Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003692.1 Kokia drynarioides strain JFW-HI SEQ_116622, 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: 34489
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:267 original size:96 final size:96
Alignment explanation
Indices: 95--286 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 96
85 CTTTTGGGAA
**
95 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAAGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCGCAATATTTCA
*
160 GAATCGAAGAT-AAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTGCCTCGATT
* * *
191 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCGCAATA-TTTC
*
255 -GAAATTCG-AGATAAAAGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAAGAACATTGCCTCGATT
287 TTAAAGTCTT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
95 2 0.02
96 77 0.91
97 6 0.07
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCGCAATATTTCA
GAATCGAAGATAAAAGAACATTGCCTCGATT
Found at i:537 original size:28 final size:29
Alignment explanation
Indices: 506--566 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
496 AAAATGAGAC
506 TTTTCGGATAC-C-GGGGGCAAAATGGTAA
1 TTTT-GGATACTCGGGGGGCAAAATGGTAA
* **
534 TTTTGGATTCTCGGGGGGTGAAATGGTAA
1 TTTTGGATACTCGGGGGGCAAAATGGTAA
563 TTTT
1 TTTT
567 AGGAAATTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 5 0.18
29 18 0.64
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.34
Consensus pattern (29 bp):
TTTTGGATACTCGGGGGGCAAAATGGTAA
Found at i:597 original size:30 final size:29
Alignment explanation
Indices: 554--970 Score: 213
Period size: 29 Copynumber: 14.3 Consensus size: 29
544 TCGGGGGGTG
* *
554 AAATGGTAATTTTAGGAAATTCGAGGTTAA
1 AAATGG-AATTTTTGGAAATTCGAGGGTAA
* *
584 AAATGGAATTTTTAGATATTC-AGGGGT-A
1 AAATGGAATTTTTGGAAATTCGA-GGGTAA
* ** * *
612 AAAGGGTAA-TTTTGAGAGTTTCGA-AGTCGA
1 AAATGG-AATTTTTG-GAAATTCGAGGGT-AA
* *
642 AAATGG-AGTTTTGGACATTCGAGGGT-A
1 AAATGGAATTTTTGGAAATTCGAGGGTAA
*
669 AAATGGTAATTTTTGGAAGTTCGAGGGTAA
1 AAATGG-AATTTTTGGAAATTCGAGGGTAA
* *
699 AAATGAGATTTTTTGGAAGTTCGAGGGTAA
1 AAATG-GAATTTTTGGAAATTCGAGGGTAA
* *
729 AAATGGAATTTTTGGAAGTTTCGAGGTTAA
1 AAATGGAATTTTTGGAA-ATTCGAGGGTAA
* * *
759 AAATGGGATTTTT-GAAAGTTTGGGGGT--
1 AAATGGAATTTTTGGAAA-TTCGAGGGTAA
* * *
786 AAA--GAATTTTTAGAAGTTTTG-GGGTTAA
1 AAATGGAATTTTTGGAA-ATTCGAGGG-TAA
* *
814 AAATGTG-ATTTTTGGAAGTTTTG-GGGTAA
1 AAATG-GAATTTTTGGAA-ATTCGAGGGTAA
* * *
843 AAATGGAATTTTTAGAAGTTTTG-GGGTCAA
1 AAATGGAATTTTTGGAA-ATTCGAGGGT-AA
* * ** *
873 AAATGGGATTTTTGGAAGTTTAAGGGTTA
1 AAATGGAATTTTTGGAAATTCGAGGGTAA
*
902 AAATGGAATTTTT-AAAAGTTTCGA-GGTCAA
1 AAATGGAATTTTTGGAAA--TTCGAGGGT-AA
* *
932 AAATGGGATTTTTGGAAGTTCG-GTGGTAA
1 AAATGGAATTTTTGGAAATTCGAG-GGTAA
*
961 AAATAGAATT
1 AAATGGAATT
971 CTTAGACAGT
Statistics
Matches: 311, Mismatches: 45, Indels: 63
0.74 0.11 0.15
Matches are distributed among these distances:
25 10 0.03
26 8 0.03
27 10 0.03
28 27 0.09
29 126 0.41
30 126 0.41
31 4 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAATTCGAGGGTAA
Found at i:730 original size:59 final size:58
Alignment explanation
Indices: 573--982 Score: 346
Period size: 59 Copynumber: 7.0 Consensus size: 58
563 TTTTAGGAAA
* * * * *
573 TTCGAGGTTAAAAATGGAATTTTTAGATA-TTC-AGGGGTAAAAGGGTAATTTTGAG-AGT
1 TTCGAGGGTAAAAATGGGATTTTTGGA-AGTTCGA-GGGTAAAATGG-AATTTTTAGAAGT
* * * *
631 TTCGA-AGTCGAAAAT-GGAGTTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTGGAAG-
1 TTCGAGGGT-AAAAATGGGATTTTTGGA-AGTTCGAGGGTAAAATGG-AATTTTTAGAAGT
* *
688 TTCGAGGGTAAAAATGAGATTTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGAGGGTAAAAATGGGA-TTTTTGGAAGTTCGAGGGT-AAAATGGAATTTTTAGAAGT
* * * *
748 TTCGAGGTTAAAAATGGGATTTTTGAAAGTTTGGGGGT-AAA--GAATTTTTAGAAGT
1 TTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGAATTTTTAGAAGT
* * *
803 TTTG-GGGTTAAAAATGTGATTTTTGGAAGTTTTG-GGGTAAAAATGGAATTTTTAGAAGT
1 TTCGAGGG-TAAAAATGGGATTTTTGGAAG-TTCGAGGGT-AAAATGGAATTTTTAGAAGT
* ** *
862 TTTG-GGGTCAAAAATGGGATTTTTGGAAGTTTAAGGGTTAAAATGGAATTTTTAAAAGT
1 TTCGAGGGT-AAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAATGGAATTTTTAGAAGT
* *
921 TTCGA-GGTCAAAAATGGGATTTTTGGAAGTTCG-GTGGTAAAAATAGAATTCTTAGACAGT
1 TTCGAGGGT-AAAAATGGGATTTTTGGAAGTTCGAG-GGT-AAAATGGAATTTTTAGA-AGT
981 TT
1 TT
983 AGGGACCTTT
Statistics
Matches: 297, Mismatches: 33, Indels: 42
0.80 0.09 0.11
Matches are distributed among these distances:
54 2 0.01
55 39 0.13
56 4 0.01
57 47 0.16
58 24 0.08
59 151 0.51
60 30 0.10
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (58 bp):
TTCGAGGGTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGAATTTTTAGAAGT
Found at i:8619 original size:96 final size:96
Alignment explanation
Indices: 8431--8622 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
8421 TTTTTGGGAA
* ** * *
8431 AAGGATATTCGATTATCTCGATTTGAATAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
* *
8496 GAATCGAAGATAAGGAAACATTGCCTTGATT
66 GAATCGAAGATAAAGAAACATTACCTTGATT
* * *
8527 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATA-TTTC
*
8591 -GAAATTC-AAGATAAA-AGAATATTACCTTGATT
65 AG-AA-TCGAAGATAAAGA-AACATTACCTTGATT
8623 TTAAAGTCTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 3 0.04
96 76 0.94
97 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTACCTTGATT
Found at i:8878 original size:29 final size:28
Alignment explanation
Indices: 8843--8905 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
8833 AAATGAGACT
8843 TTTTGGATACCCGATGGGCAAAATGGTAA
1 TTTTGGATACCCGA-GGGCAAAATGGTAA
* * **
8872 TTTTGGATTCTCGAGGGTGAAATGGTAA
1 TTTTGGATACCCGAGGGCAAAATGGTAA
8900 TTTTGG
1 TTTTGG
8906 GAAAATTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (28 bp):
TTTTGGATACCCGAGGGCAAAATGGTAA
Found at i:9023 original size:29 final size:29
Alignment explanation
Indices: 8979--9101 Score: 153
Period size: 29 Copynumber: 4.2 Consensus size: 29
8969 TTTAAAGTCG
*
8979 AAAATGG-AGTTTTGGACA-TTCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
* *
9006 AAAATGGTAGTTTTTGGAAGTTTCGAGGTTA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGGTA
* *
9037 AAAATGGAATTTTTGGAAGTTTGAGGCTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
9066 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
9095 AAAATGG
1 AAAATGG
9102 GATTAAAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
27 7 0.08
28 1 0.01
29 49 0.59
30 19 0.23
31 7 0.08
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:9041 original size:58 final size:58
Alignment explanation
Indices: 8862--9101 Score: 202
Period size: 59 Copynumber: 4.1 Consensus size: 58
8852 CCCGATGGGC
* * * **
8862 AAAATGGTAA-TTTTGGATTCTCGAGGGTGAAATGGTAATTTTGGGAAAATTCGAGGTTA
1 AAAATGG-AATTTTTGGAAT-TCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTA
* * * * ** ** * **
8921 AAAATGGAATTTTTAGAAATTTGGGGGTAAAAGGGTAATTTTAAG-AGTTTTAAAGTCG
1 AAAATGGAATTTTT-GGAATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTA
* *
8979 AAAATGG-AGTTTTGGACATTCGAGGGTAAAATGGTAGTTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGA-ATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTA
* * *
9037 AAAATGGAATTTTTGGAAGTTTGAGGCTAAAAATGG-AATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAA-TTCGAGGGT-AAAATGGTAATTTTTGGAAGTTTCGAGGTTA
9095 AAAATGG
1 AAAATGG
9102 GATTAAAAAT
Statistics
Matches: 141, Mismatches: 33, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
56 2 0.01
57 26 0.18
58 47 0.33
59 56 0.40
60 10 0.07
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAATTCGAGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTTA
Found at i:9079 original size:59 final size:59
Alignment explanation
Indices: 8891--9359 Score: 255
Period size: 59 Copynumber: 7.8 Consensus size: 59
8881 CTCGAGGGTG
* ** * * *
8891 AAATGGTAATTTTGGGAAAATTCGAGGTTAAAAATGGAATTTTTAGAAATTTGGGGGT-A
1 AAATGG-AATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTAGAAGTTTGAGGGTAA
* ** * * ** * * *
8950 AAAGGGTAATTTTAAG-AGTTTTAAAGTCGAAAATGG-AGTTTTGGACA-TTCGAGGGT-A
1 AAATGG-AATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTAGA-AGTTTGAGGGTAA
* * * *
9007 AAATGGTAGTTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGAGGCTAA
1 AAATGG-AATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTAGAAGTTTGAGGGTAA
* * * **
9067 AAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGGATTAAAAATAGAATTTTTGGAAGTTTCGG
1 AAATGGAATTTTTGGAAGTT------T--CAA--GG-TTAAAAATGGAATTTTTAGAAGTTTGAG
*
9132 GGTCA
55 GGTAA
* * * * * *
9137 AAAATAGG-ATTTTTAGAAGTTT-AGGGGTAAAAATAG-ATTTTTTGAAGTTTTG-GAGTCAA
1 AAA-T-GGAATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTAGAAG-TTTGAGGGT-AA
* * **
9196 AAATGGGATTTTTGGAAG-TTCAAGGGTAAAAATGGAATTTTTAGAAGTTTTTGCGGTCAA
1 AAATGGAATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTAGAAGTTTGAG-GGT-AA
* *
9256 AAATGGGATTTTTGTAAGTTT-AAGGGTT-AAAATGGAATTTTTAGAAGTTTTG-GGGTCAA
1 AAATGGAATTTTTGGAAGTTTCAA-GGTTAAAAATGGAATTTTTAGAAG-TTTGAGGGT-AA
* * *
9315 AAATGGGATTTTTGGAAG-TTCAAGGGTAAAAATGGAATTCTTAGA
1 AAATGGAATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTAGA
9360 TAATTTAGGG
Statistics
Matches: 327, Mismatches: 53, Indels: 60
0.74 0.12 0.14
Matches are distributed among these distances:
57 31 0.09
58 74 0.23
59 109 0.33
60 53 0.16
61 8 0.02
62 1 0.00
65 2 0.01
67 1 0.00
69 2 0.01
70 31 0.09
71 13 0.04
72 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
AAATGGAATTTTTGGAAGTTTCAAGGTTAAAAATGGAATTTTTAGAAGTTTGAGGGTAA
Found at i:9109 original size:41 final size:42
Alignment explanation
Indices: 9064--9147 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
9054 AGTTTGAGGC
* *
9064 TAAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGGAT
1 TAAAAATAGAATTTTTGGAAGTTTCG-GGGTCAAAAATAGGAT
9105 TAAAAATAGAATTTTTGGAAGTTTCGGGGTCAAAAATAGGAT
1 TAAAAATAGAATTTTTGGAAGTTTCGGGGTCAAAAATAGGAT
9147 T
1 T
9148 TTTAGAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 24 0.62
42 15 0.38
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (42 bp):
TAAAAATAGAATTTTTGGAAGTTTCGGGGTCAAAAATAGGAT
Found at i:9142 original size:30 final size:30
Alignment explanation
Indices: 9106--9334 Score: 232
Period size: 30 Copynumber: 7.7 Consensus size: 30
9096 AAATGGGATT
* * *
9106 AAAAATAGAATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
* * *
9136 AAAAATAGGATTTTTAGAAGTTTAGGGGT-
1 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
* * *
9165 AAAAAT-AGATTTTTTGAAGTTTTGGAGTC
1 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
***
9194 AAAAATGGGATTTTTGGAAGTTCAAGGGT-
1 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
* * *
9223 AAAAATGGAATTTTTAGAAGTTTTTGCGGTC
1 AAAAATGGGATTTTTGGAAG-TTTTGGGGTC
* **
9254 AAAAATGGGATTTTTGTAAGTTTAAGGGT-
1 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
* * *
9283 TAAAATGGAATTTTTAGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
9313 AAAAATGGGATTTTTGGAAGTT
1 AAAAATGGGATTTTTGGAAGTT
9335 CAAGGGTAAA
Statistics
Matches: 160, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
28 18 0.11
29 53 0.33
30 72 0.45
31 17 0.11
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAAATGGGATTTTTGGAAGTTTTGGGGTC
Found at i:9198 original size:100 final size:100
Alignment explanation
Indices: 9016--9205 Score: 244
Period size: 100 Copynumber: 1.9 Consensus size: 100
9006 AAAATGGTAG
* * *
9016 TTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGAGGCTAAAAATGGAATTTTTG
1 TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTAGAAGTTTGAGGCTAAAAATAGAATTTTTG
*
9081 GAAGTTCGAGGGTAAAAATGGGATTAAAAATAGAA
66 GAAGTTCGAGAGTAAAAATGGGATTAAAAATAGAA
* *
9116 TTTTTGGAAGTTTCGGGGTCAAAAATAGG-ATTTTTAGAAGTTT-AGGGGTAAAAATAG-ATTTT
1 TTTTTGGAAGTTTCGAGGTCAAAAAT-GGAATTTTTAGAAGTTTGA-GGCTAAAAATAGAATTTT
* *
9178 TTGAAGTTTTG-GAGTCAAAAATGGGATT
64 TGGAAG-TTCGAGAGT-AAAAATGGGATT
9206 TTTGGAAGTT
Statistics
Matches: 78, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
99 14 0.18
100 62 0.79
101 2 0.03
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (100 bp):
TTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTAGAAGTTTGAGGCTAAAAATAGAATTTTTG
GAAGTTCGAGAGTAAAAATGGGATTAAAAATAGAA
Found at i:10387 original size:15 final size:15
Alignment explanation
Indices: 10367--10433 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
10357 TTTTTTATTA
10367 ATTATTAATAATAAT
1 ATTATTAATAATAAT
*
10382 ATTATTATTAATAA-
1 ATTATTAATAATAAT
**
10396 AACATTTAATAATAAT
1 ATTA-TTAATAATAAT
*
10412 A--A-TAATAATAGT
1 ATTATTAATAATAAT
*
10424 TTTATTAATA
1 ATTATTAATA
10434 CCTGTTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
12 9 0.22
14 4 0.10
15 27 0.66
16 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
ATTATTAATAATAAT
Found at i:11135 original size:6 final size:6
Alignment explanation
Indices: 11119--11207 Score: 71
Period size: 6 Copynumber: 15.3 Consensus size: 6
11109 ACATTTAAAA
* *
11119 TAAATTT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAA-C TAAATT
1 TAAA-TT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* * * *
11166 TAAATT TAAA-A TAAACT TAATTT TAAA-A TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TA
11208 TTGGACCCAG
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
4 2 0.03
5 13 0.20
6 44 0.68
7 6 0.09
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:11144 original size:24 final size:23
Alignment explanation
Indices: 11111--11155 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
11101 GTACTTGGAC
11111 ATTTAAAATAAATTTTAAATTTAA
1 ATTTAAAATAAA-TTTAAATTTAA
*
11135 ATTTATAATAAATTTAAATTT
1 ATTTAAAATAAATTTAAATTT
11156 CAACTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAAATAAATTTAAATTTAA
Found at i:11146 original size:17 final size:17
Alignment explanation
Indices: 11126--11207 Score: 119
Period size: 17 Copynumber: 4.8 Consensus size: 17
11116 AAATAAATTT
*
11126 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
11143 TAAATTTAAATTTCAAC
1 TAAATTTAAATTTAAAA
11160 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
11177 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
11194 TAAATTTAAATTTA
1 TAAATTTAAATTTA
11208 TTGGACCCAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:12598 original size:16 final size:16
Alignment explanation
Indices: 12577--12612 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12567 ATCAATCATA
* *
12577 ATATTTTATATTTATG
1 ATATTTTAAATTTATC
12593 ATATTTTAAATTTATC
1 ATATTTTAAATTTATC
12609 ATAT
1 ATAT
12613 CATACTGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
ATATTTTAAATTTATC
Found at i:16516 original size:17 final size:17
Alignment explanation
Indices: 16494--16528 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16484 GGGAGTTTGT
16494 TTAAAATT-TTTAATAAA
1 TTAAAATTATTTAA-AAA
16511 TTAAAATTATTTAAAAA
1 TTAAAATTATTTAAAAA
16528 T
1 T
16529 GGGGTAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAATTATTTAAAAA
Found at i:18911 original size:41 final size:41
Alignment explanation
Indices: 18803--18888 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
18793 GAGTAGTCCT
*
18803 TGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCGAAA
1 TGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCAAAA
18844 TGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCAAAA
1 TGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCAAAA
18885 TGAG
1 TGAG
18889 CGTGAGGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (41 bp):
TGAGAATGAGATTATATTAAAGGAAGACTCATGTCTCAAAA
Found at i:18971 original size:40 final size:40
Alignment explanation
Indices: 18903--19002 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
18893 AGGTTTGTTT
*
18903 TTAAGAAGAAAGACTTATGACTCAGTAGAGCATAAGAGTGA
1 TTAA-AAGGAAGACTTATGACTCAGTAGAGCATAAGAGTGA
* * *
18944 TTAAAAGGATGCCTTATGACTCGGTAGAGCATAAGAGTGA
1 TTAAAAGGAAGACTTATGACTCAGTAGAGCATAAGAGTGA
18984 TTAAAAGGAAGACTTATGA
1 TTAAAAGGAAGACTTATGA
19003 ACTATGAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 49 0.92
41 4 0.08
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (40 bp):
TTAAAAGGAAGACTTATGACTCAGTAGAGCATAAGAGTGA
Found at i:21576 original size:16 final size:17
Alignment explanation
Indices: 21555--21589 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21545 TTAAATTTTA
21555 TTTTTTAT-ATTAACAT
1 TTTTTTATAATTAACAT
*
21571 TTTTTTATAATTAAGAT
1 TTTTTTATAATTAACAT
21588 TT
1 TT
21590 AAAATCGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTTTATAATTAACAT
Found at i:29586 original size:3 final size:3
Alignment explanation
Indices: 29569--29614 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
29559 CAACTAAAAT
29569 TTA TTA CTT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29614 T
1 T
29615 GTTTGGCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31223 original size:17 final size:17
Alignment explanation
Indices: 31201--31235 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31191 CTCTTGACTT
*
31201 TTAACCTTCCATCTTCC
1 TTAACCTTCCATATTCC
*
31218 TTAACCTTTCATATTCC
1 TTAACCTTCCATATTCC
31235 T
1 T
31236 GTAGCTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAACCTTCCATATTCC
Found at i:31734 original size:34 final size:35
Alignment explanation
Indices: 31683--31748 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
31673 TTTTTTTGTT
* *
31683 ATGTTATGCTTGCAAGTTTTGTTAAGGGATTACTA
1 ATGTTATGCTTGAAAGTTTTGTTAAAGGATTACTA
31718 ATGTT-TGCTTGAAAGTTTTGTTAAAGGATTA
1 ATGTTATGCTTGAAAGTTTTGTTAAAGGATTA
31749 TTTATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (35 bp):
ATGTTATGCTTGAAAGTTTTGTTAAAGGATTACTA
Done.