Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011648.1 Kokia drynarioides strain JFW-HI SEQ_126640, 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: 70043
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:9427 original size:28 final size:27
Alignment explanation
Indices: 9391--9482 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 27
9381 AAAATGAGAC
* *
9391 ATTTCGGATACCCGGGGGCAAAATGGTA
1 ATTTTGGAT-CCCGGGGGTAAAATGGTA
* *
9419 ATTTTGGATTCTCAGAGGGTAAAATGGTA
1 ATTTTGGA-TC-CCGGGGGTAAAATGGTA
* * *
9448 ATTTTGGACTCTCAGGGGTGAAATGGTA
1 ATTTTGGA-TCCCGGGGGTAAAATGGTA
9476 ATTTTGG
1 ATTTTGG
9483 GAAAATTTGG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 27 0.52
29 25 0.48
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (27 bp):
ATTTTGGATCCCGGGGGTAAAATGGTA
Found at i:9442 original size:29 final size:28
Alignment explanation
Indices: 9405--9482 Score: 120
Period size: 29 Copynumber: 2.8 Consensus size: 28
9395 CGGATACCCG
* *
9405 GGGGCAAAATGGTAATTTTGGATTCTCA
1 GGGGTAAAATGGTAATTTTGGACTCTCA
9433 GAGGGTAAAATGGTAATTTTGGACTCTCA
1 G-GGGTAAAATGGTAATTTTGGACTCTCA
*
9462 GGGGTGAAATGGTAATTTTGG
1 GGGGTAAAATGGTAATTTTGG
9483 GAAAATTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 20 0.43
29 26 0.57
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGACTCTCA
Found at i:9642 original size:30 final size:30
Alignment explanation
Indices: 9584--9863 Score: 234
Period size: 30 Copynumber: 9.5 Consensus size: 30
9574 ATTCGAGGGT
* * * *
9584 AAAATGGTAATGTTTGGAAGTTTCAGGGTCA
1 AAAATGG-AATTTTTAGAAGTTTGAGGGTTA
* *
9615 AAAATGGAATTTTAAAAAGTTTGAGGG-TA
1 AAAATGGAATTTTTAGAAGTTTGAGGGTTA
* * *
9644 AAAATGTAATTTTTGGAAGTTTCAGGGTTA
1 AAAATGGAATTTTTAGAAGTTTGAGGGTTA
* * *
9674 AAAATGGATTTTTTGGAGGTTTTG-GGGTTA
1 AAAATGGAATTTTTAGAAG-TTTGAGGGTTA
*** *
9704 AAAATATTATTTTTAGAAGTTCGAGGG-T-
1 AAAATGGAATTTTTAGAAGTTTGAGGGTTA
*
9732 AAAATGGAATTTTTAGAAGTTTTAGGGTTA
1 AAAATGGAATTTTTAGAAGTTTGAGGGTTA
* * *
9762 AAAATGGGATTTTTGGAAGTTCGAGGG-TA
1 AAAATGGAATTTTTAGAAGTTTGAGGGTTA
* *
9791 AAAAT-AAATTTTTTGGAAGTTTTG-GGGTTA
1 AAAATGGAA-TTTTTAGAAG-TTTGAGGGTTA
* * *
9821 AAAATGGGATTTTTAGAAGTTCGAGGG-CA
1 AAAATGGAATTTTTAGAAGTTTGAGGGTTA
*
9850 AAAAAGGAATTTTT
1 AAAATGGAATTTTT
9864 GTAAAGTTTA
Statistics
Matches: 198, Mismatches: 41, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
28 23 0.12
29 64 0.32
30 100 0.51
31 11 0.06
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTAGAAGTTTGAGGGTTA
Found at i:9736 original size:117 final size:118
Alignment explanation
Indices: 9600--9862 Score: 345
Period size: 117 Copynumber: 2.2 Consensus size: 118
9590 GTAATGTTTG
*
9600 GAAGTTTC-AGGGTCAAAAATGGAATTTTAAAAAGTTTGAGGG-TAAAAATGTAATTTTTGGAAG
1 GAAG-TTCGAGGG-CAAAAATGGAATTTTAAAAAGTTTGAGGGTTAAAAATGGAATTTTTGGAAG
** * **
9663 TTTC-AGGGTTAAAAATGGATTTTTTGGAGGTTTTGGGGTTAAAAATATTATTTTTA
64 -TTCGAGGG-TAAAAATAAATTTTTTGGAAGTTTTGGGGTTAAAAATAGGATTTTTA
* * * * *
9719 GAAGTTCGAGGG-TAAAATGGAATTTTTAGAAGTTTTAGGGTTAAAAATGGGATTTTTGGAAGTT
1 GAAGTTCGAGGGCAAAAATGGAATTTTAAAAAGTTTGAGGGTTAAAAATGGAATTTTTGGAAGTT
*
9783 CGAGGGTAAAAATAAATTTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTA
66 CGAGGGTAAAAATAAATTTTTTGGAAGTTTTGGGGTTAAAAATAGGATTTTTA
*
9836 GAAGTTCGAGGGCAAAAAAGGAATTTT
1 GAAGTTCGAGGGCAAAAATGGAATTTT
9863 TGTAAAGTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
117 80 0.63
118 38 0.30
119 8 0.06
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (118 bp):
GAAGTTCGAGGGCAAAAATGGAATTTTAAAAAGTTTGAGGGTTAAAAATGGAATTTTTGGAAGTT
CGAGGGTAAAAATAAATTTTTTGGAAGTTTTGGGGTTAAAAATAGGATTTTTA
Found at i:9864 original size:59 final size:59
Alignment explanation
Indices: 9600--9864 Score: 263
Period size: 59 Copynumber: 4.5 Consensus size: 59
9590 GTAATGTTTG
*** ** *
9600 GAAGTTTC-AGGGTCAAAAATGGAATTTTAAAAAG-TTTGAGGG-TAAAAATGTAATTTTTG
1 GAAG-TTCGAGGG-CAAAAATGGAATTTTTGGAAGTTTTG-GGGTTAAAAATGGGATTTTTA
* * * ***
9659 GAAGTTTC-AGGGTTAAAAATGGATTTTTTGGAGGTTTTGGGGTTAAAAATATTATTTTTA
1 GAAG-TTCGAGGG-CAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTA
* * * *
9719 GAAGTTCGAGGG-TAAAATGGAATTTTTAGAAGTTTTAGGGTTAAAAATGGGATTTTTG
1 GAAGTTCGAGGGCAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTA
* *
9777 GAAGTTCGAGGGTAAAAAT-AAATTTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTA
1 GAAGTTCGAGGGCAAAAATGGAA-TTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTA
*
9836 GAAGTTCGAGGGCAAAAAAGGAATTTTTG
1 GAAGTTCGAGGGCAAAAATGGAATTTTTG
9865 TAAAGTTTAG
Statistics
Matches: 174, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
58 51 0.29
59 95 0.55
60 28 0.16
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (59 bp):
GAAGTTCGAGGGCAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTA
Found at i:10908 original size:31 final size:32
Alignment explanation
Indices: 10832--10912 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 32
10822 GACTTTTCGT
* *
10832 TTTTTATTATTTAATAATTATTAATATCAAAACA
1 TTTTTATTA-TTAATGATTATTAAGA-CAAAACA
10866 TTTATTATTATTAATGATTATTAAGA-AAAAC-
1 TTT-TTATTATTAATGATTATTAAGACAAAACA
10897 TTATTTATTATTAATG
1 TT-TTTATTATTAATG
10913 GGGTCATTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 14 0.33
32 6 0.14
34 17 0.40
35 6 0.14
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (32 bp):
TTTTTATTATTAATGATTATTAAGACAAAACA
Found at i:11620 original size:6 final size:6
Alignment explanation
Indices: 11611--11668 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
11601 ATTTTGAAAA
* * *
11611 TAAATT TAAACT TAAA-T TAAATT TAAATT TAAA-A TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
11656 TAAATT TAAATT T
1 TAAATT TAAATT T
11669 TTAAACAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 13 0.30
6 31 0.70
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:11636 original size:11 final size:11
Alignment explanation
Indices: 11611--11667 Score: 71
Period size: 11 Copynumber: 5.1 Consensus size: 11
11601 ATTTTGAAAA
11611 TAAATTTAAACT
1 TAAATTTAAA-T
11623 TAAA-TTAAATT
1 TAAATTTAAA-T
*
11634 TAAATTTAAAA
1 TAAATTTAAAT
*
11645 TAAATTTAAAA
1 TAAATTTAAAT
11656 TAAATTTAAAT
1 TAAATTTAAAT
11667 T
1 T
11668 TTTAAACAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
11 32 0.78
12 9 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:11653 original size:28 final size:29
Alignment explanation
Indices: 11617--11682 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
11607 AAAATAAATT
* *
11617 TAAACTTAAATTAAATTTAAA-TTTAAAA
1 TAAATTTAAAATAAATTTAAATTTTAAAA
*
11645 TAAATTTAAAATAAATTTAAATTTTTAAA
1 TAAATTTAAAATAAATTTAAATTTTAAAA
*
11674 CAAATTTAA
1 TAAATTTAA
11683 TCCTAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAATTTAAAATAAATTTAAATTTTAAAA
Found at i:11668 original size:17 final size:17
Alignment explanation
Indices: 11580--11654 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
11570 TGAACTTCAT
* *
11580 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
11597 TTTAATTTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
11615 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
11632 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
11649 TTTAAA
1 TTTAAA
11655 ATAAATTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 36 0.73
18 13 0.27
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:23835 original size:80 final size:80
Alignment explanation
Indices: 23742--23903 Score: 229
Period size: 80 Copynumber: 2.0 Consensus size: 80
23732 TTAATAAAGG
** * *
23742 TAAAATTATACTTT-GACTCTTAAAAATGATAAAATTTTGATTTAATCTTTTAAAAGTTACATTT
1 TAAAATTATACTTTGGAC-CAAAAAAATGATAAAATTTTAATTTAATATTTTAAAAGTTACATTT
*
23806 TTACTGTCATAAAAAT
65 TTACTATCATAAAAAT
* *
23822 TAAAATT-TAACTTTGGACCAAAAAAATGATAAAATTTTAATTTAATATTTTAAAATTTATATTT
1 TAAAATTAT-ACTTTGGACCAAAAAAATGATAAAATTTTAATTTAATATTTTAAAAGTTACATTT
23886 TTACTATCATAAAAAT
65 TTACTATCATAAAAAT
23902 TA
1 TA
23904 CAGCTTTCAA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
79 1 0.01
80 69 0.95
81 3 0.04
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (80 bp):
TAAAATTATACTTTGGACCAAAAAAATGATAAAATTTTAATTTAATATTTTAAAAGTTACATTTT
TACTATCATAAAAAT
Found at i:38085 original size:12 final size:12
Alignment explanation
Indices: 38067--38112 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
38057 TCACGAACAA
38067 ACTCGTTTATTG
1 ACTCGTTTATTG
*
38079 GCTCGTTTATTG
1 ACTCGTTTATTG
*
38091 ACTCATTTA-TG
1 ACTCGTTTATTG
38102 ACTCGTTTATT
1 ACTCGTTTATT
38113 TATTAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.50
Consensus pattern (12 bp):
ACTCGTTTATTG
Found at i:38217 original size:12 final size:12
Alignment explanation
Indices: 38195--38239 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
38185 ATTATTCATT
38195 AACATTGTTCGTG
1 AACA-TGTTCGTG
*
38208 AACATGTTCGTT
1 AACATGTTCGTG
*
38220 TA-ATGTTCGTG
1 AACATGTTCGTG
38231 AACATGTTC
1 AACATGTTC
38240 AATTAAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 9 0.33
12 14 0.52
13 4 0.15
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:38245 original size:23 final size:23
Alignment explanation
Indices: 38200--38245 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
38190 TCATTAACAT
**
38200 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
38223 TGTTCGTGAACATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
38246 GTTAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:38849 original size:6 final size:6
Alignment explanation
Indices: 38835--38877 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
38825 TTTTCCAAAT
* *
38835 AATTGC AATTAC AATTTC AATTTC AATTTC AATTT- AA-TTC AAT
1 AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC AATTTC AAT
38878 AGTTTATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 2 0.06
5 4 0.12
6 27 0.82
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (6 bp):
AATTTC
Found at i:48901 original size:40 final size:40
Alignment explanation
Indices: 48842--49030 Score: 157
Period size: 40 Copynumber: 4.8 Consensus size: 40
48832 CAGGAATAAT
* * *
48842 TACTGAACTGG-ATGCGACACTATAAATACTGCGATACTAC
1 TACTGAACTGGCAT-TGACACTATAAACACTGCGATATTAC
*
48882 TACTGAACTGGCATTGACACTGTAAACACTGCGATATTAC
1 TACTGAACTGGCATTGACACTATAAACACTGCGATATTAC
* * * * * *
48922 TATTAAACTGACAGTGACACTATAAACACTACGACATTAC
1 TACTGAACTGGCATTGACACTATAAACACTGCGATATTAC
* * * * * *
48962 AACTGAACTGGCAGTGATACTGTAAACATTGCAATA-TAC
1 TACTGAACTGGCATTGACACTATAAACACTGCGATATTAC
* * * * * *
49001 GACTGGATTAGCAGTGACACTGTAAACACT
1 TACTGAACTGGCATTGACACTATAAACACT
49031 ACTAGATTTC
Statistics
Matches: 121, Mismatches: 27, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 27 0.22
40 92 0.76
41 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (40 bp):
TACTGAACTGGCATTGACACTATAAACACTGCGATATTAC
Found at i:52353 original size:201 final size:201
Alignment explanation
Indices: 52007--52926 Score: 885
Period size: 201 Copynumber: 4.6 Consensus size: 201
51997 TGAGGAAGTT
* * * * * *
52007 GAGTTCCTAATATCCCTTTCTTTACCACCACAATAATCTGAAACATTTGGTGTTGAAATTAAAGC
1 GAGTTCCTAACATCCATTTCTTTAACACCAGAATAATCCGAAACATTTGGTGTTGAACTTAAAGC
* * * *
52072 TTCAGAGCAACTTGATGCAAGGGTCACCGGACTTGTCATGTTTCTCATATCCAATTCATCTCTCA
66 TTCAGAGCAGCTTGATGCAAGGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCATCCCTCA
* * ** *
52137 C-GACATT-GATGGGTTCTGGAGATGAGGAAAAGGAGTTGCTGATATCCGTTTCTTTAACAA-CG
131 CAG-CATTAG-TGGGTTCTGGAGATGAGGAAATGGAGTTCCCAATATCCATTTCTTTAA-AAGCG
*
52199 GAGGGCATG
193 GACGGCATG
* *
52208 GAGTTCCT-ACAATCCATTTCTTTAACACCAGAATAATCCAAAACATTTGGTGTGGAACTTAAAG
1 GAGTTCCTAAC-ATCCATTTCTTTAACACCAGAATAATCCGAAACATTTGGTGTTGAACTTAAAG
* * * *
52272 CTTCAGAGCAGCCTGATGCAAGGGTCACTGAACTAGTCATGTTTCTTACATCCAATTCATCCCTC
65 CTTCAGAGCAGCTTGATGCAAGGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCATCCCTC
* * *
52337 GCAGCATTAGTGGGTTCTGGAGACGAGGAAATGGAGTTCCCAATATCCATTTCTTTAAAAGTGGA
130 ACAGCATTAGTGGGTTCTGGAGATGAGGAAATGGAGTTCCCAATATCCATTTCTTTAAAAGCGGA
52402 CGGCATG
195 CGGCATG
* ** * * *
52409 GAGTTCCGAACATCCACCTCTTTAACACAAGAATAATCCGAAACATTTGATGTTGAACTTATAGC
1 GAGTTCCTAACATCCATTTCTTTAACACCAGAATAATCCGAAACATTTGGTGTTGAACTTAAAGC
* * * *
52474 TTCATG-GCAGCTTGCTGCAAGGGTCACTGGACTAATCCTGTTTCTCATATCTAATTCATCCCTC
66 TTCA-GAGCAGCTTGATGCAAGGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCATCCCTC
* * *
52538 ACAACATTCA-TGGGTTCTGGAGATGAGGAAATGGAGTTCACAATATCCATTTC-TT-GAA-C--
130 ACAGCATT-AGTGGGTTCTGGAGATGAGGAAATGGAGTTCCCAATATCCATTTCTTTAAAAGCGG
52597 AC--C--G
194 ACGGCATG
* ** ** *
52601 GAG---GTAATGGT-CATTTCTTCGACACCAGAATAATCCGAAATATTTGGTGTTGAACTTAAAG
1 GAGTTCCTAA-CATCCATTTCTTTAACACCAGAATAATCCGAAACATTTGGTGTTGAACTTAAAG
* * * * * * ** *
52662 CTCCACAGAAACTTAATGTATTGGTCACTGGACTAGTCGTGTTTCTCATATCCAATTCATCCCTC
65 CTTCAGAGCAGCTTGATGCAAGGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCATCCCTC
* * ** * * * * ** * * *
52727 ATAACATTTA-TCAGTTCAGGGGATGAGGAGATGGAGTTCTCAATATCCATAACTTTAACACCAG
130 ACAGCA-TTAGTGGGTTCTGGAGATGAGGAAATGGAGTTCCCAATATCCATTTCTTTAAAAGCGG
* * **
52791 AAGGAACA
194 ACGGCATG
* *
52799 GAGTTCCTAACATCCGTTTCTTCT-ACACCAGAATAATCTGAAACATTTGGTGTTGAACTTAAAG
1 GAGTTCCTAACATCCATTTCTT-TAACACCAGAATAATCCGAAACATTTGGTGTTGAACTTAAAG
* ** * * * *
52863 CTTCAGAGAAATTTGATGTAATGGTCACTGGACTAGTCGA-GTTTCTCATATACAGTTCATCCCT
65 CTTCAGAGCAGCTTGATGCAAGGGTCACTGGACTAGTC-ATGTTTCTCATATCCAATTCATCCCT
52927 TGCTTCATAG
Statistics
Matches: 594, Mismatches: 100, Indels: 50
0.80 0.13 0.07
Matches are distributed among these distances:
189 137 0.23
190 5 0.01
191 1 0.00
192 5 0.01
194 2 0.00
196 2 0.00
198 3 0.01
199 2 0.00
200 6 0.01
201 425 0.72
202 6 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (201 bp):
GAGTTCCTAACATCCATTTCTTTAACACCAGAATAATCCGAAACATTTGGTGTTGAACTTAAAGC
TTCAGAGCAGCTTGATGCAAGGGTCACTGGACTAGTCATGTTTCTCATATCCAATTCATCCCTCA
CAGCATTAGTGGGTTCTGGAGATGAGGAAATGGAGTTCCCAATATCCATTTCTTTAAAAGCGGAC
GGCATG
Found at i:52773 original size:390 final size:394
Alignment explanation
Indices: 52038--52926 Score: 941
Period size: 390 Copynumber: 2.2 Consensus size: 394
52028 TTACCACCAC
*
52038 AATAATCTGAAACATTTGGTGTTGAAATTAAAGCTTCAGAGCAACTTGATGCAAGGGTCACCGGA
1 AATAATCTGAAACATTTGGTGTTGAACTTAAAGCTTCAGAGCAACTTGATGCAAGGGTCACCGGA
** * * *
52103 CTTGTCATGTTTCTCATATCCAATTCATCTCTCACGACATTGATGGGTTCTGGAGATGAGGAAAA
66 CTAATCATGTTTCTCATATCCAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAAA
** * * * *
52168 GGAGTTGCTGATATCCGTTTCTTTAACAACGGAGGGCATGGAGTTCCTACAATCCATTTCTTTAA
131 GGAGTTGCCAATATCCATTTCTTGAACAACGGAGGGAATGGAG--------ATCCATTTCTTCAA
* * * * *
52233 CACCAGAATAATCCAAAACATTTGGTGTGGAACTTAAAGCTTCAGAGCAGCCTGATGCAAGGGTC
188 CACCAGAATAATCCAAAACATTTGGTGTGGAACTTAAAGCTCCACAGAAACCTAATGCAAGGGTC
* * * ** *
52298 ACTGAACTAGTCATGTTTCTTACATCCAATTCATCCCTCGCAGCATTAGTGGGTTCTGGAGACGA
253 ACTGAACTAGTCATGTTTCTCACATCCAATTCATCCCTCACAACATTAGTCAGTTCAGGAGACGA
** *** * * **
52363 GGAAATGGAGTTCCCAATATCCATTTCTTTAAAAGTGGACGGCATGGAGTTCCGAACATCCACCT
318 GGAAATGGAGTTCCCAATATCCATAACTTTAAAACCAGAAGGAACAGAGTTCCGAACATCCACCT
52428 CTT-TAACACAAG
383 CTTCT-ACACAAG
* * * * * *
52440 AATAATCCGAAACATTTGATGTTGAACTTATAGCTTCATG-GCAGCTTGCTGCAAGGGTCACTGG
1 AATAATCTGAAACATTTGGTGTTGAACTTAAAGCTTCA-GAGCAACTTGATGCAAGGGTCACCGG
* *
52504 ACTAATCCTGTTTCTCATATCTAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAA
65 ACTAATCATGTTTCTCATATCCAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAA
* * * *
52569 TGGAGTT-CACAATATCCATTTCTTGAACACCGGAGGTAAT-G-G-T-CATTTCTTCGACACCAG
130 AGGAGTTGC-CAATATCCATTTCTTGAACAACGGAGGGAATGGAGATCCATTTCTTCAACACCAG
* * * * * ** *
52629 AATAATCCGAAATATTTGGTGTTGAACTTAAAGCTCCACAGAAACTTAATGTATTGGTCACTGGA
194 AATAATCCAAAACATTTGGTGTGGAACTTAAAGCTCCACAGAAACCTAATGCAAGGGTCACTGAA
* * * * * *
52694 CTAGTCGTGTTTCTCATATCCAATTCATCCCTCATAACATTTA-TCAGTTCAGGGGATGAGGAGA
259 CTAGTCATGTTTCTCACATCCAATTCATCCCTCACAACA-TTAGTCAGTTCAGGAGACGAGGAAA
* * * ***
52758 TGGAGTTCTCAATATCCATAACTTTAACACCAGAAGGAACAGAGTTCCTAACATCCGTTTCTTCT
323 TGGAGTTCCCAATATCCATAACTTTAAAACCAGAAGGAACAGAGTTCCGAACATCCACCTCTTCT
*
52823 ACACCAG
388 ACACAAG
* * * * *
52830 AATAATCTGAAACATTTGGTGTTGAACTTAAAGCTTCAGAGAAATTTGATGTAATGGTCACTGGA
1 AATAATCTGAAACATTTGGTGTTGAACTTAAAGCTTCAGAGCAACTTGATGCAAGGGTCACCGGA
* * *
52895 CTAGTCGA-GTTTCTCATATACAGTTCATCCCT
66 CTAATC-ATGTTTCTCATATCCAATTCATCCCT
52927 TGCTTCATAG
Statistics
Matches: 402, Mismatches: 79, Indels: 24
0.80 0.16 0.05
Matches are distributed among these distances:
389 1 0.00
390 249 0.62
391 5 0.01
400 1 0.00
401 2 0.00
402 143 0.36
403 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (394 bp):
AATAATCTGAAACATTTGGTGTTGAACTTAAAGCTTCAGAGCAACTTGATGCAAGGGTCACCGGA
CTAATCATGTTTCTCATATCCAATTCATCCCTCACAACATTCATGGGTTCTGGAGATGAGGAAAA
GGAGTTGCCAATATCCATTTCTTGAACAACGGAGGGAATGGAGATCCATTTCTTCAACACCAGAA
TAATCCAAAACATTTGGTGTGGAACTTAAAGCTCCACAGAAACCTAATGCAAGGGTCACTGAACT
AGTCATGTTTCTCACATCCAATTCATCCCTCACAACATTAGTCAGTTCAGGAGACGAGGAAATGG
AGTTCCCAATATCCATAACTTTAAAACCAGAAGGAACAGAGTTCCGAACATCCACCTCTTCTACA
CAAG
Found at i:53173 original size:99 final size:99
Alignment explanation
Indices: 53030--53259 Score: 327
Period size: 99 Copynumber: 2.3 Consensus size: 99
53020 TAAACAGCTC
* * *
53030 ATAGGGGCACCATTATTGCTACATGGCCTGCTAATGGGGCAATCTTCACCAGCAGTTGGTCCACT
1 ATAGGGGCATCATCATTGCTACTTGGCCTGCTAATGGGGCAATCTTCACCAGCAGTTGGTCCACT
* * *
53095 TGCAGGGGCATTTTCCCCAATACTTAATCTGCTT
66 TACAGGAGCATTTTCCCCAATACTTAACCTGCTT
* * * *
53129 ATAGGGGCATCAACATTTCTACTTGGCCTGCTAAAT-GGGTAATCTTTACCAGCAGTTGGTCCAC
1 ATAGGGGCATCATCATTGCTACTTGGCCTGCT-AATGGGGCAATCTTCACCAGCAGTTGGTCCAC
*
53193 TTACAGGAGCATTTTCCCCCATACTTAACCTGCTT
65 TTACAGGAGCATTTTCCCCAATACTTAACCTGCTT
**
53228 ATAGGGGCATCATCACCGCTACTTGGCCTGCT
1 ATAGGGGCATCATCATTGCTACTTGGCCTGCT
53260 TATAGGATCA
Statistics
Matches: 115, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 112 0.97
100 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (99 bp):
ATAGGGGCATCATCATTGCTACTTGGCCTGCTAATGGGGCAATCTTCACCAGCAGTTGGTCCACT
TACAGGAGCATTTTCCCCAATACTTAACCTGCTT
Found at i:53258 original size:33 final size:33
Alignment explanation
Indices: 53221--53341 Score: 113
Period size: 33 Copynumber: 3.7 Consensus size: 33
53211 CCATACTTAA
*
53221 CCTGCTTATAGGGGCATCATCACC-GCTACTTGG
1 CCTGCTTATAGGAGCATCATC-CCAGCTACTTGG
* *
53254 CCTGCTTATAGGATCATCATCCCAGGTACTTGAG
1 CCTGCTTATAGGAGCATCATCCCAGCTACTTG-G
* * * * *
53288 -GTGCTCACAGGGGCATCATCCCTA-CTACTAGG
1 CCTGCTTATAGGAGCATCATCCC-AGCTACTTGG
*
53320 GCTGCTTATAGGAGCATCATCC
1 CCTGCTTATAGGAGCATCATCC
53342 GTTCTACTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
32 3 0.04
33 65 0.93
34 2 0.03
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.26
Consensus pattern (33 bp):
CCTGCTTATAGGAGCATCATCCCAGCTACTTGG
Found at i:59999 original size:5 final size:5
Alignment explanation
Indices: 59989--60019 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
59979 GAACAAATAT
59989 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
60020 ATTCCATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:60390 original size:62 final size:62
Alignment explanation
Indices: 60247--60401 Score: 224
Period size: 62 Copynumber: 2.5 Consensus size: 62
60237 TGACTCTTCT
* * * *
60247 AAAAATTTTAAATTTTTTTT-ATGTTGGTCATGCAATGGCCGACACCCCTTGTTCTCGAATA
1 AAAAAATTTCAATTTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTGTTCTCGAATA
* *
60308 AAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCAATGGCCGACACTCTCTT-TTCTCGAATA
1 AAAAAATTTCAATTTTTTTTGGTGTTGGCCATGCAATGGCCGACAC-CCCTTGTTCTCGAATA
*
60370 AAAAAATTTCAATTTTTTTTGGTGTCGGCCAT
1 AAAAAATTTCAATTTTTTTTGGTGTTGGCCAT
60402 TTTATTTGGT
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
61 17 0.20
62 63 0.75
63 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (62 bp):
AAAAAATTTCAATTTTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTGTTCTCGAATA
Found at i:63374 original size:20 final size:20
Alignment explanation
Indices: 63345--63386 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
63335 ATGAAACTCA
* *
63345 GTCAATGGCGGACAAAGTCG
1 GTCAACGGCGGACAAAGGCG
*
63365 GTCAACGGCGGTCAAAGGCG
1 GTCAACGGCGGACAAAGGCG
63385 GT
1 GT
63387 TTCGAGGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.38, T:0.14
Consensus pattern (20 bp):
GTCAACGGCGGACAAAGGCG
Found at i:63655 original size:86 final size:86
Alignment explanation
Indices: 63552--63950 Score: 610
Period size: 86 Copynumber: 4.6 Consensus size: 86
63542 ATTTAAAATA
63552 TGATAAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGT
1 TGAT-AAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGT
63617 ATTGTCAAATCAACACATTATT
65 ATTGTCAAATCAACACATTATT
*
63639 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
63704 TTGTCAAATCAACACATTATT
66 TTGTCAAATCAACACATTATT
63725 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
*
63790 TTGTCAAATAAACACATTATT
66 TTGTCAAATCAACACATTATT
* * * *
63811 TGATAAAAATTGT-A-AT-ATAATAATAATTTGTACTTTAAATA-TGAAAATTTGATAAATAATA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTA-TTTAAATATTTAAAA-TTAATAAATAATG
* * *
63872 TATTGTTAAATTAACACAATATT
64 TATTGTCAAATCAACACATTATT
* **
63895 TGATATAAATTGTAATATAATAATAATCTTTTTTATTTAAATAATGTT-AAATTAAT
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAT-AT-TTAAAATTAAT
63951 TTTAAATGTA
Statistics
Matches: 288, Mismatches: 16, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
83 20 0.07
84 53 0.18
85 2 0.01
86 187 0.65
87 22 0.08
88 3 0.01
89 1 0.00
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (86 bp):
TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
TTGTCAAATCAACACATTATT
Done.