Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000584.1 Hibiscus syriacus cultivar Beakdansim tig00001140_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: 80161
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:2356 original size:68 final size:65
Alignment explanation
Indices: 2227--2374 Score: 156
Period size: 67 Copynumber: 2.2 Consensus size: 65
2217 TTTAAAGAGT
* * * * *
2227 TAAAATATAATAGTTTCCTTATCATGAATTAAAAAATTATTTCTCCATTACTGAATATTTAAATG
1 TAAAATATAA-AGTTTCCTCATCATGAATTAAAAAATAATATCTCCATTACCGAATATTT-AATC
2292 AA
64 AA
*
2294 TAAAATATAAAGTTTCCTCATCAAT-ATATTAAAAAAATAAATAT-TCCATTACCGAGTATTTAA
1 TAAAATATAAAGTTTCCTCATC-ATGA-ATT-AAAAAAT-AATATCTCCATTACCGAATATTTAA
2357 TCAA
62 TCAA
* *
2361 TTAGATATAAAGTT
1 TAAAATATAAAGTT
2375 CTAAGTTTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
66 12 0.17
67 32 0.46
68 22 0.32
69 3 0.04
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (65 bp):
TAAAATATAAAGTTTCCTCATCATGAATTAAAAAATAATATCTCCATTACCGAATATTTAATCAA
Found at i:2535 original size:14 final size:14
Alignment explanation
Indices: 2505--2545 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2495 ATATTGACCA
*
2505 AATATTTAAAT-AT
1 AATATTTATATAAT
*
2518 AATATTTGTATAAT
1 AATATTTATATAAT
2532 AATATTTATATAAT
1 AATATTTATATAAT
2546 TATTGATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
AATATTTATATAAT
Found at i:4971 original size:23 final size:23
Alignment explanation
Indices: 4941--4988 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
4931 AACTCGAGAT
*
4941 TTGCTTAAGTGATATTACACTAC
1 TTGCTTAAGTGATATTACAATAC
4964 TTGCTTAAGTGATATTACAATAC
1 TTGCTTAAGTGATATTACAATAC
4987 TT
1 TT
4989 ACCACTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (23 bp):
TTGCTTAAGTGATATTACAATAC
Found at i:5975 original size:13 final size:13
Alignment explanation
Indices: 5959--5995 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5949 GTTTATTTAT
5959 TATTTTTAAATTA
1 TATTTTTAAATTA
5972 TATTTTT-AATTA
1 TATTTTTAAATTA
5984 -ATTTTTAGAATT
1 TATTTTTA-AATT
5996 TGAATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
13 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TATTTTTAAATTA
Found at i:7079 original size:29 final size:29
Alignment explanation
Indices: 7022--7108 Score: 167
Period size: 29 Copynumber: 3.0 Consensus size: 29
7012 CTAAAGTTAA
7022 CTATCCAACCCTATA-ATCGACATCGACT
1 CTATCCAACCCTATATATCGACATCGACT
7050 CTATCCAACCCTATATATCGACATCGACT
1 CTATCCAACCCTATATATCGACATCGACT
7079 CTATCCAACCCTATATATCGACATCGACT
1 CTATCCAACCCTATATATCGACATCGACT
7108 C
1 C
7109 AAGCTTTTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 15 0.26
29 43 0.74
ACGTcount: A:0.31, C:0.36, G:0.07, T:0.26
Consensus pattern (29 bp):
CTATCCAACCCTATATATCGACATCGACT
Found at i:10543 original size:20 final size:20
Alignment explanation
Indices: 10518--10555 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10508 TTTGGTTCAC
10518 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
10538 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
10556 AGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:10786 original size:38 final size:37
Alignment explanation
Indices: 10712--10787 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 37
10702 GTTGGAAAAT
* *
10712 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
10749 ATTTATATAATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-A-TTTTCTTTAAAAAATTGAAAATCATAAA
10787 A
1 A
10788 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 7 0.21
39 18 0.55
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:16291 original size:64 final size:65
Alignment explanation
Indices: 16145--16300 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 65
16135 GAAGGTGTAT
* *** * *
16145 CGATGCACATGTAGTGCATCGATGCA-CTCTTTTAATCTAAAAACATCGAATGCAATTGGTGCAT
1 CGATGCACAAGTAGTGCATCGATGCATCTCCAGTAATCAAAAAACATCGAATGCAATTGGTGCAC
* * * * *
16209 CGATGCATAAGGCA-TGCATCGATGCATC-CCAGTAAT-AAACAAACATCGAATGTATTTTGTGC
1 CGATGCACAA-GTAGTGCATCGATGCATCTCCAGTAATCAAA-AAACATCGAATGCAATTGGTGC
16271 AC
64 AC
*
16273 CGATGCACAAGTAGTGCATCGATTCATC
1 CGATGCACAAGTAGTGCATCGATGCATC
16301 GGTAGGGAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
63 4 0.05
64 67 0.91
65 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (65 bp):
CGATGCACAAGTAGTGCATCGATGCATCTCCAGTAATCAAAAAACATCGAATGCAATTGGTGCAC
Found at i:17312 original size:103 final size:103
Alignment explanation
Indices: 17087--17304 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
17077 GTCGAGGGTC
* *
17087 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGGCACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* *
17152 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
17190 TATATGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* *
17255 TTGATCCCTAGTATATTTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
17293 TATGTGGTCCTT
1 TATGTGGTCCTT
17305 ATGGACATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:17354 original size:23 final size:23
Alignment explanation
Indices: 17320--17372 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
17310 CATTATTATA
*
17320 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
17343 TGGCACTCCGGTGCAATTATATG
1 TGGCACTACGGTGCAATTATACG
17366 TGGCACT
1 TGGCACT
17373 TATGTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:17644 original size:21 final size:21
Alignment explanation
Indices: 17612--17660 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
17602 TTGAAATGAT
17612 GATATAAATAATAAGTTTATAA
1 GATAT-AATAATAAGTTTATAA
17634 GATATAATAATAAGTTTATAA
1 GATATAATAATAAGTTTATAA
17655 GATATA
1 GATATA
17661 TGATATGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (21 bp):
GATATAATAATAAGTTTATAA
Found at i:23070 original size:103 final size:103
Alignment explanation
Indices: 22886--23103 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
22876 GTCGAGGGTC
*
22886 TATGTGGTCCTTCGTGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
22951 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
22989 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
23054 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
23092 TATGTGGTCCTT
1 TATGTGGTCCTT
23104 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:23145 original size:23 final size:23
Alignment explanation
Indices: 23110--23187 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
23100 CCTTATGGAC
* *
23110 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGCA
* *
23134 ATTCTATGTGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
23157 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
23180 ATTATATG
1 ATTATATG
23188 AGCTGTGGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 45 0.94
24 3 0.06
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:27861 original size:20 final size:20
Alignment explanation
Indices: 27836--27890 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
27826 GAAATGGTGT
*
27836 GTGCATCGATGCATCAAAGA
1 GTGCATCGGTGCATCAAAGA
27856 GTGCATCGGTGCATCAAAGA
1 GTGCATCGGTGCATCAAAGA
27876 GTGCATCGGTGCATC
1 GTGCATCGGTGCATC
27891 CCTTCACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (20 bp):
GTGCATCGGTGCATCAAAGA
Found at i:35880 original size:16 final size:17
Alignment explanation
Indices: 35828--35892 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
35818 AAAATTATAT
35828 TAAAA-AATTTAAAATA
1 TAAAATAATTTAAAATA
* * **
35844 TGAAATTATACAATCAATA
1 TAAAATAATTTAA--AATA
35863 TAAAAT-ATTTAAAATA
1 TAAAATAATTTAAAATA
35879 TAAAATAATTTAAA
1 TAAAATAATTTAAA
35893 TTTTTTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 14 0.37
17 11 0.29
18 4 0.11
19 9 0.24
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAAATAATTTAAAATA
Found at i:35892 original size:26 final size:26
Alignment explanation
Indices: 35828--35902 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
35818 AAAATTATAT
* *
35828 TAAAA-AATTTAAAATA-TGAAATTA
1 TAAAATAATTTAAAATATTTAAAATA
* *
35852 TACAATCAATATAAAATATTTAAAATA
1 TAAAAT-AATTTAAAATATTTAAAATA
* *
35879 TAAAATAATTTAAATTTTTTAAAA
1 TAAAATAATTTAAAATATTTAAAA
35903 ATACCTATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 4 0.10
26 25 0.62
27 11 0.28
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (26 bp):
TAAAATAATTTAAAATATTTAAAATA
Found at i:44555 original size:22 final size:23
Alignment explanation
Indices: 44523--44573 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
44513 CCACATTATG
*
44523 CAAATATTTACCA-AACTAACACC
1 CAAATATTTA-CATAAATAACACC
44546 CAAAT-TTTACATAAATAACACC
1 CAAATATTTACATAAATAACACC
*
44568 AAAATA
1 CAAATA
44574 AAAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.08
22 17 0.71
23 5 0.21
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (23 bp):
CAAATATTTACATAAATAACACC
Found at i:45482 original size:21 final size:21
Alignment explanation
Indices: 45445--45498 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
45435 CATTAAGTTG
* *
45445 AATAT-TTGAATAGAATTTAT
1 AATATATTAAATAGAATTTAA
*
45465 AATATATTAAATATAATTTAA
1 AATATATTAAATAGAATTTAA
*
45486 AACTATAGTAAAT
1 AA-TATATTAAAT
45499 CAATAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
AATATATTAAATAGAATTTAA
Found at i:47147 original size:22 final size:21
Alignment explanation
Indices: 47116--47169 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
47106 CCCGAACCGA
*
47116 AAAAAGATTTAATCGATACAAT
1 AAAAATATTTAA-CGATACAAT
* *
47138 AAAAATATTTTAAGGATTCAAT
1 AAAAATA-TTTAACGATACAAT
*
47160 TAAAATATTT
1 AAAAATATTT
47170 TAAAGTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.11
22 19 0.70
23 5 0.19
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAAATATTTAACGATACAAT
Found at i:47149 original size:23 final size:22
Alignment explanation
Indices: 47123--47172 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
47113 CGAAAAAAGA
47123 TTTAATCGATACAATAAAAATAT
1 TTTAA-CGATACAATAAAAATAT
* * *
47146 TTTAAGGATTCAATTAAAATAT
1 TTTAACGATACAATAAAAATAT
47168 TTTAA
1 TTTAA
47173 AGTTTAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (22 bp):
TTTAACGATACAATAAAAATAT
Found at i:51346 original size:27 final size:27
Alignment explanation
Indices: 51307--51372 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
51297 TACCAGCTTA
51307 TTGTCT-GCTATTGCAATCTATATTGC
1 TTGTCTGGCTATTGCAATCTATATTGC
51333 TTGTCTGGCTATTGCAATCTATATTGC
1 TTGTCTGGCTATTGCAATCTATATTGC
51360 TTGTCTGGCTATT
1 TTGTCTGGCTATT
51373 TCTTATTGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
26 6 0.15
27 33 0.85
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (27 bp):
TTGTCTGGCTATTGCAATCTATATTGC
Found at i:52628 original size:97 final size:97
Alignment explanation
Indices: 52458--52650 Score: 332
Period size: 97 Copynumber: 2.0 Consensus size: 97
52448 AACTCAAGTA
*
52458 TTTGGTTAATAAACTCACAAAGCAGGTTCGAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
1 TTTGGTTAATAAACTCACAAAGCAGGTTCAAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
* *
52523 GGCTTCTATAGTCTACTATAGTATGTCTGAGT
66 GGCGTCTATAGTCTACCATAGTATGTCTGAGT
* **
52555 TTTGGTTAATAAACTCACAAAGCAGGTTTAAATTCTTCTGGTTCCTCCTTTCTGGATTTAAACAT
1 TTTGGTTAATAAACTCACAAAGCAGGTTCAAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
52620 GGCGTCTATAGTCTACCATAGTATGTCTGAG
66 GGCGTCTATAGTCTACCATAGTATGTCTGAG
52651 AGTTTTTCTG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (97 bp):
TTTGGTTAATAAACTCACAAAGCAGGTTCAAATTCTTCTGGTTCCTCCTTTCTAAATTTAAACAT
GGCGTCTATAGTCTACCATAGTATGTCTGAGT
Found at i:57689 original size:19 final size:19
Alignment explanation
Indices: 57646--57692 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
57636 TCTAATATAT
*
57646 TATTTAATATTTGAATTTAG
1 TATTT-ATATTTAAATTTAG
57666 T-TTTATAGTTTAAATTTA-
1 TATTTATA-TTTAAATTTAG
57684 TATTTATAT
1 TATTTATAT
57693 ATATTTGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 18 0.75
20 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TATTTATATTTAAATTTAG
Found at i:61723 original size:2 final size:2
Alignment explanation
Indices: 61716--61771 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
61706 GCTAAATTTG
61716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61758 AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT A
61772 AATTATTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71642 original size:4 final size:4
Alignment explanation
Indices: 71633--71663 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
71623 TCCTTTGGTC
71633 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT
71664 CTTTTCAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:73389 original size:18 final size:19
Alignment explanation
Indices: 73358--73401 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
73348 TATTCTCTTA
*
73358 TTTTT-TTTACTTTAATTG
1 TTTTTATTTACTTTAATCG
73376 TTTTTATTTA-TTTAATCG
1 TTTTTATTTACTTTAATCG
73394 TTTTTATT
1 TTTTTATT
73402 ACTACTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTTATTTACTTTAATCG
Found at i:78377 original size:16 final size:16
Alignment explanation
Indices: 78356--78387 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
78346 CAATTCTAAC
78356 GGGAGAATTGAAACGG
1 GGGAGAATTGAAACGG
78372 GGGAGAATTGAAACGG
1 GGGAGAATTGAAACGG
78388 TCCTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.44, T:0.12
Consensus pattern (16 bp):
GGGAGAATTGAAACGG
Done.