Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007758.1 Hibiscus syriacus cultivar Beakdansim tig00110025_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: 87809
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:7313 original size:21 final size:19
Alignment explanation
Indices: 7266--7317 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
7256 CGGCCAAGAG
*
7266 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
7285 CATATATTTTCATTTAAAAGT
1 CATGTATTTTCA-TTAAAA-T
7306 CATGTATTTTCA
1 CATGTATTTTCA
7318 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:10127 original size:9 final size:9
Alignment explanation
Indices: 10115--10149 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
10105 TTGGCTTTTG
10115 TTTTTTGTT
1 TTTTTTGTT
*
10124 TTTTTTGCCT
1 TTTTTTG-TT
10134 TTTTTTGTT
1 TTTTTTGTT
10143 TTTTTTG
1 TTTTTTG
10150 AAAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:10148 original size:23 final size:23
Alignment explanation
Indices: 10101--10148 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
10091 AAATTTTGGC
*
10101 TTTTTTGGCTTTTGTTTTTTGTT
1 TTTTTTGCCTTTTGTTTTTTGTT
*
10124 TTTTTTGCCTTTT-TTTGTT-TT
1 TTTTTTGCCTTTTGTTTTTTGTT
10145 TTTT
1 TTTT
10149 GAAAAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 5 0.22
23 12 0.52
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.81
Consensus pattern (23 bp):
TTTTTTGCCTTTTGTTTTTTGTT
Found at i:12654 original size:22 final size:22
Alignment explanation
Indices: 12605--12658 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
12595 AGCACCATGA
* * *
12605 GTCCATGCAAATTGTAATATTC
1 GTCCATGCATATTGTAACATAC
* *
12627 GGCCATGCATATTGTAACCTAC
1 GTCCATGCATATTGTAACATAC
12649 GTCCATGCAT
1 GTCCATGCAT
12659 GCATTTCTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (22 bp):
GTCCATGCATATTGTAACATAC
Found at i:16384 original size:22 final size:22
Alignment explanation
Indices: 16335--16388 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
16325 AGCACCATGA
* * *
16335 GTCCATGCAAATTGTAATATTC
1 GTCCATGCATATTGTAACATAC
* *
16357 GGCCATGCATATTGTAACCTAC
1 GTCCATGCATATTGTAACATAC
16379 GTCCATGCAT
1 GTCCATGCAT
16389 GCATTTCTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (22 bp):
GTCCATGCATATTGTAACATAC
Found at i:18480 original size:24 final size:24
Alignment explanation
Indices: 18452--18510 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
18442 AAGAAAAATC
*
18452 AGAAAACAAAGTGAAGCACTC-AAA
1 AGAAAA-AAAGTCAAGCACTCAAAA
* *
18476 AGAAAGAAAAATCCAGCACTCAAAA
1 AGAAA-AAAAGTCAAGCACTCAAAA
18501 AGAAAAAAAG
1 AGAAAAAAAG
18511 AAAAGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.63, C:0.15, G:0.15, T:0.07
Consensus pattern (24 bp):
AGAAAAAAAGTCAAGCACTCAAAA
Found at i:21193 original size:91 final size:91
Alignment explanation
Indices: 21037--21219 Score: 267
Period size: 91 Copynumber: 2.0 Consensus size: 91
21027 GGTAGTTGAT
* *
21037 GCTTGGCCGAATAGGAAGAGAGCTCTTTATCTTGGTGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGAAGAGAACTCTTCATCTTGGTGCCTAAATGAACCACATGCAAGGCACATG
21102 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
** * * *
21128 GCTTGGCTTAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCACATGCAAGGCGCATG
1 GCTTGGCCGAATAGGAAGAGAACTCTTCATCTTGGTGCCTAAATGAACCACATGCAAGGCACATG
* * **
21193 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGATCACATGCAAAACACATG
21219 G
1 G
21220 GTGTTCTAGG
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 81 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (91 bp):
GCTTGGCCGAATAGGAAGAGAACTCTTCATCTTGGTGCCTAAATGAACCACATGCAAGGCACATG
GGGGCTGATCACATGCAAAACACATG
Found at i:34500 original size:35 final size:37
Alignment explanation
Indices: 34454--34533 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
34444 TTTGAGAATT
*
34454 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
34489 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
34526 TGGTGATG
1 TGGTGATG
34534 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:37778 original size:15 final size:15
Alignment explanation
Indices: 37728--37779 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
37718 AAAATATGGT
* *
37728 AATGAAATAAGAAAA
1 AATGAAATGATAAAA
*
37743 GATGAAA-GAATAAAGA
1 AATGAAATG-ATAAA-A
37759 AATGAAATGATAAAA
1 AATGAAATGATAAAA
37774 AATGAA
1 AATGAA
37780 GATAACTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 17 0.57
16 12 0.40
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (15 bp):
AATGAAATGATAAAA
Found at i:38449 original size:35 final size:37
Alignment explanation
Indices: 38403--38482 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
38393 TTTGAGAATT
*
38403 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGATCA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGATCA
*
38438 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGATCA
38475 TGGTGATG
1 TGGTGATG
38483 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGATCA
Found at i:40222 original size:33 final size:33
Alignment explanation
Indices: 40180--40248 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
40170 GTTGATGAAT
*
40180 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
40213 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
40246 GAA
1 GAA
40249 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:40253 original size:13 final size:12
Alignment explanation
Indices: 40234--40328 Score: 58
Period size: 13 Copynumber: 7.8 Consensus size: 12
40224 TTATTGGCGT
40234 GATATGGTGATG
1 GATATGGTGATG
40246 GAATATGGTGAT-
1 G-ATATGGTGATG
*
40258 GATATAGGCG-T-
1 GATAT-GGTGATG
40269 GATAATGGTGATG
1 GAT-ATGGTGATG
40282 GACTATGGTGAT-
1 GA-TATGGTGATG
*
40294 GATATAGGCG-T-
1 GATAT-GGTGATG
*
40305 GATAATGGAGATG
1 GAT-ATGGTGATG
40318 GATTATGGTGA
1 GA-TATGGTGA
40329 CCTTCAAGTG
Statistics
Matches: 67, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.31
12 16 0.24
13 28 0.42
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:40289 original size:36 final size:36
Alignment explanation
Indices: 40219--40328 Score: 168
Period size: 36 Copynumber: 3.1 Consensus size: 36
40209 AATGGAAGGA
* *
40219 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
40254 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
40290 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
40326 TGA
1 TGA
40329 CCTTCAAGTG
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:40433 original size:33 final size:33
Alignment explanation
Indices: 40391--40459 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
40381 GTTGATGAAT
*
40391 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
40424 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
40457 GAA
1 GAA
40460 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:40464 original size:13 final size:12
Alignment explanation
Indices: 40445--40541 Score: 71
Period size: 13 Copynumber: 8.0 Consensus size: 12
40435 TTATTGGCGT
40445 GATATGGTGATG
1 GATATGGTGATG
40457 GAATATGGTGAT-
1 G-ATATGGTGATG
40469 GATATAGGTG-T-
1 GATAT-GGTGATG
40480 GATAATGGTGATG
1 GAT-ATGGTGATG
40493 GACTATGGTGAT-
1 GA-TATGGTGATG
*
40505 GATATAGGCG-T-
1 GATAT-GGTGATG
*
40516 GATAATGGAGATG
1 GAT-ATGGTGATG
40529 GATTATGGTGATG
1 GA-TATGGTGATG
40542 AAAATAGTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 21
0.75 0.03 0.22
Matches are distributed among these distances:
11 22 0.31
12 17 0.24
13 30 0.42
14 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:40484 original size:211 final size:211
Alignment explanation
Indices: 40119--40539 Score: 833
Period size: 211 Copynumber: 2.0 Consensus size: 211
40109 AATAAATCTT
40119 CTTCAAGTGATGTTGACTTCGGCCTCCAATGGTGGTGATGAAGTATGCCTTGTTGATGAATGAAG
1 CTTCAAGTGATGTTGACTTCGGCCTCCAATGGTGGTGATGAAGTATGCCTTGTTGATGAATGAAG
40184 GATGATTTAATGGTGATGAAATGGTAATGGAAGGATGATGTTATTGGCGTGATATGGTGATGGAA
66 GATGATTTAATGGTGATGAAATGGTAATGGAAGGATGATGTTATTGGCGTGATATGGTGATGGAA
40249 TATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATGGA
131 TATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATGGA
40314 GATGGATTATGGTGAC
196 GATGGATTATGGTGAC
40330 CTTCAAGTGATGTTGACTTCGGCCTCCAATGGTGGTGATGAAGTATGCCTTGTTGATGAATGAAG
1 CTTCAAGTGATGTTGACTTCGGCCTCCAATGGTGGTGATGAAGTATGCCTTGTTGATGAATGAAG
40395 GATGATTTAATGGTGATGAAATGGTAATGGAAGGATGATGTTATTGGCGTGATATGGTGATGGAA
66 GATGATTTAATGGTGATGAAATGGTAATGGAAGGATGATGTTATTGGCGTGATATGGTGATGGAA
*
40460 TATGGTGATGATATAGGTGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATGGA
131 TATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATGGA
40525 GATGGATTATGGTGA
196 GATGGATTATGGTGA
40540 TGAAAATAGT
Statistics
Matches: 209, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 209 1.00
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.32
Consensus pattern (211 bp):
CTTCAAGTGATGTTGACTTCGGCCTCCAATGGTGGTGATGAAGTATGCCTTGTTGATGAATGAAG
GATGATTTAATGGTGATGAAATGGTAATGGAAGGATGATGTTATTGGCGTGATATGGTGATGGAA
TATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATGGA
GATGGATTATGGTGAC
Found at i:40494 original size:36 final size:36
Alignment explanation
Indices: 40430--40542 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
40420 AATGGAAGGA
* *
40430 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
40465 TGATGATATAGGTGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
40501 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
40537 TGATGA
1 TGATGA
40543 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 15 0.21
36 55 0.79
ACGTcount: A:0.27, C:0.03, G:0.36, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:45230 original size:208 final size:208
Alignment explanation
Indices: 44872--45265 Score: 752
Period size: 208 Copynumber: 1.9 Consensus size: 208
44862 TACTTGCTAC
* *
44872 GTTTGTACAACTTCCTCCATCAATGATCACCACGCAAATTTTATCTTCCACGTGACATTTGGTAT
1 GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTTCCACGTGACATTTGGTAT
*
44937 GGAAGATGTTCTCTCTTTGTTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAG
66 GGAAGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAG
45002 ATGTTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGACTTTGAAGAT
131 ATGTTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGACTTTGAAGAT
45067 GTTCAAAGTCCTT
196 GTTCAAAGTCCTT
45080 GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTTCCACGTGACATTTGGTAT
1 GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTTCCACGTGACATTTGGTAT
*
45145 GGAAGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACTACAAAG
66 GGAAGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAG
45210 ATGTTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGAC
131 ATGTTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGAC
45266 CTTATTAGAA
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
208 182 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (208 bp):
GTTTGTACAACTTCCTCCATCAATGATAACCACGCAAATTTTAACTTCCACGTGACATTTGGTAT
GGAAGATGTTCTCTCTTTATTCATCCTCTTGACTTTGAATGTTCAAAGTCCTTTTAACCACAAAG
ATGTTGGATGGAAGAGACATGTTAGCAAATAAGGAAAAATGAAATGTGTGTAGGACTTTGAAGAT
GTTCAAAGTCCTT
Found at i:45702 original size:15 final size:15
Alignment explanation
Indices: 45667--45695 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45657 GTGCTTCAAC
45667 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
45681 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
45696 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:50840 original size:16 final size:16
Alignment explanation
Indices: 50819--50857 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
50809 AAGATATGGT
50819 AATGAAACAAGAAAAA
1 AATGAAACAAGAAAAA
* * *
50835 AATGAAAGAATAAAGA
1 AATGAAACAAGAAAAA
50851 AATGAAA
1 AATGAAA
50858 TAGTAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (16 bp):
AATGAAACAAGAAAAA
Found at i:51138 original size:21 final size:20
Alignment explanation
Indices: 51076--51138 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
51066 AGTCTCTTCT
* *
51076 TTCTCTTTTTTTTGTTTTTC
1 TTCTTTTTTTTTTGTTTTTG
* *
51096 TTCTTTCTTTTTCTCTTTTTG
1 TTCTTT-TTTTTTTGTTTTTG
*
51117 TTGCTTTTTTTTTTGTTGTTG
1 TT-CTTTTTTTTTTGTTTTTG
51138 T
1 T
51139 AGCACTTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 5 0.15
21 25 0.74
22 4 0.12
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.78
Consensus pattern (20 bp):
TTCTTTTTTTTTTGTTTTTG
Found at i:52722 original size:33 final size:33
Alignment explanation
Indices: 52643--52746 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
52633 ATACAATCTG
* *
52643 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
52679 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
52712 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
52745 TC
1 TC
52747 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:58368 original size:33 final size:33
Alignment explanation
Indices: 58289--58392 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
58279 ATACAATCTG
* *
58289 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
58325 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
58358 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
58391 TC
1 TC
58393 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:61034 original size:91 final size:91
Alignment explanation
Indices: 60874--61056 Score: 285
Period size: 91 Copynumber: 2.0 Consensus size: 91
60864 GGTAGTTGAT
* * *
60874 GCTTGGCCGAATAGGGAGGGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATA
60939 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* *
60965 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGCAAGGCGCATA
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATA
* * **
61030 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGATCACATGCAAAACACATG
61056 G
1 G
61057 GTGTTCTAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGCACATA
GGGGCTGATCACATGCAAAACACATG
Found at i:62873 original size:11 final size:13
Alignment explanation
Indices: 62841--62870 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
62831 TGGCCAAAGA
62841 TGAAAAGGTATGT
1 TGAAAAGGTATGT
62854 TGAAAAGGTATG-
1 TGAAAAGGTATGT
62866 TGAAA
1 TGAAA
62871 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:72149 original size:24 final size:25
Alignment explanation
Indices: 72081--72150 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 25
72071 AAAGTCAAAG
72081 AAAGCAAGAAAAATCAGAAAAGCACTCAA
1 AAAG-AAGAAAAA--AG-AAAGCACTCAA
**
72110 AAAGAAG-AAATTGAAAGCACTC-A
1 AAAGAAGAAAAAAGAAAGCACTCAA
72133 AAAGAAGAAAAAAGAAAG
1 AAAGAAGAAAAAAGAAAG
72151 AAAAGTTGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 8 0.22
24 17 0.47
25 1 0.03
27 3 0.08
28 3 0.08
29 4 0.11
ACGTcount: A:0.64, C:0.11, G:0.17, T:0.07
Consensus pattern (25 bp):
AAAGAAGAAAAAAGAAAGCACTCAA
Found at i:74923 original size:11 final size:13
Alignment explanation
Indices: 74891--74920 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
74881 TGCCCAAAGA
74891 TGAAAAGGTATGT
1 TGAAAAGGTATGT
74904 TGAAAAGGTATG-
1 TGAAAAGGTATGT
74916 TGAAA
1 TGAAA
74921 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:77709 original size:11 final size:12
Alignment explanation
Indices: 77688--77736 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
77678 TTGAGAATTT
77688 GGTGATGATATA
1 GGTGATGATATA
77700 GGTG-TGATAT-
1 GGTGATGATATA
*
77710 GATGATGGACTAT-
1 GGTGAT-GA-TATA
77723 GGTGATGATATA
1 GGTGATGATATA
77735 GG
1 GG
77737 CGTGATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 10 0.32
12 10 0.32
13 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:77733 original size:35 final size:37
Alignment explanation
Indices: 77687--77766 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
77677 TTTGAGAATT
* *
77687 TGGTGATGATATAGGTGTGAT-AT-GATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
77722 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
77759 TGGTGATG
1 TGGTGATG
77767 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 2 0.05
37 18 0.45
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:78130 original size:20 final size:20
Alignment explanation
Indices: 78105--78160 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
78095 GAAACCCCTT
78105 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTGA
78125 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTGA
*
78145 TGAAAATACACGATTT
1 TGAAAATACATGATTT
78161 AAATGAAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTGA
Found at i:81291 original size:20 final size:20
Alignment explanation
Indices: 81253--81290 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
81243 TGCTTCACTT
*
81253 TTCTTTTGCTTTTGATTTTC
1 TTCTTTTGCTTTTCATTTTC
*
81273 TTCTTTTTCTTTTC-TTTT
1 TTCTTTTGCTTTTCATTTT
81291 TTTTGCACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (20 bp):
TTCTTTTGCTTTTCATTTTC
Found at i:81347 original size:20 final size:20
Alignment explanation
Indices: 81318--81357 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
81308 GATGTAGGAG
*
81318 TCTTTTTCTT-TTCTTTTTT
1 TCTTTTTCTTGTGCTTTTTT
81337 TCTTCTTTCTTGTGCTTTTTT
1 TCTT-TTTCTTGTGCTTTTTT
81358 GTTGTAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (20 bp):
TCTTTTTCTTGTGCTTTTTT
Found at i:81778 original size:35 final size:37
Alignment explanation
Indices: 81732--81811 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
81722 TTTGAGAATT
*
81732 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
81767 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
81804 TGGTGATG
1 TGGTGATG
81812 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:85202 original size:9 final size:9
Alignment explanation
Indices: 85152--85210 Score: 73
Period size: 9 Copynumber: 6.4 Consensus size: 9
85142 TATTTTTTTT
85152 AAAAACAAA
1 AAAAACAAA
**
85161 AAAAGGAAA
1 AAAAACAAA
*
85170 AAAAAAAAA
1 AAAAACAAA
*
85179 AAAAAAAAA
1 AAAAACAAA
85188 AAAAACAAA
1 AAAAACAAA
85197 AAAAACACAA
1 AAAAACA-AA
85207 AAAA
1 AAAA
85211 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
9 38 0.86
10 6 0.14
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:85210 original size:1 final size:1
Alignment explanation
Indices: 85152--85201 Score: 64
Period size: 1 Copynumber: 50.0 Consensus size: 1
85142 TATTTTTTTT
* ** *
85152 AAAAACAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
85202 CACAAAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.92, C:0.04, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Done.