Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014748.1 Kokia drynarioides strain JFW-HI SEQ_129787, 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: 86372
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 167 characters in sequence are not A, C, G, or T
Found at i:774 original size:38 final size:38
Alignment explanation
Indices: 723--798 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
713 GCTTGTTGAT
723 AAGTCAATTATAATGATCGAGGAACAACCTCAAACTAC
1 AAGTCAATTATAATGATCGAGGAACAACCTCAAACTAC
761 AAGTCAATTATAATGATCGAGGAACAACCTCAAACTAC
1 AAGTCAATTATAATGATCGAGGAACAACCTCAAACTAC
799 CAATCTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (38 bp):
AAGTCAATTATAATGATCGAGGAACAACCTCAAACTAC
Found at i:5239 original size:37 final size:37
Alignment explanation
Indices: 5187--5347 Score: 114
Period size: 37 Copynumber: 4.6 Consensus size: 37
5177 GCGCAATTTA
5187 TTACTTCGGATTTATCCGATGAGGCACAAGGTGCCAAT
1 TTACTTC-GATTTATCCGATGAGGCACAAGGTGCCAAT
* ** *
5225 TTACTTCGATTTATCCGATGAGACACTGGGTGTCAACT
1 TTACTTCGATTTATCCGATGAGGCACAAGGTGCCAA-T
* * * **
5263 TTA--T---TTTA-GCG-T-AGG-ACATGAT--TTA-
1 TTACTTCGATTTATCCGATGAGGCACAAGGTGCCAAT
5288 TTACTTCAGATTTATCCGATGAGGCAC-AGAGTGCCAAT
1 TTACTTC-GATTTATCCGATGAGGCACAAG-GTGCCAAT
5326 TTACTTCGATTTATCCGATGAG
1 TTACTTCGATTTATCCGATGAG
5348 ACACTGGGTG
Statistics
Matches: 92, Mismatches: 16, Indels: 31
0.66 0.12 0.22
Matches are distributed among these distances:
25 3 0.03
27 2 0.02
29 4 0.04
30 2 0.02
31 5 0.05
32 4 0.04
33 5 0.05
34 4 0.04
35 3 0.03
36 1 0.01
37 41 0.45
38 18 0.20
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (37 bp):
TTACTTCGATTTATCCGATGAGGCACAAGGTGCCAAT
Found at i:5287 original size:101 final size:101
Alignment explanation
Indices: 5102--5425 Score: 533
Period size: 101 Copynumber: 3.2 Consensus size: 101
5092 GACTATGAGT
* *
5102 CGATGAGGCACAGAGTGCCAATTTACTTCGGTTTATCCGATGAGACATTGGGTGTCAACTTTATT
1 CGATGAGGCACAGAGTGCCAATTTACTTCGATTTATCCGATGAGACACTGGGTGTCAACTTTATT
* * * ***
5167 TTAGTGCAGGGCGCAATTTATTACTTCGGATTTATC
66 TTAGCGTAGGACATGATTTATTACTTCGGATTTATC
5203 CGATGAGGCACA-AGGTGCCAATTTACTTCGATTTATCCGATGAGACACTGGGTGTCAACTTTAT
1 CGATGAGGCACAGA-GTGCCAATTTACTTCGATTTATCCGATGAGACACTGGGTGTCAACTTTAT
*
5267 TTTAGCGTAGGACATGATTTATTACTTCAGATTTATC
65 TTTAGCGTAGGACATGATTTATTACTTCGGATTTATC
5304 CGATGAGGCACAGAGTGCCAATTTACTTCGATTTATCCGATGAGACACTGGGTGTCAACTTTATT
1 CGATGAGGCACAGAGTGCCAATTTACTTCGATTTATCCGATGAGACACTGGGTGTCAACTTTATT
5369 TTAGCGTAGGACATGATTTATTACTTCGGATTTATC
66 TTAGCGTAGGACATGATTTATTACTTCGGATTTATC
* *
5405 CGATGAGGCATAGGGTGCCAA
1 CGATGAGGCACAGAGTGCCAA
5426 ACCAATTTGT
Statistics
Matches: 209, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
100 1 0.00
101 207 0.99
102 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (101 bp):
CGATGAGGCACAGAGTGCCAATTTACTTCGATTTATCCGATGAGACACTGGGTGTCAACTTTATT
TTAGCGTAGGACATGATTTATTACTTCGGATTTATC
Found at i:5877 original size:3 final size:3
Alignment explanation
Indices: 5869--5906 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5859 ATTCCCGAAC
5869 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5907 CTATTAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:7233 original size:17 final size:17
Alignment explanation
Indices: 7211--7243 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7201 TGAAAAACCT
7211 AGACATAAAGCAAGACC
1 AGACATAAAGCAAGACC
7228 AGACATAAAGCAAGAC
1 AGACATAAAGCAAGAC
7244 TTGTTGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.21, G:0.18, T:0.06
Consensus pattern (17 bp):
AGACATAAAGCAAGACC
Found at i:8650 original size:17 final size:17
Alignment explanation
Indices: 8628--8667 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
8618 AGGTGGAGAA
* *
8628 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
8645 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
8662 CTTGTT
1 CTTGTT
8668 AAGGTGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.47
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:8869 original size:49 final size:49
Alignment explanation
Indices: 8813--8915 Score: 197
Period size: 49 Copynumber: 2.1 Consensus size: 49
8803 ATTTTAATTA
8813 GAATAAGGTGTTTCAACCTTACTACGTTACTTCTATTAGTTGCTGATTG
1 GAATAAGGTGTTTCAACCTTACTACGTTACTTCTATTAGTTGCTGATTG
*
8862 GAATAAGGTGTTTCAACCTTACTACGTTACTTCTATTAGTTGTTGATTG
1 GAATAAGGTGTTTCAACCTTACTACGTTACTTCTATTAGTTGCTGATTG
8911 GAATA
1 GAATA
8916 GGCGTAGTCA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (49 bp):
GAATAAGGTGTTTCAACCTTACTACGTTACTTCTATTAGTTGCTGATTG
Found at i:12877 original size:23 final size:23
Alignment explanation
Indices: 12815--12915 Score: 100
Period size: 23 Copynumber: 4.3 Consensus size: 23
12805 GAACCTTAGC
*
12815 GTGCTCTCCGTTTAGCACGTCTCT
1 GTGCTCTCCGTTTAGCACGT-TGT
**
12839 -TGCTCTCTATTATTAGCAC-TATGT
1 GTGCTCTC-CGT-TTAGCACGT-TGT
*
12863 GTGCTCTCCGTTTAGCACTTTGT
1 GTGCTCTCCGTTTAGCACGTTGT
*
12886 GTGCTTTCCGTTTAGCACGTT-T
1 GTGCTCTCCGTTTAGCACGTTGT
12908 GTGCTCTC
1 GTGCTCTC
12916 TGTTCATTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 8 0.12
23 36 0.56
24 6 0.09
25 14 0.22
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.43
Consensus pattern (23 bp):
GTGCTCTCCGTTTAGCACGTTGT
Found at i:14847 original size:53 final size:53
Alignment explanation
Indices: 14774--14917 Score: 200
Period size: 53 Copynumber: 2.7 Consensus size: 53
14764 TACTATCACA
* * * *
14774 GATTGAAGGTCCGATGACTTTGTGTTATCGTGAGTTATTTGAATCC-TATTGCG
1 GATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTATATGAA-CCTTATTACG
* *
14827 GATTAAAGGTCTGATAACTTTGTGTCATCGTGAGTTATATGAACCTTATTACG
1 GATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTATATGAACCTTATTACG
**
14880 GATTAAAGGTCCGATGACTCCGTGTCATCGTGAGTTAT
1 GATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTAT
14918 CAAATGTGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 2 0.03
53 78 0.98
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTTTGTGTCATCGTGAGTTATATGAACCTTATTACG
Found at i:16808 original size:6 final size:6
Alignment explanation
Indices: 16797--16821 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16787 ATGACTCGTG
16797 TCATGA TCATGA TCATGA TCATGA T
1 TCATGA TCATGA TCATGA TCATGA T
16822 TTAACCTATT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TCATGA
Found at i:17801 original size:5 final size:5
Alignment explanation
Indices: 17791--17815 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
17781 TAAAATTATG
17791 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
17816 TACAAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:20130 original size:13 final size:13
Alignment explanation
Indices: 20084--20123 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 13
20074 AAAACATCTT
20084 GAAATAAAGAAAAG
1 GAAA-AAAGAAAAG
20098 GAGAAGAAAGAAAAG
1 GA-AA-AAAGAAAAG
20113 GAAAAAAGAAA
1 GAAAAAAGAAA
20124 GTGAAAAGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 7 0.29
14 4 0.17
15 13 0.54
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (13 bp):
GAAAAAAGAAAAG
Found at i:20739 original size:24 final size:24
Alignment explanation
Indices: 20707--20762 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
20697 GGGTAATTGT
* *
20707 GCTGCCATGGCTACTTCTTCCAGC
1 GCTGACATGACTACTTCTTCCAGC
*
20731 GCTGACATGACTACTTCTTCCAGT
1 GCTGACATGACTACTTCTTCCAGC
20755 GCTGACAT
1 GCTGACAT
20763 AACTGTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.32, G:0.20, T:0.30
Consensus pattern (24 bp):
GCTGACATGACTACTTCTTCCAGC
Found at i:28728 original size:6 final size:6
Alignment explanation
Indices: 28717--28743 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28707 CAATTCAACG
28717 TGAACA TGAACA TGAACA TGAACA TGA
1 TGAACA TGAACA TGAACA TGAACA TGA
28744 GCGCGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAACA
Found at i:30700 original size:3 final size:3
Alignment explanation
Indices: 30692--30717 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30682 GGTCTTCACT
30692 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
30718 GGGATGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:31294 original size:15 final size:16
Alignment explanation
Indices: 31274--31307 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
31264 AATCCTTTAA
31274 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
31289 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
31305 AAA
1 AAA
31308 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:32844 original size:19 final size:19
Alignment explanation
Indices: 32820--32864 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
32810 TGTTGTTTTA
32820 TCACTATTTTACTACCAAT
1 TCACTATTTTACTACCAAT
32839 TCACTATTTTACTACCAAT
1 TCACTATTTTACTACCAAT
32858 TCACTAT
1 TCACTAT
32865 GTTGTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (19 bp):
TCACTATTTTACTACCAAT
Found at i:32972 original size:13 final size:12
Alignment explanation
Indices: 32954--32983 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
32944 TGCAATGTTA
32954 TTTAAATATATAT
1 TTTAAATATAT-T
32967 TTTAAATATATT
1 TTTAAATATATT
32979 TTTAA
1 TTTAA
32984 TTTGTTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTAAATATATT
Found at i:33872 original size:2 final size:2
Alignment explanation
Indices: 33865--33904 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
33855 ATCTCGCATC
33865 AT 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 AT
33905 TAATAACCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36734 original size:73 final size:72
Alignment explanation
Indices: 36647--36792 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 72
36637 TAAATAAAAA
* *
36647 AAATTAAATAGGGACCAATTGTATTATTTAATCTAAAATTTTTGTTTGAAATGATAATTTAACGT
1 AAATTAAACAGGGACCAATTGCATTATTTAATCTAAAA-TTTTGTTTGAAATGATAATTTAACGT
36712 GTCATATC
65 GTCATATC
36720 AAATTAAACAGGGACCAATTGCATTATTTAATCTAAAATTTTGTTTGAAATGATAATTTAACGTG
1 AAATTAAACAGGGACCAATTGCATTATTTAATCTAAAATTTTGTTTGAAATGATAATTTAACGTG
*
36785 TTATATC
66 TCATATC
36792 A
1 A
36793 GTTTATCTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 34 0.49
73 36 0.51
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (72 bp):
AAATTAAACAGGGACCAATTGCATTATTTAATCTAAAATTTTGTTTGAAATGATAATTTAACGTG
TCATATC
Found at i:40637 original size:23 final size:23
Alignment explanation
Indices: 40607--40650 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
40597 ATCTGTTTGA
40607 TAAAAACATGTTATTTTATAAGG
1 TAAAAACATGTTATTTTATAAGG
40630 TAAAAACATGTTATTTTATAA
1 TAAAAACATGTTATTTTATAA
40651 TAATCTTATA
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:0.09, T:0.41
Consensus pattern (23 bp):
TAAAAACATGTTATTTTATAAGG
Found at i:43795 original size:60 final size:60
Alignment explanation
Indices: 43728--43872 Score: 195
Period size: 60 Copynumber: 2.4 Consensus size: 60
43718 TTAAAGCCTT
* *
43728 AATGTGGGAACAATTGCCAAGTTCAGGCCCTAACTTGGACCAAAAAAAAGTTTAGGA-CCC
1 AATGTGGGAACAATTGCCAAGTTCAGGACCTAACTTGGACCAAAAAAAAGTTCA-GACCCC
* * *
43788 AATGTGGGAACAATTGCCAAGTTTAGGACCTAAGTTGGACCAAAAAAATGTTCAGACCCC
1 AATGTGGGAACAATTGCCAAGTTCAGGACCTAACTTGGACCAAAAAAAAGTTCAGACCCC
* *
43848 AATGAGGGAA-AAGTTGCCAACTTCA
1 AATGTGGGAACAA-TTGCCAAGTTCA
43873 ATAAGCCCCA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 4 0.05
60 71 0.95
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (60 bp):
AATGTGGGAACAATTGCCAAGTTCAGGACCTAACTTGGACCAAAAAAAAGTTCAGACCCC
Found at i:52242 original size:36 final size:37
Alignment explanation
Indices: 52195--52264 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
52185 ATTTTTTTAA
* * * *
52195 TAAATTATATTTAAAT-GTTTACTATATTGATATTTG
1 TAAATAATATTTAAATAATTTAATATAATGATATTTG
52231 TAAATAATATTTAAATAATTTAATATAATGATAT
1 TAAATAATATTTAAATAATTTAATATAATGATAT
52265 AAAAAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 15 0.52
37 14 0.48
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (37 bp):
TAAATAATATTTAAATAATTTAATATAATGATATTTG
Found at i:58865 original size:26 final size:26
Alignment explanation
Indices: 58813--58865 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
58803 TTATATTTAA
* *
58813 AATTTTAAAATATTTTATATATCATT
1 AATTTTAAAATAATTTATATATAATT
*
58839 AATTTTATTAATAATTTATAT-TAATT
1 AATTTTA-AAATAATTTATATATAATT
58865 A
1 A
58866 CATAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
AATTTTAAAATAATTTATATATAATT
Found at i:60283 original size:23 final size:22
Alignment explanation
Indices: 60256--60309 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
60246 GCTGTTTTTG
* *
60256 TATTTTTTTACTGTTTTGGTTAT
1 TATTTTTGTACTGTTTT-GCTAT
**
60279 TATTTTTGTGTTGTTTTGCTAT
1 TATTTTTGTACTGTTTTGCTAT
60301 TATTTTTGT
1 TATTTTTGT
60310 TGCTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.11, C:0.04, G:0.15, T:0.70
Consensus pattern (22 bp):
TATTTTTGTACTGTTTTGCTAT
Found at i:60301 original size:22 final size:23
Alignment explanation
Indices: 60267--60309 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
60257 ATTTTTTTAC
*
60267 TGTTTTGGTTATTATTTTTGTGT
1 TGTTTTGGCTATTATTTTTGTGT
60290 TGTTTT-GCTATTATTTTTGT
1 TGTTTTGGCTATTATTTTTGT
60310 TGCTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.09, C:0.02, G:0.19, T:0.70
Consensus pattern (23 bp):
TGTTTTGGCTATTATTTTTGTGT
Found at i:60314 original size:15 final size:15
Alignment explanation
Indices: 60289--60369 Score: 53
Period size: 15 Copynumber: 5.5 Consensus size: 15
60279 TATTTTTGTG
60289 TTGTT-TTGCTATTAT
1 TTGTTGTTGCTATT-T
60304 TT-TTGTTGCTATTT
1 TTGTTGTTGCTATTT
** * *
60318 TTGTTGTTTTTAATG
1 TTGTTGTTGCTATTT
* * *
60333 TCGTTTGCTGTTATTT
1 TTG-TTGTTGCTATTT
60349 TTGTTGTTG-T-TTT
1 TTGTTGTTGCTATTT
60362 TTGTTGTT
1 TTGTTGTT
60370 TAGATGTTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
13 11 0.21
14 6 0.12
15 25 0.48
16 10 0.19
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (15 bp):
TTGTTGTTGCTATTT
Found at i:60361 original size:34 final size:33
Alignment explanation
Indices: 60313--60383 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 33
60303 TTTTTGTTGC
** *
60313 TATTTTTGTTGTT-TTTAATGTCGTTT-GCTGT
1 TATTTTTGTTGTTGTTTTTTGTCGTTTAGATGT
*
60344 TATTTTTGTTGTTGTTTTTTGTTGTTTAGATGT
1 TATTTTTGTTGTTGTTTTTTGTCGTTTAGATGT
60377 TATTTTT
1 TATTTTT
60384 TATGCCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 13 0.38
32 10 0.29
33 11 0.32
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (33 bp):
TATTTTTGTTGTTGTTTTTTGTCGTTTAGATGT
Found at i:60366 original size:22 final size:22
Alignment explanation
Indices: 60278--60366 Score: 74
Period size: 22 Copynumber: 4.1 Consensus size: 22
60268 GTTTTGGTTA
*
60278 TTATTTTTG-TGTTGTTTTGCTA
1 TTATTTTTGTTGTTGTTTT-CTG
* *
60300 TTATTTTTGTTGCTATTTT-TG
1 TTATTTTTGTTGTTGTTTTCTG
* ** * *
60321 TTGTTTTTAATGTCGTTTGCTG
1 TTATTTTTGTTGTTGTTTTCTG
*
60343 TTATTTTTGTTGTTGTTTTTTG
1 TTATTTTTGTTGTTGTTTTCTG
60365 TT
1 TT
60367 GTTTAGATGT
Statistics
Matches: 49, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
21 13 0.27
22 29 0.59
23 7 0.14
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (22 bp):
TTATTTTTGTTGTTGTTTTCTG
Found at i:60384 original size:34 final size:33
Alignment explanation
Indices: 60318--60383 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
60308 GTTGCTATTT
*
60318 TTGTTGTTTTTAATGTCGTTTGCTGTTATTTTTG
1 TTGTTGTTTTT-ATGTCGTTTGATGTTATTTTTG
*
60352 TTGTTGTTTTT-TGTTGTTTAGATGTTATTTTT
1 TTGTTGTTTTTATGTCGTTT-GATGTTATTTTT
60384 TATGCCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 7 0.24
33 11 0.38
34 11 0.38
ACGTcount: A:0.09, C:0.03, G:0.20, T:0.68
Consensus pattern (33 bp):
TTGTTGTTTTTATGTCGTTTGATGTTATTTTTG
Found at i:63721 original size:13 final size:13
Alignment explanation
Indices: 63705--63729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63695 AAAATAAAAA
63705 AAATATCAAATTC
1 AAATATCAAATTC
63718 AAATATCAAATT
1 AAATATCAAATT
63730 GAATCAAAAT
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATCAAATTC
Found at i:69161 original size:60 final size:57
Alignment explanation
Indices: 69061--69230 Score: 180
Period size: 60 Copynumber: 2.9 Consensus size: 57
69051 AATTTGAATA
* * * *
69061 TAAAAAAAACTTAGGTACCAAATT-AGGAAAATATGCCAAGTTTAGGTACCAAATTGGG
1 TAAAAAAAGCTTAGGTACCAAATTAAGAAAAATAT--CAAGTTTAAGTACCAAAATGGG
* * *
69119 TCCAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTATCAAGTTCATGTACCAAAATGGG
1 T--AAAAAAAGCTTAGGTACCAAATTAAGAAAAA-TATCAAGTTTAAGTACCAAAATGGG
* ** * *
69179 TAAAAAAAGCTTAAGTACTGAATTAAAAAAAATATCAAATTTAAGTACCAAA
1 TAAAAAAAGCTTAGGTACCAAATTAAGAAAAATATCAAGTTTAAGTACCAAA
69231 GATTATATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
57 17 0.18
58 27 0.29
60 41 0.44
61 6 0.06
62 3 0.03
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (57 bp):
TAAAAAAAGCTTAGGTACCAAATTAAGAAAAATATCAAGTTTAAGTACCAAAATGGG
Found at i:70155 original size:12 final size:12
Alignment explanation
Indices: 70138--70170 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
70128 ATCCTTTTAA
70138 ATATATACATAC
1 ATATATACATAC
70150 ATATATACATAC
1 ATATATACATAC
*
70162 ATACATACA
1 ATATATACA
70171 GGGATTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (12 bp):
ATATATACATAC
Found at i:72483 original size:18 final size:18
Alignment explanation
Indices: 72452--72490 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
72442 TTTTTGGATA
**
72452 AATTATTATTATTAATAT
1 AATTATTAAAATTAATAT
*
72470 AATTATTAAAATTAATTT
1 AATTATTAAAATTAATAT
72488 AAT
1 AAT
72491 AAAAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTATTAAAATTAATAT
Found at i:74244 original size:11 final size:11
Alignment explanation
Indices: 74230--74255 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
74220 ATTTTAAAAA
74230 TTAATTAAATG
1 TTAATTAAATG
74241 TTAATTAAATG
1 TTAATTAAATG
74252 TTAA
1 TTAA
74256 CATAACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
TTAATTAAATG
Found at i:82726 original size:29 final size:27
Alignment explanation
Indices: 82694--82747 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
82684 TGTCCTTAAA
*
82694 TAATTTTAAAATTATTTAAATTATTTTTT
1 TAATTATAAAATTA-TTAAATT-TTTTTT
82723 TAATTATAAAATTATTAAATTTTTT
1 TAATTATAAAATTATTAAATTTTTT
82748 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 7 0.29
29 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TAATTATAAAATTATTAAATTTTTTTT
Found at i:82755 original size:28 final size:30
Alignment explanation
Indices: 82689--82759 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 30
82679 TGTCATGTCC
*
82689 TTAAATAATTTTAAAATTATTTAAATTATT
1 TTAAATAATTATAAAATTATTTAAATTATT
**
82719 TT-TTTAATTATAAAATTA-TTAAATT-TT
1 TTAAATAATTATAAAATTATTTAAATTATT
*
82746 TTAAAAAATTATAA
1 TTAAATAATTATAA
82760 TCATCATCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.12
28 15 0.44
29 13 0.38
30 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTAAATAATTATAAAATTATTTAAATTATT
Found at i:85213 original size:6 final size:6
Alignment explanation
Indices: 85188--85226 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
85178 ACAATTCATA
* * *
85188 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
85227 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Done.