Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001016.1 Hibiscus syriacus cultivar Beakdansim tig00002028_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: 91452
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5682 original size:15 final size:16
Alignment explanation
Indices: 5648--5685 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5638 CCTCTCAAAA
5648 ATTTTAAATTATTATAT
1 ATTTT-AATTATTATAT
*
5665 ATTTTAATT-TTTTAT
1 ATTTTAATTATTATAT
5680 ATTTTA
1 ATTTTA
5686 TAAATCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 4 0.20
17 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTAATTATTATAT
Found at i:5734 original size:27 final size:26
Alignment explanation
Indices: 5696--5747 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5686 TAAATCTATT
* *
5696 TTATCTTCTAAAAATTTTATAAATTCG
1 TTATCTCCT-AAAATTTTAAAAATTCG
*
5723 TTATCTCCTAAAGTTTTAAAAATTC
1 TTATCTCCTAAAATTTTAAAAATTC
5748 ATCCTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (26 bp):
TTATCTCCTAAAATTTTAAAAATTCG
Found at i:6528 original size:88 final size:88
Alignment explanation
Indices: 6353--6521 Score: 302
Period size: 88 Copynumber: 1.9 Consensus size: 88
6343 CGGTTTGTAA
* *
6353 TGGTAATAAAATATTAATTTCCTATCGGAAATGAACTTAATATTTGTATTTTGAGACATTCGTAT
1 TGGTAATAAAATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGAGACATTCGTAT
*
6418 AAGACATGAGTCAAAAAGACATT
66 AAGACACGAGTCAAAAAGACATT
*
6441 TGGTAATAAAATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGATACATTCGTAT
1 TGGTAATAAAATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGAGACATTCGTAT
6506 AAGACACGAGTCAAAA
66 AAGACACGAGTCAAAA
6522 TAACATTCTC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 77 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (88 bp):
TGGTAATAAAATATTAATTTCCTATCGAAAAGGAACTTAATATTTGTATTTTGAGACATTCGTAT
AAGACACGAGTCAAAAAGACATT
Found at i:8804 original size:16 final size:16
Alignment explanation
Indices: 8781--8857 Score: 127
Period size: 16 Copynumber: 4.8 Consensus size: 16
8771 GGGTCTCCAA
8781 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* *
8797 CATTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
8813 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
8829 CGTTTATGTTCATGTT
1 CGTTTATGTTCGTGTT
8845 CGTTTATGTTCGT
1 CGTTTATGTTCGT
8858 TTATTTATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 55 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:8817 original size:10 final size:10
Alignment explanation
Indices: 8804--8861 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
8794 GTTCATTTAT
*
8804 GTTTGTGTTC
1 GTTTATGTTC
8814 GTTTATGTTC
1 GTTTATGTTC
8824 G----TGTTC
1 GTTTATGTTC
8830 GTTTATGTTC
1 GTTTATGTTC
8840 ----ATGTTC
1 GTTTATGTTC
8846 GTTTATGTTC
1 GTTTATGTTC
8856 GTTTAT
1 GTTTAT
8862 TTATTAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 16
0.70 0.02 0.29
Matches are distributed among these distances:
6 12 0.31
10 27 0.69
ACGTcount: A:0.09, C:0.10, G:0.22, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:9965 original size:65 final size:66
Alignment explanation
Indices: 9890--10054 Score: 207
Period size: 65 Copynumber: 2.6 Consensus size: 66
9880 ATTGACCGTG
*
9890 GTACAAACAT-ATATTGACATAAAAGCTGCAATTCATTTCCACATATAGATGCATTCATGCATGT
1 GTACAAACATAAT-TTGACATAAAAGCTGCAATCCATTTCCACATATAGATGCATTCATGCATGT
9954 AT
65 AT
* **
9956 GTAC-AACATAATTTGATATAGGAGCTGCAATCCATTTCCACATATAGATGCATTCATGC----A
1 GTACAAACATAATTTGACATAAAAGCTGCAATCCATTTCCACATATAGATGCATTCATGCATGTA
10016 T
66 T
* * * *
10017 GTACAAAGATAAGTTGATATAAGAGCTGCAATCCATTT
1 GTACAAACATAATTTGACATAAAAGCTGCAATCCATTT
10055 AAAATGGGTC
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
61 6 0.07
62 30 0.33
65 48 0.53
66 6 0.07
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (66 bp):
GTACAAACATAATTTGACATAAAAGCTGCAATCCATTTCCACATATAGATGCATTCATGCATGTA
T
Found at i:27990 original size:22 final size:24
Alignment explanation
Indices: 27943--27990 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
27933 AAATTTGACT
*
27943 TTTGATATTTATATCTTCTATTAA
1 TTTGATATTTATATCTTCTATAAA
*
27967 TTTGATTTTTATAT-TTC-ATAAA
1 TTTGATATTTATATCTTCTATAAA
27989 TT
1 TT
27991 AAATTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 3 0.14
24 13 0.59
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTGATATTTATATCTTCTATAAA
Found at i:36335 original size:31 final size:31
Alignment explanation
Indices: 36300--36420 Score: 118
Period size: 31 Copynumber: 3.9 Consensus size: 31
36290 GCGCATACCT
* * * *
36300 CATCATAACTTTAGTTACATGATACGTA-CGA
1 CATCATTACTTTAGTAATATGATACATATC-A
* *
36331 CATCATTATTTTAGTGATATGATACATATCA
1 CATCATTACTTTAGTAATATGATACATATCA
* *
36362 TATCATTACTTTAGTAATATGATACATGTCA
1 CATCATTACTTTAGTAATATGATACATATCA
* * *
36393 TATCATTACTTTAGATGATATGAGACAT
1 CATCATTACTTTAG-TAATATGATACAT
36421 GTCATGTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
31 65 0.84
32 12 0.16
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (31 bp):
CATCATTACTTTAGTAATATGATACATATCA
Found at i:36373 original size:62 final size:62
Alignment explanation
Indices: 36301--36425 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 62
36291 CGCATACCTC
* * *
36301 ATCATAACTTTAGTTACATGATAC-GTACGACATCATTATTTTAG-TGATATGATACATATCAT
1 ATCATAACTTTAGTAACATGATACAGT-C-ACATCATTACTTTAGATGATATGAGACATATCAT
* * * *
36363 ATCATTACTTTAGTAATATGATACATGTCATATCATTACTTTAGATGATATGAGACATGTCAT
1 ATCATAACTTTAGTAACATGATACA-GTCACATCATTACTTTAGATGATATGAGACATATCAT
36426 GTCAATAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
62 34 0.64
63 17 0.32
64 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (62 bp):
ATCATAACTTTAGTAACATGATACAGTCACATCATTACTTTAGATGATATGAGACATATCAT
Found at i:38534 original size:21 final size:21
Alignment explanation
Indices: 38510--38570 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
38500 AACTTTGAAA
38510 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
38531 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
38545 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
38566 AAATG
1 AAATG
38571 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:38601 original size:37 final size:37
Alignment explanation
Indices: 38502--38620 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
38492 TGGTAACCAA
38502 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
38539 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
38574 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
38611 -GTTGAAAAAT
1 CTTTGAAAAAT
38621 GATAATGAGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:39053 original size:16 final size:17
Alignment explanation
Indices: 39032--39063 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39022 TTACTATTCA
39032 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
39048 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
39064 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:43164 original size:37 final size:38
Alignment explanation
Indices: 43104--43187 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
43094 TGGTAACCAA
43104 CTTTGAAAAA-ATGGTTTTAAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTAAAAGTTTGGTAAATGTTT
* * *
43141 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTAAAAGTTTGGTAAATGTTT
*
43178 -GTTGAAAAAT
1 CTTTGAAAAAT
43188 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTAAAAGTTTGGTAAATGTTT
Found at i:46865 original size:64 final size:63
Alignment explanation
Indices: 46780--46940 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
46770 TTGTTTAAGG
* * * *
46780 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* **
46844 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACCAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
*
46908 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
46941 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:48547 original size:149 final size:148
Alignment explanation
Indices: 48303--48597 Score: 448
Period size: 149 Copynumber: 2.0 Consensus size: 148
48293 GGTCTACGCG
* * * * * * *
48303 GTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATACTTGGTCC
1 GTCCTTCAGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTGAGACACATACTTGATCC
* *
48368 TTAGTATATGTATATGATTCTTAAGGAATAATATGTGATCCTTAGGGACATTATTATATGGCACT
66 CTAGTATATGTATATGATTATTAAGGAATAATATGTGATCCTTAGGGACATTATTATATGGCACT
48433 ACGGTGCAATTCTACGTT
131 ACGGTGCAATTCTACGTT
* *
48451 GTCCTTCAGGATATATATATATTCTGTGGAACATGTGTGAAGTC-TTGAAAGACACATACTTGAT
1 GTCCTTCAGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTG--AGACACATACTTGAT
* *
48515 CCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATTATTATATGGCA
64 CCCTAGTATATGTATATGATTATTAAGGAATAATATGTGATCCTTAGGGACATTATTATATGGCA
48580 CTACGGTGCAATTCTACG
129 CTACGGTGCAATTCTACG
48598 CGGCACTTCG
Statistics
Matches: 132, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
147 3 0.02
148 37 0.28
149 92 0.70
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (148 bp):
GTCCTTCAGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTGAGACACATACTTGATCC
CTAGTATATGTATATGATTATTAAGGAATAATATGTGATCCTTAGGGACATTATTATATGGCACT
ACGGTGCAATTCTACGTT
Found at i:48609 original size:23 final size:23
Alignment explanation
Indices: 48576--48620 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
48566 ATTATTATAT
*
48576 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
48599 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
48621 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:53015 original size:2 final size:2
Alignment explanation
Indices: 53008--53034 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52998 ATGACAACAA
53008 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 A
53035 AAAGAAGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58489 original size:2 final size:2
Alignment explanation
Indices: 58484--58533 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
58474 CAATCTCTCA
58484 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
58526 AT AT AT AT
1 AT AT AT AT
58534 TTTACTCATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68588 original size:12 final size:12
Alignment explanation
Indices: 68571--68610 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
68561 ATGCTTTTTT
68571 AATATTTATTTA
1 AATATTTATTTA
68583 AATATTTATTT-
1 AATATTTATTTA
*
68594 -TTATTT-TTTA
1 AATATTTATTTA
68604 AATATTT
1 AATATTT
68611 TAGTTTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 3 0.12
10 5 0.21
11 5 0.21
12 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
AATATTTATTTA
Found at i:68612 original size:22 final size:22
Alignment explanation
Indices: 68573--68618 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
68563 GCTTTTTTAA
*
68573 TATTTATTTAAATATTTATTTT
1 TATTTATTTAAATATTTAGTTT
68595 TATTT-TTTAAATATTTTAGTTT
1 TATTTATTTAAATA-TTTAGTTT
68617 TA
1 TA
68619 ACATTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTTATTTAAATATTTAGTTT
Found at i:71043 original size:21 final size:21
Alignment explanation
Indices: 71018--71064 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
71008 AATGTCCAAC
*
71018 AATAACAAAATCAGTAAAAAA
1 AATAACAAAACCAGTAAAAAA
*
71039 AATAACAAAACCAGTAAAAAT
1 AATAACAAAACCAGTAAAAAA
71060 AATAA
1 AATAA
71065 TGTTTCTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.70, C:0.11, G:0.04, T:0.15
Consensus pattern (21 bp):
AATAACAAAACCAGTAAAAAA
Found at i:73471 original size:21 final size:20
Alignment explanation
Indices: 73447--73499 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
73437 CGATTATTAG
*
73447 ATTTATAAAATTATTTTAAA
1 ATTTATAAAATTATTATAAA
*
73467 TATTTGT-AAATATATTATAAA
1 -ATTTATAAAAT-TATTATAAA
*
73488 AATTATAAAATT
1 ATTTATAAAATT
73500 TTGATAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTTATAAAATTATTATAAA
Found at i:73535 original size:22 final size:22
Alignment explanation
Indices: 73510--73572 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
73500 TTGATAATCG
*
73510 AATAATAATATTATACTAATTT
1 AATAATAATATTATAATAATTT
*
73532 AATAACT-ATTTTATAATAATTT
1 AATAA-TAATATTATAATAATTT
*
73554 AATAAT-ATTTTATAATAAT
1 AATAATAATATTATAATAAT
73573 CCAATAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 14 0.37
22 23 0.61
23 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATAATATTATAATAATTT
Found at i:73563 original size:10 final size:10
Alignment explanation
Indices: 73528--73570 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
73518 TATTATACTA
73528 ATTTAATAACT
1 ATTTAATAA-T
*
73539 ATTTTATAAT
1 ATTTAATAAT
73549 AATTTAATAAT
1 -ATTTAATAAT
*
73560 ATTTTATAAT
1 ATTTAATAAT
73570 A
1 A
73571 ATCCAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 11 0.39
11 17 0.61
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
ATTTAATAAT
Found at i:74524 original size:20 final size:20
Alignment explanation
Indices: 74499--74541 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
74489 AAAGATAGTT
74499 GTTATCTCTAGAGGTCTCAA
1 GTTATCTCTAGAGGTCTCAA
74519 GTTATCTCTAGAGGTCTCAA
1 GTTATCTCTAGAGGTCTCAA
74539 GTT
1 GTT
74542 GAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
GTTATCTCTAGAGGTCTCAA
Found at i:80956 original size:24 final size:23
Alignment explanation
Indices: 80946--81070 Score: 108
Period size: 24 Copynumber: 5.2 Consensus size: 23
80936 CATAATTCAC
80946 ATCAAGTATCATATCAAAATCCA
1 ATCAAGTATCATATCAAAATCCA
* *
80969 GGTCAAGTATCATATCAGAATCCA
1 -ATCAAGTATCATATCAAAATCCA
* *
80993 AGTCAAGTATCAGATCAGAATCCA
1 A-TCAAGTATCATATCAAAATCCA
* *
81017 TGTC-AGATATCATATCATAATCCA
1 -ATCAAG-TATCATATCAAAATCCA
* * *
81041 TGTCAAGTATCAGATCAGAAATCAA
1 -ATCAAGTATCATATCA-AAATCCA
81066 ATCAA
1 ATCAA
81071 AAATCAGGTA
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
23 2 0.02
24 76 0.89
25 7 0.08
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (23 bp):
ATCAAGTATCATATCAAAATCCA
Found at i:81016 original size:48 final size:48
Alignment explanation
Indices: 80947--81060 Score: 167
Period size: 48 Copynumber: 2.4 Consensus size: 48
80937 ATAATTCACA
* *
80947 TCAAGTATCATATCAAAATCCAGGTCA-AGTATCATATCAGAATCCAAG
1 TCAAGTATCAGATCAGAATCCAGGTCAGA-TATCATATCAGAATCCAAG
* * *
80995 TCAAGTATCAGATCAGAATCCATGTCAGATATCATATCATAATCCATG
1 TCAAGTATCAGATCAGAATCCAGGTCAGATATCATATCAGAATCCAAG
81043 TCAAGTATCAGATCAGAA
1 TCAAGTATCAGATCAGAA
81061 ATCAAATCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (48 bp):
TCAAGTATCAGATCAGAATCCAGGTCAGATATCATATCAGAATCCAAG
Done.