Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005783.1 Hibiscus syriacus cultivar Beakdansim tig00013544_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: 90895
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1464 original size:32 final size:31
Alignment explanation
Indices: 1428--1532 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 31
1418 GGAACAATGA
1428 GGGCATCTTTGAAGATTTAACATCAAATGTTG
1 GGGCATCTTTG-AGATTTAACATCAAATGTTG
* *
1460 GGGCATTTTTTAGATTTAACATCAAATGTTG
1 GGGCATCTTTGAGATTTAACATCAAATGTTG
* * ** *
1491 GGGCATTTTTTGAGATTCAACATTGAATATT-
1 GGGCA-TCTTTGAGATTTAACATCAAATGTTG
1522 GGGCATCTTTG
1 GGGCATCTTTG
1533 GGAATTCAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 5 0.08
31 30 0.47
32 29 0.45
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (31 bp):
GGGCATCTTTGAGATTTAACATCAAATGTTG
Found at i:1476 original size:31 final size:32
Alignment explanation
Indices: 1435--1513 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
1425 TGAGGGCATC
1435 TTTGAAGATTTAACATCAAATGTTGGGGCATTT
1 TTTG-AGATTTAACATCAAATGTTGGGGCATTT
1468 TTT-AGATTTAACATCAAATGTTGGGGCATTT
1 TTTGAGATTTAACATCAAATGTTGGGGCATTT
*
1499 TTTGAGATTCAACAT
1 TTTGAGATTTAACAT
1514 TGAATATTGG
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
31 31 0.70
32 10 0.23
33 3 0.07
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (32 bp):
TTTGAGATTTAACATCAAATGTTGGGGCATTT
Found at i:2517 original size:36 final size:36
Alignment explanation
Indices: 2470--2695 Score: 234
Period size: 36 Copynumber: 6.4 Consensus size: 36
2460 ATTGAAAACA
* *
2470 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2506 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2542 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** * *
2571 TTTTATTTGAAACAAATTTTATCTCTCTTGAGAGAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * *
2607 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
2644 TTTCTCTTGAAACAAATTTAGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
2680 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
2696 ATCTTTGAAT
Statistics
Matches: 158, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.11
30 2 0.01
35 2 0.01
36 101 0.64
37 33 0.21
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2541 original size:101 final size:101
Alignment explanation
Indices: 2411--2659 Score: 293
Period size: 101 Copynumber: 2.5 Consensus size: 101
2401 TATGTTTTAT
* ** * *
2411 TTGAAACCAATTTCATCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA-TTGAAAACATTTCC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAACATTTGAAAACATTTCA
* *
2475 CTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCC
65 CTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
* * * ** * *
2512 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTAT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACATTTGAAAACATTTCAC
* * **
2577 TTGAAACAAATTTTATCTCTCTTGAGAGAGTTTCTT
66 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
* *
2613 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
2660 TTTAGTCTCT
Statistics
Matches: 125, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
100 4 0.03
101 84 0.67
102 37 0.30
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (101 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAACATTTGAAAACATTTCAC
TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
Found at i:2739 original size:138 final size:138
Alignment explanation
Indices: 2490--2749 Score: 403
Period size: 138 Copynumber: 1.9 Consensus size: 138
2480 AATAAATTTC
*
2490 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * ** * * *
2555 AAAATATTTGAATATGTTTTATTTGAAACAAATTTTATCTCTCTTGAGAGAGTTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTTATCTCCCTTGAGACAGTTTCTTTTGGAAC
2620 TAAGTTTT
131 TAAGTTTT
*
2628 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * *
2693 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTTATCTCCCTTGAGACAGTTTCT
2750 CTTGAAACAC
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 109 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTTATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:2757 original size:65 final size:67
Alignment explanation
Indices: 2653--2811 Score: 223
Period size: 65 Copynumber: 2.4 Consensus size: 67
2643 GTTTCTCTTG
* * **
2653 AAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
2716 TA
66 TA
* *
2718 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
2783 TA
66 TA
* *
2785 AAACAAAATTTTATTTCCCTTGAGACA
1 AAAC-AAATTTTGTCTCCCTTGAGACA
2812 TATCTTTGAG
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
65 33 0.40
66 2 0.02
67 28 0.34
68 20 0.24
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:3703 original size:106 final size:106
Alignment explanation
Indices: 3518--3866 Score: 486
Period size: 106 Copynumber: 3.3 Consensus size: 106
3508 AAGGGGCTTC
* *
3518 CCAGTTTCAAAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACATAAGCTCAA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
* *
3583 CTTCACAACGAAGGGGCGGCTGGCTGTCAACAAACATTTTT
66 CTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAATTTT
3624 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
1 CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
* ** *
3689 CTTCACAACGAAGGGGCGAATGATTGTCAACAATA-ACTTTT
66 CTTCACAACGAAGGGGCGACTGGCTGTCAACAA-ACAATTTT
* * * * *
3730 -CAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGAACTCGAGACAACACAAGC
1 CCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGC
* * *
3794 TCAACTTCACAGCGAAGGGGCGACTAGCTGTCAACAAACAATTTC
62 TCAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAATTTT
*
3839 CCAGTTCCAGAGCCAATTTCAACTTCAC
1 CCAGTTTCAGAGCCAATTTCAACTTCAC
3867 GACGGATGAT
Statistics
Matches: 215, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
105 3 0.01
106 118 0.55
107 2 0.01
108 2 0.01
109 87 0.40
110 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CCAGTTTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAA
CTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAATTTT
Found at i:4815 original size:2 final size:2
Alignment explanation
Indices: 4805--4835 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4795 TTTTTTAGAT
*
4805 TA TA AA 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
4836 TATTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:4871 original size:42 final size:39
Alignment explanation
Indices: 4821--4926 Score: 122
Period size: 42 Copynumber: 2.6 Consensus size: 39
4811 TATATATATA
4821 TATATATATATATATTATTTTTTATTATCAGTTTTATTAATT
1 TATATATATATATATTATTTTTT-TTAT-AGTTTTATTAA-T
* ** *
4863 TATGTATATATATATTTACTATTTTTTTATTTTTTTATTTAT
1 TATATATATATATA-TTA-T-TTTTTTTATAGTTTTATTAAT
4905 TATATATATATATATTATTTTT
1 TATATATATATATATTATTTTT
4927 ACTTTTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
39 4 0.07
40 1 0.02
41 3 0.05
42 27 0.48
43 11 0.20
44 5 0.09
45 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (39 bp):
TATATATATATATATTATTTTTTTTATAGTTTTATTAAT
Found at i:4895 original size:8 final size:8
Alignment explanation
Indices: 4882--4998 Score: 76
Period size: 8 Copynumber: 14.1 Consensus size: 8
4872 ATATATTTAC
4882 TATTTTTT
1 TATTTTTT
4890 TATTTTTT
1 TATTTTTT
4898 TATTTATTAT
1 TATTT-TT-T
* * *
4908 ATATATATA
1 -TATTTTTT
4917 TATTATTTT
1 TATT-TTTT
*
4926 TACTTTTT
1 TATTTTTT
*
4934 TATTATTAT
1 TATT-TTTT
*
4943 T-TTTATT
1 TATTTTTT
*
4950 TATTTGTT
1 TATTTTTT
* *
4958 TATTTATA
1 TATTTTTT
4966 TATTTTTT
1 TATTTTTT
*
4974 TCTTTTTAT
1 TATTTTT-T
4983 TA-TTTTT
1 TATTTTTT
4990 TATTTTTT
1 TATTTTTT
4998 T
1 T
4999 TGTATTTATT
Statistics
Matches: 83, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
7 6 0.07
8 58 0.70
9 13 0.16
10 2 0.02
11 4 0.05
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (8 bp):
TATTTTTT
Found at i:4905 original size:4 final size:4
Alignment explanation
Indices: 4853--5009 Score: 69
Period size: 4 Copynumber: 39.8 Consensus size: 4
4843 TATTATCAGT
* * * * * * *
4853 TTTA TTAA TTTA TGTA TATA TATA TTTA -CTA TTTT TTTA TTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * *
4900 TTTA TTATA TATA TATA TATTA -TT- TTTA CTTT- TTTA -TTA TTATT
1 TTTA TT-TA TTTA TTTA T-TTA TTTA TTTA -TTTA TTTA TTTA TT-TA
* * * * *
4944 TTTA TTTA TTTG TTTA TTTA TATA TTTT TTTC TTTT TATTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
4992 TTT- TTT- TTGTA TTTA TTT
1 TTTA TTTA TT-TA TTTA TTT
5010 TACTTACTAT
Statistics
Matches: 117, Mismatches: 23, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
3 20 0.17
4 81 0.69
5 16 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:4909 original size:38 final size:36
Alignment explanation
Indices: 4823--4942 Score: 109
Period size: 36 Copynumber: 3.1 Consensus size: 36
4813 TATATATATA
*
4823 TATATATATATATTATTTTTTATTATCAGTTTTATTAATTTAT
1 TATATATATATA-TATTATTT-TTA-C--TTTT-TT-ATTTAT
*
4866 GTATATATATATTTACTATT-TTTTTATTTTTTTATTTAT
1 -TATATATATA--TA-TATTATTTTTACTTTTTTATTTAT
4905 TATATATATATATATTATTTTTACTTTTTTA-TTAT
1 TATATATATATATATTATTTTTACTTTTTTATTTAT
4940 TAT
1 TAT
4943 TTTTATTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
35 11 0.16
36 15 0.21
38 10 0.14
39 6 0.09
40 2 0.03
41 4 0.06
44 13 0.19
45 3 0.04
46 6 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (36 bp):
TATATATATATATATTATTTTTACTTTTTTATTTAT
Found at i:4928 original size:47 final size:46
Alignment explanation
Indices: 4815--4994 Score: 151
Period size: 48 Copynumber: 3.9 Consensus size: 46
4805 TATAAATATA
* * ** *
4815 TATATATATATATATATATATTA-TTTTTTATTATCAGTTTTATTAATT
1 TATATATATATATAT-TTTTTTACTTTTTT-TTAT-TTTTTTATTTATT
*
4863 TATGTATATATATA----TTTACTATTTTTTTATTTTTTTATTTA-T
1 TATATATATATATATTTTTTTACT-TTTTTTTATTTTTTTATTTATT
4905 TATATATATATATATTATTTTTACTTTTTTATTATTATTTTTATTTATT
1 TATATATATATATATT-TTTTTACTTTTTT-TTATT-TTTTTATTTATT
* * * *
4954 TGTTTATTTATATATTTTTTT-CTTTTTATTA-TTTTTTATTT
1 TATATATATATATATTTTTTTACTTTTTTTTATTTTTTTATTT
4995 TTTTTGTATT
Statistics
Matches: 112, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
42 14 0.12
43 11 0.10
44 14 0.12
45 6 0.05
46 8 0.07
47 17 0.15
48 28 0.25
49 14 0.12
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (46 bp):
TATATATATATATATTTTTTTACTTTTTTTTATTTTTTTATTTATT
Found at i:4943 original size:42 final size:40
Alignment explanation
Indices: 4821--4985 Score: 128
Period size: 38 Copynumber: 4.1 Consensus size: 40
4811 TATATATATA
*
4821 TATATATATATATATTATTTTTTATTATCAGTTTTATTAATTTAT
1 TATATATATATATATTA-TTTTTATT-T--TTTTTATT-ATTTAT
* * *
4866 GTATATATATATTTACTATTTTT-TTATTTTT-TTATTTAT
1 -TATATATATATATATTATTTTTATTTTTTTTATTATTTAT
4905 TATATATATATATATTATTTTTACTTTTTTATTATTATTT-T
1 TATATATATATATATTATTTTTA-TTTTTT-TTATTATTTAT
* * * *
4946 TAT-T-TATTTGT-TTATTTATATATTTTTTTCTT-TTTAT
1 TATATATATATATATTATTTTTAT-TTTTTTTATTATTTAT
4983 TAT
1 TAT
4986 TTTTTATTTT
Statistics
Matches: 102, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
36 3 0.03
37 9 0.09
38 33 0.32
39 11 0.11
40 8 0.08
41 10 0.10
42 6 0.06
44 2 0.02
45 5 0.05
46 15 0.15
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (40 bp):
TATATATATATATATTATTTTTATTTTTTTTATTATTTAT
Found at i:4962 original size:18 final size:17
Alignment explanation
Indices: 4886--5065 Score: 75
Period size: 18 Copynumber: 10.3 Consensus size: 17
4876 ATTTACTATT
*
4886 TTTTTATTTTTTTATTTA
1 TTTTTATTTATTT-TTTA
* * * *
4904 TTATATATATATATATTA
1 TT-TTTATTTATTTTTTA
*
4922 TTTTTACTTTTTTATTATTA
1 TTTTTA-TTTATT-TT-TTA
4942 TTTTTATTTATTTGTTTA
1 TTTTTATTTATTT-TTTA
* * *
4960 TTTATATAT-TTTTTTC
1 TTTTTATTTATTTTTTA
4976 TTTTTA-TTATTTTTTA
1 TTTTTATTTATTTTTTA
* *
4992 TTTTT-TTT-GTATTTA
1 TTTTTATTTATTTTTTA
* *
5007 -TTTTACTTACTATTTTA
1 TTTTTATTTA-TTTTTTA
* *
5024 TTTTTGCTTTCTTTATCTTA
1 TTTTT-ATTTATTT-T-TTA
*
5044 TCTTTATTTAATTTTTT-
1 TTTTTATTT-ATTTTTTA
5061 TTTTT
1 TTTTT
5066 TTTCTTCATT
Statistics
Matches: 116, Mismatches: 31, Indels: 31
0.65 0.17 0.17
Matches are distributed among these distances:
14 4 0.03
15 8 0.07
16 21 0.18
17 14 0.12
18 29 0.25
19 21 0.18
20 19 0.16
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTTATTTATTTTTTA
Found at i:5007 original size:47 final size:50
Alignment explanation
Indices: 4885--5009 Score: 136
Period size: 46 Copynumber: 2.5 Consensus size: 50
4875 TATTTACTAT
*
4885 TTTTTTATTTTTTTATTTATTATATATATATATATTATTTTTACTTTTTTATTA
1 TTTTTTATTTTTTT-TGTATT-TAT-T-TATATATTATTTTTACTTTTTTATTA
*
4939 TTATTTT-TATTTATTTG--TTTATTTATATATT-TTTTT-C-TTTTTATTA
1 TT-TTTTAT-TTTTTTTGTATTTATTTATATATTATTTTTACTTTTTTATTA
4985 TTTTTTATTTTTTTTGTATTTATTT
1 TTTTTTATTTTTTTTGTATTTATTT
5010 TACTTACTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
45 11 0.17
46 12 0.19
47 8 0.13
48 5 0.08
49 8 0.13
50 1 0.02
51 3 0.05
52 2 0.03
54 4 0.06
55 9 0.14
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76
Consensus pattern (50 bp):
TTTTTTATTTTTTTTGTATTTATTTATATATTATTTTTACTTTTTTATTA
Found at i:6253 original size:2 final size:2
Alignment explanation
Indices: 6248--6275 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6238 CTCTCTCTCC
6248 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
6276 TCCTTTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:8612 original size:2 final size:2
Alignment explanation
Indices: 8599--8629 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8589 TGAATAACCT
*
8599 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
8630 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9627 original size:31 final size:30
Alignment explanation
Indices: 9592--9653 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
9582 TTAAAATACA
9592 TAAGATATAGTTACTTTCT-TTTTTATTTAAT
1 TAAGATATAGTTACTTT-TATTTTTA-TTAAT
*
9623 TAAGATATATTTACTTTTATTTTTATTAAT
1 TAAGATATAGTTACTTTTATTTTTATTAAT
9653 T
1 T
9654 TAAAATGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (30 bp):
TAAGATATAGTTACTTTTATTTTTATTAAT
Found at i:14983 original size:31 final size:30
Alignment explanation
Indices: 14944--15009 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
14934 TGTCAAATGG
*
14944 ATATTTTATATAAAGTTTGT-GGGTTAAATTA
1 ATATTTTATATAAA-TTT-TAAGGTTAAATTA
* *
14975 GTATTTTATGTAAATTTTAAGGTTAAATTA
1 ATATTTTATATAAATTTTAAGGTTAAATTA
15005 ATATT
1 ATATT
15010 CTGTCTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 17 0.57
31 12 0.40
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (30 bp):
ATATTTTATATAAATTTTAAGGTTAAATTA
Found at i:17195 original size:29 final size:30
Alignment explanation
Indices: 17151--17207 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
17141 TGAGCAACTC
*
17151 GAAAAAATAATATATTAA-AATTTTATTTT
1 GAAAAAATAATATATTAATAATGTTATTTT
17180 GAAAAAATAAGT-TATTAATAATGTTATT
1 GAAAAAATAA-TATATTAATAATGTTATT
17208 ATTTATGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (30 bp):
GAAAAAATAATATATTAATAATGTTATTTT
Found at i:18294 original size:21 final size:21
Alignment explanation
Indices: 18252--18297 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
18242 GTTTACTATG
* * *
18252 ATTGCGGCCATAGCGGATGCT
1 ATTGCGGCCATAACGAACGCT
*
18273 ATTGCGGTCATAACGAACGCT
1 ATTGCGGCCATAACGAACGCT
18294 ATTG
1 ATTG
18298 TAGGTATCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (21 bp):
ATTGCGGCCATAACGAACGCT
Found at i:23564 original size:20 final size:20
Alignment explanation
Indices: 23539--23591 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
23529 ATTGGAGAGG
**
23539 TTCTAGAAAATTCTAGAGCT
1 TTCTAGAAAATTCTAGAAAT
* *
23559 TTCTAGAAAAGTGTAGAAAT
1 TTCTAGAAAATTCTAGAAAT
*
23579 TTCTAGAACATTC
1 TTCTAGAAAATTC
23592 CGGAGAACTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (20 bp):
TTCTAGAAAATTCTAGAAAT
Found at i:35467 original size:40 final size:41
Alignment explanation
Indices: 35337--35470 Score: 105
Period size: 40 Copynumber: 3.3 Consensus size: 41
35327 AAAAGATAAA
* * * * *
35337 TAGCAGTGTTTGAAAAAAAACGCCACT-AATATCATAACCTT
1 TAGCGGTGTTTGTAAAAAAA-GTCGCTAAATAACATAACCTT
* * * * *
35378 TAGTGGCGTTTAG-AAAAAAAGTCGCTAAATATCATTACCTC
1 TAGCGGTGTTT-GTAAAAAAAGTCGCTAAATAACATAACCTT
* * *
35419 AAGC-GTGTTTGTAAAAAACGTTGCTAAA-AACATAACCTT
1 TAGCGGTGTTTGTAAAAAAAGTCGCTAAATAACATAACCTT
35458 TAGCGGTGTTTGT
1 TAGCGGTGTTTGT
35471 GGTTCACAAA
Statistics
Matches: 73, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
39 12 0.16
40 31 0.42
41 29 0.40
42 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (41 bp):
TAGCGGTGTTTGTAAAAAAAGTCGCTAAATAACATAACCTT
Found at i:35824 original size:21 final size:22
Alignment explanation
Indices: 35798--35847 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
35788 AGCACGTCAT
35798 CAATGCCAG-AAAAAAACTTAA
1 CAATGCCAGAAAAAAAACTTAA
35819 CAATGCCAGAAAAAAAAACTTAA
1 CAATGCCAG-AAAAAAAACTTAA
35842 CAATGC
1 CAATGC
35848 ATTACCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 9 0.33
23 18 0.67
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.14
Consensus pattern (22 bp):
CAATGCCAGAAAAAAAACTTAA
Found at i:36464 original size:82 final size:81
Alignment explanation
Indices: 36361--36860 Score: 406
Period size: 82 Copynumber: 6.1 Consensus size: 81
36351 AAAAATTGTT
** * *
36361 ACTAAAGTACGAGTCTTTAGCGAAATTTGTATAAAAATGCCACTAATGTATGAGTCTCTAGCGAC
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTATGAGTCTTTAGCGAC
36426 GTTTGTATAAAAACGCC
65 GTTTGTATAAAAACGCC
* * * * *
36443 ACTAAAGTACAAGCCTTTAGCGGCATTTGTATAAAACA-CCACTAAAGTACGAGTCTTTAGTGGC
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAA-ATCCACTAAAGTATGAGTCTTTAGCGAC
36507 GTTTGTATAAAAAC-CC
65 GTTTGTATAAAAACGCC
* * ** ** *
36523 TACTAAAGGT-TGAGTCTTTAACGGTGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCG
1 -ACTAAA-GTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTATGAGTCTTTAGCG
** *
36587 ATTTTTTTATTTTATAAAAACGCC
63 A----CGT-TTGTATAAAAACGCC
* * * * *
36611 ACTAAAATATGAGTCTTTAGCGGCATTTGTACGAAAACAT-CTCTAAAATATGAGTCTTTAGC-A
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTA-TAAAA-ATCCACTAAAGTATGAGTCTTTAGCGA
**
36674 GCGTTTGTATAAAAAAACC
64 -CGTTTGTATAAAAACGCC
* * * * * * * *
36693 ACTAAAATACGAGTCTATAGCGACGTTTGTAT-AAAATACCACTAAAGTA-CAATCTTCAGCGGC
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTATGAGTCTTTAGCGAC
36756 GTTTGTATAAAAACGCC
65 GTTTGTATAAAAACGCC
* * ** * * *
36773 ACTAAAGTAC-AATCTTCAGCGGTGTTTATATAAAAATCCCACTAAAGTACT-AGTATTTAGTGA
1 ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAAT-CCACTAAAGTA-TGAGTCTTTAGCGA
*
36836 CGTTTGTTCTAAAAACGCC
64 CGTTTG-TATAAAAACGCC
36855 ACTAAA
1 ACTAAA
36861 ATGCCACTAT
Statistics
Matches: 332, Mismatches: 65, Indels: 42
0.76 0.15 0.10
Matches are distributed among these distances:
79 17 0.05
80 55 0.17
81 83 0.25
82 111 0.33
83 2 0.01
86 3 0.01
87 53 0.16
88 6 0.02
89 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (81 bp):
ACTAAAGTACGAGTCTTTAGCGGCATTTGTATAAAAATCCACTAAAGTATGAGTCTTTAGCGACG
TTTGTATAAAAACGCC
Found at i:36665 original size:128 final size:128
Alignment explanation
Indices: 36467--36715 Score: 306
Period size: 128 Copynumber: 1.9 Consensus size: 128
36457 CTTTAGCGGC
* * * * *
36467 ATTTGTATAAAACACCACTAAAGTACGAGTCTTTAGTGGCGTTTGTATAAAAACCCTACTAAAGG
1 ATTTGTATAAAACACCACTAAAATACGAGTCTTTAGCGGCATTTGTACAAAAACCCTACTAAAGA
* * ** *
36532 TTGAGTCTTTAACGGTGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGCGATTTTTTT
66 TTGAGTCTTTAACAGCGTTTGTATAAAAAAACCACTAAAATACAAGTCTATAGCGATTTTTTT
* * * *
36595 ATTT-TATAAAAACGCCACTAAAATATGAGTCTTTAGCGGCATTTGTACGAAAACATCT-CTAAA
1 ATTTGTAT-AAAACACCACTAAAATACGAGTCTTTAGCGGCATTTGTACAAAAAC-CCTACTAAA
* *
36658 -ATATGAGTCTTTAGCAGCGTTTGTATAAAAAAACCACTAAAATACGAGTCTATAGCGA
64 GAT-TGAGTCTTTAACAGCGTTTGTATAAAAAAACCACTAAAATACAAGTCTATAGCGA
36716 CGTTTGTATA
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
127 4 0.04
128 96 0.94
129 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (128 bp):
ATTTGTATAAAACACCACTAAAATACGAGTCTTTAGCGGCATTTGTACAAAAACCCTACTAAAGA
TTGAGTCTTTAACAGCGTTTGTATAAAAAAACCACTAAAATACAAGTCTATAGCGATTTTTTT
Found at i:36785 original size:40 final size:40
Alignment explanation
Indices: 36361--36860 Score: 362
Period size: 41 Copynumber: 12.2 Consensus size: 40
36351 AAAAATTGTT
*** *
36361 ACTAAAGTACGAGTCTTTAGCGAAATTTGTATAAAAATGCC
1 ACTAAAGTAC-AGTCTTTAGCGGCGTTTGTATAAAAACGCC
* * * *
36402 ACTAATGTATGAGTCTCTAGCGACGTTTGTATAAAAACGCC
1 ACTAAAGTA-CAGTCTTTAGCGGCGTTTGTATAAAAACGCC
* * *
36443 ACTAAAGTACAAGCCTTTAGCGGCATTTGTAT-AAAACACC
1 ACTAAAGTAC-AGTCTTTAGCGGCGTTTGTATAAAAACGCC
*
36483 ACTAAAGTACGAGTCTTTAGTGGCGTTTGTATAAAAAC-CC
1 ACTAAAGTAC-AGTCTTTAGCGGCGTTTGTATAAAAACGCC
** * * *
36523 TACTAAAGGTTGAGTCTTTAACGGTGTTTGTATAAAAATGCC
1 -ACTAAA-GTACAGTCTTTAGCGGCGTTTGTATAAAAACGCC
* *** *
36565 ACTAAAGTACAAGTCTATAGCGATTTTTTTATTTTATAAAAACGCC
1 ACTAAAGTAC-AGTCTTTAGCG----GCGT-TTGTATAAAAACGCC
* * * ** **
36611 ACTAAAATATGAGTCTTTAGCGGCATTTGTACGAAAACATC
1 ACTAAAGTA-CAGTCTTTAGCGGCGTTTGTATAAAAACGCC
* * * * **
36652 TCTAAAATATGAGTCTTTAGCAGCGTTTGTATAAAAAAACC
1 ACTAAAGTA-CAGTCTTTAGCGGCGTTTGTATAAAAACGCC
* * *
36693 ACTAAAATACGAGTCTATAGCGACGTTTGTATAAAATA--CC
1 ACTAAAGTAC-AGTCTTTAGCGGCGTTTGTATAAAA-ACGCC
* *
36733 ACTAAAGTACAATCTTCAGCGGCGTTTGTATAAAAACGCC
1 ACTAAAGTACAGTCTTTAGCGGCGTTTGTATAAAAACGCC
* * * *
36773 ACTAAAGTACAATCTTCAGCGGTGTTTATATAAAAATC-CC
1 ACTAAAGTACAGTCTTTAGCGGCGTTTGTATAAAAA-CGCC
* * * *
36813 ACTAAAGTACTAGTATTTAGTGACGTTTGTTCTAAAAACGCC
1 ACTAAAGTAC-AGTCTTTAGCGGCGTTTG-TATAAAAACGCC
36855 ACTAAA
1 ACTAAA
36861 ATGCCACTAT
Statistics
Matches: 369, Mismatches: 69, Indels: 41
0.77 0.14 0.09
Matches are distributed among these distances:
38 1 0.00
39 21 0.06
40 98 0.27
41 195 0.53
42 21 0.06
45 2 0.01
46 31 0.08
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (40 bp):
ACTAAAGTACAGTCTTTAGCGGCGTTTGTATAAAAACGCC
Found at i:37328 original size:19 final size:18
Alignment explanation
Indices: 37304--37341 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
37294 ATACTCAAAA
*
37304 TAATATTAATTTATATATT
1 TAATATTAATATA-ATATT
37323 TAATATTAATATAATATT
1 TAATATTAATATAATATT
37341 T
1 T
37342 GGGTGCGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTAATATAATATT
Found at i:38608 original size:41 final size:41
Alignment explanation
Indices: 38556--38786 Score: 214
Period size: 41 Copynumber: 5.5 Consensus size: 41
38546 AAAAGTGTAT
* *
38556 GAGTCTCTAGCGATGTTTGTATAAAAACGCCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
* * * *
38597 GAGCCTTTAGCGACATTTATATAAAAACACCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
* * *
38638 GAGTCTTTAGTGGCGTTTGTATAAAAAC-CCTACTAAAGGT-T
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCC-ACTAAA-GTAC
* *
38679 GAGTCTTTAACGACGTTTGTATAAAAATGCCACTAAAGTAC
1 GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
* * ** * *
38720 AAGTCTATAGCGATTTTTTTATTTTATAAAAACGCCACTAAAGTAT
1 GAGTCTTTAGCGA----CGT-TTGTATAAAAACGCCACTAAAGTAC
* *
38766 GAGTCTTTAGCGGCATTTGTA
1 GAGTCTTTAGCGACGTTTGTA
38787 AAATATGAGT
Statistics
Matches: 150, Mismatches: 31, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
40 4 0.03
41 108 0.72
42 5 0.03
45 1 0.01
46 32 0.21
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (41 bp):
GAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTAC
Found at i:38788 original size:27 final size:27
Alignment explanation
Indices: 38758--38813 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
38748 AAAACGCCAC
* *
38758 TAAAGTATGAGTCTTTAGCGGCATTTG
1 TAAAATATGAGTCTTTAGCAGCATTTG
*
38785 TAAAATATGAGTCTTTAGCAGCGTTTG
1 TAAAATATGAGTCTTTAGCAGCATTTG
38812 TA
1 TA
38814 TAAAAAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.38
Consensus pattern (27 bp):
TAAAATATGAGTCTTTAGCAGCATTTG
Found at i:38850 original size:40 final size:39
Alignment explanation
Indices: 38806--38989 Score: 160
Period size: 40 Copynumber: 4.6 Consensus size: 39
38796 TCTTTAGCAG
*
38806 CGTTTGTATAAAAA-ACCACTAAAGTACGAGTCTATAGCGA
1 CGTTTGTATAAAAACGCCACTAAAGTAC-AGTCT-TAGCGA
* * *
38846 CGTTTGTAT-AAAATGCCACTAAAGTACAATCTTCAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACAGTCTT-AGCGA
* * *
38885 CGTTTGTTTAAAAACGCCACTAAAGTACAATCTTCAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTACAGTCTT-AGCGA
* * * *
38925 TGTTTATATAAAAATC-CCACTAAAGTACTAGTATTTAGTGA
1 CGTTTGTATAAAAA-CGCCACTAAAGTAC-AGT-CTTAGCGA
*
38966 CGTTTGT-TCTAAAACGCCACTAAA
1 CGTTTGTAT-AAAAACGCCACTAAA
38990 AATGCCACTA
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
38 1 0.01
39 20 0.17
40 75 0.62
41 23 0.19
42 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (39 bp):
CGTTTGTATAAAAACGCCACTAAAGTACAGTCTTAGCGA
Found at i:38936 original size:79 final size:82
Alignment explanation
Indices: 38796--38989 Score: 211
Period size: 79 Copynumber: 2.4 Consensus size: 82
38786 AAAATATGAG
* * * * *
38796 TCTTTAGCAGCGTTTGTATAAAAA-ACCACTAAAGTACGAGTCTATAGCGACGTTTGTAT-AAAA
1 TCTTTAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGAATCTATAGCGACGTTTATATAAAAA
*
38859 TGCCACTAAAGTAC-AA
66 TCCCACTAAAGTACTAA
* **
38875 TCTTCAGCGGCGTTTGTTTAAAAACGCCACTAAAGTAC-AATCT-TCAGCGGTGTTTATATAAAA
1 TCTTTAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGAATCTAT-AGCGACGTTTATATAAAA
*
38938 ATCCCACTAAAGTACTAG
65 ATCCCACTAAAGTACTAA
* * *
38956 TATTTAGTGACGTTTGTTCT-AAAACGCCACTAAA
1 TCTTTAGCGGCGTTTGTT-TAAAAACGCCACTAAA
38990 AATGCCACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 36 0.38
80 29 0.30
81 29 0.30
82 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (82 bp):
TCTTTAGCGGCGTTTGTTTAAAAACGCCACTAAAGTACGAATCTATAGCGACGTTTATATAAAAA
TCCCACTAAAGTACTAA
Found at i:39458 original size:19 final size:18
Alignment explanation
Indices: 39434--39471 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
39424 ATACTCAAAA
*
39434 TAATATTAATTTATATATT
1 TAATATTAATATA-ATATT
39453 TAATATTAATATAATATT
1 TAATATTAATATAATATT
39471 T
1 T
39472 GGGTGCGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTAATATAATATT
Found at i:47468 original size:22 final size:23
Alignment explanation
Indices: 47441--47485 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
47431 GGTGAGAATA
*
47441 TTATTAAT-TATTTAAAGTATAT
1 TTATTAATATATTTAAAATATAT
*
47463 TTATTAATATTTTTAAAATATAT
1 TTATTAATATATTTAAAATATAT
47486 ATAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATTAATATATTTAAAATATAT
Found at i:47483 original size:21 final size:21
Alignment explanation
Indices: 47437--47497 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
47427 TTTTGGTGAG
*
47437 AATA-TTATTAAT-TATTTAA
1 AATATTTATTAATATTTTTAA
47456 AGTATATTTATTAATATTTTTAA
1 A--ATATTTATTAATATTTTTAA
*
47479 AATATATA-TAATATTTTTA
1 AATATTTATTAATATTTTTA
47498 TTTGAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 9 0.25
22 8 0.22
23 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATATTTATTAATATTTTTAA
Found at i:52686 original size:20 final size:20
Alignment explanation
Indices: 52634--52687 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
52624 GTAGGTGGGG
52634 GTCAATATTCTTTAAAAAGGT
1 GTCAATATT-TTTAAAAAGGT
**
52655 GTCAACTATTTTTAAAGTGGT
1 GTCAA-TATTTTTAAAAAGGT
52676 GTCAATATTTTT
1 GTCAATATTTTT
52688 TTAAATGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 7 0.23
21 19 0.63
22 4 0.13
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.44
Consensus pattern (20 bp):
GTCAATATTTTTAAAAAGGT
Found at i:54933 original size:16 final size:16
Alignment explanation
Indices: 54912--54962 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
54902 AGTTTACTTT
* *
54912 TCTTCCATTGTTTGCC
1 TCTTCCATCGCTTGCC
54928 TCTTCCATCGCTTGCC
1 TCTTCCATCGCTTGCC
54944 TCTTCCATCGCTTGCC
1 TCTTCCATCGCTTGCC
54960 TCT
1 TCT
54963 ATTGAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.06, C:0.39, G:0.12, T:0.43
Consensus pattern (16 bp):
TCTTCCATCGCTTGCC
Found at i:55176 original size:78 final size:78
Alignment explanation
Indices: 55047--55197 Score: 239
Period size: 78 Copynumber: 1.9 Consensus size: 78
55037 AAGATAATGA
55047 TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAAGGAAATTAAT
1 TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAAGGAAATTAAT
*
55112 GGTTGAGTTAGCG
66 GGTAGAGTTAGCG
* * * * * *
55125 TATATTAAATGACCTTTGAGATGATACAATGAATATCGTCTATAACTGTTACCAAGGCAATTAAT
1 TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAAGGAAATTAAT
55190 GGTAGAGT
66 GGTAGAGT
55198 CAGCATCACA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (78 bp):
TATATAAAATGACCCTTGAGATAATACAATGAATATCATCTACAACTGTTACCAAGGAAATTAAT
GGTAGAGTTAGCG
Found at i:59734 original size:42 final size:42
Alignment explanation
Indices: 59674--59753 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
59664 TCAAAAGCTT
*
59674 TGATACCAATTAAGTGTAACCCCCTAGACCCAGCCTATACTC
1 TGATACCAATTAAATGTAACCCCCTAGACCCAGCCTATACTC
* *
59716 TGATACCAATTAAATGTAATCCCTTAGACCCAGCCTAT
1 TGATACCAATTAAATGTAACCCCCTAGACCCAGCCTAT
59754 GCGTTTCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26
Consensus pattern (42 bp):
TGATACCAATTAAATGTAACCCCCTAGACCCAGCCTATACTC
Found at i:61359 original size:59 final size:59
Alignment explanation
Indices: 61271--61454 Score: 291
Period size: 59 Copynumber: 3.2 Consensus size: 59
61261 ACTTTTACGC
* * * *
61271 AAATATCACC-TAACAAAAATTAATAACGTATTAGGCACCCTTTTGAAAATATTTACAA
1 AAATAGCACCTTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAA
* **
61329 AAATAGCACCTTAACAGAAATTTATTACGTATTACACACCCTTTTAAAAATATTTACAA
1 AAATAGCACCTTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAA
61388 AAATAGCACCTTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTAC-A
1 AAATAGCACCTTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAA
61446 AAATAGCAC
1 AAATAGCAC
61455 ATTTTTATAC
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
58 19 0.17
59 96 0.83
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (59 bp):
AAATAGCACCTTAACAGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAA
Found at i:63078 original size:59 final size:59
Alignment explanation
Indices: 62945--63071 Score: 200
Period size: 59 Copynumber: 2.2 Consensus size: 59
62935 GTATAAAAAT
**
62945 GTGATATTTTTGTAAATATTTTTAAAAGGGTGTTTAATACGTAATTAATTTATGGTAAG
1 GTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTATGGTAAG
* * * *
63004 GTGTTATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTCTGTTAGG
1 GTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTATGGTAAG
63063 GTGATATTT
1 GTGATATTT
63072 GCGTAAAAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (59 bp):
GTGATATTTTTGTAAATATTTTTAAAAGGGTGCCTAATACGTAATTAATTTATGGTAAG
Found at i:70904 original size:21 final size:19
Alignment explanation
Indices: 70878--70922 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 19
70868 ATATTTTTAA
70878 ATTTTTTAATAATAAAAATAT
1 ATTTTTTAATAA-AAAAA-AT
70899 ATTTTTTAATAAAAAAAAT
1 ATTTTTTAATAAAAAAAAT
70918 ATTTT
1 ATTTT
70923 AAAAAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.29
20 5 0.21
21 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTTAATAAAAAAAAT
Found at i:70913 original size:19 final size:21
Alignment explanation
Indices: 70878--70922 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
70868 ATATTTTTAA
*
70878 ATTTTTTAATAATAAAAATAT
1 ATTTTTTAATAATAAAAAAAT
70899 ATTTTTTAAT-A-AAAAAAAT
1 ATTTTTTAATAATAAAAAAAT
70918 ATTTT
1 ATTTT
70923 AAAAAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 1 0.04
21 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTTTAATAATAAAAAAAT
Found at i:71384 original size:2 final size:2
Alignment explanation
Indices: 71377--71403 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71367 CATCATTCAT
71377 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
71404 TTTTACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:72563 original size:16 final size:16
Alignment explanation
Indices: 72542--72580 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
72532 CATTAACAAC
72542 TATTTTCGGTTTGAGT
1 TATTTTCGGTTTGAGT
* *
72558 TATTTTTGGTTTGGGT
1 TATTTTCGGTTTGAGT
*
72574 TACTTTC
1 TATTTTC
72581 AGTTCAGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.10, C:0.08, G:0.23, T:0.59
Consensus pattern (16 bp):
TATTTTCGGTTTGAGT
Found at i:75775 original size:60 final size:59
Alignment explanation
Indices: 75682--75813 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 59
75672 ATTGTCAGAT
* *
75682 GACCATTTTGTAACTTGTAATAGTCAAGGGACTCAACAAAATATCGTCCTATAATCGAAG
1 GACCATTTTGTAACTTGTAATAGTCAAGGGACTCAACAAAATAGC-ACCTATAATCGAAG
* ** * * *
75742 GACCATTTTGTAACTTTTAATAGT-TGGAGGACTCAACAAAGTAGCACCTATAGTCGAGG
1 GACCATTTTGTAACTTGTAATAGTCAAG-GGACTCAACAAAATAGCACCTATAATCGAAG
75801 GACCATTTGTGTA
1 GACCATTT-TGTA
75814 CATTACCCAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 20 0.32
60 42 0.68
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (59 bp):
GACCATTTTGTAACTTGTAATAGTCAAGGGACTCAACAAAATAGCACCTATAATCGAAG
Found at i:76355 original size:16 final size:16
Alignment explanation
Indices: 76334--76373 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
76324 CGTGGAGGAG
76334 AAAGAAAATTGAAGAA
1 AAAGAAAATTGAAGAA
76350 AAAGAAAATTGAAGAA
1 AAAGAAAATTGAAGAA
76366 AAAGAAAA
1 AAAGAAAA
76374 AAAAGCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (16 bp):
AAAGAAAATTGAAGAA
Found at i:76637 original size:146 final size:146
Alignment explanation
Indices: 76407--76702 Score: 385
Period size: 146 Copynumber: 2.0 Consensus size: 146
76397 ATTTTTTCAT
* * * ** *
76407 CGACGATCGGGATCTTCGATCAACATTCCGAACGGTGAAAGGTTGCGCAAGGGTAACACCAACAA
1 CGACGATCGGGATCTCCGATCAACATTCCGAACGGTGAAAAGTTGCGCAAAGCCAACAACAACAA
** * * * * *
76472 CATACTGAAAAATTAGGACGATCAGACGGTGGACAGCGGCGGATCGGAAAAAATAAATCTAAACG
66 CATACTGAAAAACCAGGACGATCAAACAGTGGACAGAGGCGGATCGGAAAAAATAAAGCCAAACG
76537 GTTTTTGGCCTTTTGA
131 GTTTTTGGCCTTTTGA
** *
76553 CGACGATCGGGATCTCCGATCAATGTTCCGAACGGTGAAAAGTTGCGCAAAGCCAACAAGAACAA
1 CGACGATCGGGATCTCCGATCAACATTCCGAACGGTGAAAAGTTGCGCAAAGCCAACAACAACAA
* * * * * *
76618 CATACTGAAAAACCAGGACGATCAAACAGTGGACGGAGGCGGATCGGAGAAACTTAAGCCGAATG
66 CATACTGAAAAACCAGGACGATCAAACAGTGGACAGAGGCGGATCGGAAAAAATAAAGCCAAACG
*
76683 GTTTTTGGCCTTTTTA
131 GTTTTTGGCCTTTTGA
76699 CGAC
1 CGAC
76703 AAACGGAGCC
Statistics
Matches: 127, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
146 127 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (146 bp):
CGACGATCGGGATCTCCGATCAACATTCCGAACGGTGAAAAGTTGCGCAAAGCCAACAACAACAA
CATACTGAAAAACCAGGACGATCAAACAGTGGACAGAGGCGGATCGGAAAAAATAAAGCCAAACG
GTTTTTGGCCTTTTGA
Found at i:76996 original size:29 final size:29
Alignment explanation
Indices: 76964--77035 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
76954 TGAATCTTTG
*
76964 TGTTTTTCTGATTTT-GACACTTTAGTTTA
1 TGTTTTTCT-ATTTTAGACACTTAAGTTTA
* *
76993 TGTTATTT-TATTTTAGTCACTTAAGTTTC
1 TGTT-TTTCTATTTTAGACACTTAAGTTTA
77022 TGCTTTTTCTATTT
1 TG-TTTTTCTATTT
77036 ATGTCCTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 5 0.14
29 21 0.58
30 10 0.28
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (29 bp):
TGTTTTTCTATTTTAGACACTTAAGTTTA
Found at i:85273 original size:19 final size:20
Alignment explanation
Indices: 85234--85274 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
85224 ATCAGATTGT
85234 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
85254 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
85274 C
1 C
85275 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.41, G:0.29, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACCGATTCCCC
Found at i:86245 original size:24 final size:24
Alignment explanation
Indices: 86213--86260 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
86203 AACAAAAGAA
86213 AGCTCAACTTAATGCCAAGGCCAT
1 AGCTCAACTTAATGCCAAGGCCAT
86237 AGCTCAACTTAATGCCAAGGCCAT
1 AGCTCAACTTAATGCCAAGGCCAT
86261 GCACATGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (24 bp):
AGCTCAACTTAATGCCAAGGCCAT
Found at i:87565 original size:19 final size:19
Alignment explanation
Indices: 87541--87580 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
87531 ATCAGATTGT
87541 CCAGGGGGTACAGATCCCC
1 CCAGGGGGTACAGATCCCC
*
87560 CCAGGGGGTATAGATCCCC
1 CCAGGGGGTACAGATCCCC
87579 CC
1 CC
87581 CCCCCAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.38, G:0.30, T:0.12
Consensus pattern (19 bp):
CCAGGGGGTACAGATCCCC
Found at i:90386 original size:254 final size:252
Alignment explanation
Indices: 89966--90486 Score: 841
Period size: 254 Copynumber: 2.1 Consensus size: 252
89956 AAGTCAAGGC
* * *
89966 TCAACTTCACGACGAAGGGAATCGTAAACACAAGCAGCATCCATCTATAGATTGGATTTCAAACT
1 TCAACTTCACGACGAACGGAATCGTAAACACAAGAAACATCCATCTATAGATTGGATTTCAAACT
*
90031 TCACGATGAAGGATATCCAACTCAAAGAAGGAGTGTTGTCAATAAACTTTCCAATTTCAAAGTCA
66 TCACGAAGAAGGATATCCAACTCAAAGAAGGAGTGTTGTCAATAAACTTTCCAATTTCAAAGTCA
90096 ATTTCAACTTCACGACGAAGGATATTGGCCTCGAAACAACGAAACTTACATTGGATTTCAACTTC
131 ATTTCAACTTCACGACGAAGGATATTGGCCTCGAAACAACGAAACTTACATTGGATTTCAACTTC
* * *
90161 ACGACGAAGATATCCAATTTCAAGGTTC-AATTCACGACGAAGGGGCCATCCACGGTT
196 ACGACGAAGATATCCAATTTCAAGGCTCAAATTCACAACGAAGGGGCCATCC-CGATT
* *
90218 TCAACTTCACGACGAACGGAATCGTACACACCAAGAAACATCCATCTCTAGATTGGATTTC-AAC
1 TCAACTTCACGACGAACGGAATCGTAAACA-CAAGAAACATCCATCTATAGATTGGATTTCAAAC
* *
90282 TTCACGAAGAAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAG
65 TTCACGAAG-AAGGATATCCAACTCAAAGAAGGAGTGT-TGTCAATAAACTTTCCAATTTCAAAG
** *
90347 TCAATTTCAACTTCACGGTGAAGGATATTGGCCTCGAAACAACGAAACTTACATTGGATTTTAAC
128 TCAATTTCAACTTCACGACGAAGGATATTGGCCTCGAAACAACGAAACTTACATTGGATTTCAAC
* *
90412 TTCACGACGAAGGTATCCAATTTCAAGGCTCAAATTCACAATGAAGGGGCCATCCCGATT
193 TTCACGACGAAGATATCCAATTTCAAGGCTCAAATTCACAACGAAGGGGCCATCCCGATT
90472 T-AACTTCACGACGAA
1 TCAACTTCACGACGAA
90487 GAATATCGTG
Statistics
Matches: 249, Mismatches: 16, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
252 39 0.16
253 69 0.28
254 120 0.48
255 21 0.08
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (252 bp):
TCAACTTCACGACGAACGGAATCGTAAACACAAGAAACATCCATCTATAGATTGGATTTCAAACT
TCACGAAGAAGGATATCCAACTCAAAGAAGGAGTGTTGTCAATAAACTTTCCAATTTCAAAGTCA
ATTTCAACTTCACGACGAAGGATATTGGCCTCGAAACAACGAAACTTACATTGGATTTCAACTTC
ACGACGAAGATATCCAATTTCAAGGCTCAAATTCACAACGAAGGGGCCATCCCGATT
Found at i:90677 original size:123 final size:119
Alignment explanation
Indices: 90399--90717 Score: 349
Period size: 119 Copynumber: 2.7 Consensus size: 119
90389 CGAAACTTAC
* * * * *
90399 ATTGGATTTTAACTTCACGACGAAGG-TATCCAATTTCAAGGCTCAAATTCACAATGAAGGGGCC
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAA-TTCAAGGCTGAACTTCACGACGAAGGGGCC
* * * *
90463 ATCC-CGATTT-AACTTCACGACGAAGAATATCGTGCTCACCAGCAGCAATGCAA
65 ATCCACGATTTCAACTTCACAACGAAGAATATCATCCTCACCAACAGCAATGCAA
* *
90516 ACCTTGGATTTCAACTTCACGACGAAGGATGTCTAATTCAAGGCTGAACTTCACGACGAAGGGGC
1 A--TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTGAACTTCACGACGAAGGGGC
* * * * * **
90581 CATCCATGATTTCAACTTCACAACGAAGGATATCTATCCATCAGCAACATTCATCTTTAA
64 CATCCACGATTTCAACTTCACAACGAAGAATATC-ATCC-TCACCAACA-GCA-ATGCAA
* * * *
90641 ATTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGTCTG-ACTTCACGAGGAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTGAACTTCACGACGAAGGGGCCA
90705 TCCACGATTTCAA
66 TCCACGATTTCAA
90718 ATTTTATCTC
Statistics
Matches: 168, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
117 1 0.01
119 54 0.32
120 10 0.06
121 19 0.11
122 33 0.20
123 45 0.27
124 2 0.01
125 4 0.02
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (119 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTGAACTTCACGACGAAGGGGCCA
TCCACGATTTCAACTTCACAACGAAGAATATCATCCTCACCAACAGCAATGCAA
Found at i:90841 original size:36 final size:36
Alignment explanation
Indices: 90771--90887 Score: 191
Period size: 36 Copynumber: 3.3 Consensus size: 36
90761 GATAACATTT
*
90771 CCTTGAAACGAATTTTGTCTCTC-TGAGATAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTC
90806 CCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTC
* *
90842 CCTTAAAACAAATTTTGTCTCCCTTGAGATAGTTTC
1 CCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTC
*
90878 TCTTGAAACA
1 CCTTGAAACA
90888 TAACTTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 22 0.29
36 54 0.71
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
CCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTC
Done.