Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, whole genome shotgun sequence
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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 6 of 32
Found at i:2605656 original size:17 final size:17
Alignment explanation
Indices: 2605634--2605668 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2605624 GTAATTATTT
*
2605634 TGTATAAATTAAATATA
1 TGTATAAATAAAATATA
*
2605651 TGTATATATAAAATATA
1 TGTATAAATAAAATATA
2605668 T
1 T
2605669 TAAACTATTA
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:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
TGTATAAATAAAATATA
Found at i:2611828 original size:19 final size:20
Alignment explanation
Indices: 2611804--2611855 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
2611794 TTCAAAATAA
2611804 TTTTTTTATTTATTAT-ATT
1 TTTTTTTATTTATTATCATT
2611823 TTTTTTCTA-TTATTATCATT
1 TTTTTT-TATTTATTATCATT
*
2611843 TATTTTT-TTTATT
1 TTTTTTTATTTATT
2611856 TTTATTCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTTATTTATTATCATT
Found at i:2611855 original size:22 final size:19
Alignment explanation
Indices: 2611804--2611855 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
2611794 TTCAAAATAA
2611804 TTTTTTTATTTATTATATTT
1 TTTTTTTA-TTATTATATTT
*
2611824 TTTTTCTATTATTATCATTT
1 TTTTTTTATTATTAT-ATTT
*
2611844 ATTTTTT-TTATT
1 TTTTTTTATTATT
2611856 TTTATTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTTATTATTATATTT
Found at i:2611860 original size:22 final size:19
Alignment explanation
Indices: 2611804--2611860 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
2611794 TTCAAAATAA
2611804 TTTTTTTATTTATTATATTT
1 TTTTTTTATTT-TTATATTT
* *
2611824 TTTTTCTATTATTATCATTTAT
1 TTTTTTTATTTTTAT-A-TT-T
2611846 TTTTTTTATTTTTAT
1 TTTTTTTATTTTTAT
2611861 TCTATTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.13
20 10 0.33
21 2 0.07
22 14 0.47
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTTATTTTTATATTT
Found at i:2612883 original size:27 final size:27
Alignment explanation
Indices: 2612840--2612897 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
2612830 ATGTGATTCC
2612840 TTTTTCAATTATCACATTTTA-GATATAT
1 TTTTTCAATTA-CACATTTTATGATA-AT
2612868 TTTTCTCAATTA-ACATTTTATGATAAT
1 TTTT-TCAATTACACATTTTATGATAAT
2612895 TTT
1 TTT
2612898 ACTAGTTCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 13 0.46
28 8 0.29
29 7 0.25
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.55
Consensus pattern (27 bp):
TTTTTCAATTACACATTTTATGATAAT
Found at i:2626467 original size:33 final size:33
Alignment explanation
Indices: 2626402--2626467 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2626392 AACATAAAAA
* *
2626402 CCACTTTCAGATTGTACTTGAAAAACCTAACAT
1 CCACTTTCAGATTGTACTTGAAAAAACGAACAT
2626435 CCACTTTCAGATTGTACTTGAAAAAACGAACAT
1 CCACTTTCAGATTGTACTTGAAAAAACGAACAT
2626468 GTTCAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.29
Consensus pattern (33 bp):
CCACTTTCAGATTGTACTTGAAAAAACGAACAT
Found at i:2628590 original size:6 final size:6
Alignment explanation
Indices: 2628583--2628622 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
2628573 CACTGGCTCT
*
2628583 ATCTCT ATCTCC ATCTCC ATCTCC ATCTCC -TCTTCC ATCT
1 ATCTCC ATCTCC ATCTCC ATCTCC ATCTCC ATC-TCC ATCT
2628623 ATCTCTCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 2 0.06
6 27 0.87
7 2 0.06
ACGTcount: A:0.15, C:0.45, G:0.00, T:0.40
Consensus pattern (6 bp):
ATCTCC
Found at i:2642769 original size:2 final size:2
Alignment explanation
Indices: 2642762--2642792 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2642752 CTACTTGTAG
2642762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2642793 TGGATTAGGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2652968 original size:39 final size:39
Alignment explanation
Indices: 2652925--2653007 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
2652915 TAGCTTTTTT
* *
2652925 AAGAGTTATTGATAAAGCAAAAGCTAAGCCGCATAAGTC
1 AAGAGTTATTGATAAAGCAAAAACTAAGCCGCATAACTC
*
2652964 AAGAGTTATTGATAAAGCAAAAACTAAGCTGCATAACTC
1 AAGAGTTATTGATAAAGCAAAAACTAAGCCGCATAACTC
2653003 AAGAG
1 AAGAG
2653008 AAAACCTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.20
Consensus pattern (39 bp):
AAGAGTTATTGATAAAGCAAAAACTAAGCCGCATAACTC
Found at i:2654968 original size:51 final size:51
Alignment explanation
Indices: 2654911--2655104 Score: 150
Period size: 51 Copynumber: 3.7 Consensus size: 51
2654901 CGATATAACG
*
2654911 TGTAATAATTTTTTTTAATATAGTATATAATAATTTTTCAAAAACATGATA
1 TGTAATAATTTTTTTTAATATAGTGTATAATAATTTTTCAAAAACATGATA
* * * *
2654962 TGTAATAAACTTTTTTGTAATAAAATGTGTAATAACAATTTTTCAATATA-AT-ATA
1 TGTAAT-AA-TTTTTTTTAAT-ATA-GTGT-ATAATAATTTTTCAA-AAACATGATA
* * *
2655017 --TAATAATTTTTTTTAACATAATGTGTAATAATATTTT---AAACATGATA
1 TGTAATAATTTTTTTTAATATAGTGTATAATAAT-TTTTCAAAAACATGATA
* * *
2655064 TGTGATAATAATTTTTTTAATATAATGTGTAATAATATTTT
1 TGTAATAAT--TTTTTTTAATATAGTGTATAATAAT-TTTT
2655105 TTTCACGTGC
Statistics
Matches: 116, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
45 2 0.02
46 2 0.02
47 3 0.03
48 6 0.05
49 13 0.11
50 2 0.02
51 44 0.38
52 4 0.03
53 14 0.12
54 2 0.02
55 6 0.05
56 16 0.14
57 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (51 bp):
TGTAATAATTTTTTTTAATATAGTGTATAATAATTTTTCAAAAACATGATA
Found at i:2655011 original size:104 final size:102
Alignment explanation
Indices: 2654896--2655098 Score: 257
Period size: 104 Copynumber: 2.0 Consensus size: 102
2654886 AACATAATAT
* * * * *
2654896 TTTTTCGATATAACGTGTAATAATTTTTTTTAATATAGTATATAATAAT-TTTTCAAAAACATGA
1 TTTTTCAATATAACATATAATAATTTTTTTTAACATAATATATAATAATATTTT---AAACATGA
*
2654960 TATGTAATAA-ACTTTTTTGTAATAAAATGTGTAATAACAA
63 TATGTAATAATAATTTTTT-TAATAAAATGTGTAATAACAA
* * *
2655000 TTTTTCAATATAATATATAATAATTTTTTTTAACATAATGTGTAATAATATTTTAAACATGATAT
1 TTTTTCAATATAACATATAATAATTTTTTTTAACATAATATATAATAATATTTTAAACATGATAT
* *
2655065 GTGATAATAATTTTTTTAATATAATGTGTAATAA
66 GTAATAATAATTTTTTTAATAAAATGTGTAATAA
2655099 TATTTTTTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
102 34 0.40
103 7 0.08
104 41 0.48
105 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (102 bp):
TTTTTCAATATAACATATAATAATTTTTTTTAACATAATATATAATAATATTTTAAACATGATAT
GTAATAATAATTTTTTTAATAAAATGTGTAATAACAA
Found at i:2655052 original size:27 final size:27
Alignment explanation
Indices: 2655016--2655107 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 27
2655006 AATATAATAT
2655016 ATAATAATTTTTTTTAACATAATGTGTA
1 ATAAT-ATTTTTTTTAACATAATGTGTA
* * * *
2655044 ATAATA---TTTTAAACATGATATGTG
1 ATAATATTTTTTTTAACATAATGTGTA
* *
2655068 ATAATAATTTTTTTAATATAATGTGTA
1 ATAATATTTTTTTTAACATAATGTGTA
2655095 ATAATATTTTTTT
1 ATAATATTTTTTT
2655108 CACGTGCACT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
24 20 0.39
27 26 0.51
28 5 0.10
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (27 bp):
ATAATATTTTTTTTAACATAATGTGTA
Found at i:2655058 original size:24 final size:24
Alignment explanation
Indices: 2654985--2655105 Score: 116
Period size: 24 Copynumber: 4.8 Consensus size: 24
2654975 TTTGTAATAA
* *
2654985 AATGTGTAATAACAATTTTTCAATAT
1 AATGTGTAATAA-TATTTTT-AACAT
* * *
2655011 AATATATAATAATTTTTTTTAACAT
1 AATGTGTAATAA-TATTTTTAACAT
*
2655036 AATGTGTAATAATATTTTAAACAT
1 AATGTGTAATAATATTTTTAACAT
* *
2655060 GATATGTGATAATAATTTTTTTAATAT
1 -A-ATGTG-TAATAATATTTTTAACAT
2655087 AATGTGTAATAATATTTTT
1 AATGTGTAATAATATTTTT
2655106 TTCACGTGCA
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
24 22 0.28
25 20 0.26
26 21 0.27
27 15 0.19
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (24 bp):
AATGTGTAATAATATTTTTAACAT
Found at i:2655097 original size:102 final size:102
Alignment explanation
Indices: 2654913--2655098 Score: 259
Period size: 102 Copynumber: 1.8 Consensus size: 102
2654903 ATATAACGTG
* * *
2654913 TAATAATTTTTTTTAATATAGTATATAATAATTTTTCAAAAACATGATATGTAATAAACTTTTTT
1 TAATAATTTTTTTTAACATAATATATAATAATTTTT--AAAACATGATATGTAATAAAATTTTTT
2654978 GTAATAAAATGTGTAATAACAATTTTTCAATATAATATA
64 GTAATAAAATGTGTAATAACAATTTTTCAATATAATATA
* * *
2655017 TAATAATTTTTTTTAACATAATGTGTAATAATATTTT-AAACATGATATGTGATAATAATTTTTT
1 TAATAATTTTTTTTAACATAATATATAATAAT-TTTTAAAACATGATATGTAATAA-AATTTTTT
*
2655081 -TAATATAATGTGTAATAA
64 GTAATAAAATGTGTAATAA
2655099 TATTTTTTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
102 34 0.47
103 7 0.10
104 28 0.38
105 4 0.05
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (102 bp):
TAATAATTTTTTTTAACATAATATATAATAATTTTTAAAACATGATATGTAATAAAATTTTTTGT
AATAAAATGTGTAATAACAATTTTTCAATATAATATA
Found at i:2668248 original size:2 final size:2
Alignment explanation
Indices: 2668241--2668269 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2668231 TATCAGCAGC
2668241 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 A
2668270 GTAATTCAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2693844 original size:2 final size:2
Alignment explanation
Indices: 2693837--2693864 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2693827 AGACTAGATC
2693837 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2693865 ACATACAGCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2727140 original size:15 final size:15
Alignment explanation
Indices: 2727120--2727160 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2727110 GGTTATAACT
* *
2727120 TATTTTTTTTTTGTC
1 TATTTTTTTCTTATC
*
2727135 TATTTTTTTCTTATT
1 TATTTTTTTCTTATC
2727150 TATTTTTTTCT
1 TATTTTTTTCT
2727161 CAAAATTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.80
Consensus pattern (15 bp):
TATTTTTTTCTTATC
Found at i:2727863 original size:220 final size:220
Alignment explanation
Indices: 2727458--2727895 Score: 650
Period size: 220 Copynumber: 2.0 Consensus size: 220
2727448 AAATAATTGT
**
2727458 ACGTAAAGGTTAATTTAAAAAATATTAAAGGATTGAATTTAATTTAACAAAAAATATTCGAGAGA
1 ACGTAAAGGTTAATTTAAAAAATATTAAAAAATTGAATTTAATTTAACAAAAAATATTCGAGAGA
* **
2727523 TTAAATTGAAGTAATTTTTAAAATCAACATAACAATTAATTTAAATAGAAAATAATTGCTATGTG
66 TTAAATTGAAGTAATTTTTAAAATCAACATAACAATTAATTTAAAGAGAAAATAATTGCTACATG
* * * *
2727588 ACTTTTTGTGATGATGTGGTAGTGCCACAGTAATGATTAATTTAAACATAAAATATTAAAGAGAT
131 AATTTTTGTGATGACGTGGTAGTGCCACAGTAACGATTAATTTAAACAAAAAATATTAAAGAGAT
2727653 TAAATTAAAATAATTTTTAAAATCA
196 TAAATTAAAATAATTTTTAAAATCA
* * *
2727678 ACGTAACGGTTAATTTAAAAAATATTAAAAAATTTAATTTAATTTAAATAAAAAATATTCGAGAG
1 ACGTAAAGGTTAATTTAAAAAATATTAAAAAATTGAATTTAATTT-AACAAAAAATATTCGAGAG
* *
2727743 ATTAAATTGAAGTAATTTTTAAAATCAATATAACGATTAATTTAAACGA-AAAATAATTG-TCAC
65 ATTAAATTGAAGTAATTTTTAAAATCAACATAACAATTAATTTAAA-GAGAAAATAATTGCT-AC
*
2727806 ATGAATTTTT-TGATGACGTGGTAGTGCCACCA-TAACGATTAATTTAAACAAAAAATATTAGAG
128 ATGAATTTTTGTGATGACGTGGTAGTGCCA-CAGTAACGATTAATTTAAACAAAAAATATTAAAG
* * *
2727869 GGATTAAATTGAAGTAATTTTTAAAAT
192 AGATTAAATTAAAATAATTTTTAAAAT
2727896 TTAAAAATTA
Statistics
Matches: 196, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
220 112 0.57
221 83 0.42
222 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (220 bp):
ACGTAAAGGTTAATTTAAAAAATATTAAAAAATTGAATTTAATTTAACAAAAAATATTCGAGAGA
TTAAATTGAAGTAATTTTTAAAATCAACATAACAATTAATTTAAAGAGAAAATAATTGCTACATG
AATTTTTGTGATGACGTGGTAGTGCCACAGTAACGATTAATTTAAACAAAAAATATTAAAGAGAT
TAAATTAAAATAATTTTTAAAATCA
Found at i:2730042 original size:18 final size:18
Alignment explanation
Indices: 2730019--2730073 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
2730009 CCTCTATCTC
2730019 TTCTTCCTTTTTATTTTT
1 TTCTTCCTTTTTATTTTT
*
2730037 TTCTT-CTATTTAACTTTTT
1 TTCTTCCT-TTTTA-TTTTT
*
2730056 TT-TTCAATTTTTATTTTT
1 TTCTTC-CTTTTTATTTTT
2730074 CCAATCCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
17 2 0.07
18 16 0.53
19 11 0.37
20 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.75
Consensus pattern (18 bp):
TTCTTCCTTTTTATTTTT
Found at i:2739205 original size:120 final size:119
Alignment explanation
Indices: 2738976--2739201 Score: 323
Period size: 120 Copynumber: 1.9 Consensus size: 119
2738966 ATTTATAAAT
** *
2738976 AAAAAATAAAAAGAAATTAAAATAAAAATTGTATTAATTATATAATAATAAAATATTAATGTTTA
1 AAAAAATAAAAAGAAATTAAAATAAAAATCATATTAATAATATAATAATAAAATATTAATGTTTA
* **
2739041 AATTTTTAATGAAAATAGAAATTAAAAGATTGAAAATTGAAAATACAAATAGAG
66 AATTTTTAATGAAAATAGAAATTAAAAGAGTGAAAAAAGAAAATACAAATAGAG
* * * *
2739095 AAAAAATAAAAAGAAATTGAAATAAAAAATCATATTAATAATTTAATAATAAATTATTAATATTT
1 AAAAAATAAAAAGAAATTAAAAT-AAAAATCATATTAATAATATAATAATAAAATATTAAT-GTT
2739160 TAAA-TTTTAATGAAAATA-AAATTAAAAGAGT-AAAAAAGAAAA
64 TAAATTTTTAATGAAAATAGAAATTAAAAGAGTGAAAAAAGAAAA
2739202 AATATTATTA
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
118 9 0.09
119 34 0.36
120 46 0.48
121 6 0.06
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.31
Consensus pattern (119 bp):
AAAAAATAAAAAGAAATTAAAATAAAAATCATATTAATAATATAATAATAAAATATTAATGTTTA
AATTTTTAATGAAAATAGAAATTAAAAGAGTGAAAAAAGAAAATACAAATAGAG
Found at i:2740407 original size:30 final size:30
Alignment explanation
Indices: 2740372--2740428 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2740362 CTCCTAGTTC
* *
2740372 CGATGGTTACCACGCAGATGAGGATGATGA
1 CGATGGTCACCACGAAGATGAGGATGATGA
*
2740402 CGATGGTCATCACGAAGATGAGGATGA
1 CGATGGTCACCACGAAGATGAGGATGA
2740429 GGATGACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19
Consensus pattern (30 bp):
CGATGGTCACCACGAAGATGAGGATGATGA
Found at i:2743899 original size:6 final size:6
Alignment explanation
Indices: 2743888--2743915 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2743878 GGGCAAGAGC
2743888 ACTCGA ACTCGA ACTCGA ACTCGA ACTC
1 ACTCGA ACTCGA ACTCGA ACTCGA ACTC
2743916 CGTTCAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.14, T:0.18
Consensus pattern (6 bp):
ACTCGA
Found at i:2753198 original size:2 final size:2
Alignment explanation
Indices: 2753191--2753217 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2753181 GAGGCAGATG
2753191 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 A
2753218 ATTGAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2753406 original size:15 final size:15
Alignment explanation
Indices: 2753388--2753428 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
2753378 ATGATTACAG
2753388 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
2753403 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
*
2753418 GCAATGTGATT
1 GTAATGTGATT
2753429 ACAGGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:2753505 original size:54 final size:54
Alignment explanation
Indices: 2753430--2753565 Score: 254
Period size: 54 Copynumber: 2.5 Consensus size: 54
2753420 AATGTGATTA
* *
2753430 CAGGGAAAATAACATTACAGTGTTTGGTATGTAAACAAAATAATGATTAAAATG
1 CAGGGAAGATAACATTGCAGTGTTTGGTATGTAAACAAAATAATGATTAAAATG
2753484 CAGGGAAGATAACATTGCAGTGTTTGGTATGTAAACAAAATAATGATTAAAATG
1 CAGGGAAGATAACATTGCAGTGTTTGGTATGTAAACAAAATAATGATTAAAATG
2753538 CAGGGAAGATAACATTGCAGTGTTTGGT
1 CAGGGAAGATAACATTGCAGTGTTTGGT
2753566 TTACAAGTAC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (54 bp):
CAGGGAAGATAACATTGCAGTGTTTGGTATGTAAACAAAATAATGATTAAAATG
Found at i:2753674 original size:27 final size:27
Alignment explanation
Indices: 2753644--2753897 Score: 137
Period size: 27 Copynumber: 9.1 Consensus size: 27
2753634 TAATATATTT
2753644 ATATTTTTTATTATTAATTTTTATATA
1 ATATTTTTTATTATTAATTTTTATATA
** * * *
2753671 ATATCATTTCTTAAATATATTTTTAATATC
1 ATATTTTTTATT-ATTA-ATTTTT-ATATA
* *
2753701 ATATATTTTATT-TTTATTTTTATTATA
1 ATATTTTTTATTATTAATTTTTA-TATA
*
2753728 ATATTTTATA-TATT--TTTTTAATATA
1 ATATTTTTTATTATTAATTTTT-ATATA
*
2753753 TTTATATTTTTATTATTAATTTTTATATA
1 -ATAT-TTTTTATTATTAATTTTTATATA
** * * * *
2753782 ATATCATTTCTTAAATATATTTTTAATGTC
1 ATATTTTTTATT-ATTA-ATTTTT-ATATA
* *
2753812 ATATATTTTATT-TTTATTTATTATTATA
1 ATATTTTTTATTATTAATTT-TTA-TATA
*
2753840 ATATTTTATA-TATT--TTTTTAATATA
1 ATATTTTTTATTATTAATTTTT-ATATA
* *
2753865 TTTATATTTATATTATTAATTTTTATATA
1 -ATAT-TTTTTATTATTAATTTTTATATA
2753894 ATAT
1 ATAT
2753898 CATATTTTAA
Statistics
Matches: 171, Mismatches: 33, Indels: 45
0.69 0.13 0.18
Matches are distributed among these distances:
25 15 0.09
26 13 0.08
27 50 0.29
28 36 0.21
29 22 0.13
30 35 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
ATATTTTTTATTATTAATTTTTATATA
Found at i:2753781 original size:23 final size:22
Alignment explanation
Indices: 2753715--2753893 Score: 74
Period size: 23 Copynumber: 8.1 Consensus size: 22
2753705 ATTTTATTTT
2753715 TATTTTTATTATAATATTTTATA
1 TATTTTTATTATAAT-TTTTATA
*
2753738 TA-TTTT-TT-TAATATATT-TA
1 TATTTTTATTATAAT-TTTTATA
2753757 TATTTTTATTATTAATTTTTATA
1 TATTTTTATTA-TAATTTTTATA
* * * * **
2753780 TAATATCATT-T--CTTAAATA
1 TATTTTTATTATAATTTTTATA
* *
2753799 TATTTTTAATGTCATATATTTTATTTT
1 TATTTTT-AT-T-ATA-ATTTT-TATA
2753826 TATTTATTATTATAATATTTTATA
1 TATTT-TTATTATAAT-TTTTATA
*
2753850 TA-TTTT-TT-TAATATATT-TA
1 TATTTTTATTATAAT-TTTTATA
*
2753869 TATTTATATTATTAATTTTTATA
1 TATTTTTATTA-TAATTTTTATA
2753892 TA
1 TA
2753894 ATATCATATT
Statistics
Matches: 115, Mismatches: 21, Indels: 40
0.65 0.12 0.23
Matches are distributed among these distances:
19 17 0.15
20 25 0.22
21 10 0.09
22 12 0.10
23 26 0.23
24 6 0.05
25 6 0.05
26 3 0.03
27 8 0.07
28 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (22 bp):
TATTTTTATTATAATTTTTATA
Found at i:2753856 original size:112 final size:112
Alignment explanation
Indices: 2753632--2753975 Score: 597
Period size: 112 Copynumber: 3.1 Consensus size: 112
2753622 AAAATATAAA
2753632 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
2753697 TATCATATATTTTATTTTTATTT-TTATTATAATATTTTATATATTTT
65 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATATATTTT
2753744 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
*
2753809 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATATTTT
66 ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATATTTT
*
2753856 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAA
*
2753920 TATCATATATTTTATTTTTATTTATTATTAT-A-ATTTTATATTCATTTC
65 TATCATATATTTTATTTTTATTTATTATTATAATATTTTATA-T-ATTTT
2753968 TTTAATAT
1 TTTAATAT
2753976 TTTTTTTATA
Statistics
Matches: 224, Mismatches: 4, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
110 8 0.04
111 73 0.33
112 141 0.63
113 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (112 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
ATCATATATTTTATTTTTATTTATTATTATAATATTTTATATATTTT
Found at i:2753881 original size:15 final size:15
Alignment explanation
Indices: 2753819--2753892 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
2753809 GTCATATATT
*
2753819 TTATTTTTATTTATTA
1 TTATTTATATTTA-TA
*
2753835 TTA-TAATATTT-TA
1 TTATTTATATTTATA
2753848 TATATTT-T-TTTA-A
1 T-TATTTATATTTATA
2753861 TATATTTATATTTATA
1 T-TATTTATATTTATA
* *
2753877 TTATTAATTTTTATA
1 TTATTTATATTTATA
2753892 T
1 T
2753893 AATATCATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
13 14 0.30
14 4 0.09
15 24 0.51
16 5 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTATATTTATA
Found at i:2753941 original size:27 final size:26
Alignment explanation
Indices: 2753688--2753958 Score: 171
Period size: 27 Copynumber: 9.9 Consensus size: 26
2753678 TTCTTAAATA
2753688 TATTTTTAATATCATATATTTTATTTT
1 TATTTTTAATAT-ATATATTTTATTTT
* *
2753715 TATTTTTATTATA-ATATTTTATATAT
1 TATTTTTAATATATATATTTTAT-TTT
2753741 T-TTTTTAATATATTTATATTTTTATTATT
1 TATTTTTAATATA--TATA-TTTTATT-TT
* ** *
2753770 AATTTTT-ATATAATATCATTTCTTAAATA
1 TATTTTTAATAT-ATAT-A-TT-TTATTTT
*
2753799 TATTTTTAATGTCATATATTTTATTTT
1 TATTTTTAATAT-ATATATTTTATTTT
* *
2753826 TATTTATTATTATA-ATATTTTATATAT
1 TATTT-TTAATATATATATTTTAT-TTT
2753853 T-TTTTTAATATATTTATATTTATATTATT
1 TATTTTTAATATA--TATATTT-TATT-TT
* ** *
2753882 AATTTTTATATAATATCATATTTTAAATA
1 TATTTTTA-AT-ATAT-ATATTTTATTTT
2753911 TATTTTTAATATCATATATTTTATTTT
1 TATTTTTAATAT-ATATATTTTATTTT
2753938 TATTTATT-AT-TATA-ATTTTAT
1 TATTT-TTAATATATATATTTTAT
2753959 ATTCATTTCT
Statistics
Matches: 193, Mismatches: 27, Indels: 51
0.71 0.10 0.19
Matches are distributed among these distances:
24 7 0.04
25 29 0.15
26 17 0.09
27 42 0.22
28 27 0.14
29 35 0.18
30 25 0.13
31 8 0.04
32 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTTTTAATATATATATTTTATTTT
Found at i:2754043 original size:176 final size:172
Alignment explanation
Indices: 2753704--2754063 Score: 395
Period size: 176 Copynumber: 2.1 Consensus size: 172
2753694 TAATATCATA
* *
2753704 TATTTTATTTTTATTTTTAT-T-ATA--ATATTTT--ATATATTTTT--T-TAATATATTTATAT
1 TATTTTATTTTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCATATATTTATAT
* * *
2753760 TTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCATATATTTTATTT
66 TTTTATTATTAATTATAATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTATTT
* * * *
2753825 TTATTTATTATTATAATATTTTATATATTTTTTTAATATATTT
131 TAATTTATTATTACAATATTATATAAATTTTTTT-ATATATTT
2753868 ATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCATATATTT-
1 -TATTT-TATT-TTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCATATATTTA
* * * * * *
2753932 TATTTTTATTTATT-ATTATAATTTTATATTCATTTCTTTAATATTTTTTTTATATTATATATTT
63 TATTTTTA-TTATTAATTATAATATAATA-TCATTTCTTAAATATATTTTTAATATCATATATTT
**
2753996 TATTTTAATTTATT-TTACCTTATTATATAAATGTTAATTTT-TATATTT
126 TATTTTAATTTATTATTACAATATTATATAAAT-TT--TTTTATATATTT
2754044 TATTTTATTTTAATTTTTAT
1 TATTTTATTTTAATTTTTAT
2754064 TATTATATTA
Statistics
Matches: 162, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
165 5 0.03
166 4 0.02
167 10 0.06
168 1 0.01
169 3 0.02
171 7 0.04
173 21 0.13
174 4 0.02
175 37 0.23
176 66 0.41
178 4 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (172 bp):
TATTTTATTTTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCATATATTTATAT
TTTTATTATTAATTATAATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTATTT
TAATTTATTATTACAATATTATATAAATTTTTTTATATATTT
Found at i:2754047 original size:48 final size:51
Alignment explanation
Indices: 2753989--2754111 Score: 139
Period size: 48 Copynumber: 2.4 Consensus size: 51
2753979 TTTTATATTA
2753989 TATATTTTATTTTAATTT-A-TTTTACCTTATTATA-TA-A-ATGTTAATTTT
1 TATATTTTATTTTAATTTAATTTTTA--TTATTATATTATACATGTTAATTTT
* *
2754037 TATATTTTATTTTATTTTAATTTTTATTATTATATTATTACATTTTAATTTT
1 TATATTTTATTTTAATTTAATTTTTATTATTATATTA-TACATGTTAATTTT
*
2754089 AATATTTTTATTTTAATTATAAT
1 TATA-TTTTATTTTAATT-TAAT
2754112 ATTATAAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
48 25 0.40
49 3 0.05
50 5 0.08
51 1 0.02
52 13 0.21
53 12 0.19
54 4 0.06
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (51 bp):
TATATTTTATTTTAATTTAATTTTTATTATTATATTATACATGTTAATTTT
Found at i:2754059 original size:53 final size:52
Alignment explanation
Indices: 2753978--2754103 Score: 148
Period size: 53 Copynumber: 2.3 Consensus size: 52
2753968 TTTAATATTT
2753978 TTTTTATATTATATATTTTATTTTAATTTATT-TTACCT-TATTATATAAATGTTAA
1 TTTTTATATT-T-TATTTTATTTTAATTT-TTATTA-CTATATTAT-TAAATGTTAA
* * *
2754033 TTTTTATATTTTATTTTATTTTAATTTTTATTATTATATTATTACATTTTAA
1 TTTTTATATTTTATTTTATTTTAATTTTTATTACTATATTATTAAATGTTAA
*
2754085 TTTTAATATTTTTATTTTA
1 TTTTTATA-TTTTATTTTA
2754104 ATTATAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
52 18 0.28
53 35 0.55
54 1 0.02
55 10 0.16
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (52 bp):
TTTTTATATTTTATTTTATTTTAATTTTTATTACTATATTATTAAATGTTAA
Found at i:2754090 original size:34 final size:33
Alignment explanation
Indices: 2754045--2754108 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
2754035 TTTATATTTT
2754045 ATTTTATTTT-A-ATTTTTATTATTATATTATTAC
1 ATTTTATTTTAATATTTTTATT-TTA-ATTATTAC
2754078 ATTTTAATTTTAATATTTTTATTTTAATTAT
1 ATTTT-ATTTTAATATTTTTATTTTAATTAT
2754109 AATATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 5 0.18
34 10 0.36
35 4 0.14
36 9 0.32
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (33 bp):
ATTTTATTTTAATATTTTTATTTTAATTATTAC
Found at i:2765320 original size:24 final size:24
Alignment explanation
Indices: 2765263--2765325 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
2765253 AAATAAATTT
2765263 TTATTT-TTATTTTGAATTAAATAA
1 TTATTTATTATTTT-AATTAAATAA
* * *
2765287 TTAATAATTAATTTAATTAAA-ATA
1 TTATTTATTATTTTAATTAAATA-A
2765311 TTATTTATTATTTTA
1 TTATTTATTATTTTA
2765326 TGTAACATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 24 0.77
25 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATTTATTATTTTAATTAAATAA
Found at i:2765566 original size:30 final size:30
Alignment explanation
Indices: 2765531--2765608 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
2765521 AATTATTAAT
* *
2765531 TATAAAAATATATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAATTTAAAAGAAAAA
* * *
2765561 TATAAAAATTTAATTAA-ATACAAGAAAAA
1 TATAAAAATTTATTTAATTTAAAAGAAAAA
*
2765590 -ATAAAAATTTATTTGATTT
1 TATAAAAATTTATTTAATTT
2765609 TTTAAATAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 14 0.36
29 10 0.26
30 15 0.38
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (30 bp):
TATAAAAATTTATTTAATTTAAAAGAAAAA
Found at i:2783635 original size:5 final size:5
Alignment explanation
Indices: 2783627--2783651 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2783617 AGAAAACAAA
2783627 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
2783652 CTAGGAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2784970 original size:2 final size:2
Alignment explanation
Indices: 2784965--2784992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2784955 TAAGGTCTTA
2784965 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
2784993 GTAGAGAGAG
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:2785000 original size:2 final size:2
Alignment explanation
Indices: 2784995--2785026 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2784985 ATATATATGT
2784995 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2785027 GGGTTCTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2787884 original size:8 final size:7
Alignment explanation
Indices: 2787864--2787914 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
2787854 TTGTATTATT
2787864 AATTAAA
1 AATTAAA
2787871 AATTAAA
1 AATTAAA
2787878 AATTTAAA
1 AA-TTAAA
*
2787886 TATT-AA
1 AATTAAA
*
2787892 AATAAAA
1 AATTAAA
*
2787899 AATTTAA
1 AATTAAA
2787906 AA-TAAA
1 AATTAAA
2787912 AAT
1 AAT
2787915 AAATTGAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 9 0.26
7 20 0.57
8 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATTAAA
Found at i:2787899 original size:21 final size:20
Alignment explanation
Indices: 2787867--2787917 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
2787857 TATTATTAAT
*
2787867 TAAAAATTAAAAATTTAAATA
1 TAAAAATAAAAAATTTAAA-A
*
2787888 TTAAAATAAAAAATTTAAAA
1 TAAAAATAAAAAATTTAAAA
2787908 TAAAAATAAA
1 TAAAAATAAA
2787918 TTGAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAATAAAAAATTTAAAA
Found at i:2787941 original size:17 final size:16
Alignment explanation
Indices: 2787885--2787939 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 16
2787875 AAAAATTTAA
2787885 ATATTAAAATAAAAA-
1 ATATTAAAATAAAAAT
2787900 AT-TTAAAATAAAAAT
1 ATATTAAAATAAAAAT
* *
2787915 AAATTGAATATAAAAAT
1 ATATT-AAAATAAAAAT
*
2787932 TTATTAAA
1 ATATTAAA
2787940 TACGTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.38
15 3 0.09
16 4 0.12
17 13 0.41
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATATTAAAATAAAAAT
Found at i:2795530 original size:2 final size:2
Alignment explanation
Indices: 2795523--2795548 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2795513 GAAAGTTTCC
2795523 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
2795549 TGCGGAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2802494 original size:3 final size:3
Alignment explanation
Indices: 2802486--2802511 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2802476 CTGAAAATTC
2802486 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2802512 AAAAGACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2808578 original size:2 final size:2
Alignment explanation
Indices: 2808568--2808624 Score: 77
Period size: 2 Copynumber: 30.0 Consensus size: 2
2808558 TGGGGAAAAA
2808568 AT AT A- AT AT AT ACT AT -T AT -T AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2808607 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2808625 CCCCACCCCA
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.08
2 44 0.88
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2817598 original size:13 final size:13
Alignment explanation
Indices: 2817580--2817609 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2817570 TCTCATTCTC
2817580 AAAAAAAAAAAAT
1 AAAAAAAAAAAAT
*
2817593 AAAAAAATAAAAT
1 AAAAAAAAAAAAT
2817606 AAAA
1 AAAA
2817610 TTTGCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:2831226 original size:6 final size:6
Alignment explanation
Indices: 2831215--2831241 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2831205 GTGCCTATCA
2831215 ATTTTG ATTTTG ATTTTG ATTTTG ATT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATT
2831242 AAGAATCCAG
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:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
ATTTTG
Found at i:2833397 original size:23 final size:25
Alignment explanation
Indices: 2833357--2833402 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2833347 TTAATTTTAA
2833357 ATTAAATATATATATTTTAAAAACC
1 ATTAAATATATATATTTTAAAAACC
*
2833382 ATTAAATAT-T-TGTTTTAAAAA
1 ATTAAATATATATATTTTAAAAA
2833403 TCTAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 1 0.05
25 9 0.45
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTAAATATATATATTTTAAAAACC
Found at i:2833418 original size:23 final size:24
Alignment explanation
Indices: 2833361--2833427 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 24
2833351 TTTTAAATTA
* *
2833361 AATATA-TATATTTTAAAAACCATT
1 AATATATTATGTTTTAAAAATCA-T
2833385 AA-ATATT-TGTTTTAAAAATC-T
1 AATATATTATGTTTTAAAAATCAT
*
2833406 AATATATTATGTTAATAAAAAT
1 AATATATTATGTT-TTAAAAAT
2833428 TATCATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 3 0.08
22 5 0.14
23 18 0.50
24 10 0.28
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (24 bp):
AATATATTATGTTTTAAAAATCAT
Found at i:2844787 original size:24 final size:26
Alignment explanation
Indices: 2844755--2844802 Score: 82
Period size: 24 Copynumber: 1.9 Consensus size: 26
2844745 TCTCTGAACA
2844755 ACAAACAGAAC-A-AAAATATCCATG
1 ACAAACAGAACTACAAAATATCCATG
2844779 ACAAACAGAACTACAAAATATCCA
1 ACAAACAGAACTACAAAATATCCA
2844803 GTTTATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.50
25 1 0.05
26 10 0.45
ACGTcount: A:0.58, C:0.23, G:0.06, T:0.12
Consensus pattern (26 bp):
ACAAACAGAACTACAAAATATCCATG
Found at i:2858765 original size:30 final size:30
Alignment explanation
Indices: 2858729--2858805 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
2858719 CCCGACTTGA
2858729 TCCCCCCGGCCCCCCTCCCACAAGTCCCGAT
1 TCCCCCCGGCCCCCCT-CCACAAGTCCCGAT
* * *
2858760 TCCCCCCTGCCCCTCTCCACGAGTCCCGAT
1 TCCCCCCGGCCCCCCTCCACAAGTCCCGAT
*
2858790 TCCCCCCTCGCCCCCC
1 TCCCCCC-GGCCCCCC
2858806 CCCCCCCCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 20 0.50
31 20 0.50
ACGTcount: A:0.09, C:0.64, G:0.12, T:0.16
Consensus pattern (30 bp):
TCCCCCCGGCCCCCCTCCACAAGTCCCGAT
Found at i:2859383 original size:22 final size:21
Alignment explanation
Indices: 2859358--2859427 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
2859348 CTTCGGTTTA
*
2859358 TAGGCATTGCATGATTGATGTT
1 TAGGCATTGCGTGATT-ATGTT
* *
2859380 TAGGTATTGCGTGATTAGGTT
1 TAGGCATTGCGTGATTATGTT
*
2859401 ATAGGCATTGCGTGATTAATTTT
1 -TAGGCATTGCGTGATT-ATGTT
2859424 TAGG
1 TAGG
2859428 TAATGCCTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 4 0.10
22 33 0.82
23 3 0.08
ACGTcount: A:0.23, C:0.07, G:0.29, T:0.41
Consensus pattern (21 bp):
TAGGCATTGCGTGATTATGTT
Found at i:2859551 original size:23 final size:23
Alignment explanation
Indices: 2859497--2859579 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
2859487 ATGCTTTCCT
*
2859497 AACTAATCACGCAATACC-TATC
1 AACTAATCACGCAATGCCATATC
* *
2859519 AATTAGTCACGCAATGCCATATC
1 AACTAATCACGCAATGCCATATC
* *
2859542 AACTAATCACGCAATGTCACATC
1 AACTAATCACGCAATGCCATATC
* *
2859565 AACTAGTCACACAAT
1 AACTAATCACGCAAT
2859580 AATATTTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
22 15 0.29
23 36 0.71
ACGTcount: A:0.40, C:0.29, G:0.08, T:0.23
Consensus pattern (23 bp):
AACTAATCACGCAATGCCATATC
Found at i:2859605 original size:25 final size:24
Alignment explanation
Indices: 2859565--2859630 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 24
2859555 ATGTCACATC
* *
2859565 AACTAGTCACACAATAATATTTAAA
1 AACTAGTCAC-GAATAATACTTAAA
2859590 AACTAGTCACG--TAATACTTAAA
1 AACTAGTCACGAATAATACTTAAA
*
2859612 AACTAATCACG--TAATACTT
1 AACTAGTCACGAATAATACTT
2859631 GAAATCGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 28 0.74
25 10 0.26
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (24 bp):
AACTAGTCACGAATAATACTTAAA
Found at i:2859610 original size:22 final size:22
Alignment explanation
Indices: 2859579--2859630 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2859569 AGTCACACAA
* *
2859579 TAATATTTAAAAACTAGTCACG
1 TAATACTTAAAAACTAATCACG
2859601 TAATACTTAAAAACTAATCACG
1 TAATACTTAAAAACTAATCACG
2859623 TAATACTT
1 TAATACTT
2859631 GAAATCGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (22 bp):
TAATACTTAAAAACTAATCACG
Found at i:2861512 original size:20 final size:19
Alignment explanation
Indices: 2861487--2861539 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2861477 TCTTAATTTA
2861487 TAAAATTTAATTAATTAATT
1 TAAAA-TTAATTAATTAATT
* *
2861507 TAAAATAAATATAATTTATT
1 TAAAATTAAT-TAATTAATT
2861527 T-AAATTAATTAAT
1 TAAAATTAATTAAT
2861540 AAAATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 4 0.14
19 11 0.38
20 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATTAATTAATTAATT
Found at i:2861549 original size:29 final size:30
Alignment explanation
Indices: 2861486--2861551 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
2861476 ATCTTAATTT
2861486 ATAA-AATTTAATTAATTAATTTAAAATAA
1 ATAATAATTTAATTAATTAATTTAAAATAA
* *
2861515 AT-ATAATTTATTTAAATTAA-TTAATA-AA
1 ATAATAATTTAATT-AATTAATTTAAAATAA
2861543 ATAATAATT
1 ATAATAATT
2861552 CAGTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 5 0.16
29 21 0.66
30 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATAATAATTTAATTAATTAATTTAAAATAA
Found at i:2863048 original size:28 final size:29
Alignment explanation
Indices: 2863016--2863073 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
2863006 ATTTATAATA
*
2863016 ATAAATA-TAAAACTATAATGTATA-AATT
1 ATAAATAGTAAAA-TATAATATATACAATT
*
2863044 ATAAATAGTTAAATATAATATATACAATT
1 ATAAATAGTAAAATATAATATATACAATT
2863073 A
1 A
2863074 ATAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (29 bp):
ATAAATAGTAAAATATAATATATACAATT
Found at i:2863086 original size:19 final size:18
Alignment explanation
Indices: 2863064--2863102 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2863054 AAATATAATA
*
2863064 TATACAATTAATAATTTTT
1 TATACAATTAA-AATTATT
*
2863083 TATATAATTAAAATTATT
1 TATACAATTAAAATTATT
2863101 TA
1 TA
2863103 AAAATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TATACAATTAAAATTATT
Found at i:2865679 original size:18 final size:17
Alignment explanation
Indices: 2865644--2865694 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
2865634 AATATATAAG
2865644 TAAATAATATAAAA-AATA
1 TAAATAA-A-AAAATAATA
2865662 TAAATAAAAATAATAATA
1 TAAATAAAAA-AATAATA
*
2865680 TAAATTAAAAAATAA
1 TAAATAAAAAAATAA
2865695 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 2 0.07
17 8 0.27
18 20 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATAAAAAAATAATA
Found at i:2865684 original size:24 final size:22
Alignment explanation
Indices: 2865631--2865694 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
2865621 TATAGAAATT
* *
2865631 TAAAATATATAAGTAAATAATA
1 TAAAAAATATAAATAAATAATA
2865653 TAAAAAATATAAATAAA-AATAA
1 TAAAAAATATAAATAAATAAT-A
2865675 TAATATAAAT-TAAA-AAATAA
1 TAA-A-AAATATAAATAAATAA
2865695 AAAATTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.08
22 22 0.61
23 7 0.19
24 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
TAAAAAATATAAATAAATAATA
Found at i:2868114 original size:12 final size:11
Alignment explanation
Indices: 2868081--2868129 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
2868071 GACTATCCCC
2868081 TTTACATTTCA
1 TTTACATTTCA
* *
2868092 TTTTCTTTTTCA
1 TTTAC-ATTTCA
*
2868104 TTTCACCTTTCA
1 TTT-ACATTTCA
2868116 TTTACATTTCA
1 TTTACATTTCA
2868127 TTT
1 TTT
2868130 GATATTGTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 14 0.45
12 16 0.52
13 1 0.03
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTACATTTCA
Found at i:2868123 original size:18 final size:17
Alignment explanation
Indices: 2868081--2868126 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2868071 GACTATCCCC
* *
2868081 TTTACATTTCATTTTCT
1 TTTACATTTCACTTTCA
*
2868098 TTTTCATTTCACCTTTCA
1 TTTACATTTCA-CTTTCA
2868116 TTTACATTTCA
1 TTTACATTTCA
2868127 TTTGATATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTACATTTCACTTTCA
Found at i:2881778 original size:23 final size:24
Alignment explanation
Indices: 2881733--2881780 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
2881723 CTTCATTCCT
2881733 TTCTTCCTATTTTCTTTGTTTTTC
1 TTCTTCCTATTTTCTTTGTTTTTC
*
2881757 TTCTT-CTA-TTTCTTTTTATTTTC
1 TTCTTCCTATTTTCTTTGT-TTTTC
2881780 T
1 T
2881781 CAACTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 9 0.41
24 5 0.23
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (24 bp):
TTCTTCCTATTTTCTTTGTTTTTC
Found at i:2881778 original size:24 final size:24
Alignment explanation
Indices: 2881733--2881778 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2881723 CTTCATTCCT
*
2881733 TTCTTCCTATTTTCTTTGTTTTTC
1 TTCTTCCTATTTTCTTTATTTTTC
*
2881757 TTCTT-CTATTTCTTTTTATTTT
1 TTCTTCCTATTT-TCTTTATTTT
2881779 CTCAACTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (24 bp):
TTCTTCCTATTTTCTTTATTTTTC
Found at i:2887701 original size:31 final size:31
Alignment explanation
Indices: 2887651--2887713 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2887641 ATAATAATCC
* *
2887651 ATAAAAAAAAAGAATAATATAATAA-AAGAA
1 ATAAAAAAAAAGAAGAATATAACAATAAGAA
*
2887681 ATAAATAAAAATGAAGAATATAACAATAAGAA
1 ATAAA-AAAAAAGAAGAATATAACAATAAGAA
2887713 A
1 A
2887714 AACATCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 17 0.61
32 6 0.21
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (31 bp):
ATAAAAAAAAAGAAGAATATAACAATAAGAA
Found at i:2890519 original size:2 final size:2
Alignment explanation
Indices: 2890512--2890548 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2890502 ACTCTTCTTT
2890512 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2890549 GCATGTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2899803 original size:11 final size:11
Alignment explanation
Indices: 2899787--2899825 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
2899777 ACTCTGTGCA
2899787 CTCAATGAAGG
1 CTCAATGAAGG
2899798 CTCAATGAAGG
1 CTCAATGAAGG
*
2899809 CTCAATTAAAGG
1 CTCAA-TGAAGG
2899821 CTCAA
1 CTCAA
2899826 ACCGACTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (11 bp):
CTCAATGAAGG
Found at i:2911207 original size:2 final size:2
Alignment explanation
Indices: 2911200--2911224 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2911190 CATAAGTTTT
2911200 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2911225 TAACAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2917017 original size:28 final size:28
Alignment explanation
Indices: 2916956--2917162 Score: 132
Period size: 28 Copynumber: 7.5 Consensus size: 28
2916946 TTCTTTCATG
* * * *
2916956 ACATATAATAATTA-AATATTTAACATA
1 ACATATAACAATTATATTTTTTAATATA
*
2916983 ACATATAAGAATTATATTTTTTAATATA
1 ACATATAACAATTATATTTTTTAATATA
* * * *
2917011 ACGTATAACAACTA-AATCTTTAATATA
1 ACATATAACAATTATATTTTTTAATATA
*** * * * * *
2917038 GTGTATAATAACTACATTTTTCAATATT
1 ACATATAACAATTATATTTTTTAATATA
* * * *
2917066 ACATGTAATAACTATATTTTTTAACATA
1 ACATATAACAATTATATTTTTTAATATA
* * *
2917094 ACATATAACAATTA-AATTTTAAATATG
1 ACATATAACAATTATATTTTTTAATATA
* * *
2917121 ATATGTAACAATTATATTTTTTAATATG
1 ACATATAACAATTATATTTTTTAATATA
**
2917149 ATGTATAACAATTA
1 ACATATAACAATTA
2917163 AATTAATTAC
Statistics
Matches: 140, Mismatches: 37, Indels: 5
0.77 0.20 0.03
Matches are distributed among these distances:
27 56 0.40
28 84 0.60
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (28 bp):
ACATATAACAATTATATTTTTTAATATA
Found at i:2917033 original size:55 final size:55
Alignment explanation
Indices: 2916956--2917113 Score: 145
Period size: 55 Copynumber: 2.9 Consensus size: 55
2916946 TTCTTTCATG
* * * *
2916956 ACATATAATAATTAAATATTTAACATAACATATAAGAATTATATTTTTTAATATA
1 ACATATAATAACTAAATATTTAACATAACATATAACAATTAAATTTTTCAATATA
* * * * *** * * * *
2917011 ACGTATAACAACTAAATCTTTAATATAGTGTATAATAACTACATTTTTCAATATT
1 ACATATAATAACTAAATATTTAACATAACATATAACAATTAAATTTTTCAATATA
* * *
2917066 ACATGTAATAACTATATTTTTTAACATAACATATAACAATTAAATTTT
1 ACATATAATAACTA-AATATTTAACATAACATATAACAATTAAATTTT
2917114 AAATATGATA
Statistics
Matches: 77, Mismatches: 25, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
55 53 0.69
56 24 0.31
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.41
Consensus pattern (55 bp):
ACATATAATAACTAAATATTTAACATAACATATAACAATTAAATTTTTCAATATA
Found at i:2917177 original size:37 final size:37
Alignment explanation
Indices: 2917130--2917203 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
2917120 GATATGTAAC
* * * * *
2917130 AATTATATTTTTTAATATGATGTATAACAATTAAATT
1 AATTACATTTTTCAACATGACGTATAACAACTAAATT
*
2917167 AATTACATTTTTCAACATGACGTATAATAACTAAATT
1 AATTACATTTTTCAACATGACGTATAACAACTAAATT
2917204 TTTAATATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (37 bp):
AATTACATTTTTCAACATGACGTATAACAACTAAATT
Found at i:2918419 original size:5 final size:5
Alignment explanation
Indices: 2918409--2918439 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2918399 TCTTTGGGAG
*
2918409 AGGTC AGGTC AGATC AGGTC AGGTC AGGTC A
1 AGGTC AGGTC AGGTC AGGTC AGGTC AGGTC A
2918440 CCGTAGGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.19
Consensus pattern (5 bp):
AGGTC
Found at i:2931358 original size:36 final size:36
Alignment explanation
Indices: 2931318--2931407 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
2931308 AATCAACATT
* *
2931318 TCCAGGCATCCCACCTGGCA-TGCTACCAGGGAAACC
1 TCCAGGCATCCCACCTGGCATTCCT-CCAGGAAAACC
* * *
2931354 TCCAGGCATCCCTCCAGGCATTCCTCCTGGAAAACC
1 TCCAGGCATCCCACCTGGCATTCCTCCAGGAAAACC
*
2931390 TCCAGGCATACCACCTGG
1 TCCAGGCATCCCACCTGG
2931408 AAACCCACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
36 42 0.93
37 3 0.07
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (36 bp):
TCCAGGCATCCCACCTGGCATTCCTCCAGGAAAACC
Found at i:2931367 original size:12 final size:12
Alignment explanation
Indices: 2931352--2931431 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 12
2931342 ACCAGGGAAA
2931352 CCTCCAGGCATC
1 CCTCCAGGCATC
*
2931364 CCTCCAGGCATT
1 CCTCCAGGCATC
* * **
2931376 CCTCCTGGAAAA
1 CCTCCAGGCATC
*
2931388 CCTCCAGGCATA
1 CCTCCAGGCATC
* * * *
2931400 CCACCTGGAAAC
1 CCTCCAGGCATC
*
2931412 CCACCAGGCATC
1 CCTCCAGGCATC
*
2931424 CCCCCAGG
1 CCTCCAGG
2931432 TTTTCTACTG
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.24, C:0.45, G:0.17, T:0.14
Consensus pattern (12 bp):
CCTCCAGGCATC
Found at i:2931379 original size:24 final size:24
Alignment explanation
Indices: 2931364--2931431 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2931354 TCCAGGCATC
*
2931364 CCTCCAGGCATTCCTCCTGGAAAA
1 CCTCCAGGCATTCCTCCAGGAAAA
* * * *
2931388 CCTCCAGGCATACCACCTGGAAAC
1 CCTCCAGGCATTCCTCCAGGAAAA
* * *
2931412 CCACCAGGCATCCCCCCAGG
1 CCTCCAGGCATTCCTCCAGG
2931432 TTTTCTACTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.44, G:0.18, T:0.13
Consensus pattern (24 bp):
CCTCCAGGCATTCCTCCAGGAAAA
Found at i:2953151 original size:24 final size:24
Alignment explanation
Indices: 2953124--2953174 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2953114 TTATCTGCGC
2953124 AATCTATCTTATCATTAATCTTTA
1 AATCTATCTTATCATTAATCTTTA
2953148 AATCTATCTTATCATTAATCTTTA
1 AATCTATCTTATCATTAATCTTTA
2953172 AAT
1 AAT
2953175 AAGAGGGACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (24 bp):
AATCTATCTTATCATTAATCTTTA
Found at i:2956399 original size:21 final size:21
Alignment explanation
Indices: 2956340--2956473 Score: 207
Period size: 21 Copynumber: 6.2 Consensus size: 21
2956330 GGGTTTCGAG
* *
2956340 AAAACCCGGTTTTAGGGTTCTCA
1 AAAA-CCGGTTTAAGGGTT-TCC
2956363 AAGAACCGGTTTTAAGGGTTTCC
1 AA-AACCGG-TTTAAGGGTTTCC
2956386 AAAACCGGTTTAA-GGTTTCC
1 AAAACCGGTTTAAGGGTTTCC
2956406 AAAACCGGTTTAAGGGTTTCC
1 AAAACCGGTTTAAGGGTTTCC
2956427 AAAACCGGTTTAAGGGTTTCC
1 AAAACCGGTTTAAGGGTTTCC
2956448 AAAACCGGTTTAAGGGTTTCC
1 AAAACCGGTTTAAGGGTTTCC
2956469 AAAAC
1 AAAAC
2956474 GATTAACAGA
Statistics
Matches: 106, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
20 20 0.19
21 59 0.56
22 6 0.06
23 10 0.09
24 11 0.10
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (21 bp):
AAAACCGGTTTAAGGGTTTCC
Found at i:2958486 original size:69 final size:70
Alignment explanation
Indices: 2958400--2958534 Score: 184
Period size: 69 Copynumber: 1.9 Consensus size: 70
2958390 TTATATATAG
* * *
2958400 GAAAAAATAACTATTGAAAATATTAAATACATATTA-CGTTAGTTGATTG-GAATAAGAAAAATA
1 GAAAAAATAACGATTGAAAATATTAAATAAATATTATCGTTAGTTGATTGAAAATAAGAAAAATA
2958463 GGTGA
66 GGTGA
* * * *
2958468 GAAAAACATAACGGTTGAAAATATTTAATAAATATTATCTTTAGTTGATTGAAAATAAGAGAAAT
1 GAAAAA-ATAACGATTGAAAATATTAAATAAATATTATCGTTAGTTGATTGAAAATAAGAAAAAT
2958533 AG
65 AG
2958535 TTGAAAATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
68 6 0.11
69 26 0.46
70 12 0.21
71 13 0.23
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (70 bp):
GAAAAAATAACGATTGAAAATATTAAATAAATATTATCGTTAGTTGATTGAAAATAAGAAAAATA
GGTGA
Found at i:2964586 original size:29 final size:29
Alignment explanation
Indices: 2964544--2964599 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2964534 TTTGACTTAA
*
2964544 AATAAAAGTATAAGAGT-TTAATTGAATGT
1 AATAAAAGAATAAG-GTCTTAATTGAATGT
* *
2964573 AATAGAAGAATAAGGTCTTATTTGAAT
1 AATAAAAGAATAAGGTCTTAATTGAAT
2964600 TTTGTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (29 bp):
AATAAAAGAATAAGGTCTTAATTGAATGT
Found at i:2976776 original size:37 final size:37
Alignment explanation
Indices: 2976726--2976799 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
2976716 TTCTATATGC
* * **
2976726 ATTTTGCCGGGGACCCATGAAATGAAAGGCTGGCTGA
1 ATTTTGACGGGGACCCATGAAAGGAAAACCTGGCTGA
2976763 ATTTTGACGGGGACCCATGAAAGGAAAACCTGGCTGA
1 ATTTTGACGGGGACCCATGAAAGGAAAACCTGGCTGA
2976800 TATTGATCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.31, T:0.20
Consensus pattern (37 bp):
ATTTTGACGGGGACCCATGAAAGGAAAACCTGGCTGA
Found at i:2978248 original size:14 final size:14
Alignment explanation
Indices: 2978225--2978255 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2978215 AAAAATAATT
2978225 ATATTATATATATA
1 ATATTATATATATA
*
2978239 ATATTTTATATATA
1 ATATTATATATATA
2978253 ATA
1 ATA
2978256 ATGAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATATATATA
Found at i:3005159 original size:14 final size:14
Alignment explanation
Indices: 3005140--3005169 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3005130 CGGAACGAAG
3005140 AAAAGGAGAAAGAA
1 AAAAGGAGAAAGAA
*
3005154 AAAAGGTGAAAGAA
1 AAAAGGAGAAAGAA
3005168 AA
1 AA
3005170 TAGAGCTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (14 bp):
AAAAGGAGAAAGAA
Found at i:3009774 original size:2 final size:2
Alignment explanation
Indices: 3009767--3009793 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3009757 AGTTGAAATT
3009767 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3009794 GTATGCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3032142 original size:18 final size:17
Alignment explanation
Indices: 3032119--3032152 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3032109 ATCAATTTAT
3032119 ACATATATATATATATAC
1 ACATATATAT-TATATAC
3032137 ACATATATATTATATA
1 ACATATATATTATATA
3032153 AAAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (17 bp):
ACATATATATTATATAC
Found at i:3039240 original size:2 final size:2
Alignment explanation
Indices: 3039235--3039259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3039225 TTTTGACATT
3039235 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3039260 TTTGCTCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3040019 original size:2 final size:2
Alignment explanation
Indices: 3040012--3040040 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3040002 TGCCATTAGG
3040012 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
3040041 ATATATATAT
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:3053499 original size:25 final size:25
Alignment explanation
Indices: 3053462--3053510 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3053452 TATAATAAAT
*
3053462 TTTTTTGAGATAAATAAAAA-ATATG
1 TTTTTTAAGAT-AATAAAAATATATG
*
3053487 TTTTTTAATATAATAAAAATATAT
1 TTTTTTAAGATAATAAAAATATAT
3053511 AAATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTTTAAGATAATAAAAATATATG
Found at i:3074425 original size:12 final size:11
Alignment explanation
Indices: 3074407--3074433 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3074397 CATATATGTG
3074407 TAAAAAAAAAT
1 TAAAAAAAAAT
3074418 TAAAAAAAAAT
1 TAAAAAAAAAT
3074429 TAAAA
1 TAAAA
3074434 TAGTACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAAAAAAAT
Found at i:3078871 original size:2 final size:2
Alignment explanation
Indices: 3078864--3078892 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3078854 TTAGAAATGT
3078864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3078893 GGCCAATAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3097098 original size:12 final size:12
Alignment explanation
Indices: 3097077--3097106 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3097067 TCGTGAAAAA
3097077 GAAGAAGAAGAT
1 GAAGAAGAAGAT
*
3097089 GAAGATGAAGAT
1 GAAGAAGAAGAT
3097101 GAAGAA
1 GAAGAA
3097107 ACGCAGCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (12 bp):
GAAGAAGAAGAT
Found at i:3110671 original size:13 final size:13
Alignment explanation
Indices: 3110653--3110677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3110643 GAAATCTAAA
3110653 AAAAATTAAAAAT
1 AAAAATTAAAAAT
3110666 AAAAATTAAAAA
1 AAAAATTAAAAA
3110678 AACCAAAGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATTAAAAAT
Found at i:3130163 original size:11 final size:12
Alignment explanation
Indices: 3130138--3130168 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
3130128 ATAAGATAAG
3130138 TAGATAGAGAGA
1 TAGATAGAGAGA
3130150 TAGATAGA-AGA
1 TAGATAGAGAGA
3130161 TAGATAGA
1 TAGATAGA
3130169 TTGCGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.29, T:0.19
Consensus pattern (12 bp):
TAGATAGAGAGA
Found at i:3131180 original size:2 final size:2
Alignment explanation
Indices: 3131175--3131206 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3131165 CTCTCTGTCT
3131175 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
3131207 TTCTTGTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3142025 original size:22 final size:22
Alignment explanation
Indices: 3142000--3142049 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3141990 AATCAGCAAG
*
3142000 AAATCTCTCACAAAAC-AGTACC
1 AAATCACTCAC-AAACTAGTACC
*
3142022 AAATCACTCACAAACTAGTAGC
1 AAATCACTCACAAACTAGTACC
3142044 AAATCA
1 AAATCA
3142050 GCAAAAGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.48, C:0.28, G:0.06, T:0.18
Consensus pattern (22 bp):
AAATCACTCACAAACTAGTACC
Found at i:3143573 original size:21 final size:21
Alignment explanation
Indices: 3143549--3143592 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3143539 AATTGAATAC
*
3143549 AAAATTAAAATATGACAACTA
1 AAAATTAAAATATAACAACTA
*
3143570 AAAATTAAAATATAAGAACTA
1 AAAATTAAAATATAACAACTA
3143591 AA
1 AA
3143593 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAATTAAAATATAACAACTA
Found at i:3143595 original size:19 final size:20
Alignment explanation
Indices: 3143549--3143597 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
3143539 AATTGAATAC
*
3143549 AAAATTAAAATATGACAACT
1 AAAATTAAAATATAACAACT
*
3143569 AAAAATTAAAATATAAGAACT
1 -AAAATTAAAATATAACAACT
3143590 -AAATTAAA
1 AAAATTAAA
3143598 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 8 0.31
21 18 0.69
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAATTAAAATATAACAACT
Found at i:3143615 original size:23 final size:23
Alignment explanation
Indices: 3143554--3143625 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
3143544 AATACAAAAT
* * *
3143554 TAAAATATGACAACTAAA--AAT
1 TAAAATATAAAAACTAAATTAAA
*
3143575 TAAAATATAAGAACTAAATTAAA
1 TAAAATATAAAAACTAAATTAAA
* * *
3143598 TAAAATTTAAAAATTAAATTGAA
1 TAAAATATAAAAACTAAATTAAA
3143621 TAAAA
1 TAAAA
3143626 AATTAATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 16 0.38
23 26 0.62
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (23 bp):
TAAAATATAAAAACTAAATTAAA
Found at i:3143661 original size:27 final size:26
Alignment explanation
Indices: 3143611--3143661 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3143601 AATTTAAAAA
* *
3143611 TTAAATTGAATAAAAAATTAATTTTT
1 TTAAATTGAAGAAAAAAATAATTTTT
*
3143637 TTAAATTTAAGAAAAAAATATATTT
1 TTAAATTGAAGAAAAAAATA-ATTT
3143662 AGTTCACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
TTAAATTGAAGAAAAAAATAATTTTT
Found at i:3147232 original size:30 final size:30
Alignment explanation
Indices: 3147188--3147247 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3147178 CATATTACAG
3147188 GTTGCCATCAGTAAAACATATAAACTTTCC
1 GTTGCCATCAGTAAAACATATAAACTTTCC
* * **
3147218 GTTGCTATCTGTAAAACATATTGACTTTCC
1 GTTGCCATCAGTAAAACATATAAACTTTCC
3147248 TGCACAGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (30 bp):
GTTGCCATCAGTAAAACATATAAACTTTCC
Found at i:3158922 original size:2 final size:2
Alignment explanation
Indices: 3158915--3158943 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3158905 CTACTTAATT
3158915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3158944 TTCTCTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3161145 original size:2 final size:2
Alignment explanation
Indices: 3161138--3161162 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3161128 ACCCCTTAGC
3161138 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3161163 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3161167 original size:2 final size:2
Alignment explanation
Indices: 3161162--3161187 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3161152 TATATATATA
3161162 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
3161188 AAATCATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3162548 original size:2 final size:2
Alignment explanation
Indices: 3162541--3162578 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3162531 AAACACGGAC
* *
3162541 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3162579 TTGACCCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3164356 original size:30 final size:29
Alignment explanation
Indices: 3164284--3164377 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
3164274 AAAAAAGTTT
*
3164284 AAATAAATTTTTACATTTTA--TTAAATTC
1 AAATAAATTTTTATATTTTATTTTAAA-TC
**
3164312 -AATCAAAACTTTATATTGTTATTTTAAATC
1 AAAT-AAATTTTTATATT-TTATTTTAAATC
* *
3164342 AAATAAATTTTTATATTTTTATTTTTAATA
1 AAATAAATTTTTATA-TTTTATTTTAAATC
3164372 AAATAA
1 AAATAA
3164378 TTAAATTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.06
28 10 0.19
29 3 0.06
30 27 0.51
31 10 0.19
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (29 bp):
AAATAAATTTTTATATTTTATTTTAAATC
Found at i:3164705 original size:18 final size:18
Alignment explanation
Indices: 3164682--3164718 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3164672 AATTTAAAAA
3164682 AAAAT-ATTTAAATATTTT
1 AAAATAATTTAAA-ATTTT
3164700 AAAATAATTTAAAATTTT
1 AAAATAATTTAAAATTTT
3164718 A
1 A
3164719 TTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATAATTTAAAATTTT
Found at i:3171337 original size:14 final size:14
Alignment explanation
Indices: 3171318--3171347 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3171308 ATGAGCTTGG
3171318 GACTTAGAGGTTGA
1 GACTTAGAGGTTGA
3171332 GACTTAGAGGTTGA
1 GACTTAGAGGTTGA
3171346 GA
1 GA
3171348 AGTTCTCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.27
Consensus pattern (14 bp):
GACTTAGAGGTTGA
Found at i:3181785 original size:2 final size:2
Alignment explanation
Indices: 3181778--3181807 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3181768 GACTTAACAA
*
3181778 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3181808 GATCAAGAGG
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3184862 original size:18 final size:19
Alignment explanation
Indices: 3184834--3184874 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3184824 TATTACACAT
3184834 TTATTTGTAATTATATTAA
1 TTATTTGTAATTATATTAA
* *
3184853 TTATTT-TAATTTTTTTAA
1 TTATTTGTAATTATATTAA
3184871 TTAT
1 TTAT
3184875 AATTGAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTATTTGTAATTATATTAA
Found at i:3186013 original size:73 final size:74
Alignment explanation
Indices: 3185919--3186092 Score: 287
Period size: 73 Copynumber: 2.4 Consensus size: 74
3185909 ATGAAATGAG
* * * *
3185919 AAAAAGTCTCGAGTTTTCGCTTCACATTGCAAGTTGGGAAACAGTGATGATCAAAGGAATATGAA
1 AAAAACTCTCGAGTTTTCGCTTCACAGTGCAAGCTGGGAAACAGTGATGATCAAAGGAAAATGAA
3185984 AGACCTC-A
66 AGACCTCAA
3185992 AAAAACTCTCGAGTTTTCGCTTCACAGTGCAAGCTGGGAAACAGTGATGATCAAAGGAAAATGAA
1 AAAAACTCTCGAGTTTTCGCTTCACAGTGCAAGCTGGGAAACAGTGATGATCAAAGGAAAATGAA
*
3186057 AGATCTCAA
66 AGACCTCAA
3186066 AAAAACTCTCAGAGTTTTCGCTTCACA
1 AAAAACTCTC-GAGTTTTCGCTTCACA
3186093 AATATAATAC
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
73 67 0.71
74 11 0.12
75 16 0.17
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (74 bp):
AAAAACTCTCGAGTTTTCGCTTCACAGTGCAAGCTGGGAAACAGTGATGATCAAAGGAAAATGAA
AGACCTCAA
Found at i:3194989 original size:131 final size:132
Alignment explanation
Indices: 3194851--3195122 Score: 406
Period size: 131 Copynumber: 2.1 Consensus size: 132
3194841 GCAATATCCT
* *
3194851 GAGAATTCAAAAATC-TCAATGATGGTGATCCTCTGAACGTTTTGAATACTCCTTTAATGCAACA
1 GAGAATTCAAAAA-CATCAATGATGCTGATCCTCTGAACGTGTTGAATACTCCTTTAATGCAACA
* *
3194915 CACTTGAATT-AAGTGAATTATGATATGAAAAGAAATATATCTGGTTTGGGTTTGAACGCCTCCT
65 CACTTGAATTAAAGTGAATTATGATATGAAAAGAAATATATCTGGTTTGGGTCTGAACGCATCCT
3194979 TTA
130 TTA
** * *
3194982 GAGAATTC-ATGACATCAATGATGCTGATCCTCTGAACGTGTTGAATACTTCTTTAATGCAGCAC
1 GAGAATTCAAAAACATCAATGATGCTGATCCTCTGAACGTGTTGAATACTCCTTTAATGCAACAC
* * **
3195046 ACTTGGATTAAAGTGAATTGTGATATGAAAAGAAATATATCTGGTTTGGGTCTGAATTCATCCTT
66 ACTTGAATTAAAGTGAATTATGATATGAAAAGAAATATATCTGGTTTGGGTCTGAACGCATCCTT
3195111 TA
131 TA
3195113 GAGAATTCAA
1 GAGAATTCAA
3195123 TCTCCCTTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
129 1 0.01
130 56 0.44
131 68 0.54
132 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (132 bp):
GAGAATTCAAAAACATCAATGATGCTGATCCTCTGAACGTGTTGAATACTCCTTTAATGCAACAC
ACTTGAATTAAAGTGAATTATGATATGAAAAGAAATATATCTGGTTTGGGTCTGAACGCATCCTT
TA
Found at i:3197234 original size:6 final size:6
Alignment explanation
Indices: 3197225--3197271 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
3197215 AGAGCTACCC
* *
3197225 CCACCT CCACCT CCACCT CCACCT CCACCA CCGCCT CCACCT CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
3197272 GCCTCCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.68, G:0.02, T:0.13
Consensus pattern (6 bp):
CCACCT
Found at i:3198908 original size:2 final size:2
Alignment explanation
Indices: 3198901--3198933 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3198891 TTAATATGAT
*
3198901 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3198934 GTCTCAGCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3209371 original size:30 final size:30
Alignment explanation
Indices: 3209337--3209408 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
3209327 AATTATTAAT
3209337 TATAAAAATTTATTTAAT-TTAAAATAAAAA
1 TATAAAAATTTATTT-ATCTTAAAATAAAAA
*
3209367 TATAAAAACTTATTTATCTTAAAATAAAAA
1 TATAAAAATTTATTTATCTTAAAATAAAAA
*
3209397 TATAAAATTTTA
1 TATAAAAATTTA
3209409 ATAAAACACA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
TATAAAAATTTATTTATCTTAAAATAAAAA
Found at i:3222217 original size:30 final size:30
Alignment explanation
Indices: 3222154--3222219 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3222144 CAGTCAAGTG
* * * **
3222154 TTTATATTTTTATTTTGAGTCAAGTCAGTT
1 TTTATATTTTTATTTTGAATCAAATAAACT
*
3222184 TTTATATTTTTATTTTTAATCAAATAAACT
1 TTTATATTTTTATTTTGAATCAAATAAACT
3222214 TTTATA
1 TTTATA
3222220 AGTAATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (30 bp):
TTTATATTTTTATTTTGAATCAAATAAACT
Found at i:3222426 original size:14 final size:14
Alignment explanation
Indices: 3222407--3222437 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3222397 TAAAATGATA
3222407 AATAATATTTAATT
1 AATAATATTTAATT
3222421 AATAATATTTAATT
1 AATAATATTTAATT
3222435 AAT
1 AAT
3222438 TTTTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATAATATTTAATT
Found at i:3222442 original size:25 final size:24
Alignment explanation
Indices: 3222409--3222463 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3222399 AAATGATAAA
* * *
3222409 TAATATTTAATTAATAATATTTAAT
1 TAATTTTTAATT-ATAAAAATTAAT
*
3222434 TAATTTTTAATTATAAAAATTATT
1 TAATTTTTAATTATAAAAATTAAT
3222458 TAATTT
1 TAATTT
3222464 AAAATAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAATTTTTAATTATAAAAATTAAT
Found at i:3222466 original size:16 final size:16
Alignment explanation
Indices: 3222435--3222467 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3222425 ATATTTAATT
3222435 AATTTTTAATTATAAA
1 AATTTTTAATTATAAA
3222451 AATTATTTAATT-TAAA
1 AATT-TTTAATTATAAA
3222467 A
1 A
3222468 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTTTAATTATAAA
Found at i:3234718 original size:22 final size:21
Alignment explanation
Indices: 3234692--3234732 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3234682 AAAGATACAG
3234692 AAACAAAATAAAGTCCAAAAAC
1 AAACAAAATAAA-TCCAAAAAC
* *
3234714 AAACACAATCAATCCAAAA
1 AAACAAAATAAATCCAAAA
3234733 CCACCCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.66, C:0.22, G:0.02, T:0.10
Consensus pattern (21 bp):
AAACAAAATAAATCCAAAAAC
Found at i:3243550 original size:12 final size:11
Alignment explanation
Indices: 3243527--3243556 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
3243517 AACTATTTTT
3243527 ATATATATTTA
1 ATATATATTTA
3243538 ATATATATGTTA
1 ATATATAT-TTA
3243550 ATATATA
1 ATATATA
3243557 ATATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
ATATATATTTA
Done.