Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 127 of 318
Found at i:38954832 original size:13 final size:14
Alignment explanation
Indices: 38954814--38954849 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38954804 CATAAATCAC
38954814 TTTTTTTTCG-AAT
1 TTTTTTTTCGAAAT
*
38954827 TTTTTTTTGGAAAT
1 TTTTTTTTCGAAAT
38954841 TTTTTTTTC
1 TTTTTTTTC
38954850 AAACTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (14 bp):
TTTTTTTTCGAAAT
Found at i:38955619 original size:30 final size:30
Alignment explanation
Indices: 38955534--38955630 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
38955524 TAAACTAAAA
* *
38955534 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
38955564 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
38955594 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
38955623 ATGAGCTA
1 -TGAGCTA
38955631 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:38957463 original size:12 final size:11
Alignment explanation
Indices: 38957446--38957498 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
38957436 CATAAATCAC
38957446 TTTTTTTTCAA
1 TTTTTTTTCAA
38957457 TTTTTTTTCAA
1 TTTTTTTTCAA
* *
38957468 ATTTTTTT-GA
1 TTTTTTTTCAA
*
38957478 -TTTTTTTCGA
1 TTTTTTTTCAA
38957488 TTTTTTTTCAA
1 TTTTTTTTCAA
38957499 CTTGTATAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 7 0.19
10 3 0.08
11 27 0.73
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:38957495 original size:20 final size:20
Alignment explanation
Indices: 38957458--38957494 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
38957448 TTTTTTCAAT
38957458 TTTTTTTCAAATTTTTTTGA
1 TTTTTTTCAAATTTTTTTGA
*
38957478 TTTTTTTC-GATTTTTTT
1 TTTTTTTCAAATTTTTTT
38957495 TCAACTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTTTTCAAATTTTTTTGA
Found at i:38960592 original size:18 final size:19
Alignment explanation
Indices: 38960555--38960602 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
38960545 TAAAGCACAA
*
38960555 TTAATT-ATTTAAGCTGAC
1 TTAATTAATTTAAGCTAAC
38960573 TTAATTAATTTAA-CTAAC
1 TTAATTAATTTAAGCTAAC
*
38960591 TTATTTAATTTA
1 TTAATTAATTTA
38960603 TTCCAGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (19 bp):
TTAATTAATTTAAGCTAAC
Found at i:38963879 original size:27 final size:28
Alignment explanation
Indices: 38963824--38963886 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
38963814 ACTAATCCAG
* * * *
38963824 CTAACACACATTAAAAATCATGTAGTAA
1 CTAAGACACATTAAAAATAATGCACTAA
*
38963852 CTATGACACATT-AAAATAATGCACTAA
1 CTAAGACACATTAAAAATAATGCACTAA
38963879 CTAAGACA
1 CTAAGACA
38963887 AATTCAATGA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (28 bp):
CTAAGACACATTAAAAATAATGCACTAA
Found at i:38966128 original size:19 final size:19
Alignment explanation
Indices: 38966103--38966150 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
38966093 AATTACTGAT
*
38966103 CTTAGTTAATTGAGTTCAT
1 CTTAGTTAATTGAGTTCAC
* *
38966122 TTTAGTTAATTTAGTTCAC
1 CTTAGTTAATTGAGTTCAC
38966141 CTTAGTTAAT
1 CTTAGTTAAT
38966151 AACTCATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.50
Consensus pattern (19 bp):
CTTAGTTAATTGAGTTCAC
Found at i:38966394 original size:26 final size:26
Alignment explanation
Indices: 38966365--38966421 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
38966355 TTTTATTTCA
38966365 TTTA-TTGAAGTTAAGTGTTTAA-TGTG
1 TTTAGTTGAA-TT-AGTGTTTAATTGTG
*
38966391 TTTAAGTTTAATTAGTGTTTAATTGTG
1 TTT-AGTTGAATTAGTGTTTAATTGTG
38966418 TTTA
1 TTTA
38966422 ATTGTGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
26 13 0.48
27 10 0.37
28 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.54
Consensus pattern (26 bp):
TTTAGTTGAATTAGTGTTTAATTGTG
Found at i:38966395 original size:17 final size:18
Alignment explanation
Indices: 38966375--38966432 Score: 68
Period size: 17 Copynumber: 3.2 Consensus size: 18
38966365 TTTATTGAAG
38966375 TTAAGTGTTTAA-TGTGT
1 TTAAGTGTTTAATTGTGT
38966392 TTAA--GTTTAATTAGTGT
1 TTAAGTGTTTAATT-GTGT
38966409 TTAATTGTGTTTAATTGTGT
1 TTAA--GTGTTTAATTGTGT
38966429 TTAA
1 TTAA
38966433 TAAGTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.17
16 1 0.03
17 12 0.34
20 8 0.23
21 8 0.23
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (18 bp):
TTAAGTGTTTAATTGTGT
Found at i:38966420 original size:10 final size:10
Alignment explanation
Indices: 38966396--38966433 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
38966386 ATGTGTTTAA
38966396 GTTTAATTAGT
1 GTTTAATT-GT
38966407 GTTTAATTGT
1 GTTTAATTGT
38966417 GTTTAATTGT
1 GTTTAATTGT
38966427 GTTTAAT
1 GTTTAAT
38966434 AAGTTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (10 bp):
GTTTAATTGT
Found at i:38967456 original size:24 final size:25
Alignment explanation
Indices: 38967429--38967480 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
38967419 GCCTAGCCTC
38967429 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
**
38967453 TTTTGGTAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
38967478 TTT
1 TTT
38967481 CGCACTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:38967696 original size:27 final size:27
Alignment explanation
Indices: 38967674--38967845 Score: 177
Period size: 27 Copynumber: 6.4 Consensus size: 27
38967664 TTTACCCCAT
*
38967674 AAGGGTATCTCGATAATTCTACCCTAC
1 AAGGGTATTTCGATAATTCTACCCTAC
* *
38967701 AGGGGTATTTCGATATTTCTACCCTAC
1 AAGGGTATTTCGATAATTCTACCCTAC
* *
38967728 AAGGGTATTTCGGTAATTCTACCCTAT
1 AAGGGTATTTCGATAATTCTACCCTAC
* * * *
38967755 AGGGGTATTTCGGTATTTCTACCCTTC
1 AAGGGTATTTCGATAATTCTACCCTAC
** *
38967782 AAGGGTATTTC-AGTAACCCTACCCTAT
1 AAGGGTATTTCGA-TAATTCTACCCTAC
* *
38967809 AGGGGTATTTC-AGTTATTCTACCCTAC
1 AAGGGTATTTCGA-TAATTCTACCCTAC
*
38967836 AGGGGTATTT
1 AAGGGTATTT
38967846 TGGTAATTTT
Statistics
Matches: 121, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (27 bp):
AAGGGTATTTCGATAATTCTACCCTAC
Found at i:38967788 original size:81 final size:81
Alignment explanation
Indices: 38967657--38967853 Score: 216
Period size: 81 Copynumber: 2.4 Consensus size: 81
38967647 AAAGGCAAAA
* * * * * * * ***
38967657 CAGTCATTTTACCCCATAAGGGTATCTCGATAATTCTACCCTACAGGGGTATTTC-GATATTTCT
1 CAGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAG-TAACCCT
38967721 ACCCTACAAGGGTATTT
65 ACCCTACAAGGGTATTT
* * *
38967738 CGGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTTCAAGGGTATTTCAGTAACCCTA
1 CAGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAACCCTA
* *
38967803 CCCTATAGGGGTATTT
66 CCCTACAAGGGTATTT
* * *
38967819 CAGTTATTCTACCCTACAGGGGTATTTTGGTAATT
1 CAGTAATTCTACCCTATAGGGGTATTTCGGTAATT
38967854 TTACAAACTA
Statistics
Matches: 95, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
81 94 0.99
82 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (81 bp):
CAGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAACCCTA
CCCTACAAGGGTATTT
Found at i:38967866 original size:27 final size:27
Alignment explanation
Indices: 38967836--38968287 Score: 462
Period size: 27 Copynumber: 16.7 Consensus size: 27
38967826 TCTACCCTAC
38967836 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
*
38967863 AGGGGTATTTTGGTAATTTTAC-AAGT
1 AGGGGTATTTTGGTAATTTTACAAACT
* ** * *
38967889 CGAGGGTATTTCAGTAATTTCACAAATT
1 AG-GGGTATTTTGGTAATTTTACAAACT
*** *
38967917 AGGGGTATTTTGGTAATTTGGTAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
38967944 AAGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
38967971 AGGGGTATTTTGGTAATTTTATAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* * *
38967998 AAGGGTATTTTGGTAATTTTATAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
** * *
38968025 AATGGTATTTTGGTAATTCTAC-AAGT
1 AGGGGTATTTTGGTAATTTTACAAACT
* ** * *
38968051 CGAGGGTATTTCAGTAATTTCATAAA-T
1 AG-GGGTATTTTGGTAATTTTACAAACT
** *
38968078 CAGGGGTATTTTGGTAATTTTGTAAACC
1 -AGGGGTATTTTGGTAATTTTACAAACT
* *
38968106 AAGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
** *
38968133 AGGGGTATTTTGGTAATTTTGTAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
38968160 AAGGGTATTTTGGTAATTTTAC-AAGT
1 AGGGGTATTTTGGTAATTTTACAAACT
* ** * *
38968186 CGAGGGTATTTCAGTAATTTCACAAATT
1 AG-GGGTATTTTGGTAATTTTACAAACT
*
38968214 AGGGGTATTTTGGTAATTTCACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
38968241 AGGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
38968268 AGGGGTATTTTGGTAATTTT
1 AGGGGTATTTTGGTAATTTT
38968288 GCTAATCGAG
Statistics
Matches: 355, Mismatches: 62, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
26 8 0.02
27 336 0.95
28 11 0.03
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:38967872 original size:54 final size:54
Alignment explanation
Indices: 38967674--38967853 Score: 245
Period size: 54 Copynumber: 3.3 Consensus size: 54
38967664 TTTACCCCAT
* * *
38967674 AAGGGTATCTCGATAATTCTACCCTACAGGGGTATTTCGATATTTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCGATATTTCTACCCTAC
* *
38967728 AAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCCTTC
1 AAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCGATATTTCTACCCTAC
* ** *
38967782 AAGGGTATTTCAGTAACCCTACCCTATAGGGGTATTTCAGTTA-TTCTACCCTAC
1 AAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTC-GATATTTCTACCCTAC
* *
38967836 AGGGGTATTTTGGTAATT
1 AAGGGTATTTCGGTAATT
38967854 TTACAAACTA
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
54 107 0.97
55 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (54 bp):
AAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCGATATTTCTACCCTAC
Found at i:38972653 original size:30 final size:30
Alignment explanation
Indices: 38972619--38972715 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
38972609 TAAACTAAAA
38972619 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
38972649 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* * *
38972679 TGAGATAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
38972709 TGAGCTA
1 TGAGCTA
38972716 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.83
31 6 0.12
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:38974362 original size:19 final size:19
Alignment explanation
Indices: 38974338--38974377 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38974328 AGCTCCCATG
38974338 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
38974357 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
38974376 TA
1 TA
38974378 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:38976999 original size:30 final size:31
Alignment explanation
Indices: 38976928--38976999 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
38976918 CTTTTGTTTC
* *
38976928 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCATCTTCTTTTTCAATATCA
*
38976959 AATTTC-TTTTCGT-TCTCTTTTTCAATATC-
1 AATTTCTTTTTCATCT-TCTTTTTCAATATCA
*
38976988 ATTTTCTTTTTC
1 AATTTCTTTTTC
38977000 TTTTGCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 6 0.17
30 23 0.66
31 6 0.17
ACGTcount: A:0.15, C:0.22, G:0.01, T:0.61
Consensus pattern (31 bp):
AATTTCTTTTTCATCTTCTTTTTCAATATCA
Found at i:38977028 original size:12 final size:12
Alignment explanation
Indices: 38977013--38977043 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38977003 TGCTTTTTGC
38977013 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38977025 TTTTCAAAGGCT
1 TTTTCAAAGGCT
38977037 TTTTCAA
1 TTTTCAA
38977044 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:38977117 original size:21 final size:19
Alignment explanation
Indices: 38977091--38977154 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
38977081 CTCTTGCCTC
38977091 TCTTTTCCTTTTATTTCGTTT
1 TCTTTT-CTTTT-TTTCGTTT
* *
38977112 TCTTTTTCTTCTTTTGCTTTT
1 TC-TTTTCTT-TTTTTCGTTT
38977133 TCTTTTCTTTTCTTT-GTTT
1 TCTTTTCTTTT-TTTCGTTT
38977152 TCT
1 TCT
38977155 CTTTACAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.22
20 9 0.25
21 13 0.36
22 6 0.17
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.75
Consensus pattern (19 bp):
TCTTTTCTTTTTTTCGTTT
Found at i:38977131 original size:15 final size:14
Alignment explanation
Indices: 38977091--38977147 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 14
38977081 CTCTTGCCTC
38977091 TCTTTTCCTTTTAT-T
1 TCTTTT-CTTTT-TCT
38977106 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
38977121 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
38977138 TCTTTTCTTT
1 TCTTTTCTTT
38977148 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
14 5 0.14
15 17 0.46
16 8 0.22
17 7 0.19
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:38977157 original size:21 final size:20
Alignment explanation
Indices: 38977089--38977158 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
38977079 GCCTCTTGCC
38977089 TCTCTTTTCCTTTTATTTCGTTT
1 TCTCTTTT-CTTTT-TTT-GTTT
*
38977112 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTTTTTTTG-TTT
38977132 T-TCTTTTCTTTTCTTTGTTT
1 TCTCTTTTCTTTT-TTTGTTT
38977152 TCTCTTT
1 TCTCTTT
38977159 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 19 0.46
21 13 0.32
22 4 0.10
23 3 0.07
ACGTcount: A:0.01, C:0.20, G:0.04, T:0.74
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTGTTT
Found at i:38979691 original size:30 final size:30
Alignment explanation
Indices: 38979657--38979753 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
38979647 TAAACTAAAA
38979657 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
38979687 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* * *
38979717 TGATCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
38979747 TGAGCTA
1 TGAGCTA
38979754 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 6
0.69 0.23 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.83
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:38992156 original size:12 final size:13
Alignment explanation
Indices: 38992139--38992173 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
38992129 ATAAATCACT
38992139 TTTTTTTTTCG-A
1 TTTTTTTTTCGAA
38992151 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
38992164 TTTTTTTTTC
1 TTTTTTTTTC
38992174 AAACTTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:38993802 original size:10 final size:10
Alignment explanation
Indices: 38993787--38993813 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
38993777 TAAGTTGAAG
38993787 TTGAGCTGAT
1 TTGAGCTGAT
38993797 TTGAGCTGAT
1 TTGAGCTGAT
38993807 TTGAGCT
1 TTGAGCT
38993814 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:38994590 original size:30 final size:30
Alignment explanation
Indices: 38994556--38994652 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
38994546 TAAACTAAAA
38994556 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
38994586 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
38994616 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
38994646 TGAGCTA
1 TGAGCTA
38994653 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:38995511 original size:29 final size:29
Alignment explanation
Indices: 38995478--38995537 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
38995468 AAGGATTCAA
*
38995478 AGATGGGTTTATGGATATGAAG-TTTATGT
1 AGATGGGTTTATGGATATAAAGCTTT-TGT
38995507 AGATGGGTTTATGGATATAAAGCTTTTGT
1 AGATGGGTTTATGGATATAAAGCTTTTGT
38995536 AG
1 AG
38995538 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.28, C:0.02, G:0.30, T:0.40
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGCTTTTGT
Found at i:38995518 original size:14 final size:14
Alignment explanation
Indices: 38995478--38995521 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38995468 AAGGATTCAA
38995478 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
38995492 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
38995507 AGATGGGTTTATGG
1 AGATGGGTTTATGG
38995521 A
1 A
38995522 TATAAAGCTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:38999431 original size:12 final size:12
Alignment explanation
Indices: 38999412--38999445 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38999402 AGAAAGAAAA
38999412 GAGTGAAAAGGT
1 GAGTGAAAAGGT
* *
38999424 GTGTGAAAAAGT
1 GAGTGAAAAGGT
38999436 GAGTGAAAAG
1 GAGTGAAAAG
38999446 AAACGAGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (12 bp):
GAGTGAAAAGGT
Found at i:39001481 original size:30 final size:30
Alignment explanation
Indices: 39001395--39001492 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
39001385 TTAAACTAAA
* *
39001395 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
39001425 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
39001455 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
39001485 ATGAGCTA
1 ATGAGCTA
39001493 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:39003774 original size:30 final size:30
Alignment explanation
Indices: 39003703--39003785 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
39003693 CTTTTGTTTC
* *
39003703 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
39003734 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
39003763 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
39003786 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:39003785 original size:18 final size:18
Alignment explanation
Indices: 39003736--39003791 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
39003726 CACTCTCAAA
* *
39003736 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
39003753 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
39003771 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
39003790 TT
1 TT
39003792 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:39003792 original size:12 final size:12
Alignment explanation
Indices: 39003761--39003785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39003751 TTTTTCAATC
39003761 TCATTTTCTTTT
1 TCATTTTCTTTT
39003773 TCATTTTCTTTT
1 TCATTTTCTTTT
39003785 T
1 T
39003786 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:39003920 original size:16 final size:16
Alignment explanation
Indices: 39003852--39003921 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 16
39003842 GCCTTTTGCC
39003852 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTAT
*
39003868 T-TCGTTTTCTTTTTCT
1 TCTC-TTTTCTTTTTAT
39003884 TCT-TTTTCTTTTTCAT
1 TCTCTTTTCTTTTT-AT
39003900 T-TCTTTTCTTTGTT-T
1 TCTCTTTTCTTT-TTAT
39003915 TCTCTTT
1 TCTCTTT
39003922 ACTAAAATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
15 15 0.33
16 28 0.61
17 3 0.07
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (16 bp):
TCTCTTTTCTTTTTAT
Found at i:39006497 original size:30 final size:30
Alignment explanation
Indices: 39006402--39006499 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
39006392 TTAAACTAAA
* *
39006402 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAA-T
* * * * * * *
39006433 -TGAGCTGAGATTAAACTCCTAAGTTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
* *
39006462 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
39006492 ATGAGCTA
1 ATGAGCTA
39006500 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 18, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
Found at i:39007916 original size:19 final size:19
Alignment explanation
Indices: 39007871--39007916 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
39007861 ATTAACACAC
*
39007871 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
39007890 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
39007908 AATTAATAA
1 AATTAATAA
39007917 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:39008143 original size:10 final size:10
Alignment explanation
Indices: 39008130--39008164 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39008120 AAGCTCGGTT
39008130 GAGCTCAAAC
1 GAGCTCAAAC
*
39008140 GAGCTGAAAC
1 GAGCTCAAAC
*
39008150 GAGCTCAAAT
1 GAGCTCAAAC
39008160 GAGCT
1 GAGCT
39008165 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:39008173 original size:20 final size:20
Alignment explanation
Indices: 39008127--39008174 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39008117 AGTAAGCTCG
39008127 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
39008147 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
39008167 GTTGAGCT
1 GTTGAGCT
39008175 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:39009017 original size:30 final size:30
Alignment explanation
Indices: 39008974--39009070 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
39008964 AGCTCACTCC
*
39008974 TAGCTCATA-TTCAGGTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * * *
39009004 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
39009034 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
39009064 TAGCTCA
1 TAGCTCA
39009071 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:39011693 original size:9 final size:10
Alignment explanation
Indices: 39011686--39011742 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
39011676 AAGAGAAAAC
39011686 AAAGAAAAGA
1 AAAGAAAAGA
39011696 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
39011708 AAAGAAGA-A
1 AAAGAAAAGA
39011717 AAAGAAAATGA
1 AAAGAAAA-GA
39011728 AATA-AAAAGA
1 AA-AGAAAAGA
39011738 AAAGA
1 AAAGA
39011743 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:39011709 original size:21 final size:20
Alignment explanation
Indices: 39011675--39011742 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
39011665 ACATTCTTGT
39011675 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
39011696 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
39011717 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
39011738 AAAGA
1 AAAGA
39011743 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:39011710 original size:6 final size:5
Alignment explanation
Indices: 39011686--39011742 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
39011676 AAGAGAAAAC
*
39011686 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
39011733 AAAGA AAAGA
1 AAAGA AAAGA
39011743 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:39011717 original size:15 final size:14
Alignment explanation
Indices: 39011686--39011742 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
39011676 AAGAGAAAAC
39011686 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
39011702 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
39011717 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
39011733 AAAGAAAAGA
1 AAAGAAAAGA
39011743 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:39011822 original size:11 final size:12
Alignment explanation
Indices: 39011790--39011820 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39011780 TTGAGAGAAC
39011790 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39011802 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39011814 TTGAAAA
1 TTGAAAA
39011821 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:39011831 original size:12 final size:12
Alignment explanation
Indices: 39011823--39011847 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39011813 TTTGAAAAGC
39011823 AAAAAGAAAATG
1 AAAAAGAAAATG
39011835 AAAAAGAAAATG
1 AAAAAGAAAATG
39011847 A
1 A
39011848 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:39011844 original size:18 final size:18
Alignment explanation
Indices: 39011817--39011872 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
39011807 AAAGCCTTTG
39011817 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
39011836 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
39011854 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
39011871 AA
1 AA
39011873 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:39011857 original size:30 final size:31
Alignment explanation
Indices: 39011823--39011904 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
39011813 TTTGAAAAGC
*
39011823 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
39011853 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
39011883 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
39011905 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:39014151 original size:30 final size:30
Alignment explanation
Indices: 39014117--39014214 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
39014107 AGCTCACTCC
39014117 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
39014147 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
39014177 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
39014207 TAGCTCAT
1 TAGCTCAT
39014215 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:39014565 original size:16 final size:16
Alignment explanation
Indices: 39014541--39014571 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39014531 ATGTATTTGC
*
39014541 CAAATACATGAATGCA
1 CAAAAACATGAATGCA
39014557 CAAAAACATGAATGC
1 CAAAAACATGAATGC
39014572 TTGGGTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.19, G:0.13, T:0.16
Consensus pattern (16 bp):
CAAAAACATGAATGCA
Found at i:39015552 original size:14 final size:14
Alignment explanation
Indices: 39015533--39015577 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
39015523 AACTCATCTT
*
39015533 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
39015547 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
39015560 AATTTAATTTAATG
1 AGTTTAATTTAATG
39015574 AGTT
1 AGTT
39015578 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:39016585 original size:29 final size:29
Alignment explanation
Indices: 39016552--39016611 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
39016542 ATAACCAAAC
* *
39016552 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAAACCAT
*
39016581 CTACATAAACTTCATATCCATAAAACCAT
1 CTACAAAAACTTCATATCCATAAAACCAT
39016610 CT
1 CT
39016612 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAAACCAT
Found at i:39016604 original size:15 final size:15
Alignment explanation
Indices: 39016558--39016604 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
39016548 AAACCTACAA
*
39016558 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
39016573 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
39016587 AAACTTCATATCCAT
1 AAACTTCATATCCAT
39016602 AAA
1 AAA
39016605 ACCATCTTTG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:39017914 original size:34 final size:35
Alignment explanation
Indices: 39017871--39017940 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
39017861 GTATTTGACA
39017871 AAATACATGAACTTGTAAACACCTTGAATCT-GTC
1 AAATACATGAACTTGTAAACACCTTGAATCTAGTC
39017905 AAATACATGAACTTGTAAACACCTTGAATCTAGTC
1 AAATACATGAACTTGTAAACACCTTGAATCTAGTC
39017940 A
1 A
39017941 TACATGCACC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 31 0.89
35 4 0.11
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (35 bp):
AAATACATGAACTTGTAAACACCTTGAATCTAGTC
Found at i:39017932 original size:17 final size:17
Alignment explanation
Indices: 39017878--39017932 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
39017868 ACAAAATACA
39017878 TGAACTTGTAAACACCT
1 TGAACTTGTAAACACCT
* *
39017895 TGAA-TCTGTCAAATA-CA
1 TGAACT-TGT-AAACACCT
39017912 TGAACTTGTAAACACCT
1 TGAACTTGTAAACACCT
39017929 TGAA
1 TGAA
39017933 TCTAGTCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 5 0.17
17 20 0.67
18 5 0.17
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (17 bp):
TGAACTTGTAAACACCT
Found at i:39018315 original size:30 final size:30
Alignment explanation
Indices: 39018230--39018326 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39018220 TAAACTAAAA
* *
39018230 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
39018260 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
39018290 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
39018319 ATGAGCTA
1 -TGAGCTA
39018327 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:39019661 original size:17 final size:18
Alignment explanation
Indices: 39019639--39019676 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39019629 GCTACAACCG
39019639 AATTTA-TG-TTGTGTCTT
1 AATTTATTGTTTGTGT-TT
39019656 AATTTATTGTTTGTGTTT
1 AATTTATTGTTTGTGTTT
39019674 AAT
1 AAT
39019677 ATGTCTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.21, C:0.03, G:0.16, T:0.61
Consensus pattern (18 bp):
AATTTATTGTTTGTGTTT
Found at i:39019695 original size:27 final size:27
Alignment explanation
Indices: 39019650--39019702 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39019640 ATTTATGTTG
* *
39019650 TGTCTTAATTTATTGTTTGTGTTTAATA
1 TGTCTTAAGTTATTATTTGT-TTTAATA
39019678 TGTCTT-AGTTATTATTTGTTTTAAT
1 TGTCTTAAGTTATTATTTGTTTTAAT
39019703 GTGTGCTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 11 0.48
28 6 0.26
ACGTcount: A:0.21, C:0.04, G:0.13, T:0.62
Consensus pattern (27 bp):
TGTCTTAAGTTATTATTTGTTTTAATA
Found at i:39021948 original size:21 final size:21
Alignment explanation
Indices: 39021905--39021950 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39021895 GTTTTTCATA
* *
39021905 CAAGAAGCTTCTAGGGACGTT
1 CAAGAAGCTTCTAAGGAAGTT
39021926 CAAGAAGCTTC-AAGGAAGTTT
1 CAAGAAGCTTCTAAGGAAG-TT
39021947 CAAG
1 CAAG
39021951 GCAATTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (21 bp):
CAAGAAGCTTCTAAGGAAGTT
Found at i:39025229 original size:20 final size:20
Alignment explanation
Indices: 39025206--39025263 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
39025196 TAGCTCGTAT
* *
39025206 AGCTCACAACCAGCTCATCA
1 AGCTCACATCCAGCTCAACA
**
39025226 AGCTCAGTTCCAGCTCAACA
1 AGCTCACATCCAGCTCAACA
*
39025246 AGTTCACATCCAGCTCAA
1 AGCTCACATCCAGCTCAA
39025264 TTCCAGGTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.36, G:0.12, T:0.19
Consensus pattern (20 bp):
AGCTCACATCCAGCTCAACA
Found at i:39025604 original size:30 final size:30
Alignment explanation
Indices: 39025521--39025605 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
39025511 GCTCATATTC
* *
39025521 AGCTCACGTGCTAAACCTTAGCTCAGCTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* * * * * *
39025551 AGCTTAGGAGTTTAATCTCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
*
39025581 AGCTCACGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAACCTTAGCTCA
39025606 TTTTAGTTTA
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (30 bp):
AGCTCACGAGCTAAACCTTAGCTCAACTTT
Found at i:39030691 original size:10 final size:10
Alignment explanation
Indices: 39030678--39030712 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39030668 AAGCTCGGTT
39030678 GAGCTCAAAC
1 GAGCTCAAAC
*
39030688 GAGCTGAAAC
1 GAGCTCAAAC
*
39030698 GAGCTCAAAT
1 GAGCTCAAAC
39030708 GAGCT
1 GAGCT
39030713 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:39030721 original size:20 final size:20
Alignment explanation
Indices: 39030675--39030722 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39030665 AGTAAGCTCG
39030675 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
39030695 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
39030715 GTTGAGCT
1 GTTGAGCT
39030723 AGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:39044065 original size:25 final size:25
Alignment explanation
Indices: 39043998--39044066 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
39043988 CTCTTTTAAT
* *
39043998 AACTTGGGCAAAGCCCTTTTTGATA
1 AACTAGGGCAAAGCCCTTTTCGATA
* *
39044023 AACTAAGG-AAAGCCCTTTTCGGTA
1 AACTAGGGCAAAGCCCTTTTCGATA
* *
39044047 AACTGGGGCATAGCCCTTTT
1 AACTAGGGCAAAGCCCTTTT
39044067 AGCACTTCCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (25 bp):
AACTAGGGCAAAGCCCTTTTCGATA
Found at i:39044906 original size:27 final size:26
Alignment explanation
Indices: 39044876--39044953 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
39044866 GGGTATATTC
39044876 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACC-TACAGGGGTATTACG
* *
39044903 GTCACTTTACCCTACAAGGGCT-TTACG
1 GTCATTTTA-CCTAC-AGGGGTATTACG
* *
39044930 GTCTTTTTACCTATTAGGGGTATT
1 GTCATTTTACCTA-CAGGGGTATT
39044954 TTAGTCATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
26 9 0.22
27 25 0.61
28 7 0.17
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (26 bp):
GTCATTTTACCTACAGGGGTATTACG
Found at i:39045026 original size:27 final size:27
Alignment explanation
Indices: 39044993--39045222 Score: 160
Period size: 27 Copynumber: 8.4 Consensus size: 27
39044983 ATAAATCTAC
*
39044993 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
*
39045020 AAACCAAGGGTATTTCTA-TAATTTTTAA
1 AAACCAAGGGTATTTC-AGTAA-TTTTAT
*
39045048 AAAGTCAAGGGTATTTCTA-TAATTTTAT
1 AAA-CCAAGGGTATTTC-AGTAATTTTAT
* * ** *
39045076 AAATCAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
*** * * *
39045103 AAATTGAGGGTATTTCGGTAATTTCAC
1 AAACCAAGGGTATTTCAGTAATTTTAT
** *
39045130 AAACC-AGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTCAGTAATTTTAT
* * ** *
39045157 AAACTAGGGGTATTTTGGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
39045184 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTAT
* *
39045211 AAATCGAGGGTA
1 AAACCAAGGGTA
39045223 AAACGATAAT
Statistics
Matches: 171, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.01
27 135 0.79
28 17 0.10
29 17 0.10
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTAT
Found at i:39045142 original size:54 final size:53
Alignment explanation
Indices: 39044999--39045222 Score: 200
Period size: 54 Copynumber: 4.1 Consensus size: 53
39044989 CTACAAACCA
* * * * **
39044999 AGGGTATTTCAGTAATTTTGTAAACCAAGGGTATTTCT-ATAATTTTTAAAAAGTCA
1 AGGGTATTTCGGTAATTTTATAAACC-AGGGTATTT-TGGTAA-TTTTACAAA-TTG
** *
39045055 AGGGTATTTCTATAATTTTATAAATCAGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTCGGTAATTTTATAAACCA-GGGTATTTTGGTAATTTTACAAATTG
* * *
39045109 AGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAACT-
1 AGGGTATTTCGGTAATTTTATAAACCAG-GGTATTTTGGTAATTTTACAAATTG
* * * ** *
39045162 AGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
1 A-GGGTATTTCGGTAATTTTATAAACC-AGGGTATTTTGGTAATTTTACAAATTG
39045217 AGGGTA
1 AGGGTA
39045223 AAACGATAAT
Statistics
Matches: 139, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
53 2 0.01
54 91 0.65
55 13 0.09
56 33 0.24
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (53 bp):
AGGGTATTTCGGTAATTTTATAAACCAGGGTATTTTGGTAATTTTACAAATTG
Found at i:39045194 original size:81 final size:81
Alignment explanation
Indices: 39044990--39045207 Score: 210
Period size: 81 Copynumber: 2.7 Consensus size: 81
39044980 TTGATAAATC
* * ** *
39044990 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAAGGGTATTTCTA-TAATTTTTAAAAAGTC
1 TACAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTC-AGTAA-TTTCAAAAAG-C
39045054 AAGGGTATTTCTATAATTT
63 AAGGGTATTTCTATAATTT
* ** *** * * *
39045073 TATAAA-TCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAA-CCA
1 TACAAACT-AGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTCAAAAAGCAA
*
39045136 GTGGTATTT-TGGTAATTT
65 G-GGTATTTCT-ATAATTT
*
39045154 TACAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTT
1 TACAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTT
39045208 TGTAAATCGA
Statistics
Matches: 107, Mismatches: 23, Indels: 12
0.75 0.16 0.08
Matches are distributed among these distances:
80 4 0.04
81 57 0.53
82 8 0.07
83 38 0.36
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (81 bp):
TACAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTCAAAAAGCAAG
GGTATTTCTATAATTT
Found at i:39045232 original size:27 final size:27
Alignment explanation
Indices: 39045210--39045357 Score: 199
Period size: 27 Copynumber: 5.5 Consensus size: 27
39045200 AGTAATTTTG
39045210 TAAATCGAGGGTAAAACGATAATTCTA
1 TAAATCGAGGGTAAAACGATAATTCTA
* *
39045237 TAAATCGAGGGTAAAA-TAGTAATTCTG
1 TAAATCGAGGGTAAAACGA-TAATTCTA
** * *
39045264 TAAATTAAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACGATAATTCTA
39045291 TAAATCGAGGGTAAAACGATAATTCTA
1 TAAATCGAGGGTAAAACGATAATTCTA
* *
39045318 TAAATCGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGATAATTCTA
*
39045345 TAAATTGAGGGTA
1 TAAATCGAGGGTA
39045358 CTTTGGTAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
26 1 0.01
27 104 0.99
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGATAATTCTA
Found at i:39045233 original size:81 final size:80
Alignment explanation
Indices: 39045000--39045314 Score: 193
Period size: 81 Copynumber: 3.9 Consensus size: 80
39044990 TACAAACCAA
* * * ***
39045000 GGGTATTTCAGTAATTTTGTAAACCAAGGGTATTTCTA-TAATTTTTAAAAAGTCAAGGGTATTT
1 GGGTATTTTAGTAATTTTGTAAACCAAGGGTATTT-TAGTAA-TTTTATAAA-TCGAGGGTAAAA
* *
39045064 CTATAATTTTATAAATCAG
63 CGATAATTTTACAAAT-AG
* ** *** ** * * * ****
39045083 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAA-CCAGTGGTATTTTG
1 GGGTATTTTAGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTATAAATCGAG-GGTAAAACG
*
39045147 GTAATTTTACAAACTAG
65 ATAATTTTACAAA-TAG
* *
39045164 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACGA
1 GGGTATTTTAGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAACGA
* * *
39045229 TAATTCTATAAATCG
66 TAATTTTACAAATAG
*** * ** *** * *
39045244 AGGGTAAAATAGTAATTCTGTAAATTAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACG
1 -GGGTATTTTAGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAACG
39045309 ATAATT
65 ATAATT
39045315 CTATAAATCG
Statistics
Matches: 179, Mismatches: 48, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
80 5 0.03
81 132 0.74
82 11 0.06
83 31 0.17
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (80 bp):
GGGTATTTTAGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTATAAATCGAGGGTAAAACGA
TAATTTTACAAATAG
Found at i:39045365 original size:81 final size:81
Alignment explanation
Indices: 39045174--39045368 Score: 273
Period size: 81 Copynumber: 2.4 Consensus size: 81
39045164 GGGTATTTTG
* ** * * * *
39045174 GTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTATA
1 GTAATTCTGTAAATTAAGGGTAATTTGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATA
*
39045239 AATCGAGGGTAAAATA
66 AATCGAGGGTAAAACA
**
39045255 GTAATTCTGTAAATTAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATA
1 GTAATTCTGTAAATTAAGGGTAATTTGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATA
*
39045320 AATCGAGGGTAAAACG
66 AATCGAGGGTAAAACA
* *
39045336 GTAATTCTGTAAATTGAGGGTACTTTGGTAATT
1 GTAATTCTGTAAATTAAGGGTAATTTGGTAATT
39045369 TTACAAATTG
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 99 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (81 bp):
GTAATTCTGTAAATTAAGGGTAATTTGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTATA
AATCGAGGGTAAAACA
Found at i:39045368 original size:54 final size:54
Alignment explanation
Indices: 39045199--39045357 Score: 221
Period size: 54 Copynumber: 2.9 Consensus size: 54
39045189 AAGGGTATTT
* *
39045199 TAGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
** *
39045253 TAGTAATTCTGTAAATTAAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
* * * *
39045307 -CGATAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTA
1 TAG-TAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
39045358 CTTTGGTAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 91 0.99
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (54 bp):
TAGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
Found at i:39049039 original size:29 final size:29
Alignment explanation
Indices: 39049007--39049079 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
39048997 CTTCGAGCTC
*
39049007 GCACACCCAGTG-CAGTATTTTTCCAGCAT
1 GCACACCCAGTGCCA-TATATTTCCAGCAT
**
39049036 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
39049065 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
39049080 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 38 0.95
30 2 0.05
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:39058084 original size:43 final size:43
Alignment explanation
Indices: 39058033--39058137 Score: 158
Period size: 43 Copynumber: 2.4 Consensus size: 43
39058023 GGTTTAATGT
*
39058033 ATTGGCACTAAGTGTGCGATACAATTATAGCCTCGGCTAATTA
1 ATTGGCACTAAGTGTGCGATACAATTATAGCCTCAGCTAATTA
* *
39058076 ATTGGCACTAAGTGTGCGATGCAATTATAGCTTCAGCTAATTA
1 ATTGGCACTAAGTGTGCGATACAATTATAGCCTCAGCTAATTA
*
39058119 ATCT-GCACTAAGTTTGCGA
1 AT-TGGCACTAAGTGTGCGA
39058138 GTTCATTGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
43 56 0.98
44 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (43 bp):
ATTGGCACTAAGTGTGCGATACAATTATAGCCTCAGCTAATTA
Found at i:39059245 original size:2 final size:2
Alignment explanation
Indices: 39059238--39059267 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39059228 ATATGTTTAG
39059238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39059268 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39063051 original size:16 final size:16
Alignment explanation
Indices: 39063030--39063060 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39063020 ACACTTAGTG
*
39063030 CTATTTATAATCGCAA
1 CTATTTAAAATCGCAA
39063046 CTATTTAAAATCGCA
1 CTATTTAAAATCGCA
39063061 CACTTAGTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (16 bp):
CTATTTAAAATCGCAA
Found at i:39074182 original size:10 final size:10
Alignment explanation
Indices: 39074167--39074206 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
39074157 CACTTTTTTT
39074167 ATTTTTTTCGA
1 ATTTTTTT-GA
39074178 ATTTTTTTGA
1 ATTTTTTTGA
*
39074188 TTTTTTTTTGA
1 -ATTTTTTTGA
39074199 ATTTTTTT
1 ATTTTTTT
39074207 AACTTGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (10 bp):
ATTTTTTTGA
Found at i:39074192 original size:21 final size:19
Alignment explanation
Indices: 39074160--39074207 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 19
39074150 CATAAATCAC
39074160 TTTTTTTATTTTTTTCGAA
1 TTTTTTTATTTTTTTCGAA
*
39074179 TTTTTTTGATTTTTTTTTGAA
1 TTTTTTT-A-TTTTTTTCGAA
39074200 TTTTTTTA
1 TTTTTTTA
39074208 ACTTGTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 2 0.08
21 17 0.65
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTTTTATTTTTTTCGAA
Found at i:39076004 original size:30 final size:31
Alignment explanation
Indices: 39075910--39076008 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 31
39075900 TAAACTAAAA
*
39075910 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
* * * * * *
39075940 TGAGCTGAGGCTAAACTCCTAAGCTG-AAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
*
39075970 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
39076000 TGAGC-AAGG
1 TGAGCTAAGG
39076009 AGTGAGCTCG
Statistics
Matches: 53, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
29 4 0.08
30 46 0.87
31 3 0.06
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (31 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
Found at i:39076811 original size:30 final size:30
Alignment explanation
Indices: 39076716--39076812 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
39076706 AGCTCACTCC
*
39076716 TAGCTCATA-TTCAACTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
39076746 TAGCTCAGCTTCAGCTTA-GAAGTTTAATCT
1 TAGCTCAACTTCAGCTCACG-AGCTAAACCT
* * *
39076776 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
39076806 TAGCTCA
1 TAGCTCA
39076813 TGTTACTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 1 0.02
30 48 0.96
31 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:39079383 original size:9 final size:10
Alignment explanation
Indices: 39079376--39079432 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
39079366 AAGAGAAAAT
39079376 AAAGAAAAGA
1 AAAGAAAAGA
39079386 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
39079398 AAAGAAGA-A
1 AAAGAAAAGA
39079407 AAAGAAAATGA
1 AAAGAAAA-GA
39079418 AATA-AAAAGA
1 AA-AGAAAAGA
39079428 AAAGA
1 AAAGA
39079433 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:39079400 original size:6 final size:5
Alignment explanation
Indices: 39079376--39079432 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
39079366 AAGAGAAAAT
*
39079376 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
39079423 AAAGA AAAGA
1 AAAGA AAAGA
39079433 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:39079407 original size:15 final size:14
Alignment explanation
Indices: 39079376--39079432 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
39079366 AAGAGAAAAT
39079376 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
39079392 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
39079407 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
39079423 AAAGAAAAGA
1 AAAGAAAAGA
39079433 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:39079512 original size:11 final size:12
Alignment explanation
Indices: 39079480--39079510 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39079470 TTGAGAGAAC
39079480 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39079492 TTGAAAAAGCCT
1 TTGAAAAAGCCT
39079504 TTGAAAA
1 TTGAAAA
39079511 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:39079521 original size:12 final size:12
Alignment explanation
Indices: 39079513--39079537 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39079503 TTTGAAAAGC
39079513 AAAAAGAAAATG
1 AAAAAGAAAATG
39079525 AAAAAGAAAATG
1 AAAAAGAAAATG
39079537 A
1 A
39079538 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:39079534 original size:18 final size:18
Alignment explanation
Indices: 39079507--39079562 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
39079497 AAAGCCTTTG
*
39079507 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
39079526 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
39079544 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
39079561 AA
1 AA
39079563 TTTGAGAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:39079547 original size:30 final size:31
Alignment explanation
Indices: 39079513--39079594 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
39079503 TTTGAAAAGC
*
39079513 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
39079543 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
39079573 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
39079595 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:39081838 original size:30 final size:30
Alignment explanation
Indices: 39081804--39081901 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
39081794 AGCTGACTCC
39081804 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
39081834 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
39081864 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
39081894 TAGCTCAT
1 TAGCTCAT
39081902 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:39086625 original size:30 final size:30
Alignment explanation
Indices: 39086589--39086685 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39086579 AGCTCACTCC
39086589 TAGCTCATA-TTCAGCTTACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTTACGAGCTAAACCT
* * * *
39086619 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
* * * *
39086649 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
39086679 TAGCTCA
1 TAGCTCA
39086686 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTTACGAGCTAAACCT
Found at i:39089307 original size:37 final size:37
Alignment explanation
Indices: 39089256--39089326 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
39089246 CATTCTTGTA
39089256 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
39089293 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
39089327 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:39089326 original size:6 final size:6
Alignment explanation
Indices: 39089266--39089315 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
39089256 AAGAGAAAAC
*
39089266 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
39089315 A
1 A
39089316 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:39089405 original size:12 final size:12
Alignment explanation
Indices: 39089397--39089421 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39089387 TTTGAAAAGC
39089397 AAAAAGAAAATG
1 AAAAAGAAAATG
39089409 AAAAAGAAAATG
1 AAAAAGAAAATG
39089421 A
1 A
39089422 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:39089418 original size:18 final size:18
Alignment explanation
Indices: 39089391--39089446 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
39089381 AAAGCCTTTG
39089391 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
39089410 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
39089428 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
39089445 AA
1 AA
39089447 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:39089431 original size:30 final size:31
Alignment explanation
Indices: 39089397--39089478 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
39089387 TTTGAAAAGC
*
39089397 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
39089427 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
39089457 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
39089479 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:39091600 original size:30 final size:30
Alignment explanation
Indices: 39091566--39091662 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
39091556 AGCTCACTCC
39091566 TAGCTCATA-TTCAGCTTACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTTACGAGCTAAACCT
* * * *
39091596 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
* * * *
39091626 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTTACGAGCTAAACCT
39091656 TAGCTCA
1 TAGCTCA
39091663 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTTACGAGCTAAACCT
Found at i:39093423 original size:46 final size:44
Alignment explanation
Indices: 39093343--39093471 Score: 122
Period size: 46 Copynumber: 3.0 Consensus size: 44
39093333 GCTGGTATTA
* * * * *
39093343 TATTCGAGCCTTT-GAGCCTAACAGACTATTATGCCCGTGAGACAT
1 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCAGTGA-A-AT
*
39093388 TATTCGGGCCTTTCGAGCCTAGTAGGCTATAATGCCAGTGAAAT
1 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCAGTGAAAT
* * *
39093432 GATATCGGGCC--TCGAGCCTAGCAGGCGA-AATGCCGGTGAA
1 TAT-TCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCAGTGAA
39093472 TGAATAAAAG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
42 11 0.15
43 15 0.21
44 4 0.06
45 20 0.28
46 22 0.31
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (44 bp):
TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCAGTGAAAT
Found at i:39098613 original size:38 final size:38
Alignment explanation
Indices: 39098554--39098661 Score: 189
Period size: 38 Copynumber: 2.8 Consensus size: 38
39098544 TCAATCATGC
*
39098554 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTTCATAAT
*
39098593 ACTGGGCCGAAGCCTTTTCATGTTTCATATTTCATAAT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
39098631 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATT
39098662 ACTGGGCCGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 55 0.83
39 11 0.17
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (38 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTCATAAT
Found at i:39098619 original size:31 final size:31
Alignment explanation
Indices: 39098577--39098678 Score: 132
Period size: 31 Copynumber: 3.1 Consensus size: 31
39098567 CCTTTTCATA
39098577 TTTCATATTTCATAATACTGGGCCGAAGCCTTTTCAT
1 TTTCATATTTCATAATACTGGGCCGAAG-C----C-T
39098614 GTTTCATATTTCATAATACTGGGCCGAAGCCT
1 -TTTCATATTTCATAATACTGGGCCGAAGCCT
*
39098646 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
39098677 TT
1 TT
39098679 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
31 32 0.51
32 1 0.02
33 1 0.02
37 1 0.02
38 28 0.44
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:39098908 original size:24 final size:24
Alignment explanation
Indices: 39098862--39098979 Score: 143
Period size: 24 Copynumber: 4.9 Consensus size: 24
39098852 GCTTTATCAT
* *
39098862 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTCA
*
39098887 ATAACTGGGGCCA-AATCCCTTTCA
1 ATAACTGGGG-CATAAGCCCTTTCA
*
39098911 ATAACTGGGGCATAAGCCCTTT-T
1 ATAACTGGGGCATAAGCCCTTTCA
*
39098934 ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTCA
39098958 ATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTT
39098980 TTCACTTCCT
Statistics
Matches: 83, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
23 24 0.29
24 47 0.57
25 12 0.14
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTCA
Found at i:39098941 original size:47 final size:48
Alignment explanation
Indices: 39098862--39098980 Score: 163
Period size: 47 Copynumber: 2.5 Consensus size: 48
39098852 GCTTTATCAT
* *
39098862 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCCA-AATCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGG-CATAAGCCCTTTCA
*
39098911 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTCG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
39098958 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
39098981 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 2 0.03
47 42 0.65
48 9 0.14
49 12 0.18
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:39099056 original size:20 final size:20
Alignment explanation
Indices: 39099031--39099090 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
39099021 TATGATTACC
39099031 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
39099051 TCATGTGCGTATCATACATT
1 TCATGTGCATATCATACATA
39099071 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
39099091 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:39099165 original size:25 final size:25
Alignment explanation
Indices: 39099133--39099180 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39099123 ATACATAAAC
* * *
39099133 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
39099158 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
39099181 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:39101300 original size:15 final size:15
Alignment explanation
Indices: 39101280--39101327 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39101270 TCAAAGATGG
39101280 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
39101295 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
39101309 GTTTATGGATATAAA
1 GTTTATGGATATGAA
39101324 GTTT
1 GTTT
39101328 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:39101314 original size:14 final size:14
Alignment explanation
Indices: 39101274--39101317 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
39101264 AAGGATTCAA
39101274 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
39101288 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
39101303 AGATGGGTTTATGG
1 AGATGGGTTTATGG
39101317 A
1 A
39101318 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:39101343 original size:29 final size:29
Alignment explanation
Indices: 39101274--39101333 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
39101264 AAGGATTCAA
*
39101274 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
39101303 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
39101332 AG
1 AG
39101334 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:39102328 original size:14 final size:14
Alignment explanation
Indices: 39102306--39102350 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
39102296 TTAAAGAAGC
39102306 AACTCATTAAATTA
1 AACTCATTAAATTA
*
39102320 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
39102333 AACTCATTTAATTA
1 AACTCATTAAATTA
39102347 AACT
1 AACT
39102351 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:39102388 original size:22 final size:22
Alignment explanation
Indices: 39102362--39102431 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
39102352 AGATGAGTTG
39102362 TATTAATGACCAGAAACTCATT
1 TATTAATGACCAGAAACTCATT
* * *
39102384 TATTAA--ACTA-AGA-TGAGTT
1 TATTAATGACCAGAAACTCA-TT
*
39102403 GTATTAATGACCAGCAACTCATT
1 -TATTAATGACCAGAAACTCATT
39102426 TATTAA
1 TATTAA
39102432 ACTAAGAGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 9 0.26
22 15 0.43
23 3 0.09
24 2 0.06
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (22 bp):
TATTAATGACCAGAAACTCATT
Found at i:39102395 original size:42 final size:42
Alignment explanation
Indices: 39102332--39102438 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
39102322 TTCATTAAAT
39102332 AAACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAG
1 AAACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAG
39102375 AAACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAG
1 AAACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAG
*
39102417 CAACTCATTTATTAAACTAAGA
1 AAACTCATTTATTAAACTAAGA
39102439 GGCTTAAATG
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (42 bp):
AAACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAG
Found at i:39102409 original size:20 final size:20
Alignment explanation
Indices: 39102343--39102409 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
39102333 AACTCATTTA
39102343 ATTAAACTAAGATGAGTTGT
1 ATTAAACTAAGATGAGTTGT
* * *
39102363 ATTAATGACCAGAAACTCA-TT-T
1 ATTAA--ACTA-AGA-TGAGTTGT
39102385 ATTAAACTAAGATGAGTTGT
1 ATTAAACTAAGATGAGTTGT
39102405 ATTAA
1 ATTAA
39102410 TGACCAGCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 14 0.40
22 9 0.26
23 4 0.11
24 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (20 bp):
ATTAAACTAAGATGAGTTGT
Found at i:39104893 original size:18 final size:18
Alignment explanation
Indices: 39104872--39104921 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
39104862 AAACTCTTTT
39104872 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
39104890 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
39104908 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
39104922 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:39104927 original size:24 final size:24
Alignment explanation
Indices: 39104847--39104924 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
39104837 CTTGTTCACA
*
39104847 TTCTTTCTCTCTCTCAAACTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
* * * *
39104871 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTCTCTCTCTCAATCTCTTT
* *
39104895 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTCTCTCTCTCAATCTCTTT
39104919 TTCTTT
1 TTCTTT
39104925 TTCTTTCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCAATCTCTTT
Found at i:39107292 original size:10 final size:10
Alignment explanation
Indices: 39107277--39107303 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
39107267 TAAGTTGAAG
39107277 TTGAGCTGAT
1 TTGAGCTGAT
39107287 TTGAGCTGAT
1 TTGAGCTGAT
39107297 TTGAGCT
1 TTGAGCT
39107304 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:39107596 original size:11 final size:11
Alignment explanation
Indices: 39107582--39107611 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39107572 AAATTTTGTT
39107582 TTTTTTTTCAA
1 TTTTTTTTCAA
*
39107593 TTTTTTTTGAA
1 TTTTTTTTCAA
39107604 TTTTTTTT
1 TTTTTTTT
39107612 TTGAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:39107614 original size:13 final size:13
Alignment explanation
Indices: 39107580--39107616 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
39107570 TCAAATTTTG
*
39107580 TTTTTTTTTTCAA
1 TTTTTTTTTTGAA
39107593 --TTTTTTTTGAA
1 TTTTTTTTTTGAA
39107604 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
39107617 ACTTACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:39107855 original size:15 final size:15
Alignment explanation
Indices: 39107835--39107882 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39107825 TCAAAGGTGG
39107835 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
39107850 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
39107864 GTTTATGGATATAAA
1 GTTTATGGATATGAA
39107879 GTTT
1 GTTT
39107883 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:39107898 original size:29 final size:29
Alignment explanation
Indices: 39107832--39107888 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
39107822 GATTCAAAGG
*
39107832 TGGGTTTATGGATATGAAGTTTATGTAGA
1 TGGGTTTATGGATATAAAGTTTATGTAGA
*
39107861 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
39107889 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGA
Found at i:39108883 original size:14 final size:14
Alignment explanation
Indices: 39108861--39108905 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
39108851 TTAAAGAAGC
39108861 AACTCATTAAATTA
1 AACTCATTAAATTA
*
39108875 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
39108888 AACTCATTTAATTA
1 AACTCATTAAATTA
39108902 AACT
1 AACT
39108906 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:39109784 original size:38 final size:38
Alignment explanation
Indices: 39109730--39109889 Score: 214
Period size: 38 Copynumber: 4.2 Consensus size: 38
39109720 TCGAAATATG
*
39109730 ATATCAGAGTTAAATCCCGTAGGCTTCGTGCTGGTATT
1 ATATCCGAGTTAAATCCCGTAGGCTTCGTGCTGGTATT
* * *
39109768 ATATCCGAGTTGAATCCCGTAGTCTTCGTGCTGGTAAT
1 ATATCCGAGTTAAATCCCGTAGGCTTCGTGCTGGTATT
* *
39109806 ATATCCGGGTTAAATCCCGTAGGGTTCGTGCTGGTATT
1 ATATCCGAGTTAAATCCCGTAGGCTTCGTGCTGGTATT
* * * *
39109844 ATATCCGGGTTAAATCCCGCAGGCCTAGTGC-GGTATT
1 ATATCCGAGTTAAATCCCGTAGGCTTCGTGCTGGTATT
*
39109881 ATATTCGAG
1 ATATCCGAG
39109890 CCTTTGAGCC
Statistics
Matches: 107, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
37 13 0.12
38 94 0.88
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (38 bp):
ATATCCGAGTTAAATCCCGTAGGCTTCGTGCTGGTATT
Found at i:39109992 original size:42 final size:42
Alignment explanation
Indices: 39109930--39110012 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
39109920 GAGACATTAT
*
39109930 TCGGGCCTTTCGAGCCTAGCAGGCTATAATGCCGGTAAATGATA
1 TCGGGCC-TTCGAGCCTAGCAGGCGA-AATGCCGGTAAATGATA
*
39109974 TCGGGCC-TCGAGCCTAGCAGGCGAAATGCCGGTGAATGA
1 TCGGGCCTTCGAGCCTAGCAGGCGAAATGCCGGTAAATGA
39110013 ATAAAAGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 14 0.38
42 16 0.43
44 7 0.19
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.20
Consensus pattern (42 bp):
TCGGGCCTTCGAGCCTAGCAGGCGAAATGCCGGTAAATGATA
Found at i:39121714 original size:14 final size:14
Alignment explanation
Indices: 39121695--39121722 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39121685 AGAAAAGGGT
39121695 GATTAACTCTAGTA
1 GATTAACTCTAGTA
39121709 GATTAACTCTAGTA
1 GATTAACTCTAGTA
39121723 TCGAATGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GATTAACTCTAGTA
Found at i:39123657 original size:27 final size:27
Alignment explanation
Indices: 39123625--39123806 Score: 244
Period size: 27 Copynumber: 6.7 Consensus size: 27
39123615 TACATCACAT
* *
39123625 AGGGCAAAACAGTCATCTTACCATATA
1 AGGGCAAAATAGTCATTTTACCATATA
* *
39123652 AGGGCAAAATAATCATTTTACCA-CTA
1 AGGGCAAAATAGTCATTTTACCATATA
39123678 AGGGCAAAATAGTCATTTTACCATATA
1 AGGGCAAAATAGTCATTTTACCATATA
*
39123705 AGGGGCAAAATAGTCATCTTACCATATA
1 A-GGGCAAAATAGTCATTTTACCATATA
*
39123733 AGGGCAAAATAGTCATTTTACCAAATA
1 AGGGCAAAATAGTCATTTTACCATATA
* *
39123760 AGGACAAAACAGTCATTTTACCACT-TA
1 AGGGCAAAATAGTCATTTTACCA-TATA
39123787 AGGG-AGAAATAGTCATTTTA
1 AGGGCA-AAATAGTCATTTTA
39123807 TCAATTAGGG
Statistics
Matches: 137, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
26 25 0.18
27 86 0.63
28 26 0.19
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.26
Consensus pattern (27 bp):
AGGGCAAAATAGTCATTTTACCATATA
Done.