Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006190.1 Hibiscus syriacus cultivar Beakdansim tig00014729_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: 73636
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:25098 original size:249 final size:243
Alignment explanation
Indices: 24594--25186 Score: 876
Period size: 249 Copynumber: 2.4 Consensus size: 243
24584 TTTTTGGTCC
*
24594 ACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
1 ACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGACC
*
24659 CGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAACAAATATAGA
66 CGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTCAATTGAAAAAACAAATATAGA
* *
24724 GAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGTCGGGTCGGG
131 GAGTACTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TTTTT--GTCGGGTAGGG
24789 TATTTTTCACCCTAAACCCGAACCCGACTCGACCCGAATATCACACTTAAAAAA
193 TATTTTTCACCCTAAACCCGAA--C-ACTCGACCCGAATATCACACTTAAAAAA
24843 ACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGACC
1 ACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGACC
* *
24908 CGAAATAA-AAAAAATTATTTTTATTTAATAAAAACAATGACTCAATTGAAAAAA-ATTATATAT
66 CGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTCAATTGAAAAAACA--A-ATAT
*
24971 AGAGGGATACTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TTTT-T-GGGTAGG
128 AGAGAG-TACTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTGTCGGGTAGG
*
25033 GTATTTTTCACCCTAAACCCG-A-ACTCGACCCGAATATCGCACTTAAAAAAA
192 GTATTTTTCACCCTAAACCCGAACACTCGACCCGAATATCACACTT-AAAAAA
* * *
25084 CCGACCCGACCCGACTAAAATAAAGTTTCACCCGACCCGACCCGAATATATAAATTAAAAATCGA
1 ---ACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAAT---
25149 CCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
60 -CCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
25187 TATGAATAAG
Statistics
Matches: 318, Mismatches: 13, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
240 21 0.07
241 6 0.02
244 57 0.18
245 27 0.08
246 1 0.00
247 1 0.00
248 57 0.18
249 97 0.31
250 9 0.03
251 42 0.13
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (243 bp):
ACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGACC
CGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTCAATTGAAAAAACAAATATAGA
GAGTACTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTGTCGGGTAGGGTAT
TTTTCACCCTAAACCCGAACACTCGACCCGAATATCACACTTAAAAAA
Found at i:33345 original size:32 final size:32
Alignment explanation
Indices: 33297--33357 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
33287 TAGAGAATAA
*
33297 GAGCTGATGTAGCTGAA-GTTGGTATGTTGTAT
1 GAGCTGATGTAACTGAAGGTT-GTATGTTGTAT
*
33329 GAGCTGGTGTAACTGAAGGTTGTATGTTG
1 GAGCTGATGTAACTGAAGGTTGTATGTTG
33358 CCTGTAGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (32 bp):
GAGCTGATGTAACTGAAGGTTGTATGTTGTAT
Found at i:35440 original size:18 final size:20
Alignment explanation
Indices: 35394--35442 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
35384 TGGATCGGTG
35394 TTTATTA-TTATATGTGTTA
1 TTTATTATTTATATGTGTTA
* *
35413 TTAATAATTTATAT-T-TTA
1 TTTATTATTTATATGTGTTA
35431 TTTATTATTTAT
1 TTTATTATTTAT
35443 TTTATTGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 13 0.52
19 6 0.24
20 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTATTATTTATATGTGTTA
Found at i:39470 original size:32 final size:32
Alignment explanation
Indices: 39434--39515 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
39424 AAAAAGAAAA
39434 AAATGTTAGGCTTAATTTTATTTTTGAAACAT
1 AAATGTTAGGCTTAATTTTATTTTTGAAACAT
*
39466 AAATGTTAGGCTTAATTTTATTTTTGAAACGT
1 AAATGTTAGGCTTAATTTTATTTTTGAAACAT
39498 AAATGTTAGGCTTAATTT
1 AAATGTTAGGCTTAATTT
39516 CAATTGATCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (32 bp):
AAATGTTAGGCTTAATTTTATTTTTGAAACAT
Found at i:51489 original size:18 final size:18
Alignment explanation
Indices: 51468--51507 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
51458 TTAATACACG
51468 AATTTAATTCTAAAATTT
1 AATTTAATTCTAAAATTT
51486 AATTTAATTCTAAAATTT
1 AATTTAATTCTAAAATTT
51504 AATT
1 AATT
51508 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTAATTCTAAAATTT
Found at i:51549 original size:12 final size:12
Alignment explanation
Indices: 51498--51581 Score: 57
Period size: 12 Copynumber: 7.0 Consensus size: 12
51488 TTTAATTCTA
*
51498 AAATTTA-ATTA
1 AAATTTATATTT
*
51509 AAATTTAAATTT
1 AAATTTATATTT
** *
51521 AGTTTTAAATTT
1 AAATTTATATTT
51533 AAATTTGATATTT
1 AAATTT-ATATTT
*
51546 -AATTTTTGATTT
1 AAATTTAT-ATTT
*
51558 -AATTAAATATTT
1 AAATT-TATATTT
51570 AAATTTATATTT
1 AAATTTATATTT
51582 TTAAAAATTG
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
11 8 0.14
12 40 0.69
13 10 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
AAATTTATATTT
Found at i:51581 original size:24 final size:24
Alignment explanation
Indices: 51500--51581 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 24
51490 TAATTCTAAA
51500 ATTTAATTAAA-ATTTAAATTTAGT
1 ATTTAATTAAATATTTAAATTTA-T
* *
51524 -TTTAAATTTAAATTTGATATTTAATTTTT
1 ATTT-AA-TTAAA--T-AT-TTAAATTTAT
51553 GATTTAATTAAATATTTAAATTTAT
1 -ATTTAATTAAATATTTAAATTTAT
51578 ATTT
1 ATTT
51582 TTAAAAATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
23 3 0.07
24 6 0.13
25 13 0.29
26 2 0.04
27 1 0.02
29 8 0.18
30 9 0.20
31 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTAATTAAATATTTAAATTTAT
Found at i:56506 original size:77 final size:78
Alignment explanation
Indices: 56245--56568 Score: 447
Period size: 78 Copynumber: 4.1 Consensus size: 78
56235 GCAAAGGGAG
** *
56245 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGACACTGCAAATGTTTCGGA
1 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGGGACTGCAAGTGTTTCGGA
56310 ACAACGAAAAGAA
66 ACAACGAAAAGAA
* *
56323 GACAATGCTGAGGATCAAGGGAAAAGAAA-TAGGGCAAAACAAAAAAGGACTGCAATAGTGTTTC
1 GACAATGCTGAGGATCAAGGGAAAAGAAACGA-GGCAAAACAAAAAGGGACTGC-A-AGTGTTTC
* *
56387 GGAACGACAAAAAGAA
63 GGAACAACGAAAAGAA
*
56403 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAAC-AAAAGGGACTGCAAGTGTCTCGGA
1 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGGGACTGCAAGTGTTTCGGA
56467 ACAACGAAAAGAA
66 ACAACGAAAAGAA
* ** * *
56480 GACAATGCTGAGGATCAAGGGAAAAGAAACAAGGCAAAACAAAAAAAGACTGCAAATGTTTCAGA
1 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGGGACTGCAAGTGTTTCGGA
*
56545 ACGAC-AAAAGGAA
66 ACAACGAAAA-GAA
* *
56558 GATAATCCTGA
1 GACAATGCTGA
56569 AGAACAACCT
Statistics
Matches: 219, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
77 65 0.30
78 83 0.38
79 12 0.05
80 58 0.26
81 1 0.00
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (78 bp):
GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGGGACTGCAAGTGTTTCGGA
ACAACGAAAAGAA
Found at i:56516 original size:157 final size:156
Alignment explanation
Indices: 56245--56568 Score: 524
Period size: 157 Copynumber: 2.1 Consensus size: 156
56235 GCAAAGGGAG
*
56245 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGACACTGCAAATGTTTCGGA
1 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGACACTGCAAATGTCTCGGA
* * *
56310 ACAACGAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAATAGGGCAAAACAAAAAAGGACTG
66 ACAACGAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACAAGGCAAAACAAAAAAAGACTG
*
56375 CAATAGTGTTTCGGAACGACAAAAAGAA
131 CAA-A-TGTTTCAGAACGACAAAAAGAA
** *
56403 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAAC-AAAAGGGACTGCAAGTGTCTCGGA
1 GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGACACTGCAAATGTCTCGGA
56467 ACAACGAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACAAGGCAAAACAAAAAAAGACTG
66 ACAACGAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACAAGGCAAAACAAAAAAAGACTG
*
56532 CAAATGTTTCAGAACGACAAAAGGAA
131 CAAATGTTTCAGAACGACAAAAAGAA
* *
56558 GATAATCCTGA
1 GACAATGCTGA
56569 AGAACAACCT
Statistics
Matches: 155, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
155 29 0.19
156 1 0.01
157 85 0.55
158 40 0.26
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (156 bp):
GACAATGCTGAGGATCAAGGGAAAAGAAACGAGGCAAAACAAAAAGACACTGCAAATGTCTCGGA
ACAACGAAAAGAAGACAATGCTGAGGATCAAGGGAAAAGAAACAAGGCAAAACAAAAAAAGACTG
CAAATGTTTCAGAACGACAAAAAGAA
Found at i:63317 original size:2 final size:2
Alignment explanation
Indices: 63262--63297 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
63252 TGTTTTTTCC
63262 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63298 TTTTTTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63339 original size:13 final size:13
Alignment explanation
Indices: 63317--63360 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
63307 ATTTTATATA
*
63317 TAATAGATATTAT
1 TAATATATATTAT
63330 TAATATATATTA-
1 TAATATATATTAT
*
63342 TATTATATTATTAT
1 TAATATA-TATTAT
63356 TAATA
1 TAATA
63361 CTATTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.23
13 16 0.62
14 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
TAATATATATTAT
Found at i:65003 original size:17 final size:17
Alignment explanation
Indices: 64981--65041 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
64971 TACAGCCAAT
64981 AACTCTAGCTTTAGTTC
1 AACTCTAGCTTTAGTTC
* *
64998 AACTCTAAGGATATTTATGAT-
1 AACTCT-A-G--CTTTA-GTTC
65019 AACTCTAGCTTTAGTTC
1 AACTCTAGCTTTAGTTC
65036 AACTCT
1 AACTCT
65042 TAAGGATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 1 0.03
19 2 0.06
20 1 0.03
21 10 0.29
22 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (17 bp):
AACTCTAGCTTTAGTTC
Found at i:65030 original size:38 final size:39
Alignment explanation
Indices: 64979--65057 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 39
64969 GTTACAGCCA
64979 ATAACTCTAGCTTTAGTTCAACTC-TAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
65017 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
65056 AT
1 AT
65058 GTGATACATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 24 0.60
39 16 0.40
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (39 bp):
ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
Found at i:69306 original size:211 final size:207
Alignment explanation
Indices: 68866--69426 Score: 871
Period size: 211 Copynumber: 2.7 Consensus size: 207
68856 TTGTTACGCC
*
68866 TTTAGAGCCAATTTCAACTTCACAACGAATGATATTGGACT-CAGACAACGCAAGTTCAACTTCA
1 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
68930 CGACGAAGGGACCCGGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAC
66 CGACGAAGGGACGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAC
68995 GAAGGATATTGGACTCCAAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
131 GAAGGATATTGGACTCCAAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
69060 CAACTTCTCAAT
196 CAACTTCTCAAT
* *
69072 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCA
1 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
69137 CGACGAAGGGACGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCTAATTTCAACTTCACAA
66 CGACGAAGGGACGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC-A
* *
69202 CGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAA
130 CGAAGGATATTGGACTCC--A-AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
69267 TAAACAACTTCTCAAT
192 TAAACAACTTCTCAAT
* *
69283 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTGCA
1 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* ** * * **
69348 CGATGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAATCTCAG-G-GGATTTCAACTTCACG
66 CGACGAAGGGA-CGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC-
69411 ACG--GGATATTGGACTC
129 ACGAAGGATATTGGACTC
69427 GGAACAATGC
Statistics
Matches: 327, Mismatches: 22, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
206 39 0.12
207 81 0.25
208 30 0.09
210 17 0.05
211 130 0.40
212 30 0.09
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (207 bp):
TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAC
GAAGGATATTGGACTCCAAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAA
CAACTTCTCAAT
Found at i:69310 original size:106 final size:106
Alignment explanation
Indices: 68869--69426 Score: 877
Period size: 106 Copynumber: 5.4 Consensus size: 106
68859 TTACGCCTTT
*
68869 AGAGCCAATTTCAACTTCACAACGAATGATATTGGACT-CAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
68933 CGAAGGGACC-CGGGTTGTCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
68973 AGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCC--A-AACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
69034 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
*
69075 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
69140 CGAAGGGA-CGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* * *
69180 AGAGCTAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
69245 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTT
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
69286 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTGCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* ** * *
69351 TGAAGGGACCGCTGGTTGTCAATAAACAGTTTCCCAATCTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
** *
69392 AG-G-GGATTTCAACTTCACGACG--GGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
69427 GGAACAATGC
Statistics
Matches: 424, Mismatches: 23, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
101 31 0.07
102 62 0.15
103 35 0.08
104 37 0.09
105 103 0.24
106 156 0.37
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
Found at i:69925 original size:84 final size:82
Alignment explanation
Indices: 69616--69926 Score: 333
Period size: 84 Copynumber: 3.7 Consensus size: 82
69606 CTATCGGCCG
* * * * *
69616 AAAACCTTCGAGTTCGATTTCATTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGA
1 AAAACCTTCGAGTTCGATTTCATTCAGC-TCCAAGGCGCATCATTTGCAGCATAACTCAAGGCGA
69681 GAAGGGTTATCTGCCAACC
65 GAA-GGTTATCTGCCAACC
* * * * *
69700 AAAGCCTTCGAGTTCGA-TTCATTCAGCTCCAAGGCGCATTATTTGCAGCATAATTTAAGTCGAG
1 AAAACCTTCGAGTTCGATTTCATTCAGCTCCAAGGCGCATCATTTGCAGCATAACTCAAGGCGAG
69764 AAGGTTATCTGCCAACC
66 AAGGTTATCTGCCAACC
* * * *
69781 AAAAGAGCATTCGAGTTCAATTTCATTCAGCTCCAA-GCGTATCA-TTGCAGCATAAATCAAGGC
1 -AAA-A-CCTTCGAGTTCGATTTCATTCAGCTCCAAGGCGCATCATTTGCAGCATAACTCAAGGC
* *
69844 TAGAAGAGTTATCTGTCAA-C
63 GAGAAG-GTTATCTGCCAACC
* * * * *
69864 AAATACCTTCGAGTTTGATTCCACTCAGCTCCAAGGCACCATCATTTGCAGCATAGCTCAAGG
1 AAA-ACCTTCGAGTTCGATTTCATTCAGCTCCAAGGC-GCATCATTTGCAGCATAACTCAAGG
69927 AAATAAGGGC
Statistics
Matches: 193, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
81 39 0.20
82 43 0.22
83 36 0.19
84 60 0.31
85 15 0.08
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (82 bp):
AAAACCTTCGAGTTCGATTTCATTCAGCTCCAAGGCGCATCATTTGCAGCATAACTCAAGGCGAG
AAGGTTATCTGCCAACC
Found at i:70532 original size:14 final size:14
Alignment explanation
Indices: 70513--70559 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
70503 TATATAATAG
70513 ATTATTATAATAAT
1 ATTATTATAATAAT
* *
70527 ATTATTATTATTAT
1 ATTATTATAATAAT
*
70541 ATTATTATTAATACT
1 ATTATTA-TAATAAT
70556 ATTA
1 ATTA
70560 ATTTTGTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATTATAATAAT
Found at i:70535 original size:17 final size:17
Alignment explanation
Indices: 70513--70550 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
70503 TATATAATAG
70513 ATTATTATAATAATATT
1 ATTATTATAATAATATT
* *
70530 ATTATTATTATATTATT
1 ATTATTATAATAATATT
70547 ATTA
1 ATTA
70551 ATACTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTATAATAATATT
Found at i:72191 original size:17 final size:17
Alignment explanation
Indices: 72169--72229 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
72159 TACAGCCAAT
72169 AACTCTAGCTTTAGTTC
1 AACTCTAGCTTTAGTTC
* *
72186 AACTCTAAGGATATTTATGAT-
1 AACTCT-A-G--CTTTA-GTTC
72207 AACTCTAGCTTTAGTTC
1 AACTCTAGCTTTAGTTC
72224 AACTCT
1 AACTCT
72230 TAAGGATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 1 0.03
19 2 0.06
20 1 0.03
21 10 0.29
22 2 0.06
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (17 bp):
AACTCTAGCTTTAGTTC
Found at i:72218 original size:38 final size:39
Alignment explanation
Indices: 72167--72245 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 39
72157 GTTACAGCCA
72167 ATAACTCTAGCTTTAGTTCAACTC-TAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
72205 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
1 ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
72244 AT
1 AT
72246 GTGATACATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 24 0.60
39 16 0.40
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (39 bp):
ATAACTCTAGCTTTAGTTCAACTCTTAAGGATATTTATG
Done.