Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009227.1 Hibiscus syriacus cultivar Beakdansim tig00112831_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: 79972
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:10886 original size:2 final size:2
Alignment explanation
Indices: 10879--10903 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10869 GTTGATAAAA
10879 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10904 CCAGAACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21038 original size:21 final size:20
Alignment explanation
Indices: 21014--21115 Score: 62
Period size: 21 Copynumber: 4.8 Consensus size: 20
21004 TAAATTTGCA
21014 CCGAAGTGCCACATAATTGTC
1 CCGAAG-GCCACATAATTGTC
*
21035 CCGAAGAACCACATAGATT-TGC
1 CCGAAG-GCCACATA-ATTGT-C
* *
21057 ACCAAAGTGCCACATATTTGTC
1 -CCGAAG-GCCACATAATTGTC
* * *
21079 TCGGAGGACCACATATTTGTC
1 CCGAAGG-CCACATAATTGTC
*
21100 CCAAAGGACCACATAA
1 CCGAAGG-CCACATAA
21116 GACCCTCGAC
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.02
21 42 0.67
22 7 0.11
23 13 0.21
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (20 bp):
CCGAAGGCCACATAATTGTC
Found at i:21057 original size:44 final size:44
Alignment explanation
Indices: 21007--21093 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
20997 CAGCTTGTAA
*
21007 ATTTGCACCGAAGTGCCACATAATTGTCCCGAAGAACCACATAG
1 ATTTGCACCAAAGTGCCACATAATTGTCCCGAAGAACCACATAG
* * * *
21051 ATTTGCACCAAAGTGCCACATATTTGTCTCGGAGGACCACATA
1 ATTTGCACCAAAGTGCCACATAATTGTCCCGAAGAACCACATA
21094 TTTGTCCCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (44 bp):
ATTTGCACCAAAGTGCCACATAATTGTCCCGAAGAACCACATAG
Found at i:27307 original size:21 final size:21
Alignment explanation
Indices: 27283--27324 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27273 GCTCGTAAAT
*
27283 TTGTATTGAAGTG-CCACATAA
1 TTGTACTGAAG-GACCACATAA
*
27304 TTGTCCTGAAGGACCACATAA
1 TTGTACTGAAGGACCACATAA
27325 ATTTGCACCG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
TTGTACTGAAGGACCACATAA
Found at i:27368 original size:21 final size:21
Alignment explanation
Indices: 27344--27388 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27334 GAAATGTCAT
* *
27344 ATATTTGTCCCGGAGGACCAC
1 ATATTTATCCCGAAGGACCAC
*
27365 ATATTTATCCCGAAGGATCAC
1 ATATTTATCCCGAAGGACCAC
27386 ATA
1 ATA
27389 AGACCCTCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
ATATTTATCCCGAAGGACCAC
Found at i:28984 original size:20 final size:21
Alignment explanation
Indices: 28959--28998 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
28949 CTCTACATAG
28959 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
28979 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
28999 CCCAACGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:33394 original size:22 final size:22
Alignment explanation
Indices: 33369--33436 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
33359 TATAATAATT
33369 ATTTGTATTATATTAACTTGAA
1 ATTTGTATTATATTAACTTGAA
* * *
33391 ATTTATTTTATA-AAACCATT---
1 ATTTGTATTATATTAA-C-TTGAA
33411 ATTTGTATTATATTAACTTGAA
1 ATTTGTATTATATTAACTTGAA
33433 ATTT
1 ATTT
33437 ATTTTATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
19 2 0.06
20 11 0.32
21 4 0.12
22 15 0.44
23 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (22 bp):
ATTTGTATTATATTAACTTGAA
Found at i:33397 original size:20 final size:20
Alignment explanation
Indices: 33374--33439 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
33364 TAATTATTTG
33374 TATTATATTAACTTGAAATT
1 TATTATATTAACTTGAAATT
* * *
33394 TATTTTATAAAACCATT--ATTT
1 TATTATAT-TAA-C-TTGAAATT
33415 GTATTATATTAACTTGAAATT
1 -TATTATATTAACTTGAAATT
33436 TATT
1 TATT
33440 TTATAAAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
19 2 0.06
20 12 0.35
21 10 0.29
22 8 0.24
23 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (20 bp):
TATTATATTAACTTGAAATT
Found at i:33412 original size:42 final size:42
Alignment explanation
Indices: 33366--33454 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
33356 TGATATAATA
33366 ATTATTTGTATTATATTAACTTGAAATTTATTTTATAAAACC
1 ATTATTTGTATTATATTAACTTGAAATTTATTTTATAAAACC
33408 ATTATTTGTATTATATTAACTTGAAATTTATTTTATAAAACC
1 ATTATTTGTATTATATTAACTTGAAATTTATTTTATAAAACC
33450 ATTAT
1 ATTAT
33455 ATATTACCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (42 bp):
ATTATTTGTATTATATTAACTTGAAATTTATTTTATAAAACC
Found at i:33443 original size:22 final size:22
Alignment explanation
Indices: 33376--33444 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
33366 ATTATTTGTA
33376 TTATATTAACTTGAAATTTATT
1 TTATATTAACTTGAAATTTATT
* * *
33398 TTATA-AAACCATT---ATTTGTA
1 TTATATTAA-C-TTGAAATTTATT
33418 TTATATTAACTTGAAATTTATT
1 TTATATTAACTTGAAATTTATT
33440 TTATA
1 TTATA
33445 AAACCATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 2 0.06
20 11 0.31
21 4 0.11
22 16 0.46
23 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (22 bp):
TTATATTAACTTGAAATTTATT
Found at i:35458 original size:3 final size:3
Alignment explanation
Indices: 35444--35501 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
35434 TTTTTGCCCC
* * *
35444 ATT ATC ATT ATT ATT ATT A-T ATT ATT ATT ACT ATT ATT A-T ATA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
35490 AAT ATT ATT ATT
1 ATT ATT ATT ATT
35502 TTACAAATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:35472 original size:17 final size:17
Alignment explanation
Indices: 35444--35500 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
35434 TTTTTGCCCC
*
35444 ATTATCATTATTATTATT
1 ATTAT-ATTATTAATATT
*
35462 A-TATTATTATTACTATT
1 ATTA-TATTATTAATATT
*
35479 ATTATATAATTAATATT
1 ATTATATTATTAATATT
35496 ATTAT
1 ATTAT
35501 TTTACAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 30 0.88
18 4 0.12
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATTATTAATATT
Found at i:35473 original size:20 final size:20
Alignment explanation
Indices: 35444--35501 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
35434 TTTTTGCCCC
*
35444 ATTATCATTATTATTATTAT
1 ATTATTATTATTATTATTAT
*
35464 ATTATTATTACTATTATTAT
1 ATTATTATTATTATTATTAT
* *
35484 ATAATTAATATTATTATT
1 ATTATTATTATTATTATT
35502 TTACAAATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTATTATTATTATTAT
Found at i:35571 original size:20 final size:20
Alignment explanation
Indices: 35546--35590 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
35536 TAAACCAGAG
35546 GGCCCGATTACCAATTTGAA
1 GGCCCGATTACCAATTTGAA
35566 GGCCCGATTACCAATTTGAA
1 GGCCCGATTACCAATTTGAA
35586 GGCCC
1 GGCCC
35591 AAACTCGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (20 bp):
GGCCCGATTACCAATTTGAA
Found at i:35644 original size:16 final size:16
Alignment explanation
Indices: 35623--35654 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35613 ATCAAATTCA
*
35623 AATCCGGTCCATACCC
1 AATCCGGTCCAGACCC
35639 AATCCGGTCCAGACCC
1 AATCCGGTCCAGACCC
35655 GACCCAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.44, G:0.16, T:0.16
Consensus pattern (16 bp):
AATCCGGTCCAGACCC
Found at i:36314 original size:20 final size:20
Alignment explanation
Indices: 36289--36335 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36279 GGCTTTAGGG
* *
36289 TAGTGACCGGCGGTGGTGAA
1 TAGTGACCGACAGTGGTGAA
*
36309 TAGTGATCGACAGTGGTGAA
1 TAGTGACCGACAGTGGTGAA
36329 TAGTGAC
1 TAGTGAC
36336 AGGAGGTGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.38, T:0.23
Consensus pattern (20 bp):
TAGTGACCGACAGTGGTGAA
Found at i:36344 original size:20 final size:19
Alignment explanation
Indices: 36289--36344 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
36279 GGCTTTAGGG
*
36289 TAGTGACCGGCGGTGGTGAA
1 TAGTGA-CGGAGGTGGTGAA
*
36309 TAGTGATC-GACAGTGGTGAA
1 TAGTGA-CGGA-GGTGGTGAA
36329 TAGTGACAGGAGGTGG
1 TAGTGAC-GGAGGTGG
36345 CCGGAATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.25, C:0.11, G:0.43, T:0.21
Consensus pattern (19 bp):
TAGTGACGGAGGTGGTGAA
Found at i:37013 original size:18 final size:18
Alignment explanation
Indices: 36990--37032 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
36980 AAGAAAGGGT
36990 TGTCTTAAAGTAACTAGA
1 TGTCTTAAAGTAACTAGA
37008 TGTCTTAAAGTAACTAGA
1 TGTCTTAAAGTAACTAGA
37026 TGTCTTA
1 TGTCTTA
37033 TTCTGATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTCTTAAAGTAACTAGA
Found at i:39932 original size:42 final size:42
Alignment explanation
Indices: 39874--39956 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
39864 AGAGATGATC
*
39874 GATCAAGCAAAAAAGTTCCAGGATGATTCAAAGGAACAAATT
1 GATCAAGCAAAAAAGTTCCAGGATGATTCAAAAGAACAAATT
*
39916 GATCAAGCAAAAAAGTTCTAGGATGATTCAAAAGAACAAAT
1 GATCAAGCAAAAAAGTTCCAGGATGATTCAAAAGAACAAAT
39957 GACAAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.19
Consensus pattern (42 bp):
GATCAAGCAAAAAAGTTCCAGGATGATTCAAAAGAACAAATT
Found at i:42934 original size:17 final size:17
Alignment explanation
Indices: 42905--42992 Score: 94
Period size: 17 Copynumber: 5.4 Consensus size: 17
42895 TATCCATCAG
42905 AGAAAAAAA-GAAAAGA
1 AGAAAAAAAGGAAAAGA
*
42921 AGAAAAAAGGGAAAAGA
1 AGAAAAAAAGGAAAAGA
* *
42938 AAAAAAAAAGAAAAAGA
1 AGAAAAAAAGGAAAAGA
*
42955 A-AAAAAAA-GAAAAAA
1 AGAAAAAAAGGAAAAGA
*
42970 AAAAAAAAAGAGAAAAG-
1 AGAAAAAAAG-GAAAAGA
42987 AGAAAA
1 AGAAAA
42993 GAGAAAAGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
15 6 0.10
16 22 0.37
17 27 0.45
18 5 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAGGAAAAGA
Found at i:42937 original size:14 final size:14
Alignment explanation
Indices: 42908--43056 Score: 142
Period size: 14 Copynumber: 10.4 Consensus size: 14
42898 CCATCAGAGA
*
42908 AAAAAAGAAAAGAAG
1 AAAAAAGAGAA-AAG
*
42923 AAAAAAGGGAAAAG
1 AAAAAAGAGAAAAG
*
42937 AAAAAAAAAAGAAAAAG
1 --AAAAAAGAG-AAAAG
*
42954 AAAAAAAAAGAAAA-
1 -AAAAAAGAGAAAAG
42968 AAAAAA-A-AAAAG
1 AAAAAAGAGAAAAG
*
42980 AGAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
*
42994 AGAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
*
43008 AGAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
*
43022 AGAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
*
43036 AGAAAAGAGAAGAAG
1 AAAAAAGAGAA-AAG
43051 AAAAAA
1 AAAAAA
43057 TTGAATCAAG
Statistics
Matches: 121, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
11 4 0.03
12 6 0.05
13 7 0.06
14 61 0.50
15 21 0.17
16 17 0.14
17 5 0.04
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAAAAG
Found at i:42941 original size:1 final size:1
Alignment explanation
Indices: 42932--42978 Score: 58
Period size: 1 Copynumber: 47.0 Consensus size: 1
42922 GAAAAAAGGG
* * * *
42932 AAAAGAAAAAAAAAAGAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42979 GAGAAAAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:42942 original size:7 final size:7
Alignment explanation
Indices: 42908--43056 Score: 114
Period size: 7 Copynumber: 21.9 Consensus size: 7
42898 CCATCAGAGA
42908 AAAAAAG
1 AAAAAAG
42915 AAAAGAAG
1 AAAA-AAG
42923 AAAAAAG
1 AAAAAAG
**
42930 GGAAAAG
1 AAAAAAG
42937 --AAAA-
1 AAAAAAG
42941 AAAAAAG
1 AAAAAAG
42948 -AAAAAG
1 AAAAAAG
42954 AAAAAA-
1 AAAAAAG
42960 AAAGAAA-
1 AAA-AAAG
42967 AAAAAA-
1 AAAAAAG
42973 AAAAAAG
1 AAAAAAG
*
42980 AGAAAAG
1 AAAAAAG
*
42987 AGAAAAG
1 AAAAAAG
*
42994 AGAAAAG
1 AAAAAAG
*
43001 AGAAAAG
1 AAAAAAG
*
43008 AGAAAAG
1 AAAAAAG
*
43015 AGAAAAG
1 AAAAAAG
*
43022 AGAAAAG
1 AAAAAAG
*
43029 AGAAAAG
1 AAAAAAG
*
43036 AGAAAAG
1 AAAAAAG
*
43043 AGAAGAAG
1 A-AAAAAG
43051 AAAAAA
1 AAAAAA
43057 TTGAATCAAG
Statistics
Matches: 128, Mismatches: 6, Indels: 16
0.85 0.04 0.11
Matches are distributed among these distances:
5 4 0.03
6 22 0.17
7 90 0.70
8 12 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:44478 original size:52 final size:51
Alignment explanation
Indices: 44285--44466 Score: 267
Period size: 51 Copynumber: 3.6 Consensus size: 51
44275 GGTCCATATT
* *
44285 ATCCATGT-GGGTATCTTGAAGGCTCACTTCAGCATGAAAAGATAGAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* *
44335 ATCCATGTGGGGCATCTTGAAGGTTCACATAAGCATGAAAAGATAGAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
* * *
44386 ATCCATGTGGGGCATCTTGAAGGCTCACATCTGCATGAAAATGACATAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAA-GATAGAAGTA
* *
44438 ATCGATGTGGGGAATCTTGAAGGCTCACA
1 ATCCATGTGGGGCATCTTGAAGGCTCACA
44467 CCAGTTTGAA
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 8 0.07
51 76 0.64
52 35 0.29
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (51 bp):
ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTA
Found at i:46569 original size:177 final size:177
Alignment explanation
Indices: 46059--47123 Score: 1652
Period size: 177 Copynumber: 6.0 Consensus size: 177
46049 ATATTTCCTA
46059 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCA-GAATGTTTTCAAATGAGATTTT
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCATG-ATGTTTTCAAATGAGATTTT
* *
46123 ATAAACTAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAA
65 AGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAA
*
46188 TAAAGGGGTTCCTTGACAACTAAGAAACTAAGTCTTCGGGGGTTTCTT
130 TAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * * * * *
46236 GATTTGTAAGTCCTATGGGCCATCCATAAGAACTTTAATGCAGGATGTTTCCAAATGAGA-TTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
* * * *
46300 GAAACCAAGCCTTCGGGGGTTTACTAATTATTTCAAAATAGTTGTTAAAGGAAGCTAAGCCTAAC
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
*
46365 AAAGGGGTTCAC-TGACATCTAAGAAACTAAGCCTTCGGGGGTTTCTT
131 AAAGGGGTTC-CTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
*
46412 GATTTGTAAGTCCTACAGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
* *
46477 GAAACCAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGATGTTAAAGGAAGCTAAGCCTAAT
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
*
46542 AAAGGGGTTCCTTGATAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * * * *
46589 GATATGTAAGTCCTACGAGCTATCCATAAGACCTTCAGTGCAAGATGTTTTCAAATGATATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
* * * * *
46654 GAAATCAATCATTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAATGGAAGCTAAGCTTAAT
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
* * * *
46719 AAAGGGGTTCCTTAACAACTAAAAAACAAAGCCTTCGGGGGTTTTTT
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * *
46766 GATTTGTAAGTCCTACGGGCCATCCATAAAACCTTAAGTGCATGATGTTTTGAAATGAGATTTTA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
* *
46831 GAAACCAAGCCTTCAGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAAT
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
* * ** *
46896 AAAGGGGTTCTTTCACAACTAAGAAACTAAGCCTTTAGGGGTTTATT
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
* * * *
46943 GATTTGTAAG-CCTACGGGCCATCCATAAGAACTTCAGTACATGATGTTTTCAAATGATATTTAA
1 GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
* *
47007 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTCAAAGGAAGCTAAGCCTAAC
66 GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
47072 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
131 AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
47119 GATTT
1 GATTT
47124 AAGGAGATAG
Statistics
Matches: 801, Mismatches: 83, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
176 315 0.39
177 485 0.61
178 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (177 bp):
GATTTGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTA
GAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAAT
AAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTT
Found at i:47064 original size:530 final size:530
Alignment explanation
Indices: 46063--47121 Score: 1685
Period size: 530 Copynumber: 2.0 Consensus size: 530
46053 TTCCTAGATT
* *
46063 TGTAAGTCCTACGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTATAAA
1 TGTAAGTCCTACGAGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTAGAAA
*
46128 CTAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAATAAAG
66 CTAAGCATTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAATAAAG
* * * * *
46193 GGGTTCCTTGACAACTAAGAAACTAAGTCTTCGGGGGTTTCTTGATTTGTAAGTCCTATGGGCCA
131 GGGTTCCTTAACAACTAAAAAACAAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTACGGGCCA
* *
46258 TCCATAAGAACTTTAATGCAGGATGTTTCCAAATGAGATTTAGAAACCAAGCCTTCGGGGGTTTA
196 TCCATAAGAACCTTAATGCAGGATGTTTCCAAATGAGATTTAGAAACCAAGCCTTCAGGGGTTTA
* * * * * *
46323 CTAATTATTTCAAAATAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCACTGACATCTAAG
261 CTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAACAAAGGGGTTCACTCACAACTAAG
* * * *
46388 AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTACAGGCCATCCATAAGACCTTCAGTGC
326 AAACTAAGCCTTCAGGGGTTTATTGATTTGTAAGTCCTACAGGCCATCCATAAGAACTTCAGTAC
* *
46453 ATGATGTTTTCAAATGAGATTTTAGAAACCAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAG
391 ATGATGTTTTCAAATGAGATTTAAGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAG
* * *
46518 ATGTTAAAGGAAGCTAAGCCTAATAAAGGGGTTCCTTGATAACTAAGAAACTAAGCCTTCGGGGG
456 ATGTCAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGG
46583 TTTCTTGATA
521 TTTCTTGATA
* *
46593 TGTAAGTCCTACGAGCTATCCATAAGACCTTCAGTGCA-AGATGTTTTCAAATGATATTTTAGAA
1 TGTAAGTCCTACGAGCCATCCATAAGACCTTCAGTGCAGA-ATGTTTTCAAATGAGATTTTAGAA
* * *
46657 A-TCAATCATTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAATGGAAGCTAAGCTTAATAA
65 ACT-AAGCATTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAATAA
*
46721 AGGGGTTCCTTAACAACTAAAAAACAAAGCCTTCGGGGGTTTTTTGATTTGTAAGTCCTACGGGC
129 AGGGGTTCCTTAACAACTAAAAAACAAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTACGGGC
* **
46786 CATCCATAA-AACCTTAAGTGCATGATGTTTTGAAATGAGATTTTAGAAACCAAGCCTTCAGGGG
194 CATCCATAAGAACCTTAA-TGCAGGATGTTTCCAAATGAGA-TTTAGAAACCAAGCCTTCAGGGG
* **
46850 TTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAATAAAGGGGTTCTTTCACAAC
257 TTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAACAAAGGGGTTCACTCACAAC
* *
46915 TAAGAAACTAAGCCTTTAGGGGTTTATTGATTTGTAAG-CCTACGGGCCATCCATAAGAACTTCA
322 TAAGAAACTAAGCCTTCAGGGGTTTATTGATTTGTAAGTCCTACAGGCCATCCATAAGAACTTCA
*
46979 GTACATGATGTTTTCAAATGATATTTAAGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAA
387 GTACATGATGTTTTCAAATGAGATTTAAGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAA
*
47044 AGAGCTGTCAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCG
452 AGAGATGTCAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCG
47109 GGGGTTTCTTGAT
517 GGGGTTTCTTGAT
47122 TTAAGGAGAT
Statistics
Matches: 484, Mismatches: 41, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
529 9 0.02
530 362 0.75
531 113 0.23
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (530 bp):
TGTAAGTCCTACGAGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTAGAAA
CTAAGCATTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAATAAAG
GGGTTCCTTAACAACTAAAAAACAAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTACGGGCCA
TCCATAAGAACCTTAATGCAGGATGTTTCCAAATGAGATTTAGAAACCAAGCCTTCAGGGGTTTA
CTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAACAAAGGGGTTCACTCACAACTAAG
AAACTAAGCCTTCAGGGGTTTATTGATTTGTAAGTCCTACAGGCCATCCATAAGAACTTCAGTAC
ATGATGTTTTCAAATGAGATTTAAGAAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAG
ATGTCAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGG
TTTCTTGATA
Found at i:47452 original size:120 final size:122
Alignment explanation
Indices: 47124--47885 Score: 882
Period size: 120 Copynumber: 6.2 Consensus size: 122
47114 TTCTTGATTT
* * *
47124 AAGGAGATAGAGCAAC--AAAGCCATTTCCAGATAGGAGTTCATAATCTGAAGAACTCATCTGAA
1 AAGGAGATAGAGCAACTTCAA--CATTTCCAGACAGGAGTTCGTAA--TGAAGAACTCATCTGAA
* * * *
47187 GAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTTGCTTGACTCGATCGCAG
62 GAGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACC-TTTTGCTAGATTCTATCGCAG
* * ** * * * *
47249 AAGGAGATATAACAA-TAGAGTCATTTCCAGACAGGAGTTCATAATCTGAAGAACTCACCAGAAG
1 AAGGAGATAGAGCAACTTCA-ACATTTCCAGACAGGAGTTCGTAA--TGAAGAACTCATCTGAAG
* * * * *
47313 AGAAAGAAGAAATTCATAATATGAAGAACTTATTCAACCTTTTGCTCGATTCTATCGTAG
63 AGGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAG
* * *
47373 AAGGAGATAGAGCAGCTTCAACATTTCTAGA-AGGAGTTCGTAAT-AAGAACTCATTTGAAGAGG
1 AAGGAGATAGAGCAACTTCAACATTTCCAGACAGGAGTTCGTAATGAAGAACTCATCTGAAGAGG
* * *
47436 AAGAAGAAGTTTATAATCTGAAAAACTTGTTCAACCTTTTGCTAGATTCTATCGCAG
66 AAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAG
* * * *
47493 AAGGAAATAGAGCAGCTTCAACATTTCTAGA-AGGAGGTT-GTAAT-AAGAACTCATTTGAAGAG
1 AAGGAGATAGAGCAACTTCAACATTTCCAGACAGGA-GTTCGTAATGAAGAACTCATCTGAAGAG
* * *
47555 GAAGAAGAAGTTTATAATCTGAAGAACTTGTTTAACCTTTTGCTAGATTCTATCGCAG
65 GAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAG
* * * *
47613 AAGGAGATAGAACAACATCAACATTTCCAGA-AGAAGTTCGTAACAAGAAGAACTCATCTGAAGA
1 AAGGAGATAGAGCAACTTCAACATTTCCAGACAGGAGTTCGT-A-ATGAAGAACTCATCTGAAGA
* * * * *
47677 GGAAGAAGAAGTTCATAATCTAAAGAACTTATTTAACCTTTTGATCGATTCTATTGCAG
64 GGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAG
* * *
47736 AAGGAGATAGAGCAACATCAACATTTTCAGACATGAGTTCGTAATAAGAAGAACTCATCTGAAGA
1 AAGGAGATAGAGCAACTTCAACATTTCCAGACAGGAGTTCGTAAT--GAAGAACTCATCTGAAGA
* * *
47801 GGAAGAAAAAGTTCATAATCTGAAGAATTTATTCAACCTTTTGCTAGATTCTATCACAG
64 GGAAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAG
*
47860 AAGGAGAT--AG-AACATCAACATTTCCA
1 AAGGAGATAGAGCAACTTCAACATTTCCA
47886 TCTTAATCAA
Statistics
Matches: 560, Mismatches: 65, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
119 3 0.01
120 209 0.37
121 20 0.04
122 4 0.01
123 110 0.20
124 123 0.22
125 90 0.16
126 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
AAGGAGATAGAGCAACTTCAACATTTCCAGACAGGAGTTCGTAATGAAGAACTCATCTGAAGAGG
AAGAAGAAGTTCATAATCTGAAGAACTTATTCAACCTTTTGCTAGATTCTATCGCAG
Found at i:48028 original size:3 final size:3
Alignment explanation
Indices: 48002--48069 Score: 84
Period size: 3 Copynumber: 23.0 Consensus size: 3
47992 TTTTTGCGCC
* * * *
48002 ATT ATC ATT ATC ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT A-T ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
48049 ATT ATT ATT AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
48070 TTACAAATAC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:48913 original size:20 final size:20
Alignment explanation
Indices: 48875--48914 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
48865 TCGGCCACTA
*
48875 TGAATAGTGACCAGCGGTGG
1 TGAATAGTGACCAGAGGTGG
*
48895 TGAATAGTGACCTGAGGTGG
1 TGAATAGTGACCAGAGGTGG
48915 CCGACCGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.40, T:0.23
Consensus pattern (20 bp):
TGAATAGTGACCAGAGGTGG
Found at i:51090 original size:30 final size:29
Alignment explanation
Indices: 51050--51141 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
51040 TAAGGGACTA
* * *
51050 AATAATAATAGAAATTTACAGGACTAAAAC
1 AATAAAAATAGAAACTTAAAGGACT-AAAC
* *
51080 AATAAAAATAGAAACTTAAATGACTAAAT
1 AATAAAAATAGAAACTTAAAGGACTAAAC
* * * *
51109 ATTAAAAACAGAAAGTTAAAGGAGTAAAC
1 AATAAAAATAGAAACTTAAAGGACTAAAC
51138 AATA
1 AATA
51142 TTTTTTTAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 29 0.58
30 21 0.42
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.22
Consensus pattern (29 bp):
AATAAAAATAGAAACTTAAAGGACTAAAC
Found at i:51659 original size:22 final size:23
Alignment explanation
Indices: 51629--51677 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
51619 GAGCTTTCTT
*
51629 TTTTTTCTTGGT-TTTGTTTTTC-
1 TTTTCTCTTGGTGTTT-TTTTTCG
*
51651 TTTTCTCTTTGTGTTTTTTTTCG
1 TTTTCTCTTGGTGTTTTTTTTCG
51674 TTTT
1 TTTT
51678 GGTTCCCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (23 bp):
TTTTCTCTTGGTGTTTTTTTTCG
Found at i:51678 original size:17 final size:16
Alignment explanation
Indices: 51628--51678 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
51618 AGAGCTTTCT
*
51628 TTTTTTTCTTGGTTTTG
1 TTTTTTT-TTCGTTTTG
51645 TTTTTCTTTTC-TCTTTG
1 TTTTT-TTTTCGT-TTTG
51662 TGTTTTTTTTCGTTTTG
1 T-TTTTTTTTCGTTTTG
51679 GTTCCCTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.03
17 21 0.72
18 7 0.24
ACGTcount: A:0.00, C:0.10, G:0.14, T:0.76
Consensus pattern (16 bp):
TTTTTTTTTCGTTTTG
Found at i:52736 original size:29 final size:29
Alignment explanation
Indices: 52690--52772 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 29
52680 ATAATGGTTT
*
52690 CAAAAGAAACCGACTCAAAGATGATGTTG
1 CAAAAGAAACAGACTCAAAGATGATGTTG
* * *
52719 CAAAAGAAACTGAATCAAAGATGATGTTT
1 CAAAAGAAACAGACTCAAAGATGATGTTG
52748 CAAAAGAAACAGACTCAAAGATGAT
1 CAAAAGAAACAGACTCAAAGATGAT
52773 TTTGTTAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (29 bp):
CAAAAGAAACAGACTCAAAGATGATGTTG
Found at i:52877 original size:30 final size:31
Alignment explanation
Indices: 52818--52895 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
52808 TTTTTTAAAA
* * *
52818 AGAAAC-GACTCAAAGACTGTTTTGTTTTAAT
1 AGAAACAGACTCAAAGAC-ATTTCGTTTTAAG
52849 AGAAACAGACTCAAAGA-ATTTCGTTTTAAG
1 AGAAACAGACTCAAAGACATTTCGTTTTAAG
*
52879 AGAAACAAACTCAAAGA
1 AGAAACAGACTCAAAGA
52896 TACTGTCTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 26 0.62
31 6 0.14
32 10 0.24
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (31 bp):
AGAAACAGACTCAAAGACATTTCGTTTTAAG
Found at i:61146 original size:6 final size:6
Alignment explanation
Indices: 61135--61159 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61125 ATAAATTTTC
61135 ATAATT ATAATT ATAATT ATAATT A
1 ATAATT ATAATT ATAATT ATAATT A
61160 CAAATAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Done.