Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012470.1 Kokia drynarioides strain JFW-HI SEQ_127474, 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: 55146
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:6691 original size:21 final size:21
Alignment explanation
Indices: 6648--6694 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
6638 ATGTTTTATA
*
6648 TTTTATAAATTGTTTACAATT
1 TTTTATAAATTATTTACAATT
6669 TTTTATAAATTTATTT--AATT
1 TTTTATAAA-TTATTTACAATT
6689 TTTTAT
1 TTTTAT
6695 TATGATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 9 0.38
22 5 0.21
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATAAATTATTTACAATT
Found at i:8004 original size:22 final size:21
Alignment explanation
Indices: 7966--8012 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
7956 ATAGTTTATT
*
7966 TATATGATAATTATAATTATAA
1 TATAAGATAATTATAA-TATAA
*
7988 TATAAGATAATGT-TAATATTA
1 TATAAGATAAT-TATAATATAA
8009 TATA
1 TATA
8013 TTAAGAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 8 0.36
22 13 0.59
23 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (21 bp):
TATAAGATAATTATAATATAA
Found at i:31300 original size:20 final size:19
Alignment explanation
Indices: 31275--31315 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
31265 AACTAGTAAT
31275 AAAAGTCAACC-ATAACAATA
1 AAAAGT-AACCAATAA-AATA
31295 AAAAGTAACCAATAAAATA
1 AAAAGTAACCAATAAAATA
31314 AA
1 AA
31316 GCATACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.66, C:0.15, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAAGTAACCAATAAAATA
Found at i:33833 original size:23 final size:23
Alignment explanation
Indices: 33806--33859 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
33796 GAACACTAGC
33806 GCTTACTGTTTCACACTTCGTGT
1 GCTTACTGTTTCACACTTCGTGT
* **
33829 GCTTACTATTTTGCACTTCGTGT
1 GCTTACTGTTTCACACTTCGTGT
33852 GCTTACTG
1 GCTTACTG
33860 ATTTGCGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCACACTTCGTGT
Found at i:33864 original size:23 final size:23
Alignment explanation
Indices: 33825--33927 Score: 115
Period size: 23 Copynumber: 4.5 Consensus size: 23
33815 TTCACACTTC
33825 GTGTGCTTACT-ATTTTGCACT-T
1 GTGTGCTTACTGA-TTTGCACTAT
*
33847 CGTGTGCTTACTGATTTGCGCTAT
1 -GTGTGCTTACTGATTTGCACTAT
* * *
33871 GTGCGCCTACTGA-TTGCACTGT
1 GTGTGCTTACTGATTTGCACTAT
33893 GTGTGCTTACTGGA-TTGCACTAT
1 GTGTGCTTACT-GATTTGCACTAT
33916 GTGTGCTTACTG
1 GTGTGCTTACTG
33928 TTTCCCCAGC
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
22 17 0.25
23 50 0.72
24 2 0.03
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.41
Consensus pattern (23 bp):
GTGTGCTTACTGATTTGCACTAT
Found at i:33897 original size:45 final size:45
Alignment explanation
Indices: 33839--33927 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
33829 GCTTACTATT
*
33839 TTGCACTTCGTGTGCTTACT-GATTTGCGCTATGTGCGCCTACTGA
1 TTGCACTTCGTGTGCTTACTGGA-TTGCACTATGTGCGCCTACTGA
* *
33884 TTGCACTGT-GTGTGCTTACTGGATTGCACTATGTGTGCTTACTG
1 TTGCACT-TCGTGTGCTTACTGGATTGCACTATGTGCGCCTACTG
33928 TTTCCCCAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 36 0.92
46 3 0.08
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.39
Consensus pattern (45 bp):
TTGCACTTCGTGTGCTTACTGGATTGCACTATGTGCGCCTACTGA
Found at i:35988 original size:17 final size:17
Alignment explanation
Indices: 35942--35996 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
35932 TATATATTTT
35942 ATAATTAAATTCAAATAA
1 ATAATTAAATT-AAATAA
* **
35960 ATATTTTCATTAAATAA
1 ATAATTAAATTAAATAA
* *
35977 TTAATTAAATTATATAA
1 ATAATTAAATTAAATAA
35994 ATA
1 ATA
35997 TTATATTTAA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATTAAATTAAATAA
Found at i:36007 original size:34 final size:35
Alignment explanation
Indices: 35943--36008 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
35933 ATATATTTTA
*
35943 TAATTAAATTCAAATAAATATTTTCATTAAATAAT
1 TAATTAAATTCAAATAAATATTATCATTAAATAAT
*
35978 TAATTAAATT-ATATAAATATTAT-ATTTAAAT
1 TAATTAAATTCAAATAAATATTATCA-TTAAAT
36009 TTGATTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.04
34 17 0.61
35 10 0.36
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (35 bp):
TAATTAAATTCAAATAAATATTATCATTAAATAAT
Found at i:36102 original size:6 final size:6
Alignment explanation
Indices: 36093--36127 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
36083 GATTTTAATT
* *
36093 TTGATG TTGATG TTGATG TTGATA TTGATA TTGAT
1 TTGATG TTGATG TTGATG TTGATG TTGATG TTGAT
36128 AGGAGTATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (6 bp):
TTGATG
Found at i:36473 original size:17 final size:17
Alignment explanation
Indices: 36422--36476 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
36412 TTGGTCTAAC
36422 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
36439 AAAATT-AATCTTATTTT
1 AAATTTAAAT-TTATTTT
36456 AAATTTAAAATTTA-TTT
1 AAATTT-AAATTTATTTT
36473 AAAT
1 AAAT
36477 AATATCCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 3 0.09
17 24 0.73
18 3 0.09
19 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:37120 original size:12 final size:12
Alignment explanation
Indices: 37103--37143 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
37093 ATGATTTTAA
37103 TAATAATGAA-AT
1 TAATAAT-AATAT
37115 TAATAATAATAT
1 TAATAATAATAT
*
37127 TTATAATAATAT
1 TAATAATAATAT
37139 TAATA
1 TAATA
37144 GTAGTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 2 0.08
12 24 0.92
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:38030 original size:30 final size:28
Alignment explanation
Indices: 37994--38425 Score: 124
Period size: 30 Copynumber: 14.7 Consensus size: 28
37984 CCTTGAAGGT
37994 CCCTAAACTGTCCAAAAATTCTGTTTTCAC
1 CCCTAAACT-TCCAAAAATTCT-TTTTCAC
* ** *
38024 CCCTAAACTTCTAAAAACCCCATTTTTGAC
1 CCCTAAACTTCCAAAAA-TTC-TTTTTCAC
* *
38054 CTCAAAACTTCCAAAAATTCCATTTTT-AC
1 CCCTAAACTTCCAAAAATT-C-TTTTTCAC
* * * *
38083 CCCTAAACTTCAAAAAATCCCATTTTGAC
1 CCCTAAACTTCCAAAAAT-TCTTTTTCAC
** * * * *
38112 TTCAAAACTCCCAGAAATTTCGCTTTT-A-
1 CCCTAAACTTCCA-AAAATTC-TTTTTCAC
* *
38140 CCCTCAAACTTCCAAAAATCACATTTTTGAC
1 CCCT-AAACTTCCAAAAAT-TC-TTTTTCAC
* *
38171 CCCGAAAC-TCTCAAAAATTCTATTTTTA-
1 CCCTAAACTTC-CAAAAATTCT-TTTTCAC
* ** * *
38199 CCCTCGAACTTCCAAAAACCCCATTTTTGAT
1 CCCT-AAACTTCCAAAAA-TTC-TTTTTCAC
* * * *
38230 CCCGAAACTCCCAAGAATTCTATTTTTAC
1 CCCTAAACTTCCAAAAATTCT-TTTTCAC
* * * *
38259 CCTCT-AACTTTCGAAAATCCCATTTTTGA-
1 CC-CTAAACTTCCAAAAAT-TC-TTTTTCAC
* * *
38288 CCATGAAACTCCCAAAAATTCCGTTTTCAC
1 CCCT-AAACTTCCAAAAATT-CTTTTTCAC
* * *
38318 CCCCAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAAT-TC-TTTTTCAC
* *
38348 CTCGAAACTTCCAAAAATT-TTGTTTCTAC
1 CCCTAAACTTCCAAAAATTCTT-TTTC-AC
** * *
38377 CCCCGAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAAT-TC-TTTTTCAC
* *
38407 CCCAAAACCTCCAAAAATT
1 CCCTAAACTTCCAAAAATT
38426 ACCATTTTAC
Statistics
Matches: 290, Mismatches: 79, Indels: 67
0.67 0.18 0.15
Matches are distributed among these distances:
27 2 0.01
28 18 0.06
29 122 0.42
30 134 0.46
31 12 0.04
32 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTCTTTTTCAC
Found at i:38437 original size:29 final size:29
Alignment explanation
Indices: 37998--38461 Score: 249
Period size: 29 Copynumber: 15.8 Consensus size: 29
37988 GAAGGTCCCT
** * *
37998 AAACTGTCCAAAAATTCTGTTTTCACCCCT
1 AAACT-TCCAAAAATTCCATTTTGACCCCC
* ** * *
38028 AAACTTCTAAAAACCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
* *
38058 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTGACCCCC
* * ** *
38087 AAACTTCAAAAAATCCCATTTTGACTTCA
1 AAACTTCCAAAAATTCCATTTTGACCCCC
* * *
38116 AAACTCCCAGAAATTTCGC-TTTT-ACCCTC
1 AAACTTCCA-AAAATTC-CATTTTGACCCCC
*
38145 AAACTTCCAAAAA-TCACATTTTTGACCCCG
1 AAACTTCCAAAAATTC-CA-TTTTGACCCCC
* * *
38175 AAAC-TCTCAAAAATTCTATTTTTACCCTC
1 AAACTTC-CAAAAATTCCATTTTGACCCCC
* ** * *
38204 GAACTTCCAAAAACCCCATTTTTGATCCCG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
* * * * *
38234 AAACTCCCAAGAATTCTATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTGACCCCC
* * * * ***
38263 TAACTTTCGAAAATCCCATTTTTGACCATG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
* * *
38293 AAACTCCCAAAAATTCCGTTTTCACCCCC
1 AAACTTCCAAAAATTCCATTTTGACCCCC
* * *
38322 AAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
***
38352 AAACTTCCAAAAATTTTGTTTCT-ACCCCC
1 AAACTTCCAAAAATTCCATTT-TGACCCCC
* * *
38381 GAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTGACCCCC
* *
38411 AAACCTCCAAAAATTACCATTTT-ACCCTC
1 AAACTTCCAAAAATT-CCATTTTGACCCCC
* *
38440 AGA-TGTCCAAAAACTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
38462 CGATCTCGAA
Statistics
Matches: 316, Mismatches: 101, Indels: 36
0.70 0.22 0.08
Matches are distributed among these distances:
27 3 0.01
28 10 0.03
29 157 0.50
30 140 0.44
31 6 0.02
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCCCC
Found at i:38449 original size:59 final size:57
Alignment explanation
Indices: 38004--38500 Score: 425
Period size: 59 Copynumber: 8.5 Consensus size: 57
37994 CCCTAAACTG
** * * *
38004 TCCAAAAATTCTGTTTTCACCC-CTAAACTTCTAAAAACCCCATTTTTGACCTCAAAAC
1 TCCAAAAATTCCATTTT-ACCCTC-AAACTTCCAAAAATCCCATTTTTGACCTCGAAAC
* * *
38062 TTCCAAAAATTCCATTTTTACCC-CTAAACTTCAAAAAATCCCA-TTTTGACTTCAAAAC
1 -TCCAAAAATTCCA-TTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACCTCGAAAC
* * *
38120 TCCCAGAAATTTCGC-TTTTACCCTCAAACTTCCAAAAATCACATTTTTGACCCCGAAAC
1 T-CCA-AAAATTC-CATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAAAC
* * *
38179 TCTCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAACCCCATTTTTGATCC-CGAAAC
1 TC-CAAAAATTCCA-TTTTACCCTCAAACTTCCAAAAATCCCATTTTTGA-CCTCGAAAC
* * * * *
38238 TCCCAAGAATTCTATTTTTACCCTCTAACTTTCGAAAATCCCATTTTTGACCAT-GAAAC
1 T-CCAAAAATTCCA-TTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACC-TCGAAAC
* *
38297 TCCCAAAAATTCCGTTTTCACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAAAC
1 T-CCAAAAATTCCATTTT-ACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAAAC
*** * * * *
38356 TTCCAAAAATTTTGTTTCTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACC
1 -TCCAAAAATTCCATTT-TACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAAA-C
* * *
38416 TCCAAAAATTACCATTTTACCCTCAGA-TGTCCAAAAA-CTCCATTTTCGATCTCGAAAC
1 TCCAAAAATT-CCATTTTACCCTCAAACT-TCCAAAAATC-CCATTTTTGACCTCGAAAC
** *
38474 TCTTAAAATTACCCTTTTACCCTCAAA
1 TCCAAAAATT-CCATTTTACCCTCAAA
38501 TGTCTAAAAA
Statistics
Matches: 370, Mismatches: 47, Indels: 43
0.80 0.10 0.09
Matches are distributed among these distances:
57 1 0.00
58 81 0.22
59 274 0.74
60 14 0.04
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAAAC
Found at i:38461 original size:177 final size:175
Alignment explanation
Indices: 37998--38500 Score: 519
Period size: 177 Copynumber: 2.8 Consensus size: 175
37988 GAAGGTCCCT
** * * *
37998 AAACTGTCCAAAAATTCTGTTTTCACCCCTAAACTTCTAAAAACCCCATTTTTGACCTCAAAACT
1 AAACT-TCCAAAAATTCTGTTTT-ACCCCCGAACTTCCAAAAACCCCATTTTTGACCCCAAAACC
*
38063 TCCAAAAATTCCATTTTTACCC-CTAAACTT-CAAAAAATCCCA-TTTTGACTTCAAAACTCCCA
64 TCCAAAAATTCCATTTTTACCCTCT-AACTTCCAAAAACT-CCATTTTTGAC-TCAAAACTCCCA
* * *
38125 GAAATTTCGCTTTTACCCTCAAACTTCCAAAAATCACATTTTTGACCCCG
126 AAAATTCCGCTTTTACCCCCAAACTTCCAAAAATCACATTTTTGACCCCG
* * * *
38175 AAAC-TCTCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAACCCCATTTTTGATCCCGAAA-C
1 AAACTTC-CAAAAATTCT-GTTTTACCCCCGAACTTCCAAAAACCCCATTTTTGACCCCAAAACC
* * * *
38238 TCCCAAGAATTCTATTTTTACCCTCTAACTTTCGAAAA-TCCCATTTTTGAC-CATGAAACTCCC
64 T-CCAAAAATTCCATTTTTACCCTCTAACTTCCAAAAACT-CCATTTTTGACTCA--AAACTCCC
* *
38301 AAAAATTCCG-TTTTCACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCG
125 AAAAATTCCGCTTTT-ACCCCCAAACTTCCAAAAATCACATTTTTGACCCCG
* *
38352 AAACTTCCAAAAATTTTGTTTCTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACCT
1 AAACTTCCAAAAATTCTGTTT-TACCCCCGAACTTCCAAAAACCCCATTTTTGACCCCAAAACCT
* * **
38417 CCAAAAATTACCA-TTTTACCCTC-AGA-TGTCCAAAAACTCCATTTTCGATCTCGAAACT-CTT
65 CCAAAAATT-CCATTTTTACCCTCTA-ACT-TCCAAAAACTCCATTTTTGA-CTCAAAACTCCCA
*
38478 AAAATTACC-CTTTTACCCTCAAA
126 AAAATT-CCGCTTTTACCCCCAAA
38501 TGTCTAAAAA
Statistics
Matches: 274, Mismatches: 32, Indels: 41
0.79 0.09 0.12
Matches are distributed among these distances:
175 5 0.02
176 95 0.35
177 165 0.60
178 8 0.03
179 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (175 bp):
AAACTTCCAAAAATTCTGTTTTACCCCCGAACTTCCAAAAACCCCATTTTTGACCCCAAAACCTC
CAAAAATTCCATTTTTACCCTCTAACTTCCAAAAACTCCATTTTTGACTCAAAACTCCCAAAAAT
TCCGCTTTTACCCCCAAACTTCCAAAAATCACATTTTTGACCCCG
Found at i:39684 original size:17 final size:18
Alignment explanation
Indices: 39639--39685 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39629 CTGTTTAACA
39639 CTATTTTTAATTTGTCCGT
1 CTATTTTT-ATTTGTCCGT
**
39658 CTA-TAATATTTGTCCGT
1 CTATTTTTATTTGTCCGT
39675 -TATTTTTATTT
1 CTATTTTTATTT
39686 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
16 2 0.09
17 16 0.70
18 2 0.09
19 3 0.13
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (18 bp):
CTATTTTTATTTGTCCGT
Found at i:42835 original size:35 final size:37
Alignment explanation
Indices: 42765--42852 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 37
42755 TTAGTTATTA
* * *
42765 TATATATTTATACA--TTTATAATTTTTTTATTCTTT
1 TATATATTTATATATTTTTATAATATTTTTATACTTT
42800 TATATATTTATATATTTTTATAA-ATTTTTA-ACTTT
1 TATATATTTATATATTTTTATAATATTTTTATACTTT
42835 T-TATTGATTATATATATT
1 TATA-T-ATT-TATATATT
42853 ATAATTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
34 2 0.04
35 19 0.42
36 9 0.20
37 15 0.33
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (37 bp):
TATATATTTATATATTTTTATAATATTTTTATACTTT
Found at i:42836 original size:45 final size:44
Alignment explanation
Indices: 42760--42864 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 44
42750 GACGTTTAGT
* * * * *
42760 TATTATATATATTTATACATTTATAATTTTTTTATT-CTTTTATA
1 TATTATATATTTTTATAAATTTATAA-CTTTTTATTGATTATATA
*
42804 TATTTATATATTTTTATAAATTTTTAACTTTTTATTGATTATATA
1 TA-TTATATATTTTTATAAATTTATAACTTTTTATTGATTATATA
42849 TATTATA-ATTTTTATA
1 TATTATATATTTTTATA
42865 TATATTTCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
43 9 0.17
44 15 0.28
45 29 0.55
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (44 bp):
TATTATATATTTTTATAAATTTATAACTTTTTATTGATTATATA
Found at i:42925 original size:23 final size:23
Alignment explanation
Indices: 42888--42945 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 23
42878 ATTATAGGCT
42888 TTTTATATAATTT-TAATTGTATATA
1 TTTTATA-AATTTAT-ATT-TATATA
42913 TTTTATAAATTTATATTTATATA
1 TTTTATAAATTTATATTTATATA
42936 TATTTA-AAAT
1 T-TTTATAAAT
42946 AATAACTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 11 0.35
24 12 0.39
25 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTATAAATTTATATTTATATA
Found at i:42935 original size:25 final size:25
Alignment explanation
Indices: 42888--42940 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
42878 ATTATAGGCT
*
42888 TTTTATATAATTTTAATTGTATATA
1 TTTTATATAATTTTAATTATATATA
*
42913 TTTTATA-AATTTATATTTATATATA
1 TTTTATATAATTT-TAATTATATATA
42938 TTT
1 TTT
42941 AAAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTATATAATTTTAATTATATATA
Done.