Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019019.1 Corchorus olitorius cultivar O-4 contig19052, 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: 95710
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:285 original size:13 final size:13
Alignment explanation
Indices: 267--291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
257 AATTTTTCAG
267 TAATTACTGTAAC
1 TAATTACTGTAAC
280 TAATTACTGTAA
1 TAATTACTGTAA
292 ATTTGATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
TAATTACTGTAAC
Found at i:986 original size:2 final size:2
Alignment explanation
Indices: 979--1023 Score: 65
Period size: 2 Copynumber: 22.0 Consensus size: 2
969 CACTTGGTGG
979 TA TA TA TA TA TA TA TA TA TA TA CTA GT- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA TA TA TA TA
1022 TA
1 TA
1024 CTAATTTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.90
3 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1013 original size:23 final size:23
Alignment explanation
Indices: 983--1026 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
973 TGGTGGTATA
983 TATATATATATATATATACTAGT
1 TATATATATATATATATACTAGT
1006 TATATATATATATATATACTA
1 TATATATATATATATATACTA
1027 ATTTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
TATATATATATATATATACTAGT
Found at i:2127 original size:11 final size:11
Alignment explanation
Indices: 2111--2147 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
2101 CTAGCCCTAA
2111 AAAACTAGAAG
1 AAAACTAGAAG
2122 AAAACTAGAAG
1 AAAACTAGAAG
2133 AAAACTAGAAG
1 AAAACTAGAAG
2144 AAAA
1 AAAA
2148 GAAATTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:2769 original size:19 final size:18
Alignment explanation
Indices: 2736--2771 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2726 TTGAAATAGA
2736 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
2754 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
2772 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:3485 original size:21 final size:24
Alignment explanation
Indices: 3441--3520 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 24
3431 TATCTTAGAT
*
3441 ATAATATATATTATTAAATAAATA
1 ATAATATATATTACTAAATAAATA
3465 ATAA-ATATATT-CTAAAT-AAT-
1 ATAATATATATTACTAAATAAATA
*
3485 A-AATA-ATGAGTT-CAAAATAAATAA
1 ATAATATAT-A-TTACTAAATAAAT-A
3509 ATAATATATATT
1 ATAATATATATT
3521 TAATTACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 10 0.22
22 8 0.17
23 7 0.15
24 7 0.15
25 5 0.11
26 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (24 bp):
ATAATATATATTACTAAATAAATA
Found at i:3801 original size:35 final size:35
Alignment explanation
Indices: 3749--3829 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
3739 GCTCTTAAAC
* * *
3749 TCTCAAAACACCTTAATACCCTATTGAG-TTCAGTA
1 TCTCCAAACACCATAATACCCTACTG-GCTTCAGTA
*
3784 TCTCCAAACACCATAATACCCTACTGGCTTTAGTA
1 TCTCCAAACACCATAATACCCTACTGGCTTCAGTA
*
3819 TCTCCGAACAC
1 TCTCCAAACAC
3830 GTTTAGATCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 1 0.03
35 39 0.98
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.28
Consensus pattern (35 bp):
TCTCCAAACACCATAATACCCTACTGGCTTCAGTA
Found at i:11153 original size:37 final size:37
Alignment explanation
Indices: 11068--11211 Score: 139
Period size: 38 Copynumber: 3.9 Consensus size: 37
11058 TCGAGTCTAG
* * *
11068 CCAACAG-ATAACCCCTAAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACTCCTGAGGCACGGGTCCACTCTTA
* * *
11104 CCAACAGTTTAACTTCCTGAGGCATGGGTCCACAC-AA
1 CCAACAGTTTAAC-TCCTGAGGCACGGGTCCACTCTTA
* * * *
11141 CCAACAATTTAACCCCCGAGGCACGGGTCCATTCTTA
1 CCAACAGTTTAACTCCTGAGGCACGGGTCCACTCTTA
* * *
11178 CCATCAGTTTAACCTCCTGAGGCATGAGTCCACT
1 CCAACAGTTTAA-CTCCTGAGGCACGGGTCCACT
11212 ATTGCACAAC
Statistics
Matches: 84, Mismatches: 20, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
36 23 0.27
37 28 0.33
38 33 0.39
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (37 bp):
CCAACAGTTTAACTCCTGAGGCACGGGTCCACTCTTA
Found at i:14345 original size:29 final size:30
Alignment explanation
Indices: 14291--14360 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
14281 ACAAATGGTG
*
14291 AAATAAGTCCCTGAACTTCAATTTTA-GCC
1 AAATAAGTCCCTGAACTCCAATTTTAGGCC
14320 AAATAAGAT-CCTGAACTACCAA-TTTAGGCC
1 AAATAAG-TCCCTGAACT-CCAATTTTAGGCC
*
14350 AGATAAG-CCCT
1 AAATAAGTCCCT
14361 TTTGTTATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (30 bp):
AAATAAGTCCCTGAACTCCAATTTTAGGCC
Found at i:16531 original size:2 final size:2
Alignment explanation
Indices: 16524--16550 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16514 ACTCATGATA
16524 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16551 CTAAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17807 original size:32 final size:32
Alignment explanation
Indices: 17746--17827 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
17736 TAGGCGCGGG
*
17746 GGCGCCCCCCGGGGACGCCTCCACCGTGGTGA
1 GGCGCCCCACGGGGACGCCTCCACCGTGGTGA
* *
17778 GGCGCCCCAC-GGGACGCCTCC-CTTTGTGGTGG
1 GGCGCCCCACGGGGACGCCTCCAC--CGTGGTGA
17810 GGCG-CCCACGGGGACGCC
1 GGCGCCCCACGGGGACGCC
17828 CTCTGAGGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 1 0.02
31 16 0.36
32 27 0.61
ACGTcount: A:0.09, C:0.41, G:0.39, T:0.11
Consensus pattern (32 bp):
GGCGCCCCACGGGGACGCCTCCACCGTGGTGA
Found at i:17907 original size:31 final size:31
Alignment explanation
Indices: 17819--17937 Score: 175
Period size: 31 Copynumber: 3.7 Consensus size: 31
17809 GGGCGCCCAC
*
17819 GGGGACGCCCTCTGAGGATGCCTCCCACCGTGGT
1 GGGG-CGCCCTCTG-GGACGCCT-CCACCGTGGT
* *
17853 GGGGCGCTCTATGGGAACGCCTCCACCGTGGT
1 GGGGCGCCCTCTGGG-ACGCCTCCACCGTGGT
17885 GGGGCGCCCTCTGGGACGCCTCCACCGTGGT
1 GGGGCGCCCTCTGGGACGCCTCCACCGTGGT
17916 GGGGCGCCCTCTGGGACGCCTC
1 GGGGCGCCCTCTGGGACGCCTC
17938 TGCGCCTAGA
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
31 38 0.48
32 25 0.32
33 12 0.15
34 4 0.05
ACGTcount: A:0.09, C:0.36, G:0.38, T:0.17
Consensus pattern (31 bp):
GGGGCGCCCTCTGGGACGCCTCCACCGTGGT
Found at i:20373 original size:18 final size:17
Alignment explanation
Indices: 20350--20384 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20340 ATCCCAATCC
*
20350 AACTATTGTTATGATTTA
1 AACTATGGTTAT-ATTTA
20368 AACTATGGTTATATTTA
1 AACTATGGTTATATTTA
20385 CTAGGGAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (17 bp):
AACTATGGTTATATTTA
Found at i:21698 original size:23 final size:24
Alignment explanation
Indices: 21666--21728 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 24
21656 CACAATTGCT
21666 TGGCGCCCGACCACTTCCA-AAC-C
1 TGGCG-CCGACCACTTCCATAACGC
21689 TGGCGACCGACCACTTCCATAACGC
1 TGGCG-CCGACCACTTCCATAACGC
21714 -GGCGCTCGACCACTT
1 TGGCGC-CGACCACTT
21729 GTGACCACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 19 0.53
24 16 0.44
25 1 0.03
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.16
Consensus pattern (24 bp):
TGGCGCCGACCACTTCCATAACGC
Found at i:21871 original size:26 final size:27
Alignment explanation
Indices: 21810--21877 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
21800 AACCAGCTGG
*
21810 CACC-CCACACGTGACCTCCAAACGTA
1 CACCTCCACACGTGACCTCCAAACGGA
21836 CGACCT-CACACGTGACCTCC-AACGGA
1 C-ACCTCCACACGTGACCTCCAAACGGA
*
21862 CACCTCCACATGTGAC
1 CACCTCCACACGTGAC
21878 ATCGCGCGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 4 0.11
26 16 0.43
27 17 0.46
ACGTcount: A:0.28, C:0.44, G:0.15, T:0.13
Consensus pattern (27 bp):
CACCTCCACACGTGACCTCCAAACGGA
Found at i:23179 original size:54 final size:54
Alignment explanation
Indices: 23099--23204 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
23089 TTCTTTTGAC
* *
23099 GAGATGAGCTTAAAGACCATCCATGAAATGCTAGAAGCCTATATTATTGGGTAT
1 GAGATGAGCCTAAAGACCATCCATGAAAGGCTAGAAGCCTATATTATTGGGTAT
* * * *
23153 GAGATGGGCCTAAAGGCCATCCATGAAAGGCTAGAAGCCTCTATTGTTGGGT
1 GAGATGAGCCTAAAGACCATCCATGAAAGGCTAGAAGCCTATATTATTGGGT
23205 TATATTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (54 bp):
GAGATGAGCCTAAAGACCATCCATGAAAGGCTAGAAGCCTATATTATTGGGTAT
Found at i:27180 original size:15 final size:17
Alignment explanation
Indices: 27160--27203 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
27150 AATTTTGGGT
*
27160 ACCCGAATCC-AAAA-G
1 ACCCGAACCCGAAAATG
27175 ACCCGAACCCGAAAATG
1 ACCCGAACCCGAAAATG
*
27192 ACCCAAACCCGA
1 ACCCGAACCCGA
27204 TCAACCCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.36
16 4 0.16
17 12 0.48
ACGTcount: A:0.43, C:0.39, G:0.14, T:0.05
Consensus pattern (17 bp):
ACCCGAACCCGAAAATG
Found at i:28178 original size:2 final size:2
Alignment explanation
Indices: 28167--28210 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
28157 GAAAGTCTAT
28167 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28207 TA TA
1 TA TA
28211 AATCAGAGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28944 original size:14 final size:15
Alignment explanation
Indices: 28911--28953 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
28901 AAATTTTCTT
28911 AACCCGAAACTAATCC
1 AACCC-AAACTAATCC
*
28927 AACCCAAAC-AATCG
1 AACCCAAACTAATCC
28941 AACCCAAATCTAA
1 AACCCAAA-CTAA
28954 CCCTACCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 5 0.21
16 7 0.29
ACGTcount: A:0.49, C:0.35, G:0.05, T:0.12
Consensus pattern (15 bp):
AACCCAAACTAATCC
Found at i:31648 original size:7 final size:7
Alignment explanation
Indices: 31636--31669 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
31626 GGTATGCAAA
31636 TTTTGAC
1 TTTTGAC
31643 TTTTGAC
1 TTTTGAC
31650 TTTTGAC
1 TTTTGAC
31657 TTTTGAC
1 TTTTGAC
31664 TTTTGA
1 TTTTGA
31670 AGAATGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.59
Consensus pattern (7 bp):
TTTTGAC
Found at i:31730 original size:7 final size:7
Alignment explanation
Indices: 31720--31750 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
31710 TGAACCATGG
31720 ATTTTGA
1 ATTTTGA
31727 ATTTTGA
1 ATTTTGA
31734 ATTTTGA
1 ATTTTGA
31741 ATTTTGA
1 ATTTTGA
31748 ATT
1 ATT
31751 GCCTAATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
ATTTTGA
Found at i:31744 original size:21 final size:21
Alignment explanation
Indices: 31693--31750 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
31683 GAAATGCAAG
* *
31693 TTTTGAAATTTGATTTTTGAA
1 TTTTGAATTTTGAATTTTGAA
*** *
31714 CCATGGATTTTGAATTTTGAA
1 TTTTGAATTTTGAATTTTGAA
31735 TTTTGAATTTTGAATT
1 TTTTGAATTTTGAATT
31751 GCCTAATTGG
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTTGAATTTTGAATTTTGAA
Found at i:32047 original size:37 final size:37
Alignment explanation
Indices: 32004--32879 Score: 712
Period size: 37 Copynumber: 23.9 Consensus size: 37
31994 AATTTTAAAC
* * *
32004 ACCTAAACAGGGACCTTTAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* ** ** * *
32041 ATCTAAACAATGATCTCGAACAAGGTTTTCATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* * * * * *
32078 ACCTAAACAGGAATATTGAACAA-TATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
*
32115 ACCTAAACAGGGATCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* * *
32152 AGCTAAACATGGATCTTAAACAAGGATTTTGACAAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGA-TAAGAA
* *
32191 ACCTAAACAGGCA-CTTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATC-TTAAACAAGGATTTGATAAGAA
* * * * * *
32228 ACCTAAACAGGAATCATGAACAA-AATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
*
32265 ACCTAAACAGGGATCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
*
32302 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
* * *
32340 ACCTAAACAGGTACCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* * * * *
32377 ACCTAAACAGGAATCTTGAACAA-AATTTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
*
32414 ACCTAAACAGGGATCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
*
32451 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
* * *
32489 ACCTAAACAGGCATTTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* * * * * *
32526 ATCTAAACAGGAATCTTGAACAA-AATTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
*
32562 ACCTAAACAGGGATCTT----AA--A--TAATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* * * * *
32591 ACCTAAATAGGAATCTTGAACAA-GATTTTGATGAGAT
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
* * *
32628 GCCTAAACAGGGAACTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
** * * *
32665 GTCTAAACAGGAATCTTGAACAA-GATTTTGAT--GAC
1 ACCTAAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
* * * *
32700 ACCTAAAAAGGGACCTTAAATAAGAATTTGATAAGAA
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* ** * * *
32737 ACTTAAACAGGGATCTTGGACCA-GATCTTGATGAGAC
1 ACCTAAACAGGGATCTTAAACAAGGAT-TTGATAAGAA
* * * * *
32774 A-CTAAAATAGGGATCTTGAAC-CGGATTTTGATGAGAC
1 ACCT-AAACAGGGATCTTAAACAAGGA-TTTGATAAGAA
* * * * *
32811 ACCTAAATAGGGACCTAAAATAAGGATTTGATAAGAC
1 ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
* * * *
32848 GCCTAAACAGGAATCTTGAACAAGGTTTTGAT
1 ACCTAAACAGGGATCTTAAACAAGGATTTGAT
32880 GAGACTAAAT
Statistics
Matches: 664, Mismatches: 144, Indels: 62
0.76 0.17 0.07
Matches are distributed among these distances:
29 21 0.03
31 1 0.00
32 2 0.00
33 2 0.00
34 1 0.00
35 24 0.04
36 33 0.05
37 466 0.70
38 89 0.13
39 25 0.04
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (37 bp):
ACCTAAACAGGGATCTTAAACAAGGATTTGATAAGAA
Found at i:32130 original size:74 final size:74
Alignment explanation
Indices: 32062--32790 Score: 901
Period size: 74 Copynumber: 9.9 Consensus size: 74
32052 GATCTCGAAC
* * * *
32062 AAGGTTTTCATAAGAAACCTAAACAGGAATATTGAACAATATTTTGATGAGACACCTAAACAGGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGG
32127 ATCTTAAAT
66 ATCTTAAAT
* * ** *
32136 AAGGATTTGATAAGAAAGCTAAACATGG-ATCTTAAACAAGGATTTTGACAAAGAAACCTAAACA
1 AAGGATTTGATAAGAAACCTAAACA-GGAATCTTGAACAA-GATTTTGA-TGAGACACCTAAACA
*
32200 GGCA-CTTTAAAT
63 GGGATC-TTAAAT
* *
32212 AAGGATTTGATAAGAAACCTAAACAGGAATCATGAACAAAATTTTGATGAGACACCTAAACAGGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGG
32277 ATCTTAAAT
66 ATCTTAAAT
* * ** *
32286 AAGGATTTGATAAGAAACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAA-GATTTTGATGAGACACCTAAACAGG
* *
32351 TACCTTAAAT
65 GATCTTAAAT
*
32361 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGG
32426 ATCTTAAAT
66 ATCTTAAAT
* * ** *
32435 AAGGATTTGATAAGAAACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAA-GATTTTGATGAGACACCTAAACAGG
* *
32500 CATTTTAAAT
65 GATCTTAAAT
* *
32510 AAGGATTTGATAAGAAATCTAAACAGGAATCTTGAACAA-AATTTGATGAGACACCTAAACAGGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGG
32574 ATCTTAAAT
66 ATCTTAAAT
* **
32583 ----A----ATAAGAAACCTAAATAGGAATCTTGAACAAGATTTTGATGAGATGCCTAAACAGGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGG
*
32640 AACTTAAAT
66 ATCTTAAAT
** *
32649 AAGGATTTGATAAGAAGTCTAAACAGGAATCTTGAACAAGATTTTGAT--GACACCTAAAAAGGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGG
*
32712 ACCTTAAAT
66 ATCTTAAAT
* * * * * * *
32721 AAGAATTTGATAAGAAACTTAAACAGGGATCTTGGACCAGATCTTGATGAGACA-CTAAAATAGG
1 AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCT-AAACAGG
32785 GATCTT
65 GATCTT
32791 GAACCGGATT
Statistics
Matches: 560, Mismatches: 75, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
65 28 0.05
66 30 0.05
69 1 0.00
70 1 0.00
72 60 0.11
73 30 0.05
74 205 0.37
75 151 0.27
76 54 0.10
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.24
Consensus pattern (74 bp):
AAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGG
ATCTTAAAT
Found at i:32422 original size:149 final size:149
Alignment explanation
Indices: 32004--32753 Score: 1042
Period size: 149 Copynumber: 5.1 Consensus size: 149
31994 AATTTTAAAC
* * * * * * * ** * *
32004 ACCTAAACAGGGACCTTTAATAAGGA-TTTGATAAGAAATCTAAACAATG-ATCTCGAACAAGGT
1 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAAC-AGGCACCTTAAATAAGGA
* * *
32067 TTTCATAAGAAACCTAAACAGGAATATTGAACAATATTTTGATGAGACACCTAAACAGGGATCTT
65 TTTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGATCTT
32132 AAATAAGGATTTGATAAGAA
130 AAATAAGGATTTGATAAGAA
* * *
32152 AGCTAAACATGGATCTTAAACAAGGATTTTGACAAAGAAACCTAAACAGGCACTTTAAATAAGGA
1 ACCTAAACAGGGATCTTAAACAAGGATTTTGAC-AAGAAACCTAAACAGGCACCTTAAATAAGGA
*
32217 TTTGATAAGAAACCTAAACAGGAATCATGAACAAAATTTTGATGAGACACCTAAACAGGGATCTT
65 TTTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGATCTT
32282 AAATAAGGATTTGATAAGAA
130 AAATAAGGATTTGATAAGAA
*
32302 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGGTACCTTAAATAAGGAT
1 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGAT
32367 TTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGATCTTA
66 TTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGATCTTA
32432 AATAAGGATTTGATAAGAA
131 AATAAGGATTTGATAAGAA
**
32451 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGGCATTTTAAATAAGGAT
1 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGAT
*
32516 TTGATAAGAAATCTAAACAGGAATCTTGAACAAAA-TTTGATGAGACACCTAAACAGGGATCTTA
66 TTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGATCTTA
32580 AAT----A----ATAAGAA
131 AATAAGGATTTGATAAGAA
* * * ** ** * *
32591 ACCTAAATAGGAATCTTGAACAA-GATTTTGATGAGATGCCTAAACAGGGAACTTAAATAAGGAT
1 ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGAT
** * * *
32655 TTGATAAGAAGTCTAAACAGGAATCTTGAACAAGATTTTGAT--GACACCTAAAAAGGGACCTTA
66 TTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGATCTTA
*
32718 AATAAGAATTTGATAAGAA
131 AATAAGGATTTGATAAGAA
*
32737 ACTTAAACAGGGATCTT
1 ACCTAAACAGGGATCTT
32754 GGACCAGATC
Statistics
Matches: 546, Mismatches: 44, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
138 22 0.04
139 67 0.12
140 33 0.06
142 1 0.00
144 1 0.00
146 21 0.04
148 53 0.10
149 216 0.40
150 132 0.24
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.24
Consensus pattern (149 bp):
ACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGAT
TTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGATCTTA
AATAAGGATTTGATAAGAA
Found at i:32637 original size:214 final size:212
Alignment explanation
Indices: 32071--32790 Score: 671
Period size: 224 Copynumber: 3.3 Consensus size: 212
32061 CAAGGTTTTC
* * * *
32071 ATAAGAAACCTAAACAGGAATATTGAACAATATTTTGATGAGACACCT-AAACAGGGATCTTAAA
1 ATAAGAAACTTAAACAGGAATCTTGAACAAAATCTTGATGAGACA-CTAAAACAGGGATCTTAAA
* * * ** *
32135 TAAGGATTTGATAAGAAAGCTAAACATGG-ATCTTAAACAAGGATTTTGACAAAGAAACCTAAAC
65 T----A----ATAAGAAACCTAAACA-GGAATCTTGAACAA-AATTTTGA-TGAGACACCTAAAC
* * * *
32199 A-GGCACTTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCATGAACAAAATTTTGATGAG
119 AGGGAAC-TTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGA--AG
* * * * *
32263 ACACCTAAACAGGGATCTTAAATAAGGATTTG
181 AAACCTAAAAAGGCACCTTAAATAAGAATTTG
* * * * * ** * * *
32295 ATAAGAAACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAAACCT-AAACAGGTACCTTAA
1 ATAAGAAACTTAAACAGGAATCTTGAACAA-AATCTTGATGAGACA-CTAAAACAGGGATCTTAA
32359 ATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAG
64 AT----A----ATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAG
* *
32424 GGATCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGATCTTAAACAAGGATTTTGACAAGAA
121 GGAACTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAA-GATTTTG--AAGAA
* ** *
32489 ACCTAAACAGGCATTTTAAATAAGGATTTG
183 ACCTAAAAAGGCACCTTAAATAAGAATTTG
32519 ATAAGAAA-TCTAAACAGGAATCTTGAACAAAAT-TTGATGAGACACCT-AAACAGGGATCTTAA
1 ATAAGAAACT-TAAACAGGAATCTTGAACAAAATCTTGATGAGACA-CTAAAACAGGGATCTTAA
* * **
32581 ATAATAAGAAACCTAAATAGGAATCTTGAACAAGATTTTGATGAGATGCCTAAACAGGGAACTTA
64 ATAATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGAACTTA
** * * *
32646 AATAAGGATTTGATAAGAAGTCTAAACAGGAATCTTGAACAAGATTTTGATGACACCTAAAAAGG
129 AATAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGAAGAAACCTAAAAAGG
*
32711 GACCTTAAATAAGAATTTG
194 CACCTTAAATAAGAATTTG
* * * * *
32730 ATAAGAAACTTAAACAGGGATCTTGGACCAGATCTTGATGAGACACTAAAATAGGGATCTT
1 ATAAGAAACTTAAACAGGAATCTTGAACAAAATCTTGATGAGACACTAAAACAGGGATCTT
32791 GAACCGGATT
Statistics
Matches: 432, Mismatches: 54, Indels: 32
0.83 0.10 0.06
Matches are distributed among these distances:
211 57 0.13
212 24 0.06
213 7 0.02
214 95 0.22
218 1 0.00
222 26 0.06
223 56 0.13
224 102 0.24
225 63 0.15
226 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (212 bp):
ATAAGAAACTTAAACAGGAATCTTGAACAAAATCTTGATGAGACACTAAAACAGGGATCTTAAAT
AATAAGAAACCTAAACAGGAATCTTGAACAAAATTTTGATGAGACACCTAAACAGGGAACTTAAA
TAAGGATTTGATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGAAGAAACCTAAAAAGGCA
CCTTAAATAAGAATTTG
Found at i:32746 original size:72 final size:72
Alignment explanation
Indices: 32584--32786 Score: 255
Period size: 72 Copynumber: 2.8 Consensus size: 72
32574 ATCTTAAATA
* * *
32584 ATAAGAAACCTAAATAGGAATCTTGAACAAGATTTTGATGAGATGCCTAAACAGGGAACTTAAAT
1 ATAAGAAACTTAAACAGGAATCTTGAACAAGATTTTGATGAGA--CCTAAAAAGGGAACTTAAAT
*
32649 AAGGATTTG
64 AAGAATTTG
* * *
32658 ATAAG-AAGTCTAAACAGGAATCTTGAACAAGATTTTGATGACACCTAAAAAGGGACCTTAAATA
1 ATAAGAAACT-TAAACAGGAATCTTGAACAAGATTTTGATGAGACCTAAAAAGGGAACTTAAATA
32722 AGAATTTG
65 AGAATTTG
* * * *
32730 ATAAGAAACTTAAACAGGGATCTTGGACCAGATCTTGATGAGACACTAAAATAGGGA
1 ATAAGAAACTTAAACAGGAATCTTGAACAAGATTTTGATGAGAC-CTAAAA-AGGGA
32787 TCTTGAACCG
Statistics
Matches: 112, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
72 60 0.54
73 11 0.10
74 41 0.37
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.24
Consensus pattern (72 bp):
ATAAGAAACTTAAACAGGAATCTTGAACAAGATTTTGATGAGACCTAAAAAGGGAACTTAAATAA
GAATTTG
Found at i:33777 original size:87 final size:87
Alignment explanation
Indices: 33628--33796 Score: 248
Period size: 87 Copynumber: 1.9 Consensus size: 87
33618 GATTGATGCC
* * *
33628 CCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAATTAATGGTTCTAGATCAGC
1 CCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTAATGGTTCTAGATCAGC
33693 TTCCCACCTTAAGAAATATTTA
66 TTCCCACCTTAAGAAATATTTA
* * * * *
33715 CCAAATCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAGT
1 CCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTAATGGTTCTAGATCAGC
* *
33780 TTCTCATCTTAAGAAAT
66 TTCCCACCTTAAGAAAT
33797 GTTCAAACAT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (87 bp):
CCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTAATGGTTCTAGATCAGC
TTCCCACCTTAAGAAATATTTA
Found at i:33946 original size:11 final size:11
Alignment explanation
Indices: 33930--33985 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
33920 CCTTTTGATT
33930 TTTTTCTTTTC
1 TTTTTCTTTTC
33941 TTTTTCTTTTC
1 TTTTTCTTTTC
*
33952 TATTTTTCTTTGC
1 --TTTTTCTTTTC
33965 --TTTCTTTT-
1 TTTTTCTTTTC
33973 TTTTTC-TTTC
1 TTTTTCTTTTC
33983 TTT
1 TTT
33986 AGATTGCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
9 10 0.26
10 7 0.18
11 11 0.29
13 10 0.26
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:33950 original size:19 final size:18
Alignment explanation
Indices: 33916--33981 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 18
33906 AATTTGAACC
* *
33916 TTTTCCTTTTGATTTTTT
1 TTTTTCTTTTGCTTTTTT
* *
33934 TCTTTTCTTTTTCTTTTCTA
1 T-TTTTCTTTTGCTTTT-TT
33954 TTTTTC-TTTGCTTTCTTTT
1 TTTTTCTTTTGC-TT-TTTT
33973 TTTTTCTTT
1 TTTTTCTTT
33982 CTTTAGATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
18 5 0.14
19 26 0.70
20 6 0.16
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTGCTTTTTT
Found at i:34709 original size:14 final size:14
Alignment explanation
Indices: 34692--34732 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
34682 TTTTAAAAGT
34692 CATTTTTTTGAAAA
1 CATTTTTTTGAAAA
*
34706 CATTTTCTTG-AAA
1 CATTTTTTTGAAAA
34719 -ATCTTTTTTGAAAA
1 CAT-TTTTTTGAAAA
34733 AAGTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 12 0.52
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (14 bp):
CATTTTTTTGAAAA
Found at i:34711 original size:13 final size:13
Alignment explanation
Indices: 34695--34732 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
34685 TAAAAGTCAT
34695 TTTTTTGAAAA-C
1 TTTTTTGAAAATC
34707 ATTTTCTTGAAAATC
1 -TTTT-TTGAAAATC
34722 TTTTTTGAAAA
1 TTTTTTGAAAA
34733 AAGTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 11 0.48
15 1 0.04
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (13 bp):
TTTTTTGAAAATC
Found at i:39602 original size:20 final size:20
Alignment explanation
Indices: 39577--39615 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39567 CATAGATGAA
*
39577 ATTTTCAAAAATTATTATTT
1 ATTTTCAAAAATTAGTATTT
*
39597 ATTTTCAAATATTAGTATT
1 ATTTTCAAAAATTAGTATT
39616 GAATTCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTTCAAAAATTAGTATTT
Found at i:39708 original size:16 final size:16
Alignment explanation
Indices: 39635--39709 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
39625 TTTTTCCAGG
*
39635 TTCGGGTTCTGGTTTT
1 TTCGGGTTCGGGTTTT
*
39651 TTCGGGTTCGAGTTTT
1 TTCGGGTTCGGGTTTT
* * *
39667 ATCGGGTTTC-AGATTT
1 TTCGGG-TTCGGGTTTT
*
39683 TTCGAGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
*
39699 TTTGGGTTCGG
1 TTCGGGTTCGG
39710 ATTCAGGTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 3 0.06
16 41 0.87
17 3 0.06
ACGTcount: A:0.07, C:0.12, G:0.32, T:0.49
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:40432 original size:60 final size:60
Alignment explanation
Indices: 40362--40480 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
40352 AAAAGTCTAA
* *
40362 TGTTTTCCAAAATGATCAAATAAGGGTCAAATCTTTTAATTTAACCAAATAAGGGCCTAT
1 TGTTTGCCAAAATGATCAAATAAGGGTCAAATCTTTTAACTTAACCAAATAAGGGCCTAT
* * ** ** *
40422 TGTTTGCCAAAATGTTGAAATAAGGGTCCGATCTTTTAACTTGGCTAAATAAGGGCCTA
1 TGTTTGCCAAAATGATCAAATAAGGGTCAAATCTTTTAACTTAACCAAATAAGGGCCTA
40481 ACATTATCGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (60 bp):
TGTTTGCCAAAATGATCAAATAAGGGTCAAATCTTTTAACTTAACCAAATAAGGGCCTAT
Found at i:40708 original size:60 final size:58
Alignment explanation
Indices: 40552--40712 Score: 162
Period size: 60 Copynumber: 2.7 Consensus size: 58
40542 TGACTCCAGT
* *
40552 CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAACTTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTGGA-AACGTTAGGC-CTTATTTGGCCAAATTAAAAGATCGGA
* ** * * *
40612 CCCTTATTTCAGCATTTTGGCAAACAATAGACCCTTATTTGTCCAAATTAAAAGATCATG-
1 CCCTTATTTGAGCATTTTGG-AAACGTTAG-GCCTTATTTGGCCAAATTAAAAGATC-GGA
* *
40672 TCCTTATTTGAGTATTTTGGTAAACGTTAGGTCCTTATTTG
1 CCCTTATTTGAGCATTTTGG-AAACGTTAGG-CCTTATTTG
40713 AGCAATTAGC
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
60 79 0.96
61 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (58 bp):
CCCTTATTTGAGCATTTTGGAAACGTTAGGCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:43042 original size:81 final size:81
Alignment explanation
Indices: 42948--43110 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
42938 GCGTGTCGGA
42948 TATTTTTTGTTATAGATTTTGTTATTATTGTTTGAATATAGAAAGGATTTCGTTTCAAAAATTTG
1 TATTTTTTGTTATAGATTTTGTTATTATTGTTTGAATATAGAAAGGATTTCGTTTCAAAAATTTG
43013 AAATTTTATTACTATT
66 AAATTTTATTACTATT
43029 TATTTTTTGTTATAGATTTTGTTATTATTGTTTGAATATAGAAAGGATTTCGTTTCAAAAATTTG
1 TATTTTTTGTTATAGATTTTGTTATTATTGTTTGAATATAGAAAGGATTTCGTTTCAAAAATTTG
43094 AAATTTTATTACTATT
66 AAATTTTATTACTATT
43110 T
1 T
43111 TGTGTATTTG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (81 bp):
TATTTTTTGTTATAGATTTTGTTATTATTGTTTGAATATAGAAAGGATTTCGTTTCAAAAATTTG
AAATTTTATTACTATT
Found at i:43788 original size:2 final size:2
Alignment explanation
Indices: 43781--43818 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43771 GTTGCAAATA
43781 AT 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 AT
43819 TTCTTCCCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47863 original size:33 final size:33
Alignment explanation
Indices: 47821--47914 Score: 188
Period size: 33 Copynumber: 2.8 Consensus size: 33
47811 GGTGAGGAAA
47821 AAAATAAATACTAATTATTTTATTATTTCTTCT
1 AAAATAAATACTAATTATTTTATTATTTCTTCT
47854 AAAATAAATACTAATTATTTTATTATTTCTTCT
1 AAAATAAATACTAATTATTTTATTATTTCTTCT
47887 AAAATAAATACTAATTATTTTATTATTT
1 AAAATAAATACTAATTATTTTATTATTT
47915 TATTATAGGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (33 bp):
AAAATAAATACTAATTATTTTATTATTTCTTCT
Found at i:49390 original size:39 final size:39
Alignment explanation
Indices: 49335--49415 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
49325 TTTATATACT
*
49335 TGATCAATATACATGTCTTT-TCATATAGACATAACTTTA
1 TGATCAATAGACATGTCTTTCT-ATATAGACATAACTTTA
*
49374 TGATCAATAGATATGTCTTTCTATATAGACATAACTTTA
1 TGATCAATAGACATGTCTTTCTATATAGACATAACTTTA
49413 TGA
1 TGA
49416 ATAATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 38 0.97
40 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (39 bp):
TGATCAATAGACATGTCTTTCTATATAGACATAACTTTA
Found at i:52705 original size:39 final size:39
Alignment explanation
Indices: 52662--52740 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
52652 TTTATATACT
* *
52662 TGATCAATATACATGTCTTT-TCATATAGATATAACTTTA
1 TGATCAATAGACATGTCTTTCT-ATATAGACATAACTTTA
*
52701 TGATCAATAGATATGTCTTTCTATATAGACATAACTTTA
1 TGATCAATAGACATGTCTTTCTATATAGACATAACTTTA
52740 T
1 T
52741 AAATAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 35 0.97
40 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (39 bp):
TGATCAATAGACATGTCTTTCTATATAGACATAACTTTA
Found at i:52720 original size:21 final size:20
Alignment explanation
Indices: 52661--52720 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
52651 ATTTATATAC
* *
52661 TTGATCAATATACATGTCTT
1 TTGATCAATAGATATGTCTT
* **
52681 TTCAT--ATAGATATAACTT
1 TTGATCAATAGATATGTCTT
52699 TATGATCAATAGATATGTCTT
1 T-TGATCAATAGATATGTCTT
52720 T
1 T
52721 CTATATAGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
18 10 0.34
19 3 0.10
20 4 0.14
21 12 0.41
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (20 bp):
TTGATCAATAGATATGTCTT
Found at i:60329 original size:2 final size:2
Alignment explanation
Indices: 60322--60354 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
60312 ATTCTCAATG
60322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60355 TCTAAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60466 original size:30 final size:29
Alignment explanation
Indices: 60410--60467 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
60400 CATTCTGACA
*
60410 AAAGAAATTGCTTATGATCCTATTTGAAG
1 AAAGAAATTGCTTATGAACCTATTTGAAG
* *
60439 AAAGAAATTTGCTTATGAACTTTTTTGAA
1 AAAGAAA-TTGCTTATGAACCTATTTGAA
60468 AAAAATTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (29 bp):
AAAGAAATTGCTTATGAACCTATTTGAAG
Found at i:67540 original size:12 final size:12
Alignment explanation
Indices: 67520--67572 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
67510 AGTTGTTAGG
*
67520 AATATATATTCA
1 AATAAATATTCA
67532 AATAAATATTCA
1 AATAAATATTCA
67544 AAT-AA-ATT-A
1 AATAAATATTCA
*
67553 AAT-CATATTCA
1 AATAAATATTCA
67564 AATAAATAT
1 AATAAATAT
67573 AATAATATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 5 0.14
10 6 0.17
11 6 0.17
12 18 0.51
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAAATATTCA
Found at i:67580 original size:20 final size:20
Alignment explanation
Indices: 67536--67601 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
67526 TATTCAAATA
67536 AATATTCAAATAAAT-TAAAT
1 AATATTCAAATAAATAT-AAT
*
67556 CATATTCAAATAAATATAAT
1 AATATTCAAATAAATATAAT
*
67576 AATATACAGAA-AAA-ATAAT
1 AATATTCA-AATAAATATAAT
67595 ATATATT
1 A-ATATT
67602 GAAAAATTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.15
20 30 0.77
21 3 0.08
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
AATATTCAAATAAATATAAT
Found at i:70188 original size:49 final size:47
Alignment explanation
Indices: 70113--70253 Score: 171
Period size: 49 Copynumber: 2.9 Consensus size: 47
70103 CAAGCAATCA
70113 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* *
70161 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
70210 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
70254 TTGGCACGCT
Statistics
Matches: 83, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
47 17 0.20
48 24 0.29
49 41 0.49
50 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.52
Consensus pattern (47 bp):
TTTATTTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:71252 original size:15 final size:15
Alignment explanation
Indices: 71232--71278 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
71222 TGCTAGGGTG
*
71232 AATGGTGCAAACAAT
1 AATGGTGCGAACAAT
* *
71247 AATGGTGCGAATAAC
1 AATGGTGCGAACAAT
*
71262 AATGGTGTGAACAAT
1 AATGGTGCGAACAAT
71277 AA
1 AA
71279 CGGAAACGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (15 bp):
AATGGTGCGAACAAT
Found at i:81669 original size:2 final size:2
Alignment explanation
Indices: 81662--81692 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
81652 TGGCCGGTTA
81662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
81693 GTGTAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83253 original size:17 final size:17
Alignment explanation
Indices: 83233--83267 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
83223 TATTTATTGA
83233 ATAATAATTATTATTTT
1 ATAATAATTATTATTTT
*
83250 ATAATTATTATTATTTT
1 ATAATAATTATTATTTT
83267 A
1 A
83268 GTAAATAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATAATTATTATTTT
Found at i:84343 original size:23 final size:24
Alignment explanation
Indices: 84313--84360 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
84303 TCCGTGCTTA
84313 TTTTCTC-TCAGGCCCTGCGCCAC
1 TTTTCTCATCAGGCCCTGCGCCAC
*
84336 TTTTCTCTATCAGGCCCTGTGCCAC
1 TTTTCTC-ATCAGGCCCTGCGCCAC
84361 CCCCTGCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
25 15 0.68
ACGTcount: A:0.10, C:0.40, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTTCTCATCAGGCCCTGCGCCAC
Found at i:85369 original size:65 final size:64
Alignment explanation
Indices: 85265--85393 Score: 186
Period size: 65 Copynumber: 2.0 Consensus size: 64
85255 GCTTGCTATT
* * ** *
85265 GATTCCAATTTTCTGCACTAGCCCTTGCATGGGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCATGGGTAGGCCAAGGGTA-CCCATGCATGGGTAGGAC
* *
85330 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAGGGGTACCCATGCATGGGTAGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCATGGGTAGGCCAAGGGTACCCATGCATGGGTAGGAC
85394 CAGTTTTTCC
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
64 17 0.30
65 40 0.70
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (64 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCATGGGTAGGCCAAGGGTACCCATGCATGGGTAGGAC
Found at i:86555 original size:21 final size:20
Alignment explanation
Indices: 86521--86560 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
86511 TTTAAAACCT
86521 ATTGGAGCAAGTGGTACTAA
1 ATTGGAGCAAGTGGTACTAA
*
86541 ATTGGATCTAAGTGGTACTA
1 ATTGGAGC-AAGTGGTACTA
86561 GGGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (20 bp):
ATTGGAGCAAGTGGTACTAA
Found at i:89667 original size:26 final size:26
Alignment explanation
Indices: 89638--89702 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
89628 AACCCAGGCG
89638 TGGGTAGGCCAGGGGTACCCCATGAA
1 TGGGTAGGCCAGGGGTACCCCATGAA
*
89664 TGGGTAGGCCAGGGGTACCCCATGCA
1 TGGGTAGGCCAGGGGTACCCCATGAA
89690 TGGGTAGGACCAG
1 TGGGTAGG-CCAG
89703 TTTTTCCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 33 0.89
27 4 0.11
ACGTcount: A:0.22, C:0.23, G:0.40, T:0.15
Consensus pattern (26 bp):
TGGGTAGGCCAGGGGTACCCCATGAA
Found at i:91336 original size:136 final size:136
Alignment explanation
Indices: 91177--91443 Score: 507
Period size: 136 Copynumber: 2.0 Consensus size: 136
91167 CTGGGGAGAG
*
91177 GGAAAAGAAGATGCTAGGGCGCCACTTTCTGGTTGGGAGATGAAAATGTTCCTCCTAGATGGTTG
1 GGAAAAGAAGATGCTAGGGCGCCACTTTCTGGATGGGAGATGAAAATGTTCCTCCTAGATGGTTG
91242 ATGAATAATTCTTCCTTCTTCCTATCACACTTCAGCATGCCTTCGTTGCTTCTTTTGTGCTGAAA
66 ATGAATAATTCTTCCTTCTTCCTATCACACTTCAGCATGCCTTCGTTGCTTCTTTTGTGCTGAAA
91307 ATAGAA
131 ATAGAA
* *
91313 GGAAAAGGAGATGCTAGGGCGCCACTTTCTGGATGGGAGATGGAAATGTTCCTCCTAGATGGTTG
1 GGAAAAGAAGATGCTAGGGCGCCACTTTCTGGATGGGAGATGAAAATGTTCCTCCTAGATGGTTG
91378 ATGAATAATTCTTCCTTCTTCCTATCACACTTCAGCATGCCTTCGTTGCTTCTTTTGTGCTGAAA
66 ATGAATAATTCTTCCTTCTTCCTATCACACTTCAGCATGCCTTCGTTGCTTCTTTTGTGCTGAAA
91443 A
131 A
91444 CAACTAATTT
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 128 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (136 bp):
GGAAAAGAAGATGCTAGGGCGCCACTTTCTGGATGGGAGATGAAAATGTTCCTCCTAGATGGTTG
ATGAATAATTCTTCCTTCTTCCTATCACACTTCAGCATGCCTTCGTTGCTTCTTTTGTGCTGAAA
ATAGAA
Found at i:92353 original size:16 final size:16
Alignment explanation
Indices: 92329--92359 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
92319 GATGATGATT
*
92329 TTAATAATAATTATTC
1 TTAAAAATAATTATTC
92345 TTAAAAATAATTATT
1 TTAAAAATAATTATT
92360 ATTTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAAATAATTATTC
Found at i:94512 original size:49 final size:48
Alignment explanation
Indices: 94440--94568 Score: 172
Period size: 49 Copynumber: 2.7 Consensus size: 48
94430 CAAGCAATTA
**
94440 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
*
94488 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT
* *
94537 TTTAATTTT-CATTGCACTTTTTATCAATTTTT
1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTT
94569 TGATAAAATT
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
47 7 0.10
48 24 0.33
49 42 0.58
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.54
Consensus pattern (48 bp):
TTTATTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:95457 original size:8 final size:9
Alignment explanation
Indices: 95421--95458 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
95411 CCCAAATTAC
95421 TTATGGAAA
1 TTATGGAAA
*
95430 TTAAGGAAA
1 TTATGGAAA
95439 TTATGGAAA
1 TTATGGAAA
95448 TTAT-GAAA
1 TTATGGAAA
95456 TTA
1 TTA
95459 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Done.