Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 23
Found at i:704583 original size:20 final size:20
Alignment explanation
Indices: 704560--704600 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
704550 GTTCTCCTCT
*
704560 TCTCATTCTTTAATTTGAAA
1 TCTCATTCTTTAATTTAAAA
*
704580 TCTCATTTTTTAATTTAAAA
1 TCTCATTCTTTAATTTAAAA
704600 T
1 T
704601 AATAATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (20 bp):
TCTCATTCTTTAATTTAAAA
Found at i:710640 original size:43 final size:41
Alignment explanation
Indices: 710571--710651 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 41
710561 AAAAATTTAG
* *
710571 ATACATATATATAATTGCAGAGACAATAA-CCTTAATTGTAA
1 ATACATATATATAATTACAGACACAATAATCC-TAATTGTAA
*
710612 ATACATATATATAATTATATAGACACAATAATCCTAATTG
1 ATACATATATATAA-T-TACAGACACAATAATCCTAATTG
710652 AGTAAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 14 0.41
42 1 0.03
43 17 0.50
44 2 0.06
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (41 bp):
ATACATATATATAATTACAGACACAATAATCCTAATTGTAA
Found at i:711799 original size:24 final size:23
Alignment explanation
Indices: 711767--711815 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
711757 GTAAATTTTT
*
711767 AAAATTAAATTTATCA-ATATAATA
1 AAAACTAAA-TTATCATATAT-ATA
711791 AAAACTAAATTATCATATATATA
1 AAAACTAAATTATCATATATATA
711814 AA
1 AA
711816 TTAGTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAACTAAATTATCATATATATA
Found at i:714494 original size:15 final size:16
Alignment explanation
Indices: 714463--714501 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
714453 AGAATTAAAA
714463 ATAAATGAAAAATATT
1 ATAAATGAAAAATATT
*
714479 ATAAATTAAAAA-ATT
1 ATAAATGAAAAATATT
*
714494 ATATATGA
1 ATAAATGA
714502 TTTGATTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
ATAAATGAAAAATATT
Found at i:724606 original size:69 final size:70
Alignment explanation
Indices: 724494--724625 Score: 203
Period size: 69 Copynumber: 1.9 Consensus size: 70
724484 TCGGGGTTTT
* * *
724494 CGTGCAAGTCACCCCGGAATAAATATGATTAGATATTCTCATGCGAGTCACTCTAATCCTTCGGA
1 CGTGCAAGTCACCCCGAAATAAATATGATTAGATAGTCTCATGCAAGTCACTCTAATCCTTCGGA
724559 GTTCC
66 GTTCC
* * *
724564 CGTGCAAGTCA-CCCGAAATAAATATGATTAGGTGGTCTCATGCAAGTCACTCTAATTCTTCG
1 CGTGCAAGTCACCCCGAAATAAATATGATTAGATAGTCTCATGCAAGTCACTCTAATCCTTCG
724626 ACACTCCTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
69 45 0.80
70 11 0.20
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (70 bp):
CGTGCAAGTCACCCCGAAATAAATATGATTAGATAGTCTCATGCAAGTCACTCTAATCCTTCGGA
GTTCC
Found at i:733382 original size:29 final size:29
Alignment explanation
Indices: 733337--733470 Score: 115
Period size: 29 Copynumber: 4.6 Consensus size: 29
733327 ATTCAGTTTA
** *
733337 GTGCTATTCGGGGAATTAATTCGAAATGG
1 GTGCTATTTTGGGAATTAATTCGAAAAGG
* ** ** **
733366 GTGCTATTTTGGTAATTTTTTTTAAAAAA
1 GTGCTATTTTGGGAATTAATTCGAAAAGG
** * * **
733395 GTGAAATTATGGGAATTAATTTGAAATTG
1 GTGCTATTTTGGGAATTAATTCGAAAAGG
733424 GTGCTATTTTGGGAATTAATTCGAAAAGG
1 GTGCTATTTTGGGAATTAATTCGAAAAGG
*
733453 GTGCTATTTTGGTAATTA
1 GTGCTATTTTGGGAATTA
733471 TTTAAAAAAG
Statistics
Matches: 78, Mismatches: 27, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTAATTCGAAAAGG
Found at i:733479 original size:29 final size:28
Alignment explanation
Indices: 733337--733488 Score: 83
Period size: 29 Copynumber: 5.3 Consensus size: 28
733327 ATTCAGTTTA
** * **
733337 GTGCTATTCGGGGAATTAATTCGAAATGG
1 GTGCTATTTTGGGAATTAATT-AAAAAAG
* **
733366 GTGCTATTTTGGTAATTTTTTTTAAAAAA-
1 GTGCTATTTTGGGAA--TTAATTAAAAAAG
** * * **
733395 GTGAAATTATGGGAATTAATTTGAAATTG
1 GTGCTATTTTGGGAATTAA-TTAAAAAAG
* *
733424 GTGCTATTTTGGGAATTAATTCGAAAAGG
1 GTGCTATTTTGGGAATTAATT-AAAAAAG
* *
733453 GTGCTATTTTGGTAATTATTTAAAAAA-
1 GTGCTATTTTGGGAATTAATTAAAAAAG
733480 GTGCTATTT
1 GTGCTATTT
733489 GTGTAAAATG
Statistics
Matches: 92, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
27 11 0.12
28 11 0.12
29 63 0.68
30 3 0.03
31 4 0.04
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (28 bp):
GTGCTATTTTGGGAATTAATTAAAAAAG
Found at i:740614 original size:18 final size:18
Alignment explanation
Indices: 740572--740624 Score: 81
Period size: 17 Copynumber: 3.0 Consensus size: 18
740562 CGACCCATTT
*
740572 ACCCGTTGACCCAACCCG
1 ACCCGTTGACCCGACCCG
740590 A-CCGTTGACCCGACCCG
1 ACCCGTTGACCCGACCCG
*
740607 ACCCGTTGACCTGACCCG
1 ACCCGTTGACCCGACCCG
740625 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.19, C:0.47, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGTTGACCCGACCCG
Found at i:740622 original size:13 final size:13
Alignment explanation
Indices: 740601--740630 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
740591 CCGTTGACCC
740601 GACCCGACCCGTT
1 GACCCGACCCGTT
*
740614 GACCTGACCCGTT
1 GACCCGACCCGTT
740627 GACC
1 GACC
740631 GTTGACCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:740712 original size:29 final size:29
Alignment explanation
Indices: 740643--740800 Score: 147
Period size: 29 Copynumber: 5.5 Consensus size: 29
740633 TGACCGATGT
* **
740643 TATTTTGGGAATTAATTCG-ATTTAGTGC
1 TATTTTGGGAATTAATTCGAAATGGGTGC
**
740671 TATTCGGGGAATTAATTCGAAATGGGTGC
1 TATTTTGGGAATTAATTCGAAATGGGTGC
* ** ** ** *
740700 TATTTTGGTAATTTTTTTAAAAAAGGTGA
1 TATTTTGGGAATTAATTCGAAATGGGTGC
* * *
740729 TATTATGGGAATTAATTCAAAATTGGTGC
1 TATTTTGGGAATTAATTCGAAATGGGTGC
*
740758 TATTTTGGGAATTAATTCGAAAAGGGTGC
1 TATTTTGGGAATTAATTCGAAATGGGTGC
*
740787 TATTTTGGTAATTA
1 TATTTTGGGAATTA
740801 TTTTAAAAAA
Statistics
Matches: 101, Mismatches: 28, Indels: 1
0.78 0.22 0.01
Matches are distributed among these distances:
28 17 0.17
29 84 0.83
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (29 bp):
TATTTTGGGAATTAATTCGAAATGGGTGC
Found at i:740793 original size:87 final size:86
Alignment explanation
Indices: 740643--740819 Score: 255
Period size: 87 Copynumber: 2.0 Consensus size: 86
740633 TGACCGATGT
* * * *
740643 TATTTTGGGAATTAATTCGATTTAGTGCTATTCGGGGAATTAATTCGAAATGGGTGCTATTTTGG
1 TATTATGGGAATTAATTCAAATTAGTGCTATTCGGGGAATTAATTCGAAAAGGGTGCTATTTTGG
* *
740708 TAATTTTTTTAAAAAAGGTGA
66 TAATTATTTTAAAAAAAGTGA
* **
740729 TATTATGGGAATTAATTCAAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTATTTTG
1 TATTATGGGAATTAATTC-AAATTAGTGCTATTCGGGGAATTAATTCGAAAAGGGTGCTATTTTG
*
740794 GTAATTATTTTAAAAAAAGTGC
65 GTAATTATTTTAAAAAAAGTGA
740816 TATT
1 TATT
740820 TGTGTAAAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 17 0.21
87 63 0.79
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (86 bp):
TATTATGGGAATTAATTCAAATTAGTGCTATTCGGGGAATTAATTCGAAAAGGGTGCTATTTTGG
TAATTATTTTAAAAAAAGTGA
Found at i:740809 original size:29 final size:29
Alignment explanation
Indices: 740643--740820 Score: 142
Period size: 29 Copynumber: 6.2 Consensus size: 29
740633 TGACCGATGT
* ***
740643 TATTTTGGGAATTAATTCGATTTA-GTGC
1 TATTTTGGGAATTAATTCAAAAAAGGTGC
** * **
740671 TATTCGGGGAATTAATTCGAAATGGGTGC
1 TATTTTGGGAATTAATTCAAAAAAGGTGC
* ** * *
740700 TATTTTGGTAATTTTTTTAAAAAAGGTGA
1 TATTTTGGGAATTAATTCAAAAAAGGTGC
* **
740729 TATTATGGGAATTAATTCAAAATTGGTGC
1 TATTTTGGGAATTAATTCAAAAAAGGTGC
* *
740758 TATTTTGGGAATTAATTCGAAAAGGGTGC
1 TATTTTGGGAATTAATTCAAAAAAGGTGC
* * * *
740787 TATTTTGGTAATTATTTTAAAAAAAGTGC
1 TATTTTGGGAATTAATTCAAAAAAGGTGC
740816 TATTT
1 TATTT
740821 GTGTAAAATG
Statistics
Matches: 116, Mismatches: 33, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
28 19 0.16
29 97 0.84
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (29 bp):
TATTTTGGGAATTAATTCAAAAAAGGTGC
Found at i:750565 original size:18 final size:19
Alignment explanation
Indices: 750529--750569 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
750519 GTGGATAAAG
750529 AAAAAATAATAACTGAATATA
1 AAAAAATAATAAC--AATATA
750550 AAAAAATAATAA-AATATA
1 AAAAAATAATAACAATATA
750568 AA
1 AA
750570 TGTATTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
21 12 0.60
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAAAATAATAACAATATA
Found at i:752210 original size:28 final size:27
Alignment explanation
Indices: 752179--752241 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
752169 TTTCAGGATA
752179 GGGTCGGATTTAAAAAAAAATCGGGGTC
1 GGGTCGGATTT-AAAAAAAATCGGGGTC
* *
752207 GGGTCGGGCTTTAAAAAAAATCGGGTTC
1 GGGTC-GGATTTAAAAAAAATCGGGGTC
*
752235 GGTTCGG
1 GGGTCGG
752242 GTTTTTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.77
29 5 0.16
ACGTcount: A:0.29, C:0.13, G:0.35, T:0.24
Consensus pattern (27 bp):
GGGTCGGATTTAAAAAAAATCGGGGTC
Found at i:754987 original size:16 final size:16
Alignment explanation
Indices: 754968--755007 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
754958 GATATGAGAC
*
754968 AATTTAAATTTAAATT
1 AATTTAAATTTAAAAT
*
754984 AATTTAATTTTAAAAT
1 AATTTAAATTTAAAAT
755000 AATGTTAA
1 AAT-TTAA
755008 TAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:764496 original size:15 final size:16
Alignment explanation
Indices: 764461--764494 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
764451 ACTGCTTTTC
764461 AAAGTTTTTTTATCAT
1 AAAGTTTTTTTATCAT
764477 AAAGTTTTTTTATCAT
1 AAAGTTTTTTTATCAT
764493 AA
1 AA
764495 GTATATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (16 bp):
AAAGTTTTTTTATCAT
Found at i:767099 original size:14 final size:15
Alignment explanation
Indices: 767080--767109 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
767070 GCTAAAAAAA
767080 TTTAAAT-TTCAAAT
1 TTTAAATATTCAAAT
767094 TTTAAATATTCAAAT
1 TTTAAATATTCAAAT
767109 T
1 T
767110 AAAACTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAATATTCAAAT
Found at i:767417 original size:19 final size:16
Alignment explanation
Indices: 767375--767422 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 16
767365 AAATAAAAAA
767375 TTATTTTTCTTTTTCC
1 TTATTTTTCTTTTTCC
*
767391 TTCATTTTCTACTCTTTCC
1 TT-ATTTT-T-CTTTTTCC
767410 TTATTTTTTCTTT
1 TTA-TTTTTCTTT
767423 CTTTTCACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
18 3 0.12
19 13 0.50
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTTCTTTTTCC
Found at i:779809 original size:82 final size:82
Alignment explanation
Indices: 779685--779854 Score: 236
Period size: 82 Copynumber: 2.1 Consensus size: 82
779675 TAAAAGAATA
* *
779685 AATAAAGAAAAATTTATTCATCTCCCCTCAATTAAAAAAAATTATATTTCTGAAAATTAAAAAAA
1 AATAAAGAAAAATTTATTCAGCTCCCCTCAATTAAAAAAAATTATATTTATGAAAA--AAAAAAA
779750 ATACTTTAA-CCCCACCTT
64 ATACTTTAACCCCCACCTT
* * * *
779768 AATAAAGAAAACTTTATTCGGC-CCCCTCAATTTAAAAAAATTATATTTATGAAAAATAAAAAAT
1 AATAAAGAAAAATTTATTCAGCTCCCCTCAATTAAAAAAAATTATATTTATGAAAAAAAAAAAAT
* *
779832 ATTTTAACCCCCGCCTT
66 ACTTTAACCCCCACCTT
779849 AATAAA
1 AATAAA
779855 TTCCTGGTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
80 14 0.18
81 14 0.18
82 31 0.40
83 19 0.24
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.31
Consensus pattern (82 bp):
AATAAAGAAAAATTTATTCAGCTCCCCTCAATTAAAAAAAATTATATTTATGAAAAAAAAAAAAT
ACTTTAACCCCCACCTT
Found at i:783385 original size:8 final size:8
Alignment explanation
Indices: 783356--783404 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
783346 ATAAAAATTT
*
783356 AAATTTAA
1 AAATATAA
783364 AATATATAAA
1 AA-ATAT-AA
783374 AAATATAA
1 AAATATAA
783382 AAATATAA
1 AAATATAA
*
783390 AAATTTATA
1 AAATATA-A
783399 AAATAT
1 AAATAT
783405 TTAATCAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 18 0.51
9 13 0.37
10 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAATATAA
Found at i:783389 original size:17 final size:18
Alignment explanation
Indices: 783356--783404 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
783346 ATAAAAATTT
*
783356 AAATTTAAAATATATAAA
1 AAATATAAAATATATAAA
783374 AAATATAAAA-ATATAAA
1 AAATATAAAATATATAAA
*
783391 AATTTATAAAATAT
1 AA-ATATAAAATAT
783405 TTAATCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 9 0.33
18 16 0.59
19 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAAAATATATAAA
Found at i:783401 original size:9 final size:9
Alignment explanation
Indices: 783361--783404 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
783351 AATTTAAATT
783361 TAAAATATA
1 TAAAATATA
*
783370 TAAAAAATA
1 TAAAATATA
783379 TAAAA-ATA
1 TAAAATATA
*
783387 TAAAAATTTA
1 T-AAAATATA
783397 TAAAATAT
1 TAAAATAT
783405 TTAATCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 4 0.13
9 23 0.77
10 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAATATA
Found at i:784523 original size:32 final size:32
Alignment explanation
Indices: 784487--784563 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
784477 ATGGGTATAA
*
784487 ATTTTCAAATCCACACCCGCCCACGTAGGTAC
1 ATTTTCAAATCCACACCCGCCCACGCAGGTAC
*
784519 ATTTTCAAATCCACACCCGCCCACGCGGGTAC
1 ATTTTCAAATCCACACCCGCCCACGCAGGTAC
784551 ATTTTCAAATCCA
1 ATTTTCAAATCCA
784564 TCCCCACACC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.29, C:0.36, G:0.12, T:0.23
Consensus pattern (32 bp):
ATTTTCAAATCCACACCCGCCCACGCAGGTAC
Found at i:789866 original size:29 final size:29
Alignment explanation
Indices: 789824--789881 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
789814 AAGGAATTTT
*
789824 TTGCAGCTTTATGGAGGAAGAAGAAGAAG
1 TTGCAGCTTTATGGAAGAAGAAGAAGAAG
789853 TTGCAGCTTTATGGAAGAAGAAGAAGAAG
1 TTGCAGCTTTATGGAAGAAGAAGAAGAAG
789882 GGTTAACGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.21
Consensus pattern (29 bp):
TTGCAGCTTTATGGAAGAAGAAGAAGAAG
Found at i:789875 original size:26 final size:27
Alignment explanation
Indices: 789824--789878 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
789814 AAGGAATTTT
789824 TTGCAGCTTTATGGAGGAAGAAGAAGAAG
1 TTGCAGCTTTAT-G-GGAAGAAGAAGAAG
789853 TTGCAGCTTTAT-GGAAGAAGAAGAAG
1 TTGCAGCTTTATGGGAAGAAGAAGAAG
789879 AAGGGTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 14 0.54
29 12 0.46
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (27 bp):
TTGCAGCTTTATGGGAAGAAGAAGAAG
Found at i:790421 original size:37 final size:37
Alignment explanation
Indices: 790380--790451 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
790370 AAGATTTTTT
*
790380 TTAAAAAGATG-ATAAAGTCAAAATAATAATAAAATTA
1 TTAAAAAGATGTA-AAAGTCAAAATAATAAAAAAATTA
** *
790417 TTAAAATTATGTAAAAGTCAAAATATTAAAAAAAT
1 TTAAAAAGATGTAAAAGTCAAAATAATAAAAAAAT
790452 ATGAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 29 0.97
38 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (37 bp):
TTAAAAAGATGTAAAAGTCAAAATAATAAAAAAATTA
Found at i:791184 original size:2 final size:2
Alignment explanation
Indices: 791177--791207 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
791167 CAATCGTGTT
791177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
791208 TTAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:791215 original size:14 final size:14
Alignment explanation
Indices: 791184--791233 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
791174 GTTTATATAT
* *
791184 ATATATATATATAT
1 ATATATATATTTAA
791198 ATATATATATTTAA
1 ATATATATATTTAA
*
791212 ATATTTAT-TTTAA
1 ATATATATATTTAA
791225 A-ATATATAT
1 ATATATATAT
791234 AAACATGACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 5 0.16
13 7 0.23
14 19 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATATTTAA
Found at i:791613 original size:17 final size:17
Alignment explanation
Indices: 791591--791625 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
791581 ACCCTTAAAA
791591 ATTTTAAATTCTTTTAT
1 ATTTTAAATTCTTTTAT
* *
791608 ATTTTAATTTTTTTTAT
1 ATTTTAAATTCTTTTAT
791625 A
1 A
791626 AATTTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTAAATTCTTTTAT
Found at i:791933 original size:22 final size:22
Alignment explanation
Indices: 791907--791953 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
791897 AAAATATTTA
* *
791907 AAATTTTTTATAGAATAA-AAAT
1 AAATTATTAATAGAA-AATAAAT
791929 AAATTATTAATAGAAAATAAAT
1 AAATTATTAATAGAAAATAAAT
791951 AAA
1 AAA
791954 ATCTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
AAATTATTAATAGAAAATAAAT
Found at i:804000 original size:36 final size:34
Alignment explanation
Indices: 803927--804012 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 34
803917 TAGGCCATAA
* *
803927 CACTAGTATTAGAAATATGCTAGTTAGGTTATCC
1 CACTAGTATTAGAAATATACTAATTAGGTTATCC
* *
803961 CACTAGTATTTGAAATATACTCAAATTAGGTTATTC
1 CACTAGTATTAGAAATATACT--AATTAGGTTATCC
* *
803997 CACTGGTATTGGAAAT
1 CACTAGTATTAGAAAT
804013 GATCATTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
34 19 0.43
36 25 0.57
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (34 bp):
CACTAGTATTAGAAATATACTAATTAGGTTATCC
Found at i:805158 original size:23 final size:22
Alignment explanation
Indices: 805127--805171 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
805117 AGGTTGAACG
805127 ATTTATTAAATAGCTATATAAAT
1 ATTTATT-AATAGCTATATAAAT
*
805150 ATTTGTTAATAGCTATATAAAT
1 ATTTATTAATAGCTATATAAAT
805172 GTTAGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTATTAATAGCTATATAAAT
Found at i:808512 original size:31 final size:31
Alignment explanation
Indices: 808474--808536 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
808464 CCCAAGAGTT
*
808474 TGGGAGTTCCTAGTGAGAATGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
808505 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
808536 T
1 T
808537 TCACCGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.29
Consensus pattern (31 bp):
TGGGAGTTCCTAGTGAGAAGGACATATTGAA
Found at i:812274 original size:31 final size:31
Alignment explanation
Indices: 812212--812275 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
812202 AGTATCAAAA
*
812212 GTAACAAATTGATCACTAACGTTATCGATTT
1 GTAACAAATTGATCACTAACGTTAACGATTT
* * *
812243 GTAACAAATTGGTCATTCGACGTTAAC-ATTT
1 GTAACAAATTGATCACT-AACGTTAACGATTT
812274 GT
1 GT
812276 TAACGTGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (31 bp):
GTAACAAATTGATCACTAACGTTAACGATTT
Found at i:827265 original size:20 final size:20
Alignment explanation
Indices: 827240--827531 Score: 225
Period size: 20 Copynumber: 14.5 Consensus size: 20
827230 GATTTTCAAT
* *
827240 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
827260 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
827280 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
827299 CTATCGCAACGAGTATTCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
827321 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
827341 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* * *
827362 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
827382 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
827402 AATCGTAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
827422 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
827442 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
827462 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
**
827482 AATCGCAATACGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
827502 AATTGCAATGCGGAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
827522 AATCGCAACG
1 AATCGCAACG
827532 AGATTCTGAC
Statistics
Matches: 221, Mismatches: 41, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 178 0.81
21 36 0.16
22 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:827416 original size:40 final size:40
Alignment explanation
Indices: 827240--827489 Score: 270
Period size: 40 Copynumber: 6.2 Consensus size: 40
827230 GATTTTCAAT
* ** * * * **
827240 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
827280 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATTCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* *
827321 AATCGCAACGCGTATCCGTAAATCGCAATGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
*
827362 AATCGTAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
827402 AATCGTAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * *
827442 AATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
827482 AATCGCAA
1 AATCGCAA
827490 TACGAATACG
Statistics
Matches: 180, Mismatches: 25, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
39 3 0.02
40 107 0.59
41 65 0.36
42 4 0.02
43 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:827490 original size:40 final size:40
Alignment explanation
Indices: 827320--827531 Score: 257
Period size: 40 Copynumber: 5.3 Consensus size: 40
827310 AGTATTCGTA
827320 AAATCGCAACGCGTATCCGTAAATCGCAATGAC-AATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAATG-CGAATACGT
* * *
827360 AAAATCGTAACGCGTATCCGTAAATCGCAACGAGAATACGT
1 -AAATCGCAACGCGTATCCGTAAATCGCAATGCGAATACGT
* * * *
827401 AAATCGTAACGCGTATCTGTAAATCGCAACGAGAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAATGCGAATACGT
*
827441 AAATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAATGCGAATACGT
** * * * *
827481 AAATCGCAATACGAATACGTAAATTGCAATGCGGAT-CTGT
1 AAATCGCAACGCGTATCCGTAAATCGCAATGCGAATAC-GT
827521 AAATCGCAACG
1 AAATCGCAACG
827532 AGATTCTGAC
Statistics
Matches: 153, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 116 0.76
41 36 0.24
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAATGCGAATACGT
Found at i:827625 original size:20 final size:20
Alignment explanation
Indices: 827600--827709 Score: 112
Period size: 20 Copynumber: 5.4 Consensus size: 20
827590 ACAGATACGT
* *
827600 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACTC
*
827620 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACTC
** * **
827640 GTTATGATTTTACGTATTGTC
1 GTTGCGA-TTTACGGATACTC
* *
827661 GTTACGATTTACGGATACGC
1 GTTGCGATTTACGGATACTC
827681 GTTGCGATTTTACGGATACTC
1 GTTGCGA-TTTACGGATACTC
827702 GTTGCGAT
1 GTTGCGAT
827710 AGTCAGAATC
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
20 38 0.53
21 34 0.47
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATACTC
Found at i:827663 original size:41 final size:41
Alignment explanation
Indices: 827593--827709 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 41
827583 ATTCGCAACA
* *
827593 GATACGTGTTGCGA-TTTACGTATTCTCGTTGCGATTTACG
1 GATACGCGTTACGATTTTACGTATTCTCGTTGCGATTTACG
* * *
827633 GATACGCGTTATGATTTTACGTATTGTCGTTACGATTTACG
1 GATACGCGTTACGATTTTACGTATTCTCGTTGCGATTTACG
* * *
827674 GATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 GATACGCGTTACGATTTTACGTATTCTCGTTGCGAT
827710 AGTCAGAATC
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
40 11 0.17
41 54 0.83
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
GATACGCGTTACGATTTTACGTATTCTCGTTGCGATTTACG
Found at i:827726 original size:20 final size:20
Alignment explanation
Indices: 827701--827749 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
827691 TACGGATACT
827701 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
** * *
827721 CGTTGCGATTTTCATATTCG
1 CGTTGCGATAGTCAGAATCG
827741 CGTTGCGAT
1 CGTTGCGAT
827750 TATGGAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:827828 original size:20 final size:20
Alignment explanation
Indices: 827738--827832 Score: 59
Period size: 21 Copynumber: 4.7 Consensus size: 20
827728 ATTTTCATAT
* *
827738 TCGCGTTGCGATTATGGAAAA
1 TCGCGTTGCGATTCT-GAAGA
** *
827759 TCGCAATGCGATTCTTCATA-A
1 TCGCGTTGCGATTC-TGA-AGA
*
827780 TCGCGTTGCGATTCTG-GGA
1 TCGCGTTGCGATTCTGAAGA
* **
827799 ACTGATTTGCGATTCTGAAGA
1 TC-GCGTTGCGATTCTGAAGA
827820 TCGCGTTGCGATT
1 TCGCGTTGCGATT
827833 TTTATTTCGC
Statistics
Matches: 54, Mismatches: 15, Indels: 11
0.68 0.19 0.14
Matches are distributed among these distances:
19 2 0.04
20 22 0.41
21 28 0.52
22 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (20 bp):
TCGCGTTGCGATTCTGAAGA
Found at i:831781 original size:2 final size:2
Alignment explanation
Indices: 831774--831811 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
831764 TGAAAATAAT
*
831774 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
831812 ATAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:831830 original size:18 final size:17
Alignment explanation
Indices: 831809--831851 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
831799 ATATATACAT
831809 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
831827 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
831844 ATAA-AATA
1 ATAATAATA
831852 TGCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:833159 original size:105 final size:105
Alignment explanation
Indices: 832855--833516 Score: 947
Period size: 105 Copynumber: 6.3 Consensus size: 105
832845 GCATTGTTCC
* * * ** * *
832855 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* * * * *
832920 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
832961 TAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-TGA-AA-TT-TTGTTAACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
** *
833021 CAGTTGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
833061 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
833126 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
833166 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
833231 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
833271 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
833336 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
833376 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* * * *
833441 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
* * * *
833483 AGTGTCACGATATCCTTCGTCGTGGAGTTGAAAT
1 -GAGTC-CAATATCCTTCGTTGTGAAGTTGAAAT
833517 CACGGATGTT
Statistics
Matches: 506, Mismatches: 41, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
100 80 0.16
101 1 0.00
102 5 0.01
103 4 0.01
104 3 0.01
105 303 0.60
106 81 0.16
107 1 0.00
108 4 0.01
109 24 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:833732 original size:36 final size:36
Alignment explanation
Indices: 833685--833760 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
833675 TGTTTGGAGA
* * *
833685 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
833721 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
833757 GAAA
1 GAAA
833761 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:833881 original size:106 final size:105
Alignment explanation
Indices: 833660--833979 Score: 470
Period size: 106 Copynumber: 3.1 Consensus size: 105
833650 TTCGTTAAAT
* ** *
833660 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
833722 AAACTATCTCA-AGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
833761 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
833826 AAACTATCTCAAGAGAGAGAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTC-AGAGAGAGAAAAAATTCATTTCAAGGGAAA
* * * * *
833867 TGTTCTCAATGTTTATGTTTCAAGAGAAACTGTCTAAAGGGAGATAAAATTTTTTGATTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
833932 AAACTATCTCAG-GAGAGAAACAATTAATTTCAAGGGAAA
66 AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
833971 TGTTTTCAA
1 TGTTTTCAA
833980 GAGAAACTGT
Statistics
Matches: 198, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
101 46 0.23
103 3 0.02
104 51 0.26
105 3 0.02
106 95 0.48
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (105 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAGAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:834135 original size:36 final size:35
Alignment explanation
Indices: 834095--834208 Score: 102
Period size: 36 Copynumber: 3.2 Consensus size: 35
834085 CTTTCGAGTG
* *
834095 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAAT-TTGTTTTAAGA
* ** * * * **
834131 AAAACAATCTTGAGTGAAATAAATATTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAAT-TTGTTTTAAGA
*
834167 AAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TTTGTTTTAAGA
834203 AAAACA
1 AAAACA
834209 AATTTGAGTG
Statistics
Matches: 57, Mismatches: 20, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
36 56 0.98
37 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (35 bp):
AAAACAGTCTCAAGTGAGACAAATTTGTTTTAAGA
Found at i:834187 original size:72 final size:74
Alignment explanation
Indices: 834050--834224 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 74
834040 TAAAATCTTC
** * *
834050 TTAA-AAAAACAGCCTTGAGTGAAATGAAATACCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAATA-CTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
834114 CAAA-TCTTGTT
64 CAAAGT-ATGTT
*
834125 TTAAGAAAAACAATCTTGAGTGAAATAAATA-TTCTTTCGAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATACTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
834188 AAGTATGTT
66 AAGTATGTT
*
834197 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
834225 TCATCTGCAT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
72 48 0.53
73 14 0.16
75 9 0.10
76 19 0.21
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATACTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACA
AAGTATGTT
Found at i:835673 original size:183 final size:183
Alignment explanation
Indices: 835365--835901 Score: 923
Period size: 183 Copynumber: 2.9 Consensus size: 183
835355 ATCAGGTTTA
*
835365 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
835430 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCTAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCTAGGGCTTTCGAGT
835494 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
835548 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTAACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
835613 GCCAAGTGTTCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCTAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCTAGGGCTTTCGAGTT
*
835678 TCCTCTATAACTAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* ** **
835731 ACTGAATGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAATAGTGGAGCAAACAATGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
835796 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATATATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCTAGGGCTTTCGAGTT
835861 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
835902 CGGATTTAAT
Statistics
Matches: 334, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 333 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCTAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:839994 original size:2 final size:2
Alignment explanation
Indices: 839983--840012 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
839973 AAGGAAAAAA
*
839983 AT AT AA 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
840013 CAAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:840523 original size:18 final size:17
Alignment explanation
Indices: 840500--840542 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
840490 ATATATACAT
840500 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
840518 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
840535 ATAA-AATA
1 ATAATAATA
840543 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:840550 original size:56 final size:55
Alignment explanation
Indices: 840432--840550 Score: 125
Period size: 58 Copynumber: 2.1 Consensus size: 55
840422 AATATTAAAG
* * * *
840432 ATATATATATATAATAATAAAATATAGTAAAAAAATAAATGAAAATAATTTAATATAT
1 ATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAATATAC
*
840490 ATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AATATCC
1 ATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAATATAC
840546 ATATA
1 ATATA
840551 ATAAATAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
56 10 0.19
58 19 0.36
59 9 0.17
60 4 0.08
61 11 0.21
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (55 bp):
ATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAATATAC
Found at i:840950 original size:37 final size:37
Alignment explanation
Indices: 840900--841004 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
840890 GTGCTTGTGG
* * * *
840900 ATCCTATCTTTAGGATTTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
840937 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTGT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
840974 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
841005 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:841096 original size:20 final size:21
Alignment explanation
Indices: 841052--841096 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
841042 TCTAAACATT
*
841052 AAATTTTAAATTTTAATATCA
1 AAATTTTAAATTTTAATACCA
841073 AAATTTTAAATTTTAAT-CCA
1 AAATTTTAAATTTTAATACCA
841093 AAAT
1 AAAT
841097 AAATATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTTAAATTTTAATACCA
Found at i:841939 original size:25 final size:24
Alignment explanation
Indices: 841886--841950 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
841876 TAGTTTTAGT
* *
841886 TTTTTAAATATTTGAATATTTTTA
1 TTTTTAAAAATTTAAATATTTTTA
*
841910 -ATTTAAAAATTTAAATATATTTTA
1 TTTTTAAAAATTTAAATAT-TTTTA
*
841934 TTTTTAAACAAATTAAA
1 TTTTTAAA-AATTTAAA
841951 CAAGCACTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 15 0.45
24 5 0.15
25 6 0.18
26 7 0.21
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTTAAAAATTTAAATATTTTTA
Found at i:844800 original size:20 final size:20
Alignment explanation
Indices: 844775--844847 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
844765 ACTTCGACTA
844775 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
** * *
844795 TCGCATTATGATAGTCCA-AGT
1 TCGCATTGCGAT-TTACATA-T
*
844816 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
844836 TCGCATTGCGAT
1 TCGCATTGCGAT
844848 AGTCCAAGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:844825 original size:41 final size:41
Alignment explanation
Indices: 844775--844955 Score: 183
Period size: 42 Copynumber: 4.4 Consensus size: 41
844765 ACTTCGACTA
* *
844775 TCGCATTGCGATTTACATATTCGCATTATGATAGTCCAAGT
1 TCGCGTTGCGATTTACATATTCGCATTACGATAGTCCAAGT
*
844816 TCGCGTTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTACATATTCGCATTACGATAGTCCAAGT
* *
844857 TCGTGTTGCGATTTATTCCA-AGTTCG--TTACGATAGTCGAAGT
1 TCGCGTTGCGATTTA---CATA-TTCGCATTACGATAGTCCAAGT
* *
844899 TCGCGTTGCGATTTATTCCAAATTCG--TTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTA---CATATTCGCATTACGATAGTCCAAGT
* *
844941 TTGCATTGCGATTTA
1 TCGCGTTGCGATTTA
844956 TTCCAAGTTC
Statistics
Matches: 124, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
41 52 0.42
42 64 0.52
43 2 0.02
44 6 0.05
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTACATATTCGCATTACGATAGTCCAAGT
Found at i:844865 original size:21 final size:21
Alignment explanation
Indices: 844804--844980 Score: 127
Period size: 21 Copynumber: 8.5 Consensus size: 21
844794 TTCGCATTAT
844804 GATAGTCCAAGTTCGCGTTGC
1 GATAGTCCAAGTTCGCGTTGC
* * *
844825 GAT-TTACATA-TTCGCATTGC
1 GATAGTCCA-AGTTCGCGTTGC
*
844845 GATAGTCCAAGTTCGTGTTGC
1 GATAGTCCAAGTTCGCGTTGC
* *
844866 GATTTATTCCAAGTT--CGTTAC
1 GA--TAGTCCAAGTTCGCGTTGC
*
844887 GATAGTCGAAGTTCGCGTTGC
1 GATAGTCCAAGTTCGCGTTGC
* *
844908 GATTTATTCCAAATT--CGTTGC
1 GA--TAGTCCAAGTTCGCGTTGC
* *
844929 GATAGTCCAAGTTTGCATTGC
1 GATAGTCCAAGTTCGCGTTGC
*
844950 GATTTATTCCAAGTT--CGTTGC
1 GA--TAGTCCAAGTTCGCGTTGC
844971 GATAGTCCAA
1 GATAGTCCAA
844981 AATCGCAACG
Statistics
Matches: 121, Mismatches: 22, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
19 25 0.21
20 16 0.13
21 52 0.43
23 28 0.23
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (21 bp):
GATAGTCCAAGTTCGCGTTGC
Found at i:844900 original size:42 final size:42
Alignment explanation
Indices: 844804--844980 Score: 245
Period size: 42 Copynumber: 4.2 Consensus size: 42
844794 TTCGCATTAT
844804 GATAGTCCAAGTTCGCGTTGCGATTTA---CATA-TTCGCATTGC
1 GATAGTCCAAGTTCGCGTTGCGATTTATTCCA-AGTTCG--TTGC
* *
844845 GATAGTCCAAGTTCGTGTTGCGATTTATTCCAAGTTCGTTAC
1 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
* *
844887 GATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
* *
844929 GATAGTCCAAGTTTGCATTGCGATTTATTCCAAGTTCGTTGC
1 GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
844971 GATAGTCCAA
1 GATAGTCCAA
844981 AATCGCAACG
Statistics
Matches: 122, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
41 26 0.21
42 89 0.73
43 1 0.01
44 6 0.05
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
GATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
Found at i:848890 original size:22 final size:22
Alignment explanation
Indices: 848865--848924 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
848855 TCATTAGTAT
848865 TCTTTATTTTTCTTTTATTACA
1 TCTTTATTTTTCTTTTATTACA
848887 TCTTTATTTTTCTTTTATTACA
1 TCTTTATTTTTCTTTTATTACA
848909 TCTTTATTTTT-TTTTA
1 TCTTTATTTTTCTTTTA
848925 GTTTTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.13
22 33 0.87
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.72
Consensus pattern (22 bp):
TCTTTATTTTTCTTTTATTACA
Found at i:852907 original size:3 final size:3
Alignment explanation
Indices: 852899--852959 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
852889 GAATAGGGTT
852899 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
852947 TTG TTG TTG TTG T
1 TTG TTG TTG TTG T
852960 GTTTATATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:859776 original size:18 final size:18
Alignment explanation
Indices: 859754--859803 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
859744 AAAGAATAGT
*
859754 AATAATAGAAATAATAAG
1 AATAATAAAAATAATAAG
* * * *
859772 GATAATATAAAGAATAAT
1 AATAATAAAAATAATAAG
859790 AATAATAAAAATAA
1 AATAATAAAAATAA
859804 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (18 bp):
AATAATAAAAATAATAAG
Found at i:859862 original size:3 final size:3
Alignment explanation
Indices: 859854--859896 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
859844 ATATATACGT
*
859854 ATA ATA ATA ATA ATA ACA ATA ATA ATA TATA TATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA -ATA ATA A
859897 AACGTATAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:859893 original size:18 final size:17
Alignment explanation
Indices: 859853--859896 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
859843 TATATATACG
859853 TATAATAATAATA-ATA
1 TATAATAATAATATATA
*
859869 -ACAATAATAATATATA
1 TATAATAATAATATATA
859885 TATATATAATAA
1 TATA-ATAATAA
859897 AACGTATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 11 0.48
16 3 0.13
17 2 0.09
18 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAATAATAATATATA
Found at i:859905 original size:48 final size:51
Alignment explanation
Indices: 859828--859938 Score: 124
Period size: 46 Copynumber: 2.2 Consensus size: 51
859818 TATAAAAAGA
* *
859828 AATAAAATATATACATATATATACGTATAA-T-A-ATAATAATA-AC-AAT
1 AATAATATATATACATATATAAACGTATAAGTGACATAATAATATACTAAT
* *
859874 AATAATATATATATATATAATAAAACGTATAAGTGACATAATACTATACTAAT
1 AATAATATATATACATAT-AT-AAACGTATAAGTGACATAATAATATACTAAT
859927 AATACATATATA
1 AATA-ATATATA
859939 CGAGTGTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 16 0.30
47 2 0.04
48 9 0.17
49 1 0.02
50 1 0.02
51 8 0.15
52 2 0.04
53 7 0.13
54 7 0.13
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (51 bp):
AATAATATATATACATATATAAACGTATAAGTGACATAATAATATACTAAT
Found at i:859985 original size:20 final size:19
Alignment explanation
Indices: 859957--859997 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
859947 AAACACTAAT
859957 AATAATATAATATATATATA
1 AATAATATAATATA-ATATA
* *
859977 AATATTATAATGTAATATA
1 AATAATATAATATAATATA
859996 AA
1 AA
859998 AAGATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AATAATATAATATAATATA
Found at i:861020 original size:18 final size:16
Alignment explanation
Indices: 860989--861029 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
860979 AAAAAAAATG
860989 TAAATATAATTTATAA
1 TAAATATAATTTATAA
861005 TAAATATATATATTAT-A
1 TAAATATA-AT-TTATAA
861022 T-AATATAA
1 TAAATATAA
861030 GGATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 4 0.17
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATTTATAA
Found at i:861263 original size:20 final size:20
Alignment explanation
Indices: 861240--861281 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
861230 GAATCCTTCG
861240 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
* *
861260 TCGTGAAGTTGAAGTCGAAC
1 TCGTGAAATTGAAATCGAAC
861280 TC
1 TC
861282 AGAGTTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:861524 original size:105 final size:105
Alignment explanation
Indices: 861362--862286 Score: 1769
Period size: 105 Copynumber: 8.8 Consensus size: 105
861352 ATTGTTTATC
* * *
861362 GACAACCAGCGGTCCCTTCGTCATGAAGTTGAACCTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
861427 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
861467 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
861532 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
861572 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
861637 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
861677 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
861742 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
*
861782 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* *
861847 GTGAAGTTGAAATTGACTCTAAATTTGAGAAATGTTTAGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
861887 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
861952 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
*
861992 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
862057 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
*
862097 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
862162 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
*
862202 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
862267 GTGAAGTTGAAATTGGCTCT
66 GTGAAGTTGAAATTGGCTCT
862287 GGGTAAAACC
Statistics
Matches: 810, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 810 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
Found at i:862485 original size:1 final size:1
Alignment explanation
Indices: 862479--862503 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
862469 TGTTTGATGA
862479 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
862504 GAAGATGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:869713 original size:21 final size:22
Alignment explanation
Indices: 869688--869736 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
869678 TCTTTATTTG
*
869688 ATCTTCTAATATTTTTATCTTT
1 ATCTTCTAATATTTTTAGCTTT
* *
869710 -TCTTC-CATCTTTTTAGCTTT
1 ATCTTCTAATATTTTTAGCTTT
869730 ATCTTCT
1 ATCTTCT
869737 TCATCAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
ATCTTCTAATATTTTTAGCTTT
Found at i:874318 original size:18 final size:17
Alignment explanation
Indices: 874296--874344 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
874286 AAAGAATAGT
874296 AATAATAGAAATAATAAG
1 AATAATA-AAATAATAAG
* * *
874314 GATAATATAAAGAATAAT
1 AATAATA-AAATAATAAG
874332 AATAATAAAATAA
1 AATAATAAAATAA
874345 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
AATAATAAAATAATAAG
Found at i:874439 original size:46 final size:54
Alignment explanation
Indices: 874374--874474 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 54
874364 AAGAAATAAA
*
874374 ATATATACATATATACGTATAA-T-A-ATAATAATA-AC-AATAATA-ATATAT
1 ATATATACATATAAACGTATAAGTGACATAATAATATACTAATAATACATATAT
*
874422 ATATATA-ATA-AAACGTATAAGTGACATAATACTATACTAATAATACATATAT
1 ATATATACATATAAACGTATAAGTGACATAATAATATACTAATAATACATATAT
874474 A
1 A
874475 CGAGTGTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
46 9 0.20
47 4 0.09
48 8 0.18
49 8 0.18
50 2 0.04
51 7 0.16
52 7 0.16
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (54 bp):
ATATATACATATAAACGTATAAGTGACATAATAATATACTAATAATACATATAT
Found at i:874512 original size:13 final size:14
Alignment explanation
Indices: 874491--874529 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
874481 TAAAACACTA
874491 ATAATATAATATAT
1 ATAATATAATATAT
874505 AT-ATATAATAT-T
1 ATAATATAATATAT
*
874517 ATAATGTAATATA
1 ATAATATAATATA
874530 AAAGATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 3 0.14
13 17 0.77
14 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (14 bp):
ATAATATAATATAT
Found at i:875552 original size:18 final size:16
Alignment explanation
Indices: 875521--875561 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
875511 AAAAAAAATG
875521 TAAATATAATTTATAA
1 TAAATATAATTTATAA
875537 TAAATATATATATTAT-A
1 TAAATATA-AT-TTATAA
875554 T-AATATAA
1 TAAATATAA
875562 GGATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 4 0.17
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATTTATAA
Found at i:878513 original size:57 final size:57
Alignment explanation
Indices: 878406--878514 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
878396 TATATGATGC
* * * * *
878406 TTTTGAATTAAAATAAGGTAGGTATTTTCTTAAACAATCACAAATTGTGCTTTCAGA
1 TTTTGAAGTAAAATAAGGTAGATATTTGCTTAAACAAGCACAAATAGTGCTTTCAGA
* * * *
878463 TTTTGAAGTAAAATAAGGTTGATATTTGCTTAAACTAGCATAAGTAGTGCTT
1 TTTTGAAGTAAAATAAGGTAGATATTTGCTTAAACAAGCACAAATAGTGCTT
878515 ACATTATTGC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (57 bp):
TTTTGAAGTAAAATAAGGTAGATATTTGCTTAAACAAGCACAAATAGTGCTTTCAGA
Found at i:887413 original size:13 final size:13
Alignment explanation
Indices: 887397--887427 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
887387 ATTCAAAATT
887397 AAAAATAATATAA
1 AAAAATAATATAA
887410 AAAAATAATATAA
1 AAAAATAATATAA
887423 AAAAA
1 AAAAA
887428 ATCATATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAATAATATAA
Found at i:887425 original size:14 final size:14
Alignment explanation
Indices: 887397--887436 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
887387 ATTCAAAATT
887397 AAAAATAATAT-AA
1 AAAAATAATATAAA
887410 AAAAATAATATAAA
1 AAAAATAATATAAA
*
887424 AAAAATCATATAA
1 AAAAATAATATAA
887437 CTAATAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAATATAAA
Found at i:889439 original size:12 final size:12
Alignment explanation
Indices: 889422--889504 Score: 64
Period size: 12 Copynumber: 6.9 Consensus size: 12
889412 AAAAATCAAA
889422 AACAGAATTCAG
1 AACAGAATTCAG
889434 AACAGATATT-AG
1 AACAGA-ATTCAG
* *
889446 AACAGAATCCAT
1 AACAGAATTCAG
*
889458 ATA-AGAAATCAG
1 A-ACAGAATTCAG
889470 AACAGAATTCAG
1 AACAGAATTCAG
** *
889482 GTCATGTA-TCAG
1 AACA-GAATTCAG
889494 AACAGAATTCA
1 AACAGAATTCA
889505 AGTCGAAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
11 5 0.09
12 42 0.79
13 6 0.11
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:889516 original size:24 final size:24
Alignment explanation
Indices: 889463--889518 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
889453 TCCATATAAG
*
889463 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAT
**
889487 GTATCAGAACAGAATTCAAGTCGA-
1 AAATCAGAACAGAATTCAAGTC-AT
889511 AAATCAGA
1 AAATCAGA
889519 TAAAATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAT
Found at i:892012 original size:15 final size:15
Alignment explanation
Indices: 891992--892028 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
891982 GGTCAACGTC
891992 AGTCAACGATCAACG
1 AGTCAACGATCAACG
892007 AGTCAACGATCAACG
1 AGTCAACGATCAACG
*
892022 GGTCAAC
1 AGTCAAC
892029 AGGTCAGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (15 bp):
AGTCAACGATCAACG
Found at i:892014 original size:8 final size:8
Alignment explanation
Indices: 891992--892028 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
891982 GGTCAACGTC
891992 AGTCAACG
1 AGTCAACG
892000 A-TCAACG
1 AGTCAACG
892007 AGTCAACG
1 AGTCAACG
892015 A-TCAACG
1 AGTCAACG
*
892022 GGTCAAC
1 AGTCAAC
892029 AGGTCAGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (8 bp):
AGTCAACG
Found at i:892952 original size:2 final size:2
Alignment explanation
Indices: 892945--892973 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
892935 ATCTAATTGA
892945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
892974 AATAGAGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:895019 original size:23 final size:23
Alignment explanation
Indices: 894993--895070 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
894983 CACCACAGCT
894993 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
895016 CATATAATTGCATCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
895039 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
895062 TATAATAAT
1 CAT-ATAAT
895071 GTCCATAAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:895261 original size:105 final size:103
Alignment explanation
Indices: 895081--895296 Score: 360
Period size: 105 Copynumber: 2.1 Consensus size: 103
895071 GTCCATAAGA
* * *
895081 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAATTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
895146 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
*
895184 ACCACATATCATTCCTTAAGAATCATATATATATATGCCAAGGATCAAGTATGTGTCTCACCAGA
1 ACCACATATCATTCCTTAAGAATCATATACATATA--CCAAGGATCAAGTATGTGTCTCACCAGA
* *
895249 CTTTACACATGTTTCAAAGAATACATATATGTCCCGAAGG
64 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
895289 ACCACATA
1 ACCACATA
895297 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 34 0.32
105 71 0.68
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
Found at i:900334 original size:21 final size:21
Alignment explanation
Indices: 900310--900349 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
900300 TTTTCAAAGG
900310 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
900331 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
900350 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:900399 original size:19 final size:19
Alignment explanation
Indices: 900375--900413 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
900365 TCGAATGCAT
*
900375 TCCATGCACCGATGCGCTC
1 TCCATGCACCGATGCACTC
*
900394 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
900413 T
1 T
900414 AATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.18, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:900492 original size:64 final size:63
Alignment explanation
Indices: 900310--900519 Score: 201
Period size: 64 Copynumber: 3.2 Consensus size: 63
900300 TTTTCAAAGG
* ** *
900310 CATGCACCGATGCATCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCA
1 CATGCATCGATGCA-CAAT-CCATGCATCGATGCACTC--T-AATTTATTAAAACATCGAATGCA
*
900374 TTC
61 TTT
* * **
900377 CATGCACCGATGCGCTCTCCATGCATCGATGCACTCTAATTTAATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACTCTAATTT-ATTAAAACATCGAATGCATTT
* * * *
900441 GATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGTTATTT-TTCAAACATCGAATGCACT
1 CATGCATCGATGCACAATCCATGCATCGATGCACTC---TAATTTATTAAAACATCGAATGCATT
900504 T
63 T
900505 CATGCATCGATGCAC
1 CATGCATCGATGCAC
900520 TCTTAGTACA
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
63 4 0.03
64 81 0.66
65 15 0.12
66 9 0.07
67 13 0.11
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACTCTAATTTATTAAAACATCGAATGCATTT
Found at i:906361 original size:24 final size:22
Alignment explanation
Indices: 906333--906412 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
906323 CACTTAACAA
906333 TGCATCGATGCATCCTTTTGAATG
1 TGCATCGATGCATCC--TTGAATG
*
906357 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
906377 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
906401 TGCATCGATGCA
1 TGCATCGATGCA
906413 CAAGACCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 11 0.23
24 19 0.40
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:906368 original size:44 final size:42
Alignment explanation
Indices: 906313--906435 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 42
906303 TTGTGCTTAA
* *
906313 TGCACCGATGCACTTAACAATGCATCGATGCATCCTTTTGAATG
1 TGCATCGATGCACTAAACAATGCATCGATGCATCC--TTGAATG
*** *
906357 TGCATCGATGCA-TCCGCATGATGCACCGATGCATGCCTTGAATG
1 TGCATCGATGCACTAAACA--ATGCATCGATGCAT-CCTTGAATG
*
906401 TGCATCGATGCAC-AAGACCATGCATCGATGCATCC
1 TGCATCGATGCACTAA-ACAATGCATCGATGCATCC
906436 ATCGGGTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
42 2 0.03
43 16 0.25
44 30 0.47
45 14 0.22
46 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (42 bp):
TGCATCGATGCACTAAACAATGCATCGATGCATCCTTGAATG
Found at i:908866 original size:21 final size:21
Alignment explanation
Indices: 908842--908881 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
908832 TTTTCAAAGG
*
908842 CATGCACCGATGCATCAATAC
1 CATGCACCAATGCATCAATAC
*
908863 CATGCATCAATGCATCAAT
1 CATGCACCAATGCATCAAT
908882 GAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (21 bp):
CATGCACCAATGCATCAATAC
Found at i:908931 original size:19 final size:19
Alignment explanation
Indices: 908907--908945 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
908897 TCGAATGAAT
908907 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
908926 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
908945 T
1 T
908946 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:908978 original size:64 final size:65
Alignment explanation
Indices: 908842--909071 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 65
908832 TTTTCAAAGG
* * * * *
908842 CATGCACCGATGCA-TCAATACCATGCATCAATGCA-TCAATGAATAAATTGAAACATCGAATGA
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGC
*
908905 ATTC
62 ATTT
908909 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTT
* * ** * * *
908973 GATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCAT
909035 TT
64 TT
* * *
909037 CATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACT
909072 AGGAGTCCAA
Statistics
Matches: 138, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
63 2 0.01
64 99 0.72
65 14 0.10
66 7 0.05
67 14 0.10
68 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTT
Found at i:909051 original size:17 final size:19
Alignment explanation
Indices: 909023--909071 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
909013 ATTTTTCAAA
909023 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
909041 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
909060 CACCGATGCACT
1 CATCGATGCACT
909072 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:913316 original size:5 final size:5
Alignment explanation
Indices: 913308--913343 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
913298 GTCTCGTCTT
* *
913308 GGCTC GGCTC GGCTC GGCAC GGCTC GGCTT GGCTC G
1 GGCTC GGCTC GGCTC GGCTC GGCTC GGCTC GGCTC G
913344 TGGTCGTGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.36, G:0.42, T:0.19
Consensus pattern (5 bp):
GGCTC
Found at i:919758 original size:11 final size:11
Alignment explanation
Indices: 919742--919767 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
919732 GCATTTGTTT
919742 TAATAGCAAAG
1 TAATAGCAAAG
919753 TAATAGCAAAG
1 TAATAGCAAAG
919764 TAAT
1 TAAT
919768 TTAGGTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (11 bp):
TAATAGCAAAG
Found at i:919825 original size:39 final size:39
Alignment explanation
Indices: 919782--919860 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
919772 GTACTTCAAG
919782 TAAAAAATAATTTATATATTTATTTTAGTGAAAAATAAT
1 TAAAAAATAATTTATATATTTATTTTAGTGAAAAATAAT
919821 TAAAAAATAATTTATATATTTATTTTAGTGAAAAATAAT
1 TAAAAAATAATTTATATATTTATTTTAGTGAAAAATAAT
919860 T
1 T
919861 TAAGTACTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (39 bp):
TAAAAAATAATTTATATATTTATTTTAGTGAAAAATAAT
Found at i:923329 original size:2 final size:2
Alignment explanation
Indices: 923322--923352 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
923312 TAAACGTTAT
923322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
923353 GTATTTGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:924182 original size:2 final size:2
Alignment explanation
Indices: 924175--924200 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
924165 GGAATTTAAA
924175 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
924201 CTTATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:924701 original size:35 final size:35
Alignment explanation
Indices: 924662--924747 Score: 163
Period size: 35 Copynumber: 2.5 Consensus size: 35
924652 AAAATGTTAT
*
924662 ATTACCGTGTTTGGTTTGTTTGACAGTAATGTAAG
1 ATTACAGTGTTTGGTTTGTTTGACAGTAATGTAAG
924697 ATTACAGTGTTTGGTTTGTTTGACAGTAATGTAAG
1 ATTACAGTGTTTGGTTTGTTTGACAGTAATGTAAG
924732 ATTACAGTGTTTGGTT
1 ATTACAGTGTTTGGTT
924748 GAAGGAATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.44
Consensus pattern (35 bp):
ATTACAGTGTTTGGTTTGTTTGACAGTAATGTAAG
Found at i:924872 original size:15 final size:15
Alignment explanation
Indices: 924854--924883 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
924844 ATCGATAATA
924854 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
924869 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
924884 CATCGATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:928030 original size:2 final size:2
Alignment explanation
Indices: 928023--928053 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
928013 AATTTTACAT
928023 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
928054 TAATAACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:931196 original size:11 final size:11
Alignment explanation
Indices: 931180--931216 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
931170 TGGGGAAGAT
931180 GAAACATAAAA
1 GAAACATAAAA
*
931191 GAAACATAGAA
1 GAAACATAAAA
*
931202 GAAACATCAAA
1 GAAACATAAAA
931213 GAAA
1 GAAA
931217 TTGAAGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.68, C:0.11, G:0.14, T:0.08
Consensus pattern (11 bp):
GAAACATAAAA
Found at i:931794 original size:21 final size:20
Alignment explanation
Indices: 931761--931802 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
931751 ATAATTATTT
*
931761 AAAAAATTAAATAAAATATA
1 AAAAAATTAAATAAAAAATA
*
931781 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
931802 A
1 A
931803 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAATA
Found at i:934076 original size:26 final size:26
Alignment explanation
Indices: 934045--934128 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
934035 ATTATTTATA
934045 TATATTTATTTATTTATAAAAATATT
1 TATATTTATTTATTTATAAAAATATT
*
934071 TTTATTTATTTATTTATAAAAATATT
1 TATATTTATTTATTTATAAAAATATT
934097 TATATTTATTTATTTATAAAAATATT
1 TATATTTATTTATTTATAAAAATATT
934123 TATATT
1 TATATT
934129 CATCTGATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATTTATTTATTTATAAAAATATT
Found at i:934160 original size:21 final size:21
Alignment explanation
Indices: 934136--934175 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
934126 ATTCATCTGA
934136 TTAATATTT-TCGAATATATGT
1 TTAATATTTAT-GAATATATGT
*
934157 TTAATGTTTATGAATATAT
1 TTAATATTTATGAATATAT
934176 TTATTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TTAATATTTATGAATATATGT
Found at i:937483 original size:24 final size:25
Alignment explanation
Indices: 937443--937489 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
937433 ATTTAAGAAT
**
937443 AAATTCGTTTATTGATT-TCTTTAC
1 AAATTCGTTTACCGATTCTCTTTAC
937467 AAATTCGTTTACCGATTCTCTTT
1 AAATTCGTTTACCGATTCTCTTT
937490 TTCCTTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (25 bp):
AAATTCGTTTACCGATTCTCTTTAC
Found at i:938261 original size:76 final size:76
Alignment explanation
Indices: 938181--938327 Score: 242
Period size: 76 Copynumber: 1.9 Consensus size: 76
938171 GTTTAATAAG
* * *
938181 ATAATTATACGTCGTCGA-GTTAGGTGTTATACATTTTTCCAACATCCATTGTAGTAACTTCTCA
1 ATAATTATACGTCATC-ACGTTAGATGTTATACATTTTCCCAACATCCATTGTAGTAACTTCTCA
938245 CCATCTTTAAAC
65 CCATCTTTAAAC
*
938257 ATAATTATACGTCATCACGTTAGATGTTATACCTTTTCCCAACATCCATTGTAGTAACTTCTCAC
1 ATAATTATACGTCATCACGTTAGATGTTATACATTTTCCCAACATCCATTGTAGTAACTTCTCAC
938322 CATCTT
66 CATCTT
938328 CCAGCAGTCC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
75 1 0.02
76 65 0.98
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (76 bp):
ATAATTATACGTCATCACGTTAGATGTTATACATTTTCCCAACATCCATTGTAGTAACTTCTCAC
CATCTTTAAAC
Found at i:948394 original size:24 final size:25
Alignment explanation
Indices: 948357--948421 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
948347 AAATATAAAC
*
948357 AATTATT-AAGATATT-CAATACATTA
1 AATTATTAAAAATATTACAA-A-ATTA
948382 AA-TA-TAAAAATATTACAAAATTA
1 AATTATTAAAAATATTACAAAATTA
*
948405 AATTATTAAAAAAATTA
1 AATTATTAAAAATATTA
948422 ATTTAAAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 7 0.21
24 12 0.35
25 15 0.44
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (25 bp):
AATTATTAAAAATATTACAAAATTA
Found at i:952439 original size:19 final size:19
Alignment explanation
Indices: 952403--952439 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
952393 TGGAACGAAC
*
952403 TGCCTGGATTGAGACGAGT
1 TGCCTGGATCGAGACGAGT
*
952422 TGCCTGGATCGAGTCGAG
1 TGCCTGGATCGAGACGAG
952440 CCTGGGTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (19 bp):
TGCCTGGATCGAGACGAGT
Found at i:953890 original size:20 final size:20
Alignment explanation
Indices: 953867--953932 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
953857 AAATCGTAAT
953867 GCGATACTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* *
953887 GCGATTCTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
953907 GCGATTCTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
*
953927 GAGATA
1 GCGATA
953933 ATACAGAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:955097 original size:65 final size:65
Alignment explanation
Indices: 954948--955107 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
954938 TGCACCAAGT
* ***
954948 ATGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGGCTT
1 ATGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGA
* * * **
955012 GTGCATCGATACATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGA
1 ATGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGA
* * *
955077 ATGTATCGGTGCATGGAATGCATTCGATGTT
1 ATGCATCGATGCATGAAATGCATTCGATGTT
955108 CAATTAATTC
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 26 0.32
65 54 0.68
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
ATGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGA
Found at i:955347 original size:20 final size:21
Alignment explanation
Indices: 955324--955363 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
955314 GAATCGAATA
955324 TAAAAT-TATAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
955344 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
955364 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:957444 original size:44 final size:43
Alignment explanation
Indices: 957352--957447 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 43
957342 GCATGGACTC
* * *
957352 ATGCATCGATGCATATTCAAGGCATGCATCGGTGCATCATGGTG
1 ATGCATCGATACATATTCAAGGCATGCATCGATGCAT-ATGGTA
* *
957396 ATGCATCGATACATATTCAAAGGGATGCATCGATGCAT-TGTTAA
1 ATGCATCGATACATATTC-AAGGCATGCATCGATGCATATGGT-A
957440 ATGCATCG
1 ATGCATCG
957448 GTGCATAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
43 3 0.07
44 25 0.56
45 17 0.38
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (43 bp):
ATGCATCGATACATATTCAAGGCATGCATCGATGCATATGGTA
Found at i:963365 original size:65 final size:65
Alignment explanation
Indices: 963231--963390 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
963221 TGCACCAAGT
* ***
963231 ATGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGGCTT
1 ATGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGA
* * * ** *
963295 GTGCATCGATACATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGTATCGATGCATGGAGA
1 ATGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGA
* *
963360 ATGCATCGGTGCATGGAATGCATTCGATGTT
1 ATGCATCGATGCATGAAATGCATTCGATGTT
963391 CAATTAATTC
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 26 0.32
65 54 0.68
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
ATGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGA
Found at i:963630 original size:20 final size:21
Alignment explanation
Indices: 963607--963646 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
963597 GAATCGAATA
963607 TAAAAT-TATAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
963627 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
963647 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:963953 original size:20 final size:20
Alignment explanation
Indices: 963928--963983 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
963918 CAACGGGGAA
963928 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
963948 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
963968 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
963984 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:964043 original size:19 final size:19
Alignment explanation
Indices: 964002--964066 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
963992 GAAATGAAAA
964002 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
964018 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
964035 TCGCATTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
964054 TCGCATTGCGATT
1 TCGCATTGCGATT
964067 CTCTCGTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
19 25 0.60
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:965688 original size:41 final size:42
Alignment explanation
Indices: 965643--965721 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
965633 CGATGACAAT
*
965643 GGCCTCTTGAATG-GTGG-GGGAGACTCTTGAGGGATGATAGG
1 GGCCTCTTGAACGAGTGGAGGG-GACTCTTGAGGGATGATAGG
* *
965684 GGCCTCTTGAACGATTGGAGGGTACTCTTGAGGGATGA
1 GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGA
965722 CAGGTGAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 12 0.36
42 18 0.55
43 3 0.09
ACGTcount: A:0.20, C:0.14, G:0.41, T:0.25
Consensus pattern (42 bp):
GGCCTCTTGAACGAGTGGAGGGGACTCTTGAGGGATGATAGG
Found at i:966116 original size:20 final size:20
Alignment explanation
Indices: 966069--966155 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
966059 TAGTTTACTT
* *
966069 TCGCAACACGAAACAT-ACTT
1 TCGCAACGCGAAA-ATGACTA
966089 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
966109 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
966129 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
966148 TCGCAACG
1 TCGCAACG
966156 ACAAAATCGC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.26
20 42 0.74
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Done.