Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005444.1 Hibiscus syriacus cultivar Beakdansim tig00012477_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: 83122
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:13482 original size:20 final size:20
Alignment explanation
Indices: 13457--13498 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
13447 AAAATTAATC
13457 ATGTTCAAACAATCAAATTA
1 ATGTTCAAACAATCAAATTA
*
13477 ATGTTCAAAGAATCAAATTA
1 ATGTTCAAACAATCAAATTA
13497 AT
1 AT
13499 TTTTAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (20 bp):
ATGTTCAAACAATCAAATTA
Found at i:17222 original size:22 final size:21
Alignment explanation
Indices: 17180--17219 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17170 GAGTTTATTT
*
17180 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
17201 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
17220 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:26515 original size:66 final size:66
Alignment explanation
Indices: 26434--26565 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
26424 TTCTAACAAT
26434 TCTTTTCCAAATCCAATAATCTTGGGTAGAATACACCCTACAAACCAACATAGACATACTATCAA
1 TCTTTTCCAAATCCAATAATCTTGGGTAGAATACACCCTACAAACCAACATAGACATACTATCAA
26499 C
66 C
26500 TCTTTTCCAAATCCAATAATCTTGGGTAGAATACACCCTACAAACCAACATAGACATACTATCAA
1 TCTTTTCCAAATCCAATAATCTTGGGTAGAATACACCCTACAAACCAACATAGACATACTATCAA
26565 C
66 C
26566 GTCGTGTTTG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (66 bp):
TCTTTTCCAAATCCAATAATCTTGGGTAGAATACACCCTACAAACCAACATAGACATACTATCAA
C
Found at i:33467 original size:18 final size:18
Alignment explanation
Indices: 33443--33498 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
33433 CGAGGGTTAT
33443 AAGTGGTCATTCGGGACA
1 AAGTGGTCATTCGGGACA
* * *
33461 TAGTGGTCCTTCGTGACA
1 AAGTGGTCATTCGGGACA
*
33479 AAGTGGTCATTCGGAACA
1 AAGTGGTCATTCGGGACA
33497 AA
1 AA
33499 TTTTAAGTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (18 bp):
AAGTGGTCATTCGGGACA
Found at i:34737 original size:23 final size:24
Alignment explanation
Indices: 34711--34770 Score: 104
Period size: 23 Copynumber: 2.5 Consensus size: 24
34701 AAAGCACTAT
34711 ACAAACATGACAAGAAAAAGAAA-
1 ACAAACATGACAAGAAAAAGAAAC
*
34734 ACAAACATGACACGAAAAAGAAAC
1 ACAAACATGACAAGAAAAAGAAAC
34758 ACAAACATGACAA
1 ACAAACATGACAA
34771 ATATATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.65, C:0.18, G:0.12, T:0.05
Consensus pattern (24 bp):
ACAAACATGACAAGAAAAAGAAAC
Found at i:38132 original size:20 final size:20
Alignment explanation
Indices: 38107--38182 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
38097 GGCTGCTGGA
38107 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
* *
38127 AACCGGTTCTGACCGATTTT-
1 AACCGGTT-TAACCGGTTTTC
*
38147 GACCGGTTTCAACCGG--TTC
1 AACCGGTTT-AACCGGTTTTC
*
38166 GAACCGGTTTGACCGGT
1 -AACCGGTTTAACCGGT
38183 CTGACCTGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
18 2 0.05
19 6 0.14
20 27 0.61
21 9 0.20
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.30
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTC
Found at i:38159 original size:30 final size:29
Alignment explanation
Indices: 38107--38182 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 29
38097 GGCTGCTGGA
*
38107 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTC-G
*
38138 -ACCGATTTTGACCGGTTTCAACCGGTTCG
1 AACCG-GTTTGACCGGTTTCAACCGGTTCG
38167 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
38183 CTGACCTGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 11 0.28
30 21 0.52
31 8 0.20
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.30
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:38161 original size:10 final size:10
Alignment explanation
Indices: 38107--38175 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
38097 GGCTGCTGGA
38107 AACCGGTTT-
1 AACCGGTTTC
38116 AACCGGTTTTC
1 AACCGG-TTTC
38127 AACCGG-TTC
1 AACCGGTTTC
* * *
38136 TGACCGATTTT
1 -AACCGGTTTC
*
38147 GACCGGTTTC
1 AACCGGTTTC
38157 AACCGG-TTC
1 AACCGGTTTC
38166 GAACCGGTTT
1 -AACCGGTTT
38176 GACCGGTCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 12 0.25
10 26 0.54
11 10 0.21
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:38214 original size:5 final size:5
Alignment explanation
Indices: 38185--38242 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
38175 TGACCGGTCT
* * *
38185 GACCT GACCT GACCC GACCGTC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACC--C GACCC GACCC
38234 GACCC GACC
1 GACCC GACC
38243 GTTGATCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
5 37 0.80
7 9 0.20
ACGTcount: A:0.19, C:0.50, G:0.22, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:38215 original size:17 final size:17
Alignment explanation
Indices: 38190--38237 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
38180 GGTCTGACCT
*
38190 GACCTGACCCGACCGTC
1 GACCCGACCCGACCGTC
*
38207 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTC
38224 GACCCGACCCGACC
1 GACCCGACCCGACC
38238 CGACCGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (17 bp):
GACCCGACCCGACCGTC
Found at i:38215 original size:22 final size:21
Alignment explanation
Indices: 38176--38244 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
38166 GAACCGGTTT
*
38176 GACCGGTCTGACCTGACCTGACCC
1 GACC-GTC-GACCCGACC-GACCC
38200 GACCGTCGA--C--CCGACCC
1 GACCGTCGACCCGACCGACCC
*
38217 GACCGTTGACCCGACCCGACCC
1 GACCGTCGACCCGA-CCGACCC
38239 GACCGT
1 GACCGT
38245 TGATCGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
17 13 0.34
18 2 0.05
19 1 0.03
22 15 0.39
23 3 0.08
24 4 0.11
ACGTcount: A:0.17, C:0.46, G:0.25, T:0.12
Consensus pattern (21 bp):
GACCGTCGACCCGACCGACCC
Found at i:38245 original size:22 final size:22
Alignment explanation
Indices: 38206--38247 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
38196 ACCCGACCGT
38206 CGACCCGACCCGACCGTTGACC
1 CGACCCGACCCGACCGTTGACC
38228 CGACCCGACCCGACCGTTGA
1 CGACCCGACCCGACCGTTGA
38248 TCGTTGACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.10
Consensus pattern (22 bp):
CGACCCGACCCGACCGTTGACC
Found at i:45681 original size:335 final size:336
Alignment explanation
Indices: 45184--45804 Score: 919
Period size: 335 Copynumber: 1.9 Consensus size: 336
45174 ACGGTTGGCT
* * *** * *
45184 TTTTCAGAGGTCATTTAATGTAGAATTCAAGTGACTTTTCAGAAAATGGGTAAAATAGTGGTGCA
1 TTTTCAGAAGTCATTCAATGTAGAATTCAAACAACATTTCAAAAAATGGGTAAAATAGTGGTGCA
* * *
45249 TTATCATCTTCAGCAACTTTTCAATAATATATCAACTCAAATCAGAAAGCATTTTTTTAACTCAG
66 TTATCATCTTCAACAACTTTTCAATAATATATCAAATCAAATCAGAAAGAATTTTTTTAACTCAG
45314 GAAAAATAATGCACCATTCCAGCTATTTTTCAGTGAAATATGAACTCAAATCAGAAAACTTTTCA
131 GAAAAATAATGCACCATTCCAGCTATTTTTCAGTGAAATATGAACTCAAAT-AGAAAACTTTTCA
* * * *
45379 GTGTTGCATTATCACTTCAAATCA-CAAAAACGTGTATTTCAA-TCAGGCCAAATTATTTACTGT
195 GTGTTGAATTATCACTTCAAATCATAAAAAACGTATATTTCAACT-AGGCCAAATTATTCACTGT
*
45442 TTGAACAACTTTTCAATGCTCAATTAATACACGTTTCAGTAACTTTTCAAATGTCATTTATTGCA
259 TTGAACAACTTTTCAATGCACAATTAATACACGTTTCAGTAACTTTTCAAATGTCATTTATTGCA
45507 TCAATAATGCAAC
324 TCAATAATGCAAC
* * * *
45520 TTTTCAGAAGTCATTCAATGTATAATTTAAACAACATTTCAAAAAATGGGTGAAATAGTTGTGCA
1 TTTTCAGAAGTCATTCAATGTAGAATTCAAACAACATTTCAAAAAATGGGTAAAATAGTGGTGCA
* *
45585 TTATCATCTTCAACAACTTTTCAATGATATATTAAATCAAAT-A-AAA-AATGTGTTTTTAACTC
66 TTATCATCTTCAACAACTTTTCAATAATATATCAAATCAAATCAGAAAGAAT-T-TTTTTAACTC
* * *
45647 AGGCAAAATAATGCACCCTTCCAGCTATTTTTCAGTGAAATATGAACTCAAATAGAAAACTTTTT
129 AGGAAAAATAATGCACCATTCCAGCTATTTTTCAGTGAAATATGAACTCAAATAGAAAACTTTTC
* **
45712 AGTGTTGAATTATCACTTCAAATCATAAAAAACTTATATTTCAACTAGGTTAAATTATTCACTGT
194 AGTGTTGAATTATCACTTCAAATCATAAAAAACGTATATTTCAACTAGGCCAAATTATTCACTGT
*
45777 TTGAACAACTTTTCAGTGCACAATTAAT
259 TTGAACAACTTTTCAATGCACAATTAAT
45805 GCACCATTTT
Statistics
Matches: 253, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
333 2 0.01
334 39 0.15
335 119 0.47
336 93 0.37
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (336 bp):
TTTTCAGAAGTCATTCAATGTAGAATTCAAACAACATTTCAAAAAATGGGTAAAATAGTGGTGCA
TTATCATCTTCAACAACTTTTCAATAATATATCAAATCAAATCAGAAAGAATTTTTTTAACTCAG
GAAAAATAATGCACCATTCCAGCTATTTTTCAGTGAAATATGAACTCAAATAGAAAACTTTTCAG
TGTTGAATTATCACTTCAAATCATAAAAAACGTATATTTCAACTAGGCCAAATTATTCACTGTTT
GAACAACTTTTCAATGCACAATTAATACACGTTTCAGTAACTTTTCAAATGTCATTTATTGCATC
AATAATGCAAC
Found at i:46737 original size:21 final size:24
Alignment explanation
Indices: 46682--46737 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 24
46672 TGTCAGAAGG
46682 GTATCGGTACTACTATATTCAGTA
1 GTATCGGTACTACTATATTCAGTA
*
46706 GTATC-G-A-TACTGTA-T-A-TA
1 GTATCGGTACTACTATATTCAGTA
46724 GTATCGGTACTACT
1 GTATCGGTACTACT
46738 TTAGTATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
18 7 0.25
19 2 0.07
20 2 0.07
21 10 0.36
22 1 0.04
23 1 0.04
24 5 0.18
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
GTATCGGTACTACTATATTCAGTA
Found at i:50058 original size:22 final size:22
Alignment explanation
Indices: 50033--50098 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
50023 AGTTGAGGGT
*
50033 TACATAGGTCATTCAGGACATA
1 TACATAGGTCCTTCAGGACATA
* *
50055 TACACAGGTCCTT-AGGGGCATA
1 TACATAGGTCCTTCA-GGACATA
*
50077 TGCATAGGTCCTTC-GGACATA
1 TACATAGGTCCTTCAGGACATA
50098 T
1 T
50099 TTCACATGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
21 8 0.22
22 28 0.78
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (22 bp):
TACATAGGTCCTTCAGGACATA
Found at i:53924 original size:22 final size:22
Alignment explanation
Indices: 53892--53958 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
53882 AGTCGAGGGT
*
53892 TACATAAGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
*
53914 TACATAGGTCCTTCGGGAAATA
1 TACATAGGTCCTTCGGGACATA
* * **
53936 TGCATAGGTTCTTAAGGACATA
1 TACATAGGTCCTTCGGGACATA
53958 T
1 T
53959 TTCATACGCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:61836 original size:29 final size:29
Alignment explanation
Indices: 61794--61885 Score: 184
Period size: 29 Copynumber: 3.2 Consensus size: 29
61784 GTTAGGAGCA
61794 TATACAGCTTACCTTCATGTAAGATTTTG
1 TATACAGCTTACCTTCATGTAAGATTTTG
61823 TATACAGCTTACCTTCATGTAAGATTTTG
1 TATACAGCTTACCTTCATGTAAGATTTTG
61852 TATACAGCTTACCTTCATGTAAGATTTTG
1 TATACAGCTTACCTTCATGTAAGATTTTG
61881 TATAC
1 TATAC
61886 GGAGTGTATC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (29 bp):
TATACAGCTTACCTTCATGTAAGATTTTG
Found at i:64287 original size:17 final size:17
Alignment explanation
Indices: 64239--64287 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
64229 TTTAAGAAAA
*
64239 ATATATTA-ACTTTTAT
1 ATATATTATATTTTTAT
* *
64255 A-ATA-TATATATATAT
1 ATATATTATATTTTTAT
64270 ATATATTATATTTTTAT
1 ATATATTATATTTTTAT
64287 A
1 A
64288 AATAAGATCT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
14 2 0.08
15 9 0.36
16 4 0.16
17 10 0.40
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTATATTTTTAT
Found at i:64548 original size:153 final size:153
Alignment explanation
Indices: 64282--64574 Score: 391
Period size: 153 Copynumber: 1.9 Consensus size: 153
64272 ATATTATATT
* *
64282 TTTATAAATAAGATCTTTATTTATTTAGAAATATCAGAAAAAAACTTCTAGTTGCTTTAAGACAG
1 TTTATAAATAAGATATTTAGTTATTTAGAAATATCAGAAAAAAACTTCTAGTTGCTTTAAGACAG
64347 TCATTTTCTTAATATTAAAAAATAAATAAATATTAATATAACATTTTT-CTAAAAATAATTAAAA
66 TCATTTTCTTAATATTAAAAAATAAATAAATATTAATATAACATTTTTCCTAAAAATAATTAAAA
64411 T-AAATTAAATTAATATATATAA
131 TAAAATTAAATTAATATATATAA
** *
64433 TTTATAAAAGTAAGATATTTAGTTATTTA-AATATATCAGAAAATGACTTCTAGTTGTTTTAAGA
1 TTTAT-AAA-TAAGATATTTAGTTATTTAGAA-ATATCAGAAAAAAACTTCTAGTTGCTTTAAGA
* ** *
64497 TAG-C-TTTTCTTAATATT-AAAAATAAATAAATATTAAAATATGATTATTTTTCCTAAAAGTAA
63 CAGTCATTTTCTTAATATTAAAAAATAAATAAATATT--AATAT-AACATTTTTCCTAAAAATAA
* *
64559 TTTATATAAAATTAAA
125 TTAAAATAAAATTAAA
64575 GTTATTAATA
Statistics
Matches: 123, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
150 17 0.14
151 18 0.15
152 11 0.09
153 55 0.45
154 14 0.11
155 8 0.07
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (153 bp):
TTTATAAATAAGATATTTAGTTATTTAGAAATATCAGAAAAAAACTTCTAGTTGCTTTAAGACAG
TCATTTTCTTAATATTAAAAAATAAATAAATATTAATATAACATTTTTCCTAAAAATAATTAAAA
TAAAATTAAATTAATATATATAA
Found at i:65922 original size:19 final size:19
Alignment explanation
Indices: 65894--65934 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
65884 GGATCTGGCA
65894 AGATCCAACGGTTGAAAGG
1 AGATCCAACGGTTGAAAGG
*
65913 AGATCTAACGGTTGAAAGG
1 AGATCCAACGGTTGAAAGG
65932 AGA
1 AGA
65935 GGCGGCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.12, G:0.32, T:0.17
Consensus pattern (19 bp):
AGATCCAACGGTTGAAAGG
Found at i:66052 original size:3 final size:3
Alignment explanation
Indices: 66044--66168 Score: 132
Period size: 3 Copynumber: 41.0 Consensus size: 3
66034 TTTGGGCATG
* *
66044 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
66091 TAA TTAA -AA TTAA -AA TTA TAA T-A TAA TAA TAAA TACA TAAA TACA
1 TAA -TAA TAA -TAA TAA TAA TAA TAA TAA TAA T-AA TA-A T-AA TA-A
*
66136 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66169 AACCGAATGG
Statistics
Matches: 107, Mismatches: 5, Indels: 20
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.07
3 83 0.78
4 15 0.14
5 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:66671 original size:122 final size:122
Alignment explanation
Indices: 66531--67241 Score: 872
Period size: 123 Copynumber: 5.7 Consensus size: 122
66521 GAATTAAGGC
* * * *
66531 AAGGTTGAACAAATTCTTCTCATTATGAATTTTTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * * *
66596 GAACACTTCTGGAAAGGTTGATACTGATTTATCTCCTTTTGTGATACAGTCATACAA
66 GAACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATACAA
*
66653 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * *
66718 GAACTCTTTTAGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATACAA
66 GAACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATACAA
* *
66775 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
66840 GAACTCTTATGAGAACTCATCTGGAAATGTTGATGCTGATCTATCCCCTTCTGTGATAGAATCGA
66 GAA--C---T-----CT--TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTC-A
*
66905 -GCAA
118 TACAA
* * * *
66909 AAAGTTGAAGAAATTCTTCTCATTACGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * ** * *
66974 GAACTCTTTCTTGAAATGCTGATATTGATCTATCT-CTTCCTATGATAGAATC-TAGCAA
66 GAACTC-TTCTGGAAATGTTGATGCTGATCTATCTCCTT-CTGTGATAGAGTCATA-CAA
* *
67032 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * * * *
67097 GAACTTTCTCTTGAAAAGTTGATGCTGATTTATCTCCTTTTTTGATACAGTCATACAA
66 GAACTCT-TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATACAA
67155 AAGGTTGAACAAGTGT-TTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGT-TCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* *
67219 TAAACTCTTCTGAAAATGTTGAT
65 TGAACTCTTCTGGAAATGTTGAT
67242 CTATTGAGTG
Statistics
Matches: 511, Mismatches: 57, Indels: 42
0.84 0.09 0.07
Matches are distributed among these distances:
122 191 0.37
123 201 0.39
124 8 0.02
125 1 0.00
127 1 0.00
129 1 0.00
132 3 0.01
134 104 0.20
135 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (122 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATACAA
Found at i:67667 original size:22 final size:22
Alignment explanation
Indices: 67633--67708 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
67623 AAATATTTCT
67633 TCTTTGGAA-AGAGAATCTATCA
1 TCTTT-GAAGAGAGAATCTATCA
67655 TCTTTGAAGAGAGAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
* * *
67677 TCTTTAAAGAGAGATTTTATCA
1 TCTTTGAAGAGAGAATCTATCA
*
67699 TATTTGAAGA
1 TCTTTGAAGA
67709 ATGTAGATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 3 0.06
22 45 0.94
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (22 bp):
TCTTTGAAGAGAGAATCTATCA
Found at i:68672 original size:18 final size:18
Alignment explanation
Indices: 68645--68685 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
68635 TATAAAGAAT
* *
68645 AAATTGAATTTCTAAAAG
1 AAATTAAATTTCGAAAAG
*
68663 AAATTAAATTTCGAAAAT
1 AAATTAAATTTCGAAAAG
68681 AAATT
1 AAATT
68686 TGGAATCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (18 bp):
AAATTAAATTTCGAAAAG
Found at i:69048 original size:15 final size:15
Alignment explanation
Indices: 69030--69109 Score: 52
Period size: 15 Copynumber: 5.0 Consensus size: 15
69020 TCATTTTCTA
69030 TTTTTTCTTTTTTTTT
1 TTTTTTC-TTTTTTTT
* **
69046 TTTCATTTCATTTTCAT
1 TTT--TTTCTTTTTTTT
* **
69063 TTTTTTCATTTTCAT
1 TTTTTTCTTTTTTTT
*
69078 TTTTTTCTTTTCATTT
1 TTTTTTCTTTT-TTTT
69094 TTTTTTCTTTCTTTTT
1 TTTTTTCTTT-TTTTT
69110 CCTTCCTCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
15 22 0.42
16 17 0.33
17 9 0.17
18 4 0.08
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:69094 original size:20 final size:21
Alignment explanation
Indices: 69032--69108 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
69022 ATTTTCTATT
*
69032 TTTTC-TTTT-TTTTTTTTCA
1 TTTTCATTTTCTTTCTTTTCA
69051 -TTTCATTTTCATTT-TTTTCA
1 TTTTCATTTTC-TTTCTTTTCA
69071 TTTTCATTTT-TTTCTTTTCA
1 TTTTCATTTTCTTTCTTTTCA
*
69091 TTTT-TTTTTCTTTCTTTT
1 TTTTCATTTTCTTTCTTTT
69109 TCCTTCCTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
18 4 0.08
19 11 0.22
20 24 0.47
21 12 0.24
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTCATTTTCTTTCTTTTCA
Found at i:69633 original size:19 final size:19
Alignment explanation
Indices: 69609--69655 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
69599 CTCGTGCCAA
69609 TCTTTGTAAGTTTCAGTAG
1 TCTTTGTAAGTTTCAGTAG
69628 TCTTTGTAAGTTTCAGTAG
1 TCTTTGTAAGTTTCAGTAG
69647 TCTTTGTAA
1 TCTTTGTAA
69656 TGATTCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (19 bp):
TCTTTGTAAGTTTCAGTAG
Found at i:76327 original size:15 final size:15
Alignment explanation
Indices: 76303--76340 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
76293 AAATAATGCA
*
76303 ATGAATAATGAATGT
1 ATGAAAAATGAATGT
76318 ATGAAAAATGAATGT
1 ATGAAAAATGAATGT
76333 ATGCAAAA
1 ATG-AAAA
76341 GGTATTGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (15 bp):
ATGAAAAATGAATGT
Found at i:77739 original size:31 final size:31
Alignment explanation
Indices: 77641--77731 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
77631 CAATTTAAGG
77641 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
77672 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
77703 CAAAAT-GTTTTTAGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
77732 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 37 0.63
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:79623 original size:22 final size:22
Alignment explanation
Indices: 79595--79641 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
79585 CTTTGGTTTG
79595 AAAAATTCAATTTCTTAATAAA
1 AAAAATTCAATTTCTTAATAAA
*
79617 AAAAATTCAATTTCTTAATGAA
1 AAAAATTCAATTTCTTAATAAA
79639 AAA
1 AAA
79642 GGGGGAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATTCAATTTCTTAATAAA
Found at i:79839 original size:31 final size:31
Alignment explanation
Indices: 79793--79882 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
79783 CAATTTAAGG
79793 CAAAATGG-TTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
79823 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
79854 CAAAAT-GTTTTTAGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
79883 TTCAAAATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
29 11 0.19
30 19 0.33
31 28 0.48
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:80106 original size:21 final size:21
Alignment explanation
Indices: 80080--80121 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
80070 ATTTGAATAT
*
80080 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
80101 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
80122 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Done.