Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 83 of 91
Found at i:31346306 original size:2 final size:2
Alignment explanation
Indices: 31346299--31346325 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31346289 ACAATTTCAA
31346299 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 A
31346326 GCAAAAGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31347665 original size:7 final size:7
Alignment explanation
Indices: 31347659--31347693 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
31347649 GGAAAGTAAC
*
31347659 CAATAAC
1 CAATAAA
31347666 CAATAAA
1 CAATAAA
31347673 CAATAAA
1 CAATAAA
31347680 CAATAAA
1 CAATAAA
*
31347687 CAGTAAA
1 CAATAAA
31347694 GCACGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.66, C:0.17, G:0.03, T:0.14
Consensus pattern (7 bp):
CAATAAA
Found at i:31348963 original size:42 final size:42
Alignment explanation
Indices: 31348911--31348990 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
31348901 TTATATTTAC
* *
31348911 GAGTTGTGATTATAATTTCAAAAAACATTAAAATATAACTAA
1 GAGTAGTGATTATAATTTCAAAAAACATTAAAACATAACTAA
*
31348953 GAGTAGTGATTATAATTTCAAAAAATATTAAAACATAA
1 GAGTAGTGATTATAATTTCAAAAAACATTAAAACATAA
31348991 TAAATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (42 bp):
GAGTAGTGATTATAATTTCAAAAAACATTAAAACATAACTAA
Found at i:31352414 original size:20 final size:23
Alignment explanation
Indices: 31352365--31352415 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 23
31352355 TTTGTATATT
*
31352365 ATTAATAAATAAAATATTACACA
1 ATTAATAAATAAAATATTACAAA
*
31352388 GTTAATAAAT-AAAT-TTA-AAA
1 ATTAATAAATAAAATATTACAAA
31352408 ATTAATAA
1 ATTAATAA
31352416 TTCTTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 3 0.12
22 4 0.16
23 9 0.36
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTAATAAATAAAATATTACAAA
Found at i:31356384 original size:18 final size:18
Alignment explanation
Indices: 31356361--31356395 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31356351 TCATGTTGGA
31356361 AATCATCAGCAGCAGCAG
1 AATCATCAGCAGCAGCAG
31356379 AATCATCAGCAGCAGCA
1 AATCATCAGCAGCAGCA
31356396 CAGTTTCTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.29, G:0.20, T:0.11
Consensus pattern (18 bp):
AATCATCAGCAGCAGCAG
Found at i:31366716 original size:64 final size:64
Alignment explanation
Indices: 31366637--31366765 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
31366627 GCAAAGCAAG
* *
31366637 CCCATGAAAAGCCTTGAACTATTCTCTCTAGCGATAAGTC-TTTGATTTTGGTTTGAATCAATTA
1 CCCATGAAAAGCCTTGAACTATTCTCCCTAGAGATAAG-CATTTGATTTTGGTTTGAATCAATTA
*
31366701 CCCATGAAAAGCCTTGAACTATTCTCCCTAGAGATGAGCATTTGATTTTGGTTTGAATCAATTA
1 CCCATGAAAAGCCTTGAACTATTCTCCCTAGAGATAAGCATTTGATTTTGGTTTGAATCAATTA
31366765 C
1 C
31366766 TTGGTTTGAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.02
64 60 0.98
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (64 bp):
CCCATGAAAAGCCTTGAACTATTCTCCCTAGAGATAAGCATTTGATTTTGGTTTGAATCAATTA
Found at i:31381164 original size:2 final size:2
Alignment explanation
Indices: 31381157--31381233 Score: 99
Period size: 2 Copynumber: 40.0 Consensus size: 2
31381147 ATATTTAATC
* *
31381157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AN CT A- AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31381196 AT -T ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31381234 TCCTATACAT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
1 4 0.06
2 60 0.91
3 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31389890 original size:12 final size:12
Alignment explanation
Indices: 31389873--31389899 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31389863 TAATCCCAAT
31389873 TCTTGATAATTA
1 TCTTGATAATTA
31389885 TCTTGATAATTA
1 TCTTGATAATTA
31389897 TCT
1 TCT
31389900 ATTCATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (12 bp):
TCTTGATAATTA
Found at i:31393939 original size:21 final size:23
Alignment explanation
Indices: 31393890--31393939 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
31393880 ACTTTTAGAA
* *
31393890 AATTTTAAGGATAGTCTCTGCTG
1 AATTTTAAGGATAGTCCCTGCTC
31393913 AATTTTAAGGATAGTCCCT-C-C
1 AATTTTAAGGATAGTCCCTGCTC
31393934 AATTTT
1 AATTTT
31393940 TCAAACTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.24
22 1 0.04
23 18 0.72
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (23 bp):
AATTTTAAGGATAGTCCCTGCTC
Found at i:31406385 original size:2 final size:2
Alignment explanation
Indices: 31406378--31406410 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
31406368 CAAAATAATA
31406378 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 A
31406411 ATTTTGATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31407297 original size:25 final size:25
Alignment explanation
Indices: 31407263--31407313 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
31407253 TAAGAATGTG
31407263 ATATGTTTATTTCATGGTTGGATTC
1 ATATGTTTATTTCATGGTTGGATTC
31407288 ATATGTTTATTTCATGGTTGGATTC
1 ATATGTTTATTTCATGGTTGGATTC
31407313 A
1 A
31407314 CAGTTCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.51
Consensus pattern (25 bp):
ATATGTTTATTTCATGGTTGGATTC
Found at i:31416174 original size:47 final size:47
Alignment explanation
Indices: 31416104--31416199 Score: 156
Period size: 47 Copynumber: 2.0 Consensus size: 47
31416094 AACAATATTT
*
31416104 TTTTTATTTTTTATCTTTATATTTTACTAGGACATAAGCTCTTAAAG
1 TTTTTATTTTTTATCTTTATATTTTACAAGGACATAAGCTCTTAAAG
* * *
31416151 TTTTTATTTTTTATCTTTGTATTTTAGAAGGACATAAGTTCTTAAAG
1 TTTTTATTTTTTATCTTTATATTTTACAAGGACATAAGCTCTTAAAG
31416198 TT
1 TT
31416200 AAAAAAAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.54
Consensus pattern (47 bp):
TTTTTATTTTTTATCTTTATATTTTACAAGGACATAAGCTCTTAAAG
Found at i:31416390 original size:19 final size:17
Alignment explanation
Indices: 31416366--31416402 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
31416356 AAAATGACAT
31416366 ATAATAACTTTTTTTATCA
1 ATAATAA-TTTTTTT-TCA
31416385 ATAATAATTTTTTTTCA
1 ATAATAATTTTTTTTCA
31416402 A
1 A
31416403 CATATACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 7 0.39
19 7 0.39
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATAATTTTTTTTCA
Found at i:31419361 original size:125 final size:125
Alignment explanation
Indices: 31419130--31419379 Score: 428
Period size: 125 Copynumber: 2.0 Consensus size: 125
31419120 TGGAGACAAA
*
31419130 GTTTAATAGATTGTAATCAAGACTAAAGATTTTGTGGTGAAATAAAATTTTCACATTTAACATTC
1 GTTTAATAGATTGTAATCAAGACTAAAGATTTTGTGGTGAAATAAAACTTTCACATTTAACATTC
* *
31419195 AGAGTGTTCCTTATCTTTCATTCTACCTGGGATTTACGTTTAAACACCATAGCTTATGGT
66 AGAGCGTTCCTTATCTTTCATTCTACCTAGGATTTACGTTTAAACACCATAGCTTATGGT
* *
31419255 GTTTTATAGATTGTAATCAAGACTAAAGATTTTGTGGTGAAATAAAACTTTCAGATTTAACATTC
1 GTTTAATAGATTGTAATCAAGACTAAAGATTTTGTGGTGAAATAAAACTTTCACATTTAACATTC
* * *
31419320 AGCGCGTTCCTTATCTTTCCTTCTACCTAGGATTTAGGTTTAAACACCATAGCTTATGGT
66 AGAGCGTTCCTTATCTTTCATTCTACCTAGGATTTACGTTTAAACACCATAGCTTATGGT
31419380 TTTGTGCTAA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 117 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (125 bp):
GTTTAATAGATTGTAATCAAGACTAAAGATTTTGTGGTGAAATAAAACTTTCACATTTAACATTC
AGAGCGTTCCTTATCTTTCATTCTACCTAGGATTTACGTTTAAACACCATAGCTTATGGT
Found at i:31427806 original size:2 final size:2
Alignment explanation
Indices: 31427799--31427828 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31427789 TTTAGACTCG
*
31427799 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31427829 CTTTTAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:31434829 original size:11 final size:11
Alignment explanation
Indices: 31434813--31434857 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
31434803 AAAAGAAGGC
31434813 ATGAAAAAAAA
1 ATGAAAAAAAA
*
31434824 ATG-AAAAACA
1 ATGAAAAAAAA
31434834 AT-AAAAAAAA
1 ATGAAAAAAAA
*
31434844 A-GAAACAAAA
1 ATGAAAAAAAA
31434854 ATGA
1 ATGA
31434858 TTATATGGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 23 0.82
11 5 0.18
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (11 bp):
ATGAAAAAAAA
Found at i:31447515 original size:7 final size:7
Alignment explanation
Indices: 31447505--31447529 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31447495 TGGTCTTTGG
31447505 CCACTGA
1 CCACTGA
31447512 CCACTGA
1 CCACTGA
31447519 CCACTGA
1 CCACTGA
31447526 CCAC
1 CCAC
31447530 CCCGACTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.48, G:0.12, T:0.12
Consensus pattern (7 bp):
CCACTGA
Found at i:31450164 original size:2 final size:2
Alignment explanation
Indices: 31450157--31450190 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31450147 GGATAAATAA
31450157 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
31450191 GTTTCAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31452127 original size:2 final size:2
Alignment explanation
Indices: 31452120--31452152 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31452110 TTCACTGACT
*
31452120 TA TA TA TA TA CA 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 T
31452153 TTGTTTCCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31456378 original size:2 final size:2
Alignment explanation
Indices: 31456371--31456395 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31456361 AGCTCCTTCC
31456371 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 T
31456396 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31458330 original size:2 final size:2
Alignment explanation
Indices: 31458317--31458369 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
31458307 TTATCCATAC
*
31458317 AT AT AC 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
31458359 AT AT AT AT AT A
1 AT AT AT AT AT A
31458370 ACCATTTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31463293 original size:17 final size:18
Alignment explanation
Indices: 31463262--31463295 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31463252 TTACATTATA
31463262 TTAGTTAAAAATTTAAAT
1 TTAGTTAAAAATTTAAAT
*
31463280 TTAG-TAAAATTTTAAA
1 TTAGTTAAAAATTTAAA
31463296 AGGAGTATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTAGTTAAAAATTTAAAT
Found at i:31465798 original size:15 final size:15
Alignment explanation
Indices: 31465778--31465809 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31465768 TACTTTGAAT
31465778 ATGAATTAGCAATGC
1 ATGAATTAGCAATGC
*
31465793 ATGAATTAGCAGTGC
1 ATGAATTAGCAATGC
31465808 AT
1 AT
31465810 AGGAGAAGAC
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:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (15 bp):
ATGAATTAGCAATGC
Found at i:31468324 original size:2 final size:2
Alignment explanation
Indices: 31468319--31468392 Score: 114
Period size: 2 Copynumber: 37.0 Consensus size: 2
31468309 CGACTCCATC
* *
31468319 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CN CA C- CT ACT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT
31468361 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31468393 TTTCTAAACT
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.01
2 65 0.96
3 2 0.03
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:31476438 original size:17 final size:18
Alignment explanation
Indices: 31476418--31476481 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 18
31476408 ATTTTTTACT
31476418 TATA-TATATATTTTTAA
1 TATATTATATATTTTTAA
31476435 TATAATTATATATTTTTAA
1 TAT-ATTATATATTTTTAA
* *
31476454 TATAATTAAATATATTATAA
1 TAT-ATTATATAT-TTTTAA
31476474 T-TATTATA
1 TATATTATA
31476482 AAATTATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.07
18 6 0.15
19 26 0.63
20 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTATATATTTTTAA
Found at i:31476444 original size:19 final size:19
Alignment explanation
Indices: 31476422--31476466 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
31476412 TTTACTTATA
31476422 TATATATTTTTAATATAAT
1 TATATATTTTTAATATAAT
31476441 TATATATTTTTAATATAAT
1 TATATATTTTTAATATAAT
*
31476460 TAAATAT
1 TATATAT
31476467 ATTATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATATATTTTTAATATAAT
Found at i:31476446 original size:21 final size:20
Alignment explanation
Indices: 31476419--31476469 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 20
31476409 TTTTTTACTT
31476419 ATATATATATTTTTAATATA
1 ATATATATATTTTTAATATA
31476439 AT-TATATATTTTTAATATA
1 ATATATATATTTTTAATATA
*
31476458 ATTAAATATATT
1 A-TATATATATT
31476470 ATAATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 18 0.64
20 3 0.11
21 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATATATTTTTAATATA
Found at i:31489180 original size:7 final size:7
Alignment explanation
Indices: 31489168--31489200 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
31489158 TTAAATGTAC
31489168 GTGTCAA
1 GTGTCAA
31489175 GTGTCAA
1 GTGTCAA
*
31489182 GTGGCAA
1 GTGTCAA
31489189 GTGTCAA
1 GTGTCAA
31489196 GTGTC
1 GTGTC
31489201 TTTATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.27
Consensus pattern (7 bp):
GTGTCAA
Found at i:31494403 original size:2 final size:2
Alignment explanation
Indices: 31494396--31494447 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
31494386 AGATGAAGTG
*
31494396 GA GA GA GA GA GA GA GA GA GA G- GA GN GTA G- GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA
31494437 GA GA GA GA GA G
1 GA GA GA GA GA G
31494448 GATTAAGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.93
3 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.52, T:0.02
Consensus pattern (2 bp):
GA
Found at i:31496595 original size:25 final size:25
Alignment explanation
Indices: 31496550--31496597 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
31496540 GATGTTACAC
**
31496550 ATCATGATTAAAAAAGTTATTATAT
1 ATCATGATTAAAAAAAATATTATAT
31496575 ATCATG-TTGAAAAAAAATATTAT
1 ATCATGATT-AAAAAAAATATTAT
31496598 TGCTACATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (25 bp):
ATCATGATTAAAAAAAATATTATAT
Found at i:31496711 original size:15 final size:15
Alignment explanation
Indices: 31496691--31496722 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31496681 ATACATCATG
31496691 TACAAAAATATATTA
1 TACAAAAATATATTA
*
31496706 TACAAAAATATGTTA
1 TACAAAAATATATTA
31496721 TA
1 TA
31496723 TGTCATGGTT
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:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TACAAAAATATATTA
Found at i:31497266 original size:29 final size:29
Alignment explanation
Indices: 31497167--31497259 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
31497157 AGCTTTTTTC
* **
31497167 TTGTACTTGTTCACGTACAGCTTCTTCTT
1 TTGTACCTGTTCATATACAGCTTCTTCTT
* * *
31497196 TTGTACCTGTTTATATACAGCTTTTTCTC
1 TTGTACCTGTTCATATACAGCTTCTTCTT
*
31497225 TTGTACCTGTTCATATACAGCTTCTTGTT
1 TTGTACCTGTTCATATACAGCTTCTTCTT
31497254 TTGTAC
1 TTGTAC
31497260 GTATTCACGT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (29 bp):
TTGTACCTGTTCATATACAGCTTCTTCTT
Found at i:31497272 original size:29 final size:29
Alignment explanation
Indices: 31497167--31497272 Score: 113
Period size: 29 Copynumber: 3.7 Consensus size: 29
31497157 AGCTTTTTTC
*
31497167 TTGTACTTGTTCACGTACAGCTTCTTCTT
1 TTGTACCTGTTCACGTACAGCTTCTTCTT
* ** * *
31497196 TTGTACCTGTTTATATACAGCTTTTTCTC
1 TTGTACCTGTTCACGTACAGCTTCTTCTT
** *
31497225 TTGTACCTGTTCATATACAGCTTCTTGTT
1 TTGTACCTGTTCACGTACAGCTTCTTCTT
* *
31497254 TTGTACGTATTCACGTACA
1 TTGTACCTGTTCACGTACA
31497273 ACTCTTATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (29 bp):
TTGTACCTGTTCACGTACAGCTTCTTCTT
Found at i:31497880 original size:30 final size:30
Alignment explanation
Indices: 31497793--31497900 Score: 111
Period size: 30 Copynumber: 3.8 Consensus size: 30
31497783 AAAAAAGCTA
31497793 TTACACGCCATGTTGAAAAAAAATATTATTG
1 TTACACGCCATGTTG-AAAAAAATATTATTG
* *
31497824 TTACACGTCATG-T--ACAAAA-A-TA-TG
1 TTACACGCCATGTTGAAAAAAATATTATTG
*
31497848 TTACATGCCATGTTGAAAAAAATATTATTG
1 TTACACGCCATGTTGAAAAAAATATTATTG
* * *
31497878 TTACATGTCATGTTCAAAAAAAT
1 TTACACGCCATGTTGAAAAAAAT
31497901 TTTGTTATAC
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
24 12 0.19
25 3 0.05
26 1 0.02
27 10 0.16
28 1 0.02
29 2 0.03
30 24 0.38
31 11 0.17
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (30 bp):
TTACACGCCATGTTGAAAAAAATATTATTG
Found at i:31497898 original size:55 final size:55
Alignment explanation
Indices: 31497793--31497897 Score: 176
Period size: 54 Copynumber: 1.9 Consensus size: 55
31497783 AAAAAAGCTA
31497793 TTACACGCCATGTTGAAAAAAAATATTATTGTTACACGTCATGTACAAAAATATG
1 TTACACGCCATGTTGAAAAAAAATATTATTGTTACACGTCATGTACAAAAATATG
* * *
31497848 TTACATGCCATGTTG-AAAAAAATATTATTGTTACATGTCATGTTCAAAAA
1 TTACACGCCATGTTGAAAAAAAATATTATTGTTACACGTCATGTACAAAAA
31497898 AATTTTGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 33 0.70
55 14 0.30
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (55 bp):
TTACACGCCATGTTGAAAAAAAATATTATTGTTACACGTCATGTACAAAAATATG
Found at i:31497905 original size:27 final size:28
Alignment explanation
Indices: 31497810--31497907 Score: 100
Period size: 27 Copynumber: 3.6 Consensus size: 28
31497800 CCATGTTGAA
*
31497810 AAAAAATATTATTGTTACACGTCATG-T
1 AAAAAATATTATTGTTACATGTCATGTT
* *
31497837 ACAAAA-A-TA-TGTTACATGCCATGTT
1 AAAAAATATTATTGTTACATGTCATGTT
31497862 GAAAAAAATATTATTGTTACATGTCATGTT
1 --AAAAAATATTATTGTTACATGTCATGTT
31497892 CAAAAAA-ATT-TTGTTA
1 -AAAAAATATTATTGTTA
31497908 TACTTTAATG
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
24 12 0.20
25 3 0.05
26 1 0.02
27 16 0.27
28 4 0.07
29 8 0.14
30 15 0.25
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (28 bp):
AAAAAATATTATTGTTACATGTCATGTT
Found at i:31535406 original size:38 final size:38
Alignment explanation
Indices: 31535311--31535462 Score: 227
Period size: 38 Copynumber: 4.1 Consensus size: 38
31535301 TGGATCTCTG
* * * * *
31535311 ACCCAATTTGTTTCCTTCTTTATCTTTGGGCTTCATCC
1 ACCCAATTTTTTTCTTTTTTTCTCTCTGGGCTTCATCC
31535349 ACCCAA-TTTTTTC-TTTTTTCTCTCTGGGCTTCATCC
1 ACCCAATTTTTTTCTTTTTTTCTCTCTGGGCTTCATCC
31535385 ACCCAATTTTTTTCTTTTTTTCTCTCTGGGCTTCATCC
1 ACCCAATTTTTTTCTTTTTTTCTCTCTGGGCTTCATCC
**
31535423 ACCCAATTTTTTTCTTCATTTCTCTCTGGGCTTCATCC
1 ACCCAATTTTTTTCTTTTTTTCTCTCTGGGCTTCATCC
31535461 AC
1 AC
31535463 ATTCCTTCAC
Statistics
Matches: 106, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
36 26 0.25
37 13 0.12
38 67 0.63
ACGTcount: A:0.12, C:0.30, G:0.09, T:0.49
Consensus pattern (38 bp):
ACCCAATTTTTTTCTTTTTTTCTCTCTGGGCTTCATCC
Found at i:31535432 original size:74 final size:76
Alignment explanation
Indices: 31535311--31535462 Score: 236
Period size: 74 Copynumber: 2.0 Consensus size: 76
31535301 TGGATCTCTG
* *
31535311 ACCCAATTTGTTTCCTTCTTTATCTTTGGGCTTCATCCACCCAA-TTTTTTCTT-TTTTCTCTCT
1 ACCCAATTTGTTTCCTTCTTTATCTCTGGGCTTCATCCACCCAATTTTTTTCTTCATTTCTCTCT
31535374 GGGCTTCATCC
66 GGGCTTCATCC
* * * *
31535385 ACCCAATTTTTTTCTTTTTTTCTCTCTGGGCTTCATCCACCCAATTTTTTTCTTCATTTCTCTCT
1 ACCCAATTTGTTTCCTTCTTTATCTCTGGGCTTCATCCACCCAATTTTTTTCTTCATTTCTCTCT
31535450 GGGCTTCATCC
66 GGGCTTCATCC
31535461 AC
1 AC
31535463 ATTCCTTCAC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
74 39 0.56
75 9 0.13
76 22 0.31
ACGTcount: A:0.12, C:0.30, G:0.09, T:0.49
Consensus pattern (76 bp):
ACCCAATTTGTTTCCTTCTTTATCTCTGGGCTTCATCCACCCAATTTTTTTCTTCATTTCTCTCT
GGGCTTCATCC
Found at i:31552988 original size:2 final size:2
Alignment explanation
Indices: 31552981--31553030 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
31552971 TTTTAGGGTT
31552981 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
31553023 TA TA TA TA
1 TA TA TA TA
31553031 AATAAAAGAA
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):
TA
Found at i:31558904 original size:30 final size:33
Alignment explanation
Indices: 31558836--31558912 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 33
31558826 TGAATTATTG
* * *
31558836 AAATATTTTTTAAATTTGAAAATGATGAAAATA
1 AAATAATTTTAAAATTTGAAAATGATGAAAAAA
*
31558869 AAATAATTTTAAAATTTG-AGA-GAT-AAAAAA
1 AAATAATTTTAAAATTTGAAAATGATGAAAAAA
*
31558899 AAATAATTATAAAA
1 AAATAATTTTAAAA
31558913 GAAATATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 18 0.46
31 3 0.08
32 2 0.05
33 16 0.41
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (33 bp):
AAATAATTTTAAAATTTGAAAATGATGAAAAAA
Found at i:31568297 original size:66 final size:66
Alignment explanation
Indices: 31568191--31568388 Score: 396
Period size: 66 Copynumber: 3.0 Consensus size: 66
31568181 AGGAAAAAGT
31568191 AAGAGGGATGATTGCTCTTGGAGGCTTCTAGGCGTGATCCCTGTTTCTCTACCTTTAAAGACTTG
1 AAGAGGGATGATTGCTCTTGGAGGCTTCTAGGCGTGATCCCTGTTTCTCTACCTTTAAAGACTTG
31568256 C
66 C
31568257 AAGAGGGATGATTGCTCTTGGAGGCTTCTAGGCGTGATCCCTGTTTCTCTACCTTTAAAGACTTG
1 AAGAGGGATGATTGCTCTTGGAGGCTTCTAGGCGTGATCCCTGTTTCTCTACCTTTAAAGACTTG
31568322 C
66 C
31568323 AAGAGGGATGATTGCTCTTGGAGGCTTCTAGGCGTGATCCCTGTTTCTCTACCTTTAAAGACTTG
1 AAGAGGGATGATTGCTCTTGGAGGCTTCTAGGCGTGATCCCTGTTTCTCTACCTTTAAAGACTTG
31568388 C
66 C
31568389 CGGAGTTTCG
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 132 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (66 bp):
AAGAGGGATGATTGCTCTTGGAGGCTTCTAGGCGTGATCCCTGTTTCTCTACCTTTAAAGACTTG
C
Found at i:31569208 original size:45 final size:44
Alignment explanation
Indices: 31569129--31569229 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 44
31569119 ATTAAATTTA
* * * *
31569129 AATAATACTAAATAATATTTTTATTACATTTATTATATTCAAAT
1 AATAATATTAAATAATATCTTTATAACATTTATTATAGTCAAAT
* * *
31569173 AATAATATTAAATAGTATGCTTTATAATATTTATTATAGTGAAAT
1 AATAATATTAAATAATAT-CTTTATAACATTTATTATAGTCAAAT
31569218 AAT-AT-TTAAATA
1 AATAATATTAAATA
31569230 TTTTCATTTC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
43 7 0.14
44 18 0.37
45 24 0.49
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (44 bp):
AATAATATTAAATAATATCTTTATAACATTTATTATAGTCAAAT
Found at i:31571253 original size:211 final size:211
Alignment explanation
Indices: 31570889--31571315 Score: 818
Period size: 211 Copynumber: 2.0 Consensus size: 211
31570879 ACTGCTCAAG
31570889 CCTGCCTTTTGGAAACACGCAAAATATCTGTTGAGGAAATTCTAGAACGTATGTTTTAACCTTTT
1 CCTGCCTTTTGGAAACACGCAAAATATCTGTTGAGGAAATTCTAGAACGTATGTTTTAACCTTTT
*
31570954 CAATTGTAACCTTTAGCTAACTCACTTGTAGTTCAGAGGAAAATAATAAAGGAAAATGGAGATCT
66 CAATTGTAACCGTTAGCTAACTCACTTGTAGTTCAGAGGAAAATAATAAAGGAAAATGGAGATCT
31571019 CAAGTTTGGCTAGATCAGCTCCAGGGCAGTTCATACTTCCCTCTTCGAAGGGTTGGAAACTCCAT
131 CAAGTTTGGCTAGATCAGCTCCAGGGCAGTTCATACTTCCCTCTTCGAAGGGTTGGAAACTCCAT
31571084 GCTATGGGTTTAAGAT
196 GCTATGGGTTTAAGAT
31571100 CCTGCCTTTTGGAAACACGCAAAATATCTGTTGAGGAAATTCTAGAACGTATGTTTTAACCTTTT
1 CCTGCCTTTTGGAAACACGCAAAATATCTGTTGAGGAAATTCTAGAACGTATGTTTTAACCTTTT
*
31571165 CAATTGTAACCGTTAGCTAACTCATTTGTAGTTCAGAGGAAAATAATAAAGGAAAATGGAGATCT
66 CAATTGTAACCGTTAGCTAACTCACTTGTAGTTCAGAGGAAAATAATAAAGGAAAATGGAGATCT
* *
31571230 CAAGTTTGGCTAGATCAGCTCCAGGGCAGTTCATACTTCCTTCTTCGAAGGGTTGGAAACTCCCT
131 CAAGTTTGGCTAGATCAGCTCCAGGGCAGTTCATACTTCCCTCTTCGAAGGGTTGGAAACTCCAT
31571295 GCTATGGGTTTAAGAT
196 GCTATGGGTTTAAGAT
31571311 CCTGC
1 CCTGC
31571316 ATTCAGGTCA
Statistics
Matches: 212, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 212 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (211 bp):
CCTGCCTTTTGGAAACACGCAAAATATCTGTTGAGGAAATTCTAGAACGTATGTTTTAACCTTTT
CAATTGTAACCGTTAGCTAACTCACTTGTAGTTCAGAGGAAAATAATAAAGGAAAATGGAGATCT
CAAGTTTGGCTAGATCAGCTCCAGGGCAGTTCATACTTCCCTCTTCGAAGGGTTGGAAACTCCAT
GCTATGGGTTTAAGAT
Found at i:31573758 original size:17 final size:17
Alignment explanation
Indices: 31573736--31573769 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31573726 CAAGGATCTA
31573736 ATCTAT-AACCTCTTCTG
1 ATCTATAAACC-CTTCTG
31573753 ATCTATAAACCCTTCTG
1 ATCTATAAACCCTTCTG
31573770 GTAATGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.38
Consensus pattern (17 bp):
ATCTATAAACCCTTCTG
Found at i:31574311 original size:28 final size:29
Alignment explanation
Indices: 31574253--31574311 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
31574243 TTAAATATTC
*
31574253 AAATGAGACATTTTTTATTGAAATTATGA
1 AAATGAGACATTTTTTATTGAAATTAAGA
* * *
31574282 AAATGAGA-TTTTTTTATTTAAGTTAAGA
1 AAATGAGACATTTTTTATTGAAATTAAGA
31574310 AA
1 AA
31574312 GAAAGAGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (29 bp):
AAATGAGACATTTTTTATTGAAATTAAGA
Found at i:31576708 original size:25 final size:25
Alignment explanation
Indices: 31576680--31576802 Score: 183
Period size: 25 Copynumber: 4.9 Consensus size: 25
31576670 AAAACCCCAG
* *
31576680 AACCGGTTTTCGCTGTAAACCCTTA
1 AACCGGTTTTCACTGGAAACCCTTA
* *
31576705 AACCGATTTTCACTGGAAACCCGTA
1 AACCGGTTTTCACTGGAAACCCTTA
* *
31576730 AATCGGTTTTCACTGGAAACCCGTA
1 AACCGGTTTTCACTGGAAACCCTTA
*
31576755 AATCGGTTTTCACTGGAAACCCTTA
1 AACCGGTTTTCACTGGAAACCCTTA
31576780 AACCGGTTTTCACTGGAAACCCT
1 AACCGGTTTTCACTGGAAACCCT
31576803 AAAGCAGCCA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 90 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (25 bp):
AACCGGTTTTCACTGGAAACCCTTA
Found at i:31583328 original size:2 final size:2
Alignment explanation
Indices: 31583321--31583359 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
31583311 TCTATATTTA
* *
31583321 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31583360 AACCTTCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:31595574 original size:216 final size:217
Alignment explanation
Indices: 31595167--31595600 Score: 663
Period size: 216 Copynumber: 2.0 Consensus size: 217
31595157 ATAACGTTGC
* *
31595167 CAGCAAAAACAATTAATTTGGAGTTAGCACAGCATATGCAACAACTGCATATGTGATGCTTGCAT
1 CAGCAAAAACAATAAATTTGGAGTTAGCACAGCATAAGCAACAACTGCATATGTGATGCTTGCAT
* * ** *
31595232 TGTTCAGGCTGAGAGGTGAACCAGAAGGTCCTATAGCGGTTGTGTATTACTGTCATTTCTTTCTC
66 TGTTCAGGCTGAGAGGCGAACC--AAGGTCCTATAGCGGTTGTGCACAACTGTCATTTCTTGCTC
* * *
31595297 CCATCATCATCGTATTCCCCAGAGCTAGTGGCTTATCTATTCACGGTATAATTGATTTGGATACC
129 CCATCATCATCCTAATCCCCAGAGCTAGTGGCTTATCTATTCACAGTATAATTGATTTGGATACC
*
31595362 AAACAAAAGTATATTATATATGAT
194 AAACAAAAGCATATTATATATGAT
* *
31595386 CAGCAAAAACACTAAATTTGGAGTTAGGACAGCATAAGCAACAACTGCATATGTGATGCTTGCAT
1 CAGCAAAAACAATAAATTTGGAGTTAGCACAGCATAAGCAACAACTGCATATGTGATGCTTGCAT
* * * *
31595451 TGTTCAGGCTGAGAGGCGGATC-AGGTCCTATAGTGTTTGTGCACAACTGTCATTTCTTGCTCCC
66 TGTTCAGGCTGAGAGGCGAACCAAGGTCCTATAGCGGTTGTGCACAACTGTCATTTCTTGCTCCC
*
31595515 ATCATCATCCTAATCCCCAGAGCTAGTGGCTTATCTATTCACATTATAATTGATTTGGATACCAA
131 ATCATCATCCTAATCCCCAGAGCTAGTGGCTTATCTATTCACAGTATAATTGATTTGGATACCAA
* *
31595580 GCAACAGCATATTATATATGA
196 ACAAAAGCATATTATATATGA
31595601 ATTTTTTTAG
Statistics
Matches: 195, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
216 115 0.59
219 80 0.41
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (217 bp):
CAGCAAAAACAATAAATTTGGAGTTAGCACAGCATAAGCAACAACTGCATATGTGATGCTTGCAT
TGTTCAGGCTGAGAGGCGAACCAAGGTCCTATAGCGGTTGTGCACAACTGTCATTTCTTGCTCCC
ATCATCATCCTAATCCCCAGAGCTAGTGGCTTATCTATTCACAGTATAATTGATTTGGATACCAA
ACAAAAGCATATTATATATGAT
Found at i:31599227 original size:18 final size:18
Alignment explanation
Indices: 31599204--31599242 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
31599194 AATTCGTACC
31599204 TATATCTATATATAATAA
1 TATATCTATATATAATAA
31599222 TATATCTATATATAATAA
1 TATATCTATATATAATAA
31599240 TAT
1 TAT
31599243 TTCTCATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATCTATATATAATAA
Found at i:31599895 original size:13 final size:15
Alignment explanation
Indices: 31599868--31599899 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
31599858 TAAATATGTT
31599868 TATATTAAAAGTATA
1 TATATTAAAAGTATA
31599883 TATATT-AAA-TATA
1 TATATTAAAAGTATA
31599896 TATA
1 TATA
31599900 ATAATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 3 0.18
15 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TATATTAAAAGTATA
Found at i:31602348 original size:29 final size:30
Alignment explanation
Indices: 31602268--31602348 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
31602258 TATATGACTC
* * **
31602268 AAAATAAAAAATATAAAAAATTGTTTAGTTT
1 AAAAT-AAAAATATAAAAACTTGATTAGAAT
* **
31602299 AAAATAAAAATACAATGACTTGATT-GAAT
1 AAAATAAAAATATAAAAACTTGATTAGAAT
*
31602328 ATAATAAAAATATAAAAACTT
1 AAAATAAAAATATAAAAACTT
31602349 ATTTAAATTT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
29 19 0.49
30 15 0.38
31 5 0.13
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (30 bp):
AAAATAAAAATATAAAAACTTGATTAGAAT
Found at i:31615050 original size:16 final size:16
Alignment explanation
Indices: 31615029--31615060 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31615019 TTACTGGTAC
31615029 CTCTATTCTAACACAA
1 CTCTATTCTAACACAA
*
31615045 CTCTATTCTAATACAA
1 CTCTATTCTAACACAA
31615061 ATAAATGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (16 bp):
CTCTATTCTAACACAA
Found at i:31621716 original size:30 final size:27
Alignment explanation
Indices: 31621664--31621722 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
31621654 AAAATTTTAG
*
31621664 AAAATTTACATTTTTTTATTTTTCTTAA
1 AAAATCTACATTTTTTTATTTTTC-TAA
*
31621692 AAAATCTACACTTTTTTATCTTTTTCTAA
1 AAAATCTACA-TTTTTT-TATTTTTCTAA
31621721 AA
1 AA
31621723 TCGACATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 9 0.33
29 11 0.41
30 7 0.26
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (27 bp):
AAAATCTACATTTTTTTATTTTTCTAA
Found at i:31640344 original size:27 final size:26
Alignment explanation
Indices: 31640288--31640344 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
31640278 TTTTTATTTT
*
31640288 ATTT-TTTAAATATTAATAAGTGATT
1 ATTTATTTAAATATTAATAAGTGATA
* *
31640313 CTTTATTTAAAATATTAATAATTGATA
1 ATTTATTT-AAATATTAATAAGTGATA
31640340 ATTTA
1 ATTTA
31640345 ATTATTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 3 0.12
26 3 0.12
27 20 0.77
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (26 bp):
ATTTATTTAAATATTAATAAGTGATA
Found at i:31640493 original size:27 final size:27
Alignment explanation
Indices: 31640452--31640509 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
31640442 AATTTAATAT
* *
31640452 ATTT-TTTTAAATATTAATAATTTATC
1 ATTTATTTTAAATATTAATAATTGATA
*
31640478 ATTTATTTTAAATATTACTAATTGATA
1 ATTTATTTTAAATATTAATAATTGATA
31640505 ATTTA
1 ATTTA
31640510 ATTATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (27 bp):
ATTTATTTTAAATATTAATAATTGATA
Found at i:31640529 original size:123 final size:119
Alignment explanation
Indices: 31640389--31640643 Score: 393
Period size: 123 Copynumber: 2.1 Consensus size: 119
31640379 CATTTTAAAA
* *
31640389 TATTAATATTTTGTTTATAATTGAAATATTATTATGATTATTTAATTTAACTTAATTTAATATAT
1 TATTAATATTTTATTTATAATTGAAATATTATTATGACTATTTAATTTAACTTAATTTAAT-T-T
* * *
31640454 TTTTTTAAATATTAATAATTTATCATTTATTTTAAATATTACTAATTGATAATTTAAT
64 ATTTTTAAATATTAATAATTTATAATTTATTTAAAATATT--TAATTGATAATTTAAT
*
31640512 TATTAATATTTTATTTATAATTGAAATATTATTATGACTATTTAATTTAATTTAATTTAATTTAT
1 TATTAATATTTTATTTATAATTGAAATATTATTATGACTATTTAATTTAACTTAATTTAATTTAT
* *
31640577 TTTTAAATATTAATAATTTATAATTTATTTAAAATATTTTATTTATAATTTAAT
66 TTTTAAATATTAATAATTTATAATTTATTTAAAATATTTAATTGATAATTTAAT
*
31640631 CATTAATATTTTA
1 TATTAATATTTTA
31640644 AAATATTAAT
Statistics
Matches: 123, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
119 26 0.21
121 38 0.31
122 1 0.01
123 58 0.47
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (119 bp):
TATTAATATTTTATTTATAATTGAAATATTATTATGACTATTTAATTTAACTTAATTTAATTTAT
TTTTAAATATTAATAATTTATAATTTATTTAAAATATTTAATTGATAATTTAAT
Found at i:31640533 original size:26 final size:26
Alignment explanation
Indices: 31640502--31640643 Score: 92
Period size: 26 Copynumber: 5.9 Consensus size: 26
31640492 TTACTAATTG
31640502 ATAATTTAATTATTAATATTTTATTT
1 ATAATTTAATTATTAATATTTTATTT
* * * **
31640528 ATAATTGAAATATTATTATGACTA-TT
1 ATAATTTAATTATTAATAT-TTTATTT
*
31640554 -TAATTTAA-T-TT-A-ATTTAATTT
1 ATAATTTAATTATTAATATTTTATTT
* *
31640575 AT-TTTTAAATATTAATA----ATTT
1 ATAATTTAATTATTAATATTTTATTT
* *
31640596 ATAATTTATTTA-AAATATTTTATTT
1 ATAATTTAATTATTAATATTTTATTT
*
31640621 ATAATTTAATCATTAATATTTTA
1 ATAATTTAATTATTAATATTTTA
31640644 AAATATTAAT
Statistics
Matches: 85, Mismatches: 18, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
20 1 0.01
21 19 0.22
22 8 0.09
23 4 0.05
24 2 0.02
25 22 0.26
26 27 0.32
27 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
ATAATTTAATTATTAATATTTTATTT
Found at i:31640554 original size:32 final size:33
Alignment explanation
Indices: 31640496--31640626 Score: 84
Period size: 32 Copynumber: 4.2 Consensus size: 33
31640486 TAAATATTAC
* *
31640496 TAATTGATAATTTAATTATTAATATTTTATTTA
1 TAATTGATAATTTAATTATGAATATTTAATTTA
*
31640529 TAATTGA-AATATT-ATTATGACTATTTAA-TT-
1 TAATTGATAAT-TTAATTATGAATATTTAATTTA
*
31640559 TAATT--TAATTTAATT-T--ATTTTTAAATATTAA
1 TAATTGATAATTTAATTATGAATATTT-AAT-TT-A
* * * *
31640590 TAATTTATAATTTATTTA-AAATATTTTATTTA
1 TAATTGATAATTTAATTATGAATATTTAATTTA
31640622 TAATT
1 TAATT
31640627 TAATCATTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
26 4 0.05
27 2 0.03
28 3 0.04
29 8 0.10
30 5 0.06
31 7 0.09
32 21 0.27
33 20 0.26
34 2 0.03
35 5 0.06
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (33 bp):
TAATTGATAATTTAATTATGAATATTTAATTTA
Found at i:31640561 original size:5 final size:5
Alignment explanation
Indices: 31640551--31640575 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31640541 TATTATGACT
31640551 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
31640576 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:31640582 original size:21 final size:20
Alignment explanation
Indices: 31640557--31640630 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
31640547 GACTATTTAA
31640557 TTTAATTTAATTTAATTTATT
1 TTTAATTTAA-TTAATTTATT
*
31640578 TTTAAATATTAA-TAATTTATAA
1 TTT-AAT-TTAATTAATTTAT-T
* *
31640600 TTT-ATTTAAAATATTTTATT
1 TTTAATTT-AATTAATTTATT
*
31640620 TATAATTTAAT
1 TTTAATTTAAT
31640631 CATTAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
19 2 0.05
20 8 0.19
21 22 0.52
22 6 0.14
23 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATTTAATTAATTTATT
Found at i:31640621 original size:46 final size:46
Alignment explanation
Indices: 31640478--31640622 Score: 127
Period size: 46 Copynumber: 3.1 Consensus size: 46
31640468 ATAATTTATC
* * *
31640478 ATTTA-TTTTAAATATTACTAATTGATAATTTAATTATTAATATTTT
1 ATTTATTTTTAAATATTAATAATTGATAATTTATTTA-AAATATTTT
* * * ** *
31640524 ATTTATAATTGAAATATT-ATTA-TGACT-ATTTAATTTAATTTAATTTA
1 ATTTAT-TTTTAAATATTAATAATTGA-TAATTT-ATTTAAAAT-ATTTT
*
31640571 ATTTATTTTTAAATATTAATAATTTATAATTTATTTAAAATATTTT
1 ATTTATTTTTAAATATTAATAATTGATAATTTATTTAAAATATTTT
31640617 ATTTAT
1 ATTTAT
31640623 AATTTAATCA
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
46 32 0.43
47 28 0.37
48 15 0.20
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (46 bp):
ATTTATTTTTAAATATTAATAATTGATAATTTATTTAAAATATTTT
Found at i:31640626 original size:25 final size:27
Alignment explanation
Indices: 31640569--31640628 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
31640559 TAATTTAATT
*
31640569 TAATTTATTTTTAAATATTAATAATTTA
1 TAATTTATTTTAAAATATT-ATAATTTA
*
31640597 TAATTTA-TTTAAAATATT-TTATTTA
1 TAATTTATTTTAAAATATTATAATTTA
31640622 TAATTTA
1 TAATTTA
31640629 ATCATTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 13 0.43
27 10 0.33
28 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TAATTTATTTTAAAATATTATAATTTA
Found at i:31654608 original size:14 final size:14
Alignment explanation
Indices: 31654589--31654618 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31654579 TTGTTATTTA
31654589 TATTTATATTTATT
1 TATTTATATTTATT
*
31654603 TATTTATTTTTATT
1 TATTTATATTTATT
31654617 TA
1 TA
31654619 CTCATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTATATTTATT
Found at i:31654610 original size:18 final size:18
Alignment explanation
Indices: 31654560--31654618 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
31654550 TTTAAATTTT
*
31654560 TTTATTTTTTTAATTTATA
1 TTTATTTATTT-ATTTATA
31654579 TTGTTATTTA--TATTTATA
1 -T-TTATTTATTTATTTATA
*
31654597 TTTATTTATTTATTTTTA
1 TTTATTTATTTATTTATA
31654615 TTTA
1 TTTA
31654619 CTCATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 7 0.21
17 1 0.03
18 18 0.53
19 1 0.03
20 1 0.03
21 6 0.18
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTATTTATTTATTTATA
Found at i:31673015 original size:20 final size:20
Alignment explanation
Indices: 31672974--31673016 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
31672964 CAGAATATGC
*
31672974 AAAGGAAATATAAAAAAGGA
1 AAAGGAAATATAAAAAAAGA
*
31672994 AAAGTAAATA-AAAACAAAGA
1 AAAGGAAATATAAAA-AAAGA
31673014 AAA
1 AAA
31673017 CTCGTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAGGAAATATAAAAAAAGA
Found at i:31674204 original size:2 final size:2
Alignment explanation
Indices: 31674191--31674222 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31674181 CAACAATCAC
*
31674191 CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31674223 TCCTTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:31699522 original size:17 final size:17
Alignment explanation
Indices: 31699500--31699537 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
31699490 GCTCGGTGTG
31699500 GAGAGAGAAG-AGGGAAA
1 GAGAGAGAAGAAGGG-AA
31699517 GAGAGAGAAGAAGGGAA
1 GAGAGAGAAGAAGGGAA
31699534 GAGA
1 GAGA
31699538 TTGAGAGCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (17 bp):
GAGAGAGAAGAAGGGAA
Found at i:31700260 original size:33 final size:33
Alignment explanation
Indices: 31700220--31700297 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
31700210 ATTATGTTAA
* * * *
31700220 ATCAACATATCACATCGTTATTAATTATAATAT
1 ATCAACATATCAAATCATTATCAATTATAATAC
* *
31700253 ATTAACATATCAAATTATTATCAATTATAATAC
1 ATCAACATATCAAATCATTATCAATTATAATAC
31700286 ATCAACATATCA
1 ATCAACATATCA
31700298 TGTCAACATC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.37
Consensus pattern (33 bp):
ATCAACATATCAAATCATTATCAATTATAATAC
Found at i:31704035 original size:2 final size:2
Alignment explanation
Indices: 31704028--31704062 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
31704018 TATGATTTTA
31704028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31704063 GATGAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:31717675 original size:37 final size:37
Alignment explanation
Indices: 31717625--31717700 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
31717615 AGAACATTCA
*
31717625 TTGCCTCCCTGTTTATGCATTTATTCTCCTAGTTGTG
1 TTGCCTCCCTGTTTATGCATTTATGCTCCTAGTTGTG
31717662 TTGCCTCCCTGTTTATGCATTTATGCTCCTAGTTGTG
1 TTGCCTCCCTGTTTATGCATTTATGCTCCTAGTTGTG
31717699 TT
1 TT
31717701 CATTAGCTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.49
Consensus pattern (37 bp):
TTGCCTCCCTGTTTATGCATTTATGCTCCTAGTTGTG
Found at i:31723330 original size:2 final size:2
Alignment explanation
Indices: 31723323--31723367 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
31723313 GATTAATTTA
31723323 AT AT AT AT AT AT AT AT AT AT A- 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
31723364 AT AT
1 AT AT
31723368 TGAATCGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31723347 original size:21 final size:21
Alignment explanation
Indices: 31723321--31723364 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31723311 AGGATTAATT
31723321 TAATATATATATATATATATA
1 TAATATATATATATATATATA
31723342 TAATATATATATATATATATA
1 TAATATATATATATATATATA
31723363 TA
1 TA
31723365 TATTGAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATATATATATATATATA
Found at i:31731665 original size:26 final size:26
Alignment explanation
Indices: 31731597--31731665 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
31731587 GAGAGAGCGG
* *
31731597 GGTTTAATAAGGGTCCAAGAGCGCAA
1 GGTTTAGTAAGGGTGCAAGAGCGCAA
* * *
31731623 GGTTTAGTAAGGATGCATGAGCGCAG
1 GGTTTAGTAAGGGTGCAAGAGCGCAA
*
31731649 GGTTTGGTAAGGGTGCA
1 GGTTTAGTAAGGGTGCA
31731666 CTCAATCTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.28, C:0.12, G:0.38, T:0.23
Consensus pattern (26 bp):
GGTTTAGTAAGGGTGCAAGAGCGCAA
Found at i:31739930 original size:124 final size:119
Alignment explanation
Indices: 31739696--31739938 Score: 288
Period size: 124 Copynumber: 2.0 Consensus size: 119
31739686 CCAAGTTTGC
* *
31739696 AACAGTGAAGAGGCTAACCATACATATACCTATTGTTGGTATATTTTTAAAATTAAAAAATTATA
1 AACAGTGAAAAGGCTAACCATACATATACCTATTGTTGGTATATTTTTAAAATCAAAAAATTATA
* * * * * *
31739761 TCACATAATAAAAAATTATTTTAACTCGAAAGTTATATTATATAAAGTGACATA
66 TCACATAATAAAAAACTATCTTAACTCAAAAATTATATCACATAAAGTGACATA
* * *
31739815 AACAGTGAAAAGGCTAACCATACATATTCTCTATTGTTTGTTGGTGTATTTTTAAAATCAAAAAG
1 AACAGTGAAAAGGCTAACCATACATATAC-CTA----TTGTTGGTATATTTTTAAAATCAAAAAA
* * ** * *
31739880 TTATATCACATGATAAAAAGCTATCTTAGTTTAAAAATTATGTCACATAAAGTGACATA
61 TTATATCACATAATAAAAAACTATCTTAACTCAAAAATTATATCACATAAAGTGACATA
31739939 GTGTGTTTAT
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
119 27 0.26
120 3 0.03
124 72 0.71
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (119 bp):
AACAGTGAAAAGGCTAACCATACATATACCTATTGTTGGTATATTTTTAAAATCAAAAAATTATA
TCACATAATAAAAAACTATCTTAACTCAAAAATTATATCACATAAAGTGACATA
Found at i:31746458 original size:60 final size:61
Alignment explanation
Indices: 31746385--31746508 Score: 232
Period size: 60 Copynumber: 2.0 Consensus size: 61
31746375 TGTGCATTCT
31746385 TTTCATTTTTATGTGTTAGTATTTCCATTTTGTTTTAGCTGTTTTTGTCTAGATTC-AAAC
1 TTTCATTTTTATGTGTTAGTATTTCCATTTTGTTTTAGCTGTTTTTGTCTAGATTCAAAAC
*
31746445 TTTCATTTTTATGTGTTAGTATTTTCATTTTGTTTTAGCTGTTTTTGTCTAGATTCAAAAC
1 TTTCATTTTTATGTGTTAGTATTTCCATTTTGTTTTAGCTGTTTTTGTCTAGATTCAAAAC
31746506 TTT
1 TTT
31746509 ATGTTATTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 55 0.89
61 7 0.11
ACGTcount: A:0.19, C:0.10, G:0.13, T:0.58
Consensus pattern (61 bp):
TTTCATTTTTATGTGTTAGTATTTCCATTTTGTTTTAGCTGTTTTTGTCTAGATTCAAAAC
Found at i:31755096 original size:30 final size:30
Alignment explanation
Indices: 31755060--31755119 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
31755050 AATGCCTTTT
31755060 AACGATGACCCTTGTACCTCTCCATCAGAG
1 AACGATGACCCTTGTACCTCTCCATCAGAG
*
31755090 AACGATGATCCTTGTACCTCTCCATCAGAG
1 AACGATGACCCTTGTACCTCTCCATCAGAG
31755120 TCCGTAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (30 bp):
AACGATGACCCTTGTACCTCTCCATCAGAG
Found at i:31761830 original size:1 final size:1
Alignment explanation
Indices: 31761824--31761849 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
31761814 ATTCATTTGN
31761824 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
31761850 TCTTTTTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:31767681 original size:34 final size:34
Alignment explanation
Indices: 31767643--31767710 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
31767633 TTTATATTTT
* *
31767643 ATAAATTATAAGAGAAAAATTATGCGATTTAATC
1 ATAAATTATAAAAGAAAAATTATACGATTTAATC
*
31767677 ATAAATTATAAAAGAAAATTTATACGATTTAATC
1 ATAAATTATAAAAGAAAAATTATACGATTTAATC
31767711 GAATTATACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (34 bp):
ATAAATTATAAAAGAAAAATTATACGATTTAATC
Found at i:31769135 original size:17 final size:17
Alignment explanation
Indices: 31769113--31769151 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31769103 CAAAGTAAAA
* *
31769113 AATTATACTATTTAGGC
1 AATTATAATATTTAAGC
*
31769130 AATTATAATCTTTAAGC
1 AATTATAATATTTAAGC
31769147 AATTA
1 AATTA
31769152 CGCAATGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (17 bp):
AATTATAATATTTAAGC
Found at i:31769203 original size:22 final size:22
Alignment explanation
Indices: 31769177--31769220 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31769167 AATCAAAATT
* *
31769177 TGAGTTTATTCTACAAGGAAAA
1 TGAGTTTACTCTACAAAGAAAA
*
31769199 TGAGTTTACTCTATAAAGAAAA
1 TGAGTTTACTCTACAAAGAAAA
31769221 AAAAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (22 bp):
TGAGTTTACTCTACAAAGAAAA
Found at i:31787588 original size:3 final size:3
Alignment explanation
Indices: 31787580--31787609 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
31787570 CACTTATTGG
31787580 ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31787610 AATCTTGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:31787974 original size:2 final size:2
Alignment explanation
Indices: 31787969--31787994 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31787959 TATATATATA
31787969 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
31787995 GAGGGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:31796566 original size:14 final size:15
Alignment explanation
Indices: 31796548--31796589 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
31796538 ATATGTCAAG
*
31796548 TTAAATTTTATACGA
1 TTAAAATTTATACGA
*
31796563 -TAAAATTAATACGA
1 TTAAAATTTATACGA
31796577 TTAAAATTTATAC
1 TTAAAATTTATAC
31796590 AATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (15 bp):
TTAAAATTTATACGA
Found at i:31796735 original size:19 final size:18
Alignment explanation
Indices: 31796690--31796736 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
31796680 CAAATTTACA
*
31796690 AAAAAAATTATAAATATC
1 AAAAAATTTATAAATATC
*
31796708 AAAATATTTATCAAATAT-
1 AAAAAATTTAT-AAATATC
31796726 AATAAAATTTA
1 AA-AAAATTTA
31796737 ATATTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAAATTTATAAATATC
Found at i:31799249 original size:16 final size:16
Alignment explanation
Indices: 31799228--31799258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31799218 TTTCATTAAA
*
31799228 TTTTTAGAAAATAATT
1 TTTTTAAAAAATAATT
31799244 TTTTTAAAAAATAAT
1 TTTTTAAAAAATAAT
31799259 AAAATAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTTTTAAAAAATAATT
Found at i:31800328 original size:26 final size:26
Alignment explanation
Indices: 31800292--31800343 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31800282 GAGACAGAAC
31800292 TGACTCCAAATTCAAATGTATATGTA
1 TGACTCCAAATTCAAATGTATATGTA
31800318 TGACTCCAAATTCAAATGTATATGTA
1 TGACTCCAAATTCAAATGTATATGTA
31800344 CTAATCTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (26 bp):
TGACTCCAAATTCAAATGTATATGTA
Found at i:31803307 original size:2 final size:2
Alignment explanation
Indices: 31803300--31803344 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
31803290 TATGTATGTT
31803300 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
31803342 TA T
1 TA T
31803345 TTCCCTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31807737 original size:2 final size:2
Alignment explanation
Indices: 31807725--31807794 Score: 131
Period size: 2 Copynumber: 34.5 Consensus size: 2
31807715 TTTGCCATAG
31807725 AT AT CAT 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
31807768 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 A
31807795 CACATACATA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 65 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31808260 original size:2 final size:2
Alignment explanation
Indices: 31808253--31808295 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
31808243 CAATCAAAGT
31808253 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31808295 A
1 A
31808296 TTTGAAGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31809573 original size:2 final size:2
Alignment explanation
Indices: 31809566--31809610 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
31809556 NNNNNNNNNN
31809566 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31809608 TC T
1 TC T
31809611 TTGTTGGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:31810973 original size:2 final size:2
Alignment explanation
Indices: 31810960--31811048 Score: 151
Period size: 2 Copynumber: 44.0 Consensus size: 2
31810950 CGTTTTCCTA
*
31810960 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG TAG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG
*
31811003 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31811045 AG AG
1 AG AG
31811049 CGTTTCAAGA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 80 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:31822165 original size:16 final size:17
Alignment explanation
Indices: 31822135--31822168 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31822125 AGTAGTAATT
*
31822135 AATTAAGAATTAAGGAA
1 AATTAAGAATAAAGGAA
31822152 AATT-AGAATAAAGGAA
1 AATTAAGAATAAAGGAA
31822168 A
1 A
31822169 GATAAGAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (17 bp):
AATTAAGAATAAAGGAA
Found at i:31827548 original size:21 final size:21
Alignment explanation
Indices: 31827522--31827562 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
31827512 TGAAAATAAG
31827522 TATGCGGAGTGTGTAGATGGT
1 TATGCGGAGTGTGTAGATGGT
31827543 TATGCGGAGTGTGTAGATGG
1 TATGCGGAGTGTGTAGATGG
31827563 ACCGACAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.05, G:0.44, T:0.32
Consensus pattern (21 bp):
TATGCGGAGTGTGTAGATGGT
Found at i:31834147 original size:20 final size:20
Alignment explanation
Indices: 31834111--31834148 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31834101 AAAAACACAC
*
31834111 AAATAATAAAATTTAAATTT
1 AAATAATAAAATATAAATTT
31834131 AAATAATCAAAA-ATAAAT
1 AAATAAT-AAAATATAAAT
31834149 ATCTCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAAAATATAAATTT
Found at i:31834172 original size:35 final size:34
Alignment explanation
Indices: 31834119--31834190 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
31834109 ACAAATAATA
* * *
31834119 AAATTTAAATTTAAATAATCAAAAATAAATATCTC
1 AAATATAAACTTAAATAATCAAAAACAAATATC-C
*
31834154 AAATATAAACTTAAATAATTAAAAACAAATATCC
1 AAATATAAACTTAAATAATCAAAAACAAATATCC
31834188 AAA
1 AAA
31834191 CAACAACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 4 0.12
35 29 0.88
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (34 bp):
AAATATAAACTTAAATAATCAAAAACAAATATCC
Found at i:31834532 original size:22 final size:22
Alignment explanation
Indices: 31834482--31834547 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 22
31834472 TATATATTAA
*
31834482 AAATTTA-TAAATAAATTA-AT
1 AAATTTATTATATAAATTATAT
*
31834502 AATTATTATTATATAAATTATAT
1 AAAT-TTATTATATAAATTATAT
*
31834525 AAATTTATT-T-TTAATTATAT
1 AAATTTATTATATAAATTATAT
31834545 AAA
1 AAA
31834548 ATTAAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 15 0.38
21 4 0.10
22 15 0.38
23 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTTATTATATAAATTATAT
Found at i:31834895 original size:18 final size:20
Alignment explanation
Indices: 31834858--31834895 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
31834848 TTGTCACGGT
*
31834858 ATAAAGTTTACATGTTATCA
1 ATAAAGTTTACATATTATCA
31834878 ATAAA-TTTA-ATATTATCA
1 ATAAAGTTTACATATTATCA
31834896 TTTTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
ATAAAGTTTACATATTATCA
Found at i:31841374 original size:15 final size:15
Alignment explanation
Indices: 31841356--31841405 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
31841346 AACCATTTTC
31841356 CTCTTTCCTCTTCTT
1 CTCTTTCCTCTTCTT
* *
31841371 CTCTTTACTCTTCTCC
1 CTCTTTCCTCTTCT-T
31841387 CTCTCTTCTCTCTTCTT
1 CTCT-TTC-CTCTTCTT
31841404 CT
1 CT
31841406 TCTTCTTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 13 0.46
16 4 0.14
17 4 0.14
18 7 0.25
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (15 bp):
CTCTTTCCTCTTCTT
Found at i:31843171 original size:23 final size:23
Alignment explanation
Indices: 31843141--31843187 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
31843131 TTGGCTTGGT
*
31843141 CACCAATCCTCCACGCATCTGTC
1 CACCAATCCTCCACACATCTGTC
31843164 CACCAATCCTCCACACATCTGTC
1 CACCAATCCTCCACACATCTGTC
31843187 C
1 C
31843188 TTGTTGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.49, G:0.06, T:0.21
Consensus pattern (23 bp):
CACCAATCCTCCACACATCTGTC
Found at i:31847566 original size:21 final size:21
Alignment explanation
Indices: 31847542--31847593 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
31847532 TATGCCAGTG
31847542 GTGGCTGACAGGTAGCATATT
1 GTGGCTGACAGGTAGCATATT
* *
31847563 GTGGCTAACAGGTAGTATATT
1 GTGGCTGACAGGTAGCATATT
31847584 GTGGCTGACA
1 GTGGCTGACA
31847594 TGTGCATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.33, T:0.29
Consensus pattern (21 bp):
GTGGCTGACAGGTAGCATATT
Found at i:31848544 original size:93 final size:93
Alignment explanation
Indices: 31848379--31848558 Score: 324
Period size: 93 Copynumber: 1.9 Consensus size: 93
31848369 TTAAGAAGTC
*
31848379 TCCTTGTTTATAAATATTTTCAATCAATAGAATCCACTGGTGCAGGTTAGAGAAACAGGTATGTC
1 TCCTTGTTTATAAATATTTTCAATCAATAGAATACACTGGTGCAGGTTAGAGAAACAGGTATGTC
31848444 TTATTTTTCTGTATATGGAGCAGAGGTT
66 TTATTTTTCTGTATATGGAGCAGAGGTT
*
31848472 TCCTTGTTTATAAATATTTTCAATCAATAGAATACACTGGTGCAGGTTAGAGAAACAGGTATGTT
1 TCCTTGTTTATAAATATTTTCAATCAATAGAATACACTGGTGCAGGTTAGAGAAACAGGTATGTC
* *
31848537 TTTTTTTTCTGTATGTGGAGCA
66 TTATTTTTCTGTATATGGAGCA
31848559 TAACTTTGTC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (93 bp):
TCCTTGTTTATAAATATTTTCAATCAATAGAATACACTGGTGCAGGTTAGAGAAACAGGTATGTC
TTATTTTTCTGTATATGGAGCAGAGGTT
Found at i:31872905 original size:23 final size:23
Alignment explanation
Indices: 31872878--31872923 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
31872868 GACTTTTGGC
*
31872878 TTTTTGTCATTTCCAACATTTTT
1 TTTTTATCATTTCCAACATTTTT
31872901 TTTTTATCATTTCCAACATTTTT
1 TTTTTATCATTTCCAACATTTTT
31872924 AAAATAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTTATCATTTCCAACATTTTT
Found at i:31894101 original size:22 final size:22
Alignment explanation
Indices: 31894050--31894101 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
31894040 CAGATGAGAG
*
31894050 TTTATGTCTATTTCCAATAGAT
1 TTTATGTCTATTTCCAACAGAT
* *
31894072 TTGAATGTCTGTTT-CAACAGAT
1 TT-TATGTCTATTTCCAACAGAT
31894094 ATTTATGT
1 -TTTATGT
31894102 GATAATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (22 bp):
TTTATGTCTATTTCCAACAGAT
Found at i:31894222 original size:26 final size:25
Alignment explanation
Indices: 31894189--31894254 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 25
31894179 TTATATATTA
31894189 TTAATTTAATTA-ATTTTAAGCTCAT
1 TTAATTTAATTATATTTT-AGCTCAT
*
31894214 CTTAATTTATTTTATATTTTAGCTCAT
1 -TTAATTTA-ATTATATTTTAGCTCAT
31894241 TTAATTCTAATTAT
1 TTAATT-TAATTAT
31894255 TATGTACTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 18 0.51
27 12 0.34
28 5 0.14
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.56
Consensus pattern (25 bp):
TTAATTTAATTATATTTTAGCTCAT
Found at i:31905161 original size:19 final size:19
Alignment explanation
Indices: 31905129--31905173 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
31905119 GTTTTAAACA
** *
31905129 TTAATTTATTTTTAATGAT
1 TTAATTTAAATTTAATCAT
*
31905148 TTAATTTAAATTTATTCAT
1 TTAATTTAAATTTAATCAT
31905167 TTAATTT
1 TTAATTT
31905174 TATTAATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTAATTTAAATTTAATCAT
Found at i:31913633 original size:6 final size:6
Alignment explanation
Indices: 31913622--31913648 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31913612 ACAATTTCGG
31913622 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
31913649 CCTTTTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:31920089 original size:21 final size:21
Alignment explanation
Indices: 31920065--31920105 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31920055 TTCAAGTCGA
*
31920065 AAAATGTTTTT-TTATCGATTC
1 AAAACGTTTTTATTAT-GATTC
31920086 AAAACGTTTTTATTATGATT
1 AAAACGTTTTTATTATGATT
31920106 TATATATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (21 bp):
AAAACGTTTTTATTATGATTC
Found at i:31923860 original size:26 final size:26
Alignment explanation
Indices: 31923823--31923874 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
31923813 ACTGTGGGCC
31923823 TCTTTGTCCTAATGACGTCTTTACAA
1 TCTTTGTCCTAATGACGTCTTTACAA
*
31923849 TCTTTGTTCTAATGACGTCTTTACAA
1 TCTTTGTCCTAATGACGTCTTTACAA
31923875 GCCCACAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (26 bp):
TCTTTGTCCTAATGACGTCTTTACAA
Found at i:31927593 original size:8 final size:7
Alignment explanation
Indices: 31927577--31927637 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 7
31927567 CCTCTGTACA
31927577 TCTTCTC
1 TCTTCTC
31927584 T-TTCTC
1 TCTTCTC
31927590 TC-T-TC
1 TCTTCTC
31927595 TCTTCTC
1 TCTTCTC
31927602 -CTTCT-
1 TCTTCTC
*
31927607 TATTCT-
1 TCTTCTC
31927613 TCTTCT-
1 TCTTCTC
31927619 TCTTCT-
1 TCTTCTC
31927625 TCTTCT-
1 TCTTCTC
31927631 TCTTCTC
1 TCTTCTC
31927638 CCTATTTGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
5 4 0.09
6 40 0.85
7 3 0.06
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (7 bp):
TCTTCTC
Found at i:31927598 original size:18 final size:18
Alignment explanation
Indices: 31927577--31927637 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
31927567 CCTCTGTACA
31927577 TCTTCTCTTTCTCTCTTC-
1 TCTTCTCTTTCT-TCTTCT
* *
31927595 TCTTCTCCTTCTTATTCT
1 TCTTCTCTTTCTTCTTCT
31927613 TCTTCT-TCTTCTTCTTCT
1 TCTTCTCT-TTCTTCTTCT
31927631 TCTTCTC
1 TCTTCTC
31927638 CCTATTTGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 32 0.89
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTCTCTTTCTTCTTCT
Found at i:31927617 original size:3 final size:3
Alignment explanation
Indices: 31927585--31927636 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
31927575 CATCTTCTCT
* *
31927585 TTC TCTC TTC -TC TTC TCC TTC TTA TTC TTC TTC TTC TTC TTC TTC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
31927630 TTC TTC T
1 TTC TTC T
31927637 CCCTATTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:31929433 original size:16 final size:16
Alignment explanation
Indices: 31929412--31929444 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31929402 GAAGTTTAGA
31929412 TAGCCACGACAATTTT
1 TAGCCACGACAATTTT
*
31929428 TAGCCATGACAATTTT
1 TAGCCACGACAATTTT
31929444 T
1 T
31929445 GTTTCTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (16 bp):
TAGCCACGACAATTTT
Found at i:31935010 original size:2 final size:2
Alignment explanation
Indices: 31935003--31935037 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31934993 TAATTCTTTC
31935003 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
31935038 AGAAACTAAA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31943313 original size:16 final size:16
Alignment explanation
Indices: 31943294--31943326 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31943284 TTAATTAATT
31943294 AATTA-TTAATTATAAA
1 AATTATTTAATT-TAAA
31943310 AATTATTTAATTTAAA
1 AATTATTTAATTTAAA
31943326 A
1 A
31943327 TAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTATTTAATTTAAA
Found at i:31943336 original size:29 final size:27
Alignment explanation
Indices: 31943304--31943376 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 27
31943294 AATTATTAAT
*
31943304 TATAAAAATTATTTAATTTAAAATAAAAA
1 TATAAAAATTATTTAATGT--AATAAAAA
*
31943333 TATAAAATTTAATTTAATGTAATAAAAA
1 TATAAAAATT-ATTTAATGTAATAAAAA
31943361 TAATAAAAAATTATTT
1 T-AT-AAAAATTATTT
31943377 TAAATATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 9 0.24
29 15 0.39
30 14 0.37
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
TATAAAAATTATTTAATGTAATAAAAA
Found at i:31943348 original size:25 final size:27
Alignment explanation
Indices: 31943314--31943368 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 27
31943304 TATAAAAATT
31943314 ATTTAATTTAA-AATAAAAAT-ATAAA
1 ATTTAATTTAATAATAAAAATAATAAA
31943339 ATTTAATTTAATGTAATAAAAATAATAAA
1 ATTTAATTTAA--TAATAAAAATAATAAA
31943368 A
1 A
31943369 AATTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 11 0.42
28 9 0.35
29 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATTTAATTTAATAATAAAAATAATAAA
Found at i:31943379 original size:30 final size:31
Alignment explanation
Indices: 31943267--31943379 Score: 96
Period size: 30 Copynumber: 3.7 Consensus size: 31
31943257 ATATTATATA
*
31943267 AAATAATA-AATAATT-TTTTAATTAATTAAT
1 AAATAATATAAAAATTATTTTAATTAA-TAAT
* *
31943297 TATTAATTATAAAAATTA-TTTAATTTAA-AAT
1 AAATAA-TATAAAAATTATTTTAA-TTAATAAT
* *
31943328 AAA-AATATAAAATTTAATTTAATGTAATAA-
1 AAATAATATAAAAATTATTTTAAT-TAATAAT
31943358 AAATAATA-AAAAATTATTTTAA
1 AAATAATATAAAAATTATTTTAA
31943380 ATATTTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
29 11 0.16
30 29 0.43
31 12 0.18
32 11 0.16
33 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
AAATAATATAAAAATTATTTTAATTAATAAT
Found at i:31944559 original size:21 final size:21
Alignment explanation
Indices: 31944535--31944576 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
31944525 TGATTAATAA
31944535 ATTAACAATCTTAATAAATTT
1 ATTAACAATCTTAATAAATTT
*
31944556 ATTAACAATCTTTATAAATTT
1 ATTAACAATCTTAATAAATTT
31944577 GCTTGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAACAATCTTAATAAATTT
Found at i:31949106 original size:25 final size:27
Alignment explanation
Indices: 31949078--31949127 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
31949068 GGTCAATTTG
31949078 TGAGTAAT-AAGCTA-AGGCCAATAAA
1 TGAGTAATAAAGCTAGAGGCCAATAAA
* *
31949103 TGAGTGATAAAGCTAGCGGCCAATA
1 TGAGTAATAAAGCTAGAGGCCAATA
31949128 GCATAACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 6 0.29
27 8 0.38
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (27 bp):
TGAGTAATAAAGCTAGAGGCCAATAAA
Found at i:31949257 original size:102 final size:101
Alignment explanation
Indices: 31949108--31949387 Score: 348
Period size: 102 Copynumber: 2.8 Consensus size: 101
31949098 ATAAATGAGT
* * * * *
31949108 GATAAAGCTAGCGGCCAATAGCATAACATCATTACAGCCAAATTATGAGCGATAAAGCTAGCGGC
1 GATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGC
31949173 TAGAATGTGAATAAT-AAATTATGATCAAAGAATAAGC
66 T-GAATGTGAATAATGAAA-TATGATCAAAGAATAAGC
* * * * * *
31949210 GATAAAGCTTGCGACCAAAAGAAAAATATCATTGCAGCCAAAATATGAGTGGTAAAGCTTGCGGC
1 GATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGC
* *
31949275 TGAA-GTAAGAATGATGAAATATGGTCAAAGAATAAGC
66 TGAATGT--GAATAATGAAATATGATCAAAGAATAAGC
* * * *
31949312 GATAAAGCTTGCAACCAATAGTATAATATAATTACAGCCAAAATATAAGCGATAAAGCTAGCGGC
1 GATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGC
*
31949377 TGAATATGAAT
66 TGAATGTGAAT
31949388 TTTTTTTTTA
Statistics
Matches: 150, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
100 2 0.01
101 7 0.05
102 137 0.91
103 4 0.03
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (101 bp):
GATAAAGCTTGCGACCAATAGAATAATATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGGC
TGAATGTGAATAATGAAATATGATCAAAGAATAAGC
Done.