Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003612.1 Hibiscus syriacus cultivar Beakdansim tig00007641_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: 88323
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:523 original size:29 final size:28
Alignment explanation
Indices: 490--585 Score: 92
Period size: 27 Copynumber: 3.5 Consensus size: 28
480 TCATAATAAC
490 AAATATTTTTTAAAATTTAGATAAGAATA
1 AAATATTTTTT-AAATTTAGATAAGAATA
*
519 AAATATATTTTTAAA-TTAAATCAAG-ATA
1 AAATAT-TTTTTAAATTTAGAT-AAGAATA
* * *
547 AAATA-TTTTTAAATTAAGTTAATAATA
1 AAATATTTTTTAAATTTAGATAAGAATA
*
574 AAAT-TTATTTAA
1 AAATATTTTTTAA
586 TTAATATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 10 0.18
27 16 0.29
28 13 0.23
29 12 0.21
30 5 0.09
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (28 bp):
AAATATTTTTTAAATTTAGATAAGAATA
Found at i:594 original size:23 final size:24
Alignment explanation
Indices: 568--637 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 24
558 AATTAAGTTA
**
568 ATAATAAAATTTATTTAA-TTAAT
1 ATAATAAAATTTATAAAAGTTAAT
591 ATAA-AAATATTT-TAAAAGTTAAT
1 ATAATAAA-ATTTATAAAAGTTAAT
*
614 ATATATAAAATATTAT-GAAGTTAA
1 ATA-ATAAAAT-TTATAAAAGTTAA
638 GTTAATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 3 0.08
25 12 0.32
26 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
ATAATAAAATTTATAAAAGTTAAT
Found at i:599 original size:26 final size:27
Alignment explanation
Indices: 490--599 Score: 75
Period size: 26 Copynumber: 4.0 Consensus size: 27
480 TCATAATAAC
* * *
490 AAATATTTTTTAAAATTTAGATAAGAATAA
1 AAATA-TTTTT-AAATTAAGTTAAAAAT-A
* * *
520 AATATATTTTTAAATTAA-ATCAAGATA
1 AA-ATATTTTTAAATTAAGTTAAAAATA
*
547 AAATATTTTTAAATTAAGTTAATAATA
1 AAATATTTTTAAATTAAGTTAAAAATA
574 AAAT-TTATTT-AATTAA-TATAAAAATA
1 AAATATT-TTTAAATTAAGT-TAAAAATA
600 TTTTAAAAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
25 1 0.01
26 30 0.45
27 15 0.22
28 5 0.07
29 6 0.09
30 7 0.10
31 3 0.04
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATATTTTTAAATTAAGTTAAAAATA
Found at i:634 original size:25 final size:25
Alignment explanation
Indices: 589--637 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
579 TATTTAATTA
*
589 ATATAAAAATATTTTAAAAGTTAAT
1 ATATAAAAATATTATAAAAGTTAAT
*
614 ATATATAAAATATTAT-GAAGTTAA
1 ATATA-AAAATATTATAAAAGTTAA
638 GTTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
ATATAAAAATATTATAAAAGTTAAT
Found at i:645 original size:26 final size:24
Alignment explanation
Indices: 544--645 Score: 61
Period size: 27 Copynumber: 4.1 Consensus size: 24
534 TTAAATCAAG
* *
544 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATA-TTATAAGTTAA-TTAAT
570 AATAAAAT-TTAT---TTAATTAAT
1 -ATAAAATATTATAAGTTAATTAAT
*
591 ATAAAAATATTTTAAAAGTTAA-TATAT
1 AT-AAAATA--TTATAAGTTAATTA-AT
618 ATAAAATATTATGAAGTTAAGTTAAT
1 ATAAAATATTAT-AAGTTAA-TTAAT
644 AT
1 AT
646 TTATATAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 23
0.70 0.03 0.26
Matches are distributed among these distances:
20 2 0.03
21 10 0.16
22 4 0.07
24 6 0.10
25 10 0.16
26 12 0.20
27 17 0.28
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
ATAAAATATTATAAGTTAATTAAT
Found at i:11552 original size:22 final size:23
Alignment explanation
Indices: 11527--11570 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
11517 TAATCAAGTC
11527 TAAAATTAATAAT-AATAATATT
1 TAAAATTAATAATAAATAATATT
* *
11549 TAAATTTAATCATAAATAATAT
1 TAAAATTAATAATAAATAATAT
11571 ATACATAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAATTAATAATAAATAATATT
Found at i:18161 original size:16 final size:16
Alignment explanation
Indices: 18140--18179 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
18130 TTACTAATAA
18140 AGTATCATTTGTTATC
1 AGTATCATTTGTTATC
18156 AGTATCATTTGTTATC
1 AGTATCATTTGTTATC
*
18172 AGTGTCAT
1 AGTATCAT
18180 GCCCTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (16 bp):
AGTATCATTTGTTATC
Found at i:27723 original size:3 final size:3
Alignment explanation
Indices: 27715--27750 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
27705 TTAAAACATA
*
27715 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27751 GAAGAAAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:32222 original size:12 final size:12
Alignment explanation
Indices: 32205--32229 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32195 GAGATGATAA
32205 AAAAAGAAGAAG
1 AAAAAGAAGAAG
32217 AAAAAGAAGAAG
1 AAAAAGAAGAAG
32229 A
1 A
32230 GAAGGAAAAT
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:36473 original size:6 final size:6
Alignment explanation
Indices: 36440--36470 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
36430 ACGGCTCCGC
*
36440 TCGTGG TCGTGG TCGTGG TCGTGG TAGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
36471 AGTAATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.13, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:38880 original size:14 final size:14
Alignment explanation
Indices: 38858--38936 Score: 85
Period size: 14 Copynumber: 5.9 Consensus size: 14
38848 TCGGTAATAT
* *
38858 GTTCGTTTATCTTC
1 GTTCATTTATGTTC
38872 GTTCATTTATGTTC
1 GTTCATTTATGTTC
* *
38886 GTTCGTTTATGTTT
1 GTTCATTTATGTTC
38900 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
38914 G----TTTATGTGC
1 GTTCATTTATGTTC
38924 GTTCATTTATGTT
1 GTTCATTTATGTT
38937 TAGTTTAATC
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
10 9 0.17
14 44 0.83
ACGTcount: A:0.11, C:0.13, G:0.18, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:38884 original size:24 final size:24
Alignment explanation
Indices: 38855--38936 Score: 101
Period size: 24 Copynumber: 3.2 Consensus size: 24
38845 CGTTCGGTAA
*
38855 TATGTTCGTTTATCTTCGTTCATT
1 TATGTTCGTTTATGTTCGTTCATT
*
38879 TATGTTCGTTCGTTTATGTTTGTTCATT
1 TA---T-GTTCGTTTATGTTCGTTCATT
*
38907 TATGTTCGTTTATGTGCGTTCATT
1 TATGTTCGTTTATGTTCGTTCATT
38931 TATGTT
1 TATGTT
38937 TAGTTTAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 27 0.54
25 1 0.02
27 1 0.02
28 21 0.42
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTTATGTTCGTTCATT
Found at i:38891 original size:28 final size:28
Alignment explanation
Indices: 38858--38916 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
38848 TCGGTAATAT
38858 GTTCGTTTATCTTCGTTCATTTATGTTC
1 GTTCGTTTATCTTCGTTCATTTATGTTC
* *
38886 GTTCGTTTATGTTTGTTCATTTATGTTC
1 GTTCGTTTATCTTCGTTCATTTATGTTC
38914 GTT
1 GTT
38917 TATGTGCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.10, C:0.14, G:0.17, T:0.59
Consensus pattern (28 bp):
GTTCGTTTATCTTCGTTCATTTATGTTC
Found at i:55972 original size:33 final size:33
Alignment explanation
Indices: 55925--56027 Score: 156
Period size: 33 Copynumber: 3.2 Consensus size: 33
55915 ATAAAGTTTA
* *
55925 CGAT-AATTAAAATACTTAAATACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
* *
55957 TGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
55990 CGATAAATTCAAATACTTAAAAAC-TTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
56022 CGATAA
1 CGATAA
56028 TTGAAACAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 16 0.25
33 48 0.75
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTTCAAGTT
Found at i:56046 original size:21 final size:21
Alignment explanation
Indices: 56022--56063 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
56012 ACTTCAAGTT
*
56022 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAAAAAAGTTTA
56043 CGATAATTGAAAAAAAGTTTA
1 CGATAATTGAAAAAAAGTTTA
56064 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAAAAAAGTTTA
Found at i:61726 original size:29 final size:29
Alignment explanation
Indices: 61668--61734 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
61658 TGGTAACTAC
* * * *
61668 ACTTTTAAAATTTGTATTAAAGTTACTAA
1 ACTTTTAATATTTGTAATAAAGTCAATAA
*
61697 ACTTTTAATATTTGTAATATAGTCAATAA
1 ACTTTTAATATTTGTAATAAAGTCAATAA
*
61726 AATTTTAAT
1 ACTTTTAAT
61735 TCGTTTTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (29 bp):
ACTTTTAATATTTGTAATAAAGTCAATAA
Found at i:64110 original size:38 final size:38
Alignment explanation
Indices: 64059--64145 Score: 165
Period size: 38 Copynumber: 2.3 Consensus size: 38
64049 AATAATTGTT
*
64059 AATTAGTAATTTAACATATTTCTTATTATATACTAGCA
1 AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
64097 AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
1 AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
64135 AATTAGTAATT
1 AATTAGTAATT
64146 ATTAATCAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (38 bp):
AATTAGTAATTTAACATATTTCTTATCATATACTAGCA
Found at i:74382 original size:19 final size:19
Alignment explanation
Indices: 74348--74384 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
74338 ATGACCAACA
* *
74348 AAATCGCAATGTGATCTCT
1 AAATCGCAACGCGATCTCT
74367 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
74385 CATTATCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:74522 original size:20 final size:20
Alignment explanation
Indices: 74470--74522 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
74460 GATTTTAGAT
* *
74470 AATCGCAATACGAATATGTA
1 AATCGCAATGCGAATATATA
74490 AATCGCAATGCGAATATATA
1 AATCGCAATGCGAATATATA
*
74510 AATCGCAACGCGA
1 AATCGCAATGCGA
74523 TAACACGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGAATATATA
Found at i:74557 original size:20 final size:20
Alignment explanation
Indices: 74532--74584 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
74522 ATAACACGTG
74532 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
74552 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
74572 ATCGCAACGCGAT
1 ATCGCAACGCGAT
74585 AATACGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:75469 original size:24 final size:24
Alignment explanation
Indices: 75437--75490 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
75427 ATATTCGAAA
75437 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
75461 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
75485 TTTGAT
1 TTTGAT
75491 GATGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:77954 original size:6 final size:6
Alignment explanation
Indices: 77927--77975 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
77917 ACTTTCTTAG
*
77927 CATTAT CA-TAT -A-TAT TATTAT CATTAT C-TCTAT CATTAT CATTAT
1 CATTAT CATTAT CATTAT CATTAT CATTAT CAT-TAT CATTAT CATTAT
77972 CATT
1 CATT
77976 GAATTATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
4 4 0.11
5 5 0.13
6 28 0.74
7 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (6 bp):
CATTAT
Found at i:78251 original size:21 final size:21
Alignment explanation
Indices: 78225--78291 Score: 134
Period size: 21 Copynumber: 3.2 Consensus size: 21
78215 ATAATGTCCA
78225 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
78246 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
78267 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
78288 TAAG
1 TAAG
78292 AATCATATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:80031 original size:64 final size:63
Alignment explanation
Indices: 79880--80036 Score: 156
Period size: 64 Copynumber: 2.4 Consensus size: 63
79870 TAATGAATGT
** * * ** *
79880 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACCAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* * * *
79944 ATGCATCGATGCATGCCTTATGCATCGATGCATTAATTGCATTCGATGTTTCTATT-TTAAA-AG
1 ATGCATCGATGCATACC-AATGCATCGATGCATAAAATGCATTCGATG-TTCTATTATTAAAGAG
80007 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACCAATGCATCGAT
80037 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
63 4 0.05
64 64 0.83
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCATACCAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:81351 original size:20 final size:20
Alignment explanation
Indices: 81326--81547 Score: 207
Period size: 20 Copynumber: 11.7 Consensus size: 20
81316 CACATTCATT
81326 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
81346 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
81366 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
81386 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
81403 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
81420 TGACTATCGCAATGCGAATT
1 TGACTATCGCAACGCGAATA
*
81440 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
81457 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
81474 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
*
81494 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
81514 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
*
81534 TAACTATCGCAACG
1 TGACTATCGCAACG
81548 AGAAAATCGC
Statistics
Matches: 169, Mismatches: 21, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
14 16 0.09
15 2 0.01
16 2 0.01
17 6 0.04
18 2 0.01
19 2 0.01
20 139 0.82
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:81439 original size:54 final size:54
Alignment explanation
Indices: 81351--81507 Score: 251
Period size: 54 Copynumber: 2.9 Consensus size: 54
81341 GAATATGACT
* * * *
81351 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
*
81405 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
**
81459 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACG
81508 CGAATTTGAT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
Found at i:81452 original size:74 final size:74
Alignment explanation
Indices: 81331--81559 Score: 270
Period size: 74 Copynumber: 3.1 Consensus size: 74
81321 TCATTTGACT
* * *
81331 ATCGCAACGCGAATATGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGAATTTGAATATCGC
*
81396 AACGGGATA
66 AACGAGATA
* * * * *
81405 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGGGATAATCGCA-AT-G
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGA-ATTTGAATATCG
*
81468 CGAA-AATGACT-
65 C-AACGA-GA-TA
*
81479 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGATTATCGCAACGGGAATTT-AACTATCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGAATTTGAA-TATCG
*
81543 CAACGAGAAA
65 CAACGAGATA
81553 ATCGCAA
1 ATCGCAA
81560 AGTGTGTTAG
Statistics
Matches: 128, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
72 1 0.01
73 4 0.03
74 115 0.90
75 8 0.06
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (74 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGAATTTGAATATCGC
AACGAGATA
Found at i:81463 original size:34 final size:36
Alignment explanation
Indices: 81419--81530 Score: 120
Period size: 34 Copynumber: 3.0 Consensus size: 36
81409 CAATGCGAAA
81419 ATGACTATCGCAATGCGAATTTGACTATCGCAACGGG
1 ATGAC-ATCGCAATGCGAATTTGACTATCGCAACGGG
** *
81456 AT-A-ATCGCAATGCGAAAATGACTATCGCAACGCGAAA
1 ATGACATCGCAATGCGAATTTGACTATCGCAACG-G--G
* *
81493 ATGACTATCGCAACGCGAATTTGATTATCGCAACGGG
1 ATGAC-ATCGCAATGCGAATTTGACTATCGCAACGGG
81530 A
1 A
81531 ATTTAACTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
34 27 0.44
35 1 0.02
36 1 0.02
37 5 0.08
38 1 0.02
39 1 0.02
40 25 0.41
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (36 bp):
ATGACATCGCAATGCGAATTTGACTATCGCAACGGG
Found at i:83196 original size:21 final size:21
Alignment explanation
Indices: 83120--83196 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
83110 TTGGGAGAGA
* * * *
83120 CCTCTTCAACAATGACAAGGG
1 CCTCTTGAACGATGATAGGGG
* *
83141 CCTCTTGAATGGTG-TGAGGGG
1 CCTCTTGAACGATGAT-AGGGG
* **
83162 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGATAGGGG
83183 CCTCTTGAACGATG
1 CCTCTTGAACGATG
83197 GCAGGTGAGT
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 40 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (21 bp):
CCTCTTGAACGATGATAGGGG
Found at i:83717 original size:21 final size:21
Alignment explanation
Indices: 83679--83723 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
83669 ATAGTTTCTG
**
83679 AAACTTAAAATCGTAACAAGA
1 AAACTTAAAATCACAACAAGA
*
83700 AAACTTAAAATCACAACACGA
1 AAACTTAAAATCACAACAAGA
83721 AAA
1 AAA
83724 TGATTATCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.18, G:0.07, T:0.16
Consensus pattern (21 bp):
AAACTTAAAATCACAACAAGA
Found at i:83744 original size:34 final size:34
Alignment explanation
Indices: 83706--83789 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 34
83696 AAGAAAACTT
* *
83706 AAAATCACAACACGAAAATGATTATCGCAACGAG
1 AAAATCACAACGCGAAAATGACTATCGCAACGAG
*
83740 AAAATCACAACGCG-AAATGACTATTGCAACGAG
1 AAAATCACAACGCGAAAATGACTATCGCAACGAG
83773 AAAATCACAACGCGAAA
1 AAAATCACAACGCGAAA
83790 CTAAATTCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 31 0.67
34 15 0.33
ACGTcount: A:0.50, C:0.21, G:0.15, T:0.13
Consensus pattern (34 bp):
AAAATCACAACGCGAAAATGACTATCGCAACGAG
Found at i:83890 original size:20 final size:20
Alignment explanation
Indices: 83795--83954 Score: 119
Period size: 20 Copynumber: 8.6 Consensus size: 20
83785 CGAAACTAAA
*
83795 TTCGCGTTGCAATAGTCATT
1 TTCGCGTTGCGATAGTCATT
*
83815 TTCGCATTGCGAT--T-A--
1 TTCGCGTTGCGATAGTCATT
* *
83830 -TCCCGTTGAGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
*
83849 TACGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
*
83869 TTCGCGTTGCGATAGTCGTT
1 TTCGCGTTGCGATAGTCATT
* *
83889 TTTGCATTGCGAT--T-A--
1 TTCGCGTTGCGATAGTCATT
* **
83904 -TCCCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCATT
*
83923 TTCGCGTTGCGATAATCATT
1 TTCGCGTTGCGATAGTCATT
*
83943 TTCGTGTTGCGA
1 TTCGCGTTGCGA
83955 CTATTCTTCT
Statistics
Matches: 107, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
14 18 0.17
16 2 0.02
17 3 0.03
18 2 0.02
20 82 0.77
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCATT
Found at i:83917 original size:74 final size:74
Alignment explanation
Indices: 83795--83954 Score: 241
Period size: 74 Copynumber: 2.2 Consensus size: 74
83785 CGAAACTAAA
* *
83795 TTCGCGTTGCAATAGTCATTTTCGCATTGCGATTATCCCGTTGAGATAGTC-ATTTACGCGTTGC
1 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGAGATAGTCAAATT-CGCGTTGC
*
83859 GATAGTCATT
65 GATAATCATT
* * *
83869 TTCGCGTTGCGATAGTCGTTTTTGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCG
1 TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGAGATAGTCAAATTCGCGTTGCG
83934 ATAATCATT
66 ATAATCATT
*
83943 TTCGTGTTGCGA
1 TTCGCGTTGCGA
83955 CTATTCTTCT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 75 0.96
75 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (74 bp):
TTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGAGATAGTCAAATTCGCGTTGCG
ATAATCATT
Found at i:84132 original size:32 final size:31
Alignment explanation
Indices: 84073--84134 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
84063 CTACTACCGA
84073 ATGAATTTACTAAGCAATCCAAAAGACAAAT
1 ATGAATTTACTAAGCAATCCAAAAGACAAAT
*
84104 ATGAATTTACTAACTTCAA-CCAAAAGACAAA
1 ATGAATTTACTAA--GCAATCCAAAAGACAAA
84135 ACAAAGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.23
Consensus pattern (31 bp):
ATGAATTTACTAAGCAATCCAAAAGACAAAT
Found at i:86362 original size:22 final size:22
Alignment explanation
Indices: 86334--86413 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
86324 GATGGAGATA
*
86334 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAAATGGG
* * *
86356 AACGGATTTCACCAGAAATGGG
1 GACGGATTTCGCCGGAAATGGG
*
86378 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGCCGGAAATGGG
*
86400 GACGGATGTCGCCG
1 GACGGATTTCGCCG
86414 TAGAGAGTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAAATGGG
Found at i:86601 original size:20 final size:20
Alignment explanation
Indices: 86576--86640 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
86566 TTATCGCAAC
*
86576 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
86596 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
86616 GCGATAATCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
86636 GCGAT
1 GCGAT
86641 CAAGTGTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:86792 original size:19 final size:19
Alignment explanation
Indices: 86768--86804 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
86758 TGCGATAATG
* *
86768 GAGATCGCGTTGTGATTTA
1 GAGATCGCATTGCGATTTA
86787 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
86805 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Done.