Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004784.1 Hibiscus syriacus cultivar Beakdansim tig00010787_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: 61396
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:937 original size:21 final size:21
Alignment explanation
Indices: 894--938 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
884 TTTATTCGAC
**
894 TTTTAAATATTATCTCTTTTA
1 TTTTAAATATTATCTCTAATA
915 TTTTCAAATATTATCT-TAATA
1 TTTT-AAATATTATCTCTAATA
936 TTT
1 TTT
939 ATATGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAATATTATCTCTAATA
Found at i:1579 original size:22 final size:22
Alignment explanation
Indices: 1551--1602 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1541 GCTTTGCATG
1551 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
1573 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
1595 CGCC-TGCA
1 CGCCATGCA
1603 TGGAGTGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.21, C:0.31, G:0.35, T:0.13
Consensus pattern (22 bp):
CGCCATGCACGTCGGAAGAGGT
Found at i:1705 original size:29 final size:29
Alignment explanation
Indices: 1648--1706 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1638 AGGGCGCAGG
* *
1648 ACAAGGTCGCCCAGCGTGCATGGCGACCT
1 ACAAGGTCGCCCAGAGGGCATGGCGACCT
*
1677 ACAAGGTCGCCCCGGAGGGCATGGC-ACCT
1 ACAAGGTCG-CCCAGAGGGCATGGCGACCT
1706 A
1 A
1707 TGCTGGGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.22, C:0.34, G:0.32, T:0.12
Consensus pattern (29 bp):
ACAAGGTCGCCCAGAGGGCATGGCGACCT
Found at i:6813 original size:36 final size:36
Alignment explanation
Indices: 6772--6847 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
6762 ATTTTCGGGA
*
6772 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
6808 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
6844 TTTT
1 TTTT
6848 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:7289 original size:15 final size:15
Alignment explanation
Indices: 7269--7298 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7259 TATCACAATC
7269 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
7284 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
7299 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:11812 original size:36 final size:36
Alignment explanation
Indices: 11771--11846 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
11761 ATTTTCGGGA
*
11771 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
11807 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
11843 TTTT
1 TTTT
11847 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:12905 original size:8 final size:8
Alignment explanation
Indices: 12892--12944 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
12882 TCAAACTATA
12892 ATAAAAAT
1 ATAAAAAT
12900 ATAAAAAAT
1 AT-AAAAAT
12909 ATAAAAAT
1 ATAAAAAT
12917 A-AAAATAT
1 ATAAAA-AT
**
12925 ATAATTAT
1 ATAAAAAT
12933 AATAAAAAT
1 -ATAAAAAT
12942 ATA
1 ATA
12945 TTTTGTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 4 0.11
8 17 0.46
9 16 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
ATAAAAAT
Found at i:12906 original size:52 final size:51
Alignment explanation
Indices: 12810--12910 Score: 141
Period size: 52 Copynumber: 2.0 Consensus size: 51
12800 ATATTTACGC
* *
12810 TTATATATGAATCATATAATTTAAACTATAATAAATTCAAAAAAAATATTA
1 TTATATATGAATCATATAATTCAAACTATAATAAAATCAAAAAAAATATTA
* *
12861 TTATATATGAATTATATCAATTCAAACTATAATAAAAAT-ATAAAAAATAT
1 TTATATATGAATCATAT-AATTCAAACTATAAT-AAAATCAAAAAAAATAT
12911 AAAAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 16 0.36
52 24 0.55
53 4 0.09
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (51 bp):
TTATATATGAATCATATAATTCAAACTATAATAAAATCAAAAAAAATATTA
Found at i:12909 original size:15 final size:15
Alignment explanation
Indices: 12891--12928 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
12881 TTCAAACTAT
12891 AATA-AAAATATAAAA
1 AATATAAAA-ATAAAA
12906 AATATAAAAATAAAA
1 AATATAAAAATAAAA
12921 ATATATAA
1 A-ATATAA
12929 TTATAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATATAAAAATAAAA
Found at i:19043 original size:18 final size:19
Alignment explanation
Indices: 19017--19061 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
19007 AATTAATCAC
19017 TTATGATCACAT-ATCACAT
1 TTAT-ATCACATGATCACAT
*
19036 TTATATCACATGGTCACAT
1 TTATATCACATGATCACAT
19055 TTCATAT
1 TT-ATAT
19062 ATCACTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 12 0.52
20 4 0.17
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (19 bp):
TTATATCACATGATCACAT
Found at i:22645 original size:21 final size:21
Alignment explanation
Indices: 22619--22660 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
22609 CCAACTCATT
22619 ACAATGTATGAACACTTAATA
1 ACAATGTATGAACACTTAATA
22640 ACAATGTATGAACACTTAATA
1 ACAATGTATGAACACTTAATA
22661 CGCTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
ACAATGTATGAACACTTAATA
Found at i:23287 original size:18 final size:20
Alignment explanation
Indices: 23261--23305 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
23251 AATTAATCAC
23261 TTATGATCACAT-ATCACA-T
1 TTAT-ATCACATGATCACATT
*
23280 TTATATCACATGGTCACATT
1 TTATATCACATGATCACATT
23300 TTATAT
1 TTATAT
23306 ATCACTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (20 bp):
TTATATCACATGATCACATT
Found at i:24454 original size:24 final size:24
Alignment explanation
Indices: 24427--24478 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
24417 AGTTCGATTG
24427 AAGCCTAAAATTTGAGCTCAATTA
1 AAGCCTAAAATTTGAGCTCAATTA
*
24451 AAGCCTAAAATTTGAGCTCAATTG
1 AAGCCTAAAATTTGAGCTCAATTA
24475 AAGC
1 AAGC
24479 GAAAGAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (24 bp):
AAGCCTAAAATTTGAGCTCAATTA
Found at i:32355 original size:2 final size:2
Alignment explanation
Indices: 32348--32456 Score: 82
Period size: 2 Copynumber: 60.5 Consensus size: 2
32338 CCGCCTCGAT
32348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
32388 TA T- TT TA TA TA T- TT TA TA T- TA -A T- TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
32423 TT TA TA TA TT TCA TA T- TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
32457 TTTAGGGTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 28
0.73 0.04 0.23
Matches are distributed among these distances:
1 13 0.15
2 74 0.84
3 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:32410 original size:25 final size:25
Alignment explanation
Indices: 32347--32431 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 25
32337 CCCGCCTCGA
32347 TTATATATATATATATATATATATATAT
1 TTATATATA-ATA-ATATATATATAT-T
* *
32375 ATATATATAATAATATTTTATATATT
1 TTATATATAATAATA-TATATATATT
*
32401 TTATAT-TAATTATATATA-ATATT
1 TTATATATAATAATATATATATATT
32424 TTATATAT
1 TTATATAT
32432 TTCATATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
23 11 0.22
24 4 0.08
25 7 0.14
26 9 0.18
27 11 0.22
28 8 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTATATATAATAATATATATATATT
Found at i:32420 original size:32 final size:33
Alignment explanation
Indices: 32394--32460 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
32384 ATAATATTTT
32394 ATATATTTTATATTAAT-TATATATAATATTTT
1 ATATATTTTATATTAATATATATATAATATTTT
*
32426 ATATATTTCATATTAATTATATATATAATATTTT
1 ATATATTTTATATTAA-TATATATATAATATTTT
32460 A
1 A
32461 GGGTTCGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 15 0.47
33 1 0.03
34 16 0.50
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
ATATATTTTATATTAATATATATATAATATTTT
Found at i:34371 original size:25 final size:24
Alignment explanation
Indices: 34343--34442 Score: 66
Period size: 25 Copynumber: 4.0 Consensus size: 24
34333 ATATTATTCT
34343 AAATATATATTTAATAAATTTTCCA
1 AAATATATATTT-ATAAATTTTCCA
*
34368 AAATAATAATATTT-TCAATTTTAACCCA
1 AAAT-AT-ATATTTATAAATTTT---CCA
* *
34396 AAATAT-TATCTAT--ATTATT-CT
1 AAATATATATTTATAAATT-TTCCA
34417 AAATATATATTTAATAAATTTTCCA
1 AAATATATATTT-ATAAATTTTCCA
34442 A
1 A
34443 TTCTAAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 24
0.67 0.06 0.28
Matches are distributed among these distances:
21 7 0.12
22 4 0.07
23 2 0.03
24 5 0.09
25 22 0.38
26 3 0.05
27 8 0.14
28 7 0.12
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (24 bp):
AAATATATATTTATAAATTTTCCA
Found at i:34380 original size:74 final size:74
Alignment explanation
Indices: 34293--34442 Score: 300
Period size: 74 Copynumber: 2.0 Consensus size: 74
34283 GATTTTGTTA
34293 AAAATAATAATATTTTCAATTTTAACCCAAAATATTATCTATATTATTCTAAATATATATTTAAT
1 AAAATAATAATATTTTCAATTTTAACCCAAAATATTATCTATATTATTCTAAATATATATTTAAT
34358 AAATTTTCC
66 AAATTTTCC
34367 AAAATAATAATATTTTCAATTTTAACCCAAAATATTATCTATATTATTCTAAATATATATTTAAT
1 AAAATAATAATATTTTCAATTTTAACCCAAAATATTATCTATATTATTCTAAATATATATTTAAT
34432 AAATTTTCC
66 AAATTTTCC
34441 AA
1 AA
34443 TTCTAAATAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (74 bp):
AAAATAATAATATTTTCAATTTTAACCCAAAATATTATCTATATTATTCTAAATATATATTTAAT
AAATTTTCC
Found at i:34525 original size:31 final size:31
Alignment explanation
Indices: 34482--34560 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
34472 TAATAAATAT
* *
34482 ATATTTAACAAATTAGTCAATAATGTTATCG
1 ATATGTAACAAATTAGTCAATAACGTTATCG
* * *
34513 ATTTG-AAGCAAATT-GTTCACTAACGTTATTG
1 ATATGTAA-CAAATTAG-TCAATAACGTTATCG
34544 ATATGTAACAAATTAGT
1 ATATGTAACAAATTAGT
34561 AATTAGTGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
30 3 0.08
31 32 0.84
32 3 0.08
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (31 bp):
ATATGTAACAAATTAGTCAATAACGTTATCG
Found at i:34838 original size:15 final size:15
Alignment explanation
Indices: 34818--34965 Score: 163
Period size: 15 Copynumber: 9.5 Consensus size: 15
34808 TAATAAGGTT
34818 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
34833 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
* *
34848 ATTTATTATAAAAAA
1 ATTTATTTTAAAATA
* *
34863 ATTTATTATAAAAAA
1 ATTTATTTTAAAATA
34878 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
34893 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
34908 ATTTATTATAAAATATGAA
1 ATTTATT-TTAAA-AT--A
*
34927 TTGATTTATTTTTAAATA
1 ---ATTTATTTTAAAATA
34945 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
34959 ATTTATT
1 ATTTATT
34966 AGTATGGATT
Statistics
Matches: 119, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.10
15 87 0.73
16 4 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 3 0.03
22 7 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:34943 original size:22 final size:22
Alignment explanation
Indices: 34908--35012 Score: 61
Period size: 22 Copynumber: 4.7 Consensus size: 22
34898 TTTTAAAATA
* *
34908 ATTTATTATAAAATATGAATTG
1 ATTTATTTTTAAATATGAATTG
* * *
34930 ATTTATTTTTAAATAATTTATTTTA
1 ATTTATTTTTAAAT-A-TGA-ATTG
* * * *
34955 AATAATTTATT-AGTATGGATTG
1 ATTTATTT-TTAAATATGAATTG
* *
34977 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTTAAATATGAATTG
34999 ATTTA-TTTTAAATA
1 ATTTATTTTTAAATA
35013 ATTTATTAGT
Statistics
Matches: 61, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
21 9 0.15
22 35 0.57
23 2 0.03
24 3 0.05
25 10 0.16
26 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
ATTTATTTTTAAATATGAATTG
Found at i:34955 original size:14 final size:14
Alignment explanation
Indices: 34930--34965 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
34920 ATATGAATTG
34930 ATTTATTTTTAAATA
1 ATTTA-TTTTAAATA
34945 ATTTATTTTAAATA
1 ATTTATTTTAAATA
34959 ATTTATT
1 ATTTATT
34966 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:34983 original size:32 final size:32
Alignment explanation
Indices: 34945--35042 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 32
34935 TTTTTAAATA
34945 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
34977 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
34999 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
35031 ATTTATTTTAAA
1 ATTTATTTTAAA
35043 ATATGGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 14 0.25
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 26 0.46
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:35011 original size:54 final size:54
Alignment explanation
Indices: 34945--35493 Score: 446
Period size: 54 Copynumber: 10.1 Consensus size: 54
34935 TTTTTAAATA
34945 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
34999 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
35053 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT--A-AA---A----TATGGATTG
** * * * **
35111 ATTTATTTTAAA-ATATAGATTGGT-T-TATT-ATTGTAGTTGTATGGAT-T-GATTTAG
1 ATTTATTTTAAATA-ATTTATTAGTATGGATTGATT-TA-TTTTA-AAATATGGA-TT-G
*
35165 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
35219 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * *** **
35263 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAAATTG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
35325 ATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
35379 ATTTATTTTAAATAATTTATTAGCATGTATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
35433 ATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
35487 ATTTATT
1 ATTTATT
35494 ATTGTAGTTG
Statistics
Matches: 402, Mismatches: 43, Indels: 100
0.74 0.08 0.18
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
46 1 0.00
47 5 0.01
48 44 0.11
49 4 0.01
50 8 0.02
51 4 0.01
52 6 0.01
53 3 0.01
54 219 0.54
55 12 0.03
56 11 0.03
57 5 0.01
58 29 0.07
59 2 0.00
60 4 0.01
61 5 0.01
62 20 0.05
63 9 0.02
64 4 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:35085 original size:80 final size:80
Alignment explanation
Indices: 34990--35385 Score: 666
Period size: 80 Copynumber: 4.9 Consensus size: 80
34980 TATTTTAAAA
*
34990 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
35055 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
* * * *
35070 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAGATTGGT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
35135 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
35150 TATGGATTGATTTAGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGG
1 TAT-G---GA-TT-GATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGG
35215 ATTGATTTATTATTGTAGTTG
60 ATTGATTTATTATTGTAGTTG
35236 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
35301 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
** *
35316 TATAAATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
35381 TTATT
66 TTATT
35386 TTAAATAATT
Statistics
Matches: 300, Mismatches: 10, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
80 219 0.73
81 3 0.01
82 2 0.01
84 2 0.01
85 3 0.01
86 71 0.24
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:35114 original size:18 final size:18
Alignment explanation
Indices: 35067--35118 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
35057 ATTATTGTAG
35067 TTGTATGGATTGATTTAT
1 TTGTATGGATTGATTTAT
* *
35085 TT-TA---AATAATTTAT
1 TTGTATGGATTGATTTAT
35099 TTGTATGGATTGATTTAT
1 TTGTATGGATTGATTTAT
35117 TT
1 TT
35119 TAAAATATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 10 0.38
15 2 0.08
17 2 0.08
18 12 0.46
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (18 bp):
TTGTATGGATTGATTTAT
Found at i:35118 original size:166 final size:164
Alignment explanation
Indices: 34945--35493 Score: 568
Period size: 166 Copynumber: 3.4 Consensus size: 164
34935 TTTTTAAATA
*
34945 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTGATTTATTTTA
1 ATTTATTTTAAA-AATTTATT-GTATGGATTGATTTATTGTAGAAATATGGATTGATTTATTTTA
*
35009 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATG
64 AATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATG
35074 GATTGATTTATTTTAAATAATTTATTTGTATGGATTG
129 GATTGATTTATTTTAAATAATTTA-TTGTATGGATTG
** * *
35111 ATTTATTTTAAAATATAGATTGGT-T-TATT-ATTGTAGTTGTATG-GAT-T-GATTTAGATTTA
1 ATTTATTTTAAAA-ATTTATT-GTATGGATTGATT-TA-TTGTA-GAAATATGGA-TT-GATTTA
35170 TTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
59 TTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTT
*
35235 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
124 GTATGGATTGATTTATTTTAAATAATTTATT-GTATGGATTG
* * * *** **
35277 ATTTATTTT-AAAA--TA-TGGATTGATTTA-TTATTGTAGTTGTATAAATTGATTTATTTTAAA
1 ATTTATTTTAAAAATTTATTGTATGGATTGATTTATTGTAGAAATATGGATTGATTTATTTTAAA
* *
35337 TAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTA
66 TAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-
* *
35401 GCATGTATTGATTTATTTT--A-AA---A---TATGGATTG
124 GTATGGATTGATTTATTTTAAATAATTTATTGTATGGATTG
* *
35433 ATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTA-AAATATGGATTGATTTATT
1 ATTTATTTTAAA-AATTTA-TTGTATGGATTGATTTATTGTAGAAATATGGATTGATTTATT
35494 ATTGTAGTTG
Statistics
Matches: 326, Mismatches: 29, Indels: 60
0.79 0.07 0.14
Matches are distributed among these distances:
156 17 0.05
157 2 0.01
158 2 0.01
159 1 0.00
160 69 0.21
161 7 0.02
162 30 0.09
163 13 0.04
164 11 0.03
165 16 0.05
166 158 0.48
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (164 bp):
ATTTATTTTAAAAATTTATTGTATGGATTGATTTATTGTAGAAATATGGATTGATTTATTTTAAA
TAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGA
TTGATTTATTTTAAATAATTTATTGTATGGATTG
Found at i:35362 original size:32 final size:29
Alignment explanation
Indices: 35321--35587 Score: 125
Period size: 22 Copynumber: 9.9 Consensus size: 29
35311 AGTTGTATAA
35321 ATTGATTTATTTTAAATAATTTATTAGTATG
1 ATTGATTTATTTTAAATAATTTATT-G-ATG
35352 CATTGATTTATTTT-AA-AA--TA-TG--G
1 -ATTGATTTATTTTAAATAATTTATTGATG
35375 ATTGATTTATTTTAAATAATTTATTAGCATG
1 ATTGATTTATTTTAAATAATTTATT-G-ATG
35406 TATTGATTTATTTT-AA-AA--TA-TG--G
1 -ATTGATTTATTTTAAATAATTTATTGATG
35429 ATTGATTTATTTTAAATAATTTATTTGTATGG
1 ATTGATTTATTTTAAATAATTTA-TTG-AT-G
*
35461 ATTGGTTTATTTT-AA-AA--TA-TG--G
1 ATTGATTTATTTTAAATAATTTATTGATG
* * *
35483 ATTGATTTATTATT--GTAGTTGTATGGATTG
1 ATTGATTTATT-TTAAATAATT-TATTGA-TG
35513 A-T--TT-ATTTTAAATAATTTATTAGTATG
1 ATTGATTTATTTTAAATAATTTATT-G-ATG
35540 AATTGATTTATTTT-AA-AA--TA-TG--G
1 -ATTGATTTATTTTAAATAATTTATTGATG
35563 ATTGATTTATTTTAAATAATTTATT
1 ATTGATTTATTTTAAATAATTTATT
35588 ATTGTAGTTG
Statistics
Matches: 184, Mismatches: 8, Indels: 91
0.65 0.03 0.32
Matches are distributed among these distances:
22 50 0.27
23 12 0.07
24 6 0.03
25 2 0.01
26 19 0.10
27 15 0.08
28 13 0.07
29 2 0.01
30 10 0.05
31 11 0.06
32 44 0.24
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (29 bp):
ATTGATTTATTTTAAATAATTTATTGATG
Found at i:35443 original size:188 final size:188
Alignment explanation
Indices: 35236--35588 Score: 652
Period size: 188 Copynumber: 1.9 Consensus size: 188
35226 ATTGTAGTTG
35236 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*
35301 TTATTATTGTAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTT
66 TTATTATTGTAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
35366 AAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGTATTGATTTATTTTAAAA
131 AAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGTATTGATTTATTTTAAAA
* * *
35424 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
**
35489 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
35554 AAAATATGGATTGATTTATTTTAAATAATTTATTA
131 AAAATATGGATTGATTTATTTTAAATAATTTATTA
35589 TTGTAGTTGT
Statistics
Matches: 159, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
188 159 1.00
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.53
Consensus pattern (188 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATAAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AAAATATGGATTGATTTATTTTAAATAATTTATTAGCATGTATTGATTTATTTTAAAA
Found at i:35523 original size:80 final size:80
Alignment explanation
Indices: 35424--35573 Score: 273
Period size: 80 Copynumber: 1.9 Consensus size: 80
35414 TATTTTAAAA
* * *
35424 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
35489 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
35504 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
35569 TTATT
66 TTATT
35574 TTAAATAATT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:35638 original size:31 final size:31
Alignment explanation
Indices: 35603--35661 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
35593 AGTTGTATGG
* *
35603 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
35634 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
35662 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:36029 original size:14 final size:15
Alignment explanation
Indices: 36004--36032 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35994 AAAAAAAATT
36004 TCGGGTTCGGGTCGG
1 TCGGGTTCGGGTCGG
36019 TCGGG-TCGGGTCGG
1 TCGGGTTCGGGTCGG
36033 GTTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.21, G:0.55, T:0.24
Consensus pattern (15 bp):
TCGGGTTCGGGTCGG
Found at i:42904 original size:20 final size:20
Alignment explanation
Indices: 42799--42898 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
42789 GTTAAGGGCA
42799 CGAATTCGGAATTAGCGTCG
1 CGAATTCGGAATTAGCGTCG
*
42819 TGAATTCGGAATTAGCGTCG
1 CGAATTCGGAATTAGCGTCG
* * * * *
42839 CGAATTTGAAAATCGCGTTG
1 CGAATTCGGAATTAGCGTCG
*
42859 CGAAATT-GAAATTAGCGTCG
1 CG-AATTCGGAATTAGCGTCG
42879 CGAATTCGGAATTAGCGTCG
1 CGAATTCGGAATTAGCGTCG
42899 TAAATTTGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 4 0.06
20 59 0.88
21 4 0.06
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (20 bp):
CGAATTCGGAATTAGCGTCG
Found at i:42920 original size:60 final size:60
Alignment explanation
Indices: 42808--42928 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
42798 ACGAATTCGG
* * *
42808 AATTAGCGTCGTGAATTCGGAATTAGCGTCGCGAATTTGAAAATCGCGTTGCGAAATTGA
1 AATTAGCGTCGCGAATTCGGAATTAGCGTCGCAAATTTGAAAATCGCATTGCGAAATTGA
* * ** *
42868 AATTAGCGTCGCGAATTCGGAATTAGCGTCGTAAATTTGGAGTTCGCATTGCGAATTTGA
1 AATTAGCGTCGCGAATTCGGAATTAGCGTCGCAAATTTGAAAATCGCATTGCGAAATTGA
42928 A
1 A
42929 TAATCGCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (60 bp):
AATTAGCGTCGCGAATTCGGAATTAGCGTCGCAAATTTGAAAATCGCATTGCGAAATTGA
Found at i:43147 original size:17 final size:18
Alignment explanation
Indices: 43113--43147 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43103 ATTTTTAAAA
*
43113 AAAATATCCTCTAATCAT
1 AAAATATCCTCAAATCAT
43131 AAAATATCCT-AAATCAT
1 AAAATATCCTCAAATCAT
43148 CTATCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATCCTCAAATCAT
Done.