Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006223.1 Hibiscus syriacus cultivar Beakdansim tig00014832_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: 56683
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:757 original size:19 final size:19
Alignment explanation
Indices: 733--774 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
723 TATATTTATG
* * *
733 TTAAAATGGACGATTGAGA
1 TTAAAATAGACAACTGAGA
752 TTAAAATAGACAACTGAGA
1 TTAAAATAGACAACTGAGA
771 TTAA
1 TTAA
775 CAGTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (19 bp):
TTAAAATAGACAACTGAGA
Found at i:4324 original size:30 final size:30
Alignment explanation
Indices: 4290--4452 Score: 317
Period size: 30 Copynumber: 5.4 Consensus size: 30
4280 GGTTCTTCGG
*
4290 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
4320 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
4350 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
4380 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
4410 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
4440 GACCTCTGGATAG
1 GACCTCTGGATAG
4453 GTCCTTCGGA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 132 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:5358 original size:29 final size:29
Alignment explanation
Indices: 5316--5428 Score: 217
Period size: 29 Copynumber: 3.9 Consensus size: 29
5306 ATGGTTGCTG
5316 GGCGTGCATGGCGACCTGCCATGTCGCCT
1 GGCGTGCATGGCGACCTGCCATGTCGCCT
5345 GGCGTGCATGGCGACCTGCCATGTCGCCT
1 GGCGTGCATGGCGACCTGCCATGTCGCCT
5374 GGCGTGCATGGCGACCTGCCATGTCGCCT
1 GGCGTGCATGGCGACCTGCCATGTCGCCT
*
5403 GGCGTGCATGGCGACCTACCATGTCG
1 GGCGTGCATGGCGACCTGCCATGTCG
5429 TTGGGATGCC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 83 1.00
ACGTcount: A:0.12, C:0.34, G:0.35, T:0.20
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTGCCATGTCGCCT
Found at i:9940 original size:24 final size:24
Alignment explanation
Indices: 9844--9945 Score: 80
Period size: 24 Copynumber: 4.2 Consensus size: 24
9834 GAATATTTTA
* * *
9844 TCTGATTTATGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * * *
9868 TTTGACATCTGATATGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
9892 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
9916 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
*
9940 TTTGAT
1 TCTGAT
9946 TTCCGATATC
Statistics
Matches: 58, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:18605 original size:36 final size:36
Alignment explanation
Indices: 18559--18638 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
18549 TAGCAACCAA
18559 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
* *
18595 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
*
18631 -GTTGAAAA
1 CTTTGAAAA
18639 TAGGAATGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 7 0.17
36 34 0.83
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
Found at i:19449 original size:4 final size:4
Alignment explanation
Indices: 19440--19487 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
19430 TTTTACCCAT
19440 TTTA TTTA TTTA TTTA TTTA TTTA -TTA -TTA -TTA -TTA -TTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
19482 TTTA TT
1 TTTA TT
19488 ATTATTATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 18 0.42
4 25 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:19457 original size:12 final size:11
Alignment explanation
Indices: 19441--19532 Score: 79
Period size: 12 Copynumber: 8.5 Consensus size: 11
19431 TTTACCCATT
19441 TTATTTATTTA
1 TTATTTATTTA
19452 TTTATTTATTTA
1 -TTATTTATTTA
19464 TTA-TTA-TTA
1 TTATTTATTTA
19473 TTATTATTATTTA
1 TTA-T-TTATTTA
19486 TTA-TTA-TTA
1 TTATTTATTTA
*
19495 TTATTATATATA
1 TTATT-TATTTA
*
19507 TTATTATATATA
1 TTATT-TATTTA
19519 TTA-TTA-TTA
1 TTATTTATTTA
19528 TTATT
1 TTATT
19533 AAAAAATAAT
Statistics
Matches: 70, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
9 17 0.24
10 10 0.14
11 6 0.09
12 31 0.44
13 6 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:19469 original size:3 final size:3
Alignment explanation
Indices: 19461--19533 Score: 105
Period size: 3 Copynumber: 24.0 Consensus size: 3
19451 ATTTATTTAT
19461 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA
19507 TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
19534 AAAAATAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.06
3 52 0.80
4 9 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:20863 original size:12 final size:12
Alignment explanation
Indices: 20846--20910 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
20836 TTAATTCCTT
20846 TTATTTTAATTA
1 TTATTTTAATTA
*
20858 TTATTTGCAA-TA
1 TTATTT-TAATTA
20870 TTATTTTATTATTA
1 TTATTTTA--ATTA
*
20884 TTACTTTTTATTA
1 TTA-TTTTAATTA
20897 TTATTCTT-ATTA
1 TTATT-TTAATTA
20909 TT
1 TT
20911 TATATAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 1 0.02
12 22 0.50
13 12 0.27
14 5 0.11
15 4 0.09
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:20874 original size:3 final size:3
Alignment explanation
Indices: 20868--20910 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
20858 TTATTTGCAA
* *
20868 TAT TAT T-T TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
20911 TATATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:20894 original size:16 final size:15
Alignment explanation
Indices: 20873--20910 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
20863 TGCAATATTA
20873 TTTTATTATTATTACT
1 TTTTATTATTATT-CT
20889 TTTTATTATTATTCT
1 TTTTATTATTATTCT
*
20904 TATTATT
1 TTTTATT
20911 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTATTATTCT
Found at i:20913 original size:16 final size:15
Alignment explanation
Indices: 20868--20910 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
20858 TTATTTGCAA
20868 TATTATT-TTATTAT
1 TATTATTCTTATTAT
*
20882 TATTA--CTTTTTAT
1 TATTATTCTTATTAT
20895 TATTATTCTTATTAT
1 TATTATTCTTATTAT
20910 T
1 T
20911 TATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 5 0.21
15 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTCTTATTAT
Found at i:20923 original size:2 final size:2
Alignment explanation
Indices: 20911--20952 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
20901 TCTTATTATT
*
20911 TA TA TA AA 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
20953 ATAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23402 original size:14 final size:14
Alignment explanation
Indices: 23364--23402 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
23354 TTTTTAAATA
*
23364 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
23378 TTTTACATTTGCAT
1 ATTTACATTTGCAT
23392 ATTTACATTTG
1 ATTTACATTTG
23403 GCATCTCTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:26401 original size:2 final size:2
Alignment explanation
Indices: 26394--26427 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
26384 TTATCCTTTA
26394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26428 CCTTTGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26741 original size:8 final size:8
Alignment explanation
Indices: 26725--26833 Score: 98
Period size: 8 Copynumber: 13.4 Consensus size: 8
26715 TCCAGCAAAG
*
26725 AAAGGAAA
1 AAAGAAAA
26733 AAAGAAAA
1 AAAGAAAA
26741 AAAGAGGAAA
1 AAAGA--AAA
26751 AAAGAAAA
1 AAAGAAAA
26759 AAAGAAAA
1 AAAGAAAA
26767 AAA-ATAAA
1 AAAGA-AAA
*
26775 AAAGGAAA
1 AAAGAAAA
* *
26783 GAA-ATAA
1 AAAGAAAA
*
26790 AAATAAAA
1 AAAGAAAA
*
26798 AAA-ACAA
1 AAAGAAAA
26805 AAAGAAAAA
1 AAAG-AAAA
26814 AAAGAAAAA
1 AAAG-AAAA
26823 AAAGAAAA
1 AAAGAAAA
26831 AAA
1 AAA
26834 TTGAATCAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
7 11 0.13
8 50 0.59
9 16 0.19
10 8 0.09
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:26752 original size:1 final size:1
Alignment explanation
Indices: 26748--26833 Score: 64
Period size: 1 Copynumber: 86.0 Consensus size: 1
26738 AAAAAAGAGG
* * * ** * * * * *
26748 AAAAAAGAAAAAAAGAAAAAAAATAAAAAAGGAAAGAAATAAAAATAAAAAAAACAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
26813 AAAAGAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
26834 TTGAATCAAG
Statistics
Matches: 63, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.86, C:0.01, G:0.09, T:0.03
Consensus pattern (1 bp):
A
Found at i:26760 original size:9 final size:9
Alignment explanation
Indices: 26730--26833 Score: 101
Period size: 9 Copynumber: 11.6 Consensus size: 9
26720 CAAAGAAAGG
26730 AAAAAAG-A
1 AAAAAAGAA
*
26738 AAAAAAGAGG
1 AAAAAAGA-A
26748 AAAAAAG-A
1 AAAAAAGAA
26756 AAAAAAGAA
1 AAAAAAGAA
*
26765 AAAAAA-TA
1 AAAAAAGAA
*
26773 AAAAAGGAA
1 AAAAAAGAA
26782 AGAAATAA-AA
1 A-AAA-AAGAA
26792 ATAAAAA-AA
1 A-AAAAAGAA
26801 ACAAAAAGAA
1 A-AAAAAGAA
26811 AAAAAAGAA
1 AAAAAAGAA
26820 AAAAAAGAA
1 AAAAAAGAA
26829 AAAAA
1 AAAAA
26834 TTGAATCAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
8 20 0.25
9 41 0.51
10 19 0.23
11 1 0.01
ACGTcount: A:0.85, C:0.01, G:0.12, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:26785 original size:21 final size:22
Alignment explanation
Indices: 26759--26799 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
26749 AAAAAGAAAA
26759 AAAGAAA-AAAAATAAAAAAGG
1 AAAGAAATAAAAATAAAAAAGG
26780 AAAGAAATAAAAATAAAAAA
1 AAAGAAATAAAAATAAAAAA
26800 AACAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (22 bp):
AAAGAAATAAAAATAAAAAAGG
Found at i:26807 original size:16 final size:15
Alignment explanation
Indices: 26729--26833 Score: 95
Period size: 15 Copynumber: 6.7 Consensus size: 15
26719 GCAAAGAAAG
26729 GAAAAAAGAAAAAAAGA
1 GAAAAAA-AAAAAAA-A
*
26746 GGAAAAAAGAAAAAAA
1 -GAAAAAAAAAAAAAA
26762 GAAAAAAAATAAAAAA
1 GAAAAAAAA-AAAAAA
* * *
26778 GGAAAGAAATAAAAA
1 GAAAAAAAAAAAAAA
* *
26793 TAAAAAAAACAAAAA
1 GAAAAAAAAAAAAAA
26808 GAAAAAAAAGAAAAAA
1 GAAAAAAAA-AAAAAA
26824 -AAGAAAAAAA
1 GAA-AAAAAAA
26834 TTGAATCAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
15 35 0.48
16 25 0.34
17 6 0.08
18 7 0.10
ACGTcount: A:0.84, C:0.01, G:0.12, T:0.03
Consensus pattern (15 bp):
GAAAAAAAAAAAAAA
Found at i:27475 original size:32 final size:32
Alignment explanation
Indices: 27439--27500 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
27429 GTCAGACACA
*
27439 AGAAGTATCTCTACCAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
27471 AGAAGTATCTCTACAAGATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
27501 TCATTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:29312 original size:114 final size:114
Alignment explanation
Indices: 29112--29328 Score: 371
Period size: 114 Copynumber: 1.9 Consensus size: 114
29102 CACGTTCTCG
29112 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTC
* * *
29177 GGTAAGAACCCCAAAACCAATCATTGGATTTGAAAGATAAATTTGCTCA
66 GATAAGAACCCCAAAACCAATCATTGGAATTAAAAGATAAATTTGCTCA
*
29226 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTC
* * *
29291 GATAGGAATCCCAGAACCAATCATTGGAATTAAAAGAT
66 GATAAGAACCCCAAAACCAATCATTGGAATTAAAAGAT
29329 GAACTGCATG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTC
GATAAGAACCCCAAAACCAATCATTGGAATTAAAAGATAAATTTGCTCA
Found at i:31484 original size:54 final size:54
Alignment explanation
Indices: 31401--31554 Score: 265
Period size: 54 Copynumber: 2.9 Consensus size: 54
31391 AGAAATCTTG
31401 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTG-
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
31454 GACAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 G-CAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* *
31509 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGA
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGA
31555 GCCTGCTATT
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
53 1 0.01
54 93 0.98
55 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.23
Consensus pattern (54 bp):
GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:34062 original size:113 final size:113
Alignment explanation
Indices: 32362--34049 Score: 2551
Period size: 113 Copynumber: 14.9 Consensus size: 113
32352 GATTCAAATC
*
32362 CATCCCTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
32427 AGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTGTTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
32475 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** *
32540 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
32588 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
32653 ATAAGAAATTCATAATAAGAAGAATTTGTTCAAACTTTTGTTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * *
32701 CATCACTTGATGGATCAGCTTTTCCAGAAAAAATTCATAATAAGGAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** *
32766 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* *
32814 CATCATTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
32879 AGAAGAAATTCATAATGAGAAGAATTTGTTTAAACTTTTGTTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
32927 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** *
32992 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* *
33040 CATCATTTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
33105 AGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTGTTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* *
33153 CATCACTTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * ** *
33218 AGAAAAAATTCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * *
33266 CATCATTTGATGGATCAGTTTTTTCATG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTTGATGGATCAGCTTTTCCA-GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
33330 AAGAAGAAATTCATAAATGAGAAGAATTTGTTCAAACTTTTGTTTGAATT
65 AAGAAGAAATTCAT-AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* *
33380 CATCACTTGATGGATCGGCTTTTCCAGAAAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** *
33445 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
33493 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
33558 AGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTGTTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
33606 CATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
33671 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * * ** *
33719 CATCATTTGATAGATCAGCATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 CATCACTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
*
33784 GAAGAAG---TTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
64 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTTGAATT
** * **** * *
33831 CATCA-TTCGATGGATCAGCAATACCAGGGCGAGTTCATAATGAGAATAACTCATCTGAAGAAAG
1 CATCACTT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *
33895 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCGAATT
65 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * * * *
33944 CATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ** *
34009 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
34050 ATGACTCTAT
Statistics
Matches: 1434, Mismatches: 129, Indels: 24
0.90 0.08 0.02
Matches are distributed among these distances:
110 39 0.03
111 7 0.00
112 51 0.04
113 1189 0.83
114 105 0.07
115 43 0.03
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
Found at i:34115 original size:17 final size:17
Alignment explanation
Indices: 34093--34151 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
34083 CAGCATTTCC
34093 AGAAGAAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
34110 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
*
34128 AAGAAGAAGTTCACACTG
1 -AGAAGAAGTTCACAATG
34146 AGAAGA
1 AGAAGA
34152 GCTTGTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 2 0.06
19 10 0.30
20 3 0.09
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:34407 original size:3 final size:3
Alignment explanation
Indices: 34399--34477 Score: 88
Period size: 3 Copynumber: 26.0 Consensus size: 3
34389 ATTTATTTAT
* * * * *
34399 TTA TTA TTA TTA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
34447 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
34478 AAAAATAATT
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
2 2 0.03
3 63 0.89
4 6 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:35870 original size:16 final size:16
Alignment explanation
Indices: 35836--35867 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
35826 ACTTTTTATT
35836 TATATAAATAAATAAA
1 TATATAAATAAATAAA
35852 TATATATAATAAATAA
1 TATATA-AATAAATAA
35868 TATTTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATATAAATAAATAAA
Found at i:36056 original size:109 final size:109
Alignment explanation
Indices: 35922--36131 Score: 255
Period size: 109 Copynumber: 1.9 Consensus size: 109
35912 AATAATCATA
* * * * *
35922 TTTATTTATTTTTCAATATTAAGAAAGGA-CAGTCTTAAAATAACTGGATGTCCATTTTCTGATA
1 TTTATTTATTTTTCAATATGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-TTTTCTGATA
* *
35986 TTTTTAAATAAATAAATATCCTATTTTTAAATCATATATTAATTGT
65 TTTCTAAATAAATAAATATCCTATTTATAAAT-ATATATTAATTGT
* ** *
36032 TTTATTT-TTTTT-AATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATA
1 TTTATTTATTTTTCAATAT-GAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGATA
**
36095 TTTCTAAATAAATAAATATTTTATTTATAAATATATA
65 TTTCTAAATAAATAAATATCCTATTTATAAATATATA
36132 AATTAATATA
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
108 10 0.12
109 51 0.60
110 24 0.28
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (109 bp):
TTTATTTATTTTTCAATATGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTCTGATAT
TTCTAAATAAATAAATATCCTATTTATAAATATATATTAATTGT
Found at i:43478 original size:17 final size:16
Alignment explanation
Indices: 43452--43485 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
43442 TTTCACTAAT
*
43452 AGAGGAAATATTACAA
1 AGAGGAAATAGTACAA
43468 AGAGAGAAATAGTACAA
1 AGAG-GAAATAGTACAA
43485 A
1 A
43486 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAGTACAA
Found at i:45055 original size:12 final size:12
Alignment explanation
Indices: 45038--45062 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45028 AGGAACATGT
45038 AGTTCCAATTTG
1 AGTTCCAATTTG
45050 AGTTCCAATTTG
1 AGTTCCAATTTG
45062 A
1 A
45063 TCAAAATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGTTCCAATTTG
Done.