Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008520.1 Hibiscus syriacus cultivar Beakdansim tig00111387_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: 519447
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:354760 original size:294 final size:291
Alignment explanation
Indices: 354338--354883 Score: 1029
Period size: 294 Copynumber: 1.9 Consensus size: 291
354328 AAAAACACCC
* *
354338 AATTTTGGTTTGCGAAATCAGAAATCAGGCTCGGGAGTCAGTTACGTGTGGGAAATGATTAACAC
1 AATTTTGGTTTACGAAATCAGAAATCAGGCTCGGGAGTCAGTTACGCGTGGGAAATGATTAACAC
*
354403 CCCACAACGCCTAAAATTGGTACATAGTCGATTACCTTATATTTTAAATTTGGGATTTTTGAGTT
66 CCCACAACGCCTAAAATTGGTACATAGTCGATTACCCTATATTTTAAATTTGGGATTTTTGAGTT
354468 TTAATTTTTATTTATTTAAAATCCATTATGTATGTAAAATTTTAAAAAAAAAGATGTTGATTTAC
131 TTAATTTTTATTTATTTAAAATCCATTATGTATGTAAAA-TTT-AAAAAAAAGATGTTGATTTAC
354533 CAAGACCAATAACGACCACCCAAGCATAAGTGGAAGCTTCGTTATCGATCTCAATAAATTAGAAA
194 CAAGACCAATAACGACCACCCAAGCATAAGTGGAAGCTTCGTTATCGATCTCAATAAATTAGAAA
354598 TCAGAAATCAGGCTCGGGAGTCAGTTACGCCTA
259 TCAGAAATCAGGCTCGGGAGTCAGTTACGCCTA
354631 AATTTTGGTTTACGAAATCAGAAATCAGGCTCGGGAGTCAGTTACGCGTGGGAAATGATTAACAC
1 AATTTTGGTTTACGAAATCAGAAATCAGGCTCGGGAGTCAGTTACGCGTGGGAAATGATTAACA-
354696 CCCCACAACGCCTAAAATTGGTACATAGTCGATTACCCTATATTTTAAATTTGGGATTTTTGAGT
65 CCCCACAACGCCTAAAATTGGTACATAGTCGATTACCCTATATTTTAAATTTGGGATTTTTGAGT
*
354761 TTTAATTTTTATTTATTTAAAATCCATTATGTATGTAAAATTTAAAAAAAAGATGTTGATTTTCC
130 TTTAATTTTTATTTATTTAAAATCCATTATGTATGTAAAATTTAAAAAAAAGATGTTGATTTACC
354826 AAGACCAATAACGACCACCCAAGCATAAGTGGAAGCTTCGTTATCGATCTCAATAAAT
195 AAGACCAATAACGACCACCCAAGCATAAGTGGAAGCTTCGTTATCGATCTCAATAAAT
354884 GAACGTTGCC
Statistics
Matches: 248, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
292 79 0.32
293 65 0.26
294 104 0.42
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (291 bp):
AATTTTGGTTTACGAAATCAGAAATCAGGCTCGGGAGTCAGTTACGCGTGGGAAATGATTAACAC
CCCACAACGCCTAAAATTGGTACATAGTCGATTACCCTATATTTTAAATTTGGGATTTTTGAGTT
TTAATTTTTATTTATTTAAAATCCATTATGTATGTAAAATTTAAAAAAAAGATGTTGATTTACCA
AGACCAATAACGACCACCCAAGCATAAGTGGAAGCTTCGTTATCGATCTCAATAAATTAGAAATC
AGAAATCAGGCTCGGGAGTCAGTTACGCCTA
Found at i:355471 original size:326 final size:327
Alignment explanation
Indices: 354877--355519 Score: 974
Period size: 326 Copynumber: 2.0 Consensus size: 327
354867 TATCGATCTC
* *
354877 AATAAATGAACGTTGCCTTAATTTAAAAAATATGAAGCAAAGTTTTAAAAAGATGTCGGTTTACT
1 AATAAATGAACATTGCCTTAATTTAAAAAATATGAAGCAAAGTTTTAAAAAGATGTCGATTTACT
*
354942 TCGGAGATTAATAGTGGTCACTCCCAAGCAATGGCGGAGGATACACTATTAATCACCCAAATAAA
66 TCAGAGATTAATAGTGGTCACTCCCAAGCAATGGCGGAGGATACACTATTAATCACCCAAATAAA
* * * *
355007 TTAACATTGCCTTGATTTAAAAATCGAAATGCAATCAGACAATTTATTATTAAACCAAATTACAC
131 TTAACATTGCCTTGATTTAAAAATCAAAATGCAATCAAACAATTTAGTATTAAACCAAATCACAC
* *
355072 TAACTGGTTAATTAAGACAATCATCTAACTTAGAGTGTCAAATTATGAAATTTAAGGAACTTAAG
196 TAAATGGATAATTAAGACAATCATCTAACTTAGAGTGTCAAATTATGAAATTTAAGGAACTTAAG
*
355137 AGGCTAAACCTAAAATTTATAGGCTCTAATATTAATCTAAATCAAATTTAACCAATTTATAGGAT
261 AGGCTAAACCTAAAATTTATAGGCTCTAATATTAATCCAAATCAAATTTAACCAATTTATAGGAT
355202 AT
326 AT
** * *
355204 AATAAATGAACATTGCCTTAATTTAAAAAATATGTTGCAGAG-TTTATAAAGGATGTCGATTTAC
1 AATAAATGAACATTGCCTTAATTTAAAAAATATGAAGCAAAGTTTTA-AAAAGATGTCGATTTAC
355268 TTCAGAGATTAATAGTGGTCAC-CCCAAGCAATGGCGGAGGATACACTATTAATCA-CCAATATA
65 TTCAGAGATTAATAGTGGTCACTCCCAAGCAATGGCGGAGGATACACTATTAATCACCCAA-ATA
* * * * *
355331 AATTAATATTGCCTTGATTTTAAAATCAAAATGCAATCAAATAATTTAGTATTAAACCTAATCAT
129 AATTAACATTGCCTTGATTTAAAAATCAAAATGCAATCAAACAATTTAGTATTAAACCAAATCAC
* * *
355396 ACTAAATGGATGATTAA-AGTAATCCTCTAACTTAGAGTG-CAAAATTATGAAATTTAAGGAA-T
194 ACTAAATGGATAATTAAGA-CAATCATCTAACTTAGAGTGTC-AAATTATGAAATTTAAGGAACT
* * *
355458 GTAAGGGGCTAAACCTAAAATTTATAGGCTCTAATATTAATCCAAATCGATTTTAACCAATT
257 -TAAGAGGCTAAACCTAAAATTTATAGGCTCTAATATTAATCCAAATCAAATTTAACCAATT
355520 ATTGAATCGA
Statistics
Matches: 286, Mismatches: 25, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
325 7 0.02
326 205 0.72
327 74 0.26
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (327 bp):
AATAAATGAACATTGCCTTAATTTAAAAAATATGAAGCAAAGTTTTAAAAAGATGTCGATTTACT
TCAGAGATTAATAGTGGTCACTCCCAAGCAATGGCGGAGGATACACTATTAATCACCCAAATAAA
TTAACATTGCCTTGATTTAAAAATCAAAATGCAATCAAACAATTTAGTATTAAACCAAATCACAC
TAAATGGATAATTAAGACAATCATCTAACTTAGAGTGTCAAATTATGAAATTTAAGGAACTTAAG
AGGCTAAACCTAAAATTTATAGGCTCTAATATTAATCCAAATCAAATTTAACCAATTTATAGGAT
AT
Found at i:360258 original size:21 final size:21
Alignment explanation
Indices: 360232--360271 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
360222 CAGAACCCCA
*
360232 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
360253 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
360272 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:360303 original size:21 final size:23
Alignment explanation
Indices: 360252--360303 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
360242 GATTCCCCTG
*
360252 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCAGTTCCCCTTCA
**
360275 AAGGGGGAATCAGTT-CCC-TCA
1 TGGGGGGAATCAGTTCCCCTTCA
360296 TGGGGGGA
1 TGGGGGGA
360304 TCGATTCCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCAGTTCCCCTTCA
Found at i:364140 original size:22 final size:21
Alignment explanation
Indices: 364098--364137 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
364088 GAGTTTGTTT
*
364098 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
364119 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
364138 ACAATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:368982 original size:10 final size:9
Alignment explanation
Indices: 368967--369014 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
368957 ATATTAATTT
368967 TTTTTTATAA
1 TTTTTT-TAA
*
368977 TTTTTTGAA
1 TTTTTTTAA
368986 TTTTTTTATA
1 TTTTTTTA-A
*
368996 TTTTTTTTGA
1 -TTTTTTTAA
369006 TTTTTTTAA
1 TTTTTTTAA
369015 ATTTATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 17 0.53
10 8 0.25
11 7 0.22
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:368991 original size:20 final size:19
Alignment explanation
Indices: 368966--369018 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
368956 CATATTAATT
368966 TTTTTTTATAATTTTTTGAA
1 TTTTTTTATAATTTTTTG-A
*
368986 TTTTTTTATATTTTTTTTGA
1 TTTTTTTATA-ATTTTTTGA
369006 TTTTTTTA-AATTT
1 TTTTTTTATAATTT
369019 ATAAAAGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 19 0.63
21 7 0.23
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTTTTATAATTTTTTGA
Found at i:369018 original size:10 final size:10
Alignment explanation
Indices: 368966--369018 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
368956 CATATTAATT
368966 TTTTTTTATAA
1 TTTTTTTA-AA
*
368977 -TTTTTTGAA
1 TTTTTTTAAA
*
368986 TTTTTTTATA
1 TTTTTTTAAA
**
368996 TTTTTTTTGA
1 TTTTTTTAAA
369006 TTTTTTTAAA
1 TTTTTTTAAA
369016 TTT
1 TTT
369019 ATAAAAGTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
9 2 0.06
10 32 0.94
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:369048 original size:16 final size:16
Alignment explanation
Indices: 369011--369056 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
369001 TTTGATTTTT
369011 TTAAAT-TTATAA-AA
1 TTAAATATTATAATAA
*
369025 GT-AATATTATAATAA
1 TTAAATATTATAATAA
369040 TTAAATATTATGAATAA
1 TTAAATATTAT-AATAA
369057 AATAGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.12
14 7 0.27
15 3 0.12
16 8 0.31
17 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
TTAAATATTATAATAA
Found at i:371002 original size:12 final size:13
Alignment explanation
Indices: 370981--371017 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
370971 TTTATCCGAA
370981 AAAAATCCGGTAT
1 AAAAATCCGGTAT
370994 AAAAA-CCGGTA-
1 AAAAATCCGGTAT
371005 AAAAATCCGGTAT
1 AAAAATCCGGTAT
371018 GGAGTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 12 0.55
13 5 0.23
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (13 bp):
AAAAATCCGGTAT
Found at i:371394 original size:49 final size:49
Alignment explanation
Indices: 371274--371398 Score: 128
Period size: 49 Copynumber: 2.6 Consensus size: 49
371264 ATTTGATATG
* * * * *
371274 TTCCGTTGCTCTTCAAGGTAAGTTAGATCGAGAAAAGAAAAGGGATTTA
1 TTCCGCTGCTCTTCAAGGTAGGTCATATCGAGAAAAGAAAAGGGATTGA
* ** *
371323 TTCCGCTACTCTTCAAAATAGGTCATATCGAGAAAAGAAATAGGG-TCTGC
1 TTCCGCTGCTCTTCAAGGTAGGTCATATCGAGAAAAGAAA-AGGGAT-TGA
*
371373 TT-CGCTGCTCTTCAGGGTAGGTCATA
1 TTCCGCTGCTCTTCAAGGTAGGTCATA
371399 CTGGTAAAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
49 54 0.89
50 7 0.11
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (49 bp):
TTCCGCTGCTCTTCAAGGTAGGTCATATCGAGAAAAGAAAAGGGATTGA
Found at i:372363 original size:2 final size:2
Alignment explanation
Indices: 372358--372416 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
372348 TATAACTTAC
372358 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
372400 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
372417 AAATATAGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:373615 original size:21 final size:21
Alignment explanation
Indices: 373589--373631 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
373579 ATTGTAATAG
373589 ATGAACCATTTTACTCCTACC
1 ATGAACCATTTTACTCCTACC
373610 ATGAACCATTTTACTCCTACC
1 ATGAACCATTTTACTCCTACC
373631 A
1 A
373632 AAATGTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (21 bp):
ATGAACCATTTTACTCCTACC
Found at i:377217 original size:22 final size:22
Alignment explanation
Indices: 377191--377251 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
377181 TTGGGCTGCA
*
377191 ATTGGACTTCTGTTGAGTATGG
1 ATTGGGCTTCTGTTGAGTATGG
377213 ATTGGGCTTCTGTTGAGTATGG
1 ATTGGGCTTCTGTTGAGTATGG
377235 ATTGGGCTTCTGTTGAG
1 ATTGGGCTTCTGTTGAG
377252 CTTTGTAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.15, C:0.10, G:0.34, T:0.41
Consensus pattern (22 bp):
ATTGGGCTTCTGTTGAGTATGG
Found at i:378715 original size:20 final size:20
Alignment explanation
Indices: 378690--378728 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
378680 AAATCTATGT
*
378690 ATAAAATTGGAAGTCTTTAG
1 ATAAAAATGGAAGTCTTTAG
*
378710 ATAAAAATGGAAGTTTTTA
1 ATAAAAATGGAAGTCTTTA
378729 TATATATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (20 bp):
ATAAAAATGGAAGTCTTTAG
Found at i:381491 original size:105 final size:105
Alignment explanation
Indices: 381300--381506 Score: 389
Period size: 105 Copynumber: 2.0 Consensus size: 105
381290 CTACAGATCC
381300 TAGTCATCGTTCCTTTACATGGAATGTTATTGTCATTGGCATTCATAAATGAAATTCTATGGTTT
1 TAGTCATCGTTCCTTTACATGGAATGTTATTGTCATTGGCATTCATAAATGAAATTCTATGGTTT
*
381365 CGTATCCACCACAACTCCCCCCACCCCGAAAAAAAAAGAA
66 CGTATCCACCACAACTCCCCCCACCCCCAAAAAAAAAGAA
381405 TAGTCATCGTTCCTTTACATGGAATGTTATTGTCATTGGCATTCATAAAATGAAATTCTATGGTT
1 TAGTCATCGTTCCTTTACATGGAATGTTATTGTCATTGGCATTCAT-AAATGAAATTCTATGGTT
381470 TCGTATCCACCACAACT-CCCCCACCCCCAAAAAAAAA
65 TCGTATCCACCACAACTCCCCCCACCCCCAAAAAAAAA
381507 AAACAATACA
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
105 65 0.65
106 35 0.35
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (105 bp):
TAGTCATCGTTCCTTTACATGGAATGTTATTGTCATTGGCATTCATAAATGAAATTCTATGGTTT
CGTATCCACCACAACTCCCCCCACCCCCAAAAAAAAAGAA
Found at i:382342 original size:16 final size:16
Alignment explanation
Indices: 382317--382349 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
382307 ATTCATACAG
382317 AGCATCTGAATCATTC
1 AGCATCTGAATCATTC
*
382333 AGCATTTGAATCATTC
1 AGCATCTGAATCATTC
382349 A
1 A
382350 ACGCTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (16 bp):
AGCATCTGAATCATTC
Found at i:384533 original size:26 final size:26
Alignment explanation
Indices: 384504--384567 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
384494 TATATATATG
384504 ATATCATATATAATA-ATTTCAAAAAT
1 ATAT-ATATATAATAGATTTCAAAAAT
* *
384530 ATATA-ATATACATAGTTTTGAAAAAT
1 ATATATATATA-ATAGATTTCAAAAAT
384556 ATATAT-TATAAT
1 ATATATATATAAT
384568 TTTTGAAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
24 5 0.15
25 6 0.18
26 22 0.67
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (26 bp):
ATATATATATAATAGATTTCAAAAAT
Found at i:384571 original size:23 final size:25
Alignment explanation
Indices: 384511--384576 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
384501 ATGATATCAT
* *
384511 ATATA-ATAATTTCAAAAATATATA
1 ATATACATATTTTGAAAAATATATA
384535 ATATACATAGTTTTGAAAAATATATA
1 ATATACATA-TTTTGAAAAATATATA
*
384561 TTATA-AT-TTTTGAAAA
1 ATATACATATTTTGAAAA
384577 CATGTTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.24
24 5 0.14
25 5 0.14
26 18 0.49
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (25 bp):
ATATACATATTTTGAAAAATATATA
Found at i:384666 original size:43 final size:41
Alignment explanation
Indices: 384545--384697 Score: 144
Period size: 38 Copynumber: 3.9 Consensus size: 41
384535 ATATACATAG
* *
384545 TTTTGAAAA-ATATATAT-TATAATTTTTGAAAAC--ATGT
1 TTTTGAAAACATATATATATATAGTTTTTGAAAACATATTT
* *
384582 TTTTAAAAACATATA-ATATATAGTTTTCTTAAAA-ATTATTT
1 TTTTGAAAACATATATATATATAGTTTT-TGAAAACA-TATTT
*
384623 TTTTGAAAACATATATATAATATAGTTTTTGAAAACATA-AT
1 TTTTGAAAACATATATAT-ATATAGTTTTTGAAAACATATTT
* * *
384664 TTTTGGAAA-ATATATAT-TATAATTTTTTAAAACA
1 TTTTGAAAACATATATATATATAGTTTTTGAAAACA
384698 CGTTTTCCTA
Statistics
Matches: 97, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
37 10 0.10
38 28 0.29
39 5 0.05
40 8 0.08
41 26 0.27
42 9 0.09
43 11 0.11
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (41 bp):
TTTTGAAAACATATATATATATAGTTTTTGAAAACATATTT
Found at i:384677 original size:81 final size:77
Alignment explanation
Indices: 384545--384695 Score: 189
Period size: 81 Copynumber: 1.9 Consensus size: 77
384535 ATATACATAG
* *
384545 TTTTGAAAAATATATATTATAATTTTTGAAAACATGTTTTTAAAAACATATA-ATATATAGTTTT
1 TTTTGAAAAATATATATTATAATTTTTGAAAACATATTTTTAAAAACATATATAT-TATAATTTT
384609 CTTAAAAATTATTT
65 -TTAAAAATTATTT
* **
384623 TTTTGAAAACATATATATAATATAGTTTTTGAAAACATAATTTTTGGAAA-ATATATATTATAAT
1 TTTTGAAAA-ATATATAT--TATAATTTTTGAAAACAT-ATTTTTAAAAACATATATATTATAAT
384687 TTTTTAAAA
62 TTTTTAAAA
384696 CACGTTTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
78 9 0.14
79 8 0.13
80 6 0.10
81 30 0.48
82 10 0.16
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (77 bp):
TTTTGAAAAATATATATTATAATTTTTGAAAACATATTTTTAAAAACATATATATTATAATTTTT
TAAAAATTATTT
Found at i:387148 original size:21 final size:21
Alignment explanation
Indices: 387122--387162 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
387112 AAAACTTAGT
387122 TCATTTTACGTTAAGACGTAA
1 TCATTTTACGTTAAGACGTAA
387143 TCATTTTACGTTAAGACGTA
1 TCATTTTACGTTAAGACGTA
387163 TTGTTAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (21 bp):
TCATTTTACGTTAAGACGTAA
Found at i:407935 original size:14 final size:14
Alignment explanation
Indices: 407916--407948 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
407906 GTGGTACTTC
*
407916 TTCCTCGTGTTGGA
1 TTCCTCATGTTGGA
407930 TTCCTCATGTTGGA
1 TTCCTCATGTTGGA
407944 TTCCT
1 TTCCT
407949 TCCCCCTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.45
Consensus pattern (14 bp):
TTCCTCATGTTGGA
Found at i:417707 original size:166 final size:166
Alignment explanation
Indices: 417534--417897 Score: 728
Period size: 166 Copynumber: 2.2 Consensus size: 166
417524 TAGAATTATA
417534 TAACAATATTAGGATATGCAACTTATTTTATTAAAAATAAAGATTGAATGAGGTAATTTAATTAA
1 TAACAATATTAGGATATGCAACTTATTTTATTAAAAATAAAGATTGAATGAGGTAATTTAATTAA
417599 AATTTTGTAATCTAAATAAAAATTAAATTTAAGTTTAATGATTTAAGATATAAATTACTAAAAAT
66 AATTTTGTAATCTAAATAAAAATTAAATTTAAGTTTAATGATTTAAGATATAAATTACTAAAAAT
417664 TTAACATGAACCTAGCTATCTTAGTAGTTAAAAATT
131 TTAACATGAACCTAGCTATCTTAGTAGTTAAAAATT
417700 TAACAATATTAGGATATGCAACTTATTTTATTAAAAATAAAGATTGAATGAGGTAATTTAATTAA
1 TAACAATATTAGGATATGCAACTTATTTTATTAAAAATAAAGATTGAATGAGGTAATTTAATTAA
417765 AATTTTGTAATCTAAATAAAAATTAAATTTAAGTTTAATGATTTAAGATATAAATTACTAAAAAT
66 AATTTTGTAATCTAAATAAAAATTAAATTTAAGTTTAATGATTTAAGATATAAATTACTAAAAAT
417830 TTAACATGAACCTAGCTATCTTAGTAGTTAAAAATT
131 TTAACATGAACCTAGCTATCTTAGTAGTTAAAAATT
417866 TAACAATATTAGGATATGCAACTTATTTTATT
1 TAACAATATTAGGATATGCAACTTATTTTATT
417898 TTTGTAATCA
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 198 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (166 bp):
TAACAATATTAGGATATGCAACTTATTTTATTAAAAATAAAGATTGAATGAGGTAATTTAATTAA
AATTTTGTAATCTAAATAAAAATTAAATTTAAGTTTAATGATTTAAGATATAAATTACTAAAAAT
TTAACATGAACCTAGCTATCTTAGTAGTTAAAAATT
Found at i:423031 original size:28 final size:29
Alignment explanation
Indices: 422983--423047 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
422973 TTTAATTTTT
422983 AAATAAAAATAATTAATAAAA-TACTAAA
1 AAATAAAAATAATTAATAAAATTACTAAA
* * *
423011 AAATTAAAAT-ATTCATAAAAATTACT-TA
1 AAATAAAAATAATTAAT-AAAATTACTAAA
423039 AAATAAAAA
1 AAATAAAAA
423048 CACTATAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 5 0.16
28 22 0.71
29 4 0.13
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (29 bp):
AAATAAAAATAATTAATAAAATTACTAAA
Found at i:424623 original size:2 final size:2
Alignment explanation
Indices: 424616--424657 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
424606 AATATAAAAG
424616 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
424658 TACCTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435709 original size:5 final size:5
Alignment explanation
Indices: 435699--435733 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
435689 AACTATTTTT
*
435699 TATTA TATTA TATTA TATTA TATTTA TTTTA TATT
1 TATTA TATTA TATTA TATTA TA-TTA TATTA TATT
435734 TAATTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:435740 original size:15 final size:15
Alignment explanation
Indices: 435692--435742 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
435682 AAGGTAAAAC
*
435692 TATTTTTTA-TTATAT
1 TATTTTATATTTA-AT
* *
435707 TATATTATATTATATT
1 TATTTTATATT-TAAT
435723 TATTTTATATTTAAT
1 TATTTTATATTTAAT
435738 TATTT
1 TATTT
435743 GAACAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 15 0.52
16 12 0.41
17 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTATATTTAAT
Found at i:437307 original size:26 final size:28
Alignment explanation
Indices: 437277--437338 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
437267 AAAAATTTTA
437277 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
437303 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
437334 AGCTC
1 AGCTC
437339 AGCAATACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:440032 original size:30 final size:29
Alignment explanation
Indices: 439994--440122 Score: 150
Period size: 30 Copynumber: 4.3 Consensus size: 29
439984 TACCCCGCCT
*
439994 CCTCCTCAGGCGGCTCCGGTTCGCCAACC
1 CCTCCTCAGGCGGCTCCGGCTCGCCAACC
* *
440023 ACATCCTCAGGCGGCTCCGGCTCGTCAACC
1 -CCTCCTCAGGCGGCTCCGGCTCGCCAACC
*
440053 GCCTCCTCAGGCGGCTCCGGCTCGTCAAACC
1 -CCTCCTCAGGCGGCTCCGGCTCG-CCAACC
** * *
440084 CCTCCTCAGGCGGCTCTAGTTCGTCGAACC
1 CCTCCTCAGGCGGCTCCGGCTCG-CCAACC
440114 CCTCCTCAG
1 CCTCCTCAG
440123 TTGGCTCCTG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
30 83 0.95
31 4 0.05
ACGTcount: A:0.13, C:0.45, G:0.23, T:0.19
Consensus pattern (29 bp):
CCTCCTCAGGCGGCTCCGGCTCGCCAACC
Found at i:440130 original size:60 final size:60
Alignment explanation
Indices: 439994--440122 Score: 172
Period size: 60 Copynumber: 2.1 Consensus size: 60
439984 TACCCCGCCT
* * *
439994 CCTCCTCAGGCGGCTCCGGTTCGCCAACCACATCCTCAGGCGGCTCCGGCTCGTCAACCG
1 CCTCCTCAGGCGGCTCCGGCTCGCAAACCACATCCTCAGGCGGCTCCAGCTCGTCAACCG
* * *
440054 CCTCCTCAGGCGGCTCCGGCTCGTCAAACC-CCTCCTCAGGCGGCTCTAGTTCGTCGAACC-
1 CCTCCTCAGGCGGCTCCGGCTCG-CAAACCACATCCTCAGGCGGCTCCAGCTCGTC-AACCG
440114 CCTCCTCAG
1 CCTCCTCAG
440123 TTGGCTCCTG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 52 0.85
61 9 0.15
ACGTcount: A:0.13, C:0.45, G:0.23, T:0.19
Consensus pattern (60 bp):
CCTCCTCAGGCGGCTCCGGCTCGCAAACCACATCCTCAGGCGGCTCCAGCTCGTCAACCG
Found at i:448884 original size:3 final size:3
Alignment explanation
Indices: 448869--448898 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
448859 TCTAAAATCA
*
448869 TAT TAT GAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
448899 GTTTTACGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:465245 original size:3 final size:3
Alignment explanation
Indices: 465237--465263 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
465227 CATTTAACAA
465237 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
465264 CCATGGGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:466264 original size:33 final size:36
Alignment explanation
Indices: 466222--466384 Score: 167
Period size: 41 Copynumber: 4.4 Consensus size: 36
466212 TTACAAGTGT
466222 AGCATAGAGACAT-G-T-AGGTTTTAATTGGACAAC
1 AGCATAGAGACATGGATGAGGTTTTAATTGGACAAC
466255 AGCATAGAGACATGGAGACATGGAGGTTTTAATTGGACAAC
1 AGCATAGAGACAT-G-G--AT-GAGGTTTTAATTGGACAAC
466296 AGCATAGAGACATGGAGACATGGAGGTTTTAATTGGACAAC
1 AGCATAGAGACAT-G-G--AT-GAGGTTTTAATTGGACAAC
* *
466337 AGCATAGAGACAT--A-GAGATTTTAATTTGGACAAA
1 AGCATAGAGACATGGATGAGGTTTTAA-TTGGACAAC
466371 AGCATAGAGACATG
1 AGCATAGAGACATG
466385 ATACATAAAC
Statistics
Matches: 118, Mismatches: 2, Indels: 18
0.86 0.01 0.13
Matches are distributed among these distances:
33 22 0.19
34 21 0.18
35 1 0.01
36 1 0.01
39 1 0.01
41 72 0.61
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.23
Consensus pattern (36 bp):
AGCATAGAGACATGGATGAGGTTTTAATTGGACAAC
Found at i:466285 original size:41 final size:41
Alignment explanation
Indices: 466228--466354 Score: 236
Period size: 41 Copynumber: 3.1 Consensus size: 41
466218 GTGTAGCATA
*
466228 GAGACATGTAGGTTTTAATTGGACAACAGCATAGAGACATG
1 GAGACATGGAGGTTTTAATTGGACAACAGCATAGAGACATG
466269 GAGACATGGAGGTTTTAATTGGACAACAGCATAGAGACATG
1 GAGACATGGAGGTTTTAATTGGACAACAGCATAGAGACATG
*
466310 GAGACATGGAGGTTTTAATTGGACAACAGCATAGAGACATA
1 GAGACATGGAGGTTTTAATTGGACAACAGCATAGAGACATG
466351 GAGA
1 GAGA
466355 TTTTAATTTG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (41 bp):
GAGACATGGAGGTTTTAATTGGACAACAGCATAGAGACATG
Found at i:466375 original size:34 final size:33
Alignment explanation
Indices: 466310--466383 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 33
466300 TAGAGACATG
* * *
466310 GAGACATGGAGGTTTTAATTGGACAACAGCATA
1 GAGACATAGAGATTTTAATTGGACAAAAGCATA
466343 GAGACATAGAGATTTTAATTTGGACAAAAGCATA
1 GAGACATAGAGATTTTAA-TTGGACAAAAGCATA
466377 GAGACAT
1 GAGACAT
466384 GATACATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 16 0.43
34 21 0.57
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (33 bp):
GAGACATAGAGATTTTAATTGGACAAAAGCATA
Found at i:472372 original size:16 final size:17
Alignment explanation
Indices: 472351--472385 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
472341 TTACTATTCA
472351 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
472367 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
472384 CG
1 CG
472386 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:481948 original size:20 final size:19
Alignment explanation
Indices: 481905--481967 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
481895 AATTATATTA
*
481905 TTTTAAA-TTTTTTATAAT
1 TTTTAAAGTATTTTATAAT
*
481923 CCTTTAAA-TATTTTAGATAAT
1 -TTTTAAAGTATTTT--ATAAT
481944 TTTTAAAGGTATTTTATAAT
1 TTTTAAA-GTATTTTATAAT
481964 TTTT
1 TTTT
481968 TATTGCTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 11 0.30
20 15 0.41
21 5 0.14
22 6 0.16
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTAAAGTATTTTATAAT
Found at i:481969 original size:21 final size:19
Alignment explanation
Indices: 481905--481969 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
481895 AATTATATTA
* *
481905 TTTTAAATTTTTTATAATC
1 TTTTAAATATTTTATAATT
*
481924 CTTTAAATATTTTAGATAA-T
1 TTTTAAATATTTT--ATAATT
481944 TTTTAAAGGTATTTTATAATT
1 TTTTAAA--TATTTTATAATT
481965 TTTTA
1 TTTTA
481970 TTGCTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 11 0.30
20 10 0.27
21 10 0.27
22 6 0.16
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTAAATATTTTATAATT
Found at i:489573 original size:19 final size:18
Alignment explanation
Indices: 489542--489586 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
489532 CAATTTCTCT
**
489542 TTTTTA-TTTTATTACTA
1 TTTTTATTTTTATTAAAA
489559 TTTTTATTTTATATTAAAA
1 TTTTTATTTT-TATTAAAA
489578 TTTTTATTT
1 TTTTTATTT
489587 CTAATTTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 3 0.12
19 15 0.62
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATTTTTATTAAAA
Found at i:489679 original size:21 final size:20
Alignment explanation
Indices: 489654--489698 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
489644 TCACCTTAAC
* *
489654 ATTTATATTATTTTTAAAATT
1 ATTTATATTAATCTT-AAATT
*
489675 ATTTATTTTAATCTTAAATT
1 ATTTATATTAATCTTAAATT
489695 ATTT
1 ATTT
489699 TAAATTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTATATTAATCTTAAATT
Found at i:490198 original size:27 final size:25
Alignment explanation
Indices: 490166--490230 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
490156 TTAACTTAAT
490166 TTAAAAATATTTTATTACTATTATTA
1 TTAAAAATATTTTATTACTATT-TTA
**
490192 TTAAAAATATTTTTATTTTTATTTTA
1 TTAAAAATA-TTTTATTACTATTTTA
*
490218 TTAATATATATTT
1 TTAA-AAATATTT
490231 AAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TTAAAAATATTTTATTACTATTTTA
Found at i:490218 original size:63 final size:59
Alignment explanation
Indices: 490148--490265 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 59
490138 TTTAAAAACA
*
490148 TATTTTATTTAACT-TA-ATTTAAAAATATTTTATTACTATTATTATTAAAAATATTTTTATTTT
1 TATTTTA-TTAA-TATATATTTAAAAATATTTTATT-C--TTAAT-TTAAAAATATTTTTATTTT
490211 TATTTTATTAATATATATTTAAAAATATTTTATTCTTAATTTAAAAATATTTTTA
1 TATTTTATTAATATATATTTAAAAATATTTTATTCTTAATTTAAAAATATTTTTA
490266 AAATATAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
59 15 0.29
60 4 0.08
61 1 0.02
62 7 0.13
63 25 0.48
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (59 bp):
TATTTTATTAATATATATTTAAAAATATTTTATTCTTAATTTAAAAATATTTTTATTTT
Found at i:490260 original size:36 final size:35
Alignment explanation
Indices: 490187--490268 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
490177 TTATTACTAT
* * * *
490187 TATTATTAAAAATATTTTTATTTTTATTTTATTAATA
1 TATTTTTAAAAATATTTTTATTCTTAATTTA--AAAA
*
490224 TATATTTAAAAATA-TTTTATTCTTAATTTAAAAA
1 TATTTTTAAAAATATTTTTATTCTTAATTTAAAAA
490258 TATTTTTAAAA
1 TATTTTTAAAA
490269 TATAAATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
34 13 0.33
36 14 0.36
37 12 0.31
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (35 bp):
TATTTTTAAAAATATTTTTATTCTTAATTTAAAAA
Found at i:490688 original size:11 final size:11
Alignment explanation
Indices: 490672--490704 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
490662 CCACAAGTGC
490672 CCAGTCAACAT
1 CCAGTCAACAT
*
490683 CCAGTCAACGT
1 CCAGTCAACAT
490694 CCAGTCAACAT
1 CCAGTCAACAT
490705 GCTTCTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.36, G:0.12, T:0.18
Consensus pattern (11 bp):
CCAGTCAACAT
Found at i:494677 original size:35 final size:35
Alignment explanation
Indices: 494600--494677 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
494590 ATTTTCAATG
* * * * *
494600 TTCGAACAGTGCATAAAAATGCAGTGCAGATTTGG
1 TTCGAAAAGTGCAGAAAAATACAGTGCAGATTAGA
494635 TTCGAAAAGTGCAGAAAAATACAGTGCAG-TGTAGA
1 TTCGAAAAGTGCAGAAAAATACAGTGCAGAT-TAGA
*
494670 TTTGAAAA
1 TTCGAAAA
494678 TAGTGAAGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (35 bp):
TTCGAAAAGTGCAGAAAAATACAGTGCAGATTAGA
Found at i:500168 original size:22 final size:22
Alignment explanation
Indices: 500114--500179 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
500104 ATCGATTCCC
*
500114 TCAAGGAGGGAATCAGTTCCCAT
1 TCAAGG-GGGAATCGGTTCCCAT
*
500137 TCAAAGGGGGAATCGGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCAT
* *
500160 TCAAGGGGGTATCGATTCCC
1 TCAAGGGGGAATCGGTTCCC
500180 TATACTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 16 0.42
23 18 0.47
24 4 0.11
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCAT
Found at i:507676 original size:158 final size:156
Alignment explanation
Indices: 507388--507704 Score: 501
Period size: 158 Copynumber: 2.0 Consensus size: 156
507378 CAAAAACTCT
*
507388 TATGCTTTTGAAAAACATTCACAGTGAGAAGACATCTAAGGGCGAATGAATTTATAACATAAAGA
1 TATGCTTTTGAAAAACATTCACAGTGAGAAGACATCTAAGGGCGAATGAATTTATAACAGAAAGA
507453 TATCCAAGGACAAATGAATCAATCAATTAAGTATTCCGATATATTAGAAAAACATTTACCTCACG
66 TATCCAAGGACAAATGAATCAATCAATTAAGTATTCCGATATATTAGAAAAACATTTACCTCACG
*
507518 TTGAGAGTTTTTAGATATGAATA-ATTAA
131 TT---AGTTCTTAGATATGAATACATTAA
*
507546 TATGCTTTTGAAAAACATTCACAGTGAGAAGACATCTATGGGCGAATGAATTTATAACAGAAAGA
1 TATGCTTTTGAAAAACATTCACAGTGAGAAGACATCTAAGGGCGAATGAATTTATAACAGAAAGA
* * ** * * *
507611 TATCCAAGGATAAATGAATCGATCAATTAAGTATTTTGATGTCTTAGAAAAACATTTACGTCACG
66 TATCCAAGGACAAATGAATCAATCAATTAAGTATTCCGATATATTAGAAAAACATTTACCTCACG
*
507676 TTAGTTCTTATATATGAATACATTAA
131 TTAGTTCTTAGATATGAATACATTAA
507702 TAT
1 TAT
507705 AAAGTTCCTA
Statistics
Matches: 147, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
155 16 0.11
156 8 0.05
158 123 0.84
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (156 bp):
TATGCTTTTGAAAAACATTCACAGTGAGAAGACATCTAAGGGCGAATGAATTTATAACAGAAAGA
TATCCAAGGACAAATGAATCAATCAATTAAGTATTCCGATATATTAGAAAAACATTTACCTCACG
TTAGTTCTTAGATATGAATACATTAA
Found at i:514318 original size:40 final size:40
Alignment explanation
Indices: 514258--514335 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
514248 ACCACCTTAA
*
514258 ATTTAATTACGATTCAAATTAAGTAATAATATATAAAACT
1 ATTTAATTACGATTCAAATTAAGTAACAATATATAAAACT
*
514298 ATTTAATTACGATTCGAATTAAGTAACAATATATAAAA
1 ATTTAATTACGATTCAAATTAAGTAACAATATATAAAA
514336 ACATAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (40 bp):
ATTTAATTACGATTCAAATTAAGTAACAATATATAAAACT
Done.