Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000372.1 Hibiscus syriacus cultivar Beakdansim tig00000679_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: 63166
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:4537 original size:20 final size:21
Alignment explanation
Indices: 4499--4542 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4489 TTTGAACCAG
*
4499 AAAAATAAAAGACTAAAAAAT
1 AAAAATAAAAGAATAAAAAAT
*
4520 AAAAATAAACGAAT-AAAAAT
1 AAAAATAAAAGAATAAAAAAT
4540 AAA
1 AAA
4543 TAAATAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAAATAAAAGAATAAAAAAT
Found at i:4548 original size:14 final size:13
Alignment explanation
Indices: 4499--4550 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 13
4489 TTTGAACCAG
4499 AAAAATAAAAGACTA
1 AAAAATAAAA-A-TA
4514 AAAAATAAAAATA
1 AAAAATAAAAATA
*
4527 AACGAATAAAAATA
1 AA-AAATAAAAATA
4541 AATAAATAAA
1 AA-AAATAAA
4551 GAAATAAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.12
14 19 0.58
15 10 0.30
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:4633 original size:38 final size:37
Alignment explanation
Indices: 4574--4893 Score: 336
Period size: 38 Copynumber: 8.4 Consensus size: 37
4564 TATAAATCAT
*
4574 TTTTTAAAACTATA-TATTATATATATTTTCGAAAAATG
1 TTTTCAAAACTATATTA-TATATATATTTTC-AAAAATG
*
4612 TTTTCAAAACTATATTATATATATATTTTTTCGAAAATG
1 TTTTCAAAACTATATTATATATATA--TTTTCAAAAATG
*
4651 TTTCCAAAACTATA-TATTATATATATGTTTCAAAAATG
1 TTTTCAAAACTATATTA-TATATATAT-TTTCAAAAATG
4689 TTTTCGAAATTA-TATATTATATATAT-TTTTCAAAAATG
1 TTTTC-AAA--ACTATATTATATATATATTTTCAAAAATG
* *
4727 TTTACAAAACTATATATTATATATATTTTTTTCAAAAATG
1 TTTTCAAAAC--TATATTATATATA-TATTTTCAAAAATG
*
4767 TTTTCAAAACTATATATATATAAATATGCATATTCAAAAATG
1 TTTTCAAAACTATAT-TATAT--ATAT--ATTTTCAAAAATG
4809 TTTTCAAAAC--TA-TATA-ATATATTTTCAAAAATG
1 TTTTCAAAACTATATTATATATATATTTTCAAAAATG
*
4842 TTTTCAAAACTAGATATTATATATAT-TTTT-AAAAATA
1 TTTTCAAAACT--ATATTATATATATATTTTCAAAAATG
4879 TTTTCAAAACTATAT
1 TTTTCAAAACTATAT
4894 ATTCTATATA
Statistics
Matches: 246, Mismatches: 11, Indels: 53
0.79 0.04 0.17
Matches are distributed among these distances:
33 22 0.09
35 9 0.04
37 23 0.09
38 82 0.33
39 43 0.17
40 40 0.16
41 6 0.02
42 21 0.09
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTCAAAACTATATTATATATATATTTTCAAAAATG
Found at i:4713 original size:115 final size:113
Alignment explanation
Indices: 4575--4904 Score: 431
Period size: 115 Copynumber: 2.9 Consensus size: 113
4565 ATAAATCATT
*
4575 TTTTAAAACTATATATTATATATATTTTCGAAAAATGTTTTCAAAACTATATTATATATATATTT
1 TTTTCAAA-TATATATTATATATATTTTC-AAAAATGTTTTCAAAACTATA-TATATATATATTT
* *
4640 TTTCGAAAATGTTTCCAAAACTATATATTATATATATG-T-TTCAAAAATG
63 TTTCAAAAATGTTTTCAAAACTATATATTATATATATGATATTCAAAAATG
*
4689 TTTTCGAAATTATATATTATATATATTTTTCAAAAATGTTTACAAAACTATATATTATATATATT
1 TTTTC-AAA-TATATATTATATATA-TTTTCAAAAATGTTTTCAAAACTATATA-TATATATA-T
*
4754 TTTTTCAAAAATGTTTTCAAAACTATATATATATAAATATGCATATTCAAAAATG
61 TTTTTCAAAAATGTTTTCAAAACTATATAT-TATATATATG-ATATTCAAAAATG
*
4809 TTTTCAAA-ACTATA-TA-ATATATTTTCAAAAATGTTTTCAAAACTAGATAT-TATATATATTT
1 TTTTCAAATA-TATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATATATATAT-TTT
* *
4870 TT-AAAAATATTTTCAAAACTATATATTCTATATAT
64 TTCAAAAATGTTTTCAAAACTATATATTATATATAT
4905 TATGTATATA
Statistics
Matches: 195, Mismatches: 11, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
111 7 0.04
112 24 0.12
113 11 0.06
114 7 0.04
115 72 0.37
116 39 0.20
117 12 0.06
118 4 0.02
119 4 0.02
120 15 0.08
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (113 bp):
TTTTCAAATATATATTATATATATTTTCAAAAATGTTTTCAAAACTATATATATATATATTTTTT
CAAAAATGTTTTCAAAACTATATATTATATATATGATATTCAAAAATG
Found at i:8379 original size:2 final size:2
Alignment explanation
Indices: 8372--8404 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8362 TGCAATCTTA
8372 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 A
8405 CTTTGATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9579 original size:15 final size:17
Alignment explanation
Indices: 9549--9580 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
9539 GTTTTGATAC
9549 TTTTAATATATTTAAAA
1 TTTTAATATATTTAAAA
9566 TTTTAAT-T-TTTAAAA
1 TTTTAATATATTTAAAA
9581 CACATATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAATATATTTAAAA
Found at i:13745 original size:21 final size:21
Alignment explanation
Indices: 13694--13745 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
13684 GCTATAATGC
13694 ATGGCCAATTCAAAAATTTAA
1 ATGGCCAATTCAAAAATTTAA
* ** *
13715 AAGGATAATTC-GAAATATTAA
1 ATGGCCAATTCAAAAAT-TTAA
13736 ATGGCCAATT
1 ATGGCCAATT
13746 TGGGAAATTA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (21 bp):
ATGGCCAATTCAAAAATTTAA
Found at i:19069 original size:16 final size:16
Alignment explanation
Indices: 19048--19078 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19038 CGCCGCATGC
19048 TTTTCCATTTTTCTCA
1 TTTTCCATTTTTCTCA
*
19064 TTTTCCCTTTTTCTC
1 TTTTCCATTTTTCTC
19079 TTTGCAACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTCCATTTTTCTCA
Found at i:24060 original size:13 final size:13
Alignment explanation
Indices: 24044--24103 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 13
24034 TCAATGAACG
24044 TCATAAATGTGCA
1 TCATAAATGTGCA
**
24057 TCATAAATGTGTG
1 TCATAAATGTGCA
**
24070 TCATAAATGTGTG
1 TCATAAATGTGCA
*
24083 TCATAAATGCGCA
1 TCATAAATGTGCA
*
24096 TTATAAAT
1 TCATAAAT
24104 TTATGACGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (13 bp):
TCATAAATGTGCA
Found at i:24061 original size:85 final size:84
Alignment explanation
Indices: 23902--24086 Score: 185
Period size: 85 Copynumber: 2.2 Consensus size: 84
23892 CAATCACGAC
* * ** * * *
23902 ACACGAATGTGTATCATCTTTTTTTATGACATGTGCTTCAATGACACGCAATGTAAGTCATACAT
1 ACACAAATGTGTGTCATCTTAATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCATAAAT
** * *
23967 GCGTGTCATATATTTATGAT
66 GCGCATCATAAATGTATG-T
* * *
23987 ACACAAATGTGTGTCATCTTAATTTATGATAGGGGCTTCAATGACGCTCAATG-AACGTCATAAA
1 ACACAAATGTGTGTCATCTTAATTTATGACAGGGGCTTCAATGACACGCAATGTAA-GTCATAAA
* *
24051 TGTGCATCATAAATGTGTGT
65 TGCGCATCATAAATGTATGT
*
24071 -CATAAATGTGTGTCAT
1 ACACAAATGTGTGTCAT
24087 AAATGCGCAT
Statistics
Matches: 82, Mismatches: 17, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
83 15 0.18
84 3 0.04
85 64 0.78
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (84 bp):
ACACAAATGTGTGTCATCTTAATTTATGACAGGGGCTTCAATGACACGCAATGTAAGTCATAAAT
GCGCATCATAAATGTATGT
Found at i:24065 original size:26 final size:26
Alignment explanation
Indices: 24036--24091 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
24026 AATGACGCTC
24036 AATGAACGTCATAAATGTGCATCATA
1 AATGAACGTCATAAATGTGCATCATA
*** **
24062 AATGTGTGTCATAAATGTGTGTCATA
1 AATGAACGTCATAAATGTGCATCATA
24088 AATG
1 AATG
24092 CGCATTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (26 bp):
AATGAACGTCATAAATGTGCATCATA
Found at i:28042 original size:75 final size:76
Alignment explanation
Indices: 27940--28129 Score: 249
Period size: 75 Copynumber: 2.5 Consensus size: 76
27930 CCGTTGTACA
* * * *
27940 AGGGGGGAATCAGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
** *
28004 CAAAACTGTTT
66 CAAAACCATTC
* * * *
28015 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGATTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
*
28079 CCAAACCATTC
66 CAAAACCATTC
28090 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCC
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCC
28130 TTATGAGCAA
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
75 84 0.86
76 6 0.06
77 8 0.08
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
CAAAACCATTC
Found at i:28134 original size:21 final size:22
Alignment explanation
Indices: 28091--28134 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
28081 AAACCATTCA
28091 GGGGGGAATCGGTTCCTCCTATG
1 GGGGGGAATCGGTTCCT-CTATG
28114 GGGGGGAATCGGTTCCT-TATG
1 GGGGGGAATCGGTTCCTCTATG
28135 AGCAATCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
23 17 0.81
ACGTcount: A:0.14, C:0.18, G:0.41, T:0.27
Consensus pattern (22 bp):
GGGGGGAATCGGTTCCTCTATG
Found at i:30768 original size:22 final size:21
Alignment explanation
Indices: 30694--30780 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 21
30684 AACAGAACCC
*
30694 CAGGGGGGGTATCGATTCCCCT
1 CAGGGGGGGAATCGATT-CCCT
** *
30716 GTGGGGGGGAATCGGTTCCCCTT
1 CAGGGGGGGAATCGATT-CCC-T
** *
30739 CAAAGGGGGAATCGGTTCCCT
1 CAGGGGGGGAATCGATTCCCT
30760 CAGGGGGGG-ATCGATTCCCT
1 CAGGGGGGGAATCGATTCCCT
30780 C
1 C
30781 TGCACCAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 11 0.21
21 8 0.15
22 20 0.38
23 14 0.26
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (21 bp):
CAGGGGGGGAATCGATTCCCT
Found at i:34628 original size:22 final size:21
Alignment explanation
Indices: 34586--34625 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
34576 GAGTTTGTTT
*
34586 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
34607 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
34626 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:36583 original size:19 final size:20
Alignment explanation
Indices: 36546--36584 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
36536 CGTTTTACAA
36546 GGGGGGAATCGGTAATCCCTT
1 GGGGGGAATCGGT-ATCCCTT
*
36567 GGGGGGGATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
36585 CCGAGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.13, C:0.21, G:0.44, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCGGTATCCCTT
Found at i:36647 original size:75 final size:76
Alignment explanation
Indices: 36545--36734 Score: 244
Period size: 75 Copynumber: 2.5 Consensus size: 76
36535 CCGTTTTACA
*
36545 AGGGGGGAATCGGTAAT-C-CCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGG
1 AGGGGGGAATCGGT--TCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGG
** *
36607 AACAAAACTGTTT
64 AACAAAACCATTC
* * * *
36620 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGATTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
*
36684 CCAAACCATTC
66 CAAAACCATTC
36695 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCC
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGG-ATCGGTTCC
36735 TTATGAGCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
73 1 0.01
74 1 0.01
75 83 0.84
76 6 0.06
77 8 0.08
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAA
CAAAACCATTC
Found at i:36739 original size:21 final size:22
Alignment explanation
Indices: 36696--36739 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
36686 AAACCATTCA
36696 GGGGGGAATCGGTTCCTCCTATG
1 GGGGGGAATCGGTTCCT-CTATG
36719 GGGGGGAATCGGTTCCT-TATG
1 GGGGGGAATCGGTTCCTCTATG
36740 AGCAATCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
23 17 0.81
ACGTcount: A:0.14, C:0.18, G:0.41, T:0.27
Consensus pattern (22 bp):
GGGGGGAATCGGTTCCTCTATG
Found at i:37503 original size:13 final size:13
Alignment explanation
Indices: 37456--37503 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
37446 TGCGTCATAA
37456 ATTTATGA-GACGC
1 ATTTATGACG-CGC
*
37469 ATTTATGACACGC
1 ATTTATGACGCGC
37482 ATTTATGACGCGC
1 ATTTATGACGCGC
37495 ATTTATGAC
1 ATTTATGAC
37504 TTACATTGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:37587 original size:85 final size:85
Alignment explanation
Indices: 37482--37646 Score: 267
Period size: 85 Copynumber: 1.9 Consensus size: 85
37472 TATGACACGC
* ** *
37482 ATTTATGACGCGCATTTATGACTTACATTGCGCGTCATTGAATTCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
*
37547 CACACATTTGTGTGTAATAA
66 CACACATTCGTGTGTAATAA
* *
37567 ATTTATGACACGCATTTATGACTTACATTGTGTGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
37632 CACACATTCGTGTGT
66 CACACATTCGTGTGT
37647 CGTGATTGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTCGTGTGTAATAA
Found at i:43291 original size:22 final size:22
Alignment explanation
Indices: 43240--43291 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
43230 GAAGCAAATA
* * *
43240 AAAACAAATTTGAATAGTTTTC
1 AAAATAAATTTGAACAATTTTC
43262 AAAATAAATTTGAACAATTTTC
1 AAAATAAATTTGAACAATTTTC
*
43284 AAATTAAA
1 AAAATAAA
43292 AAAGTCGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (22 bp):
AAAATAAATTTGAACAATTTTC
Found at i:48037 original size:49 final size:49
Alignment explanation
Indices: 47941--48235 Score: 421
Period size: 49 Copynumber: 6.0 Consensus size: 49
47931 AATACCATGT
* * * *
47941 GTGGCACCTTTTATGTCGAAAATACATCGTTATACATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCG-AAATGCACCGTTATGCATTTAACTTTCATTA
47991 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* ** *
48040 GTGGCACCTTTTACGTTGAAATGCACCGCTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* *
48089 GTGGCACCTTTTATGCAGAAATGCACCGTTATGCATTTTACTTTTC-TTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAC-TTTCATTA
** *
48138 GTTTCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATCA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * *
48187 GTGGCACCTTTTAAGCTGAAATGCACTGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
48236 TAGAGCAGTT
Statistics
Matches: 219, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
48 4 0.02
49 194 0.89
50 21 0.10
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (49 bp):
GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
Found at i:50144 original size:23 final size:21
Alignment explanation
Indices: 50118--50172 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 21
50108 AGTACAGAGG
*
50118 GTATCGATACTCCTATATAGGGA
1 GTATCGGTACTCCTATAT--GGA
50141 GTATCGGTACTCCTATATGGA
1 GTATCGGTACTCCTATATGGA
50162 GTATCGGTACT
1 GTATCGGTACT
50173 ACCTTTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 14 0.45
23 17 0.55
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (21 bp):
GTATCGGTACTCCTATATGGA
Found at i:50157 original size:21 final size:22
Alignment explanation
Indices: 50118--50172 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
50108 AGTACAGAGG
*
50118 GTATCGATACTCCTATATAGGGA
1 GTATCGGTACTCC-ATATAGGGA
*
50141 GTATCGGTACTCC-TATATGGA
1 GTATCGGTACTCCATATAGGGA
50162 GTATCGGTACT
1 GTATCGGTACT
50173 ACCTTTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 18 0.60
23 12 0.40
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (22 bp):
GTATCGGTACTCCATATAGGGA
Found at i:51761 original size:19 final size:20
Alignment explanation
Indices: 51725--51772 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
51715 TCTAAATCAT
* *
51725 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
51745 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
51764 CTTTCAAAA
1 TTTTCAAAA
51773 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:52304 original size:13 final size:13
Alignment explanation
Indices: 52286--52333 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
52276 TGCGTTATAA
52286 ATTTATGACACGC
1 ATTTATGACACGC
52299 ATTTATGACACGC
1 ATTTATGACACGC
*
52312 ATTTATGACGCGC
1 ATTTATGACACGC
52325 ATTTATGAC
1 ATTTATGAC
52334 TTACATTGCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:52432 original size:83 final size:83
Alignment explanation
Indices: 52312--52472 Score: 277
Period size: 83 Copynumber: 1.9 Consensus size: 83
52302 TATGACACGC
* *
52312 ATTTATGACGCGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
* *
52377 CACATATTTGTGTCATAA
66 CACACATTCGTGTCATAA
*
52395 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
52460 CACACATTCGTGT
66 CACACATTCGTGT
52473 GTCGTGATTG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (83 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTCGTGTCATAA
Found at i:52581 original size:2 final size:2
Alignment explanation
Indices: 52574--52598 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52564 CGTATACTAA
52574 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 A
52599 ATACATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58111 original size:22 final size:22
Alignment explanation
Indices: 58060--58111 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
58050 GAAGCAAATA
* * *
58060 AAAACAAATTTGAATAGTTTTC
1 AAAATAAATTTGAACAATTTTC
58082 AAAATAAATTTGAACAATTTTC
1 AAAATAAATTTGAACAATTTTC
*
58104 AAATTAAA
1 AAAATAAA
58112 AAAGTCGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (22 bp):
AAAATAAATTTGAACAATTTTC
Found at i:61871 original size:14 final size:14
Alignment explanation
Indices: 61852--61880 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61842 TCGGATACTC
61852 ACTATTCTCCTCAT
1 ACTATTCTCCTCAT
61866 ACTATTCTCCTCAT
1 ACTATTCTCCTCAT
61880 A
1 A
61881 ACTTTCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTATTCTCCTCAT
Found at i:62854 original size:48 final size:49
Alignment explanation
Indices: 62744--62937 Score: 286
Period size: 48 Copynumber: 4.0 Consensus size: 49
62734 AATACCATGT
* *
62744 GTGGCACCTTTTACGTCGAAATGCACCGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
62793 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTT-ACTTTTC-TTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAC-TTTCATTA
* *
62841 GTTGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATCA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * * *
62890 GTGGCACCTTTTAAGCTG-AATACACTGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
62938 TAGAGTAGTC
Statistics
Matches: 132, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
48 73 0.55
49 59 0.45
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (49 bp):
GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
Found at i:62932 original size:97 final size:97
Alignment explanation
Indices: 62747--62932 Score: 293
Period size: 97 Copynumber: 1.9 Consensus size: 97
62737 ACCATGTGTG
* * *
62747 GCACCTTTTACGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTATGCCGA
1 GCACCTTTTACGCCGAAATGCACCGTTATGCATTTAACTTTCATCAGTGGCACCTTTTAAGCCGA
*
62812 AATGCACCGTTATGCATTTACTTTTCTTAGTT
66 AATACACCGTTATGCATTTACTTTTCTTAGTT
* *
62844 GCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATCAGTGGCACCTTTTAAGCTG-
1 GCACCTTTTACGCCGAAATGCACCGTTATGCATTTAACTTTCATCAGTGGCACCTTTTAAGCCGA
*
62908 AATACACTGTTATGCATTTAACTTT
66 AATACACCGTTATGCATTT-ACTTT
62933 CATTATAGAG
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 17 0.21
97 64 0.79
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (97 bp):
GCACCTTTTACGCCGAAATGCACCGTTATGCATTTAACTTTCATCAGTGGCACCTTTTAAGCCGA
AATACACCGTTATGCATTTACTTTTCTTAGTT
Done.