Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003594.1 Hibiscus syriacus cultivar Beakdansim tig00007588_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: 68931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1899 original size:21 final size:23
Alignment explanation
Indices: 1870--1917 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1860 ACATTTTTAT
*
1870 AAAATTATG-AAATA-ATTATAA
1 AAAAGTATGTAAATATATTATAA
*
1891 AAAAGTATGTTTAATATATTATAA
1 AAAAGTATG-TAAATATATTATAA
1915 AAA
1 AAA
1918 TATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 8 0.36
23 4 0.18
24 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (23 bp):
AAAAGTATGTAAATATATTATAA
Found at i:1957 original size:31 final size:33
Alignment explanation
Indices: 1896--1960 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1886 TATAAAAAAG
1896 TATGTTTAATATATTATAAAAATATTTATTTAA
1 TATGTTTAATATATTATAAAAATATTTATTTAA
1929 TATGTTTAATATATTAT-AAAA-ATTTATTTAA
1 TATGTTTAATATATTATAAAAATATTTATTTAA
1960 T
1 T
1961 TTTTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 11 0.34
32 4 0.12
33 17 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (33 bp):
TATGTTTAATATATTATAAAAATATTTATTTAA
Found at i:2151 original size:23 final size:23
Alignment explanation
Indices: 2119--2219 Score: 102
Period size: 23 Copynumber: 4.5 Consensus size: 23
2109 GATAATTTAA
*
2119 AAATATTATTATTTAAAATAAAT
1 AAATAATATTATTTAAAATAAAT
2142 AAATAATATTATTTAAAATAAAT
1 AAATAATATTATTTAAAATAAAT
* * *
2165 AAAT-ATATGATTTTAAA-AATT
1 AAATAATATTATTTAAAATAAAT
*
2186 AAATAGATA-T-TTTAAAATAATT
1 AAATA-ATATTATTTAAAATAAAT
**
2208 TCATAATATTAT
1 AAATAATATTAT
2220 AAATATACTT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
21 16 0.25
22 19 0.29
23 30 0.46
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATAATATTATTTAAAATAAAT
Found at i:2160 original size:19 final size:19
Alignment explanation
Indices: 2088--2205 Score: 61
Period size: 23 Copynumber: 5.9 Consensus size: 19
2078 GGTTATGTAC
2088 AATATTATTTAAAATTAAAT
1 AATATTATTTAAAA-TAAAT
2108 AGATA--ATTT--AA-AAAT
1 A-ATATTATTTAAAATAAAT
*
2123 ATTATTATTTAAAATAAATAAAT
1 AATATTATTT---A-AAATAAAT
2146 AATATTATTTAAAATAAAT
1 AATATTATTTAAAATAAAT
2165 AAATATATGATTTTAAAAATTAAAT
1 -AATAT-T-A-TTT-AAAA-TAAAT
2190 AGATA-T-TTTAAAATAA
1 A-ATATTATTTAAAATAA
2206 TTTCATAATA
Statistics
Matches: 79, Mismatches: 2, Indels: 36
0.68 0.02 0.31
Matches are distributed among these distances:
14 2 0.03
15 5 0.06
16 4 0.05
17 2 0.03
18 3 0.04
19 16 0.20
20 10 0.13
21 4 0.05
22 3 0.04
23 17 0.22
24 5 0.06
25 8 0.10
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AATATTATTTAAAATAAAT
Found at i:5438 original size:375 final size:376
Alignment explanation
Indices: 4792--5522 Score: 1038
Period size: 375 Copynumber: 1.9 Consensus size: 376
4782 AGAAAATATG
* * * *
4792 GAGAAATGAAGGAGAAGAAATGAAGAGAAAATGATGAAATGGGAGATATAAAGTTCTCATCTTTT
1 GAGAAATGAAGAAGAAGAAATGAAGAGAAAAAGATGAAATGGGAGATATAAAGCTATCATCTTTT
*
4857 AAAAAGGGTGAAATTGCACAATTGATCCTTCCTCATCTTTAAACAATTCAAAAATTATCATTTTA
66 AAAAAGGGTGAAATTGCACAATTGATCATTCCTCATCTTTAAACAATTCAAAAATTATCATTTTA
* * * *
4922 TGGCTAATTGGGCCAATTACAACTCAATTAACACCAACGAATTAAATTATTAAATTCATGGGGTC
131 TGGCTAATTGGCCCAATTACAACTCAATTAACACCAACGAATTAAATTATGAAATTCACGAGGTC
* * *
4987 CATATACCTCTCGGGTAAACCCGAAACTACTAGCGTAGAATTTGGGGTGTTACAACTCTTCATTT
196 CACATACCTCTCGGGTAAACCCGAAACTACTAGCGTAGAATTTGGGGTGTTACAACTCTCCACTT
** * *
5052 CTTAAAAGAAATTTCATCCTCGAAATTTGTTTGGGTTGAATAACGACCTATCCTTAGGTCTAAAA
261 CTTAAAAGAAATTTCATCCTCGAAATTTACTTGGGTTAAATAACGACCTATCCTTAGGTCCAAAA
*
5117 CTTAAAAATCTCTGAGCACCTAGACTCTTATCAAATGGAGAGGAAATAGTA
326 CTTAAAAATCTCTGAGCACCTAAACTCTTATCAAATGGAGAGGAAATAGTA
*
5168 GAGAAATTAAGAAGAAGAAATGAAGAGAAAAAGAT-AAATGGGAGATATAGAAGCTATCATCTTT
1 GAGAAATGAAGAAGAAGAAATGAAGAGAAAAAGATGAAATGGGAGATATA-AAGCTATCATCTTT
* * * *
5232 TAAAAAGGGTGAAATTGCATAATTGATCATTCCTCATCTTTATACAATTCAAAAA-TCTCCTTTT
65 TAAAAAGGGTGAAATTGCACAATTGATCATTCCTCATCTTTAAACAATTCAAAAATTATCATTTT
* * * * *
5296 ATTGCTAATTGGACCCAATTCCAACTCAA-TAAGC-CCGATGACTTAAATTATGAAATTCACGAG
130 ATGGCTAATTGG-CCCAATTACAACTCAATTAA-CACCAACGAATTAAATTATGAAATTCACGAG
* * * ** * * * *
5359 GTTCACATGCCTCTTGGGTAAACTTGGAACTACTAGCGTGGAATTTTGGGTGTTACAACTCTCCC
193 GTCCACATACCTCTCGGGTAAACCCGAAACTACTAGCGTAGAATTTGGGGTGTTACAACTCTCCA
*
5424 CTTCTTAAAAGAAATTTTATCCTCGAAATTTACTTGGGTTAAATAACGACCTATCCTTAGGTCCA
258 CTTCTTAAAAGAAATTTCATCCTCGAAATTTACTTGGGTTAAATAACGACCTATCCTTAGGTCCA
** * *
5489 ACGCTTATAAATCTTTGAGCACCTAAACTCTTAT
323 AAACTTAAAAATCTCTGAGCACCTAAACTCTTAT
5523 TACATATGAT
Statistics
Matches: 311, Mismatches: 41, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
375 200 0.64
376 111 0.36
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (376 bp):
GAGAAATGAAGAAGAAGAAATGAAGAGAAAAAGATGAAATGGGAGATATAAAGCTATCATCTTTT
AAAAAGGGTGAAATTGCACAATTGATCATTCCTCATCTTTAAACAATTCAAAAATTATCATTTTA
TGGCTAATTGGCCCAATTACAACTCAATTAACACCAACGAATTAAATTATGAAATTCACGAGGTC
CACATACCTCTCGGGTAAACCCGAAACTACTAGCGTAGAATTTGGGGTGTTACAACTCTCCACTT
CTTAAAAGAAATTTCATCCTCGAAATTTACTTGGGTTAAATAACGACCTATCCTTAGGTCCAAAA
CTTAAAAATCTCTGAGCACCTAAACTCTTATCAAATGGAGAGGAAATAGTA
Found at i:12976 original size:21 final size:21
Alignment explanation
Indices: 12926--13001 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
12916 TCCTTTAGGG
12926 GAAAGGATCGATCCCTTACTA
1 GAAAGGATCGATCCCTTACTA
* * * *
12947 AAAATGATCGGTCCCTTGAC-C
1 GAAAGGATCGATCCCTT-ACTA
* **
12968 GAAAGGATCGATCCCTCAGGA
1 GAAAGGATCGATCCCTTACTA
12989 GAAAGGATCGATC
1 GAAAGGATCGATC
13002 TCTTTTCAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.93
22 2 0.05
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
GAAAGGATCGATCCCTTACTA
Found at i:18378 original size:16 final size:16
Alignment explanation
Indices: 18357--18389 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
18347 TAATAAATAA
18357 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
18373 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
18389 A
1 A
18390 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:18479 original size:23 final size:23
Alignment explanation
Indices: 18449--18503 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
18439 GAACACAAAC
* * *
18449 AAACGAACATAATAAATGAATAT
1 AAACGAACACAATAAACGAACAT
18472 AAACGAACACAATAAACGAACAT
1 AAACGAACACAATAAACGAACAT
18495 AAACGAACA
1 AAACGAACA
18504 ACACAAACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.13
Consensus pattern (23 bp):
AAACGAACACAATAAACGAACAT
Found at i:18486 original size:13 final size:13
Alignment explanation
Indices: 18434--18493 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
18424 TAAACGAACG
18434 TAAACGAACACAAA
1 TAAACGAACAC-AA
* *
18448 CAAACGAACATAA
1 TAAACGAACACAA
* *
18461 TAAATG-A-A-TA
1 TAAACGAACACAA
18471 TAAACGAACACAA
1 TAAACGAACACAA
18484 TAAACGAACA
1 TAAACGAACA
18494 TAAACGAACA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 2 0.06
13 17 0.47
14 9 0.25
ACGTcount: A:0.62, C:0.18, G:0.08, T:0.12
Consensus pattern (13 bp):
TAAACGAACACAA
Found at i:19010 original size:21 final size:21
Alignment explanation
Indices: 18984--19034 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
18974 GGAACCATGG
*
18984 GATCGAAGAAGCTACATGGGA
1 GATCGAAGAAGCTACATAGGA
19005 GATCGAAGAAGCTACATAGGA
1 GATCGAAGAAGCTACATAGGA
*
19026 GACCGAAGA
1 GATCGAAGA
19035 GGACATGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.31, T:0.12
Consensus pattern (21 bp):
GATCGAAGAAGCTACATAGGA
Found at i:21674 original size:13 final size:13
Alignment explanation
Indices: 21649--21688 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
21639 TTAATTTTTT
21649 TTATTTTTAAAAA
1 TTATTTTTAAAAA
21662 TTATTATTTAAAAA
1 TTATT-TTTAAAAA
*
21676 ATATTTTTAAAAA
1 TTATTTTTAAAAA
21689 CAATTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATTTTTAAAAA
Found at i:26687 original size:19 final size:17
Alignment explanation
Indices: 26663--26702 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
26653 CTTTAATTTG
26663 TTTATTTAATTATTTTTAT
1 TTTATTTAA-T-TTTTTAT
*
26682 TTTATTTTATTTTTTAT
1 TTTATTTAATTTTTTAT
26699 TTTA
1 TTTA
26703 AAACAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
18 1 0.05
19 8 0.40
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTAATTTTTTAT
Found at i:28853 original size:21 final size:20
Alignment explanation
Indices: 28807--28863 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
28797 GATTGTCCAG
*
28807 GGGGTACAGATT-CTCCCTA
1 GGGGTACAGATTCCCCCCTA
*
28826 AGGGTACAGATTCCCCCCTA
1 GGGGTACAGATTCCCCCCTA
*
28846 TGGGGTACCGATTCCCCC
1 -GGGGTACAGATTCCCCC
28864 TTGTCTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.34
20 6 0.19
21 15 0.47
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCCTA
Found at i:32266 original size:18 final size:18
Alignment explanation
Indices: 32255--32310 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
32245 GATTGTCCAG
32255 GGGGTACAGATTCCCCCA
1 GGGGTACAGATTCCCCCA
32273 GGGGTACAGATTCCCCCTTA
1 GGGGTACAGATTCCCCC--A
*
32293 TGGGGTACCGATTCCCCC
1 -GGGGTACAGATTCCCCC
32311 TTGTCTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 17 0.50
20 1 0.03
21 16 0.47
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (18 bp):
GGGGTACAGATTCCCCCA
Found at i:32299 original size:21 final size:20
Alignment explanation
Indices: 32255--32312 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
32245 GATTGTCCAG
32255 GGGGTACAGATTCCCCC--A
1 GGGGTACAGATTCCCCCTTA
32273 GGGGTACAGATTCCCCCTTA
1 GGGGTACAGATTCCCCCTTA
*
32293 TGGGGTACCGATTCCCCCTT
1 -GGGGTACAGATTCCCCCTT
32313 GTCTAATGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 17 0.47
20 1 0.03
21 18 0.50
ACGTcount: A:0.17, C:0.33, G:0.26, T:0.24
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCTTA
Found at i:34536 original size:22 final size:23
Alignment explanation
Indices: 34501--34559 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
34491 TATCTCAAGT
* *
34501 TCATATAACTCATATAA-CATTT
1 TCATATAACACATATAATCATTG
* *
34523 TCCTATAATACATA-AATCATTG
1 TCATATAACACATATAATCATTG
34545 TCATATAACACATAT
1 TCATATAACACATAT
34560 CATATAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (23 bp):
TCATATAACACATATAATCATTG
Found at i:35025 original size:64 final size:64
Alignment explanation
Indices: 34957--35127 Score: 283
Period size: 64 Copynumber: 2.7 Consensus size: 64
34947 CATATGCATT
34957 GATGCACTACCCCATGCATCGATGCACAATTTACATTCGATGTTTCCATTTTAAGGGGTGTATC
1 GATGCACTACCCCATGCATCGATGCACAATTTACATTCGATGTTTCCATTTTAAGGGGTGTATC
35021 GATGCACTACCCCATGCATCGATGCACAATTTACATTCGATGTTTCCATTTTAAGGGGTGTATC
1 GATGCACTACCCCATGCATCGATGCACAATTTACATTCGATGTTTCCATTTTAAGGGGTGTATC
** * *
35085 GATGCACT-CCTTATGCATCGATGCACTCA-CTACATTCGATGTT
1 GATGCACTACCCCATGCATCGATGCAC-AATTTACATTCGATGTT
35128 CATTTAATTG
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
63 29 0.28
64 73 0.72
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (64 bp):
GATGCACTACCCCATGCATCGATGCACAATTTACATTCGATGTTTCCATTTTAAGGGGTGTATC
Found at i:36934 original size:5 final size:5
Alignment explanation
Indices: 36886--36951 Score: 55
Period size: 5 Copynumber: 13.0 Consensus size: 5
36876 GAGGCAACCC
* * **
36886 ATTTT ATTTC ATTTT CATTTT A-TTT ATTTC ATTCC A-TTT ATTTT ATTTTT
1 ATTTT ATTTT ATTTT -ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A-TTTT
36936 ATTTTT ATTTT ATTTT
1 A-TTTT ATTTT ATTTT
36952 TTTCTCTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
4 6 0.12
5 29 0.57
6 16 0.31
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.73
Consensus pattern (5 bp):
ATTTT
Found at i:41801 original size:458 final size:455
Alignment explanation
Indices: 40944--41860 Score: 1780
Period size: 458 Copynumber: 2.0 Consensus size: 455
40934 CTGTTTTTGC
40944 AAAAGTAGCAGGGGCAATGAAGGCTGCCGGTGGTGCTAAGCTGGGTGCTGCTGCAACTGCCATGA
1 AAAAGTAGCAGGGGCAATGAAGGCTGCCGGTGGTGCTAAGCTGGGTGCTGCTGCAACTGCCATGA
41009 CTGTGGCTGCATCAGCTGCTATGACAGGATCCAAACAGGACCCAAGAGATGGATCTAAGCGACCT
66 CTGTGGCTGCATCAGCTGCTATGACAGGATCCAAACAGGACCCAAGAGATGGATCTAAGCGACCT
41074 CCAAAATGATATGCCTTCTCTTTCTTTCTTTCGGCAGCTTCTAGATGTTTGCATTTTAGGTAGCA
131 CCAAAATGATATGCCTTCTCTTTCTTTCTTTCGGCAGCTTCTAGATGTTTGCATTTTAGGTAGCA
41139 TACTTGGCTGCTCACAGGGAAGCTTGTCGAGAGCAGATGGCTATGCTTGGCGATCCGTTTTTGGT
196 TACTTGGCTGCTCACAGGGAAGCTTGTCGAGAGCAGATGGCTATGCTTGGCGATCCGTTTTTGGT
41204 CATTACTGAGTTTTCTTTTGAAATCACTTGAAATAAGAAAAACCAACGTTTTTTATTTGAATTAA
261 CATTACTGAGTTTTCTTTTGAAATCACTTGAAATAAGAAAAACCAACGTTTTTTATTTGAATTAA
41269 GAAGATGGTATGTTGCTATTCAAGTACAAACGTGAATGTTTCTCTTACATTCTAAAGCATAAAGT
326 GAAGATGGTATGTTGCTATTCAAGTACAAACGTGAATGTTTCTCTTACATTCTAAAGCATAAAGT
41334 ACGGTTGTTTTATTTGAAGTAGCCTTTCTGGCTCACTTGCATACAGCCCAAACACACATTCCCTC
391 ACGGTTGTTTTATTT---GTAGCCTTTCTGGCTCACTTGCATACAGCCCAAACACACATTCCCTC
41399 TGA
453 TGA
41402 AAAAGTAGCAGGGGCAATGAAGGCTGCCGGTGGTGCTAAGCTGGGTGCTGCTGCAACTGCCATGA
1 AAAAGTAGCAGGGGCAATGAAGGCTGCCGGTGGTGCTAAGCTGGGTGCTGCTGCAACTGCCATGA
41467 CTGTGGCTGCATCAGCTGCTATGACAGGATCCAAACAGGACCCAAGAGATGGATCTAAGCGACCT
66 CTGTGGCTGCATCAGCTGCTATGACAGGATCCAAACAGGACCCAAGAGATGGATCTAAGCGACCT
41532 CCAAAATGATATGCCTTCTCTTTCTTTCTTTCGGCAGCTTCTAGATGTTTGCATTTTAGGTAGCA
131 CCAAAATGATATGCCTTCTCTTTCTTTCTTTCGGCAGCTTCTAGATGTTTGCATTTTAGGTAGCA
41597 TACTTGGCTGCTCACAGGGAAGCTTGTCGAGAGCAGATGGCTATGCTTGGCGATCCGTTTTTGGT
196 TACTTGGCTGCTCACAGGGAAGCTTGTCGAGAGCAGATGGCTATGCTTGGCGATCCGTTTTTGGT
41662 CATTACTGAGTTTTCTTTTGAAATCACTTGAAATAAGAAAAACCAACGTTTTTTATTTGAATTAA
261 CATTACTGAGTTTTCTTTTGAAATCACTTGAAATAAGAAAAACCAACGTTTTTTATTTGAATTAA
*
41727 GAAGATGGTATGTTGCTATTCAAGTACACACGTGAATGTTTCTCTTACATTCTAAAGCATAAAGT
326 GAAGATGGTATGTTGCTATTCAAGTACAAACGTGAATGTTTCTCTTACATTCTAAAGCATAAAGT
* *
41792 ACGGTTGTTTTATTTGTAGCCTTTCTGGCTCACTTGCATACAGCCCAAACGCACATTCCCTCTGG
391 ACGGTTGTTTTATTTGTAGCCTTTCTGGCTCACTTGCATACAGCCCAAACACACATTCCCTCTGA
41857 AAAA
1 AAAA
41861 TGGAAACATT
Statistics
Matches: 456, Mismatches: 3, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
455 52 0.11
458 404 0.89
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (455 bp):
AAAAGTAGCAGGGGCAATGAAGGCTGCCGGTGGTGCTAAGCTGGGTGCTGCTGCAACTGCCATGA
CTGTGGCTGCATCAGCTGCTATGACAGGATCCAAACAGGACCCAAGAGATGGATCTAAGCGACCT
CCAAAATGATATGCCTTCTCTTTCTTTCTTTCGGCAGCTTCTAGATGTTTGCATTTTAGGTAGCA
TACTTGGCTGCTCACAGGGAAGCTTGTCGAGAGCAGATGGCTATGCTTGGCGATCCGTTTTTGGT
CATTACTGAGTTTTCTTTTGAAATCACTTGAAATAAGAAAAACCAACGTTTTTTATTTGAATTAA
GAAGATGGTATGTTGCTATTCAAGTACAAACGTGAATGTTTCTCTTACATTCTAAAGCATAAAGT
ACGGTTGTTTTATTTGTAGCCTTTCTGGCTCACTTGCATACAGCCCAAACACACATTCCCTCTGA
Found at i:50303 original size:48 final size:48
Alignment explanation
Indices: 50204--50323 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
50194 GTTCACTTGG
* * * *
50204 CTCTCCATCATCTTGTCCACTGAGTTGCTCATGACTTCGATCACTAGA
1 CTCTCCACCACCTTGTCCACTGAGTTGCTCATGAATTCGATCACGAGA
* *
50252 CTCTCCACCACCTTGTCCACTGAGTTGTTCATGAATTTG-TGCATCGA-A
1 CTCTCCACCACCTTGTCCACTGAGTTGCTCATGAATTCGAT-CA-CGAGA
*
50300 CTCTCCACTACCTTGTCCACTGAG
1 CTCTCCACCACCTTGTCCACTGAG
50324 CTCATTTATG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
47 1 0.02
48 60 0.95
49 2 0.03
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.33
Consensus pattern (48 bp):
CTCTCCACCACCTTGTCCACTGAGTTGCTCATGAATTCGATCACGAGA
Found at i:58578 original size:23 final size:24
Alignment explanation
Indices: 58543--58603 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
58533 TTACGCGATC
*
58543 CTTCAG-GACAAATT-TACATGGCA
1 CTTCAGTG-CAAATTCTACATGACA
* * *
58566 CTTCGGTGTAAATTCTACGTGACA
1 CTTCAGTGCAAATTCTACATGACA
58590 CTTCAGTGCAAATT
1 CTTCAGTGCAAATT
58604 ATATTAGTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (24 bp):
CTTCAGTGCAAATTCTACATGACA
Found at i:63858 original size:20 final size:21
Alignment explanation
Indices: 63829--63880 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
63819 AATTGAAGTA
* * *
63829 GTATCGATACTGATGTGG-AG
1 GTATCAATACTGAAGAGGAAG
*
63849 GTATCAATAC-CAAGAGGAAG
1 GTATCAATACTGAAGAGGAAG
63869 GTATCAATACTG
1 GTATCAATACTG
63881 TTATTGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (21 bp):
GTATCAATACTGAAGAGGAAG
Found at i:67382 original size:22 final size:24
Alignment explanation
Indices: 67352--67400 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
67342 ATTGCCTTCG
* *
67352 TTGATTGTTGATTG-TGTTGAC-T
1 TTGACTGTTGATCGATGTTGACGT
67374 TTGACTGTTGATCGATGTTGACGT
1 TTGACTGTTGATCGATGTTGACGT
67398 TTG
1 TTG
67401 TCAAAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 7 0.30
24 4 0.17
ACGTcount: A:0.14, C:0.08, G:0.29, T:0.49
Consensus pattern (24 bp):
TTGACTGTTGATCGATGTTGACGT
Found at i:68386 original size:3 final size:3
Alignment explanation
Indices: 68378--68406 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
68368 TGATTTTTAA
68378 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
68407 AAAAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Done.