Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 65 of 226
Found at i:25209678 original size:27 final size:26
Alignment explanation
Indices: 25209505--25209682 Score: 77
Period size: 27 Copynumber: 6.6 Consensus size: 26
25209495 AGTTTATTAA
*
25209505 TTTTATATTTTCATAATTTATTAAAAT
1 TTTTATATTTT-ATAATTTATTATAAT
* *
25209532 TTTTATATTTTATAATAT-TTACAAGTT
1 TTTTATATTTTATAATTTATTATAA--T
*
25209559 TTTTATATTTTTTTATAATTT-TAATAA-
1 TTTTATA---TTTTATAATTTATTATAAT
* * *
25209586 GTTTATATTAATTCTAATATTTTTA-AAGT
1 TTTTATATT--TTATAAT-TTATTATAA-T
*
25209615 TTTTA-ATGTTTAATATATTTATTTTTAA-
1 TTTTATAT-TTT-ATA-ATTTA-TTATAAT
*
25209643 TTCT-T-TTTTATAATTTATTATAAT
1 TTTTATATTTTATAATTTATTATAAT
25209667 TTTTAATATTTT-TAAT
1 TTTT-ATATTTTATAAT
25209683 CATTTTTATG
Statistics
Matches: 115, Mismatches: 15, Indels: 43
0.66 0.09 0.25
Matches are distributed among these distances:
23 5 0.04
24 10 0.09
25 8 0.07
26 20 0.17
27 36 0.31
28 11 0.10
29 9 0.08
30 16 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTATATTTTATAATTTATTATAAT
Found at i:25209982 original size:23 final size:24
Alignment explanation
Indices: 25209952--25209997 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
25209942 AATTTGAAAT
25209952 TTAAAAATAAAAAGAC-TAAATTC
1 TTAAAAATAAAAAGACATAAATTC
*
25209975 TTAAAAATAAAAATACATAAATT
1 TTAAAAATAAAAAGACATAAATT
25209998 AAATTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (24 bp):
TTAAAAATAAAAAGACATAAATTC
Found at i:25220202 original size:9 final size:10
Alignment explanation
Indices: 25220165--25220205 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
25220155 TCGTTTATAT
25220165 ATTTTAATTA
1 ATTTTAATTA
*
25220175 GTTTTTAATTA
1 -ATTTTAATTA
25220186 ATTTTAATTA
1 ATTTTAATTA
25220196 A-TTTAATTA
1 ATTTTAATTA
25220205 A
1 A
25220206 CCTAAGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 9 0.32
10 10 0.36
11 9 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
ATTTTAATTA
Found at i:25220796 original size:26 final size:27
Alignment explanation
Indices: 25220759--25220810 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
25220749 CAACAAAACT
* *
25220759 AAAATACGTGCTATTAGAAGTAGACTG
1 AAAATACGTGCTATTAAAAGCAGACTG
25220786 AAAA-ACGTGCTATTAAAAGCAGACT
1 AAAATACGTGCTATTAAAAGCAGACT
25220811 CGATGAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (27 bp):
AAAATACGTGCTATTAAAAGCAGACTG
Found at i:25221905 original size:6 final size:6
Alignment explanation
Indices: 25221894--25221920 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25221884 GAACGACCGC
25221894 TAATTG TAATTG TAATTG TAATTG TAA
1 TAATTG TAATTG TAATTG TAATTG TAA
25221921 AGGATATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (6 bp):
TAATTG
Found at i:25226789 original size:15 final size:14
Alignment explanation
Indices: 25226760--25226796 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
25226750 CTTCATAACA
*
25226760 CCATTTTTTTCTTG
1 CCATTTTTCTCTTG
25226774 CCATTTTCTCTCTTG
1 CCATTTT-TCTCTTG
25226789 CCATTTTT
1 CCATTTTT
25226797 TTCTCTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.08, C:0.27, G:0.05, T:0.59
Consensus pattern (14 bp):
CCATTTTTCTCTTG
Found at i:25226806 original size:28 final size:28
Alignment explanation
Indices: 25226760--25226819 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
25226750 CTTCATAACA
25226760 CCATTTTTTTCTTGCCATTTTCTCTCTTG
1 CCATTTTTTTCTT-CCATTTTCTCTCTTG
*
25226789 CCATTTTTTTC-TCTCATTTTCTCTGTTG
1 CCATTTTTTTCTTC-CATTTTCTCTCTTG
25226817 CCA
1 CCA
25226820 AACACCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 1 0.03
28 17 0.59
29 11 0.38
ACGTcount: A:0.08, C:0.28, G:0.07, T:0.57
Consensus pattern (28 bp):
CCATTTTTTTCTTCCATTTTCTCTCTTG
Found at i:25227030 original size:21 final size:21
Alignment explanation
Indices: 25226990--25227045 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
25226980 TTTTCTCTCA
*
25226990 TTTTCTCTCTTGCCAAACACCAT
1 TTTTCT-TCTT-CAAAACACCAT
25227013 TTTTCTTCTTCAAAACACCAT
1 TTTTCTTCTTCAAAACACCAT
25227034 TTTTCTTCTTCA
1 TTTTCTTCTTCA
25227046 GTACCTAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 22 0.69
22 4 0.12
23 6 0.19
ACGTcount: A:0.21, C:0.30, G:0.02, T:0.46
Consensus pattern (21 bp):
TTTTCTTCTTCAAAACACCAT
Found at i:25228086 original size:65 final size:65
Alignment explanation
Indices: 25227981--25228102 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
25227971 GAAATGAGCC
* * *
25227981 AACCATATGTTTTGAATAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAAAAAAATGCCAAT
1 AACCATATGTTTTGAAGAAGAAAAATGGTGTTAGGAAAGAGAGAAAATGAGAAAAAAATGCCAAT
* * *
25228046 AACCATGTGTTTTGAAGAA-AAAAAGTGTTGTTAGGAAAGAGAGAAAATGAGAGAAAA
1 AACCATATGTTTTGAAGAAGAAAAA-TGGTGTTAGGAAAGAGAGAAAATGAGAAAAAA
25228103 TTTTTATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 5 0.10
65 45 0.90
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.22
Consensus pattern (65 bp):
AACCATATGTTTTGAAGAAGAAAAATGGTGTTAGGAAAGAGAGAAAATGAGAAAAAAATGCCAAT
Found at i:25232110 original size:24 final size:24
Alignment explanation
Indices: 25232068--25232115 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
25232058 ATATAATTTT
* *
25232068 ATTAAAAAATAAATTTAATGAATA
1 ATTAAAAAATAAATATAATAAATA
25232092 ATTAAAAAATGAAA-ATAATAAATA
1 ATTAAAAAAT-AAATATAATAAATA
25232116 GCGCTACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
ATTAAAAAATAAATATAATAAATA
Found at i:25235018 original size:6 final size:6
Alignment explanation
Indices: 25235009--25235033 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25234999 ATTATTTTAA
25235009 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
25235034 TATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:25236818 original size:14 final size:14
Alignment explanation
Indices: 25236799--25236826 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25236789 AACTACAAAG
25236799 GCTAATTGTATTTA
1 GCTAATTGTATTTA
25236813 GCTAATTGTATTTA
1 GCTAATTGTATTTA
25236827 TTACCTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
GCTAATTGTATTTA
Found at i:25240101 original size:29 final size:28
Alignment explanation
Indices: 25240022--25240102 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 28
25240012 TTTTAAAGGT
*
25240022 CAAATTCTTTTTACCAACTTTTAAAGGGCC
1 CAAATTTTTTTTACCAACTTTT-AA-GGCC
*
25240052 C-CATTTTTTTT---AACTTTTAAGGCC
1 CAAATTTTTTTTACCAACTTTTAAGGCC
25240076 CAAAATTTTTTTTACCAACTTTTAAGG
1 C-AAATTTTTTTTACCAACTTTTAAGG
25240103 AACTTAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
24 5 0.12
25 2 0.05
26 16 0.37
29 19 0.44
30 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (28 bp):
CAAATTTTTTTTACCAACTTTTAAGGCC
Found at i:25249164 original size:37 final size:37
Alignment explanation
Indices: 25249103--25249255 Score: 242
Period size: 37 Copynumber: 4.2 Consensus size: 37
25249093 TACGTATGAT
* *
25249103 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
25249138 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
25249175 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG-
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
25249211 CACTTATCACTTTGTCTTCTTGATCAGAT-AGTGTAGC
1 CACTTATCACTTTGT-TTCTTGATCAGATAAGTGTAGC
25249248 CACTTATC
1 CACTTATC
25249256 NNNNNNNNNN
Statistics
Matches: 110, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
35 9 0.08
36 25 0.23
37 76 0.69
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:25249208 original size:74 final size:71
Alignment explanation
Indices: 25249103--25249255 Score: 236
Period size: 73 Copynumber: 2.1 Consensus size: 71
25249093 TACGTATGAT
25249103 CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCCACCTATCACTTTGT-TTCTTGATCAGATA
1 CACTTATCACTTGTCCCTGATCAGATAAGTGTAG-CACCTATCACTTTGTCTTCTTGATCAGAT-
25249167 AGTGTAGC
64 AGTGTAGC
* * *
25249175 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCACTTATCACTTTGTCTTCTTGATCAGAT
1 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGCACCTATCACTTTGTCTTCTTGATCAGAT
25249240 AGTGTAGC
64 AGTGTAGC
25249248 CACTTATC
1 CACTTATC
25249256 NNNNNNNNNN
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
72 10 0.13
73 33 0.44
74 32 0.43
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (71 bp):
CACTTATCACTTGTCCCTGATCAGATAAGTGTAGCACCTATCACTTTGTCTTCTTGATCAGATAG
TGTAGC
Found at i:25259625 original size:16 final size:16
Alignment explanation
Indices: 25259600--25259630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25259590 TTATAGCATG
25259600 TATGTATATGTATGTC
1 TATGTATATGTATGTC
*
25259616 TATGTGTATGTATGT
1 TATGTATATGTATGT
25259631 GTGTATTGTT
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:0.23, C:0.03, G:0.23, T:0.52
Consensus pattern (16 bp):
TATGTATATGTATGTC
Found at i:25263011 original size:14 final size:14
Alignment explanation
Indices: 25262992--25263023 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
25262982 TAGCATAAGG
25262992 TACACGTGGCATAT
1 TACACGTGGCATAT
25263006 TACACGTGGCATAT
1 TACACGTGGCATAT
25263020 TACA
1 TACA
25263024 TGTCACTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (14 bp):
TACACGTGGCATAT
Found at i:25264096 original size:31 final size:31
Alignment explanation
Indices: 25264026--25264102 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
25264016 TGCTTGTATC
* *
25264026 ATTTAAATATTATTTATTATTATATTAGATT
1 ATTTAAATATAATTTATTATTATATTAGATA
*
25264057 ATTTAAATATAATTTATTTTTATATTTA-A-A
1 ATTTAAATATAATTTATTATTATA-TTAGATA
25264087 ATTTAAA-ATAATTTAT
1 ATTTAAATATAATTTAT
25264103 GTGTCATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 9 0.21
30 7 0.17
31 23 0.55
32 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
ATTTAAATATAATTTATTATTATATTAGATA
Found at i:25280424 original size:2 final size:2
Alignment explanation
Indices: 25280413--25280441 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25280403 TTCCTGTATG
25280413 TA TA -A 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
25280442 AATTAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:25281976 original size:116 final size:116
Alignment explanation
Indices: 25281849--25282089 Score: 439
Period size: 116 Copynumber: 2.1 Consensus size: 116
25281839 TCTAAGTGTC
25281849 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
1 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
* * *
25281914 GTTAATCTAACAGTCTATGATAGAAATTAGAGAAAAAACTGTTTGAATTTT
66 GTTAATCTAACAGTCTATGACAGAAATTAGAGAAAAAACTATTTAAATTTT
25281965 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
1 GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
25282030 GTTAATCTAACAGTCTATGACAGAAATTAGAGAAAAAACTATTTAAATTTT
66 GTTAATCTAACAGTCTATGACAGAAATTAGAGAAAAAACTATTTAAATTTT
*
25282081 AATTT-ATAA
1 GATTTGATAA
25282090 ATGTATGACG
Statistics
Matches: 121, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
115 4 0.03
116 117 0.97
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.36
Consensus pattern (116 bp):
GATTTGATAATTGATATATTAGATCAGTGTCTATCAATAAATACAAAAATATACTTTAGATCTAA
GTTAATCTAACAGTCTATGACAGAAATTAGAGAAAAAACTATTTAAATTTT
Found at i:25283432 original size:2 final size:2
Alignment explanation
Indices: 25283425--25283455 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25283415 TGGAAGACAA
25283425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25283456 GATCAGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25283613 original size:3 final size:3
Alignment explanation
Indices: 25283605--25283643 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25283595 ATATATGTAG
25283605 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25283644 TATTTTGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25285106 original size:18 final size:18
Alignment explanation
Indices: 25285061--25285108 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
25285051 GACAACAAAG
* *
25285061 ATTTTAGATAAAAGTTATA
1 ATTTT-GATAAAAATGATA
* *
25285080 ATATGGATAAAAATGATA
1 ATTTTGATAAAAATGATA
25285098 ATTTTGATAAA
1 ATTTTGATAAA
25285109 TATCATTCCA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (18 bp):
ATTTTGATAAAAATGATA
Found at i:25286466 original size:15 final size:17
Alignment explanation
Indices: 25286436--25286474 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
25286426 ACTAATATGC
25286436 ATAATAGAACAATGATA
1 ATAATAGAACAATGATA
25286453 ATAAT-GAA-AATGATA
1 ATAATAGAACAATGATA
25286468 ATAATAG
1 ATAATAG
25286475 TAATAATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 12 0.57
16 4 0.19
17 5 0.24
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.26
Consensus pattern (17 bp):
ATAATAGAACAATGATA
Found at i:25287042 original size:16 final size:16
Alignment explanation
Indices: 25287004--25287036 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25286994 TTTTTAAAGG
*
25287004 TGCTTTTATTTTTTTT
1 TGCTCTTATTTTTTTT
25287020 TGCTCTTATTTTTTTT
1 TGCTCTTATTTTTTTT
25287036 T
1 T
25287037 CATCTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (16 bp):
TGCTCTTATTTTTTTT
Found at i:25287742 original size:3 final size:3
Alignment explanation
Indices: 25287710--25287775 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
25287700 TTGCTATTTT
* * *
25287710 TTA TTAA TTA ATA TTA ATA TTA TTA CTA TTA TTA TCGTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA TTA TTA TTA
* *
25287758 GTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA
25287776 CTGCTATTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
3 44 0.88
4 3 0.06
5 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:25287752 original size:20 final size:20
Alignment explanation
Indices: 25287727--25287764 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25287717 TTAATATTAA
*
25287727 TATTATTACTATTATTATCG
1 TATTATTACTAGTATTATCG
*
25287747 TATTATTATTAGTATTAT
1 TATTATTACTAGTATTAT
25287765 TATTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTATTACTAGTATTATCG
Found at i:25288123 original size:18 final size:19
Alignment explanation
Indices: 25288084--25288160 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 19
25288074 ACGTATATAC
*
25288084 ATACTTATATATATTTTTT
1 ATACTTATATATATTTTAT
25288103 ATACTT-TATA-ATTTTAAT
1 ATACTTATATATATTTT-AT
* * * *
25288121 ATACATATATACA-TATAC
1 ATACTTATATATATTTTAT
*
25288139 ATACTTATATATCTTCTTAT
1 ATACTTATATATATT-TTAT
25288159 AT
1 AT
25288161 TTTTTTATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
17 5 0.11
18 21 0.48
19 13 0.30
20 5 0.11
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
ATACTTATATATATTTTAT
Found at i:25291699 original size:1 final size:1
Alignment explanation
Indices: 25291693--25291811 Score: 85
Period size: 1 Copynumber: 119.0 Consensus size: 1
25291683 CAGTGGAGGC
* * * * * * * *
25291693 AAAAAAATAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
25291758 AACAAAAAACAAAACAAAAACAAAACAAAACAAAACAAAACAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25291812 CTCTACCGGA
Statistics
Matches: 84, Mismatches: 34, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 84 1.00
ACGTcount: A:0.86, C:0.13, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:25291706 original size:7 final size:7
Alignment explanation
Indices: 25291694--25291812 Score: 140
Period size: 7 Copynumber: 17.0 Consensus size: 7
25291684 AGTGGAGGCA
*
25291694 AAAAAAT
1 AAAAAAC
25291701 AAAAAAC
1 AAAAAAC
25291708 AAAAAAC
1 AAAAAAC
25291715 AAAAAAC
1 AAAAAAC
25291722 AAAAAAC
1 AAAAAAC
25291729 AAAAAAC
1 AAAAAAC
25291736 AAAAAAC
1 AAAAAAC
25291743 --AAAA-
1 AAAAAAC
25291747 AAAAAAC
1 AAAAAAC
25291754 AAAAAAC
1 AAAAAAC
25291761 AAAAAAC
1 AAAAAAC
*
25291768 AAAACAAA
1 AAAA-AAC
25291776 AACAAAAC
1 AA-AAAAC
25291784 AAAACAA-
1 AAAA-AAC
25291791 AACAAAAC
1 AA-AAAAC
25291799 AAAACAA-
1 AAAA-AAC
25291806 AAAAAAC
1 AAAAAAC
25291813 TCTACCGGAG
Statistics
Matches: 99, Mismatches: 3, Indels: 20
0.81 0.02 0.16
Matches are distributed among these distances:
5 4 0.04
6 6 0.06
7 71 0.72
8 16 0.16
9 2 0.02
ACGTcount: A:0.85, C:0.14, G:0.00, T:0.01
Consensus pattern (7 bp):
AAAAAAC
Found at i:25292265 original size:17 final size:17
Alignment explanation
Indices: 25292243--25292296 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
25292233 TACTTCACTT
*
25292243 GAAAAAAGAAACGAAAA
1 GAAAAAAGAAAAGAAAA
25292260 GAAAAAAGAAAAGAAAAA
1 GAAAAAAGAAAAG-AAAA
*
25292278 TGGAAAAAGAAAAAGAAAA
1 -GAAAAAAG-AAAAGAAAA
25292297 ATGAGAGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 12 0.38
18 4 0.12
19 11 0.34
20 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (17 bp):
GAAAAAAGAAAAGAAAA
Found at i:25292271 original size:6 final size:6
Alignment explanation
Indices: 25292256--25292297 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
25292246 AAAAGAAACG
25292256 AAAAGA AAAA-A GAAAAGA AAAATGGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA -AAAAGA AAAA--GA AAAAGA AAAAGA AAAA
25292298 TGAGAGACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 1 0.03
6 24 0.75
7 1 0.03
8 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:25292285 original size:20 final size:20
Alignment explanation
Indices: 25292243--25292299 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
25292233 TACTTCACTT
*
25292243 GAAAAAAGAAACG-AAAA--
1 GAAAAAAGAAAAGAAAAATG
25292260 GAAAAAAGAAAAGAAAAATG
1 GAAAAAAGAAAAGAAAAATG
25292280 G-AAAAAGAAAAAGAAAAATG
1 GAAAAAAG-AAAAGAAAAATG
25292300 AGAGACCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
17 12 0.34
18 4 0.11
19 6 0.17
20 13 0.37
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (20 bp):
GAAAAAAGAAAAGAAAAATG
Found at i:25293415 original size:87 final size:87
Alignment explanation
Indices: 25293296--25293681 Score: 211
Period size: 87 Copynumber: 4.4 Consensus size: 87
25293286 ATGACGGGGA
* * *
25293296 ATCTTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGTAGC
1 ATCTTATCTCCCTAAGCAGTAGT-GG-AGCAGATTAAAGCCACCAGCCTTATCTCCCTGAGCAGC
* * *
25293359 AGTGGAGTAGGTTGAAGATTGAAG
64 AGTGGAGCAGATTGAAGATTGCAG
* **** ** * *
25293383 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTAAAGACGGTGAATCTTATCTTTCC-GAG-A-T
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAG-CCACCAGCCTTATC-TCCCTGAGCAGC
* ****
25293445 AGTAGGAAGCAGATTTAAGCCACCAG
64 AGT-GG-AGCAGATTGAAGATTGCAG
* * * **** * * *
25293471 -TCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGATCTTATCTCCCTAAGCAGTA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGCCACCAG-CCTTATCTCCCTGAGCAGCA
* *
25293535 GTGGAGCAGATCGAAGACGGTG-A-
65 GTGGAGCAGATTGAAGA--TTGCAG
* * * *
25293558 ATCTTATCTTCCC-GAG-A-TAGTAGGAAGCAGATTTAAGCCACCTATCC-TATCTCCTTGAGCA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTAAAGCCACC-AGCCTTATCTCCCTGAGCA
* *
25293619 GCAGTGGAGTAGGTTGAAGATTGCAG
62 GCAGTGGAGCAGATTGAAGATTGCAG
* *
25293645 ATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAG
25293682 ATGGTGAATC
Statistics
Matches: 220, Mismatches: 57, Indels: 44
0.69 0.18 0.14
Matches are distributed among these distances:
85 2 0.01
86 15 0.07
87 132 0.60
88 50 0.23
89 21 0.10
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (87 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGCCACCAGCCTTATCTCCCTGAGCAGCAG
TGGAGCAGATTGAAGATTGCAG
Found at i:25293448 original size:131 final size:131
Alignment explanation
Indices: 25293207--25293782 Score: 850
Period size: 131 Copynumber: 4.4 Consensus size: 131
25293197 CATCATATCA
* *
25293207 AGCCTTATCTCCCTGATCAGTAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
* * * * * *
25293272 AGTGGAGTAGATCGATGACGGGGAATCTTATCTTCCTAAGGTAGTAGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGAAGCAGATTTAAGCCAC
25293337 C
131 C
* *
25293338 AGCCTTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATTGAAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
* * * *
25293403 AGTGGAGTAGATTAAAGACGGTGAATCTTATCTTTCCGAGATAGTAGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGAAGCAGATTTAAGCCAC
25293468 C
131 C
* * *
25293469 AGTCC-TATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGATCTTATCTCCCTAAGCAG
1 AG-CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAG
* *
25293533 TAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCCCGAGATAGTAGGAAGCAGATTTAAGCCA
65 TAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGAAGCAGATTTAAGCCA
25293598 CC
130 CC
* * *
25293600 TATCC-TATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTTCCTAAGCAG
1 -AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAG
* * * *
25293664 TAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAACC
65 TAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTA-GGAAGCAGATTTAAGCC
*
25293729 ACT
129 ACC
* *
25293732 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTA
1 AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTA
25293783 CCTTCCTGTA
Statistics
Matches: 403, Mismatches: 38, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
131 340 0.84
132 63 0.16
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (131 bp):
AGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGAAGCAGATTTAAGCCAC
C
Found at i:25293683 original size:44 final size:44
Alignment explanation
Indices: 25293210--25293676 Score: 237
Period size: 44 Copynumber: 10.7 Consensus size: 44
25293200 CATATCAAGC
* * *
25293210 CTTATCTCCCTGATCAGTAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
* * * **
25293254 CTTATCTCCCTAAGCAGTAGTGGAGTAGATCGATGA-CGGGGAAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAG-AT
* * * **** *
25293298 CTTATCTTCCTAAG--GTAGTAGGAAGCAGATTTAAGCCACCAG-C
1 CTTATCTCCCTAAGCAGTAGT-GG-AGTAGATTGAAGATTGCAGAT
* * * * *
25293341 CTTATCTCCCTGAGTAGCAGTGGAGTAGGTTGAAGATTGAAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
* *
25293385 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTAAAGACGGTG-A-AT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA--TTGCAGAT
* * * * ****
25293429 CTTATCTTTCC-GAG-A-TAGTAGGAAGCAGATTTAAGCCACCAG-T
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGATTGCAGAT
* * *
25293472 CCTATCTCCCTAAGCAGTAGTGGAGTAGGTTAAAGATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
* * *
25293516 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTG-A-AT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGA--TTGCAGAT
* * * *** **
25293560 CTTATCTTCCC-GAG-A-TAGTAGGAAGCAGATTTAAG-CCACCTAT
1 CTTATC-TCCCTAAGCAGTAGT-GG-AGTAGATTGAAGATTGCAGAT
* * * * *
25293603 CCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
* *
25293647 CTTATCTTCCTAAGCAGTAGTGGAGCAGAT
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGAT
25293677 CAAAGATGGT
Statistics
Matches: 308, Mismatches: 86, Indels: 58
0.68 0.19 0.13
Matches are distributed among these distances:
42 19 0.06
43 73 0.24
44 191 0.62
45 21 0.07
46 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATTGCAGAT
Found at i:25293859 original size:220 final size:220
Alignment explanation
Indices: 25293605--25294182 Score: 798
Period size: 220 Copynumber: 2.6 Consensus size: 220
25293595 CCACCTATCC
* * * * *
25293605 TATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTTCCTAAGCAGTAGTGG
1 TATCTCCCTGAACAACAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAGCAGTAGTGG
* * * *
25293670 AGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAACCACTAGC
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
* ** * * *
25293735 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATTGTAGATCTTACCTTCCTGTATTGGCA-
131 CTTATCTCCCTGAGAAAAAGTGAAGTAGGTCGAAAATTGTAGATCTTACCTTCCTGTACTGGCAG
* *
25293799 TTAATGCAGATCGAAAGCGCCAGCCT
196 TGAA-GCAGATCGAAAGCACCAGCCT
** * * *
25293825 TATCTCCCTGAACAATGGTGGAGTAGGTTGAAGATTACAGATCCTATGTCCCTAAACAGTAGTGG
1 TATCTCCCTGAACAACAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAGCAGTAGTGG
* * *
25293890 AGTAGATCGAAGACGGCGAATCTTATTTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
* ** *
25293955 CTTATCTCCCTGAGAAAAAGTGAAGTAGGTCGAAAATTTTAGATCTTGTCTTCTTGTACTGGCAG
131 CTTATCTCCCTGAGAAAAAGTGAAGTAGGTCGAAAATTGTAGATCTTACCTTCCTGTACTGGCAG
25294020 TGAAGCAGATCGAAAGCACCAGCCT
196 TGAAGCAGATCGAAAGCACCAGCCT
* * * *
25294045 TATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAACAACAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAGCAGTAGTGG
* * * * *
25294110 AGCAGATCGAAGACGATGAATCTTATCTTCCCAAGATAGTCGGGAAGCAGATTTAAGCCACAAGT
66 AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
25294175 CTTATCTC
131 CTTATCTC
25294183 TCTAAAGTTG
Statistics
Matches: 311, Mismatches: 46, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
220 308 0.99
221 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (220 bp):
TATCTCCCTGAACAACAGTGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGC
CTTATCTCCCTGAGAAAAAGTGAAGTAGGTCGAAAATTGTAGATCTTACCTTCCTGTACTGGCAG
TGAAGCAGATCGAAAGCACCAGCCT
Found at i:25294487 original size:85 final size:85
Alignment explanation
Indices: 25294397--25294600 Score: 266
Period size: 85 Copynumber: 2.4 Consensus size: 85
25294387 TGAAGATACC
* * * * *
25294397 AATCTTATCTCCCTAAAGTTGCAG-CGGAGCATATTGAAGCTAATCCAATTTCCTTAAAGTTGCA
1 AATCTTATCTCTCTAAAGTTGCAGTC-GAGCAGATTCAAGCTAATCCAATCTCCTTAAAGTTACA
* *
25294461 GTGGAGCGGATTAAAATGATT
65 GTGGAGCGGATTAAAACGATG
* * * *
25294482 AATCTTATCTCTCTAAAGTTGCAGTCGAGCAGATTCAAGTTAATTCTATCTCCTTGAAGTTACAG
1 AATCTTATCTCTCTAAAGTTGCAGTCGAGCAGATTCAAGCTAATCCAATCTCCTTAAAGTTACAG
25294547 TGGAGCGGATTAAAACGATG
66 TGGAGCGGATTAAAACGATG
* * *
25294567 GATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 AATCTTATCTCTCTAAAGTTGCAGTCGAGCAGAT
25294601 CGAGTGGAGT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
85 103 0.99
86 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (85 bp):
AATCTTATCTCTCTAAAGTTGCAGTCGAGCAGATTCAAGCTAATCCAATCTCCTTAAAGTTACAG
TGGAGCGGATTAAAACGATG
Found at i:25294501 original size:44 final size:43
Alignment explanation
Indices: 25294451--25294596 Score: 147
Period size: 44 Copynumber: 3.4 Consensus size: 43
25294441 CCAATTTCCT
25294451 TAAAGTTGCAGTGGAGCGGATTAAAATGATTAATCTTATCTCTC
1 TAAAGTTGCAGTGGAGCGGATTAAAA-GATTAATCTTATCTCTC
* * *
25294495 TAAAGTTGCAGTCGAGCAGATT-CAAG-TTAAT-TCTATCTC-C
1 TAAAGTTGCAGTGGAGCGGATTAAAAGATTAATCT-TATCTCTC
* * **
25294535 TTGAAGTTACAGTGGAGCGGATTAAAACGATGGATCTTATCTCTC
1 -TAAAGTTGCAGTGGAGCGGATTAAAA-GATTAATCTTATCTCTC
* *
25294580 TGAAGTTGCAGTAGAGC
1 TAAAGTTGCAGTGGAGC
25294597 AGATCGAGTG
Statistics
Matches: 83, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
40 2 0.02
41 29 0.35
42 3 0.04
43 3 0.04
44 44 0.53
45 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
TAAAGTTGCAGTGGAGCGGATTAAAAGATTAATCTTATCTCTC
Found at i:25294617 original size:85 final size:84
Alignment explanation
Indices: 25294447--25294687 Score: 302
Period size: 85 Copynumber: 2.8 Consensus size: 84
25294437 TAATCCAATT
* ** * *
25294447 TCCTTAAAGTTGCAGTGGAGCGGATTAAAATGATTAATCTTATCTCTCTAAAGTTGCAGTCGAGC
1 TCCTTGAAGTTGCAGTGGAGCGGATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGC
* * *
25294512 AGATTCAAGTTAATTCTATC
66 AGA-TCGAGTGAAGTCTATC
* *
25294532 TCCTTGAAGTTACAGTGGAGCGGATTAAAACGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGC
1 TCCTTGAAGTTGCAGTGGAGCGGATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGC
*
25294597 AGATCGAGTGGAGTCTTATC
66 AGATCGAGTGAAGTC-TATC
* * * ** * *
25294617 TCCCTGAAGTTGCAATGTAGCAAATTAAAATGATGGATCTTATCTATCTGAAGTTCCAGTAGAGC
1 TCCTTGAAGTTGCAGTGGAGCGGATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGC
25294682 AGATCG
66 AGATCG
25294688 CATCAGACTT
Statistics
Matches: 135, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
84 8 0.06
85 127 0.94
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (84 bp):
TCCTTGAAGTTGCAGTGGAGCGGATTAAAATGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGC
AGATCGAGTGAAGTCTATC
Found at i:25294668 original size:44 final size:43
Alignment explanation
Indices: 25294555--25294682 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 43
25294545 AGTGGAGCGG
* *
25294555 ATTAAAACGATGGATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 ATTAAAA-GATGGATCTTATCTCTCTGAAGTTGCAATAGAGCAA
** *
25294599 A-T-CGAG-TGGAGTCTTATCTCCCTGAAGTTGCAAT-GTAGCAA
1 ATTAAAAGATGGA-TCTTATCTCTCTGAAGTTGCAATAG-AGCAA
* * *
25294640 ATTAAAATGATGGATCTTATCTATCTGAAGTTCCAGTAGAGCA
1 ATTAAAA-GATGGATCTTATCTCTCTGAAGTTGCAATAGAGCA
25294683 GATCGCATCA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
40 5 0.08
41 27 0.41
42 2 0.03
43 2 0.03
44 25 0.38
45 5 0.08
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (43 bp):
ATTAAAAGATGGATCTTATCTCTCTGAAGTTGCAATAGAGCAA
Found at i:25294856 original size:130 final size:130
Alignment explanation
Indices: 25294640--25294937 Score: 479
Period size: 130 Copynumber: 2.3 Consensus size: 130
25294630 AATGTAGCAA
* *
25294640 ATTAAAATGATGGATCTTATCTATCTGAAGTTCCAGTAGAGCAGATCGCATCAGACTTTATTTTC
1 ATTAAAATGATGGATCTTATCTATCTGAAGTTGCAGTAAAGCAGATCGCATCAGACTTTATTTTC
* *
25294705 TTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCCATCTTCCTAAAGTTGCAGTGGAGCGG
66 TTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCCATCTCCCTAAAGTTACAGTGGAGCGG
* * *
25294770 ATTAAAATGATGGATATTATCTATCTGAACTTGCAGTAAAGTAGATCGCATCAGACTTTATTTTC
1 ATTAAAATGATGGATCTTATCTATCTGAAGTTGCAGTAAAGCAGATCGCATCAGACTTTATTTTC
* * * *
25294835 TTAAAGATGCAGTAGATCAAGTTGAAGCTACCAAGTCCTATCTCCCTGAAGTTACAGTGGAGCGG
66 TTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCCATCTCCCTAAAGTTACAGTGGAGCGG
* *
25294900 ATTAAAATGATTGATCTTATCTATCTCAAGTTGCAGTA
1 ATTAAAATGATGGATCTTATCTATCTGAAGTTGCAGTA
25294938 GGTCGGATTA
Statistics
Matches: 153, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 153 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (130 bp):
ATTAAAATGATGGATCTTATCTATCTGAAGTTGCAGTAAAGCAGATCGCATCAGACTTTATTTTC
TTAAAGACGCAGTAAATCAAGTTGAAGCTACCAAGTCCCATCTCCCTAAAGTTACAGTGGAGCGG
Found at i:25295166 original size:139 final size:138
Alignment explanation
Indices: 25294855--25295184 Score: 369
Period size: 139 Copynumber: 2.4 Consensus size: 138
25294845 AGTAGATCAA
* * *
25294855 GTTGAAGCTACCAAGTCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATGATTGATCTTAT
1 GTTGAAGC-AACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACGATTGATCATAT
* ** *
25294920 CTATCTCAAGTTGCAGTAGGTCGGATTAAATTTACCACAACAAGTCTTATCTCCATGAAGTTGCA
65 CTATCTCAAGTTGCAGTAGGTCGAATTAAATTTACCACAACAAACCTTATCTCCATGAAGTCGCA
*
25294985 GTGGAGCAT
130 GTGGAGCAG
** * * * *
25294994 ACTGAACCTACTAA-TCCTATCTCCCTGAAGTTACAATGGAGTGGATTAAAACGA-TGAATCATA
1 GTTGAAGCAAC-AAGTCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACGATTG-ATCATA
* * * * ** * *
25295057 TAC-CTCTGAAGTTGCAGTAGGTCGAATTAGATCTTATCGTATCAAACCTTATCTCCCTGAAGTC
64 T-CTATCTCAAGTTGCAGTAGGTCGAATTAAAT-TTACCACAACAAACCTTATCTCCATGAAGTC
25295121 GCAGTGGAGCAG
127 GCAGTGGAGCAG
* * *
25295133 GTTGAAGCAACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAAC
1 GTTGAAGCAACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAC
25295185 CACGAATCTC
Statistics
Matches: 155, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
137 2 0.01
138 71 0.46
139 82 0.53
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (138 bp):
GTTGAAGCAACAAGTCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACGATTGATCATATC
TATCTCAAGTTGCAGTAGGTCGAATTAAATTTACCACAACAAACCTTATCTCCATGAAGTCGCAG
TGGAGCAG
Found at i:25295853 original size:17 final size:16
Alignment explanation
Indices: 25295828--25295861 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
25295818 TTTTTAAAGG
*
25295828 TGCTTTTATTATTTTTT
1 TGCTCTTATT-TTTTTT
25295845 TGCTCTTATTTTTTTT
1 TGCTCTTATTTTTTTT
25295861 T
1 T
25295862 CATCTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (16 bp):
TGCTCTTATTTTTTTT
Found at i:25296830 original size:2 final size:2
Alignment explanation
Indices: 25296823--25296888 Score: 73
Period size: 2 Copynumber: 33.5 Consensus size: 2
25296813 NNNNNNNTAT
* *
25296823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
25296865 CA TA CT- TA TA T- TT TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA T
25296889 TTTATAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
1 2 0.04
2 51 0.94
3 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25296893 original size:20 final size:20
Alignment explanation
Indices: 25296860--25296950 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
25296850 ATATATGTAC
*
25296860 ATATACATA-CTTATATTTT
1 ATATACATATTTTATATTTT
* *
25296879 ATATATATATTTTATAATTT
1 ATATACATATTTTATATTTT
* * *
25296899 GTTTACATATCTATATATATTT
1 ATATACATAT-TTTATAT-TTT
*
25296921 ATACACATATTTT-TATTTTT
1 ATATACATATTTTATA-TTTT
*
25296941 ATAAACATAT
1 ATATACATAT
25296951 GTATATACAT
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
19 8 0.15
20 29 0.53
21 8 0.15
22 10 0.18
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (20 bp):
ATATACATATTTTATATTTT
Found at i:25296998 original size:18 final size:19
Alignment explanation
Indices: 25296959--25297035 Score: 61
Period size: 18 Copynumber: 4.1 Consensus size: 19
25296949 ATGTATATAC
*
25296959 ATACTTATATATATTTTTT
1 ATACTTATATATATTTTAT
25296978 ATACTT-TATA-ATTTTAAT
1 ATACTTATATATATTTT-AT
* * * *
25296996 ATACATATATACA-TATAC
1 ATACTTATATATATTTTAT
*
25297014 ATACTTATATATCTTCTTAT
1 ATACTTATATATATT-TTAT
25297034 AT
1 AT
25297036 TTTTTTTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
17 5 0.11
18 21 0.48
19 13 0.30
20 5 0.11
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
ATACTTATATATATTTTAT
Found at i:25298542 original size:51 final size:51
Alignment explanation
Indices: 25298466--25298664 Score: 223
Period size: 51 Copynumber: 4.0 Consensus size: 51
25298456 GTAATAAGAT
* * *
25298466 TTGTAGCCTCTATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
1 TTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* *
25298517 TTGTAGCTTCAATCTGTTGCACTGCAACTTCAGGGAGATAATATTTGTAAC
1 TTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * *
25298568 TTGTAGCTTCAATATGTTCCACTGAAACTTCA-GG-G--AA-ATTAG--AT
1 TTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
* * * * *
25298612 TTGTAGCTTTAATTTGTTCTACTGCAACTTCAGGGAGATGAGATTTATAAC
1 TTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
25298663 TT
1 TT
25298665 TAATATACTC
Statistics
Matches: 123, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
44 29 0.24
45 2 0.02
46 5 0.04
47 2 0.02
48 1 0.01
49 4 0.03
50 2 0.02
51 78 0.63
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (51 bp):
TTGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC
Found at i:25298641 original size:44 final size:44
Alignment explanation
Indices: 25298568--25298688 Score: 143
Period size: 44 Copynumber: 2.8 Consensus size: 44
25298558 TATTTGTAAC
* * *
25298568 TTGTAGCTTCAATATGTTCCACTGAAACTTCAGGGAAATTAGAT
1 TTGTAGCTTTAATATGTTCTACTGAAACTTCAGGGAAATGAGAT
* * *
25298612 TTGTAGCTTTAATTTGTTCTACTGCAACTTCAGGGAGATGAGAT
1 TTGTAGCTTTAATATGTTCTACTGAAACTTCAGGGAAATGAGAT
* * ** *
25298656 TTATAACTTTAATATACTCTACTGTAACTTCAG
1 TTGTAGCTTTAATATGTTCTACTGAAACTTCAG
25298689 AGAGATAAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (44 bp):
TTGTAGCTTTAATATGTTCTACTGAAACTTCAGGGAAATGAGAT
Found at i:25298694 original size:44 final size:44
Alignment explanation
Indices: 25298585--25299053 Score: 226
Period size: 44 Copynumber: 10.6 Consensus size: 44
25298575 TTCAATATGT
* * * * * * * **
25298585 TCCACTGAAACTTCAGGGAAATTAGATTTGTAGCTTTAATTTGT
1 TCCACTGCAACTTCAGAGAGATAAGATTTATAACTTTAATATAC
* * *
25298629 TCTACTGCAACTTCAGGGAGATGAGATTTATAACTTTAATATAC
1 TCCACTGCAACTTCAGAGAGATAAGATTTATAACTTTAATATAC
* * * ** *
25298673 TCTACTGTAACTTCAGAGAGATAAGATTCACTATTTTTAATCTAC
1 TCCACTGCAACTTCAGAGAGATAAGATTTA-TAACTTTAATATAC
*
25298718 TCCACTGCAACTTCAG-GAAGATAAGATTTGTAA-TTTCAATATAC
1 TCCACTGCAACTTCAGAG-AGATAAGATTTATAACTTT-AATATAC
* *
25298762 TCCACTGCAACTTCAGAGATATAAGA-TTAGTATA-TTCAA-ACTAC
1 TCCACTGCAACTTCAGAGAGATAAGATTTA-TA-ACTTTAATA-TAC
* * * ** *
25298806 TCCACTGCAACTTTAGGGAGATAAGATTTGT-GTTTTCAATCTAC
1 TCCACTGCAACTTCAGAGAGATAAGATTTATAACTTT-AATATAC
* * * *
25298850 TCCACTACAACTTCA-AGGAGATAAGA-TTAGTATA-TTCAATCTAT
1 TCCACTGCAACTTCAGA-GAGATAAGATTTA-TA-ACTTTAATATAC
* * * * * ** *
25298894 TCCAATGCAACTTTAGGGAGATAGGATTTGT-GTTTTCAATTTAC
1 TCCACTGCAACTTCAGAGAGATAAGATTTATAACTTT-AATATAC
* * * * *
25298938 TCCACTACAACTTCA-AGGAGATAAGA-TTAGCATA-TTCAATCTAT
1 TCCACTGCAACTTCAGA-GAGATAAGATTTA-TA-ACTTTAATATAC
* * * ** * **
25298982 TCCACTGCAACTTTAGGGAGATAAGATTTGTGGCTTTAATCTGT
1 TCCACTGCAACTTCAGAGAGATAAGATTTATAACTTTAATATAC
** *
25299026 TCTTCTGCAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGAGAGATAAGATT
25299054 CGCCATGATG
Statistics
Matches: 327, Mismatches: 72, Indels: 52
0.73 0.16 0.12
Matches are distributed among these distances:
43 14 0.04
44 264 0.81
45 49 0.15
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (44 bp):
TCCACTGCAACTTCAGAGAGATAAGATTTATAACTTTAATATAC
Found at i:25298835 original size:88 final size:88
Alignment explanation
Indices: 25298632--25299012 Score: 480
Period size: 88 Copynumber: 4.3 Consensus size: 88
25298622 AATTTGTTCT
* * * * **
25298632 ACTGCAACTTCAGGGAGATGAGATTTATAACTTT-AATATACTCTACTGTAACTTC-AGAGAGAT
1 ACTGCAACTTTAGGGAGATAAGATTTGTAA-TTTCAATATACTCCACTACAACTTCAAG-GAGAT
* * *
25298695 AAGATTCACTATTTTTAATCTACTCC
64 AAGATT-AGTATATTCAATCTACTCC
* * * *
25298721 ACTGCAACTTCAGGAAGATAAGATTTGTAATTTCAATATACTCCACTGCAACTTC-AGAGATATA
1 ACTGCAACTTTAGGGAGATAAGATTTGTAATTTCAATATACTCCACTACAACTTCAAG-GAGATA
*
25298785 AGATTAGTATATTCAAACTACTCC
65 AGATTAGTATATTCAATCTACTCC
** *
25298809 ACTGCAACTTTAGGGAGATAAGATTTGTGTTTTCAATCTACTCCACTACAACTTCAAGGAGATAA
1 ACTGCAACTTTAGGGAGATAAGATTTGTAATTTCAATATACTCCACTACAACTTCAAGGAGATAA
*
25298874 GATTAGTATATTCAATCTATTCC
66 GATTAGTATATTCAATCTACTCC
* * ** *
25298897 AATGCAACTTTAGGGAGATAGGATTTGTGTTTTCAATTTACTCCACTACAACTTCAAGGAGATAA
1 ACTGCAACTTTAGGGAGATAAGATTTGTAATTTCAATATACTCCACTACAACTTCAAGGAGATAA
* *
25298962 GATTAGCATATTCAATCTATTCC
66 GATTAGTATATTCAATCTACTCC
25298985 ACTGCAACTTTAGGGAGATAAGATTTGT
1 ACTGCAACTTTAGGGAGATAAGATTTGT
25299013 GGCTTTAATC
Statistics
Matches: 265, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
88 204 0.77
89 61 0.23
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (88 bp):
ACTGCAACTTTAGGGAGATAAGATTTGTAATTTCAATATACTCCACTACAACTTCAAGGAGATAA
GATTAGTATATTCAATCTACTCC
Found at i:25299023 original size:132 final size:132
Alignment explanation
Indices: 25298585--25299053 Score: 453
Period size: 132 Copynumber: 3.5 Consensus size: 132
25298575 TTCAATATGT
* * * * * * *
25298585 TCCACTGAAACTTCAGGGAAATTAGATTTGTAGCTTTAATTTGTTCTACTGCAACTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGATTTAATCTATTCCACTGCAACTTCAGGGAGA
* * * * * *
25298650 TGAGATTTATAACTTT-AATATACTCTACTGTAACTTC-AGAGAGATAAGATTCA-CTATTTTTA
66 TAAGATTTGT-ATTTTCAATATACTCCACTGCAACTTCAAG-GAGATAAGATT-AGC-ATTTTCA
25298712 ATCTAC
127 ATCTAC
* * * * *
25298718 TCCACTGCAACTTCAGGAAGATAAGATTTGTA-ATTTCAATATACTCCACTGCAACTTCAGAGAT
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGATTT-AATCTATTCCACTGCAACTTCAGGGAG
* * * * * **
25298782 ATAAGATTAGTATATTCAA-ACTACTCCACTGCAACTTTAGGGAGATAAGATTTGTGTTTTCAAT
65 ATAAGATTTGTATTTTCAATA-TACTCCACTGCAACTTCAAGGAGATAAGATTAGCATTTTCAAT
25298846 CTAC
129 CTAC
* * * * * * *
25298850 TCCACTACAACTTCAAGGAGATAAGATTAGTATATTCAATCTATTCCAATGCAACTTTAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGATTTAATCTATTCCACTGCAACTTCAGGGAGA
* * * * *
25298915 TAGGATTTGTGTTTTCAATTTACTCCACTACAACTTCAAGGAGATAAGATTAGCATATTCAATCT
66 TAAGATTTGTATTTTCAATATACTCCACTGCAACTTCAAGGAGATAAGATTAGCATTTTCAATCT
*
25298980 AT
131 AC
* * * * **
25298982 TCCACTGCAACTTTAGGGAGATAAGATTTGTGGCTTTAATCTGTTCTTCTGCAACTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGATTTAATCTATTCCACTGCAACTTCAGGGAGA
25299047 TAAGATT
66 TAAGATT
25299054 CGCCATGATG
Statistics
Matches: 267, Mismatches: 62, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
132 179 0.67
133 87 0.33
134 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (132 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGTAGATTTAATCTATTCCACTGCAACTTCAGGGAGA
TAAGATTTGTATTTTCAATATACTCCACTGCAACTTCAAGGAGATAAGATTAGCATTTTCAATCT
AC
Found at i:25300178 original size:3 final size:3
Alignment explanation
Indices: 25300170--25300202 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
25300160 TTGGCCTCAC
*
25300170 CTT CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
25300203 TTACGTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:25301150 original size:13 final size:13
Alignment explanation
Indices: 25301132--25301157 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25301122 GACATCTCTT
25301132 GGCATAGTTGATG
1 GGCATAGTTGATG
25301145 GGCATAGTTGATG
1 GGCATAGTTGATG
25301158 CAATCTCCTT
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:0.23, C:0.08, G:0.38, T:0.31
Consensus pattern (13 bp):
GGCATAGTTGATG
Found at i:25301470 original size:3 final size:3
Alignment explanation
Indices: 25301457--25301496 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
25301447 AGGGTGATCA
*
25301457 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
25301497 TGATGTTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:25305793 original size:3 final size:3
Alignment explanation
Indices: 25305785--25305829 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
25305775 TAGAACAATG
25305785 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25305830 TATTATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25305948 original size:20 final size:20
Alignment explanation
Indices: 25305919--25305972 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
25305909 ATGGAGTAAT
25305919 AATAACAATAATAA-AATATAA
1 AATAA-AATAA-AACAATATAA
*
25305940 AATAAAATAAAACTATATAA
1 AATAAAATAAAACAATATAA
*
25305960 ATATAAAAGAAAA
1 A-ATAAAATAAAA
25305973 TAAAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 15 0.52
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (20 bp):
AATAAAATAAAACAATATAA
Found at i:25306150 original size:17 final size:18
Alignment explanation
Indices: 25306123--25306157 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
25306113 GAAAATAAAT
25306123 AAATAAATAAATCAAACA
1 AAATAAATAAATCAAACA
*
25306141 AAAT-AATAAATGAAACA
1 AAATAAATAAATCAAACA
25306158 GTTTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATAAATAAATCAAACA
Found at i:25309212 original size:14 final size:14
Alignment explanation
Indices: 25309189--25309220 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25309179 CAGTATTTAT
25309189 TTATGATTAATTAA
1 TTATGATTAATTAA
*
25309203 TTATGTTTAATTAA
1 TTATGATTAATTAA
25309217 TTAT
1 TTAT
25309221 CTCATTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
TTATGATTAATTAA
Found at i:25316529 original size:34 final size:35
Alignment explanation
Indices: 25316485--25316551 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
25316475 CAGTAAAATA
*
25316485 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
25316519 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
25316552 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:25317178 original size:18 final size:17
Alignment explanation
Indices: 25317145--25317183 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
25317135 TTTTATAAAT
25317145 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
25317163 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
25317180 TGTG
1 TGTG
25317184 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:25317422 original size:23 final size:23
Alignment explanation
Indices: 25317395--25317447 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
25317385 AGTGTTATTG
25317395 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
25317418 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
25317441 ATCAGTG
1 ATCAGTG
25317448 TGGCACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:25329668 original size:38 final size:36
Alignment explanation
Indices: 25329624--25329755 Score: 151
Period size: 38 Copynumber: 3.5 Consensus size: 36
25329614 TATGAGTACG
*
25329624 TATATGTACATATATA-AGTTATAAAAAATATGAATGTA
1 TATATGT--ATATATAGA-TTATAAAAAATATGTATGTA
* *
25329662 TCTATGTATATATAGATTAT-AAAAATGCACGTATGTA
1 TATATGTATATATAGATTATAAAAAAT--ATGTATGTA
25329699 TATATGTATATATAGATTATAAAAAATATACGTATGTA
1 TATATGTATATATAGATTATAAAAAATAT--GTATGTA
*
25329737 TATATGTATATATAAATTA
1 TATATGTATATATAGATTA
25329756 CAATGTATAA
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
35 6 0.07
36 12 0.15
37 27 0.33
38 37 0.45
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (36 bp):
TATATGTATATATAGATTATAAAAAATATGTATGTA
Found at i:25330903 original size:6 final size:6
Alignment explanation
Indices: 25330894--25330918 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25330884 GCTGTTTGTG
25330894 TTTGCT TTTGCT TTTGCT TTTGCT T
1 TTTGCT TTTGCT TTTGCT TTTGCT T
25330919 CCGTATCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTGCT
Found at i:25350087 original size:4 final size:4
Alignment explanation
Indices: 25350071--25350109 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
25350061 GTAGCACCCG
*
25350071 TAGA T-GA TTGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
25350110 CCAAACCCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (4 bp):
TAGA
Found at i:25351924 original size:20 final size:20
Alignment explanation
Indices: 25351888--25351925 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25351878 CCTTTGTCCC
*
25351888 TTCCACCATGGTGTTGTCTA
1 TTCCACCATGGCGTTGTCTA
25351908 TTCCACCA-GGCGATTGTC
1 TTCCACCATGGCG-TTGTC
25351926 CTTTCAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.16, C:0.29, G:0.21, T:0.34
Consensus pattern (20 bp):
TTCCACCATGGCGTTGTCTA
Found at i:25352129 original size:7 final size:7
Alignment explanation
Indices: 25352117--25352149 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
25352107 GATTTTTTTG
25352117 TTATTAA
1 TTATTAA
25352124 TTATTAA
1 TTATTAA
25352131 TTATTAA
1 TTATTAA
25352138 TTATTAA
1 TTATTAA
25352145 TTATT
1 TTATT
25352150 TATGTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTATTAA
Found at i:25352801 original size:16 final size:16
Alignment explanation
Indices: 25352780--25352818 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
25352770 TTAACTCATT
*
25352780 TAATTTTTATATAATG
1 TAATTTTTATATAATA
25352796 TAATTTTTATATAATA
1 TAATTTTTATATAATA
25352812 TAATTTT
1 TAATTTT
25352819 ATTTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TAATTTTTATATAATA
Found at i:25365383 original size:44 final size:44
Alignment explanation
Indices: 25365335--25365468 Score: 125
Period size: 44 Copynumber: 3.1 Consensus size: 44
25365325 CCTGGACAAC
25365335 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
** * ** * * **
25365379 AGTGGAGCAGATCGAAGATGGCGGA--TT-T-TCCCT-GGACAAC
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG-CAGT
* *
25365419 AGTGGAATAGATTGAAGATTTCAAATCTTATCTCGCTAAGCAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
25365463 AGTGGA
1 AGTGGA
25365469 GCAGATCGAA
Statistics
Matches: 64, Mismatches: 20, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
39 1 0.02
40 25 0.39
41 1 0.02
42 4 0.06
43 1 0.02
44 31 0.48
45 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
Found at i:25365407 original size:132 final size:132
Alignment explanation
Indices: 25365052--25365407 Score: 610
Period size: 132 Copynumber: 2.7 Consensus size: 132
25365042 TGGAGTACAT
*
25365052 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAATATTTCAGATCTTATCTCCCTAAGCAG
1 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
25365117 TAGT-GA--AGATCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCC
66 TAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCC
25365179 AG
131 AG
*
25365181 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATATCCCTAAGCAG
1 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
* * * ** *
25365246 TAGTGGAGCAAATCGAAGATGGTAAATTTTACCTCCTTGTGGTTATAGTGGAGTACATTGAAGCC
66 TAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCC
25365311 AG
131 AG
25365313 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
1 TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
*
25365378 TAGTGGAGCAGATCGAAGATGGCGGATTTT
66 TAGTGGAGCAGATCGAAGATGGCAGATTTT
25365408 CCCTGGACAA
Statistics
Matches: 211, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
129 67 0.32
130 2 0.01
132 142 0.67
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (132 bp):
TAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCC
AG
Found at i:25365417 original size:84 final size:84
Alignment explanation
Indices: 25365322--25365491 Score: 313
Period size: 84 Copynumber: 2.0 Consensus size: 84
25365312 GTAATTCTAC
*
25365322 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
1 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGAGC
*
25365387 AGATCGAAGATGGCGGATT
66 AGATCGAAGATGGCAGATT
*
25365406 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCGCTAAGCAGTAGTGGAGC
1 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGAGC
25365471 AGATCGAAGATGGCAGATT
66 AGATCGAAGATGGCAGATT
25365490 TT
1 TT
25365492 ACCTCCCTGT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (84 bp):
TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGAGC
AGATCGAAGATGGCAGATT
Found at i:25365436 original size:40 final size:42
Alignment explanation
Indices: 25365322--25365437 Score: 103
Period size: 44 Copynumber: 2.8 Consensus size: 42
25365312 GTAATTCTAC
**
25365322 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTA
1 TTCCCTGGACAACAGTGGAATAGATTGAAGATGGCAGA-CTTA
* ** ** * *
25365365 TCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGCGGA-TT-
1 T-TCCCTGGA-CAACAGTGGAATAGATTGAAGATGGCAGACTTA
25365406 TTCCCTGGACAACAGTGGAATAGATTGAAGAT
1 TTCCCTGGACAACAGTGGAATAGATTGAAGAT
25365438 TTCAAATCTT
Statistics
Matches: 55, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
40 23 0.42
41 2 0.04
42 2 0.04
43 2 0.04
44 26 0.47
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (42 bp):
TTCCCTGGACAACAGTGGAATAGATTGAAGATGGCAGACTTA
Found at i:25365564 original size:216 final size:216
Alignment explanation
Indices: 25365190--25365623 Score: 742
Period size: 216 Copynumber: 2.0 Consensus size: 216
25365180 GTAATTCTAC
*
25365190 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATATCCCTAAGCAGTAGTGGAGC
1 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATATCCCTAAGCAGTAGTGGAGC
* * *
25365255 AAATCGAAGATGGTAAATTTTACCTCCTTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCT
66 AAATCGAAGATGGCAAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCT
* *
25365320 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGA
131 ACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGA
*
25365385 GCAGATCGAAGATGGCGGATT
196 GCAGATCGAAGATGACGGATT
* *
25365406 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCGCTAAGCAGTAGTGGAGC
1 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATATCCCTAAGCAGTAGTGGAGC
* *
25365471 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCT
66 AAATCGAAGATGGCAAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCT
* *
25365536 ACTTTCCTAGTCAACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGA
131 ACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGA
*
25365601 GCAGATCGAGGATGACGGATT
196 GCAGATCGAAGATGACGGATT
25365622 TT
1 TT
25365624 ACCTCCCTGT
Statistics
Matches: 204, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
216 204 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (216 bp):
TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATATCCCTAAGCAGTAGTGGAGC
AAATCGAAGATGGCAAATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCT
ACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCGAAGATGACGGATT
Found at i:25365569 original size:132 final size:131
Alignment explanation
Indices: 25365409--25365851 Score: 609
Period size: 132 Copynumber: 3.4 Consensus size: 131
25365399 GCGGATTTTC
* *
25365409 CCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCGCTAAGCAGTAGTGGAGCAGA
1 CCTGGTCAACAGTGGAATAGATTGAAGATTT-AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* * *
25365474 TCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCTACT
65 TCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT
25365539 TT
130 TT
*
25365541 CCTAGTCAACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 CCTGGTCAACAGTGGAATAGATTGAAGATTTAA-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
25365606 TCGAGGATGACGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT
65 TCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT
*
25365671 TC
130 TT
* * * * *
25365673 CCTGGGCAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGTAGA
1 CCTGGTCAACAGTGGAATAGATTGAAGATTT-AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* * * * * **
25365738 TCAAAGATGGTGGATTTTACCTCACTGTGGTTACAGTAGAGTTCATTGAAGCCAGTAAACCTA-T
65 TCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT
*
25365802 CT
130 TT
* * *
25365804 CTCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCTTATCTCCCT
1 C-CTGGTCAACAGTGGAATAGATTGAAGATT-TAAATCTTATCTCCCT
25365852 GCAGTTGCAG
Statistics
Matches: 275, Mismatches: 32, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
131 4 0.01
132 269 0.98
133 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (131 bp):
CCTGGTCAACAGTGGAATAGATTGAAGATTTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
CGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTT
T
Found at i:25365695 original size:348 final size:345
Alignment explanation
Indices: 25365061--25365755 Score: 1138
Period size: 348 Copynumber: 2.0 Consensus size: 345
25365051 TTAATTCTAC
* *
25365061 TTCCCTGGACAACAGTGGAATAGATTGAATATTTCAGATCTTATCTCCCTAAGCAGTAGTGAAGA
1 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGAAGA
*
25365126 TCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCCAGTAATTCTACT
66 TCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCCAATAATTCTACT
* *
25365191 TCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATATCCCTAAGCAGTAGTGGAGCA
131 TCCCTAGACAACAGTGGAATAGATTGAAGATTTAAGATCTTATATCCCTAAGCAGTAGTGGAGCA
** * *
25365256 AATCGAAGATGGTAAATTTTACCTCCTTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTA
196 AATCGAAGATGACAAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
*
25365321 CTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
261 CTTCCCTGGACAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
*
25365386 CAGATCGAAGATGGCGGATT
326 CAGATCAAAGATGGCGGATT
*
25365406 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCGCTAAGCAGTAGTGGAGC
1 TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGT-GA--
* *
25365471 AGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTCT
63 AGATCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCCAATAATTCT
* * *
25365536 ACTTTCCTAGTCAACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGA
128 ACTTCCCTAGACAACAGTGGAATAGATTGAAGATTTAAGATCTTATATCCCTAAGCAGTAGTGGA
* * **
25365601 GCAGATCGAGGATGACGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATT
193 GCAAATCGAAGATGACAAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATT
* *
25365666 CTACTTCCCTGGGCAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTG
258 CTACTTCCCTGGACAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
* *
25365731 GAGTAGATCAAAGATGGTGGATT
323 GAGCAGATCAAAGATGGCGGATT
25365754 TT
1 TT
25365756 ACCTCACTGT
Statistics
Matches: 322, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
345 57 0.18
346 2 0.01
348 263 0.82
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (345 bp):
TTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGAAGA
TCGAAGATGGCAGATTTTACCTCCCCGTGGTTATAGTAGAGTACATTGAAGCCAATAATTCTACT
TCCCTAGACAACAGTGGAATAGATTGAAGATTTAAGATCTTATATCCCTAAGCAGTAGTGGAGCA
AATCGAAGATGACAAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
CTTCCCTGGACAACAGAGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAG
CAGATCAAAGATGGCGGATT
Found at i:25367481 original size:17 final size:17
Alignment explanation
Indices: 25367438--25367498 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
25367428 ATTTAGTTAG
*
25367438 TAGTATTATTTACTTATATA
1 TAGTATTATTT--TTA-ATT
*
25367458 TACTATTATTTTTAATT
1 TAGTATTATTTTTAATT
25367475 TAGTATTAGTTTTTAATT
1 TAGTATTA-TTTTTAATT
25367493 TAGTAT
1 TAGTAT
25367499 AGTTCTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 9 0.24
18 18 0.49
20 10 0.27
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (17 bp):
TAGTATTATTTTTAATT
Found at i:25367501 original size:17 final size:18
Alignment explanation
Indices: 25367461--25367507 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
25367451 TTATATATAC
25367461 TATTA-TTTTTAATTTAG
1 TATTAGTTTTTAATTTAG
25367478 TATTAGTTTTTAATTTAG
1 TATTAGTTTTTAATTTAG
25367496 TA-TAGTTCTTTA
1 TATTAGTT-TTTA
25367508 TTATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (18 bp):
TATTAGTTTTTAATTTAG
Found at i:25367516 original size:2 final size:2
Alignment explanation
Indices: 25367509--25367536 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25367499 AGTTCTTTAT
25367509 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
25367537 GGTATGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25369148 original size:58 final size:55
Alignment explanation
Indices: 25369058--25369179 Score: 163
Period size: 58 Copynumber: 2.2 Consensus size: 55
25369048 ATAATATTTT
* **
25369058 ATTAAAAGAAAAAAATTAATATAAAAAATTCATTGGCGCCTGTCAAATAGGCGTG
1 ATTAAAAAAAAAAAATTAATATAAAAAATTCATTGGCGCCTGTCAAATAGGCGCC
* * *
25369113 ATTAAAAAAAAGAAAATTTTAATATAAAAACTTCATTGGCGCCTGTCAGATATGCGCC
1 ATTAAAAAAAA-AAAA--TTAATATAAAAAATTCATTGGCGCCTGTCAAATAGGCGCC
25369171 ATTAAAAAA
1 ATTAAAAAA
25369180 CATACTATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 10 0.17
56 4 0.07
58 44 0.76
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (55 bp):
ATTAAAAAAAAAAAATTAATATAAAAAATTCATTGGCGCCTGTCAAATAGGCGCC
Found at i:25376560 original size:33 final size:33
Alignment explanation
Indices: 25376429--25376561 Score: 108
Period size: 33 Copynumber: 4.0 Consensus size: 33
25376419 TGACAGTATA
* *
25376429 AATACATGTGTAAGACCATAGTTGGGCTATGAC
1 AATACATGTGTAAGACCATAATTGGGCTATGGC
* *
25376462 -ATTC-TGATGATAAGACCATAATTGGGTTATGGC
1 AATACATG-TG-TAAGACCATAATTGGGCTATGGC
* ** **** *
25376495 ACTACAAATGTAAGACCATGGCAGGGCCATGGC
1 AATACATGTGTAAGACCATAATTGGGCTATGGC
* *
25376528 AATGCATGTGTAAGACCATAATTGGACTATGGC
1 AATACATGTGTAAGACCATAATTGGGCTATGGC
25376561 A
1 A
25376562 CAAAAAGAAC
Statistics
Matches: 72, Mismatches: 24, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
31 2 0.03
32 5 0.07
33 61 0.85
34 4 0.06
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (33 bp):
AATACATGTGTAAGACCATAATTGGGCTATGGC
Found at i:25383759 original size:105 final size:105
Alignment explanation
Indices: 25383564--25383760 Score: 234
Period size: 105 Copynumber: 1.9 Consensus size: 105
25383554 AATGTTTAAA
* * * * *
25383564 TGTAAGACTATAGCTGGGCTATGACATTTTAATGAAAATACTATAACTGGGTTACGACACCTTAA
1 TGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTACGACACCTCAA
** *
25383629 ACGTAAAACCATGGTTGGACGATGGCAGTATAAATACATG
66 ACGTAAAACCATGGCAGGACCATGGCAGTATAAATACATG
* * * * *
25383669 TGTAAGACCATAGGTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGCA-CTACA
1 TGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTACGACACCT-CA
* * *
25383733 AATGTAAGACCATGGCAGGGCCATGGCA
65 AACGTAAAACCATGGCAGGACCATGGCA
25383761 ATGCATGTGT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
104 2 0.03
105 73 0.97
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTACGACACCTCAA
ACGTAAAACCATGGCAGGACCATGGCAGTATAAATACATG
Found at i:25383941 original size:18 final size:18
Alignment explanation
Indices: 25383918--25383956 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
25383908 AGAAAGTGTG
25383918 TTTATTGATTATATTGTA
1 TTTATTGATTATATTGTA
25383936 TTTATTGATTATATTGTA
1 TTTATTGATTATATTGTA
25383954 TTT
1 TTT
25383957 GTTAGGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (18 bp):
TTTATTGATTATATTGTA
Found at i:25388717 original size:34 final size:33
Alignment explanation
Indices: 25388671--25388780 Score: 93
Period size: 34 Copynumber: 3.4 Consensus size: 33
25388661 AAGCATTGTA
*
25388671 TCAAAAAGTCAAATTTCTTTATTAAAAATATATG
1 TCAAAAA-TCAAATTTCATTATTAAAAATATATG
* * * **
25388705 TCAAATAATCAAA-ATGAATAAGAAAAA-AT-T-
1 TCAAA-AATCAAATTTCATTATTAAAAATATATG
* *
25388735 TCTAAAGTCAAATTTCATTATTAAAAATATATG
1 TCAAAAATCAAATTTCATTATTAAAAATATATG
25388768 TCAAATAATCAAA
1 TCAAA-AATCAAA
25388781 ATGATTAAGT
Statistics
Matches: 55, Mismatches: 15, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
29 6 0.11
30 13 0.24
31 3 0.05
32 3 0.05
33 12 0.22
34 16 0.29
35 2 0.04
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (33 bp):
TCAAAAATCAAATTTCATTATTAAAAATATATG
Found at i:25388788 original size:30 final size:30
Alignment explanation
Indices: 25388691--25388788 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
25388681 AAATTTCTTT
25388691 ATTAAAAATATATGTCAAATAATCAAAATG
1 ATTAAAAATATATGTCAAATAATCAAAATG
* * * * * *
25388721 AATAAGAAA-AAATTTCTAA-AGTCAAATTTCATT
1 ATTAA-AAATATATGTCAAATAATCAAA----ATG
25388754 ATTAAAAATATATGTCAAATAATCAAAATG
1 ATTAAAAATATATGTCAAATAATCAAAATG
25388784 ATTAA
1 ATTAA
25388789 GTATGTAATA
Statistics
Matches: 49, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
29 6 0.12
30 18 0.37
31 3 0.06
32 3 0.06
33 13 0.27
34 6 0.12
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.32
Consensus pattern (30 bp):
ATTAAAAATATATGTCAAATAATCAAAATG
Found at i:25389480 original size:14 final size:13
Alignment explanation
Indices: 25389461--25389492 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
25389451 TGGTAGATTT
25389461 TATTTTTATATATA
1 TATTTTTATATA-A
25389475 TATTTTTATATAA
1 TATTTTTATATAA
25389488 TATTT
1 TATTT
25389493 AGAATTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTTTTATATAA
Found at i:25389651 original size:16 final size:15
Alignment explanation
Indices: 25389630--25389668 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
25389620 TTTATTGTCA
25389630 AAATTAATACAAATAC
1 AAATTAATACAAAT-C
*
25389646 AAATTAATTCAAATC
1 AAATTAATACAAATC
*
25389661 AAAATAAT
1 AAATTAAT
25389669 TTAAGCGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATTAATACAAATC
Found at i:25393535 original size:2 final size:2
Alignment explanation
Indices: 25393528--25393575 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
25393518 ACTTATCATT
25393528 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
25393570 TA TA TA
1 TA TA TA
25393576 CTTTGTAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25394842 original size:16 final size:16
Alignment explanation
Indices: 25394821--25394856 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
25394811 TTGTGTTTTG
25394821 TTTTGACTGCATGACA
1 TTTTGACTGCATGACA
* *
25394837 TTTTGATTGCATTACA
1 TTTTGACTGCATGACA
25394853 TTTT
1 TTTT
25394857 CATCTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (16 bp):
TTTTGACTGCATGACA
Found at i:25398092 original size:1 final size:1
Alignment explanation
Indices: 25398086--25398206 Score: 62
Period size: 1 Copynumber: 121.0 Consensus size: 1
25398076 AGATTCAATT
* * * * * * * * *
25398086 AAAAAAAAACAAAGACAAAAACAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAGAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * *
25398151 CAAAAAAGAGAACAAAAAAGAACAAAAGAACAAAAAAACAAAAAGAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25398207 CCTCTACCGA
Statistics
Matches: 80, Mismatches: 40, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:25398119 original size:8 final size:8
Alignment explanation
Indices: 25398102--25398207 Score: 81
Period size: 8 Copynumber: 12.8 Consensus size: 8
25398092 AAACAAAGAC
25398102 AAAAACAAA
1 AAAAAC-AA
*
25398111 AAACAAAAA
1 AAA-AACAA
25398120 AAAAACAAA
1 AAAAAC-AA
25398129 AAAAACAA
1 AAAAACAA
*
25398137 AAAAAGAGA
1 AAAAACA-A
25398146 AAAAAC-A
1 AAAAACAA
* *
25398153 AAAAAGAG
1 AAAAACAA
*
25398161 AACAA-AA
1 AAAAACAA
*
25398168 AAGAACAA
1 AAAAACAA
*
25398176 AAGAACAA
1 AAAAACAA
25398184 AAAAACAAA
1 AAAAAC-AA
25398193 AAGAAACAA
1 AA-AAACAA
25398202 AAAAAC
1 AAAAAC
25398208 CTCTACCGAG
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
7 11 0.14
8 33 0.41
9 30 0.38
10 6 0.08
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:25398123 original size:18 final size:18
Alignment explanation
Indices: 25398089--25398205 Score: 112
Period size: 18 Copynumber: 6.3 Consensus size: 18
25398079 TTCAATTAAA
*
25398089 AAAAAACAAAGACAAAAAC
1 AAAAAACAAA-AAAAAAAC
25398108 AAAAAACAAAAAAAAAAC
1 AAAAAACAAAAAAAAAAC
*
25398126 AAAAAA-AACAAAAAAAGAG
1 AAAAAACAA-AAAAAAA-AC
*
25398145 AAAAAACAAAAAAGAGAAC
1 AAAAAACAAAAAA-AAAAC
* * *
25398164 AAAAAAGAACAAAAGAAC
1 AAAAAACAAAAAAAAAAC
*
25398182 AAAAAA-ACAAAAAGAAAC
1 AAAAAACA-AAAAAAAAAC
25398200 AAAAAA
1 AAAAAA
25398206 ACCTCTACCG
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
17 3 0.04
18 44 0.52
19 33 0.39
20 4 0.05
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAAC
Found at i:25398131 original size:26 final size:26
Alignment explanation
Indices: 25398089--25398205 Score: 76
Period size: 27 Copynumber: 4.2 Consensus size: 26
25398079 TTCAATTAAA
*
25398089 AAAAAACAAAGACAAAAAC-AAAAAAC
1 AAAAAACAAA-AAAAAAACAAAAAAAC
* *
25398115 AAAAAAAAAACAAAAAAAACAAAAAAAG
1 -AAAAAACAA-AAAAAAAACAAAAAAAC
* *
25398143 AGAAAAAACAAAAAAGAGAACAAAAAAGAAC
1 AAAAAA--CAAAAAA-AAAAC-AAAAA-AAC
* *
25398174 AAAAGAACAAAAAAACAA-AAAGAAAC
1 AAAA-AACAAAAAAAAAACAAAAAAAC
25398200 AAAAAA
1 AAAAAA
25398206 ACCTCTACCG
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
25 2 0.03
26 7 0.10
27 24 0.33
28 11 0.15
29 9 0.12
30 12 0.17
31 5 0.07
32 2 0.03
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (26 bp):
AAAAAACAAAAAAAAAACAAAAAAAC
Found at i:25398167 original size:56 final size:55
Alignment explanation
Indices: 25398089--25398194 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 55
25398079 TTCAATTAAA
25398089 AAAAAACAAAGACAAAAACAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAGAG
1 AAAAAACAAAGACAAAAACAAAAAACAAAAAAAAAAC-AAAAAAACAAAAAAAGAG
* * *
25398145 AAAAAACAAA-A-AAGAGAACAAAAAAGAACAAAAGAACAAAAAAACAAAAA
1 AAAAAACAAAGACAA-A-AACAAAAAACAAAAAAAAAACAAAAAAACAAAAA
25398195 GAAACAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 2 0.04
55 15 0.33
56 28 0.62
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (55 bp):
AAAAAACAAAGACAAAAACAAAAAACAAAAAAAAAACAAAAAAACAAAAAAAGAG
Found at i:25398205 original size:56 final size:56
Alignment explanation
Indices: 25398087--25398207 Score: 142
Period size: 56 Copynumber: 2.2 Consensus size: 56
25398077 GATTCAATTA
25398087 AAAAAAAACAAAGACAAAAACAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAG
1 AAAAAAAACAAAGACAAAAACAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAG
* * * *
25398143 AGAAAAAACAAA-A-AAGAGAACAAAAAAGAACAAAAGAAC-AAAAAAACAAAAAGAA-
1 AAAAAAAACAAAGACAA-A-AACAAAAAACAAAAAAAAAACAAAAAAAACAAAAA-AAG
25398198 ACAAAAAAAC
1 A-AAAAAAAC
25398208 CTCTACCGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
54 2 0.04
55 16 0.29
56 38 0.68
ACGTcount: A:0.83, C:0.11, G:0.07, T:0.00
Consensus pattern (56 bp):
AAAAAAAACAAAGACAAAAACAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAG
Found at i:25400275 original size:177 final size:177
Alignment explanation
Indices: 25399965--25400428 Score: 660
Period size: 177 Copynumber: 2.6 Consensus size: 177
25399955 TCGGCGAAAC
25399965 CACCAGCCTTGCCTCCCTGGGTTTGTAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGT
1 CACCAGCCTTGCCTCCCTGGG-TTGTAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGT
* * * *
25400030 ACTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTAGGTTTGCAGCGGAGCAGATTGA
65 ACTGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGA
* *
25400095 ATATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCAAAGA
130 ATATAGAAGATCTTGCCTTCCTGTACTGACAGAGAAGCAGATCAAAGA
* * *
25400143 CACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCTTGTA
1 CACCAGCCTTGCCTCCCTGGGTTGTAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
*
25400208 CTGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGGAGACTGAA
66 CTGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAA
* * *
25400273 TATGGAAGATCTTGCCTTCCTGTACTGACAGAGAAGCATATCGAAGA
131 TATAGAAGATCTTGCCTTCCTGTACTGACAGAGAAGCAGATCAAAGA
* * ** * * ** * *
25400320 TACCAGCCTTGTCTCCCTGGGCAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTA
1 CACCAGCCTTGCCTCCCTGGGTTGTAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
* * * *
25400385 CTGACAGA-GAAGTAGATCGAAGAGACCAGCCTTGTCTCCTTGGG
66 CTGACA-ACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGG
25400429 CAGTTGAGTA
Statistics
Matches: 255, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
177 234 0.92
178 21 0.08
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.23
Consensus pattern (177 bp):
CACCAGCCTTGCCTCCCTGGGTTGTAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
CTGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGCAGACTGAA
TATAGAAGATCTTGCCTTCCTGTACTGACAGAGAAGCAGATCAAAGA
Found at i:25400432 original size:88 final size:88
Alignment explanation
Indices: 25399965--25400428 Score: 633
Period size: 89 Copynumber: 5.2 Consensus size: 88
25399955 TCGGCGAAAC
*
25399965 CACCAGCCTTGCCTCCCTGGGTTTGTAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGT
1 CACCAGCCTTGCCTCCCTGGG-TTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGT
* *
25400030 ACTGACAGCGAAGCAGATCAAAGA
65 ACTGACAGAGAAGCAGATCGAAGA
* *
25400054 CACCAGCCTTGCCTCCCTAGGTTTGCAGCGGAGCAGATTGAATATAGCAGATCTTGCCTTCCTGT
1 CACCAGCCTTGCCTCCCT-GGGTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGT
* *
25400119 ACTGACAGCGAAGCAGATCAAAGA
65 ACTGACAGAGAAGCAGATCGAAGA
* *
25400143 CACTAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCTTGTA
1 CACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
25400208 CTGACA-ACGAAGCAGATCGAAGA
66 CTGACAGA-GAAGCAGATCGAAGA
* * *
25400231 CACCAGCCTTGCCTCCCTGGGTTTGCAGCGGAGGAGACTGAATATGGAAGATCTTGCCTTCCTGT
1 CACCAGCCTTGCCTCCCTGGG-TTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGT
*
25400296 ACTGACAGAGAAGCATATCGAAGA
65 ACTGACAGAGAAGCAGATCGAAGA
* * ** * * * ** * *
25400320 TACCAGCCTTGTCTCCCTGGGCAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTA
1 CACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
*
25400385 CTGACAGAGAAGTAGATCGAAGA
66 CTGACAGAGAAGCAGATCGAAGA
* * *
25400408 GACCAGCCTTGTCTCCTTGGG
1 CACCAGCCTTGCCTCCCTGGG
25400429 CAGTTGAGTA
Statistics
Matches: 339, Mismatches: 32, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
88 157 0.46
89 179 0.53
90 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.23
Consensus pattern (88 bp):
CACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTA
CTGACAGAGAAGCAGATCGAAGA
Found at i:25400747 original size:131 final size:130
Alignment explanation
Indices: 25400453--25400832 Score: 476
Period size: 131 Copynumber: 2.9 Consensus size: 130
25400443 AAGGATGGTG
* *
25400453 GATTTTACCT-CCTCGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
1 GATTTTACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCA-TAATTCTATCTCCCTGGTCAG
* * ** * * *
25400517 CAGTGGAATAGATTGAAGATTTCAGATATTGCCTTCCT-GCATAGACAGTGAAGCAGATCGAAGA
64 CAGTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAGCAT---TAGTGGAGCAGATCGAAGA
25400581 TGGCA
126 TGGCA
* * **
25400586 GATTTTACCTCCCTGTGGTTACGGTGGAGTACATTGAAGCTATAATTCTATCTCCCTGGTTGGCA
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCATAATTCTATCTCCCTGGTCAGCA
* *
25400651 GTGGAATAGATTGAATATTTCAGATCTTATCTCCCTAGGCATTAGTGGAGCTGATCGAAGATGGC
66 GTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTA-GCATTAGTGGAGCAGATCGAAGATGGC
25400716 A
130 A
* *
25400717 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCGTAATTCTATCTCCCTGGTCAACA
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCATAATTCTATCTCCCTGGTCAGCA
* * ** *
25400782 GTGGAATCGATCGAAGAATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAG
66 GTGGAATAGATTGAA-AATTTCAGATCTTATCTCCCT-AGCATTAGTGGAG
25400833 TAGACTGATG
Statistics
Matches: 216, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
131 93 0.43
132 80 0.37
133 36 0.17
134 7 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (130 bp):
GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCATAATTCTATCTCCCTGGTCAGCA
GTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAGCATTAGTGGAGCAGATCGAAGATGGCA
Found at i:25402578 original size:2 final size:2
Alignment explanation
Indices: 25402526--25402564 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
25402516 TTTTATAATC
* *
25402526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25402565 CCTTTGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:25429361 original size:89 final size:89
Alignment explanation
Indices: 25429202--25429368 Score: 214
Period size: 89 Copynumber: 1.9 Consensus size: 89
25429192 AAAAACTGTC
* *
25429202 TTTTTTTTTCACTCAATTGAATACTTGAATTTTCAAAATACATAAAAAAAAGTCCTTAGACTTCT
1 TTTTTTTTTCACTCAATTGAATACTTGAATTTTCAAAATACATAAAAAAAAGTCCTCAGAATTCT
25429267 TAAAAAAACAATTATGTCACTGCT
66 TAAAAAAACAATTATGTCACTGCT
* * * *** *
25429291 TTTTTTTTTCATTCAATTGGATACTTGAACTTTT-AAAATGCATAAAATGGA-TCCTCA-AATTT
1 TTTTTTTTTCACTCAATTGAATACTTGAA-TTTTCAAAATACATAAAAAAAAGTCCTCAGAATTC
25429353 TTCAAAAAAACAATTA
65 TT-AAAAAAACAATTA
25429369 AGCCCCCGCT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
87 5 0.07
88 18 0.27
89 40 0.60
90 4 0.06
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (89 bp):
TTTTTTTTTCACTCAATTGAATACTTGAATTTTCAAAATACATAAAAAAAAGTCCTCAGAATTCT
TAAAAAAACAATTATGTCACTGCT
Found at i:25429800 original size:39 final size:37
Alignment explanation
Indices: 25429741--25429819 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
25429731 AATTTTTATA
* *
25429741 TTTCTATGTATTTTATATTTTTTAGGATTTTTATATTTT
1 TTTCTATGTATTTTATATTTTTTA--ATATTTAAATTTT
25429780 TTTCTA-GT-TTTTAATAATTTTTTAATATTTAAATTTT
1 TTTCTATGTATTTT-AT-ATTTTTTAATATTTAAATTTT
25429817 TTT
1 TTT
25429820 ATTAAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
37 18 0.50
38 4 0.11
39 14 0.39
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (37 bp):
TTTCTATGTATTTTATATTTTTTAATATTTAAATTTT
Found at i:25429965 original size:54 final size:56
Alignment explanation
Indices: 25429899--25430006 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 56
25429889 CTTAATTGTT
*
25429899 TTTTTCTTGAAAA-AGTTTGAGG-GTTTTTTTGATGTATTTTGAAAGTTTAAGTTGC
1 TTTTTCTTGAAAAGA-TTTGAGGAGTTTTTTTGATATATTTTGAAAGTTTAAGTTGC
*
25429954 TTTTT-TTGAAAAGATTTGAGGACTTTTTTTTGATATATTTTGAAAGTTTAAGT
1 TTTTTCTTGAAAAGATTTGAGGA-GTTTTTTTGATATATTTTGAAAGTTTAAGT
25430007 ATTCAAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
54 14 0.29
55 6 0.12
56 28 0.58
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (56 bp):
TTTTTCTTGAAAAGATTTGAGGAGTTTTTTTGATATATTTTGAAAGTTTAAGTTGC
Found at i:25441104 original size:8 final size:9
Alignment explanation
Indices: 25441085--25441128 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 9
25441075 CGTACAAATT
25441085 AGAAAGAA-
1 AGAAAGAAG
25441093 AGAAA-AAG
1 AGAAAGAAG
25441101 AGAAAGAA-
1 AGAAAGAAG
*
25441109 AGAAAG-GG
1 AGAAAGAAG
25441117 AGAAAGAAG
1 AGAAAGAAG
25441126 AGA
1 AGA
25441129 CGCACGACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.07
8 22 0.73
9 6 0.20
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (9 bp):
AGAAAGAAG
Found at i:25441106 original size:16 final size:16
Alignment explanation
Indices: 25441085--25441124 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
25441075 CGTACAAATT
25441085 AGAAAGAAAGAAAAAG
1 AGAAAGAAAGAAAAAG
**
25441101 AGAAAGAAAGAAAGGG
1 AGAAAGAAAGAAAAAG
25441117 AGAAAGAA
1 AGAAAGAA
25441125 GAGACGCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGAAAAAG
Found at i:25444132 original size:20 final size:20
Alignment explanation
Indices: 25444107--25444148 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
25444097 TGATTTGTCT
25444107 GTGGCTCTTTCATGCCATTG
1 GTGGCTCTTTCATGCCATTG
*
25444127 GTGGCTCTTTTATGCCATTG
1 GTGGCTCTTTCATGCCATTG
25444147 GT
1 GT
25444149 AGCTATTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.21, G:0.26, T:0.43
Consensus pattern (20 bp):
GTGGCTCTTTCATGCCATTG
Found at i:25451328 original size:27 final size:24
Alignment explanation
Indices: 25451290--25451396 Score: 89
Period size: 27 Copynumber: 4.5 Consensus size: 24
25451280 GAGATGAAAG
25451290 CTTGATTGAAAACTTAATGATTAAAAA
1 CTTGA-TGAAAACTTAATGA--AAAAA
* *
25451317 CTTGATGGAAAACTTTATGAAAAGA
1 CTTGAT-GAAAACTTAATGAAAAAA
*
25451342 CTTGATGAAAAGCTTAA--AAAGAA
1 CTTGATGAAAA-CTTAATGAAAAAA
*
25451365 CTTGATGCAAACTTAA--AAAAAA
1 CTTGATGAAAACTTAATGAAAAAA
*
25451387 TTTGAT-AAAA
1 CTTGATGAAAA
25451397 GAAGTTGATG
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
21 3 0.04
22 15 0.22
23 14 0.20
24 5 0.07
25 14 0.20
26 1 0.01
27 17 0.25
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (24 bp):
CTTGATGAAAACTTAATGAAAAAA
Found at i:25451344 original size:13 final size:13
Alignment explanation
Indices: 25451307--25451353 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
25451297 GAAAACTTAA
*
25451307 TGATTAAAA-ACT
1 TGATGAAAAGACT
*
25451319 TGATGGAAA-ACT
1 TGATGAAAAGACT
*
25451331 TTATGAAAAGACT
1 TGATGAAAAGACT
25451344 TGATGAAAAG
1 TGATGAAAAG
25451354 CTTAAAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (13 bp):
TGATGAAAAGACT
Found at i:25451379 original size:22 final size:23
Alignment explanation
Indices: 25451336--25451397 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
25451326 AAACTTTATG
25451336 AAAAG-ACTTGATGAAAAGCTTA
1 AAAAGAACTTGATGAAAAGCTTA
*
25451358 AAAAGAACTTGATGCAAA-CTTA
1 AAAAGAACTTGATGAAAAGCTTA
* *
25451380 AAAAAAATTTGAT-AAAAG
1 AAAAGAACTTGATGAAAAG
25451398 AAGTTGATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.09
22 20 0.59
23 11 0.32
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.23
Consensus pattern (23 bp):
AAAAGAACTTGATGAAAAGCTTA
Found at i:25454536 original size:22 final size:22
Alignment explanation
Indices: 25454493--25454549 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
25454483 TGTAGTTTTC
25454493 TAGGTGAAA-AGTTGGATGTGA
1 TAGGTGAAAGAGTTGGATGTGA
*
25454514 TAGGTGAAAGA-TTAGGATTTGA
1 TAGGTGAAAGAGTT-GGATGTGA
25454536 TAGGTGAAAG-GTTG
1 TAGGTGAAAGAGTTG
25454550 ATGGGTGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (22 bp):
TAGGTGAAAGAGTTGGATGTGA
Found at i:25454810 original size:7 final size:7
Alignment explanation
Indices: 25454798--25454826 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
25454788 TCTCCCTGTA
25454798 AAATAAT
1 AAATAAT
25454805 AAATAAT
1 AAATAAT
25454812 AAA-AAT
1 AAATAAT
25454818 AAATAAT
1 AAATAAT
25454825 AA
1 AA
25454827 GGAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:25454834 original size:13 final size:13
Alignment explanation
Indices: 25454802--25454826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25454792 CCTGTAAAAT
25454802 AATAAATAATAAA
1 AATAAATAATAAA
25454815 AATAAATAATAA
1 AATAAATAATAA
25454827 GGAAAAATTA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAAATAATAAA
Found at i:25461689 original size:27 final size:24
Alignment explanation
Indices: 25461651--25461783 Score: 96
Period size: 27 Copynumber: 5.4 Consensus size: 24
25461641 GAGATGAAAG
25461651 CTTGATTGAAAACTTAATGATTAAAAA
1 CTTGA-TGAAAACTTAATGA--AAAAA
* *
25461678 CTTGATGGAAAACTTTATGAAAAGA
1 CTTGAT-GAAAACTTAATGAAAAAA
*
25461703 CTTGATGAAAAGCTTAA--AAAGAA
1 CTTGATGAAAA-CTTAATGAAAAAA
*
25461726 CTTGATGCAAACTT-A--AAAAAA
1 CTTGATGAAAACTTAATGAAAAAA
* *
25461747 CTTGATAAAAGAACTTGATGAAAAACA
1 CTTGAT-GAA-AACTTAATGAAAAA-A
*
25461774 CTTGAAGAAA
1 CTTGATGAAA
25461784 GAAAACACTT
Statistics
Matches: 87, Mismatches: 11, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.14
22 4 0.05
23 19 0.22
24 6 0.07
25 15 0.17
26 8 0.09
27 23 0.26
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.26
Consensus pattern (24 bp):
CTTGATGAAAACTTAATGAAAAAA
Found at i:25461740 original size:22 final size:23
Alignment explanation
Indices: 25461697--25461757 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
25461687 AAACTTTATG
25461697 AAAAG-ACTTGATGAAAAGCTTA
1 AAAAGAACTTGATGAAAAGCTTA
*
25461719 AAAAGAACTTGATGCAAA-CTTA
1 AAAAGAACTTGATGAAAAGCTTA
25461741 AAAA-AACTTGAT-AAAAG
1 AAAAGAACTTGATGAAAAG
25461758 AACTTGATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 3 0.09
21 8 0.23
22 13 0.37
23 11 0.31
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (23 bp):
AAAAGAACTTGATGAAAAGCTTA
Found at i:25461776 original size:14 final size:13
Alignment explanation
Indices: 25461659--25461783 Score: 65
Period size: 12 Copynumber: 10.1 Consensus size: 13
25461649 AGCTTGATTG
*
25461659 AAAACTTAATGATTA
1 AAAACTTGATGA--A
*
25461674 AAAACTTGATG-G
1 AAAACTTGATGAA
*
25461686 AAAACTTTATGAA
1 AAAACTTGATGAA
*
25461699 AAGACTTGATG-A
1 AAAACTTGATGAA
*
25461711 AAAGCTT-A--AA
1 AAAACTTGATGAA
25461721 AAGAACTTGATG--
1 AA-AACTTGATGAA
*
25461733 CAAACTT-A--AA
1 AAAACTTGATGAA
25461743 AAAACTTGAT-AA
1 AAAACTTGATGAA
25461755 AAGAACTTGATGAA
1 AA-AACTTGATGAA
*
25461769 AAACACTTGAAGAA
1 AAA-ACTTGATGAA
25461783 A
1 A
25461784 GAAAACACTT
Statistics
Matches: 85, Mismatches: 12, Indels: 27
0.69 0.10 0.22
Matches are distributed among these distances:
10 10 0.12
11 11 0.13
12 22 0.26
13 18 0.21
14 14 0.16
15 10 0.12
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (13 bp):
AAAACTTGATGAA
Found at i:25462236 original size:21 final size:20
Alignment explanation
Indices: 25462181--25462236 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
25462171 AAGAATTCAG
*
25462181 ATCAATCTTTAATTAGTTTA
1 ATCAATCATTAATTAGTTTA
*
25462201 ATCAAGTTATT-ATTA-TACTTA
1 ATCAA-TCATTAATTAGT--TTA
25462222 ATCAATCATTAATTA
1 ATCAATCATTAATTA
25462237 AACAAAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 15 0.52
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (20 bp):
ATCAATCATTAATTAGTTTA
Found at i:25468700 original size:15 final size:16
Alignment explanation
Indices: 25468680--25468709 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25468670 TAGTGTATTA
25468680 TATTTTTAAA-AAAAT
1 TATTTTTAAATAAAAT
25468695 TATTTTTAAATAAAA
1 TATTTTTAAATAAAA
25468710 ACTAATCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTTTAAATAAAAT
Found at i:25472405 original size:26 final size:23
Alignment explanation
Indices: 25472356--25472405 Score: 55
Period size: 23 Copynumber: 2.0 Consensus size: 23
25472346 CTCCAAAAAA
* *
25472356 AAAAAAAGAATCTGAATTCCATG
1 AAAAAAAGAATCTGAAATCAATG
25472379 AAAAAAAGAATCTAGAACATCTAATG
1 AAAAAAAGAATCT-GAA-ATC-AATG
25472405 A
1 A
25472406 CCTAGCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 3 0.14
25 2 0.09
26 4 0.18
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (23 bp):
AAAAAAAGAATCTGAAATCAATG
Found at i:25476875 original size:20 final size:19
Alignment explanation
Indices: 25476852--25476900 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
25476842 TTTCAAAACT
25476852 TTTTTATAATTTTAATTATA
1 TTTTTATAATTTTAATT-TA
25476872 TTTTTA-AA----AATTTA
1 TTTTTATAATTTTAATTTA
25476886 TTTTTATAATTTTAA
1 TTTTTATAATTTTAA
25476901 GAAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 11
0.69 0.00 0.31
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
19 4 0.17
20 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTATAATTTTAATTTA
Found at i:25479988 original size:2 final size:2
Alignment explanation
Indices: 25479981--25480008 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25479971 ATGATAATGC
25479981 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
25480009 TACAAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25481287 original size:100 final size:99
Alignment explanation
Indices: 25481144--25481451 Score: 384
Period size: 100 Copynumber: 3.1 Consensus size: 99
25481134 TGATTATTTA
* * * * * * *
25481144 CTTCAATCTGTTTAACTGCAGTGTCAGGGAAACAAGATTCGCCGCCGTGACTTCAATCTATTCCA
1 CTTCAATCT-TTTAATTGCAATGTCAAGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCCA
*
25481209 CTACACCGCCAAGGAAGTAAGATTCGCCGTTGTGG
65 CTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * *
25481244 CTTCAATCTTTTAAATTGCAATATCATGGAAACCAGATCCGCCGTCGTGGCTTCAATCTGCTCCA
1 CTTCAATCTTTT-AATTGCAATGTCAAGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCCA
* *
25481309 CTACACCGCCAGGGAAGTAAGATCCGCCATTGTGG
65 CTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
* * * *
25481344 CTTCAATCTTTTTTATTGCAATGTTAAGGAAACCAGATCCGTCGTCGT-AGCTTTAATCTGTTCC
1 CTTCAATC-TTTTAATTGCAATGTCAAGGAAACCAGATCCGCCGTCGTGA-CTTCAATCTGTTCC
* * *
25481408 ACTATACTGCCAGGGAAGCAAGATTCGCCGTTGTGG
64 ACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
25481444 CTTCAATC
1 CTTCAATC
25481452 CGTTCCACTG
Statistics
Matches: 179, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
99 3 0.02
100 172 0.96
101 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (99 bp):
CTTCAATCTTTTAATTGCAATGTCAAGGAAACCAGATCCGCCGTCGTGACTTCAATCTGTTCCAC
TACACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
Found at i:25481332 original size:50 final size:50
Alignment explanation
Indices: 25481168--25481460 Score: 163
Period size: 50 Copynumber: 5.9 Consensus size: 50
25481158 ACTGCAGTGT
* * *
25481168 CAGGGAAACAAGATTCGCCGCCGTGACTTCAATCTATTCCACTACACCGC
1 CAGGGAAACAAGATCCGCCGTCGTGGCTTCAATCTATTCCACTACACCGC
* ** * * * ** * * ****
25481218 CAAGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATAT
1 CAGGGAAACAAGATCCGCCGTCGTGGCTTCAATCTATTCCACTACACCGC
* * **
25481268 CATGGAAACCAGATCCGCCGTCGTGGCTTCAATCTGCTCCACTACACCGC
1 CAGGGAAACAAGATCCGCCGTCGTGGCTTCAATCTATTCCACTACACCGC
** * * * ** * * ** *
25481318 CAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTTATTGCAATGT
1 CAGGGAAACAAGATCCGCCGTCGTGGCTTCAATCTATTCCACTACACCGC
* * * * * * * * *
25481368 TAAGGAAACCAGATCCGTCGTCGTAGCTTTAATCTGTTCCACTATACTGC
1 CAGGGAAACAAGATCCGCCGTCGTGGCTTCAATCTATTCCACTACACCGC
* * * **
25481418 CAGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCCGTTCCACT
1 CAGGGAAACAAGATCCGCCGTCGTGGCTTCAATCTATTCCACT
25481461 GTAATGCCAA
Statistics
Matches: 169, Mismatches: 74, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
50 169 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
CAGGGAAACAAGATCCGCCGTCGTGGCTTCAATCTATTCCACTACACCGC
Done.