Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003711.1 Hibiscus syriacus cultivar Beakdansim tig00007937_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: 66733
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:5648 original size:19 final size:19
Alignment explanation
Indices: 5621--5665 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
5611 AGTGTAGACT
5621 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
*
5640 ATTGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
5659 ATCGCAA
1 ATCGCAA
5666 TGACAACTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:5705 original size:20 final size:20
Alignment explanation
Indices: 5680--5777 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
5670 AACTGAGACT
5680 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
5700 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
** * **
5721 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
5742 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
5762 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
5778 CAACGCGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 30 0.45
21 36 0.55
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:5726 original size:21 final size:21
Alignment explanation
Indices: 5700--5753 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
5690 GAAATGAAAA
5700 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
5721 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
5742 ATCGCAACGCGA
1 ATCGCAACGCGA
5754 AATGGAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:6901 original size:37 final size:37
Alignment explanation
Indices: 6832--6902 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
6822 ATAAATAATA
*
6832 TTCATATTTCAATTAAATATAAATTTATAATAACATG
1 TTCATATTTCAATTAAATATAAACTTATAATAACATG
* *
6869 TTCATATTTTAATTGAATATAAAACTTA-AATAAC
1 TTCATATTTCAATTAAATAT-AAACTTATAATAAC
6903 GTAATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 24 0.80
38 6 0.20
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (37 bp):
TTCATATTTCAATTAAATATAAACTTATAATAACATG
Found at i:17050 original size:4 final size:4
Alignment explanation
Indices: 17041--17075 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
17031 AGGGTTTGTT
17041 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
17076 TTAGAGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:21504 original size:14 final size:14
Alignment explanation
Indices: 21485--21511 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21475 TCTCTGTCGT
21485 TTGCATTCTTTCCG
1 TTGCATTCTTTCCG
21499 TTGCATTCTTTCC
1 TTGCATTCTTTCC
21512 TCCAACAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.11, T:0.52
Consensus pattern (14 bp):
TTGCATTCTTTCCG
Found at i:23351 original size:42 final size:42
Alignment explanation
Indices: 23240--23336 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
23230 TTGCAGGGAC
*
23240 ACCTCATTCAGCAGGAGAATCTAGAACAGCATAACAAAGTAA
1 ACCTCATTCAGCAGGAGAATCTAGAACTGCATAACAAAGTAA
* * *
23282 ACCTCATTCATCAGGAGAATCTAGAACTGCATAACAAATTTA
1 ACCTCATTCAGCAGGAGAATCTAGAACTGCATAACAAAGTAA
*
23324 ACCTCATGCAGCA
1 ACCTCATTCAGCA
23337 AGAAAATACT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (42 bp):
ACCTCATTCAGCAGGAGAATCTAGAACTGCATAACAAAGTAA
Found at i:29553 original size:39 final size:39
Alignment explanation
Indices: 29508--29584 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
29498 AAGTTTTAGT
*
29508 TTATATTTTATTTTAATATCTCGTTGTTAAAAATTTAAG
1 TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAAG
29547 TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAA
1 TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAA
29585 CAAAACTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (39 bp):
TTATATTTTATTTTAATATCTCGTCGTTAAAAATTTAAG
Found at i:29661 original size:49 final size:50
Alignment explanation
Indices: 29606--29709 Score: 158
Period size: 49 Copynumber: 2.1 Consensus size: 50
29596 CACGTTATAT
29606 TTTTTCA-TGTGTAATTACATCATTTATCCCTTAAT-TATTCTCACTCCTA
1 TTTTTCATTG-GTAATTACATCATTTATCCCTTAATATATTCTCACTCCTA
* *
29655 TTTTTCATTGGTAATTACATCATTTATCCCTTAATCATCTTCTCACTCTTA
1 TTTTTCATTGGTAATTACATCATTTATCCCTTAAT-ATATTCTCACTCCTA
29706 TTTT
1 TTTT
29710 GGTCATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
49 32 0.64
50 2 0.04
51 16 0.32
ACGTcount: A:0.23, C:0.22, G:0.04, T:0.51
Consensus pattern (50 bp):
TTTTTCATTGGTAATTACATCATTTATCCCTTAATATATTCTCACTCCTA
Found at i:33822 original size:20 final size:20
Alignment explanation
Indices: 33772--33824 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
33762 AGTTGTTTCT
*
33772 AGCCATTGGGAATGTTTTGG
1 AGCCATTGGGGATGTTTTGG
33792 AGCCATTGGGGATGTTTTGG
1 AGCCATTGGGGATGTTTTGG
*
33812 AGTCATTGGGGAT
1 AGCCATTGGGGAT
33825 TTATTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.09, G:0.38, T:0.34
Consensus pattern (20 bp):
AGCCATTGGGGATGTTTTGG
Found at i:33937 original size:21 final size:21
Alignment explanation
Indices: 33911--33966 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
33901 GGGCTTGATA
33911 GTATCGATACTACTATTCACG
1 GTATCGATACTACTATTCACG
* * *
33932 GTATCGATACTAGTGTTCATG
1 GTATCGATACTACTATTCACG
33953 GTATCGATACTACT
1 GTATCGATACTACT
33967 GTAGCAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (21 bp):
GTATCGATACTACTATTCACG
Found at i:34041 original size:21 final size:21
Alignment explanation
Indices: 34015--34065 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
34005 TTAGTATCGG
**
34015 TACTGTTCATGGTATTGATAC
1 TACTGTTCATGGTATCAATAC
34036 TACTGTTCATGGTATCAATAC
1 TACTGTTCATGGTATCAATAC
*
34057 TATTGTTCA
1 TACTGTTCA
34066 CAAATTATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (21 bp):
TACTGTTCATGGTATCAATAC
Found at i:34094 original size:20 final size:20
Alignment explanation
Indices: 34071--34146 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
34061 GTTCACAAAT
34071 TATCGGTACTATTCATACAA
1 TATCGGTACTATTCATACAA
* *
34091 TATCGATAATATTCATACAA
1 TATCGGTACTATTCATACAA
* *
34111 TATCAGTACTATTCATATAA
1 TATCGGTACTATTCATACAA
*
34131 T-GCGGTACTATTCATA
1 TATCGGTACTATTCATA
34147 AAAAATTTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 13 0.27
20 35 0.73
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
TATCGGTACTATTCATACAA
Found at i:35141 original size:19 final size:19
Alignment explanation
Indices: 35100--35141 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35090 ATGAAAAAAT
*
35100 GGTATCGATACCATAATAG
1 GGTATCGATACCATAATAA
* *
35119 GGTATCGGTACCATAGTAA
1 GGTATCGATACCATAATAA
35138 GGTA
1 GGTA
35142 GTATCAATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCATAATAA
Found at i:35589 original size:55 final size:54
Alignment explanation
Indices: 35516--35676 Score: 214
Period size: 54 Copynumber: 3.0 Consensus size: 54
35506 TGCAAAAAGT
* * *
35516 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGAACTATGTGTGC-AAAC
* * *
35571 TAAGAAATTCATATTAAGTATATGAATTTTCATATGGGAACTATGTGTGCAAAC
1 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGAACTATGTGTGCAAAC
* * * * *
35625 AAAGAAATCCATACTAAGTGTATGAATTTTCGTGTGGGAAATATATGTGCAA
1 TAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGAACTATGTGTGCAA
35677 TTATCATAAG
Statistics
Matches: 92, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
54 48 0.52
55 44 0.48
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (54 bp):
TAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGGAACTATGTGTGCAAAC
Found at i:35992 original size:68 final size:68
Alignment explanation
Indices: 35878--36078 Score: 242
Period size: 68 Copynumber: 3.0 Consensus size: 68
35868 ATTAATTGTC
* * * *
35878 TAACTGTGCACTTGACAGAAA-GATGTAAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 TAACTATGCATTTAACAGAAATG-TGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
35942 GGCA
65 GGCA
* * * *
35946 TAACTATGCATTTAACATAAATGTGTCAATTATGCCAGTTATATGAAATGCTAAGTGTCTTTGAG
1 TAACTATGCATTTAACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
*
36011 GCC
66 GCA
* * * * * * *
36014 TAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATAAAAGGTTAAATACCTTTGAG
1 TAACTATGCATTTAACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
36079 TAAAAGATTA
Statistics
Matches: 112, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
68 111 0.99
69 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (68 bp):
TAACTATGCATTTAACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
GCA
Found at i:36145 original size:81 final size:81
Alignment explanation
Indices: 36010--36247 Score: 422
Period size: 81 Copynumber: 2.9 Consensus size: 81
36000 GTGTCTTTGA
* * *
36010 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATAAAAGGTTAAATACCTT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTT
36075 TGAGTAAAAGATTAAT
66 TGAGTAAAAGATTAAT
* *
36091 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCACTCATGCTAGTTAGATGAAAGGTTAAATACCTT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTT
36156 TGAGTAAAAGATTAAT
66 TGAGTAAAAGATTAAT
*
36172 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATGCCTT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTT
36237 TGAGTAAAAGA
66 TGAGTAAAAGA
36248 CTAGATGTAT
Statistics
Matches: 149, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 149 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTT
TGAGTAAAAGATTAAT
Found at i:36325 original size:45 final size:45
Alignment explanation
Indices: 36256--36407 Score: 234
Period size: 45 Copynumber: 3.3 Consensus size: 45
36246 GACTAGATGT
36256 ATAACAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
1 ATAA-AATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
36302 ATAAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
1 ATAAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
* *
36347 ATGAAATGTATAATAGTGTATAAAAAGGCATG-AACGATTGCCATAA
1 ATAAAATGTATAATAGTGTAT-AAAAGGCATGAAAGGA-TGCCATAA
*
36393 ATGAAAATGCATAAT
1 AT-AAAATGTATAAT
36408 GGTACATTAT
Statistics
Matches: 99, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
45 65 0.66
46 24 0.24
47 10 0.10
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (45 bp):
ATAAAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAA
Found at i:36432 original size:92 final size:90
Alignment explanation
Indices: 36261--36444 Score: 237
Period size: 92 Copynumber: 2.0 Consensus size: 90
36251 GATGTATAAC
* * **
36261 AATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAATAGTGTATAAA
1 AATGTATAATAGTGTATAAAAGGCATGAAACGATGCCATAAATAAAATGCATAATAGTACATAAA
36326 AGGCATGAAAGGATGCCATAAATGA
66 AGGCATGAAAGGATGCCATAAATGA
*
36351 AATGTATAATAGTGTATAAAAAGGCATG-AACGATTGCCATAAATGAAAATGCATAATGGTACAT
1 AATGTATAATAGTGTAT-AAAAGGCATGAAACGA-TGCCATAAAT-AAAATGCATAATAGTACA-
* * * *
36415 TATAA-GCATGAATGGATGCTATCAATGA
62 TAAAAGGCATGAAAGGATGCCATAAATGA
36443 AA
1 AA
36445 ATAAAGAATA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
90 21 0.26
91 20 0.25
92 36 0.44
93 4 0.05
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (90 bp):
AATGTATAATAGTGTATAAAAGGCATGAAACGATGCCATAAATAAAATGCATAATAGTACATAAA
AGGCATGAAAGGATGCCATAAATGA
Found at i:40379 original size:22 final size:20
Alignment explanation
Indices: 40331--40402 Score: 101
Period size: 22 Copynumber: 3.5 Consensus size: 20
40321 AAGCAAAAAT
*
40331 GGTATCGATACCATAAT-AG
1 GGTATCGATACCATAGTAAG
40350 GGTATCGATACCATAGTAAG
1 GGTATCGATACCATAGTAAG
*
40370 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGTAAG
40392 GGTATCGATAC
1 GGTATCGATAC
40403 TTAGGAGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.33
20 13 0.27
22 19 0.40
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:40819 original size:55 final size:54
Alignment explanation
Indices: 40747--40878 Score: 174
Period size: 55 Copynumber: 2.4 Consensus size: 54
40737 GCAAAAAGTT
* * *
40747 AAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGCATTTTGTGTGCAAAACA
1 AAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGAACTATGTGTGC-AAACA
* * * * *
40802 AATAAATTCATATTAAGTGTATGAATTTCTGTATGGGAACTATGTGTGCAAACT
1 AAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGAACTATGTGTGCAAACA
*
40856 AAGAAATCCATACTAAGTGTATG
1 AAGAAATTCATACTAAGTGTATG
40879 TGTTGAGTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 24 0.36
55 42 0.64
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (54 bp):
AAGAAATTCATACTAAGTGTATGAATTTCCGTATGAGAACTATGTGTGCAAACA
Found at i:46262 original size:42 final size:42
Alignment explanation
Indices: 46199--46317 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
46189 TTCCCCGAAA
* **
46199 TCCCGTGTTTGTTTCATGTAATTCGTTTTCTGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
46241 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
*
46283 TCCCGTGTTTGTTTCACGTAATTCATTTTCCAGAA
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAA
46318 TATAATTCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATGTTT
Found at i:46519 original size:21 final size:23
Alignment explanation
Indices: 46476--46526 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
46466 CATTTTCATC
46476 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
46500 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
*
46521 ATAATA
1 AAAATA
46527 ATATAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:46540 original size:22 final size:23
Alignment explanation
Indices: 46493--46587 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 23
46483 TATTTATTAA
* *
46493 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
46514 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
46537 -ATATTTTTAATATTATATAAAATAATC
1 AATATTTATAATA--ATAT--AAT-ATT
46564 AATTATATTATAATAATATAATAT
1 AA-TAT-TTATAATAATATAATAT
46588 AAGATATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
21 11 0.19
22 15 0.25
23 4 0.07
24 4 0.07
25 2 0.03
26 6 0.10
27 2 0.03
28 5 0.08
29 3 0.05
30 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:46670 original size:29 final size:29
Alignment explanation
Indices: 46489--46674 Score: 99
Period size: 29 Copynumber: 6.3 Consensus size: 29
46479 ATATTATTTA
*
46489 TTAA-AATATTTAA-AATATATTTATTAATAT
1 TTAATAATATATAATAAT-TATTTA-T-ATAT
* *
46519 TT-ATAATAATATAATATTATATTTTTA-AT
1 TTAATAAT-ATATAATAAT-TATTTATATAT
46548 ATTATATAA-A-ATAATCAATTATATTATA-A-
1 -TTA-ATAATATATAAT-AATTAT-TTATATAT
* * *
46577 TAATATAATATA-AGATATTATATTTTTAT-T
1 TTA-ATAATATATA-ATAAT-TATTTATATAT
*
46607 TTAATAATATATAATAATTTTTTATATAT
1 TTAATAATATATAATAATTATTTATATAT
46636 TTAATAATGA-ATAAT-ATTATTTATATAT
1 TTAATAAT-ATATAATAATTATTTATATAT
46664 TTAAATAATAT
1 TT-AATAATAT
46675 TTTAGTAAAG
Statistics
Matches: 124, Mismatches: 13, Indels: 39
0.70 0.07 0.22
Matches are distributed among these distances:
28 29 0.23
29 51 0.41
30 26 0.21
31 6 0.05
32 12 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TTAATAATATATAATAATTATTTATATAT
Found at i:46804 original size:90 final size:86
Alignment explanation
Indices: 46690--46859 Score: 200
Period size: 90 Copynumber: 1.9 Consensus size: 86
46680 TAAAGATATT
* * * * * *
46690 TAAAATATGCCAATTAATATTTTTA-AAATATAA-TATAACATTATTACTTTAATAAATAATTAA
1 TAAAATATACCAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA
46753 TATAATTTATAATATTTTATTTCAC
64 -ATAATTT-TAATATTTTATTTCAC
*
46778 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATACC-A-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
46843 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
46860 AAATAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 20 0.29
89 7 0.10
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (86 bp):
TAAAATATACCAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:47042 original size:20 final size:21
Alignment explanation
Indices: 47004--47055 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
46994 TTTCCAGATG
47004 TTTTCCAGAAATGTGTAATTCA
1 TTTTCCAGAAA-GTGTAATTCA
47026 TTTTCCAGAAA-TGTAATTCA
1 TTTTCCAGAAAGTGTAATTCA
47046 TTTTCCAGAA
1 TTTTCCAGAA
47056 TTCAAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 19 0.63
22 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTTCCAGAAAGTGTAATTCA
Found at i:47063 original size:20 final size:20
Alignment explanation
Indices: 47020--47064 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
47010 AGAAATGTGT
**
47020 AATTCATTTTCCAGAAATGT
1 AATTCATTTTCCAGAAATCA
*
47040 AATTCATTTTCCAGAATTCA
1 AATTCATTTTCCAGAAATCA
47060 AATTC
1 AATTC
47065 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (20 bp):
AATTCATTTTCCAGAAATCA
Found at i:47095 original size:15 final size:15
Alignment explanation
Indices: 47038--47089 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
47028 TTCCAGAAAT
**
47038 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
47053 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
47067 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
47082 GTAATTCA
1 GTAATTCA
47090 TTTTCCGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.35
15 22 0.65
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:55519 original size:15 final size:15
Alignment explanation
Indices: 55478--55512 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
55468 ATCAAAGGAA
*
55478 GAAACGAAAAATGAG
1 GAAACAAAAAATGAG
55493 GAAACAAAAAATGAG
1 GAAACAAAAAATGAG
55508 GAAAC
1 GAAAC
55513 TCAAAATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.23, T:0.06
Consensus pattern (15 bp):
GAAACAAAAAATGAG
Found at i:61036 original size:68 final size:67
Alignment explanation
Indices: 60923--61108 Score: 300
Period size: 68 Copynumber: 2.7 Consensus size: 67
60913 TATTAATGGT
* *
60923 CTAACTGTGTATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACA-AAAGGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGA
60988 GGC
65 GGC
*
60991 CTAACTGTGCATTTGACATAAAGGTGTCAATCATGCTAGTAAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACA-AAAGGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGA
61056 GGC
65 GGC
* **
61059 CTAACTGTGCATTTGACAGAATTTGTCAATCATGCTAGTTAGATGAAAGG
1 CTAACTGTGCATTTGACAAAAGGTGTCAATCATGCTAGTTAGATGAAAGG
61109 TTAAATACCT
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 28 0.25
68 82 0.75
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (67 bp):
CTAACTGTGCATTTGACAAAAGGTGTCAATCATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAG
GC
Found at i:61180 original size:81 final size:81
Alignment explanation
Indices: 61082--61292 Score: 323
Period size: 81 Copynumber: 2.6 Consensus size: 81
61072 TGACAGAATT
* *
61082 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTAAGTAAAAGATTAATGGCCTAGTTTT
1 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGT
*
61147 GCACTTGACAGAAAGG
66 GCACTTGACAAAAAGG
* * * *
61163 TGTCACTCATGCCAGTTAGATAAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGTCTAGTTGT
1 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGT
*
61228 GCATTTGACAAAAAGG
66 GCACTTGACAAAAAGG
* **
61244 TGTCAATCATGTTAGTTAGATGAAAGGTTAAATGTCTTTGAGTAAAAGA
1 TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGA
61293 CTAGATGTAT
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 116 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TGTCAATCATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGTTGT
GCACTTGACAAAAAGG
Found at i:61367 original size:45 final size:45
Alignment explanation
Indices: 61306--61494 Score: 240
Period size: 45 Copynumber: 4.2 Consensus size: 45
61296 GATGTATAAC
*
61306 AATGTATAATAT-TGTATAAAAGGCATGAAAGGATGTCATAAATGA
1 AATGTATAAT-TGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* *
61351 AATATATAATTGTGTATAAAAGGAATGAAAGGATGCCATAAATGA
1 AATGTATAATTGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* *
61396 AATGTATAATAGTGTATAAAAGGCATGAAAGGTTGCCATAAATGA
1 AATGTATAATTGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* * * * *
61441 AATGTATAA--GTGTGTAAAAGGCATTAACGGTTACCATAAATGAA
1 AATGTATAATTGTGTATAAAAGGCATGAAAGGATGCCATAAATG-A
*
61485 AATGCATAAT
1 AATGTATAAT
61495 GGTGCATTAT
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
43 29 0.22
44 10 0.08
45 90 0.70
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (45 bp):
AATGTATAATTGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:62102 original size:2 final size:2
Alignment explanation
Indices: 62097--62143 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
62087 AATAAAAAAT
62097 TA TA TA T- TA 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 TA TA TA TA TA
62138 TA TA TA
1 TA TA TA
62144 ATAAAATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65150 original size:30 final size:30
Alignment explanation
Indices: 65114--65170 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
65104 TTCATGCATG
65114 CAGTGTTTGAGGGAGATTGTCGATCAGATT
1 CAGTGTTTGAGGGAGATTGTCGATCAGATT
65144 CAGTGTTTGAGGGAGATTGTCGATCAG
1 CAGTGTTTGAGGGAGATTGTCGATCAG
65171 TAATTCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.35, T:0.32
Consensus pattern (30 bp):
CAGTGTTTGAGGGAGATTGTCGATCAGATT
Found at i:66018 original size:24 final size:25
Alignment explanation
Indices: 65981--66040 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
65971 AACTTTTCAC
65981 TTATAATATAAATACTTAA-A-ATATT
1 TTAT-ATATAAATA-TTAATACATATT
66006 TTATATATAAATATTAATATCATATT
1 TTATATATAAATATTAATA-CATATT
66032 TTA-ATATAA
1 TTATATATAA
66041 TTTTAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.12
24 10 0.31
25 10 0.31
26 8 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (25 bp):
TTATATATAAATATTAATACATATT
Found at i:66037 original size:13 final size:12
Alignment explanation
Indices: 66001--66047 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
65991 AATACTTAAA
66001 ATATTTTATATAT
1 ATATTTTA-ATAT
* *
66014 AAATATTAATAT
1 ATATTTTAATAT
66026 CATATTTTAATAT
1 -ATATTTTAATAT
66039 A-ATTTTAAT
1 ATATTTTAAT
66048 GAATATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 8 0.28
12 5 0.17
13 16 0.55
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTTAATAT
Found at i:66073 original size:42 final size:44
Alignment explanation
Indices: 66007--66089 Score: 109
Period size: 42 Copynumber: 1.9 Consensus size: 44
65997 TAAAATATTT
66007 TATATATAAATATTAATATCATATTTTAAT-ATAATTTTAATGAA
1 TATATATAAATATTAATATCATA-TTTAATAATAATTTTAATGAA
* * *
66051 TATAT-TAATTATTAA-ATTATATTTATTAATAATTTTAAT
1 TATATATAAATATTAATATCATATTTAATAATAATTTTAAT
66090 ATTATAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 5 0.14
42 16 0.46
43 9 0.26
44 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (44 bp):
TATATATAAATATTAATATCATATTTAATAATAATTTTAATGAA
Found at i:66133 original size:18 final size:18
Alignment explanation
Indices: 66067--66152 Score: 61
Period size: 18 Copynumber: 4.6 Consensus size: 18
66057 AATTATTAAA
*
66067 TTATATTTATTAATA-ATT
1 TTATAATTA-TAATATATT
66085 TTA-ATATTATAATATTATAT
1 TTATA-ATTATAATA-TAT-T
66105 TTA-AATGTTATAATATATT
1 TTATAA--TTATAATATATT
* *
66124 TTATAATTATAGTATATA
1 TTATAATTATAATATATT
*
66142 TTATATTTATA
1 TTATAATTATA
66153 TTTGAATGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
17 6 0.11
18 26 0.46
19 7 0.12
20 10 0.18
21 8 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTATAATTATAATATATT
Found at i:66253 original size:22 final size:22
Alignment explanation
Indices: 66205--66255 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
66195 TAACTTCATA
*
66205 AAAATAATATTATTGAATATTT
1 AAAATAATATTAATGAATATTT
*
66227 AAAATATATATTAAT-AATTTTT
1 AAAATA-ATATTAATGAATATTT
*
66249 TAAATAA
1 AAAATAA
66256 AATAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.68
23 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATAATATTAATGAATATTT
Found at i:66297 original size:14 final size:15
Alignment explanation
Indices: 66278--66319 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
66268 TTATTTTTAA
66278 TATTATTATAAT-AG
1 TATTATTATAATAAG
*
66292 TATTATTTTAATAAG
1 TATTATTATAATAAG
*
66307 TAATTAATATAAT
1 T-ATTATTATAAT
66320 TAATAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 3 0.13
16 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
TATTATTATAATAAG
Found at i:66447 original size:14 final size:15
Alignment explanation
Indices: 66394--66448 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 15
66384 TAAATAATCT
66394 TAATATTTAAA-AAA
1 TAATATTTAAATAAA
66408 T-A-ATTT-AAT-AA
1 TAATATTTAAATAAA
*
66419 TAATATTGAAATAAA
1 TAATATTTAAATAAA
66434 TAAT-TTTAAATAAA
1 TAATATTTAAATAAA
66448 T
1 T
66449 TATTATAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 4 0.12
14 14 0.41
15 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
TAATATTTAAATAAA
Done.