Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007538.1 Hibiscus syriacus cultivar Beakdansim tig00021095_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: 149175
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4427 original size:85 final size:85
Alignment explanation
Indices: 4307--4484 Score: 320
Period size: 85 Copynumber: 2.1 Consensus size: 85
4297 TTCTTTGAGT
*
4307 GTCATTGAATCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
*
4372 ATGTATGACTTACATTGCGC
66 ATATATGACTTACATTGCGC
4392 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
* *
4457 ATATATGACTTACATTGTGT
66 ATATATGACTTACATTGCGC
4477 GTCATTGA
1 GTCATTGA
4485 TGCACACGTC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (85 bp):
GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
ATATATGACTTACATTGCGC
Found at i:4516 original size:85 final size:84
Alignment explanation
Indices: 4307--4516 Score: 242
Period size: 85 Copynumber: 2.5 Consensus size: 84
4297 TTCTTTGAGT
* * * ** *
4307 GTCATTGAATCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
1 GTCATTGAAGCACACGTCATAAA-TAAGACCACAAACATTTGTGCGTCATAAATTTATGACACGC
*
4372 ATGTATGACTTACATTGCGC
65 ATATATGACTTACATTGCGC
* * ** *
4392 GTCATTGAAGCCCCCGTCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGC
1 GTCATTGAAGCACACGTCATAAA-TAAGACCACAAACATTTGTGCGTCATAAATTTATGACACGC
* *
4457 ATATATGACTTACATTGTGT
65 ATATATGACTTACATTGCGC
*
4477 GTCATTGATGCACACGTCATTTAAA-AAGACCACAAACATT
1 GTCATTGAAGCACACGTCA--TAAATAAGACCACAAACATT
4517 CGTTTATCGT
Statistics
Matches: 113, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
85 109 0.96
87 4 0.04
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (84 bp):
GTCATTGAAGCACACGTCATAAATAAGACCACAAACATTTGTGCGTCATAAATTTATGACACGCA
TATATGACTTACATTGCGC
Found at i:4551 original size:2 final size:2
Alignment explanation
Indices: 4544--4643 Score: 177
Period size: 2 Copynumber: 51.0 Consensus size: 2
4534 TTTCAGAAAT
4544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4585 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4627 TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
4644 AAAAATCAAA
Statistics
Matches: 94, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 92 0.98
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:10459 original size:15 final size:15
Alignment explanation
Indices: 10434--10489 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
10424 GATGCTTTCT
*
10434 TTTTCCTTCTTTGACA
1 TTTT-CTTCTTTGACG
10450 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
10465 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
10480 TTGTCTTCTT
1 TTTTCTTCTT
10490 ACCCCATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.09, C:0.21, G:0.11, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:24820 original size:90 final size:88
Alignment explanation
Indices: 24690--24865 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 88
24680 TAATCCTGAA
* * * * *
24690 TATTTAATTTCAATTAATTAAATATATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTA
1 TATTAAATTCCAATTAATTAAATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
24755 GGGTAACTTGGATATAAAAGGAT
66 GGGTAACTTGGATATAAAAGGAT
24778 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATAT--ATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
24843 TAGGGTAACTTGGCTATAAAAGG
64 TAGGGTAACTTGGATATAAAAGG
24866 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 23 0.29
90 57 0.71
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (88 bp):
TATTAAATTCCAATTAATTAAATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
GGGTAACTTGGATATAAAAGGAT
Found at i:31606 original size:90 final size:90
Alignment explanation
Indices: 31491--31668 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
31481 TAATCCCGAA
* * * * *
31491 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAAAAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATATATTTAATTAATTTGAAAAAATAAAAACCCTAATATGAC
31556 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
31581 TATTAAATTCCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATATATTTAATTAATTTGAAAAAATAAAAACCCTAATATGAC
*
31646 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
31669 GTGTGCTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATATATTTAATTAATTTGAAAAAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:33711 original size:20 final size:20
Alignment explanation
Indices: 33686--33723 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33676 TTAATAACTA
*
33686 TTTTAAATTATTTAAATTAT
1 TTTTAAATTATCTAAATTAT
*
33706 TTTTAATTTATCTAAATT
1 TTTTAAATTATCTAAATT
33724 TTCTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAAATTATCTAAATTAT
Found at i:38005 original size:194 final size:194
Alignment explanation
Indices: 37650--38058 Score: 464
Period size: 194 Copynumber: 2.1 Consensus size: 194
37640 GTTTTGCTAC
** *
37650 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGAGAATATAAATTATCAAT
1 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCCGTGAGAATATAAATCATCAAT
** *
37715 AACGAAATCTTATTTAATTCAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGTGACGT
66 AACGAAATCTTACATAATTCAGTGAAATAATCAACTGTCATAGAATATAAATTATAAAGTGACGT
* * *
37780 TATGCATAAACGTCATTAATAATATTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAT
131 TATACATAAACGTCATCAATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAT
* * *
37844 AATATCTCTTTCGTCTCATATAGGTTGATTTTAATGTATTATCCGTGATG-ATATAAATCATCAA
1 AATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCCGTGA-GAATATAAATCATCAA
* * * ** * * * *
37908 TAACGAAATTTTACATAATTTAGTGAAATAATTAGTTGTCATTGAATATTAATTATATAGTGATG
65 TAACGAAATCTTACATAATTCAGTGAAATAATCAACTGTCATAGAATATAAATTATAAAGTGACG
* * * ** * * * * * * *
37973 TTATATATAAATGTCATCCATGCTACTATTAGGTGAC-TATATACTACGTTACTAACAATGTGAC
130 TTATACATAAACGTCATCAATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAT
* *
38037 AAT-TTTCTTTTCGTCACGTATA
1 AATATCTC-TTTCGTCACATATA
38059 CAATGAAATT
Statistics
Matches: 177, Mismatches: 36, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
192 3 0.02
193 36 0.20
194 137 0.77
195 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (194 bp):
AATATCTCTTTCGTCACATATAAGTTGATTTTAATGCATTATCCGTGAGAATATAAATCATCAAT
AACGAAATCTTACATAATTCAGTGAAATAATCAACTGTCATAGAATATAAATTATAAAGTGACGT
TATACATAAACGTCATCAATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTGAT
Found at i:42760 original size:17 final size:17
Alignment explanation
Indices: 42738--42770 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42728 TTGTGCTTCT
*
42738 ACTCTATGTTAAGATAG
1 ACTCTATGTCAAGATAG
42755 ACTCTATGTCAAGATA
1 ACTCTATGTCAAGATA
42771 TATGAGCCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (17 bp):
ACTCTATGTCAAGATAG
Found at i:51988 original size:3 final size:3
Alignment explanation
Indices: 51980--52056 Score: 68
Period size: 3 Copynumber: 25.7 Consensus size: 3
51970 ATGACCTAAA
* * *
51980 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AA- ATT AAT ATCT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * *
52025 ATTT AAT AAT TAT AAT AAT AAA AAT AA- AAT AA
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
52057 AACAATAAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
2 3 0.05
3 51 0.88
4 4 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:52320 original size:53 final size:52
Alignment explanation
Indices: 52241--52391 Score: 185
Period size: 53 Copynumber: 2.8 Consensus size: 52
52231 GACTAGCGGT
* * *
52241 TTCGCTCCCTCTTACTTTAGGAAGTAGAACTCGAACAGTCTTCTGCCGACGGG
1 TTCGCTCCCTCTT-GTTTAGGGAGTAGAACTCGAACAATCTTCTGCCGACGGG
* * * *
52294 TTCGCTCCCTATTGTTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTATGGG
1 TTCGCTCCCTCTTGTTT-AGGGAGTAGAACTCGAACAATCTTCTGCCGACGGG
* * *
52347 TTCACTTCCTCTTGCTTTAGGGGGTAGAACTCGAACAATCTTCTG
1 TTCGCTCCCTCTTG-TTTAGGGAGTAGAACTCGAACAATCTTCTG
52392 GTGTGATTCT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 3 0.04
53 78 0.93
54 3 0.04
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (52 bp):
TTCGCTCCCTCTTGTTTAGGGAGTAGAACTCGAACAATCTTCTGCCGACGGG
Found at i:52470 original size:36 final size:36
Alignment explanation
Indices: 52401--52470 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
52391 GGTGTGATTC
* * *
52401 TGCTTCACTACCCTTCTGTGAATGCTTAAGATGGTT
1 TGCTTCACTACCCTTCTATGAAGGCATAAGATGGTT
* *
52437 TGCTTCACTACTCTTCTATGAAGGCATATGATGG
1 TGCTTCACTACCCTTCTATGAAGGCATAAGATGG
52471 CCCTTGGGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (36 bp):
TGCTTCACTACCCTTCTATGAAGGCATAAGATGGTT
Found at i:55470 original size:6 final size:6
Alignment explanation
Indices: 55456--55494 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
55446 AGCTAATAAG
* * *
55456 AATGCA AATGTA AATGCG AATGCG AATGCA AATGCA AAT
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA AAT
55495 ACACAAGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.21
Consensus pattern (6 bp):
AATGCA
Found at i:58285 original size:16 final size:15
Alignment explanation
Indices: 58261--58307 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
58251 ATATAAATCT
58261 TAAACAAATTAAACC
1 TAAACAAATTAAACC
*
58276 TAAACTAAATTAAACA
1 TAAAC-AAATTAAACC
58292 TAAACAAATTAAACC
1 TAAACAAATTAAACC
58307 T
1 T
58308 CACACAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATTAAACC
Found at i:59613 original size:3 final size:3
Alignment explanation
Indices: 59592--59648 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
59582 CAATTTGTTT
* *
59592 TTA TTG TTA TTA TTG TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
59637 TTA TTA TTA TTA
1 TTA TTA TTA TTA
59649 AAAATACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61045 original size:3 final size:3
Alignment explanation
Indices: 61033--61079 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
61023 ATTTTCAGTA
*
61033 TAT T-T TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61080 ATATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:61924 original size:23 final size:24
Alignment explanation
Indices: 61898--61957 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
61888 ATATATATAC
61898 ATATTATTTTCATAATAT-TTTAT
1 ATATTATTTTCATAATATCTTTAT
* *
61921 ATATTCTTTTTTATTAATATCTTTAT
1 ATATT-ATTTTCA-TAATATCTTTAT
61947 -T-TTATTTTCAT
1 ATATTATTTTCAT
61958 GCATTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.03
23 10 0.33
24 7 0.23
25 7 0.23
26 5 0.17
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (24 bp):
ATATTATTTTCATAATATCTTTAT
Found at i:65161 original size:15 final size:15
Alignment explanation
Indices: 65141--65172 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
65131 ATCAATACAT
65141 TTTTGCATACATTCA
1 TTTTGCATACATTCA
65156 TTTTGCATACATTCA
1 TTTTGCATACATTCA
65171 TT
1 TT
65173 ATTCATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:90187 original size:16 final size:16
Alignment explanation
Indices: 90166--90197 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
90156 ATTTAATTCG
90166 AAGCCCAATTCTGGGC
1 AAGCCCAATTCTGGGC
90182 AAGCCCAATTCTGGGC
1 AAGCCCAATTCTGGGC
90198 CCACCCGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (16 bp):
AAGCCCAATTCTGGGC
Found at i:92092 original size:15 final size:16
Alignment explanation
Indices: 92072--92101 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
92062 TGTCCTAAAT
92072 TAAAATG-TTCAAAAC
1 TAAAATGCTTCAAAAC
92087 TAAAATGCTTCAAAA
1 TAAAATGCTTCAAAA
92102 AAATAAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (16 bp):
TAAAATGCTTCAAAAC
Found at i:94907 original size:44 final size:44
Alignment explanation
Indices: 94841--94930 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
94831 CTCTACTATG
* * *
94841 TACCATATATGAAGGCTCCTCTGTTGTGTGCCAGGGTAAGACCT
1 TACCATATATGAAGGCTCCTCTGTTATATGCAAGGGTAAGACCT
* * *
94885 TACCATTTCTGAAGGCTTCTCTGTTATATGCAAGGGTAAGACCT
1 TACCATATATGAAGGCTCCTCTGTTATATGCAAGGGTAAGACCT
94929 TA
1 TA
94931 TCGCTTTTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (44 bp):
TACCATATATGAAGGCTCCTCTGTTATATGCAAGGGTAAGACCT
Found at i:101783 original size:44 final size:44
Alignment explanation
Indices: 101718--101847 Score: 170
Period size: 44 Copynumber: 3.0 Consensus size: 44
101708 GGAGGAAGTT
* *
101718 TCTGAAGGCTCCTCTGCTGTGTTCTAGGGAAAGACCTTACCATA
1 TCTGAAGGCTCCTCTGCTGTGTTCAAGGGTAAGACCTTACCATA
* * * *
101762 TCTGAAGGCTCCTCTGTTGTGTTCCAGGGTAAGGCCTTACCATT
1 TCTGAAGGCTCCTCTGCTGTGTTCAAGGGTAAGACCTTACCATA
* * * *
101806 TCTGAATGATCCTCTACTATGTTCAAGGGTAAGACCTTACCA
1 TCTGAAGGCTCCTCTGCTGTGTTCAAGGGTAAGACCTTACCA
101848 CTTTTCGTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (44 bp):
TCTGAAGGCTCCTCTGCTGTGTTCAAGGGTAAGACCTTACCATA
Found at i:109870 original size:16 final size:16
Alignment explanation
Indices: 109849--109910 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
109839 AGTTTTAATT
*
109849 ATTAAAGTAAAACAAA
1 ATTAAAGTAAAAGAAA
*
109865 ATTAAA-T-TAAGAAA
1 ATTAAAGTAAAAGAAA
109879 ATATAAAGTAAAAGAAA
1 AT-TAAAGTAAAAGAAA
*
109896 ACTTTAAATTAAAAG
1 A--TTAAAGTAAAAG
109911 CTTTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 7 0.19
17 7 0.19
18 10 0.27
19 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (16 bp):
ATTAAAGTAAAAGAAA
Found at i:110540 original size:13 final size:13
Alignment explanation
Indices: 110519--110553 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
110509 CGAAACGTTT
*
110519 TTTTTCTTGTTGC
1 TTTTGCTTGTTGC
110532 TTTTGCTTGTTGC
1 TTTTGCTTGTTGC
110545 TTTTGCTTG
1 TTTTGCTTG
110554 GTTTGCTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.20, T:0.66
Consensus pattern (13 bp):
TTTTGCTTGTTGC
Found at i:110976 original size:21 final size:20
Alignment explanation
Indices: 110943--111001 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 20
110933 GGAACTGGAC
110943 AGAATAAAA-ATAAAATTAAT
1 AGAA-AAAATATAAAATTAAT
110963 A-AAATATAATATAAAA-T-AT
1 AGAAA-A-AATATAAAATTAAT
110982 AGAAAAAATA-AAAATTAAT
1 AGAAAAAATATAAAATTAAT
111001 A
1 A
111002 TAACATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
17 4 0.12
18 6 0.18
19 10 0.30
20 7 0.21
21 6 0.18
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
AGAAAAAATATAAAATTAAT
Found at i:111076 original size:34 final size:35
Alignment explanation
Indices: 111015--111185 Score: 158
Period size: 34 Copynumber: 4.9 Consensus size: 35
111005 CATAAAATAA
*
111015 TTTAAAAAACTATATATTATA-CGTTTTCAAAATCA-
1 TTTAAAAAA--ATATATTATATAGTTTTCAAAATCAT
* *
111050 TTTAAAAAAATATATTATATATTTTTCAAAACCATT
1 TTTAAAAAAATATATTATATAGTTTTCAAAATCA-T
* * *
111086 TTTAAAACAATATATTATA-CGTTTTCAAAATTACT
1 TTTAAAAAAATATATTATATAGTTTTCAAAATCA-T
*
111121 TTT--AAAAA-ATATTATATATGTTTTCAAAACCATT
1 TTTAAAAAAATATATTATATA-GTTTTCAAAATCA-T
111155 TTATAAAAAACATATATTATAT-GTTTTCAAA
1 TT-TAAAAAA-ATATATTATATAGTTTTCAAA
111186 TTTTTTTATA
Statistics
Matches: 112, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
32 8 0.07
33 14 0.12
34 25 0.22
35 24 0.21
36 18 0.16
37 13 0.12
38 1 0.01
39 9 0.08
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (35 bp):
TTTAAAAAAATATATTATATAGTTTTCAAAATCAT
Found at i:111099 original size:69 final size:70
Alignment explanation
Indices: 111015--111185 Score: 240
Period size: 69 Copynumber: 2.4 Consensus size: 70
111005 CATAAAATAA
* *
111015 TTTAAAAAACTATATATTATACGTTTTCAAAATCA-TTTAAAAAAATATATTATATAT-TTTTCA
1 TTTATAAAACAATATATTATACGTTTTCAAAATCACTTT-AAAAAA-ATATTATATATGTTTTCA
111078 AAACCAT
64 AAACCAT
* *
111085 TTT-TAAAACAATATATTATACGTTTTCAAAATTACTTTTAAAAAATATTATATATGTTTTCAAA
1 TTTATAAAACAATATATTATACGTTTTCAAAATCACTTTAAAAAAATATTATATATGTTTTCAAA
111149 ACCAT
66 ACCAT
* *
111154 TTTATAAAAAACATATATTATATGTTTTCAAA
1 TTTATAAAACA-ATATATTATACGTTTTCAAA
111186 TTTTTTTATA
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
68 11 0.12
69 49 0.54
70 12 0.13
71 19 0.21
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (70 bp):
TTTATAAAACAATATATTATACGTTTTCAAAATCACTTTAAAAAAATATTATATATGTTTTCAAA
ACCAT
Found at i:118626 original size:21 final size:23
Alignment explanation
Indices: 118596--118655 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
118586 GTCAAAATTC
*
118596 TAAACAAAAATATTTTTAAAAGA
1 TAAAGAAAAATATTTTTAAAAGA
**
118619 -AAAG-AAAATA-TAATAAAAGA
1 TAAAGAAAAATATTTTTAAAAGA
118639 TAAAGATAAAATATTTT
1 TAAAGA-AAAATATTTT
118656 ACTACAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
20 8 0.29
21 10 0.36
22 3 0.11
23 6 0.21
24 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (23 bp):
TAAAGAAAAATATTTTTAAAAGA
Found at i:127861 original size:21 final size:23
Alignment explanation
Indices: 127831--127890 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
127821 GTCAAAATTC
*
127831 TAAACAAAAATATTTTTAAAAGA
1 TAAAGAAAAATATTTTTAAAAGA
**
127854 -AAAG-AAAATA-TAATAAAAGA
1 TAAAGAAAAATATTTTTAAAAGA
127874 TAAAGATAAAATATTTT
1 TAAAGA-AAAATATTTT
127891 ACTACAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
20 8 0.29
21 10 0.36
22 3 0.11
23 6 0.21
24 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (23 bp):
TAAAGAAAAATATTTTTAAAAGA
Found at i:135557 original size:38 final size:38
Alignment explanation
Indices: 135481--135745 Score: 308
Period size: 38 Copynumber: 7.1 Consensus size: 38
135471 CGTATAACAC
* *
135481 ATATAATATATAATTTTGAAAACATTTTT-TAAAA-AT
1 ATATAATATATAGTTTTGAAAACATTTTTCAAAAATAT
*
135517 ATATAATATATAGTTTTGAAAATATTTTTCAAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTCAAAAATAT
* **
135555 ATATAATATATACTTTTGAAAACATTTTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTCAAAAATAT
**
135593 ATATAATATATAGTTTTGAAAACATTTTTCGGAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTTCAAAAATAT
* * *
135631 ATATAATATATAGTTTTG-AACCATTTTTGAAATATAT
1 ATATAATATATAGTTTTGAAAACATTTTTCAAAAATAT
* * * *
135668 A-AT-ATATATAGTTGTCAAAACATTTGTTTAAAATTAT
1 ATATAATATATAGTTTTGAAAACATTT-TTCAAAAATAT
* * *
135705 ATATTATATATATTTTTGAAAA-ATGTTTTCAAAACTAT
1 ATATAATATATAGTTTTGAAAACAT-TTTTCAAAAATAT
135743 ATA
1 ATA
135746 AAACATTTTT
Statistics
Matches: 196, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
35 11 0.06
36 36 0.18
37 28 0.14
38 105 0.54
39 16 0.08
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (38 bp):
ATATAATATATAGTTTTGAAAACATTTTTCAAAAATAT
Found at i:135612 original size:76 final size:76
Alignment explanation
Indices: 135481--135745 Score: 328
Period size: 74 Copynumber: 3.5 Consensus size: 76
135471 CGTATAACAC
*
135481 ATATAATATATAATTTTGAAAACATTTTTT-AAAA-ATATATAATATATAGTTTTGAAAATATTT
1 ATATAATATATAATTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
135544 TTCAAAAATAT
66 TTCAAAAATAT
*
135555 ATATAATATATACTTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
1 ATATAATATATAATTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
**
135620 TTCGGAAATAT
66 TTCAAAAATAT
* * * *
135631 ATATAATATATAGTTTTG-AACCA-TTTTTG-AAATATATA-ATATATATAGTTGTCAAAACATT
1 ATATAATATATAATTTTGAAAACATTTTTTGAAAATATATATA-ATATATAGTTTTGAAAACATT
* *
135692 TGTTTAAAATTAT
65 T-TTCAAAAATAT
* * * *
135705 ATATTATATATATTTTTGAAAA-ATGTTTTCAAAACTATATA
1 ATATAATATATAATTTTGAAAACATTTTTTGAAAA-TATATA
135746 AAACATTTTT
Statistics
Matches: 166, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
72 1 0.01
73 29 0.17
74 59 0.36
75 14 0.08
76 57 0.34
77 6 0.04
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (76 bp):
ATATAATATATAATTTTGAAAACATTTTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
TTCAAAAATAT
Found at i:135869 original size:4 final size:4
Alignment explanation
Indices: 135862--135914 Score: 65
Period size: 4 Copynumber: 13.2 Consensus size: 4
135852 ATTTACATTA
*
135862 TATT TATT TATT TATT TATT TATT TATT T-TT ATTTT TATTT TATT T-TT
1 TATT TATT TATT TATT TATT TATT TATT TATT -TATT TA-TT TATT TATT
135910 TATT T
1 TATT T
135915 TTATTTCAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
3 5 0.11
4 33 0.75
5 6 0.14
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TATT
Found at i:135895 original size:6 final size:6
Alignment explanation
Indices: 135884--135920 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
135874 TATTTATTTA
135884 TTTATT TTTATT TTTA-T TTTATTT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT T
135921 CAAGCCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 19 0.66
7 5 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:135915 original size:12 final size:13
Alignment explanation
Indices: 135848--135920 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 13
135838 ATTATATAGT
*
135848 TTTTATTTACATTA
1 TTTTATTTA-TTTA
135862 TATTTATTTATTTA
1 T-TTTATTTATTTA
135876 -TTTATTTATTTA
1 TTTTATTTATTTA
135888 TTTT-TATT-TTTA
1 TTTTAT-TTATTTA
135900 TTTTATTT-TTTA
1 TTTTATTTATTTA
135912 TTTTTATTT
1 -TTTTATTT
135921 CAAGCCCAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
12 27 0.51
13 14 0.26
14 4 0.08
15 8 0.15
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:137922 original size:12 final size:11
Alignment explanation
Indices: 137901--137927 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
137891 AAAAAGGTCA
137901 AAAAAGTTTTT
1 AAAAAGTTTTT
137912 AAAAAGTTTTT
1 AAAAAGTTTTT
137923 AAAAA
1 AAAAA
137928 AATAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (11 bp):
AAAAAGTTTTT
Done.