Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 137 of 172
Found at i:39400869 original size:21 final size:21
Alignment explanation
Indices: 39400828--39400873 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39400818 TCTCAATACA
*
39400828 TCAAGAACATGTCTCATGACC
1 TCAAAAACATGTCTCATGACC
39400849 TCAAAAACATGTCTCGA-GACC
1 TCAAAAACATGTCTC-ATGACC
39400870 TCAA
1 TCAA
39400874 GAATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (21 bp):
TCAAAAACATGTCTCATGACC
Found at i:39401605 original size:85 final size:86
Alignment explanation
Indices: 39401506--39401670 Score: 251
Period size: 87 Copynumber: 1.9 Consensus size: 86
39401496 AAAAATCCTC
* * * * * *
39401506 AAACTTTTTTAAAAAAGCAATTAAGTCCCT-TTTTTTTGTACTCATTTGGGTACTTGAACTTTTA
1 AAACCTTTTCAAAAAAGCAATTAAGCCCCTATTTTTTTGCACTCAATTGGGTACTTGAACTTTCA
*
39401570 AAATGCATTAAAAATGCCTTG
66 AAATGCATAAAAAATGCCTTG
39401591 AAACCTTTTCAAAAAAGCAATTAAGCCCCTACTTTTTTTGCACTCAATTGGGTACTTGAACTTTC
1 AAACCTTTTCAAAAAAGCAATTAAGCCCCTA-TTTTTTTGCACTCAATTGGGTACTTGAACTTTC
39401656 AAAATGCATAAAAAA
65 AAAATGCATAAAAAA
39401671 GACCCTCAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
85 27 0.38
87 44 0.62
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (86 bp):
AAACCTTTTCAAAAAAGCAATTAAGCCCCTATTTTTTTGCACTCAATTGGGTACTTGAACTTTCA
AAATGCATAAAAAATGCCTTG
Found at i:39401693 original size:87 final size:84
Alignment explanation
Indices: 39401502--39401692 Score: 240
Period size: 87 Copynumber: 2.2 Consensus size: 84
39401492 TGCAAAAAAT
* * * *
39401502 CCTCAAACTTTTTTAAAAAAGCAATTAAGTCCCTTTTTTTTGTACTCATTTGGGTACTTGAACTT
1 CCTCAAAC-TTTTAAAAAAAGCAATTAAGCCCCTTTTTTTTGCACTCAATTGGGTACTTGAACTT
* *
39401567 TTAAAATGCATTAAAAATGC
65 TCAAAATGCATTAAAAAAGC
* * *
39401587 CTTGAAACCTTTTCAAAAAAGCAATTAAGCCCCTACTTTTTTTGCACTCAATTGGGTACTTGAAC
1 CCTCAAA-CTTTTAAAAAAAGCAATTAAGCCCCT--TTTTTTTGCACTCAATTGGGTACTTGAAC
39401652 TTTCAAAATGCA-TAAAAAAGAC
63 TTTCAAAATGCATTAAAAAAG-C
*
39401674 CCTCAAACTTTAAAAAAAA
1 CCTCAAACTTTTAAAAAAA
39401693 AAATTAATCC
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
85 28 0.31
86 18 0.20
87 44 0.49
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (84 bp):
CCTCAAACTTTTAAAAAAAGCAATTAAGCCCCTTTTTTTTGCACTCAATTGGGTACTTGAACTTT
CAAAATGCATTAAAAAAGC
Found at i:39401698 original size:85 final size:85
Alignment explanation
Indices: 39401502--39401699 Score: 222
Period size: 85 Copynumber: 2.3 Consensus size: 85
39401492 TGCAAAAAAT
* * ** * * *
39401502 CCTCAAACTTTTTTAAAAAAGCAATTAAGTCCCTTTTTTTTGTACTCATTTGGGTACTTGAACTT
1 CCTCAAACCTTTTAAAAAAAAAAATTAAGCCCCTTTTTTTTGCACTCAATTGGGTACTTGAACTT
* *
39401567 TTAAAATGCATTAAAAATGC
66 TCAAAATGCATTAAAAAAGC
* * * **
39401587 CTTGAAACCTTTTCAAAAAAGCAATTAAGCCCCTACTTTTTTTGCACTCAATTGGGTACTTGAAC
1 CCTCAAACCTTTTAAAAAAAAAAATTAAGCCCCT--TTTTTTTGCACTCAATTGGGTACTTGAAC
39401652 TTTCAAAATGCA-TAAAAAAGAC
64 TTTCAAAATGCATTAAAAAAG-C
39401674 CCTCAAA-C-TTTAAAAAAAAAAATTAA
1 CCTCAAACCTTTTAAAAAAAAAAATTAA
39401700 TCCCTAGCTT
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
85 44 0.46
86 8 0.08
87 44 0.46
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (85 bp):
CCTCAAACCTTTTAAAAAAAAAAATTAAGCCCCTTTTTTTTGCACTCAATTGGGTACTTGAACTT
TCAAAATGCATTAAAAAAGC
Found at i:39401850 original size:20 final size:18
Alignment explanation
Indices: 39401816--39401885 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
39401806 TAAAGATTAG
39401816 AAAAAATATAAAAATCGT
1 AAAAAATATAAAAATCGT
*
39401834 AAAAGAATATAAAAAATTGT
1 AAAA-AATAT-AAAAATCGT
** **
39401854 AAAATTTTATGGAAATCGT
1 AAAA-AATATAAAAATCGT
39401873 AAAAAATTATAAA
1 AAAAAA-TATAAA
39401886 TATAGAAATA
Statistics
Matches: 38, Mismatches: 11, Indels: 5
0.70 0.20 0.09
Matches are distributed among these distances:
18 4 0.11
19 19 0.50
20 15 0.39
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (18 bp):
AAAAAATATAAAAATCGT
Found at i:39402225 original size:21 final size:19
Alignment explanation
Indices: 39402195--39402249 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
39402185 TTTTAATAAA
39402195 TTCT-AAATTTTTAAATTT
1 TTCTAAAATTTTTAAATTT
* *
39402213 TTAATTAAAA-TTTAATAATTT
1 TT--CTAAAATTTTTA-AATTT
39402234 TTCTAAAATTTTTAAA
1 TTCTAAAATTTTTAAA
39402250 AGTTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
18 2 0.07
19 7 0.25
20 9 0.32
21 10 0.36
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTCTAAAATTTTTAAATTT
Found at i:39412265 original size:23 final size:23
Alignment explanation
Indices: 39412237--39412291 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
39412227 ATTTGTTAGA
39412237 AAGCATTATTGTTTAATTTGGCG
1 AAGCATTATTGTTTAATTTGGCG
* *
39412260 AAGCATGATTTTTGTTTAATTTTGCG
1 AAGC---ATTATTGTTTAATTTGGCG
39412286 AAGCAT
1 AAGCAT
39412292 GATTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.22
26 21 0.78
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (23 bp):
AAGCATTATTGTTTAATTTGGCG
Found at i:39412276 original size:26 final size:26
Alignment explanation
Indices: 39412245--39412295 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
39412235 GAAAGCATTA
39412245 TTGTTTAATTTGGCGAAGCATGATTT
1 TTGTTTAATTTGGCGAAGCATGATTT
*
39412271 TTGTTTAATTTTGCGAAGCATGATT
1 TTGTTTAATTTGGCGAAGCATGATT
39412296 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.47
Consensus pattern (26 bp):
TTGTTTAATTTGGCGAAGCATGATTT
Found at i:39419022 original size:57 final size:58
Alignment explanation
Indices: 39418927--39419056 Score: 162
Period size: 57 Copynumber: 2.3 Consensus size: 58
39418917 ATCAAATGAA
* *
39418927 CAAAAT-T-AAATAAAAATGGAGAAATAGGAAATATTTGGAAAT-TATGAAGGTTTTCTC
1 CAAAATGTAAAATGAAAATGGAGAAATA-GAAATATTTGGAAATGAATG-AGGTTTTCTC
*
39418984 CAAAATG-AAAATGAAAATGGAGAAAT-GAAATCATTTGGAAATGAATGTGGTTTTCTC
1 CAAAATGTAAAATGAAAATGGAGAAATAGAAAT-ATTTGGAAATGAATGAGGTTTTCTC
*
39419041 CAAAATGTGAAATGAA
1 CAAAATGTAAAATGAA
39419057 TTCATTTGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
56 5 0.08
57 32 0.50
58 27 0.42
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (58 bp):
CAAAATGTAAAATGAAAATGGAGAAATAGAAATATTTGGAAATGAATGAGGTTTTCTC
Found at i:39419083 original size:44 final size:44
Alignment explanation
Indices: 39419005--39419091 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
39418995 TGAAAATGGA
*** * *
39419005 GAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGT
1 GAAATGAAATCATTTGGAAATGAACAAGGATTTCTCAAAAATGT
*
39419049 GAAATGAATTCATTTGGAAATGAACAAGGATTTCTCAAAAATG
1 GAAATGAAATCATTTGGAAATGAACAAGGATTTCTCAAAAATG
39419092 ATCGGAAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (44 bp):
GAAATGAAATCATTTGGAAATGAACAAGGATTTCTCAAAAATGT
Found at i:39421112 original size:25 final size:25
Alignment explanation
Indices: 39421084--39421174 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 25
39421074 CACAGCTTTT
*
39421084 ATGAGCATCCCGATATTTGGCTCTC
1 ATGAGCTTCCCGATATTTGGCTCTC
* *
39421109 ATGAGTTTCCC-A-ATTAATGGCTCTT
1 ATGAGCTTCCCGATATT--TGGCTCTC
* * *
39421134 ATGAGCTTCTCGATAATTGGCTCGC
1 ATGAGCTTCCCGATATTTGGCTCTC
*
39421159 ATAAGCTTCCCGATAT
1 ATGAGCTTCCCGATAT
39421175 ACAACTCACA
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
23 3 0.06
24 1 0.02
25 44 0.86
26 1 0.02
27 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCGATATTTGGCTCTC
Found at i:39424911 original size:23 final size:21
Alignment explanation
Indices: 39424855--39424907 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
39424845 TTAAATATAT
39424855 ATAATATATATTTGATTAAAA
1 ATAATATATATTTGATTAAAA
39424876 ATAATATATATTTGATTAAAA
1 ATAATATATATTTGATTAAAA
*
39424897 ATAAAATATAT
1 ATAATATATAT
39424908 ATTTAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
ATAATATATATTTGATTAAAA
Found at i:39440443 original size:27 final size:27
Alignment explanation
Indices: 39440378--39440436 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
39440368 AGCAGATCAC
* *
39440378 ATATAACCCTATCTGTATAGCGTGTAA
1 ATATTACCCTATCTATATAGCGTGTAA
39440405 ATATTACCCTATCTATATAGCGTGTAA
1 ATATTACCCTATCTATATAGCGTGTAA
39440432 ATATT
1 ATATT
39440437 CTCCTATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (27 bp):
ATATTACCCTATCTATATAGCGTGTAA
Found at i:39457153 original size:61 final size:61
Alignment explanation
Indices: 39457050--39457168 Score: 184
Period size: 61 Copynumber: 2.0 Consensus size: 61
39457040 TATTCCAGAT
* * *
39457050 GATTTATTTATACCATAAATATATCAGAATCTCTATAGTGTAAGACAACTACTAGAAAGGA
1 GATTTATTTATACCATAAAAATATCAAAATCTCTATACTGTAAGACAACTACTAGAAAGGA
* * *
39457111 GATTTATTTGTACCATAAAAATATCAAAATCTTTGTACTGTAAGACAACTACTAGAAA
1 GATTTATTTATACCATAAAAATATCAAAATCTCTATACTGTAAGACAACTACTAGAAA
39457169 AAAGTTATTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (61 bp):
GATTTATTTATACCATAAAAATATCAAAATCTCTATACTGTAAGACAACTACTAGAAAGGA
Found at i:39458769 original size:50 final size:50
Alignment explanation
Indices: 39458645--39458893 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
39458635 GATAATAACA
* * ** * *
39458645 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
39458696 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
39458746 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
39458796 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
39458851 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
39458894 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 1 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:39458824 original size:100 final size:104
Alignment explanation
Indices: 39458644--39458893 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
39458634 TGATAATAAC
** *
39458644 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATAGTGCCCATGCCATG
* *
39458709 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
39458746 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCAGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-AGTGCCCATGCCATG
39458809 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
39458851 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39458894 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATAGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:39459267 original size:29 final size:30
Alignment explanation
Indices: 39459229--39459288 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
39459219 GCCCTCGACT
*
39459229 CTAAA-TTTTTCAAAATTACAATTTTGCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
* *
39459258 CTAAACTTTTACATAATTACATTTTTGCCC
1 CTAAACTTTTACAAAATTACAATTTTGCCC
39459288 C
1 C
39459289 AAGGCTCGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (30 bp):
CTAAACTTTTACAAAATTACAATTTTGCCC
Found at i:39462050 original size:17 final size:17
Alignment explanation
Indices: 39462028--39462060 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39462018 ATAGTTCATT
39462028 TCAATTCATATT-CAATA
1 TCAATTC-TATTGCAATA
39462045 TCAATTCTATTGCAAT
1 TCAATTCTATTGCAAT
39462061 TTGTATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (17 bp):
TCAATTCTATTGCAATA
Found at i:39463488 original size:5 final size:5
Alignment explanation
Indices: 39463478--39463525 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
39463468 TATATATATA
*
39463478 ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT -TAACA ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAA
39463526 AAACATACTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 1 0.03
4 3 0.08
5 31 0.82
6 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:39463530 original size:19 final size:19
Alignment explanation
Indices: 39463493--39463530 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39463483 ATAATATAAT
**
39463493 ATAATATAATATATTAACA
1 ATAATATAATATAAAAACA
39463512 ATAATATAATATAAAAACA
1 ATAATATAATATAAAAACA
39463531 TACTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATATAATATAAAAACA
Found at i:39473588 original size:6 final size:7
Alignment explanation
Indices: 39473567--39473597 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
39473557 ATCAATATGC
39473567 TAATATTT
1 TAAT-TTT
39473575 TAATTTT
1 TAATTTT
39473582 TAATTTT
1 TAATTTT
39473589 TAATTTT
1 TAATTTT
39473596 TA
1 TA
39473598 CTTATACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TAATTTT
Found at i:39474252 original size:21 final size:24
Alignment explanation
Indices: 39474219--39474268 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
39474209 TACGAGTTTT
39474219 TTTTAGAATTATTT-AATT-T-AA
1 TTTTAGAATTATTTCAATTATAAA
39474240 TTTT-GAATATATTTCAATTATAAA
1 TTTTAGAAT-TATTTCAATTATAAA
39474264 TTTTA
1 TTTTA
39474269 TTACACTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.17
21 9 0.38
22 4 0.17
23 1 0.04
24 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTAGAATTATTTCAATTATAAA
Found at i:39477371 original size:31 final size:31
Alignment explanation
Indices: 39477333--39477467 Score: 115
Period size: 31 Copynumber: 4.4 Consensus size: 31
39477323 TCTTGGTCCG
39477333 ATTTGGTACAC-AAACTTGACACTTTTTCCTA
1 ATTTGGTAC-CTAAACTTGACACTTTTTCCTA
*
39477364 ATTTGGTACCTAAACTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* *
39477395 AGTTGGTACTTAATA-TT-----TTTTGGGATCC-A
1 ATTTGGTACCTAA-ACTTGACACTTTT----TCCTA
* *
39477424 ATTCGGTACCTAAACTTGACTCTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
39477455 ATTTGGTACCTAA
1 ATTTGGTACCTAA
39477468 TCTTTTTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
26 4 0.05
28 1 0.01
29 13 0.16
30 6 0.07
31 54 0.65
32 1 0.01
34 4 0.05
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:39477432 original size:91 final size:90
Alignment explanation
Indices: 39477273--39477467 Score: 236
Period size: 91 Copynumber: 2.1 Consensus size: 90
39477263 TTAATATAAC
* * * * * *
39477273 ATTTGGTACATGAAATTTACACTTTTTACTAATTTGGTACATAAATTTTTTCTTGGTCCGATTTG
1 ATTTGGTACCT-AAATTGACACTTTTTACTAAGTTGGTACATAAATTTTTTCTGGGTCCAATTCG
39477338 GTACAC-AAACTTGACACTTTTTCCTA
65 GTAC-CTAAACTTGACACTTTTTCCTA
*
39477364 ATTTGGTACCTAAACTTGACACTTTTT-CTTAAGTTGGTAC-TTAATATTTTT-TGGGATCCAAT
1 ATTTGGTACCTAAA-TTGACACTTTTTAC-TAAGTTGGTACATAAAT-TTTTTCTGGG-TCCAAT
*
39477426 TCGGTACCTAAACTTGACTCTTTTTCCTA
62 TCGGTACCTAAACTTGACACTTTTTCCTA
39477455 ATTTGGTACCTAA
1 ATTTGGTACCTAA
39477468 TCTTTTTTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
90 12 0.13
91 79 0.87
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (90 bp):
ATTTGGTACCTAAATTGACACTTTTTACTAAGTTGGTACATAAATTTTTTCTGGGTCCAATTCGG
TACCTAAACTTGACACTTTTTCCTA
Found at i:39477439 original size:60 final size:60
Alignment explanation
Indices: 39477363--39477475 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 60
39477353 ACTTTTTCCT
* * *
39477363 AATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTGGTACTTAATATTTTTTGGGATCC
1 AATTCGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTTGGGATCC
* * *
39477423 AATTCGGTACCTAAACTTGACTCTTTTTCCTAATTTGGTACCTAATCTTTTTT
1 AATTCGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTT
39477476 TTTGTTCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (60 bp):
AATTCGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAATATTTTTTGGGATCC
Found at i:39482559 original size:6 final size:6
Alignment explanation
Indices: 39482548--39482574 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
39482538 AGTCTAAATA
39482548 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
39482575 AAAATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:39496045 original size:2 final size:2
Alignment explanation
Indices: 39496038--39496065 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39496028 TAATAACATA
39496038 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
39496066 TCAAACATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39499164 original size:17 final size:17
Alignment explanation
Indices: 39499142--39499174 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39499132 GAGAGTTTTT
39499142 GAAGAAAGAA-AAGAAGA
1 GAAG-AAGAAGAAGAAGA
39499159 GAAGAAGAAGAAGAAG
1 GAAGAAGAAGAAGAAG
39499175 GAGAGGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAGAAGAAGA
Found at i:39501232 original size:14 final size:14
Alignment explanation
Indices: 39501213--39501247 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
39501203 GACATTTTTT
*
39501213 TTCTAATGATACTA
1 TTCTAACGATACTA
39501227 TTCTAACGATACTA
1 TTCTAACGATACTA
39501241 TTCTAAC
1 TTCTAAC
39501248 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:39501867 original size:12 final size:12
Alignment explanation
Indices: 39501850--39501883 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39501840 TTAGGGCATA
*
39501850 CGAGCCAGTGCC
1 CGAGCCAGAGCC
39501862 CGAGCCAGAGCC
1 CGAGCCAGAGCC
*
39501874 TGAGCCAGAG
1 CGAGCCAGAG
39501884 TAGAAGCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.35, T:0.06
Consensus pattern (12 bp):
CGAGCCAGAGCC
Found at i:39502497 original size:48 final size:48
Alignment explanation
Indices: 39502441--39502532 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
39502431 CAACATGAAA
* *
39502441 ACATTACAAGACTAAAACTTGGAACAAATTTTGTAATATAAATTAAAT
1 ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
* *
39502489 ACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATT
39502533 TTGTTATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (48 bp):
ACATTACAAGACTAAAAATTGGAACAAACTTTGTAATATAAATTAAAT
Found at i:39502542 original size:62 final size:62
Alignment explanation
Indices: 39502466--39502718 Score: 425
Period size: 62 Copynumber: 4.1 Consensus size: 62
39502456 AACTTGGAAC
* *
39502466 AAATTTTGTAATATAAATTAAATACATTACAATATTAAAAATTGGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
* *
39502528 AAATTTTGTTATATAAATTAAATACATTAAAACATTAAAAATTAGAACAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
* * * *
39502590 AAATTTGGTTATATAAATTAAATATATTATAACATTAAAAATTGGACCAAACTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
*
39502652 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAATTTTGTAATAT
1 AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
39502714 AAATT
1 AAATT
39502719 AGGTACATTG
Statistics
Matches: 177, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 177 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (62 bp):
AAATTTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATAT
Found at i:39509660 original size:17 final size:17
Alignment explanation
Indices: 39509634--39509667 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39509624 TAATCCATCC
* *
39509634 ATCTAGTTTAAACATTA
1 ATCTAATTTAAAAATTA
39509651 ATCTAATTTAAAAATTA
1 ATCTAATTTAAAAATTA
39509668 TAAATATATG
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:0.09, G:0.03, T:0.41
Consensus pattern (17 bp):
ATCTAATTTAAAAATTA
Found at i:39510698 original size:16 final size:15
Alignment explanation
Indices: 39510677--39510724 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
39510667 TTATGGAATA
39510677 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
39510693 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
39510708 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
39510724 A
1 A
39510725 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:39510707 original size:8 final size:8
Alignment explanation
Indices: 39510673--39510724 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
39510663 ACAATTATGG
*
39510673 AATAATAA
1 AATATTAA
39510681 AATATATAA
1 AATAT-TAA
39510690 AATA-TAA
1 AATATTAA
39510697 AATATTAA
1 AATATTAA
*
39510705 AATATCAA
1 AATATTAA
*
39510713 AATATTAG
1 AATATTAA
39510721 AATA
1 AATA
39510725 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:39510724 original size:24 final size:24
Alignment explanation
Indices: 39510672--39510728 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
39510662 AACAATTATG
*
39510672 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
39510696 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
39510720 GAATAATAA
1 GAATAATAA
39510729 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:39510903 original size:25 final size:25
Alignment explanation
Indices: 39510874--39510922 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39510864 CATGATAATA
**
39510874 TTAAAAACATGTACATAATATAGTG
1 TTAAAAACACATACATAATATAGTG
*
39510899 TTAAAAATACATACATAATATAGT
1 TTAAAAACACATACATAATATAGT
39510923 TAAGATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (25 bp):
TTAAAAACACATACATAATATAGTG
Found at i:39510937 original size:22 final size:24
Alignment explanation
Indices: 39510885--39510938 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
39510875 TAAAAACATG
39510885 TACATAATATAGTGTTAAAAATACA
1 TACATAATATAG-GTTAAAAATACA
* *
39510910 TACATAATATA-GTT-AAGATATA
1 TACATAATATAGGTTAAAAATACA
39510932 TACATAA
1 TACATAA
39510939 GATAACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 13 0.48
23 3 0.11
25 11 0.41
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (24 bp):
TACATAATATAGGTTAAAAATACA
Found at i:39511086 original size:22 final size:22
Alignment explanation
Indices: 39511022--39511093 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
39511012 TATATATACG
*
39511022 TAATATAA-ATTTA-AAATATA
1 TAATATAATATTAAGAAATATA
* *
39511042 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
39511066 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
39511089 TAATA
1 TAATA
39511094 ACAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 21 0.52
23 14 0.35
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Found at i:39511091 original size:23 final size:25
Alignment explanation
Indices: 39511048--39511093 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39511038 TATACCTAAT
39511048 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
39511073 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
39511094 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:39511608 original size:30 final size:30
Alignment explanation
Indices: 39511572--39511746 Score: 296
Period size: 30 Copynumber: 5.8 Consensus size: 30
39511562 TAGGTACAAG
* *
39511572 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
39511602 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
39511632 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
39511662 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
39511692 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
39511722 TGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
39511747 TGAGAAAAGT
Statistics
Matches: 135, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 135 1.00
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:39511665 original size:60 final size:60
Alignment explanation
Indices: 39511572--39511746 Score: 332
Period size: 60 Copynumber: 2.9 Consensus size: 60
39511562 TAGGTACAAG
*
39511572 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
39511632 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
*
39511692 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAGGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
39511747 TGAGAAAAGT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 113 1.00
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.25
Consensus pattern (60 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:39512613 original size:75 final size:75
Alignment explanation
Indices: 39512458--39512663 Score: 317
Period size: 75 Copynumber: 2.7 Consensus size: 75
39512448 TGTGAACCCA
* * * *
39512458 AGGCTCAACTCACATCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAA-TTGAAAATACCTC
39512521 AGCGTGTCCTG
65 AGCGTGTCCTG
*
39512532 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAATACCTCA
39512597 GCGTGTCCTG
66 GCGTGTCCTG
* *
39512607 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAAC-AACAGAAATTGAA
39512664 GAACATAAAT
Statistics
Matches: 122, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
74 31 0.25
75 63 0.52
76 28 0.23
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAATACCTCA
GCGTGTCCTG
Found at i:39512826 original size:14 final size:14
Alignment explanation
Indices: 39512807--39512841 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
39512797 GAGTCGATTT
39512807 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
39512821 TTGAAAACCAGAAA
1 TTGAAAAACAGAAA
39512835 TTGAAAA
1 TTGAAAA
39512842 GACCTCAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:39512885 original size:162 final size:160
Alignment explanation
Indices: 39512497--39513929 Score: 989
Period size: 162 Copynumber: 9.0 Consensus size: 160
39512487 TGATTTTTGA
* * **
39512497 AAAACAGAAATTTAAAAATACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAA-TTGAAAAGACCTCAGCTGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * *
39512561 TGATTTTTTTTA-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTA
65 T-A-ATTTTTGACA-AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTC
* **
39512625 GCAATATGAGTTGATTTTTTTTTACGAACAGAAATTG
127 GCAATATGAGTTGA---TTTTTGAAAAACAGAAATTG
* *
39512662 AAGAACATAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AA-AACAGAAATTGAAAAGACCTCAGC-TGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAG
39512727 TTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
64 TTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
*
39512792 AATATGAGTCGATTTTTGAAAAACAGAAATTG
129 AATATGAGTTGATTTTTGAAAAACAGAAATTG
39512824 AAAACCAGAAATTGAAAAGACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAA-CAGAAATTGAAAAGACCTCAGC-TGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAG
39512889 TTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
64 TTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
*
39512954 AATATGAGTCGATTTTTGAAAAACAGAAATTG
129 AATATGAGTTGATTTTTGAAAAACAGAAATTG
* * ** *
39512986 TAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAG
1 -AAAACAGAAATTGAAAAGACCTCAGC-TGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAG
* ** * * ** * *
39513051 CTAATTTTTGATGAACATAAATTAAAACCACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGC
64 TTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
* *
39513116 AATATGAGTTGATTTTTGACAAACAAAAATT-
129 AATATGAGTTGATTTTTGAAAAACAGAAATTG
*
39513147 ------GAAATT------ACCTCAGC-GT---CTTGAGGCTCAACTCACTTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAAGACCTCAGCTGTGAGC-TGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * * **
39513196 TGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCT
65 T-A---ATTTTTGACAAACAGAAATTGAAATTACCTCAGC--GTGTCCCGAGGCTCAACTCACCT
* *
39513261 CTCGCAATATAAGTTGAATTTTG-AAAACAGAAATT-
124 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG
*
39513296 ------GAAATT------ACCTCAGC-GTG-TCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAAGACCTCAGCTGTGAGC-TGAGGCTCAACTCACCTCTCGCAATATGAGT
* ** **
39513347 TGACTTTTTTTACGAACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGG
65 T-A--ATTTTT--G-AC---------A-AACAGAAATTGAAATTACCTCAGC--GTGTCCCGAGG
* *
39513412 CTCAACTCACCTCTCGC-A-ATGAGTTAATTTTTGACAAACAGAAATT-
112 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG
** * * *
39513458 ------GAAATT------ACCTCAGC-GTGTCCCGAGGCTCGACTCACCTCTCGCAATATGAGTC
1 AAAACAGAAATTGAAAAGACCTCAGCTGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * * *
39513510 GATTTTTGAAAAACAGAAATTGAAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTC
66 AATTTTTG----AC---------AAA-CAGAAATTGAAATTACCTCAGCGTGT--CCCGAGGCTC
* * *
39513575 AACTCACCTCTTGCAATATGAGCTAATTTTT--------G--A-TG
115 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG
* * **
39513610 --AACATAAATT-AAAACCACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACAGAAATTGAAAA-GACCTCAGCTGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * ** *
39513671 TGATTTTTGACAAACAAAAATTGAAATTACCTCAGC--GTCTTGAGGCTCAACTCACTTCTCGCA
65 TAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
*** * *
39513734 ATATGAGTTGATTTTTTTTGAAACATAAATTAA
130 ATATGAGTTGA-TTTTTGAAAAACAGAAATT-G
* * * ** *
39513767 AAAAAACGAAAATTGAAAATACCTGAGC-GTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAACA-G-AAATTGAAAAGACCTCAGCTGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * * *
39513831 TTGAA--ATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTT
64 TT-AATTTTTGACAA-ACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTC
* *
39513893 GCAATATGAGCTGA-TTTTGAAAAAGTAGAAATT-
127 GCAATATGAGTTGATTTTTGAAAAA-CAGAAATTG
39513926 AAAA
1 AAAA
39513930 GGTTCAACCC
Statistics
Matches: 1084, Mismatches: 112, Indels: 150
0.81 0.08 0.11
Matches are distributed among these distances:
143 1 0.00
144 55 0.05
145 6 0.01
146 4 0.00
148 53 0.05
149 29 0.03
150 48 0.04
151 36 0.03
152 1 0.00
153 1 0.00
154 7 0.01
155 1 0.00
156 6 0.01
157 1 0.00
158 5 0.00
159 17 0.02
160 87 0.08
161 70 0.06
162 473 0.44
163 56 0.05
165 83 0.08
166 9 0.01
167 35 0.03
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (160 bp):
AAAACAGAAATTGAAAAGACCTCAGCTGTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTGAAAAACAGAAATTG
Found at i:39513118 original size:73 final size:73
Alignment explanation
Indices: 39513023--39513355 Score: 347
Period size: 73 Copynumber: 4.5 Consensus size: 73
39513013 GTGTGAGCCA
* * * * **
39513023 AGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTGATGAACATAAATTAAAACCACCTCAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGA-AAACAGAAATTAAAATTACCTCAA
39513087 CGTGTCCTG
65 CGTGTCCTG
* *
39513096 AGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTGACAAACAAAAATTGAAATTACCTC-A
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGA-AAACAGAAATTAAAATTACCTCAA
* *
39513159 -GCGTCTTG
65 CGTGTCCTG
* * *
39513167 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAAAA-TACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA----ATTTTTGAAAACAGAAATT-AAAATTACC
* *
39513231 TCAGCATGTGAACC-G
61 TCA--ACGTG-TCCTG
* * *
39513246 AGGCTCAACTCACCTCTCGCAATATAAGTTGAA-TTTTGAAAACAGAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGAAAACAGAAATTAAAATTACCTCAAC
*
39513310 GTGTCTTG
66 GTGTCCTG
*
39513318 AGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTT
39513356 TTACGAACAG
Statistics
Matches: 216, Mismatches: 29, Indels: 30
0.79 0.11 0.11
Matches are distributed among these distances:
71 37 0.17
72 36 0.17
73 60 0.28
74 23 0.11
75 16 0.07
76 9 0.04
78 1 0.00
79 33 0.15
80 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (73 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTGAAAACAGAAATTAAAATTACCTCAAC
GTGTCCTG
Found at i:39513338 original size:546 final size:546
Alignment explanation
Indices: 39512431--39513929 Score: 2160
Period size: 546 Copynumber: 2.7 Consensus size: 546
39512421 AAAGTAGATT
* * * * * *
39512431 TTGAAAATACCTC-GACATGTGAACCCAAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTT
1 TTGAAAATACCTCAG-CGTGTG-AGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTT
** * **
39512495 GAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
64 GATGAACATAAA-TTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * *
39512560 TTGATTTTTTTTA-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
128 TTGA--TTTTTGACA-AACAAAAATTGAAATTACCTCAGC--GTCTTGAGGCTCAACTCACTTCT
* * * * *
39512624 AGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAGAACATAAATTGAAAAGACCTCAGC
188 CGCAATATGAGTTGATTTTTTTTT----------ATTAAAAAACAGAAATTGAAAATACCTCAGC
*
39512689 ATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT-AATTTTTGACAAACAGAAATTGAA
243 ATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA-TTTTGA-AAACAGAAATTGAA
39512753 ATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAG
306 ATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAG
*
39512818 AAATTGAAAACCAGAAATTGAAAAGACCTCAGCATGTGAGCTGAGGCTCAACTCACCTCTCGCAA
371 AAATTGAAAA-CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGC-A
39512883 TATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACC
434 -ATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACC
*
39512948 TCTCGCAATATGAGTCGATTTTTGAAAAACAGAAATTGTAAACCAGAAA
498 TCTCGCAATATGAGTCGATTTTTGAAAAACAGAAATTGAAAACCAGAAA
39512997 TTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
1 TTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
*
39513062 TGAACATAAATTAAAACCACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
66 TGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
39513127 ATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATAT
131 ATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATAT
39513192 GAGTTGA-TTTTTTTT-TT-AAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAA
196 GAGTTGATTTTTTTTTATTAAAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAA
* **
39513254 CTCACCTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGA
261 CTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGA
* * **
39513319 GGCTCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTACGAACAGAAATTGAAGAACAGAAAT
326 GGCTCAACTCACCTCTCGCAATATGAGTCGA--TTTTTGAAAAACAGAAATTGAA-AACAGAAAT
39513384 TGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATGAGTTAATTTTTGACAA
388 TGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATGAGTTAATTTTTGACAA
*
39513449 ACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCGACTCACCTCTCGCAATATGAGTCGATT
453 ACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATT
39513514 TTTGAAAAACAGAAATTGAAAACCAGAAA
518 TTTGAAAAACAGAAATTGAAAACCAGAAA
39513543 TTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
1 TTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
39513608 TGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
66 TGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
39513673 ATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATAT
131 ATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATAT
* * *
39513738 GAGTTGATTTTTTTTGAAACATAAATTAAAAAAAACGAAAATTGAAAATACCTGAGC--GTG-TC
196 GAGTTGATTTTTTTT------T--ATTAAAAAACA-G-AAATTGAAAATACCTCAGCATGTGAAC
* * * * *
39513800 CTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAA-ATTAAAACACAAAAATTGAAAATACCTC
251 C-GAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAA-ACAGAAATTGAAATTACCTC
* * *
39513864 AGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAG-CTGA-TTTTGAAAAAGTAGAAATT-
314 AGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTC-GATTTTTGAAAAA-CAGAAATTG
39513926 AAAA
377 AAAA
39513930 GGTTCAACCC
Statistics
Matches: 860, Mismatches: 50, Indels: 59
0.89 0.05 0.06
Matches are distributed among these distances:
546 374 0.43
547 76 0.09
548 74 0.09
549 2 0.00
553 3 0.00
554 9 0.01
555 7 0.01
556 9 0.01
557 96 0.11
558 1 0.00
559 26 0.03
560 35 0.04
562 29 0.03
563 1 0.00
564 53 0.06
565 46 0.05
566 18 0.02
567 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (546 bp):
TTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGA
TGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATAT
GAGTTGATTTTTTTTTATTAAAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAA
CTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGA
GGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAAAACAGAAATTGAAAACAGAAATTGA
AAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATGAGTTAATTTTTGACAAACA
GAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTT
GAAAAACAGAAATTGAAAACCAGAAA
Found at i:39513345 original size:151 final size:148
Alignment explanation
Indices: 39513095--39513373 Score: 452
Period size: 149 Copynumber: 1.9 Consensus size: 148
39513085 AACGTGTCCT
* *
39513095 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATAAGTTGAATTTTGACAAACAAAAATTGAAATTACCTCAG
* *
39513160 CGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTTAAAAACAGAAATTGAA
66 CGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--CTTTTTTTAAAAACAGAAATTGAA
39513225 AATACCTCAGCATGTGAACC
129 AATACCTCAGCATGTGAACC
*
39513245 GAGGCTCAACTCACCTCTCGCAATATAAGTTGAATTTTGA-AAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATAAGTTGAATTTTGACAAACAAAAATTGAAATTACCTCAG
**
39513309 CGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTACGAACAGAAATTGAA
66 C--GTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTAAAAACAGAAATTGAA
39513374 GAACAGAAAT
Statistics
Matches: 120, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
149 45 0.38
150 38 0.32
151 37 0.31
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (148 bp):
GAGGCTCAACTCACCTCTCGCAATATAAGTTGAATTTTGACAAACAAAAATTGAAATTACCTCAG
CGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTAAAAACAGAAATTGAAAA
TACCTCAGCATGTGAACC
Found at i:39513379 original size:14 final size:14
Alignment explanation
Indices: 39513360--39513387 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39513350 CTTTTTTTAC
39513360 GAACAGAAATTGAA
1 GAACAGAAATTGAA
39513374 GAACAGAAATTGAA
1 GAACAGAAATTGAA
39513388 AAGACCTCAG
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:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:39513499 original size:71 final size:74
Alignment explanation
Indices: 39513369--39513535 Score: 223
Period size: 73 Copynumber: 2.3 Consensus size: 74
39513359 CGAACAGAAA
* *
39513369 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGC-A-AT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATAT
*
39513432 GAGTTAATTT
65 GAGTCAATTT
* ** * *
39513442 TTGACAAACAGAAATTGAAATTACCTCAGC-GTGTCCCGAGGCTCGACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
*
39513506 AGTCGATTT
66 AGTCAATTT
39513515 TTGAAAAACAGAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
39513536 CCAGAAATTG
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
71 25 0.31
72 1 0.01
73 55 0.68
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTCAATTT
Found at i:39513534 original size:14 final size:14
Alignment explanation
Indices: 39513515--39513549 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
39513505 GAGTCGATTT
39513515 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
39513529 TTGAAAACCAGAAA
1 TTGAAAAACAGAAA
39513543 TTGAAAA
1 TTGAAAA
39513550 TACCTCAGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:39513604 original size:89 final size:87
Alignment explanation
Indices: 39513442--39513626 Score: 232
Period size: 89 Copynumber: 2.1 Consensus size: 87
39513432 GAGTTAATTT
* * *
39513442 TTGACAAA-CAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCGACTCACCTCTCGCAATATG
1 TTGA-AAACCAGAAATTGAAAATACCTCAGCGTGTCCCAAGGCTCAACTCACCTCTCGCAATATG
*
39513506 AGTCGATTTTTGAAAAACAGAAA
65 AGTCAATTTTTGAAAAACAGAAA
* *
39513529 TTGAAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATAT
1 TTGAAAACCAGAAATTGAAAATACCTCAGCGTGT--CCCAAGGCTCAACTCACCTCTCGCAATAT
** *
39513594 GAG-CTAATTTTTGATGAACATAAA
64 GAGTC-AATTTTTGAAAAACAGAAA
39513618 TT-AAAACCA
1 TTGAAAACCA
39513627 CCTCAGCGTG
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
86 3 0.04
87 29 0.34
88 8 0.09
89 45 0.53
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (87 bp):
TTGAAAACCAGAAATTGAAAATACCTCAGCGTGTCCCAAGGCTCAACTCACCTCTCGCAATATGA
GTCAATTTTTGAAAAACAGAAA
Found at i:39513664 original size:73 final size:71
Alignment explanation
Indices: 39513569--39513768 Score: 256
Period size: 73 Copynumber: 2.8 Consensus size: 71
39513559 GTGTGAGCCA
* * *
39513569 AGGCTCAACTCACCTCTTGCAATATGAGCTAATTTTTGATGAACATAAATTAAAACCACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
39513634 GTGTCCTG
66 --GTCCTG
** * * **
39513642 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
*
39513707 GTCTTG
66 GTCCTG
* **
39513713 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAACATAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATG-AACATAAATTAAAA
39513769 AAAACGAAAA
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
71 41 0.38
72 12 0.11
73 56 0.51
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGATGAACATAAATTAAAACCACCTCAGC
GTCCTG
Found at i:39513865 original size:233 final size:230
Alignment explanation
Indices: 39512658--39513910 Score: 860
Period size: 235 Copynumber: 5.3 Consensus size: 230
39512648 ACGAACAGAA
* * * *
39512658 ATTGAAGAACATAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATA
1 ATTGAAAAACAAAAATTGAAAACACCTCAGC--GTG-CCCGAGGCTCAACTCACCTCTCGCAATA
* *
39512723 TGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTC
63 TGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCG-GTCCCGAGGCTCAACTCACCTC
* ** *
39512788 TCGCAATATGAGTCGATTTTTGAAAAACAGAAATTGAAAACCAGAAATTGAAAAGACCTCAGCAT
127 TCGCAATATGAGTCGATTTTTGAAAAACAGAAATTAAAAAAAAGAAATTGAAAATACCTCAGC--
* ** *
39512853 GTGAGCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAATT
190 GTGTGCCAAGGCTCAACTCACCTCTCGCAATATGAGCTAA-T
* * * **
39512895 TTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
1 ATTGAAAAACAAAAATTGAAAACACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATG
* * * * *
39512960 AGTCGATTTTTGAAAAACAGAAATTGTAAACCAGAAATTGAAAATACCTCAGCGTGTGAGCCAAG
65 AGTTGATTTTTG----AC---------AAA-CAAAAATTGAAATTACCTCAGCG-GT--CCCGAG
* * **
39513025 GCTCAACTCACCTCTTGCAATATGAG-CTAATTTTTGATGAAC----A-T---------AAATT-
113 GCTCAACTCACCTCTCGCAATATGAGTC-GATTTTTGAAAAACAGAAATTAAAAAAAAGAAATTG
* * * * *
39513074 AAAACCACCTCAACGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
177 AAAA-TACCTCAGCGTGTGCC-AAGGCTCAACTCACCTCTCGCAATATGAGCT-AAT
* * ** ** *
39513130 TTTGACAAACAAAAATTGAAATTACCTCAGCGT-CTTGAGGCTCAACTCACTTCTCGCAATATGA
1 ATTGAAAAACAAAAATTGAAAACACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGA
* * * * **
39513194 GTTGATTTTTTTTTTAAAAACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCAC
66 GTTGA----TTTTTGACAAACAAAAATTGAAATTACCTCAGC--G-GTCCCGAGGCTCAACTCAC
* * *
39513259 CTCTCGCAATATAAGTTGAATTTTG-AAAACAGAAATT--------GAAA-T-----TACCTCAG
124 CTCTCGCAATATGAGTCGATTTTTGAAAAACAGAAATTAAAAAAAAGAAATTGAAAATACCTCAG
** *
39513309 CGTGT-CTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTACGAACAGAA
189 CGTGTGC-CAAGGCTCAACTCACCTCTCGCAATATGA---G-C------T------A-AT
* * * *
39513368 ATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGC-A-A
1 ATTGAAAAACAAAAATTGAAAACACCTCAGC--GTG-CCCGAGGCTCAACTCACCTCTCGCAATA
* * *
39513431 TGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCGACTCACCTC
63 TGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCG-GTCCCGAGGCTCAACTCACCTC
* **
39513496 TCGCAATATGAGTCGATTTTTGAAAAACAGAAATTGAAAACCAGAAATTGAAAATACCTCAGCGT
127 TCGCAATATGAGTCGATTTTTGAAAAACAGAAATTAAAAAAAAGAAATTGAAAATACCTCAGCGT
*
39513561 GTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGCTAATT
192 GT--GCCAAGGCTCAACTCACCTCTCGCAATATGAGCTAA-T
* ** * *
39513603 TTTGATGAACATAAATT-AAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 ATTGAAAAACAAAAATTGAAAA-CACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATAT
** *
39513667 GAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGC-GTCTTGAGGCTCAACTCACTTCTC
64 GAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGGTCCCGAGGCTCAACTCACCTCTC
* *** * *
39513731 GCAATATGAGTTGATTTTTTTTGAAACATAAATTAAAAAAAACGAAAATTGAAAATACCTGAGCG
129 GCAATATGAGTCGA-TTTTTGAAAAACAGAAATTAAAAAAAA-G-AAATTGAAAATACCTCAGCG
*
39513796 TGT-CCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAA-
191 TGTGCC-AAGGCTCAACTCACCTCTCGCAATATGAGCT-AAT
* *
39513836 ATT-AAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATAT
1 ATTGAAAA-ACAAAAATTGAAAACACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATAT
*
39513900 GAGCTGATTTT
64 GAGTTGATTTT
39513911 GAAAAAGTAG
Statistics
Matches: 830, Mismatches: 103, Indels: 170
0.75 0.09 0.15
Matches are distributed among these distances:
222 43 0.05
223 56 0.07
224 3 0.00
225 4 0.00
226 1 0.00
227 2 0.00
228 3 0.00
232 3 0.00
233 151 0.18
234 100 0.12
235 187 0.23
236 57 0.07
237 43 0.05
238 25 0.03
239 2 0.00
240 10 0.01
241 2 0.00
242 20 0.02
243 4 0.00
244 1 0.00
246 1 0.00
247 2 0.00
248 4 0.00
249 38 0.05
250 1 0.00
251 66 0.08
252 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (230 bp):
ATTGAAAAACAAAAATTGAAAACACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGGTCCCGAGGCTCAACTCACCTCTCGC
AATATGAGTCGATTTTTGAAAAACAGAAATTAAAAAAAAGAAATTGAAAATACCTCAGCGTGTGC
CAAGGCTCAACTCACCTCTCGCAATATGAGCTAAT
Found at i:39513929 original size:161 final size:158
Alignment explanation
Indices: 39513626--39513916 Score: 399
Period size: 161 Copynumber: 1.8 Consensus size: 158
39513616 AATTAAAACC
* ** *
39513626 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAAAAA
1 ACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAA
* ** * *
39513691 TTGAAATTACCTCAGCGTCTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAA
66 TTGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGA---TTTTTGAA
*
39513756 ACATAAATTAAAAAAAACGAAAATTGAAAAT
128 AAATAAATTAAAAAAAACGAAAATTGAAAAT
*
39513787 ACCTGAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-AATT-AAAACACAAAA
1 ACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAA-ACAAAA
*
39513850 ATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGCTGA-TTTTGAA
65 ATTGAAAATACCTCAGCGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAA
39513914 AAA
128 AAA
39513917 GTAGAAATTA
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
158 9 0.08
159 3 0.03
160 26 0.23
161 46 0.40
162 31 0.27
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (158 bp):
ACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATAATTGAAAAACAAAAA
TTGAAAATACCTCAGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTGAAAAA
TAAATTAAAAAAAACGAAAATTGAAAAT
Found at i:39513943 original size:54 final size:54
Alignment explanation
Indices: 39513879--39513983 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
39513869 GCCCCGAGGC
* * *
39513879 TCAACTCACCTCTTGCAATATGAGCTGATT-TTGAAAAAGTAGAAATTAAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTCTTGAAAAA-CAGAAATTAAAAGGT
* *
39513933 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATTCTTGAAAAACAGAAATTAAAA
39513984 TTACCTCATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
54 38 0.84
55 7 0.16
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTCTTGAAAAACAGAAATTAAAAGGT
Found at i:39514361 original size:76 final size:75
Alignment explanation
Indices: 39514056--39514396 Score: 431
Period size: 72 Copynumber: 4.5 Consensus size: 75
39514046 AGTGTGTAAT
* *
39514056 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-TTCTTTTGAAAAGCAGAAATTGAAAATAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAA-CAGAAATTGAAAATAC
*
39514120 CTCAGCATGTGAAC
65 CTCAGC--GTG-TC
* *
39514134 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAATAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTTGAAAACAGAAATTGAAAATA
*
39514198 CCTCAACGTGTC
64 CCTCAGCGTGTC
* ** * * *
39514210 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA---ATTTTGAAAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
39514272 TCAGCGTGTC
66 TCAGCGTGTC
** * *
39514282 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTAC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAA-AACAGAAATTGAAAATAC
39514347 CTCAGCGTGTC
65 CTCAGCGTGTC
*
39514358 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
39514397 GAAAAACAAA
Statistics
Matches: 235, Mismatches: 20, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
72 66 0.28
75 6 0.03
76 66 0.28
77 65 0.28
78 1 0.00
79 20 0.09
80 11 0.05
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (75 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAACAGAAATTGAAAATACC
TCAGCGTGTC
Found at i:39514673 original size:269 final size:268
Alignment explanation
Indices: 39514179--39514678 Score: 824
Period size: 269 Copynumber: 1.9 Consensus size: 268
39514169 TTTTTTTTTG
* * ** *
39514179 AAAATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTG
1 AAAACAGAAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATAAGTTG
* * * **
39514244 AATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATA
66 AATTTTGAAAACAAAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
*
39514309 TGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
131 TGAGTTGATTTTTTTTTAACAAAAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
39514374 CTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGCTAACTCACCTCTCGCAATATGA
196 CTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGCTAACTCACCTCTCGCAATATGA
39514439 GTCATTTA
261 GTCATTTA
* *
39514447 AAAACAGAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATAAGTTG
39514512 -ATTTTGAAAAACAAAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
66 AATTTTG-AAAACAAAAA-TTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
39514576 TATGAGTTGATTTTTTTTTAACAAAAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTC
129 TATGAGTTGATTTTTTTTTAACAAAAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTC
* *
39514641 ACCTCTCGCAATATGAGTTGAATTTT-AAAAACAGAAAT
194 ACCTCTAGCAATATGAGTTG-ATTTTGAAAAACAAAAAT
39514679 CGAAATTACC
Statistics
Matches: 214, Mismatches: 15, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
267 6 0.03
268 67 0.31
269 136 0.64
270 5 0.02
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (268 bp):
AAAACAGAAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACTTCTCGCAATATAAGTTG
AATTTTGAAAACAAAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTTTTTTAACAAAAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCAC
CTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGCTAACTCACCTCTCGCAATATGA
GTCATTTA
Found at i:39514708 original size:72 final size:71
Alignment explanation
Indices: 39514418--39514755 Score: 459
Period size: 72 Copynumber: 4.7 Consensus size: 71
39514408 ATTAAAAGCT
* * *
39514418 AACTCACCTCTCGCAATATGAG-TCA-TTTAAAAACAGAAATTGAAAATACCTCAGCGTGCCCCG
1 AACTCACCTCTCGCAATATGAGTTGATTTTAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
39514481 AGGCTC
66 AGGCTC
* * *
39514487 AACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTTAAAAATACCTCAGCGTGTCC
1 AACTCACCTCTCGCAATATGAGTTGATTTT-AAAAACAGAAA-TTGAAAATACCTCAGCGTGTCC
39514552 TGAGGCTC
64 TGAGGCTC
*
39514560 AACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAACAAA-AGAAATTGAAATTACCTCAGCGT
1 AACTCACCTCTCGCAATATGAGTTGA-----TTTTAA-AAACAGAAATTGAAAATACCTCAGCGT
39514624 GTCCTGAGGCTC
60 GTCCTGAGGCTC
* *
39514636 AACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATCGAAATTACCTCAGCGTGTCCT
1 AACTCACCTCTCGCAATATGAGTTG-ATTTTAAAAACAGAAATTGAAAATACCTCAGCGTGTCCT
39514701 GAGGCTC
65 GAGGCTC
* *
39514708 AACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT-AAAA
1 AACTCACCTCTCGCAATATGAGTTGATTTT-AAAAACAGAAATTGAAAA
39514756 GGCTTAACTC
Statistics
Matches: 241, Mismatches: 15, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
69 21 0.09
70 2 0.01
71 14 0.06
72 85 0.35
73 52 0.22
76 53 0.22
77 7 0.03
78 7 0.03
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (71 bp):
AACTCACCTCTCGCAATATGAGTTGATTTTAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTG
AGGCTC
Found at i:39514859 original size:121 final size:124
Alignment explanation
Indices: 39514630--39514875 Score: 349
Period size: 121 Copynumber: 2.0 Consensus size: 124
39514620 GCGTGTCCTG
* * *
39514630 AGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATCGAAATTACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTAAAAACAGAAATCAAAAATACCTCAGCG
*
39514695 TGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGTCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAA-AAAAATTAAA
* * *
39514755 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAA-CTAAAAATACCTCGGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTAAAAACAGAAATC-AAAAATACCTCAGC
* * *
39514816 GTG-CCCGAGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAA
65 GTGTCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAAATTAAA
39514875 A
1 A
39514876 ATACCTCAAC
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
120 11 0.10
121 43 0.39
122 23 0.21
123 3 0.03
124 3 0.03
125 27 0.25
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (124 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTCAATTTTAAAAACAGAAATCAAAAATACCTCAGCG
TGTCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAAAAAAATTAAA
Found at i:39514871 original size:341 final size:340
Alignment explanation
Indices: 39513933--39514929 Score: 1278
Period size: 341 Copynumber: 2.9 Consensus size: 340
39513923 ATTAAAAGGT
* * * *
39513933 TCAACCCACCTCTCGCAATATGAGTTG-ATTCTTGACAAACAGAAATTAAAATTACCTCATCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGAATT-TT-AAAAACAGAAATTGAAATTACCTCAGCGTG
* * ** ***
39513997 TCCTGAGGCTCAACTCACCTCTCGCAATATGAATTGA---AAAAAATACCACAGTGTGTAATCTG
64 TCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAA-A-CA-AAAAT-TAA----
* * * *
39514059 AAGCTCAACTCACCTCTCGCAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATACCTCA
121 AAGCTTAACTCACCTCTCGCAATATGAG-TCA---ATTT-AAAAACAGAAATTGAAAATACCTCA
* * * * *
39514124 GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAATAGAAA
181 GC--GTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA------TTTTGAAAAAAAAAA
* * * *
39514189 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA---ATTTTG
238 TTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTTG
*
39514251 AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
303 AAAAAAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
** * *
39514289 TCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTACCTCAGCG
1 TCAACTCACCTCTCGCAATATGAGTTGA----ATTTTAAAAACAGAAATTGAAATTACCTCAGCG
39514354 TGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGC-T
62 TGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGCTT
*
39514418 AACTCACCTCTCGCAATATGAGTC-ATTTAAAAACAGAAATTGAAAATACCTCAGCGTGCCCCGA
127 AACTCACCTCTCGCAATATGAGTCAATTTAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGA
*
39514482 GGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTTAAAAATACCTCAGCG
192 GGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAA-AAAAA-TTAAAAATACCTCAACG
* * *
39514547 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTAACAAAAGAAATTGAAA
255 TGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTTGAA-AAAAGAAATTGAAA
39514612 TTACCTCAGCGTGTCCTGAGGC
319 TTACCTCAGCGTGTCCTGAGGC
*
39514634 TCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATCGAAATTACCTCAGCGTGTC
1 TCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATTGAAATTACCTCAGCGTGTC
39514699 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAAC
66 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA-GCTTAAC
* * * * *
39514764 TCACCTCTCGCAATATGAGTCAATTT-AAAACATAAACTAAAAATACCTCGGCGTG-CCCGAGGT
130 TCACCTCTCGCAATATGAGTCAATTTAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGC
39514827 TCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGTGTCT
195 TCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGTGTCT
39514892 TGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
260 TGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
39514930 CCTTGGAAAG
Statistics
Matches: 577, Mismatches: 47, Indels: 50
0.86 0.07 0.07
Matches are distributed among these distances:
339 9 0.02
340 61 0.11
341 146 0.25
342 47 0.08
343 50 0.09
344 10 0.02
345 97 0.17
347 26 0.05
348 3 0.01
352 1 0.00
353 22 0.04
354 4 0.01
356 24 0.04
358 3 0.01
359 63 0.11
360 4 0.01
361 3 0.01
362 4 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (340 bp):
TCAACTCACCTCTCGCAATATGAGTTGAATTTTAAAAACAGAAATTGAAATTACCTCAGCGTGTC
CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGCTTAACT
CACCTCTCGCAATATGAGTCAATTTAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCT
CAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGTGTCTT
GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAAGAAATTGAAATTACCTC
AGCGTGTCCTGAGGC
Found at i:39514914 original size:71 final size:68
Alignment explanation
Indices: 39514755--39514929 Score: 199
Period size: 71 Copynumber: 2.5 Consensus size: 68
39514745 AAAAATTAAA
* * * * * **
39514755 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG
39514819 CCCG
65 CCCG
* *
39514823 AGGTTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTT-AAAAAAAAAACTAAAAATACCTCAACGT
**
39514888 GTCTTG
64 G-CCCG
39514894 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTT
39514930 CCTTGGAAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
67 1 0.01
68 24 0.27
69 5 0.06
70 24 0.27
71 35 0.39
72 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (68 bp):
AGGCTCAACTCACTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTGC
CCG
Found at i:39523263 original size:16 final size:15
Alignment explanation
Indices: 39523242--39523289 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
39523232 TATGGGAATA
39523242 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
39523258 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
39523273 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
39523289 A
1 A
39523290 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:39523272 original size:8 final size:8
Alignment explanation
Indices: 39523238--39523289 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
39523228 CAGTTATGGG
*
39523238 AATAATAA
1 AATATTAA
39523246 AATATATAA
1 AATAT-TAA
39523255 AATA-TAA
1 AATATTAA
39523262 AATATTAA
1 AATATTAA
*
39523270 AATATCAA
1 AATATTAA
*
39523278 AATATTAG
1 AATATTAA
39523286 AATA
1 AATA
39523290 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:39523289 original size:24 final size:24
Alignment explanation
Indices: 39523237--39523293 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
39523227 ACAGTTATGG
*
39523237 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
39523261 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
39523285 GAATAATAA
1 GAATAATAA
39523294 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:39523471 original size:25 final size:25
Alignment explanation
Indices: 39523443--39523491 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
39523433 CATCATAATA
**
39523443 TTAAAAACATGTACATAATATAGTG
1 TTAAAAACACATACATAATATAGTG
*
39523468 TTAAAAATACATACATAATATAGT
1 TTAAAAACACATACATAATATAGT
39523492 TAAGATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (25 bp):
TTAAAAACACATACATAATATAGTG
Found at i:39523506 original size:22 final size:24
Alignment explanation
Indices: 39523454--39523507 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
39523444 TAAAAACATG
39523454 TACATAATATAGTGTTAAAAATACA
1 TACATAATATAG-GTTAAAAATACA
* *
39523479 TACATAATATA-GTT-AAGATATA
1 TACATAATATAGGTTAAAAATACA
39523501 TACATAA
1 TACATAA
39523508 GATAACATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 13 0.48
23 3 0.11
25 11 0.41
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (24 bp):
TACATAATATAGGTTAAAAATACA
Found at i:39523659 original size:23 final size:25
Alignment explanation
Indices: 39523616--39523661 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39523606 TATACCTAAT
39523616 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
39523641 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
39523662 ACAAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:39524225 original size:31 final size:30
Alignment explanation
Indices: 39524148--39524240 Score: 150
Period size: 30 Copynumber: 3.1 Consensus size: 30
39524138 CAAATGGTGG
*
39524148 GGTGGAGAAGGTGTGGCTAGTGGAGTTGGT
1 GGTGGAAAAGGTGTGGCTAGTGGAGTTGGT
* *
39524178 GGTGGAAAAAGAGTGGCTAGTGGAGTTGGT
1 GGTGGAAAAGGTGTGGCTAGTGGAGTTGGT
39524208 GGTGTGAAAAGGTGTGGCTAGTGGAGTTGGT
1 GGTG-GAAAAGGTGTGGCTAGTGGAGTTGGT
39524239 GG
1 GG
39524241 AAAGGGTGGC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 31 0.54
31 26 0.46
ACGTcount: A:0.20, C:0.03, G:0.51, T:0.26
Consensus pattern (30 bp):
GGTGGAAAAGGTGTGGCTAGTGGAGTTGGT
Found at i:39530493 original size:15 final size:16
Alignment explanation
Indices: 39530473--39530502 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39530463 AAAATCGTCT
39530473 CTCTTA-TTTTCTTTC
1 CTCTTACTTTTCTTTC
39530488 CTCTTACTTTTCTTT
1 CTCTTACTTTTCTTT
39530503 TAAATTAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (16 bp):
CTCTTACTTTTCTTTC
Found at i:39534345 original size:7 final size:7
Alignment explanation
Indices: 39534333--39534358 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39534323 TCCCTATATC
39534333 TTTTATA
1 TTTTATA
39534340 TTTTATA
1 TTTTATA
39534347 TTTTATA
1 TTTTATA
39534354 TTTTA
1 TTTTA
39534359 AATATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATA
Found at i:39543923 original size:40 final size:39
Alignment explanation
Indices: 39543850--39543967 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 39
39543840 ACTGTTCATG
39543850 CCACGTCAGCAAATCGCGTCCTAGA-G-GGA-GCGATTTCCTT
1 CCACGTCAGCAAATCGCG--CT-GACGTGGACGCGATTTCC-T
39543890 CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
1 CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
* * * *
39543929 GCGCGT-ACCCTGACATCGCGCTGACGTGGACGCGATTTC
1 CCACGTCA-GC--AAATCGCGCTGACGTGGACGCGATTTC
39543968 GCGGAAAATA
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
37 2 0.03
38 4 0.06
39 9 0.13
40 27 0.40
41 26 0.38
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.21
Consensus pattern (39 bp):
CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
Found at i:39544360 original size:19 final size:19
Alignment explanation
Indices: 39544336--39544372 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
39544326 GATGTCAATA
39544336 TTAATATTATATTAAAATG
1 TTAATATTATATTAAAATG
39544355 TTAATATTATATTAAAAT
1 TTAATATTATATTAAAAT
39544373 AAAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTAATATTATATTAAAATG
Found at i:39544375 original size:24 final size:25
Alignment explanation
Indices: 39544327--39544383 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
39544317 TAATAAAAGG
* * *
39544327 ATGTCAATATTAATATTATATTAAA
1 ATGTTAATATTAATATTAAAATAAA
39544352 ATGTTAATATT-ATATTAAAATAAA
1 ATGTTAATATTAATATTAAAATAAA
*
39544376 ATTTTAAT
1 ATGTTAAT
39544384 TTTTTTGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
ATGTTAATATTAATATTAAAATAAA
Found at i:39547381 original size:6 final size:6
Alignment explanation
Indices: 39547367--39547399 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
39547357 TTGCCACCTA
*
39547367 AAAATC AAAACC AAAACC AAAACC AAAA-C AAAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAAA
39547400 GACATGTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.73, C:0.24, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAACC
Found at i:39549104 original size:5 final size:5
Alignment explanation
Indices: 39549090--39549120 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
39549080 TACAATGTTA
39549090 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
39549121 GAATAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:39552210 original size:15 final size:17
Alignment explanation
Indices: 39552178--39552215 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
39552168 TTGATGAAAG
*
39552178 TATATTTTATTAATTAT
1 TATATTATATTAATTAT
39552195 TATATTATATT-A-TAT
1 TATATTATATTAATTAT
39552210 TATATT
1 TATATT
39552216 GAAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 1 0.05
17 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTATATTAATTAT
Found at i:39553599 original size:15 final size:15
Alignment explanation
Indices: 39553562--39553600 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
39553552 TTTAAAACTA
*
39553562 TATTATTATATTATG
1 TATTATTATATCATG
**
39553577 TAAAATTATATCATG
1 TATTATTATATCATG
39553592 TATTATTAT
1 TATTATTAT
39553601 TGTAATACAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (15 bp):
TATTATTATATCATG
Found at i:39554412 original size:20 final size:21
Alignment explanation
Indices: 39554369--39554438 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 21
39554359 TTAATTTTAT
39554369 AATTTTTAAAAAATATAAATTTTGA
1 AATTTTT-AAAAAT-T--ATTTTGA
*
39554394 AATTTTTACAAA-TATTTTG-
1 AATTTTTAAAAATTATTTTGA
39554413 AA-TTTTAAAAATTATTTT-A
1 AATTTTTAAAAATTATTTTGA
39554432 AATTTTT
1 AATTTTT
39554439 CTGTAACTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 8 0.20
19 10 0.25
20 10 0.25
22 1 0.03
24 4 0.10
25 7 0.17
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (21 bp):
AATTTTTAAAAATTATTTTGA
Found at i:39556022 original size:18 final size:17
Alignment explanation
Indices: 39555999--39556048 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 17
39555989 TTTAAAATTT
*
39555999 TGAGCCCATATGCCAGTG
1 TGAGCCCACATGCC-GTG
39556017 TGAGCCCACATGTCCGTG
1 TGAGCCCACATG-CCGTG
39556035 TGAGCCCACATGCC
1 TGAGCCCACATGCC
39556049 CAGATTGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.20
Consensus pattern (17 bp):
TGAGCCCACATGCCGTG
Found at i:39558336 original size:18 final size:18
Alignment explanation
Indices: 39558313--39558373 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
39558303 GTAACATAAT
39558313 TATTATAAAAAAATTTTA
1 TATTATAAAAAAATTTTA
*
39558331 TATTATAAATCTTAAAATATTA
1 TATTATAAA----AAAATTTTA
* *
39558353 TATTATAAGAATATTTTA
1 TATTATAAAAAAATTTTA
39558371 TAT
1 TAT
39558374 ATTTTATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 19 0.54
22 16 0.46
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTATAAAAAAATTTTA
Found at i:39563498 original size:46 final size:46
Alignment explanation
Indices: 39563431--39563522 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
39563421 CTTGGACTGT
* *
39563431 GTATTCGCCTGATTTGTTCCCTCGCCATATTAGAACATCCGGCTGC
1 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
39563477 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
1 GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
39563523 ATCCTGCTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (46 bp):
GTATTCACCTGATTTGTTCCCTCGCCATATTAGAACATCCAGCTGC
Found at i:39571337 original size:3 final size:3
Alignment explanation
Indices: 39571329--39571361 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39571319 ATTAATGAAG
39571329 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39571362 TAAGATAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39571851 original size:26 final size:26
Alignment explanation
Indices: 39571799--39571851 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
39571789 TCCATTGAAT
** *
39571799 ATAATTAAAATATATTAATTTATTTA
1 ATAATTAAAATATATTAATAAAATTA
* *
39571825 ATAATTTAAATATTTTAATAAAATTA
1 ATAATTAAAATATATTAATAAAATTA
39571851 A
1 A
39571852 AGCATTTTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAATTAAAATATATTAATAAAATTA
Found at i:39576272 original size:3 final size:3
Alignment explanation
Indices: 39576264--39576288 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39576254 AGGGTAAGAC
39576264 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
39576289 GTTCAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39577392 original size:6 final size:6
Alignment explanation
Indices: 39577381--39577409 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
39577371 TGAATTATAT
39577381 TATTTA TATTTA TATTTA TATTT- TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA
39577410 GGAAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:39580927 original size:19 final size:19
Alignment explanation
Indices: 39580903--39580939 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
39580893 AGCAAAGTTA
39580903 GCATTCTCAATCTACCATG
1 GCATTCTCAATCTACCATG
39580922 GCATTCTCAATCTACCAT
1 GCATTCTCAATCTACCAT
39580940 CTTAAGCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.32
Consensus pattern (19 bp):
GCATTCTCAATCTACCATG
Found at i:39582404 original size:3 final size:3
Alignment explanation
Indices: 39582392--39582440 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
39582382 AAAAAAAAAA
*
39582392 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
39582440 A
1 A
39582441 GAGAGAAGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39586051 original size:15 final size:15
Alignment explanation
Indices: 39586031--39586081 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
39586021 TTGTGTTAAA
*
39586031 TTATATTTTAATTAT
1 TTATATTTTAATAAT
39586046 TTATA-TTTAA-AAT
1 TTATATTTTAATAAT
*
39586059 GTTATCTTTTAATAAT
1 -TTATATTTTAATAAT
39586075 TTATATT
1 TTATATT
39586082 ATGATGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.30
15 16 0.53
16 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (15 bp):
TTATATTTTAATAAT
Found at i:39590654 original size:11 final size:11
Alignment explanation
Indices: 39590624--39590679 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
39590614 AAATTAATCC
39590624 TCTCTCAATTAT
1 TCTCTCAATT-T
*
39590636 TTTCTCAATTT
1 TCTCTCAATTT
39590647 TCTCTCAATTT
1 TCTCTCAATTT
* * *
39590658 GCTTTCAAATT
1 TCTCTCAATTT
*
39590669 GCTCTCAATTT
1 TCTCTCAATTT
39590680 CCTTCCAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.52
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:39590673 original size:22 final size:22
Alignment explanation
Indices: 39590646--39590698 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
39590636 TTTCTCAATT
* *
39590646 TTCTCTCAATTTGCTTTC-AAA
1 TTCTCTCAATTTCCTTCCAAAA
39590667 TTGCTCTCAATTTCCTTCCAAAA
1 TT-CTCTCAATTTCCTTCCAAAA
39590690 TTCTCTCAA
1 TTCTCTCAA
39590699 ATCCATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 21 0.75
23 5 0.18
ACGTcount: A:0.25, C:0.28, G:0.04, T:0.43
Consensus pattern (22 bp):
TTCTCTCAATTTCCTTCCAAAA
Found at i:39590723 original size:51 final size:51
Alignment explanation
Indices: 39590662--39590759 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
39590652 CAATTTGCTT
39590662 TCAAATTGCTCTCAATTTCCT-TCCAAAATTCTCTCAAATCCATATTTAATC
1 TCAAATTGCTCTCAATTTCCTCT-CAAAATTCTCTCAAATCCATATTTAATC
* * * * *
39590713 TCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAAATTGCTCTCAATTTCCTCTCAAAATTCTCTCAAATCCATATTT
39590760 TTAATTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.02, T:0.44
Consensus pattern (51 bp):
TCAAATTGCTCTCAATTTCCTCTCAAAATTCTCTCAAATCCATATTTAATC
Found at i:39592586 original size:18 final size:18
Alignment explanation
Indices: 39592563--39592604 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39592553 GCCAGGTGCA
* *
39592563 TATCCTAGCCCTTTTATG
1 TATCCTAACCCTTATATG
39592581 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
*
39592599 TTTCCT
1 TATCCT
39592605 TTTTCTAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.07, T:0.45
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:39593079 original size:49 final size:49
Alignment explanation
Indices: 39593025--39593283 Score: 437
Period size: 49 Copynumber: 5.3 Consensus size: 49
39593015 GTTTATATTA
*
39593025 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
*
39593074 ATGTAATAAAAGACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* * * *
39593123 ATTTAATAAAATACAAAATAGTTTATTTTTAATAGTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
39593172 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* *
39593221 ATTTAGTAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
*
39593270 ATTTAATAAAATAC
1 ATGTAATAAAATAC
39593284 TGAATATTTT
Statistics
Matches: 196, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 196 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
Found at i:39596756 original size:125 final size:124
Alignment explanation
Indices: 39596497--39596907 Score: 633
Period size: 124 Copynumber: 3.3 Consensus size: 124
39596487 CCCAAACATG
* * * *
39596497 CTACTGTAGTAAAAACGTGTCTACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
* *
39596562 TTGTAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * ** *
39596621 CTACTATAGCAAAAGCGCGTCCACGTGAGAGCGATTTCAGAAATTCTTCTGATAAAGTATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
* *
39596686 TTGAAGCGTTTTTTATACTATTTGCTCAGAATCGTGAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * * *
39596746 CTATTGTAGCAAAAGCACGTTCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAACATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
39596811 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* *
39596870 TTACTGTAGCAAAAGCGCGTCCACGTGGGAGAGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
39596908 CTTAATAAAT
Statistics
Matches: 255, Mismatches: 31, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
124 144 0.56
125 111 0.44
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:39597206 original size:36 final size:36
Alignment explanation
Indices: 39597166--39597250 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
39597156 GAGAAACGGG
39597166 CAAAACGCGTCCC-CAAGGGAGCGCTTTATGTGGCAA
1 CAAAACGCG-CCCTCAAGGGAGCGCTTTATGTGGCAA
* **
39597202 CAAAACTCGCCCTTGAGGGAGCGCTTTATGTGGCAA
1 CAAAACGCGCCCTCAAGGGAGCGCTTTATGTGGCAA
*
39597238 CAAAACTCGCCCT
1 CAAAACGCGCCCT
39597251 TGAGGAGCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 3 0.07
36 42 0.93
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (36 bp):
CAAAACGCGCCCTCAAGGGAGCGCTTTATGTGGCAA
Found at i:39597251 original size:36 final size:36
Alignment explanation
Indices: 39597181--39597259 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
39597171 CGCGTCCCCA
39597181 AGGGAGCGCTTTATGTGGCAACAAAACTCGCCCTTG
1 AGGGAGCGCTTTATGTGGCAACAAAACTCGCCCTTG
39597217 AGGGAGCGCTTTATGTGGCAACAAAACTCGCCCTTG
1 AGGGAGCGCTTTATGTGGCAACAAAACTCGCCCTTG
39597253 A-GGAGCG
1 AGGGAGCG
39597260 ATTTCCGTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 6 0.14
36 37 0.86
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.20
Consensus pattern (36 bp):
AGGGAGCGCTTTATGTGGCAACAAAACTCGCCCTTG
Found at i:39609562 original size:64 final size:64
Alignment explanation
Indices: 39609484--39609613 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
39609474 TTTCTTCCAT
39609484 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
*
39609548 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTGCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
39609612 TT
1 TT
39609614 AAAATTCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.20, C:0.12, G:0.13, T:0.55
Consensus pattern (64 bp):
TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
Found at i:39611491 original size:34 final size:34
Alignment explanation
Indices: 39611429--39611495 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
39611419 AATTTGATTT
* *
39611429 TTATATTTTTGTTTTAATTTGATCATTTTTAACTC
1 TTATACTTTTGTTTTAATTTGAT-AATTTTAACTC
39611464 TTATACTTTT-TTTTAATTTTGA-AATTTTAACT
1 TTATACTTTTGTTTTAA-TTTGATAATTTTAACT
39611496 TCAACCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 9 0.31
34 6 0.21
35 14 0.48
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.63
Consensus pattern (34 bp):
TTATACTTTTGTTTTAATTTGATAATTTTAACTC
Found at i:39612965 original size:24 final size:23
Alignment explanation
Indices: 39612928--39612972 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
39612918 TTAAATCCAA
* *
39612928 AAAATAAAATGACTATATTTCTC
1 AAAATAAAAGGACTAAATTTCTC
39612951 AAAATAAAAGGGACTAAATTTC
1 AAAATAAAA-GGACTAAATTTC
39612973 AAATGTACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAATAAAAGGACTAAATTTCTC
Found at i:39614601 original size:4 final size:4
Alignment explanation
Indices: 39614592--39614617 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
39614582 TGTTGGAGTC
39614592 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
39614618 AATAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:39618614 original size:12 final size:12
Alignment explanation
Indices: 39618565--39618614 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
39618555 AGTTCTTTTT
39618565 AAGTTTTTCATC
1 AAGTTTTTCATC
*
39618577 AAGTCTTTTCATA
1 AAGT-TTTTCATC
* *
39618590 AAATTTTCCATC
1 AAGTTTTTCATC
*
39618602 AAGTTTTTAATC
1 AAGTTTTTCATC
39618614 A
1 A
39618615 TTTCGTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:39624856 original size:25 final size:26
Alignment explanation
Indices: 39624817--39624881 Score: 105
Period size: 25 Copynumber: 2.5 Consensus size: 26
39624807 GTTACTTAGG
39624817 AAGCCTTTGTGGCTAATCTTGT-GAA
1 AAGCCTTTGTGGCTAATCTTGTGGAA
**
39624842 AAGTTTTTGTGGCTAATCTTGTGGAA
1 AAGCCTTTGTGGCTAATCTTGTGGAA
39624868 AAGCCTTTGTGGCT
1 AAGCCTTTGTGGCT
39624882 TGTTATTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (26 bp):
AAGCCTTTGTGGCTAATCTTGTGGAA
Found at i:39638811 original size:18 final size:18
Alignment explanation
Indices: 39638716--39638812 Score: 106
Period size: 18 Copynumber: 5.4 Consensus size: 18
39638706 CAATCCCAAC
*
39638716 TACTGTATACGTGAACAG
1 TACTGTATACGTGAATAG
39638734 TA-TCGTATACGTGAATAG
1 TACT-GTATACGTGAATAG
* *
39638752 TTCCGTATACGTGAATAG
1 TACTGTATACGTGAATAG
* * *
39638770 TACCGTATACATGAATAA
1 TACTGTATACGTGAATAG
* *
39638788 TGCTGTATACATGAATAG
1 TACTGTATACGTGAATAG
39638806 TACTGTA
1 TACTGTA
39638813 AACGGTCGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
17 1 0.01
18 66 0.99
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:39640093 original size:20 final size:20
Alignment explanation
Indices: 39640070--39640115 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39640060 TCAAAAAAAC
39640070 TAAAAAAATAAAAAAATTTG
1 TAAAAAAATAAAAAAATTTG
** *
39640090 TAAAATTATAAAAAATTTTG
1 TAAAAAAATAAAAAAATTTG
39640110 TAAAAA
1 TAAAAA
39640116 TGGTAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAAAAAAATTTG
Found at i:39640115 original size:21 final size:20
Alignment explanation
Indices: 39640077--39640153 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
39640067 AACTAAAAAA
*
39640077 ATAAAAAAATTTGTAAAATT
1 ATAAAAAAATTTGTAAAATG
*
39640097 ATAAAAAATTTTGTAAAAATG
1 ATAAAAAAATTTGT-AAAATG
*
39640118 GTAAAAAAATTAT-TAAAAT-
1 ATAAAAAAATT-TGTAAAATG
* *
39640137 AT-TAAAAATATGTAAAA
1 ATAAAAAAATTTGTAAAA
39640154 AAGTATTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.02
18 11 0.23
19 1 0.02
20 18 0.38
21 15 0.32
22 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (20 bp):
ATAAAAAAATTTGTAAAATG
Found at i:39640123 original size:41 final size:39
Alignment explanation
Indices: 39640078--39640154 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 39
39640068 ACTAAAAAAA
*
39640078 TAAAAAAATT-TGTAAAATTATAAAAAATTTTGTAAAAATGG
1 TAAAAAAATTAT-TAAAA-TATAAAAAA-TATGTAAAAATGG
*
39640119 TAAAAAAATTATTAAAATATTAAAAATATGTAAAAA
1 TAAAAAAATTATTAAAATATAAAAAATATGTAAAAA
39640155 AGTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 9 0.27
40 8 0.24
41 15 0.45
42 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (39 bp):
TAAAAAAATTATTAAAATATAAAAAATATGTAAAAATGG
Found at i:39640136 original size:20 final size:18
Alignment explanation
Indices: 39640073--39640128 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 18
39640063 AAAAAACTAA
*
39640073 AAAAATAAAAAAATTTGT
1 AAAATTAAAAAAATTTGT
39640091 AAAATTATAAAAAATTTTGT
1 AAAATTA-AAAAAA-TTTGT
39640111 AAAAATGGTAAAAAAATT
1 -AAAAT--TAAAAAAATT
39640129 ATTAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 5 0.16
21 7 0.22
22 6 0.19
23 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (18 bp):
AAAATTAAAAAAATTTGT
Found at i:39644072 original size:4 final size:4
Alignment explanation
Indices: 39644063--39644089 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
39644053 TCAATGTAAA
39644063 ACTC ACTC ACTC ACTC ACTC ACTC ACT
1 ACTC ACTC ACTC ACTC ACTC ACTC ACT
39644090 TTTTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ACTC
Found at i:39656156 original size:20 final size:21
Alignment explanation
Indices: 39656121--39656159 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
39656111 GAAAAGAAAA
*
39656121 AATAAAATGGAAATGGGAAGG
1 AATAAAATGAAAATGGGAAGG
39656142 AATAAAA-GAAAATGGGAA
1 AATAAAATGAAAATGGGAA
39656160 AAGGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (21 bp):
AATAAAATGAAAATGGGAAGG
Found at i:39656170 original size:22 final size:20
Alignment explanation
Indices: 39656131--39656170 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
39656121 AATAAAATGG
*
39656131 AAATGGGAAGGAATAAAAGA
1 AAATGGGAAGGAAAAAAAGA
39656151 AAATGGGAAAAGGAAAAAAA
1 AAATGGG--AAGGAAAAAAA
39656171 ATGTGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (20 bp):
AAATGGGAAGGAAAAAAAGA
Found at i:39662272 original size:17 final size:19
Alignment explanation
Indices: 39662236--39662280 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
39662226 ATTATTTGAC
39662236 TATTTTATATTTAATATAT
1 TATTTTATATTTAATATAT
*
39662255 TATTTT-TA-TTAATTTA-
1 TATTTTATATTTAATATAT
39662271 T-TTTTATATT
1 TATTTTATATT
39662281 GCTTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 4 0.17
16 3 0.13
17 8 0.35
18 2 0.09
19 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTATATTTAATATAT
Found at i:39662894 original size:83 final size:80
Alignment explanation
Indices: 39662807--39663066 Score: 288
Period size: 80 Copynumber: 3.2 Consensus size: 80
39662797 AAACAAATTC
* * * *
39662807 ATTTTAAAGGGACTAAAGTGTAATTTTACTATATATTAAATTATGATTTCTTTATTTATAAGAGG
1 ATTTT-AAGGGAC-AAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGG
* *
39662872 ACTGAATTGAAAATTTTT
64 ATTAAATT-AAAATTTTT
* * **
39662890 ATTTTAAGAGGTCAAAGTGCAATTTTACTATAATATTAATTTGTAATTTATCCATTTATAAGAGG
1 ATTTTAAG-GGACAAAGTGCAATTTTACTAT-ATATTAATTTATAATTTATTTATTTATAAGAGG
*
39662955 ATTAAATTAAAATTATT
64 ATTAAATTAAAATTTTT
* * * * * *
39662972 ATTGTGAGGGACAAAATACAAATTTACTATATATTAATTTATAAATTATTTATTTATAAGAGGAT
1 ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGAT
*
39663037 TAAATTTAAAATTTTC
66 TAAA-TTAAAATTTTT
*
39663053 ATTTT-CGGGACAAA
1 ATTTTAAGGGACAAA
39663067 TCGTTTGTGT
Statistics
Matches: 149, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
80 43 0.29
81 31 0.21
82 34 0.23
83 41 0.28
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (80 bp):
ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGAT
TAAATTAAAATTTTT
Found at i:39662974 original size:82 final size:79
Alignment explanation
Indices: 39662748--39663066 Score: 284
Period size: 83 Copynumber: 3.9 Consensus size: 79
39662738 AAAATATAAA
* * * ** * *
39662748 TTTATTATGTATTAATTTATAATTT-TGTTATTTTTTGAAG-GGATTAAACAAACAAATTCATTT
1 TTTACTATATATTAATTTATAATTTAT-TTA-TTTAT-AAGAGGATTAAATTAA-AATTTTATTT
*
39662811 TAAAGGGACTAAAGTGTAAT
62 T-AAGGGAC-AAAGTGCAAT
* * * * *
39662831 TTTACTATATATTAAATTATGATTTCTTTATTTATAAGAGGACTGAATTGAAAATTTTTATTTTA
1 TTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTAAATT-AAAA-TTTTATTTTA
*
39662896 AGAGGTCAAAGTGCAAT
64 AG-GGACAAAGTGCAAT
* ** * *
39662913 TTTACTATAATATTAATTTGTAATTTATCCATTTATAAGAGGATTAAATTAAAATTATTATTGTG
1 TTTACTAT-ATATTAATTTATAATTTATTTATTTATAAGAGGATTAAATTAAAATT-TTATTTTA
* * *
39662978 AGGGACAAAATACAAA
64 AGGGACAAAGTGCAAT
*
39662994 TTTACTATATATTAATTTATAAATTATTTATTTATAAGAGGATTAAATTTAAAATTTTCATTTT-
1 TTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTAAA-TTAAAATTTT-ATTTTA
*
39663058 CGGGACAAA
64 AGGGACAAA
39663067 TCGTTTGTGT
Statistics
Matches: 194, Mismatches: 33, Indels: 21
0.78 0.13 0.08
Matches are distributed among these distances:
80 45 0.23
81 35 0.18
82 44 0.23
83 69 0.36
84 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.44
Consensus pattern (79 bp):
TTTACTATATATTAATTTATAATTTATTTATTTATAAGAGGATTAAATTAAAATTTTATTTTAAG
GGACAAAGTGCAAT
Found at i:39663988 original size:12 final size:12
Alignment explanation
Indices: 39663971--39664002 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39663961 ATTTCCTCTT
39663971 ATCATCATCACC
1 ATCATCATCACC
39663983 ATCATCATCACC
1 ATCATCATCACC
*
39663995 ACCATCAT
1 ATCATCAT
39664003 GACTCTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (12 bp):
ATCATCATCACC
Found at i:39663991 original size:15 final size:15
Alignment explanation
Indices: 39663971--39664002 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39663961 ATTTCCTCTT
*
39663971 ATCATCATCACCATC
1 ATCATCACCACCATC
39663986 ATCATCACCACCATC
1 ATCATCACCACCATC
39664001 AT
1 AT
39664003 GACTCTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (15 bp):
ATCATCACCACCATC
Found at i:39667457 original size:35 final size:35
Alignment explanation
Indices: 39667413--39667486 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
39667403 CTTGACTTTA
39667413 AAAAAAATCTGAAAAATTGAGTTAATTTTATTTTT
1 AAAAAAATCTGAAAAATTGAGTTAATTTTATTTTT
39667448 AAAAAAATCTGAAAAATTGAGTTAATTTTATTTTT
1 AAAAAAATCTGAAAAATTGAGTTAATTTTATTTTT
39667483 AAAA
1 AAAA
39667487 GGATTGAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (35 bp):
AAAAAAATCTGAAAAATTGAGTTAATTTTATTTTT
Found at i:39668970 original size:34 final size:34
Alignment explanation
Indices: 39668927--39668994 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
39668917 CTAAGAAAGA
*
39668927 GCAATGCTTTTTATTATAGTTCTGGATTGAGCTG
1 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
39668961 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
1 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
39668995 TCATTGCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.43
Consensus pattern (34 bp):
GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
Found at i:39678629 original size:17 final size:17
Alignment explanation
Indices: 39678604--39678643 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
39678594 CTAAATTATG
*
39678604 TTAATATCTCTTTCTAA
1 TTAAAATCTCTTTCTAA
39678621 TTAAAATCTCTTTCTAA
1 TTAAAATCTCTTTCTAA
39678638 TTAAAA
1 TTAAAA
39678644 CCCCTATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAATCTCTTTCTAA
Found at i:39679573 original size:6 final size:6
Alignment explanation
Indices: 39679552--39679596 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
39679542 TAATATACAC
*
39679552 AATAAA CAAAAAA AATAAA AATAAA AATAAA AATAAAA AATAAA A
1 AATAAA -AATAAA AATAAA AATAAA AATAAA AAT-AAA AATAAA A
39679597 CATATAATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.84, C:0.02, G:0.00, T:0.13
Consensus pattern (6 bp):
AATAAA
Done.