Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 137 of 199
Found at i:41625490 original size:31 final size:31
Alignment explanation
Indices: 41625445--41625514 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
41625435 ATTAAATATA
*
41625445 ATAAATAATATTTAAATAATTTAATATAATG
1 ATAAATGATATTTAAATAATTTAATATAATG
*
41625476 ATAAATGATGTTTAAATAATTTAATATAATG
1 ATAAATGATATTTAAATAATTTAATATAATG
*
41625507 ATACATGA
1 ATAAATGA
41625515 AACATAAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (31 bp):
ATAAATGATATTTAAATAATTTAATATAATG
Found at i:41625499 original size:158 final size:156
Alignment explanation
Indices: 41625322--41625634 Score: 536
Period size: 158 Copynumber: 2.0 Consensus size: 156
41625312 GTTAAATTAT
* *
41625322 ATGATATTTAAATAATTTAATATAATGATACATGAAAAATAAATCTTAAATGTATTTTAAGTAAT
1 ATGATATTTAAATAATTTAATATAATGATACATGAAAAATAAATCTTAAATGCATTTTAAATAAT
*
41625387 TAATATAAATTACCTGTAAAATTTATTATATATAAAATATTTTAAAAAATTAAATATAATAAATA
66 TAATATAAATTACCAGTAAAATTTATTATATATAAAATATTTT-AAAAATTAAATATAATAAA-A
* *
41625452 ATATTTAAATAATTTAATATAATGATAA
129 AGATTTAAATAATTAAATATAATGATAA
* *
41625480 ATGATGTTTAAATAATTTAATATAATGATACATGAAACATAAATCTTAAATGCATTTTAAATAAT
1 ATGATATTTAAATAATTTAATATAATGATACATGAAAAATAAATCTTAAATGCATTTTAAATAAT
41625545 TAATATAAATTACCAGTAAAATTTATTATATATAAAATATTTTAAAAATTAAATATAATAAAAAG
66 TAATATAAATTACCAGTAAAATTTATTATATATAAAATATTTTAAAAATTAAATATAATAAAAAG
*
41625610 ATTTATATAATTAAATATAATGATA
131 ATTTAAATAATTAAATATAATGATA
41625635 TTTCAAAATT
Statistics
Matches: 147, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
156 25 0.17
157 19 0.13
158 103 0.70
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (156 bp):
ATGATATTTAAATAATTTAATATAATGATACATGAAAAATAAATCTTAAATGCATTTTAAATAAT
TAATATAAATTACCAGTAAAATTTATTATATATAAAATATTTTAAAAATTAAATATAATAAAAAG
ATTTAAATAATTAAATATAATGATAA
Found at i:41625523 original size:31 final size:31
Alignment explanation
Indices: 41625457--41625523 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
41625447 AAATAATATT
****
41625457 TAAATAATTTAATATAATGATAAATGATGTT
1 TAAATAATTTAATATAATGATAAATGAAACA
*
41625488 TAAATAATTTAATATAATGATACATGAAACA
1 TAAATAATTTAATATAATGATAAATGAAACA
41625519 TAAAT
1 TAAAT
41625524 CTTAAATGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATAATTTAATATAATGATAAATGAAACA
Found at i:41629293 original size:20 final size:21
Alignment explanation
Indices: 41629270--41629309 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41629260 TGGACGAGCC
41629270 ACCAG-AAA-TGCAGATAAACT
1 ACCAGTAAATTGC-GATAAACT
41629290 ACCAGTAAATTGCGATAAAC
1 ACCAGTAAATTGCGATAAAC
41629310 CGCCAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 10 0.56
22 3 0.17
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.17
Consensus pattern (21 bp):
ACCAGTAAATTGCGATAAACT
Found at i:41630921 original size:102 final size:101
Alignment explanation
Indices: 41630745--41631082 Score: 448
Period size: 102 Copynumber: 3.3 Consensus size: 101
41630735 TATCGATGAA
* * *
41630745 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
41630810 TAAGTGAAGGCTA-TAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACT-ATGTGTACCGA-AAGCTTTGGT
* * *
41630847 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGAATCAATAAATGATGGTCACATGTGTAATAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
41630912 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* ** *** * *
41630949 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAA-CCGTAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
* * * * *
41631013 TATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGAT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
41631049 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
41631083 TATCGAATGA
Statistics
Matches: 212, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
100 37 0.17
101 46 0.22
102 127 0.60
103 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:41631015 original size:50 final size:50
Alignment explanation
Indices: 41630745--41631082 Score: 358
Period size: 51 Copynumber: 6.7 Consensus size: 50
41630735 TATCGATGAA
* * ***
41630745 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * * *
41630796 CACATGTGTAGTATTAAGTGAAGGCTA-TAATGTGTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACT-ACGTGAACCGTA-AAAC-TTGGT
* * ** ***
41630847 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGAATCAATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-CCGTAAAACTTGGT
* * * * *
41630898 CACATGTGTAATACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
* *
41630949 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
*
41630999 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
41631049 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
41631083 TATCGAATGA
Statistics
Matches: 240, Mismatches: 38, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
49 4 0.02
50 91 0.38
51 136 0.57
52 8 0.03
53 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:41635843 original size:51 final size:51
Alignment explanation
Indices: 41635751--41635945 Score: 198
Period size: 51 Copynumber: 3.8 Consensus size: 51
41635741 CATGAGAACT
* * * * * *
41635751 CATGTGTAGTACTATGTGTAGGCTAGTATGAGTATAAGATAGTTATGTTCA
1 CATGTGTAGTACTAAGTGTAGGCTATTATGTGTACAGGATAGTTATGGTCA
* *
41635802 CATGTGTAGTACTAAGTGCAGGCTATTATGTGTACCGGATAGCTT-TGGTCA
1 CATGTGTAGTACTAAGTGTAGGCTATTATGTGTACAGGATAG-TTATGGTCA
* * * * * *
41635853 CGTGTGTAATACTATGTGTAGGCT-TCTACGTGTGCAGGAT-GGTATTGGTCA
1 CATGTGTAGTACTAAGTGTAGGCTAT-TATGTGTACAGGATAGTTA-TGGTCA
* *
41635904 CATGTGTAGTACTAAGTGTAGGCTACTATGTGTACCGGATAG
1 CATGTGTAGTACTAAGTGTAGGCTATTATGTGTACAGGATAG
41635946 CATTGATCAT
Statistics
Matches: 115, Mismatches: 23, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
51 109 0.95
52 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (51 bp):
CATGTGTAGTACTAAGTGTAGGCTATTATGTGTACAGGATAGTTATGGTCA
Found at i:41644078 original size:26 final size:26
Alignment explanation
Indices: 41644042--41644091 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
41644032 TTAACCGCCC
41644042 ATTTAAAAGTAGAATAGAATAAGACA
1 ATTTAAAAGTAGAATAGAATAAGACA
41644068 ATTTAAAAGTAGAATAGAATAAGA
1 ATTTAAAAGTAGAATAGAATAAGA
41644092 TAAGTGTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.24
Consensus pattern (26 bp):
ATTTAAAAGTAGAATAGAATAAGACA
Found at i:41651252 original size:2 final size:2
Alignment explanation
Indices: 41651245--41651287 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
41651235 GACAAGTGAG
41651245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41651287 T
1 T
41651288 CCTAAAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41651483 original size:8 final size:8
Alignment explanation
Indices: 41651467--41651555 Score: 81
Period size: 9 Copynumber: 10.2 Consensus size: 8
41651457 TTAAGCTATT
41651467 ATATAATA
1 ATATAATA
*
41651475 ATATGATA
1 ATATAATA
*
41651483 AGTAGCAATA
1 A-TA-TAATA
41651493 ATATAAGTA
1 ATATAA-TA
41651502 ATAATAATA
1 AT-ATAATA
41651511 ATAATAATA
1 AT-ATAATA
41651520 ATAATAATA
1 AT-ATAATA
41651529 ATAATAATA
1 AT-ATAATA
41651538 ATAATAATA
1 AT-ATAATA
41651547 ATA-AATA
1 ATATAATA
41651554 AT
1 AT
41651556 GAAAGATGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
7 6 0.08
8 11 0.15
9 48 0.66
10 8 0.11
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (8 bp):
ATATAATA
Found at i:41651495 original size:3 final size:3
Alignment explanation
Indices: 41651489--41651555 Score: 109
Period size: 3 Copynumber: 22.0 Consensus size: 3
41651479 GATAAGTAGC
41651489 AAT AAT -AT AAGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41651534 AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT
41651556 GAAAGATGAC
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.03
3 53 0.87
4 6 0.10
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41653101 original size:2 final size:2
Alignment explanation
Indices: 41653094--41653133 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
41653084 GTAAACTAAC
41653094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41653134 AAGATAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41656304 original size:31 final size:31
Alignment explanation
Indices: 41656268--41656329 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41656258 TTTAATTTTG
41656268 ATTGCATACTTAGTTTCTTATTTACTTACAT
1 ATTGCATACTTAGTTTCTTATTTACTTACAT
41656299 ATTGCATACTTAGTTTCTTATTTACTTACAT
1 ATTGCATACTTAGTTTCTTATTTACTTACAT
41656330 TTATTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (31 bp):
ATTGCATACTTAGTTTCTTATTTACTTACAT
Found at i:41657495 original size:7 final size:7
Alignment explanation
Indices: 41657483--41657515 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
41657473 TTTAGTTTCC
41657483 TTTTTAT
1 TTTTTAT
41657490 TTTTTAT
1 TTTTTAT
*
41657497 TTTTGAT
1 TTTTTAT
41657504 TTTTTAT
1 TTTTTAT
41657511 TTTTT
1 TTTTT
41657516 TCATCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:41659167 original size:50 final size:50
Alignment explanation
Indices: 41659052--41659300 Score: 309
Period size: 50 Copynumber: 4.8 Consensus size: 50
41659042 GATAATAACA
* ** *
41659052 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTGG
* * * *
41659103 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* * *
41659153 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
* *
41659203 TGCCCATGCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTT--GG
*
41659258 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41659301 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
50 92 0.54
51 33 0.20
53 4 0.02
55 1 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:41659241 original size:100 final size:104
Alignment explanation
Indices: 41659051--41659300 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 104
41659041 TGATAATAAC
** *
41659051 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTGGTGCCCATGCCATG
* * *
41659116 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAAGGGACCTCTCAATCTTAAGG
* * *
41659153 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTTGTTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCCATGCCATGT
41659217 CCCAGACATGGTCTTACAAGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAAGGGACCTCTCA--ATCTTAAGG
* *
41659258 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41659301 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAAGGGACCTCTCAATCTTAAGG
Found at i:41659661 original size:30 final size:30
Alignment explanation
Indices: 41659626--41659683 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41659616 CCTCGACTCT
*
41659626 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
41659656 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
41659684 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:41661887 original size:10 final size:10
Alignment explanation
Indices: 41661872--41661947 Score: 59
Period size: 10 Copynumber: 7.3 Consensus size: 10
41661862 TATCAGTGAC
*
41661872 TTTATTTAGT
1 TTTATTTATT
41661882 TTTATTTATT
1 TTTATTTATT
41661892 TTTATTT-TT
1 TTTATTTATT
*
41661901 ATT-TTTA-T
1 TTTATTTATT
41661909 TTTATTTTATT
1 TTTA-TTTATT
41661920 TTTATGGTTACTTT
1 TTTAT--TTA--TT
41661934 TTTATTTTATT
1 TTTA-TTTATT
41661945 TTT
1 TTT
41661948 CAGATTTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
8 6 0.11
9 4 0.07
10 21 0.39
11 10 0.19
12 3 0.06
13 3 0.06
14 6 0.11
15 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.04, T:0.78
Consensus pattern (10 bp):
TTTATTTATT
Found at i:41661895 original size:6 final size:6
Alignment explanation
Indices: 41661886--41661947 Score: 67
Period size: 6 Copynumber: 10.5 Consensus size: 6
41661876 TTTAGTTTTA
* *
41661886 TTTATT TTTATT TTTATT TTTA-T TTTA-T TTTATT TTTATG GTTACTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT
41661933 TTT-TAT TTTATT TTT
1 TTTAT-T TTTATT TTT
41661948 CAGATTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
5 11 0.23
6 33 0.69
7 4 0.08
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:41661906 original size:22 final size:22
Alignment explanation
Indices: 41661881--41661947 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 22
41661871 CTTTATTTAG
41661881 TTTTA-TTTATTTTTATTTTTAT
1 TTTTATTTTA-TTTTATTTTTAT
41661903 TTTTATTTTATTTTATTTTTAT
1 TTTTATTTTATTTTATTTTTAT
41661925 GGTTACTT-TTTTATTTTATTTTT
1 --TT--TTATTTTATTTTATTTTT
41661948 CAGATTTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.43
23 4 0.10
24 2 0.05
25 15 0.38
26 2 0.05
ACGTcount: A:0.16, C:0.01, G:0.03, T:0.79
Consensus pattern (22 bp):
TTTTATTTTATTTTATTTTTAT
Found at i:41661946 original size:5 final size:5
Alignment explanation
Indices: 41661872--41661921 Score: 50
Period size: 6 Copynumber: 9.6 Consensus size: 5
41661862 TATCAGTGAC
41661872 TTTA- TTTAGT TTTA- TTTATT TTTATT TTTATT TTTAT TTTAT TTTAT
1 TTTAT TTTA-T TTTAT TTTA-T TTTA-T TTTA-T TTTAT TTTAT TTTAT
41661919 TTT
1 TTT
41661922 TATGGTTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.19
5 14 0.33
6 20 0.48
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:41667359 original size:15 final size:15
Alignment explanation
Indices: 41667327--41667355 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41667317 ATTTTTTTGA
41667327 AAATTTTAGAATTTT
1 AAATTTTAGAATTTT
41667342 AAATTTTA-AATTTT
1 AAATTTTAGAATTTT
41667356 TAAAAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
AAATTTTAGAATTTT
Found at i:41669556 original size:2 final size:2
Alignment explanation
Indices: 41669549--41669590 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41669539 NNNNNNNNNN
41669549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41669591 TCAAGGATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41670096 original size:4 final size:4
Alignment explanation
Indices: 41670087--41670127 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
41670077 CTCTGTGCAA
* * *
41670087 ACAT ACAT ACAT ACAT ACTT ACGT ACGT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
41670128 TGAGAATACA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:41676941 original size:29 final size:29
Alignment explanation
Indices: 41676904--41677002 Score: 141
Period size: 28 Copynumber: 3.5 Consensus size: 29
41676894 AAAAATAAAA
41676904 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
41676933 ATTTACCAAAATATTACAAC-TTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
* *
41676961 ATTTACCAAAATATTGC--TTTTTTTTATT
1 ATTTACCAAAATATTACAACTTTTTTT-TT
*
41676989 ATTTACTAAAATAT
1 ATTTACCAAAATAT
41677003 ATCAAAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.09
28 39 0.60
29 20 0.31
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.52
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:41677079 original size:27 final size:26
Alignment explanation
Indices: 41677041--41677097 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 26
41677031 CCTGATCACC
41677041 CCAATGCCATTGGCGGCACCAAAGGTG
1 CCAATGCCATTGGCGGCACC-AAGGTG
*
41677068 CCAATGCCATTGGCGGCACCAATGTG
1 CCAATGCCATTGGCGGCACCAAGGTG
41677094 CCAA
1 CCAA
41677098 AGGACTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (26 bp):
CCAATGCCATTGGCGGCACCAAGGTG
Found at i:41677315 original size:37 final size:37
Alignment explanation
Indices: 41677272--41677522 Score: 484
Period size: 37 Copynumber: 6.8 Consensus size: 37
41677262 TCACTTTTTT
*
41677272 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
41677309 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
41677346 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
41677383 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
41677420 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
41677457 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
*
41677494 ATTTAATAATTCTATTTTAATTTAATAAA
1 ATTTAATAACTCTATTTTAATTTAATAAA
41677523 TTAAGTAAAC
Statistics
Matches: 212, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 212 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:41678224 original size:27 final size:26
Alignment explanation
Indices: 41678188--41678244 Score: 105
Period size: 27 Copynumber: 2.2 Consensus size: 26
41678178 TTTTAGTCCT
41678188 TTGGCACATTGGTGCCGCCAATGGCA
1 TTGGCACATTGGTGCCGCCAATGGCA
41678214 TTGGCACCATTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCGCCAATGGCA
41678241 TTGG
1 TTGG
41678245 GGTGATCAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.25
Consensus pattern (26 bp):
TTGGCACATTGGTGCCGCCAATGGCA
Found at i:41678307 original size:20 final size:19
Alignment explanation
Indices: 41678265--41678308 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
41678255 CTGTGTCAGT
* * *
41678265 TTTTGTTTTTTTTTTTGTC
1 TTTTGTTTTTTTTTATATA
41678284 TTTTGTTGTTTTTTTATATA
1 TTTTGTT-TTTTTTTATATA
41678304 TTTTG
1 TTTTG
41678309 GTAAATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.07, C:0.02, G:0.11, T:0.80
Consensus pattern (19 bp):
TTTTGTTTTTTTTTATATA
Found at i:41678332 original size:28 final size:28
Alignment explanation
Indices: 41678301--41678398 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
41678291 GTTTTTTTAT
**
41678301 ATATTTTGGTAAATAATAAAAAA-AAGTA
1 ATATTTTGGTAAATAA-AAAAAAGTTGTA
*
41678329 ATATTTTCGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
41678357 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
41678385 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
41678399 TTTAATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
27 6 0.09
28 59 0.91
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:41682565 original size:135 final size:132
Alignment explanation
Indices: 41682321--41682582 Score: 389
Period size: 135 Copynumber: 2.0 Consensus size: 132
41682311 TCCAAGAAAT
* *
41682321 GCACGGTTTGTTTCCTCACCAAAGCAACTACTGCTAATTTTAAGGTGACTACTATCACCATTTTC
1 GCACAGTTTGTTTCCTCACCAAAGCAACTACTGCTAACTTTAAGGTGACTACTATCACCATTTTC
*
41682386 AGGAAAAGTACTTCTCAGATCCATGCATTCTAGAAGTCCATTAGGAAAAGATTGGCAAAGACTAG
66 AGGAAAAGTACTCCTCAGATCCATGCATTCTAGAAGTCCATTAGGAAAAGATTGGCAAAGACTAG
41682451 TC
131 TC
* *
41682453 GCACAGTTTGTTTCCTCACCAAAGCAACTACTGCTAACTTTAAGGTGACTTTTTCTATCATCATT
1 GCACAGTTTGTTTCCTCACCAAAGCAACTACTGCTAACTTTAAGGTGAC---TACTATCACCATT
* * * * * * *
41682518 TTTAGGAAGAGTGCTCCTCAGATCCGTGCATTCTAGAAGTCCTTTAGGAACAGATTGGTAAAGAC
63 TTCAGGAAAAGTACTCCTCAGATCCATGCATTCTAGAAGTCCATTAGGAAAAGATTGGCAAAGAC
41682583 CAGTTGCTTG
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
132 47 0.41
135 68 0.59
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (132 bp):
GCACAGTTTGTTTCCTCACCAAAGCAACTACTGCTAACTTTAAGGTGACTACTATCACCATTTTC
AGGAAAAGTACTCCTCAGATCCATGCATTCTAGAAGTCCATTAGGAAAAGATTGGCAAAGACTAG
TC
Found at i:41687613 original size:3 final size:3
Alignment explanation
Indices: 41687605--41687630 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41687595 TCGACATTGC
41687605 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
41687631 CTCAATAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:41690759 original size:13 final size:13
Alignment explanation
Indices: 41690741--41690765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41690731 AAAAATAAAT
41690741 ACAAATAAAAAAG
1 ACAAATAAAAAAG
41690754 ACAAATAAAAAA
1 ACAAATAAAAAA
41690766 TAGACTCGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.04, T:0.08
Consensus pattern (13 bp):
ACAAATAAAAAAG
Found at i:41691450 original size:27 final size:28
Alignment explanation
Indices: 41691419--41691472 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
41691409 AAAAAGCCCT
*
41691419 TTTTTTAA-ATTTACTGAAATGGGCCGG
1 TTTTTTAATATTTACCGAAATGGGCCGG
*
41691446 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAA-TATTTACCGAAATGGGCC
41691473 ATTTTCCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
29 15 0.65
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (28 bp):
TTTTTTAATATTTACCGAAATGGGCCGG
Found at i:41695274 original size:40 final size:39
Alignment explanation
Indices: 41695230--41695316 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
41695220 AATATGGTAC
41695230 AAATTAGTAAGATTATCAAATTA-GGTTAGGGTTTTTAATT
1 AAATTAGTAAGATTAT--AATTAGGGTTAGGGTTTTTAATT
* * * **
41695270 AAATTAAATTAGGTTATGGTTAGGGTTAGGGTTTTTAATT
1 AAATT-AGTAAGATTATAATTAGGGTTAGGGTTTTTAATT
41695310 AAATTAG
1 AAATTAG
41695317 GTTAGGGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.10
40 27 0.69
41 8 0.21
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.43
Consensus pattern (39 bp):
AAATTAGTAAGATTATAATTAGGGTTAGGGTTTTTAATT
Found at i:41695315 original size:35 final size:34
Alignment explanation
Indices: 41695271--41695373 Score: 127
Period size: 29 Copynumber: 3.3 Consensus size: 34
41695261 TTTTTAATTA
41695271 AATTAAATTAGGTTATGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGGTTA-GGTTAGGGTTAGGGTTTTT
41695306 AATT-AA--A--TTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTT
41695335 AATT-AA--A--TTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTT
41695364 AATTAAATTA
1 AATTAAATTA
41695374 AATTNNNNNN
Statistics
Matches: 65, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
29 52 0.80
30 5 0.08
32 2 0.03
34 2 0.03
35 4 0.06
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (34 bp):
AATTAAATTAGGTTAGGTTAGGGTTAGGGTTTTT
Found at i:41695320 original size:29 final size:29
Alignment explanation
Indices: 41695287--41695373 Score: 174
Period size: 29 Copynumber: 3.0 Consensus size: 29
41695277 ATTAGGTTAT
41695287 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
41695316 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
41695345 GGTTAGGGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATTAAATTA
41695374 AATTNNNNNN
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTAGGGTTTTTAATTAAATTA
Found at i:41695322 original size:40 final size:41
Alignment explanation
Indices: 41695253--41695331 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 41
41695243 TATCAAATTA
*
41695253 GGTTAGGGTTTTTAATTAAATTAAATTA-GGTTATGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTAG
**
41695293 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTT
1 GGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTT
41695332 TTTAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 26 0.74
41 9 0.26
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (41 bp):
GGTTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTAG
Found at i:41697724 original size:14 final size:15
Alignment explanation
Indices: 41697707--41697740 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41697697 AATATTTATC
41697707 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
41697721 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
41697736 TAAAA
1 TAAAA
41697741 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:41697952 original size:22 final size:21
Alignment explanation
Indices: 41697927--41697977 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
41697917 TAATATGGAG
*
41697927 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
41697949 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
41697971 TTGAGAG
1 TTGAGAG
41697978 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:41697995 original size:52 final size:52
Alignment explanation
Indices: 41697930--41698029 Score: 164
Period size: 52 Copynumber: 1.9 Consensus size: 52
41697920 TATGGAGTTG
* *
41697930 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTTA
1 AGAGAATTTTTGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
**
41697982 AGAGAATTTTTGAAGGAAATTGAGAGAATTTTTTAAGGAATTTGAGAG
1 AGAGAATTTTTGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAG
41698030 AATCTTTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (52 bp):
AGAGAATTTTTGAAGGAAATTGAGAGAATTTTGGAAGGAATTTGAGAGTTTA
Found at i:41698010 original size:22 final size:22
Alignment explanation
Indices: 41697982--41698050 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
41697972 TGAGAGTTTA
41697982 AGAGAATTTTTGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
* *
41698004 AGAGAATTTTTTAAGGAATTTG
1 AGAGAATTTTTGAAGGAAATTG
* *
41698026 AGAGAATCTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
41698048 AGA
1 AGA
41698051 TAGGATTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:41698307 original size:29 final size:27
Alignment explanation
Indices: 41698259--41698317 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
41698249 GATTTCGGGG
* *
41698259 AAACTGGCCCATTACGGTAAATAATTAAA
1 AAACCGGCCCATTACAGTAAAT--TTAAA
*
41698288 AAACCGGCCCATTTCAGTAAATTTAAA
1 AAACCGGCCCATTACAGTAAATTTAAA
41698315 AAA
1 AAA
41698318 AAAGGGCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 8 0.30
29 19 0.70
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24
Consensus pattern (27 bp):
AAACCGGCCCATTACAGTAAATTTAAA
Found at i:41698678 original size:19 final size:18
Alignment explanation
Indices: 41698651--41698721 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
41698641 AAAAAAAAAG
* *
41698651 ATATCTATAATTTTCTTAA
1 ATATTTATAATTTT-ATAA
41698670 ATATTTATAATTTTATAA
1 ATATTTATAATTTTATAA
* * *
41698688 ATTTTTATAACTTCTAAAA
1 ATATTTATAA-TTTTATAA
*
41698707 TATATTTTTAATTTT
1 -ATATTTATAATTTT
41698722 TTCCATTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 12 0.29
19 22 0.52
20 8 0.19
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTATAATTTTATAA
Found at i:41698854 original size:55 final size:54
Alignment explanation
Indices: 41698784--41698902 Score: 150
Period size: 55 Copynumber: 2.2 Consensus size: 54
41698774 TTAAAAAATC
* * *
41698784 TATAATCTCTAATATTTTATAACTTTTTCATATTTTTC-ATAACATAATAATATTT
1 TATAATTTTTAATATTTTATAA-TTTTT-ATAGTTTTCTATAACATAATAATATTT
** *
41698839 TATAATTTTTAATATTTTATAATTTTTATAGTTTTCTATAATTTTATAATATTT
1 TATAATTTTTAATATTTTATAATTTTTATAGTTTTCTATAACATAATAATATTT
41698893 TAATAATTTT
1 T-ATAATTTT
41698903 AAGCTAAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
53 8 0.14
54 20 0.36
55 28 0.50
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (54 bp):
TATAATTTTTAATATTTTATAATTTTTATAGTTTTCTATAACATAATAATATTT
Found at i:41698861 original size:10 final size:10
Alignment explanation
Indices: 41698830--41698899 Score: 64
Period size: 9 Copynumber: 7.5 Consensus size: 10
41698820 TCATAACATA
41698830 ATAATATTTT
1 ATAATATTTT
41698840 AT-A-ATTTT
1 ATAATATTTT
41698848 -TAATATTTT
1 ATAATATTTT
41698857 ATAAT-TTTT
1 ATAATATTTT
*
41698866 ATAGT-TTTCT
1 ATAATATTT-T
41698876 AT-A-ATTTT
1 ATAATATTTT
41698884 ATAATATTTT
1 ATAATATTTT
41698894 AATAAT
1 -ATAAT
41698900 TTTAAGCTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
7 1 0.02
8 9 0.18
9 21 0.42
10 14 0.28
11 5 0.10
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (10 bp):
ATAATATTTT
Found at i:41708407 original size:230 final size:230
Alignment explanation
Indices: 41708004--41708464 Score: 841
Period size: 230 Copynumber: 2.0 Consensus size: 230
41707994 CTTATTAGAA
*
41708004 GTTTACAAATTGCAGTAGGATTTTCGCATGAGGCCTTAGAAATATCAATGTTAAAAAAAGGCTAC
1 GTTTACAAATTGCAGTAGGATTTTCGCATAAGGCCTTAGAAATATCAATGTTAAAAAAAGGCTAC
*
41708069 AACCATAAGATCTTTTATCACAAAGCTCACTAAGAAGCTTTCATGCAAAATAGAACTCTGTATTG
66 AACCATAAGATCTTCTATCACAAAGCTCACTAAGAAGCTTTCATGCAAAATAGAACTCTGTATTG
* * *
41708134 ATAATTTGCAAGCCTTTGGGAGCCCGTTTCACCATTACACTTAGTATATAAAGCTTCATGGTTAA
131 ATAATTTGCAAGCCTTTAGGACCCCGTTTCACCATTACACTTAGTATACAAAGCTTCATGGTTAA
41708199 GGGAACTTCACATCTCAAACATCAGGGATCATGAT
196 GGGAACTTCACATCTCAAACATCAGGGATCATGAT
*
41708234 GTTTACAAATTGCAGTAGGATTTTCGCATAAGGCCTTAGAAATATCAATTTTAAAAAAAGGCTAC
1 GTTTACAAATTGCAGTAGGATTTTCGCATAAGGCCTTAGAAATATCAATGTTAAAAAAAGGCTAC
** *
41708299 AACTGTAAGATCTTCTATCACAGAGCTCACTAAGAAGCTTTCATGCAAAATAGAACTCTGTATTG
66 AACCATAAGATCTTCTATCACAAAGCTCACTAAGAAGCTTTCATGCAAAATAGAACTCTGTATTG
41708364 ATAATTTGCAAGCCTTTAGGACCCCGTTTCACCATTACACTTAGTATACAAAGCTTCATGGTTAA
131 ATAATTTGCAAGCCTTTAGGACCCCGTTTCACCATTACACTTAGTATACAAAGCTTCATGGTTAA
41708429 GGGAACTTCACATCTCAAACATCAGGGATCATGAT
196 GGGAACTTCACATCTCAAACATCAGGGATCATGAT
41708464 G
1 G
41708465 CATCTGATAA
Statistics
Matches: 222, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
230 222 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (230 bp):
GTTTACAAATTGCAGTAGGATTTTCGCATAAGGCCTTAGAAATATCAATGTTAAAAAAAGGCTAC
AACCATAAGATCTTCTATCACAAAGCTCACTAAGAAGCTTTCATGCAAAATAGAACTCTGTATTG
ATAATTTGCAAGCCTTTAGGACCCCGTTTCACCATTACACTTAGTATACAAAGCTTCATGGTTAA
GGGAACTTCACATCTCAAACATCAGGGATCATGAT
Found at i:41708734 original size:5 final size:5
Alignment explanation
Indices: 41708724--41708757 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
41708714 GACCAAGAAC
41708724 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
41708758 GGATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:41708898 original size:7 final size:7
Alignment explanation
Indices: 41708886--41708914 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41708876 GACACCACAA
41708886 ACTTGAC
1 ACTTGAC
41708893 ACTTGAC
1 ACTTGAC
41708900 ACTTGAC
1 ACTTGAC
41708907 ACTTGAC
1 ACTTGAC
41708914 A
1 A
41708915 TGTAACATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (7 bp):
ACTTGAC
Found at i:41717849 original size:9 final size:9
Alignment explanation
Indices: 41717837--41717902 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 9
41717827 AAAACTACGA
41717837 AAAAATTAT
1 AAAAATTAT
41717846 AAAAAAGTTAT
1 -AAAAA-TTAT
* *
41717857 TAAAATGAT
1 AAAAATTAT
41717866 AAAAGA-TATT
1 AAAA-ATTA-T
*
41717876 ATAAATTATT
1 AAAAATTA-T
41717886 AAAAATTAT
1 AAAAATTAT
41717895 AAAAATTA
1 AAAAATTA
41717903 AGAAGTATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 17 0.37
10 25 0.54
11 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:41717861 original size:20 final size:19
Alignment explanation
Indices: 41717838--41717902 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
41717828 AAACTACGAA
41717838 AAAATTATAAAAAAGTTATT
1 AAAATTAT-AAAAAGTTATT
* *
41717858 AAAATGAT-AAAAGATATT
1 AAAATTATAAAAAGTTATT
*
41717876 ATAAATTATTAAAAA-TTATA
1 A-AAATTA-TAAAAAGTTATT
41717896 AAAATTA
1 AAAATTA
41717903 AGAAGTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 10 0.27
19 11 0.30
20 12 0.32
21 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAAAGTTATT
Found at i:41720456 original size:13 final size:13
Alignment explanation
Indices: 41720438--41720463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41720428 TCTAAATCAG
41720438 AATTATTTTTGAA
1 AATTATTTTTGAA
41720451 AATTATTTTTGAA
1 AATTATTTTTGAA
41720464 CTCAAAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AATTATTTTTGAA
Found at i:41722526 original size:92 final size:91
Alignment explanation
Indices: 41722369--41722577 Score: 276
Period size: 92 Copynumber: 2.3 Consensus size: 91
41722359 TTGATTTTAG
* * *
41722369 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* * * *
41722434 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAAATATTTTAAATTATA
*
41722461 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
41722525 TATGTAATAATAAATATTTTAAATTATA
64 TATGTAATAATAAATATTTTAAATTATA
* * * *
41722553 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
41722578 GTTATAATTA
Statistics
Matches: 103, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 73 0.71
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATAAATATTTTAAATTATA
Found at i:41723145 original size:15 final size:13
Alignment explanation
Indices: 41723117--41723150 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
41723107 ATAATAAATG
41723117 TTTTAAAAAAGTT
1 TTTTAAAAAAGTT
*
41723130 TTTTCAAAAAAGGT
1 TTTT-AAAAAAGTT
41723144 TTTTAAA
1 TTTTAAA
41723151 TTTTTTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTTAAAAAAGTT
Found at i:41727021 original size:13 final size:13
Alignment explanation
Indices: 41727003--41727027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41726993 TTTTAAAATA
41727003 TTTTTATTTTTAT
1 TTTTTATTTTTAT
41727016 TTTTTATTTTTA
1 TTTTTATTTTTA
41727028 AAATAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:41732375 original size:30 final size:30
Alignment explanation
Indices: 41732314--41732375 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
41732304 AATTTAAAGT
* *
41732314 CTAAATTACAAGAAAATAGAACATAGAGGA
1 CTAAATTACAAGAAAATAGAAAATACAGGA
*
41732344 CTAAATTA-AAGAAAATGGAAAATACATGGA
1 CTAAATTACAAGAAAATAGAAAATACA-GGA
41732374 CT
1 CT
41732376 CAGAGGACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (30 bp):
CTAAATTACAAGAAAATAGAAAATACAGGA
Found at i:41734072 original size:44 final size:45
Alignment explanation
Indices: 41734019--41734545 Score: 304
Period size: 44 Copynumber: 11.6 Consensus size: 45
41734009 AATCTGACCG
* *
41734019 ACTACAACTTCAGAGG-TATAGGATTTGTCGCTTCAATCTGCTCC
1 ACTACAACTTCAGAGGAGATAAGATTTGTCGCTTCAATCTGCTCC
* * * *
41734063 AGTACAACTTCAG-GGAGATAAGATTTGTAGTTTCAATCTGCTCT
1 ACTACAACTTCAGAGGAGATAAGATTTGTCGCTTCAATCTGCTCC
* * *
41734107 ACTGCAACTTCA-AGGAGATAAGATTTGTAGCTTTC-ATTTGCTCC
1 ACTACAACTTCAGAGGAGATAAGATTTGTCGC-TTCAATCTGCTCC
* * * * **
41734151 ACTGCAACTTTA-AGGAGATAAAATTTGTTATGGTGACTTCAATCCAAC-CC
1 ACTACAACTTCAGAGGAGATAAGATTTG---T--CG-CTTCAAT-CTGCTCC
* * * *
41734201 ACTACAACTTTAGAGG-TATAGGATTTGTCGCTTCAATATGCTCC
1 ACTACAACTTCAGAGGAGATAAGATTTGTCGCTTCAATCTGCTCC
*
41734245 ACTGCAACTTCAG-GGAGATAAGATTTG-CAGCTTCAATCTGCTCC
1 ACTACAACTTCAGAGGAGATAAGATTTGTC-GCTTCAATCTGCTCC
* ** * *
41734289 ACTGA-AACTTCTG-GGAGATTTGATTTGTAGCTTTC-ATCTGCTCT
1 ACT-ACAACTTCAGAGGAGATAAGATTTGTCGC-TTCAATCTGCTCC
* * *
41734333 ACTGCAACTTCAG-GGAGATAAGATTTTCTATGGTGGCTTCAATCTAAC-CC
1 ACTACAACTTCAGAGGAGATAAGA---T-T-T-GTCGCTTCAATCT-GCTCC
* ** * * *
41734383 ATTGTAACTTCAGA--AGTATAGGATTTGTCGCTTCAATTTGTTCC
1 ACTACAACTTCAGAGGAG-ATAAGATTTGTCGCTTCAATCTGCTCC
* *
41734427 ACTGCAACTTCAG-GGAGATAAGATTTGCTATGATGGCTTCAATCTGAC-CC
1 ACTACAACTTCAGAGGAGATAAGA--T--T-TG-TCGCTTCAATCTG-CTCC
* * *
41734477 ACTGCAACTTCAGA--AGTATAGGATTTGTCGCTTCTATCTGCTCC
1 ACTACAACTTCAGAGGAG-ATAAGATTTGTCGCTTCAATCTGCTCC
*
41734521 ACTGCAACTTCAG-GGAGATAAGATT
1 ACTACAACTTCAGAGGAGATAAGATT
41734546 CGCTATGGTG
Statistics
Matches: 379, Mismatches: 60, Indels: 88
0.72 0.11 0.17
Matches are distributed among these distances:
43 7 0.02
44 249 0.66
45 14 0.04
46 3 0.01
47 4 0.01
48 3 0.01
49 14 0.04
50 80 0.21
51 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (45 bp):
ACTACAACTTCAGAGGAGATAAGATTTGTCGCTTCAATCTGCTCC
Found at i:41734226 original size:182 final size:181
Alignment explanation
Indices: 41734019--41734596 Score: 721
Period size: 182 Copynumber: 3.1 Consensus size: 181
41734009 AATCTGACCG
* * *
41734019 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTGCTCCAGTACAACTTCAGGGAGATAA
1 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATATGCTCCACTGCAACTTCAGGGAGATAA
* *
41734084 GATTTGTAGTTTCAATCTGCTCTACTGCAACTTCAAGGAGATAAGATTTGTAGCTTTCATTTGCT
66 GATTTGTAGTTTCAATCTGCTCCACTGCAACTTC-AGGAGATAAGATTTGTAGCTTTCATCTGCT
* * *
41734149 CCACTGCAACTTTAAGGAGATAAAATTTGTTATGGTGACTTCAATCCAACCC
130 CCACTGCAACTTCAGGGAGATAAGATTTGTTATGGTGACTTCAATCCAACCC
*
41734201 ACTACAACTTTAGAGGTATAGGATTTGTCGCTTCAATATGCTCCACTGCAACTTCAGGGAGATAA
1 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATATGCTCCACTGCAACTTCAGGGAGATAA
* * * * **
41734266 GATTTGCAGCTTCAATCTGCTCCACTGAAACTTCTGGGAGATTTGATTTGTAGCTTTCATCTGCT
66 GATTTGTAGTTTCAATCTGCTCCACTGCAACTTC-AGGAGATAAGATTTGTAGCTTTCATCTGCT
* * *
41734331 CTACTGCAACTTCAGGGAGATAAGATTT-TCTATGGTGGCTTCAATCTAACCC
130 CCACTGCAACTTCAGGGAGATAAGATTTGT-TATGGTGACTTCAATCCAACCC
* ** * * *
41734383 ATTGTAACTTCAGAAGTATAGGATTTGTCGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAA
1 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATATGCTCCACTGCAACTTCAGGGAGATAA
* * *
41734448 GATTTGCTATGATGGCTTCAATCTGAC-CCACTGCAACTTCAGAAGTATAGGATTTGTCGC-TTC
66 GATTTG-TA-G-T---TTCAATCTG-CTCCACTGCAACTTCAGGAG-ATAAGATTTGTAGCTTTC
* * * *
41734511 TATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATGGTGACTTCAATCCGACCT
123 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTTATGGTGACTTCAATCCAACCC
* * *
41734571 ATTACAACTTCAGGGGTATAAGATTT
1 ACTACAACTTCAGAGGTATAGGATTT
41734597 TTGGTTTCAC
Statistics
Matches: 339, Mismatches: 46, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
181 1 0.00
182 225 0.66
183 1 0.00
184 1 0.00
187 6 0.02
188 104 0.31
189 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (181 bp):
ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATATGCTCCACTGCAACTTCAGGGAGATAA
GATTTGTAGTTTCAATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGTAGCTTTCATCTGCTC
CACTGCAACTTCAGGGAGATAAGATTTGTTATGGTGACTTCAATCCAACCC
Found at i:41734243 original size:94 final size:92
Alignment explanation
Indices: 41734019--41734596 Score: 520
Period size: 94 Copynumber: 6.3 Consensus size: 92
41734009 AATCTGACCG
* *
41734019 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTGCTCCAGTACAACTTCAGGGAGATAA
1 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
** *
41734084 GATTTGTA--GT--TTCAAT-CTGCTCT
66 GATTTGTATGGTGCTTCAATCCAAC-CC
* * * * * * *
41734107 ACTGCAACTTCA-AGGAGATAAGATTTGTAGCTTTC-ATTTGCTCCACTGCAACTTTAAGGAGAT
1 ACTACAACTTCAGAGG-TATAGGATTTGTCGC-TTCAATCTGCTCCACTGCAACTTCAGGGAGAT
*
41734170 AAAATTTGTTATGGTGACTTCAATCCAACCC
64 AAGATTTG-TATGGTG-CTTCAATCCAACCC
* *
41734201 ACTACAACTTTAGAGGTATAGGATTTGTCGCTTCAATATGCTCCACTGCAACTTCAGGGAGATAA
1 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* **
41734266 GATTTGCA----GCTTCAAT-CTGCTCC
66 GATTTGTATGGTGCTTCAATCCAAC-CC
* * ** * *
41734289 ACTGA-AACTTCTG-GGAGATTTGATTTGTAGCTTTC-ATCTGCTCTACTGCAACTTCAGGGAGA
1 ACT-ACAACTTCAGAGG-TATAGGATTTGTCGC-TTCAATCTGCTCCACTGCAACTTCAGGGAGA
* *
41734351 TAAGATTTTCTATGGTGGCTTCAATCTAACCC
63 TAAGA-TTTGTATGGT-GCTTCAATCCAACCC
* ** * * *
41734383 ATTGTAACTTCAGAAGTATAGGATTTGTCGCTTCAATTTGTTCCACTGCAACTTCAGGGAGATAA
1 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* **
41734448 GATTTGCTATGATGGCTTCAATCTGACCC
66 GATTTG-TATGGT-GCTTCAATCCAACCC
* * *
41734477 ACTGCAACTTCAGAAGTATAGGATTTGTCGCTTCTATCTGCTCCACTGCAACTTCAGGGAGATAA
1 ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * *
41734542 GATTCGCTATGGTGACTTCAATCCGACCT
66 GATTTG-TATGGTG-CTTCAATCCAACCC
* * *
41734571 ATTACAACTTCAGGGGTATAAGATTT
1 ACTACAACTTCAGAGGTATAGGATTT
41734597 TTGGTTTCAC
Statistics
Matches: 397, Mismatches: 66, Indels: 48
0.78 0.13 0.09
Matches are distributed among these distances:
87 7 0.02
88 112 0.28
89 14 0.04
91 2 0.01
93 11 0.03
94 244 0.61
95 7 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (92 bp):
ACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
GATTTGTATGGTGCTTCAATCCAACCC
Found at i:41746092 original size:4 final size:4
Alignment explanation
Indices: 41746083--41746112 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
41746073 ATATTAGAAT
41746083 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
41746113 GTATTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:41747403 original size:32 final size:31
Alignment explanation
Indices: 41747351--41747411 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
41747341 TACAAATATT
41747351 TGTTTTTGTTTTTGCTTTTCTACTTTTGCTTC
1 TGTTTTTGTTTTTGCTTTTCT-CTTTTGCTTC
* *
41747383 TGTTTTTGTCTTTTTC-TTTCTTTTTTGCT
1 TGTTTTTGT-TTTTGCTTTTCTCTTTTGCT
41747412 GGTCGCGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 14 0.54
33 5 0.19
ACGTcount: A:0.02, C:0.15, G:0.11, T:0.72
Consensus pattern (31 bp):
TGTTTTTGTTTTTGCTTTTCTCTTTTGCTTC
Found at i:41756337 original size:15 final size:16
Alignment explanation
Indices: 41756317--41756347 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41756307 TATGTAAATA
41756317 CTTAT-ATTTTTATAT
1 CTTATAATTTTTATAT
41756332 CTTATAATTTTTATAT
1 CTTATAATTTTTATAT
41756348 ATATTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTATAATTTTTATAT
Found at i:41757190 original size:109 final size:109
Alignment explanation
Indices: 41756661--41757165 Score: 841
Period size: 109 Copynumber: 4.6 Consensus size: 109
41756651 TTTCTAATTG
* *
41756661 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
41756726 CGTTCAACCAAATTGCTTAATATCATTTTTTTAAAAATTTTTAAATA
66 CGTTCAACCAAATGGCTTAATATC---CTTTTAAAGATTTTAAAATA
* * *
41756773 AGGCAATATTTTGCGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTGTGTGTAGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
41756838 CGTTCAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
*
41756882 AGGCAATATTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
41756947 CGTTCAACCAAATGACTTAATATCCTTTTAAAGATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
41756991 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
41757056 CGTTCAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
* * *
41757100 AGGCAATGA-TTTGCGTTTGAAAATTTGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAAT-ATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
41757164 TC
65 TC
41757166 ATTTAACCGA
Statistics
Matches: 373, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
109 289 0.77
110 1 0.00
112 83 0.22
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (109 bp):
AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
Found at i:41761023 original size:16 final size:16
Alignment explanation
Indices: 41761004--41761034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41760994 AAGAAAAATA
*
41761004 AAAAAATTAAAAAAAC
1 AAAAAATCAAAAAAAC
41761020 AAAAAATCAAAAAAA
1 AAAAAATCAAAAAAA
41761035 TCAATGTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAATCAAAAAAAC
Found at i:41761036 original size:9 final size:9
Alignment explanation
Indices: 41760997--41761038 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
41760987 GACTCGAAAG
41760997 AAAAAT-AA
1 AAAAATCAA
*
41761005 AAAAATTAA
1 AAAAATCAA
41761014 AAAAA-C-A
1 AAAAATCAA
41761021 AAAAATCAA
1 AAAAATCAA
41761030 AAAAATCAA
1 AAAAATCAA
41761039 TGTCAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 6 0.20
8 7 0.23
9 17 0.57
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATCAA
Found at i:41761061 original size:6 final size:6
Alignment explanation
Indices: 41761052--41761090 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
41761042 CAAAAATAGG
41761052 AGAAAA AGAAAGA AGAAAA A-AGAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAA-A AGAAAA AGA-AAA AGAAAA AGAAAA AG
41761091 GAGAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 22 0.73
7 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:41762097 original size:15 final size:15
Alignment explanation
Indices: 41762079--41762116 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
41762069 ACAAAAAACA
41762079 AAAAAAGAGAAGAAG
1 AAAAAAGAGAAGAAG
41762094 -AAAAAGAAGAAGAAG
1 AAAAAAG-AGAAGAAG
*
41762109 AGAAAAGA
1 AAAAAAGA
41762117 AAAAAAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 6 0.30
15 9 0.45
16 5 0.25
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGAAGAAG
Found at i:41763472 original size:46 final size:46
Alignment explanation
Indices: 41763418--41764184 Score: 1223
Period size: 46 Copynumber: 16.6 Consensus size: 46
41763408 AATGAAGTTA
41763418 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
*
41763464 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCAAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
41763510 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* *
41763556 CAGATCTTGTCTTCCTGT-TTTGGCAGCAGAGGAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* * *
41763601 TAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* *
41763647 CAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGAGATCGAAGATAA
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* *
41763693 CAGATCTTGTCTTCCTATATTTGGCAGCGGAAGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
41763739 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
**
41763785 CAGATCTTGTCTTCCTGTATTTGGCAGTAGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* * *
41763831 CAGATCTTGTCTTCCTGTATTTGGCAGCAGAAGAGATCAAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* * * *
41763877 CAGATATTGTCTTCCTATATTTAGCAGCGGAGGAGATCCAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* *
41763923 CAGATCTTGTCTTCCTGTATTTGGCAGCAGAAGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
* *
41763969 CATATCTTGTCTTCCTATATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
41764015 CAGATCTTGTCTTCCTGTATTTTGGCAGCGGAAGGAGATCGAAGATAG
1 CAGATCTTGTCTTCCTGTA-TTTGGCAGCGG-AGGAGATCGAAGATAG
* * *
41764063 CAGATCTTGTCTTTCCTGTGTTTTGGGCAGCGAAAGAGATCGAAGATAG
1 CAGATCTTGTC-TTCCTGT-ATTT-GGCAGCGGAGGAGATCGAAGATAG
*
41764112 CAGTATATTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
1 CAG-ATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
41764159 CAGATCTTGTCTTCCTG-ATTTGGCAG
1 CAGATCTTGTCTTCCTGTATTTGGCAG
41764185 TGGAATAGAT
Statistics
Matches: 671, Mismatches: 43, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
45 51 0.08
46 505 0.75
47 36 0.05
48 30 0.04
49 35 0.05
50 14 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (46 bp):
CAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATAG
Found at i:41764297 original size:50 final size:50
Alignment explanation
Indices: 41764191--41764495 Score: 272
Period size: 50 Copynumber: 6.3 Consensus size: 50
41764181 GCAGTGGAAT
* * * *
41764191 AGATTAAAGCTACAACAGCGGATCTTGCTTCCC---C--GGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAAA
* *
41764236 AGATTGAAGCTACAACAACGGATCTTACTTCCCTAACATTACAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAAA
* * * * * * ** *
41764286 AGATTGAAGCTACAACAGCAGATCTTACTTTCTTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAAA
* * *
41764336 AGATTGAAGCTACAACAACGGATCTTGCTT-CCT--C--GGCAGA-TAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCA-ATTAAAA
* * * * * ** *
41764381 ATATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAAA
*
41764431 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAAA
*
41764481 ATATTGAAGCTACAA
1 AGATTGAAGCTACAA
41764496 TAGCAGGTTT
Statistics
Matches: 204, Mismatches: 44, Indels: 19
0.76 0.16 0.07
Matches are distributed among these distances:
45 62 0.30
46 3 0.01
47 1 0.00
48 2 0.01
49 2 0.01
50 134 0.66
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTCCCTAACATTGCAATTAAAA
Found at i:41764301 original size:95 final size:96
Alignment explanation
Indices: 41764191--41764495 Score: 354
Period size: 95 Copynumber: 3.2 Consensus size: 96
41764181 GCAGTGGAAT
* * * ** *
41764191 AGATTAAAGCTACAACAGCGGATCTTGC-TTCCCCG-GCAGTTAAAAAGATTGAAGCTACAACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCGCGTGCAGTGGAACAGATTGAAGCTACAACAA
*
41764254 CGGATCTTACTTCCCTAACATTACAATTAAAA
66 CGGATCTTACTTCCCT-ACATTGCAATTAAAA
* *
41764286 AGATTGAAGCTACAACAGCAGATCTTACTTTCTTAGCGTTGCAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTC--CGCG-TGCAGTGGAACAGATTGAAGCTACAA
* *
41764351 CAACGGATCTTGCTT-CCT-C--GGCAGA-TAAAA
63 CAACGGATCTTACTTCCCTACATTGCA-ATTAAAA
*
41764381 ATATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCC--GCG-TGCAGTGGAACAGATTGAAGCTACAA
*
41764446 CAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
63 CAACGGATCTTACTTCCCT-ACATTGCAATTAAAA
*
41764481 ATATTGAAGCTACAA
1 AGATTGAAGCTACAA
41764496 TAGCAGGTTT
Statistics
Matches: 179, Mismatches: 17, Indels: 23
0.82 0.08 0.11
Matches are distributed among these distances:
95 105 0.59
96 7 0.04
97 1 0.01
98 3 0.02
99 4 0.02
100 59 0.33
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (96 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCGCGTGCAGTGGAACAGATTGAAGCTACAACAA
CGGATCTTACTTCCCTACATTGCAATTAAAA
Found at i:41764435 original size:145 final size:145
Alignment explanation
Indices: 41764181--41764460 Score: 416
Period size: 145 Copynumber: 1.9 Consensus size: 145
41764171 TCCTGATTTG
* * *
41764181 GCAGTGGAATAGATTAAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGC
1 GCAGTGGAACAGATTAAAGCTACAACAACGGATCTTGCTTCCCCGGCAGATAAAAAGATTGAAGC
*
41764246 TACAACAACGGATCTTACTTCCCTAACATTACAATTAAAAAGATTGAAGCTACAACAGCAGATCT
66 TACAACAACGGATCTTACTTCCCTAACATTACAATGAAAAAGATTGAAGCTACAACAGCAGATCT
41764311 TACTTTCTTAGCGTT
131 TACTTTCTTAGCGTT
* * *
41764326 GCAGTGGAACAGATTGAAGCTACAACAACGGATCTTGCTTCCTCGGCAGATAAAAATATTGAAGC
1 GCAGTGGAACAGATTAAAGCTACAACAACGGATCTTGCTTCCCCGGCAGATAAAAAGATTGAAGC
* * * * * * * * *
41764391 TACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCT
66 TACAACAACGGATCTTACTTCCCTAACATTACAATGAAAAAGATTGAAGCTACAACAGCAGATCT
41764456 TACTT
131 TACTT
41764461 CCCTGACATT
Statistics
Matches: 119, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
145 119 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (145 bp):
GCAGTGGAACAGATTAAAGCTACAACAACGGATCTTGCTTCCCCGGCAGATAAAAAGATTGAAGC
TACAACAACGGATCTTACTTCCCTAACATTACAATGAAAAAGATTGAAGCTACAACAGCAGATCT
TACTTTCTTAGCGTT
Found at i:41764487 original size:145 final size:145
Alignment explanation
Indices: 41764191--41764495 Score: 387
Period size: 145 Copynumber: 2.1 Consensus size: 145
41764181 GCAGTGGAAT
* * *
41764191 AGATTAAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTTAAAAAGATTGAAGCTACAACAACG
1 AGATTGAAGCTACAACAACGGATCTTGCTTCCCCGGCAGATAAAAAGATTGAAGCTACAACAACG
* * *
41764256 GATCTTACTTCCCTAACATTACAATTAAAAAGATTGAAGCTACAACAGCAGATCTTACTTTCTTA
66 GATCTTACTTCCCTAACATTACAATGAAAAAGATTGAAGCTACAACAGCAGATCTTACTTCCTGA
* * * *
41764321 GCGTTGCAGTGGAAC
131 GCATTGCAATGAAAA
* * *
41764336 AGATTGAAGCTACAACAACGGATCTTGCTTCCTCGGCAGATAAAAATATTGAAGCTACAACAGCG
1 AGATTGAAGCTACAACAACGGATCTTGCTTCCCCGGCAGATAAAAAGATTGAAGCTACAACAACG
* * * * * * * *
41764401 GATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTGAAGCTACAACAGCGGATCTTACTTCCCTG
66 GATCTTACTTCCCTAACATTACAATGAAAAAGATTGAAGCTACAACAGCAGATCTTACTT-CCTG
*
41764466 A-CATTGCAATTAAAA
130 AGCATTGCAATGAAAA
*
41764481 ATATTGAAGCTACAA
1 AGATTGAAGCTACAA
41764496 TAGCAGGTTT
Statistics
Matches: 136, Mismatches: 23, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
145 133 0.98
146 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (145 bp):
AGATTGAAGCTACAACAACGGATCTTGCTTCCCCGGCAGATAAAAAGATTGAAGCTACAACAACG
GATCTTACTTCCCTAACATTACAATGAAAAAGATTGAAGCTACAACAGCAGATCTTACTTCCTGA
GCATTGCAATGAAAA
Found at i:41766235 original size:15 final size:16
Alignment explanation
Indices: 41766215--41766245 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41766205 CATGTAAATA
41766215 CTTAT-ATTTTTATAT
1 CTTATAATTTTTATAT
41766230 CTTATAATTTTTATAT
1 CTTATAATTTTTATAT
41766246 ATATTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
CTTATAATTTTTATAT
Found at i:41767085 original size:109 final size:109
Alignment explanation
Indices: 41766559--41767063 Score: 848
Period size: 109 Copynumber: 4.6 Consensus size: 109
41766549 TTTCTAATTG
* **
41766559 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAATGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
41766624 CGTTCAACCAAATGGCTTAATATCCTTTTTAAAAAATTTTTTAAATA
66 CGTTCAACCAAATGGCTTAATATCC-TTTT-AAAAA-TTTTAAAATA
*
41766671 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCGGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
41766736 CGTTAAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
*
41766780 AGGCAATATTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
41766845 CGTTCAACCAAATGGCTTAATATCCTTTTAAAGATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
41766889 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
41766954 CGTTCAACCAAATGGCTAAATATCCTTTTAAAAATTTTAAAATA
66 CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
* * * * *
41766998 AGGCAATGTTTTGCGTTTGAAAATTCAAGAAAACGTGCCCTAAGGTGCTGGGTATCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
41767063 C
66 C
41767064 ATTTAGCCGA
Statistics
Matches: 375, Mismatches: 18, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
109 282 0.75
110 4 0.01
111 4 0.01
112 85 0.23
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (109 bp):
AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
Found at i:41770629 original size:132 final size:132
Alignment explanation
Indices: 41770409--41770829 Score: 549
Period size: 132 Copynumber: 3.2 Consensus size: 132
41770399 AACACCAAAG
* * *
41770409 AGATAGGATTCGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGATACAGGATCTACAATCTTCA
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * **
41770474 ACCTACTCCATTGCTACTCAGGGA-AAAGGGATTGGTGGCTTAAATCTATTTCTCTACTACCTTG
66 ACCTACTCCACTGCTACTCAGGGAGATA-GGATTGGTGACTTAAATCTGCTTCTCTACTACCTTG
41770538 GAA
130 GAA
* *
41770541 AGATAAGATTTGCTGCCTTCAATCTGCTCCACTACTGCTTAGGGAGACAGGATCTATAATCTTCA
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * *
41770606 ACCTACTCCACTGTTGC-CGAGGGAGATAGGACTGGTGACTTAAATCTGCTTCTCTACTACCTTG
66 ACCTACTCCACTGCTACTC-AGGGAGATAGGATTGGTGACTTAAATCTGCTTCTCTACTACCTTG
*
41770670 GGA
130 GAA
* *** * * *
41770673 AGATAAGATTTACCATCTTCGATCTGTTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTTA
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * * *
41770738 ACCTATTCCACTACTACTCAGAGAGATAGGATTGGTGACTTAAATCTGCTTCCCTACTACTTTGG
66 ACCTACTCCACTGCTACTCAGGGAGATAGGATTGGTGACTTAAATCTGCTTCTCTACTACCTTGG
41770803 AA
131 AA
* * *
41770805 AGATAAGATTCGCCGTCTTCGATCT
1 AGATAAGATTTGCTGCCTTCGATCT
41770830 ACTTCGCTAC
Statistics
Matches: 251, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
131 1 0.00
132 247 0.98
133 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (132 bp):
AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
ACCTACTCCACTGCTACTCAGGGAGATAGGATTGGTGACTTAAATCTGCTTCTCTACTACCTTGG
AA
Found at i:41770870 original size:45 final size:45
Alignment explanation
Indices: 41770820--41771448 Score: 571
Period size: 45 Copynumber: 14.0 Consensus size: 45
41770810 AGATTCGCCG
* * * *
41770820 TCTTCGATCTACTTCGCTACCAGTACAGAAAGACAATATATGCTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
* *
41770865 TCTTCGATCTACTTCACTACC-GATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAG-TACAGGAAGACAAGATCTGCTA
* * *
41770910 CCTTCGATCTACTTCGCTGCTAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
* ** * * * * *
41770955 TTTTTTTAACTTACTCCACTG-CTGCT-CAAGG-AGACAAG-GCTTG-TGA
1 -TCTTCGATC-TACTTCGCTGCCAG-TAC-AGGAAGACAAGATC-TGCT-A
* * *
41771001 -CTTCGATCTACTTCGCCGAC-GATACAAGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAG-TACAGGAAGACAAGATCTGCTA
* *
41771045 TCTTCGATCTACTTTGCTGCCAGTACAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
* * * * *
41771090 TCTTCGACCTACTTTGCTGCCAGTACAGAAAGACAAGATCTTCCA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
* *
41771135 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
* * * * * *
41771180 TCTTCGACCTACTTTGCTGCAAGTACAGGGAGACAAAATATGCTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
** * * * *
41771225 TCTTCGATCTACTTTACTGCCAGTACAGAAAGATAAGATCTACCA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
*
41771270 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
* * * *
41771315 TCTTCGATTTACTTCGCTGCCAGTACAAGAAGATAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
* * * * * * * *
41771360 TTTTCAACCTACTTCACTG-CTGCT-CAAGG-AGATAAGGT-TGGTA
1 TCTTCGATCTACTTCGCTGCCAG-TAC-AGGAAGACAAGATCTGCTA
* * *
41771403 TCTTTGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
41771448 T
1 T
41771449 TTTCAACCTA
Statistics
Matches: 466, Mismatches: 97, Indels: 42
0.77 0.16 0.07
Matches are distributed among these distances:
43 31 0.07
44 37 0.08
45 370 0.79
46 16 0.03
47 12 0.03
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGCTA
Found at i:41773700 original size:23 final size:23
Alignment explanation
Indices: 41773673--41773717 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
41773663 TGGCCTCTCT
*
41773673 CTTTTCTTTTCTTTTTATTTTTC
1 CTTTTCTTTTCTTTTGATTTTTC
41773696 CTTTTCTTTTCTTTTGATTTTT
1 CTTTTCTTTTCTTTTGATTTTT
41773718 TTTGAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (23 bp):
CTTTTCTTTTCTTTTGATTTTTC
Found at i:41779958 original size:26 final size:27
Alignment explanation
Indices: 41779911--41779969 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
41779901 CTAAATATAA
41779911 TAAATATATATTTTTTATTTTTTAATTT
1 TAAA-ATATATTTTTTATTTTTTAATTT
* *
41779939 TAAAATATTTTTTTTA-TTTTTATTTT
1 TAAAATATATTTTTTATTTTTTAATTT
41779965 TAAAA
1 TAAAA
41779970 CAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.48
27 11 0.38
28 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TAAAATATATTTTTTATTTTTTAATTT
Found at i:41779978 original size:27 final size:27
Alignment explanation
Indices: 41779920--41779978 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
41779910 ATAAATATAT
* *
41779920 ATTTTTTATTTTTTAATTTTAAAATAT
1 ATTTTTTATTTTTTAATTTTAAAAAAA
* *
41779947 TTTTTTTA-TTTTTATTTTTAAAACAAA
1 ATTTTTTATTTTTTAATTTTAAAA-AAA
41779974 ATTTT
1 ATTTT
41779979 AGTGTTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTTTATTTTTTAATTTTAAAAAAA
Found at i:41783484 original size:9 final size:9
Alignment explanation
Indices: 41783470--41783515 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
41783460 CGAAGAAACA
*
41783470 TCATCATCC
1 TCATCGTCC
*
41783479 TCATCATCC
1 TCATCGTCC
*
41783488 TCATCGTCG
1 TCATCGTCC
41783497 TCATCGTCC
1 TCATCGTCC
41783506 TCATCGTCC
1 TCATCGTCC
41783515 T
1 T
41783516 TTTTGCAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.15, C:0.41, G:0.09, T:0.35
Consensus pattern (9 bp):
TCATCGTCC
Found at i:41784842 original size:13 final size:13
Alignment explanation
Indices: 41784824--41784954 Score: 117
Period size: 13 Copynumber: 10.2 Consensus size: 13
41784814 ATATTAAAAG
*
41784824 TTAAAACATTATA
1 TTAAAACAGTATA
*
41784837 TTAAAACAATATA
1 TTAAAACAGTATA
*
41784850 TTTATAACAGTATA
1 -TTAAAACAGTATA
*
41784864 TTAAAACAATATA
1 TTAAAACAGTATA
*
41784877 TTAAAAAAGTATA
1 TTAAAACAGTATA
* *
41784890 TTTATAATAGTATA
1 -TTAAAACAGTATA
*
41784904 TTAAAACCGTATA
1 TTAAAACAGTATA
*
41784917 TTACAA-A-T-T-
1 TTAAAACAGTATA
*
41784926 TTATAACAGTATA
1 TTAAAACAGTATA
*
41784939 TTAAAATAGTATA
1 TTAAAACAGTATA
41784952 TTA
1 TTA
41784955 CATTAAAAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 5 0.05
10 2 0.02
11 2 0.02
12 1 0.01
13 63 0.66
14 22 0.23
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (13 bp):
TTAAAACAGTATA
Found at i:41784863 original size:27 final size:27
Alignment explanation
Indices: 41784824--41784953 Score: 112
Period size: 27 Copynumber: 5.0 Consensus size: 27
41784814 ATATTAAAAG
*
41784824 TTAAAACATTATATTAAAACAATATAT
1 TTAAAACAGTATATTAAAACAATATAT
*
41784851 TTATAACAGTATATTAAAACAATATA-
1 TTAAAACAGTATATTAAAACAATATAT
* * * *
41784877 TTAAAAAAGTATATTTATAATAGTATA-
1 TTAAAACAGTATA-TTAAAACAATATAT
*
41784904 TTAAAACCGTATATT---ACAA-AT-T
1 TTAAAACAGTATATTAAAACAATATAT
* * *
41784926 TTATAACAGTATATTAAAATAGTATAT
1 TTAAAACAGTATATTAAAACAATATAT
41784953 T
1 T
41784954 ACATTAAAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
22 15 0.19
23 2 0.02
25 2 0.02
26 15 0.19
27 47 0.58
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (27 bp):
TTAAAACAGTATATTAAAACAATATAT
Found at i:41784879 original size:40 final size:40
Alignment explanation
Indices: 41784824--41784954 Score: 166
Period size: 40 Copynumber: 3.4 Consensus size: 40
41784814 ATATTAAAAG
*
41784824 TTAAAACATTATATTAAAACAATATATTTATAACAGTATA
1 TTAAAACAGTATATTAAAACAATATATTTATAACAGTATA
* *
41784864 TTAAAACAATATATTAAAA-AAGTATATTTATAATAGTATA
1 TTAAAACAGTATATTAAAACAA-TATATTTATAACAGTATA
*
41784904 TTAAAACCGTATATT---ACAA-AT-TTTATAACAGTATA
1 TTAAAACAGTATATTAAAACAATATATTTATAACAGTATA
*
41784939 TTAAAATAGTATATTA
1 TTAAAACAGTATATTA
41784955 CATTAAAAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
35 26 0.32
36 2 0.02
37 1 0.01
38 2 0.02
39 2 0.02
40 48 0.59
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (40 bp):
TTAAAACAGTATATTAAAACAATATATTTATAACAGTATA
Found at i:41787432 original size:13 final size:13
Alignment explanation
Indices: 41787414--41787438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41787404 ATTTTTAATG
41787414 TAATATACTGTTT
1 TAATATACTGTTT
41787427 TAATATACTGTT
1 TAATATACTGTT
41787439 ATAAAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:41800763 original size:24 final size:24
Alignment explanation
Indices: 41800731--41800787 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
41800721 GTCCCAAAGG
*
41800731 TTACAGTGGATTGAACCTTGAGGA
1 TTACAGTGGATTGAACCTTGAAGA
41800755 TTACAGTGGATTGAACCTTGAAGA
1 TTACAGTGGATTGAACCTTGAAGA
41800779 TTACAGTGG
1 TTACAGTGG
41800788 GGAAAATCCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (24 bp):
TTACAGTGGATTGAACCTTGAAGA
Found at i:41801158 original size:41 final size:41
Alignment explanation
Indices: 41801058--41801432 Score: 148
Period size: 44 Copynumber: 8.7 Consensus size: 41
41801048 AATTCAATCC
* * *
41801058 TATCTCCCTGAAGTTGTAGTGGAGC-GAATTTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAG-A--TAAAATCA-AG-TCT
** * ***
41801103 TATCTCTTTTAAGTTGCAGTAGAGCAGATCGCATCAAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATAAAATCAAGTCT
* * *
41801144 TATCTCCCTGAAGTTGCAGTGGAGCAGAAAAAAAAAGTCAA-TCC
1 TATCTCCCTGAAGTTGCAGTAGAGCAG---ATAAAA-TCAAGTCT
* * *
41801188 TATCTCCCTGAAGTTGCAGTGGAGCGGATTTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA--TAAAATCA-AG-TCT
* * * *** *
41801233 TATCTCTCTGTAGGTGCAGTAGAGCAGATCGCATAAAGTCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGATAAAATCAAGTCT
* *
41801274 TATCTCCCTGAGGTTGCAGTGGAGAAGACAGA-AGAAA-CTAA-TCC
1 TATCTCCCTGAAGTTGCAGT--AG-AG-CAGATA-AAATC-AAGTCT
* * ** * **
41801318 TATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAATGATAAACCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TAAAAT--CAAGTCT
* ** * **
41801362 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAATAAACCT
1 TATCTCCCTGAAGTTGCAGTAGAGCAGA-TAAAAT--CAAGTCT
*
41801406 TATCTCTCTGAAGTTGCAGTAGAGCAG
1 TATCTCCCTGAAGTTGCAGTAGAGCAG
41801433 GTTGCATCAG
Statistics
Matches: 253, Mismatches: 55, Indels: 45
0.72 0.16 0.13
Matches are distributed among these distances:
40 2 0.01
41 51 0.20
42 8 0.03
43 16 0.06
44 118 0.47
45 57 0.23
46 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (41 bp):
TATCTCCCTGAAGTTGCAGTAGAGCAGATAAAATCAAGTCT
Found at i:41801278 original size:130 final size:131
Alignment explanation
Indices: 41801045--41801351 Score: 460
Period size: 130 Copynumber: 2.4 Consensus size: 131
41801035 GAACAGATTG
* * *
41801045 AAAAATTCAATCCTATCTCCCTGAAGTTGTAGTGGAGCGAATTTAAAACCACAGATCTTATCTCT
1 AAAAACTCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTTAAAACCACAGATCTTATCTCT
* * * *
41801110 TTTAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-AA
66 TGTAAGGTGCAGTAGAGCAGATCGCATAAAGTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACAA
41801174 A
131 A
*
41801175 AAAAAGTCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTTAAAACCACAGATCTTATCTCT
1 AAAAACTCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTTAAAACCACAGATCTTATCTCT
*
41801240 CTGT-AGGTGCAGTAGAGCAGATCGCATAAAGTCTTATCTCCCTGAGGTTGCAGTGGAGAAGACA
66 -TGTAAGGTGCAGTAGAGCAGATCGCATAAAGTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACA
*
41801304 GA
130 AA
* * *
41801306 AGAAACT-AATCCTATCTTCCTGAAGTTGCAGTGGAGTGGA-TTAAAA
1 AAAAACTCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTTAAAA
41801352 TGATAAACCT
Statistics
Matches: 162, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
129 6 0.04
130 147 0.91
131 9 0.06
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (131 bp):
AAAAACTCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTTAAAACCACAGATCTTATCTCT
TGTAAGGTGCAGTAGAGCAGATCGCATAAAGTCTTATCTCCCTGAAGTTGCAGTGGAGAAGACAA
A
Found at i:41801386 original size:44 final size:44
Alignment explanation
Indices: 41801318--41801425 Score: 189
Period size: 44 Copynumber: 2.5 Consensus size: 44
41801308 AAACTAATCC
* *
41801318 TATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAATGATAAACCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAATAAACCT
41801362 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAATAAACCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAATAAACCT
*
41801406 TATCTCTCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGT
41801426 AGAGCAGGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAATAAACCT
Found at i:41804529 original size:44 final size:44
Alignment explanation
Indices: 41804492--41804815 Score: 167
Period size: 44 Copynumber: 7.3 Consensus size: 44
41804482 GGAGTAGGTT
*
41804492 AAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAAATC
1 AAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC
* *** * * * * * * *
41804536 GAAGACCCCAG-CCTTGTCTCCCTGAGTAGCAGTGGAGTAGGTTGAA
1 AAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCA-GAT--C
* *
41804582 AAAAATTACAGATCTTATCTTCCTAAGTAGTAGTGGAGCAGATC
1 AAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC
* * * * * *
41804626 GAAGATGT-TAGATCTTATGTCCCTAAGCAGTAGTGGAGCAAATT
1 AAAGAT-TACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC
* * * * * * * *
41804670 GAAG---CCAGTAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATT
1 AAAGATTACAG--ATCTTATCTCCCT-AAGTAGTAGTGGAGCAGATC
* * * * * *
41804714 AAA-ATAACATATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACC
1 AAAGATTACAGATCTTATCTCCCT-AAGTAGTAGTGGAGCAGATC
* *
41804758 GAAGAATCT-CAGATCTTATCTCCCTAAGTAGTAGTGGAGCATATC
1 AAAG-AT-TACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC
* *
41804803 GAAGATAACAGAT
1 AAAGATTACAGAT
41804816 TTTACCTACC
Statistics
Matches: 204, Mismatches: 60, Indels: 32
0.69 0.20 0.11
Matches are distributed among these distances:
41 2 0.01
43 33 0.16
44 100 0.49
45 21 0.10
46 26 0.13
47 22 0.11
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
AAAGATTACAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATC
Found at i:41804570 original size:87 final size:88
Alignment explanation
Indices: 41804458--41804630 Score: 260
Period size: 90 Copynumber: 2.0 Consensus size: 88
41804448 TCAAAAACAA
* *
41804458 AGCCTTGCCTCCCTCGGTTGCAGTGGAGTAGGTT-AAAGATTACAGATCTTATCTCCCTAAGTAG
1 AGCCTTGCCTCCCTCGGTAGCAGTGGAGTAGGTTAAAAAATTACAGATCTTATCTCCCTAAGTAG
41804522 TAGTGGAGCAAATCGAAGACCCC
66 TAGTGGAGCAAATCGAAGACCCC
* *
41804545 AGCCTTGTCTCCCT-GAGTAGCAGTGGAGTAGGTTGAAAAAAATTACAGATCTTATCTTCCTAAG
1 AGCCTTGCCTCCCTCG-GTAGCAGTGGAGTAGGTT--AAAAAATTACAGATCTTATCTCCCTAAG
*
41804609 TAGTAGTGGAGCAGATCGAAGA
63 TAGTAGTGGAGCAAATCGAAGA
41804631 TGTTAGATCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
86 1 0.01
87 30 0.39
90 46 0.60
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (88 bp):
AGCCTTGCCTCCCTCGGTAGCAGTGGAGTAGGTTAAAAAATTACAGATCTTATCTCCCTAAGTAG
TAGTGGAGCAAATCGAAGACCCC
Found at i:41804876 original size:178 final size:177
Alignment explanation
Indices: 41804590--41804925 Score: 494
Period size: 178 Copynumber: 1.9 Consensus size: 177
41804580 AAAAAAATTA
* *** ** *
41804590 CAGATCTTATCTTCCTAAGTAGTAGTGGAGCAGATCGAAGATGTTAGATCTTATGTCCCTAAGCA
1 CAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATAACAGATCTTACCTACCTAAGCA
* *
41804655 GTAGTGGAGCAAATTGAAGCCAGTAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATA
66 GTAGTGGAGCAAATTGAAGCCACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATA
*
41804720 ACATATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACCGAAGAATCT
131 ACAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACCGAAGAATCT
* * * *
41804767 CAGATCTTATCTCCCTAAGTAGTAGTGGAGCATATCGAAGATAACAGATTTTACCTACCTGAGGA
1 CAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATAACAGATCTTACCTACCTAAGCA
* *
41804832 -TACAGTGGAGTACATTGAAGCCACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
66 GT--AGTGGAGCAAATTGAAGCCACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
*
41804896 TAACAGATCTTATCTCTCTGAGGTTGCAGT
129 TAACAGATCTTATCTCTCTGAAGTTGCAGT
41804926 AGAGTAGATC
Statistics
Matches: 140, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
176 1 0.01
177 54 0.39
178 85 0.61
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (177 bp):
CAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATAACAGATCTTACCTACCTAAGCA
GTAGTGGAGCAAATTGAAGCCACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATA
ACAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACCGAAGAATCT
Found at i:41804910 original size:44 final size:44
Alignment explanation
Indices: 41804684--41805456 Score: 199
Period size: 44 Copynumber: 17.6 Consensus size: 44
41804674 CCAGTAATCC
* * *
41804684 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATAACATATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
* ** **
41804728 TATCTCTCTGAAGTTGCAGTGGAGCAGACCGAAGAATCTCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATAACAGATCT
* * * * * *
41804774 TATCTCCCT-AAGTAGTAGTGGAGCATATCGAAGATAACAGATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAATAACAGATCT
* * * * * * * * *** *
41804818 TACCTACCTGAGGATACAGTGGAGTACATTGAAGCCACTA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAC-AGATCT
*
41804862 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
* * * * ** * *
41804906 TATCTCTCTGAGGTTGCAGTAGAGTAGA-T--CGTATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
* * * * * ** * *
41804947 TATCTCCTTGGAGTTGCAGCGAAGTAGACCGAAGAATTACAGATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATAACAGATCT
* ** * * * * ***
41804993 TATCTTCCT-AAGCAGTAGTGGAGCGGATCGAAGAT-GGTGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAATAACAG-ATCT
* * * ** * *
41805037 TATCTCCCTG-AGTTTGTAGTGGAGGAGATT-GAA-GCCGGTAATCC
1 TATCTCCCTGAAG-TTGCAGTGGAGCAGATTAAAATAACAG--ATCT
* * *
41805081 TATCCCCCTGAAGTTACAGTGGAGCAGATTAAAAATAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATAACAGATCT
* * ** * * * *
41805126 TATCTCTCTGAGGTTGCAGCAGAGTAGA-TCACAT--CAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
* * ** ** * *
41805167 TATCTCCCTGAGGTTACAACGGAGCAGACCGAGAA-AGCA-AGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATAACAGA-TCT
* * * ***
41805211 TATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGAT-GGTGAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATAACAG-ATCT
* ** *** *
41805256 TATCTCCCTG-AGTTCACAGTGGAGCAGATTGAAGCTTGTA-ATCC
1 TATCTCCCTGAAGTT-GCAGTGGAGCAGATT-AAAATAACAGATCT
* * *
41805300 TATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
* ** * * * *
41805344 TATCTCTCTGAAGTTGCAGCAGAGTAGA-T--CATATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
* * * * * *
41805385 TATCTCCCTGAGGTTACAGCGGAGCAGACTGAGAA-AGCA-AGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATAACAGA-TCT
*
41805429 TATC-CCACTGAAGTTGCAGTGGGGCAGA
1 TATCTCC-CTGAAGTTGCAGTGGAGCAGA
41805457 CTGAAGACGA
Statistics
Matches: 510, Mismatches: 179, Indels: 80
0.66 0.23 0.10
Matches are distributed among these distances:
41 87 0.17
43 16 0.03
44 253 0.50
45 119 0.23
46 34 0.07
47 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCT
Found at i:41804982 original size:219 final size:218
Alignment explanation
Indices: 41804725--41805413 Score: 816
Period size: 219 Copynumber: 3.1 Consensus size: 218
41804715 AAATAACATA
* *
41804725 TCTTATCT-CTCTGAAGTTGCAGTGGAGCAGACCGAAGAATCTCAGATCTTATCTCCCTAAGTAG
1 TCTTATCTCCT-TGGAGTTGCAGCGGAGCAGACCGAAGAAT-TCAGATCTTATCTCCCTAAGTAG
* *** * * * * * *
41804789 TAGTGGAGCATATCGAAGAT-AACAGATTTTACCTACCTGAGGATACAGTGGAGTACATTGAAGC
64 TAGTGGAGCAGATCGAAGATGGTGA-ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC
* * *
41804853 CACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAACAGATCTTATCTCTCTGAG
128 CAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGATCTTATCTCTCTGAG
* *
41804918 GTTGCAGTAGAGTAGATCGTATCAGG
193 GTTGCAGCAGAGTAGATCATATCAGG
* * * * *
41804944 TCTTATCTCCTTGGAGTTGCAGCGAAGTAGACCGAAGAATTACAGATTTTATCTTCCTAAGCAGT
1 TCTTATCTCCTTGGAGTTGCAGCGGAGCAGACCGAAGAATT-CAGATCTTATCTCCCTAAGTAGT
* * ** * *
41805009 AGTGGAGCGGATCGAAGATGGTGAATCTTATCTCCCTGAGTTTGTAGTGGAGGAGATTGAAGCCG
65 AGTGGAGCAGATCGAAGATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA
* *
41805074 GTAATCCTATCCCCCTGAAGTTACAGTGGAGCAGATTAAAAATAATAGATCTTATCTCTCTGAGG
130 GTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAATAATAGATCTTATCTCTCTGAGG
*
41805139 TTGCAGCAGAGTAGATCACATCAGG
194 TTGCAGCAGAGTAGATCATATCAGG
* * * ** * *
41805164 TCTTATCTCCCT-GAGGTTACAACGGAGCAGACCG-AGAAAGCA-AGTCTTATCCCCCTAAAGTT
1 TCTTATCTCCTTGGA-GTTGCAGCGGAGCAGACCGAAGAATTCAGA-TCTTATCTCCCT-AAGTA
* *
41805226 GCAGTGGAGCAGATTGAAGATGGTGAATCTTATCTCCCTGA-GTTCACAGTGGAGCAGATTGAAG
63 GTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTCCCTGAGGTT-ACAGTGGAGCAGATTGAAG
** * *
41805290 CTTGTAATCCTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACAATAGATCTTATCTCTCTGA
127 CCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGATCTTATCTCTCTGA
*
41805355 AGTTGCAGCAGAGTAGATCATATCAGG
192 GGTTGCAGCAGAGTAGATCATATCAGG
* *
41805382 TCTTATCTCCCT-GAGGTTACAGCGGAGCAGAC
1 TCTTATCTCCTTGGA-GTTGCAGCGGAGCAGAC
41805414 TGAGAAAGCA
Statistics
Matches: 404, Mismatches: 58, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
217 1 0.00
218 94 0.23
219 232 0.57
220 77 0.19
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (218 bp):
TCTTATCTCCTTGGAGTTGCAGCGGAGCAGACCGAAGAATTCAGATCTTATCTCCCTAAGTAGTA
GTGGAGCAGATCGAAGATGGTGAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAATAGATCTTATCTCTCTGAGGTT
GCAGCAGAGTAGATCATATCAGG
Found at i:41805276 original size:45 final size:44
Alignment explanation
Indices: 41805211--41805329 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 44
41805201 AAGCAAGTCT
* * * *
41805211 TATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGATGGTGAATCT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATGGT-AATCC
* *
41805256 TATCTCCCTG-AGTTCACAGTGGAGCAGATTGAAGCTTGTAATCC
1 TATCTCCCTGAAGTT-ACAGTGGAGCAGATTGAAGATGGTAATCC
* *
41805300 TATCTCCCTGAAGTTGCAGTGGATCAGATT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT
41805330 AAAACAATAG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
44 31 0.48
45 33 0.52
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATGGTAATCC
Found at i:41805430 original size:218 final size:217
Alignment explanation
Indices: 41804833--41805463 Score: 836
Period size: 219 Copynumber: 2.9 Consensus size: 217
41804823 ACCTGAGGAT
* * * *
41804833 ACAGTGGAGTACATTGAAGCCACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATA
1 ACAGTGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATA
* * * *
41804898 ACAGATCTTATCTCTCTGAGGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCTTG-GAGTT
66 ATAGATCTTATCTCTCTGAGGTTGCAGCAGAGTAGATCATATCAGGTCTTATCTCCCTGAG-GTT
* * * * ** ** * * *
41804962 GCAGCGAAGTAGACCGAAGAATTA-C-AGATTTTATCTTCCTAAGCAGTAGTGGAGCGGATCGAA
130 ACAGCGGAGCAGACCG-AGAA--AGCAAG-TCTTATCCCCCTAAGTTGCAGTGGAGCAGATTGAA
*
41805025 GATGGTGAATCTTATCTCCCTGAGTTT
191 GATGGTGAATCTTATCTCCCTGAGTTC
** * * * *
41805052 GTAGTGGAGGAGATTGAAGCCGGTAATCCTATCCCCCTGAAGTTACAGTGGAGCAGATTAAAAAT
1 ACAGTGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAAT
*
41805117 AATAGATCTTATCTCTCTGAGGTTGCAGCAGAGTAGATCACATCAGGTCTTATCTCCCTGAGGTT
65 AATAGATCTTATCTCTCTGAGGTTGCAGCAGAGTAGATCATATCAGGTCTTATCTCCCTGAGGTT
*
41805182 ACAACGGAGCAGACCGAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGAT
130 ACAGCGGAGCAGACCGAGAAAGCAAGTCTTATCCCCCT-AAGTTGCAGTGGAGCAGATTGAAGAT
41805247 GGTGAATCTTATCTCCCTGAGTTC
194 GGTGAATCTTATCTCCCTGAGTTC
** * *
41805271 ACAGTGGAGCAGATTGAAGCTTGTAATCCTATCTCCCTGAAGTTGCAGTGGATCAGATTAAAACA
1 ACAGTGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATA
*
41805336 ATAGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATCATATCAGGTCTTATCTCCCTGAGGTTA
66 ATAGATCTTATCTCTCTGAGGTTGCAGCAGAGTAGATCATATCAGGTCTTATCTCCCTGAGGTTA
* * * *
41805401 CAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCACTGAAGTTGCAGTGGGGCAGACTGAAGA
131 CAGCGGAGCAGACCGAGAAAGCAAGTCTTATCCCCCT-AAGTTGCAGTGGAGCAGATTGAAGA
41805464 CGAAAAATCT
Statistics
Matches: 363, Mismatches: 44, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
217 1 0.00
218 135 0.37
219 151 0.42
220 75 0.21
221 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (217 bp):
ACAGTGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATA
ATAGATCTTATCTCTCTGAGGTTGCAGCAGAGTAGATCATATCAGGTCTTATCTCCCTGAGGTTA
CAGCGGAGCAGACCGAGAAAGCAAGTCTTATCCCCCTAAGTTGCAGTGGAGCAGATTGAAGATGG
TGAATCTTATCTCCCTGAGTTC
Found at i:41805733 original size:95 final size:95
Alignment explanation
Indices: 41805469--41805738 Score: 265
Period size: 95 Copynumber: 2.8 Consensus size: 95
41805459 GAAGACGAAA
* * * * *
41805469 AATCTTAC-TTCCCAGGCAGTGCAGTAGAACAGATTAAAGCCACAACGACGAATCTTACTTCCCT
1 AATCTTACTTTCCTA-GCAGTGCAGTGGAACAGATTAAAGCCACGACGGCGAATCTTATTTCCCT
*
41805533 GACATTGCAGTTAAATAGATTGAAGCCACGACAGCG
65 GACATTGCAG-----TAGATTGAAGCCACAACAGCG
* * * ** * *
41805569 AATCTTACTTTCCTAGCAGTGCAGTGGAACAGATTAAAACTACGACGGTGAATCTCGTTTCTCTA
1 AATCTTACTTTCCTAGCAGTGCAGTGGAACAGATTAAAGCCACGACGGCGAATCTTATTTCCCTG
* *
41805634 ACATTGCAGTAGATTGAAGCCATAACGGCG
66 ACATTGCAGTAGATTGAAGCCACAACAGCG
* * * * * *
41805664 AATCTTAC-TTCTTTGACGGTGTAGTGGAACAGATTGAAGCCACGACGGCGAATCTTATTTCCCC
1 AATCTTACTTTCCTAG-CAGTGCAGTGGAACAGATTAAAGCCACGACGGCGAATCTTATTTCCCT
*
41805728 GACATTACAGT
65 GACATTGCAGT
41805739 TAAACAGATT
Statistics
Matches: 139, Mismatches: 29, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
94 5 0.04
95 73 0.53
100 56 0.40
101 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (95 bp):
AATCTTACTTTCCTAGCAGTGCAGTGGAACAGATTAAAGCCACGACGGCGAATCTTATTTCCCTG
ACATTGCAGTAGATTGAAGCCACAACAGCG
Found at i:41805745 original size:50 final size:50
Alignment explanation
Indices: 41805469--41805752 Score: 188
Period size: 50 Copynumber: 5.8 Consensus size: 50
41805459 GAAGACGAAA
* * * * * * *
41805469 AATCTTACTTCCCAGGCAGTGCAG-TAGAACAGATTAAAGCCACAACGACG
1 AATCTTATTTCCCTGACATTGCAGTTA-AACAGATTGAAGCCACGACGGCG
* * *
41805519 AATCTTACTTCCCTGACATTGCAGTTAAATAGATTGAAGCCACGACAGCG
1 AATCTTATTTCCCTGACATTGCAGTTAAACAGATTGAAGCCACGACGGCG
* ** * * * *
41805569 AATCTTACTTT-CCT-AGCAGTGCAGTGGAACAGATTAAAACTACGACGGTG
1 AATCTTA-TTTCCCTGA-CATTGCAGTTAAACAGATTGAAGCCACGACGGCG
** * * **
41805619 AATCTCGTTTCTCTAACATTGCAG-T----AGATTGAAGCCATAACGGCG
1 AATCTTATTTCCCTGACATTGCAGTTAAACAGATTGAAGCCACGACGGCG
* ** ** * **
41805664 AATCTTACTTCTTTGACGGTGTAGTGGAACAGATTGAAGCCACGACGGCG
1 AATCTTATTTCCCTGACATTGCAGTTAAACAGATTGAAGCCACGACGGCG
* *
41805714 AATCTTATTTCCCCGACATTACAGTTAAACAGATTGAAG
1 AATCTTATTTCCCTGACATTGCAGTTAAACAGATTGAAG
41805753 ACAGTAATCC
Statistics
Matches: 174, Mismatches: 50, Indels: 20
0.71 0.20 0.08
Matches are distributed among these distances:
45 30 0.17
49 4 0.02
50 135 0.78
51 5 0.03
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (50 bp):
AATCTTATTTCCCTGACATTGCAGTTAAACAGATTGAAGCCACGACGGCG
Found at i:41807145 original size:5 final size:6
Alignment explanation
Indices: 41807093--41807150 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
41807083 ACCAATTTAG
* * * *
41807093 TTTATC TTTATT TTTCCTT TTTATT TCTATT TGTAATGT TTTATT TTTATT
1 TTTATT TTTATT TTT-ATT TTTATT TTTATT T-TTAT-T TTTATT TTTATT
41807144 TTTATT T
1 TTTATT T
41807151 GAATTCCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
6 30 0.71
7 10 0.24
8 2 0.05
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:41807184 original size:3 final size:3
Alignment explanation
Indices: 41807176--41807257 Score: 137
Period size: 3 Copynumber: 27.3 Consensus size: 3
41807166 TTTTTAATCC
* *
41807176 TAT TAT TAT TAT TAT TAT TAC TAC TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
41807224 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41807258 CCTTCTTTAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:41808008 original size:123 final size:123
Alignment explanation
Indices: 41807789--41808136 Score: 599
Period size: 123 Copynumber: 2.8 Consensus size: 123
41807779 TTATTTCGAG
* *
41807789 TTGACATTTCTG-GTCAAATAGTATAAAATCGCTTCTACTAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAGT-AAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
41807853 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAGAATTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAGAATTTTT
*
41807912 TTGACGTTTCTGAGTAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
41807977 AAATCACGCCCTCGTGAACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAGAATTTTT
* * *
41808035 TTAACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAATAAATTGTG
1 TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
41808100 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
41808137 CAAGTTTGGG
Statistics
Matches: 212, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 210 0.99
124 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAGAATTTTT
Found at i:41811523 original size:50 final size:50
Alignment explanation
Indices: 41811448--41811547 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
41811438 NNNNNNNNNN
* * *
41811448 GTTTTTTAATTAAGTTAGGGTAGGGGTTAGGGTTTTTAATTTAAGTTAGG
1 GTTTTTTAATTAAATTAGGGTAGGGGTTAGGGTTTTTAATTAAAATTAGG
* *
41811498 GTTTTTTAATTAAATTCGGTTAGGGGTTAGGGTTTTTAATTAAAATTAGG
1 GTTTTTTAATTAAATTAGGGTAGGGGTTAGGGTTTTTAATTAAAATTAGG
41811548 TTAGGGGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.46
Consensus pattern (50 bp):
GTTTTTTAATTAAATTAGGGTAGGGGTTAGGGTTTTTAATTAAAATTAGG
Found at i:41811579 original size:32 final size:32
Alignment explanation
Indices: 41811492--41811581 Score: 139
Period size: 31 Copynumber: 2.9 Consensus size: 32
41811482 TTTAATTTAA
*
41811492 GTTAGGGTTTTTTAA-TTAAATTCGGTTAGGG
1 GTTAGGGTTTTTTAATTTAAATTAGGTTAGGG
*
41811523 GTTAGGG-TTTTTAATTAAAATTAGGTTAGGG
1 GTTAGGGTTTTTTAATTTAAATTAGGTTAGGG
*
41811554 GTTAGGGTTTTTTAATTTAAGTTAGGTT
1 GTTAGGGTTTTTTAATTTAAATTAGGTT
41811582 CTTAATTAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 7 0.13
31 28 0.53
32 18 0.34
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (32 bp):
GTTAGGGTTTTTTAATTTAAATTAGGTTAGGG
Found at i:41811592 original size:17 final size:18
Alignment explanation
Indices: 41811565--41811598 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
41811555 TTAGGGTTTT
41811565 TTAATTTAAGTTAGGTTC
1 TTAATTTAAGTTAGGTTC
41811583 TTAA-TTAAGTTAGGTT
1 TTAATTTAAGTTAGGTT
41811599 AGGGTTAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (18 bp):
TTAATTTAAGTTAGGTTC
Found at i:41811615 original size:29 final size:29
Alignment explanation
Indices: 41811581--41811654 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
41811571 TAAGTTAGGT
41811581 TCTTAATTAAGTTAGGTTAGGGTTAGGCC
1 TCTTAATTAAGTTAGGTTAGGGTTAGGCC
**
41811610 TCTTAATTAAGTTAGGTTAGGGTTAGGGT
1 TCTTAATTAAGTTAGGTTAGGGTTAGGCC
*
41811639 TTTTAATTAAGTTAGG
1 TCTTAATTAAGTTAGG
41811655 GTTTTTAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.26, C:0.05, G:0.27, T:0.42
Consensus pattern (29 bp):
TCTTAATTAAGTTAGGTTAGGGTTAGGCC
Found at i:41811654 original size:18 final size:18
Alignment explanation
Indices: 41811631--41811796 Score: 202
Period size: 18 Copynumber: 9.3 Consensus size: 18
41811621 TTAGGTTAGG
41811631 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
41811649 GTTAGGGTTTTTAATTAAATTA
1 GTTAGGGTTTTTAATT--A--A
41811671 GGTTAGGGTTTTTAATTAA
1 -GTTAGGGTTTTTAATTAA
**
41811690 GTTA-GG---TT-A-GGA
1 GTTAGGGTTTTTAATTAA
41811702 -TTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
41811719 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
41811737 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
41811755 TTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
41811773 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
41811791 ATTAGG
1 GTTAGG
41811797 TTAGGGTTAG
Statistics
Matches: 129, Mismatches: 7, Indels: 24
0.81 0.04 0.15
Matches are distributed among these distances:
11 3 0.02
12 3 0.02
13 1 0.01
14 2 0.02
15 2 0.02
16 1 0.01
17 3 0.02
18 94 0.73
19 1 0.01
20 1 0.01
21 1 0.01
22 1 0.01
23 16 0.12
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:41811654 original size:47 final size:46
Alignment explanation
Indices: 41811612--41811996 Score: 331
Period size: 47 Copynumber: 8.3 Consensus size: 46
41811602 GTTAGGCCTC
*
41811612 TTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGG-TT
41811659 TTAATT-AA--A--TTA-GGTTAGGGTTTTTAATTAAGTTA-GGTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTT
*** ** * *
41811698 AGGATTAGGGTTTTTA-ATTA-AGTTAGGGTTTTTAATTAAGTTAGGG-T
1 TTAATTA----AATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTT
*
41811745 TT--TT-AATTA----A--TTTAGGGTTTTTAATTAAGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGG-TT
41811783 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGG--TTT--TTAA-TTA----A--GTTAGGG-TT
*
41811841 TTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTT
*
41811887 TTAATTAAATTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGG-TT
* *
41811934 TTAATTAAATTAGATTAGGGTTAGGGTTTTTAATTAAGTTAGGTTT
1 TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTT
*
41811980 TTAATCAAATTATGGTT
1 TTAATTAAATTA-GGTT
41811997 TTTATTACAT
Statistics
Matches: 284, Mismatches: 21, Indels: 66
0.77 0.06 0.18
Matches are distributed among these distances:
36 24 0.08
37 1 0.00
38 3 0.01
39 5 0.02
40 7 0.02
41 28 0.10
42 3 0.01
44 1 0.00
45 3 0.01
46 59 0.21
47 91 0.32
48 2 0.01
49 4 0.01
51 4 0.01
52 3 0.01
53 3 0.01
54 4 0.01
56 4 0.01
58 35 0.12
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.47
Consensus pattern (46 bp):
TTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGGTT
Found at i:41811706 original size:29 final size:29
Alignment explanation
Indices: 41811650--41811883 Score: 219
Period size: 29 Copynumber: 7.8 Consensus size: 29
41811640 TTTAATTAAG
41811650 TTAGGGTTTTTAATTAA---A--TTAGG-
1 TTAGGGTTTTTAATTAAGTTAGGTTAGGA
41811673 TTAGGGTTTTTAATTAAGTTAGGTTAGGA
1 TTAGGGTTTTTAATTAAGTTAGGTTAGGA
**
41811702 TTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAA
1 TTAGGGTTTTTAATTAAGTTA-GG---TT-A-GGA
* **
41811737 GTTAGGGTTTTTAATTAATTTAGGGTTTTTAATTAA
1 -TTAGGGTTTTTAATTAAGTTA-GG---TT-A-GGA
* *
41811773 GTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 -TTAGGGTTTTTAATTAAGTTAGGTTAGGA
*
41811803 TTAGGGTTTTTAATTAAGTTAGGTTAGGG
1 TTAGGGTTTTTAATTAAGTTAGGTTAGGA
*
41811832 TTAGGGTTTTTAATTAAGTTAGGTTAGGG
1 TTAGGGTTTTTAATTAAGTTAGGTTAGGA
41811861 TTAGGGTTTTTAATTAAGTTAGG
1 TTAGGGTTTTTAATTAAGTTAGG
41811884 GTTTTAATTA
Statistics
Matches: 190, Mismatches: 8, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.09
26 1 0.01
28 5 0.03
29 101 0.53
30 2 0.01
31 1 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 3 0.02
36 55 0.29
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (29 bp):
TTAGGGTTTTTAATTAAGTTAGGTTAGGA
Found at i:41811890 original size:17 final size:18
Alignment explanation
Indices: 41811860--41811946 Score: 73
Period size: 18 Copynumber: 5.3 Consensus size: 18
41811850 TTAGGTTAGG
41811860 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
41811878 GTTAGGG-TTTTAATTAA
1 GTTAGGGTTTTTAATTAA
* **
41811895 ATTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
*
41811906 GTTAGGATTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
41811924 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
41811942 ATTAG
1 GTTAG
41811947 ATTAGGGTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
11 3 0.06
12 1 0.02
13 1 0.02
14 2 0.04
15 2 0.04
16 3 0.06
17 13 0.25
18 28 0.53
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:41811934 original size:46 final size:47
Alignment explanation
Indices: 41811523--41811854 Score: 163
Period size: 47 Copynumber: 7.1 Consensus size: 47
41811513 TCGGTTAGGG
41811523 GTTAGGGTTTTTAATTAAAATTAGGTTAGGGGTTAGGGTTTTTTAATTTAA
1 GTTAGGGTTTTTAATT-AAATTAGGTTA-GGGTTAGGG-TTTTTAA-TTAA
* * * *
41811574 GTTA-GGTTCTTAATTAAGTTAGGTTAGGGTTAGGCCTCTTAATTAAGTTAG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGG-GT-TT--TTAA-TTAA
* *
41811625 GTTAGGGTTAGGGTTT--TT-AATTAAGTTAGGGTT----TTTAATTAAATTAG
1 GTTAGGGTT----TTTAATTAAATTAGGTTAGGGTTAGGGTTT--TT-AATTAA
* *
41811672 GTTAGGGTTTTTAATTAAGTTAGGTTAGGATTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
41811719 GTTAGGG--TTT--TT-AATTA----A--GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
* * * * * * *
41811755 TTTAGGGTTTTTAATTAAGTTAGGGTT---TTTA--ATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTAGGGTT--TTTA-ATTA-A
*
41811802 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
41811849 GTTAGG
1 GTTAGG
41811855 TTAGGGTTAG
Statistics
Matches: 218, Mismatches: 27, Indels: 76
0.68 0.08 0.24
Matches are distributed among these distances:
36 23 0.11
38 4 0.02
40 2 0.01
41 4 0.02
42 4 0.02
43 7 0.03
45 11 0.05
46 19 0.09
47 58 0.27
48 17 0.08
49 18 0.08
50 13 0.06
51 17 0.08
52 4 0.02
53 13 0.06
54 2 0.01
56 2 0.01
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (47 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
Found at i:41811980 original size:17 final size:18
Alignment explanation
Indices: 41811953--41812000 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
41811943 TTAGATTAGG
*
41811953 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATCAA
41811971 GTTA-GGTTTTTAATCAA
1 GTTAGGGTTTTTAATCAA
* *
41811988 ATTATGGTTTTTA
1 GTTAGGGTTTTTA
41812001 TTACATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.52
Consensus pattern (18 bp):
GTTAGGGTTTTTAATCAA
Found at i:41812048 original size:25 final size:26
Alignment explanation
Indices: 41811996--41812059 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
41811986 AAATTATGGT
41811996 TTTTATTACATCAAATAGAACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
* *
41812022 TTTTATTATATTAAATA-AACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
*
41812047 TTTTTTTACATCA
1 TTTTATTACATCA
41812060 GATAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 18 0.55
26 15 0.45
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATAGAACTTCTA
Found at i:41812495 original size:18 final size:18
Alignment explanation
Indices: 41812468--41812502 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41812458 CGGAAAAGGA
* *
41812468 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
41812486 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
41812503 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:41813164 original size:7 final size:7
Alignment explanation
Indices: 41813154--41813178 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41813144 TTATATACAT
41813154 AATACTA
1 AATACTA
41813161 AATACTA
1 AATACTA
41813168 AATACTA
1 AATACTA
41813175 AATA
1 AATA
41813179 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:41816153 original size:13 final size:13
Alignment explanation
Indices: 41816126--41816160 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41816116 TTGTTTCAAA
*
41816126 ATTATT-TTACAT
1 ATTATTATTCCAT
41816138 ATTATTATTCCAT
1 ATTATTATTCCAT
41816151 ATTATTATTC
1 ATTATTATTC
41816161 TTTTGTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTATTATTCCAT
Found at i:41817173 original size:13 final size:13
Alignment explanation
Indices: 41817155--41817246 Score: 103
Period size: 13 Copynumber: 6.9 Consensus size: 13
41817145 GGTTTCGACA
*
41817155 ATACTATTTTAAT
1 ATACTGTTTTAAT
* *
41817168 ATACTATTATAAAT
1 ATACTGTT-TTAAT
*
41817182 ATACTTTTTTAAT
1 ATACTGTTTTAAT
*
41817195 ATATTGTTTTAAT
1 ATACTGTTTTAAT
*
41817208 ATACTGTTATAAAT
1 ATACTGTT-TTAAT
41817222 ATACTGTTTTAAT
1 ATACTGTTTTAAT
*
41817235 ATATTGTTTTAA
1 ATACTGTTTTAA
41817247 CTTTTAATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
13 45 0.66
14 23 0.34
ACGTcount: A:0.37, C:0.05, G:0.04, T:0.53
Consensus pattern (13 bp):
ATACTGTTTTAAT
Found at i:41817205 original size:40 final size:40
Alignment explanation
Indices: 41817161--41817246 Score: 154
Period size: 40 Copynumber: 2.1 Consensus size: 40
41817151 GACAATACTA
*
41817161 TTTTAATATACTATTATAAATATACTTTTTTAATATATTG
1 TTTTAATATACTATTATAAATATACTGTTTTAATATATTG
*
41817201 TTTTAATATACTGTTATAAATATACTGTTTTAATATATTG
1 TTTTAATATACTATTATAAATATACTGTTTTAATATATTG
41817241 TTTTAA
1 TTTTAA
41817247 CTTTTAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (40 bp):
TTTTAATATACTATTATAAATATACTGTTTTAATATATTG
Found at i:41817227 original size:14 final size:13
Alignment explanation
Indices: 41817155--41817272 Score: 86
Period size: 13 Copynumber: 9.3 Consensus size: 13
41817145 GGTTTCGACA
* *
41817155 ATACTATTTTAAT
1 ATACTGTTTAAAT
*
41817168 ATACTATTATAAAT
1 ATACTGTT-TAAAT
* *
41817182 ATACTTTTTTAAT
1 ATACTGTTTAAAT
* *
41817195 ATATTGTTTTAAT
1 ATACTGTTTAAAT
41817208 ATACTGTTATAAAT
1 ATACTGTT-TAAAT
*
41817222 ATACTGTTTTAAT
1 ATACTGTTTAAAT
*
41817235 ATATTGTTT---T
1 ATACTGTTTAAAT
41817245 A-ACT-TTT-AAT
1 ATACTGTTTAAAT
41817255 ATACTGTTATAAAT
1 ATACTGTT-TAAAT
41817269 ATAC
1 ATAC
41817273 ATCTAATTTG
Statistics
Matches: 87, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
8 3 0.03
9 2 0.02
10 4 0.05
11 3 0.03
12 2 0.02
13 43 0.49
14 30 0.34
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (13 bp):
ATACTGTTTAAAT
Found at i:41818718 original size:19 final size:19
Alignment explanation
Indices: 41818677--41818743 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
41818667 TACATTTATT
* *
41818677 TTAGATTTTTTGAACTTCTA
1 TTAGATTTTTT-AAATTCAA
41818697 TTAGATTTTTTAAATTCAA
1 TTAGATTTTTTAAATTCAA
* * *
41818716 TTAGATTTTTTAGATTTAC
1 TTAGATTTTTTAAATTCAA
41818735 TTAGATTTT
1 TTAGATTTT
41818744 AAGTTTAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 31 0.74
20 11 0.26
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (19 bp):
TTAGATTTTTTAAATTCAA
Found at i:41818941 original size:27 final size:27
Alignment explanation
Indices: 41818911--41818962 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
41818901 TATTTCTTTG
41818911 AAGTTAAGATTAGATTTTTAA-ATTATT
1 AAGTTAA-ATTAGATTTTTAATATTATT
*
41818938 AAGTTTAATTAGATTTTTAATATTA
1 AAGTTAAATTAGATTTTTAATATTA
41818963 AATTAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (27 bp):
AAGTTAAATTAGATTTTTAATATTATT
Found at i:41819656 original size:18 final size:19
Alignment explanation
Indices: 41819635--41819670 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41819625 AAAAATTCAC
*
41819635 ATAAA-TATTTTAATTGAA
1 ATAAAGTATTTAAATTGAA
41819653 ATAAAGTATTTAAATTGA
1 ATAAAGTATTTAAATTGA
41819671 GTTGAGGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
ATAAAGTATTTAAATTGAA
Done.