Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000954.1 Hibiscus syriacus cultivar Beakdansim tig00001910_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: 93437
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:12182 original size:69 final size:67
Alignment explanation
Indices: 12004--12277 Score: 363
Period size: 69 Copynumber: 4.0 Consensus size: 67
11994 CTTTATATAT
* * *
12004 ATATATATATAACTAAGAAAAGTCGAACTATACCCGTATCTCGTAATCATAATTTGAGATCGAGT
1 ATATATATATAACTAAGAAAAGTCGAACTATACTCGTATCTCGTAATCATAATTCGAGATCAAGT
12069 AA
66 AA
** * *
12071 ATATATATATAACTAAGAAAA-TTTAATATATAAC-CGTATCTCGTAATCATAATTTGAGATCAA
1 ATATATATATAACTAAGAAAAGTCGAA-CTAT-ACTCGTATCTCGTAATCATAATTCGAGATCAA
12134 GTAA
64 GTAA
12138 ATATATACATATAACTAAGAAAAGTCGAACTATACTCGTATCTCGTAATCATATAATTCGAGATC
1 ATATAT--ATATAACTAAGAAAAGTCGAACTATACTCGTATCTCGTAATC--ATAATTCGAGATC
12203 AAGTAA
62 AAGTAA
* * * *
12209 ATATATATATAACTAAGAAAATTCGAAGTATACGTTTGTATCTCGTAATCATAATTCGAGATCGA
1 ATATATATATAACTAAGAAAAGTCGAACTATAC--TCGTATCTCGTAATCATAATTCGAGATCAA
12274 GTAA
64 GTAA
12278 CATACACAAT
Statistics
Matches: 185, Mismatches: 12, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
66 3 0.02
67 62 0.34
68 4 0.02
69 75 0.41
70 3 0.02
71 38 0.21
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (67 bp):
ATATATATATAACTAAGAAAAGTCGAACTATACTCGTATCTCGTAATCATAATTCGAGATCAAGT
AA
Found at i:14741 original size:30 final size:29
Alignment explanation
Indices: 14693--14749 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
14683 TAAAAGCATG
14693 CCCTAATAACAAATATTGAAAAAATTGGAT
1 CCCTAATAACAAATATTG-AAAAATTGGAT
* *
14723 CCCTAATAATAAGA-ATTGAGAAATTGG
1 CCCTAATAACAA-ATATTGAAAAATTGG
14750 GCTTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.33
30 15 0.62
31 1 0.04
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.26
Consensus pattern (29 bp):
CCCTAATAACAAATATTGAAAAATTGGAT
Found at i:18021 original size:21 final size:21
Alignment explanation
Indices: 17995--18039 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17985 GATTTCTGGG
* *
17995 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
18016 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
18037 CAA
1 CAA
18040 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:18716 original size:23 final size:24
Alignment explanation
Indices: 18673--18719 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
18663 ATATGGCATG
*
18673 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
18697 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
18720 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:18935 original size:31 final size:31
Alignment explanation
Indices: 18897--19050 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
18887 GGGTCGAGGG
18897 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
18928 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
18959 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
18990 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
19021 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
19051 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:22062 original size:21 final size:21
Alignment explanation
Indices: 22036--22080 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
22026 GATTTCTGGG
* *
22036 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
22057 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
22078 CAA
1 CAA
22081 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:22983 original size:31 final size:31
Alignment explanation
Indices: 22945--23098 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
22935 GGGTCGAGGG
22945 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
22976 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
23007 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
23038 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
23069 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
23099 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:23902 original size:32 final size:32
Alignment explanation
Indices: 23861--23926 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
23851 GTCCCGAAGG
23861 ACCACGTAGAACCCTCGACTCTTGGCATGCCA
1 ACCACGTAGAACCCTCGACTCTTGGCATGCCA
23893 ACCACGTAGAACCCTCGACTCTTGGCATGCCA
1 ACCACGTAGAACCCTCGACTCTTGGCATGCCA
23925 AC
1 AC
23927 TATACCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.38, G:0.18, T:0.18
Consensus pattern (32 bp):
ACCACGTAGAACCCTCGACTCTTGGCATGCCA
Found at i:27809 original size:16 final size:16
Alignment explanation
Indices: 27788--27820 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27778 TAATAAATAG
27788 ACGAACATAAAAGAAC
1 ACGAACATAAAAGAAC
*
27804 ACGAACATAAACGAAC
1 ACGAACATAAAAGAAC
27820 A
1 A
27821 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.21, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAAAGAAC
Found at i:27901 original size:10 final size:10
Alignment explanation
Indices: 27886--27960 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
27876 CATTTAATAA
27886 ATAAACGAAC
1 ATAAACGAAC
27896 ATAAACGAAC
1 ATAAACGAAC
27906 ----ACGAAC
1 ATAAACGAAC
27912 ATAAACGAAC
1 ATAAACGAAC
** *
27922 ACGAAC-ATAA
1 ATAAACGA-AC
27932 ATGAACACGAAC
1 AT-AA-ACGAAC
27944 ATAAACGAAC
1 ATAAACGAAC
27954 ATAAACG
1 ATAAACG
27961 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:27911 original size:16 final size:16
Alignment explanation
Indices: 27890--27954 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
27880 TAATAAATAA
27890 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
27906 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
27922 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
27938 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
27954 A
1 A
27955 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:28722 original size:14 final size:14
Alignment explanation
Indices: 28705--28760 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
28695 AATGAACATA
28705 AACGAACATAATCG
1 AACGAACATAATCG
28719 AACGAACAT-A---
1 AACGAACATAATCG
* *
28729 AACAAACATAACCG
1 AACGAACATAATCG
28743 AACGAACATAATCG
1 AACGAACATAATCG
28757 AACG
1 AACG
28761 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:28725 original size:24 final size:24
Alignment explanation
Indices: 28685--28759 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
28675 GATTGAGTTA
*
28685 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
28709 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
28733 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
28757 AAC
1 AAC
28760 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:40542 original size:36 final size:36
Alignment explanation
Indices: 40468--40542 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
40458 TTTTTATATT
*
40468 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
40504 TTTAATTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
40540 TTT
1 TTT
40543 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:42436 original size:2 final size:2
Alignment explanation
Indices: 42429--42460 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42419 ATGGGTTAAT
42429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42461 ATTTAGATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44316 original size:9 final size:8
Alignment explanation
Indices: 44282--44343 Score: 52
Period size: 9 Copynumber: 7.1 Consensus size: 8
44272 TAAATAAATC
44282 AAAAATAAA
1 AAAAAT-AA
44291 AGAAAATAA
1 A-AAAATAA
*
44300 TAATAATAA
1 -AAAAATAA
44309 AAACAATAA
1 AAA-AATAA
*
44318 ATAAATAA
1 AAAAATAA
*
44326 ACAAATAA
1 AAAAATAA
44334 AGAAAATAA
1 A-AAAATAA
44343 A
1 A
44344 TTGAAAGGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 15 0.34
9 23 0.52
10 6 0.14
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:44454 original size:14 final size:14
Alignment explanation
Indices: 44437--44463 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44427 CAAAAGGGAA
44437 AAATAGAAAATAAC
1 AAATAGAAAATAAC
44451 AAATAGAAAATAA
1 AAATAGAAAATAA
44464 ATCAAAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (14 bp):
AAATAGAAAATAAC
Found at i:45940 original size:37 final size:37
Alignment explanation
Indices: 45889--46072 Score: 216
Period size: 38 Copynumber: 5.0 Consensus size: 37
45879 AAAAATGTTT
45889 TTTTAAAAACTATATATTATATAAA-TTTCAAAATGA
1 TTTTAAAAACTATATATTATATAAATTTTCAAAATGA
*
45925 TTTT-AAAACTATATATTATATAAATTTTCAAAATGG
1 TTTTAAAAACTATATATTATATAAATTTTCAAAATGA
** *
45961 TTTTAAAAACTATATATTATATATGTTTTCTAAAAACG-
1 TTTTAAAAACTATATATTATATAAATTTTC--AAAATGA
* * *
45999 TTTTAAAAATTATATATTATAT-AGTTTTCAAAGGTAT-T
1 TTTTAAAAACTATATATTATATAAATTTTCAAA---ATGA
*
46037 TTTTAAAAACTATATATTATATACATTTTCAAAATG
1 TTTTAAAAACTATATATTATATAAATTTTCAAAATG
46073 TTATTTTTTT
Statistics
Matches: 128, Mismatches: 10, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
35 23 0.18
36 20 0.16
37 29 0.23
38 43 0.34
39 13 0.10
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATAAATTTTCAAAATGA
Found at i:46013 original size:38 final size:36
Alignment explanation
Indices: 45864--46074 Score: 209
Period size: 38 Copynumber: 5.7 Consensus size: 36
45854 TCAAAAAACC
*
45864 TATATTATAT--TTTTTAAAAATGTTTTTTTAAAAACTA
1 TATATTATATAATTTTCAAAAATG---TTTTAAAAACTA
*
45901 TATATTATATAAATTTC-AAAATGATTTT-AAAACTA
1 TATATTATATAATTTTCAAAAATG-TTTTAAAAACTA
45936 TATATTATATAAATTTTC-AAAATGGTTTTAAAAACTA
1 TATATTATAT-AATTTTCAAAAAT-GTTTTAAAAACTA
* * *
45973 TATATTATATATGTTTTCTAAAAACGTTTTAAAAATTA
1 TATATTATATA-ATTTTC-AAAAATGTTTTAAAAACTA
* * *
46011 TATATTATATAGTTTTCAAAGGTATTTTTTAAAAACTA
1 TATATTATATAATTTTCAAA--AATGTTTTAAAAACTA
46049 TATATTATATACATTTTC-AAAATGTT
1 TATATTATATA-ATTTTCAAAAATGTT
46075 ATTTTTTTAA
Statistics
Matches: 149, Mismatches: 14, Indels: 23
0.80 0.08 0.12
Matches are distributed among these distances:
35 17 0.11
36 27 0.18
37 39 0.26
38 54 0.36
39 12 0.08
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATTATATAATTTTCAAAAATGTTTTAAAAACTA
Found at i:46144 original size:2 final size:2
Alignment explanation
Indices: 46133--46187 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
46123 TTTTGCGAAC
* *
46133 TA TA TA -A TA TA TG TA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46174 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
46188 AAGAAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:46585 original size:14 final size:15
Alignment explanation
Indices: 46554--46590 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
46544 ATAAATTAAT
46554 TAAAA-ATTTAAAAG
1 TAAAATATTTAAAAG
*
46568 TAAATTATTTAAAA-
1 TAAAATATTTAAAAG
46582 TAAAATATT
1 TAAAATATT
46591 AATTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:46611 original size:15 final size:14
Alignment explanation
Indices: 46551--46612 Score: 51
Period size: 15 Copynumber: 4.5 Consensus size: 14
46541 ATTATAAATT
46551 AATTAAAAATTTAA
1 AATTAAAAATTTAA
* *
46565 AAGTAAATTATTTAA
1 AATTAAA-AATTTAA
46580 AA-T-AAAATATT--
1 AATTAAAAAT-TTAA
46591 AATTAAAAATTTATA
1 AATTAAAAATTTA-A
46606 AATTAAA
1 AATTAAA
46613 TTAATAGTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
11 2 0.05
12 5 0.13
13 9 0.24
14 7 0.18
15 15 0.39
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
AATTAAAAATTTAA
Found at i:46796 original size:18 final size:20
Alignment explanation
Indices: 46767--46811 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
46757 TACTATTAAA
46767 ATAATATATTTTTC-TATCT-
1 ATAATATA-TTTTCGTATCTC
46786 ATAAT-TATTTTCGTATCTC
1 ATAATATATTTTCGTATCTC
46805 ATAATAT
1 ATAATAT
46812 CAATAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 10 0.43
20 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAATATATTTTCGTATCTC
Found at i:48293 original size:3 final size:3
Alignment explanation
Indices: 48285--48309 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
48275 TATGGTGATT
48285 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
48310 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:55888 original size:31 final size:32
Alignment explanation
Indices: 55850--55927 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 32
55840 TTGGTCAAAG
*
55850 TAGGTACCT-AAAGTGTACCACCATTTTCACC
1 TAGGTACCTAAAAGTATACCACCATTTTCACC
** *
55881 TAGGTACCTAAAAAGTATACCACTTTTTTCATC
1 TAGGTACCT-AAAAGTATACCACCATTTTCACC
*
55914 TAGGTATC-AAAAGT
1 TAGGTACCTAAAAGT
55928 TGACATGCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 15 0.38
33 25 0.62
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (32 bp):
TAGGTACCTAAAAGTATACCACCATTTTCACC
Found at i:64212 original size:35 final size:35
Alignment explanation
Indices: 64143--64213 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
64133 GTTGGAAAAT
**
64143 ATTTATATTTTTCTTTAAAAAATTTAAATTTATAA
1 ATTTATATTTTTCTTTAAAAAATTTAAAAATATAA
*
64178 ATTTATATAATTTT-TTTACAAAA-TTAAAAATATAA
1 ATTTATAT--TTTTCTTTAAAAAATTTAAAAATATAA
64213 A
1 A
64214 AAGTTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 19 0.61
36 8 0.26
37 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTTATATTTTTCTTTAAAAAATTTAAAAATATAA
Found at i:65900 original size:31 final size:31
Alignment explanation
Indices: 65865--65958 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
65855 ATAATGATGA
* *
65865 AGTGATTATTTTGTTACAAATCGATAATATT
1 AGTGATCATTTTGTTACAAATCGATAACATT
* * * *
65896 AGTGATCATTCTGTTATAAGTCGATAACGTT
1 AGTGATCATTTTGTTACAAATCGATAACATT
65927 AGTGATCATTTTGTTACAAATCGATAACATT
1 AGTGATCATTTTGTTACAAATCGATAACATT
65958 A
1 A
65959 ATGACTAGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (31 bp):
AGTGATCATTTTGTTACAAATCGATAACATT
Found at i:66035 original size:71 final size:71
Alignment explanation
Indices: 65919--66061 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 71
65909 TTATAAGTCG
* * * *
65919 ATAACGTTAGTGATCATTTTGTTACAAATCGATAACATTAATGACTAGTTTGTTATTTTTAAAAC
1 ATAACGTTAGTGACCATTTTGTTACAAATCGATAACATTAATGACTAATTTATTACTTTTAAAAC
65984 TTTAAT
66 TTTAAT
* *
65990 ATAACGTTAGTGACCATTTTGTTATAAATCGAT-ACTATTAGTGACTAATTTATTACTTTTAAAA
1 ATAACGTTAGTGACCATTTTGTTACAAATCGATAAC-ATTAATGACTAATTTATTACTTTTAAAA
66054 CTTTAAT
65 CTTTAAT
66061 A
1 A
66062 GGTAAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 2 0.03
71 63 0.97
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (71 bp):
ATAACGTTAGTGACCATTTTGTTACAAATCGATAACATTAATGACTAATTTATTACTTTTAAAAC
TTTAAT
Found at i:68510 original size:5 final size:5
Alignment explanation
Indices: 68500--68543 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
68490 TGAGACCACA
68500 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
68544 ATAAATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:69010 original size:39 final size:39
Alignment explanation
Indices: 68956--69053 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
68946 AGATTGATCA
**
68956 TCCATGCTTTAAGGAAGGACGGAGGGTTGGATTTAATCG
1 TCCATGCTTTAAGGAAGGACAAAGGGTTGGATTTAATCG
* *
68995 TCCATGCTTTAAGGAAGGACAAAGGGTTGGATTTGATTG
1 TCCATGCTTTAAGGAAGGACAAAGGGTTGGATTTAATCG
*
69034 TCCACGCTTTAAGGAAGGAC
1 TCCATGCTTTAAGGAAGGAC
69054 TCAAGATTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (39 bp):
TCCATGCTTTAAGGAAGGACAAAGGGTTGGATTTAATCG
Found at i:75027 original size:20 final size:20
Alignment explanation
Indices: 75019--75062 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
75009 TTTAAAATAA
75019 TTTATTTTAAAATAATTTAT
1 TTTATTTTAAAATAATTTAT
*
75039 TTTATTTTATAATAATTTAT
1 TTTATTTTAAAATAATTTAT
75059 TTTA
1 TTTA
75063 AAATAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATTTTAAAATAATTTAT
Found at i:75082 original size:14 final size:15
Alignment explanation
Indices: 75003--75201 Score: 188
Period size: 15 Copynumber: 12.5 Consensus size: 15
74993 TAATAAGGTT
75003 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
75018 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
75033 ATTTATTTTATTTTATAATA
1 ATTTATTTTA----A-AATA
75053 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
75068 ATTTATTAT-AAATA
1 ATTTATTTTAAAATA
75082 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
75097 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
75112 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
75131 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
75149 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
75163 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
75181 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
75195 ATTTATT
1 ATTTATT
75202 AGTATGGATT
Statistics
Matches: 157, Mismatches: 10, Indels: 35
0.78 0.05 0.17
Matches are distributed among these distances:
14 35 0.22
15 73 0.46
16 7 0.04
17 3 0.02
18 11 0.07
19 2 0.01
20 16 0.10
21 4 0.03
22 6 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:75092 original size:79 final size:80
Alignment explanation
Indices: 75003--75202 Score: 251
Period size: 79 Copynumber: 2.5 Consensus size: 80
74993 TAATAAGGTT
* ***
75003 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTTTATTTTAT-AATAATTTATTTTAAAAT
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAATAATTTATTTTAAAAT
75067 AATTTATTATAAATA
66 AATTTATTATAAATA
* * *
75082 ATTTATTTTAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTAAAA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATAT-GAATAATTTATTTTAAAA
*
75147 TAATTTATTTTAAATA
65 TAATTTATTATAAATA
* * *
75163 ATTTATTAGTATGAATTGATTTATTTT-AAATAATTTATTA
1 ATTTATT--T-TAAAATAATTTATTTTAAAATAATTTATTA
75203 GTATGGATTG
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
79 41 0.39
81 37 0.36
83 13 0.12
84 13 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (80 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAATAATTTATTTTAAAAT
AATTTATTATAAATA
Found at i:75186 original size:18 final size:18
Alignment explanation
Indices: 75163--75219 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
75153 ATTTTAAATA
75163 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
75181 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
75195 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
75213 ATTTATT
1 ATTTATT
75220 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:75188 original size:32 final size:32
Alignment explanation
Indices: 75149--75614 Score: 286
Period size: 32 Copynumber: 15.4 Consensus size: 32
75139 TTTTAAAATA
*
75149 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
75181 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
75213 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
75235 ATTTATTTTAAATATTTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
75267 ATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* * *
75299 ATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 ATTTATTTT-AAATA---ATTTA-TTAGTA-TGGA-TTG
* * * * * * * **
75338 -TATAGTTTGATTTATTT-TAAATAATTTATTCG
1 ATTTATTTTAAATAATTTATTAGT-ATGGATT-G
** * ** * * *
75370 TATGGA-TTGATTTATTTTA-AAATATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTG
*
75401 ATTTATTTTAAATAATTTATTAGTATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
75433 ATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* * *
75465 ATTGA-TTT--AT--TTTA-AAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
75491 ATTTA--TT--AT--TGTAGTT-GTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTG
75517 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
75539 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
75571 ATTTATTTTAAATAATTTATTTGTATTGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
75603 ATTTATTTTAAA
1 ATTTATTTTAAA
75615 ATATGGATTG
Statistics
Matches: 345, Mismatches: 49, Indels: 80
0.73 0.10 0.17
Matches are distributed among these distances:
22 28 0.08
23 7 0.02
25 9 0.03
26 33 0.10
27 6 0.02
28 3 0.01
29 4 0.01
30 3 0.01
31 20 0.06
32 188 0.54
33 17 0.05
34 5 0.01
36 4 0.01
37 6 0.02
38 9 0.03
39 3 0.01
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:75229 original size:22 final size:22
Alignment explanation
Indices: 75204--75246 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
75194 AATTTATTAG
75204 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
75226 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
75247 TATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:75241 original size:54 final size:54
Alignment explanation
Indices: 75172--75631 Score: 290
Period size: 54 Copynumber: 8.3 Consensus size: 54
75162 AATTTATTAG
*
75172 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
75226 TATGGATTGATTTATTTTAAATATTTTATTAGTATAGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * * * ***
75279 TA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
* * *
75338 TATAGTTTGATTTATTTTAAATAATTTATTCGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
75392 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * * * * * ***
75445 TAATTTATTTGTATGGATTGATTGATTTATTT-TAAAATATGGATTGATTTATTATTGTAGTTG
1 T-ATGGA-TTG-ATTTATT--TTAAATAATTTAT-TAGTATGGATTGATTTA-T-TT-TA-AAA
** ** * ** * * *
75508 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
* *
75562 TATGGATTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
75616 TATGGATTGATTTATT
1 TATGGATTGATTTATT
75632 ATTGTAGTTG
Statistics
Matches: 303, Mismatches: 74, Indels: 58
0.70 0.17 0.13
Matches are distributed among these distances:
50 15 0.05
52 2 0.01
53 9 0.03
54 157 0.52
55 19 0.06
56 16 0.05
57 8 0.03
58 41 0.14
59 4 0.01
60 9 0.03
61 4 0.01
62 18 0.06
63 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:75367 original size:166 final size:167
Alignment explanation
Indices: 75177--75614 Score: 632
Period size: 170 Copynumber: 2.6 Consensus size: 167
75167 ATTAGTATGA
75177 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATT-GTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
*
75242 TTAAATATTTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTAT-G-GATTGATTTAT
65 TTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGTGATTGATTTAT
75305 TTTAAAATATGGATTGATTTATTATTGTAGTTGTATAG
130 TTTAAAATATGGATTGATTTATTATTGTAGTTGTATAG
*
75343 TTTGATTTATTTTAAATAATTTATTCGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATT-GTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
* *
75408 TTAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTT
65 TTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGG--TGATTGATTT
*
75473 ATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
128 ATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAG
** ** * ** * * *
75513 ATTGATTTATTTTAAA-ATATGGATTG-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA
1 ATTGATTTATTTTAAATA-ATTTATTGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTA
* *
75576 TTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAA
63 TTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
75615 ATATGGATTG
Statistics
Matches: 245, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
166 111 0.45
167 1 0.00
168 3 0.01
169 11 0.04
170 119 0.49
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (167 bp):
ATTGATTTATTTTAAATAATTTATTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTT
TAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGTGATTGATTTATT
TTAAAATATGGATTGATTTATTATTGTAGTTGTATAG
Found at i:75395 original size:22 final size:22
Alignment explanation
Indices: 75370--75412 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
75360 AATTTATTCG
75370 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
75392 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
75413 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:75420 original size:14 final size:14
Alignment explanation
Indices: 75401--75454 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
75391 ATATGGATTG
75401 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
75415 ATTTATTAGTATGGATTA
1 ATTTATT--T-T-AAATA
75433 ATTTATTTTAAATA
1 ATTTATTTTAAATA
75447 ATTTATTT
1 ATTTATTT
75455 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:75489 original size:22 final size:22
Alignment explanation
Indices: 75464--75550 Score: 111
Period size: 22 Copynumber: 3.8 Consensus size: 22
75454 TGTATGGATT
75464 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
***
75486 GATTGATTTATTATTGTAGTTGTATG
1 GATTGATTTA-T-TT-TA-AAATATG
75512 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
75534 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
75551 TAATTTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
22 31 0.56
23 3 0.05
24 4 0.07
25 3 0.05
26 14 0.25
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:75553 original size:138 final size:134
Alignment explanation
Indices: 75262--75662 Score: 537
Period size: 134 Copynumber: 3.0 Consensus size: 134
75252 TATTAGTATA
* * **
75262 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAA-ATATGGA-TTG-ATT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAATA-ATTTATTTGTATT
* * * * * * *
75324 TATT-ATTGTAGTTGTATAGT-TTGATTTATTTTAAATAATT-TA-TTCGTATGGATTGATTTAT
65 GATTGATT-TA-TTTTAAAATATGGATTGA-TTT--ATTATTGTAGTT-GTATGGATTGATTTAT
75385 TTTAAAATATG
124 TTTAAAATATG
75396 GATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTTATTTGTATGG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTTATTTG--T--
75461 ATTGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTT
62 ATTGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTT
75526 AAAATATG
127 AAAATATG
*
75534 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATTG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTTATTTGTATTG
*
75599 ATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAA
66 ATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAA
75663 TAATTTATTA
Statistics
Matches: 243, Mismatches: 13, Indels: 22
0.87 0.05 0.08
Matches are distributed among these distances:
134 117 0.48
135 4 0.02
136 1 0.00
137 5 0.02
138 88 0.36
139 11 0.05
140 14 0.06
141 3 0.01
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (134 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTTATTTGTATTG
ATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAAA
TATG
Found at i:75691 original size:112 final size:110
Alignment explanation
Indices: 75344--75703 Score: 399
Period size: 112 Copynumber: 3.2 Consensus size: 110
75334 GTTGTATAGT
* *
75344 TTGATTTATTTTAAATAATTTATTCGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTT
1 TTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGGATTGATTTA---
* *
75409 TAAATAATTTATTAGTATGGATTAATTTATTTTAAATAATTTATTTGTATGGA
63 T---T-ATTTATT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
* ** * * * * * ***
75462 TTGATTGA-TTTATTTTAA--AATATGGATTGATTTA-TTATTGTAGTTGTATGGATTGATTTA-
1 TTGATTTATTTTA-AATAATTTATTTGTATTGATTGATTTATTTTA-AAATATGGATTGATTTAT
***
75522 T-TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
64 TATTTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
75568 TTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGGATTGATTTATTA
1 TTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGGATTGATTTATTA
*
75633 TTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGA
66 TT-TA-TTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
75680 TTGATTTATTTTAAATAATTTATT
1 TTGATTTATTTTAAATAATTTATT
75704 ATTGTAGTTG
Statistics
Matches: 199, Mismatches: 33, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
106 46 0.23
107 8 0.04
108 26 0.13
109 9 0.05
110 2 0.01
111 2 0.01
112 61 0.31
115 7 0.04
116 24 0.12
117 4 0.02
118 10 0.05
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (110 bp):
TTGATTTATTTTAAATAATTTATTTGTATTGATTGATTTATTTTAAAATATGGATTGATTTATTA
TTTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
Found at i:75701 original size:32 final size:32
Alignment explanation
Indices: 75641--75704 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
75631 TATTGTAGTT
75641 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
*
75673 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAATTTATTA
75705 TTGTAGTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
GTATGAATTGATTTATTTTAAATAATTTATTA
Found at i:75754 original size:31 final size:31
Alignment explanation
Indices: 75719--75777 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
75709 AGTTGTATGG
*
75719 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGTAAAACTAAA
75750 ATTATTTAAATCTCAGTATTGTAAAACT
1 ATTATTTAAATCTCAGTATTGTAAAACT
75778 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGTAAAACTAAA
Found at i:76697 original size:30 final size:27
Alignment explanation
Indices: 76640--76697 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
76630 CTCAAAACAT
**
76640 TATTATTTTATACATTTAATATTAATA
1 TATTATTTTATACATTTAATAAAAATA
76667 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TA-CA-TTTAATAAAAATA
76697 T
1 T
76698 GAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 2 0.08
29 2 0.08
30 12 0.46
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTATTTTATACATTTAATAAAAATA
Found at i:76748 original size:21 final size:20
Alignment explanation
Indices: 76724--76793 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 20
76714 TTTATTGATA
76724 ATTTTAATAATATAATACTAT
1 ATTTTAATAATATAATA-TAT
* *
76745 ATTTTATTGATATAAT-TAT
1 ATTTTAATAATATAATATAT
76764 ATTATT-ATACTATATAATATTAT
1 ATT-TTAATA--ATATAATA-TAT
76787 ACTTTTA
1 A-TTTTA
76794 TTTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
19 7 0.18
20 2 0.05
21 21 0.55
23 6 0.16
24 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (20 bp):
ATTTTAATAATATAATATAT
Found at i:79586 original size:23 final size:23
Alignment explanation
Indices: 79553--79604 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
79543 GTAAAAGGTC
79553 TACAGTCTGCGGACCACATCTACA
1 TACA-TCTGCGGACCACATCTACA
79577 TACATCTGCGGACCACATCTACA
1 TACATCTGCGGACCACATCTACA
*
79600 GACAT
1 TACAT
79605 ATGCAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (23 bp):
TACATCTGCGGACCACATCTACA
Found at i:79765 original size:31 final size:31
Alignment explanation
Indices: 79729--79788 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
79719 AACATAAAAG
*
79729 AGTTTTGCAATACTAAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
* *
79760 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
79789 CATACAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:79836 original size:22 final size:22
Alignment explanation
Indices: 79811--80269 Score: 443
Period size: 22 Copynumber: 20.6 Consensus size: 22
79801 ATAATAAATT
79811 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
79833 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
79855 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
79877 TTTTAAAATAAAGCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
79899 TTTTAAAATAAATCAGTCCATA
1 TTTTAAAATAAATCAATTCATA
*
79921 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
79943 TTTTAAAAT-AAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
79964 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
79986 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
80008 TTTTAAAATAATAAAAT-AAATCAATCCA
1 TTTT--AA-AAT-AAATCAATTC-AT--A
* *** * **
80036 TATTTTAAA-ATAAATCAATTCATA
1 T-TTTAAAATA-AATCAATTCA-TA
***
80060 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
80082 TTTTAAAATAAATTAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
80104 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
80126 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
***
80148 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
* *
80170 TTTTAAAATAAAGCAATACATA
1 TTTTAAAATAAATCAATTCATA
*
80192 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
80214 TTTTAAAATAAATCAA-TCATA
1 TTTTAAAATAAATCAATTCATA
80235 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
80257 TTTTAAAATAAAT
1 TTTTAAAATAAAT
80270 TTTAAAATAG
Statistics
Matches: 372, Mismatches: 41, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
20 2 0.01
21 42 0.11
22 280 0.75
23 14 0.04
24 7 0.02
25 9 0.02
26 12 0.03
27 1 0.00
28 2 0.01
29 3 0.01
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:79862 original size:44 final size:44
Alignment explanation
Indices: 79811--80269 Score: 588
Period size: 44 Copynumber: 10.3 Consensus size: 44
79801 ATAATAAATT
79811 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
* *
79855 TTTTAAAATAAATCAATCCATATTTTAAAATAAAGCAATCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
* *
79899 TTTTAAAATAAATCAGTCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
**
79943 TTTTAAAAT-AAT-TTTTCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATT-CATATTTTAAAATAAATCAATCCATA
79986 TTTTAAAATAAATCAATTCATATTTTAAAATAATAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA--TT----T--TAAAATAAATCAATCCATA
*** *
80038 TTTTAAAATAAATCAATTCATATTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
*
80082 TTTTAAAATAAATTAA-TCTATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATCCATA
*** *
80126 TTTTAAAATAAATCAA-TCTATATTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATCCATA
* * **
80170 TTTTAAAATAAAGCAATACATATTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAAT-AAATCAATCCATA
*
80214 TTTTAAAATAAATCAA-TCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
80257 TTTTAAAATAAAT
1 TTTTAAAATAAAT
80270 TTTAAAATAG
Statistics
Matches: 369, Mismatches: 31, Indels: 31
0.86 0.07 0.07
Matches are distributed among these distances:
42 5 0.01
43 71 0.19
44 239 0.65
45 7 0.02
46 3 0.01
50 3 0.01
52 41 0.11
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.41
Consensus pattern (44 bp):
TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
Found at i:79881 original size:66 final size:66
Alignment explanation
Indices: 79811--80269 Score: 586
Period size: 66 Copynumber: 6.9 Consensus size: 66
79801 ATAATAAATT
79811 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
79876 A
66 A
* * *
79877 TTTTAAAATAAAGCAATCCATATTTTAAAATAAATCAGTCCATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
79942 A
66 A
** *
79943 TTTTAAAAT-AAT-TTTTCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCA
1 TTTTAAAATAAATCAATT-CATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCA
80006 TA
65 TA
* *
80008 TTTTAAAATAATAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAAT
1 --TT----T--TAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT
*** *
80073 TTTTTCATA
58 CAATCCATA
* *
80082 TTTTAAAATAAATTAA-TCTATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCA
80146 TA
65 TA
*** * * **
80148 TTTTAAAATAAATTTTTTCATATTTTAAAATAAAGCAATACATATTTTAAAATAAAAT-TTTCCA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCCA
80212 TA
65 TA
*
80214 TTTTAAAATAAATCAA-TCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT
80270 TTTAAAATAG
Statistics
Matches: 342, Mismatches: 37, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
64 5 0.01
65 82 0.24
66 189 0.55
67 8 0.02
68 1 0.00
71 1 0.00
72 2 0.01
73 6 0.02
74 47 0.14
75 1 0.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.41
Consensus pattern (66 bp):
TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
A
Found at i:80025 original size:30 final size:30
Alignment explanation
Indices: 79989--80048 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
79979 ATCCATATTT
*
79989 TAAAATAAATCAATTCATATTTTAAAATAA
1 TAAAATAAATCAATCCATATTTTAAAATAA
80019 TAAAATAAATCAATCCATATTTTAAAATAA
1 TAAAATAAATCAATCCATATTTTAAAATAA
80049 ATCAATTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (30 bp):
TAAAATAAATCAATCCATATTTTAAAATAA
Found at i:82312 original size:20 final size:20
Alignment explanation
Indices: 82273--82312 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
82263 GTAATCATAT
**
82273 TCACTGGTAATCTTTTATTC
1 TCACTGGTAATCTTACATTC
82293 TCACTGGTAATCTTACATTC
1 TCACTGGTAATCTTACATTC
82313 CGTGAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (20 bp):
TCACTGGTAATCTTACATTC
Done.