Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 21 of 27
Found at i:3514352 original size:738 final size:740
Alignment explanation
Indices: 3512727--3515698 Score: 4361
Period size: 738 Copynumber: 4.0 Consensus size: 740
3512717 TCAATCATTA
*
3512727 TAGCTAATGTCAATATCTCGTATTGTAAACTAAGATAATGCTACATAAAAATAATTAGATTTTCT
1 TAGCTAATGTCAATATCTCGTATTGTAAACTAAGACAATGCTACATAAAAATAATTAGATTTTCT
* * * ** * *
3512792 CTCAACTAATATAAATTAATTAGACTTTCTTTTAACGTGAAACTTCAAAGTTAATAAGCATCAAT
66 CTCAACTAGTATAAAGTAACTAGACTTTCTTTTAAAATAAAACTTCAAAGTTAATAAGAATCAAT
* * * * *
3512857 TTAATTAATAATTTTAAAATTTATTAAACAATTAAAAACTTGAAGTTAATAAGCATTAATT-AAC
131 TGAACTAATAATTCTAAAATTCATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATTGAAC
** *
3512921 TAATAGTGTTGAAGAAACTTGAAGTTGAA-TTTAAAAAAAAAAAGAATTTTCTTACATTTTTTTT
196 TAATAGTGTTGAAGAAACTTGAAGTTGAAGTAAAAAAAAAAAAAGAATTTTCTTACA-TTCTTTT
** * * * * * *
3512985 TAATTTATAGAATTCTGTTTTTCTGTATTTCTGAGTTCGCTATTTTTTCTTTTCAAACTATCATA
260 TAATTCGTAGAATTCTGTCTTTCTGTACTTCTAAGTCCGCTATTTTTTCTTTTCAAACTGTTATA
* **
3513050 TGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCCCTCATAATTTTTTTTAATAAAT
325 TGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCACTCACGATTTTTTTTAATAAAT
* * * *
3513115 GAGATTGAAAATAATATTGCAAACGTGCGACTTTATCTTACACTTTTTCAAA--TTTTTTTTAGG
390 GAGATTAAAAATCATACTGCAAACGTGCGACTTTATCTTACACTTTTTCAAACCTTTTTTTTAAG
* *
3513178 A-TTTTTTTAATACATTATTATTTTATTTAGATAAAAATTTACTTAAATCAAAGATAATATTTAT
455 ATTTTTTTTAATACATGATTATTTTATTTAGATAAAAATTTACTTAAATCAAAAATAATATTTAT
*
3513242 TTTATTT-AGATCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTGATTAAA
520 TTTATTTAAG-TCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTAATTAAA
*
3513306 TAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTCTCTCAAATAGATAAAGAAAA
584 TAGTATAATTATTACATATGAATTAAAAATCAAA--CTCTCTCTCTCACAAATAGATAAAGAAAA
* * *
3513371 ACACATAA-CTCTCTTCCTTGA-TTTTTTTTAAATTTAATAATTTAAGTTTAAATTTAAAATCCT
647 ACAC-TAATCTCTCTTTCTTGATTTTTTTTTAAATTTAATAATTTAAGTTTAAATTTGAAATGCT
3513434 TAGTGTTTTCTTTTTATTTATTTATTTATT
711 TAGTGTTTTCTTTTTATTTATTTATTTATT
* *
3513464 TAGCTAATGTCAATATCTCGTATTGTAAACTAAAATAATGCTACATAAAAATAATTAGATTTTCT
1 TAGCTAATGTCAATATCTCGTATTGTAAACTAAGACAATGCTACATAAAAATAATTAGATTTTCT
* * *
3513529 CTCAACTAGTATAAAGTAACTAGACTTTCTTTTAACATGAAACTTCAAAGTTAATAAGCATCAAT
66 CTCAACTAGTATAAAGTAACTAGACTTTCTTTTAAAATAAAACTTCAAAGTTAATAAGAATCAAT
* * * *
3513594 TTAATTAATAATTTTAAAATTCATTAAACAATTAAAAACTTGAAGTTAATAAGCATTAATT-AAC
131 TGAACTAATAATTCTAAAATTCATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATTGAAC
* *
3513658 TAATAGTGTTGAAGAAACTTGTAGTTAAAGTAAAAAAAAAAAAAAGAATTTTTCTTACATTCTTT
196 TAATAGTGTTGAAGAAACTTGAAGTTGAAGT-AAAAAAAAAAAAAGAA-TTTTCTTACATTCTTT
* * * * *
3513723 TTCATTTGTAGAATTCTGTCTTTCTGTATTTCTGAGTTCGCTATTTTTTCTTTTCAAACTGTTAT
259 TTAATTCGTAGAATTCTGTCTTTCTGTACTTCTAAGTCCGCTATTTTTTCTTTTCAAACTGTTAT
* *
3513788 ATGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCCCTCATGATTTTTTTTAATAAA
324 ATGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCACTCACGATTTTTTTTAATAAA
* * * * * * *
3513853 TTAAATTGAAAATCATATTACAAATGTGCGACTTTATCTTACACTTTTTCAAA-C-TTTTTTTAG
389 TGAGATTAAAAATCATACTGCAAACGTGCGACTTTATCTTACACTTTTTCAAACCTTTTTTTTAA
*
3513916 GATTTTTTTTAATACATGATTATTTTATTTAGATAACAATTTACTTAAATCAAAAATAATATTTA
454 GATTTTTTTTAATACATGATTATTTTATTTAGATAAAAATTTACTTAAATCAAAAATAATATTTA
3513981 TTTTATTTAAGTCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTAATTAAA
519 TTTTATTTAAGTCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTAATTAAA
*
3514046 TAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTCACAAATAGATAAAGAAAAGC
584 TAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTCACAAATAGATAAAGAAAAAC
* *
3514111 ACATAAT-TCTCTTACTT-ATTTTTTTTAAAATTTAATAATTTAAGTTTAAATTTGAAATGCTT-
649 AC-TAATCTCTCTTTCTTGATTTTTTTTTAAATTTAATAATTTAAGTTTAAATTTGAAATGCTTA
3514173 GATGTTTTCTTTTTATTTATTTATTTATT
713 G-TGTTTTCTTTTTATTTATTTATTTATT
* * * * * *
3514202 TAGCTAATGTCAATATCTCGTATTTTAAACTAAGACAAAGCTATATAAGAGTAATTAGATTTTTT
1 TAGCTAATGTCAATATCTCGTATTGTAAACTAAGACAATGCTACATAAAAATAATTAGATTTTCT
* *
3514267 CTCTACTAGTATAAAGTAACTAGACTTTCTTTTAAAATAAAAC-TCTAAAGTTAATAAGAATTAA
66 CTCAACTAGTATAAAGTAACTAGACTTTCTTTTAAAATAAAACTTC-AAAGTTAATAAGAATCAA
* *
3514331 TTGAACTAATAATTCTAAAATTCATTAAA-AATTAAAAATTTAAAGTTAATAAGCATCAATTGAA
130 TTGAACTAATAATTCTAAAATTCATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATTGAA
* * * *
3514395 CTAATAGTGTTGAA-AAACTTGAAATTGAAGTTAACAAAAAAAAGGAATTTTCTTACATTCTTTT
195 CTAATAGTGTTGAAGAAACTTGAAGTTGAAGTAAAAAAAAAAAAAGAATTTTCTTACATTCTTTT
* * * *
3514459 TAATTCGTAAAATTCTGTCTTTATGTACTTATAAGTCCGTTATTTTTTCTTTTCAAACTGTTATA
260 TAATTCGTAGAATTCTGTCTTTCTGTACTTCTAAGTCCGCTATTTTTTCTTTTCAAACTGTTATA
3514524 TGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCACTCACGATTTTTTTTAATAAAT
325 TGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCACTCACGATTTTTTTTAATAAAT
* * * *
3514589 GAGATTAAAAATCATACTGTAAACGTGCGAATTTATTTTACGCTTTTTCAAACCTTTTTTTTAAG
390 GAGATTAAAAATCATACTGCAAACGTGCGACTTTATCTTACACTTTTTCAAACCTTTTTTTTAAG
* *
3514654 ATTTTTTTTAATACATGGTTATTTTATTTTGATAAAAATTTACTTAAATCAAACACA-AATATTT
455 ATTTTTTTTAATACATGATTATTTTATTTAGATAAAAATTTACTTAAATCAAA-A-ATAATATTT
* * *
3514718 ATTTTATTTAGGTCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTGATTTA
518 ATTTTATTTAAGTCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTAATTAA
* * *
3514783 ATAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTCTCAAATATATAATGAAAAA
583 ATAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTCACAAATAGATAAAGAAAAA
* * *
3514848 CACTTATCTCTTTTTTTATGATTTTTTTTTAAATTTAATAATTTAAGTTTAAATTTGAAATGCTT
648 CACTAATCTCTCTTTCT-TGATTTTTTTTTAAATTTAATAATTTAAGTTTAAATTTGAAATGCTT
3514913 AGTGTTTTCTTTTTATTTATTTATTTATT
712 AGTGTTTTCTTTTTATTTATTTATTTATT
* * *
3514942 TAGCTAATGTCAATATCTCGTATTGTAAACTAAGACAACGCTACATAAGAGTAATTAGATTTTCT
1 TAGCTAATGTCAATATCTCGTATTGTAAACTAAGACAATGCTACATAAAAATAATTAGATTTTCT
* * *
3515007 CTCAACTAGTATAAAATAACTAGACTTTTTTTTAAAATAAAAC-TCTAAAGTTAATAAGAATTAA
66 CTCAACTAGTATAAAGTAACTAGACTTTCTTTTAAAATAAAACTTC-AAAGTTAATAAGAATCAA
3515071 TTGAACTAATAATTCTAAAATTCATTAAACAATTAAAAACTTATTAAAAACTTGAAGTTAATAAG
130 TTGAACTAATAATTCTAAAATTCATTAAAC--------A---ATTAAAAACTTGAAGTTAATAAG
* * *
3515136 CATCAATTGAACTAATAGTGTTAAAAAAACTTTAAGTTGAAGTTAACAAAAAAAAAAAAGAATTT
184 CATCAATTGAACTAATAGTGTTGAAGAAACTTGAAGTTGAAG-T-A-AAAAAAAAAAAAGAATTT
* * *
3515201 TCTTATATTCTTTTTCATTCGTAGAATTCTGTCTTTCTGTACTTCTAAATCCG-TAATTTTTTCT
246 TCTTACATTCTTTTTAATTCGTAGAATTCTGTCTTTCTGTACTTCTAAGTCCGCT-ATTTTTTCT
*
3515265 TTTCAAACTGTTATATGTTTCTAACAACTTT-TTTTTATAGCACAAATTAAATACGCACTCACGA
310 TTTCAAACTGTTATATGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCACTCACGA
* *
3515329 TTTTTTTTAATAAATGAGATTAAAAATCATACTGCAAACGTGCGACTTTATTTTACGCTTTTTCA
375 TTTTTTTTAATAAATGAGATTAAAAATCATACTGCAAACGTGCGACTTTATCTTACACTTTTTCA
*
3515394 AACCTTTTTTTTTAAGATTTTTTTTAATACATTG-TTATTTTATTTTGATAAAAATTTACTTAAA
440 AACC-TTTTTTTTAAGATTTTTTTTAATACA-TGATTATTTTATTTAGATAAAAATTTACTTAAA
* * *
3515458 TCAAAGATCAATATTTATTTTATTTAGGTCTATAATTTATATTATATGTGTGCAAAATTTAATTG
503 TCAAAAAT-AATATTTATTTTATTTAAGTCTATAATTTATATTATATGTGTGCAAGATTTAATTG
* *
3515523 AAAATAATGTAATTTAATAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTTTCTCTA-
567 AAAATAATGTAATTAAATAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTC-AC
* * *
3515587 AAATAGATAATGAAAAACACTTATCTCTCTTTTTTGATTTTTTTTTAAATTTAATAATTTAAGTT
631 AAATAGATAAAGAAAAACACTAATCTCTCTTTCTTGATTTTTTTTTAAATTTAATAATTTAAGTT
*
3515652 TAAATTTGAAATGCTTGGTGTTTTCTTTTTATTTATTTATTTATT
696 TAAATTTGAAATGCTTAGTGTTTTCTTTTTATTTATTTATTTATT
3515697 TA
1 TA
3515699 TTTAGTGCGA
Statistics
Matches: 2068, Mismatches: 126, Indels: 64
0.92 0.06 0.03
Matches are distributed among these distances:
735 178 0.09
736 14 0.01
737 324 0.16
738 407 0.20
739 204 0.10
740 386 0.19
741 3 0.00
749 1 0.00
752 45 0.02
753 14 0.01
754 2 0.00
755 177 0.09
756 311 0.15
757 2 0.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (740 bp):
TAGCTAATGTCAATATCTCGTATTGTAAACTAAGACAATGCTACATAAAAATAATTAGATTTTCT
CTCAACTAGTATAAAGTAACTAGACTTTCTTTTAAAATAAAACTTCAAAGTTAATAAGAATCAAT
TGAACTAATAATTCTAAAATTCATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATTGAAC
TAATAGTGTTGAAGAAACTTGAAGTTGAAGTAAAAAAAAAAAAAGAATTTTCTTACATTCTTTTT
AATTCGTAGAATTCTGTCTTTCTGTACTTCTAAGTCCGCTATTTTTTCTTTTCAAACTGTTATAT
GTTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCACTCACGATTTTTTTTAATAAATG
AGATTAAAAATCATACTGCAAACGTGCGACTTTATCTTACACTTTTTCAAACCTTTTTTTTAAGA
TTTTTTTTAATACATGATTATTTTATTTAGATAAAAATTTACTTAAATCAAAAATAATATTTATT
TTATTTAAGTCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTAATTAAATA
GTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTCACAAATAGATAAAGAAAAACAC
TAATCTCTCTTTCTTGATTTTTTTTTAAATTTAATAATTTAAGTTTAAATTTGAAATGCTTAGTG
TTTTCTTTTTATTTATTTATTTATT
Found at i:3516786 original size:21 final size:21
Alignment explanation
Indices: 3516736--3516786 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3516726 GCTAGCTTCA
3516736 GCTCGGCTTCCTTTAATTCCT
1 GCTCGGCTTCCTTTAATTCCT
* *
3516757 GCTCAGCTTCCTTTAATTGCT
1 GCTCGGCTTCCTTTAATTCCT
*
3516778 GCTTGGCTT
1 GCTCGGCTT
3516787 TTTTGCTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.10, C:0.29, G:0.18, T:0.43
Consensus pattern (21 bp):
GCTCGGCTTCCTTTAATTCCT
Found at i:3517772 original size:91 final size:91
Alignment explanation
Indices: 3517608--3517778 Score: 252
Period size: 91 Copynumber: 1.9 Consensus size: 91
3517598 CCTCAAATTG
* * *
3517608 TCCAAATCCCAGGAACTACCGCTCCTTTTTGAGCGTGGAAGATTCAACTGCGTCACAAGAAAGTT
1 TCCAAATCCCAGGAACTACAGCTCCTTTTTGAGCGTGGAAGATTCAACTACGTCACAAGAAAGTA
3517673 TAACGAAAAGAGAATTACAAAATGAT
66 TAACGAAAAGAGAATTACAAAATGAT
* * * * * *
3517699 TCCAGATCCCATGAACTACAGCTCTTTTTTGAGCTTGGAAGATTTAACTATGTCACAAGAAAGTA
1 TCCAAATCCCAGGAACTACAGCTCCTTTTTGAGCGTGGAAGATTCAACTACGTCACAAGAAAGTA
*
3517764 TAAGGAAAAGAGAAT
66 TAACGAAAAGAGAAT
3517779 CAGATAATGA
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 70 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (91 bp):
TCCAAATCCCAGGAACTACAGCTCCTTTTTGAGCGTGGAAGATTCAACTACGTCACAAGAAAGTA
TAACGAAAAGAGAATTACAAAATGAT
Found at i:3519235 original size:16 final size:17
Alignment explanation
Indices: 3519216--3519308 Score: 91
Period size: 18 Copynumber: 5.4 Consensus size: 17
3519206 ATTAAATCGG
*
3519216 TTAAAAATTTGTGA-TT
1 TTAAAAATTTGTAATTT
* *
3519232 TTAAAAATTTATGATTT
1 TTAAAAATTTGTAATTT
*
3519249 TTGAAAAATATGTAATTT
1 TT-AAAAATTTGTAATTT
3519267 TTAAAAGATTT-TAAATTT
1 TTAAAA-ATTTGT-AATTT
3519285 TTAAAAAATTTGTAATTT
1 TT-AAAAATTTGTAATTT
*
3519303 CTAAAA
1 TTAAAA
3519309 TTTAATTCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
16 13 0.20
17 13 0.20
18 34 0.52
19 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (17 bp):
TTAAAAATTTGTAATTT
Found at i:3519257 original size:18 final size:16
Alignment explanation
Indices: 3519216--3519249 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3519206 ATTAAATCGG
*
3519216 TTAAAAATTTGTGATT
1 TTAAAAATTTATGATT
3519232 TTAAAAATTTATGATT
1 TTAAAAATTTATGATT
3519248 TT
1 TT
3519250 TGAAAAATAT
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:0.00, G:0.09, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATGATT
Found at i:3519266 original size:18 final size:16
Alignment explanation
Indices: 3519216--3519320 Score: 65
Period size: 18 Copynumber: 6.2 Consensus size: 16
3519206 ATTAAATCGG
*
3519216 TTAAAAATTTGTGA-TT
1 TTAAAAA-TTGTAATTT
3519232 TTAAAAATT-TATGATTT
1 TTAAAAATTGTA--ATTT
3519249 TTGAAAAATATGTAATTT
1 TT-AAAAAT-TGTAATTT
*
3519267 TTAAAAGATTTTAAATTT
1 TTAAAA-ATTGT-AATTT
3519285 TTAAAAAATTTGTAATTT
1 TT-AAAAA-TTGTAATTT
* *
3519303 CT-AAAATT-TAATTC
1 TTAAAAATTGTAATTT
3519317 TTAA
1 TTAA
3519321 TGTGATTGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
14 7 0.10
15 5 0.07
16 12 0.17
17 10 0.14
18 28 0.39
19 8 0.11
20 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (16 bp):
TTAAAAATTGTAATTT
Found at i:3519580 original size:13 final size:14
Alignment explanation
Indices: 3519558--3519594 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
3519548 AAACACTGTT
3519558 TTCT-TCTCT-CGC
1 TTCTCTCTCTACGC
3519570 TTCTCTCTCTCACGC
1 TTCTCTCTCT-ACGC
3519585 TTCTCTCTCT
1 TTCTCTCTCT
3519595 GTCTCCGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
15 13 0.59
ACGTcount: A:0.03, C:0.43, G:0.05, T:0.49
Consensus pattern (14 bp):
TTCTCTCTCTACGC
Found at i:3519585 original size:15 final size:15
Alignment explanation
Indices: 3519562--3519594 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3519552 ACTGTTTTCT
*
3519562 TCTCTCGCTTCTCTC
1 TCTCACGCTTCTCTC
3519577 TCTCACGCTTCTCTC
1 TCTCACGCTTCTCTC
3519592 TCT
1 TCT
3519595 GTCTCCGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.45, G:0.06, T:0.45
Consensus pattern (15 bp):
TCTCACGCTTCTCTC
Found at i:3519599 original size:6 final size:6
Alignment explanation
Indices: 3519590--3519630 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
3519580 CACGCTTCTC
* *
3519590 TCTCTG TCTCCG TCTCTG TCCCTG TCTCTG TCTCTG TCTCT
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCT
3519631 TTTAATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.39, G:0.15, T:0.46
Consensus pattern (6 bp):
TCTCTG
Found at i:3521320 original size:23 final size:23
Alignment explanation
Indices: 3521294--3521339 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3521284 TCAATCCAAT
*
3521294 CTTAATTCATGATCAAA-AATTTA
1 CTTAATAC-TGATCAAATAATTTA
*
3521317 CTTAATACTTATCAAATAATTTA
1 CTTAATACTGATCAAATAATTTA
3521340 AAAATCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (23 bp):
CTTAATACTGATCAAATAATTTA
Found at i:3522890 original size:744 final size:740
Alignment explanation
Indices: 3521422--3523384 Score: 3227
Period size: 744 Copynumber: 2.7 Consensus size: 740
3521412 ATAATATCCA
* * * *
3521422 TTATTATAGCTCATGTCAATATCTCGTATTAT-AACTAATACAACGCTATATAAGAGTAATTAGA
1 TTATT-TAGCTAATGTCAATATCTCGTATTGTAAACTAATACAACGCTAAATAAGAGTAATTAAA
*
3521486 TTTTCTCTCAACTAGTATAAAGTAATTAGACTTTCTTTTAACATAAAACTCTAAAGTTAATAAGA
65 TTTTCTCTCAACTAGTATAAAGTAATTAGACTTTCTTTTAACATAAAACTCTAAAGTTAATAAGC
* *
3521551 ATTAATTGAACTAATAATTTTAAAATTCATTAAACAATTAAAAACTTGAAATTAATAAGCAGCAA
130 ATTAATTGAACTAATAATTTTAAAATT-ATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAA
*
3521616 TTGAACTAATAGTGTTGAAGAAACTTAAAGTTGAAGTTAAC--AAAAAAAAGAATTTTCTTACAT
194 TTGAACTAATAGTGTTGAAGAAACTTGAAGTTGAAGTTAACAAAAAAAAAAGAATTTTCTTACA-
* ** * *
3521679 TTTTTTTCGTTCGTGGAATTCTGTCTTTCTGTA-TTTCTGAGTCCGCTATTTTTTCTTTTTAAAC
258 TTTTTTTCATTCGTAAAATTCTGTCTTTCTGTACTTT-TGAGTCCGCAATTTTTTCTTTTCAAAC
* * **
3521743 TGTAATATATTTTTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCCTTTGCGATTTTTTTT
322 TGTAATATATTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCCCTCACGATTTTTTTT
* * *
3521808 AATAAATGAGATTGAAAATCATACTACAAACGTGCGACTTTATTTTAGGTTTTTTCAAACCTTTT
387 AATAAATGAGATTGAAAATCATACTACAACCGTGCGACTTTATTTTACGCTTTTTCAAACCTTTT
* *
3521873 TTTAAGATTTTTTTTAATATATTGTTATTTTATTTAGATAAAAATTTACTTAAATTAAATACAAA
452 TTTAAGATTTTTTTTAATATATTGTTATTTTATTTAGATAAAAATTTACTTAAATCAAAGACAAA
* *
3521938 TATTTATTTTATTTATGTCTATAATTTATATTATATGTGTGCAAGATTTAATTGAAAATAATGTG
517 TATTTATTTTATTTATGTCTATAATTTATATTATATGTGTACAAGATTTAATTGAAAATAATGTA
3522003 ATTAAATAGTATAATTATTACATATGAATTAAAAATAAAACTCTCTCTCTCTCTCAAATAGATAA
582 ATTAAATAGTATAATTATTACATATGAATTAAAAATAAAACTCTCTCTCTCTCTCAAATAGATAA
* *
3522068 AGAAAAGCACATAACTTTTTTACTTGATTTTTTTTAAAATTTAATAATTTAAGTTTAAATTTGAA
647 AGAAAAACACATAACTTTTTTACTTGAATTTTTTTAAAATTTAATAATTTAAGTTTAAATTTGAA
*
3522133 ATTTTGGTGTTTTCTTTTTATTTATTTAT
712 ATTTTGATGTTTTCTTTTTATTTATTTAT
* **
3522162 TTATTTAGCTAATGTCAATATCTCGTATTGTAAACTAAGACAACATTAAATAAGAGTAATTAAAT
1 TTATTTAGCTAATGTCAATATCTCGTATTGTAAACTAATACAACGCTAAATAAGAGTAATTAAAT
* * * *
3522227 TTTCTCTCAACTAGTATAAAGTAACTAGACTTTCTTTTAACATTAAACTTTAAATTTAATAAGCA
66 TTTCTCTCAACTAGTATAAAGTAATTAGACTTTCTTTTAACATAAAACTCTAAAGTTAATAAGCA
*
3522292 TTAATTGAATTAATAATTTTAAAATTATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATT
131 TTAATTGAACTAATAATTTTAAAATTATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATT
3522357 GAACTAATAGTGTTGAAGAAACTTGAAGTTGAAGTTAACAAAAGAAAAAAAGGAATTTTCTTACA
196 GAACTAATAGTGTTGAAGAAACTTGAAGTTGAAGTTAAC-AAA-AAAAAAA-GAATTTTCTTACA
*
3522422 TTCTTTTTCATTCGTAAAATTCTGTTTTTCTGTACTTTTGAGTCCGCAATTTTTTCTTTTCAAAC
258 TT-TTTTTCATTCGTAAAATTCTGTCTTTCTGTACTTTTGAGTCCGCAATTTTTTCTTTTCAAAC
* *
3522487 TGTCATATATTTCTAACAACTTTCTTTTTATAGCAAAAATTAAGTACGCCCTCACGATTTTTTTT
322 TGTAATATATTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCCCTCACGATTTTTTTT
3522552 AATAAATGAGATTGAAAATCATACTACAACCGTGCGACTTTATTTTACGCTTTTTCAAACCTTTT
387 AATAAATGAGATTGAAAATCATACTACAACCGTGCGACTTTATTTTACGCTTTTTCAAACCTTTT
* *
3522617 TTTAAGATTTTTTTTAATATATAGTTATTTTATTTAGATAAAAATTTACTTAAATCAAAGACCAA
452 TTTAAGATTTTTTTTAATATATTGTTATTTTATTTAGATAAAAATTTACTTAAATCAAAGACAAA
3522682 TATTTATTTTATTTATGTCTATAATTTATATTATATGTGTACAAGATTTAATTGAAAATAATGTA
517 TATTTATTTTATTTATGTCTATAATTTATATTATATGTGTACAAGATTTAATTGAAAATAATGTA
*
3522747 ATTAAATAGTATAATTATTACATATGAATTAAAAATCAAACTCTCTCTCTCTCTCAAATAGATAA
582 ATTAAATAGTATAATTATTACATATGAATTAAAAATAAAACTCTCTCTCTCTCTCAAATAGATAA
*
3522812 AGAAAAATACATAACTTTTTTACTT-AATTTTTTTAAAATTTAATAATTTAAGTTTAAATTTGAA
647 AGAAAAACACATAACTTTTTTACTTGAATTTTTTTAAAATTTAATAATTTAAGTTTAAATTTGAA
3522876 ATTTTTGATGTTTTCTTTTTATTTATTTAT
712 A-TTTTGATGTTTTCTTTTTATTTATTTAT
* *
3522906 TTATTTAGCTAATGTTAATATCTCGTATTGTAAACTAATACAACGCTACATAAGAGTAATTAAAT
1 TTATTTAGCTAATGTCAATATCTCGTATTGTAAACTAATACAACGCTAAATAAGAGTAATTAAAT
*
3522971 TTTCTCTCAACTAATATAAAGTAATTAGACTTTCTTTTAACATAAAACTCTAAAGTTAATAAGCA
66 TTTCTCTCAACTAGTATAAAGTAATTAGACTTTCTTTTAACATAAAACTCTAAAGTTAATAAGCA
* * *
3523036 TTAATTAAACTAATAATTCTAAAATTATTTAACAATTAAAAACTTGAAGTTAATAAGCATCAATT
131 TTAATTGAACTAATAATTTTAAAATTATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATT
* *
3523101 GAACTAATAGTGTT-AAGAAACTTGAAGTTAAAGTTAACAAAAAAAAAATAATTTTCTT--A---
196 GAACTAATAGTGTTGAAGAAACTTGAAGTTGAAGTTAACAAAAAAAAAAGAATTTTCTTACATTT
* *
3523160 ----CATTCGTAAAATTCTGTCTTTCTATACTTTTGAGTCCGCCATTTTTTCTTTTCAAACTGTA
261 TTTTCATTCGTAAAATTCTGTCTTTCTGTACTTTTGAGTCCGCAATTTTTTCTTTTCAAACTGTA
* *
3523221 ATATGTTTCTAACAACTTTCTTTTTATAGCACAAATTAAATACGCCCTCACGATTTTTTTTAATA
326 ATATATTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCCCTCACGATTTTTTTTAATA
* * *
3523286 AATCAGATTGAAAATCATATTACAACCGTGCGACTTTATTTTACGCTTTTTCAAACTTTTTTTTA
391 AATGAGATTGAAAATCATACTACAACCGTGCGACTTTATTTTACGCTTTTTCAAACCTTTTTTTA
3523351 AGATTTTTTTTAATATATTGTTATTTTATTTAGA
456 AGATTTTTTTTAATATATTGTTATTTTATTTAGA
3523385 CTAATGTTAC
Statistics
Matches: 1145, Mismatches: 69, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
730 214 0.19
738 1 0.00
739 99 0.09
740 127 0.11
741 7 0.01
742 4 0.00
743 71 0.06
744 619 0.54
745 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (740 bp):
TTATTTAGCTAATGTCAATATCTCGTATTGTAAACTAATACAACGCTAAATAAGAGTAATTAAAT
TTTCTCTCAACTAGTATAAAGTAATTAGACTTTCTTTTAACATAAAACTCTAAAGTTAATAAGCA
TTAATTGAACTAATAATTTTAAAATTATTAAACAATTAAAAACTTGAAGTTAATAAGCATCAATT
GAACTAATAGTGTTGAAGAAACTTGAAGTTGAAGTTAACAAAAAAAAAAGAATTTTCTTACATTT
TTTTCATTCGTAAAATTCTGTCTTTCTGTACTTTTGAGTCCGCAATTTTTTCTTTTCAAACTGTA
ATATATTTCTAACAACTTTCTTTTTATAGCACAAATTAAGTACGCCCTCACGATTTTTTTTAATA
AATGAGATTGAAAATCATACTACAACCGTGCGACTTTATTTTACGCTTTTTCAAACCTTTTTTTA
AGATTTTTTTTAATATATTGTTATTTTATTTAGATAAAAATTTACTTAAATCAAAGACAAATATT
TATTTTATTTATGTCTATAATTTATATTATATGTGTACAAGATTTAATTGAAAATAATGTAATTA
AATAGTATAATTATTACATATGAATTAAAAATAAAACTCTCTCTCTCTCTCAAATAGATAAAGAA
AAACACATAACTTTTTTACTTGAATTTTTTTAAAATTTAATAATTTAAGTTTAAATTTGAAATTT
TGATGTTTTCTTTTTATTTATTTAT
Found at i:3523772 original size:21 final size:21
Alignment explanation
Indices: 3523722--3523773 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3523712 GCTAGCTTCA
3523722 GCTCGGCTTCCTTTAATTCCT
1 GCTCGGCTTCCTTTAATTCCT
* * *
3523743 TCTCAGCTTCCTTTAATTGCT
1 GCTCGGCTTCCTTTAATTCCT
*
3523764 GCTTGGCTTC
1 GCTCGGCTTC
3523774 TTTTGCTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.31, G:0.15, T:0.44
Consensus pattern (21 bp):
GCTCGGCTTCCTTTAATTCCT
Found at i:3524132 original size:16 final size:17
Alignment explanation
Indices: 3524055--3524134 Score: 90
Period size: 18 Copynumber: 4.6 Consensus size: 17
3524045 TTTAAATCGG
*
3524055 TTAAAAATTTATGATTT
1 TTAAAAATTTATAATTT
* *
3524072 TTGAAAAATATGTAATTT
1 TT-AAAAATTTATAATTT
*
3524090 TTAAAAAATTTAAAATTT
1 TT-AAAAATTTATAATTT
*
3524108 TTTAAAATTTATAATTT
1 TTAAAAATTTATAATTT
3524125 TT-AAAATTTA
1 TTAAAAATTTA
3524135 ATTCTTAATG
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
16 8 0.15
17 17 0.32
18 28 0.53
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTATAATTT
Found at i:3524417 original size:15 final size:15
Alignment explanation
Indices: 3524397--3524428 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3524387 ACTGTTTTCT
3524397 TCTCTCGCTTCTCTC
1 TCTCTCGCTTCTCTC
*
3524412 TCTCTCGTTTCTCTC
1 TCTCTCGCTTCTCTC
3524427 TC
1 TC
3524429 CGTCTCTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTCTCGCTTCTCTC
Found at i:3525389 original size:21 final size:21
Alignment explanation
Indices: 3525339--3525390 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3525329 GCTAGCTTCA
3525339 GCTCGGCTTCCTTTAATTCCT
1 GCTCGGCTTCCTTTAATTCCT
* * *
3525360 TCTCAGCTTCCTTTAATTGCT
1 GCTCGGCTTCCTTTAATTCCT
*
3525381 GCTTGGCTTC
1 GCTCGGCTTC
3525391 TTTTGCTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.31, G:0.15, T:0.44
Consensus pattern (21 bp):
GCTCGGCTTCCTTTAATTCCT
Found at i:3525426 original size:21 final size:21
Alignment explanation
Indices: 3525386--3525427 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3525376 TTGCTGCTTG
**
3525386 GCTTCTTTTGCTTCTTGCTCA
1 GCTTCTTTTGCTTCCAGCTCA
*
3525407 GCTTTTTTTGCTTCCAGCTCA
1 GCTTCTTTTGCTTCCAGCTCA
3525428 AATTTTTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.29, G:0.14, T:0.50
Consensus pattern (21 bp):
GCTTCTTTTGCTTCCAGCTCA
Found at i:3525433 original size:21 final size:21
Alignment explanation
Indices: 3525391--3525439 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
3525381 GCTTGGCTTC
** **
3525391 TTTTGCTTCTTGCTCAGCTTT
1 TTTTGCTTCCAGCTCAAATTT
3525412 TTTTGCTTCCAGCTCAAATTT
1 TTTTGCTTCCAGCTCAAATTT
*
3525433 TTATGCT
1 TTTTGCT
3525440 CTAGCTCTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.53
Consensus pattern (21 bp):
TTTTGCTTCCAGCTCAAATTT
Found at i:3525748 original size:16 final size:17
Alignment explanation
Indices: 3525671--3525750 Score: 90
Period size: 18 Copynumber: 4.6 Consensus size: 17
3525661 TTTAAATCGG
*
3525671 TTAAAAATTTATGATTT
1 TTAAAAATTTATAATTT
* *
3525688 TTGAAAAATATGTAATTT
1 TT-AAAAATTTATAATTT
*
3525706 TTAAAAAATTTAAAATTT
1 TT-AAAAATTTATAATTT
*
3525724 TTTAAAATTTATAATTT
1 TTAAAAATTTATAATTT
3525741 TT-AAAATTTA
1 TTAAAAATTTA
3525751 ATTCTTAATG
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
16 8 0.15
17 17 0.32
18 28 0.53
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTATAATTT
Found at i:3526032 original size:15 final size:15
Alignment explanation
Indices: 3526012--3526043 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3526002 ACTGTTTTCT
*
3526012 TCTCTCGTTTCTCTC
1 TCTCTCGCTTCTCTC
3526027 TCTCTCGCTTCTCTC
1 TCTCTCGCTTCTCTC
3526042 TC
1 TC
3526044 CGTCTCCGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTCTCGCTTCTCTC
Found at i:3526979 original size:21 final size:21
Alignment explanation
Indices: 3526950--3527021 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
3526940 GCTAGCTTCA
*
3526950 GCTCGGCTTCCTTTAATTCCT
1 GCTCAGCTTCCTTTAATTCCT
*
3526971 GCTCAGCTTCCTTTAATTGCT
1 GCTCAGCTTCCTTTAATTCCT
** * ** *
3526992 GCTTGGCTTCTTTTGCTTCTT
1 GCTCAGCTTCCTTTAATTCCT
3527013 GCTCAGCTT
1 GCTCAGCTT
3527022 TTTTTGCTTA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.08, C:0.29, G:0.17, T:0.46
Consensus pattern (21 bp):
GCTCAGCTTCCTTTAATTCCT
Found at i:3527307 original size:19 final size:17
Alignment explanation
Indices: 3527285--3527370 Score: 54
Period size: 17 Copynumber: 5.0 Consensus size: 17
3527275 TAAATCGGTT
3527285 AAAAATTTATGATTTTTGAA
1 AAAAATTTA--ATTTTT-AA
* *
3527305 AAATATGTAATTTTTAA
1 AAAAATTTAATTTTTAA
* *
3527322 AAAAATTAAAATTTTT-T
1 AAAAATT-TAATTTTTAA
*
3527339 AAAATTTATAATTTTT--
1 AAAAATT-TAATTTTTAA
3527355 -AAAATTTAATTTTTAA
1 AAAAATTTAATTTTTAA
3527371 TGTGATTGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 8 0.15
15 5 0.09
17 21 0.39
18 13 0.24
20 7 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AAAAATTTAATTTTTAA
Found at i:3527323 original size:16 final size:15
Alignment explanation
Indices: 3527304--3527370 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 15
3527294 TGATTTTTGA
3527304 AAAATATGTAATTTTT
1 AAAATAT-TAATTTTT
*
3527320 AAAAAAATTAAAATTTTTT
1 -AAAATATT--AA-TTTTT
*
3527339 AAAATTTATAATTTTT
1 AAAATAT-TAATTTTT
3527355 AAAAT-TTAATTTTT
1 AAAATATTAATTTTT
3527369 AA
1 AA
3527371 TGTGATTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 11 0.26
17 8 0.19
18 7 0.16
19 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (15 bp):
AAAATATTAATTTTT
Found at i:3527366 original size:14 final size:16
Alignment explanation
Indices: 3527286--3527370 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 16
3527276 AAATCGGTTA
*
3527286 AAAATTTATGATTTTT
1 AAAATTTATAATTTTT
* *
3527302 GAAAAATATGTAATTTTT
1 --AAAATTTATAATTTTT
* *
3527320 AAAAAAATTAAAATTTTTT
1 --AAAATTTATAA-TTTTT
3527339 AAAATTTATAATTTTT
1 AAAATTTATAATTTTT
3527355 AAAA-TT-TAATTTTT
1 AAAATTTATAATTTTT
3527369 AA
1 AA
3527371 TGTGATTGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
14 10 0.18
15 2 0.04
16 9 0.16
17 9 0.16
18 21 0.38
19 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (16 bp):
AAAATTTATAATTTTT
Found at i:3527636 original size:9 final size:9
Alignment explanation
Indices: 3527622--3527655 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3527612 ACACTGTTTT
3527622 CTTCTCTCG
1 CTTCTCTCG
*
3527631 CTTCTCTCT
1 CTTCTCTCG
3527640 C-TCTCTCG
1 CTTCTCTCG
3527648 CTTCTCTC
1 CTTCTCTC
3527656 TCCGTCTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.47, G:0.06, T:0.47
Consensus pattern (9 bp):
CTTCTCTCG
Found at i:3527663 original size:17 final size:17
Alignment explanation
Indices: 3527624--3527657 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3527614 ACTGTTTTCT
3527624 TCTCTCGCTTCTCTCTC
1 TCTCTCGCTTCTCTCTC
3527641 TCTCTCGCTTCTCTCTC
1 TCTCTCGCTTCTCTCTC
3527658 CGTCTCCGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.06, T:0.47
Consensus pattern (17 bp):
TCTCTCGCTTCTCTCTC
Found at i:3529439 original size:21 final size:21
Alignment explanation
Indices: 3529367--3529470 Score: 93
Period size: 21 Copynumber: 5.0 Consensus size: 21
3529357 CTTTACCTTT
** *
3529367 GCTTCTTTTAATTCATGCTCG
1 GCTTCTTTTGCTTCCTGCTCG
** * *
3529388 GCTTCTTTTAATTGCTGCTTG
1 GCTTCTTTTGCTTCCTGCTCG
*
3529409 GCTTCTTTTGCTTCCTGCTTG
1 GCTTCTTTTGCTTCCTGCTCG
* *
3529430 GCTTCTTTTGCTTCTTGCTCA
1 GCTTCTTTTGCTTCCTGCTCG
*
3529451 GCTT-TTTCTGCTTCCAGCTC
1 GCTTCTTT-TGCTTCCTGCTC
3529471 AAATTTTTGT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 3 0.04
21 68 0.96
ACGTcount: A:0.07, C:0.27, G:0.16, T:0.50
Consensus pattern (21 bp):
GCTTCTTTTGCTTCCTGCTCG
Found at i:3534522 original size:6 final size:6
Alignment explanation
Indices: 3534511--3534595 Score: 58
Period size: 5 Copynumber: 14.8 Consensus size: 6
3534501 TTTTTTATTT
* *
3534511 ATTTAA ATTTAA A-TTAA ATATAAA AATT-A ATTT-A ATTTAA ATTATTAA
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA ATTTAA A-T-TTAA
* *
3534559 ATTT-A TTTTAA ATTTAT A-TT-A ATTTAA A-TTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA
3534596 TTAAACCTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
4 1 0.02
5 27 0.44
6 23 0.37
7 6 0.10
8 5 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:3534527 original size:11 final size:11
Alignment explanation
Indices: 3534513--3534595 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
3534503 TTTTATTTAT
3534513 TTAAATTTAAA
1 TTAAATTTAAA
*
3534524 TTAAATATAAAAA
1 TTAAAT-T-TAAA
*
3534537 TT-AATTTAAT
1 TTAAATTTAAA
3534547 TTAAA-TT--A
1 TTAAATTTAAA
**
3534555 TTAAATTTATT
1 TTAAATTTAAA
*
3534566 TTAAATTTATA
1 TTAAATTTAAA
3534577 TT-AATTTAAA
1 TTAAATTTAAA
3534587 TTAAATTTA
1 TTAAATTTA
3534596 TTAAACCTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 5 0.09
9 2 0.03
10 15 0.26
11 27 0.47
12 4 0.07
13 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:3534542 original size:23 final size:24
Alignment explanation
Indices: 3534516--3534572 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3534506 TATTTATTTA
3534516 AATTTAAATTAAA-TATAAAAATT
1 AATTTAAATTAAATTATAAAAATT
* * *
3534539 AATTTAATTTAAATTATTAAATTT
1 AATTTAAATTAAATTATAAAAATT
*
3534563 ATTTTAAATT
1 AATTTAAATT
3534573 TATATTAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTTAAATTAAATTATAAAAATT
Found at i:3535268 original size:5 final size:5
Alignment explanation
Indices: 3535255--3535291 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
3535245 TTATAAATCA
3535255 AATACT AATAT AATAT AATAT AATAT AATAT AATAT A
1 AATA-T AATAT AATAT AATAT AATAT AATAT AATAT A
3535292 TGTCTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:3537294 original size:2 final size:2
Alignment explanation
Indices: 3537287--3537316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3537277 GGTACCTGCT
3537287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3537317 AAAGAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3545599 original size:18 final size:19
Alignment explanation
Indices: 3545565--3545600 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3545555 AAATCGAAGG
*
3545565 AAAAAAAAAGACATAAATT
1 AAAAAAAAAAACATAAATT
3545584 AAAAAAAAAAAC-TAAAT
1 AAAAAAAAAAACATAAAT
3545601 CACCGGATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.14
Consensus pattern (19 bp):
AAAAAAAAAAACATAAATT
Found at i:3549708 original size:3 final size:3
Alignment explanation
Indices: 3549700--3549745 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
3549690 ATGTCATAGC
3549700 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3549746 GGATTAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3551066 original size:18 final size:19
Alignment explanation
Indices: 3551043--3551078 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3551033 TTTTTTTTGA
*
3551043 TTTATTTT-GTTAATAAAT
1 TTTATTTTAATTAATAAAT
3551061 TTTATTTTAATTAATAAA
1 TTTATTTTAATTAATAAA
3551079 AAAACTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTATTTTAATTAATAAAT
Found at i:3551293 original size:21 final size:19
Alignment explanation
Indices: 3551253--3551298 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
3551243 ATTAAATTTA
**
3551253 AAATAAAAATATTTTTATT
1 AAATAAAAATATTTAAATT
3551272 AAATAAATAATTATTTAAATT
1 AAATAAA-AA-TATTTAAATT
3551293 AAATAA
1 AAATAA
3551299 CTTTGAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATAAAAATATTTAAATT
Found at i:3551840 original size:21 final size:23
Alignment explanation
Indices: 3551794--3551845 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
3551784 TATTTTTATT
3551794 TAAAAT-TTAATTATAAAATATG
1 TAAAATATTAATTATAAAATATG
* *
3551816 T-AAATATTAA-TATAAAATTTT
1 TAAAATATTAATTATAAAATATG
3551837 TAAAATATT
1 TAAAATATT
3551846 TTTAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAAAATATTAATTATAAAATATG
Found at i:3551842 original size:22 final size:23
Alignment explanation
Indices: 3551790--3551845 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
3551780 AAAGTATTTT
3551790 TATTTAAAAT-TTAATTATAAAA
1 TATTTAAAATATTAATTATAAAA
*
3551812 TATGT-AAATATTAA-TATAAAA
1 TATTTAAAATATTAATTATAAAA
*
3551833 TTTTTAAAATATT
1 TATTTAAAATATT
3551846 TTTAATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTTAAAATATTAATTATAAAA
Found at i:3552309 original size:28 final size:28
Alignment explanation
Indices: 3552277--3552358 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
3552267 ATACATTAAA
3552277 TATATTATATTAAATATATTTAATTATT
1 TATATTATATTAAATATATTTAATTATT
3552305 TATATTGAGT-TT-AATATA-TT-ATT-TT
1 TATATT-A-TATTAAATATATTTAATTATT
3552330 TATATT-TATTAAATAAATATTTATATTAT
1 TATATTATATTAAAT--ATATTTA-ATTAT
3552359 ATTTTATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 18
0.71 0.00 0.29
Matches are distributed among these distances:
22 1 0.02
23 2 0.05
24 3 0.07
25 8 0.18
26 6 0.14
27 4 0.09
28 12 0.27
29 6 0.14
30 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TATATTATATTAAATATATTTAATTATT
Found at i:3552341 original size:23 final size:26
Alignment explanation
Indices: 3552277--3552372 Score: 65
Period size: 28 Copynumber: 3.6 Consensus size: 26
3552267 ATACATTAAA
3552277 TATATTATATTAAATATATTTAATTATT
1 TATATT-TATT-AATATATTTAATTATT
*
3552305 TATATTGAGTTTAATATA-TT-ATT-TT
1 TATATTTA--TTAATATATTTAATTATT
** *
3552330 TATATTTATTAA-ATAAATATTTATAT
1 TATATTTATTAATATATTTAATTAT-T
3552356 TATATTTTATATAATAT
1 TATA-TTTAT-TAATAT
3552373 TTAAAACTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
22 3 0.05
23 5 0.09
24 2 0.04
25 10 0.18
26 8 0.15
27 8 0.15
28 15 0.27
29 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TATATTTATTAATATATTTAATTATT
Found at i:3552373 original size:23 final size:22
Alignment explanation
Indices: 3552275--3552375 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 22
3552265 ATATACATTA
* * *
3552275 AATATATTATATTAAATATATTT
1 AATAT-TTATATTTATTATATAT
*
3552298 AATTATTTATATTGAGTTTAATATAT
1 AA-TATTTATATTTA--TT-ATATAT
* * *
3552324 TATTTTTATATTTATTAAATA-
1 AATATTTATATTTATTATATAT
*
3552345 AATATTTATATTATATTTTATAT
1 AATATTTATATT-TATTATATAT
3552368 AATATTTA
1 AATATTTA
3552376 AAACTATCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
21 10 0.16
22 11 0.18
23 20 0.33
24 3 0.05
25 11 0.18
26 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATATTTATATTTATTATATAT
Found at i:3554124 original size:2 final size:2
Alignment explanation
Indices: 3554117--3554146 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3554107 TAAAATAAGA
3554117 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
3554147 TGGATGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3557663 original size:27 final size:28
Alignment explanation
Indices: 3557626--3557695 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
3557616 CCACTTATTT
*
3557626 ATTTGTTAAAAATGGTGGTTAT-TTTGTG
1 ATTTGTCAAAAATGGTGGTTATCTTTG-G
* *
3557654 -TTTGTCAAAAATGATGGTTTTCTTTGG
1 ATTTGTCAAAAATGGTGGTTATCTTTGG
*
3557681 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
3557696 AGGCTTGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 19 0.54
28 16 0.46
ACGTcount: A:0.26, C:0.04, G:0.23, T:0.47
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATCTTTGG
Found at i:3557797 original size:20 final size:20
Alignment explanation
Indices: 3557772--3557813 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3557762 AAATAGAGGT
*
3557772 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
*
3557792 TCCCTCATCCCTCTCATGTA
1 TCCCTCATCCCTCTCAAGTA
3557812 TC
1 TC
3557814 TCTCTTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.48, G:0.05, T:0.33
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:3560299 original size:21 final size:22
Alignment explanation
Indices: 3560270--3560315 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3560260 TGTTCAGACA
** *
3560270 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
3560292 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
3560313 AGT
1 AGT
3560316 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:3560702 original size:21 final size:21
Alignment explanation
Indices: 3560678--3560723 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
3560668 GGTATTTGCA
3560678 AAGAAAGATGGATCTTCTAGC
1 AAGAAAGATGGATCTTCTAGC
3560699 AAGAAAGATGGATCTTCTAGC
1 AAGAAAGATGGATCTTCTAGC
3560720 AAGA
1 AAGA
3560724 TTCACTAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (21 bp):
AAGAAAGATGGATCTTCTAGC
Found at i:3562257 original size:28 final size:27
Alignment explanation
Indices: 3562203--3562273 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
3562193 GTCACCCATT
*
3562203 TGTTTGTAAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
*
3562230 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT-TTTG
*
3562258 -GATTTGTCAAATATGG
1 TG-TTTGTCAAAAATGG
3562274 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:3563062 original size:2 final size:2
Alignment explanation
Indices: 3563052--3563087 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3563042 ACACACATAC
3563052 AT AT A- 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 AT AT AT A
3563088 AAGAGCTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3563524 original size:21 final size:22
Alignment explanation
Indices: 3563498--3563546 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3563488 TTTTTAATAT
* *
3563498 TTATAAATTTTGA-TTATATTA
1 TTATAAATTTTAATTTATAGTA
3563519 TTAT-AATTTTAATTTATAGTA
1 TTATAAATTTTAATTTATAGTA
3563540 TTA-AAAT
1 TTATAAAT
3563547 ATTATCCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TTATAAATTTTAATTTATAGTA
Found at i:3567764 original size:2 final size:2
Alignment explanation
Indices: 3567757--3567792 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3567747 ACTTTTCAAC
3567757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3567793 AACCAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3569138 original size:560 final size:560
Alignment explanation
Indices: 3568079--3569198 Score: 2195
Period size: 560 Copynumber: 2.0 Consensus size: 560
3568069 GGTAAGTGAA
3568079 AAAAATTTGCTACTTTGCTCAAAAAGTTTCTTAAGCAATTGTTCATCAACCCCAGGATTCACAAG
1 AAAAATTTGCTACTTTGCTCAAAAAGTTTCTTAAGCAATTGTTCATCAACCCCAGGATTCACAAG
3568144 GTAAAAGAAACCATAATCAACGCATGCCTGTTGAAAACCTCATATTTTTTAAAAGCAACTTTATG
66 GTAAAAGAAACCATAATCAACGCATGCCTGTTGAAAACCTCATATTTTTTAAAAGCAACTTTATG
3568209 GCATTGGGAAAGTTAGAAATTGTATGCAAATAAGATTTCATTGCTTCTTAGACATTTTTCTGGTG
131 GCATTGGGAAAGTTAGAAATTGTATGCAAATAAGATTTCATTGCTTCTTAGACATTTTTCTGGTG
3568274 AGGACAAGTCAACGATGGGAAGTTGAAGAGGGTCAGACATTTTTCTTTTTTGGTTTCTGCTGCAA
196 AGGACAAGTCAACGATGGGAAGTTGAAGAGGGTCAGACATTTTTCTTTTTTGGTTTCTGCTGCAA
*
3568339 ATTACTTTGCATTGAGCAAGGAGTTTTATATATTAAAAAAGGGATAATTTAATCTTCCATTTGTC
261 ATTACTTTGCATTGAACAAGGAGTTTTATATATTAAAAAAGGGATAATTTAATCTTCCATTTGTC
*
3568404 TATGGCCTATCATGGTATCATATAGTATTTTATTTCACTTGTATAAAATACAAGGGTTTCATGCT
326 TATGGCCTATCATGGTATCATATAGTATTTTATTTCACTTGTATAAAATACAAGGGTGTCATGCT
*
3568469 CATATTAGACAAAGTTAAGGCCAATACTAAGACAATGTCCAAAAGATTTTCGGTTTGGGATTACC
391 CATATTAGACAAAGTTAAGGCCAATACTAAGACAATGTCCAAAAGACTTTCGGTTTGGGATTACC
3568534 TGCTGCCCTTCTCAAAGGGAGCGATATTATCATGTACGACCCTAAGAACGCAAAGTGCGTTCACA
456 TGCTGCCCTTCTCAAAGGGAGCGATATTATCATGTACGACCCTAAGAACGCAAAGTGCGTTCACA
3568599 CAAACAGTTATGTCAGTTGACCAGCGGGGTAGATCAGGTG
521 CAAACAGTTATGTCAGTTGACCAGCGGGGTAGATCAGGTG
3568639 AAAAATTTGCTACTTTGCTCAAAAAGTTTCTTAAGCAATTGTTCATCAACCCCAGGATTCACAAG
1 AAAAATTTGCTACTTTGCTCAAAAAGTTTCTTAAGCAATTGTTCATCAACCCCAGGATTCACAAG
3568704 GTAAAAGAAACCATAATCAACGCATGCCTGTTGAAAACCTCATATTTTTTAAAAGCAACTTTATG
66 GTAAAAGAAACCATAATCAACGCATGCCTGTTGAAAACCTCATATTTTTTAAAAGCAACTTTATG
3568769 GCATTGGGAAAGTTAGAAATTGTATGCAAATAAGATTTCATTGCTTCTTAGACATTTTTCTGGTG
131 GCATTGGGAAAGTTAGAAATTGTATGCAAATAAGATTTCATTGCTTCTTAGACATTTTTCTGGTG
3568834 AGGACAAGTCAACGATGGGAAGTTGAAGAGGGTCAGACATTTTTCTTTTTTGGTTTCTGCTGCAA
196 AGGACAAGTCAACGATGGGAAGTTGAAGAGGGTCAGACATTTTTCTTTTTTGGTTTCTGCTGCAA
*
3568899 ATTACTTTGCATTGAACAAGGAGTTTTATTTATTAAAAAAGGGATAATTTAATCTTCCATTTGTC
261 ATTACTTTGCATTGAACAAGGAGTTTTATATATTAAAAAAGGGATAATTTAATCTTCCATTTGTC
*
3568964 TATGGCCTATCATGGTATCGTATAGTATTTTATTTCACTTGTATAAAATACAAGGGTGTCATGCT
326 TATGGCCTATCATGGTATCATATAGTATTTTATTTCACTTGTATAAAATACAAGGGTGTCATGCT
3569029 CATATTAGACAAAGTTAAGGCCAATACTAAGACAATGTCCAAAAGACTTTCGGTTTGGGATTACC
391 CATATTAGACAAAGTTAAGGCCAATACTAAGACAATGTCCAAAAGACTTTCGGTTTGGGATTACC
3569094 TGCTGCCCTTCTCAAAGGGAGCGATATTATCATGTACGACCCTAAGAACGCAAAGTGCGTTCACA
456 TGCTGCCCTTCTCAAAGGGAGCGATATTATCATGTACGACCCTAAGAACGCAAAGTGCGTTCACA
3569159 CAAACAGTTATGTCAGTTGACCAGCGGGGTAGATCAGGTG
521 CAAACAGTTATGTCAGTTGACCAGCGGGGTAGATCAGGTG
3569199 GACAACTCAA
Statistics
Matches: 555, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
560 555 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (560 bp):
AAAAATTTGCTACTTTGCTCAAAAAGTTTCTTAAGCAATTGTTCATCAACCCCAGGATTCACAAG
GTAAAAGAAACCATAATCAACGCATGCCTGTTGAAAACCTCATATTTTTTAAAAGCAACTTTATG
GCATTGGGAAAGTTAGAAATTGTATGCAAATAAGATTTCATTGCTTCTTAGACATTTTTCTGGTG
AGGACAAGTCAACGATGGGAAGTTGAAGAGGGTCAGACATTTTTCTTTTTTGGTTTCTGCTGCAA
ATTACTTTGCATTGAACAAGGAGTTTTATATATTAAAAAAGGGATAATTTAATCTTCCATTTGTC
TATGGCCTATCATGGTATCATATAGTATTTTATTTCACTTGTATAAAATACAAGGGTGTCATGCT
CATATTAGACAAAGTTAAGGCCAATACTAAGACAATGTCCAAAAGACTTTCGGTTTGGGATTACC
TGCTGCCCTTCTCAAAGGGAGCGATATTATCATGTACGACCCTAAGAACGCAAAGTGCGTTCACA
CAAACAGTTATGTCAGTTGACCAGCGGGGTAGATCAGGTG
Found at i:3569914 original size:13 final size:12
Alignment explanation
Indices: 3569869--3569912 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
3569859 CACGAATCTT
3569869 ATTTTTATTTTA
1 ATTTTTATTTTA
* *
3569881 AATTTTATTTTT
1 ATTTTTATTTTA
*
3569893 ATTTTT-TATTA
1 ATTTTTATTTTA
3569904 ATTTTTATT
1 ATTTTTATT
3569913 ATATTTATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:3573967 original size:13 final size:13
Alignment explanation
Indices: 3573951--3573988 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3573941 TACATATTTT
3573951 AAATATAATTAAA
1 AAATATAATTAAA
3573964 AAAT-TAATT-AA
1 AAATATAATTAAA
3573975 AAATATAAATTAAA
1 AAATAT-AATTAAA
3573989 CACATAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 6 0.27
13 8 0.36
14 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATTAAA
Found at i:3574112 original size:12 final size:14
Alignment explanation
Indices: 3574085--3574117 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
3574075 CGAATGTATC
3574085 AAATATTAATCTAA
1 AAATATTAATCTAA
3574099 AAATATT-A-CTAA
1 AAATATTAATCTAA
3574111 AAATATT
1 AAATATT
3574118 TGTTAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 1 0.05
14 7 0.37
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATTAATCTAA
Found at i:3577152 original size:30 final size:30
Alignment explanation
Indices: 3577108--3577165 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3577098 GCACTTAGAT
* *
3577108 TCATACGTGTGAAAAGACAGAACTATGGAC
1 TCATACATGAGAAAAGACAGAACTATGGAC
*
3577138 TCATACATGAGAAAAGACAGATCTATGG
1 TCATACATGAGAAAAGACAGAACTATGG
3577166 TTAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (30 bp):
TCATACATGAGAAAAGACAGAACTATGGAC
Found at i:3581114 original size:17 final size:17
Alignment explanation
Indices: 3581092--3581124 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3581082 TTTTTAAAAT
3581092 AATAAAACAA-ATATTTC
1 AATAAAA-AATATATTTC
3581109 AATAAAAAATATATTT
1 AATAAAAAATATATTT
3581125 TTAAAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAAAAATATATTTC
Found at i:3581840 original size:22 final size:22
Alignment explanation
Indices: 3581799--3581840 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3581789 TATTAACTTA
*
3581799 AATATTTAAATACTTAAAAAAT
1 AATATTTAAATAATTAAAAAAT
* *
3581821 AATATTTAATTAATTTAAAA
1 AATATTTAAATAATTAAAAA
3581841 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATATTTAAATAATTAAAAAAT
Found at i:3583701 original size:16 final size:16
Alignment explanation
Indices: 3583682--3583725 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3583672 AATTCAAGTT
3583682 ATTTTTTAATT-TTATA
1 ATTTTTTAATTATTA-A
*
3583698 ATTTTTAAATTATTAA
1 ATTTTTTAATTATTAA
*
3583714 TTTTTTTAATTA
1 ATTTTTTAATTA
3583726 AAATCAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTTAATTATTAA
Found at i:3583772 original size:26 final size:27
Alignment explanation
Indices: 3583705--3583776 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
3583695 ATAATTTTTA
*
3583705 AATT-ATTAATTTTTTTAATTAAAATC
1 AATTGATTAATTTTTTAAATTAAAATC
** *
3583731 AATTTGATCGA--GTTTAAATTAAAAT-
1 AA-TTGATTAATTTTTTAAATTAAAATC
3583756 AATTGATTAATTTTTTAAATT
1 AATTGATTAATTTTTTAAATT
3583777 CACATCAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
24 6 0.17
25 2 0.06
26 22 0.63
27 2 0.06
28 3 0.09
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (27 bp):
AATTGATTAATTTTTTAAATTAAAATC
Found at i:3584404 original size:18 final size:19
Alignment explanation
Indices: 3584381--3584424 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3584371 TTAAATTTAT
3584381 ATTTTTTT-GTTTTAATTA
1 ATTTTTTTAGTTTTAATTA
*
3584399 ATTTTTTTATTTTTAATTA
1 ATTTTTTTAGTTTTAATTA
*
3584418 AATTTTT
1 ATTTTTT
3584425 AATTTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTTTTTTAGTTTTAATTA
Found at i:3584406 original size:19 final size:20
Alignment explanation
Indices: 3584381--3584424 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
3584371 TTAAATTTAT
*
3584381 ATTTTTTT-GTTTTAATT-A
1 ATTTTTTTATTTTTAATTAA
3584399 ATTTTTTTATTTTTAATTAA
1 ATTTTTTTATTTTTAATTAA
3584419 ATTTTT
1 ATTTTT
3584425 AATTTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 7 0.30
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTTTTTTATTTTTAATTAA
Found at i:3584429 original size:19 final size:19
Alignment explanation
Indices: 3584390--3584429 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3584380 TATTTTTTTG
* *
3584390 TTTTAATTAATTTTTTTAT
1 TTTTAATTAAATTTTTAAT
3584409 TTTTAATTAAATTTTTAAT
1 TTTTAATTAAATTTTTAAT
3584428 TT
1 TT
3584430 AAGTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTAATTAAATTTTTAAT
Found at i:3584430 original size:23 final size:23
Alignment explanation
Indices: 3584390--3584458 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
3584380 TATTTTTTTG
*
3584390 TTTTAATT-AA-TTTT--TTTAT
1 TTTTAATTAAATTTTTAATTTAA
3584409 TTTTAATTAAATTTTTAATTTAA
1 TTTTAATTAAATTTTTAATTTAA
* * *
3584432 GTTTAAATAAGTTTTTAATTTAGA
1 TTTTAATTAAATTTTTAATTTA-A
3584456 TTT
1 TTT
3584459 AAATAAGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.20
20 2 0.05
21 4 0.10
23 23 0.57
24 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTAATTAAATTTTTAATTTAA
Found at i:3584459 original size:23 final size:23
Alignment explanation
Indices: 3584410--3584468 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
3584400 TTTTTTTATT
* *
3584410 TTTAATTAAATTTTTAATTTAAG
1 TTTAAATAAGTTTTTAATTTAAG
3584433 TTTAAATAAGTTTTTAATTT-AG
1 TTTAAATAAGTTTTTAATTTAAG
3584455 ATTTAAATAAGTTT
1 -TTTAAATAAGTTT
3584469 AAGTTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTAAATAAGTTTTTAATTTAAG
Found at i:3584570 original size:9 final size:9
Alignment explanation
Indices: 3584553--3584615 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
3584543 TAACAATAAA
*
3584553 AAATCAATT
1 AAATTAATT
3584562 AAATTAATT
1 AAATTAATT
*
3584571 -AATTAAATC
1 AAATT-AATT
3584580 AATATT--TT
1 AA-ATTAATT
*
3584588 AAATTGATT
1 AAATTAATT
3584597 AAATTAATTT
1 AAATTAA-TT
3584607 AAATTAATT
1 AAATTAATT
3584616 TTTTTAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
7 3 0.07
8 7 0.16
9 21 0.48
10 10 0.23
11 3 0.07
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (9 bp):
AAATTAATT
Found at i:3584628 original size:18 final size:19
Alignment explanation
Indices: 3584600--3584635 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3584590 ATTGATTAAA
*
3584600 TTAATTTAAATTAATTTTT
1 TTAATTTAAATCAATTTTT
3584619 TTAA-TTAAATCAATTTT
1 TTAATTTAAATCAATTTT
3584636 AATCCAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAATTTAAATCAATTTTT
Found at i:3592019 original size:2 final size:2
Alignment explanation
Indices: 3592012--3592053 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3592002 TGAAAAGAAC
3592012 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
3592054 GAAGTTCTTG
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:3592716 original size:21 final size:21
Alignment explanation
Indices: 3592673--3592717 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3592663 TAGATTTGGG
** *
3592673 TTAAAAAATTTAAATTTGGAT
1 TTAAAAAATCAAAATTTGCAT
*
3592694 TTAAAAAATCAAAATTTTCAT
1 TTAAAAAATCAAAATTTGCAT
3592715 TTA
1 TTA
3592718 GATGTTGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (21 bp):
TTAAAAAATCAAAATTTGCAT
Found at i:3593016 original size:22 final size:21
Alignment explanation
Indices: 3592988--3593041 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
3592978 GTCTAAATAA
**
3592988 AAAATTTTAAATTCATGAATTT
1 AAAATTTTAAATT-ATGAAACT
*
3593010 AAAA-TTTATAATTTTGAAACT
1 AAAATTTTA-AATTATGAAACT
3593031 AAAATTTTAAA
1 AAAATTTTAAA
3593042 ATTAAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
AAAATTTTAAATTATGAAACT
Found at i:3593941 original size:17 final size:16
Alignment explanation
Indices: 3593901--3593941 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
3593891 TTTTTAAAAA
*
3593901 TTAACTAATATATTAT
1 TTAAATAATATATTAT
3593917 TTATAATAATATATTATT
1 TTA-AATAATATATTA-T
3593935 TTAAATA
1 TTAAATA
3593942 TAATAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 15 0.68
18 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAATAATATATTAT
Found at i:3595160 original size:2 final size:2
Alignment explanation
Indices: 3595147--3595182 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3595137 TCATGAAACC
*
3595147 AT AT AC 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
3595183 GTATGTACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3598238 original size:16 final size:16
Alignment explanation
Indices: 3598217--3598251 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3598207 ATCATATAAG
3598217 ATTAAG-AAAATAAAAT
1 ATTAAGCAAAAT-AAAT
3598233 ATTAAGCAAAATAAAT
1 ATTAAGCAAAATAAAT
3598249 ATT
1 ATT
3598252 TTATTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
ATTAAGCAAAATAAAT
Found at i:3599754 original size:26 final size:26
Alignment explanation
Indices: 3599725--3599775 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3599715 TATTAACTTA
3599725 TTAAA-ATAA-TATAAATTATAAATATT
1 TTAAATATAATTAT-AA-TATAAATATT
3599751 TTAAATATAATTATAATATAAATAT
1 TTAAATATAATTATAATATAAATAT
3599776 ATAAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 14 0.61
27 6 0.26
28 3 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAAATATAATTATAATATAAATATT
Found at i:3600411 original size:24 final size:24
Alignment explanation
Indices: 3600384--3600429 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3600374 GATTTTTTTT
* *
3600384 TTTTAAATTATATTTAAAAAATTA
1 TTTTAAATTAAATTAAAAAAATTA
**
3600408 TTTTTTATTAAATTAAAAAAAT
1 TTTTAAATTAAATTAAAAAAAT
3600430 AATATATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTAAATTAAATTAAAAAAATTA
Found at i:3604265 original size:29 final size:30
Alignment explanation
Indices: 3604210--3604328 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 30
3604200 ATAATTAAAA
*
3604210 TATTATAATTTTATATAAATTTTAATATTAT
1 TATTATTATTTTATATA-ATTTTAATATTAT
3604241 TATTATTATTTTATAT-ATTTTAATA-TATT
1 TATTATTATTTTATATAATTTTAATATTA-T
* *
3604270 TATT-TTATATTCATATTATTTT--TATTAT
1 TATTATTAT-TTTATATAATTTTAATATTAT
*
3604298 AAATTA-TATTTTA-ATAATTTTATATATTAT
1 -TATTATTATTTTATATAATTTTA-ATATTAT
3604328 T
1 T
3604329 TTTTAAATCA
Statistics
Matches: 73, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
27 7 0.10
28 12 0.16
29 28 0.38
30 11 0.15
31 15 0.21
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTATTATTTTATATAATTTTAATATTAT
Found at i:3605258 original size:21 final size:21
Alignment explanation
Indices: 3605220--3605260 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3605210 AAATTTTAAA
*
3605220 ATTAATTAATATATTATTTAT
1 ATTAATAAATATATTATTTAT
3605241 ATTAATAAATAT-TATATTTA
1 ATTAATAAATATAT-TATTTA
3605261 ATTTATTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTAATAAATATATTATTTAT
Found at i:3605347 original size:24 final size:25
Alignment explanation
Indices: 3605310--3605371 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
3605300 ACAAATAAAT
*
3605310 AAATAAAATTTATAA-TTATT-ATA
1 AAATTAAATTTATAATTTATTCATA
3605333 AAATTAAATTATATAATTTATTCATA
1 AAATTAAATT-TATAATTTATTCATA
*
3605359 ATATATAAATTTA
1 AAAT-TAAATTTA
3605372 AACGTCGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 9 0.27
24 5 0.15
25 5 0.15
26 8 0.24
27 6 0.18
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AAATTAAATTTATAATTTATTCATA
Found at i:3608093 original size:2 final size:2
Alignment explanation
Indices: 3608086--3608118 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3608076 TTACAAGGAA
3608086 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3608119 ATTATTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3608596 original size:12 final size:12
Alignment explanation
Indices: 3608579--3608603 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3608569 ATGATATAAA
3608579 AAATATATAATT
1 AAATATATAATT
3608591 AAATATATAATT
1 AAATATATAATT
3608603 A
1 A
3608604 TTTTTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATAATT
Found at i:3613410 original size:17 final size:17
Alignment explanation
Indices: 3613368--3613442 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 17
3613358 ATTTTTTAAT
3613368 TTTTATATTAAA-A-ATA
1 TTTTA-ATTAAATATATA
3613384 TTATTAAATTAAATATATA
1 TT-TT-AATTAAATATATA
* *
3613403 TTTTAATTAATTATTTA
1 TTTTAATTAAATATATA
* * *
3613420 TTAT-ATTTAATATTTA
1 TTTTAATTAAATATATA
3613436 -TTTAATT
1 TTTTAATT
3613443 TTAAAATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
15 2 0.04
16 15 0.31
17 22 0.46
18 4 0.08
19 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAATTAAATATATA
Found at i:3613445 original size:17 final size:18
Alignment explanation
Indices: 3613399--3613457 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 18
3613389 AAATTAAATA
3613399 TATATTTTAATTAATTATT
1 TATATTTTAA-TAATTATT
*
3613418 TATTATATTTAATATTTATT
1 TA-TAT-TTTAATAATTATT
3613438 TA-ATTTTAA-AATTATT
1 TATATTTTAATAATTATT
3613454 TATA
1 TATA
3613458 AATATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 8 0.23
17 6 0.17
18 2 0.06
19 2 0.06
20 12 0.34
21 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTTAATAATTATT
Found at i:3613744 original size:18 final size:19
Alignment explanation
Indices: 3613709--3613746 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3613699 TACATAATTA
*
3613709 TCATTTATAAATATAAAAT
1 TCATATATAAATATAAAAT
3613728 TCATATATAAA-ATAAAAT
1 TCATATATAAATATAAAAT
3613746 T
1 T
3613747 GAAAGACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
TCATATATAAATATAAAAT
Found at i:3615251 original size:10 final size:9
Alignment explanation
Indices: 3615225--3615250 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3615215 CTGTCCATGC
3615225 CTTTTTTTA
1 CTTTTTTTA
3615234 CTTTTTTTA
1 CTTTTTTTA
3615243 CTTTTTTT
1 CTTTTTTT
3615251 TTTCGTTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
CTTTTTTTA
Found at i:3615420 original size:31 final size:29
Alignment explanation
Indices: 3615349--3615422 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
3615339 ATTTATTTGT
*
3615349 TTATATTTGTATTATTTTTTATTTAAAATA
1 TTATATTT-TATTATTTTTTATATAAAATA
*
3615379 TTATATTTTTATATATTTTTTATATATTAATAA
1 TTATA-TTTTAT-TATTTTTTATATA-AAAT-A
3615412 TT-TATTTTATT
1 TTATATTTTATT
3615423 TAATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 9 0.24
31 21 0.55
32 5 0.13
33 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATATTTTATTATTTTTTATATAAAATA
Found at i:3616109 original size:488 final size:500
Alignment explanation
Indices: 3615292--3616192 Score: 1253
Period size: 488 Copynumber: 1.8 Consensus size: 500
3615282 AGGAAAGGAG
** *
3615292 AGAAAGGAGAAAAGAAGAAAAAGGAACAAAAGAAAGAAGAGAGAAAAATTTATTTGTTTATATTT
1 AGAAAGGAGAAAAGAAGAAAAAGGAACAAAAGAAAGAAGAGAGAAAAATTTAAGTGTTCATATTT
*
3615357 GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTAT
66 GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTTAT
* * * * *
3615422 TTAATATATATTTTTATATGTACGTATATTTATATTATACGTATTTATTTTTATATTATATTTTT
131 TTAATATATATTTTTATATGTACATATATTCATATTATACGCATTTATTTTCATAGTATATTTTT
* *
3615487 AAATATTTTTTATAAATATCGCGTTTATATTATTTTTTTATATTTAAAATAAAATAAATTTATAT
196 AAATATTTTTTATAAACATCGCGTTTATATTAGTTTTTTATATTTAAAATAAAATAAATTTATAT
* * * * * *
3615552 AAATTTTTACATGTTAATTATTTATTTATCTATATTTTAACATATTCGTGTATACATACTATATT
261 AAATTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATATT
* *
3615617 TATATTATTTTTCATGTTATATTTTAATTTTTTATCTATATGTTAAATGTGTATTATATCTCAAT
326 TATATTATCTTTCATGTTATATTTTAATTTTTT-T-TATATGTTAAATGTATATTATATCTCAAT
3615682 TCATGTTATATTTT-ATATAGCTAATCACTATGATTCATATAAAATCAACTACACAAACTAATAT
389 TCATGTTATATTTTGA-ATAGCTAATCACTATGATTCATATAAAATCAACTACACAAACTAATAT
3615746 GGTGCTAACATGTGACTTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
453 GGTGCTAACATGTGACTTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
* *
3615794 AGAAAGGAGAAGAA-AAGAAAGAGGAA-AGAAAGAAA-AAGA-A-AAAATTTTAAGTGTTCATA-
1 AGAAAGGAGAA-AAGAAGAAAAAGGAACA-AAAGAAAGAAGAGAGAAAAATTTAAGTGTTCATAT
*
3615853 TT-TA-TGTTTTTTATTTAAAATATTATATTTTTATAT-TTTTTTACATATTAATAATTTATTTT
64 TTGTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTT
* * * * * **
3615915 ATTTTATGTATA-TTTTATATGTACATGTATTCGTGTTATGTGCATATTATTTTCAT-GT-TA-T
129 ATTTAATATATATTTTTATATGTACATATATTCATATTATACGCAT-TTATTTTCATAGTATATT
* * *
3615976 TTTAAATATTTTTTATAAACATCGTG-TT-TA-T-GTTTTTTATGTTTAAAATAAAATAAATTTT
193 TTTAAATATTTTTTATAAACATCGCGTTTATATTAGTTTTTTATATTTAAAATAAAATAAATTTA
* * * *
3616037 TATAAATTTTTACACGTTAATTATTCATATATCTATATTTTGACATATTCATGCATTCGTACCGT
258 TATAAATTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCAT
* * * *
3616102 GTTTATATTATCTTTCATGTTGTGTTTTAATTTTTTTTATATGTTAAATTTATATTATATCTCAA
323 ATTTATATTATCTTTCATGTTATATTTTAATTTTTTTTATATGTTAAATGTATATTATATCTCAA
*
3616167 TTTATGTTATATTTTGAATAGCTAAT
388 TTCATGTTATATTTTGAATAGCTAAT
3616193 TACCGTGATT
Statistics
Matches: 354, Mismatches: 41, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
486 49 0.14
487 2 0.01
488 114 0.32
489 1 0.00
490 2 0.01
491 2 0.01
492 25 0.07
493 2 0.01
494 26 0.07
495 44 0.12
496 31 0.09
497 2 0.01
498 2 0.01
499 15 0.04
500 1 0.00
501 5 0.01
502 29 0.08
503 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (500 bp):
AGAAAGGAGAAAAGAAGAAAAAGGAACAAAAGAAAGAAGAGAGAAAAATTTAAGTGTTCATATTT
GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTTAT
TTAATATATATTTTTATATGTACATATATTCATATTATACGCATTTATTTTCATAGTATATTTTT
AAATATTTTTTATAAACATCGCGTTTATATTAGTTTTTTATATTTAAAATAAAATAAATTTATAT
AAATTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATATT
TATATTATCTTTCATGTTATATTTTAATTTTTTTTATATGTTAAATGTATATTATATCTCAATTC
ATGTTATATTTTGAATAGCTAATCACTATGATTCATATAAAATCAACTACACAAACTAATATGGT
GCTAACATGTGACTTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
Found at i:3616933 original size:20 final size:17
Alignment explanation
Indices: 3616902--3616980 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
3616892 ATTTATTTGA
3616902 ATAATT-TATTTATCAAATT
1 ATAATTATATTTA--AAA-T
3616921 ATAATTATATTTAAAAT
1 ATAATTATATTTAAAAT
* *
3616938 ATTATAATATTTAAAAT
1 ATAATTATATTTAAAAT
* *
3616955 ATTATTATATTT-ATAT
1 ATAATTATATTTAAAAT
*
3616971 ATATTTATAT
1 ATAATTATAT
3616981 ATATTTATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
16 11 0.21
17 27 0.51
18 3 0.06
19 6 0.11
20 6 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAATTATATTTAAAAT
Found at i:3616948 original size:8 final size:9
Alignment explanation
Indices: 3616927--3616991 Score: 71
Period size: 10 Copynumber: 7.2 Consensus size: 9
3616917 AATTATAATT
*
3616927 ATATTTAAA
1 ATATTTATA
3616936 ATA-TTATA
1 ATATTTATA
*
3616944 ATATTTAAA
1 ATATTTATA
*
3616953 ATA-TTATT
1 ATATTTATA
3616961 ATATTTATA
1 ATATTTATA
3616970 TATATTTATA
1 -ATATTTATA
3616980 TATATTTATA
1 -ATATTTATA
3616990 AT
1 AT
3616992 TAATATTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
8 13 0.27
9 16 0.33
10 19 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATATTTATA
Found at i:3616949 original size:17 final size:17
Alignment explanation
Indices: 3616927--3616987 Score: 77
Period size: 17 Copynumber: 3.4 Consensus size: 17
3616917 AATTATAATT
3616927 ATATTTAAAATATTATA
1 ATATTTAAAATATTATA
*
3616944 ATATTTAAAATATTATT
1 ATATTTAAAATATTATA
*
3616961 ATATTTATATATATTTATA
1 ATATTTA-AAATA-TTATA
3616980 TATATTTA
1 -ATATTTA
3616988 TAATTAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.61
18 4 0.11
19 4 0.11
20 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTTAAAATATTATA
Found at i:3616957 original size:26 final size:26
Alignment explanation
Indices: 3616927--3617024 Score: 62
Period size: 26 Copynumber: 3.8 Consensus size: 26
3616917 AATTATAATT
3616927 ATATTTAAAATATTATAATATTTAAA
1 ATATTTAAAATATTATAATATTTAAA
** *
3616953 ATA-TTATTATATTTATATATATTTATAT
1 ATATTTAAAATA-TTATA-ATATTTA-AA
* * * *
3616981 ATATTTATAAT-TAATATTATAT-AA
1 ATATTTAAAATATTATAATATTTAAA
*
3617005 AT-TTTAAAGTATT-TAATATT
1 ATATTTAAAATATTATAATATT
3617025 ATATTTTTAT
Statistics
Matches: 54, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
23 11 0.20
24 4 0.07
25 6 0.11
26 12 0.22
27 11 0.20
28 4 0.07
29 6 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
ATATTTAAAATATTATAATATTTAAA
Found at i:3617043 original size:17 final size:19
Alignment explanation
Indices: 3617021--3617064 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
3617011 AAGTATTTAA
3617021 TATTATATTT-TTATTT-T
1 TATTATATTTATTATTTCT
3617038 TATTATATTTAATTATTTCT
1 TATTATATTT-ATTATTTCT
3617058 TATTATA
1 TATTATA
3617065 ATGATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
19 6 0.25
20 8 0.33
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTATATTTATTATTTCT
Found at i:3617168 original size:4 final size:4
Alignment explanation
Indices: 3617161--3617196 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
3617151 TTATGTAGTG
*
3617161 AGAA AGAA AGAA AGAA AAAA AGAA AGAA AG-A AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
3617197 AAAAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3617184 original size:16 final size:17
Alignment explanation
Indices: 3617163--3617198 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
3617153 ATGTAGTGAG
3617163 AAAGAAAGAAAGAA-AA
1 AAAGAAAGAAAGAAGAA
3617179 AAAGAAAGAAAGAAGAA
1 AAAGAAAGAAAGAAGAA
3617196 AAA
1 AAA
3617199 AAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAGAAGAA
Found at i:3617201 original size:20 final size:20
Alignment explanation
Indices: 3617161--3617200 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
3617151 TTATGTAGTG
3617161 AGAAAGAAAGAAAGAAAAAA
1 AGAAAGAAAGAAAGAAAAAA
3617181 AGAAAGAAAG-AAGAAAAAA
1 AGAAAGAAAGAAAGAAAAAA
3617200 A
1 A
3617201 AAATTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AGAAAGAAAGAAAGAAAAAA
Found at i:3617279 original size:26 final size:24
Alignment explanation
Indices: 3617229--3617297 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 24
3617219 TATGTTGTAT
3617229 TTATATTTTTTTATTTTTAAAATA
1 TTATATTTTTTTATTTTTAAAATA
* *
3617253 TTATATTTTTGTATATTTTTGACATA
1 TTATATTTTT-T-TATTTTTAAAATA
3617279 TTAATAATTTATTTTATTT
1 TT-AT-ATTT-TTTTATTT
3617298 ATGTATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 13 0.34
27 7 0.18
28 5 0.13
29 2 0.05
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.65
Consensus pattern (24 bp):
TTATATTTTTTTATTTTTAAAATA
Found at i:3617406 original size:17 final size:17
Alignment explanation
Indices: 3617371--3617408 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3617361 TATTATTTAA
3617371 AATATTATAAATTTATGT
1 AATATTATAAA-TTATGT
3617389 AATATTTATAAA-TATGT
1 AATA-TTATAAATTATGT
3617406 AAT
1 AAT
3617409 TATATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATTATAAATTATGT
Found at i:3623093 original size:24 final size:25
Alignment explanation
Indices: 3623046--3623095 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
3623036 CAGATAAATA
3623046 TTTGAAATATATTTAAATTTATATT
1 TTTGAAATATATTTAAATTTATATT
*
3623071 TTTGAAA-A-ATTATAACTTTATATT
1 TTTGAAATATATT-TAAATTTATATT
3623095 T
1 T
3623096 ATGTCGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 3 0.13
24 13 0.57
25 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTGAAATATATTTAAATTTATATT
Found at i:3633472 original size:360 final size:353
Alignment explanation
Indices: 3632744--3633690 Score: 1237
Period size: 360 Copynumber: 2.7 Consensus size: 353
3632734 CAACTCCCTG
* *
3632744 CACATGCTCTGCATCGAGCTTCACTGCCAAATTCCTTGCTTTCACGGATTGCTAGTGGATGCTTG
1 CACATGCTCTGCATCGAACTTCACTGCCAAATTCCTTGCTTTCACGGACTGCTAGTGGATGCTTG
* * * *
3632809 TGGGCGCCATGTTGAATCTTATCAGCATCTTTGGACTCTATC-GTGGGAAGTAAGGCGCATTTGA
66 TGAGCGCAATGTTGAATCTTATCGGCATCTTTGGACT-T-TCAGTCGGAAGTAAGGCGCATTTGA
* * * *
3632873 CATGCAGTTGGAATTTACAATTTACGCAGCAATAGGCCAAGACTGAGCCATCTTCATCACAAGCC
129 CATCCAGTTGGAAATTAC-ATTTACGCAGCAATAGGCCAAGCCTGAGCCAACTTCATCACAA-CC
* * * * *
3632938 TTACACCGGTAAGGAAAGCTG-CTGAGTGC--AATGAGAGGGTGTAGGGGATGAAAGATATGACG
192 TTACACTGGTAAGG-TAGCTGTCTGTGAGCAGAATGAGAGGGTGTAGGGGATGAAAGAGATGACG
** *
3633000 GATTTCTTGTAGTAACTCAACAGCACACGTTCTGTGTAAAAAGAAATCGCATGACCGTTTGACAC
256 GATTTCCAGTAGTAACTCAACAGCACACGTTCTGTGCAAAAAGAAATCGCATGACCGTTTGACAC
3633065 AACCAAAACAGGGGTCTAATAAGCAGTTTTCCC
321 AACCAAAACAGGGGTCTAATAAGCAGTTTTCCC
*
3633098 CACATGCTCTGCATCGAACTTCACTGCCAAATTCCTTGCTTTCACGGAGTGCTAGTGGATGCTTG
1 CACATGCTCTGCATCGAACTTCACTGCCAAATTCCTTGCTTTCACGGACTGCTAGTGGATGCTTG
* * *
3633163 TGAGCGCTATGTTGAATCTTATCGGCATCTTTGGACTTTGCAGTCGGAAGTAAGGCGCACTTGGC
66 TGAGCGCAATGTTGAATCTTATCGGCATCTTTGGACTTT-CAGTCGGAAGTAAGGCGCATTTGAC
* * ** *
3633228 ATCCAGTAGGAAGTTACATGTTGTGCAGCAATAGGCCAAGCCTGAGCCAACTTCTTCACAACCAT
130 ATCCAGTTGGAAATTACAT-TTACGCAGCAATAGGCCAAGCCTGAGCCAACTTCATCACAACC-T
*
3633293 TACACTGGTAGCGGTTAGGCATGTCTGTGAGCAGAATGAGAGGGTGTAGGGGATGAAAGAGATGA
193 TACACTGGTA-AGG-TA-GC-TGTCTGTGAGCAGAATGAGAGGGTGTAGGGGATGAAAGAGATGA
* * * * * *
3633358 TGGATTTCCAGTCGTAACTCAACAGCACACTTTCTGTGCAAAAAGAAGTCGCATGATCTTTTG-C
254 CGGATTTCCAGTAGTAACTCAACAGCACACGTTCTGTGCAAAAAGAAATCGCATGACCGTTTGAC
* * *
3633422 TGCAACCAAAAGAGGGGTCTAATAAGCAAG-TTTCTC
319 -ACAACCAAAACAGGGGTCTAATAAGC-AGTTTTCCC
* * *
3633458 CACATGCTCTGCATCGAACTTCACGGCCAAACTCCTTGCTTTCACGGACTGCTAGTGGATGATTG
1 CACATGCTCTGCATCGAACTTCACTGCCAAATTCCTTGCTTTCACGGACTGCTAGTGGATGCTTG
* *
3633523 TGAGCGCAATGTTGAATCTTATTGGCATCTTTGGACTCTACAGTCGGAAGTAAGGCGCATTTGAC
66 TGAGCGCAATGTTGAATCTTATCGGCATCTTTGGACT-TTCAGTCGGAAGTAAGGCGCATTTGAC
** * * **
3633588 ATCCAGTTGGAAACGACACTTTCCGCAGCGAA-AGGCCAAGCCTGAGCCAGCTTCGCCACAACCC
130 ATCCAGTTGGAAATTACA-TTTACGCAGC-AATAGGCCAAGCCTGAGCCAACTTCATCACAA-CC
3633652 TTACACTGGTAAGGTA-C-GTCTGTGAGCAGAATGAGAGGG
192 TTACACTGGTAAGGTAGCTGTCTGTGAGCAGAATGAGAGGG
3633691 CATGACGGGT
Statistics
Matches: 523, Mismatches: 54, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
352 1 0.00
353 6 0.01
354 199 0.38
355 3 0.01
356 3 0.01
357 2 0.00
358 8 0.02
359 3 0.01
360 290 0.55
361 8 0.02
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (353 bp):
CACATGCTCTGCATCGAACTTCACTGCCAAATTCCTTGCTTTCACGGACTGCTAGTGGATGCTTG
TGAGCGCAATGTTGAATCTTATCGGCATCTTTGGACTTTCAGTCGGAAGTAAGGCGCATTTGACA
TCCAGTTGGAAATTACATTTACGCAGCAATAGGCCAAGCCTGAGCCAACTTCATCACAACCTTAC
ACTGGTAAGGTAGCTGTCTGTGAGCAGAATGAGAGGGTGTAGGGGATGAAAGAGATGACGGATTT
CCAGTAGTAACTCAACAGCACACGTTCTGTGCAAAAAGAAATCGCATGACCGTTTGACACAACCA
AAACAGGGGTCTAATAAGCAGTTTTCCC
Found at i:3641402 original size:21 final size:22
Alignment explanation
Indices: 3641379--3641425 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3641369 AGATTAATAA
3641379 TTTATATTATATAA-ATTTTAAT
1 TTTATA-TATATAACATTTTAAT
* *
3641401 TTTATATATTTAACATTTTTAT
1 TTTATATATATAACATTTTAAT
3641423 TTT
1 TTT
3641426 TTTATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATATATATAACATTTTAAT
Found at i:3641462 original size:25 final size:23
Alignment explanation
Indices: 3641417--3641468 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
3641407 TATTTAACAT
* * *
3641417 TTTTATTTTTTTATTATATTATG
1 TTTTATTTTTTTATAAAATTATA
3641440 TTTTATTTTATTTTATAAAATTATA
1 TTTTA-TTT-TTTTATAAAATTATA
3641465 TTTT
1 TTTT
3641469 TATAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 3 0.12
25 16 0.67
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTTATTTTTTTATAAAATTATA
Found at i:3642051 original size:16 final size:16
Alignment explanation
Indices: 3642027--3642072 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
3642017 TATACTGTCG
*
3642027 ATAAAATAAT-TAGAAT
1 ATAATATAATATAG-AT
3642043 ATAATATAATATAGAT
1 ATAATATAATATAGAT
3642059 ATAATATAAATATA
1 ATAATAT-AATATA
3642073 TTAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
ATAATATAATATAGAT
Found at i:3643316 original size:2 final size:2
Alignment explanation
Indices: 3643309--3643345 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3643299 AAGAGATGAA
3643309 AT AT AT AT AT AT -T AT AT A- 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 AT AT AT AT A
3643346 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3647723 original size:29 final size:29
Alignment explanation
Indices: 3647666--3647723 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3647656 CTTAGGAATG
* *
3647666 TAATTTTAATTACTATTTTAAATATAATT
1 TAATTTTAATTACTATTTTAAAAAAAATT
*
3647695 TAATTTTAATT-TTATTTTTAAAAAAAATT
1 TAATTTTAATTACTA-TTTTAAAAAAAATT
3647724 AATAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (29 bp):
TAATTTTAATTACTATTTTAAAAAAAATT
Found at i:3648131 original size:25 final size:25
Alignment explanation
Indices: 3648087--3648156 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 25
3648077 ATGTATTTAA
*
3648087 AAATAAATATAAAACATAAAT-TTTT
1 AAATAAATATAAAA-TTAAATATTTT
3648112 AAATAAATAATAAAATTAAATATTTT
1 AAATAAAT-ATAAAATTAAATATTTT
3648138 AATATTAAATA-AAAATTAA
1 AA-A-TAAATATAAAATTAA
3648157 TCTTTAACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 13 0.32
26 20 0.50
27 2 0.05
28 5 0.12
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (25 bp):
AAATAAATATAAAATTAAATATTTT
Found at i:3649850 original size:3 final size:3
Alignment explanation
Indices: 3649844--3649868 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3649834 ACAAAAAAAA
3649844 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3649869 GTAGTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3653375 original size:24 final size:21
Alignment explanation
Indices: 3653343--3653386 Score: 52
Period size: 24 Copynumber: 2.0 Consensus size: 21
3653333 GAAAGATTTT
3653343 TAATGAAATTAAAATTCTTATTAC
1 TAATGAAA-T-AAATT-TTATTAC
*
3653367 TAATTAAATAAATTTTATTA
1 TAATGAAATAAATTTTATTA
3653387 AAATAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 5 0.26
23 1 0.05
24 7 0.37
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (21 bp):
TAATGAAATAAATTTTATTAC
Found at i:3653470 original size:18 final size:19
Alignment explanation
Indices: 3653435--3653471 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
3653425 GAATACCTAT
3653435 AATTATTTTTATTAATTCA
1 AATTATTTTTATTAATTCA
3653454 AATT-TTTTT-TTATATTCA
1 AATTATTTTTATTA-ATTCA
3653472 TACTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTATTTTTATTAATTCA
Found at i:3653492 original size:14 final size:14
Alignment explanation
Indices: 3653475--3653508 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3653465 ATATTCATAC
3653475 TTATATATTATAAA
1 TTATATATTATAAA
*
3653489 TTATAGATTATAAA
1 TTATATATTATAAA
3653503 -TATATA
1 TTATATA
3653509 CTCTTAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TTATATATTATAAA
Found at i:3661090 original size:3 final size:3
Alignment explanation
Indices: 3661082--3661124 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3661072 AAATGTCCTT
3661082 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3661125 CATAAGCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3661678 original size:4 final size:4
Alignment explanation
Indices: 3661671--3661723 Score: 106
Period size: 4 Copynumber: 13.2 Consensus size: 4
3661661 TCAATGTGTG
3661671 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
3661719 TGTA T
1 TGTA T
3661724 ACATACATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:3661741 original size:2 final size:2
Alignment explanation
Indices: 3661734--3661783 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3661724 ACATACATAC
3661734 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
3661776 AT AT AT AT
1 AT AT AT AT
3661784 TGAGAGACAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3664358 original size:16 final size:16
Alignment explanation
Indices: 3664315--3664370 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
3664305 CGATTTTTTT
*
3664315 TTAAATAATT-AAATTT
1 TTAAAT-ATTAAAATTA
3664331 TTAAA-A-TAAAA-TA
1 TTAAATATTAAAATTA
3664344 TATAAATATTAAAATTA
1 T-TAAATATTAAAATTA
3664361 TTAAATATTA
1 TTAAATATTA
3664371 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
15 1 0.03
16 19 0.56
17 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATATTAAAATTA
Found at i:3665741 original size:18 final size:19
Alignment explanation
Indices: 3665712--3665750 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3665702 CTGATGATAT
3665712 ATAAAGTTAAAT-ATAATTA
1 ATAAAGTTAAATGAT-ATTA
3665731 ATAAA-TTAAATGATATTA
1 ATAAAGTTAAATGATATTA
3665749 AT
1 AT
3665751 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
ATAAAGTTAAATGATATTA
Found at i:3666683 original size:16 final size:16
Alignment explanation
Indices: 3666662--3666716 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
3666652 ATTATAATCG
3666662 TATTTAAAATATTTTA
1 TATTTAAAATATTTTA
* *
3666678 TATTTATAAAAATTTAA
1 TATTTA-AAATATTTTA
*
3666695 TATATTAATATATTTATA
1 TAT-TTAAAATATTT-TA
3666713 TATT
1 TATT
3666717 CGTATCATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.19
17 18 0.58
18 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTAAAATATTTTA
Found at i:3667274 original size:7 final size:7
Alignment explanation
Indices: 3667257--3667285 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3667247 AACGAATTTT
3667257 AAAAT-A
1 AAAATAA
3667263 AAAATAA
1 AAAATAA
3667270 AAAATAA
1 AAAATAA
3667277 AAAATAA
1 AAAATAA
3667284 AA
1 AA
3667286 CCCTTTCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:3674825 original size:45 final size:45
Alignment explanation
Indices: 3674761--3674847 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
3674751 TCGGTCCATT
* * * *
3674761 TTATAGCCCCTCGTTGATAGTCCTTTTCGCCATCTTGATTGGTAC
1 TTATAGCCCATCGTGGATAGCCCTTGTCGCCATCTTGATTGGTAC
3674806 TTATAGCCCATCGTGGATAGCCCTTGTCGCCATCTTGATTGG
1 TTATAGCCCATCGTGGATAGCCCTTGTCGCCATCTTGATTGG
3674848 CACTGGAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (45 bp):
TTATAGCCCATCGTGGATAGCCCTTGTCGCCATCTTGATTGGTAC
Found at i:3678374 original size:22 final size:22
Alignment explanation
Indices: 3678325--3678390 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 22
3678315 TATAAATTTG
3678325 AATTTAT-TATTTATTATATTA
1 AATTTATATATTTATTATATTA
*
3678346 AA--AATATATTT-TTATATTA
1 AATTTATATATTTATTATATTA
3678365 ATATTTATATA-TTA-TA-ATTA
1 A-ATTTATATATTTATTATATTA
3678385 AATTTA
1 AATTTA
3678391 AATAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
19 16 0.42
20 11 0.29
21 6 0.16
22 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTATATATTTATTATATTA
Found at i:3679032 original size:14 final size:14
Alignment explanation
Indices: 3679007--3679040 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3678997 ACCTTTTAAC
3679007 AAATTT-TTTATTA
1 AAATTTATTTATTA
3679020 AAATTTATTTATTA
1 AAATTTATTTATTA
3679034 AAATTTA
1 AAATTTA
3679041 AATCTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AAATTTATTTATTA
Found at i:3679056 original size:29 final size:29
Alignment explanation
Indices: 3679024--3679079 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3679014 TTATTAAAAT
* *
3679024 TTATTTATTA-AAATTTAAATCTTTATTTA
1 TTATTTAATATAAATATAAAT-TTTATTTA
3679053 TTATTTAATATAAATATAAATTTTATT
1 TTATTTAATATAAATATAAATTTTATT
3679080 ATTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATTTAATATAAATATAAATTTTATTTA
Found at i:3679101 original size:25 final size:26
Alignment explanation
Indices: 3679049--3679107 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
3679039 TAAATCTTTA
* *
3679049 TTTATTATTTAATATAAATATA-AAT
1 TTTATTATTTAAAATAAATAGATAAT
**
3679074 TTTATTATTTAAAATAAATAGATTTT
1 TTTATTATTTAAAATAAATAGATAAT
3679100 TTTATTAT
1 TTTATTAT
3679108 AGATACAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTATTATTTAAAATAAATAGATAAT
Found at i:3682396 original size:26 final size:24
Alignment explanation
Indices: 3682354--3682410 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
3682344 TTATAAAATT
* *
3682354 TTAATAAATTAAATTATGCTATTTTA
1 TTAA-AAAATAAATTAT-ATATTTTA
*
3682380 TTAAAAAATAAACTTATATATTTTC
1 TTAAAAAATAAA-TTATATATTTTA
3682405 TTAAAA
1 TTAAAA
3682411 TTAATGAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (24 bp):
TTAAAAAATAAATTATATATTTTA
Found at i:3683790 original size:2 final size:2
Alignment explanation
Indices: 3683785--3683815 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3683775 TCTCTCTCTC
*
3683785 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3683816 TTCTGCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Done.