Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008534.1 Hibiscus syriacus cultivar Beakdansim tig00111412_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: 53398
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:10390 original size:12 final size:12
Alignment explanation
Indices: 10375--10428 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
10365 AAGAGAAAAG
10375 AAAAAAGAAG-A
1 AAAAAAGAAGAA
10386 AAAAAA-AAGAGA
1 AAAAAAGAAGA-A
10398 AAAAAA-AAGAA
1 AAAAAAGAAGAA
10409 AAAAAAG-AGAA
1 AAAAAAGAAGAA
*
10420 GAAAAAGAA
1 AAAAAAGAA
10429 AGGGGGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 3 0.08
11 23 0.61
12 12 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:10391 original size:11 final size:10
Alignment explanation
Indices: 10370--10429 Score: 68
Period size: 10 Copynumber: 5.8 Consensus size: 10
10360 GCTTGAAGAG
10370 AAAAGAAAAA
1 AAAAGAAAAA
*
10380 AGAAGAAAAA
1 AAAAGAAAAA
10390 AAAAGAGAAAA
1 AAAAGA-AAAA
10401 AAAA-AGAAAA
1 AAAAGA-AAAA
*
10411 AAAAGAGAAGA
1 AAAAGA-AAAA
10422 AAAAGAAA
1 AAAAGAAA
10430 GGGGGTCAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
10 26 0.58
11 19 0.42
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:10410 original size:21 final size:21
Alignment explanation
Indices: 10373--10429 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
10363 TGAAGAGAAA
*
10373 AGAAAAAAGAAGAAAAAAAAAG
1 AGAAAAAAAAAG-AAAAAAAAG
10395 AGAAAAAAAAAGAAAAAAAAG
1 AGAAAAAAAAAGAAAAAAAAG
*
10416 AG-AAGAAAAAGAAA
1 AGAAAAAAAAAGAAA
10430 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.33
21 11 0.33
22 11 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAGAAAAAAAAG
Found at i:10767 original size:16 final size:16
Alignment explanation
Indices: 10746--10785 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
10736 ATACAATTCT
*
10746 ATTTATTTCAAG-TTCA
1 ATTTATTT-AAGAGTCA
10762 ATTTATTTAAGAGTCA
1 ATTTATTTAAGAGTCA
10778 ATTTATTT
1 ATTTATTT
10786 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTATTTAAGAGTCA
Found at i:11995 original size:84 final size:84
Alignment explanation
Indices: 11553--11985 Score: 800
Period size: 84 Copynumber: 5.2 Consensus size: 84
11543 ATATCTTAGT
11553 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
11617 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
11636 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
11700 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
11719 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
11784 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
11803 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
11868 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
11887 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
11952 CTAATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
11971 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
11986 AAAAGATGAA
Statistics
Matches: 344, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
83 117 0.34
84 222 0.65
85 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:12909 original size:113 final size:110
Alignment explanation
Indices: 12612--13720 Score: 1567
Period size: 113 Copynumber: 9.9 Consensus size: 110
12602 ATCTATCAAT
* **
12612 TGATGGATTATTTTTGAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 TGATGGATAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
12677 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCAC
66 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTGAATTC-ATCAC
* *
12723 TTGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
1 -TGATGGATAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
12788 GTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATC
65 GTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TGAATTCATCA-C
** * *
12836 TGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TGATGGAT-AATTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
12900 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCAC
64 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTGAATTC-ATCAC
*
12948 TTGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 -TGATGGATAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* * * *
13013 GTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
65 GTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTGAATTCATCAC
** *
13060 TGGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 T-GATGGAT-AATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* * *
13125 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAC
64 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTGAATTCATCAC
* * *
13173 TTGATGGATTATTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 -TGATGGATAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
13238 GTTCATAATAAGAAGAATTTGTTCAACCTTTAAT-CTGAATTCATCAC
65 GTTCATAATGAGAAGAATTTGTTCAACCTTT--TGCTGAATTCATCAC
*
13285 TGGATGGAATATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 T-GATGG-ATAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
13350 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
64 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTGAATTCATCAC
* *
13398 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 -TGATGGATAATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
13463 AGTTCATAATAAGAAGAATTTGTTCAACCTTTAAT-CTGAATTCATCAC
64 AGTTCATAATGAGAAGAATTTGTTCAACCTTT--TGCTGAATTCATCAC
* *
13511 TGGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGA
1 T-GATGGA-TAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
13576 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAT
64 AGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTGAATTCATC-AC
***
13625 TGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGAT-AATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
*
13690 GTTCATAATGAGAAGAGTTTGTTCAACCTTT
65 GTTCATAATGAGAAGAATTTGTTCAACCTTT
13721 GTTTGATGCT
Statistics
Matches: 907, Mismatches: 63, Indels: 53
0.89 0.06 0.05
Matches are distributed among these distances:
111 4 0.00
112 309 0.34
113 582 0.64
114 11 0.01
115 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (110 bp):
TGATGGATAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTGAATTCATCAC
Found at i:13026 original size:225 final size:224
Alignment explanation
Indices: 12629--13720 Score: 1658
Period size: 225 Copynumber: 4.8 Consensus size: 224
12619 TTATTTTTGA
12629 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
12694 TTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATGA
66 TTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATGA
* * *
12759 GAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTT-TGCT
131 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTAT-C-
12823 TGAATTCATCATCT-GATGGATCAACATTGCC
194 TGAATTCATCA-CTGGATGGATCAACATTGCC
*
12854 AG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 AGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
12918 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATG
65 TTTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATG
* * * *
12983 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTT
130 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC-CTTTATC
*
13048 TGAATTCATCATTGGATGGATCAACATTGCC
194 TGAATTCATCACTGGATGGATCAACATTGCC
*
13079 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* * ** * *
13144 TTGTTCAACTTTTTGTTTGAAT-TCATCACTTGATGGATTATTTTGCCAGAGAAGGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCT-ATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATG
*
13208 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTAATC
130 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT-ATC
*** *
13273 TGAATTCATCACTGGATGGAAT-ATTTTTTCC
194 TGAATTCATCACTGGATGG-ATCAACATTGCC
13304 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* ** *
13369 TTGTTCAACCTTTTGTTTGAAT-TCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAAT
66 TTGTTCAACCTTTTGCTCAAATCT-ATCACTTGATGGATTATTTTT-CCAGAGAAAGTTCATAAT
*
13433 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTAAT
129 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT-AT
* *** *
13498 CTGAATTCATCACTGGATGGATTATTTTTTCC
193 CTGAATTCATCACTGGATGGATCAACATTGCC
*
13530 AGAGAAAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
* * * * * **
13595 TTGTTCAACCTTTTACCTGAATTC-ATCAATTGATGGATCAGCCTTTCCAGAGAAAGTTCATAAT
66 TTGTTCAACCTTTT-GCTCAAATCTATCACTTGATGGATTA-TTTTTCCAGAGAAAGTTCATAAT
*
13659 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTT
129 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
13721 GTTTGATGCT
Statistics
Matches: 814, Mismatches: 40, Indels: 25
0.93 0.05 0.03
Matches are distributed among these distances:
224 6 0.01
225 514 0.63
226 287 0.35
227 7 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (224 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCTATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATGA
GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTATCTG
AATTCATCACTGGATGGATCAACATTGCC
Found at i:13355 original size:338 final size:335
Alignment explanation
Indices: 12606--13726 Score: 1673
Period size: 338 Copynumber: 3.3 Consensus size: 335
12596 ATTCAAATCT
* * **
12606 ATCAATTGATGGATTATTTTTGAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 ATCACTTGATGGAATATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
* * * *
12671 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTCAAATCTATCACTTGATGGATTAT
66 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC-ATCACTTGATGGATAAT
* *
12735 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAG
130 TTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * ** *
12800 AAGAACTTGTTCAA-TCTTTTGCTTGAATTCATCA-TCTGATGGATCAACATTGCCAG-GTAGAG
195 AAGAACTTGTTCAACT-TTTTGTTTGAATTCATCACT-TGATGGAT-TATTTTGCCAGAGAAG-G
12862 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
256 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
* *
12927 CCTTT-TGCTCAAATC
321 CCTTTAT-CTGAATTC
*
12942 TATCACTTGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 -ATCACTTGATGGAATATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
13007 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCA-TTGGATGGATCA
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTT-GATGGAT-A
**
13071 ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
128 ATTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
13136 AGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCACTTGATGGATTATTTTGCCAGAGAAGGTT
193 AGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCACTTGATGGATTATTTTGCCAGAGAAGGTT
*
13201 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACC
258 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
13266 TTTAATCTGAATTC
323 TTT-ATCTGAATTC
*
13280 ATCACTGGATGGAATATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGAATA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
13345 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATTAT
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGA-TAA
* *
13410 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
129 TTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * ** * * * *
13475 GAAGAATTTGTTCAACCTTTAATCTGAATTCATCACTGGATGGATTATTTTTTCCAGAGAAAGTT
194 GAAGAACTTGTTCAACTTTTTGTTTGAATTCATCACTTGATGGATTA-TTTTGCCAGAGAAGGTT
*
13540 CATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
258 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
*
13605 TTTTACCTGAATTC
323 -TTTATCTGAATTC
* **
13619 ATCAATTGATGG-ATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGAAT-A-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
13683 AGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACC-TTTGTTTGA
64 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGA
13727 TGCTATCACA
Statistics
Matches: 723, Mismatches: 47, Indels: 27
0.91 0.06 0.03
Matches are distributed among these distances:
336 2 0.00
337 201 0.28
338 334 0.46
339 183 0.25
340 3 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (335 bp):
ATCACTTGATGGAATATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGATAATT
TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACTTTTTGTTTGAATTCATCACTTGATGGATTATTTTGCCAGAGAAGGTTCAT
AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
ATCTGAATTC
Found at i:14050 original size:3 final size:3
Alignment explanation
Indices: 14042--14153 Score: 197
Period size: 3 Copynumber: 37.3 Consensus size: 3
14032 TACCCATATC
14042 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
14090 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATC ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14138 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
14154 AATATAAAAT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 105 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:14686 original size:15 final size:16
Alignment explanation
Indices: 14666--14695 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14656 ACAGAACCGG
14666 AGAGAAA-AAAAAAAC
1 AGAGAAAGAAAAAAAC
14681 AGAGAAAGAAAAAAA
1 AGAGAAAGAAAAAAA
14696 AAACAACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAAAAAC
Found at i:14690 original size:29 final size:28
Alignment explanation
Indices: 14636--14690 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
14626 AAAAAAAAGA
* * *
14636 GGAGAGACAAAAAAACCGAGACAGAACC
1 GGAGAGAAAAAAAAACAGAGAAAGAACC
14664 GGAGAGAAAAAAAAAACAGAGAAAGAA
1 GGAGAG-AAAAAAAAACAGAGAAAGAA
14691 AAAAAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.62, C:0.13, G:0.25, T:0.00
Consensus pattern (28 bp):
GGAGAGAAAAAAAAACAGAGAAAGAACC
Found at i:22802 original size:43 final size:42
Alignment explanation
Indices: 22749--22950 Score: 145
Period size: 43 Copynumber: 4.7 Consensus size: 42
22739 TTTTTAATAG
* *
22749 AAACGCCGCAAAACATCAATACCTATTGTGGCGTTTGTGAAAA
1 AAACGCCGCTAAACATCAATACCTATTGTGGCGTTT-TGAGAA
* * * * * * *
22792 AAACGTCGCAAAACATCAACACATACTGCGGCGTTTTAGCGAA
1 AAACGCCGCTAAACATCAATACCTATTGTGGCGTTTT-GAGAA
* * * * *
22835 AAATGCCTCTAAACATC-ATAACCTATTGCGGCGTTTTTATGAC
1 AAACGCCGCTAAACATCAAT-ACCTATTGTGGCGTTTTGA-GAA
* * * * * *
22878 AAACGCCACTAAATATCAACACCTATTGTGGCGTTTGTCACAC
1 AAACGCCGCTAAACATCAATACCTATTGTGGCGTTT-TGAGAA
* * *
22921 AAATGTCGCTAAATATCAATACCTATTGTG
1 AAACGCCGCTAAACATCAATACCTATTGTG
22951 ATGTTTTTTT
Statistics
Matches: 126, Mismatches: 28, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
42 2 0.02
43 121 0.96
44 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAACATCAATACCTATTGTGGCGTTTTGAGAA
Found at i:26338 original size:21 final size:22
Alignment explanation
Indices: 26303--26352 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
26293 TAGGTATGTT
*
26303 TATTTTTACTCTATTT-TTTTAA
1 TATTTTTACTATATTTCTTTT-A
*
26325 TATTTTTA-TATATTTCTTTTG
1 TATTTTTACTATATTTCTTTTA
26346 TATTTTT
1 TATTTTT
26353 GCATGTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTTACTATATTTCTTTTA
Found at i:28858 original size:20 final size:21
Alignment explanation
Indices: 28824--28863 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
28814 TATTTGTGTT
28824 TATTAATAAAAATAT-TATAG
1 TATTAATAAAAATATATATAG
* *
28844 TATTAATATATATATATATA
1 TATTAATAAAAATATATATA
28864 TATATATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TATTAATAAAAATATATATAG
Found at i:33257 original size:103 final size:103
Alignment explanation
Indices: 33109--33319 Score: 246
Period size: 103 Copynumber: 2.0 Consensus size: 103
33099 ATTTGACACA
* * * * * * **
33109 ATTATCAATATAAATTGTGATGATTTCCTTGACACTGAAAATATATTTTGTGACCATTAATATTG
1 ATTATCAATAGAAATTGTGATAATTTACTTGACACTCAAAATATATATTGCGACCACCAATATTG
* *
33174 TCACACTAAGTT-TTTTTAGTGACCAATTGTTCGATACT
66 TCAAACTAA-TTCTTTTTAGTGACCAAATGTTCGATACT
* * *
33212 ATTATCAATAGAAATTGTGATAAATTTATTTGACAC-CAAAGTATATATTGCGACCACCAATGTT
1 ATTATCAATAGAAATTGTGAT-AATTTACTTGACACTCAAAATATATATTGCGACCACCAATATT
* *
33276 GTCAAAGTAATTGCTTTTTAGTTACCAAATGTTCGATACT
65 GTCAAACTAATT-CTTTTTAGTGACCAAATGTTCGATACT
33316 ATTA
1 ATTA
33320 ATAATAACTC
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
102 2 0.02
103 49 0.54
104 39 0.43
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (103 bp):
ATTATCAATAGAAATTGTGATAATTTACTTGACACTCAAAATATATATTGCGACCACCAATATTG
TCAAACTAATTCTTTTTAGTGACCAAATGTTCGATACT
Found at i:34925 original size:40 final size:40
Alignment explanation
Indices: 34841--34926 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 40
34831 ATTATTGTCG
*
34841 TCACAAATCACCAAATATGACTAGTGACAAATATTTATCG
1 TCACAAATCACCAAATATGACTAGTGACAAATATTTATCA
* *
34881 TCACAAATCACCAACTAAT-ACTAGTGACAAA-ATGTTTTCA
1 TCACAAATCACCAAAT-ATGACTAGTGACAAATAT-TTATCA
34921 TCACAA
1 TCACAA
34927 TTATAAATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
39 2 0.05
40 37 0.90
41 2 0.05
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (40 bp):
TCACAAATCACCAAATATGACTAGTGACAAATATTTATCA
Found at i:36777 original size:32 final size:31
Alignment explanation
Indices: 36722--36782 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
36712 TAAGCTAGTC
36722 AAAATTTTGCTCGACTCGAGCTCGTTAAAAA
1 AAAATTTTGCTCGACTCGAGCTCGTTAAAAA
*
36753 AAAATTGTTGCTC-AGCTCGTGCTCGTTAAA
1 AAAATT-TTGCTCGA-CTCGAGCTCGTTAAA
36783 TTCGTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (31 bp):
AAAATTTTGCTCGACTCGAGCTCGTTAAAAA
Found at i:40527 original size:3 final size:3
Alignment explanation
Indices: 40519--40605 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
40509 TTCATGTTGA
40519 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40567 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40606 ATAATTGTCA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41449 original size:2 final size:2
Alignment explanation
Indices: 41393--41432 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
41383 AATTGTGACC
41393 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
41433 TAATGTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42519 original size:12 final size:12
Alignment explanation
Indices: 42502--42533 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
42492 CACAGTGTTG
42502 ATGTGACAGTCT
1 ATGTGACAGTCT
42514 ATGTGACAGTCT
1 ATGTGACAGTCT
42526 ATGTGACA
1 ATGTGACA
42534 TGTTTGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (12 bp):
ATGTGACAGTCT
Found at i:45084 original size:101 final size:101
Alignment explanation
Indices: 44946--45146 Score: 307
Period size: 101 Copynumber: 2.0 Consensus size: 101
44936 GTAAATTACA
* *
44946 TATTTAGTACCTAAAGTATAAGTTTGATCCGTTTTAGTATCTAAACTTTCAA-TTTTTTCAAAAT
1 TATTTAGTACCTAAAGTATAAGTTTGATCCATTTTAGTATCTAAACTTTCAATTTTTTTCAAAAC
45010 CATACATAATATTTAGTTTTTGTTT-ATTTTAGTACG
66 CATACATAATATTTAG-TTTTGTTTCATTTTAGTACG
* * *
45046 TATTTAGTACCTAAATTATCAATTTTGATCCATTTTAGTATCTAAACTTTTAATTTTTTTCAAAA
1 TATTTAGTACCTAAAGTAT-AAGTTTGATCCATTTTAGTATCTAAACTTTCAATTTTTTTCAAAA
* *
45111 CCATACCTAATGTTTAGTTTTGTTTCATTTTAGTAC
65 CCATACATAATATTTAGTTTTGTTTCATTTTAGTAC
45147 CTAGCCATTA
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
100 18 0.20
101 38 0.42
102 35 0.38
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.49
Consensus pattern (101 bp):
TATTTAGTACCTAAAGTATAAGTTTGATCCATTTTAGTATCTAAACTTTCAATTTTTTTCAAAAC
CATACATAATATTTAGTTTTGTTTCATTTTAGTACG
Found at i:48727 original size:30 final size:30
Alignment explanation
Indices: 48689--48813 Score: 77
Period size: 30 Copynumber: 4.2 Consensus size: 30
48679 TGTGTTTGTT
48689 TATT-TTTAAAGATGTTTATGTTCGATTTG
1 TATTGTTTAAAGATGTTTATGTTCGATTTG
* * *
48718 TGTTGTTTAATG-TGTTT-TGTTTG-TTT-
1 TATTGTTTAAAGATGTTTATGTTCGATTTG
* * *
48744 AACCTTCGATATAAAGATGTTTGTGTTC-ATTTG
1 TA--TT-G-TTTAAAGATGTTTATGTTCGATTTG
48777 TTTATT-TTTGAAA-ATGTTTATGTTCGATTTG
1 --TATTGTTT-AAAGATGTTTATGTTCGATTTG
48808 TATTGT
1 TATTGT
48814 CTAACGAGTT
Statistics
Matches: 71, Mismatches: 11, Indels: 27
0.65 0.10 0.25
Matches are distributed among these distances:
27 3 0.04
28 7 0.10
29 13 0.18
30 25 0.35
31 13 0.18
32 7 0.10
33 2 0.03
35 1 0.01
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (30 bp):
TATTGTTTAAAGATGTTTATGTTCGATTTG
Found at i:50641 original size:12 final size:12
Alignment explanation
Indices: 50624--50652 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
50614 TACTAATACC
50624 GCATCTGCTTCT
1 GCATCTGCTTCT
50636 GCATCTGCTTCT
1 GCATCTGCTTCT
50648 GCATC
1 GCATC
50653 AGCTCTTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.34, G:0.17, T:0.38
Consensus pattern (12 bp):
GCATCTGCTTCT
Done.