Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003536.1 Hibiscus syriacus cultivar Beakdansim tig00007462_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: 136306
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1040 original size:26 final size:28
Alignment explanation
Indices: 1003--1058 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 28
993 AGAATTATAG
1003 AATTGCCCCTGAAGTATAAAATGA-CTA
1 AATTGCCCCTGAAGTATAAAATGACCTA
*
1030 AATT-CCCCTGAAGTGTAAAATGACCTA
1 AATTGCCCCTGAAGTATAAAATGACCTA
1057 AA
1 AA
1059 GTATCTCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (28 bp):
AATTGCCCCTGAAGTATAAAATGACCTA
Found at i:2343 original size:13 final size:13
Alignment explanation
Indices: 2325--2350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2315 GTCATGGAAC
2325 TATATATATATAT
1 TATATATATATAT
2338 TATATATATATAT
1 TATATATATATAT
2351 ATGGTGTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:16731 original size:14 final size:14
Alignment explanation
Indices: 16712--16774 Score: 99
Period size: 14 Copynumber: 4.5 Consensus size: 14
16702 ACTTAGATTT
*
16712 AGTCAACTTGTCTG
1 AGTCAACTCGTCTG
* *
16726 AGTCAACTAGTCCG
1 AGTCAACTCGTCTG
16740 AGTCAACTCGTCTG
1 AGTCAACTCGTCTG
16754 AGTCAACTCGTCTG
1 AGTCAACTCGTCTG
16768 AGTCAAC
1 AGTCAAC
16775 ATATTTAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 45 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (14 bp):
AGTCAACTCGTCTG
Found at i:16808 original size:13 final size:14
Alignment explanation
Indices: 16783--16812 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
16773 ACATATTTAG
16783 TTTGACACGTTGAC
1 TTTGACACGTTGAC
16797 TTTGAC-CGTTGAC
1 TTTGACACGTTGAC
16810 TTT
1 TTT
16813 AACCCACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (14 bp):
TTTGACACGTTGAC
Found at i:26585 original size:21 final size:21
Alignment explanation
Indices: 26559--26598 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26549 TGCATCAAGG
26559 CTTTTGTAGACGCCATGAAAT
1 CTTTTGTAGACGCCATGAAAT
* *
26580 CTTTTGTCGAGGCCATGAA
1 CTTTTGTAGACGCCATGAA
26599 TTAGTGCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
CTTTTGTAGACGCCATGAAAT
Found at i:28181 original size:21 final size:19
Alignment explanation
Indices: 28143--28188 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
28133 AATTAATCAT
28143 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
28163 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
28184 A-TAAT
1 ACTAAT
28189 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:32959 original size:5 final size:6
Alignment explanation
Indices: 32944--32968 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32934 TTCGCTTCAT
32944 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
32969 CCTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:38462 original size:18 final size:19
Alignment explanation
Indices: 38424--38462 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
38414 TTTCAAGGCT
*
38424 ATGTGCATCGATGCACATCA
1 ATGTGCACCGATG-ACATCA
38444 ATGTGCACCGATG-CATCA
1 ATGTGCACCGATGACATCA
38462 A
1 A
38463 GGATAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (19 bp):
ATGTGCACCGATGACATCA
Found at i:38942 original size:25 final size:25
Alignment explanation
Indices: 38887--38948 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
38877 ATAAGTCTAG
*
38887 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCACA
* *
38913 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCA-CA
38938 ATTCATATTAT
1 ATTCATATTAT
38949 ATGCATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCACA
Found at i:39040 original size:31 final size:30
Alignment explanation
Indices: 38991--39050 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
38981 TTATATAAGC
*
38991 TATGTGATACAATGATGGAACATGATATGTT
1 TATGTGATACAAGGATGGAA-ATGATATGTT
*
39022 TATGTGATA-AAGGTATGGAAATTATATGT
1 TATGTGATACAAGG-ATGGAAATGATATGT
39051 CTATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
TATGTGATACAAGGATGGAAATGATATGTT
Found at i:39334 original size:23 final size:23
Alignment explanation
Indices: 39290--39334 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39280 CGGTGCACGC
*
39290 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTATACGT
*
39313 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
39335 AGTTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGT
Found at i:58457 original size:22 final size:23
Alignment explanation
Indices: 58413--58457 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
58403 CAATCTTATA
*
58413 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
58436 TGGCACT-CGGTGTATTTATACG
1 TGGCACTACGGTGCAATTATACG
58458 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:59157 original size:44 final size:45
Alignment explanation
Indices: 59053--59157 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 45
59043 GGGTATGAAC
* * * * * *
59053 TGGGTCACATAGCATTAGCATCTCACAAGTACCATAGGTGAGGTT
1 TGGGTCACATAGCATCAACACCTCACAAGTAACATAGCTGAGGTA
*
59098 TGGGTCACATAGCATCAACACCTCAC-AGTAACTTAAGCT-AGGTA
1 TGGGTCACATAGCATCAACACCTCACAAGTAACAT-AGCTGAGGTA
59142 TGGGTCACATAGCATC
1 TGGGTCACATAGCATC
59158 GGTACCTTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 26 0.50
45 26 0.50
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (45 bp):
TGGGTCACATAGCATCAACACCTCACAAGTAACATAGCTGAGGTA
Found at i:61409 original size:20 final size:21
Alignment explanation
Indices: 61386--61435 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
61376 GTCATTACCA
* *
61386 TTCATCTAA-AGTCGTGACTT
1 TTCATCCAAGAGTCATGACTT
*
61406 TTCA-CCAAGAGTCATGTCTT
1 TTCATCCAAGAGTCATGACTT
61426 TTCAT-CAAGA
1 TTCATCCAAGA
61436 TTGGTATCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (21 bp):
TTCATCCAAGAGTCATGACTT
Found at i:62243 original size:26 final size:26
Alignment explanation
Indices: 62207--62259 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
62197 GCCTACCCTA
62207 TGTCCTTACTTCTACTACCTTTAACT
1 TGTCCTTACTTCTACTACCTTTAACT
62233 TGTCCTTACTTCTACTACCTTTAACT
1 TGTCCTTACTTCTACTACCTTTAACT
62259 T
1 T
62260 TTCTTTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.04, T:0.47
Consensus pattern (26 bp):
TGTCCTTACTTCTACTACCTTTAACT
Found at i:63174 original size:107 final size:107
Alignment explanation
Indices: 63041--63254 Score: 428
Period size: 107 Copynumber: 2.0 Consensus size: 107
63031 CCTAAATTTT
63041 TAAACATATAAACCTTAATTTTTTAAATCCCTAAATTATTATATTATAAACCCTTGTTGCATACT
1 TAAACATATAAACCTTAATTTTTTAAATCCCTAAATTATTATATTATAAACCCTTGTTGCATACT
63106 AATCTTGGATGGCTCATTGCGTAATTTCCAACAATGATAGGA
66 AATCTTGGATGGCTCATTGCGTAATTTCCAACAATGATAGGA
63148 TAAACATATAAACCTTAATTTTTTAAATCCCTAAATTATTATATTATAAACCCTTGTTGCATACT
1 TAAACATATAAACCTTAATTTTTTAAATCCCTAAATTATTATATTATAAACCCTTGTTGCATACT
63213 AATCTTGGATGGCTCATTGCGTAATTTCCAACAATGATAGGA
66 AATCTTGGATGGCTCATTGCGTAATTTCCAACAATGATAGGA
63255 AGCAAATGGC
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (107 bp):
TAAACATATAAACCTTAATTTTTTAAATCCCTAAATTATTATATTATAAACCCTTGTTGCATACT
AATCTTGGATGGCTCATTGCGTAATTTCCAACAATGATAGGA
Found at i:69307 original size:19 final size:20
Alignment explanation
Indices: 69283--69325 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
69273 AATCATTATA
69283 AAAAAAATTAGTTT-TG-ATG
1 AAAAAAATTA-TTTGTGAATG
69302 AAAAAAATTATTTGTGAATG
1 AAAAAAATTATTTGTGAATG
69322 AAAA
1 AAAA
69326 TTATTAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.55
20 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (20 bp):
AAAAAAATTATTTGTGAATG
Found at i:69315 original size:17 final size:16
Alignment explanation
Indices: 69283--69330 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
69273 AATCATTATA
69283 AAAAAAATTAGTTTTGATG
1 AAAAAAATTA--TTTG-TG
69302 AAAAAAATTATTTGTG
1 AAAAAAATTATTTGTG
*
69318 AATGAAAATTATT
1 AA-AAAAATTATT
69331 AGTTAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 4 0.15
17 13 0.48
19 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAAAAATTATTTGTG
Found at i:71807 original size:22 final size:22
Alignment explanation
Indices: 71758--71809 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
71748 GGTGGGATGG
*
71758 TGTGGGTGGCCTGATGCACCGG
1 TGTGGGTGGCCTGATGCACCGC
71780 TGTGGGTGGCCTGATGCACCAGC
1 TGTGGGTGGCCTGATGCACC-GC
71803 T-TGGGTG
1 TGTGGGTG
71810 CCATGAACGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.10, C:0.21, G:0.44, T:0.25
Consensus pattern (22 bp):
TGTGGGTGGCCTGATGCACCGC
Found at i:71809 original size:28 final size:22
Alignment explanation
Indices: 71756--71799 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
71746 GGGGTGGGAT
71756 GGTGTGGGTGGCCTGATGCACC
1 GGTGTGGGTGGCCTGATGCACC
71778 GGTGTGGGTGGCCTGATGCACC
1 GGTGTGGGTGGCCTGATGCACC
71800 AGCTTGGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.45, T:0.23
Consensus pattern (22 bp):
GGTGTGGGTGGCCTGATGCACC
Found at i:78032 original size:18 final size:16
Alignment explanation
Indices: 78007--78051 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
77997 AATAATATAC
78007 AAATTAAAATATAAACT
1 AAATTAAAATATAAA-T
*
78024 AATATTAAAAAATAAAT
1 AA-ATTAAAATATAAAT
78041 AAA-TAAAATAT
1 AAATTAAAATAT
78052 TCTCAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 1 0.04
17 5 0.20
18 12 0.48
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTAAAATATAAAT
Found at i:83565 original size:22 final size:20
Alignment explanation
Indices: 83537--83589 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
83527 TATTAATATA
83537 ATATTTAAGAAAATATATTAAT
1 ATATTTAAGAAAATAT-TT-AT
83559 ATATTTATA-AAAATATTTAT
1 ATATTTA-AGAAAATATTTAT
*
83579 TTATTT-AGAAA
1 ATATTTAAGAAA
83590 TATCAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 7 0.25
21 2 0.07
22 14 0.50
23 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
ATATTTAAGAAAATATTTAT
Found at i:83574 original size:20 final size:21
Alignment explanation
Indices: 83537--83585 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
83527 TATTAATATA
*
83537 ATATTTAAGAAAATATATTAAT
1 ATATTT-ATAAAATATATTAAT
*
83559 ATATTTATAAAA-ATATTTAT
1 ATATTTATAAAATATATTAAT
*
83579 TTATTTA
1 ATATTTA
83586 GAAATATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.54
21 5 0.21
22 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATTTATAAAATATATTAAT
Found at i:83999 original size:23 final size:23
Alignment explanation
Indices: 83964--84027 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
83954 TTTATATGAC
*
83964 TATATAATA-AAATAATATTTAAA
1 TATATAA-ACAAATAATATTAAAA
*
83987 TATATAAACAAATAAAATTAAAA
1 TATATAAACAAATAATATTAAAA
84010 TATAAATAAAC-AATAATA
1 TAT--ATAAACAAATAATA
84028 AAAATACAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 22 0.63
24 6 0.17
25 6 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
TATATAAACAAATAATATTAAAA
Found at i:84029 original size:21 final size:21
Alignment explanation
Indices: 83982--84033 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
83972 AAAATAATAT
*
83982 TTAAATATATAAACAAATAAAA
1 TTAAA-ATATAAACAAACAAAA
*
84004 TTAAAATATAAATAAACAATAA
1 TTAAAATATAAACAAACAA-AA
*
84026 TAAAAATA
1 TTAAAATA
84034 CAATTAGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAAAATATAAACAAACAAAA
Found at i:85395 original size:3 final size:3
Alignment explanation
Indices: 85387--85462 Score: 89
Period size: 3 Copynumber: 24.7 Consensus size: 3
85377 TTATTTATTA
* * *
85387 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAAT AAT AAT ACT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
**
85434 AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
85463 ATTTAAATGA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:86226 original size:113 final size:113
Alignment explanation
Indices: 85697--86548 Score: 1180
Period size: 113 Copynumber: 7.5 Consensus size: 113
85687 AGGTTGAATA
* * * *
85697 AGTTCTTCTCATTATGAACTTT-TACCTGGCAATGCTGATCCATCGAGTGATGGATTTGAGCAAA
1 AGTTCTTCTCATTATGAACTTTCT--CTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAA
* *
85761 AAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
64 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
* * * * * *
85811 AGTTCTTCTCATTATG-ACCTTCTACCTGGCAATGTTGATCCATCGAGTGATGGATTTGAGCAAA
1 AGTTCTTCTCATTATGAACTTTCT--CTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAA
* ** *
85875 AGGTTGAACAAATTCTTCTCATTATGAATTTATTCTT-CTTC-AGATGACG
64 AGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA-GATG
* * * * * * * *
85924 AGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAA
1 AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAA
* *
85988 GGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATG
65 GGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
* * * * * * * * * *
86036 ACAAGTTCTTCTCATTATGAACTCTATTTGGAAATGTTAATCCATCAAATAATGAATTTAAACAA
1 ---AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAA
86101 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
63 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
86152 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
86217 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
*
86265 AGTTCTTCTCATTATGAATTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
*
86330 GTTGAACAAATTCTTCTCATTATGAATTTATTCTTCCTTCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
* *
86378 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTAATCCATTAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
86443 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTCCTTCAGATG
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTT-CTTCAGATG
*
86491 AGTTCTTCTCATTATGAAC-TTCTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
1 AGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
86549 ATCTTTGCTA
Statistics
Matches: 676, Mismatches: 49, Indels: 27
0.90 0.07 0.04
Matches are distributed among these distances:
112 79 0.12
113 399 0.59
114 93 0.14
115 95 0.14
116 10 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
Found at i:86974 original size:22 final size:22
Alignment explanation
Indices: 86949--87025 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
86939 GATAAAGCTT
** *
86949 TCATCTTTGAAAAGAGAAAATG
1 TCATCTTTGAAAAGAGAATCTA
* *
86971 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
86993 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
87015 TCATCTTTGAA
1 TCATCTTTGAA
87026 GAGTGTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:89786 original size:93 final size:92
Alignment explanation
Indices: 89628--89813 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 92
89618 CTACGAGAAA
*
89628 ATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 ATTCATCTTCCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
89693 AACACTTCCAGAAGATGCTATGAGCAC
66 AACACTTCCAGAAGATGCTATGAGCAC
* *
89720 ATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 ATTCATCTTCCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
89785 GAACACTTCCAGAAGATGCTATGAGCAC
65 GAACACTTCCAGAAGATGCTATGAGCAC
89813 A
1 A
89814 CAACACTTGT
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 24 0.27
93 66 0.73
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (92 bp):
ATTCATCTTCCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGAGCAC
Found at i:92048 original size:2 final size:2
Alignment explanation
Indices: 92041--92068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
92031 ACAACAAAGG
92041 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
92069 TAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97037 original size:16 final size:17
Alignment explanation
Indices: 97016--97048 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
97006 AAATATAATA
97016 TATTTA-TAAAAATATT
1 TATTTATTAAAAATATT
97032 TATTTATTTAAAAATAT
1 TATTTA-TTAAAAATAT
97049 CAGAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTATTAAAAATATT
Found at i:97045 original size:19 final size:18
Alignment explanation
Indices: 96996--97045 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
96986 TATTAATATA
96996 ATATTTAAGAAAATATAAT
1 ATATTTAA-AAAATATAAT
*
97015 ATATTTATAAAAATATTTAT
1 ATATTTA-AAAAATA-TAAT
*
97035 TTATTTAAAAA
1 ATATTTAAAAA
97046 TATCAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATATTTAAAAAATATAAT
Found at i:97444 original size:22 final size:21
Alignment explanation
Indices: 97416--97470 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
97406 TATTTATGAC
*
97416 TATATAATAAAATAATATTTAA
1 TATATAATAAAATAA-AATTAA
97438 TATATAA-ACAAATAAAATTAA
1 TATATAATA-AAATAAAATTAA
*
97459 AATATAAATAAA
1 TATAT-AATAAA
97471 CAATAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 10 0.36
22 17 0.61
23 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TATATAATAAAATAAAATTAA
Found at i:98845 original size:3 final size:3
Alignment explanation
Indices: 98837--98912 Score: 80
Period size: 3 Copynumber: 24.7 Consensus size: 3
98827 TTATTTATTA
* * * *
98837 AAT AAT AAT AAT ATAT AAT ATT ACT ATT AAT AAT AAAT AAT AAT ACT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
**
98884 AAT AAT AAT AAT TTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
98913 ATTTAATTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:98868 original size:22 final size:22
Alignment explanation
Indices: 98839--98912 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
98829 ATTTATTAAA
* *
98839 TAATAATAATATATAATATTAC
1 TAATAATAATAAATAATAATAC
*
98861 TATTAATAATAAATAATAATAC
1 TAATAATAATAAATAATAATAC
** *
98883 TAATAATAAT-AATTTTAATAA
1 TAATAATAATAAATAATAATAC
98904 TAATAATAA
1 TAATAATAA
98913 ATTTAATTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 17 0.38
22 28 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATAATAATAAATAATAATAC
Found at i:99198 original size:18 final size:18
Alignment explanation
Indices: 99175--99211 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
99165 TCGTTTCACT
99175 CACACTCGGCGATGACAC
1 CACACTCGGCGATGACAC
99193 CACACTCGGCGATGACAC
1 CACACTCGGCGATGACAC
99211 C
1 C
99212 CAGACAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.41, G:0.22, T:0.11
Consensus pattern (18 bp):
CACACTCGGCGATGACAC
Found at i:114664 original size:17 final size:17
Alignment explanation
Indices: 114642--114679 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
114632 ATTAACAGTG
*
114642 GGAATAAAAGATTATCA
1 GGAATAAAAGATTACCA
114659 GGAATAAAAGATTACCA
1 GGAATAAAAGATTACCA
114676 GGAA
1 GGAA
114680 ATAGGATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.18
Consensus pattern (17 bp):
GGAATAAAAGATTACCA
Found at i:119229 original size:31 final size:31
Alignment explanation
Indices: 119191--119250 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
119181 ATTACACGAT
**
119191 TTTTATTTAGGATTTAAGATTTATAATTTTA
1 TTTTATTTAAAATTTAAGATTTATAATTTTA
*
119222 TTTTATTTAAAATTTAAGATTTGTAATTT
1 TTTTATTTAAAATTTAAGATTTATAATTT
119251 AACAAGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (31 bp):
TTTTATTTAAAATTTAAGATTTATAATTTTA
Done.