Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014153.1 Kokia drynarioides strain JFW-HI SEQ_129186, 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: 52941
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2872 original size:96 final size:96
Alignment explanation
Indices: 2688--2879 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
2678 CTTTTGCGAA
* ** *
2688 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCA
* *
2753 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAACCGAAGATAAAGAAACATTGCCTCGATT
* * *
2784 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGTAAAT-TTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCG-AAATATTTC
*
2848 -GAAACCCGAA-ATAAA-AGAATATTGCCTCGATT
65 AG-AA-CCGAAGATAAAGA-AACATTGCCTCGATT
2880 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 2 0.02
96 73 0.89
97 7 0.09
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCA
GAACCGAAGATAAAGAAACATTGCCTCGATT
Found at i:3204 original size:29 final size:28
Alignment explanation
Indices: 3168--3378 Score: 162
Period size: 29 Copynumber: 7.1 Consensus size: 28
3158 ATTTCAAACA
*
3168 TTCGAGGGTAAAAGGGTAATTTTTGGAAGG
1 TTCG-GGGTAAAATGGTAATTTTTGGAA-G
*
3198 TTCAGGGTCAAAAAT-G-AGATTTTTGGAAG
1 TTCGGGGT--AAAATGGTA-ATTTTTGGAAG
* *
3227 TTTAGGGGGGGTAAAATGGTAAATTTTGGAAGG
1 -TT---CGGGGTAAAATGGTAATTTTTGGAA-G
* *
3260 TTCGGGGTCAAAATGG-GACTTTTGGAAG
1 TTCGGGGT-AAAATGGTAATTTTTGGAAG
3288 TTCGGGGGTAAAATGGTAATTTTTGGAATG
1 TTC-GGGGTAAAATGGTAATTTTTGGAA-G
*
3318 TTTGGGGTCAAAAAT-G-AGATTTTTGGAAG
1 TTCGGGGT--AAAATGGTA-ATTTTTGGAAG
3347 TTCGGGGATAAAATGGTAATTTTTGGATAG
1 TTCGGGG-TAAAATGGTAATTTTTGGA-AG
3377 TT
1 TT
3379 TAGGGACCTC
Statistics
Matches: 148, Mismatches: 12, Indels: 42
0.73 0.06 0.21
Matches are distributed among these distances:
28 16 0.11
29 57 0.39
30 43 0.29
31 14 0.09
32 12 0.08
33 6 0.04
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.33
Consensus pattern (28 bp):
TTCGGGGTAAAATGGTAATTTTTGGAAG
Found at i:5423 original size:17 final size:17
Alignment explanation
Indices: 5378--5474 Score: 122
Period size: 17 Copynumber: 5.6 Consensus size: 17
5368 GGTTTTATTT
5378 TAAATTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* * *
5397 TAATTTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
5414 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
5431 TAAATTTAAATTTTAAA
1 TAAATTTAAATTTAAAA
* *
5448 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
5465 TAAATTTAAA
1 TAAATTTAAA
5475 GGGAGTATGG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 55 0.83
18 8 0.12
19 3 0.05
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:9703 original size:96 final size:95
Alignment explanation
Indices: 9529--9713 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 95
9519 GAAAAGGATT
** *
9529 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTTAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAA-TTTTAGAATCGA
*
9594 AGATAAGGAAATATTGCCTCGATTAAGGGTA
65 AGATAAGAAAATATTGCCTCGATTAAGGGTA
* *
9625 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGTGCAAA-TTTACGAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTA-G-AA-TC
9689 GAA-ATAA-AATAATATTGCCTCGATT
63 GAAGATAAGAA-AATATTGCCTCGATT
9714 TTAAAGTTTA
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
94 4 0.05
95 2 0.03
96 68 0.86
97 5 0.06
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (95 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTAGAATCGAA
GATAAGAAAATATTGCCTCGATTAAGGGTA
Found at i:10067 original size:59 final size:60
Alignment explanation
Indices: 10004--10119 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
9994 GTTAAAAATG
10004 GAATTTTTAGACACCCGAGGGT-AAACGATAAATTTTAAAAAAATCGAGATCAAAAAGCA
1 GAATTTTTAGACACCCGAGGGTAAAACGATAAATTTTAAAAAAATCGAGATCAAAAAGCA
* * * * * * ** *
10063 GAATTTTTGGACATCCGGGGGTAAAATGGTAAGTTTTAGGAAAATCGGGATCAAAAA
1 GAATTTTTAGACACCCGAGGGTAAAACGATAAATTTTAAAAAAATCGAGATCAAAAA
10120 TGGAATTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 19 0.40
60 28 0.60
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.24
Consensus pattern (60 bp):
GAATTTTTAGACACCCGAGGGTAAAACGATAAATTTTAAAAAAATCGAGATCAAAAAGCA
Found at i:10126 original size:59 final size:58
Alignment explanation
Indices: 9967--10157 Score: 192
Period size: 59 Copynumber: 3.2 Consensus size: 58
9957 TCTAGAGGGC
* * * *
9967 AAAATGGTAATTTT-GGAAAAGTTCGAGG-TTAAAAATGGAATTTTTAGACACCCGAGGGT
1 AAAATGGTAATTTTAGGAAAA--TCG-GGATCAAAAATGGAATTTTTGGACATCCGGGGGT
* * ** *
10026 -AAACGATAAATTTTAAAAAAATCGAGATCAAAAA-GCAGAATTTTTGGACATCCGGGGGT
1 AAAATGGT-AATTTTAGGAAAATCGGGATCAAAAATG--GAATTTTTGGACATCCGGGGGT
*
10085 AAAATGGTAAGTTTTAGGAAAATCGGGATCAAAAATGGAATTTTTGGACATTCGGGGGT
1 AAAATGGTAA-TTTTAGGAAAATCGGGATCAAAAATGGAATTTTTGGACATCCGGGGGT
*
10144 AAAAAGGTAATTTT
1 AAAATGGTAATTTT
10158 TGAAAGTTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
57 2 0.02
58 18 0.17
59 57 0.53
60 30 0.28
61 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (58 bp):
AAAATGGTAATTTTAGGAAAATCGGGATCAAAAATGGAATTTTTGGACATCCGGGGGT
Found at i:10139 original size:29 final size:27
Alignment explanation
Indices: 10063--10159 Score: 68
Period size: 29 Copynumber: 3.3 Consensus size: 27
10053 TCAAAAAGCA
* *
10063 GAATTTTTGGACATCCGGGGGTAAAATG
1 GAATTTTTGGACATTC-GGGATAAAATG
* * *
10091 GTAAGTTTTAGGAAAATCGGGATCAAAAATG
1 G-AA-TTTTTGGACATTCGGGAT--AAAATG
* *
10122 GAATTTTTGGACATTCGGGGGTAAAAAG
1 GAATTTTTGGACATTC-GGGATAAAATG
10150 GTAATTTTTG
1 G-AATTTTTG
10160 AAAGTTTTAG
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
28 7 0.13
29 24 0.45
30 15 0.28
31 7 0.13
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (27 bp):
GAATTTTTGGACATTCGGGATAAAATG
Found at i:10172 original size:29 final size:29
Alignment explanation
Indices: 10140--10379 Score: 209
Period size: 30 Copynumber: 8.1 Consensus size: 29
10130 GGACATTCGG
* *
10140 GGGTAAAAAGGTAATTTTTGAAAGTTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTTTA
* ***
10169 GGGTTAAAAATGTATTTTTTGGAAGTTCGG
1 GGG-TAAAAATGTAATTTTTGGAAGTTTTA
*
10199 GGGTAAAAAAGTAATTTTTGGAAGTTTTA
1 GGGTAAAAATGTAATTTTTGGAAGTTTTA
* *
10228 GGGTCAAAAATGTAATTTTTGGGAG-TATA
1 GGGT-AAAAATGTAATTTTTGGAAGTTTTA
* *
10257 GGGGTAAAAATGTAATTTTTTGAAG-TTTC
1 -GGGTAAAAATGTAATTTTTGGAAGTTTTA
* **
10286 GTGGTCAAAAATGGAATTTTTAGG-AGTTCAA
1 G-GGT-AAAAATGTAATTTTT-GGAAGTTTTA
* * *
10317 GGGTAAAAATATAATTTTTTGGAAGTATTG
1 GGGTAAAAATGTAA-TTTTTGGAAGTTTTA
*
10347 GGGTTAAAAATGGAATTTTTGGACAG-TTTA
1 GGG-TAAAAATGTAATTTTTGGA-AGTTTTA
10377 GGG
1 GGG
10380 ACCTTCAGGG
Statistics
Matches: 167, Mismatches: 33, Indels: 21
0.76 0.15 0.10
Matches are distributed among these distances:
28 1 0.01
29 64 0.38
30 88 0.53
31 14 0.08
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTTA
Found at i:10178 original size:59 final size:59
Alignment explanation
Indices: 10113--10369 Score: 254
Period size: 59 Copynumber: 4.3 Consensus size: 59
10103 AAAATCGGGA
10113 TCAAAAATGGAATTTTTGGACATTCGGGGGTAAAAAGGTAA-TTTTTGAAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGGA-ATTCGGGGGTAAAAAGGTAATTTTTTGAAAGTTTTAGGG
* * * * *
10172 TTAAAAATGTATTTTTTGGAAGTTCGGGGGTAAAAAAGTAA-TTTTTGGAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGGAA-TTCGGGGGTAAAAAGGTAATTTTTTGAAAGTTTTAGGG
* * * * *
10231 TCAAAAATGTAATTTTTGGGAGTAT-AGGGGTAAAAATGTAATTTTTTG-AAG-TTTCGTGG
1 TCAAAAATGGAATTTTT-GGAAT-TCGGGGGTAAAAAGGTAATTTTTTGAAAGTTTTAG-GG
* ** ** * * *
10290 TCAAAAATGGAATTTTTAGGAGTTCAAGGGTAAAAATATAATTTTTTGGAAGTATTGGGG
1 TCAAAAATGGAATTTTT-GGAATTCGGGGGTAAAAAGGTAATTTTTTGAAAGTTTTAGGG
*
10350 TTAAAAATGGAATTTTTGGA
1 TCAAAAATGGAATTTTTGGA
10370 CAGTTTAGGG
Statistics
Matches: 172, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
58 6 0.03
59 132 0.77
60 31 0.18
61 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (59 bp):
TCAAAAATGGAATTTTTGGAATTCGGGGGTAAAAAGGTAATTTTTTGAAAGTTTTAGGG
Found at i:17957 original size:28 final size:28
Alignment explanation
Indices: 17911--17970 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
17901 AAATGAGACT
17911 TTTTGGATACCCGACGGCAAAATGGAAA
1 TTTTGGATACCCGACGGCAAAATGGAAA
* * * *
17939 TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTGGATACCCGACGGCAAAATGGAAA
17967 TTTT
1 TTTT
17971 AGGAAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGACGGCAAAATGGAAA
Found at i:18025 original size:59 final size:58
Alignment explanation
Indices: 17929--18181 Score: 172
Period size: 58 Copynumber: 4.3 Consensus size: 58
17919 ACCCGACGGC
* * ** * * *
17929 AAAATGGAAATTTTGGATTCTCGAGGGCAAAATGGTAATTTTAGGAAAGTTCAGGGTTA
1 AAAATGGAATTTTTAGACACTCGGGGGTAAAACGGTAATTTTA-GAAAGTTCAGGGTTA
* * * * *
17988 AAAATGGAATTTTTAGACACTCGGGGGTAAAACGGTAACTTTAAAAAATTC-GAGATCA
1 AAAATGGAATTTTTAGACACTCGGGGGTAAAACGGTAATTTTAGAAAGTTCAG-GGTTA
* * ** * * * *
18046 AAAACGAAATTTTTAGACA-TCCGGGGGTAAAACAATAATTTTTAAGAAA-ATCA-AGATC
1 AAAATGGAATTTTTAGACACT-CGGGGGTAAAACGGTAA-TTTT-AGAAAGTTCAGGGTTA
* * ** * **
18104 AAAATGGAATTTTTGGACATTCGGGGGTAAATGGGTAATTTTTGAAAGTTTTGGGGTTA
1 AAAATGGAATTTTTAGACACTCGGGGGTAAAACGGTAATTTTAGAAAG-TTCAGGGTTA
*
18163 AAAATAGAATTTTTAGACA
1 AAAATGGAATTTTTAGACA
18182 TTTAAGGGAA
Statistics
Matches: 145, Mismatches: 40, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
56 4 0.03
57 6 0.04
58 71 0.49
59 60 0.41
60 4 0.03
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (58 bp):
AAAATGGAATTTTTAGACACTCGGGGGTAAAACGGTAATTTTAGAAAGTTCAGGGTTA
Found at i:18143 original size:58 final size:59
Alignment explanation
Indices: 17987--18146 Score: 191
Period size: 58 Copynumber: 2.7 Consensus size: 59
17977 GTTCAGGGTT
* * *
17987 AAAAATGGAATTTTTAGACACTCGGGGGTAAAACGGTAA-CTTTAAAAAATTCGAGATC
1 AAAAATGGAATTTTTAGACATTCGGGGGTAAAACGGTAATTTTTAAAAAATTCAAGATC
* * * **
18045 AAAAACGAAATTTTTAGACATCCGGGGGTAAAACAATAATTTTTAAGAAAA-TCAAGATC
1 AAAAATGGAATTTTTAGACATTCGGGGGTAAAACGGTAATTTTTAA-AAAATTCAAGATC
* **
18104 -AAAATGGAATTTTTGGACATTCGGGGGTAAATGGGTAATTTTT
1 AAAAATGGAATTTTTAGACATTCGGGGGTAAAACGGTAATTTTT
18147 GAAAGTTTTG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 68 0.81
59 12 0.14
60 4 0.05
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.29
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGACATTCGGGGGTAAAACGGTAATTTTTAAAAAATTCAAGATC
Found at i:18175 original size:29 final size:29
Alignment explanation
Indices: 18143--18300 Score: 83
Period size: 30 Copynumber: 5.4 Consensus size: 29
18133 AATGGGTAAT
18143 TTTTGAAAGTTTTGGGGTTAAAAATAGAA
1 TTTTGAAAGTTTTGGGGTTAAAAATAGAA
* **
18172 TTTTTAGACA-TTTAAGGG--AAAAATAGTAA
1 -TTTT-GAAAGTTTTGGGGTTAAAAATAG-AA
* * * * *
18201 TTTTTAGAAGTTTTGAGGTAAAAAATGGACG
1 TTTTGA-AAGTTTTGGGGTTAAAAATAGA-A
* *
18232 TTTTGGAAG-TTTGGGGGTAAAAAT-GTAA
1 TTTTGAAAGTTTTGGGGTTAAAAATAG-AA
* * * *
18260 TTTTTAGAAGTTTTAGGGTCAAAAATGGAA
1 TTTTGA-AAGTTTTGGGGTTAAAAATAGAA
*
18290 TTTTGGAAGTT
1 TTTTGAAAGTT
18301 AGAGGGTAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 23
0.67 0.16 0.16
Matches are distributed among these distances:
27 1 0.01
28 18 0.19
29 28 0.30
30 32 0.34
31 15 0.16
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTTGAAAGTTTTGGGGTTAAAAATAGAA
Found at i:18201 original size:59 final size:57
Alignment explanation
Indices: 18138--18424 Score: 211
Period size: 59 Copynumber: 4.9 Consensus size: 57
18128 GGGTAAATGG
* * *
18138 GTAATTTTT-GAAAGTTTTGGGGTTAAAAATAGAATTTTTAGACATTTAAGGG-AAAAAT
1 GTAATTTTTAG-AAGTTTTGGGGTAAAAAATGGAA-TTTTGGA-ATTTAAGGGTAAAAAT
* * **
18196 AGTAATTTTTAGAAGTTTTGAGGTAAAAAATGGACGTTTTGGAAGTTTGGGGGTAAAAAT
1 -GTAATTTTTAGAAGTTTTGGGGTAAAAAATGGA-ATTTTGGAA-TTTAAGGGTAAAAAT
* * *
18256 GTAATTTTTAGAAGTTTTAGGGTCAAAAATGGAATTTTGGAAGTTAGAGGGTAAAAAT
1 GTAATTTTTAGAAGTTTTGGGGTAAAAAATGGAATTTTGGAATTTA-AGGGTAAAAAT
* ** ** * * * **
18314 GTAATTTTTGGAAGTTTCAGCATCAAAAATGGGATTTTTTGGAGTTCGAGGGTAAAAAT
1 GTAATTTTTAGAAGTTTTGGGGTAAAAAAT-GGA-ATTTTGGAATTTAAGGGTAAAAAT
** * * *
18373 AAAATTTTT-GAAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAGTTTAAGG
1 GTAATTTTTAG-AAGTTTTGGGGTAAAAAATGGAA-TTTTGGA-A-TTTAAGG
18425 ACCTCCAAGG
Statistics
Matches: 184, Mismatches: 33, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
57 2 0.01
58 56 0.30
59 106 0.58
60 20 0.11
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
GTAATTTTTAGAAGTTTTGGGGTAAAAAATGGAATTTTGGAATTTAAGGGTAAAAAT
Found at i:18306 original size:29 final size:29
Alignment explanation
Indices: 18104--18420 Score: 213
Period size: 29 Copynumber: 10.8 Consensus size: 29
18094 AATCAAGATC
* *
18104 AAAATGGAATTTTTGGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTA
*
18132 -AAATGGGTAATTTTTGAAAGTTTTG-GGGTTA
1 AAAAT-GG-AATTTTTGGAAG-TTTGAGGG-TA
* * *
18163 AAAATAGAATTTTTAGACA-TTTAAGGG-A
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTA
* *
18191 AAAATAGTAATTTTTAGAAGTTTTGA-GGTAA
1 AAAAT-GGAATTTTTGGAAG-TTTGAGGGT-A
** *
18222 AAAATGGACGTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
* * *
18251 AAAATGTAATTTTTAGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGT-A
*
18281 AAAATGGAA-TTTTGGAAGTTAGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
* * **
18309 AAAATGTAATTTTTGGAAGTTTCAGCATCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGT-A
* *
18339 AAAATGGGATTTTTTGG-AGTTCGAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTGAGGGTA
** *
18368 AAAATAAAATTTTTGAAAGTTTCGA-GGTCA
1 AAAATGGAATTTTTGGAAGTTT-GAGGGT-A
18398 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
18421 AAGGACCTCC
Statistics
Matches: 223, Mismatches: 43, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
27 4 0.02
28 26 0.12
29 96 0.43
30 71 0.32
31 22 0.10
32 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTA
Found at i:20313 original size:6 final size:6
Alignment explanation
Indices: 20302--20379 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
20292 TTTGGACATT
* * *
20302 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * *
20348 AA-GTA AATTTA AACTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
20380 CTGTTGGGCC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
4 2 0.04
5 12 0.22
6 39 0.71
7 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:20340 original size:34 final size:34
Alignment explanation
Indices: 20302--20379 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
20292 TTTGGACATT
* * * *
20302 AATTTAAATTTAAATTTAACTCAAATTTATAATA
1 AATTTAAATTTAAAGTAAACTCAAACTTAAAATA
* * *
20336 AATTTAAATTTTAAGTAAATTTAAACTTAAAATA
1 AATTTAAATTTAAAGTAAACTCAAACTTAAAATA
20370 AATTTAAATT
1 AATTTAAATT
20380 CTGTTGGGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (34 bp):
AATTTAAATTTAAAGTAAACTCAAACTTAAAATA
Found at i:20344 original size:17 final size:18
Alignment explanation
Indices: 20302--20379 Score: 74
Period size: 17 Copynumber: 4.6 Consensus size: 18
20292 TTTGGACATT
* *
20302 AATTTAAATTTA-AATTT
1 AATTTAAATTTATAAGTA
* *
20319 AACTCAAATTTATAA-TA
1 AATTTAAATTTATAAGTA
20336 AATTTAAATTT-TAAGTA
1 AATTTAAATTTATAAGTA
* *
20353 AATTTAAACTTA-AAATA
1 AATTTAAATTTATAAGTA
20370 AATTTAAATT
1 AATTTAAATT
20380 CTGTTGGGCC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
16 3 0.06
17 45 0.90
18 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (18 bp):
AATTTAAATTTATAAGTA
Found at i:20662 original size:20 final size:17
Alignment explanation
Indices: 20619--20653 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20609 ATTAAAATGA
20619 AATTAATTATTTTTTTT
1 AATTAATTATTTTTTTT
20636 AATTAATTATTTTTTTT
1 AATTAATTATTTTTTTT
20653 A
1 A
20654 TAGTATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTAATTATTTTTTTT
Found at i:20824 original size:15 final size:17
Alignment explanation
Indices: 20804--20835 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20794 TCATTTCATT
20804 TATAT-AATG-ATAAAA
1 TATATAAATGCATAAAA
20819 TATATAAATGCATAAAA
1 TATATAAATGCATAAAA
20836 AGATTTTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
TATATAAATGCATAAAA
Found at i:21084 original size:24 final size:22
Alignment explanation
Indices: 21049--21115 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 22
21039 TTACTATATT
* **
21049 AATATAGAATATACTAATAAAATC
1 AATATA-AATATAAT-ATAAAAGA
21073 AATATAACATATAATATAAAAGA
1 AATATAA-ATATAATATAAAAGA
*
21096 AATATAATTA-AGATATAAAA
1 AATATAAATATA-ATATAAAA
21116 AAGATATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.27
23 14 0.38
24 12 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (22 bp):
AATATAAATATAATATAAAAGA
Found at i:21131 original size:20 final size:21
Alignment explanation
Indices: 21085--21132 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
21075 TATAACATAT
21085 AATATAAAAGAAATATAATTAA
1 AATATAAAAGAAATAT-ATTAA
*
21107 GATATAAAA-AAGATAT-TTAA
1 AATATAAAAGAA-ATATATTAA
21127 AATATA
1 AATATA
21133 GATAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.39
21 2 0.09
22 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (21 bp):
AATATAAAAGAAATATATTAA
Found at i:21756 original size:24 final size:21
Alignment explanation
Indices: 21728--21796 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
21718 ACAAAAAAGA
21728 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCTAAGTCACTTC---TCTT
* **
21752 TTTGTCCAAGTTGCTTCTCTT
1 TTTGTCTAAGTCACTTCTCTT
*
21773 TTTGTCTAACTCACTTACT-TT
1 TTTGTCTAAGTCACTT-CTCTT
21794 TTT
1 TTT
21797 CTTTGTGAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 21 0.57
22 2 0.05
24 14 0.38
ACGTcount: A:0.13, C:0.22, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTGTCTAAGTCACTTCTCTT
Found at i:26620 original size:18 final size:18
Alignment explanation
Indices: 26593--26633 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
26583 AGGTCACGAC
*
26593 CAATAGCGTCACTAGCAT
1 CAATAGCGTCAATAGCAT
* *
26611 CAATATCGTCAATATCAT
1 CAATAGCGTCAATAGCAT
26629 CAATA
1 CAATA
26634 ACGATATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (18 bp):
CAATAGCGTCAATAGCAT
Found at i:33400 original size:7 final size:8
Alignment explanation
Indices: 33383--33408 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
33373 TAATTAAAGT
33383 AAAATGAA
1 AAAATGAA
33391 AAAATGAA
1 AAAATGAA
33399 AAAATGAA
1 AAAATGAA
33407 AA
1 AA
33409 TTTAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:35181 original size:15 final size:15
Alignment explanation
Indices: 35158--35190 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35148 CTTGTTGTTC
35158 ATTTCTTTCTTCTTT
1 ATTTCTTTCTTCTTT
*
35173 ATTTTTTTCTTCTTT
1 ATTTCTTTCTTCTTT
35188 ATT
1 ATT
35191 CAAACTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTCTTTCTTCTTT
Found at i:36044 original size:6 final size:6
Alignment explanation
Indices: 36035--36139 Score: 56
Period size: 6 Copynumber: 17.5 Consensus size: 6
36025 TCTGAAAAAG
* * * * *
36035 AAATAA AAATAA TATTAA TAAATAA AATTTA AAATAA AAATAA AGAT--
1 AAATAA AAATAA AAATAA -AAATAA AAATAA AAATAA AAATAA AAATAA
* ** * *
36082 AAATAG AAATAGA AATATAA ATAATTG AAAT-A AATTAA TAAT-A AAATAA
1 AAATAA AAATA-A AA-ATAA A-AATAA AAATAA AAATAA AAATAA AAATAA
36131 AAATAA AAA
1 AAATAA AAA
36140 ACAATGGGTT
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
4 3 0.04
5 7 0.10
6 48 0.66
7 11 0.15
8 4 0.05
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (6 bp):
AAATAA
Found at i:36091 original size:22 final size:21
Alignment explanation
Indices: 36066--36115 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
36056 ATAAAATTTA
36066 AAATAAAAATA-AAGATAAATAG
1 AAATAAAAATATAA-AT-AATAG
* *
36088 AAATAGAAATATAAATAATTG
1 AAATAAAAATATAAATAATAG
36109 AAATAAA
1 AAATAAA
36116 TTAATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 12 0.50
23 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAAAATATAAATAATAG
Found at i:39721 original size:15 final size:15
Alignment explanation
Indices: 39698--39730 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39688 CTTGTTGTTC
39698 ATTTCTTTCTTCTTT
1 ATTTCTTTCTTCTTT
*
39713 ATTTTTTTCTTCTTT
1 ATTTCTTTCTTCTTT
39728 ATT
1 ATT
39731 CAAACTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTCTTTCTTCTTT
Found at i:40603 original size:6 final size:6
Alignment explanation
Indices: 40594--40698 Score: 56
Period size: 6 Copynumber: 17.5 Consensus size: 6
40584 TCTGAAAAAG
* * * * *
40594 AAATAA AAATAA TATTAA TAAATAA AATTTA AAATAA AAATAA AGAT--
1 AAATAA AAATAA AAATAA -AAATAA AAATAA AAATAA AAATAA AAATAA
* ** * *
40641 AAATAG AAATAGA AATATAA ATAATTG AAAT-A AATTAA TAAT-A AAATAA
1 AAATAA AAATA-A AA-ATAA A-AATAA AAATAA AAATAA AAATAA AAATAA
40690 AAATAA AAA
1 AAATAA AAA
40699 ACAATGGGTT
Statistics
Matches: 73, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
4 3 0.04
5 7 0.10
6 48 0.66
7 11 0.15
8 4 0.05
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (6 bp):
AAATAA
Found at i:40650 original size:22 final size:21
Alignment explanation
Indices: 40625--40674 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
40615 ATAAAATTTA
40625 AAATAAAAATA-AAGATAAATAG
1 AAATAAAAATATAA-AT-AATAG
* *
40647 AAATAGAAATATAAATAATTG
1 AAATAAAAATATAAATAATAG
40668 AAATAAA
1 AAATAAA
40675 TTAATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 12 0.50
23 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAAAATATAAATAATAG
Found at i:49219 original size:13 final size:14
Alignment explanation
Indices: 49201--49229 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49191 CTGAATATTC
49201 AAATAAAAA-TAAA
1 AAATAAAAAGTAAA
49214 AAATAAAAAGTAAA
1 AAATAAAAAGTAAA
49228 AA
1 AA
49230 TAATAACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (14 bp):
AAATAAAAAGTAAA
Found at i:52315 original size:19 final size:18
Alignment explanation
Indices: 52268--52320 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
52258 CATTAGGATG
*
52268 CCCCTCCTTCCACCTTTC
1 CCCCTCCTTCCCCCTTTC
*
52286 TCCCTCCTTCCCCCTTTCC
1 CCCCTCCTTCCCCCTTT-C
*
52305 CCCCTCTTTCCCCCTT
1 CCCCTCCTTCCCCCTT
52321 CTTTCATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.02, C:0.62, G:0.00, T:0.36
Consensus pattern (18 bp):
CCCCTCCTTCCCCCTTTC
Found at i:52342 original size:18 final size:18
Alignment explanation
Indices: 52319--52361 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52309 TCTTTCCCCC
*
52319 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
52337 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
52355 TGCTTTC
1 TTCTTTC
52362 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Done.