Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003365.1 Hibiscus syriacus cultivar Beakdansim tig00007077_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: 70630
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:11767 original size:100 final size:100
Alignment explanation
Indices: 11589--11792 Score: 331
Period size: 100 Copynumber: 2.0 Consensus size: 100
11579 TCTTCCATGT
* * *
11589 CTTAGCTCCACAAGTTCATCTTCTTCCCCGTTAAACCTTATCTTTCCCAAAAAAAAAGAGAGAAA
1 CTTACCTCCACAAGTTCATCTTCTTCCCCATTAAACCTTATCTTCCCCAAAAAAAAAGAGAGAAA
11654 AAAAACATGACCATCTCTGGTTGTCCAGACTGGTC
66 AAAAACATGACCATCTCTGGTTGTCCAGACTGGTC
* *
11689 CTTACCTCCACAAGTTGATCTTCTTCCCCATTAAACCTTATCTTCCCCAAAAAAGACAG-GA-AA
1 CTTACCTCCACAAGTTCATCTTCTTCCCCATTAAACCTTATCTTCCCCAAAAAA-AAAGAGAGAA
11752 TAAAAAACATGACCATCTCTGGTTGTCCAGACTGGTC
65 -AAAAAACATGACCATCTCTGGTTGTCCAGACTGGTC
11789 CTTA
1 CTTA
11793 GCTTCAACAG
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
99 2 0.02
100 92 0.95
101 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27
Consensus pattern (100 bp):
CTTACCTCCACAAGTTCATCTTCTTCCCCATTAAACCTTATCTTCCCCAAAAAAAAAGAGAGAAA
AAAAACATGACCATCTCTGGTTGTCCAGACTGGTC
Found at i:12906 original size:18 final size:18
Alignment explanation
Indices: 12883--12921 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12873 CTTTAGGTAA
12883 CTTCTCAATCCCTAATCT
1 CTTCTCAATCCCTAATCT
*
12901 CTTCTCAATCCCTAATTT
1 CTTCTCAATCCCTAATCT
12919 CTT
1 CTT
12922 TCGATCCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.44
Consensus pattern (18 bp):
CTTCTCAATCCCTAATCT
Found at i:15428 original size:21 final size:22
Alignment explanation
Indices: 15387--15430 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
15377 AATGTCAGAG
*
15387 GGGAACCGATTCCCCTACTACA
1 GGGAACCGATTACCCTACTACA
*
15409 GGGAACCGA-TACCCTGCTACA
1 GGGAACCGATTACCCTACTACA
15430 G
1 G
15431 TACTTCCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTACCCTACTACA
Found at i:16068 original size:24 final size:24
Alignment explanation
Indices: 16041--16108 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
16031 CACCACAGCT
*
16041 CGTATAAATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
16065 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
* *
16089 TGTAGAAA-TGCACCGTAGTG
1 CGTAGAAATTGCACCGAAGTG
16109 TCATATAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 11 0.29
24 27 0.71
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.22
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:18693 original size:2 final size:2
Alignment explanation
Indices: 18636--18677 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
18626 AATATTTTGC
18636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18678 GCAAAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19720 original size:19 final size:19
Alignment explanation
Indices: 19693--19729 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19683 AAATGACCAA
*
19693 ATAAATCGCAATGCGATCG
1 ATAAATCGCAACGCGATCG
*
19712 ATAATTCGCAACGCGATC
1 ATAAATCGCAACGCGATC
19730 TCCGGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (19 bp):
ATAAATCGCAACGCGATCG
Found at i:19808 original size:20 final size:21
Alignment explanation
Indices: 19757--19802 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
19747 GTTTCCAGAT
19757 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
19778 TCGCAACGCGAACTT-GACTA
1 TCGCAACGCGAACTTCGACTA
19798 TCGCA
1 TCGCA
19803 TTGCGATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:19822 original size:21 final size:21
Alignment explanation
Indices: 19798--19921 Score: 103
Period size: 21 Copynumber: 5.9 Consensus size: 21
19788 AACTTGACTA
*
19798 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
19819 TCGCGTTACGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
* * *
19840 TCGCGTTGCGATTTATTACAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
*
19863 T--CGTTGTGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
19882 TCGCGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
19905 T--CGTTGCGATAGTCCAA
1 TCGCGTTGCGATAGTCCAA
19922 AATCGCAACG
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
19 15 0.19
21 50 0.62
23 16 0.20
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:19874 original size:42 final size:42
Alignment explanation
Indices: 19822--19921 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
19812 TCCAAGTTCG
* *
19822 CGTTACGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
* *
19864 CGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
19906 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
19922 AATCGCAACG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
Found at i:21095 original size:6 final size:6
Alignment explanation
Indices: 21084--21143 Score: 84
Period size: 6 Copynumber: 10.0 Consensus size: 6
21074 GCCATCCCTA
* *
21084 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT AGTGGT AGTGGT
1 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
* *
21132 AGTGGT AGTGGT
1 CGTGGT CGTGGT
21144 AATACGTGTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.07, C:0.10, G:0.50, T:0.33
Consensus pattern (6 bp):
CGTGGT
Found at i:21256 original size:19 final size:19
Alignment explanation
Indices: 21232--21298 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 19
21222 TCGTTGCGAT
21232 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
21251 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
*
21274 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
21293 TTTGGA
1 TTTGGA
21299 AAATCGCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 16 0.40
21 14 0.35
23 10 0.25
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:21304 original size:19 final size:19
Alignment explanation
Indices: 21240--21306 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
21230 ATTTTGGACT
21240 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* **
21261 ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAA
21282 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
21301 ATCGCA
1 ATCGCA
21307 TTGCGATAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.39
21 14 0.37
22 1 0.03
23 8 0.21
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:21331 original size:21 final size:21
Alignment explanation
Indices: 21302--21354 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
21292 ATTTGGAAAA
* *
21302 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTAGAAGT
*
21323 TCGCGTTGCGATAGTAGATGT
1 TCGCGTTGCGATAGTAGAAGT
21344 TCGCGTTGCGA
1 TCGCGTTGCGA
21355 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTAGAAGT
Found at i:22439 original size:21 final size:22
Alignment explanation
Indices: 22401--22441 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
22391 TAAAATCTTA
*
22401 TTTAGAGATAAATTTATAAAAT
1 TTTAGAGATAAATATATAAAAT
*
22423 TTTAGA-ATATATATATAAA
1 TTTAGAGATAAATATATAAA
22442 CTTTCATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
TTTAGAGATAAATATATAAAAT
Found at i:24569 original size:21 final size:21
Alignment explanation
Indices: 24528--24569 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
24518 TTATAATTCC
**
24528 ATTTAAATATAATTACTTTTA
1 ATTTAAATATAATTAAATTTA
24549 ATTTAAA-ATAAATTAAATTTA
1 ATTTAAATAT-AATTAAATTTA
24570 GTTTGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTAAATATAATTAAATTTA
Found at i:29082 original size:2 final size:2
Alignment explanation
Indices: 29075--29102 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29065 TAACTTTTTA
29075 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
29103 CACAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36686 original size:54 final size:54
Alignment explanation
Indices: 36623--36736 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
36613 GAATGATATT
* * * * ** *
36623 GATATTGTTCGTCGGGTATCAATATAATGGTATTGATG-TTTTTCGAGTAGTATC
1 GATACTGTTCATCGGATACCAATATAATGGTATTGATGCCATTT-GAGGAGTATC
**
36677 GATACTGTTCATTTGATACCAATATAATGGTATTGATGCCATTTGAGGAGTATC
1 GATACTGTTCATCGGATACCAATATAATGGTATTGATGCCATTTGAGGAGTATC
36731 GATACT
1 GATACT
36737 TTTTGGAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 47 0.94
55 3 0.06
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.39
Consensus pattern (54 bp):
GATACTGTTCATCGGATACCAATATAATGGTATTGATGCCATTTGAGGAGTATC
Found at i:41668 original size:16 final size:16
Alignment explanation
Indices: 41647--41679 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41637 AAATGTTTTC
41647 ATTTTAATAAAAT-TTA
1 ATTTTAA-AAAATATTA
41663 ATTTTAAAAAATATTA
1 ATTTTAAAAAATATTA
41679 A
1 A
41680 AACACGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTAAAAAATATTA
Found at i:43229 original size:29 final size:30
Alignment explanation
Indices: 43160--43218 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
43150 AATTTAAGGT
43160 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
43191 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
43219 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:43324 original size:21 final size:21
Alignment explanation
Indices: 43298--43376 Score: 131
Period size: 21 Copynumber: 3.8 Consensus size: 21
43288 AGGGTGTCAA
43298 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
43319 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
43340 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
43361 AGTGCATCGATGCACC
1 AGTGCATCCATGCACC
43377 TGCACTAGTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:43443 original size:20 final size:20
Alignment explanation
Indices: 43418--43485 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
43408 AATGCAATTA
*
43418 GTGCATCGATGCATCCTTTT
1 GTGCATCGATGCATCCTATT
* *
43438 GTGCATCGATGAAT-CAAGGTT
1 GTGCATCGATGCATCCTA--TT
*
43459 GTGCATCGATGCATCCTACT
1 GTGCATCGATGCATCCTATT
43479 GTGCATC
1 GTGCATC
43486 CACGCACGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 21 0.54
21 15 0.38
22 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTATT
Found at i:43642 original size:20 final size:22
Alignment explanation
Indices: 43604--43643 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
43594 TTTGAGTGGA
43604 AAAACCATCCCCAAACGACTCC
1 AAAACCATCCCCAAACGACTCC
43626 AAAA-CATCCCC-AACGACT
1 AAAACCATCCCCAAACGACT
43644 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.42, C:0.42, G:0.05, T:0.10
Consensus pattern (22 bp):
AAAACCATCCCCAAACGACTCC
Found at i:44530 original size:30 final size:30
Alignment explanation
Indices: 44496--44552 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
44486 CAGAGGTTAC
*
44496 AAAGAACCCCGGTAACTATCCAGATGTCAT
1 AAAGAACCCCGGCAACTATCCAGATGTCAT
* * *
44526 AAAGATCCTCGGCAACTATCCATATGT
1 AAAGAACCCCGGCAACTATCCAGATGT
44553 TCCTTTCAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (30 bp):
AAAGAACCCCGGCAACTATCCAGATGTCAT
Found at i:45380 original size:64 final size:64
Alignment explanation
Indices: 45226--45382 Score: 146
Period size: 64 Copynumber: 2.5 Consensus size: 64
45216 CAATAAGGGT
* **
45226 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCGATGTTGTATTATTATTAAG
* * * * *
45290 ATGCATCGATGCA-TGCCTTATACATCGATGCACT-AATTGCATTCGATG-T-TATTATT-TTAA
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATGTTGTATTATTATT--
45350 AAG
62 AAG
45353 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
45383 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
61 2 0.03
62 7 0.09
63 4 0.05
64 57 0.76
65 5 0.07
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTGTATTATTATTAAG
Found at i:49096 original size:34 final size:30
Alignment explanation
Indices: 49057--49125 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
49047 TTGATATAAC
*
49057 AATTTAAGGCAAAATGGTTTTTTGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
49091 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
49120 AATTTA
1 AATTTA
49126 TTTAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:49136 original size:29 final size:30
Alignment explanation
Indices: 49066--49125 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
49056 CAATTTAAGG
*
49066 CAAAATGGTTTTTTGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
49097 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
49126 TTTAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:49231 original size:21 final size:20
Alignment explanation
Indices: 49205--49303 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
49195 AGGGTGTCAA
49205 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
49226 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
49247 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
** *
49268 TAGTGCATTGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
49289 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
49304 TCAAACACCG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.53
22 12 0.18
23 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:49349 original size:20 final size:20
Alignment explanation
Indices: 49324--49417 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
49314 AATGCAATTA
* *
49324 GTGCATCGATGCTTCCTTTT
1 GTGCATCGATGCATCCTGTT
*
49344 GTGCATCGATGCAAT-CTTTT
1 GTGCATCGATGC-ATCCTGTT
**
49364 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC-CTGTT
*
49385 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGTT
*
49405 GTGCATCCATGCA
1 GTGCATCGATGCA
49418 CGAAGGCTGC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.68
21 18 0.29
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGTT
Found at i:52090 original size:39 final size:39
Alignment explanation
Indices: 52032--52106 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
52022 CTGCTTCAAT
*
52032 TTCACTTCTTGACAATGCTAAGCCAGACTCTACTTCCAA
1 TTCACTTCTTAACAATGCTAAGCCAGACTCTACTTCCAA
* * *
52071 TTCACTTGTTAACACTGCTAGGCCAGACTCTACTTC
1 TTCACTTCTTAACAATGCTAAGCCAGACTCTACTTC
52107 TACTTTGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (39 bp):
TTCACTTCTTAACAATGCTAAGCCAGACTCTACTTCCAA
Found at i:54977 original size:47 final size:47
Alignment explanation
Indices: 54907--55000 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
54897 ATACACTTTT
* *
54907 GCTCTTGGTAAGGATGATTCCTTATCTTTAGTTCATATATCTTTCAA
1 GCTCTTGGTAAGGATGATACCTTATCTTCAGTTCATATATCTTTCAA
* * *
54954 GCTCTTGGTAATGATGATACCTTATCTTCATTTCATATCTCTTTCAA
1 GCTCTTGGTAAGGATGATACCTTATCTTCAGTTCATATATCTTTCAA
55001 TAGAGTACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (47 bp):
GCTCTTGGTAAGGATGATACCTTATCTTCAGTTCATATATCTTTCAA
Found at i:64516 original size:2 final size:2
Alignment explanation
Indices: 64509--64552 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
64499 AAACAAGAGC
64509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64551 TA
1 TA
64553 AGGAATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65272 original size:29 final size:30
Alignment explanation
Indices: 65219--65283 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
65209 AAAAAATTGA
65219 TATTTTATATAAATTCTAAGATT-AATTAG
1 TATTTTATATAAATTCTAAGATTAAATTAG
* *
65248 TATTTTCTATAAAATT-TAA-AGTTAAATTAT
1 TATTTTATAT-AAATTCTAAGA-TTAAATTAG
65278 TATTTT
1 TATTTT
65284 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 14 0.45
30 16 0.52
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TATTTTATATAAATTCTAAGATTAAATTAG
Found at i:65502 original size:2 final size:2
Alignment explanation
Indices: 65497--65546 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
65487 TAACTGAAAT
65497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65539 TA TA TA TA
1 TA TA TA TA
65547 CTGTCCACCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65709 original size:21 final size:21
Alignment explanation
Indices: 65683--65728 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
65673 TACTCTTTTT
*
65683 TTTTTCT-AAAAATATATATTA
1 TTTTTCTCAAAAATAAATA-TA
65704 TTTTTCTCAAAAATAAATATA
1 TTTTTCTCAAAAATAAATATA
65725 TTTT
1 TTTT
65729 ATTTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTCTCAAAAATAAATATA
Found at i:65776 original size:17 final size:15
Alignment explanation
Indices: 65744--65801 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
65734 ATAAAAAATA
65744 TTTAATAT-TATATT
1 TTTAATATATATATT
*
65758 TTACAATATATATATT
1 TT-TAATATATATATT
*
65774 TTTAATATATTTATT
1 TTTAATATATATATT
65789 TCTTAATAT-TATA
1 T-TTAATATATATA
65802 ATTGTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.05
15 20 0.54
16 15 0.41
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATATATATATT
Found at i:67757 original size:62 final size:63
Alignment explanation
Indices: 67660--67787 Score: 213
Period size: 62 Copynumber: 2.0 Consensus size: 63
67650 CAAATATTGA
* * *
67660 AAATCAAGTTGATAGGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGA-ACAGATACATC
1 AAATCAAGTAGATAAGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAGACAAATACATC
*
67722 AAATCAAGTAGATAAGTTGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAGACAAATACATC
1 AAATCAAGTAGATAAGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAGACAAATACATC
67785 AAA
1 AAA
67788 GAGTGCAACC
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
62 48 0.79
63 13 0.21
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (63 bp):
AAATCAAGTAGATAAGTCGGAGGAGCCATCAGCAAAGAAACAATGCCTTGAGACAAATACATC
Done.