Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012090.1 Kokia drynarioides strain JFW-HI SEQ_127089, 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: 43425
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:252 original size:17 final size:17
Alignment explanation
Indices: 232--318 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
222 CCAATTTTAA
*
232 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
* *
249 ATTTTAAGTTCAAATTT
1 ATTTTAAATTTAAATTT
*
266 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
283 ATTTTTGAGTTTAAATTT
1 A-TTTTAAATTTAAATTT
301 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
318 A
1 A
319 AAATTTAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 44 0.76
18 14 0.24
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:279 original size:6 final size:6
Alignment explanation
Indices: 227--326 Score: 62
Period size: 6 Copynumber: 16.8 Consensus size: 6
217 TGAACCCAAT
* * * * *
227 TTTAAA TTTTAAA TTTTAA TTT-AT TTTAAG TTCAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * *
274 TTTAAA CTTATT TTTGAG TTTAAA TTT-AT TTTAAA TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
322 TTTAA
1 TTTAA
327 TTATAAATCC
Statistics
Matches: 70, Mismatches: 19, Indels: 9
0.71 0.19 0.09
Matches are distributed among these distances:
5 12 0.17
6 46 0.66
7 12 0.17
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:306 original size:35 final size:34
Alignment explanation
Indices: 232--314 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 34
222 CCAATTTTAA
* *
232 ATTTTAAATTTTAATTTATTTTAAGTTCAAATTT
1 ATTTTAAATTTAAACTTATTTTAAGTTCAAATTT
* *
266 ATTTTAAATTTAAACTTATTTTTGAGTTTAAATTT
1 ATTTTAAATTTAAACTTA-TTTTAAGTTCAAATTT
301 ATTTTAAATTTAAA
1 ATTTTAAATTTAAA
315 TTTAAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 16 0.36
35 28 0.64
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (34 bp):
ATTTTAAATTTAAACTTATTTTAAGTTCAAATTT
Found at i:1768 original size:30 final size:30
Alignment explanation
Indices: 1725--2092 Score: 249
Period size: 30 Copynumber: 12.5 Consensus size: 30
1715 TGTTTTGTCT
* * * *
1725 AAAAATAATATTTTGACCCTCGAACTTTTC
1 AAAAATTACATTTTTACCCTCAAACTTTTC
* *
1755 AAAAATCACATTTTAACCC-CTAAACTTTTC
1 AAAAATTACATTTTTACCCTC-AAACTTTTC
* **
1785 AAAAATTATATTTCGACCCTCAAACTTTTC
1 AAAAATTACATTTTTACCCTCAAACTTTTC
* *
1815 CAAAATTACCATTTTGACCCT-AAACTTTTC
1 AAAAATTA-CATTTTTACCCTCAAACTTTTC
* * * * * *
1845 CAAAATTATATTTTTATCCTCGAAC-ATCC
1 AAAAATTACATTTTTACCCTCAAACTTTTC
* * *
1874 AAAAAATACCATTATGACCCT-AAACTTTTC
1 AAAAATTA-CATTTTTACCCTCAAACTTTTC
*
1904 CAAAATTACCA-TTTTACCCTTCAAAC-TTTC
1 AAAAATTA-CATTTTTACCC-TCAAACTTTTC
* * *
1934 -AAAATCACATTTTTACCCTCGAACTTCTC
1 AAAAATTACATTTTTACCCTCAAACTTTTC
* *
1963 AAAAATTACATTTTTACCCTCGAACTTCT-
1 AAAAATTACATTTTTACCCTCAAACTTTTC
* * * *
1992 AAAAATCATATTTTTACCC-CGAACTTTCC
1 AAAAATTACATTTTTACCCTCAAACTTTTC
* *
2021 CAAAATGACATTTTTACCC-CTAAA-TCTTTC
1 AAAAATTACATTTTTACCCTC-AAACT-TTTC
* * * *
2051 CAAATTTACATTTTAACCC-CAAACTCTTC
1 AAAAATTACATTTTTACCCTCAAACTTTTC
*
2080 AAAACTT-CATTTT
1 AAAAATTACATTTT
2093 CGACCCCATT
Statistics
Matches: 274, Mismatches: 49, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
28 20 0.07
29 90 0.33
30 149 0.54
31 15 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAAATTACATTTTTACCCTCAAACTTTTC
Found at i:1959 original size:59 final size:58
Alignment explanation
Indices: 1734--2039 Score: 246
Period size: 59 Copynumber: 5.2 Consensus size: 58
1724 TAAAAATAAT
* * * *
1734 ATTTTGACCCTCGAACTTTTCAAAAATCACATTTTAACCC-CTAAACTTTTCAAAAATTAT
1 ATTTTTACCCTCGAAC-TTTC-AAAATCACATTTTGACCCTC-AAACTTTTCCAAAATTAC
** * * *
1794 ATTTCGACCCTCAAACTTTTCCAAAATTACCATTTTGACCCT-AAACTTTTCCAAAATTAT
1 ATTTTTACCCTCGAAC-TTT-CAAAATCA-CATTTTGACCCTCAAACTTTTCCAAAATTAC
* * * *
1854 ATTTTTATCCTCGAACATCCAAAAAAT-ACCATTATGACCCT-AAACTTTTCCAAAATTACC
1 ATTTTTACCCTCGAACTTTC--AAAATCA-CATTTTGACCCTCAAACTTTTCCAAAATTA-C
* * * * *
1914 A-TTTTACCCTTCAAACTTTCAAAATCACATTTTTACCCTCGAACTTCTCAAAAATTAC
1 ATTTTTACCC-TCGAACTTTCAAAATCACATTTTGACCCTCAAACTTTTCCAAAATTAC
* * * * * *
1972 ATTTTTACCCTCGAACTTCTAAAAATCATATTTTTACCC-CGAACTTTCCCAAAATGAC
1 ATTTTTACCCTCGAACTT-TCAAAATCACATTTTGACCCTCAAACTTTTCCAAAATTAC
2030 ATTTTTACCC
1 ATTTTTACCC
2040 CTAAATCTTT
Statistics
Matches: 206, Mismatches: 29, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
58 50 0.24
59 79 0.38
60 66 0.32
61 11 0.05
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
ATTTTTACCCTCGAACTTTCAAAATCACATTTTGACCCTCAAACTTTTCCAAAATTAC
Found at i:3752 original size:169 final size:170
Alignment explanation
Indices: 3297--3797 Score: 801
Period size: 170 Copynumber: 3.0 Consensus size: 170
3287 AACAGTAAGA
* **
3297 ACAGTAAAAATGAAAATAGCATCCTCTTTAGTGAGA-T-TATATGAACAAATGCCCGAACCTAAA
1 ACAGTAAAAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAA
* * * *
3360 TACGTTATTGCTCTGGGCACGTGTACAATTACAGGAGGGATGTTCAATAATGATTCTTATAGTAC
66 TATGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTAC
* *
3425 TGTTTGGGGGGTAGATAAGCTAATTCTCGTGGATGTCTAT
131 TGTTCGGGGGGTAGATAAGCTAATTCCCGTGGATGTCTAT
* * * *
3465 ATAGTAATAATGAAAATGACGCCCTCTTTAGTGAGATTATATATAAACAAATGCCCGAACCTAAA
1 ACAGTAAAAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAA
3530 TATGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTAC
66 TATGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTAC
* *
3595 TATTCGGGGGGTCGATAAGCTAATTCCCGTGGATGTCTAT
131 TGTTCGGGGGGTAGATAAGCTAATTCCCGTGGATGTCTAT
* *
3635 ACAGTAACAATGAAAATGGCGCCCAC-TTAGTGAGATTATATATGAACAAATGCCCGAACCTAAA
1 ACAGTAAAAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAA
* *
3699 TATGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAGTAT
66 TATGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTAC
*
3764 TGTTCGGGGGGTGGATAAGCTAATTCCCGTGGAT
131 TGTTCGGGGGGTAGATAAGCTAATTCCCGTGGAT
3798 ATGCATTTGT
Statistics
Matches: 307, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
168 30 0.10
169 133 0.43
170 144 0.47
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (170 bp):
ACAGTAAAAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAA
TATGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTAC
TGTTCGGGGGGTAGATAAGCTAATTCCCGTGGATGTCTAT
Found at i:3878 original size:17 final size:17
Alignment explanation
Indices: 3851--3890 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3841 ATAAATTCTA
*
3851 AATAGACTAAACAGAAAT
1 AATA-ACTAAACAAAAAT
*
3869 AATAACTAAATAAAAAT
1 AATAACTAAACAAAAAT
3886 AATAA
1 AATAA
3891 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (17 bp):
AATAACTAAACAAAAAT
Found at i:3906 original size:11 final size:12
Alignment explanation
Indices: 3882--3910 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3872 AACTAAATAA
3882 AAATAATAATTT
1 AAATAATAATTT
3894 AAATAAT-ATTT
1 AAATAATAATTT
3905 AAATAA
1 AAATAA
3911 AATAATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATAATAATTT
Found at i:3927 original size:28 final size:29
Alignment explanation
Indices: 3865--3957 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 29
3855 GACTAAACAG
** *
3865 AAATAATAACTAAATAAAAATAATAATTT
1 AAATAATATTTAAATAAAAATAATAATAT
*
3894 AAATAATATTTAAAT-AAAATAATGATAT
1 AAATAATATTTAAATAAAAATAATAATAT
* * * * *
3922 ATATAATA-ATAGAT-AGAATAATAAAAT
1 AAATAATATTTAAATAAAAATAATAATAT
3949 AAATAATAT
1 AAATAATAT
3958 AGATATAGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
27 21 0.40
28 18 0.35
29 13 0.25
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (29 bp):
AAATAATATTTAAATAAAAATAATAATAT
Found at i:3929 original size:15 final size:15
Alignment explanation
Indices: 3911--3962 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3901 ATTTAAATAA
*
3911 AATAAT-GATATATAT
1 AATAATAGATAGA-AT
3926 AATAATAGATAGAAT
1 AATAATAGATAGAAT
3941 AATAA-A-ATA-AAT
1 AATAATAGATAGAAT
3953 AAT-ATAGATA
1 AATAATAGATA
3963 TAGATTTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 1 0.03
12 7 0.21
13 6 0.18
14 1 0.03
15 13 0.39
16 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (15 bp):
AATAATAGATAGAAT
Found at i:4003 original size:22 final size:21
Alignment explanation
Indices: 3978--4056 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 21
3968 TTCTAAATCG
3978 AAATATATTAATATAAATATAA
1 AAAT-TATTAATATAAATATAA
4000 AAATATATTAAT-TACTAATATAA
1 AAAT-TATTAATATA--AATATAA
* *
4023 ATATTATTAATTACTTAATATAA
1 AAATTATTAA-TA-TAAATATAA
*
4046 AGATTATTAAT
1 AAATTATTAAT
4057 TACTTAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.04
22 19 0.39
23 27 0.55
25 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (21 bp):
AAATTATTAATATAAATATAA
Found at i:4023 original size:23 final size:23
Alignment explanation
Indices: 3993--4066 Score: 114
Period size: 23 Copynumber: 3.2 Consensus size: 23
3983 TATTAATATA
3993 AATATAAAAATATATTAATTAC-T
1 AATATAAAAAT-TATTAATTACTT
*
4016 AATATAAATATTATTAATTACTT
1 AATATAAAAATTATTAATTACTT
*
4039 AATATAAAGATTATTAATTACTT
1 AATATAAAAATTATTAATTACTT
4062 AATAT
1 AATAT
4067 TAATAACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.21
23 38 0.79
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (23 bp):
AATATAAAAATTATTAATTACTT
Found at i:4177 original size:20 final size:21
Alignment explanation
Indices: 4147--4185 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
4137 TTGTTATATA
4147 ATTTCGATTGTTAATTGGTTT
1 ATTTCGATTGTTAATTGGTTT
4168 ATTT-GATTGTTAATTGGT
1 ATTTCGATTGTTAATTGGT
4186 ATTAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.56
Consensus pattern (21 bp):
ATTTCGATTGTTAATTGGTTT
Found at i:4339 original size:40 final size:40
Alignment explanation
Indices: 4295--4370 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
4285 AGGTCATGTT
** *
4295 CTTTAGCGGCATTTGTGGTAAAAGCGCCGCTAAAGACCAG
1 CTTTAGCAACATTTGTGGGAAAAGCGCCGCTAAAGACCAG
* *
4335 CTTTAGCAACGTTTGTGGGGAAAGCGCCGCTAAAGA
1 CTTTAGCAACATTTGTGGGAAAAGCGCCGCTAAAGA
4371 TCATATTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (40 bp):
CTTTAGCAACATTTGTGGGAAAAGCGCCGCTAAAGACCAG
Found at i:5214 original size:40 final size:40
Alignment explanation
Indices: 5159--5243 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
5149 TGATTAACAA
5159 CTCAAAAGCACACCATCTTTATACAAAATCTCTCAAGAAT
1 CTCAAAAGCACACCATCTTTATACAAAATCTCTCAAGAAT
5199 CTCAAAAGCACACCATCTTTATACAAAATCTCTCAAGAAT
1 CTCAAAAGCACACCATCTTTATACAAAATCTCTCAAGAAT
5239 CTCAA
1 CTCAA
5244 GATTATTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.42, C:0.28, G:0.05, T:0.25
Consensus pattern (40 bp):
CTCAAAAGCACACCATCTTTATACAAAATCTCTCAAGAAT
Found at i:6901 original size:27 final size:28
Alignment explanation
Indices: 6871--6926 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
6861 TTTATAATTT
*
6871 ATAAAATTTTAAAT-TAATAATGATAAA
1 ATAAAATTTTAAATCTAAAAATGATAAA
* *
6898 ATAATATTTTGAATCTAAAAATGATAAA
1 ATAAAATTTTAAATCTAAAAATGATAAA
6926 A
1 A
6927 AATTGATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (28 bp):
ATAAAATTTTAAATCTAAAAATGATAAA
Found at i:7264 original size:17 final size:17
Alignment explanation
Indices: 7234--7270 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7224 AAGTACTTAC
*
7234 AAGAATATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
*
7251 AAGAAGATGGAAGGTTA
1 AAGAAGATGAAAGGTTA
7268 AAG
1 AAG
7271 GTCAAGAGAG
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:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGGTTA
Found at i:7270 original size:24 final size:24
Alignment explanation
Indices: 7243--7290 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
7233 CAAGAATATG
*
7243 AAAGGTTAAAGA-AGATGGAAGGTT
1 AAAGG-TAAAGAGAGATGAAAGGTT
*
7267 AAAGGTCAAGAGAGATGAAAGGTT
1 AAAGGTAAAGAGAGATGAAAGGTT
7291 GAACATCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.19
Consensus pattern (24 bp):
AAAGGTAAAGAGAGATGAAAGGTT
Found at i:17733 original size:72 final size:72
Alignment explanation
Indices: 17590--17726 Score: 211
Period size: 72 Copynumber: 1.9 Consensus size: 72
17580 TACTCCATTT
* * ** *
17590 GAAGTGAATTGATTCGAAATCTATCAAATGATTTAAATTTTGTCATCTCGTTTAGATAAAATCAT
1 GAAGTGAATTGATTCGAAATCTATCAAACGATATAAATTTTAACATCTCGTTTAAATAAAATCAT
17655 CTTAATA
66 CTTAATA
* *
17662 GAAGTGAATTGATTCGAAATCTATCAGACGATATAAATTTTAACATCTCGTTTAAATAAAGTCAT
1 GAAGTGAATTGATTCGAAATCTATCAAACGATATAAATTTTAACATCTCGTTTAAATAAAATCAT
17727 TGTAATAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (72 bp):
GAAGTGAATTGATTCGAAATCTATCAAACGATATAAATTTTAACATCTCGTTTAAATAAAATCAT
CTTAATA
Found at i:24819 original size:15 final size:16
Alignment explanation
Indices: 24787--24819 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
24777 ATTTAAAAGT
*
24787 AATGGGGAAAATTTGG
1 AATGAGGAAAATTTGG
24803 AATGAGGAAAA-TTGG
1 AATGAGGAAAATTTGG
24818 AA
1 AA
24820 GTTTTGTGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.21
Consensus pattern (16 bp):
AATGAGGAAAATTTGG
Found at i:38114 original size:13 final size:13
Alignment explanation
Indices: 38096--38125 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
38086 AGCACTTATA
38096 TGTGCAAAGTGTG
1 TGTGCAAAGTGTG
38109 TGTGCAAAGTGTG
1 TGTGCAAAGTGTG
38122 TGTG
1 TGTG
38126 AGTTGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.40, T:0.33
Consensus pattern (13 bp):
TGTGCAAAGTGTG
Found at i:38451 original size:5 final size:5
Alignment explanation
Indices: 38441--38465 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38431 ATAGGAAAAC
38441 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
38466 GAGAGAGAGA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:41442 original size:21 final size:22
Alignment explanation
Indices: 41416--41463 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
41406 AGAACTGAAC
41416 TTTTAAGATTTTT-T-TTTTATA
1 TTTTAA-ATTTTTATCTTTTATA
*
41437 TTTT-AATTTTTATCTTTTTTA
1 TTTTAAATTTTTATCTTTTATA
41458 TTTTAA
1 TTTTAA
41464 CTTTGACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 6 0.26
20 2 0.09
21 14 0.61
22 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTAAATTTTTATCTTTTATA
Done.