Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001190.1 Hibiscus syriacus cultivar Beakdansim tig00002361_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: 54154
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1096 original size:24 final size:24
Alignment explanation
Indices: 1069--1153 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
1059 GATATTAGAA
* *
1069 ATCAAAACAGAATTCAGATCAGAT
1 ATCAGAACAGAATCCAGATCAGAT
* * *
1093 ATCAGAACATAATCCATATCAGAA
1 ATCAGAACAGAATCCAGATCAGAT
* *
1117 ATCAGAACAGAATCCAGGTCAGGT
1 ATCAGAACAGAATCCAGATCAGAT
1141 ATCAGAACAGAAT
1 ATCAGAACAGAAT
1154 TCAAATCATA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATCCAGATCAGAT
Found at i:5462 original size:24 final size:24
Alignment explanation
Indices: 5435--5531 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
5425 GATATTAGAA
**
5435 ATCAAAACAAAATTTAGATCAGAT
1 ATCAAAACAAAATCCAGATCAGAT
* *
5459 ATCAGAACAAAATCCAGATCAGAA
1 ATCAAAACAAAATCCAGATCAGAT
* * * *
5483 ATCAGAACAGAATCCAGGTCAGGT
1 ATCAAAACAAAATCCAGATCAGAT
* * *
5507 ATCAAAACAGAATTCAAATCAGAT
1 ATCAAAACAAAATCCAGATCAGAT
5531 A
1 A
5532 AAATATTCAT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGATCAGAT
Found at i:5488 original size:12 final size:12
Alignment explanation
Indices: 5431--5494 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
5421 CGGAGATATT
*
5431 AGAAATCAAAAC
1 AGAAATCAGAAC
* *
5443 A-AAATTTAGATC
1 AGAAA-TCAGAAC
*
5455 AGATATCAGAAC
1 AGAAATCAGAAC
*
5467 A-AAATCCAGATC
1 AGAAAT-CAGAAC
5479 AGAAATCAGAAC
1 AGAAATCAGAAC
5491 AGAA
1 AGAA
5495 TCCAGGTCAG
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
11 6 0.15
12 27 0.69
13 6 0.15
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (12 bp):
AGAAATCAGAAC
Found at i:19835 original size:17 final size:16
Alignment explanation
Indices: 19796--19863 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
19786 TGTAAAAGAA
*
19796 ATTAATTAAA-TATAAT
1 ATTAAATAAATTA-AAT
*
19812 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
19828 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
19845 ATTAAATATAATAAAAT
1 ATTAAATA-AATTAAAT
19862 AT
1 AT
19864 ACCTTAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
16 19 0.42
17 26 0.58
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:20622 original size:2 final size:2
Alignment explanation
Indices: 20615--20646 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20605 ATCATATACA
20615 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
20647 CTTCATATTT
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):
AT
Found at i:22288 original size:29 final size:30
Alignment explanation
Indices: 22235--22299 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
22225 TCAACAGATG
*
22235 CGTCTTTGTATGGCAGCTTGGAACTCTCGA
1 CGTCTTTGCATGGCAGCTTGGAACTCTCGA
*
22265 CGTCTTTGCATGG-AGGTTGGAACTCTCGA
1 CGTCTTTGCATGGCAGCTTGGAACTCTCGA
*
22294 CATCTT
1 CGTCTT
22300 CAACACAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (30 bp):
CGTCTTTGCATGGCAGCTTGGAACTCTCGA
Found at i:24395 original size:2 final size:2
Alignment explanation
Indices: 24388--24413 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24378 TCTACTTTTA
24388 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
24414 GAATGTTTTT
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:25549 original size:20 final size:19
Alignment explanation
Indices: 25504--25548 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
25494 ACTTGAATTT
*
25504 AAAAAATCAGAAAACATAC
1 AAAAAAACAGAAAACATAC
25523 AAAAAAACAGAAAA-ATTAC
1 AAAAAAACAGAAAACA-TAC
25542 AAAAAAA
1 AAAAAAA
25549 AAAATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.76, C:0.11, G:0.04, T:0.09
Consensus pattern (19 bp):
AAAAAAACAGAAAACATAC
Found at i:25606 original size:115 final size:113
Alignment explanation
Indices: 25410--25625 Score: 274
Period size: 115 Copynumber: 1.9 Consensus size: 113
25400 ACTTGAATTT
* * * *
25410 AAAAAAATCAGAAAAATTACAAAAAAAATAGTATGTTTACGTATCTAATTTTAATGTATTTTTAT
1 AAAAAAATCAGAAAAATTACAAAAAAAATAATATGTTTACGTATCTAATTTCAATATATATTTAT
* * *
25475 CTATCTTGCAAATTAATATACTTGAATTTAAAAAATCAGAAAACATAC
66 CTATATTACAAATTAATATACTTGAATTAAAAAAATCAGAAAACATAC
**
25523 AAAAAAA-CAGAAAAATTACAAAAAAAAAAATTAATATGTTTATTTATCTAATTTCAATATA-AT
1 AAAAAAATCAGAAAAATTAC---AAAAAAAA-TAATATGTTTACGTATCTAATTTCAATATATAT
* * *
25586 TTATCTATATTATAATTTAATATATTTGAATTAAAAAAAT
62 TTATCTATATTACAAATTAATATACTTGAATTAAAAAAAT
25626 TAAATTATAG
Statistics
Matches: 87, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
112 12 0.14
113 7 0.08
115 43 0.49
116 25 0.29
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (113 bp):
AAAAAAATCAGAAAAATTACAAAAAAAATAATATGTTTACGTATCTAATTTCAATATATATTTAT
CTATATTACAAATTAATATACTTGAATTAAAAAAATCAGAAAACATAC
Found at i:28980 original size:28 final size:28
Alignment explanation
Indices: 28947--29000 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
28937 TCCCCGTTGC
**
28947 TTTCAAGCATTTACTCGACGACATAATG
1 TTTCAAGCACATACTCGACGACATAATG
*
28975 TTTCAAGCACATGCTCGACGACATAA
1 TTTCAAGCACATACTCGACGACATAA
29001 CATAGACGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACATACTCGACGACATAATG
Found at i:33828 original size:17 final size:17
Alignment explanation
Indices: 33796--33830 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
33786 TTTCTCACAC
* *
33796 TTAAAGTCTTAGAAAAA
1 TTAAAGTCTCAAAAAAA
33813 TTAAAGTCTCAAAAAAA
1 TTAAAGTCTCAAAAAAA
33830 T
1 T
33831 ATCTATGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (17 bp):
TTAAAGTCTCAAAAAAA
Found at i:37451 original size:149 final size:149
Alignment explanation
Indices: 37174--37616 Score: 544
Period size: 149 Copynumber: 3.0 Consensus size: 149
37164 GTAACGTCAG
* * * * * * * * *
37174 GAGGAAGTCTACCTACCAATGAGACAAGCCATACATCTGCCTGCTGAGCTAACAAGTTGGACTCG
1 GAGGGAGTCTATCTACCAAGGAGACGATCCATACATTTGCCTACTGAGGTAACAAGTTAGACTCG
* * * * ** * *
37239 AGACAATTCGACGCTGAAGCCAACAATTGAAGATCACGAATTAGCTCGAAAGATTTCTAGAAGTA
66 AGACGATTCAACACCGAAGCCAACAATTGAAGATCACGAACCAGCTCGAAAGATTTTTGGAAGTA
*
37304 GGAAATGAAGTAGAAGCTA
131 GGAAATGAAGTAGAAGATA
* *
37323 GAGGGAGTCTATCTACCAAGGAGACGATCCAGACATTTGCCTACTGAGGTAACAAGTTAGACTTG
1 GAGGGAGTCTATCTACCAAGGAGACGATCCATACATTTGCCTACTGAGGTAACAAGTTAGACTCG
* * * *
37388 AGACGATTCAACTCCGAAGCCAACAGTTGAAGATCACAAACCAACTCGAAAGATTTTTGGAAGTA
66 AGACGATTCAACACCGAAGCCAACAATTGAAGATCACGAACCAGCTCGAAAGATTTTTGGAAGTA
* * *
37453 AGAAAGGAAGTAGGAGATA
131 GGAAATGAAGTAGAAGATA
* * * *
37472 GAGAGAGTCTATCTACCAAGGAGACGATCCATATATTTTCCTATTGAGGTAACAAGTTAGACTCG
1 GAGGGAGTCTATCTACCAAGGAGACGATCCATACATTTGCCTACTGAGGTAACAAGTTAGACTCG
* * ** * *
37537 AGAAGATTCAACACCGAAGTCAACAATTGAAGATTGCGAACCAGCTCGAAATATTTTTGAAAGTA
66 AGACGATTCAACACCGAAGCCAACAATTGAAGATCACGAACCAGCTCGAAAGATTTTTGGAAGTA
*
37602 GGAGATGAAGTAGAA
131 GGAAATGAAGTAGAA
37617 ATTTTGAAGA
Statistics
Matches: 248, Mismatches: 46, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
149 248 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (149 bp):
GAGGGAGTCTATCTACCAAGGAGACGATCCATACATTTGCCTACTGAGGTAACAAGTTAGACTCG
AGACGATTCAACACCGAAGCCAACAATTGAAGATCACGAACCAGCTCGAAAGATTTTTGGAAGTA
GGAAATGAAGTAGAAGATA
Found at i:38689 original size:2 final size:2
Alignment explanation
Indices: 38682--38716 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38672 TGTATACCCA
*
38682 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38717 ATGTTGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40182 original size:36 final size:36
Alignment explanation
Indices: 40133--40291 Score: 230
Period size: 36 Copynumber: 4.4 Consensus size: 36
40123 CTTTGAATTT
*
40133 GTTTCCCTTGAAACAAGA-TTTGTCTCCCTTGAGATA
1 GTTTCCCTTGAAACAA-ATTTTGTCTCCCTTGAGACA
* *
40169 GTTTCCCTAGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
40205 GTTTCCTTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* **
40241 GTTTCTCTTGAAACAAATTTTGTCTCTATTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
40277 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
40292 TAAAATCTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 1 0.01
36 111 0.99
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:40318 original size:31 final size:30
Alignment explanation
Indices: 40277--40389 Score: 84
Period size: 31 Copynumber: 3.5 Consensus size: 30
40267 TATTGAGACA
*
40277 GTTTCTCTTGAAACATAAAATCTTTGAATCT
1 GTTTCCCTTGAAACATAAAATCTTTGAAT-T
** *
40308 GTTTCCCTTGAAACA-AAGTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACATAA----AATCT-TTGA-ATT
* * *
40343 GTTTCTCTTGAAACACAAAATCTTTGAGTTT
1 GTTTCCCTTGAAACATAAAATCTTTGA-ATT
40374 GTTTCCCTTGAAACAT
1 GTTTCCCTTGAAACAT
40390 GTTTTATCTC
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
30 2 0.03
31 34 0.53
32 3 0.05
34 3 0.05
35 18 0.28
36 4 0.06
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (30 bp):
GTTTCCCTTGAAACATAAAATCTTTGAATT
Found at i:40413 original size:133 final size:134
Alignment explanation
Indices: 40241--40491 Score: 328
Period size: 133 Copynumber: 1.9 Consensus size: 134
40231 CCTTGAGACA
* * * *
40241 GTTTCTCTTGAAACAAATTTTGTCTCTATTGAGACAGTTTCTCTTGAAACATAAAATCTTTGA-A
1 GTTTCCCTTGAAACAAATTTTATCTCTACTGAGACAGTTTCTCTTGAAACA-AAAACCTTTGAGA
* * * * *
40305 TCTGTTTCCCTTGAAACAAA-GTTGTCTCTCTTGAGA-TAGTTTCTCTTGAAACACAAAATCTTT
65 T-TGTTTCCCTCGAAACAAATGTTGTCTCGCTTGAGACAAATTTCCCTTGAAACACAAAATCTTT
40368 GAGTTT
129 GAGTTT
** * **
40374 GTTTCCCTTGAAACATGTTTTATCTCTCCTGAGACAGTTTCTCTTGAAACACCAACCTTTGAGAT
1 GTTTCCCTTGAAACAAATTTTATCTCTACTGAGACAGTTTCTCTTGAAACAAAAACCTTTGAGAT
*
40439 TGTTTCCCTCGAAACAAATTTTGTCTCGCTTGAGACAAATTTCCCTTGAAACA
66 TGTTTCCCTCGAAACAAATGTTGTCTCGCTTGAGACAAATTTCCCTTGAAACA
40492 AGAAATTTTA
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
132 25 0.25
133 61 0.61
134 14 0.14
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (134 bp):
GTTTCCCTTGAAACAAATTTTATCTCTACTGAGACAGTTTCTCTTGAAACAAAAACCTTTGAGAT
TGTTTCCCTCGAAACAAATGTTGTCTCGCTTGAGACAAATTTCCCTTGAAACACAAAATCTTTGA
GTTT
Found at i:40424 original size:67 final size:67
Alignment explanation
Indices: 40169--40491 Score: 330
Period size: 66 Copynumber: 4.8 Consensus size: 67
40159 CCTTGAGATA
* **
40169 GTTTCCCTAGAAACAAATTTTGTCTCTCTTGAGACAGTTTC-CTTTGAAACA-AATTTTGTCTCC
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTC-TTGAAACACAA---AATCT--
***
40232 CTTGAGACA
60 -TTGAGTTT
* * * *
40241 GTTTCTCTTGAAACAAATTTTGTCTCTATTGAGACAGTTTCTCTTGAAACATAAAATCTTTGAAT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAGT
*
40306 CT
66 TT
* *
40308 GTTTCCCTTGAAACAAA-GTTGTCTCTCTTGAGATAGTTTCTCTTGAAACACAAAATCTTTGAGT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAGT
40372 TT
66 TT
** * * * * *
40374 GTTTCCCTTGAAACATGTTTTATCTCTCCTGAGACAGTTTCTCTTGAAACAC-CAACCTTTGAGA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAGT
40438 TT
66 TT
* * * *
40440 GTTTCCCTCGAAACAAATTTTGTCTCGCTTGAGACAAATTTCCCTTGAAACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC-AGTTTCTCTTGAAACA
40492 AGAAATTTTA
Statistics
Matches: 215, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
66 98 0.46
67 65 0.30
70 3 0.01
72 46 0.21
73 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (67 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTGAGT
TT
Found at i:41833 original size:21 final size:21
Alignment explanation
Indices: 41807--41848 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41797 CCAGAATGGG
*
41807 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
41828 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
41849 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:44222 original size:34 final size:32
Alignment explanation
Indices: 44169--44238 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
44159 CCTTACAAAC
*
44169 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
44201 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
44235 TCCC
1 TCCC
44239 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:44549 original size:21 final size:21
Alignment explanation
Indices: 44523--44562 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44513 AGAATGGGGG
* *
44523 GAATCGGTACCCTTTCATAGA
1 GAATCGATACCCCTTCATAGA
44544 GAATCGATACCCCTTCATA
1 GAATCGATACCCCTTCATA
44563 CTGTTCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
GAATCGATACCCCTTCATAGA
Found at i:44685 original size:29 final size:31
Alignment explanation
Indices: 44653--44712 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
44643 AAATTTTGAA
*
44653 TAAATTCAA-TTAAGTCCAAATA-CATTTTG
1 TAAATTCAATTTAAGTCCAAAAACCATTTTG
44682 TAAATTCAATTTAAGTCCAAAAACCATTTTG
1 TAAATTCAATTTAAGTCCAAAAACCATTTTG
44713 CCTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 12 0.43
31 7 0.25
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTTAAGTCCAAAAACCATTTTG
Found at i:49689 original size:14 final size:14
Alignment explanation
Indices: 49666--49703 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
49656 TCTGTCTATA
*
49666 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
49679 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
49694 TGCAGGGATT
1 TGCAGGGATT
49704 ACTGCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:50011 original size:19 final size:20
Alignment explanation
Indices: 49985--50025 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49975 TTCTTTTTAA
*
49985 ATTTTTAATAATTAATTTTT
1 ATTTTAAATAATTAATTTTT
* *
50005 ATTTTAAATATTTATTTTTT
1 ATTTTAAATAATTAATTTTT
50025 A
1 A
50026 AACATTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTAAATAATTAATTTTT
Found at i:50169 original size:21 final size:21
Alignment explanation
Indices: 50130--50171 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
50120 TCATTATTTA
*
50130 TTGTGAACAATCATATCAATG
1 TTGTGAACAATCACATCAATG
*
50151 TTGTGAACAATCACGTCAATG
1 TTGTGAACAATCACATCAATG
50172 CTATCAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (21 bp):
TTGTGAACAATCACATCAATG
Found at i:52938 original size:59 final size:59
Alignment explanation
Indices: 52865--52983 Score: 197
Period size: 59 Copynumber: 2.0 Consensus size: 59
52855 AAGGAAAAAG
*
52865 AAAACTTGCA-TTTTTCAGATAAATCAGACTATTTTTTAGAGTTTATTATATCCAAACAC
1 AAAACTTGCATTTTTTCAGATAAATCAGACTA-TTTTTAGAGTTTATTACATCCAAACAC
52924 AAAACTTG-AGTTTTTTCAGATAAATCAGACTATTTTTAGAGTTTATTACATCCAAACAC
1 AAAACTTGCA-TTTTTTCAGATAAATCAGACTATTTTTAGAGTTTATTACATCCAAACAC
52983 A
1 A
52984 CACACATATT
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
58 1 0.02
59 35 0.61
60 21 0.37
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (59 bp):
AAAACTTGCATTTTTTCAGATAAATCAGACTATTTTTAGAGTTTATTACATCCAAACAC
Done.