Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 2 of 214
Found at i:389015 original size:29 final size:29
Alignment explanation
Indices: 388971--389026 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
388961 TAGCTATTTG
* *
388971 AACTAATTAATTACATTGTAAAAATATTA
1 AACTAATTAATAACATTATAAAAATATTA
389000 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACATTATAAAAATAT
389027 AGAGACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTAATTAATAACATTATAAAAATATTA
Found at i:408387 original size:15 final size:17
Alignment explanation
Indices: 408366--408406 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
408356 TAATCTTTTA
408366 AAAATTATAAAAATA-T
1 AAAATTATAAAAATAGT
*
408382 -AAATTATTAAAATAGT
1 AAAATTATAAAAATAGT
408398 AAAATTATA
1 AAAATTATA
408407 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 13 0.62
16 1 0.05
17 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAGT
Found at i:430591 original size:39 final size:39
Alignment explanation
Indices: 430532--430609 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
430522 ACGTATGTCT
* *
430532 TGATTTTTTGTCAAAAATATATTTGAACACTGAAACAAA
1 TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
* *
430571 TGATCTTTTGTCAAAAATATATATGTACATTGAAACAAA
1 TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
430610 ATTATAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (39 bp):
TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
Found at i:432772 original size:3 final size:3
Alignment explanation
Indices: 432764--432796 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
432754 TTAAAACAAC
432764 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
432797 AAGACGAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:438402 original size:85 final size:86
Alignment explanation
Indices: 438235--438419 Score: 230
Period size: 85 Copynumber: 2.2 Consensus size: 86
438225 CGCTAAAGAC
* *
438235 CAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGAACCTTTAGCGACACTTTT
1 CAGGACCTTTAGCGGCACTTTTCACACAAACGCCGCTATAGATCAGAACCTTTAGCGACACTTTT
*
438300 CCCACAAACGCCGCTATAAAT
66 CCCACAAACGCCACTATAAAT
* * *
438321 CAGGACCTTTAGTGGCACTTTT-ACACAAACGCCGCTATAGATCA-AGACCTTTAGCGGCGCTTT
1 CAGGACCTTTAGCGGCACTTTTCACACAAACGCCGCTATAGATCAGA-ACCTTTAGCGACACTTT
*** * *
438384 TTTTATAAACGCCACTATAGAT
65 TCCCACAAACGCCACTATAAAT
* *
438406 CATGACTTTTAGCG
1 CAGGACCTTTAGCG
438420 ACGTTTTTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
84 1 0.01
85 63 0.75
86 20 0.24
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (86 bp):
CAGGACCTTTAGCGGCACTTTTCACACAAACGCCGCTATAGATCAGAACCTTTAGCGACACTTTT
CCCACAAACGCCACTATAAAT
Found at i:438404 original size:43 final size:43
Alignment explanation
Indices: 438219--438443 Score: 220
Period size: 43 Copynumber: 5.3 Consensus size: 43
438209 GCGCCGCCAA
* * * *
438219 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * *
438262 AAACGCCGCTATAGATC-AGAACCTTTAGCGACACTTTTCCCAC
1 AAACGCCGCTATAGATCAAG-ACCTTTAGCGGCGCTTTTTCCAC
* * * * *
438305 AAACGCCGCTATAAATCAGGACCTTTAGTGGCAC-TTTTACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
** *
438347 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTTTAT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
* * * * * ***
438390 AAACGCCACTATAGATCATGACTTTTAGCGACGTTTTTTTTGC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
438433 AAACGCCGCTA
1 AAACGCCGCTA
438444 AAAGTGCCAT
Statistics
Matches: 153, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 37 0.24
43 115 0.75
44 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTTCCAC
Found at i:443027 original size:21 final size:21
Alignment explanation
Indices: 443003--443043 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
442993 AACCCTAAAT
443003 CCCTAACTCTTAACCCCTAAC
1 CCCTAACTCTTAACCCCTAAC
*
443024 CCCTAACTCTTAATCCCTAA
1 CCCTAACTCTTAACCCCTAA
443044 ACCTTAAATC
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:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
CCCTAACTCTTAACCCCTAAC
Found at i:443280 original size:23 final size:24
Alignment explanation
Indices: 443241--443294 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
443231 TACATGAAAT
*
443241 TATTTAATATATAAATTAAAAAAA
1 TATTTAATAAATAAATTAAAAAAA
443265 TATTTAA-AAATAAATT-AAAAAA
1 TATTTAATAAATAAATTAAAAAAA
*
443287 TAATTAAT
1 TATTTAAT
443295 CTAAACCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 8 0.30
24 7 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATTTAATAAATAAATTAAAAAAA
Found at i:443359 original size:22 final size:23
Alignment explanation
Indices: 443318--443387 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 23
443308 CCTAACTTGA
* *
443318 CCCATGAACTCATAAACCCTAAAT
1 CCCAT-AACTCATAACCCCTAAAC
*
443342 CCC-TAACTCTTAACCCCTAAAC
1 CCCATAACTCATAACCCCTAAAC
443364 CCCATAAC-CACTAACCCCTAAAC
1 CCCATAACTCA-TAACCCCTAAAC
443387 C
1 C
443388 TTAAATCTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 19 0.47
23 18 0.45
24 3 0.08
ACGTcount: A:0.37, C:0.43, G:0.01, T:0.19
Consensus pattern (23 bp):
CCCATAACTCATAACCCCTAAAC
Found at i:443424 original size:14 final size:15
Alignment explanation
Indices: 443407--443440 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
443397 AACCCTTAAA
443407 CCATAATCCCT-AAT
1 CCATAATCCCTCAAT
*
443421 CCATAATCCTTCAAT
1 CCATAATCCCTCAAT
443436 CCATA
1 CCATA
443441 CTCCATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (15 bp):
CCATAATCCCTCAAT
Found at i:443719 original size:41 final size:41
Alignment explanation
Indices: 443673--443788 Score: 155
Period size: 41 Copynumber: 2.8 Consensus size: 41
443663 TAAAATGTTT
443673 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCCTA-CCA
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCC-AGCCA
* * *
443714 TTAGCGGCGC-TTATCCAAAAACGCCGCTAAAGACCCAGGCA
1 TTAGCGGCGCTTTAT-AAAAAACGCCGCTAAAGCCCCAGCCA
* *
443755 TTAGCGGCGCTTTTTGAAAAACGCCGCTAAAGCC
1 TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCC
443789 ACGAAATGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
40 5 0.08
41 58 0.88
42 3 0.05
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTTATAAAAAACGCCGCTAAAGCCCCAGCCA
Found at i:443868 original size:39 final size:39
Alignment explanation
Indices: 443824--443902 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
443814 TGGGCTAAGG
* * *
443824 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCA
443864 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
443903 ATCTTTAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 19 0.53
40 17 0.47
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCATTTTTTTAAAAACGCCACTAATGCTCA
Found at i:443874 original size:40 final size:40
Alignment explanation
Indices: 443824--443961 Score: 136
Period size: 40 Copynumber: 3.5 Consensus size: 40
443814 TGGGCTAAGG
*
443824 TTTTTTGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
* *
443864 TTTTTAGCGGCATTTTTTT-AAAAACGCCACTAATGCTCAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTC-A
* * * *** * *
443904 TCTTTAGTGGCGATTTCCAG-AAAGCGCCGCTAATGCTTAA
1 TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGC-TCA
*
443944 TTTTTACCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
443962 GTCCAAACGC
Statistics
Matches: 76, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 18 0.24
40 57 0.75
41 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTTGAAAAACGCCGCTAATGCTCA
Found at i:448107 original size:4 final size:4
Alignment explanation
Indices: 448098--448123 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
448088 ACTTCCACTT
448098 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
448124 ATCGTCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:463663 original size:22 final size:22
Alignment explanation
Indices: 463637--463686 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
463627 GACTCACATA
463637 CTTTTCTTCT-AATCCGCAATAT
1 CTTTTCTTCTAAATCCGCAA-AT
**
463659 CTTTT-TTCTAAATCTTCAAAT
1 CTTTTCTTCTAAATCCGCAAAT
463680 CTTTTCT
1 CTTTTCT
463687 GACTGACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (22 bp):
CTTTTCTTCTAAATCCGCAAAT
Found at i:472664 original size:16 final size:16
Alignment explanation
Indices: 472643--472678 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
472633 TAACTCAGGA
472643 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
472659 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
472675 GCTG
1 GCTG
472679 TGATTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.19
Consensus pattern (16 bp):
GCTGCAGGAGTACATG
Found at i:473521 original size:120 final size:120
Alignment explanation
Indices: 473395--473684 Score: 485
Period size: 120 Copynumber: 2.4 Consensus size: 120
473385 AATTATTTTA
* * *
473395 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTT-TCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATATTAATTATTT-AAATTTATATTT
* *
473459 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
473515 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAAT-ATTAATTATTTAAATTTATATTT
473579 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
473635 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATATTAATTAT
473685 GTTTAAATAT
Statistics
Matches: 160, Mismatches: 7, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
119 7 0.04
120 150 0.94
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATATTAATTATTTAAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:473577 original size:15 final size:14
Alignment explanation
Indices: 473525--473580 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 14
473515 AATTTTATTA
473525 AATTATA-TATTTT
1 AATTATATTATTTT
*
473538 AATTATAATATATTT
1 AATTATATTAT-TTT
*
473553 AATAATTATTATTTT
1 AATTA-TATTATTTT
473568 AATT-TA-TATTTT
1 AATTATATTATTTT
473580 A
1 A
473581 CAGTATCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.19
13 9 0.24
14 3 0.08
15 13 0.35
16 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATATTATTTT
Found at i:473641 original size:61 final size:61
Alignment explanation
Indices: 473456--473642 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
473446 TCAAATTTTC
*
473456 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGACTATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
* * * * * * *
473517 TTTTATTA-AATTATATATT-TTAATT-A-T-AATAT-ATTTAATAATTATT-ATT-TTAATTTA
1 TTTTA-TAGTATCATATATTATGATTTGAGTAAAT-TCATATAAGAA-TATTAATTATTAA--GA
473574 TA
61 -A
*
473576 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
473637 TTTTAT
1 TTTTAT
473643 TAAATTATAT
Statistics
Matches: 95, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
56 4 0.04
57 12 0.13
58 8 0.08
59 16 0.17
60 8 0.08
61 21 0.22
62 9 0.09
63 13 0.14
64 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (61 bp):
TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
Found at i:473670 original size:16 final size:16
Alignment explanation
Indices: 473649--473690 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
473639 TTATTAAATT
*
473649 ATATATTTTAATTATA
1 ATATATTTTAATAATA
473665 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
473680 AT-TATGTTTAA
1 ATATAT-TTTAA
473691 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:473675 original size:15 final size:15
Alignment explanation
Indices: 473640--473681 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
473630 TTAAGAATTT
*
473640 TATTAAATTAT-ATA
1 TATTTAATTATAATA
473654 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
473668 TATTTAATAATAAT
1 TATTTAATTATAAT
473682 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:473784 original size:147 final size:149
Alignment explanation
Indices: 473624--473898 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
473614 ATAAGAATAT
* *
473624 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
473689 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
473752 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
473771 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
473836 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
473899 CAATAATCAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 90 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:473811 original size:18 final size:17
Alignment explanation
Indices: 473783--473817 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
473773 ATTATTAAGA
*
473783 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
473800 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
473818 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:474028 original size:44 final size:45
Alignment explanation
Indices: 473979--474073 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
473969 TTACACCTCT
* * *
473979 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
** *
474023 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
474068 ATTACA
1 ATTACA
474074 CCTCTAATCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACATCTATTCC
Found at i:474073 original size:16 final size:16
Alignment explanation
Indices: 474054--474105 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
474044 GATTTGCTAT
* * *
474054 TACACATCTATTCCAT
1 TACACCTCTAATCCAA
474070 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
474086 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
474102 TACA
1 TACA
474106 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:474467 original size:12 final size:12
Alignment explanation
Indices: 474437--474469 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
474427 CAAGCACATC
*
474437 TCTAAAAATTTT
1 TCTAGAAATTTT
474449 TCT-GAAATTTT
1 TCTAGAAATTTT
474460 TCTAGAAATT
1 TCTAGAAATT
474470 CTAATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (12 bp):
TCTAGAAATTTT
Found at i:476505 original size:17 final size:17
Alignment explanation
Indices: 476475--476519 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
476465 CTGATATAAT
* *
476475 AAATATATTTATTTTTA
1 AAATATTTTTAATTTTA
476492 AAAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
476508 AAATATTTTTAA
1 AAATATTTTTAA
476520 AATACTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:478528 original size:15 final size:15
Alignment explanation
Indices: 478508--478559 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
478498 AAAAATAAAT
478508 TTTAATAATTTATTG
1 TTTAATAATTTATTG
* *
478523 TTTAAT-ATTAAAT-
1 TTTAATAATTTATTG
478536 TTTAATAATTTATTG
1 TTTAATAATTTATTG
478551 TTTAATAAT
1 TTTAATAAT
478560 AAATGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.19
14 10 0.32
15 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TTTAATAATTTATTG
Found at i:478534 original size:28 final size:28
Alignment explanation
Indices: 478501--478572 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
478491 ATTATTAAAA
478501 AATAAATTTTAATAATTTATTGTTTAAT
1 AATAAATTTTAATAATTTATTGTTTAAT
*
478529 ATTAAATTTTAATAATTTATTGTTTAAT
1 AATAAATTTTAATAATTTATTGTTTAAT
*
478557 AATAAATGTTAA-AATT
1 AATAAATTTTAATAATT
478573 CATGTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 4 0.10
28 37 0.90
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
AATAAATTTTAATAATTTATTGTTTAAT
Found at i:478579 original size:12 final size:12
Alignment explanation
Indices: 478562--478586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
478552 TTAATAATAA
478562 ATGTTAAAATTC
1 ATGTTAAAATTC
478574 ATGTTAAAATTC
1 ATGTTAAAATTC
478586 A
1 A
478587 AGCCATAACT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTAAAATTC
Found at i:484040 original size:23 final size:23
Alignment explanation
Indices: 483995--484040 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
483985 TGTTAAAATT
* *
483995 GTATCGTGAAAATTGTATTTTTA
1 GTATCGTGAAAATTATATATTTA
484018 GTATCGTGAAAA-TATATAATTTA
1 GTATCGTGAAAATTATAT-ATTTA
484041 ATTCCGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (23 bp):
GTATCGTGAAAATTATATATTTA
Found at i:489601 original size:13 final size:13
Alignment explanation
Indices: 489583--489609 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
489573 AGCTATCCCA
489583 AACTCTCATGCTT
1 AACTCTCATGCTT
489596 AACTCTCATGCTT
1 AACTCTCATGCTT
489609 A
1 A
489610 TAACATGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (13 bp):
AACTCTCATGCTT
Found at i:492912 original size:20 final size:17
Alignment explanation
Indices: 492878--492932 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 17
492868 ATATAAAAAA
492878 TAAATTTTAAAAAATTAT
1 TAAATTTTAAAAAATT-T
492896 TAAATTTTAATAAAAATTT
1 TAAATTTT-A-AAAAATTT
492915 TCAAATTTATTAAAAAAT
1 T-AAA-TT-TTAAAAAAT
492933 AGAATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 8 0.25
19 3 0.09
20 16 0.50
21 3 0.09
22 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTTAAAAAATTT
Found at i:492930 original size:19 final size:20
Alignment explanation
Indices: 492878--492922 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
492868 ATATAAAAAA
492878 TAAATTTT-A-AAAAATTAT
1 TAAATTTTAATAAAAATTAT
492896 TAAATTTTAATAAAAATT-T
1 TAAATTTTAATAAAAATTAT
492915 TCAAATTT
1 T-AAATTT
492923 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 3 0.12
20 13 0.54
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAATTTTAATAAAAATTAT
Found at i:493171 original size:10 final size:9
Alignment explanation
Indices: 493154--493238 Score: 54
Period size: 8 Copynumber: 9.6 Consensus size: 9
493144 ACTTTATAAA
493154 ATTTTATAT
1 ATTTTATAT
*
493163 -TTCTATAT
1 ATTTTATAT
493171 ATTTTATA-
1 ATTTTATAT
493179 ATTTTATACT
1 ATTTTATA-T
*
493189 ATTTTAATAAA
1 ATTTT-AT-AT
* * *
493200 AGTTTACAA
1 ATTTTATAT
493209 ATTTTATAT
1 ATTTTATAT
493218 -TTTTATGAT
1 ATTTTAT-AT
493227 -TTTTATAT
1 ATTTTATAT
493235 -TTTT
1 ATTTT
493239 TTAACTGTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
8 27 0.44
9 22 0.35
10 6 0.10
11 6 0.10
12 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTATAT
Found at i:493176 original size:17 final size:18
Alignment explanation
Indices: 493154--493194 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
493144 ACTTTATAAA
493154 ATTTTAT-ATTTCTATA-T
1 ATTTTATAATTT-TATACT
493171 ATTTTATAATTTTATACT
1 ATTTTATAATTTTATACT
493189 ATTTTA
1 ATTTTA
493195 ATAAAAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTATAATTTTATACT
Found at i:493199 original size:46 final size:44
Alignment explanation
Indices: 493098--493237 Score: 117
Period size: 46 Copynumber: 3.1 Consensus size: 44
493088 TTTTATAAAT
* * * *
493098 TATTTTATGAAA-TTTATATTTCTTTACATTGTATAATTTTCTTAC
1 TATTTTATAAAATTTTATATTTCTATATATTTTATAA-TTT-TTAC
* *
493143 GACTTTATAAAATTTTATATTTCTATATATTTTATAATTTTATAC
1 TATTTTATAAAATTTTATATTTCTATATATTTTATAATTTT-TAC
* * *
493188 TATTTTAATAAAAGTTTACAAATTT-TATAT-TTTTATGATTTTTA-
1 TATTTT-ATAAAA-TTT-TATATTTCTATATATTTTATAATTTTTAC
493232 TATTTT
1 TATTTT
493238 TTTAACTGTT
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
44 7 0.09
45 21 0.27
46 38 0.48
47 8 0.10
48 5 0.06
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.58
Consensus pattern (44 bp):
TATTTTATAAAATTTTATATTTCTATATATTTTATAATTTTTAC
Found at i:493554 original size:92 final size:95
Alignment explanation
Indices: 493362--493566 Score: 255
Period size: 92 Copynumber: 2.2 Consensus size: 95
493352 ATTTCTTTTT
*
493362 CTTTTTTTTTGAAAAAGTTTGAAGGTCTTTTTTTATGCATTTTGAAAGTTCAAGTACCTAAATGA
1 CTTTTTTTTTGAAAAAGTTTGAAGGTCTTTTTTTATGCATTTTGAAAGTTCAAGTACCAAAATGA
* * * * * *
493427 GTGCAAAAAAAGAGAGTAGGGGTTTAATTG
66 GTGCAAAAAAAGAAAGCAGAGGCTTAAATA
*
493457 C-TTTTTTTT-AAAAAGTTTG-A-GTGCTTTTTTTATGCATTTTGAAAGTTTAAGTACCAAAATG
1 CTTTTTTTTTGAAAAAGTTTGAAGGT-CTTTTTTTATGCATTTTGAAAGTTCAAGTACCAAAATG
493518 AGTG-AAAAAAA-AAAGCAGAGGCTTAAATA
65 AGTGCAAAAAAAGAAAGCAGAGGCTTAAATA
* *
493547 C--ATTTTTTGAAAAAATTTGA
1 CTTTTTTTTTGAAAAAGTTTGA
493567 GGGCTTCTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
89 6 0.06
90 22 0.23
91 9 0.09
92 41 0.42
93 10 0.10
94 8 0.08
95 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (95 bp):
CTTTTTTTTTGAAAAAGTTTGAAGGTCTTTTTTTATGCATTTTGAAAGTTCAAGTACCAAAATGA
GTGCAAAAAAAGAAAGCAGAGGCTTAAATA
Found at i:494682 original size:3 final size:3
Alignment explanation
Indices: 494674--494711 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
494664 AATTAAGGAA
494674 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
494712 GATTTCCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:506968 original size:17 final size:18
Alignment explanation
Indices: 506938--506971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
506928 CCTAATATTG
506938 TTATATTAATAATATTTT
1 TTATATTAATAATATTTT
*
506956 TTATTTTAA-AATATTT
1 TTATATTAATAATATTT
506972 AAAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTAATAATATTTT
Found at i:510831 original size:23 final size:25
Alignment explanation
Indices: 510803--510850 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
510793 AATTTGGTAA
510803 TTTTTT-TCATATTGA-CTCCTAAAT
1 TTTTTTATCATATTGATC-CCTAAAT
510827 TTTTTTATCATATTGATCCCTAAA
1 TTTTTTATCATATTGATCCCTAAA
510851 GTTGACATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 15 0.68
26 1 0.05
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (25 bp):
TTTTTTATCATATTGATCCCTAAAT
Found at i:511036 original size:20 final size:19
Alignment explanation
Indices: 510983--511036 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
510973 TAATCATTTT
*
510983 TTAAAAAATTTAACAAAAAC
1 TTAAAAAATATAA-AAAAAC
* *
511003 TTAAAAATTA-AAAAAGAAG
1 TTAAAAAATATAAAAA-AAC
511022 TTAAAAAATATAAAA
1 TTAAAAAATATAAAA
511037 GTATATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.11
19 13 0.46
20 12 0.43
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (19 bp):
TTAAAAAATATAAAAAAAC
Found at i:511120 original size:21 final size:22
Alignment explanation
Indices: 511079--511120 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
511069 AATTGAAAAT
*
511079 AAATAAATTAAATATGTTTAAA
1 AAATAAATTAAATATGGTTAAA
*
511101 AAATAAA-TAAATTTGGTTAA
1 AAATAAATTAAATATGGTTAA
511121 CTTTTTAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATAAATTAAATATGGTTAAA
Found at i:511756 original size:35 final size:35
Alignment explanation
Indices: 511717--511788 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
511707 TATATTAAGC
511717 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
1 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
511752 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
1 ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
511787 AT
1 AT
511789 ATGCGTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (35 bp):
ATTAAAAAAACTAATGGTGTTCACCATAGAAACCG
Found at i:520224 original size:16 final size:15
Alignment explanation
Indices: 520203--520234 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
520193 TAATATTATT
520203 TAATATTAAATATAAA
1 TAATATTAAAT-TAAA
520219 TAATATTAAATTAAA
1 TAATATTAAATTAAA
520234 T
1 T
520235 TTAATACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATATTAAATTAAA
Found at i:520240 original size:26 final size:26
Alignment explanation
Indices: 520190--520240 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
520180 AACTATTCAA
*
520190 AAATAATATTATTTAATATTAAATAT
1 AAATAATATTAATTAATATTAAATAT
*
520216 AAATAATATTAAATTAA-ATTTAATA
1 AAATAATATT-AATTAATATTAAATA
520241 CTTATCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATAATATTAATTAATATTAAATAT
Found at i:524135 original size:24 final size:27
Alignment explanation
Indices: 524108--524173 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
524098 AAATAAAAAA
*
524108 TTACCAAAATGT-TATAA-CTTTTT-T
1 TTACCAAAATATATATAATCTTTTTAT
* *
524132 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATATATATAATCTTTTTAT
524159 TTACCAAAATATATA
1 TTACCAAAATATATA
524174 AAAAAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.29
25 5 0.14
26 5 0.14
27 15 0.43
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (27 bp):
TTACCAAAATATATATAATCTTTTTAT
Found at i:524174 original size:25 final size:23
Alignment explanation
Indices: 524108--524174 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 23
524098 AAATAAAAAA
*
524108 TTACCAAAATGTTATAACTTTTTT
1 TTACCAAAAT-ATATAACTTTTTT
*
524132 TTACCAAAAAATATATAATTTTTTTAT
1 TTACC--AAAATATATAA-CTTTTT-T
524159 TTACCAAAATATATAA
1 TTACCAAAATATATAA
524175 AAAAGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
24 5 0.14
25 16 0.43
26 10 0.27
27 6 0.16
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.45
Consensus pattern (23 bp):
TTACCAAAATATATAACTTTTTT
Found at i:524255 original size:27 final size:27
Alignment explanation
Indices: 524214--524267 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
524204 AACTCCCTGG
*
524214 GTGGAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAACCAGGTTGGCGGCACCA
524241 GTGGAGGGAACCAGGTTGGCGGCACCA
1 GTGGAGGGAACCAGGTTGGCGGCACCA
524268 CCCTTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.46, T:0.11
Consensus pattern (27 bp):
GTGGAGGGAACCAGGTTGGCGGCACCA
Found at i:524347 original size:10 final size:10
Alignment explanation
Indices: 524316--524387 Score: 63
Period size: 10 Copynumber: 6.6 Consensus size: 10
524306 ATGAGAGGGG
*
524316 AAGAAGAAGA
1 AAGAAAAAGA
524326 AAGAAAGGAAGA
1 AAGAAA--AAGA
524338 AAGAAAAAGA
1 AAGAAAAAGA
*
524348 AGGAAAAAGA
1 AAGAAAAAGA
524358 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
524372 AAGAAAAAGA
1 AAGAAAAAGA
*
524382 AGGAAA
1 AAGAAA
524388 GAAAAGGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 29 0.56
11 2 0.04
12 12 0.23
13 2 0.04
14 7 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:524356 original size:28 final size:30
Alignment explanation
Indices: 524316--524391 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 30
524306 ATGAGAGGGG
524316 AAGAAGAAGAAAGAAAGGA-A-GAAAGAAA
1 AAGAAGAAGAAAGAAAGGAGAGGAAAGAAA
524344 AAGAAGGAA-AAAGAAAGGAGAGGAAAGAAA
1 AAGAA-GAAGAAAGAAAGGAGAGGAAAGAAA
*
524374 GAAAAAGAAGGAAAGAAA
1 -AAGAAGAA-GAAAGAAA
524392 AGGAAAGGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 15 0.37
29 4 0.10
30 11 0.27
31 4 0.10
32 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (30 bp):
AAGAAGAAGAAAGAAAGGAGAGGAAAGAAA
Found at i:524358 original size:38 final size:38
Alignment explanation
Indices: 524316--524465 Score: 117
Period size: 38 Copynumber: 4.1 Consensus size: 38
524306 ATGAGAGGGG
*
524316 AAGAAGAAGAAAGAAAGG-AAGAAAGAAAAAGAAGGAAA
1 AAGAA-AAGAAAGAGAGGAAAGAAAGAAAAAGAAGGAAA
524354 AAG-AAAG---GAGAGGAAAGAAAGAAAAAGAAGG--A
1 AAGAAAAGAAAGAGAGGAAAGAAAGAAAAAGAAGGAAA
* *
524386 AAGAAAAGGAAAGGGGAGGAAAGAAAGAAAAATAAGG--A
1 AAGAAAA-GAAA-GAGAGGAAAGAAAGAAAAAGAAGGAAA
* * *
524424 AAGAAAATGAAATGAGA--AGAGAAA-AAAAAGAAAGAAG
1 AAGAAAA-GAAA-GAGAGGAAAGAAAGAAAAAGAAGGAAA
524461 AAGAA
1 AAGAA
524466 GAGGGAAGGA
Statistics
Matches: 93, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
32 4 0.04
33 8 0.09
34 18 0.19
35 8 0.09
36 9 0.10
37 6 0.06
38 40 0.43
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (38 bp):
AAGAAAAGAAAGAGAGGAAAGAAAGAAAAAGAAGGAAA
Found at i:524394 original size:10 final size:10
Alignment explanation
Indices: 524336--524459 Score: 64
Period size: 10 Copynumber: 12.7 Consensus size: 10
524326 AAGAAAGGAA
*
524336 GAAAGAAAAA
1 GAAAGAAAAG
* *
524346 GAAGGAAAAA
1 GAAAGAAAAG
* *
524356 GAAAGGAGAG
1 GAAAGAAAAG
524366 GAAAG-AAA-
1 GAAAGAAAAG
524374 GAAA-AAGAAG
1 GAAAGAA-AAG
524384 GAAAGAAAAG
1 GAAAGAAAAG
***
524394 GAAAGGGGAG
1 GAAAGAAAAG
524404 GAAAG-AAA-
1 GAAAGAAAAG
524412 GAAA-AATAAG
1 GAAAGAA-AAG
*
524422 GAAAGAAAAT
1 GAAAGAAAAG
*
524432 GAAATGAGAAG
1 GAAA-GAAAAG
*
524443 AGAAA-AAAAA
1 -GAAAGAAAAG
524453 GAAAGAA
1 GAAAGAA
524460 GAAGAAGAGG
Statistics
Matches: 87, Mismatches: 16, Indels: 22
0.70 0.13 0.18
Matches are distributed among these distances:
8 10 0.11
9 11 0.13
10 54 0.62
11 8 0.09
12 4 0.05
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:524395 original size:28 final size:28
Alignment explanation
Indices: 524319--524398 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
524309 AGAGGGGAAG
524319 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
524344 AAGAAGGAAAAAGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG--AAAG-AA--A-AGGAAAGAAAGAAA
524378 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
524399 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
28 11 0.24
29 1 0.02
30 1 0.02
31 2 0.04
32 5 0.11
33 3 0.07
34 17 0.37
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:524436 original size:18 final size:18
Alignment explanation
Indices: 524330--524429 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
524320 AGAAGAAAGA
*
524330 AAGG-AAGAAAGAAAAAG
1 AAGGAAAGAAAGAAAAAT
*
524347 AAGG-AA-AAAGAAAGGA-
1 AAGGAAAGAAAGAAA-AAT
* *
524363 GAGGAAAGAAAGAAAAAG
1 AAGGAAAGAAAGAAAAAT
***
524381 AAGGAAAGAAAAGGAAAGGG
1 AAGGAAAG-AAA-GAAAAAT
*
524401 GAGGAAAGAAAGAAAAAT
1 AAGGAAAGAAAGAAAAAT
524419 AAGGAAAGAAA
1 AAGGAAAGAAA
524430 ATGAAATGAG
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
16 10 0.15
17 10 0.15
18 28 0.42
19 6 0.09
20 12 0.18
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (18 bp):
AAGGAAAGAAAGAAAAAT
Found at i:524456 original size:21 final size:22
Alignment explanation
Indices: 524315--524464 Score: 67
Period size: 24 Copynumber: 6.4 Consensus size: 22
524305 AATGAGAGGG
524315 GAAGAAGAAGAAAGAAAGGAAGAAA
1 GAAGAAG-AGAAAGAAA--AAGAAA
*
524340 GAA-AA-AGAAGGAAAAAGAAA
1 GAAGAAGAGAAAGAAAAAGAAA
*
524360 GGAGAGGAA-AGAAAGAAAAAGAAG
1 -GA-A-GAAGAGAAAGAAAAAGAAA
* *
524384 GAAAGAAAAGGAAAGGGGAGGAAAGAAA
1 G-AAGAAGA-GAAA---GA-AAAAGAAA
* * *
524412 GAAAAATAAGGAAAGAAAATGAAA
1 GAAGAA-GA-GAAAGAAAAAGAAA
524436 TG-AGAAGAGAAA-AAAAAGAAA
1 -GAAGAAGAGAAAGAAAAAGAAA
524457 GAAGAAGA
1 GAAGAAGA
524465 AGAGGGAAGG
Statistics
Matches: 100, Mismatches: 11, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
20 7 0.07
21 16 0.16
22 16 0.16
23 4 0.04
24 31 0.31
25 6 0.06
27 6 0.06
28 14 0.14
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (22 bp):
GAAGAAGAGAAAGAAAAAGAAA
Found at i:525211 original size:13 final size:13
Alignment explanation
Indices: 525193--525218 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
525183 TTATGGGTTT
525193 TATAAAAAAATAA
1 TATAAAAAAATAA
525206 TATAAAAAAATAA
1 TATAAAAAAATAA
525219 AAAATTACCA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:525260 original size:27 final size:27
Alignment explanation
Indices: 525223--525290 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 27
525213 AAATAAAAAA
525223 TTACCAAAATAT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTAT
525250 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
525277 TTACCAAAATATAT
1 TTACCAAAATATAT
525291 CAAAAAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:525324 original size:17 final size:17
Alignment explanation
Indices: 525292--525323 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
525282 AAAATATATC
525292 AAAAAAAAGTAAAAAAT
1 AAAAAAAAGTAAAAAAT
525309 AAAAAAAA-TAAAAAA
1 AAAAAAAAGTAAAAAA
525324 AAGGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAAAAAGTAAAAAAT
Found at i:526656 original size:17 final size:17
Alignment explanation
Indices: 526634--526670 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
526624 ATGGGGTAAG
526634 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
526651 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
526668 ATG
1 ATG
526671 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:527674 original size:15 final size:14
Alignment explanation
Indices: 527634--527662 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
527624 TTTTTGTATC
527634 AATTTAATTATTCT
1 AATTTAATTATTCT
527648 AATTTAATTATTCT
1 AATTTAATTATTCT
527662 A
1 A
527663 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:530067 original size:18 final size:18
Alignment explanation
Indices: 530041--530078 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
530031 ATCCCAATGA
* *
530041 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
530059 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
530077 TC
1 TC
530079 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:530085 original size:18 final size:18
Alignment explanation
Indices: 530044--530085 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
530034 CCAATGATCG
* *
530044 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
530062 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
530080 CCACCA
1 CCACCA
530086 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:530754 original size:39 final size:38
Alignment explanation
Indices: 530703--530779 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
530693 AATAACTAAC
* *
530703 ACTAATAATATTAATAATTTTA-TATACAAAATAATACTA
1 ACTAATAATATTAATAA-CTAACTATA-AAAATAATACTA
530742 ACTAA-AATTATTAATAACTAACTATAAAAATAATACTA
1 ACTAATAA-TATTAATAACTAACTATAAAAATAATACTA
530780 GTTTTTTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 16 0.47
39 18 0.53
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (38 bp):
ACTAATAATATTAATAACTAACTATAAAAATAATACTA
Found at i:531155 original size:27 final size:27
Alignment explanation
Indices: 531114--531219 Score: 86
Period size: 27 Copynumber: 3.9 Consensus size: 27
531104 AACACGAGTA
* ** **
531114 GTGCCGCCAATCTGGTTGGCAGGACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
*
531141 GTGCCGCCAACCTGGTTCCCTCCACTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
* *****
531168 GTGCCGCCAACCTGCTTCCCTTGTTTG
1 GTGCCGCCAACCTGGTTCCCACCACTG
* *
531195 GTGCCGCCAACCTGCTTCCCTCCAC
1 GTGCCGCCAACCTGGTTCCCACCAC
531220 CCAGGGAGTT
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.11, C:0.40, G:0.25, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAACCTGGTTCCCACCACTG
Found at i:531309 original size:24 final size:25
Alignment explanation
Indices: 531280--531329 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
531270 TTTGTTTTTT
*
531280 TTATATA-TTTTGGTAAATAAAAAA
1 TTATATATTTTTGATAAATAAAAAA
531304 TTATATATTTTTTGATAAATAAAAAA
1 TTATATA-TTTTTGATAAATAAAAAA
531330 AAGTTATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
26 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (25 bp):
TTATATATTTTTGATAAATAAAAAA
Found at i:534465 original size:97 final size:97
Alignment explanation
Indices: 534299--534493 Score: 381
Period size: 97 Copynumber: 2.0 Consensus size: 97
534289 CTGGTCTTCT
534299 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
1 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
534364 TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
66 TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
534396 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
1 TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
*
534461 TGGTTGTTGAGAGGGGCAGTCTGCATCATCGA
66 TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
534493 T
1 T
534494 TGAATACATG
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (97 bp):
TGGGGTCTTACGATGGCCTACTCCAATCACATCTGAGGGAGTAATTTTTTTCATTGGCTAACATC
TGGTTGTTGAGAGGGGCAGTCTACATCATCGA
Found at i:537876 original size:34 final size:35
Alignment explanation
Indices: 537838--537904 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
537828 CAGTAAAATA
*
537838 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
537872 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
537905 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:537878 original size:20 final size:20
Alignment explanation
Indices: 537853--537892 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
537843 CGTAAAATGA
*
537853 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
537873 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
537893 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:537908 original size:14 final size:15
Alignment explanation
Indices: 537832--537908 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
537822 GATTCCCAGT
* *
537832 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
537846 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
537860 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
537880 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
537895 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
537909 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:542426 original size:43 final size:43
Alignment explanation
Indices: 542365--542450 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
542355 ACGCATGTCG
*
542365 TTAGTGAAACTCCCATGGCGAAACCTAGGGTTGAAGAGGTCAC
1 TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
542408 TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
1 TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
542451 GTGGGAGTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (43 bp):
TTAGTGAAACTCCCATGGCGAAACCTAGCGTTGAAGAGGTCAC
Found at i:544460 original size:21 final size:22
Alignment explanation
Indices: 544419--544460 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
544409 TAAATATTAG
*
544419 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
544441 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
544461 ATCTACAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:549563 original size:15 final size:15
Alignment explanation
Indices: 549539--549572 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
549529 AAAAAATTTT
549539 ATATACATATATTAA
1 ATATACATATATTAA
* *
549554 ATATATATATTTTAA
1 ATATACATATATTAA
549569 ATAT
1 ATAT
549573 TGATAAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATACATATATTAA
Found at i:556206 original size:19 final size:20
Alignment explanation
Indices: 556166--556212 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
556156 GTATGTAATG
* *
556166 AAATTT-ATAACATATTTGA
1 AAATTTAATAACATAATTAA
556185 AAATTTAATAA-ATAATTAA
1 AAATTTAATAACATAATTAA
556204 AAATATTAA
1 AAAT-TTAA
556213 AATTACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATTTAATAACATAATTAA
Found at i:556358 original size:16 final size:15
Alignment explanation
Indices: 556332--556362 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
556322 AAATTTATTC
556332 AAAATATTAAAAATT
1 AAAATATTAAAAATT
556347 AAAATAATTAAAAATT
1 AAAAT-ATTAAAAATT
556363 TTAGTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATATTAAAAATT
Found at i:557275 original size:13 final size:13
Alignment explanation
Indices: 557257--557282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
557247 AGAAGTGTAA
557257 AATTTACATTCAT
1 AATTTACATTCAT
557270 AATTTACATTCAT
1 AATTTACATTCAT
557283 CTATGAAGAA
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:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTACATTCAT
Found at i:559204 original size:19 final size:19
Alignment explanation
Indices: 559180--559238 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
559170 TATGTGTTAT
559180 TTTTAAACACAAATATGAG
1 TTTTAAACACAAATATGAG
*
559199 TTTTAAATAC--AT-T-A-
1 TTTTAAACACAAATATGAG
*
559213 TTTCAAACACAAATATGAG
1 TTTTAAACACAAATATGAG
559232 TTTTAAA
1 TTTTAAA
559239 TACATTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 8 0.26
15 1 0.03
16 3 0.10
17 3 0.10
18 1 0.03
19 15 0.48
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (19 bp):
TTTTAAACACAAATATGAG
Found at i:559222 original size:33 final size:33
Alignment explanation
Indices: 559184--559249 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
559174 TGTTATTTTT
559184 AAACACAAATATGAGTTTTAAATACATTATTTC
1 AAACACAAATATGAGTTTTAAATACATTATTTC
559217 AAACACAAATATGAGTTTTAAATACATTATTTC
1 AAACACAAATATGAGTTTTAAATACATTATTTC
559250 CTCAAGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (33 bp):
AAACACAAATATGAGTTTTAAATACATTATTTC
Found at i:569107 original size:58 final size:55
Alignment explanation
Indices: 568930--569114 Score: 155
Period size: 58 Copynumber: 3.2 Consensus size: 55
568920 TAAATTTACT
*
568930 ATTAAATTTAATTTAATTATTATATTAAT-AGTACTTTATTAATTTAATATTAAAGTG
1 ATTAAATTTAATTTAATT-TTAT-TTGATAAGTA-TTTATTAATTTAATATTAAAGTG
* * *
568987 ATT--ATCTTAATATTAATTTTAATTAAGATAAATATTCTATTAATTTAATAAATTTAA-T-
1 ATTAAAT-TTAAT-TTAATTTT-ATT-TGATAAGTATT-TATTAATTTAAT--ATTAAAGTG
* *
569045 ATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTGAATATTAAAGTG
1 ATTAAATTTAATTTAAT-TTTAT-TTGATAAGTATT-TATTAATTTAATATTAAAGTG
*
569103 ATTAAGTTTAAT
1 ATTAAATTTAAT
569115 AATAGTTGAA
Statistics
Matches: 103, Mismatches: 11, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
55 2 0.02
56 13 0.13
57 16 0.16
58 55 0.53
59 10 0.10
60 7 0.07
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (55 bp):
ATTAAATTTAATTTAATTTTATTTGATAAGTATTTATTAATTTAATATTAAAGTG
Found at i:574532 original size:30 final size:30
Alignment explanation
Indices: 574491--574550 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
574481 AGTAATTTGT
* *
574491 AAAGGGTTTTAGTTAAGCTACAAAAACTAG
1 AAAGGGCTTTAGTTAAGCCACAAAAACTAG
*
574521 AAAGGGCTTTAGTTTAGCCACAAAAACTAG
1 AAAGGGCTTTAGTTAAGCCACAAAAACTAG
574551 GGGAAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (30 bp):
AAAGGGCTTTAGTTAAGCCACAAAAACTAG
Found at i:587373 original size:24 final size:23
Alignment explanation
Indices: 587337--587382 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
587327 AAATGAGTCT
* *
587337 TGAACTTGATAATTGTTCTCAATC
1 TGAACTAGATAATTATT-TCAATC
*
587361 TGAACTAGGTAATTATTTCAAT
1 TGAACTAGATAATTATTTCAAT
587383 ATTCTTAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (23 bp):
TGAACTAGATAATTATTTCAATC
Found at i:596379 original size:31 final size:30
Alignment explanation
Indices: 596295--596379 Score: 71
Period size: 31 Copynumber: 2.8 Consensus size: 30
596285 ATACATGAAT
* *
596295 TTTAATTTTGTGTAATTATACACGTAAAAC
1 TTTAATTTTGTTTAATTATATACGTAAAAC
* * * * * * *
596325 TCTAATTGTGGTTCAAATGTATACTTGAAAC
1 TTTAATT-TTGTTTAATTATATACGTAAAAC
596356 TTTAATTTTGATTTAATTATATAC
1 TTTAATTTTG-TTTAATTATATAC
596380 ATTTAAAAAA
Statistics
Matches: 39, Mismatches: 14, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
30 8 0.21
31 31 0.79
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (30 bp):
TTTAATTTTGTTTAATTATATACGTAAAAC
Found at i:601770 original size:20 final size:19
Alignment explanation
Indices: 601745--601817 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
601735 ACATTAAAAA
601745 ATATAAATATGAAAATAAAT
1 ATATAAATAT-AAAATAAAT
* * *
601765 ATATAAAAAATAAAAAAAAC
1 ATAT-AAATATAAAATAAAT
601785 ATATAAATTATAAAAATAAAT
1 ATATAAA-TAT-AAAATAAAT
*
601806 -TATAAAAATAAA
1 ATATAAATATAAA
601818 TTTTGTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 3 0.07
19 5 0.12
20 23 0.53
21 12 0.28
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (19 bp):
ATATAAATATAAAATAAAT
Found at i:601803 original size:13 final size:13
Alignment explanation
Indices: 601737--601819 Score: 73
Period size: 13 Copynumber: 6.2 Consensus size: 13
601727 GTATATACAC
601737 ATTA-AAAAATATA
1 ATTATAAAAATA-A
* *
601750 AATATGAAAATAA
1 ATTATAAAAATAA
601763 ATATATAAAAAATAA
1 AT-TAT-AAAAATAA
*
601778 A--AAAAACATATAA
1 ATTATAAA-A-ATAA
601791 ATTATAAAAATAA
1 ATTATAAAAATAA
601804 ATTATAAAAATAA
1 ATTATAAAAATAA
601817 ATT
1 ATT
601820 TTGTTTATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
11 3 0.05
12 2 0.04
13 30 0.53
14 10 0.18
15 12 0.21
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (13 bp):
ATTATAAAAATAA
Found at i:601810 original size:40 final size:38
Alignment explanation
Indices: 601740--601817 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 38
601730 TATACACATT
*
601740 AAAAAATATAAATATGAAAATAAATATATAAAAAATAAA
1 AAAAAATATAAATATAAAAATAAATATAT-AAAAATAAA
601779 AAAAACATATAAATTATAAAAATAAAT-TATAAAAATAAA
1 AAAAA-ATATAAA-TATAAAAATAAATATATAAAAATAAA
601818 TTTTGTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 14 0.39
40 10 0.28
41 12 0.33
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (38 bp):
AAAAAATATAAATATAAAAATAAATATATAAAAATAAA
Found at i:617430 original size:45 final size:45
Alignment explanation
Indices: 617376--617461 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 45
617366 CAAATCGGAT
*
617376 ACATGTGGTCAAGCCACTAT-ATTGCA-ACCAAGCTGCCAGAACAA
1 ACATGTGGTCAAGCCACCATAATTGCAGA-CAAGCTGCCAGAACAA
617420 ACATAGTGGTCAAGCCACCATAATTGCAGACAAGCTGCCAGA
1 ACAT-GTGGTCAAGCCACCATAATTGCAGACAAGCTGCCAGA
617462 CAGAATTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
44 4 0.11
45 15 0.39
46 18 0.47
47 1 0.03
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17
Consensus pattern (45 bp):
ACATGTGGTCAAGCCACCATAATTGCAGACAAGCTGCCAGAACAA
Found at i:643126 original size:24 final size:24
Alignment explanation
Indices: 643098--643150 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
643088 ATTAGTAATT
* *
643098 TAAATAAACTATGCTAATAAATGC
1 TAAATAAACTATACTAATAAATAC
* *
643122 TAAATATATTATACTAATAAATAC
1 TAAATAAACTATACTAATAAATAC
643146 TAAAT
1 TAAAT
643151 TTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATAAACTATACTAATAAATAC
Found at i:645987 original size:7 final size:7
Alignment explanation
Indices: 645974--646007 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
645964 GATTCTGACG
645974 AATGGCC
1 AATGGCC
*
645981 TATGGCC
1 AATGGCC
*
645988 TATGGCC
1 AATGGCC
645995 AATGGCC
1 AATGGCC
646002 AATGGC
1 AATGGC
646008 AGTGGGAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (7 bp):
AATGGCC
Found at i:646501 original size:15 final size:13
Alignment explanation
Indices: 646473--646499 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
646463 AATGAGATTG
646473 ATATAAGCAAAAA
1 ATATAAGCAAAAA
646486 ATATAAGCAAAAA
1 ATATAAGCAAAAA
646499 A
1 A
646500 AACCCACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (13 bp):
ATATAAGCAAAAA
Found at i:649081 original size:50 final size:47
Alignment explanation
Indices: 648989--649088 Score: 105
Period size: 50 Copynumber: 2.0 Consensus size: 47
648979 GAAATATAAG
648989 GATTAAAACTAAAATTTAACCATTATTATATAATCTCAAAAAAGTAAAAA
1 GATTAAAACTAAAATTTAACCA-TATTATATAATCTCAAAAAA--AAAAA
* * *
649039 GATTAGAACTAAAATTT-AGCA-ATTATATATTCTCATGTAAAAAAAAAA
1 GATTAAAACTAAAATTTAACCATATTATATAATCTCA---AAAAAAAAAA
649087 GA
1 GA
649089 GAAAAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
47 13 0.30
48 7 0.16
49 3 0.07
50 21 0.48
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (47 bp):
GATTAAAACTAAAATTTAACCATATTATATAATCTCAAAAAAAAAAA
Found at i:656006 original size:15 final size:14
Alignment explanation
Indices: 655976--656019 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
655966 TGTATATTTA
*
655976 ATAATATTTAAAATT
1 ATAATATTTTAAA-T
*
655991 ATAATATTTTATAT
1 ATAATATTTTAAAT
656005 -TAATATTTTAAAT
1 ATAATATTTTAAAT
656018 AT
1 AT
656020 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.48
14 2 0.08
15 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATATTTTAAAT
Found at i:659343 original size:27 final size:27
Alignment explanation
Indices: 659305--659357 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
659295 TAGCCACAAA
*
659305 GGTGCCGCCTTTTTATTCCTCTCCATT
1 GGTGCCGCCTTTTTATTCCCCTCCATT
659332 GGTGCCGCCTTTTTATTCCCCTCCAT
1 GGTGCCGCCTTTTTATTCCCCTCCAT
659358 CACCCTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.08, C:0.36, G:0.15, T:0.42
Consensus pattern (27 bp):
GGTGCCGCCTTTTTATTCCCCTCCATT
Found at i:660149 original size:41 final size:41
Alignment explanation
Indices: 660104--660207 Score: 147
Period size: 41 Copynumber: 2.5 Consensus size: 41
660094 CTTCCCTCTT
* *
660104 CTTCTTCTTCTTTTTTTTCTCTTCCCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTTTTTTCTCTTCCCCTTTCCTCTTCTTTC
*
660145 CTTCTTTTTCTTTCTTTTT-TCTTCTCCTTTCCTCTTCTTTC
1 CTTCTTTTTCTTT-TTTTTCTCTTCCCCTTTCCTCTTCTTTC
* *
660186 CTTCTTTTTCTTTCTTTCCTCT
1 CTTCTTTTTCTTTTTTTTCTCT
660208 CCTTCATTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 3 0.05
41 48 0.86
42 5 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (41 bp):
CTTCTTTTTCTTTTTTTTCTCTTCCCCTTTCCTCTTCTTTC
Found at i:660158 original size:4 final size:4
Alignment explanation
Indices: 660137--660233 Score: 69
Period size: 4 Copynumber: 24.0 Consensus size: 4
660127 CCCCTTTCCT
*
660137 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * *
660182 TTTC CTTC -TT- TTTC TTTC TTTCC TCTC CTTC ATTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC -TTTC TTTC TTTC TTTC
660230 TTTC
1 TTTC
660234 CCTCTCCTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
3 11 0.14
4 48 0.62
5 13 0.17
6 5 0.06
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (4 bp):
TTTC
Found at i:660218 original size:77 final size:76
Alignment explanation
Indices: 660083--660228 Score: 181
Period size: 77 Copynumber: 1.9 Consensus size: 76
660073 TTACCTTTTT
* * *
660083 TTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTTTTTTTTCTCTTCCCCTTTCCTTTTCTTTCCTT
1 TTTTTTCCTTCCTTCCCTCTTCTTCTCCTTCTTTTTTTTCTCTTCCCCCTTCCATTTCTTTCCTT
660148 CTTTTTCTTTC
66 CTTTTTCTTTC
* *
660159 TTTTTTCTTCTCCTTTCCTCTTCTT-TCCTTCTTTTTCTTTCT-TTCCTCTCCTT-CATTTCTTT
1 TTTTTTCCT-TCCTTCCCTCTTCTTCTCCTTCTTTTT-TTTCTCTTCC-C-CCTTCCATTTCTTT
*
660221 CTTTCTTT
62 CCTTCTTT
660229 CTTTCCCTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
76 22 0.37
77 35 0.58
78 3 0.05
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (76 bp):
TTTTTTCCTTCCTTCCCTCTTCTTCTCCTTCTTTTTTTTCTCTTCCCCCTTCCATTTCTTTCCTT
CTTTTTCTTTC
Found at i:660424 original size:20 final size:21
Alignment explanation
Indices: 660404--660444 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
660394 TTTAGGTATA
660404 TTTTGGTAAATAAAAAAATATT
1 TTTTGGTAAATAAAAAAATA-T
660426 TTTTGGTAAATAAAAAAAT
1 TTTTGGTAAATAAAAAAAT
660445 TATAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTTGGTAAATAAAAAAATAT
Found at i:665317 original size:21 final size:22
Alignment explanation
Indices: 665288--665328 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
665278 CCTATACACT
*
665288 CTCTCTCCTCTAATTTCCTCGG
1 CTCTCTCCTCTAATCTCCTCGG
*
665310 CTCT-TCCTCTCATCTCCTC
1 CTCTCTCCTCTAATCTCCTC
665329 TCTTGCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.46, G:0.05, T:0.41
Consensus pattern (22 bp):
CTCTCTCCTCTAATCTCCTCGG
Found at i:681905 original size:10 final size:10
Alignment explanation
Indices: 681892--681919 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
681882 AATTAAATAT
681892 AATTTAAAAA
1 AATTTAAAAA
681902 AATTTAAAAA
1 AATTTAAAAA
681912 AATTTAAA
1 AATTTAAA
681920 GTTAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTTAAAAA
Found at i:687626 original size:52 final size:48
Alignment explanation
Indices: 687607--687809 Score: 256
Period size: 46 Copynumber: 4.3 Consensus size: 48
687597 TGACAAGTGG
* *
687607 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
687653 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* * *
687705 AAAGTGATAAGTGATCGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
687751 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
687797 AAAGTGATAAGTG
1 AAAGTGATAAGTG
687810 GCTACACTTA
Statistics
Matches: 142, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
46 99 0.70
52 43 0.30
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:687661 original size:98 final size:98
Alignment explanation
Indices: 687541--687809 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
687531 TTTGAGTACT
*
687541 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
687606 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
687639 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
687704 AAAAGTGATAAGTGATCGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
687737 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
687802 GATAAGTG
65 GAAAAGTG
687810 GCTACACTTA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 148 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:687817 original size:37 final size:37
Alignment explanation
Indices: 687773--687918 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
687763 GATAGCTTTA
*
687773 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
687810 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
687847 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
687884 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
687919 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:689640 original size:11 final size:11
Alignment explanation
Indices: 689611--689676 Score: 61
Period size: 10 Copynumber: 6.4 Consensus size: 11
689601 AACACCAATT
689611 TTTTAAAAA-A
1 TTTTAAAAATA
*
689621 TTTAAAAAAGTA
1 TTTTAAAAA-TA
689633 TTTTAAAAATA
1 TTTTAAAAATA
689644 TTTT--AAA-A
1 TTTTAAAAATA
*
689652 TTTAAAAAATA
1 TTTTAAAAATA
*
689663 -TATAAAAATA
1 TTTTAAAAATA
689673 TTTT
1 TTTT
689677 TTATTATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
8 4 0.09
9 3 0.07
10 19 0.43
11 9 0.20
12 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:689652 original size:31 final size:29
Alignment explanation
Indices: 689617--689676 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
689607 AATTTTTTAA
*
689617 AAAATTTAAAAAAGTATTTTAAAAATATTTT
1 AAAATTTAAAAAA-TA-TATAAAAATATTTT
689648 AAAATTTAAAAAATATATAAAAATATTTT
1 AAAATTTAAAAAATATATAAAAATATTTT
689677 TTATTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 13 0.46
30 2 0.07
31 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATTTAAAAAATATATAAAAATATTTT
Found at i:694298 original size:32 final size:31
Alignment explanation
Indices: 694250--694343 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 31
694240 ATCTCAATAG
*
694250 TATTTTATT-AATTTAATATTAAAGTGATTA
1 TATTATATTAAATTTAATATTAAAGTGATTA
* * * * *
694280 TCTTAATATTAAATTTAAT-CTAATATTTATCAA
1 TATT-ATATTAAATTTAATATTAA-AGTGAT-TA
*
694313 TATTAGATTAAATTTAATATTAAAGTGATTA
1 TATTATATTAAATTTAATATTAAAGTGATTA
694344 AGTTTAATAA
Statistics
Matches: 47, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
30 3 0.06
31 8 0.17
32 29 0.62
33 7 0.15
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (31 bp):
TATTATATTAAATTTAATATTAAAGTGATTA
Found at i:694355 original size:68 final size:67
Alignment explanation
Indices: 694214--694343 Score: 185
Period size: 68 Copynumber: 2.0 Consensus size: 67
694204 TTTAATAAAT
* * **
694214 TTAATATTAAATTTAATTTAATACTTATCTCAATAGTATTTTATTAATTTAATATTAAAGTGATT
1 TTAATATTAAATTTAATCTAATACTTATATCAATAGTAGATTA-TAATTTAATATTAAAGTGATT
694279 ATC
65 ATC
*
694282 TTAATATTAAATTTAATCTAATA-TT-TATCAATATTAGATTA-AATTTAATATTAAAGTGATTA
1 TTAATATTAAATTTAATCTAATACTTATATCAATAGTAGATTATAATTTAATATTAAAGTGATTA
694344 AGTTTAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
64 21 0.37
66 12 0.21
67 2 0.04
68 22 0.39
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (67 bp):
TTAATATTAAATTTAATCTAATACTTATATCAATAGTAGATTATAATTTAATATTAAAGTGATTA
TC
Found at i:696646 original size:29 final size:30
Alignment explanation
Indices: 696572--696650 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
696562 CAAAATTCAA
*
696572 AAAAGTATAGGGACTAAAATTGAGCAATATG
1 AAAA-TATAGGGACTAAATTTGAGCAATATG
* *
696603 AAAA-ATAAGGAGACTAAATTTGATCAA-ATT
1 AAAATAT-AGG-GACTAAATTTGAGCAATATG
696633 AAAATATAGGGACTAAAT
1 AAAATATAGGGACTAAAT
696651 CTGCAACTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 10 0.24
30 12 0.29
31 20 0.48
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (30 bp):
AAAATATAGGGACTAAATTTGAGCAATATG
Found at i:701919 original size:2 final size:2
Alignment explanation
Indices: 701912--701936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
701902 ATCTTTTACA
701912 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 A
701937 AATGGAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:704380 original size:25 final size:25
Alignment explanation
Indices: 704334--704382 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
704324 TATATATTAA
* * *
704334 AAATATATATTTTTTATTTTTAATC
1 AAATATATATTATATATATTTAATC
704359 AAATATATATTATATATATTTAAT
1 AAATATATATTATATATATTTAAT
704383 ATATATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AAATATATATTATATATATTTAATC
Found at i:704712 original size:26 final size:24
Alignment explanation
Indices: 704683--704731 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
704673 AAATTAATAT
704683 TAATAAATATAAAATTAATTAAGTGA
1 TAATAAATATAAAA-TAA-TAAGTGA
* *
704709 TAATCAATTTAAAATAATAAGTG
1 TAATAAATATAAAATAATAAGTG
704732 GAGTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
TAATAAATATAAAATAATAAGTGA
Found at i:706221 original size:26 final size:25
Alignment explanation
Indices: 706187--706240 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 25
706177 TTTAAAATAC
706187 TTTTAAAATAATTTTTTATTTTTTAT
1 TTTTAAAATAATTTTTTA-TTTTTAT
706213 TTTTAAAATAATTTTTTATTTTTAT
1 TTTTAAAATAATTTTTTATTTTTAT
706238 TTT
1 TTT
706241 ACAAAATGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTAAAATAATTTTTTATTTTTAT
Found at i:706246 original size:26 final size:26
Alignment explanation
Indices: 706187--706247 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
706177 TTTAAAATAC
706187 TTTT-AAAATAATTTTTTATTTTTTA
1 TTTTCAAAATAATTTTTTATTTTTTA
*
706212 TTTTTAAAATAATTTTTTA-TTTTTA
1 TTTTCAAAATAATTTTTTATTTTTTA
706237 TTTTACAAAAT
1 TTTT-CAAAAT
706248 GGGCCGGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 14 0.42
26 19 0.58
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTCAAAATAATTTTTTATTTTTTA
Found at i:706472 original size:26 final size:27
Alignment explanation
Indices: 706433--706488 Score: 105
Period size: 26 Copynumber: 2.1 Consensus size: 27
706423 TTTAAAATAC
706433 TTTTAAAATAAATTTTTTATTTTTTAT
1 TTTTAAAATAAATTTTTTATTTTTTAT
706460 TTTTAAAAT-AATTTTTTATTTTTTAT
1 TTTTAAAATAAATTTTTTATTTTTTAT
706486 TTT
1 TTT
706489 ACAAAATGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTAAAATAAATTTTTTATTTTTTAT
Found at i:706489 original size:38 final size:39
Alignment explanation
Indices: 706398--706489 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 39
706388 TAATAAATAC
*
706398 ATATTTTTTATTTTTATTTTTTAATTTTAAAATACTTTTA
1 ATATTTTTTA-TTTTATTTTTTAATTTTAAAATAATTTTA
* *** *
706438 AAATAAATT-TTTTATTTTTTATTTTTAAAATAATTTT-
1 ATATTTTTTATTTTATTTTTTAATTTTAAAATAATTTTA
*
706475 TTATTTTTTATTTTA
1 ATATTTTTTATTTTA
706490 CAAAATGGGT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
37 4 0.10
38 31 0.77
40 5 0.12
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (39 bp):
ATATTTTTTATTTTATTTTTTAATTTTAAAATAATTTTA
Found at i:706494 original size:27 final size:27
Alignment explanation
Indices: 706433--706495 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
706423 TTTAAAATAC
706433 TTTT-AAAATAAATTTTTTATTTTTTA
1 TTTTCAAAATAAATTTTTTATTTTTTA
*
706459 TTTTTAAAAT-AATTTTTTATTTTTTA
1 TTTTCAAAATAAATTTTTTATTTTTTA
706485 TTTTACAAAAT
1 TTTT-CAAAAT
706496 GGGTCGGGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 24 0.71
27 10 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTTCAAAATAAATTTTTTATTTTTTA
Found at i:706552 original size:248 final size:248
Alignment explanation
Indices: 706108--706869 Score: 1284
Period size: 238 Copynumber: 3.1 Consensus size: 248
706098 CCTCGGGCAT
* * * *
706108 AACTTTTT-T-GGCCCGGCCCG-GCCTGGCCCGAATATAATAAATATATATTTTTTATTTTTATT
1 AACTTTTTCTAGGCCCGGCTCGAACCCGGCCCGAATATAATAAATACATATTTTTTATTTTTATT
*
706170 TTTAAATTTTAAAATACTTTTAAAAT-AATTTTTTATTTTTTATTTTTAAAATAATTTTTTA-TT
66 TTTTAATTTTAAAATACTTTTAAAATAAATTTTTTATTTTTTATTTTTAAAATAATTTTTTATTT
*
706233 TTTATTTTACAAAATGGGCCGGGCTGGGCCGGGCTCGGGCTTATGATATTTTTCCCGGGCCAAGC
131 TTTATTTTACAAAATGGGTCGGGCTGGGCCGGGCTCGGGCTTATGATATTTTTCCCGGGCCAAGC
706298 CTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGCTTAGGAAGCGGGCCGAA
196 CTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGCTTAGGAAGCGGGCCGAA
706351 AACTTTTTCTAGGCCCGGCTCGAACCCGGCCCGAATATAATAAATACATATTTTTTATTTTTATT
1 AACTTTTTCTAGGCCCGGCTCGAACCCGGCCCGAATATAATAAATACATATTTTTTATTTTTATT
706416 TTTTAATTTTAAAATACTTTTAAAATAAATTTTTTATTTTTTATTTTTAAAATAATTTTTTATTT
66 TTTTAATTTTAAAATACTTTTAAAATAAATTTTTTATTTTTTATTTTTAAAATAATTTTTTATTT
706481 TTTATTTTACAAAATGGGTCGGGCTGGGCCGGGCTCGGGCTTATGATATTTTTCCCGGGCCAAGC
131 TTTATTTTACAAAATGGGTCGGGCTGGGCCGGGCTCGGGCTTATGATATTTTTCCCGGGCCAAGC
* * *
706546 CTGGGCAAAATTTCAGGCCCATATTTCGGCCCGGACTTAGGAAGCGGGCCAAA
196 CTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGCTTAGGAAGCGGGCCGAA
*
706599 AATTTTTTCTAGGCCCGGCTCGAACCCGGCCCGAATATAATAAATACATATTTTTTATTTTTA--
1 AACTTTTTCTAGGCCCGGCTCGAACCCGGCCCGAATATAATAAATACATATTTTTTATTTTTATT
*
706662 -TTT--TTTT---A-A-TTTTAAAATAATTTTTTTATTTTTTATTTTTAAAATAATTTTTTATTT
66 TTTTAATTTTAAAATACTTTTAAAATAAATTTTTTATTTTTTATTTTTAAAATAATTTTTTATTT
706719 TTTATTTTACAAAATGGGTCGGGCTGGGCCGGGCTCGGGCTTATGATATTTTTCCCGGGCCAAGC
131 TTTATTTTACAAAATGGGTCGGGCTGGGCCGGGCTCGGGCTTATGATATTTTTCCCGGGCCAAGC
*
706784 CTGGGCAAAATTTCAGGCCCATATTTCGGGTCGGGCTTAGGAAGCGGGCCGAA
196 CTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGCTTAGGAAGCGGGCCGAA
* * *
706837 AATTTTTTCCAAGCCCGGCTCGAACCCGGCCCG
1 AACTTTTTCTAGGCCCGGCTCGAACCCGGCCCG
706870 GCCCATGGAC
Statistics
Matches: 497, Mismatches: 17, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
238 192 0.39
239 1 0.00
240 1 0.00
243 12 0.02
244 1 0.00
245 13 0.03
246 64 0.13
247 35 0.07
248 178 0.36
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (248 bp):
AACTTTTTCTAGGCCCGGCTCGAACCCGGCCCGAATATAATAAATACATATTTTTTATTTTTATT
TTTTAATTTTAAAATACTTTTAAAATAAATTTTTTATTTTTTATTTTTAAAATAATTTTTTATTT
TTTATTTTACAAAATGGGTCGGGCTGGGCCGGGCTCGGGCTTATGATATTTTTCCCGGGCCAAGC
CTGGGCAAAATTTCAGGCCCATATTTCGGGCCGGGCTTAGGAAGCGGGCCGAA
Found at i:706733 original size:27 final size:26
Alignment explanation
Indices: 706656--706727 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 26
706646 ATATTTTTTA
706656 TTTTTATTTTTTTAATTTTAAAATAATT
1 TTTTTA-TTTTTT-ATTTTAAAATAATT
706684 TTTTTATTTTTTATTTTTAAAATAA-T
1 TTTTTATTTTTTA-TTTTAAAATAATT
706710 TTTTTATTTTTTATTTTA
1 TTTTTATTTTTTATTTTA
706728 CAAAATGGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
25 5 0.12
26 15 0.35
27 17 0.40
28 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTTATTTTTTATTTTAAAATAATT
Found at i:707788 original size:32 final size:31
Alignment explanation
Indices: 707743--707804 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
707733 TTTTCCAGAG
707743 TTTTTATATTTTTT-TGAATTTTGAATATTATT
1 TTTTTATATTTTTTAT-AATTTTGAA-ATTATT
*
707775 TTTTTA-ATATTTTTATAATTTTTAAATTAT
1 TTTTTATAT-TTTTTATAATTTTGAAATTAT
707805 CTATTGACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 7 0.26
32 19 0.70
33 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (31 bp):
TTTTTATATTTTTTATAATTTTGAAATTATT
Found at i:712597 original size:89 final size:89
Alignment explanation
Indices: 712446--712610 Score: 231
Period size: 89 Copynumber: 1.9 Consensus size: 89
712436 TCAGGGGAGG
* * * * * *
712446 AAATCTGATTTGTCGTTCTCTTATTGGAAATGGATATAGATGACACGGAATTAAAGTTTCATACA
1 AAATCTCATTTGTCATTCTCCTATTGAAAATGGATAGAGATGACACGGAATCAAAGTTTCATACA
712511 ATCCTTTCTCAACATCAAGAGAAA
66 ATCCTTTCTCAACATCAAGAGAAA
* ** *
712535 AAATCTCATTTGTCATTCTCCTATTGAAAATGGATAGGGATGACGTGGAATCACAGTTTCATACA
1 AAATCTCATTTGTCATTCTCCTATTGAAAATGGATAGAGATGACACGGAATCAAAGTTTCATACA
*
712600 ATTCTTTCTCA
66 ATCCTTTCTCA
712611 TTAATTAATT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (89 bp):
AAATCTCATTTGTCATTCTCCTATTGAAAATGGATAGAGATGACACGGAATCAAAGTTTCATACA
ATCCTTTCTCAACATCAAGAGAAA
Found at i:725019 original size:4 final size:4
Alignment explanation
Indices: 725010--725048 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
725000 GGTATTAAAC
725010 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
725049 AAGAAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:726045 original size:15 final size:15
Alignment explanation
Indices: 726021--726067 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
726011 TGATAAATTA
726021 AAAAATTAAGTGTTG
1 AAAAATTAAGTGTTG
726036 AAAAGA-TAAGTGTTG
1 AAAA-ATTAAGTGTTG
*
726051 AAAAATTAAGTATTG
1 AAAAATTAAGTGTTG
726066 AA
1 AA
726068 TTTAAGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (15 bp):
AAAAATTAAGTGTTG
Done.