Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006135.1 Hibiscus syriacus cultivar Beakdansim tig00014552_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: 53459
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:911 original size:24 final size:25
Alignment explanation
Indices: 876--924 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
866 TTTTGACTAA
876 AATGAATAGTTTG-AAATATTTTAC
1 AATGAATAGTTTGAAAATATTTTAC
*
900 AATGAATTGTTTGAAAATATTTTAC
1 AATGAATAGTTTGAAAATATTTTAC
925 GCTTCGAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (25 bp):
AATGAATAGTTTGAAAATATTTTAC
Found at i:10353 original size:45 final size:45
Alignment explanation
Indices: 10174--10356 Score: 240
Period size: 45 Copynumber: 4.1 Consensus size: 45
10164 AATACCATGA
* ** * *
10174 GTGGCACCTTTTATACCGTTAATGCACCGTTATGCATTTTCATTA
1 GTGGCACCTTTTATGCCAATAATGCACAGTTATGCATTTTCATTT
* * *
10219 GTGGCACATTTTATGCCAAAAATGCACCGTTATGCATTTTCATTT
1 GTGGCACCTTTTATGCCAATAATGCACAGTTATGCATTTTCATTT
** *
10264 GTGGCACCTTTTATGCTGATAATGCACAGTCATGCATTTTCATTT
1 GTGGCACCTTTTATGCCAATAATGCACAGTTATGCATTTTCATTT
* **
10309 GTGGCACCTTTTATGTCAATAATGCACAGTTACACATTTTCATTT
1 GTGGCACCTTTTATGCCAATAATGCACAGTTATGCATTTTCATTT
10354 GTG
1 GTG
10357 TTCATCCATT
Statistics
Matches: 120, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 120 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
GTGGCACCTTTTATGCCAATAATGCACAGTTATGCATTTTCATTT
Found at i:11276 original size:14 final size:14
Alignment explanation
Indices: 11257--11283 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11247 TATATAGTGA
11257 ACCTTTTTTCTAGT
1 ACCTTTTTTCTAGT
11271 ACCTTTTTTCTAG
1 ACCTTTTTTCTAG
11284 GTCTGAAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (14 bp):
ACCTTTTTTCTAGT
Found at i:12208 original size:10 final size:10
Alignment explanation
Indices: 12193--12221 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
12183 TCAATACCTT
12193 TATTGCATTG
1 TATTGCATTG
12203 TATTGCATTG
1 TATTGCATTG
12213 TATTGCATT
1 TATTGCATT
12222 TGCAATTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (10 bp):
TATTGCATTG
Found at i:23304 original size:22 final size:22
Alignment explanation
Indices: 23276--23321 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
23266 GGAGTAGTAA
23276 AGCTTGCACAAATGCTCATGGT
1 AGCTTGCACAAATGCTCATGGT
23298 AGCTTGCACAAATGCTCATGGT
1 AGCTTGCACAAATGCTCATGGT
23320 AG
1 AG
23322 ATTACACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (22 bp):
AGCTTGCACAAATGCTCATGGT
Found at i:23329 original size:22 final size:22
Alignment explanation
Indices: 23282--23329 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
23272 GTAAAGCTTG
* *
23282 CACAAATGCTCATGGTAGCTTG
1 CACAAATGCTCATGGTAGATTA
23304 CACAAATGCTCATGGTAGATTA
1 CACAAATGCTCATGGTAGATTA
23326 CACA
1 CACA
23330 TTTTGATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (22 bp):
CACAAATGCTCATGGTAGATTA
Found at i:25419 original size:3 final size:3
Alignment explanation
Indices: 25411--25472 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
25401 GAGTTCTTTA
25411 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
25459 TAT TGT TAT TAT TA
1 TAT TAT TAT TAT TA
25473 ATAATATCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:28827 original size:2 final size:2
Alignment explanation
Indices: 28815--28851 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
28805 GTTTTAGCTG
28815 AT AT GAT 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
28852 GGATTGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35686 original size:5 final size:5
Alignment explanation
Indices: 35676--35706 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
35666 GAGAGCGATC
*
35676 GAAAG GAAAG GAAAA GAAAG GAAAG GAAAG G
1 GAAAG GAAAG GAAAG GAAAG GAAAG GAAAG G
35707 GCAGAATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:36371 original size:21 final size:21
Alignment explanation
Indices: 36345--36442 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 21
36335 GCGAATAAGT
36345 AAATCGCAACGCGATTTGGGA
1 AAATCGCAACGCGATTTGGGA
*
36366 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGATTTGGGA
* * ** *
36387 AAATCGCAATGCGA-ATAAGT
1 AAATCGCAACGCGATTTGGGA
36407 AAATCGCAACGCGATTTGGGA
1 AAATCGCAACGCGATTTGGGA
* *
36428 AAATCACAATGCGAT
1 AAATCGCAACGCGAT
36443 ACTGACTATC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 15 0.24
21 48 0.76
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
AAATCGCAACGCGATTTGGGA
Found at i:36459 original size:20 final size:20
Alignment explanation
Indices: 36438--36544 Score: 90
Period size: 20 Copynumber: 5.3 Consensus size: 20
36428 AAATCACAAT
*
36438 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* * *
36458 GCGATAAT-ACAAAATCGTAAC
1 GCGATACTGAC--TATCGCAAC
* * *
36479 GAGATACTTACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
36499 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* * *
36519 GCGATTCTGACTTTCACAAC
1 GCGATACTGACTATCGCAAC
36539 GCGATA
1 GCGATA
36545 ATACATAATC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
19 2 0.03
20 54 0.77
21 12 0.17
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:36474 original size:62 final size:60
Alignment explanation
Indices: 36328--36461 Score: 180
Period size: 62 Copynumber: 2.2 Consensus size: 60
36318 TTTTCCCAAT
* *
36328 TCGCAATGCGAATAAGTAAATCGCAACGCGATTTGGGAAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAG-AAATCGCAACGCGATTTGGGAAAATCACAACGCGAACT-GGAAAA
* **
36390 TCGCAATGCGAATAAGTAAATCGCAACGCGATTTGGGAAAATCACAATGCGATACT-GACTA
1 TCGCAATGCGAATAAG-AAATCGCAACGCGATTTGGGAAAATCACAACGCGA-ACTGGAAAA
36451 TCGCAATGCGA
1 TCGCAATGCGA
36462 TAATACAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
61 14 0.21
62 50 0.76
63 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.19
Consensus pattern (60 bp):
TCGCAATGCGAATAAGAAATCGCAACGCGATTTGGGAAAATCACAACGCGAACTGGAAAA
Found at i:36760 original size:22 final size:22
Alignment explanation
Indices: 36732--36775 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36722 CACTCTCTCA
36732 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
36754 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
36776 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:37201 original size:12 final size:11
Alignment explanation
Indices: 37172--37199 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
37162 TATTTTTGGT
37172 ATTTTTATTTA
1 ATTTTTATTTA
37183 ATTTTTATTTA
1 ATTTTTATTTA
37194 ATTTTT
1 ATTTTT
37200 TAAATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTTATTTA
Found at i:39202 original size:38 final size:37
Alignment explanation
Indices: 39128--39210 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
39118 GAAGTTTAGT
* *
39128 TTTGTTTCATACCGGGTGTTCTATGACCGTGAAAAGC
1 TTTGTTTCATACAGGGTGTGCTATGACCGTGAAAAGC
* *
39165 TTTGTTTCATACAGGCTTGTGCTATGACTGT-ACAAAGC
1 TTTGTTTCATACAGG-GTGTGCTATGACCGTGA-AAAGC
39203 TGTTGTTT
1 T-TTGTTT
39211 TCAGACAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 15 0.38
38 18 0.46
39 6 0.15
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (37 bp):
TTTGTTTCATACAGGGTGTGCTATGACCGTGAAAAGC
Found at i:39831 original size:31 final size:31
Alignment explanation
Indices: 39783--39852 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
39773 CGTGGCACTG
*
39783 CCACATCATCATCTATGATGATTTGTGCATA
1 CCACGTCATCATCTATGATGATTTGTGCATA
* *
39814 CCACGTCATCATGTATGATGATTTGTGCATG
1 CCACGTCATCATCTATGATGATTTGTGCATA
39845 CCACGTCA
1 CCACGTCA
39853 GATGGATCCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (31 bp):
CCACGTCATCATCTATGATGATTTGTGCATA
Found at i:41509 original size:80 final size:81
Alignment explanation
Indices: 41245--41580 Score: 462
Period size: 81 Copynumber: 4.2 Consensus size: 81
41235 TGTTAAACAT
* * * * * * * *
41245 TTAATCTTTTAC-CTAAAGGCATTTAGCCTTTCATCTATCTTGCATGATTGAAAC-CTTCTTGCC
1 TTAATCTTTTACTC-AAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTC-TGTC
*
41308 AAATGCACAGTTAGGCCA
64 AAATGCACAGCTAGGCCA
* * * * *
41326 TTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAAATGGCATAATTGACACCTTTATGCCAA
1 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
*
41391 ATGCACCGCTAGGCCA
66 ATGCACAGCTAGGCCA
* *
41407 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGAATAATTAACACATTTCTGTC-A
1 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
41471 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
*
41487 TTAATGTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
1 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
*
41552 ATGCACAGCTAGGCTA
66 ATGCACAGCTAGGCCA
41568 TTAATCTTTTACT
1 TTAATCTTTTACT
41581 TTAGATATGT
Statistics
Matches: 227, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
80 76 0.33
81 148 0.65
82 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (81 bp):
TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
ATGCACAGCTAGGCCA
Found at i:41794 original size:55 final size:55
Alignment explanation
Indices: 41751--42356 Score: 907
Period size: 55 Copynumber: 11.3 Consensus size: 55
41741 ATAAACTCAT
* *
41751 TATGAATTTCTT-AGTTCTGCACACAAAGTGCCCATACGAAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTT-TACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
* * * * *
41806 TATGAATTTCTTAAGTTCACACACAAAGTGTCCATATGGAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
* * *
41861 TATGAATTTCTTAAGTTCACACATAAAGTGTCCATACGGAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
41916 TATG------TT-A---T--ACATAAAGTGCCCATACGAAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
* *
41959 TATGAATTTCTTAAGTTTACACATAAAGTTCCCATACGGAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
*
42014 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
* *
42069 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATA-GGAAATTCATCCAATTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
*
42123 TATGAATTTCTTAAGTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
*
42178 TATGAATTTCTTAAGTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
42233 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
* ** *
42288 TATGAATTTCTTAAGTTAACACATAAAGTGTTCATACGAAAATTCATCCACGTAG
1 TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
*
42343 TATAAATTTCTTAA
1 TATGAATTTCTTAA
42357 CTTTTTGCAC
Statistics
Matches: 514, Mismatches: 23, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
43 37 0.07
48 1 0.00
49 4 0.01
50 1 0.00
53 1 0.00
54 52 0.10
55 414 0.81
56 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (55 bp):
TATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATCCACTTAG
Found at i:41947 original size:43 final size:43
Alignment explanation
Indices: 41881--41962 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
41871 TTAAGTTCAC
* *
41881 ACATAAAGTGTCCATACGGAAATTCATCCACTTAGTATGTTAT
1 ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGTTAT
41924 ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATG
1 ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATG
41963 AATTTCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (43 bp):
ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGTTAT
Found at i:42312 original size:219 final size:220
Alignment explanation
Indices: 41924--42356 Score: 751
Period size: 219 Copynumber: 2.0 Consensus size: 220
41914 AGTATGTTAT
*
41924 ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTT
1 ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTG
* *
41989 CCCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGGA
66 CCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAA
* *
42054 AATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA-GGAAATTCATCCA
131 AATTCATCCACTTAGTATGAATTTCTTAAGTTAACACATAAAGTGCCCATACGAAAATTCATCCA
* *
42118 ATTAGTATGAATTTCTTAAGTTTAC
196 AGTAGTATAAATTTCTTAAGTTTAC
* *
42143 ACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATATAGTG
1 ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTG
42208 CCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAA
66 CCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAA
**
42273 AATTCATCCACTTAGTATGAATTTCTTAAGTTAACACATAAAGTGTTCATACGAAAATTCATCCA
131 AATTCATCCACTTAGTATGAATTTCTTAAGTTAACACATAAAGTGCCCATACGAAAATTCATCCA
*
42338 CGTAGTATAAATTTCTTAA
196 AGTAGTATAAATTTCTTAA
42357 CTTTTTGCAC
Statistics
Matches: 201, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
219 173 0.86
220 28 0.14
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (220 bp):
ACATAAAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTG
CCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAA
AATTCATCCACTTAGTATGAATTTCTTAAGTTAACACATAAAGTGCCCATACGAAAATTCATCCA
AGTAGTATAAATTTCTTAAGTTTAC
Found at i:42759 original size:19 final size:21
Alignment explanation
Indices: 42723--42762 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
42713 ACCATGGCAT
42723 CGATACTACTATACTATGGTAC
1 CGATACTACTATA-TATGGTAC
42745 CGATACT-CTAT-TATGGTA
1 CGATACTACTATATATGGTA
42763 TTGATATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (21 bp):
CGATACTACTATATATGGTAC
Found at i:44075 original size:22 final size:22
Alignment explanation
Indices: 44033--44075 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
44023 TTCTATAAGA
*
44033 TATAAATGAATGATAAGATGGG
1 TATAAATGAATGATAACATGGG
*
44055 TATAATTG-ATGATTAACATGG
1 TATAAATGAATGA-TAACATGG
44076 AAACCTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.33
Consensus pattern (22 bp):
TATAAATGAATGATAACATGGG
Found at i:44178 original size:56 final size:55
Alignment explanation
Indices: 44092--44247 Score: 188
Period size: 56 Copynumber: 2.8 Consensus size: 55
44082 GATTTTTTTA
* *
44092 GAAAATAGGTTTTAGGTTGGAAAACCGATTTTAGATTGAAAAATAGGTTTTAGGTT
1 GAAAATTGATTTTAGGTT-GAAAACCGATTTTAGATTGAAAAATAGGTTTTAGGTT
* * *
44148 -AAAACTTGATTTTAGGTTGAAAACCTGATTTTAGTTTGGAACATAGGTTTTAGGTT
1 GAAAA-TTGATTTTAGGTTGAAAACC-GATTTTAGATTGAAAAATAGGTTTTAGGTT
* * *
44204 GGAAAATTGATTTTAGGTTGGAAACCAGATTTTAGGTTGCAAAA
1 -GAAAATTGATTTTAGGTTGAAAACC-GATTTTAGATTGAAAAA
44248 CCTAATTTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
55 11 0.13
56 38 0.44
57 33 0.38
58 4 0.05
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.37
Consensus pattern (55 bp):
GAAAATTGATTTTAGGTTGAAAACCGATTTTAGATTGAAAAATAGGTTTTAGGTT
Found at i:44235 original size:57 final size:56
Alignment explanation
Indices: 44092--44297 Score: 202
Period size: 58 Copynumber: 3.6 Consensus size: 56
44082 GATTTTTTTA
* *
44092 GAAAATAGGTTTTAGGTTGGAAAACC-GATTTTAGATTGAAAAATAGGTTTTAGGTT
1 GAAAATAGATTTTAGGTTGG-AAACCAGATTTTAGATTGAAACATAGGTTTTAGGTT
* * * * *
44148 -AAAACTTGATTTTAGGTTGAAAACCTGATTTTAGTTTGGAACATAGGTTTTAGGTT
1 GAAAA-TAGATTTTAGGTTGGAAACCAGATTTTAGATTGAAACATAGGTTTTAGGTT
* * * * * *
44204 GGAAAATTGATTTTAGGTTGGAAACCAGATTTTAGGTTGCAAAACCTA-ATTTTTGTTT
1 -GAAAATAGATTTTAGGTTGGAAACCAGATTTTAGATTG--AAACATAGGTTTTAGGTT
* *
44262 AGAAAATAGGTTTTAGGTTGGAAACCAGGTTTTAGA
1 -GAAAATAGATTTTAGGTTGGAAACCAGATTTTAGA
44298 AGGATTAGAG
Statistics
Matches: 125, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
55 9 0.07
56 39 0.31
57 30 0.24
58 42 0.34
59 5 0.04
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (56 bp):
GAAAATAGATTTTAGGTTGGAAACCAGATTTTAGATTGAAACATAGGTTTTAGGTT
Found at i:44285 original size:19 final size:19
Alignment explanation
Indices: 44092--44285 Score: 146
Period size: 19 Copynumber: 10.2 Consensus size: 19
44082 GATTTTTTTA
*
44092 GAAAATAGGTTTTAGGTTG
1 GAAAATAGATTTTAGGTTG
** *
44111 GAAAACCGATTTTAGATTG
1 GAAAATAGATTTTAGGTTG
* *
44130 AAAAATAGGTTTTAGGTT-
1 GAAAATAGATTTTAGGTTG
*
44148 -AAAACTTGATTTTAGGTT-
1 GAAAA-TAGATTTTAGGTTG
*
44166 GAAAACCT-GATTTTAGTTTG
1 GAAAA--TAGATTTTAGGTTG
* *
44186 GAACATAGGTTTTAGGTTG
1 GAAAATAGATTTTAGGTTG
*
44205 GAAAATTGATTTTAGGTTG
1 GAAAATAGATTTTAGGTTG
**
44224 GAAACCAGATTTTAGGTTG
1 GAAAATAGATTTTAGGTTG
* * * *
44243 CAAAACCTA-ATTTTTGTTTA
1 GAAAA--TAGATTTTAGGTTG
*
44263 GAAAATAGGTTTTAGGTTG
1 GAAAATAGATTTTAGGTTG
44282 GAAA
1 GAAA
44286 CCAGGTTTTA
Statistics
Matches: 135, Mismatches: 32, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
17 4 0.03
18 14 0.10
19 98 0.73
20 18 0.13
21 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.38
Consensus pattern (19 bp):
GAAAATAGATTTTAGGTTG
Found at i:44481 original size:37 final size:37
Alignment explanation
Indices: 44439--44566 Score: 184
Period size: 37 Copynumber: 3.5 Consensus size: 37
44429 CGAAATTAAA
* * *
44439 ATGACTCACACGGGAGCACATAATCATATTATTCTGG
1 ATGACTCGCACGGGAGCACCTAATTATATTATTCTGG
* * *
44476 GTGACTCGCACGGGAACACCTAATTATATTATTTTGG
1 ATGACTCGCACGGGAGCACCTAATTATATTATTCTGG
*
44513 ATGACTCGCACAGGAGCACCTAATTATATTATTCTGG
1 ATGACTCGCACGGGAGCACCTAATTATATTATTCTGG
*
44550 ATGACTCGCATGGGAGC
1 ATGACTCGCACGGGAGC
44567 TACGAAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 79 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (37 bp):
ATGACTCGCACGGGAGCACCTAATTATATTATTCTGG
Found at i:44482 original size:66 final size:66
Alignment explanation
Indices: 44308--44486 Score: 166
Period size: 66 Copynumber: 2.7 Consensus size: 66
44298 AGGATTAGAG
* * * * * **
44308 TGACTCGCACAGGAGCACTTGATCATATTGTTCTGTGTGACTCGCA-GGGAGCCTCGAAGGATTA
1 TGACTCACAC-GGAGCACATAATCATATTATTCTGAGTGACTCGCACAAGAGCCTCGAA-GATTA
* *
44372 GAG
64 AAA
* * * * *
44375 TGACTCACACGGAACACCTATTCATATTATTCTAAGAGACTCGCACAAGAGGCC-CGAA-ATTAA
1 TGACTCACACGGAGCACATAATCATATTATTCTGAGTGACTCGCACAAGA-GCCTCGAAGATTAA
44438 AA
65 AA
*
44440 TGACTCACACGGGAGCACATAATCATATTATTCTGGGTGACTCGCAC
1 TGACTCACAC-GGAGCACATAATCATATTATTCTGAGTGACTCGCAC
44487 GGGAACACCT
Statistics
Matches: 90, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
65 15 0.17
66 57 0.63
67 15 0.17
68 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (66 bp):
TGACTCACACGGAGCACATAATCATATTATTCTGAGTGACTCGCACAAGAGCCTCGAAGATTAAA
A
Found at i:46433 original size:23 final size:25
Alignment explanation
Indices: 46407--46452 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
46397 TTTACTTGGT
46407 GTTG-GTTATGGTTTTG-ATGAAAC
1 GTTGTGTTATGGTTTTGAATGAAAC
* *
46430 GTTGTTTTATGTTTTTGAATGAA
1 GTTGTGTTATGGTTTTGAATGAA
46453 GAATTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 10 0.53
25 5 0.26
ACGTcount: A:0.22, C:0.02, G:0.26, T:0.50
Consensus pattern (25 bp):
GTTGTGTTATGGTTTTGAATGAAAC
Found at i:48656 original size:54 final size:54
Alignment explanation
Indices: 48582--48813 Score: 249
Period size: 54 Copynumber: 4.4 Consensus size: 54
48572 TTTCTTGAGA
* * * *
48582 TGCACA-TGTAGTGCCGATACGGTTGTTTATAAACATATTATGAATTCTGTGGGT
1 TGCACACT-TAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGT
* * * *
48636 TACACACTTAGTGCCTATACGATCGTTCATCAACATATGATGAATT-TCGTAGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCT-GTGGGT
* * * * * *
48690 TGCACACTTAGTGCCTTTATGGTCATTCATAAACACATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGT
* * *
48744 TGTACACTTAGTGCCTATAAGGTCGTTCATCAACATATGATGAATTC---GGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGT
*
48795 TGCACACATAGTGCCTATA
1 TGCACACTTAGTGCCTATA
48814 GTACACATAG
Statistics
Matches: 148, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
51 21 0.14
53 1 0.01
54 125 0.84
55 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATGATGAATTCTGTGGGT
Found at i:48759 original size:108 final size:105
Alignment explanation
Indices: 48610--48810 Score: 312
Period size: 108 Copynumber: 1.9 Consensus size: 105
48600 ACGGTTGTTT
* * *
48610 ATAAACATATTATGAATTCTGTGGGTTACACACTTAGTGCCTATACGATCGTTCATCAACATATG
1 ATAAACACATTATGAATTCCGTGGGTTACACACTTAGTGCCTATAAGATCGTTCATCAACATATG
*
48675 ATGAATTTCGTAGGTTGCACACTTAGTGCCTTTATGGTCATTC
66 ATGAA-TTCG--GGTTGCACACATAGTGCCTTTATGGTCATTC
** *
48718 ATAAACACATTATGAATTCCGTGGGTTGTACACTTAGTGCCTATAAGGTCGTTCATCAACATATG
1 ATAAACACATTATGAATTCCGTGGGTTACACACTTAGTGCCTATAAGATCGTTCATCAACATATG
48783 ATGAATTCGGGTTGCACACATAGTGCCT
66 ATGAATTCGGGTTGCACACATAGTGCCT
48811 ATAGTACACA
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 18 0.21
107 4 0.05
108 64 0.74
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (105 bp):
ATAAACACATTATGAATTCCGTGGGTTACACACTTAGTGCCTATAAGATCGTTCATCAACATATG
ATGAATTCGGGTTGCACACATAGTGCCTTTATGGTCATTC
Found at i:49275 original size:18 final size:19
Alignment explanation
Indices: 49233--49280 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
49223 GGAGTCCATG
* *
49233 GTATCGATACCTTCCTCATA
1 GTATCGATACCTACATCA-A
49253 GTATCGATACCTACATC-A
1 GTATCGATACCTACATCAA
49271 GTATCGATAC
1 GTATCGATAC
49281 TAATTGCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (19 bp):
GTATCGATACCTACATCAA
Found at i:50884 original size:21 final size:22
Alignment explanation
Indices: 50858--50903 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
50848 CAAGCAATAG
50858 CTTAAGTTT-GGGGTGTGATAA
1 CTTAAGTTTGGGGGTGTGATAA
50879 CTTAAGTTTGGGGGTGTGATAA
1 CTTAAGTTTGGGGGTGTGATAA
50901 CTT
1 CTT
50904 CGTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.39
Consensus pattern (22 bp):
CTTAAGTTTGGGGGTGTGATAA
Found at i:51195 original size:20 final size:21
Alignment explanation
Indices: 51163--51202 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
51153 AGACTACAGT
51163 GAGGAACAAATTTATCTTGCC
1 GAGGAACAAATTTATCTTGCC
51184 GAGGAA-AAATTTATCTTGC
1 GAGGAACAAATTTATCTTGC
51203 AGATCTGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (21 bp):
GAGGAACAAATTTATCTTGCC
Done.