Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007531.1 Hibiscus syriacus cultivar Beakdansim tig00021029_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: 78709
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1496 original size:23 final size:20
Alignment explanation
Indices: 1463--1510 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 20
1453 ACTCCTTATT
1463 TTTTCTAATTAATATCTTCT-A
1 TTTTCTAATT-A-ATCTTCTCA
1484 TTTTCTACTATTAATCTTCTCA
1 TTTTCTA--ATTAATCTTCTCA
1506 TTTTC
1 TTTTC
1511 ACAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 14 0.58
22 7 0.29
23 3 0.12
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTCTAATTAATCTTCTCA
Found at i:1520 original size:22 final size:21
Alignment explanation
Indices: 1476--1516 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1466 TCTAATTAAT
*
1476 ATCTTCTATTTTCTACTATTA
1 ATCTTCTATTTTCTACAATTA
1497 ATCTTCTCATTTTC-ACAATT
1 ATCTTCT-ATTTTCTACAATT
1517 TAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (21 bp):
ATCTTCTATTTTCTACAATTA
Found at i:3304 original size:2 final size:2
Alignment explanation
Indices: 3297--3328 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3287 ATATTAAGCC
3297 TA TA 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 TA TA
3329 AACTTAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3742 original size:21 final size:21
Alignment explanation
Indices: 3696--3765 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
3686 AATATGTTCG
* *
3696 TAAATATTAAATAAATGTATTTA
1 TAAATGTTAAATAAA--TATATA
* *
3719 TAAATGTTAGATGAATATATA
1 TAAATGTTAAATAAATATATA
* *
3740 TAAATTTTAAATAAATATACA
1 TAAATGTTAAATAAATATATA
3761 TAAAT
1 TAAAT
3766 AAAATTTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 27 0.69
23 12 0.31
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (21 bp):
TAAATGTTAAATAAATATATA
Found at i:3913 original size:60 final size:60
Alignment explanation
Indices: 3840--3976 Score: 136
Period size: 60 Copynumber: 2.3 Consensus size: 60
3830 AATCTACGGT
* * * *
3840 AAAG-TATACAAATGGTCTCCCGACAATAAGATA-TTACTTTGTCGA-GTCCTTTGACTATTA
1 AAAGTTATA-AAATGGTCCCCCAACAATAAGA-AGTTACTTCGT-GATGTCCTTTGACTATGA
* * * * * *
3900 AAAGTTATAAAATGATCCCCCAACTATAGGAAGTTACTTCGTTATGTCTTTTTACTATGA
1 AAAGTTATAAAATGGTCCCCCAACAATAAGAAGTTACTTCGTGATGTCCTTTGACTATGA
3960 AAAGTTATAAAATGGTC
1 AAAGTTATAAAATGGTC
3977 ACTCAATTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
59 2 0.03
60 57 0.90
61 4 0.06
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (60 bp):
AAAGTTATAAAATGGTCCCCCAACAATAAGAAGTTACTTCGTGATGTCCTTTGACTATGA
Found at i:7611 original size:38 final size:36
Alignment explanation
Indices: 7553--7630 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 36
7543 AATTTAACGT
7553 TAAATTTTGAATGGGGTACTAAAAT-AAA-ATAAAAC
1 TAAATTTTGAATGGGGTACTAAAATGAAACA-AAAAC
*
7588 TAAAGTTTTTAATGGCGGATACTAAAATGAAACAAAAAC
1 TAAA-TTTTGAATGG-GG-TACTAAAATGAAACAAAAAC
7627 TAAA
1 TAAA
7631 ATTTAGATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 4 0.11
36 9 0.24
37 2 0.05
38 9 0.24
39 12 0.32
40 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (36 bp):
TAAATTTTGAATGGGGTACTAAAATGAAACAAAAAC
Found at i:9372 original size:16 final size:17
Alignment explanation
Indices: 9353--9388 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
9343 GTTGATTTAA
*
9353 TTTTGT-AAATATATAT
1 TTTTGTAAAACATATAT
9369 TTTTGTAAAACATATAT
1 TTTTGTAAAACATATAT
9386 TTT
1 TTT
9389 AGAAGAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTGTAAAACATATAT
Found at i:14134 original size:57 final size:58
Alignment explanation
Indices: 14058--14211 Score: 213
Period size: 57 Copynumber: 2.7 Consensus size: 58
14048 GCTTGGCGGT
* * *
14058 TTCAATTACTTCCTAAGTCCCTACTAGTTTT-AAATTATGCACCCCAAATTTGGTGGG
1 TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGG
*
14115 TTCAATTACTTCCCGAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGG
1 TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGG
* *** *
14173 TTCAATGACTTTTGAAGT-CCTAGTAGTTTTGAAACTATG
1 TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATG
14212 AAAAATAAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 49 0.57
58 37 0.43
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (58 bp):
TTCAATTACTTCCCAAGTCCCTACTAGTTTTGAAACTATGCACCCCAAATTTAGTGGG
Found at i:21043 original size:60 final size:60
Alignment explanation
Indices: 20933--21047 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
20923 GTTTGGGGAT
*
20933 TAATTTAGAATGAAGATCACAATTTGAGGATGAATATGAAACATTAAAAAGTTTAAAGAC
1 TAATTTAGAATGAAGATCACAATTTGAGGATGAATATAAAACATTAAAAAGTTTAAAGAC
* * * * *
20993 TAATTTAGAATGATAG-TTATAGTTTGAGGATGAA-ATTAAAATATTTAAAAGTTTA
1 TAATTTAGAATGA-AGATCACAATTTGAGGATGAATA-TAAAACATTAAAAAGTTTA
21048 GGGATCACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 44 0.94
61 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (60 bp):
TAATTTAGAATGAAGATCACAATTTGAGGATGAATATAAAACATTAAAAAGTTTAAAGAC
Found at i:24473 original size:33 final size:33
Alignment explanation
Indices: 24431--24510 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
24421 TAACCACGTT
*
24431 AAGTCTCGTCTCTTCGAGGAATACTTTCGGATG
1 AAGTCTCGTCTCTTCGAGGAACACTTTCGGATG
* * * **
24464 AAGTCTCGTCTATTTGAGGAGCGTTTTCGGATG
1 AAGTCTCGTCTCTTCGAGGAACACTTTCGGATG
* *
24497 AATTATCGTCTCTT
1 AAGTCTCGTCTCTT
24511 TGGGGAGAGC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (33 bp):
AAGTCTCGTCTCTTCGAGGAACACTTTCGGATG
Found at i:26589 original size:74 final size:74
Alignment explanation
Indices: 26460--26601 Score: 248
Period size: 74 Copynumber: 1.9 Consensus size: 74
26450 AGTGATCAAT
* *
26460 TTGTAACAAACGATAACATTAGCTTTCTCAATTTGTGACTTTTCAAATATTAATAGTGAAAACGA
1 TTGTAACAAACGATAACATTAGCTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
26525 ACACTCATA
66 ACACTCATA
* *
26534 TTGTAACAAACGATAACGTTAGTTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
1 TTGTAACAAACGATAACATTAGCTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
26599 ACA
66 ACA
26602 TTTATCTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (74 bp):
TTGTAACAAACGATAACATTAGCTTTCTCAATTTGTGACTTTTCAAACATCAATAGTGAAAACGA
ACACTCATA
Found at i:31477 original size:20 final size:20
Alignment explanation
Indices: 31439--31477 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31429 GTGCTCCCAC
*
31439 TAAGAAGCACCCCATAAGCT
1 TAAGAAGCACCCCAGAAGCT
* *
31459 TAAGAATCACCCCGGAAGC
1 TAAGAAGCACCCCAGAAGC
31478 CATCTCTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
TAAGAAGCACCCCAGAAGCT
Found at i:41625 original size:28 final size:28
Alignment explanation
Indices: 41593--41648 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
41583 AATAGCACAA
*
41593 ACCTGTACACATTCGTTCGATGCATCTT
1 ACCTGTACACATTCGTTCAATGCATCTT
41621 ACCTGTACACATTCGTTCAATGCATCTT
1 ACCTGTACACATTCGTTCAATGCATCTT
41649 GCATGCTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (28 bp):
ACCTGTACACATTCGTTCAATGCATCTT
Found at i:46636 original size:17 final size:17
Alignment explanation
Indices: 46614--46647 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
46604 CACACCAAAG
46614 AATGAACTAACCAAGAA
1 AATGAACTAACCAAGAA
46631 AATGAACTAACCAAGAA
1 AATGAACTAACCAAGAA
46648 TGTACTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
AATGAACTAACCAAGAA
Found at i:51315 original size:31 final size:30
Alignment explanation
Indices: 51218--51319 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
51208 TGTGTCATAT
* *
51218 GTCCTCAAACTATGAATCTCATTTTAAATTG
1 GTCCTTAAACTATGAATCT-ATTTTAAATTA
* * *
51249 GTCCCTAAACTTTTGAA--TATTTTAATTTCA
1 GTCCTTAAAC-TATGAATCTATTTTAAATT-A
*
51279 -TCCTTAAACTATGAATCTAATTCTAAATTA
1 GTCCTTAAACTATGAATCT-ATTTTAAATTA
51309 GTCCTTAAACT
1 GTCCTTAAACT
51320 CTTAAACATT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
28 5 0.09
29 17 0.30
30 3 0.05
31 26 0.46
32 5 0.09
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (30 bp):
GTCCTTAAACTATGAATCTATTTTAAATTA
Found at i:51318 original size:60 final size:60
Alignment explanation
Indices: 51219--51401 Score: 217
Period size: 60 Copynumber: 3.0 Consensus size: 60
51209 GTGTCATATG
* * * * *
51219 TCCTCAAACTATGAATCTCATTTTAAATTGGTCCCTAAACTTTTGAATATTTTAATTTCA
1 TCCTTAAACTATGAATCTAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
* * * * *
51279 TCCTTAAACTATGAATCTAATTCTAAATTAGTCCTTAAACTCTTAAACATTCTAATTTCA
1 TCCTTAAACTATGAATCTAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
* * *
51339 TCAC-TAAACTATG-ATCTTATTTCTAAATTGGTCCATAAACTTTTGAATATTCAAAATTCA
1 TC-CTTAAACTATGAATC-TAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
51399 TCC
1 TCC
51402 CCAAATCTAT
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
59 4 0.04
60 99 0.95
61 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.41
Consensus pattern (60 bp):
TCCTTAAACTATGAATCTAATTCTAAATTGGTCCATAAACTTTTGAATATTCTAATTTCA
Found at i:51965 original size:14 final size:14
Alignment explanation
Indices: 51946--51978 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51936 ACTTATCAAA
51946 TTCACATTCA-TAAG
1 TTCACATT-ATTAAG
51960 TTCACATTATTAAG
1 TTCACATTATTAAG
51974 TTCAC
1 TTCAC
51979 TAGCCCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (14 bp):
TTCACATTATTAAG
Found at i:52080 original size:23 final size:22
Alignment explanation
Indices: 52054--52120 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
52044 CACCACAACT
*
52054 CGTATAATTGCACCGAAGTGCAA
1 CGTAGAATTGCACCGAAGTGC-A
* * *
52077 CGTAGAATTGCATCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTG-CA
*
52100 CGTAGAATTGCACCGTAGTGC
1 CGTAGAATTGCACCGAAGTGC
52121 CATATAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (22 bp):
CGTAGAATTGCACCGAAGTGCA
Found at i:52230 original size:2 final size:2
Alignment explanation
Indices: 52225--52264 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
52215 ATTCCAAAGA
52225 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
52265 CCCGAAGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52400 original size:30 final size:30
Alignment explanation
Indices: 52359--52427 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
52349 ACATAGTTTG
* *
52359 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCATTTTCATACCTT
52389 TATCACATAGACATATCATTTTCATACCTT
1 TATCACATAGACATATCATTTTCATACCTT
52419 TATCACATA
1 TATCACATA
52428 ACTCATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (30 bp):
TATCACATAGACATATCATTTTCATACCTT
Found at i:54390 original size:174 final size:174
Alignment explanation
Indices: 54100--54449 Score: 682
Period size: 174 Copynumber: 2.0 Consensus size: 174
54090 TGATTAGTTG
54100 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
1 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
*
54165 AGTGATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
66 AGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
54230 TGAGCATTCAATGTCGAACTGTTGAGAGATAATATCAACTATCA
131 TGAGCATTCAATGTCGAACTGTTGAGAGATAATATCAACTATCA
54274 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
1 TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
*
54339 CGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
66 AGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
54404 TGAGCATTCAATGTCGAACTGTTGAGAGATAATATCAACTATCA
131 TGAGCATTCAATGTCGAACTGTTGAGAGATAATATCAACTATCA
54448 TT
1 TT
54450 ATTATCTCAA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (174 bp):
TTTAATTAATTAATTTAGGTCTGGAAAACATTTAATTATATATCCCGCACAAACCGAATGACCTC
AGTAATAAAAGAATTATTGTTATTCTTTGAGGACCTAAGTCCGAACACCGTAAATACTAGAGATT
TGAGCATTCAATGTCGAACTGTTGAGAGATAATATCAACTATCA
Found at i:58314 original size:182 final size:184
Alignment explanation
Indices: 57996--58368 Score: 606
Period size: 182 Copynumber: 2.0 Consensus size: 184
57986 ATTAAATTTT
* *
57996 AAATTTTAAATATATTATATATAACATATGGGGTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
* ** *
58061 TTTAAGATCCAATAATTTTTAAACCTAAATCAATATTAATTAATTAAAATTTTATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTA
*
58126 TATTTTATAATTATATATTATTTAAATTAATTGTAAAC-TTTTTTT-AATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
* * * * *
58178 AAATATTATATATATTATATATAACATATGGGCTCTGCCTAAATCATTTAAAATTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
*
58243 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATCTAAAATTTA
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTA
58308 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
*
58362 AACTATT
1 AAATATT
58369 TTTTTTATAT
Statistics
Matches: 175, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
182 155 0.89
183 7 0.04
184 13 0.07
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTA
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
Found at i:58364 original size:19 final size:20
Alignment explanation
Indices: 58336--58373 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
58326 TATTTAAATT
*
58336 AATTATAAACT-TTTTTTTG
1 AATTAAAAACTATTTTTTTG
58355 AATTAAAAACTATTTTTTT
1 AATTAAAAACTATTTTTTT
58374 TATATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
AATTAAAAACTATTTTTTTG
Found at i:58807 original size:60 final size:60
Alignment explanation
Indices: 58739--58890 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
58729 TTGATGAATT
* * * * * *
58739 GGGATGAAATTGGAA-GATCTAAATATTTTGA-GACAAATTTAGAATGAGATTCATAGTTTG
1 GGGATGAAATTGGAATG-T-TAAAAAGTTTAAGGACAAATTTAAAATGAGAGTCATACTTTG
*
58799 GGGATGAAATTGGAATGTTAAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATACTTTG
1 GGGATGAAATTGGAATGTTAAAAAGTTTAAGGACAAATTTAAAATGAGAGTCATACTTTG
* * *
58859 AGGATGAAATAT-GAATGTTTAAAATTTTAAGG
1 GGGATGAAAT-TGGAATGTTAAAAAGTTTAAGG
58891 GTCATAGTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
59 9 0.11
60 68 0.86
61 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
GGGATGAAATTGGAATGTTAAAAAGTTTAAGGACAAATTTAAAATGAGAGTCATACTTTG
Found at i:59219 original size:20 final size:18
Alignment explanation
Indices: 59177--59219 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
59167 AATAATTATT
* *
59177 TAATTTAAACATGTGTCA
1 TAATTTAAACATGTATAA
59195 TAATTTAGAACATGGTATAA
1 TAATTTA-AACAT-GTATAA
59215 TAATT
1 TAATT
59220 GAATTGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 9 0.43
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (18 bp):
TAATTTAAACATGTATAA
Found at i:76068 original size:6 final size:6
Alignment explanation
Indices: 76048--76102 Score: 89
Period size: 6 Copynumber: 9.7 Consensus size: 6
76038 CGTCCGTCTC
76048 GTCG-G GTCG-G GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
76094 GTCG-G GTCG
1 GTCGTG GTCG
76103 GGTAATACGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 14 0.29
6 35 0.71
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GTCGTG
Found at i:76287 original size:20 final size:20
Alignment explanation
Indices: 76264--76324 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
76254 AGATCGCGTT
76264 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* ** *
76284 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTTCAACTATCGCAAC
76304 GCGATTTTCAACTATCGCAAC
1 GCGA-TTTCAACTATCGCAAC
76325 ACGAATTGCG
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
19 1 0.03
20 17 0.57
21 12 0.40
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Done.