Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000396.1 Hibiscus syriacus cultivar Beakdansim tig00000729_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: 44122
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:6954 original size:9 final size:9
Alignment explanation
Indices: 6940--7022 Score: 70
Period size: 9 Copynumber: 9.9 Consensus size: 9
6930 ACACTTGAAT
6940 AAAAATAAG
1 AAAAATAAG
6949 AAAAATAAG
1 AAAAATAAG
6958 AAAAA-AAG
1 AAAAATAAG
***
6966 AAAAAGGGG
1 AAAAATAAG
*
6975 AAAAAAAAG
1 AAAAATAAG
6984 -AAAA-AA-
1 AAAAATAAG
*
6990 AAGAA-AAG
1 AAAAATAAG
6998 AAAAATAAG
1 AAAAATAAG
*
7007 -AAAATAAT
1 AAAAATAAG
7015 AAAAATAA
1 AAAAATAA
7023 TGAATAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
7 7 0.11
8 23 0.38
9 31 0.51
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (9 bp):
AAAAATAAG
Found at i:6966 original size:17 final size:17
Alignment explanation
Indices: 6940--7022 Score: 73
Period size: 17 Copynumber: 4.9 Consensus size: 17
6930 ACACTTGAAT
6940 AAAAATAAGAAAAATAAG
1 AAAAA-AAGAAAAATAAG
***
6958 AAAAAAAGAAAAAGGGG
1 AAAAAAAGAAAAATAAG
6975 AAAAAAA-AGAAAA-AA-
1 AAAAAAAGA-AAAATAAG
*
6990 AAGAAAAGAAAAATAAG
1 AAAAAAAGAAAAATAAG
* *
7007 AAAATAATAAAAATAA
1 AAAAAAAGAAAAATAA
7023 TGAATAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
15 10 0.19
16 4 0.08
17 33 0.63
18 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (17 bp):
AAAAAAAGAAAAATAAG
Found at i:6996 original size:14 final size:14
Alignment explanation
Indices: 6975--7010 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6965 GAAAAAGGGG
6975 AAAA-AAAAGAAAA
1 AAAAGAAAAGAAAA
6988 AAAAGAAAAGAAAA
1 AAAAGAAAAGAAAA
*
7002 ATAAGAAAA
1 AAAAGAAAA
7011 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAGAAAA
Found at i:7033 original size:18 final size:16
Alignment explanation
Indices: 6949--7035 Score: 52
Period size: 17 Copynumber: 5.2 Consensus size: 16
6939 TAAAAATAAG
*
6949 AAAAATAAGAAAAAAAG
1 AAAAATAAG-AAAAAAT
***
6966 AAAAAGGGGAAAAAA-
1 AAAAATAAGAAAAAAT
* *
6981 AAGAAA-AAAAAGAAAAG
1 AA-AAATAAGAA-AAAAT
6998 AAAAATAAGAAAATAAT
1 AAAAATAAGAAAA-AAT
7015 AAAAATAATGAATAAAAT
1 AAAAATAA-GAA-AAAAT
7033 AAA
1 AAA
7036 TGAGGGTTCA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
15 4 0.07
16 18 0.33
17 22 0.40
18 9 0.16
19 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (16 bp):
AAAAATAAGAAAAAAT
Found at i:10197 original size:3 final size:3
Alignment explanation
Indices: 10189--10221 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
10179 CACCTTCGTC
10189 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10222 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11900 original size:22 final size:22
Alignment explanation
Indices: 11875--11917 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11865 ATATTTATTA
*
11875 ATATTTCTAATAATATAATAAT
1 ATATTTCTAATAATAAAATAAT
*
11897 ATATTTTTAATAATAAAATAA
1 ATATTTCTAATAATAAAATAA
11918 AATAATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTTCTAATAATAAAATAAT
Found at i:12114 original size:23 final size:23
Alignment explanation
Indices: 12088--12132 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12078 AATAATATTT
12088 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
12111 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
12133 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:12210 original size:33 final size:29
Alignment explanation
Indices: 12172--12242 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 29
12162 AATATAATTT
12172 ATAATATTTTTATTTCAATAAAA-TATACCAA
1 ATAATATTTTTA-TT-AATAAAATTATA-CAA
12203 TATTAATATTTTTATTAATAAAATTATACAA
1 -A-TAATATTTTTATTAATAAAATTATACAA
12234 ATAATATTT
1 ATAATATTT
12243 AATAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
29 8 0.22
30 1 0.03
31 10 0.27
32 7 0.19
33 11 0.30
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTATACAA
Found at i:12265 original size:27 final size:26
Alignment explanation
Indices: 12235--12311 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
12225 ATTATACAAA
12235 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATTT
* *
12262 TAATATTT-TAA-AAAT-AATAATAT
1 TAATATTTATAATAAATAAATTATTT
*
12285 TAA-ATTTTATGATAAATAATATTATTT
1 TAATA-TTTATAATAAATAA-ATTATTT
12312 ATTGTATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
22 1 0.03
23 12 0.30
24 6 0.15
25 7 0.17
26 1 0.03
27 13 0.32
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATTT
Found at i:12513 original size:15 final size:14
Alignment explanation
Indices: 12461--12519 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
12451 TCAGAAATGT
12461 AATTCATTTTCCAG
1 AATTCATTTTCCAG
** *
12475 AATTCAAATTCTAG
1 AATTCATTTTCCAG
12489 TAATTCATTTTCCAG
1 -AATTCATTTTCCAG
12504 AATTCAATTTT-CAG
1 AATTC-ATTTTCCAG
12518 AA
1 AA
12520 AACTAATTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 21 0.57
15 16 0.43
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (14 bp):
AATTCATTTTCCAG
Found at i:14867 original size:9 final size:8
Alignment explanation
Indices: 14839--14884 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
14829 TCTCATATTA
14839 TTTGTTTT
1 TTTGTTTT
*
14847 TTTGGTTT
1 TTTGTTTT
14855 TTTGTTTT
1 TTTGTTTT
14863 ATTTGTTTT
1 -TTTGTTTT
14872 TGTT-TTTT
1 T-TTGTTTT
14880 TTTGT
1 TTTGT
14885 GTGGTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 2 0.06
8 21 0.64
9 10 0.30
ACGTcount: A:0.02, C:0.00, G:0.15, T:0.83
Consensus pattern (8 bp):
TTTGTTTT
Found at i:14871 original size:15 final size:16
Alignment explanation
Indices: 14839--14880 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
14829 TCTCATATTA
14839 TTTGTTTTTTTGGTTT
1 TTTGTTTTTTTGGTTT
14855 TTTGTTTTATTT-G-TT
1 TTTGTTTT-TTTGGTTT
14870 TTTGTTTTTTT
1 TTTGTTTTTTT
14881 TTGTGTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 9 0.36
17 3 0.12
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.83
Consensus pattern (16 bp):
TTTGTTTTTTTGGTTT
Found at i:22870 original size:35 final size:34
Alignment explanation
Indices: 22797--22872 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 34
22787 ATTTTACACT
*
22797 AAAAATATTATATAATTACATGTTTTGTTACATCA
1 AAAAATATTATATAATTACATGTTTCGTTACAT-A
*
22832 AAAAGTATTATATAATTGCACATGTTTCG-TA-ATA
1 AAAAATATTATATAATT--ACATGTTTCGTTACATA
22866 AAAAATA
1 AAAAATA
22873 ATAATTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 7 0.19
35 18 0.50
36 2 0.06
37 9 0.25
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (34 bp):
AAAAATATTATATAATTACATGTTTCGTTACATA
Found at i:26950 original size:98 final size:99
Alignment explanation
Indices: 26781--26980 Score: 375
Period size: 98 Copynumber: 2.0 Consensus size: 99
26771 CAGTTGTTAC
26781 GATCTTTTAATGGGCAATGAATCCTACCACTGGAGTTTGTATTTTGTTTAGCAAGCTTTAAGAAA
1 GATCTTTTAATGGGCAATGAATCCTACCACTGGAGTTTGTATTTTGTTTAGCAAGCTTTAAGAAA
26846 TCACAAACA-TCTTGGTATTTAGTTGATAAATTT
66 TCACAAACATTCTTGGTATTTAGTTGATAAATTT
26879 GATCTTTTAATGGGCAATGAATCCTACCACTGGAGTTTGTATTTTGTTTAGCAAGCTTTAAGAAA
1 GATCTTTTAATGGGCAATGAATCCTACCACTGGAGTTTGTATTTTGTTTAGCAAGCTTTAAGAAA
26944 TCACAAACATCTTCTTGGTATTTAGTTGATAAATTT
66 TCACAAACA--TTCTTGGTATTTAGTTGATAAATTT
26980 G
1 G
26981 TTTGTATGCG
Statistics
Matches: 99, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
98 74 0.75
101 25 0.25
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (99 bp):
GATCTTTTAATGGGCAATGAATCCTACCACTGGAGTTTGTATTTTGTTTAGCAAGCTTTAAGAAA
TCACAAACATTCTTGGTATTTAGTTGATAAATTT
Found at i:29160 original size:21 final size:20
Alignment explanation
Indices: 29125--29165 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29115 TGAGATAAAA
*
29125 ATAATATTTATTTTAAATTT
1 ATAATATTTAATTTAAATTT
*
29145 ATAATAATTTAATTTATATTT
1 ATAAT-ATTTAATTTAAATTT
29166 TTATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATAATATTTAATTTAAATTT
Found at i:29168 original size:8 final size:8
Alignment explanation
Indices: 29157--29218 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
29147 AATAATTTAA
29157 TTTATATT
1 TTTATATT
29165 TTTATATT
1 TTTATATT
29173 TTTATA-T
1 TTTATATT
* *
29180 GTAATATT
1 TTTATATT
29188 TTGTATA-T
1 TT-TATATT
*
29196 TTTAAATT
1 TTTATATT
29204 TTTAAATATT
1 TTT--ATATT
29214 TTTAT
1 TTTAT
29219 TCTTAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
7 8 0.19
8 25 0.58
9 3 0.07
10 7 0.16
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (8 bp):
TTTATATT
Found at i:29730 original size:64 final size:64
Alignment explanation
Indices: 29651--29790 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 64
29641 CAGATCTTGG
* * * *
29651 CAGGTCGGGTAAAATCAGGTACAAGTCA-ACTCAGGTTGATTTGATACCAGATCCAGATCGGGTT
1 CAGGTCAGGTCAAATCA-GTACAAGTCATACTCAGGTTGATTTGACACCAGATCCAGATCGGGTC
* **** * **
29715 CAGGTTAGGTCAAATCAGTTTGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTC
1 CAGGTCAGGTCAAATCAGTACAAGTCATACTCAGGTTGATTTGACACCAGATCCAGATCGGGTC
29779 CAGGTCAGGTCA
1 CAGGTCAGGTCA
29791 TTTTTAGTTC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
63 5 0.08
64 57 0.92
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (64 bp):
CAGGTCAGGTCAAATCAGTACAAGTCATACTCAGGTTGATTTGACACCAGATCCAGATCGGGTC
Found at i:30501 original size:17 final size:16
Alignment explanation
Indices: 30470--30516 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
30460 AAATTGAAAA
30470 AATATAATATATATAT
1 AATATAATATATATAT
*
30486 AATATAAGTTTATATAT
1 AATATAA-TATATATAT
30503 AA-ACT-ATATATATA
1 AATA-TAATATATATA
30517 AACTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.26
16 9 0.33
17 11 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
AATATAATATATATAT
Found at i:30512 original size:13 final size:13
Alignment explanation
Indices: 30496--30631 Score: 75
Period size: 13 Copynumber: 10.4 Consensus size: 13
30486 AATATAAGTT
30496 TATATATAAACTA
1 TATATATAAACTA
30509 TATATATAAACTA
1 TATATATAAACTA
* *
30522 TAT-T-TATATTA
1 TATATATAAACTA
*
30533 TAAACTATATAA-T-
1 TATA-TATA-AACTA
**
30546 TAT-TATAAGTTA
1 TATATATAAACTA
**
30558 TATATATAAGTTA
1 TATATATAAACTA
* *
30571 TGTTTATATGAACTA
1 --TATATATAAACTA
* *
30586 TATATAAAAACTT
1 TATATATAAACTA
*
30599 TATATGTAAACTA
1 TATATATAAACTA
30612 TATATATGTAAACTA
1 TATATA--TAAACTA
30627 TATAT
1 TATAT
30632 GTGTAAACTA
Statistics
Matches: 94, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
10 1 0.01
11 12 0.13
12 4 0.04
13 52 0.55
14 3 0.03
15 22 0.23
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:30513 original size:30 final size:30
Alignment explanation
Indices: 30477--30566 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 30
30467 AAAAATATAA
30477 TATATATATAATATAAGTTTATATATAAAC
1 TATATATATAATATAAGTTTATATATAAAC
30507 TATATATATAA-ACTATA-TTTATATTATAAAC
1 TATATATATAATA-TA-AGTTTATA-TATAAAC
*
30538 TATATA-ATTATTATAAGTTATATATATAA
1 TATATATA-TAATATAAGTT-TATATATAA
30567 GTTATGTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
29 1 0.02
30 21 0.40
31 25 0.48
32 5 0.10
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
TATATATATAATATAAGTTTATATATAAAC
Found at i:30514 original size:15 final size:15
Alignment explanation
Indices: 30496--30643 Score: 96
Period size: 15 Copynumber: 10.0 Consensus size: 15
30486 AATATAAGTT
30496 TATATATAAAC--TA
1 TATATATAAACTATA
30509 TATATATAAACTATA
1 TATATATAAACTATA
30524 TTTATATTATAAACTATA
1 --TATA-TATAAACTATA
*
30542 TA-ATTATTATAAGT-TA
1 TATA-TA-TA-AACTATA
** *
30558 TATATATAAGTTATG
1 TATATATAAACTATA
* *
30573 TTTATATGAACTATA
1 TATATATAAACTATA
30588 TATA-A-AAACT-T-
1 TATATATAAACTATA
*
30599 TATATGTAAACTATA
1 TATATATAAACTATA
*
30614 TATATGTAAACTATA
1 TATATATAAACTATA
* *
30629 TATGTGTAAACTATA
1 TATATATAAACTATA
30644 AAAAGTATAT
Statistics
Matches: 109, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
11 4 0.04
12 1 0.01
13 20 0.18
14 4 0.04
15 51 0.47
16 10 0.09
17 8 0.07
18 11 0.10
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:30549 original size:18 final size:18
Alignment explanation
Indices: 30507--30565 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
30497 ATATATAAAC
30507 TATATA-TATAAACTATA
1 TATATATTATAAACTATA
*
30524 TTTATATTATAAACTATA
1 TATATATTATAAACTATA
**
30542 TA-ATTATTATAAGTTATA
1 TATA-TATTATAAACTATA
30560 TATATA
1 TATATA
30566 AGTTATGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.17
18 28 0.80
19 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (18 bp):
TATATATTATAAACTATA
Found at i:30821 original size:17 final size:18
Alignment explanation
Indices: 30799--30842 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
30789 TTGGGAAATT
30799 TTGAGAATATAGA-GAAA
1 TTGAGAATATAGAGGAAA
*
30816 TTGAGAATTTAGAGGGAAA
1 TTGAGAATATAGA-GGAAA
30835 TTGAGAAT
1 TTGAGAAT
30843 TGAGATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.50
19 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (18 bp):
TTGAGAATATAGAGGAAA
Found at i:30843 original size:19 final size:17
Alignment explanation
Indices: 30799--30843 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
30789 TTGGGAAATT
*
30799 TTGAGAATATAGAGAAA
1 TTGAGAATTTAGAGAAA
30816 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGA--GAAA
30835 TTGAGAATT
1 TTGAGAATT
30844 GAGATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.48
19 13 0.52
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (17 bp):
TTGAGAATTTAGAGAAA
Found at i:31024 original size:10 final size:11
Alignment explanation
Indices: 31000--31079 Score: 63
Period size: 10 Copynumber: 8.2 Consensus size: 11
30990 ATATAAACTT
31000 TATATAGTATA
1 TATATAGTATA
*
31011 TATAT-GTATG
1 TATATAGTATA
*
31021 TATA-ACTA-A
1 TATATAGTATA
31030 TATA-AGTA-A
1 TATATAGTATA
*
31039 TCTATAG-AT-
1 TATATAGTATA
31048 TATATA-TATA
1 TATATAGTATA
31058 TATATA-TATA
1 TATATAGTATA
31068 TATATA-TATA
1 TATATAGTATA
31078 TA
1 TA
31080 GAAATACTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
9 19 0.33
10 34 0.59
11 5 0.09
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (11 bp):
TATATAGTATA
Found at i:31055 original size:2 final size:2
Alignment explanation
Indices: 31048--31079 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31038 ATCTATAGAT
31048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31080 GAAATACTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31183 original size:22 final size:21
Alignment explanation
Indices: 31133--31194 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
31123 TTATAAAAAC
31133 CATAAACCCTAAATCC-TAAAT
1 CATAAACCCTAAA-CCTTAAAT
31154 CATAAACCCTAAACCTTCAAAT
1 CATAAACCCTAAACCTT-AAAT
* *
31176 CCTTAACCCTAAACCTTAA
1 CATAAACCCTAAACCTTAA
31195 TCCCCTGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.05
21 16 0.43
22 19 0.51
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
CATAAACCCTAAACCTTAAAT
Found at i:31406 original size:21 final size:20
Alignment explanation
Indices: 31382--31429 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
31372 TCATAACTCC
31382 TAAATCCTAAACTTTAAACCA
1 TAAA-CCTAAACTTTAAACCA
31403 TAAACACTAAACTTTAAACCA
1 TAAAC-CTAAACTTTAAACCA
*
31424 CAAACC
1 TAAACC
31430 CTAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAACCTAAACTTTAAACCA
Found at i:31433 original size:21 final size:21
Alignment explanation
Indices: 31387--31433 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
31377 ACTCCTAAAT
*
31387 CCTAAACTTTAAACCATAAAC
1 CCTAAACTTTAAACCACAAAC
*
31408 ACTAAACTTTAAACCACAAAC
1 CCTAAACTTTAAACCACAAAC
31429 CCTAA
1 CCTAA
31434 TATAAATGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (21 bp):
CCTAAACTTTAAACCACAAAC
Found at i:31827 original size:13 final size:13
Alignment explanation
Indices: 31826--31857 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31816 AAACTATATA
*
31826 TATATATATAACC
1 TATATATATAAAC
31839 TATATATATAAAC
1 TATATATATAAAC
31852 TATATA
1 TATATA
31858 AAGTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:31833 original size:19 final size:19
Alignment explanation
Indices: 31793--31848 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
31783 AATATGTATG
* *
31793 TATAAACCATGTATAGTATA
1 TATAAACTATATATA-TATA
31813 TATAAACTATATATATATA
1 TATAAACTATATATATATA
*
31832 TATAACCTATATATATA
1 TATAAACTATATATATA
31849 AACTATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (19 bp):
TATAAACTATATATATATA
Found at i:31936 original size:7 final size:7
Alignment explanation
Indices: 31926--32005 Score: 88
Period size: 7 Copynumber: 11.4 Consensus size: 7
31916 ATAGTTTATA
31926 TAAACCC
1 TAAACCC
31933 TAAACCC
1 TAAACCC
**
31940 TAAACTT
1 TAAACCC
31947 TAAACCC
1 TAAACCC
*
31954 TAAACAC
1 TAAACCC
31961 TAAACCC
1 TAAACCC
**
31968 TAAACTT
1 TAAACCC
* *
31975 TAAGCCA
1 TAAACCC
*
31982 TAAACCA
1 TAAACCC
31989 TAAACCC
1 TAAACCC
31996 TAAACCC
1 TAAACCC
32003 TAA
1 TAA
32006 TATATGTATT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:31963 original size:28 final size:27
Alignment explanation
Indices: 31925--32000 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 27
31915 TATAGTTTAT
31925 ATAAACCCTAAACCCTAAACTTTAAACC
1 ATAAA-CCTAAACCCTAAACTTTAAACC
* *
31953 CTAAACACTAAACCCTAAACTTTAAGCC
1 ATAAAC-CTAAACCCTAAACTTTAAACC
31981 ATAAACCATAAACCCTAAAC
1 ATAAACC-TAAACCCTAAAC
32001 CCTAATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.05
28 41 0.95
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (27 bp):
ATAAACCTAAACCCTAAACTTTAAACC
Found at i:32030 original size:17 final size:16
Alignment explanation
Indices: 32005--32046 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
31995 CTAAACCCTA
*
32005 ATATATGTATTATATGC
1 ATATGTGTA-TATATGC
32022 ATATGTGTATATATGC
1 ATATGTGTATATATGC
32038 ATAATGTGT
1 AT-ATGTGT
32047 GTATTAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (16 bp):
ATATGTGTATATATGC
Found at i:32105 original size:7 final size:7
Alignment explanation
Indices: 32093--32139 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
32083 GGTGTCATCT
32093 AAGTATA
1 AAGTATA
32100 AAGTATA
1 AAGTATA
32107 AAGTATA
1 AAGTATA
32114 AAGTATA
1 AAGTATA
32121 TAA-TATA
1 -AAGTATA
32128 AAGTAATA
1 AAGT-ATA
32136 AAGT
1 AAGT
32140 GTTGTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 2 0.05
7 26 0.70
8 9 0.24
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (7 bp):
AAGTATA
Found at i:33818 original size:19 final size:18
Alignment explanation
Indices: 33786--33853 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
33776 TTCATTGAAA
33786 AACCGAAAAACCGAACCG
1 AACCGAAAAACCGAACCG
33804 AACCGAAAAACCCGAACCG
1 AACCGAAAAA-CCGAACCG
*
33823 TTAA---AAAAACTGAACCG
1 --AACCGAAAAACCGAACCG
33840 AACCGATAAAACCG
1 AACCGA-AAAACCG
33854 GTTTCGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 7 0.17
18 16 0.39
19 14 0.34
21 2 0.05
ACGTcount: A:0.50, C:0.29, G:0.15, T:0.06
Consensus pattern (18 bp):
AACCGAAAAACCGAACCG
Found at i:34838 original size:17 final size:17
Alignment explanation
Indices: 34812--34844 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34802 TAATTTGTTG
34812 TTTTAATTAAAATGAAT
1 TTTTAATTAAAATGAAT
*
34829 TTTTATTTAAAATGAA
1 TTTTAATTAAAATGAA
34845 AACGATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TTTTAATTAAAATGAAT
Found at i:43696 original size:55 final size:54
Alignment explanation
Indices: 43612--44118 Score: 729
Period size: 55 Copynumber: 9.4 Consensus size: 54
43602 TGAAGAGTCT
* *
43612 TACTCTCGGAAGAGAATA-GAACAGACACGATTGTTGAAGATTGTTCGAGTCTTA
1 TACTCTCTGAAG-GAATAGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
* ** *
43666 TACTCTCTGAAGGAATATGGAGTAGACACGATTGAAGAAGA-TGTTCGAGTATTA
1 TACTCTCTGAAGGAATA-GGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
* * * *
43720 TACTCTCTGAAGGAATAGAGAGCAAATACGATTGTTGAAAATTGTTTGAGTCTTA
1 TACTCTCTGAAGGAATAG-GAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
43775 TACTCTCTGAAGGAATAGAGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
1 TACTCTCTGAAGGAATAG-GAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
*
43830 TACTCTCTGAAGGAATAGAGAGCAGACACGATTGTTGAATATTGTTCGAGTCTTA
1 TACTCTCTGAAGGAATAG-GAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
*
43885 TACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGCTCGAGTCTTA
1 TACTCTCTGAAGGAATA-GGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
**
43940 TACTCTCTGAAACAATAGGGAGCAGACACGATTGTTGAAGATTG-TCGAGTCTTA
1 TACTCTCTGAAGGAATA-GGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
* * *
43994 TACTCTCTGAAGAAATAGGAGTAGACACG-TTGTTGAAGATT-ATCGAGTCTTA
1 TACTCTCTGAAGGAATAGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
* *
44046 TACTCTCTGAAGGAATGGGGAGCAGACACGATTGTTGAAGA-TATTCGAGTCTTA
1 TACTCTCTGAAGGAAT-AGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
44100 TACTCTCTGAAGGAATAGG
1 TACTCTCTGAAGGAATAGG
44119 GAGC
Statistics
Matches: 413, Mismatches: 31, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
52 37 0.09
53 31 0.08
54 117 0.28
55 227 0.55
56 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (54 bp):
TACTCTCTGAAGGAATAGGAGCAGACACGATTGTTGAAGATTGTTCGAGTCTTA
Done.