Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003519.1 Hibiscus syriacus cultivar Beakdansim tig00007438_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: 93259
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3094 original size:8 final size:8
Alignment explanation
Indices: 3083--3120 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
3073 AAATAAAAGA
3083 GAAAAAAT
1 GAAAAAAT
3091 G-AAAAAT
1 GAAAAAAT
3098 GAAAAAA-
1 GAAAAAAT
3105 GAGAAAAAT
1 GA-AAAAAT
3114 GAAAAAA
1 GAAAAAA
3121 AGAGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 9 0.33
8 16 0.59
9 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:3112 original size:17 final size:17
Alignment explanation
Indices: 3091--3127 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
3081 GAGAAAAAAT
3091 GAAAAATG-AAAAAAGA
1 GAAAAATGAAAAAAAGA
3107 GAAAAATGAAAAAAAGA
1 GAAAAATGAAAAAAAGA
3124 GAAA
1 GAAA
3128 TAAAAGGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (17 bp):
GAAAAATGAAAAAAAGA
Found at i:3128 original size:15 final size:15
Alignment explanation
Indices: 3083--3132 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
3073 AAATAAAAGA
*
3083 GAAAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
3098 GAAAAAAGAGAAAAAT
1 GAAAAAA-AGAAAAAT
*
3114 GAAAAAAAGAGAAAT
1 GAAAAAAAGAAAAAT
3129 -AAAA
1 GAAAA
3133 GGAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 4 0.12
15 14 0.44
16 14 0.44
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:4618 original size:56 final size:55
Alignment explanation
Indices: 4447--4912 Score: 538
Period size: 55 Copynumber: 8.6 Consensus size: 55
4437 GTTGAAGATT
* * * ** *
4447 GAGTCCTATACTCTCTGAATGAATAGGGAGTGGACAAGTTCATTGAAGA---TT-
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
* * * * ** **
4498 GAGTCATATACTCTCTGAATGAATAGGGAGTGGACAAGTTCGTTGAAGA---TT-
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
*
4549 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTGTTC
* * *
4605 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
* *
4660 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTGTTC
* * *
4716 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
*
4771 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCG-TTTATTGAAGATTGTTC
* * * * *
4827 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTT-TATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTAT-TGAAGATTGTTC
* *
4882 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCCTATACTCT-CTGAAGGAATAGAGAGC
4913 AGGCTCGTCA
Statistics
Matches: 370, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
51 81 0.22
52 10 0.03
54 2 0.01
55 143 0.39
56 134 0.36
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (55 bp):
GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTATTGAAGATTGTTC
Found at i:4697 original size:111 final size:111
Alignment explanation
Indices: 4498--4912 Score: 594
Period size: 111 Copynumber: 3.8 Consensus size: 111
4488 ATTGAAGATT
* * * * ** ** *
4498 GAGTCATATACTCTCTGAATGAATAGGGAGTGGACAAGTTCGTTGAAGA---TT-GAGTCCTATA
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
4559 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
4605 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
4670 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
4716 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
*
4781 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
* * * * *
4827 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACAC-GTTT-TATGAAGATTGTTCGAG-TCTT
1 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGAC-CTGTTTAT-TGAAGATTTTTCGAGTTC-T
*
4889 ATACT-TCCTGAAGGAATAGGGAGC
63 ATACTCT-CTGAAGGAATAGAGAGC
4913 AGGCTCGTCA
Statistics
Matches: 284, Mismatches: 16, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
107 41 0.14
110 6 0.02
111 236 0.83
112 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (111 bp):
GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTGTTTATTGAAGATTTTTCGAGTTCTATA
CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
Found at i:4914 original size:55 final size:56
Alignment explanation
Indices: 4549--4912 Score: 515
Period size: 56 Copynumber: 6.6 Consensus size: 56
4539 GTTGAAGATT
* *
4549 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
4605 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTG-TTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
4660 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
4716 GAGTCCTATACTCTCTGAAAGAATAGAGAGCGGACCTG-TTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
4771 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
4827 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
4882 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
4913 AGGCTCGTCA
Statistics
Matches: 276, Mismatches: 25, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
54 1 0.00
55 136 0.49
56 138 0.50
57 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:21093 original size:31 final size:30
Alignment explanation
Indices: 21036--21103 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
21026 AGAATTAATG
* *
21036 GGTCAAATTGATATTTTATCTAAAGTTTAG
1 GGTCAAAATGATATTTTATCTAAAGTTTAA
21066 GAGTCAAAATGATATCTTT-TC-AGAAGTTTAA
1 G-GTCAAAATGATAT-TTTATCTA-AAGTTTAA
21097 GGTCAAA
1 GGTCAAA
21104 TCAATATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 8 0.24
31 22 0.67
32 3 0.09
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (30 bp):
GGTCAAAATGATATTTTATCTAAAGTTTAA
Found at i:22158 original size:31 final size:32
Alignment explanation
Indices: 22123--22195 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 32
22113 TTTTTAAAGA
22123 GAAATTATAA-ATGCCTGTTTCTATACATACT
1 GAAATTATAATATGCCTGTTTCTATACATACT
22154 GAAATTATATATATGCCTGTTTCTATACATACT
1 GAAATTATA-ATATGCCTGTTTCTATACATACT
*
22187 -AAAATATAA
1 GAAATTATAA
22196 CACATAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
31 10 0.26
32 8 0.21
33 21 0.54
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (32 bp):
GAAATTATAATATGCCTGTTTCTATACATACT
Found at i:24586 original size:15 final size:14
Alignment explanation
Indices: 24562--24600 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
24552 ATCCATTTTT
24562 CATAACATATCACA
1 CATAACATATCACA
24576 CATACACATATCACA
1 CATA-ACATATCACA
* *
24591 TATAATATAT
1 CATAACATAT
24601 TTATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (14 bp):
CATAACATATCACA
Found at i:24728 original size:23 final size:23
Alignment explanation
Indices: 24693--24758 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
24683 CACCACAACT
*
24693 CGTATAAATGCACCGAAGTGTCA
1 CGTAGAAATGCACCGAAGTGTCA
*
24716 CGTAG-AATCGCACCGAAGTGTCG
1 CGTAGAAAT-GCACCGAAGTGTCA
*
24739 CGTAGAAATGCACAGAAGTG
1 CGTAGAAATGCACCGAAGTG
24759 CCATATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.84
24 3 0.08
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGTCA
Found at i:27074 original size:26 final size:27
Alignment explanation
Indices: 27014--27074 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 27
27004 TTTTTATTGT
*
27014 TTTTAATTTTTATTAATGGAAGAAATAA
1 TTTTAACTTTTATTAAT-GAAGAAATAA
27042 TTCTTAACTTTTATTAAT-AA-AAATAA
1 TT-TTAACTTTTATTAATGAAGAAATAA
27068 TCTTTAA
1 T-TTTAA
27075 ATAAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 11 0.37
27 3 0.10
28 2 0.07
29 14 0.47
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (27 bp):
TTTTAACTTTTATTAATGAAGAAATAA
Found at i:31465 original size:14 final size:14
Alignment explanation
Indices: 31446--31473 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31436 CTTGAAATAT
31446 AATATTAAAACTTG
1 AATATTAAAACTTG
31460 AATATTAAAACTTG
1 AATATTAAAACTTG
31474 GCTCGAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AATATTAAAACTTG
Found at i:32346 original size:199 final size:201
Alignment explanation
Indices: 31993--32393 Score: 747
Period size: 199 Copynumber: 2.0 Consensus size: 201
31983 AATTCGTTTT
31993 GTCATCAAATTAACAGCCATTAAAGTTTTTTATTGCTGGTACTTGCATGTCGTAGGAGATTTATC
1 GTCATCAAATTAACAGCCATTAAAG-TTTTTATTGCTGGTACTTGCATGTCGTAGGAGATTTATC
32058 TGTGTACACAATCTTGATTTTTTAATATTTGTTGAGTCTTAGAATATTAATTGTTTGGCCCTAAT
65 TGTGTACACAATCTTGATTTTTTAATATTTGTTGAGTCTTAGAATATTAATTGTTTGGCCCTAAT
32123 AAATCATGACTTTTAGGTTCACTAATATACAATAATGTATAACTACGCATATTCAAATCTATGAC
130 AAATCATGACTTTTAGGTTCACTAATATAC-A-AATGTATAACTACGCATATTCAAATCTATGAC
32188 C-AAACTAA
193 CAAAACTAA
32196 GTCATCAAATTAACAGCCATTAAAG-TTTTATTGCTGGTACTTGCATGTCGTAGGAGATTTATCT
1 GTCATCAAATTAACAGCCATTAAAGTTTTTATTGCTGGTACTTGCATGTCGTAGGAGATTTATCT
32260 GTGTACACAATCTTGATTTTTT-A-ATTTGTTGAGTCTTAGAATATTAATTGTTTGGCCCTAATA
66 GTGTACACAATCTTGATTTTTTAATATTTGTTGAGTCTTAGAATATTAATTGTTTGGCCCTAATA
32323 AATCATGACTTTTAGGTTCACTAATATACAAATGTATAACTACGCATATTCAAATCTATGACCAA
131 AATCATGACTTTTAGGTTCACTAATATACAAATGTATAACTACGCATATTCAAATCTATGACCAA
32388 AACTAA
196 AACTAA
32394 TTATTTCTTT
Statistics
Matches: 197, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
197 33 0.17
198 8 0.04
199 69 0.35
200 1 0.01
201 61 0.31
203 25 0.13
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (201 bp):
GTCATCAAATTAACAGCCATTAAAGTTTTTATTGCTGGTACTTGCATGTCGTAGGAGATTTATCT
GTGTACACAATCTTGATTTTTTAATATTTGTTGAGTCTTAGAATATTAATTGTTTGGCCCTAATA
AATCATGACTTTTAGGTTCACTAATATACAAATGTATAACTACGCATATTCAAATCTATGACCAA
AACTAA
Found at i:49981 original size:25 final size:26
Alignment explanation
Indices: 49930--49981 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
49920 ATAACATGGG
*
49930 CATTTTCACTTATCTCATTTCACTATA
1 CATTTTCAC-TATCACATTTCACTATA
49957 CATTTTCA-TATCACATGTTCA-TATA
1 CATTTTCACTATCACAT-TTCACTATA
49982 AGCTCATAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 11 0.48
26 4 0.17
27 8 0.35
ACGTcount: A:0.29, C:0.23, G:0.02, T:0.46
Consensus pattern (26 bp):
CATTTTCACTATCACATTTCACTATA
Found at i:50668 original size:20 final size:20
Alignment explanation
Indices: 50643--50761 Score: 202
Period size: 20 Copynumber: 5.8 Consensus size: 20
50633 TTCCCCTTGA
50643 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
50663 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
50683 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
50703 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
50723 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
50746 ATGTGCATCGATGCAT
1 A-GTGCATCGATGCAT
50762 GGGTATCGAT
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
20 77 0.81
22 1 0.01
23 3 0.03
24 14 0.15
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:53996 original size:11 final size:11
Alignment explanation
Indices: 53980--54010 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
53970 CATTCCTATC
53980 ATTATCATTTT
1 ATTATCATTTT
53991 ATTATCATTTT
1 ATTATCATTTT
54002 ATTATCATT
1 ATTATCATT
54011 CATATTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATCATTTT
Found at i:54789 original size:16 final size:17
Alignment explanation
Indices: 54768--54801 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54758 CATAACTTAT
*
54768 ATCACA-AAGTCATATC
1 ATCACATAAATCATATC
54784 ATCACATAAATCATATC
1 ATCACATAAATCATATC
54801 A
1 A
54802 CATAGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (17 bp):
ATCACATAAATCATATC
Found at i:55279 original size:19 final size:19
Alignment explanation
Indices: 55255--55326 Score: 144
Period size: 19 Copynumber: 3.8 Consensus size: 19
55245 TTTTAAGGGG
55255 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
55274 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
55293 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
55312 ATGCATCGATGCACT
1 ATGCATCGATGCACT
55327 AATTGCATTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:55409 original size:101 final size:102
Alignment explanation
Indices: 55275--55487 Score: 410
Period size: 101 Copynumber: 2.1 Consensus size: 102
55265 GCACTCCTTA
55275 TGCATCGATGCACTCCTTATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGAT
1 TGCATCGATG-ACTCCTTATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGAT
55340 GTTTCTTCTTTAAAGATTGCATCGATACACATTGAATG
65 GTTTCTTCTTTAAAGATTGCATCGATACACATTGAATG
55378 TGCATCGATG-CTCCTTATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATG
1 TGCATCGATGACTCCTTATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATG
55442 TTTCTTCTTTAAAGATTGCATCGATACACATTGAATG
66 TTTCTTCTTTAAAGATTGCATCGATACACATTGAATG
55479 TGCATCGAT
1 TGCATCGAT
55488 ACACCTTGCC
Statistics
Matches: 110, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
101 100 0.91
103 10 0.09
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (102 bp):
TGCATCGATGACTCCTTATGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATG
TTTCTTCTTTAAAGATTGCATCGATACACATTGAATG
Found at i:55412 original size:19 final size:19
Alignment explanation
Indices: 55378--55427 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
55368 ACATTGAATG
55378 TGCATCGATG--CTCCTTA
1 TGCATCGATGCACTCCTTA
55395 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
55414 TGCATCGATGCACT
1 TGCATCGATGCACT
55428 AATTGCATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.32
19 21 0.68
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:56210 original size:2 final size:2
Alignment explanation
Indices: 56203--56237 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56193 TTACAAATTG
56203 AT AT AT 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 AT AT AT A
56238 CTCATCTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68905 original size:22 final size:21
Alignment explanation
Indices: 68853--68909 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
68843 CCCTCTATAT
*
68853 ATAATTTTTTT-TTGAATTAA
1 ATAATTTTTTTATTGAATAAA
* *
68873 GTCATTGTTTTTATTGAATAAAA
1 ATAATT-TTTTTATTGAAT-AAA
68896 ATAATTTTTTTATT
1 ATAATTTTTTTATT
68910 ATTTCGGGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.14
21 5 0.17
22 14 0.48
23 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
ATAATTTTTTTATTGAATAAA
Found at i:69023 original size:32 final size:33
Alignment explanation
Indices: 68982--69061 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
68972 TATTTTGTTT
68982 GGGTCGGGTCGGGTTTTTT-AAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
69014 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
1 GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
69047 GGGTCGGGTCGGGTT
1 GGGTCGGGTCGGGTT
69062 CGGGTTTAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 19 0.40
33 28 0.60
ACGTcount: A:0.11, C:0.10, G:0.41, T:0.38
Consensus pattern (33 bp):
GGGTCGGGTCGGGTTTTTTAAAGTGTGATATTC
Found at i:69622 original size:17 final size:18
Alignment explanation
Indices: 69596--69635 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
69586 ATATGGAATT
* *
69596 AGATTCCAATT-CTTGAC
1 AGATTACAATTCCTTCAC
69613 AGATTACAATTCCTTCAC
1 AGATTACAATTCCTTCAC
69631 AGATT
1 AGATT
69636 CTAATTCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (18 bp):
AGATTACAATTCCTTCAC
Found at i:69641 original size:18 final size:17
Alignment explanation
Indices: 69596--69643 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
69586 ATATGGAATT
*
69596 AGATTCCAATT-CTTGAC
1 AGATT-CAATTCCTTCAC
69613 AGATTACAATTCCTTCAC
1 AGATT-CAATTCCTTCAC
69631 AGATTCTAATTCC
1 AGATTC-AATTCC
69644 CCCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (17 bp):
AGATTCAATTCCTTCAC
Found at i:76461 original size:21 final size:21
Alignment explanation
Indices: 76413--76463 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
76403 TATCGGAAAC
* *
76413 ATTATTATTTCTACTGATTTT
1 ATTATTTTTTCTACCGATTTT
76434 ATTATTTTTTCTACCGATTTT
1 ATTATTTTTTCTACCGATTTT
*
76455 GTTATTTTT
1 ATTATTTTT
76464 GAGCATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.65
Consensus pattern (21 bp):
ATTATTTTTTCTACCGATTTT
Found at i:76771 original size:2 final size:2
Alignment explanation
Indices: 76764--76794 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76754 TTTCTTCATC
76764 AT 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 AT A
76795 GGTTTACTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80987 original size:35 final size:35
Alignment explanation
Indices: 80944--81079 Score: 164
Period size: 35 Copynumber: 3.9 Consensus size: 35
80934 ATTGAAGTGT
* * * ** *
80944 TTTAGAATTTGGGGTTTAAAATTTAATTGAATTAT
1 TTTAGAAATTAGGGTTTAGAATGAAATTGAATTAC
* * *
80979 TTTGGAATTTAGGGTTTAGAATGAAATTAAATTAC
1 TTTAGAAATTAGGGTTTAGAATGAAATTGAATTAC
*
81014 TTTAGAAATTAGGGTTTAGAATGAAAGTGAATTAC
1 TTTAGAAATTAGGGTTTAGAATGAAATTGAATTAC
* *
81049 TTTGGAAATTGGGGTTTAGAATGAAATTGAA
1 TTTAGAAATTAGGGTTTAGAATGAAATTGAA
81080 GACTGTTTTG
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 87 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.40
Consensus pattern (35 bp):
TTTAGAAATTAGGGTTTAGAATGAAATTGAATTAC
Found at i:81020 original size:70 final size:70
Alignment explanation
Indices: 80944--81076 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 70
80934 ATTGAAGTGT
* * ** * * *
80944 TTTAGAATTTGGGGTTTAAAATTTAATTGAATTATTTTGGAATTTAGGGTTTAGAATGAAATTAA
1 TTTAGAAATTAGGGTTTAAAATGAAAGTGAATTACTTTGGAAATTAGGGTTTAGAATGAAATTAA
81009 ATTAC
66 ATTAC
* *
81014 TTTAGAAATTAGGGTTTAGAATGAAAGTGAATTACTTTGGAAATTGGGGTTTAGAATGAAATT
1 TTTAGAAATTAGGGTTTAAAATGAAAGTGAATTACTTTGGAAATTAGGGTTTAGAATGAAATT
81077 GAAGACTGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
70 54 1.00
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.41
Consensus pattern (70 bp):
TTTAGAAATTAGGGTTTAAAATGAAAGTGAATTACTTTGGAAATTAGGGTTTAGAATGAAATTAA
ATTAC
Found at i:84512 original size:17 final size:17
Alignment explanation
Indices: 84452--84512 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
84442 TAGTATGCTG
84452 AATTT-TACATTTTTTA
1 AATTTATACATTTTTTA
* *
84468 AATTTAGT-CCTTATTTA
1 AATTTA-TACATTTTTTA
84485 ACATGTATATACATTTTTTA
1 A-AT-T-TATACATTTTTTA
84505 AATTTATA
1 AATTTATA
84513 GTTTAGCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
16 5 0.14
17 12 0.34
18 4 0.11
19 4 0.11
20 10 0.29
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.54
Consensus pattern (17 bp):
AATTTATACATTTTTTA
Found at i:86230 original size:45 final size:49
Alignment explanation
Indices: 86155--86254 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 49
86145 ATTTATTTTC
* *
86155 ATTTTTTCGAATAAATGTATGCGAACTAGATATCATGCGGTTAGG-TTT
1 ATTTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
*
86203 ATTTTTT-GAAT-AA-GCATGCGAATTAGATATCATGAGGTTAGGATTT
1 ATTTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
*
86249 CTTTTT
1 ATTTTT
86255 GTGGAAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 26 0.55
46 10 0.21
47 4 0.09
48 7 0.15
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (49 bp):
ATTTTTTCGAATAAATGCATGCGAACTAGATATCATGAGGTTAGGATTT
Done.