Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018099.1 Corchorus olitorius cultivar O-4 contig18132, 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: 64816
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:3355 original size:14 final size:14
Alignment explanation
Indices: 3336--3365 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3326 CGAATTGACA
3336 AACAGAATAATGAT
1 AACAGAATAATGAT
3350 AACAGAATAATGAT
1 AACAGAATAATGAT
3364 AA
1 AA
3366 TAATAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (14 bp):
AACAGAATAATGAT
Found at i:9071 original size:385 final size:382
Alignment explanation
Indices: 7971--9093 Score: 2049
Period size: 377 Copynumber: 2.9 Consensus size: 382
7961 TTCTGCTGGC
*
7971 ATTATTGAAATAGTGAAAGGTTGATGTTTTATTCTTGGTAATTCTTAAAGAGTGACAGAACAAAC
1 ATTATTGAAATAGTGAAAGGTTGATGTTTTATTCTTGGTAATTCTTAAAGAGTGACAGAACAGAC
* * *
8036 TTATTGAGATGAAACTAGATTTGGAACTATTTCGAAAATGTTAATCAAATGAATATATTGTGTGT
66 TTAATGAGATGAAACTAGATTTGGAACTATTTTGATAATGTTAATCAAATGAATATATTGTGTGT
8101 CAATGATCCATAGCCTTATTGATTGATTTCAACCATTGGAAGGAAAGTATGTCTTTTTAATTAAT
131 CAATGATCCATAGCCTTATTGATTGATTTCAACCATTGGAAGGAAAGTATGTCTTTTTAATTAAT
* *
8166 TGTTTTCTAAGTAGTTTTCAAGTCTTTATTTTGTCTTTAATTAATTACTTGTTAAGTTTTATTTT
196 TGTTTTCTAAGTAGTTTTCGAGTCTTTATTTTGTCTTTAATTAATTACTTGTTAAGCTTTATTTT
8231 TAATCAATCTTTGTTCAAGTATTCTTTATAGATCAGGTTTAGAAATTGATTTTCAGTTATTCCCT
261 TAATCAATCTTTGTTCAAGTATTCTTTATAGATCAGGTTTAGAAATTGATTTTCAGTTATTCCCT
*
8296 CCCTGTGGGATCGACCTTTGCTTTTGGGGATTGAAGTGGCCAATTATTCAATTAGAA
326 CCCTGTGGGATCGACCCTTGCTTTTGGGGATTGAAGTGGCCAATTATTCAATTAGAA
*
8353 ATTATTGAAATAGTGAAAGGTTGATGTTTTATTCTTGGTAATTCTTAAAGACTGACAGAACAGAC
1 ATTATTGAAATAGTGAAAGGTTGATGTTTTATTCTTGGTAATTCTTAAAGAGTGACAGAACAGAC
*
8418 TTAGTGAGATGAAACTAGATTTGGAACTATTTTGATAATGTTAATCAAATGAATATATTGTGTGT
66 TTAATGAGATGAAACTAGATTTGGAACTATTTTGATAATGTTAATCAAATGAATATATTGTGTGT
8483 CAATGATCCATAGCCTTATTGATTGATTTCAACC-----AAGGAAAGTATGTCTTTTTAATTAAT
131 CAATGATCCATAGCCTTATTGATTGATTTCAACCATTGGAAGGAAAGTATGTCTTTTTAATTAAT
*
8543 TGTTTTCTAAGTAGTTTTTGAGTCTTTATTTTGTCTTTAATTAATTACTTGTTAAGCTTTATTTT
196 TGTTTTCTAAGTAGTTTTCGAGTCTTTATTTTGTCTTTAATTAATTACTTGTTAAGCTTTATTTT
*
8608 TAATCAATCTTTGTTCAAGTATTCTTTATAGATCAGGTTTAGAAATTGATTTTCAGTTATTCCCC
261 TAATCAATCTTTGTTCAAGTATTCTTTATAGATCAGGTTTAGAAATTGATTTTCAGTTATTCCCT
8673 CCCTGTGGGATCGACCCTTGCTTTTGGGGATTGAAGTGGCCAATTATTCAATTAGAAA
326 CCCTGTGGGATCGACCCTTGCTTTTGGGGATTGAAGTGGCCAATTATTCAATTAG-AA
8731 TTATTATTGAAATAGTGAAAGGTTGATGTTTTATTCTTGGTAATTCTTAAAGAGTGACAGAACAG
1 --ATTATTGAAATAGTGAAAGGTTGATGTTTTATTCTTGGTAATTCTTAAAGAGTGACAGAACAG
*
8796 ACTTAATGAGATGAAACTAGATTTGGAACTATTTTGATAATTTTAATCAAATGAATATATTGTGT
64 ACTTAATGAGATGAAACTAGATTTGGAACTATTTTGATAATGTTAATCAAATGAATATATTGTGT
8861 GTCAATGATCCATAGCCTTATTGATTGATTTCAACCATTGGAAGGAAAGTATGTCTTTTTAATTA
129 GTCAATGATCCATAGCCTTATTGATTGATTTCAACCATTGGAAGGAAAGTATGTCTTTTTAATTA
*
8926 ATTGTTTTCTAATTAGTTTTCGAGTCTTTATTTTGTCTTTAATTAATTACTTGTTAAGCTTTATT
194 ATTGTTTTCTAAGTAGTTTTCGAGTCTTTATTTTGTCTTTAATTAATTACTTGTTAAGCTTTATT
8991 TTTAATCAATCTTTGTTCAAGTATTCTTTATAGATCAGGTTTAGAAATTGATTTTCAGTTATTCC
259 TTTAATCAATCTTTGTTCAAGTATTCTTTATAGATCAGGTTTAGAAATTGATTTTCAGTTATTCC
* *
9056 CTCCCTTTGGGATCGACCCTTACTTTTGGGGATTGAAG
324 CTCCCTGTGGGATCGACCCTTGCTTTTGGGGATTGAAG
9094 CGTTCATGCA
Statistics
Matches: 715, Mismatches: 18, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
377 206 0.29
378 2 0.00
380 161 0.23
382 159 0.22
385 187 0.26
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.42
Consensus pattern (382 bp):
ATTATTGAAATAGTGAAAGGTTGATGTTTTATTCTTGGTAATTCTTAAAGAGTGACAGAACAGAC
TTAATGAGATGAAACTAGATTTGGAACTATTTTGATAATGTTAATCAAATGAATATATTGTGTGT
CAATGATCCATAGCCTTATTGATTGATTTCAACCATTGGAAGGAAAGTATGTCTTTTTAATTAAT
TGTTTTCTAAGTAGTTTTCGAGTCTTTATTTTGTCTTTAATTAATTACTTGTTAAGCTTTATTTT
TAATCAATCTTTGTTCAAGTATTCTTTATAGATCAGGTTTAGAAATTGATTTTCAGTTATTCCCT
CCCTGTGGGATCGACCCTTGCTTTTGGGGATTGAAGTGGCCAATTATTCAATTAGAA
Found at i:10582 original size:17 final size:17
Alignment explanation
Indices: 10560--10595 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
10550 TGTACATTAT
*
10560 TTTGTTTTTGTGTTTTG
1 TTTGTTTTTATGTTTTG
10577 TTTGTTTTTATGTTTTG
1 TTTGTTTTTATGTTTTG
10594 TT
1 TT
10596 GGATCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.00, G:0.19, T:0.78
Consensus pattern (17 bp):
TTTGTTTTTATGTTTTG
Found at i:11349 original size:3 final size:3
Alignment explanation
Indices: 11341--11395 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
11331 CACTCTTAAA
11341 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11389 AAT AAT A
1 AAT AAT A
11396 TGGTTAGTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11765 original size:16 final size:16
Alignment explanation
Indices: 11746--11777 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11736 TCTTATGGTC
11746 TTTGTATTTTTACTAA
1 TTTGTATTTTTACTAA
11762 TTTGTATTTTTACTAA
1 TTTGTATTTTTACTAA
11778 CTTATATTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTGTATTTTTACTAA
Found at i:11785 original size:16 final size:16
Alignment explanation
Indices: 11750--11785 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11740 ATGGTCTTTG
* *
11750 TATTTTTACTAATTTG
1 TATTTTTACTAACTTA
11766 TATTTTTACTAACTTA
1 TATTTTTACTAACTTA
11782 TATT
1 TATT
11786 GCATTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTTTTACTAACTTA
Found at i:12780 original size:34 final size:33
Alignment explanation
Indices: 12742--13022 Score: 267
Period size: 34 Copynumber: 8.2 Consensus size: 33
12732 TATTCAATTT
*
12742 AGTTTTCAAATTGGGAAAGTTCCCATCGAGTTCA
1 AGTTTTCAAATTGGGAAAGTTCCCATC-AGTTTA
*
12776 AGTTTTCAAATTGGGAAAGTTCCCATCGGGTTTA
1 AGTTTTCAAATTGGGAAAGTTCCCATC-AGTTTA
* * *
12810 AGTTTTCAAATTGGAAAAATTTCCATCAGTGAATTA
1 AGTTTTCAAATTGGGAAAGTTCCCATCAGT---TTA
*
12846 AGTTTTCAAATTGGGAAAATTCCCATCAGGTTTA
1 AGTTTTCAAATTGGGAAAGTTCCCATCA-GTTTA
* *
12880 GGTTTTCAAATTGGGAAAGTTTCCATCAGGTTTA
1 AGTTTTCAAATTGGGAAAGTTCCCATCA-GTTTA
* * *
12914 GGTTTTCAAATTGGGAAAGTTCCC-TCCGGGTTTT
1 AGTTTTCAAATTGGGAAAGTTCCCAT-C-AGTTTA
* * **
12948 AGTTTTTAAAATCGGGAAAGTTCCCATCAGGTCAA
1 AG-TTTTCAAATTGGGAAAGTTCCCATCA-GTTTA
* * * * *
12983 AATTTTCAAATTGGAAAAGTTCTCACCATGTTTT
1 AGTTTTCAAATTGGGAAAGTTCCCATCA-GTTTA
13017 AGTTTT
1 AGTTTT
13023 TTTTTTTCAA
Statistics
Matches: 206, Mismatches: 32, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
33 3 0.01
34 147 0.71
35 24 0.12
36 30 0.15
37 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (33 bp):
AGTTTTCAAATTGGGAAAGTTCCCATCAGTTTA
Found at i:12922 original size:104 final size:104
Alignment explanation
Indices: 12737--12927 Score: 303
Period size: 104 Copynumber: 1.8 Consensus size: 104
12727 CAAGGTATTC
* *
12737 AATTTAGTTTTCAAATTGGGAAAGTTCCCATCGAGTTCAAGTTTTCAAATTGGGAAAGTTCCCAT
1 AATTAAGTTTTCAAATTGGGAAAATTCCCATCGAGTTCAAGTTTTCAAATTGGGAAAGTTCCCAT
*
12802 CGGGTTTAAGTTTTCAAATTGGAAAAATTTCCATCAGTG
66 CAGGTTTAAGTTTTCAAATTGGAAAAATTTCCATCAGTG
* * *
12841 AATTAAGTTTTCAAATTGGGAAAATTCCCATC-AGGTTTAGGTTTTCAAATTGGGAAAGTTTCCA
1 AATTAAGTTTTCAAATTGGGAAAATTCCCATCGA-GTTCAAGTTTTCAAATTGGGAAAGTTCCCA
*
12905 TCAGGTTTAGGTTTTCAAATTGG
65 TCAGGTTTAAGTTTTCAAATTGG
12928 GAAAGTTCCC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 1 0.01
104 78 0.99
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (104 bp):
AATTAAGTTTTCAAATTGGGAAAATTCCCATCGAGTTCAAGTTTTCAAATTGGGAAAGTTCCCAT
CAGGTTTAAGTTTTCAAATTGGAAAAATTTCCATCAGTG
Found at i:13018 original size:138 final size:137
Alignment explanation
Indices: 12739--13015 Score: 341
Period size: 138 Copynumber: 2.0 Consensus size: 137
12729 AGGTATTCAA
12739 TTTA-GTTTTCAAATTGGGAAAGTTCCCATCGAGTTCAAGTTTTCAAATTGGGAAAGTTCCCATC
1 TTTAGGTTTTCAAATTGGGAAAGTTCCCATCGAGTTCAAGTTTTCAAATTGGGAAAGTTCCCATC
* * * *
12803 GGGTTTAAGTTTTCAAATTGGAAAAATTTCCATCAGTGAATTAAGTTTTCAAATTGGGAAAATTC
66 GGGTTTAAGTTTTAAAATCGGAAAAATTCCCATCAGTCAA-TAAGTTTTCAAATTGGGAAAATTC
*
12868 CCATCAGG
130 CCACCAGG
* * *
12876 TTTAGGTTTTCAAATTGGGAAAGTTTCCATC-AGGTTTAGGTTTTCAAATTGGGAAAGTTCCC-T
1 TTTAGGTTTTCAAATTGGGAAAGTTCCCATCGA-GTTCAAGTTTTCAAATTGGGAAAGTTCCCAT
* * *
12939 CCGGGTTTTAGTTTTTAAAATCGGGAAAGTTCCCATCAGGTCAA-AA-TTTTCAAATT-GGAAAA
65 -CGGGTTTAAG-TTTTAAAATCGGAAAAATTCCCATCA-GTCAATAAGTTTTCAAATTGGGAAAA
* *
13001 GTTCTCACCATG
127 -TTCCCACCAGG
13013 TTT
1 TTT
13016 TAGTTTTTTT
Statistics
Matches: 121, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
136 6 0.05
137 27 0.22
138 63 0.52
139 21 0.17
140 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (137 bp):
TTTAGGTTTTCAAATTGGGAAAGTTCCCATCGAGTTCAAGTTTTCAAATTGGGAAAGTTCCCATC
GGGTTTAAGTTTTAAAATCGGAAAAATTCCCATCAGTCAATAAGTTTTCAAATTGGGAAAATTCC
CACCAGG
Found at i:15617 original size:17 final size:17
Alignment explanation
Indices: 15595--15630 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
15585 TTAAAGTGAC
15595 GACGACGGCCTTTAATT
1 GACGACGGCCTTTAATT
15612 GACGACGGCCTTTAATT
1 GACGACGGCCTTTAATT
15629 GA
1 GA
15631 ACAAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (17 bp):
GACGACGGCCTTTAATT
Found at i:16448 original size:104 final size:104
Alignment explanation
Indices: 16268--16474 Score: 396
Period size: 104 Copynumber: 2.0 Consensus size: 104
16258 AACTACGACA
16268 GTAGTGATTTTGAGCCTCCGAATAATTCAATGTTGTATATTGAATTTTGAATTATTGTTGATCTT
1 GTAGTGATTTTGAGCCTCCGAATAATTCAATGTTGTATATTGAATTTTGAATTATTGTTGATCTT
*
16333 ATAAGTTGGGGGGGGGGGGGTGGACATAGAAATTATATC
66 ATAAGTGGGGGGGGGGGGGGTGGACATAGAAATTATATC
16372 GTAGTGATTTTGAGCCTCCGAATAATTCAATGTTGTATATTGAATTTTGAATTATTGTTGATCTT
1 GTAGTGATTTTGAGCCTCCGAATAATTCAATGTTGTATATTGAATTTTGAATTATTGTTGATCTT
*
16437 CTAAGTGGGGGGGGGGGGGGTGGACATAGAAATTATAT
66 ATAAGTGGGGGGGGGGGGGGTGGACATAGAAATTATAT
16475 TTTGGCCCCT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.37
Consensus pattern (104 bp):
GTAGTGATTTTGAGCCTCCGAATAATTCAATGTTGTATATTGAATTTTGAATTATTGTTGATCTT
ATAAGTGGGGGGGGGGGGGGTGGACATAGAAATTATATC
Found at i:21054 original size:24 final size:23
Alignment explanation
Indices: 21027--21084 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
21017 ATTACCTGGT
21027 ATTTATAGGATTCGGATACCTAAA
1 ATTTATAGG-TTCGGATACCTAAA
* *
21051 ATTTTATAGGTTTGGATACCTGAA
1 A-TTTATAGGTTCGGATACCTAAA
21075 ATTCTATAGG
1 ATT-TATAGG
21085 GTTAGCGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.07
24 20 0.67
25 8 0.27
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (23 bp):
ATTTATAGGTTCGGATACCTAAA
Found at i:30941 original size:3 final size:3
Alignment explanation
Indices: 30933--31010 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
30923 ATCTTGTGAT
30933 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30981 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31011 AAAGTTCTGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32964 original size:256 final size:255
Alignment explanation
Indices: 32509--33021 Score: 918
Period size: 256 Copynumber: 2.0 Consensus size: 255
32499 ACAAAACTTA
32509 AAGCAACTTTTCACCCTTACTGTTATCATCTGGCACCAGTATCGATTCTTTTGCATCCTCCCCCT
1 AAGCAACTTTTCACCCTTACTGTTATCATCTGGCACCAGTATCGATTCTTTTGCATCCTCCCCCT
* *
32574 TTTCTGGACTACTTTCTCTGCTAACTGCAGAAACTTACTATGATAAATACACTACGCTTTTAACT
66 TTTCTGGACTACTTTCTCTGCTAACTGCAGAAACTTACTATAATAAACACACTACGCTTTTAACT
* *
32639 AAAAAAGCAATCAGGAAAAGAAGGGTACAAAATTTCATAAATAGCTGCACACAATCATAATGTTA
131 AAAAAAGCAAGCAGGAAAAGAAGGGTACAAAATTTCACAAATAGCTGCACACAATCATAATGTTA
* *
32704 AGCCAACAATTTATCATGGAAAAATGTAACTTCATCCCATAAAAAAATAAAAAAATAAAAC
196 AGCCAACAATATATCATGGAAAAATGTAACTTCATCCCATAAAAAAAT-AAAAAACAAAAC
*
32765 AAGCAACTTTTCACCCTTACTGTTATCATCTGGCACCAGTATCGATTCTTTTGCATCCTCCCCTT
1 AAGCAACTTTTCACCCTTACTGTTATCATCTGGCACCAGTATCGATTCTTTTGCATCCTCCCCCT
32830 TTTCTGGACTACTTTCTCTGCTAACTGCAGAAACTTACTATAATAAACACACTACGCTTTTAACT
66 TTTCTGGACTACTTTCTCTGCTAACTGCAGAAACTTACTATAATAAACACACTACGCTTTTAACT
*
32895 AAAAAAGCAAGCAGGAAAAGAAGGGTACAAAATTTCACAAATAGCTGCACTCAATCATAATGTTA
131 AAAAAAGCAAGCAGGAAAAGAAGGGTACAAAATTTCACAAATAGCTGCACACAATCATAATGTTA
* * *
32960 AGCCAACAATATATCATGGAAAAATGTAACTTCATCGCATACAAAAATCAAAAACAAAAC
196 AGCCAACAATATATCATGGAAAAATGTAACTTCATCCCATAAAAAAATAAAAAACAAAAC
33020 AA
1 AA
33022 CTAACTGCCC
Statistics
Matches: 246, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
255 12 0.05
256 234 0.95
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (255 bp):
AAGCAACTTTTCACCCTTACTGTTATCATCTGGCACCAGTATCGATTCTTTTGCATCCTCCCCCT
TTTCTGGACTACTTTCTCTGCTAACTGCAGAAACTTACTATAATAAACACACTACGCTTTTAACT
AAAAAAGCAAGCAGGAAAAGAAGGGTACAAAATTTCACAAATAGCTGCACACAATCATAATGTTA
AGCCAACAATATATCATGGAAAAATGTAACTTCATCCCATAAAAAAATAAAAAACAAAAC
Found at i:33718 original size:15 final size:15
Alignment explanation
Indices: 33698--33727 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33688 ATTCACATCT
33698 TCATTAGTAACAAAA
1 TCATTAGTAACAAAA
33713 TCATTAGTAACAAAA
1 TCATTAGTAACAAAA
33728 ATACGTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
TCATTAGTAACAAAA
Found at i:37325 original size:20 final size:20
Alignment explanation
Indices: 37283--37325 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
37273 CATAAATGAA
*
37283 ATTTTCAAAAATTATTATTT
1 ATTTTCAAAAATTATTATGT
*
37303 ATTTTCAAATATATATTA-GT
1 ATTTTCAAAAAT-TATTATGT
37323 ATT
1 ATT
37326 GAATTCGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTCAAAAATTATTATGT
Found at i:38628 original size:24 final size:23
Alignment explanation
Indices: 38583--38633 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
38573 CATAGACAAC
*
38583 TTCATAATTAATTAGTATTTAATA
1 TTCATAATTAACTAGTATTTAA-A
38607 TTCATAATTAACTAGT-TCTTAAA
1 TTCATAATTAACTAGTAT-TTAAA
38630 TTCA
1 TTCA
38634 CGTGCGTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (23 bp):
TTCATAATTAACTAGTATTTAAA
Found at i:40450 original size:29 final size:29
Alignment explanation
Indices: 40402--40479 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
40392 GCTAAATACC
* *
40402 CAAAA-AATCCCTTATGGTTTTTTTTGGGA
1 CAAAATAATTCCTTAT-GTTTTTTTTGCGA
40431 CAAAATAATTCCTTATGTTTTTTTTGCGA
1 CAAAATAATTCCTTATGTTTTTTTTGCGA
*
40460 CAAATTAA-TCCGTTATGTTT
1 CAAAATAATTCC-TTATGTTT
40480 CAAGAATGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 3 0.07
29 32 0.73
30 9 0.20
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (29 bp):
CAAAATAATTCCTTATGTTTTTTTTGCGA
Found at i:40670 original size:13 final size:13
Alignment explanation
Indices: 40654--40685 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
40644 AATTTATTAA
40654 AATTTTTTAAACT
1 AATTTTTTAAACT
40667 AATTTTTTAAACT
1 AATTTTTTAAACT
40680 AATTTT
1 AATTTT
40686 AAAGAATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTTTAAACT
Found at i:40688 original size:11 final size:12
Alignment explanation
Indices: 40639--40685 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
40629 AAAAAGAGAG
40639 AAACTAATTTATT
1 AAACTAATTT-TT
*
40652 AAA--ATTTTTT
1 AAACTAATTTTT
40662 AAACTAATTTTTT
1 AAACTAA-TTTTT
40675 AAACTAATTTT
1 AAACTAATTTT
40686 AAAGAATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
10 5 0.17
11 4 0.14
12 5 0.17
13 15 0.52
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (12 bp):
AAACTAATTTTT
Found at i:40936 original size:3 final size:3
Alignment explanation
Indices: 40930--40954 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40920 GTTTTTTTTT
40930 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
40955 CCCTCAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:41177 original size:30 final size:31
Alignment explanation
Indices: 41136--41210 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 31
41126 CTCACTTTTG
* *
41136 AAACGTAAGGGATTAATTTGTCCCGAAA-AA
1 AAACATAAGGGATTAATTTGTCCCAAAAGAA
*
41166 AAACATAAGGGATTATTTTGTCCCAAAAGAA
1 AAACATAAGGGATTAATTTGTCCCAAAAGAA
*
41197 AAACAGAAGGGATT
1 AAACATAAGGGATT
41211 TTTTTGGGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 25 0.62
31 15 0.38
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTGTCCCAAAAGAA
Found at i:43789 original size:29 final size:29
Alignment explanation
Indices: 43734--43810 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
43724 TTTTTCTGAA
* * *
43734 TTTGTTTAAGTTGCGGGTTGCGCACTTGTG
1 TTTGTTTAAG-TGTGGGTTGCACACTTGGG
*
43764 TTTGTTTAAGTGTGGGTTGTACACTTGGG
1 TTTGTTTAAGTGTGGGTTGCACACTTGGG
* *
43793 ATTGTTTTGAGTGTGGGT
1 TTTG-TTTAAGTGTGGGT
43811 CCGCACTCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.12, C:0.08, G:0.35, T:0.45
Consensus pattern (29 bp):
TTTGTTTAAGTGTGGGTTGCACACTTGGG
Found at i:55320 original size:20 final size:21
Alignment explanation
Indices: 55287--55330 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
55277 CATATCAAGG
* *
55287 AATAGGCAAGCAAG-CAAAGC
1 AATAGCCAAGCAAGACAAAAC
*
55307 AATAGCCAATCAAGACAAAAC
1 AATAGCCAAGCAAGACAAAAC
55328 AAT
1 AAT
55331 GCAAAGGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.55, C:0.20, G:0.16, T:0.09
Consensus pattern (21 bp):
AATAGCCAAGCAAGACAAAAC
Found at i:58857 original size:27 final size:27
Alignment explanation
Indices: 58816--58878 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
58806 TAAAATTTTT
*
58816 TTTTCTTTTAACGCAAAAAGCAGAGAAA-
1 TTTT-TTTTAACGCAAAAAGAAGA-AAAC
*
58844 TTTTTTTTATCGCAAAAAGAAGAAAAC
1 TTTTTTTTAACGCAAAAAGAAGAAAAC
58871 TTTTTTTT
1 TTTTTTTT
58879 TATATTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 3 0.09
27 25 0.78
28 4 0.12
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (27 bp):
TTTTTTTTAACGCAAAAAGAAGAAAAC
Found at i:59013 original size:49 final size:49
Alignment explanation
Indices: 58960--59106 Score: 213
Period size: 49 Copynumber: 3.0 Consensus size: 49
58950 TTTTCAAAAC
* * * * **
58960 GCAAAACCAAGAGAAAATTCTTGAGATTAGTCACTTCCTTCCTTCCCCG
1 GCAAAACCAAGAGAAAGTTTTTAAGATGAGTCTTTTCCTTCCTTCCCCG
* *
59009 GCAAAACCAATAGAAAGTTTTTAAGATGAGTCTTTTCCTTCCTTCCCCA
1 GCAAAACCAAGAGAAAGTTTTTAAGATGAGTCTTTTCCTTCCTTCCCCG
*
59058 GCAAAACCAAGAGAAAGTTTTTAAGATGAGTCTTTTCCTTCTTTCCCCG
1 GCAAAACCAAGAGAAAGTTTTTAAGATGAGTCTTTTCCTTCCTTCCCCG
59107 ACAATGGCGC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 87 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (49 bp):
GCAAAACCAAGAGAAAGTTTTTAAGATGAGTCTTTTCCTTCCTTCCCCG
Found at i:63808 original size:21 final size:21
Alignment explanation
Indices: 63782--63852 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
63772 TGCTAGGAGA
63782 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
63803 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
63824 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
63845 TCATTGGA
1 TCATTGGA
63853 ATTGCCTAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 2 0.04
21 46 0.96
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.