Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 51 of 93
Found at i:6450801 original size:24 final size:24
Alignment explanation
Indices: 6450748--6450802 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
6450738 AAATTAGTTT
6450748 AATATTAAATATTAGATAATACTA
1 AATATTAAATATTAGATAATACTA
** *
6450772 TGTATTAAATATTATATAATA-TAA
1 AATATTAAATATTAGATAATACT-A
6450796 AATATTA
1 AATATTA
6450803 TATAATGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
AATATTAAATATTAGATAATACTA
Found at i:6450879 original size:22 final size:21
Alignment explanation
Indices: 6450799--6450882 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
6450789 AATATAAAAT
* * *
6450799 ATTATATAATGTTAATTAGTTA
1 ATTAT-TAATATTAAATATTTA
**
6450821 ATTAATTTAATATTAAATATGAA
1 ATT-A-TTAATATTAAATATTTA
* *
6450844 ACTATATAAAATTAAATATTTA
1 ATTAT-TAATATTAAATATTTA
6450866 ATTATTGAATATTAAAT
1 ATTATT-AATATTAAAT
6450883 TTAATATTGC
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
21 2 0.04
22 30 0.64
23 14 0.30
24 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTATTAATATTAAATATTTA
Found at i:6451155 original size:20 final size:20
Alignment explanation
Indices: 6451130--6451170 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6451120 GATATTGGAG
*
6451130 GCGTCATTCCATGGAGAAAA
1 GCGTCATTCCATCGAGAAAA
6451150 GCGTCATTCCATCGAGAAAA
1 GCGTCATTCCATCGAGAAAA
6451170 G
1 G
6451171 AGGAATCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (20 bp):
GCGTCATTCCATCGAGAAAA
Found at i:6455442 original size:66 final size:68
Alignment explanation
Indices: 6455371--6455498 Score: 233
Period size: 66 Copynumber: 1.9 Consensus size: 68
6455361 AAATAGTCAA
*
6455371 TTTTATTAAATTAAATTACAAGTTTTTAGGTGAAAA-ATAAATAAAAT-AAAGAGATATTTTGTA
1 TTTTATTAAATTAAATTACAAGTTTTTAGGTGAAAAGATAAATAAAATAAAAAAGATATTTTGTA
6455434 TAT
66 TAT
6455437 TTTTATTAAATTAAATTACAAGTTTTTAGGTGAAAAGATAAATAAAATAAAAAAGATATTTT
1 TTTTATTAAATTAAATTACAAGTTTTTAGGTGAAAAGATAAATAAAATAAAAAAGATATTTT
6455499 TGTTAATTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
66 36 0.61
67 11 0.19
68 12 0.20
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (68 bp):
TTTTATTAAATTAAATTACAAGTTTTTAGGTGAAAAGATAAATAAAATAAAAAAGATATTTTGTA
TAT
Found at i:6458092 original size:11 final size:13
Alignment explanation
Indices: 6458065--6458103 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
6458055 TTATACAAAT
6458065 TTTAATTATATTA
1 TTTAATTATATTA
6458078 TTTAATT-TA-TA
1 TTTAATTATATTA
*
6458089 TTTAATTATAATA
1 TTTAATTATATTA
6458102 TT
1 TT
6458104 GTTTAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 4 0.17
13 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATTATATTA
Found at i:6458128 original size:27 final size:27
Alignment explanation
Indices: 6458072--6458170 Score: 68
Period size: 27 Copynumber: 3.9 Consensus size: 27
6458062 AATTTTAATT
* * *
6458072 ATATTATTTAATTTATATTTAATTATA
1 ATATTATTTAAATGATATTAAATTATA
*
6458099 ATATTGTTTAAATGATATTAAATTCA-A
1 ATATTATTTAAATGATATTAAATT-ATA
* *
6458126 ATA-AAATTAAATG--A-TAAA--ATA
1 ATATTATTTAAATGATATTAAATTATA
*
6458147 ATATTATTTAAATGTTATTTAAAT
1 ATATTATTTAAATGATA-TTAAAT
6458171 ATTATTTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
20 1 0.02
21 4 0.07
22 8 0.15
23 4 0.07
24 2 0.04
26 11 0.20
27 24 0.44
28 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (27 bp):
ATATTATTTAAATGATATTAAATTATA
Found at i:6458166 original size:11 final size:11
Alignment explanation
Indices: 6458146--6458182 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
6458136 ATGATAAAAT
6458146 AATATTATTTA
1 AATATTATTTA
*
6458157 AATGTTATTTA
1 AATATTATTTA
6458168 AATATTATTTA
1 AATATTATTTA
6458179 AATA
1 AATA
6458183 ATATAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (11 bp):
AATATTATTTA
Found at i:6458214 original size:18 final size:19
Alignment explanation
Indices: 6458139--6458214 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 19
6458129 AAATTAAATG
*
6458139 ATAAAATAATATTATTTAA
1 ATAATATAATATTATTTAA
* *
6458158 ATGTTATTTAAATATTATTTAA
1 A--TAATAT-AATATTATTTAA
6458180 ATAATATAAT-TTATTT-A
1 ATAATATAATATTATTTAA
6458197 ATAAATATAATATT-TTTA
1 AT-AATATAATATTATTTA
6458215 TTTAATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.07
18 17 0.37
19 6 0.13
20 4 0.09
21 3 0.07
22 13 0.28
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (19 bp):
ATAATATAATATTATTTAA
Found at i:6458252 original size:20 final size:19
Alignment explanation
Indices: 6458208--6458254 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
6458198 TAAATATAAT
6458208 ATTTTTATTTAATTTTTAA
1 ATTTTTATTTAATTTTTAA
* * *
6458227 AATTTTATTTTATTTATTGA
1 ATTTTTATTTAATTT-TTAA
6458247 ATTTTTAT
1 ATTTTTAT
6458255 ATTTGGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTATTTAATTTTTAA
Found at i:6460372 original size:2 final size:2
Alignment explanation
Indices: 6460367--6460396 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6460357 TTTTTTATTT
6460367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6460397 GACACACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6471909 original size:23 final size:21
Alignment explanation
Indices: 6471867--6471916 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
6471857 CTAATTGAGC
*
6471867 TTTTA-TATTTTAATATAAAT
1 TTTTATTATTTTAATAAAAAT
6471887 TTTTATTATTTTAACTAGAAAAT
1 TTTTATTATTTTAA-TA-AAAAT
*
6471910 TATTATT
1 TTTTATT
6471917 TTACTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 8 0.32
22 2 0.08
23 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATTTTAATAAAAAT
Found at i:6473228 original size:86 final size:86
Alignment explanation
Indices: 6473057--6473215 Score: 221
Period size: 86 Copynumber: 1.8 Consensus size: 86
6473047 TAAAAATAAG
* * *
6473057 AATGTATTTTGTATTAGATTTGTCAATATGAATTTGATACAAATTTTTTATATTTTACATGCATT
1 AATGTATTTTGTATTAGATTTGTCAACACGAATTTAATACAAATTTTTTATATTTTACATGCATT
* *
6473122 ATATATGAGTTAGATAAAATA
66 ATATACGAGTCAGATAAAATA
* * * *
6473143 AATGTATTTTGTTTTCGATTTGTCAACACGAATTTAATACAAATTTTTTATTTTTTATATGCATT
1 AATGTATTTTGTATTAGATTTGTCAACACGAATTTAATACAAATTTTTTATATTTTACATGCATT
6473208 -TGATACGA
66 AT-ATACGA
6473216 TACAGTACAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 1 0.02
86 63 0.98
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (86 bp):
AATGTATTTTGTATTAGATTTGTCAACACGAATTTAATACAAATTTTTTATATTTTACATGCATT
ATATACGAGTCAGATAAAATA
Found at i:6477706 original size:16 final size:14
Alignment explanation
Indices: 6477674--6477716 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
6477664 TCATAAAACA
*
6477674 ATATAATTTGATATG
1 ATATAATTT-ATTTG
6477689 ATATGAATTGTATTTG
1 ATAT-AATT-TATTTG
6477705 ATATAATTTATT
1 ATATAATTTATT
6477717 ATAAAGTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 12 0.48
17 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (14 bp):
ATATAATTTATTTG
Found at i:6478041 original size:15 final size:16
Alignment explanation
Indices: 6478001--6478051 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
6477991 AATAAAATTG
* *
6478001 TATTAAATAAATTTACT
1 TATTAAATAAA-TAAAT
**
6478018 TATTAAATATTTAAAT
1 TATTAAATAAATAAAT
6478034 TATT-AATAAATAAAT
1 TATTAAATAAATAAAT
6478049 TAT
1 TAT
6478052 ATTTAAGTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 12 0.43
16 7 0.25
17 9 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTAAATAAATAAAT
Found at i:6479101 original size:16 final size:17
Alignment explanation
Indices: 6479070--6479102 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6479060 TTGTAATAAA
6479070 ATGATAAATGTTTAATTT
1 ATGATAAA-GTTTAATTT
6479088 ATGATAAA-TTTAATT
1 ATGATAAAGTTTAATT
6479103 AAATTTAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
ATGATAAAGTTTAATTT
Found at i:6479835 original size:142 final size:142
Alignment explanation
Indices: 6479579--6479860 Score: 483
Period size: 142 Copynumber: 2.0 Consensus size: 142
6479569 CTAGTTTATT
* * *
6479579 AGTTTATTATTTAGTTATTGTAACTTGATTATTATGTAATGGTTGATTATATAGATGTAATACTT
1 AGTTTATTATTCAGTGATTGTAACTTGATTATTATGTAATGATTGATTATATAGATGTAATACTT
* * *
6479644 GATTATAATTATATTTAATAATTGATTTTATGCATAATATACTTGATTATAATTCTAATTTTAAA
66 AATTATAATTATATTTAATAATTGATTTTATGCATAATATACTTGATTATAATTATAATTTAAAA
6479709 AAAATAAGAGAA
131 AAAATAAGAGAA
6479721 AGTTTATTATTCAGTGATTGTAACTTGATTATTATGTAATGATTGATTATATAGATGTAATACTT
1 AGTTTATTATTCAGTGATTGTAACTTGATTATTATGTAATGATTGATTATATAGATGTAATACTT
* * *
6479786 AATTATAATTTTATTTAATAGTTGATTTTATGTATAATATACTTGATTATAATTATAATTTAAAA
66 AATTATAATTATATTTAATAATTGATTTTATGCATAATATACTTGATTATAATTATAATTTAAAA
6479851 AAAATAAGAG
131 AAAATAAGAG
6479861 GATTATTTTT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 131 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.46
Consensus pattern (142 bp):
AGTTTATTATTCAGTGATTGTAACTTGATTATTATGTAATGATTGATTATATAGATGTAATACTT
AATTATAATTATATTTAATAATTGATTTTATGCATAATATACTTGATTATAATTATAATTTAAAA
AAAATAAGAGAA
Found at i:6480039 original size:25 final size:26
Alignment explanation
Indices: 6479998--6480054 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
6479988 AACCAATCTA
*
6479998 TTTTTTTTCCTTCTTTTCATTTTTCC
1 TTTTTTTTCCCTCTTTTCATTTTTCC
*
6480024 TTTTTTTTCCCT-TTTTCCTTTTTCC
1 TTTTTTTTCCCTCTTTTCATTTTTCC
6480049 TTTTTT
1 TTTTTT
6480055 GCTTTTCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTTTTCCCTCTTTTCATTTTTCC
Found at i:6480045 original size:15 final size:15
Alignment explanation
Indices: 6480027--6480064 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6480017 TTTTTCCTTT
6480027 TTTTTCCCTTTTTCC
1 TTTTTCCCTTTTTCC
* *
6480042 TTTTTCCTTTTTTGC
1 TTTTTCCCTTTTTCC
6480057 -TTTTCCCT
1 TTTTTCCCT
6480065 CCTTTTCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTTCCCTTTTTCC
Found at i:6480054 original size:8 final size:8
Alignment explanation
Indices: 6480000--6480060 Score: 54
Period size: 8 Copynumber: 7.5 Consensus size: 8
6479990 CCAATCTATT
6480000 TTTTTTCC
1 TTTTTTCC
6480008 TTCTTTT-C
1 TT-TTTTCC
*
6480016 ATTTTTCC
1 TTTTTTCC
6480024 TTTTTTTTCC
1 --TTTTTTCC
*
6480034 CTTTTTCC
1 TTTTTTCC
6480042 -TTTTTCC
1 TTTTTTCC
*
6480049 TTTTTTGC
1 TTTTTTCC
6480057 TTTT
1 TTTT
6480061 CCCTCCTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
7 11 0.25
8 22 0.50
9 4 0.09
10 7 0.16
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.74
Consensus pattern (8 bp):
TTTTTTCC
Found at i:6480054 original size:16 final size:17
Alignment explanation
Indices: 6480001--6480046 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
6479991 CAATCTATTT
*
6480001 TTTTTCCTTCTTTT-CA
1 TTTTTCCTTTTTTTCCA
*
6480017 TTTTTCCTTTTTTTTCCC
1 TTTTTCC-TTTTTTTCCA
6480035 TTTTTCCTTTTT
1 TTTTTCCTTTTT
6480047 CCTTTTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 11 0.42
18 8 0.31
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTCCTTTTTTTCCA
Found at i:6480071 original size:31 final size:27
Alignment explanation
Indices: 6479998--6480114 Score: 78
Period size: 31 Copynumber: 4.1 Consensus size: 27
6479988 AACCAATCTA
* * *
6479998 TTTT-TTTTCCTTCTTTTCATTTTTC-C
1 TTTTCTTTTCCCT-TTTTCCTTTTTCTT
6480024 TTTT-TTTTCCCTTTTTCCTTTTTCCTT
1 TTTTCTTTTCCCTTTTTCCTTTTT-CTT
* *
6480051 TTTTGCTTTTCCCTCCTTTTCTTTCTTTATT
1 TTTT-CTTTTCCCT--TTTTCCTT-TTTCTT
6480082 TTTTCTTATTCCCTTTTTTTCTCTTTTTCTT
1 TTTTCTT-TTCCC--TTTTTC-CTTTTTCTT
6480113 TT
1 TT
6480115 ACTTTCTTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
25 10 0.14
26 12 0.16
27 4 0.05
29 8 0.11
30 3 0.04
31 30 0.41
32 5 0.07
33 1 0.01
ACGTcount: A:0.03, C:0.24, G:0.01, T:0.73
Consensus pattern (27 bp):
TTTTCTTTTCCCTTTTTCCTTTTTCTT
Found at i:6481039 original size:29 final size:29
Alignment explanation
Indices: 6480968--6481044 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
6480958 ATTTTCATAC
* *
6480968 AAATAAGCCGTTAATATATTATTTGTATTT
1 AAATAAGCC-TTAATATATTATTTATATCT
*
6480998 AAATAAACTCTTAATAT-TTATTTATATCT
1 AAATAAGC-CTTAATATATTATTTATATCT
6481027 AAATAAGTCCTTAATATA
1 AAATAAG-CCTTAATATA
6481045 AATTAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 24 0.60
30 15 0.38
31 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (29 bp):
AAATAAGCCTTAATATATTATTTATATCT
Found at i:6481074 original size:17 final size:16
Alignment explanation
Indices: 6481043--6481083 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
6481033 GTCCTTAATA
*
6481043 TAAATTAATATTTTATT
1 TAAA-TAATAATTTATT
6481060 TGAAATAATAATTTATT
1 T-AAATAATAATTTATT
6481077 TAAATAA
1 TAAATAA
6481084 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 13 0.59
18 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TAAATAATAATTTATT
Found at i:6481146 original size:28 final size:27
Alignment explanation
Indices: 6481080--6481147 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
6481070 ATTTATTTAA
*
6481080 ATAAAAATAAAAAAATAAATACTTATT
1 ATAAAAATAAAAAAATAAACACTTATT
* * *
6481107 AGATATAATAAAAATATAAACACTTATT
1 ATA-AAAATAAAAAAATAAACACTTATT
*
6481135 TTAAAAAGTAAAA
1 ATAAAAA-TAAAA
6481148 TAATTCGACA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.29
Consensus pattern (27 bp):
ATAAAAATAAAAAAATAAACACTTATT
Found at i:6489562 original size:56 final size:57
Alignment explanation
Indices: 6489493--6489611 Score: 150
Period size: 57 Copynumber: 2.1 Consensus size: 57
6489483 AAAATCATAC
* * * *
6489493 TAATTTGTCATTTATAAGATGGG-TATTTATCATTTAAGACATAATGGGCATTAAAG
1 TAATTTGACATTTATAAAAGGGGTTATTTATCATTTAAGAAATAATGGGCATTAAAG
* * * * *
6489549 TGATTTGACATTTATAAAAGGGGTTTTTTGTCATTTAAGAAATGATGGGCATTATAG
1 TAATTTGACATTTATAAAAGGGGTTATTTATCATTTAAGAAATAATGGGCATTAAAG
6489606 TAATTT
1 TAATTT
6489612 ATTATTTAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
56 19 0.37
57 33 0.63
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (57 bp):
TAATTTGACATTTATAAAAGGGGTTATTTATCATTTAAGAAATAATGGGCATTAAAG
Found at i:6489870 original size:60 final size:61
Alignment explanation
Indices: 6489827--6489967 Score: 162
Period size: 61 Copynumber: 2.3 Consensus size: 61
6489817 TTTTGGTAAG
6489827 AAGACATTTTCATAATTAT-GATAAAAG-GATATTATAGTAATTTTAATCAATCATGATAGT
1 AAGACATTTTCATAATTATAG-TAAAAGAGATATTATAGTAATTTTAATCAATCATGATAGT
* ** ** * *
6489887 GAGACATTTTCATAATTATAGTAGGAGAGATATTATAGTAATTTTAGCCAATTATAGGAT-GA
1 AAGACATTTTCATAATTATAGTAAAAGAGATATTATAGTAATTTTAATCAATCAT--GATAGT
*
6489949 AAGGCATTTTCATAATTAT
1 AAGACATTTTCATAATTAT
6489968 GATATAAAGG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
60 22 0.32
61 25 0.37
62 18 0.26
63 3 0.04
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (61 bp):
AAGACATTTTCATAATTATAGTAAAAGAGATATTATAGTAATTTTAATCAATCATGATAGT
Found at i:6489990 original size:61 final size:59
Alignment explanation
Indices: 6489827--6489990 Score: 161
Period size: 61 Copynumber: 2.7 Consensus size: 59
6489817 TTTTGGTAAG
* *
6489827 AAGACATTTTCATAATTATGATAAAAGGATATTATAGTAATTTTAATCAATCATGATAGT
1 AAGACATTTTCATAATTATGATAAAAGG-TATTATAGTAATTTTAACCAATCATGATAGA
* * * * *
6489887 GAGACATTTTCATAATTAT-AGTAGGAGAGATATTATAGTAATTTTAGCCAATTATAGGAT-GA
1 AAGACATTTTCATAATTATGA-TA--AAAGGTATTATAGTAATTTTAACCAATCAT--GATAGA
* * *
6489949 AAGGCATTTTCATAATTATGATATAAAGGTATCATAATAATT
1 AAGACATTTTCATAATTATGATA-AAAGGTATTATAGTAATT
6489991 CGTCATTTAT
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
59 1 0.01
60 20 0.24
61 36 0.43
62 23 0.27
63 4 0.05
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (59 bp):
AAGACATTTTCATAATTATGATAAAAGGTATTATAGTAATTTTAACCAATCATGATAGA
Found at i:6499846 original size:3 final size:3
Alignment explanation
Indices: 6499838--6499885 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
6499828 ACCAATGAAT
6499838 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6499886 ATTTTGTCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6500077 original size:17 final size:17
Alignment explanation
Indices: 6500037--6500077 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6500027 ATTAAAATGT
*
6500037 TAAAAATATATAATAAA
1 TAAAAATATAAAATAAA
* *
6500054 TATAAATATAAAATACA
1 TAAAAATATAAAATAAA
6500071 TAAAAAT
1 TAAAAAT
6500078 CAAAATTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAATATAAAATAAA
Found at i:6500679 original size:2 final size:2
Alignment explanation
Indices: 6500672--6500702 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6500662 CACATTATCA
6500672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6500703 ACAACAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6505835 original size:17 final size:18
Alignment explanation
Indices: 6505813--6505846 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6505803 AACCTTATGC
6505813 AAAGAAAAAA-AAAAAGG
1 AAAGAAAAAAGAAAAAGG
6505830 AAAGAAAAAAGAAAAAG
1 AAAGAAAAAAGAAAAAG
6505847 TGAAGAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAAGG
Found at i:6507428 original size:14 final size:13
Alignment explanation
Indices: 6507403--6507439 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
6507393 TGCATATGCA
6507403 TTTCTTTGTTTTTT
1 TTTCTTT-TTTTTT
6507417 TTTCTGTTTTTTTT
1 TTTCT-TTTTTTTT
6507431 TTTCTTTTT
1 TTTCTTTTT
6507440 ACTTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 16 0.73
15 2 0.09
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.86
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:6511945 original size:191 final size:192
Alignment explanation
Indices: 6511439--6512019 Score: 943
Period size: 191 Copynumber: 3.0 Consensus size: 192
6511429 AACTTTAGCT
** * *
6511439 TTTGTTTATTCCAACATGAAACTGATTACTATTGTTTTCTTTTTTTGCTAAAATTTGAAAAACAC
1 TTTGTTTATTCCAACACAAAACTTATTACTATGGTTTTCTTTTTTTGCTAAAATTTGAAAAACAC
6511504 TTTATGATCTGGTCTGTTCTGTCTGAAATGAGGATATAAAGGTTTAAATAGTATACTTTTTGTTA
66 TTTATGATCTGGTCTGTTCTGTCTGAAATGAGGATATAAAGGTTTAAATAGTATACTTTTTGTTA
* *
6511569 TACAGGCTCATGGACCTGCTGACCCTTCGTTTTATTTTTATTCAAATGAGTCATCATTGACTA
131 TACAGGCTCATGGACCTGCTGAACCATCGTTTTATTTTTATTC-AATGAGTCATCATTGACTA
* *
6511632 TTTGTTTATTCCAACACATAACTTATTACTATGGGTTTT-TTTTTATTGCTGAAATTTGAAAAAC
1 TTTGTTTATTCCAACACAAAACTTATTACTAT-GGTTTTCTTTTT-TTGCTAAAATTTGAAAAAC
*
6511696 ACTTTATGATCTGGTCCT-TTCTGTCTGAAATGAGGATATAAAGGTCTAAATAGTATACTTTTTG
64 ACTTTATGATCTGGT-CTGTTCTGTCTGAAATGAGGATATAAAGGTTTAAATAGTATACTTTTTG
* * * *
6511760 TTCTACAGGCTTATGGACCTACTGAACCATCATTTTATTTTTATTCAATGAGTCATCATTGACTA
128 TTATACAGGCTCATGGACCTGCTGAACCATCGTTTTATTTTTATTCAATGAGTCATCATTGACTA
*
6511825 TTTGTTTATACCAACACAAAACTTATTACTATGGTTTTCTTTTTTTGCTAAAATTTG-AAAACAC
1 TTTGTTTATTCCAACACAAAACTTATTACTATGGTTTTCTTTTTTTGCTAAAATTTGAAAAACAC
*
6511889 TTTATGATCTGGTCTGTTCTGTCTGAAATGAGGATATAAAGGTTTAAATTGTATACTTTTTGTTA
66 TTTATGATCTGGTCTGTTCTGTCTGAAATGAGGATATAAAGGTTTAAATAGTATACTTTTTGTTA
* * *
6511954 TACATGCTCATGGACCTGCTGAGCCATCGTTTTATTTTTATTCAACGAGTCATCATTGACTA
131 TACAGGCTCATGGACCTGCTGAACCATCGTTTTATTTTTATTCAATGAGTCATCATTGACTA
6512016 TTTG
1 TTTG
6512020 CTTGTTGGTA
Statistics
Matches: 358, Mismatches: 25, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
190 2 0.01
191 126 0.35
192 18 0.05
193 87 0.24
194 123 0.34
195 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (192 bp):
TTTGTTTATTCCAACACAAAACTTATTACTATGGTTTTCTTTTTTTGCTAAAATTTGAAAAACAC
TTTATGATCTGGTCTGTTCTGTCTGAAATGAGGATATAAAGGTTTAAATAGTATACTTTTTGTTA
TACAGGCTCATGGACCTGCTGAACCATCGTTTTATTTTTATTCAATGAGTCATCATTGACTA
Found at i:6515328 original size:3 final size:3
Alignment explanation
Indices: 6515298--6515411 Score: 99
Period size: 3 Copynumber: 39.0 Consensus size: 3
6515288 ATCGGTGTAG
* * * * * *
6515298 ATT ATT -TT ACT ATT ATT TTT ATT TTT ATT ATT AAT AAT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
6515345 ATT GTT -TT GTT GTT ACT ATT ACT AGT ATT A-T ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6515391 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
6515412 CTTGATCTGA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
2 6 0.06
3 87 0.94
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:6516251 original size:14 final size:14
Alignment explanation
Indices: 6516197--6516299 Score: 53
Period size: 12 Copynumber: 7.6 Consensus size: 14
6516187 TTTTTTTTTC
6516197 ATTTTAT-TTTTAT
1 ATTTTATATTTTAT
* *
6516210 TTTTTGA-ATTTATTT
1 ATTTT-ATATTT-TAT
6516225 ATTTATATCATTTTAT
1 ATTT-TAT-ATTTTAT
6516241 ATTTTATATTTTA-
1 ATTTTATATTTTAT
*
6516254 AGTTT-TATTTT-T
1 ATTTTATATTTTAT
*
6516266 ATTTTA-AGTTTTTT
1 ATTTTATA-TTTTAT
6516280 ATTATT-TA-TTTA-
1 ATT-TTATATTTTAT
6516292 ATTTTATA
1 ATTTTATA
6516300 GATTTTTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 27
0.67 0.07 0.26
Matches are distributed among these distances:
11 2 0.03
12 16 0.23
13 15 0.21
14 14 0.20
15 12 0.17
16 7 0.10
17 4 0.06
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (14 bp):
ATTTTATATTTTAT
Found at i:6516271 original size:18 final size:18
Alignment explanation
Indices: 6516240--6516286 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
6516230 TATCATTTTA
6516240 TATTTTATATTTTAAGTTT
1 TATTTT-TATTTTAAGTTT
6516259 TATTTTTATTTTAAGTTT
1 TATTTTTATTTTAAGTTT
*
6516277 T-TTATTATTT
1 TATTTTTATTT
6516287 ATTTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.30
18 13 0.48
19 6 0.22
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (18 bp):
TATTTTTATTTTAAGTTT
Found at i:6516291 original size:20 final size:19
Alignment explanation
Indices: 6516234--6516296 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
6516224 TATTTATATC
*
6516234 ATTTTATATTTTATATTTTA
1 ATTTTTTATTTT-TATTTTA
*
6516254 A-GTTTTATTTTTATTTTA
1 ATTTTTTATTTTTATTTTA
6516272 AGTTTTTTATTATTTA-TTTA
1 A-TTTTTTATT-TTTATTTTA
6516292 ATTTT
1 ATTTT
6516297 ATAGATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.22
19 12 0.32
20 13 0.35
21 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
ATTTTTTATTTTTATTTTA
Found at i:6542310 original size:26 final size:26
Alignment explanation
Indices: 6542274--6542328 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
6542264 TAAAAAACAA
6542274 AGTTGGTGCTAAAAAGAATTCTCTTG
1 AGTTGGTGCTAAAAAGAATTCTCTTG
6542300 AGTTGGTGCTAAAAAGAATTCTCTTG
1 AGTTGGTGCTAAAAAGAATTCTCTTG
6542326 AGT
1 AGT
6542329 CAACATGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.35
Consensus pattern (26 bp):
AGTTGGTGCTAAAAAGAATTCTCTTG
Found at i:6543932 original size:3 final size:3
Alignment explanation
Indices: 6543914--6544039 Score: 148
Period size: 3 Copynumber: 42.3 Consensus size: 3
6543904 ATTGGTGTCG
* **
6543914 ATT ATT -TT ACT ATT ATT ATT ATT ATT -TT ATT AGA ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * *
6543960 ATT ATTT ATT ATT ATT GCT ATT ATT GTT ATT GTT ACT AGT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6544006 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6544040 CTACTACTAC
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
2 4 0.04
3 96 0.93
4 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:6544044 original size:3 final size:3
Alignment explanation
Indices: 6544038--6544075 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6544028 TTATTATTAT
6544038 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
6544076 TTCTTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:6544874 original size:6 final size:6
Alignment explanation
Indices: 6544865--6544971 Score: 58
Period size: 6 Copynumber: 16.7 Consensus size: 6
6544855 AGGTTTTCTT
6544865 TTTTTA -TTTTA TTTTTA TTGTTTGA -TTTTA TTTTTTA TCATTTTA TATTTTA
1 TTTTTA TTTTTA TTTTTA TT-TTT-A TTTTTA -TTTTTA T--TTTTA T-TTTTA
** * * *
6544917 TATTTTA AGTTTA TTTATA TTTATA TTTTAA GTTTTTTA TTATTTA -TTTTA
1 T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA --TTTTTA TT-TTTA TTTTTA
6544968 TTTT
1 TTTT
6544972 AATTGAGTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
5 10 0.12
6 34 0.41
7 26 0.32
8 12 0.15
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:6544910 original size:8 final size:7
Alignment explanation
Indices: 6544864--6544968 Score: 60
Period size: 7 Copynumber: 14.9 Consensus size: 7
6544854 TAGGTTTTCT
*
6544864 TTTTTTA
1 TTTTATA
6544871 TTTTAT-
1 TTTTATA
6544877 TTTTAT-
1 TTTTATA
*
6544883 TGTTT-GA
1 T-TTTATA
*
6544890 TTTTATT
1 TTTTATA
6544897 TTTTATCA
1 TTTTAT-A
6544905 TTTTATA
1 TTTTATA
6544912 TTTTATA
1 TTTTATA
6544919 TTTTA-A
1 TTTTATA
*
6544925 GTTTATTTA
1 -TTT-TATA
6544934 TATTTATA
1 T-TTTATA
6544942 TTTTA-A
1 TTTTATA
*
6544948 GTTTTTTA
1 -TTTTATA
6544956 TTATT-TA
1 TT-TTATA
6544963 TTTTAT
1 TTTTAT
6544969 TTTAATTGAG
Statistics
Matches: 78, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
6 14 0.18
7 46 0.59
8 15 0.19
9 3 0.04
ACGTcount: A:0.23, C:0.01, G:0.04, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:6544939 original size:23 final size:22
Alignment explanation
Indices: 6544905--6544963 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 22
6544895 TTTTTTATCA
6544905 TTTTATATTTTATATTTTAAGTT
1 TTTTATA-TTTATATTTTAAGTT
6544928 TATTTATATTTATATTTTAAGTT
1 T-TTTATATTTATATTTTAAGTT
6544951 TTTTATTATTTAT
1 TTTTA-TATTTAT
6544964 TTTATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.12
23 24 0.71
24 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTTATATTTATATTTTAAGTT
Found at i:6545980 original size:19 final size:21
Alignment explanation
Indices: 6545956--6546000 Score: 76
Period size: 19 Copynumber: 2.2 Consensus size: 21
6545946 CCAAAAATTA
6545956 ATAAAATATTATTTT-T-AAT
1 ATAAAATATTATTTTATAAAT
6545975 ATAAAATATTATTTTATAAAT
1 ATAAAATATTATTTTATAAAT
6545996 ATAAA
1 ATAAA
6546001 TATAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.62
20 1 0.04
21 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAATATTATTTTATAAAT
Found at i:6551552 original size:185 final size:185
Alignment explanation
Indices: 6551240--6551609 Score: 695
Period size: 185 Copynumber: 2.0 Consensus size: 185
6551230 TTTGAGGTTG
*
6551240 TTAACAACTGTTTGGAAACCTATTTTATATGTATGAACGAGGAAAAGCCTAAATAGTGGGCAAAA
1 TTAACAACTGTTTGGAAACCTATTTTAGATGTATGAACGAGGAAAAGCCTAAATAGTGGGCAAAA
*
6551305 GAGATACCATAGGCTAAGTGGTGCTATAACACTAGTTACCACATGTCCATACAAACCACCCCATA
66 GAGATACCATAGGCTAAGTAGTGCTATAACACTAGTTACCACATGTCCATACAAACCACCCCATA
6551370 TGAGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGGAGAT
131 TGAGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGGAGAT
6551425 TTAACAACTGTTTGGAAACCTATTTTAGATGTATGAACGAGGAAAAGCCTAAATAGTGGGCAAAA
1 TTAACAACTGTTTGGAAACCTATTTTAGATGTATGAACGAGGAAAAGCCTAAATAGTGGGCAAAA
* *
6551490 GAGATACCATAGGCTAAGTAGTGGTATATCACTAGTTACCACATGTCCATACAAACCACCCCATA
66 GAGATACCATAGGCTAAGTAGTGCTATAACACTAGTTACCACATGTCCATACAAACCACCCCATA
*
6551555 TGAGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGTAGAT
131 TGAGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGGAGAT
6551610 AGTCTATGGT
Statistics
Matches: 180, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 180 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (185 bp):
TTAACAACTGTTTGGAAACCTATTTTAGATGTATGAACGAGGAAAAGCCTAAATAGTGGGCAAAA
GAGATACCATAGGCTAAGTAGTGCTATAACACTAGTTACCACATGTCCATACAAACCACCCCATA
TGAGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGGAGAT
Found at i:6551629 original size:49 final size:49
Alignment explanation
Indices: 6551557--6551701 Score: 272
Period size: 49 Copynumber: 3.0 Consensus size: 49
6551547 ACCCCATATG
6551557 AGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGT
1 AGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGT
6551606 AGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGT
1 AGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGT
* *
6551655 AGATAGTCTATGGTTGGTCAGCCTTAACTCATATGCCTTACCTACCT
1 AGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCT
6551702 ATGCCTTACC
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 94 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (49 bp):
AGATAGTCTATGGTTAGCCAGCCTTAACTCATATGCCTTACCTACCTGT
Found at i:6551640 original size:23 final size:23
Alignment explanation
Indices: 6551565--6551640 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
6551555 TGAGATAGTC
6551565 TATGGTTAGCCAGCCTTAACTCA
1 TATGGTTAGCCAGCCTTAACTCA
* *
6551588 TATGCCTTA-CCTA-CCTGTAGATAGTC-
1 TATG-GTTAGCC-AGCCT-T--A-ACTCA
6551614 TATGGTTAGCCAGCCTTAACTCA
1 TATGGTTAGCCAGCCTTAACTCA
6551637 TATG
1 TATG
6551641 CCTTACCTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 3 0.08
23 14 0.35
24 5 0.12
25 5 0.12
26 10 0.25
27 3 0.08
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (23 bp):
TATGGTTAGCCAGCCTTAACTCA
Found at i:6551706 original size:15 final size:15
Alignment explanation
Indices: 6551686--6551716 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6551676 CCTTAACTCA
6551686 TATGCCTTACCTACC
1 TATGCCTTACCTACC
6551701 TATGCCTTACCTACC
1 TATGCCTTACCTACC
6551716 T
1 T
6551717 GGAGATAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.39, G:0.06, T:0.35
Consensus pattern (15 bp):
TATGCCTTACCTACC
Found at i:6551741 original size:64 final size:64
Alignment explanation
Indices: 6551637--6551762 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 64
6551627 CCTTAACTCA
* * ***
6551637 TATGCCTTACCTACCTGTAGATAGTCTATGGTTGGTCAGCCTTAACTCATATGCCTTACCTACC
1 TATGCCTTACCTACCTGGAGATAGACTATGGTTAACCAGCCTTAACTCATATGCCTTACCTACC
*
6551701 TATGCCTTACCTACCTGGAGATAGACTATGGTTAACCAGCCTTAACTCGTATGCCTTACCTA
1 TATGCCTTACCTACCTGGAGATAGACTATGGTTAACCAGCCTTAACTCATATGCCTTACCTA
6551763 TCTGGAGATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (64 bp):
TATGCCTTACCTACCTGGAGATAGACTATGGTTAACCAGCCTTAACTCATATGCCTTACCTACC
Found at i:6554776 original size:17 final size:16
Alignment explanation
Indices: 6554745--6554778 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6554735 CCTATTTAAT
*
6554745 ATAAAATTATTTTATA
1 ATAAAAATATTTTATA
6554761 ATAAAAATATTATTATA
1 ATAAAAATATT-TTATA
6554778 A
1 A
6554779 ATAATAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAAATATTTTATA
Found at i:6557290 original size:91 final size:91
Alignment explanation
Indices: 6557128--6557301 Score: 224
Period size: 91 Copynumber: 1.9 Consensus size: 91
6557118 CTAAGGAAAG
* * * * * * *
6557128 AAAGACCACAAATTCTAAGATTAAGAAAACATGAGTCATAATGTCATGTTTAAAATATGGAAAAA
1 AAAGACCACAAATGCTAAGATTAAAAAAACATGAATCACAATGGCATGCTCAAAATATGGAAAAA
*
6557193 AAGGTCATAATAAAAGGTCTTGTAAT
66 AAGGTCACAATAAAAGGTCTTGTAAT
* * *
6557219 AAAGACCACAAATGCTAAGGTTAAAAAAACATGAATCACAATGGCATGCTCAAAATGT-GAACAG
1 AAAGACCACAAATGCTAAGATTAAAAAAACATGAATCACAATGGCATGCTCAAAATATGGAA-AA
*
6557283 AAGGGTCACAATAAAAGGT
65 AAAGGTCACAATAAAAGGT
6557302 TTTGCAAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
90 3 0.04
91 67 0.96
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (91 bp):
AAAGACCACAAATGCTAAGATTAAAAAAACATGAATCACAATGGCATGCTCAAAATATGGAAAAA
AAGGTCACAATAAAAGGTCTTGTAAT
Found at i:6562278 original size:2 final size:2
Alignment explanation
Indices: 6562271--6562297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6562261 TGCTAAAATC
6562271 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
6562298 TAAAAAACAC
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:6563646 original size:27 final size:29
Alignment explanation
Indices: 6563616--6563671 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
6563606 GGTAAAAAAA
*
6563616 TATT-TTTTTAATTTT-TTAATAATATTT
1 TATTATTTTAAATTTTATTAATAATATTT
*
6563643 TATTATTTTAAATTTTATTATTAATATTT
1 TATTATTTTAAATTTTATTAATAATATTT
6563672 ATGCATGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.16
28 10 0.40
29 11 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTATTTTAAATTTTATTAATAATATTT
Found at i:6563660 original size:12 final size:14
Alignment explanation
Indices: 6563626--6563671 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
6563616 TATTTTTTTA
*
6563626 ATTTT-TTAATAAT
1 ATTTTATTATTAAT
6563639 ATTTTATTATTTTAA-
1 ATTTTATTA--TTAAT
6563654 ATTTTATTATTAAT
1 ATTTTATTATTAAT
6563668 ATTT
1 ATTT
6563672 ATGCATGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 9 0.32
14 7 0.25
15 9 0.32
16 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTATTATTAAT
Found at i:6563682 original size:29 final size:28
Alignment explanation
Indices: 6563625--6563683 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
6563615 ATATTTTTTT
* *
6563625 AATTTTTTAATAATATTTTATTATTTTA
1 AATTTTTTAATAATATTTTATCATGTTA
*
6563653 AATTTTATTATTAATA-TTTATGCATGTTA
1 AATTTT-TTAATAATATTTTAT-CATGTTA
6563682 AA
1 AA
6563684 ATGATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
AATTTTTTAATAATATTTTATCATGTTA
Found at i:6566691 original size:18 final size:17
Alignment explanation
Indices: 6566646--6566746 Score: 84
Period size: 18 Copynumber: 5.9 Consensus size: 17
6566636 ATTACTTATC
*
6566646 AAAAT-AAATAAATAAT
1 AAAATAAAATAAAAAAT
* *
6566662 GAAAT-CAATAAAAAAT
1 AAAATAAAATAAAAAAT
*
6566678 AAATATAAAAT-AAATAT
1 AAA-ATAAAATAAAAAAT
* *
6566695 AAAAT-AGATATAAAAAG
1 AAAATAAAATA-AAAAAT
6566712 AAAATAAAATCAAAAAAT
1 AAAATAAAAT-AAAAAAT
6566730 AAAATAAAATAGAAAAA
1 AAAATAAAATA-AAAAA
6566747 AGAAAACCTG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
15 3 0.04
16 17 0.25
17 20 0.30
18 26 0.39
19 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAATAAAATAAAAAAT
Found at i:6566718 original size:22 final size:22
Alignment explanation
Indices: 6566646--6566738 Score: 75
Period size: 22 Copynumber: 4.1 Consensus size: 22
6566636 ATTACTTATC
*
6566646 AAAAT-AAATAAATAATGAAATCA
1 AAAATAAAATAAAT-ATAAAAT-A
*
6566669 ATAA-AAAATAAATATAAAATA
1 AAAATAAAATAAATATAAAATA
* *
6566690 AATATAAAATAGATATAAAA-A
1 AAAATAAAATAAATATAAAATA
*
6566711 GAAAATAAAATCAAAAAATAAAATA
1 -AAAATAAAAT--AAATATAAAATA
6566736 AAA
1 AAA
6566739 TAGAAAAAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
21 4 0.07
22 29 0.52
23 11 0.20
24 11 0.20
25 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.20
Consensus pattern (22 bp):
AAAATAAAATAAATATAAAATA
Found at i:6566726 original size:6 final size:5
Alignment explanation
Indices: 6566673--6566740 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
6566663 AAATCAATAA
* *
6566673 AAAAT AAATAT AAAAT AAATAT AAAAT AGATAT AAAAAG AAAAT AAAAT
1 AAAAT AAA-AT AAAAT AAA-AT AAAAT A-AAAT -AAAAT AAAAT AAAAT
*
6566722 -CAA- AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT A
6566741 GAAAAAAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
4 4 0.08
5 31 0.61
6 15 0.29
7 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:6566746 original size:13 final size:11
Alignment explanation
Indices: 6566646--6566738 Score: 66
Period size: 11 Copynumber: 8.3 Consensus size: 11
6566636 ATTACTTATC
6566646 AAAAT-AAATA
1 AAAATAAAATA
*
6566656 AATAATGAAATCA
1 AA-AATAAAAT-A
*
6566669 ATAA-AAAATA
1 AAAATAAAATA
*
6566679 AATATAAAATA
1 AAAATAAAATA
*
6566690 AATATAAAATA
1 AAAATAAAATA
* *
6566701 GATATAAAA-A
1 AAAATAAAATA
6566711 GAAAATAAAATCAA
1 -AAAATAAAAT--A
6566725 AAAATAAAATA
1 AAAATAAAATA
6566736 AAA
1 AAA
6566739 TAGAAAAAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
10 6 0.09
11 43 0.63
12 6 0.09
13 12 0.18
14 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:6567579 original size:3 final size:3
Alignment explanation
Indices: 6567555--6567621 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
6567545 CAAAATAAAA
* * * * * * *
6567555 AAT AAG AAT AAG AAT GAT AAT AAT AAT AAT GAT GAT GAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
6567603 AAT AAT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT A
6567622 GTAGTAGTAG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:6567622 original size:6 final size:6
Alignment explanation
Indices: 6567599--6567715 Score: 73
Period size: 6 Copynumber: 19.8 Consensus size: 6
6567589 ATGATGATAA
* * * * * *
6567599 TAATAA TAATAA TAATAG TAATAG TAGTAG TAGTAG TAGTAG TAGTAG
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG
* * * * *
6567647 TAGTAG TAGTAG TAGTAG TAGTAG TAGTAG TAATA- -ACATAG TATAATA-
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TA-ATAG --TAATAG
6567695 TAATA- TAATA- TAATAG TAATA
1 TAATAG TAATAG TAATAG TAATA
6567716 AACTAATAAT
Statistics
Matches: 102, Mismatches: 3, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
4 1 0.01
5 18 0.18
6 79 0.77
8 3 0.03
9 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.19, T:0.34
Consensus pattern (6 bp):
TAATAG
Found at i:6567626 original size:3 final size:3
Alignment explanation
Indices: 6567614--6567678 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
6567604 ATAATAATAA
*
6567614 TAG TAA TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
6567662 TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TA
6567679 ATAACATAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:6579770 original size:16 final size:16
Alignment explanation
Indices: 6579740--6579785 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
6579730 ATAAATTACT
6579740 TAATGAAAATAAATAAA
1 TAATG-AAATAAATAAA
*
6579757 TAATGAAATCAATAAA
1 TAATGAAATAAATAAA
*
6579773 AAATGAAAATAAA
1 TAATG-AAATAAA
6579786 ATATATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (16 bp):
TAATGAAATAAATAAA
Found at i:6579815 original size:40 final size:38
Alignment explanation
Indices: 6579745--6579826 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 38
6579735 TTACTTAATG
*
6579745 AAAATAAATAAATAATGAAATCAAT-AAAAAATGAAAAT
1 AAAATAAATAAATAATCAAATCAATAAAAAAAT-AAAAT
*
6579783 AAAATATATATAAA-AATCAAATCAAATCAAAAAATAAAAT
1 AAAATA-A-ATAAATAATCAAATC-AATAAAAAAATAAAAT
6579823 AAAA
1 AAAA
6579827 AAAAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
38 6 0.15
39 9 0.23
40 17 0.44
41 7 0.18
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (38 bp):
AAAATAAATAAATAATCAAATCAATAAAAAAATAAAAT
Found at i:6579822 original size:13 final size:12
Alignment explanation
Indices: 6579767--6579838 Score: 51
Period size: 13 Copynumber: 5.8 Consensus size: 12
6579757 TAATGAAATC
6579767 AATAAAAAATGAA
1 AATAAAAAAT-AA
6579780 AATAAAATATATATA
1 AATAAAA-A-ATA-A
* *
6579795 AA-AATCAAATCA
1 AATAA-AAAATAA
6579807 AATCAAAAAATAA
1 AAT-AAAAAATAA
6579820 AATAAAAAA-AA
1 AATAAAAAATAA
6579831 AA-AAAAAA
1 AATAAAAAA
6579839 CCTATGATGG
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
12 9 0.18
13 17 0.35
14 7 0.14
15 6 0.12
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.17
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:6580621 original size:3 final size:3
Alignment explanation
Indices: 6580615--6580764 Score: 111
Period size: 3 Copynumber: 52.3 Consensus size: 3
6580605 TAAAAATTAA
* * * *
6580615 AAT AAT AAT AGT AAT AAT GAT AAT AAT TAT AAT AA- ATAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* *
6580660 AAT AAC AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAG AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * *
6580707 AGC AAT AA- CAT AGT -AT ACT -AT AA- ATAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
*
6580747 AGT AAT AA- AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
6580765 TGTTATACTA
Statistics
Matches: 112, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
2 13 0.12
3 97 0.87
4 2 0.02
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6585234 original size:43 final size:43
Alignment explanation
Indices: 6585132--6585234 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 43
6585122 AGTATTTAGA
6585132 GGTGATATCCGAG-TATTAAAGTATGGAATTACATTTTCTCGGT
1 GGTGATAT-CGAGATATTAAAGTATGGAATTACATTTTCTCGGT
* ** *
6585175 GGTGATATTTGA-ATATTAAAGTAT-GAATTTTATTTTCTTGGT
1 GGTGATA-TCGAGATATTAAAGTATGGAATTACATTTTCTCGGT
6585217 GGTGATATCGAAGATATT
1 GGTGATATCG-AGATATT
6585235 TTCAAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
41 2 0.04
42 23 0.45
43 25 0.49
44 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (43 bp):
GGTGATATCGAGATATTAAAGTATGGAATTACATTTTCTCGGT
Found at i:6585339 original size:137 final size:137
Alignment explanation
Indices: 6585163--6585444 Score: 377
Period size: 137 Copynumber: 2.1 Consensus size: 137
6585153 TATGGAATTA
* * ** * * *
6585163 CATTTTCTCGGTGGTGATATTTGAATATTAAAGTATGAATTTTATTTTCTTGGTGGTGATATCGA
1 CATTTTTTCGATGGTGATATCCGAATATTAAAGTATGAATTTCATTTTCTTAGTGGTGATATCCA
* * * * *
6585228 AGATATTTTCAAAATTACTCGATGGTAATAT-TCAAGTTTAGAGTTTGAATTTGTATTCTTTCTC
66 AAACATTTTCAAAATCACTCGATGGTAATATCT-AAGTTTAAAGTTTGAATTTGCATTCTTTCTC
6585292 TACATTTG
130 TACATTTG
*
6585300 CATTTTTTCGATGGTGATATCCGAGTATTAAAGTATGAATTTCATTTTCTTAGTGGTGATATCCA
1 CATTTTTTCGATGGTGATATCCGAATATTAAAGTATGAATTTCATTTTCTTAGTGGTGATATCCA
* * * *
6585365 AAACATTTTCAAAATCATTCGGTGGTGATATCTGAGTTTAAAGTTTGAATTTGCATTCTTTCTCT
66 AAACATTTTCAAAATCACTCGATGGTAATATCTAAGTTTAAAGTTTGAATTTGCATTCTTTCTCT
*
6585430 ACATTTT
131 ACATTTG
*
6585437 TATTTTTT
1 CATTTTTT
6585445 TTATGATGAT
Statistics
Matches: 125, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
137 124 0.99
138 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (137 bp):
CATTTTTTCGATGGTGATATCCGAATATTAAAGTATGAATTTCATTTTCTTAGTGGTGATATCCA
AAACATTTTCAAAATCACTCGATGGTAATATCTAAGTTTAAAGTTTGAATTTGCATTCTTTCTCT
ACATTTG
Found at i:6585654 original size:42 final size:42
Alignment explanation
Indices: 6585608--6585695 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
6585598 ATTAAAAGTC
* * *
6585608 ATTGTATCTTCTCGGTATTGATATCCGAGTGTTAAAACTGGA
1 ATTGTATCTTCTCGGCAGTGATATCCAAGTGTTAAAACTGGA
* * * *
6585650 ATTGTATTTTCTCGGCAGTGGTATCCAAGTGTTAAAGCTTGA
1 ATTGTATCTTCTCGGCAGTGATATCCAAGTGTTAAAACTGGA
6585692 ATTG
1 ATTG
6585696 CATTTTCTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (42 bp):
ATTGTATCTTCTCGGCAGTGATATCCAAGTGTTAAAACTGGA
Found at i:6588412 original size:119 final size:119
Alignment explanation
Indices: 6588255--6588497 Score: 353
Period size: 119 Copynumber: 2.0 Consensus size: 119
6588245 AATTTCATTC
* * * *
6588255 TACTTAACATATGATTTAAATTTCAAACCTTCACATTAATATTTTAAATTTTAACTATCGAGATG
1 TACTTAACATATGATTTAAATTTAAAACCTCCAAATTAATATTTTAAATTCTAACTATCGAGATG
* * * * *
6588320 TCTCTTAAAAATAAAAGAGA-AAAATATATGAATTGAATTATTTTATGTGTATAA
66 TCTCCT-AAAATAAAAGAGAGAAAATATATAAATTGAATCATTTTAAGTGCATAA
* * *
6588374 TACTTTACATATGATTTAAATTTAAAACCTCCAAATTAATATTTTAAGTTCTAACTATTGAGATG
1 TACTTAACATATGATTTAAATTTAAAACCTCCAAATTAATATTTTAAATTCTAACTATCGAGATG
6588439 TCTCCTAAAATAAAAGAGAGGAAAATATATAAATTGAATCATTTTAAGTGCATAA
66 TCTCCTAAAATAAAAGAGA-GAAAATATATAAATTGAATCATTTTAAGTGCATAA
6588494 TACT
1 TACT
6588498 ATATGTTGAG
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
118 13 0.12
119 63 0.57
120 34 0.31
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (119 bp):
TACTTAACATATGATTTAAATTTAAAACCTCCAAATTAATATTTTAAATTCTAACTATCGAGATG
TCTCCTAAAATAAAAGAGAGAAAATATATAAATTGAATCATTTTAAGTGCATAA
Found at i:6590161 original size:2 final size:2
Alignment explanation
Indices: 6590154--6590182 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6590144 TACTAAAATC
6590154 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
6590183 TAAAAAAGAC
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:6590614 original size:5 final size:5
Alignment explanation
Indices: 6590606--6590647 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
6590596 ACTTATTTAA
6590606 TTTTC TTTTC TTTT- TTTTC TTTTTC TTTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC TTTTC TTTTC T
6590648 GATCTACTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
5 20 0.57
6 11 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:6591553 original size:21 final size:21
Alignment explanation
Indices: 6591512--6591564 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
6591502 AAATATTTTT
*
6591512 TTTTTATT-TTTTGAATATTA
1 TTTTTATTATTTTAAATATTA
6591532 TTTTTATTATTTTAAA-ATTTA
1 TTTTTATTATTTTAAATA-TTA
* *
6591553 TTATTAGTATTT
1 TTTTTATTATTT
6591565 ATGCTTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTTTATTATTTTAAATATTA
Found at i:6594547 original size:6 final size:5
Alignment explanation
Indices: 6594524--6594578 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
6594514 AATTCAGTAA
* *
6594524 AAAAT GAAAAT AAAAT AAATAT AAAAAG AAAAT AAAAT -CAA- AAAAT
1 AAAAT -AAAAT AAAAT AAA-AT -AAAAT AAAAT AAAAT AAAAT AAAAT
6594570 AAAAT AAAA
1 AAAAT AAAA
6594579 AGAAAAAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.10
5 26 0.63
6 8 0.20
7 3 0.07
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:6594547 original size:11 final size:11
Alignment explanation
Indices: 6594524--6594584 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
6594514 AATTCAGTAA
*
6594524 AAAATGAAAAT
1 AAAATAAAAAT
*
6594535 AAAATAAATAT
1 AAAATAAAAAT
6594546 AAAA-AGAAAAT
1 AAAATA-AAAAT
6594557 AAAATCAAAAAAT
1 AAAAT--AAAAAT
*
6594570 AAAATAAAAAG
1 AAAATAAAAAT
6594581 AAAA
1 AAAA
6594585 AAACCTATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 1 0.02
11 30 0.71
13 10 0.24
14 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:6594561 original size:18 final size:18
Alignment explanation
Indices: 6594530--6594578 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
6594520 GTAAAAAATG
6594530 AAAATAAAAT-AAAT-ATA
1 AAAATAAAATAAAATCA-A
*
6594547 AAAAGAAAATAAAATCAA
1 AAAATAAAATAAAATCAA
6594565 AAAATAAAATAAAA
1 AAAATAAAATAAAA
6594579 AGAAAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.32
18 18 0.64
19 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAAATAAAATCAA
Found at i:6594584 original size:18 final size:17
Alignment explanation
Indices: 6594530--6594586 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
6594520 GTAAAAAATG
* *
6594530 AAAATAAAATAAATATA
1 AAAATAAAATAAAAAAA
* *
6594547 AAAAGAAAATAAAATCAA
1 AAAATAAAATAAAA-AAA
6594565 AAAATAAAATAAAAAGAA
1 AAAATAAAATAAAAA-AA
6594583 AAAA
1 AAAA
6594587 ACCTATGATC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.14
Consensus pattern (17 bp):
AAAATAAAATAAAAAAA
Found at i:6595484 original size:3 final size:3
Alignment explanation
Indices: 6595478--6595548 Score: 97
Period size: 3 Copynumber: 23.7 Consensus size: 3
6595468 AATAATAATA
* * *
6595478 ATG ATG ATG ATG ATG ATC ATG ATG ATG ATC ATG ATG ATG ATG ATA ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
* *
6595526 ATG ATA ATA ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG AT
6595549 AATAATAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:6595563 original size:3 final size:3
Alignment explanation
Indices: 6595557--6595582 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6595547 ATAATAATAA
6595557 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
6595583 ATAATAACAT
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:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:6596154 original size:111 final size:111
Alignment explanation
Indices: 6595930--6596204 Score: 293
Period size: 111 Copynumber: 2.5 Consensus size: 111
6595920 CAAAGCTGAG
* * * * * * *
6595930 ATCGAACGATCGACATTGAACCACAAGTCTAGAAAACTGAGCTGGATCGAGTCGAGGTTAAATGA
1 ATCGAATGACCGAAATTGAACCACAAGTCTAGAAAACTGACCTAGATCGAGTCAAGGTCAAATGA
* * ** **
6595995 TCAGGATTGAGCCGTAAGTTTGGAAAACAATTAAGATGGAGCCAAA
66 TCAGGAATGAACCGTAAGCCTGGAAAACAATTAAGACAGAGCCAAA
*
6596041 ATCTAATGACCGAAATTGAACCACAAGTCT-GAAAAACTGACCTAGATCGAGTCAAGGTCAAATG
1 ATCGAATGACCGAAATTGAACCACAAGTCTAG-AAAACTGACCTAGATCGAGTCAAGGTCAAATG
* ***
6596105 ATCAGGAATGAACCGTAAGCCTGGAAAACAACTT-GGACAGAGTTGAA
65 ATCAGGAATGAACCGTAAGCCTGGAAAACAA-TTAAGACAGAGCCAAA
* * * * * * *
6596152 ATCGAATGATCGAGATTGAATCACAAGTTTAGAAAACTAACTTAGATTGAGTC
1 ATCGAATGACCGAAATTGAACCACAAGTCTAGAAAACTGACCTAGATCGAGTC
6596205 GACGCCAAAC
Statistics
Matches: 135, Mismatches: 26, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
110 1 0.01
111 131 0.97
112 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (111 bp):
ATCGAATGACCGAAATTGAACCACAAGTCTAGAAAACTGACCTAGATCGAGTCAAGGTCAAATGA
TCAGGAATGAACCGTAAGCCTGGAAAACAATTAAGACAGAGCCAAA
Found at i:6608567 original size:3 final size:3
Alignment explanation
Indices: 6608559--6608661 Score: 104
Period size: 3 Copynumber: 35.0 Consensus size: 3
6608549 AAAGAAAAGA
* *
6608559 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAC AAT -AT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
6608605 AAT AAC AAT GAT AAT AAT AA- ATAT AAC AAC AAC AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
6608650 AAT AAT AAT AAT
1 AAT AAT AAT AAT
6608662 TACATAGTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
2 5 0.06
3 80 0.93
4 1 0.01
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:6608706 original size:10 final size:11
Alignment explanation
Indices: 6608560--6608713 Score: 83
Period size: 12 Copynumber: 14.2 Consensus size: 11
6608550 AAGAAAAGAA
6608560 ATAATAATAAT
1 ATAATAATAAT
6608571 AATAATAATAAT
1 -ATAATAATAAT
* *
6608583 AAAATAACAAT
1 ATAATAATAAT
6608594 ATAATAAT-A-
1 ATAATAATAAT
* *
6608603 GTAATAACAAT
1 ATAATAATAAT
6608614 GATAATAATAAAT
1 -ATAATAAT-AAT
* * *
6608627 ATAACAACAACA
1 ATAATAATAA-T
*
6608639 ACAATAATAAT
1 ATAATAATAAT
6608650 AATAATAATAAT
1 -ATAATAATAAT
*
6608662 -TACATAGT-AT
1 ATA-ATAATAAT
6608672 ACT-AT-A-AAT
1 A-TAATAATAAT
*
6608681 ATTAT-ATAAT
1 ATAATAATAAT
*
6608691 ATAATAGTAAT
1 ATAATAATAAT
6608702 A-AATAATAAT
1 ATAATAATAAT
6608712 AT
1 AT
6608714 GTTATACTAT
Statistics
Matches: 107, Mismatches: 21, Indels: 29
0.68 0.13 0.18
Matches are distributed among these distances:
8 1 0.01
9 12 0.11
10 24 0.22
11 26 0.24
12 41 0.38
13 3 0.03
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:6612820 original size:24 final size:24
Alignment explanation
Indices: 6612792--6612849 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
6612782 TTTTGTCAAT
**
6612792 AAAATAAAATATTTTTATGGAAGG
1 AAAATAAAATATTTTTACAGAAGG
6612816 AAAATAAAATATTTTTACAGAAGG
1 AAAATAAAATATTTTTACAGAAGG
6612840 AAAATAAAAT
1 AAAATAAAAT
6612850 TTTGAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (24 bp):
AAAATAAAATATTTTTACAGAAGG
Found at i:6613386 original size:37 final size:35
Alignment explanation
Indices: 6613297--6613391 Score: 111
Period size: 34 Copynumber: 2.7 Consensus size: 35
6613287 ATGCATTGGT
*
6613297 ATTTTTAGAAAAGACATTTGCATTTCATGTGCATC
1 ATTTTAAGAAAAGACATTTGCATTTCATGTGCATC
* *
6613332 ATTTTAAGAAAACACA-TTGCATTTCATTTGCATC
1 ATTTTAAGAAAAGACATTTGCATTTCATGTGCATC
* *
6613366 ATCAGTTTAATAGAAGACATTTGCAT
1 AT---TTTAAGAAAAGACATTTGCAT
6613392 CATAGTGGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 19 0.38
35 14 0.28
37 11 0.22
38 6 0.12
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (35 bp):
ATTTTAAGAAAAGACATTTGCATTTCATGTGCATC
Found at i:6613859 original size:136 final size:137
Alignment explanation
Indices: 6613653--6613921 Score: 423
Period size: 136 Copynumber: 2.0 Consensus size: 137
6613643 TTTTTCAGTA
* * ** * *
6613653 GTGATATTCGAGTATTAAAGTATGAATTTCATTTTCTTAGTGGTCATATCCAAGATATTTTCAAA
1 GTGATATCCGAATATTAAAGTATGAATTTCATTTTCTTAGTAATCATATCCAAAACATTTTCAAA
* * * *
6613718 ATCACTCGATGGTGATTTTTGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTGCATTTT
66 ATCACTCGATGGTGATATTTGAGTTTAAAGGTTGAATTTGCATGCTTTCTCTACATTTACATTTT
6613783 CTCGGTG
131 CTCGGTG
* *
6613790 GTGATATCCGAATATTAAAGTATGAATTTCA-TTTCTTGGTAATGATATCCAAAACATTTTCAAA
1 GTGATATCCGAATATTAAAGTATGAATTTCATTTTCTTAGTAATCATATCCAAAACATTTTCAAA
6613854 ATCACTCGATGGTGATATTTGAGTTTAAAGGTTGAATTTGCATGCTTTCTCTACATTTACATTTT
66 ATCACTCGATGGTGATATTTGAGTTTAAAGGTTGAATTTGCATGCTTTCTCTACATTTACATTTT
6613919 CTC
131 CTC
6613922 TATAATGATA
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
136 91 0.76
137 29 0.24
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (137 bp):
GTGATATCCGAATATTAAAGTATGAATTTCATTTTCTTAGTAATCATATCCAAAACATTTTCAAA
ATCACTCGATGGTGATATTTGAGTTTAAAGGTTGAATTTGCATGCTTTCTCTACATTTACATTTT
CTCGGTG
Found at i:6614129 original size:42 final size:42
Alignment explanation
Indices: 6614013--6614178 Score: 140
Period size: 42 Copynumber: 4.0 Consensus size: 42
6614003 TTTGTCCTTT
** * * *
6614013 AGTGGTGATATCCAAGTGTTAAAAAT-CATTTGCATTTTCTC
1 AGTGGTGATATCTGAGTGTTAAAACTAGAATTGCATTTTCTC
* * * * * * * * *
6614054 AATGATAATAT-TAAGTATTAAAAGT-CATTTGCATCTTCTC
1 AGTGGTGATATCTGAGTGTTAAAACTAGAATTGCATTTTCTC
*
6614094 GGTGGTGATATCTGAGTGTTAAAACTAGAATTGCATTTTCTC
1 AGTGGTGATATCTGAGTGTTAAAACTAGAATTGCATTTTCTC
* * * *
6614136 AGTGGTGGTATCTGAGTGTTAAAGCTTGAATTACATTTTCTC
1 AGTGGTGATATCTGAGTGTTAAAACTAGAATTGCATTTTCTC
6614178 A
1 A
6614179 ATAGGGATAT
Statistics
Matches: 101, Mismatches: 22, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
40 32 0.32
41 19 0.19
42 50 0.50
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (42 bp):
AGTGGTGATATCTGAGTGTTAAAACTAGAATTGCATTTTCTC
Found at i:6614533 original size:10 final size:10
Alignment explanation
Indices: 6614520--6614552 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
6614510 TTATTATTTA
6614520 TTTCTTTTTT
1 TTTCTTTTTT
6614530 TTTC-TTTTT
1 TTTCTTTTTT
6614539 TTTCTTTTCTT
1 TTTCTTTT-TT
6614550 TTT
1 TTT
6614553 TGGTCTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 7 0.33
11 5 0.24
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:6614546 original size:14 final size:13
Alignment explanation
Indices: 6614524--6614553 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
6614514 TATTTATTTC
6614524 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
6614537 TTTTTCTTTTCTTT
1 TTTTT-TTTTCTTT
6614551 TTT
1 TTT
6614554 GGTCTACTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:6614849 original size:17 final size:17
Alignment explanation
Indices: 6614815--6614852 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6614805 CAAGAATACC
6614815 AAACAAAAAAAAACAAA
1 AAACAAAAAAAAACAAA
*
6614832 AAACACAAACAAAA-AAA
1 AAACA-AAAAAAAACAAA
6614849 AAAC
1 AAAC
6614853 TCAATCCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
AAACAAAAAAAAACAAA
Found at i:6615485 original size:21 final size:21
Alignment explanation
Indices: 6615450--6615505 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
6615440 TTTTTTGGAT
*
6615450 TTTTTGATTATTTTTTAATATTA
1 TTTTT-ATTA-TTTTAAATATTA
*
6615473 TTTTTATTATTTTAAATTTTA
1 TTTTTATTATTTTAAATATTA
* *
6615494 TTATTAGTATTT
1 TTTTTATTATTT
6615506 ATGCTTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 20 0.69
22 4 0.14
23 5 0.17
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTATTATTTTAAATATTA
Found at i:6616932 original size:121 final size:121
Alignment explanation
Indices: 6616778--6617015 Score: 395
Period size: 121 Copynumber: 2.0 Consensus size: 121
6616768 ATTCTGCTTA
* *
6616778 ACATATGATTTAAATTTCAAACCTCCAAATTAATATTTTAAATTTTAACTATTGAGATGTATCTT
1 ACATATGATTTAAATTTAAAACCTCCAAATTAATATTTTAAATTCTAACTATTGAGATGTATCTT
* *
6616843 AAAAATAAAAGAGAGAAAAATATATTAATTAAATTATTTTAAGTGCATAATATTTT
66 AAAAATAAAAGAGAGAAAAATATATAAATTAAATCATTTTAAGTGCATAATATTTT
* * *
6616899 ACATATGATTTATATTTAAAACCTCCAAATTAATATTTTAAGTTCTAACTATTGAGATGTCTCTT
1 ACATATGATTTAAATTTAAAACCTCCAAATTAATATTTTAAATTCTAACTATTGAGATGTATCTT
* *
6616964 AAAAATAAAAGAGAGGAAAATATATAAATTGAATCATTTTAAGTGCATAATA
66 AAAAATAAAAGAGAGAAAAATATATAAATTAAATCATTTTAAGTGCATAATA
6617016 CTATATGTTG
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 108 1.00
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (121 bp):
ACATATGATTTAAATTTAAAACCTCCAAATTAATATTTTAAATTCTAACTATTGAGATGTATCTT
AAAAATAAAAGAGAGAAAAATATATAAATTAAATCATTTTAAGTGCATAATATTTT
Found at i:6620565 original size:13 final size:13
Alignment explanation
Indices: 6620542--6620591 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
6620532 TGAAAAGTGT
6620542 AAAAA-AAAGAAA
1 AAAAAGAAAGAAA
*
6620554 AAAGAGAAAGAAA
1 AAAAAGAAAGAAA
*
6620567 AAAAAGAAGGAAA
1 AAAAAGAAAGAAA
*
6620580 AAGAAG-AAGAAA
1 AAAAAGAAAGAAA
6620592 CTAATGGGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAA
Found at i:6620570 original size:25 final size:25
Alignment explanation
Indices: 6620542--6620591 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6620532 TGAAAAGTGT
6620542 AAAAAAAAGAAAAAAG-AGAAAGAAA
1 AAAAAAAAGAAAAAAGAAG-AAGAAA
* *
6620567 AAAAAGAAGGAAAAAGAAGAAGAAA
1 AAAAAAAAGAAAAAAGAAGAAGAAA
6620592 CTAATGGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAGAAGAAGAAA
Found at i:6620893 original size:8 final size:8
Alignment explanation
Indices: 6620877--6620935 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
6620867 TGGAAAAATG
6620877 AAAAC-AA
1 AAAACAAA
6620884 AAAACAAA
1 AAAACAAA
*
6620892 AAAGCAAAA
1 AAAAC-AAA
*
6620901 AAAACGAA
1 AAAACAAA
**
6620909 AAAATGAA
1 AAAACAAA
*
6620917 AAAACGAA
1 AAAACAAA
6620925 AAAACAAA
1 AAAACAAA
6620933 AAA
1 AAA
6620936 TGAAGACTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
7 5 0.11
8 32 0.73
9 7 0.16
ACGTcount: A:0.81, C:0.10, G:0.07, T:0.02
Consensus pattern (8 bp):
AAAACAAA
Found at i:6622151 original size:45 final size:46
Alignment explanation
Indices: 6622046--6622171 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 46
6622036 ACTATCTTCA
* * *
6622046 AATGTGAATCCTTGAAATTTAAGATGTGAAACCCTAAAAGTTTTTG
1 AATGTGAATCTTTGAAATTTTAGATGTGAAACCATAAAAGTTTTTG
* * * * *
6622092 AATGAGAATCTTTGAAATTTTAGTTGTGAAA-TATTAAAGTTTTTT
1 AATGTGAATCTTTGAAATTTTAGATGTGAAACCATAAAAGTTTTTG
*
6622137 AATGTGAATTTTTGAAATCTTT-GATGTGAAACCAT
1 AATGTGAATCTTTGAAAT-TTTAGATGTGAAACCAT
6622172 GATTTTTTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
45 34 0.52
46 32 0.48
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (46 bp):
AATGTGAATCTTTGAAATTTTAGATGTGAAACCATAAAAGTTTTTG
Found at i:6622360 original size:17 final size:17
Alignment explanation
Indices: 6622334--6622383 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
6622324 AGTTTTGGCA
6622334 AACCTAAATTTCTTACG
1 AACCTAAATTTCTTACG
*
6622351 AACCTTAATTTCTTACG
1 AACCTAAATTTCTTACG
*
6622368 AACCTAAATCTCTTAC
1 AACCTAAATTTCTTAC
6622384 AAATCTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (17 bp):
AACCTAAATTTCTTACG
Found at i:6622423 original size:16 final size:18
Alignment explanation
Indices: 6622389--6622439 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
6622379 CTTACAAATC
* *
6622389 TTTAAAGTTCTT-GCGAA
1 TTTAAAGTTCTTATCAAA
*
6622406 TTTGAA-TTCTTA-CAAA
1 TTTAAAGTTCTTATCAAA
6622422 TTTAAAGTTCTTATCAAA
1 TTTAAAGTTCTTATCAAA
6622440 GATATTGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 13 0.46
17 11 0.39
18 4 0.14
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (18 bp):
TTTAAAGTTCTTATCAAA
Found at i:6622496 original size:17 final size:17
Alignment explanation
Indices: 6622454--6622508 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
6622444 TTGTGAACTT
* *
6622454 TAAAGGTCTTGCGAACA
1 TAAAGTTCTTGCGAACC
*
6622471 TGAAA-TTCTTGAGAACC
1 T-AAAGTTCTTGCGAACC
*
6622488 TAAAGTTCTTGCGAATC
1 TAAAGTTCTTGCGAACC
6622505 TAAA
1 TAAA
6622509 CTTTTGTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 3 0.10
17 25 0.81
18 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (17 bp):
TAAAGTTCTTGCGAACC
Found at i:6622574 original size:17 final size:17
Alignment explanation
Indices: 6622547--6622653 Score: 83
Period size: 17 Copynumber: 6.2 Consensus size: 17
6622537 CTGAATTCTA
*
6622547 GCAAATCTGAAACCTTT
1 GCAAATTTGAAACCTTT
* *
6622564 GTAAATTTGAAATCTTT
1 GCAAATTTGAAACCTTT
* * *
6622581 GGGAAACTTGAAATCTTT
1 -GCAAATTTGAAACCTTT
* *
6622599 GCGAATCT-AGAACCTTT
1 GCAAATTTGA-AACCTTT
*
6622616 GCAAATCTTGAAA-TTTT
1 GCAAAT-TTGAAACCTTT
*
6622633 GCAAATTTGAAACTTTT
1 GCAAATTTGAAACCTTT
6622650 GCAA
1 GCAA
6622654 TATGGAACTT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
16 7 0.10
17 46 0.64
18 18 0.25
19 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (17 bp):
GCAAATTTGAAACCTTT
Found at i:6622662 original size:16 final size:17
Alignment explanation
Indices: 6622613--6622663 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
6622603 ATCTAGAACC
*
6622613 TTTGCAAATCTTGAAA-T
1 TTTGCAAAT-ATGAAACT
*
6622630 TTTGCAAATTTGAAACT
1 TTTGCAAATATGAAACT
*
6622647 TTTGC-AATATGGAACT
1 TTTGCAAATATGAAACT
6622663 T
1 T
6622664 CTGTGAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (17 bp):
TTTGCAAATATGAAACT
Found at i:6622672 original size:85 final size:85
Alignment explanation
Indices: 6622527--6622689 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 85
6622517 AATATGGAAT
*
6622527 CTTTGCAAATCTGAATTCTAGCAAATCTGAAACCTTTGTAAATTTGAAATCTTTGGGAAACTTGA
1 CTTTGCAAATCTGAATTCTAGCAAATCTGAAACCTTTGTAAATATGAAATCTTTGGGAAACTTGA
6622592 AATCTTTGCGAATCTAGAAC
66 AATCTTTGCGAATCTAGAAC
* * * * * *
6622612 CTTTGCAAATCTTGAAATT-TTGCAAATTTGAAACTTTTG-CAATATGGAA-CTTCTGTGAAACT
1 CTTTGCAAATC-TG-AATTCTAGCAAATCTGAAACCTTTGTAAATATGAAATCTT-TGGGAAACT
* *
6622674 TGGAATCTTTGTGAAT
63 TGAAATCTTTGCGAAT
6622690 TTGGGACCTC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
84 3 0.05
85 40 0.61
86 19 0.29
87 4 0.06
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (85 bp):
CTTTGCAAATCTGAATTCTAGCAAATCTGAAACCTTTGTAAATATGAAATCTTTGGGAAACTTGA
AATCTTTGCGAATCTAGAAC
Found at i:6624437 original size:24 final size:25
Alignment explanation
Indices: 6624393--6624443 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
6624383 TTGTACTATT
* *
6624393 TTATTTTTATTTTTTG-TTTTTATA
1 TTATTTTTATTTTATGATTTTAATA
6624417 TTATTTTTATATTTAT-ATTTTAATA
1 TTATTTTTAT-TTTATGATTTTAATA
6624442 TT
1 TT
6624444 CATTATGGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (25 bp):
TTATTTTTATTTTATGATTTTAATA
Found at i:6624664 original size:21 final size:22
Alignment explanation
Indices: 6624633--6624689 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
6624623 ATGATCATTA
*
6624633 ATATTACTGCATGATAGTTTAT
1 ATATTATTGCATGATAGTTTAT
6624655 -TATTATTGCATGATAGTTTAT
1 ATATTATTGCATGATAGTTTAT
*
6624676 ATCATTATTTCATG
1 AT-ATTATTGCATG
6624690 GTATTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 20 0.65
22 1 0.03
23 10 0.32
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (22 bp):
ATATTATTGCATGATAGTTTAT
Found at i:6624852 original size:14 final size:14
Alignment explanation
Indices: 6624835--6624861 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6624825 AATACATTTT
6624835 TTTTAAAAAAAATA
1 TTTTAAAAAAAATA
6624849 TTTTAAAAAAAAT
1 TTTTAAAAAAAAT
6624862 CCTATCAATA
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTTAAAAAAAATA
Found at i:6626495 original size:21 final size:22
Alignment explanation
Indices: 6626465--6626512 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
6626455 ACCTCCGAAT
*
6626465 ATAATTTTTAAGA-TCTCC-GGC
1 ATAATCTTTAAGACT-TCCGGGC
6626486 ATAATCTTTAAGACTTCCGGGC
1 ATAATCTTTAAGACTTCCGGGC
6626508 ATAAT
1 ATAAT
6626513 TTTGATTCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (22 bp):
ATAATCTTTAAGACTTCCGGGC
Found at i:6626661 original size:132 final size:129
Alignment explanation
Indices: 6626393--6626865 Score: 475
Period size: 132 Copynumber: 3.6 Consensus size: 129
6626383 GTAGCAATAG
* ** * * *
6626393 ATGTTGTCCCGATTGATTCCTTATTTTTTGACTTACGATGTTGTCCTAGTTGATTCTGTAAGACC
1 ATGTTGTCCCGATCGATTCCTTATTTTTTGACTTTGGATGTTATCCCAGTCGATTCTGTAAGACC
* ** * * *
6626458 TCCGAATATAATTTTTAAGATCTCCGGCATAATCTTTAAGACTTCCGGGCATAATTTTGATTCGC
66 TTCG-GCATGATTTTTAAGAACTCGGGCATAATCTTTAAGACTT-CGGGCATAATTTTGATTCGC
6626523 A
129 A
* * * *
6626524 GTGTTGTCCCGATTGATTCCTTATTTTTTAACTTTGGATGTTATCCCAGTCGATTTTGTAAGACC
1 ATGTTGTCCCGATCGATTCCTTATTTTTTGACTTTGGATGTTATCCCAGTCGATTCTGTAAGACC
* *
6626589 TTCAGGCATGATTTTCAAGAACTCTGGGCATAATCTTTAAGACTTCTAGGCATAATTTTGATTCG
66 TTC-GGCATGATTTTTAAGAACTC-GGGCATAATCTTTAAGACTTC-GGGCATAATTTTGATTCG
6626654 CA
128 CA
* * * * * *
6626656 ATGTTGTCTCGATCAATTTCTTATTTTTTGAC-TTGCGGTGTTATCTCAGTCGATTCTATAAGAC
1 ATGTTGTCCCGATCGATTCCTTATTTTTTGACTTTG-GATGTTATCCCAGTCGATTCTGTAAGAC
* **
6626720 CTTCGGACATGATTTTTAAGACCTCGAGATATAATCTTTAAGACATTCGGGCATAATTTTGATTC
65 CTTCGG-CATGATTTTTAAGAACTCG-GGCATAATCTTTAAGAC-TTCGGGCATAATTTTGATTC
* *
6626785 ACG
127 GCA
* * * * * * * * *
6626788 GTGTTGTCCCAATCGATTCTTTATTTTTGGGCTTATGG-TGTTGTCCCAATCAATTCTCT-AGAC
1 ATGTTGTCCCGATCGATTCCTTATTTTTTGACTT-TGGATGTTATCCCAGTCGATTCTGTAAGAC
*
6626851 CTTCAGGCATAATTT
65 CTTC-GGCATGATTT
6626866 CGATTCACGG
Statistics
Matches: 285, Mismatches: 47, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
131 95 0.33
132 183 0.64
133 5 0.02
134 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (129 bp):
ATGTTGTCCCGATCGATTCCTTATTTTTTGACTTTGGATGTTATCCCAGTCGATTCTGTAAGACC
TTCGGCATGATTTTTAAGAACTCGGGCATAATCTTTAAGACTTCGGGCATAATTTTGATTCGCA
Found at i:6626739 original size:22 final size:22
Alignment explanation
Indices: 6626714--6626779 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
6626704 GTCGATTCTA
*
6626714 TAAGACCTTCGGACATGATTTT
1 TAAGACCTTCGGACATAATTTT
* *
6626736 TAAGACC-TCGAGATATAATCTT
1 TAAGACCTTCG-GACATAATTTT
* *
6626758 TAAGACATTCGGGCATAATTTT
1 TAAGACCTTCGGACATAATTTT
6626780 GATTCACGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.09
22 29 0.83
23 3 0.09
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAGACCTTCGGACATAATTTT
Found at i:6626915 original size:87 final size:87
Alignment explanation
Indices: 6626760--6626922 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 87
6626750 ATAATCTTTA
* * * * *
6626760 AGACATTCGGGCATAATTTTGATTCACGGTGTTGTCCCAATCGATTCTTTATTTTTGGGCTTATG
1 AGACATTCAGGCATAATTTCGATTCACGGTGTTGTCCCAATAGATTCCTTATTTTTGGACTTATG
6626825 GTGTTGTCCCAATCAATTCTCT
66 GTGTTGTCCCAATCAATTCTCT
* * *
6626847 AGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCGATAGATTCCTTATTTTAT-GACTTGT
1 AGACATTCAGGCATAATTTCGATTCACGGTGTTGTCCCAATAGATTCCTTATTTT-TGGACTTAT
6626911 GGTGTTGTCCCA
65 GGTGTTGTCCCA
6626923 GTTGATTCTG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
87 66 0.99
88 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (87 bp):
AGACATTCAGGCATAATTTCGATTCACGGTGTTGTCCCAATAGATTCCTTATTTTTGGACTTATG
GTGTTGTCCCAATCAATTCTCT
Found at i:6626931 original size:87 final size:88
Alignment explanation
Indices: 6626758--6626940 Score: 235
Period size: 87 Copynumber: 2.1 Consensus size: 88
6626748 ATATAATCTT
* * * * * *
6626758 TAAGACATTCGGGCATAATTTTGATTCACGGTGTTGTCCCAATCGATTCTTTATTTTTGGGCTTA
1 TAAGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCAATAGATTCCTTATTTTTGGACTTA
6626823 TGGTGTTGTCCCAATCAATTCTC
66 TGGTGTTGTCCCAATCAATTCTC
*
6626846 T-AGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCGATAGATTCCTTATTTTAT-GACTT
1 TAAGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCAATAGATTCCTTATTTT-TGGACTT
* * ** *
6626909 GTGGTGTTGTCCCAGTTGATTCTG
65 ATGGTGTTGTCCCAATCAATTCTC
6626933 TAAGACCT
1 TAAGACCT
6626941 CCGAGCATGA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 73 0.90
88 8 0.10
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (88 bp):
TAAGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCAATAGATTCCTTATTTTTGGACTTA
TGGTGTTGTCCCAATCAATTCTC
Found at i:6627070 original size:111 final size:110
Alignment explanation
Indices: 6626842--6627084 Score: 310
Period size: 111 Copynumber: 2.2 Consensus size: 110
6626832 CCCAATCAAT
*
6626842 TCTCT-AGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCGATAGATTCCTTATTTTATGA
1 TCTCTAAGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCGATAGATTCCTTATTTTATCA
** **
6626906 CTTGTGGTGTTGTCCCAGTTGATTCTGTAAGACCTCCGAGCATGA
66 CTTACGGTGTTGTCCCAGTCAATTCTGTAAGACCTCCGAGCATGA
* * ** ** * * *
6626951 TCTCTAAGACCTACAGGCATAATTTTGATTTGCGGTGTTGTCTTGATCGATTCTTTATTTTTTTC
1 TCTCTAAGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCGATAGATTCCTTA-TTTTATC
*
6627016 ACTTACGGTGTTGTCCTAGTCAATTCTGTAAGACCTCCG-GACATGA
65 ACTTACGGTGTTGTCCCAGTCAATTCTGTAAGACCTCCGAG-CATGA
*
6627062 TTTCTAAGACCTTCAGGCATAAT
1 TCTCTAAGACCTTCAGGCATAAT
6627085 CTTTAAGACC
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
109 5 0.04
110 44 0.39
111 65 0.57
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (110 bp):
TCTCTAAGACCTTCAGGCATAATTTCGATTCACGGTGTTGTCCCGATAGATTCCTTATTTTATCA
CTTACGGTGTTGTCCCAGTCAATTCTGTAAGACCTCCGAGCATGA
Found at i:6627202 original size:22 final size:22
Alignment explanation
Indices: 6627170--6627238 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
6627160 GTCCTAGTTG
*
6627170 ATTTTGTAAGACCTCTGAGCATA
1 ATTTT-TAAGACCTCTGGGCATA
*
6627193 ATTTTTAAGACCTATGGGCATA
1 ATTTTTAAGACCTCTGGGCATA
6627215 ATTTTTAAGACCTCTGGGCATA
1 ATTTTTAAGACCTCTGGGCATA
6627237 AT
1 AT
6627239 CTTGATCGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
22 38 0.88
23 5 0.12
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (22 bp):
ATTTTTAAGACCTCTGGGCATA
Found at i:6627215 original size:132 final size:131
Alignment explanation
Indices: 6626945--6627306 Score: 388
Period size: 132 Copynumber: 2.7 Consensus size: 131
6626935 AGACCTCCGA
* * * * * *
6626945 GCATGATCTCTAAGACCTACAGGCATAATTTTGATTTGCGGTGTTGTCTTGATCGATTCTTTATT
1 GCATAATCTTTAAGACCTCCAGGCATAA-TTTGATTTGCGGTGTTGTCTCGATTGATTCCTTA-T
* * * * *
6627010 TTTTTCACTTACGGTGTTGTCCTAGTCAATTCTGTAAGACCTCCGGACATGATTTCTAAGACCTT
64 TTTTTGACTTGCGGTATTGTCCTAGTCGATTCTGTAAGACCTCCGGACATAATTTCTAAGACCTT
6627075 CAG
129 CAG
* * * *
6627078 GCATAATCTTTAAGACCTCCAAGCATAATTTCAATTTACGGTGTTGTCTCAATTGATTCCTTATT
1 GCATAATCTTTAAGACCTCCAGGCATAATTT-GATTTGCGGTGTTGTCTCGATTGATTCCTTATT
* * * * *
6627143 TTTTGACTTGCGGCATTGTCCTAGTTGATTTTGTAAGACCT-CTGAGCATAATTTTTAAGACCTA
65 TTTTGACTTGCGGTATTGTCCTAGTCGATTCTGTAAGACCTCCGGA-CATAATTTCTAAGACCT-
*
6627207 T-GG
128 TCAG
* ** ** **
6627210 GCATAATTTTTAAGACCTCTGGGCATAATCTTGATCGGCAATGTTGTC-CTGATTGATTCCTTAT
1 GCATAATCTTTAAGACCTCCAGGCATAAT-TTGATTTGCGGTGTTGTCTC-GATTGATTCCTTAT
6627274 TTTTTGACTTGCGGTATTGTCCTAGTCGATTCT
64 TTTTTGACTTGCGGTATTGTCCTAGTCGATTCT
6627307 TTATTCCTTG
Statistics
Matches: 189, Mismatches: 35, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
131 4 0.02
132 133 0.70
133 52 0.28
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (131 bp):
GCATAATCTTTAAGACCTCCAGGCATAATTTGATTTGCGGTGTTGTCTCGATTGATTCCTTATTT
TTTGACTTGCGGTATTGTCCTAGTCGATTCTGTAAGACCTCCGGACATAATTTCTAAGACCTTCA
G
Found at i:6627305 original size:37 final size:37
Alignment explanation
Indices: 6627251--6627396 Score: 134
Period size: 37 Copynumber: 3.9 Consensus size: 37
6627241 TGATCGGCAA
* * *
6627251 TGTTGTCCT-GATTGATTCCTTATTTTTTGACTTGCGG
1 TGTTGTCCTAG-TCGATTCTTTATTTCTTGACTTGCGG
* * *
6627288 TATTGTCCTAGTCGATTCTTTATTCCTTGACTTGTGG
1 TGTTGTCCTAGTCGATTCTTTATTTCTTGACTTGCGG
* * *
6627325 TGTTGT-CTCAGTTGATTCTTTATTTCTCGACTCGCGG
1 TGTTGTCCT-AGTCGATTCTTTATTTCTTGACTTGCGG
* * **
6627362 CGTTGTCCTAGTCGTTGTCTTTATCACTTGACTTG
1 TGTTGTCCTAGTCGAT-TCTTTATTTCTTGACTTG
6627397 AGATTCAAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
36 2 0.02
37 67 0.78
38 17 0.20
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.48
Consensus pattern (37 bp):
TGTTGTCCTAGTCGATTCTTTATTTCTTGACTTGCGG
Found at i:6627655 original size:7 final size:7
Alignment explanation
Indices: 6627633--6627681 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
6627623 TAATATTGAA
6627633 AAAAAAT
1 AAAAAAT
6627640 ACTAAAAAT
1 A--AAAAAT
6627649 AAAAAAT
1 AAAAAAT
6627656 AAAAAAT
1 AAAAAAT
6627663 AAAAAA-
1 AAAAAAT
*
6627669 AAAGAAAC
1 AAA-AAAT
6627677 AAAAA
1 AAAAA
6627682 GTGGCAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 3 0.08
7 25 0.66
8 3 0.08
9 7 0.18
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:6629162 original size:14 final size:14
Alignment explanation
Indices: 6629143--6629216 Score: 62
Period size: 14 Copynumber: 5.2 Consensus size: 14
6629133 CTTCAATTAA
6629143 AAAATCTAAACCCT
1 AAAATCTAAACCCT
* *
6629157 AAAATCGAAAACCT
1 AAAATCTAAACCCT
* *
6629171 AAAACCAAAACCCT
1 AAAATCTAAACCCT
*
6629185 AAACTCTTTATAACCC-
1 AAAATC--TA-AACCCT
6629201 AAAA-CTAAACCCT
1 AAAATCTAAACCCT
6629214 AAA
1 AAA
6629217 TCCTCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 27 0.57
15 1 0.02
16 4 0.09
17 5 0.11
ACGTcount: A:0.53, C:0.28, G:0.01, T:0.18
Consensus pattern (14 bp):
AAAATCTAAACCCT
Found at i:6629296 original size:36 final size:36
Alignment explanation
Indices: 6629256--6629338 Score: 157
Period size: 36 Copynumber: 2.3 Consensus size: 36
6629246 GAAATCAAAT
*
6629256 CCCTAAACCCTCGAAACCATAAAACAAATCCTTAAA
1 CCCTAAACCCTCCAAACCATAAAACAAATCCTTAAA
6629292 CCCTAAACCCTCCAAACCATAAAACAAATCCTTAAA
1 CCCTAAACCCTCCAAACCATAAAACAAATCCTTAAA
6629328 CCCTAAACCCT
1 CCCTAAACCCT
6629339 AAACCCTCCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.45, C:0.37, G:0.01, T:0.17
Consensus pattern (36 bp):
CCCTAAACCCTCCAAACCATAAAACAAATCCTTAAA
Found at i:6629358 original size:43 final size:45
Alignment explanation
Indices: 6629288--6629386 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 45
6629278 AACAAATCCT
6629288 TAAACCCTAAACCCTCCAAACCATAAAA-C-AAATCCTTAAAC-CC
1 TAAACCCTAAACCCTCCAAACCATAAAATCGAAA-CCTTAAACACC
**
6629331 TAAACCCTAAACCCTCCAAGTTC-TAAAATCGAAACCTTAAACATCC
1 TAAACCCTAAACCCTCCAA-ACCATAAAATCGAAACCTTAAACA-CC
6629377 -AAACCCTAAA
1 TAAACCCTAAA
6629387 ATTGAAACCC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
43 24 0.49
44 10 0.20
45 13 0.27
46 2 0.04
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.18
Consensus pattern (45 bp):
TAAACCCTAAACCCTCCAAACCATAAAATCGAAACCTTAAACACC
Found at i:6629396 original size:14 final size:14
Alignment explanation
Indices: 6629353--6629499 Score: 127
Period size: 14 Copynumber: 10.4 Consensus size: 14
6629343 CCTCCAAGTT
6629353 CTAAAATCGAAACC
1 CTAAAATCGAAACC
* *
6629367 TTAAACATCCAAACC
1 CTAAA-ATCGAAACC
*
6629382 CTAAAATTGAAACC
1 CTAAAATCGAAACC
6629396 CTAAAATCGAAACC
1 CTAAAATCGAAACC
* *
6629410 C-CAAATCTCAAACC
1 CTAAAATC-GAAACC
*
6629424 CTAAAATTGAAACC
1 CTAAAATCGAAACC
* *
6629438 CTAAACCTC-AAATC
1 CTAAA-ATCGAAACC
* * *
6629452 TTAAAATCAAAACT
1 CTAAAATCGAAACC
*
6629466 CTAAACATCCAAACC
1 CTAAA-ATCGAAACC
*
6629481 CTAAAATCGAAAAC
1 CTAAAATCGAAACC
6629495 CTAAA
1 CTAAA
6629500 CCCCAAAATC
Statistics
Matches: 104, Mismatches: 23, Indels: 12
0.75 0.17 0.09
Matches are distributed among these distances:
13 7 0.07
14 68 0.65
15 29 0.28
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (14 bp):
CTAAAATCGAAACC
Found at i:6629400 original size:43 final size:41
Alignment explanation
Indices: 6629353--6629499 Score: 152
Period size: 42 Copynumber: 3.4 Consensus size: 41
6629343 CCTCCAAGTT
6629353 CTAAAATCGAAACCTTAAACATCCAAACCCTAAAATTGAAACC
1 CTAAAATCGAAACC-TAAA-ATCCAAACCCTAAAATTGAAACC
**
6629396 CTAAAATCGAAACCCCAAATCTCAAACCCTAAAATTGAAACC
1 CTAAAATCGAAACCTAAAATC-CAAACCCTAAAATTGAAACC
* * * * **
6629438 CTAAACCTC-AAATCTTAAAATCAAAACTCTAAACATCCAAACC
1 CTAAA-ATCGAAA-CCTAAAATCCAAACCCTAAA-ATTGAAACC
6629481 CTAAAATCGAAAACCTAAA
1 CTAAAATCG-AAACCTAAA
6629500 CCCCAAAATC
Statistics
Matches: 86, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
41 3 0.03
42 41 0.48
43 39 0.45
44 3 0.03
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (41 bp):
CTAAAATCGAAACCTAAAATCCAAACCCTAAAATTGAAACC
Found at i:6629521 original size:28 final size:28
Alignment explanation
Indices: 6629437--6629543 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 28
6629427 AAATTGAAAC
*
6629437 CCTAAACCTC-AAATCTTAAAATC-AAAA
1 CCTAAACCCCAAAATC-TAAAATCAAAAA
* ** *
6629464 CTCTAAACATCCAAACCCTAAAATCGAAAA
1 C-CTAAAC-CCCAAAATCTAAAATCAAAAA
*
6629494 CCTAAACCCCAAAATCTGAAACTCAAAAA
1 CCTAAACCCCAAAATCT-AAAATCAAAAA
* *
6629523 CCT-AACCCTAAAATCCAAAAT
1 CCTAAACCCCAAAATCTAAAAT
6629544 GCTAAACCCT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.08
28 24 0.38
29 26 0.41
30 8 0.13
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (28 bp):
CCTAAACCCCAAAATCTAAAATCAAAAA
Done.