Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007212.1 Hibiscus syriacus cultivar Beakdansim tig00019065_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: 72686
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:4592 original size:17 final size:17
Alignment explanation
Indices: 4572--4606 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4562 TAAACAATCC
4572 ATGAA-GAAGAACATATG
1 ATGAATGAAGAA-ATATG
4589 ATGAATGAAGAAATATG
1 ATGAATGAAGAAATATG
4606 A
1 A
4607 AGCTAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (17 bp):
ATGAATGAAGAAATATG
Found at i:6611 original size:20 final size:20
Alignment explanation
Indices: 6561--6610 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
6551 CACTTAAGGA
6561 ACCGATTCCCCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
6581 ACCGATTCCCCATA-GGGGT
1 ACCGATTCCCCATAGGGGGT
6600 ACCGATTCCCC
1 ACCGATTCCCC
6611 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.20, C:0.36, G:0.24, T:0.20
Consensus pattern (20 bp):
ACCGATTCCCCATAGGGGGT
Found at i:13646 original size:12 final size:12
Alignment explanation
Indices: 13629--13657 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13619 AGATGAGCCT
13629 GAGCAGCCCGAG
1 GAGCAGCCCGAG
13641 GAGCAGCCCGAG
1 GAGCAGCCCGAG
13653 GAGCA
1 GAGCA
13658 AGCACAACAA
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:0.28, C:0.31, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:14008 original size:24 final size:23
Alignment explanation
Indices: 13958--14031 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
13948 GCTTCAACTT
* *
13958 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
13981 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
14005 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
14028 TTTG
1 TTTG
14032 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:14687 original size:22 final size:22
Alignment explanation
Indices: 14661--14715 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
14651 CTCATAGGGA
*
14661 ACCGATTCCCCATCAAGGGGGT
1 ACCGATTCCCCACCAAGGGGGT
14683 ACCGATTCCCCACCAAGGGGGT
1 ACCGATTCCCCACCAAGGGGGT
14705 ACCGATTCCCC
1 ACCGATTCCCC
14716 CCTGAATGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.38, G:0.24, T:0.16
Consensus pattern (22 bp):
ACCGATTCCCCACCAAGGGGGT
Found at i:16522 original size:99 final size:99
Alignment explanation
Indices: 16402--16591 Score: 281
Period size: 99 Copynumber: 1.9 Consensus size: 99
16392 TTATAATATT
* * * * * *
16402 ATATGTATACAATAAAACTTGAGATGTCCCTCTAGAGTAATTGGTTAAACGCTCCGGCTTTATGG
1 ATATATATACAATAAAACTTGAGATGTCCCTCCAGAGCAATTGGTTAAACACACCAGCTTTATGG
*
16467 ATAAGATTCAGCTAACCTGATAAAGGTGATTATA
66 ATAAGATTCAACTAACCTGATAAAGGTGATTATA
* * *
16501 ATATATATATAATAAAGCTTGAGTTGTCCCTCCAGAGCAATTGGTTAAACACACCAGCTTTATGG
1 ATATATATACAATAAAACTTGAGATGTCCCTCCAGAGCAATTGGTTAAACACACCAGCTTTATGG
*
16566 ATAAGATTCAACTAGCCTGATAAAGG
66 ATAAGATTCAACTAACCTGATAAAGG
16592 AAAATTACAA
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (99 bp):
ATATATATACAATAAAACTTGAGATGTCCCTCCAGAGCAATTGGTTAAACACACCAGCTTTATGG
ATAAGATTCAACTAACCTGATAAAGGTGATTATA
Found at i:18504 original size:41 final size:42
Alignment explanation
Indices: 18422--18508 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 42
18412 GAGCATTCAG
* * *
18422 TAAGTCTTTCGAGCATGATGGTTAAATCCTTCGGGTCATCTA
1 TAAGTCTTTCGAGCAAGATGGATAAATCCTTCCGGTCATCTA
*
18464 TAAGTCTTTCGAGCAAGAT-GATAAGTCCTTCCGGTCATCTA
1 TAAGTCTTTCGAGCAAGATGGATAAATCCTTCCGGTCATCTA
18505 TAAG
1 TAAG
18509 ACCTTCAGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 23 0.56
42 18 0.44
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAGTCTTTCGAGCAAGATGGATAAATCCTTCCGGTCATCTA
Found at i:18723 original size:42 final size:41
Alignment explanation
Indices: 18640--18763 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 41
18630 TTCTTACTAA
* * * *
18640 ATAAGTCCTTTGGGCCATCAGTAAGCCTTTTGAGCATGATG
1 ATAAATCCTTTGGGCCATCTGTAAGCCTTTCGAGCAAGATG
* * *
18681 ATTAAATTCTTTGGGTCATCTGTAAGCCTTTCGAACAAGATG
1 A-TAAATCCTTTGGGCCATCTGTAAGCCTTTCGAGCAAGATG
* * *
18723 ATAACTCCTTCGGGCCATCTATAAGACCTTTCG-GCAAGATG
1 ATAAATCCTTTGGGCCATCTGTAAG-CCTTTCGAGCAAGATG
18764 TTTTCATATG
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 27 0.40
42 41 0.60
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTTGGGCCATCTGTAAGCCTTTCGAGCAAGATG
Found at i:18747 original size:239 final size:236
Alignment explanation
Indices: 18300--19061 Score: 802
Period size: 239 Copynumber: 3.1 Consensus size: 236
18290 ATTAAGTTAT
* * * *
18300 TTTGAAAAATGCA-AAAGAAATGTCCAAA-TTTCTCATTTAAATCCTTTATGAAAATGAAATTTT
1 TTTGAAAAATG-AGAAAGAGATTTCCAAAGTTTCTCATTTAAATCCTTTTTGAAAATGAAAATTT
* *** * *
18363 TGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTGGTAAGTCATTCGAG-CATTCAGTAAGT
65 TGAAAAGTAAGAAAA-CATTTCCAAAGTTTCTTACTAAATAAGTCCTTCGGGCCA-TCAGTAAGT
* * * *
18427 CTTTCGAGCATGATGGTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCC
128 CTTTCGAGCATGATGATTAAATTCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCC
* * * * *
18492 TTCCGGTCATCTATAAGACCTTCAGGTAGGATGTTTTCACGTGATT
193 TTCGGGCCATCTATAAGACCTTC-GGCAGGATGTTTTCACATGA-A
18538 TTTGAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCCTTTTTGAAAATGAAAATTTT
1 TTTGAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCCTTTTTGAAAATGAAAATTTT
* * *
18603 GAAAAGTAAGAAAACATTTTCCAATGTTTCTTACTAAATAAGTCCTTTGGGCCATCAGTAAGCCT
66 GAAAAGTAAGAAAACA-TTTCCAAAGTTTCTTACTAAATAAGTCCTTCGGGCCATCAGTAAGTCT
* * * *
18668 TTTGAGCATGATGATTAAATTCTTTGGGTCATCTGTAAGCCTTTCGAACAAGATGATAACTCCTT
130 TTCGAGCATGATGATTAAATTCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTT
* *
18733 CGGGCCATCTATAAGACCTTTCGGCAAGATGTTTTCATATGAA
195 CGGGCCATCTATAAGACC-TTCGGCAGGATGTTTTCACATGAA
* * * * *
18776 TTTGAAAAATGAGAAAGTGATTTTTCAAAGTTTTTCATTT-AAT-GTTTTCAGAAAATG-AAATC
1 TTTGAAAAATGAGAAAGAGA-TTTCCAAAGTTTCTCATTTAAATCCTTTT-TGAAAATGAAAAT-
* *
18838 TTTGAAAAGAAAGAAAGCAATTTCCAAAGTTTCTTACTTAGTAGACTATTTCTGAAGATTATAAG
63 TTTGAAAAGTAAGAAAAC-ATTTCCAAAGTTTCTTAC----TA-A--A----T-AAG----T---
*
18903 ACCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGATTAAA-TCATTCGGGTCATCTGTAAGCC
108 -CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATTC-TTCGGGTCATCTGTAAGCC
* * *
18967 TTTCGAGCAAGATGATAAGTCCTTCGTGCCATATATAAGACCTTCGGGAGGGATG-TTTCACATG
171 TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGCA-GGATGTTTTCACATG
19031 AA
235 AA
* *
19033 TTTGAAAAATGAGAAAGTGATTTTCAAAG
1 TTTGAAAAATGAGAAAGAGATTTCCAAAG
19062 AAAGTGATTT
Statistics
Matches: 445, Mismatches: 48, Indels: 44
0.83 0.09 0.08
Matches are distributed among these distances:
237 9 0.02
238 86 0.19
239 192 0.43
240 5 0.01
242 2 0.00
243 1 0.00
245 1 0.00
249 1 0.00
250 3 0.01
254 1 0.00
256 9 0.02
257 38 0.09
258 97 0.22
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (236 bp):
TTTGAAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAATCCTTTTTGAAAATGAAAATTTT
GAAAAGTAAGAAAACATTTCCAAAGTTTCTTACTAAATAAGTCCTTCGGGCCATCAGTAAGTCTT
TCGAGCATGATGATTAAATTCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTC
GGGCCATCTATAAGACCTTCGGCAGGATGTTTTCACATGAA
Found at i:19414 original size:196 final size:195
Alignment explanation
Indices: 19170--19523 Score: 530
Period size: 196 Copynumber: 1.8 Consensus size: 195
19160 TTTCGAGTAA
* *
19170 GATGATAAGTCCTTCGGGCTATCCATAAGACCTTCGGGTAGGATGTTTTCACATGATTTTGAAAA
1 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGACTTTGAAAA
** * * *
19235 ATGAGAAAGTGATTTCCAAAGTTTCACATTTAAATCATTTT-TGAAAATAAAATTTTTGAAAAGT
66 ATGAGAAAGCAATTTCCAAAGTTTCACATTT-AAT-ATTTTCAGAAAATAAAATCTTTCAAAAGT
*
19299 AAGAAAATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAACCCTTTTGAGC
129 AAGAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAACCCTTTTGAGC
19364 AG
194 AG
* * * *
19366 GATGATAAGTCCTTCGGGCCATCTATAAGATCTTTGGGTAGGATGTTTTCATATGACTTTGAAAA
1 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGACTTTGAAAA
* * * *
19431 ATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTCAAAAGTAA
66 ATGAGAAAGCAATTTCCAAAGTTTCACATTTAATATTTTCAGAAAATAAAATCTTTCAAAAGTAA
*
19496 GAAAGCGATTTCCAAAGTTTCTTACTTA
131 GAAAACGATTTCCAAAGTTTCTTACTTA
19524 ATAGACTATT
Statistics
Matches: 140, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
194 4 0.03
195 50 0.36
196 86 0.61
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (195 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGACTTTGAAAA
ATGAGAAAGCAATTTCCAAAGTTTCACATTTAATATTTTCAGAAAATAAAATCTTTCAAAAGTAA
GAAAACGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAACCCTTTTGAGCAG
Found at i:19701 original size:257 final size:244
Alignment explanation
Indices: 19543--20398 Score: 778
Period size: 236 Copynumber: 3.5 Consensus size: 244
19533 TTCTGAAGAT
* * * *
19543 GATAAGACCTTCGGGGCATCAGTAAGTCTTTCGAGCATGATGATTAATTCCTTTGGGTCATCTGT
1 GATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT
* * * *
19608 GAGCCTTTCGAGGAAGATGATAAGTCCTTAGAGCCATCTATAAGACCTTCGGGCTA-GATGTTTT
66 -AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGG-TAGGATGTTTT
*
19672 CACATGAATTTGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGA
129 CACATGATTTTGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGA
*
19737 AATCTTTGAAAAGTTAGAAAGCGATTTCCAAAGTTTCTTAC------TT-A
194 AATCTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACTTAGAATTAA
* * *
19781 G-TAAGTCATTCGAGCCATCAATAAG-CATTTCGAGCATGATGATTAAATCCTTCGGGTCATCTG
1 GATAAGTCCTTCGGGCCATCAGTAAGTC-TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTG
* * * *
19844 TAAGTCTTTTGAGGAAGATGATAAGTCCTTCGGGCCATCCATAAGATCTTC-GGTAGGATGTTTT
65 T-AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTTT
** * * *
19908 CACATGATTTTGAAAAATGAGAAAGCGGTTTCCAAAGTTTCT-ATTTAAATCCTTTT-TGAAAAT
129 CACATGATTTTGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTT-AAT-GTTTTCAGAAAAT
* * **
19971 GAAATTTTTGAAAAGTATGAAAATGATTTCCAAAG--T-TT-CTT--AATT-A
192 GAAATCTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACTTAGAATTAA
* * * *
20017 -ATAAGTCCTTAGGGCTATCACTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTCATCTGT
1 GATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT
* * * * * * *
20081 --T-TTT-GAGCAAGATTACAAGTCTTTCGGGCCATCCATAAGACCTTGGGGCAGGATGTTCTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTTTCA
* * * * * * * * *
20142 CGTGATTTTTAAAAAATGAG--AGCGATTTTCAAATTTTATATCGTTTAGTATTTTTAGAAAATG
131 CATGA-TTTTGAAAAATGAGAAAGCAATTTTCAAA-GTT-TCTCATTTAATGTTTTCAGAAAATG
* * *
20205 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTGCTTA-TTAGTAAACTATTTCCAAAA
193 AAATCTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACTTAG---A--A-TT----AA
* * * **
20266 TTAGTAAGTCCTTCGGGCCATCAGTAAGACTTTCGAGCATAATGATTAAATCCTTTAGGTCATCT
1 -GA-TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCT
* * * * * *
20331 GTCAGTCTTTCGTGCTAGATGATAAGTCATTCGGGCCATCTATAAAACCTTCGAGTATGATGTTT
64 GT-AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTT
20396 TCA
128 TCA
20399 AATTCTCAAA
Statistics
Matches: 505, Mismatches: 72, Indels: 63
0.79 0.11 0.10
Matches are distributed among these distances:
231 46 0.09
232 27 0.05
233 59 0.12
234 4 0.01
235 6 0.01
236 150 0.30
237 102 0.20
238 1 0.00
241 1 0.00
243 1 0.00
244 2 0.00
249 1 0.00
251 1 0.00
252 55 0.11
255 1 0.00
256 3 0.01
257 45 0.09
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (244 bp):
GATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT
AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTTTCA
CATGATTTTGAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAA
TCTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACTTAGAATTAA
Found at i:19985 original size:236 final size:232
Alignment explanation
Indices: 19559--20252 Score: 803
Period size: 236 Copynumber: 3.0 Consensus size: 232
19549 ACCTTCGGGG
* * * * *
19559 CATCAGTAAGTCTTTCGAGCATGATGATTAATTCCTTTGGGTCATCTGTGAGCCTTTCGAGGAAG
1 CATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT-AGTCTTTTGAGGAAG
* * * *
19624 ATGATAAGTCCTTAGAGCCATCTATAAGACCTTCGGGCTA-GATGTTTTCACATGAATTTGAAAA
65 ATGATAAGTCCTTCGGGCCATCCATAAGACCTTC-GG-TAGGATGTTTTCACATGATTTTGAAAA
* * * *
19688 ATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTGAAAAGTTA
128 ATGAGAAAGCGATTTTCAAAGTTTCT-ATTTAATATTTT-TGAAAATGAAATTTTTGAAAAGTTA
* *
19753 GAAAGCGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGAGC
191 GAAAGTGATTTCCAAAGTTTCTTA-TTAGTAAGTCATTAGAGC
19796 CATCAATAAG-CATTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGGAA
1 CATCAATAAGTC-TTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT-AGTCTTTTGAGGAA
*
19860 GATGATAAGTCCTTCGGGCCATCCATAAGATCTTCGGTAGGATGTTTTCACATGATTTTGAAAAA
64 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGTAGGATGTTTTCACATGATTTTGAAAAA
* * *
19925 TGAGAAAGCGGTTTCCAAAGTTTCTATTTAAATCCTTTTTGAAAATGAAATTTTTGAAAAG-TAT
129 TGAGAAAGCGATTTTCAAAGTTTCTATTT-AAT-ATTTTTGAAAATGAAATTTTTGAAAAGTTA-
* * * *
19989 GAAAATGATTTCCAAAGTTTCTTAATTAATAAGTCCTTAGGGC
191 GAAAGTGATTTCCAAAGTTTCTT-ATTAGTAAGTCATTAGAGC
* * * *
20032 TATCACTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTCATC--T-GT-TTTTGAGCAAGA
1 CATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAGTCTTTTGAGGAAGA
* * * * * * * *
20093 TTACAAGTCTTTCGGGCCATCCATAAGACCTTGGGGCAGGATGTTCTCACGTGATTTTTAAAAAA
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTT-CGGTAGGATGTTTTCACATGA-TTTTGAAAAA
* * * *
20158 TGAG--AGCGATTTTCAAATTTTATATCGTTTAGTATTTTTAGAAAATGAAATTTTTGAAAAGTA
129 TGAGAAAGCGATTTTCAAAGTTTCTA---TTTAATATTTTT-GAAAATGAAATTTTTGAAAAGTT
*
20221 AGAAAGTGATTTCCAAAGTTGCTTATTAGTAA
190 AGAAAGTGATTTCCAAAGTTTCTTATTAGTAA
20253 ACTATTTCCA
Statistics
Matches: 397, Mismatches: 46, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
231 55 0.14
232 31 0.08
233 57 0.14
234 5 0.01
235 8 0.02
236 148 0.37
237 93 0.23
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (232 bp):
CATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAGTCTTTTGAGGAAGA
TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGTAGGATGTTTTCACATGATTTTGAAAAATG
AGAAAGCGATTTTCAAAGTTTCTATTTAATATTTTTGAAAATGAAATTTTTGAAAAGTTAGAAAG
TGATTTCCAAAGTTTCTTATTAGTAAGTCATTAGAGC
Found at i:20937 original size:2 final size:2
Alignment explanation
Indices: 20895--20925 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20885 ATAATGTTGA
20895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20926 AACAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22473 original size:37 final size:36
Alignment explanation
Indices: 22432--22507 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 36
22422 TTCGGGAGCG
* *
22432 GGTCGGGTTTTTTAAGTTTGATATTTGGGTTGGGTCT
1 GGTCGGGTTTTTTAAGTGTGATATTTGGGTCGGGT-T
*
22469 GGTCGTGTTTTTTAAGTGTGATATTTGGGTCGGGTT
1 GGTCGGGTTTTTTAAGTGTGATATTTGGGTCGGGTT
22505 GGT
1 GGT
22508 TTTTTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 4 0.11
37 32 0.89
ACGTcount: A:0.11, C:0.05, G:0.37, T:0.47
Consensus pattern (36 bp):
GGTCGGGTTTTTTAAGTGTGATATTTGGGTCGGGTT
Found at i:22623 original size:33 final size:33
Alignment explanation
Indices: 22557--22709 Score: 216
Period size: 33 Copynumber: 4.6 Consensus size: 33
22547 ATAATTCAGG
* * *
22557 TTCGGGTCGAGTCAGGTTTTTTTAAAGTTTGATA
1 TTCGGGTCGGGTCGGGTTTTTTT-AAGTGTGATA
22591 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
* *
22624 TTCGGGTCGGATCGGGTTTTTTTAAGTTTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
* *
22657 TTCAGGTCGGGTCAGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
*
22690 TTCAGGTCGGGTTCGGGTTT
1 TTCGGGTCGGG-TCGGGTTT
22710 AGGGTGAAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 80 0.74
34 28 0.26
ACGTcount: A:0.15, C:0.10, G:0.32, T:0.43
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:30262 original size:30 final size:30
Alignment explanation
Indices: 30228--30293 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
30218 AGTTTAATTA
*
30228 ATGAAATAACTTTA-TTAATGAATTAAATGC
1 ATGAAAT-ACTTTATTTAATGAAGTAAATGC
* * *
30258 ATGAAGTAGTTTATTTAATGAAGTAGATGC
1 ATGAAATACTTTATTTAATGAAGTAAATGC
30288 AT-AAAT
1 ATGAAAT
30294 GGACTACTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (30 bp):
ATGAAATACTTTATTTAATGAAGTAAATGC
Found at i:36282 original size:20 final size:18
Alignment explanation
Indices: 36249--36287 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
36239 TTTATAATAT
*
36249 TCGAATATAATATTTAAA
1 TCGAATATAATATTAAAA
36267 TCGAATATAAAATATTAAAA
1 TCGAATAT--AATATTAAAA
36287 T
1 T
36288 TATTTAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (18 bp):
TCGAATATAATATTAAAA
Found at i:36410 original size:16 final size:16
Alignment explanation
Indices: 36389--36422 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
36379 GATTTTCTTT
36389 TTGAAAAAATTTACTC
1 TTGAAAAAATTTACTC
36405 TTGAAAAAATTTACTC
1 TTGAAAAAATTTACTC
36421 TT
1 TT
36423 ACTCCCCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (16 bp):
TTGAAAAAATTTACTC
Found at i:36679 original size:14 final size:16
Alignment explanation
Indices: 36646--36682 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
36636 TTCAATTAAG
*
36646 TTCAAAATGCTAATCA
1 TTCAAAATGCTAAACA
36662 TTCAAAAT-C-AAACA
1 TTCAAAATGCTAAACA
36676 TTCAAAA
1 TTCAAAA
36683 CACAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 11 0.55
15 1 0.05
16 8 0.40
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (16 bp):
TTCAAAATGCTAAACA
Found at i:37677 original size:16 final size:16
Alignment explanation
Indices: 37634--37677 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
37624 TTTGATTGAT
37634 TTTTGTGTTTTGGATA
1 TTTTGTGTTTTGGATA
*
37650 TTTGGT-TGTTTGGATA
1 TTTTGTGT-TTTGGATA
37666 TTTTGTGTTTTG
1 TTTTGTGTTTTG
37678 AATGTTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.09, C:0.00, G:0.27, T:0.64
Consensus pattern (16 bp):
TTTTGTGTTTTGGATA
Found at i:37694 original size:30 final size:31
Alignment explanation
Indices: 37631--37709 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 31
37621 CATTTTGATT
* *
37631 GATTTTTGTGTTTTGGATATTTGGTTGTTTG
1 GATTTTTGTGTTTTGAATATTTGGATGTTTG
*
37662 GATATTTTGTGTTTTGAATGTTT-GAT-TTTG
1 GAT-TTTTGTGTTTTGAATATTTGGATGTTTG
*
37692 GATTATTTGTATTTTGAA
1 GATT-TTTGTGTTTTGAA
37710 CTTAATTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.02
30 19 0.45
31 5 0.12
32 17 0.40
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.59
Consensus pattern (31 bp):
GATTTTTGTGTTTTGAATATTTGGATGTTTG
Found at i:37707 original size:16 final size:15
Alignment explanation
Indices: 37635--37707 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
37625 TTGATTGATT
*
37635 TTTGTGTTTTGGATA
1 TTTGTATTTTGGATA
37650 TTTGGT-TGTTTGGATA
1 TTT-GTAT-TTTGGATA
* * *
37666 TTTTGTGTTTTGAATG
1 -TTTGTATTTTGGATA
37682 TTTG-ATTTTGGATTA
1 TTTGTATTTTGGA-TA
37697 TTTGTATTTTG
1 TTTGTATTTTG
37708 AACTTAATTG
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.13
15 13 0.28
16 24 0.51
17 4 0.09
ACGTcount: A:0.14, C:0.00, G:0.25, T:0.62
Consensus pattern (15 bp):
TTTGTATTTTGGATA
Found at i:37976 original size:15 final size:16
Alignment explanation
Indices: 37933--37966 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
37923 AAGGGGCAGT
*
37933 AAGAGTTAATTTTTTC
1 AAGAGTAAATTTTTTC
37949 AAGAGTAAATTTTTTC
1 AAGAGTAAATTTTTTC
37965 AA
1 AA
37967 AGTGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
AAGAGTAAATTTTTTC
Found at i:40626 original size:2 final size:2
Alignment explanation
Indices: 40619--40683 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
40609 CGAACCTCTA
40619 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
40661 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
40684 CTAACATCAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41009 original size:2 final size:2
Alignment explanation
Indices: 41004--41032 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40994 TGTATATATA
41004 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
41033 ATTTATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:49821 original size:22 final size:22
Alignment explanation
Indices: 49795--49844 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
49785 AAAGGAAATG
49795 TGGTTCTTCATATTCAATAGCT
1 TGGTTCTTCATATTCAATAGCT
49817 TGGTTCTTCATATTCAATAGCT
1 TGGTTCTTCATATTCAATAGCT
49839 TGGTTC
1 TGGTTC
49845 ATATGAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (22 bp):
TGGTTCTTCATATTCAATAGCT
Found at i:50383 original size:17 final size:17
Alignment explanation
Indices: 50361--50465 Score: 88
Period size: 17 Copynumber: 6.2 Consensus size: 17
50351 AATTAAGAGT
* *
50361 TAGTTTGATTAATGCAC
1 TAGTTTAATTAATGAAC
* *
50378 TAGTTTAATGATTGAAC
1 TAGTTTAATTAATGAAC
50395 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
50412 TAACTTT-ATTAATGAAC
1 T-AGTTTAATTAATGAAC
* * * *
50429 TAAATGT-ATGAATGAAT
1 T-AGTTTAATTAATGAAC
*
50446 TAGTTTATTTAATGAAC
1 TAGTTTAATTAATGAAC
50463 TAG
1 TAG
50466 ATGCATAAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
16 3 0.04
17 63 0.90
18 4 0.06
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:50443 original size:34 final size:34
Alignment explanation
Indices: 50405--50485 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
50395 TAGTTTAATT
* *
50405 AATGAACTAACTTTA-TTAATGAACTAAATGTATG
1 AATGAACT-ACTTTATTTAATGAACTAAATGCATA
* * *
50439 AATGAATTAGTTTATTTAATGAACTAGATGCATA
1 AATGAACTACTTTATTTAATGAACTAAATGCATA
50473 AATGAACTACTTT
1 AATGAACTACTTT
50486 CCCTAAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 5 0.13
34 34 0.87
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (34 bp):
AATGAACTACTTTATTTAATGAACTAAATGCATA
Found at i:50477 original size:51 final size:51
Alignment explanation
Indices: 50385--50481 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
50375 CACTAGTTTA
* ** *
50385 ATGATTGAACTAGTTTAATTAATGAACTAACTTTATTAATGAACTAAATGT
1 ATGAATGAACTAGTTTAATTAATGAACTAACTGCATAAATGAACTAAATGT
* *
50436 ATGAATGAATTAGTTTATTTAATGAACTAGA-TGCATAAATGAACTA
1 ATGAATGAACTAGTTTAATTAATGAACTA-ACTGCATAAATGAACTA
50482 CTTTCCCTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 38 0.97
52 1 0.03
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.37
Consensus pattern (51 bp):
ATGAATGAACTAGTTTAATTAATGAACTAACTGCATAAATGAACTAAATGT
Found at i:51743 original size:24 final size:24
Alignment explanation
Indices: 51702--51752 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
51692 TTTTATTTTC
* *
51702 TTTGCCTCGTTTTGGTCAGTCTCT
1 TTTGCCTCATTTTGGTCACTCTCT
*
51726 TTTGCCTCAATTTT-GTCACTCTTT
1 TTTGCCTC-ATTTTGGTCACTCTCT
51750 TTT
1 TTT
51753 TTTACTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.55
Consensus pattern (24 bp):
TTTGCCTCATTTTGGTCACTCTCT
Found at i:53931 original size:18 final size:19
Alignment explanation
Indices: 53891--53932 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
53881 AACGCTTCCG
*
53891 TGGCAAGTAGTGTTGTCGA
1 TGGCAAGTAGTATTGTCGA
*
53910 -GGCAAGTGGTATTGTC-A
1 TGGCAAGTAGTATTGTCGA
53927 TGGCAA
1 TGGCAA
53933 ATGTTGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.24, C:0.12, G:0.36, T:0.29
Consensus pattern (19 bp):
TGGCAAGTAGTATTGTCGA
Found at i:55040 original size:17 final size:17
Alignment explanation
Indices: 54987--55043 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
54977 GTTAACTTTA
* *
54987 TTAATGAACTAAATGCA
1 TTAATGAACTAGATGCT
* * * **
55004 TGAATGAAGTAGTTTAT
1 TTAATGAACTAGATGCT
55021 TTAATGAACTAGATGCT
1 TTAATGAACTAGATGCT
55038 TTAATG
1 TTAATG
55044 CAATGCATGC
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (17 bp):
TTAATGAACTAGATGCT
Found at i:55053 original size:17 final size:17
Alignment explanation
Indices: 55020--55074 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
55010 AAGTAGTTTA
*
55020 TTTAATGAACTAG-ATGC
1 TTTAATGAAC-GGCATGC
*
55037 TTTAATGCAA-TGCATGC
1 TTTAATG-AACGGCATGC
*
55054 TTAAATGAACGGCATGC
1 TTTAATGAACGGCATGC
55071 TTTA
1 TTTA
55075 TTAAATGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 3 0.10
17 26 0.84
18 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (17 bp):
TTTAATGAACGGCATGC
Found at i:56920 original size:24 final size:26
Alignment explanation
Indices: 56860--56957 Score: 121
Period size: 26 Copynumber: 3.9 Consensus size: 26
56850 AGTCTTTGGT
*
56860 ATAAATGGCACTTTCGAGTGCAATTG
1 ATAAATGGCACTTTCGAGTGCAAGTG
* *
56886 ATAAATGGCACTTTCTAGAGCAAGT-
1 ATAAATGGCACTTTCGAGTGCAAGTG
*
56911 A-AAATGGCACTTTCGAGTGCAAGAG
1 ATAAATGGCACTTTCGAGTGCAAGTG
* *
56936 ATAAAGGGCACTAT-GAGTGCAA
1 ATAAATGGCACTTTCGAGTGCAA
56958 AGATGGTAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
24 20 0.32
25 10 0.16
26 32 0.52
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (26 bp):
ATAAATGGCACTTTCGAGTGCAAGTG
Found at i:57195 original size:117 final size:117
Alignment explanation
Indices: 56989--57218 Score: 316
Period size: 117 Copynumber: 2.0 Consensus size: 117
56979 TGTAATATGG
* * * *
56989 CACTTTGTGTGCAAGGATGATAGTCATAATGAATTACCACTCCAGAATTATTAGTATAGTGTTGT
1 CACTTTGTGTGCAACGAAGATAGTCATAACGAATTACCACTCCAGAATTATTAGTATAGTGTCGT
* * * *
57054 TTTATACTATAGTACATATACATCATTGTGGAACTTAGGTTCTTATTGGGCA
66 TGTATACCACAGTACATATACATCATTGTGGAACTTAGGTGCTTATTGGGCA
* * * *
57106 CACTTTGTGTGCAACGAAGATATTCATAACGAATTACTACTCCGGAATTGTTAGTATAGTGTCGT
1 CACTTTGTGTGCAACGAAGATAGTCATAACGAATTACCACTCCAGAATTATTAGTATAGTGTCGT
* * * *
57171 TGTGTACCACAGTACCTATACATCATTGTGGCACTTATGTGCTTATTG
66 TGTATACCACAGTACATATACATCATTGTGGAACTTAGGTGCTTATTG
57219 TGTACCTTGC
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 97 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (117 bp):
CACTTTGTGTGCAACGAAGATAGTCATAACGAATTACCACTCCAGAATTATTAGTATAGTGTCGT
TGTATACCACAGTACATATACATCATTGTGGAACTTAGGTGCTTATTGGGCA
Found at i:66851 original size:61 final size:61
Alignment explanation
Indices: 66737--66856 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
66727 GTGCAAGTTG
* * * *
66737 TGGGCACAACCTTATGTGTCATATCTGGATTAGCACTAGAGTATAAACCTAGTGTAGGTGA
1 TGGGCACAACCCTATGTGTCATATCCGGATTAGCACTAGAGCATAAACCTAGTGCAGGTGA
* * * *
66798 TGGGCACGACCCTATGTGTCATATCCGGATTAGCACTAGAGCGTAAGCTTAGTGCAGGT
1 TGGGCACAACCCTATGTGTCATATCCGGATTAGCACTAGAGCATAAACCTAGTGCAGGT
66857 TTAGCACTAC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (61 bp):
TGGGCACAACCCTATGTGTCATATCCGGATTAGCACTAGAGCATAAACCTAGTGCAGGTGA
Found at i:71024 original size:19 final size:19
Alignment explanation
Indices: 71002--71043 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
70992 TTTGACCAGT
71002 TTTGAACCGT-TCGAACCGG
1 TTTGAACCGTCT-GAACCGG
71021 TTTG-ACCGTCTGAACCGG
1 TTTGAACCGTCTGAACCGG
*
71039 GTTGA
1 TTTGA
71044 CCCGACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
TTTGAACCGTCTGAACCGG
Found at i:71080 original size:17 final size:17
Alignment explanation
Indices: 71039--71112 Score: 116
Period size: 16 Copynumber: 4.4 Consensus size: 17
71029 TCTGAACCGG
*
71039 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
71056 GTTTGACCCGACCCGACC
1 G-TTGACCCGACCCGACC
71074 GTTGACCC-ACCCGACC
1 GTTGACCCGACCCGACC
71090 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
71107 G-TGACC
1 GTTGACC
71113 GTGACCATGA
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
16 21 0.39
17 17 0.31
18 16 0.30
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:72062 original size:30 final size:30
Alignment explanation
Indices: 71989--72062 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
71979 CTAATGTGAC
* *
71989 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTA-GTAGGCCCTGCGGCCCTAAGATCAT
** **
72020 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTT
1 TCT-TAGTAGGCCCTGCGGCCCTAAGATCAT
72051 TCTTAGTAGGCC
1 TCTTAGTAGGCC
72063 TCACGGCCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (30 bp):
TCTTAGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:72070 original size:30 final size:32
Alignment explanation
Indices: 72036--72110 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 32
72026 GTAGGCCCTG
72036 CGGCCCTAAGATGTTTCTT-AGTAGGC-CTCA
1 CGGCCCTAAGATGTTTCTTGAGTAGGCTCTCA
** * * *
72066 CGGCCCCGA-ATCTATCTTGGGTAGGCTCTCA
1 CGGCCCTAAGATGTTTCTTGAGTAGGCTCTCA
72097 -GGCCCTAAGATGTT
1 CGGCCCTAAGATGTT
72111 CCCTTAGGTA
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
29 7 0.21
30 19 0.58
31 7 0.21
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (32 bp):
CGGCCCTAAGATGTTTCTTGAGTAGGCTCTCA
Done.