Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001588.1 Hibiscus syriacus cultivar Beakdansim tig00003168_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: 84376
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:4581 original size:17 final size:16
Alignment explanation
Indices: 4550--4583 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4540 CACGTGAGGA
4550 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
4566 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
4583 T
1 T
4584 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:21595 original size:131 final size:130
Alignment explanation
Indices: 21422--21789 Score: 450
Period size: 131 Copynumber: 2.8 Consensus size: 130
21412 ATAATTTTAA
** * * **
21422 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGATCTTTCATGCCTTAAAATA
1 GAGAGAAAATGATAATATAAAATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGCA
* * * *
21487 GTCATTTATTACTCCGATTGAAATGAAGAGATATCACTATTCCGTATTAAAATTCAATATCGATT
66 GTCATTTATTACTCC-ATCGAAATGAAGAGATATCACTATTCCATATTAAAAATCAATATCAATT
21552 C
130 C
* *
21553 GAGTGAAAATGATAATATAAAATAATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGCA
1 GAGAGAAAATGATAATATAAAATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGCA
** * * *
21618 GTCATTTATTGTTTCAGTCGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTAATT
66 GTCATTTATTACTCCA-TCGAAATGAAGAGATATCACTATTCCATATTAAAAATCAATATCAATT
21683 C
130 C
* * ** * * **
21684 TAGAG-AAATAATAATATTGAATTATTTCCAATCTAGAATAAATGACCTCTCATACCTTAGTGCA
1 GAGAGAAAATGATAATATAAAATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGCA
* * *
21748 GTCATTTATTACTCCAACCGAAATGAAAAGATATTACTATTC
66 GTCATTTATTACTCC-ATCGAAATGAAGAGATATCACTATTC
21790 TCAATATCGC
Statistics
Matches: 202, Mismatches: 33, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
130 86 0.43
131 116 0.57
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (130 bp):
GAGAGAAAATGATAATATAAAATTATTTCCAATCGAGAATAAATGATCTCTCATACCTTAAAGCA
GTCATTTATTACTCCATCGAAATGAAGAGATATCACTATTCCATATTAAAAATCAATATCAATTC
Found at i:25123 original size:22 final size:22
Alignment explanation
Indices: 25095--25195 Score: 120
Period size: 22 Copynumber: 4.8 Consensus size: 22
25085 GAGGGTTTAT
25095 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
** **
25117 AGTGGTCCTTCGAAATGTATCC
1 AGTGGTCCTTCGGGACATATCC
25139 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACATATCC
* *
25161 AGTGGTCCTTAGGGACGTA---
1 AGTGGTCCTTCGGGACATATCC
25180 A-TGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
25196 AATATTCACT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 13 0.19
19 1 0.01
22 53 0.79
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.28
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATCC
Found at i:26477 original size:134 final size:133
Alignment explanation
Indices: 26253--27111 Score: 903
Period size: 134 Copynumber: 6.4 Consensus size: 133
26243 TTCAGGGTTG
* * * * *
26253 ATCAGAT-TGAGAAATGTTTATTCATTTCACTGTTCTTCAGGGAAGATTAAATCGATGTAGACTT
1 ATCAGATCT-AGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTT
* * * * * *
26317 GTTCCATTGTTGCTCAAGGAAGATCAAATCTTGAAAACAAGGGATATGTTCTACTTCTTTTTGAG
65 GTTCCACTGTTCCTCAGGGAATATCAAATCTTGAAAA-AAGGGATATGTTCTGCTTCTTCTTGAG
*
26382 AGAAA
129 GGAAA
* * ** * * * *
26387 ATCAGATATGGGGACGTTGATTCATTCCACTATTCTTCAGGGACA-ATTAAATCGAGGCATACTT
1 ATCAGATCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGA-AGATTGAATCGAGGCAGACTT
* * * *
26451 GTTCAACTATTACTCAGGGAATATCAAATCTT-AAAAGAGAGGGATATGTTCCGCTTCTTCTTGA
65 GTTCCACTGTTCCTCAGGGAATATCAAATCTTGAAAA-A-AGGGATATGTTCTGCTTCTTCTTGA
*
26515 GGGGAA
128 GGGAAA
* * *
26521 ATCAGATCTGGAAATGTTGATTCATTCTACTGTTCTTCAGGGAAGATTGAATTGAGGCAGACTTG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
*** * *
26586 TTCTGTTGTTCCTCAGGGAATATCAAATCTGGAAAAAAGGGATATATT-T-CGTTGCTTCTTGAG
66 TTCCACTGTTCCTCAGGGAATATCAAATCTTGAAAAAAGGGATATGTTCTGC-TT-CTTCTTGAG
26649 GGAAA
129 GGAAA
* * * *
26654 ATCAGATTTGGAAATGTTGACTT-ATTCCACTATTCTTCAAGGAAGATTGAATCGAGGCAGACTT
1 ATCAGATCTAGAAATGTTGA-TTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTT
** * * * * * * *
26718 GTTCCACTGTTCCTCATAGAAGATCAAATCTGGAAAAAAGTGGGATCTGTTCCGCTGCTTTTTAA
65 GTTCCACTGTTCCTCAGGGAATATCAAATCTTGAAAAAA--GGGATATGTTCTGCTTCTTCTTGA
26783 GGGAAA
128 GGGAAA
* * * * *
26789 ATCAGATCTAGAAATGTTGACTCGTTCCACTATTCTTCAGGGAAGATTAAATCGAGGCAAACTTG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
** * *
26854 TTCCACTGTTCCTCAGGGAATATCAAAT-TTGGAAAAAAATGATAAGTTCCT-CTGCTTCTTG-G
66 TTCCACTGTTCCTCAGGGAATATCAAATCTT-GAAAAAAGGGATATGTT-CTGCTTCTTCTTGAG
*
26916 GAAAAA
129 G-GAAA
* * * * *
26922 ATCAAATCTAGAAATTTTGACTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAGGCATACTTG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
** * *
26987 TTCCACTGTTCCTCAGGGAA-AGTCAAATC-TGAAAAAAAAAAGATATGTTTTGCTACTTCTTGA
66 TTCCACTGTTCCTCAGGGAATA-TCAAATCTTG--AAAAAAGGGATATGTTCTGCTTCTTCTTGA
27050 GGGAAA
128 GGGAAA
*
27056 ATCAGATCTAGAAATGTTGACTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
1 ATCAGATCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
27112 TTTGATTCTT
Statistics
Matches: 612, Mismatches: 91, Indels: 44
0.82 0.12 0.06
Matches are distributed among these distances:
131 1 0.00
132 6 0.01
133 221 0.36
134 266 0.43
135 116 0.19
136 1 0.00
137 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (133 bp):
ATCAGATCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
TTCCACTGTTCCTCAGGGAATATCAAATCTTGAAAAAAGGGATATGTTCTGCTTCTTCTTGAGGG
AAA
Found at i:33984 original size:131 final size:131
Alignment explanation
Indices: 33738--34104 Score: 418
Period size: 131 Copynumber: 2.8 Consensus size: 131
33728 ACAATTTTAA
* * * *
33738 AAGAAAAAATGATATTATCTAATTATTTCC-AATCGAGAATAAATGACCTTTCATGCCTTAAAAC
1 AAGAGAAAATGATAATATCTAATTATTTCCAAAT-GAGAATAAATGACCTCTCATGCCTTAAAGC
* * * ** * * *
33802 AGTCATTTGTTACTCCGATTGAAATGAAGAGATATCACTATTTCGTATTAAAATTCAATATCGAT
65 AGTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATCCCATATTAAAAATCAATATCAAT
33867 TC
130 TC
* * * * *
33869 GAGTGAAAATGATAATATCTAATGATTTCCAAATGAGAATAAATGACATCTCATACCTTAAAGCA
1 AAGAGAAAATGATAATATCTAATTATTTCCAAATGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
33934 GTCATTTATTGCTCCAATCGAAATGAAGAGATATCACTATCCCATCTTAAAAATCAATATTAATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATCCCATATTAAAAATCAATATCAATT
33999 C
131 C
* * *
34000 AAGAGAGAATGATAATAT-TGAATTATTTCCAATTGAGAATAAAAT-ACCTCTCATGCCTTAGAG
1 AAGAGAAAATGATAATATCT-AATTATTTCCAAATGAGAAT-AAATGACCTCTCATGCCTTAAAG
* * * * *
34063 CAATCCTTAATTACTCCAA-CTGAAATGAAAAGATATTACTAT
64 CAGTCATTTATTACTCCAATC-GAAATGAAGAGATATCACTAT
34105 TCTTAATATC
Statistics
Matches: 198, Mismatches: 34, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
130 2 0.01
131 189 0.95
132 7 0.04
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (131 bp):
AAGAGAAAATGATAATATCTAATTATTTCCAAATGAGAATAAATGACCTCTCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATCCCATATTAAAAATCAATATCAATT
C
Found at i:35482 original size:110 final size:110
Alignment explanation
Indices: 35289--35515 Score: 427
Period size: 110 Copynumber: 2.1 Consensus size: 110
35279 TCTATAAAAG
* *
35289 TCGACCCATTCGCTAGTCGTTTGGCTGCATCCAGTCATCGCCGTCAGGGACGCCGCGCCTCTACC
1 TCGACCCATTCGCTAGTCGTTTGGCTGCATCCAGTCACCGCCGTCAGGGACGCCGCGCCTCCACC
35354 GTCGTCGGTGGCTTTTAGATACCAAATTTTACCCGAAGATCCACC
66 GTCGTCGGTGGCTTTTAGATACCAAATTTTACCCGAAGATCCACC
35399 TCGACCCATTCGCTAGTCGTTTGGCTGCATCCAGTCACCGCCGTCAGGGACGCCGCGCCTCCACC
1 TCGACCCATTCGCTAGTCGTTTGGCTGCATCCAGTCACCGCCGTCAGGGACGCCGCGCCTCCACC
*
35464 GTCGTCGGTGGCTTTTAGATACCAAATTTTACCCGAAGATCCGCC
66 GTCGTCGGTGGCTTTTAGATACCAAATTTTACCCGAAGATCCACC
35509 TCGACCC
1 TCGACCC
35516 TCTCGTTTTA
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 114 1.00
ACGTcount: A:0.18, C:0.35, G:0.23, T:0.24
Consensus pattern (110 bp):
TCGACCCATTCGCTAGTCGTTTGGCTGCATCCAGTCACCGCCGTCAGGGACGCCGCGCCTCCACC
GTCGTCGGTGGCTTTTAGATACCAAATTTTACCCGAAGATCCACC
Found at i:37564 original size:24 final size:24
Alignment explanation
Indices: 37537--37587 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
37527 GGAACCTGTC
*
37537 TACCCCA-TCCCCTCTTCTTATAAA
1 TACCCCACT-CCCTCTTCCTATAAA
*
37561 TA-CCCACTCCTTCTTCCTATAAA
1 TACCCCACTCCCTCTTCCTATAAA
37584 TACC
1 TACC
37588 ATACCCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.25, C:0.41, G:0.00, T:0.33
Consensus pattern (24 bp):
TACCCCACTCCCTCTTCCTATAAA
Found at i:37891 original size:24 final size:25
Alignment explanation
Indices: 37841--37892 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
37831 TTAATTATTG
* *
37841 TTAATGTTTTATTTATTTTTTAGTA
1 TTAATGTTTTATTTAATTTCTAGTA
37866 TTAAT-TTTTATTTTAATTTCTA-TA
1 TTAATGTTTTA-TTTAATTTCTAGTA
37890 TTA
1 TTA
37893 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (25 bp):
TTAATGTTTTATTTAATTTCTAGTA
Found at i:40027 original size:24 final size:23
Alignment explanation
Indices: 39972--40027 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
39962 TGTTTATTAA
39972 TATTTTTATTATTTAATTGTTTG
1 TATTTTTATTATTTAATTGTTTG
* * *
39995 AATTTTTTATTATTTAGTTGTTTT
1 TA-TTTTTATTATTTAATTGTTTG
40019 TATTATTTA
1 TATT-TTTA
40028 ATTTCTTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (23 bp):
TATTTTTATTATTTAATTGTTTG
Found at i:44571 original size:64 final size:64
Alignment explanation
Indices: 44457--44601 Score: 159
Period size: 64 Copynumber: 2.2 Consensus size: 64
44447 GTGCACCAAG
* * * * * *
44457 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCT
1 TGTGCATCGATGCATGAAATGCATTCGATATTTGAAAATAGCATGAGTGCATCGATGCATGGAT
** *
44521 TGTGCATCGATGCATGAAATGCATTCGATATTT-AATTTATTCAATG-GTGCATCGATGCATGGA
1 TGTGCATCGATGCATGAAATGCATTCGATATTTGAAAATA-GC-ATGAGTGCATCGATGCATGGA
44584 T
64 T
*
44585 TGATGCATCGGTGCATG
1 TG-TGCATCGATGCATG
44602 CCTTTGAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
63 4 0.06
64 49 0.72
65 15 0.22
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (64 bp):
TGTGCATCGATGCATGAAATGCATTCGATATTTGAAAATAGCATGAGTGCATCGATGCATGGAT
Found at i:47519 original size:55 final size:55
Alignment explanation
Indices: 47478--48061 Score: 693
Period size: 55 Copynumber: 10.9 Consensus size: 55
47468 TAACGAGTTT
* * *
47478 GCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAACAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGTGTCC
* * *
47533 GCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGTGTCC
*
47588 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * ** *
47643 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCATGAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* *
47698 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * * *
47753 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
47804 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAGCAATCTTCATA-AAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGTGTCC
* * *
47859 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * * *
47914 GGTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * * *
47965 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
48016 GCTCCCTGTTCTTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
48062 AATTTGCTTC
Statistics
Matches: 481, Mismatches: 39, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
51 161 0.33
54 2 0.00
55 315 0.65
56 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
Found at i:47855 original size:161 final size:161
Alignment explanation
Indices: 47478--47995 Score: 761
Period size: 161 Copynumber: 3.2 Consensus size: 161
47468 TAACGAGTTT
* * * * * *
47478 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCA-ACAAACGTGTCTGCTCCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTAT
* * ** *
47542 TCATTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTCAGA
65 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACTTGTCCGCTCCCTATTCCTTCAGA
* * *
47606 GAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
129 GAGTATAGGACT----CAATCTTCAACGAACTTGTCC
* * * *
47643 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCATGAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
*
47708 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGA
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGA
47773 GTATAGGACTCAATCTTCAACGAACTTGTCC
131 GTATAGGACTCAATCTTCAACGAACTTGTCC
*
47804 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* *
47869 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCCGGTCCCTATTCCTTCAGAGA
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGA
47934 GTATAGGACTCAATCTTCAACGAACTTGTCC
131 GTATAGGACTCAATCTTCAACGAACTTGTCC
*
47965 GCTCCCTATTCATTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
47996 AATCTTCAAC
Statistics
Matches: 323, Mismatches: 28, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
161 202 0.63
164 1 0.00
165 120 0.37
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (161 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGA
GTATAGGACTCAATCTTCAACGAACTTGTCC
Found at i:49437 original size:20 final size:18
Alignment explanation
Indices: 49385--49437 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
49375 TTTATTTCTC
49385 TTTTT-TTCACTTTTCATT
1 TTTTTCTTC-CTTTTCATT
49403 TTTTTCTTCCATTTTCCATT
1 TTTTTCTTCC-TTTT-CATT
49423 TTTTTCTTCTCTTTT
1 TTTTTCTTC-CTTTT
49438 TTTCATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.19
19 7 0.23
20 17 0.55
21 1 0.03
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTCTTCCTTTTCATT
Found at i:49478 original size:40 final size:42
Alignment explanation
Indices: 49395--49481 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 42
49385 TTTTTTTCAC
*
49395 TTTTCATTTTTTTCTTCCATTTTCCATTTTTTTCTTCTCTTT
1 TTTTCATTTTTTTCTTCCATTTTCCATTATTTTCTTCTCTTT
49437 TTTTCA-TTTTTT-TT-CATTTATCCATTCATTTT-TTCAT-TTT
1 TTTTCATTTTTTTCTTCCATTT-TCCATT-ATTTTCTTC-TCTTT
49477 TTTTC
1 TTTTC
49482 TTCAAGCGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
39 5 0.12
40 19 0.46
41 11 0.27
42 6 0.15
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.71
Consensus pattern (42 bp):
TTTTCATTTTTTTCTTCCATTTTCCATTATTTTCTTCTCTTT
Found at i:62756 original size:15 final size:15
Alignment explanation
Indices: 62738--62769 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62728 GATTTCATCT
62738 TCCCGAATTTCTCCA
1 TCCCGAATTTCTCCA
62753 TCCCGAATTTCTCCA
1 TCCCGAATTTCTCCA
62768 TC
1 TC
62770 ATAGTAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.06, T:0.34
Consensus pattern (15 bp):
TCCCGAATTTCTCCA
Found at i:66091 original size:18 final size:18
Alignment explanation
Indices: 66064--66106 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
66054 GGGCCTTCTG
66064 TATA-TTTAAAATTATTA
1 TATATTTTAAAATTATTA
*
66081 TATATTTTAAAATTTTTA
1 TATATTTTAAAATTATTA
66099 TATATTTT
1 TATATTTT
66107 TATTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTTTAAAATTATTA
Found at i:80370 original size:15 final size:15
Alignment explanation
Indices: 80350--80378 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
80340 GTTATATGAG
80350 CTATGTGATAAGAAA
1 CTATGTGATAAGAAA
80365 CTATGTGATAAGAA
1 CTATGTGATAAGAA
80379 GCTACGAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (15 bp):
CTATGTGATAAGAAA
Found at i:81218 original size:14 final size:14
Alignment explanation
Indices: 81189--81228 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
81179 AAAATGAGGA
*
81189 GCAAAGCAATGATAG
1 GCAAGGCAA-GATAG
*
81204 GCAAGGTAAGATAG
1 GCAAGGCAAGATAG
81218 GCAAGGCAAGA
1 GCAAGGCAAGA
81229 CAGGTCAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.45, C:0.12, G:0.33, T:0.10
Consensus pattern (14 bp):
GCAAGGCAAGATAG
Done.