Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004889.1 Hibiscus syriacus cultivar Beakdansim tig00011008_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: 67073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:5567 original size:20 final size:20
Alignment explanation
Indices: 5428--5578 Score: 89
Period size: 20 Copynumber: 7.6 Consensus size: 20
5418 AAATGACCAA
*
5428 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * * *
5448 CAATTTCTCAAC-CCAGTTTT
1 CAAATTCGCAACGCGA-ATTT
* *
5468 CAATTTCGCAACGCAAATATGT
1 CAAATTCGCAACGCGAAT-T-T
** *
5490 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
*
5508 CCAAATTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
*
5529 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
5548 CAAATTTGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
5568 -AATTTCGCAAC
1 CAAATTCGCAAC
5579 AGGTTTTAGT
Statistics
Matches: 98, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
18 1 0.01
19 25 0.26
20 57 0.58
21 14 0.14
22 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:6497 original size:24 final size:24
Alignment explanation
Indices: 6470--6523 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
6460 GTATTCGAAA
6470 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
6494 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
6518 TTTGAT
1 TTTGAT
6524 GATGTGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:9133 original size:20 final size:20
Alignment explanation
Indices: 9085--9134 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
9075 ATGTTGCGAT
9085 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
9105 CAACACGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
9125 CAATGCGAAA
1 CAACGCGAAA
9135 TAAGCGTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:9678 original size:24 final size:24
Alignment explanation
Indices: 9651--9701 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
9641 TTTCATATGT
9651 AATTAGAGTTTGAATTTAAATTTC
1 AATTAGAGTTTGAATTTAAATTTC
* * *
9675 AATTTGAGTTTGAGTTTGAATTTC
1 AATTAGAGTTTGAATTTAAATTTC
9699 AAT
1 AAT
9702 ATAAATTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (24 bp):
AATTAGAGTTTGAATTTAAATTTC
Found at i:10054 original size:39 final size:39
Alignment explanation
Indices: 10011--10097 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
10001 TCTGATGCTC
10011 ATCAAAATCCAAAGCTCATATGGTG-CAAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGTC-AAGCAAAAGGAA
*
10050 ATCAAAATCCAAATCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
10089 ATCAAAATC
1 ATCAAAATC
10098 TACAACTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 45 0.98
40 1 0.02
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
Found at i:10296 original size:20 final size:20
Alignment explanation
Indices: 10271--10313 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
10261 ATGTTGCGAT
*
10271 CAACGCGAAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
10291 CAACGCAAAAGTCAAATTCG
1 CAACGCAAAAGTCAAATTCG
10311 CAA
1 CAA
10314 ACCGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (20 bp):
CAACGCAAAAGTCAAATTCG
Found at i:11988 original size:21 final size:21
Alignment explanation
Indices: 11964--12058 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
11954 GGCGAGACCA
*
11964 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* *
11985 CTTGAACGATGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
12006 CTTCG-ATGATGAGA-GGGCCT
1 CTT-GAACGATGAGAGGGGCCT
* *
12026 ATTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
12047 CTTGAATGATGA
1 CTTGAACGATGA
12059 TAGGTGCATC
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.03
20 13 0.22
21 41 0.71
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:12034 original size:41 final size:41
Alignment explanation
Indices: 11964--12058 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
11954 GGCGAGACCA
* * * * * *
11964 CTTGAACGATGACAGGGGCCTCTTGAACGATGGGAGGGGCTT
1 CTTGAATGATGAGA-GGGCCTATTGAACGATAGGAGGCGCCT
12006 CTTCG-ATGATGAGAGGGCCTATTGAACGATAGGAGGCGCCT
1 CTT-GAATGATGAGAGGGCCTATTGAACGATAGGAGGCGCCT
12047 CTTGAATGATGA
1 CTTGAATGATGA
12059 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 33 0.73
42 10 0.22
43 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
CTTGAATGATGAGAGGGCCTATTGAACGATAGGAGGCGCCT
Found at i:14234 original size:20 final size:20
Alignment explanation
Indices: 14211--14248 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14201 AGAAGTTTCT
*
14211 GAAACTGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
14231 GAAAATGAAAATCGCAAC
1 GAAAATGAAAATCGCAAC
14249 ACGATTTTAG
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:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:14474 original size:14 final size:14
Alignment explanation
Indices: 14457--14504 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
14447 AATTTCAAAA
14457 TAAAAATAAGAGAT
1 TAAAAATAAGAGAT
* * *
14471 TAAAAA-AACTATAA
1 TAAAAATAA-GAGAT
14485 TAAAAATAAGAGAT
1 TAAAAATAAGAGAT
14499 TAAAAA
1 TAAAAA
14505 AACTAACCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.21
Consensus pattern (14 bp):
TAAAAATAAGAGAT
Found at i:14475 original size:28 final size:28
Alignment explanation
Indices: 14453--14510 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
14443 CAAAAATTTC
14453 AAAATAAAAATAAGAGATTAAAAAAACT
1 AAAATAAAAATAAGAGATTAAAAAAACT
*
14481 ATAATAAAAATAAGAGATTAAAAAAACT
1 AAAATAAAAATAAGAGATTAAAAAAACT
14509 AA
1 AA
14511 CCATCGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (28 bp):
AAAATAAAAATAAGAGATTAAAAAAACT
Found at i:14782 original size:20 final size:20
Alignment explanation
Indices: 14757--14800 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
14747 GCGTAAAAAT
* * *
14757 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCACGTTGCAA
14777 ATTTGACTATCACGTTGCAA
1 ATTTGACTATCACGTTGCAA
14797 ATTT
1 ATTT
14801 AGAAAATCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTTGACTATCACGTTGCAA
Found at i:16661 original size:6 final size:6
Alignment explanation
Indices: 16639--16679 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
16629 GTATATCCAT
*
16639 CTCAT- CTCATG -TCATG CTCATG CTGATG CTCATG CTCATG C
1 CTCATG CTCATG CTCATG CTCATG CTCATG CTCATG CTCATG C
16680 ATGCCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (6 bp):
CTCATG
Found at i:17867 original size:23 final size:23
Alignment explanation
Indices: 17812--17872 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
17802 TCAAACAATC
* *
17812 AAAAATT-ACTAA-AAACATAAA
1 AAAAATTAACCAATAAAGATAAA
17833 AAAAATTAACC-ATAAAGATAAA
1 AAAAATTAACCAATAAAGATAAA
17855 AGAAAA-TATACCAATAAA
1 A-AAAATTA-ACCAATAAA
17873 ATAGAATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 8 0.24
22 13 0.39
23 7 0.21
24 5 0.15
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (23 bp):
AAAAATTAACCAATAAAGATAAA
Found at i:18161 original size:2 final size:2
Alignment explanation
Indices: 18154--18181 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18144 ATCTAATAAT
18154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18182 AAAGTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19960 original size:13 final size:13
Alignment explanation
Indices: 19944--20007 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
19934 TGTGTAAATA
19944 TATTAAATATTTT
1 TATTAAATATTTT
*
19957 TATTTAATATTTTT
1 TATTAAATA-TTTT
**
19971 TGAACAAATATTTT
1 T-ATTAAATATTTT
* *
19985 TATTTAATATTAT
1 TATTAAATATTTT
19998 T-TT-AATATTT
1 TATTAAATATTT
20008 AAACGGTGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
11 6 0.15
12 2 0.05
13 17 0.43
14 10 0.25
15 5 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTAAATATTTT
Found at i:20510 original size:24 final size:24
Alignment explanation
Indices: 20483--20544 Score: 61
Period size: 27 Copynumber: 2.4 Consensus size: 24
20473 GAAATTTATT
* *
20483 TTCGTCCTCTTAAAATTTTTTAAG
1 TTCGTCCTCTTAAAATTCTATAAG
*
20507 TTCGTCTCTCCTTTAAAGTTCTATAAG
1 TTCGTC-CT-C-TTAAAATTCTATAAG
20534 TTCGCTCCTCT
1 TTCG-TCCTCT
20545 AACATAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 6 0.19
25 3 0.10
26 2 0.06
27 18 0.58
28 2 0.06
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.47
Consensus pattern (24 bp):
TTCGTCCTCTTAAAATTCTATAAG
Found at i:29234 original size:64 final size:64
Alignment explanation
Indices: 29155--29292 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 64
29145 CGGATCCTGG
* * *
29155 CAGGTCGGGTAAAATCAGATACAGGTCAAGTT-AGGTAAATTTGATACCATATCCAGATCGGGTT
1 CAGGTCAGGTAAAATCAG-TACAGGTCAAGTTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
* * * * ** **
29219 CAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
1 CAGGTCAGGTAAAATCAGTACAGGTCAAGTTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
29283 CAGGTCAGGT
1 CAGGTCAGGT
29293 TATTTTCAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
63 8 0.13
64 54 0.87
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (64 bp):
CAGGTCAGGTAAAATCAGTACAGGTCAAGTTCAGGTAAATTTGACACCAGATCCAGATCGGGTT
Found at i:30078 original size:215 final size:215
Alignment explanation
Indices: 29580--30204 Score: 924
Period size: 215 Copynumber: 2.9 Consensus size: 215
29570 ATCTTATGAA
* *
29580 AAATACAAATTTA-AGAATTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
1 AAATA-AAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
* * *
29644 AACAACACACATTGATGAGGGATCAACTTGAAATAATTTTAAGTTGTGAGGTTGAAATTAATACA
65 AACAACACACATTGAT-AGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACA
* * * *
29709 AAAAAATACTAAATTATACCCATTTAAAAAGTTATGGGCCAAATAAAAAAATAGAATTAAGTAAT
129 AAAAAGTACTAAATTATACCTATTTAAAAAGTTATGGGCC-AATATAAAAATAGAAATAAGTAAT
*
29774 AAGTATAGATCAATTTCATATGC
193 AAGTATAGATCAATTTCAGATGC
* * *
29797 AAATAAAATTTGGATGACTAAATTGAAAAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
*
29862 ACAACACACATTGATTAGGGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATAC-A
66 ACAACACACATTGA-TAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
* *
29926 AAAAGTACTAAATTATACCTATTTAAAAAGTTATGGGTCAATCTAAAAATAGAAATAAGTAATAA
130 AAAAGTACTAAATTATACCTATTTAAAAAGTTATGGGCCAATATAAAAATAGAAATAAGTAATAA
* *
29991 GTATTGGTCAATTTCAGATGC
195 GTATAGATCAATTTCAGATGC
*
30012 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAA
1 AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* * *
30077 ACAACACA-A---A-AGGGATCAAATCAAAATAATTTTTAATTTTGAGGTTGAAATTAATACAAA
66 ACAACACACATTGATAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAA
* * *
30137 AAAGTACTAAATTATA-CTCATTTAAAAAGTTACGGGCCAATTTAAAAATATAAATAAGTAATAA
131 AAAGTACTAAATTATACCT-ATTTAAAAAGTTATGGGCCAATATAAAAATAGAAATAAGTAATAA
30201 GTAT
195 GTAT
30205 GGGTATGGGT
Statistics
Matches: 374, Mismatches: 30, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
209 45 0.12
210 63 0.17
211 1 0.00
214 1 0.00
215 110 0.29
216 43 0.11
217 110 0.29
218 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (215 bp):
AAATAAAATTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACACATTGATAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAA
AAAGTACTAAATTATACCTATTTAAAAAGTTATGGGCCAATATAAAAATAGAAATAAGTAATAAG
TATAGATCAATTTCAGATGC
Found at i:30270 original size:33 final size:32
Alignment explanation
Indices: 30227--30290 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
30217 TTATATACTA
* *
30227 TATTTTATACTATTTATATAAACTATAGTTTG
1 TATTTTATACTATATACATAAACTATAGTTTG
*
30259 TATTTATATACTATATACATGAACTATAGTTT
1 TATTT-TATACTATATACATAAACTATAGTTT
30291 ACATATAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (32 bp):
TATTTTATACTATATACATAAACTATAGTTTG
Found at i:30356 original size:18 final size:18
Alignment explanation
Indices: 30335--30449 Score: 97
Period size: 18 Copynumber: 5.9 Consensus size: 18
30325 AAGGTTGATA
30335 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* *
30353 TTTACATATAAACTATATAG
1 TTTATATATGAAC--TATAG
30373 TTTATATACT-AACTATAG
1 TTTATATA-TGAACTATAG
*
30391 TTTATATATAAACTATAG
1 TTTATATATGAACTATAG
30409 TTAATATTTACATATGAACTATAG
1 TT--TA--T--ATATGAACTATAG
* *
30433 TTTACATATGAAATATA
1 TTTATATATGAACTATA
30450 TATATAAACT
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
17 1 0.01
18 45 0.56
20 17 0.21
21 1 0.01
22 3 0.04
24 14 0.17
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:30377 original size:38 final size:39
Alignment explanation
Indices: 30332--30454 Score: 153
Period size: 38 Copynumber: 3.1 Consensus size: 39
30322 ACTAAGGTTG
30332 ATATTTATATATGAACTATAGTTTACATATAAACTATAT
1 ATATTTATATATGAACTATAGTTTACATATAAACTATAT
* *
30371 A-GTTTATATACT-AACTATAGTTTATATATAAACTATAGTT
1 ATATTTATATA-TGAACTATAGTTTACATATAAACTATA--T
*
30411 AATATTTACATATGAACTATAGTTTACATATGAAA-TATAT
1 -ATATTTATATATGAACTATAGTTTACATAT-AAACTATAT
30451 ATAT
1 ATAT
30455 AAACTATATA
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
38 32 0.44
39 6 0.08
40 2 0.03
41 2 0.03
42 27 0.38
43 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (39 bp):
ATATTTATATATGAACTATAGTTTACATATAAACTATAT
Found at i:30460 original size:31 final size:30
Alignment explanation
Indices: 30420--30549 Score: 111
Period size: 33 Copynumber: 4.5 Consensus size: 30
30410 TAATATTTAC
30420 ATATGAACTATAGTTTACATATGAAATATAT
1 ATAT-AACTATAGTTTACATATGAAATATAT
*
30451 ATATAAACTATATAGTTTACATATGACATATAT
1 ATAT-AAC--TATAGTTTACATATGAAATATAT
*
30484 ATAT-ACTATAG-TT-GATAT----T-TAT
1 ATATAACTATAGTTTACATATGAAATATAT
*
30506 ATACT-A-TATAGTTTACATATGACATATAT
1 ATA-TAACTATAGTTTACATATGAAATATAT
30535 ATAT-ACTATAGTTTA
1 ATATAACTATAGTTTA
30550 TATTCATATA
Statistics
Matches: 84, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
22 11 0.13
23 5 0.06
24 4 0.05
27 4 0.05
28 5 0.06
29 20 0.24
31 9 0.11
33 26 0.31
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (30 bp):
ATATAACTATAGTTTACATATGAAATATAT
Found at i:30473 original size:51 final size:52
Alignment explanation
Indices: 30415--30544 Score: 155
Period size: 51 Copynumber: 2.6 Consensus size: 52
30405 ATAGTTAATA
30415 TTTACATATGAAC-TATAGT-T-TACATATGAAAT-ATATATATAAACTATATAG
1 TTTACATATGAACATATA-TATATAC-TAT-AAATGATATATATAAACTATATAG
** * *
30466 TTTACATATG-ACATATATATATACTATAGTTGATATTTATATACTATATAG
1 TTTACATATGAACATATATATATACTATAAATGATATATATAAACTATATAG
30517 TTTACATATG-ACATATATATATACTATA
1 TTTACATATGAACATATATATATACTATA
30545 GTTTATATTC
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
50 5 0.07
51 63 0.89
52 3 0.04
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (52 bp):
TTTACATATGAACATATATATATACTATAAATGATATATATAAACTATATAG
Found at i:30482 original size:20 final size:18
Alignment explanation
Indices: 30459--30568 Score: 53
Period size: 15 Copynumber: 6.4 Consensus size: 18
30449 ATATATAAAC
30459 TATATAGTTTACATATGACA
1 TATATA-TTTACATAT-ACA
* *
30479 TATATATATAC-TATA-G
1 TATATATTTACATATACA
30495 T-TGATATTT--ATATAC-
1 TAT-ATATTTACATATACA
30510 TATATAGTTTACATATGACA
1 TATATA-TTTACATAT-ACA
* *
30530 TATATATATAC-TATA-G
1 TATATATTTACATATACA
*
30546 TTTATA-TT-CATATAC-
1 TATATATTTACATATACA
30561 TATATATT
1 TATATATT
30569 ATATAGATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 28
0.66 0.08 0.26
Matches are distributed among these distances:
14 1 0.01
15 19 0.27
16 16 0.23
17 2 0.03
18 10 0.14
19 10 0.14
20 12 0.17
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATATTTACATATACA
Found at i:30545 original size:51 final size:51
Alignment explanation
Indices: 30447--30566 Score: 204
Period size: 51 Copynumber: 2.4 Consensus size: 51
30437 CATATGAAAT
* *
30447 ATATATATAAACTATATAGTTTACATATGACATATATATATACTATAGTTG
1 ATATTTATATACTATATAGTTTACATATGACATATATATATACTATAGTTG
*
30498 ATATTTATATACTATATAGTTTACATATGACATATATATATACTATAGTTT
1 ATATTTATATACTATATAGTTTACATATGACATATATATATACTATAGTTG
*
30549 ATATTCATATACTATATA
1 ATATTTATATACTATATA
30567 TTATATAGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (51 bp):
ATATTTATATACTATATAGTTTACATATGACATATATATATACTATAGTTG
Found at i:30570 original size:20 final size:20
Alignment explanation
Indices: 30529--30587 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
30519 TACATATGAC
*
30529 ATATATATATACTATAGT-TT
1 ATATACATATACTATA-TATT
*
30549 ATATTCATATACTATATATT
1 ATATACATATACTATATATT
* *
30569 ATATAGATAAACTATATAT
1 ATATACATATACTATATAT
30588 ACTATATAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (20 bp):
ATATACATATACTATATATT
Found at i:30573 original size:29 final size:28
Alignment explanation
Indices: 30503--30574 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
30493 AGTTGATATT
*
30503 TATATACTATATAGTTTACATATGACATA
1 TATATA-TATATAGTTTACATATCACATA
* *
30532 TATATATACTATAGTTTATAT-TCATATA
1 TATATATA-TATAGTTTACATATCACATA
30560 CTATATATTATATAG
1 -TATATA-TATATAG
30575 ATAAACTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 7 0.19
29 28 0.76
30 2 0.05
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (28 bp):
TATATATATATAGTTTACATATCACATA
Found at i:30692 original size:33 final size:33
Alignment explanation
Indices: 30650--30862 Score: 228
Period size: 33 Copynumber: 6.5 Consensus size: 33
30640 CCCTAAACCC
*
30650 TAAACTATATATTATATAGTTTATTAGTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
* * *
30683 TAAACTATATAACATATATAG-ACTATATCGTATATA
1 TAAACTATAT-A-TTATATAGTTC-AT-TAGTATATA
*
30719 TAAACTATACATTATATATAGTTCATTAGTATATA
1 TAAACTATATA-T-TATATAGTTCATTAGTATATA
30754 TAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
* *
30787 TAACCTATATAGTATAT-G-------GTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
*
30812 CAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATATATTATATAGTTCATTAGTATATA
*
30845 TAAACTATATAGTATATA
1 TAAACTATATATTATATA
30863 TAAACTATAT
Statistics
Matches: 149, Mismatches: 17, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
25 21 0.14
26 1 0.01
32 1 0.01
33 69 0.46
34 2 0.01
35 28 0.19
36 26 0.17
37 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.42
Consensus pattern (33 bp):
TAAACTATATATTATATAGTTCATTAGTATATA
Found at i:30753 original size:17 final size:17
Alignment explanation
Indices: 30731--30788 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
30721 AACTATACAT
30731 TATATATAGTTCATTAG
1 TATATATAGTTCATTAG
**
30748 TATATATA-AAC-TATA-
1 TATATATAGTTCAT-TAG
30763 TATTATATAGTTCATTAG
1 TA-TATATAGTTCATTAG
30781 TATATATA
1 TATATATA
30789 ACCTATATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (17 bp):
TATATATAGTTCATTAG
Found at i:30771 original size:18 final size:18
Alignment explanation
Indices: 30674--30873 Score: 126
Period size: 18 Copynumber: 11.1 Consensus size: 18
30664 TATAGTTTAT
30674 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
** *
30692 TAACATATATAGACTATA
1 TAGTATATATAAACTATA
*
30710 TCGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * **
30728 CATTATATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
30745 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* ** *
30763 TATTATATAGTTCATTAGTA
1 TAGTATATA-TAAACTA-TA
* *
30783 TA-TATAACCTATATAGTATA
1 TAGTAT-A--TATAAACTATA
* *
30803 TGGTATATACAAACTATA
1 TAGTATATATAAACTATA
**
30821 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
30836 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
30854 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
30872 TA
1 TA
30874 TTAATTTATT
Statistics
Matches: 135, Mismatches: 33, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
15 4 0.03
16 7 0.05
17 20 0.15
18 79 0.59
19 7 0.05
20 9 0.07
21 7 0.05
22 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:30818 original size:58 final size:58
Alignment explanation
Indices: 30747--30861 Score: 212
Period size: 58 Copynumber: 2.0 Consensus size: 58
30737 TAGTTCATTA
* *
30747 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATG
30805 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATAT
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATAT
30862 ATAAACTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATG
Found at i:30819 original size:25 final size:25
Alignment explanation
Indices: 30780--30828 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
30770 TAGTTCATTA
* *
30780 GTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATAGTATATG
*
30805 GTATATACAAACTATATATTATAT
1 GTATATACAAACTATATAGTATAT
30829 AGTTCATTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (25 bp):
GTATATACAAACTATATAGTATATG
Found at i:30861 original size:91 final size:94
Alignment explanation
Indices: 30688--30862 Score: 275
Period size: 91 Copynumber: 1.9 Consensus size: 94
30678 ATATATAAAC
*
30688 TATATAACATATATAGACTATATCGTATATATAAACTATACATTATATATAGTTCATTAGTATAT
1 TATATAACATATATAGA-TATATCGTATATACAAACTATACATTATATATAGTTCATTAGTATAT
*
30753 ATAAACTATATATTATATAGTTCATTAGTA
65 ATAAACTATATAGTATATAGTTCATTAGTA
* * *
30783 TATATAACCTATATAG-TATATGGTATATACAAACTATATA-T-TATATAGTTCATTAGTATATA
1 TATATAACATATATAGATATATCGTATATACAAACTATACATTATATATAGTTCATTAGTATATA
30845 TAAACTATATAGTATATA
66 TAAACTATATAGTATATA
30863 TAAACTATAT
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
91 38 0.51
92 1 0.01
93 21 0.28
95 15 0.20
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (94 bp):
TATATAACATATATAGATATATCGTATATACAAACTATACATTATATATAGTTCATTAGTATATA
TAAACTATATAGTATATAGTTCATTAGTA
Found at i:30897 original size:51 final size:51
Alignment explanation
Indices: 30799--30897 Score: 112
Period size: 51 Copynumber: 1.9 Consensus size: 51
30789 ACCTATATAG
* * * *
30799 TATATGGTATATACAAACTATATATTATATAGTTCATTAGTATATATAAAC
1 TATATAGTATATACAAACTATATATTATATAGTTAATTAGAACATATAAAC
* *
30850 TATATAGTATATATAAACTATATATTAATTTA-TTAATATA-AACATATA
1 TATATAGTATATACAAACTATATATT-ATATAGTTAAT-TAGAACATATA
30898 TATTAATTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
51 34 0.85
52 6 0.15
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (51 bp):
TATATAGTATATACAAACTATATATTATATAGTTAATTAGAACATATAAAC
Found at i:33949 original size:20 final size:20
Alignment explanation
Indices: 33924--33977 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
33914 TTCTGCTTTA
* * *
33924 TTCTGTTTTATGTTGTTTGC
1 TTCTGTTTGATATTGCTTGC
33944 TTCTGTTTGATATTGCTTGC
1 TTCTGTTTGATATTGCTTGC
**
33964 TTCTACTTGATATT
1 TTCTGTTTGATATT
33978 TGTAAGGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (20 bp):
TTCTGTTTGATATTGCTTGC
Found at i:35916 original size:2 final size:2
Alignment explanation
Indices: 35909--35949 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
35899 ACTCGAGAGC
* *
35909 TA TA TA TA TG TG 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 TA TA TA TA TA TA T
35950 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41510 original size:21 final size:20
Alignment explanation
Indices: 41486--41529 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41476 TTATGCATTT
*
41486 TTAAAAGTAATAAAATAACTA
1 TTAAAAGTAATAAAAGAA-TA
* *
41507 TTAAAATTACTAAAAGAATA
1 TTAAAAGTAATAAAAGAATA
41527 TTA
1 TTA
41530 TATTTTCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TTAAAAGTAATAAAAGAATA
Found at i:60946 original size:23 final size:23
Alignment explanation
Indices: 60918--60962 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
60908 GGGTTGGAAT
60918 CATTAGTAAAATGGAAAACTAAC
1 CATTAGTAAAATGGAAAACTAAC
60941 CATTAGTAAAATGGAAAACTAA
1 CATTAGTAAAATGGAAAACTAA
60963 TATAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.22
Consensus pattern (23 bp):
CATTAGTAAAATGGAAAACTAAC
Done.