Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012088.1 Kokia drynarioides strain JFW-HI SEQ_127087, 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: 75098
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 163 characters in sequence are not A, C, G, or T
Found at i:252 original size:43 final size:43
Alignment explanation
Indices: 170--254 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
160 ATTAACATGT
* * *
170 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGAATCGTATTAATATGCTTGCATGTTAC
* *
213 TAAATTATATTACTTTAATCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGAATCGTATTAATATGCTTG-CATGTTA
255 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGAATCGTATTAATATGCTTGCATGTTAC
Found at i:891 original size:21 final size:21
Alignment explanation
Indices: 865--905 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
855 TCATCGTGAT
*
865 ACTCTATTCCTCCCGGGCAAG
1 ACTCTACTCCTCCCGGGCAAG
*
886 ACTCTACTCCTCCGGGGCAA
1 ACTCTACTCCTCCCGGGCAA
906 ATGGACCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22
Consensus pattern (21 bp):
ACTCTACTCCTCCCGGGCAAG
Found at i:3132 original size:19 final size:18
Alignment explanation
Indices: 3101--3145 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3091 AATAAATTTG
*
3101 TTAAAAATTAAATAAAAT
1 TTAAAAATAAAATAAAAT
*
3119 TTAATAAATAAAATACAATT
1 TTAA-AAATAAAATA-AAAT
3139 TTAAAAA
1 TTAAAAA
3146 GATATCATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAATAAAATAAAAT
Found at i:3205 original size:4 final size:4
Alignment explanation
Indices: 3185--3237 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
3175 AACACATTAC
* * *
3185 CTTT CTCT CTTT C-TT CTTT CTTT CCTCT CCTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
3233 CTTT C
1 CTTT C
3238 CCGTTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 3 0.07
4 35 0.85
5 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:4686 original size:25 final size:25
Alignment explanation
Indices: 4654--4706 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
4644 ATAAATTAAC
4654 AAATAATAATTATTTGTTTCATATG
1 AAATAATAATTATTTGTTTCATATG
4679 AAATAATAATTATTTGTTTCATATG
1 AAATAATAATTATTTGTTTCATATG
4704 AAA
1 AAA
4707 AGCTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (25 bp):
AAATAATAATTATTTGTTTCATATG
Found at i:4807 original size:28 final size:28
Alignment explanation
Indices: 4751--4806 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4741 TAATTTGAAA
* *
4751 ATATGATTAAATTTTTCACTCAACTTTT
1 ATATGATTAAATTTTACACTAAACTTTT
*
4779 ATATGATTGAATTTTACTACTAAACTTT
1 ATATGATTAAATTTTAC-ACTAAACTTT
4807 AAATTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.48
Consensus pattern (28 bp):
ATATGATTAAATTTTACACTAAACTTTT
Found at i:11797 original size:53 final size:53
Alignment explanation
Indices: 11726--11829 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
11716 AATATAATTT
11726 TTTTTTTTTTGAAACTCCAGGGCAGAAAGAGTAGGTGAAAGTCGAAAATATAA
1 TTTTTTTTTTGAAACTCCAGGGCAGAAAGAGTAGGTGAAAGTCGAAAATATAA
11779 TTTTTTTTTTGAAACTCCAGGGCAGAAAGAGTAGGTGAAAGTCGAAAATAT
1 TTTTTTTTTTGAAACTCCAGGGCAGAAAGAGTAGGTGAAAGTCGAAAATAT
11830 TGGTGCCTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.31
Consensus pattern (53 bp):
TTTTTTTTTTGAAACTCCAGGGCAGAAAGAGTAGGTGAAAGTCGAAAATATAA
Found at i:15626 original size:14 final size:14
Alignment explanation
Indices: 15607--15637 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15597 AGAATAGATT
15607 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
15621 TTTAATTAATTAAA
1 TTTAATTAAATAAA
15635 TTT
1 TTT
15638 TTTTTAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:19203 original size:21 final size:21
Alignment explanation
Indices: 19177--19225 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
19167 GAAGAGATGA
*
19177 TGATACACTACCTGAATTAAT
1 TGATACACTACCTGAACTAAT
*
19198 TGATACCCTACCTGAACTAAT
1 TGATACACTACCTGAACTAAT
*
19219 TCATACA
1 TGATACA
19226 AAAATTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (21 bp):
TGATACACTACCTGAACTAAT
Found at i:30368 original size:19 final size:20
Alignment explanation
Indices: 30341--30380 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
30331 TTAGTAATGC
*
30341 TTTTATCTCACAAGTG-TTT
1 TTTTATCTCAAAAGTGCTTT
*
30360 TTTTGTCTCAAAAGTGCTTT
1 TTTTATCTCAAAAGTGCTTT
30380 T
1 T
30381 GAAAAGCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (20 bp):
TTTTATCTCAAAAGTGCTTT
Found at i:32359 original size:44 final size:41
Alignment explanation
Indices: 32222--32413 Score: 199
Period size: 42 Copynumber: 4.5 Consensus size: 41
32212 GAGGGTATAC
* *
32222 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTT
1 TAAAGGAAGACTCATGACTC-GGAAGAGCATGAGATTATGTT
* * * *
32264 AAAAAGGAAGACTCGTGATTCAGGAAGAGCAT-AGATTATAATT
1 -TAAAGGAAGACTCATGACTC-GGAAGAGCATGAGATTAT-GTT
* *
32307 T-AAGGAAGACTCATGACTCGGAAGAAGTATGAGGTTATGTTT
1 TAAAGGAAGACTCATGACTCGGAAG-AGCATGAGATTATG-TT
* *
32349 TAAAAGGAAGACTCATGACTCGAGATGAGCATGAGATTTTGTT
1 T-AAAGGAAGACTCATGACTCG-GAAGAGCATGAGATTATGTT
*
32392 TAAAGGAAGACTTATGACTCGG
1 TAAAGGAAGACTCATGACTCGG
32414 TTGATTATGT
Statistics
Matches: 124, Mismatches: 18, Indels: 16
0.78 0.11 0.10
Matches are distributed among these distances:
40 5 0.04
41 21 0.17
42 35 0.28
43 30 0.24
44 30 0.24
45 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCATGACTCGGAAGAGCATGAGATTATGTT
Found at i:43141 original size:31 final size:31
Alignment explanation
Indices: 43097--43185 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 31
43087 CTTTTTTTTT
* *
43097 TTTTTGCCCAATTTGATACTTGAACTTGACAC
1 TTTTT-CCTAATTTGATACTTAAACTTGACAC
* *
43129 TTTTTCTTAATTTGATACTTAAACTTGACAT
1 TTTTTCCTAATTTGATACTTAAACTTGACAC
*
43160 TTTTTCCTAATTTGATACCTAAACTT
1 TTTTTCCTAATTTGATACTTAAACTT
43186 TTTTTTGACT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 46 0.90
32 5 0.10
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTTTCCTAATTTGATACTTAAACTTGACAC
Found at i:43729 original size:31 final size:31
Alignment explanation
Indices: 43654--43788 Score: 98
Period size: 31 Copynumber: 4.5 Consensus size: 31
43644 CCCAAAAAAG
* * * *
43654 TTTAAGTACCAACTTAAGAAAAAATATCAAT
1 TTTAGGTACCAAATTAGGAAAAAATATCAAA
* *
43685 TTTAGGTACCAAATTAGGAAAAATTTTCAAA
1 TTTAGGTACCAAATTAGGAAAAAATATCAAA
* * **
43716 TTTGGGTATCAAATT-GGACCAAA-A--AAA
1 TTTAGGTACCAAATTAGGAAAAAATATCAAA
* * * * *
43743 TTTAAGTACCAAATTAAGAAAAATTGTCAAG
1 TTTAGGTACCAAATTAGGAAAAAATATCAAA
*
43774 TTTAAGTACCAAATT
1 TTTAGGTACCAAATT
43789 TATATTAAAC
Statistics
Matches: 79, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
27 15 0.19
28 4 0.05
30 5 0.06
31 55 0.70
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (31 bp):
TTTAGGTACCAAATTAGGAAAAAATATCAAA
Found at i:45270 original size:39 final size:41
Alignment explanation
Indices: 45182--45276 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 41
45172 TTTGTATTTT
* * *
45182 TATTTGAAATAATTATTTGGAATATTTCACATATAAACATAATAA
1 TATTTGAAATAATTAATCGAAATATTTCACATAT----ATAATAA
45227 TATTTGAAATAATTAATCGAAATATTTCACATAT-TAA-AA
1 TATTTGAAATAATTAATCGAAATATTTCACATATATAATAA
45266 TATTTGAAATA
1 TATTTGAAATA
45277 TCATACCCAC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 13 0.28
40 3 0.06
45 31 0.66
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (41 bp):
TATTTGAAATAATTAATCGAAATATTTCACATATATAATAA
Found at i:46089 original size:19 final size:19
Alignment explanation
Indices: 46053--46098 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
46043 ATCTCTTTTA
46053 AAAAATTATTACAAAATTC
1 AAAAATTATTACAAAATTC
* *
46072 TAAAATTATTA-ATTAATTC
1 AAAAATTATTACA-AAATTC
46091 AAAAATTA
1 AAAAATTA
46099 AATAATTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTATTACAAAATTC
Found at i:49716 original size:5 final size:5
Alignment explanation
Indices: 49706--49736 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
49696 GAATAAGTTC
49706 GGTTT GGTTT GGTTT GGTTT GGTTT GGTTT G
1 GGTTT GGTTT GGTTT GGTTT GGTTT GGTTT G
49737 TGCTTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.42, T:0.58
Consensus pattern (5 bp):
GGTTT
Found at i:52868 original size:29 final size:28
Alignment explanation
Indices: 52838--53126 Score: 102
Period size: 29 Copynumber: 9.9 Consensus size: 28
52828 TGGATACCCG
52838 GGGGGCAAAATGGAATTTTTAGACATTC
1 GGGGGCAAAATGGAATTTTTAGACATTC
* * * * **
52866 GGGGGTAAAAGGGTAATGTTGAGAGTTTC
1 GGGGGCAAAATGG-AATTTTTAGACATTC
* * *
52895 GAGGTCGAAAATGGAGTTTTTAGACATTC
1 GGGGGC-AAAATGGAATTTTTAGACATTC
* * *
52924 GGGGACAAAATGGTAAATTTT-GATAGTTTC
1 GGGGGCAAAATGG-AATTTTTAGACA--TTC
* * * * **
52954 GAGGTCAAAAATGGAAATTTTGGAGGTTC
1 GGGGGC-AAAATGGAATTTTTAGACATTC
* *
52983 GAGGGCAAAAATGGAATTTTTGGA-AGTTTC
1 GGGGGC-AAAATGGAATTTTTAGACA--TTC
** * *
53013 AAGGTCAAAATTGGAATTTTTGGA-AGTTC
1 GGGGGCAAAA-TGGAATTTTTAGACA-TTC
* * *
53042 GGGGGTAAAAATGGAATTTTTGGA-AGTTTT
1 GGGGG-CAAAATGGAATTTTTAGACA--TTC
* *
53072 GAGGGTCAAAATGGAATTTTTGGA-AGTTC
1 G-GGGGCAAAATGGAATTTTTAGACA-TTC
** *
53101 AGGGGTAAAAATGGAATTTTTGGACA
1 -GGGGGCAAAATGGAATTTTTAGACA
53127 GTTCAGGGAC
Statistics
Matches: 205, Mismatches: 41, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
28 21 0.10
29 104 0.51
30 68 0.33
31 12 0.06
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.31
Consensus pattern (28 bp):
GGGGGCAAAATGGAATTTTTAGACATTC
Found at i:52915 original size:58 final size:59
Alignment explanation
Indices: 52844--52974 Score: 183
Period size: 58 Copynumber: 2.2 Consensus size: 59
52834 CCCGGGGGGC
** *
52844 AAAATGGAATTTTTAGACATTCGGGGGTAAAAGGGT-AATGTTGAGAGTTTCGAGGTCG
1 AAAATGGAATTTTTAGACATTCGGGGACAAAAGGGTAAATGTTGAGAGTTTCGAGGTCA
* * * *
52902 AAAATGGAGTTTTTAGACATTCGGGGACAAAATGGTAAATTTTGATAGTTTCGAGGTCA
1 AAAATGGAATTTTTAGACATTCGGGGACAAAAGGGTAAATGTTGAGAGTTTCGAGGTCA
*
52961 AAAATGGAAATTTT
1 AAAATGGAATTTTT
52975 GGAGGTTCGA
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
58 32 0.51
59 31 0.49
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.31
Consensus pattern (59 bp):
AAAATGGAATTTTTAGACATTCGGGGACAAAAGGGTAAATGTTGAGAGTTTCGAGGTCA
Found at i:52972 original size:30 final size:30
Alignment explanation
Indices: 52889--53129 Score: 223
Period size: 29 Copynumber: 8.1 Consensus size: 30
52879 TAATGTTGAG
* * *
52889 AGTTTCGAGGTCGAAAATGGAGTTTTTAGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* * *
52919 CA--TTCGGGGAC-AAAATGGTAAATTTT-GA
1 -AGTTTCGAGGTCAAAAATGG-AATTTTTGGA
*
52947 TAGTTTCGAGGTCAAAAATGGAAATTTTGG-
1 -AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* *
52977 AGGTTCGAGGGCAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* *
53007 AGTTTCAAGGTCAAAATTGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
*
53037 AG-TTCGGGGGT-AAAAATGGAATTTTTGGA
1 AGTTTC-GAGGTCAAAAATGGAATTTTTGGA
*
53066 AGTTTTGAGGGTC-AAAATGGAATTTTTGGA
1 AGTTTCGA-GGTCAAAAATGGAATTTTTGGA
*
53096 AG-TTCAGGGGT-AAAAATGGAATTTTTGGA
1 AGTTTC-GAGGTCAAAAATGGAATTTTTGGA
53125 CAGTT
1 -AGTT
53130 CAGGGACCTC
Statistics
Matches: 175, Mismatches: 21, Indels: 28
0.78 0.09 0.12
Matches are distributed among these distances:
28 10 0.06
29 83 0.47
30 72 0.41
31 10 0.06
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (30 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGA
Found at i:52992 original size:59 final size:59
Alignment explanation
Indices: 52889--53129 Score: 237
Period size: 59 Copynumber: 4.1 Consensus size: 59
52879 TAATGTTGAG
* * *
52889 AGTTTCGAGGTCGAAAATGGAGTTTTTAGACA-TTCG-GGGACAAAATGGTAAATTTT-GA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGACAAAATGG-AAATTTTGGA
* * *
52947 TAGTTTCGAGGTCAAAAATGGAAATTTTGGAGGTTCGAGGG-CAAAAATGGAATTTTTGGA
1 -AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGAC-AAAATGGAAATTTTGGA
* * * *
53007 AGTTTCAAGGTCAAAATTGGAATTTTTGGAAGTTCGGGGGTA-AAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGG-ACAAAATGGAAATTTTGGA
* *
53066 AGTTTTGAGGGTC-AAAATGGAATTTTTGGAAGTTC-AGGGGTA-AAAATGGAATTTTTGGA
1 AGTTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTCGA-GGG-ACAAAATGGAAATTTTGGA
53125 CAGTT
1 -AGTT
53130 CAGGGACCTC
Statistics
Matches: 158, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
59 138 0.87
60 20 0.13
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (59 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGACAAAATGGAAATTTTGGA
Found at i:54240 original size:3 final size:3
Alignment explanation
Indices: 54232--54320 Score: 61
Period size: 3 Copynumber: 28.7 Consensus size: 3
54222 GTTTTCCTTT
* * * *
54232 TTA TTA TTAA TTA TTA ATA ATA TTA TTAA TTA CTA ATA GTTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA
* * * ** *
54280 TTA ATA ATA ATA TTA TTA TTA TTA TTA AAA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54321 GCCATTAATA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
3 64 0.89
4 8 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:55036 original size:6 final size:6
Alignment explanation
Indices: 55021--55086 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
55011 TTGAACATTG
* * *
55021 TTTAAT TTTAAA TTTATAA --TAAA TTTAAA TTTAAA -ATAAA TTTAAT
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
55067 TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
55087 TGTTGGGTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.04
5 10 0.21
6 34 0.71
7 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:55049 original size:17 final size:17
Alignment explanation
Indices: 55027--55086 Score: 102
Period size: 17 Copynumber: 3.5 Consensus size: 17
55017 ATTGTTTAAT
*
55027 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
55044 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
55061 TTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
55078 TTTAAATTT
1 TTTAAATTT
55087 TGTTGGGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:55642 original size:29 final size:27
Alignment explanation
Indices: 55566--55647 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 27
55556 TTTGAAACAC
55566 AATTAAAATTTCATATGTATAATTACATCA
1 AATTAAAA-TTCATA--TATAATTACATCA
*
55596 AATTAAAATTAATGTATATAATTACACATCA
1 AATTAAAATTCA--TATATAATT--ACATCA
55627 AATTAAAATTCATATATAATT
1 AATTAAAATTCATATATAATT
55648 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 19 0.41
30 8 0.17
31 19 0.41
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (27 bp):
AATTAAAATTCATATATAATTACATCA
Found at i:59667 original size:28 final size:28
Alignment explanation
Indices: 59632--59754 Score: 90
Period size: 28 Copynumber: 4.3 Consensus size: 28
59622 GGATACTCGG
59632 GGGGTAAAATGGTAATTTTGGATTTTTA
1 GGGGTAAAATGGTAATTTTGGATTTTTA
*
59660 GGGGTAAAATGGTTATTTTGGGAAATTTTTA
1 GGGGTAAAATGGTAATTTT-GG--ATTTTTA
* * * ** *
59691 -GGTTAAGAAT-GAAATTTTAGACATTCA
1 GGGGTAA-AATGGTAATTTTGGATTTTTA
* *
59718 GGGGTAAAAGGGTAATTTTGAGAGTTTT-
1 GGGGTAAAATGGTAATTTTG-GATTTTTA
*
59746 GAGGTAAAA
1 GGGGTAAAA
59755 AATGGAGATT
Statistics
Matches: 72, Mismatches: 16, Indels: 14
0.71 0.16 0.14
Matches are distributed among these distances:
27 6 0.08
28 38 0.53
29 7 0.10
30 11 0.15
31 10 0.14
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGATTTTTA
Found at i:59817 original size:30 final size:29
Alignment explanation
Indices: 59763--60070 Score: 291
Period size: 30 Copynumber: 10.4 Consensus size: 29
59753 AAAATGGAGA
* *
59763 TTTTGG-AGGTTCGAGGATAAAAATGAAAT
1 TTTTGGAAGTTTCG-GGGTAAAAATGAAAT
* *
59792 TTTTAGAAGTTTCGGGGTCAAAAATGACAT
1 TTTTGGAAGTTTCGGGGT-AAAAATGAAAT
59822 TTTTGGAAG-TTCGAGGGTAAAAATGAAAT
1 TTTTGGAAGTTTCG-GGGTAAAAATGAAAT
*
59851 TTTTGGAAGTTTTAGGGGTAAAAATGAAAT
1 TTTTGGAAG-TTTCGGGGTAAAAATGAAAT
* *
59881 TTTTGGAAGTTTCAGGGTCAAAAATGACAT
1 TTTTGGAAGTTTCGGGGT-AAAAATGAAAT
* *
59911 TTTTGGAAGTTT-GGGGATAAAAGTGGAAT
1 TTTTGGAAGTTTCGGGG-TAAAAATGAAAT
* * * *
59940 TTTTGGTAGTGTTAGGGTTAAAAATGGAAT
1 TTTTGGAAGT-TTCGGGGTAAAAATGAAAT
* **
59970 TTTTGGAAGTTTTGGGGTTAAAAATGGTAT
1 TTTTGGAAGTTTCGGGG-TAAAAATGAAAT
** * *
60000 TTTTGGAAGTTTTAGGGTTAAAATGGAAT
1 TTTTGGAAGTTTCGGGGTAAAAATGAAAT
* *
60029 TTTTGAAAG-TTCAGGGGTAAAAATGTAAT
1 TTTTGGAAGTTTC-GGGGTAAAAATGAAAT
*
60058 TTTTAGATAGTTT
1 TTTTGGA-AGTTT
60071 AAGGACCTTC
Statistics
Matches: 235, Mismatches: 31, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
28 2 0.01
29 99 0.42
30 126 0.54
31 8 0.03
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
TTTTGGAAGTTTCGGGGTAAAAATGAAAT
Found at i:59874 original size:89 final size:89
Alignment explanation
Indices: 59780--60070 Score: 379
Period size: 89 Copynumber: 3.3 Consensus size: 89
59770 GGTTCGAGGA
*
59780 TAAAAATGAAATTTTTAGAAGTTTCGGGGTCAAAAATGACATTTTTGGAAGTTCGAGGGTAAAAA
1 TAAAAATGAAATTTTTAGAAGTTTCGGGGTCAAAAATGACATTTTTGGAAGTTTGAGGGTAAAAA
*
59845 TGAAATTTTTGGAAGTTTTAGGGG
66 TGGAATTTTTGGAAGTTTTAGGGG
* *
59869 TAAAAATGAAATTTTTGGAAGTTTCAGGGTCAAAAATGACATTTTTGGAAGTTTG-GGGATAAAA
1 TAAAAATGAAATTTTTAGAAGTTTCGGGGTCAAAAATGACATTTTTGGAAGTTTGAGGG-TAAAA
* * * *
59933 GTGGAATTTTTGGTAGTGTTAGGGT
65 ATGGAATTTTTGGAAGTTTTAGGGG
* * * * ** * *
59958 TAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGTATTTTTGGAAGTTTTAGGGTTAAAA
1 TAAAAATGAAATTTTTAGAAGTTTCGGGGTCAAAAATGACATTTTTGGAAGTTTGAGGGTAAAAA
* *
60023 TGGAATTTTTGAAAG-TTCAGGGG
66 TGGAATTTTTGGAAGTTTTAGGGG
*
60046 TAAAAATGTAATTTTTAGATAGTTT
1 TAAAAATGAAATTTTTAGA-AGTTT
60071 AAGGACCTTC
Statistics
Matches: 175, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
88 25 0.14
89 147 0.84
90 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (89 bp):
TAAAAATGAAATTTTTAGAAGTTTCGGGGTCAAAAATGACATTTTTGGAAGTTTGAGGGTAAAAA
TGGAATTTTTGGAAGTTTTAGGGG
Found at i:60070 original size:59 final size:58
Alignment explanation
Indices: 59780--60070 Score: 286
Period size: 59 Copynumber: 4.9 Consensus size: 58
59770 GGTTCGAGGA
* * **
59780 TAAAAATGAAATTTTTAGAAGTTTC-GGGGTCAAAAATG-ACATTTTTGGAAGTTCGAGGG
1 TAAAAATGGAATTTTTGGAAG-TTCAGGGGT-AAAAATGTA-ATTTTTGGAAGTTTTAGGG
* * * *
59839 TAAAAATGAAATTTTTGGAAGTTTTAGGGGTAAAAATGAAATTTTTGGAAGTTTCAGGG
1 TAAAAATGGAATTTTTGGAAG-TTCAGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGG
* * * * *
59898 TCAAAAAT-GACATTTTTGGAAGTT-TGGGGATAAAAGTGGAATTTTTGGTAGTGTTAGGG
1 T-AAAAATGGA-ATTTTTGGAAGTTCAGGGG-TAAAAATGTAATTTTTGGAAGTTTTAGGG
**
59957 TTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGT-ATTTTTGGAAGTTTTAGGG
1 -TAAAAATGGAATTTTTGGAAGTTCAGGGG-TAAAAAT-GTAATTTTTGGAAGTTTTAGGG
* * *
60017 TTAAAATGGAATTTTTGAAAGTTCAGGGGTAAAAATGTAATTTTTAGATAGTTT
1 TAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTGGA-AGTTT
60071 AAGGACCTTC
Statistics
Matches: 200, Mismatches: 21, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.01
58 19 0.09
59 124 0.62
60 54 0.27
61 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (58 bp):
TAAAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGG
Found at i:61151 original size:12 final size:12
Alignment explanation
Indices: 61136--61182 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
61126 ATTATTAATG
61136 TTATTAATATTA
1 TTATTAATATTA
61148 TTA-TAGATATTA
1 TTATTA-ATATTA
61160 TTATTAATACCATTA
1 TTATTAAT---ATTA
61175 TTATTAAT
1 TTATTAAT
61183 GCTATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.07
12 14 0.47
13 2 0.07
15 12 0.40
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:61885 original size:17 final size:17
Alignment explanation
Indices: 61859--61895 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
61849 CTTTTAATTT
* *
61859 TAAATTTAAATTTAAGA
1 TAAATCTAAATTTAAAA
61876 TAAATCTAAATTTAAAA
1 TAAATCTAAATTTAAAA
61893 TAA
1 TAA
61896 CTTAAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAATCTAAATTTAAAA
Found at i:64114 original size:14 final size:15
Alignment explanation
Indices: 64078--64118 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
64068 CATAACAGAC
*
64078 ATATTTTTTTATTTA
1 ATATTTTATTATTTA
64093 A-ATATTTATT-TTTA
1 ATAT-TTTATTATTTA
64107 ATATTTTATTAT
1 ATATTTTATTAT
64119 ATACATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATATTTTATTATTTA
Found at i:64248 original size:16 final size:15
Alignment explanation
Indices: 64210--64250 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
64200 CCATGGTCCC
64210 TTAAAGTTTAATTTTT
1 TTAAA-TTTAATTTTT
*
64226 TTTAATTTAATTTTT
1 TTAAATTTAATTTTT
64241 TGTAAATTTA
1 T-TAAATTTA
64251 CATTATGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (15 bp):
TTAAATTTAATTTTT
Found at i:64452 original size:31 final size:31
Alignment explanation
Indices: 64396--64465 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
64386 TTAAATTAGT
*
64396 AATGAT-AAAATTACATTTTATCCCTTCCAAA
1 AATGATAAAAATTACATTTTAACCCTT-CAAA
*
64427 AATGATAAAAATTTA-A-TTTAACCCTTTAAA
1 AATGATAAAAA-TTACATTTTAACCCTTCAAA
*
64457 AATAATAAA
1 AATGATAAA
64466 TATATAAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 11 0.32
31 15 0.44
32 5 0.15
33 3 0.09
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (31 bp):
AATGATAAAAATTACATTTTAACCCTTCAAA
Found at i:64947 original size:21 final size:21
Alignment explanation
Indices: 64909--64952 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
64899 GAAGATGAAG
* * *
64909 TTTAGATTTTTTGGTTTTTTT
1 TTTAAATTTTTTGCTTTTATT
*
64930 TTTAAATTTTTTTCTTTTATT
1 TTTAAATTTTTTGCTTTTATT
64951 TT
1 TT
64953 GGTTAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (21 bp):
TTTAAATTTTTTGCTTTTATT
Found at i:65275 original size:28 final size:26
Alignment explanation
Indices: 65226--65299 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
65216 ACAATTTGTG
* *
65226 AAATAAGGACTTAAAAGCAAAAGAAGTT
1 AAATAAGGGCTTAAAA--AAAAAAAGTT
65254 AAATAAGGGCTTCAAAAAAAAAAAGTT
1 AAATAAGGGCTT-AAAAAAAAAAAGTT
* * *
65281 GAACAAGGGCTTTAAAAAA
1 AAATAAGGGCTTAAAAAAA
65300 TAAATACTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.15
27 19 0.47
28 11 0.28
29 4 0.10
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.18
Consensus pattern (26 bp):
AAATAAGGGCTTAAAAAAAAAAAGTT
Found at i:65479 original size:32 final size:31
Alignment explanation
Indices: 65440--65523 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 31
65430 ATAAGTACTT
*
65440 AAATAAGGGCTTAAAAATAAAATAAAAAATTG
1 AAATAAGGGCTTAAAAATAAAA-AAAAAAGTG
* *
65472 AAATAAGGGCTT-AAAAGAAAAAAATAAGTG
1 AAATAAGGGCTTAAAAATAAAAAAAAAAGTG
*
65502 AAACAAGGGCTTCAAAAATAAA
1 AAATAAGGGCTT-AAAAATAAA
65524 TGGAAAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
30 18 0.40
31 8 0.18
32 19 0.42
ACGTcount: A:0.61, C:0.06, G:0.15, T:0.18
Consensus pattern (31 bp):
AAATAAGGGCTTAAAAATAAAAAAAAAAGTG
Found at i:65510 original size:30 final size:30
Alignment explanation
Indices: 65342--65518 Score: 116
Period size: 30 Copynumber: 6.0 Consensus size: 30
65332 TAAAAGTGCA
*
65342 AAAAAAAT-AGTGAAATAAGGACTTAAAAG
1 AAAAAAATAAGTGAAATAAGGGCTTAAAAG
* * * *
65371 CAAAAAA-AAGTTAAGTAAGGGCATCAAAA-
1 AAAAAAATAAGTGAAATAAGGGC-TTAAAAG
* * *
65400 ATAAAAAA-AAATG-AACAAGGGCTTTAAAG
1 A-AAAAAATAAGTGAAATAAGGGCTTAAAAG
* * * * *
65429 -AATAAGT-ACTTAAATAAGGGCTTAAAAAT
1 AAAAAAATAAGTGAAATAAGGGCTT-AAAAG
* *
65458 AAAATAAAAAATTGAAATAAGGGCTTAAAAG
1 AAAA-AAATAAGTGAAATAAGGGCTTAAAAG
*
65489 AAAAAAATAAGTGAAACAAGGGCTTCAAAA
1 AAAAAAATAAGTGAAATAAGGGCTT-AAAA
65519 ATAAATGGAA
Statistics
Matches: 109, Mismatches: 28, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
27 6 0.06
28 14 0.13
29 27 0.25
30 34 0.31
31 14 0.13
32 14 0.13
ACGTcount: A:0.59, C:0.07, G:0.16, T:0.18
Consensus pattern (30 bp):
AAAAAAATAAGTGAAATAAGGGCTTAAAAG
Found at i:71375 original size:21 final size:21
Alignment explanation
Indices: 71351--71401 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
71341 TATGCATAGG
*
71351 TTAATATTTGAATTTATATCA
1 TTAATATTTGAACTTATATCA
71372 TTAATATTTGAACTTATATCA
1 TTAATATTTGAACTTATATCA
71393 -TAAGTATTT
1 TTAA-TATTT
71402 ATAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (21 bp):
TTAATATTTGAACTTATATCA
Found at i:71459 original size:24 final size:25
Alignment explanation
Indices: 71399--71459 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 25
71389 ATCATAAGTA
71399 TTTATA-AATA-TTTATTTTACCATT
1 TTTATACAATATTTTATTTTA-CATT
* * *
71423 TTAAT-CAAAATTTTATTTT-GATT
1 TTTATACAATATTTTATTTTACATT
71446 TTTATACAATATTT
1 TTTATACAATATTT
71460 CCAATGACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
23 7 0.24
24 14 0.48
25 8 0.28
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTATACAATATTTTATTTTACATT
Found at i:73147 original size:18 final size:18
Alignment explanation
Indices: 73115--73165 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
73105 AAAAAATCAG
73115 AATAATTTTCAAAAATTAAA
1 AATAATTTT--AAAATTAAA
*
73135 AATAATTTTAAAATTCAA
1 AATAATTTTAAAATTAAA
73153 AAT-ATTTATAAAA
1 AATAATTT-TAAAA
73166 AAAATTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 16 0.55
20 9 0.31
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAATTTTAAAATTAAA
Found at i:73447 original size:23 final size:23
Alignment explanation
Indices: 73404--73450 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
73394 TGTAACAAGA
* *
73404 TTTTAATTTAACATTATTAATTT
1 TTTTAATTTAACATGAATAATTT
73427 TTTTAATTTAAC-TCGAATAATTT
1 TTTTAATTTAACAT-GAATAATTT
73450 T
1 T
73451 GCTTGATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATTTAACATGAATAATTT
Found at i:74453 original size:24 final size:24
Alignment explanation
Indices: 74417--74470 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
74407 AAATACCCCT
*
74417 AAAATAATCAAAATTTAACTGAGAA
1 AAAATAATAAAAATTTAA-TGAGAA
*
74442 AAAATAA-AAAAATTTAATTAGAA
1 AAAATAATAAAAATTTAATGAGAA
74465 AAAATA
1 AAAATA
74471 CGAGACACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 11 0.41
24 9 0.33
25 7 0.26
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.24
Consensus pattern (24 bp):
AAAATAATAAAAATTTAATGAGAA
Done.