Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007329.1 Hibiscus syriacus cultivar Beakdansim tig00019594_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: 80837
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6217 original size:7 final size:7
Alignment explanation
Indices: 6205--6235 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
6195 GTCAAAGAAA
6205 GTCAACG
1 GTCAACG
6212 GTCAACG
1 GTCAACG
6219 GTCAACG
1 GTCAACG
6226 GTCAACG
1 GTCAACG
6233 GTC
1 GTC
6236 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:6242 original size:5 final size:5
Alignment explanation
Indices: 6232--6289 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
6222 AACGGTCAAC
* *
6232 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
6281 GGTCG GGTC
1 GGTCG GGTC
6290 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:6253 original size:22 final size:22
Alignment explanation
Indices: 6225--6289 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
6215 AACGGTCAAC
6225 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
6247 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
6269 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
6290 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:6309 original size:19 final size:18
Alignment explanation
Indices: 6286--6364 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
6276 GGTCGGGTCG
6286 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
6304 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
6323 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
6343 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
6362 GGT
1 GGT
6365 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:6343 original size:29 final size:31
Alignment explanation
Indices: 6311--6385 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
6301 ACCGAGTCAG
6311 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
6340 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
6370 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
6386 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:6385 original size:9 final size:9
Alignment explanation
Indices: 6286--6384 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
6276 GGTCGGGTCG
*
6286 GGTCAGACC
1 GGTCAAACC
6295 GGTCAAACC
1 GGTCAAACC
*
6304 GAGTCAGACC
1 G-GTCAAACC
6314 GGTCAAACC
1 GGTCAAACC
*
6323 GGTTCGAACC
1 GG-TCAAACC
*
6333 GGTTGAAACC
1 GG-TCAAACC
6343 GGTCAAACC
1 GGTCAAACC
6352 GGTCAGAACC
1 GGTCA-AACC
*
6362 GGTTGAAAACC
1 GG-T-CAAACC
*
6373 GGTTAAACC
1 GGTCAAACC
6382 GGT
1 GGT
6385 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:15468 original size:26 final size:26
Alignment explanation
Indices: 15390--15470 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
15380 GAGATAACTT
*
15390 GATTTGTGCTCCATTTTAATTTTTTA
1 GATTTGTGCTTCATTTTAATTTTTTA
* ** * ***
15416 GAATACTG-TTACAAATTTAACAATTTA
1 GATTTGTGCTT-C-ATTTTAATTTTTTA
15443 GATTTGTGCTTCATTTTAATTTTTTA
1 GATTTGTGCTTCATTTTAATTTTTTA
15469 GA
1 GA
15471 ATACATTACA
Statistics
Matches: 37, Mismatches: 15, Indels: 6
0.64 0.26 0.10
Matches are distributed among these distances:
25 1 0.03
26 18 0.49
27 16 0.43
28 2 0.05
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.51
Consensus pattern (26 bp):
GATTTGTGCTTCATTTTAATTTTTTA
Found at i:15563 original size:24 final size:23
Alignment explanation
Indices: 15536--15581 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
15526 TTTAATTTTT
*
15536 AATATTGCTTTGAACTATTAAAAA
1 AATAATGCTTTGAACTA-TAAAAA
*
15560 AATAATGCTTTGAATTATAAAA
1 AATAATGCTTTGAACTATAAAA
15582 CCTAATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (23 bp):
AATAATGCTTTGAACTATAAAAA
Found at i:16652 original size:14 final size:14
Alignment explanation
Indices: 16633--16665 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16623 GTTCGCCATA
*
16633 AATTTATACTTGTT
1 AATTTATACATGTT
16647 AATTTATACATGTT
1 AATTTATACATGTT
16661 AATTT
1 AATTT
16666 TAGTTTAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (14 bp):
AATTTATACATGTT
Found at i:18917 original size:20 final size:20
Alignment explanation
Indices: 18892--18931 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18882 ATATTTACTT
18892 AGCGGTAATTCTGAAGGTGC
1 AGCGGTAATTCTGAAGGTGC
18912 AGCGGTAATTCTGAAGGTGC
1 AGCGGTAATTCTGAAGGTGC
18932 TGTTCTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (20 bp):
AGCGGTAATTCTGAAGGTGC
Found at i:21665 original size:25 final size:25
Alignment explanation
Indices: 21631--21689 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
21621 ATCATCACTC
21631 CACTGCCTCCATCACCTTCAACCTT
1 CACTGCCTCCATCACCTTCAACCTT
*
21656 CACTGCCTCCATCTCCTTCAACCTT
1 CACTGCCTCCATCACCTTCAACCTT
21681 CACTGCCTC
1 CACTGCCTC
21690 AACCCTCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.17, C:0.49, G:0.05, T:0.29
Consensus pattern (25 bp):
CACTGCCTCCATCACCTTCAACCTT
Found at i:29483 original size:45 final size:45
Alignment explanation
Indices: 29423--29509 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
29413 TGCAATTATC
* * *
29423 TAATTGTTGTTTTGATCCGATAGATTCTTTTGATAGTTCCACTAA
1 TAATTATTATTTTGATCCGATAGATTCTCTTGATAGTTCCACTAA
29468 TAATTATTATTTTGATCCGATAGATTCTCTTGATAGTTCCAC
1 TAATTATTATTTTGATCCGATAGATTCTCTTGATAGTTCCAC
29510 ACAAAAAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (45 bp):
TAATTATTATTTTGATCCGATAGATTCTCTTGATAGTTCCACTAA
Found at i:29713 original size:2 final size:2
Alignment explanation
Indices: 29706--29757 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
29696 AATTATAAAT
* *
29706 TA TA TA TA TA TA TA TG TA TA TG 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
29748 TA TA TA TA TA
1 TA TA TA TA TA
29758 AACTTGCTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30747 original size:20 final size:20
Alignment explanation
Indices: 30706--30747 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
30696 AACTATTAAG
* *
30706 AATAAAAAAAAATAGGTTAT
1 AATAAAAAAAAATAGATAAT
30726 AATAAAGAAAAAATA-ATAAT
1 AATAAA-AAAAAATAGATAAT
30746 AA
1 AA
30748 AAATACCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (20 bp):
AATAAAAAAAAATAGATAAT
Found at i:31819 original size:21 final size:20
Alignment explanation
Indices: 31793--31845 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
31783 AAATAACGAT
*
31793 AAAAAAATATATCAAAAGGCAA
1 AAAAAAATATAT--AAAGACAA
31815 AAAAAAATGATATAAAGACAA
1 AAAAAAAT-ATATAAAGACAA
31836 AAAAAAATAT
1 AAAAAAATAT
31846 GACAAAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 15 0.52
22 8 0.28
23 4 0.14
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAAAATATATAAAGACAA
Found at i:31847 original size:23 final size:22
Alignment explanation
Indices: 31793--31852 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
31783 AAATAACGAT
*
31793 AAAAAAATAT-ATCAAAAGGCA
1 AAAAAAATATGATCAAAAGACA
31814 AAAAAAA-ATGAT-ATAAAGACAA
1 AAAAAAATATGATCA-AAAGAC-A
31836 AAAAAAATATGA-CAAAA
1 AAAAAAATATGATCAAAA
31853 ACATAGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 3 0.09
21 14 0.42
22 11 0.33
23 5 0.15
ACGTcount: A:0.72, C:0.07, G:0.08, T:0.13
Consensus pattern (22 bp):
AAAAAAATATGATCAAAAGACA
Found at i:31951 original size:25 final size:25
Alignment explanation
Indices: 31921--31969 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
31911 TAATTATACG
31921 TTGACTAATAGACTAAGTGGATATA
1 TTGACTAATAGACTAAGTGGATATA
31946 TTGACTAATAGACTAAGTGGATAT
1 TTGACTAATAGACTAAGTGGATAT
31970 GATCAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (25 bp):
TTGACTAATAGACTAAGTGGATATA
Found at i:35586 original size:2 final size:2
Alignment explanation
Indices: 35579--35630 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
35569 TTTAAAAATG
35579 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
35621 AT AT AT AT AT
1 AT AT AT AT AT
35631 TGTATAACTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35847 original size:17 final size:18
Alignment explanation
Indices: 35803--35848 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
35793 ATCAATTGAT
*
35803 TATTAATAAAATATTATA
1 TATTTATAAAATATTATA
35821 TATTT-T-AAATATT-TA
1 TATTTATAAAATATTATA
*
35836 TTTTTATAAAATA
1 TATTTATAAAATA
35849 ATTTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 6 0.25
16 8 0.33
17 6 0.25
18 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTATAAAATATTATA
Found at i:35921 original size:2 final size:2
Alignment explanation
Indices: 35916--35949 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
35906 TATTATTCAA
* *
35916 AT AT AT AC AC 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
35950 TAAATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:40012 original size:8 final size:8
Alignment explanation
Indices: 39999--40039 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
39989 CTCATTTTCA
39999 GAGAATTT
1 GAGAATTT
40007 GAGAATTT
1 GAGAATTT
*
40015 -AGAGTTT
1 GAGAATTT
*
40022 GGGAATTT
1 GAGAATTT
40030 GAGAATTT
1 GAGAATTT
40038 GA
1 GA
40040 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:40300 original size:104 final size:104
Alignment explanation
Indices: 40120--40426 Score: 569
Period size: 104 Copynumber: 3.0 Consensus size: 104
40110 ACTATTCACA
*
40120 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCATA
*
40185 TTATGTCACTCATGTCCCTCAGGGACACTATTCAGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCAGGACT
*
40224 TGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCATA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCATA
40289 TTATGTCACTCATGTCCCTCGGGGACACTATTCAGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCAGGACT
* *
40328 TGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCATA
40393 TTATGTCACTCATGTCCCTCGGGGACACTATTCA
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCA
40427 TATCAGTACC
Statistics
Matches: 197, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 197 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (104 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCATA
TTATGTCACTCATGTCCCTCGGGGACACTATTCAGGACT
Found at i:40551 original size:128 final size:128
Alignment explanation
Indices: 40323--40675 Score: 661
Period size: 128 Copynumber: 2.8 Consensus size: 128
40313 ACACTATTCA
*
40323 GGACTTGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
1 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
*
40388 CCTTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
66 CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
40451 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
1 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
* * *
40516 CCCTATTATGTCACTCATGTCTCTCAGGGATACTATTCATATCAGTACCTATTATTTCTCAGG
66 CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
40579 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
1 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
40644 CCCTATTATGTCACTCATGTCCCTCGGGGACA
66 CCCTATTATGTCACTCATGTCCCTCGGGGACA
40676 ATAGATGGAT
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 217 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
Found at i:41059 original size:21 final size:21
Alignment explanation
Indices: 41006--41099 Score: 118
Period size: 21 Copynumber: 4.5 Consensus size: 21
40996 TATGATATAA
* *
41006 AACCCTGCGGGCTAGGCATAT
1 AACCCTGCGGGCTAGGAATGT
*
41027 AA-CCTGGTGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
41048 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
* *
41069 AACCCCGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
41090 AACCCTGCGG
1 AACCCTGCGG
41100 AGATGGCATA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:41123 original size:42 final size:43
Alignment explanation
Indices: 41006--41123 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 43
40996 TATGATATAA
41006 AACCCTGCGGGCTAGGCATAT-AACCTGGTGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGCATATGAACCTGGTGGGCTAGGAATGT
* ** * *
41048 AACCCTGCGGGCTCGG-A-ATGTAACCCCGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGCATATG-AACCTGGTGGGCTAGGAATGT
*
41090 AACCCTGCGGAGAT-GGCATATGAA-CTGGTGGGCT
1 AACCCTGCGG-GCTAGGCATATGAACCTGGTGGGCT
41124 TGGCATATGA
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
40 2 0.03
41 1 0.02
42 51 0.82
43 5 0.08
44 3 0.05
ACGTcount: A:0.22, C:0.25, G:0.34, T:0.19
Consensus pattern (43 bp):
AACCCTGCGGGCTAGGCATATGAACCTGGTGGGCTAGGAATGT
Found at i:41129 original size:21 final size:21
Alignment explanation
Indices: 41103--41150 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
41093 CCTGCGGAGA
* *
41103 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAAATGGAGGGCT
41124 TGGCATATGAAATGGAGGGCT
1 TGGCATATGAAATGGAGGGCT
*
41145 GGGCAT
1 TGGCAT
41151 GTACCCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATGAAATGGAGGGCT
Found at i:42689 original size:16 final size:17
Alignment explanation
Indices: 42663--42760 Score: 51
Period size: 17 Copynumber: 5.6 Consensus size: 17
42653 ATCAGTATCC
*
42663 AAAATAATATACATTAT
1 AAAATAATATAAATTAT
42680 AAAA-AATATAAATTAAT
1 AAAATAATATAAATT-AT
* *
42697 ATAAATTCATAATAACTT-T
1 A-AAA-TAAT-ATAAATTAT
*
42716 AAAATAAAAATAAATT-T
1 AAAAT-AATATAAATTAT
* *
42733 AAATATTAACATTAATTAT
1 AAA-A-TAATATAAATTAT
42752 AAAA-AATAT
1 AAAATAATAT
42761 TACCATATCG
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
16 13 0.21
17 18 0.29
18 17 0.27
19 7 0.11
20 2 0.03
21 6 0.10
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATAATATAAATTAT
Found at i:42938 original size:18 final size:17
Alignment explanation
Indices: 42884--42940 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
42874 TCTAAATAAA
*
42884 TAATAATTATATAAATAT
1 TAATATTTA-ATAAATAT
* *
42902 T-AT-TTTAATAAAAAA
1 TAATATTTAATAAATAT
42917 TAATATTTACATAAATAT
1 TAATATTTA-ATAAATAT
42935 TAATAT
1 TAATAT
42941 AAAATATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 6 0.19
18 13 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATATTTAATAAATAT
Found at i:42952 original size:33 final size:32
Alignment explanation
Indices: 42877--42982 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 32
42867 TAATAATTCT
* * * *
42877 AAATAAATAATAATTATATAAATATTATTTTAA
1 AAAT-AATAATATTTAAATAAATATTAATATAA
* *
42910 TAAAAAATAATATTTACATAAATATTAATATAA
1 -AAATAATAATATTTAAATAAATATTAATATAA
* * *
42943 AATATAATAACTATTTAAAAAAATACTAACATAA
1 AA-ATAATAA-TATTTAAATAAATATTAATATAA
42977 AAATAA
1 AAATAA
42983 ATTTCTTACC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.03
33 34 0.57
34 24 0.40
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (32 bp):
AAATAATAATATTTAAATAAATATTAATATAA
Found at i:42967 original size:34 final size:32
Alignment explanation
Indices: 42911--42982 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
42901 TTATTTTAAT
* * * *
42911 AAAA-AATAATATTTACATAAATATTAATATA
1 AAAATAATAATATTTAAAAAAATACTAACATA
42942 AAATATAATAACTATTTAAAAAAATACTAACATA
1 AAA-ATAATAA-TATTTAAAAAAATACTAACATA
42976 AAAATAA
1 AAAATAA
42983 ATTTCTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 3 0.09
32 1 0.03
33 9 0.26
34 21 0.62
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (32 bp):
AAAATAATAATATTTAAAAAAATACTAACATA
Found at i:43874 original size:38 final size:37
Alignment explanation
Indices: 43797--43874 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
43787 TTTTTATATT
43797 TTTAATTTTGTAAAAAAAATTATATAAATATTATAAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATAAA
* * *
43834 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAAAAAAATTATATAAATATTATA-AA
43872 TTT
1 TTT
43875 GTAATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 19 0.53
38 17 0.47
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATAAA
Found at i:44225 original size:2 final size:2
Alignment explanation
Indices: 44218--44253 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44208 TTAAGAGTGA
44218 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
44254 TAACAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62129 original size:21 final size:22
Alignment explanation
Indices: 62058--62138 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 22
62048 CTTTATAATG
* *
62058 TAATGTAATAATTGAT-TATAT
1 TAATGTGATAATTTATATATAT
*
62079 TAGTGTGATAATTTAT-TATAT
1 TAATGTGATAATTTATATATAT
* * *
62100 TGATATGATATTTTATATA-AT
1 TAATGTGATAATTTATATATAT
62121 TAATGTGAT-ATTTCATAT
1 TAATGTGATAATTT-ATAT
62139 GTGAATAATG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
20 3 0.06
21 43 0.90
22 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (22 bp):
TAATGTGATAATTTATATATAT
Found at i:62753 original size:7 final size:7
Alignment explanation
Indices: 62741--62767 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
62731 ATTTGGTTAA
62741 ATTATAT
1 ATTATAT
62748 ATTATAT
1 ATTATAT
62755 ATTATAT
1 ATTATAT
62762 ATTATA
1 ATTATA
62768 CAATATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTATAT
Found at i:63093 original size:8 final size:8
Alignment explanation
Indices: 63082--63140 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
63072 ATTTTATAAT
63082 TTTTTATA
1 TTTTTATA
63090 TTTTTA-A
1 TTTTTATA
* *
63097 ATTTAATA
1 TTTTTATA
63105 TTTTTATAA
1 TTTTTAT-A
63114 TGTTTTAGTA
1 T-TTTTA-TA
*
63124 ATTTTATA
1 TTTTTATA
63132 TTTTT-TA
1 TTTTTATA
63139 TT
1 TT
63141 AAAATTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
7 9 0.22
8 18 0.44
9 7 0.17
10 6 0.15
11 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (8 bp):
TTTTTATA
Found at i:63093 original size:17 final size:17
Alignment explanation
Indices: 63071--63139 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 17
63061 CATAATTGAT
63071 TATTTTATAATTTTTTA
1 TATTTTATAATTTTTTA
* *
63088 TATTTT-TAA-ATTTAA
1 TATTTTATAATTTTTTA
*
63103 TATTTTTATAATGTTTTA
1 TA-TTTTATAATTTTTTA
63121 GTAATTTTAT-ATTTTTTA
1 -T-ATTTTATAATTTTTTA
63139 T
1 T
63140 TAAAATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
15 6 0.14
16 7 0.17
17 10 0.24
18 11 0.26
19 7 0.17
20 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTTATAATTTTTTA
Found at i:63334 original size:49 final size:49
Alignment explanation
Indices: 63281--63430 Score: 145
Period size: 45 Copynumber: 3.2 Consensus size: 49
63271 GTAATGATTG
*
63281 AATGATAAAATTGATATAATTTAATAAATTAAAATATGAAATTAATATA
1 AATGATAAAATTGATATAATTTAATAAATTTAAATATGAAATTAATATA
* * * * * * *
63330 AATGA-AAAAAT-AT-TAA-TTATTTAGATTTACA-ACGTAA-TGAT-T-
1 AATGATAAAATTGATATAATTTA-ATAAATTTAAATATGAAATTAATATA
*
63372 AATGATAAAGTTGATATAATTTAATAAATTTAAATATGAAATTAATATA
1 AATGATAAAATTGATATAATTTAATAAATTTAAATATGAAATTAATATA
*
63421 AATGAAAAAA
1 AATGATAAAA
63431 ATATTAATTA
Statistics
Matches: 74, Mismatches: 18, Indels: 18
0.67 0.16 0.16
Matches are distributed among these distances:
42 5 0.07
43 5 0.07
44 5 0.07
45 18 0.24
46 17 0.23
47 5 0.07
48 6 0.08
49 13 0.18
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (49 bp):
AATGATAAAATTGATATAATTTAATAAATTTAAATATGAAATTAATATA
Found at i:63386 original size:91 final size:93
Alignment explanation
Indices: 63271--63451 Score: 330
Period size: 91 Copynumber: 2.0 Consensus size: 93
63261 ATTAATATTT
63271 GTAATGATTGAATGATAAAATTGATATAATTTAATAAATTAAAATATGAAATTAATATAAATG-A
1 GTAATGATTGAATGATAAAATTGATATAATTTAATAAATTAAAATATGAAATTAATATAAATGAA
63335 AAAAATATTAATTATTTAGATTTACAAC
66 AAAAATATTAATTATTTAGATTTACAAC
* *
63363 GTAATGATT-AATGATAAAGTTGATATAATTTAATAAATTTAAATATGAAATTAATATAAATGAA
1 GTAATGATTGAATGATAAAATTGATATAATTTAATAAATTAAAATATGAAATTAATATAAATGAA
63427 AAAAATATTAATTATTTAGATTTAC
66 AAAAATATTAATTATTTAGATTTAC
63452 TGTAAAGATA
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 51 0.59
92 35 0.41
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (93 bp):
GTAATGATTGAATGATAAAATTGATATAATTTAATAAATTAAAATATGAAATTAATATAAATGAA
AAAAATATTAATTATTTAGATTTACAAC
Found at i:63422 original size:42 final size:41
Alignment explanation
Indices: 63288--63423 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 41
63278 TTGAATGATA
*
63288 AAATTGATATAATTTAATAAATTAAAATATGAAATTAATAT
1 AAATTGATATAATTTAATAAATTTAAATATGAAATTAATAT
* *
63329 AAA-TGAAAAAATATTAATTATTTAGATTTACAACGTAATG--ATTAATGAT
1 AAATTGATATAAT-TTAA-TA---A-ATTTA-AA--T-ATGAAATTAAT-AT
63378 AAAGTTGATATAATTTAATAAATTTAAATATGAAATTAATAT
1 AAA-TTGATATAATTTAATAAATTTAAATATGAAATTAATAT
63420 AAAT
1 AAAT
63424 GAAAAAAATA
Statistics
Matches: 75, Mismatches: 5, Indels: 30
0.68 0.05 0.27
Matches are distributed among these distances:
40 7 0.09
41 11 0.15
42 8 0.11
43 6 0.08
44 2 0.03
45 6 0.08
46 5 0.07
47 2 0.03
48 6 0.08
49 8 0.11
50 7 0.09
51 7 0.09
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.38
Consensus pattern (41 bp):
AAATTGATATAATTTAATAAATTTAAATATGAAATTAATAT
Found at i:65055 original size:14 final size:15
Alignment explanation
Indices: 65038--65071 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65028 TTTAAAAATG
65038 TATTTTT-AAAATAA
1 TATTTTTGAAAATAA
*
65052 TATTTTTGAAATTAA
1 TATTTTTGAAAATAA
65067 TATTT
1 TATTT
65072 ATTCGTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TATTTTTGAAAATAA
Found at i:70843 original size:24 final size:24
Alignment explanation
Indices: 70833--70950 Score: 139
Period size: 24 Copynumber: 4.9 Consensus size: 24
70823 CATAATTCAC
*
70833 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
70857 GTCAAGTGTCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
70881 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
* *
70905 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
*
70929 GTCAAGTGTCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
70951 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 2 0.02
24 76 0.90
25 6 0.07
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:70902 original size:48 final size:48
Alignment explanation
Indices: 70833--70947 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
70823 CATAATTCAC
* * *
70833 GTCAAGTATCATATCAAAATCCAAGTCA-AGTGTCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAAGTCAGA-TATCAGATCAGAATCCAA
* *
70881 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAAGTCAGATATCAGATCAGAATCCAA
*
70929 GTCAAGTGTCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
70948 ATCAAATCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAAGTCAGATATCAGATCAGAATCCAA
Found at i:70964 original size:48 final size:48
Alignment explanation
Indices: 70809--70964 Score: 129
Period size: 48 Copynumber: 3.2 Consensus size: 48
70799 AAATGAATAT
* * * * * * *
70809 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* ** *
70857 GTCA-AGTGTCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * * *
70905 GTCAGATATCAGATCAGAATCCATGTCAAGTGTCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAA
70953 ATC-GAAAATCAG
1 ATCAG-AAATCAG
70965 GTAAAATATT
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.02
48 82 0.93
49 4 0.05
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:70964 original size:72 final size:71
Alignment explanation
Indices: 70813--70964 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 71
70803 GAATATATCA
* * * *
70813 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAAGTCAAGTGTCAGATCAGAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAAGTCAAGTGTCAGATCAGAATC
*
70878 CAAGTC
66 CAAATC
* * * *
70884 AAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTGTCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCAGATCAAAATCCAAGTCAAGTGTCAGATCAG-A
70948 AT-CAAATC
63 ATCCAAATC
70956 GAAAATCAG
1 -AAAATCAG
70965 GTAAAATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 4 0.06
72 58 0.87
73 5 0.07
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAAGTCAAGTGTCAGATCAGAATC
CAAATC
Found at i:73442 original size:18 final size:17
Alignment explanation
Indices: 73418--73473 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
73408 CGGCCAACGA
73418 GTCGGGTCAACGGATCG
1 GTCGGGTCAACGGATCG
73435 GATCGGGTCAAC--A--G
1 G-TCGGGTCAACGGATCG
*
73449 GTCGGGTCAACGGGTCGG
1 GTCGGGTCAACGGATC-G
73467 GTCGGGT
1 GTCGGGT
73474 TGTGACTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 10 0.31
14 2 0.06
16 1 0.03
17 1 0.03
18 18 0.56
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCGGGTCAACGGATCG
Found at i:73453 original size:13 final size:13
Alignment explanation
Indices: 73437--73469 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
73427 ACGGATCGGA
73437 TCGGGTCAACAGG
1 TCGGGTCAACAGG
*
73450 TCGGGTCAACGGG
1 TCGGGTCAACAGG
73463 TCGGGTC
1 TCGGGTC
73470 GGGTTGTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.42, T:0.18
Consensus pattern (13 bp):
TCGGGTCAACAGG
Done.