Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 17 of 113
Found at i:5768706 original size:22 final size:21
Alignment explanation
Indices: 5768654--5768706 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
5768644 TTGGATTAAT
*
5768654 AAAATATAAATCATATAAAAA
1 AAAATAAAAATCATATAAAAA
** *
5768675 ATTTAGAAAAATCATATGAAAAA
1 A-AAATAAAAATCATAT-AAAAA
5768698 AAAATAAAA
1 AAAATAAAA
5768707 GTTAAAGTTA
Statistics
Matches: 23, Mismatches: 7, Indels: 3
0.70 0.21 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.70
23 6 0.26
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAATAAAAATCATATAAAAA
Found at i:5769072 original size:3 final size:3
Alignment explanation
Indices: 5769064--5769093 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5769054 AAGTCATGCA
*
5769064 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5769094 TTTTATCGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5790437 original size:2 final size:2
Alignment explanation
Indices: 5790432--5790456 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5790422 AAAAACCCAA
5790432 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
5790457 AGTAGCAATC
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:5791761 original size:18 final size:17
Alignment explanation
Indices: 5791710--5791762 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
5791700 TATTGTGAGT
5791710 AATTAATATAAAATATTAA
1 AATT-ATATAAAATA-TAA
* *
5791729 AATTATTTAATATATAA
1 AATTATATAAAATATAA
5791746 AATTATGATAAAATATA
1 AATTAT-ATAAAATATA
5791763 TTTAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AATTATATAAAATATAA
Found at i:5791762 original size:20 final size:19
Alignment explanation
Indices: 5791710--5791763 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
5791700 TATTGTGAGT
5791710 AATTAATATAAAATAT-TAA
1 AATT-ATATAAAATATATAA
*
5791729 AATTAT-T-TAATATATAA
1 AATTATATAAAATATATAA
5791746 AATTATGATAAAATATAT
1 AATTAT-ATAAAATATAT
5791764 TTAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 5 0.17
17 10 0.34
18 2 0.07
19 5 0.17
20 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTATATAAAATATATAA
Found at i:5791786 original size:29 final size:27
Alignment explanation
Indices: 5791709--5791786 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 27
5791699 GTATTGTGAG
*
5791709 TAATTAATATAAAATATTAAAATTATT
1 TAATTAATATAAAATTTTAAAATTATT
5791736 TAA-T-ATATAAAATTATGATAAAATATATT
1 TAATTAATATAAAATT-T--TAAAAT-TATT
*
5791765 TAATTAATAAATAAATTTTAAA
1 TAATTAATATA-AAATTTTAAA
5791787 TTTTAAATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
25 9 0.21
26 2 0.05
27 3 0.07
28 6 0.14
29 11 0.26
30 1 0.02
31 5 0.12
32 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
TAATTAATATAAAATTTTAAAATTATT
Found at i:5799099 original size:11 final size:13
Alignment explanation
Indices: 5799074--5799105 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5799064 TTTCCTCAAT
5799074 TTCTTCCCTCTTC
1 TTCTTCCCTCTTC
5799087 TT-TTCCC-CTTC
1 TTCTTCCCTCTTC
5799098 TTCTTCCC
1 TTCTTCCC
5799106 ACCTTTTCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 10 0.56
13 2 0.11
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (13 bp):
TTCTTCCCTCTTC
Found at i:5810609 original size:21 final size:20
Alignment explanation
Indices: 5810563--5810626 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
5810553 AAATTAAATT
5810563 AATATAATTTTTTTATTA-A
1 AATATAATTTTTTTATTATA
* *
5810582 AA-AT--TTTTTTAATTGTA
1 AATATAATTTTTTTATTATA
*
5810599 ATTATAATTTTTTTATTATA
1 AATATAATTTTTTTATTATA
5810619 AATATAAT
1 AATATAAT
5810627 AAATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.26
17 2 0.06
18 4 0.11
19 2 0.06
20 18 0.51
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
AATATAATTTTTTTATTATA
Found at i:5811837 original size:42 final size:41
Alignment explanation
Indices: 5811781--5811882 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 41
5811771 AACTAGATTT
*
5811781 TTTACAATAGTTACCAAACAACACTA-AAAGATTACCAAAATTC
1 TTTAAAAT-GTTACCAAAC-ACACTACAAAGATTACC-AAATTC
* * *
5811824 TTTAAAATGTTACCAAACACAGTACAAAGCTTATCAAATTC
1 TTTAAAATGTTACCAAACACACTACAAAGATTACCAAATTC
5811865 -TTACAAATGATTACCAAA
1 TTTA-AAATG-TTACCAAA
5811883 ATACTATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 3 0.06
41 16 0.31
42 26 0.50
43 7 0.13
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (41 bp):
TTTAAAATGTTACCAAACACACTACAAAGATTACCAAATTC
Found at i:5812499 original size:5 final size:5
Alignment explanation
Indices: 5812491--5812517 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5812481 CTCTTCTCTT
5812491 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
5812518 TACATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5815471 original size:582 final size:581
Alignment explanation
Indices: 5814305--5816049 Score: 2704
Period size: 582 Copynumber: 3.0 Consensus size: 581
5814295 TTTTTTTTAT
* *
5814305 TTGTAATCAATTAATCCTTCCAATATTTATTTACATCCAATTAAGTCTTTATTTGAATGACAAAA
1 TTGTAATCAATTAATCCTTCCAATATTTATTTACTTCC-ATTAAATCTTTATTTGAA-GACAAAA
*
5814370 TTAACACCGTTAAATTTTTTACCAATTAAGATAAAATTATATGTGACATTAATAAAATAGATGAA
64 TTAACACCGTTAATTTTTTTACCAATTAAGATAAAATTATATGTGACATTAATAAAATAGATGAA
* * * *
5814435 ATTTTGATATATAATGTAATTAATATATGTGAAAATTAAATAAAATAAATTTATTTTCCTTCTTT
129 AATTTGATATATAACGTATTTAATATATGTGAAAATTAAATAAAATAAATTTATTTTTCTTCTTT
* * * *
5814500 ATTTTTTTTCACTTCTCTTTCTAATATCTTCTAAGGGTTAAATTTTACCACACGAAT-AATTTTA
194 A-TTTTTTCCACTTCTCTTTCTAAGATCTTCTAAGGGTTCAATTTTACCACATGAATAAATTTTA
* *
5814564 GTCTAA-TAAAGGATTTAATTAAATCGAAATAAAAGATTAAAGTCTTGATTAATTATAAAAAAAT
258 -TCTAATTAAA-GATTTAATTAAATCGAAATAAAATATTAAAGTCTTAATTAATTATAAAAAAAT
* **
5814628 TAAAAATTTAAACAAATTTTTAATTATAATTCAGAATATATATTAGTCTTTAATCAAGTTATTTC
321 TAAAAATTTAAACAAAATTTTAATTATAATTCAGAATATATATTAGTCTTTAATCAAGAGATTTC
5814693 TGTTATCTATCTCCAATTCCTATATTTTTATGTCTTCACAAACAATAAAGTAATTTTATCTATGC
386 TGTTATCTATCTCCAATTCCTATATTTTTATGTCTTCACAAACAATAAAGTAATTTTATCTATG-
* *
5814758 TCTGGGACATTAATCCAAAGTGGTTTTTTATTTCAAGGTCAAACATTTAATGTGAAATAAATCTT
450 TCTGGGACATTAATCCAAAAT-GTTTTTTTTTTCAAGGTCAAACATTTAATGTGAAATAAATCTT
* *
5814823 GCAAAATTAAATGGTTATTTTCACCTCCCCCAGCTTAATACATTTGTAAGTGTTAGAGAGGCCAT
514 GCAAAATTAAATGGTTACTTTCACCTCCCCCAGCTTAATACATTTGTAAGTGTTAAAGAGGCCAT
5814888 TAA
579 TAA
** *
5814891 TTGTAATCAATTAATCCTTTGAATCTTTATTTACGTTCCATTAAATCTTTA-TTGAAGA-AAAAT
1 TTGTAATCAATTAATCCTTCCAATATTTATTTAC-TTCCATTAAATCTTTATTTGAAGACAAAAT
5814954 TAACACCGTTAATTTTTTTACCAATTAAGATAAAATTATATGTGACATTAATAAAATAGATGAAA
65 TAACACCGTTAATTTTTTTACCAATTAAGATAAAATTATATGTGACATTAATAAAATAGATGAAA
*
5815019 ATTTGATATATAACATATTTAATATATGTGAAAATTAAATAAAATAAATTTATTTTTCTTCTTTA
130 ATTTGATATATAACGTATTTAATATATGTGAAAATTAAATAAAATAAATTTATTTTTCTTCTTTA
* * *
5815084 TTTTTTCCACTTCTCTTTTTAAGATCTTCCAACGGTTCAATTTTACCACATGAATAAATTTTATC
195 TTTTTTCCACTTCTCTTTCTAAGATCTTCTAAGGGTTCAATTTTACCACATGAATAAATTTTATC
*
5815149 TAATTAAAGATTTAATTAAATTGAAATAAAATATTAAAGTCTTAAATT-ATTATAAAAAAATT-A
260 TAATTAAAGATTTAATTAAATCGAAATAAAATATTAAAGTCTT-AATTAATTATAAAAAAATTAA
* * *
5815212 AAATTTAAGCAAAATTTTAATTATAATTCAGAATATATGTTAGTCTTTAATCAAGAGATTTATGT
324 AAATTTAAACAAAATTTTAATTATAATTCAGAATATATATTAGTCTTTAATCAAGAGATTTCTGT
* * * * *
5815277 CAACTATCTCCAATTGCTATATTCTTATGTCTTCACAAACAATAAAGTAATTTTATCAATGTGCT
389 TATCTATCTCCAATTCCTATATTTTTATGTCTTCACAAACAATAAAGTAATTTTATCTATGT-CT
5815342 GGGACATTAATCCAAAATGTTTTTTTTTTTTCAAGGTCAAACATTTAATGTGAAATAAATCTTGC
453 GGGACATTAATCCAAAATG--TTTTTTTTTTCAAGGTCAAACATTTAATGTGAAATAAATCTTGC
* * *
5815407 AAAATTAAATTGTTACTTTCACCTCCCTCAGCTTAATACATTTGTAAGTGTCAAAGAGGCCATTA
516 AAAATTAAATGGTTACTTTCACCTCCCCCAGCTTAATACATTTGTAAGTGTTAAAGAGGCCATTA
5815472 A
581 A
* ** *
5815473 TTGTAATCAATTAATCCGTCCAATATTTATTTACATTTAATTAAATCTTTATTTGAA-AGAAAA-
1 TTGTAATCAATTAATCCTTCCAATATTTATTTAC-TTCCATTAAATCTTTATTTGAAGACAAAAT
*** * *
5815536 -AA-ATTTTTAATTTTTTTACCAATTAAGATAAAATTACATGTGGCATTAATAAAATAGATGAAA
65 TAACACCGTTAATTTTTTTACCAATTAAGATAAAATTATATGTGACATTAATAAAATAGATGAAA
* * *
5815599 ATTTGATAAATAACGTATTTAATATATGTAAAAATTAAATAAAATAAATTTATTTTTATTCTTTA
130 ATTTGATATATAACGTATTTAATATATGTGAAAATTAAATAAAATAAATTTATTTTTCTTCTTT-
* * ***
5815664 ATTTTTTCCACTTCTCTTTCTAAGATATTCTAAGGGTTCAATTTTACTACATGAATAAATTCCGT
194 ATTTTTTCCACTTCTCTTTCTAAGATCTTCTAAGGGTTCAATTTTACCACATGAATAAATTTTAT
* *
5815729 CCAATTAATGATTTAATTAAATCGAAATAAAATATTAAAGTCTTAATTAATTATAAAAAAATTAA
259 CTAATTAAAGATTTAATTAAATCGAAATAAAATATTAAAGTCTTAATTAATTATAAAAAAATTAA
* **
5815794 AAATTTAAATAAGCTTTTAATTATAATTCAGAATATATATTAGTCTTTAATCAAGAGATTTCTGT
324 AAATTTAAACAAAATTTTAATTATAATTCAGAATATATATTAGTCTTTAATCAAGAGATTTCTGT
*
5815859 TATCTATCTCCAATTCCTATATTTTTATGTCTTCACAAACAATAAAATAATTTTATCTATGTTCT
389 TATCTATCTCCAATTCCTATATTTTTATGTCTTCACAAACAATAAAGTAATTTTATCTATG-TCT
5815924 GGGACATTAATCCAAAATG-TTTTTTTTTCAAGGTCAAACATTTAATGTGAAATAAATCTTGCAA
453 GGGACATTAATCCAAAATGTTTTTTTTTTCAAGGTCAAACATTTAATGTGAAATAAATCTTGCAA
5815988 AATTAAATGGTTACTTTCACCTCCCCCAGCTTAATACATTTGTAAGTGTTAGAA-AGGCCATT
518 AATTAAATGGTTACTTTCACCTCCCCCAGCTTAATACATTTGTAAGTGTTA-AAGAGGCCATT
5816050 TTGATCTATA
Statistics
Matches: 1064, Mismatches: 81, Indels: 35
0.90 0.07 0.03
Matches are distributed among these distances:
579 101 0.09
580 124 0.12
581 249 0.23
582 385 0.36
583 153 0.14
584 2 0.00
585 5 0.00
586 42 0.04
587 3 0.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.41
Consensus pattern (581 bp):
TTGTAATCAATTAATCCTTCCAATATTTATTTACTTCCATTAAATCTTTATTTGAAGACAAAATT
AACACCGTTAATTTTTTTACCAATTAAGATAAAATTATATGTGACATTAATAAAATAGATGAAAA
TTTGATATATAACGTATTTAATATATGTGAAAATTAAATAAAATAAATTTATTTTTCTTCTTTAT
TTTTTCCACTTCTCTTTCTAAGATCTTCTAAGGGTTCAATTTTACCACATGAATAAATTTTATCT
AATTAAAGATTTAATTAAATCGAAATAAAATATTAAAGTCTTAATTAATTATAAAAAAATTAAAA
ATTTAAACAAAATTTTAATTATAATTCAGAATATATATTAGTCTTTAATCAAGAGATTTCTGTTA
TCTATCTCCAATTCCTATATTTTTATGTCTTCACAAACAATAAAGTAATTTTATCTATGTCTGGG
ACATTAATCCAAAATGTTTTTTTTTTCAAGGTCAAACATTTAATGTGAAATAAATCTTGCAAAAT
TAAATGGTTACTTTCACCTCCCCCAGCTTAATACATTTGTAAGTGTTAAAGAGGCCATTAA
Found at i:5817506 original size:26 final size:26
Alignment explanation
Indices: 5817455--5817515 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
5817445 TACACAGATT
* *
5817455 TTTATTATATTTTTTATAATTTTAAA
1 TTTATTATAATTTTTATAATTATAAA
*
5817481 TTTATTTTAATTTTTAT-ATCTATAAA
1 TTTATTATAATTTTTATAAT-TATAAA
*
5817507 TATA-TATAA
1 TTTATTATAA
5817516 AAATAGTCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATTATAATTTTTATAATTATAAA
Found at i:5817798 original size:20 final size:21
Alignment explanation
Indices: 5817773--5817814 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
5817763 TGAATTTAAA
*
5817773 TATGGTTTTGTT-TTTTTGGT
1 TATGGTTTTGTTCTGTTTGGT
5817793 TATGGTTTTGTTCTGTTTGGT
1 TATGGTTTTGTTCTGTTTGGT
5817814 T
1 T
5817815 GATGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.05, C:0.02, G:0.26, T:0.67
Consensus pattern (21 bp):
TATGGTTTTGTTCTGTTTGGT
Found at i:5820217 original size:30 final size:30
Alignment explanation
Indices: 5820168--5820226 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
5820158 AAAAAATATA
* *
5820168 AAGTTAAAAACTATGTTTTTATTATATAAT
1 AAGTCAAAAACTACGTTTTTATTATATAAT
* *
5820198 AAGTCAAATACTACGTTTTTCTTATATAA
1 AAGTCAAAAACTACGTTTTTATTATATAA
5820227 GTGCAGTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (30 bp):
AAGTCAAAAACTACGTTTTTATTATATAAT
Found at i:5820895 original size:13 final size:12
Alignment explanation
Indices: 5820875--5820912 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
5820865 AAAAGTATCA
5820875 TAAATATTATAT
1 TAAATATTATAT
5820887 TATAATATTATAT
1 TA-AATATTATAT
*
5820900 TAATTATTATAT
1 TAAATATTATAT
5820912 T
1 T
5820913 TTCAACGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAAATATTATAT
Found at i:5822668 original size:27 final size:28
Alignment explanation
Indices: 5822624--5822677 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
5822614 ATGGAGTAAT
*
5822624 TCTCAAGATATCATCATCATAAAACAAGC
1 TCTCAAGATATCAGCATCA-AAAACAAGC
*
5822653 TCTCAA-A-ATCAGCATCAAAACCAAG
1 TCTCAAGATATCAGCATCAAAAACAAG
5822678 AAAATACTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 9 0.39
28 1 0.04
29 6 0.26
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.20
Consensus pattern (28 bp):
TCTCAAGATATCAGCATCAAAAACAAGC
Found at i:5825736 original size:35 final size:35
Alignment explanation
Indices: 5825686--5825756 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 35
5825676 ATATCAACTA
*
5825686 CCTAAATACTTTGTTAAAGTTAGTTTTTCCATTTT
1 CCTAAATACTTTGTTAAACTTAGTTTTTCCATTTT
5825721 CCTAAATA-TTATGTTAAACTTAGTTTTTCCATTTT
1 CCTAAATACTT-TGTTAAACTTAGTTTTTCCATTTT
5825756 C
1 C
5825757 TTCCATACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (35 bp):
CCTAAATACTTTGTTAAACTTAGTTTTTCCATTTT
Found at i:5830128 original size:13 final size:13
Alignment explanation
Indices: 5830106--5830143 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5830096 TTAATAAAAA
5830106 TTTA-ATTATATT
1 TTTATATTATATT
5830118 TTTATATTATATT
1 TTTATATTATATT
* *
5830131 ATTATATCATATT
1 TTTATATTATATT
5830144 ATATTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:5830156 original size:13 final size:13
Alignment explanation
Indices: 5830110--5830145 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
5830100 TAAAAATTTA
*
5830110 ATTATATTTTTAT
1 ATTATATTATTAT
5830123 ATTATATTATTAT
1 ATTATATTATTAT
*
5830136 ATCATATTAT
1 ATTATATTAT
5830146 ATTATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATATTATTAT
Found at i:5837325 original size:132 final size:133
Alignment explanation
Indices: 5837087--5837353 Score: 430
Period size: 132 Copynumber: 2.0 Consensus size: 133
5837077 TGCACAAAGA
** *
5837087 TCAATCATGAAAATAAAATGTAAATATGACTGCCACAATGTATGTCACCTGAGGCATAAATTTAT
1 TCAATCATGAAAATAAAACCTAAATATGACTGCCACAATGTACGTCACCTGAGGCATAAATTTAT
5837152 CCAATCATACTAGTAACCATCTTAGGATACATTGATGTCAAAATCAAATTTATCC-CAGTCAATC
66 CCAATCATACTAGTAACCATCTTAGGATACATTGATGTCAAAATCAAATTTATCCTCA-TCAATC
5837216 AAAT
130 AAAT
*
5837220 TCAATCATGAAAATAAAACCTAAATA-GACTGCCACAATGTACGTCACCTGAGGCATAAATTTTT
1 TCAATCATGAAAATAAAACCTAAATATGACTGCCACAATGTACGTCACCTGAGGCATAAATTTAT
*** * *
5837284 CTGGTCATACTAGTAACCATTTTAGGATACATTGATGTCAAAATCAAATTTATCCTCATCGATCA
66 CCAATCATACTAGTAACCATCTTAGGATACATTGATGTCAAAATCAAATTTATCCTCATCAATCA
5837349 AAT
131 AAT
5837352 TC
1 TC
5837354 TACTAACACT
Statistics
Matches: 124, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
132 98 0.79
133 26 0.21
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (133 bp):
TCAATCATGAAAATAAAACCTAAATATGACTGCCACAATGTACGTCACCTGAGGCATAAATTTAT
CCAATCATACTAGTAACCATCTTAGGATACATTGATGTCAAAATCAAATTTATCCTCATCAATCA
AAT
Found at i:5841368 original size:29 final size:27
Alignment explanation
Indices: 5841316--5841370 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
5841306 TATCATATTA
*
5841316 ATTAATAATTTATAATTTATGTATCAC
1 ATTAATAATTTATAATTTAAGTATCAC
*
5841343 ATTATATAATTTTTAAATTTAAGTATCA
1 ATTA-ATAATTTAT-AATTTAAGTATCA
5841371 TAATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 8 0.33
29 12 0.50
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (27 bp):
ATTAATAATTTATAATTTAAGTATCAC
Found at i:5844995 original size:21 final size:19
Alignment explanation
Indices: 5844946--5845004 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
5844936 ATTTTATATA
**
5844946 TATTTAATAAATTAATTTT
1 TATTTAATAAATTAAAATT
5844965 TATTTAAT-AATATAAAATT
1 TATTTAATAAAT-TAAAATT
5844984 TATTTTATATAAATTAAAATT
1 TA-TTTA-ATAAATTAAAATT
5845005 AATATATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.09
19 15 0.44
20 4 0.12
21 9 0.26
22 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTAATAAATTAAAATT
Found at i:5845030 original size:20 final size:21
Alignment explanation
Indices: 5844995--5845033 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5844985 ATTTTATATA
*
5844995 AATTAAAATTAATATATTTTT
1 AATTAAAATAAATATATTTTT
5845016 AATTAAAA-AAATATATTT
1 AATTAAAATAAATATATTT
5845034 ATAAAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTAAAATAAATATATTTTT
Found at i:5849354 original size:29 final size:30
Alignment explanation
Indices: 5849307--5849396 Score: 110
Period size: 31 Copynumber: 3.0 Consensus size: 30
5849297 TTTAACATCT
*
5849307 TTAAATAAGTCTTTAATTTTTTTATTTATAA
1 TTAAATAAAT-TTTAATTTTTTTATTTATAA
* *
5849338 TTAAATAAATTTT-ATTTTTTAATTTATAT
1 TTAAATAAATTTTAATTTTTTTATTTATAA
**
5849367 TTAAATAAAATTTTAAAATTTTTATTTATA
1 TTAAAT-AAATTTTAATTTTTTTATTTATA
5849397 CTTTAAAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 20 0.39
30 10 0.20
31 21 0.41
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TTAAATAAATTTTAATTTTTTTATTTATAA
Found at i:5849379 original size:25 final size:25
Alignment explanation
Indices: 5849321--5849394 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 25
5849311 ATAAGTCTTT
* *
5849321 AATTTTTTTATTTATAATTAAATAA
1 AATTTTTTAATTTATATTTAAATAA
5849346 ATTTTATTTTTTAATTTATATTTAAATAA
1 A----ATTTTTTAATTTATATTTAAATAA
** *
5849375 AATTTTAAAATTTTTATTTA
1 AATTTTTTAATTTATATTTA
5849395 TACTTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
25 17 0.43
29 23 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
AATTTTTTAATTTATATTTAAATAA
Found at i:5850652 original size:38 final size:38
Alignment explanation
Indices: 5850601--5850676 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
5850591 ATGCGGTGAT
*
5850601 AGTGAACTCAAAGGATTTTCTTTTGTGTATTTGTTTTG
1 AGTGAACTCAAAGGATTTTCGTTTGTGTATTTGTTTTG
5850639 AGTGAACTCAAAGGATTTTCGTTTGTGTATTTGTTTTG
1 AGTGAACTCAAAGGATTTTCGTTTGTGTATTTGTTTTG
5850677 TTTTCATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.08, G:0.22, T:0.49
Consensus pattern (38 bp):
AGTGAACTCAAAGGATTTTCGTTTGTGTATTTGTTTTG
Found at i:5860390 original size:2 final size:2
Alignment explanation
Indices: 5860383--5860423 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5860373 CAGAAGCTTT
5860383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5860424 GATTGACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5860477 original size:2 final size:2
Alignment explanation
Indices: 5860465--5860496 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5860455 CAGAGGCTTT
*
5860465 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5860497 AAACAGCAAA
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5860478 original size:82 final size:82
Alignment explanation
Indices: 5860341--5860496 Score: 294
Period size: 82 Copynumber: 1.9 Consensus size: 82
5860331 TCCTATGGAC
*
5860341 TGATTGACAAAGAATGTCACATGCATGGTGGTCAGAAGCTTTTATATATATATATATATATATAT
1 TGATTGACAAAGAATGTCACATGCATGGTGGTCAGAAGCTTTTATAGATATATATATATATATAT
5860406 ATATATATATATATATA
66 ATATATATATATATATA
*
5860423 TGATTGACAAAGAATGTCACATGCATGGTGGTCAGAGGCTTTTATAGATATATATATATATATAT
1 TGATTGACAAAGAATGTCACATGCATGGTGGTCAGAAGCTTTTATAGATATATATATATATATAT
5860488 ATATATATA
66 ATATATATA
5860497 AAACAGCAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (82 bp):
TGATTGACAAAGAATGTCACATGCATGGTGGTCAGAAGCTTTTATAGATATATATATATATATAT
ATATATATATATATATA
Found at i:5870152 original size:27 final size:28
Alignment explanation
Indices: 5870117--5870171 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
5870107 TTAATTAATT
*
5870117 ATTTAATTATGAAA-ATATTTATTTATTA
1 ATTTAATTAT-AAATAAATTTATTTATTA
5870145 ATTT-ATTATAAATAAATTTATTTATTA
1 ATTTAATTATAAATAAATTTATTTATTA
5870172 TATTAACTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 18 0.72
28 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATTTAATTATAAATAAATTTATTTATTA
Found at i:5871805 original size:2 final size:2
Alignment explanation
Indices: 5871798--5871826 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5871788 ATATGTGCTT
5871798 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
5871827 TATGTGTGTA
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:5873108 original size:14 final size:16
Alignment explanation
Indices: 5873084--5873116 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5873074 TATTACTTAT
5873084 TATTGTATT-AAAATA
1 TATTGTATTAAAAATA
5873099 TATT-TATTAAAAATA
1 TATTGTATTAAAAATA
5873114 TAT
1 TAT
5873117 AAAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TATTGTATTAAAAATA
Found at i:5884383 original size:2 final size:2
Alignment explanation
Indices: 5884376--5884407 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5884366 ACGCTTCCTA
5884376 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5884408 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5889530 original size:29 final size:29
Alignment explanation
Indices: 5889478--5889537 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
5889468 AATTATAATG
* * * *
5889478 AAAATATTTAATATGATATTTAAATTTTA
1 AAAATATTTAATATAAGATATAAATTATA
*
5889507 AAAATATTTAATTTAAGATATAAATTATA
1 AAAATATTTAATATAAGATATAAATTATA
5889536 AA
1 AA
5889538 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
AAAATATTTAATATAAGATATAAATTATA
Found at i:5889674 original size:29 final size:29
Alignment explanation
Indices: 5889614--5889677 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
5889604 TTTCATATTA
* * **
5889614 ATTAAGAAATTTATAATTTAAATATTTTT
1 ATTAAAAAATTTAAAATTTAAATATTCAT
5889643 ATTAAAAAATTTTAAAATTTAAATA-TCAT
1 ATTAAAAAA-TTTAAAATTTAAATATTCAT
5889672 ATTAAA
1 ATTAAA
5889678 TATTTTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTAAAAAATTTAAAATTTAAATATTCAT
Found at i:5893726 original size:23 final size:22
Alignment explanation
Indices: 5893696--5893742 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
5893686 ATATATTAAA
*
5893696 TTTTAAATAATTATTATAATTT
1 TTTTAAATAATAATTATAATTT
5893718 TTTTGAAATAATAATTATAATTT
1 TTTT-AAATAATAATTATAATTT
5893741 TT
1 TT
5893743 AATTTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTAAATAATAATTATAATTT
Found at i:5893900 original size:125 final size:124
Alignment explanation
Indices: 5893771--5894012 Score: 278
Period size: 125 Copynumber: 1.9 Consensus size: 124
5893761 ATTAAAAATA
* * ***
5893771 TTTTTGA-CAAAAAATATATTTAATAAT-TTTCTCATAAATTTTTATGAAATAATTATTCAAGGT
1 TTTTTGACCAAAAAAGAT-TTTAATAATCTTT-TCATAAATTTTTATGAAATAATTACTCAAAAA
*
5893834 A-TTTTTCA-CAAAAAATGCATTGA-ATAATCTCAAAATTTTTTTTAATAGGGTTATTGAAAGCG
64 AGTTTTT-ATC-AAAAATGC-TTGAGATAATCTCAAAATTTTTTTTAAT-GGATTATTGAAAGCG
* * * ** *
5893896 TTTTTGACCAAAAACGCTTTTAATAATCTTTTTATAAATTTTTATGAGGTGATTACTCAAAAAAG
1 TTTTTGACCAAAAAAGATTTTAATAATCTTTTCATAAATTTTTATGAAATAATTACTCAAAAAAG
*
5893961 TTTTTATCAAAAATGCTTTAGATAATCTCAAAATTTTTTTTAATGGATTATT
66 TTTTTATCAAAAATGCTTGAGATAATCTCAAAATTTTTTTTAATGGATTATT
5894013 AATTGTATTT
Statistics
Matches: 99, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
124 10 0.10
125 73 0.74
126 16 0.16
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.44
Consensus pattern (124 bp):
TTTTTGACCAAAAAAGATTTTAATAATCTTTTCATAAATTTTTATGAAATAATTACTCAAAAAAG
TTTTTATCAAAAATGCTTGAGATAATCTCAAAATTTTTTTTAATGGATTATTGAAAGCG
Found at i:5894025 original size:125 final size:123
Alignment explanation
Indices: 5893836--5894141 Score: 307
Period size: 125 Copynumber: 2.5 Consensus size: 123
5893826 TTCAAGGTAT
* * * *
5893836 TTTTCACAAAAAATGCATT-GAATAATCTCAAAATTTTTTTTAATAGGGTTATTGAAAGCGTTTT
1 TTTTCACCAAAAATGCTTTAG-ATAATCTCAAAATTTTTTTTAAT-GGATTATT-AAAGAGTTTT
* * *
5893900 T-GACCAAAAAC-GCTTTTAATAATCTTTTTATAAATTTTTATGAGGTGATTACTCAAAAAAG
63 TAG-CCAAAAACATC-TTTAATAATCTATTCATAAATTTTTATGAGGTGATTACTCAAAAAAG
* * * *
5893961 TTTTTATCAAAAATGCTTTAGATAATCTCAAAATTTTTTTTAATGGATTATTAATTGTATTTTTT
1 TTTTCACCAAAAATGCTTTAGATAATCTCAAAATTTTTTTTAATGGATTATTAA-AG-AGTTTTT
* * * * *
5894026 AGTCAAAAACATCTTTGATAATCTATTCATACATTTTTATGAGGTGATTACTCAAGATAG
64 AGCCAAAAACATCTTTAATAATCTATTCATAAATTTTTATGAGGTGATTACTCAAAAAAG
** * * * *
5894086 TTTTCACCAAAAACACTTGA-ATAATTTTGAAAA-TTTTTTTAATAGATTATTAAAGA
1 TTTTCACCAAAAATGCTTTAGATAA-TCTCAAAATTTTTTTTAATGGATTATTAAAGA
5894142 CATTTCTAAT
Statistics
Matches: 150, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
122 1 0.01
123 3 0.02
124 31 0.21
125 112 0.75
126 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (123 bp):
TTTTCACCAAAAATGCTTTAGATAATCTCAAAATTTTTTTTAATGGATTATTAAAGAGTTTTTAG
CCAAAAACATCTTTAATAATCTATTCATAAATTTTTATGAGGTGATTACTCAAAAAAG
Found at i:5894514 original size:61 final size:60
Alignment explanation
Indices: 5894375--5894516 Score: 153
Period size: 60 Copynumber: 2.3 Consensus size: 60
5894365 ATTTATGAGA
* *
5894375 AAATTATTGAAGACGTTTTTAATCAAAAAATACTTTCAATAACAACATTAAATTTTTTTTTG
1 AAATTATT-AAGACATTTTTAACCAAAAAATACTTTCAATAAC-ACATTAAATTTTTTTTTG
* * * * *
5894437 AGATTATTTAGGCATTTTT-ACCAAAAAATACTTTTAATAATC-CTATTAATTTTTTTTTTG
1 AAATTATTAAGACATTTTTAACCAAAAAATACTTTCAATAA-CAC-ATTAAATTTTTTTTTG
*
5894497 AAATTATTCAAAACATTTTT
1 AAATTATT-AAGACATTTTT
5894517 TATAAAAATA
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 1 0.02
60 41 0.62
61 17 0.26
62 7 0.11
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.46
Consensus pattern (60 bp):
AAATTATTAAGACATTTTTAACCAAAAAATACTTTCAATAACACATTAAATTTTTTTTTG
Found at i:5894597 original size:126 final size:127
Alignment explanation
Indices: 5894451--5894697 Score: 295
Period size: 126 Copynumber: 2.0 Consensus size: 127
5894441 TATTTAGGCA
** **
5894451 TTTTTACCAAAAAATACTTTTAATAA-TCCTATTAATTTTTTTTTTGAAATTATTCAAAACATTT
1 TTTTTACCAAAAAATACTTTTAATAACT-CTATTAAAATTTTTTTAAAAATTATTCAAAACATTT
* * * * *
5894515 TTTAT-AAAAATAACATTGAATAATCAT-CTTATAAAAATTTATGAAGAGATTATTAAATACGTT
65 TTAATAAAAAAT-ACATCGAATAATC-TCCTCATAAAAATTTATGAAAAAATTATTAAATACGTT
* * * * *
5894578 TTTTTATCAAAAAA-GCTTTTAATAACTTTATTAAAATTTTTTTAAAAATTATTCAAGATATTTT
1 TTTTTACCAAAAAATACTTTTAATAACTCTATTAAAATTTTTTTAAAAATTATTCAAAACATTTT
* *
5894642 TAATAAAAAATATATCGAATAATCTCCTCATAAAGATTTATGAAAAAATTATTAAA
66 TAATAAAAAATACATCGAATAATCTCCTCATAAAAATTTATGAAAAAATTATTAAA
5894698 AATATTTTTA
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
125 1 0.01
126 80 0.79
127 20 0.20
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (127 bp):
TTTTTACCAAAAAATACTTTTAATAACTCTATTAAAATTTTTTTAAAAATTATTCAAAACATTTT
TAATAAAAAATACATCGAATAATCTCCTCATAAAAATTTATGAAAAAATTATTAAATACGTT
Found at i:5894706 original size:126 final size:127
Alignment explanation
Indices: 5894451--5894740 Score: 288
Period size: 126 Copynumber: 2.3 Consensus size: 127
5894441 TATTTAGGCA
** **
5894451 TTTTTACCAAAAAATACTTTTAATAATCCTATTAATTTTTTTTTTGAAATTATTCAAAACATTTT
1 TTTTTACCAAAAAATACTTTTAATAATCCTATTAAAATTTTTTTAAAAATTATTCAAAACATTTT
* * * * * * *
5894516 TTATAAAAATAACATTGAATAATCATCTTATAAAAATTTATGAAGAGATTATTAAATACGTT
66 TAATAAAAATAACATCGAATAATCATCTCATAAAAATTTATGAAAAAATTATTAAAAACATT
* * * * *
5894578 TTTTTATCAAAAAA-GCTTTTAATAA-CTTTATTAAAATTTTTTTAAAAATTATTCAAGATATTT
1 TTTTTACCAAAAAATACTTTTAATAATC-CTATTAAAATTTTTTTAAAAATTATTCAAAACATTT
* * *
5894641 TTAATAAAAA-ATATATCGAATAATC-TCCTCATAAAGATTTATGAAAAAATTATT-AAAA-ATA
65 TTAATAAAAATA-ACATCGAATAATCAT-CTCATAAAAATTTATGAAAAAATTATTAAAAACATT
** *
5894702 TTTTTAATAAAAAATAC-TTTAAGTAATCTTATTCAAAAT
1 TTTTTACCAAAAAATACTTTTAA-TAATCCTATT-AAAAT
5894741 GATAATAGTT
Statistics
Matches: 134, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
124 18 0.13
125 15 0.11
126 88 0.66
127 13 0.10
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (127 bp):
TTTTTACCAAAAAATACTTTTAATAATCCTATTAAAATTTTTTTAAAAATTATTCAAAACATTTT
TAATAAAAATAACATCGAATAATCATCTCATAAAAATTTATGAAAAAATTATTAAAAACATT
Found at i:5900088 original size:16 final size:16
Alignment explanation
Indices: 5900067--5900099 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5900057 AAACAAATCC
5900067 CTAAAAACTTAACAAT
1 CTAAAAACTTAACAAT
5900083 CTAAAAACTTAACAAT
1 CTAAAAACTTAACAAT
5900099 C
1 C
5900100 AGAATAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (16 bp):
CTAAAAACTTAACAAT
Found at i:5900192 original size:25 final size:25
Alignment explanation
Indices: 5900156--5900214 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
5900146 ATAAATTAAA
*
5900156 AATCAAA-CTGCACTAATATAAGAG
1 AATCAAATTTGCACTAATATAAGAG
* * *
5900180 AATCAGATTTGCACTAATGTAGGAG
1 AATCAAATTTGCACTAATATAAGAG
5900205 AATCAAATTT
1 AATCAAATTT
5900215 CTACACTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (25 bp):
AATCAAATTTGCACTAATATAAGAG
Found at i:5918485 original size:22 final size:22
Alignment explanation
Indices: 5918460--5918504 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5918450 ATATATATTT
*
5918460 ATATTTGTATATCTAAAATTAA
1 ATATTTATATATCTAAAATTAA
* *
5918482 ATATTTATATTTTTAAAATTAA
1 ATATTTATATATCTAAAATTAA
5918504 A
1 A
5918505 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTTATATATCTAAAATTAA
Found at i:5918511 original size:28 final size:28
Alignment explanation
Indices: 5918454--5918511 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
5918444 TAATATATAT
* **
5918454 ATATTTATATTTGTATATCTAAAATTAA
1 ATATTTATATTTGTAAATCTAAAAAAAA
*
5918482 ATATTTATATTTTTAAAAT-TAAAAAAAA
1 ATATTTATATTTGT-AAATCTAAAAAAAA
5918510 AT
1 AT
5918512 TAAAATAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
ATATTTATATTTGTAAATCTAAAAAAAA
Found at i:5923954 original size:26 final size:26
Alignment explanation
Indices: 5923925--5923978 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
5923915 TAATCTTTGA
5923925 CATAATATATAATTAATGGATAAATT
1 CATAATATATAATTAATGGATAAATT
5923951 CATAATATATAATTAATGGATAAATT
1 CATAATATATAATTAATGGATAAATT
5923977 CA
1 CA
5923979 AATGCGAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (26 bp):
CATAATATATAATTAATGGATAAATT
Found at i:5953721 original size:21 final size:21
Alignment explanation
Indices: 5953673--5953721 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5953663 TCTACATTAT
* *
5953673 ATCAAATGTTACCCAAATTGT
1 ATCAAATGTTACCAAAATTGC
*
5953694 ATAAAATGTTACCAAAACTT-C
1 ATCAAATGTTACCAAAA-TTGC
5953715 ATCAAAT
1 ATCAAAT
5953722 ATTTATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (21 bp):
ATCAAATGTTACCAAAATTGC
Found at i:5953924 original size:21 final size:21
Alignment explanation
Indices: 5953900--5953984 Score: 63
Period size: 20 Copynumber: 4.1 Consensus size: 21
5953890 AATGATAATC
*
5953900 AAAATTATATAAAATATTACAA
1 AAAATTATATAAAATGTTAC-A
* *
5953922 AAAATT-TATTAAGA-GTTACT
1 AAAATTATA-TAAAATGTTACA
* *
5953942 AAAATTATAT-TAATGTTACC
1 AAAATTATATAAAATGTTACA
5953962 AAAATTATATGAAAA-GTTA-A
1 AAAATTATAT-AAAATGTTACA
5953982 AAA
1 AAA
5953985 GCTATATCAC
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
19 1 0.02
20 25 0.50
21 12 0.24
22 12 0.24
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (21 bp):
AAAATTATATAAAATGTTACA
Found at i:5953947 original size:20 final size:20
Alignment explanation
Indices: 5953899--5953971 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
5953889 CAATGATAAT
* *
5953899 CAAAATTATATAAAATATTAC
1 CAAAATTATATTAAA-GTTAC
*
5953920 AAAAAATT-TATTAAGAGTTAC
1 -CAAAATTATATTAA-AGTTAC
* *
5953941 TAAAATTATATTAATGTTAC
1 CAAAATTATATTAAAGTTAC
5953961 CAAAATTATAT
1 CAAAATTATAT
5953972 GAAAAGTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 21 0.49
21 15 0.35
22 7 0.16
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (20 bp):
CAAAATTATATTAAAGTTAC
Found at i:5954048 original size:11 final size:11
Alignment explanation
Indices: 5954027--5954075 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
5954017 AATGACTATC
5954027 AAAATTGTATTA
1 AAAATT-TATTA
5954039 AAAATTTATT-
1 AAAATTTATTA
*
5954049 AAAATATATTA
1 AAAATTTATTA
*
5954060 AAATTTTA-TA
1 AAAATTTATTA
5954070 AAAATT
1 AAAATT
5954076 ATCAAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 16 0.50
11 10 0.31
12 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
AAAATTTATTA
Found at i:5954058 original size:21 final size:20
Alignment explanation
Indices: 5954034--5954097 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
5954024 ATCAAAATTG
*
5954034 TATTAAAAATTTATTAAAAT
1 TATTAAAAATTTATAAAAAT
*
5954054 ATATTAAAATTTTATAAAAAT
1 -TATTAAAAATTTATAAAAAT
*
5954075 TA-TCAAAATTGTATAAATAAT
1 TATTAAAAATT-TATAAA-AAT
5954096 TA
1 TA
5954098 CCGCACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.16
20 8 0.22
21 23 0.62
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
TATTAAAAATTTATAAAAAT
Found at i:5954071 original size:10 final size:11
Alignment explanation
Indices: 5954027--5954075 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
5954017 AATGACTATC
*
5954027 AAAATTGTATT
1 AAAATTTTATT
*
5954038 AAAAATTTATT
1 AAAATTTTATT
*
5954049 AAAA-TATATT
1 AAAATTTTATT
*
5954059 AAAATTTTATA
1 AAAATTTTATT
5954070 AAAATT
1 AAAATT
5954076 ATCAAAATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
AAAATTTTATT
Found at i:5973375 original size:3 final size:3
Alignment explanation
Indices: 5973367--5973394 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5973357 TTGACAAAAC
5973367 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5973395 AAGGTAGATG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5974711 original size:21 final size:19
Alignment explanation
Indices: 5974681--5974719 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
5974671 AATATAATTT
5974681 TATAATTAAAATAATAAAAA
1 TATAATTAAAATAA-AAAAA
5974701 TATATATTAAAATAAAAAA
1 TATA-ATTAAAATAAAAAA
5974720 TTTTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TATAATTAAAATAAAAAAA
Found at i:5983385 original size:98 final size:98
Alignment explanation
Indices: 5983270--5983470 Score: 359
Period size: 98 Copynumber: 2.1 Consensus size: 98
5983260 ACAGGAGTAC
*
5983270 AATT-ATTAAATAAAAAATAAATAGAGTACAAAAGCAGATGGATGGGATGTTTACTGAGAAACAG
1 AATTAATTAAATAAAAAATAAATAGAGTACAAAAGCAGACGGATGGGATGTTTACTGAGAAACAG
*
5983334 ATATGGCGGAATATTTCAGTATACCTGGTTTCA
66 ATATGACGGAATATTTCAGTATACCTGGTTTCA
*
5983367 AATTAATTAAATAAAAAATAAATAGAGTACAAAAGCAGACGGATGGGATGTTTACTGAGAGACAG
1 AATTAATTAAATAAAAAATAAATAGAGTACAAAAGCAGACGGATGGGATGTTTACTGAGAAACAG
*
5983432 ATATGATGGAATATTTCAGTATACCTGGTTTCA
66 ATATGACGGAATATTTCAGTATACCTGGTTTCA
5983465 AATTAA
1 AATTAA
5983471 CCCCAACAGC
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 4 0.04
98 95 0.96
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (98 bp):
AATTAATTAAATAAAAAATAAATAGAGTACAAAAGCAGACGGATGGGATGTTTACTGAGAAACAG
ATATGACGGAATATTTCAGTATACCTGGTTTCA
Found at i:5989044 original size:19 final size:19
Alignment explanation
Indices: 5989020--5989061 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
5989010 CAGCAGCTTA
5989020 AACTCCTAGGCAGAGCCAG
1 AACTCCTAGGCAGAGCCAG
5989039 AACTCCTAGGCAGAGCCAG
1 AACTCCTAGGCAGAGCCAG
5989058 AACT
1 AACT
5989062 GTGGCCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.31, G:0.24, T:0.12
Consensus pattern (19 bp):
AACTCCTAGGCAGAGCCAG
Found at i:5996525 original size:31 final size:31
Alignment explanation
Indices: 5996464--5996525 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
5996454 AAAATGTTAT
*
5996464 TTTTTAAATTAAAAAAAATATTTTAGTTTAA
1 TTTTTAAATTAAAAAAAATATTGTAGTTTAA
*
5996495 TTTTTAAATATAAGAATAAA-ATTGTA-TTTAA
1 TTTTTAAAT-TAA-AAAAAATATTGTAGTTTAA
5996526 AAGATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 14 0.52
32 8 0.30
33 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTTTAAATTAAAAAAAATATTGTAGTTTAA
Found at i:6007201 original size:15 final size:15
Alignment explanation
Indices: 6007172--6007213 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
6007162 AGGGAAGAGG
*
6007172 AAAAAAAAG-AAAGT
1 AAAAGAAAGTAAAGT
*
6007186 AAAGGAAAGTAAAGT
1 AAAAGAAAGTAAAGT
*
6007201 AAAAGAATGTAAA
1 AAAAGAAAGTAAA
6007214 AGAAACAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (15 bp):
AAAAGAAAGTAAAGT
Found at i:6007365 original size:14 final size:15
Alignment explanation
Indices: 6007336--6007365 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6007326 AATTTGGAGG
6007336 AAAAGTTAAGAAAAT
1 AAAAGTTAAGAAAAT
6007351 AAAAGTTAA-AAAAT
1 AAAAGTTAAGAAAAT
6007365 A
1 A
6007366 TTTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
AAAAGTTAAGAAAAT
Found at i:6008187 original size:22 final size:24
Alignment explanation
Indices: 6008134--6008187 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
6008124 TATGAATTTT
*
6008134 AAAAAATATATTTATTTTAAGAAA
1 AAAAAATATATTTAGTTTAAGAAA
*
6008158 AAACAATA-ATTT-GTTTAA-AAA
1 AAAAAATATATTTAGTTTAAGAAA
6008179 ATAAAAATA
1 A-AAAAATA
6008188 GTAAAAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 11 0.42
23 4 0.15
24 7 0.27
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAAAATATATTTAGTTTAAGAAA
Found at i:6008993 original size:2 final size:2
Alignment explanation
Indices: 6008986--6009010 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6008976 TATAAAAAGA
6008986 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
6009011 AAGCATTATT
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:6010501 original size:18 final size:18
Alignment explanation
Indices: 6010478--6010514 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6010468 TGGGATTAAA
6010478 AAAATAATAAT-AATATAT
1 AAAATAA-AATAAATATAT
6010496 AAAATAAAATAAATATAT
1 AAAATAAAATAAATATAT
6010514 A
1 A
6010515 TTGACATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAAAATAAATATAT
Found at i:6010582 original size:16 final size:16
Alignment explanation
Indices: 6010552--6010595 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
6010542 TATAATTTGA
*
6010552 TAATATTTATTATAAAC
1 TAATATTTAATA-AAAC
6010569 TATATATTTAATAAAAC
1 TA-ATATTTAATAAAAC
6010586 TAATATTTAA
1 TAATATTTAA
6010596 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 8 0.32
17 8 0.32
18 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTTAATAAAAC
Found at i:6011968 original size:17 final size:18
Alignment explanation
Indices: 6011948--6011984 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6011938 ATTTAACAAT
6011948 TTTTTAAAT-TTATTTTA
1 TTTTTAAATATTATTTTA
*
6011965 TTTTTATATATTATTTTA
1 TTTTTAAATATTATTTTA
6011983 TT
1 TT
6011985 ATGATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTAAATATTATTTTA
Found at i:6011997 original size:24 final size:23
Alignment explanation
Indices: 6011956--6012000 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
6011946 ATTTTTTAAA
* *
6011956 TTTATTTTATTTTTATATATTAT
1 TTTATTTGATTTTAATATATTAT
6011979 TTTATTATGATTTTAATATATT
1 TTTATT-TGATTTTAATATATT
6012001 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTGATTTTAATATATTAT
Found at i:6019616 original size:5 final size:6
Alignment explanation
Indices: 6019601--6019625 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6019591 AATCGGCCCT
6019601 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
6019626 GGGTAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:6024249 original size:2 final size:2
Alignment explanation
Indices: 6024244--6024282 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
6024234 TCTCTCACTC
*
6024244 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6024283 GGTTTATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:6025899 original size:2 final size:2
Alignment explanation
Indices: 6025892--6025917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6025882 CTTTATTTCC
6025892 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
6025918 TTCAGATATG
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:6027608 original size:21 final size:21
Alignment explanation
Indices: 6027574--6027613 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6027564 AATGAACACA
*
6027574 TTTTTTGTAATTCTTTTTTTT
1 TTTTTTGTAATTCTATTTTTT
**
6027595 TTTTTTGTGTTTCTATTTT
1 TTTTTTGTAATTCTATTTT
6027614 CATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTTGTAATTCTATTTTTT
Found at i:6027619 original size:21 final size:21
Alignment explanation
Indices: 6027572--6027619 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
6027562 CAAATGAACA
*
6027572 CATTTTTTGTAATTCTTTTTT
1 CATTTTTTGTAATTCTATTTT
** **
6027593 TTTTTTTTGTGTTTCTATTTT
1 CATTTTTTGTAATTCTATTTT
6027614 CATTTT
1 CATTTT
6027620 AAAAAAATCA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.75
Consensus pattern (21 bp):
CATTTTTTGTAATTCTATTTT
Found at i:6028772 original size:27 final size:25
Alignment explanation
Indices: 6028721--6028772 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
6028711 TATCCAAATT
* * *
6028721 TGAAAAAAAAGAGATATTGAAAAGA
1 TGAAAAAAAAAAAATATTAAAAAGA
6028746 TGAAAAAAAAAAAATATATAAATAAGA
1 TGAAAAAAAAAAAATAT-TAAA-AAGA
6028773 AAGAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 3 0.14
27 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.17
Consensus pattern (25 bp):
TGAAAAAAAAAAAATATTAAAAAGA
Found at i:6039378 original size:13 final size:13
Alignment explanation
Indices: 6039360--6039384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6039350 CAATTTAAGT
6039360 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
6039373 TTTTTTCTTTTT
1 TTTTTTCTTTTT
6039385 GTCTTTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:6042088 original size:2 final size:2
Alignment explanation
Indices: 6042083--6042108 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6042073 TGTACGCGCG
6042083 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
6042109 TATATATGGA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6042455 original size:2 final size:2
Alignment explanation
Indices: 6042448--6042474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6042438 GACCTTAGGT
6042448 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 T
6042475 AGTGTATCAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6059129 original size:27 final size:28
Alignment explanation
Indices: 6059071--6059125 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
6059061 CCCGTTGATT
*
6059071 TCATCATCGCCGTCCAGATCTTCACTCCCA
1 TCATCATCGACGTCC--ATCTTCACTCCCA
6059101 TCATCATCGACGTCC-TCTTC-CTCCC
1 TCATCATCGACGTCCATCTTCACTCCC
6059126 CATCGTCGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 5 0.21
30 14 0.58
ACGTcount: A:0.16, C:0.45, G:0.09, T:0.29
Consensus pattern (28 bp):
TCATCATCGACGTCCATCTTCACTCCCA
Found at i:6077122 original size:13 final size:12
Alignment explanation
Indices: 6077098--6077126 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6077088 TTCTTTTCTC
6077098 TCTTTCTATTTT
1 TCTTTCTATTTT
6077110 TCTTTCTATTTT
1 TCTTTCTATTTT
6077122 T-TTTC
1 TCTTTC
6077127 ATGATTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTCTATTTT
Found at i:6086070 original size:40 final size:40
Alignment explanation
Indices: 6086009--6086090 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
6085999 CTCAGGATAG
*
6086009 GTTTATCATCATGCCACAATTGAATAACACAACAGATGAA
1 GTTTATCATCATACCACAATTGAATAACACAACAGATGAA
* *
6086049 GTTTATCATCATACCAGAATTGACTAACACAACAGATGAA
1 GTTTATCATCATACCACAATTGAATAACACAACAGATGAA
6086089 GT
1 GT
6086091 ATTAGTATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (40 bp):
GTTTATCATCATACCACAATTGAATAACACAACAGATGAA
Found at i:6093558 original size:2 final size:2
Alignment explanation
Indices: 6093551--6093583 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6093541 AAGGGAAGAC
6093551 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 A
6093584 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6093879 original size:22 final size:22
Alignment explanation
Indices: 6093854--6093895 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6093844 TATATATTTA
* *
6093854 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
6093876 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
6093896 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:6100998 original size:15 final size:15
Alignment explanation
Indices: 6100978--6101007 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6100968 GGTAGAAAAT
6100978 TTGAGTAACAATAAA
1 TTGAGTAACAATAAA
6100993 TTGAGTAACAATAAA
1 TTGAGTAACAATAAA
6101008 AGAACATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
TTGAGTAACAATAAA
Found at i:6102116 original size:2 final size:2
Alignment explanation
Indices: 6102109--6102139 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6102099 ATTAGGGAGT
6102109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6102140 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6104477 original size:16 final size:16
Alignment explanation
Indices: 6104452--6104490 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
6104442 ATCAAAAATG
* *
6104452 ATATTTTAATTTAATC
1 ATATTATAATTTAATA
6104468 ATATTATAATTTAATA
1 ATATTATAATTTAATA
6104484 ATATTAT
1 ATATTAT
6104491 TATAATCAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTATAATTTAATA
Found at i:6106930 original size:29 final size:29
Alignment explanation
Indices: 6106898--6106957 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
6106888 TCTCTCCTGA
6106898 TTTTCTTTTTCATTTCTTCTCTCTTTTTT
1 TTTTCTTTTTCATTTCTTCTCTCTTTTTT
*
6106927 TTTTTTTTTTCATTTCTTCTCTCTTTTTT
1 TTTTCTTTTTCATTTCTTCTCTCTTTTTT
6106956 TT
1 TT
6106958 GCAATAACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTCTTTTTCATTTCTTCTCTCTTTTTT
Found at i:6112109 original size:24 final size:24
Alignment explanation
Indices: 6112081--6112127 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6112071 AATTATTACC
6112081 TTTAAA-AATAATAATCTATTTATA
1 TTTAAATAATAATAA-CTATTTATA
* *
6112105 TTTAAATAGTTATAACTATTTAT
1 TTTAAATAATAATAACTATTTAT
6112128 TATATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAAATAATAATAACTATTTATA
Found at i:6122747 original size:13 final size:13
Alignment explanation
Indices: 6122729--6122756 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6122719 AATTTATTTA
6122729 AATATATAAAAAT
1 AATATATAAAAAT
6122742 AATATATAAAAAT
1 AATATATAAAAAT
6122755 AA
1 AA
6122757 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATATATAAAAAT
Found at i:6122760 original size:21 final size:20
Alignment explanation
Indices: 6122736--6122789 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
6122726 TTAAATATAT
6122736 AAAAATAATATATAAAAATAA
1 AAAAATAA-ATATAAAAATAA
* *
6122757 AAAATTTAAATTTAAAAATCAA
1 AAAA-ATAAATATAAAAAT-AA
*
6122779 TAAAATAAATA
1 AAAAATAAATA
6122790 AAATTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATAAATATAAAAATAA
Found at i:6122764 original size:36 final size:34
Alignment explanation
Indices: 6122724--6122792 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
6122714 ATCAAAATTT
6122724 ATTTAAATATATAAAAAT-AATATATAA-AAATAAAAA
1 ATTTAAAT-T-TAAAAATCAATA-A-AATAAATAAAAA
6122760 ATTTAAATTTAAAAATCAATAAAATAAATAAAA
1 ATTTAAATTTAAAAATCAATAAAATAAATAAAA
6122793 TTAAATCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 2 0.06
34 16 0.52
35 5 0.16
36 8 0.26
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (34 bp):
ATTTAAATTTAAAAATCAATAAAATAAATAAAAA
Found at i:6124145 original size:17 final size:17
Alignment explanation
Indices: 6124123--6124158 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6124113 ATATTTGAAT
* *
6124123 TTAATAATTGATTAATA
1 TTAATAATCGATAAATA
6124140 TTAATAATCGATAAATA
1 TTAATAATCGATAAATA
6124157 TT
1 TT
6124159 GTATTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (17 bp):
TTAATAATCGATAAATA
Found at i:6131326 original size:18 final size:18
Alignment explanation
Indices: 6131293--6131337 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
6131283 GCCTTTGGGA
* *
6131293 CGTGGTCGGGGTCGTGGC
1 CGTGGTCGTGGACGTGGC
*
6131311 CGTGGTCGTGGACGTGGT
1 CGTGGTCGTGGACGTGGC
*
6131329 CGAGGTCGT
1 CGTGGTCGT
6131338 TAAATATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.04, C:0.20, G:0.51, T:0.24
Consensus pattern (18 bp):
CGTGGTCGTGGACGTGGC
Found at i:6133972 original size:3 final size:3
Alignment explanation
Indices: 6133964--6133989 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6133954 GAATGTATAG
6133964 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6133990 ATTAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6134936 original size:21 final size:20
Alignment explanation
Indices: 6134908--6134950 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
6134898 ATTTACAAAT
*
6134908 TTTATTAAGTAT-GAATTAAA
1 TTTATTAA-TATAAAATTAAA
6134928 TTTATTTAATATAAAATTAAA
1 TTTA-TTAATATAAAATTAAA
6134949 TT
1 TT
6134951 AAATTCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTATTAATATAAAATTAAA
Found at i:6134960 original size:21 final size:21
Alignment explanation
Indices: 6134921--6134960 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6134911 ATTAAGTATG
* *
6134921 AATTAAATTTATTTAATATAA
1 AATTAAATTAAATTAATATAA
*
6134942 AATTAAATTAAATTCATAT
1 AATTAAATTAAATTAATAT
6134961 GTAATAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTAAATTAAATTAATATAA
Found at i:6135766 original size:18 final size:18
Alignment explanation
Indices: 6135743--6135780 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
6135733 TGGAAGTGTC
6135743 ATTGATACATCTGATTTT
1 ATTGATACATCTGATTTT
6135761 ATTGATACATCTGATTTT
1 ATTGATACATCTGATTTT
6135779 AT
1 AT
6135781 CTTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
ATTGATACATCTGATTTT
Found at i:6137659 original size:18 final size:19
Alignment explanation
Indices: 6137636--6137674 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6137626 TCCTTCTGGG
* *
6137636 TGTTGTT-CTTTTTTTTTT
1 TGTTGTTGCATTTTTGTTT
6137654 TGTTGTTGCATTTTTGTTT
1 TGTTGTTGCATTTTTGTTT
6137673 TG
1 TG
6137675 GGTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.03, C:0.05, G:0.18, T:0.74
Consensus pattern (19 bp):
TGTTGTTGCATTTTTGTTT
Found at i:6144467 original size:26 final size:23
Alignment explanation
Indices: 6144421--6144513 Score: 64
Period size: 26 Copynumber: 3.8 Consensus size: 23
6144411 AACGAGTTTG
6144421 TTCATAAATATTAAATAAATATA
1 TTCATAAATATTAAATAAATATA
*
6144444 TTCATTAACATATATAAATGAATATA
1 TTCA-TAA-ATAT-TAAATAAATATA
* * *
6144470 TAT-ATGAATAATAAACAAATTATA
1 T-TCATAAATATTAAATAAA-TATA
*
6144494 ATCAAATAAAT-TTAAATAAA
1 TTC--ATAAATATTAAATAAA
6144514 AAAATTCTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
23 11 0.21
24 10 0.19
25 13 0.25
26 18 0.34
27 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
TTCATAAATATTAAATAAATATA
Found at i:6146792 original size:13 final size:13
Alignment explanation
Indices: 6146774--6146798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6146764 TGTTTTGAAT
6146774 TTTTTATTTTTTA
1 TTTTTATTTTTTA
6146787 TTTTTATTTTTT
1 TTTTTATTTTTT
6146799 TATTAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:6149084 original size:18 final size:18
Alignment explanation
Indices: 6149061--6149098 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6149051 GTGCTTCATT
*
6149061 TTAATTGTTTCATTATTG
1 TTAATTGCTTCATTATTG
6149079 TTAATTGCTTCATTATTG
1 TTAATTGCTTCATTATTG
6149097 TT
1 TT
6149099 TACTATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.61
Consensus pattern (18 bp):
TTAATTGCTTCATTATTG
Found at i:6152497 original size:52 final size:52
Alignment explanation
Indices: 6152411--6152567 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
6152401 TATAACCATA
* * ** *
6152411 CAAACTTGCCCATTAAGAATTTCACTCCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
*
6152463 CAAACTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
* ** * *
6152515 CAAACTTACCTATTAAGAATCCTCTTT-CTCTGGGAATTCTTCTTTTACAAGT
1 CAAACTTGCCTATTAAGAAT-CTCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
6152567 C
1 C
6152568 TTCTTATCCA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 86 0.93
53 6 0.07
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:6167730 original size:2 final size:2
Alignment explanation
Indices: 6167723--6167753 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6167713 GTACTGTAAA
*
6167723 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6167754 GAAGATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6168031 original size:2 final size:2
Alignment explanation
Indices: 6168024--6168054 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6168014 TTATTTAGTG
6168024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6168055 TAGCCTAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6168881 original size:31 final size:31
Alignment explanation
Indices: 6168814--6168881 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
6168804 TGGGACGGAA
* * *
6168814 GAAAATAATATAAATGTAAACAAGGTAGGTT
1 GAAAGTAATATAAACGTAAACAAGGTAGGCT
* *
6168845 CAAAGTAATATAAACGTAAAGAAGGTAGGCT
1 GAAAGTAATATAAACGTAAACAAGGTAGGCT
6168876 GAAAGT
1 GAAAGT
6168882 CCAATCTGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (31 bp):
GAAAGTAATATAAACGTAAACAAGGTAGGCT
Found at i:6169410 original size:2 final size:2
Alignment explanation
Indices: 6169399--6169431 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
6169389 TGAGAAGAGA
*
6169399 AT AT -T AT AT AT AA 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 AT AT AT
6169432 GAAAGGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6169583 original size:20 final size:19
Alignment explanation
Indices: 6169560--6169616 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
6169550 ACATATTCAA
6169560 AATATATGTAAAATATAAAT
1 AATATAT-TAAAATATAAAT
6169580 AATATAATTAAAATATCAAAT
1 AATAT-ATTAAAATAT-AAAT
*
6169601 CATA-ATTAAAA-ATAAA
1 AATATATTAAAATATAAA
6169617 ACTTTTAACT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 7 0.21
20 13 0.38
21 9 0.26
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (19 bp):
AATATATTAAAATATAAAT
Found at i:6176771 original size:169 final size:170
Alignment explanation
Indices: 6176478--6176806 Score: 491
Period size: 169 Copynumber: 1.9 Consensus size: 170
6176468 AACTAACCTG
*
6176478 TACAATACATGATCCATTGGTTATGGTTGACAAAAGCGCCAGTATTATTTTATGCCATAAAACCT
1 TACAATACATGATCCATTGGTTATGGTTGACAAAAGCGCCAGTATTATTTTATCCCATAAAACCT
* ** *
6176543 CGCTTCTTACCTACTACATTATCCATTGATGTTATCACTTGATCTTATTACTGTTGATATTAATA
66 CGCTTCTTACCTACTACATTATCCATTGATGTTATCAATCAATCTTATTACTATTGATATTAATA
*
6176608 GTAATCAAGAAAAAACCTTGCTTTTCCTTCAACCAACCCT
131 CTAATCAAGAAAAAACCTTGCTTTTCCTTCAACCAACCCT
* * *
6176648 TACAATAC-TGATTCATTGGTTATGGTTGACAAAAGCGCC-TTAATTATTTTGTCCCATAAAACC
1 TACAATACATGATCCATTGGTTATGGTTGACAAAAGCGCCAGT-ATTATTTTATCCCATAAAACC
** * * *
6176711 TTTCTTCTTCCCTACTGCATTATCCATTGATGTTATCAATCAATCTTGTTACTATTGATATTAAT
65 TCGCTTCTTACCTACTACATTATCCATTGATGTTATCAATCAATCTTATTACTATTGATATTAAT
* *
6176776 ACTGATCAAGAAAAAACCTTGCTTTTTCTTC
130 ACTAATCAAGAAAAAACCTTGCTTTTCCTTC
6176807 TCGTTTAGTT
Statistics
Matches: 142, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
168 1 0.01
169 133 0.94
170 8 0.06
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (170 bp):
TACAATACATGATCCATTGGTTATGGTTGACAAAAGCGCCAGTATTATTTTATCCCATAAAACCT
CGCTTCTTACCTACTACATTATCCATTGATGTTATCAATCAATCTTATTACTATTGATATTAATA
CTAATCAAGAAAAAACCTTGCTTTTCCTTCAACCAACCCT
Found at i:6194266 original size:16 final size:19
Alignment explanation
Indices: 6194245--6194282 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
6194235 CTTACCGCAG
6194245 TTTACA-ATTT-TG-TTTT
1 TTTACAGATTTATGATTTT
6194261 TTTACAGATTTATGATTTT
1 TTTACAGATTTATGATTTT
6194280 TTT
1 TTT
6194283 TTTTGGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 4 0.21
18 2 0.11
19 7 0.37
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.66
Consensus pattern (19 bp):
TTTACAGATTTATGATTTT
Found at i:6198344 original size:11 final size:11
Alignment explanation
Indices: 6198328--6198359 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
6198318 ATTTATAAAA
6198328 AAAATTCATTT
1 AAAATTCATTT
*
6198339 AAAATTTATTT
1 AAAATTCATTT
6198350 AAAATTCATT
1 AAAATTCATT
6198360 CATTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATTCATTT
Found at i:6198500 original size:25 final size:24
Alignment explanation
Indices: 6198472--6198531 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
6198462 GTTCGTTTGA
6198472 GTTTGTTTATATTAATTTATGATT-T
1 GTTTGTTTATATTAATTTA--ATTAT
* *
6198497 GTTTGTTTAAATTTATTTAATTAT
1 GTTTGTTTATATTAATTTAATTAT
6198521 GATTTGTTTAT
1 G-TTTGTTTAT
6198532 TGTTTATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 2 0.07
25 25 0.83
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.63
Consensus pattern (24 bp):
GTTTGTTTATATTAATTTAATTAT
Found at i:6200779 original size:17 final size:18
Alignment explanation
Indices: 6200751--6200784 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6200741 ACATGGTCAT
6200751 AAATATTATTTTATTAAA
1 AAATATTATTTTATTAAA
*
6200769 AAATA-TATTTTTTTAA
1 AAATATTATTTTATTAA
6200785 TTTTAATTAA
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:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATATTATTTTATTAAA
Found at i:6201411 original size:34 final size:34
Alignment explanation
Indices: 6201373--6201495 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 34
6201363 ATATTTTTAA
*
6201373 TATTTTAATAATAAATAGTATTATATTATATTAT
1 TATTTTAATAATAAATAGTATTATATAATATTAT
* *
6201407 TATTTTAATAATAAATACAGATATAGTAAATAATTTTTAT
1 TATTTTAATAATAAAT--AG-TAT--TATATAA-TATTAT
* *
6201447 TATTTTAATAATTAATATTGT-TTCATATAATAATAT
1 TATTTTAATAA-TAA-ATAGTATT-ATATAATATTAT
6201483 TATTTTAATAATA
1 TATTTTAATAATA
6201496 TGACTATTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
34 16 0.22
35 2 0.03
36 18 0.25
37 8 0.11
38 1 0.01
39 6 0.08
40 17 0.23
41 3 0.04
42 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (34 bp):
TATTTTAATAATAAATAGTATTATATAATATTAT
Found at i:6201495 original size:17 final size:17
Alignment explanation
Indices: 6201444--6201508 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 17
6201434 AAATAATTTT
6201444 TATTATTTTAATAATTAA
1 TATTATTTTAATAA-TAA
* *
6201462 TATTGTTTCATATAATAA
1 TATTATTTTA-ATAATAA
6201480 TATTATTTTAATAAT-A
1 TATTATTTTAATAATAA
*
6201496 TGACTATTTTAAT
1 T-ATTATTTTAAT
6201509 CATGTTTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.05
17 15 0.38
18 19 0.47
19 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TATTATTTTAATAATAA
Found at i:6201858 original size:24 final size:25
Alignment explanation
Indices: 6201829--6201876 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
6201819 ATAATGTTAA
*
6201829 TAATAAAT-ATTTTCAATATTTTAC
1 TAATAAATAATTTTCAAAATTTTAC
*
6201853 TAATAAATAATTTTGAAAATTTTA
1 TAATAAATAATTTTCAAAATTTTA
6201877 ATAGTTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
TAATAAATAATTTTCAAAATTTTAC
Found at i:6202007 original size:20 final size:20
Alignment explanation
Indices: 6201970--6202009 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6201960 AATAATATTG
*
6201970 ACTATTTTGTATACATAAAA
1 ACTATTTTATATACATAAAA
* *
6201990 ACTATTTTATTTAGATAAAA
1 ACTATTTTATATACATAAAA
6202010 TCCTATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (20 bp):
ACTATTTTATATACATAAAA
Found at i:6202068 original size:30 final size:30
Alignment explanation
Indices: 6202032--6202091 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
6202022 TATTATTATG
6202032 AACATAATTTGTAACTTTTGTAAAGACTAT
1 AACATAATTTGTAACTTTTGTAAAGACTAT
6202062 AACATAATTTGTAACTTTTGTAAAGACTAT
1 AACATAATTTGTAACTTTTGTAAAGACTAT
6202092 CTTTTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (30 bp):
AACATAATTTGTAACTTTTGTAAAGACTAT
Found at i:6202182 original size:7 final size:7
Alignment explanation
Indices: 6202170--6202199 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
6202160 TTTTATTGTG
6202170 TTTAATT
1 TTTAATT
6202177 TTTAATT
1 TTTAATT
6202184 TTTAATT
1 TTTAATT
6202191 TTTAATT
1 TTTAATT
6202198 TT
1 TT
6202200 ATATTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTAATT
Found at i:6203417 original size:47 final size:47
Alignment explanation
Indices: 6203364--6203457 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
6203354 TTTTAATTTT
*
6203364 AACTGTTAGAGGTGAGAATCTAGTAAGTGAAATGAAATGAGTTTTCA
1 AACTGTTAGAGGTAAGAATCTAGTAAGTGAAATGAAATGAGTTTTCA
* * * * *
6203411 AACTGTTAGATGTAAGAGTCTAGTATGTGAAATGGAGTGAGTTTTCA
1 AACTGTTAGAGGTAAGAATCTAGTAAGTGAAATGAAATGAGTTTTCA
6203458 TTTGCAAGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (47 bp):
AACTGTTAGAGGTAAGAATCTAGTAAGTGAAATGAAATGAGTTTTCA
Found at i:6207738 original size:5 final size:5
Alignment explanation
Indices: 6207728--6207809 Score: 91
Period size: 5 Copynumber: 16.6 Consensus size: 5
6207718 TAGGTGTTTG
6207728 TTATT TTATT TTATT TTATTT TTATT TTATT TTATTT TTATTT TTATT
1 TTATT TTATT TTATT TTA-TT TTATT TTATT TTA-TT TTA-TT TTATT
* *
6207776 TT-TA TT-TT TTATT TT-TA TT-TT TTATT TTATT TTA
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTA
6207810 GGATATTAGC
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
4 12 0.17
5 41 0.59
6 16 0.23
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:6207752 original size:6 final size:6
Alignment explanation
Indices: 6207731--6207808 Score: 103
Period size: 6 Copynumber: 13.5 Consensus size: 6
6207721 GTGTTTGTTA
6207731 TTTTA- TTTTA- TTTTAT TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
6207775 TTTTATT TTTTAT TTTTAT TTTT-T ATTTTAT TTT
1 TTTTA-T TTTTAT TTTTAT TTTTAT -TTTTAT TTT
6207809 AGGATATTAG
Statistics
Matches: 68, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
5 21 0.31
6 40 0.59
7 7 0.10
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:6209032 original size:59 final size:60
Alignment explanation
Indices: 6208817--6209103 Score: 355
Period size: 58 Copynumber: 5.0 Consensus size: 60
6208807 TTTCAAACAA
* *
6208817 AAAAATTAAAAAATTAAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAA-TAAAAATTTAAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* ** *
6208878 CAAAATAAAAATTT-CTAAAA-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAATAAAAATTTAAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
** *
6208936 AAAAATAAAAATTTTTAAAAATAT-TTTTGGAG-AAAAGTTGAAAGTATCAATTTTT-TT
1 AAAAATAAAAATTTAAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* *
6208993 GAAAAT-AAAATTTAAAAAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAA-TTTT-TT
1 AAAAATAAAAATTT-AAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* *
6209051 AAAAAT-AAAA-TTAAAAAAA-ATA-TTTTAAGAAAAAATTGAAAGTATCAATTTTT
1 AAAAATAAAAATTTAAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTT
6209104 ATTGTATAAA
Statistics
Matches: 205, Mismatches: 15, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
54 25 0.12
55 7 0.03
56 14 0.07
57 17 0.08
58 95 0.46
59 33 0.16
60 10 0.05
61 4 0.02
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (60 bp):
AAAAATAAAAATTTAAAAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
Found at i:6209101 original size:26 final size:26
Alignment explanation
Indices: 6209019--6209102 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
6209009 AAAAATATAT
*
6209019 TTTTAAGAAAAAGTTGAAAGTATCAA
1 TTTTAAGAAAAAATTGAAAGTATCAA
* * **
6209045 TTTTTTAAAAATAAAATT-AAA-AAAAATA
1 --TTTTAAGAA-AAAATTGAAAGTATCA-A
6209073 TTTTAAGAAAAAATTGAAAGTATCAA
1 TTTTAAGAAAAAATTGAAAGTATCAA
6209099 TTTT
1 TTTT
6209103 TATTGTATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
25 6 0.14
26 16 0.37
27 4 0.09
28 12 0.28
29 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (26 bp):
TTTTAAGAAAAAATTGAAAGTATCAA
Found at i:6212571 original size:8 final size:8
Alignment explanation
Indices: 6212560--6212612 Score: 63
Period size: 8 Copynumber: 6.4 Consensus size: 8
6212550 AAAAGGTTTC
*
6212560 AAAGATAA
1 AAAGAAAA
6212568 AAAGAAAAA
1 AAAG-AAAA
6212577 AAAGAAAA
1 AAAGAAAA
6212585 AAAGTAAAA
1 AAAG-AAAA
6212594 CAAAG-AAA
1 -AAAGAAAA
6212602 AAAGAAAA
1 AAAGAAAA
6212610 AAA
1 AAA
6212613 ATGAATGGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 4 0.10
8 21 0.52
9 11 0.28
10 4 0.10
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (8 bp):
AAAGAAAA
Done.