Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008095.1 Hibiscus syriacus cultivar Beakdansim tig00110614_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: 106976
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1521 original size:18 final size:19
Alignment explanation
Indices: 1500--1542 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1490 TTAAAAATTA
*
1500 AAATTATATTG-TATAAAT
1 AAATTATATCGTTATAAAT
**
1518 AAATGCTATCGTTATAAAT
1 AAATTATATCGTTATAAAT
1537 AAATTA
1 AAATTA
1543 AAATTGGATT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (19 bp):
AAATTATATCGTTATAAAT
Found at i:13565 original size:20 final size:20
Alignment explanation
Indices: 13540--13586 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
13530 AATGTGTGAT
13540 GCCAGTGACTACACAGTAGG
1 GCCAGTGACTACACAGTAGG
*
13560 GCCAGTGACTACGCAGTAGG
1 GCCAGTGACTACACAGTAGG
*
13580 GGCAGTG
1 GCCAGTG
13587 CTAAGGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.36, T:0.15
Consensus pattern (20 bp):
GCCAGTGACTACACAGTAGG
Found at i:20168 original size:23 final size:23
Alignment explanation
Indices: 20141--20185 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
20131 AATATTTTAT
20141 TTTAACTAATTTACCTTTAAATG
1 TTTAACTAATTTACCTTTAAATG
*
20164 TTTAACTAATTTAGCTTTAAAT
1 TTTAACTAATTTACCTTTAAAT
20186 TTGAGTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTAACTAATTTACCTTTAAATG
Found at i:22742 original size:3 final size:3
Alignment explanation
Indices: 22736--22767 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
22726 AAAATAATAA
*
22736 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
22768 CATTTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:23431 original size:30 final size:30
Alignment explanation
Indices: 23397--23462 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
23387 TTGTTTTTTA
* * *
23397 TATTTGTGGTTTAGCCCTTTAATTTTTTGT
1 TATTTGTAGTTTAGCCATTTAATTTTATGT
* * *
23427 TATTTCTATTTTAGTCATTTAATTTTATGT
1 TATTTGTAGTTTAGCCATTTAATTTTATGT
23457 T-TTTGT
1 TATTTGT
23463 TATTTTACTC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.64
Consensus pattern (30 bp):
TATTTGTAGTTTAGCCATTTAATTTTATGT
Found at i:23467 original size:30 final size:30
Alignment explanation
Indices: 23414--23480 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
23404 GGTTTAGCCC
* *
23414 TTTAATTTTTTGTTATTTCTATTTTAGTCA
1 TTTAATTTTATGTTATTTCTATTTTACTCA
* *
23444 TTTAATTTTATGTT-TTTGTTATTTTACTCC
1 TTTAATTTTATGTTATTT-CTATTTTACTCA
23474 TTTAATT
1 TTTAATT
23481 AATTAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.67
Consensus pattern (30 bp):
TTTAATTTTATGTTATTTCTATTTTACTCA
Found at i:23517 original size:19 final size:20
Alignment explanation
Indices: 23477--23528 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
23467 TTACTCCTTT
* *
23477 AATTAATTAAT-TTGAATCA
1 AATTAATCAATATTTAATCA
23496 AATTAATCAATATTTAAT-A
1 AATTAATCAATATTTAATCA
*
23515 AATGAATC-ATATTT
1 AATTAATCAATATTT
23529 TAACTTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 18 0.62
20 5 0.17
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTAATCAATATTTAATCA
Found at i:26467 original size:64 final size:65
Alignment explanation
Indices: 26346--26468 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 65
26336 TTCACAAGCT
* * * * *
26346 ATGCATCGATGCACTCTTGAATATTTTGAAACATCGAATGCATTTTGTGTACCGATGCAGAGACC
1 ATGCATCGATGCACTCCTGAATATTTTGAAACATCAAATGCAATTAGTGTAACGATGCAGAGACC
** * * *
26411 ATGCATCGATGCACTCCTGGCTCTTTT-AAACATCAAATGTAATTAGTGTAATGATGCA
1 ATGCATCGATGCACTCCTGAATATTTTGAAACATCAAATGCAATTAGTGTAACGATGCA
26469 CCCCTAGTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
64 25 0.52
65 23 0.48
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTCCTGAATATTTTGAAACATCAAATGCAATTAGTGTAACGATGCAGAGACC
Found at i:34373 original size:12 final size:12
Alignment explanation
Indices: 34356--34389 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
34346 TTTTAGTGCT
34356 AGAAACAAGAAA
1 AGAAACAAGAAA
34368 AGAAACAAGAAA
1 AGAAACAAGAAA
34380 AGAAACAAGA
1 AGAAACAAGA
34390 TTAAAATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.74, C:0.09, G:0.18, T:0.00
Consensus pattern (12 bp):
AGAAACAAGAAA
Found at i:40671 original size:11 final size:11
Alignment explanation
Indices: 40657--40695 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
40647 AAATTTTGGC
40657 TTTTTTGGCTT
1 TTTTTTGGCTT
40668 TTTTTTGGCTT
1 TTTTTTGGCTT
*
40679 TTTTTTTG-TT
1 TTTTTTGGCTT
40689 TTTTTTG
1 TTTTTTG
40696 TTTTTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.79
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:40703 original size:8 final size:9
Alignment explanation
Indices: 40678--40702 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40668 TTTTTTGGCT
40678 TTTTTTTTG
1 TTTTTTTTG
40687 TTTTTTTTG
1 TTTTTTTTG
40696 TTTTTTT
1 TTTTTTT
40703 GAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:42820 original size:65 final size:64
Alignment explanation
Indices: 42750--42887 Score: 179
Period size: 65 Copynumber: 2.1 Consensus size: 64
42740 CACACCCATT
* * * *
42750 TCGAATGTATTTTGTGTATCGATGCAC-AAGCTATGCATCTATGCACTCTTGAATATTTTGAAAC
1 TCGAATGTATTTTGTGTACCGATGCACGAA-CCATGCATCGATGCACTCTTGAAT-CTTTGAAAC
42814 A
64 A
* **
42815 TCGAATGCATTTTGTGTACCGATGCACGAACCATGCATCGATGCACTCTTGGCTCTTTGAAACA
1 TCGAATGTATTTTGTGTACCGATGCACGAACCATGCATCGATGCACTCTTGAATCTTTGAAACA
*
42879 TCAAATGTA
1 TCGAATGTA
42888 ATTATTACAC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 16 0.25
65 45 0.71
66 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (64 bp):
TCGAATGTATTTTGTGTACCGATGCACGAACCATGCATCGATGCACTCTTGAATCTTTGAAACA
Found at i:47546 original size:124 final size:124
Alignment explanation
Indices: 47326--47655 Score: 498
Period size: 124 Copynumber: 2.7 Consensus size: 124
47316 AAAACAATTC
* * * * *
47326 TTGGATTTTAACTTCATGACGAAGGATATCCAATTCGAGGCTCAAATTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGGGACAT
* * * *
47391 CCACGATTTTAACTTCATGACAAAGGATATCGTGTCTACCAGCAATATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
*
47450 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGGGTCAT
1 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGGGACAT
**
47515 CCACGATTTCAACTTCACGACGGAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
* * * * **
47574 TTGGATTTCAACTTCACGATGAAGGATATCCAACTCAAGGCTCAACTTCACGACAAATTAGACAT
1 TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGGGACAT
47639 CCACGATTTCAACTTCA
66 CCACGATTTCAACTTCA
47656 TGATGAAAGA
Statistics
Matches: 188, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 188 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (124 bp):
TTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAATGGGACAT
CCACGATTTCAACTTCACGACAAAGGATATCGTGTCCACCAGCAACATTCATCTTTAGA
Found at i:48087 original size:3 final size:3
Alignment explanation
Indices: 48081--48118 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
48071 TTAAAAATAA
*
48081 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
48119 CATTTTTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:48448 original size:19 final size:19
Alignment explanation
Indices: 48395--48449 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
48385 TGCCACCGAG
48395 CCACCAACGCCGAGCCATC
1 CCACCAACGCCGAGCCATC
* * * *
48414 TCATCGACGCCAAGCCATC
1 CCACCAACGCCGAGCCATC
*
48433 CCACCAACGCTGAGCCA
1 CCACCAACGCCGAGCCA
48450 CTGAATGTTC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.09
Consensus pattern (19 bp):
CCACCAACGCCGAGCCATC
Found at i:49638 original size:21 final size:23
Alignment explanation
Indices: 49605--49648 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
49595 AATGTTTAAT
49605 TTTTTTTATTATTT-TGGCTTAG
1 TTTTTTTATTATTTGTGGCTTAG
*
49627 TTTTTTTA-TATTTGTGGTTTAG
1 TTTTTTTATTATTTGTGGCTTAG
49649 CCCTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.68
Consensus pattern (23 bp):
TTTTTTTATTATTTGTGGCTTAG
Found at i:49678 original size:30 final size:30
Alignment explanation
Indices: 49644--49718 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
49634 ATATTTGTGG
*
49644 TTTAGCCCTTTAATTTTTTGTTATTT-CTAT
1 TTTAGCCCTTTAATTTTATGTT-TTTGCTAT
*** *
49674 TTTAGTAATTTAATTTTATGTTTTTGTTAT
1 TTTAGCCCTTTAATTTTATGTTTTTGCTAT
49704 TTTA-CTCCTTTAATT
1 TTTAGC-CCTTTAATT
49719 AATTATTTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (30 bp):
TTTAGCCCTTTAATTTTATGTTTTTGCTAT
Found at i:50549 original size:22 final size:23
Alignment explanation
Indices: 50463--50550 Score: 60
Period size: 22 Copynumber: 4.0 Consensus size: 23
50453 TACAATAAAT
**
50463 AATATTATTTATTATAAAACTTAA
1 AATATTATTTATTAT-AATTTTAA
* * * *
50487 TATTATTATTT-TTAAAATATTGA
1 -AATATTATTTATTATAATTTTAA
*
50510 AATA--ATTTATT-TATTTTTAA
1 AATATTATTTATTATAATTTTAA
50530 AATATTATTT-TTATAATTTTA
1 AATATTATTTATTATAATTTTA
50551 TTAATAAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 11
0.69 0.16 0.16
Matches are distributed among these distances:
20 13 0.27
21 4 0.08
22 14 0.29
23 5 0.10
24 3 0.06
25 9 0.19
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (23 bp):
AATATTATTTATTATAATTTTAA
Found at i:50780 original size:27 final size:25
Alignment explanation
Indices: 50713--50800 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 25
50703 ATATTAATAT
*
50713 TAAATATATAAATAATATTATTCATTA
1 TAAATA-ATAAATAATATTATT-TTTA
* *
50740 TTAATAATTTAATAATATTATTTTTA
1 TAAATAA-TAAATAATATTATTTTTA
* *
50766 TGAAATTAATAAATAATATAAATTTTA
1 T-AAA-TAATAAATAATATTATTTTTA
*
50793 TTAATAAT
1 TAAATAAT
50801 TTATTATATA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 36 0.72
28 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TAAATAATAAATAATATTATTTTTA
Found at i:50894 original size:22 final size:23
Alignment explanation
Indices: 50866--50912 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
50856 TTGATTATTT
*
50866 TATTATAATGTTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
50888 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
50911 TA
1 TA
50913 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:50899 original size:30 final size:34
Alignment explanation
Indices: 50839--50918 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
50829 ATAATATCTT
* *
50839 ATATTATTATAATATAATTGATTATTTTATTAT-A
1 ATATTAATA-AATATAATTGATTATATTATTATAA
*
50873 ATGTTAA-AAATATAA-T-ATTATATTATTATAA
1 ATATTAATAAATATAATTGATTATATTATTATAA
50904 ATATTAATAAATATA
1 ATATTAATAAATATA
50919 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 12 0.30
31 8 0.20
32 14 0.35
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
ATATTAATAAATATAATTGATTATATTATTATAA
Found at i:53817 original size:15 final size:16
Alignment explanation
Indices: 53797--53826 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53787 TTTTCTCTGG
53797 AGAGAA-GGAAAGAAT
1 AGAGAAGGGAAAGAAT
53812 AGAGAAGGGAAAGAA
1 AGAGAAGGGAAAGAA
53827 ATGGGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (16 bp):
AGAGAAGGGAAAGAAT
Found at i:58309 original size:17 final size:16
Alignment explanation
Indices: 58286--58349 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
58276 CTAATCAAAA
58286 CAAAG-AGAAAAAGAG
1 CAAAGAAGAAAAAGAG
* *
58301 CAAAGAGAGAAAAAAAA
1 CAAAGA-AGAAAAAGAG
58318 CAAAGAA-AAATATAGAG
1 CAAAGAAGAAA-A-AGAG
*
58335 CAAAGAAAAAAAAGA
1 CAAAGAAGAAAAAGA
58350 AGAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 8 0.20
16 5 0.12
17 24 0.60
18 3 0.08
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.03
Consensus pattern (16 bp):
CAAAGAAGAAAAAGAG
Found at i:58318 original size:32 final size:32
Alignment explanation
Indices: 58282--58361 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
58272 AGATCTAATC
*
58282 AAAACAAAGAGAAA-A-AGAGCAAAGAGAGAAAA
1 AAAACAAAGAAAAATATAGAGCAAAGA-A-AAAA
58314 AAAACAAAGAAAAATATAGAGCAAAGAAAAAA
1 AAAACAAAGAAAAATATAGAGCAAAGAAAAAA
*
58346 AAGAAGAAA-AAAAATA
1 AA-AACAAAGAAAAATA
58362 AAAGAAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 26 0.60
33 7 0.16
34 10 0.23
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (32 bp):
AAAACAAAGAAAAATATAGAGCAAAGAAAAAA
Found at i:58354 original size:12 final size:12
Alignment explanation
Indices: 58337--58387 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
58327 ATATAGAGCA
58337 AAGAAAAAAAAG
1 AAGAAAAAAAAG
*
58349 AAGAAAAAAAAT
1 AAGAAAAAAAAG
*
58361 AA-AAGAAAAAG
1 AAGAAAAAAAAG
*
58372 AAAACAACAAAAAG
1 AAGA-AA-AAAAAG
58386 AA
1 AA
58388 AACAAGAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 9 0.28
12 14 0.44
13 1 0.03
14 8 0.25
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:58359 original size:14 final size:14
Alignment explanation
Indices: 58340--58395 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
58330 TAGAGCAAAG
*
58340 AAAAAAAAGAAGAA
1 AAAAAAAACAAGAA
58354 AAAAAATAA-AAGAA
1 AAAAAA-AACAAGAA
* *
58368 AAAGAAAACAACAA
1 AAAAAAAACAAGAA
*
58382 AAAGAAAACAAGAA
1 AAAAAAAACAAGAA
58396 GTACATGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (14 bp):
AAAAAAAACAAGAA
Found at i:58384 original size:20 final size:19
Alignment explanation
Indices: 58308--58389 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 19
58298 GAGCAAAGAG
*
58308 AGAAAAAAAACAAAGAAAA
1 AGAAAAAAAAAAAAGAAAA
* *
58327 ATATAGAGCAAAGAAAAAA-AAGA
1 AGA-A-A--AAA-AAAAAAGAAAA
58350 AGAAAAAAAATAAAAGAAAA
1 AGAAAAAAAA-AAAAGAAAA
*
58370 AGAAAACAACAAAAAGAAAA
1 AGAAAA-AAAAAAAAGAAAA
58390 CAAGAAGTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
18 2 0.04
19 9 0.18
20 19 0.39
21 5 0.10
22 1 0.02
23 8 0.16
24 5 0.10
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.04
Consensus pattern (19 bp):
AGAAAAAAAAAAAAGAAAA
Found at i:62361 original size:29 final size:28
Alignment explanation
Indices: 62300--62424 Score: 108
Period size: 29 Copynumber: 4.3 Consensus size: 28
62290 TTTGACGTTC
* *
62300 ATTGTAATTTATAAAAAAAGTTTGTCGTAT
1 ATTGTAATTTAT--AAAAAGTTTGTCCTTT
*
62330 ATTGTAATTTATAAAAGGTTCTGTCCTTT
1 ATTGTAATTTATAAAAAGTT-TGTCCTTT
* * *
62359 ATTATAATTTATAAAAAGTTTTATCCATT
1 ATTGTAATTTATAAAAAG-TTTGTCCTTT
* * *
62388 AATGCAATTTAT-AAAAGATTTATTCCTTT
1 ATTGTAATTTATAAAAAG-TTT-GTCCTTT
62417 ATTGTAAT
1 ATTGTAAT
62425 ACAATTTTGA
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
28 15 0.19
29 48 0.62
30 14 0.18
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (28 bp):
ATTGTAATTTATAAAAAGTTTGTCCTTT
Found at i:63263 original size:64 final size:63
Alignment explanation
Indices: 63172--63343 Score: 188
Period size: 63 Copynumber: 2.7 Consensus size: 63
63162 TTGAAATTTT
* * *
63172 TTTTGTCTCTCGAGACAGTTTCTTTTGAAAAAAATCTTTGAGT-TTG-TTACTTTGGAAAAAAA
1 TTTTGTCTCTTGAGACAGTTTCTTTTGAAAAAAATCTTTGAGTATCGTTTACATT-GAAAAAAA
* * * * *
63234 GTTTTGTCTCCTTGAGACAATTTCCTTTGAGAAAAAACCTTTGA-TATCGTTTCCATTGAAACAA
1 -TTTTGTCT-CTTGAGACAGTTTCTTTTGA-AAAAAATCTTTGAGTATCGTTTACATTGAAAAAA
63298 A
63 A
* * *
63299 TTTTGTCTCTTGAGACAGCTTCTTTTGAGAAAAATCCTTGAGTAT
1 TTTTGTCTCTTGAGACAGTTTCTTTTGAAAAAAATCTTTGAGTAT
63344 GTGTTGAGTT
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
62 10 0.11
63 28 0.31
64 26 0.29
65 21 0.23
66 5 0.06
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (63 bp):
TTTTGTCTCTTGAGACAGTTTCTTTTGAAAAAAATCTTTGAGTATCGTTTACATTGAAAAAAA
Found at i:64903 original size:13 final size:14
Alignment explanation
Indices: 64858--64904 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 14
64848 TCTAATTATT
*
64858 CAAAACTAAACATC
1 CAAAACAAAACATC
*
64872 CAAATTACAAAATATC
1 CAAA--ACAAAACATC
64888 CAAAAC-AAACATC
1 CAAAACAAAACATC
64901 CAAA
1 CAAA
64905 TATTCAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 6 0.21
16 12 0.43
ACGTcount: A:0.60, C:0.26, G:0.00, T:0.15
Consensus pattern (14 bp):
CAAAACAAAACATC
Found at i:72819 original size:17 final size:18
Alignment explanation
Indices: 72787--72824 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
72777 CATCCAAATC
72787 ACAAATTATCCAAAACAA
1 ACAAATTATCCAAAACAA
*
72805 ACAAA-TATTCAAAACAA
1 ACAAATTATCCAAAACAA
72822 ACA
1 ACA
72825 TCCAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.63, C:0.21, G:0.00, T:0.16
Consensus pattern (18 bp):
ACAAATTATCCAAAACAA
Found at i:72823 original size:21 final size:21
Alignment explanation
Indices: 72799--72838 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72789 AAATTATCCA
72799 AAACAAACAAATATTCAAAAC
1 AAACAAACAAATATTCAAAAC
**
72820 AAACATCCAAATATTCAAA
1 AAACAAACAAATATTCAAA
72839 TACATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.20, G:0.00, T:0.17
Consensus pattern (21 bp):
AAACAAACAAATATTCAAAAC
Found at i:74298 original size:21 final size:21
Alignment explanation
Indices: 74274--74313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74264 AAAATATCTA
74274 AAACAAACAAATATTCAAAAC
1 AAACAAACAAATATTCAAAAC
**
74295 AAACATCCAAATATTCAAA
1 AAACAAACAAATATTCAAA
74314 TACATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.20, G:0.00, T:0.17
Consensus pattern (21 bp):
AAACAAACAAATATTCAAAAC
Found at i:74732 original size:12 final size:12
Alignment explanation
Indices: 74717--74756 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
74707 TCTTGAGCCA
*
74717 GAGCCAGAGCTG
1 GAGCCGGAGCTG
*
74729 GAGCCGGAGCTA
1 GAGCCGGAGCTG
74741 GAGCCGGAGCTG
1 GAGCCGGAGCTG
74753 GAGC
1 GAGC
74757 AGCTTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.45, T:0.07
Consensus pattern (12 bp):
GAGCCGGAGCTG
Found at i:74738 original size:18 final size:18
Alignment explanation
Indices: 74711--74756 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
74701 TCAAGCTCTT
* *
74711 GAGCCAGAGCCAGAGCTG
1 GAGCCGGAGCCAGAGCCG
*
74729 GAGCCGGAGCTAGAGCCG
1 GAGCCGGAGCCAGAGCCG
*
74747 GAGCTGGAGC
1 GAGCCGGAGC
74757 AGCTTGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.43, T:0.07
Consensus pattern (18 bp):
GAGCCGGAGCCAGAGCCG
Found at i:81741 original size:23 final size:23
Alignment explanation
Indices: 81715--81773 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
81705 TATATGTCCT
81715 GAAGGACCGCGTAGAAATGTCTC
1 GAAGGACCGCGTAGAAATGTCTC
* *** * *
81738 GAAGGGCCATATGGAATTGTCTC
1 GAAGGACCGCGTAGAAATGTCTC
81761 GAAGGACCGCGTA
1 GAAGGACCGCGTA
81774 TAACCCTCGA
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.19
Consensus pattern (23 bp):
GAAGGACCGCGTAGAAATGTCTC
Found at i:86289 original size:20 final size:21
Alignment explanation
Indices: 86245--86290 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
86235 TTTGGCTAGT
*
86245 GGTATCAATACTTGTTCTTTA
1 GGTATCAATACTTGTTCTATA
*
86266 GGTATCAATA-TTGTTCTATC
1 GGTATCAATACTTGTTCTATA
86286 GGTAT
1 GGTAT
86291 TGATACTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (21 bp):
GGTATCAATACTTGTTCTATA
Found at i:88896 original size:7 final size:6
Alignment explanation
Indices: 88860--88912 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
88850 CAGCAGTTGG
* * *
88860 AAAAGG AAAAGA AAAAGA AAAA-A AAAAGA AAACAGA AAGAGA CATAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA AAAAGA -AAAAGA
88909 AAAA
1 AAAA
88913 ATGGAAAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 5 0.13
6 25 0.64
7 9 0.23
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:89731 original size:26 final size:27
Alignment explanation
Indices: 89702--89752 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
89692 CTGACGTGGT
*
89702 AGTTTT-TAAAAGGTCCAGTCAGCATC
1 AGTTTTCTAAAAGATCCAGTCAGCATC
*
89728 AGTTTTCTAAAAGATCTAGTCAGCA
1 AGTTTTCTAAAAGATCCAGTCAGCA
89753 CTTTTTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (27 bp):
AGTTTTCTAAAAGATCCAGTCAGCATC
Found at i:90024 original size:29 final size:29
Alignment explanation
Indices: 89973--90030 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
89963 TAAAGTTCTC
* *
89973 TATTTTCTTTTCTTTTCAAGTTTTCATTTT
1 TATTTTATTTTATTTTCAAGTTTT-ATTTT
90003 TATTTTATTTTATTTT-AAGTTTTATTTT
1 TATTTTATTTTATTTTCAAGTTTTATTTT
90031 CAAACATGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 7 0.27
30 14 0.54
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (29 bp):
TATTTTATTTTATTTTCAAGTTTTATTTT
Found at i:91954 original size:16 final size:16
Alignment explanation
Indices: 91933--91971 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
91923 TATTTTAAAA
*
91933 TTAAATTTT-TTTAGT
1 TTAAATTTTATTTAAT
91948 TTCAAATTTTATTTAAT
1 TT-AAATTTTATTTAAT
91965 TTAAATT
1 TTAAATT
91972 CCACTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 12 0.57
17 7 0.33
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAAATTTTATTTAAT
Found at i:100955 original size:31 final size:31
Alignment explanation
Indices: 100848--100956 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 31
100838 CCTTAGGTCC
*
100848 ATAAGGAATTACCAGTCGGTGTTGAACCTAT
1 ATAAGGAATTACCAGTCGATGTTGAACCTAT
* * * *
100879 ACAAGGAATTTATAGCAG-CGA--CTGAACCTGCCAG
1 ATAAGGAA--T-TACCAGTCGATGTTGAACCT---AT
*
100913 AGATAGGAATTACCAGTCGATGTTGAACCTAT
1 ATA-AGGAATTACCAGTCGATGTTGAACCTAT
100945 ATAAGGAATTAC
1 ATAAGGAATTAC
100957 TAGCAATGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 20
0.66 0.11 0.23
Matches are distributed among these distances:
31 23 0.40
32 8 0.14
33 7 0.12
34 8 0.14
35 12 0.21
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (31 bp):
ATAAGGAATTACCAGTCGATGTTGAACCTAT
Found at i:100961 original size:66 final size:66
Alignment explanation
Indices: 100851--100980 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
100841 TAGGTCCATA
* *
100851 AGGAATTACCAGTCGGTGTTGAACCTATACAAGGAATTTATAGCAGCGACTGAACCTGCCAGAGA
1 AGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTTATAGCAACGACTGAACCTGCCAGAGA
100916 T
66 T
* * * *
100917 AGGAATTACCAGTCGATGTTGAACCTATATAAGGAA-TTACTAGCAATGACTGGACCTGTCAGAG
1 AGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTTA-TAGCAACGACTGAACCTGCCAGAG
100981 TCTTTATACC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 3 0.05
66 54 0.95
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (66 bp):
AGGAATTACCAGTCGATGTTGAACCTATACAAGGAATTTATAGCAACGACTGAACCTGCCAGAGA
T
Done.