Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000003.1 Hibiscus syriacus cultivar Beakdansim tig00000008_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: 105507
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2477 original size:56 final size:55
Alignment explanation
Indices: 2388--2501 Score: 156
Period size: 56 Copynumber: 2.1 Consensus size: 55
2378 CTTGGGTCTG
* * * *
2388 AGACATTGGTGCAAGTGTCCGACAGGGAGGTTCAAGATAGAGTGTCGGGCTTGCTA
1 AGACATTAGTGCAAGTGTCCGACAGGGAGGTTCAAGATAGA-TATCAGGCTTGCCA
* * *
2444 AGACATTAGTGCAAGTGTCTGATAGGGATGTTCAAGATAGATATCAGGCTTGCCA
1 AGACATTAGTGCAAGTGTCCGACAGGGAGGTTCAAGATAGATATCAGGCTTGCCA
2499 AGA
1 AGA
2502 TCACCAGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 14 0.27
56 37 0.73
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.25
Consensus pattern (55 bp):
AGACATTAGTGCAAGTGTCCGACAGGGAGGTTCAAGATAGATATCAGGCTTGCCA
Found at i:9341 original size:29 final size:29
Alignment explanation
Indices: 9308--9376 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
9298 GGAGAGAGTA
9308 AAGTTCAATGACAAAAAATCAAATGTATT
1 AAGTTCAATGACAAAAAATCAAATGTATT
9337 AAGTTCAATGACAAAAAATCAAATGTATT
1 AAGTTCAATGACAAAAAATCAAATGTATT
9366 AAGTTCAATGA
1 AAGTTCAATGA
9377 AAATACGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.28
Consensus pattern (29 bp):
AAGTTCAATGACAAAAAATCAAATGTATT
Found at i:20730 original size:15 final size:14
Alignment explanation
Indices: 20710--20777 Score: 97
Period size: 15 Copynumber: 4.9 Consensus size: 14
20700 TTTACCGGAT
20710 AAAAAACCGGTTTGA
1 AAAAAACCGGTTT-A
20725 AAAAAACCGG-TT-
1 AAAAAACCGGTTTA
20737 AAAAAACCGGTTTGA
1 AAAAAACCGGTTT-A
20752 AAAAAACCGG-TTA
1 AAAAAACCGGTTTA
20765 AAAAAACCGGTTT
1 AAAAAACCGGTTT
20778 TTATCCGGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.20
13 13 0.27
14 6 0.12
15 20 0.41
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (14 bp):
AAAAAACCGGTTTA
Found at i:20739 original size:27 final size:27
Alignment explanation
Indices: 20703--20777 Score: 132
Period size: 27 Copynumber: 2.7 Consensus size: 27
20693 CGGTTTTTTT
*
20703 ACCGGATAAAAAACCGGTTTGAAAAAA
1 ACCGGTTAAAAAACCGGTTTGAAAAAA
20730 ACCGGTTAAAAAACCGGTTTGAAAAAA
1 ACCGGTTAAAAAACCGGTTTGAAAAAA
20757 ACCGGTTAAAAAAACCGGTTT
1 ACCGGTT-AAAAAACCGGTTT
20778 TTATCCGGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 33 0.72
28 13 0.28
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (27 bp):
ACCGGTTAAAAAACCGGTTTGAAAAAA
Found at i:23095 original size:21 final size:21
Alignment explanation
Indices: 23071--23110 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23061 TTTATTTTAT
23071 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
23092 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
23111 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:23158 original size:33 final size:33
Alignment explanation
Indices: 23105--23203 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
23095 TTTGTTTCAA
23105 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
23137 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
23170 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
23203 T
1 T
23204 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:23465 original size:21 final size:21
Alignment explanation
Indices: 23439--23495 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
23429 TGGAGCGTGG
*
23439 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
**
23460 GGGAATCGGTTTTCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
23481 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
23496 AAGTGTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:23687 original size:15 final size:15
Alignment explanation
Indices: 23662--23717 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
23652 ATCTGGAATA
*
23662 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
23677 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
23692 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
23709 TTAAAACCG
1 TTAAAACCG
23718 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:23726 original size:21 final size:18
Alignment explanation
Indices: 23681--23714 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23671 GTTTTTTTAT
23681 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
23698 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
23715 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:23834 original size:15 final size:17
Alignment explanation
Indices: 23808--23839 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
23798 TTCTATGAGA
23808 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
23824 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
23840 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:24504 original size:22 final size:22
Alignment explanation
Indices: 24479--24533 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
24469 CCTTTGTTTT
24479 TTCCTCTCAACCTTCTATCTTC
1 TTCCTCTCAACCTTCTATCTTC
24501 TTCCTCTCAACCTTCTATCTTC
1 TTCCTCTCAACCTTCTATCTTC
24523 TTCCTCTCAAC
1 TTCCTCTCAAC
24534 GGCACCTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.44
Consensus pattern (22 bp):
TTCCTCTCAACCTTCTATCTTC
Found at i:36201 original size:17 final size:17
Alignment explanation
Indices: 36137--36202 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 17
36127 TGTTAGATAC
*
36137 AAAAATATAATAAAAT-
1 AAAAAAATAATAAAATA
*
36153 -AAAGAA-AAT-AAATA
1 AAAAAAATAATAAAATA
** *
36167 AATAAATTTAACAAAATA
1 AA-AAAAATAATAAAATA
36185 AAAAAAATAATAAAATA
1 AAAAAAATAATAAAATA
36202 A
1 A
36203 TAAAGACAAG
Statistics
Matches: 36, Mismatches: 9, Indels: 9
0.67 0.17 0.17
Matches are distributed among these distances:
13 4 0.11
14 3 0.08
15 5 0.14
16 2 0.06
17 15 0.42
18 7 0.19
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAAATAATAAAATA
Found at i:36248 original size:26 final size:26
Alignment explanation
Indices: 36187--36256 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
36177 ACAAAATAAA
36187 AAAAATAATAAA-ATAATAAAGACAAG
1 AAAAATAATAAATA-AATAAAGACAAG
36213 AAACAA-AATAAATAAATAAAGA-ATAG
1 AAA-AATAATAAATAAATAAAGACA-AG
* *
36239 GAAAATAAT-AGTAAATAA
1 AAAAATAATAAATAAATAA
36257 TAATATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 11 0.29
26 24 0.63
27 3 0.08
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (26 bp):
AAAAATAATAAATAAATAAAGACAAG
Found at i:36360 original size:30 final size:28
Alignment explanation
Indices: 36326--36386 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
36316 AAACATAAAG
36326 ATAATGAAGCAAAAAGTA-TAATATATATAT
1 ATAATG-A-CAAAAAG-AGTAATATATATAT
* *
36356 ATAATGATAAAAAGAGTAATATATGTAT
1 ATAATGACAAAAAGAGTAATATATATAT
36384 ATA
1 ATA
36387 GATAATAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 20 0.71
29 1 0.04
30 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.31
Consensus pattern (28 bp):
ATAATGACAAAAAGAGTAATATATATAT
Found at i:36443 original size:11 final size:11
Alignment explanation
Indices: 36405--36505 Score: 59
Period size: 11 Copynumber: 9.2 Consensus size: 11
36395 AATGAAACAC
36405 TAAAATATATA
1 TAAAATATATA
*
36416 TAATTATATATACA
1 TAA--A-ATATATA
36430 TAAAATATATA
1 TAAAATATATA
36441 TAAAATA-A-A
1 TAAAATATATA
* *
36450 -AAAATAAAGA
1 TAAAATATATA
* * *
36460 AAAAATAAAGA
1 TAAAATATATA
36471 -AAAATA-ATAA
1 TAAAATATAT-A
36481 TAATAATATATA
1 TAA-AATATATA
*
36493 TAAAAAATATA
1 TAAAATATATA
36504 TA
1 TA
36506 GATATAATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
8 6 0.08
9 3 0.04
10 9 0.12
11 37 0.49
12 9 0.12
13 3 0.04
14 9 0.12
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (11 bp):
TAAAATATATA
Found at i:36453 original size:19 final size:19
Alignment explanation
Indices: 36431--36486 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
36421 ATATATACAT
36431 AAAATATATATAAAATAAA-
1 AAAATATA-ATAAAATAAAG
* *
36450 AAAATAAAGAAAAAATAAAG
1 AAAATATA-ATAAAATAAAG
36470 AAAA-ATAATAATAATAA
1 AAAATATAATAA-AATAA
36487 TATATATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.10
19 23 0.77
20 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAATATAATAAAATAAAG
Found at i:38636 original size:110 final size:110
Alignment explanation
Indices: 38495--38787 Score: 390
Period size: 110 Copynumber: 2.6 Consensus size: 110
38485 TTGACAGCTA
* *
38495 GCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCGAGTACAATATCCTTCACTGTGAAGTTGAG
1 GCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT-CAATATCCTTCACTGTGAAGTTGAA
* * * *
38560 ATTGA-ATCTGAATGAAACTGAAAAGTTTTTTGTTGACAGTCAGTC
65 ATTGACATCTAAATGAAACTAAAAAGTTATTTGTTGACAATCAGTC
* * *
38605 GCCCCATCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCGCTATGAAGTTGAA
1 GCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTC-AATATCCTTCACTGTGAAGTTGAA
*
38670 ATTGACTCTCTAAATGAAACTAAAAAGTTATTTGTTGACAATCAGTC
65 ATTGAC-ATCTAAATGAAACTAAAAAGTTATTTGTTGACAATCAGTC
* * * * *
38717 GCCCCTTTTTGTTATGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCTCTGTGAAGTTG
1 GCCCC--TTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT-CAATATCCTTCACTGTGAAGTTG
38782 AAATTG
63 AAATTG
38788 GCTCTGAAAC
Statistics
Matches: 160, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
109 1 0.01
110 63 0.39
112 40 0.25
114 55 0.34
115 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (110 bp):
GCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCAATATCCTTCACTGTGAAGTTGAAA
TTGACATCTAAATGAAACTAAAAAGTTATTTGTTGACAATCAGTC
Found at i:39919 original size:10 final size:10
Alignment explanation
Indices: 39904--39953 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
39894 ACCCACCTTA
39904 TTTTTTTTTC
1 TTTTTTTTTC
39914 -TTTTTTTTC
1 TTTTTTTTTC
39923 TTTTTTTTTC
1 TTTTTTTTTC
*
39933 TCTTTTTTTCC
1 T-TTTTTTTTC
39944 TTTTTCTTTT
1 TTTTT-TTTT
39954 TTCAATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 9 0.26
10 14 0.40
11 12 0.34
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:50069 original size:19 final size:18
Alignment explanation
Indices: 50040--50133 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 18
50030 TAAAATATAT
*
50040 ATAATTATATATACATAAA
1 ATAAATATATATA-ATAAA
* *
50059 ATATATATATAATAAAAAA
1 ATAAATATAT-ATAATAAA
* *
50078 ATAAATAATAAATAAAGAAA
1 ATAAAT-ATATAT-AATAAA
50098 ATAAATAATAATATATATAAA
1 ATAAAT-AT-ATATA-ATAAA
* *
50119 ATATATAGATATAAT
1 ATAAATATATATAAT
50134 TATTAATGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.03
19 24 0.40
20 22 0.37
21 12 0.20
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAATATATATAATAAA
Found at i:50083 original size:23 final size:23
Alignment explanation
Indices: 50057--50119 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 23
50047 TATATACATA
50057 AAATATATATATAATAAAAAAAT
1 AAATATATATATAATAAAAAAAT
50080 -AA-ATA-ATA-AATAAAGAAAAT
1 AAATATATATATAATAAA-AAAAT
50100 AAATA-ATAATATATATAAAA
1 AAATATAT-ATATA-ATAAAA
50120 TATATAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 6 0.18
22 3 0.09
23 3 0.09
24 2 0.06
25 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATATATATATAATAAAAAAAT
Found at i:50100 original size:20 final size:19
Alignment explanation
Indices: 50056--50108 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
50046 ATATATACAT
*
50056 AAAATATAT-ATATAATAAA
1 AAAATAAATAATA-AATAAA
50075 AAAATAAATAATAAATAAA
1 AAAATAAATAATAAATAAA
50094 GAAAATAAATAATAA
1 -AAAATAAATAATAA
50109 TATATATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATAAATAATAAATAAA
Found at i:69149 original size:3 final size:3
Alignment explanation
Indices: 69141--69167 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
69131 CTATCTTCAT
69141 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
69168 AATGTCCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:75971 original size:2 final size:2
Alignment explanation
Indices: 75966--75992 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
75956 CTTTCGTTTT
75966 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 T
75993 GATGTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77431 original size:20 final size:19
Alignment explanation
Indices: 77402--77441 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
77392 TCTCATCTCG
*
77402 TTGTTTCCCTCTCCATTTTC
1 TTGTTCCCCTC-CCATTTTC
*
77422 TTGTTCCCCTCCGATTTTC
1 TTGTTCCCCTCCCATTTTC
77441 T
1 T
77442 CAAGTGGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.05, C:0.35, G:0.07, T:0.53
Consensus pattern (19 bp):
TTGTTCCCCTCCCATTTTC
Found at i:80050 original size:2 final size:2
Alignment explanation
Indices: 80043--80070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
80033 GTCATGTGTT
80043 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
80071 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:80146 original size:15 final size:13
Alignment explanation
Indices: 80077--80149 Score: 80
Period size: 12 Copynumber: 5.8 Consensus size: 13
80067 CACATATATA
*
80077 TATATATATAT-A
1 TATATATATATGG
*
80089 TATATATATAT-A
1 TATATATATATGG
*
80101 TATATATATAT-A
1 TATATATATATGG
80113 TATATATATATGG
1 TATATATATATGG
80126 TATATATATATGG
1 TATATATATATGG
* *
80139 TTTGTATATAT
1 TATATATATAT
80150 TGGGTGCAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
12 35 0.61
13 22 0.39
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (13 bp):
TATATATATATGG
Found at i:80149 original size:2 final size:2
Alignment explanation
Indices: 80070--80136 Score: 116
Period size: 2 Copynumber: 33.0 Consensus size: 2
80060 ACACACACAC
80070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
80112 AT AT AT AT AT AT GGT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT
80137 GGTTTGTATA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 61 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84087 original size:45 final size:47
Alignment explanation
Indices: 84014--84119 Score: 162
Period size: 45 Copynumber: 2.3 Consensus size: 47
84004 TTTATTTTCG
*
84014 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTTGAAT-AATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
84061 TTTTTTGAATAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
84107 TTTTTGTGAATAA
1 TTTTT-TGAATAA
84120 CAAAGCATAG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
45 28 0.51
46 11 0.20
47 16 0.29
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:93770 original size:8 final size:8
Alignment explanation
Indices: 93752--93907 Score: 96
Period size: 8 Copynumber: 19.6 Consensus size: 8
93742 AGAAATGAAA
93752 AAAAGAATG
1 AAAA-AATG
93761 AAAAAATG
1 AAAAAATG
93769 AAAAAATG
1 AAAAAATG
93777 AAAAAATG
1 AAAAAATG
93785 -AAAAATG
1 AAAAAATG
93792 -AAAAATG
1 AAAAAATG
93799 -AAAAATG
1 AAAAAATG
93806 -AAAAATGAG
1 AAAAAAT--G
93815 AAAAAAATG
1 -AAAAAATG
***
93824 GTGAAA-G
1 AAAAAATG
*
93831 AAAAAAAG
1 AAAAAATG
*
93839 AAAAAAAAG
1 -AAAAAATG
93848 AAGAAAAATG
1 -A-AAAAATG
93858 --AAAA-G
1 AAAAAATG
* *
93863 AGAAAATA
1 AAAAAATG
93871 AAAAAATG
1 AAAAAATG
*
93879 AAAAAATA
1 AAAAAATG
*
93887 AAAAAGAAG
1 AAAAA-ATG
93896 AAAAAA-G
1 AAAAAATG
93903 AAAAA
1 AAAAA
93908 GAAATAAAAG
Statistics
Matches: 123, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
5 1 0.01
6 4 0.03
7 41 0.33
8 43 0.35
9 22 0.18
10 6 0.05
11 6 0.05
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:93780 original size:7 final size:7
Alignment explanation
Indices: 93744--93818 Score: 91
Period size: 7 Copynumber: 10.4 Consensus size: 7
93734 TTTGAAGAAG
93744 AAATGAA
1 AAATGAA
93751 AAA--AA
1 AAATGAA
*
93756 GAATGAAA
1 AAATG-AA
93764 AAATGAAA
1 AAATG-AA
93772 AAATGAAA
1 AAATG-AA
93780 AAATGAA
1 AAATGAA
93787 AAATGAA
1 AAATGAA
93794 AAATGAA
1 AAATGAA
93801 AAATGAA
1 AAATGAA
93808 AAATGAGA
1 AAATGA-A
93816 AAA
1 AAA
93819 AAATGGTGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
5 4 0.06
7 32 0.52
8 26 0.42
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:93844 original size:7 final size:7
Alignment explanation
Indices: 93827--93911 Score: 59
Period size: 7 Copynumber: 12.0 Consensus size: 7
93817 AAAAATGGTG
93827 AAAGAAA
1 AAAGAAA
93834 AAA-AGAA
1 AAAGA-AA
93841 AAA-AAA
1 AAAGAAA
*
93847 GAAGAAA
1 AAAGAAA
*
93854 AATGAAA
1 AAAGAAA
*
93861 AGAGAAA
1 AAAGAAA
93868 ATAA-AAA
1 A-AAGAAA
*
93875 AATGAAA
1 AAAGAAA
*
93882 AAATAAA
1 AAAGAAA
93889 AAAGAAGA
1 AAAGAA-A
*
93897 AAAAAGAA
1 AAAGA-AA
93905 AAAGAAA
1 AAAGAAA
93912 TAAAAGGAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
6 6 0.10
7 42 0.70
8 11 0.18
9 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:93916 original size:16 final size:14
Alignment explanation
Indices: 93833--93916 Score: 69
Period size: 14 Copynumber: 5.6 Consensus size: 14
93823 GGTGAAAGAA
93833 AAAAAGAAAAAAAAG
1 AAAAA-AAAAAAAAG
*
93848 AAGAAAAATGAAAAGAG
1 AA-AAAAA--AAAAAAG
* *
93865 AAAATAAAAAAATG
1 AAAAAAAAAAAAAG
*
93879 AAAAAATAAAAAAG
1 AAAAAAAAAAAAAG
93893 AAGAAAAAAGAAAAAG
1 AA-AAAAAA-AAAAAG
*
93909 AAATAAAA
1 AAAAAAAA
93917 GGAGGGTTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.33
15 14 0.25
16 15 0.27
17 8 0.15
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:95854 original size:55 final size:55
Alignment explanation
Indices: 95241--95844 Score: 925
Period size: 55 Copynumber: 11.0 Consensus size: 55
95231 TTTATAAAGA
* * *
95241 TCGAG-TCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
95296 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
95351 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
95406 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
95461 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * *
95516 TCGAGTTCTATACTCTCTAAAGGAATAGAGAACGGACCCGTTTTTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* **
95571 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGTGGACTAGTTT-TATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
*
95626 TCAAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
95681 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTAGGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTT--GAAGATTGT
* * * *
95737 TCGAG-TCTTATACTCTCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
* * * *
95792 TCGAG-TCTTATACTC-CTTAAAAGAATAGGGAGCAGACCCGTTAT-TTGAAGATT
1 TCGAGTTC-TATACTCTC-TGAAGGAATAGAGAGCGGACCCGTT-TGTTGAAGATT
95845 TTTCAAGTCT
Statistics
Matches: 517, Mismatches: 23, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
54 4 0.01
55 462 0.89
56 49 0.09
57 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:102872 original size:21 final size:21
Alignment explanation
Indices: 102846--102885 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
102836 TCTGCTGAAA
* *
102846 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTTCGGAGTATG
102867 CTCCACCTGCTTCGGAGTA
1 CTCCACCTGCTTCGGAGTA
102886 CTACTTGTCT
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:0.15, C:0.30, G:0.23, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTTCGGAGTATG
Done.