Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001165.1 Hibiscus syriacus cultivar Beakdansim tig00002322_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: 60767
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:2287 original size:18 final size:17
Alignment explanation
Indices: 2260--2293 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2250 TGACAGAAGA
2260 GAAAGAACAAATGATAT
1 GAAAGAACAAATGATAT
2277 GAAATGAACAAATGATA
1 GAAA-GAACAAATGATA
2294 ATGCACATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
GAAAGAACAAATGATAT
Found at i:2393 original size:22 final size:22
Alignment explanation
Indices: 2362--2412 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2352 GTCTACGCGA
2362 TCCTTCGGGACAAATACATAAG
1 TCCTTCGGGACAAATACATAAG
* *
2384 TCCTTGGGGACAAATACATAGG
1 TCCTTCGGGACAAATACATAAG
*
2406 TCATTCG
1 TCCTTCG
2413 AGAGAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (22 bp):
TCCTTCGGGACAAATACATAAG
Found at i:3556 original size:23 final size:22
Alignment explanation
Indices: 3496--3559 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
3486 CAGCTCGTAT
* *
3496 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACAG-AGTGCCACATAG
*
3519 AATTGCATCAGAGTGCCGCATAG
1 AATTGCA-CAGAGTGCCACATAG
*
3542 AATTGCACTGTAGTGCCA
1 AATTGCACAG-AGTGCCA
3560 TAAAATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACAGAGTGCCACATAG
Found at i:3758 original size:103 final size:103
Alignment explanation
Indices: 3579--3786 Score: 353
Period size: 103 Copynumber: 2.0 Consensus size: 103
3569 GTCCATAAGA
* * *
3579 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGGCTCACCAGACT
3644 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
*
3682 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGGCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGGCTCACCAGACT
* * *
3747 TCACATATGTTCCAAAGAATATATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
3785 AC
1 AC
3787 TGCGTAGACC
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGGCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATATCCCGAAGG
Found at i:5455 original size:12 final size:12
Alignment explanation
Indices: 5438--5473 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
5428 TTGACAAGTC
5438 AAATTCAACTTA
1 AAATTCAACTTA
5450 AAATTCAACTTA
1 AAATTCAACTTA
5462 AAATTCAACTTA
1 AAATTCAACTTA
5474 TCAACTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTCAACTTA
Found at i:11403 original size:24 final size:23
Alignment explanation
Indices: 11362--11410 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
11352 AATAACCTCA
*
11362 TTTTGAGAGTTTAAGATTGAGAG
1 TTTTGAGAGTTTAAGATTGAAAG
11385 TTTTGA-AGTTTCAAAGATTGAAAG
1 TTTTGAGAGTTT--AAGATTGAAAG
11409 TT
1 TT
11411 AGAAGGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 6 0.26
24 12 0.52
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (23 bp):
TTTTGAGAGTTTAAGATTGAAAG
Found at i:11844 original size:171 final size:169
Alignment explanation
Indices: 11526--12059 Score: 680
Period size: 170 Copynumber: 3.1 Consensus size: 169
11516 CCTTTTTTAT
* * * *
11526 CAGAGATTCTCTGAGAAAAAGAAAAATG-TTTCCCTGGAACGCGCCTTTCTTTTTCGTCAGATTT
1 CAGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACACGCCTTTCTTTTT-GTCAGATTT
* * * * *
11590 TATCTGGAAGTCTCAGTCCATTATATTGAGATTTATGTAGTCATTA-GGGAACTATTCCTGCCAG
65 TATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCAG
* * *
11654 -ACGGATATAATGTTTGATGGGGTGAGACATTATAACATGG
130 AAC-GATATAATGTTTGATGGGATGAGACACTATGACATGG
* ***
11694 CAGAGATTCTTTGAGAAAAGGAAAAACGCTTCCCCTGGGACACACTTTTTTCTTTTTGTCAGATT
1 CAGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCT-GGA-ACACGCCTTTCTTTTTGTCAGATT
* * *
11759 TTATCTGGAAGTCTCAGTCCAATATGTTGAGATTTCTATAGGCAGTAGGGGAACTATTCCCGTCA
64 TTATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCA
*
11824 GAACGATATAATGTTTGATGGGATGAGACACTATGACATTG
129 GAACGATATAATGTTTGATGGGATGAGACACTATGACATGG
* * * ** *
11865 CAGAAAATCTCT-ACGAAAAGGACAAACGCTTCCCCTGGAATGCGCCTTTCATTTTTCTCAGATT
1 CAGAGATTCTCTGA-GAAAAGGAAAAACGCTTCCCCTGGAACACGCCTTTC-TTTTTGTCAGATT
* * * *
11929 TTATCTAGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGAAGTAGGAGAACTATTCCTATCA
64 TTATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCA
* * *
11994 TACCGATATAATGTTTAATGGGATGAGACACTATGACATGG
129 GAACGATATAATGTTTGATGGGATGAGACACTATGACATGG
*
12035 CAAAGATTCTCTGAGAAAAGGAAAA
1 CAGAGATTCTCTGAGAAAAGGAAAA
12060 GTGTTTCCCA
Statistics
Matches: 313, Mismatches: 45, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
168 25 0.08
169 12 0.04
170 182 0.58
171 92 0.29
172 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (169 bp):
CAGAGATTCTCTGAGAAAAGGAAAAACGCTTCCCCTGGAACACGCCTTTCTTTTTGTCAGATTTT
ATCTGGAAGTCTCAGTCCATTATGTTGAGATTTCTGTAGGCAGTAGGGGAACTATTCCTGTCAGA
ACGATATAATGTTTGATGGGATGAGACACTATGACATGG
Found at i:13625 original size:24 final size:25
Alignment explanation
Indices: 13592--13641 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
13582 AACCGTTACA
*
13592 ATTAAAAAACTAAAT-AATAAAAAC
1 ATTAAAAAACAAAATAAATAAAAAC
*
13616 ATTAAGAAACAAAATAAATAAAAAC
1 ATTAAAAAACAAAATAAATAAAAAC
13641 A
1 A
13642 CATAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.72, C:0.08, G:0.02, T:0.18
Consensus pattern (25 bp):
ATTAAAAAACAAAATAAATAAAAAC
Found at i:14812 original size:17 final size:18
Alignment explanation
Indices: 14790--14837 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
14780 TTTAATTTTA
14790 ATTTTAATTTCATTAAT-
1 ATTTTAATTTCATTAATG
*
14807 ATTTTAAATTGTTTATTAATG
1 ATTTT-AA-T-TTCATTAATG
14828 ATTTTAATTT
1 ATTTTAATTT
14838 TAATTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 2 0.08
20 10 0.38
21 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
ATTTTAATTTCATTAATG
Found at i:15465 original size:55 final size:55
Alignment explanation
Indices: 15379--15491 Score: 145
Period size: 55 Copynumber: 2.1 Consensus size: 55
15369 AATTGTGTGC
* * * * *
15379 CATAAATCTATGACGCGCATTTATGACGCTCATTGCACGTCATTGAAGCCCTCGT
1 CATAAATCTATGACACACATGTATGACGCTCATTGCACGTCATTGAAGCACACGT
* * **
15434 CATAAATTTATGACACACATGTATGATGCTCATTGCGTGTCATTGAAGCACACGT
1 CATAAATCTATGACACACATGTATGACGCTCATTGCACGTCATTGAAGCACACGT
15489 CAT
1 CAT
15492 TAAAAAAGGT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (55 bp):
CATAAATCTATGACACACATGTATGACGCTCATTGCACGTCATTGAAGCACACGT
Found at i:15546 original size:2 final size:2
Alignment explanation
Indices: 15539--15567 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15529 TTTTGTAAAT
15539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15568 TGTAGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20003 original size:16 final size:17
Alignment explanation
Indices: 19972--20004 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19962 ACTTTTGTTA
*
19972 ATGTTATTATAAATTTT
1 ATGTTATTACAAATTTT
19989 ATGTTATT-CAAATTTT
1 ATGTTATTACAAATTTT
20005 CAATCGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (17 bp):
ATGTTATTACAAATTTT
Found at i:20061 original size:12 final size:12
Alignment explanation
Indices: 20044--20068 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20034 CAATTAAATT
20044 TTATCTTTTATA
1 TTATCTTTTATA
20056 TTATCTTTTATA
1 TTATCTTTTATA
20068 T
1 T
20069 ATATGTCAAA
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATCTTTTATA
Found at i:26016 original size:14 final size:14
Alignment explanation
Indices: 25997--26027 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25987 CAAACAAAGG
25997 CTTTTAACTATTGT
1 CTTTTAACTATTGT
26011 CTTTTAACTATTGT
1 CTTTTAACTATTGT
26025 CTT
1 CTT
26028 AAGCATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (14 bp):
CTTTTAACTATTGT
Found at i:28018 original size:60 final size:60
Alignment explanation
Indices: 27950--28075 Score: 243
Period size: 60 Copynumber: 2.1 Consensus size: 60
27940 TTCTGATATA
*
27950 TTTGATTCTTATGATAGTTTTGATATGTTATTTAATATTTTTCAGGTCAGCTGGTTTAGT
1 TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
28010 TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
1 TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
28070 TTTGAT
1 TTTGAT
28076 CCGGATTTCC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (60 bp):
TTTGATTCTTATGATAGTTTTGATATGTGATTTAATATTTTTCAGGTCAGCTGGTTTAGT
Found at i:43772 original size:12 final size:12
Alignment explanation
Indices: 43737--43774 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
43727 TTTTAATATT
43737 TATCGGGTCGGG
1 TATCGGGTCGGG
* *
43749 TATCGAGCCGGG
1 TATCGGGTCGGG
43761 TATCGGGTCGGG
1 TATCGGGTCGGG
43773 TA
1 TA
43775 ATCAGAGCGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.13, C:0.18, G:0.45, T:0.24
Consensus pattern (12 bp):
TATCGGGTCGGG
Found at i:44134 original size:20 final size:20
Alignment explanation
Indices: 44104--44270 Score: 149
Period size: 20 Copynumber: 8.3 Consensus size: 20
44094 GTTTCAAGAT
*
44104 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
44124 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
* * *
44144 TTCGCAATGCGAATATGTA-AA
1 -TCGCAATGCGATTCTG-ACTA
*
44165 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
44185 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
44205 TCGCAACGCGATTCTGATTA
1 TCGCAATGCGATTCTGACTA
* * *
44225 TCGCAACGAGATTTTGACTA
1 TCGCAATGCGATTCTGACTA
* *
44245 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
44265 TCGCAA
1 TCGCAA
44271 CACTGAATTT
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.02
20 105 0.86
21 13 0.11
22 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:44271 original size:20 final size:20
Alignment explanation
Indices: 44164--44271 Score: 153
Period size: 20 Copynumber: 5.4 Consensus size: 20
44154 GAATATGTAA
* *
44164 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
44184 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
44204 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
* *
44224 ATCGCAACGAGATTTTGACT
1 ATCGCAACGCGATTCTGACT
44244 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
44264 GTCGCAAC
1 ATCGCAAC
44272 ACTGAATTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:45119 original size:24 final size:24
Alignment explanation
Indices: 45092--45145 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
45082 GTATTCGAAA
45092 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
45116 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
45140 TTTGAT
1 TTTGAT
45146 GATGTTTCAG
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:47655 original size:20 final size:20
Alignment explanation
Indices: 47605--47769 Score: 84
Period size: 20 Copynumber: 8.8 Consensus size: 20
47595 TTACACATTC
47605 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
**
47625 ATTTGGCTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* * *
47645 ATTTGATTATCACAACTC-A
1 ATTTGAATATCGCAACGCGA
*
47664 A----AA-ATCACAACGCGA
1 ATTTGAATATCGCAACGCGA
*
47679 ATTTGACTATCGCAA--CGA
1 ATTTGAATATCGCAACGCGA
*
47697 A----AAAATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* ** *
47713 ATTTGACTATCGCAGTGTGA
1 ATTTGAATATCGCAACGCGA
* * * *
47733 ATTTGATTAACGCAACGGGT
1 ATTTGAATATCGCAACGCGA
* *
47753 ATTCGACTATCGCAACG
1 ATTTGAATATCGCAACG
47770 AGAAAATCGC
Statistics
Matches: 107, Mismatches: 26, Indels: 24
0.68 0.17 0.15
Matches are distributed among these distances:
14 17 0.16
15 3 0.03
16 4 0.04
18 4 0.04
19 3 0.03
20 76 0.71
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:47724 original size:34 final size:34
Alignment explanation
Indices: 47633--47726 Score: 143
Period size: 34 Copynumber: 2.8 Consensus size: 34
47623 GAATTTGGCT
* * **
47633 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
*
47667 ATCACAACGCGAATTTGACTATCGCAACGAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
47701 ATCGCAACGCGAATTTGACTATCGCA
1 ATCGCAACGCGAATTTGACTATCGCA
47727 GTGTGAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
Found at i:47838 original size:20 final size:21
Alignment explanation
Indices: 47809--47866 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
47799 GCAACGCGAA
47809 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
* *
47829 TTG-GCTTTCGCATTGTGATT
1 TTGAGCTTTCGCGTTGCGATT
*
47849 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
47867 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.45
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:50026 original size:18 final size:18
Alignment explanation
Indices: 50003--50086 Score: 105
Period size: 20 Copynumber: 4.4 Consensus size: 18
49993 GAAACTTAAA
50003 ATCGCAACACGAATGACT
1 ATCGCAACACGAATGACT
*
50021 ATCGCAACACAAATGACT
1 ATCGCAACACGAATGACT
*
50039 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG--AATGACT
*
50059 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAA--TGACT
50079 ATCGCAAC
1 ATCGCAAC
50087 GAGAGAATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
18 28 0.47
20 31 0.53
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (18 bp):
ATCGCAACACGAATGACT
Found at i:50056 original size:20 final size:20
Alignment explanation
Indices: 50014--50087 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
50004 TCGCAACACG
*
50014 AATGACTATCGCAACAC--A
1 AATGACTATCGCAACGCGAA
50032 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
50052 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
50072 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
50088 AGAGAATCGC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
18 16 0.31
20 35 0.69
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:50155 original size:20 final size:20
Alignment explanation
Indices: 50130--50177 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
50120 GTGATTCTTT
50130 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
50150 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCATTTTCG
50170 CGTTGCGA
1 CGTTGCGA
50178 AAGTAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:50746 original size:18 final size:18
Alignment explanation
Indices: 50720--50768 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
50710 CGAGTCGATC
50720 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
50738 AGGTAATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
50756 AGGTGATGGCTCT
1 AGGTGATGGCTCT
50769 CGAAGTGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.14, C:0.12, G:0.45, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:51792 original size:57 final size:57
Alignment explanation
Indices: 51704--51820 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
51694 AGATCGCTAG
51704 TCATGGTTTGAAGAAACAGATGGGTCAACATAGCATCTCCACCCGAATGTTGTACTT
1 TCATGGTTTGAAGAAACAGATGGGTCAACATAGCATCTCCACCCGAATGTTGTACTT
51761 TCATGGTTTGAAGAAACAGATGGGTCAACATAGCATCTCCACCCGAATGTTGTACTT
1 TCATGGTTTGAAGAAACAGATGGGTCAACATAGCATCTCCACCCGAATGTTGTACTT
51818 TCA
1 TCA
51821 GCCATGGCCC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (57 bp):
TCATGGTTTGAAGAAACAGATGGGTCAACATAGCATCTCCACCCGAATGTTGTACTT
Found at i:52205 original size:20 final size:20
Alignment explanation
Indices: 52147--52220 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
52137 GAAACTTAAA
**
52147 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
52167 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
**
52187 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAAAATGACT
* *
52207 ATTGCAACGCGAAA
1 ATCGCAACACGAAA
52221 CTAAAATCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:52631 original size:22 final size:22
Alignment explanation
Indices: 52605--52647 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
52595 GAGATAGATG
52605 GATTTCGCCAGAGATGGGGACT
1 GATTTCGCCAGAGATGGGGACT
* *
52627 GATTTCGTCGGAGATGGGGAC
1 GATTTCGCCAGAGATGGGGAC
52648 GGATGTCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (22 bp):
GATTTCGCCAGAGATGGGGACT
Found at i:52849 original size:20 final size:20
Alignment explanation
Indices: 52824--52917 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
52814 GCGCTTTGAA
*
52824 AATCGCATTGTGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
52844 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
52864 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
52884 AATCGCATTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAG
52904 AATCGCATTGCGAT
1 AATCGCATTGCGAT
52918 TTACATATTC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:52929 original size:20 final size:20
Alignment explanation
Indices: 52906--52956 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
52896 ATAGTTAGAA
52906 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
52926 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
52946 TCGCATTGCGA
1 TCGCATTGCGA
52957 ATTCGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:52977 original size:21 final size:21
Alignment explanation
Indices: 52946--53019 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
52936 ATTTACATAT
* **
52946 TCGCATTGCGAATTCGGAAAA
1 TCGCAATGCGAATTTAGAAAA
*
52967 TCGCAACGCGAATTTAGAAAA
1 TCGCAATGCGAATTTAGAAAA
52988 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTTAGAAAA
53009 TCGCAATGCGA
1 TCGCAATGCGA
53020 TAGTCAGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:53547 original size:27 final size:27
Alignment explanation
Indices: 53516--53570 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
53506 ACAAAGTATA
*
53516 AATTACGACCATTAGATTAATAAATTT
1 AATTACGACCACTAGATTAATAAATTT
* *
53543 AATTATGATCACTAGATTAATAAATTT
1 AATTACGACCACTAGATTAATAAATTT
53570 A
1 A
53571 TTTCTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.38
Consensus pattern (27 bp):
AATTACGACCACTAGATTAATAAATTT
Found at i:53786 original size:13 final size:13
Alignment explanation
Indices: 53768--53792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53758 TTAACTTTAT
53768 TTATATATATATA
1 TTATATATATATA
53781 TTATATATATAT
1 TTATATATATAT
53793 CACAAAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:54783 original size:20 final size:21
Alignment explanation
Indices: 54758--54796 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
54748 TTAATTCGAT
*
54758 GAATTAATCGAT-TTTAAACC
1 GAATTAACCGATGTTTAAACC
54778 GAATTAACCGATGTTTAAA
1 GAATTAACCGATGTTTAAA
54797 ACAATCATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (21 bp):
GAATTAACCGATGTTTAAACC
Found at i:60454 original size:35 final size:36
Alignment explanation
Indices: 60408--60476 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
60398 TACTAAACCG
60408 TCCCCGTCCCCGTTTAACATAAC-GTTTTTCCCTCA
1 TCCCCGTCCCCGTTTAACATAACAGTTTTTCCCTCA
* *
60443 TCCCCGTCCCCGTTTAGCATAACATTTTTTCCCT
1 TCCCCGTCCCCGTTTAACATAACAGTTTTTCCCT
60477 TCACCATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 22 0.71
36 9 0.29
ACGTcount: A:0.16, C:0.39, G:0.09, T:0.36
Consensus pattern (36 bp):
TCCCCGTCCCCGTTTAACATAACAGTTTTTCCCTCA
Done.