Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 24
Found at i:4728146 original size:9 final size:9
Alignment explanation
Indices: 4728132--4728197 Score: 80
Period size: 9 Copynumber: 7.0 Consensus size: 9
4728122 ATTATGCTTG
*
4728132 AAGAAAAGA
1 AAGAAAAAA
4728141 AAGAAAAAAA
1 AAG-AAAAAA
4728151 AAGAAAAAA
1 AAGAAAAAA
4728160 AAGGAAAAAA
1 AA-GAAAAAA
4728170 AAGAAAAAA
1 AAGAAAAAA
4728179 GAA-AAAAAA
1 -AAGAAAAAA
4728188 AGAGAAAAAA
1 A-AGAAAAAA
4728198 TGGGGGGTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
8 1 0.02
9 25 0.49
10 25 0.49
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:4728153 original size:10 final size:10
Alignment explanation
Indices: 4728135--4728197 Score: 76
Period size: 10 Copynumber: 6.5 Consensus size: 10
4728125 ATGCTTGAAG
*
4728135 AAAAGAAAGA
1 AAAAAAAAGA
4728145 AAAAAAAAG-
1 AAAAAAAAGA
*
4728154 AAAAAAAAGG
1 AAAAAAAAGA
4728164 AAAAAAAAGA
1 AAAAAAAAGA
*
4728174 AAAAAGAA-A
1 AAAAAAAAGA
*
4728183 AAAAAAGAGA
1 AAAAAAAAGA
4728193 AAAAA
1 AAAAA
4728198 TGGGGGGTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
9 16 0.35
10 30 0.65
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:4728156 original size:19 final size:18
Alignment explanation
Indices: 4728132--4728197 Score: 89
Period size: 19 Copynumber: 3.6 Consensus size: 18
4728122 ATTATGCTTG
4728132 AAGAAAAGAAAGAAAAAAA
1 AAGAAAA-AAAGAAAAAAA
*
4728151 AAGAAAAAAAAGGAAAAAA
1 AAG-AAAAAAAGAAAAAAA
4728170 AAG-AAAAAAGAAAAAAA
1 AAGAAAAAAAGAAAAAAA
4728187 AAGAGAAAAAA
1 AAGA-AAAAAA
4728198 TGGGGGGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 16 0.38
19 22 0.52
20 4 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAGAAAAAAA
Found at i:4728183 original size:26 final size:26
Alignment explanation
Indices: 4728135--4728197 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
4728125 ATGCTTGAAG
*
4728135 AAAAG-AAAGAAA-AAAAAAGAAAAA
1 AAAAGAAAAAAAAGAAAAAAGAAAAA
*
4728159 AAAGGAAAAAAAAGAAAAAAGAAAAA
1 AAAAGAAAAAAAAGAAAAAAGAAAAA
*
4728185 AAAAGAGAAAAAA
1 AAAAGAAAAAAAA
4728198 TGGGGGGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 4 0.12
25 6 0.18
26 23 0.70
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (26 bp):
AAAAGAAAAAAAAGAAAAAAGAAAAA
Found at i:4729583 original size:164 final size:166
Alignment explanation
Indices: 4729312--4729798 Score: 876
Period size: 164 Copynumber: 3.0 Consensus size: 166
4729302 ATATCCTAGT
* * *
4729312 CCAATCATTGAATTTAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
4729377 TGATCTGGTTAGACAGAACCAATCATTGAATTTAG-A-ATGAATGTGTTCATAGCATCTTCTGGA
66 TGATCTGGTTAGACAGAACCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGA
4729440 AGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAA
131 AGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAA
4729476 CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAG-T-TC
1 CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
4729539 TGATCTGGTTAGACAGAACCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGA
66 TGATCTGGTTAGACAGAACCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGA
4729604 AGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAA
131 AGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAA
4729640 CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
* * *
4729705 TGATCTGGTTTGGCAGAACCAAT-ATTTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGG
66 TGATCTGGTTAGACAGAACCAATCA-TTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGG
4729769 AAGTGTTCTTTGAGTTATCTGATCTGGTTT
130 AAGTGTTCTTTGAGTTATCTGATCTGGTTT
4729799 GGTAGGAACT
Statistics
Matches: 312, Mismatches: 6, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
162 37 0.12
163 2 0.01
164 180 0.58
165 2 0.01
166 91 0.29
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (166 bp):
CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTAGACAGAACCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAA
Found at i:4729668 original size:83 final size:83
Alignment explanation
Indices: 4729312--4729798 Score: 835
Period size: 83 Copynumber: 5.9 Consensus size: 83
4729302 ATATCCTAGT
*
4729312 CCAATCATTGAATTTAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
4729377 TGATCTGG-TTAGACAGAA
66 TGATCTGGTTTAG-CAGAA
4729395 CCAATCATTGAATTTAG-A-ATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
4729458 TGATCTGGTTTAGCAGAA
66 TGATCTGGTTTAGCAGAA
* *
4729476 CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAG-T-TC
1 CCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
4729539 TGATCTGG-TTAGACAGAA
66 TGATCTGGTTTAG-CAGAA
4729557 CCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
4729622 TGATCTGGTTTAGCAGAA
66 TGATCTGGTTTAGCAGAA
* *
4729640 CCAATCATTGAATTTGGAAGATGAATGTGTTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
4729705 TGATCTGGTTTGGCAGAA
66 TGATCTGGTTTAGCAGAA
*
4729723 CCAAT-ATTTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCA-TTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
4729787 CTGATCTGGTTT
65 CTGATCTGGTTT
4729799 GGTAGGAACT
Statistics
Matches: 387, Mismatches: 9, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
80 4 0.01
81 146 0.38
82 9 0.02
83 224 0.58
84 4 0.01
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
CCAATCATTGAATTTAGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTAGCAGAA
Found at i:4730956 original size:222 final size:226
Alignment explanation
Indices: 4730539--4731401 Score: 1410
Period size: 222 Copynumber: 3.9 Consensus size: 226
4730529 TGACATTTCC
4730539 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
4730603 GTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAG
66 GTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAG
*
4730668 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAATCTTTTACCTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
4730732 AATTCATCACTTGATGGATTATTTTTGCCAG
196 AATTCATCACTTGATGGATTATTTTTGCCAG
*
4730763 AGAAGGTTCATAATGAG-AGAACTC-TCTGAAGAAGGAAG-AGAAGTTCATAATGAGAAGAA-TT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
4730824 GTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAG-AAGTTCATAATGAG
66 GTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAG
*
4730888 AAGAACTCATCTGAAGAAGGAATAAGAAGTTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
131 AAGAACTCATCTGAAGAAGGAAGAAGAAG-TTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
*
4730953 GAATTCATCACTTGATGGATTATTTTTACCAG
195 GAATTCATCACTTGATGGATTATTTTTGCCAG
*
4730985 AGAAGGTTCATAAT--G-AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA-AATTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
4731046 GTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAG
66 GTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAG
4731111 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA-CTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
4731175 AATTCATCACTTGATGGATTA-TTTTGCCAG
196 AATTCATCACTTGATGGATTATTTTTGCCAG
*
4731205 AGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAG-A-AAGTTCATAATGAGAAGAATTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
* * * * * *
4731268 GTTCAACCTTTT-GTCTGAATTCATCACTTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATG
66 GTTCAACCTTTTACT-TGAATCCATCATTTGATGGATCATCATTT-CCAGAGAAAGTTCATAATG
**
4731331 AGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCATAAT--GAAGAATTTGTTCAACCTTTTGTC
129 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
*
4731391 TAAATTCATCA
194 TGAATTCATCA
4731402 TCTAAAGAAG
Statistics
Matches: 609, Mismatches: 16, Indels: 34
0.92 0.02 0.05
Matches are distributed among these distances:
217 21 0.03
218 11 0.02
219 15 0.02
220 70 0.11
221 129 0.21
222 274 0.45
223 73 0.12
224 16 0.03
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (226 bp):
AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
GTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAG
AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
AATTCATCACTTGATGGATTATTTTTGCCAG
Found at i:4730972 original size:334 final size:336
Alignment explanation
Indices: 4730518--4731401 Score: 1315
Period size: 331 Copynumber: 2.7 Consensus size: 336
4730508 CAAAACTATT
* *
4730518 ATTTGATGGATTGA-CATTTCCAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAG
1 ATTTGATGGA-TCATCATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAG
* * * * *
4730581 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATT
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT-TTT
*
4730646 T-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
129 TACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
* * * *
4730710 GAA-TTGTTCAATCTTTTACCTGAATTCATCACTTGATGGATTAT-TTTTGCCAGAGAAGGTTCA
194 GAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCATTT-CCAGAGAAAGTTCA
4730773 TAATGAG-AGAACTC-TCTGAAGAAGGAAG-AGAAGTTCATAATGAGAAGAA-TTGTTCAACCTT
258 TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
4730834 TTACTTGAATCCATC
323 TTAC-TGAATCCATC
4730849 ATTTGATGGATCATCATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAG
1 ATTTGATGGATCATCATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AAG
4730914 AAGTTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTT
65 AAG-TTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTT
4730979 TACCAGAGAAGGTTCATAAT--G-AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
129 TACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
* * *
4731041 -AATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCAT
194 GAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCATTTCCAGAGAAAGTTCAT
4731105 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
259 AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
*
4731170 TACTGAATTCATC
324 TACTGAATCCATC
* * * *
4731183 ACTTGATGGATTAT--TTTGCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 ATTTGATGGATCATCATTT-CCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAA
**
4731246 -AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTT
64 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTT
*
4731310 TGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCATAAT--GAA
129 TACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
** *
4731370 GAATTTGTTCAACCTTTTGTCTAAATTCATCA
194 GAATTTGTTCAACCTTTTACCTGAATTCATCA
4731402 TCTAAAGAAG
Statistics
Matches: 508, Mismatches: 28, Indels: 35
0.89 0.05 0.06
Matches are distributed among these distances:
329 3 0.01
330 30 0.06
331 210 0.41
332 52 0.10
333 32 0.06
334 165 0.32
335 16 0.03
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (336 bp):
ATTTGATGGATCATCATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTA
CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCATCATTTCCAGAGAAAGTTCATAA
TGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA
CTGAATCCATC
Found at i:4731432 original size:443 final size:442
Alignment explanation
Indices: 4730539--4731432 Score: 1378
Period size: 443 Copynumber: 2.0 Consensus size: 442
4730529 TGACATTTCC
*
4730539 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGAAGGTTCATAAT-AGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTTG
4730604 TTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGA
65 TTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGA
*
4730669 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTGTTCAATCTTTTACCTGAA
130 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACCTGAA
*
4730734 TTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAGAACTCTCTGAAGAAGGA
195 TTCATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAGAACTCTCTGAAGAAGGA
*
4730799 AGAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCATC
260 AGAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACTTGAATCCATCACTTGATGGATCATC
4730864 ATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTTCATAATGAG
325 ATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-A-AAGAAGTTTCATAAT-AG
* * * ** ** * *
4730929 AAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTATTTTTACCAG
387 AAGAATTTGTTCAACCTTTTACCTAAATTCATCACTAGAAGGAGAAAGTTCACAAG
4730985 AGAAGGTTCATAAT-G-AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA-AATTTG
1 AGAAGGTTCATAATAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTG
4731047 TTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGA
65 TTCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGA
4731112 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTA-CTGA
130 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACCTGA
*
4731176 ATTCATCACTTGATGGATTA-TTTTGCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGAA
194 ATTCATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAG-AGAACTC-TCTGAAGAA
* *
4731240 GGAAGA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GTCTGAATTCATCACTTGATGGA
257 GGAAGAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACT-TGAATCCATCACTTGATGGA
* *
4731303 TTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AAGAAG-TTCATA
320 TCATCATTT-CCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAGAAGTTTCATA
** *
4731365 AT-GAAGAATTTGTTCAACCTTTTGTCTAAATTCATCATCTAAAGAAGAGAGAAAGTTCATAAG
383 ATAGAAGAATTTGTTCAACCTTTTACCTAAATTCATCA-CT--AGAAG-GAGAAAGTTCACAAG
4731428 AGAAG
1 AGAAG
4731433 AACTCATCAA
Statistics
Matches: 415, Mismatches: 21, Indels: 27
0.90 0.05 0.06
Matches are distributed among these distances:
439 32 0.08
440 2 0.00
441 8 0.02
442 33 0.08
443 201 0.48
444 94 0.23
445 32 0.08
446 13 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (442 bp):
AGAAGGTTCATAATAGAAGAACTCATCTGAAGAAGGAGAAGAAGTTCATAATGAGAAGAATTTGT
TCAACCTTTTACTTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAA
GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACCTGAAT
TCATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAGAACTCTCTGAAGAAGGAA
GAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACTTGAATCCATCACTTGATGGATCATCA
TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAGAAGTTTCATAATAGAAGA
ATTTGTTCAACCTTTTACCTAAATTCATCACTAGAAGGAGAAAGTTCACAAG
Found at i:4731685 original size:3 final size:3
Alignment explanation
Indices: 4731677--4731728 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
4731667 TTTTTACCCA
* *
4731677 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4731724 TAT TA
1 TAT TA
4731729 AATATATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4734228 original size:27 final size:25
Alignment explanation
Indices: 4734169--4734239 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 25
4734159 TTTTAATTTT
4734169 AATATTAATTTTGTAA-A-TAAATTA
1 AATATTAATTTT-TAATATTAAATTA
*
4734193 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTTAATATTAAATTA
4734218 TAGATATTAA-TTTTAATATTAA
1 -A-ATATTAATTTTTAATATTAA
4734240 TTTTTAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.07
24 13 0.32
25 6 0.15
26 12 0.29
27 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (25 bp):
AATATTAATTTTTAATATTAAATTA
Found at i:4734267 original size:35 final size:39
Alignment explanation
Indices: 4734193--4734273 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 39
4734183 AAATAAATTA
*
4734193 AATATTAATTTTTAATATTATATTATAGATATTAATTTT
1 AATATTAATTTTTAATATTAAATTATAGATATTAATTTT
*
4734232 AATATTAATTTTTAA-A-TAAATTA-A-ATATTATTTTT
1 AATATTAATTTTTAATATTAAATTATAGATATTAATTTT
4734267 AATATTA
1 AATATTA
4734274 TATTATAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 17 0.43
36 1 0.03
37 6 0.15
38 1 0.03
39 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (39 bp):
AATATTAATTTTTAATATTAAATTATAGATATTAATTTT
Found at i:4734270 original size:61 final size:63
Alignment explanation
Indices: 4734146--4734294 Score: 252
Period size: 61 Copynumber: 2.4 Consensus size: 63
4734136 TATTTAATTT
*
4734146 ATATTATATT-T-GATTTTAATTTTAATATTAATTTTGTAAATAAATTAAATATTAATTTTTA
1 ATATTATATTATAGATATTAATTTTAATATTAATTTTGTAAATAAATTAAATATTAATTTTTA
4734207 ATATTATATTATAGATATTAATTTTAATATTAATTTT-TAAATAAATTAAATATT-ATTTTTA
1 ATATTATATTATAGATATTAATTTTAATATTAATTTTGTAAATAAATTAAATATTAATTTTTA
4734268 ATATTATATTATAGATATTTAATTTTA
1 ATATTATATTATAGATA-TTAATTTTA
4734295 TATCATATAA
Statistics
Matches: 84, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
61 34 0.40
62 27 0.32
63 23 0.27
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (63 bp):
ATATTATATTATAGATATTAATTTTAATATTAATTTTGTAAATAAATTAAATATTAATTTTTA
Found at i:4734506 original size:13 final size:14
Alignment explanation
Indices: 4734480--4734518 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
4734470 ATTAATATTT
4734480 TAAAATATAAAATA
1 TAAAATATAAAATA
4734494 TAAAATA-AAAATA
1 TAAAATATAAAATA
*
4734507 AAAAATTATAAA
1 TAAAA-TATAAA
4734519 TTATGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 10 0.45
14 9 0.41
15 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAATATAAAATA
Found at i:4734522 original size:7 final size:7
Alignment explanation
Indices: 4734480--4734518 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
4734470 ATTAATATTT
4734480 TAAAATA
1 TAAAATA
4734487 TAAAATA
1 TAAAATA
4734494 TAAAATA
1 TAAAATA
4734501 -AAAATA
1 TAAAATA
*
4734507 AAAAATTA
1 TAAAA-TA
4734515 TAAA
1 TAAA
4734519 TTATGTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 6 0.21
7 18 0.62
8 5 0.17
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAAATA
Found at i:4735329 original size:20 final size:20
Alignment explanation
Indices: 4735304--4735341 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4735294 TTTTAATTTA
4735304 TGTTAAAAATGATATATTGC
1 TGTTAAAAATGATATATTGC
4735324 TGTTAAAAATGATATATT
1 TGTTAAAAATGATATATT
4735342 AAATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTTAAAAATGATATATTGC
Found at i:4740027 original size:2 final size:2
Alignment explanation
Indices: 4740020--4740062 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
4740010 TAATTAAAGA
4740020 AT AT AT AT AT AT AT AT AT ACT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
4740063 GAATTCACGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.