Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015380.1 Kokia drynarioides strain JFW-HI SEQ_130427, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 614474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 461 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:7775 original size:29 final size:30
Alignment explanation
Indices: 7711--7776 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
7701 ATACCAAAAC
* *
7711 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGATTT-ATATGCAATTG
* *
7742 TATACATGAACTTTGATTT-TATGCAATTT
1 TATACATGAACTATGATTTATATGCAATTG
7771 TATACA
1 TATACA
7777 GAAATTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.45
31 17 0.55
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (30 bp):
TATACATGAACTATGATTTATATGCAATTG
Found at i:7785 original size:29 final size:29
Alignment explanation
Indices: 7734--7791 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
7724 TGGTTTAATG
*
7734 TGCAATTGTATACATGAACTTTGATTTTA
1 TGCAATTGTATACATGAACTTTGACTTTA
* *
7763 TGCAATTTTATACA-GAAATTTTGACTTTA
1 TGCAATTGTATACATG-AACTTTGACTTTA
7792 CCCAATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (29 bp):
TGCAATTGTATACATGAACTTTGACTTTA
Found at i:7994 original size:29 final size:30
Alignment explanation
Indices: 7962--8020 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
7952 TCACGTGTAT
*
7962 AATTACAC-TAAATTAAAGTTCATATATAC
1 AATTACACATAAATCAAAGTTCATATATAC
*
7991 AATTACACATTAAATCAAAGTTCATGTATA
1 AATTACACA-TAAATCAAAGTTCATATATA
8021 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (30 bp):
AATTACACATAAATCAAAGTTCATATATAC
Found at i:8023 original size:29 final size:27
Alignment explanation
Indices: 7957--8023 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
7947 CAGTTTCACG
*
7957 TGTATAATTACACTAAATTAAAGTTCA
1 TGTATAATTACACTAAATCAAAGTTCA
*
7984 TATATACAATTACACATTAAATCAAAGTTCA
1 TGTAT--AATTACAC--TAAATCAAAGTTCA
8015 TGTATAATT
1 TGTATAATT
8024 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 4 0.12
29 12 0.36
31 17 0.52
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (27 bp):
TGTATAATTACACTAAATCAAAGTTCA
Found at i:8265 original size:20 final size:18
Alignment explanation
Indices: 8236--8276 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
8226 GTTTAGGTCC
*
8236 AAATTGAATATTGAAATATT
1 AAATTAAATATT-AAA-ATT
8256 AAATTAAATATTAAAATT
1 AAATTAAATATTAAAATT
8274 AAA
1 AAA
8277 CTCAAGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 3 0.15
20 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTAAATATTAAAATT
Found at i:8353 original size:2 final size:2
Alignment explanation
Indices: 8348--8383 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8338 ATATATAGGA
8348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8384 GATAATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9114 original size:6 final size:6
Alignment explanation
Indices: 9103--9136 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
9093 AGTGCAGCCC
9103 CATGGT CATGGT CATGGT CATGGT CATGGAT CAT
1 CATGGT CATGGT CATGGT CATGGT CATGG-T CAT
9137 ATGATCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (6 bp):
CATGGT
Found at i:12037 original size:19 final size:19
Alignment explanation
Indices: 12013--12055 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12003 AAACATGAAT
12013 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
12032 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
12051 TAAAT
1 TAAAT
12056 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:15957 original size:6 final size:6
Alignment explanation
Indices: 15932--15970 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
15922 ACAATTCATA
* * *
15932 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
15971 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:28429 original size:5 final size:5
Alignment explanation
Indices: 28419--28444 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28409 ACACAAAAAA
28419 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
28445 GTTATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:31042 original size:104 final size:104
Alignment explanation
Indices: 30858--31066 Score: 391
Period size: 104 Copynumber: 2.0 Consensus size: 104
30848 TAATTGGGTA
*
30858 GAAGATCCCTTCTCTTTCATCGTGGAGGGGATTTATAAGGGAAATCCCCTTGTTTAGTAGCGGCG
1 GAAGATCCCTTCTCTTACATCGTGGAGGGGATTTATAAGGGAAATCCCCTTGTTTAGTAGCGGCG
*
30923 ATATGGCAGGTCGTTACTAATGGGTTGTTATCATGGAGT
66 ATATGGCAGGCCGTTACTAATGGGTTGTTATCATGGAGT
*
30962 GAAGATCCCTTCTCTTACATCGTGGAGGGGATTTATAAGGGAAATCCCCTTGTTTAGTAGCGGTG
1 GAAGATCCCTTCTCTTACATCGTGGAGGGGATTTATAAGGGAAATCCCCTTGTTTAGTAGCGGCG
31027 ATATGGCAGGCCGTTACTAATGGGTTGTTATCATGGAGT
66 ATATGGCAGGCCGTTACTAATGGGTTGTTATCATGGAGT
31066 G
1 G
31067 CGTGGGGGAC
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.32
Consensus pattern (104 bp):
GAAGATCCCTTCTCTTACATCGTGGAGGGGATTTATAAGGGAAATCCCCTTGTTTAGTAGCGGCG
ATATGGCAGGCCGTTACTAATGGGTTGTTATCATGGAGT
Found at i:31778 original size:21 final size:21
Alignment explanation
Indices: 31727--31811 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
31717 GATTGATTTT
*
31727 AGTGAAATTAAAATAGTGATGAC
1 AGTGAAATT-AAATATTG-TGAC
* * *
31750 ACTAAAATTAATTATTGTGAC
1 AGTGAAATTAAATATTGTGAC
* * *
31771 AGTGAAATTGAGTATTGTAAC
1 AGTGAAATTAAATATTGTGAC
* *
31792 GGTGAGATTAAA-ATTAGTGA
1 AGTGAAATTAAATATT-GTGA
31812 TTAAGTATGT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.06
21 31 0.66
22 6 0.13
23 7 0.15
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (21 bp):
AGTGAAATTAAATATTGTGAC
Found at i:32341 original size:16 final size:15
Alignment explanation
Indices: 32310--32340 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32300 GTTAACAAAT
*
32310 ATTTAAAAAATAAAA
1 ATTTAAAAAAAAAAA
32325 ATTTAAAAAAAAAAA
1 ATTTAAAAAAAAAAA
32340 A
1 A
32341 AAGCATGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATTTAAAAAAAAAAA
Found at i:34664 original size:3 final size:3
Alignment explanation
Indices: 34656--34702 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
34646 CTACATTGAT
34656 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
34703 TTATTAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:44920 original size:21 final size:20
Alignment explanation
Indices: 44892--44946 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
44882 AACAATAATG
*
44892 AATCGATTTAAAACAACAAAA
1 AATCGA-TTAAAAAAACAAAA
* * *
44913 AATTGATTGAAATAAACAAAG
1 AATCGATT-AAAAAAACAAAA
44934 AATCGATTAAAAA
1 AATCGATTAAAAA
44947 GAAGCAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.22
Consensus pattern (20 bp):
AATCGATTAAAAAAACAAAA
Found at i:44995 original size:55 final size:55
Alignment explanation
Indices: 44934--45238 Score: 270
Period size: 55 Copynumber: 5.4 Consensus size: 55
44924 ATAAACAAAG
* * * *
44934 AATCGATTAAAAAGAAGCAATATTCCACCATAACAATCGATTTGAACATATAATC
1 AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATAAAC
* * * * *
44989 AATCGATTCAAAAGAAGTAGA-ATTCCAACATGACAATCAATTTAAACGTATAAAT
1 AATCGATTCAAAAGAAGCA-ATATTCCAACATAACAATCGATTTAAACATATAAAC
* * *** ** *
45044 AATCGATCCAAAAGATGCGGGATTCCAACATAACAATTAATTTAAACATATAAGC
1 AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATAAAC
* * *
45099 AATCTATTCAAAAGAAGAAGAAACAATATTCCACCATAACAATCGATTTAAACATAAAAAC
1 AATCGATTC--AA-AAGAAG---CAATATTCCAACATAACAATCGATTTAAACATATAAAC
* * * * * * * *
45160 AATCTATTCGAAAGAAGCAGTATTCCAACATGATAATCGTTTTAAATATAAAAAC
1 AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATAAAC
* *
45215 AATTGATCCAAAAGAAGCAATATT
1 AATCGATTCAAAAGAAGCAATATT
45239 TTTGAGAAAT
Statistics
Matches: 200, Mismatches: 42, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
55 146 0.73
56 1 0.00
57 2 0.01
58 11 0.05
59 1 0.00
61 39 0.19
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (55 bp):
AATCGATTCAAAAGAAGCAATATTCCAACATAACAATCGATTTAAACATATAAAC
Found at i:45204 original size:116 final size:110
Alignment explanation
Indices: 44934--45231 Score: 265
Period size: 116 Copynumber: 2.7 Consensus size: 110
44924 ATAAACAAAG
** * * * * *
44934 AATCGATTAAAAAGAAGCAATATTCCACCATAACAATCGATTTGAACATATAATCAATCGATTCA
1 AATCGATCCAAAAGAAGCAGTATTCCAACATAACAATCGATTTAAACATATAAACAATCTATTCA
* * * * *
44999 AAAGAAGTAGAATTCCAACATGACAATCAATTTAAACGTATAAAT
66 AAAGAAGAAGAATTCCAACATAACAATCAATTTAAACATAAAAAC
* * * ** *
45044 AATCGATCCAAAAGATGCGGGATTCCAACATAACAATTAATTTAAACATATAAGCAATCTATTCA
1 AATCGATCCAAAAGAAGCAGTATTCCAACATAACAATCGATTTAAACATATAAACAATCTATTCA
* *
45109 AAAGAAGAAGAAACAATATTCCACCATAACAATCGATTTAAACATAAAAAC
66 AAAGAAGAAG-----A-ATTCCAACATAACAATCAATTTAAACATAAAAAC
* * * * * * * * *
45160 AATCTATTCGAAAGAAGCAGTATTCCAACATGATAATCGTTTTAAATATAAAAACAAT-TGATCC
1 AATCGATCCAAAAGAAGCAGTATTCCAACATAACAATCGATTTAAACATATAAACAATCT-ATTC
45224 AAAAGAAG
65 AAAAGAAG
45232 CAATATTTTT
Statistics
Matches: 147, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
110 62 0.42
115 2 0.01
116 83 0.56
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (110 bp):
AATCGATCCAAAAGAAGCAGTATTCCAACATAACAATCGATTTAAACATATAAACAATCTATTCA
AAAGAAGAAGAATTCCAACATAACAATCAATTTAAACATAAAAAC
Found at i:52027 original size:29 final size:29
Alignment explanation
Indices: 51963--52031 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
51953 TTTAATAGTC
* * *
51963 TATATTTTTATAATTTTAAAGGATTAAAT
1 TATAATTTTATAATTTTAAAGGATCAAAA
* * *
51992 TAAAATTTTATAATTTTAAGGGGTCAAAA
1 TATAATTTTATAATTTTAAAGGATCAAAA
52021 TATAATTTTAT
1 TATAATTTTAT
52032 CTTTATTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (29 bp):
TATAATTTTATAATTTTAAAGGATCAAAA
Found at i:54372 original size:5 final size:5
Alignment explanation
Indices: 54362--54392 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
54352 TTGTCTTCCC
*
54362 CATTG CATTG CATTG GATTG CATTG CATTG C
1 CATTG CATTG CATTG CATTG CATTG CATTG C
54393 TTACTGGTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (5 bp):
CATTG
Found at i:84481 original size:18 final size:16
Alignment explanation
Indices: 84460--84495 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
84450 ATTTTAAATT
84460 TTTAATTAATCAAATTTA
1 TTTAATTAA--AAATTTA
84478 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
84494 TT
1 TT
84496 ATCATCCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:103302 original size:21 final size:21
Alignment explanation
Indices: 103278--103325 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
103268 TATTAGTAAG
*
103278 AATATA-GAAAATTAATATTTT
1 AATATATGAAAAGTAA-ATTTT
103299 AATATATGAAAAGTAAATTTT
1 AATATATGAAAAGTAAATTTT
103320 AA-ATAT
1 AATATAT
103326 TTTTTAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 13 0.52
22 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (21 bp):
AATATATGAAAAGTAAATTTT
Found at i:104063 original size:25 final size:25
Alignment explanation
Indices: 104010--104064 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
104000 AAAAGTGCTT
104010 TTAAAAAGCACTACTAAACAAATCC
1 TTAAAAAGCACTACTAAACAAATCC
** *
104035 -TAAAAAGCTTTATTAAACACAA-CC
1 TTAAAAAGCACTACTAAACA-AATCC
104059 TTAAAA
1 TTAAAA
104065 TTAAGTAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.24
Consensus pattern (25 bp):
TTAAAAAGCACTACTAAACAAATCC
Found at i:116550 original size:20 final size:20
Alignment explanation
Indices: 116517--116576 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
116507 GACTTGTTTT
116517 AAAACTATTTTAACTTTGATT-
1 AAAAC-ATTTTAAC-TTGATTG
*
116538 AAAA-ATGTTTAACTCGATTG
1 AAAACAT-TTTAACTTGATTG
116558 AAAACATTTTAACTTGATT
1 AAAACATTTTAACTTGATT
116577 TAAAGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 7 0.21
20 21 0.62
21 6 0.18
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAACATTTTAACTTGATTG
Found at i:119928 original size:21 final size:21
Alignment explanation
Indices: 119902--119952 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
119892 AGAACAAGGG
*
119902 TCAGCAAAAGGACCAACAAGC
1 TCAGCAAAAAGACCAACAAGC
119923 TCAGCAAAAAGACCAACAAGC
1 TCAGCAAAAAGACCAACAAGC
119944 TCAGCAAAA
1 TCAGCAAAA
119953 CACACATGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.51, C:0.27, G:0.16, T:0.06
Consensus pattern (21 bp):
TCAGCAAAAAGACCAACAAGC
Found at i:131461 original size:24 final size:24
Alignment explanation
Indices: 131440--131594 Score: 177
Period size: 24 Copynumber: 6.5 Consensus size: 24
131430 TTATGCTCAT
*
131440 CAGCTAAGATACGTTTACGCTCGC
1 CAGCTAATATACGTTTACGCTCGC
*
131464 CAGCTAATATGCGTTTACGCTCGC
1 CAGCTAATATACGTTTACGCTCGC
* *
131488 CAGCTAATATACATTTACGCT-GAT
1 CAGCTAATATACGTTTACGCTCG-C
* * *
131512 CAGCTAATATGCGTTTACACTTGC
1 CAGCTAATATACGTTTACGCTCGC
* *
131536 CAGCTAATATACGTTTACACTCGT
1 CAGCTAATATACGTTTACGCTCGC
* * *
131560 CAACTAATATGCGTTTACGCTTGC
1 CAGCTAATATACGTTTACGCTCGC
*
131584 TAGCTAATATA
1 CAGCTAATATA
131595 AGAAACATTG
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
23 1 0.01
24 107 0.98
25 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (24 bp):
CAGCTAATATACGTTTACGCTCGC
Found at i:131516 original size:48 final size:48
Alignment explanation
Indices: 131440--131594 Score: 222
Period size: 48 Copynumber: 3.2 Consensus size: 48
131430 TTATGCTCAT
* * *
131440 CAGCTAAGATACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGC
1 CAGCTAATATACGTTTACGCTCGTCAGCTAATATGCGTTTACGCTTGC
* *
131488 CAGCTAATATACATTTACGCT-GATCAGCTAATATGCGTTTACACTTGC
1 CAGCTAATATACGTTTACGCTCG-TCAGCTAATATGCGTTTACGCTTGC
* *
131536 CAGCTAATATACGTTTACACTCGTCAACTAATATGCGTTTACGCTTGC
1 CAGCTAATATACGTTTACGCTCGTCAGCTAATATGCGTTTACGCTTGC
*
131584 TAGCTAATATA
1 CAGCTAATATA
131595 AGAAACATTG
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.01
48 93 0.98
49 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (48 bp):
CAGCTAATATACGTTTACGCTCGTCAGCTAATATGCGTTTACGCTTGC
Found at i:131542 original size:72 final size:72
Alignment explanation
Indices: 131425--131594 Score: 207
Period size: 72 Copynumber: 2.4 Consensus size: 72
131415 GCAAGTTCAG
* * * * * *
131425 TACATTTATGCTCATCAGCTAAGATACGTTTACGCTCGCCAGCTAATATGCGTTTACGCTCGCCA
1 TACATTTACGCTGATCAGCTAATATACGTTTACACTCGCCAGCTAATATACGTTTACACTCGCCA
*
131490 GCTAATA
66 ACTAATA
* * *
131497 TACATTTACGCTGATCAGCTAATATGCGTTTACACTTGCCAGCTAATATACGTTTACACTCGTCA
1 TACATTTACGCTGATCAGCTAATATACGTTTACACTCGCCAGCTAATATACGTTTACACTCGCCA
131562 ACTAATA
66 ACTAATA
* * *
131569 TGCGTTTACGCTTGCT-AGCTAATATA
1 TACATTTACGC-TGATCAGCTAATATA
131595 AGAAACATTG
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 80 0.96
73 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (72 bp):
TACATTTACGCTGATCAGCTAATATACGTTTACACTCGCCAGCTAATATACGTTTACACTCGCCA
ACTAATA
Found at i:131651 original size:21 final size:21
Alignment explanation
Indices: 131627--131668 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
131617 TTATTTGATC
131627 CATCGAAATTTACTTAACATA
1 CATCGAAATTTACTTAACATA
131648 CATCGAAATTTACTTAACATA
1 CATCGAAATTTACTTAACATA
131669 TTTATTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
CATCGAAATTTACTTAACATA
Found at i:141705 original size:6 final size:6
Alignment explanation
Indices: 141696--141724 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
141686 AAAAAGAGAA
141696 AGGGGG AGGGGG AGGGGG AGGGGG AGGGG
1 AGGGGG AGGGGG AGGGGG AGGGGG AGGGG
141725 TATCATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (6 bp):
AGGGGG
Found at i:146592 original size:3 final size:3
Alignment explanation
Indices: 146584--146618 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
146574 ATAGAAAAAC
*
146584 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
146619 AACGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:147237 original size:6 final size:6
Alignment explanation
Indices: 147226--147250 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
147216 GGTTTTCTCT
147226 TTTTGC TTTTGC TTTTGC TTTTGC T
1 TTTTGC TTTTGC TTTTGC TTTTGC T
147251 GGAGGTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGC
Found at i:154280 original size:6 final size:6
Alignment explanation
Indices: 154264--154302 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
154254 CTTGGTTATT
* * *
154264 GTCTTC TTCTTC GTCTTC GTCGTC GTCTTC GTCATC GTC
1 GTCTTC GTCTTC GTCTTC GTCTTC GTCTTC GTCTTC GTC
154303 GTCTACTTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.46
Consensus pattern (6 bp):
GTCTTC
Found at i:162084 original size:22 final size:24
Alignment explanation
Indices: 162040--162084 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
162030 TTTCTTTTAG
*
162040 TTTTTATCTGTCTTTGTGGCACGT
1 TTTTTATCTGTCTTTGTGACACGT
*
162064 TTTTTCTCTGTC-TTG-GACACG
1 TTTTTATCTGTCTTTGTGACACG
162085 CTTCTGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 3 0.16
24 11 0.58
ACGTcount: A:0.09, C:0.20, G:0.20, T:0.51
Consensus pattern (24 bp):
TTTTTATCTGTCTTTGTGACACGT
Found at i:163770 original size:5 final size:5
Alignment explanation
Indices: 163757--163789 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
163747 GCCTAGGAAG
*
163757 CAACG CAACC CAACC CAACC CAACC CAACC CAA
1 CAACC CAACC CAACC CAACC CAACC CAACC CAA
163790 GTGGCAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.42, C:0.55, G:0.03, T:0.00
Consensus pattern (5 bp):
CAACC
Found at i:178943 original size:26 final size:27
Alignment explanation
Indices: 178903--178960 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
178893 GCTTGTTTGG
* *
178903 TTTTTGAAAATAA-TTTCTATTTTT-T
1 TTTTTGAAAAGAATTTTCAATTTTTAT
178928 TTTTTGAAAAAGAATTTTCAATTTTTAT
1 TTTTTG-AAAAGAATTTTCAATTTTTAT
178956 TTTTT
1 TTTTT
178961 ACAAATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 6 0.21
26 6 0.21
27 10 0.36
28 6 0.21
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.62
Consensus pattern (27 bp):
TTTTTGAAAAGAATTTTCAATTTTTAT
Found at i:180594 original size:31 final size:30
Alignment explanation
Indices: 180495--180688 Score: 153
Period size: 30 Copynumber: 6.5 Consensus size: 30
180485 ATTCGAGGTA
* * *
180495 AAAATGTAATTTTGGAAAAGTTTGA-GGTC
1 AAAATATAATTTTTGAAAAGTTTAAGGGTC
* * * *
180524 AAAATGTGA-TTTTGAGATAGTTT-TGGGTC
1 AAAATATAATTTTTGA-AAAGTTTAAGGGTC
* *
180553 AAAATGTAATTTTTGAAAAGTGTAAGGGTC
1 AAAATATAATTTTTGAAAAGTTTAAGGGTC
* * * *
180583 AAAAATATAATTTTGGAGAAGTTT-GGGGCTT
1 -AAAATATAATTTTTGAAAAGTTTAAGGG-TC
* * * *
180614 AAAATATAATTTTAGAGAAGTTTGAGGGTT
1 AAAATATAATTTTTGAAAAGTTTAAGGGTC
*
180644 AAAATATGATTTTTGGAAAAGTTTAAGGGTC
1 AAAATATAATTTTT-GAAAAGTTTAAGGGTC
*
180675 AAAATATGATTTTT
1 AAAATATAATTTTT
180689 AAAGAAAATA
Statistics
Matches: 136, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
28 5 0.04
29 31 0.23
30 50 0.37
31 50 0.37
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
AAAATATAATTTTTGAAAAGTTTAAGGGTC
Found at i:180642 original size:61 final size:59
Alignment explanation
Indices: 180495--180679 Score: 185
Period size: 61 Copynumber: 3.1 Consensus size: 59
180485 ATTCGAGGTA
* * * *
180495 AAAATGTAATTTTGGAAAAGTTTGA-GGTCAAAATGTGATTTT-GAGATAGTTTTGGGTC
1 AAAATGTAATTTTAGAAAAGTTTGAGGGTCAAAATATAATTTTGGAGA-AGTTTGGGGTC
* * * *
180553 AAAATGTAATTTTTGAAAAGTGTAAGGGTCAAAAATATAATTTTGGAGAAGTTTGGGGCTT
1 AAAATGTAATTTTAGAAAAGTTTGAGGGTC-AAAATATAATTTTGGAGAAGTTTGGGG-TC
* * * * * *
180614 AAAATATAATTTTAGAGAAGTTTGAGGGTTAAAATATGATTTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTAGAAAAGTTTGAGGGTCAAAATAT-AATTTTGGAGAAGTTT-GGGGTC
180675 AAAAT
1 AAAAT
180680 ATGATTTTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
58 22 0.21
59 4 0.04
60 26 0.25
61 49 0.47
62 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTAGAAAAGTTTGAGGGTCAAAATATAATTTTGGAGAAGTTTGGGGTC
Found at i:181669 original size:21 final size:21
Alignment explanation
Indices: 181628--181672 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
181618 TTGTTTGAAA
*
181628 ATAATAAATGACATTAATAAT
1 ATAATAAATGAAATTAATAAT
*
181649 ATAATAAAT-AAATATATTAAT
1 ATAATAAATGAAAT-TAATAAT
181670 ATA
1 ATA
181673 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATAAATGAAATTAATAAT
Found at i:182186 original size:17 final size:18
Alignment explanation
Indices: 182164--182201 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
182154 AAGGGTCATT
182164 AATAAATTT-AAATTTAA
1 AATAAATTTAAAATTTAA
182181 AATAAATTTAAAATTTAA
1 AATAAATTTAAAATTTAA
182199 AAT
1 AAT
182202 TATTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATTTAAAATTTAA
Found at i:182686 original size:39 final size:39
Alignment explanation
Indices: 182643--183215 Score: 212
Period size: 39 Copynumber: 14.7 Consensus size: 39
182633 GTTGATGGTG
* *
182643 ATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTACA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * *
182682 ATCTGTCCCAAGCTCGGGGTAAAAGATCGGATGGCTACA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * *** * * *
182721 ATTTACCCTTGGCTCGGGGTAAGAGATTGGCTG-ATGG-T--G
1 ATCTGCCCCAAGATCGGGGTAAAAGA-T--C-GAATGGCTACA
* * * * **
182760 ATCTACCCCAAGCTCGGAGTAAAAGATCGGATGGCTGTA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * * * * * *
182799 ATCTACCCCAGGCTTGAGGTAAGAGATTGACTGATGG-T--A
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGA---ATGGCTACA
* * * * *
182838 ATTTGCCCCAAGCTCGGGGTAAAAGATTGAATGGTTGCA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * * * * *
182877 ATTTACCCCAAGCTCGGAGTAAAAGATCGGATGGCTGCA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * *
182916 ATCTGCCACAAGCTCGGGGTAAGAGATTGGCTG-ATGG-T--A
1 ATCTGCCCCAAGATCGGGGTAAAAGA-T--C-GAATGGCTACA
** * ** * **
182955 ATCTGCCTTAAGCTCGGGGTAAAAGATTAAATGGTTGTA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * * * *
182994 ATCTGTCCCAAGCTTGGGGTAAGAGATTGGCTG-ATGG-T--G
1 ATCTGCCCCAAGATCGGGGTAAAAGA-T--C-GAATGGCTACA
* * *
183033 ATCTGCCCCAAGTTCGGGGTAAAAAATCGAATGGCTGCA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * * * * *
183072 ATTTGCCACAAGCTTGGGGTAAGAGATTGGCTG-ATGG-T--G
1 ATCTGCCCCAAGATCGGGGTAAAAGA-T--C-GAATGGCTACA
* * *
183111 ATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* * *
183150 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCA
1 ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
* *
183189 ATCTGCCCCAAGCTCGGGGTAAGAGAT
1 ATCTGCCCCAAGATCGGGGTAAAAGAT
183216 TGGCTGATGG
Statistics
Matches: 418, Mismatches: 78, Indels: 76
0.73 0.14 0.13
Matches are distributed among these distances:
35 3 0.01
36 23 0.06
37 5 0.01
38 4 0.01
39 348 0.83
40 4 0.01
41 5 0.01
42 23 0.06
43 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGATCGGGGTAAAAGATCGAATGGCTACA
Found at i:182702 original size:78 final size:78
Alignment explanation
Indices: 182582--183293 Score: 473
Period size: 78 Copynumber: 9.1 Consensus size: 78
182572 TTGATTTAAA
* * * * * * * * *
182582 GGTAAAAGATTGGATGATTGCAATCTGCCCCTA-TTGCAGGGTAAGAGATTGGTTGATGGTGATC
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCT-CGGGGTAAAAGATTGGATGATGGTAATC
* *
182646 TGCCCCATGATCGG
65 TGCCCCAAGCTCGG
* * * *
182660 GGTAAAAGATCGAATGGTTACAATCTGTCCCAAGCTCGGGGTAAAAGATCGGATG--GCTACAAT
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGATGGT--AAT
* * ***
182723 TTACCCTTGGCTCGG
64 CTGCCCCAAGCTCGG
* * ** * * ** * * * *
182738 GGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGAGTAAAAGATCGGATGGCT-GTAATC
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGAT-GATGGTAATC
* * * *
182802 TACCCCAGGCTTGA
65 TGCCCCAAGCTCGG
* * * * * * * * * * * *
182816 GGTAAGAGATTGACTGATGGTAATTTGCCCCAAGCTCGGGGTAAAAGATTGAATGGTTGCAATTT
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGATGGTAATCT
*
182881 ACCCCAAGCTCGG
66 GCCCCAAGCTCGG
* * * * * *
182894 AGTAAAAGATCGGATGGCTGCAATCTGCCACAAGCTCGGGGTAAGAGATTGGCTGATGGTAATCT
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGATGGTAATCT
**
182959 GCCTTAAGCTCGG
66 GCCCCAAGCTCGG
** * * * * * *
182972 GGTAAAAGATTAAATGGTTGTAATCTGTCCCAAGCTTGGGGTAAGAGATTGGCTGATGGTGATCT
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGATGGTAATCT
*
183037 GCCCCAAGTTCGG
66 GCCCCAAGCTCGG
* * * * * * * *
183050 GGTAAAAAATCGAATGGCTGCAATTTGCCACAAGCTTGGGGTAAGAGATTGGCTGATGGTGATCT
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGATGGTAATCT
*
183115 GCCCCAAGCTCGA
66 GCCCCAAGCTCGG
* * * * * *
183128 GGTAAAAGATCGAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCAATCT
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGATGGTAATCT
183193 GCCCCAAGCTCGG
66 GCCCCAAGCTCGG
* * ** * * ** * * * *
183206 GGTAAGAGATTGGCTGATGGTGATCTGTCCCAGGCTCGGGGTAAAAGATCGGATGACT-GTGATC
1 GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGA-TGGTAATC
*
183270 TGCCCCATA-ATCGG
65 TGCCCCA-AGCTCGG
*
183284 GGTAAGAGAT
1 GGTAAAAGAT
183294 TGAAATCTTC
Statistics
Matches: 502, Mismatches: 123, Indels: 18
0.78 0.19 0.03
Matches are distributed among these distances:
76 2 0.00
77 2 0.00
78 493 0.98
79 4 0.01
80 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (78 bp):
GGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGATGGTAATCT
GCCCCAAGCTCGG
Found at i:182788 original size:117 final size:115
Alignment explanation
Indices: 182620--183293 Score: 579
Period size: 117 Copynumber: 5.8 Consensus size: 115
182610 CCCTATTGCA
* * * * * * *
182620 GGGTAAGAGATTGGTTGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTACAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGAGTAAAAGATCGGATGGCTGCAATC
* * ***
182685 TGTCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATTTACCCTTGGCTCG
66 TGCCCCAAGCTCGGGGTAAAAGATCGGATGG-T-CAATTTGCCCCAAGCTCG
* *
182737 GGGTAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGAGTAAAAGATCGGATGGCTGTAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGAGTAAAAGATCGGATGGCTGCAATC
* * * * * *
182802 TACCCCAGGCTTGAGGTAAGAGATTGACTGATGGT-AATTTGCCCCAAGCTCG
66 TGCCCCAAGCTCGGGGTAAAAGA-T--CGGATGGTCAATTTGCCCCAAGCTCG
* ** * * ** * *
182854 GGGTAAAAGATTGAATGGTTGCAATTTACCCCAAGCTCGGAGTAAAAGATCGGATGGCTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGAGTAAAAGATCGGATGGCTGCAATC
* * * * **
182919 TGCCACAAGCTCGGGGTAAGAGATTGGCTGATGGT-AATCTGCCTTAAGCTCG
66 TGCCCCAAGCTCGGGGTAAAAGA-T--CGGATGGTCAATTTGCCCCAAGCTCG
* *** * * * * * * * *
182971 GGGTAAAAGATTAAATGGTTGTAATCTGTCCCAAGCTTGGGGTAAGAGATTGGCTGATGG-TG--
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGAGTAAAAGA-T--CGGATGGCTGCA
* * * * *
183033 ATCTGCCCCAAGTTCGGGGTAAAAAATCGAATGGCTGCAATTTGCCACAAGCTTG
63 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGG-T-CAATTTGCCCCAAGCTCG
*
183088 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC-GAGGTAAAAGATCGAATGGCTGCAAT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGA-GTAAAAGATCGGATGGCTGCAAT
* *
183152 CTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCAAGCTCG
65 CTGCCCCAAGCTCGGGGTAAAAGATCGGATGG-T-CAATTTGCCCCAAGCTCG
* * * * **
183205 GGGTAAGAGATTGGCTGATGGTGATCTGTCCCAGGCTCGGGGTAAAAGATCGGATGACTGTGATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGAGTAAAAGATCGGATGGCTGCAATC
* *
183270 TGCCCCATA-ATCGGGGTAAGAGAT
66 TGCCCCA-AGCTCGGGGTAAAAGAT
183294 TGAAATCTTC
Statistics
Matches: 457, Mismatches: 85, Indels: 30
0.80 0.15 0.05
Matches are distributed among these distances:
114 10 0.02
115 3 0.01
116 3 0.01
117 422 0.92
118 4 0.01
119 3 0.01
120 12 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (115 bp):
GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGAGTAAAAGATCGGATGGCTGCAATC
TGCCCCAAGCTCGGGGTAAAAGATCGGATGGTCAATTTGCCCCAAGCTCG
Found at i:183232 original size:39 final size:39
Alignment explanation
Indices: 182732--183295 Score: 364
Period size: 39 Copynumber: 14.5 Consensus size: 39
182722 TTTACCCTTG
* *
182732 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
* * * * * * *
182771 GCTCGGAGTAAAAGATCGGATGGCT-GTAATCTACCCCAG
1 GCTCGGGGTAAAAGATTGGCT-GATGGTGATCTGCCCCAA
* * * * * *
182810 GCTTGAGGTAAGAGATTGACTGATGGTAATTTGCCCCAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
** * * ** * *
182849 GCTCGGGGTAAAAGATTGAATGGTTGCAATTTACCCCAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
* * *
182888 GCTCGGAGTAAAAGA-T--CGGATGGCTGCAATCTGCCACAA
1 GCTCGGGGTAAAAGATTGGCTGATGG-TG--ATCTGCCCCAA
* * **
182927 GCTCGGGGTAAGAGATTGGCTGATGGTAATCTGCCTTAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
*** * * * *
182966 GCTCGGGGTAAAAGATTAAATGGTTGTAATCTGTCCCAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
* *
183005 GCTTGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
* * * *
183044 GTTCGGGGTAAAA-AAT--C-GAATGGCTGCAATTTGCCACAA
1 GCTCGGGGTAAAAGATTGGCTG-ATGG-TG--ATCTGCCCCAA
* *
183083 GCTTGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
*
183122 GCTCGAGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCCCAA
1 GCTCGGGGTAAAAGATTGGCTG-ATGG-TG--ATCTGCCCCAA
* ** * * **
183161 GCTCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCAA
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
* * *
183200 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAG
1 GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
* *
183239 GCTCGGGGTAAAAGATCGGATGACT-GTGATCTGCCCCATA
1 GCTCGGGGTAAAAGATTGGCTGA-TGGTGATCTGCCCCA-A
* *
183279 -ATCGGGGTAAGAGATTG
1 GCTCGGGGTAAAAGATTG
183296 AAATCTTCAA
Statistics
Matches: 399, Mismatches: 100, Indels: 52
0.72 0.18 0.09
Matches are distributed among these distances:
35 2 0.01
36 13 0.03
37 4 0.01
38 6 0.02
39 350 0.88
40 6 0.02
41 3 0.01
42 13 0.03
43 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (39 bp):
GCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCAA
Found at i:191423 original size:25 final size:25
Alignment explanation
Indices: 191389--191438 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
191379 AAATGGTTTT
191389 GCAACTGCACTTGCACTTGCTCTTA
1 GCAACTGCACTTGCACTTGCTCTTA
191414 GCAACTGCACTTGCACTTGCTCTTA
1 GCAACTGCACTTGCACTTGCTCTTA
191439 CATTTCCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (25 bp):
GCAACTGCACTTGCACTTGCTCTTA
Found at i:195037 original size:24 final size:24
Alignment explanation
Indices: 194984--195035 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
194974 TTGGCAAAAT
*
194984 TAAATAGAACAATTAAGCAGATAAA
1 TAAATAGAAAAATTAAGCA-ATAAA
195009 TAAAT-GAAAAATTAAGC-ATAACA
1 TAAATAGAAAAATTAAGCAATAA-A
195032 TAAA
1 TAAA
195036 ATACGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 5 0.20
24 11 0.44
25 5 0.20
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.21
Consensus pattern (24 bp):
TAAATAGAAAAATTAAGCAATAAA
Found at i:195229 original size:30 final size:30
Alignment explanation
Indices: 195182--195371 Score: 181
Period size: 30 Copynumber: 6.4 Consensus size: 30
195172 ATTCAAGGTA
* * *
195182 AAAATGTAATTTTGGAAAACTTT-GGGGTT
1 AAAATGTGATTTTGGAAAAGTTTAGGGGTC
*
195211 AAAATGTGATTTTAGG-AAA-TTTTGGGGTC
1 AAAATGTGATTTT-GGAAAAGTTTAGGGGTC
* *
195240 AAAATGTGATTTTTGAAAAGTTTAGGAGTC
1 AAAATGTGATTTTGGAAAAGTTTAGGGGTC
* * * *
195270 AAAATGTAATTTTGGAGAGGTTT-GAGGTC
1 AAAATGTGATTTTGGAAAAGTTTAGGGGTC
* * * *
195299 AAAATGTAATTTTGGAGAAGTTTAAGGGTT
1 AAAATGTGATTTTGGAAAAGTTTAGGGGTC
* * *
195329 AAAATATGATTTTAGAAAAATTTAGGGGTC
1 AAAATGTGATTTTGGAAAAGTTTAGGGGTC
*
195359 AAAATATGATTTT
1 AAAATGTGATTTT
195372 TAAAGAAAAC
Statistics
Matches: 134, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
28 4 0.03
29 62 0.46
30 68 0.51
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTGATTTTGGAAAAGTTTAGGGGTC
Found at i:195282 original size:59 final size:58
Alignment explanation
Indices: 195182--195363 Score: 204
Period size: 59 Copynumber: 3.1 Consensus size: 58
195172 ATTCAAGGTA
* *
195182 AAAATGTAATTTTGGAAAACTTTGGGGTTAAAATGTGATTTTAGGAAATTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGGAAATTTTGGGGTC
* * * * ** *
195240 AAAATGTGATTTTTGAAAAGTTTAGGAGTCAAAATGTAATTTT-GGAGAGGTTTGAGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGG-GTTAAAATGTGATTTTAGGA-AATTTTGGGGTC
* * * *
195299 AAAATGTAATTTTGGAGAAGTTTAAGGGTTAAAATATGATTTTAGAAAAATTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATGTGATTTTAG-GAAATTTTGGGGTC
195359 AAAAT
1 AAAAT
195364 ATGATTTTTA
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
58 25 0.25
59 56 0.57
60 17 0.17
61 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTGATTTTAGGAAATTTTGGGGTC
Found at i:196311 original size:21 final size:21
Alignment explanation
Indices: 196270--196314 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
196260 ATGTTTGAAA
*
196270 ATAATAAATGACATTAATAAT
1 ATAATAAATGAAATTAATAAT
*
196291 ATAATAAAT-AAATATATTAAT
1 ATAATAAATGAAAT-TAATAAT
196312 ATA
1 ATA
196315 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATAAATGAAATTAATAAT
Found at i:196326 original size:25 final size:24
Alignment explanation
Indices: 196267--196329 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
196257 TGCATGTTTG
196267 AAAATAATAAATGACATTAATAATAT
1 AAAAT-ATAAAT-ACATTAATAATAT
* *
196293 AATAA-ATAAATATATTAATATATTT
1 AA-AATATAAATACATTAATA-ATAT
196318 AAAATATAAATA
1 AAAATATAAATA
196330 GTTTTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 10 0.31
25 18 0.56
26 2 0.06
27 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAATATAAATACATTAATAATAT
Found at i:198219 original size:6 final size:6
Alignment explanation
Indices: 198208--198240 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
198198 CCCCAGCAGC
198208 AGGACG AGGACG AGGACG AGGACG AGGACG AGG
1 AGGACG AGGACG AGGACG AGGACG AGGACG AGG
198241 GCTTCCTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.52, T:0.00
Consensus pattern (6 bp):
AGGACG
Found at i:200613 original size:16 final size:16
Alignment explanation
Indices: 200594--200651 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
200584 CTTTTTCAGA
200594 AGAATAATTTTTGTTT
1 AGAATAATTTTTGTTT
*
200610 AGAATAGTTTTTGTTCT
1 AGAATAATTTTTGTT-T
* **
200627 A-AACAATCATTGTTT
1 AGAATAATTTTTGTTT
200642 GAGAATAATT
1 -AGAATAATT
200652 ACATTCAGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 1 0.03
16 24 0.75
17 7 0.22
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (16 bp):
AGAATAATTTTTGTTT
Found at i:201509 original size:62 final size:62
Alignment explanation
Indices: 201434--201558 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
201424 GAAAGGAGAG
* * *
201434 TATTTTGAGATGTAAACTAAGGCTGGGAAATGGCTCGAGAAGGAAAGTGAGATGAGGATATC
1 TATTTTGAAATGTAAACCAAGGCTGGGAAATGGCTCGAGAAGGAAAATGAGATGAGGATATC
* * *
201496 TATTTTGAAATGTAAACCAAGGTTGGGAAATGGCTTGAGAAGGAAAATGAGATGAGGGTATC
1 TATTTTGAAATGTAAACCAAGGCTGGGAAATGGCTCGAGAAGGAAAATGAGATGAGGATATC
201558 T
1 T
201559 GTATATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.36, C:0.07, G:0.31, T:0.26
Consensus pattern (62 bp):
TATTTTGAAATGTAAACCAAGGCTGGGAAATGGCTCGAGAAGGAAAATGAGATGAGGATATC
Found at i:201894 original size:45 final size:45
Alignment explanation
Indices: 201804--201890 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
201794 TTTGTCTGCA
201804 ATTTTTTTTATAATTTTTATATTTTGTCATTTATAATGATTTTAT
1 ATTTTTTTTATAATTTTTATATTTTGTCATTTATAATGATTTTAT
* *
201849 ATTTTTTTTCTATATTTATTATTTTTTG-CATTT-TAAT-ATTTT
1 ATTTTTTTTATA-ATTT-TTATATTTTGTCATTTATAATGATTTT
201891 TATAATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 5 0.13
45 15 0.39
46 9 0.24
47 9 0.24
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (45 bp):
ATTTTTTTTATAATTTTTATATTTTGTCATTTATAATGATTTTAT
Found at i:201918 original size:18 final size:18
Alignment explanation
Indices: 201840--201919 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
201830 TCATTTATAA
201840 TGATTTTATATTTTTTTT
1 TGATTTTATATTTTTTTT
* *
201858 CT-ATATT-TATTATTTTT
1 -TGATTTTATATTTTTTTT
**
201875 TGCATTTTAATATTTTTATAA
1 TG-ATTTT-ATATTTTT-TTT
201896 T-ATTTTATATTTTTTTT
1 TGATTTTATATTTTTTTT
201913 TGATTTT
1 TGATTTT
201920 TTAAATATAA
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.02
17 11 0.23
18 21 0.45
19 6 0.13
20 6 0.13
21 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.71
Consensus pattern (18 bp):
TGATTTTATATTTTTTTT
Found at i:201919 original size:37 final size:35
Alignment explanation
Indices: 201840--201919 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 35
201830 TCATTTATAA
* **
201840 TGATTTTATATTTTTTTTCTATATTTATTATTTTT
1 TGATTTTATATTTTTATAATATATTTATTATTTTT
* *
201875 TGCATTTTAATATTTTTATAATATTTTATATTTTTTTT
1 TG-ATTTT-ATATTTTTATAATATATT-TATTATTTTT
201913 TGATTTT
1 TGATTTT
201920 TTAAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 2 0.05
36 5 0.14
37 19 0.51
38 11 0.30
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.71
Consensus pattern (35 bp):
TGATTTTATATTTTTATAATATATTTATTATTTTT
Found at i:203583 original size:58 final size:58
Alignment explanation
Indices: 203493--203605 Score: 217
Period size: 58 Copynumber: 1.9 Consensus size: 58
203483 AAACTATTTA
*
203493 AAGGATGAAATTCATTTTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCATTG
1 AAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCATTG
203551 AAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCA
1 AAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCA
203606 CAGCATCTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (58 bp):
AAGGATGAAATTCATATTCACTCTAACTAAGTTCAAGTTAAACAAAACATTAGCATTG
Found at i:215366 original size:12 final size:13
Alignment explanation
Indices: 215340--215396 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
215330 TGGGGTTTGA
215340 GGTTAAGGTTAAG
1 GGTTAAGGTTAAG
215353 GGTTAAGG-TAAG
1 GGTTAAGGTTAAG
*
215365 GGTTGAGTGCTTAAG
1 GGTTAAG-G-TTAAG
* * *
215380 GTTTAAAGTTTAG
1 GGTTAAGGTTAAG
215393 GGTT
1 GGTT
215397 TAAGTTGATG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 10 0.29
13 16 0.46
14 1 0.03
15 8 0.23
ACGTcount: A:0.26, C:0.02, G:0.37, T:0.35
Consensus pattern (13 bp):
GGTTAAGGTTAAG
Found at i:215720 original size:21 final size:21
Alignment explanation
Indices: 215691--215747 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
215681 GGCTTGGGGT
* *
215691 TTTAGGGTTCAAGGTCTATTG
1 TTTAAGGTTCAAGGTCTATGG
* *
215712 TTTATGGTTCAATGTCTATGG
1 TTTAAGGTTCAAGGTCTATGG
*
215733 TTCAAGGTTCAAGGT
1 TTTAAGGTTCAAGGT
215748 TTCACGGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (21 bp):
TTTAAGGTTCAAGGTCTATGG
Found at i:217793 original size:24 final size:23
Alignment explanation
Indices: 217752--217796 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
217742 ACATGTCCAC
217752 GAACATTAAATGAACATGTTCGT
1 GAACATTAAATGAACATGTTCGT
*
217775 GAACATATAATTGAACATGTTC
1 GAACAT-TAAATGAACATGTTC
217797 ACGAACAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (23 bp):
GAACATTAAATGAACATGTTCGT
Found at i:217802 original size:24 final size:23
Alignment explanation
Indices: 217716--217803 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
217706 TTAATGTTCA
**
217716 TGAACATGTTCATTTAA-ATTAAT
1 TGAACATGTTCA-CGAACATTAAT
* * *
217739 CGAACATGTCCACGAACATTAAA
1 TGAACATGTTCACGAACATTAAT
**
217762 TGAACATGTTCGTGAACATATAAT
1 TGAACATGTTCACGAACAT-TAAT
217786 TGAACATGTTCACGAACA
1 TGAACATGTTCACGAACA
217804 ATATTAATGA
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 2 0.04
23 30 0.59
24 19 0.37
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (23 bp):
TGAACATGTTCACGAACATTAAT
Found at i:228513 original size:191 final size:192
Alignment explanation
Indices: 228187--228569 Score: 633
Period size: 191 Copynumber: 2.0 Consensus size: 192
228177 TCCCCATGAA
*
228187 GCTTTGTGGTTGTTTTCCCAGTGGTTCTTCTTTATCAAGCATTCTATGATTTTTAAATGAGATTT
1 GCTTTGTGGTTGTTTTCCCAGTGGTTCTTATTTATCAAGCATTCTATGATTTTTAAATGAGATTT
* *
228252 AACCAGAGTTATCTCACACTACTGCAGCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGTA
66 AACCAGAGTTATCTCACACTACTGCACCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
** * * *
228317 TGAGCAGGCATGTGGTT-GGGTGTACATTTGTTACTTCTGCATGTGTGAATGAGTTTTGTTG
131 TGAGCAGGCAAATGGTTGGGGTGTACATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
* * *
228378 GCTTTGTGGTTGTTTTCCTAGTGGTTCTTATTTATCAAGCTTTCTATGATTTTTAAATGAGTTTT
1 GCTTTGTGGTTGTTTTCCCAGTGGTTCTTATTTATCAAGCATTCTATGATTTTTAAATGAGATTT
*
228443 AACCAGAGTTATCTCACACTACTGCACCTAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
66 AACCAGAGTTATCTCACACTACTGCACCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
* *
228508 TGAGCATGCAAATGGTTGGGGTGTGCATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
131 TGAGCAGGCAAATGGTTGGGGTGTACATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
228570 CACAGTTTTT
Statistics
Matches: 177, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
191 137 0.77
192 40 0.23
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (192 bp):
GCTTTGTGGTTGTTTTCCCAGTGGTTCTTATTTATCAAGCATTCTATGATTTTTAAATGAGATTT
AACCAGAGTTATCTCACACTACTGCACCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGCA
TGAGCAGGCAAATGGTTGGGGTGTACATTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
Found at i:234514 original size:17 final size:18
Alignment explanation
Indices: 234494--234527 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
234484 TTATAATCTC
234494 TTTTTATTT-TGTTTTAT
1 TTTTTATTTGTGTTTTAT
234511 TTTTTATTTGTGTTTTA
1 TTTTTATTTGTGTTTTA
234528 AACCCTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (18 bp):
TTTTTATTTGTGTTTTAT
Found at i:245634 original size:104 final size:103
Alignment explanation
Indices: 245452--245658 Score: 236
Period size: 104 Copynumber: 2.0 Consensus size: 103
245442 GCTTCATATC
* * * * * * **
245452 AAAGAACTAATTGAACTAAATTCAAGTAGATGGAGATTTAGACTAATTGTAGTTTTGATAAATTT
1 AAAGAACTAATTGAACTAAATTCAAGGAGATAGAGATTTAAACTAAGTGTAATTTTGACAAACCT
*
245517 TTAATGTTGATATAAAAAAAAAAGCTTGTTTATTATACA
66 TTAATGCTGATAT-AAAAAAAAAGCTTGTTTATTATACA
* * * *
245556 AAAGATCTAATTGAGCTAAATTCAAGGAGATAGAGATTTACAATTAAGTGTAATTTTGACAAGCC
1 AAAGAACTAATTGAACTAAATTCAAGGAGATAGAGATTTA-AACTAAGTGTAATTTTGACAAACC
* ** *
245621 TTTAATGCT-ATATATAAGGAAGGCTTGTTTATTATACA
65 TTTAATGCTGATATAAAAAAAAAGCTTGTTTATTATACA
245659 TTTACGAGAT
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
103 21 0.25
104 40 0.47
105 24 0.28
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (103 bp):
AAAGAACTAATTGAACTAAATTCAAGGAGATAGAGATTTAAACTAAGTGTAATTTTGACAAACCT
TTAATGCTGATATAAAAAAAAAGCTTGTTTATTATACA
Found at i:246037 original size:140 final size:139
Alignment explanation
Indices: 245780--246055 Score: 446
Period size: 140 Copynumber: 2.0 Consensus size: 139
245770 TACAAGTTAG
* *
245780 TATAATGGTAAGATTATATTTTAATCTTTTAAAAAAAAAAGCTATTCACTTTTGAACTCTTAAAA
1 TATAATGGTAAAATTATATTTTAATCTTTTAAAAAAAAAAACTATTCACTTTTGAACTCTTAAAA
* * *
245845 TAGTTTTCTAATTTTGCCCCTGCTTATTTTGTTTGTATGAGGAACTTATTTCAATACAAATTATT
66 CAGTTTTCTAATTTTGCCCCTGCTTATTTTGCTTATATGAGGAACTTATTTCAATACAAATTATT
245910 ATAAATTAA
131 ATAAATTAA
*
245919 TATAATGGTAAAATTATATTTTAATCTTTTAAAAAAAAAAATACTATTCATTTTTGAACTCTTAA
1 TATAATGGTAAAATTATATTTTAATCTTTT-AAAAAAAAAA-ACTATTCACTTTTGAACTCTTAA
* * *
245984 AACAGTTTTTTAATTTTG-CTCTGCTTATTTTGCTTATATGAGGAACTTATTTCAATGCAAATTA
64 AACAGTTTTCTAATTTTGCCCCTGCTTATTTTGCTTATATGAGGAACTTATTTCAATACAAATTA
246048 TTATAAAT
129 TTATAAAT
246056 AAAATGTTCT
Statistics
Matches: 126, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
139 29 0.23
140 60 0.48
141 37 0.29
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.45
Consensus pattern (139 bp):
TATAATGGTAAAATTATATTTTAATCTTTTAAAAAAAAAAACTATTCACTTTTGAACTCTTAAAA
CAGTTTTCTAATTTTGCCCCTGCTTATTTTGCTTATATGAGGAACTTATTTCAATACAAATTATT
ATAAATTAA
Found at i:246971 original size:15 final size:16
Alignment explanation
Indices: 246946--246978 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
246936 TTTAGTACTT
*
246946 ATTTTTATACCAACTA
1 ATTTTTATACCAAATA
246962 ATTTTT-TACCAAATA
1 ATTTTTATACCAAATA
246977 AT
1 AT
246979 CTAATTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTTATACCAAATA
Found at i:255680 original size:26 final size:26
Alignment explanation
Indices: 255650--255701 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
255640 TTGAATTAAA
*
255650 AATATTTGAATTACG-TTTTTATTTTT
1 AATATTTCAA-TACGTTTTTTATTTTT
*
255676 AATATTTCAATATGTTTTTTATTTTT
1 AATATTTCAATACGTTTTTTATTTTT
255702 TAAATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (26 bp):
AATATTTCAATACGTTTTTTATTTTT
Found at i:258071 original size:24 final size:24
Alignment explanation
Indices: 258055--258105 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
258045 AGTTTGACTT
258055 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
258079 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
258103 AAA
1 AAA
258106 AATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:258537 original size:20 final size:21
Alignment explanation
Indices: 258493--258540 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
258483 TATAACTATT
*
258493 CAAAAAATTTAAAATTTATAA
1 CAAAAAATATAAAATTTATAA
258514 -AAAAAATATAAAA-TTA-AA
1 CAAAAAATATAAAATTTATAA
*
258532 CCAAAAATA
1 CAAAAAATA
258541 ATTTAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.08
19 10 0.42
20 12 0.50
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (21 bp):
CAAAAAATATAAAATTTATAA
Found at i:260264 original size:31 final size:31
Alignment explanation
Indices: 260226--260289 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
260216 TCGCACCCGC
260226 TTGGTTGCATATAAAAGATATATTATATATT
1 TTGGTTGCATATAAAAGATATATTATATATT
*
260257 TTGGTTGCATATAAAAGATATATTATTTATT
1 TTGGTTGCATATAAAAGATATATTATATATT
260288 TT
1 TT
260290 AAGTATAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (31 bp):
TTGGTTGCATATAAAAGATATATTATATATT
Found at i:260565 original size:22 final size:21
Alignment explanation
Indices: 260539--260579 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
260529 ATAATTCAAA
260539 AAATTATAAAAACAAAAAATAT
1 AAATTA-AAAAACAAAAAATAT
*
260561 AAATTAAAAAATAAAAAAT
1 AAATTAAAAAACAAAAAAT
260580 TCATAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATTAAAAAACAAAAAATAT
Found at i:263234 original size:80 final size:80
Alignment explanation
Indices: 263101--263261 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
263091 GGATGGTTAG
263101 ACCCTTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGA
1 ACCCTTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGA
*
263166 ACCATTGCCGTCTAT
66 ACCATTACCGTCTAT
263181 ACCCTTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGA
1 ACCCTTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGA
263246 ACCATTACCGTCTAT
66 ACCATTACCGTCTAT
263261 A
1 A
263262 TGTTTTTCTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (80 bp):
ACCCTTGATACGCCTTTGATTTCTCAAATATTGGTTAATGGTAAAACTCAGAGAGTTGAATATGA
ACCATTACCGTCTAT
Found at i:272809 original size:29 final size:30
Alignment explanation
Indices: 272745--272809 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
272735 ACAATTAAAC
*
272745 CTAAATTTTGAAATATGAAAAGTAAAGTGA
1 CTAAATTTTGAAATATGAAAAGTAAAGAGA
*
272775 CAAAATTCTTGAAA-AT-AAAAGTATAA-AGA
1 CTAAATT-TTGAAATATGAAAAGTA-AAGAGA
272804 CTAAAT
1 CTAAAT
272810 ATCAAATTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 14 0.47
30 10 0.33
31 6 0.20
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.28
Consensus pattern (30 bp):
CTAAATTTTGAAATATGAAAAGTAAAGAGA
Found at i:273555 original size:24 final size:25
Alignment explanation
Indices: 273499--273549 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
273489 TCAAATTTTG
* *
273499 ATACCAAATTAAAAA-AAAAATTAA
1 ATACCAAATTAAAAATATATATTAA
273523 ATACCAAATTAAAAATATATATTAA
1 ATACCAAATTAAAAATATATATTAA
273548 AT
1 AT
273550 TCAAATACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (25 bp):
ATACCAAATTAAAAATATATATTAA
Found at i:273581 original size:25 final size:24
Alignment explanation
Indices: 273535--273581 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
273525 ACCAAATTAA
*
273535 AAATATATATTAAATTCAAATACC
1 AAATATATATTAAATGCAAATACC
273559 AAATATTATATTAAA-GCATAATA
1 AAATA-TATATTAAATGCA-AATA
273582 AATTGATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATATATATTAAATGCAAATACC
Found at i:274618 original size:31 final size:31
Alignment explanation
Indices: 274583--274652 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
274573 TTACAAAATT
*
274583 GTCACTAAACTATTCAAAAATTTTC-ATTTAA
1 GTCACTAAACTATT-AAAAAGTTTCTATTTAA
* *
274614 GTCACTAAACTATTTAGAAGTTTCTATTTAA
1 GTCACTAAACTATTAAAAAGTTTCTATTTAA
274645 GTCA-TAAA
1 GTCACTAAA
274653 GTCATTAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (31 bp):
GTCACTAAACTATTAAAAAGTTTCTATTTAA
Found at i:279246 original size:213 final size:206
Alignment explanation
Indices: 278877--279263 Score: 551
Period size: 213 Copynumber: 1.8 Consensus size: 206
278867 TCCTTCTGAA
* * *
278877 TTATGATCTTGATCATCATAATCATGAAGTGTTTTTGTTAATCTCTTTTTAATATTCTTTATTAA
1 TTATGATCTTGATCATCATAATCACGAAGTGTTTTTATTAATCTCTTTTAAATATTCTTTATTAA
*
278942 TTTATTTCTGCAGGGAGAAGAGGTTTTCAGTTATGTTTTCTTTTTAGCTAAATTCTCCTTAAATT
66 TTTATTTCTGCAGGGAGAAGAGGTTTTCAGTTATCTTTTCTTTTTAGCTAAATTCTCCTTAAATT
* * *
279007 AGTTACTAAATCTTTCTATGGATTTGAAAATTTGAGAAATTATTCTTTGTTAATCTTTATTATCA
131 AGTTACTAAATATTTCTATAGATTTGAAAATTAGAGAAATTATTCTTTGTTAATCTTTATTATCA
279072 AATATTCTTTG
196 AATATTCTTTG
* *
279083 TTATGATCTTGATCATCATAATTACGAAGTGTTTTTATTAATCT-TTTTCAAAAATATTCTTTGT
1 TTATGATCTTGATCATCATAATCACGAAGTGTTTTTATTAATCTCTTTT---AAATATTCTTTAT
* * * * *
279147 TAATTTATTTTTTCCGGGAGAAGAGAACAAGTTTTCAGTTATCTTTTCTTTTTAGCTACATTTTC
63 TAATTTATTTCTGCAGGGAGAAGAG-----GTTTTCAGTTATCTTTTCTTTTTAGCTAAATTCTC
* *
279212 CTTAAATTAGTTGCTAAATATTTCTTTAGATTTGAAAATTAGAGAAATTATT
123 CTTAAATTAGTTACTAAATATTTCTATAGATTTGAAAATTAGAGAAATTATT
279264 ATGCCTCTTT
Statistics
Matches: 157, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
205 4 0.03
206 41 0.26
208 33 0.21
213 79 0.50
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.49
Consensus pattern (206 bp):
TTATGATCTTGATCATCATAATCACGAAGTGTTTTTATTAATCTCTTTTAAATATTCTTTATTAA
TTTATTTCTGCAGGGAGAAGAGGTTTTCAGTTATCTTTTCTTTTTAGCTAAATTCTCCTTAAATT
AGTTACTAAATATTTCTATAGATTTGAAAATTAGAGAAATTATTCTTTGTTAATCTTTATTATCA
AATATTCTTTG
Found at i:284129 original size:46 final size:45
Alignment explanation
Indices: 284074--284162 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 45
284064 TATTCAAACG
* * * *
284074 ATATTAAAAATG-ACAATGAAACAACATTAAAAACAATAGCAAAATA
1 ATATAAAAAATGCACAA-AAAACAACACT-AAAACAATAACAAAATA
*
284120 ATATAAAAAATGCACAAAAAACAACACTCAAACAATAACAAAA
1 ATATAAAAAATGCACAAAAAACAACACTAAAACAATAACAAAA
284163 ACAACAGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 13 0.35
46 20 0.54
47 4 0.11
ACGTcount: A:0.65, C:0.15, G:0.04, T:0.16
Consensus pattern (45 bp):
ATATAAAAAATGCACAAAAAACAACACTAAAACAATAACAAAATA
Found at i:284162 original size:23 final size:21
Alignment explanation
Indices: 284136--284184 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 21
284126 AAAATGCACA
284136 AAAAACAACACTCAAACAATAAC
1 AAAAACAACACT-AAA-AATAAC
*
284159 AAAAACAACAGTAAAAATAAC
1 AAAAACAACACTAAAAATAAC
284180 AAAAA
1 AAAAA
284185 AATAGTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.44
22 3 0.12
23 11 0.44
ACGTcount: A:0.71, C:0.18, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAAACAACACTAAAAATAAC
Found at i:284186 original size:23 final size:24
Alignment explanation
Indices: 284133--284185 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
284123 TAAAAAATGC
284133 ACAAAAAACAACACTCAAACAATA
1 ACAAAAAACAACACTCAAACAATA
*
284157 AC-AAAAACAACAGT-AAA-AATA
1 ACAAAAAACAACACTCAAACAATA
284178 ACAAAAAA
1 ACAAAAAA
284186 ATAGTGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 6 0.22
22 8 0.30
23 11 0.41
24 2 0.07
ACGTcount: A:0.72, C:0.19, G:0.02, T:0.08
Consensus pattern (24 bp):
ACAAAAAACAACACTCAAACAATA
Found at i:284803 original size:33 final size:33
Alignment explanation
Indices: 284737--284806 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
284727 TTCTATTATT
* *
284737 AAAT-GAATTAATTTAATTTGTATATTATTAAA
1 AAATAGAATAAATTTAATTTGTATATTATAAAA
284769 AAATAGAATAAATTTAATATT-TACTA-TATAAAA
1 AAATAGAATAAATTTAAT-TTGTA-TATTATAAAA
284802 AAATA
1 AAATA
284807 TATTGAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 4 0.12
33 25 0.76
34 4 0.12
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (33 bp):
AAATAGAATAAATTTAATTTGTATATTATAAAA
Found at i:294264 original size:21 final size:21
Alignment explanation
Indices: 294238--294277 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
294228 TAAATTTTAA
294238 AATTTCAAAAAGTAAAAATTG
1 AATTTCAAAAAGTAAAAATTG
* *
294259 AATTTCTAAAATTAAAAAT
1 AATTTCAAAAAGTAAAAAT
294278 ATAGAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
AATTTCAAAAAGTAAAAATTG
Found at i:295024 original size:16 final size:16
Alignment explanation
Indices: 295003--295051 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
294993 TATATCTCAC
295003 TTTAATTTTGACATAA
1 TTTAATTTTGACATAA
* *
295019 TTTAA-TTT-ATATAT
1 TTTAATTTTGACATAA
295033 TTTAATTTTGACATAA
1 TTTAATTTTGACATAA
295049 TTT
1 TTT
295052 GATACCTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (16 bp):
TTTAATTTTGACATAA
Found at i:303337 original size:21 final size:21
Alignment explanation
Indices: 303313--303375 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
303303 CGATATTTGA
303313 GTAAGTTCTACCGATACAAGT
1 GTAAGTTCTACCGATACAAGT
* *
303334 GTAACTTCTACCAATACAAGT
1 GTAAGTTCTACCGATACAAGT
* *
303355 -TATGCTTCTATCGATACAAGT
1 GTAAG-TTCTACCGATACAAGT
303376 CATGCTTCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (21 bp):
GTAAGTTCTACCGATACAAGT
Found at i:303380 original size:21 final size:21
Alignment explanation
Indices: 303338--303391 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
303328 ACAAGTGTAA
* * *
303338 CTTCTACCAATACAAGTTATG
1 CTTCTATCGATACAAGTCATG
303359 CTTCTATCGATACAAGTCATG
1 CTTCTATCGATACAAGTCATG
303380 CTTCTATCGATA
1 CTTCTATCGATA
303392 TTAAAAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (21 bp):
CTTCTATCGATACAAGTCATG
Found at i:304163 original size:52 final size:52
Alignment explanation
Indices: 304090--304380 Score: 406
Period size: 52 Copynumber: 5.6 Consensus size: 52
304080 ATTTCATTTA
* * **
304090 ATACTCACGATGACACATAGTCATTGAACGTCATAATTTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * *
304142 ATATTCACGATGACACATAGTCATAAGAA-CTCGTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCAT-CGAACCTCATAATCCGTAAAGGATTCAT
* *
304194 ATACTCACGACGACACATAGTCATC-AGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGA-ACCTCATAATCCGTAAAGGATTCAT
* * *
304246 ATACTCATGATGACACATAGTTATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
* * *
304298 ATACTCACGATAACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
*
304350 ATACTCATGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGAACCT
304381 TTCGTTTACG
Statistics
Matches: 212, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
50 1 0.00
51 1 0.00
52 207 0.98
53 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCAT
Found at i:311829 original size:13 final size:14
Alignment explanation
Indices: 311810--311849 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
311800 AAGTTTTATT
311810 TAATTTTTATATAA
1 TAATTTTTATATAA
311824 -AATTTTTATA-AA
1 TAATTTTTATATAA
311836 TATATTTTTATATA
1 TA-ATTTTTATATA
311850 CACTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 11 0.48
14 9 0.39
15 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTTTTATATAA
Found at i:314718 original size:41 final size:41
Alignment explanation
Indices: 314661--314748 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
314651 TTAAGATTCA
*
314661 AGATGAAAAGCGAAGAGGCAAGAAAAGAACCAAAGGATTAT
1 AGATGAAAAGAGAAGAGGCAAGAAAAGAACCAAAGGATTAT
314702 AGATGAAAAGAGAAGAGGCAAGAAAAGAACCAAAGGATTAT
1 AGATGAAAAGAGAAGAGGCAAGAAAAGAACCAAAGGATTAT
314743 AGATGA
1 AGATGA
314749 GCATTTCGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.55, C:0.08, G:0.27, T:0.10
Consensus pattern (41 bp):
AGATGAAAAGAGAAGAGGCAAGAAAAGAACCAAAGGATTAT
Found at i:321220 original size:312 final size:309
Alignment explanation
Indices: 320619--321230 Score: 938
Period size: 312 Copynumber: 2.0 Consensus size: 309
320609 AAAGTTGCTT
* *
320619 TTCTGAGGAAGACTGACCAGAAGCAATTTCTTTTGTAACTAATTGAAGCTCATTTAGCTCTTCTG
1 TTCTGAGGAAGACTGACCAGAAGAAATTTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTTCTG
* ** * *
320684 TTTCTCCAGCTGATGAGTCTTCATGGTTCCCATCGTGAAGCTTTTCAGTTTCTTTCCTTTTTCTT
66 TTTCTCCAGCTGACGAGTCTTCACAGTTCCCATCGTCAAGCTTTTCAGCTTCTTTCCTTTTTCTT
* * * *
320749 TCGTTTGCTTCAACCTCTTGTGATTCCTCTGTTATGGAAGCCTGAGCAATAATGGTTTCTTGATC
131 TCGTTTGCTTCAACATCTTGAGATTCCACTGTTATGGAAGCCTGAACAATAATGGTTTCTTGATC
*
320814 GATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTTTCCC
196 CATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTTTCCC
* *
320879 CCTCTTCTTCATTGGCCTCAGCTCCATGCTTTAGGTTCTCTTTAGTCAA
261 CCTCTTCTTCATTGGCCTCAGCGCCATGCTTTAGGCTCTCTTTAGTCAA
*
320928 TTCTGAGGAAGACTGTCCAGAAGAAAGTTCTTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTT
1 TTCTGAGGAAGACTGACCAGAAGAAA--T-TTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTT
* * * **
320993 CTGTTTCTCCAGCTGACGAGTCTTTACAGTTCCTATCGTCCAGCTTTTTGGCTTCTTTCC-TTTT
63 CTGTTTCTCCAGCTGACGAGTCTTCACAGTTCCCATCGTCAAGCTTTTCAGCTTCTTTCCTTTTT
* * * *
321057 CTCTTCGTTTGGTTCAATATCTTGAGATTCCACTGTTATTGAAGCCTGAACTATAATGGTTTCTT
128 CT-TTCGTTTGCTTCAACATCTTGAGATTCCACTGTTATGGAAGCCTGAACAATAATGGTTTCTT
*
321122 GATCCATAACAGCTTTAGGCTCCTGAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTT
192 GATCCATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTT
**
321187 TCTTCCTCTTCTTCATTGGCCTCAGCGCCATGCTTTAGGCTCTC
257 TCCCCCTCTTCTTCATTGGCCTCAGCGCCATGCTTTAGGCTCTC
321231 AACAGTCAAC
Statistics
Matches: 272, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
309 24 0.09
311 7 0.03
312 241 0.89
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (309 bp):
TTCTGAGGAAGACTGACCAGAAGAAATTTCTCTTGTAACTAATTGAAGCTCATTTAGCTCTTCTG
TTTCTCCAGCTGACGAGTCTTCACAGTTCCCATCGTCAAGCTTTTCAGCTTCTTTCCTTTTTCTT
TCGTTTGCTTCAACATCTTGAGATTCCACTGTTATGGAAGCCTGAACAATAATGGTTTCTTGATC
CATAACAGCTTTAGGCTCCTCAGGTCCTTCCTTTTCGAGAATTTCCACTTCCTTCACCTTTTCCC
CCTCTTCTTCATTGGCCTCAGCGCCATGCTTTAGGCTCTCTTTAGTCAA
Found at i:330111 original size:20 final size:20
Alignment explanation
Indices: 330086--330128 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
330076 TTCCTTAATT
* *
330086 TCAGCAACTTATATCCCTAA
1 TCAGCAAATCATATCCCTAA
330106 TCAGCAAATCATATCCCTAA
1 TCAGCAAATCATATCCCTAA
330126 TCA
1 TCA
330129 CATCCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.30, G:0.05, T:0.28
Consensus pattern (20 bp):
TCAGCAAATCATATCCCTAA
Found at i:342988 original size:137 final size:137
Alignment explanation
Indices: 342742--343368 Score: 936
Period size: 137 Copynumber: 4.6 Consensus size: 137
342732 GCACAATACG
* *
342742 TGTAAGATGAAAGAACTTTACCACTACTGAAATGGGTTCTTGGATGATCACTGCTTCAGTTGCCA
1 TGTAAGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
* * * * * *
342807 TTGTTTCCTGCACAAGTTATCGAATTCGAGTTAGAGAGCTTATCATTTCAAACACTCGTAAACTG
66 TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
342872 TGAATCA
131 TGAATCA
*
342879 TGTAAGATGAAAGAACTTTACCACTA-TGAAAATGGGTTCTTGAATGATCACTGATTCAGTTGCC
1 TGTAAGATGAAAGAACTTTACCACTATTG-AAATGGGTTCTTGAATGATCACTGCTTCAGTTGCC
* *
342943 ATTTTTTCCTGCACAAGTGGTCGAATTCGAGTTTGAGATCCTATCATTTCAAACATTCATAAACT
65 ATTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACT
343008 GTGAATCA
130 GTGAATCA
* * *
343016 TGTAGGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGATTCAGATGCCA
1 TGTAAGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
* *
343081 TTTTTTCCTGCACAAGTGATTGACTTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
66 TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
343146 TGAATCA
131 TGAATCA
*
343153 TGTAGGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
1 TGTAAGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
* * * ** *
343218 TTTCTTCCTGCACAAGTAATAGAATTCGAGTTTGAGAGCCTATCATTTTGAACATTCATAAATTG
66 TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
343283 TGAAT--
131 TGAATCA
* * * **
343288 TTTAAAGATGAAAGAACTTCACCACTATGGAAACAGGTTCTTGAATGATCACTGCTTCAGTTGCC
1 TGT-AAGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCC
343353 ATCTACTTTTCCTGCA
65 AT-T--TTTTCCTGCA
343369 GAAATAATAG
Statistics
Matches: 452, Mismatches: 32, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
135 2 0.00
136 60 0.13
137 379 0.84
138 2 0.00
139 9 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (137 bp):
TGTAAGATGAAAGAACTTTACCACTATTGAAATGGGTTCTTGAATGATCACTGCTTCAGTTGCCA
TTTTTTCCTGCACAAGTGATCGAATTCGAGTTTGAGAGCCTATCATTTCAAACATTCATAAACTG
TGAATCA
Found at i:350386 original size:2 final size:2
Alignment explanation
Indices: 350379--350403 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
350369 TTAAACATGA
350379 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
350404 ATTGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:357063 original size:23 final size:23
Alignment explanation
Indices: 356941--357051 Score: 159
Period size: 23 Copynumber: 4.8 Consensus size: 23
356931 GCTGGGGAAA
356941 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * * *
356964 CAATAGGCACACGCAGTGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
356987 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
357010 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
357033 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
357052 TGAACAGTAA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:360898 original size:11 final size:11
Alignment explanation
Indices: 360884--360920 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
360874 TAAAAAAATT
*
360884 AAATTACTTTA
1 AAATTACTATA
360895 AAATTA-TATA
1 AAATTACTATA
360905 AAA-TACTATA
1 AAATTACTATA
360915 AAATTA
1 AAATTA
360921 TTAAATCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 2 0.09
10 13 0.57
11 8 0.35
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATTACTATA
Found at i:360911 original size:20 final size:19
Alignment explanation
Indices: 360860--360925 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
360850 CTATATTCTT
*
360860 AATTA-TAAAATAAT-TAA
1 AATTATTAAAATACTATAA
** * *
360877 AAAAATTAAATTACTTTAA
1 AATTATTAAAATACTATAA
360896 AATTATATAAAATACTATAA
1 AATTAT-TAAAATACTATAA
360916 AATTATTAAA
1 AATTATTAAA
360926 TCATAATTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 7 0.18
19 11 0.29
20 17 0.45
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTATTAAAATACTATAA
Found at i:360936 original size:20 final size:18
Alignment explanation
Indices: 360860--360943 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 18
360850 CTATATTCTT
360860 AATTA-TAAAATAATTAA
1 AATTATTAAAATAATTAA
** * *
360877 AAAAATTAAATTACTTTAA
1 AATTATTAAAATA-ATTAA
*
360896 AATTATATAAAATACTATAA
1 AATTAT-TAAAATAAT-TAA
360916 AATTATTAAATCATAATTAA
1 AATTATTAAA--ATAATTAA
360936 AATATATT
1 AAT-TATT
360944 TTACTTCTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
17 3 0.06
18 6 0.12
19 13 0.25
20 21 0.41
21 8 0.16
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATTAAAATAATTAA
Found at i:370711 original size:21 final size:21
Alignment explanation
Indices: 370663--370726 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
370653 AAATCTCGAA
* * *
370663 TAATTATTTAAATGATTTTTTT
1 TAATAATTT-AATAATTATTTT
370685 TAAATAATTTAATAATTATTTT
1 T-AATAATTTAATAATTATTTT
* *
370707 TAATAATTTATTCATTATTT
1 TAATAATTTAATAATTATTT
370727 ATAACATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.47
22 12 0.33
23 7 0.19
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATAATTTAATAATTATTTT
Found at i:378334 original size:29 final size:28
Alignment explanation
Indices: 378304--378647 Score: 232
Period size: 29 Copynumber: 11.9 Consensus size: 28
378294 GTTCATGGTC
*
378304 AAAAATGTAATTTTTTGAAGTTTGAGGT
1 AAAAATGTAATTTTTAGAAGTTTGAGGT
* *
378332 CAAAAATGGAATTTTTAG-ACTTTCGAGGGT
1 -AAAAATGTAATTTTTAGAAGTTT-GA-GGT
* *
378362 -AAAATGGTAATTTTT-TAAGTTCGAGGT
1 AAAAAT-GTAATTTTTAGAAGTTTGAGGT
* * **
378389 CAAAAATGGAATTTTTGGAAGTTCAAGGT
1 -AAAAATGTAATTTTTAGAAGTTTGAGGT
*
378418 CAAAAATGTAATTTTTAGAAGTTTGGGGT
1 -AAAAATGTAATTTTTAGAAGTTTGAGGT
** * *
378447 TTAAATGTAATTTTTAAAAGTTTAAGGGT
1 AAAAATGTAATTTTTAGAAGTTTGA-GGT
* * *
378476 AAAAATATAATTTTTGGAAAGTTTGGGGTT
1 AAAAATGTAATTTTTAG-AAGTTTGAGG-T
*
378506 AAAAATGTAATTTTTAGAAGTTCGAGGGT
1 AAAAATGTAATTTTTAGAAGTTTGA-GGT
* *
378535 -AAAATAG-AATTTTTGGAAAGTTCGAGGGT
1 AAAAAT-GTAATTTTTAG-AAGTTTGA-GGT
* *
378564 AAAAATGTAATTTTTTGAAAGTTTAGGGGT
1 AAAAATGTAATTTTTAG-AAGTTT-GAGGT
* * *
378594 -AAAATGGAATTTTTAAAAAGTTTGGGGGT
1 AAAAATGTAATTTTT-AGAAGTTT-GAGGT
* * *
378623 CAAAATGTAGTTTTTGGAAAGTTTG
1 AAAAATGTAATTTTTAG-AAGTTTG
378648 GGAGTCAAAA
Statistics
Matches: 253, Mismatches: 43, Indels: 38
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.01
28 52 0.21
29 130 0.51
30 67 0.26
31 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (28 bp):
AAAAATGTAATTTTTAGAAGTTTGAGGT
Found at i:378376 original size:57 final size:57
Alignment explanation
Indices: 378237--378578 Score: 268
Period size: 58 Copynumber: 5.9 Consensus size: 57
378227 TTGTGGATAC
* * * * * *
378237 TCGAGGGTAAAACTGTAA-TTTTGGACACTTCGGAGG-CAAAATGGTAATTTTCAAAAAGT
1 TCGAGGGTAAAAATGTAATTTTTGGA-AGTT-TGAGGTAAAAAT-GTAATTTT-TAGAAGT
* * * **
378296 TC-ATGGTCAAAAATGTAATTTTTTGAAGTTTGAGGTCAAAAATGGAATTTTTAGACTT
1 TCGAGGGT-AAAAATGTAATTTTTGGAAGTTTGAGGT-AAAAATGTAATTTTTAGAAGT
* * * *
378354 TCGAGGGT-AAAATGGTAATTTTT-TAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGT
1 TCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTGAGGT-AAAAATGTAATTTTTAGAAGT
* * * ** *
378411 TC-AAGGTCAAAAATGTAATTTTTAGAAGTTTGGGGTTTAAATGTAATTTTTAAAAGT
1 TCGAGGGT-AAAAATGTAATTTTTGGAAGTTTGAGGTAAAAATGTAATTTTTAGAAGT
** * *
378468 TTAAGGGTAAAAATATAATTTTTGGAAAGTTTGGGGTTAAAAATGTAATTTTTAGAAGT
1 TCGAGGGTAAAAATGTAATTTTTGG-AAGTTTGAGG-TAAAAATGTAATTTTTAGAAGT
*
378527 TCGAGGGT-AAAATAG-AATTTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTT
1 TCGAGGGTAAAAAT-GTAATTTTTGG-AAGTTTGA-GGTAAAAATGTAATTTTT
378579 TGAAAGTTTA
Statistics
Matches: 231, Mismatches: 38, Indels: 29
0.78 0.13 0.10
Matches are distributed among these distances:
56 4 0.02
57 77 0.33
58 87 0.38
59 52 0.23
60 11 0.05
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (57 bp):
TCGAGGGTAAAAATGTAATTTTTGGAAGTTTGAGGTAAAAATGTAATTTTTAGAAGT
Found at i:378540 original size:58 final size:58
Alignment explanation
Indices: 378305--378637 Score: 279
Period size: 58 Copynumber: 5.8 Consensus size: 58
378295 TTCATGGTCA
* * * * **
378305 AAAATGTAATTTTTTG-AAGTTTGAGGTCAAAAATGGAATTTTTAGACTTTCGAGGGT
1 AAAATGTAATTTTTAGAAAGTTTGGGGTTAAAAATGTAATTTTTAGAAGTTCGAGGGT
* * * * * * *
378362 AAAATGGTAATTTTT--TAAGTTCGAGGTCAAAAATGGAATTTTTGGAAGTTC-AAGGT
1 AAAAT-GTAATTTTTAGAAAGTTTGGGGTTAAAAATGTAATTTTTAGAAGTTCGAGGGT
* * **
378418 CAAAAATGTAATTTTTAG-AAGTTTGGGGTT-TAAATGTAATTTTTAAAAGTTTAAGGGT
1 --AAAATGTAATTTTTAGAAAGTTTGGGGTTAAAAATGTAATTTTTAGAAGTTCGAGGGT
* *
378476 AAAAATATAATTTTTGGAAAGTTTGGGGTTAAAAATGTAATTTTTAGAAGTTCGAGGGT
1 -AAAATGTAATTTTTAGAAAGTTTGGGGTTAAAAATGTAATTTTTAGAAGTTCGAGGGT
* * * *
378535 AAAATAG-AATTTTTGGAAAGTTCGAGGG-TAAAAATGTAATTTTTTGAAAGTT-TAGGGGT
1 AAAAT-GTAATTTTTAGAAAGTTTG-GGGTTAAAAATGTAATTTTTAG-AAGTTCGA-GGGT
* * * * *
378594 AAAATGGAATTTTTAAAAAGTTTGGGGGTCAAAATGTAGTTTTT
1 AAAATGTAATTTTTAGAAAGTTTGGGGTTAAAAATGTAATTTTT
378638 GGAAAGTTTG
Statistics
Matches: 232, Mismatches: 29, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
56 4 0.02
57 77 0.33
58 82 0.35
59 69 0.30
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTTAGAAAGTTTGGGGTTAAAAATGTAATTTTTAGAAGTTCGAGGGT
Found at i:378647 original size:30 final size:30
Alignment explanation
Indices: 378419--378658 Score: 233
Period size: 30 Copynumber: 8.2 Consensus size: 30
378409 GTTCAAGGTC
378419 AAAAATGTAATTTTTAG-AAGTTT-GGGGT
1 AAAAATGTAATTTTTAGAAAGTTTGGGGGT
** **
378447 TTAAATGTAATTTTTA-AAAGTTTAAGGGT
1 AAAAATGTAATTTTTAGAAAGTTTGGGGGT
* * *
378476 AAAAATATAATTTTTGGAAAGTTTGGGGTT
1 AAAAATGTAATTTTTAGAAAGTTTGGGGGT
* *
378506 AAAAATGTAATTTTTAG-AAGTTCGAGGGT
1 AAAAATGTAATTTTTAGAAAGTTTGGGGGT
* * *
378535 -AAAATAG-AATTTTTGGAAAGTTCGAGGGT
1 AAAAAT-GTAATTTTTAGAAAGTTTGGGGGT
* *
378564 AAAAATGTAATTTTTTGAAAGTTTAGGGGT
1 AAAAATGTAATTTTTAGAAAGTTTGGGGGT
* *
378594 -AAAATGGAATTTTTAAAAAGTTTGGGGGT
1 AAAAATGTAATTTTTAGAAAGTTTGGGGGT
* * * *
378623 CAAAATGTAGTTTTTGGAAAGTTTGGGAGT
1 AAAAATGTAATTTTTAGAAAGTTTGGGGGT
*
378653 CAAAAT
1 AAAAAT
378659 ATGATTTCAG
Statistics
Matches: 175, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
28 33 0.19
29 64 0.37
30 78 0.45
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAAATGTAATTTTTAGAAAGTTTGGGGGT
Found at i:379799 original size:3 final size:3
Alignment explanation
Indices: 379793--379833 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
379783 TTCTTTTATT
*
379793 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TTAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T
379834 TATTACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:379838 original size:3 final size:3
Alignment explanation
Indices: 379832--379880 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
379822 ATAATTAATA
* *
379832 ATT ATT ACT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
379880 A
1 A
379881 AATATTGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:380548 original size:17 final size:17
Alignment explanation
Indices: 380526--380580 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
380516 GGACTTTTAA
*
380526 TAAATTTAAAATAATTT
1 TAAATTTAAAATAAATT
*
380543 TAAATTTAGAATAAATT
1 TAAATTTAAAATAAATT
*
380560 T-AATCTTAAAGTAAATT
1 TAAAT-TTAAAATAAATT
380577 TAAA
1 TAAA
380581 AGGGTTTGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 3 0.09
17 27 0.84
18 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:381241 original size:161 final size:161
Alignment explanation
Indices: 381056--381399 Score: 535
Period size: 161 Copynumber: 2.1 Consensus size: 161
381046 TCGACCTGCC
** *
381056 TCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCACATCGAGCTTGGCTTCATTGAT
1 TCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAAATTTGCTCACATCGAGCTTGGCTACATTGAT
* *
381121 TTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTG
66 TTGATCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTG
*
381186 TATCTCATCAGGAAGACGAATTTGGTCCACT
131 TATCTCATCAGGAAGACGAATCTGGTCCACT
* * ** *
381217 TCTCAATATCTCATCAGAAAGCTGGGGTTCGAAAATTTGCTCATTTTGAGCTTGGCTACATTGAT
1 TCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAAATTTGCTCACATCGAGCTTGGCTACATTGAT
* * *
381282 TTGATCTTCTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTGTTTCAATCCGCTTCTCTG
66 TTGATCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTG
* * *
381347 TGTCTCATCAGGAAGACGGATCTGGTTCACT
131 TATCTCATCAGGAAGACGAATCTGGTCCACT
381378 TCTCAGTATCTCATCAGGAAGC
1 TCTCAGTATCTCATCAGGAAGC
381400 AAACCATTTT
Statistics
Matches: 164, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
161 164 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (161 bp):
TCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAAATTTGCTCACATCGAGCTTGGCTACATTGAT
TTGATCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTG
TATCTCATCAGGAAGACGAATCTGGTCCACT
Found at i:381586 original size:370 final size:370
Alignment explanation
Indices: 380905--381609 Score: 1050
Period size: 370 Copynumber: 1.9 Consensus size: 370
380895 AGTCTGGTTT
* * *
380905 CATTGATTTGGCCTACTTCTCAGCATCTCATTAGGAAGATGACCGCATCACTTGTTTCAATCCGC
1 CATTGATTTGACCTACTTCTCAGCATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGC
* * * * *
380970 TTCTCTGTATCTCATTAGGAAGACAAATTTGATCCACTTCTCAGTATCTCATCAGGGAGCTAACT
66 TTCTCTGTATCTCATCAGGAAGACAAATCTGATCCACTTCTCAGTATCTCATCAGGAAGCAAACC
* * * *
381035 ATTTTATTGCTTCGACCTGCCTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGGTTTGCTCAC
131 ATTTTATTGCTTCAACCTGCCTCTCAGTACCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
* *
381100 ATCGAGCTTGGCTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCAC
196 ATCGAGCTTGGCTTCATTGATTTGGCCTTCTTCTCAATATCTCATCAAGAAGATGACCGCATCAC
**
381165 TTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCA
261 TTGTTACAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCA
381230 TCAGAAAGCTGGGGTTCGAAAATTTGCTCATTTTGAGCTTGGCTA
326 TCAGAAAGCTGGGGTTCGAAAATTTGCTCATTTTGAGCTTGGCTA
* * * * * *
381275 CATTGATTTGATCTTCTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTGTTTCAATCCGC
1 CATTGATTTGACCTACTTCTCAGCATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGC
* ** * *
381340 TTCTCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCAGTATCTCATCAGGAAGCAAACC
66 TTCTCTGTATCTCATCAGGAAGACAAATCTGATCCACTTCTCAGTATCTCATCAGGAAGCAAACC
* * * *
381405 ATTTTATTGCTTTAACTTGCTTCTCAGTACCTCATCAAGAAGTTGGGGTTCGAAGATTTGCTCAC
131 ATTTTATTGCTTCAACCTGCCTCTCAGTACCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
* * * * *
381470 TTTGAGCTTGGCTTTATTGATTTGGCCTTTTTCTCAATATCTCATCAGGAAGATGACCGCATCAC
196 ATCGAGCTTGGCTTCATTGATTTGGCCTTCTTCTCAATATCTCATCAAGAAGATGACCGCATCAC
* * *
381535 TTGTTACAATCTGCTTCTCTGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCA
261 TTGTTACAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCA
*
381600 TCAGGAAGCT
326 TCAGAAAGCT
381610 AACCATTTTA
Statistics
Matches: 295, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
370 295 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (370 bp):
CATTGATTTGACCTACTTCTCAGCATCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCGC
TTCTCTGTATCTCATCAGGAAGACAAATCTGATCCACTTCTCAGTATCTCATCAGGAAGCAAACC
ATTTTATTGCTTCAACCTGCCTCTCAGTACCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
ATCGAGCTTGGCTTCATTGATTTGGCCTTCTTCTCAATATCTCATCAAGAAGATGACCGCATCAC
TTGTTACAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCA
TCAGAAAGCTGGGGTTCGAAAATTTGCTCATTTTGAGCTTGGCTA
Found at i:381722 original size:209 final size:206
Alignment explanation
Indices: 381215--381748 Score: 692
Period size: 209 Copynumber: 2.5 Consensus size: 206
381205 ATTTGGTCCA
* * * *
381215 CTTCTCAATATCTCATC-AGAAAGCTGGGGTTCGAAAATTTGCTCATTTTGAGCTTGGCTACATT
1 CTTCTCAGTATCTCATCAAG-AAGTTGGGGTTCG-AAGTTTGCTCA-TTTGAGCTTGG-TTCATT
* * * *
381279 GATTTGATCTTCTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTGTTTCAATCCGCTTCT
62 GATTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTACAATCCGCTTCT
* * *
381344 CTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCAGTATCTCATCAGGAAGCAAACCATTT
127 CTGTATCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTCATCAGGAAGCAAACCATTT
* *
381409 TATTGCTTTAACTTG
192 TATTGCTTCAACCTG
* *
381424 CTTCTCAGTACCTCATCAAGAAGTTGGGGTTCGAAGATTTGCTCACTTTGAGCTTGGCTTTATTG
1 CTTCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAG-TTTGCTCA-TTTGAGCTTGG-TTCATTG
* * ** * *
381489 ATTTGGCCTTTTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTACAATCTGCTTCTC
63 ATTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTACAATCCGCTTCTC
* * *
381554 TGTATCTCATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTT
128 TGTATCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTCATCAGGAAGCAAACCATTTT
381619 ATTGCTTCAACCTG
193 ATTGCTTCAACCTG
* *
381633 CTTCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAGTTTCGCTCGTATTGAGCTTTGTTCCATTG
1 CTTCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAGTTT-GCTCAT-TTGAGCTTGGTT-CATTG
* * * * *
381698 AGTTGGTATACTTCTTTGTATCTCAACAGGAAGATGACCGCCTCACTTGTT
63 ATTTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTT
381749 TTGGGTAATC
Statistics
Matches: 281, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
208 8 0.03
209 271 0.96
210 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAGTTTGCTCATTTGAGCTTGGTTCATTGATT
TGGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTACAATCCGCTTCTCTGT
ATCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTCATCAGGAAGCAAACCATTTTATT
GCTTCAACCTG
Found at i:383906 original size:3 final size:3
Alignment explanation
Indices: 383898--383946 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
383888 GGTCATCACT
383898 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
383946 T
1 T
383947 ACCTCGATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:390982 original size:19 final size:19
Alignment explanation
Indices: 390960--391042 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 19
390950 ATTAGAAGTA
390960 TTGATATCCATTAAAAATT
1 TTGATATCCATTAAAAATT
* *
390979 TTGACATCCATT--AAATA
1 TTGATATCCATTAAAAATT
*
390996 TTGATATCGCCA-AAAAAATT
1 TTGATAT--CCATTAAAAATT
* * * *
391016 TCGGTGTCAATTAAAAATT
1 TTGATATCCATTAAAAATT
391035 TTGATATC
1 TTGATATC
391043 TCTTTTACTC
Statistics
Matches: 46, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
17 10 0.22
18 2 0.04
19 26 0.57
20 8 0.17
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (19 bp):
TTGATATCCATTAAAAATT
Found at i:394382 original size:6 final size:7
Alignment explanation
Indices: 394364--394388 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
394354 NNNNNNNNNN
394364 AGGGGGA
1 AGGGGGA
394371 AGGGGGA
1 AGGGGGA
394378 AGGGGGA
1 AGGGGGA
394385 AGGG
1 AGGG
394389 AAAGGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (7 bp):
AGGGGGA
Found at i:403598 original size:3 final size:3
Alignment explanation
Indices: 403590--403618 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
403580 TTTAGGGAAT
403590 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
403619 GTAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:416121 original size:29 final size:29
Alignment explanation
Indices: 416089--416168 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 29
416079 AAATGCAAAA
416089 AAAAAATATAAAAACTATTTTTAA-AAATT
1 AAAAAATATAAAAA-TATTTTTAATAAATT
*
416118 -AAAAATA-ATTAAAT-TTATTTAATAAATT
1 AAAAAATATA-AAAATATT-TTTAATAAATT
416146 ATAAAAATATAAAAAATATTTTT
1 A-AAAAATAT-AAAAATATTTTT
416169 TTATTTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
26 2 0.05
27 7 0.17
28 15 0.37
30 7 0.17
31 7 0.17
32 3 0.07
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAAAATATAAAAATATTTTTAATAAATT
Found at i:436973 original size:17 final size:18
Alignment explanation
Indices: 436953--436989 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
436943 CCACTCTCTC
436953 TTATTTTCAA-TTTTACT
1 TTATTTTCAATTTTTACT
*
436970 TTATTTTTAATTTTTACT
1 TTATTTTCAATTTTTACT
436988 TT
1 TT
436990 TGGAAGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTTCAATTTTTACT
Found at i:438220 original size:14 final size:15
Alignment explanation
Indices: 438201--438248 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
438191 TCAGTTGTAA
438201 TTAATTTAAAATT-T
1 TTAATTTAAAATTAT
438215 TTAATTAATTAAAATTAT
1 TTAA-T--TTAAAATTAT
*
438233 TTAATTAAAAATTAT
1 TTAATTTAAAATTAT
438248 T
1 T
438249 CTTATCCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.14
15 11 0.38
17 9 0.31
18 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATTTAAAATTAT
Found at i:438221 original size:18 final size:18
Alignment explanation
Indices: 438198--438240 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
438188 TTTTCAGTTG
438198 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
438216 TAATTAATTAAAATTATT
1 TAATTAATTAAAATTATT
438234 TAATTAA
1 TAATTAA
438241 AAATTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:440488 original size:16 final size:17
Alignment explanation
Indices: 440469--440515 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
440459 TTAATGCGAG
440469 TAATA-TTTAAAATAAA
1 TAATAGTTTAAAATAAA
*
440485 TAATATTTTATAAAT-AA
1 TAATAGTTTA-AAATAAA
440502 -AATAGTTTAAAATA
1 TAATAGTTTAAAATA
440516 GTATAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 6 0.22
18 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TAATAGTTTAAAATAAA
Found at i:440540 original size:11 final size:11
Alignment explanation
Indices: 440526--440550 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
440516 GTATAGAAAT
440526 TTAAAACTATA
1 TTAAAACTATA
440537 TTAAAACTATA
1 TTAAAACTATA
440548 TTA
1 TTA
440551 GAAAGTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAACTATA
Found at i:443066 original size:19 final size:20
Alignment explanation
Indices: 443044--443083 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
443034 AACTTTAGAG
* *
443044 ATTATTATTAA-AAATGATA
1 ATTATAATTAATAAAAGATA
443063 ATTATAATTAATAAAAGATA
1 ATTATAATTAATAAAAGATA
443083 A
1 A
443084 AAACACACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTATAATTAATAAAAGATA
Found at i:444911 original size:26 final size:27
Alignment explanation
Indices: 444879--444929 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
444869 ACAATTCAAC
444879 TATTTTTAAAAGATTGAGA-TCAAATA
1 TATTTTTAAAAGATTGAGAGTCAAATA
* * *
444905 TATTTTTTAATGGTTGAGAGTCAAA
1 TATTTTTAAAAGATTGAGAGTCAAA
444930 GTTAGCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (27 bp):
TATTTTTAAAAGATTGAGAGTCAAATA
Found at i:451322 original size:28 final size:28
Alignment explanation
Indices: 451282--451383 Score: 100
Period size: 28 Copynumber: 3.5 Consensus size: 28
451272 TTAAAATTAC
*
451282 AAAATTTATTAAAATTACTTAAAGTATAAA
1 AAAAATTA-TAAAATTACTTAAA-TATAAA
**
451312 AAAAA-TATAAAATTACAAAAATATTTAAA
1 AAAAATTATAAAATTACTTAAATA--TAAA
* *
451341 AAAAATTACAAAATTA-TTAAAAATAGAA
1 AAAAATTATAAAATTACTTAAATATA-AA
451369 AAAAATTATAAAATT
1 AAAAATTATAAAATT
451384 TTATGAAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
27 4 0.07
28 28 0.47
29 15 0.25
30 13 0.22
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAATTATAAAATTACTTAAATATAAA
Found at i:451348 original size:22 final size:21
Alignment explanation
Indices: 451320--451363 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
451310 AAAAAAATAT
451320 AAAATTACAAAAATATTTAAAA
1 AAAATTACAAAAATA-TTAAAA
*
451342 AAAATTACAAAATTATTAAAA
1 AAAATTACAAAAATATTAAAA
451363 A
1 A
451364 TAGAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATTACAAAAATATTAAAA
Done.