Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004310.1 Hibiscus syriacus cultivar Beakdansim tig00009454_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: 82949
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:999 original size:20 final size:20
Alignment explanation
Indices: 974--1012 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
964 TAAATTAAAT
*
974 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
994 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
1013 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1050 original size:19 final size:20
Alignment explanation
Indices: 1026--1063 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1016 TCTATTAGTT
*
1026 ATTAGATAGGATC-ATTTTA
1 ATTAGATAGAATCAATTTTA
1045 ATTAGATAGAATCAATTTT
1 ATTAGATAGAATCAATTTT
1064 TTTTTATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTAGATAGAATCAATTTTA
Found at i:1054 original size:51 final size:51
Alignment explanation
Indices: 973--1119 Score: 244
Period size: 51 Copynumber: 2.9 Consensus size: 51
963 CTAAATTAAA
973 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCA-TTTTTATTCTATTAGT
*
1025 TATTAGATAGGATCA-TTTTAATTAGATAGAATCAATTTTT-TTTTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATC-ATTTTTATTCTATTAGT
*
1075 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTATTCT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCATTTTTATTCT
1120 TTTGCTAATT
Statistics
Matches: 90, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
50 30 0.33
51 44 0.49
52 16 0.18
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.48
Consensus pattern (51 bp):
TATTAGATAGGATCAGTTTTAATTAGATAGAATCATTTTTATTCTATTAGT
Found at i:1101 original size:20 final size:20
Alignment explanation
Indices: 1076--1115 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1066 TTTATTAGTT
*
1076 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1096 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1116 TTCTTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:5690 original size:20 final size:20
Alignment explanation
Indices: 5665--5703 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5655 TAAATTAAAT
*
5665 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
5685 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
5704 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:5749 original size:19 final size:20
Alignment explanation
Indices: 5717--5754 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5707 TCTATTAGTT
5717 ATTAGATATGATCA-TTTTA
1 ATTAGATATGATCAGTTTTA
5736 ATTAGATA-GAATCAGTTTT
1 ATTAGATATG-ATCAGTTTT
5755 TTATTCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 12 0.71
20 4 0.24
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTAGATATGATCAGTTTTA
Found at i:5756 original size:52 final size:52
Alignment explanation
Indices: 5664--5813 Score: 266
Period size: 52 Copynumber: 2.9 Consensus size: 52
5654 CTAAATTAAA
5664 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
5716 TATTAGATATGATCA-TTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
5768 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
1 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCT
5814 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
51 20 0.21
52 54 0.57
53 20 0.21
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:5794 original size:20 final size:21
Alignment explanation
Indices: 5769--5809 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5759 TCTATTAGTT
*
5769 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
5789 ATTAGATAGAATCAGTTTTTA
1 ATTAGATAGAATCAGTTTTTA
5810 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:10579 original size:25 final size:25
Alignment explanation
Indices: 10551--10606 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
10541 CCACCATGCT
10551 TATTTTCCCAAAATCGTTTGAGCTA
1 TATTTTCCCAAAATCGTTTGAGCTA
* * *
10576 TATTTTCCCAGAATTGTTTGAGTTA
1 TATTTTCCCAAAATCGTTTGAGCTA
*
10601 CATTTT
1 TATTTT
10607 ATGGATCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.46
Consensus pattern (25 bp):
TATTTTCCCAAAATCGTTTGAGCTA
Found at i:13234 original size:73 final size:73
Alignment explanation
Indices: 13112--13343 Score: 383
Period size: 73 Copynumber: 3.2 Consensus size: 73
13102 AAAAATGCGC
* *
13112 GAGTGTTTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATCTAAAAATGCGCGCGAGCGAC
1 GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
13177 ATTGAAGT
66 ATTGAAGT
* * *
13185 GAGTGTTTGTCTTTATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCAAC
1 GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
13250 ATTGAAGT
66 ATTGAAGT
* * *
13258 GAGGGTGTGTCTATATGCGGTCTAACGGTCTTGATTCTTCAGATTTAAAATTGCGCGCGAGCGAC
1 GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
13323 ATTGAAGT
66 ATTGAAGT
*
13331 GAGCGTGTGTCTA
1 GAGTGTGTGTCTA
13344 CGTGCGCGGT
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 149 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (73 bp):
GAGTGTGTGTCTATATGCGGCCTAACGGTCTTGATTCTTCAGATTTAAAAATGCGCGCGAGCGAC
ATTGAAGT
Found at i:13517 original size:93 final size:91
Alignment explanation
Indices: 13359--13687 Score: 304
Period size: 93 Copynumber: 3.6 Consensus size: 91
13349 GCGGTTTTTT
* * * * * * *
13359 TTTTCTGTCTATATGCAGCCTAACGGTCTTGATTCTTCCTAAATGGAATATCGCAG-GCTGTATT
1 TTTT-TGTCAATATACAGCGTAACGGTCTTGATTCCTCCTAAA-GGAA-ATCACAGAACTGCATT
* *
13423 TAAGTGAGTGTGCATCTGCAAGTGTGCGCG
63 TAAGT-AGTGTGCATCTACAAGTGTGCACG
* * *
13453 TTTTTGTTAATATACGGCGTAACGGTCTTGATTTCTCCTAAAGGAAATCACATGAACTGCATTTA
1 TTTTTGTCAATATACAGCGTAACGGTCTTGATTCCTCCTAAAGGAAATCACA-GAACTGCATTTA
* * * *
13518 TGTAAGTGTGTATCCACAAGTGTGCATG
65 AGT-AGTGTGCATCTACAAGTGTGCACG
* * * *
13546 TTTTTGTCAGTATACAGTGTAACGGTCTTGATTCCTCCTAAA-TAGAATCACACAGACTGCATTT
1 TTTTTGTCAATATACAGCGTAACGGTCTTGATTCCTCCTAAAGGA-AATCACAGA-ACTGCATTT
* * * * * *
13610 AAGT-TTGTGCGTCTAAAAGTTTTCACA
64 AAGTAGTGTGCATCTACAAGTGTGCACG
* * *
13637 TTTTGGTCAATATACAGCGTAATGGTCTTGATTCCTCCTAAAGGCAATCAC
1 TTTTTGTCAATATACAGCGTAACGGTCTTGATTCCTCCTAAAGGAAATCAC
13688 GTGAGCGCAT
Statistics
Matches: 190, Mismatches: 40, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
91 63 0.33
92 7 0.04
93 116 0.61
94 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (91 bp):
TTTTTGTCAATATACAGCGTAACGGTCTTGATTCCTCCTAAAGGAAATCACAGAACTGCATTTAA
GTAGTGTGCATCTACAAGTGTGCACG
Found at i:19390 original size:150 final size:152
Alignment explanation
Indices: 18805--19418 Score: 651
Period size: 153 Copynumber: 4.0 Consensus size: 152
18795 CCAAGTCAAC
* *
18805 CAAACCCAAGGATGGTGACAATGCTACCAAAGCCAAGGATCATGCCCGTAAAAGTGGTAGTAGAC
1 CAAACCCAAGGA-GGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGAC
** * * * * *
18870 CAGTTGTTGTTGCTTTAGAAGTGAGCAGTAAACCCAAAACTGAGGTCAGTGTCGTCACGCCCAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
*
18935 TCAACCAAACCCAAGGGCGACGA
130 TCAACCAAACCCAAGGACGACGA
* * *
18958 CAAACCCAAGGATGGTGACAATGCTACCAAAGGCAAGGATCATACCCGCAAAAGTGGTAGTAGAC
1 CAAACCCAAGGA-GGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGAC
** * * * ** * *
19023 CAGTTGTTGTTGCTTTAGAAGTGAGCAGCGAACCCAAAACTGAGGAGGGTGTCGACAGGCCTAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
* *
19088 TCAACCAAACCCAAGGCCGATGA
130 TCAACCAAACCCAAGGACGACGA
* * * * * * *
19111 CAAACCGAAGGATGGCAACAATGTTATCGAAGCCAACGATCATACCCCTAAAAGTGGTAGTAGAC
1 CAAACCCAAGGA-GGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGAC
* * ** * ** *
19176 CAGTTGACGATGCTTCAAAAGTGGGCAGCAAGTCCAAAACTGAGGACGGTGTCGTTACGGCCAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
* * *
19241 CCAACCAAACCGAAGGACGACAA
130 TCAACCAAACCCAAGGACGACGA
* * * * * *
19264 CAAACCCAA-G-CGCGACAATGTTACCAAAGCCAAGGATCATACCAC-TAACACTGTTAGTGGAC
1 CAAACCCAAGGAGGCGACAATGCTACCAAAGCCAAGGATCATACC-CGTAAAAGTGGTAGTAGAC
* * * * *
19326 CAGTTGACGTTGCTTCAAAAGTGGGCAGCAAATCCAAAAATGAGGACAGTGTTGACACTCCCAAG
65 CAGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAG
* * * *
19391 TCTACTAAACCCGAGGACGA-GC
130 TCAACCAAACCCAAGGACGACGA
19413 CAAACC
1 CAAACC
19419 AAGACACTAC
Statistics
Matches: 391, Mismatches: 69, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
149 6 0.02
150 112 0.29
151 1 0.00
152 1 0.00
153 271 0.69
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (152 bp):
CAAACCCAAGGAGGCGACAATGCTACCAAAGCCAAGGATCATACCCGTAAAAGTGGTAGTAGACC
AGTTGACGTTGCTTCAAAAGTGAGCAGCAAACCCAAAACTGAGGACAGTGTCGACACGCCCAAGT
CAACCAAACCCAAGGACGACGA
Found at i:20445 original size:21 final size:21
Alignment explanation
Indices: 20420--20461 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
20410 TAGTGCTCAA
20420 GTATTTGAACTATGCTTTCTT
1 GTATTTGAACTATGCTTTCTT
* *
20441 GTATTTGAATTATGTTTTCTT
1 GTATTTGAACTATGCTTTCTT
20462 ATGTTAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.10, G:0.14, T:0.57
Consensus pattern (21 bp):
GTATTTGAACTATGCTTTCTT
Found at i:21273 original size:28 final size:29
Alignment explanation
Indices: 21229--21286 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
21219 TGAAGACTTC
21229 TACAATAAATTAATAAAAAATAATTAAAT
1 TACAATAAATTAATAAAAAATAATTAAAT
**
21258 TACAAT-AATTAATAAAGCATAATTAAAT
1 TACAATAAATTAATAAAAAATAATTAAAT
21286 T
1 T
21287 CACTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (29 bp):
TACAATAAATTAATAAAAAATAATTAAAT
Found at i:23664 original size:18 final size:18
Alignment explanation
Indices: 23641--23698 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
23631 TTTTATTAAT
23641 ATTTATGTATGATGTGGC
1 ATTTATGTATGATGTGGC
*
23659 ATTTATGTATGATGTGGA
1 ATTTATGTATGATGTGGC
* *
23677 ATTTATGTATAATGTGAC
1 ATTTATGTATGATGTGGC
23695 ATTT
1 ATTT
23699 TTCCTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (18 bp):
ATTTATGTATGATGTGGC
Found at i:23960 original size:29 final size:28
Alignment explanation
Indices: 23914--23970 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
23904 TAAAGTAGAG
23914 GGAATATTTTTTAATTTAATTATAATTTT
1 GGAATATTTTTTAATTTAA-TATAATTTT
** *
23943 GGAATATTTTTTGTTTTAATGTAATTTT
1 GGAATATTTTTTAATTTAATATAATTTT
23971 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (28 bp):
GGAATATTTTTTAATTTAATATAATTTT
Found at i:25725 original size:23 final size:23
Alignment explanation
Indices: 25699--25742 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
25689 ATTTGAAATA
*
25699 TTAAGACCTAATAA-ATTTTAACC
1 TTAA-ACCCAATAATATTTTAACC
*
25722 TTAAACCCATTAATATTTTAA
1 TTAAACCCAATAATATTTTAA
25743 AACTCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (23 bp):
TTAAACCCAATAATATTTTAACC
Found at i:30708 original size:10 final size:10
Alignment explanation
Indices: 30693--30718 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
30683 TAAAAGAACG
30693 TTTAATTATT
1 TTTAATTATT
30703 TTTAATTATT
1 TTTAATTATT
30713 TTTAAT
1 TTTAAT
30719 AATAAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTAATTATT
Found at i:37754 original size:14 final size:15
Alignment explanation
Indices: 37735--37766 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
37725 ACTAAATTAT
37735 TTTGAAAACTTA-GA
1 TTTGAAAACTTAGGA
37749 TTTGAAAACTTAGGA
1 TTTGAAAACTTAGGA
37764 TTT
1 TTT
37767 TGGAGTCGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (15 bp):
TTTGAAAACTTAGGA
Found at i:40114 original size:11 final size:12
Alignment explanation
Indices: 40084--40115 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40074 TAATCAACAC
40084 TCCAATATTAAA
1 TCCAATATTAAA
40096 TCCAATATTAAA
1 TCCAATATTAAA
40108 T-CAATATT
1 TCCAATATT
40116 TTAATATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (12 bp):
TCCAATATTAAA
Found at i:44026 original size:32 final size:31
Alignment explanation
Indices: 43960--44043 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 31
43950 TAAAGTTTAG
43960 TTTTTGTTTCATTTTAGTACCCGTCGTTAAC
1 TTTTTGTTTCATTTTAGTACCCGTCGTTAAC
*
43991 TTTTTATTTCATTTTAGTACATCAC-T-GTTAAC
1 TTTTTGTTTCATTTTAGTAC--C-CGTCGTTAAC
*
44023 TTTTTGTTTCGTTTTAGTACC
1 TTTTTGTTTCATTTTAGTACC
44044 TAATTTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 1 0.02
31 19 0.40
32 24 0.51
33 2 0.04
34 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.11, T:0.55
Consensus pattern (31 bp):
TTTTTGTTTCATTTTAGTACCCGTCGTTAAC
Found at i:45373 original size:13 final size:12
Alignment explanation
Indices: 45355--45402 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
45345 ACATATAAAT
45355 TAAATGAATATAA
1 TAAAT-AATATAA
45368 TAAATGAATATAA
1 TAAAT-AATATAA
45381 T-AATAA-ATAA
1 TAAATAATATAA
*
45391 TTAATAATATAA
1 TAAATAATATAA
45403 GTTGCAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 7 0.21
13 14 0.42
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (12 bp):
TAAATAATATAA
Found at i:45385 original size:16 final size:14
Alignment explanation
Indices: 45364--45399 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
45354 TTAAATGAAT
45364 ATAATAAATGAATATA
1 ATAATAAAT-AAT-TA
45380 ATAATAAATAATTA
1 ATAATAAATAATTA
45394 ATAATA
1 ATAATA
45400 TAAGTTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 3 0.15
16 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATAATAAATAATTA
Found at i:53297 original size:30 final size:31
Alignment explanation
Indices: 53261--53320 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
53251 AAAAACTTAA
*
53261 TATG-TTTAGTACATAAACTATCAGTTTTTG
1 TATGTTTTAGTACATAAACTATCAATTTTTG
* *
53291 TATGTTTTAGTTCATAAACTTTCAATTTTT
1 TATGTTTTAGTACATAAACTATCAATTTTT
53321 TTGTACTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATGTTTTAGTACATAAACTATCAATTTTTG
Found at i:54986 original size:22 final size:22
Alignment explanation
Indices: 54944--54987 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54934 AATGTGTACT
*
54944 AAATCCACAAAAATTTGAATTA
1 AAATCCACAAAAATATGAATTA
*
54966 AAATCCATTAAAAATAT-AATTA
1 AAATCCA-CAAAAATATGAATTA
54988 TAAGATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATCCACAAAAATATGAATTA
Found at i:56036 original size:38 final size:36
Alignment explanation
Indices: 55960--56036 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
55950 TTTTTATATT
*
55960 TTTAATTTTGTAAAAAAAATATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
* * *
55996 TTTAATTTTTTAAAGAAAATATATAAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATATAT-AAATATTAT-CAA
56034 TTT
1 TTT
56037 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 22 0.63
37 8 0.23
38 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
Found at i:56198 original size:18 final size:19
Alignment explanation
Indices: 56175--56217 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
56165 CCTAGTAATC
56175 TTATTCC-CTGGTAATCTT
1 TTATTCCACTGGTAATCTT
56193 TTATTCCAACTGGTAATCTT
1 TTATTCC-ACTGGTAATCTT
*
56213 ATATT
1 TTATT
56218 TCGTGGACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (19 bp):
TTATTCCACTGGTAATCTT
Found at i:58259 original size:18 final size:19
Alignment explanation
Indices: 58222--58259 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
58212 CACGGAATGT
*
58222 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GAGAATAA
58242 AAGATTACCA-GAGAATAA
1 AAGATTACCAGGAGAATAA
58260 GATTACTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:64986 original size:2 final size:2
Alignment explanation
Indices: 64979--65007 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64969 TGGTTTCAAT
64979 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 T
65008 TCATATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67595 original size:19 final size:19
Alignment explanation
Indices: 67568--67610 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
67558 ACAACTCAAG
*
67568 CTTATACTCCACTTGAGTT
1 CTTAAACTCCACTTGAGTT
67587 CTTAAACTCCACTTGAGTT
1 CTTAAACTCCACTTGAGTT
67606 CTTAA
1 CTTAA
67611 CGAACCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (19 bp):
CTTAAACTCCACTTGAGTT
Found at i:74022 original size:32 final size:32
Alignment explanation
Indices: 73944--74048 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 32
73934 GTGCTTAATT
* * *
73944 GGTGATGTGGTACATATCAGGTCATCACTTTG
1 GGTGATGTGGTACATGTCATGTCATCACCTTG
*** *
73976 GGTGACACGATACATGTCATGTCAAT-ACCTTG
1 GGTGATGTGGTACATGTCATGTC-ATCACCTTG
* * *
74008 GGTGATGTGGTACATGTCATATTATCA-CTTT
1 GGTGATGTGGTACATGTCATGTCATCACCTTG
74039 GGTGATGTGG
1 GGTGATGTGG
74049 CGTATGATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
31 15 0.26
32 40 0.70
33 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (32 bp):
GGTGATGTGGTACATGTCATGTCATCACCTTG
Found at i:75865 original size:3 final size:3
Alignment explanation
Indices: 75857--75918 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
75847 GCACCTCTAA
75857 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
75905 GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GA
75919 AGAAGAAGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:79980 original size:169 final size:168
Alignment explanation
Indices: 79697--80035 Score: 624
Period size: 169 Copynumber: 2.0 Consensus size: 168
79687 ATTAACAAAA
79697 TTAAAACACTTAGATAAATATGATTTTTTTTAGGTTTACGGGCTAATTCGGAGGCTTTCGAGTCT
1 TTAAAACACTTAGATAAATATGATTTTTTTTAGGTTTACGGGCTAATTCGGAGGCTTTCGAGTCT
* *
79762 AAATTTGACCAAACTGATTGCGGAATCGAAATCAGTATATCGAAAAACATAAAATATGATTTTTT
66 AAATTTGACCAAACCGATTGCGGAATCGAAATCAGTATATCGAAAAACATAAAATATGACTTTTT
*
79827 TAAAATTCGAATTCTTGGTCAAGGTCAAAGTCAACGGG
131 GAAAATTCGAATTCTTGGTCAAGGTCAAAGTCAACGGG
*
79865 TTAACACACTTAGATAAATATGATTTTTTTTCAGGTTTACGGGCTAATTCGGAGGCTTTCGAGTC
1 TTAAAACACTTAGATAAATATGATTTTTTTT-AGGTTTACGGGCTAATTCGGAGGCTTTCGAGTC
79930 TAAATTTGACCAAACCGATTGCGGAATCGAAATCAGTATATCGAAAAACATAAAATATGACTTTT
65 TAAATTTGACCAAACCGATTGCGGAATCGAAATCAGTATATCGAAAAACATAAAATATGACTTTT
*
79995 TGAAAATTCGAATTCTTGGTCAAGGTCAAAGTCAATGGG
130 TGAAAATTCGAATTCTTGGTCAAGGTCAAAGTCAACGGG
80034 TT
1 TT
80036 TGACTAAAGA
Statistics
Matches: 165, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
168 30 0.18
169 135 0.82
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (168 bp):
TTAAAACACTTAGATAAATATGATTTTTTTTAGGTTTACGGGCTAATTCGGAGGCTTTCGAGTCT
AAATTTGACCAAACCGATTGCGGAATCGAAATCAGTATATCGAAAAACATAAAATATGACTTTTT
GAAAATTCGAATTCTTGGTCAAGGTCAAAGTCAACGGG
Found at i:80263 original size:28 final size:28
Alignment explanation
Indices: 80201--80334 Score: 189
Period size: 28 Copynumber: 4.8 Consensus size: 28
80191 ACATTTTTTT
* * *
80201 AATAATTACGAGAATATCAACCTTTTCGA
1 AATAATTACCAAAATATC-ACTTTTTCGA
* *
80230 AATAATTACCAAAATATTACTTTTTCAA
1 AATAATTACCAAAATATCACTTTTTCGA
*
80258 AATAATTACCAAAATATCACTTTTTTGA
1 AATAATTACCAAAATATCACTTTTTCGA
*
80286 AATAATTATCAAAATATCAC-TTTTCGA
1 AATAATTACCAAAATATCACTTTTTCGA
80313 AATAATTACCAAAATATCACTT
1 AATAATTACCAAAATATCACTT
80335 GTTTAACAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 25 0.27
28 53 0.57
29 15 0.16
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (28 bp):
AATAATTACCAAAATATCACTTTTTCGA
Found at i:80318 original size:55 final size:56
Alignment explanation
Indices: 80201--80334 Score: 189
Period size: 55 Copynumber: 2.4 Consensus size: 56
80191 ACATTTTTTT
* * * *
80201 AATAATTACGAGAATATCAACCTTTTCGAAATAATTACCAAAATATTACTTTTTCAA
1 AATAATTACCAAAATATC-ACTTTTTCGAAATAATTACCAAAATATCACTTTTTCAA
* * *
80258 AATAATTACCAAAATATCACTTTTTTGAAATAATTATCAAAATATCAC-TTTTCGA
1 AATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATATCACTTTTTCAA
80313 AATAATTACCAAAATATCACTT
1 AATAATTACCAAAATATCACTT
80335 GTTTAACAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
55 28 0.40
56 26 0.37
57 16 0.23
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (56 bp):
AATAATTACCAAAATATCACTTTTTCGAAATAATTACCAAAATATCACTTTTTCAA
Done.