Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008801.1 Hibiscus syriacus cultivar Beakdansim tig00111951_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: 46671
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2289 original size:18 final size:18
Alignment explanation
Indices: 2266--2300 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2256 TTCCATCCGG
*
2266 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
2284 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
2301 GCCATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:12547 original size:18 final size:18
Alignment explanation
Indices: 12524--12558 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12514 TTCCATCCGG
*
12524 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
12542 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
12559 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:13908 original size:13 final size:13
Alignment explanation
Indices: 13875--13911 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
13865 GTTAACGGGT
*
13875 CGGGTCGAGTCAA
1 CGGGTCGGGTCAA
13888 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
13901 CGGGTCGGGTC
1 CGGGTCGGGTC
13912 GGGTCGTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.24, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:16618 original size:3 final size:3
Alignment explanation
Indices: 16602--16682 Score: 90
Period size: 3 Copynumber: 27.0 Consensus size: 3
16592 TTAATATATT
* * * * *
16602 TAA TAA AAA AAA TAA TAA TAA TAA AAA TAA TAA TGA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
16650 TAA TGA TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16683 AATGGATAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:16691 original size:18 final size:18
Alignment explanation
Indices: 16602--16684 Score: 103
Period size: 18 Copynumber: 4.4 Consensus size: 18
16592 TTAATATATT
* *
16602 TAATAAAAAAAATAATAA
1 TAATAAAAATAATAATGA
16620 TAATAAAAATAATAATGA
1 TAATAAAAATAATAATGA
* *
16638 TAATAATATTAATAATGA
1 TAATAAAAATAATAATGA
16656 TAATAATATTAATAATAATGA
1 TAATAA-A--AATAATAATGA
16677 TAATAAAA
1 TAATAAAA
16685 TGGATAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
18 39 0.70
20 1 0.02
21 16 0.29
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
TAATAAAAATAATAATGA
Found at i:17269 original size:118 final size:119
Alignment explanation
Indices: 16929--17614 Score: 1221
Period size: 118 Copynumber: 5.8 Consensus size: 119
16919 GCTCTTGATG
*
16929 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
* * * *
16990 TAC-CTGGTAATGTTGATCCATCAA-CTGATGAATTCAAGCAAAAGGTTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
17042 A-TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
17106 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
*
17160 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
17225 TCCTCTGGAAATGATGATCCATCAA-TTGATGAATTCAAGCAAAAGGTTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
17278 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
17343 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
17397 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
17462 T-CTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
17515 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
* * *
17580 TTCTTTGGAAATGATGATCCATCAA-GTGATGAATT
66 TCCTCTGGAAATGATGATCCATCAATTTGATGAATT
17615 TGAATCTTTG
Statistics
Matches: 555, Mismatches: 9, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
112 36 0.06
113 1 0.00
115 21 0.04
116 3 0.01
117 19 0.03
118 272 0.49
119 203 0.37
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (119 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
TCCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:17338 original size:237 final size:235
Alignment explanation
Indices: 16929--17614 Score: 1213
Period size: 237 Copynumber: 2.9 Consensus size: 235
16919 GCTCTTGATG
* *
16929 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTC-A-GATGAGTTCTTCTCATTATGAACT-TT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAATGACGAGTTCTTCTCATTATGAACTCTT
* * *
16991 AC-CTGGTAATGTTGATCCATCAACTGATGAATTCAAGCAAAAGGTTGAACAA-TTCTTCTCATT
66 -CTCTGGAAATGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATT
17054 ATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATG
130 ATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATG
17119 ATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
195 ATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
17160 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AATGACGAGTTCTTCTCATTATGAACTCT
17225 TCCTCTGGAAATGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
65 T-CTCTGGAAATGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
17290 TATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAT
129 TATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAT
17355 GATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
194 GATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
17397 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-ATGACGAGTTCTTCTCATTATGAACTCT
17462 TCTCTGGAAATGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
65 TCTCTGGAAATGATGATCCATCAA-TTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
* *
17527 TATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTTCTTTGGAAAT
129 TATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAT
*
17592 GATGATCCATCAA-GTGATGAATT
194 GATGATCCATCAATTTGATGAATT
17615 TGAATCTTTG
Statistics
Matches: 438, Mismatches: 9, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
231 34 0.08
233 1 0.00
234 23 0.05
235 3 0.01
236 80 0.18
237 297 0.68
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (235 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAATGACGAGTTCTTCTCATTATGAACTCTT
CTCTGGAAATGATGATCCATCAATTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTA
TGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGA
TGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:18249 original size:52 final size:52
Alignment explanation
Indices: 18168--18725 Score: 1053
Period size: 52 Copynumber: 10.7 Consensus size: 52
18158 CACTTCTTCG
* *
18168 GATCAAATAACTCAAAGAACACTTTCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
18220 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
18272 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
18324 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
18376 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATATTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
18428 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
* *
18480 GATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATGTTATGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
18532 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
18584 GGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
18636 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
18688 GATCAGATAACTCAAATAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
18726 TGAGCACATA
Statistics
Matches: 495, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 495 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.23
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:19340 original size:16 final size:16
Alignment explanation
Indices: 19304--19341 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19294 TGAATTTCCA
19304 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
19320 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
19336 AAAATA
1 AAAATA
19342 GATATAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:19671 original size:6 final size:6
Alignment explanation
Indices: 19660--19732 Score: 62
Period size: 6 Copynumber: 12.0 Consensus size: 6
19650 CTTGACCCCC
*
19660 TTTCTT TTTCTT CTCTT-TT TTTCAT TTTCTAT TTT-TT CTTTCTT TTTC-T
1 TTTCTT TTTCTT -T-TTCTT TTTCTT TTTCT-T TTTCTT -TTTCTT TTTCTT
* *
19709 CTTCTT TTTCTT TTTTTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT
19733 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
5 7 0.13
6 36 0.67
7 9 0.17
8 2 0.04
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:19678 original size:11 final size:10
Alignment explanation
Indices: 19659--19732 Score: 77
Period size: 9 Copynumber: 7.7 Consensus size: 10
19649 CCTTGACCCC
19659 CTTTCTTTTT
1 CTTTCTTTTT
19669 C-TTCTCTTTT
1 CTTTCT-TTTT
*
19679 -TTTCATTTT
1 CTTTCTTTTT
*
19688 CTAT-TTTTT
1 CTTTCTTTTT
19697 CTTTCTTTTT
1 CTTTCTTTTT
19707 CTCTTCTTTTT
1 CT-TTCTTTTT
19718 CTTT-TTTTT
1 CTTTCTTTTT
19727 -TTTCTT
1 CTTTCTT
19733 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
8 3 0.06
9 22 0.41
10 19 0.35
11 10 0.19
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:19703 original size:38 final size:33
Alignment explanation
Indices: 19660--19732 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 33
19650 CTTGACCCCC
*
19660 TTTCTTT-TTCTTCTCTT-TTTTTCATTTTCTATTT
1 TTTCTTTCTTTTTCTCTTCTTTTTC-TTTT-T-TTT
19694 TTTCTTTCTTTTTCTCTTCTTTTTCTTTTTTTT
1 TTTCTTTCTTTTTCTCTTCTTTTTCTTTTTTTT
19727 TTTCTT
1 TTTCTT
19733 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 9 0.25
34 8 0.22
35 13 0.36
36 6 0.17
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTCTTTCTTTTTCTCTTCTTTTTCTTTTTTTT
Found at i:19716 original size:29 final size:27
Alignment explanation
Indices: 19664--19732 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 27
19654 ACCCCCTTTC
19664 TTTTTC-TTCTCTTTTTTTCATTTTCTAT
1 TTTTTCTTTCT-TTTTTTTCATTTTCT-T
*
19692 TTTTTCTTTCTTTTTCTCTTCTTTTTCTT
1 TTTTTCTTTCTTTTT-T-TTCATTTTCTT
*
19721 TTTTTTTTTCTT
1 TTTTTCTTTCTT
19733 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 10 0.28
29 17 0.47
30 9 0.25
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTCTTTCTTTTTTTTCATTTTCTT
Found at i:19724 original size:19 final size:18
Alignment explanation
Indices: 19660--19725 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
19650 CTTGACCCCC
19660 TTTCTTTTTCTTCTCTTTT
1 TTTCTTTTT-TTCTCTTTT
* *
19679 TTTC--ATTTTCT-ATTT
1 TTTCTTTTTTTCTCTTTT
19694 TTTCTTTCTTTTTCTCTTCTT
1 TTTC-TT-TTTTTCTCTT-TT
19715 TTTCTTTTTTT
1 TTTCTTTTTTT
19726 TTTTCTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
15 7 0.19
16 4 0.11
17 2 0.05
19 15 0.41
20 3 0.08
21 6 0.16
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTTTCTCTTTT
Found at i:30290 original size:18 final size:18
Alignment explanation
Indices: 30267--30301 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30257 ATACTTGCAA
30267 ATAAAACATA-TAAATATT
1 ATAAAA-ATATTAAATATT
30285 ATAAAAATATTAAATAT
1 ATAAAAATATTAAATAT
30302 AAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAATATTAAATATT
Found at i:32445 original size:3 final size:3
Alignment explanation
Indices: 32430--32515 Score: 111
Period size: 3 Copynumber: 29.0 Consensus size: 3
32420 TTAATATATT
* * *
32430 TAA TAA -AA AAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
32477 TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32516 AATGGATAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:32523 original size:12 final size:11
Alignment explanation
Indices: 32432--32529 Score: 64
Period size: 12 Copynumber: 8.9 Consensus size: 11
32422 AATATATTTA
* *
32432 ATAAAAAAATA
1 ATAATAAAATG
*
32443 ATAATAATAATA
1 ATAATAA-AATG
32455 ATAATAATAATG
1 ATAATAA-AATG
*
32467 ATAATAATAT-
1 ATAATAAAATG
32477 -TAAT--AATG
1 ATAATAAAATG
32485 ATAATAATAAT-
1 ATAATAA-AATG
32496 ATTAATAATAATG
1 A-TAATAA-AATG
32509 ATAATAAAATGG
1 ATAATAAAAT-G
32521 ATAA-AAAAT
1 ATAATAAAAT
32530 AGTATCTTCA
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
7 2 0.03
9 8 0.11
11 17 0.23
12 46 0.62
13 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (11 bp):
ATAATAAAATG
Found at i:32524 original size:18 final size:18
Alignment explanation
Indices: 32439--32524 Score: 111
Period size: 18 Copynumber: 4.8 Consensus size: 18
32429 TTAATAAAAA
*
32439 AATAATAATAATAATAAT
1 AATAATAATGATAATAAT
32457 AATAATAATGATAATAAT
1 AATAATAATGATAATAAT
*
32475 ATTAATAATGATAATAAT
1 AATAATAATGATAATAAT
* * *
32493 AATATTAATAATAATGAT
1 AATAATAATGATAATAAT
32511 AATAA-AATGGATAA
1 AATAATAAT-GATAA
32525 AAAATAGTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
17 3 0.05
18 56 0.95
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
AATAATAATGATAATAAT
Found at i:35614 original size:18 final size:18
Alignment explanation
Indices: 35591--35625 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35581 TTCCATCCGG
*
35591 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
35609 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
35626 GTCATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:36943 original size:13 final size:13
Alignment explanation
Indices: 36925--36949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36915 CAGTCAACGG
36925 GTCAACGGGTCGA
1 GTCAACGGGTCGA
36938 GTCAACGGGTCG
1 GTCAACGGGTCG
36950 GGTCGGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:36953 original size:18 final size:19
Alignment explanation
Indices: 36916--36963 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
36906 GGTCAACGAC
36916 AGTCAACGGGTCAACGGGTCG
1 AGTCAACGGGT--ACGGGTCG
36937 AGTCAACGGGT-CGGGTCG
1 AGTCAACGGGTACGGGTCG
*
36955 GGTCAACGG
1 AGTCAACGG
36964 ATCAGGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 15 0.58
21 11 0.42
ACGTcount: A:0.21, C:0.23, G:0.42, T:0.15
Consensus pattern (19 bp):
AGTCAACGGGTACGGGTCG
Found at i:36957 original size:31 final size:31
Alignment explanation
Indices: 36922--36989 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
36912 CGACAGTCAA
* *
36922 CGGGTCAACGGGTC-GAGTCAACGGGTCGGGT
1 CGGGTCAACGGATCAG-GTAAACGGGTCGGGT
36953 CGGGTCAACGGATCAGGTAAACGGGTCGGGT
1 CGGGTCAACGGATCAGGTAAACGGGTCGGGT
36984 CGGGTC
1 CGGGTC
36990 GGGTTGTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.44, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGATCAGGTAAACGGGTCGGGT
Found at i:42351 original size:3 final size:3
Alignment explanation
Indices: 42343--42378 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
42333 GTTGTCATAT
*
42343 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42379 GGCTAAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Done.