Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 30
Found at i:420197 original size:2 final size:2
Alignment explanation
Indices: 420190--420268 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
420180 AAATTGACAA
420190 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
420232 AT AT AT AT AT AT AT AT AT -T 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
420269 TTGTACTTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:423025 original size:24 final size:24
Alignment explanation
Indices: 422998--423058 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
422988 AGTCCTAAAT
422998 GTTTCATGAGTTTCAATTACAATA
1 GTTTCATGAGTTTCAATTACAATA
423022 GTTTCATGAGTTTCAATTACAATA
1 GTTTCATGAGTTTCAATTACAATA
423046 GTTTCATGAGTTT
1 GTTTCATGAGTTT
423059 TAGTTGTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (24 bp):
GTTTCATGAGTTTCAATTACAATA
Found at i:425438 original size:25 final size:25
Alignment explanation
Indices: 425410--425487 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 25
425400 ATAAAAATGA
425410 TTTGCGGGTTATAATTGATTAATTG
1 TTTGCGGGTTATAATTGATTAATTG
** * * *
425435 TTTG-ATG-AATAATAT-ATAAAAATG
1 TTTGCGGGTTATAAT-TGAT-TAATTG
425459 ATTTGCGGGTTATAATTGATTAATTG
1 -TTTGCGGGTTATAATTGATTAATTG
425485 TTT
1 TTT
425488 ATATATTTAT
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
23 7 0.19
24 6 0.16
25 11 0.30
26 6 0.16
27 7 0.19
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (25 bp):
TTTGCGGGTTATAATTGATTAATTG
Found at i:425452 original size:50 final size:50
Alignment explanation
Indices: 425377--425487 Score: 204
Period size: 50 Copynumber: 2.2 Consensus size: 50
425367 TATACCCTAA
* *
425377 ATTAATTGTTTGCTGATTAATATATAAAAATGATTTGCGGGTTATAATTG
1 ATTAATTGTTTGATGAATAATATATAAAAATGATTTGCGGGTTATAATTG
425427 ATTAATTGTTTGATGAATAATATATAAAAATGATTTGCGGGTTATAATTG
1 ATTAATTGTTTGATGAATAATATATAAAAATGATTTGCGGGTTATAATTG
425477 ATTAATTGTTT
1 ATTAATTGTTT
425488 ATATATTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (50 bp):
ATTAATTGTTTGATGAATAATATATAAAAATGATTTGCGGGTTATAATTG
Found at i:426673 original size:21 final size:21
Alignment explanation
Indices: 426643--426683 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
426633 AATGTTAAAA
*
426643 AAATATTAATGTTTTAGGTAG
1 AAATAATAATGTTTTAGGTAG
426664 AAATAATAATGTTTTAGGTA
1 AAATAATAATGTTTTAGGTA
426684 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (21 bp):
AAATAATAATGTTTTAGGTAG
Found at i:437171 original size:71 final size:69
Alignment explanation
Indices: 437046--437217 Score: 177
Period size: 71 Copynumber: 2.4 Consensus size: 69
437036 GGGTGTATCG
* * * *
437046 CGTCGAACTGAATGTTTAAAAAAGTTCGAGC-TCAAGCTGGAACTTGCCTGGAACAAACATAACA
1 CGTCGAACTGAATGCTT-AAAAAGCTCGAGCTTCAAGCTGGAACTCGCCTCGAACAAACATAACA
437110 CTCAAAC
65 --CAAAC
* * * *
437117 CGTCGAACTGAATGCTTGAAAAAGCTCGAGCTTGAA-TTTGAACTCGCCTCGAACAAACGTAACA
1 CGTCGAACTGAATGCTT-AAAAAGCTCGAGCTTCAAGCTGGAACTCGCCTCGAACAAACATAACA
437181 CAAAC
65 CAAAC
** **
437186 AATCCCACTGAATGCTTAAGAAAGCTCGAGCT
1 CGTCGAACTGAATGCTTAA-AAAGCTCGAGCT
437218 CGAACTTGGC
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
68 2 0.02
69 30 0.35
71 51 0.59
72 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (69 bp):
CGTCGAACTGAATGCTTAAAAAGCTCGAGCTTCAAGCTGGAACTCGCCTCGAACAAACATAACAC
AAAC
Found at i:439808 original size:2 final size:2
Alignment explanation
Indices: 439801--439834 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
439791 AAATTAAAAT
439801 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
439835 GAAAACGCAA
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):
TA
Found at i:440598 original size:59 final size:59
Alignment explanation
Indices: 440471--440598 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 59
440461 ACTCATGATC
* * * *
440471 ACTTAATTACAAGAGGATTATAATTTAACAGTTATTTTTTTAATTTTATCAATCAAACT
1 ACTTAATTATAAGAGGATTATAATTGAACAGTTAATCTTTTAATTTTATCAATCAAACT
* * * * * *
440530 ACTTAATTATGAGAGGATTATAATATGACCA-TTAATCTTTTAATTTTGTTAATCATATT
1 ACTTAATTATAAGAGGATTATAAT-TGAACAGTTAATCTTTTAATTTTATCAATCAAACT
440589 ACTTAATTAT
1 ACTTAATTAT
440599 TTAAACGATA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 54 0.93
60 4 0.07
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (59 bp):
ACTTAATTATAAGAGGATTATAATTGAACAGTTAATCTTTTAATTTTATCAATCAAACT
Found at i:442014 original size:2 final size:2
Alignment explanation
Indices: 442007--442068 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
441997 CCGATTAGTT
442007 TA TA TA 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 TA TA TA
442049 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
442069 ATGAATTATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:446917 original size:7 final size:7
Alignment explanation
Indices: 446905--446929 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
446895 GTTTTTATTA
446905 TAAATAT
1 TAAATAT
446912 TAAATAT
1 TAAATAT
446919 TAAATAT
1 TAAATAT
446926 TAAA
1 TAAA
446930 CTAGTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAATAT
Found at i:447686 original size:13 final size:13
Alignment explanation
Indices: 447677--447714 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
447667 TTTTTATTTT
447677 TTATTATT-ATTAA
1 TTATTATTAATT-A
*
447690 TTATTATTAACTA
1 TTATTATTAATTA
447703 TTATTATTAATT
1 TTATTATTAATT
447715 TTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:447695 original size:10 final size:10
Alignment explanation
Indices: 447679--447708 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
447669 TTTATTTTTT
447679 ATTATTATTA
1 ATTATTATTA
447689 ATTATTATTA
1 ATTATTATTA
*
447699 ACTATTATTA
1 ATTATTATTA
447709 TTAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:462404 original size:135 final size:129
Alignment explanation
Indices: 462117--462425 Score: 345
Period size: 135 Copynumber: 2.3 Consensus size: 129
462107 TCAACATCAG
* ** * * *
462117 CTGACCAGATCTCCTCATCACGTAGGAGCAACGTCAACATTAGATAACCAGCCGTCCTCATTACG
1 CTGACCAGATATCCTCATCACGTAGGAGC-GTGTCACCCTTAGATAACCAGCCGTCCTCATCACG
* *
462182 TAGGAACTATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGTAGGAGCAGTGTCATCCC
65 TAGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
* * *
462247 CTGACTAGATATCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCATCGCG
1 CTGACCAGATATCCTCATCACGTAGGAG-CGTGTCACCCTTAGATAACCAGCCGTCCTCATCACG
* *
462312 TAGGAACCGA-GTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGCATGAGTC-GTG
65 TAGGAA-CGATGTTATCA--C-T-ATAAA-ATGGCCAAGAACTCTTCATCACGCAGGAG-CAGTG
462375 TCAT-CC
123 TCATCCC
* * * *
462381 TTCGACCAGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGA
1 CT-GACCAGATATCCTCATCACGTA-GGAGCGTGTCACCCTTAGA
462426 CGACCCGAAC
Statistics
Matches: 151, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
130 67 0.44
131 3 0.02
132 1 0.01
133 1 0.01
134 7 0.05
135 69 0.46
136 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (129 bp):
CTGACCAGATATCCTCATCACGTAGGAGCGTGTCACCCTTAGATAACCAGCCGTCCTCATCACGT
AGGAACGATGTTATCACTATAAAATGGCCAAGAACTCTTCATCACGCAGGAGCAGTGTCATCCC
Found at i:462443 original size:43 final size:40
Alignment explanation
Indices: 462348--462451 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 40
462338 AAGATGGCCA
* ** *
462348 AGAACTCTTCATCACGCATGAGTCGTGTCATCCTTCGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
** *
462388 AGATTTCCTCATCACGTATGAACCGTGTCACCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAACCGTGTCACCCTT---CGACC
*
462431 CGAACTCTTCATCACGTATGA
1 AGAACTCTTCATCACGTATGA
462452 GCAGTGTCGT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
40 28 0.56
43 22 0.44
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAACCGTGTCACCCTTCGACC
Found at i:462638 original size:13 final size:13
Alignment explanation
Indices: 462629--462666 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
462619 TTTTTATTTT
462629 TTATTATT-ATTAA
1 TTATTATTAATT-A
*
462642 TTATTATTAACTA
1 TTATTATTAATTA
462655 TTATTATTAATT
1 TTATTATTAATT
462667 TTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:462647 original size:10 final size:10
Alignment explanation
Indices: 462631--462660 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
462621 TTTATTTTTT
462631 ATTATTATTA
1 ATTATTATTA
462641 ATTATTATTA
1 ATTATTATTA
*
462651 ACTATTATTA
1 ATTATTATTA
462661 TTAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:470360 original size:94 final size:92
Alignment explanation
Indices: 470235--470515 Score: 341
Period size: 93 Copynumber: 3.0 Consensus size: 92
470225 GGATAAAAAC
* * * *
470235 CGCTAGTTAACAAATGTTTAACGCTCTAAAATAGGGCCCTTTTACCCTAAAATGAAATAATAGGG
1 CGCTAGTTAATAGATGATTAACGCTCCAAAATAGGG--CTTTTACCCTAAAATGAAATAATAGGG
470300 GCCAAAATGCTCTAGAAGAAAAGAATAA-
64 GCCAAAATGCTCTAGAAGAAAAGAATAAT
* * *
470328 CTGCTAGTTAATAGATGATTAACGCTCCAAAATA-GGTTTTTCATCCTAAAAATGAAATAATAAG
1 C-GCTAGTTAATAGATGATTAACGCTCCAAAATAGGGCTTTT-ACCCT-AAAATGAAATAATAGG
470392 GGCCAAAATGCTCTAGAAGAAAAGAATAAT
63 GGCCAAAATGCTCTAGAAGAAAAGAATAAT
** ** *
470422 CGCTAGTTAATAGACCATTAACGCTCCAAAATAGGGGGGTTTACCCTAAAATGAAATATTAGCGG
1 CGCTAGTTAATAGATGATTAACGCTCCAAAATA-GGGCTTTTACCCTAAAATGAAATAATAG-GG
***
470487 TAAAAAAATGCTCTAGAAGAAAAGAATAA
64 -GCCAAAATGCTCTAGAAGAAAAGAATAA
470516 GGGTGAAAGT
Statistics
Matches: 163, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
91 4 0.02
92 4 0.02
93 90 0.55
94 35 0.21
95 30 0.18
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (92 bp):
CGCTAGTTAATAGATGATTAACGCTCCAAAATAGGGCTTTTACCCTAAAATGAAATAATAGGGGC
CAAAATGCTCTAGAAGAAAAGAATAAT
Found at i:475632 original size:17 final size:17
Alignment explanation
Indices: 475610--475653 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
475600 GTCGCATGGT
475610 CCCTAGAGTTGTCATAA
1 CCCTAGAGTTGTCATAA
475627 CCCTAGAGTTGTCATAA
1 CCCTAGAGTTGTCATAA
475644 CCCTAGAGTT
1 CCCTAGAGTT
475654 ACTTCTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (17 bp):
CCCTAGAGTTGTCATAA
Found at i:475853 original size:3 final size:3
Alignment explanation
Indices: 475845--475908 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
475835 ACCTGTTTTG
* * * *
475845 TAA TAA TAA TATT TAT TAA TAA TAA TAA TAA AAA TAA TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
475891 TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
475909 ACAGGCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 50 0.96
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:476845 original size:97 final size:97
Alignment explanation
Indices: 476679--476876 Score: 387
Period size: 97 Copynumber: 2.0 Consensus size: 97
476669 ATTTTGGCCT
476679 TGAACGTTTTATTTTGGGGTAAAAAGACCCCTCAATAGATAGAAATTGTTAGCTAACATACTATT
1 TGAACGTTTTATTTTGGGGTAAAAAGACCCCTCAATAGATAGAAATTGTTAGCTAACATACTATT
476744 AACACTTCCAAATAAAGGTTTTTGCACTAATA
66 AACACTTCCAAATAAAGGTTTTTGCACTAATA
*
476776 TGAACGTTTTATTTTGGGGTAAAAATACCCCTCAATAGATAGAAATTGTTAGCTAACATACTATT
1 TGAACGTTTTATTTTGGGGTAAAAAGACCCCTCAATAGATAGAAATTGTTAGCTAACATACTATT
476841 AACACTTCCAAATAAAGGTTTTTGCACTAATA
66 AACACTTCCAAATAAAGGTTTTTGCACTAATA
476873 TGAA
1 TGAA
476877 ACATTGATAG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (97 bp):
TGAACGTTTTATTTTGGGGTAAAAAGACCCCTCAATAGATAGAAATTGTTAGCTAACATACTATT
AACACTTCCAAATAAAGGTTTTTGCACTAATA
Found at i:480346 original size:21 final size:20
Alignment explanation
Indices: 480260--480417 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
480250 AAATGACCAA
**
480260 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
480279 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
480299 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
480319 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
480340 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
480361 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
480381 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
480402 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
480418 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:480479 original size:20 final size:20
Alignment explanation
Indices: 480385--480613 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
480375 GATTTTCCAG
* ** *
480385 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
480405 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
480425 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
480445 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
480465 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
480485 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
480505 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
480525 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * **
480545 AATCGCAACGAGAATCTATA
1 AATCGCAACGCGTATCCGTA
*
480565 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
480585 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
480605 AATCACAAC
1 AATCGCAAC
480614 ACTGAAATTT
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 173 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:481326 original size:24 final size:24
Alignment explanation
Indices: 481299--481352 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
481289 GTATTCGAAA
*
481299 TTTGATCTTGGTCAATATC-CGGAC
1 TTTGATATTGGTCAATA-CACGGAC
*
481323 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
481347 TTTGAT
1 TTTGAT
481353 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:481544 original size:12 final size:12
Alignment explanation
Indices: 481527--481551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
481517 ATATAATCCT
481527 GAAGAAGAAAAA
1 GAAGAAGAAAAA
481539 GAAGAAGAAAAA
1 GAAGAAGAAAAA
481551 G
1 G
481552 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:483901 original size:20 final size:19
Alignment explanation
Indices: 483850--484035 Score: 204
Period size: 19 Copynumber: 10.4 Consensus size: 19
483840 GCAACGAGAG
483850 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
483869 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
483883 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
483903 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
*
483922 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
483936 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
483956 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
483975 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
483989 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
484008 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
484028 AATCGCAA
1 AATCGCAA
484036 CGAGAGAATC
Statistics
Matches: 141, Mismatches: 8, Indels: 35
0.77 0.04 0.19
Matches are distributed among these distances:
14 32 0.23
15 2 0.01
16 4 0.03
17 5 0.04
18 1 0.01
19 53 0.38
20 44 0.31
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:483993 original size:86 final size:84
Alignment explanation
Indices: 483836--484015 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
483826 CGGAAATTAC
483836 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
*
483901 AAAATCGCAATGTGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
483922 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
483985 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
484008 AATCGCAA
1 AATCGCAA
484016 TGCGGAAATG
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:484012 original size:33 final size:33
Alignment explanation
Indices: 483836--484015 Score: 161
Period size: 33 Copynumber: 5.2 Consensus size: 33
483826 CGGAAATTAC
*
483836 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
483869 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
* * * * *
483903 AATCGCAATGTG-AAAT-GAAAAT-CGCAACGAGA
1 AATCGCAACGAGAAAATCG-CAATGCGAAATGA-A
483935 GAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAA
*
483975 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
484008 AATCGCAA
1 AATCGCAA
484016 TGCGGAAATG
Statistics
Matches: 118, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
31 5 0.04
32 4 0.03
33 65 0.55
34 17 0.14
36 2 0.02
37 1 0.01
39 9 0.08
40 8 0.07
41 7 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:484067 original size:53 final size:53
Alignment explanation
Indices: 483850--484053 Score: 349
Period size: 53 Copynumber: 3.8 Consensus size: 53
483840 GCAACGAGAG
* *
483850 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
*
483903 AATCGCAATGTGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
483956 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
484008 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCG
484054 ATTTTAATTT
Statistics
Matches: 144, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
52 19 0.13
53 124 0.86
54 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:484107 original size:52 final size:52
Alignment explanation
Indices: 484044--484178 Score: 243
Period size: 52 Copynumber: 2.6 Consensus size: 52
484034 AACGAGAGAA
* * *
484044 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCAATTTTCATT
484096 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCAATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCAATTTTCATT
484148 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
484179 AGTCATTTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 80 1.00
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCAATTTTCATT
Found at i:484186 original size:19 final size:19
Alignment explanation
Indices: 484044--484178 Score: 155
Period size: 19 Copynumber: 7.6 Consensus size: 19
484034 AACGAGAGAA
* *
484044 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
484063 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
484079 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
484096 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
484115 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
484131 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
484148 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
484167 TCGCATTGCGAT
1 TCGCATTGCGAT
484179 AGTCATTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 11 0.11
16 14 0.14
17 13 0.13
19 60 0.61
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:484304 original size:14 final size:14
Alignment explanation
Indices: 484285--484321 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
484275 CATCAATTAC
484285 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
484299 ACAAATCATCTTTT
1 ACAAATCAACTTTT
484313 ACAAATCAA
1 ACAAATCAA
484322 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:486270 original size:19 final size:19
Alignment explanation
Indices: 486228--486381 Score: 148
Period size: 19 Copynumber: 8.6 Consensus size: 19
486218 TAGTTTACTT
* *
486228 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
486248 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
486267 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
486286 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
486305 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
486319 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
486338 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
486352 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
486371 TCGCAATGCGA
1 TCGCAACGCGA
486382 TTTTGGTTTC
Statistics
Matches: 111, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
14 16 0.14
16 11 0.10
17 11 0.10
19 61 0.55
20 12 0.11
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:486322 original size:14 final size:14
Alignment explanation
Indices: 486303--486359 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
486293 GCGAAATGAA
*
486303 AATCGCAACGACAG
1 AATCGCAACGAAAG
486317 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
486334 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
486350 AATCGCAACG
1 AATCGCAACG
486360 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:486330 original size:33 final size:33
Alignment explanation
Indices: 486246--486376 Score: 181
Period size: 33 Copynumber: 3.8 Consensus size: 33
486236 CGAAACTTAA
* *
486246 AATCGCAACGCGAAATGATAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
486284 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
486317 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
486350 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
486377 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
33 59 0.67
34 1 0.01
36 1 0.01
38 27 0.31
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:486423 original size:33 final size:33
Alignment explanation
Indices: 486381--486471 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
486371 TCGCAATGCG
486381 ATTTTGGTTTCGCGTTGCGATTTTGTCGTTGCA
1 ATTTTGGTTTCGCGTTGCGATTTTGTCGTTGCA
* *
486414 ATTTTGGTTTCGCGTTGCGATTCTT-TTGTTGCG
1 ATTTTGGTTTCGCGTTGCGATT-TTGTCGTTGCA
**
486447 ATTTTCATTTCGCGTTGCGATTTTG
1 ATTTTGGTTTCGCGTTGCGATTTTG
486472 GTTTCGCGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
32 2 0.04
33 48 0.92
34 2 0.04
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (33 bp):
ATTTTGGTTTCGCGTTGCGATTTTGTCGTTGCA
Found at i:486431 original size:19 final size:19
Alignment explanation
Indices: 486377--486505 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
486367 AAAATCGCAA
486377 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
486396 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
486410 TGCAATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
486429 TGCGATTCT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
486443 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
486462 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
486481 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
486501 TGCGA
1 TGCGA
486506 AAGTAAACTA
Statistics
Matches: 91, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 21 0.23
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 47 0.52
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:486686 original size:93 final size:93
Alignment explanation
Indices: 486550--486832 Score: 523
Period size: 93 Copynumber: 3.1 Consensus size: 93
486540 ATGGATTGCA
486550 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
486614 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
486642 TTACTTTCAACCAAAAGACAAAACAAATACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
**
486707 TAGCAGAATTGGCAGCAACCGAACATTT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
486735 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
486800 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
486828 TTACT
1 TTACT
486833 AAGCAATCTA
Statistics
Matches: 183, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
92 4 0.02
93 179 0.98
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:488564 original size:20 final size:20
Alignment explanation
Indices: 488533--488596 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
488523 TTTTGGTTGA
488533 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*** *
488553 AATGACTGTCGCAACGAGATA
1 AATGAAAATCGCAACGAGA-G
488574 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
488594 AAT
1 AAT
488597 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:488599 original size:14 final size:14
Alignment explanation
Indices: 488580--488636 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
488570 GATAAATGAA
488580 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
488594 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
488613 AATCGCAACAAGAG
1 AATCGCAACGAGAG
488627 AATCGCAACG
1 AATCGCAACG
488637 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:488613 original size:33 final size:33
Alignment explanation
Indices: 488531--488653 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
488521 TCTTTTGGTT
*
488531 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
488570 GATAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 G--AAATGAAAATCGCAACGAGAGAATCGCAACGC
*
488605 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
488638 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
488654 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
33 47 0.59
35 9 0.11
38 1 0.01
39 1 0.01
40 1 0.01
41 21 0.26
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:488689 original size:14 final size:14
Alignment explanation
Indices: 488670--488726 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
488660 TTTGGTTTCG
488670 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
488684 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
488703 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
488717 CGTTGCGATT
1 CGTTGCGATT
488727 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:488702 original size:33 final size:33
Alignment explanation
Indices: 488654--488734 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
488644 AAAATCGCAA
**
488654 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
488687 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
488720 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
488735 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:488737 original size:21 final size:21
Alignment explanation
Indices: 488711--488786 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
488701 CGCGTTGCGA
488711 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
488732 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
488752 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
488773 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
488787 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:488767 original size:41 final size:41
Alignment explanation
Indices: 488710--488787 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
488700 TCGCGTTGCG
*
488710 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
488751 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
488788 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:488908 original size:33 final size:33
Alignment explanation
Indices: 488866--488936 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
488856 AATACTAACT
488866 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
488899 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
488932 TGAAA
1 TGAAA
488937 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:489341 original size:20 final size:20
Alignment explanation
Indices: 489316--489508 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
489306 CTTTAAATAT
489316 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
489336 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
489358 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
489377 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
489397 CACATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
489417 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
489437 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
489457 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
489477 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
489497 CGCGTTGCGATT
1 CGCGTTGCGATT
489509 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 129 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:493992 original size:26 final size:26
Alignment explanation
Indices: 493956--494007 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
493946 ACCATTTATA
493956 TCGAATTAGCTCTTAAAGGGTGTTTG
1 TCGAATTAGCTCTTAAAGGGTGTTTG
493982 TCGAATTAGCTCTTAAAGGGTGTTTG
1 TCGAATTAGCTCTTAAAGGGTGTTTG
494008 GTTCAAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (26 bp):
TCGAATTAGCTCTTAAAGGGTGTTTG
Found at i:494431 original size:37 final size:36
Alignment explanation
Indices: 494356--494431 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
494346 TTTTTTTATT
*
494356 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
494392 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
494429 TTT
1 TTT
494432 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:494613 original size:20 final size:20
Alignment explanation
Indices: 494577--494614 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
494567 ATCCTATTCT
**
494577 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
494597 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
494615 GTGAACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:494686 original size:21 final size:21
Alignment explanation
Indices: 494662--494708 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
494652 ATATTGTTAT
494662 GTATCGATACATTTTTATAAA
1 GTATCGATACATTTTTATAAA
494683 GTATCGATACATTTTTATAAA
1 GTATCGATACATTTTTATAAA
494704 GTATC
1 GTATC
494709 AACACTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (21 bp):
GTATCGATACATTTTTATAAA
Found at i:494909 original size:111 final size:111
Alignment explanation
Indices: 494766--495224 Score: 699
Period size: 111 Copynumber: 4.1 Consensus size: 111
494756 AATACTTATA
* * * * *
494766 ATAAAGTACCAACACTATCAACATATCCGGTAGCGCTTTATCTGTTTTGTCATTTATAG-TCCGG
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGAT-CGG
*
494830 TGTTGTCATTTTTTACCT-TATATATTGTTATGGATCAATACATTTTT
65 TTTTGTCATTTTTTACCTGT-TATATTGTTATGGATCAATACATTTTT
* * * *
494877 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACATGTTTTTTCATTTATAGATTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
*
494942 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
494988 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
*
495053 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * * * *
495099 ATAAAGTATCGACACTTTCAATATATCCGATAGCG-TTTGACCTGTTTTTTCATTTATAAACCGA
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTT-ACCTGTTTTGTCATTTATAGATCGG
* *
495163 TTTTGTCATTTTTTACCTGTTATATTGTTATGAATCAATATATTTTT
65 TTTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
495210 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
495225 AAACCGACAA
Statistics
Matches: 322, Mismatches: 23, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
110 3 0.01
111 317 0.98
112 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (111 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
TTTGTCATTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:508290 original size:22 final size:21
Alignment explanation
Indices: 508248--508287 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
508238 GAGTTTGTTT
*
508248 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
508269 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
508288 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:513221 original size:22 final size:22
Alignment explanation
Indices: 513158--513236 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
513148 GAACCCCATA
*
513158 GGGGTATCGATTCCCC-T--AG
1 GGGGAATCGATTCCCCTTAAAG
* *
513177 GGGGAATTGGTTCCCCTTCAAAG
1 GGGGAATCGATTCCCCTT-AAAG
513200 GGGGAATCGATTCCCCTTAAAG
1 GGGGAATCGATTCCCCTTAAAG
*
513222 GGGGTATCGATTCCC
1 GGGGAATCGATTCCC
513237 TCTGCCCTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.26
20 1 0.02
22 18 0.36
23 18 0.36
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGAATCGATTCCCCTTAAAG
Found at i:523801 original size:21 final size:21
Alignment explanation
Indices: 523777--523821 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
523767 TGGTTTTGAA
523777 AAAAATGAAA-GTTTAGGTACT
1 AAAAATGAAATG-TTAGGTACT
* *
523798 AAAATTGATATGTTAGGTACT
1 AAAAATGAAATGTTAGGTACT
523819 AAA
1 AAA
523822 CGTGCAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (21 bp):
AAAAATGAAATGTTAGGTACT
Found at i:527402 original size:21 final size:21
Alignment explanation
Indices: 527378--527476 Score: 66
Period size: 21 Copynumber: 5.0 Consensus size: 21
527368 ATATTTCAAT
*
527378 ATTTTATAATTATTTTAATAA
1 ATTTTATAATTCTTTTAATAA
* * *
527399 ATTTT-CAATTTTTTTCAT-A
1 ATTTTATAATTCTTTTAATAA
* *
527418 ATTTT-T-ATACTTTCAA-ATA
1 ATTTTATAATTCTTTTAATA-A
***
527437 ATTTTATAATTCTCAAAATAA
1 ATTTTATAATTCTTTTAATAA
527458 ATTTTATAA-TCTTTTAATA
1 ATTTTATAATTCTTTTAATA
527477 TTGGTATGTC
Statistics
Matches: 58, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
18 6 0.10
19 12 0.21
20 18 0.31
21 21 0.36
22 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTATAATTCTTTTAATAA
Found at i:527476 original size:20 final size:20
Alignment explanation
Indices: 527378--527476 Score: 53
Period size: 20 Copynumber: 5.0 Consensus size: 20
527368 ATATTTCAAT
*
527378 ATTTTATAATTATTTTAATAA
1 ATTTTATAA-TCTTTTAATAA
* * *
527399 ATTTTCA-ATTTTTTTCATAA
1 ATTTT-ATAATCTTTTAATAA
* *
527419 TTTTTAT-A-CTTTCAA-ATA
1 ATTTTATAATCTTTTAATA-A
***
527437 ATTTTATAATTCTCAAAATAA
1 ATTTTATAA-TCTTTTAATAA
527458 ATTTTATAATCTTTTAATA
1 ATTTTATAATCTTTTAATA
527477 TTGGTATGTC
Statistics
Matches: 56, Mismatches: 15, Indels: 15
0.65 0.17 0.17
Matches are distributed among these distances:
17 1 0.02
18 11 0.20
19 2 0.04
20 20 0.36
21 20 0.36
22 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTATAATCTTTTAATAA
Found at i:527627 original size:23 final size:23
Alignment explanation
Indices: 527601--527661 Score: 78
Period size: 18 Copynumber: 2.9 Consensus size: 23
527591 CAATGTTAGG
527601 TTAGGCATAGAATCAATGGTGGA
1 TTAGGCATAGAATCAATGGTGGA
*
527624 TTAGGC-----ATCAATGGTGGG
1 TTAGGCATAGAATCAATGGTGGA
527642 TTAGGCATAGAATCAATGGT
1 TTAGGCATAGAATCAATGGT
527662 CAAAATAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
18 17 0.53
23 15 0.47
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (23 bp):
TTAGGCATAGAATCAATGGTGGA
Found at i:535869 original size:69 final size:69
Alignment explanation
Indices: 535758--535911 Score: 272
Period size: 69 Copynumber: 2.2 Consensus size: 69
535748 GTTGTCATGC
* *
535758 AGAAAAGCTTAGGTTTATGCAAGATCAGGTTATTTCTGCAAATACGATATGCTCTCGTAAATTTC
1 AGAAAAGCTTAGGTTTATGCAAGATCAGGTTATTTCTGCAAATACGATATGCTCTCGTAAATATA
535823 GTAG
66 GTAG
*
535827 AGAAAAGCTTAGGTTTATGCAATATCAGGTTATTTCTGCAAATACGATATGCTCTCGTAAATATA
1 AGAAAAGCTTAGGTTTATGCAAGATCAGGTTATTTCTGCAAATACGATATGCTCTCGTAAATATA
535892 GTAG
66 GTAG
*
535896 AGAAAAGCTTGGGTTT
1 AGAAAAGCTTAGGTTT
535912 GCAGAAACTC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (69 bp):
AGAAAAGCTTAGGTTTATGCAAGATCAGGTTATTTCTGCAAATACGATATGCTCTCGTAAATATA
GTAG
Found at i:547801 original size:26 final size:26
Alignment explanation
Indices: 547772--547823 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
547762 AGACAAGCCT
*
547772 CAGAAAACTCAGCGATAAATGGGCCA
1 CAGAAAACTCAGCGAGAAATGGGCCA
* *
547798 CAGAAAATTCAGCGAGAGATGGGCCA
1 CAGAAAACTCAGCGAGAAATGGGCCA
547824 AACAAGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.27, T:0.12
Consensus pattern (26 bp):
CAGAAAACTCAGCGAGAAATGGGCCA
Found at i:549003 original size:4 final size:4
Alignment explanation
Indices: 548996--549024 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
548986 TTCAAACCAA
548996 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
549025 GAGATAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:551618 original size:2 final size:2
Alignment explanation
Indices: 551611--551644 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
551601 TGTATATGTG
551611 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
551645 GACAGTTCTT
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):
TA
Found at i:553101 original size:3 final size:3
Alignment explanation
Indices: 553093--553131 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
553083 AGTACAAATA
553093 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
553132 GTACTTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:553857 original size:13 final size:13
Alignment explanation
Indices: 553839--553864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
553829 CCGGTTCTCC
553839 TTTTTTTATTTTA
1 TTTTTTTATTTTA
553852 TTTTTTTATTTTA
1 TTTTTTTATTTTA
553865 AATATTGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTATTTTA
Found at i:558572 original size:21 final size:21
Alignment explanation
Indices: 558548--558591 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
558538 GTAATGAGAG
558548 ATCATAATAAGATATAAATTT
1 ATCATAATAAGATATAAATTT
558569 ATCATAATAAGATATAAATTT
1 ATCATAATAAGATATAAATTT
558590 AT
1 AT
558592 ATGGTTGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
ATCATAATAAGATATAAATTT
Found at i:560130 original size:15 final size:15
Alignment explanation
Indices: 560086--560130 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
560076 TGTCAATAAA
*
560086 ATTTAAAATAATTAT
1 ATTTAAAATATTTAT
560101 -TTTAAAATATGTTAT
1 ATTTAAAATAT-TTAT
*
560116 ATTTAAATTATTTAT
1 ATTTAAAATATTTAT
560131 GTAATATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 9 0.35
15 8 0.31
16 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTAAAATATTTAT
Found at i:569303 original size:2 final size:2
Alignment explanation
Indices: 569291--569368 Score: 128
Period size: 2 Copynumber: 41.0 Consensus size: 2
569281 TAGTTATTAT
569291 TA TA TA T- TA TA TA TA TA TA -A 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 TA TA TA
569331 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
569369 ATGAATTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 4 0.06
2 68 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:569340 original size:27 final size:27
Alignment explanation
Indices: 569291--569368 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
569281 TAGTTATTAT
569291 TATATAT-TATATATATATAATATATA
1 TATATATATATATATATATAATATATA
*
569317 TATATATATATATATATATTATATATA
1 TATATATATATATATATATAATATATA
569344 TATATATATATATATATATAATATA
1 TATATATATATATATATATAATATA
569369 ATGAATTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 7 0.14
27 42 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATATATATATATATATAATATATA
Found at i:569382 original size:27 final size:27
Alignment explanation
Indices: 569291--569383 Score: 111
Period size: 29 Copynumber: 3.4 Consensus size: 27
569281 TAGTTATTAT
569291 TATATATTATATATATATAATAT-AT-A
1 TATATA-TATATATATATAATATAATAA
*
569317 TATATATATATATATATATTATATATATA
1 TATATATATATATATATAATATA-ATA-A
569346 TATATATATATATATATAATATAATGAA
1 TATATATATATATATATAATATAAT-AA
*
569374 T-TATTTATAT
1 TATATATATAT
569384 TATGAATTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
25 15 0.25
26 6 0.10
27 10 0.17
28 4 0.07
29 24 0.41
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TATATATATATATATATAATATAATAA
Found at i:569388 original size:16 final size:16
Alignment explanation
Indices: 569364--569394 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
569354 TATATATATA
569364 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
569380 ATATTATGAATTATT
1 ATATAATGAATTATT
569395 AGATTTTGTA
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:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:571816 original size:4 final size:4
Alignment explanation
Indices: 571807--571874 Score: 61
Period size: 4 Copynumber: 16.8 Consensus size: 4
571797 CAAAAAATTA
* *
571807 AAAT AAAT AAAT AAAT AATAT AAAT AAAT ATA- AAAT -TAT AAAT -AAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
571853 AATAT AAAT AATAT ATAAT AAA
1 AA-AT AAAT AA-AT A-AAT AAA
571875 AACTATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
3 7 0.13
4 31 0.58
5 14 0.26
6 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:571831 original size:27 final size:27
Alignment explanation
Indices: 571811--571862 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
571801 AAATTAAAAT
571811 AAATAAATAAATAATATAAATAAATATA
1 AAAT-AATAAATAATATAAATAAATATA
* *
571839 AAATTATAAATAATA-ATATAAATA
1 AAATAATAAATAATATAAATAAATA
571863 ATATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 10 0.45
28 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
AAATAATAAATAATATAAATAAATATA
Found at i:571850 original size:35 final size:35
Alignment explanation
Indices: 571813--571881 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 35
571803 ATTAAAATAA
*
571813 ATAAATAAATAATATAAAT-A-A-AT-AT-AAAATT
1 ATAAAT-AATAATATAAATAATATATAATAAAAACT
571844 ATAAATAATAATATAAATAATATATAATAAAAACT
1 ATAAATAATAATATAAATAATATATAATAAAAACT
571879 ATA
1 ATA
571882 TAACATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 12 0.38
31 7 0.22
32 1 0.03
33 2 0.06
34 2 0.06
35 8 0.25
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (35 bp):
ATAAATAATAATATAAATAATATATAATAAAAACT
Found at i:571861 original size:39 final size:39
Alignment explanation
Indices: 571800--571874 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
571790 CTGTTAACAA
571800 AAAATTAAAATAAATAAATAAATAATATA-AATAAATAT
1 AAAATTAAAATAAATAAATAAATAATATATAATAAATAT
571838 AAAATTATAAAT-AATAATATAAATAATATATAATAAA
1 AAAATTA-AAATAAATAA-ATAAATAATATATAATAAA
571875 AACTATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
38 12 0.35
39 16 0.47
40 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (39 bp):
AAAATTAAAATAAATAAATAAATAATATATAATAAATAT
Found at i:574432 original size:2 final size:2
Alignment explanation
Indices: 574427--574451 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
574417 TATATGTGTG
574427 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 T
574452 TACATAAGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:575579 original size:16 final size:17
Alignment explanation
Indices: 575545--575582 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
575535 AAAATCGTCG
*
575545 ACCCGAAAGTTCTGGGT
1 ACCCGAAAATTCTGGGT
575562 ACCCGAAAATTC-GGGT
1 ACCCGAAAATTCTGGGT
575578 ACCCG
1 ACCCG
575583 GATTTGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (17 bp):
ACCCGAAAATTCTGGGT
Found at i:585208 original size:41 final size:42
Alignment explanation
Indices: 585143--585479 Score: 250
Period size: 41 Copynumber: 8.0 Consensus size: 42
585133 GAAAATGATT
* * *
585143 AAATTAGGATCTTAAATTATAAAAGT-AAAAGTAAGATTGAAA
1 AAATTAGGGTC-TCAATTATAAAAGTAAAAAGTGAGATTGAAA
* *
585185 AAATTAGGGTCTCAACTATAAAAGGTAAAAAGTGATATT-AAA
1 AAATTAGGGTCTCAATTATAAAA-GTAAAAAGTGAGATTGAAA
** * *
585227 AAA-TAGGCACCTCAATTTTAAAGGTAAAAAGTGAGATTGAAA
1 AAATTAGG-GTCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
* * * * *
585269 AAA-TATGGCCT-ATATTATATAAGCAAAAACTG-GAATTGGAAAA
1 AAATTAGGGTCTCA-ATTATAAAAGTAAAAAGTGAG-ATT-G-AAA
* *
585312 AAATCAGGGTCTCAATTATAAAGGTAAAAAGTGAGATT--AA
1 AAATTAGGGTCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
* * *
585352 AAATTAGGGGTCTCAAATATAAATA-TAGAAAGTGAGATTCAAA
1 AAATTA-GGGTCTCAATTATAAA-AGTAAAAAGTGAGATTGAAA
* * *
585395 AAATTAGAAG-CTC-AGT-T-AAAGTAAAAAGTGAGATTGAAG
1 AAATTAG-GGTCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
* * *
585434 AAATTAGAGTCATCAATTATAAATGTAAGAAAATGAGATTGAAA
1 AAATTAGGGTC-TCAATTATAAAAGTAA-AAAGTGAGATTGAAA
585478 AA
1 AA
585480 TTATATGTCT
Statistics
Matches: 234, Mismatches: 38, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
38 3 0.01
39 25 0.11
40 12 0.05
41 80 0.34
42 43 0.18
43 31 0.13
44 38 0.16
45 2 0.01
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.26
Consensus pattern (42 bp):
AAATTAGGGTCTCAATTATAAAAGTAAAAAGTGAGATTGAAA
Found at i:585912 original size:54 final size:55
Alignment explanation
Indices: 585823--585936 Score: 160
Period size: 55 Copynumber: 2.1 Consensus size: 55
585813 TTAAACTATT
*
585823 AACAATGCATACACATGTTACAATACAGATCCTCGG-TTCAAGACTTCAAGAGAG
1 AACAATGCATACACATGTTACAATACAGATCCTCGGACTCAAGACTTCAAGAGAG
* * * *
585877 AACAATGCATACACATGTTATAGATATAGAT-CTCGGACTCAGGACTTCAAGAGAT
1 AACAATGCATACACATGTTACA-ATACAGATCCTCGGACTCAAGACTTCAAGAGAG
585932 AACAA
1 AACAA
585937 AACGATTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
54 26 0.49
55 27 0.51
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (55 bp):
AACAATGCATACACATGTTACAATACAGATCCTCGGACTCAAGACTTCAAGAGAG
Found at i:592033 original size:14 final size:14
Alignment explanation
Indices: 592016--592061 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
592006 TTAATGAGAT
592016 TAATTTAATGATTA
1 TAATTTAATGATTA
592030 TAATTTAA--ATTTA
1 TAATTTAATGA-TTA
*
592043 TAATATAATGATTA
1 TAATTTAATGATTA
592057 TAATT
1 TAATT
592062 AATATAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 1 0.04
13 10 0.37
14 15 0.56
15 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (14 bp):
TAATTTAATGATTA
Found at i:592776 original size:24 final size:24
Alignment explanation
Indices: 592747--592793 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
592737 AAATTATATT
* *
592747 AAAATTTTAAGGGTGTAAAATTAC
1 AAAATTTAAAGGATGTAAAATTAC
*
592771 AAAATTTAAAGGATGTGAAATTA
1 AAAATTTAAAGGATGTAAAATTA
592794 GATTATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (24 bp):
AAAATTTAAAGGATGTAAAATTAC
Found at i:595880 original size:32 final size:33
Alignment explanation
Indices: 595844--595931 Score: 90
Period size: 37 Copynumber: 2.5 Consensus size: 33
595834 AACCTTTTTT
595844 ATATTTTTAATTTTGTAAAAAAAAT-TATATAA
1 ATATTTTTAATTTTGTAAAAAAAATATATATAA
* *
595876 ATATTATGAATTTAATTTTTTAAAGAAAATATATATAA
1 ATA-T-T---TTTAATTTTGTAAAAAAAATATATATAA
595914 ATATTTTATAA-TTTGTAA
1 ATATTTT-TAATTTTGTAA
595932 TATTATACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
32 3 0.07
33 9 0.20
34 4 0.09
36 1 0.02
37 19 0.41
38 10 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (33 bp):
ATATTTTTAATTTTGTAAAAAAAATATATATAA
Found at i:596747 original size:27 final size:28
Alignment explanation
Indices: 596706--596774 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
596696 GAATATTAAC
* *
596706 TATAATATATTTAT-ATATATATATATAT
1 TATAATTTAATTATAATATA-ATATATAT
*
596734 TATCA-TTAATTATAATATAATATATAT
1 TATAATTTAATTATAATATAATATATAT
596761 TATAATTTAATTAT
1 TATAATTTAATTAT
596775 TAAATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
TATAATTTAATTATAATATAATATATAT
Found at i:596764 original size:12 final size:12
Alignment explanation
Indices: 596706--596766 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
596696 GAATATTAAC
596706 TATAATATAT-T
1 TATAATATATAT
596717 TAT-ATATATA-
1 TATAATATATAT
596727 TAT-ATAT-TAT
1 TATAATATATAT
* *
596737 CATTAAT-TATAA
1 TA-TAATATATAT
596749 TATAATATATAT
1 TATAATATATAT
596761 TATAAT
1 TATAAT
596767 TTAATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.05
10 14 0.35
11 9 0.22
12 15 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TATAATATATAT
Found at i:596766 original size:17 final size:16
Alignment explanation
Indices: 596706--596764 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 16
596696 GAATATTAAC
596706 TATAATATAT-TTATA
1 TATAATATATATTATA
596721 TAT-ATATATA-TAT-
1 TATAATATATATTATA
*
596734 TATCAT-TA-ATTATAA
1 TATAATATATATTAT-A
596749 TATAATATATATTATA
1 TATAATATATATTATA
596765 ATTTAATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
12 1 0.03
13 8 0.22
14 11 0.31
15 8 0.22
16 3 0.08
17 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TATAATATATATTATA
Found at i:597551 original size:39 final size:39
Alignment explanation
Indices: 597462--597556 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 39
597452 CAATGCTAAT
* * *
597462 GTGAAATAAATTAAGAAATTAAGAATTTATATTGTTATG
1 GTGAAATAATTTAAGAAATTAAGAATTTAGAATGTTATG
* *
597501 GTGGTAA-AATTTAAGAAATTAGGAATTTAGAATGTTA-G
1 GT-GAAATAATTTAAGAAATTAAGAATTTAGAATGTTATG
*
597539 AGTGAAATAATTTGAGAA
1 -GTGAAATAATTTAAGAA
597557 TAATAAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
38 4 0.09
39 39 0.85
40 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (39 bp):
GTGAAATAATTTAAGAAATTAAGAATTTAGAATGTTATG
Found at i:599511 original size:144 final size:145
Alignment explanation
Indices: 599359--599770 Score: 560
Period size: 144 Copynumber: 2.8 Consensus size: 145
599349 TACTTTTCGG
* * *
599359 TTTCGGGAGGGACCGAGGTTTCCGACGACTTCTTGATGCTCACATCGACATTGCTATGCCCCGTC
1 TTTCGGGAGGGACCGAGGTTTCCAACGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGTC
* **
599424 GGCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCGAGTGATTGAAGAAAAGCCTC
66 GGCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAAACGATTGAAGAAAAGCCTC
*
599489 GACGTC-CTCGTTGT
131 GACGTCACTCGTTGA
* * * *
599503 TTTGGGGAGGGACCGAGGTTTCCAAGGACTTCTTGATGTTCACATCGACATTGTTATTCTCCGT-
1 TTTCGGGAGGGACCGAGGTTTCCAACGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGTC
* *
599567 GCGCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAAACGATTGAATAAAAGCGT
66 G-GCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAAACGATTGAAGAAAAGCCT
* *
599632 CGCCGTCGTAGTCGTTGA
130 CGACGTC--ACTCGTTGA
* * *
599650 TTTCGGGAGGAACCGAGGTTT-CAATTGACTTCTTGATGTTCCCATCGACATTGTTATGCCCCGT
1 TTTCGGGAGGGACCGAGGTTTCCAA-CGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGT
* * * * *
599714 CGGCATGCCGTCCCCGGATGACATATCACCTTGCAAGTGGGCATCCATCGATTGAAG
65 CGGCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAAACGATTGAAG
599771 TGAAGGCTCT
Statistics
Matches: 235, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
143 1 0.00
144 121 0.51
146 3 0.01
147 109 0.46
148 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (145 bp):
TTTCGGGAGGGACCGAGGTTTCCAACGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGTC
GGCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAAACGATTGAAGAAAAGCCTC
GACGTCACTCGTTGA
Found at i:599787 original size:147 final size:146
Alignment explanation
Indices: 599281--599791 Score: 558
Period size: 144 Copynumber: 3.5 Consensus size: 146
599271 TTCTCTGCCA
* * * * ** *
599281 GCATGGAGTCCCCTGG-TGACATATTACCATGCAACTCGGCACCGCTCGGTTGAAGT-AAAGCGT
1 GCATGCAGTCCCC-GGATGACATATCACCTTGCAACTCGGCATCAATCGATTGAAGTAAAAGC-T
* * * * *
599344 -T-GTCGTACT-TTTCGGTTTCGGGAGGGACCGAGGTTTCCGACGACTTCTTGATGCTCACATCG
64 CTCGTCGTAGTCGTT-GATTTCGGGAGGGACCGAGGTTTCCAACGACTTCTTGATGTTCACATCG
*
599406 ACATTGCTATGCCCCGTCG
128 ACATTGTTATGCCCCGTCG
*
599425 GCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCGAGT-GATTGAAG-AAAAGC-C
1 GCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATC-AATCGATTGAAGTAAAAGCTC
* ** * * *
599487 TCGACGTCCTCGTTGTTTTGGGGAGGGACCGAGGTTTCCAAGGACTTCTTGATGTTCACATCGAC
65 TCGTCGTAGTCGTTGATTTCGGGAGGGACCGAGGTTTCCAACGACTTCTTGATGTTCACATCGAC
* *
599552 ATTGTTATTCTCCGT-G
130 ATTGTTATGCCCCGTCG
*
599568 CGCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAAACGATTGAA-TAAAAGCGT
1 -GCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAATCGATTGAAGTAAAAGC-T
* * * *
599632 CGCCGTCGTAGTCGTTGATTTCGGGAGGAACCGAGGTTT-CAATTGACTTCTTGATGTTCCCATC
64 C-TCGTCGTAGTCGTTGATTTCGGGAGGGACCGAGGTTTCCAA-CGACTTCTTGATGTTCACATC
599696 GACATTGTTATGCCCCGTCG
127 GACATTGTTATGCCCCGTCG
* * * * * *
599716 GCATGCCGTCCCCGGATGACATATCACCTTGCAAGTGGGCATCCATCGATTGAAGTGAAGGCTCT
1 GCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAATCGATTGAAGTAAAAGCTCT
*
599781 ATGTCGTAGTC
66 -CGTCGTAGTC
599792 ATCGATTGCG
Statistics
Matches: 311, Mismatches: 40, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
143 5 0.02
144 168 0.54
145 3 0.01
146 4 0.01
147 125 0.40
148 6 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (146 bp):
GCATGCAGTCCCCGGATGACATATCACCTTGCAACTCGGCATCAATCGATTGAAGTAAAAGCTCT
CGTCGTAGTCGTTGATTTCGGGAGGGACCGAGGTTTCCAACGACTTCTTGATGTTCACATCGACA
TTGTTATGCCCCGTCG
Found at i:599815 original size:147 final size:143
Alignment explanation
Indices: 599371--599818 Score: 485
Period size: 147 Copynumber: 3.1 Consensus size: 143
599361 TCGGGAGGGA
* * * *
599371 CCGAGGTTTCCGACGACTTCTTGATGCTCACATCGACATTGCTATGCCCCGTCGGCATGCAGTCC
1 CCGAGGTTT-CAAGGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGTCGGCATGCAGTCC
* * * * *
599436 CCGGATGACATATCACCTTGCAACTCGGCATCGAGT-GATTGAAGAAAAGCCTCGACGTCCTCGT
65 CCGGATGACATATCACCTTGCAACTCGGCATC-AATCGATTGAAGTAAAGGCTCGACGTCGTAGT
* *
599500 -TG-TTTTGGGGAGGG
129 CTGATTTCGGGGA-AG
* *
599514 ACCGAGGTTTCCAAGGACTTCTTGATGTTCACATCGACATTGTTATTCTCCGT-GCGCATGCAGT
1 -CCGAGGTTT-CAAGGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGTCG-GCATGCAGT
* * *
599578 CCCCGGATGACATATCACCTTGCAACTCGGCATCAAACGATTGAA-TAAAAGCGTCGCCGTCGTA
63 CCCCGGATGACATATCACCTTGCAACTCGGCATCAATCGATTGAAGTAAAGGC-TCGACGTCGTA
599642 GTCGTTGATTTCGGGAGGAA-
127 GTC--TGATTTC-GG-GGAAG
* * *
599662 CCGAGGTTTCAATTGACTTCTTGATGTTCCCATCGACATTGTTATGCCCCGTCGGCATGCCGTCC
1 CCGAGGTTTCAA-GGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGTCGGCATGCAGTCC
* * * * * *
599727 CCGGATGACATATCACCTTGCAAGTGGGCATCCATCGATTGAAGTGAAGGCTCTATGTCGTAGTC
65 CCGGATGACATATCACCTTGCAACTCGGCATCAATCGATTGAAGTAAAGGCTCGACGTCGTAGTC
*
599792 ATCGATTGCGGGGAAG
130 -T-GATTTCGGGGAAG
599808 CCTGAGGTTTC
1 CC-GAGGTTTC
599819 CGACGACAGG
Statistics
Matches: 257, Mismatches: 32, Indels: 27
0.81 0.10 0.09
Matches are distributed among these distances:
143 6 0.02
144 106 0.41
145 4 0.02
146 8 0.03
147 119 0.46
148 9 0.04
149 2 0.01
150 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.27
Consensus pattern (143 bp):
CCGAGGTTTCAAGGACTTCTTGATGTTCACATCGACATTGTTATGCCCCGTCGGCATGCAGTCCC
CGGATGACATATCACCTTGCAACTCGGCATCAATCGATTGAAGTAAAGGCTCGACGTCGTAGTCT
GATTTCGGGGAAG
Found at i:604027 original size:11 final size:11
Alignment explanation
Indices: 604011--604091 Score: 54
Period size: 11 Copynumber: 7.2 Consensus size: 11
604001 TGTATGATCA
604011 ATGATGCATGT
1 ATGATGCATGT
*
604022 ATGATGTATGT
1 ATGATGCATGT
*
604033 ATGATACATGT
1 ATGATGCATGT
* * *
604044 ATAATACATAT
1 ATGATGCATGT
* ** *
604055 ATATATATATAT
1 AT-GATGCATGT
*
604067 ATGCATGTATGT
1 ATG-ATGCATGT
604079 ATGATGCATGT
1 ATGATGCATGT
604090 AT
1 AT
604092 ATATATATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
11 39 0.68
12 18 0.32
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (11 bp):
ATGATGCATGT
Found at i:604093 original size:35 final size:35
Alignment explanation
Indices: 604040--604110 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
604030 TGTATGATAC
*
604040 ATGTATAATACATATATATATATATATATGCATGT
1 ATGTATAATACATATATATATATATATATACATGT
* * * *
604075 ATGTATGATGCATGTATATATATATTTATACATGT
1 ATGTATAATACATATATATATATATATATACATGT
604110 A
1 A
604111 ATTGTAATCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (35 bp):
ATGTATAATACATATATATATATATATATACATGT
Found at i:607780 original size:2 final size:2
Alignment explanation
Indices: 607773--607799 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
607763 TCATACAAAC
607773 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 A
607800 AATTATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:608032 original size:28 final size:28
Alignment explanation
Indices: 607996--608066 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
607986 TTTAATAGTT
607996 TTAT-TTAAATTATTTTTAAATAATAATAA
1 TTATATTAAATTATTTTTAAA-AATAA-AA
* *
608025 -TATA-TAAAATA-TATTAAAAATAAAA
1 TTATATTAAATTATTTTTAAAAATAAAA
608050 TTATATTAAAATTATTT
1 TTATATT-AAATTATTT
608067 AGAGAATCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
25 2 0.06
26 9 0.27
27 7 0.21
28 14 0.42
29 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TTATATTAAATTATTTTTAAAAATAAAA
Found at i:608044 original size:111 final size:107
Alignment explanation
Indices: 607870--608100 Score: 367
Period size: 111 Copynumber: 2.1 Consensus size: 107
607860 GTAAGACTTA
* *
607870 AAAAATGAGTTTAATAATTTTTTACAATTATTTTTAAATAATAATATATAAATTATATTAAAAAT
1 AAAAATAAGTTTAATAATTTTTTACAATTATTTTTAAATAATAATATATAAAATATATTAAAAAT
*
607935 AAAATTTTATTAAAATTATTTAGAGAATCCAAATCACAAAAT
66 AAAATTATATTAAAATTATTTAGAGAATCCAAATCACAAAAT
*
607977 AAAAATAAGTTTAATAGTTTTATTTA-AATTATTTTTAAATAATAATAATATATAAAATATATTA
1 AAAAATAAGTTTAATA-ATTT-TTTACAATTATTTTT--A-AATAATAATATATAAAATATATTA
608041 AAAATAAAATTATATTAAAATTATTTAGAGAATCCAAATCACAAAAT
61 AAAATAAAATTATATTAAAATTATTTAGAGAATCCAAATCACAAAAT
608088 AAAAATAA-TTTAA
1 AAAAATAAGTTTAA
608101 CTTAAAAATA
Statistics
Matches: 115, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
107 15 0.13
108 13 0.11
109 4 0.03
110 6 0.05
111 77 0.67
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (107 bp):
AAAAATAAGTTTAATAATTTTTTACAATTATTTTTAAATAATAATATATAAAATATATTAAAAAT
AAAATTATATTAAAATTATTTAGAGAATCCAAATCACAAAAT
Found at i:608049 original size:16 final size:17
Alignment explanation
Indices: 608028--608060 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
608018 ATAATAATAT
608028 ATAAAA-TATATTAAAA
1 ATAAAATTATATTAAAA
608044 ATAAAATTATATTAAAA
1 ATAAAATTATATTAAAA
608061 TTATTTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAAATTATATTAAAA
Found at i:608054 original size:26 final size:27
Alignment explanation
Indices: 608011--608065 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
608001 TAAATTATTT
608011 TTAAATAATAATAATATA-TAAAATATA
1 TTAAATAATAATAATATATTAAAAT-TA
608038 TTAAA-AATAA-AATTATATTAAAATTA
1 TTAAATAATAATAA-TATATTAAAATTA
608064 TT
1 TT
608066 TAGAGAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.08
26 13 0.50
27 11 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TTAAATAATAATAATATATTAAAATTA
Found at i:608123 original size:21 final size:22
Alignment explanation
Indices: 608083--608123 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
608073 TCCAAATCAC
**
608083 AAAATAAAAATAATTTAACTTA
1 AAAATAAAAATAATAAAACTTA
608105 AAAATAAAAAT-ATAAAACT
1 AAAATAAAAATAATAAAACT
608124 CATTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATAAAAATAATAAAACTTA
Found at i:614372 original size:31 final size:31
Alignment explanation
Indices: 614336--614397 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
614326 CGACCCGTTT
* *
614336 ACCCGACCCGTTTATCCGA-CCAGTTGACCCG
1 ACCCGACCCGTTGACCCGACCCA-TTGACCCG
614367 ACCCGACCCGTTGACCCGACCCATTGACCCG
1 ACCCGACCCGTTGACCCGACCCATTGACCCG
614398 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCATTGACCCG
Found at i:614374 original size:18 final size:18
Alignment explanation
Indices: 614351--614388 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
614341 ACCCGTTTAT
614351 CCGACCAGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
*
614369 CCGACCCGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
614387 CC
1 CC
614389 ATTGACCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
CCGACCAGTTGACCCGAC
Found at i:614382 original size:8 final size:8
Alignment explanation
Indices: 614371--614435 Score: 59
Period size: 8 Copynumber: 8.5 Consensus size: 8
614361 GACCCGACCC
614371 GACCCGTT
1 GACCCGTT
614379 GACCC---
1 GACCCGTT
*
614384 GACCCATT
1 GACCCGTT
614392 GACCCGTT
1 GACCCGTT
614400 GA-CCGTT
1 GACCCGTT
*
614407 GACCTGTT
1 GACCCGTT
614415 GA-CCGTT
1 GACCCGTT
614422 GACCGGCGTT
1 GACC--CGTT
614432 GACC
1 GACC
614436 ATTGTTGACC
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
5 5 0.11
7 13 0.28
8 21 0.45
10 8 0.17
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:614388 original size:13 final size:13
Alignment explanation
Indices: 614326--614371 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
614316 GGTCATAACT
614326 CGACCCGTTTACC
1 CGACCCGTTTACC
*
614339 CGACCCGTTTATC
1 CGACCCGTTTACC
* *
614352 CGACCAGTTGACC
1 CGACCCGTTTACC
614365 CGACCCG
1 CGACCCG
614372 ACCCGTTGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.43, G:0.20, T:0.20
Consensus pattern (13 bp):
CGACCCGTTTACC
Found at i:614393 original size:13 final size:13
Alignment explanation
Indices: 614366--614397 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
614356 CAGTTGACCC
*
614366 GACCCGACCCGTT
1 GACCCGACCCATT
614379 GACCCGACCCATT
1 GACCCGACCCATT
614392 GACCCG
1 GACCCG
614398 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:614407 original size:7 final size:7
Alignment explanation
Indices: 614390--614426 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
614380 ACCCGACCCA
614390 TTGACCCG
1 TTGA-CCG
614398 TTGACCG
1 TTGACCG
614405 TTGACCTG
1 TTGACC-G
614413 TTGACCG
1 TTGACCG
614420 TTGACCG
1 TTGACCG
614427 GCGTTGACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 17 0.61
8 11 0.39
ACGTcount: A:0.14, C:0.30, G:0.27, T:0.30
Consensus pattern (7 bp):
TTGACCG
Found at i:614410 original size:15 final size:15
Alignment explanation
Indices: 614390--614435 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
614380 ACCCGACCCA
614390 TTGACCCGTTGACCG
1 TTGACCCGTTGACCG
*
614405 TTGACCTGTTGACCG
1 TTGACCCGTTGACCG
614420 TTGACCGGCGTTGACC
1 TTGACC--CGTTGACC
614436 ATTGTTGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 20 0.74
17 7 0.26
ACGTcount: A:0.13, C:0.30, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGACCCGTTGACCG
Found at i:615740 original size:18 final size:18
Alignment explanation
Indices: 615714--615748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
615704 TCGAAAGGAC
*
615714 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
615732 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
615749 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:619384 original size:31 final size:31
Alignment explanation
Indices: 619348--619409 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
619338 CGACCCGTTT
* *
619348 ACCCGACCCGTTTATCCGA-CCAGTTGACCCG
1 ACCCGACCCGTTGACCCGACCCA-TTGACCCG
619379 ACCCGACCCGTTGACCCGACCCATTGACCCG
1 ACCCGACCCGTTGACCCGACCCATTGACCCG
619410 TTGACCGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCGTTGACCCGACCCATTGACCCG
Found at i:619386 original size:18 final size:18
Alignment explanation
Indices: 619363--619400 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
619353 ACCCGTTTAT
619363 CCGACCAGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
*
619381 CCGACCCGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
619399 CC
1 CC
619401 ATTGACCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
CCGACCAGTTGACCCGAC
Found at i:619394 original size:8 final size:8
Alignment explanation
Indices: 619383--619447 Score: 59
Period size: 8 Copynumber: 8.5 Consensus size: 8
619373 GACCCGACCC
619383 GACCCGTT
1 GACCCGTT
619391 GACCC---
1 GACCCGTT
*
619396 GACCCATT
1 GACCCGTT
619404 GACCCGTT
1 GACCCGTT
619412 GA-CCGTT
1 GACCCGTT
*
619419 GACCTGTT
1 GACCCGTT
619427 GA-CCGTT
1 GACCCGTT
619434 GACCGGCGTT
1 GACC--CGTT
619444 GACC
1 GACC
619448 ATTGTTGACC
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
5 5 0.11
7 13 0.28
8 21 0.45
10 8 0.17
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:619400 original size:13 final size:13
Alignment explanation
Indices: 619335--619383 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
619325 ACCGGTCATA
619335 ACCCGACCCGTTT
1 ACCCGACCCGTTT
619348 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* * *
619361 ATCCGACCAGTTG
1 ACCCGACCCGTTT
619374 ACCCGACCCG
1 ACCCGACCCG
619384 ACCCGTTGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:619405 original size:13 final size:13
Alignment explanation
Indices: 619378--619409 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
619368 CAGTTGACCC
*
619378 GACCCGACCCGTT
1 GACCCGACCCATT
619391 GACCCGACCCATT
1 GACCCGACCCATT
619404 GACCCG
1 GACCCG
619410 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:619419 original size:7 final size:7
Alignment explanation
Indices: 619402--619438 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
619392 ACCCGACCCA
619402 TTGACCCG
1 TTGA-CCG
619410 TTGACCG
1 TTGACCG
619417 TTGACCTG
1 TTGACC-G
619425 TTGACCG
1 TTGACCG
619432 TTGACCG
1 TTGACCG
619439 GCGTTGACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 17 0.61
8 11 0.39
ACGTcount: A:0.14, C:0.30, G:0.27, T:0.30
Consensus pattern (7 bp):
TTGACCG
Found at i:619422 original size:15 final size:15
Alignment explanation
Indices: 619402--619447 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
619392 ACCCGACCCA
619402 TTGACCCGTTGACCG
1 TTGACCCGTTGACCG
*
619417 TTGACCTGTTGACCG
1 TTGACCCGTTGACCG
619432 TTGACCGGCGTTGACC
1 TTGACC--CGTTGACC
619448 ATTGTTGACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 20 0.74
17 7 0.26
ACGTcount: A:0.13, C:0.30, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGACCCGTTGACCG
Found at i:620751 original size:18 final size:18
Alignment explanation
Indices: 620725--620759 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
620715 TCGAAAGGAC
*
620725 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
620743 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
620760 CCGGATGGAA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:626855 original size:22 final size:22
Alignment explanation
Indices: 626796--626863 Score: 97
Period size: 21 Copynumber: 3.2 Consensus size: 22
626786 TTTTGTAAAT
*
626796 AAATAATTTTTTTTAA--ATTAA
1 AAATAA-TATTTTTAATTATTAA
626817 AAATAATATTTTT-ATTATTAA
1 AAATAATATTTTTAATTATTAA
626838 AAATAATATTTTTAATTATTAA
1 AAATAATATTTTTAATTATTAA
626860 AAAT
1 AAAT
626864 TAAAATTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 1 0.02
20 6 0.14
21 24 0.56
22 12 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATAATATTTTTAATTATTAA
Found at i:626873 original size:21 final size:21
Alignment explanation
Indices: 626812--626863 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 21
626802 TTTTTTTTAA
*
626812 ATTAAAAATAATATTTTTATT
1 ATTAAAAATAATATTTTAATT
626833 ATTAAAAATAATATTTTTAATT
1 ATTAAAAATAATA-TTTTAATT
626855 ATTAAAAAT
1 ATTAAAAAT
626864 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAAAAATAATATTTTAATT
Found at i:630382 original size:60 final size:61
Alignment explanation
Indices: 630283--630398 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
630273 TGATTCACCA
* * * *
630283 ACTATAGGATATTATTTTTGTTGAGTCACTCGACTATTAAAAGTTATAAAATGATCTTCTG
1 ACTATAGGATATTATTTTTATTGAGTCACCCGACTATTAAAAATTACAAAATGATCTTCTG
* * *
630344 ACTATAGGATGTTA-TTTTATTGAGTCCCCCGATTATTAAAAATTACAAAATGATC
1 ACTATAGGATATTATTTTTATTGAGTCACCCGACTATTAAAAATTACAAAATGATC
630399 ACATGACTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 35 0.73
61 13 0.27
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (61 bp):
ACTATAGGATATTATTTTTATTGAGTCACCCGACTATTAAAAATTACAAAATGATCTTCTG
Found at i:636215 original size:34 final size:36
Alignment explanation
Indices: 636172--636272 Score: 170
Period size: 34 Copynumber: 2.8 Consensus size: 36
636162 TTAGATCTGG
636172 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT-
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTC
*
636206 TAGGATTCAAACTCCTAAAAATAGGATAAAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTT-C
636243 TAGGATTCAAACTCCTAAAAATAGGATAGA
1 TAGGATTCAAACTCCTAAAAATAGGATAGA
636273 GTTATACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTC
Found at i:636595 original size:23 final size:24
Alignment explanation
Indices: 636564--636609 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
636554 GTTATTTTTT
636564 TTTTCATGTAATATT-TTTTTTACA
1 TTTTCATGT-ATATTCTTTTTTACA
*
636588 TTTT-ATGTATTTTCTTTTTTAC
1 TTTTCATGTATATTCTTTTTTAC
636610 TTTAGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTCATGTATATTCTTTTTTACA
Found at i:636632 original size:26 final size:25
Alignment explanation
Indices: 636577--636649 Score: 60
Period size: 26 Copynumber: 2.8 Consensus size: 25
636567 TCATGTAATA
* * *
636577 TTTTTTTTACATTTTATGTATTTTCT
1 TTTTTTTTAGA-TATATATATTTTCT
636603 TTTTTACTTTAG-TATATATATTTT-T
1 TTTTT--TTTAGATATATATATTTTCT
636628 ATTTTTTTTAGATTATATATAT
1 -TTTTTTTTAGA-TATATATAT
636650 AAATATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
24 5 0.13
25 1 0.03
26 29 0.74
28 4 0.10
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTTTTTAGATATATATATTTTCT
Found at i:636715 original size:6 final size:6
Alignment explanation
Indices: 636715--636825 Score: 50
Period size: 6 Copynumber: 17.7 Consensus size: 6
636705 TTTTTTATTT
* *
636715 TTTTTA TTTTATA TATATTA TTTTTA CTTTTTTA TTATTA -TTTTA TTTATT-
1 TTTTTA TTTT-TA T-TTTTA TTTTTA --TTTTTA TTTTTA TTTTTA TTT-TTA
* * * *
636766 TGTTTTA TTTCTA TATTTT- TTCTTC TTTTTC TTCTTT- TTCTTTA TTTTTA
1 T-TTTTA TTTTTA T-TTTTA TTTTTA TTTTTA TT-TTTA TT-TTTA TTTTTA
*
636816 TATTTA TTTT
1 TTTTTA TTTT
636826 ACTTACTATT
Statistics
Matches: 83, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
5 7 0.08
6 49 0.59
7 19 0.23
8 8 0.10
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:636716 original size:9 final size:9
Alignment explanation
Indices: 636699--636814 Score: 63
Period size: 9 Copynumber: 12.0 Consensus size: 9
636689 TATATATATA
*
636699 TTTACTTTT
1 TTTATTTTT
636708 TTTATTTTT
1 TTTATTTTT
636717 TTTATTTTAT
1 TTTATTTT-T
* *
636727 ATATATTATT
1 -TTTATTTTT
636737 TTTACTTTTT
1 TTTA-TTTTT
636747 TATTATTATTTT
1 T-TTA-T-TTTT
*
636759 ATTTATTTGT
1 -TTTATTTTT
*
636769 TTTA-TTTC
1 TTTATTTTT
*
636777 TATATTTTT
1 TTTATTTTT
*
636786 TCTTCTTTTT
1 T-TTATTTTT
* *
636796 CTTCTTTTT
1 TTTATTTTT
636805 CTTTATTTTT
1 -TTTATTTTT
636815 ATATTTATTT
Statistics
Matches: 82, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
8 5 0.06
9 35 0.43
10 23 0.28
11 11 0.13
12 7 0.09
13 1 0.01
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTATTTTT
Found at i:636728 original size:29 final size:28
Alignment explanation
Indices: 636695--636825 Score: 97
Period size: 29 Copynumber: 4.4 Consensus size: 28
636685 TATATATATA
636695 TATATTTACTTTTTTTATTTTTTTTATTT
1 TATATTTA-TTTTTTTATTTTTTTTATTT
*
636724 TATATATATTATTTTTACTTTTTTATTATTAT
1 TATATTTATT-TTTTTA-TTTTTT-TTATT-T
* * *
636756 TTTATTTATTTGTTTTA-TTTCTATATTT
1 TATATTTATTT-TTTTATTTTTTTTATTT
* *
636784 T-T-TCTTCTTTTTCTTCTTTTTCTTTATTTT
1 TATAT-TTATTTTT-TTATTTTT-TTTA-TTT
636814 TATATTTATTTT
1 TATATTTATTTT
636826 ACTTACTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
26 3 0.04
27 8 0.10
28 7 0.09
29 20 0.25
30 14 0.17
31 13 0.16
32 15 0.19
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.76
Consensus pattern (28 bp):
TATATTTATTTTTTTATTTTTTTTATTT
Done.