Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008859.1 Hibiscus syriacus cultivar Beakdansim tig00112082_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: 67518
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8575 original size:30 final size:32
Alignment explanation
Indices: 8522--8580 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
8512 TGCAAATAAA
*
8522 ATGAAATATTAATAAGAAAATATATAAATACT
1 ATGAAATATTAATAAGAAAATATAAAAATACT
* *
8554 ATGAAA-A-TAATAAGTATATATAAAAAT
1 ATGAAATATTAATAAGAAAATATAAAAAT
8581 TTTGAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.71
31 1 0.04
32 6 0.25
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (32 bp):
ATGAAATATTAATAAGAAAATATAAAAATACT
Found at i:10718 original size:3 final size:3
Alignment explanation
Indices: 10710--10773 Score: 82
Period size: 3 Copynumber: 22.7 Consensus size: 3
10700 TTATATATAT
*
10710 TAA TAA TAA TAA T-A TGA TAA TAA TAA TAA T-A TAA TAA TAA -AA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
10754 TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
10774 TGGATAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
2 8 0.15
3 46 0.85
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:10730 original size:17 final size:17
Alignment explanation
Indices: 10710--10780 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
10700 TTATATATAT
10710 TAATAATAATAATATGA
1 TAATAATAATAATATGA
*
10727 TAATAATAATAATATAA
1 TAATAATAATAATATGA
*
10744 TAATAAAATATAATAT--
1 TAATAATA-ATAATATGA
10760 TAATAATAATAATATGGA
1 TAATAATAATAATAT-GA
10778 TAA
1 TAA
10781 AAAATTAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
15 7 0.15
16 7 0.15
17 23 0.49
18 10 0.21
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (17 bp):
TAATAATAATAATATGA
Found at i:10731 original size:14 final size:13
Alignment explanation
Indices: 10712--10773 Score: 81
Period size: 14 Copynumber: 4.7 Consensus size: 13
10702 ATATATATTA
10712 ATAATAATAATAT
1 ATAATAATAATAT
10725 GATAATAATAATAAT
1 -ATAATAATAAT-AT
*
10740 ATAATAATAAAAT
1 ATAATAATAATAT
*
10753 ATAATATTAATA-
1 ATAATAATAATAT
10765 ATAATAATA
1 ATAATAATA
10774 TGGATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 8 0.19
13 12 0.28
14 21 0.49
15 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:17402 original size:44 final size:44
Alignment explanation
Indices: 17353--17704 Score: 456
Period size: 44 Copynumber: 8.0 Consensus size: 44
17343 TGTTACCGAA
* * *
17353 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTACA
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
17397 ATAAATGAAAATGCATAAAGGTGCATTACTAGG-ACAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTA-TTGGCAGAAAGGTGCC
** * *
17441 ATAAATGAAAATGCATAACAATGCATTATTGGCATAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
17485 ATAAATGAAAATGCATAACGGTGTATTATTTGTAG-AAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
17528 ATAAATGAAAATGTATAACGATGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
17572 ATAAATAAAAATGCATAGCGGTGTATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
17616 ATAAATAAAAATGCATAACGGTGTATTATTGGCATAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
17660 ATAAATGAAAATGCATAACGGTGCATTATTAGCATAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
17704 A
1 A
17705 CTCATGGTAT
Statistics
Matches: 267, Mismatches: 38, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
43 40 0.15
44 224 0.84
45 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:17646 original size:175 final size:175
Alignment explanation
Indices: 17353--17689 Score: 491
Period size: 175 Copynumber: 1.9 Consensus size: 175
17343 TGTTACCGAA
*
17353 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTACAATAAATGAAAATGCATAAAGG
1 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTACAATAAATAAAAATGCATAAAGG
* * *
17418 TGCATTACTAGGACAAATGTGCCATAAATGAAAATGCATAACAATGCATTATTGGCATAAAGGTT
66 TGCATTACTAGGACAAAGGTGCCATAAATAAAAATGCATAACAATGCATTATTGGCATAAAGGTG
*
17483 CCATAAATGAAAATGCATAACGGTGTATTATTTGTAGAAGGTGCC
131 CCATAAATGAAAATGCATAACGGTGCATTATTTGTAGAAGGTGCC
* * **
17528 ATAAATGAAAATGTATAAC-GATGCATTATTGGCAGAAAGGTGTC-ATAAATAAAAATGCATAGC
1 ATAAATGAAAATGCATAACAG-TGCATTATTGGCAGAAAGGT-ACAATAAATAAAAATGCATAAA
* * * ** *
17591 GGTGTATTA-TTGGCAGAAAGGTGCCATAAATAAAAATGCATAACGGTGTATTATTGGCATAAAG
64 GGTGCATTACTAGG-ACAAAGGTGCCATAAATAAAAATGCATAACAATGCATTATTGGCATAAAG
17655 GTGCCATAAATGAAAATGCATAACGGTGCATTATT
128 GTGCCATAAATGAAAATGCATAACGGTGCATTATT
17690 AGCATAAAGG
Statistics
Matches: 144, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
174 4 0.03
175 139 0.97
176 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (175 bp):
ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTACAATAAATAAAAATGCATAAAGG
TGCATTACTAGGACAAAGGTGCCATAAATAAAAATGCATAACAATGCATTATTGGCATAAAGGTG
CCATAAATGAAAATGCATAACGGTGCATTATTTGTAGAAGGTGCC
Found at i:20417 original size:15 final size:16
Alignment explanation
Indices: 20385--20424 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
20375 TGGAGCTTTC
20385 AAATTTTGAAAAATTA
1 AAATTTTGAAAAATTA
20401 AAATTTTGAAAAA-TA
1 AAATTTTGAAAAATTA
*
20416 AATTTTTGA
1 AAATTTTGA
20425 TTTGAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATTTTGAAAAATTA
Found at i:21326 original size:29 final size:29
Alignment explanation
Indices: 21284--21339 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
21274 TAAAAATGCA
* *
21284 ATTTTCTAGAAAAACGATCGATCCCTTGC
1 ATTTTATAGAAAAACGATCAATCCCTTGC
*
21313 ATTTTATAGAAAAATGATCAATCCCTT
1 ATTTTATAGAAAAACGATCAATCCCTT
21340 TGTAAGAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (29 bp):
ATTTTATAGAAAAACGATCAATCCCTTGC
Found at i:21369 original size:21 final size:21
Alignment explanation
Indices: 21325--21382 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
21315 TTTATAGAAA
*
21325 AATGATCAATCCCTTTGTAAG
1 AATGATCGATCCCTTTGTAAG
* **
21346 AATGATCGATCCCTTTTTGTG
1 AATGATCGATCCCTTTGTAAG
*
21367 AATTATCGATCCCTTT
1 AATGATCGATCCCTTT
21383 AGGCCAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (21 bp):
AATGATCGATCCCTTTGTAAG
Found at i:27903 original size:89 final size:89
Alignment explanation
Indices: 27752--27931 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 89
27742 GCTGAAAAAT
27752 TATGGCTAATACCATTAGAATTACAAAACTCATTAAATACAAGATTTTCAAATTCAGTGCCATGA
1 TATGGCTAATACCATTAGAATTACAAAACTCATTAAATACAAGATTTTCAAATTCAGTGCCATGA
27817 TCACTTCTAACACTAGTGATAGAG
66 TCACTTCTAACACTAGTGATAGAG
*
27841 TATGGCTAATACCATTAGAATTACAAAACTCATTAAATCCAAGATTTTCAAATTCAGTGCCATGA
1 TATGGCTAATACCATTAGAATTACAAAACTCATTAAATACAAGATTTTCAAATTCAGTGCCATGA
27906 TCACTTCTAACACTAGTGATAGAG
66 TCACTTCTAACACTAGTGATAGAG
27930 TA
1 TA
27932 ACCTTTTTCG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (89 bp):
TATGGCTAATACCATTAGAATTACAAAACTCATTAAATACAAGATTTTCAAATTCAGTGCCATGA
TCACTTCTAACACTAGTGATAGAG
Found at i:33445 original size:21 final size:21
Alignment explanation
Indices: 33374--33439 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
33364 ATATGTTTGG
* *
33374 GATTGGTCCCTTCACCAAAAG
1 GATTGATCCCTTCACCAAAAT
**
33395 GATTGATCCCTTCAGGAAAAT
1 GATTGATCCCTTCACCAAAAT
33416 GATTGATCCCTTCACCAAAAT
1 GATTGATCCCTTCACCAAAAT
33437 GAT
1 GAT
33440 CAATCCTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (21 bp):
GATTGATCCCTTCACCAAAAT
Found at i:37181 original size:20 final size:20
Alignment explanation
Indices: 37142--37181 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
37132 ACACCAAATC
* *
37142 CTCTCAAATACTTTCTACTT
1 CTCTCAAATACTCTCAACTT
*
37162 CTCTCAAATCCTCTCAACTT
1 CTCTCAAATACTCTCAACTT
37182 AAGGTATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (20 bp):
CTCTCAAATACTCTCAACTT
Found at i:37244 original size:13 final size:12
Alignment explanation
Indices: 37193--37255 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
37183 AGGTATATTT
*
37193 TATTATATTTAA
1 TATTTTATTTAA
*
37205 TATTTTA-TTAG
1 TATTTTATTTAA
37216 TATTTTATTT-A
1 TATTTTATTTAA
*
37227 -ATTAT-TTTAA
1 TATTTTATTTAA
37237 TATTTTATTTAA
1 TATTTTATTTAA
*
37249 TTTTTTA
1 TATTTTA
37256 CAGTTATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
9 3 0.07
10 5 0.12
11 14 0.34
12 19 0.46
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:42963 original size:14 final size:14
Alignment explanation
Indices: 42946--42973 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42936 GTATCTAATG
42946 AGATAAATTATATC
1 AGATAAATTATATC
42960 AGATAAATTATATC
1 AGATAAATTATATC
42974 GTTGCTCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AGATAAATTATATC
Found at i:44334 original size:20 final size:21
Alignment explanation
Indices: 44311--44349 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
44301 TTAAACAAAC
44311 AAATTATTATTT-AATTAAAT
1 AAATTATTATTTAAATTAAAT
44331 AAATTATTATTTAAATTAA
1 AAATTATTATTTAAATTAA
44350 TTGTAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTATTATTTAAATTAAAT
Found at i:44351 original size:16 final size:17
Alignment explanation
Indices: 44311--44351 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
44301 TTAAACAAAC
44311 AAATT-ATTATTTAATT
1 AAATTAATTATTTAATT
* *
44327 AAATAAATTA-TTATTT
1 AAATTAATTATTTAATT
44343 AAATTAATT
1 AAATTAATT
44352 GTAAATTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTAATTATTTAATT
Found at i:44487 original size:24 final size:24
Alignment explanation
Indices: 44460--44525 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
44450 TTTACAAGTT
44460 TAATTTGTTTGTTTAATTAAATAA
1 TAATTTGTTTGTTTAATTAAATAA
*
44484 TAATTTGTTTGTTTAATTAAATAT
1 TAATTTGTTTGTTTAATTAAATAA
44508 TAATTTGTTTGTTTAATT
1 TAATTTGTTTGTTTAATT
44526 TTTTATCCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (24 bp):
TAATTTGTTTGTTTAATTAAATAA
Found at i:44996 original size:28 final size:30
Alignment explanation
Indices: 44936--45006 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 30
44926 TAACAGCGCG
44936 GTGGTCTGATTGAATCAAATAAAAAATTTA
1 GTGGTCTGATTGAATCAAATAAAAAATTTA
*
44966 GTGGTCTGATTGAGA-C-AA-AAAAAGTTTA
1 GTGGTCTGATTGA-ATCAAATAAAAAATTTA
*
44994 GTGGTCAGATTGA
1 GTGGTCTGATTGA
45007 TTATTGATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 21 0.55
29 2 0.05
30 14 0.37
31 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (30 bp):
GTGGTCTGATTGAATCAAATAAAAAATTTA
Found at i:46146 original size:21 final size:20
Alignment explanation
Indices: 46106--46146 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
46096 TATAATTTCA
*
46106 ATAAAAAAATTGGATTTTTT
1 ATAAAAAAATTGAATTTTTT
*
46126 ATAAATAAATTGAACTTTTTT
1 ATAAAAAAATTGAA-TTTTTT
46147 CTATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (20 bp):
ATAAAAAAATTGAATTTTTT
Found at i:47934 original size:18 final size:17
Alignment explanation
Indices: 47912--47960 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
47902 AAAGAATAGT
47912 AATAATAGAAATAATAAG
1 AATAATA-AAATAATAAG
* * *
47930 GATAATATAAAGAATAAT
1 AATAATA-AAATAATAAG
47948 AATAATAAAATAA
1 AATAATAAAATAA
47961 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
AATAATAAAATAATAAG
Found at i:47955 original size:21 final size:21
Alignment explanation
Indices: 47894--47961 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
47884 ATAATTACAT
*
47894 GAATAAATAAAGAATAGTAATAATA
1 GAAT-AAT-AAGAATA-AAATAA-A
* *
47919 GAAATAATAAGGATAATATAAA
1 G-AATAATAAGAATAAAATAAA
*
47941 GAATAATAATAATAAAATAAA
1 GAATAATAAGAATAAAATAAA
47962 AATGGTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
21 17 0.47
22 2 0.06
23 4 0.11
24 6 0.17
25 4 0.11
26 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
GAATAATAAGAATAAAATAAA
Found at i:48134 original size:20 final size:19
Alignment explanation
Indices: 48106--48146 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
48096 AAACACTAAT
48106 AATAATATAATATATATATA
1 AATAATATAATATA-ATATA
* *
48126 AATATTATAATGTAATATA
1 AATAATATAATATAATATA
48145 AA
1 AA
48147 AAGATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AATAATATAATATAATATA
Found at i:49174 original size:18 final size:16
Alignment explanation
Indices: 49143--49183 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
49133 AAAAAAAATG
49143 TAAATATAATTTATAA
1 TAAATATAATTTATAA
49159 TAAATATATATATTAT-A
1 TAAATATA-AT-TTATAA
49176 T-AATATAA
1 TAAATATAA
49184 GGATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 4 0.17
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATTTATAA
Found at i:49419 original size:20 final size:20
Alignment explanation
Indices: 49396--49437 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
49386 GAATCCTTCG
49396 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
* *
49416 TCGTGAAGTTGAAGTCGAAC
1 TCGTGAAATTGAAATCGAAC
49436 TC
1 TC
49438 AGAGTTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:49680 original size:105 final size:105
Alignment explanation
Indices: 49518--50127 Score: 1202
Period size: 105 Copynumber: 5.8 Consensus size: 105
49508 ATTGTTTATC
* *
49518 GACAACCAGCGGTCCCTTCGTCATGAAGTTGAACCTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
49583 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
49623 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
49688 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
49728 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
49793 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
49833 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
49898 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
49938 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
50003 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
50043 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
50108 GTGAAGTTGAAATTGGCTCT
66 GTGAAGTTGAAATTGGCTCT
50128 GGGTAAAACC
Statistics
Matches: 503, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 503 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
Found at i:50326 original size:1 final size:1
Alignment explanation
Indices: 50320--50346 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
50310 CGTTTGATGA
50320 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
50347 GAAGATGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:61669 original size:14 final size:14
Alignment explanation
Indices: 61650--61677 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61640 TGAAAGATAT
61650 AAAAAAAAAAGGTA
1 AAAAAAAAAAGGTA
61664 AAAAAAAAAAGGTA
1 AAAAAAAAAAGGTA
61678 TACATACACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (14 bp):
AAAAAAAAAAGGTA
Found at i:62131 original size:18 final size:17
Alignment explanation
Indices: 62109--62157 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
62099 AAAGAATAGT
62109 AATAATAGAAATAATAAG
1 AATAATA-AAATAATAAG
* * *
62127 GATAATATAAAGAATAAT
1 AATAATA-AAATAATAAG
62145 AATAATAAAATAA
1 AATAATAAAATAA
62158 AAATGGTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
AATAATAAAATAATAAG
Found at i:62152 original size:21 final size:21
Alignment explanation
Indices: 62091--62158 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
62081 ATAATTACAT
*
62091 GAATAAATAAAGAATAGTAATAATA
1 GAAT-AAT-AAGAATA-AAATAA-A
* *
62116 GAAATAATAAGGATAATATAAA
1 G-AATAATAAGAATAAAATAAA
*
62138 GAATAATAATAATAAAATAAA
1 GAATAATAAGAATAAAATAAA
62159 AATGGTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
21 17 0.47
22 2 0.06
23 4 0.11
24 6 0.17
25 4 0.11
26 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
GAATAATAAGAATAAAATAAA
Done.