Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003419.1 Hibiscus syriacus cultivar Beakdansim tig00007197_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: 72424
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:474 original size:21 final size:21
Alignment explanation
Indices: 427--505 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
417 GTTCTTCGGG
* * **
427 ACATATATGTGATCTTTTGGA
1 ACATATATGTGGTCCTTCAGA
* *
448 ACATATATGTGGTCCTTCGGT
1 ACATATATGTGGTCCTTCAGA
* * *
469 ATATAT-TTTGGTCCTTTAGA
1 ACATATATGTGGTCCTTCAGA
489 ACATATATGTGGTCCTT
1 ACATATATGTGGTCCTT
506 AGGGACAATT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.33
21 31 0.67
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (21 bp):
ACATATATGTGGTCCTTCAGA
Found at i:550 original size:20 final size:20
Alignment explanation
Indices: 527--568 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
517 TATGTGATTC
* * *
527 TTCGGATATTTATGTGGTCA
1 TTCGGACATATATGGGGTCA
547 TTCGGACATATATGGGGTCA
1 TTCGGACATATATGGGGTCA
567 TT
1 TT
569 TGGGACAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (20 bp):
TTCGGACATATATGGGGTCA
Found at i:4758 original size:21 final size:21
Alignment explanation
Indices: 4734--4792 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
4724 GGTTCTACGC
*
4734 TCCTTCGAAACATATATGTAA
1 TCCTTCGAAACATATATGCAA
* * **
4755 TCCTTTGGAACATATATGCGG
1 TCCTTCGAAACATATATGCAA
*
4776 TCCTTCGAGACATATAT
1 TCCTTCGAAACATATAT
4793 TTGGTTCTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (21 bp):
TCCTTCGAAACATATATGCAA
Found at i:4857 original size:20 final size:20
Alignment explanation
Indices: 4834--4895 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
4824 GGGACAACTC
*
4834 TATGTGGTCCTTTGGGATAT
1 TATGTGGTCCTTAGGGATAT
* *
4854 TATGTGGTCCTTCGGGAAAT
1 TATGTGGTCCTTAGGGATAT
* *
4874 ATATATGGTCATTAGGGATAT
1 -TATGTGGTCCTTAGGGATAT
4895 T
1 T
4896 TCTACGTGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (20 bp):
TATGTGGTCCTTAGGGATAT
Found at i:8295 original size:54 final size:54
Alignment explanation
Indices: 8166--8550 Score: 538
Period size: 54 Copynumber: 7.3 Consensus size: 54
8156 GGTGTACTAC
*
8166 CGGCACTAA--GTGCAACCCACAGAATTCATAATAAGTTTAT-AA--ATCGTAT
1 CGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTAT
** * *
8215 CAACACTAA--GTGCAACCCACATAATTCATAATATGTTTATGAACGACCGTAT
1 CGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTAT
8267 CGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTAT
1 CGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTAT
* ***
8321 CGGAACTAAGTGTGCAACCCAC-GAAATTCATAATATA-TTTATGAATTTCCGTAT
1 CGGCACTAAGTGTGCAACCCACAG-AATTCATAATA-AGTTTATGAACGACCGTAT
* *
8375 CGGCACTAAGTGTGCAACCCACGGAATTTATAATAAGTTTATGAACGACCGTAT
1 CGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTAT
* *
8429 CGGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACTGTAT
1 CGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTAT
8483 CGGCACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGACCGTAT
1 CGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCGTAT
* *
8537 AGGCACTACGTGTG
1 CGGCACTAAGTGTG
8551 TACCCAAAGA
Statistics
Matches: 300, Mismatches: 26, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
49 36 0.12
50 2 0.01
52 13 0.04
53 3 0.01
54 244 0.81
55 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (54 bp):
CGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTAT
Found at i:10494 original size:18 final size:18
Alignment explanation
Indices: 10471--10505 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10461 TTTTTTTTTT
*
10471 CTTTTATTCTTTCGTGCG
1 CTTTTATTCATTCGTGCG
10489 CTTTTATTCATTCGTGC
1 CTTTTATTCATTCGTGC
10506 CCAAGTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.23, G:0.14, T:0.54
Consensus pattern (18 bp):
CTTTTATTCATTCGTGCG
Found at i:13932 original size:24 final size:24
Alignment explanation
Indices: 13900--13962 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
13890 TTAGTTACGA
*
13900 AAGCTTGTGCTTTTGCAGTC-GATG
1 AAGCTTGTGCTTTTGCA-ACAGATG
13924 AAGCTTGTGCTTTTGCAACAGATG
1 AAGCTTGTGCTTTTGCAACAGATG
*
13948 AAGCTTATGCTTTTG
1 AAGCTTGTGCTTTTG
13963 TAGCATATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (24 bp):
AAGCTTGTGCTTTTGCAACAGATG
Found at i:16801 original size:23 final size:23
Alignment explanation
Indices: 16771--16861 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
16761 GTTCCACGTA
16771 TTTGTCCCGAAGGACCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
* *
16794 TTTGTCCCGAATGATCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
* * *
16817 TTTATCCTGAAAGACCACATAGT
1 TTTGTCCCGAAGGACCACATAGT
*
16840 TTTGTCCCAAAGGACCACATAG
1 TTTGTCCCGAAGGACCACATAG
16862 AACCCTCGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (23 bp):
TTTGTCCCGAAGGACCACATAGT
Found at i:17617 original size:22 final size:22
Alignment explanation
Indices: 17589--17646 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
17579 ACTCTTCTTG
17589 TAGTACCGATACTTCTCTTATA
1 TAGTACCGATACTTCTCTTATA
17611 TAGTACCGATACTTCTCTTATA
1 TAGTACCGATACTTCTCTTATA
*
17633 TGGTACCGATACTT
1 TAGTACCGATACTT
17647 ACTTCAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (22 bp):
TAGTACCGATACTTCTCTTATA
Found at i:20639 original size:13 final size:14
Alignment explanation
Indices: 20623--20683 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
20613 AATAAAATTA
20623 AATA-AATAAATAT
1 AATATAATAAATAT
20636 AATATAATAAATAT
1 AATATAATAAATAT
20650 AA-ATAATAAATAAT
1 AATATAATAAAT-AT
20664 AATATAACT-AATAT
1 AATATAA-TAAATAT
*
20678 TATATA
1 AATATA
20684 TATATAAAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
13 13 0.30
14 22 0.51
15 7 0.16
16 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AATATAATAAATAT
Found at i:20644 original size:18 final size:16
Alignment explanation
Indices: 20612--20662 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
20602 GAACTGTTAA
20612 AAATAAAAT--TAAAT
1 AAATAAAATAATAAAT
20626 AAATAAATATAATATAAT
1 AAATAAA-ATAATA-AAT
20644 AAATATAAATAATAAAT
1 AAATA-AAATAATAAAT
20661 AA
1 AA
20663 TAATATAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.22
15 2 0.06
17 7 0.22
18 14 0.44
19 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAAAATAATAAAT
Found at i:20651 original size:20 final size:19
Alignment explanation
Indices: 20623--20676 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
20613 AATAAAATTA
20623 AATAA-ATAAAT-ATAATAT
1 AATAATATAAATAATAA-AT
20641 AATAAATATAAATAATAAAT
1 AAT-AATATAAATAATAAAT
*
20661 AATAATATAACTAATA
1 AATAATATAAATAATA
20677 TTATATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.09
19 14 0.44
20 11 0.34
21 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAATATAAATAATAAAT
Found at i:20652 original size:28 final size:27
Alignment explanation
Indices: 20617--20679 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 27
20607 GTTAAAAATA
20617 AAATTAAATAAATAAAT-ATAATATAAT
1 AAATTAAAT-AATAAATAATAATATAAT
20644 AAATATAAATAATAAATAATAATATAACT
1 AAAT-TAAATAATAAATAATAATATAA-T
20673 AATATTA
1 AA-ATTA
20680 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
27 11 0.34
28 14 0.44
29 5 0.16
30 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATTAAATAATAAATAATAATATAAT
Found at i:20665 original size:14 final size:13
Alignment explanation
Indices: 20609--20661 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 13
20599 TTGGAACTGT
20609 TAAA-AATAAA-A
1 TAAATAATAAATA
20620 TTAAATAAATAAATA
1 -TAAAT-AATAAATA
20635 TAATATAATAAATA
1 TAA-ATAATAAATA
20649 TAAATAATAAATA
1 TAAATAATAAATA
20662 ATAATATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 4 0.11
13 10 0.27
14 20 0.54
15 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAATAATAAATA
Found at i:20690 original size:28 final size:28
Alignment explanation
Indices: 20617--20670 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
20607 GTTAAAAATA
20617 AAAT-TAAATAAATAAAT-ATAATATAAT
1 AAATATAAAT-AATAAATAATAATATAAT
20644 AAATATAAATAATAAATAATAATATAA
1 AAATATAAATAATAAATAATAATATAA
20671 CTAATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATATAAATAATAAATAATAATATAAT
Found at i:20837 original size:62 final size:60
Alignment explanation
Indices: 20771--20892 Score: 165
Period size: 62 Copynumber: 2.0 Consensus size: 60
20761 AAAAATTATA
**
20771 TATATTATATATGTTTTCAAAAACCG-TTTTAAAAACTATATATATATATATGTTTTCAAAAT
1 TATATTATATACATTTTCAAAAACCGTTTTTAAAAACTATATAT-T-T-TATGTTTTCAAAAT
* * *
20833 TATATTATATACATTTTCGAAAACTGTTTTTTAAAACTATATATTTTATGTTTTCAAAAT
1 TATATTATATACATTTTCAAAAACCGTTTTTAAAAACTATATATTTTATGTTTTCAAAAT
20893 ACGTTTTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 14 0.26
61 1 0.02
62 23 0.43
63 16 0.30
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (60 bp):
TATATTATATACATTTTCAAAAACCGTTTTTAAAAACTATATATTTTATGTTTTCAAAAT
Found at i:20849 original size:23 final size:25
Alignment explanation
Indices: 20809--20855 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
20799 TTAAAAACTA
**
20809 TATATATATATATGTTTTC-AAAAT
1 TATATATATATACATTTTCGAAAAT
20833 TATAT-TATATACATTTTCGAAAA
1 TATATATATATACATTTTCGAAAA
20856 CTGTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (25 bp):
TATATATATATACATTTTCGAAAAT
Found at i:20922 original size:87 final size:85
Alignment explanation
Indices: 20823--20990 Score: 216
Period size: 87 Copynumber: 2.0 Consensus size: 85
20813 TATATATATG
* * *
20823 TTTTCAAAATTATAT-TATATACATTTTCGAA-AACTGTTTT-TTAAAACTATATATTTTATGTT
1 TTTTCAAAATTATATAT-TATACATTTTC-AATAACTGTTTTCTAAAAACTATATA-TATACGTT
*
20885 TTCAAAATACGTTTTCAAAAACCGT
63 TTAAAAATA--TTTTCAAAAACCGT
* *
20910 TTTTCGAAATTATATATTATATATTTTCAATAACTGTTTTCTAAAAACTATATATATACGTTTTA
1 TTTTCAAAATTATATATTATACATTTTCAATAACTGTTTTCTAAAAACTATATATATACGTTTTA
20975 AAAATATTTTCAAAAA
66 AAAATATTTTCAAAAA
20991 TTATACTGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
85 10 0.14
86 2 0.03
87 47 0.65
88 13 0.18
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (85 bp):
TTTTCAAAATTATATATTATACATTTTCAATAACTGTTTTCTAAAAACTATATATATACGTTTTA
AAAATATTTTCAAAAACCGT
Found at i:20949 original size:50 final size:50
Alignment explanation
Indices: 20841--20957 Score: 128
Period size: 50 Copynumber: 2.3 Consensus size: 50
20831 ATTATATTAT
* * * * * *
20841 ATACATTTTCGAAAACTGTTTTTTAAAACTATATATTTTATGTTTTCAAA
1 ATACGTTTTCAAAAACCGTTTTTCAAAACTATATATTATATATTTTCAAA
* * *
20891 ATACGTTTTCAAAAACCGTTTTTCGAAATTATATATTATATATTTTCAAT
1 ATACGTTTTCAAAAACCGTTTTTCAAAACTATATATTATATATTTTCAAA
20941 A-ACTGTTTTCTAAAAAC
1 ATAC-GTTTTC-AAAAAC
20958 TATATATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
49 2 0.04
50 48 0.86
51 6 0.11
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (50 bp):
ATACGTTTTCAAAAACCGTTTTTCAAAACTATATATTATATATTTTCAAA
Found at i:25887 original size:15 final size:15
Alignment explanation
Indices: 25867--25897 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25857 ATTATCGATG
25867 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
25882 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
25897 A
1 A
25898 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:31599 original size:22 final size:21
Alignment explanation
Indices: 31574--31621 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
31564 TTCTTTAAAC
*
31574 TAAAATTTATGAAAATTAA-ATA
1 TAAAATTT-T-AAAACTAATATA
31596 T-AAATTTTAAAACTAATATA
1 TAAAATTTTAAAACTAATATA
31616 TAAAAT
1 TAAAAT
31622 AAATATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 7 0.30
20 5 0.22
21 10 0.43
22 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATTTTAAAACTAATATA
Found at i:32317 original size:5 final size:5
Alignment explanation
Indices: 32278--32318 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
32268 AGTTGCCATC
* * *
32278 ACCCC ACCCC ACCCC ACCCT ACCCT ACCCT ACCCT ACCCT A
1 ACCCT ACCCT ACCCT ACCCT ACCCT ACCCT ACCCT ACCCT A
32319 TAAATATCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.22, C:0.66, G:0.00, T:0.12
Consensus pattern (5 bp):
ACCCT
Found at i:32434 original size:28 final size:27
Alignment explanation
Indices: 32402--32467 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 27
32392 TTATAAGGTA
32402 TATTTTATT-CTATTTAATATTTTGTTAG
1 TATTTTATTACTATTTAA-ATTTT-TTAG
*
32430 TATTTTATTTAATTATTTAAATTTTTTAG
1 TATTTTA-TT-ACTATTTAAATTTTTTAG
32459 TATTTTATT
1 TATTTTATT
32468 TAATTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 9 0.26
29 13 0.38
30 5 0.15
31 7 0.21
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (27 bp):
TATTTTATTACTATTTAAATTTTTTAG
Found at i:32463 original size:29 final size:31
Alignment explanation
Indices: 32412--32476 Score: 116
Period size: 29 Copynumber: 2.2 Consensus size: 31
32402 TATTTTATTC
32412 TATTTAATATTTTGTTAGTATTTTATTTAAT
1 TATTTAATATTTTGTTAGTATTTTATTTAAT
32443 TATTTAA-ATTTT-TTAGTATTTTATTTAAT
1 TATTTAATATTTTGTTAGTATTTTATTTAAT
32472 TATTT
1 TATTT
32477 TATTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 22 0.65
30 5 0.15
31 7 0.21
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (31 bp):
TATTTAATATTTTGTTAGTATTTTATTTAAT
Found at i:32477 original size:13 final size:13
Alignment explanation
Indices: 32430--32481 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
32420 ATTTTGTTAG
32430 TATTTTATTTAAT
1 TATTTTATTTAAT
* * *
32443 TATTTAAATTTTTTAG
1 TATTT---TATTTAAT
32459 TATTTTATTTAAT
1 TATTTTATTTAAT
32472 TATTTTATTT
1 TATTTTATTT
32482 TATTTGCAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
13 20 0.67
16 10 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:38884 original size:64 final size:65
Alignment explanation
Indices: 38760--38915 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 65
38750 ACACCTCATT
* * * * *
38760 TCGAATACATTTTGTGTACCGATGCACAATGCATGCATCGATGCATTCCTGAATATTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAATCCATGCATCAATGAATTCCAGAATATTTTGAAACA
**
38824 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATGCATCAATGAACTT-CAGGCTCA-TTTGAA
1 TCGAATGCATTTTGTGTACCGATGCACA-ATCCATGCATCAATGAA-TTCCAGAAT-ATTTTGAA
38886 ACA
63 ACA
* * * *
38889 TCGAATGTATTTTATGCATCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
38916 CCCTAGTGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
64 46 0.60
65 31 0.40
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAATCCATGCATCAATGAATTCCAGAATATTTTGAAACA
Found at i:46641 original size:21 final size:21
Alignment explanation
Indices: 46617--46656 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46607 AAGACTTTAT
46617 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
46638 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
46657 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:50553 original size:23 final size:22
Alignment explanation
Indices: 50472--50553 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
50462 ATACTAGTTA
*
50472 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CTCTTGAAT
* * *
50495 GTGCATCGATTCAC-CATGAAG
1 GTGCATCGATGCACTCTTGAAT
*
50516 GTGCACCGATGCACTCTTTGAAT
1 GTGCATCGATGCACTC-TTGAAT
*
50539 GTGCATCGATACACT
1 GTGCATCGATGCACT
50554 AGTCGGGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
21 17 0.35
22 2 0.04
23 29 0.60
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCACTCTTGAAT
Found at i:53329 original size:64 final size:65
Alignment explanation
Indices: 53205--53360 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 65
53195 ACACCTCATT
* * *
53205 TCGAATGCATTTTGTGTACCGATGCACAAGGCACGCATCAATGCACTCCTGAATATTTTG-AACA
1 TCGAATGCATTTTGTGTACCGATGCACAAGCCACGCATCAATGCAATCCAGAATATTTTGAAACA
* * * **
53269 TCGAATGCATTTTGTGTACCGATGCAC-AGACCATGCATCGATGTAATCCAGGCTCA-TTTGAAA
1 TCGAATGCATTTTGTGTACCGATGCACAAG-CCACGCATCAATGCAATCCAGAAT-ATTTTGAAA
53332 CA
64 CA
* * * *
53334 TCGAATGTATTTTATGCATCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
53361 CCTTAGTGTA
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.03
64 47 0.61
65 28 0.36
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGCCACGCATCAATGCAATCCAGAATATTTTGAAACA
Found at i:54138 original size:29 final size:30
Alignment explanation
Indices: 54074--54142 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
54064 AACTCAACAA
*
54074 GATTGTTGGGTGATATTTACGGGTTGAAAG
1 GATTGTTGTGTGATATTTACGGGTTGAAAG
* **
54104 GTTTGTTGTGTGAGT-TTT-CGGGTTGAGCG
1 GATTGTTGTGTGA-TATTTACGGGTTGAAAG
54133 GATTGTTGTG
1 GATTGTTGTG
54143 AATGTGTACG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 18 0.55
30 14 0.42
31 1 0.03
ACGTcount: A:0.14, C:0.04, G:0.39, T:0.42
Consensus pattern (30 bp):
GATTGTTGTGTGATATTTACGGGTTGAAAG
Found at i:54330 original size:51 final size:50
Alignment explanation
Indices: 54218--54341 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 50
54208 ATAATTATAA
* * * *
54218 AAGGCGCGACCCATGTACCACGTCTATCTGGCGCGTGTGTCACACGAAAG
1 AAGGCGCGGCCCATGCACCACGCCTATCTGGCGCATGTGTCACACGAAAG
* * *
54268 ATAGGCACGGCCCATGCACCGCGCCTATCTGGCGCATGTGTCACACGACAG
1 A-AGGCGCGGCCCATGCACCACGCCTATCTGGCGCATGTGTCACACGAAAG
* *
54319 TAAGGCGCGGCCTATACACCACG
1 -AAGGCGCGGCCCATGCACCACG
54342 ACAGTAAGAC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 1 0.02
51 59 0.97
52 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.27, T:0.16
Consensus pattern (50 bp):
AAGGCGCGGCCCATGCACCACGCCTATCTGGCGCATGTGTCACACGAAAG
Found at i:54346 original size:27 final size:27
Alignment explanation
Indices: 54311--54365 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
54301 GCATGTGTCA
*
54311 CACGACAGTAAGGCGCGGCCTATACAC
1 CACGACAGTAAGACGCGGCCTATACAC
54338 CACGACAGTAAGACGCGGCCTATACAC
1 CACGACAGTAAGACGCGGCCTATACAC
54365 C
1 C
54366 GCGCCTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.35, G:0.24, T:0.11
Consensus pattern (27 bp):
CACGACAGTAAGACGCGGCCTATACAC
Found at i:56185 original size:21 final size:21
Alignment explanation
Indices: 56159--56212 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
56149 AGAGACTTGT
56159 AGTATCAGTACTACGTCTATC
1 AGTATCAGTACTACGTCTATC
56180 AGTATCAGTACTACGTCTATC
1 AGTATCAGTACTACGTCTATC
*
56201 AGTATCAATACT
1 AGTATCAGTACT
56213 CCCTGCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (21 bp):
AGTATCAGTACTACGTCTATC
Found at i:58923 original size:4 final size:4
Alignment explanation
Indices: 58914--58972 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
58904 AAAAAAACAA
58914 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
58962 ATAC ATAC ATA
1 ATAC ATAC ATA
58973 TACATATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:59433 original size:19 final size:19
Alignment explanation
Indices: 59406--59444 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
59396 CTTCAAAGCA
59406 AAAACTGGATGGTATCGAT
1 AAAACTGGATGGTATCGAT
*
59425 AAAATTGGATGGTATCGAT
1 AAAACTGGATGGTATCGAT
59444 A
1 A
59445 CTAAGTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (19 bp):
AAAACTGGATGGTATCGAT
Found at i:59542 original size:20 final size:20
Alignment explanation
Indices: 59479--59546 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
59469 CTACAAGAAT
* **
59479 AGTATCGGTACTATATGAAC
1 AGTATCGATACTGGATGAAC
* * *
59499 AATATTGATACTGAGCAAGAAC
1 AGTATCGATACTG-G-ATGAAC
59521 AGTATCGATACTGGATGAAC
1 AGTATCGATACTGGATGAAC
59541 AGTATC
1 AGTATC
59547 AGTACTAAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
20 20 0.54
21 1 0.03
22 16 0.43
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (20 bp):
AGTATCGATACTGGATGAAC
Found at i:65451 original size:20 final size:20
Alignment explanation
Indices: 65423--65460 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
65413 AACAGTATCG
*
65423 GGTATTGTTATAGTAGTACC
1 GGTACTGTTATAGTAGTACC
65443 GGTACTGTTATAGTAGTA
1 GGTACTGTTATAGTAGTA
65461 TCAGTACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (20 bp):
GGTACTGTTATAGTAGTACC
Found at i:65467 original size:20 final size:20
Alignment explanation
Indices: 65428--65468 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
65418 TATCGGGTAT
*
65428 TGTTATAGTAGTACCGGTAC
1 TGTTATAGTAGTACCAGTAC
*
65448 TGTTATAGTAGTATCAGTAC
1 TGTTATAGTAGTACCAGTAC
65468 T
1 T
65469 ACTTTGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTTATAGTAGTACCAGTAC
Found at i:65869 original size:34 final size:34
Alignment explanation
Indices: 65780--65869 Score: 155
Period size: 34 Copynumber: 2.6 Consensus size: 34
65770 ATGACTATCA
*
65780 TATCTTAAT-TCGTATGTTAACACTTAGCTCGGAT
1 TATCTTAATAT-GTATGTTAACGCTTAGCTCGGAT
65814 TATCTTAATATGTATGTTAACGCTTAGCTCGGAT
1 TATCTTAATATGTATGTTAACGCTTAGCTCGGAT
65848 TATCTTAATATGTATGTTAACG
1 TATCTTAATATGTATGTTAACG
65870 TTTAACTCAG
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
34 53 0.98
35 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (34 bp):
TATCTTAATATGTATGTTAACGCTTAGCTCGGAT
Found at i:70584 original size:6 final size:6
Alignment explanation
Indices: 70573--70603 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
70563 AGCTCTCCTC
70573 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT C
1 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT C
70604 TTCTCTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCCTTT
Done.