Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006044.1 Hibiscus syriacus cultivar Beakdansim tig00014291_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: 78754
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:543 original size:36 final size:36
Alignment explanation
Indices: 491--602 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
481 TGATCTATTT
*
491 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
527 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
563 TC-TCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
597 ACATCA
1 TCATCA
603 TCCTTCCATT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 12 0.18
35 21 0.31
36 35 0.51
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:617 original size:33 final size:33
Alignment explanation
Indices: 573--641 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
563 TCTCACCATA
*
573 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
606 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
639 TTC
1 TTC
642 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:6135 original size:36 final size:36
Alignment explanation
Indices: 6083--6195 Score: 149
Period size: 36 Copynumber: 3.2 Consensus size: 36
6073 GATACTATTT
6083 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* * *
6119 TCATCACCATAGTCCATCACCATTATCACGCTTATA
1 TCATCACCATAATCCATCTCCATTATCACGCCTATA
* *
6155 TCATCACCATATTCCAT-TACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCT-CCATTATCACGCCTATA
*
6190 ACATCA
1 TCATCA
6196 TCCTTCCATT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
35 16 0.24
36 52 0.76
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCTCCATTATCACGCCTATA
Found at i:6208 original size:33 final size:33
Alignment explanation
Indices: 6166--6234 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
6156 CATCACCATA
*
6166 TTCCATTACCATATCA-CGCCAATAACATCATCC
1 TTCCATTACCATATCATCACCAATAA-ATCATCC
* *
6199 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATTACCATATCATCACCAATAAATCATCC
6232 TTC
1 TTC
6235 ATTCATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATTACCATATCATCACCAATAAATCATCC
Found at i:6590 original size:11 final size:12
Alignment explanation
Indices: 6536--6620 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 12
6526 CATCAAAGTT
*
6536 GGTGATAATATA
1 GGTGATGATATA
*
6548 GGCG-TGATAT-
1 GGTGATGATATA
*
6558 GGTGAAGGA-ATA
1 GGTG-ATGATATA
6570 TGGTGATGATATA
1 -GGTGATGATATA
6583 GGTG-TGATA-A
1 GGTGATGATATA
6593 TGGTGATGGACTAT-
1 -GGTGAT-GA-TATA
6607 GGTGATGATATA
1 GGTGATGATATA
6619 GG
1 GG
6621 CGTGATAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 22
0.68 0.06 0.26
Matches are distributed among these distances:
10 4 0.07
11 19 0.33
12 17 0.30
13 15 0.26
14 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:6608 original size:36 final size:36
Alignment explanation
Indices: 6535--6639 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6525 ACATCAAAGT
* * *
6535 TGGTGATAATATAGGCGTGAT-ATGGTGAAGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
6570 TGGTGATGATATAGGTGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
6606 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
6640 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:6610 original size:13 final size:12
Alignment explanation
Indices: 6553--6638 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 12
6543 ATATAGGCGT
*
6553 GATATGGTGAAG
1 GATATGGTGATG
6565 GAATATGGTGAT-
1 G-ATATGGTGATG
6577 GATATAGGTG-T-
1 GATAT-GGTGATG
6588 GATAATGGTGATG
1 GAT-ATGGTGATG
6601 GACTATGGTGAT-
1 GA-TATGGTGATG
*
6613 GATATAGGCG-T-
1 GATAT-GGTGATG
6624 GATAATGGTGATG
1 GAT-ATGGTGATG
6637 GA
1 GA
6639 CAGATTGTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
11 22 0.36
12 17 0.28
13 21 0.34
14 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:8152 original size:19 final size:20
Alignment explanation
Indices: 8128--8176 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
8118 CGTCCAAGAG
* *
8128 CATGTATTTTCGTT-AAAGT
1 CATGTATTTTCATTAAAAAT
8147 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
8167 CATGTATTTT
1 CATGTATTTT
8177 AAAAGGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:12142 original size:18 final size:18
Alignment explanation
Indices: 12109--12143 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12099 TAGATCAAGA
*
12109 AAACACCATTTATAACAT
1 AAACACCATGTATAACAT
*
12127 AAACACCATGTCTAACA
1 AAACACCATGTATAACA
12144 GTGTCGATTC
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:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (18 bp):
AAACACCATGTATAACAT
Found at i:12486 original size:15 final size:15
Alignment explanation
Indices: 12466--12501 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12456 ATTATTAGCT
*
12466 TTATAATATATGTTA
1 TTATAATATATATTA
12481 TTATAATATATATTA
1 TTATAATATATATTA
*
12496 TGATAA
1 TTATAA
12502 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:12677 original size:42 final size:42
Alignment explanation
Indices: 12618--12701 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
12608 TATACATCAA
12618 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
12660 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
12702 ATATTAACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (42 bp):
GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
Found at i:14193 original size:18 final size:18
Alignment explanation
Indices: 14150--14193 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
14140 TCAGCAAAGG
14150 AAAAAG-AAGCACTCAAA
1 AAAAAGAAAGCACTCAAA
* **
14167 AGATTGAAAGCACTCAAA
1 AAAAAGAAAGCACTCAAA
14185 AAAAAGAAA
1 AAAAAGAAA
14194 AAGAAAGAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.09
Consensus pattern (18 bp):
AAAAAGAAAGCACTCAAA
Found at i:16970 original size:42 final size:42
Alignment explanation
Indices: 16911--16994 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
16901 TATACATCAA
16911 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
16953 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
16995 ATATTAACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (42 bp):
GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
Found at i:18935 original size:15 final size:15
Alignment explanation
Indices: 18910--18945 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
18900 GGTCCACGTC
18910 TCCTT-TAGCCAGAT
1 TCCTTCTAGCCAGAT
18924 TCCTTCTAGCCAGAT
1 TCCTTCTAGCCAGAT
18939 TCCTTCT
1 TCCTTCT
18946 CTTTTGCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.17, C:0.33, G:0.11, T:0.39
Consensus pattern (15 bp):
TCCTTCTAGCCAGAT
Found at i:19719 original size:17 final size:17
Alignment explanation
Indices: 19699--19731 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19689 GAGGATCCAT
19699 AATACATCAATTTCCTA
1 AATACATCAATTTCCTA
19716 AATACATCAATTTCCT
1 AATACATCAATTTCCT
19732 CTCTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.36
Consensus pattern (17 bp):
AATACATCAATTTCCTA
Found at i:21318 original size:80 final size:77
Alignment explanation
Indices: 21173--21338 Score: 174
Period size: 80 Copynumber: 2.1 Consensus size: 77
21163 GAATTAATAA
* *
21173 TAAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTATAATC-T
1 TAAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTT
* *
21237 TTAATGTTTATT
66 TTAATGCTTACT
* * * * *
21249 TAAAATCTTATTTAATT-ATTAGGAATTACATATACCAATTAAAAGAGTTGTAATCTAAATTACA
1 TAAAATATTATTTAATTAATT--CAATTAAATATA-C-ATT-AAAGACTTATAATCTAAATTACA
*
21313 TTCTTTTAATGCTTACT
61 ATCTTTTAATGCTTACT
*
21330 TAATATATT
1 TAAAATATT
21339 CGAGATAATT
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
75 3 0.04
76 16 0.22
77 10 0.14
78 1 0.01
79 3 0.04
80 21 0.29
81 18 0.25
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (77 bp):
TAAAATATTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTAAATTACAATCTT
TTAATGCTTACT
Found at i:23830 original size:19 final size:21
Alignment explanation
Indices: 23806--23858 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
23796 CAGCCAAGAG
*
23806 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
23825 CATGTATTTTCATTTAAAAAAT
1 CATGTATTTTCATTT-AAAAAT
23847 CATGTATTTTCA
1 CATGTATTTTCA
23859 AAGGGGATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
22 17 0.57
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:24634 original size:18 final size:17
Alignment explanation
Indices: 24585--24634 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
24575 AATTGGAGTG
24585 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAA-AAAAAGA
**
24603 CAAAAAGAAGAAAAAATT
1 CAAAAAGAA-AAAAAAGA
24621 CAGAAAAGAAAAAA
1 CA-AAAAGAAAAAA
24635 GAAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAAAAAAGA
Found at i:34615 original size:14 final size:15
Alignment explanation
Indices: 34587--34640 Score: 74
Period size: 14 Copynumber: 3.6 Consensus size: 15
34577 TGGTTTTGCT
34587 TTCTTTTTGAATTTC
1 TTCTTTTTGAATTTC
*
34602 TTCTTTTT-ATTTTC
1 TTCTTTTTGAATTTC
*
34616 TTCTTTTCTGAATTTT
1 TTCTTTT-TGAATTTC
34632 TTCTTTTTG
1 TTCTTTTTG
34641 TCTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.35
15 11 0.32
16 11 0.32
ACGTcount: A:0.09, C:0.13, G:0.06, T:0.72
Consensus pattern (15 bp):
TTCTTTTTGAATTTC
Found at i:40761 original size:20 final size:20
Alignment explanation
Indices: 40736--40782 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
40726 GATGCTCACC
40736 AACCAGCTAGTAAAGAGGTT
1 AACCAGCTAGTAAAGAGGTT
*
40756 AACCAGCTAGTGAAGAGGTT
1 AACCAGCTAGTAAAGAGGTT
40776 AACCAGC
1 AACCAGC
40783 CCACCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (20 bp):
AACCAGCTAGTAAAGAGGTT
Found at i:43038 original size:15 final size:15
Alignment explanation
Indices: 43027--43055 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43017 ACTCAAAAAG
43027 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
43042 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
43056 GTTGAAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:44677 original size:6 final size:7
Alignment explanation
Indices: 44660--44711 Score: 52
Period size: 7 Copynumber: 6.9 Consensus size: 7
44650 TTTTTTTTCA
44660 AAAAAAC
1 AAAAAAC
44667 AAAAAAC
1 AAAAAAC
44674 AAAAAAGGC
1 AAAAAA--C
44683 AAAAAA-
1 AAAAAAC
44689 AAAAAAGGC
1 AAAAAA--C
44698 AAAAAAAC
1 -AAAAAAC
44706 AAAAAA
1 AAAAAA
44712 AGAGCCAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.15
7 19 0.49
8 1 0.03
9 7 0.18
10 6 0.15
ACGTcount: A:0.83, C:0.10, G:0.08, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:44678 original size:15 final size:16
Alignment explanation
Indices: 44658--44711 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
44648 ATTTTTTTTT
44658 CAAAAAA-ACAAAAAA
1 CAAAAAAGACAAAAAA
*
44673 CAAAAAAGGCAAAAAA
1 CAAAAAAGACAAAAAA
*
44689 -AAAAAAGGCAAAAAAA
1 CAAAAAAGAC-AAAAAA
44705 CAAAAAA
1 CAAAAAA
44712 AGAGCCAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 16 0.46
16 13 0.37
17 6 0.17
ACGTcount: A:0.81, C:0.11, G:0.07, T:0.00
Consensus pattern (16 bp):
CAAAAAAGACAAAAAA
Found at i:44730 original size:20 final size:20
Alignment explanation
Indices: 44686--44723 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44676 AAAAGGCAAA
*
44686 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
44706 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
44724 GCCAAAATTT
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:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:51594 original size:11 final size:13
Alignment explanation
Indices: 51562--51591 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51552 TGGCCAAAGA
51562 TGAAAAGGTATGT
1 TGAAAAGGTATGT
51575 TGAAAAGGTATG-
1 TGAAAAGGTATGT
51587 TGAAA
1 TGAAA
51592 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:56791 original size:15 final size:16
Alignment explanation
Indices: 56762--56816 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
56752 AGTAATATGC
56762 AAAT-ATTAAAGAAAG
1 AAATGATTAAAGAAAG
56777 AAATGATTAAA-AAAG
1 AAATGATTAAAGAAAG
*
56792 AATATGA-AAGAAGAAAGG
1 AA-ATGATTA-AAGAAA-G
56810 AAATGAT
1 AAATGAT
56817 AAGAAAAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 11 0.33
16 12 0.36
17 7 0.21
18 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (16 bp):
AAATGATTAAAGAAAG
Found at i:56838 original size:16 final size:16
Alignment explanation
Indices: 56776--56830 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
56766 ATTAAAGAAA
56776 GAAATGATTAA-AAAA-
1 GAAATGA-TAAGAAAAG
56791 GAATATGA-AAGAAGAAAG
1 GAA-ATGATAAG-A-AAAG
56809 GAAATGATAAGAAAAG
1 GAAATGATAAGAAAAG
56825 GAAATG
1 GAAATG
56831 GATAGAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.06
15 3 0.09
16 15 0.44
17 8 0.24
18 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (16 bp):
GAAATGATAAGAAAAG
Found at i:57052 original size:13 final size:13
Alignment explanation
Indices: 57034--57059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57024 TTATAGGCGT
57034 GAAAATGGTGATG
1 GAAAATGGTGATG
57047 GAAAATGGTGATG
1 GAAAATGGTGATG
57060 AACAGATAGT
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:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
GAAAATGGTGATG
Found at i:57445 original size:19 final size:20
Alignment explanation
Indices: 57403--57445 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
57393 GAAACCCCTT
*
57403 TGAAAACACATGATTTTAAA
1 TGAAAACACATAATTTTAAA
*
57423 TGAAAATACATAATTTT-AA
1 TGAAAACACATAATTTTAAA
57442 TGAA
1 TGAA
57446 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (20 bp):
TGAAAACACATAATTTTAAA
Found at i:58189 original size:20 final size:21
Alignment explanation
Indices: 58151--58189 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
58141 GATCATCTAG
* *
58151 AAGCTAAGATAACATGTATAT
1 AAGCTAAGATAAAAGGTATAT
58172 AAGCT-AGATAAAAGGTAT
1 AAGCTAAGATAAAAGGTAT
58190 TGGACGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:60804 original size:28 final size:26
Alignment explanation
Indices: 60772--60829 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
60762 TTTGAATGTA
60772 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTC-TTTT
* *
60800 CTTTGAATTTTTCTTCTTTTTCTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTT
60826 CTTT
1 CTTT
60830 CTTTGGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 7 0.26
28 12 0.44
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (26 bp):
CTTTGAATCTTTCTTCCTTTTCTTTT
Found at i:60888 original size:17 final size:17
Alignment explanation
Indices: 60863--60896 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
60853 AGGAGTATTC
60863 TTTTTTTCTTT-TTGTT
1 TTTTTTTCTTTCTTGTT
60879 TTTTTCTTCTTTCTTGTT
1 TTTTT-TTCTTTCTTGTT
60897 GCAGCACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTCTTGTT
Found at i:61218 original size:19 final size:20
Alignment explanation
Indices: 61190--61229 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
61180 GGATAATAAT
61190 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
*
61210 ATAAG-AATGAAATTAAATA
1 ATAAGTAATGAAAATAAATA
61229 A
1 A
61230 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:68501 original size:24 final size:21
Alignment explanation
Indices: 68463--68508 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
68453 ATTGGCACAT
*
68463 TCTTTTGAATTTCAAGAGGTACA
1 TCTTTTGAATGTCAA-AGG-ACA
68486 TCTTTTGAAATGTCAAAGGACA
1 TCTTTTG-AATGTCAAAGGACA
68508 T
1 T
68509 GTCTTGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 10 0.48
24 7 0.33
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (21 bp):
TCTTTTGAATGTCAAAGGACA
Found at i:69800 original size:15 final size:15
Alignment explanation
Indices: 69765--69793 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
69755 GTGCTTCAAC
69765 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
69779 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
69794 CTTTTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:69816 original size:27 final size:28
Alignment explanation
Indices: 69786--69847 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
69776 CTTTTCTTTG
* *
69786 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
69813 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
69841 CTTTTCT
1 CTTTTCT
69848 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:73121 original size:14 final size:15
Alignment explanation
Indices: 73099--73131 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
73089 AACAAAACAA
*
73099 AAAACAAAAAAAGGC
1 AAAACAAAAAAAGCC
73114 AAAA-AAAAAAAGCC
1 AAAACAAAAAAAGCC
73128 AAAA
1 AAAA
73132 TTTCAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAAGCC
Done.