Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002019.1 Hibiscus syriacus cultivar Beakdansim tig00004123_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: 98956
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:359 original size:16 final size:16
Alignment explanation
Indices: 334--364 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
324 TCGACACGAG
334 TTCTCCAACATACATA
1 TTCTCCAACATACATA
*
350 TTCTCGAACATACAT
1 TTCTCCAACATACAT
365 CAAACACGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (16 bp):
TTCTCCAACATACATA
Found at i:8715 original size:26 final size:24
Alignment explanation
Indices: 8653--8703 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
8643 GTTTTTATTG
8653 TTTATAAAATTTTGGAATTTTTTC
1 TTTATAAAATTTTGGAATTTTTTC
8677 TTTATAAAATTTTGGAATTTTTT-
1 TTTATAAAATTTTGGAATTTTTTC
8700 TTTA
1 TTTA
8704 AATTATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (24 bp):
TTTATAAAATTTTGGAATTTTTTC
Found at i:10326 original size:15 final size:16
Alignment explanation
Indices: 10297--10329 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
10287 TTAAATTATT
10297 TTAAAATATAAATATA
1 TTAAAATATAAATATA
10313 TTAAAATA-AAATATA
1 TTAAAATATAAATATA
10328 TT
1 TT
10330 TTAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATATAAATATA
Found at i:10335 original size:16 final size:16
Alignment explanation
Indices: 10289--10340 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
10279 ACTTATTTTT
10289 AAAT-TATTTTAAAATA
1 AAATATATTTT-AAATA
*
10305 TAAATATA-TTAAAATA
1 -AAATATATTTTAAATA
10321 AAATATATTTTAAATTA
1 AAATATATTTTAAA-TA
10338 AAA
1 AAA
10341 AAAATTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 7 0.23
16 10 0.33
17 11 0.37
18 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATTTTAAATA
Found at i:22223 original size:16 final size:16
Alignment explanation
Indices: 22202--22238 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
22192 AACAATTATG
22202 AAAGGGAAAA-AAAAGA
1 AAAGGGAAAAGAAAA-A
22218 AAAGGGAAAAGAAAAA
1 AAAGGGAAAAGAAAAA
22234 AAAGG
1 AAAGG
22239 TACCTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAAGGGAAAAGAAAAA
Found at i:26780 original size:2 final size:2
Alignment explanation
Indices: 26773--26806 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26763 CAAAAGTAAC
26773 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
26807 CAAATTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33148 original size:2 final size:2
Alignment explanation
Indices: 33141--33166 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33131 AAAGACATAC
33141 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
33167 TATTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39532 original size:6 final size:6
Alignment explanation
Indices: 39521--39553 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
39511 TATGCATACG
*
39521 ATATCT ATATCT ATATCT ATATCT ATATAT ATA
1 ATATCT ATATCT ATATCT ATATCT ATATCT ATA
39554 AATTTATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATCT
Found at i:41626 original size:37 final size:37
Alignment explanation
Indices: 41550--41626 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
41540 TTTTTATATT
*
41550 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
41587 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
41624 TTT
1 TTT
41627 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:47514 original size:2 final size:2
Alignment explanation
Indices: 47509--47534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47499 TTATTTTTAA
47509 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
47535 TACTTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48936 original size:3 final size:3
Alignment explanation
Indices: 48928--48954 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48918 CCCTATAAAT
48928 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
48955 AACCAGTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54251 original size:2 final size:2
Alignment explanation
Indices: 54241--54293 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
54231 TTTTTGTGTG
*
54241 TA TA CA TA TA 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 TA TA TA TA TA
54283 TA TA TA TA TA T
1 TA TA TA TA TA T
54294 GTATGTGTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55831 original size:23 final size:22
Alignment explanation
Indices: 55776--55832 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
55766 AAAATAAAAA
*
55776 ATTTATATTATATTTTAAAATT
1 ATTTATAATATATTTTAAAATT
*
55798 ATTAATAAATATATTTTAAGGAATT
1 ATTTAT-AATATATTTTAA--AATT
55823 -TTTATAATAT
1 ATTTATAATAT
55833 TATAGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.17
23 16 0.55
24 4 0.14
25 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTATAATATATTTTAAAATT
Found at i:66163 original size:32 final size:32
Alignment explanation
Indices: 66099--66190 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 32
66089 TCGAATTACA
* *
66099 TAGTTCAATATCCAAACATAATT-AAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
66130 TAGTCCAACATCCAAACATAATTAAAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
66162 TAGTCCAACATCCAAACATAATTAAAAAA
1 TAGTCCAACATCCAAACATAATTAAAAAA
66191 AATATCATGT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 21 0.36
32 37 0.64
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.26
Consensus pattern (32 bp):
TAGTCCAACATCCAAACATAATTAAAAAATGT
Found at i:66321 original size:31 final size:31
Alignment explanation
Indices: 66286--66462 Score: 111
Period size: 31 Copynumber: 5.3 Consensus size: 31
66276 AAAATAATCG
66286 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
** ** ** *
66317 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATGG
1 AGTGACCAAA-ACATAAATTA-GAT-AAT-AT-AT-A
66354 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
* ** ** * *
66385 AGTGACCAAATAGATAGTTTACCCTAAATAACAATCG
1 AGTGACCAAA-ACATAAATTA-GAT-AAT-A-TAT-A
66422 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
*
66453 AGTAACCAAA
1 AGTGACCAAA
66463 TAGGTAGTTT
Statistics
Matches: 105, Mismatches: 29, Indels: 24
0.66 0.18 0.15
Matches are distributed among these distances:
31 29 0.28
32 17 0.16
33 5 0.05
34 12 0.11
35 5 0.05
36 17 0.16
37 20 0.19
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTAGATAATATATA
Found at i:66357 original size:68 final size:68
Alignment explanation
Indices: 66278--66480 Score: 370
Period size: 68 Copynumber: 3.0 Consensus size: 68
66268 TTTGGAAAAA
66278 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
66343 AAT
66 AAT
* *
66346 AATAATGGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGATAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
66411 AAT
66 AAT
* *
66414 AACAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTAACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
66479 AA
66 AA
66481 AAAATCCCTA
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 129 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (68 bp):
AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
AAT
Found at i:66358 original size:37 final size:36
Alignment explanation
Indices: 66307--66431 Score: 107
Period size: 37 Copynumber: 3.5 Consensus size: 36
66297 CATAAATTAG
* *
66307 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATA-ATGAGTGACCAAATAGATAGTTTACCCTAA
* ** **
66344 ATAATAATGGAGTGACCAAA-ACATAAATTA-GAT-A
1 ATAATAAT-GAGTGACCAAATAGATAGTTTACCCTAA
*
66378 AT-AT-ATAAGTGACCAAATAGATAGTTTACCCTAA
1 ATAATAATGAGTGACCAAATAGATAGTTTACCCTAA
*
66412 ATAACAATCGAGTGACCAAA
1 ATAATAAT-GAGTGACCAAA
66432 ACATAAATTA
Statistics
Matches: 66, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
31 10 0.15
32 9 0.14
33 3 0.05
34 6 0.09
35 2 0.03
36 10 0.15
37 26 0.39
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (36 bp):
ATAATAATGAGTGACCAAATAGATAGTTTACCCTAA
Found at i:75132 original size:2 final size:2
Alignment explanation
Indices: 75127--75153 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
75117 AAAAAAAAAT
75127 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 T
75154 TGAAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77046 original size:4 final size:4
Alignment explanation
Indices: 77039--77075 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
77029 AACATCACAC
*
77039 ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
77076 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:77080 original size:4 final size:4
Alignment explanation
Indices: 77045--77105 Score: 68
Period size: 4 Copynumber: 15.2 Consensus size: 4
77035 ACACACATAC
* * * * * *
77045 ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
77093 ATAT ATAT ATAT A
1 ATAT ATAT ATAT A
77106 CAGAGAGAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:81129 original size:21 final size:21
Alignment explanation
Indices: 81105--81164 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
81095 ACTAAATCAC
81105 TAAAAAATTAAATATATATAT
1 TAAAAAATTAAATATATATAT
* *
81126 TAAAAATACTAAA-ACTA-CTAT
1 TAAAAA-ATTAAATA-TATATAT
81147 T-AAAAATTAAATATATAT
1 TAAAAAATTAAATATATAT
81165 TATAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
19 7 0.23
20 6 0.19
21 11 0.35
22 7 0.23
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAATTAAATATATATAT
Found at i:81171 original size:18 final size:17
Alignment explanation
Indices: 81120--81180 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 17
81110 AATTAAATAT
81120 ATATATTAAAAATACTAAA
1 ATATATTAAAAAT--TAAA
81139 ACTACTATTAAAAATTAAA
1 A-TA-TATTAAAAATTAAA
*
81158 TATATATTATAAATTAAA
1 -ATATATTAAAAATTAAA
81176 ATATA
1 ATATA
81181 ATTTGTAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 5 0.13
18 13 0.34
19 7 0.18
20 3 0.08
21 10 0.26
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATATTAAAAATTAAA
Found at i:81195 original size:29 final size:26
Alignment explanation
Indices: 81161--81224 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
81151 AATTAAATAT
* *
81161 ATATTATAAATTAAAATATAATTTGTAA
1 ATATTATAAAAT-AAACATAATTT-TAA
*
81189 AGTATTAAAAAATAAACATAATTTTAA
1 A-TATTATAAAATAAACATAATTTTAA
81216 ATATATATA
1 ATAT-TATA
81225 TTATGCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
26 3 0.10
27 7 0.23
28 11 0.37
29 9 0.30
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (26 bp):
ATATTATAAAATAAACATAATTTTAA
Found at i:81533 original size:20 final size:22
Alignment explanation
Indices: 81493--81548 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
81483 ATATATATAT
81493 TATTTAAATTTTTAGTAATTTAA
1 TATTT-AATTTTTAGTAATTTAA
*
81516 TATTT-ATTTTTAGT-ATTTTA
1 TATTTAATTTTTAGTAATTTAA
81536 TATTTAATTTTTA
1 TATTTAATTTTTA
81549 TTGAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.32
21 16 0.52
23 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TATTTAATTTTTAGTAATTTAA
Found at i:83527 original size:41 final size:41
Alignment explanation
Indices: 83456--83732 Score: 229
Period size: 41 Copynumber: 6.7 Consensus size: 41
83446 CGCAACTCAG
* * * * *
83456 TTTCCAAATTCACGTTGCGATAGTTCAAAATCACAACGCGA
1 TTTCCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGA
*
83497 TTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGA
1 TTTCCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGA
* * * * * * * *
83538 TTTTCCAT-TTCGCGTTGCGAT-TTGCAGATTCGTATTGCGAAGA
1 -TTTCCATATTCGCATTGCGATAGTCCAAAATCGCA--ACG-CGA
* * *
83581 TTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGTGA
1 TTTCCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGA
* * * * **
83622 TTTTCCAT-TTCGCGTTGCGAT-TTGCAAATTCGCATTGCGA
1 -TTTCCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGA
* *
83662 TTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACACGA
1 TTTCCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGA
* * *
83703 TTTTCAGATTCGCATTACGATAGTCCAAAA
1 TTTCCATATTCGCATTGCGATAGTCCAAAA
83733 CCTTAAGTCT
Statistics
Matches: 182, Mismatches: 45, Indels: 18
0.74 0.18 0.07
Matches are distributed among these distances:
39 6 0.03
40 33 0.18
41 101 0.55
42 20 0.11
43 14 0.08
44 8 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (41 bp):
TTTCCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGA
Found at i:83537 original size:21 final size:21
Alignment explanation
Indices: 83472--83538 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
83462 AATTCACGTT
* *
83472 GCGATAGTTCAAAATCACAAC
1 GCGATAGTCCAAAATCGCAAC
* * * * **
83493 GCGAT-TTGCATATTCGCATT
1 GCGATAGTCCAAAATCGCAAC
83513 GCGATAGTCCAAAATCGCAAC
1 GCGATAGTCCAAAATCGCAAC
83534 GCGAT
1 GCGAT
83539 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
GCGATAGTCCAAAATCGCAAC
Found at i:83569 original size:20 final size:20
Alignment explanation
Indices: 83546--83682 Score: 87
Period size: 20 Copynumber: 6.7 Consensus size: 20
83536 GATTTTCCAT
*
83546 TTCGCGTTGCGATTTGCAGA
1 TTCGCATTGCGATTTGCAGA
* *
83566 TTCGTATTGCGAAGATTTTCAGA
1 TTCGCATTGC---GATTTGCAGA
* * *
83589 TTCGCATTGCGATAGTCCAAA
1 TTCGCATTGCGAT-TTGCAGA
* ** * * *
83610 ATCGCAACGTGATTTTCCA-T
1 TTCGCATTGCGA-TTTGCAGA
* *
83630 TTCGCGTTGCGATTTGCAAA
1 TTCGCATTGCGATTTGCAGA
*
83650 TTCGCATTGCGATTTGCATA
1 TTCGCATTGCGATTTGCAGA
83670 TTCGCATTGCGAT
1 TTCGCATTGCGAT
83683 AGTCCAAAAT
Statistics
Matches: 89, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
19 5 0.06
20 49 0.55
21 16 0.18
22 1 0.01
23 18 0.20
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
TTCGCATTGCGATTTGCAGA
Found at i:83588 original size:23 final size:23
Alignment explanation
Indices: 83556--83600 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
83546 TTCGCGTTGC
*
83556 GATTTGCAGATTCGTATTGCGAA
1 GATTTGCAGATTCGCATTGCGAA
*
83579 GATTTTCAGATTCGCATTGCGA
1 GATTTGCAGATTCGCATTGCGA
83601 TAGTCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (23 bp):
GATTTGCAGATTCGCATTGCGAA
Found at i:83603 original size:84 final size:81
Alignment explanation
Indices: 83493--83707 Score: 349
Period size: 84 Copynumber: 2.6 Consensus size: 81
83483 AAATCACAAC
83493 GCGATTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGA
1 GCGATTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGA
* *
83558 TTTGCAGATTCGTATT
66 TTTGCAAATTCGCATT
* * *
83574 GCGAAGATTTTCAGATTCGCATTGCGATAGTCCAAAATCGCAACGTGATTTTCCATTTCGCGTTG
1 GC---GATTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCCATTTCGCGTTG
83639 CGATTTGCAAATTCGCATT
63 CGATTTGCAAATTCGCATT
*
83658 GCGATTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACACGATTTTC
1 GCGATTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTC
83708 AGATTCGCAT
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
81 46 0.38
84 76 0.62
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (81 bp):
GCGATTTGCATATTCGCATTGCGATAGTCCAAAATCGCAACGCGATTTTCCATTTCGCGTTGCGA
TTTGCAAATTCGCATT
Found at i:83722 original size:20 final size:20
Alignment explanation
Indices: 83639--83723 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
83629 TTTCGCGTTG
*
83639 CGATTTGCAAATTCGCATTG
1 CGATTTGCAAATTCGCATTA
* *
83659 CGATTTGCATATTCGCATTG
1 CGATTTGCAAATTCGCATTA
* * * **
83679 CGATAGTCCAAAATCGCAACA
1 CGAT-TTGCAAATTCGCATTA
* *
83700 CGATTTTCAGATTCGCATTA
1 CGATTTGCAAATTCGCATTA
83720 CGAT
1 CGAT
83724 AGTCCAAAAC
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 37 0.74
21 13 0.26
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (20 bp):
CGATTTGCAAATTCGCATTA
Found at i:84240 original size:41 final size:41
Alignment explanation
Indices: 84183--84305 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 41
84173 CGTTTTACCG
* *
84183 TTGCGATTTTAGACTATCGTAATGCGAATATGCAAATCGCA
1 TTGCGATTTTGGACTATCGCAATGCGAATATGCAAATCGCA
* *
84224 TTGCGATTTTGGACTATCGCAATGCGAATCTGCAAATCGCG
1 TTGCGATTTTGGACTATCGCAATGCGAATATGCAAATCGCA
* *
84265 TTGCGATTTTGGACTATCGCAACGCGAA-ATGGAAAATCGCA
1 TTGCGATTTTGGACTATCGCAATGCGAATAT-GCAAATCGCA
84306 ACGCGAATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 72 0.99
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (41 bp):
TTGCGATTTTGGACTATCGCAATGCGAATATGCAAATCGCA
Found at i:84243 original size:21 final size:21
Alignment explanation
Indices: 84183--84285 Score: 75
Period size: 20 Copynumber: 5.0 Consensus size: 21
84173 CGTTTTACCG
* *
84183 TTGCGATTTTAGACTATCGTA
1 TTGCGATTTTGGACTATCGCA
* * * * *
84204 ATGCGAATATGCA-AATCGCA
1 TTGCGATTTTGGACTATCGCA
84224 TTGCGATTTTGGACTATCGCA
1 TTGCGATTTTGGACTATCGCA
* * * * * *
84245 ATGCGAATCTGCA-AATCGCG
1 TTGCGATTTTGGACTATCGCA
84265 TTGCGATTTTGGACTATCGCA
1 TTGCGATTTTGGACTATCGCA
84286 ACGCGAAATG
Statistics
Matches: 56, Mismatches: 24, Indels: 4
0.67 0.29 0.05
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (21 bp):
TTGCGATTTTGGACTATCGCA
Found at i:85771 original size:2 final size:2
Alignment explanation
Indices: 85766--85795 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
85756 TTACATATTT
85766 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
85796 AGTTAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86509 original size:34 final size:33
Alignment explanation
Indices: 86433--86539 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
86423 GTGGTAAGAA
* *
86433 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
86467 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
86502 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
86536 ATTT
1 ATTT
86540 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:86521 original size:36 final size:34
Alignment explanation
Indices: 86466--86544 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
86456 TTTAAATAGT
*
86466 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
86498 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
86532 TATTATTTATTTA
1 TATTATTTTTTTA
86545 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:86708 original size:17 final size:17
Alignment explanation
Indices: 86686--86739 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
86676 AATGTTAATA
86686 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
86703 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
86720 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
86737 TTT
1 TTT
86740 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:87379 original size:35 final size:35
Alignment explanation
Indices: 87339--87450 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
87329 TCTAAACCTT
* * *
87339 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
87374 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
87409 AAATTGAATTAATTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
87444 AAATTGA
1 AAATTGA
87451 GGACTGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Done.