Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 104 of 214
Found at i:30840898 original size:27 final size:27
Alignment explanation
Indices: 30840852--30840981 Score: 138
Period size: 27 Copynumber: 4.8 Consensus size: 27
30840842 CGAAGACATT
* *
30840852 CATTTCCATAGATCGCCACAAAGGC-TC
1 CATTT-CACAGATTGCCACAAAGGCTTC
*
30840879 CTATTTCACAGATTGCCACAAAGCCTTC
1 C-ATTTCACAGATTGCCACAAAGGCTTC
* * *
30840907 CATTTCACAGATTTCCATAAAGCCTTC
1 CATTTCACAGATTGCCACAAAGGCTTC
* *
30840934 CATTTCATCA-ATTTCCATAAAGGCTTC
1 CATTTCA-CAGATTGCCACAAAGGCTTC
*
30840961 CATTTCATAGATTGCCACAAA
1 CATTTCACAGATTGCCACAAA
30840982 AGCTCCTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
26 1 0.01
27 80 0.89
28 9 0.10
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (27 bp):
CATTTCACAGATTGCCACAAAGGCTTC
Found at i:30849382 original size:3 final size:3
Alignment explanation
Indices: 30849376--30849402 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
30849366 TTATTAATAC
30849376 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
30849403 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:30853743 original size:17 final size:18
Alignment explanation
Indices: 30853721--30853754 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
30853711 CGACCGCGAC
30853721 AAACGCGA-CGCGACCGA
1 AAACGCGACCGCGACCGA
30853738 AAACGCGACCGCGACCG
1 AAACGCGACCGCGACCG
30853755 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.38, G:0.29, T:0.00
Consensus pattern (18 bp):
AAACGCGACCGCGACCGA
Found at i:30874483 original size:339 final size:339
Alignment explanation
Indices: 30873863--30874539 Score: 1318
Period size: 339 Copynumber: 2.0 Consensus size: 339
30873853 AGAAGAACCA
*
30873863 GTCAAGCTAAGTGTTGAACCTGAATATACAACTGTCATGTCGACTTCTGCAAGTGCTTCAAAGAA
1 GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
30873928 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
66 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
* *
30873993 AATATGCAAAAATTAGAGATGACTCAATTCGAAATACTTTTAAGAATATATCTAATACTTTTGTT
131 AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
30874058 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
196 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
30874123 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
261 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
30874188 TTAATTATTTTTAG
326 TTAATTATTTTTAG
30874202 GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
1 GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
30874267 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
66 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
30874332 AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
131 AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
30874397 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
196 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
*
30874462 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTGTTATTTAT
261 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
30874527 TTAATTATTTTTA
326 TTAATTATTTTTA
30874540 AGTCTTTAGG
Statistics
Matches: 334, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
339 334 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (339 bp):
GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
TTAATTATTTTTAG
Found at i:30880118 original size:25 final size:25
Alignment explanation
Indices: 30880023--30880129 Score: 108
Period size: 25 Copynumber: 4.3 Consensus size: 25
30880013 AGCTCCCCTA
** *
30880023 AGCTGAATAACAGTAAAATCCT-CTG
1 AGCTGAATAACAGTAAGCTCATAC-G
* *
30880048 AGCTGAATAACAGTAAGCTCCTTCG
1 AGCTGAATAACAGTAAGCTCATACG
*
30880073 AGCTGAATAACGGTAAGCTCATACG
1 AGCTGAATAACAGTAAGCTCATACG
* * * *
30880098 AGCTGAGTATCAGTATGCTCATAAG
1 AGCTGAATAACAGTAAGCTCATACG
30880123 AGCTGAA
1 AGCTGAA
30880130 ATCGATAACC
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
25 69 0.99
26 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (25 bp):
AGCTGAATAACAGTAAGCTCATACG
Found at i:30880253 original size:45 final size:45
Alignment explanation
Indices: 30880189--30880279 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
30880179 TCAAATGGGG
* * *
30880189 CTCGGTAATCGTCGTACGTCGTTCGACAAGCAATCGATATTCATT
1 CTCGGTAATCATCATACGTCGTTAGACAAGCAATCGATATTCATT
* *
30880234 CTCGGTAGTCATCATACGTCGTTAGATAAGCAATCGATATTCATT
1 CTCGGTAATCATCATACGTCGTTAGACAAGCAATCGATATTCATT
30880279 C
1 C
30880280 ATGGCAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
CTCGGTAATCATCATACGTCGTTAGACAAGCAATCGATATTCATT
Found at i:30881585 original size:316 final size:316
Alignment explanation
Indices: 30881012--30881626 Score: 1176
Period size: 316 Copynumber: 1.9 Consensus size: 316
30881002 TTTTTAATTG
30881012 TTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAACCTTTATAAACATTATTTAT
1 TTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAACCTTTATAAACATTATTTAT
30881077 TACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGCTATTTACCATATAAGAACC
66 TACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGCTATTTACCATATAAGAACC
*
30881142 TCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAACACAACTTTCGCACTTTAT
131 TCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAACACAACTTTCGCACTTTAC
*
30881207 GTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATCGGTAAAATTTCTTAACAAAATTTTTATA
196 GTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATCGGTAAAATTTCTCAACAAAATTTTTATA
* *
30881272 CGATAATACTATCATGCTACAGATCATAAATTATTATTATTAACTAAATTACAAAT
261 CGATAATACTATCATGCTACAGATCATAAAATAATATTATTAACTAAATTACAAAT
30881328 TTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAACCTTTATAAACATTATTTAT
1 TTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAACCTTTATAAACATTATTTAT
30881393 TACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGCTATTTACCATATAAGAACC
66 TACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGCTATTTACCATATAAGAACC
* *
30881458 TCCAATTTAAATTTCTATAGCTATTAGACACCTTTATCTATTAGAACACAACTTTTGCACTTTAC
131 TCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAACACAACTTTCGCACTTTAC
30881523 GTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATCGGTAAAATTTCTCAACAAAATTTTTATA
196 GTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATCGGTAAAATTTCTCAACAAAATTTTTATA
30881588 CGATAATACTATCATGCTACAGATCATAAAATAATATTA
261 CGATAATACTATCATGCTACAGATCATAAAATAATATTA
30881627 AAATAATTTT
Statistics
Matches: 293, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
316 293 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (316 bp):
TTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAACCTTTATAAACATTATTTAT
TACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGCTATTTACCATATAAGAACC
TCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAACACAACTTTCGCACTTTAC
GTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATCGGTAAAATTTCTCAACAAAATTTTTATA
CGATAATACTATCATGCTACAGATCATAAAATAATATTATTAACTAAATTACAAAT
Found at i:30884627 original size:18 final size:18
Alignment explanation
Indices: 30884601--30884635 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30884591 TCCCATGTTC
30884601 AAGGATTTATGCGAGTTT
1 AAGGATTTATGCGAGTTT
*
30884619 AAGGCTTTATGCGAGTT
1 AAGGATTTATGCGAGTT
30884636 GGGAGCTAGC
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:0.26, C:0.09, G:0.29, T:0.37
Consensus pattern (18 bp):
AAGGATTTATGCGAGTTT
Found at i:30887628 original size:18 final size:18
Alignment explanation
Indices: 30887605--30887651 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
30887595 TCTTGTCAAA
*
30887605 AAAATAATTAATTTTTAC
1 AAAATAATTAATATTTAC
30887623 AAAATAATTAATATTTAC
1 AAAATAATTAATATTTAC
30887641 AAAATAATTAA
1 AAAATAATTAA
30887652 AGTGCACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATTAATATTTAC
Found at i:30894194 original size:27 final size:28
Alignment explanation
Indices: 30894110--30894207 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
30894100 CATGAGATTG
* * * *
30894110 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
30894139 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
30894167 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
30894194 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
30894208 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:30894218 original size:27 final size:27
Alignment explanation
Indices: 30894138--30894220 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
30894128 TAAATTGTAC
* *
30894138 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
30894166 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
30894193 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
30894220 A
1 A
30894221 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:30894221 original size:29 final size:27
Alignment explanation
Indices: 30894110--30894221 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
30894100 CATGAGATTG
** * *
30894110 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
30894139 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
30894167 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
30894194 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
30894222 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:30899320 original size:25 final size:25
Alignment explanation
Indices: 30899262--30899317 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
30899252 CTAAATTTTA
*
30899262 AATTAATTATTTAATTTTTTCAATT
1 AATTAATTATTTAATATTTTCAATT
*
30899287 TATTGAATTA-TTAATATTTT-ATATT
1 AATT-AATTATTTAATATTTTCA-ATT
30899312 AATTAA
1 AATTAA
30899318 ATTTTTGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 3 0.12
25 18 0.69
26 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTAATTATTTAATATTTTCAATT
Found at i:30905208 original size:22 final size:21
Alignment explanation
Indices: 30905183--30905253 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
30905173 CATTGCATTT
30905183 TTAGTGTCATTGCATTTTAATG
1 TTAGTG-CATTGCATTTTAATG
*
30905205 TTAGTGCATTGCATTTTTA-G
1 TTAGTGCATTGCATTTTAATG
30905225 -T-GT-CATTGCATTTTAATG
1 TTAGTGCATTGCATTTTAATG
30905243 TTAGTGCATTG
1 TTAGTGCATTG
30905254 AGGACAATGC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
17 12 0.28
18 3 0.07
19 2 0.05
20 3 0.07
21 17 0.40
22 6 0.14
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (21 bp):
TTAGTGCATTGCATTTTAATG
Found at i:30905224 original size:38 final size:38
Alignment explanation
Indices: 30905173--30905253 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
30905163 TGCACATTTT
30905173 CATTGCATTTTTAGTGTCATTGCATTTTAATGTTAGTG
1 CATTGCATTTTTAGTGTCATTGCATTTTAATGTTAGTG
30905211 CATTGCATTTTTAGTGTCATTGCATTTTAATGTTAGTG
1 CATTGCATTTTTAGTGTCATTGCATTTTAATGTTAGTG
30905249 CATTG
1 CATTG
30905254 AGGACAATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (38 bp):
CATTGCATTTTTAGTGTCATTGCATTTTAATGTTAGTG
Found at i:30905239 original size:16 final size:17
Alignment explanation
Indices: 30905172--30905238 Score: 89
Period size: 17 Copynumber: 3.7 Consensus size: 17
30905162 GTGCACATTT
30905172 TCATTGCATTTTTAGTG
1 TCATTGCATTTTTAGTG
*
30905189 TCATTGCATTTTAATGTTAG
1 TCATTGCATTTTTA-G-T-G
30905209 TGCATTGCATTTTTAGTG
1 T-CATTGCATTTTTAGTG
30905227 TCATTGCATTTT
1 TCATTGCATTTT
30905239 AATGTTAGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 24 0.55
18 3 0.07
19 2 0.05
20 3 0.07
21 12 0.27
ACGTcount: A:0.19, C:0.12, G:0.16, T:0.52
Consensus pattern (17 bp):
TCATTGCATTTTTAGTG
Found at i:30909105 original size:20 final size:20
Alignment explanation
Indices: 30909080--30909119 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30909070 AGTTTGATTT
30909080 GTTAAAAGAC-TTTTAACTTG
1 GTTAAAA-ACATTTTAACTTG
*
30909100 GTTAAAATCATTTTAACTTG
1 GTTAAAAACATTTTAACTTG
30909120 ATTTTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (20 bp):
GTTAAAAACATTTTAACTTG
Found at i:30915072 original size:21 final size:21
Alignment explanation
Indices: 30915046--30915121 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
30915036 AATCATATCT
30915046 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
30915067 TCTAAGATTGCATATATCATA
1 TCTAAGATTGTATATATCATA
*
30915088 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
30915107 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
30915122 CCTAGAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.36
21 32 0.64
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:30915081 original size:19 final size:19
Alignment explanation
Indices: 30915059--30915122 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
30915049 AAGATTGTAT
30915059 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
30915078 ATATATCATATCTAAGATTGC
1 --ATATCATATCTAAGATTGC
*
30915099 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
30915118 ATATC
1 ATATC
30915123 CTAGAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:30934424 original size:24 final size:24
Alignment explanation
Indices: 30934392--30934440 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30934382 GAACTAAGGA
30934392 TGTGAAAAGGATAGTCAGTTCAGG
1 TGTGAAAAGGATAGTCAGTTCAGG
30934416 TGTGAAAAGGATAGTCAGTTCAGG
1 TGTGAAAAGGATAGTCAGTTCAGG
30934440 T
1 T
30934441 TTATCCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.27
Consensus pattern (24 bp):
TGTGAAAAGGATAGTCAGTTCAGG
Found at i:30934890 original size:15 final size:16
Alignment explanation
Indices: 30934863--30934899 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
30934853 CCTAATCTCT
30934863 ATAGA-ATCTTTCTTC
1 ATAGATATCTTTCTTC
30934878 ATAGATATC-TTCTTC
1 ATAGATATCTTTCTTC
30934893 ATA-ATAT
1 ATAGATAT
30934900 AAGTCTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 14 0.67
16 3 0.14
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (16 bp):
ATAGATATCTTTCTTC
Found at i:30939272 original size:13 final size:13
Alignment explanation
Indices: 30939254--30939279 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30939244 TTTTTATGAT
30939254 TCGTTAGAACATC
1 TCGTTAGAACATC
30939267 TCGTTAGAACATC
1 TCGTTAGAACATC
30939280 CTAGTGTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TCGTTAGAACATC
Found at i:30940899 original size:13 final size:13
Alignment explanation
Indices: 30940881--30940918 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
30940871 ATGGGTTGGG
30940881 CGGCCCGGCCCGA
1 CGGCCCGGCCCGA
30940894 CGGCCCGGCCCGA
1 CGGCCCGGCCCGA
*
30940907 CAGCCC-GCCCGA
1 CGGCCCGGCCCGA
30940919 AATATGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.11, C:0.55, G:0.34, T:0.00
Consensus pattern (13 bp):
CGGCCCGGCCCGA
Found at i:30941172 original size:14 final size:14
Alignment explanation
Indices: 30941153--30941185 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
30941143 AATCAACCTT
30941153 CACCTCCACCAATC
1 CACCTCCACCAATC
*
30941167 CACCTCCACCGATC
1 CACCTCCACCAATC
30941181 CACCT
1 CACCT
30941186 TCGGTCCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.58, G:0.03, T:0.15
Consensus pattern (14 bp):
CACCTCCACCAATC
Found at i:30943476 original size:19 final size:18
Alignment explanation
Indices: 30943425--30943491 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
30943415 ACCCCAAACA
*
30943425 TATTTTTTGTTTTATCTT
1 TATTTTTTGTTTTATTTT
* * *
30943443 T-TTTCTT-TATCATTTT
1 TATTTTTTGTTTTATTTT
30943459 CTATTTTTTGTTTTATTTT
1 -TATTTTTTGTTTTATTTT
30943478 TAATTTTTTGTTTT
1 T-ATTTTTTGTTTT
30943492 TGACATTCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 6 0.16
17 6 0.16
18 7 0.18
19 19 0.50
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (18 bp):
TATTTTTTGTTTTATTTT
Found at i:30952853 original size:17 final size:17
Alignment explanation
Indices: 30952811--30952855 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
30952801 AATTCAATTT
30952811 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
30952827 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
30952845 TAATATAAATA
1 TAATATAAATA
30952856 GTAGATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.08
16 2 0.08
17 11 0.44
18 8 0.32
19 2 0.08
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:30953118 original size:30 final size:31
Alignment explanation
Indices: 30953079--30953138 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
30953069 AGAGGTGGGA
*
30953079 TGGGAAGGGAATAAAAGTTTT-AGGGCAAAAG
1 TGGGAAGGGAATAAAAATTTTGAGGG-AAAAG
*
30953110 TGGG-AGGGAGTAAAAATTTTGAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAA
30953139 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
Found at i:30953366 original size:9 final size:9
Alignment explanation
Indices: 30953352--30953388 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30953342 TATAGTTTGA
30953352 TATTCGAAT
1 TATTCGAAT
30953361 TATTCGAAT
1 TATTCGAAT
*
30953370 TATTCGAGT
1 TATTCGAAT
30953379 TATTCGAAT
1 TATTCGAAT
30953388 T
1 T
30953389 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:30956420 original size:42 final size:42
Alignment explanation
Indices: 30956325--30956464 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 42
30956315 GTCTCAAATG
* * * *
30956325 TGGTCTTACATGTAATCAAATAACGATGCCACTGTTCCAGACA
1 TGGTCTTACACGTAATCATAT-ACGATGCCAATGTCCCAGACA
* * *
30956368 GGGTCTTACACGTAATCATATACGACGCCAATGTCCCAAACA
1 TGGTCTTACACGTAATCATATACGATGCCAATGTCCCAGACA
* * *
30956410 TGGTCTTACACGTAAATC-TCAAATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGT-AATCAT-ATA-CGATGCCAATGTCCCAGACA
30956454 TGGTCTTACAC
1 TGGTCTTACAC
30956465 AATATCACAT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.37
43 24 0.30
44 27 0.33
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
TGGTCTTACACGTAATCATATACGATGCCAATGTCCCAGACA
Found at i:30958701 original size:13 final size:13
Alignment explanation
Indices: 30958685--30958721 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 13
30958675 ATTAAGGCAG
30958685 TAAATATTTTTAT
1 TAAATATTTTTAT
30958698 TAAATATATTTTTAT
1 T-AA-ATATTTTTAT
30958713 TAAATATTT
1 TAAATATTT
30958722 ATAGAGTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 4 0.18
15 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:30958708 original size:15 final size:15
Alignment explanation
Indices: 30958688--30958719 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30958678 AAGGCAGTAA
30958688 ATATTTTTATTAAAT
1 ATATTTTTATTAAAT
30958703 ATATTTTTATTAAAT
1 ATATTTTTATTAAAT
30958718 AT
1 AT
30958720 TTATAGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTTTATTAAAT
Found at i:30960787 original size:48 final size:48
Alignment explanation
Indices: 30960715--30960812 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
30960705 GTAATTAAGT
* *
30960715 GAAGTATGCAAGTTTAATCTTGAGTTTAAGAAAGAAATGGTAAGTTTG
1 GAAGTATGCAAGTTTAATCCTGAGTCTAAGAAAGAAATGGTAAGTTTG
* *
30960763 GAAGTATGCAAGTTTCATCCTGAGTCTAAGCAAGAAATGGTAAGTTTG
1 GAAGTATGCAAGTTTAATCCTGAGTCTAAGAAAGAAATGGTAAGTTTG
30960811 GA
1 GA
30960813 TGAGTATGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.31
Consensus pattern (48 bp):
GAAGTATGCAAGTTTAATCCTGAGTCTAAGAAAGAAATGGTAAGTTTG
Found at i:30961478 original size:54 final size:54
Alignment explanation
Indices: 30961394--30961527 Score: 198
Period size: 54 Copynumber: 2.5 Consensus size: 54
30961384 GTGTAGGTTT
* * * **
30961394 CACACGGTCTG-GCACACGGCCATGTAACCCAACATCGAATTGAATAGGGTCTAG
1 CACACGGCCTGCG-ACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
30961448 CACACGGCCTGCGACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
1 CACACGGCCTGCGACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
*
30961502 CATACGGCCTGCGACACGGCCATGTG
1 CACACGGCCTGCGACACGGCCATGTG
30961528 GAATTATTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
54 72 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (54 bp):
CACACGGCCTGCGACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
Found at i:30964013 original size:19 final size:20
Alignment explanation
Indices: 30963969--30964014 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
30963959 TCTTGTTGCC
*
30963969 TTTCTT-TCTCTACCCTTTG
1 TTTCTTCTCTCAACCCTTTG
*
30963988 TTCTCTTCTCTCAACTCTTT-
1 TT-TCTTCTCTCAACCCTTTG
30964008 TTTCTTC
1 TTTCTTC
30964015 AATCTTCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 10 0.43
ACGTcount: A:0.07, C:0.33, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTCTTCTCTCAACCCTTTG
Found at i:30977215 original size:40 final size:40
Alignment explanation
Indices: 30977171--30977433 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
30977161 GCTCCTCGTT
* *
30977171 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
30977211 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
30977251 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
30977290 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
30977329 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * *
30977368 CAAATGCCTTC-GGATCTTGGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
30977409 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
30977434 CATCATTCAA
Statistics
Matches: 202, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 110 0.54
40 73 0.36
41 17 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:30983395 original size:27 final size:28
Alignment explanation
Indices: 30983323--30983398 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
30983313 AGATATTACG
*
30983323 TAAACTTTTATTATATTAAGTCAAGTTT
1 TAAAGTTTTATTATATTAAGTCAAGTTT
*
30983351 TATAGTTTTATTATATTACA-T-AACGTTT
1 TAAAGTTTTATTATATTA-AGTCAA-GTTT
30983379 TAAAG-TTTATTATATTAAGT
1 TAAAGTTTTATTATATTAAGT
30983399 TTTATAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 1 0.02
27 15 0.36
28 25 0.60
29 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (28 bp):
TAAAGTTTTATTATATTAAGTCAAGTTT
Found at i:30986298 original size:41 final size:41
Alignment explanation
Indices: 30986241--30986354 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
30986231 AGTAAGATGA
*
30986241 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
30986282 TTCAGACTTTACGTCTAGCTGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
30986323 TTTAGACTTTACGTCTAGCAGGC-TAATTGCCG
1 TTCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
30986355 ATGTACTGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.04
41 65 0.96
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
Found at i:30986916 original size:97 final size:97
Alignment explanation
Indices: 30986806--30987069 Score: 474
Period size: 97 Copynumber: 2.7 Consensus size: 97
30986796 CAATTGGTTG
30986806 TAATATTTGTTAAGCATATGTATATATGCATTCGGCTATTCATGTTTATAGTAAATATACATTCG
1 TAATATTTGTTAAGCATATGTATATATGCATTCGGCTATTCATGTTTATAGTAAATATACATTCG
30986871 GTTCATGTTCAAAGTGTATATACATTTGGAGC
66 GTTCATGTTCAAAGTGTATATACATTTGGAGC
*
30986903 TAATATTTGTTAAGCATATGTATATATGCATTCAGCTATTCATGTTTATAGTAAATATACATTCG
1 TAATATTTGTTAAGCATATGTATATATGCATTCGGCTATTCATGTTTATAGTAAATATACATTCG
*
30986968 ATTCATGTTCAAAGTGTATATACATTTGGAGC
66 GTTCATGTTCAAAGTGTATATACATTTGGAGC
* *
30987000 TAATATTTGTTAAGCATATATGTATATATGCATTCGACTATTCATGTTTATAGTGAATATACATT
1 TAATATTTGTTAAGC--ATATGTATATATGCATTCGGCTATTCATGTTTATAGTAAATATACATT
30987065 CGGTT
64 CGGTT
30987070 TTAAGAGTTG
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
97 110 0.69
99 49 0.31
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (97 bp):
TAATATTTGTTAAGCATATGTATATATGCATTCGGCTATTCATGTTTATAGTAAATATACATTCG
GTTCATGTTCAAAGTGTATATACATTTGGAGC
Found at i:30997641 original size:34 final size:35
Alignment explanation
Indices: 30997558--30997649 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 35
30997548 CACTAATTAT
* * *
30997558 TTCGTCGGTTTATCCGACTAGCGCTGAGTGCAACT
1 TTCGTCAGTTTATCTGACTAGCGCTGAGTGCAACA
* * *
30997593 TTCATTAGTTTATCTGACTAGTGCTG-G-GCACACA
1 TTCGTCAGTTTATCTGACTAGCGCTGAGTGCA-ACA
30997627 TTCGTCAGTTTATCTGACTAGCG
1 TTCGTCAGTTTATCTGACTAGCG
30997650 TTGGGCGCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 3 0.06
34 23 0.49
35 21 0.45
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (35 bp):
TTCGTCAGTTTATCTGACTAGCGCTGAGTGCAACA
Found at i:30997735 original size:75 final size:75
Alignment explanation
Indices: 30997499--30997735 Score: 238
Period size: 75 Copynumber: 3.2 Consensus size: 75
30997489 GATTCTTTCA
* * *
30997499 ACTACCGCTGGGCGCAAATACCATTAATTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
1 ACTAGCGCTGGGCGCAAATACTATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
*
30997564 GGTTTATCCG
66 GATTTATCCG
* * * * ** * *
30997574 ACTAGCGCTGAGTGCAACT-TTCATTAGTTTATCTGACTAGTGCTGGG--CAC--A-CA-TTCGT
1 ACTAGCGCTGGGCGCAAATACT-ATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGT
*
30997632 C-AGTTTATCTG
65 CGA-TTTATCCG
* * **
30997643 ACTAGCGTTGGGCGCAAATACTATTGGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTTTTC
1 ACTAGCGCTGGGCGCAAATACTATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
30997708 GATTTATCCG
66 GATTTATCCG
*
30997718 ACTAGCGCTGGGTGCAAA
1 ACTAGCGCTGGGCGCAAA
30997736 CTCTTTCGCG
Statistics
Matches: 124, Mismatches: 28, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
69 49 0.40
70 2 0.02
71 4 0.03
73 4 0.03
74 1 0.01
75 63 0.51
76 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (75 bp):
ACTAGCGCTGGGCGCAAATACTATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
GATTTATCCG
Found at i:31003102 original size:17 final size:17
Alignment explanation
Indices: 31003080--31003112 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31003070 TCTGCCACTT
31003080 TTTTCTCTG-TTGTTCTC
1 TTTTCT-TGTTTGTTCTC
31003097 TTTTCTTGTTTGTTCT
1 TTTTCTTGTTTGTTCT
31003113 ATTTCCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.00, C:0.18, G:0.12, T:0.70
Consensus pattern (17 bp):
TTTTCTTGTTTGTTCTC
Found at i:31005254 original size:56 final size:50
Alignment explanation
Indices: 31005031--31005278 Score: 232
Period size: 50 Copynumber: 4.9 Consensus size: 50
31005021 TGATAATAAA
* * * *
31005031 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGCGA--TGT-TTCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * * * ** *
31005078 TACTGCCAATGTCATATCTCAGATATGGTCTTACATGGGAGTTCTCATATTG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * *
31005130 GTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * * *
31005180 GTGCGAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CT---TG
*
31005236 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31005279 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 31 0.19
50 81 0.50
51 2 0.01
52 4 0.02
53 2 0.01
56 40 0.25
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
Found at i:31012581 original size:12 final size:11
Alignment explanation
Indices: 31012565--31012595 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
31012555 AGAAAAAGAA
31012565 GAAAAAAACAG
1 GAAAAAAACAG
31012576 GAAAAAAACAG
1 GAAAAAAACAG
31012587 GAAAAAAAC
1 GAAAAAAAC
31012596 GTACAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.10, G:0.16, T:0.00
Consensus pattern (11 bp):
GAAAAAAACAG
Found at i:31012765 original size:37 final size:37
Alignment explanation
Indices: 31012715--31012867 Score: 288
Period size: 37 Copynumber: 4.1 Consensus size: 37
31012705 ATACAGAAGC
31012715 TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
31012752 TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
*
31012789 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
*
31012826 TTAACCATTGAACTATCAAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
31012863 TTAAC
1 TTAAC
31012868 TTAAGTTGAG
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 113 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (37 bp):
TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
Found at i:31015062 original size:49 final size:49
Alignment explanation
Indices: 31015008--31015107 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
31014998 CATGAATTTG
31015008 AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
1 AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
*
31015057 AATATCATTTAAATATATATTTTATTTTATAACTTATCTAAAAAAATAA
1 AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
31015106 AA
1 AA
31015108 GATTATCAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (49 bp):
AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
Found at i:31018210 original size:16 final size:16
Alignment explanation
Indices: 31018181--31018214 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
31018171 TTTGTTTCTC
31018181 TTTTCTTTTATTCTCTT
1 TTTTCTTTTATTCT-TT
31018198 TTTTCTTTT-TTCTTT
1 TTTTCTTTTATTCTTT
31018213 TT
1 TT
31018215 AGTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTATTCTTT
Found at i:31019602 original size:40 final size:40
Alignment explanation
Indices: 31019514--31019618 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
31019504 ATCTCGTGCT
* * *
31019514 TAGGAGCATCATATTTTGGATGATCAGTTTAAGCTCATGCC
1 TAGGAGCATCATATTTTGG-TGAACAATTTAAGCTCATACC
* * *
31019555 TAAGAGCACCATATTTTGGTGAACAATTTAAGCTCATACG
1 TAGGAGCATCATATTTTGGTGAACAATTTAAGCTCATACC
*
31019595 TAGGAGCATCATTTTTTGGGTGAA
1 TAGGAGCATCATATTTT-GGTGAA
31019619 TGGTTAAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 31 0.57
41 23 0.43
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (40 bp):
TAGGAGCATCATATTTTGGTGAACAATTTAAGCTCATACC
Found at i:31019629 original size:41 final size:41
Alignment explanation
Indices: 31019514--31019632 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
31019504 ATCTCGTGCT
* *
31019514 TAGGAGCATCATATTTTGGATG-ATCAGTTTAAGCTCATGCC
1 TAGGAGCATCATATTTTGGGTGAAT-AGTTTAAGCTCATACC
* * * * *
31019555 TAAGAGCACCATATTTT-GGTGAACAATTTAAGCTCATACG
1 TAGGAGCATCATATTTTGGGTGAATAGTTTAAGCTCATACC
* * *
31019595 TAGGAGCATCATTTTTTGGGTGAATGGTTAAAGCTCAT
1 TAGGAGCATCATATTTTGGGTGAATAGTTTAAGCTCAT
31019633 TGATAGCAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
40 30 0.48
41 32 0.52
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (41 bp):
TAGGAGCATCATATTTTGGGTGAATAGTTTAAGCTCATACC
Found at i:31025698 original size:11 final size:11
Alignment explanation
Indices: 31025684--31025710 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31025674 TTTATTTGAA
31025684 AAAATATATTT
1 AAAATATATTT
31025695 AAAATATATTT
1 AAAATATATTT
31025706 AAAAT
1 AAAAT
31025711 TTAAATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATATATTT
Found at i:31026141 original size:22 final size:22
Alignment explanation
Indices: 31026084--31026149 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
31026074 CTGGCTCGAA
31026084 TTAT-ATATTAAATATATATTT
1 TTATGATATTAAATATATATTT
** *
31026105 TTATTTTAATCAAATATATA-TT
1 TTATGAT-ATTAAATATATATTT
31026127 TTATAGATATTAAATATATATTT
1 TTAT-GATATTAAATATATATTT
31026150 AATATGGGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 4 0.11
22 18 0.50
23 14 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATGATATTAAATATATATTT
Found at i:31027237 original size:23 final size:23
Alignment explanation
Indices: 31027194--31027237 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
31027184 TAACTTTGGA
* *
31027194 TTAAATTAAATTTTGATTTAAAG
1 TTAAATTAAATTTTCAATTAAAG
*
31027217 TTAAATTAAGTTTTCAATTAA
1 TTAAATTAAATTTTCAATTAA
31027238 TTTTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (23 bp):
TTAAATTAAATTTTCAATTAAAG
Found at i:31030142 original size:58 final size:57
Alignment explanation
Indices: 31030067--31030203 Score: 175
Period size: 58 Copynumber: 2.4 Consensus size: 57
31030057 TATTGTTATT
* * *
31030067 AAATTTTAATAAAATTATTATTAAAAATAATTGCATAAAAATAATAAATAATTTAACC
1 AAATTTTAATATAATTATTATTAAAAATAATTGAAT-AAAATAATAAATAATTTAACA
* * * * * *
31030125 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAAAATAATTGAATAAAATAATAAATAATTTAACA
31030182 AAATTCTTAATATAATTATTAT
1 AAATT-TTAATATAATTATTAT
31030204 ATGAATTAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
57 22 0.33
58 45 0.67
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAAAATAATTGAATAAAATAATAAATAATTTAACA
Found at i:31031363 original size:30 final size:30
Alignment explanation
Indices: 31031327--31031418 Score: 116
Period size: 30 Copynumber: 3.0 Consensus size: 30
31031317 GGCCCATTTT
31031327 TATTTTAAAAATTTTAAAAAATTAAAAAAG
1 TATTTTAAAAATTTTAAAAAATTAAAAAAG
31031357 TATTTTAAAATTATTTT--AAAATTAAAAAAAG
1 TATTTTAAAA--ATTTTAAAAAATT-AAAAAAG
*
31031388 TATTTTAAAAATATTTAAAAATTTTAAAAAA
1 TATTTTAAAAAT-TTTAAAAA-ATTAAAAAA
31031419 ATTTAAAAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
29 2 0.04
30 19 0.35
31 17 0.31
32 14 0.26
33 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAG
Found at i:31031366 original size:11 final size:10
Alignment explanation
Indices: 31031327--31031450 Score: 67
Period size: 10 Copynumber: 12.1 Consensus size: 10
31031317 GGCCCATTTT
31031327 TATTTTAAAA
1 TATTTTAAAA
31031337 -ATTTTAAAA
1 TATTTTAAAA
* **
31031346 AATTAAAAAA
1 TATTTTAAAA
31031356 GTATTTTAAAA
1 -TATTTTAAAA
31031367 TTATTTTAAAA
1 -TATTTTAAAA
***
31031378 T-TAAAAAAA
1 TATTTTAAAA
31031387 GTATTTTAAAA
1 -TATTTTAAAA
31031398 -ATATTTAAAA
1 TAT-TTTAAAA
31031408 -ATTTTAAAAA
1 TATTTT-AAAA
* *
31031418 AATTTAAAAA
1 TATTTTAAAA
**
31031428 GTATGTAAAAAA
1 -TAT-TTTAAAA
31031440 TATTTTAAAA
1 TATTTTAAAA
31031450 T
1 T
31031451 TAAAAAAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
9 19 0.22
10 32 0.36
11 31 0.35
12 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:31031388 original size:31 final size:30
Alignment explanation
Indices: 31031327--31031419 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 30
31031317 GGCCCATTTT
31031327 TATTTTAAAA-ATTTTAAAAAATT-AAAAAAG
1 TATTTTAAAATATTTT--AAAATTAAAAAAAG
31031357 TATTTTAAAATTATTTTAAAATTAAAAAAAG
1 TATTTTAAAA-TATTTTAAAATTAAAAAAAG
*
31031388 TATTTTAAAAATATTTAAAAATTTTAAAAAAA
1 TATTTT-AAAATATTTTAAAA--TTAAAAAAA
31031420 TTTAAAAAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
30 16 0.29
31 22 0.39
32 9 0.16
33 9 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TATTTTAAAATATTTTAAAATTAAAAAAAG
Found at i:31031405 original size:41 final size:42
Alignment explanation
Indices: 31031326--31031452 Score: 129
Period size: 41 Copynumber: 3.1 Consensus size: 42
31031316 CGGCCCATTT
*
31031326 TTATTTTAAAAATTTTAAAAA--AT-TAAAAAAGTATTTTAAAA
1 TTATTTTAAAAA-TTAAAAAAGTATGTAAAAAA-TATTTTAAAA
* * *
31031367 TTATTTT-AAAATTAAAAAAAGTATTTTAAAAATATTTAAAAA
1 TTATTTTAAAAATT-AAAAAAGTATGTAAAAAATATTTTAAAA
** *
31031409 TT-TTAAAAAAATTTAAAAAGTATGTAAAAAATATTTTAAAA
1 TTATTTTAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
31031450 TTA
1 TTA
31031453 AAAAAAATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
39 2 0.03
40 9 0.13
41 35 0.49
42 19 0.27
43 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (42 bp):
TTATTTTAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
Found at i:31039881 original size:20 final size:20
Alignment explanation
Indices: 31039856--31039897 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
31039846 AATTATCTGA
31039856 AAAAATAGGTATATTATATG
1 AAAAATAGGTATATTATATG
*
31039876 AAAAATATGTATATTATATG
1 AAAAATAGGTATATTATATG
31039896 AA
1 AA
31039898 CAATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (20 bp):
AAAAATAGGTATATTATATG
Found at i:31041015 original size:30 final size:31
Alignment explanation
Indices: 31040974--31041034 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
31040964 GGGTTGGGAG
* *
31040974 GGGAGAGGAGTAAAAATTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
*
31041005 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
31041035 TAAAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
Found at i:31041166 original size:30 final size:30
Alignment explanation
Indices: 31041093--31041168 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 30
31041083 TATTCGAATT
***
31041093 ATTCGAGTT-ATTCG-AATTCGAAAACTCA
1 ATTCGAGTTGATTCGAAATTCGAAAAAAAA
*
31041121 ACTCGA-TTCGAATTCGAAATTCGAAAAAAAA
1 ATTCGAGTT-G-ATTCGAAATTCGAAAAAAAA
31041152 ATTCGAGTTGATTCGAA
1 ATTCGAGTTGATTCGAA
31041169 TAACTCGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
27 2 0.05
28 5 0.13
30 12 0.32
31 17 0.45
32 2 0.05
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (30 bp):
ATTCGAGTTGATTCGAAATTCGAAAAAAAA
Found at i:31048085 original size:5 final size:5
Alignment explanation
Indices: 31048075--31048121 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
31048065 TTTAGTTGAT
* *
31048075 AAATA AAATA AAATA AACA-A ATATA TAATA AAA-A AAATA AAATA AAA
1 AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA AAA
31048122 AAGAATTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 5 0.14
5 29 0.83
6 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:31048120 original size:14 final size:14
Alignment explanation
Indices: 31048073--31048123 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
31048063 AATTTAGTTG
*
31048073 ATAAATAAAATAAA
1 ATAAAAAAAATAAA
* *
31048087 ATAAACAAATATATA
1 ATAAA-AAAAATAAA
31048102 ATAAAAAAAATAAA
1 ATAAAAAAAATAAA
31048116 ATAAAAAA
1 ATAAAAAA
31048124 GAATTATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAAAAAATAAA
Found at i:31057736 original size:20 final size:20
Alignment explanation
Indices: 31057699--31057736 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31057689 TCTCTTCACA
*
31057699 ATTTTTGGTCCAACTTCTCT
1 ATTTTTGGTCCAAATTCTCT
*
31057719 ATTTTTGGTTCAAATTCT
1 ATTTTTGGTCCAAATTCT
31057737 AAAGTCCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (20 bp):
ATTTTTGGTCCAAATTCTCT
Found at i:31075052 original size:27 final size:27
Alignment explanation
Indices: 31075018--31075072 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
31075008 AGCTATGGAG
*
31075018 AAGAGAAGAGAAAACTAA-AACCCTAA
1 AAGAGAAGAGAAAACTAAGAAACCTAA
*
31075044 AAGATGAAGAGAAACCTAAGAAACCTAA
1 AAGA-GAAGAGAAAACTAAGAAACCTAA
31075072 A
1 A
31075073 CTAAACTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 13 0.52
28 8 0.32
ACGTcount: A:0.60, C:0.15, G:0.16, T:0.09
Consensus pattern (27 bp):
AAGAGAAGAGAAAACTAAGAAACCTAA
Found at i:31079474 original size:24 final size:26
Alignment explanation
Indices: 31079441--31079494 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
31079431 TCTTCTTAGA
*
31079441 TTTAGTCTTTA-GTTT-TTCTC-TTTT
1 TTTAGGCTTTAGGTTTATT-TCATTTT
31079465 TTTAGGCTTTAGGTTTATTTCATTTT
1 TTTAGGCTTTAGGTTTATTTCATTTT
31079491 TTTA
1 TTTA
31079495 TTTGCTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 10 0.38
25 6 0.23
26 10 0.38
ACGTcount: A:0.13, C:0.09, G:0.11, T:0.67
Consensus pattern (26 bp):
TTTAGGCTTTAGGTTTATTTCATTTT
Found at i:31080688 original size:19 final size:19
Alignment explanation
Indices: 31080666--31080703 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31080656 ATCACTGTCA
31080666 CCCACCATAATCAAATTTG
1 CCCACCATAATCAAATTTG
* *
31080685 CCCATCGTAATCAAATTTG
1 CCCACCATAATCAAATTTG
31080704 TTATTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (19 bp):
CCCACCATAATCAAATTTG
Found at i:31081301 original size:29 final size:31
Alignment explanation
Indices: 31081263--31081324 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
31081253 GGGGGTAGGA
31081263 TGGGAAGGGAGCAAAAGTTATGGG-GGAAAG
1 TGGGAAGGGAGCAAAAGTTATGGGAGGAAAG
* *
31081293 TGGG-AGGGAGTAAAAGTTTTGGGAGGAAAG
1 TGGGAAGGGAGCAAAAGTTATGGGAGGAAAG
31081323 TG
1 TG
31081325 AAGAGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.34, C:0.02, G:0.47, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAGCAAAAGTTATGGGAGGAAAG
Found at i:31094363 original size:88 final size:88
Alignment explanation
Indices: 31094244--31094417 Score: 339
Period size: 88 Copynumber: 2.0 Consensus size: 88
31094234 GTTTATAGTT
31094244 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
1 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
*
31094309 AATAATGATTTGTTTTGATTTTA
66 AAGAATGATTTGTTTTGATTTTA
31094332 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
1 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
31094397 AAGAATGATTTGTTTTGATTT
66 AAGAATGATTTGTTTTGATTT
31094418 GAACTACTAT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.43
Consensus pattern (88 bp):
ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
AAGAATGATTTGTTTTGATTTTA
Found at i:31096997 original size:276 final size:277
Alignment explanation
Indices: 31096454--31097002 Score: 749
Period size: 276 Copynumber: 2.0 Consensus size: 277
31096444 ATTTCAATTC
*
31096454 ACATTCATCGGTTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
1 ACATTCATCGATTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
* * * * *
31096519 TATATGCATCAGCCGATCATTGTATCAAATCAATCTAAAAAATCATTTATTCCAATTACATTATA
66 TAAATGCATCAGCCAATCATTGTATCAAATCAATATAAAAAATCATGTATTCCAATTACATTACA
* * * *
31096584 CATGTCCCTATTAACCTAACTCAAACTCGAACTAATACACGAATCCAACCTACACACCAATTTGG
131 CATGTCCCTATTAACCTAACTCAAACTCAAACAAATACACGAATCCAACCAACACAACAATTTGG
* * * * *
31096649 CACCTAATGCCTGATGGATAAATTCGTAATAATGAATTGCGCACTACGCTGGCTGGTAAAACTAA
196 CACCTAATCCCTGACGGATAAATCCGTAATAATGAATTGCGCACTACACTGGCTAGTAAAACTAA
31096714 AAAATAAATGTGTGATT
261 AAAATAAATGTGTGATT
* * * * * *
31096731 ACATTTATCGATTTTTCATGTTTCCATATTGGCCCCCTGGGCTTATATAACTGATTTTCAATATG
1 ACATTCATCGATTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
* * *
31096796 TAAATTCATCAGTCAATCATTGTATCAAATCAATAT-GAAAATCATGTATTCCAATTACATTACA
66 TAAATGCATCAGCCAATCATTGTATCAAATCAATATAAAAAATCATGTATTCCAATTACATTACA
* * * * * *
31096860 TATGTCTCTATTAACCTAACTTAGACTCAAACAAATACATGGATCCAACCAACACAACAATTTGG
131 CATGTCCCTATTAACCTAACTCAAACTCAAACAAATACACGAATCCAACCAACACAACAATTTGG
** * * * * *
31096925 CATTTAGTCCCTGACGGATAAATCCGTAATAATGAATTGTGCCCTACACTGGCTAGTAAAATTGA
196 CACCTAATCCCTGACGGATAAATCCGTAATAATGAATTGCGCACTACACTGGCTAGTAAAACTAA
*
31096990 CAAATAAATGTGT
261 AAAATAAATGTGT
31097003 CCAACACTGG
Statistics
Matches: 234, Mismatches: 38, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
276 145 0.62
277 89 0.38
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (277 bp):
ACATTCATCGATTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
TAAATGCATCAGCCAATCATTGTATCAAATCAATATAAAAAATCATGTATTCCAATTACATTACA
CATGTCCCTATTAACCTAACTCAAACTCAAACAAATACACGAATCCAACCAACACAACAATTTGG
CACCTAATCCCTGACGGATAAATCCGTAATAATGAATTGCGCACTACACTGGCTAGTAAAACTAA
AAAATAAATGTGTGATT
Found at i:31102937 original size:16 final size:18
Alignment explanation
Indices: 31102916--31102952 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31102906 GCTCACATTC
31102916 TCTTTTT-A-TCTCTTCT
1 TCTTTTTCATTCTCTTCT
*
31102932 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATTCTCTTCT
31102950 TCT
1 TCT
31102953 CACAACTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTTTTCATTCTCTTCT
Found at i:31102961 original size:28 final size:28
Alignment explanation
Indices: 31102911--31102965 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
31102901 TTCAAGCTCA
* **
31102911 CATTCTCTTTTTATCTCTTCTTCTTTTT
1 CATTCTCTTTTTATCACAACTTCTTTTT
*
31102939 CATTCTCTTTTTCTCACAACTTCTTTT
1 CATTCTCTTTTTATCACAACTTCTTTT
31102966 CTCACACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (28 bp):
CATTCTCTTTTTATCACAACTTCTTTTT
Found at i:31103024 original size:20 final size:21
Alignment explanation
Indices: 31102984--31103042 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
31102974 CTCACTTTTT
31102984 ATTTCCTTTTCTTTTTCTCTC
1 ATTTCCTTTTCTTTTTCTCTC
* *
31103005 ATTTCTTTTTTTTTCTTCTCTC
1 ATTTCCTTTTCTTT-TTCTCTC
* *
31103027 AATCTCCTTTACTTTT
1 -ATTTCCTTTTCTTTT
31103043 CTTTCTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 12 0.40
22 8 0.27
23 10 0.33
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTCCTTTTCTTTTTCTCTC
Found at i:31103119 original size:30 final size:31
Alignment explanation
Indices: 31103078--31103140 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
31103068 CTTCTCTCTT
31103078 TTCTTAATTTCTTTT-TTTTCTC-AATTTTC
1 TTCTTAATTTCTTTTATTTTCTCTAATTTTC
*
31103107 TTCTTCAATTTCTTTTAGTTTTCTCTCATTTTC
1 TTCTT-AATTTCTTTTA-TTTTCTCTAATTTTC
31103140 T
1 T
31103141 CTCATTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
32 7 0.24
33 7 0.24
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.67
Consensus pattern (31 bp):
TTCTTAATTTCTTTTATTTTCTCTAATTTTC
Found at i:31109713 original size:33 final size:36
Alignment explanation
Indices: 31109664--31109731 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
31109654 ACTTTATTTA
* *
31109664 ATGCAAAACACATAATG-T-ATGTCATAATTAAAAG
1 ATGCAAAACACATAATGATCAAGACATAATTAAAAG
*
31109698 ATGC-AAACACTTAATGATCAAGACATAATTAAAA
1 ATGCAAAACACATAATGATCAAGACATAATTAAAA
31109732 ATTGTAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 11 0.38
34 5 0.17
35 13 0.45
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.25
Consensus pattern (36 bp):
ATGCAAAACACATAATGATCAAGACATAATTAAAAG
Found at i:31114226 original size:48 final size:48
Alignment explanation
Indices: 31114155--31114253 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
31114145 TTAGAAATAG
*
31114155 ATAACATCTAGGCGAATTCCTAAGAGCTAATCTCCTATTTGCGGAATC
1 ATAACATCTAGGCGAATTCCTAAGAGCTAATCCCCTATTTGCGGAATC
* *
31114203 ATAACATCTAGGCGAATTTCTAAGAGCTAATCCCCTGTTTGCGGAATC
1 ATAACATCTAGGCGAATTCCTAAGAGCTAATCCCCTATTTGCGGAATC
31114251 ATA
1 ATA
31114254 CATATGAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (48 bp):
ATAACATCTAGGCGAATTCCTAAGAGCTAATCCCCTATTTGCGGAATC
Found at i:31114727 original size:22 final size:22
Alignment explanation
Indices: 31114609--31114736 Score: 87
Period size: 22 Copynumber: 5.9 Consensus size: 22
31114599 TCCTTTGCCA
* * *
31114609 CCCAT-AAGAGCTCTAATATGT
1 CCCATAAAGGGCTCTCATACGT
* * *
31114630 CCCATAAAGAGCTTTTATACGT
1 CCCATAAAGGGCTCTCATACGT
* * * * *
31114652 CCTAGAAAGGGTTTTCATATGT
1 CCCATAAAGGGCTCTCATACGT
* * * * *
31114674 CTCATAAAAGGCTCTTATGCAT
1 CCCATAAAGGGCTCTCATACGT
*
31114696 CCCATTAAGGGCTCTCATACGT
1 CCCATAAAGGGCTCTCATACGT
*
31114718 CCCATAAAGGGCTTTCATA
1 CCCATAAAGGGCTCTCATA
31114737 TATTGGTGTC
Statistics
Matches: 79, Mismatches: 27, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
21 5 0.06
22 74 0.94
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (22 bp):
CCCATAAAGGGCTCTCATACGT
Found at i:31117088 original size:34 final size:34
Alignment explanation
Indices: 31117039--31117103 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
31117029 TTTTAATTAA
31117039 TATAAAATTATAAAATCAATTAAATAATAATATG
1 TATAAAATTATAAAATCAATTAAATAATAATATG
* * *
31117073 TATACAATTGTAAAATTAATTAAATAATAAT
1 TATAAAATTATAAAATCAATTAAATAATAAT
31117104 TAATATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (34 bp):
TATAAAATTATAAAATCAATTAAATAATAATATG
Found at i:31124634 original size:3 final size:3
Alignment explanation
Indices: 31124626--31124664 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
31124616 TTTCGACTCT
31124626 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
31124665 ATCATCACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:31129678 original size:36 final size:36
Alignment explanation
Indices: 31129638--31129706 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
31129628 AAGGGTGATG
*
31129638 ATTCATTAATCTCTACATATAATCCAATTGAAGATA
1 ATTCAATAATCTCTACATATAATCCAATTGAAGATA
31129674 ATTCAATAATCTCTACATATAATCCAATTGAAG
1 ATTCAATAATCTCTACATATAATCCAATTGAAG
31129707 GTGGAGTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (36 bp):
ATTCAATAATCTCTACATATAATCCAATTGAAGATA
Found at i:31134830 original size:12 final size:12
Alignment explanation
Indices: 31134815--31134846 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31134805 TAAAAAGGAA
31134815 AATAATAATAGT
1 AATAATAATAGT
31134827 AATAATAATAGT
1 AATAATAATAGT
31134839 AA-AATAAT
1 AATAATAAT
31134847 TAATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:31140346 original size:47 final size:47
Alignment explanation
Indices: 31140288--31140778 Score: 829
Period size: 47 Copynumber: 10.4 Consensus size: 47
31140278 CAGCCAAGAC
*
31140288 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31140335 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31140382 AGTGTATATATGTGATAAGGCCTAATGTCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31140429 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31140478 AGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
31140525 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31140572 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31140619 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
31140666 CGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
31140713 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
31140760 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
31140779 TCCCGAAGGG
Statistics
Matches: 420, Mismatches: 22, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 374 0.89
49 46 0.11
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:31140953 original size:37 final size:37
Alignment explanation
Indices: 31140897--31140975 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
31140887 CCGAGCTCTA
* *
31140897 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
31140934 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
31140971 AAGAC
1 AAGAC
31140976 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:31148077 original size:27 final size:27
Alignment explanation
Indices: 31147997--31148078 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
31147987 TAAAATTTTG
* * * *
31147997 AAAATAATAAGTGAAAAATAACATATT
1 AAAAAAATAAATGAAAAGTAATATATT
* *
31148024 ATAAAAAACCAAATGGAAAGTAATATATT
1 A-AAAAAA-TAAATGAAAAGTAATATATT
*
31148053 AAAAAAATAACTGAAAAGTAATATAT
1 AAAAAAATAAATGAAAAGTAATATAT
31148079 CCAAATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
27 17 0.39
28 11 0.25
29 16 0.36
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.24
Consensus pattern (27 bp):
AAAAAAATAAATGAAAAGTAATATATT
Found at i:31149883 original size:31 final size:31
Alignment explanation
Indices: 31149845--31149908 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
31149835 GCTTGGGAAG
*
31149845 AAAAAATAAAAGGG-AAAGAAAGAAAGGGAGA
1 AAAAAATAAAAGGGAAAAGAAAAAAAGGG-GA
31149876 AAAAAATAAAAGGGAAAAGAAAAAAAGGGGA
1 AAAAAATAAAAGGGAAAAGAAAAAAAGGGGA
31149907 AA
1 AA
31149909 CCTCTCATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (31 bp):
AAAAAATAAAAGGGAAAAGAAAAAAAGGGGA
Found at i:31149901 original size:15 final size:15
Alignment explanation
Indices: 31149852--31149904 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
31149842 AAGAAAAAAT
31149852 AAAAGGG-AAAGAAA
1 AAAAGGGAAAAGAAA
* *
31149866 GAAAGGGAGAAAAAAA
1 AAAAGGGA-AAAGAAA
31149882 TAAAAGGGAAAAGAAA
1 -AAAAGGGAAAAGAAA
31149898 AAAAGGG
1 AAAAGGG
31149905 GAAACCTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 12 0.38
17 7 0.22
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (15 bp):
AAAAGGGAAAAGAAA
Found at i:31153274 original size:29 final size:29
Alignment explanation
Indices: 31153215--31153275 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
31153205 AATATATATC
* ***
31153215 TAAAAGATTATAAACACTTTTTTTTAAAA
1 TAAAAGATTATAAACACATTTAAATAAAA
31153244 TAAAA-ATTATAAACACATTTAAATAACAA
1 TAAAAGATTATAAACACATTTAAATAA-AA
31153273 TAA
1 TAA
31153276 TACTTTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAAAGATTATAAACACATTTAAATAAAA
Found at i:31156491 original size:9 final size:9
Alignment explanation
Indices: 31156479--31156503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31156469 AAAAACTTCT
31156479 AAAAATATA
1 AAAAATATA
31156488 AAAAATATA
1 AAAAATATA
31156497 AAAAATA
1 AAAAATA
31156504 ATATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATATA
Found at i:31156758 original size:40 final size:40
Alignment explanation
Indices: 31156702--31156781 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
31156692 TTATTAAATA
*
31156702 AAGTATGGGCCAAACATGTGTAGATACTCTAATAATTAAT
1 AAGTATGGGCCAAACATGTATAGATACTCTAATAATTAAT
* *
31156742 AAGTATGGGTCTAACATGTATAGATACTCTAATAATTAAT
1 AAGTATGGGCCAAACATGTATAGATACTCTAATAATTAAT
31156782 TTCTAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (40 bp):
AAGTATGGGCCAAACATGTATAGATACTCTAATAATTAAT
Found at i:31157378 original size:36 final size:35
Alignment explanation
Indices: 31157318--31157387 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 35
31157308 AATAATTGAG
* * * *
31157318 TTTTCTGTTCTTTATCGACCAATAAGTCGTTTATA
1 TTTTCTGCTCTTCATCGACCAATAAATCATTTATA
31157353 TTTTGCTGCTCTTCATCGACCAATAAATCATTTAT
1 TTTT-CTGCTCTTCATCGACCAATAAATCATTTAT
31157388 TGCTTCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.13
36 26 0.87
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCTGCTCTTCATCGACCAATAAATCATTTATA
Found at i:31157512 original size:5 final size:5
Alignment explanation
Indices: 31157502--31157526 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31157492 TACGGTAATT
31157502 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
31157527 AGGAGTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:31157863 original size:41 final size:41
Alignment explanation
Indices: 31157769--31157930 Score: 234
Period size: 42 Copynumber: 3.9 Consensus size: 41
31157759 TAACGAAAAA
* * * *
31157769 CGCCGCTAAGGAACATGATCTTTAGTGGCGTTTTTCCTTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-TTTAAG
31157811 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTAAG
* *
31157852 CGCCTCTAAAGAACATGTTCATTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT-TAAG
* *
31157894 CGCCTCTAAAGAACATGTTCTTTAGCGGCGCTTTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT
31157931 ACAAAAATGC
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
41 40 0.36
42 71 0.64
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTAAG
Found at i:31157903 original size:83 final size:83
Alignment explanation
Indices: 31157769--31157930 Score: 236
Period size: 83 Copynumber: 2.0 Consensus size: 83
31157759 TAACGAAAAA
* * *
31157769 CGCCGCTAAGGAACATGATCTTTAGTGGCGTTTTTCCTTAAGCGCCGCTAAAGAACATGTTCTTT
1 CGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTCCTTAAGCGCCGCTAAAGAACATGTTCTTT
*
31157834 AGCGGCGTTTTTTTTAAG
66 AGCGGCGCTTTTTTTAAG
* * * *
31157852 CGCCTCTAAAGAACATGTTCATTAGCGGCGTTTTT-TTCTAAGCGCCTCTAAAGAACATGTTCTT
1 CGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTCCT-TAAGCGCCGCTAAAGAACATGTTCTT
31157916 TAGCGGCGCTTTTTT
65 TAGCGGCGCTTTTTT
31157931 ACAAAAATGC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
82 1 0.01
83 69 0.99
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (83 bp):
CGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTCCTTAAGCGCCGCTAAAGAACATGTTCTTT
AGCGGCGCTTTTTTTAAG
Found at i:31158334 original size:21 final size:21
Alignment explanation
Indices: 31158310--31158360 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
31158300 TTCTTTTGAA
*
31158310 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
31158331 CCTCTACTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
31158352 CATCTGCTT
1 CCTCTGCTT
31158361 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.45, G:0.16, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:31160765 original size:9 final size:9
Alignment explanation
Indices: 31160735--31161059 Score: 353
Period size: 9 Copynumber: 35.8 Consensus size: 9
31160725 ATTTACACGG
31160735 GTAAGTTAT
1 GTAAGTTAT
* *
31160744 TTAATTTAT
1 GTAAGTTAT
*
31160753 GTAAGTTAA
1 GTAAGTTAT
31160762 GTAAGTTAT
1 GTAAGTTAT
31160771 GTAAGTTAT
1 GTAAGTTAT
* *
31160780 TTAATTTAT
1 GTAAGTTAT
*
31160789 GTAGGTTAT
1 GTAAGTTAT
* *
31160798 GTAAGTCCAC
1 GTAAGT-TAT
* *
31160808 GGAATTTAT
1 GTAAGTTAT
31160817 GTAAGTTAT
1 GTAAGTTAT
* *
31160826 TTAATTTAT
1 GTAAGTTAT
31160835 GTAAGTTAT
1 GTAAGTTAT
31160844 GTAAGTTAT
1 GTAAGTTAT
* *
31160853 TTAATTTAT
1 GTAAGTTAT
*
31160862 GTAGGTTAT
1 GTAAGTTAT
31160871 GTAAGTTAT
1 GTAAGTTAT
* *
31160880 TTAATTTAT
1 GTAAGTTAT
*
31160889 GCAAGTTTAT
1 GTAAG-TTAT
31160899 GTAAGTTAT
1 GTAAGTTAT
31160908 GTAAGTTAT
1 GTAAGTTAT
* *
31160917 TTAATTTAT
1 GTAAGTTAT
31160926 GTAAGTTAT
1 GTAAGTTAT
31160935 GTAAGTTAT
1 GTAAGTTAT
* *
31160944 TTAATTTAT
1 GTAAGTTAT
*
31160953 GTAGGTTAT
1 GTAAGTTAT
31160962 GTAAGTTAT
1 GTAAGTTAT
31160971 GTAAGTTAT
1 GTAAGTTAT
* *
31160980 TTAATTTAT
1 GTAAGTTAT
*
31160989 GCAAGTTTAT
1 GTAAG-TTAT
31160999 GTAAGTTAT
1 GTAAGTTAT
31161008 GTAAGTTAT
1 GTAAGTTAT
* *
31161017 TTAATTTAT
1 GTAAGTTAT
31161026 GTAAGTTAT
1 GTAAGTTAT
31161035 GTAAGTTAT
1 GTAAGTTAT
* *
31161044 TTAATTTAT
1 GTAAGTTAT
31161053 GTAAGTT
1 GTAAGTT
31161060 TCTATATATA
Statistics
Matches: 253, Mismatches: 60, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
9 232 0.92
10 21 0.08
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:31160935 original size:100 final size:100
Alignment explanation
Indices: 31160735--31161059 Score: 481
Period size: 100 Copynumber: 3.2 Consensus size: 100
31160725 ATTTACACGG
* * *
31160735 GTAAGTTATTTAATTTATGTAAGTTAAGTAAGTTATGTAAGTTATTTAATTTATG-TAGGTTATG
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATG
* * * * * * * *
31160799 TAAGTCCACGGAATTTATGTAAGTTATTTAATTTAT
66 TAAGT-TATGTAAGTTATTTAATTTATGTAAGTTAT
* * * * *
31160835 GTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTTATTTAATTTATGCAAGTTTATG
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATG
31160900 TAAGTTATGTAAGTTATTTAATTTATGTAAGTTAT
66 TAAGTTATGTAAGTTATTTAATTTATGTAAGTTAT
*
31160935 GTAAGTTATTTAATTTATGTAGGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATG
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATG
31161000 TAAGTTATGTAAGTTATTTAATTTATGTAAGTTAT
66 TAAGTTATGTAAGTTATTTAATTTATGTAAGTTAT
31161035 GTAAGTTATTTAATTTATGTAAGTT
1 GTAAGTTATTTAATTTATGTAAGTT
31161060 TCTATATATA
Statistics
Matches: 201, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 189 0.94
101 12 0.06
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (100 bp):
GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATG
TAAGTTATGTAAGTTATTTAATTTATGTAAGTTAT
Found at i:31161122 original size:21 final size:21
Alignment explanation
Indices: 31161101--31161176 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
31161091 ATTATGTTAT
* *
31161101 TATATAAGTTATGTAA-ATTA
1 TATATAAGTTATGCAAGCTTA
*
31161121 TTATGTAAGTTATGCAAGCTTA
1 -TATATAAGTTATGCAAGCTTA
*
31161143 AATATAAGTTATGCAAGCTTA
1 TATATAAGTTATGCAAGCTTA
*
31161164 TATACAAGTTATG
1 TATATAAGTTATG
31161177 TATTATAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 44 0.94
22 3 0.06
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (21 bp):
TATATAAGTTATGCAAGCTTA
Found at i:31161148 original size:42 final size:39
Alignment explanation
Indices: 31161102--31161273 Score: 110
Period size: 42 Copynumber: 4.4 Consensus size: 39
31161092 TTATGTTATT
31161102 ATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAA
1 ATATAAGTTATGTAAATTATTATGTAAGTTATG-AA--TTAA
* * ** *
31161144 ATATAAGTTATGCAAGCTTA-TATACAAGTTATGTATTATA
1 ATATAAGTTATGTAA-ATTATTATGTAAGTTATGAATTA-A
* * *
31161184 ACATAAAGTATTATGT-AA-T-TTAT-TATG-T-T--ATTAT
1 ATAT-AAG--TTATGTAAATTATTATGTAAGTTATGAATTAA
31161218 ATATAAGTTATGTAAATTATTATGTAAGTTATGCAAGCTTAA
1 ATATAAGTTATGTAAATTATTATGTAAGTTATG-AA--TTAA
31161260 ATATAAGTTATGTA
1 ATATAAGTTATGTA
31161274 TTATATAAGT
Statistics
Matches: 99, Mismatches: 14, Indels: 34
0.67 0.10 0.23
Matches are distributed among these distances:
31 6 0.06
32 2 0.02
33 4 0.04
34 7 0.07
35 7 0.07
36 1 0.01
37 2 0.02
38 1 0.01
39 5 0.05
40 9 0.09
41 4 0.04
42 43 0.43
43 8 0.08
ACGTcount: A:0.40, C:0.05, G:0.13, T:0.42
Consensus pattern (39 bp):
ATATAAGTTATGTAAATTATTATGTAAGTTATGAATTAA
Found at i:31161420 original size:16 final size:16
Alignment explanation
Indices: 31161395--31161432 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
31161385 GAAAACGAAG
*
31161395 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
31161410 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
31161426 TAAATTT
1 TAAATTT
31161433 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:31161447 original size:13 final size:13
Alignment explanation
Indices: 31161429--31161456 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31161419 ATACAAATAA
31161429 ATTTAGAAAACTT
1 ATTTAGAAAACTT
31161442 ATTTAGAAAACTT
1 ATTTAGAAAACTT
31161455 AT
1 AT
31161457 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:31161464 original size:17 final size:17
Alignment explanation
Indices: 31161425--31161474 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
31161415 TTTAATACAA
31161425 ATAAATTTAGAAAAC-T
1 ATAAATTTAGAAAACTT
31161441 -T--ATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
31161455 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
31161472 ATA
1 ATA
31161475 TAGATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 2 0.07
17 16 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:31189790 original size:62 final size:62
Alignment explanation
Indices: 31189639--31189791 Score: 164
Period size: 62 Copynumber: 2.5 Consensus size: 62
31189629 CGTGTAACTC
* * * *
31189639 ACACGGCCTAGGTACATGCCCGTGTCCTTGGCCATATGGCTTTGTGCCACAAACAATGAGTT
1 ACACGGCCTGGGTACACGCCCGTGTCCCTGGCCATATGGCTTTGTACCACAAACAATGAGTT
* * ** * * * *
31189701 ACACGGCTTGGGCACACATCCGTGTCCCTGGTCATGTGG-TATTGTACCATAAACAGTGAGTT
1 ACACGGCCTGGGTACACGCCCGTGTCCCTGGCCATATGGCT-TTGTACCACAAACAATGAGTT
* *
31189763 ACATGGCCTGGGTACACGCCCATGTCCCT
1 ACACGGCCTGGGTACACGCCCGTGTCCCT
31189792 TACCCGTGCG
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
61 1 0.01
62 71 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (62 bp):
ACACGGCCTGGGTACACGCCCGTGTCCCTGGCCATATGGCTTTGTACCACAAACAATGAGTT
Found at i:31197454 original size:25 final size:26
Alignment explanation
Indices: 31197410--31197459 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
31197400 GGTTTTATTT
*
31197410 TCTTTTCATTTTTAGATTAGGTTTTC
1 TCTTTTCATTTTTAGATTAGATTTTC
*
31197436 TCTTTTC-TTTTTAGGTTAGATTTT
1 TCTTTTCATTTTTAGATTAGATTTT
31197460 AGTTTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.14, C:0.10, G:0.12, T:0.64
Consensus pattern (26 bp):
TCTTTTCATTTTTAGATTAGATTTTC
Found at i:31202559 original size:24 final size:24
Alignment explanation
Indices: 31202514--31202561 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31202504 TTAGCCAAAG
* *
31202514 GCTAAAGGACTTAAACTGCAATTA
1 GCTAAAGGACTCAAAATGCAATTA
31202538 GCTAAAGGAC-CAAAATGACAATTA
1 GCTAAAGGACTCAAAATG-CAATTA
31202562 AACCATAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (24 bp):
GCTAAAGGACTCAAAATGCAATTA
Found at i:31205117 original size:16 final size:15
Alignment explanation
Indices: 31205098--31205131 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31205088 TAATTCTAAA
31205098 AAAAATTAAAAATAAT
1 AAAAATTAAAAAT-AT
*
31205114 AAAAATTTAAAATAT
1 AAAAATTAAAAATAT
31205129 AAA
1 AAA
31205132 TTTCTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATTAAAAATAT
Found at i:31207921 original size:13 final size:13
Alignment explanation
Indices: 31207903--31207927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31207893 TGGGCCTACA
31207903 TGCTTGTGTGGCT
1 TGCTTGTGTGGCT
31207916 TGCTTGTGTGGC
1 TGCTTGTGTGGC
31207928 CCCACACGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.40, T:0.44
Consensus pattern (13 bp):
TGCTTGTGTGGCT
Found at i:31216464 original size:14 final size:14
Alignment explanation
Indices: 31216445--31216472 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31216435 TACAAAAACC
31216445 ACAATTTCAACGTT
1 ACAATTTCAACGTT
31216459 ACAATTTCAACGTT
1 ACAATTTCAACGTT
31216473 TAAGCAACTC
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:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
ACAATTTCAACGTT
Found at i:31218269 original size:8 final size:8
Alignment explanation
Indices: 31218256--31218282 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31218246 TATGTGTTTT
31218256 TTTTATAA
1 TTTTATAA
31218264 TTTTATAA
1 TTTTATAA
31218272 TTTTATAA
1 TTTTATAA
31218280 TTT
1 TTT
31218283 AGTCTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTATAA
Found at i:31226762 original size:23 final size:23
Alignment explanation
Indices: 31226734--31226788 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
31226724 GCTATTTTAT
31226734 TGTTGTTTCGCAACTATTTATTA
1 TGTTGTTTCGCAACTATTTATTA
* * * *
31226757 TGTTGTTTTGTACCTGTTTATTA
1 TGTTGTTTCGCAACTATTTATTA
*
31226780 TATTGTTTC
1 TGTTGTTTC
31226789 ACTGTCGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.11, G:0.15, T:0.58
Consensus pattern (23 bp):
TGTTGTTTCGCAACTATTTATTA
Found at i:31231966 original size:21 final size:21
Alignment explanation
Indices: 31231940--31231995 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
31231930 AACAGCGGTG
*
31231940 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
31231961 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
31231982 GCAGTGAAATTAGA
1 GCGGTGAGATTAGA
31231996 AACAGCGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:31234992 original size:6 final size:6
Alignment explanation
Indices: 31234981--31235042 Score: 106
Period size: 6 Copynumber: 10.2 Consensus size: 6
31234971 TTTGCAACTC
*
31234981 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
31235029 AAGGGG AAAGGGG A
1 AAGGGG -AAGGGG A
31235043 GAAGAAGGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
6 47 0.89
7 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:31235049 original size:18 final size:18
Alignment explanation
Indices: 31234981--31235050 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
31234971 TTTGCAACTC
** *
31234981 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGAAGAAGGGG
**
31234999 AAGGGGAAGGGGAAGGGG
1 AAGGGGAAGAAGAAGGGG
**
31235017 AAGGGGAAGGGGAAGGGG
1 AAGGGGAAGAAGAAGGGG
31235035 AAAGGGG-AGAAGAAGG
1 -AAGGGGAAGAAGAAGG
31235051 TAACATACAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
18 42 0.88
19 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGAAGAAGGGG
Found at i:31242704 original size:21 final size:22
Alignment explanation
Indices: 31242675--31242721 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
31242665 CAGAAGGAGT
*
31242675 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
31242697 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
31242718 GAGT
1 GAGT
31242722 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:31245913 original size:21 final size:22
Alignment explanation
Indices: 31245884--31245930 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
31245874 CAGAAGGAGT
*
31245884 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
31245906 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
31245927 GAGT
1 GAGT
31245931 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:31248658 original size:2 final size:2
Alignment explanation
Indices: 31248651--31248685 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31248641 ACCATCATTT
*
31248651 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31248686 TTTTGCAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:31253903 original size:20 final size:20
Alignment explanation
Indices: 31253878--31253916 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31253868 TGGAGCAAGA
*
31253878 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
31253898 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
31253917 AGCATCGATA
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:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:31253923 original size:20 final size:20
Alignment explanation
Indices: 31253880--31253928 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
31253870 GAGCAAGAAT
* *
31253880 ATCGATACCTTAGGAAATAT
1 ATCGATACCTTAAGAAATAC
31253900 ATCGATACCTTAAGAAA-AGC
1 ATCGATACCTTAAGAAATA-C
31253920 ATCGATACC
1 ATCGATACC
31253929 AGATCGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (20 bp):
ATCGATACCTTAAGAAATAC
Found at i:31254943 original size:24 final size:24
Alignment explanation
Indices: 31254916--31254963 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31254906 AAGTCTAGGT
31254916 ACATATAAGCATGTGAAGTGATAA
1 ACATATAAGCATGTGAAGTGATAA
31254940 ACATATAAGCATGTGAAGTGATAA
1 ACATATAAGCATGTGAAGTGATAA
31254964 GTAAATTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (24 bp):
ACATATAAGCATGTGAAGTGATAA
Found at i:31256259 original size:20 final size:20
Alignment explanation
Indices: 31256236--31256383 Score: 97
Period size: 20 Copynumber: 7.6 Consensus size: 20
31256226 AATTTTTTAT
*
31256236 CGATACAAAAATTTTTAACG
1 CGATACCAAAATTTTTAACG
* ** * *
31256256 CGATATCACTATTTCTAA-T
1 CGATACCAAAATTTTTAACG
*
31256275 CAATACC-AAATTTTTAAC-
1 CGATACCAAAATTTTTAACG
* *
31256293 TGATGCCAAAATTTTTAACG
1 CGATACCAAAATTTTTAACG
* * * *
31256313 AGATACCAATATTTCTAATG
1 CGATACCAAAATTTTTAACG
* * *
31256333 TGATACCAATATTTTTAACA
1 CGATACCAAAATTTTTAACG
* *
31256353 TGATACTAAAATTTTTAAC-
1 CGATACCAAAATTTTTAACG
*
31256372 CGACACCAAAAT
1 CGATACCAAAAT
31256384 AGCTAATGTG
Statistics
Matches: 97, Mismatches: 28, Indels: 7
0.73 0.21 0.05
Matches are distributed among these distances:
18 11 0.11
19 25 0.26
20 61 0.63
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (20 bp):
CGATACCAAAATTTTTAACG
Found at i:31256380 original size:59 final size:58
Alignment explanation
Indices: 31256222--31256401 Score: 195
Period size: 57 Copynumber: 3.1 Consensus size: 58
31256212 TAATGACAAG
* * * **
31256222 ACCAAATTTTTTA-TCGATACAAAAATTTTTAACGCGATATCACTATTTCTAAT-CAAT
1 ACCAAATTTTTAACT-GATACAAAAATTTTTAACGCGATACCAATATTTCTAATGTGAT
* * *
31256279 ACCAAATTTTTAACTGATGCCAAAATTTTTAACGAGATACCAATATTTCTAATGTGAT
1 ACCAAATTTTTAACTGATACAAAAATTTTTAACGCGATACCAATATTTCTAATGTGAT
* * * **
31256337 ACCAATATTTTTAACATGATACTAAAATTTTTAAC-CGACACCAAAATAGCTAATGTGAT
1 ACCAA-ATTTTTAAC-TGATACAAAAATTTTTAACGCGATACCAATATTTCTAATGTGAT
31256396 ACCAAA
1 ACCAAA
31256402 ATTTCTAGGC
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
57 45 0.43
58 9 0.09
59 33 0.32
60 17 0.16
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (58 bp):
ACCAAATTTTTAACTGATACAAAAATTTTTAACGCGATACCAATATTTCTAATGTGAT
Found at i:31256382 original size:19 final size:19
Alignment explanation
Indices: 31256277--31256383 Score: 99
Period size: 20 Copynumber: 5.5 Consensus size: 19
31256267 TTTCTAATCA
31256277 ATACC-AAATTTTTAACTG
1 ATACCAAAATTTTTAACTG
* *
31256295 ATGCCAAAATTTTTAACGAG
1 ATACCAAAATTTTTAAC-TG
* * *
31256315 ATACCAATATTTCTAATGTG
1 ATACCAAAATTTTTAA-CTG
*
31256335 ATACCAATATTTTTAACATG
1 ATACCAAAATTTTTAAC-TG
* *
31256355 ATACTAAAATTTTTAACCG
1 ATACCAAAATTTTTAACTG
*
31256374 ACACCAAAAT
1 ATACCAAAAT
31256384 AGCTAATGTG
Statistics
Matches: 71, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
18 4 0.06
19 20 0.28
20 47 0.66
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (19 bp):
ATACCAAAATTTTTAACTG
Found at i:31256530 original size:15 final size:15
Alignment explanation
Indices: 31256510--31256539 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31256500 TAAGGCACGT
31256510 GTATTTAATTGTTGA
1 GTATTTAATTGTTGA
31256525 GTATTTAATTGTTGA
1 GTATTTAATTGTTGA
31256540 TGCAACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (15 bp):
GTATTTAATTGTTGA
Done.