Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009198.1 Kokia drynarioides strain JFW-HI SEQ_123903, 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: 115384
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:3354 original size:17 final size:18
Alignment explanation
Indices: 3321--3356 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3311 TAGTAAAATG
3321 TGTATAATAAAATTAAAA
1 TGTATAATAAAATTAAAA
*
3339 TGTATAA-AATATTAAAA
1 TGTATAATAAAATTAAAA
3356 T
1 T
3357 CAAGCTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
TGTATAATAAAATTAAAA
Found at i:6576 original size:6 final size:6
Alignment explanation
Indices: 6565--6603 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
6555 TCTACTTAAT
6565 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGT
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGT
6604 ATGTAGAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.18
Consensus pattern (6 bp):
GGTGGA
Found at i:16143 original size:45 final size:45
Alignment explanation
Indices: 16078--16312 Score: 283
Period size: 45 Copynumber: 5.2 Consensus size: 45
16068 TGACAATCCT
*
16078 ACTGCTCGTAGGCTT-AATGAAATGAGAGGTGAATGTACCAGCCCC
1 ACTGCTCGTAAG-TTGAATGAAATGAGAGGTGAATGTACCAGCCCC
* * * *
16123 ACTGCTAGCAGGTTGAATGAAATGAGAGGTGAATGTCCCAGCCCC
1 ACTGCTCGTAAGTTGAATGAAATGAGAGGTGAATGTACCAGCCCC
* * **
16168 ACTGCTCGTAAGTCGAATGAATTGAGAATTGAATGTACCAGCCCC
1 ACTGCTCGTAAGTTGAATGAAATGAGAGGTGAATGTACCAGCCCC
* * * *
16213 ACCGCTTGTAAGTTGAATGAACTGAGAGCTGAATGTACCAGCCCC
1 ACTGCTCGTAAGTTGAATGAAATGAGAGGTGAATGTACCAGCCCC
* * * ** *
16258 ACTGCTCGTAAGTTCAGTGAATTGAGAATTGAATGTACCAGCTCC
1 ACTGCTCGTAAGTTGAATGAAATGAGAGGTGAATGTACCAGCCCC
16303 ACTGCTCGTA
1 ACTGCTCGTA
16313 GGCTTAATGA
Statistics
Matches: 164, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 2 0.01
45 162 0.99
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (45 bp):
ACTGCTCGTAAGTTGAATGAAATGAGAGGTGAATGTACCAGCCCC
Found at i:16322 original size:90 final size:90
Alignment explanation
Indices: 16093--16323 Score: 313
Period size: 90 Copynumber: 2.6 Consensus size: 90
16083 TCGTAGGCTT
* ** * *
16093 AATGAAATGAGAGGTGAATGTACCAGCCCCACTGCTAGCAGGTTGAATGAAATGAGAGGTGAATG
1 AATGAATTGAGAATTGAATGTACCAGCCCCACTGCTAGTAGGTTGAATGAAATGAGAGCTGAATG
*
16158 TCCCAGCCCCACTGCTCGTAAGTCG
66 TACCAGCCCCACTGCTCGTAAGTCG
* * * *
16183 AATGAATTGAGAATTGAATGTACCAGCCCCACCGCTTGTAAGTTGAATGAACTGAGAGCTGAATG
1 AATGAATTGAGAATTGAATGTACCAGCCCCACTGCTAGTAGGTTGAATGAAATGAGAGCTGAATG
16248 TACCAGCCCCACTGCTCGTAAGTTC-
66 TACCAGCCCCACTGCTCGTAAG-TCG
* * *
16273 AGTGAATTGAGAATTGAATGTACCAGCTCCACTGCTCGTAGGCTT-AATGAA
1 AATGAATTGAGAATTGAATGTACCAGCCCCACTGCTAGTAGG-TTGAATGAA
16324 GGGTCCGATA
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
90 120 0.97
91 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (90 bp):
AATGAATTGAGAATTGAATGTACCAGCCCCACTGCTAGTAGGTTGAATGAAATGAGAGCTGAATG
TACCAGCCCCACTGCTCGTAAGTCG
Found at i:18780 original size:6 final size:6
Alignment explanation
Indices: 18769--18793 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18759 AATTTTTTAA
18769 GCTTTT GCTTTT GCTTTT GCTTTT G
1 GCTTTT GCTTTT GCTTTT GCTTTT G
18794 ATCCTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.20, T:0.64
Consensus pattern (6 bp):
GCTTTT
Found at i:19879 original size:13 final size:13
Alignment explanation
Indices: 19861--19885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19851 TTTTACTTAA
19861 TATTATTTTATTT
1 TATTATTTTATTT
19874 TATTATTTTATT
1 TATTATTTTATT
19886 ATATATACTC
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTATTTTATTT
Found at i:22024 original size:15 final size:17
Alignment explanation
Indices: 21999--22030 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21989 AATGCTTATT
21999 TATTATATTAT-GTTTA
1 TATTATATTATGGTTTA
22015 TATT-TATTATGGTTTA
1 TATTATATTATGGTTTA
22031 CTTTGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
TATTATATTATGGTTTA
Found at i:24494 original size:29 final size:31
Alignment explanation
Indices: 24432--24498 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
24422 TTACCATTTT
*
24432 GTCACTAAACTATTCGGAAGTTTTCATTTAA
1 GTCACTAAACTATTCGAAAGTTTTCATTTAA
* *
24463 GTCA-TAAACTATTC-AAAGTTTTTATTTGA
1 GTCACTAAACTATTCGAAAGTTTTCATTTAA
24492 GTCACTA
1 GTCACTA
24499 GGTTGTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.50
30 12 0.38
31 4 0.12
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (31 bp):
GTCACTAAACTATTCGAAAGTTTTCATTTAA
Found at i:26484 original size:17 final size:17
Alignment explanation
Indices: 26462--26519 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
26452 TACAAATACA
26462 GTCACAGATACAATCAT
1 GTCACAGATACAATCAT
26479 GTCACAGAT---A-CA-
1 GTCACAGATACAATCAT
* *
26491 GTTACAAATACAATCAT
1 GTCACAGATACAATCAT
26508 GTCACAGATACA
1 GTCACAGATACA
26520 GTTACGAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
12 7 0.22
13 2 0.06
14 1 0.03
15 1 0.03
16 2 0.06
17 19 0.59
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.22
Consensus pattern (17 bp):
GTCACAGATACAATCAT
Found at i:26491 original size:29 final size:29
Alignment explanation
Indices: 26457--26548 Score: 132
Period size: 29 Copynumber: 3.2 Consensus size: 29
26447 ACAATTACAA
*
26457 ATACAGTCACAGATACAATCATGTCACAG
1 ATACAGTTACAGATACAATCATGTCACAG
*
26486 ATACAGTTACAAATACAATCATGTCACAG
1 ATACAGTTACAGATACAATCATGTCACAG
* *
26515 ATACAGTTAC-GAATGCAATCATGTCACAT
1 ATACAGTTACAG-ATACAATCATGTCACAG
26544 ATACA
1 ATACA
26549 ATTATGGATG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (29 bp):
ATACAGTTACAGATACAATCATGTCACAG
Found at i:26559 original size:29 final size:29
Alignment explanation
Indices: 26472--26581 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
26462 GTCACAGATA
* *
26472 CAATCATGTCACAGATACAGTTACAAATA
1 CAATCATGTCACAGATACAGTTACGAATG
26501 CAATCATGTCACAGATACAGTTACGAATG
1 CAATCATGTCACAGATACAGTTACGAATG
* * * *
26530 CAATCATGTCACATATACAATTATGGATG
1 CAATCATGTCACAGATACAGTTACGAATG
* *
26559 CAAACATGAT-ATAGATACAGTTA
1 CAATCATG-TCACAGATACAGTTA
26582 TATATGCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 69 0.99
30 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (29 bp):
CAATCATGTCACAGATACAGTTACGAATG
Found at i:26582 original size:29 final size:29
Alignment explanation
Indices: 26482--26599 Score: 98
Period size: 29 Copynumber: 4.1 Consensus size: 29
26472 CAATCATGTC
** * *
26482 ACAGATACAGTTACAAATACAATCATG-T
1 ACAGATACAGTTATGAATGCAAACATGAT
* *
26510 CACAGATACAGTTACGAATGCAATCATG-T
1 -ACAGATACAGTTATGAATGCAAACATGAT
* * *
26539 CACATATACAATTATGGATGCAAACATGAT
1 -ACAGATACAGTTATGAATGCAAACATGAT
*
26569 ATAGATACAGTTAT-ATATGCAAACATGAT
1 ACAGATACAGTTATGA-ATGCAAACATGAT
26598 AC
1 AC
26600 CCCTATCCGT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
29 74 0.99
30 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (29 bp):
ACAGATACAGTTATGAATGCAAACATGAT
Found at i:26745 original size:40 final size:40
Alignment explanation
Indices: 26705--26940 Score: 199
Period size: 40 Copynumber: 6.0 Consensus size: 40
26695 GTAAACTTGT
* * *
26705 AGTGTTTATAGTGTCACTGTCGGTTCAGTTATAATATTGT
1 AGTGTTTACAGTGTCACTGCCGGTTCAGTTATAATATTGC
* * ** **
26745 AGTGTTTAAAGTGTCACTGCCAGTTCAGTGGTAACCTTGC
1 AGTGTTTACAGTGTCACTGCCGGTTCAGTTATAATATTGC
* * * * *
26785 GGT-TTCTACAGTGTCACTGTCGGTTCAATTATAATGTTGT
1 AGTGTT-TACAGTGTCACTGCCGGTTCAGTTATAATATTGC
* * * ** *
26825 AGTGTTCACAGTGTTACTGCCAGTTCAGTGGTAACATTGC
1 AGTGTTTACAGTGTCACTGCCGGTTCAGTTATAATATTGC
* * ** * *
26865 AGTTTTTACAGTGTCACTACCTATTCAATTATAATGTTGC
1 AGTGTTTACAGTGTCACTGCCGGTTCAGTTATAATATTGC
*
26905 AGTGTTTAAAGTGTCACTGCCGGTTCAG-TA-AATATT
1 AGTGTTTACAGTGTCACTGCCGGTTCAGTTATAATATT
26941 CTTAAGTGGT
Statistics
Matches: 147, Mismatches: 47, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
38 5 0.03
39 4 0.03
40 136 0.93
41 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (40 bp):
AGTGTTTACAGTGTCACTGCCGGTTCAGTTATAATATTGC
Found at i:26802 original size:80 final size:80
Alignment explanation
Indices: 26714--26933 Score: 314
Period size: 80 Copynumber: 2.8 Consensus size: 80
26704 TAGTGTTTAT
* *
26714 AGTGTCACTGTCGGTTCAGTTATAATATTGTAGTGTTTAAAGTGTCACTGCCAGTTCAGTGGTAA
1 AGTGTCACTGTCGGTTCAATTATAATGTTGTAGTGTTTAAAGTGTCACTGCCAGTTCAGTGGTAA
* *
26779 CCTTGCGGTTTCTAC
66 CATTGCAGTTTCTAC
* * *
26794 AGTGTCACTGTCGGTTCAATTATAATGTTGTAGTGTTCACAGTGTTACTGCCAGTTCAGTGGTAA
1 AGTGTCACTGTCGGTTCAATTATAATGTTGTAGTGTTTAAAGTGTCACTGCCAGTTCAGTGGTAA
*
26859 CATTGCAGTTTTTAC
66 CATTGCAGTTTCTAC
** ** * *
26874 AGTGTCACTACCTATTCAATTATAATGTTGCAGTGTTTAAAGTGTCACTGCCGGTTCAGT
1 AGTGTCACTGTCGGTTCAATTATAATGTTGTAGTGTTTAAAGTGTCACTGCCAGTTCAGT
26934 AAATATTCTT
Statistics
Matches: 123, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 123 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (80 bp):
AGTGTCACTGTCGGTTCAATTATAATGTTGTAGTGTTTAAAGTGTCACTGCCAGTTCAGTGGTAA
CATTGCAGTTTCTAC
Found at i:29762 original size:17 final size:17
Alignment explanation
Indices: 29740--29801 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
29730 TACAAATATA
*
29740 GTCACAGATGCAATCAT
1 GTCACAGATACAATCAT
29757 GTCACAGAT---A-CA-
1 GTCACAGATACAATCAT
* *
29769 GTTACAGATACAGTCAT
1 GTCACAGATACAATCAT
29786 GTCACAGATACAATCA
1 GTCACAGATACAATCA
29802 CGAATGCAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
12 8 0.22
13 2 0.06
14 1 0.03
16 2 0.06
17 23 0.64
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (17 bp):
GTCACAGATACAATCAT
Found at i:29785 original size:29 final size:30
Alignment explanation
Indices: 29743--29867 Score: 136
Period size: 29 Copynumber: 4.3 Consensus size: 30
29733 AAATATAGTC
*
29743 ACAG-ATGCAATCATGTCACAGATACAGTT
1 ACAGAATGCAGTCATGTCACAGATACAGTT
* * *
29772 ACAG-ATACAGTCATGTCACAGATACAATC
1 ACAGAATGCAGTCATGTCACAGATACAGTT
*
29801 AC-GAATGCAGTCATGTCACAAATACAGTT
1 ACAGAATGCAGTCATGTCACAGATACAGTT
* *
29830 AC-GAATGTAGACATGAT-ACAGATACAGTT
1 ACAGAATGCAGTCATG-TCACAGATACAGTT
29859 ACA-AATGCA
1 ACAGAATGCA
29868 AACGTGATAC
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 79 0.98
30 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (30 bp):
ACAGAATGCAGTCATGTCACAGATACAGTT
Found at i:37034 original size:2 final size:2
Alignment explanation
Indices: 37029--37053 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37019 AAAAAAGAGA
37029 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
37054 ACATTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37317 original size:13 final size:13
Alignment explanation
Indices: 37299--37342 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
37289 TCCCAAATAA
*
37299 AAATTTGAAAAAT
1 AAATTTTAAAAAT
*
37312 AAATTTTAAAAAA
1 AAATTTTAAAAAT
*
37325 AATATTTTTAAAAT
1 AA-ATTTTAAAAAT
37339 AAAT
1 AAAT
37343 CAGACTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:40569 original size:44 final size:44
Alignment explanation
Indices: 40506--40599 Score: 170
Period size: 44 Copynumber: 2.1 Consensus size: 44
40496 GCTTCTAAGT
40506 ACTTCCTTTTACGCGTTTCCTTCCACACATTTATAACCCCAAAC
1 ACTTCCTTTTACGCGTTTCCTTCCACACATTTATAACCCCAAAC
*
40550 ACTTCCTTTTACTCGTTTCCTTCCACACATTTATAACCCCAAAC
1 ACTTCCTTTTACGCGTTTCCTTCCACACATTTATAACCCCAAAC
*
40594 TCTTCC
1 ACTTCC
40600 CTTCATCCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.23, C:0.37, G:0.03, T:0.36
Consensus pattern (44 bp):
ACTTCCTTTTACGCGTTTCCTTCCACACATTTATAACCCCAAAC
Found at i:41898 original size:4 final size:4
Alignment explanation
Indices: 41889--41946 Score: 75
Period size: 4 Copynumber: 15.0 Consensus size: 4
41879 ATTCATTAGC
* * *
41889 ATGT ATGT ATGT ATGT ATGT ATTT ATGT GTGT ATGT GTGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
41937 A--T ATGT ATGT
1 ATGT ATGT ATGT
41947 GTGTGCGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
4 44 0.96
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
ATGT
Found at i:41975 original size:8 final size:8
Alignment explanation
Indices: 41889--41976 Score: 59
Period size: 8 Copynumber: 10.8 Consensus size: 8
41879 ATTCATTAGC
*
41889 ATGTATGT
1 ATGTGTGT
*
41897 ATGTATGT
1 ATGTGTGT
* *
41905 ATGTATTT
1 ATGTGTGT
41913 ATGTGTGT
1 ATGTGTGT
41921 ATGTGTGT
1 ATGTGTGT
*
41929 ATGTATGTAT
1 ATG--TGTGT
*
41939 ATGTATGT
1 ATGTGTGT
* *
41947 GTGTGCGT
1 ATGTGTGT
* *
41955 GTGTGCGT
1 ATGTGTGT
*
41963 GTGTGTGT
1 ATGTGTGT
41971 ATGTGT
1 ATGTGT
41977 CTGATATGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
8 60 0.90
10 7 0.10
ACGTcount: A:0.16, C:0.02, G:0.33, T:0.49
Consensus pattern (8 bp):
ATGTGTGT
Found at i:60769 original size:60 final size:59
Alignment explanation
Indices: 60704--60849 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 59
60694 ATAATTGTCT
* * * *
60704 AGTTCAAGCCCCATTATGAGAACAATTACTAAGTTCAAGGACTAACTTGAATAAAAAACA
1 AGTTCAAGCCCCAATGTGAGAACAATTACCAAGTTCAAGGACTAACTTGAACAAAAAA-A
* * * ** * *
60764 AGTTCAAGCTCCAATGTGGGAATAATTACCAAGTTCAAGGGTTAATTTGGACAAAAAAA
1 AGTTCAAGCCCCAATGTGAGAACAATTACCAAGTTCAAGGACTAACTTGAACAAAAAAA
*
60823 AGTTCAAACCCCAATGTGAGAACAATT
1 AGTTCAAGCCCCAATGTGAGAACAATT
60850 GTTTAGTTCA
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 24 0.34
60 47 0.66
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.24
Consensus pattern (59 bp):
AGTTCAAGCCCCAATGTGAGAACAATTACCAAGTTCAAGGACTAACTTGAACAAAAAAA
Found at i:62914 original size:16 final size:17
Alignment explanation
Indices: 62893--62934 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
62883 AAATTTTACA
*
62893 AAAAAATTTTAAA-ATT
1 AAAAAATTATAAATATT
*
62909 AAAAAATTATAAATTTT
1 AAAAAATTATAAATATT
62926 AAAAAATTA
1 AAAAAATTA
62935 CAAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAAATTATAAATATT
Found at i:62914 original size:17 final size:16
Alignment explanation
Indices: 62893--62939 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
62883 AAATTTTACA
*
62893 AAAAAATTTTAAAATT
1 AAAAAATTATAAAATT
*
62909 AAAAAATTATAAATTTT
1 AAAAAATTATAAA-ATT
*
62926 AAAAAATTACAAAA
1 AAAAAATTATAAAA
62940 AATATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAAATTATAAAATT
Found at i:63002 original size:18 final size:20
Alignment explanation
Indices: 62970--63023 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 20
62960 AACTTACAAA
* *
62970 AAAAATATTTTAAAACTATT
1 AAAATTATTATAAAACTATT
62990 -AAATTATTA-AAAA-TATT
1 AAAATTATTATAAAACTATT
*
63007 AAAATTTTTATAAAACT
1 AAAATTATTATAAAACT
63024 TCAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.14
18 12 0.43
19 11 0.39
20 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTATTATAAAACTATT
Found at i:63286 original size:72 final size:74
Alignment explanation
Indices: 63165--63317 Score: 170
Period size: 72 Copynumber: 2.1 Consensus size: 74
63155 AAACTTTAGT
* * * * *
63165 ATTTTTATATTTTATAATTTTTTTTGTAAGTTTATATTTTTCCTATTTTAATCA-TTTT-GTAAT
1 ATTTTTTTATTTTATAATTTTTTTTATAAATTTATATTTTTCATATTTTAAT-AGTTTTAATAAT
63228 TTTTA-AATA
65 TTTTAGAATA
* * * *
63237 ATTTTTTTAGTTTT-TAATTTTTTTTATAAATTTGTATTTTTTATGTTTTAGTAGTTTTAATAAT
1 ATTTTTTTA-TTTTATAATTTTTTTTATAAATTTATATTTTTCATATTTTAATAGTTTTAATAAT
63301 TTTTAGAATA
65 TTTTAGAATA
*
63311 GTTTTTT
1 ATTTTTT
63318 GTAAATTTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
71 1 0.01
72 43 0.64
73 13 0.19
74 10 0.15
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (74 bp):
ATTTTTTTATTTTATAATTTTTTTTATAAATTTATATTTTTCATATTTTAATAGTTTTAATAATT
TTTAGAATA
Found at i:67742 original size:7 final size:7
Alignment explanation
Indices: 67732--67774 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
67722 TTGAAAATAA
67732 AAAATTT
1 AAAATTT
67739 AAAATTT
1 AAAATTT
*
67746 AAAGTTT
1 AAAATTT
*
67753 CATAATTT
1 -AAAATTT
67761 AAAA-TT
1 AAAATTT
67767 AAAATTT
1 AAAATTT
67774 A
1 A
67775 TCAAACAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
6 6 0.20
7 19 0.63
8 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (7 bp):
AAAATTT
Found at i:67802 original size:7 final size:7
Alignment explanation
Indices: 67790--67829 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
67780 CAATCTAATT
67790 ATATTTA
1 ATATTTA
67797 ATATTTA
1 ATATTTA
67804 ATATTTA
1 ATATTTA
67811 ATATTTA
1 ATATTTA
67818 ATATTTA
1 ATATTTA
67825 A-ATTT
1 ATATTT
67830 TAAATAACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.12
7 29 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:68155 original size:57 final size:57
Alignment explanation
Indices: 68093--68205 Score: 226
Period size: 57 Copynumber: 2.0 Consensus size: 57
68083 TAATAAAAAA
68093 TATAATAATTATGCATGAACCAAGCTATGAACAATGATGATTGATGAATTAAAAAGC
1 TATAATAATTATGCATGAACCAAGCTATGAACAATGATGATTGATGAATTAAAAAGC
68150 TATAATAATTATGCATGAACCAAGCTATGAACAATGATGATTGATGAATTAAAAAG
1 TATAATAATTATGCATGAACCAAGCTATGAACAATGATGATTGATGAATTAAAAAG
68206 TAACCCAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (57 bp):
TATAATAATTATGCATGAACCAAGCTATGAACAATGATGATTGATGAATTAAAAAGC
Found at i:73653 original size:20 final size:20
Alignment explanation
Indices: 73608--73654 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
73598 TACAATAAAA
73608 AATAAAATATTATAAACAAT
1 AATAAAATATTATAAACAAT
** *
73628 GTTAAAAT-TTATCAACTAAT
1 AATAAAATATTATAAAC-AAT
73648 AATAAAA
1 AATAAAA
73655 AAATAATAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (20 bp):
AATAAAATATTATAAACAAT
Found at i:85405 original size:3 final size:3
Alignment explanation
Indices: 85397--85431 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
85387 TTGGTTTTCC
85397 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
85432 TATAACTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:88531 original size:21 final size:21
Alignment explanation
Indices: 88493--88532 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
88483 GTTTTTAGTA
*
88493 TCGATAGAAGTATGACTTGAT
1 TCGATAGAAGTATCACTTGAT
88514 TCGATAGAAGCT-TCACTTG
1 TCGATAGAAG-TATCACTTG
88533 TATCAGTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (21 bp):
TCGATAGAAGTATCACTTGAT
Found at i:90194 original size:24 final size:24
Alignment explanation
Indices: 90167--90225 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
90157 TTTAGCCCAC
90167 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
90191 ACGAGACCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
90215 AGGAGCCCAGA
1 ACGAGCCCAGA
90226 TAGAGTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:100705 original size:19 final size:19
Alignment explanation
Indices: 100681--100782 Score: 82
Period size: 19 Copynumber: 5.4 Consensus size: 19
100671 TAGAGAATAC
100681 AACTTCATTCCCATAACCA
1 AACTTCATTCCCATAACCA
** * *
100700 AACTTCAAACCAAATTA-CA
1 AACTTCATTCC-CATAACCA
*
100719 AATTTCATTCCCATAACCA
1 AACTTCATTCCCATAACCA
** * *
100738 AACTTCAAACCAAATTA-CA
1 AACTTCATTCC-CATAACCA
*
100757 AATTTCATTCCCATAACCA
1 AACTTCATTCCCATAACCA
100776 AACTTCA
1 AACTTCA
100783 AACCTTCAAC
Statistics
Matches: 59, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
18 6 0.10
19 47 0.80
20 6 0.10
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.26
Consensus pattern (19 bp):
AACTTCATTCCCATAACCA
Found at i:100726 original size:38 final size:38
Alignment explanation
Indices: 100684--100786 Score: 206
Period size: 38 Copynumber: 2.7 Consensus size: 38
100674 AGAATACAAC
100684 TTCATTCCCATAACCAAACTTCAAACCAAATTACAAAT
1 TTCATTCCCATAACCAAACTTCAAACCAAATTACAAAT
100722 TTCATTCCCATAACCAAACTTCAAACCAAATTACAAAT
1 TTCATTCCCATAACCAAACTTCAAACCAAATTACAAAT
100760 TTCATTCCCATAACCAAACTTCAAACC
1 TTCATTCCCATAACCAAACTTCAAACC
100787 TTCAACCTGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (38 bp):
TTCATTCCCATAACCAAACTTCAAACCAAATTACAAAT
Found at i:106742 original size:16 final size:17
Alignment explanation
Indices: 106721--106754 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
106711 TCCTTTAACA
*
106721 ATTTTTA-AATATTTTT
1 ATTTTTATAAAATTTTT
106737 ATTTTTATAAAATTTTT
1 ATTTTTATAAAATTTTT
106754 A
1 A
106755 ATGATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTATAAAATTTTT
Found at i:107351 original size:58 final size:60
Alignment explanation
Indices: 107233--107367 Score: 175
Period size: 58 Copynumber: 2.3 Consensus size: 60
107223 TCAAATTAGA
** * *
107233 AAAAAAAAAAGTCAAGTTCAGGTATCAAATTGGGTCCAAACAAAGTTTAAGTACCAAATT
1 AAAAAAAAGTGTCAAGTTCAGATATCAAATTGGGTCCAAACAAAATTTAAGTACCAAATT
** * *
107293 AGGAAAAAGTGTCAAGTTTAGATATCAAATTGGGT-CAAA-AAAATTTAGGTACCAAATT
1 AAAAAAAAGTGTCAAGTTCAGATATCAAATTGGGTCCAAACAAAATTTAAGTACCAAATT
*
107351 AAAAAAAAGTATCAAGT
1 AAAAAAAAGTGTCAAGT
107368 ACATGTACCA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 31 0.48
59 4 0.06
60 29 0.45
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (60 bp):
AAAAAAAAGTGTCAAGTTCAGATATCAAATTGGGTCCAAACAAAATTTAAGTACCAAATT
Found at i:107380 original size:58 final size:59
Alignment explanation
Indices: 107269--107380 Score: 129
Period size: 58 Copynumber: 1.9 Consensus size: 59
107259 AAATTGGGTC
* ** * ** *
107269 CAAACAAAGTTTAAGTACCAAATTAGGAAAAAGTGTCAAGTTTAGATATCAAATTGGGT
1 CAAACAAAATTTAAGTACCAAATTAAAAAAAAGTATCAAGTACAGATACCAAATTGGGT
*
107328 CAAA-AAAATTTAGGTACCAAATTAAAAAAAAGTATCAAGTACATG-TACCAAAT
1 CAAACAAAATTTAAGTACCAAATTAAAAAAAAGTATCAAGTACA-GATACCAAAT
107381 GTTATATTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
58 39 0.89
59 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (59 bp):
CAAACAAAATTTAAGTACCAAATTAAAAAAAAGTATCAAGTACAGATACCAAATTGGGT
Found at i:109931 original size:63 final size:65
Alignment explanation
Indices: 109847--109969 Score: 162
Period size: 63 Copynumber: 1.9 Consensus size: 65
109837 CCAAAATAAC
* *
109847 ATAATTTATGAAAAAATAAAAATTAGACTATAAATA-TATAT-GA-AAAATATTTAAATTTATAT
1 ATAATTTATCAAAAAATAAAAATTAAACTATAAATAGTATATCGAGAAAATATTTAAATTTATAT
* *
109909 ATAATTTATCAAGAAACTAAAAATTAAATTATAAATATGTATATGCGAGAAAATATTTAAA
1 ATAATTTATCAA-AAAATAAAAATTAAACTATAAATA-GTATAT-CGAGAAAATATTTAAA
109970 AATATCGATA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
62 11 0.22
63 21 0.41
65 5 0.10
67 2 0.04
68 12 0.24
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (65 bp):
ATAATTTATCAAAAAATAAAAATTAAACTATAAATAGTATATCGAGAAAATATTTAAATTTATAT
Done.