Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 41 of 208
Found at i:11263918 original size:28 final size:28
Alignment explanation
Indices: 11263878--11263945 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
11263868 TATCTAAATA
*
11263878 GTCTCGAGACAAAGTGGTCTTTGTCTTT
1 GTCTCGAGACAAAGTGGTCTTTGCCTTT
*
11263906 GTCTCAAGACAAAGTGGTCTTTGCCTTT
1 GTCTCGAGACAAAGTGGTCTTTGCCTTT
11263934 GTCTCGAGACAA
1 GTCTCGAGACAA
11263946 GAAAACATCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (28 bp):
GTCTCGAGACAAAGTGGTCTTTGCCTTT
Found at i:11266218 original size:17 final size:18
Alignment explanation
Indices: 11266178--11266218 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
11266168 TTTATTTTAT
11266178 TATTTTTCCCAACATCTC
1 TATTTTTCCCAACATCTC
* *
11266196 TA-TTTTCCC-ACGTTTC
1 TATTTTTCCCAACATCTC
11266212 TATTTTT
1 TATTTTT
11266219 TCTCTTACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 11 0.55
18 2 0.10
ACGTcount: A:0.17, C:0.27, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTTTTCCCAACATCTC
Found at i:11276056 original size:18 final size:18
Alignment explanation
Indices: 11276033--11276070 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
11276023 GATAGTGAGT
11276033 CATGTCATGACGTCAAAC
1 CATGTCATGACGTCAAAC
11276051 CATGTCATGACGTCAAAC
1 CATGTCATGACGTCAAAC
11276069 CA
1 CA
11276071 CTTGACATCG
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:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (18 bp):
CATGTCATGACGTCAAAC
Found at i:11277211 original size:22 final size:23
Alignment explanation
Indices: 11277161--11277212 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
11277151 ACACCACACT
* *
11277161 AGTAGGCACCGAAGTGCTTTAAC
1 AGTAGGCACCAAAGTGCTTGAAC
*
11277184 AGTAGGCACCAAAGTGC-TGAGC
1 AGTAGGCACCAAAGTGCTTGAAC
11277206 AGTAGGC
1 AGTAGGC
11277213 CTCGTAGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (23 bp):
AGTAGGCACCAAAGTGCTTGAAC
Found at i:11279554 original size:24 final size:24
Alignment explanation
Indices: 11279525--11279574 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
11279515 AAAGCATAGG
*
11279525 TACTTTTTGGAAAAAATTTATTAC
1 TACTTTTTCGAAAAAATTTATTAC
**
11279549 TACTTTTTCGAAAAGGTTTATTAC
1 TACTTTTTCGAAAAAATTTATTAC
11279573 TA
1 TA
11279575 TAAATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (24 bp):
TACTTTTTCGAAAAAATTTATTAC
Found at i:11281775 original size:3 final size:3
Alignment explanation
Indices: 11281767--11281826 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
11281757 AAAATGCAAG
11281767 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
11281815 GAA GAA GAA GAA
1 GAA GAA GAA GAA
11281827 AACCATCGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11282504 original size:15 final size:16
Alignment explanation
Indices: 11282484--11282513 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11282474 ATTGTATTAT
11282484 TTAATTGTT-TAATAG
1 TTAATTGTTGTAATAG
11282499 TTAATTGTTGTAATA
1 TTAATTGTTGTAATA
11282514 CAATAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (16 bp):
TTAATTGTTGTAATAG
Found at i:11282694 original size:37 final size:37
Alignment explanation
Indices: 11282624--11282694 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
11282614 TTTAACTTAC
* * *
11282624 AAGTATATGGTTATTTGATACATGAATGGAAATGAGT
1 AAGTATATGGTTACTTGATACATGAACGAAAATGAGT
* * *
11282661 AAGTGTATGGTTACTTGATATATGTACGAAAATG
1 AAGTATATGGTTACTTGATACATGAACGAAAATG
11282695 TTCAAGAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (37 bp):
AAGTATATGGTTACTTGATACATGAACGAAAATGAGT
Found at i:11283500 original size:36 final size:36
Alignment explanation
Indices: 11283453--11283533 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
11283443 TGTTAAGTGA
11283453 TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
1 TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
*
11283489 TGTACTTGTGAATGTAACAGGATGCCAAATGTTATT
1 TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
11283525 TGTACTTGT
1 TGTACTTGT
11283534 TACATTATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (36 bp):
TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
Found at i:11284675 original size:23 final size:23
Alignment explanation
Indices: 11284649--11284693 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
11284639 TGAACAATAC
11284649 GACCATGTTCCATAGCTTCGCAT
1 GACCATGTTCCATAGCTTCGCAT
11284672 GACCATGTTCCATAGCTTCGCA
1 GACCATGTTCCATAGCTTCGCA
11284694 AGGCCTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (23 bp):
GACCATGTTCCATAGCTTCGCAT
Found at i:11285382 original size:4 final size:4
Alignment explanation
Indices: 11285369--11285399 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
11285359 TGGTTTTTTA
11285369 AATT -ATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
11285400 GAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
AATT
Found at i:11285980 original size:18 final size:17
Alignment explanation
Indices: 11285952--11285985 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11285942 AAAGTAGTGA
11285952 AAATTTATTTTAGGAAT
1 AAATTTATTTTAGGAAT
*
11285969 AAATTCTATTTTTGGAA
1 AAATT-TATTTTAGGAA
11285986 AATTGCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
AAATTTATTTTAGGAAT
Found at i:11289650 original size:42 final size:42
Alignment explanation
Indices: 11289536--11289698 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 42
11289526 CAAAAATATC
* * *
11289536 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
* * * * *
11289578 ATAACGATGCCACTGTCCTAGAC-CGAGTCTTACACGTAATCAT
1 AT-ACAATGCCAATGTCCCAGACATG-GTCTTACACGTAATCAA
*
11289621 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCGCAA
1 ATACAATGCCAATGTCCCAGACATGGTCTTACACGT-AAT--CAA
*
11289666 AT-CAATGCCAATGTCCTAGACA-GGTCTTACACG
1 ATACAATGCCAATGTCCCAGACATGGTCTTACACG
11289699 ATATCACATA
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
42 32 0.31
43 48 0.47
44 18 0.18
45 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
ATACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCAA
Found at i:11289693 original size:85 final size:84
Alignment explanation
Indices: 11289536--11289698 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 84
11289526 CAAAAATATC
* * * *
11289536 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCACTGTCCTAGAC
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAAT-ACAATGCCAATGTCCTAGAC
*
11289601 CGAGTCTTACACGTAATCAT
65 AGAGTCTTACACGTAATCAT
* *
11289621 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCGCAAAT-CAATGCCAATGTCCTAG
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGT-AAT--CAAATACAATGCCAATGTCCTAG
11289685 ACAG-GTCTTACACG
63 ACAGAGTCTTACACG
11289699 ATATCACATA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
85 42 0.62
86 21 0.31
88 5 0.07
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (84 bp):
ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATACAATGCCAATGTCCTAGACA
GAGTCTTACACGTAATCAT
Found at i:11296263 original size:2 final size:2
Alignment explanation
Indices: 11296256--11296292 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
11296246 TTTAACTATA
*
11296256 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
11296293 AAGTATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:11302147 original size:40 final size:40
Alignment explanation
Indices: 11302071--11302148 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
11302061 ATGCACACAC
* * *
11302071 GTGCCCCTATTTGTACTTCGATACCCCTGGATGCATATAT
1 GTGCCCCTATTAGTACTTCGATACCCCTGAAGGCATATAT
* * *
11302111 GTGCCCCTATTAGTACTTTGGTACTCCTGAAGGCATAT
1 GTGCCCCTATTAGTACTTCGATACCCCTGAAGGCATAT
11302149 TCATGCTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (40 bp):
GTGCCCCTATTAGTACTTCGATACCCCTGAAGGCATATAT
Found at i:11308419 original size:26 final size:27
Alignment explanation
Indices: 11308390--11308447 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
11308380 AACCTTAAAG
11308390 TAAAC-TTGTTTTCTCATTTTAATACC
1 TAAACTTTGTTTTCTCATTTTAATACC
* *
11308416 TAAACTTTTTTTTTCTCATTTTGATACC
1 TAAAC-TTTGTTTTCTCATTTTAATACC
11308444 TAAA
1 TAAA
11308448 GTACTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.18
28 23 0.82
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.52
Consensus pattern (27 bp):
TAAACTTTGTTTTCTCATTTTAATACC
Found at i:11308669 original size:90 final size:83
Alignment explanation
Indices: 11308521--11308696 Score: 235
Period size: 89 Copynumber: 2.0 Consensus size: 83
11308511 TGCAAAAAGT
* *
11308521 CCTCAAACTTAAAAAAAAAATTAAGCCCCTGATTTTTTTTTCACTCAATTGGGTACTTGAACTTT
1 CCTCAAACTTAAAAAAAAAATTAAGCCCATGATTTTTTTTTCACTCAATTGGGTACTTGAACTAT
*
11308586 CAAAATGCATAAAAAATGC
66 C-AAATGCATAAAAAAGGC
* *
11308605 CCTCAAACTTAAAAAAAAAGCAATTATGCCCATGTTTTTTTTTTTTGCACTCAATTGGGTACTTG
1 CCTCAAACTT-AAAAAAAA--AATTAAGCCCATG--ATTTTTTTTT-CACTCAATTGGGTACTTG
*
11308670 AACTATCAAATGCATCAAAAAGGC
60 AACTATCAAATGCATAAAAAAGGC
11308694 CCT
1 CCT
11308697 TTGATCGTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
84 10 0.12
85 8 0.10
87 11 0.14
89 27 0.34
90 24 0.30
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (83 bp):
CCTCAAACTTAAAAAAAAAATTAAGCCCATGATTTTTTTTTCACTCAATTGGGTACTTGAACTAT
CAAATGCATAAAAAAGGC
Found at i:11308836 original size:19 final size:19
Alignment explanation
Indices: 11308814--11308873 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
11308804 ATAAAAAATA
*
11308814 AAAATAAATAAAATTTATT
1 AAAATAATTAAAATTTATT
* *
11308833 AAAAT-ATTAAATTTTAATA
1 AAAATAATTAAAATTT-ATT
*
11308852 AAAATATTTAAAATTTATT
1 AAAATAATTAAAATTTATT
11308871 AAA
1 AAA
11308874 TATTAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.24
19 17 0.52
20 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATAATTAAAATTTATT
Found at i:11308848 original size:18 final size:18
Alignment explanation
Indices: 11308822--11308878 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
11308812 TAAAAATAAA
11308822 TAAAATTTATTAAAATAT
1 TAAAATTTATTAAAATAT
* *
11308840 TAAATTTTAATAAAAATATT
1 TAAAATTT-ATTAAAATA-T
11308860 TAAAATTTATT-AAATAT
1 TAAAATTTATTAAAATAT
11308877 TA
1 TA
11308879 GAAAAAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 10 0.30
20 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTTATTAAAATAT
Found at i:11309120 original size:20 final size:19
Alignment explanation
Indices: 11309083--11309130 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
11309073 TTTTTATATG
11309083 AATTTTAT-ATTTCTTTAC
1 AATTTTATAATTTCTTTAC
11309101 ATATTTTATAATTT-TCTTAC
1 A-ATTTTATAATTTCT-TTAC
*
11309121 AACTTTATAA
1 AATTTTATAA
11309131 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTATAATTTCTTTAC
Found at i:11309205 original size:20 final size:19
Alignment explanation
Indices: 11309162--11309223 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
11309152 TTTCTATATG
11309162 TTTTATAAAATTTTACGAT
1 TTTTATAAAATTTTACGAT
*
11309181 TTTTATAAAATTTTACAGTT
1 TTTTATAAAATTTTAC-GAT
**
11309201 TTTTATAATTTTTTTACGAT
1 TTTTATAA-AATTTTACGAT
11309221 TTT
1 TTT
11309224 GTAATTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 16 0.43
20 15 0.41
21 6 0.16
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTACGAT
Found at i:11309262 original size:19 final size:19
Alignment explanation
Indices: 11309191--11309263 Score: 51
Period size: 19 Copynumber: 3.7 Consensus size: 19
11309181 TTTTATAAAA
* *
11309191 TTTTACAGTTTTTTATAATT
1 TTTTATAGTTTTTAAT-ATT
11309211 TTTT-TACGATTTTGTAAT-TGT
1 TTTTATA-G-TTTT-TAATAT-T
* *
11309232 TTTTCTAATTTTTAATATT
1 TTTTATAGTTTTTAATATT
11309251 TTTTATAGTTTTT
1 TTTTATAGTTTTT
11309264 TAATTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
19 17 0.40
20 11 0.26
21 9 0.21
22 5 0.12
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTATAGTTTTTAATATT
Found at i:11309591 original size:13 final size:13
Alignment explanation
Indices: 11309573--11309597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11309563 ATAACAAATA
11309573 TAAAAATATATAT
1 TAAAAATATATAT
11309586 TAAAAATATATA
1 TAAAAATATATA
11309598 AAATAGAAGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAATATATAT
Found at i:11315713 original size:12 final size:12
Alignment explanation
Indices: 11315696--11315720 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11315686 GTAAAAGTGC
11315696 ATATTTTATTAA
1 ATATTTTATTAA
11315708 ATATTTTATTAA
1 ATATTTTATTAA
11315720 A
1 A
11315721 ATTAGTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTTATTAA
Found at i:11317067 original size:27 final size:27
Alignment explanation
Indices: 11317026--11317079 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
11317016 TTGCACTCCA
*
11317026 AAATAGATAATGTTTATTAACTTTGTT
1 AAATAGATAAAGTTTATTAACTTTGTT
*
11317053 AAATATATAAAGTTTATTAACTTTGTT
1 AAATAGATAAAGTTTATTAACTTTGTT
11317080 GATGTGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (27 bp):
AAATAGATAAAGTTTATTAACTTTGTT
Found at i:11320761 original size:19 final size:18
Alignment explanation
Indices: 11320729--11320764 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11320719 CAATTTAGAA
*
11320729 ACGAAAATATTAATAATG
1 ACGAAAATAATAATAATG
11320747 ACGATAAATAATAATAAT
1 ACGA-AAATAATAATAAT
11320765 AACAATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (18 bp):
ACGAAAATAATAATAATG
Found at i:11320772 original size:19 final size:19
Alignment explanation
Indices: 11320733--11320773 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
11320723 TTAGAAACGA
* * *
11320733 AAATATTAATAATGACGAT
1 AAATAATAATAATAACAAT
11320752 AAATAATAATAATAACAAT
1 AAATAATAATAATAACAAT
11320771 AAA
1 AAA
11320774 CAATTTAAGG
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:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAATAATAATAATAACAAT
Found at i:11320960 original size:3 final size:3
Alignment explanation
Indices: 11320952--11320998 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
11320942 AAAAGGGGGA
11320952 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11320999 CAGAAAACAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11322686 original size:44 final size:44
Alignment explanation
Indices: 11322585--11322781 Score: 182
Period size: 44 Copynumber: 4.4 Consensus size: 44
11322575 TATCTACAGT
11322585 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAAC
1 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAAC
** *
11322629 CCACTTCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAAC
1 CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAAC
* * ** * *** * *
11322673 CTGCCCCATTACAACTTCAAGGG-GATAAGGTTTATGGCTTCCAT
1 CTGCTCCACTACAACTTC-AGGGAGATAAGACTTGTTATTTCAAC
* * * *
11322717 CTACTCCACTGCAACTTTAGGGAGATAAGA-TTGATTTATTTGTAAC
1 CTGCTCCACTACAACTTCAGGGAGATAAGACTTG--TTATTT-CAAC
*
11322763 CTGCTCCACTGCAACTTCA
1 CTGCTCCACTACAACTTCA
11322782 ATGAGGTCAG
Statistics
Matches: 117, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
43 6 0.05
44 86 0.74
45 7 0.06
46 18 0.15
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
CTGCTCCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAAC
Found at i:11322935 original size:89 final size:89
Alignment explanation
Indices: 11322779--11323015 Score: 404
Period size: 89 Copynumber: 2.7 Consensus size: 89
11322769 CACTGCAACT
* *
11322779 TCAATGAGGTCAGGCTGGTATCTTCGATCTGCTTCGCTGCC-AGTACAGGAAGACAAGATCTGCT
1 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGA-TACAGGAAGACAAGATCTGCT
11322843 ATCTTCAGTCTGTTCCGCTACAAAC
65 ATCTTCAGTCTGTTCCGCTACAAAC
11322868 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGATCTGCTA
1 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGATCTGCTA
*
11322933 TCTTCAGTCTGTTCCGCTGCAAAC
66 TCTTCAGTCTGTTCCGCTACAAAC
* * *
11322957 TCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCTGGTACAGGAAGACAAGAT
1 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGAT
11323016 ATGTTATTTT
Statistics
Matches: 141, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
89 140 0.99
90 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (89 bp):
TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGATCTGCTA
TCTTCAGTCTGTTCCGCTACAAAC
Found at i:11324055 original size:51 final size:51
Alignment explanation
Indices: 11323947--11324256 Score: 431
Period size: 51 Copynumber: 6.3 Consensus size: 51
11323937 CTTGCGTATG
** *
11323947 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* **
11323997 ATCACTTGCCATTTACCACTGATCAGATAAGTGTAGCTGAAGCTACCAC-T
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
11324047 -T-A--T--CACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
11324092 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
11324143 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* * *
11324194 ATCACTTGCCATTTGTCACTAATTAGATAAGTGTAGCTG-AGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
11324244 ATCACTTGTCACT
1 ATCACTTGCCACT
11324257 GATCAGAAGT
Statistics
Matches: 234, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
44 36 0.15
45 1 0.00
46 2 0.01
47 1 0.00
48 1 0.00
49 2 0.01
50 54 0.23
51 137 0.59
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
Found at i:11331595 original size:16 final size:16
Alignment explanation
Indices: 11331570--11331620 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
11331560 AATAAAGAGC
11331570 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
11331586 AAATATGCTAGTAAAT
1 AAATACGCTAGTAAAT
* *
11331602 AAACACGCGAGTAAAT
1 AAATACGCTAGTAAAT
11331618 AAA
1 AAA
11331621 ATACTAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:11332539 original size:19 final size:19
Alignment explanation
Indices: 11332506--11332557 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
11332496 GCAATTTAGA
*
11332506 AACGA-AAATATTAATAAT
1 AACGATAAATAATAATAAT
*
11332524 GACGATAAATAATAATAAT
1 AACGATAAATAATAATAAT
* *
11332543 AACAATAAACAATAA
1 AACGATAAATAATAA
11332558 ACAATTTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (19 bp):
AACGATAAATAATAATAAT
Found at i:11332775 original size:3 final size:3
Alignment explanation
Indices: 11332767--11332818 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
11332757 AAAAGGGAAC
* *
11332767 ATA ATA ATA ATA ATA ATA ATA ATA AGA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11332815 ATA A
1 ATA A
11332819 CAGCAAACAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:11334445 original size:22 final size:22
Alignment explanation
Indices: 11334397--11334449 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
11334387 AGGTAGTGTT
* * *
11334397 GCGACACCGATCTTGTGATGTT
1 GCGACATCGATCCTGTGATGTC
*
11334419 ACGACATCGATCCTGTGATGTC
1 GCGACATCGATCCTGTGATGTC
11334441 GCGACATCG
1 GCGACATCG
11334450 GGCAATGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCGACATCGATCCTGTGATGTC
Found at i:11339872 original size:18 final size:18
Alignment explanation
Indices: 11339849--11339883 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11339839 TTATTGATTG
11339849 AATTGAA-TACTTGAATTT
1 AATTGAAGTACTT-AATTT
11339867 AATTGAAGTACTTAATT
1 AATTGAAGTACTTAATT
11339884 GAATGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
AATTGAAGTACTTAATTT
Found at i:11340868 original size:28 final size:28
Alignment explanation
Indices: 11340836--11340914 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
11340826 GAATCATTGC
* ** *
11340836 AATATAGCACACATTAAGTGTTGAGTCA
1 AATATAACACACATTAACCGTTGAATCA
11340864 AATATAACACACATTAACCGTTGAATCA
1 AATATAACACACATTAACCGTTGAATCA
** *
11340892 AATATAACATGCATTAAGCGTTG
1 AATATAACACACATTAACCGTTG
11340915 GATCTCCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (28 bp):
AATATAACACACATTAACCGTTGAATCA
Found at i:11342299 original size:4 final size:4
Alignment explanation
Indices: 11342290--11342316 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
11342280 TCTTCCTCAA
11342290 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
11342317 GCATGACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:11342770 original size:21 final size:21
Alignment explanation
Indices: 11342725--11342800 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
11342715 ATCTTCAAGG
*
11342725 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
11342744 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
11342765 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
11342786 TTATGCAATCTTAGA
1 ATATGCAATCTTAGA
11342801 ATATATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.34
21 35 0.66
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:11342822 original size:23 final size:24
Alignment explanation
Indices: 11342745--11342823 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 24
11342735 TTAGATATGA
*
11342745 TATGCAATCTTAG---ATATGATA
1 TATGCAATCTTAGAATATATGATT
11342766 TATGCAATCTTAG---ATATGATT
1 TATGCAATCTTAGAATATATGATT
11342787 TATGCAATCTTAGAATATATGATT
1 TATGCAATCTTAGAATATATGATT
*
11342811 T-TGTAATCTTAGA
1 TATGCAATCTTAGA
11342824 GATTTAATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 33 0.62
23 11 0.21
24 9 0.17
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (24 bp):
TATGCAATCTTAGAATATATGATT
Found at i:11343102 original size:4 final size:4
Alignment explanation
Indices: 11343093--11343131 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
11343083 TTAGTTCTTT
11343093 TTTA TTTA -TTA -TTA TTTA TTTA -TTA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
11343132 TTATTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 12 0.38
4 20 0.62
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:11343111 original size:7 final size:7
Alignment explanation
Indices: 11343094--11343137 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
11343084 TAGTTCTTTT
11343094 TTATTTA
1 TTATTTA
11343101 TTA-TTA
1 TTATTTA
11343107 TTTATTTA
1 -TTATTTA
11343115 TTATTTA
1 TTATTTA
11343122 TTATTTA
1 TTATTTA
11343129 TT-TTTA
1 TTATTTA
11343135 TTA
1 TTA
11343138 AATTTGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 9 0.26
7 22 0.65
8 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:11343175 original size:20 final size:20
Alignment explanation
Indices: 11343119--11343178 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
11343109 TATTTATTAT
* *
11343119 TTATTATTTATTTTTATTAAAT
1 TTATTA-TTATTGTTATT-AAG
*
11343141 TTGATT-TTCTTGTTATTAAG
1 TT-ATTATTATTGTTATTAAG
11343161 TTATTATTATTGTTATTA
1 TTATTATTATTGTTATTA
11343179 TTACCAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.09
20 15 0.47
21 9 0.28
22 2 0.06
23 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.65
Consensus pattern (20 bp):
TTATTATTATTGTTATTAAG
Found at i:11343354 original size:17 final size:17
Alignment explanation
Indices: 11343323--11343421 Score: 73
Period size: 17 Copynumber: 5.9 Consensus size: 17
11343313 GCATAACTTT
*
11343323 ATATAC-ATATATATAC
1 ATATACTATTTATATAC
*
11343339 ATTTACTATTTATATAC
1 ATATACTATTTATATAC
* *
11343356 ATATACTATTTTATTTCC
1 ATATACTA-TTTATATAC
* *
11343374 TTA-ACT-TTTATATGC
1 ATATACTATTTATATAC
*
11343389 ATATA-TATATATATATAT
1 ATATACTAT-T-TATATAC
11343407 ATATACT-TTTATATA
1 ATATACTATTTATATA
11343422 TTTTTTACTT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
15 10 0.15
16 13 0.20
17 21 0.32
18 20 0.31
19 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (17 bp):
ATATACTATTTATATAC
Found at i:11347207 original size:19 final size:18
Alignment explanation
Indices: 11347183--11347223 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
11347173 CATATTGCCT
11347183 AAAAAGATGGCGCAAACAA
1 AAAAAGATGGCGCAAA-AA
11347202 AAAAAGATGGCGCAAAAA
1 AAAAAGATGGCGCAAAAA
11347220 AAAA
1 AAAA
11347224 CTCTATCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.63, C:0.12, G:0.20, T:0.05
Consensus pattern (18 bp):
AAAAAGATGGCGCAAAAA
Found at i:11347905 original size:2 final size:2
Alignment explanation
Indices: 11347898--11347924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11347888 CTCCCAAGCT
11347898 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11347925 TGCCAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11348190 original size:41 final size:40
Alignment explanation
Indices: 11348061--11348190 Score: 120
Period size: 41 Copynumber: 3.2 Consensus size: 40
11348051 TTAAAAACAG
* * *
11348061 ATTCACCGGCATTTAGCCTGCTAGGCTTAAAGCCTG-ATT
1 ATTCACCGGCATTTAGCCTGCTAGACATAAAGTCTGAATT
* **
11348100 CAGTACACCGGCATTTAGCCTGCTAGACATTTAGTCTGAAATGT
1 -A-TTCACCGGCATTTAGCCTGCTAGACATAAAGTCTG-AAT-T
* * *
11348144 A-TCACCGGCATTAAGCCAGCTAGACGTAAAGTCTGAATT
1 ATTCACCGGCATTTAGCCTGCTAGACATAAAGTCTGAATT
11348183 ACTTCACC
1 A-TTCACC
11348191 ACCTTATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
39 2 0.03
40 4 0.06
41 62 0.86
43 3 0.04
44 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (40 bp):
ATTCACCGGCATTTAGCCTGCTAGACATAAAGTCTGAATT
Found at i:11356958 original size:13 final size:13
Alignment explanation
Indices: 11356940--11356965 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11356930 CAATCAAATG
11356940 CACACAAAATAAT
1 CACACAAAATAAT
11356953 CACACAAAATAAT
1 CACACAAAATAAT
11356966 ATTAATAATA
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:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
CACACAAAATAAT
Found at i:11358773 original size:44 final size:43
Alignment explanation
Indices: 11358725--11359131 Score: 124
Period size: 44 Copynumber: 9.3 Consensus size: 43
11358715 AATAGCAGAT
* *
11358725 CTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGATACTAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATAC-AGC
**** * * ** * *
11358769 CTTGCCTCCCTG-GGTTACAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATA-CAG-C
* *
11358813 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATA-CAGC
* **** * * ** * *
11358857 CTTACCTCCCTGGGTTG-TAGC-AGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGCACCGACAGCGA-AGCAGATCGAAGATA-CAG-C
* * * * *
11358901 CTTGCCTTCCTGCACTGACATCGAAGCAGATCGAAGACACCAAC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATA-CAGC
* **** * * ** * * *
11358945 CTTGCCTCCTTGGGTTG-CAGCGGAGCAGGTTAAAAATAGTAGAT
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATA-CAG-C
* * *
11358989 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATA-CAGC
**** ** *
11359033 CTTGCCTCCCTGGGTTG-CAGCGAAGCAGATTAAAAATAGCAG-
1 CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATA-CAGC
* * * * *
11359075 ATCTGTCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CT-TGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATA-CAGC
*
11359120 CTTACCTCCCTG
1 CTTGCCTCCCTG
11359132 GGTTGTAGCG
Statistics
Matches: 240, Mismatches: 111, Indels: 24
0.64 0.30 0.06
Matches are distributed among these distances:
42 2 0.01
43 77 0.32
44 109 0.45
45 51 0.21
46 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.21
Consensus pattern (43 bp):
CTTGCCTCCCTGCACCGACAGCGAAGCAGATCGAAGATACAGC
Found at i:11358781 original size:88 final size:88
Alignment explanation
Indices: 11358632--11359197 Score: 882
Period size: 88 Copynumber: 6.4 Consensus size: 88
11358622 GTGAAGATAA
* * *
11358632 CAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATTGAAGACACCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
11358697 GTAGCAGAGCAGGTTAGAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
11358720 CAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGATACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
11358785 ACAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
11358808 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
11358873 GTAGCAGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
11358896 CAGATCTTGCCTTCCTGCACTGACATCGAAGCAGATCGAAGACACCAACCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
11358961 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
11358984 TAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
11359049 GCAGCGAAGCAGATTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
11359072 CAGATC-TGTCTTCTTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
11359136 GTAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
11359159 CAGATCTTTCCTTCCTGCACCGACAACGAAGCAGATCGA
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
11359198 TGACCCCAAC
Statistics
Matches: 435, Mismatches: 42, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
87 80 0.18
88 355 0.82
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:11359746 original size:44 final size:44
Alignment explanation
Indices: 11359649--11359759 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
11359639 GAAGATGGCG
* *
11359649 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAAATTAAAACCAAT
* * **
11359693 AATCCTATCTTCCTGAAGCTGCAGTGGAGCGGATTAAAACCACA-
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAAATTAAAACCA-AT
*
11359737 GATCTTATC-TCTCTGAAGTTGCA
1 AATCTTATCTTC-CTGAAGTTGCA
11359760 ATAGAGTAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
43 2 0.04
44 53 0.95
45 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAAATTAAAACCAAT
Found at i:11360233 original size:19 final size:20
Alignment explanation
Indices: 11360211--11360259 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
11360201 AAGGATACGT
11360211 AATCTTAGATATG-ATATGC
1 AATCTTAGATATGAATATGC
11360230 AATCTTAGATATGATATATGC
1 AATCTTAGATATGA-ATATGC
11360251 AATCTTAGA
1 AATCTTAGA
11360260 AGATATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 13 0.46
21 15 0.54
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (20 bp):
AATCTTAGATATGAATATGC
Found at i:11360264 original size:19 final size:19
Alignment explanation
Indices: 11360211--11360265 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
11360201 AAGGATACGT
*
11360211 AATCTTAG-ATATGATATGC
1 AATCTTAGAAGAT-ATATGC
11360230 AATCTTAGATATGATATATGC
1 AATCTTAGA-A-GATATATGC
11360251 AATCTTAGAAGATAT
1 AATCTTAGAAGATAT
11360266 GATTTTGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.41
20 1 0.03
21 16 0.50
22 2 0.06
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
AATCTTAGAAGATATATGC
Found at i:11360281 original size:23 final size:24
Alignment explanation
Indices: 11360217--11360282 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 24
11360207 ACGTAATCTT
11360217 AGATATG--ATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
11360236 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
11360260 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
11360283 GATTTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.17
21 12 0.30
23 12 0.30
24 9 0.22
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:11360564 original size:3 final size:3
Alignment explanation
Indices: 11360556--11360653 Score: 67
Period size: 3 Copynumber: 32.0 Consensus size: 3
11360546 TCTTTTTTAT
* * *
11360556 TTA TTA TTA TTTA TTTA TTA TTTA TTT TTA TTA -AA TT- TTA TT- TTC
1 TTA TTA TTA -TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
11360601 TTG TTA TTAA GTTA TTA TTA TTA TTG TTA TTA TTA CCA TTA TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11360648 TTA TTA
1 TTA TTA
11360654 CTATATATAC
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
2 5 0.07
3 57 0.75
4 12 0.16
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:11360569 original size:7 final size:7
Alignment explanation
Indices: 11360552--11360588 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
11360542 TTAGTCTTTT
11360552 TTATTTA
1 TTATTTA
11360559 TTA-TTA
1 TTATTTA
11360565 TTTATTTA
1 -TTATTTA
11360573 TTATTTA
1 TTATTTA
11360580 TT-TTTA
1 TTATTTA
11360586 TTA
1 TTA
11360589 AATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 9 0.33
7 15 0.56
8 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:11360810 original size:17 final size:17
Alignment explanation
Indices: 11360779--11360822 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
11360769 CATAACTTTT
*
11360779 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
11360795 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
11360812 ATATACATTTT
1 ATATACATTTT
11360823 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:11360949 original size:23 final size:24
Alignment explanation
Indices: 11360903--11360951 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
11360893 TATACGTATG
11360903 TTTTCTTATATTATTCTTCATAAA
1 TTTTCTTATATTATTCTTCATAAA
*
11360927 TTTT-TTATATATATTTTTC-TAAA
1 TTTTCTTATAT-TATTCTTCATAAA
11360950 TT
1 TT
11360952 AATTAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTCTTATATTATTCTTCATAAA
Found at i:11360975 original size:19 final size:21
Alignment explanation
Indices: 11360951--11360989 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
11360941 TTTTCTAAAT
11360951 TAATTAAT-TTTA-ATATATG
1 TAATTAATATTTATATATATG
*
11360970 TAATTATTATTTATATATAT
1 TAATTAATATTTATATATAT
11360990 ATATGTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TAATTAATATTTATATATATG
Found at i:11361041 original size:30 final size:30
Alignment explanation
Indices: 11360963--11361026 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 30
11360953 ATTAATTTTA
*
11360963 ATATATGTAATTA--TTATTTAT-A--TAT
1 ATATATGTAATTATCTTTTTTATAATCTAT
11360988 ATATATGTAATTATCTTTTTTATAATCTAT
1 ATATATGTAATTATCTTTTTTATAATCTAT
11361018 ATATATGTA
1 ATATATGTA
11361027 TATACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 13 0.39
27 7 0.21
28 1 0.03
30 12 0.36
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (30 bp):
ATATATGTAATTATCTTTTTTATAATCTAT
Found at i:11361206 original size:4 final size:4
Alignment explanation
Indices: 11361186--11361238 Score: 56
Period size: 4 Copynumber: 13.5 Consensus size: 4
11361176 GCTTTGCATG
* * *
11361186 TTAT TGAT TTA- TT-T TTAT TTAT TTAT TTAT TTAT TTGT TTGT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
11361232 ATTAT TT
1 -TTAT TT
11361239 CTATGCCATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 4 0.10
4 34 0.81
5 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:11361553 original size:2 final size:2
Alignment explanation
Indices: 11361548--11361584 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11361538 ATTTTTTAAA
11361548 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 A
11361585 AAGGAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11367054 original size:24 final size:23
Alignment explanation
Indices: 11367023--11367070 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
11367013 GTTGTTGCTG
11367023 ATATTATTAAAAAT-TTATTCATT
1 ATATTATTAAAAATATTATT-ATT
11367046 ATATATATTAAAAATATTATTATT
1 ATAT-TATTAAAAATATTATTATT
11367070 A
1 A
11367071 AAGTGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTATTAAAAATATTATTATT
Found at i:11367121 original size:56 final size:56
Alignment explanation
Indices: 11367055--11367165 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
11367045 TATATATATT
*
11367055 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTATAATTATTTTGACATA
1 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACATA
11367111 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACAT
1 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACAT
11367166 GTTATAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (56 bp):
AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACATA
Found at i:11376956 original size:26 final size:25
Alignment explanation
Indices: 11376900--11376977 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
11376890 AATAATTTTC
* *
11376900 TCAAAATTTTATCGAGGGTAAAATCG
1 TCAAAATTTTATCG-GGGTAAATTTG
*
11376926 CCAAAATTTTATCAGGGGTAAATTTG
1 TCAAAATTTTATC-GGGGTAAATTTG
*
11376952 TCAAAAAATTTA-CTGGGGTAAATTTG
1 TC-AAAATTTTATC-GGGGTAAATTTG
11376978 CGATAAGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
26 35 0.80
27 9 0.20
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (25 bp):
TCAAAATTTTATCGGGGTAAATTTG
Found at i:11407779 original size:24 final size:24
Alignment explanation
Indices: 11407731--11407779 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
11407721 TAAATGAAAA
* *
11407731 AAATAAATTTTTAGCTTATATTTT
1 AAATAAATTTTGAGATTATATTTT
11407755 AAATAAA-TTTGAGATTATATATTT
1 AAATAAATTTTGAGATTATAT-TTT
11407779 A
1 A
11407780 TAAATTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
AAATAAATTTTGAGATTATATTTT
Found at i:11411037 original size:50 final size:50
Alignment explanation
Indices: 11410983--11411180 Score: 243
Period size: 50 Copynumber: 3.8 Consensus size: 50
11410973 GATCATAACA
* * ** * **
11410983 TGCCAAAGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTTATCTCTG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
11411033 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* *
11411083 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCGCATGATCCCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT--C-TCAT--CTAGG
* *
11411138 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
11411181 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
50 83 0.63
52 1 0.01
53 4 0.03
54 1 0.01
55 4 0.03
56 38 0.29
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:11411553 original size:30 final size:30
Alignment explanation
Indices: 11411519--11411576 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
11411509 CCTCGAATCT
11411519 AACTTTGGA-AAAATTACAATTTTGCCCCTA
1 AACTTT-GACAAAATTACAATTTTGCCCCTA
* * *
11411549 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
11411577 AAGGCTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:11430914 original size:46 final size:44
Alignment explanation
Indices: 11430862--11430961 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
11430852 AACAGAAAAA
11430862 GAGAAATGAGAAACATTG-AGAAATGATTAT-GGTTTTCTCCAAAATG
1 GAGAAATGA-AAACATTGCA-AAATGATTATAGG-TTTC-CCAAAATG
*
11430908 GAGAAATGAAATCATTGCAAAATGATTATAGGTTTCCCAAAAT-
1 GAGAAATGAAAACATTGCAAAATGATTATAGGTTTCCCAAAATG
11430951 G-GAAATGAAAA
1 GAGAAATGAAAA
11430962 TAGAAATGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
42 9 0.18
43 1 0.02
44 7 0.14
45 21 0.42
46 12 0.24
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (44 bp):
GAGAAATGAAAACATTGCAAAATGATTATAGGTTTCCCAAAATG
Found at i:11430962 original size:6 final size:6
Alignment explanation
Indices: 11430947--11431022 Score: 125
Period size: 6 Copynumber: 12.7 Consensus size: 6
11430937 AGGTTTCCCA
* *
11430947 AAATGG AAATGA AAATAG AAATGG AAATGG AAATGG AAATGG AAATGG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
*
11430995 AAATGG AAATGG AAATGA AAATGG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAAT
11431023 AAAAAAGAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:11430970 original size:18 final size:18
Alignment explanation
Indices: 11430947--11431039 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
11430937 AGGTTTCCCA
*
11430947 AAATGGAAATGAAAATAG
1 AAATGGAAATGAAAATGG
*
11430965 AAATGGAAATGGAAATGG
1 AAATGGAAATGAAAATGG
*
11430983 AAATGGAAATGGAAATGG
1 AAATGGAAATGAAAATGG
11431001 AAATGGAAATGAAAATGG
1 AAATGGAAATGAAAATGG
** *
11431019 AAATAAAAAAGAAAATGG
1 AAATGGAAATGAAAATGG
11431037 AAA
1 AAA
11431040 CTTGCAATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (18 bp):
AAATGGAAATGAAAATGG
Found at i:11431213 original size:26 final size:26
Alignment explanation
Indices: 11431184--11431243 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
11431174 TTTTTTCAAA
11431184 ATTTTATTAAGGGTAAAATCGTAAAT
1 ATTTTATTAAGGGTAAAATCGTAAAT
* * * *
11431210 ATTTTACTAGGGGTAAAATTGTCAAT
1 ATTTTATTAAGGGTAAAATCGTAAAT
11431236 ATTTTATT
1 ATTTTATT
11431244 GGGATAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (26 bp):
ATTTTATTAAGGGTAAAATCGTAAAT
Found at i:11433633 original size:7 final size:7
Alignment explanation
Indices: 11433621--11433652 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
11433611 AGTGTCGATT
*
11433621 ATATGTG
1 ATATGTA
11433628 ATATGTA
1 ATATGTA
11433635 ATATGTA
1 ATATGTA
11433642 ATATGTA
1 ATATGTA
11433649 ATAT
1 ATAT
11433653 ATGAGAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (7 bp):
ATATGTA
Found at i:11435015 original size:80 final size:80
Alignment explanation
Indices: 11434882--11435043 Score: 297
Period size: 80 Copynumber: 2.0 Consensus size: 80
11434872 CATAAACGGA
* *
11434882 TCTAGGATCTATTCTACTTAGTTCATGTTTGATGTAGTGTCAGTTTTTTCAGTCATATCTATGTC
1 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
11434947 TTTATCTTTTAAGAT
66 TTTATCTTTTAAGAT
11434962 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
1 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
*
11435027 TTTATCTTTTAGGAT
66 TTTATCTTTTAAGAT
11435042 TC
1 TC
11435044 ATTTGCTTCG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (80 bp):
TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
TTTATCTTTTAAGAT
Found at i:11439292 original size:51 final size:50
Alignment explanation
Indices: 11439231--11439400 Score: 162
Period size: 58 Copynumber: 3.2 Consensus size: 50
11439221 CATTTCCGAG
*
11439231 TCATTTTCATTTAGGAGAAAACCACATTCATTTCCAAATGATTCCACTTCT
1 TCATTTTCATTTAGGAGAAAACCA-ATTCATTTCCAAATGTTTCCACTTCT
* *
11439282 CCATTTTCATTTTA-GAGAAAACCATTATCATTTCCAAATGTTTCCCATTTCTTCATTT
1 TCATTTTCA-TTTAGGAGAAAACCAAT-TCATTTCCAAATGTTT-CCA---CTTC---T
* * * *
11439340 TTATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTCATTTCT
1 TCATTTTCATTTAGGAGAAAACCA-ATTCATTTCCAAATGTTTC-CACTTCT
11439392 TCATTTTCA
1 TCATTTTCA
11439401 CCATTTCTAT
Statistics
Matches: 97, Mismatches: 10, Indels: 23
0.75 0.08 0.18
Matches are distributed among these distances:
50 1 0.01
51 33 0.34
52 16 0.16
55 7 0.07
57 4 0.04
58 36 0.37
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (50 bp):
TCATTTTCATTTAGGAGAAAACCAATTCATTTCCAAATGTTTCCACTTCT
Found at i:11439348 original size:58 final size:58
Alignment explanation
Indices: 11439284--11439398 Score: 203
Period size: 58 Copynumber: 2.0 Consensus size: 58
11439274 CCACTTCTCC
*
11439284 ATTTTCATTTTAGAGAAAACCATTATCATTTCCAAATGTTTCCCATTTCTTCATTTTT
1 ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTTCATTTTT
* *
11439342 ATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTCATTTCTTCATTTT
1 ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTTCATTTT
11439399 CACCATTTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (58 bp):
ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTTCATTTTT
Found at i:11449683 original size:25 final size:25
Alignment explanation
Indices: 11449629--11449721 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
11449619 GGATACTTCG
* *
11449629 CAGCTCGTGA-GAGCATACCAATTTA
1 CAGCTCATGATGAGCATACCGA-TTA
*
11449654 TAGCTCATGA-GAGCATACCGATCTA
1 CAGCTCATGATGAGCATACCGAT-TA
*
11449679 CAGCTCA-AATGAGCATACCGATTCA
1 CAGCTCATGATGAGCATACCGATT-A
11449704 CAGCTCAT-ATGAGCATAC
1 CAGCTCATGATGAGCATAC
11449722 TTGTACATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.05
25 56 0.95
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (25 bp):
CAGCTCATGATGAGCATACCGATTA
Found at i:11460297 original size:2 final size:2
Alignment explanation
Indices: 11460290--11460316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11460280 CAATAATAAA
11460290 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
11460317 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11460745 original size:16 final size:16
Alignment explanation
Indices: 11460724--11460759 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
11460714 TTTGGTTCGC
11460724 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
11460740 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
11460756 TGTA
1 TGTA
11460760 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:11460824 original size:44 final size:45
Alignment explanation
Indices: 11460740--11460830 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
11460730 GGATTAGAGG
* * *
11460740 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
11460785 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
11460829 TG
1 TG
11460831 AAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:11460847 original size:39 final size:42
Alignment explanation
Indices: 11460750--11460853 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 42
11460740 TGTATTGGAT
11460750 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGTAATGGAA
1 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATG-AA--GAA
* ***
11460795 TAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAATG-A-AA
1 TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGAAGAA
11460834 TAGAGGTGTAATAGCATAAT
1 TAGAGGTGTAATAGC-TAAT
11460854 GGAAAAAACT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
39 15 0.29
41 4 0.08
42 1 0.02
44 19 0.37
45 13 0.25
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.34
Consensus pattern (42 bp):
TAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAATGAAGAA
Found at i:11461016 original size:18 final size:17
Alignment explanation
Indices: 11460995--11461029 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11460985 TTATTATTAA
*
11460995 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
11461013 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
11461030 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:11461166 original size:156 final size:157
Alignment explanation
Indices: 11460882--11461197 Score: 571
Period size: 156 Copynumber: 2.0 Consensus size: 157
11460872 TAGAATACCC
11460882 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
11460947 TTATGAGTAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
11461012 TATATAATTTAATAAAATTCTT-ATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
11461038 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
*
11461103 TTATCAGTAATAAATAATTTAATCATATTTAAACATAATTTTTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
*
11461168 TATATAATTTAATAAATTTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
11461195 TTA
1 TTA
11461198 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
156 146 0.95
157 7 0.05
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (157 bp):
TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:11461171 original size:16 final size:16
Alignment explanation
Indices: 11461131--11461172 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
11461121 TTAATCATAT
*
11461131 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
11461147 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
11461162 TTAAAATATAT
1 TTAAAATATAT
11461173 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:11461278 original size:120 final size:119
Alignment explanation
Indices: 11461134--11461358 Score: 387
Period size: 120 Copynumber: 1.9 Consensus size: 119
11461124 ATCATATTTA
* * *
11461134 AACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAATTTCTTAATAATTAA
1 AACATAAATATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
11461199 TATTCTTATATTAATTTACTCAAATCATAATATTTGATACTGTAAAATATAAATT
66 TATTCTTATA-TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
11461254 AACATAAATATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTCA
1 AACATAAATATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
11461319 TATTCTTATATAATTTATTCAAATCATAATATATGATACT
66 TATTCTTATATAATTTACTCAAATCATAATATATGATACT
11461359 ATAATTTAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 28 0.28
120 71 0.72
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (119 bp):
AACATAAATATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:11461292 original size:18 final size:17
Alignment explanation
Indices: 11461271--11461305 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11461261 ATATTATTAA
*
11461271 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
11461289 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
11461306 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:11464866 original size:23 final size:23
Alignment explanation
Indices: 11464839--11464911 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
11464829 TTATATTAAT
11464839 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
* * * ***
11464862 ATTATAT-TTC-AATTAAAAAT-
1 ATTATATAATCAAAATGATTTTA
11464882 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
11464905 ATTATAT
1 ATTATAT
11464912 TTTAATATAC
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 7 0.20
21 7 0.20
22 7 0.20
23 14 0.40
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (23 bp):
ATTATATAATCAAAATGATTTTA
Found at i:11468656 original size:26 final size:24
Alignment explanation
Indices: 11468613--11468664 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
11468603 TATATACTAC
*
11468613 ATAAATTAATAATAAAATAATAAAAT
1 ATAAATTAAAAATAAAAT--TAAAAT
*
11468639 ATAAATTAAAAATCAAATTAAAAT
1 ATAAATTAAAAATAAAATTAAAAT
11468663 AT
1 AT
11468665 TAATAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
26 16 0.67
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
ATAAATTAAAAATAAAATTAAAAT
Found at i:11470447 original size:2 final size:2
Alignment explanation
Indices: 11470440--11470470 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11470430 ATCAACATCA
11470440 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
11470471 TATAATCACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11473282 original size:47 final size:47
Alignment explanation
Indices: 11473213--11473307 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
11473203 TTTTTCAAAC
11473213 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
1 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
11473260 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
1 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
11473307 A
1 A
11473308 TATTATCCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (47 bp):
AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
Found at i:11479439 original size:24 final size:23
Alignment explanation
Indices: 11479368--11479430 Score: 63
Period size: 27 Copynumber: 2.5 Consensus size: 23
11479358 ATTAATAATA
* *
11479368 AGTTAGTGAAACGATTAGTTTTG
1 AGTTAATGAAACGATGAGTTTTG
11479391 ATTTAGTTAATGAAACGATGAGTTTTG
1 ----AGTTAATGAAACGATGAGTTTTG
11479418 AGTTAAATGAAAC
1 AGTT-AATGAAAC
11479431 ATGGCGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
27 21 0.64
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (23 bp):
AGTTAATGAAACGATGAGTTTTG
Found at i:11480061 original size:17 final size:17
Alignment explanation
Indices: 11480039--11480082 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
11480029 ATAGAAATAA
11480039 AGTCCAAAA-CCCAAAAC
1 AGTCCAAAAGCCC-AAAC
*
11480056 AGTCCAAAATGTCCAAAC
1 AGTCCAAAA-GCCCAAAC
11480074 AGTCCAAAA
1 AGTCCAAAA
11480083 TTTACAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 9 0.38
18 13 0.54
19 2 0.08
ACGTcount: A:0.50, C:0.30, G:0.09, T:0.11
Consensus pattern (17 bp):
AGTCCAAAAGCCCAAAC
Found at i:11480090 original size:18 final size:18
Alignment explanation
Indices: 11480052--11480090 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11480042 CCAAAACCCA
*
11480052 AAACAGTCCAAAATGTCC
1 AAACAGTCCAAAATGTAC
*
11480070 AAACAGTCCAAAATTTAC
1 AAACAGTCCAAAATGTAC
11480088 AAA
1 AAA
11480091 ACTCTTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (18 bp):
AAACAGTCCAAAATGTAC
Found at i:11480504 original size:20 final size:20
Alignment explanation
Indices: 11480481--11480519 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11480471 AATAAAACAA
11480481 ATTTAATTTAAT-TAAAAATT
1 ATTT-ATTTAATCTAAAAATT
*
11480501 ATTTATTTTATCTAAAAAT
1 ATTTATTTAATCTAAAAAT
11480520 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATTTAATCTAAAAATT
Found at i:11489698 original size:64 final size:64
Alignment explanation
Indices: 11489574--11489737 Score: 195
Period size: 64 Copynumber: 2.6 Consensus size: 64
11489564 ACGGGTAAGG
* * * * *
11489574 CACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGTGTTAGGATTTGGAGCCATATGGGCAAAA
1 CACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTAGAGACACACGGGCAAAA
* * * *
11489638 CACACGGGCATGTGTCCAGGCTGTGTAACTC-CTTGAGTTCGTATTTAGAGACACACGGGCAAGA
1 CACACGGGCATGTGTCCAGGCCGTGTAACTCTC-TGAGTTAGGATTTAGAGACACACGGGCAAAA
* * * *
11489702 GACACGGGCATGTGTCCAAGCCATGTAACTCACTGA
1 CACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGA
11489738 CTTCAGATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 1 0.01
64 83 0.98
65 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (64 bp):
CACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTAGAGACACACGGGCAAAA
Found at i:11490231 original size:20 final size:21
Alignment explanation
Indices: 11490198--11490237 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
11490188 ATATACCTAT
*
11490198 TGGTGTGTAGAGTGGGTGGAGA
1 TGGTGTGTA-AGTGGATGGAGA
11490220 TGGTGTGT-AGTGGATGGA
1 TGGTGTGTAAGTGGATGGA
11490238 ATAGGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (21 bp):
TGGTGTGTAAGTGGATGGAGA
Found at i:11490342 original size:60 final size:60
Alignment explanation
Indices: 11490261--11490387 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 60
11490251 TCTGTATCTA
* * *
11490261 TACCGTATGACATATACATCTGATCGTATTTGTGTTATATGTGCATTTGTACTAATATGC
1 TACCATATGACATATACATCTGATCGTATTTGTGTTATACGTGCATCTGTACTAATATGC
* * * *
11490321 TACCATATGACATGTGCATCTGATCGTATTTGTGTTATACGTGCATCTGTATTAATCTGC
1 TACCATATGACATATACATCTGATCGTATTTGTGTTATACGTGCATCTGTACTAATATGC
11490381 TA-CATAT
1 TACCATAT
11490388 AAGGACTGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
59 5 0.08
60 55 0.92
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (60 bp):
TACCATATGACATATACATCTGATCGTATTTGTGTTATACGTGCATCTGTACTAATATGC
Found at i:11494428 original size:2 final size:2
Alignment explanation
Indices: 11494421--11494453 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11494411 AAAAGGAAAT
11494421 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11494454 AGAAAAAAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11498017 original size:21 final size:21
Alignment explanation
Indices: 11497991--11498032 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11497981 CAATGAATTA
*
11497991 ACTTTTCTTGTTTTGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
11498012 ACTTTTCTTGTTTCGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
11498033 TTGATCACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (21 bp):
ACTTTTCTTGTTTCGATTTTG
Found at i:11499998 original size:16 final size:16
Alignment explanation
Indices: 11499977--11500039 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
11499967 CGCTGTATTA
*
11499977 GAATAGAGGCATAATG
1 GAATAGAGGCGTAATG
11499993 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATG
*
11500009 GAATAGAGGTGTAATG
1 GAATAGAGGCGTAATG
* *
11500025 GATTAGAGGTGTAAT
1 GAATAGAGGCGTAAT
11500040 AGCAAATCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.24
Consensus pattern (16 bp):
GAATAGAGGCGTAATG
Found at i:11500068 original size:45 final size:44
Alignment explanation
Indices: 11500018--11500112 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 44
11500008 GGAATAGAGG
* *
11500018 TGTAATGGATTAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* * *
11500063 TGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
11500107 TGTAAT
1 TGTAAT
11500113 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 22 0.50
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:11500290 original size:16 final size:16
Alignment explanation
Indices: 11500253--11500294 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
11500243 TTAATCATAT
*
11500253 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
11500269 TT-AAATATATTATAA
1 TTAAAATATATTATAA
11500284 TTAAAATATAT
1 TTAAAATATAT
11500295 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:11500301 original size:14 final size:15
Alignment explanation
Indices: 11500262--11500303 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
11500252 TTTAAACATA
*
11500262 ATTATTATTAAATAT
1 ATTATAATTAAATAT
11500277 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
11500291 A-TATAATTTAATA
1 ATTATAATTAAATA
11500304 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:11500401 original size:120 final size:120
Alignment explanation
Indices: 11500256--11500598 Score: 661
Period size: 120 Copynumber: 2.9 Consensus size: 120
11500246 ATCATATTTA
11500256 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
11500321 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
11500376 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
11500441 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
11500496 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
11500561 TATTCTTATATGAATTTACTCAAATCATAATATA-GATA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATA
11500599 ATTTAACATA
Statistics
Matches: 220, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
119 4 0.02
120 216 0.98
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:11500421 original size:14 final size:15
Alignment explanation
Indices: 11500372--11500423 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
11500362 ATAAAATATA
11500372 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
11500387 TATTAAATATATTAT
1 AATTAAATATATTAT
11500402 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
11500415 AATTTAATA
1 AATTAAATA
11500424 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:11500532 original size:16 final size:16
Alignment explanation
Indices: 11500488--11500534 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
11500478 TACTATAAAA
*
11500488 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
11500504 TATTATT-AAATATAT
1 TATAATTAAAATATAT
11500519 TATAATTAAAATATAT
1 TATAATTAAAATATAT
11500535 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:11504583 original size:44 final size:44
Alignment explanation
Indices: 11504520--11504609 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
11504510 TAAAATCATA
*
11504520 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGCAAAG
1 AGATATGCTCGTTATATGTGATGAATTTCAGTATAATAGCAAAG
* * *
11504564 AGATATGCTCGTTCTATGTGATGAATTTCATTGTAATAGCAAAG
1 AGATATGCTCGTTATATGTGATGAATTTCAGTATAATAGCAAAG
11504608 AG
1 AG
11504610 CATACTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (44 bp):
AGATATGCTCGTTATATGTGATGAATTTCAGTATAATAGCAAAG
Found at i:11510779 original size:21 final size:21
Alignment explanation
Indices: 11510754--11510801 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
11510744 AGAGTTGAAG
11510754 AAGCTACCTGGAAACAAGAAA
1 AAGCTACCTGGAAACAAGAAA
* * *
11510775 AAGCTACCTGGGAACCAGAAG
1 AAGCTACCTGGAAACAAGAAA
11510796 AAGCTA
1 AAGCTA
11510802 TGAAAGTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (21 bp):
AAGCTACCTGGAAACAAGAAA
Found at i:11512145 original size:38 final size:38
Alignment explanation
Indices: 11512005--11512178 Score: 186
Period size: 41 Copynumber: 4.4 Consensus size: 38
11511995 TTCAAATTGG
* * * *
11512005 GTGTTATTCAGGCTTTGTGCCTAGCAGGCTTAATGTCG
1 GTGTTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCA
*
11512043 GTGTACTGATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCA
1 GTGT--T-ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCA
* * * * *
11512084 GTGTATTGATTCAGGCTTTGTGCCTAGGAGACTTAGCGCTA
1 GTG--TT-ATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCA
11512125 GTGTTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCA
1 GTGTTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCA
* *
11512163 GCGTTACTCAGGCTTA
1 GTGTTATTCAGGCTTA
11512179 AAGCATAGTA
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 46 0.39
39 2 0.02
40 1 0.01
41 67 0.57
43 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (38 bp):
GTGTTATTCAGGCTTAGTGCCTAGCAGGCTTAGTGCCA
Found at i:11516672 original size:2 final size:2
Alignment explanation
Indices: 11516665--11516691 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11516655 TTGGTATGTT
11516665 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11516692 TAAAATAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11517507 original size:22 final size:22
Alignment explanation
Indices: 11517442--11517507 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
11517432 TTTATTGTTC
*
11517442 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
11517464 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
11517486 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
11517508 TGTAGGTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:11519023 original size:11 final size:12
Alignment explanation
Indices: 11518986--11519054 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 12
11518976 TTGGGAATGT
11518986 TATTAAATTATA
1 TATTAAATTATA
11518998 TATT--ATTAT-
1 TATTAAATTATA
11519007 TATTAAATTATA
1 TATTAAATTATA
*
11519019 T-TTAATAATAATTA
1 TATT-A-AATTA-TA
11519033 TATTAAA--ATA
1 TATTAAATTATA
11519043 TGATTAAATTAT
1 T-ATTAAATTAT
11519055 TCATTATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 19
0.70 0.02 0.29
Matches are distributed among these distances:
9 4 0.09
10 8 0.17
11 14 0.30
12 6 0.13
13 8 0.17
14 4 0.09
15 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (12 bp):
TATTAAATTATA
Found at i:11519061 original size:58 final size:55
Alignment explanation
Indices: 11518987--11519096 Score: 159
Period size: 55 Copynumber: 1.9 Consensus size: 55
11518977 TGGGAATGTT
*
11518987 ATTAAATTATATATTATTATTATTAAATTATATTTAATAATAATTATATTAAAATATG
1 ATTAAA-T-TATA-TATTATTATTAAATTATATTTAATAATAATCATATTAAAATATG
*
11519045 ATTAAATTAT-TCATTATTATTAAATTATATTTAATAATAATCCTATTAAAAT
1 ATTAAATTATAT-ATTATTATTAAATTATATTTAATAATAATCATATTAAAAT
11519097 TTAATAACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
54 1 0.02
55 38 0.78
56 3 0.06
57 1 0.02
58 6 0.12
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (55 bp):
ATTAAATTATATATTATTATTAAATTATATTTAATAATAATCATATTAAAATATG
Found at i:11521731 original size:20 final size:21
Alignment explanation
Indices: 11521706--11521747 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
11521696 TTGTAAATTA
11521706 ATTTAATT-TTT-TGATTTATT
1 ATTTAATTGTTTATGA-TTATT
11521726 ATTTAATTGTTTATGATTATT
1 ATTTAATTGTTTATGATTATT
11521747 A
1 A
11521748 ATTGAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 9 0.45
22 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATTTAATTGTTTATGATTATT
Found at i:11529897 original size:13 final size:13
Alignment explanation
Indices: 11529879--11529917 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
11529869 AGATAAATTG
11529879 AACATCTTTTTGT
1 AACATCTTTTTGT
*
11529892 AACATC-TTTAGTT
1 AACATCTTTTTG-T
11529905 AACATCTTTTTGT
1 AACATCTTTTTGT
11529918 TGATATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (13 bp):
AACATCTTTTTGT
Found at i:11531165 original size:20 final size:22
Alignment explanation
Indices: 11531125--11531165 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11531115 ATTAACTATC
*
11531125 ACACTCTAACCTATCAGATTTG
1 ACACTCTAACCTATCAAATTTG
11531147 ACACTCTAA-C-ATCAAATTT
1 ACACTCTAACCTATCAAATTT
11531166 AATAGACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (22 bp):
ACACTCTAACCTATCAAATTTG
Found at i:11537392 original size:11 final size:12
Alignment explanation
Indices: 11537359--11537392 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11537349 TTTACTCTAC
11537359 ATTTATTTTGAT
1 ATTTATTTTGAT
*
11537371 ATTTGTTTTGAT
1 ATTTATTTTGAT
11537383 -TTTATTTTGA
1 ATTTATTTTGA
11537393 AACTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (12 bp):
ATTTATTTTGAT
Found at i:11545104 original size:23 final size:23
Alignment explanation
Indices: 11545074--11545127 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
11545064 GAAGTCCTAA
11545074 TTGGTGTGATAGGTTGGTTGGAG
1 TTGGTGTGATAGGTTGGTTGGAG
11545097 TTGGTGTGATAGGTTGGTTGGAG
1 TTGGTGTGATAGGTTGGTTGGAG
11545120 TTGGTGTG
1 TTGGTGTG
11545128 TAGCGAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.11, C:0.00, G:0.48, T:0.41
Consensus pattern (23 bp):
TTGGTGTGATAGGTTGGTTGGAG
Found at i:11545114 original size:13 final size:13
Alignment explanation
Indices: 11545074--11545114 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
11545064 GAAGTCCTAA
11545074 TTGGTGTGATAGG
1 TTGGTGTGATAGG
*
11545087 TTGGT-TG-GA-G
1 TTGGTGTGATAGG
11545097 TTGGTGTGATAGG
1 TTGGTGTGATAGG
11545110 TTGGT
1 TTGGT
11545115 TGGAGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 6 0.26
11 3 0.13
12 3 0.13
13 11 0.48
ACGTcount: A:0.12, C:0.00, G:0.46, T:0.41
Consensus pattern (13 bp):
TTGGTGTGATAGG
Done.