Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009374.1 Kokia drynarioides strain JFW-HI SEQ_124081, 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: 135424
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:149 original size:47 final size:47
Alignment explanation
Indices: 67--158 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 47
57 CATAATTGCA
* * * * *
67 TTGAAATTTAACACATTTGTCTCATCTATTTTACTTCTAATTGGGCT
1 TTGAAATTTAACACACTTGTATCATCAATTCTACTTCTAAATGGGCT
* * *
114 TTGAAATTTGACACACTTGTATTATCAATTCTACTTTTAAATGGG
1 TTGAAATTTAACACACTTGTATCATCAATTCTACTTCTAAATGGG
159 TGGTTAATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (47 bp):
TTGAAATTTAACACACTTGTATCATCAATTCTACTTCTAAATGGGCT
Found at i:697 original size:18 final size:17
Alignment explanation
Indices: 655--704 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
645 TCATGTCAGC
*
655 AAAAAA-AATTAAAGTT
1 AAAAAATAATTAAAATT
*
671 AAAACATAATTAAAATT
1 AAAAAATAATTAAAATT
688 AAAAAAATAATTTAAAA
1 -AAAAAATAA-TTAAAA
705 CACCCTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 8 0.29
19 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAAAATAATTAAAATT
Found at i:1249 original size:27 final size:28
Alignment explanation
Indices: 1216--1269 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
1206 GTCGAATTAA
1216 GGGATTTTGGTTAAGAG-TTTTGATTTG
1 GGGATTTTGGTTAAGAGTTTTTGATTTG
* * *
1243 GGGATTTTTGTTTAGGGTTTTTGATTT
1 GGGATTTTGGTTAAGAGTTTTTGATTT
1270 TGAGATCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (28 bp):
GGGATTTTGGTTAAGAGTTTTTGATTTG
Found at i:1264 original size:14 final size:15
Alignment explanation
Indices: 1233--1269 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1223 TGGTTAAGAG
*
1233 TTTTGATTTGGGGAT
1 TTTTGATTTAGGGAT
1248 TTTTG-TTTAGGG-T
1 TTTTGATTTAGGGAT
1261 TTTTGATTT
1 TTTTGATTT
1270 TGAGATCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 6 0.30
14 9 0.45
15 5 0.25
ACGTcount: A:0.11, C:0.00, G:0.27, T:0.62
Consensus pattern (15 bp):
TTTTGATTTAGGGAT
Found at i:1764 original size:21 final size:23
Alignment explanation
Indices: 1712--1776 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 23
1702 AATTATATTG
* *
1712 TTATTTTGGTGCTGTTTTGGT-TA
1 TTATTTT-TTGCTATTTTGGTGTA
1735 TTATTTTTTGCTATTTTGGTGT-
1 TTATTTTTTGCTATTTTGGTGTA
*
1757 TT-TTTTTTACTATTTTGGTG
1 TTATTTTTTGCTATTTTGGTG
1777 CTGTCTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 17 0.45
22 13 0.34
23 8 0.21
ACGTcount: A:0.09, C:0.05, G:0.20, T:0.66
Consensus pattern (23 bp):
TTATTTTTTGCTATTTTGGTGTA
Found at i:1807 original size:12 final size:12
Alignment explanation
Indices: 1790--1849 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
1780 TCTTTATTAT
1790 TATTTTTGTTGC
1 TATTTTTGTTGC
*
1802 TATTTTTCTAT--
1 TATTTTTGT-TGC
1813 TATTTTTGTTGC
1 TATTTTTGTTGC
* * *
1825 TGTTTTGGTTGT
1 TATTTTTGTTGC
*
1837 TATTTTGGTTGC
1 TATTTTTGTTGC
1849 T
1 T
1850 TGGATGTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 8 0.21
12 28 0.74
13 1 0.03
ACGTcount: A:0.08, C:0.07, G:0.18, T:0.67
Consensus pattern (12 bp):
TATTTTTGTTGC
Found at i:1813 original size:23 final size:23
Alignment explanation
Indices: 1787--1830 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1777 CTGTCTTTAT
1787 TATTATTTTTGTTGCTATTTTTC
1 TATTATTTTTGTTGCTATTTTTC
*
1810 TATTATTTTTGTTGCTGTTTT
1 TATTATTTTTGTTGCTATTTT
1831 GGTTGTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.70
Consensus pattern (23 bp):
TATTATTTTTGTTGCTATTTTTC
Found at i:2685 original size:22 final size:22
Alignment explanation
Indices: 2654--2734 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 22
2644 ATAACTTTAT
*
2654 ATTTTTAAAAAAATTTAAATTA
1 ATTTTAAAAAAAATTTAAATTA
2676 ATTTTAAAAAAAATTTAAAAATTTTA
1 ATTTTAAAAAAAATTT--AAA--TTA
*
2702 TATTTTAAAAAAATAATTTTAA-TA
1 -ATTTTAA-AAAA-AATTTAAATTA
2726 ATTTTAAAA
1 ATTTTAAAA
2735 TCATTTGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
22 17 0.34
23 7 0.14
24 5 0.10
26 3 0.06
27 9 0.18
28 4 0.08
29 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTTTAAAAAAAATTTAAATTA
Found at i:2702 original size:49 final size:50
Alignment explanation
Indices: 2624--2734 Score: 136
Period size: 49 Copynumber: 2.2 Consensus size: 50
2614 GATGATGATT
* * * * *
2624 ATAATTTTTAAATAATTTTAATAACTTTATATTTT-TAAAAA-AATTTAA
1 ATAATTTTAAAAAAAATTTAAAAACTTTATATTTTAAAAAAATAATTTAA
* *
2672 ATTAATTTTAAAAAAAATTTAAAAATTTTATATTTTAAAAAAATAATTTTA
1 A-TAATTTTAAAAAAAATTTAAAAACTTTATATTTTAAAAAAATAATTTAA
2723 ATAATTTTAAAA
1 ATAATTTTAAAA
2735 TCATTTGTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 1 0.02
49 29 0.55
50 16 0.30
51 7 0.13
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (50 bp):
ATAATTTTAAAAAAAATTTAAAAACTTTATATTTTAAAAAAATAATTTAA
Found at i:2731 original size:30 final size:27
Alignment explanation
Indices: 2622--2714 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
2612 ATGATGATGA
* * * * *
2622 TTATAATTTTTAAATAATTTTAATAACT
1 TTAT-ATTTTAAAAAAAATTTAAAAATT
*
2650 TTATATTTTTAAAAAAATTT--AAA--
1 TTATATTTTAAAAAAAATTTAAAAATT
2673 TTA-ATTTTAAAAAAAATTTAAAAATT
1 TTATATTTTAAAAAAAATTTAAAAATT
2699 TTATATTTTAAAAAAA
1 TTATATTTTAAAAAAA
2715 TAATTTTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
22 15 0.27
23 3 0.05
24 3 0.05
25 2 0.04
26 3 0.05
27 26 0.46
28 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATATTTTAAAAAAAATTTAAAAATT
Found at i:3243 original size:15 final size:14
Alignment explanation
Indices: 3225--3277 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
3215 CTACTTGGGT
3225 CAAATCTAATTGACC
1 CAAA-CTAATTGACC
***
3240 CAAACTAACTTGGGT
1 CAAACTAA-TTGACC
3255 CAAATCTAATTGACC
1 CAAA-CTAATTGACC
3270 CAAACTAA
1 CAAACTAA
3278 ACCTAAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
14 8 0.27
15 18 0.60
16 4 0.13
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (14 bp):
CAAACTAATTGACC
Found at i:3275 original size:30 final size:30
Alignment explanation
Indices: 3208--3277 Score: 124
Period size: 30 Copynumber: 2.3 Consensus size: 30
3198 CCTATTACAC
3208 CCCAAACCT-ACTTGGGTCAAATCTAATTGA
1 CCCAAA-CTAACTTGGGTCAAATCTAATTGA
3238 CCCAAACTAACTTGGGTCAAATCTAATTGA
1 CCCAAACTAACTTGGGTCAAATCTAATTGA
3268 CCCAAACTAA
1 CCCAAACTAA
3278 ACCTAAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.24
Consensus pattern (30 bp):
CCCAAACTAACTTGGGTCAAATCTAATTGA
Found at i:3896 original size:11 final size:11
Alignment explanation
Indices: 3880--3952 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 11
3870 TTGCATATTA
3880 AATAAATAATT
1 AATAAATAATT
*
3891 AATAAAATATTT
1 AAT-AAATAATT
*
3903 ATTAAATAAAATT
1 AATAAAT--AATT
3916 AAT-AATAA-T
1 AATAAATAATT
3925 AAT-AATATATT
1 AATAAATA-ATT
3936 AATAAAT-ATT
1 AATAAATAATT
3946 AAATAAA
1 -AATAAA
3953 AAAAAAAGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
9 8 0.16
10 6 0.12
11 17 0.33
12 15 0.29
13 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAAATAATT
Found at i:3943 original size:12 final size:12
Alignment explanation
Indices: 3874--3944 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
3864 CATTTGTTGC
3874 ATATTAAATAAAT
1 ATATT-AATAAAT
3887 A-ATTAATAAA-
1 ATATTAATAAAT
*
3897 ATATTTATTAAAT
1 ATA-TTAATAAAT
*
3910 AAAATTAAT-AAT
1 -ATATTAATAAAT
3922 A-A-TAAT-AAT
1 ATATTAATAAAT
3931 ATATTAATAAAT
1 ATATTAATAAAT
3943 AT
1 AT
3945 TAAATAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
9 8 0.17
10 3 0.06
11 12 0.25
12 18 0.38
13 5 0.10
14 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATTAATAAAT
Found at i:5022 original size:30 final size:29
Alignment explanation
Indices: 4972--5166 Score: 107
Period size: 30 Copynumber: 6.6 Consensus size: 29
4962 CCCAAAACTA
4972 TCCAAAAATTACCA--TTTTACCCTCGAATT
1 TCCAAAAATT-CCATTTTTTACCC-CGAATT
* *
5001 TCTAAAAATTCCATTTTTTACCCCGATTTT
1 TCCAAAAATTCCATTTTTTACCCCGA-ATT
*
5031 TCCAAAAATTACCA--TTTTACGCCCGATTTT
1 TCCAAAAATT-CCATTTTTTAC-CCCGA-ATT
* * *
5061 TCCAAAAATAACCA--TTTTACCCTCCAACT
1 TCCAAAAAT-TCCATTTTTTACCC-CGAATT
* * * **
5090 TCCAAAAATTCTATTTTTGACCCTGTTTCT
1 TCCAAAAATTCCATTTTTTACCCCGAAT-T
* * *
5120 TCCAAAAATTACCATTTTAT-CCCCGGATG
1 TCCAAAAATT-CCATTTTTTACCCCGAATT
* *
5149 TCTAAAAATTTCATTTTT
1 TCCAAAAATTCCATTTTT
5167 GCCCCCGAGT
Statistics
Matches: 130, Mismatches: 25, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
28 11 0.08
29 39 0.30
30 71 0.55
31 9 0.07
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.39
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTTACCCCGAATT
Found at i:5123 original size:89 final size:89
Alignment explanation
Indices: 4972--5138 Score: 255
Period size: 89 Copynumber: 1.9 Consensus size: 89
4962 CCCAAAACTA
* * * * *
4972 TCCAAAAATTACCATTTTACCCTCGAATTTCTAAAAATTCCATTTTTTACCCCGATTTTTCCAAA
1 TCCAAAAATAACCATTTTACCCTCCAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTCCAAA
5037 AATTACCATTTTACGCCCGATTTT
66 AATTACCATTTTACGCCCGATTTT
* *
5061 TCCAAAAATAACCATTTTACCCTCCAACTTCCAAAAATTCTATTTTTGACCCTG-TTTCTTCCAA
1 TCCAAAAATAACCATTTTACCCTCCAACTTCCAAAAATTCCATTTTTGACCCCGATTT-TTCCAA
5125 AAATTACCATTTTA
65 AAATTACCATTTTA
5139 TCCCCGGATG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
88 3 0.04
89 67 0.96
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (89 bp):
TCCAAAAATAACCATTTTACCCTCCAACTTCCAAAAATTCCATTTTTGACCCCGATTTTTCCAAA
AATTACCATTTTACGCCCGATTTT
Found at i:5171 original size:28 final size:30
Alignment explanation
Indices: 5123--5200 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 30
5113 TGTTTCTTCC
*
5123 AAAAATTACCATTTTATCCCCGGA-TGTCT
1 AAAAATTACCATTTTATCCCCCGAGTGTCT
*
5152 AAAAATT-TCATTTT-TGCCCCCGAGTGTCT
1 AAAAATTACCATTTTAT-CCCCCGAGTGTCT
5181 --AAATTACCATTTTA-CCCCCG
1 AAAAATTACCATTTTATCCCCCG
5201 GGTATCCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
27 12 0.29
28 18 0.43
29 12 0.29
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (30 bp):
AAAAATTACCATTTTATCCCCCGAGTGTCT
Found at i:8131 original size:6 final size:6
Alignment explanation
Indices: 8111--8184 Score: 55
Period size: 6 Copynumber: 12.7 Consensus size: 6
8101 ATTTTGAAAA
* ** *
8111 TAAATT T-ATTT TAAATT TAAATT T-GTTT TAAAATT TAAATT T-AATA
1 TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* * *
8157 TAAATT TATATT TATATT TATATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAA
8185 AATTATTATA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 11 0.20
6 40 0.74
7 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (6 bp):
TAAATT
Found at i:8146 original size:18 final size:17
Alignment explanation
Indices: 8098--8184 Score: 86
Period size: 17 Copynumber: 5.0 Consensus size: 17
8088 ATTTTAAAAT
*
8098 TTTATTTTGAAA-ATAAA
1 TTTATTTT-AAATTTAAA
8115 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
*
8132 TTTGTTTTAAAATTTAAA
1 TTTATTTT-AAATTTAAA
* * *
8150 TTTAATATAAATTTATA
1 TTTATTTTAAATTTAAA
*
8167 TTTATATTTATATTTAAA
1 TTTAT-TTTAAATTTAAA
8185 AATTATTATA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
16 3 0.05
17 31 0.54
18 23 0.40
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:8919 original size:15 final size:16
Alignment explanation
Indices: 8877--8938 Score: 56
Period size: 15 Copynumber: 4.0 Consensus size: 16
8867 ATATTTAGTC
*
8877 TTAATAAT-AATAATA
1 TTAATAATAAATATTA
* *
8892 TTGACAATAAATATTA
1 TTAATAATAAATATTA
* **
8908 TTATTAAT-AATAACA
1 TTAATAATAAATATTA
8923 TTAATAATAAATATTA
1 TTAATAATAAATATTA
8939 GCAATGAATA
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
15 18 0.53
16 16 0.47
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (16 bp):
TTAATAATAAATATTA
Found at i:8986 original size:21 final size:21
Alignment explanation
Indices: 8951--9012 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
8941 AATGAATAGC
*
8951 ATTAATAAGTATTAATAAGAAT
1 ATTAATAA-TATTAATAAAAAT
8973 ATTAATAATATTAATAAAAAT
1 ATTAATAATATTAATAAAAAT
* *
8994 ATCAATAATTTTAATAAAA
1 ATTAATAATATTAATAAAA
9013 GAAAATTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 29 0.78
22 8 0.22
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (21 bp):
ATTAATAATATTAATAAAAAT
Found at i:10172 original size:29 final size:29
Alignment explanation
Indices: 10141--10426 Score: 130
Period size: 29 Copynumber: 9.9 Consensus size: 29
10131 AAAAATTATA
10141 TTTTAACCCTCTAACTTTCCAAAATTCCAT
1 TTTTAACCC-CTAACTTTCCAAAATTCCAT
* * ** *
10171 TTTTGACCCCGATTTTTCCAAAAAATACCA-
1 TTTTAACCCCTAACTTTCC--AAAATTCCAT
*
10201 TTTT-ACCCTTGAAC-TTCCAAATATTCCAT
1 TTTTAACCCCT-AACTTTCCAAA-ATTCCAT
* * ** * *
10230 TTTTAACCTCGATTTTTCTAAAGATT--AC
1 TTTTAACCCCTAACTTTCCAAA-ATTCCAT
*
10258 TATT-ACCCCTAAAC-TTCCTAAAATTCCAT
1 TTTTAACCCCT-AACTTTCC-AAAATTCCAT
*
10287 TTTTAA-CCCTAATTTTTCCAAAAATTACCA-
1 TTTTAACCCCTAA-CTTTCC-AAAATT-CCAT
* *
10317 TTTTACCCCCAAACTTTCCAAAATTCCAT
1 TTTTAACCCCTAACTTTCCAAAATTCCAT
* ** *
10346 TTTTAACCCC--ATTTTTAAAAATTATCA-
1 TTTTAACCCCTAACTTTCCAAAATT-CCAT
* * * *
10373 TTTTACCCCCGAACTTTCAAAAATTTCAT
1 TTTTAACCCCTAACTTTCCAAAATTCCAT
* *
10402 TTTTGACCCC-AATTTTCCCAAAATT
1 TTTTAACCCCTAACTTT-CCAAAATT
10427 ATCATTTTAC
Statistics
Matches: 191, Mismatches: 43, Indels: 45
0.68 0.15 0.16
Matches are distributed among these distances:
27 32 0.17
28 28 0.15
29 69 0.36
30 46 0.24
31 16 0.08
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTTAACCCCTAACTTTCCAAAATTCCAT
Found at i:10227 original size:59 final size:57
Alignment explanation
Indices: 10128--10437 Score: 308
Period size: 59 Copynumber: 5.4 Consensus size: 57
10118 CCCTAAACTA
* *
10128 TCCAAAAATTA-TATTTTAACCCTCT-AACTTTCCAAAATTCCATTTTTGACCCCGATTTT
1 TCCAAAAATTACCATTTT-ACCC-CTAAAC-TTCCAAAATTCCATTTTTAACCCC-ATTTT
* * * *
10187 TCCAAAAAATACCATTTTACCCTTGAACTTCCAAATATTCCATTTTTAACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCCTAAACTTCCAAA-ATTCCATTTTTAACC-CCATTTT
* * * *
10246 TCTAAAGATTA-C-TATTACCCCTAAACTTCCTAAAATTCCATTTTTAACCCTAATTTT
1 TCCAAAAATTACCATTTTACCCCTAAACTTCC-AAAATTCCATTTTTAACCC-CATTTT
*
10303 TCCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCATTTT
1 TCCAAAAATTACCATTTTACCCCTAAAC-TTCCAAAATTCCATTTTTAACCCCATTTT
* ** * * * *
10361 T--AAAAATTATCATTTTACCCCCGAACTTTCAAAAATTTCATTTTTGACCCCAATTT
1 TCCAAAAATTACCATTTTACCCCTAAAC-TTCCAAAATTCCATTTTTAACCCCATTTT
* *
10417 TCCCAAAATTATCATTTTACC
1 TCCAAAAATTACCATTTTACC
10438 TCGGCTGCCT
Statistics
Matches: 216, Mismatches: 24, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
56 51 0.24
57 44 0.20
58 36 0.17
59 75 0.35
60 10 0.05
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (57 bp):
TCCAAAAATTACCATTTTACCCCTAAACTTCCAAAATTCCATTTTTAACCCCATTTT
Found at i:10482 original size:29 final size:29
Alignment explanation
Indices: 10141--10482 Score: 82
Period size: 29 Copynumber: 11.9 Consensus size: 29
10131 AAAAATTATA
* *
10141 TTTTAACCCTCTAACTTTCCAAAATTCCAT
1 TTTTAA-CCTCGAACTTCCCAAAATTCCAT
* * ** * *
10171 TTTTGACCCCGATTTTTCCAAAAAATACCA-
1 TTTTAACCTCGA-ACTTCC-CAAAATTCCAT
* *
10201 TTTTACCCTTGAACTT-CCAAATATTCCAT
1 TTTTAACCTCGAACTTCCCAAA-ATTCCAT
** * * *
10230 TTTTAACCTCGATTTTTCTAAAGATT--AC
1 TTTTAACCTCGAACTTCCCAAA-ATTCCAT
* * * *
10258 TATT-ACCCCTAAACTTCCTAAAATTCCAT
1 TTTTAACCTC-GAACTTCCCAAAATTCCAT
* * *
10287 TTTTAACC-CTAATTTTTCCAAAAATTACCA-
1 TTTTAACCTCGAA--CTTCCCAAAATT-CCAT
* * * *
10317 TTTTACCCCCAAACTTTCCAAAATTCCAT
1 TTTTAACCTCGAACTTCCCAAAATTCCAT
* * *** *
10346 TTTTAACC-C-CATTTTTAAAAATTATCA-
1 TTTTAACCTCGAACTTCCCAAAATT-CCAT
* * * * *
10373 TTTTACCCCCGAACTTTCAAAAATTTCAT
1 TTTTAACCTCGAACTTCCCAAAATTCCAT
* * * *
10402 TTTTGACC-CCAATTTTCCCAAAATTATCA-
1 TTTTAACCTCGAA-CTTCCCAAAATT-CCAT
* * *
10431 TTTT-ACCTCG-GCTGCCTAAAATTCCAT
1 TTTTAACCTCGAACTTCCCAAAATTCCAT
10458 TTTTAACCTCGAACTTCCCAAAATT
1 TTTTAACCTCGAACTTCCCAAAATT
10483 ATCATTTTGC
Statistics
Matches: 224, Mismatches: 64, Indels: 49
0.66 0.19 0.15
Matches are distributed among these distances:
26 2 0.01
27 40 0.18
28 42 0.19
29 80 0.36
30 46 0.21
31 14 0.06
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTTAACCTCGAACTTCCCAAAATTCCAT
Found at i:10490 original size:29 final size:29
Alignment explanation
Indices: 10363--10490 Score: 95
Period size: 29 Copynumber: 4.5 Consensus size: 29
10353 CCCATTTTTA
* * * *
10363 AAAATTATCATTTTACCCCCGAACTTTCA
1 AAAATTATCATTTTAACCTCGAACTTCCC
* * *
10392 AAAATT-TCATTTTTGACC-CCAATTTTCCC
1 AAAATTATCA-TTTTAACCTCGAA-CTTCCC
* * *
10421 AAAATTATCATTTT-ACCTCG-GCTGCCT
1 AAAATTATCATTTTAACCTCGAACTTCCC
*
10448 AAAATT-CCATTTTTAACCTCGAACTTCCC
1 AAAATTATCA-TTTTAACCTCGAACTTCCC
10477 AAAATTATCATTTT
1 AAAATTATCATTTT
10491 GCCCTCAAGT
Statistics
Matches: 75, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
26 2 0.03
27 13 0.17
28 15 0.20
29 40 0.53
30 5 0.07
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTATCATTTTAACCTCGAACTTCCC
Found at i:10496 original size:29 final size:29
Alignment explanation
Indices: 10363--10522 Score: 84
Period size: 29 Copynumber: 5.6 Consensus size: 29
10353 CCCATTTTTA
* * * *
10363 AAAATTATCATTTTACCCCCGAACTTTCA
1 AAAATTATCATTTTGCCCTCGAACTTCCC
*
10392 AAAATT-TCATTTTTGACCC-C-AATTTTCCC
1 AAAATTATCA-TTTTG-CCCTCGAA-CTTCCC
* * * *
10421 AAAATTATCATTTT-ACCTCG-GCTGCCT
1 AAAATTATCATTTTGCCCTCGAACTTCCC
* **
10448 AAAATT-CCATTTTTAACCTCGAACTTCCC
1 AAAATTATCA-TTTTGCCCTCGAACTTCCC
* *
10477 AAAATTATCATTTTGCCCTC-AAGTAT-CT
1 AAAATTATCATTTTGCCCTCGAACT-TCCC
*
10505 AAAATTACCATTTTGCCC
1 AAAATTATCATTTTGCCC
10523 CTGGGTATCC
Statistics
Matches: 101, Mismatches: 19, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
26 2 0.02
27 15 0.15
28 33 0.33
29 43 0.43
30 8 0.08
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAATTATCATTTTGCCCTCGAACTTCCC
Found at i:17692 original size:50 final size:50
Alignment explanation
Indices: 17497--17841 Score: 251
Period size: 50 Copynumber: 6.9 Consensus size: 50
17487 TTACAGGTCT
* * * * *
17497 CAGTTCCATGAAGATATGAAGGGAAAGATCTAATACCGCAATGGCGGATC
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGAATC
** * * * * *
17547 CAGTACCACAAAGATACA-AAAGGGAAAGGTCTAAG-TCACAACGGC-AAGAC
1 CAGTACCATGAAG--ACATGAAGGGAAAGATCTAAGACCGCAACGGCGAA-TC
* * * * *
17597 CGTGTACCTTAGAAGACACGAAGGGAAAGATTTAAG-CCGCAACGGTGAATC
1 C-AGTACCAT-GAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGAATC
* *
17648 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATC
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGAATC
** * * * *
17698 CAGTACCACAAAGATACA-AAAGGGAAAGGTCTAAG-TCGCAACGGCGGA-C
1 CAGTACCATGAAG--ACATGAAGGGAAAGATCTAAGACCGCAACGGCGAATC
* * *
17747 CGTGTACC-TCAGAAGACAAGAAGGGAAAGATTTAAGTA--GCAACGGCGAATC
1 C-AGTACCAT--GAAGACATGAAGGGAAAGATCTAAG-ACCGCAACGGCGAATC
* *
17798 CACTACCATGAAGACATGAAGGGAAAGATCTAAGACCACAACGG
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGG
17842 TAGATCCAAT
Statistics
Matches: 229, Mismatches: 46, Indels: 40
0.73 0.15 0.13
Matches are distributed among these distances:
48 1 0.00
49 52 0.23
50 103 0.45
51 63 0.28
52 10 0.04
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (50 bp):
CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGAATC
Found at i:17823 original size:150 final size:150
Alignment explanation
Indices: 17497--17975 Score: 690
Period size: 150 Copynumber: 3.2 Consensus size: 150
17487 TTACAGGTCT
* * * * *
17497 CAGTTCCATGAAGATATGAAGGGAAAGATCTAATACCGCAATGGCGGATCCAGTACCACAAAGAT
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACAAAGAT
* * * *
17562 ACAAAAGGGAAAGGTCTAAGTCACAACGGCAAGACCGTGTACCTTAGAAGACACGAAGGGAAAGA
66 ACAAAAGGGAAAGGTCTAAGTCGCAACGGC-GGACCGTGTACCTCAGAAGACAAGAAGGGAAAGA
*
17627 TTTAAGCCGCAACGGTGAATC
130 TTTAAGTCGCAACGGTGAATC
17648 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACAAAGAT
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACAAAGAT
17713 ACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGAT
66 ACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGAT
* *
17778 TTAAGTAGCAACGGCGAATC
131 TTAAGTCGCAACGGTGAATC
* * * *
17798 CACTACCATGAAGACATGAAGGGAAAGATCTAAGACCACAACGGTAGATCCAATACCACAAAGAT
1 CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACAAAGAT
* * * * *
17863 ACAAAAGGGAAAGGTTTAAGCCGCAATGGTGGACCGTGTACCTCAGAAGATAAGAAGGGAAAG-T
66 ACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGAT
* *
17927 CTTAAGTCGTAATGGTGAATC
131 -TTAAGTCGCAACGGTGAATC
* **
17948 CAGTACCACGAAGATTTGAAGGGGAAAG
1 CAGTACCATGAAGACATGAA-GGGAAAG
17976 GTTTAAGTCG
Statistics
Matches: 297, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
149 1 0.00
150 200 0.67
151 96 0.32
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.15
Consensus pattern (150 bp):
CAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATCCAGTACCACAAAGAT
ACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGAT
TTAAGTCGCAACGGTGAATC
Found at i:17954 original size:50 final size:50
Alignment explanation
Indices: 17600--17954 Score: 257
Period size: 50 Copynumber: 7.1 Consensus size: 50
17590 GCAAGACCGT
* *
17600 GTACCTTAGAAGACACGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCA
1 GTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCA
* * *
17650 GTA-C-CATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATCCA
1 GTACCTCA-GAAGACAAGAAGGGAAAGATTTAAG-CCGCAACGGTGAATCCA
* * * * * * *
17700 GTACCACA-AAGATACAA-AAGGGAAAGGTCTAAGTCGCAACGGCGGA-CCGT
1 GTACCTCAGAAG--ACAAGAAGGGAAAGATTTAAGCCGCAACGGTGAATCC-A
** *
17750 GTACCTCAGAAGACAAGAAGGGAAAGATTTAAGTAGCAACGGCGAATCCA
1 GTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCA
* * * *
17800 CTA-C-CATGAAGACATGAAGGGAAAGATCTAAGACCACAACGGT-AGATCCA
1 GTACCTCA-GAAGACAAGAAGGGAAAGATTTAAG-CCGCAACGGTGA-ATCCA
* * * * * *
17850 ATACCACA-AAGATACAA-AAGGGAAAGGTTTAAGCCGCAATGGTGGA-CCGT
1 GTACCTCAGAAG--ACAAGAAGGGAAAGATTTAAGCCGCAACGGTGAATCC-A
* * * *
17900 GTACCTCAGAAGATAAGAAGGGAAAG-TCTTAAGTCGTAATGGTGAATCCA
1 GTACCTCAGAAGACAAGAAGGGAAAGAT-TTAAGCCGCAACGGTGAATCCA
17950 GTACC
1 GTACC
17955 ACGAAGATTT
Statistics
Matches: 245, Mismatches: 37, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
48 3 0.01
49 61 0.25
50 130 0.53
51 41 0.17
52 10 0.04
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.15
Consensus pattern (50 bp):
GTACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCA
Found at i:18004 original size:50 final size:49
Alignment explanation
Indices: 17549--18004 Score: 206
Period size: 50 Copynumber: 9.1 Consensus size: 49
17539 GGCGGATCCA
* * * * **
17549 GTACCACA-AAGATACAAAAGGGAAAGGTCTAAGTCACAACGGCAAGACCG
1 GTACCACAGAAGATA-AGAAGGGAAAGGTTTAAGTCGCAATGGTGA-ACCG
** * * * * * *
17599 TGTACCTTAGAAGACACGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCA
1 -GTACCACAGAAGATAAGAAGGGAAAGGTTTAAGTCGCAATGGTGAA-CCG
* * * * * * * * *
17650 GTACCA-TGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGTGGATCCA
1 GTACCACAGAAGATAAGAAGGGAAAGGTTTAAG-TCGCAATGGT-GAACCG
* * * * *
17700 GTACCACA-AAGATACAAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCG
1 GTACCACAGAAGATA-AGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCG
* * * * * * *
17749 TGTACCTCAGAAGACAAGAAGGGAAAGATTTAAGTAGCAACGGCGAATCCA
1 -GTACCACAGAAGATAAGAAGGGAAAGGTTTAAGTCGCAATGGTGAA-CCG
* * * * * * * * * * *
17800 CTACCA-TGAAGACATGAAGGGAAAGATCTAAGACCACAACGGTAGATCCA
1 GTACCACAGAAGATAAGAAGGGAAAGGTTTAAG-TCGCAATGGT-GAACCG
* * * *
17850 ATACCACA-AAGATACAAAAGGGAAAGGTTTAAGCCGCAATGGTGGACCG
1 GTACCACAGAAGATA-AGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCG
* * *
17899 TGTACCTCAGAAGATAAGAAGGGAAA-GTCTTAAGTCGTAATGGTGAATCCA
1 -GTACCACAGAAGATAAGAAGGGAAAGGT-TTAAGTCGCAATGGTGAA-CCG
** *
17950 GTACCAC-GAAGATTTGAAGGGGAAAGGTTTAAGTCGCAATGGCGAACCCG
1 GTACCACAGAAGATAAGAA-GGGAAAGGTTTAAGTCGCAATGGTGAA-CCG
18000 GTACC
1 GTACC
18005 TTAGAAACAT
Statistics
Matches: 315, Mismatches: 71, Indels: 39
0.74 0.17 0.09
Matches are distributed among these distances:
49 63 0.20
50 167 0.53
51 80 0.25
52 5 0.02
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (49 bp):
GTACCACAGAAGATAAGAAGGGAAAGGTTTAAGTCGCAATGGTGAACCG
Found at i:18393 original size:195 final size:194
Alignment explanation
Indices: 18055--18533 Score: 733
Period size: 195 Copynumber: 2.5 Consensus size: 194
18045 TCAATATGAG
* * *
18055 CAAATCTTCGAACCCCAGGTTCCTGATGAGATACTGAGAAGCAGGGTGAAGCAATAAAAAAGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
* *
18120 GCTTCTTGATAAGATACGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGA
66 GCTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGA
* * * * *
18185 TTGAAATAAGTGAGGCAGTCATCTTCCTGATGAGATACAGAGACGTATGCTAACTCAAATGCGAA
131 TTGAAACAAGTGAGGCAGTCATCTTCCCGATGAGATACAGAGAAGTATACCAACTC-AATGCGAA
* * * * *
18250 CAAATCTTCGAACCCCAACTTCTTGATGAGAAACTAAGAAGCAGGGCGAAGCAATAAAATGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
* * * *
18315 GCTTCTTAATGAGATACTGAGAAGTGGACCAAATTCTTCTTCCTGATGAGGTACAGAGAAGCGGA
66 GCTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGA
* *
18380 TTGAAACAAGTGAGGCGGTCATCTTCCCGATGAGATATAGAGAAGTATACCAACTCAATGCGAA
131 TTGAAACAAGTGAGGCAGTCATCTTCCCGATGAGATACAGAGAAGTATACCAACTCAATGCGAA
* *
18444 CAAATCTTCGAACCCCAGCTTCCTGATGAGATGCTGAGAAGCAAGGCGAAGCAATAAAAAGGTTA
1 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
*
18509 GCTTCCTGATGAGATACAGAGAAGT
66 GCTTCTTGATGAGATACAGAGAAGT
18534 ATACCAACTC
Statistics
Matches: 254, Mismatches: 30, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
194 88 0.35
195 166 0.65
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (194 bp):
CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTA
GCTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGA
TTGAAACAAGTGAGGCAGTCATCTTCCCGATGAGATACAGAGAAGTATACCAACTCAATGCGAA
Found at i:18543 original size:108 final size:108
Alignment explanation
Indices: 18402--18641 Score: 408
Period size: 108 Copynumber: 2.2 Consensus size: 108
18392 AGGCGGTCAT
* *
18402 CTTCCCGATGAGATATAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCC
*
18467 TGATGAGATGCTGAGAAGCAAGGCGAAGCAATAAAAAGGTTAG
66 TGATGAGATACTGAGAAGCAAGGCGAAGCAATAAAAAGGTTAG
18510 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCC
1 CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCC
* * *
18575 TGATGAGATATTGAGAAGCAGGGCGAAGCAATAAAAATGTTAG
66 TGATGAGATACTGAGAAGCAAGGCGAAGCAATAAAAAGGTTAG
* *
18618 CTTCCTGATGAGACACTGAGAAGT
1 CTTCCTGATGAGATACAGAGAAGT
18642 GGACCAAATT
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 124 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (108 bp):
CTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCAGCTTCC
TGATGAGATACTGAGAAGCAAGGCGAAGCAATAAAAAGGTTAG
Found at i:18805 original size:201 final size:194
Alignment explanation
Indices: 18504--18891 Score: 562
Period size: 201 Copynumber: 2.0 Consensus size: 194
18494 GCAATAAAAA
18504 GGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCA
1 GGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCA
* *
18569 GCTTCCTGATGAGATATTGAGAAGCAGGGCGAAGCAATAAAAAT-GTTAGCTTCCTGATGAGACA
66 GCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAAT-AAAATGGTTAGCTTCCTGATGAAACA
* *
18633 CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAAGGGGGC
130 CTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCAGATTGAAACAAAGGGGGC
* * * * *
18698 GGTTATCTTCTTGATGAGATACAGAGAAGTATATCAACTCAGGGCTCGATGTGAGCAAATCTTCG
1 GGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCA-------ATGCGAACAAATCTTCG
* * * *
18763 AATCTCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTCTGAT
59 AACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAATGGTTAGCTTCCTGAT
* *
18828 GAAATACTGAGAAGTAGACCAAATTTGTCTTCCTGATGAGGTACAGAGAAGCAGATTGAAACAA
124 GAAACACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCAGATTGAAACAA
18892 GCGATGCGGT
Statistics
Matches: 171, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
194 38 0.22
200 5 0.03
201 128 0.75
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.24
Consensus pattern (194 bp):
GGTTAGCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCGAACAAATCTTCGAACCCCA
GCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAATGGTTAGCTTCCTGATGAAACAC
TGAGAAGTAGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCAGATTGAAACAAAGGGGGC
Found at i:19168 original size:17 final size:17
Alignment explanation
Indices: 19146--19254 Score: 110
Period size: 17 Copynumber: 6.2 Consensus size: 17
19136 ACTCATTTTA
* *
19146 AAATTTATTTTGAATAT
1 AAATTTATTTTAAATTT
19163 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
19180 AAATTTATTTTAAAATTT
1 AAATTTATTTT-AAATTT
* *
19198 AAATTTAATATAAATTT
1 AAATTTATTTTAAATTT
* *
19215 AGATTTGTATTTAAATTT
1 AAATTTAT-TTTAAATTT
* *
19233 AAAACTTATTATAAATATT
1 -AAATTTATTTTAAAT-TT
19252 AAA
1 AAA
19255 AGTCCAAAGA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
17 37 0.49
18 32 0.42
19 7 0.09
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:19182 original size:6 final size:6
Alignment explanation
Indices: 19162--19235 Score: 64
Period size: 6 Copynumber: 12.7 Consensus size: 6
19152 ATTTTGAATA
* * *
19162 TAAATT T-ATTT TAAATT TAAATT T-ATTT TAAAATT TAAATT T-AATA
1 TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT
* **
19208 TAAATT TAGATT TGTATT TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAA
19236 ACTTATTATA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
5 12 0.23
6 37 0.70
7 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:19291 original size:23 final size:24
Alignment explanation
Indices: 19264--19311 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
19254 AAGTCCAAAG
* *
19264 ATTACAAGCCCAAA-CAATATCCA
1 ATTACAAGACCAAATAAATATCCA
19287 ATTACAAGACCAAATAAATATCCA
1 ATTACAAGACCAAATAAATATCCA
19311 A
1 A
19312 ATGGTCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.52, C:0.25, G:0.04, T:0.19
Consensus pattern (24 bp):
ATTACAAGACCAAATAAATATCCA
Found at i:27872 original size:18 final size:18
Alignment explanation
Indices: 27849--27884 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27839 CATCTAATAC
*
27849 TGTTCCTTGTAATTATTT
1 TGTTCCTTGTAAATATTT
27867 TGTTCCTTGTAAATATTT
1 TGTTCCTTGTAAATATTT
27885 GGCAATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (18 bp):
TGTTCCTTGTAAATATTT
Found at i:28374 original size:49 final size:49
Alignment explanation
Indices: 28300--28917 Score: 375
Period size: 49 Copynumber: 12.7 Consensus size: 49
28290 CTACAAGTCT
* *
28300 CAGTACCACGAA-ACATGAAGGGAAAGATTTAAGCCGCAACAGTGAATC
1 CAGTACCAAGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * * *
28348 CAGTACCAAGAAGATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAA-C
1 CAGTACCAAGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * *
28396 CTAGTACCTTAGAAG-CATGAAGGGAAATATTTAAGCCGTAACAGCGAATC
1 C-AGTACC-AAGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * * * *
28446 CAGTACCAAGAAGATATGGAGGGAAAGGTTTAAG-CGACAACGGTGAA-C
1 CAGTACCAAGAAGACATGAAGGGAAAGATTTAAGCCG-CAACAGCGAATC
* * * *
28494 CGTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATC
1 C-AGTACC-AAGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
*
28544 CAGTACCACAG-AGACATGAAGGGAAAGATTTAAGCCTCAACAGCGAATC
1 CAGTACCA-AGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * * * *
28593 CAGTACCACA-AAGACATGAAGGGAAGGGTTTAAGTCGCAACGGC-AAAC
1 CAGTACCA-AGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * * * * *
28641 CTTGTACCTCAGAAG-CATGAAGGGAAATATCTAAGCCGTAAC-GACGGATC
1 C-AGTACC-AAGAAGACATGAAGGGAAAGATTTAAGCCGCAACAG-CGAATC
* * * * * * *
28691 CAGTACCGCAA-AGATACA-AAAAGGAAAGGTGTAAGTCGCAAC-GAC-AAAC
1 CAGTA-C-CAAGA-AGACATGAAGGGAAAGATTTAAGCCGCAACAG-CGAATC
* * * * **
28740 CTAGTACCTCAG-AGACATGAAGGGAAGGATCTAAGCCGCAACGGTTAATC
1 C-AGTACC-AAGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * * **
28790 CAGTACCACA-AAGACA-CAAGGGAAAG--GTAAGTCGCAATGGCGAA-C
1 CAGTACCA-AGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * * * *
28835 CTAGTACCTCA-AAGGCATGAAAGGGAAAGATTTAAGCCACAACGGCAAATC
1 C-AGTACC-AAGAAGACATG-AAGGGAAAGATTTAAGCCGCAACAGCGAATC
* * * *
28886 CAGTACTACGAAG--ATGAGGGGAAAGGTTTAAG
1 CAGTACCAAGAAGACATGAAGGGAAAGATTTAAG
28918 TCGTAATGGC
Statistics
Matches: 442, Mismatches: 90, Indels: 77
0.73 0.15 0.13
Matches are distributed among these distances:
45 2 0.00
46 25 0.06
47 14 0.03
48 54 0.12
49 267 0.60
50 75 0.17
51 5 0.01
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (49 bp):
CAGTACCAAGAAGACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATC
Found at i:28586 original size:147 final size:147
Alignment explanation
Indices: 28300--28952 Score: 434
Period size: 147 Copynumber: 4.5 Consensus size: 147
28290 CTACAAGTCT
* * * * * *
28300 CAGTACCACGAA-ACATGAAGGGAAAGATTTAAGCCGCAACAGTG-AATCC-AGTACC-AAGAAG
1 CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAAC-G-GCAAACCGTGTACCTCAGAAG
* * * * * ** *
28361 ATATGGAGGGAAAGGTTTAAGTCGCAACAGCGAA-CCTAGTACCTTAGAAGCATGAAGGGAAATA
64 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACAGAAGCATGAAGGGAAAGA
28425 TTTAAGCCGTAACAGCGAATC
127 TTTAAGCCGTAACAGCGAATC
* * **
28446 CAGTACCA-AGAAGATATGGAGGGAAAGGTTTAAG-CGACAACGGTGAACCGTGTACCTCAGAAG
1 CAGTACCACA-AAGACATGAAGGGAAAGGTTTAAGTCG-CAACGGCAAACCGTGTACCTCAGAAG
*
28509 CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACAG-AGACATGAAGGGAAAGAT
64 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAGAAG-CATGAAGGGAAAGAT
28573 TTAAGCC-TCAACAGCGAATC
128 TTAAGCCGT-AACAGCGAATC
* *
28593 CAGTACCACAAAGACATGAAGGGAAGGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAGAAGCA
1 CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAACCGTGTACCTCAGAAGCA
* * * * * * * * *
28658 TGAAGGGAAATATCTAAGCCGTAACGACGGATCCAGTACCGCA-AAG-ATACAAAAAGGAAAGGT
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAGAAGCAT---GAAGGGAAAGAT
* * * *
28721 GTAAGTCGCAAC-GAC-AAAC
128 TTAAGCCGTAACAG-CGAATC
* * * * * * * *
28740 CTAGTACCTCAGAGACATGAAGGG-AAGGATCTAAGCCGCAACGGTTAATCC-AGTACCACA-AA
1 C-AGTACCACAAAGACATGAAGGGAAAGG-TTTAAGTCGCAACGG-CAAACCGTGTACCTCAGAA
* * * * *
28802 GACA-CAAGGGAAAG--GTAAGTCGCAATGGCGAA-CCTAGTACCTCA-AAGGCATGAAAGGGAA
63 G-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACAGAA-GCATG-AAGGGAA
** * *
28862 AGATTTAAGCCACAACGGCAAATC
124 AGATTTAAGCCGTAACAGCGAATC
* * * * * * * * *
28886 CAGTACTACGAAG--ATGAGGGGAAAGGTTTAAGTCGTAATGGCGAACCCTATACCTCATAAGCA
1 CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAACCGTGTACCTCAGAAGCA
28949 TGAA
66 TGAA
28953 AAGAAATTTA
Statistics
Matches: 398, Mismatches: 78, Indels: 64
0.74 0.14 0.12
Matches are distributed among these distances:
142 3 0.01
143 26 0.07
144 11 0.03
145 52 0.13
146 25 0.06
147 207 0.52
148 70 0.18
149 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (147 bp):
CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCAAACCGTGTACCTCAGAAGCA
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAGAAGCATGAAGGGAAAGATTTA
AGCCGTAACAGCGAATC
Found at i:28634 original size:98 final size:99
Alignment explanation
Indices: 28300--28939 Score: 467
Period size: 98 Copynumber: 6.6 Consensus size: 99
28290 CTACAAGTCT
* * * * *
28300 CAGTACCACGAA-ACATGAAGGGAAAGATTTAAGCCGCAACAGTGAATCC-AGTACCA-AGAAGA
1 CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACCACAG-AGA
* * * * * *
28362 TATGGAGGGAAAGGTTTAAGTCGCAACAGCGAA-C
65 CATGAAGGGAAAGATTTAAGCCACAACGGCGAATC
** ** * * *
28396 CTAGTACCTTAGAAG-CATGAAGGGAAATATTTAAGCCGTAACAGCGAATCC-AGTACCA-AGAA
1 C-AGTACCACA-AAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACCACAG-A
* * * * *
28458 GATATGGAGGGAAAGGTTTAAGCGACAACGGTGAA-C
63 GACATGAAGGGAAAGATTTAAGCCACAACGGCGAATC
* * * * *
28494 CGTGTACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCC-AGTACCACAGAG
1 C-AGTACCACA-AAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACCACAGAG
* *
28557 ACATGAAGGGAAAGATTTAAGCCTCAACAGCGAATC
64 ACATGAAGGGAAAGATTTAAGCCACAACGGCGAATC
* * * *
28593 CAGTACCACAAAGACATGAAGGGAAGGGTTTAAGTCGCAACGGC-AAACCTTGTACCTCAGA-AG
1 CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACCACAGAGA-
* * ** * *
28656 CATGAAGGGAAATATCTAAGCCGTAACGACGGATC
65 CATGAAGGGAAAGATTTAAGCCACAACGGCGAATC
* * * * * * *
28691 CAGTACCGCAAAGATACA-AAAAGGAAAGGTGTAAGTCGCAACGAC-AAACCTAGTACCTCAGAG
1 CAGTACCACAAAG--ACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACCACAGAG
* * * **
28754 ACATGAAGGGAAGGATCTAAGCCGCAACGGTTAATC
64 ACATGAAGGGAAAGATTTAAGCCACAACGGCGAATC
* * * * *
28790 CAGTACCACAAAGACA-CAAGGGAAAGG--TAAGTCGCAATGGCGAA-CCTAGTACCTCAAAGGC
1 CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACCACAGAGAC
*
28851 ATGAAAGGGAAAGATTTAAGCCACAACGGCAAATC
66 ATG-AAGGGAAAGATTTAAGCCACAACGGCGAATC
* * * * * *
28886 CAGTACTACGAAG--ATGAGGGGAAAGGTTTAAGTCGTAATGGCGAACCCTA-TACC
1 CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACC
28940 TCATAAGCAT
Statistics
Matches: 455, Mismatches: 72, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
94 1 0.00
95 39 0.09
96 40 0.09
97 46 0.10
98 243 0.53
99 82 0.18
100 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (99 bp):
CAGTACCACAAAGACATGAAGGGAAAGGTTTAAGTCGCAACGGCGAATCCTAGTACCACAGAGAC
ATGAAGGGAAAGATTTAAGCCACAACGGCGAATC
Found at i:28759 original size:99 final size:97
Alignment explanation
Indices: 28513--28891 Score: 365
Period size: 99 Copynumber: 3.9 Consensus size: 97
28503 CAGAAGCATG
* * * * * * *
28513 AAGGGAAAGATTTAAGCCGCAACGGTGAATCC-AGTACCACAGAGACATGAAGGGAAAGATTTAA
1 AAGGGAAAGGTGTAAGTCGCAACGG-CAAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAA
*
28577 GCC-TCAAC-AGCGAATCCAGTACCACAAAGACATG
65 GCCGT-AACGA-CGAATCCAGTACCACAAAGACA-A
* * * *
28611 AAGGGAAGGGTTTAAGTCGCAACGGCAAACCTTGTACCTCAGA-AGCATGAAGGGAAATATCTAA
1 AAGGGAAAGGTGTAAGTCGCAACGGCAAACCTAGTACCTCAGAGA-CATGAAGGGAAAGATCTAA
* *
28675 GCCGTAACGACGGATCCAGTACCGCAAAGATACAA
65 GCCGTAACGACGAATCCAGTACCACAAAG--ACAA
* * *
28710 AAAGGAAAGGTGTAAGTCGCAACGACAAACCTAGTACCTCAGAGACATGAAGGGAAGGATCTAAG
1 AAGGGAAAGGTGTAAGTCGCAACGGCAAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAG
* *** *
28775 CCGCAACGGTTAATCCAGTACCACAAAGACAC
66 CCGTAACGACGAATCCAGTACCACAAAGACAA
* * * * *
28807 AAGGGAAA-G-GTAAGTCGCAATGGCGAACCTAGTACCTCAAAGGCATGAAAGGGAAAGATTTAA
1 AAGGGAAAGGTGTAAGTCGCAACGGCAAACCTAGTACCTCAGAGACATG-AAGGGAAAGATCTAA
** * *
28870 GCCACAACGGCAAATCCAGTAC
65 GCCGTAACGACGAATCCAGTAC
28892 TACGAAGATG
Statistics
Matches: 236, Mismatches: 37, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
95 33 0.14
96 33 0.14
97 15 0.06
98 71 0.30
99 80 0.34
100 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.15
Consensus pattern (97 bp):
AAGGGAAAGGTGTAAGTCGCAACGGCAAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAG
CCGTAACGACGAATCCAGTACCACAAAGACAA
Found at i:29828 original size:3 final size:3
Alignment explanation
Indices: 29820--29862 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
29810 CCCATACCAT
*
29820 TTA TTA TTA TTA TTG TTA TTA TTA TTA TT- TTCA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
29863 TAAAAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:29986 original size:15 final size:15
Alignment explanation
Indices: 29912--29986 Score: 51
Period size: 15 Copynumber: 5.4 Consensus size: 15
29902 TATTGCATAT
29912 TAAATAA-ATAATTAA
1 TAAATAATAT-ATTAA
*
29927 T-AA-AATAT-TTAT
1 TAAATAATATATTAA
29939 TAAATAA-A-ATTAA
1 TAAATAATATATTAA
29952 TAATTATAATA-A-TAA
1 TAA--ATAATATATTAA
29967 T-AATAATATATTAA
1 TAAATAATATATTAA
29981 TAAATA
1 TAAATA
29987 TTAAATAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 20
0.69 0.03 0.29
Matches are distributed among these distances:
12 10 0.21
13 12 0.25
14 11 0.23
15 13 0.27
16 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATAATATATTAA
Found at i:31340 original size:118 final size:118
Alignment explanation
Indices: 31078--31421 Score: 548
Period size: 118 Copynumber: 2.9 Consensus size: 118
31068 CCTTAAACTA
* * * * *
31078 TCCAAAAATTACCATTTTA-CCCTCAAATTTCTAAAAATTCTATTTTTTATCCTGATTTTTCCAA
1 TCCAAAAATTACCATTTTATCCCT-AAACTTCCAAAAATTCCATTTTTTACCCTGATTCTTCCAA
31142 AAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTTGACCTCGATTTT
65 AAATTACCATTTTACCCCCGAACTTCCAAAAATTCCA-TTTTTGACCTCGATTTT
* *
31197 TCCAAAAATTACCATTTTATCCCTAAACTTCCAAAAATTCCATTTTTGACCCTGATTCTTCTAAA
1 TCCAAAAATTACCATTTTATCCCTAAACTTCCAAAAATTCCATTTTTTACCCTGATTCTTCCAAA
31262 AATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGATTTT
66 AATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGATTTT
31315 TCCAAAAATTACCATTTTATCCCTAAACTTCCAAAAATTCCATTTTTTACCCTGATTCTTCCAAA
1 TCCAAAAATTACCATTTTATCCCTAAACTTCCAAAAATTCCATTTTTTACCCTGATTCTTCCAAA
* * * *
31380 AATTACCATTTGACCCTCGAA-TGTCTAAAAATTCTATTTTTG
66 AATTACCATTTTACCCCCGAACT-TCCAAAAATTCCATTTTTG
31422 CCCTTGAGTG
Statistics
Matches: 210, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
117 1 0.00
118 116 0.55
119 89 0.42
120 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (118 bp):
TCCAAAAATTACCATTTTATCCCTAAACTTCCAAAAATTCCATTTTTTACCCTGATTCTTCCAAA
AATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGATTTT
Found at i:31410 original size:59 final size:58
Alignment explanation
Indices: 31078--31420 Score: 440
Period size: 59 Copynumber: 5.8 Consensus size: 58
31068 CCTTAAACTA
* * *
31078 TCCAAAAATTACCATTTTACCCTCAAATTTCTAAAAATTCTATTTTTTATCCTGATTTT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTA-CCTGATTTT
* *
31137 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTTGACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTT-ACCT-GATTTT
* *
31197 TCCAAAAATTACCATTTTATCCCT-AAACTTCCAAAAATTCCATTTTTGACCCTGATTCT
1 TCCAAAAATTACCATTTTA-CCCTCAAACTTCCAAAAATTCCATTTTTTA-CCTGATTTT
* * * *
31256 TCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGATTTT
1 TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACCT-GATTTT
*
31315 TCCAAAAATTACCATTTTATCCCT-AAACTTCCAAAAATTCCATTTTTTACCCTGATTCT
1 TCCAAAAATTACCATTTTA-CCCTCAAACTTCCAAAAATTCCATTTTTTA-CCTGATTTT
* * * *
31374 TCCAAAAATTACCATTTGACCCTCGAA-TGTCTAAAAATTCTATTTTT
1 TCCAAAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTT
31421 GCCCTTGAGT
Statistics
Matches: 252, Mismatches: 22, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
58 11 0.04
59 181 0.72
60 57 0.23
61 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTTACCTGATTTT
Found at i:32906 original size:13 final size:14
Alignment explanation
Indices: 32883--32912 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
32873 TAGGGATTTA
32883 CAATATTACATAAT
1 CAATATTACATAAT
32897 CAAT-TTACATAAT
1 CAATATTACATAAT
32910 CAA
1 CAA
32913 ATCAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (14 bp):
CAATATTACATAAT
Found at i:33334 original size:180 final size:181
Alignment explanation
Indices: 33023--33388 Score: 565
Period size: 180 Copynumber: 2.0 Consensus size: 181
33013 TCCAAACTTC
* * * *
33023 AATCTAACATCCTTCTCCAACAACTCTTTGAATCGGGTTAACTCTCGTGGGTCAAATGAGCCTCA
1 AATCTAACAACCTTCTCCAACAACTCTTTGAATCAGGTTAACTCTCGTCGGTCAAATGAGCCCCA
33088 TCTAACTAATAGACCTTATTGGGACACATTTTATGCAATGGTCACAGGCTTTGAACTATGGCCCA
66 TCTAACTAATAGACCTTATTGGGACACATTTTATGCAATGGTCACAGGCTTTGAACTATGGCCCA
33153 TG-ATTTGTTCATGCATAAACAATGTTGAGAAACTTATGAACTAATTATTT
131 TGAATTTGTTCATGCATAAACAATGTTGAGAAACTTATGAACTAATTATTT
* *
33203 AATCTAACAACCTTCTTCAACAACTCTTTGAATCAGGTTAGCTCTCGTCGGTCAAATGAGCCCCA
1 AATCTAACAACCTTCTCCAACAACTCTTTGAATCAGGTTAACTCTCGTCGGTCAAATGAGCCCCA
* * * * * ** *
33268 TCTAATTGATAGACCTTCTTGGGACACATTTTGTGCAATTGTCATGGGCTTTGAACTGCT-GCCC
66 TCTAACTAATAGACCTTATTGGGACACATTTTATGCAATGGTCACAGGCTTTGAACT-ATGGCCC
*
33332 ATGACATTTGTTCATGCATAAACAATGTTGAGAAGCTTATGAACTAATTATTT
130 ATGA-ATTTGTTCATGCATAAACAATGTTGAGAAACTTATGAACTAATTATTT
33385 AATC
1 AATC
33389 CAAACAAGGT
Statistics
Matches: 168, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
180 116 0.69
181 1 0.01
182 51 0.30
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (181 bp):
AATCTAACAACCTTCTCCAACAACTCTTTGAATCAGGTTAACTCTCGTCGGTCAAATGAGCCCCA
TCTAACTAATAGACCTTATTGGGACACATTTTATGCAATGGTCACAGGCTTTGAACTATGGCCCA
TGAATTTGTTCATGCATAAACAATGTTGAGAAACTTATGAACTAATTATTT
Found at i:33913 original size:4 final size:4
Alignment explanation
Indices: 33906--33939 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
33896 AAAGAAAGTC
33906 TAAT TAAT TAAT TAAT TAAT TAAGCT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAA--T TAAT TAAT
33940 ACCTAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 24 0.86
6 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:37791 original size:31 final size:31
Alignment explanation
Indices: 37750--37814 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
37740 GTGCTCCACA
*
37750 TTTTTATATTTTTCGTACA-TTTAAAATTT-AG
1 TTTTTATATTTTT--TAAATTTTAAAATTTAAG
*
37781 TTTTTTTATTTTTTAAATTTTAAAATTTAAG
1 TTTTTATATTTTTTAAATTTTAAAATTTAAG
37812 TTT
1 TTT
37815 AATTGTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.10
30 10 0.33
31 17 0.57
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (31 bp):
TTTTTATATTTTTTAAATTTTAAAATTTAAG
Found at i:40390 original size:21 final size:21
Alignment explanation
Indices: 40364--40403 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40354 GCATGGATAT
*
40364 TTCTACCGATACTTAAATTAG
1 TTCTACCGATACTAAAATTAG
*
40385 TTCTACTGATACTAAAATT
1 TTCTACCGATACTAAAATT
40404 GACAGTGAGC
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:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCTACCGATACTAAAATTAG
Found at i:41173 original size:37 final size:36
Alignment explanation
Indices: 41132--41234 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 36
41122 ACAAAGCCTG
41132 CTAGGCACATAGCCCAAGTACACTGGCACGAAGCATA
1 CTAGGCACATAGCCCAA-TACACTGGCACGAAGCATA
* * * *
41169 CTAGGCACATAGCCTAAAAACACCGGCACGAAGCCTA
1 CTAGGCACATAGCC-CAATACACTGGCACGAAGCATA
* * *
41206 CTAGGTACATAACCTGAATACACTGGCAC
1 CTAGGCACATAGCC-CAATACACTGGCAC
41235 ATAGCTTGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 54 0.96
38 2 0.04
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (36 bp):
CTAGGCACATAGCCCAATACACTGGCACGAAGCATA
Found at i:41237 original size:58 final size:58
Alignment explanation
Indices: 41172--41300 Score: 143
Period size: 58 Copynumber: 2.2 Consensus size: 58
41162 AAGCATACTA
** * * *
41172 GGCACATAGCCTAAAAACACCGGCAC-GAAGCCTACTAGGTACATAACCTGAATACACT
1 GGCACATAGCCTAAAAACACCAACACAG-AGCCTACTAGGCACATAACCTAAATACACC
* * * **
41230 GGCACATAGCTTGAATACACCAACACAGAGCCTACTAGGCACATAGTCTAAATACACC
1 GGCACATAGCCTAAAAACACCAACACAGAGCCTACTAGGCACATAACCTAAATACACC
*
41288 GGCACAAAGCCTA
1 GGCACATAGCCTA
41301 CTAAGCACAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
58 56 0.98
59 1 0.02
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.16
Consensus pattern (58 bp):
GGCACATAGCCTAAAAACACCAACACAGAGCCTACTAGGCACATAACCTAAATACACC
Found at i:41284 original size:37 final size:37
Alignment explanation
Indices: 41230--41313 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
41220 TGAATACACT
* *
41230 GGCACATAGCTTGAATACACCAACACAGAGCCTACTA
1 GGCACATAGCTTAAATACACCAACACAAAGCCTACTA
**
41267 GGCACATAG-TCTAAATACACCGGCACAAAGCCTACTA
1 GGCACATAGCT-TAAATACACCAACACAAAGCCTACTA
*
41304 AGCACATAGC
1 GGCACATAGC
41314 CTGAATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 1 0.03
37 39 0.98
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.15
Consensus pattern (37 bp):
GGCACATAGCTTAAATACACCAACACAAAGCCTACTA
Found at i:46910 original size:28 final size:29
Alignment explanation
Indices: 46862--46933 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 29
46852 AAAGTTATAT
* *
46862 TTTGTTTAG-TAATTATTATTTTAAATT-A
1 TTTGTTTTGTTAATT-TAATTTTAAATTGA
*
46890 TTTGTTTTGTTAATTTAATTTTTAATTGA
1 TTTGTTTTGTTAATTTAATTTTAAATTGA
46919 TTT-TTTAT-TTAATTT
1 TTTGTTT-TGTTAATTT
46934 TTTTATTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 28 0.74
29 10 0.26
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTGTTTTGTTAATTTAATTTTAAATTGA
Found at i:47296 original size:47 final size:47
Alignment explanation
Indices: 47242--47336 Score: 129
Period size: 47 Copynumber: 2.0 Consensus size: 47
47232 GGTGTGGATA
* *
47242 CCATTTTGGTATATAAATATT-TATTTTGTATCATTTTGGTAAATAAT
1 CCATTTTGGTATATAAATATTAT-TTTTGTATCATATTGGTAAAAAAT
* * *
47289 CCATTTTGGTATTTAATTATTATTTTTGTATTATATTGGTAAAAAAT
1 CCATTTTGGTATATAAATATTATTTTTGTATCATATTGGTAAAAAAT
47336 C
1 C
47337 ATAAAAATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
47 41 0.98
48 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.52
Consensus pattern (47 bp):
CCATTTTGGTATATAAATATTATTTTTGTATCATATTGGTAAAAAAT
Found at i:48569 original size:43 final size:43
Alignment explanation
Indices: 48478--48571 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
48468 TTATTCATTG
* * * *
48478 ACATGTTATTAAATTATATTACTTGATTCATGTTAATATGGTT
1 ACATGTTACTAAATTATATTACTTGACTCATATTAATATGCTT
* *
48521 GCATGTTACTAAATTATATTACTTGACTCTTATTAATAT-CTT
1 ACATGTTACTAAATTATATTACTTGACTCATATTAATATGCTT
48563 AACATGTTA
1 -ACATGTTA
48572 TTAATTGTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.47
Consensus pattern (43 bp):
ACATGTTACTAAATTATATTACTTGACTCATATTAATATGCTT
Found at i:51951 original size:110 final size:110
Alignment explanation
Indices: 51755--51977 Score: 383
Period size: 110 Copynumber: 2.0 Consensus size: 110
51745 TAAAATCAGG
*
51755 TTGCCACCGTTTTCCTTCCTCTTTCATGGTTCATTATTTCCAGGAAACTCCTCCTTTAAATCACC
1 TTGCCACCGTTTTCCTTCCTCTTTCATGGTTCATTATTTCCAAGAAACTCCTCCTTTAAATCACC
* *
51820 AAACTCTTATACGATGTTTATGACCATTTTTCTTTTAATTAGGGT
66 AAACTCTTATACGATGATTATGACCATTTTTCTTTTAATTAAGGT
* * **
51865 TTGCCACTGTTTTCCTTCCTCTTTCATGGTTCATTATTTCCAAGAAATTCCTCCTTTAGTTCACC
1 TTGCCACCGTTTTCCTTCCTCTTTCATGGTTCATTATTTCCAAGAAACTCCTCCTTTAAATCACC
51930 AAACTCTTATACGATGATTATGACCATTTTTCTTTTAATTAAGGT
66 AAACTCTTATACGATGATTATGACCATTTTTCTTTTAATTAAGGT
51975 TTG
1 TTG
51978 GATGTGACAG
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 106 1.00
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (110 bp):
TTGCCACCGTTTTCCTTCCTCTTTCATGGTTCATTATTTCCAAGAAACTCCTCCTTTAAATCACC
AAACTCTTATACGATGATTATGACCATTTTTCTTTTAATTAAGGT
Found at i:60733 original size:31 final size:31
Alignment explanation
Indices: 60698--60763 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
60688 GTTACAAAAT
60698 AGTCACTAAATTA-TTCAAAAGTTTTCATTTA
1 AGTCACTAAATTATTTC-AAAGTTTTCATTTA
*
60729 AGTCACTAAATTATTTCAAAGTTTTTATTTA
1 AGTCACTAAATTATTTCAAAGTTTTCATTTA
60760 AGTC
1 AGTC
60764 GCTGGACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTCACTAAATTATTTCAAAGTTTTCATTTA
Found at i:61489 original size:16 final size:15
Alignment explanation
Indices: 61468--61499 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
61458 AATCACCATC
61468 TTTCTTCTTTTTTTTT
1 TTTCTT-TTTTTTTTT
61484 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
61499 T
1 T
61500 ATAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:61490 original size:13 final size:13
Alignment explanation
Indices: 61472--61499 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
61462 ACCATCTTTC
61472 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
61485 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
61498 TT
1 TT
61500 ATAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:65647 original size:23 final size:23
Alignment explanation
Indices: 65599--65648 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
65589 TAACTGTTTA
* **
65599 TATATTTATATAATTTTTAAATT
1 TATATATATATAATTTCAAAATT
65622 TATATATATAT-ATTTCAAAATAT
1 TATATATATATAATTTCAAAAT-T
65645 TATA
1 TATA
65649 GATTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATATATATAATTTCAAAATT
Found at i:65767 original size:18 final size:18
Alignment explanation
Indices: 65744--65778 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
65734 TTATTCAAAA
65744 TTTT-AATTTGGTTGATAG
1 TTTTAAATTTGG-TGATAG
65762 TTTTAAATTTGGTGATA
1 TTTTAAATTTGGTGATA
65779 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (18 bp):
TTTTAAATTTGGTGATAG
Found at i:68571 original size:20 final size:20
Alignment explanation
Indices: 68546--68583 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
68536 TTGAGAAAAT
*
68546 AAAAAAAAAAAGTATTATTG
1 AAAAAAAAAAAGCATTATTG
*
68566 AAAAAATAAAAGCATTAT
1 AAAAAAAAAAAGCATTAT
68584 GGTAAATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (20 bp):
AAAAAAAAAAAGCATTATTG
Found at i:72233 original size:34 final size:30
Alignment explanation
Indices: 72184--72249 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 30
72174 ATAAACCAAG
72184 AATCACAAAAACTCAAAAACACATTAATCAAAAC
1 AATCACAAAAACTC-AAAAC-CATTAA--AAAAC
* *
72218 AATCCCAAAAGCTCAAAACCATTAAAAAAC
1 AATCACAAAAACTCAAAACCATTAAAAAAC
72248 AA
1 AA
72250 CAGGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 7 0.23
32 6 0.20
33 5 0.17
34 12 0.40
ACGTcount: A:0.61, C:0.24, G:0.02, T:0.14
Consensus pattern (30 bp):
AATCACAAAAACTCAAAACCATTAAAAAAC
Found at i:77432 original size:57 final size:57
Alignment explanation
Indices: 77335--77450 Score: 146
Period size: 57 Copynumber: 2.0 Consensus size: 57
77325 AGAAATGGTG
* * *
77335 AAATGGAGAAATCGAAACATTTGGAAATGATTACGTTTTTCTCCAAAATGAAAAA-GA
1 AAATGGAGAAATCGAAACATTTGGAAATGAATACGGTTTTCACCAAAAT-AAAAATGA
* **
77392 AAATGGAGAAAT-GAAATTATTTGGAAATGAATGTGGTTTTCACCAAAATAAAAATGA
1 AAATGGAGAAATCGAAA-CATTTGGAAATGAATACGGTTTTCACCAAAATAAAAATGA
77449 AA
1 AA
77451 GACTTGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
56 9 0.18
57 42 0.82
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAATCGAAACATTTGGAAATGAATACGGTTTTCACCAAAATAAAAATGA
Found at i:78622 original size:21 final size:20
Alignment explanation
Indices: 78584--78722 Score: 89
Period size: 23 Copynumber: 6.1 Consensus size: 20
78574 ATACGGAACA
* *
78584 AACAGAGAGTATCAAAGTACT
1 AACAGAGAGCA-CAAAGTGCT
78605 AACAGAGAGCACATAAGTGCT
1 AACAGAGAGCACA-AAGTGCT
*
78626 GGGCAATAGAGAGCACACACAGTGCT
1 ----AACAGAGAGCACA-A-AGTGCT
*
78652 AAACAGAGAGTACACAAAGTACT
1 -AACAGAGAG--CACAAAGTGCT
78675 AATCAGAGAGCACACAAAGTGCT
1 AA-CAGAGAG--CACAAAGTGCT
78698 AATCAGAGAGCACACAAAGTGCT
1 AA-CAGAGAG--CACAAAGTGCT
78721 AA
1 AA
78723 TAACAGAGAG
Statistics
Matches: 100, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.02
21 16 0.16
22 2 0.02
23 56 0.56
24 1 0.01
25 17 0.17
26 6 0.06
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (20 bp):
AACAGAGAGCACAAAGTGCT
Found at i:78666 original size:23 final size:23
Alignment explanation
Indices: 78633--78735 Score: 143
Period size: 23 Copynumber: 4.4 Consensus size: 23
78623 GCTGGGCAAT
*
78633 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACAAAGTGCTAAAC
* * *
78656 AGAGAGTACACAAAGTACTAATC
1 AGAGAGCACACAAAGTGCTAAAC
*
78679 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAAAC
78702 AGAGAGCACACAAAGTGCTAATAAC
1 AGAGAGCACACAAAGTGCT-A-AAC
78727 AGAGAGCAC
1 AGAGAGCAC
78736 GAGACGTGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
23 59 0.83
24 1 0.01
25 11 0.15
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAAAC
Found at i:78683 original size:46 final size:47
Alignment explanation
Indices: 78633--78756 Score: 162
Period size: 46 Copynumber: 2.6 Consensus size: 47
78623 GCTGGGCAAT
*
78633 AGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT-C
1 AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATAC
* * *
78679 AGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATAAC
1 AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT-AC
* *
78727 AGAGAGCACGAGAC-GTGTTAAACAGAGAGC
1 AGAGAGCAC-ACACAGTGCTAAACAGAGAGC
78757 GCGCTAGTGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 41 0.61
48 24 0.36
49 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (47 bp):
AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATAC
Found at i:78706 original size:69 final size:67
Alignment explanation
Indices: 78583--78732 Score: 187
Period size: 69 Copynumber: 2.1 Consensus size: 67
78573 TATACGGAAC
* * *
78583 AAACAGAGAGTATCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAATAGAGAGCACACACAG
1 AAACAGAGAGTAACAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AATAGAGAGCACACAAAG
78648 TGCT-
63 TGCTA
78652 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAA
1 AAACAGAGAGTA-ACAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAAT-AGAGAGCACACAAA
78716 GTGCTA
62 GTGCTA
78722 ATAACAGAGAG
1 A-AACAGAGAG
78733 CACGAGACGT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 3 0.04
69 30 0.42
70 12 0.17
71 20 0.28
72 7 0.10
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTAACAAAGTACTAACAGAGAGCACAAAAGTGCTGAATAGAGAGCACACAAAGTGC
TA
Found at i:82433 original size:29 final size:32
Alignment explanation
Indices: 82377--82437 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
82367 AGAAAAAAAA
82377 TTGTAATGGTTGTATAATATTATATATTTAAAT
1 TTGTAATGGTTGTAT-ATATTATATATTTAAAT
82410 TTGTAATGGTTGTAT-T-TTA-ATATTTAAA
1 TTGTAATGGTTGTATATATTATATATTTAAA
82438 ATATAGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 9 0.32
30 3 0.11
31 1 0.04
33 15 0.54
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
TTGTAATGGTTGTATATATTATATATTTAAAT
Found at i:92947 original size:15 final size:15
Alignment explanation
Indices: 92929--92958 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
92919 TAGTTTTTTC
92929 AAAAATAATTATATT
1 AAAAATAATTATATT
*
92944 AAAAATGATTATATT
1 AAAAATAATTATATT
92959 TTGAAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AAAAATAATTATATT
Found at i:95106 original size:21 final size:22
Alignment explanation
Indices: 95080--95121 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
95070 AAGAAATATA
*
95080 TAAAAATAT-ATAAATATTTTT
1 TAAAAATATAATAAAAATTTTT
95101 TAAAAATATAATAAAAATTTT
1 TAAAAATATAATAAAAATTTT
95122 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAAATATAATAAAAATTTTT
Found at i:95558 original size:25 final size:24
Alignment explanation
Indices: 95517--95564 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
95507 ATAGGAGATT
95517 TTTATTTTATTTAATATTAATATA
1 TTTATTTTATTTAATATTAATATA
*
95541 TTTATATTTATTTCATATTAATAT
1 TTTAT-TTTATTTAATATTAATAT
95565 TACTGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATTTTATTTAATATTAATATA
Found at i:96742 original size:29 final size:28
Alignment explanation
Indices: 96688--96743 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
96678 AATATTACAG
*
96688 AAATAAATTAAAACCAAAATATCCAATC
1 AAATAAATTAAAACCAAAATAACCAATC
*
96716 AAATATAATTAAAACTAAACA-AACCAAT
1 AAATA-AATTAAAACCAAA-ATAACCAAT
96744 TTCCTTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 18 0.75
30 1 0.04
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.21
Consensus pattern (28 bp):
AAATAAATTAAAACCAAAATAACCAATC
Found at i:96916 original size:14 final size:16
Alignment explanation
Indices: 96891--96923 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
96881 AGGATATTGC
96891 AAAATAAAATATAA-G
1 AAAATAAAATATAATG
96906 AAAAT-AAATATAATG
1 AAAATAAAATATAATG
96921 AAA
1 AAA
96924 GTTTAAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAATAAAATATAATG
Found at i:97819 original size:30 final size:31
Alignment explanation
Indices: 97749--97819 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
97739 CTTTTTATTT
* * *
97749 TCCCTCAAAACTTTTACTTCCTCTCACTTTCC
1 TCCC-CAAAACTTTTACTTCCCCTCACATCCC
* *
97781 -CCCTAAAACTTTTA-TTCCCCTCCCATCCC
1 TCCCCAAAACTTTTACTTCCCCTCACATCCC
97810 TCCCCAAAAC
1 TCCCCAAAAC
97820 CTCCAAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
29 11 0.34
30 18 0.56
31 3 0.09
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (31 bp):
TCCCCAAAACTTTTACTTCCCCTCACATCCC
Found at i:102695 original size:10 final size:9
Alignment explanation
Indices: 102668--102705 Score: 58
Period size: 9 Copynumber: 4.0 Consensus size: 9
102658 AGTTGAGTCA
102668 AAATCTTTTT
1 AAAT-TTTTT
102678 GAAATTTTTT
1 -AAATTTTTT
102688 AAATTTTTT
1 AAATTTTTT
102697 AAATTTTTT
1 AAATTTTTT
102706 GTTGCATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.67
10 5 0.19
11 4 0.15
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (9 bp):
AAATTTTTT
Found at i:104372 original size:19 final size:20
Alignment explanation
Indices: 104348--104385 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104338 AATTATTTGT
104348 AAAATT-TAATTTAAATATA
1 AAAATTATAATTTAAATATA
*
104367 AAAATTATATTTTAAATAT
1 AAAATTATAATTTAAATAT
104386 TATTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTATAATTTAAATATA
Found at i:104671 original size:33 final size:33
Alignment explanation
Indices: 104633--104703 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
104623 TAATAAAAGT
*
104633 AAAATTATACTTTAACTCTCTAAAAATGATAAA
1 AAAATTATAATTTAACTCTCTAAAAATGATAAA
* * *
104666 AAAATTTTAATTTAATTCTTTAAAAATGATAAA
1 AAAATTATAATTTAACTCTCTAAAAATGATAAA
*
104699 GAAAT
1 AAAAT
104704 AAACTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (33 bp):
AAAATTATAATTTAACTCTCTAAAAATGATAAA
Found at i:109688 original size:24 final size:24
Alignment explanation
Indices: 109655--109710 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
109645 ATACTCCACT
109655 CACCACCATCCACTTCCTTCCCCA
1 CACCACCATCCACTTCCTTCCCCA
*
109679 TACCACCATCCACTTCCTTCCCCA
1 CACCACCATCCACTTCCTTCCCCA
109703 CACCACCA
1 CACCACCA
109711 CTGAAAATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.23, C:0.57, G:0.00, T:0.20
Consensus pattern (24 bp):
CACCACCATCCACTTCCTTCCCCA
Found at i:109769 original size:33 final size:34
Alignment explanation
Indices: 109680--109776 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 34
109670 CCTTCCCCAT
*
109680 ACCACCATCCACTTCCTTCCCCACACCACCACTG
1 ACCACCATCCACTTCCTTCCCCACACCACCACTC
* * *
109714 A--A-AATCC-C-TCAACCTCTCCACACC-CCACTC
1 ACCACCATCCACTTC--CTTCCCCACACCACCACTC
109744 ACCACCATCCACTTCCTTCCCCACACCACCACT
1 ACCACCATCCACTTCCTTCCCCACACCACCACT
109777 AAAAAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
29 2 0.04
30 7 0.15
31 14 0.29
32 2 0.04
33 14 0.29
34 7 0.15
35 2 0.04
ACGTcount: A:0.26, C:0.56, G:0.01, T:0.18
Consensus pattern (34 bp):
ACCACCATCCACTTCCTTCCCCACACCACCACTC
Found at i:112066 original size:52 final size:52
Alignment explanation
Indices: 111986--112172 Score: 275
Period size: 52 Copynumber: 3.6 Consensus size: 52
111976 AAATGAAAAA
*
111986 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
* * *
112038 AGGTCTGATGACTACGTGTCATCATGAGTATATGAATCCTTTATGAATTGTG
1 AGGTCCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
* * * * *
112090 AGGTCCGATAACTACTTGTCATCGTGAGTATACGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
* *
112142 AGGTCTGATGACTATGTGTCATCATGAGTAT
1 AGGTCCGATGACTACGTGTCATCATGAGTAT
112173 TAAACGAAAT
Statistics
Matches: 118, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACGAATTATG
Found at i:114214 original size:16 final size:18
Alignment explanation
Indices: 114187--114220 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
114177 ATTTTCATTT
114187 ATTTATTATAA-TAAATA
1 ATTTATTATAATTAAATA
114204 ATTTA-TATAATTAAATA
1 ATTTATTATAATTAAATA
114221 TAAATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTATTATAATTAAATA
Found at i:124038 original size:30 final size:30
Alignment explanation
Indices: 124003--124075 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
123993 ATGCTTCATT
124003 GTATCGGTAGAACTCTGAGGGTTTCATTTG
1 GTATCGGTAGAACTCTGAGGGTTTCATTTG
124033 GTATCGGTAGAACTCTGAGGGTTTCATTTG
1 GTATCGGTAGAACTCTGAGGGTTTCATTTG
124063 GTATCGGTAGAAC
1 GTATCGGTAGAAC
124076 CCATCAAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (30 bp):
GTATCGGTAGAACTCTGAGGGTTTCATTTG
Found at i:124163 original size:21 final size:21
Alignment explanation
Indices: 124137--124189 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
124127 TTGACTTATT
* *
124137 TCGGTAGAAGTCTTCAAGGTA
1 TCGGTAGAAGTCATCAAAGTA
**
124158 TCGGTAGAACCCATCAAAGTA
1 TCGGTAGAAGTCATCAAAGTA
*
124179 TCGATAGAAGT
1 TCGGTAGAAGT
124190 ACTTTTGAGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
TCGGTAGAAGTCATCAAAGTA
Found at i:125290 original size:40 final size:41
Alignment explanation
Indices: 125213--125307 Score: 131
Period size: 40 Copynumber: 2.3 Consensus size: 41
125203 GAATTTTATT
* *
125213 TTAACAAGAATTTTAGTTACCTAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCTAATTCTAACAATCTCCACC
*
125254 TTAACAAGAATTCTAGTCATCC-AA-TCTAATAATCTCCACC
1 TTAACAAGAATTCTAGTCA-CCTAATTCTAACAATCTCCACC
*
125294 TTGACAAGAATTCT
1 TTAACAAGAATTCT
125308 CTACGAACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 28 0.57
41 19 0.39
42 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCTAATTCTAACAATCTCCACC
Found at i:125319 original size:17 final size:17
Alignment explanation
Indices: 125297--125335 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
125287 CTCCACCTTG
* *
125297 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
125314 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
125331 ACAAG
1 ACAAG
125336 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:135219 original size:33 final size:33
Alignment explanation
Indices: 135182--135261 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
135172 TCATCACAAG
* *
135182 TGATTGGAACATCTATCAGCT-CCACTTCATTAA
1 TGATTGGAACATCTATCAG-TGCAACTTCATCAA
*
135215 TGATTGGAACATCTATCAGTGCAACTTCATCAT
1 TGATTGGAACATCTATCAGTGCAACTTCATCAA
*
135248 TGATTCGAACATCT
1 TGATTGGAACATCT
135262 CTCAAGGCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.02
33 41 0.98
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGTGCAACTTCATCAA
Done.