Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 179 of 208
Found at i:54692195 original size:19 final size:19
Alignment explanation
Indices: 54692154--54692195 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54692144 AGATTTGTTT
*
54692154 TTTATTTTTGAATTATAGT
1 TTTATTTTTGAATTATAGA
54692173 TTTATTTTATGAATT-TAGA
1 TTTATTTT-TGAATTATAGA
54692192 TTTA
1 TTTA
54692196 AAAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (19 bp):
TTTATTTTTGAATTATAGA
Found at i:54698186 original size:28 final size:27
Alignment explanation
Indices: 54698130--54698191 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
54698120 GTATGCTTTA
**
54698130 ATAAAAAAAATTAAGTACTTAATTGGG
1 ATAAAAAAAATTAAGTACTTAATCAGG
*
54698157 ATAAAAAAATTTTAAGTA-TTAAATCAGG
1 ATAAAAAAA-ATTAAGTACTT-AATCAGG
54698185 ATAAAAA
1 ATAAAAA
54698192 TTTCTCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.29
Consensus pattern (27 bp):
ATAAAAAAAATTAAGTACTTAATCAGG
Found at i:54698614 original size:25 final size:27
Alignment explanation
Indices: 54698586--54698643 Score: 93
Period size: 25 Copynumber: 2.2 Consensus size: 27
54698576 TTAAAAATCT
*
54698586 TTTTCATAAATA-TTTCAAAA-AAAAG
1 TTTTCATAAATATTTTAAAAAGAAAAG
54698611 TTTTCATAAATATTTTAAAAAGAAAAG
1 TTTTCATAAATATTTTAAAAAGAAAAG
54698638 TTTTCA
1 TTTTCA
54698644 AGTAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 12 0.40
26 7 0.23
27 11 0.37
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (27 bp):
TTTTCATAAATATTTTAAAAAGAAAAG
Found at i:54702846 original size:14 final size:14
Alignment explanation
Indices: 54702827--54702853 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54702817 CAGTGCTTAT
54702827 AAAATTTAGTACTA
1 AAAATTTAGTACTA
54702841 AAAATTTAGTACT
1 AAAATTTAGTACT
54702854 TAATTTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAATTTAGTACTA
Found at i:54703503 original size:113 final size:111
Alignment explanation
Indices: 54703304--54703528 Score: 387
Period size: 113 Copynumber: 2.0 Consensus size: 111
54703294 TTTTGTATGA
*
54703304 TGATGGCCACACATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTTACCTT
1 TGATGGCCACACATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACCTT
54703369 TAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
66 TAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
*
54703415 TGATGGCCACACATATATATCTCAAGCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACC
1 TGATGGCCACAC--ATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACC
* * *
54703480 TTTAACTAGTATTTAATGTAAGCTCATCTACATTAGATAAATTATTGT
64 TTTAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
54703528 T
1 T
54703529 TATAATATTT
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 12 0.11
113 95 0.89
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (111 bp):
TGATGGCCACACATATATCTCAACCTAAAGTAAGAAGATTTAAGCAATTCCTATGTATTGACCTT
TAACTACTATTTAACGGAAGCTCATCTACATTAGATAAATTATTGT
Found at i:54707323 original size:2 final size:2
Alignment explanation
Indices: 54707316--54707344 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
54707306 ATTTACTTAG
54707316 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54707345 TAAAGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54716569 original size:18 final size:18
Alignment explanation
Indices: 54716543--54716585 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
54716533 GTTTATGTTA
54716543 AAGTGTCATATATTGGAT
1 AAGTGTCATATATTGGAT
* *
54716561 AAGTTTCATATATTGTAT
1 AAGTGTCATATATTGGAT
54716579 AAGTGTC
1 AAGTGTC
54716586 TTTCTCTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (18 bp):
AAGTGTCATATATTGGAT
Found at i:54721282 original size:49 final size:50
Alignment explanation
Indices: 54721214--54721311 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
54721204 TCTTATAAAG
* * * *
54721214 AACATATGGAAAGCATT-AAACACGTTATGTTCTTTCCAAAAAGAATTAT
1 AACATATGGAAAACATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
*
54721263 AACATATGGAAAACATTAAAAAACATTATATTTTTTCCAAAAAGAATTA
1 AACATATGGAAAACATTAAAAAACATTATATTCTTTCCAAAAAGAATTA
54721312 AAACTACCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 16 0.37
50 27 0.63
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (50 bp):
AACATATGGAAAACATTAAAAAACATTATATTCTTTCCAAAAAGAATTAT
Found at i:54723649 original size:9 final size:9
Alignment explanation
Indices: 54723635--54723662 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
54723625 TGAGTTTTCG
54723635 AATTCGAAT
1 AATTCGAAT
54723644 AATTCGAAT
1 AATTCGAAT
54723653 AATTCGAAT
1 AATTCGAAT
54723662 A
1 A
54723663 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54723737 original size:17 final size:17
Alignment explanation
Indices: 54723715--54723755 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
54723705 CATTTTACTT
54723715 TTCCTTCAAAACTTTTA
1 TTCCTTCAAAACTTTTA
54723732 TTCCTTCAAAACTTTTA
1 TTCCTTCAAAACTTTTA
*
54723749 CTCCTTC
1 TTCCTTC
54723756 CTACTTTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.46
Consensus pattern (17 bp):
TTCCTTCAAAACTTTTA
Found at i:54727433 original size:11 final size:11
Alignment explanation
Indices: 54727417--54727466 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
54727407 TACAAAATTA
54727417 TTTAAAATGTT
1 TTTAAAATGTT
*
54727428 TTTAAATTGTAAT
1 TTTAAAATGT--T
54727441 TTTAAAAATGTT
1 TTT-AAAATGTT
*
54727453 TTTAAAATATT
1 TTTAAAATGTT
54727464 TTT
1 TTT
54727467 GAATAATACT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 19 0.58
12 4 0.12
13 4 0.12
14 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (11 bp):
TTTAAAATGTT
Found at i:54732350 original size:11 final size:11
Alignment explanation
Indices: 54732334--54732409 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
54732324 GATAATCACT
54732334 TTAATATTAAA
1 TTAATATTAAA
54732345 TTAATA--AAA
1 TTAATATTAAA
54732354 -TAATATTAAA
1 TTAATATTAAA
*
54732364 ATAAGTATTAAA
1 TTAA-TATTAAA
54732376 TTTAAT-TTAATA
1 -TTAATATTAA-A
54732388 TTAAATTATTAAA
1 TT-AA-TATTAAA
*
54732401 ATAATATTA
1 TTAATATTA
54732410 TTTTTGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
8 5 0.09
9 3 0.06
10 3 0.06
11 20 0.37
12 13 0.24
13 6 0.11
14 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:54755844 original size:179 final size:179
Alignment explanation
Indices: 54755544--54755901 Score: 562
Period size: 179 Copynumber: 2.0 Consensus size: 179
54755534 AATTATTCTA
* *
54755544 GGGACCCCACAATAAATAACCCAATTTAATTTAAACAAAATATAAAAATTAAATATAAAAAGGGC
1 GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATATAAAAAATAAATATAAAAAGGGC
*
54755609 TAAATTACGGAATAAAGCCCTTTTTTTCAAATTTACGAAAATAGGCCAGTTTTTTTTAAATGACA
66 TAAATTACGGAATAAAGCCCTTTTTTTCAAAATTACGAAAATAGGCCAGTTTTTTTTAAATGACA
* * * *
54755674 TAAATGGGCCGATTTTTCTAAAACGCATCTAACTAGTGTTGTTTTTATG
131 GAAATGGGCCGATTTTGCTAAAACGCATCCAACTAGTGTCGTTTTTATG
54755723 GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATA-AAAAAATAAATAT-AAAA-GGC
1 GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATATAAAAAATAAATATAAAAAGGGC
*
54755785 TAAATTACGGAATAAAGCCCATTTTTTTCAAAATTAC-AGAAATAGGCTAGTTTTTTTTTTAAAT
66 TAAATTACGGAATAAAGCCC-TTTTTTTCAAAATTACGA-AAATAGGCCAG--TTTTTTTTAAAT
**
54755849 GACAGAAATGGGCCGATTTTGCTAAAACGTGTCCAACTAGTGTCGTTTTTATG
127 GACAGAAATGGGCCGATTTTGCTAAAACGCATCCAACTAGTGTCGTTTTTATG
54755902 AGAAAATAAA
Statistics
Matches: 165, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
176 24 0.15
177 29 0.18
178 12 0.07
179 100 0.61
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (179 bp):
GGGACCCCACAATAAATAACCCAAATTAATTTAAACAAAATATAAAAAATAAATATAAAAAGGGC
TAAATTACGGAATAAAGCCCTTTTTTTCAAAATTACGAAAATAGGCCAGTTTTTTTTAAATGACA
GAAATGGGCCGATTTTGCTAAAACGCATCCAACTAGTGTCGTTTTTATG
Found at i:54756131 original size:11 final size:12
Alignment explanation
Indices: 54756117--54756145 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
54756107 ACCCAAATTC
54756117 TATTTTTATT-A
1 TATTTTTATTAA
54756128 TATTTTTATTAA
1 TATTTTTATTAA
54756140 TATTTT
1 TATTTT
54756146 CAAGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTTTATTAA
Found at i:54756306 original size:20 final size:22
Alignment explanation
Indices: 54756260--54756306 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
54756250 CCACTTTTCA
*
54756260 TTTTTATTACTTCTAAAATGTT
1 TTTTTATTACTTCTAAAATATT
* *
54756282 ATTTTATT-C-TCTCAAATATT
1 TTTTTATTACTTCTAAAATATT
54756302 TTTTT
1 TTTTT
54756307 TGTTTAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTATTACTTCTAAAATATT
Found at i:54756910 original size:2 final size:2
Alignment explanation
Indices: 54756903--54756929 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54756893 TCTAAACAAT
54756903 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
54756930 TTATCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54759630 original size:24 final size:24
Alignment explanation
Indices: 54759595--54759645 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
54759585 ACAAAGTTAC
* *
54759595 TTGTTAATGTGTCATAATGTTCTA
1 TTGTTAACGTGTCATAATATTCTA
54759619 TTGTTAACGTGTCATAATATTCTA
1 TTGTTAACGTGTCATAATATTCTA
54759643 TTG
1 TTG
54759646 ATGCTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (24 bp):
TTGTTAACGTGTCATAATATTCTA
Found at i:54760195 original size:93 final size:95
Alignment explanation
Indices: 54760095--54760281 Score: 333
Period size: 93 Copynumber: 2.0 Consensus size: 95
54760085 TTTGTAAAAT
*
54760095 CTAACATTTTGCTAGTAAAGTTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
54760160 ATATCAAATTATTAA-T-TATTAATTGTTA
66 ATATCAAATTATTAATTGTATTAATTGTTA
* *
54760188 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
54760253 ATATCAAATTATTAATTGTATTAATTGTT
66 ATATCAAATTATTAATTGTATTAATTGTT
54760282 GTAACAAAAT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 77 0.87
94 1 0.01
95 11 0.12
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (95 bp):
CTAACATTTTGCTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTACTAAAATTATCAAATT
ATATCAAATTATTAATTGTATTAATTGTTA
Found at i:54760220 original size:19 final size:19
Alignment explanation
Indices: 54760196--54760246 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
54760186 TACTAACATT
54760196 TTGTTAGTAAAATTATTAA
1 TTGTTAGTAAAATTATTAA
*
54760215 TTG-T--T-AATTGTATTAA
1 TTGTTAGTAAAAT-TATTAA
54760231 TTGTTAGTAAAATTAT
1 TTGTTAGTAAAATTAT
54760247 CAAATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
15 3 0.12
16 10 0.40
17 1 0.04
18 1 0.04
19 7 0.28
20 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
TTGTTAGTAAAATTATTAA
Found at i:54769092 original size:21 final size:19
Alignment explanation
Indices: 54769049--54769097 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
54769039 TGATTGAACC
54769049 AATTTTTTTATTTTTAAAT
1 AATTTTTTTATTTTTAAAT
*
54769068 -ATTTTTTTATGATTTTTAAT
1 AATTTTTTTAT--TTTTAAAT
*
54769088 AATTTATTTA
1 AATTTTTTTA
54769098 ATAGAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
AATTTTTTTATTTTTAAAT
Found at i:54770259 original size:19 final size:18
Alignment explanation
Indices: 54770235--54770274 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54770225 GAAATTTTGG
54770235 AATGGAAAAGAAGAGAGAA
1 AATGG-AAAGAAGAGAGAA
* *
54770254 AATGGAGAGAAGAGAGGA
1 AATGGAAAGAAGAGAGAA
54770272 AAT
1 AAT
54770275 ATGTGAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.07
Consensus pattern (18 bp):
AATGGAAAGAAGAGAGAA
Found at i:54772808 original size:10 final size:10
Alignment explanation
Indices: 54772795--54772825 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
54772785 ATATATATAT
54772795 ATATATCACA
1 ATATATCACA
54772805 ATATATCACA
1 ATATATCACA
*
54772815 CTATATCACA
1 ATATATCACA
54772825 A
1 A
54772826 GACTTGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (10 bp):
ATATATCACA
Found at i:54775765 original size:24 final size:24
Alignment explanation
Indices: 54775737--54775783 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
54775727 GAGATAAAAA
54775737 ATGG-TTTGAAAAAAAATAAATGAG
1 ATGGTTTTG-AAAAAAATAAATGAG
54775761 ATGGTTTTGAAAAAAATAAATGA
1 ATGGTTTTGAAAAAAATAAATGA
54775784 TCAACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (24 bp):
ATGGTTTTGAAAAAAATAAATGAG
Found at i:54777975 original size:45 final size:46
Alignment explanation
Indices: 54777926--54778022 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
54777916 TTGTAATTGA
* *
54777926 AATTTTCAAGTTTGT-ATTAATTTAATTATAACAACTATTTGGCTT
1 AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATATTTGACTT
* *
54777971 AATTTTCAAGTTTGTAATTAATTTAATTATAGCAAATGTTTGACTT
1 AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATATTTGACTT
54778017 AATTTT
1 AATTTT
54778023 ATTTGAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 15 0.32
46 32 0.68
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.49
Consensus pattern (46 bp):
AATTTTCAAGTTTGTAATTAATTTAATTATAACAAATATTTGACTT
Found at i:54789029 original size:2 final size:2
Alignment explanation
Indices: 54789022--54789058 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54789012 AGAGTAAAAG
54789022 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54789059 TATTTACTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54805488 original size:21 final size:20
Alignment explanation
Indices: 54805462--54805500 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54805452 TAAGGTAGTT
54805462 TTGAAATGGAAAAGTATTGAA
1 TTGAAAT-GAAAAGTATTGAA
*
54805483 TTGAAATGTAAAGTATTG
1 TTGAAATGAAAAGTATTG
54805501 CATGGAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGAAATGAAAAGTATTGAA
Found at i:54807387 original size:18 final size:18
Alignment explanation
Indices: 54807364--54807424 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 18
54807354 ACTCCCCCTA
*
54807364 TTTACTTTCCCTCAAACT
1 TTTACTTTCCCTAAAACT
54807382 TTTAC--TCCCTAAAACTT
1 TTTACTTTCCCTAAAAC-T
* *
54807399 TTTATCTTCCCCTTAAACT
1 TTTA-CTTTCCCTAAAACT
54807418 TTTACTT
1 TTTACTT
54807425 CTCACCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.25
17 5 0.14
18 9 0.25
19 5 0.14
20 8 0.22
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTACTTTCCCTAAAACT
Found at i:54808152 original size:20 final size:20
Alignment explanation
Indices: 54808110--54808150 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
54808100 TACAACACAA
*
54808110 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
54808130 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
54808149 TT
1 TT
54808151 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:54809528 original size:12 final size:12
Alignment explanation
Indices: 54809503--54809541 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54809493 ACTCGCTTCT
* *
54809503 TTACTTACTCAC
1 TTACTTGCTTAC
*
54809515 TTACTTGTTTAC
1 TTACTTGCTTAC
54809527 TTACTTGCTTAC
1 TTACTTGCTTAC
54809539 TTA
1 TTA
54809542 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:54809821 original size:49 final size:49
Alignment explanation
Indices: 54809758--54809982 Score: 168
Period size: 50 Copynumber: 4.4 Consensus size: 49
54809748 GCTATGTCCT
* * *
54809758 AGACATAGTCTTACATGGGATGTTTTC-TGTAC-TGCCAATGCCATATCCC
1 AGACATGGTCTTACATGGGA-GTTCTCATAT-CGTGCCAATGCCATATCCC
* * *
54809807 AGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCC
1 AGACATGGTCTTACATGGGAGTTCTCATATC-GTGCCAATGCCATATCCC
* ** * * * *
54809857 AGACATGGTCTTAC-GGGGAACCTCTCATCTCGATGCCAACGCCATGTCCT
1 AGACATGGTCTTACATGGG-AGTTCTCATATCG-TGCCAATGCCATATCCC
** * *
54809907 AGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCTAATGCCATGTCCC
1 AGACATGGTCTTACATGGGAGTTCTCAT-A--TC---G-TGCCAATGCCATATCCC
54809963 AGACATGGTCTTACATGGGA
1 AGACATGGTCTTACATGGGA
54809983 TCCCATTCCT
Statistics
Matches: 145, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
48 6 0.04
49 24 0.17
50 74 0.51
51 3 0.02
53 2 0.01
56 36 0.25
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (49 bp):
AGACATGGTCTTACATGGGAGTTCTCATATCGTGCCAATGCCATATCCC
Found at i:54809858 original size:50 final size:50
Alignment explanation
Indices: 54809790--54809982 Score: 217
Period size: 50 Copynumber: 3.7 Consensus size: 50
54809780 TTTTCTGTAC
* * ** *
54809790 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
* * *
54809840 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATATCGA
* *
54809890 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GA
*
54809946 TGCTAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
54809983 TCCCATTCCT
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 75 0.63
51 3 0.03
53 2 0.02
56 36 0.30
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGA
Found at i:54809918 original size:100 final size:103
Alignment explanation
Indices: 54809790--54809976 Score: 245
Period size: 100 Copynumber: 1.8 Consensus size: 103
54809780 TTTTCTGTAC
* * ** * *
54809790 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCAT-A-TC-GGTGCCCATGCCAT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
54809852 GTCCCAGACATGGTCTTACGGGGAACCTCTCATCTCGA
66 GTCCCAGACATGGTCTTACGGGGAACCTCTCATCTCGA
* * *
54809890 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCTAATGC
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATAA-CTC-A-GATGCCAATGC
54809955 CATGTCCCAGACATGGTCTTAC
63 CATGTCCCAGACATGGTCTTAC
54809977 ATGGGATCCC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 39 0.54
101 1 0.01
103 2 0.03
106 30 0.42
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (103 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATAACTCAGATGCCAATGCCAT
GTCCCAGACATGGTCTTACGGGGAACCTCTCATCTCGA
Found at i:54813147 original size:15 final size:15
Alignment explanation
Indices: 54813127--54813162 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54813117 TTATACTGTT
*
54813127 ACATTCTTGGTAATC
1 ACATTCTTGGCAATC
54813142 ACATTCTTGGCAATC
1 ACATTCTTGGCAATC
*
54813157 ATATTC
1 ACATTC
54813163 CCTTGGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (15 bp):
ACATTCTTGGCAATC
Found at i:54813948 original size:9 final size:9
Alignment explanation
Indices: 54813934--54813958 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54813924 CAAATCAAAG
54813934 AAAAGAGAA
1 AAAAGAGAA
54813943 AAAAGAGAA
1 AAAAGAGAA
54813952 AAAAGAG
1 AAAAGAG
54813959 GGATTCGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAGAGAA
Found at i:54814362 original size:11 final size:11
Alignment explanation
Indices: 54814346--54814374 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
54814336 GAGCTCTCTG
54814346 TTTTTTTTTCT
1 TTTTTTTTTCT
54814357 TTTTTTTTTCT
1 TTTTTTTTTCT
54814368 TTTTTTT
1 TTTTTTT
54814375 CGTTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:54822231 original size:22 final size:22
Alignment explanation
Indices: 54822195--54822302 Score: 144
Period size: 22 Copynumber: 4.9 Consensus size: 22
54822185 TTCGTAAATT
54822195 CGTACTAAGCTCTCATGTTTAA
1 CGTACTAAGCTCTCATGTTTAA
* * * **
54822217 CGAACTAAACCCTCATGGCTAA
1 CGTACTAAGCTCTCATGTTTAA
**
54822239 CGTACTAAGCTCTCATGGCTAA
1 CGTACTAAGCTCTCATGTTTAA
*
54822261 CGTACTAAGCTCTCATGTTTCA
1 CGTACTAAGCTCTCATGTTTAA
54822283 CGTACTAAGCTCTCATGTTT
1 CGTACTAAGCTCTCATGTTT
54822303 GAACAATAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (22 bp):
CGTACTAAGCTCTCATGTTTAA
Found at i:54824835 original size:15 final size:15
Alignment explanation
Indices: 54824808--54824840 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54824798 ATATTTGGTA
54824808 ATTATGCATTGAATTG
1 ATTATGCATTGAA-TG
54824824 ATTATG-ATTGAATG
1 ATTATGCATTGAATG
54824838 ATT
1 ATT
54824841 CATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (15 bp):
ATTATGCATTGAATG
Found at i:54827196 original size:5 final size:5
Alignment explanation
Indices: 54827169--54827236 Score: 81
Period size: 5 Copynumber: 14.2 Consensus size: 5
54827159 TTTTTATGTT
*
54827169 TTATA -TATA TTAT- TT-TA TTATA TAATA -TATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
*
54827215 TTATA TTATTT TTATA TTATA T
1 TTATA TTA-TA TTATA TTATA T
54827237 AAATTAAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
3 1 0.02
4 11 0.20
5 38 0.70
6 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:54827197 original size:24 final size:24
Alignment explanation
Indices: 54827170--54827238 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
54827160 TTTTATGTTT
54827170 TATATATATTATTTTATTATATAA
1 TATATATATTATTTTATTATATAA
*
54827194 TATATAT-TATATTATATTATAT--
1 TATATATAT-TATTTTATTATATAA
54827216 TATAT-TATT-TTTATATTATATAA
1 TATATATATTATTT-TATTATATAA
54827239 ATTAAATAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 6 0.16
23 1 0.03
24 19 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TATATATATTATTTTATTATATAA
Found at i:54828474 original size:24 final size:26
Alignment explanation
Indices: 54828447--54828515 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
54828437 GTGAATTTGT
*
54828447 GAAATAATTATTG-ATTGAAAG-GTG-
1 GAAA-AATGATTGAATTGAAAGTGTGA
54828471 GAAAAATGATTGAATTGAAAGTGTGA
1 GAAAAATGATTGAATTGAAAGTGTGA
**
54828497 GAAACTGTGATTGAATTGA
1 GAAA-AATGATTGAATTGA
54828516 GAATATATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 7 0.18
24 12 0.32
25 3 0.08
26 4 0.11
27 12 0.32
ACGTcount: A:0.42, C:0.01, G:0.26, T:0.30
Consensus pattern (26 bp):
GAAAAATGATTGAATTGAAAGTGTGA
Found at i:54831245 original size:40 final size:41
Alignment explanation
Indices: 54831154--54831261 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 41
54831144 AGCGGCACTT
*
54831154 TTAGCGGCGTTTGGAGCAAAAACGCTGCTAAAAATCGAGAA
1 TTAGCGGCGTTTGGAGCAAAAACGCCGCTAAAAATCGAGAA
* * * * * *
54831195 ATAGCAGCGTTT-TAGGAAAAGCGCCGCTAAAAAGT-GAGCA
1 TTAGCGGCGTTTGGAGCAAAAACGCCGCTAAAAA-TCGAGAA
* *
54831235 TTAGCGGCGTTTAGA-AAAAAACGCCGC
1 TTAGCGGCGTTTGGAGCAAAAACGCCGC
54831262 AAATAATACA
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
40 41 0.77
41 12 0.23
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGTTTGGAGCAAAAACGCCGCTAAAAATCGAGAA
Found at i:54832244 original size:2 final size:2
Alignment explanation
Indices: 54832239--54832273 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54832229 AAAAAATCCC
54832239 AT AT 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 A
54832274 CACTTGTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54835907 original size:13 final size:13
Alignment explanation
Indices: 54835889--54835983 Score: 61
Period size: 13 Copynumber: 7.2 Consensus size: 13
54835879 GTTAATTTGG
54835889 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
54835902 TTAAATATGTTAC
1 TTAAATTTATTAC
54835915 TTAAATGCATTACTTAC
1 TTAAAT---TTA-TTAC
* *
54835932 TAAAATTT-GT--
1 TTAAATTTATTAC
54835942 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
54835955 TTAAATATGTTAC
1 TTAAATTTATTAC
**
54835968 TTAAATACATTAC
1 TTAAATTTATTAC
54835981 TTA
1 TTA
54835984 CTAAAAATTA
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 7 0.11
11 1 0.02
12 1 0.02
13 42 0.67
14 2 0.03
16 1 0.02
17 9 0.14
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:54835919 original size:26 final size:26
Alignment explanation
Indices: 54835889--54835983 Score: 102
Period size: 26 Copynumber: 3.6 Consensus size: 26
54835879 GTTAATTTGG
*
54835889 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTCATTACTTAAATATGTTAC
* * **
54835915 TTAAATGCATTACTTACTAAAAT-TTGT
1 TTAAATTCATTACTTA--AATATGTTAC
*
54835942 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTCATTACTTAAATATGTTAC
*
54835968 TTAAATACATTACTTA
1 TTAAATTCATTACTTA
54835984 CTAAAAATTA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
25 4 0.07
26 30 0.56
27 16 0.30
28 4 0.07
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (26 bp):
TTAAATTCATTACTTAAATATGTTAC
Found at i:54835962 original size:53 final size:53
Alignment explanation
Indices: 54835882--54835989 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
54835872 TTTGTAAGTT
*
54835882 AATTTGGTTAAATTTATTACTTAAATATGTTACTTAAATGCATTACTTACTAA
1 AATTTGGTTAAATTTATTACTTAAATATGTTACTTAAATACATTACTTACTAA
*
54835935 AATTTGTTTAAATTTATTACTTAAATATGTTACTTAAATACATTACTTACTAA
1 AATTTGGTTAAATTTATTACTTAAATATGTTACTTAAATACATTACTTACTAA
54835988 AA
1 AA
54835990 ATTAAGTATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (53 bp):
AATTTGGTTAAATTTATTACTTAAATATGTTACTTAAATACATTACTTACTAA
Found at i:54836208 original size:16 final size:16
Alignment explanation
Indices: 54836187--54836241 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
54836177 CTTATATGTA
54836187 AACTTACATAATACAT
1 AACTTACATAATACAT
*
54836203 AACTTACAT-GT---T
1 AACTTACATAATACAT
*
54836215 ACCTTACATAATACAT
1 AACTTACATAATACAT
*
54836231 AACTTATATAA
1 AACTTACATAA
54836242 AATTTTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
12 9 0.30
13 1 0.03
15 1 0.03
16 19 0.63
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:54836333 original size:9 final size:9
Alignment explanation
Indices: 54836315--54836649 Score: 244
Period size: 9 Copynumber: 38.8 Consensus size: 9
54836305 CTTGTGGTTA
*
54836315 AACTTGCAT
1 AACTTACAT
54836324 AACTTACAT
1 AACTTACAT
*
54836333 AA-TAACAT
1 AACTTACAT
54836341 AACAACTTACAT
1 ---AACTTACAT
54836353 AA--TACAT
1 AACTTACAT
*
54836360 AACATACAT
1 AACTTACAT
54836369 AACTTACAT
1 AACTTACAT
*
54836378 AACTTATAT
1 AACTTACAT
*
54836387 AA--TACAA
1 AACTTACAT
54836394 AACTTACAT
1 AACTTACAT
*
54836403 AACTTAAAT
1 AACTTACAT
* *
54836412 ATCTTACAC
1 AACTTACAT
54836421 AACTTACAT
1 AACTTACAT
*
54836430 AACCTACAT
1 AACTTACAT
54836439 AA--TACAT
1 AACTTACAT
54836446 AACTTACAT
1 AACTTACAT
*
54836455 AATACATA-AT
1 -A-ACTTACAT
54836465 AACTTAC--
1 AACTTACAT
54836472 AACTTACAT
1 AACTTACAT
*
54836481 AACATACAT
1 AACTTACAT
* **
54836490 TACTTTGAT
1 AACTTACAT
54836499 AACTTACAT
1 AACTTACAT
*
54836508 AAGTTACAT
1 AACTTACAT
54836517 AA--TACAT
1 AACTTACAT
54836524 AACTTAC--
1 AACTTACAT
54836531 AACTTACAT
1 AACTTACAT
*
54836540 AACATACAT
1 AACTTACAT
* **
54836549 TACTTTGAT
1 AACTTACAT
54836558 AACTTACAT
1 AACTTACAT
*
54836567 AAGTTACAT
1 AACTTACAT
54836576 AA-TATAC--
1 AACT-TACAT
54836583 AACTTACAT
1 AACTTACAT
* *
54836592 AGCTTACTT
1 AACTTACAT
54836601 AA--TACAT
1 AACTTACAT
54836608 AACTTACAT
1 AACTTACAT
54836617 AACTT--AT
1 AACTTACAT
*
54836624 ACACGTACAT
1 A-ACTTACAT
54836634 AACTTACAT
1 AACTTACAT
*
54836643 AATTTAC
1 AACTTAC
54836650 TTAATACATA
Statistics
Matches: 256, Mismatches: 42, Indels: 56
0.72 0.12 0.16
Matches are distributed among these distances:
7 54 0.21
8 14 0.05
9 171 0.67
10 6 0.02
11 6 0.02
12 5 0.02
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:54836369 original size:16 final size:16
Alignment explanation
Indices: 54836321--54836660 Score: 169
Period size: 16 Copynumber: 20.3 Consensus size: 16
54836311 GTTAAACTTG
54836321 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
54836338 CATAACAACTTACATAATA
1 CAT---AACTTACATAATA
*
54836357 CATAACATACATAACTTA
1 CATAACTTACATAA--TA
*
54836375 CATAACTTATATAATA
1 CATAACTTACATAATA
*
54836391 CAAAACTTACATAACTTA
1 CATAACTTACATAA--TA
* * *
54836409 AATATCTTACACAACTTA
1 CATAACTTACATAA--TA
*
54836427 CATAACCTACATAATA
1 CATAACTTACATAATA
54836443 CATAACTTACATAATA
1 CATAACTTACATAATA
*
54836459 CATAA-TAAC-T--TA
1 CATAACTTACATAATA
54836471 C--AACTTACATAACATA
1 CATAACTTACAT-A-ATA
* **
54836487 CATTACTTTGATAACTTA
1 CATAACTTACATAA--TA
*
54836505 CATAAGTTACATAATA
1 CATAACTTACATAATA
*
54836521 CATAACTTACA-ACTTA
1 CATAACTTACATA-ATA
* * *
54836537 CATAACATACATTACTTT
1 CATAACTTACA-TA-ATA
*
54836555 GATAACTTACATAAGTTA
1 CATAACTTACATAA--TA
*
54836573 CATAA-TATACA-ACTTA
1 CATAACT-TACATA-ATA
* *
54836589 CATAGCTTACTTAATA
1 CATAACTTACATAATA
54836605 CATAACTTACATAACT-
1 CATAACTTACATAA-TA
* *
54836621 TATACACGTACATAACTTA
1 CATA-ACTTACATAA--TA
* *
54836640 CATAATTTACTTAATA
1 CATAACTTACATAATA
54836656 CATAA
1 CATAA
54836661 ATTATGTAAC
Statistics
Matches: 248, Mismatches: 45, Indels: 61
0.70 0.13 0.17
Matches are distributed among these distances:
10 2 0.01
11 3 0.01
12 4 0.02
14 1 0.00
15 4 0.02
16 107 0.43
17 20 0.08
18 88 0.35
19 7 0.03
20 12 0.05
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:54836376 original size:25 final size:26
Alignment explanation
Indices: 54836334--54836577 Score: 152
Period size: 25 Copynumber: 9.5 Consensus size: 26
54836324 AACTTACATA
*
54836334 ATAACATA-ACAACTTACATAA-TAC
1 ATAACATACATAACTTACATAACTAC
*
54836358 ATAACATACATAACTTACATAACT-T
1 ATAACATACATAACTTACATAACTAC
* *
54836383 ATATA-ATACAAAACTTACATAACTTAA
1 ATA-ACATACATAACTTACATAAC-TAC
* * *
54836410 ATATCTTACACAACTTACATAACCTAC
1 ATAACATACATAACTTACATAA-CTAC
54836437 AT-A-ATACATAACTTACATAA-TAC
1 ATAACATACATAACTTACATAACTAC
* *
54836460 ATAATA-ACTTACAACTTACATAACATAC
1 ATAACATAC--ATAACTTACATAAC-TAC
* * ** *
54836488 ATTACTTTGATAACTTACATAAGTTAC
1 ATAACATACATAACTTACATAA-CTAC
54836515 AT-A-ATACATAACTTAC--AACTTAC
1 ATAACATACATAACTTACATAAC-TAC
* **
54836538 ATAACATACATTACTTTGATAACTTAC
1 ATAACATACATAACTTACATAAC-TAC
**
54836565 ATAAGTTACATAA
1 ATAACATACATAA
54836578 TATACAACTT
Statistics
Matches: 171, Mismatches: 29, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
23 12 0.07
24 12 0.07
25 68 0.40
26 16 0.09
27 56 0.33
28 7 0.04
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.32
Consensus pattern (26 bp):
ATAACATACATAACTTACATAACTAC
Found at i:54836539 original size:78 final size:73
Alignment explanation
Indices: 54836342--54836541 Score: 197
Period size: 78 Copynumber: 2.6 Consensus size: 73
54836332 TAATAACATA
* *
54836342 ACAACTTACATAATACATAACATACATAACTTACATAACTTATATAATACAAAACTTACATAACT
1 ACAACTTACATAATACAT-A-ATACATAACTTAC--AACTTACATAATACAAAACTTACATAACA
54836407 TAAATATCTTAC
62 TAAATATCTTAC
* *
54836419 ACAACTTACATAACCTACATAATACATAACTTACATA-ATACATAATAACTTACAACTTACATAA
1 ACAACTTACATAA--TACATAATACATAACTTACA-ACTTACATAAT-AC--AAAACTTACATAA
* **
54836483 CATACAT-TACTTTG
60 CATAAATAT-CTTAC
*
54836497 ATAACTTACATAAGTTACATAATACATAACTTACAACTTACATAA
1 ACAACTTACATAA--TACATAATACATAACTTACAACTTACATAA
54836542 CATACATTAC
Statistics
Matches: 104, Mismatches: 11, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
75 8 0.08
76 3 0.03
77 28 0.27
78 60 0.58
79 5 0.05
ACGTcount: A:0.48, C:0.20, G:0.01, T:0.31
Consensus pattern (73 bp):
ACAACTTACATAATACATAATACATAACTTACAACTTACATAATACAAAACTTACATAACATAAA
TATCTTAC
Found at i:54836592 original size:25 final size:25
Alignment explanation
Indices: 54836511--54836618 Score: 80
Period size: 25 Copynumber: 4.3 Consensus size: 25
54836501 CTTACATAAG
54836511 TTACATAA--TACATAACT-TACAAC
1 TTACATAAGTTACATAA-TATACAAC
** * * *
54836534 TTACATAACATACATTACTTTGATAAC
1 TTACATAAGTTACA-TAATAT-ACAAC
54836561 TTACATAAGTTACATAATATACAAC
1 TTACATAAGTTACATAATATACAAC
* * *
54836586 TTACAT-AGCTTACTTAATACATAAC
1 TTACATAAG-TTACATAATATACAAC
54836611 TTACATAA
1 TTACATAA
54836619 CTTATACACG
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
23 8 0.12
24 2 0.03
25 34 0.50
26 8 0.12
27 16 0.24
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (25 bp):
TTACATAAGTTACATAATATACAAC
Found at i:54836607 original size:59 final size:59
Alignment explanation
Indices: 54836441--54836590 Score: 246
Period size: 59 Copynumber: 2.5 Consensus size: 59
54836431 ACCTACATAA
*
54836441 TACATAACTTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGATAACT
1 TACATAAGTTACATAAT--AT-ATAACTTACAACTTACATAACATACATTACTTTGATAACT
*
54836503 TACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTACTTTGATAACT
1 TACATAAGTTACATAATATATAACTTACAACTTACATAACATACATTACTTTGATAACT
*
54836562 TACATAAGTTACATAATATACAACTTACA
1 TACATAAGTTACATAATATATAACTTACA
54836591 TAGCTTACTT
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
59 67 0.80
60 1 0.01
62 16 0.19
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (59 bp):
TACATAAGTTACATAATATATAACTTACAACTTACATAACATACATTACTTTGATAACT
Found at i:54836619 original size:59 final size:59
Alignment explanation
Indices: 54836315--54836622 Score: 245
Period size: 59 Copynumber: 5.1 Consensus size: 59
54836305 CTTGTGGTTA
* * *
54836315 AACTTGCATAACTTACATAATAACATAACAACTTACATA-ATACATAACATACATAACTTACAT
1 AACTTACATAAGTTACATAAT---AT-ACAACTTACA-ACTTACATAACATACATAACTTACAT
* * * * * *
54836378 AACTTATATAA--TACAAAACT-TACATAACTTAAATATCTTACACAACTTACATAACCTACAT
1 AACTTACATAAGTTACATAA-TATAC--AACTTACA-A-CTTACATAACATACATAACTTACAT
* * * **
54836439 AA--TACATAACTTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGAT
1 AACTTACATAAGTTACATAAT--AT-ACAACTTACAACTTACATAACATACATAACTTACAT
* * * **
54836499 AACTTACATAAGTTACATAATACATAACTTACAACTTACATAACATACATTACTTTGAT
1 AACTTACATAAGTTACATAATATACAACTTACAACTTACATAACATACATAACTTACAT
*
54836558 AACTTACATAAGTTACATAATATACAACTTACATAGCTTAC-TTA-ATACATAACTTACAT
1 AACTTACATAAGTTACATAATATACAACTTACA-A-CTTACATAACATACATAACTTACAT
54836617 AACTTA
1 AACTTA
54836623 TACACGTACA
Statistics
Matches: 204, Mismatches: 26, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
57 2 0.01
58 1 0.00
59 100 0.49
60 26 0.13
61 40 0.20
62 24 0.12
63 10 0.05
64 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (59 bp):
AACTTACATAAGTTACATAATATACAACTTACAACTTACATAACATACATAACTTACAT
Found at i:54836622 original size:25 final size:25
Alignment explanation
Indices: 54836556--54836660 Score: 115
Period size: 25 Copynumber: 4.2 Consensus size: 25
54836546 CATTACTTTG
* * *
54836556 ATAACTTACATAAGTTACATAATAT
1 ATAACTTACATAACTTACTTAATAC
* *
54836581 ACAACTTACATAGCTTACTTAATAC
1 ATAACTTACATAACTTACTTAATAC
54836606 ATAACTTACATAACTTA--TACACGTAC
1 ATAACTTACATAACTTACTTA-A--TAC
*
54836632 ATAACTTACATAATTTACTTAATAC
1 ATAACTTACATAACTTACTTAATAC
54836657 ATAA
1 ATAA
54836661 ATTATGTAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.03
24 1 0.01
25 42 0.63
26 19 0.28
27 1 0.01
28 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (25 bp):
ATAACTTACATAACTTACTTAATAC
Found at i:54842223 original size:21 final size:21
Alignment explanation
Indices: 54842197--54842244 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
54842187 CAACAACTTA
*
54842197 AAGCAGAGGC-GACAGCGAGGG
1 AAGCAGAGGCTG-CAGCGAGAG
54842218 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
54842239 AAGCAG
1 AAGCAG
54842245 CGAGAGAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:54842246 original size:12 final size:12
Alignment explanation
Indices: 54842229--54842256 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
54842219 AGCAGAGGCT
54842229 GCAGCGAGAGAA
1 GCAGCGAGAGAA
54842241 GCAGCGAGAGAA
1 GCAGCGAGAGAA
54842253 GCAG
1 GCAG
54842257 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:54843956 original size:9 final size:9
Alignment explanation
Indices: 54843942--54843972 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54843932 GTTAAACGAA
54843942 TCGAGTTAT
1 TCGAGTTAT
*
54843951 TCGAGTTAA
1 TCGAGTTAT
54843960 TCGAGTTAT
1 TCGAGTTAT
54843969 TCGA
1 TCGA
54843973 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:54850960 original size:26 final size:26
Alignment explanation
Indices: 54850931--54850980 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54850921 AAAATATATA
*
54850931 TTTATATT-TAATTATTTTATATATTT
1 TTTAT-TTATAATGATTTTATATATTT
*
54850957 TTTATTTATTATGATTTTATATAT
1 TTTATTTATAATGATTTTATATAT
54850981 AGTCATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTATTTATAATGATTTTATATATTT
Found at i:54856770 original size:41 final size:42
Alignment explanation
Indices: 54856687--54856791 Score: 149
Period size: 41 Copynumber: 2.5 Consensus size: 42
54856677 TGCGGCGTTT
* *
54856687 TTATAGAACATGACCTTTAGCAGTGCTTTTCCCACAAACACCG
1 TTATAAAACATGACCTTTAGCAAT-CTTTTCCCACAAACACCG
*
54856730 TTATAAAACATGACCTTTAGGAAT-TTTTCCCACAAACACCG
1 TTATAAAACATGACCTTTAGCAATCTTTTCCCACAAACACCG
* *
54856771 CTATAAAATATGACCTTTAGC
1 TTATAAAACATGACCTTTAGC
54856792 GAAAATAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 35 0.62
43 21 0.38
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (42 bp):
TTATAAAACATGACCTTTAGCAATCTTTTCCCACAAACACCG
Found at i:54857853 original size:14 final size:14
Alignment explanation
Indices: 54857820--54857859 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
54857810 AAAAATAGGC
*
54857820 ATTGGGGGTAACTGA
1 ATTGGGGG-AAATGA
*
54857835 TTTGGGGGAAATGA
1 ATTGGGGGAAATGA
54857849 ATTGGGGGAAA
1 ATTGGGGGAAA
54857860 AAGGGGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.30, C:0.03, G:0.42, T:0.25
Consensus pattern (14 bp):
ATTGGGGGAAATGA
Found at i:54865138 original size:43 final size:43
Alignment explanation
Indices: 54865075--54865202 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 43
54865065 GGATCTCTGG
* *
54865075 TATGTGTTTTCGTATAAGACCACGTCTGGGACGTTGGCATTGA
1 TATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATTGA
*
54865118 CT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA
1 -TATGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATTGA
* * * *
54865161 TATGTGATTACATGTAAGACCACGTCTAGGACGTTGGTATTG
1 TATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATTG
54865203 TACGAGCTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
42 3 0.04
43 65 0.92
44 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATTGA
Found at i:54866500 original size:2 final size:2
Alignment explanation
Indices: 54866493--54866533 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
54866483 ACGGACATGT
54866493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54866534 TAGTGATGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54872403 original size:24 final size:24
Alignment explanation
Indices: 54872376--54872426 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
54872366 AGCCTATAAC
*
54872376 GGGTAGCTCCAAAGAGTAATTAAT
1 GGGTAGCTCCAAAGAGCAATTAAT
*
54872400 GGGTAGCTCCGAAGAGCAATTAAT
1 GGGTAGCTCCAAAGAGCAATTAAT
54872424 GGG
1 GGG
54872427 AAGTACCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (24 bp):
GGGTAGCTCCAAAGAGCAATTAAT
Found at i:54879511 original size:17 final size:17
Alignment explanation
Indices: 54879436--54879512 Score: 51
Period size: 17 Copynumber: 4.8 Consensus size: 17
54879426 TTTGAAATGT
54879436 TTAGAAATTAAA-T-AA
1 TTAGAAATTAAATTAAA
54879451 TT-GAAA-TAACA-TAAA
1 TTAGAAATTAA-ATTAAA
*
54879466 -TAAACAATTAAA-TAAA
1 TTAGA-AATTAAATTAAA
*
54879482 TTAGAAATAAAATTAAA
1 TTAGAAATTAAATTAAA
* *
54879499 TTGGGAATTAAATT
1 TTAGAAATTAAATT
54879513 CGGATTTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 3 0.06
14 7 0.14
15 5 0.10
16 13 0.27
17 21 0.43
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (17 bp):
TTAGAAATTAAATTAAA
Found at i:54883172 original size:17 final size:17
Alignment explanation
Indices: 54883150--54883184 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54883140 AACAATTAAA
54883150 TAAATTGGAAATAAAAT
1 TAAATTGGAAATAAAAT
* *
54883167 TAAATTGGGAATTAAAT
1 TAAATTGGAAATAAAAT
54883184 T
1 T
54883185 CGGATTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (17 bp):
TAAATTGGAAATAAAAT
Found at i:54884223 original size:124 final size:124
Alignment explanation
Indices: 54884004--54884258 Score: 309
Period size: 124 Copynumber: 2.1 Consensus size: 124
54883994 AAATAGTGGG
** * * * * * *
54884004 AAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTGGACGCAATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTATGAAACAGCGCCCTCGTGGACGCAATT
* * *
54884069 TTGCTACAGTGGTCATGTGAGAAATAAA-TTTTTTTGACATTTGCTGAGGAAATAGTATA
66 TCGCTACAGTGGTCATGTGAGAAATAAATTTTTTTTGACATTT-ATGAGCAAATAGTATA
* * *
54884128 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTATGAAACCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTATGAAACAGCGCCCTCGTGGACGCAATT
* * *
54884193 TCGCTACAGTTGGTCATGT-AGGAAAT-AATTTTTTTTGACGTTTATGAGCAAATAGTGTC
66 TCGCTACAG-TGGTCATGTGA-GAAATAAATTTTTTTTGACATTTATGAGCAAATAGTATA
54884252 AAATCGC
1 AAATCGC
54884259 GCCCTCGTGG
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
124 84 0.76
125 27 0.24
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTATGAAACAGCGCCCTCGTGGACGCAATT
TCGCTACAGTGGTCATGTGAGAAATAAATTTTTTTTGACATTTATGAGCAAATAGTATA
Found at i:54887205 original size:22 final size:22
Alignment explanation
Indices: 54887175--54887216 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54887165 ATTTGGAGAT
*
54887175 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
54887197 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
54887217 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:54887237 original size:52 final size:51
Alignment explanation
Indices: 54887166--54887268 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
54887156 TTAATATGGA
* * *
54887166 TTTGGAGATTTTTTGAAGGAAATTGAGAG-GATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTT-GAAGGGAA-TTGAGAG
*
54887217 TTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
54887269 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAAATTTTGAAGGGAATTGAGAG
Found at i:54887299 original size:22 final size:22
Alignment explanation
Indices: 54887218--54887302 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
54887208 ATTTGAGAGT
*
54887218 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGAAAGG-AA
* *
54887240 TTGATAGAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGGAA
54887262 TTGAGAGAAATTTTGAAAGGAA
1 TTGAGAGAAATTTTGAAAGGAA
*
54887284 TTGAGAGAATTTTTGAAAG
1 TTGAGAGAAATTTTGAAAG
54887303 AAGTTGATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 46 0.82
23 10 0.18
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (22 bp):
TTGAGAGAAATTTTGAAAGGAA
Found at i:54889667 original size:26 final size:25
Alignment explanation
Indices: 54889638--54889688 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
54889628 AATTTTTAAT
54889638 ATAC-TTTATAATTTATATATACATAC
1 ATACATTTATAA--TATATATACATAC
54889664 ATACATTTTATAATATATATACATA
1 ATACA-TTTATAATATATATACATA
54889689 TACGTGTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 16 0.70
28 7 0.30
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (25 bp):
ATACATTTATAATATATATACATAC
Found at i:54889899 original size:35 final size:36
Alignment explanation
Indices: 54889859--54889940 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 36
54889849 ACCCCTTTTT
*
54889859 TACATATATAGTTTT-TATATTTTATAATTCGTATA
1 TACATATATAGTTTTCTATATTTTACAATTCGTATA
* *
54889894 TACATACATATTTTTCGTATATTTTACAATTCGTATA
1 TACATATATAGTTTTC-TATATTTTACAATTCGTATA
* *
54889931 CATATATATA
1 TACATATATA
54889941 TCCACATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 13 0.33
37 26 0.67
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (36 bp):
TACATATATAGTTTTCTATATTTTACAATTCGTATA
Found at i:54891535 original size:14 final size:14
Alignment explanation
Indices: 54891516--54891545 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54891506 ATGGATTCAA
54891516 ATCTAATGGTTGAC
1 ATCTAATGGTTGAC
54891530 ATCTAATGGTTGAC
1 ATCTAATGGTTGAC
54891544 AT
1 AT
54891546 TTTGGTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (14 bp):
ATCTAATGGTTGAC
Found at i:54891679 original size:26 final size:27
Alignment explanation
Indices: 54891645--54891707 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
54891635 ATAAAAAATA
54891645 ACCAAAATATTATAAA-TTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
54891671 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
54891698 ACCAAAATAT
1 ACCAAAATAT
54891708 ACAAAAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 16 0.44
27 20 0.56
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:54891787 original size:27 final size:27
Alignment explanation
Indices: 54891757--54891835 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
54891747 GGCCAATCAC
*
54891757 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
54891784 ATTGGCGGCACCAATGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
*
54891811 ATTGGCAGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
54891836 GACTAAAATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.32, C:0.23, G:0.32, T:0.14
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:54892111 original size:20 final size:20
Alignment explanation
Indices: 54892086--54892123 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54892076 ATTTTATTAT
54892086 TAAAGTAAATA-TATTTTACC
1 TAAAGTAAA-ACTATTTTACC
54892106 TAAAGTAAAACTATTTTA
1 TAAAGTAAAACTATTTTA
54892124 AAAAGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAAGTAAAACTATTTTACC
Found at i:54892405 original size:19 final size:19
Alignment explanation
Indices: 54892381--54892437 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 19
54892371 TCTAATTAAG
54892381 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
54892400 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
54892418 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
54892437 T
1 T
54892438 TAAAAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:54892786 original size:26 final size:26
Alignment explanation
Indices: 54892757--54892815 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
54892747 TTTTTTTAGT
54892757 ATATTTTGATAAATAAAAAAATTATA
1 ATATTTTGATAAATAAAAAAATTATA
* *
54892783 ATATTTTGGTAAATAAAAAATTTATA
1 ATATTTTGATAAATAAAAAAATTATA
54892809 ATATTTT
1 ATATTTT
54892816 AGTTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (26 bp):
ATATTTTGATAAATAAAAAAATTATA
Found at i:54903252 original size:23 final size:23
Alignment explanation
Indices: 54903226--54903271 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54903216 AAATCACTGG
54903226 GCTGTTAAATCTTTTTTAAGCCT
1 GCTGTTAAATCTTTTTTAAGCCT
54903249 GCTGTTAAATCTTTTTTAAGCCT
1 GCTGTTAAATCTTTTTTAAGCCT
54903272 AGTCAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (23 bp):
GCTGTTAAATCTTTTTTAAGCCT
Found at i:54907573 original size:2 final size:2
Alignment explanation
Indices: 54907566--54907599 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54907556 TTATTAATTA
*
54907566 AT AT AT AT AT AT AT AT AT AC 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
54907600 TGTATTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:54908555 original size:41 final size:41
Alignment explanation
Indices: 54908510--54908683 Score: 260
Period size: 41 Copynumber: 4.2 Consensus size: 41
54908500 GGCTCGGTGC
* * **
54908510 CTAGCAGGCTTGATGCCAGTGATATGTTTCAGACTTTAAGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
54908551 CTAGCAGGCTTG-TCGCCGGTGAAACATTTCAGACTTTAAGT
1 CTAGCAGGCTTGAT-GCCGGTGAAACATTTCAGACTTTAAGT
* **
54908592 TTAGCAGGCTTGGCGCCGGTGAAACATTTCAGACTTTAAGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
*
54908633 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTATGT
1 CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
54908674 CTAGCAGGCT
1 CTAGCAGGCT
54908684 AAGTGCCAGT
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 120 0.99
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (41 bp):
CTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTAAGT
Found at i:54908713 original size:82 final size:81
Alignment explanation
Indices: 54908538--54908737 Score: 222
Period size: 82 Copynumber: 2.4 Consensus size: 81
54908528 GTGATATGTT
* * *
54908538 TCAGACTTTAAGTCTAGCAGGCTTGTCGCCGGTGAAACATTTCAGACTTTAAGTTTAGCAGGCTT
1 TCAGACCTTAAGTCTAGCAGGCTTGT-GCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTA
* * *
54908603 GGCGCCGGTGAAACATT
65 AGCGCCAGTGAAACATA
* *
54908620 TCAGACTTTAAGTCTAGCAGGCTTGATGCCGGTGAAACATTTCAGACTTTATGTCTAGCAGGCTA
1 TCAGACCTTAAGTCTAGCAGGCTTG-TGCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTA
* ***
54908685 AGTGCCAGTGTATTGA-A
65 AGCGCCAGTG-AAACATA
* * *
54908702 TCAGGCCTTAAGCCTAGCAGGTTTTGTGCCGGTGAA
1 TCAGACCTTAAGTCTAGCAGG-CTTGTGCCGGTGAA
54908738 TCTATTCATA
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
82 95 0.94
83 6 0.06
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (81 bp):
TCAGACCTTAAGTCTAGCAGGCTTGTGCCGGTGAAACATTTCAGACTTTAAGTCTAGCAGGCTAA
GCGCCAGTGAAACATA
Found at i:54910928 original size:20 final size:20
Alignment explanation
Indices: 54910887--54910930 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
54910877 AAAATATTAA
*
54910887 AAAATTGTAAAAAGATCTTT
1 AAAATTGTAAAAAGATCGTT
*
54910907 AAAATTGTACAAAA-ATGGTT
1 AAAATTGTA-AAAAGATCGTT
54910927 AAAA
1 AAAA
54910931 ATGAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (20 bp):
AAAATTGTAAAAAGATCGTT
Found at i:54915559 original size:17 final size:17
Alignment explanation
Indices: 54915519--54915560 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
54915509 ATAAATAAAC
*
54915519 AATT-AATTAAATTTGA
1 AATTAAATTAAATTGGA
* *
54915535 AATAAAATTAAATTGGG
1 AATTAAATTAAATTGGA
54915552 AATTAAATT
1 AATTAAATT
54915561 TGGATTTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
AATTAAATTAAATTGGA
Found at i:54927279 original size:16 final size:18
Alignment explanation
Indices: 54927247--54927281 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54927237 AAGTTGTGAG
54927247 AATTATATATTTCAAAAT
1 AATTATATATTTCAAAAT
54927265 AATTATA-ATTT-AAAAT
1 AATTATATATTTCAAAAT
54927281 A
1 A
54927282 CAATTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 4 0.24
18 7 0.41
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTATATATTTCAAAAT
Found at i:54927286 original size:18 final size:17
Alignment explanation
Indices: 54927247--54927299 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
54927237 AAGTTGTGAG
54927247 AATTATATATTTCAAAAT-
1 AATTATA-ATTT-AAAATA
54927265 AATTATAATTTAAAATA
1 AATTATAATTTAAAATA
* *
54927282 CAATTATTATTAAAAATA
1 -AATTATAATTTAAAATA
54927300 TTGTGCTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 5 0.16
17 4 0.13
18 22 0.71
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTATAATTTAAAATA
Found at i:54928155 original size:19 final size:19
Alignment explanation
Indices: 54928118--54928156 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54928108 AAAAAATTAA
*
54928118 TATTATTTTTGTATTTTTT
1 TATTATTTTTGTATATTTT
54928137 TATT-TTTTTGTAATATTTT
1 TATTATTTTTGT-ATATTTT
54928156 T
1 T
54928157 GTAAAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TATTATTTTTGTATATTTT
Found at i:54936189 original size:17 final size:17
Alignment explanation
Indices: 54936149--54936190 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
54936139 ATAAATAAAC
*
54936149 AATTAAA-TAAATTTGA
1 AATTAAATTAAATTGGA
* *
54936165 AATAAAATTAAATTGGG
1 AATTAAATTAAATTGGA
54936182 AATTAAATT
1 AATTAAATT
54936191 CGGATTTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (17 bp):
AATTAAATTAAATTGGA
Found at i:54936973 original size:2 final size:2
Alignment explanation
Indices: 54936966--54937007 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
54936956 CTACCACTTT
54936966 TA TA TA 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 TA TA TA
54937008 ATTTACTAAA
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):
TA
Found at i:54940451 original size:18 final size:18
Alignment explanation
Indices: 54940430--54940464 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54940420 TAAAAAATTA
54940430 TAAAAAACATAAAAAACG
1 TAAAAAACATAAAAAACG
* *
54940448 TAAAAAAGATGAAAAAC
1 TAAAAAACATAAAAAAC
54940465 AAAAAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.09, G:0.09, T:0.11
Consensus pattern (18 bp):
TAAAAAACATAAAAAACG
Found at i:54942063 original size:12 final size:12
Alignment explanation
Indices: 54942046--54942074 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
54942036 AAAAACTAGT
54942046 AGTCCTCATTCC
1 AGTCCTCATTCC
54942058 AGTCCTCATTCC
1 AGTCCTCATTCC
54942070 AGTCC
1 AGTCC
54942075 AGCTTTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.41, G:0.10, T:0.31
Consensus pattern (12 bp):
AGTCCTCATTCC
Found at i:54956745 original size:29 final size:29
Alignment explanation
Indices: 54956703--54956765 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
54956693 GTTGACCAAT
54956703 CTTTTAAAGAATGTTTACAAAATTAATAA
1 CTTTTAAAGAATGTTTACAAAATTAATAA
*
54956732 CTTTTAAAGAATGTTTACAAAATTTATAA
1 CTTTTAAAGAATGTTTACAAAATTAATAA
*
54956761 TTTTT
1 CTTTT
54956766 TACTAGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (29 bp):
CTTTTAAAGAATGTTTACAAAATTAATAA
Found at i:54957423 original size:34 final size:32
Alignment explanation
Indices: 54957381--54957467 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 32
54957371 ATTAGTTGTA
54957381 AAATTAATGATACATAAAATATTACAAAAATTT
1 AAATTAATGATACATAAAATATTA-AAAAATTT
* * * *
54957414 AAATATAATGATAAATAATAT-TTAAATAGTTT
1 AAAT-TAATGATACATAAAATATTAAAAAATTT
54957446 -AATCTAATGATACATAAAATAT
1 AAAT-TAATGATACATAAAATAT
54957468 AAATTAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 17 0.38
32 7 0.16
33 7 0.16
34 14 0.31
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (32 bp):
AAATTAATGATACATAAAATATTAAAAAATTT
Found at i:54961395 original size:8 final size:8
Alignment explanation
Indices: 54961382--54961406 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54961372 AGAATTATTG
54961382 TCAATTTT
1 TCAATTTT
54961390 TCAATTTT
1 TCAATTTT
54961398 TCAATTTT
1 TCAATTTT
54961406 T
1 T
54961407 AAGTTTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TCAATTTT
Found at i:54962411 original size:10 final size:9
Alignment explanation
Indices: 54962370--54962414 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
54962360 ATTAAATTAT
54962370 TATTTA-AA
1 TATTTATAA
54962378 TATTT-T-A
1 TATTTATAA
*
54962385 TATTTATGA
1 TATTTATAA
54962394 TATTTATAA
1 TATTTATAA
54962403 TATTTTATAA
1 TA-TTTATAA
54962413 TA
1 TA
54962415 AATAAGTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
7 6 0.19
8 6 0.19
9 11 0.34
10 9 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
TATTTATAA
Found at i:54966263 original size:5 final size:5
Alignment explanation
Indices: 54966253--54966296 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
54966243 AAAAAAATAT
*
54966253 TTATA TTATA TTA-A TT-TA ATAT- TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
54966297 TTTTTATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 8 0.24
5 26 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:54966306 original size:27 final size:27
Alignment explanation
Indices: 54966249--54966306 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
54966239 TTTTAAAAAA
54966249 ATAT-TTATATTATATTAATTTAATATT
1 ATATATTATATTATATTAATTT-ATATT
*
54966276 -TATATTATATTATATTATATTT-TTTT
1 ATATATTATATTATATTA-ATTTATATT
54966302 ATATA
1 ATATA
54966307 ATCATCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
26 6 0.22
27 17 0.63
28 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATATTATATTATATTAATTTATATT
Found at i:54970938 original size:20 final size:20
Alignment explanation
Indices: 54970891--54970951 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
54970881 TAACAGTTAT
* *
54970891 TATATTAATA-ATTATAAAA
1 TATATTATTACATTATATAA
*
54970910 TATATTATTTCATTATATAA
1 TATATTATTACATTATATAA
54970930 TACTA-TATTACA-TACTATAA
1 TA-TATTATTACATTA-TATAA
54970950 TA
1 TA
54970952 GTAGAGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.29
20 23 0.66
21 2 0.06
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATTATTACATTATATAA
Found at i:54987170 original size:13 final size:13
Alignment explanation
Indices: 54987154--54987183 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54987144 TTGTATTGCA
*
54987154 TGTTTGATTTTCT
1 TGTTTGATTTCCT
54987167 TGTTTGATTTCCT
1 TGTTTGATTTCCT
54987180 TGTT
1 TGTT
54987184 AACCCCTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.10, G:0.17, T:0.67
Consensus pattern (13 bp):
TGTTTGATTTCCT
Found at i:54989107 original size:40 final size:40
Alignment explanation
Indices: 54989040--54989189 Score: 223
Period size: 40 Copynumber: 3.7 Consensus size: 40
54989030 ACCAAAAATT
54989040 TATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
54989084 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
54989124 -ATTTTAAAATTAAAAAAATTAAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAATT-AAAAAAAGTATTTTAAAAA
*
54989164 TATTTTAAAGTTAAAAAAA-TAAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAA
54989190 TAAAAAATAA
Statistics
Matches: 102, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
39 26 0.25
40 45 0.44
41 19 0.19
43 6 0.06
44 6 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:54989108 original size:8 final size:9
Alignment explanation
Indices: 54989090--54989150 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
54989080 AAAATATTTT
54989090 AAAATTAAA
1 AAAATTAAA
54989099 AAAATTAAAA
1 AAAATT-AAA
*
54989109 AAAGTATTTTAA
1 AAA--A-TTAAA
**
54989121 AAAATT-TT
1 AAAATTAAA
54989129 AAAATTAAA
1 AAAATTAAA
54989138 AAAATTAAA
1 AAAATTAAA
54989147 AAAA
1 AAAA
54989151 AGTATTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
8 6 0.14
9 21 0.50
10 7 0.17
12 6 0.14
13 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAATTAAA
Found at i:54989162 original size:11 final size:11
Alignment explanation
Indices: 54989148--54989172 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54989138 AAAATTAAAA
54989148 AAAAGTATTTT
1 AAAAGTATTTT
54989159 AAAAGTATTTT
1 AAAAGTATTTT
54989170 AAA
1 AAA
54989173 GTTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:54989189 original size:7 final size:7
Alignment explanation
Indices: 54989177--54989208 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
54989167 TTTAAAGTTA
54989177 AAAAAAT
1 AAAAAAT
54989184 AAAAAAT
1 AAAAAAT
54989191 AAAAAAT
1 AAAAAAT
54989198 -AAAAAT
1 AAAAAAT
54989204 AAAAA
1 AAAAA
54989209 TATTTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:54989194 original size:14 final size:13
Alignment explanation
Indices: 54989177--54989208 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
54989167 TTTAAAGTTA
54989177 AAAAAATAAAAAAT
1 AAAAAAT-AAAAAT
54989191 AAAAAATAAAAAT
1 AAAAAATAAAAAT
54989204 AAAAA
1 AAAAA
54989209 TATTTTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:54995893 original size:18 final size:18
Alignment explanation
Indices: 54995872--54995982 Score: 93
Period size: 18 Copynumber: 5.9 Consensus size: 18
54995862 ATACTAAGAA
54995872 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
*
54995890 TTTTGTTAAATTATAT-T
1 TTTTATTAAATTATATAT
* *
54995907 TTATATT-ATTATATATTAT
1 TTTTATTAAAT-TATA-TAT
*
54995926 GATTTTAGTAAATTCATATA-
1 --TTTTATTAAATT-ATATAT
54995946 TTTTATTAAATTATATATT
1 TTTTATTAAATTATATA-T
54995965 ATTATTATTAAATTATAT
1 -TT-TTATTAAATTATAT
54995983 TTAATAATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
16 2 0.03
17 15 0.20
18 27 0.36
19 1 0.01
20 2 0.03
21 22 0.30
22 5 0.07
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:54995995 original size:21 final size:21
Alignment explanation
Indices: 54995950--54995995 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54995940 CATATATTTT
* *
54995950 ATTAAATTATATATTATTATT
1 ATTAAATTATATATTATAATA
54995971 ATTAAATTATAT-TTAATAATA
1 ATTAAATTATATATT-ATAATA
54995992 ATTA
1 ATTA
54995996 TGTTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAAATTATATATTATAATA
Found at i:55002310 original size:3 final size:3
Alignment explanation
Indices: 55002302--55002339 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
55002292 TAATTCCCAC
55002302 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55002340 CTTACCTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:55003410 original size:9 final size:9
Alignment explanation
Indices: 55003396--55003423 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
55003386 CATTTAAATA
55003396 AATAATTAT
1 AATAATTAT
55003405 AATAATTAT
1 AATAATTAT
55003414 AATAATTAT
1 AATAATTAT
55003423 A
1 A
55003424 TACATATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AATAATTAT
Found at i:55006078 original size:18 final size:17
Alignment explanation
Indices: 55006045--55006083 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
55006035 TTTTATAAAT
55006045 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
55006063 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
55006080 TGTG
1 TGTG
55006084 GAAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:55006334 original size:23 final size:23
Alignment explanation
Indices: 55006307--55006359 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
55006297 AGTGTTATTG
55006307 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* *
55006330 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
55006353 ATCAGTG
1 ATCAGTG
55006360 TGGCACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCAGCTACAT
Found at i:55008474 original size:67 final size:67
Alignment explanation
Indices: 55008371--55008750 Score: 546
Period size: 67 Copynumber: 5.8 Consensus size: 67
55008361 CAATTGCAAT
*
55008371 AGTATTTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGCGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGCGAAT
55008436 TG
66 TG
* * *
55008438 AGTAATTAAATGTATGTATTTAATTAAATCGATTATATGTATGTGATTTGAGAAAGTATGTGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGCGAAT
55008503 TG
66 TG
* *
55008505 AATAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGCGAAT
55008570 TG
66 TG
* *
55008572 AGTAATTAAATGTATGTAGTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGCGAAT
55008637 TG
66 TG
* * *
55008639 AGTATTTAAATGT-T-TA---AATCG-ATT-A-TATA--TATGTGATTTGAGAAGGTATGCGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGCGAAT
*
55008694 TA
66 TG
* * * *
55008696 AGTATTTAAATGTATGTACTTAATTGAATAGATTATATATATGTGATTTGAGAAA
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAA
55008751 TTGAATTATT
Statistics
Matches: 284, Mismatches: 19, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
57 38 0.13
58 1 0.00
59 6 0.02
60 1 0.00
61 3 0.01
62 8 0.03
63 2 0.01
64 1 0.00
65 6 0.02
66 1 0.00
67 217 0.76
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (67 bp):
AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGCGAAT
TG
Found at i:55008983 original size:23 final size:23
Alignment explanation
Indices: 55008897--55009020 Score: 65
Period size: 23 Copynumber: 5.3 Consensus size: 23
55008887 GACTCACTAC
55008897 AGCTCATATGAGCTTACCGATATTTT
1 AGCTCATATGAGCTTACC---ATTTT
* * * **
55008923 AGCTCGTAAGAGCCTACTGTTTT
1 AGCTCATATGAGCTTACCATTTT
*
55008946 CAGTTCAT-TAGAGCTTACCATTTT
1 -AGCTCATAT-GAGCTTACCATTTT
* * *
55008970 AGCTCGTATGAGCTTACTA-TTC
1 AGCTCATATGAGCTTACCATTTT
* * *
55008992 AGCTCATCA-AAGCTTACCGTTTC
1 AGCTCAT-ATGAGCTTACCATTTT
55009015 AGCTCA
1 AGCTCA
55009021 ATAGAGCCTA
Statistics
Matches: 74, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
22 15 0.20
23 28 0.38
24 17 0.23
26 14 0.19
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.35
Consensus pattern (23 bp):
AGCTCATATGAGCTTACCATTTT
Found at i:55009008 original size:45 final size:46
Alignment explanation
Indices: 55008918--55009035 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 46
55008908 GCTTACCGAT
* * * *
55008918 ATTTTAGCTCGTAAGAGCCTACTGTTTTCAGTTCATTAGAGCTTACC
1 ATTTTAGCTCGTAAGAGCCTAC-GTATTCAGCTCATCAAAGCTTACC
* *
55008965 ATTTTAGCTCGTATGAGCTTAC-TATTCAGCTCATCAAAGCTTACC
1 ATTTTAGCTCGTAAGAGCCTACGTATTCAGCTCATCAAAGCTTACC
* * *
55009010 GTTTCAGCTC-AATAGAGCCTAC-TATT
1 ATTTTAGCTCGTA-AGAGCCTACGTATT
55009036 TATCAGCTCA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
44 1 0.02
45 38 0.64
47 20 0.34
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (46 bp):
ATTTTAGCTCGTAAGAGCCTACGTATTCAGCTCATCAAAGCTTACC
Found at i:55017684 original size:17 final size:18
Alignment explanation
Indices: 55017662--55017696 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55017652 TAATAATAAT
*
55017662 TTATATAATA-AAATTAA
1 TTATATAAAAGAAATTAA
55017679 TTATATAAAAGAAATTAA
1 TTATATAAAAGAAATTAA
55017697 AAAAAACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TTATATAAAAGAAATTAA
Found at i:55023631 original size:15 final size:15
Alignment explanation
Indices: 55023611--55023641 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55023601 CTCAACTTTA
55023611 AAAAAGTGACAAAAC
1 AAAAAGTGACAAAAC
55023626 AAAAAGTGACAAAAC
1 AAAAAGTGACAAAAC
55023641 A
1 A
55023642 GTCTTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.13, G:0.13, T:0.06
Consensus pattern (15 bp):
AAAAAGTGACAAAAC
Found at i:55024708 original size:30 final size:31
Alignment explanation
Indices: 55024643--55024711 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
55024633 ACTATTAATC
* * *
55024643 AGTGATTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
*
55024674 AGTGACTGTTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
55024703 GAGTGACTG
1 -AGTGACTG
55024712 AAATGAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 14 0.42
31 14 0.42
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:55026334 original size:18 final size:18
Alignment explanation
Indices: 55026311--55026353 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55026301 ACCTAATCTA
**
55026311 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
55026329 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
55026347 AACCCAA
1 AACCCAA
55026354 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:55026471 original size:9 final size:9
Alignment explanation
Indices: 55026457--55026505 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
55026447 GTAGTGATTC
55026457 AATTCGGTT
1 AATTCGGTT
55026466 AATTCGGTT
1 AATTCGGTT
55026475 AATTCGAG-T
1 AATTCG-GTT
55026484 AATTCGAG-T
1 AATTCG-GTT
55026493 AATTCGGTT
1 AATTCGGTT
55026502 AATT
1 AATT
55026506 TTTAACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 1 0.03
9 36 0.95
10 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55031837 original size:18 final size:17
Alignment explanation
Indices: 55031814--55031865 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 17
55031804 ATTATTATTA
55031814 TTATTATTTTTACTTTAT
1 TTATTA-TTTTACTTTAT
* *
55031832 TTATTACTTTATTTTA-
1 TTATTATTTTACTTTAT
55031848 TT-TTATTTTAC-TTAT
1 TTATTATTTTACTTTAT
55031863 TTA
1 TTA
55031866 GATATTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 2 0.07
17 8 0.29
18 6 0.21
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTATTTTACTTTAT
Found at i:55031852 original size:27 final size:30
Alignment explanation
Indices: 55031800--55031863 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
55031790 GAGGCAACCC
*
55031800 ACTTATTATTATTATTATTATTTTTACTTT
1 ACTTATTACTATTATTATTATTTTTACTTT
* *
55031830 ATTTATTACT-TTATT-TTA-TTTTATTTT
1 ACTTATTACTATTATTATTATTTTTACTTT
55031857 ACTTATT
1 ACTTATT
55031864 TAGATATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 14 0.47
28 3 0.10
29 5 0.17
30 8 0.27
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (30 bp):
ACTTATTACTATTATTATTATTTTTACTTT
Found at i:55031865 original size:23 final size:23
Alignment explanation
Indices: 55031805--55031865 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
55031795 AACCCACTTA
55031805 TTATTATTATTA-TTATTTTTACT
1 TTATT-TTATTATTTATTTTTACT
*
55031828 TTA-TTTATTACTTTA-TTTTATT
1 TTATTTTATTA-TTTATTTTTACT
55031850 TTATTTTACTTATTTA
1 TTATTTTA-TTATTTA
55031866 GATATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 6 0.18
22 10 0.30
23 14 0.42
24 3 0.09
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTTTATTATTTATTTTTACT
Done.