Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011992.1 Kokia drynarioides strain JFW-HI SEQ_126990, 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: 129845
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:1222 original size:27 final size:27
Alignment explanation
Indices: 1192--1246 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1182 CTCTTGGTCG
1192 AATCTAGCCTAGTCCATTCAGCTCCTT
1 AATCTAGCCTAGTCCATTCAGCTCCTT
*
1219 AATCTAGCCTAGTCCATTCATCTCCTT
1 AATCTAGCCTAGTCCATTCAGCTCCTT
1246 A
1 A
1247 CTTAATTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.35
Consensus pattern (27 bp):
AATCTAGCCTAGTCCATTCAGCTCCTT
Found at i:1888 original size:22 final size:24
Alignment explanation
Indices: 1861--1904 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1851 TTAGAAGTGC
*
1861 AAAG-TTTGAAA-TATTAAAAATA
1 AAAGTTTTGAAAGTATAAAAAATA
1883 AAAGTTTTGAAAGTATAAAAAA
1 AAAGTTTTGAAAGTATAAAAAA
1905 AACTAAAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 7 0.37
24 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (24 bp):
AAAGTTTTGAAAGTATAAAAAATA
Found at i:4179 original size:15 final size:15
Alignment explanation
Indices: 4159--4189 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4149 GGTAAAAAAT
4159 TAGTTTGCATGGGTA
1 TAGTTTGCATGGGTA
4174 TAGTTTGCATGGGTA
1 TAGTTTGCATGGGTA
4189 T
1 T
4190 TCTTTAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.42
Consensus pattern (15 bp):
TAGTTTGCATGGGTA
Found at i:4482 original size:23 final size:23
Alignment explanation
Indices: 4456--4505 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
4446 AAGTTCGTAA
4456 ATTTATTAAATTAATTATATATT
1 ATTTATTAAATTAATTATATATT
* * *
4479 ATTTCTTGAATTAATTATATGTT
1 ATTTATTAAATTAATTATATATT
4502 ATTT
1 ATTT
4506 CTTGATTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTTATTAAATTAATTATATATT
Found at i:4506 original size:23 final size:23
Alignment explanation
Indices: 4464--4510 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
4454 AAATTTATTA
4464 AATTAATTATATATTATTTCTTG
1 AATTAATTATATATTATTTCTTG
*
4487 AATTAATTATATGTTATTTCTTG
1 AATTAATTATATATTATTTCTTG
4510 A
1 A
4511 TTCAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (23 bp):
AATTAATTATATATTATTTCTTG
Found at i:5004 original size:52 final size:52
Alignment explanation
Indices: 4933--5251 Score: 348
Period size: 52 Copynumber: 6.2 Consensus size: 52
4923 GAAAAGCTAG
*
4933 CGAGCGTAAACGCATATTTATAAGCTGATGAGTGTAAACGTGTGCAAGCTGA
1 CGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGA
* * * * * *
4985 CGAGCGTAAACGCATATTTATAATCAGACGAGCGTAAACATGTGCAAGATGG
1 CGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGA
* * *
5037 CGAGCATAAACTCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGT
1 CGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGA
* * * * *
5089 CAAGCGTAAACGCATATTTATAATGCTGACGAGCGTAAATGTGTGCAAGTTGG
1 CGAGCGTAAACGCATATTTATAA-GCTGATGAGCGTAAACGTGTGCAAGCTGA
*
5142 CGAGCGT-AACGCATATTTATAACGCTGA-CATGCGTAAACGTGTGCAAGCTTGTA
1 CGAGCGTAAACGCATATTTATAA-GCTGATGA-GCGTAAACGTGTGCAAGC-TG-A
* * * **
5196 --AGCATAAACGCATA--T-T-AGCTGGTGAGCGTAAACGTATGTTAGCTGA
1 CGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGA
5242 CGAGCGTAAA
1 CGAGCGTAAA
5252 TGTACTGAAC
Statistics
Matches: 224, Mismatches: 35, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
46 1 0.00
47 2 0.01
48 26 0.12
49 2 0.01
50 1 0.00
51 2 0.01
52 149 0.67
53 41 0.18
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
CGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGA
Found at i:5112 original size:104 final size:105
Alignment explanation
Indices: 4932--5211 Score: 406
Period size: 104 Copynumber: 2.7 Consensus size: 105
4922 TGAAAAGCTA
* * *
4932 GCGAGCGTAAACGCATATTTATAAGCTGATGAGTGTAAACGTGTGCAAGCTGACGAGCGTAAACG
1 GCGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGTCAAGCGTAAACG
4997 CATATTTATAAT-CAGACGAGCGTAAACATGTGCAAGATG
66 CATATTTATAATGCAGACGAGCGTAAACATGTGCAAGATG
* *
5036 GCGAGCATAAACTCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGTCAAGCGTAAACG
1 GCGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGTCAAGCGTAAACG
* ** *
5101 CATATTTATAATGCTGACGAGCGTAAATGTGTGCAAGTTG
66 CATATTTATAATGCAGACGAGCGTAAACATGTGCAAGATG
* *
5141 GCGAGCGT-AACGCATATTTATAACGCTGA-CATGCGTAAACGTGTGCAAGCTTGT-AAGCATAA
1 GCGAGCGTAAACGCATATTTATAA-GCTGATGA-GCGTAAACGTGTGCAAGC-TGTCAAGCGTAA
5203 ACGCATATT
63 ACGCATATT
5212 AGCTGGTGAG
Statistics
Matches: 159, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
104 87 0.55
105 69 0.43
106 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (105 bp):
GCGAGCGTAAACGCATATTTATAAGCTGATGAGCGTAAACGTGTGCAAGCTGTCAAGCGTAAACG
CATATTTATAATGCAGACGAGCGTAAACATGTGCAAGATG
Found at i:5215 original size:24 final size:24
Alignment explanation
Indices: 5188--5240 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5178 AACGTGTGCA
*
5188 AGCTTGTAAGCATAAACGCATATT
1 AGCTGGTAAGCATAAACGCATATT
* * * *
5212 AGCTGGTGAGCGTAAACGTATGTT
1 AGCTGGTAAGCATAAACGCATATT
5236 AGCTG
1 AGCTG
5241 ACGAGCGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (24 bp):
AGCTGGTAAGCATAAACGCATATT
Found at i:5246 original size:24 final size:24
Alignment explanation
Indices: 5200--5251 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5190 CTTGTAAGCA
**
5200 TAAACGCATATTAGCTGGTGAGCG
1 TAAACGCATATTAGCTGACGAGCG
* *
5224 TAAACGTATGTTAGCTGACGAGCG
1 TAAACGCATATTAGCTGACGAGCG
5248 TAAA
1 TAAA
5252 TGTACTGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (24 bp):
TAAACGCATATTAGCTGACGAGCG
Found at i:5668 original size:12 final size:12
Alignment explanation
Indices: 5641--5681 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
5631 GGCTATAGGG
*
5641 AATGATTATATGA
1 AATGA-TATGTGA
5654 AATGATATGTGA
1 AATGATATGTGA
5666 AATGATATGTGTA
1 AATGATATGTG-A
5679 AAT
1 AAT
5682 TGAGATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.37
Consensus pattern (12 bp):
AATGATATGTGA
Found at i:7830 original size:14 final size:14
Alignment explanation
Indices: 7811--7838 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7801 AGTGATTGTT
7811 TTGTCAGCTACCTC
1 TTGTCAGCTACCTC
7825 TTGTCAGCTACCTC
1 TTGTCAGCTACCTC
7839 AAAGTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (14 bp):
TTGTCAGCTACCTC
Found at i:10302 original size:91 final size:90
Alignment explanation
Indices: 10155--10397 Score: 278
Period size: 91 Copynumber: 2.7 Consensus size: 90
10145 GCCTTCAAAT
* * * *
10155 TTTTTTTCAAAAAAA-TAATCAAGCCCCTGCTTTTATTTTACA-TTCATTTG-GATACTTGAACT
1 TTTTTTT-AAAAAAAGTAATTAAGCCTCTGCTTTTATTTTGCACTT-AATTGAG-TACTTGAACT
10217 TTCAAAATGCATAAAAAAAACCCTAAAA
63 TTCAAAATGCATAAAAAAAACCCTAAAA
*
10245 CTTTTTTTAAAAAAAGTAATTAAGCCTCTGCTTTTATTTTGCACTTAATTGAGTACTTAAACTTT
1 -TTTTTTTAAAAAAAGTAATTAAGCCTCTGCTTTTATTTTGCACTTAATTGAGTACTTGAACTTT
* ** *
10310 CAAAATGTATAAAAAAAATTCTCAAA
65 CAAAATGCATAAAAAAAACCCTAAAA
* * * * *
10336 -TTTTTTCAAAAAAGTAATTAAGCCTCTGATTGTTTTTTTTGTACTCAATTGAGTACTTGAAC
1 TTTTTTTAAAAAAAGTAATTAAGCCTCTG-CT-TTTATTTTGCACTTAATTGAGTACTTGAAC
10398 CGTTCCTATT
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
89 27 0.20
90 8 0.06
91 94 0.71
92 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (90 bp):
TTTTTTTAAAAAAAGTAATTAAGCCTCTGCTTTTATTTTGCACTTAATTGAGTACTTGAACTTTC
AAAATGCATAAAAAAAACCCTAAAA
Found at i:10525 original size:25 final size:24
Alignment explanation
Indices: 10488--10561 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 24
10478 TTTTTGATGC
* *
10488 ATTTTATAAATTTTTTCTAATTTTA
1 ATTTTTTATATTTTTT-TAATTTTA
* *
10513 ATTTTTTATATTTCTATTAAATTTAAA
1 ATTTTTTATATTT-T-TTTAATTT-TA
*
10540 ATTTTTTAT-TTTTTATAATTTT
1 ATTTTTTATATTTTTTTAATTTT
10562 TTTGCCACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
24 6 0.15
25 12 0.31
26 9 0.23
27 12 0.31
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
ATTTTTTATATTTTTTTAATTTTA
Found at i:21719 original size:25 final size:24
Alignment explanation
Indices: 21683--21729 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
21673 AGTTAATAAT
21683 AATTCTCTTTGACTTTTTCTTTAAG
1 AATTCTCTTTGACTTTTT-TTTAAG
*
21708 AATTGCTC-TTGAGTTTTTTTTA
1 AATT-CTCTTTGACTTTTTTTTA
21730 GAAGTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 13 0.65
26 3 0.15
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (24 bp):
AATTCTCTTTGACTTTTTTTTAAG
Found at i:30691 original size:19 final size:19
Alignment explanation
Indices: 30667--30710 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
30657 ACTTTGAATT
*
30667 GTTGTCCATCCAAGATGAA
1 GTTGTCCATCCAAAATGAA
* * *
30686 GTTGTCGATGCAAAATGAT
1 GTTGTCCATCCAAAATGAA
30705 GTTGTC
1 GTTGTC
30711 ATGCCATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (19 bp):
GTTGTCCATCCAAAATGAA
Found at i:48175 original size:51 final size:52
Alignment explanation
Indices: 48106--48236 Score: 183
Period size: 52 Copynumber: 2.5 Consensus size: 52
48096 CTTTCATACG
* * * * * *
48106 TTTACACTTGTCAACTTGCACATGTTTACGCTCGTTAGC-TATATATATGCA
1 TTTACACTCGCCAGCTTGCACACGTTTACACTCGTCAGCTTATATATATGCA
*
48157 TTTACACTCGCCAGCTTGCACACGTTTACACTCGTCAGCTTATATATATGCG
1 TTTACACTCGCCAGCTTGCACACGTTTACACTCGTCAGCTTATATATATGCA
*
48209 TTTACGCTCGCCAGCTTGCACACGTTTA
1 TTTACACTCGCCAGCTTGCACACGTTTA
48237 GAAATTCACC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 33 0.46
52 38 0.54
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (52 bp):
TTTACACTCGCCAGCTTGCACACGTTTACACTCGTCAGCTTATATATATGCA
Found at i:48188 original size:24 final size:24
Alignment explanation
Indices: 48157--48236 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
48147 TATATATGCA
48157 TTTACACTCGCCAGCTTGCACACG
1 TTTACACTCGCCAGCTTGCACACG
* ** *
48181 TTTACACTCGTCAGCTTATATATATGCG
1 TTTACACTCGCCAGC-T-TGCACA--CG
*
48209 TTTACGCTCGCCAGCTTGCACACG
1 TTTACACTCGCCAGCTTGCACACG
48233 TTTA
1 TTTA
48237 GAAATTCACC
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
24 20 0.47
25 1 0.02
26 6 0.14
27 1 0.02
28 15 0.35
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (24 bp):
TTTACACTCGCCAGCTTGCACACG
Found at i:48225 original size:28 final size:27
Alignment explanation
Indices: 48142--48224 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 27
48132 TACGCTCGTT
*
48142 AGCTATATATATGCATTTACACTCGCC
1 AGCTATATATATGCGTTTACACTCGCC
** * *
48169 AGCT-TGCACA--CGTTTACACTCGTC
1 AGCTATATATATGCGTTTACACTCGCC
*
48193 AGCTTATATATATGCGTTTACGCTCGCC
1 AGC-TATATATATGCGTTTACACTCGCC
48221 AGCT
1 AGCT
48225 TGCACACGTT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
24 15 0.36
25 1 0.02
26 6 0.14
27 5 0.12
28 15 0.36
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (27 bp):
AGCTATATATATGCGTTTACACTCGCC
Found at i:50575 original size:34 final size:34
Alignment explanation
Indices: 50537--50609 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
50527 AGTTTATTTG
* * * * *
50537 ACTAGTGTTAGGTACACATTCGTTGGTTTATCCA
1 ACTAGTGCTAGGCACAAAATCGTTGGTTAATCCA
*
50571 ACTAGTGCTGGGCACAAAATCGTTGGTTAATCCA
1 ACTAGTGCTAGGCACAAAATCGTTGGTTAATCCA
50605 ACTAG
1 ACTAG
50610 AGATTGACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (34 bp):
ACTAGTGCTAGGCACAAAATCGTTGGTTAATCCA
Found at i:50869 original size:183 final size:184
Alignment explanation
Indices: 50561--50900 Score: 434
Period size: 183 Copynumber: 1.9 Consensus size: 184
50551 CACATTCGTT
* * *
50561 GGTTTATCCAACTAGTGCTGGGCACAAAATCGTTGGTTAATCCAACTAGAGATTGACTCATTTTT
1 GGTTTATCCAACTAGCGCTGGGCACAAAATCGTTGGTTAATCCAACTAGAGATGGACTCACTTTT
* ** * * ** *
50626 GCGGTTTATCCGCTAGGCACTGGGTGCCAAGATTTGACGGACTATTTGTTGGTTAATCCAACTAG
66 ACAATTTATCCACTAGGCACTAGGTGCCAAGAAATGACGAACTATTTGTTGGTTAATCCAACTAG
* *
50691 AGTTGGGTTCAATT-TTACAGTTTATCGACTAGGCACTAGGTGTCAGGATTGTG
131 AGCTGGGCTCAATTATTACAGTTTATCGACTAGGCACTAGGTGTCAGGATTGTG
* * * * *
50744 GGTTTATCCCACTAGCGTTGGGCGCAAAATTGTTGGTTAATCCAACTAGA-ACTGGGCTCACTTT
1 GGTTTATCCAACTAGCGCTGGGCACAAAATCGTTGGTTAATCCAACTAGAGA-TGGACTCACTTT
* * *
50808 TACAATTTATCCACTGGGCACTAGGTGCCAGGAAATGACGAAAT-TATTGTTGGTTAATCCAACT
65 TACAATTTATCCACTAGGCACTAGGTGCCAAGAAATGACGAACTAT-TTGTTGGTTAATCCAACT
* *
50872 AGAGCTGGGCTCACTTATTATAGTTTATC
129 AGAGCTGGGCTCAATTATTACAGTTTATC
50901 CGCTAAGCAC
Statistics
Matches: 131, Mismatches: 23, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
182 2 0.02
183 118 0.90
184 11 0.08
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (184 bp):
GGTTTATCCAACTAGCGCTGGGCACAAAATCGTTGGTTAATCCAACTAGAGATGGACTCACTTTT
ACAATTTATCCACTAGGCACTAGGTGCCAAGAAATGACGAACTATTTGTTGGTTAATCCAACTAG
AGCTGGGCTCAATTATTACAGTTTATCGACTAGGCACTAGGTGTCAGGATTGTG
Found at i:53843 original size:95 final size:95
Alignment explanation
Indices: 53639--53909 Score: 253
Period size: 95 Copynumber: 2.8 Consensus size: 95
53629 GGTGGTGGAT
** * * *** * * *
53639 ACCTTACCGATGGTTAAGATTCTGCATATATTATGGATTCTTCACAATATCGTGTAAGCAGCATC
1 ACCTTACTAATGGCTAAAATTCTGCATATATTGCAGATTCATCACAA-CTCGTGTAAGCAACATC
** *
53704 GTGTAACT-AATAATGTTTC-A-ACTTACTAGAT
65 GTGTAA-TGGTTAATG--TCAAGACTTACTAGAC
* * * *
53735 ACCTTACTGATGGCTAAAATTCTGCATATATTGTAGATTCATCACAGCTCGTGTGAGCAACATCG
1 ACCTTACTAATGGCTAAAATTCTGCATATATTGCAGATTCATCACAACTCGTGTAAGCAACATCG
53800 TGTAATGGTTAATGTCAAGACTTACTAGAC
66 TGTAATGGTTAATGTCAAGACTTACTAGAC
* * * * * * *
53830 ACCTTA-TCAATGGCTAAGATTCTGCATGTGTTGCGGATTCTTCACAACTTGTGTAAGCAGCATC
1 ACCTTACT-AATGGCTAAAATTCTGCATATATTGCAGATTCATCACAACTCGTGTAAGCAACATC
53894 GTGTAATGGTTAATGT
65 GTGTAATGGTTAATGT
53910 TCGATTCATA
Statistics
Matches: 147, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
93 2 0.01
94 3 0.02
95 102 0.69
96 40 0.27
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (95 bp):
ACCTTACTAATGGCTAAAATTCTGCATATATTGCAGATTCATCACAACTCGTGTAAGCAACATCG
TGTAATGGTTAATGTCAAGACTTACTAGAC
Found at i:60775 original size:110 final size:110
Alignment explanation
Indices: 60582--60800 Score: 402
Period size: 110 Copynumber: 2.0 Consensus size: 110
60572 CAATATTTAG
* *
60582 AATTATTTATAGTCCATTTTCAACTCATAAACAAGAGAATAATCCGTTTCAACACATTCAAATCC
1 AATTACTTATAGTCCATTCTCAACTCATAAACAAGAGAATAATCCGTTTCAACACATTCAAATCC
60647 ACATATTCCTGCATCGACAATAATACTCATATCAACCGAGTTAAC
66 ACATATTCCTGCATCGACAATAATACTCATATCAACCGAGTTAAC
*
60692 AATTACTTATAGTCCATTCTCAACTCATAAACAAGAGAATAATCCGTTTCAACACATTCAAATTC
1 AATTACTTATAGTCCATTCTCAACTCATAAACAAGAGAATAATCCGTTTCAACACATTCAAATCC
*
60757 ACATCTTCCTGCATCGACAATAATACTCATATCAACCGAGTTAA
66 ACATATTCCTGCATCGACAATAATACTCATATCAACCGAGTTAA
60801 GAGTTAATCG
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (110 bp):
AATTACTTATAGTCCATTCTCAACTCATAAACAAGAGAATAATCCGTTTCAACACATTCAAATCC
ACATATTCCTGCATCGACAATAATACTCATATCAACCGAGTTAAC
Found at i:69206 original size:315 final size:315
Alignment explanation
Indices: 68634--69265 Score: 1210
Period size: 315 Copynumber: 2.0 Consensus size: 315
68624 TCTTTTCCAA
*
68634 AAGCCCTCTGCAAATTTACATTTGAAAAATAAATGCGCAGTTGTCTCTAGTTCCTTTTCACACCA
1 AAGCCCTCTACAAATTTACATTTGAAAAATAAATGCGCAGTTGTCTCTAGTTCCTTTTCACACCA
68699 AGGGCACTCTTTCTTCACTTAAGGTCTACACACCCCTCTTTATTAGAAAATTTTTTGTTGGAATT
66 AGGGCACTCTTTCTTCACTTAAGGTCTACACACCCCTCTTTATTAGAAAATTTTTTGTTGGAATT
* * *
68764 CTTCCAATAGCCATCATCCAAAGAAAGGATTTCACTCTTGGCGGTACTTTTAATTTCCAAATCTT
131 CTTCCAATAGCCATCATCCAAAGAAAGGACTTCACTCTTAGCGGTACTTTTAATTTCCAAATATT
*
68829 GTCAAAATCAAAACCTAAAACTTTCTCCCCATCTTATATTAGCAATTCCAGTATCTTCTTGACTG
196 GTCAAAATCAAAACCTAAAACTTTCTCCCCATATTATATTAGCAATTCCAGTATCTTCTTGACTG
68894 AAAAATCTCCCTTATTGTTATGCACCCAACTTAAACTATCTTCCTTACCTAATTT
261 AAAAATCTCCCTTATTGTTATGCACCCAACTTAAACTATCTTCCTTACCTAATTT
68949 AAGCCCTCTACAAATTTACATTTGAAAAATAAATGCGCAGTTGTCTCTAGTTCCTTTTCACACCA
1 AAGCCCTCTACAAATTTACATTTGAAAAATAAATGCGCAGTTGTCTCTAGTTCCTTTTCACACCA
*
69014 AGGGCACTCTTTCTTCACTTAAGGTTTACACACCCCTCTTTATTAGAAAATTTTTTGTTGGAATT
66 AGGGCACTCTTTCTTCACTTAAGGTCTACACACCCCTCTTTATTAGAAAATTTTTTGTTGGAATT
69079 CTTCCAATAGCCATCATCCAAAGAAAGGACTTCACTCTTAGCGGTACTTTTAATTTCCAAATATT
131 CTTCCAATAGCCATCATCCAAAGAAAGGACTTCACTCTTAGCGGTACTTTTAATTTCCAAATATT
69144 GTCAAAATCAAAACCTAAAACTTTCTCCCCATATTATATTAGCAATTCCAGTATCTTCTTGACTG
196 GTCAAAATCAAAACCTAAAACTTTCTCCCCATATTATATTAGCAATTCCAGTATCTTCTTGACTG
69209 AAAAATCTCCCTTATTGTTATGCACCCAACTTAAACTATCTTCCTTACCTAATTT
261 AAAAATCTCCCTTATTGTTATGCACCCAACTTAAACTATCTTCCTTACCTAATTT
69264 AA
1 AA
69266 TCATCTCCCG
Statistics
Matches: 311, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
315 311 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.35
Consensus pattern (315 bp):
AAGCCCTCTACAAATTTACATTTGAAAAATAAATGCGCAGTTGTCTCTAGTTCCTTTTCACACCA
AGGGCACTCTTTCTTCACTTAAGGTCTACACACCCCTCTTTATTAGAAAATTTTTTGTTGGAATT
CTTCCAATAGCCATCATCCAAAGAAAGGACTTCACTCTTAGCGGTACTTTTAATTTCCAAATATT
GTCAAAATCAAAACCTAAAACTTTCTCCCCATATTATATTAGCAATTCCAGTATCTTCTTGACTG
AAAAATCTCCCTTATTGTTATGCACCCAACTTAAACTATCTTCCTTACCTAATTT
Found at i:70693 original size:21 final size:21
Alignment explanation
Indices: 70667--70722 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
70657 AATAGTACAG
* *
70667 ACTTCTACCGATATACGTGAC
1 ACTTCTACCGATACAAGTGAC
*
70688 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
*
70709 TCTTCTACCGATAC
1 ACTTCTACCGATAC
70723 TAAAAACTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:70731 original size:21 final size:21
Alignment explanation
Indices: 70690--70731 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
70680 TACGTGACAG
**
70690 TTCTACCGATACAAGTGACTC
1 TTCTACCGATACAAGAAACTC
70711 TTCTACCGATACTAA-AAACTC
1 TTCTACCGATAC-AAGAAACTC
70732 CAGAGAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAAGAAACTC
Found at i:74445 original size:17 final size:18
Alignment explanation
Indices: 74408--74446 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
74398 TAGAGGGAAT
74408 AGCATACTGACTCGTTTG
1 AGCATACTGACTCGTTTG
* *
74426 AGCATATTGGCTCG-TTG
1 AGCATACTGACTCGTTTG
74443 AGCA
1 AGCA
74447 AAAATTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (18 bp):
AGCATACTGACTCGTTTG
Found at i:74527 original size:19 final size:19
Alignment explanation
Indices: 74425--74530 Score: 99
Period size: 19 Copynumber: 5.6 Consensus size: 19
74415 TGACTCGTTT
*
74425 GAGC-ATATTGGCTCGT-T
1 GAGCAATATTGGCTCGTAA
* **
74442 GAGCAAAAATTAACTCGTAA
1 GAGC-AATATTGGCTCGTAA
* * * *
74462 GAGCAATACTAGTTCATAA
1 GAGCAATATTGGCTCGTAA
*
74481 GAGCAATACTGGCTCGTAA
1 GAGCAATATTGGCTCGTAA
*
74500 GAGTAATATTGGCTCGTAA
1 GAGCAATATTGGCTCGTAA
74519 GAGCAATATTGG
1 GAGCAATATTGG
74531 ATCACAAGGA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
17 4 0.06
19 63 0.89
20 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (19 bp):
GAGCAATATTGGCTCGTAA
Found at i:80216 original size:21 final size:21
Alignment explanation
Indices: 80190--80249 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
80180 AATAGTGCAG
80190 ACTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
*
80211 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
*
80232 TCTTCTACCGATACAAGT
1 ACTTCTACCGATACAAGT
80250 CTTACTTCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:80257 original size:21 final size:20
Alignment explanation
Indices: 80190--80261 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
80180 AATAGTGCAG
80190 ACTTCTACCGATACAAGTGAC-
1 ACTTCTACCGATACAAGT--CT
*
80211 AGTTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAGT--CT
80233 -CTTCTACCGATACAAGTCTT
1 ACTTCTACCGATACAAGTC-T
80253 ACTTCTACC
1 ACTTCTACC
80262 AATGTTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 44 0.96
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (20 bp):
ACTTCTACCGATACAAGTCT
Found at i:82116 original size:20 final size:20
Alignment explanation
Indices: 82080--82129 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
82070 TCATTAAGCT
*
82080 TTAATTAATCACTTTTA-ATC
1 TTAATTAAACACTTTTACA-C
82100 TTAATTAAAC-CTATTTACAC
1 TTAATTAAACACT-TTTACAC
82120 TTAATATAAA
1 TTAAT-TAAA
82130 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTACAC
Found at i:95403 original size:20 final size:20
Alignment explanation
Indices: 95364--95409 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
95354 TTTTGAAGTG
* *
95364 TATTTTGACTTATTTCAAAT
1 TATTTTGACATATTTAAAAT
*
95384 TATTTTGACATGTTTAAAAT
1 TATTTTGACATATTTAAAAT
*
95404 CATTTT
1 TATTTT
95410 AACTTGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (20 bp):
TATTTTGACATATTTAAAAT
Found at i:97914 original size:15 final size:15
Alignment explanation
Indices: 97894--97924 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
97884 CATATTAGTT
97894 TGAAATGATCTCTAA
1 TGAAATGATCTCTAA
*
97909 TGAAATGATGTCTAA
1 TGAAATGATCTCTAA
97924 T
1 T
97925 CTCAATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (15 bp):
TGAAATGATCTCTAA
Found at i:112937 original size:20 final size:20
Alignment explanation
Indices: 112859--112943 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
112849 GCCTAGTGCT
* *
112859 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACATGTTT-AAAATC
*
112880 ATTTTGA-A-GTGTTAAAATG
1 ATTTTGACATGT-TTAAAATC
* *
112899 ATTTTGACTTAGTTT-AAATG
1 ATTTTGACAT-GTTTAAAATC
112919 ATTTTGACATGTTTAAAATC
1 ATTTTGACATGTTTAAAATC
112939 ATTTT
1 ATTTT
112944 AACTTGATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
19 17 0.32
20 25 0.47
21 9 0.17
22 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (20 bp):
ATTTTGACATGTTTAAAATC
Found at i:127203 original size:6 final size:6
Alignment explanation
Indices: 127192--127221 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
127182 TATATTATCA
127192 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT
127222 ATACATGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
TGAGAT
Done.