Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 125 of 127
Found at i:25203057 original size:2 final size:2
Alignment explanation
Indices: 25203050--25203077 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25203040 GATTGCTATC
25203050 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
25203078 GATAGCAATC
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:25203488 original size:2 final size:2
Alignment explanation
Indices: 25203465--25203508 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
25203455 TCCATTAATC
* * *
25203465 TA TA TC TA TA TT TA TGA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
25203508 T
1 T
25203509 GGATGTTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25213652 original size:20 final size:20
Alignment explanation
Indices: 25213627--25213666 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25213617 TAATTATTTA
25213627 TTTATATATAT-TTATAAAAT
1 TTTATATATATATTA-AAAAT
*
25213647 TTTATATTTATATTAAAAAT
1 TTTATATATATATTAAAAAT
25213667 AATATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATATATATATTAAAAAT
Found at i:25213658 original size:22 final size:22
Alignment explanation
Indices: 25213633--25213699 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 22
25213623 TTTATTTATA
25213633 TATATTTATAAAATTTTATATT
1 TATATTTATAAAATTTTATATT
**
25213655 TATA-TTA-AAAATAATAT-TT
1 TATATTTATAAAATTTTATATT
* *
25213674 TATATTT-TAAAAATTAATATT
1 TATATTTATAAAATTTTATATT
25213695 T-TATT
1 TATATT
25213700 AAGTTCGAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 6 0.17
20 20 0.56
21 6 0.17
22 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATTTATAAAATTTTATATT
Found at i:25213674 original size:25 final size:22
Alignment explanation
Indices: 25213640--25213698 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
25213630 ATATATATTT
*
25213640 ATAAAATTTTATATTTATATTAAAA
1 ATAATATTTTATATTT-TA--AAAA
25213665 ATAATATTTTATATTTTAAAAA
1 ATAATATTTTATATTTTAAAAA
*
25213687 TTAATATTTTAT
1 ATAATATTTTAT
25213699 TAAGTTCGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 15 0.47
24 2 0.06
25 15 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAATATTTTATATTTTAAAAA
Found at i:25213699 original size:20 final size:20
Alignment explanation
Indices: 25213635--25213699 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
25213625 TATTTATATA
* *
25213635 TATTTATAAAATTTTATA-TT
1 TATTT-TAAAAATTAATATTT
*
25213655 TATATTAAAAA-TAATATTTT
1 TATTTTAAAAATTAATA-TTT
25213675 ATATTTTAAAAATTAATATTT
1 -TATTTTAAAAATTAATATTT
25213696 TATT
1 TATT
25213700 AAGTTCGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.11
19 5 0.14
20 10 0.27
21 13 0.35
22 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTAAAAATTAATATTT
Found at i:25229106 original size:199 final size:198
Alignment explanation
Indices: 25228738--25229138 Score: 775
Period size: 199 Copynumber: 2.0 Consensus size: 198
25228728 TCTGATTGCT
*
25228738 CTCCGCAAAAGTCTGAGCCTTTTCTTCTTGCTTTGCTTCCTTCGCTACTGATCAATCAACACCAA
1 CTCCGCAAAAGTCTGAGCCTTTTCTTCTTGCTTTGCTTCCTTCGCCACTGATCAATCAACACCAA
25228803 CGTGGGCCTTGTTTAAGGAACTTTTACTTATTGGGCTATAAAAGCCCAAGAAATTGACTTTTCAT
66 CGTGGGCCTTGTTTAAGGAACTTTTACTTATTGGGCTATAAAAGCCCAAGAAATTGACTTTTCAT
25228868 TGGGGGCCGTTGCTGCGTCAATGCCATGGACTCCATGCTCGAAAAGAATTTGTGGTAATTTTAAT
131 TGGGGGCCGTTGCTGCGTCAATGCCATGGACTCCATGCTCGAAAAGAATTTGTGGTAATTTTAAT
25228933 TGG
196 TGG
25228936 CTCCGCAAAAGTCTGAGCCTTTTCTTCTTGCTTTGCTTCCTTCGCCACTGATCAATCAACACCAA
1 CTCCGCAAAAGTCTGAGCCTTTTCTTCTTGCTTTGCTTCCTTCGCCACTGATCAATCAACACCAA
*
25229001 CGTGGGCCTTGTTTAAGGAATCTTTTACTTATTGGGCTATGAAAGCCCAAGAAATTGACTTTTCA
66 CGTGGGCCTTGTTTAAGGAA-CTTTTACTTATTGGGCTATAAAAGCCCAAGAAATTGACTTTTCA
25229066 TTGGGGGCCGTTGCTGCGTCAATGCCATGGACTCCATGCTCGAAAAGAATTTGTGGTAATTTTAA
130 TTGGGGGCCGTTGCTGCGTCAATGCCATGGACTCCATGCTCGAAAAGAATTTGTGGTAATTTTAA
25229131 TTGG
195 TTGG
25229135 CTCC
1 CTCC
25229139 AACCTCTCCT
Statistics
Matches: 200, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
198 84 0.42
199 116 0.58
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (198 bp):
CTCCGCAAAAGTCTGAGCCTTTTCTTCTTGCTTTGCTTCCTTCGCCACTGATCAATCAACACCAA
CGTGGGCCTTGTTTAAGGAACTTTTACTTATTGGGCTATAAAAGCCCAAGAAATTGACTTTTCAT
TGGGGGCCGTTGCTGCGTCAATGCCATGGACTCCATGCTCGAAAAGAATTTGTGGTAATTTTAAT
TGG
Found at i:25233965 original size:14 final size:16
Alignment explanation
Indices: 25233941--25233979 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
25233931 AAAAGGCTGT
*
25233941 AGTTTTTAATTAA-AA
1 AGTTATTAATTAAGAA
25233956 A-TTATTAATTAAGAA
1 AGTTATTAATTAAGAA
25233971 AGTTATTAA
1 AGTTATTAA
25233980 CAGTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 10 0.48
15 4 0.19
16 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
AGTTATTAATTAAGAA
Found at i:25234515 original size:27 final size:24
Alignment explanation
Indices: 25234461--25234509 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 24
25234451 TTGGTTTCGA
*
25234461 TAAAATTAAAAATAATGATGATTG
1 TAAAATTAAAAATAATGATGAATG
25234485 TAAAATTAAATATTATAATGATGAA
1 TAAAATTAAA-A--ATAATGATGAA
25234510 ATTAAAGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 1 0.05
27 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (24 bp):
TAAAATTAAAAATAATGATGAATG
Found at i:25241478 original size:22 final size:22
Alignment explanation
Indices: 25241450--25241498 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
25241440 AACGAGATTG
25241450 AAGGGTTTACTGTAGCAACATT
1 AAGGGTTTACTGTAGCAACATT
25241472 AAGGGTTTACTGTAGCAACATT
1 AAGGGTTTACTGTAGCAACATT
25241494 AAGGG
1 AAGGG
25241499 GAAATGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (22 bp):
AAGGGTTTACTGTAGCAACATT
Found at i:25254301 original size:4 final size:4
Alignment explanation
Indices: 25254292--25254317 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
25254282 CATGACAATA
25254292 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
25254318 ATTCTGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:25263529 original size:13 final size:13
Alignment explanation
Indices: 25263506--25263547 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
25263496 TCTATCAGTA
25263506 AAATATTAAATTTT
1 AAATATTAAA-TTT
25263520 AAAT-TTAAATTT
1 AAATATTAAATTT
*
25263532 AAATGATTAAAATT
1 AAAT-ATTAAATTT
25263546 AA
1 AA
25263548 GATCTTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 7 0.28
13 5 0.20
14 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AAATATTAAATTT
Found at i:25269466 original size:9 final size:8
Alignment explanation
Indices: 25269452--25269476 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25269442 CGGTGTTCAA
25269452 TTTTTTTC
1 TTTTTTTC
25269460 TTTTTTTC
1 TTTTTTTC
25269468 TTTTTTTC
1 TTTTTTTC
25269476 T
1 T
25269477 AGCACATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:25293110 original size:5 final size:5
Alignment explanation
Indices: 25293102--25293126 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
25293092 GATAATATTA
25293102 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
25293127 AATATTATTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:25293221 original size:17 final size:18
Alignment explanation
Indices: 25293199--25293236 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25293189 TCAAAATTTT
*
25293199 TTTAAA-AATTTATATAA
1 TTTAAATAATTAATATAA
*
25293216 TTTAAATTATTAATATAA
1 TTTAAATAATTAATATAA
25293234 TTT
1 TTT
25293237 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATAATTAATATAA
Found at i:25293352 original size:16 final size:16
Alignment explanation
Indices: 25293331--25293361 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25293321 AACATAAGAT
25293331 ATCTAATCTTTTTATA
1 ATCTAATCTTTTTATA
*
25293347 ATCTAATTTTTTTAT
1 ATCTAATCTTTTTAT
25293362 TTAAATACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
ATCTAATCTTTTTATA
Found at i:25296761 original size:68 final size:68
Alignment explanation
Indices: 25296648--25296783 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
25296638 ACAAATTCAC
25296648 AAACTACAATCTGGACAGGAAAAGGAAATGAAGAAACAAAAAGCATTGATGTAAGCCAGTATACA
1 AAACTACAATCTGGACAGGAAAAGGAAATGAAGAAACAAAAAGCATTGATGTAAGCCAGTATACA
25296713 TGT
66 TGT
* *
25296716 AAACTACAATCTGGA-AGGGAAAAGGAAATGAAGAAACAAAGAGCATTGGTGTAAGCCAGTATAC
1 AAACTACAATCTGGACA-GGAAAAGGAAATGAAGAAACAAAAAGCATTGATGTAAGCCAGTATAC
25296780 ATGT
65 ATGT
25296784 CAATACCCCA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 1 0.02
68 64 0.98
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.18
Consensus pattern (68 bp):
AAACTACAATCTGGACAGGAAAAGGAAATGAAGAAACAAAAAGCATTGATGTAAGCCAGTATACA
TGT
Found at i:25299930 original size:7 final size:7
Alignment explanation
Indices: 25299918--25299946 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
25299908 ACATCATATC
25299918 TCTTAAG
1 TCTTAAG
25299925 TCTTAAG
1 TCTTAAG
25299932 TCTTAAG
1 TCTTAAG
25299939 TCTTAAG
1 TCTTAAG
25299946 T
1 T
25299947 TACAGCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (7 bp):
TCTTAAG
Found at i:25301756 original size:10 final size:11
Alignment explanation
Indices: 25301738--25301775 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
25301728 CAATTTATAA
25301738 TTATATAAAAT
1 TTATATAAAAT
25301749 TTAT-TAAAATT
1 TTATATAAAA-T
25301760 TTATATAAAAT
1 TTATATAAAAT
25301771 TTATA
1 TTATA
25301776 CTTATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATATAAAAT
Found at i:25301803 original size:43 final size:40
Alignment explanation
Indices: 25301729--25301816 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 40
25301719 ATTTAATCAC
25301729 AATTTATAATTATATAAAATTTATTAAAATTTTATA-TAA
1 AATTTATAATTATATAAAATTTATTAAAATTTTATACTAA
* *
25301768 AATTTATACTTATAAATATAAATTT-TTACATAATTTTATACTAT
1 AATTTATAATTAT--ATA-AAATTTATTA-A-AATTTTATACTAA
25301812 AATTT
1 AATTT
25301817 TTTTGACCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 12 0.29
41 6 0.15
42 7 0.17
43 9 0.22
44 7 0.17
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (40 bp):
AATTTATAATTATATAAAATTTATTAAAATTTTATACTAA
Found at i:25307233 original size:30 final size:30
Alignment explanation
Indices: 25307200--25307320 Score: 111
Period size: 30 Copynumber: 4.0 Consensus size: 30
25307190 ATATTTTGAC
* *
25307200 GTAGTGAGAGCTGATTTTGTTACAGAAGAC
1 GTAGTGAGAGCTGATTTTGTTACTGAAGAA
* ** *
25307230 GTAG-AAGGAGCTGATTTCATAACTGAAGAA
1 GTAGTGA-GAGCTGATTTTGTTACTGAAGAA
* * *
25307260 GTAATGGGAGCTGATTTTGGTACTGAAGAA
1 GTAGTGAGAGCTGATTTTGTTACTGAAGAA
* *
25307290 GTGGTG-GCAGCTGATCTTGTTACTGAAGAA
1 GTAGTGAG-AGCTGATTTTGTTACTGAAGAA
25307320 G
1 G
25307321 ATCGACCAGT
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
29 2 0.03
30 69 0.97
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (30 bp):
GTAGTGAGAGCTGATTTTGTTACTGAAGAA
Found at i:25319831 original size:30 final size:31
Alignment explanation
Indices: 25319794--25319866 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
25319784 TGGATAGGGG
*
25319794 TATATATATATATAAAAATATGAGCATATACA
1 TATATATATATAT-AAAATATGAACATATACA
*
25319826 TATATA-ATGA-ATAAAATATGAACATATATA
1 TATATATAT-ATATAAAATATGAACATATACA
25319856 TATATATATAT
1 TATATATATAT
25319867 GCTCATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
30 23 0.64
31 6 0.17
32 7 0.19
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.37
Consensus pattern (31 bp):
TATATATATATATAAAATATGAACATATACA
Found at i:25322104 original size:6 final size:6
Alignment explanation
Indices: 25322093--25322118 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25322083 TTAGAGCTCT
25322093 AATGCA AATGCA AATGCA AATGCA AA
1 AATGCA AATGCA AATGCA AATGCA AA
25322119 AGGTACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AATGCA
Found at i:25330929 original size:21 final size:20
Alignment explanation
Indices: 25330905--25330950 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
25330895 GTTTAATTAT
25330905 ATTTTAAATAAAATAAAATAA
1 ATTTTAAATAAAATAAAA-AA
**
25330926 ATTTTCATTTAAAATAAAAAA
1 ATTTT-AAATAAAATAAAAAA
25330947 ATTT
1 ATTT
25330951 ATTTAAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTTAAATAAAATAAAAAA
Found at i:25330939 original size:22 final size:19
Alignment explanation
Indices: 25330913--25330966 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
25330903 ATATTTTAAA
25330913 TAAAATAAAATAAATTTTCATT
1 TAAAATAAAA-AAA-TTT-ATT
25330935 TAAAATAAAAAAATTTATT
1 TAAAATAAAAAAATTTATT
25330954 T-AAATACAAAAAA
1 TAAAATA-AAAAAA
25330967 ACAAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.16
19 10 0.32
20 3 0.10
21 3 0.10
22 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATAAAAAAATTTATT
Found at i:25330956 original size:19 final size:21
Alignment explanation
Indices: 25330913--25330967 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
25330903 ATATTTTAAA
25330913 TAAAATAAAATAAATTTTCATT
1 TAAAATAAAA-AAATTTTCATT
25330935 TAAAATAAAAAAA-TTT-ATT
1 TAAAATAAAAAAATTTTCATT
*
25330954 TAAATACAAAAAAA
1 TAAA-ATAAAAAAA
25330968 CAAATTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 11 0.35
21 3 0.10
22 10 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAATAAAAAAATTTTCATT
Found at i:25331019 original size:19 final size:19
Alignment explanation
Indices: 25330992--25331032 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
25330982 TAAAAAATAA
*
25330992 AATAATTTAATTTTTTTTT
1 AATAATTTAATATTTTTTT
* *
25331011 AATATTTTAGTATTTTTTT
1 AATAATTTAATATTTTTTT
25331030 AAT
1 AAT
25331033 TTATCAGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
AATAATTTAATATTTTTTT
Found at i:25349433 original size:22 final size:22
Alignment explanation
Indices: 25349408--25349467 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
25349398 TTATAAATTT
*
25349408 TATTTATTTAAATTTATATGAA
1 TATTTATTTAAATTTATATAAA
* *
25349430 TATTAATTTAGATTGTATATAAA
1 TATTTATTTAAATT-TATATAAA
*
25349453 T-TTTTTTTATAATTT
1 TATTTATTTA-AATTT
25349468 TTAAGATTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TATTTATTTAAATTTATATAAA
Found at i:25357837 original size:24 final size:24
Alignment explanation
Indices: 25357806--25357851 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25357796 AAAAAATTAA
25357806 TAAAAATA-AAAAATCCCTAAAATT
1 TAAAAATATAAAAA-CCCTAAAATT
*
25357830 TAAAAATATAAAAACCTTAAAA
1 TAAAAATATAAAAACCCTAAAA
25357852 ATAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAAAATATAAAAACCCTAAAATT
Found at i:25357858 original size:24 final size:24
Alignment explanation
Indices: 25357807--25357859 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
25357797 AAAAATTAAT
* *
25357807 AAAAATAAAAAATCCCTAAAATTT
1 AAAAATAAAAAATCCCTAAAAATA
*
25357831 AAAAATATAAAAA-CCTTAAAAATA
1 AAAAATA-AAAAATCCCTAAAAATA
25357855 AAAAA
1 AAAAA
25357860 AACTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (24 bp):
AAAAATAAAAAATCCCTAAAAATA
Found at i:25357908 original size:19 final size:19
Alignment explanation
Indices: 25357864--25357910 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
25357854 AAAAAAAACT
*
25357864 AAAATTTCTTAAAAAATGTA
1 AAAATTT-TAAAAAAATGTA
*
25357884 ACAATTTTAAAAAAAT-TCA
1 AAAATTTTAAAAAAATGT-A
25357903 AAAATTTT
1 AAAATTTT
25357911 TGAAAAACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATTTTAAAAAAATGTA
Found at i:25358528 original size:3 final size:3
Alignment explanation
Indices: 25358520--25358576 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
25358510 TTCTTAAATG
25358520 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25358568 TAT TAT TAT
1 TAT TAT TAT
25358577 ATGTTCAACT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25364624 original size:29 final size:29
Alignment explanation
Indices: 25364586--25364646 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
25364576 GTACTGAGAA
25364586 AAAAGAAATACGACAGCTCTTTTGATGAG
1 AAAAGAAATACGACAGCTCTTTTGATGAG
*
25364615 AAAAGAAATACGACTGCTCTTTTGATGAG
1 AAAAGAAATACGACAGCTCTTTTGATGAG
25364644 AAA
1 AAA
25364647 TGTACAAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.25
Consensus pattern (29 bp):
AAAAGAAATACGACAGCTCTTTTGATGAG
Found at i:25371224 original size:35 final size:35
Alignment explanation
Indices: 25371184--25371253 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
25371174 ATGTGATATC
*
25371184 GTTCAACCTTATCCAATTAATAAATGTGGAATTAT
1 GTTCAAACTTATCCAATTAATAAATGTGGAATTAT
*
25371219 GTTCAAACTTATCTAATTAATAAATGTGGAATTAT
1 GTTCAAACTTATCCAATTAATAAATGTGGAATTAT
25371254 AGTCAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (35 bp):
GTTCAAACTTATCCAATTAATAAATGTGGAATTAT
Found at i:25374358 original size:2 final size:2
Alignment explanation
Indices: 25374351--25374379 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25374341 TATCAACCCT
25374351 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
25374380 TTTAAGTTTC
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:25374626 original size:3 final size:3
Alignment explanation
Indices: 25374620--25374645 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25374610 TCATCATCTT
25374620 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
25374646 ATATCATCAG
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:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:25376474 original size:2 final size:2
Alignment explanation
Indices: 25376467--25376496 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25376457 ATGAATTGTT
25376467 TA TA TA TA TA TA TA -A 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
25376497 GGATTATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25376485 original size:15 final size:15
Alignment explanation
Indices: 25376467--25376495 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25376457 ATGAATTGTT
25376467 TATATATATATATAA
1 TATATATATATATAA
25376482 TATATATATATATA
1 TATATATATATATA
25376496 TGGATTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:25376486 original size:13 final size:13
Alignment explanation
Indices: 25376468--25376493 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25376458 TGAATTGTTT
25376468 ATATATATATATA
1 ATATATATATATA
25376481 ATATATATATATA
1 ATATATATATATA
25376494 TATGGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:25384546 original size:32 final size:32
Alignment explanation
Indices: 25384505--25384569 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
25384495 CTCCTCTAAT
*
25384505 CCACTCACAAACAAACATACAAACCCATAAGA
1 CCACTCACAAACAAAAATACAAACCCATAAGA
*
25384537 CCACTCACAAATAAAAATACAAACCCATAAGA
1 CCACTCACAAACAAAAATACAAACCCATAAGA
25384569 C
1 C
25384570 GTAGAGCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.54, C:0.32, G:0.03, T:0.11
Consensus pattern (32 bp):
CCACTCACAAACAAAAATACAAACCCATAAGA
Found at i:25384786 original size:52 final size:52
Alignment explanation
Indices: 25384730--25384835 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
25384720 TTCCTGTAAC
* * * * * *
25384730 TCAAACTTGCCTATTAAAAATCTTTTTTCTTTTAAAATTTTTCTCTTGCAAG
1 TCAAACTTACCTATTAAAAATCATATTTCTCTTAAAATTCTTCTCTTACAAG
* *
25384782 TCAAACTTACCTATTAAGAATCATATTTCTCTTAAAATTCTTCTTTTACAAG
1 TCAAACTTACCTATTAAAAATCATATTTCTCTTAAAATTCTTCTCTTACAAG
25384834 TC
1 TC
25384836 TTCTTGTCCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (52 bp):
TCAAACTTACCTATTAAAAATCATATTTCTCTTAAAATTCTTCTCTTACAAG
Found at i:25384878 original size:11 final size:11
Alignment explanation
Indices: 25384860--25384901 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
25384850 GCAATATCTG
25384860 ACAAATCTCAA
1 ACAAATCTCAA
* *
25384871 ATAAATCTCTA
1 ACAAATCTCAA
*
25384882 ACAAATTTCAA
1 ACAAATCTCAA
25384893 ACAAATCTC
1 ACAAATCTC
25384902 TTATAAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:25384885 original size:22 final size:22
Alignment explanation
Indices: 25384860--25384902 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25384850 GCAATATCTG
*
25384860 ACAAATCTCAAATAAATCTCTA
1 ACAAATCTCAAACAAATCTCTA
*
25384882 ACAAATTTCAAACAAATCTCT
1 ACAAATCTCAAACAAATCTCT
25384903 TATAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (22 bp):
ACAAATCTCAAACAAATCTCTA
Found at i:25392332 original size:29 final size:30
Alignment explanation
Indices: 25392289--25392351 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 30
25392279 CTGTTTTATG
25392289 TTATGACAAG-AAGAAAGACGTATTGCATT
1 TTATGACAAGAAAGAAAGACGTATTGCATT
*
25392318 TTATGACAATTAGAAGAAAGACGTATTGCATT
1 TTATGACAA-GA-AAGAAAGACGTATTGCATT
25392350 TT
1 TT
25392352 TTGTTAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 9 0.30
32 21 0.70
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (30 bp):
TTATGACAAGAAAGAAAGACGTATTGCATT
Found at i:25396783 original size:28 final size:28
Alignment explanation
Indices: 25396729--25396784 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
25396719 TCCTTGTGAG
*
25396729 TTAAGTTTTTAATTTTTAATGTAACTTC
1 TTAAGTTTTTAATTTTTAATATAACTTC
*
25396757 TTAAGTTTTTAATTTTTAATATTACTTC
1 TTAAGTTTTTAATTTTTAATATAACTTC
25396785 CTGTTAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (28 bp):
TTAAGTTTTTAATTTTTAATATAACTTC
Found at i:25404429 original size:2 final size:2
Alignment explanation
Indices: 25404422--25404456 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25404412 TCTTGCCTAG
25404422 AT AT 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 AT AT A
25404457 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25404461 original size:2 final size:2
Alignment explanation
Indices: 25404456--25404487 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
25404446 ATATATATAT
*
25404456 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25404488 GTTACAGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25412165 original size:15 final size:15
Alignment explanation
Indices: 25412136--25412164 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25412126 TATATACTCT
25412136 TAAAATTATTAAAAA
1 TAAAATTATTAAAAA
25412151 TAAAATT-TTAAAAA
1 TAAAATTATTAAAAA
25412165 AACCTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATTATTAAAAA
Found at i:25414841 original size:17 final size:17
Alignment explanation
Indices: 25414821--25414862 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
25414811 ATTTAATTTG
*
25414821 ATATTATATAAAATTAT
1 ATATAATATAAAATTAT
*
25414838 ATATAATCTAAAATTA-
1 ATATAATATAAAATTAT
*
25414854 ATAAAATAT
1 ATATAATAT
25414863 TATTTTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAAAATTAT
Found at i:25415884 original size:24 final size:24
Alignment explanation
Indices: 25415857--25415905 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
25415847 TTAGACATTA
*
25415857 AGTTTATATATTTAATATATTGAT
1 AGTTTATAAATTTAATATATTGAT
*
25415881 AGTTTATAAATTTTATATATTGAT
1 AGTTTATAAATTTAATATATTGAT
25415905 A
1 A
25415906 ATGAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (24 bp):
AGTTTATAAATTTAATATATTGAT
Found at i:25415936 original size:21 final size:21
Alignment explanation
Indices: 25415912--25415962 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
25415902 GATAATGAAT
*
25415912 TAAAT-AATATTATTTTATTAA
1 TAAATAAATATTA-ATTATTAA
25415933 TAAATAAATATTAATTATT-A
1 TAAATAAATATTAATTATTAA
25415953 -AAATAAATAT
1 TAAATAAATAT
25415963 ATAAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.36
20 1 0.04
21 10 0.36
22 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATAAATATTAATTATTAA
Found at i:25430012 original size:22 final size:21
Alignment explanation
Indices: 25429987--25430029 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25429977 ATTATAACGC
25429987 AGATTCTTTTTCTTTTTCTTTT
1 AGATT-TTTTTCTTTTTCTTTT
* *
25430009 AGATTTTTTTTTTTTTTTTTT
1 AGATTTTTTTCTTTTTCTTTT
25430030 GTAAATCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.09, C:0.07, G:0.05, T:0.79
Consensus pattern (21 bp):
AGATTTTTTTCTTTTTCTTTT
Found at i:25432930 original size:21 final size:22
Alignment explanation
Indices: 25432899--25432939 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
25432889 CCTACTAAGC
25432899 TAATCTTTTTTATTC-TTCCATA
1 TAATCTTTTTT-TTCATTCCATA
25432921 TAAT-TTTTTTTTCATTCCA
1 TAATCTTTTTTTTCATTCCA
25432940 CTCACGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 11 0.61
22 4 0.22
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATCTTTTTTTTCATTCCATA
Found at i:25436571 original size:16 final size:16
Alignment explanation
Indices: 25436541--25436574 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
25436531 TCACAACAAC
25436541 AATTTCTGATATTGGT
1 AATTTCTGATATTGGT
25436557 AATTATCTGAT-TTGGT
1 AATT-TCTGATATTGGT
25436573 AA
1 AA
25436575 AATTGTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (16 bp):
AATTTCTGATATTGGT
Found at i:25443012 original size:24 final size:24
Alignment explanation
Indices: 25442993--25443046 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
25442983 TGTATATATT
25442993 ATATATAAGTTATTTTTATACATAA
1 ATATATAAGTT-TTTTTATACATAA
*
25443018 ATATATAGGTTTTTTTA-A-ATAA
1 ATATATAAGTTTTTTTATACATAA
25443040 ATATATA
1 ATATATA
25443047 GTTCAAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.39
23 1 0.04
24 6 0.21
25 10 0.36
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (24 bp):
ATATATAAGTTTTTTTATACATAA
Found at i:25443584 original size:3 final size:3
Alignment explanation
Indices: 25443576--25443601 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25443566 AGGCATGTCA
25443576 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
25443602 AATATATAAC
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:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:25443993 original size:2 final size:2
Alignment explanation
Indices: 25443986--25444011 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25443976 TCAAATTAGT
25443986 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
25444012 CATAACAAGT
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):
TA
Found at i:25444506 original size:13 final size:13
Alignment explanation
Indices: 25444490--25444538 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
25444480 TTTGTATATT
25444490 ATTTTAATATAAA
1 ATTTTAATATAAA
25444503 ATTTTAATAT---
1 ATTTTAATATAAA
25444513 A-TTTAA-ATAAA
1 ATTTTAATATAAA
25444524 A-TTTAATATAAA
1 ATTTTAATATAAA
25444536 ATT
1 ATT
25444539 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 5 0.16
10 1 0.03
11 6 0.19
12 6 0.19
13 11 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTAATATAAA
Found at i:25444530 original size:20 final size:22
Alignment explanation
Indices: 25444492--25444533 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
25444482 TGTATATTAT
25444492 TTTAATATAAAATTTTAATATA
1 TTTAATATAAAATTTTAATATA
25444514 TTTAA-ATAAAA-TTTAATATA
1 TTTAATATAAAATTTTAATATA
25444534 AAATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 6 0.30
22 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAATATAAAATTTTAATATA
Found at i:25444578 original size:17 final size:16
Alignment explanation
Indices: 25444552--25444589 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
25444542 ATTTTTATTT
25444552 TATAAAATTAAAAATA
1 TATAAAATTAAAAATA
25444568 TATATAAATTAAAAATA
1 TATA-AAATTAAAAATA
25444585 TATAA
1 TATAA
25444590 TTTAATTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATAAAATTAAAAATA
Found at i:25444587 original size:15 final size:16
Alignment explanation
Indices: 25444552--25444594 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
25444542 ATTTTTATTT
25444552 TATA-AAATTAAAAATA
1 TATATAAATT-AAAATA
25444568 TATATAAATTAAAA-A
1 TATATAAATTAAAATA
*
25444583 TATATAATTTAA
1 TATATAAATTAA
25444595 TTCGATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 12 0.48
16 8 0.32
17 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TATATAAATTAAAATA
Found at i:25444844 original size:22 final size:21
Alignment explanation
Indices: 25444819--25444911 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 21
25444809 AATTATTATA
25444819 ATTTAAAATTATATGAAATTTT
1 ATTTAAAATTATAT-AAATTTT
25444841 ATTTAAAAAATTATATAAATTTT
1 ATTT--AAAATTATATAAATTTT
*
25444864 A-TTAAAATTTTATACGAGATTTAT
1 ATTTAAAATTATATA--A-ATTT-T
* *
25444888 ATTTACAAATGATAAAAATTTT
1 ATTTA-AAATTATATAAATTTT
25444910 AT
1 AT
25444912 ATAATTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
20 10 0.17
22 10 0.17
23 16 0.27
24 13 0.22
25 3 0.05
26 7 0.12
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTTAAAATTATATAAATTTT
Found at i:25444854 original size:24 final size:22
Alignment explanation
Indices: 25444823--25444870 Score: 78
Period size: 24 Copynumber: 2.1 Consensus size: 22
25444813 ATTATAATTT
25444823 AAAATTATATGAAATTTTATTTAA
1 AAAATTATAT-AAATTTTA-TTAA
25444847 AAAATTATATAAATTTTATTAA
1 AAAATTATATAAATTTTATTAA
25444869 AA
1 AA
25444871 TTTTATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.25
23 8 0.33
24 10 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AAAATTATATAAATTTTATTAA
Found at i:25444877 original size:46 final size:45
Alignment explanation
Indices: 25444827--25444919 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 45
25444817 TAATTTAAAA
* * *
25444827 TTATATGAAATTT-TATTTAAAAAATTATATAAATTTTATTAAAATT
1 TTATACGAAATTTATATTT-AAAAATGATAAAAATTTTA-TAAAATT
* * *
25444873 TTATACGAGATTTATATTTACAAATGATAAAAATTTTATATAATT
1 TTATACGAAATTTATATTTAAAAATGATAAAAATTTTATAAAATT
25444918 TT
1 TT
25444920 TTAATTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 8 0.20
46 27 0.68
47 5 0.12
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (45 bp):
TTATACGAAATTTATATTTAAAAATGATAAAAATTTTATAAAATT
Found at i:25444930 original size:14 final size:14
Alignment explanation
Indices: 25444911--25444956 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
25444901 AAAAATTTTA
25444911 TATAATTTTTTAAT
1 TATAATTTTTTAAT
*
25444925 TATAA-TTTGTAA-
1 TATAATTTTTTAAT
*
25444937 -ATAATTTTTTTAT
1 TATAATTTTTTAAT
25444950 TATAATT
1 TATAATT
25444957 AAATAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 6 0.23
14 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
TATAATTTTTTAAT
Found at i:25444946 original size:25 final size:24
Alignment explanation
Indices: 25444904--25444964 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
25444894 AAATGATAAA
*
25444904 AATTTTATATAATTTTTTAATTAT
1 AATTTTAAATAATTTTTTAATTAT
*
25444928 AATTTGTAAATAATTTTTTTATTAT
1 AATTT-TAAATAATTTTTTAATTAT
25444953 AA--TTAAATAATT
1 AATTTTAAATAATT
25444965 ATAAAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 9 0.26
23 1 0.03
24 5 0.15
25 19 0.56
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
AATTTTAAATAATTTTTTAATTAT
Found at i:25478096 original size:42 final size:42
Alignment explanation
Indices: 25478049--25478135 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
25478039 AAATTAAAGT
25478049 TGTCATATATAATTAAATAAACGTCAAAAACAGGTGAGAAAA
1 TGTCATATATAATTAAATAAACGTCAAAAACAGGTGAGAAAA
25478091 TGTCATATATAATTAAATAAACGTCAAAAACAGGTGAGAAAA
1 TGTCATATATAATTAAATAAACGTCAAAAACAGGTGAGAAAA
25478133 TGT
1 TGT
25478136 ACTTTGTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.25
Consensus pattern (42 bp):
TGTCATATATAATTAAATAAACGTCAAAAACAGGTGAGAAAA
Found at i:25481995 original size:16 final size:16
Alignment explanation
Indices: 25481974--25482004 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25481964 ACTTGTTTAT
25481974 ATAAATATACATATAA
1 ATAAATATACATATAA
*
25481990 ATAAATATATATATA
1 ATAAATATACATATA
25482005 TGTATTACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATATACATATAA
Found at i:25483978 original size:28 final size:29
Alignment explanation
Indices: 25483947--25484029 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 29
25483937 CTAAATTGAG
25483947 GAAAATTTAGAAATAAAACTTATAAAA-A
1 GAAAATTTAGAAATAAAACTTATAAAAGA
** * * *
25483975 GAAAATTTCTAAAT-AGAC-CA-AAATAGT
1 GAAAATTTAGAAATAAAACTTATAAA-AGA
25484002 GAAAAATTTAGAAATAAAACTTATAAAA
1 G-AAAATTTAGAAATAAAACTTATAAAA
25484030 TTTTTTTTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
25 3 0.08
26 2 0.05
27 4 0.10
28 23 0.57
29 3 0.08
30 2 0.05
31 3 0.08
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.25
Consensus pattern (29 bp):
GAAAATTTAGAAATAAAACTTATAAAAGA
Found at i:25484040 original size:56 final size:55
Alignment explanation
Indices: 25483921--25484086 Score: 172
Period size: 56 Copynumber: 3.0 Consensus size: 55
25483911 CTAACAAAAG
* * *
25483921 TTTTTTCTAAATAGATCTAAAT-TGAGGAAAATTTAGAAATAAAACTTATAAAAAGA
1 TTTTTTCTAAATAGACCAAAATGTGA--AAAATTTAGAAATAAAACTTATAAAATGA
*** **
25483977 AAATTTCTAAATAGACCAAAATAGTGAAAAATTTAGAAATAAAACTTATAAAATTT
1 TTTTTTCTAAATAGACCAAAAT-GTGAAAAATTTAGAAATAAAACTTATAAAATGA
* * * * *
25484033 TTTTTTCTAAATTGGCCCAAATGCTGAAAAATTAAGAAATAAAACTTGTAAAAT
1 TTTTTTCTAAATAGACCAAAATG-TGAAAAATTTAGAAATAAAACTTATAAAAT
25484087 AAAAAATAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
55 1 0.01
56 87 0.96
58 3 0.03
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.33
Consensus pattern (55 bp):
TTTTTTCTAAATAGACCAAAATGTGAAAAATTTAGAAATAAAACTTATAAAATGA
Found at i:25485248 original size:8 final size:7
Alignment explanation
Indices: 25485164--25485356 Score: 70
Period size: 8 Copynumber: 27.3 Consensus size: 7
25485154 AGCCCATTTG
25485164 TTTATT-
1 TTTATTA
25485170 TTTATT-
1 TTTATTA
*
25485176 TTTATTT
1 TTTATTA
25485183 TTTATCTA
1 TTTAT-TA
*
25485191 TTTATAAA
1 TTTAT-TA
*
25485199 TATATATA
1 TTTAT-TA
*
25485207 TCT-TTA
1 TTTATTA
25485213 -TTATTA
1 TTTATTA
25485219 TTTATCTA
1 TTTAT-TA
*
25485227 TTAATT-
1 TTTATTA
25485233 TTT-TTA
1 TTTATTA
25485239 TTTATCTA
1 TTTAT-TA
25485247 TTAATATATA
1 TT--TAT-TA
**
25485257 TACATT-
1 TTTATTA
25485263 TTTATTA
1 TTTATTA
25485270 TTTATTAA
1 TTTATT-A
* *
25485278 TATATTT
1 TTTATTA
25485285 TTTATTA
1 TTTATTA
25485292 TTTATCTA
1 TTTAT-TA
*
25485300 TTAATGTA
1 TTTAT-TA
25485308 TTT-TT-
1 TTTATTA
25485313 TTTA-TA
1 TTTATTA
25485319 TTTATCTA
1 TTTAT-TA
25485327 TTAATATT-
1 TT--TATTA
25485335 TTTA-TA
1 TTTATTA
25485341 TTTATCTA
1 TTTAT-TA
25485349 -TTATTA
1 TTTATTA
25485355 TT
1 TT
25485357 ATTGTTATCA
Statistics
Matches: 143, Mismatches: 21, Indels: 45
0.68 0.10 0.22
Matches are distributed among these distances:
5 8 0.06
6 39 0.27
7 35 0.24
8 51 0.36
9 1 0.01
10 9 0.06
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.66
Consensus pattern (7 bp):
TTTATTA
Found at i:25485264 original size:27 final size:25
Alignment explanation
Indices: 25485231--25485351 Score: 124
Period size: 27 Copynumber: 4.8 Consensus size: 25
25485221 TATCTATTAA
25485231 TTTTTTTATTTATCTATTAATATAT
1 TTTTTTTATTTATCTATTAATATAT
* *
25485256 ATACATTTTTA-TTATTTATTAATATAT
1 -T--TTTTTTATTTATCTATTAATATAT
*
25485283 TTTTTATTATTTATCTATTAATGTATT
1 TTTTT-TTATTTATCTATTAATATA-T
25485310 TTTTTTATATTTATCTATT-A-ATA-
1 TTTTTT-TATTTATCTATTAATATAT
*
25485333 TTTTTATATTTATCTATTA
1 TTTTTTTATTTATCTATTA
25485352 TTATTATTGT
Statistics
Matches: 81, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
22 12 0.15
23 5 0.06
24 3 0.04
25 5 0.06
26 17 0.21
27 33 0.41
28 6 0.07
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (25 bp):
TTTTTTTATTTATCTATTAATATAT
Found at i:25485321 original size:49 final size:53
Alignment explanation
Indices: 25485172--25485351 Score: 171
Period size: 49 Copynumber: 3.4 Consensus size: 53
25485162 TGTTTATTTT
* * *
25485172 TATTTTTATTTTTTATCTATTTATAAATATATATATCTTTATTATTATTTATCT-ATTA
1 TATTTTTATTATTTATCTA--T-T-AATATATATA-ATTT-TTATTATTTATCTAATAA
25485230 -ATTTTT-TTATTTATCTATTAATATATATACATTTTTATTATTTAT-TAAT-A
1 TATTTTTATTATTTATCTATTAATATATATA-ATTTTTATTATTTATCTAATAA
* * *
25485280 TATTTTTTATTATTTATCTATTAATGTAT-T-TTTTTTA-TATTTATCTATTAA
1 TA-TTTTTATTATTTATCTATTAATATATATAATTTTTATTATTTATCTAATAA
25485331 TATTTTTA-TATTTATCTATTA
1 TATTTTTATTATTTATCTATTA
25485352 TTATTATTGT
Statistics
Matches: 110, Mismatches: 6, Indels: 21
0.80 0.04 0.15
Matches are distributed among these distances:
49 20 0.18
50 17 0.15
51 17 0.15
52 19 0.17
53 20 0.18
54 1 0.01
56 10 0.09
57 6 0.05
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (53 bp):
TATTTTTATTATTTATCTATTAATATATATAATTTTTATTATTTATCTAATAA
Found at i:25485329 original size:53 final size:50
Alignment explanation
Indices: 25485172--25485351 Score: 145
Period size: 53 Copynumber: 3.4 Consensus size: 50
25485162 TGTTTATTTT
* * *
25485172 TATTTTTATTTTTTATCTATTTATAAATATATATATC-TTTATTATTATTTATCTAT
1 TATTTTTATTATTTATCTA--T-T-AATATATATA-CATTT-TTATTATCTAT-TAA
*
25485228 TAATTTTT-TTATTTATCTATTAATATATATACATTTTTATTATTTATTAATA
1 T-ATTTTTATTATTTATCTATTAATATATATACATTTTTATTATCTATT-A-A
* **
25485280 TATTTTTTATTATTTATCTATTAATGTAT-T-TTTTTTATATTTATCTATTAA
1 TA-TTTTTATTATTTATCTATTAATATATATACATTTT-TA-TTATCTATTAA
25485331 TATTTTTA-TATTTATCTATTA
1 TATTTTTATTATTTATCTATTA
25485352 TTATTATTGT
Statistics
Matches: 110, Mismatches: 6, Indels: 23
0.79 0.04 0.17
Matches are distributed among these distances:
49 13 0.12
50 7 0.06
51 21 0.19
52 23 0.21
53 28 0.25
54 1 0.01
56 11 0.10
57 6 0.05
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (50 bp):
TATTTTTATTATTTATCTATTAATATATATACATTTTTATTATCTATTAA
Found at i:25485329 original size:80 final size:80
Alignment explanation
Indices: 25485181--25485333 Score: 199
Period size: 80 Copynumber: 1.9 Consensus size: 80
25485171 TTATTTTTAT
*
25485181 TTTTTATCTATTTATAAATATATATATCTTTATTATTATTTATCTATTAATTTTTTTATTTATCT
1 TTTTTATCTATTTATAAATATATATATCTTTATTATTATCTATCTATTAATTTTTTTATTTATCT
25485246 ATTAATATATATACA
66 ATTAATATATATACA
* *
25485261 TTTTTAT-TATTTATTAATATAT-T-T-TTTATTATTTATCTAT-TAATGTATTTTTTTTATATT
1 TTTTTATCTATTTATAAATATATATATCTTTATTA-TTATCTATCT-AT-TA-ATTTTTT-TATT
25485321 TATCTATTAATAT
61 TATCTATTAATAT
25485334 TTTTATATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
76 8 0.12
77 10 0.15
78 3 0.05
79 20 0.31
80 24 0.37
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (80 bp):
TTTTTATCTATTTATAAATATATATATCTTTATTATTATCTATCTATTAATTTTTTTATTTATCT
ATTAATATATATACA
Found at i:25485339 original size:22 final size:23
Alignment explanation
Indices: 25485311--25485356 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
25485301 TAATGTATTT
25485311 TTTTTA-TATTTATCTATTAATA
1 TTTTTATTATTTATCTATTAATA
*
25485333 TTTTTA-TATTTATCTATTATTA
1 TTTTTATTATTTATCTATTAATA
25485355 TT
1 TT
25485357 ATTGTTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTATTATTTATCTATTAATA
Found at i:25485644 original size:21 final size:21
Alignment explanation
Indices: 25485614--25485658 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25485604 TTCGAACAGC
25485614 TTTAGGAATTTATGAGAATTTT
1 TTTAGGAATTTATGA-AATTTT
* *
25485636 TTTA-GAATTTTTGAAGTTTT
1 TTTAGGAATTTATGAAATTTT
25485656 TTT
1 TTT
25485659 CTGGAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.58
Consensus pattern (21 bp):
TTTAGGAATTTATGAAATTTT
Found at i:25486213 original size:12 final size:12
Alignment explanation
Indices: 25486173--25486239 Score: 66
Period size: 12 Copynumber: 5.6 Consensus size: 12
25486163 AATTATTTAG
25486173 TATTTCTTATC-T
1 TATTT-TTATCTT
* *
25486185 TATTTTATTTTTT
1 TATTTT-TATCTT
25486198 TATTTTTATCTT
1 TATTTTTATCTT
* *
25486210 TATTTTTGTTTT
1 TATTTTTATCTT
25486222 TATTTTTAT-TT
1 TATTTTTATCTT
25486233 TATTTTT
1 TATTTTT
25486240 TTGATTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
11 10 0.22
12 29 0.63
13 7 0.15
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (12 bp):
TATTTTTATCTT
Found at i:25486240 original size:24 final size:23
Alignment explanation
Indices: 25486173--25486241 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 23
25486163 AATTATTTAG
*
25486173 TATTTCTTATCTTATTTTATTTTTT
1 TATTT-TTATTTTATTTT-TTTTTT
*
25486198 TATTTTTATCTTTATTTTTGTTTT
1 TATTTTTAT-TTTATTTTTTTTTT
25486222 TATTTTTATTTTATTTTTTT
1 TATTTTTATTTTATTTTTTT
25486242 GATTTTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 10 0.25
24 18 0.45
25 12 0.30
ACGTcount: A:0.14, C:0.04, G:0.01, T:0.80
Consensus pattern (23 bp):
TATTTTTATTTTATTTTTTTTTT
Found at i:25486247 original size:6 final size:6
Alignment explanation
Indices: 25486184--25486239 Score: 69
Period size: 6 Copynumber: 9.3 Consensus size: 6
25486174 ATTTCTTATC
* * *
25486184 TTATTT TATTTTT TTATTT TTATCT TTATTT TTGTTT TTATTT TTA-TT
1 TTATTT T-TATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
25486232 TTATTT TT
1 TTATTT TT
25486240 TTGATTTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
5 5 0.12
6 32 0.76
7 5 0.12
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (6 bp):
TTATTT
Found at i:25486328 original size:58 final size:59
Alignment explanation
Indices: 25486260--25486485 Score: 273
Period size: 59 Copynumber: 3.8 Consensus size: 59
25486250 TTAAATAAAA
*
25486260 TTCTAAAAAAATATTTTTGA-AGAGAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTT
1 TTCTAAAAAAATATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTT
* * * *
25486319 TTCTAAAAAAATATTTTTGAGTAGAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGTT
1 TTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTT
* * *
25486378 TT-TTAAAAAATATTTTCGAGAAAAAGTTGAAAGTATCAA-TTTTCTTTGGAAATAA-TT
1 TTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAGTT
* * *
25486435 TTCTAAAAAAAGTTTTTTTTTA-AGAAAAGTTGAATGTATCAATTTTTCTTG
1 TTCTAAAAAAA--TATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTG
25486486 TACAAAAGCA
Statistics
Matches: 145, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
57 8 0.06
58 48 0.33
59 58 0.40
60 26 0.18
61 5 0.03
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (59 bp):
TTCTAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTT
Found at i:25490354 original size:17 final size:17
Alignment explanation
Indices: 25490332--25490366 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
25490322 CATATACAGA
25490332 TGTCGACAGAGAATGTG
1 TGTCGACAGAGAATGTG
25490349 TGTCGACAGAGAATGTG
1 TGTCGACAGAGAATGTG
25490366 T
1 T
25490367 ATCCCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (17 bp):
TGTCGACAGAGAATGTG
Found at i:25492210 original size:2 final size:2
Alignment explanation
Indices: 25492205--25492233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25492195 GTGTGTGTGT
25492205 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
25492234 GGATGGCGTG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25509840 original size:2 final size:2
Alignment explanation
Indices: 25509833--25509858 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25509823 TTGGGGGCAA
25509833 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
25509859 TATTTGAAAA
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:25511975 original size:20 final size:21
Alignment explanation
Indices: 25511936--25511975 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
25511926 CACAGTACCA
*
25511936 TTGGAGGATTTTTCAGTCTCC
1 TTGGAGGATTGTTCAGTCTCC
*
25511957 TTGGAGGA-TGTTGAGTCTC
1 TTGGAGGATTGTTCAGTCTC
25511976 TGTTGACTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (21 bp):
TTGGAGGATTGTTCAGTCTCC
Found at i:25514450 original size:7 final size:7
Alignment explanation
Indices: 25514440--25514473 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
25514430 GATAAAAATT
25514440 TTAAAAA
1 TTAAAAA
25514447 TTAAAAA
1 TTAAAAA
*
25514454 ATAAAAA
1 TTAAAAA
25514461 TTAATAAA
1 TTAA-AAA
25514469 TTAAA
1 TTAAA
25514474 TCAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:25521023 original size:25 final size:25
Alignment explanation
Indices: 25520989--25521038 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
25520979 CATACTTAGT
25520989 TGCTTCAACCACTAACACACTAACA
1 TGCTTCAACCACTAACACACTAACA
*
25521014 TGCTTCAACCACTAACACATTAACA
1 TGCTTCAACCACTAACACACTAACA
25521039 GAACAACATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.34, G:0.04, T:0.22
Consensus pattern (25 bp):
TGCTTCAACCACTAACACACTAACA
Found at i:25522422 original size:2 final size:2
Alignment explanation
Indices: 25522415--25522440 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25522405 AATGTGGAGT
25522415 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
25522441 AGAATCAACA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:25523700 original size:2 final size:2
Alignment explanation
Indices: 25523693--25523717 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25523683 GGTTCACTTG
25523693 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 A
25523718 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25523722 original size:2 final size:2
Alignment explanation
Indices: 25523717--25523746 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25523707 ATATATATAT
25523717 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
25523747 TAAATATCTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25525959 original size:4 final size:4
Alignment explanation
Indices: 25525950--25525974 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25525940 ATAAAATCCA
25525950 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
25525975 GTAATTCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:25529910 original size:2 final size:2
Alignment explanation
Indices: 25529905--25529943 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25529895 AAACACACGC
25529905 AT AT AT AT 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 AT AT AT AT A
25529944 AAGGAGGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25532488 original size:17 final size:18
Alignment explanation
Indices: 25532457--25532490 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25532447 TAAAAATAAG
25532457 AATAACTTTAATAATTTA
1 AATAACTTTAATAATTTA
*
25532475 AATAA-TTTATTAATTT
1 AATAACTTTAATAATTT
25532491 TATAAATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAACTTTAATAATTTA
Found at i:25535557 original size:6 final size:6
Alignment explanation
Indices: 25535520--25535556 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
25535510 CCACTGGATC
25535520 TTTTC- TTTTCT TTTTCT TTTTCT TTTT-T TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
25535557 TGGGGGGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 15 0.48
6 16 0.52
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
TTTTCT
Found at i:25535557 original size:17 final size:17
Alignment explanation
Indices: 25535520--25535555 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25535510 CCACTGGATC
25535520 TTTTCTTTTCTTTTTCT
1 TTTTCTTTTCTTTTTCT
25535537 TTTTCTTTT-TTTTT-T
1 TTTTCTTTTCTTTTTCT
25535552 TTTT
1 TTTT
25535556 TTGGGGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 5 0.26
17 9 0.47
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTCT
Found at i:25539456 original size:7 final size:7
Alignment explanation
Indices: 25539439--25539507 Score: 65
Period size: 7 Copynumber: 10.0 Consensus size: 7
25539429 TGATATAATA
25539439 TTAAA-T
1 TTAAATT
25539445 TTAAATT
1 TTAAATT
25539452 TTAAATT
1 TTAAATT
25539459 TTAAATT
1 TTAAATT
*
25539466 TT-GA-T
1 TTAAATT
25539471 TTAAATT
1 TTAAATT
25539478 TGATAAAATT
1 T--T-AAATT
*
25539488 TTAATTT
1 TTAAATT
25539495 TTAAA-T
1 TTAAATT
25539501 TTAAATT
1 TTAAATT
25539508 AAAATAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
5 3 0.06
6 13 0.25
7 28 0.54
8 1 0.02
9 1 0.02
10 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (7 bp):
TTAAATT
Found at i:25539730 original size:21 final size:21
Alignment explanation
Indices: 25539704--25539743 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25539694 ATTTGAACGA
*
25539704 TAAATTTAATTTAATTTAATT
1 TAAATTTAATTTAAATTAATT
*
25539725 TAAATTTTATTTAAATTAA
1 TAAATTTAATTTAAATTAA
25539744 AATCAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAATTTAATTTAAATTAATT
Found at i:25539736 original size:11 final size:11
Alignment explanation
Indices: 25539704--25539741 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
25539694 ATTTGAACGA
25539704 TAAATTTAATT
1 TAAATTTAATT
25539715 T-AATTTAATT
1 TAAATTTAATT
*
25539725 TAAATTTTATT
1 TAAATTTAATT
25539736 TAAATT
1 TAAATT
25539742 AAAATCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TAAATTTAATT
Found at i:25539736 original size:16 final size:16
Alignment explanation
Indices: 25539706--25539744 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
25539696 TTGAACGATA
25539706 AATTT-AATTTAATTT
1 AATTTAAATTTAATTT
*
25539721 AATTTAAATTTTATTT
1 AATTTAAATTTAATTT
*
25539737 AAATTAAA
1 AATTTAAA
25539745 ATCAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTTAAATTTAATTT
Found at i:25541748 original size:1 final size:1
Alignment explanation
Indices: 25541742--25541768 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
25541732 TGTGCGTGTG
25541742 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
25541769 GCAGTCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:25542681 original size:3 final size:3
Alignment explanation
Indices: 25542673--25542700 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25542663 CATTAAACAC
25542673 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
25542701 TAGAAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:25548190 original size:23 final size:21
Alignment explanation
Indices: 25548147--25548193 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 21
25548137 CGTACTTATA
25548147 AATAATATTATATTAATAAAT
1 AATAATATTATATTAATAAAT
*
25548168 AATATTATTATATGGTAATAAAT
1 AATAATATTATAT--TAATAAAT
25548191 AAT
1 AAT
25548194 TCAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.52
23 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
AATAATATTATATTAATAAAT
Found at i:25548207 original size:52 final size:52
Alignment explanation
Indices: 25548146--25548394 Score: 142
Period size: 52 Copynumber: 4.7 Consensus size: 52
25548136 TCGTACTTAT
* *
25548146 AAATAATATTATATTA-ATAAAT-AATATTATTATATGGTAATAAATAATTCAA
1 AAATAATATTATAATATATAAATAAATAATATTAT-T-GTAATAAATAATTCAA
* *
25548198 AAATAATATTATAATATATGAATAAATAATATTATTTTAATAAATAATAT-AA
1 AAATAATATTATAATATATAAATAAATAATATTATTGTAATAAATAAT-TCAA
* * * * *
25548250 TAATAAAATATTATAA-AT-TTAATTAATAA-A-TATTATAATAATATAA--GAA
1 -AA-ATAATATTATAATATATAAATAAATAATATTATTGTAATAA-ATAATTCAA
* *
25548299 TAAATAACATATTATTAATAAATAATATACTATTAATATACTATAT-TAATAAATATTATT-AA
1 -AAAT-A-ATATTA-TAATATATAA-ATA--AATAATAT--TAT-TGTAATAAATA--ATTCAA
* *
25548361 TAATAATATTATAATATATGAATAAATAATATTA
1 AAATAATATTATAATATATAAATAAATAATATTA
25548395 AGAATAATAA
Statistics
Matches: 156, Mismatches: 17, Indels: 47
0.71 0.08 0.21
Matches are distributed among these distances:
48 1 0.01
49 6 0.04
50 16 0.10
51 8 0.05
52 38 0.24
53 15 0.10
54 23 0.15
55 7 0.04
56 4 0.03
57 4 0.03
58 8 0.05
59 9 0.06
60 10 0.06
61 5 0.03
62 2 0.01
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (52 bp):
AAATAATATTATAATATATAAATAAATAATATTATTGTAATAAATAATTCAA
Found at i:25548211 original size:23 final size:23
Alignment explanation
Indices: 25548194--25548254 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 23
25548184 AATAAATAAT
25548194 TCAA-AAATAATATTATAATATA
1 TCAATAAATAATATTATAATATA
*
25548216 TGAATAAATAATATTAT--T-T-
1 TCAATAAATAATATTATAATATA
*
25548235 T-AATAAATAATATAATAATA
1 TCAATAAATAATATTATAATA
25548255 AAATATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 14 0.42
19 1 0.03
20 2 0.06
21 1 0.03
22 3 0.09
23 12 0.36
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TCAATAAATAATATTATAATATA
Found at i:25548226 original size:38 final size:38
Alignment explanation
Indices: 25548144--25548389 Score: 170
Period size: 41 Copynumber: 6.2 Consensus size: 38
25548134 AATCGTACTT
25548144 ATAAATAATATTATATTAATAAATAATATTAT--TATATG-
1 ATAAATAA-A-TA-ATTAATAAATAATATTATAATATATGA
*
25548182 GT-AATAAATAATTCAA-AAATAATATTATAATATATGA
1 ATAAATAAATAATT-AATAAATAATATTATAATATATGA
* *
25548219 ATAAATAATATTATTTTAATAAATAATATAATAATA-A--A
1 ATAAATAA-A-TA-ATTAATAAATAATATTATAATATATGA
* * * *
25548257 ATATTATAAATTTAATTAATAAATATTATAATAATATAAGA
1 ATA-AATAAA--TAATTAATAAATAATATTATAATATATGA
25548298 ATAAATAACATATTATTAATAAATAATATACTATTAATATACT-A
1 ATAAATAA-ATA--ATTAATAAATAATAT--TA-TAATATA-TGA
*
25548342 TATTAATAAATATTATTAAT-AATAATATTATAATATATGA
1 -ATAAATAAATA--ATTAATAAATAATATTATAATATATGA
25548382 ATAAATAA
1 ATAAATAA
25548390 TATTAAGAAT
Statistics
Matches: 172, Mismatches: 13, Indels: 45
0.75 0.06 0.20
Matches are distributed among these distances:
34 15 0.09
35 4 0.02
36 7 0.04
37 6 0.03
38 31 0.18
39 19 0.11
40 17 0.10
41 38 0.22
43 9 0.05
44 19 0.11
45 7 0.04
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (38 bp):
ATAAATAAATAATTAATAAATAATATTATAATATATGA
Found at i:25548300 original size:79 final size:79
Alignment explanation
Indices: 25548144--25548394 Score: 266
Period size: 79 Copynumber: 3.2 Consensus size: 79
25548134 AATCGTACTT
* * * ***
25548144 ATAAATAATATTATATTAATAAATAATATTATTATATGGTA--ATAAA--TAATTCAA-AAATAA
1 ATAAATAATATTATTTTAATAAATAATATAATAATAAAATATTATAAATTTAATT-AATAAATAA
25548204 TATTATAATATATGA
65 TATTATAATATATGA
*
25548219 ATAAATAATATTATTTTAATAAATAATATAATAATAAAATATTATAAATTTAATTAATAAATATT
1 ATAAATAATATTATTTTAATAAATAATATAATAATAAAATATTATAAATTTAATTAATAAATAAT
* *
25548284 ATAATAATATAAGA
66 ATTATAATATATGA
* *
25548298 ATAAATAACA-TATTATTAATAAATAATATACTATTAATATACTATATTAATAAATATT-ATTAA
1 ATAAATAATATTATT-TTAATAAATAATATA--A-TAATA-A-AATATT-ATAAAT-TTAATTAA
25548361 T-AATAATATTATAATATATGA
58 TAAATAATATTATAATATATGA
25548382 ATAAATAATATTA
1 ATAAATAATATTA
25548395 AGAATAATAA
Statistics
Matches: 147, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
75 35 0.24
77 5 0.03
78 6 0.04
79 47 0.32
81 1 0.01
82 5 0.03
83 1 0.01
84 31 0.21
85 14 0.10
86 2 0.01
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (79 bp):
ATAAATAATATTATTTTAATAAATAATATAATAATAAAATATTATAAATTTAATTAATAAATAAT
ATTATAATATATGA
Found at i:25548392 original size:38 final size:39
Alignment explanation
Indices: 25548144--25548394 Score: 202
Period size: 38 Copynumber: 6.3 Consensus size: 39
25548134 AATCGTACTT
25548144 ATAAATAATATTATATTAATAAATAATATTAT--TATATG-
1 ATAAATAATA-T-TATTAATAAATAATATTATAATATATGA
* *
25548182 GT-AATAA-ATAATTCAA-AAATAATATTATAATATATGA
1 ATAAATAATATTATT-AATAAATAATATTATAATATATGA
*
25548219 ATAAATAATATTATTTTAATAAATAATATAATAATA-A--A
1 ATAAATAATATTA--TTAATAAATAATATTATAATATATGA
* * * *
25548257 ATATTATAA-ATTTAATTAATAAATATTATAATAATATAAGA
1 ATA-AATAATA-TT-ATTAATAAATAATATTATAATATATGA
25548298 ATAAATAACATATTATTAATAAATAATATACTATTAATATACT-A
1 ATAAAT-A-ATATTATTAATAAATAATAT--TA-TAATATA-TGA
*
25548342 TATTAATAAATATTATTAAT-AATAATATTATAATATATGA
1 -ATAAAT-AATATTATTAATAAATAATATTATAATATATGA
25548382 ATAAATAATATTA
1 ATAAATAATATTA
25548395 AGAATAATAA
Statistics
Matches: 176, Mismatches: 13, Indels: 48
0.74 0.05 0.20
Matches are distributed among these distances:
34 15 0.09
35 3 0.02
36 7 0.04
37 6 0.03
38 38 0.22
39 16 0.09
40 14 0.08
41 38 0.22
42 3 0.02
43 10 0.06
44 19 0.11
45 7 0.04
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (39 bp):
ATAAATAATATTATTAATAAATAATATTATAATATATGA
Found at i:25548395 original size:35 final size:35
Alignment explanation
Indices: 25548147--25548231 Score: 77
Period size: 34 Copynumber: 2.4 Consensus size: 35
25548137 CGTACTTATA
* *
25548147 AATAATATTATATTAATAAATAATATTAT--TATATGG
1 AATAA-ATAATATTAA-GAATAATATTATAATATAT-G
* *
25548183 TAATAAATAAT-TCAAAAATAATATTATAATATATG
1 -AATAAATAATATTAAGAATAATATTATAATATATG
25548218 AATAAATAATATTA
1 AATAAATAATATTA
25548232 TTTTAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
34 22 0.52
35 6 0.14
36 9 0.21
37 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (35 bp):
AATAAATAATATTAAGAATAATATTATAATATATG
Found at i:25548395 original size:79 final size:79
Alignment explanation
Indices: 25548183--25548407 Score: 214
Period size: 84 Copynumber: 2.8 Consensus size: 79
25548173 TATTATATGG
* * *
25548183 TAATAAATA--ATTCAAAAATAATATTATAATATATGAATAAATAATATTATTTTAATAA-ATAA
1 TAATAAATATTATT-AATAATAATATTATAATATATGAATAAATAATATTA-ATAAATAATATAA
25548245 TATAATAATAAAATAT
64 TATAATAATAAAATAT
* * *
25548261 T-ATAAAT-TTAATTAATAAATATTATAATAATATAAGAATAAATAACATATTATTAATAAATAA
1 TAATAAATATT-ATTAAT-AATAATATTATAATATATGAATAAAT---A-A-TATTAATAAATAA
* **
25548324 TATACTATTAAT-ATACTATAT
59 TATAATA-TAATAATAAAATAT
*
25548345 TAATAAATATTATTAATAATAATATTATAATATATGAATAAATAATATTAA-GAATAATA-AATA
1 TAATAAATATTATTAATAATAATATTATAATATATGAATAAATAATATTAATAAATAATATAATA
25548408 GTTTTATTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 27
0.75 0.09 0.17
Matches are distributed among these distances:
77 9 0.08
78 10 0.08
79 32 0.27
80 1 0.01
81 1 0.01
82 1 0.01
83 7 0.06
84 41 0.34
85 16 0.13
86 2 0.02
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (79 bp):
TAATAAATATTATTAATAATAATATTATAATATATGAATAAATAATATTAATAAATAATATAATA
TAATAATAAAATAT
Found at i:25548404 original size:15 final size:15
Alignment explanation
Indices: 25548208--25548401 Score: 50
Period size: 16 Copynumber: 12.0 Consensus size: 15
25548198 AAATAATATT
*
25548208 ATAATATATGAATAA
1 ATAATATAAGAATAA
**
25548223 ATAATATTATTTTAATAA
1 ATAATA-TA--AGAATAA
*
25548241 ATAATATAATAATAAA
1 ATAATATAAGAAT-AA
* *
25548257 ATATTATAA-ATTTAA
1 ATAATATAAGA-ATAA
* * *
25548272 TTAATA-AATATTATA
1 ATAATATAAGAATA-A
25548287 ATAATATAAGAATAA
1 ATAATATAAGAATAA
**
25548302 ATAACATATTATTAATAA
1 AT-A-ATA-TAAGAATAA
** *
25548320 ATAATATACTATTAA
1 ATAATATAAGAATAA
* **
25548335 TATACTATATTAATAA
1 -ATAATATAAGAATAA
* *
25548351 ATATTATTAATAATAATATT
1 ATA--A-T-ATAAGAATA-A
*
25548371 ATAATATATGAATAA
1 ATAATATAAGAATAA
25548386 ATAATATTAAGAATAA
1 ATAATA-TAAGAATAA
25548402 TAAATAGTTT
Statistics
Matches: 138, Mismatches: 23, Indels: 35
0.70 0.12 0.18
Matches are distributed among these distances:
14 5 0.04
15 43 0.31
16 49 0.36
17 7 0.05
18 23 0.17
19 8 0.06
20 3 0.02
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAATATAAGAATAA
Found at i:25548407 original size:23 final size:23
Alignment explanation
Indices: 25548362--25548407 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
25548352 TATTATTAAT
* *
25548362 AATAATATTATAATATATGAATA
1 AATAATATTAGAATATATAAATA
25548385 AATAATATTAAGAATA-ATAAATA
1 AATAATATT-AGAATATATAAATA
25548408 GTTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
AATAATATTAGAATATATAAATA
Found at i:25548500 original size:15 final size:15
Alignment explanation
Indices: 25548480--25548520 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
25548470 TATAATTATT
*
25548480 TTTTAATATTAATAA
1 TTTTAATATAAATAA
25548495 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
25548511 TTTTAATATA
1 TTTTAATATA
25548521 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:25548523 original size:10 final size:9
Alignment explanation
Indices: 25548483--25548530 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
25548473 AATTATTTTT
*
25548483 TAATATTAA
1 TAATTTTAA
25548492 TAATTTTAA
1 TAATTTTAA
*
25548501 TAA--TAAA
1 TAATTTTAA
25548508 TAATTTTAA
1 TAATTTTAA
25548517 TATATTTTAA
1 TA-ATTTTAA
25548527 TAAT
1 TAAT
25548531 CAATCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 6 0.18
9 18 0.55
10 9 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATTTTAA
Found at i:25548523 original size:26 final size:26
Alignment explanation
Indices: 25548483--25548553 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
25548473 AATTATTTTT
*
25548483 TAATATTAATA-ATTTTAATAATAAA
1 TAATTTTAATATATTTTAATAATAAA
*
25548508 TAATTTTAATATATTTTAATAATCAA
1 TAATTTTAATATATTTTAATAATAAA
* *
25548534 TCATTTTTA-ATATTTTAATA
1 TAATTTTAATATATTTTAATA
25548554 GTTATATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 21 0.51
26 20 0.49
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATTTTAATATATTTTAATAATAAA
Found at i:25563433 original size:21 final size:21
Alignment explanation
Indices: 25563394--25563434 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25563384 AGAAGGGGCA
* *
25563394 AAAGGTATTAAATCAAACCAT
1 AAAGGCATTAAACCAAACCAT
*
25563415 AAAGGCATTAAACCCAACCA
1 AAAGGCATTAAACCAAACCA
25563435 CAAGACCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAGGCATTAAACCAAACCAT
Found at i:25566164 original size:2 final size:2
Alignment explanation
Indices: 25566157--25566186 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25566147 ATGATTATTT
25566157 TA TA TA TA -A 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
25566187 GCGTGTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25575104 original size:31 final size:31
Alignment explanation
Indices: 25575066--25575128 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
25575056 AAACCCACAG
* *
25575066 TTAACCATATTATTGCATTTGATGGGAGACA
1 TTAACCATATTATTCCATTTAATGGGAGACA
25575097 TTAACCATATTATTCCATTTAATGGGAGACA
1 TTAACCATATTATTCCATTTAATGGGAGACA
25575128 T
1 T
25575129 CACTAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (31 bp):
TTAACCATATTATTCCATTTAATGGGAGACA
Found at i:25598991 original size:26 final size:26
Alignment explanation
Indices: 25598962--25599013 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
25598952 TAATTAATTG
25598962 TTTAGAGAGTAGAAATTAAGAAACTC
1 TTTAGAGAGTAGAAATTAAGAAACTC
25598988 TTTAGAGAGTAGAAATTAAGAAACTC
1 TTTAGAGAGTAGAAATTAAGAAACTC
25599014 ACACTAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (26 bp):
TTTAGAGAGTAGAAATTAAGAAACTC
Found at i:25601452 original size:2 final size:2
Alignment explanation
Indices: 25601447--25601473 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25601437 AAAAACATAA
25601447 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
25601474 CACATTCTCC
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:25606594 original size:5 final size:5
Alignment explanation
Indices: 25606584--25606609 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25606574 CTCAATGCTT
25606584 GACTG GACTG GACTG GACTG GACTG G
1 GACTG GACTG GACTG GACTG GACTG G
25606610 GGATACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (5 bp):
GACTG
Done.