Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 26 of 199
Found at i:10750110 original size:6 final size:6
Alignment explanation
Indices: 10750101--10750126 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10750091 TTTTGGTTTA
10750101 TTTTGT TTTTGT TTTTGT TTTTGT TT
1 TTTTGT TTTTGT TTTTGT TTTTGT TT
10750127 AATTAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:10766816 original size:6 final size:6
Alignment explanation
Indices: 10766805--10766838 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
10766795 AGATGTCAAA
*
10766805 TGATGG TGATGG TGATGG TAATGG TGATGG TGAT
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGAT
10766839 TGGTAATGCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (6 bp):
TGATGG
Found at i:10766830 original size:18 final size:19
Alignment explanation
Indices: 10766807--10766846 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
10766797 ATGTCAAATG
10766807 ATGGTGATGGTGA-TGGTA
1 ATGGTGATGGTGATTGGTA
10766825 ATGGTGATGGTGATTGGTA
1 ATGGTGATGGTGATTGGTA
10766844 ATG
1 ATG
10766847 CGCCGCCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (19 bp):
ATGGTGATGGTGATTGGTA
Found at i:10768826 original size:3 final size:3
Alignment explanation
Indices: 10768818--10768850 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
10768808 TTTGGGATGC
*
10768818 AGA AGA AGA AGA TGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
10768851 GCATAGCGGG
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:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:10773763 original size:13 final size:13
Alignment explanation
Indices: 10773726--10773763 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
10773716 TTAATTTATA
10773726 AAAAATTAAA-AT
1 AAAAATTAAATAT
10773738 AATTAAATTAAATAT
1 AA--AAATTAAATAT
10773753 AAAAATTAAAT
1 AAAAATTAAAT
10773764 CCACAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 8 0.35
15 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:10783918 original size:50 final size:51
Alignment explanation
Indices: 10783788--10783934 Score: 190
Period size: 50 Copynumber: 2.9 Consensus size: 51
10783778 TAAATGATAC
* * ** *
10783788 CCGGTTCACATAGTAGCCTGTACATAGTACTACACATGTGATCGAAGTTATT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCTAGTCATT
* *
10783840 -CAGTACGCATAGTAGCCTGCACATAGTACTACACATGTGACCTA-TCATT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCTAGTCATT
* *
10783889 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCTAG
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCTAG
10783935 CAACTTCACT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
49 4 0.05
50 42 0.51
51 36 0.44
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (51 bp):
CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCTAGTCATT
Found at i:10784116 original size:15 final size:16
Alignment explanation
Indices: 10784087--10784118 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10784077 AATCCAGTCC
10784087 AAAAATCACATTTTTG
1 AAAAATCACATTTTTG
*
10784103 AAAAATTACATTTTTG
1 AAAAATCACATTTTTG
10784119 CCCCTACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
AAAAATCACATTTTTG
Found at i:10785091 original size:28 final size:26
Alignment explanation
Indices: 10785047--10785098 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
10785037 TTAATTCCAA
*
10785047 CTTTTATAACATGTATATATATACATAT
1 CTTTTATAACA--TATATAAATACATAT
*
10785075 CTTTTATAATATATATAAATACAT
1 CTTTTATAACATATATAAATACAT
10785099 GCACATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
28 10 0.45
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (26 bp):
CTTTTATAACATATATAAATACATAT
Found at i:10792425 original size:22 final size:22
Alignment explanation
Indices: 10792400--10792455 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 22
10792390 GAATGTGTAT
10792400 ATATGAGATAATTTCATGTTTG
1 ATATGAGATAATTTCATGTTTG
10792422 ATATGAGTGCGGATAATTTCATGTTTG
1 ATATGA-----GATAATTTCATGTTTG
10792449 ATATGAG
1 ATATGAG
10792456 TGCTTAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
22 7 0.24
27 22 0.76
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.41
Consensus pattern (22 bp):
ATATGAGATAATTTCATGTTTG
Found at i:10792436 original size:27 final size:27
Alignment explanation
Indices: 10792406--10792458 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
10792396 GTATATATGA
10792406 GATAATTTCATGTTTGATATGAGTGCG
1 GATAATTTCATGTTTGATATGAGTGCG
10792433 GATAATTTCATGTTTGATATGAGTGC
1 GATAATTTCATGTTTGATATGAGTGC
10792459 TTAGTATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.42
Consensus pattern (27 bp):
GATAATTTCATGTTTGATATGAGTGCG
Found at i:10805132 original size:29 final size:29
Alignment explanation
Indices: 10805097--10805161 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
10805087 CTTAATATCC
10805097 AGCCCAATATTTTAAATCAATATACGAAT
1 AGCCCAATATTTTAAATCAATATACGAAT
* * *
10805126 AGTCCAATATTTTAAATTAATTTACGAAT
1 AGCCCAATATTTTAAATCAATATACGAAT
10805155 AGCCCAA
1 AGCCCAA
10805162 AACAGACCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (29 bp):
AGCCCAATATTTTAAATCAATATACGAAT
Found at i:10813959 original size:64 final size:64
Alignment explanation
Indices: 10813855--10813984 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
10813845 AAGACAATAC
*
10813855 TGATAAATCATCTAAAACAGTACACATGACATTCCCGGTCCTAATTATAACACATCATGTGCTT
1 TGATAAATCATCTAAAACAGTACACATGACATTCCCGGTCCAAATTATAACACATCATGTGCTT
* * * *
10813919 TGATAAATCATCTAAAACAGTACACATGATATTCCTGGTCCAAATTCTAACACATTATGTGCTT
1 TGATAAATCATCTAAAACAGTACACATGACATTCCCGGTCCAAATTATAACACATCATGTGCTT
10813983 TG
1 TG
10813985 TTATGCATGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (64 bp):
TGATAAATCATCTAAAACAGTACACATGACATTCCCGGTCCAAATTATAACACATCATGTGCTT
Found at i:10834612 original size:15 final size:15
Alignment explanation
Indices: 10834579--10834611 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
10834569 TTTATAAATT
10834579 AAAA-AAATATATAA
1 AAAATAAATATATAA
10834593 AAAATAAATAATATAA
1 AAAATAAAT-ATATAA
10834609 AAA
1 AAA
10834612 TTCAAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 4 0.24
16 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAAATATATAA
Found at i:10855821 original size:29 final size:29
Alignment explanation
Indices: 10855779--10855836 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
10855769 CTGGGTACCC
10855779 GTCCACCCGCAATCCTAATTGCAGATGGA
1 GTCCACCCGCAATCCTAATTGCAGATGGA
10855808 GTCCACCCGCAATCCTAATTGCAGATGGA
1 GTCCACCCGCAATCCTAATTGCAGATGGA
10855837 CATCTTCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (29 bp):
GTCCACCCGCAATCCTAATTGCAGATGGA
Found at i:10856351 original size:51 final size:51
Alignment explanation
Indices: 10856278--10856398 Score: 206
Period size: 51 Copynumber: 2.4 Consensus size: 51
10856268 TATTTTAAAA
*
10856278 AAGGAAATTGAGAGTAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
* * *
10856329 AAGGAATTTGAGAGGAATTTGAAATTAAATATGGATTTGAGTGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
10856380 AAGGAAATTGAGAGGAAAT
1 AAGGAAATTGAGAGGAAAT
10856399 ATGAGAGGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (51 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
Found at i:10866925 original size:26 final size:25
Alignment explanation
Indices: 10866877--10866951 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 25
10866867 TGACTAATGG
*
10866877 AGGTGCCAACTTGAGAAAAAAAATAGTTT
1 AGGTACCAACTTGAG---AAAAA-AGTTT
10866906 AGGTACACAACTTGAGAAAAAAGTTT
1 AGGTAC-CAACTTGAGAAAAAAGTTT
* *
10866932 AGGTACCAATTTGGGAAAAA
1 AGGTACCAACTTGAGAAAAA
10866952 GAGTATAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 12 0.29
26 11 0.26
27 5 0.12
29 5 0.12
30 9 0.21
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (25 bp):
AGGTACCAACTTGAGAAAAAAGTTT
Found at i:10871188 original size:236 final size:236
Alignment explanation
Indices: 10870775--10871249 Score: 869
Period size: 236 Copynumber: 2.0 Consensus size: 236
10870765 ACAAAAGCTC
* *
10870775 ATCTATGAGTATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
1 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
10870840 GAAGAGAGAAAAACAAAAAGGAGCAAAACACACCAGTCAAAATTCTACTTTTCACAAAATATTTT
66 GAAGAGAGAAAAACAAAAAGGAGCAAAACACACCAGTCAAAATTCTACTTTTCACAAAATATTTT
* *
10870905 TTTTTCTTAAAACTGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
131 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
*
10870970 ACTGCCAACAAGTTCTTACAATATGTAAATACTAAAATTTA
196 ACTGCCAAAAAGTTCTTACAATATGTAAATACTAAAATTTA
10871011 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
1 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
* * *
10871076 GAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTTTCACTAAATATTTT
66 GAAGAGAGAAAAACAAAAAGGAGCAAAACACACCAGTCAAAATTCTACTTTTCACAAAATATTTT
10871141 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
131 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
*
10871206 ACTGCGAAAAAGTTCTTACAATATGTAAATACTAAAATTTA
196 ACTGCCAAAAAGTTCTTACAATATGTAAATACTAAAATTTA
10871247 ATC
1 ATC
10871250 GTGAAGTATA
Statistics
Matches: 230, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
236 230 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (236 bp):
ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
GAAGAGAGAAAAACAAAAAGGAGCAAAACACACCAGTCAAAATTCTACTTTTCACAAAATATTTT
ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
ACTGCCAAAAAGTTCTTACAATATGTAAATACTAAAATTTA
Found at i:10875091 original size:19 final size:19
Alignment explanation
Indices: 10875046--10875093 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
10875036 ATAAAATTCT
10875046 AATAAATTATAAAAATAATA
1 AATAAA-TATAAAAATAATA
10875066 AGA-AAATATAAAACAT-ATA
1 A-ATAAATATAAAA-ATAATA
10875085 AATAAATAT
1 AATAAATAT
10875094 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
18 1 0.04
19 17 0.68
20 6 0.24
21 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AATAAATATAAAAATAATA
Found at i:10875175 original size:10 final size:9
Alignment explanation
Indices: 10875038--10875178 Score: 59
Period size: 10 Copynumber: 14.4 Consensus size: 9
10875028 AAAACCCTAT
*
10875038 AAAATTCTA
1 AAAATTATA
10875047 ATAAATTATA
1 A-AAATTATA
*
10875057 AAAATAATA
1 AAAATTATA
*
10875066 AGAAAATATA
1 A-AAATTATA
10875076 AAACA-TATAA
1 AAA-ATTAT-A
*
10875086 ATAAATATTTA
1 A-AAAT-TATA
*
10875097 AAATTTTATA
1 AAA-ATTATA
* *
10875107 TAAACTTACA
1 -AAAATTATA
10875117 AAAATTATA
1 AAAATTATA
*
10875126 AAAATATAAAA
1 AAAAT-T-ATA
*
10875137 AAAATCATCA
1 AAAATTAT-A
**
10875147 AATTTTATA
1 AAAATTATA
*
10875156 AATATTATA
1 AAAATTATA
10875165 AAAACTTATA
1 AAAA-TTATA
10875175 AAAA
1 AAAA
10875179 ACCATACTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 25
0.69 0.13 0.17
Matches are distributed among these distances:
9 39 0.39
10 44 0.44
11 15 0.15
12 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:10875175 original size:19 final size:19
Alignment explanation
Indices: 10874998--10875176 Score: 53
Period size: 19 Copynumber: 9.3 Consensus size: 19
10874988 AAAAAATATG
* *
10874998 TATAAA-ATCATAACAACT
1 TATAAATATTATAAAAACT
* * *
10875016 TATAAGTATTATAAAACCC
1 TATAAATATTATAAAAACT
*
10875035 TATAAA-ATTCTAATAAA-T
1 TATAAATATTATAA-AAACT
* * *
10875053 TATAAAAATAATAAGAAAAT
1 TATAAATATTATAA-AAACT
* * * *
10875073 ATAAAACATATAAATAAATATT
1 -TATAA-ATAT-TATAAAAACT
* *
10875095 TA-AAATTTTATATAAACT
1 TATAAATATTATAAAAACT
* *
10875113 TACAAAAATTATAAAAA-T
1 TATAAATATTATAAAAACT
* * * * **
10875131 ATAAAAAAAATCATCAAATTT
1 -T-ATAAATATTATAAAAACT
10875152 TATAAATATTATAAAAACT
1 TATAAATATTATAAAAACT
10875171 TATAAA
1 TATAAA
10875177 AAACCATACT
Statistics
Matches: 116, Mismatches: 34, Indels: 21
0.68 0.20 0.12
Matches are distributed among these distances:
18 26 0.22
19 56 0.48
20 16 0.14
21 7 0.06
22 6 0.05
23 5 0.04
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.32
Consensus pattern (19 bp):
TATAAATATTATAAAAACT
Found at i:10876821 original size:27 final size:28
Alignment explanation
Indices: 10876755--10876821 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
10876745 TAAATCTCAA
* * *
10876755 AATTATATATGAATTTTAATTTAATGTGT
1 AATTATACATGAATTTTAATTT-AGGTGC
10876784 AATTGTATACATGAATTTTAATTT-GGTGC
1 AA-T-TATACATGAATTTTAATTTAGGTGC
10876813 AATTATACA
1 AATTATACA
10876822 CGTGAAACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 6 0.18
28 1 0.03
29 7 0.21
30 1 0.03
31 18 0.55
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.46
Consensus pattern (28 bp):
AATTATACATGAATTTTAATTTAGGTGC
Found at i:10881761 original size:13 final size:13
Alignment explanation
Indices: 10881743--10881769 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10881733 ACAAGCAATC
10881743 TGTAAGTAGAATT
1 TGTAAGTAGAATT
10881756 TGTAAGTAGAATT
1 TGTAAGTAGAATT
10881769 T
1 T
10881770 CCTGTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TGTAAGTAGAATT
Found at i:10889787 original size:21 final size:21
Alignment explanation
Indices: 10889746--10889787 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10889736 CTTCCTCCAT
*
10889746 CTCCTCTTCATCAATTTCTTC
1 CTCCTCTTCATCAATTACTTC
10889767 CTCCTCTTCATC-ATATACTTC
1 CTCCTCTTCATCAAT-TACTTC
10889788 TTCTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTCTTCATCAATTACTTC
Found at i:10893415 original size:3 final size:3
Alignment explanation
Indices: 10893407--10893449 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
10893397 TGCATTTTCA
10893407 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
10893450 AAGTTTCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
AGT
Found at i:10903283 original size:2 final size:2
Alignment explanation
Indices: 10903276--10903305 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10903266 AAATATGAAT
*
10903276 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10903306 AGAAATGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10906656 original size:24 final size:24
Alignment explanation
Indices: 10906603--10906657 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
10906593 ATTAAGGATA
**
10906603 AAAAAAATTGAAAAAAAAAGCTTC
1 AAAAAAATTGAAAAAAAAAGCAAC
10906627 AAAAAAATTGAAAAAAAAAG-AAC
1 AAAAAAATTGAAAAAAAAAGCAAC
10906650 AATAAAAA
1 AA-AAAAA
10906658 AATGTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.13
Consensus pattern (24 bp):
AAAAAAATTGAAAAAAAAAGCAAC
Found at i:10924356 original size:5 final size:5
Alignment explanation
Indices: 10924346--10924372 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
10924336 TAGTCATGAC
10924346 TTTTG TTTTG TTTTG TTTTG TTTTG TT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TT
10924373 CCCTTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:10925344 original size:27 final size:26
Alignment explanation
Indices: 10925299--10925349 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
10925289 AAAATTAAAT
*
10925299 ATAAAATATTTTAGTAATATGAAAAAA
1 ATAAAATATTTTAGAAATAT-AAAAAA
10925326 ATAAAATCATTTTA-AAATATAAAA
1 ATAAAAT-ATTTTAGAAATATAAAA
10925350 GTAACTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 12 0.55
28 6 0.27
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
ATAAAATATTTTAGAAATATAAAAAA
Found at i:10926060 original size:20 final size:20
Alignment explanation
Indices: 10926024--10926063 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
10926014 CTGGAATTTG
10926024 ATTAAAAATTAAGAAATAGA
1 ATTAAAAATTAAGAAATAGA
10926044 ATTAGAAAATTAA-AAATAGA
1 ATTA-AAAATTAAGAAATAGA
10926064 GAAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
ATTAAAAATTAAGAAATAGA
Found at i:10929053 original size:9 final size:9
Alignment explanation
Indices: 10929039--10929082 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
10929029 TGGTTAAAAA
*
10929039 TTAACCAAC
1 TTAACCGAC
*
10929048 TTAACCGAT
1 TTAACCGAC
10929057 TTAACCGAC
1 TTAACCGAC
10929066 TTAACCGAC
1 TTAACCGAC
10929075 TTAACCGA
1 TTAACCGA
10929083 TTTAGTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (9 bp):
TTAACCGAC
Found at i:10930808 original size:18 final size:19
Alignment explanation
Indices: 10930775--10930810 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10930765 ATTATCCTGC
10930775 AAAATTCGGTTAAACCGAA
1 AAAATTCGGTTAAACCGAA
10930794 AAAATTCGGTT-AACCGA
1 AAAATTCGGTTAAACCGA
10930811 CCGGTTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (19 bp):
AAAATTCGGTTAAACCGAA
Found at i:10931815 original size:40 final size:39
Alignment explanation
Indices: 10931759--10931893 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
10931749 ACCAGTTTGG
10931759 CACCCAGTGCCTCATCGGATAATTTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATTTGAAGT-ATAAATTGA
* * * * ** *
10931799 TACCCAATGTCTCATCGGCTAAACTGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGGATAATTTGAAGTATAAATTGA
* * *
10931836 CACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTAA
1 CACCCAGTGCCTCATCGGA-TAATTTGAAGTA-TAAATTGA
*
10931877 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
10931894 ACTCGAATTC
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
37 21 0.29
38 7 0.10
40 23 0.32
41 22 0.30
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATTTGAAGTATAAATTGA
Found at i:10931881 original size:41 final size:40
Alignment explanation
Indices: 10931759--10931894 Score: 118
Period size: 41 Copynumber: 3.5 Consensus size: 40
10931749 ACCAGTTTGG
* *
10931759 CACCCAGTGCCTCATCGGA-TAATTTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATTAA-TTGAAGTAGTAAATTGA
* * * ** * * *
10931799 TACCCAATGTCTCATCGGCTAAACTG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATTAATTGAAGTAGTAAATTGA
*
10931836 CACCCAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTAA
1 CACCCAGTGCCTCATCGAATTAATT-GAAGTAGTAAATTGA
*
10931877 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
10931895 CTCGAATTCG
Statistics
Matches: 73, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
37 26 0.36
38 1 0.01
39 2 0.03
40 17 0.23
41 27 0.37
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATTAATTGAAGTAGTAAATTGA
Found at i:10932431 original size:18 final size:19
Alignment explanation
Indices: 10932405--10932440 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10932395 TAAAATAAAT
*
10932405 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
10932423 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
10932441 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:10932738 original size:11 final size:10
Alignment explanation
Indices: 10932722--10932783 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 10
10932712 GTCTTTCTCC
10932722 TTTTCTTTCCT
1 TTTTCTTT-CT
10932733 TTTTCTTTCT
1 TTTTCTTTCT
10932743 TTTTCCTTT-T
1 TTTT-CTTTCT
10932753 TGTTTCGTTTCT
1 T-TTTC-TTTCT
* *
10932765 ATCTTGTTTCT
1 -TTTTCTTTCT
10932776 TTTTCTTT
1 TTTTCTTT
10932784 TATTTAATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 15 0.36
11 23 0.55
12 3 0.07
13 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:10932819 original size:18 final size:17
Alignment explanation
Indices: 10932797--10932830 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
10932787 TTAATTGTTT
10932797 TATTATTAT-ATA-ATA
1 TATTATTATAATATATA
10932812 TATTATTATAATATATA
1 TATTATTATAATATATA
10932829 TA
1 TA
10932831 CTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATTATAATATATA
Found at i:10932823 original size:13 final size:13
Alignment explanation
Indices: 10932800--10932854 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
10932790 ATTGTTTTAT
10932800 TATTA-TATAATA
1 TATTATTATAATA
10932812 TATTATTATAATA
1 TATTATTATAATA
*
10932825 TATATACTA-AATA
1 TAT-TATTATAATA
10932838 TATTTTATTATAATA
1 TA--TTATTATAATA
10932853 TA
1 TA
10932855 CATTAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
12 5 0.14
13 16 0.44
14 8 0.22
15 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TATTATTATAATA
Found at i:10932861 original size:26 final size:27
Alignment explanation
Indices: 10932809--10932862 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
10932799 TTATTATATA
*
10932809 ATATATTATTATAATATATATACTAAAT
1 ATATATTATTATAATATACATA-TAAAT
*
10932837 ATATTTTATTATAATATACAT-TAAAT
1 ATATATTATTATAATATACATATAAAT
10932863 TTTACATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
28 19 0.79
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATTATTATAATATACATATAAAT
Found at i:10934527 original size:136 final size:133
Alignment explanation
Indices: 10934361--10934634 Score: 503
Period size: 136 Copynumber: 2.0 Consensus size: 133
10934351 TCTCGACTCA
10934361 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
1 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
10934426 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTTGAAAGTGACTATATGTTTG
66 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTA-TTTTGAAAGTGAC--TATGTTTG
10934491 AATTGT
128 AATTGT
* *
10934497 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTTATTCAATTTTTGA
1 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
10934562 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATGTTTGAAT
66 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATGTTTGAAT
10934627 TGT
131 TGT
10934630 GCAAA
1 GCAAA
10934635 CTAGGTTGTT
Statistics
Matches: 136, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
133 19 0.14
135 13 0.10
136 104 0.76
ACGTcount: A:0.26, C:0.07, G:0.22, T:0.45
Consensus pattern (133 bp):
GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATGTTTGAAT
TGT
Found at i:10942286 original size:21 final size:20
Alignment explanation
Indices: 10942257--10942295 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10942247 TTAGAAATGT
10942257 TTTCATTTT-GTCTTTTTTAA
1 TTTCATTTTAGT-TTTTTTAA
10942277 TTTCAATTTTAGTTTTTTT
1 TTTC-ATTTTAGTTTTTTT
10942296 CAACTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTCATTTTAGTTTTTTTAA
Found at i:10958325 original size:14 final size:15
Alignment explanation
Indices: 10958300--10958328 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10958290 ATGGTTACTC
10958300 TTTTTAATAATTTTA
1 TTTTTAATAATTTTA
10958315 TTTTTAA-AATTTTA
1 TTTTTAATAATTTTA
10958329 ACTTCATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATAATTTTA
Found at i:10959640 original size:88 final size:88
Alignment explanation
Indices: 10959533--10959768 Score: 239
Period size: 88 Copynumber: 2.6 Consensus size: 88
10959523 GTTTAAAGTG
* * * *
10959533 TAAAAAAAA-ACCCT-AAACTTTTTCAAAAAAAGTAATTAAGTCT-TTGTTTTCTTTTCACTTAA
1 TAAAAAAAATACCCTCAAACTTTTTAAAAAAAAGCAATTAAGCCTCTT-TTTT-TTTTCACTCAA
*
10959595 TTAGATACTTAAATTTTCAAAATGCA
64 TT-GATACTTAAAATTTCAAAATGCA
** ***
10959621 T-AAAAAAATGTCCTC-AACTTAAAAAAAGAAGAAGCAATTAAGCCTCTTTTTTTTTTCACTCAA
1 TAAAAAAAATACCCTCAAACTTTTTAAAA-AA-AAGCAATTAAGCCTCTTTTTTTTTTCACTCAA
*
10959684 TTGGTACTTAAAATTTCAAAATGCA
64 TTGATACTTAAAATTTCAAAATGCA
* * *
10959709 TAAAAAAAATACCCTCAAACTTTTTTAAAAAAAGCAAGTAAACCCCTACTTTTTTTTTTC
1 TAAAAAAAATACCCTCAAACTTTTTAAAAAAAAGCAA-TTAA-GCCT-CTTTTTTTTTTC
10959769 GCACTCATTT
Statistics
Matches: 119, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
87 7 0.06
88 40 0.34
89 31 0.26
90 27 0.23
91 14 0.12
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (88 bp):
TAAAAAAAATACCCTCAAACTTTTTAAAAAAAAGCAATTAAGCCTCTTTTTTTTTTCACTCAATT
GATACTTAAAATTTCAAAATGCA
Found at i:10959928 original size:10 final size:10
Alignment explanation
Indices: 10959913--10960050 Score: 66
Period size: 10 Copynumber: 14.4 Consensus size: 10
10959903 GGCATGTGGC
10959913 AAAAAATTAT
1 AAAAAATTAT
10959923 AAAAAA--AT
1 AAAAAATTAT
*
10959931 AATAAATGT-T
1 AAAAAAT-TAT
10959941 ATAAAAATTA-
1 A-AAAAATTAT
**
10959951 ATAAATTTTAAT
1 A-AAAAATT-AT
10959963 AAAAAA--AT
1 AAAAAATTAT
10959971 AAAAATATT-T
1 AAAAA-ATTAT
10959981 -AAAAA-T-T
1 AAAAAATTAT
10959988 AAAAAA-TAT
1 AAAAAATTAT
*
10959997 ATAAAAATCAT
1 A-AAAAATTAT
* *
10960008 AAAATATTGT
1 AAAAAATTAT
*
10960018 AAAAATTTAT
1 AAAAAATTAT
*
10960028 -AAAAATCAT
1 AAAAAATTAT
10960037 AAAAAATTAT
1 AAAAAATTAT
10960047 AAAA
1 AAAA
10960051 TGCATCAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
7 2 0.02
8 21 0.22
9 14 0.14
10 47 0.48
11 12 0.12
12 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:10959944 original size:20 final size:20
Alignment explanation
Indices: 10959918--10960003 Score: 83
Period size: 19 Copynumber: 4.5 Consensus size: 20
10959908 GTGGCAAAAA
10959918 ATTATAAAAAAATAATAAAT
1 ATTATAAAAAAATAATAAAT
* *
10959938 GTTAT-AAAAATTAATAAAT
1 ATTATAAAAAAATAATAAAT
*
10959957 TTTAATAAAAAAATAA-AAAT
1 ATT-ATAAAAAAATAATAAAT
* *
10959977 ATT-T-AAAAATTAAAAAAT
1 ATTATAAAAAAATAATAAAT
10959995 A-TATAAAAA
1 ATTATAAAAA
10960004 TCATAAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
17 9 0.16
18 7 0.13
19 19 0.35
20 12 0.22
21 8 0.15
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (20 bp):
ATTATAAAAAAATAATAAAT
Found at i:10959983 original size:18 final size:19
Alignment explanation
Indices: 10959913--10960022 Score: 79
Period size: 19 Copynumber: 5.8 Consensus size: 19
10959903 GGCATGTGGC
10959913 AAAAA-ATTATAAAAAAAT
1 AAAAATATTATAAAAAAAT
* *
10959931 AATAAATGTTAT-AAAAATT
1 AA-AAATATTATAAAAAAAT
*
10959950 AATAAATTTTAATAAAAAAAT
1 AA-AAATATT-ATAAAAAAAT
*
10959971 AAAAATATT-T-AAAAATT
1 AAAAATATTATAAAAAAAT
*
10959988 AAAAA-A-TATATAAAAAT
1 AAAAATATTATAAAAAAAT
*
10960005 CATAAAATATTGTAAAAA
1 -A-AAAATATTATAAAAA
10960023 TTTATAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.01
16 2 0.03
17 16 0.22
18 4 0.06
19 22 0.31
20 13 0.18
21 14 0.19
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATTATAAAAAAAT
Found at i:10960011 original size:19 final size:19
Alignment explanation
Indices: 10959914--10960050 Score: 90
Period size: 18 Copynumber: 7.2 Consensus size: 19
10959904 GCATGTGGCA
*
10959914 AAAAAT-TATAAAAA-AAT
1 AAAAATATATAAAAATTAT
*
10959931 AATAAATGTTATAAAAATTA-
1 AA-AAAT-ATATAAAAATTAT
* * *
10959951 ATAAATTTTAATAAAAA-AAT
1 A-AAAATAT-ATAAAAATTAT
*
10959971 AAAAATATTTAAAAATTA-
1 AAAAATATATAAAAATTAT
*
10959989 AAAAATATATAAAAATCAT
1 AAAAATATATAAAAATTAT
*
10960008 -AAAATATTGTAAAAATTTAT
1 AAAAATA-TATAAAAA-TTAT
10960028 AAAAATCATA-AAAAATTAT
1 AAAAAT-ATATAAAAATTAT
10960047 AAAA
1 AAAA
10960051 TGCATCAAAA
Statistics
Matches: 95, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
17 2 0.02
18 32 0.34
19 24 0.25
20 28 0.29
21 8 0.08
22 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAAATATATAAAAATTAT
Found at i:10960022 original size:29 final size:29
Alignment explanation
Indices: 10959961--10960050 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
10959951 ATAAATTTTA
*
10959961 ATAAAAA-A-ATAAAAAT-ATTTAAAAATT
1 ATAAAAATATATAAAAATCA-TAAAAAATT
*
10959988 A-AAAAATATATAAAAATCATAAAATATT
1 ATAAAAATATATAAAAATCATAAAAAATT
* *
10960016 GTAAAAATTTATAAAAATCATAAAAAATT
1 ATAAAAATATATAAAAATCATAAAAAATT
10960045 ATAAAA
1 ATAAAA
10960051 TGCATCAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.09
27 2 0.04
28 15 0.28
29 31 0.58
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (29 bp):
ATAAAAATATATAAAAATCATAAAAAATT
Found at i:10960062 original size:20 final size:19
Alignment explanation
Indices: 10959961--10960050 Score: 73
Period size: 19 Copynumber: 4.8 Consensus size: 19
10959951 ATAAATTTTA
10959961 ATAAAAAA--ATAAAAAT-
1 ATAAAAAATTATAAAAATC
*
10959977 ATTTAAAAATTA-AAAAAT-
1 A-TAAAAAATTATAAAAATC
* *
10959995 ATATAAAAATCATAAAATATT
1 ATA-AAAAATTATAAAA-ATC
* *
10960016 GTAAAAATTTATAAAAATC
1 ATAAAAAATTATAAAAATC
10960035 ATAAAAAATTATAAAA
1 ATAAAAAATTATAAAA
10960051 TGCATCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.02
17 7 0.12
18 14 0.24
19 21 0.36
20 13 0.22
21 2 0.03
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATC
Found at i:10960265 original size:18 final size:19
Alignment explanation
Indices: 10960232--10960268 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
10960222 TTGGTACAGT
*
10960232 AATTTATATTTTTTTTACA
1 AATTTATATATTTTTTACA
10960251 AATTT-TATATTTTTTACA
1 AATTTATATATTTTTTACA
10960269 TTTTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTATATATTTTTTACA
Found at i:10960451 original size:17 final size:17
Alignment explanation
Indices: 10960429--10960463 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10960419 AACATTTTTA
10960429 TATTTTTTATTAAAAAT
1 TATTTTTTATTAAAAAT
* *
10960446 TATTTTTTTTTATAAAT
1 TATTTTTTATTAAAAAT
10960463 T
1 T
10960464 TAATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTTATTAAAAAT
Found at i:10960469 original size:19 final size:19
Alignment explanation
Indices: 10960425--10960477 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
10960415 ATTAAACATT
*
10960425 TTTATATTTTTTATTA-AAA
1 TTTA-ATTTTTTTTTATAAA
*
10960444 ATT-ATTTTTTTTTATAAA
1 TTTAATTTTTTTTTATAAA
*
10960462 TTTAATTTATTTTTAT
1 TTTAATTTTTTTTTAT
10960478 TTTTTATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 10 0.36
18 5 0.18
19 13 0.46
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTTTTTTATAAA
Found at i:10963408 original size:49 final size:49
Alignment explanation
Indices: 10963329--10963457 Score: 195
Period size: 49 Copynumber: 2.6 Consensus size: 49
10963319 GATAATAACA
* * * *
10963329 TGCCAAAGCCATGTCCCAGACATGGCCTTACATGGAATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGAATGTTTCCTGTAC
* *
10963378 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGTCTTACATGGAATGTTTCCTGTAC
*
10963427 TGCCAATGTCATATCCCAGATATGGTCTTAC
1 TGCCAATGCCATATCCCAGATATGGTCTTAC
10963458 CTGAGAGTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 72 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAGATATGGTCTTACATGGAATGTTTCCTGTAC
Found at i:10963520 original size:50 final size:50
Alignment explanation
Indices: 10963466--10963614 Score: 138
Period size: 50 Copynumber: 2.9 Consensus size: 50
10963456 ACCTGAGAGT
* * *
10963466 TCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACC
1 TCTCATATCAGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGG-ACC
* * * *
10963516 TCTCATCTCAGTGTCAACGCCATGTCCTAGACATGGTCTTACATGGGACC
1 TCTCATATCAGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACC
* * *
10963566 TCTCATAATCTCAATGATACCAATGTCATGTCCCAGACATGGTCTTACA
1 TCTCAT-A--TC-A-G-TGCCAACGCCATGTCCCAGACATGGTCTTACA
10963615 TGAGATCTCT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
50 45 0.57
51 3 0.04
53 2 0.03
54 1 0.01
55 1 0.01
56 27 0.34
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (50 bp):
TCTCATATCAGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACC
Found at i:10965813 original size:23 final size:20
Alignment explanation
Indices: 10965779--10965832 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
10965769 TAGCAATTTT
*
10965779 TAAATATTTTTATCATTTTAA
1 TAAATATTTTTAT-AGTTTAA
10965800 TAAATATATATTTATAGTTTAA
1 TAAATAT-T-TTTATAGTTTAA
*
10965822 T-GATATTTTTA
1 TAAATATTTTTA
10965833 AAATTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 4 0.14
20 1 0.03
21 11 0.38
22 8 0.28
23 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TAAATATTTTTATAGTTTAA
Found at i:10970920 original size:26 final size:26
Alignment explanation
Indices: 10970891--10970946 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
10970881 TTTTTGATAA
* * *
10970891 AAATGTGTTTTAAGGATTAAATTGTG
1 AAATGTGTATGAAGGATCAAATTGTG
* *
10970917 AAATTTGTATGAAGGGTCAAATTGTG
1 AAATGTGTATGAAGGATCAAATTGTG
10970943 AAAT
1 AAAT
10970947 AAATTGAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (26 bp):
AAATGTGTATGAAGGATCAAATTGTG
Found at i:10981402 original size:14 final size:14
Alignment explanation
Indices: 10981385--10981411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10981375 AACGTTCAGA
10981385 GTTTAAGGATTAAG
1 GTTTAAGGATTAAG
10981399 GTTTAAGGATTAA
1 GTTTAAGGATTAA
10981412 AATTTATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (14 bp):
GTTTAAGGATTAAG
Found at i:10984300 original size:45 final size:45
Alignment explanation
Indices: 10984236--10984429 Score: 289
Period size: 45 Copynumber: 4.3 Consensus size: 45
10984226 GAACGGCATG
**
10984236 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTTGTGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
10984281 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * *
10984326 AATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * * *
10984371 AATTTAAGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
10984416 AAATTGAGGAAGCA
1 AAATTAAGGAAGCA
10984430 CCATGGCCGA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (45 bp):
AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
Found at i:10990796 original size:45 final size:45
Alignment explanation
Indices: 10990732--10990925 Score: 289
Period size: 45 Copynumber: 4.3 Consensus size: 45
10990722 GAACGGCATG
**
10990732 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTTGTGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
10990777 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * *
10990822 AATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * * *
10990867 AATTTAAGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
10990912 AAATTGAGGAAGCA
1 AAATTAAGGAAGCA
10990926 CCATGGCCGA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (45 bp):
AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
Found at i:10998880 original size:5 final size:5
Alignment explanation
Indices: 10998867--10998902 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
10998857 GTAAGCTAAA
* *
10998867 CGCAC CGCAT CGCAC CGCAT CGCAC CGCAC CGCAC C
1 CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC CGCAC C
10998903 CAATCGCCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.56, G:0.19, T:0.06
Consensus pattern (5 bp):
CGCAC
Found at i:10998882 original size:10 final size:10
Alignment explanation
Indices: 10998867--10998902 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
10998857 GTAAGCTAAA
10998867 CGCACCGCAT
1 CGCACCGCAT
10998877 CGCACCGCAT
1 CGCACCGCAT
*
10998887 CGCACCGCAC
1 CGCACCGCAT
10998897 CGCACC
1 CGCACC
10998903 CAATCGCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.19, C:0.56, G:0.19, T:0.06
Consensus pattern (10 bp):
CGCACCGCAT
Found at i:11003128 original size:6 final size:6
Alignment explanation
Indices: 11003119--11003150 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
11003109 TTTTCTTTTT
11003119 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TG
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAAAA TG
11003151 GCTTTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAAAA
Found at i:11007330 original size:14 final size:14
Alignment explanation
Indices: 11007313--11007352 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
11007303 CCATTATATT
11007313 AATT-ATTTTATTAA
1 AATTAATTTT-TTAA
11007327 AATTAATTTTTT-A
1 AATTAATTTTTTAA
11007340 AA-TAATTTTTTAA
1 AATTAATTTTTTAA
11007353 GTGAGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.38
13 4 0.17
14 6 0.25
15 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTAATTTTTTAA
Found at i:11016578 original size:22 final size:21
Alignment explanation
Indices: 11016550--11016601 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
11016540 AAAAATTAAC
*
11016550 AATAAAATAATAGTAATATAAT
1 AATAAAATAATAGCAA-ATAAT
* *
11016572 AATAAAATGATAGCAAATAGT
1 AATAAAATAATAGCAAATAAT
*
11016593 AGTAAAATA
1 AATAAAATA
11016602 GTAAAAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.27
Consensus pattern (21 bp):
AATAAAATAATAGCAAATAAT
Found at i:11020786 original size:7 final size:7
Alignment explanation
Indices: 11020774--11020812 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
11020764 ATATACCGAA
*
11020774 CTTTTGC
1 CTTTTAC
*
11020781 CTTTTGC
1 CTTTTAC
11020788 CTTTTAC
1 CTTTTAC
11020795 CTTTTAC
1 CTTTTAC
11020802 CTTTTAC
1 CTTTTAC
11020809 CTTT
1 CTTT
11020813 ACTTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.08, C:0.28, G:0.05, T:0.59
Consensus pattern (7 bp):
CTTTTAC
Found at i:11021684 original size:19 final size:18
Alignment explanation
Indices: 11021647--11021685 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11021637 AGTGAATATT
*
11021647 AAAATTAAATTAAACATA
1 AAAATTAAATCAAACATA
*
11021665 AAAATTAAACTCACACATA
1 AAAATTAAA-TCAAACATA
11021684 AA
1 AA
11021686 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATTAAATCAAACATA
Found at i:11023886 original size:9 final size:9
Alignment explanation
Indices: 11023874--11023912 Score: 64
Period size: 8 Copynumber: 4.6 Consensus size: 9
11023864 TTTATTTTAA
11023874 TGTAATATT
1 TGTAATATT
11023883 TGT-ATATT
1 TGTAATATT
11023891 TGTAATATT
1 TGTAATATT
11023900 TGT-ATATT
1 TGTAATATT
11023908 TGTAA
1 TGTAA
11023913 ATCTTTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 16 0.57
9 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (9 bp):
TGTAATATT
Found at i:11023894 original size:17 final size:17
Alignment explanation
Indices: 11023874--11023912 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
11023864 TTTATTTTAA
11023874 TGTAATATTTGTATATT
1 TGTAATATTTGTATATT
11023891 TGTAATATTTGTATATT
1 TGTAATATTTGTATATT
11023908 TGTAA
1 TGTAA
11023913 ATCTTTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (17 bp):
TGTAATATTTGTATATT
Found at i:11027670 original size:2 final size:2
Alignment explanation
Indices: 11027663--11027708 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
11027653 AGAATGCAGT
11027663 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
11027705 CA CA
1 CA CA
11027709 TGAAACAGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:11032457 original size:61 final size:60
Alignment explanation
Indices: 11032359--11032481 Score: 153
Period size: 61 Copynumber: 2.0 Consensus size: 60
11032349 GTCATTACAT
11032359 TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGCATT-AAATTTTGAACAAGGA
1 TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGC-TTCAAATTTTGAACAAGGA
* ** *
11032419 TGAATGCTTTAG-TTTTTCTCTAGTTTATTTTTGA-GGAGTTGCTTCAAATTTTGAACGAGGA
1 TGAATGCTTTAGCTGTTT-T-TAGTTTATGATT-ATGGAGTTGCTTCAAATTTTGAACAAGGA
11032480 TG
1 TG
11032482 GACAAGGCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
59 4 0.07
60 15 0.27
61 35 0.64
62 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (60 bp):
TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGCTTCAAATTTTGAACAAGGA
Found at i:11039537 original size:26 final size:27
Alignment explanation
Indices: 11039487--11039539 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
11039477 CCAGAACAAT
11039487 AAAGAAACGTGCCAAAAAACAGCAGAC
1 AAAGAAACGTGCCAAAAAACAGCAGAC
*
11039514 AAAGAAACGTGCC-AAAAACGGCAGAC
1 AAAGAAACGTGCCAAAAAACAGCAGAC
11039540 TCATTCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.53, C:0.23, G:0.21, T:0.04
Consensus pattern (27 bp):
AAAGAAACGTGCCAAAAAACAGCAGAC
Found at i:11043552 original size:31 final size:30
Alignment explanation
Indices: 11043495--11043561 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
11043485 GTATATATAT
*
11043495 TAATTTGGTGCAATTATACACGTGAAACTC
1 TAATTTGGTGCAAATATACACGTGAAACTC
* * * *
11043525 TAATTGTGGTTCAAATATATACTTGAAACTT
1 TAATT-TGGTGCAAATATACACGTGAAACTC
11043556 TAATTT
1 TAATTT
11043562 TGACTTAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (30 bp):
TAATTTGGTGCAAATATACACGTGAAACTC
Found at i:11044810 original size:29 final size:30
Alignment explanation
Indices: 11044752--11044820 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
11044742 AAAACAATAC
* *
11044752 ATGAACTTTGATTTAATATGCAATTATATAT
1 ATGAATTTTGATTT-ATATGCAATTATATAA
* *
11044783 ATGAATTTTGATTT-TATGTAATTTTATAA
1 ATGAATTTTGATTTATATGCAATTATATAA
*
11044812 ATAAATTTT
1 ATGAATTTT
11044821 TTATTGATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 20 0.61
31 13 0.39
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.51
Consensus pattern (30 bp):
ATGAATTTTGATTTATATGCAATTATATAA
Found at i:11045332 original size:25 final size:25
Alignment explanation
Indices: 11045304--11045356 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
11045294 TCTTTTCTTC
*
11045304 TTTTACAAAATTTAATCA-TTTTATT
1 TTTTACAAAAGTTAAT-ATTTTTATT
* *
11045329 TTTTCCATAAGTTAATATTTTTATT
1 TTTTACAAAAGTTAATATTTTTATT
11045354 TTT
1 TTT
11045357 GCGCAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTACAAAAGTTAATATTTTTATT
Found at i:11045536 original size:21 final size:21
Alignment explanation
Indices: 11045510--11045553 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
11045500 TTCAGGATTT
*
11045510 GGGTTCGAGATTTAAGGTTTA
1 GGGTTCGAGATTCAAGGTTTA
11045531 GGGTTCGAGATTCAAGGTTTA
1 GGGTTCGAGATTCAAGGTTTA
11045552 GG
1 GG
11045554 TCTAGGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.36, T:0.34
Consensus pattern (21 bp):
GGGTTCGAGATTCAAGGTTTA
Found at i:11046708 original size:16 final size:17
Alignment explanation
Indices: 11046677--11046718 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
11046667 CAGGCCCAAA
11046677 CCCAAAATAAACAGTGG
1 CCCAAAATAAACAGTGG
*
11046694 CCCAAAAT-TACAGTGG
1 CCCAAAATAAACAGTGG
11046710 CCCAAAATA
1 CCCAAAATA
11046719 GTTTCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.14
Consensus pattern (17 bp):
CCCAAAATAAACAGTGG
Found at i:11048551 original size:16 final size:17
Alignment explanation
Indices: 11048520--11048583 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 17
11048510 TTTTGAAATT
*
11048520 TTTCTCTTGATTCTTTG
1 TTTCTCTTGATTCTTTC
*
11048537 TTTCT-TTGTTTCTTTC
1 TTTCTCTTGATTCTTTC
*
11048553 TTTCATTCTTTGATTCATT-
1 TTTC--TC-TTGATTCTTTC
*
11048572 TTTCTTTTGATT
1 TTTCTCTTGATT
11048584 TACTATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
16 19 0.50
17 6 0.16
18 1 0.03
19 4 0.11
20 8 0.21
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.69
Consensus pattern (17 bp):
TTTCTCTTGATTCTTTC
Found at i:11049412 original size:19 final size:20
Alignment explanation
Indices: 11049385--11049424 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11049375 ATTAGTTTAA
11049385 TATTAATTTATTATTATTAT
1 TATTAATTTATTATTATTAT
* *
11049405 TATT-ATTTGTTATTGTTAT
1 TATTAATTTATTATTATTAT
11049424 T
1 T
11049425 GACATTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TATTAATTTATTATTATTAT
Found at i:11049803 original size:24 final size:24
Alignment explanation
Indices: 11049776--11049825 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
11049766 TTACCTTTAA
11049776 ATTTCCCTTTAG-ATTCATTTATAT
1 ATTT-CCTTTAGAATTCATTTATAT
* *
11049800 ATTTTCTTTCGAATTCATTTATAT
1 ATTTCCTTTAGAATTCATTTATAT
11049824 AT
1 AT
11049826 ACACATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTCCTTTAGAATTCATTTATAT
Found at i:11054463 original size:31 final size:31
Alignment explanation
Indices: 11054428--11054490 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
11054418 TACGTTTAAT
11054428 GAAGTAACACACACTCATAAGCATACAATAA
1 GAAGTAACACACACTCATAAGCATACAATAA
11054459 GAAGTAACACACACTCATAAGCATACAATAA
1 GAAGTAACACACACTCATAAGCATACAATAA
11054490 G
1 G
11054491 GAAAACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.22, G:0.11, T:0.16
Consensus pattern (31 bp):
GAAGTAACACACACTCATAAGCATACAATAA
Found at i:11064723 original size:67 final size:67
Alignment explanation
Indices: 11064642--11064776 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
11064632 AAAACGGCAT
11064642 CTATTTTTATTTATCAGCATGCAGAATGTGCAGTTAATTCATTATGAACTTCAAATAGGATTCGT
1 CTATTTTTATTTATCAGCATGCAGAATGTGCAGTTAATTCATTATGAACTTCAAATAGGATTCGT
11064707 GA
66 GA
11064709 CTATTTTTATTTATCAGCATGCAGAATGTGCAGTTAATTCATTATGAACTTCAAATAGGATTCGT
1 CTATTTTTATTTATCAGCATGCAGAATGTGCAGTTAATTCATTATGAACTTCAAATAGGATTCGT
11064774 GA
66 GA
11064776 C
1 C
11064777 AAATGTACCT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (67 bp):
CTATTTTTATTTATCAGCATGCAGAATGTGCAGTTAATTCATTATGAACTTCAAATAGGATTCGT
GA
Found at i:11073534 original size:24 final size:28
Alignment explanation
Indices: 11073498--11073553 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
11073488 ATATAATTTC
11073498 TTTTTATATTT-A-A-ATTTATGTTATG
1 TTTTTATATTTAACATATTTATGTTATG
* *
11073523 TTTTTTTATTAAACATATTTATGTTATG
1 TTTTTATATTTAACATATTTATGTTATG
11073551 TTT
1 TTT
11073554 AAATTATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.35
26 1 0.04
27 1 0.04
28 15 0.58
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTTATATTTAACATATTTATGTTATG
Found at i:11077306 original size:6 final size:6
Alignment explanation
Indices: 11077295--11077319 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11077285 TTAATATTGA
11077295 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
11077320 TAGAATGAAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:11085136 original size:17 final size:16
Alignment explanation
Indices: 11085111--11085147 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
11085101 ATTAATAAGT
*
11085111 TTATTATTATTTAATTA
1 TTATGATTATTT-ATTA
11085128 TTATGATTATTTATTA
1 TTATGATTATTTATTA
11085144 TTAT
1 TTAT
11085148 ATTTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATGATTATTTATTA
Found at i:11085439 original size:20 final size:20
Alignment explanation
Indices: 11085410--11085454 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
11085400 ACTAATTATT
11085410 AAAA-ATTAATTTTTAATGA
1 AAAAGATTAATTTTTAATGA
11085429 AAAAGATTAATTTTTAATGA
1 AAAAGATTAATTTTTAATGA
11085449 AAAAGA
1 AAAAGA
11085455 GAATTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (20 bp):
AAAAGATTAATTTTTAATGA
Found at i:11085459 original size:19 final size:20
Alignment explanation
Indices: 11085417--11085460 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
11085407 ATTAAAAATT
*
11085417 AATTTTTAATGAAAAAGATT
1 AATTTTTAATGAAAAAGATG
11085437 AATTTTTAATGAAAAAGA-G
1 AATTTTTAATGAAAAAGATG
11085456 AATTT
1 AATTT
11085461 CTTTTGGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (20 bp):
AATTTTTAATGAAAAAGATG
Found at i:11086575 original size:24 final size:23
Alignment explanation
Indices: 11086548--11086593 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11086538 AAAAGAAAAA
*
11086548 GTCTGTCGTATTGGCATGTTTTTC
1 GTCTG-CGTATTGGCACGTTTTTC
*
11086572 GTCTGCTTATTGGCACGTTTTT
1 GTCTGCGTATTGGCACGTTTTT
11086594 TTTCTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.09, C:0.17, G:0.24, T:0.50
Consensus pattern (23 bp):
GTCTGCGTATTGGCACGTTTTTC
Found at i:11170588 original size:37 final size:38
Alignment explanation
Indices: 11170529--11170761 Score: 149
Period size: 37 Copynumber: 6.0 Consensus size: 38
11170519 CAAAGATAGT
* *
11170529 AATCCTATCTCCTTG-AGATTACAATGGAGCGGATTAA-
1 AATCCTATCTCCCTGAAG-TTACAGTGGAGCGGATTAAG
*
11170566 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGAAATAAG
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGG-ATTAAG
* * * * **
11170605 GATCTTATCTCTCTG-AGTTACAGTGAGTACCGAGAATT-TC
1 AATCCTATCTCCCTGAAGTTACAGTG-G-AGCG-G-ATTAAG
* * *
11170645 AATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT--A---AG
* * *
11170688 AGAT-CTATCT-CCTGAA-TTACAGCGGAG-AGATCGAAG
1 A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAAG
11170724 ACATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAA
1 A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAA
11170762 AATAAAGGAT
Statistics
Matches: 152, Mismatches: 25, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
36 5 0.03
37 36 0.24
38 23 0.15
39 28 0.18
40 24 0.16
41 23 0.15
42 5 0.03
43 6 0.04
44 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (38 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAG
Found at i:11170901 original size:44 final size:44
Alignment explanation
Indices: 11170808--11170901 Score: 102
Period size: 44 Copynumber: 2.1 Consensus size: 44
11170798 TAGATCACAT
* *
11170808 CAGATTGAAGCTGGAGATCTTATCTCCCTGAGATTACAATGGAG
1 CAGATTGAAGCTGGAGATCCTATCTCCCTGAGATTACAACGGAG
* * * *
11170852 TAGATTGAAGCTAGTA-ATCCTATTTCCCTG-GAGTTACAGCGGAG
1 CAGATTGAAGCT-GGAGATCCTATCTCCCTGAGA-TTACAACGGAG
11170896 CAGATT
1 CAGATT
11170902 AAAACACAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.05
44 37 0.90
45 2 0.05
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (44 bp):
CAGATTGAAGCTGGAGATCCTATCTCCCTGAGATTACAACGGAG
Found at i:11172276 original size:3 final size:3
Alignment explanation
Indices: 11172204--11172267 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
11172194 GTACTTTTGC
*
11172204 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT CT-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* *
11172252 TAC TAT TAT TAG TAT T
1 TAT TAT TAT TAT TAT T
11172268 GGTATTATTG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:11172475 original size:35 final size:35
Alignment explanation
Indices: 11172398--11172475 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
11172388 AATTTGTTTA
* *
11172398 ATATATATACGTATACTCATATTTCTTTTATATAT
1 ATATATATACATATACTCATATTTATTTTATATAT
* *
11172433 ATCTATATACATATACAT-ATTTTTATTTTATA-AGT
1 ATATATATACATATAC-TCATATTTATTTTATATA-T
11172468 ATATATAT
1 ATATATAT
11172476 TTATATGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 1 0.03
35 34 0.94
36 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (35 bp):
ATATATATACATATACTCATATTTATTTTATATAT
Found at i:11172731 original size:18 final size:19
Alignment explanation
Indices: 11172700--11172737 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
11172690 TATACACCTA
11172700 TATATATGTACATATTTTTT
1 TATATATG-ACATATTTTTT
11172720 TATATATG-CATATTTTTT
1 TATATATGACATATTTTTT
11172738 CTTCTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
20 8 0.44
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (19 bp):
TATATATGACATATTTTTT
Found at i:11174516 original size:13 final size:13
Alignment explanation
Indices: 11174498--11174532 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
11174488 ACTTTTCAAA
11174498 AGCACTTTTTCAC
1 AGCACTTTTTCAC
11174511 -GTCACTTTTTCAC
1 AG-CACTTTTTCAC
11174524 AGCACTTTT
1 AGCACTTTT
11174533 CAAAAACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.43
Consensus pattern (13 bp):
AGCACTTTTTCAC
Found at i:11174722 original size:16 final size:16
Alignment explanation
Indices: 11174666--11174734 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
11174656 ATTTTTAAAT
*
11174666 TAAAA-ATATTTAAT-
1 TAAAATATAATTAATA
* *
11174680 TAAAATGTATTTAATA
1 TAAAATATAATTAATA
*
11174696 TTAAATATAATTACATA
1 TAAAATATAATTA-ATA
*
11174713 TAAAAT-TAATTGATTA
1 TAAAATATAATT-AATA
11174729 TAAAAT
1 TAAAAT
11174735 GATTTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.11
15 8 0.18
16 23 0.51
17 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAAATATAATTAATA
Found at i:11174934 original size:10 final size:9
Alignment explanation
Indices: 11174909--11174933 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11174899 ACAAAGACAT
11174909 GAAAAAATA
1 GAAAAAATA
11174918 GAAAAAATA
1 GAAAAAATA
11174927 GAAAAAA
1 GAAAAAA
11174934 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
GAAAAAATA
Found at i:11175345 original size:17 final size:18
Alignment explanation
Indices: 11175325--11175365 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
11175315 CATTTTTTAA
11175325 AAAATT-ATT-TATTTTCT
1 AAAATTGATTCTATTTT-T
*
11175342 AAAATTGTTTCTATTTTT
1 AAAATTGATTCTATTTTT
11175360 AAAATT
1 AAAATT
11175366 CTTGCATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
AAAATTGATTCTATTTTT
Found at i:11175955 original size:28 final size:25
Alignment explanation
Indices: 11175918--11175984 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
11175908 AAAATAAATT
*
11175918 TTTACTAAAATACTACAAGTTTTTTTTA
1 TTTACCAAAATA-TACAA--TTTTTTTA
*
11175946 TTTACCAAAATATATAATTTTTTTA
1 TTTACCAAAATATACAATTTTTTTA
11175971 TTTACCAAAATATA
1 TTTACCAAAATATA
11175985 TCAAAAAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 22 0.59
27 4 0.11
28 11 0.30
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.48
Consensus pattern (25 bp):
TTTACCAAAATATACAATTTTTTTA
Found at i:11175966 original size:25 final size:25
Alignment explanation
Indices: 11175938--11175985 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
11175928 TACTACAAGT
11175938 TTTTTTTATTTACCAAAATATATAA
1 TTTTTTTATTTACCAAAATATATAA
11175963 TTTTTTTATTTACCAAAATATAT
1 TTTTTTTATTTACCAAAATATAT
11175986 CAAAAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTTTATTTACCAAAATATATAA
Found at i:11177192 original size:27 final size:27
Alignment explanation
Indices: 11177162--11177215 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
11177152 TTTGGTTTTT
11177162 TTTTATATATTTT-AGTAAATAAAAAAA
1 TTTTATATATTTTGA-TAAATAAAAAAA
11177189 TTTTATATATTTTGATAAATAAAAAAA
1 TTTTATATATTTTGATAAATAAAAAAA
11177216 CTTGTAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (27 bp):
TTTTATATATTTTGATAAATAAAAAAA
Found at i:11177226 original size:27 final size:27
Alignment explanation
Indices: 11177165--11177235 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
11177155 GGTTTTTTTT
*
11177165 TATATATTTT-AGTAAATAAAAAAATTT
1 TATATATTTTGA-TAAATAAAAAAATTG
11177192 TATATATTTTGATAAATAAAAAAACTTG
1 TATATATTTTGATAAATAAAAAAA-TTG
* *
11177220 TA-GTATTTTGGTAAAT
1 TATATATTTTGATAAAT
11177236 TTTTATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 34 0.87
28 5 0.13
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (27 bp):
TATATATTTTGATAAATAAAAAAATTG
Found at i:11177945 original size:58 final size:60
Alignment explanation
Indices: 11177803--11177950 Score: 185
Period size: 58 Copynumber: 2.5 Consensus size: 60
11177793 AAATGTGCTA
* * *
11177803 CATAACAATCGATTTAAACATATAAACAATTGATTCAAAAGAAGAAAAAACAGTATTCTAC
1 CATAACAATTGATTTAAACATATAAACAATTGATTC-AAAGAACAAAAAACAATATTCTAC
* * * * *
11177864 TATAAC-ATTCGATTTAAATATATAAACAATTTATTC-AA-AACAATAAGCAATATTCTAC
1 CATAACAATT-GATTTAAACATATAAACAATTGATTCAAAGAACAAAAAACAATATTCTAC
11177922 CATAACAATTGATTTAAACATATAAACAA
1 CATAACAATTGATTTAAACATATAAACAA
11177951 CAAATTCGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
58 39 0.52
59 5 0.07
60 2 0.03
61 29 0.39
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.29
Consensus pattern (60 bp):
CATAACAATTGATTTAAACATATAAACAATTGATTCAAAGAACAAAAAACAATATTCTAC
Found at i:11179886 original size:14 final size:14
Alignment explanation
Indices: 11179867--11179899 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11179857 ATTGTTATAT
11179867 AAATTCATTT-AATA
1 AAATTC-TTTCAATA
11179881 AAATTCTTTCAATA
1 AAATTCTTTCAATA
11179895 AAATT
1 AAATT
11179900 AAAATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTCTTTCAATA
Found at i:11188612 original size:3 final size:3
Alignment explanation
Indices: 11188604--11188632 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11188594 CTACATACAA
11188604 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11188633 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11194868 original size:20 final size:17
Alignment explanation
Indices: 11194833--11194877 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
11194823 ATTTGTATGG
11194833 TTTTATGATTTTTAATAAT
1 TTTTAT-ATTTTTAAT-AT
11194852 TATTTATATTTTGTAATAT
1 T-TTTATATTTT-TAATAT
11194871 TTTTATA
1 TTTTATA
11194878 ATACTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTATATTTTTAATAT
Found at i:11198670 original size:20 final size:22
Alignment explanation
Indices: 11198641--11198681 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11198631 AACAATTTAT
11198641 TAAAAATA-T-TTTTTAAAATA
1 TAAAAATATTGTTTTTAAAATA
*
11198661 TAAAATTATTGTTTTTAAAAT
1 TAAAAATATTGTTTTTAAAAT
11198682 TTATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAAATATTGTTTTTAAAATA
Found at i:11216977 original size:16 final size:16
Alignment explanation
Indices: 11216937--11216980 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
11216927 AAAACACGCA
11216937 TATTTAAAATAACAAT
1 TATTTAAAATAACAAT
* *
11216953 T-TTAAAAAATAACCAT
1 TATT-TAAAATAACAAT
11216969 TATTTAAAATAA
1 TATTTAAAATAA
11216981 GCGCTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (16 bp):
TATTTAAAATAACAAT
Found at i:11221075 original size:2 final size:2
Alignment explanation
Indices: 11221068--11221096 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11221058 CCTACTCTTT
11221068 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11221097 TATTGTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11231415 original size:26 final size:26
Alignment explanation
Indices: 11231386--11231438 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11231376 CATTCTAGGA
11231386 ACCAAAACATGGCTGCCAACTAAACT
1 ACCAAAACATGGCTGCCAACTAAACT
11231412 ACCAAAACATGGCTGCCAACTAAACT
1 ACCAAAACATGGCTGCCAACTAAACT
11231438 A
1 A
11231439 AGCATAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.15
Consensus pattern (26 bp):
ACCAAAACATGGCTGCCAACTAAACT
Found at i:11261004 original size:18 final size:17
Alignment explanation
Indices: 11260971--11261009 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11260961 TTGTATAAAT
11260971 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
11260989 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
11261006 TGTG
1 TGTG
11261010 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:11261254 original size:23 final size:23
Alignment explanation
Indices: 11261227--11261302 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
11261217 AGTGTTATTG
11261227 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
11261250 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11261273 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11261296 ATCAGTG
1 ATCAGTG
11261303 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:11268319 original size:18 final size:17
Alignment explanation
Indices: 11268286--11268324 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11268276 TTGTATAAAT
11268286 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
11268304 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
11268321 TGTG
1 TGTG
11268325 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:11268570 original size:23 final size:23
Alignment explanation
Indices: 11268543--11268618 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
11268533 AGTGTTATTG
11268543 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
11268566 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11268589 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11268612 ATCAGTG
1 ATCAGTG
11268619 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:11270760 original size:42 final size:42
Alignment explanation
Indices: 11270701--11270784 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
11270691 TTGATTTTCT
11270701 CCGTATTTGATACAATGTGCGTGTATTAAAAAGGGGAAAAGA
1 CCGTATTTGATACAATGTGCGTGTATTAAAAAGGGGAAAAGA
*
11270743 CCGTATTTGATACAATGTGCGTGTGTTAAAAAGGGGAAAAGA
1 CCGTATTTGATACAATGTGCGTGTATTAAAAAGGGGAAAAGA
11270785 GCCCCTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (42 bp):
CCGTATTTGATACAATGTGCGTGTATTAAAAAGGGGAAAAGA
Found at i:11295189 original size:12 final size:13
Alignment explanation
Indices: 11295172--11295200 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11295162 CCAATTGAAG
11295172 AAATAAATAAAT-
1 AAATAAATAAATC
11295184 AAATAAATAAATC
1 AAATAAATAAATC
11295197 AAAT
1 AAAT
11295201 GAACCCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAATC
Found at i:11300020 original size:81 final size:81
Alignment explanation
Indices: 11299885--11300044 Score: 302
Period size: 81 Copynumber: 2.0 Consensus size: 81
11299875 AAAATCTGAT
* *
11299885 TTGTCATTTTCCTATTGAGAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATTCCTTCT
1 TTGTCATTTTCCTATTGAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATCCCTTCT
11299950 CTTTTGACATAATGAG
66 CTTTTGACATAATGAG
11299966 TTGTCATTTTCCTATTGAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATCCCTTCT
1 TTGTCATTTTCCTATTGAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATCCCTTCT
11300031 CTTTTGACATAATG
66 CTTTTGACATAATG
11300045 CCTAGAACTA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (81 bp):
TTGTCATTTTCCTATTGAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATCCCTTCT
CTTTTGACATAATGAG
Found at i:11318403 original size:23 final size:21
Alignment explanation
Indices: 11318353--11318403 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
11318343 ATAAACGTCT
11318353 TAAAATTTCTAAAATTTCGAA
1 TAAAATTTCTAAAATTTCGAA
*
11318374 AATAAATTTCTTAAAATATTAC-AA
1 TA-AAATTTC-TAAAAT-TT-CGAA
11318398 TAAAAT
1 TAAAAT
11318404 AATTCAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.04
22 7 0.29
23 10 0.42
24 5 0.21
25 1 0.04
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAATTTCTAAAATTTCGAA
Found at i:11330769 original size:24 final size:24
Alignment explanation
Indices: 11330742--11330788 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
11330732 TTCATGTGAA
11330742 CATAGACTCATTCAGATT-TAATTT
1 CATA-ACTCATTCAGATTCTAATTT
* *
11330766 CATATCTCATTCAGCTTCTAATT
1 CATAACTCATTCAGATTCTAATT
11330789 CAATTTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (24 bp):
CATAACTCATTCAGATTCTAATTT
Found at i:11331597 original size:46 final size:46
Alignment explanation
Indices: 11331519--11331795 Score: 437
Period size: 46 Copynumber: 6.0 Consensus size: 46
11331509 ACATTGCTAT
* * *
11331519 AACTTAGTATGATTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * *
11331565 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGATTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
11331611 AACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCACCGAAACACCATACCTACTTTTCAC
** * *
11331657 AACTCAGTATGGGTTTCTTCACTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGATTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
11331703 AACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCACCGAAACACCATACCTACTTTTCAC
*
11331749 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCACCGAAACACCATACCTACTTTTCAC
11331795 A
1 A
11331796 CTTTGCCATG
Statistics
Matches: 210, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 210 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGATTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:11331674 original size:92 final size:92
Alignment explanation
Indices: 11331517--11331793 Score: 500
Period size: 92 Copynumber: 3.0 Consensus size: 92
11331507 TCACATTGCT
* * * *
11331517 ATAACTTAGTATGATTTTCTTCACGGAAATACCATACCTACTTTTCACAACTCAGTATGGTTTTC
1 ATAACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCACAACTCAGTATGGTTTTC
11331582 TTCACTGAAACACCATACCTACTTTTC
66 TTCACTGAAACACCATACCTACTTTTC
*
11331609 ATAACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCACAACTCAGTATGGGTTTC
1 ATAACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCACAACTCAGTATGGTTTTC
11331674 TTCACTGAAACACCATACCTACTTTTC
66 TTCACTGAAACACCATACCTACTTTTC
11331701 ATAACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCACAACTCAGTATGGTTTTC
1 ATAACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCACAACTCAGTATGGTTTTC
*
11331766 TTCACCGAAACACCATACCTACTTTTC
66 TTCACTGAAACACCATACCTACTTTTC
11331793 A
1 A
11331794 CACTTTGCCA
Statistics
Matches: 178, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 178 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (92 bp):
ATAACTCAGTATGATTTTATTCACCGAAACACCATACCTACTTTTCACAACTCAGTATGGTTTTC
TTCACTGAAACACCATACCTACTTTTC
Found at i:11332951 original size:17 final size:17
Alignment explanation
Indices: 11332929--11332962 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11332919 AATGACACTC
11332929 CATAAATATTTATAAAA
1 CATAAATATTTATAAAA
11332946 CATAAATATTTATAAAA
1 CATAAATATTTATAAAA
11332963 ATATTTATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
CATAAATATTTATAAAA
Found at i:11333084 original size:16 final size:17
Alignment explanation
Indices: 11333038--11333085 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
11333028 AAATTCTTTT
*
11333038 TAAACCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
11333055 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
11333072 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
11333086 TTCTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Done.