Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014247.1 Kokia drynarioides strain JFW-HI SEQ_129280, 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: 48643
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:670 original size:20 final size:21
Alignment explanation
Indices: 645--685 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
635 AGCTAATTTA
*
645 TTTAAATTAAA-AATTTAAAT
1 TTTAAATTAAACAAATTAAAT
665 TTTAAATTAAACAAATTAAAT
1 TTTAAATTAAACAAATTAAAT
686 GAAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAATTAAACAAATTAAAT
Found at i:785 original size:19 final size:20
Alignment explanation
Indices: 755--796 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
745 TTTATCATTC
* *
755 AATTTAATTTAATTTTTTTA
1 AATTTAATTTAAGTTTTTCA
775 AATTT-ATTTAAGTTTTTCA
1 AATTTAATTTAAGTTTTTCA
794 AAT
1 AAT
797 ATTTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTTAATTTAAGTTTTTCA
Found at i:857 original size:222 final size:216
Alignment explanation
Indices: 405--984 Score: 545
Period size: 222 Copynumber: 2.6 Consensus size: 216
395 TTATTTTTTC
* * * * *
405 AAATATTTCTATAAGTTAATTTATTTAAATTAATATTTTCAAATTTAAATTAATTCAATGAATAA
1 AAATATTTATATAAGTTAATTTATTTAAATTAAAAATTTCAAATTTAAATTAATTAAATGAAAAA
*
470 AATATTTTATATTAAAAAAAATTAGATAAATTTAAAATTTAAAAAGTTCATTTATCCATTCAATT
66 AATATTTTATATTAAAAAAAATTAGATAAATATAAAATTTAAAAAGTTCATTTATCCATTCAATT
*
535 TAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATATTTTTATAAGTTTAATTTATTTATC
131 TAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATATTTTTATAAGTTTAATTTATTTACC
* * *
600 GTAATTTTTTTTCACATTAAATA
196 ATAA--TCTTTTCAAATTAAATA
*
623 AAA-ATTTATATAAGCTAATTTATTTAAATTAAAAATTT-AAATTTTAAATTAAACAAATTAAAT
1 AAATATTTATATAAGTTAATTTATTTAAATTAAAAATTTCAAA-TTTAAATT-----AATTAAAT
** **
686 GAAAAAAATATTTTA-ATTAAAAATTATTAGATAAATATAAAATTTAAAAAGGACATTTTTTTAT
60 GAAAAAAATATTTTATATTAAAAAAAATTAGATAAATATAAAATTTAAAAA-G---TTCATTTAT
* *** * ** **
750 -CATTCAATTTAATTTAATTTTTTTAAATTT-ATTTAAGTTTTTCAAATATTTTTATAAG-TTAA
121 CCATTCAATTTAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATATTTTTATAAGTTTAA
*
812 TTTATTTACCATAA-CTTTTCAAATACTAGATA
186 TTTATTTACCATAATCTTTTCAAAT--TAAATA
* * * * *
844 AAATATTTATATAATTTAATTTATTTTAATTAAAATTTTCGAATTTATATTAAATAAATTCAATG
1 AAATATTTATATAAGTTAATTTATTTAAATTAAAAATTTC-AA---AT-TTAAATTAATTAAATG
*** * * * *
909 GGTAAAATGTTTTTTAATAAAAAATATAATTACAT-AATATAAAA-TTAAAAA--TCATTTATCC
61 AAAAAAATATTTTAT-ATTAAAAA-A-AATTAGATAAATATAAAATTTAAAAAGTTCATTTATCC
970 ATTCAA-TTAAATTAA
123 ATTCAATTTAAATTAA
985 ATAAAGCCTT
Statistics
Matches: 295, Mismatches: 43, Indels: 48
0.76 0.11 0.12
Matches are distributed among these distances:
216 3 0.01
217 39 0.13
218 17 0.06
219 15 0.05
221 40 0.14
222 86 0.29
223 24 0.08
224 41 0.14
225 16 0.05
226 7 0.02
227 7 0.02
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (216 bp):
AAATATTTATATAAGTTAATTTATTTAAATTAAAAATTTCAAATTTAAATTAATTAAATGAAAAA
AATATTTTATATTAAAAAAAATTAGATAAATATAAAATTTAAAAAGTTCATTTATCCATTCAATT
TAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATATTTTTATAAGTTTAATTTATTTACC
ATAATCTTTTCAAATTAAATA
Found at i:2086 original size:3 final size:3
Alignment explanation
Indices: 2078--2119 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2068 ATACCTTCAC
2078 TTA TTA 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
2120 AAATTTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3757 original size:3 final size:3
Alignment explanation
Indices: 3749--3777 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3739 TACGTATGTG
3749 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3778 TTCAATCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5076 original size:4 final size:4
Alignment explanation
Indices: 5067--5094 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5057 TCACTTGATA
5067 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
5095 CAGTCGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:12947 original size:87 final size:87
Alignment explanation
Indices: 12798--12964 Score: 246
Period size: 87 Copynumber: 1.9 Consensus size: 87
12788 ACAACAGGGT
* * *
12798 TTCACAGCACCCTTTGTAGCCGAGGATCGGTGGTTCGGTGAAGCCACACCGCTCACTTCTGTTTA
1 TTCACAGCACCCTGTATAGCCGAGGATCGGTGGTTCGGTGAAGCCACACCGCTCACTCCTGTTTA
*
12863 TTGATGCATGCAGTTAGAAATG
66 TTCATGCATGCAGTTAGAAATG
* * * *
12885 TTCACAGCAGCCTGTATAGCCGGGGA-CTGGTGGTTCGGTGAAGCTACACCGGTCACTCCTGTTT
1 TTCACAGCACCCTGTATAGCCGAGGATC-GGTGGTTCGGTGAAGCCACACCGCTCACTCCTGTTT
12949 ATTCATGCATGCAGTT
65 ATTCATGCATGCAGTT
12965 TTTAAAAGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 1 0.01
87 70 0.99
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (87 bp):
TTCACAGCACCCTGTATAGCCGAGGATCGGTGGTTCGGTGAAGCCACACCGCTCACTCCTGTTTA
TTCATGCATGCAGTTAGAAATG
Found at i:20229 original size:6 final size:6
Alignment explanation
Indices: 20218--20249 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20208 GGTTTGAAAT
20218 TGTTGA TGTTGA TGTTGA TGTTGA -G-TGA TGTT
1 TGTTGA TGTTGA TGTTGA TGTTGA TGTTGA TGTT
20250 ACAATGCAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 3 0.12
5 2 0.08
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGTTGA
Found at i:27018 original size:97 final size:98
Alignment explanation
Indices: 26830--27020 Score: 251
Period size: 97 Copynumber: 2.0 Consensus size: 98
26820 ACAACAATCA
* * *
26830 CCATCAAACAATGCTGCTCCAAGATACAATACCAATACTCGACCACGAATTCAAATAATAAGATA
1 CCATAAAACAATGCTGCTACAAGATACAATACCAATACTCGACCACAAATTCAAATAATAAGATA
*
26895 ATAATACTCCAACAATTCTAAGATCCTGCAGTC
66 ATAATACTCCAACAATTATAAGATCCTGCAGTC
* * * * * *
26928 CCATAAAACAATGCTGCTAC-AGATACAATATCTATATTCGACTACAAATTCACATCATAAGATA
1 CCATAAAACAATGCTGCTACAAGATACAATACCAATACTCGACCACAAATTCAAATAATAAGATA
* *
26992 ATAATATTCCAACAGTTAATAA-ATCCTGC
66 ATAATACTCCAACAATT-ATAAGATCCTGC
27021 TGCACAAGGT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
97 59 0.74
98 21 0.26
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.25
Consensus pattern (98 bp):
CCATAAAACAATGCTGCTACAAGATACAATACCAATACTCGACCACAAATTCAAATAATAAGATA
ATAATACTCCAACAATTATAAGATCCTGCAGTC
Found at i:38540 original size:12 final size:11
Alignment explanation
Indices: 38524--38563 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
38514 TTTTAAAATA
38524 TATTTTAATTT
1 TATTTTAATTT
38535 TAATTTTAATTT
1 T-ATTTTAATTT
*
38547 T-TTTGAATTT
1 TATTTTAATTT
38557 TATTTTA
1 TATTTTA
38564 TGAATAGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.36
11 5 0.20
12 11 0.44
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
TATTTTAATTT
Found at i:41082 original size:8 final size:8
Alignment explanation
Indices: 41073--41131 Score: 109
Period size: 8 Copynumber: 7.4 Consensus size: 8
41063 TTTACCGTAC
*
41073 GAATTAAC
1 GAATTAAT
41081 GAATTAAT
1 GAATTAAT
41089 GAATTAAT
1 GAATTAAT
41097 GAATTAAT
1 GAATTAAT
41105 GAATTAAT
1 GAATTAAT
41113 GAATTAAT
1 GAATTAAT
41121 GAATTAAT
1 GAATTAAT
41129 GAA
1 GAA
41132 ATTTTTTTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 50 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.34
Consensus pattern (8 bp):
GAATTAAT
Found at i:47063 original size:96 final size:96
Alignment explanation
Indices: 46890--47070 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
46880 AAGATGTTCG
* ** * *
46890 ATTATCTCGATTTGAGGAAAGGTTTCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATCGAAGAT
*
46955 AAGGAAACATTGCCTCGATTAAGGGTATTCA
66 AAAGAAACATTGCCTCGATTAAGGGTATTCA
*
46986 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTC-GAAACTCGAA-
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTCAG-AA-TCGAAG
*
47049 ATAAA-AGAATATTGCCTCGATT
64 ATAAAGA-AACATTGCCTCGATT
47071 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 67 0.91
97 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTCAGAATCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCA
Found at i:47395 original size:30 final size:29
Alignment explanation
Indices: 47332--47704 Score: 162
Period size: 30 Copynumber: 12.6 Consensus size: 29
47322 TCCCGGGCGC
* *
47332 AAAATGGTAATTTTGGGAAAATTCG-GGGTTA
1 AAAATGG-AATTTTTGG--AATTCGAGGGGTA
*
47363 AAAATGGAATTTTTAGACATTCGAGGGGT-
1 AAAATGGAATTTTTGGA-ATTCGAGGGGTA
* * *
47392 AAAAGGGTAA-TTTTGAGAGTTTTGA--GGTAA
1 AAAATGG-AATTTTTG-GA-ATTCGAGGGGT-A
* *
47422 AAAATGGAGTTTTTGGACA-TCGAGGGG-C
1 AAAATGGAATTTTTGGA-ATTCGAGGGGTA
* ** *
47450 AAAATGGTAATTTTTGAAAGTTTTA-GGCTA
1 AAAATGG-AATTTTTGGAA-TTCGAGGGGTA
* * *
47480 AAAATGGAAATTTTGGAGGTTTGA-GGGTA
1 AAAATGGAATTTTTGGA-ATTCGAGGGGTA
* ** * * *
47509 AAAATAGAATTTTTGGAAGTTTTAAGGTTG
1 AAAATGGAATTTTTGGAA-TTCGAGGGGTA
47539 AAAATGGAATTTTTGGAAGTTCG-GGGGTA
1 AAAATGGAATTTTTGGAA-TTCGAGGGGTA
* ** *
47568 AAAATGGAATTTTTTGAAGTTTTA-AGGTCA
1 AAAATGGAATTTTTGGAA-TTCGAGGGGT-A
*
47598 AAAATGGGATTTTTGGAAGTTCG-GGGGTAA
1 AAAATGGAATTTTTGGAA-TTCGAGGGGT-A
* * *
47628 AAAATGAAATTTTTGGAAGTTTTGA-GGTTA
1 AAAATGGAATTTTTGGAA--TTCGAGGGGTA
* **
47658 AAAATGGGATTTTTGGAAGTTTTA-GGGTA
1 AAAATGGAATTTTTGGAA-TTCGAGGGGTA
*
47687 AAAATGGAAATTTTGGAA
1 AAAATGGAATTTTTGGAA
47705 GTTTTGGGGT
Statistics
Matches: 262, Mismatches: 59, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
28 15 0.06
29 113 0.43
30 121 0.46
31 13 0.05
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAATTCGAGGGGTA
Found at i:47482 original size:29 final size:29
Alignment explanation
Indices: 47450--47735 Score: 295
Period size: 30 Copynumber: 9.7 Consensus size: 29
47440 ATCGAGGGGC
* *
47450 AAAATGGTAATTTTTGAAAGTTTTAGGCTA
1 AAAATGG-AATTTTTGGAAGTTTTAGGGTA
* * *
47480 AAAATGGAAATTTTGGAGGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTA
* * *
47509 AAAATAGAATTTTTGGAAGTTTTAAGGTTG
1 AAAATGGAATTTTTGGAAGTTTT-AGGGTA
***
47539 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTA
* *
47568 AAAATGGAATTTTTTGAAGTTTTAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAGGGT-A
* ***
47598 AAAATGGGATTTTTGGAAGTTCGGGGGTAA
1 AAAATGGAATTTTTGGAAGTTTTAGGGT-A
* *
47628 AAAATGAAATTTTTGGAAGTTTTGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTT-AGGGTA
*
47658 AAAATGGGATTTTTGGAAGTTTTAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTAGGGTA
* *
47687 AAAATGGAAATTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAGGGT-A
*
47717 AAAATATG-ATTTTTGGAAG
1 AAAAT-GGAATTTTTGGAAG
47736 CTCGAGGGGT
Statistics
Matches: 208, Mismatches: 43, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
29 92 0.44
30 112 0.54
31 4 0.02
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTAGGGTA
Found at i:47758 original size:59 final size:59
Alignment explanation
Indices: 47362--47759 Score: 312
Period size: 59 Copynumber: 6.7 Consensus size: 59
47352 ATTCGGGGTT
* * *** *
47362 AAAAATGGAATTTTTAGACA-TTCGAGGGGTAAAAGGGTAA-TTTT-GAGAGTTTTGAGGTA
1 AAAAATGGGATTTTTGGA-AGTTCG-GGGGTAAAAATATAATTTTTGGA-AGTTTTGAGGTC
* * *
47421 AAAAAT-GGAGTTTTTGGACA--TCGAGGGG-CAAAATGGTAATTTTTGAAAGTTTT-AGG-C
1 AAAAATGGGA-TTTTTGGA-AGTTCG-GGGGTAAAAAT-ATAATTTTTGGAAGTTTTGAGGTC
* * * * * * * *
47478 TAAAAATGGAAATTTTGGAGGTTTGAGGGTAAAAATAGAATTTTTGGAAGTTTTAAGGTT
1 -AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTGGAAGTTTTGAGGTC
* * ** * *
47538 GAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTTGAAGTTTTAAGGTC
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTGGAAGTTTTGAGGTC
*
47597 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA-ATGAAATTTTTGGAAGTTTTGAGGTT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAT--AATTTTTGGAAGTTTTGAGGTC
*** ** * *
47657 AAAAATGGGATTTTTGGAAGTTTTAGGGTAAAAATGGAAATTTTGGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTGGAAGTTTTGAGGTC
** * *
47716 AAAAATATGATTTTTGGAAGCTCGAGGGGTAGAAATATAATTTT
1 AAAAATGGGATTTTTGGAAGTTCG-GGGGTAAAAATATAATTTT
47760 CGAATAGTTT
Statistics
Matches: 274, Mismatches: 50, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
57 3 0.01
58 48 0.18
59 158 0.58
60 65 0.24
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTGGAAGTTTTGAGGTC
Found at i:47758 original size:119 final size:117
Alignment explanation
Indices: 47409--47759 Score: 343
Period size: 119 Copynumber: 3.0 Consensus size: 117
47399 TAATTTTGAG
* * * ** * *
47409 AGTTTTGAGGTAAAAAATGGAGTTTTTGGACA--TCGAGGGGCAAAATGGTAATTTTTGAAAGTT
1 AGTTTTAAGGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGG-AAATTTTGGAAGTT
* * * * * *
47472 TT-AGG-CTAAAAAT-GGAAATTTTGGAGGTTTGAGGGTAAAAATAGAATTTTTGGA
64 TTAAGGTC-AAAAATAGG-ATTTTTGGAAGCTCGGGGGT-AAAATATAATTTTTGGA
* * * *
47526 AGTTTTAAGGTTGAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTTGAAGTTTT
1 AGTTTTAAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAAATTTTGGAAGTTTT
* * *
47591 AAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAATGAAATTTTTGGA
66 AAGGTCAAAAATAGGATTTTTGGAAGCTCGGGGGTAAAATAT--AATTTTTGGA
* * **
47645 AGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTTAGGGTAAAAATGGAAATTTTGGAAGTTTT
1 AGTTTTAAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAAATTTTGGAAGTTTT
** *
47710 GGGGTCAAAAATATGATTTTTGGAAGCTCGAGGGGTAGAAATATAATTTT
66 AAGGTCAAAAATAGGATTTTTGGAAGCTCG-GGGGTA-AAATATAATTTT
47760 CGAATAGTTT
Statistics
Matches: 196, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
116 1 0.01
117 45 0.23
118 38 0.19
119 101 0.52
120 6 0.03
121 5 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (117 bp):
AGTTTTAAGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAAATTTTGGAAGTTTT
AAGGTCAAAAATAGGATTTTTGGAAGCTCGGGGGTAAAATATAATTTTTGGA
Found at i:47759 original size:89 final size:89
Alignment explanation
Indices: 47478--47751 Score: 297
Period size: 89 Copynumber: 3.1 Consensus size: 89
47468 AGTTTTAGGC
* * * * * * *
47478 TAAAAATGGAAATTTTGGAGGTTTGAGGGTAAAAATAGAATTTTTGGAAGTTTTAAGGTTGAAAA
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTT-GGGGTAAAAA
*
47543 T-GGAATTTTTGGAAGTTCG-GGGG
65 TATGAATTTTTGGAAGTTCGAGGGG
* * * **
47566 TAAAAATGGAATTTTTTGAAGTTTTAAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGT-AAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAA
* *
47631 -ATGAAATTTTTGGAAGTTTTGA-GGT
65 TATG-AATTTTTGGAAG-TTCGAGGGG
* *
47656 TAAAAATGGGATTTTTGGAAGTTTTAGGGTAAAAATGGAAATTTTGGAAGTTTTGGGGTCAAAAA
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGT-AAAAA
*
47721 TATG-ATTTTTGGAAGCTCGAGGGG
65 TATGAATTTTTGGAAGTTCGAGGGG
*
47745 TAGAAAT
1 TAAAAAT
47752 ATAATTTTCG
Statistics
Matches: 152, Mismatches: 26, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
88 36 0.24
89 76 0.50
90 37 0.24
91 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (89 bp):
TAAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAAT
ATGAATTTTTGGAAGTTCGAGGGG
Done.