Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 10 of 214
Found at i:3013130 original size:19 final size:19
Alignment explanation
Indices: 3013086--3013144 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
3013076 GAGTATGAGA
*
3013086 TTATGTTCTAGTATGCACT
1 TTATGTGCTAGTATGCACT
**
3013105 TCGTGTGCTAGATATGCA-T
1 TTATGTGCTAG-TATGCACT
*
3013124 TTATGTGCCAGTATGCACT
1 TTATGTGCTAGTATGCACT
3013143 TT
1 TT
3013145 GTGTACCAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 6 0.19
19 20 0.62
20 6 0.19
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (19 bp):
TTATGTGCTAGTATGCACT
Found at i:3015073 original size:20 final size:20
Alignment explanation
Indices: 3015048--3015087 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3015038 CGTAAAATGA
*
3015048 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
3015068 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
3015088 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:3015835 original size:21 final size:21
Alignment explanation
Indices: 3015796--3015836 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3015786 CTAATTAATT
3015796 TAAAATTTTATGATGTAAAAA
1 TAAAATTTTATGATGTAAAAA
*
3015817 TAAATATTTTAT-ATTTAAAA
1 TAAA-ATTTTATGATGTAAAA
3015837 TAGTGGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TAAAATTTTATGATGTAAAAA
Found at i:3016741 original size:19 final size:18
Alignment explanation
Indices: 3016717--3016769 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3016707 GAAAAACAAG
3016717 TAAAAAAAACCTAAAAAAA
1 TAAAAAAAACC-AAAAAAA
* *
3016736 TAAAAACAACCACAAAAA
1 TAAAAAAAACCAAAAAAA
**
3016754 TAACTAAAA-CAAAAAA
1 TAAAAAAAACCAAAAAA
3016770 CTAAGCAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 10 0.36
ACGTcount: A:0.75, C:0.15, G:0.00, T:0.09
Consensus pattern (18 bp):
TAAAAAAAACCAAAAAAA
Found at i:3016752 original size:18 final size:19
Alignment explanation
Indices: 3016717--3016756 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3016707 GAAAAACAAG
3016717 TAAAAAAAACCTAAAAAAA
1 TAAAAAAAACCTAAAAAAA
* *
3016736 TAAAAACAACC-ACAAAAA
1 TAAAAAAAACCTAAAAAAA
3016754 TAA
1 TAA
3016757 CTAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.75, C:0.15, G:0.00, T:0.10
Consensus pattern (19 bp):
TAAAAAAAACCTAAAAAAA
Found at i:3021511 original size:9 final size:9
Alignment explanation
Indices: 3021497--3021536 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
3021487 GTAGTGATTC
*
3021497 AATTCGGTA
1 AATTCGGTT
3021506 AATTCGAG-T
1 AATTCG-GTT
3021515 AATTCGGTT
1 AATTCGGTT
3021524 AATTCGGTT
1 AATTCGGTT
3021533 AATT
1 AATT
3021537 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:3026925 original size:11 final size:11
Alignment explanation
Indices: 3026902--3026936 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3026892 CAGCTCGTCA
3026902 ATATTATTTTTT
1 ATATTA-TTTTT
3026914 ATATTATTTTT
1 ATATTATTTTT
*
3026925 ATATAATTTTT
1 ATATTATTTTT
3026936 A
1 A
3026937 AATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:3026929 original size:13 final size:13
Alignment explanation
Indices: 3026902--3026941 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
3026892 CAGCTCGTCA
3026902 ATATTATTTTT-T
1 ATATTATTTTTAT
3026914 ATATTATTTTTAT
1 ATATTATTTTTAT
*
3026927 ATA--ATTTTTAA
1 ATATTATTTTTAT
3026938 ATAT
1 ATAT
3026942 ATATAATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 10 0.40
12 11 0.44
13 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATATTATTTTTAT
Found at i:3027087 original size:30 final size:30
Alignment explanation
Indices: 3027053--3027115 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3027043 ACTTAACAAG
*
3027053 CAAATACGTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
3027083 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
3027113 CAA
1 CAA
3027116 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:3027420 original size:20 final size:20
Alignment explanation
Indices: 3027395--3027434 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3027385 TGCAACTTTG
3027395 AAAATT-TTTAATGTTTCCAA
1 AAAATTCTTTAA-GTTTCCAA
*
3027415 AAAATTCTTTGAGTTTCCAA
1 AAAATTCTTTAAGTTTCCAA
3027435 TTTAGTCCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (20 bp):
AAAATTCTTTAAGTTTCCAA
Found at i:3027971 original size:21 final size:20
Alignment explanation
Indices: 3027943--3028010 Score: 50
Period size: 23 Copynumber: 3.2 Consensus size: 20
3027933 CACAACTTTT
3027943 TTAA-CTAATAATTCT-AAA
1 TTAATCTAATAATTCTAAAA
* *
3027961 TTAAATTCTAAATATTTTTAAAA
1 TT-AA-TCT-AATAATTCTAAAA
3027984 TTAATCTAATAATATACTAAAAA
1 TTAATCTAATAAT-T-CT-AAAA
3028007 TTAA
1 TTAA
3028011 AGGGCATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 5 0.13
21 6 0.16
22 10 0.26
23 13 0.34
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATCTAATAATTCTAAAA
Found at i:3033808 original size:20 final size:21
Alignment explanation
Indices: 3033766--3033807 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3033756 CAATATTTGT
3033766 ATTTGTAGACTCGCTTAAAAA
1 ATTTGTAGACTCGCTTAAAAA
*
3033787 ATTTGTAGACTTGCTTAAAAA
1 ATTTGTAGACTCGCTTAAAAA
3033808 TACCGATGTT
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:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
ATTTGTAGACTCGCTTAAAAA
Found at i:3036008 original size:27 final size:27
Alignment explanation
Indices: 3035967--3036041 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 27
3035957 AGTATTGACA
* * *
3035967 CCTATTTGGAAGGCGTCAATGGTGGTG
1 CCTATCTGGGAGGCGCCAATGGTGGTG
3035994 CCTATCTAGGG-GGCGCCAATGGTGGTG
1 CCTATCT-GGGAGGCGCCAATGGTGGTG
*
3036021 CTTATCTGGGAGGCGCCAATG
1 CCTATCTGGGAGGCGCCAATG
3036042 CTTTGATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.88
28 2 0.05
ACGTcount: A:0.17, C:0.20, G:0.37, T:0.25
Consensus pattern (27 bp):
CCTATCTGGGAGGCGCCAATGGTGGTG
Found at i:3036082 original size:19 final size:19
Alignment explanation
Indices: 3036058--3036098 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3036048 TTTTTTCGGG
*
3036058 TTTAGGGTTATGTTATAAA
1 TTTAGGATTATGTTATAAA
*
3036077 TTTAGGATTATGTTATAGA
1 TTTAGGATTATGTTATAAA
3036096 TTT
1 TTT
3036099 TTGTGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (19 bp):
TTTAGGATTATGTTATAAA
Found at i:3036341 original size:19 final size:19
Alignment explanation
Indices: 3036309--3036360 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
3036299 ATTCATACAA
3036309 ATTAT-TTA-AAATTTAGG
1 ATTATGTTATAAATTTAGG
3036326 ATTATGTTATAAATTTAGG
1 ATTATGTTATAAATTTAGG
3036345 ATTATGTTATAAATTT
1 ATTATGTTATAAATTT
3036361 TTGTGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.15
18 3 0.09
19 25 0.76
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (19 bp):
ATTATGTTATAAATTTAGG
Found at i:3036511 original size:8 final size:8
Alignment explanation
Indices: 3036498--3036561 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
3036488 CATACAAAAA
3036498 ATTACAAT
1 ATTACAAT
3036506 ATTACAAT
1 ATTACAAT
* *
3036514 ATATCCCAAC
1 AT-T-ACAAT
3036524 ATTACAAT
1 ATTACAAT
*
3036532 ATTCACACAAA
1 ATT---ACAAT
3036543 ATTACAAT
1 ATTACAAT
3036551 ATTACAAT
1 ATTACAAT
3036559 ATT
1 ATT
3036562 CATATAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 31 0.69
9 2 0.04
10 5 0.11
11 7 0.16
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (8 bp):
ATTACAAT
Found at i:3036527 original size:18 final size:19
Alignment explanation
Indices: 3036501--3036553 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
3036491 ACAAAAAATT
*
3036501 ACAATATTACAATATATC-C
1 ACAAAATTACAATAT-TCAC
*
3036520 -CAACATTACAATATTCAC
1 ACAAAATTACAATATTCAC
3036538 ACAAAATTACAATATT
1 ACAAAATTACAATATT
3036554 ACAATATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 14 0.47
19 14 0.47
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (19 bp):
ACAAAATTACAATATTCAC
Found at i:3036528 original size:260 final size:262
Alignment explanation
Indices: 3036058--3036565 Score: 939
Period size: 260 Copynumber: 1.9 Consensus size: 262
3036048 TTTTTTCGGG
* *
3036058 TTTAGGGTTATGTTATAAATTTAGGATTATGTTATAGATTTTTGTGTTTGTAATTATTTAAAATT
1 TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATT
3036123 CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
66 CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
3036188 TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
131 TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
* *
3036253 TATATCCCGACATTACAATATTCATACAAAATTACAATATTACAATATTCATACAAATTATTTAA
196 TATATCCCAACATTACAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAA
3036318 AA
261 AA
*
3036320 TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAATTT
1 TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATT
*
3036385 TAATTTATTAGTAATAAATTACAAAATTACTAATAAG-T-TACTAATAAATTTATAACATAATCC
66 CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
*
3036448 TAAATTACTAACAAATTAATTATAAAATAATTTCAATATTCATACAAAAAATTACAATATTACAA
131 TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
3036513 TATATCCCAACATTACAATATTCACACAAAATTACAATATTACAATATTCATA
196 TATATCCCAACATTACAATATTCACACAAAATTACAATATTACAATATTCATA
3036566 TAAAATTGCA
Statistics
Matches: 239, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
260 140 0.59
261 1 0.00
262 98 0.41
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.40
Consensus pattern (262 bp):
TTTAGGATTATGTTATAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATT
CAATTTATTAGTAATAAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCC
TAAATTACTAACAAATTAATTATAAAATAATTACAATATTCATACAAAAAATTACAATATTACAA
TATATCCCAACATTACAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAA
AA
Found at i:3036560 original size:27 final size:27
Alignment explanation
Indices: 3036524--3036580 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3036514 ATATCCCAAC
3036524 ATTACAATATTCACACAAAATTACAAT
1 ATTACAATATTCACACAAAATTACAAT
* * *
3036551 ATTACAATATTCATATAAAATTGCAAT
1 ATTACAATATTCACACAAAATTACAAT
3036578 ATT
1 ATT
3036581 TTTTTGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCACACAAAATTACAAT
Found at i:3036704 original size:49 final size:48
Alignment explanation
Indices: 3036616--3036714 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 48
3036606 GATTATCTAT
*
3036616 ATTTAGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATTATA
1 ATTTAGTATGAATATTGCAATTTTTTGTATGAATATTGTAATATTATA
* *
3036664 ATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTA
1 ATTTAGTATGAATATTGCAA-TTTTTTGTATGAATATTGTAATATTATA
3036713 AT
1 AT
3036715 ATTATAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 18 0.38
49 29 0.62
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (48 bp):
ATTTAGTATGAATATTGCAATTTTTTGTATGAATATTGTAATATTATA
Found at i:3036709 original size:8 final size:8
Alignment explanation
Indices: 3036696--3036767 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
3036686 TTTTTGTATG
3036696 AATATTGT
1 AATATTGT
3036704 AATATTGT
1 AATATTGT
*
3036712 AATATTAT
1 AATATTGT
*
3036720 AATTTTGTAT
1 AATATTG--T
3036730 GAATATTGT
1 -AATATTGT
* * *
3036739 AATGTCGGG
1 AATAT-TGT
3036748 ATATATTGT
1 A-ATATTGT
3036757 AATATTGT
1 AATATTGT
3036765 AAT
1 AAT
3036768 TTTTTGTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
8 34 0.69
9 5 0.10
10 4 0.08
11 6 0.12
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.47
Consensus pattern (8 bp):
AATATTGT
Found at i:3036953 original size:27 final size:27
Alignment explanation
Indices: 3036922--3036988 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
3036912 TAACATAAAT
*
3036922 TTCATTGGCGCCTCTCTATAAGGCACC
1 TTCATTGGCGCCTCTCTATAAGACACC
*
3036949 TTCATTGGCGCCTCTCTATGAGACACC
1 TTCATTGGCGCCTCTCTATAAGACACC
* *
3036976 TTTATTAGCGCCT
1 TTCATTGGCGCCT
3036989 ACCTGATAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATAAGACACC
Found at i:3044683 original size:40 final size:40
Alignment explanation
Indices: 3044635--3044773 Score: 144
Period size: 40 Copynumber: 3.5 Consensus size: 40
3044625 AACACACCAG
*
3044635 TTTGCACCCAGTGCCTCATCGGATAATTC-GAAATAATAA
1 TTTGCACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
* * *
3044674 TTTGACACCCAGTGTCTCATCGGCTAA-ACTGAAGT-A-AA
1 TTTG-CACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
* **
3044712 TTAGCACCCAGTGCCTCATCAAAT-ATATCTGAAGTAATAA
1 TTTGCACCCAGTGCCTCATCGGATAAT-TCTGAAGTAATAA
*
3044752 TTTGACACCCAGTGTCTCATCG
1 TTTG-CACCCAGTGCCTCATCG
3044774 ACTCGAAGTC
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
36 1 0.01
37 16 0.20
38 12 0.15
39 7 0.09
40 29 0.36
41 15 0.19
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
TTTGCACCCAGTGCCTCATCGGATAATTCTGAAGTAATAA
Found at i:3045930 original size:16 final size:16
Alignment explanation
Indices: 3045909--3045941 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3045899 TAATTTCTCC
*
3045909 TTTCTTTCTTTCTCTT
1 TTTCTTTCTTTCCCTT
3045925 TTTCTTTCTTTCCCTT
1 TTTCTTTCTTTCCCTT
3045941 T
1 T
3045942 CTGTTTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTTTCTTTCCCTT
Found at i:3060884 original size:29 final size:29
Alignment explanation
Indices: 3060851--3060946 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 29
3060841 CAATTACAAA
3060851 TAAAATTATTTTATATTAATTATTGCAAT
1 TAAAATTATTTTATATTAATTATTGCAAT
* * *
3060880 TAAAATATAATATT-TA-CAATTATTTACAAT
1 TAAAAT-T-ATTTTATATTAATTA-TTGCAAT
3060910 ATAAAAATTATTTTATATTAATTATTGCAAT
1 -T-AAAATTATTTTATATTAATTATTGCAAT
3060941 TAAAAT
1 TAAAAT
3060947 ATAATATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
29 16 0.30
30 14 0.26
31 14 0.26
32 10 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAAATTATTTTATATTAATTATTGCAAT
Found at i:3060931 original size:61 final size:59
Alignment explanation
Indices: 3060844--3060956 Score: 208
Period size: 61 Copynumber: 1.9 Consensus size: 59
3060834 TTACTTACAA
3060844 TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
1 TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
3060903 TTACAATATAAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTA
1 TTACAA-AT-AAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTA
3060957 AAAAATTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
59 6 0.12
60 2 0.04
61 44 0.85
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (59 bp):
TTACAAATAAAATTATTTTATATTAATTATTGCAATTAAAATATAATATTTACAATTAT
Found at i:3061930 original size:4 final size:4
Alignment explanation
Indices: 3061923--3061948 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3061913 TAAATTGATG
3061923 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
3061949 AATGTGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:3069170 original size:16 final size:16
Alignment explanation
Indices: 3069146--3069198 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3069136 TAGCCAAAAT
*
3069146 ATTATTTATTTAATCA
1 ATTAATTATTTAATCA
*
3069162 ATTAATTATTTAATTA
1 ATTAATTATTTAATCA
* *
3069178 AATAATTTTTTCAATCCA
1 ATTAATTATTT-AAT-CA
3069196 ATT
1 ATT
3069199 CTAATTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 23 0.79
17 3 0.10
18 3 0.10
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATTATTTAATCA
Found at i:3069569 original size:15 final size:15
Alignment explanation
Indices: 3069551--3069581 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3069541 AGGGCTTAAA
3069551 TAATTATAATATTAT
1 TAATTATAATATTAT
3069566 TAATTATAATATTAT
1 TAATTATAATATTAT
3069581 T
1 T
3069582 TAGTCATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATAATATTAT
Found at i:3072854 original size:90 final size:89
Alignment explanation
Indices: 3072673--3072897 Score: 337
Period size: 90 Copynumber: 2.5 Consensus size: 89
3072663 TATGTAGCAT
* * * * *
3072673 CACCAAGGTGGTCATGCTAAAGAGAATGGTTCCACCAAAAT-AAAAT-AAAAATCATTTTTATGG
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATAATTTTTATGG
3072736 TGGTCACACCATTCTCAATGGCAC
66 TGGTCACACCATTCTCAATGGCAC
3072760 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATTAATTTTTATG
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAA-TAATTTTTATG
*
3072825 GTGGTCACGCCATTCTCAATGGCAC
65 GTGGTCACACCATTCTCAATGGCAC
* * * *
3072850 CACCAAAGTGGTCACGTCAAAGTGAATGACTCCACTAAAATAAAAATA
1 CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATA
3072898 TTTTATTATT
Statistics
Matches: 125, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
87 37 0.30
88 5 0.04
89 5 0.04
90 78 0.62
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (89 bp):
CACCAAAGTGGTCACGCCAAAGAGAATGGCTCCACCAAAATAAAAATAAAAAATAATTTTTATGG
TGGTCACACCATTCTCAATGGCAC
Found at i:3075192 original size:22 final size:22
Alignment explanation
Indices: 3075134--3075192 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
3075124 TTTTTGCATG
* * *
3075134 TTATTTTCTTGTTATTTTGCTA
1 TTATTTTATTGTTATGTTACTA
* * * *
3075156 CTGTTTTACTATTATGTTACTA
1 TTATTTTATTGTTATGTTACTA
3075178 TTATTTTATTGTTAT
1 TTATTTTATTGTTAT
3075193 TGTTTGTATA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (22 bp):
TTATTTTATTGTTATGTTACTA
Found at i:3075259 original size:30 final size:30
Alignment explanation
Indices: 3075225--3075284 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3075215 TATTTTATTA
3075225 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
3075255 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
3075285 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:3075420 original size:11 final size:11
Alignment explanation
Indices: 3075406--3075431 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3075396 TATATATGTT
3075406 TAAAAATAATA
1 TAAAAATAATA
3075417 TAAAAATAATA
1 TAAAAATAATA
3075428 TAAA
1 TAAA
3075432 TAATTAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:3075718 original size:13 final size:14
Alignment explanation
Indices: 3075697--3075730 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3075687 AACATACAAA
3075697 AATAATT-AAAAAT
1 AATAATTAAAAAAT
*
3075710 AATATTTAAAAAAT
1 AATAATTAAAAAAT
3075724 AATAATT
1 AATAATT
3075731 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATTAAAAAAT
Found at i:3077392 original size:30 final size:31
Alignment explanation
Indices: 3077332--3077392 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
3077322 TTGTTATTTT
* *
3077332 ATATATTTTTATAATTAAATTTTAATTTAAA
1 ATATATTTTTATAATTAAATTTGAAATTAAA
*
3077363 ATAT-TTTTTATTATTGAAA-TTGAAATTAAA
1 ATATATTTTTATAATT-AAATTTGAAATTAAA
3077393 CCGACATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
ATATATTTTTATAATTAAATTTGAAATTAAA
Found at i:3083075 original size:16 final size:16
Alignment explanation
Indices: 3083051--3083086 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3083041 CAGATTATGG
* *
3083051 ATTTTAAAATGTTAGT
1 ATTTCAAAATATTAGT
3083067 ATTTCAAAATATTAGT
1 ATTTCAAAATATTAGT
3083083 ATTT
1 ATTT
3083087 GTGATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (16 bp):
ATTTCAAAATATTAGT
Found at i:3084413 original size:8 final size:9
Alignment explanation
Indices: 3084384--3084411 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3084374 TAATCGATTC
3084384 AATTAAAAA
1 AATTAAAAA
3084393 AATTAAAAA
1 AATTAAAAA
3084402 AATTAAAAA
1 AATTAAAAA
3084411 A
1 A
3084412 TTTCGGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AATTAAAAA
Found at i:3088549 original size:8 final size:8
Alignment explanation
Indices: 3088536--3088561 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3088526 TTATTGATTA
3088536 ATAAAATT
1 ATAAAATT
3088544 ATAAAATT
1 ATAAAATT
3088552 ATAAAATT
1 ATAAAATT
3088560 AT
1 AT
3088562 TATCTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAAAATT
Found at i:3088843 original size:17 final size:16
Alignment explanation
Indices: 3088823--3088865 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
3088813 AATATAAAAA
*
3088823 ATTATATATATTAAATT
1 ATTATAAAT-TTAAATT
3088840 ATTATAAATTTAAATT
1 ATTATAAATTTAAATT
3088856 -TTATACAATT
1 ATTATA-AATT
3088866 AACAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATAAATTTAAATT
Found at i:3088867 original size:15 final size:15
Alignment explanation
Indices: 3088821--3088867 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3088811 TAAATATAAA
*
3088821 AAATTA-TATATATT
1 AAATTATTATAAATT
3088835 AAATTATTATAAATTT
1 AAATTATTATAAA-TT
3088851 AAATT-TTATACAATT
1 AAATTATTATA-AATT
3088866 AA
1 AA
3088868 CAAAATCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.21
15 14 0.48
16 9 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTATTATAAATT
Found at i:3092764 original size:13 final size:13
Alignment explanation
Indices: 3092746--3092796 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
3092736 AGTTGTTTAT
*
3092746 TGCTTTTGAGAAG
1 TGCTTTTCAGAAG
3092759 TGCTTTTCAGAAG
1 TGCTTTTCAGAAG
*
3092772 TACTTTTCAGAAG
1 TGCTTTTCAGAAG
*
3092785 TGCTTTTGAGAA
1 TGCTTTTCAGAA
3092797 ATTTGAGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (13 bp):
TGCTTTTCAGAAG
Found at i:3093433 original size:22 final size:22
Alignment explanation
Indices: 3093380--3093423 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3093370 AAGCATATGA
* *
3093380 AAATGATTTGGTTATATTCAAT
1 AAATAATTTGGTTATATACAAT
3093402 AAATAATTTGGTTA-ATACAAT
1 AAATAATTTGGTTATATACAAT
3093423 A
1 A
3093424 CTTACATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (22 bp):
AAATAATTTGGTTATATACAAT
Found at i:3100032 original size:20 final size:20
Alignment explanation
Indices: 3099988--3100033 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3099978 ATCTATATTG
*
3099988 AAGTATCAATACCTTTCCTA
1 AAGTATCAATACCTTTACTA
*
3100008 TAGTATCAATA-CTTTGACTA
1 AAGTATCAATACCTTT-ACTA
3100028 AAGTAT
1 AAGTAT
3100034 TGATACCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
AAGTATCAATACCTTTACTA
Found at i:3104825 original size:12 final size:13
Alignment explanation
Indices: 3104805--3104843 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
3104795 TATTTTCTGA
3104805 AATTAAATATAAT
1 AATTAAATATAAT
3104818 AATT-AATATAA-
1 AATTAAATATAAT
3104829 AATTAAATATAAT
1 AATTAAATATAAT
3104842 AA
1 AA
3104844 ATTGGACCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.17
12 14 0.58
13 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAATATAAT
Found at i:3113549 original size:229 final size:229
Alignment explanation
Indices: 3113143--3113605 Score: 908
Period size: 229 Copynumber: 2.0 Consensus size: 229
3113133 TAGGCTCTTA
*
3113143 ACATATTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
1 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
3113208 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
66 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
*
3113273 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTATCGTTAATA
131 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
3113338 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
196 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
3113372 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
1 ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
3113437 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
66 AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
3113502 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
131 ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
3113567 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
196 AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
3113601 ACATT
1 ACATT
3113606 GATCTTTTAA
Statistics
Matches: 232, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 232 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (229 bp):
ACATTTTTGGTCACCCTGGGGATCATGTCAAGCTTTCTATGACGTTGCTTTTGCAGCATGATAAT
AGAAGAGGGGTGCAACGAGAGTTAGATCAGTTGTGGCCTTCCTTTCATAAAATGGTTGGGTGTAA
ATATAAAGCTGTGTCTCTATATAGGTAGGAGAGATTGGAAGTCTAAAAAATGTTTACCGTTAATA
AAAATTTAATTGTTAGATTTAGATATTTCAAGTT
Found at i:3126891 original size:41 final size:41
Alignment explanation
Indices: 3126834--3127031 Score: 297
Period size: 41 Copynumber: 4.8 Consensus size: 41
3126824 TTATATAAAA
* * * *
3126834 CACCGGCATAAAGCCTGCTAGGCACAAAGTCCGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
3126875 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTGTTACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
3126916 CACCGGCACAGAGCTTGCTAGGCATAAAGCCCAATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
*
3126957 CACTGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
* *
3126998 CACCGGTACAGAGCCTGCTAGGCATAAAACCCGA
1 CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGA
3127032 ACTTACAAAG
Statistics
Matches: 141, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 141 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (41 bp):
CACCGGCACAGAGCCTGCTAGGCATAAAGCCCGATACATTT
Found at i:3127235 original size:47 final size:47
Alignment explanation
Indices: 3127179--3127506 Score: 228
Period size: 47 Copynumber: 6.6 Consensus size: 47
3127169 ACATTCGGTC
* *
3127179 ATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAACT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * * * *
3127226 ATAGATTAATTCATTTCAATGTATAACAAAAATATATATATACATTCGACC
1 ATAGATTAATTCATTTCTATGCATAAC---AAT-TACATATACATTCAACT
* * * *
3127277 ATAGTTTAATTTATTTCTTTGCATAACAATTACATATACATTCAGCT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * *
3127324 ATAGATTAATTCATTTCAATGTATAACAAATATATATATACATTCGGCCATAACCT
1 ATAGATTAATTCATTTCTATGCATAAC-AAT-TACATATACATT----C--AA-CT
* * * * ** *
3127380 AT-GTAATTTCAAATAATTTATTTCAATGCATAACAAATATATATACATTCGGCC
1 ATAG--A--T----TAATTCATTTCTATGCATAACAATTACATATACATTCAACT
* * *
3127434 ATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCT
1 ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
3127481 ATAGATTAATTCATTT-TCATGCATAA
1 ATAGATTAATTCATTTCT-ATGCATAA
3127507 AAAATATATT
Statistics
Matches: 219, Mismatches: 39, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
46 1 0.00
47 114 0.52
48 6 0.03
49 11 0.05
50 3 0.01
51 37 0.17
53 1 0.00
54 3 0.01
55 3 0.01
56 4 0.02
57 2 0.01
59 1 0.00
61 12 0.05
62 2 0.01
63 19 0.09
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (47 bp):
ATAGATTAATTCATTTCTATGCATAACAATTACATATACATTCAACT
Found at i:3127286 original size:98 final size:96
Alignment explanation
Indices: 3127136--3127375 Score: 390
Period size: 98 Copynumber: 2.5 Consensus size: 96
3127126 TAACTTCAAA
* ** *
3127136 TAATTTATTTCAATACATAACAAATATATATATACATTCGGTCATAGTTTAATTCATTTCTCTGC
1 TAATTCATTTCAATGTATAACAAATATATATATACATTCGGCCATAGTTTAATTCATTTCTCTGC
3127201 ATAACAATTACATATACATTCAACTATAGAT
66 ATAACAATTACATATACATTCAACTATAGAT
* * *
3127232 TAATTCATTTCAATGTATAACAAAAATATATATATACATTCGACCATAGTTTAATTTATTTCTTT
1 TAATTCATTTCAATGTATAAC--AAATATATATATACATTCGGCCATAGTTTAATTCATTTCTCT
*
3127297 GCATAACAATTACATATACATTCAGCTATAGAT
64 GCATAACAATTACATATACATTCAACTATAGAT
3127330 TAATTCATTTCAATGTATAACAAATATATATATACATTCGGCCATA
1 TAATTCATTTCAATGTATAACAAATATATATATACATTCGGCCATA
3127376 ACCTATGTAA
Statistics
Matches: 133, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
96 42 0.32
98 91 0.68
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (96 bp):
TAATTCATTTCAATGTATAACAAATATATATATACATTCGGCCATAGTTTAATTCATTTCTCTGC
ATAACAATTACATATACATTCAACTATAGAT
Found at i:3127440 original size:157 final size:159
Alignment explanation
Indices: 3127232--3127520 Score: 458
Period size: 157 Copynumber: 1.8 Consensus size: 159
3127222 AACTATAGAT
* * *
3127232 TAATTCATTTCAATGTATAACAAAAATATATATATACATTCGACCATAGTTTAATTTATTTCTTT
1 TAATTCATTTCAATGCATAAC--AAATATATATATACATTCGACCATAGTTTAATTCATTTCTCT
* *
3127297 GCATAACAATTACATATACATTCAGCTATAGATTAATTCA-TTTCAATGTATAACAAATATATAT
64 GCATAACAATTACATATACATTCAGCTATAGATTAATTCATTTTC-ATGCATAAAAAATATATAT
3127361 ATACATTCGGCCATAACCTATGTAATTTCAAA
128 ATACATTCGGCCATAACCTATGTAATTTCAAA
* *
3127393 TAATTTATTTCAATGCATAAC-AA-ATATATATACATTCGGCCATAGTTTAATTCATTTCTCTGC
1 TAATTCATTTCAATGCATAACAAATATATATATACATTCGACCATAGTTTAATTCATTTCTCTGC
*
3127456 ATAACAATTACATATACATTCAGCTATAGATTAATTCATTTTCATGCATAAAAAATATATTTATA
66 ATAACAATTACATATACATTCAGCTATAGATTAATTCATTTTCATGCATAAAAAATATATATATA
3127521 TATATACATA
Statistics
Matches: 119, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
157 94 0.79
158 6 0.05
161 19 0.16
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (159 bp):
TAATTCATTTCAATGCATAACAAATATATATATACATTCGACCATAGTTTAATTCATTTCTCTGC
ATAACAATTACATATACATTCAGCTATAGATTAATTCATTTTCATGCATAAAAAATATATATATA
CATTCGGCCATAACCTATGTAATTTCAAA
Found at i:3138449 original size:45 final size:46
Alignment explanation
Indices: 3138382--3138505 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
3138372 CATATGACCT
*
3138382 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3138425 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3138471 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3138506 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:3138488 original size:46 final size:45
Alignment explanation
Indices: 3138382--3138579 Score: 207
Period size: 37 Copynumber: 4.8 Consensus size: 45
3138372 CATATGACCT
*
3138382 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3138425 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
3138471 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3138508 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
3138545 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3138580 CACTTATCAC
Statistics
Matches: 140, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
37 64 0.46
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.06
44 6 0.04
45 21 0.15
46 34 0.24
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:3138509 original size:37 final size:37
Alignment explanation
Indices: 3138468--3138606 Score: 233
Period size: 37 Copynumber: 3.8 Consensus size: 37
3138458 GCTGAAGCTA
* *
3138468 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3138505 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3138542 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3138579 CCACTTATCACTTTGTTTCTTGATCAGA
1 CCACTTATCACTTTGTCTCTTGATCAGA
3138607 AGTACTCAAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:3146103 original size:45 final size:45
Alignment explanation
Indices: 3146036--3146159 Score: 198
Period size: 46 Copynumber: 2.8 Consensus size: 45
3146026 CATATGACCT
* *
3146036 CTTATCACTTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
3146079 CTTATCACTTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTT-CACTTGATCAGATAAGTGTAGCTGAAGCTACCA
3146125 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTT-TCACTTGATCAGATAAGTGTAGC
3146160 CACTTATCAC
Statistics
Matches: 75, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
43 11 0.15
44 1 0.01
45 21 0.28
46 41 0.55
47 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (45 bp):
CTTATCACTTTTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:3146163 original size:37 final size:37
Alignment explanation
Indices: 3146121--3146297 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
3146111 AGCTGAAGCT
* **
3146121 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
3146158 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
3146195 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
3146232 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
3146269 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
3146298 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:3151974 original size:17 final size:17
Alignment explanation
Indices: 3151954--3151990 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3151944 ACTTATACAC
*
3151954 ATTTAGTACAATTTCTA
1 ATTTAGCACAATTTCTA
*
3151971 ATTTAGCATAATTTCTA
1 ATTTAGCACAATTTCTA
3151988 ATT
1 ATT
3151991 AGCCCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (17 bp):
ATTTAGCACAATTTCTA
Found at i:3158318 original size:88 final size:83
Alignment explanation
Indices: 3158193--3158411 Score: 278
Period size: 84 Copynumber: 2.6 Consensus size: 83
3158183 AAGTCACTGT
* * *
3158193 TTTTTTTTTACACTCAATTGGGTACTTGAACTT-TCAAAATGCATAAAAAGGCCCTCAAACTTTT
1 TTTTTTTTTGCACTCAATTGGATACTTGAA-TTGTCAAAATACATAAAAAGGCCCTCAAACTTTT
*
3158257 TCAAATAAAGCAATTAAGCCCC
65 TCAAA-AAA--AATTAAGCCAC
* *
3158279 TACTTTTTTTTGCACTTAATTGGATAATTGAATTGTCAAAATACATCAAAAAGGCCCTCAAACTT
1 T--TTTTTTTTGCACTCAATTGGATACTTGAATTGTCAAAATACAT-AAAAAGGCCCTCAAACTT
**
3158344 TTTCAAAAAAAATTAATTCAC
63 TTTCAAAAAAAATTAAGCCAC
* *
3158365 TTTTTTTTTGCACTCAATTGGATACTTGAACTGCCAAAATACATAAA
1 TTTTTTTTTGCACTCAATTGGATACTTGAATTGTCAAAATACATAAA
3158412 TTTATAAAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
83 3 0.03
84 39 0.33
86 10 0.09
87 2 0.02
88 38 0.32
89 25 0.21
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (83 bp):
TTTTTTTTTGCACTCAATTGGATACTTGAATTGTCAAAATACATAAAAAGGCCCTCAAACTTTTT
CAAAAAAAATTAAGCCAC
Found at i:3158822 original size:9 final size:10
Alignment explanation
Indices: 3158787--3158882 Score: 78
Period size: 9 Copynumber: 9.9 Consensus size: 10
3158777 TTCTTTTTCT
3158787 ATATTTCTAT-
1 ATATTT-TATA
3158797 ATATTTTATA
1 ATATTTTATA
*
3158807 ATATTTTATG
1 ATATTTTATA
3158817 AT-TTTTATA
1 ATATTTTATA
*
3158826 AAATTTTA-A
1 ATATTTTATA
3158835 ATATTTT-TA
1 ATATTTTATA
*
3158844 TATTTTTTATTA
1 -ATATTTTA-TA
* *
3158856 AAATTTAATA
1 ATATTTTATA
3158866 AT-TTTTATA
1 ATATTTTATA
3158875 AT-TTTTAT
1 ATATTTTAT
3158883 TGATTTTTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
9 32 0.46
10 31 0.44
11 5 0.07
12 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
ATATTTTATA
Found at i:3158822 original size:19 final size:19
Alignment explanation
Indices: 3158787--3158849 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
3158777 TTCTTTTTCT
3158787 ATATTTCTATATATTTTATA
1 ATATTT-TATATATTTTATA
3158807 ATATTTTATGAT-TTTTATA
1 ATATTTTAT-ATATTTTATA
* *
3158826 AAATTTTAAATATTTT-T-
1 ATATTTTATATATTTTATA
3158843 ATATTTT
1 ATATTTT
3158850 TTATTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 21 0.55
20 8 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATATTTTATATATTTTATA
Found at i:3158872 original size:10 final size:10
Alignment explanation
Indices: 3158800--3158891 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 10
3158790 TTTCTATATA
3158800 TTTT-ATAAT
1 TTTTAATAAT
*
3158809 ATTTT-ATGAT
1 -TTTTAATAAT
*
3158819 TTTTATAAAAT
1 TTTTA-ATAAT
*
3158830 TTTAAAT-AT
1 TTTTAATAAT
*
3158839 TTTT-ATATT
1 TTTTAATAAT
* *
3158848 TTTTATTAAA
1 TTTTAATAAT
*
3158858 ATTTAATAAT
1 TTTTAATAAT
3158868 TTTT-ATAAT
1 TTTTAATAAT
* *
3158877 TTTTATTGAT
1 TTTTAATAAT
3158887 TTTTA
1 TTTTA
3158892 TTTTTTATCA
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
8 2 0.03
9 23 0.38
10 29 0.48
11 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:3158881 original size:19 final size:18
Alignment explanation
Indices: 3158800--3158906 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 18
3158790 TTTCTATATA
*
3158800 TTTTATAATATTTTATGAT
1 TTTTATAAT-TTTTATAAT
* *
3158819 TTTTATAAAATTTTAAATAT
1 TTTTAT-AATTTTTATA-AT
* *
3158839 TTTTATATTTTTTATTAAAA
1 TTTTATAATTTTTA-T-AAT
*
3158859 TTTAATAATTTTTATAAT
1 TTTTATAATTTTTATAAT
*
3158877 TTTTATTGATTTTTAT--T
1 TTTTA-TAATTTTTATAAT
*
3158894 TTTTATCATTTTT
1 TTTTATAATTTTT
3158907 TGCCACATGT
Statistics
Matches: 70, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
16 7 0.10
17 6 0.09
18 6 0.09
19 27 0.39
20 23 0.33
21 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATAATTTTTATAAT
Found at i:3158881 original size:48 final size:47
Alignment explanation
Indices: 3158787--3158897 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 47
3158777 TTCTTTTTCT
* * * * *
3158787 ATATTTCTATATATTTTATAATATTTTATGATTTTTATAAAATTTTAA
1 ATATTTTTATATTTTTTATAAAATTTAATAATTTTTATAAAATTTT-A
*
3158835 ATATTTTTATATTTTTTATTAAAATTTAATAATTTTTAT-AATTTTTA
1 ATATTTTTATATTTTTTA-TAAAATTTAATAATTTTTATAAAATTTTA
*
3158882 TTGATTTTTAT-TTTTT
1 AT-ATTTTTATATTTTT
3158898 ATCATTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
47 7 0.13
48 30 0.56
49 17 0.31
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (47 bp):
ATATTTTTATATTTTTTATAAAATTTAATAATTTTTATAAAATTTTA
Found at i:3158891 original size:29 final size:28
Alignment explanation
Indices: 3158799--3158906 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 28
3158789 ATTTCTATAT
* *
3158799 ATTTTATAATATTTTATGATTTTTATAAA
1 ATTTTATAAT-TTTTATAATTTTTATTAA
* *
3158828 ATTTTAAATATTTTTATATTTTTTATTAAA
1 ATTTTATA-ATTTTTATAATTTTTATT-AA
* *
3158858 ATTTAATAATTTTTATAATTTTTATT-G
1 ATTTTATAATTTTTATAATTTTTATTAA
* *
3158885 ATTTT-TATTTTTTATCATTTTT
1 ATTTTATAATTTTTATAATTTTT
3158907 TGCCACATGT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 15 0.23
27 4 0.06
29 37 0.56
30 10 0.15
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (28 bp):
ATTTTATAATTTTTATAATTTTTATTAA
Found at i:3158892 original size:10 final size:10
Alignment explanation
Indices: 3158837--3158893 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
3158827 AATTTTAAAT
3158837 ATTTTTA-TA
1 ATTTTTATTA
*
3158846 TTTTTTATTA
1 ATTTTTATTA
** *
3158856 AAATTTAATA
1 ATTTTTATTA
3158866 ATTTTTA-TA
1 ATTTTTATTA
*
3158875 ATTTTTATTG
1 ATTTTTATTA
3158885 ATTTTTATT
1 ATTTTTATT
3158894 TTTTATCATT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
9 15 0.39
10 23 0.61
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:3160793 original size:90 final size:93
Alignment explanation
Indices: 3160631--3160862 Score: 244
Period size: 93 Copynumber: 2.5 Consensus size: 93
3160621 CGCCCCTAGC
* * * * *
3160631 CTTTTTGATGCATTTTTG-CAGTTCAAGTGCCCAATT-AGTACTAAAAAAGAGCAGATGCTTAAT
1 CTTTTTGATGCA-TTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGATGATTAAT
*
3160694 TGCT-TTTTTTGGAAAAAGTTTAAGG-GA
65 TGCTGTTTTTTGGAAAAAGTTTAAGGTCA
*
3160721 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAGAAAAAAAAG-AGGTGATTAAT
1 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCA-AAAAAAAAGCAGATGATTAAT
**** * *
3160785 TG-TGTTTTTTTTTTTAAATTTTGAGGTCA
65 TGCTG-TTTTTTGGAAAAAGTTTAAGGTCA
* * *
3160814 TTTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-AAAAAAAA
1 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAA
3160863 CAAGACTTAA
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
89 5 0.04
90 30 0.25
91 22 0.18
92 24 0.20
93 39 0.32
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (93 bp):
CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAGCAGATGATTAATT
GCTGTTTTTTGGAAAAAGTTTAAGGTCA
Found at i:3161459 original size:39 final size:38
Alignment explanation
Indices: 3161386--3161492 Score: 119
Period size: 39 Copynumber: 2.8 Consensus size: 38
3161376 ATGTGATGCC
* * **
3161386 AAAATCTTTAACGGATGTCAAAATCTCTAACAAATA-T
1 AAAATCTCTAACTGATACCAAAATCTCTAACAAATACT
3161423 AAAAAAT-TCTAACTGATACCAAAATCTCTAACCAAATACT
1 --AAAATCTCTAACTGATACCAAAATCTCTAA-CAAATACT
* *
3161463 AAAGTCTCTAATTGATACCAAAATCTCTAA
1 AAAATCTCTAACTGATACCAAAATCTCTAA
3161493 TGGATACCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
38 24 0.41
39 34 0.58
40 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.28
Consensus pattern (38 bp):
AAAATCTCTAACTGATACCAAAATCTCTAACAAATACT
Found at i:3161489 original size:19 final size:19
Alignment explanation
Indices: 3161379--3161505 Score: 87
Period size: 19 Copynumber: 6.6 Consensus size: 19
3161369 AAGCCTAATG
* *
3161379 TGATGCCAAAATCTTTAAC
1 TGATACCAAAATCTCTAAC
* **
3161398 GGATGTCAAAATCTCTAAC
1 TGATACCAAAATCTCTAAC
** **
3161417 AAATATAAAAAAT-TCTAAC
1 TGATA-CCAAAATCTCTAAC
3161436 TGATACCAAAATCTCTAACC
1 TGATACCAAAATCTCTAA-C
** * * *
3161456 AAATACTAAAGTCTCTAAT
1 TGATACCAAAATCTCTAAC
3161475 TGATACCAAAATCTCTAA-
1 TGATACCAAAATCTCTAAC
3161493 TGGATACCAAAAT
1 T-GATACCAAAAT
3161506 TTGTAACCAA
Statistics
Matches: 83, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
18 6 0.07
19 57 0.69
20 20 0.24
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.28
Consensus pattern (19 bp):
TGATACCAAAATCTCTAAC
Found at i:3161541 original size:13 final size:13
Alignment explanation
Indices: 3161523--3161548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3161513 CAAATACCAC
3161523 AATCTCTAACAAA
1 AATCTCTAACAAA
3161536 AATCTCTAACAAA
1 AATCTCTAACAAA
3161549 TACCAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
AATCTCTAACAAA
Found at i:3161562 original size:19 final size:19
Alignment explanation
Indices: 3161404--3161564 Score: 102
Period size: 19 Copynumber: 8.7 Consensus size: 19
3161394 TAACGGATGT
*
3161404 CAAAATCTCTAACAAATATA
1 CAAAATCTCTAACAAATA-C
* **
3161424 AAAAAT-TCTAACTGATAC
1 CAAAATCTCTAACAAATAC
3161442 CAAAATCTCTAACCAAATAC
1 CAAAATCTCTAA-CAAATAC
* * ***
3161462 TAAAGTCTCTAATTGATAC
1 CAAAATCTCTAACAAATAC
***
3161481 CAAAATCTCTAATGGATAC
1 CAAAATCTCTAACAAATAC
* *
3161500 CAAAATTTGTAACCAAATAC
1 CAAAATCTCTAA-CAAATAC
*
3161520 CACAATCTCTAAC----A-
1 CAAAATCTCTAACAAATAC
3161534 -AAAATCTCTAACAAATAC
1 CAAAATCTCTAACAAATAC
*
3161552 CAAAATTTCTAAC
1 CAAAATCTCTAAC
3161565 CATATATAGA
Statistics
Matches: 107, Mismatches: 25, Indels: 19
0.71 0.17 0.13
Matches are distributed among these distances:
13 11 0.10
15 1 0.01
17 1 0.01
18 5 0.05
19 56 0.52
20 33 0.31
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (19 bp):
CAAAATCTCTAACAAATAC
Found at i:3168629 original size:35 final size:33
Alignment explanation
Indices: 3168548--3168632 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
3168538 AAAACACGAG
* * *
3168548 AATTTTTGAAAACACGAGAATTTGTAAACACGAA
1 AATTTTT-AAAACACGAAAATTTGTAAAAAAGAA
*
3168582 AA-TTTTAGAAACACGAAAATTTTTAGAAAAAAGAA
1 AATTTTTA-AAACACGAAAATTTGT--AAAAAAGAA
3168617 AATTTTTAAAACACGA
1 AATTTTTAAAACACGA
3168633 CATTTTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
32 1 0.02
33 18 0.42
34 2 0.05
35 17 0.40
36 5 0.12
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (33 bp):
AATTTTTAAAACACGAAAATTTGTAAAAAAGAA
Found at i:3168740 original size:52 final size:52
Alignment explanation
Indices: 3168683--3168895 Score: 150
Period size: 52 Copynumber: 4.1 Consensus size: 52
3168673 GCGAGAATAT
* *
3168683 TTTGAAACACAAATTTTTTTTTAAACACGAGAATTTTTGAAAACATGAAAAC
1 TTTGAAACACGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
* * ** * *
3168735 TTTGAAACACCGGA-GTTTTTGAAAACACGAGAATTTGTG-AAACACGAAAAT
1 TTTGAAACA-CGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
* * * * **
3168786 TTGTGAAAACACGTATTTTTTTTTAAAAACACGAAAATTTTTG-AAACGCCAGAATT
1 TT-TG-AAACACGAATTTTTTTTT--AAACACGAGAATTTTTGAAAACACGA-AAAC
** ** *
3168842 TTTGAAAACACGAA-GATTTTCAAAACACGAAAATTTTTGAAAACAC-AAAA-
1 TTTG-AAACACGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
3168892 TTTG
1 TTTG
3168896 TTGAACAGGG
Statistics
Matches: 129, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
50 4 0.03
51 14 0.11
52 53 0.41
53 17 0.13
54 4 0.03
55 32 0.25
56 5 0.04
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (52 bp):
TTTGAAACACGAATTTTTTTTTAAACACGAGAATTTTTGAAAACACGAAAAC
Found at i:3168793 original size:35 final size:35
Alignment explanation
Indices: 3168699--3168900 Score: 144
Period size: 35 Copynumber: 5.7 Consensus size: 35
3168689 ACACAAATTT
* * *
3168699 TTTTTTAAACACGAGAATTTTTGAAAACATGAAAA
1 TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
* * * *
3168734 -CTTTGAAACACCG-GAGTTTTTGAAAACACGAGAA
1 TTTTTGAAACA-CGAAAATTTTTGAAAACACGAAAA
* * ***
3168768 TTTGTGAAACACGAAAATTTGTGAAAACACGTATTTT
1 TTTTTGAAACACGAAAATTTTTGAAAACACG-A-AAA
* * * *
3168805 TTTTTAAAAACACGAAAATTTTTG-AAACGCCAGAA
1 TTTTT-GAAACACGAAAATTTTTGAAAACACGAAAA
* *
3168840 TTTTTGAAAACACGAAGA-TTTTCAAAACACGAAAA
1 TTTTTG-AAACACGAAAATTTTTGAAAACACGAAAA
3168875 TTTTTGAAAACAC-AAAATTTGTTGAA
1 TTTTTG-AAACACGAAAATTT-TTGAA
3168901 CAGGGAATTT
Statistics
Matches: 128, Mismatches: 29, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
34 35 0.27
35 62 0.48
36 6 0.05
37 9 0.07
38 16 0.12
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (35 bp):
TTTTTGAAACACGAAAATTTTTGAAAACACGAAAA
Found at i:3168853 original size:90 final size:89
Alignment explanation
Indices: 3168716--3168887 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 89
3168706 AACACGAGAA
* * * * *
3168716 TTTTTGAAAACATGAAAACTTTGAAACACCGGAGTTTTTGAAAACACG-AGAATTTGT-GAAACA
1 TTTTTAAAAACACGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAG-ATTT-TCAAAACA
3168779 CGAAAATTTGTGAAAACACGTATTTT
64 CGAAAATTTGTGAAAACACGTATTTT
* *
3168805 TTTTTAAAAACACGAAAATTTTTGAAACGCCAGAATTTTTGAAAACACGAAGATTTTCAAAACAC
1 TTTTTAAAAACACGAAAA-CTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTTCAAAACAC
*
3168870 GAAAATTTTTGAAAACAC
65 GAAAATTTGTGAAAACAC
3168888 AAAATTTGTT
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 17 0.24
90 53 0.74
91 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (89 bp):
TTTTTAAAAACACGAAAACTTTGAAACACCAGAATTTTTGAAAACACGAAGATTTTCAAAACACG
AAAATTTGTGAAAACACGTATTTT
Found at i:3168899 original size:18 final size:18
Alignment explanation
Indices: 3168532--3168900 Score: 194
Period size: 18 Copynumber: 21.4 Consensus size: 18
3168522 ACGAAAGTTT
* *
3168532 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
3168550 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
3168568 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
3168584 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
3168601 TTTTTAGAAAA-AAGAAAA
1 TTTTT-GAAAACACGAAAA
**
3168619 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
3168637 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
*
3168651 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
* ** *
3168665 --ATTG-AAATGCGAGAA
1 TTTTTGAAAACACGAAAA
*
3168680 TATTTTG-AAACAC-AAATT
1 T-TTTTGAAAACACGAAA-A
** *
3168698 TTTTTTTAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
3168716 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
3168734 -CTTTG-AAACACCG-GAG
1 TTTTTGAAAACA-CGAAAA
*
3168750 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
3168768 TTTGTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* ***
3168785 TTTGTGAAAACACGTATTTT
1 TTTTTGAAAACACG-A-AAA
*
3168805 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
3168823 TTTTTG-AAACGCCAGAA
1 TTTTTGAAAACACGAAAA
*
3168840 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
*
3168858 -TTTTCAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
3168875 TTTTTGAAAACAC-AAAA
1 TTTTTGAAAACACGAAAA
3168892 TTTGTTGAA
1 TTT-TTGAA
3168901 CAGGGAATTT
Statistics
Matches: 268, Mismatches: 54, Indels: 58
0.71 0.14 0.15
Matches are distributed among these distances:
12 8 0.03
14 7 0.03
15 3 0.01
16 24 0.09
17 87 0.32
18 120 0.45
19 7 0.03
20 12 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:3168968 original size:18 final size:16
Alignment explanation
Indices: 3168940--3169001 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 16
3168930 AATTGATCAT
3168940 CGAAATTTTTGAGAACA
1 CGAAATTTTTGA-AACA
3168957 CGAAATTTTTTGAAACA
1 CGAAA-TTTTTGAAACA
* *
3168974 CCAGGATTTTTGAAAACA
1 CGA-AATTTTTG-AAACA
3168992 CGAAATTTTT
1 CGAAATTTTT
3169002 TTAAATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 23 0.61
18 15 0.39
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (16 bp):
CGAAATTTTTGAAACA
Found at i:3169002 original size:18 final size:17
Alignment explanation
Indices: 3168532--3169001 Score: 153
Period size: 18 Copynumber: 27.3 Consensus size: 17
3168522 ACGAAAGTTT
*
3168532 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
3168550 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
*
3168568 --TTTGTAAACACGAAA
1 TTTTTGAAAACACGAAA
*
3168583 ATTTT-AGAAACACGAAAA
1 TTTTTGA-AAACACG-AAA
*
3168601 TTTTTAGAAAA-AAGAAAA
1 TTTTT-GAAAACACG-AAA
*
3168619 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-A-A
3168637 TTTTTG-AAACACG--A
1 TTTTTGAAAACACGAAA
*
3168651 --TTT-AAAAAAC-AAA
1 TTTTTGAAAACACGAAA
** **
3168664 -AATTG-AAATGCGAGAA
1 TTTTTGAAAACACGA-AA
3168680 TATTTTG-AAACAC-AAA
1 T-TTTTGAAAACACGAAA
**
3168696 TTTTTTTTTAAACACGAGAA
1 --TTTTTGAAAACACGA-AA
*
3168716 TTTTTGAAAACATGAAA
1 TTTTTGAAAACACGAAA
** * *
3168733 ACTTTG-AAACACCGGAG
1 TTTTTGAAAACA-CGAAA
3168750 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGA-AA
*
3168768 TTTGTG-AAACACGAAAA
1 TTTTTGAAAACACG-AAA
* **
3168785 TTTGTGAAAACACGTATTTT
1 TTTTTGAAAACACG-A--AA
*
3168805 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
* *
3168823 TTTTTG-AAACGCCAGAA
1 TTTTTGAAAACACGA-AA
3168840 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAA-A
*
3168858 -TTTTCAAAACACGAAAA
1 TTTTTGAAAACACG-AAA
*
3168875 TTTTTGAAAACACAAAA
1 TTTTTGAAAACACGAAA
* *
3168892 TTTGTTG--AACAGGGAATT
1 TTT-TTGAAAACA-CGAA-A
**
3168910 TTTTTGAAAACGAAAAAAA
1 TTTTTGAAAAC--ACGAAA
*** *
3168929 AAATTG--ATCATCGAAA
1 TTTTTGAAAACA-CGAAA
*
3168945 TTTTTGAGAACACGAAA
1 TTTTTGAAAACACGAAA
* *
3168962 TTTTTTG-AAACACCAGGA
1 -TTTTTGAAAACACGA-AA
3168980 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
3168997 TTTTT
1 TTTTT
3169002 TTAAATATTT
Statistics
Matches: 336, Mismatches: 67, Indels: 99
0.67 0.13 0.20
Matches are distributed among these distances:
12 8 0.02
13 1 0.00
14 6 0.02
15 4 0.01
16 37 0.11
17 110 0.33
18 141 0.42
19 10 0.03
20 18 0.05
21 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
TTTTTGAAAACACGAAA
Found at i:3169331 original size:10 final size:9
Alignment explanation
Indices: 3169313--3169370 Score: 62
Period size: 10 Copynumber: 6.0 Consensus size: 9
3169303 ATTAAAACCC
3169313 TTTTTTTCT
1 TTTTTTTCT
3169322 TTTTTCTTCT
1 TTTTT-TTCT
*
3169332 TTTATCTTCT
1 TTT-TTTTCT
*
3169342 TTTTTCCTCT
1 TTTTT-TTCT
3169352 CTTTTTTTCT
1 -TTTTTTTCT
3169362 TTTTTTTCT
1 TTTTTTTCT
3169371 GGACTGGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 15 0.37
10 20 0.49
11 6 0.15
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:3169343 original size:20 final size:18
Alignment explanation
Indices: 3169312--3169370 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 18
3169302 AATTAAAACC
3169312 CTTTTTTTCTTTTTTCTT
1 CTTTTTTTCTTTTTTCTT
3169330 CTTTTATCTTCTTTTTTCCTCT
1 CTTTT-T-TTCTTTTTT-CT-T
3169352 CTTTTTTTCTTTTTT-TT
1 CTTTTTTTCTTTTTTCTT
3169369 CT
1 CT
3169371 GGACTGGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.08
18 6 0.16
19 1 0.03
20 18 0.49
21 3 0.08
22 6 0.16
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
CTTTTTTTCTTTTTTCTT
Found at i:3169419 original size:22 final size:23
Alignment explanation
Indices: 3169391--3169440 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
3169381 GGCCTGTTGG
*
3169391 GCTGCTG-CTAGGCCTGGGGGCT
1 GCTGCTGACTAGGCCTGGGGCCT
3169413 GCTGCTGCACTAGGCCTGGGGCCT
1 GCTGCTG-ACTAGGCCTGGGGCCT
3169437 GCTG
1 GCTG
3169441 GGCCTGCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.06, C:0.30, G:0.42, T:0.22
Consensus pattern (23 bp):
GCTGCTGACTAGGCCTGGGGCCT
Found at i:3169657 original size:20 final size:20
Alignment explanation
Indices: 3169628--3169705 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 20
3169618 GACTGTGATA
3169628 TTTTTCTTTTT-TTTTTCCT
1 TTTTTCTTTTTCTTTTTCCT
3169647 TTTTTCTTTTT-TTCTTT-CT
1 TTTTTCTTTTTCTT-TTTCCT
*
3169666 CTTTTTCTTCTCTCTTTTTCCT
1 -TTTTTCTT-TTTCTTTTTCCT
*
3169688 TCTTTCTTTTTCTTTTTC
1 TTTTTCTTTTTCTTTTTC
3169706 TTCTTCTTCT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
19 15 0.29
20 20 0.39
21 12 0.24
22 4 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTTCCT
Found at i:3169664 original size:12 final size:13
Alignment explanation
Indices: 3169628--3169716 Score: 87
Period size: 14 Copynumber: 6.8 Consensus size: 13
3169618 GACTGTGATA
3169628 TTTTTCTT-TTT-
1 TTTTTCTTCTTTC
*
3169639 TTTTTCCTTTTTTC
1 TTTTT-CTTCTTTC
3169653 TTTTT-TTCTTTCTC
1 TTTTTCTTC-TT-TC
*
3169667 TTTTTCTTCTCTC
1 TTTTTCTTCTTTC
3169680 TTTTTCCTTCTTTC
1 TTTTT-CTTCTTTC
3169694 TTTTTCTT-TTTC
1 TTTTTCTTCTTTC
*
3169706 TTCTTCTTCTT
1 TTTTTCTTCTT
3169717 CGGGCCGTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
11 5 0.08
12 16 0.24
13 17 0.26
14 25 0.38
15 3 0.05
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:3169670 original size:27 final size:26
Alignment explanation
Indices: 3169628--3169710 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 26
3169618 GACTGTGATA
*
3169628 TTTTTCTTTTTTTTTTCCTTTTTTCTT
1 TTTTTC-TTTCTTTTTCCTTTTTTCTT
* * *
3169655 TTTTTCTTTCTCTTTTTCTTCTCTCTT
1 TTTTTCTTTCT-TTTTCCTTTTTTCTT
*
3169682 TTTCCTTCTTTCTTTTTCTTTTTCTTCTT
1 TTT--TTCTTTCTTTTTCCTTTT-TTCTT
3169711 CTTCTTCGGG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 4 0.09
27 21 0.48
28 7 0.16
29 12 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTCTTTCTTTTTCCTTTTTTCTT
Found at i:3169670 original size:33 final size:33
Alignment explanation
Indices: 3169630--3169713 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
3169620 CTGTGATATT
* * * *
3169630 TTTCTTTTTTTTTTC-CT-TTTTTCTTTTTTTC
1 TTTCTCTTTTTCTTCTCTCTTTTTCCTTCTTTC
3169661 TTTCTCTTTTTCTTCTCTCTTTTTCCTTCTTTC
1 TTTCTCTTTTTCTTCTCTCTTTTTCCTTCTTTC
*
3169694 TTTTTCTTTTTCTTCT-TCTT
1 TTTCTCTTTTTCTTCTCTCTT
3169714 CTTCGGGCCG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.28
32 6 0.13
33 27 0.59
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (33 bp):
TTTCTCTTTTTCTTCTCTCTTTTTCCTTCTTTC
Found at i:3169701 original size:6 final size:6
Alignment explanation
Indices: 3169628--3169713 Score: 79
Period size: 6 Copynumber: 14.3 Consensus size: 6
3169618 GACTGTGATA
* * *
3169628 TTTTTC TTTTT- TTTTTC CTTTT- TTCTT- TTTTTC TTTCTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
3169673 TTCTCTC TTTTTCC TTCTTTC TTTTTC TTTTTC TTCTTC TT
1 TT-TTTC TTTTT-C TT-TTTC TTTTTC TTTTTC TTTTTC TT
3169714 CTTCGGGCCG
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
5 12 0.18
6 40 0.61
7 11 0.17
8 3 0.05
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:3170277 original size:30 final size:29
Alignment explanation
Indices: 3170243--3170401 Score: 133
Period size: 29 Copynumber: 5.4 Consensus size: 29
3170233 TATGGGGCTA
* * *
3170243 AAATGTAATTTATAGAAAGTTTAGGGGCCC
1 AAATGTAATTTAGA-AAAGTTTAGGGGTCG
* * **
3170273 AAATGAAATTTAGAAAATTTTAGGGGTAT
1 AAATGTAATTTAGAAAAGTTTAGGGGTCG
* * *
3170302 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTG
1 AAATGT-AATTTAGA-AAAGTTTAGGGGTCG
*
3170332 AAATGTAATTTCA-AAAAGTTTAGGGGTTG
1 AAATGTAATTT-AGAAAAGTTTAGGGGTCG
** * *
3170361 AAATGTAATTTAGAAAAGTACAGGGGCCA
1 AAATGTAATTTAGAAAAGTTTAGGGGTCG
3170390 AAATGTAATTTA
1 AAATGTAATTTA
3170402 TATTTTTTTA
Statistics
Matches: 105, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.01
29 70 0.67
30 34 0.32
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (29 bp):
AAATGTAATTTAGAAAAGTTTAGGGGTCG
Found at i:3170309 original size:59 final size:58
Alignment explanation
Indices: 3170243--3170401 Score: 162
Period size: 59 Copynumber: 2.7 Consensus size: 58
3170233 TATGGGGCTA
* * * *
3170243 AAATGTAATTTATAGAAAGTTTAGGGGCCCAAATGAAATTTAGAAAATTTTAGGGGTAT-
1 AAATGTAATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTTA-AAAAGTTTAGGGGT-TG
* * ***
3170302 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTGAAATGTAATTTCAAAAAGTTTAGGGGTTG
1 AAATGT-AATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTT-AAAAAGTTTAGGGGTTG
**
3170361 AAATGTAATTTAGA-AAAGTACAGGGGCCAAAATGTAATTTA
1 AAATGTAATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTTA
3170402 TATTTTTTTA
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
57 1 0.01
58 26 0.32
59 48 0.59
60 6 0.07
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (58 bp):
AAATGTAATTTAGAGAAAGTTTAGGGGCCAAAATGTAATTTAAAAAGTTTAGGGGTTG
Found at i:3170351 original size:29 final size:29
Alignment explanation
Indices: 3170243--3170379 Score: 136
Period size: 29 Copynumber: 4.7 Consensus size: 29
3170233 TATGGGGCTA
* ***
3170243 AAATGTAATTTATAGAAAGTTTAGGGGCCC
1 AAATGTAATTTAGA-AAAGTTTAGGGGTTG
* *
3170273 AAATGAAATTTAGAAAATTTTAGGGGTAT-
1 AAATGTAATTTAGAAAAGTTTAGGGGT-TG
* *
3170302 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTG
1 AAATGT-AATTTAGA-AAAGTTTAGGGGTTG
3170332 AAATGTAATTTCA-AAAAGTTTAGGGGTTG
1 AAATGTAATTT-AGAAAAGTTTAGGGGTTG
3170361 AAATGTAATTTAGAAAAGT
1 AAATGTAATTTAGAAAAGT
3170380 ACAGGGGCCA
Statistics
Matches: 89, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.01
29 54 0.61
30 34 0.38
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (29 bp):
AAATGTAATTTAGAAAAGTTTAGGGGTTG
Found at i:3170932 original size:163 final size:163
Alignment explanation
Indices: 3170755--3172573 Score: 2300
Period size: 163 Copynumber: 11.5 Consensus size: 163
3170745 AAAAATAGAT
* *
3170755 ATTGAAAATACCTCAGCGTAACCCGAGGCTCAAAC-CATCTCTCGCATTATGAGTTGATTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTC-AACTCACCTCTCGCATTATGAGTTGA-TTTTTT
* *
3170819 TG-AAAAAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAAGCTCAACTCACTTCTCGGAAT
64 TGAAAAAAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAT
3170883 ATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
129 ATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
**
3170918 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTTACATTATGAGTTGATTTTTTTG
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG
* * *
3170983 AAAAAAGAAATTTAAAAGAAATTCATCAGCGTGCGACTCGAGGCTCAACTCACTTCTCGCAATAT
66 AAAAAAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATAT
*
3171048 GAGTTAATTTTTTTGAAAAACAGAGAAACATAA
131 GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
*
3171081 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTG
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG
*
3171146 AAAAAAGAAATTTAAAAGAAATTCCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATAT
66 AAAAAAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATAT
3171211 GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
131 GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
3171244 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTTTCACATTATGAGTTGATTTTTTTG
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG
*
3171309 AAAAAAGAAATTTAAAAGAAATTCCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATAT
66 AAAAAAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATAT
3171374 GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
131 GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
3171407 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG
* *
3171472 AAAAGAGAAATTTAAAAGAAATACCTCAGCGTGCGACCTGAGGCTCAACTCACTTCTCGCAATAT
66 AAAAAAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATAT
3171537 GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
131 GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* * * *
3171570 ATTGAAAATACCTCAGCGTGACCTGAGGTTCAACTCACCTCTCGCATTATGAATT--TATTTTTG
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG
* * * * * * *
3171633 AAAAACGAAAATTTGAAAGAAATACCTCGGCAT--GACCCGAGGCTCAACTCACATCT-GTATTA
66 AAAAAAG-AAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATA
**
3171695 TGAGTTGA--TTTTTGAAAAAC-GA-AAATTTGAA
130 TGAGTTGATTTTTTTGAAAAACAGAGAAACAT-AA
* * **
3171726 A--G-AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTGTTATGAGTTGA--TTTTTG
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG
* * * * *
3171785 AAAAACGAAAATTTAAAAGAAATACCTC-GACAT--GACCCGAGGCTCAACTCACCTCT-GTATT
66 AAAAAAG-AAATTTAAAAGAAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACTTCTCGCAAT
**
3171846 ATGAGTTGA--TTTTTGAAAAAC-GA-AAATTTGAA
129 ATGAGTTGATTTTTTTGAAAAACAGAGAAACAT-AA
* * * * *
3171878 A--G-AAATACCTCGGCATGACCCGAGGCTCAACTCACTTCTGGCAATATGAGTTGATTTTTTTT
1 ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTT
*
3171940 GAAAAACAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
65 GAAAAA-AGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAAT
3172005 ATGAGTTGA-TTTTTTGAAAAAC--A-AAA-AT--
129 ATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
3172033 -TTAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
1 ATTGAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
* *
3172095 TGAAAAAACAGAAATTT---A-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCA
64 TG-AAAAA-AGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCA
*
3172156 ATATGAGTTGA--TTTTTGAAAAA-ACAG-AA-AT--
127 ATATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
3172186 -TT-AAAATACCTCAGCGTGCGACCCGAGGCTCAACCCACTTCTCGCATTATGAGTTGA--TTTT
1 ATTGAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
* *
3172247 TGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGTAA
64 TGAAAAA-AGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAA
*
3172310 TATGAGTTGA--TTTTTGAAAAA-ACAG-AA-AT--
128 TATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
* *
3172339 -TT-AAAATACCTCAGCGTGCAATCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGA--TTTT
1 ATTGAAAATACCTCAGCGTG--ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
*
3172400 TGAAAAACAGAAATTTAAAAGAAATACCTCAGCGT--GACCTGAGGCTCAACTCAGC-TCTCGCA
64 TGAAAAA-AGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCA-CTTCTCGCA
*
3172462 ATATGAGTTGATTTTTTTGAAAAA-ACAG-AA-AT--
127 ATATGAGTTGATTTTTTTGAAAAACAGAGAAACATAA
*
3172494 -TT-AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
1 ATTGAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTT
* *
3172555 TGAAAACAGAAATTGAAAA
64 TGAAAAAAGAAATTTAAAA
3172574 ATATTTTTTA
Statistics
Matches: 1544, Mismatches: 75, Indels: 83
0.91 0.04 0.05
Matches are distributed among these distances:
151 16 0.01
152 211 0.14
153 284 0.18
154 15 0.01
155 98 0.06
156 44 0.03
157 41 0.03
158 24 0.02
159 64 0.04
160 33 0.02
161 11 0.01
162 33 0.02
163 670 0.43
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (163 bp):
ATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTG
AAAAAAGAAATTTAAAAGAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATAT
GAGTTGATTTTTTTGAAAAACAGAGAAACATAA
Found at i:3171717 original size:76 final size:76
Alignment explanation
Indices: 3171575--3172568 Score: 1224
Period size: 76 Copynumber: 12.9 Consensus size: 76
3171565 CATAAATTGA
* * * * *
3171575 AAATACCTCAGCGTGACCTGAGGTTCAACTCACCTCTCGCATTATGAATTTATTTTTGAAAAAC-
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
3171639 GAAAATTTGAAAG
66 G-AAATTT-AAAG
* * * * *
3171652 AAATACCTCGGCATGACCCGAGGCTCAACTCACATCT-GTATTATGAGTTGATTTTTGAAAAAC-
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
3171715 GAAAATTTGAAAG
66 G-AAATTT-AAAG
* * ***
3171728 AAATACCTCGGCATGACCCGAGGCTCAACTCACCTCT-GTGTTATGAGTTGATTTTTGAAAAAC-
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
3171791 GAAAATTTAAAAG
66 G-AAATTT-AAAG
* * *
3171804 AAATACCTC-GACATGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTGAAAAAC
1 AAATACCTCAG-CGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
3171867 -GAAAATTTGAAAG
65 AG-AAATTT-AAAG
* * * *
3171880 AAATACCTCGGCATGACCCGAGGCTCAACTCACTTCTGGCAATATGAGTTGATTTTTTTTGAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAA
3171945 ACAGAAATTTAAAAG
63 ACAGAAATTT-AAAG
3171960 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAA
*
3172025 ACAAAAATTT-AA-
63 ACAGAAATTTAAAG
3172037 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
3172102 ACAGAAATTT--A-
63 ACAGAAATTTAAAG
*
3172113 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
3172178 ACAGAAATTT--A-
63 ACAGAAATTTAAAG
* * *
3172189 AAATACCTCAGCGTGCGACCCGAGGCTCAACCCACTTCTCGCATTATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
3172254 CAGAAATTTAAAAG
64 CAGAAATTT-AAAG
*
3172268 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAAAC
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAAC
3172333 AGAAATTT--A-
65 AGAAATTTAAAG
* * *
3172342 AAATACCTCAGCGTGCAATCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTGAAAAA
1 AAATACCTCAGCGTG--ACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
3172407 CAGAAATTTAAAAG
64 CAGAAATTT-AAAG
* *
3172421 AAATACCTCAGCGTGACCTGAGGCTCAACTCAGCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG-AAAA
3172486 ACAGAAATTT--A-
63 ACAGAAATTTAAAG
3172497 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA
1 AAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
3172561 CAGAAATT
64 CAGAAATT
3172569 GAAAAATATT
Statistics
Matches: 848, Mismatches: 43, Indels: 55
0.90 0.05 0.06
Matches are distributed among these distances:
74 27 0.03
75 30 0.04
76 412 0.49
77 185 0.22
78 54 0.06
79 35 0.04
80 68 0.08
81 1 0.00
82 36 0.04
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (76 bp):
AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
GAAATTTAAAG
Found at i:3173485 original size:17 final size:18
Alignment explanation
Indices: 3173459--3173492 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3173449 TTTTGTCTGT
3173459 TTTTTCTGTTCTTTTTTC
1 TTTTTCTGTTCTTTTTTC
*
3173477 TTTTT-TGTTGTTTTTT
1 TTTTTCTGTTCTTTTTT
3173493 TAAGCATAAT
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:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (18 bp):
TTTTTCTGTTCTTTTTTC
Found at i:3178891 original size:35 final size:35
Alignment explanation
Indices: 3178795--3179223 Score: 225
Period size: 35 Copynumber: 12.5 Consensus size: 35
3178785 ACGAAAGTTT
* *
3178795 TTTTTA-AAACACGAGAATTTTTGAAAACACGAGAA
1 TTTTTAGAAACACGAAAATTTTT-AAAACACGAAAA
*
3178830 TTTGT--AAACACGAAAA-TTTTAGAAACACGAAAA
1 TTTTTAGAAACACGAAAATTTTTA-AAACACGAAAA
* * * *
3178863 TTTTTAGAAAAACAAAAATTTTTAAAACACGACAT
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* ** * *
3178898 TTTTTTGAAACACGGGAATTTTTAAAACAGGGAAA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* *
3178933 -TTTTAGAAACACGAAAATTTTTAAAACACGACAT
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* *
3178967 TTTTTTGAAACACG---A--TTTAAAAAAC-AAAA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
* * * * *
3178996 --ATT-GAAATACGAGAATATTTTGAAACAC-AAATT
1 TTTTTAGAAACACGAAAAT-TTTTAAAACACGAAA-A
** * * *
3179029 TTTTTTTAAACGCGAGAATTTTTGAAAACATGAAAA
1 TTTTTAGAAACACGAAAATTTTT-AAAACACGAAAA
* * * *
3179065 -ATTT-GAAACACCG-GAGTTTTTGAAAACACGAGAA
1 TTTTTAGAAACA-CGAAAATTTTT-AAAACACGAAAA
* * * **
3179099 TTTGT-GAAACATGAAAATTTGTGAAAACACGTAATTT
1 TTTTTAGAAACACGAAAATTT-TTAAAACACG-AA-AA
* * ** * *
3179136 TTTTTAAAAACACGAAAATTTTTGAAATGCTAGAA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
*
3179171 TTTTT-GAAAACACGAAGATTTTTAAAACACGAAAA
1 TTTTTAG-AAACACGAAAATTTTTAAAACACGAAAA
3179206 TTTTT-GAAAACACGAAAA
1 TTTTTAG-AAACACGAAAA
3179224 CACAAAATTT
Statistics
Matches: 295, Mismatches: 74, Indels: 50
0.70 0.18 0.12
Matches are distributed among these distances:
26 7 0.02
27 2 0.01
29 3 0.01
30 9 0.03
32 13 0.04
33 18 0.06
34 60 0.20
35 135 0.46
36 23 0.08
37 12 0.04
38 13 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
TTTTTAGAAACACGAAAATTTTTAAAACACGAAAA
Found at i:3178953 original size:69 final size:71
Alignment explanation
Indices: 3178795--3178980 Score: 231
Period size: 69 Copynumber: 2.7 Consensus size: 71
3178785 ACGAAAGTTT
* * * *
3178795 TTTTTA-AAACACGAGAATTTTTGAAAACACGAGA-ATTTGT-AAACAC-GAAAATTTTAGAAAC
1 TTTTTAGAAACACGAAAATTTTT-AAAACACGACATTTTTTTGAAACACGGAAAATTTTAGAAAC
3178856 ACGAAAA
65 ACGAAAA
* * * *
3178863 TTTTTAGAAAAACAAAAATTTTTAAAACACGACATTTTTTTGAAACACGGGAATTTTTA-AAACA
1 TTTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACGGAAAATTTTAGAAACA
* *
3178927 GGGAAA
66 CGAAAA
3178933 -TTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACG
1 TTTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACG
3178981 ATTTAAAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
68 16 0.16
69 63 0.62
70 15 0.15
71 8 0.08
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (71 bp):
TTTTTAGAAACACGAAAATTTTTAAAACACGACATTTTTTTGAAACACGGAAAATTTTAGAAACA
CGAAAA
Found at i:3179221 original size:18 final size:18
Alignment explanation
Indices: 3178794--3179223 Score: 232
Period size: 18 Copynumber: 25.0 Consensus size: 18
3178784 AACGAAAGTT
* *
3178794 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
3178812 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
3178830 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
3178846 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
3178863 TTTTTAGAAAA-ACAAAAA
1 TTTTT-GAAAACACGAAAA
**
3178881 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
**
3178899 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
3178916 TTTTT-AAAACAGGGAAA
1 TTTTTGAAAACACGAAAA
*
3178933 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
3178950 TTTTT-AAAACACGACATT
1 TTTTTGAAAACACGA-AAA
3178968 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
*
3178982 --TTT-AAAAAAC-AAAA
1 TTTTTGAAAACACGAAAA
* * *
3178996 --ATTG-AAATACGAGAA
1 TTTTTGAAAACACGAAAA
*
3179011 TATTTTG-AAACAC-AAATT
1 T-TTTTGAAAACACGAAA-A
** * *
3179029 TTTTTTTAAACGCGAGAA
1 TTTTTGAAAACACGAAAA
*
3179047 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* * *
3179065 -ATTTG-AAACACCG-GAG
1 TTTTTGAAAACA-CGAAAA
*
3179081 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
3179099 TTTGTG-AAACATGAAAA
1 TTTTTGAAAACACGAAAA
* **
3179116 TTTGTGAAAACACGTAATTT
1 TTTTTGAAAACACG-AA-AA
*
3179136 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
** * *
3179154 TTTTTG-AAATGCTAGAA
1 TTTTTGAAAACACGAAAA
*
3179171 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
3179189 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
3179206 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
3179224 CACAAAATTT
Statistics
Matches: 313, Mismatches: 66, Indels: 66
0.70 0.15 0.15
Matches are distributed among these distances:
12 8 0.03
14 8 0.03
15 3 0.01
16 24 0.08
17 118 0.38
18 131 0.42
19 9 0.03
20 12 0.04
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:3179307 original size:17 final size:16
Alignment explanation
Indices: 3179285--3179343 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
3179275 TGATCATCGG
3179285 AATTTTTGAGAACACAA
1 AATTTTTGA-AACACAA
*
3179302 AATTTTTTGAAACACCAG
1 AA-TTTTTGAAACA-CAA
* *
3179320 GATTTTTGAAAACACGA
1 AATTTTTG-AAACACAA
3179337 AATTTTT
1 AATTTTT
3179344 TGAATATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
AATTTTTGAAACACAA
Found at i:3179310 original size:18 final size:17
Alignment explanation
Indices: 3179287--3179347 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
3179277 ATCATCGGAA
3179287 TTTTTGAGAACACAAAAT
1 TTTTTGA-AACACAAAAT
**
3179305 TTTTTGAAACACCAGGA-
1 TTTTTGAAACA-CAAAAT
*
3179322 TTTTTGAAAACACGAAAT
1 TTTTTG-AAACACAAAAT
3179340 TTTTTGAA
1 TTTTTGAA
3179348 TATTTACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (17 bp):
TTTTTGAAACACAAAAT
Found at i:3179677 original size:10 final size:10
Alignment explanation
Indices: 3179659--3179717 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
3179649 ATTAAAACCC
3179659 TTTTT-TTCT
1 TTTTTCTTCT
3179668 TTTTTCTTCT
1 TTTTTCTTCT
*
3179678 TTTATCTTCT
1 TTTTTCTTCT
*
3179688 TTTTTCCTCT
1 TTTTTCTTCT
3179698 CTTTTT-TTCT
1 -TTTTTCTTCT
*
3179708 TTTTTTTTCT
1 TTTTTCTTCT
3179718 GGACTGGGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
9 10 0.23
10 28 0.65
11 5 0.12
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:3179689 original size:20 final size:18
Alignment explanation
Indices: 3179658--3179717 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 18
3179648 AATTAAAACC
3179658 CTTTTTTTCTTTTTTCTT
1 CTTTTTTTCTTTTTTCTT
3179676 CTTTTATCTTCTTTTTTCCTCT
1 CTTTT-T-TTCTTTTTT-CT-T
*
3179698 CTTTTTTTCTTTTTTTTT
1 CTTTTTTTCTTTTTTCTT
3179716 CT
1 CT
3179718 GGACTGGGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
18 8 0.22
19 2 0.05
20 18 0.49
21 3 0.08
22 6 0.16
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
CTTTTTTTCTTTTTTCTT
Found at i:3179837 original size:13 final size:13
Alignment explanation
Indices: 3179819--3179875 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
3179809 TGCATTTGGG
3179819 CTGCTTCTTTCTT
1 CTGCTTCTTTCTT
3179832 CTGCTTCTTTCTTT
1 CTGCTTCTTTC-TT
* * *
3179846 CTTTCTTTTTTCTG
1 C-TGCTTCTTTCTT
*
3179860 CTGCTTCTTTTTT
1 CTGCTTCTTTCTT
3179873 CTG
1 CTG
3179876 TTTTGGTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
13 22 0.63
14 5 0.14
15 8 0.23
ACGTcount: A:0.00, C:0.26, G:0.09, T:0.65
Consensus pattern (13 bp):
CTGCTTCTTTCTT
Found at i:3179851 original size:25 final size:23
Alignment explanation
Indices: 3179823--3179874 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
3179813 TTTGGGCTGC
*
3179823 TTCTTTCTTCTGCTTCTTTCTTTCT
1 TTCTTTCTTCTGCTGC-TTCTTT-T
*
3179848 TTCTTTTTTCTGCTGCTTCTTTT
1 TTCTTTCTTCTGCTGCTTCTTTT
3179871 TTCT
1 TTCT
3179875 GTTTTGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
25 14 0.56
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (23 bp):
TTCTTTCTTCTGCTGCTTCTTTT
Found at i:3180000 original size:6 final size:6
Alignment explanation
Indices: 3179984--3180063 Score: 70
Period size: 6 Copynumber: 12.3 Consensus size: 6
3179974 GACTGTGATA
* *
3179984 TTTTTC TTTTTTC TTTTTTTC TTTCTC TTTTTC TTCTCTC TTTTTCC TTCTTTC
1 TTTTTC -TTTTTC --TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT-C TT-TTTC
* *
3180038 TTTTTC TTTTTC TTCTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TT
3180064 CGGGCCGTAC
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
6 37 0.58
7 17 0.27
8 10 0.16
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:3180012 original size:14 final size:14
Alignment explanation
Indices: 3179984--3180051 Score: 54
Period size: 14 Copynumber: 5.0 Consensus size: 14
3179974 GACTGTGATA
*
3179984 TTTTTCTTTTTTCTT
1 TTTTTC-TTTCTCTT
3179999 TTTTTCTTTCTC--
1 TTTTTCTTTCTCTT
*
3180011 TTTTTC-TTCTCTC
1 TTTTTCTTTCTCTT
*
3180024 TTTTTCCTTCT-TT
1 TTTTTCTTTCTCTT
*
3180037 CTTTTTCTTTTTCTT
1 -TTTTTCTTTCTCTT
3180052 CTTCTTCTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
11 5 0.11
12 6 0.14
13 7 0.16
14 18 0.41
15 8 0.18
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTCTCTT
Found at i:3180025 original size:27 final size:27
Alignment explanation
Indices: 3179984--3180060 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
3179974 GACTGTGATA
* *
3179984 TTTTTCTTTTTTCTTTTT-TTCTTTCT
1 TTTTTCTTCTCTCTTTTTCTTCTTTCT
3180010 CTTTTTCTTCTCTCTTTTTCCTTCTTTC-
1 -TTTTTCTTCTCTCTTTTT-CTTCTTTCT
* *
3180038 TTTTTCTT-TTTCTTCTTCTTCTT
1 TTTTTCTTCTCTCTTTTTCTTCTT
3180061 CTTCGGGCCG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
25 6 0.14
26 7 0.16
27 24 0.55
29 7 0.16
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTTCTTCTCTCTTTTTCTTCTTTCT
Found at i:3180038 original size:33 final size:32
Alignment explanation
Indices: 3179991--3180057 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
3179981 ATATTTTTCT
* *
3179991 TTTTTCTTTTTTTCTTTCTCTTTTTCTTCTCTC
1 TTTTTCCTTCTTTCTTTCTCTTTTTCTTCT-TC
*
3180024 TTTTTCCTTCTTTCTTTTTCTTTTTCTTCTTC
1 TTTTTCCTTCTTTCTTTCTCTTTTTCTTCTTC
3180056 TT
1 TT
3180058 CTTCTTCGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 4 0.13
33 27 0.87
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTCCTTCTTTCTTTCTCTTTTTCTTCTTC
Found at i:3180693 original size:29 final size:29
Alignment explanation
Indices: 3180615--3180727 Score: 106
Period size: 29 Copynumber: 3.9 Consensus size: 29
3180605 TTAGGAGCCC
* * *
3180615 AAATGAAATTTAGAAAATTTTAGGGGTAT-
1 AAATGTAATTTAGAAAAGTTCAGGGGT-TG
* * *
3180644 AAGTGTAAATTT-GAGAGAGTTTAGGGGTTG
1 AAATGT-AATTTAGA-AAAGTTCAGGGGTTG
3180674 AAATGTAATTTCA-AAAAGTTCAGGGGTTG
1 AAATGTAATTT-AGAAAAGTTCAGGGGTTG
*
3180703 AAATGTAATTTAGAAAAGTACAGGG
1 AAATGTAATTTAGAAAAGTTCAGGG
3180728 CCAAAATGTA
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.01
29 47 0.67
30 22 0.31
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.31
Consensus pattern (29 bp):
AAATGTAATTTAGAAAAGTTCAGGGGTTG
Found at i:3189430 original size:71 final size:71
Alignment explanation
Indices: 3189347--3189488 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
3189337 AGCCAAGAGT
3189347 TAGTTGCTCTTACTCTCGAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
1 TAGTTGCTCTTACTCTCGAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
3189412 AGTAAA
66 AGTAAA
3189418 TAGTTGCTCTTACTCTCGAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
1 TAGTTGCTCTTACTCTCGAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
3189483 AGTAAA
66 AGTAAA
3189489 GAAATTGCGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (71 bp):
TAGTTGCTCTTACTCTCGAAAGAGATATTAGCATACTTTAGAGATTTTTACGAATTAAGATACTA
AGTAAA
Found at i:3195647 original size:21 final size:19
Alignment explanation
Indices: 3195608--3195650 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
3195598 GTATGTAATT
3195608 TATATGAAATTAAATTAAA
1 TATATGAAATTAAATTAAA
3195627 TATAT-AATATTATAATGTAAA
1 TATATGAA-ATTA-AAT-TAAA
3195648 TAT
1 TAT
3195651 TAAAGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.10
19 9 0.43
20 3 0.14
21 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
TATATGAAATTAAATTAAA
Found at i:3198557 original size:22 final size:22
Alignment explanation
Indices: 3198529--3198571 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3198519 GCACTAACGA
*
3198529 ACAGAGAGCACTAAGGTGCTAT
1 ACAGAGAGCACGAAGGTGCTAT
*
3198551 ACAGAGAGCACGAATGTGCTA
1 ACAGAGAGCACGAAGGTGCTA
3198572 AATGGATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (22 bp):
ACAGAGAGCACGAAGGTGCTAT
Found at i:3201327 original size:27 final size:27
Alignment explanation
Indices: 3201289--3201344 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3201279 GCTTCATGGA
*
3201289 TATCAATAGGTACAGTAGCAGATAAAC
1 TATCAATAGGTACAATAGCAGATAAAC
* * *
3201316 TATCAGTAGGTACAATATCAGATGAAC
1 TATCAATAGGTACAATAGCAGATAAAC
3201343 TA
1 TA
3201345 GTTACCCTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (27 bp):
TATCAATAGGTACAATAGCAGATAAAC
Found at i:3210210 original size:31 final size:31
Alignment explanation
Indices: 3210172--3210232 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3210162 CCTTCCATCA
* *
3210172 TTGCGATAGCTGCCTTGTACTCTAGTGATCC
1 TTGCGATAGCTGCCTCGTACTCCAGTGATCC
3210203 TTGCGATAGCTGCCTCGTACTCCAGTGATC
1 TTGCGATAGCTGCCTCGTACTCCAGTGATC
3210233 AATTTGCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (31 bp):
TTGCGATAGCTGCCTCGTACTCCAGTGATCC
Found at i:3219209 original size:58 final size:56
Alignment explanation
Indices: 3219138--3219313 Score: 211
Period size: 58 Copynumber: 3.2 Consensus size: 56
3219128 GCTAAGCTAC
* *
3219138 CACTTATCACTTGTCGCTTGTCACTGATTAGATAAGTGTAGCTAATGCTACCAATTAT
1 CACTTATCACTTGTC-CTTGTCACTGATCAGATAAGTGTAGCTAA-GCTACCACTTAT
* *
3219196 GACTTATCA------CTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
1 CACTTATCACTTGTCCTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTAT
* *
3219247 CACTTGTCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTATCACTTGTC-CTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTAT
3219305 CACTTATCA
1 CACTTATCA
3219314 GAAGTACTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
51 43 0.43
52 2 0.02
58 55 0.55
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (56 bp):
CACTTATCACTTGTCCTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTAT
Found at i:3219212 original size:51 final size:51
Alignment explanation
Indices: 3219093--3219313 Score: 277
Period size: 51 Copynumber: 4.2 Consensus size: 51
3219083 CTTACGTATG
3219093 ATCACTTATCACTTGTC-CTTGATCAGATAAGTGTAGCTAAGCTACCACTT
1 ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTT
* * * *
3219143 ATCACTTGTCGCTTGTCAC-TGATTAGATAAGTGTAGCTAATGCTACCAATT
1 ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAA-GCTACCACTT
* *
3219194 ATGACTTATCACTTGTCAC-TGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTT
*
3219245 ATCACTTGTCACTTGTCACTTGTCACTAATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTATCACTTGTCACTTG------ATCAGATAAGTGTAGCT-AAGCTACCACTT
3219303 ATCACTTATCA
1 ATCACTTATCA
3219314 GAAGTACTTA
Statistics
Matches: 146, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
50 35 0.24
51 69 0.47
52 4 0.03
58 38 0.26
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
ATCACTTATCACTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTT
Found at i:3219258 original size:14 final size:14
Alignment explanation
Indices: 3219239--3219276 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
3219229 GCTGAAGCTA
3219239 TCACTTATCACTTG
1 TCACTTATCACTTG
*
3219253 TCACTTGTCACTTG
1 TCACTTATCACTTG
*
3219267 TCACTAATCA
1 TCACTTATCA
3219277 GATAAGTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (14 bp):
TCACTTATCACTTG
Found at i:3224928 original size:44 final size:44
Alignment explanation
Indices: 3224865--3225173 Score: 300
Period size: 44 Copynumber: 6.6 Consensus size: 44
3224855 TTTGAGTACT
*
3224865 TCTGATCAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
3224909 TCTGATCAGTGACACGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTG--AC-----AAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
3224960 TCTGATCAGTGACAAGTGATAAGTGATAAATGGTAGC-TTAGCTACTCTTA
1 TCTGATCAGTGACAAGTGATAA--G-----TGGTAGCTTTAGCTACACTTA
* *
3225010 TCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAGTG---A----CAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
3225061 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
** * *
3225105 TCTGATCAGTGACAAGTGGCAAGTGATAAG-TGGTAGC-ACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGT-AGCT-TTAGCTACACTTA
*
3225149 TCTGATCAGGGACAAGTGATAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
3225174 ATCATACGTA
Statistics
Matches: 225, Mismatches: 16, Indels: 48
0.78 0.06 0.17
Matches are distributed among these distances:
44 103 0.46
45 5 0.02
46 2 0.01
48 1 0.00
49 2 0.01
50 29 0.13
51 71 0.32
53 1 0.00
55 1 0.00
57 10 0.04
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:3224949 original size:51 final size:51
Alignment explanation
Indices: 3224872--3225175 Score: 404
Period size: 51 Copynumber: 6.3 Consensus size: 51
3224862 ACTTCTGATC
3224872 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
3224923 CGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
3224974 AGTGATAAGTGATAAATGGTAGC-TTAGCTACTCTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
** * *
3225024 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGAC-
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
*
3225074 ------AAGTGATAAGTGGTAGCTTTAACTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
** *
3225119 AGTGGCAAGTGATAAGT-G--G---TAGC-ACACTTATCTGATCAGGGACA
1 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
3225163 AGTGATAAGTGAT
1 AGTGATAAGTGAT
3225176 CATACGTAAG
Statistics
Matches: 228, Mismatches: 17, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
44 72 0.32
45 3 0.01
48 1 0.00
50 46 0.20
51 106 0.46
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30
Consensus pattern (51 bp):
AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:3225615 original size:29 final size:30
Alignment explanation
Indices: 3225592--3225680 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
3225582 ATTTTTATTT
*
3225592 TTGCATTTTGACCCCTAAAATTTTCTAAAA
1 TTGCATTTTAACCCCTAAAATTTTCTAAAA
*
3225622 TTGCATTTTAACCCCT-AAACTTTCTCAAAA
1 TTGCATTTTAACCCCTAAAATTTTCT-AAAA
* *
3225652 TTACATTTCT-ACCCCTAAAATTTTTTAAA
1 TTGCATTT-TAACCCCTAAAATTTTCTAAA
3225681 TTACATTCGG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.16
30 35 0.69
31 8 0.16
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (30 bp):
TTGCATTTTAACCCCTAAAATTTTCTAAAA
Found at i:3225626 original size:30 final size:30
Alignment explanation
Indices: 3225595--3225752 Score: 114
Period size: 29 Copynumber: 5.4 Consensus size: 30
3225585 TTTATTTTTG
*
3225595 CATTTTGACCCCTAAAATTTTCTAAAATTG
1 CATTTTGACCCCTAAAATTTTCTAAAATTA
* *
3225625 CATTTTAACCCCT-AAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAAATTTTCT-AAAATTA
*
3225655 CATTTCT-ACCCCTAAAATTTT-TTAAATTA
1 CATTT-TGACCCCTAAAATTTTCTAAAATTA
** * * *
3225684 CATTCGGGCCCTTAAAA-TATCTATAAATTA
1 CATTTTGACCCCTAAAATTTTCTA-AAATTA
* * *
3225714 CA-TTTGGCCCC--ATATTTTCCTAAAATTG
1 CATTTTGACCCCTAAAATTTT-CTAAAATTA
*
3225742 CATTTTTACCC
1 CATTTTGACCC
3225753 TAGAAACTTT
Statistics
Matches: 100, Mismatches: 19, Indels: 19
0.72 0.14 0.14
Matches are distributed among these distances:
27 2 0.02
28 11 0.11
29 42 0.42
30 38 0.38
31 7 0.07
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.39
Consensus pattern (30 bp):
CATTTTGACCCCTAAAATTTTCTAAAATTA
Found at i:3226118 original size:35 final size:35
Alignment explanation
Indices: 3226073--3226139 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3226063 CAACTAGCAA
3226073 AACAACCAAAA-AGCAAAAAAAAAAAAGAAAGAAAC
1 AACAACCAAAAGAG-AAAAAAAAAAAAGAAAGAAAC
* *
3226108 AACAAGCAAAAGAGAAAAAAAAAAGAGAAAGA
1 AACAACCAAAAGAGAAAAAAAAAAAAGAAAGA
3226140 GAAAAGAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.76, C:0.10, G:0.13, T:0.00
Consensus pattern (35 bp):
AACAACCAAAAGAGAAAAAAAAAAAAGAAAGAAAC
Found at i:3226262 original size:4 final size:4
Alignment explanation
Indices: 3226253--3226317 Score: 62
Period size: 4 Copynumber: 15.8 Consensus size: 4
3226243 GGCTGATCGG
*
3226253 GAAA GAAA GAAA AAATA GAAA GAAAA GAGAA GAAA GAAA GAAA GAAA -AAGA
1 GAAA GAAA GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAA-A
*
3226304 GAAA -ACA GAAA GAA
1 GAAA GAAA GAAA GAA
3226318 GGAAGGAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 4 0.08
4 34 0.67
5 13 0.25
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:3226288 original size:31 final size:30
Alignment explanation
Indices: 3226253--3226331 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
3226243 GGCTGATCGG
*
3226253 GAAAGAAAGAAAAAATAGAAAGAAAAGAG-AA
1 GAAAGAAAGAAAAAA-A-AAAGAAAACAGAAA
*
3226284 GAAAGAAAGAAAGAAAAAGAGAAAACAGAAA
1 GAAAGAAAGAAA-AAAAAAAGAAAACAGAAA
* *
3226315 GAAGGAAGGAAAAAAAA
1 GAAAGAAAGAAAAAAAA
3226332 GGGAGATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 14 0.33
31 25 0.60
32 3 0.07
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (30 bp):
GAAAGAAAGAAAAAAAAAAGAAAACAGAAA
Found at i:3226313 original size:23 final size:22
Alignment explanation
Indices: 3226254--3226317 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
3226244 GCTGATCGGG
*
3226254 AAAGA-AAGAAAAAATAGAAAGA
1 AAAGAGAAGAAAGAA-AGAAAGA
3226276 AAAGAGAAGAAAGAAAGAAAGAA
1 AAAGAGAAGAAAGAAAGAAAG-A
3226299 AAAGAGAA-AACAGAAAGAA
1 AAAGAGAAGAA-AGAAAGAA
3226318 GGAAGGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
22 13 0.34
23 25 0.66
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAGAGAAGAAAGAAAGAAAGA
Found at i:3226327 original size:19 final size:19
Alignment explanation
Indices: 3226258--3226317 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
3226248 ATCGGGAAAG
* *
3226258 AAAGAAAAAATAGAAAGAA
1 AAAGAGAAAACAGAAAGAA
*
3226277 AAGAGAAGAAAGAAAGAAAGAA
1 AA-AG-AGAAA-ACAGAAAGAA
3226299 AAAGAGAAAACAGAAAGAA
1 AAAGAGAAAACAGAAAGAA
3226318 GGAAGGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 11 0.31
20 7 0.20
21 6 0.17
22 11 0.31
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAGAGAAAACAGAAAGAA
Done.