Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006117.1 Hibiscus syriacus cultivar Beakdansim tig00014498_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: 83772
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:5287 original size:21 final size:22
Alignment explanation
Indices: 5256--5312 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
5246 AGATTTTCAC
*
5256 TTCAGAGATGACAAAATT-TCTT
1 TTCAAAGATGA-AAAATTCTCTT
* *
5278 TT-AAAGATGATAGATTCTCTT
1 TTCAAAGATGAAAAATTCTCTT
5299 TTCAAAGATGAAAA
1 TTCAAAGATGAAAA
5313 CTTTATGGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 11 0.39
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (22 bp):
TTCAAAGATGAAAAATTCTCTT
Found at i:5308 original size:22 final size:20
Alignment explanation
Indices: 5232--5309 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 20
5222 TACATCTACA
5232 CTTTTAAAGATGATAGATTTT
1 CTTTTAAAGATGATAGA-TTT
* * * * *
5253 CACTTCAGAGATGACAAAATTT
1 C-TTTTAAAGATGA-TAGATTT
5275 CTTTTAAAGATGATAGATTCT
1 CTTTTAAAGATGATAGATT-T
5296 CTTTTCAAAGATGA
1 CTTTT-AAAGATGA
5310 AAACTTTATG
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
20 4 0.09
21 16 0.37
22 21 0.49
23 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (20 bp):
CTTTTAAAGATGATAGATTT
Found at i:6093 original size:166 final size:164
Alignment explanation
Indices: 5812--6133 Score: 504
Period size: 166 Copynumber: 1.9 Consensus size: 164
5802 AGAATAAGCA
* * * *
5812 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAACATAATGAGAAAATGA
1 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATTT-AAAAACATAATGAGAAAACGA
* **
5877 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGA-TTTT
65 TTTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTT
5941 CTTAGTTTTTTTACTTATTAAACTATTTCCAACAACC
130 CTTAG-TTTTTTACTTATTAAAC-ATTTCCAACAACC
*
5978 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATCTT-GAAACATAATGAGAAAACGA
1 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTAT-TTAAAAACATAATGAGAAAACGA
*
6042 TTTCCAAAGTTTCTCATTCAATCTTTTCTGAAAATGAAATTGTTGAAAAGTAAGAAAACTATTTT
65 TTTCCAAAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
6107 TCTTAGTTTTTTACTTATTAAACATTT
129 TCTTAGTTTTTTACTTATTAAACATTT
6134 TCCTTCGAAA
Statistics
Matches: 144, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
165 48 0.33
166 85 0.59
167 11 0.08
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (164 bp):
TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATTTAAAAACATAATGAGAAAACGAT
TTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTTC
TTAGTTTTTTACTTATTAAACATTTCCAACAACC
Found at i:6194 original size:36 final size:36
Alignment explanation
Indices: 6141--6339 Score: 168
Period size: 36 Copynumber: 5.4 Consensus size: 36
6131 TTTTCCTTCG
6141 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAA-AATTTATCTCACTTGAGATTGTTTTTCTTA
* * ** ** **
6178 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
1 AAACAAAATTTATCTCACTTGAGATTGTTTTTCTTA
* *
6214 AAACAGCAATTTATCTCACTTGAGATTTTTTTTCTTA
1 AAACA-AAATTTATCTCACTTGAGATTGTTTTTCTTA
* * * ** *
6251 AAACAAAATTTGTCTCGCTCGAGACAG--TTTCATTCG
1 AAACAAAATTTATCTCACTTGAGATTGTTTTTC-TT-A
* *
6287 AAACAACAATTTATCTCACTTGAAATTGTTTTCCTTA
1 AAACAA-AATTTATCTCACTTGAGATTGTTTTTCTTA
*
6324 AAACAAAATTTGTCTC
1 AAACAAAATTTATCTC
6340 GCTCGAGACA
Statistics
Matches: 121, Mismatches: 35, Indels: 13
0.72 0.21 0.08
Matches are distributed among these distances:
34 4 0.03
35 2 0.02
36 57 0.47
37 53 0.44
38 2 0.02
39 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (36 bp):
AAACAAAATTTATCTCACTTGAGATTGTTTTTCTTA
Found at i:6257 original size:73 final size:73
Alignment explanation
Indices: 6138--6364 Score: 400
Period size: 73 Copynumber: 3.1 Consensus size: 73
6128 ACATTTTCCT
*
6138 TCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGAC
1 TCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGAC
6203 AGTTTCAC
66 AGTTTCAC
* *
6211 TCGAAACAGCAATTTATCTCACTTGAGATTTTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGAC
1 TCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGAC
*
6276 AGTTTCAT
66 AGTTTCAC
* *
6284 TCGAAACAACAATTTATCTCACTTGAAATTGTTTTCCTTAAAACAAAATTTGTCTCGCTCGAGAC
1 TCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGAC
6349 AGTTTCAC
66 AGTTTCAC
6357 TCGAAACA
1 TCGAAACA
6365 TAATTTCCAT
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 145 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (73 bp):
TCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGAC
AGTTTCAC
Found at i:6364 original size:36 final size:36
Alignment explanation
Indices: 6178--6370 Score: 163
Period size: 36 Copynumber: 5.3 Consensus size: 36
6168 GTTTTTCTTA
6178 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
* * * *** ** **
6214 AAACAGCAATTTATCTCACTTGAGATTTTTTTTCTTA
1 AAACA-AAATTTGTCTCACTCGAGACAGTTTCACTCG
* *
6251 AAACAAAATTTGTCTCGCTCGAGACAGTTTCATTCG
1 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
* * * ** **
6287 AAACAACAATTTATCTCACTTGAAATTGTTTTC-CTTA
1 AAACAA-AATTTGTCTCACTCGAGACAG-TTTCACTCG
*
6324 AAACAAAATTTGTCTCGCTCGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
*
6360 AAACATAATTT
1 AAACAAAATTT
6371 CCATCACTCG
Statistics
Matches: 113, Mismatches: 40, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
35 4 0.04
36 57 0.50
37 48 0.42
38 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (36 bp):
AAACAAAATTTGTCTCACTCGAGACAGTTTCACTCG
Found at i:6874 original size:39 final size:39
Alignment explanation
Indices: 6830--6906 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
6820 CCCTCCATCC
*
6830 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
* *
6869 AGCAGCCCCTCCACGCATCAGTTGCAGCAGCTTCCAGC
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGC
6907 ACTGCCAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.43, G:0.18, T:0.17
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
Found at i:8350 original size:12 final size:11
Alignment explanation
Indices: 8335--8410 Score: 68
Period size: 12 Copynumber: 6.7 Consensus size: 11
8325 ATTTCATTAT
8335 TTATTTGTAATA
1 TTATTT-TAATA
8347 TTATTTT--TA
1 TTATTTTAATA
8356 TTACTTTTAATA
1 TTA-TTTTAATA
8368 -TATTTTAATTTA
1 TTATTTTAA--TA
*
8380 TTACTTTAATTA
1 TTATTTTAA-TA
*
8392 TTATTTTATTA
1 TTATTTTAATA
8403 TTATTTTA
1 TTATTTTA
8411 GTCTTATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
9 5 0.09
10 10 0.18
11 13 0.24
12 20 0.36
13 7 0.13
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:8381 original size:24 final size:25
Alignment explanation
Indices: 8352--8410 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
8342 TAATATTATT
8352 TTTATTACTTTTAA-TA-TATTTTAA
1 TTTATTACTTTTAATTATTATTTT-A
8376 TTTATTAC-TTTAATTATTATTTTA
1 TTTATTACTTTTAATTATTATTTTA
8400 -TTATTA-TTTTA
1 TTTATTACTTTTA
8411 GTCTTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 15 0.47
24 11 0.34
25 6 0.19
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTATTACTTTTAATTATTATTTTA
Found at i:8401 original size:20 final size:22
Alignment explanation
Indices: 8344--8402 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 22
8334 TTTATTTGTA
8344 ATATTATTTTTATTACTTTTAAT
1 ATATTA-TTTTATTACTTTTAAT
*
8367 ATATTTTAATTTATTAC-TTTAAT
1 ATA--TTATTTTATTACTTTTAAT
8390 -TATTATTTTATTA
1 ATATTATTTTATTA
8403 TTATTTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 10 0.31
22 2 0.06
23 9 0.28
24 8 0.25
25 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATTATTTTATTACTTTTAAT
Found at i:8427 original size:2 final size:2
Alignment explanation
Indices: 8415--8447 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
8405 ATTTTAGTCT
*
8415 TA TA AA 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 TA TA TA T
8448 TTGTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8561 original size:21 final size:19
Alignment explanation
Indices: 8537--8584 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
8527 ATATTCTTAA
8537 ATAAATAAATATCTTACTTTT
1 ATAAATAAATATC-TA-TTTT
*
8558 ATAAAT-TATATCTATTTT
1 ATAAATAAATATCTATTTT
8576 -TAAATAAAT
1 ATAAATAAAT
8585 GTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 6 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATAAATATCTATTTT
Found at i:8635 original size:129 final size:127
Alignment explanation
Indices: 8460--8692 Score: 323
Period size: 129 Copynumber: 1.8 Consensus size: 127
8450 GTTTAAATAA
*
8460 TAATATTTATTTATTTTTAATATCAAAGAAAATGGGTTGTCTTAAAGCACCTAGAAGT-CATTTT
1 TAATATTTATTTATTTTTAATATCAAAGAAAATGAGTTGTCTTAAAGCACCTAGAA-TCCATTTT
8524 CTGATATTCT-TAAATAAATAAATATCTTACTTT-TATAAATTATATCTATTTTTAAATAAATGT
65 CTGATATT-TATAAAT-AA-AAATATCTTA-TTTATATAAATTATATCTATTTTTAAATAAATGT
8587 TT
126 TT
* * *
8589 TAATATTTATTTATTCATTTTATAT-TAAGAAAA-GAGTTGTCTTAAAGCACCTAGAATCCCTTT
1 TAATATTTATTTATT--TTTAATATCAAAGAAAATGAGTTGTCTTAAAGCACCTAGAATCCATTT
*
8652 TCTGATATTTATAAATAAAAATATCTTATTTATATATATTA
64 TCTGATATTTATAAATAAAAATATCTTATTTATATAAATTA
8693 ATAGATTTTC
Statistics
Matches: 94, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
126 3 0.03
127 18 0.19
128 4 0.04
129 55 0.59
130 7 0.07
131 7 0.07
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (127 bp):
TAATATTTATTTATTTTTAATATCAAAGAAAATGAGTTGTCTTAAAGCACCTAGAATCCATTTTC
TGATATTTATAAATAAAAATATCTTATTTATATAAATTATATCTATTTTTAAATAAATGTTT
Found at i:13190 original size:45 final size:45
Alignment explanation
Indices: 13140--13258 Score: 152
Period size: 45 Copynumber: 2.7 Consensus size: 45
13130 TAATTTTTTT
* * * * * *
13140 AATTATATATTAATAAATTAATAATAAATATTGTACTTTTACACA
1 AATTATATATTAATAAAATAATAATAAAAACTATAATTTTACAAA
13185 AATTATATATTAATAAAATAATAATAAAAACTATAATTTTACAAA
1 AATTATATATTAATAAAATAATAATAAAAACTATAATTTTACAAA
*
13230 AATTTATATATTAAAAAAATAA-AA-AAAAA
1 AA-TTATATATTAATAAAATAATAATAAAAA
13259 TCATTTTACA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
44 5 0.08
45 43 0.65
46 18 0.27
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (45 bp):
AATTATATATTAATAAAATAATAATAAAAACTATAATTTTACAAA
Found at i:13805 original size:16 final size:16
Alignment explanation
Indices: 13771--13811 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
13761 GTTTACTTCA
13771 GAATGATT-AAACACT
1 GAATGATTCAAACACT
**
13786 GAATGATTCAAATGCT
1 GAATGATTCAAACACT
13802 GAATGATTCA
1 GAATGATTCA
13812 GATACTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACACT
Found at i:25369 original size:14 final size:15
Alignment explanation
Indices: 25350--25379 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25340 CTAAAATAGG
25350 TTTATAGTGG-GTTT
1 TTTATAGTGGCGTTT
25364 TTTATAGTGGCGTTT
1 TTTATAGTGGCGTTT
25379 T
1 T
25380 AATACGCCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.03, G:0.27, T:0.57
Consensus pattern (15 bp):
TTTATAGTGGCGTTT
Found at i:25541 original size:42 final size:41
Alignment explanation
Indices: 25472--25590 Score: 139
Period size: 42 Copynumber: 2.9 Consensus size: 41
25462 TTACTTTAAC
* * *
25472 AAACGCCGCGAAAGGTTAAGTTATATAGCGGCGTTTTTATAA
1 AAACGCCGC-AAAAGTTAGGTTCTATAGCGGCGTTTTTATAA
* *
25514 AAACGCCGCAAAAAGTTAGGCTCTATAGCGGCATTTTTATAA
1 AAACGCCGC-AAAAGTTAGGTTCTATAGCGGCGTTTTTATAA
* * **
25556 AAGCGCCGCAACAGGAAGGTTCTATAGCGGCGTTT
1 AAACGCCGCAAAAGTTAGGTTCTATAGCGGCGTTT
25591 ATGATATGAA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
41 21 0.32
42 44 0.68
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (41 bp):
AAACGCCGCAAAAGTTAGGTTCTATAGCGGCGTTTTTATAA
Found at i:27983 original size:80 final size:81
Alignment explanation
Indices: 27879--28033 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 81
27869 TATTTATTAA
** * *
27879 AAAAATTGGAAGGAAGGTAGTTTTGGGTTAGAAAAATTATATGGATATTTATTAC-AAAACACCA
1 AAAAATTGGAAGGAAGAAAGTTTTGGGTTAAAAAAATTATATAGATATTTATTACAAAAACACCA
*
27943 CTAAGGTACAGTCAAC
66 CTAAAGTACAGTCAAC
* *
27959 AAAAGTTGGAAGGAAGAAAGTTTTGGGTTAAAAAAATTATATAGATATTTATTACAAAAACGCCA
1 AAAAATTGGAAGGAAGAAAGTTTTGGGTTAAAAAAATTATATAGATATTTATTACAAAAACACCA
28024 CTAAAGTACA
66 CTAAAGTACA
28034 TGATTATTCT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
80 50 0.75
81 17 0.25
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (81 bp):
AAAAATTGGAAGGAAGAAAGTTTTGGGTTAAAAAAATTATATAGATATTTATTACAAAAACACCA
CTAAAGTACAGTCAAC
Found at i:28094 original size:42 final size:41
Alignment explanation
Indices: 28005--28112 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
27995 TTATATAGAT
* *
28005 ATTTATTACAAAAACGCCACTAAAGTACATGATTATTCTAG
1 ATTTATTACAAAAACGCCACTAAAGCACATGACTATTCTAG
* * *
28046 CATTTATTACAAAAATGCCACTAAAGCACATTACTATTGT-G
1 -ATTTATTACAAAAACGCCACTAAAGCACATGACTATTCTAG
* *
28087 ATGTTTATTACAAAAGCACCACTAAA
1 A--TTTATTACAAAAACGCCACTAAA
28113 ATATATGACT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 1 0.02
42 54 0.96
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.31
Consensus pattern (41 bp):
ATTTATTACAAAAACGCCACTAAAGCACATGACTATTCTAG
Found at i:31957 original size:12 final size:12
Alignment explanation
Indices: 31940--31964 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31930 TGATTAATAA
31940 TTTTTTTCTTGT
1 TTTTTTTCTTGT
31952 TTTTTTTCTTGT
1 TTTTTTTCTTGT
31964 T
1 T
31965 GCTTGCAGAA
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:0.08, G:0.08, T:0.84
Consensus pattern (12 bp):
TTTTTTTCTTGT
Found at i:42407 original size:42 final size:42
Alignment explanation
Indices: 42326--42409 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
42316 TTTGCAGCCC
* *
42326 CACCGTTAACCACCGCGCTAAGGCATTGCGGCAACGATTGAA
1 CACCGTTAACCACCACGCTAAGGCATTGCAGCAACGATTGAA
* * *
42368 CACCGTTAACCACCACGC-ATAGGCGTTGCAGCGAGGATTGAA
1 CACCGTTAACCACCACGCTA-AGGCATTGCAGCAACGATTGAA
42410 TTAGACACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.29, C:0.30, G:0.25, T:0.17
Consensus pattern (42 bp):
CACCGTTAACCACCACGCTAAGGCATTGCAGCAACGATTGAA
Found at i:43848 original size:19 final size:19
Alignment explanation
Indices: 43802--43841 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43792 AGGCATTGAA
43802 TTTCACATTCATTTGTATG
1 TTTCACATTCATTTGTATG
43821 TTTCACATTCATTTGTATG
1 TTTCACATTCATTTGTATG
43840 TT
1 TT
43842 CTACATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (19 bp):
TTTCACATTCATTTGTATG
Found at i:46012 original size:66 final size:66
Alignment explanation
Indices: 45931--46062 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
45921 CATATATTCC
45931 AACATTTTTCAACACGATTTTTACTCCCATTAAAATATCGCGTATGTGACTAAATTAACCTTAAC
1 AACATTTTTCAACACGATTTTTACTCCCATTAAAATATCGCGTATGTGACTAAATTAACCTTAAC
45996 A
66 A
*
45997 AACATTTTTCAACACGATTTTTACTTCCATTAAAATATCGCGTATGTGACTAAATTAACCTTAAC
1 AACATTTTTCAACACGATTTTTACTCCCATTAAAATATCGCGTATGTGACTAAATTAACCTTAAC
46062 A
66 A
46063 TAAATATAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (66 bp):
AACATTTTTCAACACGATTTTTACTCCCATTAAAATATCGCGTATGTGACTAAATTAACCTTAAC
A
Found at i:47687 original size:20 final size:19
Alignment explanation
Indices: 47664--47710 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
47654 CGATATACCA
47664 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
47684 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
47704 GGTAAAA
1 GGTAAAA
47711 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:47798 original size:181 final size:182
Alignment explanation
Indices: 47452--47924 Score: 741
Period size: 181 Copynumber: 2.6 Consensus size: 182
47442 GATCCAAATT
* * * **
47452 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
47517 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
47582 GCGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
131 GCGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
47634 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
47699 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
47763 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GCGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
47815 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
47880 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
47925 CGTAAGTACG
Statistics
Matches: 267, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
181 169 0.63
182 98 0.37
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GCGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:47868 original size:20 final size:19
Alignment explanation
Indices: 47845--47891 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
47835 CGATATAACA
47845 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
47865 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
47885 GGTAAAA
1 GGTAAAA
47892 CGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:47896 original size:17 final size:19
Alignment explanation
Indices: 47856--47896 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
47846 GTAAAAATAT
*
47856 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
47876 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
47893 GATA
1 GATA
47897 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:50129 original size:21 final size:21
Alignment explanation
Indices: 50103--50167 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
50093 AAGACAATCA
*
50103 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
*
50124 AGAGTCAAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
50145 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
50166 AG
1 AG
50168 GTATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:50232 original size:25 final size:25
Alignment explanation
Indices: 50204--50258 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
50194 TAGATGGAGT
*
50204 GGTGAAAGAAGTAGAGGTGTTGAGG
1 GGTGAAAGAAGTAGAGGTGTTAAGG
* *
50229 GGTGAAAGAAGTTGGGGTGTTAAGG
1 GGTGAAAGAAGTAGAGGTGTTAAGG
50254 GGTGA
1 GGTGA
50259 TATTAAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.49, T:0.22
Consensus pattern (25 bp):
GGTGAAAGAAGTAGAGGTGTTAAGG
Found at i:52107 original size:18 final size:19
Alignment explanation
Indices: 52047--52096 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
52037 AATGTAGGGT
52047 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
52066 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
52085 TAATTTTGTATA
1 TAATTTTGTATA
52097 TGAATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:53289 original size:200 final size:200
Alignment explanation
Indices: 52350--53270 Score: 1610
Period size: 200 Copynumber: 4.6 Consensus size: 200
52340 GTGCAACCAT
* *
52350 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
*
52415 TCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
* *
52480 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTACAACAATAAAGTTTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
52545 TATAA
196 TATAA
*
52550 AAAGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
52615 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
*
52680 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCTATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
52745 TATAA
196 TATAA
*
52750 AAAGTGTCGATCCCATAAACATCGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* *
52815 CCGGTACAAGTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
52880 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
52945 TATAA
196 TATAA
* *
52950 AAAATGTCGATCCCATAAACATCGAAATCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* * *
53015 CCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATAATGTGTTGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
* *
53080 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAATAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
53145 TATAA
196 TATAA
* * *
53150 AAAGTGTCGATCTCATAAACATCGAAACCCAAAAGTATAATGTATTAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* * * *
53215 CCGGTATAAGTATACCGGTTTTATGGGAGAATTGGTATATAAT-ATGTATCGACACT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTA-AATAATGTATCGACACT
53271 GTTTAATGTT
Statistics
Matches: 688, Mismatches: 32, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
200 685 1.00
201 3 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
TATAA
Found at i:53876 original size:183 final size:183
Alignment explanation
Indices: 53565--54001 Score: 811
Period size: 183 Copynumber: 2.4 Consensus size: 183
53555 GTCAGAAGCG
* *
53565 CGATATAAATATACCAGTTTTATGAGTGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
53630 GTGTCAGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACA
53695 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
* * *
53748 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATAAT
1 CGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
53813 GTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACA
53878 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
*
53931 CGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCAACACTTTTTAATATT
1 CGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
53996 GTGTCG
66 GTGTCG
54002 CTAATTTTAA
Statistics
Matches: 245, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 245 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (183 bp):
CGATATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACA
TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:57379 original size:23 final size:23
Alignment explanation
Indices: 57350--57397 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
57340 AAATAGGTCA
*
57350 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
* *
57373 ATATAAGCGCTTCCTAATATGTT
1 ATATAAGCGCTACCTAATATATT
57396 AT
1 AT
57398 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:57448 original size:87 final size:87
Alignment explanation
Indices: 57350--57512 Score: 265
Period size: 87 Copynumber: 1.9 Consensus size: 87
57340 AAATAGGTCA
*
57350 ATATAAGCGCTACCTATTATATTATATAAGCGCTT-CCTAATATGTTATTGTACTTGATAATATT
1 ATATAAGCGCTACCTATTACATTATATAAGCG-TTACCTAATATGTTATTGTACTTGATAATATT
57414 TCCCGTTAAATACCTATTTTATT
65 TCCCGTTAAATACCTATTTTATT
* *
57437 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTATTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
* *
57502 TCGGTTAAATA
66 CCCGTTAAATA
57513 ATATAACATA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
86 2 0.03
87 68 0.97
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:57484 original size:23 final size:23
Alignment explanation
Indices: 57434--57478 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
57424 TACCTATTTT
* *
57434 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
57457 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
57479 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:70562 original size:64 final size:63
Alignment explanation
Indices: 70494--70650 Score: 197
Period size: 64 Copynumber: 2.5 Consensus size: 63
70484 TTCAATGTGT
* * *
70494 ATCGATGCACAAGAAGTGCATCGATGCACCCCTTAAAAATGGAAACATCAAATGCAATTGGTGC
1 ATCGATGCATAAGAAGTGCATCGATGCACCCCTT-AAAATGAAAACATCAAAGGCAATTGGTGC
* * * * *
70558 ATCGATGCATAAGGAGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTTGTGT
1 ATCGATGCATAAGAAGTGCATCGATGCA-CCCCTTAAAATGAAAACATCAAAGGCAATTGGTGC
** *
70622 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAAGAAGTGCATCGATGCAC
70651 ATGTTAAAGA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
63 1 0.01
64 74 0.91
65 6 0.07
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAAGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCAAAGGCAATTGGTGC
Found at i:71121 original size:6 final size:6
Alignment explanation
Indices: 71110--71136 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
71100 GCAGGATTAT
71110 ATAAGA ATAAGA ATAAGA ATAAGA ATA
1 ATAAGA ATAAGA ATAAGA ATAAGA ATA
71137 GGATGTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
ATAAGA
Found at i:71201 original size:13 final size:14
Alignment explanation
Indices: 71172--71202 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
71162 AACCATGCAA
71172 GTGATATGAACTAT
1 GTGATATGAACTAT
71186 GTGATATGAA-TAT
1 GTGATATGAACTAT
71199 GTGA
1 GTGA
71203 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:82767 original size:29 final size:30
Alignment explanation
Indices: 82734--82799 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
82724 AAAAAAAATA
*
82734 TAAGATATGATCGCTTT-A-TTTTATTTAAT
1 TAAGATATGATC-ATTTAATTTTTATTTAAT
*
82763 TAAGATATGGTCATTTACATTTTTATTTAAT
1 TAAGATATGATCATTTA-ATTTTTATTTAAT
82794 TAAGAT
1 TAAGAT
82800 GTGGTCACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 3 0.09
29 11 0.34
30 1 0.03
31 17 0.53
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (30 bp):
TAAGATATGATCATTTAATTTTTATTTAAT
Done.