Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 155 of 208
Found at i:47230294 original size:16 final size:16
Alignment explanation
Indices: 47230258--47230311 Score: 74
Period size: 16 Copynumber: 3.3 Consensus size: 16
47230248 CTAAAGAAAG
47230258 AAAAATGAAAATAAAAT
1 AAAAAT-AAAATAAAAT
47230275 -AAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
*
47230290 AAAAACAAAATAAAAT
1 AAAAATAAAATAAAAT
47230306 ATAAAA
1 A-AAAA
47230312 ACTCACAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 10 0.29
16 20 0.59
17 4 0.12
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:47234647 original size:43 final size:43
Alignment explanation
Indices: 47234480--47234673 Score: 169
Period size: 43 Copynumber: 4.5 Consensus size: 43
47234470 AGATACTGGT
* * * * *
47234480 CTAAAGAACATGATCTTTAGTGGCGCTTCCCATAAAAATGTCG
1 CTAAAGAACATGATCTTTAGCGACGCTTCACACAAAAATGCCG
* * * * * *
47234523 TTAAAGAACATGATCTTTAGCGGTAC-TTTTAC-TAAAAACGCCA
1 CTAAAGAACATGATCTTTAGC-G-ACGCTTCACACAAAAATGCCG
* * * * *
47234566 CTATAA-AAAATGATATTTCGCGGCGCTTCTCACAAAAATGCCG
1 CTA-AAGAACATGATCTTTAGCGACGCTTCACACAAAAATGCCG
*
47234609 CTATAGAACATGATCTTTAGCGACGCTTCACACAAAAATGCCG
1 CTAAAGAACATGATCTTTAGCGACGCTTCACACAAAAATGCCG
* *
47234652 CTAAAGATCATGTTCTTTAGCG
1 CTAAAGAACATGATCTTTAGCG
47234674 GCATTTGTAA
Statistics
Matches: 116, Mismatches: 29, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
41 1 0.01
42 5 0.04
43 103 0.89
44 6 0.05
45 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (43 bp):
CTAAAGAACATGATCTTTAGCGACGCTTCACACAAAAATGCCG
Found at i:47234675 original size:86 final size:86
Alignment explanation
Indices: 47234480--47234675 Score: 200
Period size: 86 Copynumber: 2.3 Consensus size: 86
47234470 AGATACTGGT
* * * *
47234480 CTAAAGAACATGATCTTTAGTGGCGCTTCCCATAAAAATGTCGTTAAAGAACATGATCTTTAGCG
1 CTAAAGAACATGATCTTTAGCGGCGCTTCCCACAAAAATGCCGCTAAAGAACATGATCTTTAGCG
* * *
47234545 GTACTTTTACTAAAAACGCCA
66 GTACCTTCACCAAAAACGCCA
* * * * *
47234566 CTATAA-AAAATGATATTTCGCGGCGCTTCTCACAAAAATGCCGCTATAGAACATGATCTTTAGC
1 CTA-AAGAACATGATCTTTAGCGGCGCTTCCCACAAAAATGCCGCTAAAGAACATGATCTTTAGC
* *
47234630 -G-ACGCTTCACACAAAAATGCCG
65 GGTAC-CTTCAC-CAAAAACGCCA
* *
47234652 CTAAAGATCATGTTCTTTAGCGGC
1 CTAAAGAACATGATCTTTAGCGGC
47234676 ATTTGTAAGA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
84 2 0.02
85 7 0.08
86 76 0.87
87 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (86 bp):
CTAAAGAACATGATCTTTAGCGGCGCTTCCCACAAAAATGCCGCTAAAGAACATGATCTTTAGCG
GTACCTTCACCAAAAACGCCA
Found at i:47249040 original size:21 final size:22
Alignment explanation
Indices: 47249011--47249057 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
47249001 CAGAAGGAGT
*
47249011 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
*
47249033 GAGT-GTACTCCGTAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
47249054 GAGT
1 GAGT
47249058 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:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:47252399 original size:2 final size:2
Alignment explanation
Indices: 47252388--47252416 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
47252378 AATTTTTATT
47252388 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47252417 CACACGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47255052 original size:62 final size:60
Alignment explanation
Indices: 47254944--47255062 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 60
47254934 TTTTAATATA
*
47254944 TTTGTACAAACTATTTTTATATTATTTCATTTAATAAAATAGAAGTTGTTTTGAATATTT
1 TTTGTACAAACTATTTTTATATTATTTCATTTAATAAAATAGAAGTTCTTTTGAATATTT
* * *
47255004 TTTGTATAAATTATTTTTATATT-TTGTCCTATTTAATAAAATATAAGTTCTTTTGAATA
1 TTTGTACAAACTATTTTTATATTATT-T-C-ATTTAATAAAATAGAAGTTCTTTTGAATA
47255063 AGGCAATGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 22 0.42
61 1 0.02
62 27 0.52
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (60 bp):
TTTGTACAAACTATTTTTATATTATTTCATTTAATAAAATAGAAGTTCTTTTGAATATTT
Found at i:47256241 original size:43 final size:42
Alignment explanation
Indices: 47256192--47256272 Score: 126
Period size: 43 Copynumber: 1.9 Consensus size: 42
47256182 ATTTCATTTG
*
47256192 TCATCTCATAATCATTTTTCATATTTGCCATTTCAATATTTTC
1 TCATCTCATAATCATTTCTCATATTTGCCATTT-AATATTTTC
* *
47256235 TCATCTCATATTCATTTCTCATATTTTCCATTTAATAT
1 TCATCTCATAATCATTTCTCATATTTGCCATTTAATAT
47256273 CAATCACATA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 5 0.14
43 30 0.86
ACGTcount: A:0.26, C:0.21, G:0.01, T:0.52
Consensus pattern (42 bp):
TCATCTCATAATCATTTCTCATATTTGCCATTTAATATTTTC
Found at i:47263135 original size:126 final size:125
Alignment explanation
Indices: 47262904--47263387 Score: 528
Period size: 126 Copynumber: 3.9 Consensus size: 125
47262894 TAAGCAGGAG
* * * *
47262904 CATCTTCTCAAAATTA-TTTTGCAGAAACTATTGTAGAAAAAGAGCATCCAGCTGGGAGCTTTTT
1 CATCTTCTCAAAATTATTTTTTCAGAAACTATTATAGAAAAAGAGCGTCCAGCTGAGAGCTTTTT
* * * ** * ** *
47262968 TTAGTACTTTTGCTGACAATGTGTCCTGGTTGAAGTGTTTTTTACCTTATTTTTTCAGAA
66 TCAGTACTTTTACTGACAGTGCATCCTGCTTGAAGCATTTTTTACCTTATTTTTTTAGAA
* * * * *
47263028 TCATCTT-TCCAAAATTATATTTCCAGAAATTACTT-TAGAAAAAGAGCGTCTAG-TTAGGAGCT
1 -CATCTTCT-CAAAATTATTTTTTCAGAAACTA-TTATAGAAAAAGAGCGTCCAGCTGA-GAGCT
* * * *
47263090 GTTTTCAGTACTTTTACTGACAGTGCATCCTGTTTGAAGCGTTTTTTACCTAATTTTTTTAGAA
62 TTTTTCAGTACTTTTACTGACAGTGCATCCTGCTTGAAGCATTTTTTACCTTATTTTTTTAGAA
* * * * * * * *
47263154 CCATCTTTTTAAAATTATTTTTTAAGAAACTACTGTAGAAAAAGAACGTCTAGCTGAGAACTTTT
1 -CATCTTCTCAAAATTATTTTTTCAGAAACTATTATAGAAAAAGAGCGTCCAGCTGAGAGCTTTT
* *
47263219 TTCAGTACTTTTACTGATAGTGCATCCTGCTTGAAGCATTTTTTACCATATTTTTTTAGAA
65 TTCAGTACTTTTACTGACAGTGCATCCTGCTTGAAGCATTTTTTACCTTATTTTTTTAGAA
* * * *
47263280 CTATCTTCTTAAAATTATTTTTTC-GAAAACTATTATAGAAAAATAGCGTCCAACTGTGAGCTTT
1 C-ATCTTCTCAAAATTATTTTTTCAG-AAACTATTATAGAAAAAGAGCGTCCAGCTGAGAGCTTT
* *
47263344 TTTCAGTACTTTTGCTGACAGTGCATCCTACTTGAAGCATTTTT
64 TTTCAGTACTTTTACTGACAGTGCATCCTGCTTGAAGCATTTTT
47263388 GAACACAAGT
Statistics
Matches: 304, Mismatches: 46, Indels: 17
0.83 0.13 0.05
Matches are distributed among these distances:
124 1 0.00
125 18 0.06
126 280 0.92
127 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (125 bp):
CATCTTCTCAAAATTATTTTTTCAGAAACTATTATAGAAAAAGAGCGTCCAGCTGAGAGCTTTTT
TCAGTACTTTTACTGACAGTGCATCCTGCTTGAAGCATTTTTTACCTTATTTTTTTAGAA
Found at i:47269128 original size:18 final size:18
Alignment explanation
Indices: 47269105--47269145 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
47269095 AAAATATATC
47269105 AACTAAAAATCAAATTTA
1 AACTAAAAATCAAATTTA
*
47269123 AACTAAAAATTAAATTTA
1 AACTAAAAATCAAATTTA
47269141 AACTA
1 AACTA
47269146 TTTATAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (18 bp):
AACTAAAAATCAAATTTA
Found at i:47270216 original size:17 final size:17
Alignment explanation
Indices: 47270194--47270237 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
47270184 TTAAATTATC
47270194 CATTAAATATTTAAATT
1 CATTAAATATTTAAATT
*
47270211 CATTAAATATTTATATT
1 CATTAAATATTTAAATT
* *
47270228 TAGTAAATAT
1 CATTAAATAT
47270238 AAAATATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (17 bp):
CATTAAATATTTAAATT
Found at i:47281608 original size:3 final size:3
Alignment explanation
Indices: 47281587--47281703 Score: 108
Period size: 3 Copynumber: 39.0 Consensus size: 3
47281577 TTTAAGATTT
* * * ** * * * * *
47281587 TTA TTA TTG TTA TTC TTA TTA TTA TTA ATA CCA TCA TCA TCA TCA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
47281635 TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA CCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
47281683 TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
47281704 AATTGTTTTA
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:47285228 original size:14 final size:14
Alignment explanation
Indices: 47285209--47285241 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
47285199 GCCATGTTTG
47285209 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
47285223 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
47285237 TTTGG
1 TTTGG
47285242 TTTTGGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:47285682 original size:44 final size:44
Alignment explanation
Indices: 47285569--47285682 Score: 104
Period size: 44 Copynumber: 2.6 Consensus size: 44
47285559 TGTCGGCTTT
* * * * * *
47285569 AATCTGTTCCATTACAACTTCAGGGAGATAAGATTTGCCATCTTC
1 AATCTGCTCCACTACTAC-TCAGGGAGATAAGATCTACAATCTTC
* * *
47285614 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
1 AATCTGCTCCACTACTACTCAGGGAGATAAGATCTACAATCTTC
* *
47285658 AA-CTTTCTCCACTGCTACTCAGGGA
1 AATC-TGCTCCACTACTACTCAGGGA
47285683 AACAAGGCTT
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.74
45 13 0.24
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTACTACTCAGGGAGATAAGATCTACAATCTTC
Found at i:47300816 original size:14 final size:14
Alignment explanation
Indices: 47300797--47300829 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
47300787 GCCATGTTTG
47300797 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
47300811 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
47300825 TTTGG
1 TTTGG
47300830 TTTTGGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:47306892 original size:25 final size:24
Alignment explanation
Indices: 47306864--47306925 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
47306854 AATAAAGATA
*
47306864 AAATATTTAAATCCAAATATTTTAC
1 AAATATTAAAAT-CAAATATTTTAC
** *
47306889 AAATTAAAAAAATCAAATATTTTGC
1 AAA-TATTAAAATCAAATATTTTAC
*
47306914 AAATATTCAAAT
1 AAATATTAAAAT
47306926 TTTACTCTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 6 0.21
25 17 0.59
26 6 0.21
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATTAAAATCAAATATTTTAC
Found at i:47311520 original size:7 final size:7
Alignment explanation
Indices: 47311508--47311534 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
47311498 ATTTCATATT
47311508 AATTTTA
1 AATTTTA
47311515 AATTTTA
1 AATTTTA
47311522 AATTTTA
1 AATTTTA
47311529 AATTTT
1 AATTTT
47311535 TTTTATAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:47316475 original size:19 final size:20
Alignment explanation
Indices: 47316439--47316476 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
47316429 TTTTTTTGAA
**
47316439 ATTTTTAAACTTTAATTAAT
1 ATTTTTAAAAGTTAATTAAT
47316459 ATTTTTAAAAGTT-ATTAA
1 ATTTTTAAAAGTTAATTAA
47316477 AAACATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTTTAAAAGTTAATTAAT
Found at i:47317715 original size:43 final size:43
Alignment explanation
Indices: 47317668--47317975 Score: 368
Period size: 43 Copynumber: 7.2 Consensus size: 43
47317658 TAAATAATGT
* *
47317668 CGCTAAAGATCATGACCTTTAGCGGCGCATTTCTCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGC
* * * *
47317711 CGCTAAAGACCAAGACCTTTAGCAGCGCTTTAAC-CACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTT-TCTCACAAACGC
** * * *
47317754 CATTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAATGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGC
* * *
47317797 CGCTAAAGACCAAGACCTTTAGCGGCGCTTTAAC-CACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTT-TCTCACAAACGC
* * *
47317840 CGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGC
* * *
47317883 CGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGC
* * *
47317926 CGCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAACGC
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGC
*
47317969 AGCTAAA
1 CGCTAAA
47317976 AATACAACTC
Statistics
Matches: 236, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
42 2 0.01
43 232 0.98
44 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (43 bp):
CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGC
Found at i:47317773 original size:86 final size:86
Alignment explanation
Indices: 47317668--47317975 Score: 427
Period size: 86 Copynumber: 3.6 Consensus size: 86
47317658 TAAATAATGT
* *
47317668 CGCTAAAGATCATGACCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
*
47317733 CAGCGCTTTAACCACAAACGC
66 CGGCGCTTTAACCACAAACGC
** * * *
47317754 CATTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAATGCCGCTAAAGACCAAGACCTTTAG
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
47317819 CGGCGCTTTAACCACAAACGC
66 CGGCGCTTTAACCACAAACGC
* * * * * * *
47317840 CGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACATGAGCTTTAG
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
**
47317905 CGGCGCTTTTCCCACAAACGC
66 CGGCGCTTTAACCACAAACGC
* * * *
47317926 CGCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAACGCAGCTAAA
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAA
47317976 AATACAACTC
Statistics
Matches: 194, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 194 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (86 bp):
CGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
CGGCGCTTTAACCACAAACGC
Found at i:47317989 original size:129 final size:128
Alignment explanation
Indices: 47317668--47318016 Score: 389
Period size: 129 Copynumber: 2.7 Consensus size: 128
47317658 TAAATAATGT
* * * *
47317668 CGCTAAAGATCATGACCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGACCAAGACCTTTAG
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAAC-AGACCTTTAG
* * * * *
47317733 CAGCGCTTTAACCACAAACGCCATTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAATGC
65 CGGCGCTTTAACCACAAACGCCACTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * * * *
47317797 CGCTAAAGACCAAGACCTTTAGCGGCGCTTTAACCACAAACGCCGCTATAGAACATGAGCTTTAG
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACA-GACCTTTAG
** * * * *
47317862 CGGCGCTTTTCCCACAAACGCCGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCACAAACGC
65 CGGCGCTTTAACCACAAACGCCACTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGC
* * * *
47317926 CGCTAAAGAACATGATCTTTAGCGACGCTTTTATCACAAACGCAGCTAAAAATACA-ACTCTTTA
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGA-ACAGAC-CTTTA
* *
47317990 GCGGCG-TTTATA-GAAAAACGCCACTAA
64 GCGGCGCTTTA-ACCACAAACGCCACTAA
47318017 TTTTAACAAA
Statistics
Matches: 180, Mismatches: 36, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
128 16 0.09
129 161 0.89
130 3 0.02
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (128 bp):
CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAACAGACCTTTAGC
GGCGCTTTAACCACAAACGCCACTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGC
Found at i:47318973 original size:40 final size:40
Alignment explanation
Indices: 47318910--47318993 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
47318900 TAGCTTGAAC
* * *
47318910 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
47318950 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
47318990 ATCA
1 ATCA
47318994 TGTATAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:47319175 original size:86 final size:88
Alignment explanation
Indices: 47319005--47319175 Score: 211
Period size: 88 Copynumber: 2.0 Consensus size: 88
47318995 GTATAATGTA
* * * * * * *
47319005 TTTACATGCAAAAAATTAGCAAAAATTAACAATTCATGTATAATGTATTTTACCAAAAACCGGAC
1 TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTTCACCAAAAACCAGAC
*
47319070 CAACTTGTCAATTTTTATAACAT
66 CAAATTGTCAATTTTTATAACAT
* * *
47319093 TTTAAATGCAACAAATTAACACAAATTAACAATACAAGT-TCATATA-TTCACCAAAAACCAGAC
1 TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTTCACCAAAAACCAGAC
* *
47319156 TAAATTTTCAATTTTTATAA
66 CAAATTGTCAATTTTTATAA
47319176 AATGAGAGGA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
86 32 0.46
87 5 0.07
88 33 0.47
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (88 bp):
TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTTCACCAAAAACCAGAC
CAAATTGTCAATTTTTATAACAT
Found at i:47323915 original size:21 final size:22
Alignment explanation
Indices: 47323878--47323918 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
47323868 CTAAATTAAC
*
47323878 TATATATATATACCCTAAACCA
1 TATATATATAAACCCTAAACCA
47323900 TATATAT-TAAACCCTAAAC
1 TATATATATAAACCCTAAAC
47323919 TATAATGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (22 bp):
TATATATATAAACCCTAAACCA
Found at i:47324232 original size:41 final size:41
Alignment explanation
Indices: 47324168--47324322 Score: 202
Period size: 41 Copynumber: 3.8 Consensus size: 41
47324158 TGTTTTTGCA
* * * ** * *
47324168 GCGCTTTTTCAAAAACACTGCTAAAGCCCTGAACATTAGTG
1 GCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCG
* ** *
47324209 GCGCTTCTTGGAAAACGCCGCTAAAGATCTGAGCACTAGCG
1 GCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCG
47324250 GCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCG
1 GCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCG
*
47324291 GCGCTTTTTTAAAAACGCCACTAAAGATCTGA
1 GCGCTTTTTTAAAAACGCCGCTAAAGATCTGA
47324323 AAGGTACAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCG
Found at i:47324397 original size:39 final size:40
Alignment explanation
Indices: 47324354--47324448 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 40
47324344 CGGCTTAGGT
*
47324354 TTTTTGCGGCGTTTTTCCAAAAAATGCCGCTAATGC-TAA
1 TTTTTGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTAA
* * * *
47324393 TTTTTAGCGGCG-CTTTCCTAGAAACGCCGCTAATGCTTGA
1 TTTTT-GCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTAA
*
47324433 TCTTTAGCGGCGTTTT
1 T-TTTTGCGGCGTTTT
47324449 ACGTAAAGCG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 25 0.56
40 15 0.33
41 5 0.11
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (40 bp):
TTTTTGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTAA
Found at i:47324397 original size:40 final size:41
Alignment explanation
Indices: 47324353--47324489 Score: 118
Period size: 40 Copynumber: 3.4 Consensus size: 41
47324343 TCGGCTTAGG
* *
47324353 TTTTTTGCGGCGTTTTTCCAAAAAATGCCGCTAATGC-TAA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTAA
* * * *
47324393 TTTTTAGCGGCG-CTTTCCTAGAAACGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTAA
* * ** * **
47324433 TCTTTAGCGGCG-TTTTACGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTAA
* *
47324473 TTTTTAGTGGCATTTTT
1 TTTTTAGCGGCGTTTTT
47324490 TGTCCAAACG
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 20 0.26
40 54 0.69
41 4 0.05
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTTAA
Found at i:47325968 original size:14 final size:14
Alignment explanation
Indices: 47325949--47325978 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47325939 TTAGAGAACT
47325949 AGATTATGCAATTA
1 AGATTATGCAATTA
47325963 AGATTATGCAATTA
1 AGATTATGCAATTA
47325977 AG
1 AG
47325979 CCCTGGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (14 bp):
AGATTATGCAATTA
Found at i:47331236 original size:108 final size:108
Alignment explanation
Indices: 47331034--47331250 Score: 373
Period size: 108 Copynumber: 2.0 Consensus size: 108
47331024 ACATTAGCAT
47331034 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
1 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
*
47331099 ACCATCAACAACCAAGGACTAGTTGAGAACTCCAAACCCGACA
66 ACCATCAACAACCAAGGACCAGTTGAGAACTCCAAACCCGACA
*
47331142 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGTCAAGG
1 TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
* * *
47331207 ACCATTAACAACCCAA-GACCAGTTTAGAACTCCAAACCTGACA
66 ACCATCAACAA-CCAAGGACCAGTTGAGAACTCCAAACCCGACA
47331250 T
1 T
47331251 AACACCAATA
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
108 99 0.96
109 4 0.04
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.18
Consensus pattern (108 bp):
TTGGCCAAAGCAACCTTCCACAAAGATCACCTCGTAAGAGATTTCAAGACTATCAGCAGCCAAGG
ACCATCAACAACCAAGGACCAGTTGAGAACTCCAAACCCGACA
Found at i:47337212 original size:12 final size:13
Alignment explanation
Indices: 47337190--47337220 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
47337180 GATATGAAAT
47337190 AAAAACAAAAAAA
1 AAAAACAAAAAAA
47337203 AAAAACAAAAAAA
1 AAAAACAAAAAAA
47337216 AAAAA
1 AAAAA
47337221 GGTTAGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAAAA
Found at i:47339575 original size:2 final size:2
Alignment explanation
Indices: 47339570--47339614 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
47339560 TTTGCTCAAT
* *
47339570 TC TC TC TT TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
47339612 TC T
1 TC T
47339615 TGCTGTAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:47340811 original size:15 final size:15
Alignment explanation
Indices: 47340764--47340811 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
47340754 AAAATATATA
47340764 TTTATATTATTTTAAT
1 TTTATA-TATTTTAAT
*
47340780 TTTATAT-TTAATAAT
1 TTTATATATT-TTAAT
*
47340795 TTTATATATTTTTAT
1 TTTATATATTTTAAT
47340810 TT
1 TT
47340812 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 2 0.07
15 17 0.63
16 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATATTTTAAT
Found at i:47344378 original size:44 final size:44
Alignment explanation
Indices: 47344325--47344420 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
47344315 ATATTACTTT
* * *
47344325 AATCCGCTCCACTACGACTTCAGGGAGATAGGATTATCAGCTCC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCAGCTCC
* ** * *
47344369 AATTTGCTCCACTGTAACTTCAGGGAGATAAGATTATCGGCTTC
1 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCAGCTCC
47344413 AATCTGCT
1 AATCTGCT
47344421 TCTTTACACT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTGCTCCACTACAACTTCAGGGAGATAAGATTATCAGCTCC
Found at i:47344591 original size:132 final size:132
Alignment explanation
Indices: 47344433--47344758 Score: 444
Period size: 132 Copynumber: 2.5 Consensus size: 132
47344423 TTTACACTTG
* * *
47344433 AAGATAAGATTTGCCGTC-TTGAATCTGCTCCGCTACTACTTAGGGAGACAAGATCTG-TAAT-T
1 AAGATAAGATTTGTCGTCTTTG-ATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGCT-ATCT
* * * *
47344495 TCCAACCTATTCCACTGCTGAC-CAGGGGGACAAGGCTCGGTGACTTAAATCTGCTTCCTACTAT
64 T-CAACCTACTCCACTGCTG-CTCAGGGAGACAAGGCTCGATGACTTAAATCTGCTTCCCACTAT
47344559 CCTGGA
127 CCTGGA
* *
47344565 AAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGGTCTGCTATCTTC
1 AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGCTATCTTC
** * * * *
47344630 AACCTACTCTGCTGCTGCTCAGGGAGACTAGGTTCGATGGCTTAAATCTGCTTCCCACTATCTTG
66 AACCTACTCCACTGCTGCTCAGGGAGACAAGGCTCGATGACTTAAATCTGCTTCCCACTATCCTG
47344695 GA
131 GA
*
47344697 AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTACTATC
1 AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGCTATC
47344759 CTTACTGATC
Statistics
Matches: 172, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
131 1 0.01
132 165 0.96
133 6 0.03
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (132 bp):
AAGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGCTATCTTC
AACCTACTCCACTGCTGCTCAGGGAGACAAGGCTCGATGACTTAAATCTGCTTCCCACTATCCTG
GA
Found at i:47344614 original size:44 final size:44
Alignment explanation
Indices: 47344566--47344750 Score: 112
Period size: 44 Copynumber: 4.2 Consensus size: 44
47344556 TATCCTGGAA
*
47344566 AGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * ** * *
47344610 AGATAAGGTCTG-CTATCTTCAACCTACTCTGCTGCTGCTCAGGG
1 AGATAAGATTTGTC-GTCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * *
47344654 AGACT-AGGTTCGAT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGA-TAAGATTTG-TCGTCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* *
47344698 AGATAAGATTTGTCGTCTTTGATCTGCTCCGCTACTGCTTAGGG
1 AGATAAGATTTGTCGTCTTTAATCTGCTCCACTACTGCTTAGGG
47344742 AGATAAGAT
1 AGATAAGAT
47344751 CTACTATCCT
Statistics
Matches: 99, Mismatches: 30, Indels: 24
0.65 0.20 0.16
Matches are distributed among these distances:
42 5 0.05
43 7 0.07
44 79 0.80
45 5 0.05
46 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (44 bp):
AGATAAGATTTGTCGTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:47345605 original size:17 final size:18
Alignment explanation
Indices: 47345585--47345622 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
47345575 TATTTTCAAG
* *
47345585 AATAACATATTCAATA-A
1 AATAAAATATGCAATACA
47345602 AATAAAATATGCAATACA
1 AATAAAATATGCAATACA
47345620 AAT
1 AAT
47345623 CAAGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAAAATATGCAATACA
Found at i:47353352 original size:25 final size:24
Alignment explanation
Indices: 47353314--47353368 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
47353304 TTCCTGATAT
* *
47353314 ATGGCTATCCGGAGCTTCCCGATTA
1 ATGGCTATCAGGAGCTACCCG-TTA
*
47353339 ATGGCTATTAGGAGCTACCCGTTA
1 ATGGCTATCAGGAGCTACCCGTTA
*
47353363 TTGGCT
1 ATGGCT
47353369 CGCATGAGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
ATGGCTATCAGGAGCTACCCGTTA
Found at i:47356720 original size:17 final size:17
Alignment explanation
Indices: 47356695--47356729 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47356685 TAGAATTGGG
* *
47356695 TTGAGAAAATTATTTAA
1 TTGAAAAAATAATTTAA
47356712 TTGAAAAAATAATTTAA
1 TTGAAAAAATAATTTAA
47356729 T
1 T
47356730 AAATAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (17 bp):
TTGAAAAAATAATTTAA
Found at i:47358459 original size:27 final size:25
Alignment explanation
Indices: 47358429--47358483 Score: 58
Period size: 27 Copynumber: 2.0 Consensus size: 25
47358419 TTTTATTATC
47358429 AAAG-TATGCTTTGTTTTTTTAACAAAA
1 AAAGATATGC-TT-TTTTTTTAA-AAAA
47358456 AAAGAATTATGCTTTTTTTTTAAAAAA
1 AAAG-A-TATGCTTTTTTTTTAAAAAA
47358483 A
1 A
47358484 TTTTAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
27 9 0.36
28 9 0.36
29 2 0.08
30 5 0.20
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (25 bp):
AAAGATATGCTTTTTTTTTAAAAAA
Found at i:47360968 original size:23 final size:23
Alignment explanation
Indices: 47360942--47360993 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
47360932 TGATTTTTAA
*
47360942 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
47360965 ATTTAGGATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
47360988 ATTTAG
1 ATTTAG
47360994 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:47360969 original size:13 final size:13
Alignment explanation
Indices: 47360951--47360993 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
47360941 AATTTTGAAT
47360951 TATTTAGTGATAA
1 TATTTAGTGATAA
47360964 TATTTAG-GAT--
1 TATTTAGTGATAA
47360974 TATTTAGTGATAA
1 TATTTAGTGATAA
47360987 TATTTAG
1 TATTTAG
47360994 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:47360994 original size:23 final size:23
Alignment explanation
Indices: 47360949--47360995 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
47360939 TAAATTTTGA
47360949 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
47360972 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
47360995 A
1 A
47360996 AAAATCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (23 bp):
ATTATTTAGTGATAATATTTAGG
Found at i:47368402 original size:18 final size:18
Alignment explanation
Indices: 47368379--47368416 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
47368369 ACCCAGGGAG
47368379 ACATGCTCGGTCGAATAA
1 ACATGCTCGGTCGAATAA
47368397 ACATGCTCGGTCGAATAA
1 ACATGCTCGGTCGAATAA
47368415 AC
1 AC
47368417 CCTCGATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (18 bp):
ACATGCTCGGTCGAATAA
Found at i:47375391 original size:17 final size:18
Alignment explanation
Indices: 47375361--47375397 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
47375351 GTTTGAAAAA
47375361 AATAAAATATATATAAAT
1 AATAAAATATATATAAAT
47375379 AATAAAA-ATATATAAAT
1 AATAAAATATATATAAAT
47375396 AA
1 AA
47375398 AAGTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATATATATAAAT
Found at i:47381159 original size:10 final size:10
Alignment explanation
Indices: 47381141--47381311 Score: 81
Period size: 10 Copynumber: 16.8 Consensus size: 10
47381131 CCCATTTTTT
*
47381141 TTTTTAAAAA
1 TTTTAAAAAA
47381151 TTTTAAAAAA
1 TTTTAAAAAA
*
47381161 TTTAAAAAAA
1 TTTTAAAAAA
*
47381171 TTTTTTAAAAAT
1 --TTTTAAAAAA
**
47381183 TTTTTTAAAA
1 TTTTAAAAAA
*
47381193 TTTAAAAAAA
1 TTTTAAAAAA
**
47381203 TTAAAAAAAAGTA
1 TT-TTAAAAA--A
47381216 TTTTAAAAATA
1 TTTTAAAAA-A
47381227 TTTT--AAAA
1 TTTTAAAAAA
47381235 -TTTAAAAAA
1 TTTTAAAAAA
*
47381244 -TTAAAAAAGTA
1 TTTTAAAAA--A
47381255 TTTTAAAAATA
1 TTTTAAAAA-A
47381266 TTTT-AAAAA
1 TTTTAAAAAA
47381275 ---TAAAAAA
1 TTTTAAAAAA
*
47381282 -TTAAAAAAGTA
1 TTTTAAAAA--A
47381293 TTTTAAAAATA
1 TTTTAAAAA-A
47381304 TTTTAAAA
1 TTTTAAAA
47381312 TTAAAAAAAT
Statistics
Matches: 128, Mismatches: 17, Indels: 31
0.73 0.10 0.18
Matches are distributed among these distances:
6 1 0.01
7 8 0.06
8 1 0.01
9 20 0.16
10 38 0.30
11 30 0.23
12 27 0.21
13 3 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:47381160 original size:11 final size:11
Alignment explanation
Indices: 47381146--47381311 Score: 73
Period size: 11 Copynumber: 15.2 Consensus size: 11
47381136 TTTTTTTTTT
47381146 AAAAATTTT-A
1 AAAAATTTTAA
47381156 AAAAA-TTTAA
1 AAAAATTTTAA
**
47381166 AAAAATTTTTT
1 AAAAATTTTAA
**
47381177 AAAAATTTTTT
1 AAAAATTTTAA
*
47381188 TAAAA-TTTAA
1 AAAAATTTTAA
**
47381198 AAAAATTAAAA
1 AAAAATTTTAA
47381209 AAAAGTATTTTAA
1 AAAA--ATTTTAA
*
47381222 AAATATTTT--
1 AAAAATTTTAA
47381231 -AAAA-TTT-A
1 AAAAATTTTAA
47381239 AAAAA--TTAA
1 AAAAATTTTAA
47381248 AAAAGTATTTTAA
1 AAAA--ATTTTAA
*
47381261 AAATATTTTAAAA
1 AAAAATTTT--AA
**
47381274 ATAAAAAATTAA
1 A-AAAATTTTAA
47381286 AAAAGTATTTTAA
1 AAAA--ATTTTAA
*
47381299 AAATATTTTAA
1 AAAAATTTTAA
47381310 AA
1 AA
47381312 TTAAAAAAAT
Statistics
Matches: 120, Mismatches: 19, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
7 3 0.03
8 5 0.04
9 12 0.10
10 18 0.15
11 48 0.40
12 3 0.03
13 26 0.22
14 5 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:47381193 original size:32 final size:31
Alignment explanation
Indices: 47381140--47381204 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
47381130 GCCCATTTTT
47381140 TTTTTTAAAAATTTTAAAAAATTTAAAAAAA
1 TTTTTTAAAAATTTTAAAAAATTTAAAAAAA
**
47381171 TTTTTTAAAAATTTTTTTAAAATTTAAAAAAA
1 TTTTTTAAAAA-TTTTAAAAAATTTAAAAAAA
47381203 TT
1 TT
47381205 AAAAAAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTTTTAAAAATTTTAAAAAATTTAAAAAAA
Found at i:47381279 original size:38 final size:39
Alignment explanation
Indices: 47381142--47381355 Score: 251
Period size: 38 Copynumber: 5.5 Consensus size: 39
47381132 CCATTTTTTT
* * *
47381142 TTTTAAAAATTTTAAAAAATTTAAAAAAATTTTTTAAAAATTT
1 TTTT-AAAA-TTTAAAAAA-TTAAAAAAGTATTTTAAAAA-TA
47381185 TTTTAAAATTTAAAAAAATTAAAAAAAAGTATTTTAAAAATA
1 TTTTAAAATTT-AAAAAATT--AAAAAAGTATTTTAAAAATA
47381227 TTTTAAAATTTAAAAAATTAAAAAAGTATTTTAAAAATA
1 TTTTAAAATTTAAAAAATTAAAAAAGTATTTTAAAAATA
*
47381266 TTTTAAAA-ATAAAAAATTAAAAAAGTATTTTAAAAATA
1 TTTTAAAATTTAAAAAATTAAAAAAGTATTTTAAAAATA
* * *
47381304 TTTTAAAATTAAAAAAATT----AA-TATGTAAAAAATA
1 TTTTAAAATTTAAAAAATTAAAAAAGTATTTTAAAAATA
*
47381338 TTTTAAAATTAAAAAAAT
1 TTTTAAAATTTAAAAAAT
47381356 AAATATATTT
Statistics
Matches: 159, Mismatches: 8, Indels: 17
0.86 0.04 0.09
Matches are distributed among these distances:
34 29 0.18
35 2 0.01
38 37 0.23
39 36 0.23
41 13 0.08
42 22 0.14
43 20 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (39 bp):
TTTTAAAATTTAAAAAATTAAAAAAGTATTTTAAAAATA
Found at i:47381317 original size:17 final size:17
Alignment explanation
Indices: 47381295--47381352 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
47381285 AAAAAGTATT
47381295 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
47381312 TTAAAAA-A-ATTAATA
1 TTAAAAATATTTTAAAA
47381327 TGTAAAAAATATTTTAAAA
1 T-T-AAAAATATTTTAAAA
47381346 TTAAAAA
1 TTAAAAA
47381353 AATAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 6 0.18
16 2 0.06
17 17 0.52
18 2 0.06
19 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:47381355 original size:34 final size:34
Alignment explanation
Indices: 47381297--47381361 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
47381287 AAAGTATTTT
*
47381297 AAAAATATTTTAAAATTAAAAAAATTAATATGTA
1 AAAAATATTTTAAAATTAAAAAAATAAATATGTA
47381331 AAAAATATTTTAAAATTAAAAAAATAAATAT
1 AAAAATATTTTAAAATTAAAAAAATAAATAT
47381362 ATTTATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (34 bp):
AAAAATATTTTAAAATTAAAAAAATAAATATGTA
Found at i:47386731 original size:55 final size:56
Alignment explanation
Indices: 47386670--47386940 Score: 273
Period size: 55 Copynumber: 4.9 Consensus size: 56
47386660 CACATGCTTA
* * * *
47386670 ATTATGATATGTGCA-TAATGAAACTAGTAAGCATGATTATATACATGCATACCCT
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
* * * * * *
47386725 ATTATGATATGTGCA-GAATAAAACTAGTGAGCATGACTATGTACATGCATGCTCA
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
* * *
47386780 ATTTTTATATGTGCACT-ATGAAACTAGTAAGCATCACTATGTACATGCATGCTCT
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
* * * * * *
47386835 ATTTTGATATGTGCACTTA-GAAACTAATGATCATCACTATGTACATGCATGCCTT
1 ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
* * *
47386890 ATTATGATATTTGCACTATAT-ACATGTCTAGTGAGCATCACTATGTACATG
1 ATTATGATATGTGCACTA-ATGA-A--ACTAGTAAGCATCACTATGTACATG
47386941 GTTGTTACAT
Statistics
Matches: 182, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
55 156 0.86
56 3 0.02
57 1 0.01
59 22 0.12
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (56 bp):
ATTATGATATGTGCACTAATGAAACTAGTAAGCATCACTATGTACATGCATGCCCT
Found at i:47386905 original size:110 final size:109
Alignment explanation
Indices: 47386662--47386940 Score: 303
Period size: 110 Copynumber: 2.5 Consensus size: 109
47386652 TATTAATGCA
* * *
47386662 CATGCTTAATTATGATATGTGCA-TAATGAAACTAGTAAGCATGATTATATACATGCATACCCTA
1 CATGCTT-ATTATGATATGTGCACT-ATGAAACTAGTAAGCATCACTATGTACATGCATACCCTA
* *
47386726 TTATGATATGTGCAGAATAAAACTAGTGAGCATGACTATGTACATG
64 TTATGATATGTGCAGAATAAAACTAATGAGCATCACTATGTACATG
* * * * *
47386772 CATGCTCAATTTTTATATGTGCACTATGAAACTAGTAAGCATCACTATGTACATGCATGCTCTAT
1 CATGCT-TATTATGATATGTGCACTATGAAACTAGTAAGCATCACTATGTACATGCATACCCTAT
* ** *
47386837 TTTGATATGTGCA-CTTAGAAACTAATGATCATCACTATGTACATG
65 TATGATATGTGCAGAATA-AAACTAATGAGCATCACTATGTACATG
* *
47386882 CATGCCTTATTATGATATTTGCACTAT-ATACATGTCTAGTGAGCATCACTATGTACATG
1 CATG-CTTATTATGATATGTGCACTATGA-A-A---CTAGTAAGCATCACTATGTACATG
47386941 GTTGTTACAT
Statistics
Matches: 141, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
109 3 0.02
110 111 0.79
111 4 0.03
114 23 0.16
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (109 bp):
CATGCTTATTATGATATGTGCACTATGAAACTAGTAAGCATCACTATGTACATGCATACCCTATT
ATGATATGTGCAGAATAAAACTAATGAGCATCACTATGTACATG
Found at i:47390457 original size:250 final size:250
Alignment explanation
Indices: 47390016--47390518 Score: 988
Period size: 250 Copynumber: 2.0 Consensus size: 250
47390006 GGCTGCTCAA
47390016 GTGCCATTGACGGCGGATCATGTACACGGTGGTCGCACTTCTATTGGTGGCCGAGGGAGAGGTTT
1 GTGCCATTGACGGCGGATCATGTACACGGTGGTCGCACTTCTATTGGTGGCCGAGGGAGAGGTTT
47390081 TTGCCTACGTGTTCAGTGTCAGATTTGTGGAAGATTTGGCCACGTGGCTCAACAGTGTTTTTACC
66 TTGCCTACGTGTTCAGTGTCAGATTTGTGGAAGATTTGGCCACGTGGCTCAACAGTGTTTTTACC
47390146 ATTTTAATCGCGTATATGATAGTTCTCCTTCGGTGACGACTCTGGAGCCAGTGGCCGGTGTTGCT
131 ATTTTAATCGCGTATATGATAGTTCTCCTTCGGTGACGACTCTGGAGCCAGTGGCCGGTGTTGCT
47390211 TGCGACTCGACTGCGGGGTTTGGTGTACCTACGGTGAGTAATGATGGCGGTCCTG
196 TGCGACTCGACTGCGGGGTTTGGTGTACCTACGGTGAGTAATGATGGCGGTCCTG
47390266 GTGCCATTGACGGCGGATCATGTACACGGTGGTCGCACTTCTATTGGTGGCCGAGGGAGAGGTTT
1 GTGCCATTGACGGCGGATCATGTACACGGTGGTCGCACTTCTATTGGTGGCCGAGGGAGAGGTTT
*
47390331 TTGCCTACGTGTTCAGTGTCAGATTTGTGGAAGATTTGGCCACGTGGCTCAACATTGTTTTTACC
66 TTGCCTACGTGTTCAGTGTCAGATTTGTGGAAGATTTGGCCACGTGGCTCAACAGTGTTTTTACC
*
47390396 GTTTTAATCGCGTATATGATAGTTCTCCTTCGGTGACGACTCTGGAGCCAGTGGCCGGTGTTGCT
131 ATTTTAATCGCGTATATGATAGTTCTCCTTCGGTGACGACTCTGGAGCCAGTGGCCGGTGTTGCT
47390461 TGCGACTCGACTGCGGGGTTTGGTGTACCTACGGTGAGTAATGATGGCGGTCCTG
196 TGCGACTCGACTGCGGGGTTTGGTGTACCTACGGTGAGTAATGATGGCGGTCCTG
47390516 GTG
1 GTG
47390519 TCTTCATTTT
Statistics
Matches: 251, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
250 251 1.00
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.31
Consensus pattern (250 bp):
GTGCCATTGACGGCGGATCATGTACACGGTGGTCGCACTTCTATTGGTGGCCGAGGGAGAGGTTT
TTGCCTACGTGTTCAGTGTCAGATTTGTGGAAGATTTGGCCACGTGGCTCAACAGTGTTTTTACC
ATTTTAATCGCGTATATGATAGTTCTCCTTCGGTGACGACTCTGGAGCCAGTGGCCGGTGTTGCT
TGCGACTCGACTGCGGGGTTTGGTGTACCTACGGTGAGTAATGATGGCGGTCCTG
Found at i:47398220 original size:23 final size:23
Alignment explanation
Indices: 47398190--47398271 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 23
47398180 CAGCTCGTAT
*
47398190 GAGCTTACCGTTTCAGGTT-TATA
1 GAGCTTACCGTTTCA-GTTCGATA
*
47398213 GAGCTTACCGTTTTAGTTCGATA
1 GAGCTTACCGTTTCAGTTCGATA
* *
47398236 GAGCTTACCGTTTATCAGCTCGAAAA
1 GAGCTTACCG-TT-TCAGTTCG-ATA
47398262 GAGCTTACCG
1 GAGCTTACCG
47398272 ATCATGGCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.06
23 27 0.54
24 2 0.04
25 6 0.12
26 12 0.24
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGTTCGATA
Found at i:47398271 original size:26 final size:23
Alignment explanation
Indices: 47398212--47398289 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
47398202 TCAGGTTTAT
* *
47398212 AGAGCTTACCGTTTTAGTTCGAT
1 AGAGCTTACCGTTTTAGCTCGAA
47398235 AGAGCTTACCGTTTATCAGCTCGAAA
1 AGAGCTTACCGTTT-T-AGCTCG-AA
** *
47398261 AGAGCTTACCGATCATGGCTCGAA
1 AGAGCTTACCG-TTTTAGCTCGAA
47398285 AGAGC
1 AGAGC
47398290 AGAAATGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 14 0.30
24 8 0.17
25 10 0.22
26 13 0.28
27 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (23 bp):
AGAGCTTACCGTTTTAGCTCGAA
Found at i:47398281 original size:25 final size:25
Alignment explanation
Indices: 47398230--47398289 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
47398220 CCGTTTTAGT
* * *
47398230 TCGATAGAGCTTACCGTTTATCAGC
1 TCGAAAGAGCTTACCGATCATCAGC
*
47398255 TCGAAAAGAGCTTACCGATCAT-GGC
1 TCG-AAAGAGCTTACCGATCATCAGC
47398280 TCGAAAGAGC
1 TCGAAAGAGC
47398290 AGAAATGACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.23
25 8 0.27
26 15 0.50
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (25 bp):
TCGAAAGAGCTTACCGATCATCAGC
Found at i:47399107 original size:11 final size:11
Alignment explanation
Indices: 47399081--47399107 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
47399071 TTAAAAAAAT
47399081 AAAATTATTTA
1 AAAATTATTTA
47399092 AAAATTATTTA
1 AAAATTATTTA
47399103 AAAAT
1 AAAAT
47399108 AGGGATTTAA
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):
AAAATTATTTA
Found at i:47399148 original size:51 final size:51
Alignment explanation
Indices: 47399104--47399203 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
47399094 AATTATTTAA
47399104 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * *
47399155 AAATATGGATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
47399204 GGAAATTGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:47399188 original size:22 final size:23
Alignment explanation
Indices: 47399163--47399231 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 23
47399153 TTAAATATGG
47399163 ATTTGAGAGAAATTTGGA-AGGA
1 ATTTGAGAGAAATTTGGAGAGGA
47399185 ATTTGAGAGCAAA-TT-GAGAGGA
1 ATTTGAGAG-AAATTTGGAGAGGA
*
47399207 AATTGAGAGGAAATTTGAGAGAGGA
1 ATTTGAGA-GAAATTTG-GAGAGGA
47399232 TTAGTTTGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 2 0.05
22 25 0.62
23 6 0.15
25 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.33, T:0.23
Consensus pattern (23 bp):
ATTTGAGAGAAATTTGGAGAGGA
Found at i:47399231 original size:14 final size:11
Alignment explanation
Indices: 47399128--47399227 Score: 68
Period size: 11 Copynumber: 9.4 Consensus size: 11
47399118 GAGAAATTTA
47399128 AGAGGAAATTG
1 AGAGGAAATTG
*
47399139 AGAGCAAATTG
1 AGAGGAAATTG
**
47399150 AGATTAAA-T-
1 AGAGGAAATTG
* *
47399159 A-TGG-ATTTG
1 AGAGGAAATTG
47399168 AGA-GAAATTTG
1 AGAGGAAA-TTG
*
47399179 -GAAGGAATTTG
1 AG-AGGAAATTG
*
47399190 AGAGCAAATTG
1 AGAGGAAATTG
47399201 AGAGGAAATTG
1 AGAGGAAATTG
47399212 AGAGGAAATTTG
1 AGAGGAAA-TTG
47399224 AGAG
1 AGAG
47399228 AGGATTAGTT
Statistics
Matches: 67, Mismatches: 13, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 3 0.04
10 3 0.04
11 48 0.72
12 11 0.16
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:47400304 original size:18 final size:19
Alignment explanation
Indices: 47400283--47400325 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
47400273 AATGTTTTTA
* *
47400283 AAAAAATTA-TAAATCTGT
1 AAAAAATTATTAAATATAT
*
47400301 AAAATATTATTAAATATAT
1 AAAAAATTATTAAATATAT
47400320 AAAAAA
1 AAAAAA
47400326 ATTTAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAAATTATTAAATATAT
Found at i:47400701 original size:21 final size:21
Alignment explanation
Indices: 47400664--47400756 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 21
47400654 TTTATTAATT
*
47400664 TTTAATATTTTT-GAAATTTA
1 TTTAATATTTTTAAAAATTTA
*
47400684 TTTAATATTTTTATAAATTTA
1 TTTAATATTTTTAAAAATTTA
**
47400705 AATAAT-TTTTTAAAAATTTA
1 TTTAATATTTTTAAAAATTTA
**
47400725 --T-A-ATTTTTAAAAAAATA
1 TTTAATATTTTTAAAAATTTA
*
47400742 TTAAAT-TTTTTAAAA
1 TTTAATATTTTTAAAA
47400757 TAATATTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
17 13 0.22
18 1 0.02
20 35 0.58
21 11 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
TTTAATATTTTTAAAAATTTA
Found at i:47400724 original size:37 final size:35
Alignment explanation
Indices: 47400683--47400773 Score: 82
Period size: 37 Copynumber: 2.6 Consensus size: 35
47400673 TTTGAAATTT
47400683 ATTTAATATTTTTATAAATTTAA-ATAATTTTTTAAAA
1 ATTTAATATTTTTA-AAATTTAATA-AATTTTTT-AAA
** *
47400720 ATTT-ATAATTTTTAAAAAAATATTAAATTTTTTAAA
1 ATTTAAT-ATTTTT-AAAATTTAATAAATTTTTTAAA
47400756 A--TAATATTTTTAAAATTT
1 ATTTAATATTTTTAAAATTT
47400774 TTTAAAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
33 5 0.11
34 7 0.16
35 2 0.04
36 6 0.13
37 23 0.51
38 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
ATTTAATATTTTTAAAATTTAATAAATTTTTTAAA
Found at i:47400738 original size:19 final size:20
Alignment explanation
Indices: 47400706--47400763 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
47400696 ATAAATTTAA
*
47400706 ATAATTTTT-TAAAAAT-TT
1 ATAATTTTTAAAAAAATATT
47400724 ATAATTTTTAAAAAAATATT
1 ATAATTTTTAAAAAAATATT
*
47400744 A-AATTTTTTAAAATAATATT
1 ATAA-TTTTTAAAAAAATATT
47400764 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.26
19 8 0.23
20 18 0.51
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTTTAAAAAAATATT
Found at i:47400761 original size:20 final size:20
Alignment explanation
Indices: 47400706--47400763 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
47400696 ATAAATTTAA
47400706 ATAATTTTTT-AAAAAT-TT
1 ATAATTTTTTAAAAAATATT
*
47400724 ATAATTTTTAAAAAAATATT
1 ATAATTTTTTAAAAAATATT
47400744 A-AATTTTTTAAAATAATATT
1 ATAATTTTTTAAAA-AATATT
47400764 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.26
19 17 0.49
20 9 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTTTTAAAAAATATT
Found at i:47401765 original size:25 final size:24
Alignment explanation
Indices: 47401728--47401774 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
47401718 TAGATTTTTT
47401728 TTTTATGTATAATG-ATGTAGATAA
1 TTTTATGTATAATGTATG-AGATAA
*
47401752 TTTTATTGTTTAATGTATGAGAT
1 TTTTA-TGTATAATGTATGAGAT
47401775 GATGGTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 12 0.60
26 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
TTTTATGTATAATGTATGAGATAA
Found at i:47407556 original size:16 final size:17
Alignment explanation
Indices: 47407535--47407566 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47407525 AACTATGCAA
47407535 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
47407551 TCACATAACTTCATAT
1 TCACATAACTTCATAT
47407567 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:47407871 original size:84 final size:84
Alignment explanation
Indices: 47407727--47407885 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 84
47407717 GACTAGTACA
* * *
47407727 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGACAGGGT
47407792 CTTACACAAATCAAATACG
66 CTTACACAAATCAAATACG
* * *
47407811 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACA-AGTCGATGCCAAC-GTCCTAGACATG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATA-TCGATGCC-ACTGTCCCAGACAGG
47407874 GTCTTACACAAA
64 GTCTTACACAAA
47407886 AACACATATC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 1 0.01
84 64 0.96
85 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCGATGCCACTGTCCCAGACAGGGT
CTTACACAAATCAAATACG
Found at i:47407882 original size:43 final size:42
Alignment explanation
Indices: 47407727--47407897 Score: 188
Period size: 43 Copynumber: 4.0 Consensus size: 42
47407717 GACTAGTACA
* * *
47407727 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACA-ATCG
*
47407770 ATGCC-ACTGTCCCAGACAGGGTCTTACAC--AAATCA-AATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAA-CACAAT-CG
*
47407811 ATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAGTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAA-TCG
* **
47407854 ATGCCAACGTCCTAGACATGGTCTTACACAAAAACACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACA-ATCG
47407897 A
1 A
47407898 AATCCTATGT
Statistics
Matches: 109, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
40 2 0.02
41 30 0.28
42 7 0.06
43 68 0.62
44 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAATCG
Found at i:47414923 original size:22 final size:24
Alignment explanation
Indices: 47414895--47414957 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 24
47414885 CATCCTGCTA
47414895 TTTTTTTTACTATTTT-TTGTTG-
1 TTTTTTTTACTATTTTCTTGTTGC
*
47414917 -TTTTTTTATTATTTTCTTGTTGC
1 TTTTTTTTACTATTTTCTTGTTGC
47414940 TGTTTTTTTCACTATTTT
1 T-TTTTTTT-ACTATTTT
47414958 ACTACCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 14 0.41
22 6 0.18
25 7 0.21
26 7 0.21
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.75
Consensus pattern (24 bp):
TTTTTTTTACTATTTTCTTGTTGC
Found at i:47418753 original size:9 final size:9
Alignment explanation
Indices: 47418699--47418876 Score: 57
Period size: 9 Copynumber: 19.2 Consensus size: 9
47418689 TATTAGTACG
47418699 ATAATTTTT
1 ATAATTTTT
47418708 ATATATTTTTT
1 ATA-A-TTTTT
47418719 ATGAA-TTTT
1 AT-AATTTTT
47418728 AT-ATTTCTT
1 ATAATTT-TT
*
47418737 -TCATTTTTT
1 AT-AATTTTT
47418746 ATAATTTTCT
1 ATAATTTT-T
**
47418756 -TACAACTTT
1 ATA-ATTTTT
*
47418765 ATAAAATTTT
1 AT-AATTTTT
47418775 ATAATTTTT
1 ATAATTTTT
**
47418784 ACCATTTTT
1 ATAATTTTT
* *
47418793 CTAATTTTAA
1 ATAATTTT-T
**
47418803 ATAAAATTT
1 ATAATTTTT
*
47418812 A-AATATTT
1 ATAATTTTT
*
47418820 A-GATATTTT
1 ATAAT-TTTT
47418829 AT-ATTTTT
1 ATAATTTTT
*
47418837 ATTAATATTT
1 A-TAATTTTT
47418847 A-ATATTTTT
1 ATA-ATTTTT
*
47418856 ATAATATTT
1 ATAATTTTT
47418865 ATTAATTTTT
1 A-TAATTTTT
47418875 AT
1 AT
47418877 TTTTATCATT
Statistics
Matches: 126, Mismatches: 23, Indels: 40
0.67 0.12 0.21
Matches are distributed among these distances:
7 1 0.01
8 18 0.14
9 60 0.48
10 37 0.29
11 9 0.07
12 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:47418784 original size:19 final size:19
Alignment explanation
Indices: 47418762--47418876 Score: 55
Period size: 19 Copynumber: 6.3 Consensus size: 19
47418752 TTCTTACAAC
47418762 TTTATAAAATTTTATAATT
1 TTTATAAAATTTTATAATT
** * *
47418781 TTTA-CCATTTTTCTAATT
1 TTTATAAAATTTTATAATT
* *
47418799 TTAAATAAAA-TTTA-AATA
1 TT-TATAAAATTTTATAATT
* *
47418817 TTTA-GATATTTTAT-ATT
1 TTTATAAAATTTTATAATT
* *
47418834 TTTATTAATATTTAAT-ATT
1 TTTA-TAAAATTTTATAATT
*
47418853 TTTATAATA-TTTATTAATT
1 TTTATAAAATTTTA-TAATT
47418872 TTTAT
1 TTTAT
47418877 TTTTATCATT
Statistics
Matches: 71, Mismatches: 17, Indels: 16
0.68 0.16 0.15
Matches are distributed among these distances:
16 2 0.03
17 14 0.20
18 23 0.32
19 31 0.44
20 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTATAAAATTTTATAATT
Found at i:47418841 original size:28 final size:29
Alignment explanation
Indices: 47418810--47418869 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 29
47418800 TAAATAAAAT
*
47418810 TTAAATATTTAGATA-TTTTAT-ATTTTTA
1 TTAAATATTTA-ATATTTTTATAATATTTA
47418838 TT-AATATTTAATATTTTTATAATATTTA
1 TTAAATATTTAATATTTTTATAATATTTA
47418866 TTAA
1 TTAA
47418870 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.11
27 14 0.50
28 10 0.36
29 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTAAATATTTAATATTTTTATAATATTTA
Found at i:47418854 original size:18 final size:19
Alignment explanation
Indices: 47418822--47418876 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
47418812 AAATATTTAG
*
47418822 ATATTTTATA-TTTTTATTA
1 ATATTTAATATTTTTTA-TA
47418841 ATATTTAATA-TTTTTATA
1 ATATTTAATATTTTTTATA
* *
47418859 ATATTTATTAATTTTTAT
1 ATATTTAATATTTTTTAT
47418877 TTTTATCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATATTTAATATTTTTTATA
Found at i:47421058 original size:11 final size:10
Alignment explanation
Indices: 47421034--47421070 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
47421024 AGTAAGTCTG
*
47421034 AAAAATATTC
1 AAAAAAATTC
47421044 AAAAAAATTC
1 AAAAAAATTC
*
47421054 AAAAAAATTT
1 AAAAAAATTC
47421064 AAAAAAA
1 AAAAAAA
47421071 ATTCGTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:47421071 original size:11 final size:11
Alignment explanation
Indices: 47421034--47421073 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
47421024 AGTAAGTCTG
47421034 AAAAATATTCAA
1 AAAAAT-TTCAA
47421046 AAAAA-TTCAA
1 AAAAATTTCAA
*
47421056 AAAAATTTAAA
1 AAAAATTTCAA
47421067 AAAAATT
1 AAAAATT
47421074 CGTGAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.38
11 11 0.42
12 5 0.19
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
AAAAATTTCAA
Found at i:47421071 original size:21 final size:22
Alignment explanation
Indices: 47421034--47421074 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
47421024 AGTAAGTCTG
*
47421034 AAAAATATTCAAAAAAATTCAA
1 AAAAATATTAAAAAAAATTCAA
47421056 AAAAAT-TTAAAAAAAATTC
1 AAAAATATTAAAAAAAATTC
47421075 GTGAAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAATATTAAAAAAAATTCAA
Found at i:47422238 original size:18 final size:18
Alignment explanation
Indices: 47422217--47422279 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
47422207 AGATTGAGAA
*
47422217 TGAAAAAGAAAGAGAGTT
1 TGAAAAAGAAAAAGAGTT
**
47422235 TG-AAAAGAAATCGAG--
1 TGAAAAAGAAAAAGAGTT
47422250 TGAAAAAAGAAAAAGAGTT
1 TG-AAAAAGAAAAAGAGTT
*
47422269 TGCAAAAGAAA
1 TGAAAAAGAAA
47422280 CGAGTGAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
15 2 0.06
17 22 0.61
18 10 0.28
19 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.24, T:0.14
Consensus pattern (18 bp):
TGAAAAAGAAAAAGAGTT
Found at i:47422241 original size:35 final size:35
Alignment explanation
Indices: 47422219--47422292 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 35
47422209 ATTGAGAATG
*
47422219 AAAAAGAAAGAGAGTTTG-AAAAGAAATCGAGTGA
1 AAAAAGAAAAAGAGTTTGCAAAAGAAATCGAGTGA
47422253 AAAAAGAAAAAGAGTTTGCAAAAGAAA-CGAGTGA
1 AAAAAGAAAAAGAGTTTGCAAAAGAAATCGAGTGA
*
47422287 AGAAAG
1 AAAAAG
47422293 CAATCAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 29 0.78
35 8 0.22
ACGTcount: A:0.58, C:0.04, G:0.26, T:0.12
Consensus pattern (35 bp):
AAAAAGAAAAAGAGTTTGCAAAAGAAATCGAGTGA
Found at i:47441576 original size:2 final size:2
Alignment explanation
Indices: 47441569--47441628 Score: 54
Period size: 2 Copynumber: 31.0 Consensus size: 2
47441559 CAAATTCAAG
* * * *
47441569 TA TA TA TA TA CA TA TA GA TA CA TA TA TA -A T- TA TT TGA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
47441609 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
47441629 CCTTTATACC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:47448731 original size:41 final size:41
Alignment explanation
Indices: 47448671--47448761 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
47448661 ACCAGCACTT
*
47448671 AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCATTA
1 AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCAATA
* * *
47448712 AGCCTGCTAGACATTTAGTCTGAAGTGTTTCACCGGCAATA
1 AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCAATA
47448753 AGCCTGCTA
1 AGCCTGCTA
47448762 AGCGCTAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCAATA
Found at i:47448776 original size:41 final size:41
Alignment explanation
Indices: 47448671--47448776 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
47448661 ACCAGCACTT
* * * *
47448671 AGCCTGCTAGACA-TATAGTCTGAAATATTTCACCGGCATTA
1 AGCCTGCTAGACACTA-AGCCTGAAGTGTTTCACCGGCAATA
* * *
47448712 AGCCTGCTAGACATTTAGTCTGAAGTGTTTCACCGGCAATA
1 AGCCTGCTAGACACTAAGCCTGAAGTGTTTCACCGGCAATA
*
47448753 AGCCTGCTA-AGCGCTAAGCCTGAA
1 AGCCTGCTAGA-CACTAAGCCTGAA
47448777 AATCTCAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 53 0.96
42 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACACTAAGCCTGAAGTGTTTCACCGGCAATA
Found at i:47449173 original size:2 final size:2
Alignment explanation
Indices: 47449166--47449233 Score: 70
Period size: 2 Copynumber: 35.0 Consensus size: 2
47449156 CAAATTCAAG
* * * *
47449166 TA TA TA TA TA CA TA TA GA TA CA TA TA TA -A T- TA TT TGA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
47449206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47449234 CCTTTATACC
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:47450402 original size:13 final size:13
Alignment explanation
Indices: 47450384--47450408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47450374 CAATCAAATG
47450384 CACACAAAATAAA
1 CACACAAAATAAA
47450397 CACACAAAATAA
1 CACACAAAATAA
47450409 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:47456395 original size:41 final size:41
Alignment explanation
Indices: 47456350--47456440 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
47456340 ACCAGCACTT
*
47456350 AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCATTA
1 AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCAATA
* * *
47456391 AGCCTGCTAGACATTTAGTCTGAAGTGTTTCACCGGCAATA
1 AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCAATA
47456432 AGCCTGCTA
1 AGCCTGCTA
47456441 AGCGCTAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATATAGTCTGAAATATTTCACCGGCAATA
Found at i:47456455 original size:41 final size:41
Alignment explanation
Indices: 47456350--47456455 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
47456340 ACCAGCACTT
* * * *
47456350 AGCCTGCTAGACA-TATAGTCTGAAATATTTCACCGGCATTA
1 AGCCTGCTAGACACTA-AGCCTGAAGTGTTTCACCGGCAATA
* * *
47456391 AGCCTGCTAGACATTTAGTCTGAAGTGTTTCACCGGCAATA
1 AGCCTGCTAGACACTAAGCCTGAAGTGTTTCACCGGCAATA
*
47456432 AGCCTGCTA-AGCGCTAAGCCTGAA
1 AGCCTGCTAGA-CACTAAGCCTGAA
47456456 AATCTCAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 53 0.96
42 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACACTAAGCCTGAAGTGTTTCACCGGCAATA
Found at i:47456848 original size:2 final size:2
Alignment explanation
Indices: 47456841--47456900 Score: 54
Period size: 2 Copynumber: 31.0 Consensus size: 2
47456831 CAAATTCAAG
* * * *
47456841 TA TA TA TA TA CA TA TA GA TA CA TA TA TA -A T- TA TT TGA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
47456881 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
47456901 CCTTTATACC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:47466157 original size:22 final size:22
Alignment explanation
Indices: 47466129--47466171 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
47466119 TTTATTGTTC
47466129 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
47466151 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
47466172 TAAATCCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:47468961 original size:23 final size:23
Alignment explanation
Indices: 47468929--47468972 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
47468919 AAAAATGCTA
*
47468929 AAAATCATTTAAAATTAAAAAAT
1 AAAATAATTTAAAATTAAAAAAT
* *
47468952 AAAATAATTTGAATTTAAAAA
1 AAAATAATTTAAAATTAAAAA
47468973 TATATATTAA
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:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATAATTTAAAATTAAAAAAT
Found at i:47473203 original size:21 final size:20
Alignment explanation
Indices: 47473156--47473208 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
47473146 TCCATTTTTT
*
47473156 CTAATCTCACCGCTATAGTA
1 CTAATCTCACCGCTACAGTA
*
47473176 TTCAATCTCACCGCTACAGTAA
1 CT-AATCTCACCGCTACAGT-A
47473198 CTAATCTCACC
1 CTAATCTCACC
47473209 ACCACCGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (20 bp):
CTAATCTCACCGCTACAGTA
Found at i:47475082 original size:21 final size:21
Alignment explanation
Indices: 47475058--47475123 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
47475048 ATGAAATGAT
*
47475058 TCTTTTCAATCCATTGTTTTC
1 TCTTTTCAATCAATTGTTTTC
*
47475079 TCTTTACAATCAATTGTTTTGC
1 TCTTTTCAATCAATTGTTTT-C
* **
47475101 TGTTTT-AATTTATTGTTTTC
1 TCTTTTCAATCAATTGTTTTC
47475121 TCT
1 TCT
47475124 ATCTACTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 3 0.08
21 29 0.78
22 5 0.14
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.59
Consensus pattern (21 bp):
TCTTTTCAATCAATTGTTTTC
Found at i:47482138 original size:36 final size:37
Alignment explanation
Indices: 47482069--47482138 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
47482059 TAGATTTCTT
* *
47482069 ATATCATTATATTAAATTATTTAAATATTATTTAAAA
1 ATATCATTATAGTAAATTATTTAAATATAATTTAAAA
47482106 ATATCATTATAGTAAA-TATTTAAATATAATTTA
1 ATATCATTATAGTAAATTATTTAAATATAATTTA
47482139 TTATTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 16 0.52
37 15 0.48
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATATCATTATAGTAAATTATTTAAATATAATTTAAAA
Found at i:47482433 original size:13 final size:13
Alignment explanation
Indices: 47482415--47482439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47482405 TTCCAAACCA
47482415 AACTTTTCAAAAG
1 AACTTTTCAAAAG
47482428 AACTTTTCAAAA
1 AACTTTTCAAAA
47482440 TTGGCCCTAA
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:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
AACTTTTCAAAAG
Found at i:47484535 original size:3 final size:3
Alignment explanation
Indices: 47484520--47484610 Score: 98
Period size: 3 Copynumber: 30.7 Consensus size: 3
47484510 TAGGTTTTTT
* * * *
47484520 TTA TT- TTA ATA TTA TTA ATA TTG TTA -TA TTGCA TTA TTA CTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA TTA TTA TTA
*
47484564 GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
47484611 TCTATACATA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.07
3 65 0.89
5 3 0.04
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:47486950 original size:109 final size:109
Alignment explanation
Indices: 47486536--47486938 Score: 607
Period size: 109 Copynumber: 3.7 Consensus size: 109
47486526 AGAATTCAAG
* * * * * * *
47486536 AGGATATTTGGCTACTTGGTTAAACGAG--AAATAGACACCCAGCACATTAGGGCACG-TTCCTC
1 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* * *
47486598 GCATTTCCCAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* * *
47486642 AGGATA-TTTGACTATTTGGCTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCT
1 AGGATACTTAG-CTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
*
47486706 CGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTAAA
65 CGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
*
47486751 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGACACGTTTTCTC
1 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
47486816 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* **
47486860 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAGCCCAGCACATTAGGGCTTGTTTTCTC
1 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
47486925 GAATTTCCAAACGC
66 GAATTTCCAAACGC
47486939 TATATATTGC
Statistics
Matches: 271, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
105 3 0.01
106 20 0.07
108 25 0.09
109 220 0.81
110 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (109 bp):
AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:47487683 original size:12 final size:12
Alignment explanation
Indices: 47487668--47487716 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
47487658 ACGTGTAAAT
*
47487668 ATAATGATAGTA
1 ATAATAATAGTA
* *
47487680 ATAATGATATTA
1 ATAATAATAGTA
* *
47487692 GTAATAATACTA
1 ATAATAATAGTA
47487704 ATAATAATAGTA
1 ATAATAATAGTA
47487716 A
1 A
47487717 GGATATTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:47487714 original size:21 final size:21
Alignment explanation
Indices: 47487681--47487733 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
47487671 ATGATAGTAA
* * *
47487681 TAATGATATTAGTAATAATAC
1 TAATAATAATAGTAAGAATAC
* *
47487702 TAATAATAATAGTAAGGATAT
1 TAATAATAATAGTAAGAATAC
47487723 TAATAATAATA
1 TAATAATAATA
47487734 ACATTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (21 bp):
TAATAATAATAGTAAGAATAC
Found at i:47487739 original size:15 final size:16
Alignment explanation
Indices: 47487721--47487760 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
47487711 TAGTAAGGAT
47487721 ATTAATAATAAT-AAC
1 ATTAATAATAATGAAC
47487736 ATTAA-AATAATGAAC
1 ATTAATAATAATGAAC
*
47487751 A-AAATAATAA
1 ATTAATAATAA
47487761 AATTGCTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (16 bp):
ATTAATAATAATGAAC
Found at i:47489607 original size:45 final size:45
Alignment explanation
Indices: 47489556--47489911 Score: 410
Period size: 45 Copynumber: 7.9 Consensus size: 45
47489546 TTCATTGTTT
* * * *
47489556 TTCGATCTGCTTCGCTGCTAGTATAGGAAGACAAGATCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* *
47489601 TTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * *
47489646 TTCGATCTACTTCACTGCCAATACATGAAGACAAGACCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * *
47489691 TTCGATCTACTTCGCTGCCAGTACAGGAAGACAATATTTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* *
47489736 TTC-AGTCTACTTTGCTGCCAATACAGGAAGACAAGACCTGCTATC
1 TTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * * * * *
47489781 TTTGATCTATTTCAC-GCCAATACATGAAGACAAGATCTGTTTTC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
** * ** *
47489825 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * * * *
47489870 TTCGATCCACTTCACTACCAATATAGGAAGACAGGATCTGCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT
47489912 GCTTTTCAAC
Statistics
Matches: 260, Mismatches: 48, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
44 38 0.15
45 221 0.85
46 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (45 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
Found at i:47492586 original size:16 final size:16
Alignment explanation
Indices: 47492565--47492597 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47492555 TCTCGCATGA
47492565 TAGTCACATTGTGCAT
1 TAGTCACATTGTGCAT
47492581 TAGTCACATTGTGCAT
1 TAGTCACATTGTGCAT
47492597 T
1 T
47492598 TGTGCCGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (16 bp):
TAGTCACATTGTGCAT
Found at i:47493476 original size:19 final size:17
Alignment explanation
Indices: 47493454--47493496 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 17
47493444 GTGAAATTTG
47493454 ATGCATGCAATGAAATGTA
1 ATGCATGC-ATGAAATG-A
47493473 ATGCAGATGCATGAAATGA
1 ATGC--ATGCATGAAATGA
47493492 ATGCA
1 ATGCA
47493497 AAAAGAGACG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.05
19 9 0.41
20 8 0.36
21 4 0.18
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (17 bp):
ATGCATGCATGAAATGA
Found at i:47495086 original size:106 final size:107
Alignment explanation
Indices: 47494894--47495096 Score: 264
Period size: 106 Copynumber: 1.9 Consensus size: 107
47494884 TGGATTAAGA
* * * * *
47494894 TTTAAGAGGATATTTGGCTATTTGGTCAAACGAAAAAATAGAAGCCCAGCATATTAGGGCACGTT
1 TTTAAGAGGATATTCGGCTATTTGGTCAAACGAAAAAATAGAAACCCAACACATTAGGGAACGTT
* * *
47494959 TCCTCTAATTTCTAAACGCAAAATATTACCTTACTCTGAAAT
66 TCCTCGAATTCCCAAACGCAAAATATTACCTTACTCTGAAAT
** * *
47495001 TTTAA-AGGATATTCGGCTATTTGGTTGAACGAAAAAATCGAAACCCAACACATTATGGAACGTT
1 TTTAAGAGGATATTCGGCTATTTGGTCAAACGAAAAAATAGAAACCCAACACATTAGGGAACGTT
* * *
47495065 TTCTCGAATTCCCAAATGCAAAATATTGCCTT
66 TCCTCGAATTCCCAAACGCAAAATATTACCTT
47495097 TATTATTTTT
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
106 76 0.94
107 5 0.06
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (107 bp):
TTTAAGAGGATATTCGGCTATTTGGTCAAACGAAAAAATAGAAACCCAACACATTAGGGAACGTT
TCCTCGAATTCCCAAACGCAAAATATTACCTTACTCTGAAAT
Found at i:47496109 original size:106 final size:107
Alignment explanation
Indices: 47495920--47496118 Score: 312
Period size: 106 Copynumber: 1.9 Consensus size: 107
47495910 ATAATAAAGG
* * * *
47495920 CAATATTTTGTATTTGGGAATTCGAGAAAGCGTGCCCTAATGTGTTGGGTTTCGATTTTTTCGTT
1 CAATATTTTGCATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTGGGCTTCGATTTTTTCGTT
*
47495985 CGACCAAATAGCCGAATATCCT-TTAAAATTTCAGAGTAAGA
66 CGACCAAATAGCCAAATATCCTCTTAAAATTTCAGAGTAAGA
*
47496026 CAATATTTTGCGTTTGGAAATTCGAGGAAA-CGTGCCCTAATGTGCTGGGCTTCGATTTTTTCGT
1 CAATATTTTGCATTTGGAAATTCGA-GAAAGCGTGCCCTAATGTGCTGGGCTTCGATTTTTTCGT
*
47496090 TTGACCAAATAGCCAAATATCCTCTTAAA
65 TCGACCAAATAGCCAAATATCCTCTTAAA
47496119 TCTTAATCCA
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
106 75 0.89
107 9 0.11
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (107 bp):
CAATATTTTGCATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTGGGCTTCGATTTTTTCGTT
CGACCAAATAGCCAAATATCCTCTTAAAATTTCAGAGTAAGA
Found at i:47498214 original size:55 final size:56
Alignment explanation
Indices: 47498155--47498295 Score: 180
Period size: 57 Copynumber: 2.5 Consensus size: 56
47498145 TTGTTATTAA
* *
47498155 ATTTTAATA-AGATTATTATTAAATATAATTTAAT-AATAATAAATAATTTAATCAC
1 ATTTTAATATA-ATTATTATTAAAAATAATTTAATAAATAATAAATAATTTAATAAC
* * *
47498210 ATTTTAATATAATTTTTGTTAAAAATAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAAAATAATTTAAT-AAATAATAAATAATTTAATAAC
*
47498267 ATTCTTAATATAAATATTA-TAAAAATAAT
1 ATT-TTAATATAATTATTATTAAAAATAAT
47498296 ATATAATCTG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 29 0.39
56 1 0.01
57 32 0.43
58 12 0.16
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (56 bp):
ATTTTAATATAATTATTATTAAAAATAATTTAATAAATAATAAATAATTTAATAAC
Found at i:47498603 original size:21 final size:21
Alignment explanation
Indices: 47498578--47498631 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
47498568 TGATTTGTTA
*
47498578 TTTTTGCTACTGTTTTTTCA-
1 TTTTTGCTACTGTTTTCTCAC
*
47498598 TGTTTTGCTATTGTTTTCTCAC
1 T-TTTTGCTACTGTTTTCTCAC
*
47498620 TTTTTGCCACTG
1 TTTTTGCTACTG
47498632 CCTTCCATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.09, C:0.19, G:0.13, T:0.59
Consensus pattern (21 bp):
TTTTTGCTACTGTTTTCTCAC
Found at i:47499598 original size:15 final size:14
Alignment explanation
Indices: 47499558--47499599 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
47499548 GAATGCATGT
47499558 ATAAATATCACAATA
1 ATAAATA-CACAATA
*
47499573 ACAAATA-ACAATA
1 ATAAATACACAATA
47499586 ATAAATACGACAAT
1 ATAAATAC-ACAAT
47499600 TGTATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 12 0.52
15 11 0.48
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (14 bp):
ATAAATACACAATA
Found at i:47499722 original size:16 final size:16
Alignment explanation
Indices: 47499696--47499747 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
47499686 AAAAAATATG
* *
47499696 AAAACATAAATCAACA
1 AAAAAATAAATAAACA
*
47499712 AACAAATAAATAAACA
1 AAAAAATAAATAAACA
*
47499728 AAAAAAT--ATAAAGA
1 AAAAAATAAATAAACA
47499742 AAAAAA
1 AAAAAA
47499748 GTGCATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 12 0.39
16 19 0.61
ACGTcount: A:0.77, C:0.10, G:0.02, T:0.12
Consensus pattern (16 bp):
AAAAAATAAATAAACA
Found at i:47499920 original size:18 final size:18
Alignment explanation
Indices: 47499880--47499923 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
47499870 TAGAAAGTAT
47499880 AATATATATACGTACATA
1 AATATATATACGTACATA
* *
47499898 TATATATATAAGGTA-ATA
1 AATATATAT-ACGTACATA
47499916 AATATATA
1 AATATATA
47499924 AATCATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (18 bp):
AATATATATACGTACATA
Found at i:47501735 original size:132 final size:132
Alignment explanation
Indices: 47501575--47502159 Score: 954
Period size: 132 Copynumber: 4.4 Consensus size: 132
47501565 ATAAGATTAT
* * *
47501575 TGGCTTTAATTTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTCGATCTGCTCCACTA
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTA
*
47501640 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCTCTGCTGCTCAAGGAGACAAGGCTT
66 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAAGGAGACAAGGCTT
47501705 GG
131 GG
* *
47501707 TGGCTTAAATCAGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACAA
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTA
* * *
47501772 CTGCTTAGAGAGGTAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAAGGAGACAAGGCTT
66 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAAGGAGACAAGGCTT
47501837 GG
131 GG
* * *
47501839 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTATTTGATCTACTCCACTA
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTA
*
47501904 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGCTT
66 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAAGGAGACAAGGCTT
47501969 GG
131 GG
* * * *
47501971 TGGCTTAAATCTGCTTCTCACTATCTTAGAAAGATAAGATTTTCCATCTTTAATCTGCTCCACTA
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTA
* * * ** * *
47502036 CTGCCTAGGGAGACAAGATCTACAATCTTCAGCCTACTCTACTGCTACTCAGGGAGACAAGGCTT
66 CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAAGGAGACAAGGCTT
47502101 GG
131 GG
47502103 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTG
1 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTG
47502160 TCTCGCTGTC
Statistics
Matches: 418, Mismatches: 35, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 418 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATCTTTGATCTGCTCCACTA
CTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAAGGAGACAAGGCTT
GG
Found at i:47505338 original size:41 final size:41
Alignment explanation
Indices: 47505293--47505472 Score: 213
Period size: 41 Copynumber: 4.4 Consensus size: 41
47505283 AGATTCACTA
* ** * *
47505293 GCACTTCA-CCTGATAGGCTTATAGTTTAATTCCGTTCACCG
1 GCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
*
47505334 GCACTTAGCCTGCTAGGCCTATAGCCTGATTCAGTTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
* *
47505375 GCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAATTCACCG
1 GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
* * *
47505416 GCACTTAGCCTGCT-GGACGTATAGTCC-GATTCAATTCATCG
1 GCACTTAGCCTGCTAGG-CTTATAG-CCTGATTCAGTTCACCG
47505457 GCACTTAGCCTGCTAG
1 GCACTTAGCCTGCTAG
47505473 ACGTATAGTC
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
40 3 0.02
41 117 0.95
42 3 0.02
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (41 bp):
GCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCG
Found at i:47505476 original size:41 final size:41
Alignment explanation
Indices: 47505327--47505485 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 41
47505317 TTTAATTCCG
* * *
47505327 TTCACCGGCACTTAGCCTGCTAGGCCTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
* * *
47505368 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
*
47505409 TTCACCGGCACTTAGCCTGCTGGACGTATAGTCC-GATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAA
* *
47505450 TTCATCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
47505486 ATAATTTCAC
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
40 1 0.01
41 103 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAA
Found at i:47513226 original size:24 final size:24
Alignment explanation
Indices: 47513197--47513242 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
47513187 ATCATCTTTT
*
47513197 GCTGCTCATT-CATTTGCTTTTGAA
1 GCTGCTC-TTGCATTTCCTTTTGAA
47513221 GCTGCTCTTGCATTTCCTTTTG
1 GCTGCTCTTGCATTTCCTTTTG
47513243 GGATTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (24 bp):
GCTGCTCTTGCATTTCCTTTTGAA
Found at i:47517256 original size:16 final size:16
Alignment explanation
Indices: 47517209--47517256 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
47517199 ATAGAAAGTA
47517209 TAATATATATATATACG
1 TAATATATATATA-ACG
47517226 TACATATATATATAACG
1 TA-ATATATATATAACG
*
47517243 TAATAAATATATAA
1 TAATATATATATAA
47517257 ATCATAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 11 0.38
17 7 0.24
18 11 0.38
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (16 bp):
TAATATATATATAACG
Found at i:47522042 original size:22 final size:22
Alignment explanation
Indices: 47522017--47522061 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
47522007 TTAACCTTGA
47522017 AATGGTTAAGTAAATTTTGACT
1 AATGGTTAAGTAAATTTTGACT
47522039 AATGGTTAAGTAAATTTTGACT
1 AATGGTTAAGTAAATTTTGACT
47522061 A
1 A
47522062 TCTCTGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (22 bp):
AATGGTTAAGTAAATTTTGACT
Found at i:47528605 original size:31 final size:31
Alignment explanation
Indices: 47528570--47528694 Score: 91
Period size: 31 Copynumber: 4.1 Consensus size: 31
47528560 TTGGTAGAAG
*
47528570 TTAGGTCCTAAACTTGGCAATTGTTCCCACA
1 TTAGGTCCTGAACTTGGCAATTGTTCCCACA
* * * *
47528601 TTAGGACCTGCACTTGGTAGCTT-TTCCCACA
1 TTAGGTCCTGAACTTGGCA-ATTGTTCCCACA
** *
47528632 TT-GGTGCCTGAACTT--CTTTTTGGT-CCA-A
1 TTAGGT-CCTGAACTTGGC-AATTGTTCCCACA
*
47528660 GTTAGGGCCTGAACTTGGCAATTGTTCCCACA
1 -TTAGGTCCTGAACTTGGCAATTGTTCCCACA
47528692 TTA
1 TTA
47528695 AGGCTTGAAC
Statistics
Matches: 69, Mismatches: 15, Indels: 20
0.66 0.14 0.19
Matches are distributed among these distances:
28 1 0.01
29 16 0.23
30 9 0.13
31 40 0.58
32 3 0.04
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (31 bp):
TTAGGTCCTGAACTTGGCAATTGTTCCCACA
Found at i:47528676 original size:91 final size:91
Alignment explanation
Indices: 47528516--47528694 Score: 268
Period size: 91 Copynumber: 2.0 Consensus size: 91
47528506 TTATTTGGGG
* * * *
47528516 CCTGAACTTGGAAACTTTTCCCACATTGGGGTCTGAACTTTTTTTTGGTAGAAGTTAGGTCCTAA
1 CCTGAACTTGGAAACTTTTCCCACATTGGGGCCTGAACTTCTTTTTGGTACAAGTTAGGGCCTAA
47528581 ACTTGGCAATTGTTCCCACATTAGGA
66 ACTTGGCAATTGTTCCCACATTAGGA
* * * * * *
47528607 CCTGCACTTGGTAGCTTTTCCCACATTGGTGCCTGAACTTCTTTTTGGTCCAAGTTAGGGCCTGA
1 CCTGAACTTGGAAACTTTTCCCACATTGGGGCCTGAACTTCTTTTTGGTACAAGTTAGGGCCTAA
47528672 ACTTGGCAATTGTTCCCACATTA
66 ACTTGGCAATTGTTCCCACATTA
47528695 AGGCTTGAAC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (91 bp):
CCTGAACTTGGAAACTTTTCCCACATTGGGGCCTGAACTTCTTTTTGGTACAAGTTAGGGCCTAA
ACTTGGCAATTGTTCCCACATTAGGA
Found at i:47536301 original size:43 final size:43
Alignment explanation
Indices: 47536178--47536304 Score: 114
Period size: 43 Copynumber: 3.0 Consensus size: 43
47536168 GATGCCGCTT
* * *
47536178 AAGATCATGTTCTTTAGCGGAGCTTGGTA-AAAAAACGCCACTA
1 AAGATAATGTTCTTTAGCGGAGCTT-TTATAAAAAACGCCACAA
* * * * * ** *
47536221 TAGATCATGTTCTTTAGCGGCGCTTTCATCACGAACGCCGCGAA
1 AAGATAATGTTCTTTAGCGGAGCTTTTATAAAAAACGCCAC-AA
*
47536265 AAG-TAATGTTCTTTAGCGGTGCTTTTATAAAAAACGCCAC
1 AAGATAATGTTCTTTAGCGGAGCTTTTATAAAAAACGCCAC
47536305 TAATTTTGGG
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
42 1 0.02
43 61 0.94
44 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
AAGATAATGTTCTTTAGCGGAGCTTTTATAAAAAACGCCACAA
Found at i:47536715 original size:21 final size:21
Alignment explanation
Indices: 47536691--47536739 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
47536681 GCTTCTCTCG
47536691 CTGCTTCTCGCGCTGCAGCCT
1 CTGCTTCTCGCGCTGCAGCCT
* *
47536712 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCGCGCTGCAGCCT
47536733 CTGCTTC
1 CTGCTTC
47536740 CTTCGTTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.41, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCGCGCTGCAGCCT
Found at i:47538722 original size:7 final size:7
Alignment explanation
Indices: 47538710--47538741 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
47538700 CAGAAATAGC
47538710 AAAACAG
1 AAAACAG
47538717 AAAACAG
1 AAAACAG
*
47538724 AAAATAG
1 AAAACAG
47538731 AAAACAG
1 AAAACAG
47538738 AAAA
1 AAAA
47538742 TAAAGAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.75, C:0.09, G:0.12, T:0.03
Consensus pattern (7 bp):
AAAACAG
Found at i:47538724 original size:21 final size:21
Alignment explanation
Indices: 47538698--47538741 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
47538688 CACTTCATTC
47538698 AACAG-AAATAGCAAAACAGAA
1 AACAGAAAATAG-AAAACAGAA
47538719 AACAGAAAATAGAAAACAGAA
1 AACAGAAAATAGAAAACAGAA
47538740 AA
1 AA
47538742 TAAAGAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.70, C:0.11, G:0.14, T:0.05
Consensus pattern (21 bp):
AACAGAAAATAGAAAACAGAA
Found at i:47538756 original size:15 final size:14
Alignment explanation
Indices: 47538717--47538756 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
47538707 AGCAAAACAG
*
47538717 AAAACAGAAAATAG
1 AAAACAGAAAATAA
47538731 AAAACAGAAAATAA
1 AAAACAGAAAATAA
*
47538745 AGAAACATAAAA
1 A-AAACAGAAAA
47538757 ATGGTATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAACAGAAAATAA
Done.