Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 131 of 255
Found at i:42026221 original size:47 final size:47
Alignment explanation
Indices: 42026152--42026506 Score: 304
Period size: 47 Copynumber: 7.6 Consensus size: 47
42026142 TATAATGCCA
* * *
42026152 ATGCCATGTCCCAGACCTGGTCTTACACCGGCTCTCATGCTAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGCTAAGCCG
* * * * *
42026199 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTAACGTTAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGCTAAGCCG
* * * *
42026246 ATGCAATTTCCCAGACATGGTCTTACACTGACTCTCATG-TATCCATGACG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGCTA---A-GCCG
* *
42026296 ATGCCATGTCCCAGACATGGTCTT-CTACTGACACATCATG-T-AGCCG
1 ATGCCATGTCCCAGACATGGTCTTAC-ACTGGCTC-TCATGCTAAGCCG
*
42026342 ATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATGCT--AAGCCG
* * *
42026388 ATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCGT-CTCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGCT-AA-GCCG
** ** *
42026434 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGCT-AAGCCG
42026482 ATG-CATGTCCCAGACAT-GTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
42026507 GTAGCACACA
Statistics
Matches: 260, Mismatches: 31, Indels: 35
0.80 0.10 0.11
Matches are distributed among these distances:
42 1 0.00
43 4 0.02
44 10 0.04
45 16 0.06
46 60 0.23
47 105 0.40
48 23 0.09
49 3 0.01
50 32 0.12
51 6 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGCTAAGCCG
Found at i:42035392 original size:18 final size:18
Alignment explanation
Indices: 42035369--42035420 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
42035359 TAATTATTTA
42035369 AAATATCATTATTTTTTC
1 AAATATCATTATTTTTTC
* * *
42035387 AAATATC-TAAAATATTTC
1 AAATATCAT-TATTTTTTC
*
42035405 AAATATCATTGTTTTT
1 AAATATCATTATTTTT
42035421 CATCTATATA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (18 bp):
AAATATCATTATTTTTTC
Found at i:42036618 original size:28 final size:28
Alignment explanation
Indices: 42036594--42036709 Score: 103
Period size: 28 Copynumber: 4.2 Consensus size: 28
42036584 ATCGCCATAG
42036594 AGGCTGATCTTTTCATACTTTGCCACAA
1 AGGCTGATCTTTTCATACTTTGCCACAA
** *
42036622 AGGCTTTTCTTTTCTTACTTTGCCACAA
1 AGGCTGATCTTTTCATACTTTGCCACAA
* * ** *
42036650 AGG-TTATTATTTTCATACTTCACCACAG
1 AGGCTGA-TCTTTTCATACTTTGCCACAA
* *
42036678 AGGCT-TTCATTTCATGA-TTTGCCACAA
1 AGGCTGATCTTTTCAT-ACTTTGCCACAA
42036705 AGGCT
1 AGGCT
42036710 TCATTTCCTA
Statistics
Matches: 70, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
27 21 0.30
28 48 0.69
29 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (28 bp):
AGGCTGATCTTTTCATACTTTGCCACAA
Found at i:42036668 original size:56 final size:55
Alignment explanation
Indices: 42036603--42036707 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 55
42036593 GAGGCTGATC
** * *
42036603 TTTTCATACTTTGCCACAAAGGCTTTTCTTTTC-TTACTTTGCCACAAAGGTTATTA
1 TTTTCATACTTCACCACAAAGGC-TTTCATTTCATGA-TTTGCCACAAAGGTTATTA
*
42036659 TTTTCATACTTCACCACAGAGGCTTTCATTTCATGATTTGCCACAAAGG
1 TTTTCATACTTCACCACAAAGGCTTTCATTTCATGATTTGCCACAAAGG
42036708 CTTCATTTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
55 21 0.49
56 22 0.51
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (55 bp):
TTTTCATACTTCACCACAAAGGCTTTCATTTCATGATTTGCCACAAAGGTTATTA
Found at i:42042079 original size:79 final size:81
Alignment explanation
Indices: 42041911--42042095 Score: 211
Period size: 79 Copynumber: 2.3 Consensus size: 81
42041901 GTTACTCGTT
* *
42041911 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
*
42041975 AATTTAGTAACACGCAC
65 AATATAGTAACACGCAC
* **
42041992 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* * *
42042054 GATATGGTCACTTA-GCA-
65 AATATAGTAAC--ACGCAC
42042071 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
42042096 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 24 0.27
81 4 0.04
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA
ATATAGTAACACGCAC
Found at i:42042095 original size:40 final size:40
Alignment explanation
Indices: 42041892--42042095 Score: 202
Period size: 40 Copynumber: 5.1 Consensus size: 40
42041882 CGGAATTTAA
* * ** *
42041892 CCGGATATAGTTACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGC
* * *
42041932 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGC
* * *
42041972 CCGAATTTAGTAAC-ACGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTA-GCACAAATGCCTTCGGGACTTAGC
* *
42042011 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTAGCACAAATGCCTTCGGGA-CTTAGC
* *
42042051 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAGC
42042091 CCGGA
1 CCGGA
42042096 CATCATTCGA
Statistics
Matches: 135, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
38 2 0.01
39 29 0.21
40 92 0.68
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGC
Found at i:42050263 original size:79 final size:81
Alignment explanation
Indices: 42050095--42050279 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
42050085 GCTACTCGTT
* *
42050095 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
42050159 AATTTAGTAACTCGCAC
65 AATATAGTAACTAGCAC
* **
42050176 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* * *
42050238 GATATGGTCACTTAGCA-
65 AATATAGTAAC-TAGCAC
42050255 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
42050280 CATCATTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 25 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGA
ATATAGTAACTAGCAC
Found at i:42050279 original size:40 final size:40
Alignment explanation
Indices: 42050076--42050279 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
42050066 CGGAATTTAA
** *
42050076 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42050116 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
42050156 CCGAATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42050195 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42050235 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42050275 CCGGA
1 CCGGA
42050280 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42058514 original size:25 final size:25
Alignment explanation
Indices: 42058484--42058546 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
42058474 GTTTCGACCC
* *
42058484 ACAGCTCGTGTGAGTATATCGATTT
1 ACAGCTCGTGTGAGCATATCGATCT
* **
42058509 ATAGCTCGTAAGAGCATATCGATCT
1 ACAGCTCGTGTGAGCATATCGATCT
*
42058534 ACAGCTCGAGTGA
1 ACAGCTCGTGTGA
42058547 ATACCGATTC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCATATCGATCT
Found at i:42059955 original size:17 final size:17
Alignment explanation
Indices: 42059933--42059966 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42059923 TAAATTCTAG
*
42059933 TAGCTATAAGGATCAAA
1 TAGCTATAAGAATCAAA
*
42059950 TAGCTATGAGAATCAAA
1 TAGCTATAAGAATCAAA
42059967 ACTAGAGGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
TAGCTATAAGAATCAAA
Found at i:42080579 original size:48 final size:51
Alignment explanation
Indices: 42080419--42080612 Score: 283
Period size: 51 Copynumber: 3.9 Consensus size: 51
42080409 CGGATACATG
* *
42080419 GTGGCCTTCACATAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAA
*
42080470 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAACTATTATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
*
42080521 GTGGCATTCACATAGTA-CACACTTGTGTCC-AAGCTA-TATATTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* *
42080569 GTGACCTTCACATAATACC-CACTTGTGTCCAAAGCTATT-TATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
42080613 CTAAGGTTCA
Statistics
Matches: 131, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
48 37 0.28
49 17 0.13
50 15 0.11
51 62 0.47
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
Found at i:42080714 original size:26 final size:26
Alignment explanation
Indices: 42080634--42080715 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 26
42080624 CGGAAATTTC
42080634 TCACTTAGCACAATGCCATGGACTTATT
1 TCACTTAGC-C-ATGCCATGGACTTATT
42080662 TCACTTAG--ATGCCATGGACTTATT
1 TCACTTAGCCATGCCATGGACTTATT
42080686 TCACTTAGCCATTGCCAT-GACTTATT
1 TCACTTAGCCA-TGCCATGGACTTATT
42080712 TCAC
1 TCAC
42080716 GTAGATGTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
24 24 0.47
26 13 0.25
27 6 0.12
28 8 0.16
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (26 bp):
TCACTTAGCCATGCCATGGACTTATT
Found at i:42087256 original size:51 final size:51
Alignment explanation
Indices: 42087179--42087427 Score: 331
Period size: 51 Copynumber: 4.9 Consensus size: 51
42087169 CGGATACACG
* * *
42087179 ATGGCCTTCATATAGTACCACCCTTGTAG-CCAAAGCTATTTTATTCACAAA
1 ATGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAAA
* * *
42087230 ATGGCCTTCACATAGTGCTACACTTGTGTCC-AAGCTATTATATTTACAAA
1 ATGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* *
42087280 TTGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTATATTCACAAA
1 ATGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* * *
42087331 GTGGCCTTCACATAGTACCACACTTGTGTCTAAAGCTATTATCTTCACAAA
1 ATGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
* * * * *
42087382 CTGACCTTCACATAGTACCGCACCTGTGTCCAAAGCTATTTTATTC
1 ATGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
42087428 CTAAGGTTCA
Statistics
Matches: 174, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
50 45 0.26
51 129 0.74
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
ATGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAA
Found at i:42087355 original size:101 final size:102
Alignment explanation
Indices: 42087180--42087427 Score: 354
Period size: 101 Copynumber: 2.4 Consensus size: 102
42087170 GGATACACGA
* * *
42087180 TGGCCTTCATATAGTACCACCCTTGTAGCCAAAGCTATTTTATTCACAAAATGGCCTTCACATAG
1 TGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTCACAAAATGGCCTTCACATAG
* * * * *
42087245 TGCTACACTTGTGTC-CAAGCTATTATATTTACAAAT
66 TACCACACTTGTGTCTAAAGCTATTATATTCACAAAC
* *
42087281 TGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTATATTCACAAAGTGGCCTTCACATAG
1 TGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTCACAAAATGGCCTTCACATAG
*
42087346 TACCACACTTGTGTCTAAAGCTATTATCTTCACAAAC
66 TACCACACTTGTGTCTAAAGCTATTATATTCACAAAC
* * * *
42087383 TGACCTTCACATAGTACCGCACCTGTGTCCAAAGCTATTTTATTC
1 TGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTC
42087428 CTAAGGTTCA
Statistics
Matches: 130, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 73 0.56
102 57 0.44
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (102 bp):
TGGCCTTCACATAGTACCACACTTGTATCCAAAGCTATTTTATTCACAAAATGGCCTTCACATAG
TACCACACTTGTGTCTAAAGCTATTATATTCACAAAC
Found at i:42087497 original size:49 final size:49
Alignment explanation
Indices: 42087438--42087536 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
42087428 CTAAGGTTCA
* * *
42087438 ACCGGGAAATTTCTCACTTAGCACAATGGCATGGACTTATTTCACTTAG
1 ACCGGGAAATTTCTCACTTAGCACAATGCCAAGGACTTAATTCACTTAG
*
42087487 ACCGGGAAATTTCTCACTTAGTACAATGCCAAGGACTTAATTCACTTAG
1 ACCGGGAAATTTCTCACTTAGCACAATGCCAAGGACTTAATTCACTTAG
42087536 A
1 A
42087537 TGCCATAGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (49 bp):
ACCGGGAAATTTCTCACTTAGCACAATGCCAAGGACTTAATTCACTTAG
Found at i:42087547 original size:24 final size:24
Alignment explanation
Indices: 42087512--42087583 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
42087502 ACTTAGTACA
*
42087512 ATGCCA-AGGACTTAATTCACTTAG
1 ATGCCATA-GACTTATTTCACTTAG
42087536 ATGCCATAGACTTATTTCACTTAG
1 ATGCCATAGACTTATTTCACTTAG
* *
42087560 ATGCCATGGTCTTATTTCACTTAG
1 ATGCCATAGACTTATTTCACTTAG
42087584 CACAATGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (24 bp):
ATGCCATAGACTTATTTCACTTAG
Found at i:42088755 original size:50 final size:51
Alignment explanation
Indices: 42088632--42088839 Score: 330
Period size: 51 Copynumber: 4.1 Consensus size: 51
42088622 ACAGATACAC
* * * * *
42088632 AGTGACCTTCACATAGTACCACCCTTGTAG-GCAAAGTTATTTTATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGT-GTCCAAAGCTATTATATTCACAA
*
42088683 AGTGGCCTTTACATAGTACCACACTTGTGTCCAAAGCTATTATATTCAC-A
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
*
42088733 AGTGGCCTTCACATAGTACCACACTTGTGTTCAAAGCTATTATATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
42088784 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
1 AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
42088835 AGTGG
1 AGTGG
42088840 AATTCTATAA
Statistics
Matches: 146, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
50 49 0.34
51 97 0.66
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (51 bp):
AGTGGCCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
Found at i:42088812 original size:101 final size:102
Alignment explanation
Indices: 42088632--42088839 Score: 339
Period size: 101 Copynumber: 2.0 Consensus size: 102
42088622 ACAGATACAC
* * * * *
42088632 AGTGACCTTCACATAGTACCACCCTTGTAGGCAAAGTTATTTTATTCACAAAGTGGCCTTTACAT
1 AGTGGCCTTCACATAGTACCACACTTGTAGGCAAAGCTATTATATTCACAAAGTGGCCTTCACAT
42088697 AGTACCACACTTGTGTCCAAAGCTATTATATTCAC-A
66 AGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
*
42088733 AGTGGCCTTCACATAGTACCACACTTGT-GTTCAAAGCTATTATATTCACAAAGTGGCCTTCACA
1 AGTGGCCTTCACATAGTACCACACTTGTAG-GCAAAGCTATTATATTCACAAAGTGGCCTTCACA
42088797 TAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
65 TAGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
42088835 AGTGG
1 AGTGG
42088840 AATTCTATAA
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
100 1 0.01
101 92 0.93
102 6 0.06
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (102 bp):
AGTGGCCTTCACATAGTACCACACTTGTAGGCAAAGCTATTATATTCACAAAGTGGCCTTCACAT
AGTACCACACTTGTGTCCAAAGCTATTATATTCACAA
Found at i:42104356 original size:47 final size:44
Alignment explanation
Indices: 42104252--42104422 Score: 130
Period size: 44 Copynumber: 3.8 Consensus size: 44
42104242 ATATATGCAT
42104252 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTG
* * * * * * *
42104296 GCCGATGCGTGTCCCAAACACGTCTTACACTGGC-TATCTCTGTCGAG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-T---G
** * * *
42104343 GCTGATGCATGTCCCAGACATGTCTTATTCTGGCACTCATAAT-ATG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCA--CA-ACTCTTG
* * *
42104389 GATGAAGCATGTCCCAGGCATGTCTTACACTAGC
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGC
42104423 CCTCGTCTGG
Statistics
Matches: 96, Mismatches: 23, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
43 5 0.05
44 30 0.31
46 29 0.30
47 29 0.30
49 1 0.01
50 1 0.01
51 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (44 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTG
Found at i:42105194 original size:12 final size:12
Alignment explanation
Indices: 42105177--42105202 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42105167 TAAAAAATGT
42105177 GAAAATCATCAA
1 GAAAATCATCAA
42105189 GAAAATCATCAA
1 GAAAATCATCAA
42105201 GA
1 GA
42105203 TCACTTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (12 bp):
GAAAATCATCAA
Found at i:42109017 original size:28 final size:28
Alignment explanation
Indices: 42108951--42109078 Score: 157
Period size: 28 Copynumber: 4.5 Consensus size: 28
42108941 CTTGAGATTG
* * **
42108951 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
42108980 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
42109008 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
*
42109037 GCACTAAGTGTGTGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
42109065 ACACTAAGGGTGCG
1 GCACTAAGTGTGCG
42109079 GACTTACTAT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
28 43 0.50
29 43 0.50
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:42109040 original size:57 final size:57
Alignment explanation
Indices: 42108951--42109078 Score: 168
Period size: 57 Copynumber: 2.2 Consensus size: 57
42108941 CTTGAGATTG
*
42108951 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* * * **
42109008 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGTGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTGTGCAAGTTTGATTATATA
* *
42109065 ACACTAAGGGTGCG
1 GCACTAAGTGTGCG
42109079 GACTTACTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 59 0.95
58 3 0.05
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATATA
Found at i:42112191 original size:45 final size:45
Alignment explanation
Indices: 42112132--42112219 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
42112122 GAACTATGTG
* * *
42112132 ATCTGAACTAATTGAGTTGTTGTTTGAGTTCATGATATATGTGGC
1 ATCTGAACTAATTGAGTTATGGTCTGAGTTCATGATATATGTGGC
* *
42112177 ATCTGAACTCATTGAGTTATGGTCTGAGTTCATGATGTATGTG
1 ATCTGAACTAATTGAGTTATGGTCTGAGTTCATGATATATGTG
42112220 ACACATGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (45 bp):
ATCTGAACTAATTGAGTTATGGTCTGAGTTCATGATATATGTGGC
Found at i:42114097 original size:52 final size:52
Alignment explanation
Indices: 42114041--42114159 Score: 220
Period size: 52 Copynumber: 2.3 Consensus size: 52
42114031 GGGAAATTTC
42114041 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
* *
42114093 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
42114145 TCACTTAGCACAATG
1 TCACTTAGCACAATG
42114160 TCATATACTA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
Found at i:42114118 original size:28 final size:27
Alignment explanation
Indices: 42114041--42114156 Score: 163
Period size: 24 Copynumber: 4.4 Consensus size: 27
42114031 GGGAAATTTC
42114041 TCACTTAGCACAATGCCATGGACTTATT
1 TCACTTAGCAC-ATGCCATGGACTTATT
42114069 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
42114093 TCACTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
42114121 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
42114145 TCACTTAGCACA
1 TCACTTAGCACA
42114157 ATGTCATATA
Statistics
Matches: 80, Mismatches: 1, Indels: 15
0.83 0.01 0.16
Matches are distributed among these distances:
24 46 0.57
25 1 0.01
27 2 0.03
28 31 0.39
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:42124647 original size:40 final size:40
Alignment explanation
Indices: 42124586--42124661 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
42124576 CGGTACCTTA
*
42124586 TGGTGTGTAGGATTGGATGGGTTGATTATATCCCCATACT
1 TGGTGTGTAGGATTGGATGGGTCGATTATATCCCCATACT
* * *
42124626 TGGTGTGTAGGGTTGGGTGGGTCGATTCTATCCCCA
1 TGGTGTGTAGGATTGGATGGGTCGATTATATCCCCA
42124662 CATGGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.16, C:0.14, G:0.34, T:0.36
Consensus pattern (40 bp):
TGGTGTGTAGGATTGGATGGGTCGATTATATCCCCATACT
Found at i:42126827 original size:43 final size:43
Alignment explanation
Indices: 42126726--42127028 Score: 349
Period size: 43 Copynumber: 7.1 Consensus size: 43
42126716 AAAGCGCCAT
* *
42126726 TAAAGAACGTGACCTTTAGCGACGCTTTTCACACAAAC-TCGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* *
42126768 TAAAGAACGTGACCTTTAGGGGCGCTTTTCACACAAACGCTGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * *
42126811 TAAAGAACGTGACCTTTAGTGGTGCTTTTCACACAAACGCCAC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * *
42126854 TAAAGAACGTGACCTGTAGCGGCGCTTTTCTCAAAAACGCCGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * * * *
42126897 TAAAGAACTTGACCTTTAGCGGCGCTTTT-ATAAAAAATGCCGT
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCA-CACAAACGCCGC
* * * * * *
42126940 TAAAGAACATGACCTTTAGCGGCACTTTTCATACTAATGACGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * * * *
42126983 TAAAGAACATGACCTTTAGCGGCGATTTTCTCAAAAACGCCAC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
42127026 TAA
1 TAA
42127029 TTTTAACATA
Statistics
Matches: 222, Mismatches: 36, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 36 0.16
43 185 0.83
44 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (43 bp):
TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
Found at i:42126899 original size:86 final size:86
Alignment explanation
Indices: 42126682--42127028 Score: 344
Period size: 86 Copynumber: 4.0 Consensus size: 86
42126672 AAAAAGGCTG
* * * * **
42126682 CTAAAGAACATGA-CTTTCAGCGGC-CTTTTTTGAGAAAGCGCCATTAAAGAACGTGACCTTTAG
1 CTAAAGAACGTGACCTTT-AGCGGCGCTTTTCTCACAAA-CGCCGCTAAAGAACGTGACCTTTAG
* * * *
42126745 CGACGCTTTTCACACAAAC-TCG
64 CGGCGCTTTTCACAAAAACGCCA
* * * *
42126767 CTAAAGAACGTGACCTTTAGGGGCGCTTTTCACACAAACGCTGCTAAAGAACGTGACCTTTAGTG
1 CTAAAGAACGTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACGTGACCTTTAGCG
* *
42126832 GTGCTTTTCACACAAACGCCA
66 GCGCTTTTCACAAAAACGCCA
* * *
42126853 CTAAAGAACGTGACCTGTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACTTGACCTTTAGCG
1 CTAAAGAACGTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACGTGACCTTTAGCG
* * *
42126918 GCGCTTTT-ATAAAAAATGCCG
66 GCGCTTTTCA-CAAAAACGCCA
* * * * * * *
42126939 TTAAAGAACATGACCTTTAGCGGCACTTTTCAT-ACTAATGACGCTAAAGAACATGACCTTTAGC
1 CTAAAGAACGTGACCTTTAGCGGCGCTTTTC-TCACAAACGCCGCTAAAGAACGTGACCTTTAGC
* *
42127003 GGCGATTTTCTCAAAAACGCCA
65 GGCGCTTTTCACAAAAACGCCA
42127025 CTAA
1 CTAA
42127029 TTTTAACATA
Statistics
Matches: 215, Mismatches: 41, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
85 56 0.26
86 158 0.73
87 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (86 bp):
CTAAAGAACGTGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACGTGACCTTTAGCG
GCGCTTTTCACAAAAACGCCA
Found at i:42126946 original size:129 final size:129
Alignment explanation
Indices: 42126670--42127028 Score: 384
Period size: 129 Copynumber: 2.8 Consensus size: 129
42126660 GTGTTTATGT
* * *** * *
42126670 AAAAAAAGGCTGCTAAAGAACATGA-CTTTCAGCGGC-CTTTTTTGAGAAAGCGCCATTAAAGAA
1 AAAAAAACGCCGCTAAAGAACATGACCTTT-AGCGGCACTTTTCACACAAA-CGCCACTAAAGAA
* * * * *
42126733 CGTGACCTTTAGCGACGCTTTTCACACAAAC-TCGCTAAAGAACGTGACCTTTAGGGGCGCTTTT
64 CGTGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTT
42126797 C
129 C
* * * * * **
42126798 ACACAAACGCTGCTAAAGAACGTGACCTTTAGTGGTGCTTTTCACACAAACGCCACTAAAGAACG
1 AAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCACACAAACGCCACTAAAGAACG
* *
42126863 TGACCTGTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACTTGACCTTTAGCGGCGCTTTT-
66 TGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTC
* * * * * * *
42126926 ATAAAAAATGCCGTTAAAGAACATGACCTTTAGCGGCACTTTTCATACTAATGACGCTAAAGAAC
1 A-AAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCACACAAACGCCACTAAAGAAC
* * *
42126991 ATGACCTTTAGCGGCGATTTTCTCAAAAACGCCACTAA
65 GTGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAA
42127029 TTTTAACATA
Statistics
Matches: 191, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
128 65 0.34
129 126 0.66
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (129 bp):
AAAAAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCACACAAACGCCACTAAAGAACG
TGACCTTTAGCGGCGCTTTTCTCAAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCGCTTTTC
Found at i:42127760 original size:13 final size:14
Alignment explanation
Indices: 42127727--42127762 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
42127717 AATGAATATT
42127727 CCATTATAATTAAA
1 CCATTATAATTAAA
*
42127741 CCATTATGATTAAA
1 CCATTATAATTAAA
42127755 -CATTATAA
1 CCATTATAA
42127763 ATATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (14 bp):
CCATTATAATTAAA
Found at i:42132294 original size:9 final size:9
Alignment explanation
Indices: 42132276--42132317 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
42132266 TATTTATGTA
42132276 TTATGTAAG
1 TTATGTAAG
*
42132285 TTAAGTAAG
1 TTATGTAAG
*
42132294 TTTTGTAAG
1 TTATGTAAG
42132303 TTATGTAAG
1 TTATGTAAG
42132312 TTATGT
1 TTATGT
42132318 TATGATATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42132421 original size:27 final size:27
Alignment explanation
Indices: 42132340--42132421 Score: 103
Period size: 30 Copynumber: 2.9 Consensus size: 27
42132330 TTATATAAGG
42132340 TATGTAAGTTATGATATGATATATATT
1 TATGTAAGTTATGATATGATATATATT
*
42132367 CATGTATTA-TACTATGATATGATATATATT
1 TATGTA--AGT--TATGATATGATATATATT
*
42132397 TATGTAAGTTATTATATGATATATA
1 TATGTAAGTTATGATATGATATATA
42132422 ATTAACATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 20 0.43
28 2 0.04
29 2 0.04
30 23 0.49
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (27 bp):
TATGTAAGTTATGATATGATATATATT
Found at i:42132715 original size:14 final size:14
Alignment explanation
Indices: 42132693--42132723 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42132683 CTTGTTTTAA
42132693 TATGATAATGGCAT
1 TATGATAATGGCAT
*
42132707 TATGGTAATGGCAT
1 TATGATAATGGCAT
42132721 TAT
1 TAT
42132724 TGACAAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (14 bp):
TATGATAATGGCAT
Found at i:42134993 original size:9 final size:9
Alignment explanation
Indices: 42134975--42135025 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
42134965 GAAACAAATT
*
42134975 CAAAATGCA
1 CAAAACGCA
42134984 CAAAACGCA
1 CAAAACGCA
42134993 CATAAAC-C-
1 CA-AAACGCA
42135001 CAAAACGCA
1 CAAAACGCA
42135010 CAAAACGCA
1 CAAAACGCA
42135019 CATAAAC
1 CA-AAAC
42135026 CCAAACCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 4 0.11
8 3 0.08
9 22 0.59
10 8 0.22
ACGTcount: A:0.55, C:0.31, G:0.08, T:0.06
Consensus pattern (9 bp):
CAAAACGCA
Found at i:42135004 original size:26 final size:26
Alignment explanation
Indices: 42134975--42135030 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
42134965 GAAACAAATT
*
42134975 CAAAATGCACAAAACGCACATAAACC
1 CAAAACGCACAAAACGCACATAAACC
42135001 CAAAACGCACAAAACGCACATAAACC
1 CAAAACGCACAAAACGCACATAAACC
42135027 CAAA
1 CAAA
42135031 CCCAAAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.55, C:0.32, G:0.07, T:0.05
Consensus pattern (26 bp):
CAAAACGCACAAAACGCACATAAACC
Found at i:42135030 original size:17 final size:16
Alignment explanation
Indices: 42134984--42135015 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42134974 TCAAAATGCA
42134984 CAAAACGCACATAAACC
1 CAAAACGCACA-AAACC
42135001 CAAAACGCACAAAAC
1 CAAAACGCACAAAAC
42135016 GCACATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.34, G:0.06, T:0.03
Consensus pattern (16 bp):
CAAAACGCACAAAACC
Found at i:42135153 original size:17 final size:19
Alignment explanation
Indices: 42135112--42135156 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
42135102 GACAGCAGTG
* *
42135112 GAGAGAAGAGGGTGTGACA
1 GAGAGAAGAGGATGCGACA
*
42135131 GAGAGAAGAGGATGCGACG
1 GAGAGAAGAGGATGCGACA
42135150 GAGAGAA
1 GAGAGAA
42135157 AACGAATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.47, T:0.07
Consensus pattern (19 bp):
GAGAGAAGAGGATGCGACA
Found at i:42139954 original size:29 final size:29
Alignment explanation
Indices: 42139911--42139985 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
42139901 CATGATTATG
* *
42139911 AATGTGA-CTGGGCCTAACGGGCCATATA
1 AATGTGATTTGGGCCTAACAGGCCATATA
**
42139939 AATGTGATTTGGGCCTAGTAGGCCATATA
1 AATGTGATTTGGGCCTAACAGGCCATATA
* *
42139968 CAGGTGATTTGGGCCTAA
1 AATGTGATTTGGGCCTAA
42139986 TGAGTCATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 7 0.18
29 32 0.82
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAACAGGCCATATA
Found at i:42139994 original size:29 final size:29
Alignment explanation
Indices: 42139919--42139995 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
42139909 TGAATGTGAC
* * *
42139919 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGAGCCATATAAAGGTGATT
* *
42139948 TGGGCCTAGT-AGGCCATATACAGGTGATT
1 TGGGCCTAATGA-GCCATATAAAGGTGATT
*
42139977 TGGGCCTAATGAGTCATAT
1 TGGGCCTAATGAGCCATAT
42139996 GAATATGATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGAGCCATATAAAGGTGATT
Found at i:42151329 original size:42 final size:43
Alignment explanation
Indices: 42151229--42151378 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 43
42151219 CAATGCCAGG
* ** * *
42151229 GTCCCAGATATGGTCTTACATGTAATCAAATATTGATGCCACT
1 GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
* * * *
42151272 GTCCCTGACAGGGTCTTACACAAAATCATATA-CGATGCCAAT
1 GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
* * *
42151314 GTCCCAGACATGGTCTTACATTTAAATCAAAAATCGATGCCAAC
1 GTCCCAGACATGGTCTTACA-TAAAATCAAATATCGATGCCAAT
**
42151358 GTCCCAGATGTGGTCTTACAT
1 GTCCCAGACATGGTCTTACAT
42151379 GATAACACAC
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
42 26 0.30
43 34 0.39
44 27 0.31
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATAAAATCAAATATCGATGCCAAT
Found at i:42156605 original size:42 final size:43
Alignment explanation
Indices: 42156540--42156622 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 43
42156530 TCTTCCATGT
* *
42156540 AATCAAATATCGATGCCACTGTCCCTGACAGGGTCCTACACGA
1 AATCAAATATCGATGCCAATGTCCCAGACAGGGTCCTACACGA
* * * *
42156583 AATCATATA-CGATGTCAATGTCCCAGACATGGTCTTACAC
1 AATCAAATATCGATGCCAATGTCCCAGACAGGGTCCTACAC
42156623 ATAAATCACA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 26 0.76
43 8 0.24
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
AATCAAATATCGATGCCAATGTCCCAGACAGGGTCCTACACGA
Found at i:42159758 original size:117 final size:116
Alignment explanation
Indices: 42159562--42159807 Score: 359
Period size: 117 Copynumber: 2.1 Consensus size: 116
42159552 ACAGGCATGC
* * * *
42159562 CACATGCCCATGTGCTAGGCCATGTGGTTAATTAATGTTTTTTGAACCTAGGTGTAGGATTCACA
1 CACACGCCCATGTGCTAGGCCATGTGGTTAATTAATGTTTTTTGAAACTAGGTGCAGGAATCACA
**
42159627 CGACCAAGACACATG-CTCGTGTTCTAGGCTTTGTAGCACACACGGCTAAGA
66 CGACCAAGACACATGCCT-GTGTTCTAGGCCGTGTAGCACACACGGCTAAGA
* * * *
42159678 CACACGCCCGTGTGCTAGGCCGTGTGGTTAATTAACTTTTTTTTGAAATTAGGTGCAGGAATCAC
1 CACACGCCCATGTGCTAGGCCATGTGGTTAATTAA-TGTTTTTTGAAACTAGGTGCAGGAATCAC
*
42159743 ACGACCAAGACACATGCCTGTGTTCTAGGCCGTGTAGCACACACGGCTGAGA
65 ACGACCAAGACACATGCCTGTGTTCTAGGCCGTGTAGCACACACGGCTAAGA
*
42159795 CACACGCCTATGT
1 CACACGCCCATGT
42159808 CTCTGCCCGT
Statistics
Matches: 115, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
116 32 0.28
117 81 0.70
118 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (116 bp):
CACACGCCCATGTGCTAGGCCATGTGGTTAATTAATGTTTTTTGAAACTAGGTGCAGGAATCACA
CGACCAAGACACATGCCTGTGTTCTAGGCCGTGTAGCACACACGGCTAAGA
Found at i:42167454 original size:162 final size:162
Alignment explanation
Indices: 42167185--42167503 Score: 575
Period size: 162 Copynumber: 2.0 Consensus size: 162
42167175 AGTACTTGAA
*
42167185 ATGAATTATCATTGTATAAGATCCTTATACAAAGCAATATGAACCAGAAGTTAAACAGATAATTC
1 ATGAATTATCATTGTATAAGATCCTTATACAAAGAAATATGAACCAGAAGTTAAACAGATAATTC
* *
42167250 ATTTTACAAATCAACTGCTAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
66 ATTTTACAAATCAACTACCAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
*
42167315 GCTAAAAATGTTCCAATACGAATTGATACTCT
131 ACTAAAAATGTTCCAATACGAATTGATACTCT
* *
42167347 ATGAATTATCATTGTATAAGATCCTTGTACAAAGAAATATGAACCAGAAGTTCAACAGATAATTC
1 ATGAATTATCATTGTATAAGATCCTTATACAAAGAAATATGAACCAGAAGTTAAACAGATAATTC
*
42167412 ATTTTACAAATCAACTACCAGATTCATTTATTGACTTAAAGAGAATTACAAAATCTCACATATCA
66 ATTTTACAAATCAACTACCAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
42167477 ACTAAAAATGTTCCAATACGAATTGAT
131 ACTAAAAATGTTCCAATACGAATTGAT
42167504 GTCCCAATAG
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 150 1.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (162 bp):
ATGAATTATCATTGTATAAGATCCTTATACAAAGAAATATGAACCAGAAGTTAAACAGATAATTC
ATTTTACAAATCAACTACCAGATTCATTTATTGACCTAAAGAGAATTACAAAATCTCACATATCA
ACTAAAAATGTTCCAATACGAATTGATACTCT
Found at i:42173118 original size:14 final size:13
Alignment explanation
Indices: 42173095--42173126 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
42173085 GGGATATCAA
42173095 AACAATAATTAAG
1 AACAATAATTAAG
42173108 AACACATAATTAAG
1 AACA-ATAATTAAG
42173122 AACAA
1 AACAA
42173127 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:42183252 original size:47 final size:47
Alignment explanation
Indices: 42183160--42183254 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 47
42183150 ATGGGTAAGG
**
42183160 TGTCGATGCCATGTCCCAGACACGATCTTACACTGGCTTATATCTCA
1 TGTCGATGCCATGTCCCAGACACGATCTTACACTAACTTATATCTCA
* * * *
42183207 TGTCGATGCCATGTTCCAGACATGGTGTTACACTAAC-TATCATCTCA
1 TGTCGATGCCATGTCCCAGACACGATCTTACACTAACTTAT-ATCTCA
42183254 T
1 T
42183255 AGCCTATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 3 0.07
47 38 0.93
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (47 bp):
TGTCGATGCCATGTCCCAGACACGATCTTACACTAACTTATATCTCA
Found at i:42187662 original size:50 final size:50
Alignment explanation
Indices: 42187608--42187708 Score: 139
Period size: 50 Copynumber: 2.0 Consensus size: 50
42187598 CGTGTGAGGC
* * **
42187608 ACACGGCCTGCTTGCACAAGCATGTGACATGTGAATGTAATTTTTTTCTA
1 ACACGGCCTGCTTACACAAGCATGTGACATGTGAACGTAAAATTTTTCTA
* * *
42187658 ACACGGCCTGCTTACACAGGCGTGTGACCTGTGAACGTAAAATTTTTCTA
1 ACACGGCCTGCTTACACAAGCATGTGACATGTGAACGTAAAATTTTTCTA
42187708 A
1 A
42187709 GTGTTTGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (50 bp):
ACACGGCCTGCTTACACAAGCATGTGACATGTGAACGTAAAATTTTTCTA
Found at i:42188372 original size:20 final size:20
Alignment explanation
Indices: 42188347--42188394 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
42188337 AAATAGGGTC
42188347 ACACGCCCATGTGGCTAGGG
1 ACACGCCCATGTGGCTAGGG
* *
42188367 ACACGCCGATGTGGCTTGGG
1 ACACGCCCATGTGGCTAGGG
42188387 ACACGCCC
1 ACACGCCC
42188395 GTGTCCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.15
Consensus pattern (20 bp):
ACACGCCCATGTGGCTAGGG
Found at i:42202242 original size:43 final size:44
Alignment explanation
Indices: 42202195--42202293 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 44
42202185 CATCAATTTG
*
42202195 TGATTTACATGTAAGAAC-ATGTCTGAGACATTGGCATC-ATATA
1 TGATTTACATGTAAG-ACTATGTCTGAGACAGTGGCATCGATATA
* * * *
42202238 TGATTT-CGTGTAAGACTCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTACATGTAAGACTATGTCTGAGACAGTGGCATCGATATA
42202281 TGA-TTACATGTAA
1 TGATTTACATGTAA
42202294 AACCACGTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.04
42 26 0.55
43 19 0.40
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (44 bp):
TGATTTACATGTAAGACTATGTCTGAGACAGTGGCATCGATATA
Found at i:42202314 original size:85 final size:85
Alignment explanation
Indices: 42202160--42202316 Score: 198
Period size: 85 Copynumber: 1.8 Consensus size: 85
42202150 ATGTGTTATT
* *
42202160 GTGTAAGACTGCGTCTGGGACGTTGCATCAATTTGTGATTTACATGTAAGAACATGTCTGAGACA
1 GTGTAAGACTGCGTCTGGGACGTGGCATCAATTTGTGATTTACATGTAAGAACACGTCTGAGACA
42202225 TTGGCATCATATATGATTTC
66 TTGGCATCATATATGATTTC
*
42202245 GTGTAAGACT-CTGTCTGGGACAGTGGCATCGATATT-TGA-TTACATGTAA-AACCACGTCT-A
1 GTGTAAGACTGC-GTCTGGGAC-GTGGCATCAAT-TTGTGATTTACATGTAAGAA-CACGTCTGA
*
42202305 GGACGTTGGCAT
62 -GACATTGGCAT
42202317 TGTACGAGCT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
84 4 0.06
85 45 0.71
86 12 0.19
87 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (85 bp):
GTGTAAGACTGCGTCTGGGACGTGGCATCAATTTGTGATTTACATGTAAGAACACGTCTGAGACA
TTGGCATCATATATGATTTC
Found at i:42202315 original size:43 final size:42
Alignment explanation
Indices: 42202171--42202316 Score: 113
Period size: 43 Copynumber: 3.4 Consensus size: 42
42202161 TGTAAGACTG
42202171 CGTCTGGGACGTT-GCATCA-ATTTGTGATTTACATGTAAGAA-CA
1 CGTCTGGGACGTTGGCATCATA-TT-TGA-TTACATGTAA-AACCA
* * * * * * *
42202214 TGTCTGAGACATTGGCATCATATATGATTTCGTGTAAGACTC-
1 CGTCTGGGACGTTGGCATCATATTTGATTACATGTAAAAC-CA
*
42202256 TGTCTGGGACAG-TGGCATCGATATTTGATTACATGTAAAACCA
1 CGTCTGGGAC-GTTGGCATC-ATATTTGATTACATGTAAAACCA
*
42202299 CGTCTAGGACGTTGGCAT
1 CGTCTGGGACGTTGGCAT
42202317 TGTACGAGCT
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
42 26 0.32
43 45 0.56
44 7 0.09
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (42 bp):
CGTCTGGGACGTTGGCATCATATTTGATTACATGTAAAACCA
Found at i:42210446 original size:9 final size:9
Alignment explanation
Indices: 42210434--42210500 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
42210424 TGATATATAT
42210434 TTATGTAAG
1 TTATGTAAG
42210443 TTATGTAAG
1 TTATGTAAG
*
42210452 TTATGATATG
1 TTATG-TAAG
* * *
42210462 ATATAT-AT
1 TTATGTAAG
42210470 TTATGT-A-
1 TTATGTAAG
42210477 TTATGTAAG
1 TTATGTAAG
42210486 TTATGTAAG
1 TTATGTAAG
42210495 TTATGT
1 TTATGT
42210501 TGCAACGCCC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 30 0.62
10 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42210448 original size:36 final size:34
Alignment explanation
Indices: 42210407--42210490 Score: 150
Period size: 36 Copynumber: 2.4 Consensus size: 34
42210397 ATCCAAAGTT
42210407 TTATGTAAGTTATGATATGATATATATTTATGTAA
1 TTATGTAAGTTATGATATGATATATATTTATGT-A
42210442 GTTATGTAAGTTATGATATGATATATATTTATGTA
1 -TTATGTAAGTTATGATATGATATATATTTATGTA
42210477 TTATGTAAGTTATG
1 TTATGTAAGTTATG
42210491 TAAGTTATGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 14 0.29
35 1 0.02
36 33 0.69
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.49
Consensus pattern (34 bp):
TTATGTAAGTTATGATATGATATATATTTATGTA
Found at i:42212167 original size:46 final size:45
Alignment explanation
Indices: 42212100--42212255 Score: 151
Period size: 48 Copynumber: 3.4 Consensus size: 45
42212090 GCTAGTATAA
42212100 GACATGCATCGGCCT-CGAGATGTAAG-CTAGTGTAAGA-CATGTCTGG
1 GACATGCATCGG-CTACGAGATGT--GTC-AGTGTAAGACCATGTCTGG
*
42212146 GACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTTTGG
1 GACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTGG
* * * *
42212191 GACATGGTATC-GATACGTATAGAGGTGTCAGTGTAAGACTATGTCTGG
1 GACAT-GCATCGGCTACG---AGATGTGTCAGTGTAAGACCATGTCTGG
42212239 GACATGGCATCGG-TACG
1 GACAT-GCATCGGCTACG
42212256 GATATACGAG
Statistics
Matches: 95, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
44 10 0.11
45 21 0.22
46 24 0.25
48 39 0.41
49 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (45 bp):
GACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTGG
Found at i:42212279 original size:50 final size:48
Alignment explanation
Indices: 42212128--42212296 Score: 163
Period size: 48 Copynumber: 3.6 Consensus size: 48
42212118 GATGTAAGCT
* * *
42212128 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACG---AGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GATACGTATAGAGGTCTC
* * *
42212172 AGTGTAAGACCATGTTTGGGACATGGTATCGATACGTATAGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGATACGTATAGAGGTCTC
* *
42212220 AGTGTAAGACTATGTCTGGGACATGGCATCGGTACGGATATACGAGAG-CT-
1 AGTGTAAGACCATGTCTGGGACATGGCATCGATAC-G-TATA-GAG-GTCTC
*
42212270 AGTGTAAGACCATGTCTGGTACATGGC
1 AGTGTAAGACCATGTCTGGGACATGGC
42212297 GTTGGCCTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
44 9 0.09
45 18 0.17
46 4 0.04
48 39 0.37
49 1 0.01
50 29 0.28
51 4 0.04
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGATACGTATAGAGGTCTC
Found at i:42237531 original size:47 final size:48
Alignment explanation
Indices: 42237462--42237554 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 48
42237452 ATTCCATGTG
* *
42237462 ACATCACCAGATTCGGTCATAACGTTTAGGCCGGGTTT-GGGTGTTTC
1 ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTTTC
42237509 ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTT
1 ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTT
42237555 ACATATGTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
47 36 0.84
48 7 0.16
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (48 bp):
ACATCACCAGATTCGGTCATAACGTCTAGGCCAGGTTTGGGGTGTTTC
Found at i:42237673 original size:35 final size:35
Alignment explanation
Indices: 42237634--42237700 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
42237624 TTTTTTTATT
*
42237634 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATATTTATGTAAGTTATGATAATCATAAA
* *
42237669 CTTTAATTATTTATGTAAGTTATGATTATCAT
1 CTTTAAATATTTATGTAAGTTATGATAATCAT
42237701 CTTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (35 bp):
CTTTAAATATTTATGTAAGTTATGATAATCATAAA
Found at i:42238168 original size:35 final size:35
Alignment explanation
Indices: 42238132--42238199 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
42238122 CTATGAAAAT
*
42238132 TTTAACTTTAAAACT-AAATATAA-AAATTAATAAA
1 TTTAAATTTAAAACTCAAA-ATAATAAATTAATAAA
* *
42238166 TTTAAATTTAGAATTCAAAATAATAAATTAATAA
1 TTTAAATTTAAAACTCAAAATAATAAATTAATAA
42238200 CATAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (35 bp):
TTTAAATTTAAAACTCAAAATAATAAATTAATAAA
Found at i:42238266 original size:19 final size:20
Alignment explanation
Indices: 42238242--42238279 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42238232 TATCTTAAAT
42238242 TTTAAAAT-AAAAATAAAAA
1 TTTAAAATCAAAAATAAAAA
*
42238261 TTTAAAATCAAAACTAAAA
1 TTTAAAATCAAAAATAAAA
42238280 TAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (20 bp):
TTTAAAATCAAAAATAAAAA
Found at i:42238280 original size:19 final size:18
Alignment explanation
Indices: 42238237--42238293 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
42238227 CAAGTTATCT
*
42238237 TAAATTTTAAAATAAAAA
1 TAAAATTTAAAATAAAAA
*
42238255 TAAAAATTTAAAATCAAAAC
1 T-AAAATTTAAAAT-AAAAA
*
42238275 TAAAA-TAAATAATAAAAA
1 TAAAATTTAA-AATAAAAA
42238293 T
1 T
42238294 TGAATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.28
19 18 0.56
20 5 0.16
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAATTTAAAATAAAAA
Found at i:42238731 original size:72 final size:72
Alignment explanation
Indices: 42238654--42238845 Score: 198
Period size: 72 Copynumber: 2.7 Consensus size: 72
42238644 AAATGGTTCC
* *
42238654 ACTTAATATCAAAATTCAATAAGTTGAACTAAATTAACCTCTTTAAAAAT-TCA-AAATTGA-AC
1 ACTTAATATCAAAATTCAATAAATTGAACTAAATTAACCT-TTTAAAAATGT-ATAAATAGATA-
*
42238716 AAATGTCTT-T
63 AAAGGT-TTCT
* ** * * * *
42238726 ACTTAATATCAAATTTCAATAAATCAAACTAAATTAAGCTTCTAAAAATGTATAACTAGATAAAC
1 ACTTAATATCAAAATTCAATAAATTGAACTAAATTAACCTTTTAAAAATGTATAAATAGATAAAA
42238791 GGTTTCT
66 GGTTTCT
42238798 -CTTAATATCAAAACTT-AATAAATTGAACTAAATTAACCTTTTTAAAAA
1 ACTTAATATCAAAA-TTCAATAAATTGAACTAAATTAACC-TTTTAAAAA
42238846 CACATAATTA
Statistics
Matches: 99, Mismatches: 15, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
71 42 0.42
72 56 0.57
73 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (72 bp):
ACTTAATATCAAAATTCAATAAATTGAACTAAATTAACCTTTTAAAAATGTATAAATAGATAAAA
GGTTTCT
Found at i:42243944 original size:22 final size:22
Alignment explanation
Indices: 42243901--42243944 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42243891 AACATATAAT
*
42243901 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
42243923 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
42243945 CAGCAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:42244783 original size:25 final size:24
Alignment explanation
Indices: 42244749--42244795 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
42244739 GGATAGGATT
42244749 TTGTCAAATGAAATAATAAAAATAA
1 TTGTCAAATGAAATAA-AAAAATAA
*
42244774 TTGTTAAATGAAATAAAAAAAT
1 TTGTCAAATGAAATAAAAAAAT
42244796 TGGGTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (24 bp):
TTGTCAAATGAAATAAAAAAATAA
Found at i:42244890 original size:20 final size:20
Alignment explanation
Indices: 42244865--42244904 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42244855 TGAGAAATGA
42244865 AATAAAACTTGCTTATCATT
1 AATAAAACTTGCTTATCATT
42244885 AATAAAACTTGCTTATCATT
1 AATAAAACTTGCTTATCATT
42244905 CATTTTTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (20 bp):
AATAAAACTTGCTTATCATT
Found at i:42245268 original size:40 final size:40
Alignment explanation
Indices: 42245215--42245315 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
42245205 AAAATGATAC
* **
42245215 TTTGCGGCCTTTTTCTCATAAC-GTAGCTAATGCTTGAAC-T
1 TTTGCGGCGTTTTTCTCATAACACCA-CTAATGCTTG-ACTT
*
42245255 TTTGCAGCGTTTTTCTCATAACACCACTAATGCTTGACTT
1 TTTGCGGCGTTTTTCTCATAACACCACTAATGCTTGACTT
*
42245295 TTTGTGGCGTTTTTCTCATAA
1 TTTGCGGCGTTTTTCTCATAA
42245316 ACGCCAGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.04
40 50 0.94
41 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (40 bp):
TTTGCGGCGTTTTTCTCATAACACCACTAATGCTTGACTT
Found at i:42245346 original size:41 final size:40
Alignment explanation
Indices: 42245224--42245351 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 40
42245214 CTTTGCGGCC
** * * *
42245224 TTTTTCTCATAAC-GTAGCTAATGCTTGAACTTTTGCAGCG
1 TTTTTCTCATAACACCA-CTAATGCTTGACCTATTGTAGCG
* * *
42245264 TTTTTCTCATAACACCACTAATGCTTGACTTTTTGTGGCG
1 TTTTTCTCATAACACCACTAATGCTTGACCTATTGTAGCG
* * * *
42245304 TTTTTCTCATAAACGCCAGTACTGCTTTACCTATTGTAGCG
1 TTTTTCTCAT-AACACCACTAATGCTTGACCTATTGTAGCG
42245345 TTTTTCT
1 TTTTTCT
42245352 GTTAGCTCCA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 42 0.58
41 31 0.42
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (40 bp):
TTTTTCTCATAACACCACTAATGCTTGACCTATTGTAGCG
Found at i:42251923 original size:99 final size:99
Alignment explanation
Indices: 42251810--42252008 Score: 389
Period size: 99 Copynumber: 2.0 Consensus size: 99
42251800 ATGATTGCCG
*
42251810 AGGTGTTGAAAGTAAGTATAATTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
1 AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
42251875 GAAAGTATGTAAGTTTGTATATAAATAATACATT
66 GAAAGTATGTAAGTTTGTATATAAATAATACATT
42251909 AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
1 AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
42251974 GAAAGTATGTAAGTTTGTATATAAATAATACATT
66 GAAAGTATGTAAGTTTGTATATAAATAATACATT
42252008 A
1 A
42252009 TCTTTATTAT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (99 bp):
AGGTGTTGAAAGTAAGTATAAGTATGATGATTTAAATGTTCAATATTAATTCGACATGGAAATGA
GAAAGTATGTAAGTTTGTATATAAATAATACATT
Found at i:42252386 original size:66 final size:65
Alignment explanation
Indices: 42252229--42252386 Score: 162
Period size: 67 Copynumber: 2.4 Consensus size: 65
42252219 ATTATGATGT
* * * * *
42252229 AGCTAGGTCACATGGGTGATACT-A-TGTGTACACCATGTAGACAAGAGAGCTACGGGATATATG
1 AGCTAGGTCACATGGGTGGTACTAAGTGAGGACACCATGTAGACAAGAGAGCTACGAGATAAATG
* * * * *
42252292 TAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGTA-AGTTACGAGATAA
1 -AGCTAGGTCACATGGGTGGTACTAAGTG-AGGACACCATGTAGACAAG-AGAGCTACGAGATAA
42252356 ACTG
63 A-TG
42252360 -GCTAGGTCACATGGGTGGTACTAAGTG
1 AGCTAGGTCACATGGGTGGTACTAAGTG
42252387 TTCACCATGT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
64 18 0.24
65 1 0.01
66 25 0.33
67 28 0.37
68 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (65 bp):
AGCTAGGTCACATGGGTGGTACTAAGTGAGGACACCATGTAGACAAGAGAGCTACGAGATAAATG
Found at i:42266511 original size:30 final size:29
Alignment explanation
Indices: 42266477--42266540 Score: 110
Period size: 30 Copynumber: 2.2 Consensus size: 29
42266467 ATGAATCGGA
42266477 AGCTTTGGCACTAAGTGTGCGATTTAAACT
1 AGCTTTGGCACTAAGTGTGCGATTT-AACT
*
42266507 AGCTTTGGCACTAAGTGTGTGATTTAACT
1 AGCTTTGGCACTAAGTGTGCGATTTAACT
42266536 AGCTT
1 AGCTT
42266541 CGGTTACTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (29 bp):
AGCTTTGGCACTAAGTGTGCGATTTAACT
Found at i:42267384 original size:87 final size:87
Alignment explanation
Indices: 42267277--42267451 Score: 314
Period size: 87 Copynumber: 2.0 Consensus size: 87
42267267 GGTTTATAAG
*
42267277 TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAGCTTAAAGAATGGTTGATT
1 TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
*
42267342 GGGTTGTACATATATGTTTGAT
66 GGGTTGTACATATATGCTTGAT
*
42267364 TATGTAAATTATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
1 TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
*
42267429 GGGTTGTACGTATATGCTTGAT
66 GGGTTGTACATATATGCTTGAT
42267451 T
1 T
42267452 CCTTGTTTGT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (87 bp):
TATGTAAATGATTGATAATATTATGGCATGAATGATGTATGTTTTAACTTAAAGAATGGTTGATT
GGGTTGTACATATATGCTTGAT
Found at i:42277499 original size:22 final size:21
Alignment explanation
Indices: 42277469--42277518 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
42277459 TATTTTTATT
*
42277469 TAAATTTAATTATAAA-ATATA
1 TAAATTTAA-AATAAACATATA
42277490 TAAATATTAAAATAAACATATA
1 TAAAT-TTAAAATAAACATATA
*
42277512 TATATTT
1 TAAATTT
42277519 CTTAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTAAAATAAACATATA
Found at i:42279141 original size:51 final size:50
Alignment explanation
Indices: 42279072--42279189 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 50
42279062 TTCAAGTTTT
* *
42279072 TTTCATTTTTCATTTTCATTTTGGAGAAAACCATATTCATTTCCAAATAA
1 TTTCATTTCTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATAA
* * **
42279122 TTTCATTTCTCTATTTTCATTTTGGAGAAAATCATAATCATTTTCAAATGT
1 TTTCATTTCTC-ATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATAA
42279173 TTTCTATTTCTCCATTT
1 TTTC-ATTTCT-CATTT
42279190 CTCTATTTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 10 0.17
51 38 0.64
52 10 0.17
53 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (50 bp):
TTTCATTTCTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATAA
Found at i:42279209 original size:10 final size:10
Alignment explanation
Indices: 42279194--42279227 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
42279184 CCATTTCTCT
42279194 ATTTCTATTC
1 ATTTCTATTC
42279204 ATTTCTATTC
1 ATTTCTATTC
*
42279214 ATTTCTTTTC
1 ATTTCTATTC
42279224 ATTT
1 ATTT
42279228 AATTCAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTCTATTC
Found at i:42280445 original size:12 final size:13
Alignment explanation
Indices: 42280428--42280460 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42280418 TCTTATTTTA
42280428 TTTATTTTGA-TT
1 TTTATTTTGATTT
*
42280440 TTTATTTTTATTT
1 TTTATTTTGATTT
42280453 TTTATTTT
1 TTTATTTT
42280461 ATATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTATTTTGATTT
Found at i:42286069 original size:23 final size:22
Alignment explanation
Indices: 42286023--42286074 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42286013 AAAATTCGGC
42286023 AAAGG-GA-AAAAGGAAAATAA
1 AAAGGAGAGAAAAGGAAAATAA
*
42286043 AAAGGTAGAGAAAAGAGAAAA-AG
1 AAAGG-AGAGAAAAG-GAAAATAA
42286066 AAAGGAGAG
1 AAAGGAGAG
42286075 TTTCAGTAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.19
22 6 0.22
23 11 0.41
24 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (22 bp):
AAAGGAGAGAAAAGGAAAATAA
Found at i:42300104 original size:13 final size:13
Alignment explanation
Indices: 42300086--42300114 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42300076 GGTTGTTTAT
42300086 TAAACTAATTAAC
1 TAAACTAATTAAC
42300099 TAAACTAATTAAC
1 TAAACTAATTAAC
42300112 TAA
1 TAA
42300115 TTAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:42304096 original size:47 final size:45
Alignment explanation
Indices: 42303931--42304285 Score: 224
Period size: 47 Copynumber: 7.6 Consensus size: 45
42303921 TTACCAATGC
* * *
42303931 CATGTCCCAGACATGGTCTTACACT-GCCTCTCATATACGCATGCTGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCATCTC-TAT--G-AGGCCGATG
* *
42303980 CATGTCCCAGACATGTCTTACACTAGCACAACTCT-T-A-GCCGATG
1 CATGTCCCAGACATGTCTTACACT-G-GCATCTCTATGAGGCCGATG
*** * * * *
42304024 TGCGTCCCGGAAATGTATTACACTGGCTATCTCTATCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTGGC-ATCTCTAT-GAGGCCGATG
* * *
42304071 CATGTCCCAGACATGTCTTACACTGGCACTAATCTCTG-TGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCA-T-CTCTATGAGGCCGATG
* * *
42304117 CCATGTCCCAGACATGGTCTTACACTAGC-TATC-ATAGTATGGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCATCTCTAT-G-A-GGCCGATG
* * * *
42304165 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCT-GGATGCCGATG
1 CATGTCCCAGACATGTCTTACACT-GGCATC-TCTATGAGGCCGATG
* * *
42304211 CCATGTCCCAGACATGGTCTTACACTGGC-TCTCATGATGTGGCCAAAG
1 -CATGTCCCAGACAT-GTCTTACACTGGCATCTC-T-ATGAGGCCGATG
42304259 CATGTCCCAGACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
42304286 GCACAAATCA
Statistics
Matches: 242, Mismatches: 39, Indels: 53
0.72 0.12 0.16
Matches are distributed among these distances:
42 1 0.00
43 6 0.02
44 26 0.11
45 7 0.03
46 41 0.17
47 89 0.37
48 50 0.21
49 17 0.07
50 1 0.00
51 4 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTGGCATCTCTATGAGGCCGATG
Found at i:42304183 original size:94 final size:93
Alignment explanation
Indices: 42303927--42304282 Score: 359
Period size: 94 Copynumber: 3.8 Consensus size: 93
42303917 TATATTACCA
* * * * **
42303927 ATGCCATGTCCCAGACATGGTCTTACACTGCCTCTCATATACGCATGCTGATGCATGTCCCAGAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGTATG---GCCAATGCATGTCCCAGAC
42303992 ATGTCTTACACTAGCAC-AA-CTCT-TAGCCG
63 ATGTCTTACACTAGCACTAATCTCTGT-GCCG
* * * * *
42304021 ATGTGC--GTCCCGGAAAT-GTATTACACTGGCTATC-TCTATCGAGGCCAATGCATGTCCCAGA
1 ATG-CCATGTCCCAGACATGGTCTTACACTGGCTATCATGTAT---GGCCAATGCATGTCCCAGA
*
42304082 CATGTCTTACACTGGCACTAATCTCTGTGCCG
62 CATGTCTTACACTAGCACTAATCTCTGTGCCG
* **
42304114 ATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATAGTATGGCTGATGCATGTCCCAGACAT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-GTATGGCCAATGCATGTCCCAGACAT
* ** *
42304179 GTCTTACACTAGCCCTCGTCT-GGATGCCG
65 GTCTTACACTAGCACTAATCTCTG-TGCCG
* * *
42304208 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATGATGTGGCCAAAGCATGTCCCAGACAT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATG-TATGGCCAATGCATGTCCCAGACAT
42304273 GTCTTACACT
65 GTCTTACACT
42304283 GGCGCACAAA
Statistics
Matches: 218, Mismatches: 30, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
91 36 0.17
92 17 0.08
93 22 0.10
94 123 0.56
95 16 0.07
96 1 0.00
97 3 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (93 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGTATGGCCAATGCATGTCCCAGACATG
TCTTACACTAGCACTAATCTCTGTGCCG
Found at i:42308029 original size:14 final size:13
Alignment explanation
Indices: 42308006--42308037 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
42307996 GGGATATCAA
42308006 AACAATAATTAAG
1 AACAATAATTAAG
42308019 AACACATAATTAAG
1 AACA-ATAATTAAG
42308033 AACAA
1 AACAA
42308038 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:42308497 original size:52 final size:51
Alignment explanation
Indices: 42308435--42308574 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 51
42308425 GTGTTTGAGC
*
42308435 CTGCCAAATTGACACGGTCGTGTGGTCTGCCCGTGTGAATCATGCTTCGATT
1 CTGCCAAATTGACACGG-CGTGTGGTCTGCCCGTGTGAATCATGCTTCAATT
* *
42308487 TTGCCAAATTGACACGGCTGTGTGGTCTGCCCGTGTGAATCGTGCTTCAATT
1 CTGCCAAATTGACACGGC-GTGTGGTCTGCCCGTGTGAATCATGCTTCAATT
*
42308539 CTACCAAATTGACACGGCCGTGTGAG-CTGCCCGTGT
1 CTGCCAAATTGACACGG-CGTGTG-GTCTGCCCGTGT
42308575 AAGGAAGTCC
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
51 1 0.01
52 77 0.96
53 2 0.03
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (51 bp):
CTGCCAAATTGACACGGCGTGTGGTCTGCCCGTGTGAATCATGCTTCAATT
Found at i:42316591 original size:13 final size:13
Alignment explanation
Indices: 42316573--42316625 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
42316563 GCTTGGCAGG
*
42316573 GACATACCCGTGT
1 GACACACCCGTGT
*
42316586 GACATACCCGTGT
1 GACACACCCGTGT
42316599 GACACACCCGTGT
1 GACACACCCGTGT
*
42316612 GACACGCCCGTGT
1 GACACACCCGTGT
42316625 G
1 G
42316626 CGATTACTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (13 bp):
GACACACCCGTGT
Found at i:42317262 original size:71 final size:71
Alignment explanation
Indices: 42317170--42317308 Score: 251
Period size: 71 Copynumber: 2.0 Consensus size: 71
42317160 TTATAAGGAC
* *
42317170 TATTTTGTAAAAGATGTAAATGTGTGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
42317235 AGAGAA
66 AGAGAA
*
42317241 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCATA
1 TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
42317306 AGA
66 AGA
42317309 AGGAAAAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (71 bp):
TATTCTGTAAAAGATGTAAATGTATGGTAGAAATGAGAAAATAATGGATAATGTGGGCTACCACA
AGAGAA
Found at i:42318177 original size:21 final size:21
Alignment explanation
Indices: 42318151--42318196 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
42318141 ATTCCATCGG
42318151 GATTTCCTAGAAACTCAACGA
1 GATTTCCTAGAAACTCAACGA
42318172 GATTTCCTAGAAACTCAACGA
1 GATTTCCTAGAAACTCAACGA
42318193 GATT
1 GATT
42318197 AATTGATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (21 bp):
GATTTCCTAGAAACTCAACGA
Found at i:42331274 original size:12 final size:12
Alignment explanation
Indices: 42331259--42331285 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42331249 CTATTTTCAT
42331259 TTTCCATTTCCA
1 TTTCCATTTCCA
42331271 TTTCCATTTCCA
1 TTTCCATTTCCA
42331283 TTT
1 TTT
42331286 TGGAAACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.30, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTCCATTTCCA
Found at i:42333239 original size:53 final size:54
Alignment explanation
Indices: 42333148--42333615 Score: 240
Period size: 54 Copynumber: 9.0 Consensus size: 54
42333138 TCGGGAACCT
* * * * * * **
42333148 TTTCCTTTTTGAACTTACCATTGCCTTGTCTTGACATGGTCTTATGTGGTATCC
1 TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
* * *
42333202 TTTCCTTAT-GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CTT
1 TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATC-C
** * * *
42333255 TTTCCTTATAGTAACTCATTAATGCCATGTCTTGACATGGTCTTACATGATTTCC
1 TTTCCTTATAG-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
* * * * *
42333310 TTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCC
1 TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
** *
42333364 TTAT-C-T-T---AC-CA--AATGCCATGTTCC-AAACATGGTCTT-GATGGTATCC
1 TT-TCCTTATAGAACTCACCAATGCCATG--CCTTGACATGGTCTTACATGGTATCC
* *** **
42333410 TTGT-C-T-TAG---T-GCCAATGCCACATCTTGATGTGGTCTTACATGG-AGTCC
1 TT-TCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTA-TCC
** * * *
42333458 -TTAATTA-ATG---T---CGATGCCATGTCTTGACATGGTCTTACATGGGA-CC
1 TTTCCTTATA-GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
* * * *
42333504 TTTTCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCC
1 -TTTCCTTATAG-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
* * * * *
42333560 TTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCC
1 TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
42333614 TT
1 TT
42333616 ATCTTTCCAA
Statistics
Matches: 325, Mismatches: 58, Indels: 62
0.73 0.13 0.14
Matches are distributed among these distances:
46 27 0.08
47 45 0.14
48 26 0.08
49 5 0.02
52 3 0.01
53 43 0.13
54 91 0.28
55 82 0.25
56 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (54 bp):
TTTCCTTATAGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
Found at i:42333294 original size:55 final size:54
Alignment explanation
Indices: 42333169--42333607 Score: 240
Period size: 55 Copynumber: 8.5 Consensus size: 54
42333159 AACTTACCAT
* ** * * *
42333169 TGCCTTGTCTTGACATGGTCTTATGTGGTATCCTTTCCTTAT-G-AACTCACCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGAT-TTTTCCTTATAGTAACTCATCAA
* * *
42333222 TGCCATGCCTTGGCATGGTCTTACATGGGACTTTTTCCTTATAGTAACTCATTAA
1 TGCCATGTCTTGACATGGTCTTACATGGGA-TTTTTCCTTATAGTAACTCATCAA
*
42333277 TGCCATGTCTTGACATGGTCTTACAT--GATTTCCTTACCTTATAG-AACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGATTT--TT-CCTTATAGTAACTCATCAA
* * * * *
42333331 TGCCATGCCTTGGCATGGTCTTACAT--GA--TATCCTTAT-CTTAC-CA--AA
1 TGCCATGTCTTGACATGGTCTTACATGGGATTTTTCCTTATAGTAACTCATCAA
*** * * * *
42333377 TGCCATGTTCCAAACATGGTCTT-GATGGTATCCTTGT-C-T-TAGT---GC--CAA
1 TGCCATG-TCTTGACATGGTCTTACATGGGAT--TTTTCCTTATAGTAACTCATCAA
** ** * * * *
42333425 TGCCACATCTTGATGTGGTCTTACAT-GGA---GTCCTTA-ATTAA-T-GTCGA
1 TGCCATGTCTTGACATGGTCTTACATGGGATTTTTCCTTATAGTAACTCATCAA
*
42333472 TGCCATGTCTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGA-TTTTTCCTTATAGTAACTCATCAA
*
42333527 TGCCATGTCTTGACATGGTCTTACAT--GATTTCCTTGCCTTATAG-AACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGGGATTT--TT-CCTTATAGTAACTCATCAA
* *
42333581 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGTCTTGACATGGTCTTACATG
42333608 ATATCCTTAT
Statistics
Matches: 297, Mismatches: 52, Indels: 72
0.71 0.12 0.17
Matches are distributed among these distances:
42 2 0.01
43 1 0.00
44 3 0.01
46 11 0.04
47 46 0.15
48 15 0.05
49 9 0.03
50 3 0.01
51 1 0.00
52 14 0.05
53 41 0.14
54 74 0.25
55 77 0.26
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (54 bp):
TGCCATGTCTTGACATGGTCTTACATGGGATTTTTCCTTATAGTAACTCATCAA
Found at i:42333649 original size:47 final size:47
Alignment explanation
Indices: 42333594--42333715 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
42333584 CATGCCTTGG
* * * *
42333594 CATGGTCTTACATGATATCCTTATCTTTCCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAACGCCATGTTCCAAA
42333641 CATGGTCTTACATGGTATCCTTGTCTTACCAAACGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAACGCCATGTTCCAAA
* *
42333688 CATGTTCGTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
42333716 ATGCCAATGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAACGCCATGTTCCAAA
Found at i:42333702 original size:250 final size:248
Alignment explanation
Indices: 42333221--42333702 Score: 759
Period size: 250 Copynumber: 1.9 Consensus size: 248
42333211 GAACTCACCA
* * *
42333221 ATGCCATGCCTTGGCATGGTCTTACATGGGACTTTTTCCTTATAGTAACTCATTAATGCCATGTC
1 ATGCCATGCCTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
42333286 TTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
66 TTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
*
42333351 TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCTTGTCT
131 TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTCATGGTATCCTTGTCT
* *** ** *
42333416 TAGTGCCAATGCCACATCTTGATGTGGTCTTACATGGAGTCCTTAATTAATGTCG
196 TA--GCCAACGCCACATCCAAACATGGTCGTACATGGAGTCCTTAATTAATGTCG
*
42333471 ATGCCATGTCTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
1 ATGCCATGCCTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
*
42333536 TTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
66 TTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
*
42333601 TTACATGATATCCTTATCTTTCCAAATGCCATGTTCCAAACATGGTCTTACATGGTATCCTTGTC
131 TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTT-CATGGTATCCTTGTC
** *
42333666 TTA-CCAAACGCCATGTTCCAAACATGTTCGTACATGG
195 TTAGCC-AACGCCA-CATCCAAACATGGTCGTACATGG
42333703 TATCCTTGTC
Statistics
Matches: 212, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
248 2 0.01
249 6 0.03
250 187 0.88
251 17 0.08
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (248 bp):
ATGCCATGCCTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCCATGTC
TTGACATGGTCTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTC
TTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTCATGGTATCCTTGTCT
TAGCCAACGCCACATCCAAACATGGTCGTACATGGAGTCCTTAATTAATGTCG
Found at i:42333759 original size:298 final size:299
Alignment explanation
Indices: 42333169--42333804 Score: 815
Period size: 298 Copynumber: 2.1 Consensus size: 299
42333159 AACTTACCAT
* ** *
42333169 TGCCTTGTCTTGACATGGTCTTATGTGGTATCC-TTTCCTTATGAACTCACCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGGGATCCTTTTCCTTATGAACTCACCAATGCCATGCCTT
* * *
42333233 GGCATGGTCTTACATGGGACTTTTTCCTTATAGTAACTCATTAATGCCATGTCTTGACATGGTCT
66 GACATGGTCTTACAT-GGACTTTTTCCTTATAGTAACTCATCAATGCCATGCCTTGACATGGTCT
* * ***
42333298 TACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATC
130 TACATGATATCCTTACCTTAT---ACTCA-CAATGCCATGCCTAAACATGGTCTTACATGATATC
* ** *
42333363 CTTATCTTACCAAATGCCATGTTCCAAACATGGTCTTGATGGTATCCTTGTCTTAGTGCCAATGC
191 CTTATCTTACCAAACGCCATGTTCCAAACATGGTCTACATGGTATCCTTGTCTTAATGCCAATGC
* * * * *
42333428 CACATCTTGATGTGGTCTTACATGGAGTCCTTAATTAATGTCGA
256 CACATCTTAATGTGGCCTTACATGGAATCCTTAATCAATGCCGA
* *
42333472 TGCCATGTCTTGACATGGTCTTACATGGGA-CCTTTTCCTTATAGTAACTCATCAATGCCATGTC
1 TGCCATGTCTTGACATGGTCTTACATGGGATCCTTTTCCTTAT-G-AACTCACCAATGCCATGCC
* *
42333536 TTGACATGGTCTTACAT-GA-TTTCCTTGCCTTATAG-AACTTATCAATGCCATGCCTTGGCATG
64 TTGACATGGTCTTACATGGACTTT--TT-CCTTATAGTAACTCATCAATGCCATGCCTTGACATG
* *
42333598 GTCTTACATGATATCCTTATCTT-T-C-CA-AATGCCATGTTCC-AAACATGGTCTTACATGGTA
126 GTCTTACATGATATCCTTACCTTATACTCACAATGCCATG--CCTAAACATGGTCTTACATGATA
* *
42333658 TCCTTGTCTTACCAAACGCCATGTTCCAAACATGTTCGTACATGGTATCCTTGTCTTAATGCCAA
189 TCCTTATCTTACCAAACGCCATGTTCCAAACATGGTC-TACATGGTATCCTTGTCTTAATGCCAA
42333723 TGCCACATCTTAATGTGGCCTTACATGGAATCCTTAATCAATGCCGA
253 TGCCACATCTTAATGTGGCCTTACATGGAATCCTTAATCAATGCCGA
*
42333770 TGCCATGTCTTGACATGGTCTTACACGGGATCCTT
1 TGCCATGTCTTGACATGGTCTTACATGGGATCCTT
42333805 GCCTTACCAA
Statistics
Matches: 293, Mismatches: 30, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
296 9 0.03
297 50 0.17
298 98 0.33
299 5 0.02
302 5 0.02
303 38 0.13
304 47 0.16
305 41 0.14
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (299 bp):
TGCCATGTCTTGACATGGTCTTACATGGGATCCTTTTCCTTATGAACTCACCAATGCCATGCCTT
GACATGGTCTTACATGGACTTTTTCCTTATAGTAACTCATCAATGCCATGCCTTGACATGGTCTT
ACATGATATCCTTACCTTATACTCACAATGCCATGCCTAAACATGGTCTTACATGATATCCTTAT
CTTACCAAACGCCATGTTCCAAACATGGTCTACATGGTATCCTTGTCTTAATGCCAATGCCACAT
CTTAATGTGGCCTTACATGGAATCCTTAATCAATGCCGA
Found at i:42342467 original size:28 final size:29
Alignment explanation
Indices: 42342435--42342490 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
42342425 ACTGGTCAAT
*
42342435 ACTGTAAAA-CTAGAAAACAGGGGACAAA
1 ACTGTAAAATCTAAAAAACAGGGGACAAA
* *
42342463 ACTGTAAAATTTAAAAAATAGGGGACAA
1 ACTGTAAAATCTAAAAAACAGGGGACAA
42342491 CTATAAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.54, C:0.11, G:0.20, T:0.16
Consensus pattern (29 bp):
ACTGTAAAATCTAAAAAACAGGGGACAAA
Found at i:42342492 original size:27 final size:28
Alignment explanation
Indices: 42342435--42342507 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
42342425 ACTGGTCAAT
* *
42342435 ACTGTAAAA-CTAGAAAACAGGGGACAAA
1 ACTGTAAAATTTAAAAAACAGGGGAC-AA
*
42342463 ACTGTAAAATTTAAAAAATAGGGGAC-A
1 ACTGTAAAATTTAAAAAACAGGGGACAA
*
42342490 ACTAT-AAATCTTAAAAAA
1 ACTGTAAAAT-TTAAAAAA
42342508 ATAAAGTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 4 0.10
27 13 0.33
28 9 0.23
29 13 0.33
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (28 bp):
ACTGTAAAATTTAAAAAACAGGGGACAA
Found at i:42342553 original size:27 final size:27
Alignment explanation
Indices: 42342460--42342625 Score: 102
Period size: 29 Copynumber: 5.9 Consensus size: 27
42342450 AACAGGGGAC
*
42342460 AAAACTGTAAAATTTAAAAAATAGGGG
1 AAAACTATAAAATTTAAAAAATAGGGG
* * **
42342487 ACAACTAT-AAATCTTAAAAAAATAAAGTC
1 AAAACTATAAAAT-TT-AAAAAAT-AGGGG
* *
42342516 AAAA-TCGTAAAATTTCAAAAATAGGGG
1 AAAACT-ATAAAATTTAAAAAATAGGGG
* * *
42342543 AAAACTATAAAATCTGAAAAGAAAAAAGGGA
1 AAAACTATAAAAT-T--TAA-AAAATAGGGG
* *
42342574 AAAACTATAAAATCTAAAAAATGGGGGGG
1 AAAACTATAAAATTTAAAAAAT--AGGGG
* *
42342603 GAAACTATAAAATCTAAAAAATA
1 AAAACTATAAAATTTAAAAAATA
42342626 AGGAACACAC
Statistics
Matches: 104, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
26 4 0.04
27 24 0.23
28 18 0.17
29 32 0.31
30 5 0.05
31 21 0.20
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (27 bp):
AAAACTATAAAATTTAAAAAATAGGGG
Found at i:42342581 original size:31 final size:32
Alignment explanation
Indices: 42342532--42342593 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
42342522 GTAAAATTTC
* *
42342532 AAAAATAGGGGAAAACTATAAAATCTGAAAAG
1 AAAAATAGGGAAAAACTATAAAATCTAAAAAG
42342564 AAAAA-AGGGAAAAACTATAAAATCTAAAAA
1 AAAAATAGGGAAAAACTATAAAATCTAAAAA
42342594 ATGGGGGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (32 bp):
AAAAATAGGGAAAAACTATAAAATCTAAAAAG
Found at i:42346425 original size:14 final size:14
Alignment explanation
Indices: 42346406--42346445 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
42346396 TCAGGTATAT
42346406 TTTATTATAATTTA
1 TTTATTATAATTTA
*
42346420 TTTATTAT-ATCATA
1 TTTATTATAAT-TTA
42346434 TTTATTATAATT
1 TTTATTATAATT
42346446 GGAGATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATTATAATTTA
Found at i:42349536 original size:40 final size:40
Alignment explanation
Indices: 42349444--42349555 Score: 97
Period size: 40 Copynumber: 2.8 Consensus size: 40
42349434 GCCATCTCAA
* * *
42349444 ATAACCGAAGCTATCT-CAGTATCGTACACTTAGTGCCTCGT
1 ATAACCGAAGCTAT-TGCAAT-TCGCACACTTAGTGCCTAGT
* * *
42349485 ATAGCCAAAGCTATTGCAATTCGCACACTTAGTG-CTAATT
1 ATAACCGAAGCTATTGCAATTCGCACACTTAGTGCCT-AGT
*
42349525 ATAACCGAAGCTGTTTG-AA-TCGCACACTTAG
1 ATAACCGAAGCT-ATTGCAATTCGCACACTTAG
42349556 CTCCGAACAT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
39 14 0.24
40 27 0.46
41 18 0.31
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (40 bp):
ATAACCGAAGCTATTGCAATTCGCACACTTAGTGCCTAGT
Found at i:42350725 original size:12 final size:12
Alignment explanation
Indices: 42350708--42350740 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
42350698 CTAGACACAC
42350708 GCCCGTGTGTCT
1 GCCCGTGTGTCT
42350720 GCCCGTGTGTCT
1 GCCCGTGTGTCT
*
42350732 ACCCGTGTG
1 GCCCGTGTG
42350741 GACAATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.33, G:0.33, T:0.30
Consensus pattern (12 bp):
GCCCGTGTGTCT
Found at i:42355894 original size:20 final size:20
Alignment explanation
Indices: 42355835--42355899 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
42355825 TTTAATCATA
* *
42355835 TAATAAATTA-TTGATATAAT
1 TAATAAATTATTTAATAT-TT
* **
42355855 TAATATAATTTTTTTTTATTT
1 TAATA-AATTATTTAATATTT
42355876 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
42355896 TAAT
1 TAAT
42355900 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 21 0.58
21 10 0.28
22 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:42356703 original size:14 final size:14
Alignment explanation
Indices: 42356684--42356719 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
42356674 AAAAAGTAAG
42356684 TTATTTTCCAGAAA
1 TTATTTTCCAGAAA
42356698 TTATTTTCCAGAAA
1 TTATTTTCCAGAAA
*
42356712 TCATTTTC
1 TTATTTTC
42356720 TGAAAACCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (14 bp):
TTATTTTCCAGAAA
Found at i:42361566 original size:16 final size:17
Alignment explanation
Indices: 42361540--42361578 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
42361530 TTTTTTTATT
42361540 ATTTATATATATTTT-AA
1 ATTT-TATATATTTTAAA
42361557 ATTTTATATATTTTAAA
1 ATTTTATATATTTTAAA
42361574 ATTTT
1 ATTTT
42361579 TAAAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATATATTTTAAA
Found at i:42361579 original size:18 final size:17
Alignment explanation
Indices: 42361540--42361580 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
42361530 TTTTTTTATT
*
42361540 ATTTATATATATTTTAA
1 ATTTTTATATATTTTAA
42361557 A-TTTTATATATTTTAAA
1 ATTTTTATATATTTT-AA
42361574 ATTTTTA
1 ATTTTTA
42361581 AAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 12 0.57
17 4 0.19
18 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTATATATTTTAA
Found at i:42362155 original size:23 final size:23
Alignment explanation
Indices: 42362127--42362174 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
42362117 CTTTTTGACC
42362127 TTAATTTCAAGTCCCTAGTCATT
1 TTAATTTCAAGTCCCTAGTCATT
42362150 TTAATTTCAAGTCCCTAGTCATT
1 TTAATTTCAAGTCCCTAGTCATT
42362173 TT
1 TT
42362175 TCTTTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (23 bp):
TTAATTTCAAGTCCCTAGTCATT
Found at i:42367492 original size:17 final size:18
Alignment explanation
Indices: 42367465--42367499 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
42367455 ATGTGAAAAA
42367465 AATTATATATATTTTATT
1 AATTATATATATTTTATT
42367483 AATT-TATATATTTTATT
1 AATTATATATATTTTATT
42367500 TTTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATATATATTTTATT
Found at i:42368212 original size:18 final size:19
Alignment explanation
Indices: 42368171--42368212 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42368161 AATAGTATTT
*
42368171 AAATTAAATTGAAATTACG
1 AAATTAAATTGAAATGACG
42368190 AAATTAAA-T-AAATGACGG
1 AAATTAAATTGAAATGAC-G
42368208 AAATT
1 AAATT
42368213 GAGATGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (19 bp):
AAATTAAATTGAAATGACG
Found at i:42368995 original size:27 final size:26
Alignment explanation
Indices: 42368965--42369026 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
42368955 AGATAATTAA
42368965 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
42368992 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
42369019 AATAAAAT
1 AATAAAAT
42369027 GGAGTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:42374336 original size:20 final size:20
Alignment explanation
Indices: 42374313--42374360 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
42374303 TAAATTCTAA
*
42374313 AAAGATAAATACAA-TTAATT
1 AAAGATAAATA-AAGATAATT
42374333 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
42374353 AAA-ATAAA
1 AAAGATAAA
42374361 ATCTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:42374385 original size:27 final size:26
Alignment explanation
Indices: 42374355--42374416 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
42374345 AGATAATTAA
42374355 AATAAAATCTTAAAATTAAATAATCCT
1 AATAAAATCTTAAAATT-AATAATCCT
* * *
42374382 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTTAAAATTAATAATCCT
42374409 AATAAAAT
1 AATAAAAT
42374417 GGAGTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 18 0.60
28 10 0.33
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAAAATCTTAAAATTAATAATCCT
Found at i:42376479 original size:52 final size:52
Alignment explanation
Indices: 42376417--42376547 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
42376407 ATCAACCATC
* *
42376417 TAAGAAATAATCATTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
* *
42376469 TAAGATATAATCCTTGATAAATTGAAATATGAAAAATAGAAGAAAACAAAAA
1 TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
*
42376521 TAAGATATAATCCTTGACAAATCGAAA
1 TAAGATATAATCCTTGACAAATTGAAA
42376548 ATAAGATGGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.21
Consensus pattern (52 bp):
TAAGATATAATCCTTGACAAATTGAAAGATGAAAAATAGAAGAAAACAAAAA
Found at i:42386321 original size:17 final size:18
Alignment explanation
Indices: 42386281--42386322 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
42386271 TATAAAATAC
*
42386281 AAATTATAAAAATATAAT
1 AAATAATAAAAATATAAT
* *
42386299 ATATAATAAAATTAT-AT
1 AAATAATAAAAATATAAT
42386316 AAATAAT
1 AAATAAT
42386323 TTAATATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAATAAAAATATAAT
Found at i:42386329 original size:29 final size:26
Alignment explanation
Indices: 42386269--42386320 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
42386259 TGTTAAAAAG
*
42386269 AATATAAAATACAAATTATAAAAATAT
1 AATATATAATA-AAATTATAAAAATAT
*
42386296 AATATATAATAAAATTATATAAATA
1 AATATATAATAAAATTATAAAAATA
42386321 ATTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AATATATAATAAAATTATAAAAATAT
Found at i:42386339 original size:29 final size:28
Alignment explanation
Indices: 42386269--42386337 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
42386259 TGTTAAAAAG
*
42386269 AATATAAAATACAAA-T-TATAAAAATAT
1 AATATATAATA-AAATTATATAAAAATAT
*
42386296 AATATATAATAAAATTATATAAATAATTT
1 AATATATAATAAAATTATATAAA-AATAT
*
42386325 AATAT-TTATAAAA
1 AATATATAATAAAA
42386338 ATAATTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.08
27 11 0.31
28 13 0.36
29 9 0.25
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (28 bp):
AATATATAATAAAATTATATAAAAATAT
Found at i:42397615 original size:27 final size:29
Alignment explanation
Indices: 42397580--42397634 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
42397570 TTATTACAGA
*
42397580 TAAATAATATTATAATTA-ATTATAAATT
1 TAAATAATATTATAATTATAATATAAATT
*
42397608 TAAA-AATATTTTAATTATAATATAAAT
1 TAAATAATATTATAATTATAATATAAAT
42397635 ATTATCTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAATAATATTATAATTATAATATAAATT
Found at i:42397957 original size:28 final size:29
Alignment explanation
Indices: 42397925--42397979 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
42397915 TAAATTTTAA
* *
42397925 TTCAATTATATACATT-TAAAAATAAAAT
1 TTCAATTATACACATTAAAAAAATAAAAT
42397953 TTCAATTATACACATTAAAAAAATAAA
1 TTCAATTATACACATTAAAAAAATAAA
42397980 TTTATTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (29 bp):
TTCAATTATACACATTAAAAAAATAAAAT
Found at i:42398805 original size:17 final size:17
Alignment explanation
Indices: 42398783--42398817 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42398773 GAAGAATAAG
*
42398783 TAATATTTATAAATTAA
1 TAATATATATAAATTAA
*
42398800 TAATATATATATATTAA
1 TAATATATATAAATTAA
42398817 T
1 T
42398818 TTTAGGGAAG
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:0.00, T:0.49
Consensus pattern (17 bp):
TAATATATATAAATTAA
Found at i:42398809 original size:21 final size:21
Alignment explanation
Indices: 42398777--42398818 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42398767 ATTTAAGAAG
*
42398777 AATAAGTAATATTTATAAATT
1 AATAAGTAATATATATAAATT
*
42398798 AATAA-TATATATATATTAATT
1 AATAAGTA-ATATATATAAATT
42398819 TTAGGGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATAAGTAATATATATAAATT
Found at i:42405161 original size:23 final size:23
Alignment explanation
Indices: 42405135--42405180 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
42405125 ACTATGTCCA
42405135 CAAATTAGGTTTAAATTATGATT
1 CAAATTAGGTTTAAATTATGATT
*
42405158 CAAATTAGGTTTAATTTATGATT
1 CAAATTAGGTTTAAATTATGATT
42405181 TGGCTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (23 bp):
CAAATTAGGTTTAAATTATGATT
Found at i:42406281 original size:15 final size:15
Alignment explanation
Indices: 42406261--42406310 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
42406251 AAAACAAATG
42406261 ATAAGATGAAAGAAA
1 ATAAGATGAAAGAAA
**
42406276 ATAAGA-GACAA-ATG
1 ATAAGATGA-AAGAAA
42406290 ATAAGATGAAAGAAA
1 ATAAGATGAAAGAAA
42406305 ATAAGA
1 ATAAGA
42406311 GACGAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.64, C:0.02, G:0.20, T:0.14
Consensus pattern (15 bp):
ATAAGATGAAAGAAA
Found at i:42406296 original size:29 final size:29
Alignment explanation
Indices: 42406254--42406313 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
42406244 TCATTCCAAA
42406254 ACAAATGATAAGATGAAAGAAAATAAGAG
1 ACAAATGATAAGATGAAAGAAAATAAGAG
42406283 ACAAATGATAAGATGAAAGAAAATAAGAG
1 ACAAATGATAAGATGAAAGAAAATAAGAG
42406312 AC
1 AC
42406314 GAGTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.62, C:0.05, G:0.20, T:0.13
Consensus pattern (29 bp):
ACAAATGATAAGATGAAAGAAAATAAGAG
Found at i:42406503 original size:16 final size:16
Alignment explanation
Indices: 42406482--42406519 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42406472 ATATATTTAT
42406482 TTTTCTATCCCTTCAA
1 TTTTCTATCCCTTCAA
**
42406498 TTTTCTATCTTTTCAA
1 TTTTCTATCCCTTCAA
42406514 TTTTCT
1 TTTTCT
42406520 TTCCACCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTCTATCCCTTCAA
Found at i:42406759 original size:17 final size:17
Alignment explanation
Indices: 42406737--42406778 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
42406727 CAAATACCAA
42406737 TATATATTATAATTT-TT
1 TATATATT-TAATTTATT
42406754 TATATATTTAATTTATT
1 TATATATTTAATTTATT
42406771 TCATATAT
1 T-ATATAT
42406779 GTATTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 11 0.48
18 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTTAATTTATT
Found at i:42411863 original size:40 final size:40
Alignment explanation
Indices: 42411786--42412041 Score: 342
Period size: 40 Copynumber: 6.4 Consensus size: 40
42411776 AAACCAAGTA
* * * *
42411786 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGAATATAG-TAACTCGCACAAATG
** *
42411825 CCTTCGGGACTTAGCCCGAATATAGTAGTTTGCACAAATG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
*
42411865 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
*
42411905 CCTTCGGGACTTAGCCCGAA-ATTAGTAACTCGCAAAAATG
1 CCTTCGGGACTTAGCCCGAATA-TAGTAACTCGCACAAATG
42411945 CCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATG
* *
42411985 CCTTCGGGACTTAGCCCGGAAT-TAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATG
42412025 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
42412042 CGTTATCATC
Statistics
Matches: 196, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
39 14 0.07
40 179 0.91
41 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
Found at i:42415604 original size:35 final size:35
Alignment explanation
Indices: 42415553--42415628 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
42415543 TATTGATATT
42415553 AGAATGGGTTTATCTATCAACTATAAAATGTTAAAA
1 AGAA-GGGTTTATCTATCAACTATAAAATGTTAAAA
*
42415589 AGAAGGGTTTATCTATCAGCTATAAAATGTTAAAA
1 AGAAGGGTTTATCTATCAACTATAAAATGTTAAAA
42415624 AGAAG
1 AGAAG
42415629 TGTAGGATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (35 bp):
AGAAGGGTTTATCTATCAACTATAAAATGTTAAAA
Done.