Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007775.1 Hibiscus syriacus cultivar Beakdansim tig00110056_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: 599510
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:532236 original size:24 final size:24
Alignment explanation
Indices: 532207--532278 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
532197 GGTCCAACAT
*
532207 CATTTGATTATGCTCATTGCTCAA
1 CATTTGAATATGCTCATTGCTCAA
*
532231 CATTTGACTATGCTCATTGCTCAA
1 CATTTGAATATGCTCATTGCTCAA
532255 CATTTGAATATGCTCATTGCTCAA
1 CATTTGAATATGCTCATTGCTCAA
532279 TACCCATCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.39
Consensus pattern (24 bp):
CATTTGAATATGCTCATTGCTCAA
Found at i:540149 original size:142 final size:145
Alignment explanation
Indices: 539947--540295 Score: 389
Period size: 142 Copynumber: 2.4 Consensus size: 145
539937 TTCGCTACGT
* * * ** * *
539947 GTATGCAAATTCCAATTGCTCGAGTTGTCAATCACCTTTAGGAACCAATGGTATTTTGAATAGTT
1 GTATGCTAATTCCAATAGCTCGAGTAGTCAATCACCTTTAGGAACCAATACTATTCTGAATAGTG
* * * *
540012 AACTCTTTAATTGTTGCGAGGGTGTGAAGATAAATCATATGAACTTTTAAGCCCTTTT-TCTTTT
66 AACTCTTAAAATGTTGCGAGGATGTGAAGATAAATCATATGAACTTTTAAGCCCTTTTGTCTTAT
540076 GAACAT-CACT-TGA
131 GAACATCCACTCTGA
* ** *
540089 GTATGCTAATTTCAATAGCTCGAGTAGTCAATCACCTTTAGGAACCTGTACTATTCTGAATTGTG
1 GTATGCTAATTCCAATAGCTCGAGTAGTCAATCACCTTTAGGAACCAATACTATTCTGAATAGTG
* * * * **
540154 GATTGTTAAAATGTTGCTAGGATGTGAAGATAAATCATATGAACTTTTAAGGGCTTTTGTCTTAT
66 AACTCTTAAAATGTTGCGAGGATGTGAAGATAAATCATATGAACTTTTAAGCCCTTTTGTCTTAT
* *
540219 GGATATGCCACTCTGA
131 GAACAT-CCACTCTGA
* * * ** * **
540235 GTACGCTAATTCCAATAGCTTGAGTAGTCATTCTGCTTTAGGAACCACTGTTATTCTGAAT
1 GTATGCTAATTCCAATAGCTCGAGTAGTCAATCACCTTTAGGAACCAATACTATTCTGAAT
540296 TGAGGAATGA
Statistics
Matches: 170, Mismatches: 33, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
142 103 0.61
143 9 0.05
145 4 0.02
146 54 0.32
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (145 bp):
GTATGCTAATTCCAATAGCTCGAGTAGTCAATCACCTTTAGGAACCAATACTATTCTGAATAGTG
AACTCTTAAAATGTTGCGAGGATGTGAAGATAAATCATATGAACTTTTAAGCCCTTTTGTCTTAT
GAACATCCACTCTGA
Found at i:541626 original size:99 final size:99
Alignment explanation
Indices: 541455--541653 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
541445 AGTTCTTAAC
541455 TGATAAGTTTCACGAGTGATGGATCACCTTTTGTCAAGGAGGATAGGGTAAAATGTCTTATGGTT
1 TGATAAGTTTCACGAGTGATGGATCACCTTTTGTCAAGGAGGATAGGGTAAAATGTCTTATGGTT
541520 GGATGGTTCAATGTTGGTCTTATTCAGCTAAGTT
66 GGATGGTTCAATGTTGGTCTTATTCAGCTAAGTT
541554 TGATAAGTTTCACGAGTGATGGATCACCTTTTGTCAAGGAGGATAGGGTAAAATGTCTTATGGTT
1 TGATAAGTTTCACGAGTGATGGATCACCTTTTGTCAAGGAGGATAGGGTAAAATGTCTTATGGTT
541619 GGATGGTTCAATGTTGGTCTTATTCAGCTAAGTT
66 GGATGGTTCAATGTTGGTCTTATTCAGCTAAGTT
541653 T
1 T
541654 CTCCTGTGAT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (99 bp):
TGATAAGTTTCACGAGTGATGGATCACCTTTTGTCAAGGAGGATAGGGTAAAATGTCTTATGGTT
GGATGGTTCAATGTTGGTCTTATTCAGCTAAGTT
Found at i:549406 original size:19 final size:21
Alignment explanation
Indices: 549382--549425 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
549372 GGTTGAAGTT
549382 TAATTTTTAATT-AA-TAAAA
1 TAATTTTTAATTGAACTAAAA
549401 TAATTTTTAATTGAACTAAAA
1 TAATTTTTAATTGAACTAAAA
549422 -AATT
1 TAATT
549426 GACAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.52
20 6 0.26
21 5 0.22
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TAATTTTTAATTGAACTAAAA
Found at i:549872 original size:17 final size:17
Alignment explanation
Indices: 549850--549882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
549840 TATAATAAAC
549850 TATAAAAAATTAAATTA
1 TATAAAAAATTAAATTA
*
549867 TATAAAAATTTAAATT
1 TATAAAAAATTAAATT
549883 TTCAGAAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATAAAAAATTAAATTA
Found at i:557878 original size:29 final size:29
Alignment explanation
Indices: 557836--557906 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
557826 GGTTTGAGGT
557836 GTGCTAATATGCGTCAGCCCCATGCAAGA
1 GTGCTAATATGCGTCAGCCCCATGCAAGA
557865 GTGCTAATATGCGTCAGCCCCATGCAAGA
1 GTGCTAATATGCGTCAGCCCCATGCAAGA
*
557894 GTGCTAACATGCG
1 GTGCTAATATGCG
557907 CCTATCTCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (29 bp):
GTGCTAATATGCGTCAGCCCCATGCAAGA
Found at i:558157 original size:13 final size:14
Alignment explanation
Indices: 558129--558157 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
558119 ATAACAAAAG
558129 AAAATTGAAAACTA
1 AAAATTGAAAACTA
558143 AAAATTGAAAA-TA
1 AAAATTGAAAACTA
558156 AA
1 AA
558158 TTAAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAATTGAAAACTA
Found at i:568669 original size:17 final size:18
Alignment explanation
Indices: 568630--568667 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
568620 TTCTTCCCAA
*
568630 AAAGAAAAAAATTAAAAC
1 AAAGAAAAAAATAAAAAC
*
568648 AAAGAAGAAAATAAAAAC
1 AAAGAAAAAAATAAAAAC
568666 AA
1 AA
568668 GACCAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAGAAAAAAATAAAAAC
Found at i:570856 original size:21 final size:21
Alignment explanation
Indices: 570831--570887 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
570821 TATTTCATCG
570831 TTTATTTTATATGTTCACTCT
1 TTTATTTTATATGTTCACTCT
* **
570852 TTTATTTTAAAAT-TTCTTTCT
1 TTTATTTT-ATATGTTCACTCT
*
570873 TTTATTTTATTTGTT
1 TTTATTTTATATGTT
570888 AAAAAGATCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.83
22 3 0.10
ACGTcount: A:0.19, C:0.09, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTATTTTATATGTTCACTCT
Found at i:574782 original size:44 final size:44
Alignment explanation
Indices: 574733--574859 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
574723 TTAAACATTA
574733 TATTTTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
1 TATTTTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
*
574777 TATTTTA-ATTAAGTTTTAGG-A---TA---T---TAT-TTTTA-
1 TATTTTATATT-TGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
* *
574809 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
574853 TATTTTA
1 TATTTTA
574860 ATTAGGATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
32 15 0.23
33 8 0.12
34 3 0.05
36 2 0.03
37 1 0.02
39 1 0.02
40 2 0.03
42 2 0.03
43 9 0.14
44 22 0.34
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.61
Consensus pattern (44 bp):
TATTTTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
Found at i:574837 original size:76 final size:74
Alignment explanation
Indices: 574730--574945 Score: 324
Period size: 76 Copynumber: 2.9 Consensus size: 74
574720 ATTTTAAACA
*
574730 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTA
574795 GGATATTATTT
65 GGATATTA-TT
* *
574806 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTA
574871 GGATATTATT
65 GGATATTATT
* * * * *
574881 TTAAATATTATTTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAAGATTTA
574946 AGATCTTTTA
Statistics
Matches: 131, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
74 5 0.04
75 57 0.44
76 69 0.53
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.58
Consensus pattern (74 bp):
TTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGATTTAG
GATATTATT
Found at i:581277 original size:5 final size:5
Alignment explanation
Indices: 581253--581299 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
581243 TTCAGCGAAC
* * * *
581253 TTTAT TTCAT TCTA- TTTAT TTTAT TTTAA TTAAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
581300 TCTCTGAACA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:583420 original size:44 final size:43
Alignment explanation
Indices: 583371--583497 Score: 125
Period size: 44 Copynumber: 3.2 Consensus size: 43
583361 TTAAACATCA
583371 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTA-TTTAAATAGGTTTTAG
**
583415 TATTTTAAT-TAAGTTTTAGG-A---TA-TT--AT---TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTATTTAAATAGGTTTTAG
583447 TATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTT-ATTTAAATAGGTTTTAG
583491 TATTTTA
1 TATTTTA
583498 ATTAGGATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
31 2 0.03
32 15 0.23
33 6 0.09
36 3 0.05
37 1 0.02
38 4 0.06
40 4 0.06
43 6 0.09
44 22 0.34
45 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.60
Consensus pattern (43 bp):
TATTTTATCTTTGTTTTAGGTATTTTATTTAAATAGGTTTTAG
Found at i:583479 original size:76 final size:75
Alignment explanation
Indices: 583370--583575 Score: 317
Period size: 76 Copynumber: 2.7 Consensus size: 75
583360 TTTAAACATC
*
583370 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGG
1 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGG
583435 ATATTATTTTT
66 ATATTA-TTTT
* *
583446 ATATTTTATCTTTGTTTTAGGTATTTTAATTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGG
1 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGG
583511 ATATTATTTT
66 ATATTATTTT
* * * *
583521 AAATATTATTTTTATTTTAGGTATTTTAGTTTAAATA-GTTTTAAGT-TTTTAATTA
1 ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTA
583576 GGAAATTAAA
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
74 14 0.12
75 39 0.32
76 68 0.56
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (75 bp):
ATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGG
ATATTATTTT
Found at i:583498 original size:24 final size:24
Alignment explanation
Indices: 583383--583500 Score: 80
Period size: 25 Copynumber: 4.7 Consensus size: 24
583373 TTTTATCTTT
*
583383 GTTTTAGGTATTTTAGTTTAAATAG
1 GTTTTA-GTATTTTAATTTAAATAG
*
583408 GTTTTAGTATTTTAA-TTAAGTTTTAG
1 GTTTTAGTATTTTAATTTAA---ATAG
* ** **
583434 GATATTA-T-TTTTATATTTTATCTTT
1 G-TTTTAGTATTTTA-A-TTTAAATAG
583459 GTTTTAGGTATTTTAATTTAAATAG
1 GTTTTA-GTATTTTAATTTAAATAG
583484 GTTTTAGTATTTTAATT
1 GTTTTAGTATTTTAATT
583501 AGGATTTAGG
Statistics
Matches: 71, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
23 4 0.06
24 23 0.32
25 24 0.34
26 8 0.11
27 9 0.13
28 3 0.04
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (24 bp):
GTTTTAGTATTTTAATTTAAATAG
Found at i:589354 original size:25 final size:23
Alignment explanation
Indices: 589326--589381 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
589316 TACAAAATTT
*
589326 ACAAATTACAATAATTATTAATTAA
1 ACAAATTAC-ATAATT-TAAATTAA
* *
589351 ACAAATATTCATAATTTAAATTAC
1 ACAAAT-TACATAATTTAAATTAA
589375 ACAAATT
1 ACAAATT
589382 TAATATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 12 0.44
25 12 0.44
26 2 0.07
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.36
Consensus pattern (23 bp):
ACAAATTACATAATTTAAATTAA
Found at i:589945 original size:107 final size:107
Alignment explanation
Indices: 589819--590014 Score: 288
Period size: 107 Copynumber: 1.8 Consensus size: 107
589809 ATTAAAAAGG
* * * *
589819 TGAAGAAATAATGATGTAAAAGTTAAAAATAAATAATATTTTAATCATTATAACCTT-TCCATTC
1 TGAAGAAATAATGATGTAAAAGTTAAAAATAAATAATATTTTAATCAATACAAACTTCT-CATGC
589883 ACGTTAAACAACACAACACCAAAAAAAAATGGTTGGGCAACAT
65 ACGTTAAACAACACAACACCAAAAAAAAATGGTTGGGCAACAT
* *
589926 TGAAGAAA-AGATTATGTAAAAGTTAAAAGTAAATAATATTTTAATCAATACAAACTTCTCATGC
1 TGAAGAAATA-ATGATGTAAAAGTTAAAAATAAATAATATTTTAATCAATACAAACTTCTCATGC
* *
589990 ACTTTAAACAACACAACACCCAAAA
65 ACGTTAAACAACACAACACCAAAAA
590015 TATTGGTGTG
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
106 1 0.01
107 77 0.97
108 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (107 bp):
TGAAGAAATAATGATGTAAAAGTTAAAAATAAATAATATTTTAATCAATACAAACTTCTCATGCA
CGTTAAACAACACAACACCAAAAAAAAATGGTTGGGCAACAT
Found at i:590531 original size:20 final size:21
Alignment explanation
Indices: 590506--590598 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
590496 TTTTCCCAAT
*
590506 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
590526 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
590547 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
590567 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
590588 TCGCAATGCGA
1 TCGCAATGCGA
590599 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:590613 original size:41 final size:41
Alignment explanation
Indices: 590506--590598 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
590496 TTTTCCCAAT
590506 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
590547 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
590588 TCGCAATGCGA
1 TCGCAATGCGA
590599 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:590677 original size:20 final size:20
Alignment explanation
Indices: 590631--590681 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
590621 ATACAAAATT
* *
590631 GCAACGAGATACTGACTTTC
1 GCAACGCGATTCTGACTTTC
590651 GCAACGCGATTCTGACTTTC
1 GCAACGCGATTCTGACTTTC
590671 GCAACGCGATT
1 GCAACGCGATT
590682 TACATAGCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (20 bp):
GCAACGCGATTCTGACTTTC
Found at i:591260 original size:19 final size:19
Alignment explanation
Indices: 591200--591280 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
591190 TTCGAGAATG
591200 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
591220 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
591236 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
591253 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
591272 AAAATCGCA
1 AAAATCGCA
591281 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:591298 original size:19 final size:19
Alignment explanation
Indices: 591276--591460 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
591266 GAAACCAAAA
*
591276 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
591295 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
591314 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
591333 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
591353 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
591369 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
591386 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
591400 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
591419 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
591439 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
591459 TC
1 TC
591461 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:591353 original size:39 final size:38
Alignment explanation
Indices: 591276--591460 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
591266 GAAACCAAAA
*
591276 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
591314 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
591353 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
591386 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
591419 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
591459 TC
1 TC
591461 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:591437 original size:20 final size:20
Alignment explanation
Indices: 591403--591460 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
591393 GCGATTCTCT
**
591403 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
591423 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
591443 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
591461 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:593534 original size:21 final size:21
Alignment explanation
Indices: 593510--593576 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
593500 TCATTCCTCG
593510 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
593531 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
593552 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
593573 AGAG
1 AGAG
593577 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:593534 original size:42 final size:42
Alignment explanation
Indices: 593455--593576 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
593445 GCCCGACTCG
* * * * * * *
593455 CTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCC
1 CTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCCA
*
593497 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCCA
* * *
593539 CTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
593577 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 4 0.06
42 60 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (42 bp):
CTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCCA
Found at i:594950 original size:14 final size:14
Alignment explanation
Indices: 594931--594966 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
594921 ATTGTTTAAT
594931 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
594945 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
594959 TGATTTGT
1 TGATTTGT
594967 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:595149 original size:19 final size:20
Alignment explanation
Indices: 595105--595144 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
595095 GCAACGAGAG
595105 AATCGCAACGCGAAAATAAA
1 AATCGCAACGCGAAAATAAA
*
595125 AATCGCAACGCGAAATTAAA
1 AATCGCAACGCGAAAATAAA
595145 TTCGCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.15, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAAAATAAA
Found at i:595167 original size:19 final size:19
Alignment explanation
Indices: 595145--595294 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
595135 CGAAATTAAA
595145 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
595164 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
595179 -CCTCGTTGCGA-TTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
595196 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
595210 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
595229 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
595244 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
595262 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
595281 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
595295 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 29
0.66 0.14 0.20
Matches are distributed among these distances:
14 28 0.29
15 3 0.03
16 3 0.03
17 6 0.06
18 8 0.08
19 37 0.39
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:595191 original size:33 final size:32
Alignment explanation
Indices: 595149--595274 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
595139 ATTAAATTCG
595149 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
595182 CGTTGCGA-TTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
595214 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
595247 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
595275 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
31 3 0.04
32 25 0.30
33 53 0.63
34 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:595236 original size:65 final size:66
Alignment explanation
Indices: 595142--595273 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 66
595132 ACGCGAAATT
*
595142 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGA-TTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
595206 G
66 G
*
595207 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
595272 G
66 G
595273 A
1 A
595274 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 46 0.72
66 18 0.28
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:597560 original size:12 final size:12
Alignment explanation
Indices: 597543--597567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
597533 TCTTCGGGGA
597543 CTTTTTCTTCTT
1 CTTTTTCTTCTT
597555 CTTTTTCTTCTT
1 CTTTTTCTTCTT
597567 C
1 C
597568 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:597773 original size:24 final size:24
Alignment explanation
Indices: 597739--597792 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
597729 CTGAAACATC
*
597739 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
597763 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
597787 ATCAAA
1 ATCAAA
597793 TTTCGAATAC
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:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:597806 original size:24 final size:24
Alignment explanation
Indices: 597755--597806 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
597745 ATCCGTGTAT
** *
597755 TGACCAATATCAAAGTCCGGGTAT
1 TGACCAATATCAAAGTCCGAATAC
* *
597779 TGACCAATATCAAATTTCGAATAC
1 TGACCAATATCAAAGTCCGAATAC
597803 TGAC
1 TGAC
597807 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
TGACCAATATCAAAGTCCGAATAC
Found at i:598847 original size:20 final size:20
Alignment explanation
Indices: 598822--598859 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
598812 ATTCATTTGA
*
598822 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
598842 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
598860 CGCAATGCGA
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:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:598902 original size:33 final size:33
Alignment explanation
Indices: 598865--598935 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
598855 AAAATCGCAA
*
598865 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCAT
** ** **
598898 TGCGATTTTCATTTCGCATTGCGATTTTCTCAT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCAT
598931 TGCGA
1 TGCGA
598936 TAGCCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCAT
Found at i:598919 original size:19 final size:16
Alignment explanation
Indices: 598878--598936 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 16
598868 GAAATGAAAA
598878 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
598894 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
598908 ATTTCGCATTGCGATTTTC
1 ---TCGCATTGCGATTTTC
598927 T--CATTGCGAT
1 TCGCATTGCGAT
598937 AGCCATTTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 20 0.53
16 4 0.11
17 3 0.08
19 11 0.29
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:598936 original size:33 final size:33
Alignment explanation
Indices: 598878--598955 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
598868 GAAATGAAAA
* ***
598878 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCATTGCGATAGCCATT
598911 TCGCATTGCGATTTTCTCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCATTGCGATAGCCATT
*
598944 TCGCGTTGCGAT
1 TCGCATTGCGAT
598956 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCATTGCGATAGCCATT
Done.