Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 60 of 313
Found at i:20220554 original size:23 final size:23
Alignment explanation
Indices: 20220524--20220610 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
20220514 GCTTTATCGA
* *
20220524 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
20220547 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
20220568 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
20220590 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
20220611 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:20223569 original size:35 final size:35
Alignment explanation
Indices: 20223523--20223643 Score: 125
Period size: 35 Copynumber: 3.5 Consensus size: 35
20223513 CAAGGTTCCT
*
20223523 TATATCATCACATATGGCCAAATATACAAGTATAA
1 TATAACATCACATATGGCCAAATATACAAGTATAA
* * * * * *
20223558 TAAAACATCACATGTAGTCAAATATTCAAGTTTAA
1 TATAACATCACATATGGCCAAATATACAAGTATAA
* * * *
20223593 TATAACATCATATGTGGCCAAAGATACAAGTACAA
1 TATAACATCACATATGGCCAAATATACAAGTATAA
* *
20223628 TATATCATCATATATG
1 TATAACATCACATATG
20223644 TACATACCTA
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.30
Consensus pattern (35 bp):
TATAACATCACATATGGCCAAATATACAAGTATAA
Found at i:20229968 original size:30 final size:29
Alignment explanation
Indices: 20229912--20229972 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 29
20229902 ATCCAAGATG
20229912 ACTTGACTCGAGCCTTCTTGCAAAGACCAT
1 ACTTGACTCGAGCCTTC-TGCAAAGACCAT
*
20229942 ACTTGACTCGAGCCCTTC-GACGAAGACCAT
1 ACTTGACTCGAG-CCTTCTG-CAAAGACCAT
20229972 A
1 A
20229973 GCACCCATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 1 0.04
30 22 0.79
31 5 0.18
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (29 bp):
ACTTGACTCGAGCCTTCTGCAAAGACCAT
Found at i:20230966 original size:22 final size:22
Alignment explanation
Indices: 20230941--20230989 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20230931 ATAACAGAAT
* *
20230941 ATATCATAGCATATCAGATTTC
1 ATATCAGAGCATATCAGATATC
* *
20230963 ATATCGGAGCATATCATATATC
1 ATATCAGAGCATATCAGATATC
20230985 ATATC
1 ATATC
20230990 GTATCGTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
ATATCAGAGCATATCAGATATC
Found at i:20230980 original size:27 final size:27
Alignment explanation
Indices: 20230945--20231021 Score: 66
Period size: 27 Copynumber: 2.9 Consensus size: 27
20230935 CAGAATATAT
*
20230945 CATAGCATATCAGATTTCATATCGGAG
1 CATATCATATCAGATTTCATATCGGAG
* * * * *
20230972 CATATCATAT-ATCATATCGTATCGTAT
1 CATATCATATCA-GATTTCATATCGGAG
* *
20230999 CATATCATATCTGTTTTCATATC
1 CATATCATATCAGATTTCATATC
20231022 ATGTTGTAGC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (27 bp):
CATATCATATCAGATTTCATATCGGAG
Found at i:20230990 original size:22 final size:22
Alignment explanation
Indices: 20230948--20230990 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20230938 AATATATCAT
*
20230948 AGCATATCAGATTTCATATCGG
1 AGCATATCAGATATCATATCGG
*
20230970 AGCATATCATATATCATATCG
1 AGCATATCAGATATCATATCG
20230991 TATCGTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (22 bp):
AGCATATCAGATATCATATCGG
Found at i:20230999 original size:15 final size:15
Alignment explanation
Indices: 20230981--20231056 Score: 53
Period size: 15 Copynumber: 4.8 Consensus size: 15
20230971 GCATATCATA
*
20230981 TATCATATCGTATCG
1 TATCATATCATATCG
20230996 TATCATATCATATCTG
1 TATCATATCATATC-G
* * *
20231012 TTTTCATATCATGTTG
1 -TATCATATCATATCG
* * *
20231028 TAGCATGTTTCATATCT
1 TATCA--TATCATATCG
20231045 TATCATATCATA
1 TATCATATCATA
20231057 ACTCATGCCA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
15 22 0.49
16 2 0.04
17 21 0.47
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (15 bp):
TATCATATCATATCG
Found at i:20231090 original size:22 final size:22
Alignment explanation
Indices: 20231037--20231092 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
20231027 GTAGCATGTT
* *
20231037 TCATATCTTATCATATCATAAC
1 TCATATCATGTCATATCATAAC
** *
20231059 TCATGCCATGTCATATCATATC
1 TCATATCATGTCATATCATAAC
20231081 TCATATCATGTC
1 TCATATCATGTC
20231093 CTACCCCAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.39
Consensus pattern (22 bp):
TCATATCATGTCATATCATAAC
Found at i:20232199 original size:16 final size:17
Alignment explanation
Indices: 20232168--20232200 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20232158 AAAAAAACTC
*
20232168 AAAGAAAAGTGAAAGAA
1 AAAGAAAAGAGAAAGAA
20232185 AAAGAAAA-AGAAAGAA
1 AAAGAAAAGAGAAAGAA
20232201 CAAAAGGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAGAAAAGAGAAAGAA
Found at i:20234230 original size:19 final size:20
Alignment explanation
Indices: 20234206--20234250 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
20234196 TTGAGATGGA
20234206 ATGATATTCAACTTTGTGG-
1 ATGATATTCAACTTTGTGGT
* *
20234225 ATGATATTTAACTTTTTGGT
1 ATGATATTCAACTTTGTGGT
20234245 ATGATA
1 ATGATA
20234251 GGGACATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (20 bp):
ATGATATTCAACTTTGTGGT
Found at i:20240289 original size:191 final size:191
Alignment explanation
Indices: 20239948--20240328 Score: 600
Period size: 191 Copynumber: 2.0 Consensus size: 191
20239938 ATAATCTCTC
* * *
20239948 TTACATGAAATAGTCATACCTTTTTCCCTCCTATGACTAAGTTGTCTCCACTTCAAACGAGTCGA
1 TTACACGAAATAGTCATACCTTTTTCCCTCCTATGACCAAGTTGTCTCCACTTCAAACGAGTCCA
* *** * *
20240013 GTTTAACTCTTTAACAGATGTGGGACGTCTGGTTTCACCGGTCACCGTTGATCCTTCCAAAACAT
66 GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
* * *
20240078 AAAGACTTTTAATATTTTTACCTTTCATAGAAAAGAAGAGCCTCATGAGATACCTTAATGT
131 AAAGACTTTCAATATTTTTACCTTTCATAAAAAAGAAGAGCCTCATAAGATACCTTAATGT
* **
20240139 TTACACGAAATAGTCATACCTTTTTCTCTCCTATGACCAAGTTGTCTCTGCTTCAAACGAGTCCA
1 TTACACGAAATAGTCATACCTTTTTCCCTCCTATGACCAAGTTGTCTCCACTTCAAACGAGTCCA
20240204 GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
66 GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
* * *
20240269 AAAGACTTTCAATCTTTTTACCTTTTATAAAAAAGAAGAGCCTTATAAGATACCTTAATG
131 AAAGACTTTCAATATTTTTACCTTTCATAAAAAAGAAGAGCCTCATAAGATACCTTAATG
20240329 CCGCTTGAAT
Statistics
Matches: 172, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
191 172 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (191 bp):
TTACACGAAATAGTCATACCTTTTTCCCTCCTATGACCAAGTTGTCTCCACTTCAAACGAGTCCA
GTTCAACTCTTTAACAGACAAGGGACGTCCGGTTTCACAGGTCACCGTTGATCCTTCCAAAACAT
AAAGACTTTCAATATTTTTACCTTTCATAAAAAAGAAGAGCCTCATAAGATACCTTAATGT
Found at i:20246566 original size:7 final size:7
Alignment explanation
Indices: 20246554--20246578 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20246544 AGTCGTTTCA
20246554 TATTTAG
1 TATTTAG
20246561 TATTTAG
1 TATTTAG
20246568 TATTTAG
1 TATTTAG
20246575 TATT
1 TATT
20246579 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20247141 original size:30 final size:30
Alignment explanation
Indices: 20247077--20247141 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
20247067 AACGACACAG
* * * * *
20247077 GCCCATCAACAGCGGCTACACAATCGCCGG
1 GCCCATCAACAACGCCCACACAATCACCGA
*
20247107 GCCCATCAACAACGCCCACACAATCATCGA
1 GCCCATCAACAACGCCCACACAATCACCGA
20247137 GCCCA
1 GCCCA
20247142 ATGCCTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.43, G:0.17, T:0.09
Consensus pattern (30 bp):
GCCCATCAACAACGCCCACACAATCACCGA
Found at i:20250506 original size:46 final size:46
Alignment explanation
Indices: 20250328--20250585 Score: 156
Period size: 46 Copynumber: 5.5 Consensus size: 46
20250318 TTTGTGCGCT
* * * * *
20250328 AGTGTAAGA-AATGTCCGGGACATGCATTGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGA-GATGA-AGCC
** * * * * * *
20250374 AGTGTAAGACCATGTCTAAGACATGGCAACGAC-ATTGTGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTA-CGAGATGA-AGCC
* *
20250422 AGTGTAAGA-CATGTATGGGGCATGCATCGGCCT-CGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGG-CTACGAGATG-AAGCC
* * *
20250468 AGTGTAAGA-CATGTCTGGGACATGCATTGGCTATGAGATG-AGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGAGATGAAGCC
* * *
20250512 AGTGTAAGACCACGTTTGGGACATGACATCAGC-ACGGAGATGCGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATG-CATCGGCTAC-GAGAT--GA-AGCC
20250562 AGTGTAAGACCATGTCT-GGACATG
1 AGTGTAAGACCATGTCTGGGACATG
20250586 GCGTTAGACT
Statistics
Matches: 162, Mismatches: 35, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
44 12 0.07
45 16 0.10
46 64 0.40
47 23 0.14
48 22 0.14
49 7 0.04
50 18 0.11
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCTACGAGATGAAGCC
Found at i:20252178 original size:30 final size:30
Alignment explanation
Indices: 20252142--20252210 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
20252132 ATGGGGCAGA
20252142 CCGTGTGTCACACACGGCCTAGACACATGC
1 CCGTGTGTCACACACGGCCTAGACACATGC
*
20252172 CCGTGTGTCACACATGGCCTAGACACATGC
1 CCGTGTGTCACACACGGCCTAGACACATGC
20252202 CCGTGTGTC
1 CCGTGTGTC
20252211 CAACCTTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (30 bp):
CCGTGTGTCACACACGGCCTAGACACATGC
Found at i:20253407 original size:45 final size:45
Alignment explanation
Indices: 20253343--20253429 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
20253333 CCAAAACATG
*
20253343 TGTCACATATATTACGAACTCAGACCACAACTCAATGAGTTCGGA
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
* * *
20253388 TGTCATATATATCATGAACTCAGATCACAACTCAATGAGTTC
1 TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTC
20253430 AGATTACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (45 bp):
TGTCACATATATCACGAACTCAGACCACAACTCAATGAGTTCGGA
Found at i:20262035 original size:44 final size:41
Alignment explanation
Indices: 20261938--20262037 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 41
20261928 CAATTGTATT
*
20261938 TGGCACTAAGTGTGCGATTCAAAATAGCTTCGGCTATATGA
1 TGGCACTAAGTGTGCGATCCAAAATAGCTTCGGCTATATGA
* * *
20261979 -GGCACTAAGTGTGCGATACCGAGATAGCTTCGGTTA-ATTGAGA
1 TGGCACTAAGTGTGCGAT-CCAAAATAGCTTCGGCTATA-T--GA
20262022 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
20262038 GAATCGTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
40 18 0.36
41 15 0.30
43 2 0.04
44 15 0.30
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGATCCAAAATAGCTTCGGCTATATGA
Found at i:20264457 original size:126 final size:125
Alignment explanation
Indices: 20264232--20264731 Score: 673
Period size: 125 Copynumber: 4.0 Consensus size: 125
20264222 GGCCAATTAT
* * * * * *
20264232 GAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTTAGACATTTTGCTGACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATA-ATTTTGCTGACAGTGCATC
* *
20264297 CTGCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTCTGAAAATTATTTTTTCAA
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
**
20264358 GAACTACTGTAGAAAAAGAGCGTTTACGTAGGAGCTTTTTCCTATAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTT-CTATAATTTTGCTGACAGTGCATC
* * * * * *
20264423 CTGCTTGAGGCATTTTTGACACTATTTGTTCAG-AACTTCTTCTCATAATTATCTTTTCAT
65 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* * ** * *
20264483 GAACTAATTTAGAAAAAGAGCGTCCACGT-GGTAGCTTTTTTCCCTAATTTTGCTGACAATACAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGG-AGC-TTTTTCTATAATTTTGCTGACAGTGCAT
* * *
20264547 CCTGCTTGAAGCGTTTTTGGCACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTT-AG
64 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
* *
20264608 GAACTACTGTAGAAAAAGAGCGTCCAAGTAGGAGCTTTTTCTATATTTTTGCTGACAGTGCATCC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATAATTTTGCTGACAGTGCATCC
* **
20264673 TGCTTGAAGCGTTTTTGACACTATTTATTCAGAAACGCCTTCTCAAAATTATTTTTTCA
66 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCA
20264732 GTGTAAAAAT
Statistics
Matches: 323, Mismatches: 45, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
124 79 0.24
125 130 0.40
126 111 0.34
127 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTAGGAGCTTTTTCTATAATTTTGCTGACAGTGCATCC
TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAA
Found at i:20264814 original size:30 final size:29
Alignment explanation
Indices: 20264782--20264904 Score: 120
Period size: 29 Copynumber: 4.0 Consensus size: 29
20264772 GTTATTTTTA
*
20264782 AAAAAACTAAACCCTAATTTAATTTATTT
1 AAAAACCTAAACCCTAATTTAATTTATTT
*
20264811 AAAACCCTAGAACCCTAATTTAGTTAATTTATTT
1 AAAAACCTA-AACCCTAA--T--TTAATTTATTT
* *
20264845 AAAAATCGTAAACCCCAATTTAATTTATTT
1 AAAAA-CCTAAACCCTAATTTAATTTATTT
* * * *
20264875 AAAACCCCAAACCCTAATTTACTTAATTT
1 AAAAACCTAAACCCTAATTTAATTTATTT
20264904 A
1 A
20264905 TTTTAAAATC
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
29 27 0.35
30 23 0.30
32 2 0.03
34 22 0.29
35 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAACCTAAACCCTAATTTAATTTATTT
Found at i:20264843 original size:34 final size:32
Alignment explanation
Indices: 20264788--20264931 Score: 138
Period size: 34 Copynumber: 4.5 Consensus size: 32
20264778 TTTAAAAAAA
20264788 CTAAACCCTAA--T-TTAATTTATTTAAAACC
1 CTAAACCCTAATTTATTAATTTATTTAAAACC
*
20264817 CTAGAACCCTAATTTAGTTAATTTATTTAAAAATC
1 CTA-AACCCTAATTTA-TTAATTTATTT-AAAACC
* *
20264852 GTAAACCCCAA--T-TTAATTTATTTAAAACC
1 CTAAACCCTAATTTATTAATTTATTTAAAACC
* *
20264881 CCAAACCCTAATTTACTTAATTTATTTTAAAATC
1 CTAAACCCTAATTTA-TTAATTTA-TTTAAAACC
**
20264915 CTAAATTCTAATTTATT
1 CTAAACCCTAATTTATT
20264932 TAAAACCCTA
Statistics
Matches: 93, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
29 16 0.17
30 19 0.20
31 1 0.01
32 2 0.02
33 10 0.11
34 38 0.41
35 7 0.08
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (32 bp):
CTAAACCCTAATTTATTAATTTATTTAAAACC
Found at i:20264901 original size:63 final size:64
Alignment explanation
Indices: 20264778--20264919 Score: 214
Period size: 64 Copynumber: 2.2 Consensus size: 64
20264768 CAATGTTATT
** * * *
20264778 TTTAAAAAAACTAAACCCTAATTTAATTTATTTAAAACCCTAGAACCCTAATTTAGTTAATTTA
1 TTTAAAAATCCTAAACCCCAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
*
20264842 TTTAAAAATCGTAAACCCCAATTTAATTTATTTAAAACCCCA-AACCCTAATTTACTTAATTTA
1 TTTAAAAATCCTAAACCCCAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
*
20264905 TTTTAAAATCCTAAA
1 TTTAAAAATCCTAAA
20264920 TTCTAATTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
63 33 0.47
64 37 0.53
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (64 bp):
TTTAAAAATCCTAAACCCCAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
Found at i:20264927 original size:25 final size:23
Alignment explanation
Indices: 20264897--20264954 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
20264887 CCTAATTTAC
*
20264897 TTAATTTATTTTAAAATCCTAAAT
1 TTAATTTATTTTAAAACCCT-AAT
20264921 TCTAATTTA-TTTAAAACCCTAAT
1 T-TAATTTATTTTAAAACCCTAAT
20264944 TTAATTTATTT
1 TTAATTTATTT
20264955 GAAACCTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 7 0.23
23 6 0.19
24 11 0.35
25 7 0.23
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTTATTTTAAAACCCTAAT
Found at i:20264928 original size:63 final size:64
Alignment explanation
Indices: 20264778--20264933 Score: 217
Period size: 63 Copynumber: 2.5 Consensus size: 64
20264768 CAATGTTATT
** * *
20264778 TTTAAAAAAACTAAACCCTAATTTAATTTATTTAAAACCCTAGAACCCTAATTTAGTTAATTTA
1 TTTAAAAATCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
* *
20264842 TTTAAAAATCGTAAACCCCAATTTAATTTATTTAAAACCCCA-AACCCTAATTTACTTAATTTA
1 TTTAAAAATCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
* **
20264905 TTTTAAAATCCTAAATTCTAATTT-ATTTA
1 TTTAAAAATCCTAAACCCTAATTTAATTTA
20264934 AAACCCTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 5 0.06
63 39 0.48
64 37 0.46
ACGTcount: A:0.42, C:0.17, G:0.02, T:0.40
Consensus pattern (64 bp):
TTTAAAAATCCTAAACCCTAATTTAATTTATTTAAAACCCCAGAACCCTAATTTACTTAATTTA
Found at i:20264951 original size:22 final size:23
Alignment explanation
Indices: 20264897--20264965 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 23
20264887 CCTAATTTAC
*
20264897 TTAATTTATTTTAAAATCCTAAAT
1 TTAATTTA-TTTAAAACCCTAAAT
20264921 TCTAATTTATTTAAAACCCT-AAT
1 T-TAATTTATTTAAAACCCTAAAT
* *
20264944 TTAATTTATTTGAAACCTTAAA
1 TTAATTTATTTAAAACCCTAAA
20264966 AACCCTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
22 16 0.40
23 6 0.15
24 11 0.28
25 7 0.17
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (23 bp):
TTAATTTATTTAAAACCCTAAAT
Found at i:20267834 original size:48 final size:48
Alignment explanation
Indices: 20267776--20267928 Score: 209
Period size: 48 Copynumber: 3.2 Consensus size: 48
20267766 TAGCCGGGCT
* * *
20267776 ATTGGTATCGATATGTGATCCCATGTAAGACTATGTCTAGGACATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
** **
20267824 ATTGGCATCGACCTACGATCCCATGTAAGACCATGT-TCGGGACATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCT-GGGACATGGC
* *
20267872 ATTGGCATCGATATGTGATCCCATGTAAGACCATATCTGGGATATGGC
1 ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
20267920 ATTGGCATC
1 ATTGGCATC
20267929 CTACCATATG
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
47 1 0.01
48 88 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (48 bp):
ATTGGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACATGGC
Found at i:20270199 original size:41 final size:40
Alignment explanation
Indices: 20270154--20270311 Score: 176
Period size: 41 Copynumber: 3.9 Consensus size: 40
20270144 GATTCTTAGT
*
20270154 ACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGATTAGACC
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTAGA-C
* * * * *
20270195 ACTGGCTCGAAGGCCCTTCGGAACTAAGTTCGG-TTATGAC
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTA-GAC
* * *
20270235 ACTGGCTCTAAAGCCCTTCGAAACTAAGTTCGGTTATTAG-C
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGG--ATTAGAC
*
20270276 ACTGGCTCAAAGGCCCTTCGAAACCAAGCTCGGATT
1 ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATT
20270312 TAAACCCTGA
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.03
40 34 0.34
41 59 0.59
42 1 0.01
43 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
ACTGGCTCAAAAGCCCTTCGAAACCAAGCTCGGATTAGAC
Found at i:20284418 original size:48 final size:48
Alignment explanation
Indices: 20284347--20284486 Score: 190
Period size: 48 Copynumber: 2.9 Consensus size: 48
20284337 TAGGGTTATG
*
20284347 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACC
1 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACA
* *
20284395 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGATA
1 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACA
** * * * **
20284443 TGTGATCCCATGTAAGACCATATCCGGGATATGGAATTGGCATC
1 TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATC
20284487 CTACCATGTG
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 82 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (48 bp):
TACGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCAACA
Found at i:20293626 original size:44 final size:43
Alignment explanation
Indices: 20293578--20293734 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
20293568 TGTGTTATCG
* * *
20293578 TGTAAGACCACTTATGGGACATTGGCATCA-ACTTATGATTTACG
1 TGTAAGACCACTTCTAGGACATTGGCATCATA-TT-TGATTTACA
* * *
20293622 TGTAAGACCACTTTTGGGACATTGGCATTATATTTGATTT-CA
1 TGTAAGACCACTTCTAGGACATTGGCATCATATTTGATTTACA
*
20293664 TGTAAGACC-CTGTCTAGGACAGTGGCATCGATATTTGA-TTACA
1 TGTAAGACCACT-TCTAGGACATTGGCATC-ATATTTGATTTACA
*
20293707 TGTAAGACCACGTCTAGGACATTGGCAT
1 TGTAAGACCACTTCTAGGACATTGGCAT
20293735 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.02
42 25 0.25
43 40 0.40
44 31 0.31
45 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACTTCTAGGACATTGGCATCATATTTGATTTACA
Found at i:20293897 original size:21 final size:21
Alignment explanation
Indices: 20293871--20293914 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
20293861 GAGGATAAGG
20293871 TAAGTACAAAGCATATGTATA
1 TAAGTACAAAGCATATGTATA
20293892 TAAGTACAAAGCATATGTATA
1 TAAGTACAAAGCATATGTATA
20293913 TA
1 TA
20293915 TGTGAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.30
Consensus pattern (21 bp):
TAAGTACAAAGCATATGTATA
Found at i:20294500 original size:9 final size:9
Alignment explanation
Indices: 20294486--20294514 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
20294476 AGATTGAATG
20294486 ATGGATATT
1 ATGGATATT
20294495 ATGGATATT
1 ATGGATATT
20294504 ATGGATATT
1 ATGGATATT
20294513 AT
1 AT
20294515 TCAGTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
ATGGATATT
Found at i:20304278 original size:129 final size:129
Alignment explanation
Indices: 20304048--20304298 Score: 344
Period size: 129 Copynumber: 1.9 Consensus size: 129
20304038 CGCTAAACTG
* * * * * **
20304048 ATTAGTGATAGACTGAAAGTCCCTTCTGATAGGCAGAAGTCTTACATAGATCTGAAATGTTGTGA
1 ATTAGTGATAAACTAAAAGTCCCTTCTGATAAGCAAAAGTCTTACACAGATCTGAAACATTGTGA
* *
20304113 CATCAAGTTTTAGGTTGGGGATCGAGTGTTCCTTAAGGTTTCACCTTGGGAA-AAAGTGAAATTT
66 CATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCA-CTTGGGAAGAAAGTGAAATTT
* * * *
20304177 ATTAGTGATAAACTAAAAG-CTGCTTGTGATAAGCAAAAGTCTTACGCAGATTTGAAACATTGTG
1 ATTAGTGATAAACTAAAAGTC-CCTTCTGATAAGCAAAAGTCTTACACAGATCTGAAACATTGTG
*
20304241 ACATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCACTTTGGAAGAAAGT
65 ACATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCACTTGGGAAGAAAGT
20304299 TCTAATATTC
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
128 8 0.08
129 98 0.92
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (129 bp):
ATTAGTGATAAACTAAAAGTCCCTTCTGATAAGCAAAAGTCTTACACAGATCTGAAACATTGTGA
CATCAAGTTTCAAGTTGGGGATCGAGTGTTCCTTAAGGTTTCACTTGGGAAGAAAGTGAAATTT
Found at i:20313426 original size:27 final size:27
Alignment explanation
Indices: 20313364--20313734 Score: 251
Period size: 27 Copynumber: 13.8 Consensus size: 27
20313354 CCAAACTATT
* * *
20313364 TAAAATTATCGAAATACCCCCA-TTTG
1 TAAAATTACCGAAATACCCCTAGATTG
* ** *
20313390 AAAAATTACCGAAATACCTTTAGATTA
1 TAAAATTACCGAAATACCCCTAGATTG
* *
20313417 TAAAATTACCAAAATA-CCCTCAGTTTG
1 TAAAATTACCGAAATACCCCT-AGATTG
* * * *
20313444 TAAAATCACTGAAA-AACCCTCGAATTG
1 TAAAATTACCGAAATACCCCTAG-ATTG
** *
20313471 TAAAATTATTGAAATA-CCCTAGTTTG
1 TAAAATTACCGAAATACCCCTAGATTG
* ** *
20313497 TAAAATTATCGAAATACCTTTAGATTA
1 TAAAATTACCGAAATACCCCTAGATTG
*
20313524 TAAAATTACCAAAATACCCCT-GATTTG
1 TAAAATTACCGAAATACCCCTAGA-TTG
* * * *
20313551 TAAAATCACCAAAATACCCTTGGATTG
1 TAAAATTACCGAAATACCCCTAGATTG
*
20313578 TAAAATTATCGAAATACCCCT-GATTTG
1 TAAAATTACCGAAATACCCCTAGA-TTG
* *
20313605 TAAAATTACCAAAAT-GCCCTCAGATTG
1 TAAAATTACCGAAATACCCCT-AGATTG
** *
20313632 TAAAATTAATGAAAGACTCCC--GATTTG
1 TAAAATTACCGAAATAC-CCCTAGA-TTG
* * *
20313659 TAAAATTACCAAAATACCCC-CGATTTA
1 TAAAATTACCGAAATACCCCTAGA-TTG
* * *
20313686 TAAAATTACTGAAATA-CCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTAG-ATTG
20313713 TAAAATTACCGAAATACCCCTA
1 TAAAATTACCGAAATACCCCTA
20313735 TAGGGTAAAA
Statistics
Matches: 269, Mismatches: 58, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
26 55 0.20
27 201 0.75
28 10 0.04
29 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCTAGATTG
Found at i:20313616 original size:54 final size:54
Alignment explanation
Indices: 20313364--20313731 Score: 317
Period size: 54 Copynumber: 6.9 Consensus size: 54
20313354 CCAAACTATT
* * * * *
20313364 TAAAATTATCGAAATACCCC-CATTTGAAAAATTACCGAAATACCTTTAGATTA
1 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
* * * * * *
20313417 TAAAATTACCAAAATA-CCCTCAGTTTGTAAAATCACTGAAAA-ACCCTC-GAATTG
1 TAAAATTATCGAAATACCCCTGA-TTTGTAAAATTAC-CAAAATACCCTCAG-ATTA
* * * * *
20313471 TAAAATTATTGAAATA-CCCT-AGTTTGTAAAATTATCGAAATACCTTTAGATTA
1 TAAAATTATCGAAATACCCCTGA-TTTGTAAAATTACCAAAATACCCTCAGATTA
* * * ** *
20313524 TAAAATTACCAAAATACCCCTGATTTGTAAAATCACCAAAATACCCTTGGATTG
1 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
* *
20313578 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATGCCCTCAGATTG
1 TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
* *
20313632 TAAAATTAAT-GAAAGACTCCC-GATTTGTAAAATTACCAAAATACCC-CCGATTTA
1 TAAAATT-ATCGAAATAC-CCCTGATTTGTAAAATTACCAAAATACCCTCAGA-TTA
* * *
20313686 TAAAATTA-CTGAAATACCCTTG-TAGTGTAAAATTACCGAAATACCC
1 TAAAATTATC-GAAATACCCCTGAT-TTGTAAAATTACCAAAATACCC
20313732 CTATAGGGTA
Statistics
Matches: 258, Mismatches: 42, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
52 6 0.02
53 57 0.22
54 186 0.72
55 9 0.03
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30
Consensus pattern (54 bp):
TAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAATACCCTCAGATTA
Found at i:20313742 original size:27 final size:27
Alignment explanation
Indices: 20313686--20313745 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
20313676 CCCCGATTTA
* * * *
20313686 TAAAATTACTGAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTATAGGG
20313713 TAAAATTACCGAAATACCCCTATAGGG
1 TAAAATTACCGAAATACCCCTATAGGG
20313740 TAAAAT
1 TAAAAT
20313746 GAATGTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCTATAGGG
Found at i:20314248 original size:27 final size:27
Alignment explanation
Indices: 20314190--20314251 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
20314180 CTATGTACCT
* * *
20314190 ATCATATTTATCGATGACTCTGTGTCG
1 ATCATATTTACCCATGACTCTGTGTAG
*
20314217 ATCATATTTACCCATGACTGTGTGCTAG
1 ATCATATTTACCCATGACTCTGTG-TAG
20314245 -TCATATT
1 ATCATATT
20314252 ACCGTCACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (27 bp):
ATCATATTTACCCATGACTCTGTGTAG
Found at i:20314590 original size:27 final size:27
Alignment explanation
Indices: 20314531--20314590 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
20314521 AGATGCGCTA
* ** *
20314531 GGCCCAATTGATTCTGTTATGGGCTGT
1 GGCCCAAATGATAATGTAATGGGCTGT
* *
20314558 GACCCAAATGATAATGTAATGGGCTTT
1 GGCCCAAATGATAATGTAATGGGCTGT
20314585 GGCCCA
1 GGCCCA
20314591 CTTATGCTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (27 bp):
GGCCCAAATGATAATGTAATGGGCTGT
Found at i:20315299 original size:20 final size:20
Alignment explanation
Indices: 20315274--20315322 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
20315264 CAGCCTGTGG
20315274 TATCGATATCGCTT-TAAAAA
1 TATCGATA-CGCTTATAAAAA
**
20315294 TATCGATACTTTTATAAAAA
1 TATCGATACGCTTATAAAAA
20315314 TATCGATAC
1 TATCGATAC
20315323 TTGTGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (20 bp):
TATCGATACGCTTATAAAAA
Found at i:20315323 original size:20 final size:21
Alignment explanation
Indices: 20315288--20315342 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
20315278 GATATCGCTT
*
20315288 TAAAAATATCGATACTT-TTA
1 TAAAAATATCGATACTTGTGA
20315308 TAAAAATATCGATACTTGTGA
1 TAAAAATATCGATACTTGTGA
*
20315329 -AAAAATATCAATAC
1 TAAAAATATCGATAC
20315343 CAATATGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (21 bp):
TAAAAATATCGATACTTGTGA
Found at i:20322498 original size:41 final size:41
Alignment explanation
Indices: 20322452--20322531 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
20322442 GTGATTCCTT
20322452 AGGACAAGATTGATATCTAGCACACAAGCATACATTAAATA
1 AGGACAAGATTGATATCTAGCACACAAGCATACATTAAATA
*
20322493 AGGACAATATTGATATCTAGCACACAAGCATACATTAAA
1 AGGACAAGATTGATATCTAGCACACAAGCATACATTAAA
20322532 CATAATCTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (41 bp):
AGGACAAGATTGATATCTAGCACACAAGCATACATTAAATA
Found at i:20325192 original size:22 final size:22
Alignment explanation
Indices: 20325143--20325215 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
20325133 ATAGCTCGTA
*
20325143 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTG-TTCAGCTCAAT
* *
20325166 GGAGCTTACTGTTCAGCTCAAC
1 AGAGCTTACTGTTCAGCTCAAT
*
20325188 AGAGCTTACCATTTTCAGCTCAAT
1 AGAGCTTA-C-TGTTCAGCTCAAT
20325212 AGAG
1 AGAG
20325216 ACTATTGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 16 0.38
23 11 0.26
24 15 0.36
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCAAT
Found at i:20335287 original size:22 final size:23
Alignment explanation
Indices: 20335241--20335287 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
20335231 CATTGGAGCC
*
20335241 TACTGATTCAGCTCGAAAGAGCT
1 TACTGATTCAGCTCGAAAGAACT
20335264 TACT-ATTCAGCTC-AACAGAACT
1 TACTGATTCAGCTCGAA-AGAACT
20335286 TA
1 TA
20335288 GCGTTTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 16 0.73
23 4 0.18
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (23 bp):
TACTGATTCAGCTCGAAAGAACT
Found at i:20345661 original size:22 final size:22
Alignment explanation
Indices: 20345622--20345732 Score: 136
Period size: 22 Copynumber: 5.0 Consensus size: 22
20345612 GAGTCATGGT
* *
20345622 CGGTAAGCTCCT-TCGAGCAGAA
1 CGGTAAGCT-CTATTGAGCTGAA
*
20345644 CAGTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCTCTATTGAGCTG-AA
20345667 CGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
20345689 CGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
* *
20345711 CGATAAGCT-TCAATGAGCTGAA
1 CGGTAAGCTCT-ATTGAGCTGAA
20345733 ACATAAGCTC
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
21 3 0.04
22 56 0.70
23 21 0.26
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (22 bp):
CGGTAAGCTCTATTGAGCTGAA
Found at i:20345673 original size:45 final size:44
Alignment explanation
Indices: 20345622--20345719 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
20345612 GAGTCATGGT
20345622 CGGTAAGCTCCT-TCGAGCAGAACAGTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCT-CTATCGAGCAGAACAGTAAGCTCTATTGAGCTG-AA
* * *
20345667 CGGTAAGCTCTATTGAGCTGAACGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATCGAGCAGAACAGTAAGCTCTATTGAGCTGAA
*
20345711 CGATAAGCT
1 CGGTAAGCT
20345720 TCAATGAGCT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
44 12 0.25
45 36 0.75
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (44 bp):
CGGTAAGCTCTATCGAGCAGAACAGTAAGCTCTATTGAGCTGAA
Found at i:20355321 original size:40 final size:41
Alignment explanation
Indices: 20355277--20355371 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 41
20355267 AGCGATTCTG
* *
20355277 ACTTGTTTTAAAATCATTTT-GA-TGTGTTAAAATGATTTTA
1 ACTTGTTTTAAAATCATTTTGGATTG-GTTAAAATCAATTTA
* * * *
20355317 ACTTG-ATTGAAATCATTTTGGCTTGGTTAAAATCAATTTC
1 ACTTGTTTTAAAATCATTTTGGATTGGTTAAAATCAATTTA
20355357 ACTTGATTTTAAAAT
1 ACTTG-TTTTAAAAT
20355372 TGTTTCAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
39 12 0.28
40 23 0.53
41 2 0.05
42 6 0.14
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (41 bp):
ACTTGTTTTAAAATCATTTTGGATTGGTTAAAATCAATTTA
Found at i:20355334 original size:20 final size:20
Alignment explanation
Indices: 20355284--20355364 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
20355274 CTGACTTGTT
*
20355284 TTAAAATCATTTTGA-TGTG-
1 TTAAAATCATTTTAACT-TGA
*
20355303 TTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
* ** *
20355323 TTGAAATCATTTTGGCTTGG
1 TTAAAATCATTTTAACTTGA
* *
20355343 TTAAAATCAATTTCACTTGA
1 TTAAAATCATTTTAACTTGA
20355363 TT
1 TT
20355365 TTAAAATTGT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
19 15 0.31
20 33 0.69
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.46
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:20359217 original size:51 final size:50
Alignment explanation
Indices: 20359125--20359226 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 50
20359115 AAAGTTGGAA
20359125 CAGGGGATCCAGAAATCGCTCTTGCCCTATTTCACCAAAACTCAGATACC
1 CAGGGGATCCAGAAATCGCTCTTGCCCTATTTCACCAAAACTCAGATACC
* *
20359175 CNAGGGGATCCAGAAATTGCTCCTTTCCCTATTTCACC-AAACTCAGATACC
1 C-AGGGGATCCAGAAATCGCT-CTTGCCCTATTTCACCAAAACTCAGATACC
20359226 C
1 C
20359227 TATAAAATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
50 1 0.02
51 32 0.67
52 15 0.31
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.24
Consensus pattern (50 bp):
CAGGGGATCCAGAAATCGCTCTTGCCCTATTTCACCAAAACTCAGATACC
Found at i:20360048 original size:48 final size:46
Alignment explanation
Indices: 20359979--20360099 Score: 127
Period size: 48 Copynumber: 2.6 Consensus size: 46
20359969 TGTCTTCGAC
** * * *
20359979 ATGGACTTACATGAATTATTCCTGTCTCC-AATGCCATATATATATAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAT-CCATATAGAT-GAT
* * *
20360026 AATGGGCTTACATGGCTCATTCCTATCTCCAAATCCATATAGCTGAT
1 -ATGGACTTACATGGCTCATTCCTGTCTCCAAATCCATATAGATGAT
*
20360073 ATGGACTTACATGGCTCATTTCTGTCT
1 ATGGACTTACATGGCTCATTCCTGTCT
20360100 TGTCCTGTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
46 24 0.39
47 2 0.03
48 32 0.52
49 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.36
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAATCCATATAGATGAT
Found at i:20364722 original size:13 final size:13
Alignment explanation
Indices: 20364692--20364730 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
20364682 AAATATATAC
* *
20364692 AAAATATTAAATT
1 AAAATATAAAAAT
*
20364705 CAAATATAAAAAT
1 AAAATATAAAAAT
20364718 AAAATATAAAAAT
1 AAAATATAAAAAT
20364731 TAAACAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATATAAAAAT
Found at i:20364923 original size:17 final size:18
Alignment explanation
Indices: 20364903--20364941 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
20364893 TTTAATAAAA
20364903 AAATAAAATTT-AGAGAG
1 AAATAAAATTTAAGAGAG
*
20364920 AAATAAAATTTAAGTGAG
1 AAATAAAATTTAAGAGAG
20364938 AAAT
1 AAAT
20364942 TAAGAGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (18 bp):
AAATAAAATTTAAGAGAG
Found at i:20372952 original size:91 final size:90
Alignment explanation
Indices: 20372833--20373009 Score: 264
Period size: 91 Copynumber: 2.0 Consensus size: 90
20372823 ATAAATTCCC
* *
20372833 TAAAAATATTTCAAGAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCTTTT
1 TAAAAATATTTCAAAAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCATTT
20372898 AATTGTTTAGCTAAATCCACTTTCT
66 AATTGTTTAGCTAAATCCACTTTCT
* * ** *
20372923 TAAAAATATTTCAAAAAAAGCTATTTTAAATGAAACAAACATATATTTGGCTTTTTCTTTTCATT
1 TAAAAATATTTC-AAAAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCATT
* *
20372988 TAATTGTTTAGTTAAATTCACT
65 TAATTGTTTAGCTAAATCCACT
20373010 AAACAAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 12 0.16
91 65 0.84
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (90 bp):
TAAAAATATTTCAAAAAAGCTATTTTAAACGAAACAAACATACATTTGAATTTTTCTTGTCATTT
AATTGTTTAGCTAAATCCACTTTCT
Found at i:20377402 original size:16 final size:16
Alignment explanation
Indices: 20377378--20377408 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20377368 GAGAAGAAAT
20377378 TATGAGTTTTGAGAAG
1 TATGAGTTTTGAGAAG
*
20377394 TATGGGTTTTGAGAA
1 TATGAGTTTTGAGAA
20377409 AAAGAATAGC
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:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (16 bp):
TATGAGTTTTGAGAAG
Found at i:20380989 original size:26 final size:26
Alignment explanation
Indices: 20380960--20381009 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
20380950 CACCAATATT
* *
20380960 GCAGCAGAGCTGCCAGTAACAGTAAC
1 GCAGCAAAGCTACCAGTAACAGTAAC
* *
20380986 GCAGCAAAGTTACCAGTATCAGTA
1 GCAGCAAAGCTACCAGTAACAGTA
20381010 TATGGCACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (26 bp):
GCAGCAAAGCTACCAGTAACAGTAAC
Found at i:20381037 original size:20 final size:20
Alignment explanation
Indices: 20381013--20381090 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
20381003 ATCAGTATAT
*
20381013 GGCACAAAGCCATCAATAGT
1 GGCACAAAGCCATCAATAGC
20381033 GGCACAAAGCCATCAATAGC
1 GGCACAAAGCCATCAATAGC
20381053 GGCACAAAGCCATCAATAGC
1 GGCACAAAGCCATCAATAGC
*
20381073 GGCACAAAGCCATAAATA
1 GGCACAAAGCCATCAATA
20381091 TCACAGTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.42, C:0.27, G:0.19, T:0.12
Consensus pattern (20 bp):
GGCACAAAGCCATCAATAGC
Found at i:20381408 original size:27 final size:27
Alignment explanation
Indices: 20381378--20381442 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
20381368 GGGTAAAATA
*
20381378 GTCATTTTATCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
*
20381405 GTCAGTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
20381432 GTCATTTTACC
1 GTCATTTTACC
20381443 TGCCTTAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTTG
Found at i:20384976 original size:20 final size:20
Alignment explanation
Indices: 20384922--20385019 Score: 81
Period size: 20 Copynumber: 4.9 Consensus size: 20
20384912 ATCAATATAT
*
20384922 GGCACAAAGCCA-CGAGTAGC
1 GGCACAAAGCCATC-AGTAGA
* *
20384942 GGCTCAAAGCTATCAGTAGA
1 GGCACAAAGCCATCAGTAGA
* * *
20384962 GGCACAATGCCATCAATAGT
1 GGCACAAAGCCATCAGTAGA
* * *
20384982 GGCACAAAGACATCAATAGC
1 GGCACAAAGCCATCAGTAGA
* *
20385002 GACACAAAGCCATAAGTA
1 GGCACAAAGCCATCAGTA
20385020 TCGCAACAAT
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 61 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (20 bp):
GGCACAAAGCCATCAGTAGA
Found at i:20392009 original size:22 final size:22
Alignment explanation
Indices: 20391982--20392039 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
20391972 TCTCCGATTA
20391982 TTAGCACATTAATGCTCT-TCGT
1 TTAGCACATTAATGCTCTCT-GT
**
20392004 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTAATGCTCTCTGT
* *
20392026 ATAGCATATTAATG
1 TTAGCACATTAATG
20392040 ATCCCTATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAATGCTCTCTGT
Found at i:20395963 original size:42 final size:43
Alignment explanation
Indices: 20395891--20395993 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 43
20395881 TATGATTTAC
* *
20395891 GTGTAAGACCATGTCTGGGACTTCGACATCG-TATTTGATTTT
1 GTGTAAGACCATGTCTGGAACGTCGACATCGATATTTGATTTT
* * **
20395933 GTGTAAGACCCTGTCTGGAACAGT-GGCATCGATATTTGATTAC
1 GTGTAAGACCATGTCTGGAAC-GTCGACATCGATATTTGATTTT
* *
20395976 ATGTAAGACCACGTCTGG
1 GTGTAAGACCATGTCTGG
20395994 GATGTTGGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
42 25 0.50
43 25 0.50
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGAACGTCGACATCGATATTTGATTTT
Found at i:20396003 original size:43 final size:44
Alignment explanation
Indices: 20395834--20396004 Score: 133
Period size: 43 Copynumber: 4.0 Consensus size: 44
20395824 CATAGGATCT
* * * *
20395834 GATATGTGATTTCGTGTAAGACCACGTTTGGGAC-ATTGGCAT-
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACTGTTGGCATC
* * * *
20395876 TA-ACTTATGATTTACGTGTAAGACCATGTCTGGGACT-TCGACATC
1 GATA-TT-TGA-TTACGTGTAAGACCACGTCTGGGACTGTTGGCATC
** * *
20395921 G-TATTTGATTTTGTGTAAGACC-CTGTCTGGAACAG-TGGCATC
1 GATATTTGATTACGTGTAAGACCAC-GTCTGGGACTGTTGGCATC
*
20395963 GATATTTGATTACATGTAAGACCACGTCTGGGA-TGTTGGCAT
1 GATATTTGATTACGTGTAAGACCACGTCTGGGACTGTTGGCAT
20396005 TGTATGATCT
Statistics
Matches: 98, Mismatches: 20, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
41 1 0.01
42 29 0.30
43 37 0.38
44 30 0.31
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (44 bp):
GATATTTGATTACGTGTAAGACCACGTCTGGGACTGTTGGCATC
Found at i:20402892 original size:21 final size:21
Alignment explanation
Indices: 20402866--20402921 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
20402856 AGCAGCGGTG
*
20402866 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
20402887 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
*
20402908 ACGGTGAGATTAGA
1 GCGGTGAGATTAGA
20402922 AACAATGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:20406020 original size:49 final size:47
Alignment explanation
Indices: 20405910--20406035 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 47
20405900 ATAGGGTACG
* * *
20405910 ATGTCGACGCCATGTTCCAAACATGGTCTTACGCTGGCTCTCACATCT
1 ATGTCGATGCCATGTCCCAAACA-GGTCTTACACTGGCTCTCACATCT
* **
20405958 AAGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCGTTTATCT
1 ATGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTC--ACATCT
*
20406007 ATGTCGATGCCATGTCCCAAACAGTTCTT
1 ATGTCGATGCCATGTCCCAAACAGGTCTT
20406036 GTAATGGCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 17 0.25
48 20 0.29
49 31 0.46
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.30
Consensus pattern (47 bp):
ATGTCGATGCCATGTCCCAAACAGGTCTTACACTGGCTCTCACATCT
Found at i:20414021 original size:30 final size:29
Alignment explanation
Indices: 20413977--20414033 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
20413967 TCCGAGCCTT
20413977 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATG-AAAAGTTTA
* * *
20414007 GGGGCAAAATTGTAATTTTGAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAGTT
20414034 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGGAAAAAATGTAATTATGAAAAGTTTA
Found at i:20414263 original size:13 final size:13
Alignment explanation
Indices: 20414245--20414276 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
20414235 TTTCCAGCAA
20414245 TTATGAATTTATT
1 TTATGAATTTATT
20414258 TTATGAATTTATT
1 TTATGAATTTATT
*
20414271 TGATGA
1 TTATGA
20414277 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:20414495 original size:50 final size:49
Alignment explanation
Indices: 20414377--20414562 Score: 219
Period size: 50 Copynumber: 3.6 Consensus size: 49
20414367 GTAAAGAGAT
* * *
20414377 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC---AGA-C--GAGAAGA
* *
20414433 CCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGATGA
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACC-AGACGAGAAGA
* *
20414483 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCATCACGAGAACA
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCA-GACGAGAAGA
20414533 TCCCATGTAAGACCATGTCTGGGACATGGC
1 -CCCATGTAAGACCATGTCTGGGACATGGC
20414563 TTTGGCATGT
Statistics
Matches: 119, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
49 1 0.01
50 49 0.41
51 29 0.24
52 1 0.01
53 3 0.03
55 2 0.02
56 34 0.29
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (49 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAGACGAGAAGA
Found at i:20414514 original size:26 final size:26
Alignment explanation
Indices: 20414485--20414562 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 26
20414475 CGAGATGACC
20414485 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
* ** * **
20414511 CATG--GGCACCATCAC-GAGAACATCC
1 CATGTAAG-ACCATGTCTG-GGACATGG
20414536 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
20414562 C
1 C
20414563 TTTGGCATGT
Statistics
Matches: 35, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
24 2 0.06
25 15 0.43
26 16 0.46
27 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (26 bp):
CATGTAAGACCATGTCTGGGACATGG
Found at i:20423047 original size:17 final size:17
Alignment explanation
Indices: 20423021--20423056 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20423011 TCAATCACAC
*
20423021 AAAAATGAAAAAAAAAG
1 AAAAAAGAAAAAAAAAG
*
20423038 AAAAAAGAAAAAAGAAG
1 AAAAAAGAAAAAAAAAG
20423055 AA
1 AA
20423057 TAAGATAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:20433373 original size:21 final size:21
Alignment explanation
Indices: 20433335--20433374 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20433325 ATTACTCCAA
*
20433335 GGAAGCCGATTGATTCATCTC
1 GGAAGCCGATTCATTCATCTC
20433356 GGAAGCCGGATTCA-TCATC
1 GGAAGCC-GATTCATTCATC
20433375 AAGACTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
GGAAGCCGATTCATTCATCTC
Found at i:20442515 original size:47 final size:46
Alignment explanation
Indices: 20442363--20442536 Score: 153
Period size: 47 Copynumber: 3.7 Consensus size: 46
20442353 TGTAACCCGC
* * ** *
20442363 CCATAAGTGAACTC-GAACTCAACTCAATGAGCTC-GGGTGTTCGCAT
1 CCATAAGTGAACTCAG-ACTCAACTCAACGAGTTCAGCAT-TTCACAT
*
20442409 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC--A-G-C-ATTTCACAT
* * *
20442459 -C-TTA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTTCACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCAG-CATTTCACAT
20442503 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTC
20442537 GGATGTTCAA
Statistics
Matches: 103, Mismatches: 14, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
43 3 0.03
44 6 0.06
45 2 0.02
46 32 0.31
47 51 0.50
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGTTCAGCATTTCACAT
Found at i:20451187 original size:39 final size:39
Alignment explanation
Indices: 20451134--20451261 Score: 175
Period size: 39 Copynumber: 3.3 Consensus size: 39
20451124 TATGAGATTG
* *
20451134 AAAATATCCAGACATGAGGTCCGCAGGCTATATGCCGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * *
20451173 AAAATATTCGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
* * **
20451212 AATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
20451251 AAAATATCCGG
1 AAAATATCCGG
20451262 GTTAAAGACC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 76 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (39 bp):
AAAATATCCGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:20451275 original size:78 final size:76
Alignment explanation
Indices: 20451133--20451287 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 76
20451123 GTATGAGATT
* * * *
20451133 GAAAATATCCAGACATGAGGTCCGCAGGCTATATGCCGGAAAAATATTCGGACATGAGATCCGCA
1 GAAAATATCCAGACATGAGGTCCGCAGGCTACATGCCGGAAAAATATCCGGACATAAGACCCGCA
20451198 GGCTATATGCTA
66 GGCT-TATGCTA
* * * * **
20451210 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAGACCCG
1 GAAA-ATATCCAGACATGAGGTCCGCAGGCTACATGCCGGAAAAATATCCGGACAT-AAGACCCG
20451274 CAGGCTTATGCTA
64 CAGGCTTATGCTA
20451287 G
1 G
20451288 TAATGTATTC
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
77 13 0.20
78 53 0.80
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (76 bp):
GAAAATATCCAGACATGAGGTCCGCAGGCTACATGCCGGAAAAATATCCGGACATAAGACCCGCA
GGCTTATGCTA
Found at i:20459090 original size:39 final size:39
Alignment explanation
Indices: 20459037--20459164 Score: 184
Period size: 39 Copynumber: 3.3 Consensus size: 39
20459027 TATGAGATTG
**
20459037 AAAATATCCAGACATGAGGTCCGCAGGCTATATGCTGGA
1 AAAATATCTGGACATGAGGTCCGCAGGCTATATGCTGGA
* *
20459076 AAAATATCTGGACATGAGATCCGCAGGCTATATGCTAGA
1 AAAATATCTGGACATGAGGTCCGCAGGCTATATGCTGGA
* * **
20459115 AATATATCTGGACTTGAGGTCCGCAGGCTACGTGCTGGA
1 AAAATATCTGGACATGAGGTCCGCAGGCTATATGCTGGA
20459154 AAAATATCTGG
1 AAAATATCTGG
20459165 GTTAAAGACC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (39 bp):
AAAATATCTGGACATGAGGTCCGCAGGCTATATGCTGGA
Found at i:20462431 original size:15 final size:16
Alignment explanation
Indices: 20462411--20462443 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20462401 AAATAATTTA
*
20462411 TTTCTCTTA-TTTTCT
1 TTTCTCTCACTTTTCT
20462426 TTTCTCTCACTTTTCT
1 TTTCTCTCACTTTTCT
20462442 TT
1 TT
20462444 CCTACCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCTCTCACTTTTCT
Found at i:20462881 original size:21 final size:20
Alignment explanation
Indices: 20462855--20462897 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
20462845 TTAAATTAGA
20462855 ATAAAA-ATGATAAGTTTTTTT
1 ATAAAATAT-ATAA-TTTTTTT
*
20462876 ATAAAATATTTAATTTTTTT
1 ATAAAATATATAATTTTTTT
20462896 AT
1 AT
20462898 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 9 0.45
22 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
ATAAAATATATAATTTTTTT
Found at i:20463033 original size:8 final size:8
Alignment explanation
Indices: 20463020--20463049 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
20463010 AAAAAATATT
20463020 TTTTATAA
1 TTTTATAA
20463028 TTTTATAA
1 TTTTATAA
20463036 TTTTTATAA
1 -TTTTATAA
20463045 TTTTA
1 TTTTA
20463050 ATACAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTATAA
Found at i:20463040 original size:9 final size:9
Alignment explanation
Indices: 20463019--20463048 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20463009 TAAAAAATAT
20463019 TTTTTATAA
1 TTTTTATAA
20463028 -TTTTATAA
1 TTTTTATAA
20463036 TTTTTATAA
1 TTTTTATAA
20463045 TTTT
1 TTTT
20463049 AATACAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTATAA
Found at i:20463189 original size:29 final size:31
Alignment explanation
Indices: 20463129--20463200 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
20463119 CTTATGTTTA
*
20463129 TATAATTTTTTAAATAATGTTTACAACTTTT
1 TATAATTTTTTAAATAATGTTTACAAATTTT
* *
20463160 TATAA-TTTTT-AATAATTTTTAAAATATTTT
1 TATAATTTTTTAAATAATGTTTACAA-ATTTT
*
20463190 TAT-GTTTTTTA
1 TATAATTTTTTA
20463201 TGCTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 12 0.35
30 17 0.50
31 5 0.15
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (31 bp):
TATAATTTTTTAAATAATGTTTACAAATTTT
Found at i:20463241 original size:28 final size:28
Alignment explanation
Indices: 20463185--20463241 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
20463175 TTTTTAAAAT
* *
20463185 ATTTTTATGTTTTTTATGCTTTTTTTCA
1 ATTTTTATGTTTTTTATGATTTTTCTCA
20463213 ATTTTTAT-TTTTTTAAT-ATTTTTACTCA
1 ATTTTTATGTTTTTT-ATGATTTTT-CTCA
20463241 A
1 A
20463242 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (28 bp):
ATTTTTATGTTTTTTATGATTTTTCTCA
Found at i:20463443 original size:22 final size:21
Alignment explanation
Indices: 20463416--20463456 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
20463406 ACTTAATAGG
*
20463416 TTTTTTATTTATTTATAAGCTT
1 TTTTTTATATATTT-TAAGCTT
20463438 TTTTTTATATATTTTAAGC
1 TTTTTTATATATTTTAAGC
20463457 CTAACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTTTATATATTTTAAGCTT
Found at i:20463569 original size:15 final size:16
Alignment explanation
Indices: 20463548--20463587 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
20463538 AATCCCTTCA
20463548 AAAATTATA-AAAAAT
1 AAAATTATATAAAAAT
*
20463563 TAAATTA-ATAAAAAT
1 AAAATTATATAAAAAT
20463578 AAAATTATAT
1 AAAATTATAT
20463588 TTTAGCTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.86
16 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:20467724 original size:24 final size:24
Alignment explanation
Indices: 20467679--20467731 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
20467669 TTTAAAATAA
*
20467679 ATTTAATTTAATATAATTATTTTT
1 ATTTAATTTAATATAATAATTTTT
20467703 ATTTAATATTAATATAA-AATTTTT
1 ATTTAAT-TTAATATAATAATTTTT
20467727 ATTTA
1 ATTTA
20467732 TTTTTTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTAATTTAATATAATAATTTTT
Found at i:20471477 original size:29 final size:29
Alignment explanation
Indices: 20471435--20471493 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20471425 TTCCCATTTG
20471435 TTTCTCTTGAAAATAGACTCATTCAGGAT
1 TTTCTCTTGAAAATAGACTCATTCAGGAT
20471464 TTTCTCTTGAAAATAGACTCATTCAGGAT
1 TTTCTCTTGAAAATAGACTCATTCAGGAT
20471493 T
1 T
20471494 CTAAACATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTCTCTTGAAAATAGACTCATTCAGGAT
Found at i:20473926 original size:31 final size:31
Alignment explanation
Indices: 20473891--20473958 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
20473881 TTAACAACCC
**
20473891 AGTGACTTAAAT-AAAAACTTTTGAATAATTT
1 AGTGACTTAAATGAAAAA-TTTCAAATAATTT
*
20473922 AGTGACTTAAATGAAAAATTTCAAATAGTTT
1 AGTGACTTAAATGAAAAATTTCAAATAATTT
20473953 AGTGAC
1 AGTGAC
20473959 CAACTTGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (31 bp):
AGTGACTTAAATGAAAAATTTCAAATAATTT
Found at i:20477845 original size:5 final size:5
Alignment explanation
Indices: 20477821--20477864 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
20477811 GATGTGTAAA
* *
20477821 ATAAT A-AAT ATAATT ATAAT ATAAT ATCAT ATAAT ATGAT ATAA
1 ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
20477865 GCAAATAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:20478763 original size:109 final size:109
Alignment explanation
Indices: 20478572--20478771 Score: 357
Period size: 109 Copynumber: 1.8 Consensus size: 109
20478562 GGATTTATTT
20478572 TTATCTATGATAATTATATTTTATTGATATAAAACAATTGCAATTCCATTTAATTTGATCATAAA
1 TTATCTATGATAATTATATTTTATTGATATAAAACAATTGCAATTCCATTTAATTTGATCATAAA
*
20478637 TACTTTTTGGATGTCTTATAATATATATTTGTACGTCAACTTTA
66 TACTTTTTAGATGTCTTATAATATATATTTGTACGTCAACTTTA
* *
20478681 TTATCTAT-ATTAATTATATTTTATTGATATAAAACAATTGCAGTTTCATTTAATTTGATCATAA
1 TTATCTATGA-TAATTATATTTTATTGATATAAAACAATTGCAATTCCATTTAATTTGATCATAA
20478745 ATACTTTTTAGATGTCTTATAATATAT
65 ATACTTTTTAGATGTCTTATAATATAT
20478772 GTTCTTTGCT
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
108 1 0.01
109 86 0.99
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (109 bp):
TTATCTATGATAATTATATTTTATTGATATAAAACAATTGCAATTCCATTTAATTTGATCATAAA
TACTTTTTAGATGTCTTATAATATATATTTGTACGTCAACTTTA
Found at i:20492667 original size:21 final size:20
Alignment explanation
Indices: 20492639--20492677 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
20492629 CAAAACTTGT
20492639 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
20492659 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
20492678 CAAAATACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:20495975 original size:34 final size:34
Alignment explanation
Indices: 20495928--20495998 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
20495918 TTAGGCCCTC
*
20495928 TTTCAGCAGCAGTAACAGTCTGGGCCTGAGCCCA
1 TTTCAGCAGCAGTAACAGTCTGGGCCTCAGCCCA
* * * *
20495962 TTTCAGTATCAGTAGCAGTTTGGGCCTCAGCCCA
1 TTTCAGCAGCAGTAACAGTCTGGGCCTCAGCCCA
20495996 TTT
1 TTT
20495999 TAGAATAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (34 bp):
TTTCAGCAGCAGTAACAGTCTGGGCCTCAGCCCA
Found at i:20499959 original size:39 final size:39
Alignment explanation
Indices: 20499915--20500101 Score: 329
Period size: 39 Copynumber: 4.8 Consensus size: 39
20499905 TATCAGGACA
*
20499915 AAGCCTGCGGGACTTTAACCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
*
20499954 AAGCCTGCGGGACTTTGGCCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
* *
20499993 AAGCCTGTGGGACTTTAGTCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
*
20500032 AAGCCTGCGGGACTTTGGCCCGGATACATTTCCAGCACG
1 AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
20500071 AAGCCTGCGGGACTTTAGCCCGGATACATTT
1 AAGCCTGCGGGACTTTAGCCCGGATACATTT
20500102 TCAGTGTCTT
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 139 1.00
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.22
Consensus pattern (39 bp):
AAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACG
Found at i:20510792 original size:21 final size:21
Alignment explanation
Indices: 20510768--20510836 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
20510758 CTATGCGACC
20510768 TAGCTACATCATAATGTCTCG
1 TAGCTACATCATAATGTCTCG
* * *
20510789 TAGCT-C-TC-TAGTGCACATCACC
1 TAGCTACATCATAATG----TCTCG
20510811 TAGCTACATCATAATGTCTCG
1 TAGCTACATCATAATGTCTCG
20510832 TAGCT
1 TAGCT
20510837 CTCTTGTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
18 4 0.11
19 2 0.06
20 1 0.03
21 13 0.37
22 8 0.23
23 1 0.03
24 2 0.06
25 4 0.11
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (21 bp):
TAGCTACATCATAATGTCTCG
Found at i:20510826 original size:43 final size:43
Alignment explanation
Indices: 20510765--20510849 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
20510755 CACCTATGCG
*
20510765 ACCTAGCTACATCATAATGTCTCGTAGCTCTCTAGTGCACATC
1 ACCTAGCTACATCATAATGTCTCGTAGCTCTCTAGTACACATC
*
20510808 ACCTAGCTACATCATAATGTCTCGTAGCTCTCTTGTACACAT
1 ACCTAGCTACATCATAATGTCTCGTAGCTCTCTAGTACACAT
20510850 GATGTGCACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (43 bp):
ACCTAGCTACATCATAATGTCTCGTAGCTCTCTAGTACACATC
Found at i:20511387 original size:30 final size:30
Alignment explanation
Indices: 20511353--20511413 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
20511343 TCCTTACCTC
20511353 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
20511383 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
20511413 A
1 A
20511414 GGCTAGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:20522518 original size:21 final size:20
Alignment explanation
Indices: 20522490--20522528 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
20522480 CAAAACTTGT
20522490 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
20522510 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
20522529 CAAAATGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:20537138 original size:29 final size:28
Alignment explanation
Indices: 20537086--20537157 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
20537076 CTTATGGTCT
*
20537086 ACTAGGCCCAATCTCATTCATATGGCCC
1 ACTAGGCCCAATCACATTCATATGGCCC
*
20537114 ATTAGGCCCAAATCACA-TCTATATGGCCC
1 ACTAGGCCC-AATCACATTC-ATATGGCCC
*
20537143 ACTAGGCCTAATCAC
1 ACTAGGCCCAATCAC
20537158 TTTTACAGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 16 0.42
29 22 0.58
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (28 bp):
ACTAGGCCCAATCACATTCATATGGCCC
Found at i:20541654 original size:50 final size:49
Alignment explanation
Indices: 20541595--20541872 Score: 301
Period size: 50 Copynumber: 5.6 Consensus size: 49
20541585 CATCAAAGTC
* *
20541595 GATGCCATGTCCTAGACATGGTCTTACATTGACTCTCACGTATCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCAC-TATCGAGGCT
* * *
20541645 GATGCCATGTCCCAGACATGGTCTTACACT-AGCTCTCACATATTGAAGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTCAC-TATCGAGGCT
* * * *
20541695 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATCTATCGATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCA-CTATCGAGGCT
* * * * *
20541745 GATGCCATGTCCCAGACGTGGTCTTACACTGACACACACATGTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCAC-TATCGAGGCT
* * * * *
20541795 AATGCCATGTCCCTGACATGGTCTTACACAGGCTCTCA-TAAT-GTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACT-ATCGAGGCT
*
20541843 GACGCCATGTCCCAGACATGGTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
20541873 ATCACACATA
Statistics
Matches: 190, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
48 31 0.16
49 3 0.02
50 155 0.82
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACTATCGAGGCT
Found at i:20541768 original size:100 final size:101
Alignment explanation
Indices: 20541590--20541873 Score: 348
Period size: 100 Copynumber: 2.9 Consensus size: 101
20541580 TCATACATCA
* * *
20541590 AAGTCGATGCCATGTCCTAGACATGGTCTTACATTGACTCTCA-CGTATCGAGGCTGATGCCATG
1 AAGTCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATC-TATCGATGCTGATGCCATG
* * *
20541654 TCCCAGACATGGTCTTACACTAG-CTCTCACATATTG
65 TCCCAGACATGGTCTTACACTAGACACACACATATCG
* *
20541690 AAGTTGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATCTATCGATGCCGATGCCATGT
1 AAGTCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATCTATCGATGCTGATGCCATGT
* *
20541755 CCCAGACGTGGTCTTACACT-GACACACACATGTCG
66 CCCAGACATGGTCTTACACTAGACACACACATATCG
* * * * * *
20541790 AGGCCAATGCCATGTCCCT-GACATGGTCTTACACAGGCTCTCAT-AAT-G-TGGCTGACGCCAT
1 AAGTCGATGCCATGT-CCTAGACATGGTCTTACACTGGCTCTCATCTATCGAT-GCTGATGCCAT
20541851 GTCCCAGACATGGTCTTACACTA
64 GTCCCAGACATGGTCTTACACTA
20541874 TCACACATAT
Statistics
Matches: 160, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
97 1 0.01
98 31 0.19
99 3 0.02
100 121 0.76
101 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (101 bp):
AAGTCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATCTATCGATGCTGATGCCATGT
CCCAGACATGGTCTTACACTAGACACACACATATCG
Found at i:20548442 original size:59 final size:59
Alignment explanation
Indices: 20548377--20548492 Score: 232
Period size: 59 Copynumber: 2.0 Consensus size: 59
20548367 TGTCCTCCAT
20548377 ACGGCGGAGAGACACGACCATGTCTCTACCCGTGTGTCTACTAGCATGCATACTGACAC
1 ACGGCGGAGAGACACGACCATGTCTCTACCCGTGTGTCTACTAGCATGCATACTGACAC
20548436 ACGGCGGAGAGACACGACCATGTCTCTACCCGTGTGTCTACTAGCATGCATACTGAC
1 ACGGCGGAGAGACACGACCATGTCTCTACCCGTGTGTCTACTAGCATGCATACTGAC
20548493 TTGTAAAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.21
Consensus pattern (59 bp):
ACGGCGGAGAGACACGACCATGTCTCTACCCGTGTGTCTACTAGCATGCATACTGACAC
Found at i:20550303 original size:36 final size:36
Alignment explanation
Indices: 20550263--20550333 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
20550253 CACTTCGTCG
20550263 CCGATCTCAAACTCAATGTCTTTTCTTTTCAAATCA
1 CCGATCTCAAACTCAATGTCTTTTCTTTTCAAATCA
20550299 CCGATCTCAAACTCAATGTCTTTTCTTTTCAAATC
1 CCGATCTCAAACTCAATGTCTTTTCTTTTCAAATC
20550334 TGTATATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (36 bp):
CCGATCTCAAACTCAATGTCTTTTCTTTTCAAATCA
Found at i:20554461 original size:30 final size:29
Alignment explanation
Indices: 20554427--20554487 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
20554417 ATGAGTTGAA
20554427 AGCTTTGGCACTAAATGTGCAATTTAAACT
1 AGCTTTGGCACTAAATGTGCAATTT-AACT
* *
20554457 AGCTTTGGCACTAAGTGTGCGATTTAACT
1 AGCTTTGGCACTAAATGTGCAATTTAACT
20554486 AG
1 AG
20554488 TTTCGACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (29 bp):
AGCTTTGGCACTAAATGTGCAATTTAACT
Found at i:20557019 original size:39 final size:41
Alignment explanation
Indices: 20556924--20557107 Score: 197
Period size: 40 Copynumber: 4.6 Consensus size: 41
20556914 TTGAATGATG
* *
20556924 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAATGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGAT-ACTAATA
* *
20556963 TCCGGACAAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
20557003 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
20557042 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAATA
* *
20557082 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20557108 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
39 53 0.43
40 58 0.47
41 12 0.10
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:20557129 original size:79 final size:79
Alignment explanation
Indices: 20556976--20557140 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
20556966 GGACAAAGAT
* ** *
20556976 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
20557041 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20557055 CCGAAGGCATTTGTGTGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
20557117 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
20557134 CCGAAGG
1 CCGAAGG
20557141 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 45 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:20568230 original size:55 final size:55
Alignment explanation
Indices: 20568146--20568255 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
20568136 GACAATTCAG
*
20568146 ATACTTGAGGATATGTTGAGATGTTGCATCCTCGAGTTCAGTGGTTCATGGGAAC
1 ATACTTGAGGATATGTTGAGATGTTGCATCCTCGAGTTCAGTAGTTCATGGGAAC
20568201 ATACTTGAGGATATGTTGAGATGTTGCATCCTCGAGTTCAGTAGTTCATGGGAAC
1 ATACTTGAGGATATGTTGAGATGTTGCATCCTCGAGTTCAGTAGTTCATGGGAAC
20568256 GGTATTTACC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (55 bp):
ATACTTGAGGATATGTTGAGATGTTGCATCCTCGAGTTCAGTAGTTCATGGGAAC
Found at i:20568719 original size:148 final size:148
Alignment explanation
Indices: 20568446--20568737 Score: 426
Period size: 148 Copynumber: 2.0 Consensus size: 148
20568436 TCCGTGAAAA
* * *
20568446 TCTGAAAGCAGCCACAGATCGTCAAAAATCGTATGCGGATTTGAAACGAAAGGACATTGAATATC
1 TCTGAAAGCAGCCACAGATCGTCAAAAATCGTACGCGGATTTGAAACGAAAAGACATTCAATATC
* * * * *
20568511 AGGTGGGAGATAAAGTGTTTCTTACAGTTTCACCTTGGAAGAAGGTACTCAGATTTGGCCGTAAG
66 AGGTGGGAGACAAAGTGTTCCTTACAGTTTCACCTTGGAAAAAGATACTCAGATTCGGCCGTAAG
20568576 GGCAAGTTGAGCCCGAAG
131 GGCAAGTTGAGCCCGAAG
* * * * *
20568594 TCTGAAGGTAGCCACGGATCGTCAGAAATCGTACGCTGATTTGAAACGAAAAGACA-TCAAGTAT
1 TCTGAAAGCAGCCACAGATCGTCAAAAATCGTACGCGGATTTGAAACGAAAAGACATTCAA-TAT
*
20568658 CAGGTGGGAGACAAAGTGTTCCTTA-AGGTTTCACCTTGGAAAAAGATACTCAGGTTCGGCCGTA
65 CAGGTGGGAGACAAAGTGTTCCTTACA-GTTTCACCTTGGAAAAAGATACTCAGATTCGGCCGTA
20568722 AGGGCAAGTTGAGCCC
129 AGGGCAAGTTGAGCCC
20568738 AAGATTCATT
Statistics
Matches: 128, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
147 4 0.03
148 124 0.97
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (148 bp):
TCTGAAAGCAGCCACAGATCGTCAAAAATCGTACGCGGATTTGAAACGAAAAGACATTCAATATC
AGGTGGGAGACAAAGTGTTCCTTACAGTTTCACCTTGGAAAAAGATACTCAGATTCGGCCGTAAG
GGCAAGTTGAGCCCGAAG
Found at i:20570416 original size:39 final size:41
Alignment explanation
Indices: 20570321--20570504 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
20570311 TTGAATGATG
*
20570321 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
20570360 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
20570400 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
20570439 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
20570479 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20570505 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:20570456 original size:79 final size:81
Alignment explanation
Indices: 20570321--20570504 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
20570311 TTGAATGATG
20570321 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
20570384 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
20570399 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
20570460 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
20570479 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20570505 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:20570526 original size:79 final size:79
Alignment explanation
Indices: 20570373--20570537 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
20570363 GGACTAAGAT
* ** *
20570373 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
20570438 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
20570452 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
20570514 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
20570531 CCGAAGG
1 CCGAAGG
20570538 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:20578448 original size:46 final size:46
Alignment explanation
Indices: 20578395--20578508 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 46
20578385 GAGGTCTTGT
* *
20578395 ATATGTTGCAGACTCGAGAATACAGGAATAGGTTCTAAGCTCCTAC
1 ATATGTTGCAAACTCGAGAATACAGGAATAGGTTCCAAGCTCCTAC
* * * * ** *
20578441 ATGTGTTGCAAACTTGAGAATCCATGTTTAGGTTCCAAGCTCCTGC
1 ATATGTTGCAAACTCGAGAATACAGGAATAGGTTCCAAGCTCCTAC
*
20578487 ATATGTTGCATACTCGAGAATA
1 ATATGTTGCAAACTCGAGAATA
20578509 TAAGCCCTGG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (46 bp):
ATATGTTGCAAACTCGAGAATACAGGAATAGGTTCCAAGCTCCTAC
Found at i:20579424 original size:27 final size:27
Alignment explanation
Indices: 20579317--20579424 Score: 171
Period size: 27 Copynumber: 4.0 Consensus size: 27
20579307 NNNNNNNNNC
*
20579317 GTTTTACCCTCGATTTACAGAATTACC
1 GTTTTACCCTCGATTTACAGAATTACT
*
20579344 GTTTTACCCTCGATTTATAGAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
* *
20579371 ATTTTACCCTTGATTTACAGAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
*
20579398 GTTTTACCCTCGATTTACAAAATTACT
1 GTTTTACCCTCGATTTACAGAATTACT
20579425 AAAATACCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (27 bp):
GTTTTACCCTCGATTTACAGAATTACT
Found at i:20579432 original size:27 final size:27
Alignment explanation
Indices: 20579402--20579596 Score: 173
Period size: 27 Copynumber: 7.2 Consensus size: 27
20579392 ATTACTGTTT
* *
20579402 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * *
20579429 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
20579456 TACCC-CTAATTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
* *
20579483 TACCCT-TAGTTTGTAAAATTACCAAAA
1 TACCCTCGA-TTTATAAAATTACCAAAA
* * * *
20579510 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCGATTTATAAAATTACCAAAA
* *
20579537 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* *
20579564 TACCC-CTGATTTACAAAATTACAAAAA
1 TACCCTC-GATTTATAAAATTACCAAAA
20579591 TACCCT
1 TACCCT
20579597 TGACTTTCTA
Statistics
Matches: 140, Mismatches: 21, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.03
27 134 0.96
28 2 0.01
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:20579433 original size:54 final size:54
Alignment explanation
Indices: 20579321--20579436 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
20579311 NNNNNCGTTT
* * * ***
20579321 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTATAGAATTACTATTT
1 TACCCTTGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAA
*
20579375 TACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAA
20579429 TACCCTTG
1 TACCCTTG
20579437 GTTTGTAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTTGATTTACAGAATTACCGTTTTACCCTCGATTTACAAAATTACTAAAA
Found at i:20579449 original size:54 final size:54
Alignment explanation
Indices: 20579337--20579505 Score: 160
Period size: 54 Copynumber: 3.1 Consensus size: 54
20579327 CGATTTACAG
* *** * ** *
20579337 AATTACCGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAG
1 AATTACCGTTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
* *
20579391 AATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAA
1 AATTACCGTTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
**** * * * *
20579445 AATTACCAAAATACCC-CTAATTTGTAAAATTACCAAAATACCCTTAGTTTGTAA
1 AATTACCGTTTTACCCTC-GATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
20579499 AATTACC
1 AATTACC
20579506 AAAATACCAC
Statistics
Matches: 94, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
53 1 0.01
54 93 0.99
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (54 bp):
AATTACCGTTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTGTAA
Found at i:20579476 original size:81 final size:81
Alignment explanation
Indices: 20579402--20579598 Score: 267
Period size: 81 Copynumber: 2.4 Consensus size: 81
20579392 ATTACTGTTT
*
20579402 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCC-CTAAT
1 TACCCTCGATTTACAAAATTACAAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTC-AAT
20579466 TTGTAAAATTACCAAAA
65 TTGTAAAATTACCAAAA
* ** * * *
20579483 TACCCT-TAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGAAATTACCGAAATACCCTCAA
1 TACCCTCGA-TTTACAAAATTACAAAAATACC-CTTGGTTTGTAAAATTACCAAAATACCCTCAA
20579546 TTTGTAAAATTACCAAAA
64 TTTGTAAAATTACCAAAA
20579564 TACCC-CTGATTTACAAAATTACAAAAATACCCTTG
1 TACCCTC-GATTTACAAAATTACAAAAATACCCTTG
20579599 ACTTTCTAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
80 2 0.02
81 95 0.95
82 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACAAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTCAATT
TGTAAAATTACCAAAA
Found at i:20579506 original size:54 final size:54
Alignment explanation
Indices: 20579416--20579597 Score: 256
Period size: 54 Copynumber: 3.4 Consensus size: 54
20579406 CTCGATTTAC
* * *
20579416 AAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTGATTTGT
* *
20579470 AAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCACTGGTTTGT
1 AAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTGATTTGT
* * * * **
20579524 GAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTGATTTGT
*
20579578 AAAATTACAAAAATACCCTT
1 AAAATTACCAAAATACCCTT
20579598 GACTTTCTAA
Statistics
Matches: 111, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 111 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTGATTTGT
Found at i:20579733 original size:26 final size:27
Alignment explanation
Indices: 20579713--20579781 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
20579703 CCCCTATTAG
20579713 GTAAAAAGACCGTAAAGCCCTTGTAGC
1 GTAAAAAGACCGTAAAGCCCTTGTAGC
** * * *
20579740 GTAAAGTGACTGTAAAGCCCCTGTAGG
1 GTAAAAAGACCGTAAAGCCCTTGTAGC
**
20579767 GTAAAGTGACCGTAA
1 GTAAAAAGACCGTAA
20579782 TACCCCTGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (27 bp):
GTAAAAAGACCGTAAAGCCCTTGTAGC
Found at i:20579798 original size:27 final size:27
Alignment explanation
Indices: 20579720--20579791 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
20579710 TAGGTAAAAA
* *
20579720 GACCGTAAAGCCCTTGTAGCGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
*
20579747 GACTGTAAAGCCCCTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
20579774 GACCGTAATA-CCCCTGTA
1 GACCGTAA-AGCCCCTGTA
20579792 TGTTAAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (27 bp):
GACCGTAAAGCCCCTGTAGGGTAAAGT
Found at i:20580745 original size:25 final size:26
Alignment explanation
Indices: 20580595--20580788 Score: 270
Period size: 26 Copynumber: 7.5 Consensus size: 26
20580585 TGCAAAATGA
*
20580595 CTTATGCCCCAGTTTACCGAAAAGGG
1 CTTATGCCCCAGTTTACTGAAAAGGG
*
20580621 CTTATGCCCCAGTTTATTGAAAAGGG
1 CTTATGCCCCAGTTTACTGAAAAGGG
*
20580647 CTTATACCCCAGTTTACTGAAAAGGG
1 CTTATGCCCCAGTTTACTGAAAAGGG
20580673 CTTATGCCCCAGTTTA-TGGAAAAAGGG
1 CTTATGCCCCAGTTTACT-G-AAAAGGG
*
20580700 CTTATGCCCTAGTTTACTGAAAAGGG
1 CTTATGCCCCAGTTTACTGAAAAGGG
*
20580726 CTTATG-CCCAGTTTATTGAAAAGGG
1 CTTATGCCCCAGTTTACTGAAAAGGG
* **
20580751 CTT-TGCCTCAGTTTACCAAAAAGGG
1 CTTATGCCCCAGTTTACTGAAAAGGG
20580776 CTT-TGCCCCAGTT
1 CTTATGCCCCAGTT
20580789 ATTAAAGAGG
Statistics
Matches: 151, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
24 2 0.01
25 48 0.32
26 77 0.51
27 23 0.15
28 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (26 bp):
CTTATGCCCCAGTTTACTGAAAAGGG
Found at i:20580992 original size:42 final size:42
Alignment explanation
Indices: 20580933--20581024 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
20580923 TAGTCTCCCC
* ** * *
20580933 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATACTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGAGACTG
*
20580975 AAATGGGCTTGCATACATCCATTGACATTACATGTGAGATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGAGACTG
20581017 AAATGGGC
1 AAATGGGC
20581025 CTAAGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGAGACTG
Found at i:20581083 original size:31 final size:31
Alignment explanation
Indices: 20581048--20581124 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
20581038 TATTTACAGT
*
20581048 AAAGGCTTAGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* *
20581079 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
20581110 AAAGGCTTCGGCCCA
1 AAAGGCTTCGGCCCA
20581125 GTAACCGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:20583001 original size:313 final size:313
Alignment explanation
Indices: 20582424--20583048 Score: 1198
Period size: 313 Copynumber: 2.0 Consensus size: 313
20582414 ATCTCGTGAT
20582424 TTTATACGATAACTCAATGCAGACTGATATGTATGGTCAAAATCATAATAAAAATACATATCACA
1 TTTATACGATAACTCAATGCAGACTGATATGTATGGTCAAAATCATAATAAAAATACATATCACA
20582489 AACCAACTTCCTATACATGCCACTCACTTGATATTTCTAATATTTGAATTAATTTTCCCAAAAAT
66 AACCAACTTCCTATACATGCCACTCACTTGATATTTCTAATATTTGAATTAATTTTCCCAAAAAT
*
20582554 GATAGTTTGATAGTGTGATTTTGCCTCCGACGATCTCCAACCCCGAGCTGACCTACCAATACTAA
131 GATAGTTTGAGAGTGTGATTTTGCCTCCGACGATCTCCAACCCCGAGCTGACCTACCAATACTAA
20582619 AGAAATAGAGAGGATGGGTAAGCTTTACGCTTAGTAAGTTCATATGAAAATAATAAGCAATTACT
196 AGAAATAGAGAGGATGGGTAAGCTTTACGCTTAGTAAGTTCATATGAAAATAATAAGCAATTACT
20582684 ACCATGCTTTTCAAGATAAAACACTATAATTGTACAATTACACATATTCAGGG
261 ACCATGCTTTTCAAGATAAAACACTATAATTGTACAATTACACATATTCAGGG
20582737 TTTATACGATAACTCAATGCAGACTGATATGTATGGTCAAAATCATAATAAAAATACATATCACA
1 TTTATACGATAACTCAATGCAGACTGATATGTATGGTCAAAATCATAATAAAAATACATATCACA
20582802 AACCAACTTCCTATACATGCCACTCACTTGATATTTCTAATATTTGAATTAATTTTCCCAAAAAT
66 AACCAACTTCCTATACATGCCACTCACTTGATATTTCTAATATTTGAATTAATTTTCCCAAAAAT
*
20582867 GATAGTTTGAGAGTGTGATTTTGCCTCCGACGATCTCCAACCCTGAGCTGACCTACCAATACTAA
131 GATAGTTTGAGAGTGTGATTTTGCCTCCGACGATCTCCAACCCCGAGCTGACCTACCAATACTAA
*
20582932 AGAAATGGAGAGGATGGGTAAGCTTTACGCTTAGTAAGTTCATATGAAAATAATAAGCAAATT-C
196 AGAAATAGAGAGGATGGGTAAGCTTTACGCTTAGTAAGTTCATATGAAAATAATAAGC-AATTAC
*
20582996 TACCATGCTTTTCAAGATAAAACACTATAATTTTACAATTACACATATTCAGG
260 TACCATGCTTTTCAAGATAAAACACTATAATTGTACAATTACACATATTCAGG
20583049 ACAGGCTGTT
Statistics
Matches: 307, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
313 303 0.99
314 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (313 bp):
TTTATACGATAACTCAATGCAGACTGATATGTATGGTCAAAATCATAATAAAAATACATATCACA
AACCAACTTCCTATACATGCCACTCACTTGATATTTCTAATATTTGAATTAATTTTCCCAAAAAT
GATAGTTTGAGAGTGTGATTTTGCCTCCGACGATCTCCAACCCCGAGCTGACCTACCAATACTAA
AGAAATAGAGAGGATGGGTAAGCTTTACGCTTAGTAAGTTCATATGAAAATAATAAGCAATTACT
ACCATGCTTTTCAAGATAAAACACTATAATTGTACAATTACACATATTCAGGG
Found at i:20583968 original size:50 final size:49
Alignment explanation
Indices: 20583849--20584023 Score: 174
Period size: 50 Copynumber: 3.5 Consensus size: 49
20583839 TGGTACGTAC
* * **
20583849 AGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACAT
1 AGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACAT
* *
20583898 AGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACACGT
1 AGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACAT
* * * *** *
20583948 AGTAGCCTGCACTTAATACTACACACGTGATC-ATAGTTTTCGGGTACGCAT
1 AGTAGCCTGCACTTAGTACTACACACGTGACCAACAG---TCTAATACACAT
20583999 AGTAGCCTGCACTTAGTACTACACA
1 AGTAGCCTGCACTTAGTACTACACA
20584024 TGCGACCTCA
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 28 0.27
50 39 0.38
51 35 0.34
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (49 bp):
AGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACAT
Found at i:20596978 original size:39 final size:39
Alignment explanation
Indices: 20596929--20597008 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
20596919 AATGGATGAT
*
20596929 TACTTATGGATTGTTTTGAGATATTATTGATAGGGATTA
1 TACTTATGGATTATTTTGAGATATTATTGATAGGGATTA
* *
20596968 TACTTATGGATTATTTTTAGATATTATTTATAGGGATTA
1 TACTTATGGATTATTTTGAGATATTATTGATAGGGATTA
20597007 TA
1 TA
20597009 AATTGAGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (39 bp):
TACTTATGGATTATTTTGAGATATTATTGATAGGGATTA
Found at i:20597425 original size:13 final size:13
Alignment explanation
Indices: 20597407--20597443 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20597397 GAAGCAATCG
20597407 CACACGGGCGTGT
1 CACACGGGCGTGT
*
20597420 CACACGGGCATGT
1 CACACGGGCGTGT
*
20597433 CACACGAGCGT
1 CACACGGGCGT
20597444 ATCCCTGTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:20605704 original size:38 final size:38
Alignment explanation
Indices: 20605642--20605715 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
20605632 AAGATAAGGC
*
20605642 TTAAAGATAAGGCTCTAGTCACTTCAAGTGATTTTCCT
1 TTAAAGATAAGGCTCTAATCACTTCAAGTGATTTTCCT
* * *
20605680 TTAAAGATAAGGTTTTAATTACTTCAAGTGATTTTC
1 TTAAAGATAAGGCTCTAATCACTTCAAGTGATTTTC
20605716 ACAATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (38 bp):
TTAAAGATAAGGCTCTAATCACTTCAAGTGATTTTCCT
Done.