Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006924.1 Hibiscus syriacus cultivar Beakdansim tig00017760_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: 78934
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1803 original size:4 final size:4
Alignment explanation
Indices: 1548--1792 Score: 346
Period size: 4 Copynumber: 61.2 Consensus size: 4
1538 CCACTGTCTC
*
1548 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * * *
1596 GCAT GTAT GCAT GTAT GCAT GTAT GCAT GTAT GCAT GCAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
1644 GTAT GTAT GCAT GCAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
1692 GCAT GTAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GCAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
1740 GTAT GTAT GCAT GTAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1788 GTAT G
1 GTAT G
1793 CATGCATGCA
Statistics
Matches: 217, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 217 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (4 bp):
GTAT
Found at i:8198 original size:2 final size:2
Alignment explanation
Indices: 8191--8228 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8181 TCTATTATTA
8191 AT AT 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 AT AT
8229 GAATAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8969 original size:2 final size:2
Alignment explanation
Indices: 8962--8989 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8952 AGACTGTATG
8962 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
8990 TCGTAAAAGG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:17404 original size:25 final size:24
Alignment explanation
Indices: 17376--17443 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
17366 TATGATATAA
17376 ATTTATATAATATTAACTTAAAA-AT
1 ATTT-TAT-ATATTAACTTAAAATAT
17401 ATTTT-TATATTAACTTATTAAATAT
1 ATTTTATATATTAACTTA--AAATAT
17426 ATTTTAT-TATTAACTTAA
1 ATTTTATATATTAACTTAA
17444 TTTAAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
22 11 0.28
23 2 0.05
24 4 0.10
25 21 0.54
26 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTTTATATATTAACTTAAAATAT
Found at i:17413 original size:22 final size:23
Alignment explanation
Indices: 17385--17443 Score: 84
Period size: 22 Copynumber: 2.5 Consensus size: 23
17375 AATTTATATA
17385 ATATTAACTTAAAAATAT-TTTT
1 ATATTAACTTAAAAATATATTTT
*
17407 ATATTAACTTATTAAATATATTTT
1 ATATTAACTTA-AAAATATATTTT
17431 ATTATTAACTTAA
1 A-TATTAACTTAA
17444 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 11 0.34
23 6 0.19
24 5 0.16
25 10 0.31
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTAACTTAAAAATATATTTT
Found at i:26881 original size:19 final size:19
Alignment explanation
Indices: 26836--26875 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
26826 ATATTTCATT
26836 ATCATTTTAGTACATGAAG
1 ATCATTTTAGTACATGAAG
26855 ATCATTTTAGTACATGAAG
1 ATCATTTTAGTACATGAAG
26874 AT
1 AT
26876 TTTTTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
ATCATTTTAGTACATGAAG
Found at i:32310 original size:18 final size:18
Alignment explanation
Indices: 32287--32321 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32277 TATATATATG
*
32287 AATAAAATAAAAATAAAA
1 AATAAAACAAAAATAAAA
*
32305 AATAAAACAATAATAAA
1 AATAAAACAAAAATAAA
32322 TACTATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (18 bp):
AATAAAACAAAAATAAAA
Found at i:32824 original size:18 final size:18
Alignment explanation
Indices: 32789--32826 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
32779 AATTGCAATT
32789 AATATTGACTAAAGTAAA
1 AATATTGACTAAAGTAAA
*
32807 AATATATGATTAAA-TAAA
1 AATAT-TGACTAAAGTAAA
32825 AA
1 AA
32827 AAATAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (18 bp):
AATATTGACTAAAGTAAA
Found at i:33912 original size:62 final size:62
Alignment explanation
Indices: 33814--33944 Score: 156
Period size: 62 Copynumber: 2.1 Consensus size: 62
33804 GGAATTTTTG
* * *
33814 GTTGAGGATGGCATCGTGGTAGCAGCTGGATGGGGAATACAACGACAGAGCAATTCGGAGTA
1 GTTGAAGATGGCATCGTGGTAGCAGCTGGATAGGGAACACAACGACAGAGCAATTCGGAGTA
* * *** * *
33876 GTTGAAGATGGCATCGTGGTAGCAGCT-TACTAGGGAACATAACGGTGGAGCAGTTCGGAGTG
1 GTTGAAGATGGCATCGTGGTAGCAGCTGGA-TAGGGAACACAACGACAGAGCAATTCGGAGTA
33938 GTTGAAG
1 GTTGAAG
33945 GCGGTGCCGG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 1 0.02
62 57 0.98
ACGTcount: A:0.27, C:0.14, G:0.37, T:0.21
Consensus pattern (62 bp):
GTTGAAGATGGCATCGTGGTAGCAGCTGGATAGGGAACACAACGACAGAGCAATTCGGAGTA
Found at i:34231 original size:3 final size:3
Alignment explanation
Indices: 34225--34270 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
34215 ATTATTTATT
* *
34225 TAA TAA TAA AAA TAA -AA TAA TAA TAT TAA TAA TAA TAA -AA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34270 T
1 T
34271 TAACAACCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:34254 original size:23 final size:22
Alignment explanation
Indices: 34228--34270 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
34218 ATTTATTTAA
34228 TAATAAAAATAAAATAATAATAT
1 TAATAAAAATAAAA-AATAATAT
*
34251 TAATAATAATAAAAAATAAT
1 TAATAAAAATAAAAAATAAT
34271 TAACAACCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAAAATAAAAAATAATAT
Found at i:34650 original size:123 final size:123
Alignment explanation
Indices: 34392--34956 Score: 914
Period size: 123 Copynumber: 4.6 Consensus size: 123
34382 CTCTTGACAG
* * * * * *
34392 AAAATGTTGAACAAGTTCTTCATATTATGAACTTTTTCTTCTTCTTCAGATGAGTTATTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * * * * *
34457 ACGAACTCGTGTCTAGAAATGTTGATGTTGTTCTATCTCCTTCTGCGATAGAGTCAAGA
66 ACGAACTCCT-TCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
* *
34516 AAAAGGTTGAATACGTTCTTCAGATTACGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
34581 ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
66 ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
*
34639 AAAAGGTTGAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * * *
34704 ACGAACTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTTTGCGATAGAGTTGAGC
66 ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
34762 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* *
34827 ACGAACTCCTTCTGGAAATATTGATGTTGCTTTATCTCCTTCTACGATAGAGTCGAGC
66 ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
* *
34885 AAAAGGTTGAATAAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
34950 ACGAACT
66 ACGAACT
34957 TTATAAATCA
Statistics
Matches: 413, Mismatches: 28, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
123 347 0.84
124 66 0.16
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (123 bp):
AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
ACGAACTCCTTCTGGAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
Found at i:35234 original size:39 final size:39
Alignment explanation
Indices: 35170--35259 Score: 126
Period size: 39 Copynumber: 2.3 Consensus size: 39
35160 TTAGTTTTTT
*
35170 ATAAAATCTTTTGCTTCAAGAGAAACTATCTCAAGCAAG
1 ATAAAATCTTCTGCTTCAAGAGAAACTATCTCAAGCAAG
* * * *
35209 ATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 ATAAAATCTTCTGCTTCAAGAGAAACTATCTCAAGCAAG
*
35248 ACAAAATCTTCT
1 ATAAAATCTTCT
35260 TTTTTCATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (39 bp):
ATAAAATCTTCTGCTTCAAGAGAAACTATCTCAAGCAAG
Found at i:36595 original size:51 final size:51
Alignment explanation
Indices: 36458--36654 Score: 277
Period size: 51 Copynumber: 3.8 Consensus size: 51
36448 TATCCCAACA
* * *
36458 TTTTCATGCTGGTATGAGCCTTCAAGATGCCCTACATGGATTACTTCTGTC
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCACATGGATTACTTCTATC
* * *
36509 TTTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATTGATTATTTCTATC
1 -TTTTCATGCTGATATGAGCCTTCAAGATGCCCCACATGGATTACTTCTATC
* * * *
36561 TTTTCATGCTGATGTGAGCCTTCAATATGGCCCACGTGGATTACTTCTATC
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCACATGGATTACTTCTATC
* *
36612 TTTTCATGATGATATGAGCCTTCAAGATACCCCACATGGATTA
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCACATGGATTA
36655 TATGGACCTT
Statistics
Matches: 128, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
51 83 0.65
52 45 0.35
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (51 bp):
TTTTCATGCTGATATGAGCCTTCAAGATGCCCCACATGGATTACTTCTATC
Found at i:38201 original size:8 final size:8
Alignment explanation
Indices: 38190--38273 Score: 93
Period size: 8 Copynumber: 10.9 Consensus size: 8
38180 TTTTTTGTTA
38190 TCTTTTTT
1 TCTTTTTT
38198 TC-TTTTT
1 TCTTTTTT
*
38205 TC-CTTTT
1 TCTTTTTT
* *
38212 TCCTTATT
1 TCTTTTTT
*
38220 GCTTTTTT
1 TCTTTTTT
38228 TCTTTTTT
1 TCTTTTTT
38236 TCTTTTTT
1 TCTTTTTT
38244 TCTTTTTT
1 TCTTTTTT
*
38252 T-TTCTTT
1 TCTTTTTT
*
38259 TCTCTTTT
1 TCTTTTTT
38267 TCTTTTT
1 TCTTTTT
38274 CTCTCTCTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
7 19 0.30
8 44 0.70
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:38235 original size:31 final size:30
Alignment explanation
Indices: 38191--38274 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
38181 TTTTTGTTAT
38191 CTTTTTTTC-TTTTTTCCTTTTTCCTTATTG
1 CTTTTTTTCTTTTTTTCCTTTTTCCTT-TTG
* * *
38221 CTTTTTTTCTTTTTTTCTTTTTTTCTTTTT
1 CTTTTTTTCTTTTTTTCCTTTTTCCTTTTG
* *
38251 TTTTCTTTTCTCTTTTT-CTTTTTC
1 CTTT-TTTTCTTTTTTTCCTTTTTC
38275 TCTCTCTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 19 0.42
31 26 0.58
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (30 bp):
CTTTTTTTCTTTTTTTCCTTTTTCCTTTTG
Found at i:41744 original size:46 final size:47
Alignment explanation
Indices: 41692--41784 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 47
41682 ATATATACAT
* * *
41692 CCTAACCTCATGATTTCTAGTTC-CATG-GTTTATTTGGAAAACTAAA
1 CCTAACCACATGATTTCTAGTTCACATGAATTTATTCGGAAAA-TAAA
41738 CCTAACCACATGATTTCTAGTTCACATGAATTTATTCGGAAAATAAA
1 CCTAACCACATGATTTCTAGTTCACATGAATTTATTCGGAAAATAAA
41785 ACAATACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 22 0.52
47 8 0.19
48 12 0.29
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (47 bp):
CCTAACCACATGATTTCTAGTTCACATGAATTTATTCGGAAAATAAA
Found at i:44191 original size:62 final size:62
Alignment explanation
Indices: 44091--44229 Score: 181
Period size: 62 Copynumber: 2.2 Consensus size: 62
44081 TTGGAAGTTT
* * *
44091 TGGTTGAGGACGGCGTCATGGCAGCAGCTGGATGGGGAACACAACGGCAGAGCAGTTCGGAG
1 TGGTTGAAGACGGCGTCATGGCAGCAGCTGGATAGGGAACACAACGGCAGAGCAGTTCAGAG
* * * * *
44153 TGGTTGAAGATGGCGTCGTGGCAGCAGCT-TACTAGGGAACATAACGGCGGAGCAGTTCAGAG
1 TGGTTGAAGACGGCGTCATGGCAGCAGCTGGA-TAGGGAACACAACGGCAGAGCAGTTCAGAG
*
44215 TGGTTGAAGGCGGCG
1 TGGTTGAAGACGGCG
44230 CCAGAATAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
61 1 0.02
62 65 0.98
ACGTcount: A:0.24, C:0.18, G:0.41, T:0.17
Consensus pattern (62 bp):
TGGTTGAAGACGGCGTCATGGCAGCAGCTGGATAGGGAACACAACGGCAGAGCAGTTCAGAG
Found at i:44510 original size:3 final size:3
Alignment explanation
Indices: 44504--44543 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
44494 ATTATTTATT
44504 TAA TAA TAA T-A TAA TAA -AA TAA TAA TAA TAA -AA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
44544 TAACAACCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 6 0.18
3 28 0.82
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:44519 original size:8 final size:8
Alignment explanation
Indices: 44505--44542 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
44495 TTATTTATTT
44505 AATAATAA
1 AATAATAA
*
44513 TATAATAA
1 AATAATAA
44521 AATAAT--
1 AATAATAA
44527 AATAATAA
1 AATAATAA
44535 AATAATAA
1 AATAATAA
44543 TTAACAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AATAATAA
Found at i:44520 original size:11 final size:11
Alignment explanation
Indices: 44504--44543 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
44494 ATTATTTATT
44504 TAATAATAATA
1 TAATAATAATA
44515 TAATAA-AATAA
1 TAATAATAAT-A
*
44526 TAATAATAAAA
1 TAATAATAATA
44537 TAATAAT
1 TAATAAT
44544 TAACAACCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 3 0.12
11 21 0.81
12 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAATAATA
Found at i:44533 original size:14 final size:14
Alignment explanation
Indices: 44508--44543 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
44498 TTTATTTAAT
44508 AATAAT-ATAATAA
1 AATAATAATAATAA
44521 AATAATAATAATAA
1 AATAATAATAATAA
44535 AATAATAAT
1 AATAATAAT
44544 TAACAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:45291 original size:30 final size:30
Alignment explanation
Indices: 45257--45314 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
45247 GATTTGATTT
* * *
45257 TTATAATTGATAAGTAGAATGACTTGGTCG
1 TTATAATCGATAAATAGAATGACATGGTCG
*
45287 TTATAATCGATAAATAGAGTGACATGGT
1 TTATAATCGATAAATAGAATGACATGGT
45315 TATAACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.34
Consensus pattern (30 bp):
TTATAATCGATAAATAGAATGACATGGTCG
Found at i:46345 original size:2 final size:2
Alignment explanation
Indices: 46338--46369 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46328 AATCTTTCCC
46338 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46370 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:46374 original size:2 final size:2
Alignment explanation
Indices: 46369--46401 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46359 TCTCTCTCTC
46369 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46402 GCGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53590 original size:3 final size:3
Alignment explanation
Indices: 53582--53660 Score: 70
Period size: 3 Copynumber: 24.3 Consensus size: 3
53572 TATAACATAC
* *
53582 TAT TAT TAT TGCT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCT ATAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
53629 TAT ATAT ATAT ATAT ATAT ATAT TAT T-T TAT T
1 TAT -TAT -TAT -TAT -TAT -TAT TAT TAT TAT T
53661 TTTTACTATT
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.03
3 43 0.63
4 23 0.34
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:54520 original size:17 final size:17
Alignment explanation
Indices: 54480--54521 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
54470 TTTTAAGAAT
54480 TTTTATTTAAAATAAAAA
1 TTTT-TTTAAAATAAAAA
*
54498 TATTTTTAAAA-AAAATA
1 TTTTTTTAAAATAAAA-A
54515 TTTTTTT
1 TTTTTTT
54522 TCAAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTTTTAAAATAAAAA
Found at i:56765 original size:27 final size:27
Alignment explanation
Indices: 56723--56780 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
56713 CTTTCAATTG
* *
56723 CATCAATGAGTATTTATGAGAATCTAA
1 CATCAATGAGTATTTATGACAATCCAA
*
56750 CATCAATGAGTGTTTATGACAATCCAA
1 CATCAATGAGTATTTATGACAATCCAA
56777 CATC
1 CATC
56781 GTATTTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (27 bp):
CATCAATGAGTATTTATGACAATCCAA
Found at i:57225 original size:23 final size:23
Alignment explanation
Indices: 57199--57248 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
57189 CTATAGGTTC
**
57199 AAATTATAATTATAAATTAGTT-A
1 AAATTATAAAGATAAATTA-TTCA
*
57222 AAATTTTAAAGATAAATTATTCA
1 AAATTATAAAGATAAATTATTCA
57245 AAAT
1 AAAT
57249 AAAGGGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
AAATTATAAAGATAAATTATTCA
Found at i:58221 original size:27 final size:25
Alignment explanation
Indices: 58189--58245 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
58179 TATTAAATTA
58189 ATTTTACATCTTAACATTAAAAAATAT
1 ATTTTA-ATCTTAAC-TTAAAAAATAT
* **
58216 -TTTTTATCTTAACTTATTAAATAT
1 ATTTTAATCTTAACTTAAAAAATAT
58240 ATTTTA
1 ATTTTA
58246 TTTTGTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 9 0.36
25 12 0.48
26 4 0.16
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTAATCTTAACTTAAAAAATAT
Found at i:58244 original size:24 final size:25
Alignment explanation
Indices: 58175--58246 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 25
58165 AACTTAAATC
58175 AACA-TATTAAAT-TAATTTTACATCTT
1 AACATTATTAAATAT-ATTTT--ATCTT
** *
58201 AACATTAAAAAATATTTTTTATCTT
1 AACATTATTAAATATATTTTATCTT
58226 AAC-TTATTAAATATATTTTAT
1 AACATTATTAAATATATTTTAT
58247 TTTGTTCTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 15 0.39
25 8 0.21
26 4 0.11
27 10 0.26
28 1 0.03
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (25 bp):
AACATTATTAAATATATTTTATCTT
Found at i:58283 original size:26 final size:28
Alignment explanation
Indices: 58232--58283 Score: 65
Period size: 26 Copynumber: 1.9 Consensus size: 28
58222 TCTTAACTTA
*
58232 TTAAATATATTTTATTTTGTTCTTAACC
1 TTAAATATATTTTATTTTATTCTTAACC
58260 TTAAA-AT-TTTTATTCTTATT-TTAA
1 TTAAATATATTTTATT-TTATTCTTAA
58284 TTCAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 11 0.50
27 6 0.27
28 5 0.23
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (28 bp):
TTAAATATATTTTATTTTATTCTTAACC
Found at i:58314 original size:29 final size:28
Alignment explanation
Indices: 58196--58361 Score: 105
Period size: 29 Copynumber: 6.0 Consensus size: 28
58186 TTAATTTTAC
*
58196 ATCTTAACATTAAAAAATATTTTTTATCTT
1 ATCTTAA-ATTAAAAAATATTTTAT-TCTT
* *
58226 AACTT--ATT-AAATATATTTTATT-TT
1 ATCTTAAATTAAAAAATATTTTATTCTT
* *
58250 GTTCTTAACCTT--AAAAT-TTTTATTCTT
1 -ATCTTAA-ATTAAAAAATATTTTATTCTT
* *
58277 AT-TTTAATTCAAAAAATATTTTAATCTT
1 ATCTTAAATT-AAAAAATATTTTATTCTT
**
58305 ATCTTAAATTAAAAACATAACTTATTCTT
1 ATCTTAAATTAAAAA-ATATTTTATTCTT
* * *
58334 ATCTTAACTTAAATATTATATTTATTCT
1 ATCTTAAATTAAAAAATAT-TTTATTCT
58362 GATAGTATTT
Statistics
Matches: 104, Mismatches: 20, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
24 4 0.04
25 7 0.07
26 19 0.18
27 14 0.13
28 20 0.19
29 36 0.35
30 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (28 bp):
ATCTTAAATTAAAAAATATTTTATTCTT
Found at i:58486 original size:56 final size:56
Alignment explanation
Indices: 58410--58563 Score: 147
Period size: 56 Copynumber: 2.8 Consensus size: 56
58400 TGTAATTAAA
** * * *
58410 ATAA-AATATATATTTTTAATTTAAGATAAGAATAAAAGATATTTAATAATTTAAGG
1 ATAAGAATATATATTAATAATTTAAGATAAGAATAAAATATATGTAATAAGTT-AGG
* * *
58466 -TAAGAATATATATTAATAATTTAAGTTAAG--T-ATATTTATGTAATAAGTTAGG
1 ATAAGAATATATATTAATAATTTAAGATAAGAATAAAATATATGTAATAAGTTAGG
* *
58518 ATAAGTATATAATTATGTAATAAGTTAAGATAAGAATAAAATATAT
1 ATAAGAATAT-A-TAT-TAATAATTTAAGATAAGAATAAAATATAT
58564 ATTTTAAGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
52 3 0.04
53 21 0.27
54 2 0.03
55 6 0.08
56 38 0.49
58 1 0.01
59 6 0.08
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (56 bp):
ATAAGAATATATATTAATAATTTAAGATAAGAATAAAATATATGTAATAAGTTAGG
Found at i:58538 original size:29 final size:27
Alignment explanation
Indices: 58453--58551 Score: 110
Period size: 26 Copynumber: 3.6 Consensus size: 27
58443 AAAAGATATT
* * * *
58453 TAATAATTTAAGGTAAGAATATATAT-
1 TAATAAGTTAAGATAAGTATATTTATG
* *
58479 TAATAATTTAAGTTAAGTATATTTATG
1 TAATAAGTTAAGATAAGTATATTTATG
*
58506 TAATAAGTTAGGATAAGTATATAATTATG
1 TAATAAGTTAAGATAAGTATAT--TTATG
58535 TAATAAGTTAAGATAAG
1 TAATAAGTTAAGATAAG
58552 AATAAAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.37
27 19 0.30
29 21 0.33
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (27 bp):
TAATAAGTTAAGATAAGTATATTTATG
Found at i:58570 original size:25 final size:25
Alignment explanation
Indices: 58542--58631 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 25
58532 ATGTAATAAG
*
58542 TTAAGATAAGAATAAAATATATATT
1 TTAAGTTAAGAATAAAATATATATT
58567 TTAAGTTAAG-ATAAATATTAAATATATT
1 TTAAGTTAAGAATAAA-A-T--ATATATT
*
58595 TTAAGTTAA-AATAATAAAATATATTT
1 TTAAGTTAAGAATAA-AATATATA-TT
*
58621 TTAGGTTAAGA
1 TTAAGTTAAGA
58632 CAAGAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
24 5 0.09
25 15 0.28
26 11 0.20
27 1 0.02
28 21 0.39
29 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (25 bp):
TTAAGTTAAGAATAAAATATATATT
Found at i:58598 original size:23 final size:25
Alignment explanation
Indices: 58542--58621 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 25
58532 ATGTAATAAG
*
58542 TTAAGATAAGAATAA-AATATATATT
1 TTAAGATAA-AATAATAAAATATATT
* *
58567 TTAAGTTAAGATAAATATTAAATATATT
1 TTAAGATAAAAT-AATA--AAATATATT
*
58595 TTAAGTTAAAATAATAAAATATATT
1 TTAAGATAAAATAATAAAATATATT
58620 TT
1 TT
58622 TAGGTTAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
24 2 0.04
25 21 0.45
26 1 0.02
27 4 0.09
28 19 0.40
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
TTAAGATAAAATAATAAAATATATT
Found at i:66894 original size:15 final size:16
Alignment explanation
Indices: 66876--66908 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
66866 TATTTAAAAT
66876 AAAAACA-TTTTTTCA
1 AAAAACATTTTTTTCA
*
66891 AAAAATATTTTTTTCA
1 AAAAACATTTTTTTCA
66907 AA
1 AA
66909 TCTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAACATTTTTTTCA
Found at i:71686 original size:41 final size:41
Alignment explanation
Indices: 71606--71687 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
71596 ACCAACAGTG
*
71606 CTGAACATTGATACACAAATATACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACAAATATACCAAAGCTGAAATGATAA
* * * *
71647 CTGAACATTGATACACGAATGTACTAAAGTTGAAATGATAA
1 CTGAACATTGATACACAAATATACCAAAGCTGAAATGATAA
71688 GCACTCACTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (41 bp):
CTGAACATTGATACACAAATATACCAAAGCTGAAATGATAA
Found at i:71840 original size:18 final size:18
Alignment explanation
Indices: 71814--71879 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 18
71804 GTCTTATATT
* * *
71814 ATCTAATAACTGTAGATC
1 ATCTGATAACTGAAAATC
71832 ATCTGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
* * * *
71850 ATATGATCACTAAAAATT
1 ATCTGATAACTGAAAATC
71868 ATCTGATAACTG
1 ATCTGATAACTG
71880 TAAACATTAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (18 bp):
ATCTGATAACTGAAAATC
Done.