Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007164.1 Hibiscus syriacus cultivar Beakdansim tig00018775_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: 72492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2633 original size:20 final size:20
Alignment explanation
Indices: 2608--2650 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2598 GAGTACATGC
2608 AACTAGAAATGAGATAAATA
1 AACTAGAAATGAGATAAATA
2628 AACTAGAAATGAGATAAATA
1 AACTAGAAATGAGATAAATA
2648 AAC
1 AAC
2651 GCTACTTATC
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:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (20 bp):
AACTAGAAATGAGATAAATA
Found at i:5106 original size:60 final size:60
Alignment explanation
Indices: 4988--5115 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
4978 ATAGTTGGAT
* *
4988 GACCATTTTATAACTTTCAATAGTTGAGGGACTCAACAAAATAACACTCTATAATCGAAG
1 GACCATTTTATAACTTTCAATAGTTGAGAGACTCAACAAAACAACACTCTATAATCGAAG
* * * ** * * *
5048 GATCATTTTATAATTTTTAATAGTTGAGAGACTCAATGAAACAACA-TTTCATAGTCGAAT
1 GACCATTTTATAACTTTCAATAGTTGAGAGACTCAACAAAACAACACTCT-ATAATCGAAG
5108 GACCATTT
1 GACCATTT
5116 GCATTTTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 2 0.04
60 54 0.96
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (60 bp):
GACCATTTTATAACTTTCAATAGTTGAGAGACTCAACAAAACAACACTCTATAATCGAAG
Found at i:10637 original size:33 final size:33
Alignment explanation
Indices: 10596--10690 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
10586 ACAGCCACGA
** * *
10596 AGAT-GCCCTGGTTTTCTTAGGGATTCTTACAT
1 AGATGGCCCTGGGGTTCTTAGGAATTCTTACAG
* *
10628 AGATGGCCCTGGGGTTCTTAGGAATTTTTACGG
1 AGATGGCCCTGGGGTTCTTAGGAATTCTTACAG
* *
10661 AGATGCCCCTGGGGTTCTTAGGTATTCTTA
1 AGATGGCCCTGGGGTTCTTAGGAATTCTTA
10691 GGTCATTACA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 4 0.08
33 49 0.92
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (33 bp):
AGATGGCCCTGGGGTTCTTAGGAATTCTTACAG
Found at i:13044 original size:32 final size:31
Alignment explanation
Indices: 12965--13049 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
12955 ATTTTTTGAG
* * *
12965 AAATTTAAAAATTGTTTTATAATAATTTAAT
1 AAATTTAATAATTATTTTATAATAATATAAT
12996 AAATTTAATGAA-TATTTTATAATAATATAAT
1 AAATTTAAT-AATTATTTTATAATAATATAAT
13027 AAAATTTAATAATTATTTTATAA
1 -AAATTTAATAATTATTTTATAA
13050 GTATTTGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
31 27 0.56
32 21 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
AAATTTAATAATTATTTTATAATAATATAAT
Found at i:19069 original size:27 final size:28
Alignment explanation
Indices: 19007--19069 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
18997 ACGTGTCACG
* * * *
19007 TTTATAAAATTTAAATTTTTTATTTAAA
1 TTTATAAAACTCAAAATTGTTATTTAAA
*
19035 TTTA-AAAACTCAAAATTGTTATTT-AT
1 TTTATAAAACTCAAAATTGTTATTTAAA
19061 TTTATAAAA
1 TTTATAAAA
19070 AACCCAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 5 0.17
27 20 0.69
28 4 0.14
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTATAAAACTCAAAATTGTTATTTAAA
Found at i:21726 original size:3 final size:3
Alignment explanation
Indices: 21718--21780 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
21708 TCTAATTTTA
* *
21718 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT AACT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
21763 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
21781 TAATACATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.95
4 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:23806 original size:22 final size:22
Alignment explanation
Indices: 23781--23824 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
23771 TCAAACGATG
*
23781 CAATGTGTGTTATTTTAAGTGA
1 CAATGTCTGTTATTTTAAGTGA
* * *
23803 CAATTTCTTTTATTTTATGTGA
1 CAATGTCTGTTATTTTAAGTGA
23825 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTCTGTTATTTTAAGTGA
Found at i:25323 original size:32 final size:32
Alignment explanation
Indices: 25287--25349 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
25277 ATTTTACATG
*
25287 TACTAACTTATTTTTTCTCTTTTGCTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGCTTGTGTA
*
25319 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGCTTGTGT
25350 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.14, C:0.16, G:0.10, T:0.60
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGCTTGTGTA
Found at i:29587 original size:25 final size:27
Alignment explanation
Indices: 29526--29587 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 27
29516 TCTTGAGACA
29526 GTTTCTCTTGAAGTAAATCTTTGAATAT
1 GTTTCTCTTGAAG-AAATCTTTGAATAT
* *
29554 G-TTCATCTTG-A-AAATCTTTGAGTTT
1 GTTTC-TCTTGAAGAAATCTTTGAATAT
29579 GTTTCTCTT
1 GTTTCTCTT
29588 AACAAAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 17 0.57
26 3 0.10
27 4 0.13
28 6 0.20
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (27 bp):
GTTTCTCTTGAAGAAATCTTTGAATAT
Found at i:30542 original size:40 final size:40
Alignment explanation
Indices: 30487--30951 Score: 170
Period size: 40 Copynumber: 10.6 Consensus size: 40
30477 TGGCCAACCG
* * *
30487 TCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
* * **
30527 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGACC
* *
30569 GTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCAT--CC--CC---AGA---CCAGACC
* * * * *
30620 TCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
* *
30660 TCCTCTTCACGTAGGAGCCGTGTCA-CCCCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCC-AG---ACCAGACC
* *
30702 GTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCAT--CC--CC---AGA---CC-AGACC
* * * * *
30754 TCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGA-CC
* *
30795 -CCTCATCACGTAGGAGCCGTTTCA-CCCCTAGATAACCA-ACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCC-AG---ACCAGACC
* *
30836 GTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCAT--CC--CC---AGA---CCAGACC
* * * * *
30887 TCTTCATCACGTATGAGCCGTGTCATCCACC-GACCAAATC
1 TCCTCATCACGTAGGAACCGTGTCATCC-CCAGACCAGACC
30927 TCCTCATCACGTAGGAACCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
30952 CCCTTAGATG
Statistics
Matches: 320, Mismatches: 55, Indels: 100
0.67 0.12 0.21
Matches are distributed among these distances:
39 8 0.03
40 106 0.33
41 5 0.02
42 3 0.01
43 84 0.26
44 2 0.01
45 2 0.01
46 6 0.02
47 7 0.02
48 8 0.03
49 2 0.01
50 59 0.18
51 27 0.08
52 1 0.00
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
Found at i:30577 original size:43 final size:43
Alignment explanation
Indices: 30519--30982 Score: 171
Period size: 43 Copynumber: 10.5 Consensus size: 43
30509 TCATCCCCAG
* *
30519 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * *
30562 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTG---TCA---TCC-ATAGATA
* * * * ***
30612 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * * *
30652 ACCAGATCTCCTCTTCACGTAGGAGCCGTGTCACCCCTAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * *
30695 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTG---TCA---TCC-ATAGATA
* * * * ***
30745 GCCAAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCG---
1 ACC-AGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * * *
30786 ACCAAATCC-CCTCATCACGTAGGAGCCGTTTCACCCCTAGATA
1 ACCAGA-CCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * *
30829 ACCA-ACCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTG---TCA---TCC-ATAGATA
* * * * **
30879 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * * * * *
30919 ACCAAATCTCCTCATCACGTAGGAACCGTGTCACCCTTAGATG
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * *
30962 ACCCGAACTCTTCATCACGTA
1 ACCAGACCTCCTCATCACGTA
30983 TGAGTAGTGT
Statistics
Matches: 310, Mismatches: 72, Indels: 78
0.67 0.16 0.17
Matches are distributed among these distances:
40 89 0.29
41 5 0.02
42 3 0.01
43 94 0.30
44 7 0.02
45 3 0.01
46 9 0.03
47 6 0.02
48 3 0.01
49 6 0.02
50 60 0.19
51 24 0.08
52 1 0.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
Found at i:30820 original size:134 final size:133
Alignment explanation
Indices: 30468--30960 Score: 799
Period size: 133 Copynumber: 3.7 Consensus size: 133
30458 AAACCATAAC
* * * * ** * *
30468 TCCTAAAGATGGCCA-ACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTC
1 TCCTAAAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTC
* *
30532 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
65 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
30597 ACCT
130 ACCT
* *
30601 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCT
1 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTCA
30666 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
30731 CCT
131 CCT
*
30734 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCCCCTC
1 TCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTC
* *
30799 ATCACGTAGGAGCCGTTTCACCCCTAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATC
65 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
30864 ACCT
130 ACCT
*
30868 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAAATCTCCTCA
1 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTCA
* *
30933 TCACGTAGGAACCGTGTCACCCTTAGAT
66 TCACGTAGGAGCCGTGTCACCCCTAGAT
30961 GACCCGAACT
Statistics
Matches: 338, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
133 208 0.62
134 130 0.38
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.23
Consensus pattern (133 bp):
TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTCA
TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
CCT
Found at i:31168 original size:3 final size:3
Alignment explanation
Indices: 31160--31213 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
31150 TCTAATTTTA
* *
31160 ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT AACT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
31205 ATT ATT ATT
1 ATT ATT ATT
31214 TAATACATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.93
4 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:33216 original size:22 final size:22
Alignment explanation
Indices: 33191--33234 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
33181 TCAAACGATG
*
33191 CAATGTGTGTTATTTTAAGTGA
1 CAATGTCTGTTATTTTAAGTGA
* * *
33213 CAATTTCTTTTATTTTATGTGA
1 CAATGTCTGTTATTTTAAGTGA
33235 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTCTGTTATTTTAAGTGA
Found at i:36087 original size:12 final size:12
Alignment explanation
Indices: 36070--36094 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36060 TGGTTTAAAC
36070 TCTATTAAAAAT
1 TCTATTAAAAAT
36082 TCTATTAAAAAT
1 TCTATTAAAAAT
36094 T
1 T
36095 TAAAGTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTATTAAAAAT
Found at i:37211 original size:51 final size:51
Alignment explanation
Indices: 37137--37280 Score: 220
Period size: 51 Copynumber: 2.8 Consensus size: 51
37127 TTCATACTAC
*
37137 AAAAAATGTATCATTTAACACATA-TTACACCGGTGTAAGTGAA-TAAAATA
1 AAAAAATGTATCACTTAACACATACTTACACCGGTGTAAGT-AACTAAAATA
*
37187 AAAATAGTGTATCACTTAACACATACTTACACCGGTGTAAGTAACTAAAATA
1 AAAA-AATGTATCACTTAACACATACTTACACCGGTGTAAGTAACTAAAATA
* *
37239 AAAAAATGTAACACTTAACACATACTTACACTGGTGTAAGTA
1 AAAAAATGTATCACTTAACACATACTTACACCGGTGTAAGTA
37281 TATACATCTC
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
50 4 0.05
51 55 0.64
52 27 0.31
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (51 bp):
AAAAAATGTATCACTTAACACATACTTACACCGGTGTAAGTAACTAAAATA
Found at i:38730 original size:6 final size:6
Alignment explanation
Indices: 38719--38754 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
38709 AAGCAAAAGG
* *
38719 AAATCA AAATCA CAATCA AAATCA AAATCA TAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
38755 CAACCGGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATCA
Found at i:38742 original size:18 final size:18
Alignment explanation
Indices: 38719--38754 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38709 AAGCAAAAGG
38719 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
38737 AAATCAAAATCATAATCA
1 AAATCAAAATCACAATCA
38755 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:40523 original size:21 final size:21
Alignment explanation
Indices: 40499--40555 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
40489 GTAGGAGATA
*
40499 CCTCTTGAACGATGATAGAGG
1 CCTCTTGAACGATGAGAGAGG
* * *
40520 CCTCTTGAACGGTGGGAGTGG
1 CCTCTTGAACGATGAGAGAGG
*
40541 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
40556 CAGGTGAATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGAGG
Found at i:40941 original size:21 final size:21
Alignment explanation
Indices: 40917--40966 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
40907 ACCATTGTCG
* *
40917 TCACGTAAAGTACCGACCTTA
1 TCACGTAAAGTACCAACCTCA
* *
40938 TCACGCAAAGTACTAACCTCA
1 TCACGTAAAGTACCAACCTCA
40959 TCACGTAA
1 TCACGTAA
40967 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGTACCAACCTCA
Found at i:42587 original size:20 final size:20
Alignment explanation
Indices: 42502--42580 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
42492 TCGTGTTGCG
*
42502 ATTTTCGTGTTGTGAATTTC
1 ATTTTCGTGTTGCGAATTTC
42522 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
* *
42542 ATTTTCATATTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
42562 ATTTTCGTGTTGCAAATTT
1 ATTTTCGTGTTGCGAATTT
42581 ATGTTTCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:42932 original size:22 final size:22
Alignment explanation
Indices: 42907--42964 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
42897 GATGTAGATA
42907 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
**
42929 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
42951 GACGGATATCGCCG
1 GACGGATTTCGCCG
42965 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.41, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:44058 original size:15 final size:16
Alignment explanation
Indices: 44038--44070 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44028 CAAAATACAA
44038 TATTCCC-AGTAATCT
1 TATTCCCTAGTAATCT
*
44053 TATTCCCTGGTAATCT
1 TATTCCCTAGTAATCT
44069 TA
1 TA
44071 CATTCCCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (16 bp):
TATTCCCTAGTAATCT
Found at i:44084 original size:20 final size:20
Alignment explanation
Indices: 44059--44096 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44049 ATCTTATTCC
*
44059 CTGGTAATCTTACATTCCCA
1 CTGGTAATCATACATTCCCA
44079 CTGGTAATCATACATTCC
1 CTGGTAATCATACATTCC
44097 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (20 bp):
CTGGTAATCATACATTCCCA
Found at i:48266 original size:2 final size:2
Alignment explanation
Indices: 48259--48329 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
48249 CAGTTGAATC
48259 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
48301 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 A
48330 GTGGCGGATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48998 original size:16 final size:17
Alignment explanation
Indices: 48948--48999 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
48938 AAAATAAAAA
48948 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
48965 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
48980 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
48996 AATT
1 AATT
49000 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:55326 original size:2 final size:2
Alignment explanation
Indices: 55319--55354 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
55309 TTATAAGTTC
55319 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
55355 TAATAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55836 original size:2 final size:2
Alignment explanation
Indices: 55829--55863 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
55819 ATTCATCTTT
*
55829 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55864 TTAGTGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:66667 original size:3 final size:3
Alignment explanation
Indices: 66659--66696 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
66649 CAAATTGTCC
66659 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T
66697 AACAAGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:67766 original size:30 final size:31
Alignment explanation
Indices: 67719--67789 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
67709 ACTGATTTTT
*
67719 TTGTTTGTATCCGTTCATTAAGAAATTTAGC
1 TTGTTTGTGTCCGTTCATTAAGAAATTTAGC
*
67750 TTGTTTGTGT-CGTTCATTAATAAATTTAGC
1 TTGTTTGTGTCCGTTCATTAAGAAATTTAGC
*
67780 TTGTTCGTGT
1 TTGTTTGTGT
67790 TCATTCATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 28 0.76
31 9 0.24
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.49
Consensus pattern (31 bp):
TTGTTTGTGTCCGTTCATTAAGAAATTTAGC
Found at i:71212 original size:5 final size:6
Alignment explanation
Indices: 71180--71217 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
71170 GACACATATT
71180 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
71218 GAGACGAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:71889 original size:21 final size:21
Alignment explanation
Indices: 71865--71918 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
71855 GATTTACATA
71865 TTCGCATTGCGATAATCCAAG
1 TTCGCATTGCGATAATCCAAG
*
71886 TTCGCATTGCGATAATCGAAG
1 TTCGCATTGCGATAATCCAAG
*
71907 TTCGCGTTGCGA
1 TTCGCATTGCGA
71919 ACTTGGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAATCCAAG
Done.