Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000131.1 Hibiscus syriacus cultivar Beakdansim tig00000237_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: 100514
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4127 original size:2 final size:2
Alignment explanation
Indices: 4120--4153 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4110 GCTATAAATG
4120 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4154 GTTATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8636 original size:2 final size:2
Alignment explanation
Indices: 8629--8687 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
8619 CTATAAAGTA
8629 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
8671 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
8688 CTATGTTATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9044 original size:24 final size:24
Alignment explanation
Indices: 9012--9062 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
9002 AAGTAATGAA
9012 GAACAATGAGATAGGC-TCTCAAAG
1 GAACAATGAGATAGGCGT-TCAAAG
*
9036 GAACAATGAGATGGGCGTTCAAAG
1 GAACAATGAGATAGGCGTTCAAAG
9060 GAA
1 GAA
9063 AAAGAGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.41, C:0.14, G:0.29, T:0.16
Consensus pattern (24 bp):
GAACAATGAGATAGGCGTTCAAAG
Found at i:13640 original size:17 final size:18
Alignment explanation
Indices: 13602--13655 Score: 74
Period size: 17 Copynumber: 3.0 Consensus size: 18
13592 AATACAAGAA
13602 AAAATACAACTCAAACAAT
1 AAAA-ACAACTCAAACAAT
*
13621 AAAAACAACT-AAATAAT
1 AAAAACAACTCAAACAAT
*
13638 AAAAACAATTCAAACAAT
1 AAAAACAACTCAAACAAT
13656 TAAATAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.48
18 12 0.39
19 4 0.13
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAACAACTCAAACAAT
Found at i:13643 original size:26 final size:26
Alignment explanation
Indices: 13614--13694 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 26
13604 AATACAACTC
*
13614 AAACAATAAAAACAACTAAATAATAA
1 AAACAATAAAAACAAATAAATAATAA
** *
13640 AAACAATTCAAACAATTAAATAATAA
1 AAACAATAAAAACAAATAAATAATAA
13666 AAA-AACTAACAAACCAAATAAATAA-AA
1 AAACAA-TAA-AAA-CAAATAAATAATAA
13693 AA
1 AA
13695 GTCCATAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
25 2 0.04
26 27 0.59
27 7 0.15
28 10 0.22
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (26 bp):
AAACAATAAAAACAAATAAATAATAA
Found at i:15982 original size:20 final size:18
Alignment explanation
Indices: 15949--15985 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
15939 AAAAATTAGT
15949 ATAATAAAATTGAATAAA
1 ATAATAAAATTGAATAAA
15967 ATAATAAATTATTGAATAA
1 ATAATAAA--ATTGAATAA
15986 TTATAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
ATAATAAAATTGAATAAA
Found at i:18459 original size:6 final size:7
Alignment explanation
Indices: 18439--18467 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
18429 GTGTTTTCTT
18439 CCGCCCC
1 CCGCCCC
18446 CCGCCCC
1 CCGCCCC
18453 CCGCCCC
1 CCGCCCC
18460 CCGCCCC
1 CCGCCCC
18467 C
1 C
18468 AACAATCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.86, G:0.14, T:0.00
Consensus pattern (7 bp):
CCGCCCC
Found at i:23539 original size:1 final size:1
Alignment explanation
Indices: 23533--23558 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
23523 CAAAAGAAAT
23533 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
23559 TAATAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:24278 original size:42 final size:42
Alignment explanation
Indices: 24199--24278 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
24189 CGAAGAACTT
* * *
24199 ATCATCTTGCTTGAAAGACTTATAAATGACCCGAAGGATGTA
1 ATCATCATGCTCGAAAGACTTATAAATGACCCAAAGGATGTA
*
24241 ATCATCATGCTCGAAAGACTTACT-AATGGCCCAAAGGA
1 ATCATCATGCTCGAAAGACTTA-TAAATGACCCAAAGGA
24279 CTTACCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.97
43 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTATAAATGACCCAAAGGATGTA
Found at i:24395 original size:257 final size:256
Alignment explanation
Indices: 23854--24678 Score: 1156
Period size: 257 Copynumber: 3.2 Consensus size: 256
23844 TTACTAGGTA
* * * *
23854 AGAAACTTTGGAAATCATTTTCTCATTTTTTCCGAAAAACATGTAAAAAACATCTTGCTCGAAGG
1 AGAAACTTTGGAAATCATTTTCTCATTTTTTTCGAAAAACATGT-GAAAACATCCTGCCCGAAGG
* * *
23919 TCTTATGGATGGCCCGAA-AGACTTATCATCTTGGTCGAAAGACTTATAAATGAACCAAAGGATT
65 TCTTATGGATGGCCCGAAGA-ACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAAGGATT
*
23983 TAATTATCATGCTCGAAAGACTTACTGATGG-CCAGAAGGACTTACCAATTTTGGAAATAGTTTA
129 TAATCATCATGCTCGAAAGACTTACTGATGGCCCA-AAGGACTTACCAATTTTGGAAATAGTTTA
* * * *
24047 CTAGGTAAAAAACTTTGGAAA-CTGTTTTTTACTTTTCAAAAATTTCAATTTTCAAATTTTAATG
193 CTAGGTAAGAAACTTTGGAAATC-GTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
* * *
24111 AGAAACTTTGGAAATCATTTTCTCATTTTTTTCGAAATACAAGTGAAAACATCCTGCCCAAAGGT
1 AGAAACTTTGGAAATCATTTTCTCATTTTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGT
* *
24176 CTTATGGATGGCCCGAAGAACTTATCATCTTGCTTGAAAGACTTATAAATGACCCGAAGGATGTA
66 CTTATGGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAAGGATTTA
*
24241 ATCATCATGCTCGAAAGACTTACTAATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTA
131 ATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTA
*
24306 GGTAAGAAACTTTGGAAATCGTTTACTTACTTTTCAAAAATTTCATTTTTCAGATTTAAATG
196 GGTAAGAAACTTTGGAAATCGTTT-CTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
** *
24368 AGAAACTTTGGAAATTGTTTTCTCATTTTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGA
1 AGAAACTTTGGAAATCATTTTCTCATTTTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGT
* * * *
24433 CTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTA
66 CTTATGGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAAGGATTTA
* * * * *
24498 ATCATCATTCTTGAAAGATTTACTGATGGCGCGAAGGACTTACCAATTTTGGAAATAGTTTACTA
131 ATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTA
* *
24563 GGTAAGAAACTTTGAAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTCAAGAAAGATTTAAA
196 GGTAAGAAACTTTGGAAATC-GTTTCTTACTTTTCAAAAATTTCAATTTTC-----AGATTTAAA
24628 TG
255 TG
* ** *
24630 AGTAACTTTGGAAATTGTTTTTTTTTCA-TTTTTT-GAAAAACATGTGAAA
1 AGAAACTTTGGAAA---TCATTTTCTCATTTTTTTCGAAAAACATGTGAAA
24679 TAACTTAATG
Statistics
Matches: 512, Mismatches: 43, Indels: 20
0.89 0.07 0.03
Matches are distributed among these distances:
256 155 0.30
257 300 0.59
258 3 0.01
262 24 0.05
263 15 0.03
264 6 0.01
265 9 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (256 bp):
AGAAACTTTGGAAATCATTTTCTCATTTTTTTCGAAAAACATGTGAAAACATCCTGCCCGAAGGT
CTTATGGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTTATAAATGACCCGAAGGATTTA
ATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAATTTTGGAAATAGTTTACTA
GGTAAGAAACTTTGGAAATCGTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
Found at i:34288 original size:31 final size:31
Alignment explanation
Indices: 34250--34374 Score: 128
Period size: 31 Copynumber: 4.0 Consensus size: 31
34240 GATCCTCGAC
* *
34250 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* **
34281 AACTGTCCATATATTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
34312 TACTGTTCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
34343 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
34375 CCCTCGACTC
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
30 3 0.04
31 47 0.63
32 22 0.29
33 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:38701 original size:32 final size:32
Alignment explanation
Indices: 38580--38703 Score: 98
Period size: 31 Copynumber: 3.9 Consensus size: 32
38570 ATCCTTGGCA
* * * ** *
38580 ACTGTTCATAGGTTCCGAAGAACCTAGATAA-
1 ACTGTCCATATGTTCCGTAGAAAATAGGTAAT
* *
38611 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAAAATAGGTAAT
38642 ACTGTCCATATG-TCTCG-A-AAGACATAGGTAATT
1 ACTGTCCATATGTTC-CGTAGAA-A-ATAGGTAA-T
38675 A-TGTCCATATGTTCCGTAGAAAATAGGTA
1 ACTGTCCATATGTTCCGTAGAAAATAGGTA
38704 CCCTCGACTC
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
29 2 0.03
30 4 0.05
31 42 0.55
32 20 0.26
33 6 0.08
34 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAAAATAGGTAAT
Found at i:41109 original size:3 final size:3
Alignment explanation
Indices: 41068--41132 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
41058 ATACAAAAGA
* * * *
41068 AAT AA- AAT AAA AAT AAA AAT AA- AACA AAT AAT TAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
41112 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
41133 TGATAATTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:41140 original size:7 final size:7
Alignment explanation
Indices: 41128--41167 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
41118 AATAATAATA
41128 ATAATTG
1 ATAATTG
41135 ATAATTG
1 ATAATTG
41142 ATAATTG
1 ATAATTG
41149 ATAATTG
1 ATAATTG
41156 ATAATTG
1 ATAATTG
41163 ATAAT
1 ATAAT
41168 AATATTAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (7 bp):
ATAATTG
Found at i:43527 original size:54 final size:54
Alignment explanation
Indices: 43445--43555 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
43435 GATTGTTGAG
*
43445 TAATAGTTCGTATTTCTAATGTGATGATGTATTTTTTTCATTAATATTATATTT
1 TAATAGTTCGTATTTCGAATGTGATGATGTATTTTTTTCATTAATATTATATTT
43499 TAATAGTTCGTATTTCGAATGTGATGATGTATTTTTTTCATTAATATTATATTT
1 TAATAGTTCGTATTTCGAATGTGATGATGTATTTTTTTCATTAATATTATATTT
43553 TAA
1 TAA
43556 ATTTTATGTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (54 bp):
TAATAGTTCGTATTTCGAATGTGATGATGTATTTTTTTCATTAATATTATATTT
Found at i:43840 original size:14 final size:14
Alignment explanation
Indices: 43806--43841 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
43796 CACTGATGAC
43806 ACTTAATAAGTTCG
1 ACTTAATAAGTTCG
*
43820 ACTTTAATAAGTTCT
1 AC-TTAATAAGTTCG
43835 ACTTAAT
1 ACTTAAT
43842 GTAGACGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (14 bp):
ACTTAATAAGTTCG
Found at i:46959 original size:14 final size:15
Alignment explanation
Indices: 46940--46968 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46930 GTGATAATTG
46940 ATAAAT-TGAAAAAA
1 ATAAATGTGAAAAAA
46954 ATAAATGTGAAAAAA
1 ATAAATGTGAAAAAA
46969 TGATAAAATG
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:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
ATAAATGTGAAAAAA
Found at i:74705 original size:21 final size:21
Alignment explanation
Indices: 74679--74731 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
74669 GTTTCCAGAT
74679 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
74700 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
74721 TCGCAATGCGA
1 TCGCAACGCGA
74732 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:74770 original size:21 final size:21
Alignment explanation
Indices: 74740--75040 Score: 185
Period size: 21 Copynumber: 14.6 Consensus size: 21
74730 GATTTACATA
*
74740 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
74761 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
74782 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
74803 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
74822 TTCGCGTTGCAATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
74843 TT--CGTTGCGATAGGCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
74862 TTCGCGTTGTGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* **
74885 TT--TGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** * *
74904 TTCTCGTTGCGATTTTTCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
74925 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
74944 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
74967 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
74986 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
75009 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
75028 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
75041 TTATTCCAAA
Statistics
Matches: 206, Mismatches: 56, Indels: 36
0.69 0.19 0.12
Matches are distributed among these distances:
19 64 0.31
21 119 0.58
23 23 0.11
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:74787 original size:42 final size:40
Alignment explanation
Indices: 74740--75065 Score: 418
Period size: 42 Copynumber: 7.9 Consensus size: 40
74730 GATTTACATA
* * *
74740 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATT--CGTTGCGATAGTCGAAG
* *
74782 TTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
* * *
74822 TTCGCGTTGCAATTTTCCAAATTCGTTGCGATAGGCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
* * *
74862 TTCGCGTTGTGATTTATTCCAAATTTGTTGCGATAGTTGAAG
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTCGAAG
* * *
74904 TTCTCGTTGCGATTTTTCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
*
74944 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTCGAAG
74986 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTCGAAG
*
75028 TTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTC
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTC
75066 CAAAATCGCA
Statistics
Matches: 256, Mismatches: 24, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
40 99 0.39
42 157 0.61
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (40 bp):
TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:74894 original size:82 final size:82
Alignment explanation
Indices: 74765--75065 Score: 471
Period size: 82 Copynumber: 3.7 Consensus size: 82
74755 TCCAAGTTCG
*
74765 CGTTGCGATAGTCGAAGTTCGCATTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
74828 TTGCAATTTTCCAAATT
66 TTGCAATTTTCCAAATT
* * * * *
74845 CGTTGCGATAGGCGAAGTTCGCGTTGTGATTTATTCCAAATTTGTTGCGATAGTTGAAGTTCTCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
* *
74910 TTGCGATTTTTCAAATT
66 TTGCAATTTTCCAAATT
*
74927 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
*
74992 TTGCGATTTATTCCAAATT
66 TTGC-AATT-TTCCAAATT
*
75011 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTC
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
75066 CAAAATCGCA
Statistics
Matches: 199, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
80 26 0.13
81 2 0.01
82 107 0.54
83 2 0.01
84 62 0.31
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
TTGCAATTTTCCAAATT
Found at i:75058 original size:21 final size:21
Alignment explanation
Indices: 74907--75061 Score: 112
Period size: 21 Copynumber: 7.5 Consensus size: 21
74897 GTTGAAGTTC
74907 TCGTTGCGATTT-TT-CAAAT
1 TCGTTGCGATTTATTCCAAAT
* * *
74926 TCGTTGCGA--TAGTCGAAGT
1 TCGTTGCGATTTATTCCAAAT
74945 TCGCGTTGCGATTTATTCCAAAT
1 T--CGTTGCGATTTATTCCAAAT
*
74968 TCGTTGCGA--TAGT-CAAAGT
1 TCGTTGCGATTTATTCCAAA-T
74987 TCGCGTTGCGATTTATTCCAAAT
1 T--CGTTGCGATTTATTCCAAAT
* * *
75010 TCGTTGCGA--TAGTCGAAGT
1 TCGTTGCGATTTATTCCAAAT
75029 TCGCGTTGCGATTTATTCCAAAT
1 T--CGTTGCGATTTATTCCAAAT
*
75052 TCATTGCGAT
1 TCGTTGCGAT
75062 AGTCCAAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
17 1 0.01
18 5 0.05
19 26 0.25
21 48 0.46
23 21 0.20
24 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (21 bp):
TCGTTGCGATTTATTCCAAAT
Found at i:78017 original size:64 final size:65
Alignment explanation
Indices: 77867--78020 Score: 224
Period size: 65 Copynumber: 2.4 Consensus size: 65
77857 TTGAACATTA
* * * *
77867 AATGCATTTCATGCATCGATGCAC-TCTCCATGCATCGATGCACTCGGGTTTTAATGAAAACATC
1 AATGCATTTGATGCATCGATGCACATCACCATGCATCGATGCACTCGGCTTTT-ATCAAAACATC
77931 G
65 G
*
77932 AATGCATTTGATGCATCGATGCACAT-ACCATGCATTGATGCACTCAGGCTTTT-TCAAAACATC
1 AATGCATTTGATGCATCGATGCACATCACCATGCATCGATGCACTC-GGCTTTTATCAAAACATC
77995 G
65 G
77996 AATGCATTTGATGCATCGATGCACA
1 AATGCATTTGATGCATCGATGCACA
78021 CTTAGTGCAC
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
64 35 0.43
65 40 0.49
66 7 0.09
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (65 bp):
AATGCATTTGATGCATCGATGCACATCACCATGCATCGATGCACTCGGCTTTTATCAAAACATCG
Found at i:78036 original size:64 final size:63
Alignment explanation
Indices: 77867--78039 Score: 206
Period size: 64 Copynumber: 2.7 Consensus size: 63
77857 TTGAACATTA
* * * * *
77867 AATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACTCGGGTTTTAATGAAAACATCG
1 AATGCATTTGATGCATCGATGCACACT-TATGCATCGATGCACTCGGCTTTT-ATCAAAACATCG
* *
77932 AATGCATTTGATGCATCGATGCACA-TACCATGCATTGATGCACTCAGGCTTTT-TCAAAACATC
1 AATGCATTTGATGCATCGATGCACACT--TATGCATCGATGCACTC-GGCTTTTATCAAAACATC
77995 G
63 G
*
77996 AATGCATTTGATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AATGCATTTGATGCATCGATGCACACTTA-TGCATCGATGCACT
78040 AAGTGTTCCA
Statistics
Matches: 96, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
63 1 0.01
64 48 0.50
65 41 0.43
66 6 0.06
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (63 bp):
AATGCATTTGATGCATCGATGCACACTTATGCATCGATGCACTCGGCTTTTATCAAAACATCG
Found at i:79743 original size:3 final size:3
Alignment explanation
Indices: 79735--79792 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
79725 ATTTAAAATT
* *
79735 TAA TAA TAA TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
79783 TAA TAG TAA T
1 TAA TAA TAA T
79793 GTTCTAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:80065 original size:28 final size:27
Alignment explanation
Indices: 80030--80086 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
80020 TCATGTGTAG
*
80030 TTTTTATTTAGAT-GTATTTTGATTATA
1 TTTTTATTTAGATCG-ATTTTAATTATA
*
80057 TTTTATATTTAGTTCGATTTTAATTATA
1 TTTT-TATTTAGATCGATTTTAATTATA
80085 TT
1 TT
80087 ATTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
28 21 0.81
29 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.63
Consensus pattern (27 bp):
TTTTTATTTAGATCGATTTTAATTATA
Found at i:85147 original size:17 final size:18
Alignment explanation
Indices: 85125--85173 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
85115 CAAAGAGGTT
85125 TTATATTTAATTTT-ATA
1 TTATATTTAATTTTAATA
*
85142 TTATATTTGATTTTAATA
1 TTATATTTAATTTTAATA
85160 TTA-ATATTAATTTT
1 TTATAT-TTAATTTT
85174 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATATTTAATTTTAATA
Found at i:85208 original size:32 final size:32
Alignment explanation
Indices: 85166--85269 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 32
85156 AATATTAATA
*
85166 TTAATTTTTTAAATAAATTAAATATTAAATTT
1 TTAATATTTTAAATAAATTAAATATTAAATTT
* ** *
85198 TTAATATTTTATTATAGATATT-AAT-TTTTA-TA
1 TTAATATTTTA-AATA-A-ATTAAATATTAAATTT
* *
85230 TTAATTTTTTAAATAAATTAAATATTAATTTT
1 TTAATATTTTAAATAAATTAAATATTAAATTT
85262 TTAATATT
1 TTAATATT
85270 ATATTATAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
29 3 0.06
30 4 0.07
31 5 0.09
32 29 0.54
33 6 0.11
34 4 0.07
35 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
TTAATATTTTAAATAAATTAAATATTAAATTT
Found at i:85234 original size:64 final size:65
Alignment explanation
Indices: 85127--85294 Score: 242
Period size: 64 Copynumber: 2.7 Consensus size: 65
85117 AAGAGGTTTT
* * *
85127 ATATTTAA-TTTT-ATATTATATT-T-GAT-TTTAATATTAATATTAATTTTTTAAATAAATTAA
1 ATATTAAATTTTTAATATTATATTATAGATATTTAATTTTTATATTAATTTTTTAAATAAATTAA
*
85187 ATATTAAATTTTTAATATTTTATTATAGATA-TTAATTTTTATATTAATTTTTTAAATAAATTAA
1 ATATTAAATTTTTAATATTATATTATAGATATTTAATTTTTATATTAATTTTTTAAATAAATTAA
*
85251 ATATTAATTTTTTAATATTATATTATAGATATTTAA-TTTTATAT
1 ATATTAAATTTTTAATATTATATTATAGATATTTAATTTTTATAT
85295 CATATAAATT
Statistics
Matches: 96, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
60 7 0.07
61 4 0.04
62 9 0.09
63 1 0.01
64 71 0.74
65 4 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (65 bp):
ATATTAAATTTTTAATATTATATTATAGATATTTAATTTTTATATTAATTTTTTAAATAAATTAA
Found at i:86490 original size:12 final size:12
Alignment explanation
Indices: 86458--86512 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
86448 GTTATTTAAA
*
86458 CGGGTATTAGGC
1 CGGGTATTGGGC
*
86470 CGGGTATTGGGT
1 CGGGTATTGGGC
*
86482 CGGGTATTGAGC
1 CGGGTATTGGGC
* * *
86494 CGAGAATCGGGC
1 CGGGTATTGGGC
86506 CGGGTAT
1 CGGGTAT
86513 ATATATATAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.16, C:0.16, G:0.44, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:86517 original size:2 final size:2
Alignment explanation
Indices: 86510--86553 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
86500 TCGGGCCGGG
* * *
86510 TA TA TA TA TA TA TA TA TA TA AA T- TA AA TA TA TA AA 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
86551 TA T
1 TA T
86554 TTTTATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:86600 original size:33 final size:34
Alignment explanation
Indices: 86514--86611 Score: 107
Period size: 33 Copynumber: 3.0 Consensus size: 34
86504 GCCGGGTATA
* *
86514 TATATATATATATATAAATTAAATATATAAATA-
1 TATATATATATATATAAATTAAATTTATTAATAT
* * *
86547 TATATATTTTTATTTAAATTAAATTTATTAATAT
1 TATATATATATATATAAATTAAATTTATTAATAT
*
86581 TATATATATATAAAT-AATT--ATTT-TTAATAT
1 TATATATATATATATAAATTAAATTTATTAATAT
86611 T
1 T
86612 TATCGGGTCG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 8 0.15
31 4 0.07
33 32 0.58
34 11 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TATATATATATATATAAATTAAATTTATTAATAT
Found at i:89780 original size:36 final size:35
Alignment explanation
Indices: 89678--89804 Score: 114
Period size: 35 Copynumber: 3.6 Consensus size: 35
89668 CTTATATCCG
* *
89678 TAAGGAATTACCAGTTCGATCGGT-CTGAACCTATA
1 TAAGGAATTACCAGTT-GATCGGTGTTGAACCTACA
* * * *
89713 TAAGGAATTACTAGTTTGA-CTGAGTTAAACCTACCA
1 TAAGGAATTACCAG-TTGATCGGTGTTGAACCTA-CA
* *
89749 TAAGGAGTTACCAGTTGATCGGTGTTGAACCTATA
1 TAAGGAATTACCAGTTGATCGGTGTTGAACCTACA
* *
89784 TAAGAAATTATCAGCTTGATC
1 TAAGGAATTACCAG-TTGATC
89805 AGAACTGAAC
Statistics
Matches: 72, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
34 2 0.03
35 38 0.53
36 32 0.44
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (35 bp):
TAAGGAATTACCAGTTGATCGGTGTTGAACCTACA
Found at i:91588 original size:20 final size:20
Alignment explanation
Indices: 91565--91607 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
91555 GGTTAACTTG
*
91565 GTTCGAGTCAGGTTGACTCA
1 GTTCAAGTCAGGTTGACTCA
*
91585 GTTCAAGTTAGGTTGACTCA
1 GTTCAAGTCAGGTTGACTCA
91605 GTT
1 GTT
91608 AGGGTCGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (20 bp):
GTTCAAGTCAGGTTGACTCA
Found at i:92295 original size:3 final size:3
Alignment explanation
Indices: 92287--92327 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
92277 GAGTATGAAA
92287 ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT -TT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
92328 TTACCTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:93606 original size:141 final size:141
Alignment explanation
Indices: 93428--93709 Score: 492
Period size: 141 Copynumber: 2.0 Consensus size: 141
93418 CATTTGTTTA
* *
93428 GTCTCCATATTCCTTTATATTTGCATGTGATTGATTCTTTGGATTTGTTTTCCATACATATTTAA
1 GTCTCCATATTCCTTTACATTTGCATGTGATTGATTCTTTGGATTTGTTTTCCATAAATATTTAA
* ** *
93493 TCATTTGGTGTATTTATATATTATATTTATTGTATATAAATTTGATTAGGTTCGTTTCTTTGTTT
66 GCATTTGGTGTATCCATATATTATATTTATTGTATATAAATTTGATTAGGTTCATTTCTTTGTTT
*
93558 ACTATATATTT
131 ACCATATATTT
93569 GTCTCCATATTCCTTTACATTTGCATGTGATTGATTCTTTGGATTTGTTTTCCATAAATATTTAA
1 GTCTCCATATTCCTTTACATTTGCATGTGATTGATTCTTTGGATTTGTTTTCCATAAATATTTAA
*
93634 GCATTTGGTGTATCCATATATTATATTTATTGTATATACATTTGATTAGGTTCATTTCTTTGTTT
66 GCATTTGGTGTATCCATATATTATATTTATTGTATATAAATTTGATTAGGTTCATTTCTTTGTTT
93699 ACCATATATTT
131 ACCATATATTT
93710 TAATAATTCT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 133 1.00
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.53
Consensus pattern (141 bp):
GTCTCCATATTCCTTTACATTTGCATGTGATTGATTCTTTGGATTTGTTTTCCATAAATATTTAA
GCATTTGGTGTATCCATATATTATATTTATTGTATATAAATTTGATTAGGTTCATTTCTTTGTTT
ACCATATATTT
Found at i:94345 original size:12 final size:12
Alignment explanation
Indices: 94328--94352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94318 ATTTTTTGCG
94328 AGGTTACTATTC
1 AGGTTACTATTC
94340 AGGTTACTATTC
1 AGGTTACTATTC
94352 A
1 A
94353 TATGAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Done.