Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007130.1 Kokia drynarioides strain JFW-HI SEQ_121742, 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: 23627
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Found at i:650 original size:29 final size:29
Alignment explanation
Indices: 606--1075 Score: 349
Period size: 29 Copynumber: 16.6 Consensus size: 29
596 CTTAAATTTT
606 CAAAAATTCCATTTTTACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * * * *
635 TAAAAATCCCAATTTTGACCCTAAAGCTTC
1 CAAAAATTCC-ATTTTTACCCCAAAACTTC
*
665 CAAAAATTCCATTTTTACCCTC-GAACTTC
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
* **
694 CAAAAATTCCATTTTGACTTCAAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * *
723 CAAAAATTCCATTTTTACACTAGAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * *
752 TAAAAATCCCATTTTTTACCCCGAAACTTC
1 CAAAAATTCCA-TTTTTACCCCAAAACTTC
* *
782 CAAAAATTCCATTTTTACCCTAGAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
811 CAAAAATTCAATTTTT-------AAC-CC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * ** *
832 CAAAAATTCCATTTTTACCTCGAACTTCC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
861 AAAAAT-TCCATTTTTAACCCCAAAA-TTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
*
889 C----A-----TTTTTACCCTC-AAACTTT
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
*
909 CAAAAATTCTATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
* *
939 CAAAAAGTCCATTTTTTACCCTC-GAACTTC
1 CAAAAATTCCA-TTTTTACCC-CAAAACTTC
969 CAAAAA-TCTCATTTTTAACCCCAAAACTTC
1 CAAAAATTC-CATTTTT-ACCCCAAAACTTC
* *
999 CAAAAATTTCATTTTTACCCTC-GAACTTC
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
** *
1028 CAAAAAACCCATTTTTAACCTCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
1058 CAAAAATTCCATTTTTAC
1 CAAAAATTCCATTTTTAC
1076 TCTCGAACTT
Statistics
Matches: 347, Mismatches: 59, Indels: 70
0.73 0.12 0.15
Matches are distributed among these distances:
19 7 0.02
20 9 0.03
21 16 0.05
22 3 0.01
24 1 0.00
28 13 0.04
29 160 0.46
30 131 0.38
31 7 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCAAAACTTC
Found at i:699 original size:59 final size:58
Alignment explanation
Indices: 606--1097 Score: 468
Period size: 59 Copynumber: 8.7 Consensus size: 58
596 CTTAAATTTT
* * *
606 CAAAAATTCCATTTTTACCC-CAAAACTTCTAAAAATCCCAATTTTGACCCTAAAGCTTC
1 CAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCAATTTT-ACCCTAAAACTTC
* *
665 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCC-ATTTTGA-CTTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTT-ACCCT-AAAACTTC
* * * * **
723 CAAAAATTCCATTTTTACACTAGAACTTCTAAAAATCCCATTTTTTACCCCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCA-ATTTTACCCTAAAACTTC
* * *
782 CAAAAATTCCATTTTTACCCTAGAACTTCCAAAAAT-TCAATTTT----T--AAC-CC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCTAAAACTTC
*
832 CAAAAATTCCATTTTTA-CCTCGAACTTCCAAAAATTCC-ATTTT----T--AAC--C
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCTAAAACTTC
* * * * * * *
880 CCAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTT-ACCCTAAAACTTC
* * * *
939 CAAAAAGTCCATTTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCCAAAACTTC
1 CAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAATCCCAATTTT-ACCCTAAAACTTC
* * * *
999 CAAAAATTTCATTTTTACCCTCGAACTTCCAAAAAACCCATTTTTAACCTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCT-AAAACTTC
* *
1058 CAAAAATTCCATTTTTACTCTCGAACTTCTAAAAATCCCA
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCA
1098 CTGAACATCC
Statistics
Matches: 370, Mismatches: 44, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
48 17 0.05
49 44 0.12
50 23 0.06
51 3 0.01
57 9 0.02
58 54 0.15
59 162 0.44
60 58 0.16
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCTAAAACTTC
Found at i:874 original size:49 final size:50
Alignment explanation
Indices: 781--1000 Score: 257
Period size: 49 Copynumber: 4.2 Consensus size: 50
771 CCCGAAACTT
*
781 CCAAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCAATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAACC
*
831 CCAAAAATTCCATTTTTA-CCTCGAACTTCCAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAACC
* * *
880 CC-AAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAAC
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAA---C----C
*
936 TTCCAAAAAGTCCATTTTTTACCCTCGAACTTCCAAAAATCTC-ATTTTTAACC
1 --CCAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAAT-TCAATTTTTAACC
*
989 CCAAAACTTCCA
1 CCAAAAATTCCA
1001 AAAATTTCAT
Statistics
Matches: 147, Mismatches: 10, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
48 15 0.10
49 57 0.39
50 18 0.12
51 10 0.07
52 1 0.01
53 1 0.01
56 1 0.01
57 1 0.01
58 2 0.01
59 8 0.05
60 31 0.21
61 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (50 bp):
CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAACC
Found at i:899 original size:19 final size:21
Alignment explanation
Indices: 862--904 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
852 CGAACTTCCA
862 AAAATTCCATTTTTAACCC-C
1 AAAATTCCATTTTTAACCCTC
882 AAAATTCCATTTTT-ACCCTC
1 AAAATTCCATTTTTAACCCTC
902 AAA
1 AAA
905 CTTTCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTCCATTTTTAACCCTC
Found at i:943 original size:30 final size:30
Alignment explanation
Indices: 882--1093 Score: 231
Period size: 30 Copynumber: 7.2 Consensus size: 30
872 TTTTAACCCC
*
882 AAAATTCCATTTTT-ACCCTCAAACTTTCA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
*
911 AAAATTCTATTTTTAACCC-CAAAACTTCCA
1 AAAATTCCATTTTTAACCCTC-AAACTTCCA
* * *
941 AAAAGTCCATTTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
971 AAAA-TCTCATTTTTAACCC-CAAAACTTCCA
1 AAAATTC-CATTTTTAACCCTC-AAACTTCCA
* *
1001 AAAATTTCATTTTT-ACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
**
1030 AAAAACCCATTTTTAA-CCTCAAAACTTCCA
1 AAAATTCCATTTTTAACCCTC-AAACTTCCA
* * *
1060 AAAATTCCATTTTT-ACTCTCGAACTTCTA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
1089 AAAAT
1 AAAAT
1094 CCCACTGAAC
Statistics
Matches: 154, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
29 57 0.37
30 95 0.62
31 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCTCAAACTTCCA
Found at i:1742 original size:215 final size:213
Alignment explanation
Indices: 1366--1778 Score: 711
Period size: 215 Copynumber: 1.9 Consensus size: 213
1356 TTTTACCATT
*
1366 TTATTTACTTCGCATTATTCAATATCCATTATTAACTACTATTTCATATTAATTAGCATGTTTGT
1 TTATTTACTTCGCATTATTCAATATCCATTATTAACTACTATTTCATATTAACTAGCATGTTTGT
* *
1431 TTTCAAAATTGTTTTCATAAAAACTTTAAAATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAA
66 TTTCAAAATTATTTTCATAAAAACTTTAAAATCGAGACAATATTCTTTTATTTCGAGTTTCGAAA
1496 ATTTGCGCCTTAACTTACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAATCG
131 ATTTGCGCCTTAACTTACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAATCG
1561 AGGTAATGTTTATTCGTG
196 AGGTAATGTTTATTCGTG
** * * *
1579 TTATCTTACTTCGTGTTATTTAATATCCATTATTAACTGCT-TATTCATATTAAACTCGCATGTT
1 TTAT-TTACTTCGCATTATTCAATATCCATTATTAACTACTAT-TTCATATT-AACTAGCATGTT
1643 TGTTTTCAAAATTATTTTCATAAAAACTTTAAAATCGAGACAATATTCTTTTATTTCGAGTTTCG
63 TGTTTTCAAAATTATTTTCATAAAAACTTTAAAATCGAGACAATATTCTTTTATTTCGAGTTTCG
*
1708 AAAATTTGCGCCTTAACTTACTAGGTGTAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
128 AAAATTTGCGCCTTAACTTACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
1773 TCGAGG
193 TCGAGG
1779 CAACGTTTTT
Statistics
Matches: 188, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
213 5 0.03
214 40 0.21
215 143 0.76
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (213 bp):
TTATTTACTTCGCATTATTCAATATCCATTATTAACTACTATTTCATATTAACTAGCATGTTTGT
TTTCAAAATTATTTTCATAAAAACTTTAAAATCGAGACAATATTCTTTTATTTCGAGTTTCGAAA
ATTTGCGCCTTAACTTACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAATCG
AGGTAATGTTTATTCGTG
Found at i:13216 original size:37 final size:37
Alignment explanation
Indices: 13175--13245 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
13165 AAACGGTTAG
* *
13175 CTTCCTAATGAAATATAGGGAAGTGAACCAAAACCAT
1 CTTCCTAATGAAACATAGAGAAGTGAACCAAAACCAT
* * *
13212 CTTCCTGATGAAACATAGAGAAGTGGATCAAAAC
1 CTTCCTAATGAAACATAGAGAAGTGAACCAAAAC
13246 AAGTGATATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (37 bp):
CTTCCTAATGAAACATAGAGAAGTGAACCAAAACCAT
Found at i:13295 original size:49 final size:49
Alignment explanation
Indices: 13209--13332 Score: 122
Period size: 49 Copynumber: 2.5 Consensus size: 49
13199 GAACCAAAAC
* * * * * * * * *
13209 CATCTTCCTGATGAAACATAGAGAAGTGGATCAAAACAAGTGATATGTT
1 CATCTTCCTGATGAGATACAGAGAAGCGAATCAAAACAAATGACACGGT
** *
13258 CATCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAATGACGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGCGAATCAAAACAAATGACACGGT
* *
13307 CATCTTCCTAATGAGATACTGAGAAG
1 CATCTTCCTGATGAGATACAGAGAAG
13333 AAGTCCAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (49 bp):
CATCTTCCTGATGAGATACAGAGAAGCGAATCAAAACAAATGACACGGT
Found at i:13500 original size:37 final size:38
Alignment explanation
Indices: 13430--13501 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
13420 AAACGGTTAG
* * *
13430 CTTCCTGATGAAATACAGGGGAAGTGAACCAAAACCAT
1 CTTCCTGATAAAACACAGGAGAAGTGAACCAAAACCAT
* *
13468 CTTCCTGATAAAACACA-GAGAAGTGGATCAAAAC
1 CTTCCTGATAAAACACAGGAGAAGTGAACCAAAAC
13502 AGGTGATATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 14 0.48
38 15 0.52
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (38 bp):
CTTCCTGATAAAACACAGGAGAAGTGAACCAAAACCAT
Found at i:13624 original size:256 final size:252
Alignment explanation
Indices: 13052--13539 Score: 742
Period size: 255 Copynumber: 1.9 Consensus size: 252
13042 GCGATGCGGT
* ** * * ** *
13052 CATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAATCCACGCTCGATGTGAGAAAATCTT
1 CATCTTCCT-AAGAGATACGGAGAAGAAGTCCAAATCAAACCCAAACTCGATGTGAGCAAATCTT
*
13117 CGAACCACAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACGGTTAGCTTCCTA
65 CGAACCACAGCTTCCTGATAAGATACTGAGAAGCAAGTCGAAGTAATAAAACGGTTAGCTTCCTA
* * *
13182 ATGAAATATAGGGAAGTGAACCAAAACCATCTTCCTGATGAAACATAGAGAAGTGGATCAAAACA
130 ATGAAATACAGGGAAGTGAACCAAAACCATCTTCCTGATAAAACACAGAGAAGTGGATCAAAACA
* * *
13247 AGTGATATGTTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAATGACGCGG
195 AGTGATATGGTCATCTTCCTGATGAGATACAGAGAAGCCAATTGAAACAAA-GACGCAG
* *
13306 TCATCTTCCTAATGAGATACTGAGAAGAAGTCCAAATCAAACCCACACTCGATGTGAGCAAATCT
1 -CATCTTCCTAA-GAGATACGGAGAAGAAGTCCAAATCAAACCCAAACTCGATGTGAGCAAATCT
*
13371 TCGAACCACAGCTTCCTGATAAGATACTGAGAAGCAAGTTGAAGTAATAAAACGGTTAGCTTCCT
64 TCGAACCACAGCTTCCTGATAAGATACTGAGAAGCAAGTCGAAGTAATAAAACGGTTAGCTTCCT
*
13436 GATGAAATACAGGGGAAGTGAACCAAAACCATCTTCCTGATAAAACACAGAGAAGTGGATCAAAA
129 AATGAAATACA-GGGAAGTGAACCAAAACCATCTTCCTGATAAAACACAGAGAAGTGGATCAAAA
* *
13501 CAGGTGATATGGTCATCTTCCTGATGAGATACTGAGAAG
193 CAAGTGATATGGTCATCTTCCTGATGAGATACAGAGAAG
13540 AAGGCCAAGT
Statistics
Matches: 216, Mismatches: 15, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
254 1 0.00
255 128 0.59
256 87 0.40
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (252 bp):
CATCTTCCTAAGAGATACGGAGAAGAAGTCCAAATCAAACCCAAACTCGATGTGAGCAAATCTTC
GAACCACAGCTTCCTGATAAGATACTGAGAAGCAAGTCGAAGTAATAAAACGGTTAGCTTCCTAA
TGAAATACAGGGAAGTGAACCAAAACCATCTTCCTGATAAAACACAGAGAAGTGGATCAAAACAA
GTGATATGGTCATCTTCCTGATGAGATACAGAGAAGCCAATTGAAACAAAGACGCAG
Found at i:15849 original size:29 final size:29
Alignment explanation
Indices: 15799--15942 Score: 195
Period size: 29 Copynumber: 5.0 Consensus size: 29
15789 GAAGGTCCCT
*
15799 AAACTTCCAAAATTC-CATTTTTACCCCC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
* *
15827 GAACTTCCAAAAATCTCATTTTTGA-CCCT
1 AAACTTCCAAAAATCTCATTTTT-ACCCCC
*
15856 AAAGCTTCCAAAAAT-TCCATTTTTACCCTC
1 AAA-CTTCCAAAAATCT-CATTTTTACCCCC
*
15886 AAACTTCCAAAAATCCCATTTTTACCCCC
1 AAACTTCCAAAAATCTCATTTTTACCCCC
15915 AAACTTCCAAAAATCTCATTTTTACCCC
1 AAACTTCCAAAAATCTCATTTTTACCCC
15943 TAAAACTCTC
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
28 13 0.13
29 64 0.63
30 24 0.24
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCTCATTTTTACCCCC
Found at i:15891 original size:59 final size:58
Alignment explanation
Indices: 15795--15942 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 58
15785 CCCTGAAGGT
* *
15795 CCCTAAACTTCC-AAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTT-AC
*
15852 CCCTAAAGCTTCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAC
1 CCCTAAA-CTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAC
*
15911 CCCCAAACTTCCAAAAA-TCTCATTTTTACCCC
1 CCCTAAACTTCCAAAAATTC-CATTTTTACCCC
15943 TAAAACTCTC
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
57 9 0.11
58 27 0.33
59 46 0.56
ACGTcount: A:0.32, C:0.34, G:0.02, T:0.32
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAC
Found at i:16386 original size:96 final size:96
Alignment explanation
Indices: 16280--16464 Score: 266
Period size: 96 Copynumber: 1.9 Consensus size: 96
16270 AAAACTTTAA
16280 AATCGAGGCAATA-TTATTTTAT-TTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTTA-TTTATCTTCGA-TTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAA
** *
16343 TTTTTCTTCAAATCGAAATAATCGAATACCCTT
64 CCTTTCATCAAATCGAAATAATCGAATACCCTT
* * *
16376 AATCGAGGCAATGTTTATTTATCTTCGATTTTGAAAATTTGCGCTTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTATTTATCTTCGATTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
**
16441 TTTCATCAAATCGGGATAATCGAA
66 TTTCATCAAATCGAAATAATCGAA
16465 CATCCTTTCC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 71 0.90
97 8 0.10
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTATTTATCTTCGATTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCATCAAATCGAAATAATCGAATACCCTT
Found at i:17739 original size:23 final size:22
Alignment explanation
Indices: 17707--17759 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
17697 AATAGTGAAA
17707 AAAAAAACAAAAAGAAAATGAGT
1 AAAAAAACAAAAAGAAAA-GAGT
*
17730 AAAAACACAAAAAGAAAAGAGT
1 AAAAAAACAAAAAGAAAAGAGT
17752 AAGAAAAA
1 AA-AAAAA
17760 GTGTGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.75, C:0.06, G:0.13, T:0.06
Consensus pattern (22 bp):
AAAAAAACAAAAAGAAAAGAGT
Found at i:17840 original size:25 final size:23
Alignment explanation
Indices: 17795--17840 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
17785 CGTCACTAAT
* *
17795 AGAAAAAGAGAAAGCTTACTCGA
1 AGAAAAAGAAAAAGCATACTCGA
17818 AGAACAAAGAAAATAGCATACTC
1 AGAA-AAAGAAAA-AGCATACTC
17841 ATAGGCTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.13
Consensus pattern (23 bp):
AGAAAAAGAAAAAGCATACTCGA
Found at i:20409 original size:22 final size:22
Alignment explanation
Indices: 20381--20424 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20371 ATATATAGTG
*
20381 TTGTGATAGTTGCATCCACTTT
1 TTGTGATAGCTGCATCCACTTT
20403 TTGTGATAGCTGCATCCACTTT
1 TTGTGATAGCTGCATCCACTTT
20425 GGTCTATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (22 bp):
TTGTGATAGCTGCATCCACTTT
Found at i:22391 original size:28 final size:28
Alignment explanation
Indices: 22337--22390 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
22327 CAAAAATGTA
*
22337 TATAAGAAATAAAAATTCATATAAAAAT
1 TATAAAAAATAAAAATTCATATAAAAAT
* *
22365 TATAAAAAATACAAATT-GTATAAAAA
1 TATAAAAAATAAAAATTCATATAAAAA
22391 AAATGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (28 bp):
TATAAAAAATAAAAATTCATATAAAAAT
Found at i:22420 original size:39 final size:38
Alignment explanation
Indices: 22359--22432 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 38
22349 AAATTCATAT
*
22359 AAAAATTATAAAAAATACAAATTGTATAAAAAAAATGC
1 AAAAATTACAAAAAATACAAATTGTATAAAAAAAATGC
*
22397 AAAACATTACAAAAGAATA-AAATTTTATAAAAAAAA
1 AAAA-ATTACAAAA-AATACAAATTGTATAAAAAAAA
22433 CTTAAATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 4 0.12
39 24 0.75
40 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.23
Consensus pattern (38 bp):
AAAAATTACAAAAAATACAAATTGTATAAAAAAAATGC
Found at i:23214 original size:15 final size:15
Alignment explanation
Indices: 23196--23261 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
23186 TACTACAAAC
23196 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
23211 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
23230 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
23245 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
23258 ATTT
1 ATTT
23262 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:23336 original size:21 final size:21
Alignment explanation
Indices: 23310--23370 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
23300 TAAAATAAAA
23310 TTAAAATATTAAATAATTTAT
1 TTAAAATATTAAATAATTTAT
*
23331 TTAAAATAATAAATAA--TA-
1 TTAAAATATTAAATAATTTAT
*
23349 TTAATTATATT-AATAATTTAT
1 TTAA-AATATTAAATAATTTAT
23370 T
1 T
23371 ATATGACTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.27
19 6 0.18
20 2 0.06
21 16 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATATTAAATAATTTAT
Found at i:23373 original size:16 final size:18
Alignment explanation
Indices: 23342--23374 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
23332 TAAAATAATA
23342 AATAATATTAATTATATT
1 AATAATATTAATTATATT
23360 AATAAT-TT-ATTATAT
1 AATAATATTAATTATAT
23375 GACTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATAATATTAATTATATT
Done.