Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 19 of 345
Found at i:5613046 original size:16 final size:16
Alignment explanation
Indices: 5613025--5613055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5613015 ATATTCATTT
*
5613025 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
5613041 TATTTAATATTAAAA
1 TATTTAATATTAAAA
5613056 TAATAAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:5615351 original size:18 final size:18
Alignment explanation
Indices: 5615330--5615375 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
5615320 TAATAGTAAC
5615330 AAAAATAATACCAATGGT
1 AAAAATAATACCAATGGT
5615348 AAAAATAATACCAATGGT
1 AAAAATAATACCAATGGT
*
5615366 AATAATAATA
1 AAAAATAATA
5615376 ATAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (18 bp):
AAAAATAATACCAATGGT
Found at i:5615371 original size:3 final size:3
Alignment explanation
Indices: 5615365--5615404 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5615355 ATACCAATGG
5615365 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5615405 GATAGTAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5626797 original size:20 final size:22
Alignment explanation
Indices: 5626750--5626801 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 22
5626740 CTTGTGGAAG
5626750 AAACAA-AACAGATTTGCAAGGGA
1 AAACAAGAACAGATTTGCAA--GA
5626773 AAACAAGAACAGATTTG-AA-A
1 AAACAAGAACAGATTTGCAAGA
5626793 AAACAAGAA
1 AAACAAGAA
5626802 AAAAATGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.36
23 8 0.29
24 10 0.36
ACGTcount: A:0.60, C:0.12, G:0.17, T:0.12
Consensus pattern (22 bp):
AAACAAGAACAGATTTGCAAGA
Found at i:5639871 original size:88 final size:87
Alignment explanation
Indices: 5639722--5640570 Score: 1079
Period size: 88 Copynumber: 9.7 Consensus size: 87
5639712 CGAATTTGGG
* ** * * *
5639722 AGATCGAAGCTACAAATCTCTTCTCCCTGAAATAACATTTGAGCGACTTGAAGCCACAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGCG-CTCGAAGCCACAATTCGTA
*
5639787 TCTCCTTGAAGTTCCAGCAGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
5639810 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGCAGCTCGAAGCCACAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGC-GCTCGAAGCCACAATTCGTA
* *
5639875 TCTCTTTGAAGTTCTAGCGGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* * * *
5639898 AGACCGCAGCTACAAATCTCTTCTCCCTGAAATGGCACTGAAGCAGCTCGAAGCCACAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGC-GCTCGAAGCCACAATTCGTA
* **
5639963 TCTCCTTGAAGTTTCAGTAGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* * *
5639986 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCATTGGAGCGGCTCGAAGCCATAATTTGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGC-GCTCGAAGCCACAATTCGTA
*
5640051 TCTCCTTAAAGTT-CAGCGGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* * * * *
5640073 AGATCGAAGCTACAGATCTCTTTTCCCTGAAATGGCACTAGAGCTGCTCGAAGCCACAATTTGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGC-GCTCGAAGCCACAATTCGTA
* **
5640138 TCTCCTTAAAGTTTTAGCGGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* * * * * *
5640161 AGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGAATTAGAGCGGCTTGAAGCCATAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGC-GCTCGAAGCCACAATTCGTA
* * *
5640226 TCTCCTTAAAGTTTCAGCAGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* * *
5640249 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAACGGCTCAAAGCCATAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGC-GCTCGAAGCCACAATTCGTA
* *
5640314 TCTGCTTGAAGTTTCAGCGGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* * * *
5640337 AGATCGAAGCTACAAATATCTTCTCCCTGAAATGGCATTGGAGCGACTCGAAGCTACAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGCG-CTCGAAGCCACAATTCGTA
* *
5640402 TCTCCTTAAAGTTCCAGCAGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* ** *
5640425 AGATCGAAGCTATAAATCTCTTCTCCCTAAAATCACACTGGAGCAGGTCGAAGCCACAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGC-GCTCGAAGCCACAATTCGTA
* *
5640490 TCTCTTTGAAGTTCTAGCGGAGT
65 TCTCCTTGAAGTTCCAGCGGAGT
* * * * *
5640513 AGATCGCAGCTACAAATCTCTTCTCCCTAAAATAGCATTGGAGCGATTGAAGCCACAA
1 AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGCGCTCGAAGCCACAA
5640571 ACCTTATCTC
Statistics
Matches: 670, Mismatches: 87, Indels: 9
0.87 0.11 0.01
Matches are distributed among these distances:
87 91 0.14
88 577 0.86
89 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (87 bp):
AGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGAGCGCTCGAAGCCACAATTCGTAT
CTCCTTGAAGTTCCAGCGGAGT
Found at i:5640567 original size:439 final size:439
Alignment explanation
Indices: 5639722--5640570 Score: 1278
Period size: 439 Copynumber: 1.9 Consensus size: 439
5639712 CGAATTTGGG
*
5639722 AGATCGAAGCTACAAATCTCTTCTCCCTGAAATAACATTTGAGCGACTTGAAGCCACAATTCGTA
1 AGATCGAAGCTACAAATCTCTTCTCCCTGAAATAACATTAGAGCGACTTGAAGCCACAATTCGTA
*
5639787 TCTCCTTGAAGTTCCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGA
66 TCTCCTTAAAGTTCCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGA
* * * *
5639852 GCAGCTCGAAGCCACAATTCGTATCTCTTTGAAGTTCTAGCGGAGTAGACCGCAGCTACAAATCT
131 ACAGCTCAAAGCCACAATTCGTATCTCTTTGAAGTTCTAGCGGAGTAGACCGAAGCTACAAATAT
* * *
5639917 CTTCTCCCTGAAATGGCACTGAAGCAGCTCGAAGCCACAATTCGTATCTCCTTGAAGTTTCAGTA
196 CTTCTCCCTGAAATGGCACTGAAGCAGCTCGAAGCCACAATTCGTATCTCCTTAAAGTTCCAGCA
** * *
5639982 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCATTGGAGCGGCTCGAAGCCATAATT
261 GAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATCACACTGGAGCGGCTCGAAGCCACAATT
* * * * *
5640047 TGTATCTCCTTAAAGTTCAGCGGAGTAGATCGAAGCTACAGATCTCTTTTCCCTGAAATGGCACT
326 CGTATCTCCTTAAAGTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATAGCACT
*
5640112 AGAGCTGCTCGAAGCCACAATTTGTATCTCCTTAAAGTTTTAGCGGAGT
391 AGAGCTGATCGAAGCCACAATTTGTATCTCCTTAAAGTTTTAGCGGAGT
* * *
5640161 AGATCGAAGCTACAAATCTCTTCTCCCTGAAATGGA-ATTAGAGCGGCTTGAAGCCATAATTCGT
1 AGATCGAAGCTACAAATCTCTTCTCCCTGAAAT-AACATTAGAGCGACTTGAAGCCACAATTCGT
*
5640225 ATCTCCTTAAAGTTTCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGG
65 ATCTCCTTAAAGTTCCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGG
* * *
5640290 AACGGCTCAAAGCCATAATTCGTATCTGC-TTGAAGTT-TCAGCGGAGTAGATCGAAGCTACAAA
130 AACAGCTCAAAGCCACAATTCGTATCT-CTTTGAAGTTCT-AGCGGAGTAGACCGAAGCTACAAA
* * *
5640353 TATCTTCTCCCTGAAATGGCATTGGAGC-GACTCGAAGCTACAATTCGTATCTCCTTAAAGTTCC
193 TATCTTCTCCCTGAAATGGCACTGAAGCAG-CTCGAAGCCACAATTCGTATCTCCTTAAAGTTCC
*
5640417 AGCAGAGTAGATCGAAGCTATAAATCTCTTCTCCCTAAAATCACACTGGAGCAGG-TCGAAGCCA
257 AGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATCACACTGGAGC-GGCTCGAAGCCA
* * *
5640481 CAATTCGTATCTCTTTGAAGTTCTAGCGGAGTAGATCGCAGCTACAAATCTCTTCTCCCTAAAAT
321 CAATTCGTATCTCCTTAAAGTTC-AGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAAT
* * *
5640546 AGCATTGGAGC-GATTGAAGCCACAA
385 AGCACTAGAGCTGATCGAAGCCACAA
5640571 ACCTTATCTC
Statistics
Matches: 368, Mismatches: 36, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
438 2 0.01
439 317 0.86
440 49 0.13
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (439 bp):
AGATCGAAGCTACAAATCTCTTCTCCCTGAAATAACATTAGAGCGACTTGAAGCCACAATTCGTA
TCTCCTTAAAGTTCCAGCAGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATGGCACTGGA
ACAGCTCAAAGCCACAATTCGTATCTCTTTGAAGTTCTAGCGGAGTAGACCGAAGCTACAAATAT
CTTCTCCCTGAAATGGCACTGAAGCAGCTCGAAGCCACAATTCGTATCTCCTTAAAGTTCCAGCA
GAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATCACACTGGAGCGGCTCGAAGCCACAATT
CGTATCTCCTTAAAGTTCAGCGGAGTAGATCGAAGCTACAAATCTCTTCTCCCTAAAATAGCACT
AGAGCTGATCGAAGCCACAATTTGTATCTCCTTAAAGTTTTAGCGGAGT
Found at i:5640711 original size:45 final size:46
Alignment explanation
Indices: 5640569--5640957 Score: 164
Period size: 45 Copynumber: 8.7 Consensus size: 46
5640559 TTGAAGCCAC
* * * *
5640569 AAACCTTATCTCCCTAAAGTTTCAGT-GAAGCAG-GTTGAAGTTAC-
1 AAACCTTATCTCCCTGAAGTTGCAGTAG-AGCAGAGTTAAAGCTACT
** * * * ** * *
5640613 AAGTCTTATCTCCCTGAAGTTGTAGTGGAG-AAAACTGAAGATAGC-
1 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAGTTAAAGCTA-CT
* * *
5640658 AAATCTTATCTCTCTGAAATTGCAGTAGAGCAGAGTTAAAGCTA-T
1 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAGTTAAAGCTACT
* * * ** *
5640703 AAACCTTATCCCCCTGAAGTGGCAGT-GAG--GTAGGTAGAATTTACG
1 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAG-AGTTA-AAGCTACT
** * * * * *
5640748 AGTCC-TATCTCCCTAAAGTTGCAGTAAAGCCGA-TTGAAGATAGC-
1 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAGTTAAAGCTA-CT
* ** *
5640792 AAATCTTATCTCTTTGAAGTTGCAGTAGAGCAGAGTTAAAACTA-T
1 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAGTTAAAGCTACT
* * * * * *
5640837 AAACCTTATCCCCCTGAAGTTGCAGTGGGGCAG-GTTGAAGTTACC
1 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAGTTAAAGCTACT
*** * * * *
5640882 AGTTCTTATC-CCTCTGAAGTTGCAGTGGGGCA-AGTTGAAGTTAC-
1 AAACCTTATCTCC-CTGAAGTTGCAGTAGAGCAGAGTTAAAGCTACT
** *
5640926 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 AAACCTTATCTCCCTGAAGTTGCAGTAGAGCA
5640958 AACTGAAGAA
Statistics
Matches: 261, Mismatches: 65, Indels: 38
0.72 0.18 0.10
Matches are distributed among these distances:
42 1 0.00
43 5 0.02
44 95 0.36
45 144 0.55
46 15 0.06
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
AAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGAGTTAAAGCTACT
Found at i:5640933 original size:134 final size:134
Alignment explanation
Indices: 5640569--5640957 Score: 478
Period size: 134 Copynumber: 2.9 Consensus size: 134
5640559 TTGAAGCCAC
* * * *
5640569 AAACCTTATCTCCCTAAAGTTTCAGTGAAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
1 AAACCTTATCCCCCTGAAGTTGCAGTGAGGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
* * ** * *
5640634 GTAGTGGAGAAAACTGAAGATAGCAAATCTTATCTCTCTGAAATTGCAGTAGAGCAGAGTTAAAG
66 GCAGTGGAGCAAGTTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGTTAAAA
5640699 CTAT
131 CTAT
* * * * * * *
5640703 AAACCTTATCCCCCTGAAGTGGCAGTGAGGTAGGTAGAATTTACGAGTCCTATCTCCCTAAAGTT
1 AAACCTTATCCCCCTGAAGTTGCAGTGAGGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
** * *
5640768 GCAGTAAAGC-CGATTGAAGATAGCAAATCTTATCTCTTTGAAGTTGCAGTAGAGCAGAGTTAAA
66 GCAGTGGAGCAAG-TTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGTTAAA
5640832 ACTAT
130 ACTAT
* *
5640837 AAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACCAGTTCTTATC-CCTCTGAAG
1 AAACCTTATCCCCCTGAAGTTGCAGTGAGGCAGGTTGAAGTTACAAG-TCTTATCTCC-CTGAAG
* * * * *
5640901 TTGCAGTGGGGCAAGTTGAAGTTA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
64 TTGCAGTGGAGCAAGTTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCA
5640958 AACTGAAGAA
Statistics
Matches: 213, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
134 184 0.86
135 28 0.13
136 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (134 bp):
AAACCTTATCCCCCTGAAGTTGCAGTGAGGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
GCAGTGGAGCAAGTTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAGTTAAAA
CTAT
Found at i:5640979 original size:134 final size:133
Alignment explanation
Indices: 5640569--5641003 Score: 401
Period size: 134 Copynumber: 3.2 Consensus size: 133
5640559 TTGAAGCCAC
* * *
5640569 AAACCTTATCTCCCTAAAGTTTCAGTGAAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
1 AAACCTTATCCCCCTGAAGTTGCAGTGAAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
* * ** * **
5640634 GTAGTGGAGAAAACTGAAGATAGCAAATCTTATCTCTCTGAAATTGCAGTAGAGCAGAGTTAAAG
66 GCAGTGGAGCAAGTTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCA-AACTAAAG
**
5640699 CTAT
130 AAAT
* * * * * * * *
5640703 AAACCTTATCCCCCTGAAGTGGCAGTGAGGTAGGTAGAATTTACGAGTCCTATCTCCCTAAAGTT
1 AAACCTTATCCCCCTGAAGTTGCAGTGAAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
** * * **
5640768 GCAGTAAAGC-CGATTGAAGATAGCAAATCTTATCTCTTTGAAGTTGCAGTAGAGCAGAGTTAAA
66 GCAGTGGAGCAAG-TTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCA-AACTAAA
*
5640832 -ACTAT
129 GA-AAT
** *
5640837 AAACCTTATCCCCCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACCAGTTCTTATC-CCTCTGAAG
1 AAACCTTATCCCCCTGAAGTTGCAGTGAAGCAGGTTGAAGTTACAAG-TCTTATCTCC-CTGAAG
* * * * * *
5640901 TTGCAGTGGGGCAAGTTGAAGTTA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAA
64 TTGCAGTGGAGCAAGTTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAACTAAA
5640965 GAAAGT
129 GAAA-T
* * * * * *
5640971 AGATCTTATCTCCTTGAAGTTGCAATGGAGCAG
1 AAACCTTATCCCCCTGAAGTTGCAGTGAAGCAG
5641004 ATCAAACTAT
Statistics
Matches: 246, Mismatches: 48, Indels: 14
0.80 0.16 0.05
Matches are distributed among these distances:
133 5 0.02
134 212 0.86
135 28 0.11
136 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (133 bp):
AAACCTTATCCCCCTGAAGTTGCAGTGAAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTT
GCAGTGGAGCAAGTTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAACTAAAGA
AAT
Found at i:5640993 original size:45 final size:44
Alignment explanation
Indices: 5640885--5641002 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 44
5640875 AGTTACCAGT
* ** **
5640885 TCTTATC-CCTCTGAAGTTGCAGTGGGGCAAGTTGAAGTTACAAG
1 TCTTATCTCCT-TGAAGTTGCAGTGGAGCAAACTGAAGAAACAAG
* **
5640929 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGAAAGTAG
1 TCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTGAAGAAACAAG
*
5640973 ATCTTATCTCCTTGAAGTTGCAATGGAGCA
1 -TCTTATCTCCTTGAAGTTGCAGTGGAGCA
5641003 GATCAAACTA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 33 0.53
45 29 0.47
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
TCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTGAAGAAACAAG
Found at i:5641559 original size:14 final size:15
Alignment explanation
Indices: 5641535--5641567 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5641525 ATGCAACACG
*
5641535 CAAACGAAGAAGAAA
1 CAAACGAAGAAAAAA
5641550 CAAA-GAAGAAAAAA
1 CAAACGAAGAAAAAA
5641564 CAAA
1 CAAA
5641568 AAAAGAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (15 bp):
CAAACGAAGAAAAAA
Found at i:5642554 original size:3 final size:3
Alignment explanation
Indices: 5642546--5642570 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5642536 ATTAATCCTC
5642546 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
5642571 CAATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5642683 original size:27 final size:25
Alignment explanation
Indices: 5642654--5642737 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 25
5642644 TTATTTAAAC
5642654 TTTATTAGTTTTTATTGTTATTATTT
1 TTTATTA-TTTTTATTGTTATTATTT
5642680 CTTTATTATTTGTTCACTTGATTATTATTT
1 -TTTATTATTT-TT-A-TTG-TTATTATTT
5642710 TTT-TTATTTTTATT-TTATT-TTT
1 TTTATTATTTTTATTGTTATTATTT
5642732 TTTATT
1 TTTATT
5642738 TTATAATCGA
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
22 6 0.12
23 7 0.13
25 2 0.04
26 4 0.08
27 11 0.21
28 7 0.13
29 6 0.12
30 9 0.17
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.74
Consensus pattern (25 bp):
TTTATTATTTTTATTGTTATTATTT
Found at i:5642718 original size:9 final size:9
Alignment explanation
Indices: 5642704--5642739 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
5642694 CACTTGATTA
5642704 TTATTTTTT
1 TTATTTTTT
5642713 TTATTTTTATT
1 TTA-TTTT-TT
5642724 TTATTTTTT
1 TTATTTTTT
5642733 TTATTTT
1 TTATTTT
5642740 ATAATCGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.48
10 8 0.32
11 5 0.20
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTATTTTTT
Found at i:5642729 original size:20 final size:20
Alignment explanation
Indices: 5642704--5642768 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
5642694 CACTTGATTA
5642704 TTATTTTTTTTATTTTTATT
1 TTATTTTTTTTATTTTTATT
*
5642724 TTATTTTTTTTATTTTATAAT
1 TTATTTTTTTTATTTT-TATT
** *
5642745 CGATTTATTTTATTTTTACTT
1 TTATTTTTTTTATTTTTA-TT
5642766 TTA
1 TTA
5642769 CCCATATTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (20 bp):
TTATTTTTTTTATTTTTATT
Found at i:5642732 original size:12 final size:11
Alignment explanation
Indices: 5642701--5642734 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5642691 GTTCACTTGA
5642701 TTATTATTTTTT
1 TTATT-TTTTTT
*
5642713 TTATTTTTATT
1 TTATTTTTTTT
5642724 TTATTTTTTTT
1 TTATTTTTTTT
5642735 ATTTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:5642739 original size:14 final size:15
Alignment explanation
Indices: 5642704--5642741 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
5642694 CACTTGATTA
*
5642704 TTATTTTTTTTATTT
1 TTATTTTATTTATTT
5642719 TTATTTTATTT-TTT
1 TTATTTTATTTATTT
5642733 TTATTTTAT
1 TTATTTTAT
5642742 AATCGATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTTTATTTATTT
Found at i:5642760 original size:5 final size:5
Alignment explanation
Indices: 5642704--5642741 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
5642694 CACTTGATTA
5642704 TTATT TT-TT TTATTT TTATT TTATT TT-TT TTATT TTAT
1 TTATT TTATT TTA-TT TTATT TTATT TTATT TTATT TTAT
5642742 AATCGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.27
5 17 0.57
6 5 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTATT
Found at i:5648493 original size:49 final size:49
Alignment explanation
Indices: 5648301--5648845 Score: 893
Period size: 47 Copynumber: 11.4 Consensus size: 49
5648291 ATTTTGTTAC
5648301 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
5648350 GATGAATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
*
5648397 GATGAATGTGAAAGTGTATGTATA--TGATAAGGCCGAATGACCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
5648444 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
* *
5648493 GATGAATGTGAAAGTGTATGTATGTGTGATAAGGCCGAGTGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
*
5648542 GATGAATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCGAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
*
5648589 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATTT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
5648638 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
5648687 GATGAATGTGAAAGTGT-TG--TATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
5648733 GATGAATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
* * * *
5648780 GATGAATGTGAAA--GTATATATATATGATAAGGCCGAATGGTCAATGG
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
*
5648827 GATGGAA-GTGGAAGTGTAT
1 GAT-GAATGTGAAAGTGTAT
5648846 AACTGTGATA
Statistics
Matches: 469, Mismatches: 15, Indels: 24
0.92 0.03 0.05
Matches are distributed among these distances:
45 4 0.01
46 44 0.09
47 211 0.45
48 5 0.01
49 205 0.44
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (49 bp):
GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
Found at i:5648596 original size:145 final size:145
Alignment explanation
Indices: 5648301--5648845 Score: 926
Period size: 145 Copynumber: 3.8 Consensus size: 145
5648291 ATTTTGTTAC
5648301 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
5648366 TATG--TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATATGATAAGG
66 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
*
5648429 CCGAATGACCAATGT
131 CCGAATGGCCAATGT
5648444 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
5648509 TATGTATGTGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
66 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
*
5648574 CCGAATGGCGAATGT
131 CCGAATGGCCAATGT
*
5648589 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATTTGATGAATGTGAAAGTG
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
5648654 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGT-TGTATGTGATAAGG
66 TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
5648718 CCGAATGGCCAATGT
131 CCGAATGGCCAATGT
5648733 GATGAATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA--G
1 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* * * * *
5648794 TATATATATATGATAAGGCCGAATGGTCAATGGGATGGAA-GTGGAAGTGTAT
66 TATGTATATGTGATAAGGCCGAATGGCCAATGTGAT-GAATGTGAAAGTGTAT
5648846 AACTGTGATA
Statistics
Matches: 383, Mismatches: 15, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
140 42 0.11
141 4 0.01
142 39 0.10
143 69 0.18
144 48 0.13
145 181 0.47
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (145 bp):
GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
TATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGG
CCGAATGGCCAATGT
Found at i:5648689 original size:22 final size:22
Alignment explanation
Indices: 5648661--5648735 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
5648651 GTGTATGTAT
5648661 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ****
5648683 ATGTGATGAATG-TGAAAGTGTTGT
1 ATGTGAT-AAGGCCG-AA-TGGCCA
5648707 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
5648729 ATGTGAT
1 ATGTGAT
5648736 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 12, Indels: 8
0.65 0.21 0.14
Matches are distributed among these distances:
22 17 0.46
23 10 0.27
24 10 0.27
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.27
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:5650753 original size:40 final size:40
Alignment explanation
Indices: 5650698--5651010 Score: 513
Period size: 40 Copynumber: 7.9 Consensus size: 40
5650688 TTCAGTATGT
5650698 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
*
5650738 TATATCCGGGCTAAGTCCCAAAGAGCATT-GTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* * *
5650777 TGTATCCGGGGTAAGTTCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
5650817 TGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
*
5650857 TGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
5650897 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
5650937 TATATCCGGGTTAAGTCTCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
5650977 TGTATCCGGGCTAAGCCCCGAAG-GCATTCGTGCT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
5651011 TGGACGAAAT
Statistics
Matches: 258, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 46 0.18
40 212 0.82
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
Found at i:5651306 original size:25 final size:25
Alignment explanation
Indices: 5651256--5651306 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
5651246 TGTGTGACAA
* *
5651256 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
5651281 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
5651306 C
1 C
5651307 GAGTTCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:5655149 original size:47 final size:47
Alignment explanation
Indices: 5655057--5655315 Score: 475
Period size: 47 Copynumber: 5.5 Consensus size: 47
5655047 ATTTTGTTAC
5655057 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGT
* *
5655106 GATGAATGTGAAAGTGTATGTTTGTGATAAGGCTGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
5655153 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAAT-T
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
5655199 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
5655246 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
5655293 GATGAATGTGAAAGTGTATGTAT
1 GATGAATGTGAAAGTGTATGTAT
5655316 ATGTGAAAGT
Statistics
Matches: 205, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
46 46 0.22
47 139 0.68
49 20 0.10
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.29
Consensus pattern (47 bp):
GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGT
Found at i:5655311 original size:140 final size:139
Alignment explanation
Indices: 5655057--5655625 Score: 572
Period size: 140 Copynumber: 3.9 Consensus size: 139
5655047 ATTTTGTTAC
5655057 GATGAATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 GATGAATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
5655122 TATGTTTGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCC
64 TATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCC
5655187 GAATGGCCAATT
129 GAATGGCCAA-T
5655199 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
5655264 TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATATGTGA-AAGTGT
66 TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATG--TATGTGATAAG-G-
**
5655328 ATGTATATGTGATAAGGCCGAAT
127 CCG---A----AT--GGCC-AAT
** * * * *
5655351 GACCAATGTGATGAATGTGAAAGTGTATGT-AT-ATG-TGATAAGGCCGAATGGCCAATGTGATG
1 GATGAATGTGA--AA-GTG-TA-TGTATGTGATAAGGCCGA-ATGG-C-------CAATGTGATG
5655413 AATGTGAAAGTGTATGTATATGTGATAAGGCCGAAT-GCCAATGTGATGAATGTGAAAGTGTATG
52 AATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATG
5655477 -ATGTGATAAGG--GAATGGCCAAT
115 TATGTGATAAGGCCGAATGGCCAAT
5655499 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG-AA---TA
1 GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * * * *
5655560 TATATATGATAAGGCCGAATGGTCAATGGGATGGAA-GTGGAAGTGTAT-AACTGTGATAAGTCC
66 TGTATGTGATAAGGCCGAATGGCCAATGTGAT-GAATGTGAAAGTGTATGTA-TGTGATAAGGCC
5655623 GAA
129 GAA
5655626 GGACATTTGT
Statistics
Matches: 365, Mismatches: 22, Indels: 87
0.77 0.05 0.18
Matches are distributed among these distances:
131 17 0.05
132 21 0.06
133 15 0.04
135 3 0.01
136 2 0.01
137 16 0.04
140 92 0.25
141 3 0.01
142 28 0.08
143 8 0.02
144 4 0.01
145 8 0.02
146 5 0.01
148 12 0.03
149 4 0.01
150 2 0.01
151 2 0.01
152 14 0.04
153 2 0.01
154 4 0.01
155 9 0.02
156 4 0.01
157 7 0.02
158 1 0.00
161 7 0.02
162 3 0.01
163 26 0.07
164 28 0.08
165 18 0.05
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.28
Consensus pattern (139 bp):
GATGAATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
TGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTATGTGATAAGGCCGA
ATGGCCAAT
Found at i:5655321 original size:18 final size:18
Alignment explanation
Indices: 5655298--5655339 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
5655288 AATGTGATGA
5655298 ATGTGAAAGTGTATGTAT
1 ATGTGAAAGTGTATGTAT
5655316 ATGTGAAAGTGTATGTAT
1 ATGTGAAAGTGTATGTAT
5655334 ATGTGA
1 ATGTGA
5655340 TAAGGCCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.38
Consensus pattern (18 bp):
ATGTGAAAGTGTATGTAT
Found at i:5655350 original size:67 final size:65
Alignment explanation
Indices: 5655251--5655388 Score: 249
Period size: 67 Copynumber: 2.1 Consensus size: 65
5655241 AATGTGATGA
*
5655251 ATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTAT
1 ATGTGAAAGTGTATGTATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATGTAT
5655316 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATGT
1 ATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATGT
5655381 AT
64 AT
5655383 ATGTGA
1 ATGTGA
5655389 TAAGGCCGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 15 0.21
67 55 0.79
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (65 bp):
ATGTGAAAGTGTATGTATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATGTAT
Found at i:5655369 original size:49 final size:49
Alignment explanation
Indices: 5655316--5655607 Score: 411
Period size: 49 Copynumber: 6.3 Consensus size: 49
5655306 GTGTATGTAT
*
5655316 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGACCAATGTGATGA
1 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGA
5655365 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGA
5655414 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAAT-GCCAATGTGATGA
1 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGA
5655462 ATGTGAAAGTGTATG---ATGTGATAAGG--GAATGGCCAA--TGATGA
1 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGA
5655504 ATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * *
5655551 ATGTG-AA---TA--TATATATGATAAGGCCGAATGGTCAATGGGATGGA
1 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGAT-GA
*
5655595 A-GTGGAAGTGTAT
1 ATGTGAAAGTGTAT
5655608 AACTGTGATA
Statistics
Matches: 225, Mismatches: 4, Indels: 29
0.87 0.02 0.11
Matches are distributed among these distances:
42 21 0.09
43 47 0.21
44 10 0.04
45 21 0.09
46 2 0.01
47 13 0.06
48 28 0.12
49 83 0.37
ACGTcount: A:0.34, C:0.07, G:0.31, T:0.28
Consensus pattern (49 bp):
ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:5655386 original size:27 final size:27
Alignment explanation
Indices: 5655356--5655438 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
5655346 CGAATGACCA
5655356 ATGTGATGAATGTGAAAGTGTATGTAT
1 ATGTGATGAATGTGAAAGTGTATGTAT
* * *
5655383 ATGTGAT-AAGGCCG-AA-TG---GCCA-
1 ATGTGATGAATG-TGAAAGTGTATG-TAT
5655405 ATGTGATGAATGTGAAAGTGTATGTAT
1 ATGTGATGAATGTGAAAGTGTATGTAT
5655432 ATGTGAT
1 ATGTGAT
5655439 AAGGCCGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 2 0.05
25 2 0.05
26 6 0.15
27 16 0.39
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.33
Consensus pattern (27 bp):
ATGTGATGAATGTGAAAGTGTATGTAT
Found at i:5655423 original size:116 final size:112
Alignment explanation
Indices: 5655204--5655437 Score: 423
Period size: 116 Copynumber: 2.1 Consensus size: 112
5655194 CAATTGATGA
*
5655204 ATGTGAAAGTGTATGTATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTAT
1 ATGTGAAAGTGTATGTATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATGTAT
5655269 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTAT
66 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTAT
5655316 ATGTGAAAGTGTATGTATATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATGT
1 ATGTGAAAGTGTATG--TATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATG-
5655381 ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTAT
63 -TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTAT
5655432 ATGTGA
1 ATGTGA
5655438 TAAGGCCGAA
Statistics
Matches: 117, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
112 15 0.13
114 46 0.39
116 56 0.48
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (112 bp):
ATGTGAAAGTGTATGTATGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAAGTGTATGTAT
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATGTAT
Found at i:5662595 original size:43 final size:43
Alignment explanation
Indices: 5662534--5662618 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
5662524 TCCTATTCTC
*
5662534 TCCAAGAACCATCGATTTTGGTTTCAAAAATACCCAAAGAAAT
1 TCCAAGAACCATCGATTTTGGTTTAAAAAATACCCAAAGAAAT
5662577 TCCAAGAACCATCGATTTTGGTTTAAAAAATACCCAAAGAAA
1 TCCAAGAACCATCGATTTTGGTTTAAAAAATACCCAAAGAAA
5662619 CTAATGCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.25
Consensus pattern (43 bp):
TCCAAGAACCATCGATTTTGGTTTAAAAAATACCCAAAGAAAT
Found at i:5662830 original size:40 final size:40
Alignment explanation
Indices: 5662799--5662993 Score: 250
Period size: 41 Copynumber: 4.8 Consensus size: 40
5662789 AATTATACAT
*
5662799 TAGCAGCATTTTTAGTAAAACGCCGCTAAAAAACAGAGCAA
1 TAGCGGCATTTTT-GTAAAACGCCGCTAAAAAACAGAGCAA
*
5662840 TAGCGGCATTTTTGGTAAAATGCCGCT-AAAAACAGAGCAA
1 TAGCGGCATTTTT-GTAAAACGCCGCTAAAAAACAGAGCAA
* *
5662880 TAGCGGCGTTTTTGGTAAGACGCCGCTAAAAAACAGAGCAA
1 TAGCGGCATTTTT-GTAAAACGCCGCTAAAAAACAGAGCAA
* *
5662921 TAGCGGCATTTTTGTTAAAACGCTGCTAAAAATCAGAGCAA
1 TAGCGGCATTTTTG-TAAAACGCCGCTAAAAAACAGAGCAA
* *
5662962 TAGCAGCGTTTTTGTTCAAAACGCCGC-AAAAA
1 TAGCGGCATTTTTG-T-AAAACGCCGCTAAAAA
5662994 GTCATATAAC
Statistics
Matches: 138, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
40 38 0.28
41 91 0.66
42 9 0.07
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (40 bp):
TAGCGGCATTTTTGTAAAACGCCGCTAAAAAACAGAGCAA
Found at i:5662921 original size:81 final size:82
Alignment explanation
Indices: 5662799--5662993 Score: 295
Period size: 81 Copynumber: 2.4 Consensus size: 82
5662789 AATTATACAT
* * *
5662799 TAGCAGCATTTTTAGTAAAACGCCGCTAAAAAACAGAGCAATAGCGGCATTTTTGGTAAAATGCC
1 TAGCAGCGTTTTTGGTAAAACGCCGCTAAAAAACAGAGCAATAGCGGCATTTTTGGTAAAACGCC
5662864 GCTAAAAA-CAGAGCAA
66 GCTAAAAATCAGAGCAA
* * * *
5662880 TAGCGGCGTTTTTGGTAAGACGCCGCTAAAAAACAGAGCAATAGCGGCATTTTTGTTAAAACGCT
1 TAGCAGCGTTTTTGGTAAAACGCCGCTAAAAAACAGAGCAATAGCGGCATTTTTGGTAAAACGCC
5662945 GCTAAAAATCAGAGCAA
66 GCTAAAAATCAGAGCAA
*
5662962 TAGCAGCGTTTTTGTTCAAAACGCCGC-AAAAA
1 TAGCAGCGTTTTTGGT-AAAACGCCGCTAAAAA
5662994 GTCATATAAC
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
81 66 0.65
82 27 0.26
83 9 0.09
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (82 bp):
TAGCAGCGTTTTTGGTAAAACGCCGCTAAAAAACAGAGCAATAGCGGCATTTTTGGTAAAACGCC
GCTAAAAATCAGAGCAA
Found at i:5663449 original size:22 final size:22
Alignment explanation
Indices: 5663390--5663459 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
5663380 TTTTAGGGCA
*
5663390 TATGGA-TACGGGTTTAAGGTT
1 TATGGACTATGGGTTTAAGGTT
5663411 TATGAGTTACTAT---TTTAAGGTT
1 TATG-G--ACTATGGGTTTAAGGTT
* *
5663433 TATGGACTATGGGTTTAGGGAT
1 TATGGACTATGGGTTTAAGGTT
5663455 TATGG
1 TATGG
5663460 TTTAATGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
19 5 0.13
21 5 0.13
22 26 0.67
24 1 0.03
25 2 0.05
ACGTcount: A:0.24, C:0.04, G:0.30, T:0.41
Consensus pattern (22 bp):
TATGGACTATGGGTTTAAGGTT
Found at i:5663559 original size:22 final size:22
Alignment explanation
Indices: 5663516--5663577 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
5663506 AGGTTCTCGG
* *
5663516 TTAA-GGTTTATGTTTTAG-GA
1 TTAAGGGTTTAAGGTTTAGAGA
*
5663536 TTTAGGGTTTAAGGTTTAGAGA
1 TTAAGGGTTTAAGGTTTAGAGA
* *
5663558 TTAAGAGTTTAGGGTTTAGA
1 TTAAGGGTTTAAGGTTTAGA
5663578 TTAATTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 19 0.56
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (22 bp):
TTAAGGGTTTAAGGTTTAGAGA
Found at i:5664014 original size:6 final size:6
Alignment explanation
Indices: 5664003--5664030 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5663993 TTTTTATATT
5664003 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTT
5664031 CTTACATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:5664536 original size:116 final size:114
Alignment explanation
Indices: 5664300--5664520 Score: 271
Period size: 116 Copynumber: 1.9 Consensus size: 114
5664290 TTTTAGTGAT
** **
5664300 CGCAAAAGGATATGCTTTAGTGGCGTTTTCTCAGAAAACGCCGCTAATATGTTGGAAGAGATAGC
1 CGCAAAA-GATAACCTTTAGTGGCGTTTTCTCAGAAAACGCCGCTAATAAATTGGAAGAGATAGC
* * *
5664365 GAAACGCTGCCGTTTTTATATGATTTTTAGTGGCGTTTTTTATAAAACGC
65 AAAACGCTGCCGTTTCTATATGATTTCTAGTGGCGTTTTTTATAAAACGC
** ** * *
5664415 CGCAAATAGATAACCTTTAGTGGCGTTTTCCTCTTAAAACGCCGCTAATAAATTTTAAGAGTTGG
1 CGCAAA-AGATAACCTTTAGTGGCGTTTT-CTCAGAAAACGCCGCTAATAAATTGGAAGAGATAG
* * *
5664480 CAAAACGTTGTCGTTTCTATATGCTTTCTAGTGGCGTTTTT
64 CAAAACGCTGCCGTTTCTATATGATTTCTAGTGGCGTTTTT
5664521 ACTAGAGTGC
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
115 25 0.28
116 63 0.72
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (114 bp):
CGCAAAAGATAACCTTTAGTGGCGTTTTCTCAGAAAACGCCGCTAATAAATTGGAAGAGATAGCA
AAACGCTGCCGTTTCTATATGATTTCTAGTGGCGTTTTTTATAAAACGC
Found at i:5664718 original size:16 final size:14
Alignment explanation
Indices: 5664696--5664734 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 14
5664686 TTTCCCCCAA
5664696 TTTCCCCAAAGTTAT
1 TTTCCCCAAA-TTAT
5664711 TCTTCCCCAAATTAT
1 T-TTCCCCAAATTAT
5664726 TTTCCCCAA
1 TTTCCCCAA
5664735 TTTTCCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 9 0.39
ACGTcount: A:0.26, C:0.33, G:0.03, T:0.38
Consensus pattern (14 bp):
TTTCCCCAAATTAT
Found at i:5664915 original size:2 final size:2
Alignment explanation
Indices: 5664908--5664936 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5664898 CAACTGATAG
5664908 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5664937 TATATGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5665631 original size:24 final size:24
Alignment explanation
Indices: 5665604--5665698 Score: 154
Period size: 24 Copynumber: 4.0 Consensus size: 24
5665594 ATTATTATTG
*
5665604 AAATATTCTCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
5665628 AAATATTATCGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
* *
5665652 AAATATTATCGTCCATTTTATCAA
1 AAATATTATCGTCCGTTTTATCAC
*
5665676 AAATATTATCATCCGTTTTATCA
1 AAATATTATCGTCCGTTTTATCA
5665699 TTTAAGTTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:5665927 original size:15 final size:15
Alignment explanation
Indices: 5665882--5665936 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
5665872 AAAGACATGT
5665882 ATATTATTTAATTAAA
1 ATATTATTTAATT-AA
*
5665898 ATATT-TTT--TTCA
1 ATATTATTTAATTAA
5665910 ATATTATTTAATTAA
1 ATATTATTTAATTAA
5665925 ATATTATTTAAT
1 ATATTATTTAAT
5665937 CTCGTAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
12 6 0.18
13 5 0.15
15 18 0.53
16 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:5666102 original size:9 final size:9
Alignment explanation
Indices: 5666073--5666173 Score: 66
Period size: 9 Copynumber: 11.6 Consensus size: 9
5666063 TATTTGATAT
*
5666073 CATAATTTA
1 CATAACTTA
5666082 CATAA--TA
1 CATAACTTA
5666089 CATAACTTA
1 CATAACTTA
* *
5666098 TATAACCTA
1 CATAACTTA
* *
5666107 GATAA-ATA
1 CATAACTTA
*
5666115 TATAACTTA
1 CATAACTTA
*
5666124 CACAACTTA
1 CATAACTTA
*
5666133 CATAA-ATA
1 CATAACTTA
* * *
5666141 TATATCATA
1 CATAACTTA
5666150 TCATAACTTA
1 -CATAACTTA
5666160 CATAACTTA
1 CATAACTTA
5666169 CATAA
1 CATAA
5666174 TACTTAAATA
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
7 7 0.10
8 11 0.15
9 48 0.67
10 6 0.08
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:5666119 original size:26 final size:26
Alignment explanation
Indices: 5666080--5666144 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
5666070 TATCATAATT
* * *
5666080 TACAT-AATACATAACTTATATAACC
1 TACATAAATATATAACTTACACAACC
* *
5666105 TAGATAAATATATAACTTACACAACT
1 TACATAAATATATAACTTACACAACC
5666131 TACATAAATATATA
1 TACATAAATATATA
5666145 TCATATCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 4 0.12
26 29 0.88
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (26 bp):
TACATAAATATATAACTTACACAACC
Found at i:5672427 original size:15 final size:15
Alignment explanation
Indices: 5672403--5672442 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5672393 TACTTTAGCC
*
5672403 ATTTATTTTATTGTA
1 ATTTAATTTATTGTA
*
5672418 ATTTAATTTATTTTA
1 ATTTAATTTATTGTA
5672433 ATTTTAATTT
1 A-TTTAATTT
5672443 TAATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTTAATTTATTGTA
Found at i:5672438 original size:6 final size:6
Alignment explanation
Indices: 5672407--5672452 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
5672397 TTAGCCATTT
*
5672407 ATTTT- ATTGTA A-TTTA A-TTT- ATTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
5672451 AT
1 AT
5672453 AATTTTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
4 1 0.03
5 14 0.39
6 21 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:5672464 original size:21 final size:20
Alignment explanation
Indices: 5672431--5672469 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5672421 TAATTTATTT
5672431 TAATTTTAATTTTAATTTTAA
1 TAATTTTAATTTT-ATTTTAA
**
5672452 TAATTTTTCTTTTATTTT
1 TAATTTTAATTTTATTTT
5672470 GTTTCTACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TAATTTTAATTTTATTTTAA
Found at i:5677007 original size:18 final size:18
Alignment explanation
Indices: 5676970--5677005 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5676960 CATGGGTACG
5676970 TCATTGACCTCGCCTATT
1 TCATTGACCTCGCCTATT
*
5676988 TCATTGCCCTCGCC-ATT
1 TCATTGACCTCGCCTATT
5677005 T
1 T
5677006 TCCATCAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.14, C:0.36, G:0.11, T:0.39
Consensus pattern (18 bp):
TCATTGACCTCGCCTATT
Found at i:5682102 original size:85 final size:86
Alignment explanation
Indices: 5682003--5682221 Score: 230
Period size: 85 Copynumber: 2.6 Consensus size: 86
5681993 CCATTAGCGG
*
5682003 CGCTTTT-ATCACAAACGCCGCTAAAGGCCATTACTTTTAACGGCGCTTTCTC-ACAAACGCCGC
1 CGCTTTTCA-CACAAACGCCGCTAAAGGCCATTACTTTTAGCGGCGCTTTCTCTACAAACGCCGC
*
5682066 TAAAGGCCACGACTTTTAGTGA
65 TAAAAGCCACGACTTTTAGTGA
** *** * *
5682088 CGCTTTTCACACAAACGCCGCTAAAGGCCACGACTTTTAGTTACG-TTTTTCTACAAATGCCGCT
1 CGCTTTTCACACAAACGCCGCTAAAGGCCATTACTTTTAGCGGCGCTTTCTCTACAAACGCCGCT
*** * *
5682152 AAAAGCTTTGGCTTTTAGTGG
66 AAAAGCCACGACTTTTAGTGA
* * * *
5682173 CGCTTTTCTCACAAACACCGCTAAAAGCC-TTGACTTTTAGCGGCACTTT
1 CGCTTTTCACACAAACGCCGCTAAAGGCCATT-ACTTTTAGCGGCGCTTT
5682222 TTCAGATAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
84 5 0.05
85 98 0.92
86 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (86 bp):
CGCTTTTCACACAAACGCCGCTAAAGGCCATTACTTTTAGCGGCGCTTTCTCTACAAACGCCGCT
AAAAGCCACGACTTTTAGTGA
Found at i:5682222 original size:43 final size:43
Alignment explanation
Indices: 5681996--5682222 Score: 235
Period size: 43 Copynumber: 5.3 Consensus size: 43
5681986 CTAAAAGCCA
*
5681996 TTAGCGGCGCTTTTATCACAAACGCCGCTAAAGGCCATT-ACTT
1 TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGGCC-TTGACTT
* **
5682039 TTAACGGCGC-TTTCTCACAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGGCCTTGACTT
* * * **
5682081 TTAGTGACGCTTTTCACACAAACGCCGCTAAAGGCCACGACTT
1 TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGGCCTTGACTT
*** * * * * *
5682124 TTAGTTACGTTTTTCT-ACAAATGCCGCTAAAAGCTTTGGCTT
1 TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGGCCTTGACTT
* * *
5682166 TTAGTGGCGCTTTTCTCACAAACACCGCTAAAAGCCTTGACTT
1 TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGGCCTTGACTT
*
5682209 TTAGCGGCACTTTT
1 TTAGCGGCGCTTTT
5682223 TCAGATAAAC
Statistics
Matches: 155, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
42 68 0.44
43 87 0.56
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (43 bp):
TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGGCCTTGACTT
Found at i:5684750 original size:19 final size:19
Alignment explanation
Indices: 5684594--5684743 Score: 126
Period size: 19 Copynumber: 7.9 Consensus size: 19
5684584 GTGCCGATAT
*
5684594 GAGCATATGGGCCCCACAA
1 GAGCATATGGGCCCCACAC
*
5684613 GAGCATATGGGTCCCACAC
1 GAGCATATGGGCCCCACAC
* * *
5684632 GAGCACATAGACCCCACAC
1 GAGCATATGGGCCCCACAC
5684651 G-GACATAT-GGCCCCACAC
1 GAG-CATATGGGCCCCACAC
* *
5684669 -AGACATGTGGGCCCTACAC
1 GAG-CATATGGGCCCCACAC
* * *
5684688 GGGTATGTGGGCCCCACAC
1 GAGCATATGGGCCCCACAC
* * *
5684707 GGGTATGTGGGCCCCACAC
1 GAGCATATGGGCCCCACAC
* *
5684726 GGGTATATGGGCCCCACA
1 GAGCATATGGGCCCCACA
5684744 TGAGTATGTG
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.14
19 96 0.85
20 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.13
Consensus pattern (19 bp):
GAGCATATGGGCCCCACAC
Found at i:5684751 original size:38 final size:37
Alignment explanation
Indices: 5684643--5684756 Score: 131
Period size: 38 Copynumber: 3.0 Consensus size: 37
5684633 AGCACATAGA
** * *
5684643 CCCCACACGGACATAT-GGCCCCACACAGACATGTGGG
1 CCCCACACGGGTATATGGGCCCCACAGAG-TATGTGGG
* * *
5684680 CCCTACACGGGTATGTGGGCCCCACACGGGTATGTGGG
1 CCCCACACGGGTATATGGGCCCCACA-GAGTATGTGGG
5684718 CCCCACACGGGTATATGGGCCCCACATGAGTATGTGGG
1 CCCCACACGGGTATATGGGCCCCACA-GAGTATGTGGG
5684756 C
1 C
5684757 TGCACAGGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
37 12 0.19
38 51 0.80
39 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.31, T:0.16
Consensus pattern (37 bp):
CCCCACACGGGTATATGGGCCCCACAGAGTATGTGGG
Found at i:5684762 original size:19 final size:19
Alignment explanation
Indices: 5684659--5684756 Score: 133
Period size: 19 Copynumber: 5.2 Consensus size: 19
5684649 ACGGACATAT
* **
5684659 GGCCCCACACAGACATGTG
1 GGCCCCACACGGGTATGTG
*
5684678 GGCCCTACACGGGTATGTG
1 GGCCCCACACGGGTATGTG
5684697 GGCCCCACACGGGTATGTG
1 GGCCCCACACGGGTATGTG
*
5684716 GGCCCCACACGGGTATATG
1 GGCCCCACACGGGTATGTG
* *
5684735 GGCCCCACATGAGTATGTG
1 GGCCCCACACGGGTATGTG
5684754 GGC
1 GGC
5684757 TGCACAGGGG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.19, C:0.31, G:0.34, T:0.16
Consensus pattern (19 bp):
GGCCCCACACGGGTATGTG
Found at i:5687176 original size:5 final size:5
Alignment explanation
Indices: 5687166--5687195 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5687156 AGATTTGGGA
*
5687166 AAAAG AAAAG AAAAG AAAAG AAAAG GAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
5687196 TGAAAGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5689458 original size:19 final size:19
Alignment explanation
Indices: 5689434--5689471 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5689424 GAATTTGATT
5689434 GAAAGTGAAAGTGAATTGA
1 GAAAGTGAAAGTGAATTGA
*
5689453 GAAAGTGAAATTGAATTGA
1 GAAAGTGAAAGTGAATTGA
5689472 TTCGTAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (19 bp):
GAAAGTGAAAGTGAATTGA
Found at i:5689704 original size:38 final size:39
Alignment explanation
Indices: 5689644--5689740 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
5689634 CAGATAGATT
* * *
5689644 CGATGAGGTACTGGGTACCAACT-TTACTTCG-GCTAGGC
1 CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTA-GC
* * * *
5689682 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTAGC
5689721 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
5689741 TATTGGTGTG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 19 0.40
39 26 0.54
40 3 0.06
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTACTTCGAACTAGC
Found at i:5689865 original size:18 final size:18
Alignment explanation
Indices: 5689842--5689890 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
5689832 ATGAGAAAAA
*
5689842 GAAATT-GAATTATGAATT
1 GAAATTGGAATT-GGAATT
5689860 GAAATTGGAATTGGAATT
1 GAAATTGGAATTGGAATT
*
5689878 GGAATTGGAATTG
1 GAAATTGGAATTG
5689891 TAATAGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.35
Consensus pattern (18 bp):
GAAATTGGAATTGGAATT
Found at i:5689871 original size:6 final size:6
Alignment explanation
Indices: 5689855--5689890 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
5689845 ATTGAATTAT
*
5689855 GAATTG AAATTG GAATTG GAATTG GAATTG GAATTG
1 GAATTG GAATTG GAATTG GAATTG GAATTG GAATTG
5689891 TAATAGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (6 bp):
GAATTG
Found at i:5690055 original size:15 final size:15
Alignment explanation
Indices: 5690044--5690074 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5690034 AAATTAATTG
5690044 TTATGTATTTAATAT
1 TTATGTATTTAATAT
*
5690059 TTATGTATTTATTAT
1 TTATGTATTTAATAT
5690074 T
1 T
5690075 GTTGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (15 bp):
TTATGTATTTAATAT
Found at i:5691428 original size:19 final size:19
Alignment explanation
Indices: 5691406--5691672 Score: 216
Period size: 19 Copynumber: 14.1 Consensus size: 19
5691396 TGGGCCATAA
*
5691406 GAGCATATGGGCCCCATAC
1 GAGCATATGGGCCCCACAC
* * *
5691425 GAGCATACGGGCCCCATAA
1 GAGCATATGGGCCCCACAC
*
5691444 GAGCATACGGGCCCCACAC
1 GAGCATATGGGCCCCACAC
* * *
5691463 AAGCATATGGGTCCCACAT
1 GAGCATATGGGCCCCACAC
* * *
5691482 GAACACATGGGTCCCACAC
1 GAGCATATGGGCCCCACAC
* * *
5691501 GAGCACATGGGTCCTACAC
1 GAGCATATGGGCCCCACAC
* *
5691520 GAGCACATGGGCCTCACAC
1 GAGCATATGGGCCCCACAC
*
5691539 -AGGCATATGGGCCTCACA-
1 GA-GCATATGGGCCCCACAC
* * * *
5691557 TAGACATATGGACCCCATAT
1 GAG-CATATGGGCCCCACAC
* * *
5691577 GGGCATATGGACCACACAC
1 GAGCATATGGGCCCCACAC
*
5691596 GGGCATATGGGCCCCACAC
1 GAGCATATGGGCCCCACAC
* *
5691615 -AGAAATATGGACCCCACAC
1 GAG-CATATGGGCCCCACAC
* *
5691634 GAGTATATGGGCCCTACAC
1 GAGCATATGGGCCCCACAC
*
5691653 GAGCATGTGGGCCCCACAC
1 GAGCATATGGGCCCCACAC
5691672 G
1 G
5691673 GACATGTGAG
Statistics
Matches: 205, Mismatches: 37, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
18 3 0.01
19 199 0.97
20 3 0.01
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (19 bp):
GAGCATATGGGCCCCACAC
Found at i:5694212 original size:27 final size:27
Alignment explanation
Indices: 5693997--5694210 Score: 275
Period size: 27 Copynumber: 7.9 Consensus size: 27
5693987 GTTAAGACAT
*
5693997 TGATTTGTGAAATTACCGAAACACCCC
1 TGATTTGTGAAATTACCGAAATACCCC
* * *
5694024 TAATTTGTGGAATTATCGAAATACCCC
1 TGATTTGTGAAATTACCGAAATACCCC
* * *
5694051 TGACTTGTGAAATTATCGAAATACCCT
1 TGATTTGTGAAATTACCGAAATACCCC
*
5694078 TGATTTGTGAAATTACAGAAATACCCC
1 TGATTTGTGAAATTACCGAAATACCCC
* * *
5694105 TGATTTGTGAAATTACTGAAATACTCT
1 TGATTTGTGAAATTACCGAAATACCCC
* *
5694132 TGACTTGTGAAATTACTGAAATACCCC
1 TGATTTGTGAAATTACCGAAATACCCC
* *
5694159 TGATTTGTAAAATTACCGAAATACCTC
1 TGATTTGTGAAATTACCGAAATACCCC
* *
5694186 TAACTTGTGAAATTACCGAAATACC
1 TGATTTGTGAAATTACCGAAATACC
5694211 TCCGTTTTCA
Statistics
Matches: 162, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 162 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (27 bp):
TGATTTGTGAAATTACCGAAATACCCC
Found at i:5694414 original size:27 final size:27
Alignment explanation
Indices: 5694384--5694453 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
5694374 AGTACTGTAC
*
5694384 TGGTGACTATGTCAC-ATCCACTGATAT
1 TGGTGACTATGCCACAAT-CACTGATAT
* *
5694411 TGGTGGCTATGCCACAATTACTGATAT
1 TGGTGACTATGCCACAATCACTGATAT
* *
5694438 TGGTGGCTTTGCCACA
1 TGGTGACTATGCCACA
5694454 TTTACTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 36 0.95
28 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (27 bp):
TGGTGACTATGCCACAATCACTGATAT
Found at i:5694458 original size:27 final size:27
Alignment explanation
Indices: 5694403--5694459 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
5694393 TGTCACATCC
5694403 ACTGATATTGGTGGCTATGCCACAATT
1 ACTGATATTGGTGGCTATGCCACAATT
* *
5694430 ACTGATATTGGTGGCTTTGCCACATTT
1 ACTGATATTGGTGGCTATGCCACAATT
5694457 ACT
1 ACT
5694460 ATTTCTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (27 bp):
ACTGATATTGGTGGCTATGCCACAATT
Found at i:5697212 original size:27 final size:26
Alignment explanation
Indices: 5697177--5697266 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 26
5697167 AATAAAAATG
5697177 AAATAAAATAATATATAAAATAAATTTA
1 AAAT-AAATAATATATAAAA-AAATTTA
* * *
5697205 GAGTAAATAATATAT--AAAAGTTTA
1 AAATAAATAATATATAAAAAAATTTA
5697229 AAATAAATAATATATGAAAAAAATTTA
1 AAATAAATAATATAT-AAAAAAATTTA
5697256 AAATAAATAAT
1 AAATAAATAAT
5697267 GCATATGACA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
24 19 0.36
25 2 0.04
27 30 0.57
28 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (26 bp):
AAATAAATAATATATAAAAAAATTTA
Found at i:5697222 original size:22 final size:24
Alignment explanation
Indices: 5697208--5697436 Score: 121
Period size: 24 Copynumber: 9.0 Consensus size: 24
5697198 AAATTTAGAG
5697208 TAAATAATATATAAAAGTTTAAAA
1 TAAATAATATATAAAAGTTTAAAA
*
5697232 TAAATAATATATGAAAAAAATTTAAAA
1 TAAATAATATAT---AAAAGTTTAAAA
* *
5697259 TAAATAATGCATATGACAA-TAT-AAA
1 TAAATAAT--ATAT-AAAAGTTTAAAA
5697284 T-AAT-ATATA-AAAAGGTTTAAAA
1 TAAATAATATATAAAA-GTTTAAAA
*
5697306 TAAATAATATGTAAAAAGAAATTTAAAA
1 TAAATAATATAT-AAAAG---TTTAAAA
* * * *
5697334 TAGATAATACACAAAACAATTTAAAA
1 TAAATAATATA-TAAA-AGTTTAAAA
* **
5697360 GTAAATGATATATATATAA--TCCAAA
1 -TAAAT-A-ATATATAAAAGTTTAAAA
*
5697385 TAAATAATACATATAACAGTTTAAAA
1 TAAATAAT--ATATAAAAGTTTAAAA
*
5697411 TAAATAATATATAAAAAATTTAAAA
1 TAAATAATATAT-AAAAGTTTAAAA
5697436 T
1 T
5697437 GGATTTGAAA
Statistics
Matches: 156, Mismatches: 24, Indels: 49
0.68 0.10 0.21
Matches are distributed among these distances:
19 3 0.02
21 5 0.03
22 6 0.04
23 6 0.04
24 34 0.22
25 20 0.13
26 25 0.16
27 27 0.17
28 21 0.13
29 9 0.06
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (24 bp):
TAAATAATATATAAAAGTTTAAAA
Found at i:5697228 original size:24 final size:25
Alignment explanation
Indices: 5697177--5697436 Score: 176
Period size: 26 Copynumber: 10.2 Consensus size: 25
5697167 AATAAAAATG
5697177 AAATAAAATAATATATAAAATAAATTTA
1 AAAT-AAATAATATAT-AAA-AAATTTA
* * *
5697205 GAGTAAATAATATAT-AAAAGTTTA
1 AAATAAATAATATATAAAAAATTTA
5697229 AAATAAATAATATATGAAAAAAATTTA
1 AAATAAATAATATAT--AAAAAATTTA
* *
5697256 AAATAAATAATGCATAT-GACAA--T-
1 AAATAAATAAT--ATATAAAAAATTTA
*
5697279 --ATAAATAATATATAAAAAGGTTTA
1 AAATAAATAATATATAAAAA-ATTTA
*
5697303 AAATAAATAATATGTAAAAAGAAATTTA
1 AAATAAATAATA--TATAAA-AAATTTA
* * *
5697331 AAATAGATAATACACAAAACAATTTA
1 AAATAAATAATATATAAAA-AATTTA
* * * **
5697357 AAAGTAAATGATATATATATAA-TCC
1 AAA-TAAATAATATATAAAAAATTTA
* * *
5697382 AAATAAATAATACATATAACAGTTTA
1 AAATAAATAATATATA-AAAAATTTA
5697408 AAATAAATAATATATAAAAAATTTA
1 AAATAAATAATATATAAAAAATTTA
5697433 AAAT
1 AAAT
5697437 GGATTTGAAA
Statistics
Matches: 179, Mismatches: 34, Indels: 41
0.70 0.13 0.16
Matches are distributed among these distances:
19 4 0.02
20 2 0.01
21 9 0.05
23 1 0.01
24 31 0.17
25 20 0.11
26 44 0.25
27 40 0.22
28 22 0.12
29 6 0.03
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.30
Consensus pattern (25 bp):
AAATAAATAATATATAAAAAATTTA
Found at i:5697331 original size:28 final size:26
Alignment explanation
Indices: 5697279--5697514 Score: 129
Period size: 25 Copynumber: 9.3 Consensus size: 26
5697269 ATATGACAAT
*
5697279 ATAAATAATATATAAAAAGGTTTAAA
1 ATAAATAATATATAAAAAGATTTAAA
*
5697305 ATAAATAATATGTAAAAAGAAATTTAAA
1 ATAAATAATATATAAAAAG--ATTTAAA
* * *
5697333 ATAGATAATACACAAAACA-ATTTAAA
1 ATAAATAATATATAAAA-AGATTTAAA
* * * **
5697359 AGTAAATGATATATATATA-A-TCCAA
1 A-TAAATAATATATAAAAAGATTTAAA
* *
5697384 ATAAATAATACATATAACAG-TTTAAA
1 ATAAATAATATATA-AAAAGATTTAAA
5697410 ATAAATAATATATAAAAA-ATTTAAA
1 ATAAATAATATATAAAAAGATTTAAA
** * *
5697435 ATGGAT--T-T-GAAATAG-TTTAAA
1 ATAAATAATATATAAAAAGATTTAAA
* * * *
5697456 ATACATAATATGTGAAAA-ACTTAAA
1 ATAAATAATATATAAAAAGATTTAAA
* *
5697481 GTAAATTATA-ATAAAACA-ATTTAAA
1 ATAAATAATATATAAAA-AGATTTAAA
5697506 ATAAATAAT
1 ATAAATAAT
5697515 GTATGAGAAA
Statistics
Matches: 155, Mismatches: 40, Indels: 31
0.69 0.18 0.14
Matches are distributed among these distances:
21 14 0.09
22 1 0.01
23 2 0.01
24 16 0.10
25 48 0.31
26 44 0.28
27 10 0.06
28 19 0.12
29 1 0.01
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
ATAAATAATATATAAAAAGATTTAAA
Found at i:5700713 original size:25 final size:25
Alignment explanation
Indices: 5700661--5700717 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
5700651 AGCTCTTATA
* *
5700661 AGCTTCCCGTTACATGGCTTACATG
1 AGCTTCCCGTTACATGGCTGACAAG
*
5700686 AGCTTCCCGTTATATGGCTCGA-AAG
1 AGCTTCCCGTTACATGGCT-GACAAG
5700711 AGCTTCC
1 AGCTTCC
5700718 TGATTGCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCTTCCCGTTACATGGCTGACAAG
Found at i:5702408 original size:21 final size:22
Alignment explanation
Indices: 5702366--5702408 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5702356 AATTGAAAAA
*
5702366 TGTGAAAATTGTGTGATATATG
1 TGTGAAAATTGTGTAATATATG
*
5702388 TGTG-AAATTGTGTAATGTATG
1 TGTGAAAATTGTGTAATATATG
5702409 GGCTGTTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (22 bp):
TGTGAAAATTGTGTAATATATG
Found at i:5705592 original size:52 final size:51
Alignment explanation
Indices: 5705514--5705620 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 51
5705504 CAATACATTT
5705514 CATATTCAATAAGGCTCAATTTACATTCTAGGCAAAATTACCATTTTTCCCC
1 CATATTCAATAAGGCTCAATTTACATTCTAGGCAAAATTACCA-TTTTCCCC
** *
5705566 CATATTCAATTGGGCTCAATTTACATTCTCGGCAAAATTACCATTTTCCCC
1 CATATTCAATAAGGCTCAATTTACATTCTAGGCAAAATTACCATTTTCCCC
5705617 CATA
1 CATA
5705621 CTTTTTATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 12 0.23
52 40 0.77
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (51 bp):
CATATTCAATAAGGCTCAATTTACATTCTAGGCAAAATTACCATTTTCCCC
Found at i:5713689 original size:6 final size:6
Alignment explanation
Indices: 5713675--5713708 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
5713665 TTTATTGCAA
*
5713675 TTTACT TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
5713709 CTAATTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:5727098 original size:44 final size:44
Alignment explanation
Indices: 5727035--5727251 Score: 287
Period size: 44 Copynumber: 5.0 Consensus size: 44
5727025 GGGTTACATT
5727035 GAGTTGGCTTC-GAGCCATGATATTGGCACTTAGTGTGCGAGATC
1 GAGTTGGCTTCAG-GCCATGATATTGGCACTTAGTGTGCGAGATC
*
5727079 GAGTTGGCTTCAGGCCATGATATTGGCACTTAGTGTACGAGATC
1 GAGTTGGCTTCAGGCCATGATATTGGCACTTAGTGTGCGAGATC
* *
5727123 GAGTTGGCTTCGGGCCATGATATTGGCACTTAGTGTGGGAGATC
1 GAGTTGGCTTCAGGCCATGATATTGGCACTTAGTGTGCGAGATC
* * ** *
5727167 GAGCTAGCTTTGGGCTATGATATTGGCACTTAGTGTGCGAGATC
1 GAGTTGGCTTCAGGCCATGATATTGGCACTTAGTGTGCGAGATC
* * * * *
5727211 GAGGTAGCTT-AGGCTATG-TATTGGCAATTAGTGAGCGAGAT
1 GAGTTGGCTTCAGGCCATGATATTGGCACTTAGTGTGCGAGAT
5727252 TCCTGAGTAT
Statistics
Matches: 159, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
42 21 0.13
43 7 0.04
44 130 0.82
45 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.30
Consensus pattern (44 bp):
GAGTTGGCTTCAGGCCATGATATTGGCACTTAGTGTGCGAGATC
Found at i:5737858 original size:14 final size:14
Alignment explanation
Indices: 5737823--5737867 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
5737813 ATAATAAAAT
5737823 ATAATGTTATATTTA
1 ATAAT-TTATATTTA
5737838 ATAATTTAT-TTTA
1 ATAATTTATATTTA
5737851 ATATATTTA-A-TTA
1 ATA-ATTTATATTTA
5737864 ATAA
1 ATAA
5737868 ATTGGGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.04
13 13 0.46
14 9 0.32
15 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
ATAATTTATATTTA
Found at i:5749463 original size:9 final size:9
Alignment explanation
Indices: 5749415--5749531 Score: 53
Period size: 10 Copynumber: 12.6 Consensus size: 9
5749405 TTTCTCATAG
5749415 AAAATTATTA
1 AAAATTA-TA
*
5749425 AAAGATCATA
1 AAA-ATTATA
5749435 AAAA--ATA
1 AAAATTATA
**
5749442 AAAACCATAA
1 AAAATTAT-A
5749452 AAAATTATAA
1 AAAATTAT-A
* *
5749462 AAAAATATT
1 AAAATTATA
* *
5749471 GAAACTATTA
1 AAAATTA-TA
*
5749481 AATATTA-A
1 AAAATTATA
5749489 AAATATT-TA
1 AAA-ATTATA
5749498 AAAACTTATA
1 AAAA-TTATA
5749508 AAAACTTATA
1 AAAA-TTATA
*
5749518 AATATTATA
1 AAAATTATA
5749527 AAAAT
1 AAAAT
5749532 AAATTTTAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
7 7 0.08
8 4 0.05
9 26 0.31
10 44 0.52
11 3 0.04
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:5749509 original size:10 final size:10
Alignment explanation
Indices: 5749496--5749530 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5749486 TAAAAATATT
5749496 TAAAAACTTA
1 TAAAAACTTA
5749506 TAAAAACTTA
1 TAAAAACTTA
*
5749516 TAAATA-TTA
1 TAAAAACTTA
5749525 TAAAAA
1 TAAAAA
5749531 TAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAAAACTTA
Found at i:5749634 original size:10 final size:10
Alignment explanation
Indices: 5749486--5749654 Score: 53
Period size: 10 Copynumber: 16.6 Consensus size: 10
5749476 TATTAAATAT
5749486 TAAAAATATT-
1 TAAAAAT-TTA
*
5749496 TAAAAACTTA
1 TAAAAATTTA
*
5749506 TAAAAACTTA
1 TAAAAATTTA
*
5749516 TAAATA-TTA
1 TAAAAATTTA
*
5749525 TAAAAATAAATTT
1 TAAAAAT---TTA
*
5749538 TAATATAGTTTA
1 TAA-A-AATTTA
* *
5749550 AAAAAATTAA
1 TAAAAATTTA
*
5749560 TAGAATATATT-
1 TA-AAAAT-TTA
*
5749571 TAAAATTTTA
1 TAAAAATTTA
* **
5749581 TGAAAACATA
1 TAAAAATTTA
* *
5749591 TAAAAAATCA
1 TAAAAATTTA
5749601 T-AAAATTTA
1 TAAAAATTTA
***
5749610 TTGTAATTTA
1 TAAAAATTTA
5749620 T-AAAATTTA
1 TAAAAATTTA
*
5749629 TAAAAATTGA
1 TAAAAATTTA
5749639 TATAAAA-TTA
1 TA-AAAATTTA
5749649 TAAAAA
1 TAAAAA
5749655 AATCATAAAA
Statistics
Matches: 116, Mismatches: 30, Indels: 27
0.67 0.17 0.16
Matches are distributed among these distances:
9 30 0.26
10 62 0.53
11 11 0.09
12 5 0.04
13 5 0.04
14 1 0.01
15 2 0.02
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.37
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:5749636 original size:19 final size:19
Alignment explanation
Indices: 5749488--5749654 Score: 63
Period size: 19 Copynumber: 8.3 Consensus size: 19
5749478 TTAAATATTA
*
5749488 AAAATATTTA-AAAACTTAT
1 AAAA-ATTTATAAAATTTAT
*
5749507 AAAAACTTAT-AAATATTAT
1 AAAAATTTATAAAAT-TTAT
* *
5749526 AAAAATAAATTTTAATATAGTTTAA
1 AAAAAT---TTATAA-A-A-TTTAT
*
5749551 AAAAATTAATAGAATATATT-T
1 AAAAATTTATA-AA-AT-TTAT
* **
5749572 AAAATTTTATGAAAACATAT
1 AAAAATTTAT-AAAATTTAT
* *
5749592 AAAAAATCATAAAATTTAT
1 AAAAATTTATAAAATTTAT
***
5749611 TGTAATTTATAAAATTTAT
1 AAAAATTTATAAAATTTAT
5749630 AAAAATTGATATAAAA-TTAT
1 AAAAATT--TATAAAATTTAT
5749650 AAAAA
1 AAAAA
5749655 AATCATAAAA
Statistics
Matches: 108, Mismatches: 25, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
18 7 0.06
19 39 0.36
20 18 0.17
21 18 0.17
22 12 0.11
23 2 0.02
24 1 0.01
25 10 0.09
26 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAAATTTATAAAATTTAT
Found at i:5750280 original size:31 final size:31
Alignment explanation
Indices: 5750227--5750314 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
5750217 ATTTAAATTT
** *
5750227 TTTTTATAAGTTTTTAAGAATTTTTAT-ACA
1 TTTTTATAAAATTTTAATAATTTTTATGACA
* **
5750257 TTTTTATAAAATTTTAAATAATTTTTTTGTTA
1 TTTTTATAAAATTTT-AATAATTTTTATGACA
* *
5750289 ATTTTATAAAATTTTTATAATTTTTA
1 TTTTTATAAAATTTTAATAATTTTTA
5750315 AAATTTGTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 13 0.28
31 19 0.40
32 15 0.32
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTTTATAAAATTTTAATAATTTTTATGACA
Found at i:5750309 original size:19 final size:19
Alignment explanation
Indices: 5750287--5750326 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
5750277 ATTTTTTTGT
5750287 TAATTTTATAAAATTT-TTA
1 TAATTTT-TAAAATTTGTTA
5750306 TAATTTTTAAAATTTGTTA
1 TAATTTTTAAAATTTGTTA
5750325 TA
1 TA
5750327 TTTATAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TAATTTTTAAAATTTGTTA
Found at i:5755542 original size:30 final size:31
Alignment explanation
Indices: 5755485--5755549 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
5755475 AATAGCCTAG
*
5755485 TGACTTAAATAAAAACTTTTGAATAGTTCAA
1 TGACTTAAATAAAAACTTTTAAATAGTTCAA
* *
5755516 TGACTTAAATGAGAA-TTTTAAATAGTTCAA
1 TGACTTAAATAAAAACTTTTAAATAGTTCAA
5755546 TGAC
1 TGAC
5755550 CAACTTCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTAAATAGTTCAA
Found at i:5758602 original size:16 final size:16
Alignment explanation
Indices: 5758583--5758698 Score: 74
Period size: 16 Copynumber: 6.8 Consensus size: 16
5758573 ATAATTTACA
5758583 AATAAAAATATATAAT
1 AATAAAAATATATAAT
* **
5758599 AATATAAATCATATAGC
1 AATAAAAAT-ATATAAT
*
5758616 AATAAAAATATAT-GT
1 AATAAAAATATATAAT
5758631 AATAAAATATATATAATAT
1 AATAAAA-ATATAT-A-AT
5758650 AATATAAAGAATATATAA-
1 -A-ATAAA-AATATATAAT
* *
5758668 AATAATAATAATCTAAT
1 AATAAAAAT-ATATAAT
5758685 AAGTATAAAATATA
1 AA-TA-AAAATATA
5758699 GTAAATTAGT
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
15 11 0.14
16 27 0.35
17 16 0.21
18 4 0.05
19 6 0.08
20 2 0.03
21 11 0.14
22 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAAAAATATATAAT
Found at i:5758685 original size:51 final size:48
Alignment explanation
Indices: 5758583--5758686 Score: 111
Period size: 51 Copynumber: 2.1 Consensus size: 48
5758573 ATAATTTACA
** ** *
5758583 AATAAAAATATATAATAATATAAATCATATAGCAATAAAAATATATGT
1 AATAAAAATATATAATAATATAAAGAATATAAAAATAAAAATATATCT
*
5758631 AATAAAATATATATAATATAATATAAAGAATATATAAAATAATAATA-ATCT
1 AATAAAA-ATATAT-A-ATAATATAAAGAATATA-AAAATAAAAATATATCT
5758682 AATAA
1 AATAA
5758687 GTATAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
48 7 0.15
49 6 0.13
50 1 0.02
51 23 0.50
52 9 0.20
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (48 bp):
AATAAAAATATATAATAATATAAAGAATATAAAAATAAAAATATATCT
Found at i:5758805 original size:14 final size:14
Alignment explanation
Indices: 5758788--5758971 Score: 69
Period size: 14 Copynumber: 12.6 Consensus size: 14
5758778 ATAATTAGTA
5758788 ATATATAAAATAAT
1 ATATATAAAATAAT
5758802 ATATACTAAAAT-AT
1 ATATA-TAAAATAAT
5758816 ATA-ATATAAATAAT
1 ATATATA-AAATAAT
5758830 ATATA-ATAAAT-AT
1 ATATATA-AAATAAT
* *
5758843 ATGATAAAAATATTTAAA
1 AT-ATATAAA-A--TAAT
*
5758861 ATGTATAACAATAAT
1 ATATATAA-AATAAT
* *
5758876 ATA-AT-AGATAAA
1 ATATATAAAATAAT
*
5758888 ATATAGTACAATAAAT
1 ATATA-TAAAAT-AAT
*
5758904 AATATATAATAAAAAT
1 -ATATATAA-AATAAT
5758920 ATATATAACATATAAT
1 ATATATAA-A-ATAAT
* * *
5758936 AAAATACAAATATAAC
1 -ATATATAAA-ATAAT
*
5758952 A-AAAT-AAATAAT
1 ATATATAAAATAAT
5758964 ATATATAA
1 ATATATAA
5758972 TAAATAAGTC
Statistics
Matches: 128, Mismatches: 21, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
12 14 0.11
13 16 0.12
14 32 0.25
15 26 0.20
16 17 0.13
17 19 0.15
18 4 0.03
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (14 bp):
ATATATAAAATAAT
Found at i:5758821 original size:22 final size:21
Alignment explanation
Indices: 5758767--5758941 Score: 71
Period size: 22 Copynumber: 8.0 Consensus size: 21
5758757 ATGTATAATA
*
5758767 ATATGAATAATATAATTAGTAATAT
1 ATAT-AATAATAT-A-TA-TAAAAT
*
5758792 ATAAAATAATATATACTAAAAT
1 ATATAATAATATATA-TAAAAT
5758814 ATATAAT-ATA-A-AT--AAT
1 ATATAATAATATATATAAAAT
5758830 ATATAATAAATATATGATAAAAAT
1 ATATAAT-AATATAT-AT-AAAAT
* * *
5758854 ATTTAA-AATGTATAACAATAAT
1 ATATAATAATATAT-ATAA-AAT
* *
5758876 ATAATAGATAAAATATAGTACAAT
1 AT-ATA-ATAATATATA-TAAAAT
*
5758900 AAATAAT-ATATA-ATAAAA-
1 ATATAATAATATATATAAAAT
*
5758918 ATATATATAACATATAATAAAAT
1 ATATA-ATAATATAT-ATAAAAT
5758941 A
1 A
5758942 CAAATATAAC
Statistics
Matches: 114, Mismatches: 18, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
16 10 0.09
18 8 0.07
19 8 0.07
20 6 0.05
21 11 0.10
22 33 0.29
23 7 0.06
24 22 0.19
25 9 0.08
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (21 bp):
ATATAATAATATATATAAAAT
Found at i:5758830 original size:9 final size:9
Alignment explanation
Indices: 5758763--5758973 Score: 56
Period size: 9 Copynumber: 23.8 Consensus size: 9
5758753 TAAAATGTAT
*
5758763 AATAATATG
1 AATAATATA
5758772 AATAATATA
1 AATAATATA
* *
5758781 ATTAGTA-A
1 AATAATATA
*
5758789 TAT-ATA-A
1 AATAATATA
5758796 AATAATATA
1 AATAATATA
* *
5758805 TACTAAAATA
1 -AATAATATA
*
5758815 TATAATATA
1 AATAATATA
5758824 AATAATATA
1 AATAATATA
5758833 TAATAA-ATA
1 -AATAATATA
* * *
5758842 TATGATAAA
1 AATAATATA
*
5758851 AAT-ATTTA
1 AATAATATA
*
5758859 AA-ATGTATAA
1 AATA-ATAT-A
5758869 CAATAATAT-
1 -AATAATATA
5758878 AATAGATA-A
1 AATA-ATATA
5758887 AAT-ATAGTA
1 AATAATA-TA
5758896 CAATAA-AT-
1 -AATAATATA
5758904 AATATATAATA
1 AATA-AT-ATA
5758915 AA-AATATA
1 AATAATATA
* *
5758923 TATAACATA
1 AATAATATA
*
5758932 TAATAAAATA
1 -AATAATATA
*
5758942 CA-AATATA
1 AATAATATA
5758950 ACA-AA-ATA
1 A-ATAATATA
5758958 AATAATATA
1 AATAATATA
*
5758967 TATAATA
1 AATAATA
5758974 AATAAGTCTC
Statistics
Matches: 147, Mismatches: 30, Indels: 50
0.65 0.13 0.22
Matches are distributed among these distances:
7 13 0.09
8 33 0.22
9 65 0.44
10 27 0.18
11 8 0.05
12 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (9 bp):
AATAATATA
Found at i:5758881 original size:27 final size:26
Alignment explanation
Indices: 5758787--5758912 Score: 90
Period size: 24 Copynumber: 5.0 Consensus size: 26
5758777 TATAATTAGT
*
5758787 AATATA-TAAAAT-AAT-ATATACTAA
1 AATATAGTACAATAAATAATATA-TAA
5758811 AATATA-TA-ATATAAATAATATATAA
1 AATATAGTACA-ATAAATAATATATAA
** *
5758836 TAA-ATA-TATGATAAA-AATATTTAA
1 -AATATAGTACAATAAATAATATATAA
* *
5758860 AATGTA-TAACAATAATATAATAGATAA
1 AATATAGT-ACAATAA-ATAATATATAA
5758887 AATATAGTACAATAAATAATATATAA
1 AATATAGTACAATAAATAATATATAA
5758913 TAAAAATATA
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
23 3 0.04
24 21 0.25
25 21 0.25
26 18 0.22
27 19 0.23
28 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.33
Consensus pattern (26 bp):
AATATAGTACAATAAATAATATATAA
Found at i:5758969 original size:21 final size:23
Alignment explanation
Indices: 5758902--5758971 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 23
5758892 AGTACAATAA
* *
5758902 ATAATATATAATAAAA-ATATAT
1 ATAACATATAATAAATAATATAT
5758924 ATAACATATAATAAAATACA-A-AT
1 ATAACATATAAT-AAATA-ATATAT
5758947 ATAACA-A-AATAAATAATATAT
1 ATAACATATAATAAATAATATAT
5758968 ATAA
1 ATAA
5758972 TAAATAAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 1 0.02
20 6 0.15
21 9 0.22
22 12 0.29
23 11 0.27
24 1 0.02
25 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAACATATAATAAATAATATAT
Found at i:5758972 original size:66 final size:65
Alignment explanation
Indices: 5758821--5758978 Score: 144
Period size: 66 Copynumber: 2.4 Consensus size: 65
5758811 AATATATAAT
* * * *
5758821 ATAAATAATATATAATAAATATATGATAAAAATATTTAAAATGTATAACAATAATATAATAGATA
1 ATAAATAATATAT-AT-AATATATAATAAAAATATTTAAAATATATAACAATAAAATAATAGACA
5758886 AA
64 AA
* * *
5758888 ATATAGTACA-ATAAATAATATATAATAAAAATATATATAACATATAATAA-AATACAAAT-ATA
1 ATA-AATA-ATATATATAATATATAATAAAAATAT-T-TAAAATAT-ATAACAATA-AAATAATA
5758950 -ACAAA
60 GACAAA
*
5758955 ATAAATAATATATATAATAAATAA
1 ATAAATAATATATATAATATATAA
5758979 GTCTCCTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
65 1 0.01
66 33 0.45
67 13 0.18
68 19 0.26
69 8 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (65 bp):
ATAAATAATATATATAATATATAATAAAAATATTTAAAATATATAACAATAAAATAATAGACAAA
Found at i:5766945 original size:40 final size:40
Alignment explanation
Indices: 5766901--5766976 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
5766891 CGGCTAAGAA
*
5766901 TGGCACTTAGTGTGCGGTTTGAA-ATAGCTTCGGCTAAATG
1 TGGCACTTAGTGTGCGATTT-AAGATAGCTTCGGCTAAATG
* *
5766941 TGGCACTTGGTGTGTGATTTAAGATAGCTTCGGCTA
1 TGGCACTTAGTGTGCGATTTAAGATAGCTTCGGCTA
5766977 TATATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.34
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTTAAGATAGCTTCGGCTAAATG
Found at i:5767030 original size:28 final size:30
Alignment explanation
Indices: 5766998--5767064 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 30
5766988 ATATATGTGG
5766998 CACTTAGTGTGTG-AA-ATATTGAGAATGA
1 CACTTAGTGTGTGCAAGATATTGAGAATGA
* *
5767026 CACTT-G-GTGTGCAAGATATTGAGTATGG
1 CACTTAGTGTGTGCAAGATATTGAGAATGA
5767054 CACTTAGTGTG
1 CACTTAGTGTG
5767065 CGAGACATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 5 0.15
27 3 0.09
28 21 0.64
29 1 0.03
30 3 0.09
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.33
Consensus pattern (30 bp):
CACTTAGTGTGTGCAAGATATTGAGAATGA
Found at i:5767637 original size:14 final size:14
Alignment explanation
Indices: 5767618--5767645 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5767608 TTAATGAGTC
5767618 TATTTTCAAAAGAA
1 TATTTTCAAAAGAA
5767632 TATTTTCAAAAGAA
1 TATTTTCAAAAGAA
5767646 ATAAACAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
TATTTTCAAAAGAA
Found at i:5769723 original size:96 final size:96
Alignment explanation
Indices: 5769559--5769793 Score: 355
Period size: 96 Copynumber: 2.4 Consensus size: 96
5769549 CCATGGCAAT
* * *
5769559 ATATGTATGCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACATTATGAGAGCCAGTATA
1 ATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATAAGAGCCAGTATA
5769624 AGACCATGTCT-GAGACATGGCATCGGCATTG
66 AGACCATGTCTAG-GACATGGCATCGGCATTG
*
5769655 ATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATAAGAGCCAGTGTA
1 ATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATAAGAGCCAGTATA
5769720 AGACCATGTCTAGGACATGGCATCGGCATTG
66 AGACCATGTCTAGGACATGGCATCGGCATTG
* * * * * * *
5769751 AGACGAGAGCTAGTGTAAGACCATATCTGGGATATGGCATCGG
1 ATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGG
5769794 TATCGATATA
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
96 126 0.99
97 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (96 bp):
ATATGTGTGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATAAGAGCCAGTATA
AGACCATGTCTAGGACATGGCATCGGCATTG
Found at i:5769793 original size:48 final size:47
Alignment explanation
Indices: 5769570--5769844 Score: 245
Period size: 48 Copynumber: 5.7 Consensus size: 47
5769560 TATGTATGCT
* *
5769570 AGTGTAAGACCATGTTTGGGACATGGCATCGACCACATT-AT-GAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCG---GCATTGATAGAGAGCC
* * * * *
5769618 AGTATAAGACCATGTCTGAGACATGGCATCGGCATTGATATGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATA-GAGAGCC
*
5769666 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATT-ATA-AGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG---CATTGATAGAGAGCC
* * *
5769714 AGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATA-GAGAGCC
* * * * * *
5769762 AGTGTAAGACCATATCTGGGATATGGCATCGGTATCGATATATGATCCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAGA-GA-GCC
* * *
5769811 A-TGTAAGACCATATCTGGGATATGGCATTGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
5769845 CTTATTATGT
Statistics
Matches: 188, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
45 8 0.04
46 4 0.02
47 1 0.01
48 166 0.88
49 2 0.01
50 3 0.02
51 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAGAGAGCC
Found at i:5769816 original size:96 final size:95
Alignment explanation
Indices: 5769567--5769844 Score: 310
Period size: 96 Copynumber: 2.9 Consensus size: 95
5769557 ATATATGTAT
* * * * * *
5769567 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGACCACATTATGAGAGCCAGTATAAGACCATG
1 GCTAGTGTAAGACCATATCTGGGACATGGCATCGGCCACATTATAAGACCCAGTGTAAGACCATG
* * * *
5769632 TCTGAGACATGGCATCGGCATTGATATGTGT
66 TCTG-GACATGGCATCGGCATTGAGACGAGA
* * *
5769663 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCACATTATAAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATATCTGGGACATGGCATCGGCCACATTATAAGACCCAGTGTAAGACCATG
5769728 TCTAGGACATGGCATCGGCATTGAGACGAGA
66 TCT-GGACATGGCATCGGCATTGAGACGAGA
* * *
5769759 GCTAGTGTAAGACCATATCTGGGATATGGCATCGG-TATCGA-TATATGATCCCA-TGTAAGACC
1 GCTAGTGTAAGACCATATCTGGGACATGGCATCGGCCA-C-ATTATAAGA-CCCAGTGTAAGACC
* * *
5769821 ATATCTGGGATATGGCATTGGCAT
63 ATGTCT-GGACATGGCATCGGCAT
5769845 CTTATTATGT
Statistics
Matches: 161, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
95 1 0.01
96 155 0.96
97 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (95 bp):
GCTAGTGTAAGACCATATCTGGGACATGGCATCGGCCACATTATAAGACCCAGTGTAAGACCATG
TCTGGACATGGCATCGGCATTGAGACGAGA
Found at i:5773689 original size:20 final size:20
Alignment explanation
Indices: 5773664--5773704 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5773654 AATATAAAAG
5773664 AAAAATA-AACATAAAAATAA
1 AAAAATAGAA-ATAAAAATAA
*
5773684 AAAAATAGAAATAGAAATAA
1 AAAAATAGAAATAAAAATAA
5773704 A
1 A
5773705 TGGACCCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAAATAGAAATAAAAATAA
Found at i:5784363 original size:40 final size:40
Alignment explanation
Indices: 5784319--5784394 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
5784309 CGGCTACGAA
*
5784319 TGGCACTTGGTGTGCGGTTTGAA-ATAGCTTCGGCTAAATG
1 TGGCACTTGGTGTGCGATTT-AAGATAGCTTCGGCTAAATG
*
5784359 TGGCACTTGGTGTGTGATTTAAGATAGCTTCGGCTA
1 TGGCACTTGGTGTGCGATTTAAGATAGCTTCGGCTA
5784395 TATATATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (40 bp):
TGGCACTTGGTGTGCGATTTAAGATAGCTTCGGCTAAATG
Found at i:5784485 original size:28 final size:28
Alignment explanation
Indices: 5784419--5784487 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
5784409 CATATATGTA
5784419 GCACTTAGTGTGCAAAATATTGAGAATG
1 GCACTTAGTGTGCAAAATATTGAGAATG
* * * * *
5784447 ACATTTGGTGTGCAAGATATTGAGTATG
1 GCACTTAGTGTGCAAAATATTGAGAATG
5784475 GCACTTAGTGTGC
1 GCACTTAGTGTGC
5784488 GAGACATCGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTTAGTGTGCAAAATATTGAGAATG
Found at i:5787712 original size:95 final size:99
Alignment explanation
Indices: 5787602--5787848 Score: 304
Period size: 101 Copynumber: 2.5 Consensus size: 99
5787592 CGCTAGGACC
* * *
5787602 AAAAACGCTGCTATAGATTGAGAATTAGCGGCGCTTTTTGAAAAACACCG-AAAAAAATTAAGC-
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGCAAAAAAATTAAGCA
* *
5787665 AC-G-AGCTTTAGTGGCATTAGCGATGCTTTCTG
66 ACGGCAGCATTAGTGGCATTAGCGACGCTTTCTG
*** * *
5787697 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAATGTCGCAAAAATATTCAGCA
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGCAAAAAAATTAAGC-
* *
5787762 AGACGGCAGCATTAGTGGCATTAGCGACGTTTTTTG
65 A-ACGGCAGCATTAGTGGCATTAGCGACGCTTTCTG
* * * *
5787798 AAAAACGCCGCTATAGATCGAGCTTTAACGGCGCTTTTTGATAAACGCCGC
1 AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGC
5787849 TATAGATCAA
Statistics
Matches: 129, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
95 44 0.34
96 11 0.09
99 2 0.02
100 1 0.01
101 71 0.55
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (99 bp):
AAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAACACCGCAAAAAAATTAAGCA
ACGGCAGCATTAGTGGCATTAGCGACGCTTTCTG
Found at i:5787967 original size:14 final size:14
Alignment explanation
Indices: 5787941--5788046 Score: 70
Period size: 14 Copynumber: 7.6 Consensus size: 14
5787931 AATCAATTTA
5787941 GTTTATGGG-TTATG
1 GTTTA-GGGTTTATG
5787955 GTTTAGGGTTTATG
1 GTTTAGGGTTTATG
* *
5787969 TTTTAGAGTTTATG
1 GTTTAGGGTTTATG
** * *
5787983 ACTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
5787997 GTTTAGGGTTTATA
1 GTTTAGGGTTTATG
* * * * *
5788011 ATTTATGATTTCTA
1 GTTTAGGGTTTATG
* *
5788025 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
5788039 GTTTAGGG
1 GTTTAGGG
5788047 GTAAATATGG
Statistics
Matches: 69, Mismatches: 22, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
13 3 0.04
14 66 0.96
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:5788667 original size:43 final size:42
Alignment explanation
Indices: 5788551--5788673 Score: 113
Period size: 43 Copynumber: 2.9 Consensus size: 42
5788541 GAGATATGGG
*
5788551 TTATGATATAATGTTTATTATTTTGGGGTTTAAGGTTTATGAT
1 TTATGATATAATGTTTATTATTTT-GGGTTTAAGGTTTAGGAT
* * * * ** * *
5788594 TTAAGATTTAAGGTTTAATATCCAT-GGTTTAGGTGTTTAGGGT
1 TTATGATATAATGTTTATTAT-TTTGGGTTTAAG-GTTTAGGAT
* *
5788637 TTATGATATAATATTTATTATTTTGGGTTTAAAGTTT
1 TTATGATATAATGTTTATTATTTTGGGTTTAAGGTTT
5788674 TTGGTTTAGG
Statistics
Matches: 59, Mismatches: 18, Indels: 7
0.70 0.21 0.08
Matches are distributed among these distances:
42 12 0.20
43 46 0.78
44 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (42 bp):
TTATGATATAATGTTTATTATTTTGGGTTTAAGGTTTAGGAT
Found at i:5789148 original size:17 final size:18
Alignment explanation
Indices: 5789126--5789159 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5789116 CATTTATTTT
5789126 AATATA-TTAAAATTATC
1 AATATAGTTAAAATTATC
*
5789143 AATATAGTTTAAATTAT
1 AATATAGTTAAAATTAT
5789160 TTAAGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AATATAGTTAAAATTATC
Found at i:5789551 original size:25 final size:25
Alignment explanation
Indices: 5789517--5789569 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5789507 TTTCCCCAAA
5789517 TCGGCAGCCCGCTGCTGTATCTCCG
1 TCGGCAGCCCGCTGCTGTATCTCCG
5789542 TCGGCAGCCCGCTGCTGTATCTCCG
1 TCGGCAGCCCGCTGCTGTATCTCCG
5789567 TCG
1 TCG
5789570 ACATATGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.08, C:0.40, G:0.28, T:0.25
Consensus pattern (25 bp):
TCGGCAGCCCGCTGCTGTATCTCCG
Found at i:5792996 original size:40 final size:40
Alignment explanation
Indices: 5792880--5793047 Score: 133
Period size: 40 Copynumber: 4.1 Consensus size: 40
5792870 TATAATGGCA
* * * *
5792880 TTTGTGAGAAAAGCGCCACTAAAGGT-TTATTTTATAGTGGTG
1 TTTGTG-GAAAAGCGCCGCTAAAGGTCATA-TTT-TAGCGGCG
* * ** *
5792922 TTCGTGACAAAAGCGTTGCTAAAGGT-TTATTTTTAGCGGCG
1 TTTGTG-GAAAAGCGCCGCTAAAGGTCATA-TTTTAGCGGCG
* * *
5792963 TTTGTGGGAAAGTGTCGCTAAAGGTCATATTTTAGCGGCG
1 TTTGTGGAAAAGCGCCGCTAAAGGTCATATTTTAGCGGCG
* *
5793003 TTTGTGGAAAAGCGCCACTAAAGGTCATGTTCTATAGCGGCG
1 TTTGTGGAAAAGCGCCGCTAAAGGTCATATT-T-TAGCGGCG
5793045 TTT
1 TTT
5793048 TTTGTGGCGC
Statistics
Matches: 105, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
40 52 0.50
41 14 0.13
42 39 0.37
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (40 bp):
TTTGTGGAAAAGCGCCGCTAAAGGTCATATTTTAGCGGCG
Found at i:5797575 original size:25 final size:25
Alignment explanation
Indices: 5797547--5797597 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5797537 AGCAAGTAAC
5797547 ATAACCATGCAATTATACGAAATCA
1 ATAACCATGCAATTATACGAAATCA
5797572 ATAACCATGCAATTATACGAAATCA
1 ATAACCATGCAATTATACGAAATCA
5797597 A
1 A
5797598 CATTTGCATA
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:0.49, C:0.20, G:0.08, T:0.24
Consensus pattern (25 bp):
ATAACCATGCAATTATACGAAATCA
Found at i:5797907 original size:46 final size:46
Alignment explanation
Indices: 5797838--5798014 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
5797828 ATAATCTCAC
*
5797838 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGGTG-TTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTT-GCAT
* *
5797884 CCATAATGAACTCGGAACACAACTC-ACGAGTTTGGATGCTTGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCAT
* * *
5797929 CCATAGGTAAACTCGGAACGCAACTCAACGAGTTCGGATGCCT-CAT
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCAT
* * *
5797975 -AATTCTCACGAACTCGGAACGCAACTCAACGAGTTCGGAT
1 CCA---TAATGAACTCGGAACGCAACTCAACGAGTTCGGAT
5798015 CTCAAATTCC
Statistics
Matches: 112, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
45 21 0.19
46 46 0.41
47 44 0.39
48 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTGCAT
Found at i:5797929 original size:45 final size:47
Alignment explanation
Indices: 5797838--5798014 Score: 209
Period size: 47 Copynumber: 3.8 Consensus size: 47
5797828 ATAATCTCAC
*
5797838 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGGTG-TTCGCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* *
5797884 CCATAATGAACTCGGAACACAACTC-ACGAGTTTGGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
* * * **
5797929 CCATAGGTAAACTCGGAACGCAACTCAACGAGTTCGGATGCCTCATAAT
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTC-GCAT
* * *
5797978 TC-TCACGAACTCGGAACGCAACTCAACGAGTTCGGAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGAT
5798015 CTCAAATTCC
Statistics
Matches: 111, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
45 20 0.18
46 43 0.39
47 44 0.40
48 1 0.01
49 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (47 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCGCAT
Found at i:5809026 original size:25 final size:26
Alignment explanation
Indices: 5808989--5809039 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
5808979 ATTATTATAT
5808989 ATATATTTAAAAAATATAATAAATAAA
1 ATATATTTAAAAAATATAA-AAATAAA
*
5809016 ATATA-TT-AAAAATATTAAAATAAA
1 ATATATTTAAAAAATATAAAAATAAA
5809040 TGTTTATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 2 0.09
27 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
ATATATTTAAAAAATATAAAAATAAA
Found at i:5810463 original size:12 final size:12
Alignment explanation
Indices: 5810446--5810471 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5810436 TGTTTGTAAC
5810446 CTCTGCGAACCT
1 CTCTGCGAACCT
5810458 CTCTGCGAACCT
1 CTCTGCGAACCT
5810470 CT
1 CT
5810472 TATGTTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.42, G:0.15, T:0.27
Consensus pattern (12 bp):
CTCTGCGAACCT
Found at i:5817794 original size:16 final size:16
Alignment explanation
Indices: 5817773--5817847 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
5817763 AGTCATAGTG
5817773 ATGTGTGAGTTGTGTA
1 ATGTGTGAGTTGTGTA
**** *
5817789 ATGTGTGAGCTACAATG
1 ATGTGTGAG-TTGTGTA
*
5817806 ATGTGCGAGTTGTGTA
1 ATGTGTGAGTTGTGTA
*
5817822 ATGTGTGAGCTGTAGTA
1 ATGTGTGAGTTGT-GTA
5817839 ATGTGTGAG
1 ATGTGTGAG
5817848 CTGCGAAAAT
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 22 0.50
17 22 0.50
ACGTcount: A:0.23, C:0.05, G:0.36, T:0.36
Consensus pattern (16 bp):
ATGTGTGAGTTGTGTA
Found at i:5817841 original size:17 final size:17
Alignment explanation
Indices: 5817768--5817850 Score: 80
Period size: 17 Copynumber: 5.0 Consensus size: 17
5817758 TTGCGAGTCA
* *
5817768 TAGTGATGTGTGAGTTG
1 TAGTAATGTGTGAGCTG
*
5817785 T-GTAATGTGTGAGCTA
1 TAGTAATGTGTGAGCTG
* * * * *
5817801 CAATGATGTGCGAGTTG
1 TAGTAATGTGTGAGCTG
5817818 T-GTAATGTGTGAGCTG
1 TAGTAATGTGTGAGCTG
5817834 TAGTAATGTGTGAGCTG
1 TAGTAATGTGTGAGCTG
5817851 CGAAAATATG
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
16 24 0.48
17 26 0.52
ACGTcount: A:0.22, C:0.06, G:0.36, T:0.36
Consensus pattern (17 bp):
TAGTAATGTGTGAGCTG
Found at i:5817843 original size:33 final size:33
Alignment explanation
Indices: 5817767--5817843 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
5817757 TTTGCGAGTC
*
5817767 ATAGTGATGTGTGAGTTGTGTAATGTGTGAGCT
1 ATAGTGATGTGCGAGTTGTGTAATGTGTGAGCT
* *
5817800 ACAATGATGTGCGAGTTGTGTAATGTGTGAGCT
1 ATAGTGATGTGCGAGTTGTGTAATGTGTGAGCT
* *
5817833 GTAGTAATGTG
1 ATAGTGATGTG
5817844 TGAGCTGCGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.36
Consensus pattern (33 bp):
ATAGTGATGTGCGAGTTGTGTAATGTGTGAGCT
Found at i:5821235 original size:22 final size:20
Alignment explanation
Indices: 5821192--5821230 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5821182 CAATTTAAAA
*
5821192 TATAAAAATTTATTAATATG
1 TATATAAATTTATTAATATG
5821212 TATATAAATTTATTAATAT
1 TATATAAATTTATTAATAT
5821231 ATGTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATAAATTTATTAATATG
Found at i:5821330 original size:34 final size:33
Alignment explanation
Indices: 5821288--5821352 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
5821278 AAACAACAGA
5821288 AAATA-TTTTTAGTAAATCATTTTCCAGAAAAGT
1 AAATATTTTTTAG-AAATCATTTTCCAGAAAAGT
* *
5821321 AAATCATTTTTTAGAATTCATTTTCCGGAAAA
1 AAAT-ATTTTTTAGAAATCATTTTCCAGAAAA
5821353 TATTTTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 17 0.61
35 7 0.25
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (33 bp):
AAATATTTTTTAGAAATCATTTTCCAGAAAAGT
Found at i:5823467 original size:14 final size:15
Alignment explanation
Indices: 5823439--5823467 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5823429 ATACTCACAC
5823439 ATAGAGCATGCAAGA
1 ATAGAGCATGCAAGA
5823454 ATAGAGCA-GCAAGA
1 ATAGAGCATGCAAGA
5823468 TACTCCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.14, G:0.28, T:0.10
Consensus pattern (15 bp):
ATAGAGCATGCAAGA
Found at i:5825186 original size:16 final size:16
Alignment explanation
Indices: 5825165--5825213 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
5825155 CTCTAAATCC
5825165 TAATGGAATAGAGCTG
1 TAATGGAATAGAGCTG
*
5825181 TAATGGAATAAAGCTG
1 TAATGGAATAGAGCTG
*
5825197 TAATGGAATAGGGCTG
1 TAATGGAATAGAGCTG
5825213 T
1 T
5825214 TATCAGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.27
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:5834933 original size:5 final size:6
Alignment explanation
Indices: 5834894--5834936 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
5834884 ATAATTTCAT
*
5834894 AAATAA AAATAA AAATCTAA AACTAA AAATAA AAATAA AAATA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATA
5834937 TATAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 28 0.85
8 5 0.15
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:5834967 original size:9 final size:9
Alignment explanation
Indices: 5834953--5835002 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
5834943 TTTATACAAA
*
5834953 TAATTCGAT
1 TAATTCGGT
5834962 TAATTCGGT
1 TAATTCGGT
* *
5834971 TAATTAGGG
1 TAATTCGGT
5834980 TAATTCGGT
1 TAATTCGGT
5834989 TAATTCGGT
1 TAATTCGGT
5834998 TAATT
1 TAATT
5835003 TTATACTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:5835366 original size:28 final size:28
Alignment explanation
Indices: 5835255--5835369 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 28
5835245 GTGAGCATGA
* *
5835255 ATATGAATGTGACTGGG-TCTAATAGGCC
1 ATATGAATGTGATTGGGCT-TAATGGGCC
* * *
5835283 ATATAAATGTGATTTGGGCCTAATGGGCT
1 ATATGAATGTGA-TTGGGCTTAATGGGCC
* *
5835312 ATAT-ACAGGTGATCTGGGCTGAATGGGCC
1 ATATGA-ATGTGAT-TGGGCTTAATGGGCC
*
5835341 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCTTAATGGGCC
5835369 A
1 A
5835370 GATATAGGTA
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
28 28 0.40
29 41 0.59
30 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCTTAATGGGCC
Found at i:5841641 original size:45 final size:45
Alignment explanation
Indices: 5841558--5841659 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
5841548 TAACGGTAGC
*
5841558 AGTAACAGTAACAATATTCAACACACAAAGTACTGAATCTGTAAT
1 AGTAACAGTAACAATATTCAACACACAAAGTACTGAATCGGTAAT
* * *
5841603 AGTAACGGTAACAATATTCGACACACAAAGTA-TCGAATCGGTAAC
1 AGTAACAGTAACAATATTCAACACACAAAGTACT-GAATCGGTAAT
*
5841648 AATAACAGTAAC
1 AGTAACAGTAAC
5841660 GGTAACAGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (45 bp):
AGTAACAGTAACAATATTCAACACACAAAGTACTGAATCGGTAAT
Found at i:5841664 original size:18 final size:18
Alignment explanation
Indices: 5841641--5841675 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5841631 AGTATCGAAT
5841641 CGGTAACAATAACAGTAA
1 CGGTAACAATAACAGTAA
*
5841659 CGGTAACAGTAACAGTA
1 CGGTAACAATAACAGTA
5841676 GTCGGCACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (18 bp):
CGGTAACAATAACAGTAA
Found at i:5841955 original size:40 final size:39
Alignment explanation
Indices: 5841875--5841981 Score: 99
Period size: 40 Copynumber: 2.7 Consensus size: 39
5841865 AATTCATTAC
* * * * *
5841875 TTCAGTAATTTCACAGTTCAATGCAGTACACATAATAATA
1 TTCAGTAA-TTCATAATTCAATTCAGTACACAAAACAATA
**
5841915 TTCAGTAACTTCATAATTCAATTCAGTACTTAAAACAATA
1 TTCAGTAA-TTCATAATTCAATTCAGTACACAAAACAATA
* *
5841955 TTCAAT-ATTCCATAATTCAGTTCAGTA
1 TTCAGTAATT-CATAATTCAATTCAGTA
5841982 TCAGTCTCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
38 2 0.04
39 17 0.30
40 37 0.66
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (39 bp):
TTCAGTAATTCATAATTCAATTCAGTACACAAAACAATA
Done.