Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000684.1 Hibiscus syriacus cultivar Beakdansim tig00001337_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: 79726
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:2760 original size:22 final size:22
Alignment explanation
Indices: 2714--2780 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
2704 TATTTTATAA
* * *
2714 TTATGTCTCTATGATATAATTTT
1 TTATATCTTTATGACAT-ATTTT
2737 TTATATCTTTATGACATATTTT
1 TTATATCTTTATGACATATTTT
* *
2759 TTTTATCTTCATGACAT-TTTT
1 TTATATCTTTATGACATATTTT
2780 T
1 T
2781 ATCATTTGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 5 0.13
22 20 0.51
23 14 0.36
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (22 bp):
TTATATCTTTATGACATATTTT
Found at i:8553 original size:26 final size:26
Alignment explanation
Indices: 8523--8574 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
8513 TGAATTTTAC
8523 AAACCTCATATTTAATGGAAATTTCA
1 AAACCTCATATTTAATGGAAATTTCA
8549 AAACCTCATATTTAATGGAAATTTCA
1 AAACCTCATATTTAATGGAAATTTCA
8575 TATCCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (26 bp):
AAACCTCATATTTAATGGAAATTTCA
Found at i:12875 original size:24 final size:24
Alignment explanation
Indices: 12823--12875 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
12813 AGGATTGTGT
12823 CACAAGAGCTGAGAAAACGAGTGC
1 CACAAGAGCTGAGAAAACGAGTGC
*
12847 AACAAGAGCAT-AGAAAAC-ACGTGC
1 CACAAGAGC-TGAGAAAACGA-GTGC
12871 CACAA
1 CACAA
12876 AAACAGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 1 0.04
24 23 0.92
25 1 0.04
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.08
Consensus pattern (24 bp):
CACAAGAGCTGAGAAAACGAGTGC
Found at i:13467 original size:5 final size:5
Alignment explanation
Indices: 13459--13483 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13449 TGGCCCAAAA
13459 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
13484 TTGCCATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:18210 original size:15 final size:16
Alignment explanation
Indices: 18186--18218 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18176 GTTCTTTTCT
18186 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
18201 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
18217 TT
1 TT
18219 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:19769 original size:3 final size:3
Alignment explanation
Indices: 19761--19801 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
19751 ATTTTTTATT
*
19761 TAA TAA TAA TAA T-A TAA TAA -AT TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
19802 AATGAACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:20671 original size:76 final size:76
Alignment explanation
Indices: 19931--20645 Score: 1297
Period size: 76 Copynumber: 9.4 Consensus size: 76
19921 GAAATGTTGA
* * *
19931 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
19996 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
20007 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
20072 AGGCTTTTTGG
66 AGGCTTTTTGG
*
20083 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
20148 AGGCTTTTTGG
66 AGGCTTTTTGG
20159 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
20224 AGGCTTTTTGG
66 AGGCTTTTTGG
*
20235 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
20300 AGGCTTTTTGG
66 AGGCTTTTTGG
*
20311 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
20376 AGGCTTTTTGG
66 AGGCTTTTTGG
*
20387 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
20452 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
20463 AAACATCATGCACTGAAGGACTTATAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
20528 AGGCTTTTTGG
66 AGGCTTTTTGG
*
20539 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGCTCTCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAA-AACATCAAAAAGCTCCCG
20603 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
20615 AAACATCATGCACTGAAGGACTTATAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
20646 GGGAAATAGT
Statistics
Matches: 622, Mismatches: 16, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 2 0.00
76 620 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:21427 original size:113 final size:113
Alignment explanation
Indices: 21047--21717 Score: 944
Period size: 112 Copynumber: 6.0 Consensus size: 113
21037 ATAGAATTAT
* * *
21047 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * **
21112 ATTATGAAC-TTCTCTAGAAAAGTTGTTCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
* *
21159 GCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
21224 ATTATGAACCTTCTCTGGCAAA--ATAATCCATCAAGTGATGAATTC-A
66 ATTATGAACTTTCTCTGG-AAATGATGATCCATCAAATGATGGATTCAA
21270 GACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
21335 CATTATGAACTTTCTCTGGAAATGATGATCCATCAAATAATAGATTCAA
65 CATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
* *
21384 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
21449 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
66 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
* *
21497 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
21562 ATTATGAAC-TTCTATGGAAATG-TCAATCCATCGAATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAATGAT-GATCCATCAAATGATGGATTCAA
* *
21609 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTATC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * **
21674 ATTATGAACTCGAC-CTGG-AATGTTGATCCATTGAATGATGGATT
66 ATTATGAACT-TTCTCTGGAAATGATGATCCATCAAATGATGGATT
21718 TGAACTTTGC
Statistics
Matches: 512, Mismatches: 37, Indels: 20
0.90 0.07 0.04
Matches are distributed among these distances:
111 6 0.01
112 291 0.57
113 209 0.41
114 6 0.01
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
Found at i:21447 original size:225 final size:223
Alignment explanation
Indices: 21047--21682 Score: 961
Period size: 225 Copynumber: 2.8 Consensus size: 223
21037 ATAGAATTAT
* *
21047 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
* * * *
21112 ATTATGAACTTCTCTAGAAAAGTTGTTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 ATTATGAACTTCTCTGGAAATG-TGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
21177 TCTTCTTATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG
*
21242 CAAA-ATAATCCATCAAGTGATGAATTC-A
195 -AAAGATAATCCATCAAATGATGAATTCAA
*
21270 GACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCT
* * ** *
21335 CATTATGAACTTTCTCTGGAAATGATGATCCATCAAATAATAGATTCAAGTAAAAGGTTGAACAA
65 CATTATGAAC-TTCTCTGGAAATG-TGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAA
* *
21400 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCT
128 ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCT
* *
21465 GGAAATGATGATCCATCAAATGATGGATTCAA
193 GGAAA-GATAATCCATCAAATGATGAATTCAA
* *
21497 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
* * *
21562 ATTATGAACTTCTATGGAAATGTCAATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAAT
66 ATTATGAACTTCTCTGGAAATGT-GATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
21627 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAAC
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
21683 TCGACCTGGA
Statistics
Matches: 374, Mismatches: 33, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
223 1 0.00
224 74 0.20
225 206 0.55
226 91 0.24
227 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (223 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
ATTATGAACTTCTCTGGAAATGTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGA
AAGATAATCCATCAAATGATGAATTCAA
Found at i:21551 original size:24 final size:23
Alignment explanation
Indices: 21516--21560 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
21506 TGAACAAATT
21516 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
21540 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
21561 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:22145 original size:22 final size:22
Alignment explanation
Indices: 22120--22174 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
22110 CATAAAGTTT
*
22120 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
22142 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
22164 TCATCTTTGAA
1 TCATCTTTGAA
22175 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:24847 original size:83 final size:83
Alignment explanation
Indices: 24708--24963 Score: 476
Period size: 83 Copynumber: 3.1 Consensus size: 83
24698 CTTATTTCTC
*
24708 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
24773 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
24791 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
24856 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
24874 CTATGAGCAGATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
24939 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
24957 CTATGAG
1 CTATGAG
24964 TCTCTTTCAG
Statistics
Matches: 169, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 169 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:31965 original size:20 final size:20
Alignment explanation
Indices: 31942--31985 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31932 TGAAAGAAAA
* *
31942 AATTAAATATAGA-AATTTTT
1 AATT-AATAGAGACAATTTAT
31962 AATTAATAGAGACAATTTAT
1 AATTAATAGAGACAATTTAT
31982 AATT
1 AATT
31986 GATTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
AATTAATAGAGACAATTTAT
Found at i:32491 original size:15 final size:16
Alignment explanation
Indices: 32467--32499 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
32457 GCTCTTTTCT
32467 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
32482 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
32498 TT
1 TT
32500 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:32972 original size:2 final size:2
Alignment explanation
Indices: 32965--33028 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
32955 ATTTACCTAA
32965 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
33007 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
33029 TCTGATAAGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34114 original size:18 final size:18
Alignment explanation
Indices: 34091--34125 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34081 TTTTATTTAA
34091 TAATAA-TATATAATAAAT
1 TAATAATTA-ATAATAAAT
34109 TAATAATTAATAATAAA
1 TAATAATTAATAATAAA
34126 ATGAACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATTAATAATAAAT
Found at i:43994 original size:11 final size:10
Alignment explanation
Indices: 43956--44033 Score: 106
Period size: 10 Copynumber: 7.7 Consensus size: 10
43946 GGAAAATCGG
43956 TTTGACCGGT
1 TTTGACCGGT
*
43966 TTTGAACCAG-
1 TTTG-ACCGGT
43976 TTTGACCGGT
1 TTTGACCGGT
43986 TTTGAACCGGT
1 TTTG-ACCGGT
43997 TTTGACCGGT
1 TTTGACCGGT
44007 TTTGAACCGGT
1 TTTG-ACCGGT
44018 TTTGACCGG-
1 TTTGACCGGT
44027 TTTGACC
1 TTTGACC
44034 CGACCCGACC
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
9 11 0.18
10 27 0.44
11 24 0.39
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (10 bp):
TTTGACCGGT
Found at i:44002 original size:21 final size:21
Alignment explanation
Indices: 43956--44029 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
43946 GGAAAATCGG
*
43956 TTTGACCGGTTTTGAACCAG-
1 TTTGACCGGTTTTGAACCGGT
43976 TTTGACCGGTTTTGAACCGGT
1 TTTGACCGGTTTTGAACCGGT
43997 TTTGACCGGTTTTGAACCGGT
1 TTTGACCGGTTTTGAACCGGT
44018 TTTGACCGGTTT
1 TTTGACCGGTTT
44030 GACCCGACCC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 19 0.37
21 33 0.63
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.39
Consensus pattern (21 bp):
TTTGACCGGTTTTGAACCGGT
Found at i:44057 original size:17 final size:17
Alignment explanation
Indices: 44035--44072 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
44025 GGTTTGACCC
44035 GACCCGACCAGACCGTT
1 GACCCGACCAGACCGTT
*
44052 GACCCGACCCGACCGTT
1 GACCCGACCAGACCGTT
44069 GACC
1 GACC
44073 GTTGACTTTC
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:0.21, C:0.45, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCAGACCGTT
Found at i:45659 original size:36 final size:36
Alignment explanation
Indices: 45606--45675 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
45596 GGGGGTTACA
* *
45606 GAGACTATTCAAAGAGTTCACAAAACATTTACCATT
1 GAGACTACTCAAAGAGTTCACAAAACATTAACCATT
*
45642 GAGACTACTCAATGAGTTCACAAAACATTAACCA
1 GAGACTACTCAAAGAGTTCACAAAACATTAACCA
45676 CTTATTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.24
Consensus pattern (36 bp):
GAGACTACTCAAAGAGTTCACAAAACATTAACCATT
Found at i:56312 original size:18 final size:18
Alignment explanation
Indices: 56285--56336 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
56275 GTGAAGTATG
*
56285 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
56303 AATGGTGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
56321 AATGGTGTTGTCGTGG
1 AATGGTGTTGTCGTGG
56337 TAAGTGTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.15, C:0.12, G:0.40, T:0.33
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:57555 original size:18 final size:17
Alignment explanation
Indices: 57510--57582 Score: 74
Period size: 18 Copynumber: 4.2 Consensus size: 17
57500 AACATATAAA
*
57510 GAACTAGTTTAATTAAT
1 GAACTAGTTTAATGAAT
* *
57527 GAACCAATTTAAATGAAT
1 GAACTAGTTT-AATGAAT
* *
57545 GAACTAGTTTAATTAGT
1 GAACTAGTTTAATGAAT
*
57562 GAACTAGCTTTATTGAAT
1 GAACTAG-TTTAATGAAT
57580 GAA
1 GAA
57583 AGAGGATACT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 20 0.45
18 24 0.55
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTAATGAAT
Found at i:57566 original size:17 final size:17
Alignment explanation
Indices: 57510--57582 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
57500 AACATATAAA
57510 GAACTAGTTTAATTAAT
1 GAACTAGTTTAATTAAT
* * *
57527 GAACCAATTTAAATGAAT
1 GAACTAGTTT-AATTAAT
*
57545 GAACTAGTTTAATTAGT
1 GAACTAGTTTAATTAAT
57562 GAACTAGCTTT-ATTGAAT
1 GAACTAG-TTTAATT-AAT
57580 GAA
1 GAA
57583 AGAGGATACT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
17 23 0.51
18 22 0.49
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTAATTAAT
Found at i:57720 original size:20 final size:20
Alignment explanation
Indices: 57682--57720 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57672 CAACTTAATG
* *
57682 TCATGAAAATTTATTAACAC
1 TCATGAAAATTCATAAACAC
*
57702 TCATGCAAATTCATAAACA
1 TCATGAAAATTCATAAACA
57721 AGTAAAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (20 bp):
TCATGAAAATTCATAAACAC
Found at i:59604 original size:9 final size:9
Alignment explanation
Indices: 59580--59630 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
59570 CCTCTTTAAA
*
59580 TTTTTTTCT
1 TTTTTTTAT
59589 TTCTTTTTAT
1 TT-TTTTTAT
59599 TTTTTTTAT
1 TTTTTTTAT
*
59608 TTTTTTGAT
1 TTTTTTTAT
59617 TTGTTTTTGAT
1 TT-TTTTT-AT
59628 TTT
1 TTT
59631 GTACTGACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 19 0.53
10 13 0.36
11 4 0.11
ACGTcount: A:0.08, C:0.04, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:59613 original size:18 final size:18
Alignment explanation
Indices: 59580--59630 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
59570 CCTCTTTAAA
* *
59580 TTTTTTTCTTTCTTTTTAT
1 TTTTTTTATTT-TTTTGAT
59599 TTTTTTTATTTTTTTGAT
1 TTTTTTTATTTTTTTGAT
59617 TTGTTTTTGATTTT
1 TT-TTTTT-ATTTT
59631 GTACTGACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.29
19 15 0.54
20 5 0.18
ACGTcount: A:0.08, C:0.04, G:0.06, T:0.82
Consensus pattern (18 bp):
TTTTTTTATTTTTTTGAT
Found at i:59860 original size:12 final size:12
Alignment explanation
Indices: 59820--59852 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
59810 GGAAATGATA
59820 TGAAATAATAAT
1 TGAAATAATAAT
59832 TGAAATAATAAT
1 TGAAATAATAAT
59844 TGAAATAAT
1 TGAAATAAT
59853 GAATGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (12 bp):
TGAAATAATAAT
Found at i:59970 original size:18 final size:18
Alignment explanation
Indices: 59943--59994 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
59933 GTGAAGTATG
*
59943 AATGGCGTTGTCGTGGAA
1 AATGGTGTTGTCGTGGAA
*
59961 AATGGTGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGAA
59979 AATGGTGTTGTCGTGG
1 AATGGTGTTGTCGTGG
59995 TAAGTGTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.10, G:0.40, T:0.33
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGAA
Found at i:61206 original size:18 final size:17
Alignment explanation
Indices: 61169--61259 Score: 119
Period size: 18 Copynumber: 5.2 Consensus size: 17
61159 AACATATAAA
*
61169 GAACTAGTTTAATTAAT
1 GAACTAGTTTAATGAAT
61186 GAACTAGTTTAAATGAAT
1 GAACTAGTTT-AATGAAT
61204 GAACTAGTTTAAATGAAT
1 GAACTAGTTT-AATGAAT
* *
61222 GAACTAGTTTAATTAGT
1 GAACTAGTTTAATGAAT
*
61239 GAACTAGCTTTATTGAAT
1 GAACTAG-TTTAATGAAT
61257 GAA
1 GAA
61260 AGAGGATACT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
17 22 0.33
18 44 0.67
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTAATGAAT
Found at i:61215 original size:35 final size:34
Alignment explanation
Indices: 61169--61259 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 34
61159 AACATATAAA
61169 GAACTAGTTTAATTAATGAACTAGTTTAAATGAAT
1 GAACTAGTTTAATTAATGAACTAGTTT-AATGAAT
* * *
61204 GAACTAGTTTAAATGAATGAACTAGTTTAATTAGT
1 GAACTAGTTT-AATTAATGAACTAGTTTAATGAAT
61239 GAACTAGCTTT-ATTGAATGAA
1 GAACTAG-TTTAATT-AATGAA
61260 AGAGGATACT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
34 2 0.04
35 28 0.57
36 19 0.39
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (34 bp):
GAACTAGTTTAATTAATGAACTAGTTTAATGAAT
Found at i:61276 original size:53 final size:53
Alignment explanation
Indices: 61164--61277 Score: 124
Period size: 53 Copynumber: 2.2 Consensus size: 53
61154 ATGAAAACAT
** **
61164 ATAAA-GAACTAGTTTAATTAATGAACTAGTTTAAATGAATGAACTAGTTTAA
1 ATAAATGAACTAGTTTAATTAATGAACTAGTTTAAATGAATGAAAGAGGATAA
* * * *
61216 ATGAATGAACTAGTTTAATTAGTGAACTAGCTTT-ATTGAATGAAAGAGGATAC
1 ATAAATGAACTAGTTTAATTAATGAACTAG-TTTAAATGAATGAAAGAGGATAA
*
61269 TTAAATGAA
1 ATAAATGAA
61278 GTAGCTTCAT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
52 4 0.08
53 43 0.86
54 3 0.06
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (53 bp):
ATAAATGAACTAGTTTAATTAATGAACTAGTTTAAATGAATGAAAGAGGATAA
Found at i:61397 original size:20 final size:20
Alignment explanation
Indices: 61359--61397 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61349 CAACTTAATG
* *
61359 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
61379 TCATGCAAATTCATGAACA
1 TCATGCAAATTCATGAACA
61398 AGTAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Found at i:64026 original size:24 final size:25
Alignment explanation
Indices: 63991--64038 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
63981 TATAGCATAG
63991 TATATATAATATAGTTTTT-GAAAA
1 TATATATAATATAGTTTTTAGAAAA
64015 TATATA-ATATATAGTTTTTAGAAA
1 TATATATA-ATATAGTTTTTAGAAA
64039 CTTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.05
24 17 0.77
25 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (25 bp):
TATATATAATATAGTTTTTAGAAAA
Found at i:64120 original size:35 final size:35
Alignment explanation
Indices: 64006--64409 Score: 381
Period size: 35 Copynumber: 11.5 Consensus size: 35
63996 ATAATATAGT
* *
64006 TTTTGAAAATATATAATATATAGTTTTTAGAAACTTATT
1 TTTTGAAAACATATAATATATAGTTTTTA-AAA--TA-A
* * ***
64045 TTTTAAAAAAATATAATATATAGTTTTTTAAAACGG
1 TTTTGAAAACATATAATATATAG-TTTTTAAAATAA
*
64081 TTTTGAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* *
64116 TTTTGGAAAACATATAATATATAGTTTTTAAAGTAG
1 TTTT-GAAAACATATAATATATAGTTTTTAAAATAA
* * ***
64152 TTTTGAAAGCGTATAATATATAGTTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
*
64187 TTTTGAAAATATATAATATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
*
64222 TTTTGAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* *
64257 TTTTGAAAACGTAT-A-ATATAGTTTTTAAATTAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
** * * * *
64290 TTTTGAAATGA-ATAATAATATACTTTTGAAAACAT
1 TTTTGAAAACATATAAT-ATATAGTTTTTAAAATAA
* *
64325 TTTTAAAAACGTATAATATAT-GTTTTTAAAA-ACA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATA-A
* * * *
64359 TTTTTGAAAACGTAT-A-ATATGGTTTTGAAAATGAT
1 -TTTTGAAAACATATAATATATAGTTTTTAAAAT-AA
*
64394 TTTTGAAAATATATAA
1 TTTTGAAAACATATAA
64410 ATTTTTGAAA
Statistics
Matches: 303, Mismatches: 50, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.01
33 31 0.10
34 30 0.10
35 152 0.50
36 58 0.19
39 24 0.08
40 6 0.02
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (35 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAATAA
Found at i:64464 original size:3 final size:3
Alignment explanation
Indices: 64456--64509 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
64446 AATATAGTCT
*
64456 TTA TTA TTA TTA TT- TTA -TA TTTA TT- TAA GTTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA
64499 TTA TTA TTA TT
1 TTA TTA TTA TT
64510 TATTTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 7 0.16
3 32 0.74
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:66611 original size:18 final size:20
Alignment explanation
Indices: 66571--66608 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
66561 GGGGTAGGAA
*
66571 TTTTTTTATTTTTCATTATTC
1 TTTTATTATTTTT-ATTATTC
66592 TTTTATTATTTTT-TTAT
1 TTTTATTATTTTTATTAT
66609 CTTACTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
21 12 0.75
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTATTATTTTTATTATTC
Found at i:69602 original size:21 final size:21
Alignment explanation
Indices: 69573--69632 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
69563 GGCATGTGAA
* *
69573 ATCTATGTCCTGAAGGACATC
1 ATCTGTGTCCCGAAGGACATC
69594 ATCTGTGTCCCGAAGGACATC
1 ATCTGTGTCCCGAAGGACATC
69615 ATCTGTGTCCCGAAGGAC
1 ATCTGTGTCCCGAAGGAC
69633 CTATCCATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (21 bp):
ATCTGTGTCCCGAAGGACATC
Found at i:69688 original size:31 final size:31
Alignment explanation
Indices: 69631--69695 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
69621 GTCCCGAAGG
**
69631 ACCTATCCATATGTTTCGAAGAACATAGATA
1 ACCTATCCATATGTCCCGAAGAACATAGATA
* *
69662 ACCTGTCCATATGTCCCGAA-AGACATAGGTA
1 ACCTATCCATATGTCCCGAAGA-ACATAGATA
69693 ACC
1 ACC
69696 CTCGACTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (31 bp):
ACCTATCCATATGTCCCGAAGAACATAGATA
Found at i:79712 original size:30 final size:30
Alignment explanation
Indices: 79626--79726 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
79616 GTAAGACCTA
* * *
79626 TCCATATGTTTCGAAGAACATAGGTAACCTG
1 TCCATATG-TCCGAAGGACATAGGTAAACTG
79657 TCCATATGTACCGAAGGAC--AGGTAAACTG
1 TCCATATGT-CCGAAGGACATAGGTAAACTG
79686 TCCATATGTCCGAAGGACATAGGTAAACTG
1 TCCATATGTCCGAAGGACATAGGTAAACTG
79716 TCCATATGTCC
1 TCCATATGTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
28 9 0.14
29 18 0.28
30 22 0.34
31 15 0.23
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCGAAGGACATAGGTAAACTG
Done.