Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007196.1 Hibiscus syriacus cultivar Beakdansim tig00018968_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: 63368
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1716 original size:32 final size:32
Alignment explanation
Indices: 1680--1743 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1670 TCTCTGGTTC
*
1680 CTCACTTACTCTTTGATTGCTTTTGTTTAGGG
1 CTCACTTACTCTTTGATTGCTTTTCTTTAGGG
1712 CTCACTTACTCTTTGATTGCTTTTCTTTAGGG
1 CTCACTTACTCTTTGATTGCTTTTCTTTAGGG
1744 ATTTGGGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.12, C:0.20, G:0.17, T:0.50
Consensus pattern (32 bp):
CTCACTTACTCTTTGATTGCTTTTCTTTAGGG
Found at i:6626 original size:37 final size:36
Alignment explanation
Indices: 6551--6626 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
6541 TTTTTATATT
*
6551 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
6587 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
6624 TTT
1 TTT
6627 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:13715 original size:16 final size:17
Alignment explanation
Indices: 13691--13723 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13681 TCTCTTTAAA
*
13691 GTTTTGGAT-AAAATGG
1 GTTTCGGATCAAAATGG
13707 GTTTCGGATCAAAATGG
1 GTTTCGGATCAAAATGG
13724 TGTAGCTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (17 bp):
GTTTCGGATCAAAATGG
Found at i:29290 original size:13 final size:13
Alignment explanation
Indices: 29272--29297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29262 TCAACTATGA
29272 ACCAAAAAACCAC
1 ACCAAAAAACCAC
29285 ACCAAAAAACCAC
1 ACCAAAAAACCAC
29298 TAAACTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (13 bp):
ACCAAAAAACCAC
Found at i:29628 original size:14 final size:14
Alignment explanation
Indices: 29609--29658 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
29599 AATATATTCG
*
29609 TTTATGTTCTTTCA
1 TTTATGTTCGTTCA
*
29623 TTTATGTTCGTTCG
1 TTTATGTTCGTTCA
*
29637 TTTATGTGCGTTCA
1 TTTATGTTCGTTCA
29651 TTTATGTT
1 TTTATGTT
29659 TAACCCAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (14 bp):
TTTATGTTCGTTCA
Found at i:29650 original size:28 final size:28
Alignment explanation
Indices: 29605--29658 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
29595 CGGTAATATA
* *
29605 TTCGTTTATGTTCTTTCATTTATGTTCG
1 TTCGTTTATGTGCGTTCATTTATGTTCG
29633 TTCGTTTATGTGCGTTCATTTATGTT
1 TTCGTTTATGTGCGTTCATTTATGTT
29659 TAACCCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (28 bp):
TTCGTTTATGTGCGTTCATTTATGTTCG
Found at i:29898 original size:23 final size:23
Alignment explanation
Indices: 29825--29912 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
29815 AAAATCTATT
* *
29825 TTCATTTATGTTCATTTATTGTG
1 TTCATTTATATTCGTTTATTGTG
* *
29848 TTCGTTTACATTCGTTCGT-TTGTG
1 TTCATTTATATTCGTT--TATTGTG
* *
29872 TTCATTAATATTCGTTTATTGTT
1 TTCATTTATATTCGTTTATTGTG
*
29895 TTCATTTATGTTCGTTTA
1 TTCATTTATATTCGTTTA
29913 CATCCATTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 18 0.35
25 1 0.02
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (23 bp):
TTCATTTATATTCGTTTATTGTG
Found at i:36181 original size:46 final size:46
Alignment explanation
Indices: 36118--36226 Score: 209
Period size: 46 Copynumber: 2.3 Consensus size: 46
36108 TTCTGTGAAG
36118 CAAACATCTGCATTAGCATTGGGGAGTGTAATGACTATTCTCCCAAC
1 CAAACA-CTGCATTAGCATTGGGGAGTGTAATGACTATTCTCCCAAC
36165 CAAACACTGCATTAGCATTGGGGAGTGTAATGACTATTCTCCCAAC
1 CAAACACTGCATTAGCATTGGGGAGTGTAATGACTATTCTCCCAAC
36211 CAAACACTGCATTAGC
1 CAAACACTGCATTAGC
36227 TTTTATGTAC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 56 0.90
47 6 0.10
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (46 bp):
CAAACACTGCATTAGCATTGGGGAGTGTAATGACTATTCTCCCAAC
Found at i:42126 original size:21 final size:21
Alignment explanation
Indices: 42108--42157 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
42098 CATCGAAGTG
42108 CCACATAATTGTCCCGAAGGA
1 CCACATAATTGTCCCGAAGGA
*
42129 CCACATAATTGTCTCGAAGGA
1 CCACATAATTGTCCCGAAGGA
42150 CCACATAA
1 CCACATAA
42158 ACCCTCGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (21 bp):
CCACATAATTGTCCCGAAGGA
Found at i:50411 original size:59 final size:56
Alignment explanation
Indices: 50332--50513 Score: 161
Period size: 59 Copynumber: 3.1 Consensus size: 56
50322 GGATGTTACA
* *
50332 AAACTATGATCCCATTCTAAATTATCCCCAAACTTTTAAACATTCTAATTTTATCCCT
1 AAACTATGATCTCATTCTAAATTAT-CCTAAA-TTTTAAACATTCTAATTTTATCCCT
* ** *
50390 AAACTATGACTCTCATTCTAAATTAGTTCCTACAATTTTAAACATTTTGAA-TCCAT-CAT
1 AAACTATGA-TCTCATTCTAAATTA--TCCTA-AATTTTAAACATTCT-AATTTTATCCCT
* * * *
50449 CAAACTATGATCTTCATTCTATATTTATCCTAAAATTTTGAATATTCTAATTTTATCCCC
1 -AAACTATGATC-TCATTCTA-AATTATCCT-AAATTTTAAACATTCTAATTTTATCCCT
50509 AAACT
1 AAACT
50514 TTTGAATGAT
Statistics
Matches: 99, Mismatches: 14, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
58 11 0.11
59 42 0.42
60 37 0.37
61 9 0.09
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (56 bp):
AAACTATGATCTCATTCTAAATTATCCTAAATTTTAAACATTCTAATTTTATCCCT
Found at i:50504 original size:28 final size:29
Alignment explanation
Indices: 50464--50520 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
50454 TATGATCTTC
*
50464 ATTCTATATTTAT-CCTAAAATTTTGAAT
1 ATTCTATATTTATCCCCAAAATTTTGAAT
*
50492 ATTCTA-ATTTTATCCCCAAACTTTTGAAT
1 ATTCTATA-TTTATCCCCAAAATTTTGAAT
50521 GATTTAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 11 0.44
29 13 0.52
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (29 bp):
ATTCTATATTTATCCCCAAAATTTTGAAT
Found at i:50702 original size:60 final size:59
Alignment explanation
Indices: 50540--50706 Score: 174
Period size: 60 Copynumber: 2.8 Consensus size: 59
50530 TAAGTTGTTG
* * * *
50540 GAATGTTCAAAAGTTTGAGGACTAATTTAGAATGAGAGTCATAGTTTGGGGATGAATTTG
1 GAATGTTCAAAAGTTT-AGGACTAATTTAAAATGACAGTCATAGTTTAGGGATGAATTTA
* * * * * * *
50600 GAATATTCAAAAATTAAAGAATCATTTTAAAATGACAATCATAGTTTAGGGATGAATTTA
1 GAATGTTCAAAAGTTTAGGACT-AATTTAAAATGACAGTCATAGTTTAGGGATGAATTTA
* *
50660 GAATGTTTAAAAGTTTATGGACTACTTTAAAATGA-ATGTCATAGTTT
1 GAATGTTCAAAAGTTTA-GGACTAATTTAAAATGACA-GTCATAGTTT
50707 GAGGATGTAT
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
59 5 0.06
60 77 0.91
61 3 0.04
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (59 bp):
GAATGTTCAAAAGTTTAGGACTAATTTAAAATGACAGTCATAGTTTAGGGATGAATTTA
Found at i:52033 original size:186 final size:185
Alignment explanation
Indices: 51220--52633 Score: 1443
Period size: 187 Copynumber: 7.7 Consensus size: 185
51210 AGGTTGCGTC
* ** *
51220 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCGTTATATTATCCCAGTATAAGAAAATATGTTTA
1 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTAT-CCAGTATAAGAAAATAAGTTTA
** *
51285 AAACTGAAAAATATTATGAACATATATAAGAAATATGGA-TGCATCCAATAATTTCATGGTTCAA
65 AAACTG-AAAATATTATGAACATATATAAGAAATAT-GATTGCGCCCAATAATGTCATGGTTCAA
* * *
51349 TAATAAAAGAGGTTATAATCTGGAATGTTAATACTTTTAATAATAAAACAGGTTG-ATT
128 TAATAAAAGAGGTTGTAATCTGGAATGTTAATAC-TTTAATAATAAAATAGGTTGCACT
* * *
51407 CGAAAATGTTATCAGAGTTTAAGCTGATGAAGTCTT-GAGTTATCCCAATATAAGAAAATAAGTT
1 -GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGA-TTAT-CCAGTATAAGAAAATAAGTT
* * * * *
51471 TAAAATTGAAAATGTTATGAACATACATAAGAAATACT-ATT--TCTCAATAATGTCATGGTTCA
63 TAAAACTGAAAATATTATGAACATATATAAGAAATA-TGATTGCGCCCAATAATGTCATGGTTCA
* * * * **
51533 ATAATAAAA-AAGTTGTAATATGGAATGTTAATAATTTTAATAATAAAGTAGGTTG-TGT
127 ATAATAAAAGAGGTTGTAATCTGGAATGTTAAT-ACTTTAATAATAAAATAGGTTGCACT
* * * ** * *
51591 CAAAATTGTTATCAGATTTTAAGCTGATAGAGCGATGGATTATCCCAATATAAGAAAATAAATTT
1 GAAAA-TGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTAT-CCAGTATAAGAAAATAAGTTT
* * * *
51656 AAAACT-AAAAAAGTTATGAACATATATAAGAAATATGGTTGTGCACAATAATGTCATGGTTCAA
64 AAAACTGAAAATA-TTATGAACATATATAAGAAATATGATTGCGCCCAATAATGTCATGGTTCAA
* * *
51720 TAATAAAAGATGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAATAGGTTGCGCC
128 TAATAAAAGAGGTTGTAATCTGGAATGTTAATAC-TTTAATAATAAAATAGGTTGCACT
* * * * *
51779 AAAAATATTATCACAGTTTAAGATGATGGAGCATTGGATTATCCTAGTATAAGAAAATAAGTTTA
1 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATCC-AGTATAAGAAAATAAGTTTA
* * * * *
51844 AAACTGAAAATATTATTAGCATATATAATAAATATGATTACGCCCAATAATGTCAAGGTTCAATA
65 AAACTGAAAATATTATGAACATATATAAGAAATATGATTGCGCCCAATAATGTCATGGTTCAATA
*
51909 ATAAAAGAAGTTGTAATCTGGAATGTTAATACTTTAATAATAAAATAGGTTGCACT
130 ATAAAAGAGGTTGTAATCTGGAATGTTAATACTTTAATAATAAAATAGGTTGCACT
* * *
51965 GAAAATATTATCAGAGTTTAAGCTGATGGAGCCTTTGATTATCTCAATATAAGAAAATAAGTTTA
1 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATC-CAGTATAAGAAAATAAGTTTA
* * * * *
52030 AAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCGTCCAATAATGTGAAT-GTTCAAT
65 AAACTGAAAATATTATGAACATATATAAGAAATATGATTGCGCCCAATAATGT-CATGGTTCAAT
*
52094 AATAAAAGAGGTTGTAATCTAGAATGTTAATACTTTTAATAATAAAATAGGTAGTGC-C-
129 AATAAAAGAGGTTGTAATCTGGAATGTTAATAC-TTTAATAATAAAATAGGT--TGCACT
* * * * *
52152 GAAAATGTTATCATAATTTAAGCTGATTGAGCCTTGGATTATCTCAGTGTAAGAAAATAAGATTA
1 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATC-CAGTATAAGAAAATAAGTTTA
* * * * *
52217 AAACTGAAAATATTATG----------AG-CA-A-CA---CACTCAATAATGTCATGGTTGAA-A
65 AAACTGAAAATATTATGAACATATATAAGAAATATGATTGCGCCCAATAATGTCATGGTTCAATA
* * *
52265 ATTAAAATAGGTTGTAATCTAGAATGTTAATATTTTTAATAATAAAATAGGGTTGCGAC-
130 A-TAAAAGAGGTTGTAATCTGGAATGTTAATA-CTTTAATAATAAAATA-GGTTGC-ACT
* *
52324 GAAAATGTTAT-TGAATTTTAAGCTGATGGAGCCTTGGATTATCCTAGTATAAGAAAATAAGTTT
1 GAAAATGTTATCAG-AGTTTAAGCTGATGGAGCCTTGGATTATCC-AGTATAAGAAAATAAG-TT
* * * * * * * * *
52388 TAAAACTTAAAATGTTATGAACATATATAATAAATA-CAGTTGTGCCAAAAAATGTCATGGCTAA
63 TAAAACTGAAAATATTATGAACATATATAAGAAATATGA-TTGCGCCCAATAATGTCATGGTTCA
* * * * * * * *
52452 AAAATAAAACAGGTTCTAATATGAAATGTTAATATTTTAATAATAAAATAGTTTGCACC
127 ATAATAAAAGAGGTTGTAATCTGGAATGTTAATACTTTAATAATAAAATAGGTTGCACT
* * *
52511 GAAAATATTATCAGAGTTTAAACAGATGGAGCCTTGGATTATCCGAGTATAAGAAAATAAGTTTA
1 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATCC-AGTATAAGAAAATAAGTTTA
* * * * * * *
52576 AAATTAAAAATTTTATGAACATATATAAGAAATATGGTTGCACTCATTAATGTCATGG
65 AAACTGAAAATATTATGAACATATATAAGAAATATGATTGCGCCCAATAATGTCATGG
52634 GTCACCAAGA
Statistics
Matches: 1034, Mismatches: 143, Indels: 100
0.81 0.11 0.08
Matches are distributed among these distances:
170 7 0.01
171 60 0.06
172 57 0.06
173 18 0.02
175 1 0.00
176 1 0.00
177 2 0.00
183 10 0.01
184 117 0.11
185 32 0.03
186 245 0.24
187 348 0.34
188 90 0.09
189 44 0.04
190 2 0.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (185 bp):
GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATCCAGTATAAGAAAATAAGTTTAA
AACTGAAAATATTATGAACATATATAAGAAATATGATTGCGCCCAATAATGTCATGGTTCAATAA
TAAAAGAGGTTGTAATCTGGAATGTTAATACTTTAATAATAAAATAGGTTGCACT
Found at i:52080 original size:373 final size:370
Alignment explanation
Indices: 51220--52633 Score: 1593
Period size: 373 Copynumber: 3.8 Consensus size: 370
51210 AGGTTGCGTC
* ** * *
51220 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCGTTATATTATCCCAGTATAAGAAAATATGTTTA
1 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATCCCAATATAAGAAAATAAGTTTA
* * * * *
51285 AAACTGAAAAATATTATGAACATATATAAGAAATATGGATGCATCCAATAATTTCATGGTTCAAT
66 AAACTG-AAAATGTTATGAACATATATAAGAAATACGGTTGC-GCCAATAATGTCATGGTTCAAT
* * *** *
51350 AATAAAAGAGGTTATAATCTGGAATGTTAATACTTTTAATAATAAAACAGGTTGATTCGAAAATG
129 AATAAAAGAGGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAATAGGTTGCGCCGAAAATA
* * * * * *
51415 TTATCAGAGTTTAAGCTGATGAAGTCTT-GAGTTATCCCAATATAAGAAAATAAGTTTAAAATTG
194 TTATCAGAGTTTAAGATGATGGAGCCTTGGA-TTATCCTAGTATAAGAAAATAAGTTTAAAACTG
* * *
51479 AAAATGTTATGAACATACATAAGAAATACTATT--TCTCAATAATGTCATGGTTCAATAATAAAA
258 AAAATATTATGAACATATATAAGAAATA-TATTACACTCAATAATGTCATGGTTCAATAATAAAA
* * **
51542 AAGTTGTAATATGGAATGTTAATAATTTTAATAATAAAGTAGGTTG-TGT
322 AAGTTGTAATCTGGAATGTTAAT-ATTTTAATAATAAAATAGGTTGCACT
* * * ** *
51591 CAAAATTGTTATCAGATTTTAAGCTGATAGAGCGATGGATTATCCCAATATAAGAAAATAAATTT
1 GAAAA-TGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATCCCAATATAAGAAAATAAGTTT
* * * *
51656 AAAACTAAAAAAGTTATGAACATATATAAGAAATATGGTTGTGCACAATAATGTCATGGTTCAAT
65 AAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCGC-CAATAATGTCATGGTTCAAT
* *
51721 AATAAAAGATGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAATAGGTTGCGCCAAAAATA
129 AATAAAAGAGGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAATAGGTTGCGCCGAAAATA
* *
51786 TTATCACAGTTTAAGATGATGGAGCATTGGATTATCCTAGTATAAGAAAATAAGTTTAAAACTGA
194 TTATCAGAGTTTAAGATGATGGAGCCTTGGATTATCCTAGTATAAGAAAATAAGTTTAAAACTGA
* * * * * *
51851 AAATATTATTAGCATATATAATAAATATGATTACGCCCAATAATGTCAAGGTTCAATAATAAAAG
259 AAATATTATGAACATATATAAGAAATAT-ATTACACTCAATAATGTCATGGTTCAATAATAAAA-
*
51916 AAGTTGTAATCTGGAATGTTAATACTTTAATAATAAAATAGGTTGCACT
322 AAGTTGTAATCTGGAATGTTAATATTTTAATAATAAAATAGGTTGCACT
* * *
51965 GAAAATATTATCAGAGTTTAAGCTGATGGAGCCTTTGATTATCTCAATATAAGAAAATAAGTTTA
1 GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATCCCAATATAAGAAAATAAGTTTA
*
52030 AAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCGTCCAATAATGTGAAT-GTTCAAT
66 AAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCG-CCAATAATGT-CATGGTTCAAT
* * * *
52094 AATAAAAGAGGTTGTAATCTAGAATGTTAATACTTTTAATAATAAAATAGGTAGTGCCGAAAATG
129 AATAAAAGAGGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAATAGGTTGCGCCGAAAATA
* * * * * *
52159 TTATCATAATTTAAGCTGATTGAGCCTTGGATTAT-CTCAGTGTAAGAAAATAAGATTAAAACTG
194 TTATCAGAGTTTAAGATGATGGAGCCTTGGATTATCCT-AGTATAAGAAAATAAGTTTAAAACTG
* * *
52223 AAAATATTATG----------AG---CA-A-CACACTCAATAATGTCATGGTTGAA-AATTAAAA
258 AAAATATTATGAACATATATAAGAAATATATTACACTCAATAATGTCATGGTTCAATAA-TAAAA
* *
52272 TAGGTTGTAATCTAGAATGTTAATATTTTTAATAATAAAATAGGGTTGCGAC-
322 -AAGTTGTAATCTGGAATGTTAATA-TTTTAATAATAAAATA-GGTTGC-ACT
* * * *
52324 GAAAATGTTAT-TGAATTTTAAGCTGATGGAGCCTTGGATTATCCTAGTATAAGAAAATAAGTTT
1 GAAAATGTTATCAG-AGTTTAAGCTGATGGAGCCTTGGATTATCCCAATATAAGAAAATAAG-TT
* * * * * * *
52388 TAAAACTTAAAATGTTATGAACATATATAATAAATACAGTTGTGCCAAAAAATGTCATGGCTAAA
64 TAAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCGCC-AATAATGTCATGGTTCAA
* * * * * * *
52453 AAATAAAACAGGTTCTAATATGAAATGTTAATA-TTTTAATAATAAAATAGTTTGCACCGAAAAT
128 TAATAAAAGAGGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAATAGGTTGCGCCGAAAAT
* * *
52517 ATTATCAGAGTTTAA-ACAGATGGAGCCTTGGATTATCCGAGTATAAGAAAATAAGTTTAAAATT
193 ATTATCAGAGTTTAAGA-TGATGGAGCCTTGGATTATCCTAGTATAAGAAAATAAGTTTAAAACT
* * * * *
52581 AAAAATTTTATGAACATATATAAGAAATATGGTTGCACTCATTAATGTCATGG
257 GAAAATATTATGAACATATATAAGAAATAT-ATTACACTCAATAATGTCATGG
52634 GTCACCAAGA
Statistics
Matches: 880, Mismatches: 126, Indels: 70
0.82 0.12 0.07
Matches are distributed among these distances:
356 2 0.00
357 47 0.05
358 17 0.02
359 150 0.17
360 84 0.10
363 1 0.00
369 2 0.00
370 2 0.00
371 190 0.22
372 62 0.07
373 276 0.31
374 30 0.03
375 17 0.02
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (370 bp):
GAAAATGTTATCAGAGTTTAAGCTGATGGAGCCTTGGATTATCCCAATATAAGAAAATAAGTTTA
AAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCGCCAATAATGTCATGGTTCAATAA
TAAAAGAGGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAATAGGTTGCGCCGAAAATATT
ATCAGAGTTTAAGATGATGGAGCCTTGGATTATCCTAGTATAAGAAAATAAGTTTAAAACTGAAA
ATATTATGAACATATATAAGAAATATATTACACTCAATAATGTCATGGTTCAATAATAAAAAAGT
TGTAATCTGGAATGTTAATATTTTAATAATAAAATAGGTTGCACT
Found at i:54737 original size:22 final size:22
Alignment explanation
Indices: 54709--54784 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
54699 ATGTATCATA
54709 AAGCGTTGAACAATTAGGAGCC
1 AAGCGTTGAACAATTAGGAGCC
54731 AAGCGTTGAACAATTAGGAGCC
1 AAGCGTTGAACAATTAGGAGCC
*
54753 AAGCGTTGAACAATTAGGAGTC
1 AAGCGTTGAACAATTAGGAGCC
*
54775 ATGCGTTGAA
1 AAGCGTTGAA
54785 AGAAATTAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.21
Consensus pattern (22 bp):
AAGCGTTGAACAATTAGGAGCC
Found at i:55045 original size:33 final size:32
Alignment explanation
Indices: 54984--55051 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
54974 GAGATTTAAC
* * * * *
54984 TGACTGGCTTGTTGATTGGTCTATATTTTTCGA
1 TGACTGACTGGTTGATTGGCCCACATTTTT-GA
55017 TGACTGACTGGTTGATTGGCCCACATTTTTGA
1 TGACTGACTGGTTGATTGGCCCACATTTTTGA
55049 TGA
1 TGA
55052 GTTGTTTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 5 0.17
33 25 0.83
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.43
Consensus pattern (32 bp):
TGACTGACTGGTTGATTGGCCCACATTTTTGA
Found at i:56431 original size:23 final size:23
Alignment explanation
Indices: 56387--56485 Score: 74
Period size: 23 Copynumber: 4.3 Consensus size: 23
56377 TGAAGTGCCA
* *
56387 CATAGAAATGT-CTCGAAGGACCT
1 CATAGAAATGTCCT-GAAAGACCG
* * *
56410 TATAGTATTGTCCTGAAAGACCG
1 CATAGAAATGTCCTGAAAGACCG
* *
56433 CATAGAAATGTCCTGAATGACCA
1 CATAGAAATGTCCTGAAAGACCG
* * * *
56456 CGTAGAATTGTCCCGAAGGACCG
1 CATAGAAATGTCCTGAAAGACCG
*
56479 CGTAGAA
1 CATAGAA
56486 CCTTCGACTT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 58 0.97
24 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (23 bp):
CATAGAAATGTCCTGAAAGACCG
Found at i:56616 original size:44 final size:44
Alignment explanation
Indices: 56562--56703 Score: 185
Period size: 44 Copynumber: 3.2 Consensus size: 44
56552 TTATAACTTT
* *** *
56562 TCACATAGCTTATATAACATAGACAAATAATCACATAGATCATG
1 TCACATAGCTTATATCACATTTTCAAATAATCACATAGATCATA
* * * *
56606 TCACACAGCTTCTATCACATTTTCATATAATCACATAGTTCAATA
1 TCACATAGCTTATATCACATTTTCAAATAATCACATAGATC-ATA
*
56651 TCACATAGCTTATATCACATTTTCACATAATCACATAGATCATA
1 TCACATAGCTTATATCACATTTTCAAATAATCACATAGATCATA
56695 TCACATAGC
1 TCACATAGC
56704 ATGAAATATA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 45 0.54
45 39 0.46
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (44 bp):
TCACATAGCTTATATCACATTTTCAAATAATCACATAGATCATA
Found at i:56640 original size:16 final size:15
Alignment explanation
Indices: 56618--56686 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
56608 ACACAGCTTC
56618 TATCACATTTTCATA
1 TATCACATTTTCATA
*
56633 TAATCACATAGTTCA-A
1 T-ATCACAT-TTTCATA
** *
56649 TATCACA-TAGCTTA
1 TATCACATTTTCATA
*
56663 TATCACATTTTCACA
1 TATCACATTTTCATA
56678 TAATCACAT
1 T-ATCACAT
56687 AGATCATATC
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
13 1 0.03
14 8 0.20
15 11 0.28
16 16 0.40
17 4 0.10
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (15 bp):
TATCACATTTTCATA
Found at i:56699 original size:14 final size:14
Alignment explanation
Indices: 56591--56702 Score: 61
Period size: 14 Copynumber: 7.6 Consensus size: 14
56581 TAGACAAATA
*
56591 ATCACATAGATCAT
1 ATCACATAGTTCAT
* *
56605 GTCACACAGCTTC-T
1 ATCACATAG-TTCAT
*
56619 ATCACAT-TTTCATAT
1 ATCACATAGTTC--AT
56634 AATCACATAGTTCAAT
1 -ATCACATAGTTC-AT
56650 ATCACATAGCTT-AT
1 ATCACATAG-TTCAT
*
56664 ATCACAT-TTTCACAT
1 ATCACATAGTT--CAT
*
56679 AATCACATAGATCAT
1 -ATCACATAGTTCAT
56694 ATCACATAG
1 ATCACATAG
56703 CATGAAATAT
Statistics
Matches: 75, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
12 5 0.07
14 31 0.41
15 17 0.23
16 18 0.24
17 4 0.05
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (14 bp):
ATCACATAGTTCAT
Done.