Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009590.1 Kokia drynarioides strain JFW-HI SEQ_124305, 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: 21457
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4734 original size:40 final size:40
Alignment explanation
Indices: 4690--4768 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
4680 GCAGTGGAGC
*
4690 TGGATTCAAACTACATCATTTCATTTTTACCCTTAATCAT
1 TGGATTCAAACTACAACATTTCATTTTTACCCTTAATCAT
4730 TGGATTCAAACTACAACATTTCATTTTTACCCTTAATCA
1 TGGATTCAAACTACAACATTTCATTTTTACCCTTAATCA
4769 AGAAAGGCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (40 bp):
TGGATTCAAACTACAACATTTCATTTTTACCCTTAATCAT
Found at i:4911 original size:78 final size:78
Alignment explanation
Indices: 4786--5410 Score: 518
Period size: 78 Copynumber: 7.9 Consensus size: 78
4776 CAGATTAAAA
* * *
4786 ATTCTGATCTCTT-ACCTCGAGCCTAGGGTAGATCA-TATCAGCCAATCTCTTACCCCGAGCCTA
1 ATTC-GATCT-TTCACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTA
*
4849 GGGCAGATTGCAGCC
64 GGGCAGATTGCAACC
* * ** * * * * * *
4864 ATCCAATCTTTCACCCTAAACCTAGGGCAAAACACCATCAGCTAATCTCTTACCCCGAGCTTGGG
1 ATTCGATCTTTCACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
4929 GCAGATTGCAACC
66 GCAGATTGCAACC
* * *
4942 ATTCGATCTTTTACCCCGAGCCT-GGAGCAGATCACCATCAGCCAATCTCTTACTCCGAG-CTTG
1 ATTCGATCTTTCACCCCGAGCCTAGG-GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAG
*
5005 AGGCAGATTGTAACC
65 -GGCAGATTGCAACC
* * **
5020 ATTCGATC-TT-ACCCCGAGCCTAGGGCAAATCACCATCAGTCAATCTCTTACCTTGAGCCTAGG
1 ATTCGATCTTTCACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
*
5083 GCAGATTGCAATC
66 GCAGATTGCAACC
* * * * * *
5096 ATTCGATCTTTTACCCCGAGCCT-GAGGTAGATCACCATCAGCTAATCTCTTATCTCGAGCCTGG
1 ATTCGATCTTTCACCCCGAGCCTAG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAG
* * **
5160 GGTAGATTGTAGTC
65 GGCAGATTGCAACC
* *
5174 ATTCAATC-TT-ACCCCGAGCCTAGGGCAAATCATAGGGCAAATCACCATCAGTCAATCTCTTAC
1 ATTCGATCTTTCACCCCGAGCCTAGGG-----C--A--G---ATCACCATCAGCCAATCTCTTAC
* *
5237 CCCGAG-CTTGAGGCAGATTGCAGCC
54 CCCGAGCCTAG-GGCAGATTGCAACC
* * * * * * * *
5262 ATTCGATCTTTTACCCCGAGCAT-GAAGTAGATCACCATCAACCAATCTCCTACCCCGAGCTTGG
1 ATTCGATCTTTCACCCCGAGCCTAG-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAG
*
5326 GGCAGATTGCAGCC
65 GGCAGATTGCAACC
* * * * * * *
5340 -TCCGATCTTTCACCCCGAACCTAAGGCAGATCACCATTAGCCAATCTCTTACCTCGAGACAAGG
1 ATTCGATCTTTCACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
5404 GCAGATT
66 GCAGATT
5411 ATAACCATCC
Statistics
Matches: 440, Mismatches: 79, Indels: 57
0.76 0.14 0.10
Matches are distributed among these distances:
76 74 0.17
77 91 0.21
78 209 0.47
79 2 0.00
81 1 0.00
83 2 0.00
85 1 0.00
87 3 0.01
88 43 0.10
89 3 0.01
90 11 0.03
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (78 bp):
ATTCGATCTTTCACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
GCAGATTGCAACC
Found at i:5011 original size:39 final size:38
Alignment explanation
Indices: 4792--5147 Score: 136
Period size: 39 Copynumber: 9.2 Consensus size: 38
4782 AAAAATTCTG
* * * *
4792 ATCTCTTACCTCGAGCCTAGGGTAGATCA-TATCAGCCA
1 ATCTCTTACCCCGAG-CTTGGGCAGATCACCATCAGCCA
*
4830 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCAT---CCA
1 ATCTCTTACCCCGAG-CTTGGGCAGA-T-CA-CCATCAGCCA
** * * * * *
4869 ATCT-TTCACCCTAAACCTAGGGCAAAACACCATCAGCTA
1 ATCTCTT-ACCC-CGAGCTTGGGCAGATCACCATCAGCCA
** * * ** *
4908 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATTCG
1 ATCTCTTACCCCGAGCTT-GGGCAGATCACCATCAGCCA
* *
4947 ATCTTTTACCCCGAGCCTGGAGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGG-GCAGATCACCATCAGCCA
* ** *
4986 ATCTCTTACTCCGAGCTTGAGGCAGAT---TGT-AACCA
1 ATCTCTTACCCCGAGCTTG-GGCAGATCACCATCAGCCA
* * * *
5021 TTCGATCTTACCCCGAGCCTAGGGCAAATCACCATCAGTCA
1 ATC--TCTTACCCCGAG-CTTGGGCAGATCACCATCAGCCA
** * ** * ** *
5062 ATCTCTTACCTTGAGCCTAGGGCAGATTGCAATCATTCG
1 ATCTCTTACCCCGAG-CTTGGGCAGATCACCATCAGCCA
* * * *
5101 ATCTTTTACCCCGAGCCTGAGGTAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCTTG-GGCAGATCACCATCAGCCA
5140 ATCTCTTA
1 ATCTCTTA
5148 TCTCGAGCCT
Statistics
Matches: 228, Mismatches: 69, Indels: 41
0.67 0.20 0.12
Matches are distributed among these distances:
35 6 0.03
36 5 0.02
37 19 0.08
38 36 0.16
39 148 0.65
40 7 0.03
41 5 0.02
42 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCTTGGGCAGATCACCATCAGCCA
Found at i:5069 original size:154 final size:156
Alignment explanation
Indices: 4786--5397 Score: 637
Period size: 154 Copynumber: 3.9 Consensus size: 156
4776 CAGATTAAAA
* * *
4786 ATTCTGATCTCTTACCTCGAGCCTAGG-GTAGATCA-TATCAGCCAATCTCTTACCCCGAGCCT-
1 ATTC-GATCTTTTACCCCGAGCCT-GGAGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTG
** *
4848 AGGGCAGATTGCAGCCATCCAATCTTTCACCCTAAACCTAGGGCAAAACACCATCAG-CTAATCT
64 A-GGCAGATTGCAGCCATCCAATCTTTCACCCCGAACCTAGGGCAAATCACCATCAGTC-AATCT
4912 CTTACCCCGAGCTTGGGGCAGATTGCAACC
127 CTTACCCCGAGCTTGGGGCAGATTGCAACC
* * *
4942 ATTCGATCTTTTACCCCGAGCCTGGAGCAGATCACCATCAGCCAATCTCTTACTCCGAGCTTGAG
1 ATTCGATCTTTTACCCCGAGCCTGGAGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAG
* * * * *
5007 GCAGATTGTAACCATTCGATC-TT-ACCCCGAGCCTAGGGCAAATCACCATCAGTCAATCTCTTA
66 GCAGATTGCAGCCATCCAATCTTTCACCCCGAACCTAGGGCAAATCACCATCAGTCAATCTCTTA
** * * *
5070 CCTTGAGCCTAGGGCAGATTGCAATC
131 CCCCGAGCTTGGGGCAGATTGCAACC
* * * *
5096 ATTCGATCTTTTACCCCGAGCCT-GAGGTAGATCACCATCAGCTAATCTCTTATCTCGAGCCTGG
1 ATTCGATCTTTTACCCCGAGCCTGGA-GTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGA
* * * * * * *
5160 GGTAGATTGTAGTCATTCAATCTTACCCCGAGCCTAGGGCAAATCATAGGGCAAATCACCATCAG
65 GGCAGATTGCAGCCATCCAATCTTTCACC---CC----G--AA-CCTAGGGCAAATCACCATCAG
* *
5225 TCAATCTCTTACCCCGAGCTTGAGGCAGATTGCAGCC
120 TCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACC
* * * * * *
5262 ATTCGATCTTTTACCCCGAGCATGAAGTAGATCACCATCAACCAATCTCCTACCCCGAGCTTGGG
1 ATTCGATCTTTTACCCCGAGCCTGGAGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAG
* * * * *
5327 GCAGATTGCAGCC-TCCGATCTTTCACCCCGAACCTAAGGCAGATCACCATTAGCCAATCTCTTA
66 GCAGATTGCAGCCATCCAATCTTTCACCCCGAACCTAGGGCAAATCACCATCAGTCAATCTCTTA
*
5391 CCTCGAG
131 CCCCGAG
5398 ACAAGGGCAG
Statistics
Matches: 376, Mismatches: 62, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
153 2 0.01
154 129 0.34
155 61 0.16
156 50 0.13
157 1 0.00
158 1 0.00
159 2 0.01
162 2 0.01
163 1 0.00
165 11 0.03
166 115 0.31
167 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (156 bp):
ATTCGATCTTTTACCCCGAGCCTGGAGTAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAG
GCAGATTGCAGCCATCCAATCTTTCACCCCGAACCTAGGGCAAATCACCATCAGTCAATCTCTTA
CCCCGAGCTTGGGGCAGATTGCAACC
Found at i:7630 original size:30 final size:30
Alignment explanation
Indices: 7594--7665 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
7584 CTTAAAAGGT
* *
7594 CCTTAAACTTCTTAAAAATTACATTTTGAC
1 CCTTAAACTTCTCAAAAATTACATGTTGAC
*
7624 CCTTAAATTTCTCAAAAATTACATGTTGAC
1 CCTTAAACTTCTCAAAAATTACATGTTGAC
*
7654 CC-CAAACTTCTC
1 CCTTAAACTTCTC
7666 TAACATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
CCTTAAACTTCTCAAAAATTACATGTTGAC
Found at i:7773 original size:30 final size:29
Alignment explanation
Indices: 7714--7789 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
7704 TTTTTTACCT
* *
7714 CAAATTTTCCAAAAGTTTTATTTTAATCC
1 CAAATTTTCCAAAAATTTAATTTTAATCC
*
7743 CAAATTTTCCAAAAATTTCAATTTTGATCC
1 CAAATTTTCCAAAAATTT-AATTTTAATCC
7773 CTAAA-TTTCTCAAAAAT
1 C-AAATTTTC-CAAAAAT
7790 GACGTTTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 17 0.41
30 14 0.34
31 10 0.24
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (29 bp):
CAAATTTTCCAAAAATTTAATTTTAATCC
Found at i:9794 original size:23 final size:23
Alignment explanation
Indices: 9768--9819 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
9758 TTTTGTTCTA
*
9768 GCTTTTATT-TGCTTTTGTGGTAC
1 GCTTTTATTCTG-TCTTGTGGTAC
*
9791 GCTTTTCTTCTGTCTTGTGGTAC
1 GCTTTTATTCTGTCTTGTGGTAC
9814 GCTTTT
1 GCTTTT
9820 GCCTTATGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.06, C:0.17, G:0.21, T:0.56
Consensus pattern (23 bp):
GCTTTTATTCTGTCTTGTGGTAC
Found at i:10181 original size:19 final size:20
Alignment explanation
Indices: 10144--10185 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
10134 ACGTTTCGTT
*
10144 TTTTAGTTTTTTTAATTTTC
1 TTTTAGTTTTGTTAATTTTC
10164 TTTT-GTTTTGTT-ATTTT-
1 TTTTAGTTTTGTTAATTTTC
10181 TTTTA
1 TTTTA
10186 CTACATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 7 0.35
20 4 0.20
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTTAGTTTTGTTAATTTTC
Found at i:16528 original size:24 final size:24
Alignment explanation
Indices: 16494--16539 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16484 TATATGAAAT
* *
16494 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
16518 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
16540 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:16772 original size:30 final size:29
Alignment explanation
Indices: 16739--16796 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
16729 GAAGGGTGAA
16739 AAAAAAAATTAAGCACCAAAAGTGCTTTT
1 AAAAAAAATTAAGCACCAAAAGTGCTTTT
*
16768 AAAAATAATTAAGCACCAAAAGTGCTTTT
1 AAAAAAAATTAAGCACCAAAAGTGCTTTT
16797 GGTAGAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (29 bp):
AAAAAAAATTAAGCACCAAAAGTGCTTTT
Found at i:20542 original size:28 final size:27
Alignment explanation
Indices: 20511--20881 Score: 221
Period size: 29 Copynumber: 12.8 Consensus size: 27
20501 TTATGCTCGA
* *
20511 GGGTAAAATGGTAATTTTTTAGGTTTAG
1 GGGTAAAATGGTAATTTTTGAAGTTT-G
* * *
20539 GGGTAAAACGGTATTTTTTAGACA-TTCG
1 GGGTAAAATGGTAATTTTT-GA-AGTTTG
* * *
20567 GGGCAAAATGATAATTTTTGGAAATTTCG
1 GGGTAAAATGGTAATTTTT-GAAGTTT-G
* *
20596 TGGTAAAATGGTAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTG-AAGTTT-G
*
20625 GGGTCAAAAATGG-AATTTTTTAAAAGTTTG
1 GGGT--AAAATGGTAA-TTTTT-GAAGTTTG
*
20655 GTGGTAAAATGGTAATTTTTGGAAGTTCAG
1 G-GGTAAAATGGTAATTTTT-GAAGTT-TG
* *
20685 GAGTAGAAAT-GTGATTTTTGGAAGTTTGG
1 GGGTA-AAATGGTAATTTTT-GAAGTTT-G
*
20714 GGGTAAAATGGTAATTTTAGAAGTTTG
1 GGGTAAAATGGTAATTTTTGAAGTTTG
*
20741 AGGGTAAAATTGTAATTTTTGAAAAGTTTG
1 -GGGTAAAATGGTAATTTTTG--AAGTTTG
* *
20771 GGGTCAAAATGGTAATATTTGGAAGTTCG
1 GGGT-AAAATGGTAAT-TTTTGAAGTTTG
* **
20800 AGGGTAAAAAT-ATAATTTTTGTGAAGTTCAA
1 -GGGT-AAAATGGTAA-TTTT-TGAAGTT-TG
* *
20831 GGGCAAAATGGTAATTTTTAAAAAGTTTAG
1 GGGTAAAATGGTAATTTTT--GAAGTTT-G
20861 GGGTTAAAAT-GTAATTTTTGA
1 GGG-TAAAATGGTAATTTTTGA
20882 GAAGTTCAAG
Statistics
Matches: 268, Mismatches: 46, Indels: 58
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.01
28 69 0.26
29 100 0.37
30 68 0.25
31 29 0.11
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTTGAAGTTTG
Found at i:20595 original size:29 final size:29
Alignment explanation
Indices: 20511--20880 Score: 210
Period size: 28 Copynumber: 12.7 Consensus size: 29
20501 TTATGCTCGA
* ** *
20511 GGGTAAAATGGTAATTTTT-TAGGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAATTTCG
* * * *
20539 GGGTAAAACGGTATTTTTTAGACA-TTCG
1 GGGTAAAATGGTAATTTTTGGAAATTTCG
* *
20567 GGGCAAAATGATAATTTTTGGAAATTTCG
1 GGGTAAAATGGTAATTTTTGGAAATTTCG
* *
20596 TGGTAAAATGGTAA-TTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAA-TTTCG
**
20625 GGGTCAAAAATGG-AATTTTTTAAAAGTTT-G
1 GGGT--AAAATGGTAATTTTTGGAAA-TTTCG
*
20655 GTGGTAAAATGGTAATTTTTGG-AAGTTCAG
1 G-GGTAAAATGGTAATTTTTGGAAATTTC-G
* * * *
20685 GAGTAGAAAT-GTGATTTTTGGAAGTTTGG
1 GGGTA-AAATGGTAATTTTTGGAAATTTCG
* *
20714 GGGTAAAATGGTAA-TTTTAGAAGTTT-G
1 GGGTAAAATGGTAATTTTTGGAAATTTCG
* *
20741 AGGGTAAAATTGTAATTTTTGAAAAGTTT-G
1 -GGGTAAAATGGTAATTTTTGGAAA-TTTCG
* *
20771 GGGTCAAAATGGTAATATTTGG-AAGTTCG
1 GGGT-AAAATGGTAATTTTTGGAAATTTCG
* * *
20800 AGGGTAAAAAT-ATAATTTTTGTG-AAGTTCAA
1 -GGGT-AAAATGGTAATTTTTG-GAAATTTC-G
* ** *
20831 GGGCAAAATGGTAATTTTTAAAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAA-TTTCG
20861 GGGTTAAAAT-GTAATTTTTG
1 GGG-TAAAATGGTAATTTTTG
20881 AGAAGTTCAA
Statistics
Matches: 266, Mismatches: 51, Indels: 48
0.73 0.14 0.13
Matches are distributed among these distances:
27 1 0.00
28 79 0.30
29 79 0.30
30 79 0.30
31 28 0.11
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAATTTCG
Found at i:20642 original size:59 final size:57
Alignment explanation
Indices: 20571--20880 Score: 261
Period size: 59 Copynumber: 5.3 Consensus size: 57
20561 CATTCGGGGC
*
20571 AAAATGATAATTTTTGGAAATTTCGTGGTAAAATGGTAATTTTGGAAAGTTTAGGGGTCA
1 AAAATG-TAATTTTTGGAAATTTCGGGGTAAAATGGTAATTTTGG-AAGTTTAGGGGT-A
* ** * *
20631 AAAATGGAATTTTTTAAAAGTTT-GGTGGTAAAATGGTAATTTTTGGAAGTTCAGGAGTA
1 AAAATGTAATTTTTGGAAA-TTTCGG-GGTAAAATGGTAA-TTTTGGAAGTTTAGGGGTA
* * * * *
20690 GAAATGTGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTAGAAGTTT-GAGGGTA
1 AAAATGTAATTTTTGGAAATTTCGGGGTAAAATGGTAATTTTGGAAGTTTAG-GGGTA
* * *
20747 AAATTGTAATTTTTGAAAAGTTT-GGGGTCAAAATGGTAATATTTGGAAG-TTCGAGGGTA
1 AAAATGTAATTTTTGGAAA-TTTCGGGGT-AAAATGGTAAT-TTTGGAAGTTTAG-GGGTA
* * * * ** *
20806 AAAATATAATTTTTGTG-AAGTTCAAGGGCAAAATGGTAATTTTTAAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTG-GAAATTTC-GGGGTAAAATGGTAA-TTTT-GGAAGTTTAGGGGTA
20866 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
20881 AGAAGTTCAA
Statistics
Matches: 203, Mismatches: 32, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
56 1 0.00
57 33 0.16
58 34 0.17
59 69 0.34
60 57 0.28
61 9 0.04
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAATTTCGGGGTAAAATGGTAATTTTGGAAGTTTAGGGGTA
Found at i:20810 original size:30 final size:29
Alignment explanation
Indices: 20507--20922 Score: 220
Period size: 30 Copynumber: 14.2 Consensus size: 29
20497 TTTTTTATGC
* *
20507 TCGAGGGTAAAATGGTAATTTTT-TAGGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAGT
* * * *
20535 T-TAGGGGTAAAACGGTATTTTTTAGACA-T
1 TCGA-GGGTAAAATGGTAATTTTTGGA-AGT
* * *
20564 TCG-GGGCAAAATGATAATTTTTGGAAATT
1 TCGAGGGTAAAATGGTAATTTTTGG-AAGT
*
20593 TCG-TGGTAAAATGGTAA-TTTTGGAAAGT
1 TCGAGGGTAAAATGGTAATTTTTGG-AAGT
* **
20621 T-TAGGGGTCAAAAATGG-AATTTTTTAAAAGT
1 TCGA-GGGT--AAAATGGTAA-TTTTTGGAAGT
*
20652 TTG-GTGGTAAAATGGTAATTTTTGGAAGT
1 TCGAG-GGTAAAATGGTAATTTTTGGAAGT
*
20681 TC-AGGAGTAGAAAT-GTGATTTTTGGAAGT
1 TCGAGG-GTA-AAATGGTAATTTTTGGAAGT
* * *
20710 TTGGGGGTAAAATGGTAA-TTTTAGAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAGT
* * *
20738 TTGAGGGTAAAATTGTAATTTTTGAAAAGT
1 TCGAGGGTAAAATGGTAATTTTTG-GAAGT
* *
20768 TTG-GGGTCAAAATGGTAATATTTGGAAGT
1 TCGAGGGT-AAAATGGTAATTTTTGGAAGT
*
20797 TCGAGGGTAAAAAT-ATAATTTTTGTGAAGT
1 TCGAGGGT-AAAATGGTAATTTTTG-GAAGT
* * **
20827 TCAAGGGCAAAATGGTAATTTTTAAAAAGT
1 TCGAGGGTAAAATGGTAATTTTT-GGAAGT
*
20857 T-TAGGGGTTAAAAT-GTAATTTTTGAGAAGT
1 TCGA-GGG-TAAAATGGTAATTTTTG-GAAGT
* ** *
20887 TCAAGCCTGAAAAT-ATAATTTTTGGACAGT
1 TCGAGGGT-AAAATGGTAATTTTTGGA-AGT
20917 TC-AGGG
1 TCGAGGG
20923 ACCATTTGGG
Statistics
Matches: 301, Mismatches: 54, Indels: 65
0.72 0.13 0.15
Matches are distributed among these distances:
27 1 0.00
28 76 0.25
29 97 0.32
30 102 0.34
31 21 0.07
32 4 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAGT
Done.