
541431 ACAACTGAGG
Statistics
Matches: 122, Mismatches: 27, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
36 47 0.39
37 45 0.37
39 13 0.11
40 17 0.14
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (36 bp):
TTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAA
Found at i:541348 original size:76 final size:76
Alignment explanation
Indices: 541258--541409 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
541248 ACTTTAGATA
541258 GTTTCACTCGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAATTTGTCTCAC
1 GTTTCACTCGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAATTTGTCTCAC
541323 TTGAGACAATT
66 TTGAGACAATT
* * *
541334 GTTTCGCTCGAAACAAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTTGTCTCAC
1 GTTTCACTCGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAATTTGTCTCAC
541399 TTGAGACAATT
66 TTGAGACAATT
541410 TTCCCTCAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (76 bp):
GTTTCACTCGAAACAAAAATTTATCTCACTCGAGATAGTTTTTCTTAAAACAAAATTTGTCTCAC
TTGAGACAATT
Found at i:541834 original size:20 final size:20
Alignment explanation
Indices: 541771--541835 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
541761 TCGAGTAGAG
541771 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* ** **
541791 CG-TCCGAA-GAGGAAGAAAA
1 AGTTCATAATGA-GAAGAACT
541810 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
541830 TGTTCA
1 AGTTCA
541836 ATCTTTTGGT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:542160 original size:139 final size:139
Alignment explanation
Indices: 541876--542233 Score: 486
Period size: 140 Copynumber: 2.6 Consensus size: 139
541866 ATAGATCAAC
* * * * *
541876 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTTGTCCGATGAGGAAAAAGAAGTTCAT
1 ATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCAT
* * * * *
541941 AATGAGAAGAACTTGTTTGAACCTTAGCTTGATTCATCACATATGGAGTTGAATCAACGACACCT
66 AATGAGAAGAAATCGTTTCAACCTTAGCTTGATTCACCACATATGGAGTTAAATCAACGACACCT
*
542006 CACTCAAGGG
131 CACTCAA-GA
* * * * *
542016 ATCAACATTTTCAATGAAGAGTTCATAATGAGAAAAACTCATCTGAAGGGGAAGAATAAGTTCTT
1 ATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCAT
*
542081 AATGAGAAGAAATCG-TTCAACCTTAGCTTGATTCACCGCATATGGAGTTAAATCAACGACACCT
66 AATGAGAAGAAATCGTTTCAACCTTAGCTTGATTCACCACATATGGAGTTAAATCAACGACACCT
*
542145 CACTTGAA-A
131 CAC-TCAAGA
* *
542154 ATTCAACATTTTCAATGGAAAAGTTCATAATGAGAAGAACTCGTTTGAAGAGGAAGAAGAAGTTC
1 A-TCAACATTTTCAAT-GAAGAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTC
542219 ATAATGAGAAGAAAT
64 ATAATGAGAAGAAAT
542234 TTTTTCAATA
Statistics
Matches: 190, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
138 1 0.01
139 62 0.33
140 127 0.67
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (139 bp):
ATCAACATTTTCAATGAAGAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAAATCGTTTCAACCTTAGCTTGATTCACCACATATGGAGTTAAATCAACGACACCT
CACTCAAGA
Found at i:542378 original size:3 final size:3
Alignment explanation
Indices: 542370--542404 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
542360 TCCCATTTTA
542370 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
542405 AAAACTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:542386 original size:14 final size:14
Alignment explanation
Indices: 542367--542404 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
542357 TTTTCCCATT
542367 TTATATTATTATTA
1 TTATATTATTATTA
542381 TTATATTATTATTA
1 TTATATTATTATTA
542395 TTATTATTAT
1 TTA-TATTAT
542405 AAAACTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:543374 original size:2 final size:2
Alignment explanation
Indices: 543367--543420 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
543357 CACATTAACC
543367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
543409 AT AT AT AT AT AT
1 AT AT AT AT AT AT
543421 CTTTCTAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:545287 original size:29 final size:29
Alignment explanation
Indices: 545206--545294 Score: 135
Period size: 29 Copynumber: 3.1 Consensus size: 29
545196 AGTCCATTAT
* *
545206 TCTTTTACTCAATATTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
* *
545235 TATCTTACTC-ACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
545263 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
545292 TCT
1 TCT
545295 AACTGGCATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 24 0.45
29 29 0.55
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAACCGTTCA
Found at i:545410 original size:81 final size:81
Alignment explanation
Indices: 545263--545411 Score: 190
Period size: 81 Copynumber: 1.8 Consensus size: 81
545253 TAACCGTTCA
* * * *
545263 TCTTTTACTCAACAGTGTTTAACCGTTCATCTAACTGGCATAATTAACACATTTCTGCCAATTGC
1 TCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTAACACATTTCAGCCAAATGC
545328 ACAGATAGGTCATTAT
66 ACAGATAGGTCATTAT
* ** * * * * *
545344 TCTTTTACTCAACGGTATTTAACTTTTCATTTAGCTAGCATAATTGACACCTTTCAGTCAAATGC
1 TCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTAACACATTTCAGCCAAATGC
545409 ACA
66 ACA
545412 ATTAGGCCGT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 56 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTAACACATTTCAGCCAAATGC
ACAGATAGGTCATTAT
Found at i:545819 original size:47 final size:47
Alignment explanation
Indices: 545768--546048 Score: 216
Period size: 47 Copynumber: 6.1 Consensus size: 47
545758 TTAATTTCAT
* * *
545768 TTATGGCATCATTTCATACCTTAATGTATCCATTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTTAG
* * **
545815 TTATGGCATCCTTTCATTCCTTAATGCATCCTTTCAT--A-CCTTA-
1 TTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTTAG
** * * *
545858 --AT-GCATCCGCTCATGCAGTTTTAGTTATGGCATCCTTTCATGC---CTTA-
1 TTATGGCATCCTTTCATGC---CTTA---AT-GCATCCATTCATGCATTTTTAG
*
545905 --AT-GCATCCTTTCATGCCTTAATGCAT-CATTTCATGCATATTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCA-TTCATGCATTTTTAG
* **
545949 TTAAGGCATTTTTTCATGCCTTAATGCAT-CATTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCA-TTCATGCATTTTTAG
*
545996 TTATGGCATCCTTTAATGCCTTAATGCATCCATTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTTAG
546043 TTATGG
1 TTATGG
546049 ACTTGATTTA
Statistics
Matches: 193, Mismatches: 23, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
39 1 0.01
40 22 0.11
41 4 0.02
43 6 0.03
44 6 0.03
45 1 0.01
46 3 0.02
47 148 0.77
48 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTTAG
Found at i:545844 original size:67 final size:67
Alignment explanation
Indices: 545773--545985 Score: 302
Period size: 67 Copynumber: 3.2 Consensus size: 67
545763 TTCATTTATG
* *
545773 GCATCATTTCATACCTTAATGTATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATTCCTTA
1 GCATCATTTCATACCTTAATGCATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
545838 AT
66 AT
* ** *
545840 GCATCCTTTCATACCTTAATGCATCCGCTCATGCAGTTTTAGTTATGGCATCCTTTCATGCCTTA
1 GCATCATTTCATACCTTAATGCATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
545905 AT
66 AT
* * * * **
545907 GCATCCTTTCATGCCTTAATGCAT-CATTTCATGCATATTTAGTTAAGGCATTTTTTCATGCCTT
1 GCATCATTTCATACCTTAATGCATCCA-TTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTT
545971 AAT
65 AAT
545974 GCATCATTTCAT
1 GCATCATTTCAT
545986 GCATTTTTAG
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
66 1 0.01
67 129 0.99
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.42
Consensus pattern (67 bp):
GCATCATTTCATACCTTAATGCATCCATTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
AT
Found at i:545845 original size:20 final size:20
Alignment explanation
Indices: 545820--545940 Score: 125
Period size: 20 Copynumber: 5.7 Consensus size: 20
545810 TTTAGTTATG
*
545820 GCATCCTTTCATTCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
545840 GCATCCTTTCATACCTTAAT
1 GCATCCTTTCATGCCTTAAT
** *
545860 GCATCCGCTCATGCAGTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
545886 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
545907 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
545927 GCATCATTTCATGC
1 GCATCCTTTCATGC
545941 ATATTTAGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
20 63 0.74
21 2 0.02
23 3 0.04
24 3 0.04
26 2 0.02
27 12 0.14
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.40
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:545977 original size:20 final size:20
Alignment explanation
Indices: 545949--545987 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
545939 GCATATTTAG
**
545949 TTAAGGCATTTTTTCATGCC
1 TTAAGGCATCATTTCATGCC
*
545969 TTAATGCATCATTTCATGC
1 TTAAGGCATCATTTCATGC
545988 ATTTTTAGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (20 bp):
TTAAGGCATCATTTCATGCC
Found at i:550567 original size:29 final size:28
Alignment explanation
Indices: 550534--550644 Score: 114
Period size: 28 Copynumber: 3.9 Consensus size: 28
550524 CATTATTCTT
**
550534 TTACTCAACAGTGTTTGCCCGTTCATATC
1 TTACTC-ACAGTGTTTAACCGTTCATATC
* * *
550563 TTACTCATAGTATTTAACCGTTCCTATC
1 TTACTCACAGTGTTTAACCGTTCATATC
* * * *
550591 TTACTCATAGTGTTTAACTGTTCATCTT
1 TTACTCACAGTGTTTAACCGTTCATATC
*
550619 TTACTCAACAATGTTTAACCGTTCAT
1 TTACTC-ACAGTGTTTAACCGTTCAT
550645 CTAACTGGCA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
28 46 0.68
29 22 0.32
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (28 bp):
TTACTCACAGTGTTTAACCGTTCATATC
Found at i:550714 original size:80 final size:80
Alignment explanation
Indices: 550615--550856 Score: 326
Period size: 80 Copynumber: 3.0 Consensus size: 80
550605 TAACTGTTCA
550615 TCTTTTACTCAACAATGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGC
1 TCTTTTACTCAACAATGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGC
*
550680 ATATTAGGCCATTAT
66 AAATTAGGCCATTAT
* * * *
550695 TCTTTTACTCAACACTGTTTAACCGTTCATCTAACTGGAATAATTGACACATTTCTGCCAATTGC
1 TCTTTTACTCAACAATGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGC
550760 ACAATTAGGCCATTAT
66 A-AATTAGGCCATTAT
* * * * * *
550776 TCTTTTACTCAACGGTAT-TTTAACCGTTTATTTAGCTGGCATAATTGACACCTTTCA-GTCAAA
1 TCTTTTACTCAAC--AATGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTT-ATGCCAAT
550839 TGCAAAGTTAGGCCATTA
63 TGCAAA-TTAGGCCATTA
550857 AGCTTGTATT
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
80 62 0.44
81 28 0.20
82 51 0.36
83 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (80 bp):
TCTTTTACTCAACAATGTTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAATTGC
AAATTAGGCCATTAT
Found at i:551222 original size:21 final size:20
Alignment explanation
Indices: 551198--551243 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
551188 TCGTTAATTT
551198 CATTTATGGAATCCTCTCATA
1 CATTTAT-GAATCCTCTCATA
* * *
551219 CATTAATGCATCCTCTCATG
1 CATTTATGAATCCTCTCATA
551239 CATTT
1 CATTT
551244 TTAGTTATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (20 bp):
CATTTATGAATCCTCTCATA
Found at i:551272 original size:47 final size:47
Alignment explanation
Indices: 551201--551512 Score: 362
Period size: 47 Copynumber: 6.9 Consensus size: 47
551191 TTAATTTCAT
* * * * *
551201 TTATGGAATCCTCTCATACATTAATGCATCCTCTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
*
551248 TTATGGCATCCTTTCATGCCTTAATGTATCCTTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* * * *
551295 TTATGGCATCTTTTTATACCTTAATGCAT-CTGCTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCT-TTCATGCATTTTTAG
*
551342 TTATGGCATCCTTTCATGCCTTAATGCAT--TTT--T--A--GTTA-
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* * *
551380 --AT-ACATCCTTTAATGCCTTATTGCATCCTTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
* * *
551424 TTATGGAATCCTTGCATGCCTTAATGCATCATTTCATGCATTTTTAG
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
*
551471 TTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGCATT
1 TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATT
551513 AATGCATCCT
Statistics
Matches: 222, Mismatches: 30, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
35 21 0.09
36 2 0.01
37 3 0.01
39 4 0.02
41 2 0.01
43 4 0.02
45 1 0.00
46 5 0.02
47 180 0.81
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (47 bp):
TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTTAG
Found at i:551376 original size:35 final size:35
Alignment explanation
Indices: 551330--551405 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
551320 GCATCTGCTC
* *
551330 ATGCATTTTTAGTT-ATGGCATCCTTTCATGCCTTA
1 ATGCATTTTTAGTTAAT-ACATCCTTTAATGCCTTA
551365 ATGCATTTTTAGTTAATACATCCTTTAATGCCTTA
1 ATGCATTTTTAGTTAATACATCCTTTAATGCCTTA
*
551400 TTGCAT
1 ATGCAT
551406 CCTTTCATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (35 bp):
ATGCATTTTTAGTTAATACATCCTTTAATGCCTTA
Found at i:551408 original size:129 final size:129
Alignment explanation
Indices: 551236--551499 Score: 397
Period size: 129 Copynumber: 2.0 Consensus size: 129
551226 GCATCCTCTC
* * *
551236 ATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGTATCCTTTCATGCATTTTTAGTTATGG
1 ATGCATTTTTAGTTATGACATCCTTTAATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGG
* * ** *
551301 CATCTTTTTATACCTTAATGCATC-TGCTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTA
66 AATCCTTGCATACCTTAATGCATCAT-CTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTA
*
551365 ATGCATTTTTAGTTAAT-ACATCCTTTAATGCCTTATTGCATCCTTTCATGCATTTTTAGTTATG
1 ATGCATTTTTAGTT-ATGACATCCTTTAATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATG
* *
551429 GAATCCTTGCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTA
65 GAATCCTTGCATACCTTAATGCATCATCTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTA
551494 ATGCAT
1 ATGCAT
551500 CCTTTCATGC
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
129 119 0.98
130 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (129 bp):
ATGCATTTTTAGTTATGACATCCTTTAATGCCTTAATGCATCCTTTCATGCATTTTTAGTTATGG
AATCCTTGCATACCTTAATGCATCATCTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTA
Found at i:551420 original size:82 final size:82
Alignment explanation
Indices: 551283--551452 Score: 236
Period size: 82 Copynumber: 2.1 Consensus size: 82
551273 GTATCCTTTC
* * *
551283 ATGCATTTTTAGTTATGGCATCTTTTTATACCTTAATGCATCTGCTCATGCATTTTTAGTTATGG
1 ATGCATTTTTAGTTATGACATCCTTTAATACCTTAATGCATCTGCTCATGCATTTTTAGTTATGG
* *
551348 CATCCTTTCATGCCTTA
66 AATCCTTGCATGCCTTA
* * *
551365 ATGCATTTTTAGTTAAT-ACATCCTTTAATGCCTTATTGCATCCT-TTCATGCATTTTTAGTTAT
1 ATGCATTTTTAGTT-ATGACATCCTTTAATACCTTAATGCAT-CTGCTCATGCATTTTTAGTTAT
551428 GGAATCCTTGCATGCCTTA
64 GGAATCCTTGCATGCCTTA
551447 ATGCAT
1 ATGCAT
551453 CATTTCATGC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
82 74 0.95
83 4 0.05
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.45
Consensus pattern (82 bp):
ATGCATTTTTAGTTATGACATCCTTTAATACCTTAATGCATCTGCTCATGCATTTTTAGTTATGG
AATCCTTGCATGCCTTA
Found at i:551501 original size:20 final size:20
Alignment explanation
Indices: 551476--551575 Score: 101
Period size: 20 Copynumber: 4.7 Consensus size: 20
551466 TTTAGTTATG
* *
551476 GCATCCTTTAATGCCTTAAT
1 GCATCCTTTCATGCATTAAT
551496 GCATCCTTTCATGCATTAAT
1 GCATCCTTTCATGCATTAAT
551516 GCATCCTTTCATGCATTTTTAGTTAT
1 GCATCCTTTCATGCA---TTA---AT
*
551542 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCATTAAT
*
551563 GCATCCATTCATG
1 GCATCCTTTCATG
551576 TATTTTTAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
20 45 0.65
21 2 0.03
23 3 0.04
24 3 0.04
26 2 0.03
27 14 0.20
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCATTAAT
Found at i:551519 original size:114 final size:114
Alignment explanation
Indices: 551377--551626 Score: 385
Period size: 114 Copynumber: 2.2 Consensus size: 114
551367 GCATTTTTAG
* * * *
551377 TTAATACATCCTTTAATGCCTTATTGCATCCTTTCATGCATTTTTAGTTATGGAATCCTTGCATG
1 TTAATGCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGAATCCTTGCATG
*
551442 CCTTAATGCAT-CATTTCATGCATTTTTAGTTATGGCATCCTTTAATGCC
66 CCTTAATGCATCCA-TTCATGCATTTTTAGTTATGGAATCCTTTAATGCC
* *
551491 TTAATGCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATG
1 TTAATGCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGAATCCTTGCATG
* *
551556 CCTTAATGCATCCATTCATGTATTTTTAGTTATGGAATCCTTTCATGCC
66 CCTTAATGCATCCATTCATGCATTTTTAGTTATGGAATCCTTTAATGCC
**
551605 TTAATGCATCCGATCATGCATT
1 TTAATGCATCCTTTCATGCATT
551627 TTTAGTTATG
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
114 122 0.98
115 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (114 bp):
TTAATGCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGAATCCTTGCATG
CCTTAATGCATCCATTCATGCATTTTTAGTTATGGAATCCTTTAATGCC
Found at i:551539 original size:67 final size:67
Alignment explanation
Indices: 551431--551575 Score: 245
Period size: 67 Copynumber: 2.2 Consensus size: 67
551421 TAGTTATGGA
* *
551431 ATCCTTGCATGCCTTAATGCATCATTTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTAAT
1 ATCCTTTCATGCATTAATGCATCATTTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTAAT
551496 GC
66 GC
* *
551498 ATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 ATCCTTTCATGCATTAATGCATCATTTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTAAT
551563 GC
66 GC
*
551565 ATCCATTCATG
1 ATCCTTTCATG
551576 TATTTTTAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 73 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.42
Consensus pattern (67 bp):
ATCCTTTCATGCATTAATGCATCATTTCATGCATTTTTAGTTATGGCATCCTTTAATGCCTTAAT
GC
Found at i:551547 original size:47 final size:47
Alignment explanation
Indices: 551496--551684 Score: 297
Period size: 47 Copynumber: 4.0 Consensus size: 47
551486 ATGCCTTAAT
* *
551496 GCATCCTTTCATGCATTAATGCATCCTTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATG
* *
551543 GCATCCTTTCATGCCTTAATGCATCCATTCATGTATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATG
* *
551590 GAATCCTTTCATGCCTTAATGCATCCGATCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATG
* * *
551637 ACATCCTTTCATGCCTTATTGCATCCGTTCATGCATTTTTGGTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATG
551684 G
1 G
551685 ATTTGATTTA
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 129 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (47 bp):
GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATG
Found at i:554412 original size:72 final size:74
Alignment explanation
Indices: 554358--554493 Score: 222
Period size: 72 Copynumber: 1.9 Consensus size: 74
554348 AAATTTCTAC
554358 AAGTTTCATATAATTTTTAACTTCAAAAATTTAAAAATTTT-A-ATTTTTTTCAAATTTATTAAA
1 AAGTTTCATATAATTTTTAACTTCAAAAATTTAAAAATTTTAATATTTTTTTCAAATTTATTAAA
554421 AAATTAAAA
66 AAATTAAAA
* ** *
554430 AAGTTTCATATTATTTTTAACTTCGGAATTTTAAAAATTTTAATATTTTTTTCAAATTTATTAA
1 AAGTTTCATATAATTTTTAACTTCAAAAATTTAAAAATTTTAATATTTTTTTCAAATTTATTAA
554494 TTACACTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 37 0.64
73 1 0.02
74 20 0.34
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (74 bp):
AAGTTTCATATAATTTTTAACTTCAAAAATTTAAAAATTTTAATATTTTTTTCAAATTTATTAAA
AAATTAAAA
Found at i:559170 original size:17 final size:16
Alignment explanation
Indices: 559139--559172 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
559129 CACGTGAGGA
559139 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
559155 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
559172 T
1 T
559173 ACCGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:565560 original size:19 final size:21
Alignment explanation
Indices: 565523--565565 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
565513 TAACTTTTTC
565523 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
565543 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
565563 TTT
1 TTT
565566 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:565571 original size:19 final size:20
Alignment explanation
Indices: 565522--565571 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
565512 TTAACTTTTT
*
565522 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
565542 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
565561 CTTTTACCTTT
1 CTTTTACCTTT
565572 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:569429 original size:17 final size:16
Alignment explanation
Indices: 569398--569431 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
569388 CACGTGAGGA
569398 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
569414 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
569431 T
1 T
569432 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:576636 original size:20 final size:20
Alignment explanation
Indices: 576611--576653 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
576601 TGTCCATAAG
576611 GCCGAACATTGAGACTTAAT
1 GCCGAACATTGAGACTTAAT
576631 GCCGAACATTGAGACTTAAT
1 GCCGAACATTGAGACTTAAT
576651 GCC
1 GCC
576654 ATTTATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (20 bp):
GCCGAACATTGAGACTTAAT
Found at i:581413 original size:26 final size:27
Alignment explanation
Indices: 581384--581435 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
581374 GGTCTGACGT
581384 GGCAG-TTTCTAGAAGGTCCAGTCAGC
1 GGCAGTTTTCTAGAAGGTCCAGTCAGC
* *
581410 GGCAGTTTTCTAGAAGTTCTAGTCAG
1 GGCAGTTTTCTAGAAGGTCCAGTCAG
581436 TGCACCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (27 bp):
GGCAGTTTTCTAGAAGGTCCAGTCAGC
Found at i:589748 original size:3 final size:3
Alignment explanation
Indices: 589727--589799 Score: 92
Period size: 3 Copynumber: 23.3 Consensus size: 3
589717 AATGTAACAA
*
589727 AAT AATT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT ATAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
589774 AAT AAT AAAT GAT ATT AAT AAT AAT A
1 AAT AAT -AAT AAT AAT AAT AAT AAT A
589800 TTTTGCAGAC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
3 52 0.85
4 9 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:589751 original size:19 final size:18
Alignment explanation
Indices: 589727--589799 Score: 92
Period size: 19 Copynumber: 3.9 Consensus size: 18
589717 AATGTAACAA
*
589727 AATAATTAATAATAGTAAT
1 AATAA-TAATAATAATAAT
589746 AATAATAATAATAATAAT
1 AATAATAATAATAATAAT
589764 ATATAATAATAATAATAAAT
1 A-ATAATAATAATAAT-AAT
* *
589784 GATATTAATAATAATA
1 AATAATAATAATAATA
589800 TTTTGCAGAC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.29
19 32 0.65
20 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AATAATAATAATAATAAT
Found at i:590220 original size:130 final size:128
Alignment explanation
Indices: 589981--590280 Score: 288
Period size: 130 Copynumber: 2.3 Consensus size: 128
589971 AGTTATAGTC
* * * * *
589981 GTCTAAGGGTGATACTGCTCTTACGTGATGAGGAGATCA-GGTCGGT-GA-CACAGTTCCTACGC
1 GTCTAAGGGTG--ACGGCTCCTACGTGATGAGGAGGT-ATGGTCAGTGGATGACA-TTCCTACGC
* * * **
590043 GATGAGGACGGTAGGCCATCTTTAGGAGACTGATAACACATTTCCTACGCGATGAGGATGACTGG
62 GATGAGGACGGCAGGCCATCTTTAGGAGACTGATAACACAGTTCCTACGCGATAAGGACAACTGG
590108 TT
127 TT
* * *
590110 GTCTAGGGGTGACACGG-TACCTACGTGATGAGGAGGTTTGGTCAGTGGATGACATTCCTACGTG
1 GTCTAAGGGTG--ACGGCT-CCTACGTGATGAGGAGGTATGGTCAGTGGATGACATTCCTACGCG
* * * * **
590174 ATGAGGATGGCATGCCAT-TTTAGGA-ATGGTGATAACACGGTTCCTACGTTATAAGGACAACTG
63 ATGAGGACGGCAGGCCATCTTTAGGAGA--CTGATAACACAGTTCCTACGCGATAAGGACAACTG
590237 GTT
126 GTT
* *
590240 TTCTAAGGTTGACGGCTCCTACGTGATGAGGAGGTATGGTC
1 GTCTAAGGGTGACGGCTCCTACGTGATGAGGAGGTATGGTC
590281 CTACGTGATG
Statistics
Matches: 140, Mismatches: 24, Indels: 15
0.78 0.13 0.08
Matches are distributed among these distances:
128 29 0.21
129 44 0.31
130 64 0.46
131 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (128 bp):
GTCTAAGGGTGACGGCTCCTACGTGATGAGGAGGTATGGTCAGTGGATGACATTCCTACGCGATG
AGGACGGCAGGCCATCTTTAGGAGACTGATAACACAGTTCCTACGCGATAAGGACAACTGGTT
Done.