Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011550.1 Corchorus capsularis cultivar CVL-1 contig11571, 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: 54751
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Found at i:964 original size:21 final size:21
Alignment explanation
Indices: 914--1001 Score: 79
Period size: 21 Copynumber: 4.0 Consensus size: 21
904 CTAAATTGGA
* *
914 ATAA-TTAATATTTTAATTTAG
1 ATAAGTTAATATATTAATTT-C
*
935 ATAAATTAATATATTAATTTC
1 ATAAGTTAATATATTAATTTC
* *
956 ATAAGTTAATATATTGATTCC
1 ATAAGTTAATATATTAATTTC
*
977 ATAAGTGAAGTTATAATTAATTTC
1 ATAAGTTAA--TAT-ATTAATTTC
1001 A
1 A
1002 ACCAAACCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
21 30 0.55
22 14 0.25
23 3 0.05
24 8 0.15
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATAAGTTAATATATTAATTTC
Found at i:3249 original size:23 final size:21
Alignment explanation
Indices: 3201--3243 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3191 TTAGATAAAT
*
3201 ATATATTAATTTCATAAGTGA
1 ATATATTAATTCCATAAGTGA
*
3222 ATATATTGATTCCATAAGTGA
1 ATATATTAATTCCATAAGTGA
3243 A
1 A
3244 GTTATAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (21 bp):
ATATATTAATTCCATAAGTGA
Found at i:4692 original size:21 final size:20
Alignment explanation
Indices: 4680--4734 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
4670 AATTAGTAGT
4680 TTAATTTACATAAATTAATATA
1 TTAATTT-CAT-AATTAATATA
*
4702 TTAATTTCATAAGTGAATATA
1 TTAATTTCATAA-TTAATATA
* *
4723 TTGATTCCATAA
1 TTAATTTCATAA
4735 GTGAATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
TTAATTTCATAATTAATATA
Found at i:4735 original size:21 final size:21
Alignment explanation
Indices: 4696--4755 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
4686 TACATAAATT
*
4696 AATATATTAATTTCATAAGTG
1 AATATATTAATTCCATAAGTG
*
4717 AATATATTGATTCCATAAGTG
1 AATATATTAATTCCATAAGTG
4738 AATTTATAATTAATTCCA
1 AA--TAT-ATTAATTCCA
4756 CCAAAACTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.64
23 3 0.09
24 9 0.27
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (21 bp):
AATATATTAATTCCATAAGTG
Found at i:4958 original size:513 final size:502
Alignment explanation
Indices: 3681--5231 Score: 1751
Period size: 513 Copynumber: 3.1 Consensus size: 502
3671 CTCAATTGAA
* * * * * *
3681 AAATTAATATTTTAATTTACATAAATTAATGTATTAATTTCATTAAGTGAAG-T-T-ATTAATTC
1 AAATTAATATATTAATTT-CATAAGTGAATATATTGATTCCA-TAAGTGAAGTTATAATTAATTC
* * * * ** * * * *
3743 TATCATACCTTAACACAGTTAAACAAACAGTTTGGTTAATGGGTGTCAGGGGC-ACTCGTGAAGA
64 CACCAAACGTTATTACAATTAAACAAACTGTTTGGCTAATGGGTGCCA-GGGCAAC-CGTGAAGA
* * * *
3807 GCCAATTATTATCCTAATATCAATCAATTTCTACTGTCCTCAACC-TCTTAATTGGAATAATGAA
127 GCCAATTATTATCCCAATATCAATC-ATTTTTACGGTCCTC-ACCATCTGAATTGGAATAATGAA
* * * *
3871 TATTTTAAAGGTCTCATCATCTCAATTGGAGTAATTAATATTT-TTTTAGAAAAATTAATATATT
190 TATTTTAAGGGTCTCATCATCTCAATT-GAATAATTAATATTTAATTTAGATAAATTAATATATT
* * *
3935 AATTCCATAAATGAAGTTATTATTTCTACCAAATTTTATTACAATTAAACAAACGGTTTGGCTAA
254 AATTCCATAAATAAAGTTATTA-TTCTACCAAATCTTATCACAATTAAACAAACGGTTTGGCTAA
* * * * * *
4000 TGGATACCCTATGGGCACCCATGAAGAGCCGATTATTATTTTGAAGTTTGTGCTAAAAGTATTTC
318 TGGGTACCCCA-GGGCACCCGTGGAGAGCCGGTTATTATTTTGAAGTTTGTGCTAAAAGTATGTC
* * * *
4065 TCCTACATAG-TG---TAACACAATATTACCTCTATAATAATTATTATTTAGCCTTGAATTATAA
382 TCCTAAAT-GTTGTAATAAGACAATAATACC-CTGTAATAATTATTATTTAGCCTTGAATTATAA
* *
4126 TATTGATTGATTTTAA--GTC----TC-CATTGGAATAATTAATATTTTATTTTAGAT
445 TATTTATTGATTTTAAGGGTCTATATCTCATTGGAATAATTAATATTTTAATTTAGAT
* * ** *
4177 AAATTAATATATTATATTTTCATAAGTCAATATATTGCTTTGATAAGTGAAGTTATGATTAATTC
1 AAATTAATATATTA-A-TTTCATAAGTGAATATATTGATTCCATAAGTGAAGTTATAATTAATTC
* *
4242 CACCAAACGTTATTACAATTAAACAAACAT-TTTGACTAATGGGTGCCAGGGCACCCGTGAAGAG
64 CACCAAACGTTATTACAATTAAACAAAC-TGTTTGGCTAATGGGTGCCAGGGCAACCGTGAAGAG
* * * *
4306 CCAATTGTTATCCCAATTATGAATCAGTTTTTGCGGTCCTCACCATCTGAATTGGAAGAATGAAT
128 CCAATTATTATCCCAA-TATCAATCA-TTTTTACGGTCCTCACCATCTGAATTGGAATAATGAAT
* * *
4371 ATTTTAAGGGTCTCATAATCTCAATTGAATTAATTAGTATTTTAATTTAGATAAACTAATATATT
191 ATTTTAAGGGTCTCATCATCTCAATTGAA-TAATTAATA-TTTAATTTAGATAAATTAATATATT
* * * * ***
4436 AACTCCATAAATTAAGTTATTGATTCTACCAAACCTTATCACAATTAAACATACTCCTTGGCTAA
254 AATTCCATAAATAAAGTTATT-ATTCTACCAAATCTTATCACAATTAAACAAACGGTTTGGCTAA
* * * *
4501 TGGGTACCCCAGGGATATCCGTGGAGAGCCGGTTATTATTTTGAAGTTTATGCTAAATGTATGTC
318 TGGGTACCCCAGGG-CACCCGTGGAGAGCCGGTTATTATTTTGAAGTTTGTGCTAAAAGTATGTC
* *
4566 TCCTAAATGTTGTAATAAGACAATAATACCCATGTAATAATTATTGTTTAGCCTTGAATGATAAT
382 TCCTAAATGTTGTAATAAGACAATAATACCC-TGTAATAATTATTATTTAGCCTTGAATTATAAT
* * *
4631 ATTTATTGATTTTAAGGGTCTAATAATCTCAATTGGAATAATTAGTAGTTTAATTTACAT
446 ATTTATTGATTTTAAGGGTCT-AT-ATCTC-ATTGGAATAATTAATATTTTAATTTAGAT
*
4691 AAATTAATATATTAATTTCATAAGTGAATATATTGATTCCATAAGTGAATTTATAATTAATTCCA
1 AAATTAATATATTAATTTCATAAGTGAATATATTGATTCCATAAGTGAAGTTATAATTAATTCCA
* *
4756 CCAAAAC-TTCTTACAATTAAACAAACTGTTTGGCTAAT-GGTGCCTAGGAGCAACCTTGAAGAG
66 CC-AAACGTTATTACAATTAAACAAACTGTTTGGCTAATGGGTGCC-AGG-GCAACCGTGAAGAG
* * **
4819 CCAATTATTATGCCCAATATCAACCGATTTTTACGGTCATCACCATCTGAATTGGAATAGGGAAT
128 CCAATTATTAT-CCCAATATCAATC-ATTTTTACGGTCCTCACCATCTGAATTGGAATAATGAAT
*
4884 ATTTTAAGGGTCTCATCATCTCAATTAGAATAATTAATGATTTAATTTGGATAAATTAATATATT
191 ATTTTAAGGGTCTCATCATCTCAATT-GAATAATTAAT-ATTTAATTTAGATAAATTAATATATT
* * * *
4949 AATTCCATAAATAAAATTATTAATTCTACCAAATCTTATCACAATAAAACAAAAGGTTTGCCTAA
254 AATTCCATAAATAAAGTTATT-ATTCTACCAAATCTTATCACAATTAAACAAACGGTTTGGCTAA
* * * * ** *
5014 TGGGAACCACACA-GGCACCCGTGGAGAGTCGGTTATTATTTTTAAGCTTGTGAGAAAACTATGT
318 TGGGTACC-C-CAGGGCACCCGTGGAGAGCCGGTTATTATTTTGAAGTTTGTGCTAAAAGTATGT
* * * *
5078 CTCTTAAATGTTGTAATAAGACAATAATACCCCTGTAAAAATTATTTTTTAGCTTTGAATTATAA
381 CTCCTAAATGTTGTAATAAGACAATAATA-CCCTGTAATAATTATTATTTAGCCTTGAATTATAA
*
5143 TATTTATTGATTTTAAGGGTCTCATCATTTCCATTGG-ATAATTAATATTTTAATTTAGAT
445 TATTTATTGATTTTAAGGGTCT-AT-ATCT-CATTGGAATAATTAATATTTTAATTTAGAT
*
5203 AAATTAATAAATTAATTTCATTAAGTGAA
1 AAATTAATATATTAATTTCA-TAAGTGAA
5232 GTTTTTAATT
Statistics
Matches: 891, Mismatches: 121, Indels: 69
0.82 0.11 0.06
Matches are distributed among these distances:
496 22 0.02
497 19 0.02
498 37 0.04
499 113 0.13
500 7 0.01
501 132 0.15
502 1 0.00
503 1 0.00
504 57 0.06
506 3 0.00
511 7 0.01
512 117 0.13
513 317 0.36
514 56 0.06
515 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (502 bp):
AAATTAATATATTAATTTCATAAGTGAATATATTGATTCCATAAGTGAAGTTATAATTAATTCCA
CCAAACGTTATTACAATTAAACAAACTGTTTGGCTAATGGGTGCCAGGGCAACCGTGAAGAGCCA
ATTATTATCCCAATATCAATCATTTTTACGGTCCTCACCATCTGAATTGGAATAATGAATATTTT
AAGGGTCTCATCATCTCAATTGAATAATTAATATTTAATTTAGATAAATTAATATATTAATTCCA
TAAATAAAGTTATTATTCTACCAAATCTTATCACAATTAAACAAACGGTTTGGCTAATGGGTACC
CCAGGGCACCCGTGGAGAGCCGGTTATTATTTTGAAGTTTGTGCTAAAAGTATGTCTCCTAAATG
TTGTAATAAGACAATAATACCCTGTAATAATTATTATTTAGCCTTGAATTATAATATTTATTGAT
TTTAAGGGTCTATATCTCATTGGAATAATTAATATTTTAATTTAGAT
Found at i:5882 original size:21 final size:21
Alignment explanation
Indices: 5843--5882 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5833 CCCAATTGGA
*
5843 ATAATTAATATTTTAATTTAG
1 ATAATTAATATATTAATTTAG
*
5864 ATAATTAATATATTGATTT
1 ATAATTAATATATTAATTT
5883 CAAAAGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
ATAATTAATATATTAATTTAG
Found at i:6021 original size:21 final size:21
Alignment explanation
Indices: 5979--6021 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5969 CAATTGGAAT
* **
5979 AATTAATATTTTAATTGGATA
1 AATTAATATATTAATTCCATA
*
6000 AATTAATATATTGATTCCATA
1 AATTAATATATTAATTCCATA
6021 A
1 A
6022 GTGAAGTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTAATATATTAATTCCATA
Found at i:6765 original size:647 final size:628
Alignment explanation
Indices: 5951--7235 Score: 1650
Period size: 647 Copynumber: 2.0 Consensus size: 628
5941 ATTTTGTGCC
* * *
5951 CCAATTATTACACCATCTCAATTGGAATAATTAATATTTTAATTGGATAAATTAATATATTGATT
1 CCAATTATTACACCATCTCAATTGAAATAATTAAGATTTTAATTAGATAAATTAATATATTGATT
*
6016 CCATAAGTGAAGTTATAATTAATTCCAGCAAATCTTATCACAATTAAAATAAATGTTTGGGTAAT
66 CCATAAGTGAAGTTATAATTAATTCCAGCAAATCTTATCACAATTAAAATAAATGTTTGGCTAAT
* * * *
6081 GGGTGCGTCAGGGGCACCCGTGAAGAGCCAGTTATTATCCCCAATATCAATCAATTTCTACGATC
131 GGGTGCCTCAAGGGCACCAGTGAAGAGCCAATTATTATCCCCAATATCAATCAATTTCTACGATC
* * * * * * *
6146 CTCACCATCTGAATTTCAATAATGAATATTTTAAGAGTCTCATCATCTCAATTGGGATAATTA-T
196 CTCACAATCTGAATTGCAATAATGAATATTTTAAGAGTATAATAATCTCAATCGGAATAATTAGT
* ** * *
6210 CATTTTAATTTAGATAAATT-A-GTA-TATTAATTCCATAAAAGAAGTCATTAATTCTACCAAAC
261 -ATTTAAATCCAGATAAATTAATATATTATTAATTCCATAAAAGAAGTCATTAATTCTAACAAAC
* *
6272 CTTATCACAATTAAACAAACGGTTTGGCTAATGGGTATCCCAAGGGCACCCGTGGAGAGCCGGTT
325 CTTATCACAATTAAAC--A----------AAT-GGT-T----A----ACCCATGGAAAGCCGGTT
* *
6337 ATTATTTTGAAATTTGTGCTAAAAGTATGTCTCCTAAATGTTTTAATAAGACAATAATACCCCTG
368 ATTATTTTGAAATTTGTGCTAAAAGAATGTCTCCTAAATGTTGTAATAAGACAATAATACCCCTG
* *
6402 TAATAATTATTGTTCAGCCTTGAATTATAATATTTATTGATATTAAGTGTCTCATTATCCCAATT
433 TAATAA-TATTGTTCAG-CTTGAATTATAATATTTATTGATATTAAGGGTCTCATAATCCCAA-T
* * *
6467 TG-AATAATTAATATTTTAATTTAGATGAATTAATATATTAATTTCATAAATGAA-TT-T-ATTA
495 TGCAATAATTAATATTTTAA-TTAGATAAATTAATATATTAATTCCATAAATCAAGTTATAATTA
* * * *
6528 ATTCTACCAAACCTTAACATAGTTAAACATACAGTTTGGCTAATGGGTGCCCAAAGACACCCATG
559 ATTCTACCAAACATTAACACAATTAAACAAACAGTTTGGCTAATGGGTGCCCAAAGACACCCATG
6593 AAGAG
624 AAGAG
**
6598 CCAATTATTACACGGTCTCAATTGAAATAATTAAGATTTTAATTAGATAAATTAATATATTGATT
1 CCAATTATTACACCATCTCAATTGAAATAATTAAGATTTTAATTAGATAAATTAATATATTGATT
* * * *
6663 CCTTAAGTGAAGTTATAATTAATTCCAGCAAATCTTTTCACAATTAAACTAACTGTTTGGCTAAT
66 CCATAAGTGAAGTTATAATTAATTCCAGCAAATCTTATCACAATTAAAATAAATGTTTGGCTAAT
* *
6728 GGGTGCCTCAAGGGCACCAGTGAAGAGTCAATTATTATCGCCAATATCAATCAATTTCTACGATC
131 GGGTGCCTCAAGGGCACCAGTGAAGAGCCAATTATTATCCCCAATATCAATCAATTTCTACGATC
* * *
6793 CTTACAATCTGAATTGGAATAATGAATATTTTAAGGGTATAATAATCTCAATCGGAATAATTAGT
196 CTCACAATCTGAATTGCAATAATGAATATTTTAAGAGTATAATAATCTCAATCGGAATAATTAGT
* * *
6858 ATTTAAATCCAGATAAATTAATATATTATTAATTCCATAAATGAAGTTATTAATTCTAAGAAACC
261 ATTTAAATCCAGATAAATTAATATATTATTAATTCCATAAAAGAAGTCATTAATTCTAACAAACC
* * * *
6923 TTATTACAATTAAACAAATGGTTAACCCATGGAAAGTCGGTTATTATTTTGAAGTTTTTGCTAAA
326 TTATCACAATTAAACAAATGGTTAACCCATGGAAAGCCGGTTATTATTTTGAAATTTGTGCTAAA
* *
6988 AGAATGTCTCCTAAATGTTGTAATAAGATAATAATACCCCTGTAATAATATTGTTTAGCTTGAAT
391 AGAATGTCTCCTAAATGTTGTAATAAGACAATAATACCCCTGTAATAATATTGTTCAGCTTGAAT
* *
7053 TATAATATTTATTGATTTTAAGGGTCTCATAATCTCAATTGCAATAATTAATATTTTAATTAGAT
456 TATAATATTTATTGATATTAAGGGTCTCATAATCCCAATTGCAATAATTAATATTTTAATTAGAT
* * * * * *
7118 AAATTAATATATTGATTCCATAAGTCAAGTTATAATTAATTGTACTAAATATTATCACAATTAAA
521 AAATTAATATATTAATTCCATAAATCAAGTTATAATTAATTCTACCAAACATTAACACAATTAAA
* * ** * * *
7183 CAAACTGTTTGGCTGATGGGTGCCCAGGGTCATCCGTGAAGAG
586 CAAACAGTTTGGCTAATGGGTGCCCAAAGACACCCATGAAGAG
*
7226 TCAATTATTA
1 CCAATTATTA
7236 TCCCCGATAT
Statistics
Matches: 561, Mismatches: 69, Indels: 35
0.84 0.10 0.05
Matches are distributed among these distances:
625 32 0.06
626 60 0.11
627 10 0.02
628 149 0.27
632 1 0.00
636 1 0.00
637 3 0.01
638 3 0.01
647 248 0.44
648 3 0.01
649 2 0.00
650 49 0.09
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (628 bp):
CCAATTATTACACCATCTCAATTGAAATAATTAAGATTTTAATTAGATAAATTAATATATTGATT
CCATAAGTGAAGTTATAATTAATTCCAGCAAATCTTATCACAATTAAAATAAATGTTTGGCTAAT
GGGTGCCTCAAGGGCACCAGTGAAGAGCCAATTATTATCCCCAATATCAATCAATTTCTACGATC
CTCACAATCTGAATTGCAATAATGAATATTTTAAGAGTATAATAATCTCAATCGGAATAATTAGT
ATTTAAATCCAGATAAATTAATATATTATTAATTCCATAAAAGAAGTCATTAATTCTAACAAACC
TTATCACAATTAAACAAATGGTTAACCCATGGAAAGCCGGTTATTATTTTGAAATTTGTGCTAAA
AGAATGTCTCCTAAATGTTGTAATAAGACAATAATACCCCTGTAATAATATTGTTCAGCTTGAAT
TATAATATTTATTGATATTAAGGGTCTCATAATCCCAATTGCAATAATTAATATTTTAATTAGAT
AAATTAATATATTAATTCCATAAATCAAGTTATAATTAATTCTACCAAACATTAACACAATTAAA
CAAACAGTTTGGCTAATGGGTGCCCAAAGACACCCATGAAGAG
Found at i:7140 original size:21 final size:21
Alignment explanation
Indices: 7098--7140 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
7088 CAATTGCAAT
* *
7098 AATTAATATTTTAATTAGATA
1 AATTAATATATTAATTACATA
* *
7119 AATTAATATATTGATTCCATA
1 AATTAATATATTAATTACATA
7140 A
1 A
7141 GTCAAGTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
AATTAATATATTAATTACATA
Found at i:7515 original size:27 final size:27
Alignment explanation
Indices: 7484--7535 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
7474 TACCTACCAA
*
7484 ATACACAAATAAATCAAATTACAAACT
1 ATACACAAATAAACCAAATTACAAACT
7511 ATACACAAATAAACCAAATTACAAA
1 ATACACAAATAAACCAAATTACAAA
7536 TTGAACTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (27 bp):
ATACACAAATAAACCAAATTACAAACT
Found at i:9372 original size:2 final size:2
Alignment explanation
Indices: 9365--9390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9355 CTATTAAATA
9365 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9391 CCTTATGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12172 original size:37 final size:37
Alignment explanation
Indices: 12122--12196 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
12112 ACCCAAAATT
**
12122 AGTCATTTGATTAAGATCAATTACCAATAATTCAATC
1 AGTCATTCAATTAAGATCAATTACCAATAATTCAATC
*
12159 AGTCATTCAATTAAGATTAATTACCAATAATTCAATC
1 AGTCATTCAATTAAGATCAATTACCAATAATTCAATC
12196 A
1 A
12197 AGTAACCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (37 bp):
AGTCATTCAATTAAGATCAATTACCAATAATTCAATC
Found at i:14660 original size:5 final size:5
Alignment explanation
Indices: 14650--14675 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
14640 TTGAGCAGAC
14650 ATCAT ATCAT ATCAT ATCAT ATCAT A
1 ATCAT ATCAT ATCAT ATCAT ATCAT A
14676 CTTACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (5 bp):
ATCAT
Found at i:15899 original size:19 final size:18
Alignment explanation
Indices: 15875--15911 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
15865 GTTTTGTTCA
15875 TTTCATCATTTTCTTTCTT
1 TTTCAT-ATTTTCTTTCTT
*
15894 TTTCATTTTTTCTTTCTT
1 TTTCATATTTTCTTTCTT
15912 CTTCCCAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCATATTTTCTTTCTT
Found at i:17067 original size:137 final size:137
Alignment explanation
Indices: 16821--17075 Score: 501
Period size: 137 Copynumber: 1.9 Consensus size: 137
16811 GAGATAAGGT
16821 GATTTTCTGACATATCTTGGATATTGTGTTGGAAGAGATAAGGATTCAAATTAACGGTCACATTT
1 GATTTTCTGACATATCTTGGATATTGTGTTGGAAGAGATAAGGATTCAAATTAACGGTCACATTT
16886 GAATCTCACTTTTAATCCAACGGTTAGATTGAGATAAGGTTAGATTCTATGAAATTATTGACTAT
66 GAATCTCACTTTTAATCCAACGGTTAGATTGAGATAAGGTTAGATTCTATGAAATTATTGACTAT
16951 TGTGTAA
131 TGTGTAA
16958 GATTTTCTGACATATCTTGGATATTGTGTTGGAAGAGATAAGGATTCAAATTAACGGTCACATTT
1 GATTTTCTGACATATCTTGGATATTGTGTTGGAAGAGATAAGGATTCAAATTAACGGTCACATTT
*
17023 GAATCTCACTTTTAATCCAACGGTTAGATTGAGATAAGGTTAGATTCTCTGAA
66 GAATCTCACTTTTAATCCAACGGTTAGATTGAGATAAGGTTAGATTCTATGAA
17076 GATAAAATTA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 117 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (137 bp):
GATTTTCTGACATATCTTGGATATTGTGTTGGAAGAGATAAGGATTCAAATTAACGGTCACATTT
GAATCTCACTTTTAATCCAACGGTTAGATTGAGATAAGGTTAGATTCTATGAAATTATTGACTAT
TGTGTAA
Found at i:21564 original size:26 final size:27
Alignment explanation
Indices: 21531--21598 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
21521 CCTAGGGGTG
*
21531 TTTTGGTCATTTTTGCACT-AAGGGCA
1 TTTTGGTCATTTTTACACTCAAGGGCA
* * *
21557 TTTTGGTCATTTGTACATTCAGGGGCA
1 TTTTGGTCATTTTTACACTCAAGGGCA
*
21584 TTTTGGTCACTTTTA
1 TTTTGGTCATTTTTA
21599 AGTCCACTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 16 0.46
27 19 0.54
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTTGGTCATTTTTACACTCAAGGGCA
Found at i:23946 original size:9 final size:9
Alignment explanation
Indices: 23919--23965 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
23909 TTTATTTATT
23919 TATATATAA
1 TATATATAA
23928 TA-A-A-AA
1 TATATATAA
23934 TATATATAA
1 TATATATAA
23943 TATATATAA
1 TATATATAA
23952 TATATATAA
1 TATATATAA
23961 TATAT
1 TATAT
23966 TTTAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.11
7 2 0.06
8 2 0.06
9 27 0.77
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TATATATAA
Found at i:23987 original size:20 final size:20
Alignment explanation
Indices: 23931--23987 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 20
23921 TATATAATAA
* *
23931 AAATATATATAATATA-TAT
1 AAATATATATAATAAATTTT
*
23950 -AATATATATAATATATTTT
1 AAATATATATAATAAATTTT
* *
23969 AAATATATTTTATAAATTT
1 AAATATATATAATAAATTT
23988 CTGAGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 15 0.47
19 2 0.06
20 15 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATATATAATAAATTTT
Found at i:24146 original size:58 final size:58
Alignment explanation
Indices: 24078--24242 Score: 303
Period size: 58 Copynumber: 2.8 Consensus size: 58
24068 AACATTTTGT
24078 AGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTGTTGC
1 AGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTGTTGC
* *
24136 AGAGGTTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTGTTGC
1 AGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTGTTGC
*
24194 AGAGATTCCCTTCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTC
1 AGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTC
24243 AACTTTTGAC
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 102 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (58 bp):
AGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTGTTGC
Found at i:31580 original size:7 final size:7
Alignment explanation
Indices: 31548--31663 Score: 50
Period size: 7 Copynumber: 17.1 Consensus size: 7
31538 TTATTTATTT
31548 ATATATA
1 ATATATA
*
31555 ATA-AAA
1 ATATATA
*
31561 ACATAT-
1 ATATATA
31567 ATAATATA
1 AT-ATATA
31575 ATATATA
1 ATATATA
*
31582 AAATATA
1 ATATATA
* *
31589 TTTTA-A
1 ATATATA
31595 ATATAT-
1 ATATATA
* *
31601 TTA-AAA
1 ATATATA
*
31607 ATATATT
1 ATATATA
31614 ATATATTA
1 ATATA-TA
31622 A-ATATTA
1 ATATA-TA
31629 A-ATATA
1 ATATATA
*
31635 TTATATA
1 ATATATA
31642 ATATATTA
1 ATATA-TA
31650 A-ATATA
1 ATATATA
*
31656 TTATATA
1 ATATATA
31663 A
1 A
31664 AAATATCTAT
Statistics
Matches: 79, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
5 1 0.01
6 17 0.22
7 54 0.68
8 7 0.09
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:31589 original size:21 final size:21
Alignment explanation
Indices: 31549--31663 Score: 110
Period size: 21 Copynumber: 5.3 Consensus size: 21
31539 TATTTATTTA
31549 TATATAATA-A-AAACATATAT
1 TATATAATATATAAA-ATATAT
*
31569 AATATAATATATAAAATATAT
1 TATATAATATATAAAATATAT
*
31590 TTTA-AATATATTTAAAAATATAT
1 TATATAATATA--T-AAAATATAT
* *
31613 TATATATTAAATATTAAATATAT
1 TATATA--ATATATAAAATATAT
*
31636 TATATAATATATTAAATATAT
1 TATATAATATATAAAATATAT
31657 TATATAA
1 TATATAA
31664 AAATATCTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
20 14 0.17
21 30 0.38
22 4 0.05
23 26 0.32
24 2 0.03
26 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAATATATAAAATATAT
Found at i:31625 original size:28 final size:31
Alignment explanation
Indices: 31585--31657 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 31
31575 ATATATAAAA
*
31585 TATATTTTAAATATATTTAAA-A-A-TATAT
1 TATATATTAAATATATTTAAATATATTATAT
31613 TATATATT-AA-ATA-TTAAATATATTATAT
1 TATATATTAAATATATTTAAATATATTATAT
*
31641 AATATATTAAATATATT
1 TATATATTAAATATATT
31658 ATATAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 5 0.14
26 4 0.11
27 3 0.08
28 19 0.51
29 2 0.05
30 3 0.08
31 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TATATATTAAATATATTTAAATATATTATAT
Found at i:31657 original size:9 final size:9
Alignment explanation
Indices: 31574--31658 Score: 61
Period size: 9 Copynumber: 9.0 Consensus size: 9
31564 TATATAATAT
*
31574 AATATATAA
1 AATATATTA
31583 AATATATTTTA
1 AATATA--TTA
31594 AATATATTTAAA
1 AATATA-TT--A
31606 AATATATT-
1 AATATATTA
31614 -ATATATT-
1 AATATATTA
31621 AA-ATATTA
1 AATATATTA
31629 AATATATTATA
1 AATATA-T-TA
31640 TAATATATTA
1 -AATATATTA
31650 AATATATTA
1 AATATATTA
31659 TATAAAAATA
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
7 12 0.18
8 3 0.05
9 18 0.28
10 6 0.09
11 13 0.20
12 13 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AATATATTA
Found at i:32053 original size:17 final size:17
Alignment explanation
Indices: 32031--32084 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
32021 TTGTGACTGA
32031 TTGTTTCAATTTGAGGC
1 TTGTTTCAATTTGAGGC
*
32048 TTGTTT-ATGTTTGA---
1 TTGTTTCA-ATTTGAGGC
32062 TTGTTTCAATTTGAGGC
1 TTGTTTCAATTTGAGGC
32079 TTGTTT
1 TTGTTT
32085 ATGTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 11 0.37
15 1 0.03
16 1 0.03
17 17 0.57
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (17 bp):
TTGTTTCAATTTGAGGC
Found at i:32063 original size:31 final size:31
Alignment explanation
Indices: 32028--32090 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
32018 TGATTGTGAC
32028 TGATTGTTTCAATTTGAGGCTTGTTTATGTT
1 TGATTGTTTCAATTTGAGGCTTGTTTATGTT
32059 TGATTGTTTCAATTTGAGGCTTGTTTATGTT
1 TGATTGTTTCAATTTGAGGCTTGTTTATGTT
32090 T
1 T
32091 CTTTTTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.56
Consensus pattern (31 bp):
TGATTGTTTCAATTTGAGGCTTGTTTATGTT
Found at i:39841 original size:2 final size:2
Alignment explanation
Indices: 39834--39860 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39824 CTAAATACCA
39834 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39861 GTACCCTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43937 original size:2 final size:2
Alignment explanation
Indices: 43930--43963 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
43920 GACTTTATGT
43930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43964 TAATGGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44207 original size:31 final size:31
Alignment explanation
Indices: 44169--44233 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
44159 TTGGGTTATC
44169 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
44200 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
44231 AGT
1 AGT
44234 TAGTTCAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:49252 original size:438 final size:438
Alignment explanation
Indices: 48367--49373 Score: 1260
Period size: 438 Copynumber: 2.3 Consensus size: 438
48357 TGCGTTGACT
* * *
48367 TTTATTTTTGTAATTTC-TT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTGAAAGGT
1 TTTATTTTTTTATTTTCTTTGTTCTATTTGTCCGATTAA-GTGATTCAAGTGTCTATTAAAAGGT
* * * * * * * *
48430 AATTTCATGATCTATAATTTTAATGCAGAACTCAAAAGCCAATTTTAATATTTTAATTTTAAAAA
65 AATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAA
* * * * *
48495 ATGCTTCCGAAATTTTGTGGTTTTGATTGCCGGTCAATTTAATATCGTATAATTTTTTGTCAACA
130 ATGCTTCCGAAATTTGGTCGTTTTGATTGCCGGTCAATTTAATACCATATAATTTTTCGTCAACA
* * * * *
48560 TGTCCGATTGAAGTTATTGAAGTGTCAGTTAAATGGTTATTGCATGATTTACGACTTTCATGAAG
195 TGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAG
* * * * *
48625 GAGCCGAAAGCTAAATTTGATCTATGAGTTTCATAAAGGGTTCAAAAGGGAAATTTTATGCTTCA
260 AACCCGAAAGCTAAATTTGATCTACGAATTTCATAAAGGGTTCAAAAGCGAAATTTTATGCTTCA
* * ** *
48690 AGATCTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACTTTCATATTTTTCTAC
325 AGATATCCATTAACAAACATTTTCTTATTTGGATTAGTTATCAAATGACACTCATACTTTTCTAC
* *
48755 TTTATACTATTTAGTCCTTTACAAATTATATCTTAATCTAATGTTAAGA
390 TTTATACTACTTAGTCATTTACAAATTATATCTTAATCTAATGTTAAGA
* * *
48804 TTTATTTTTTTATTTT-TTTGTTCTATTTGTCCGATTAAGTTGATTTATGTGTCTATCAAAAGGT
1 TTTATTTTTTTATTTTCTTTGTTCTATTTGTCCGATTAAG-TGATTCAAGTGTCTATTAAAAGGT
* *
48868 AATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTTAATTCAAAAAA
65 AATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAA
* ** * *
48933 ATGCTTCCTAAATTTGGTCGTTTCT-ATTGTTGGTCTATTTAATACCATATAA-TTTTCGATCTA
130 ATGCTTCCGAAATTTGGTCGTTT-TGATTGCCGGTCAATTTAATACCATATAATTTTTCG-TCAA
* *
48996 CATGTCCGATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGA
193 CATGTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGA
* * *
49061 AGAACCCGAAAG-TTAATTTGATCTACGAATTTCATGAAGGGTTCAAAA-CGAAATTTTTATGTT
258 AGAACCCGAAAGCTAAATTTGATCTACGAATTTCATAAAGGGTTCAAAAGCGAAA-TTTTATGCT
* *
49124 TCAAGATATCCATTAAGAAATATTTTCTTATTTGGATTAGTTATCAAATGACACTCATACTTTTC
322 TCAAGATATCCATTAACAAACATTTTCTTATTTGGATTAGTTATCAAATGACACTCATACTTTTC
* * * * *
49189 TATTTTATGCTACTTAGTCATTTACAAATTTTATCTTATTC-GAT-TTAACGCTTA
387 TACTTTATACTACTTAGTCATTTACAAATTATATCTTAATCTAATGTTAA-G---A
* * *
49243 TTT-TTTTTTTATTTTCTTTGTTCTATTTGTCCAATTAAAGTAATTCAGGTGTCTATTAAAAGGT
1 TTTATTTTTTTATTTTCTTTGTTCTATTTGTCCGATT-AAGTGATTCAAGTGTCTATTAAAAGGT
* * * * * * **
49307 AATTTTATGATTTACAACTTTCATGAAAGACTCAAAAGCTAATCTTCATGTTTCCATTCTAAAAA
65 AATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAA
49372 AT
130 AT
49374 ATTTTTGAAA
Statistics
Matches: 489, Mismatches: 69, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
435 4 0.01
436 7 0.01
437 155 0.32
438 218 0.45
439 102 0.21
440 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (438 bp):
TTTATTTTTTTATTTTCTTTGTTCTATTTGTCCGATTAAGTGATTCAAGTGTCTATTAAAAGGTA
ATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCTAAAAAA
TGCTTCCGAAATTTGGTCGTTTTGATTGCCGGTCAATTTAATACCATATAATTTTTCGTCAACAT
GTCCGATTAAAGTTATTCAAGTGTCAGTTAAAAGGTTACTGCATGATCTACGACTTTCATGAAGA
ACCCGAAAGCTAAATTTGATCTACGAATTTCATAAAGGGTTCAAAAGCGAAATTTTATGCTTCAA
GATATCCATTAACAAACATTTTCTTATTTGGATTAGTTATCAAATGACACTCATACTTTTCTACT
TTATACTACTTAGTCATTTACAAATTATATCTTAATCTAATGTTAAGA
Found at i:50623 original size:441 final size:439
Alignment explanation
Indices: 49787--50955 Score: 1690
Period size: 441 Copynumber: 2.7 Consensus size: 439
49777 CCCGCTTATA
* * **
49787 ATAAACAAATA-TATTTTTGCTGGTTTATTTATCAAATGATCCCTATACTTTTATGCTTTATATT
1 ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCCTATACTTTTATGCTTTATGCT
* * * * *
49851 ATTTAGTCCCTCATAATTTTTGGGTTCGACAATCGAACGTTTCGGCTTTAATTCTTTTATTTTTT
66 ATTTAGTCCCTCA-AATTTTTGGGTTGGACGATTGAACGTTTCGACTTTAATTCTTTTA-TTTTC
* * * * * ** *
49916 TGTTTTGTTTGTCCGATGAAGGTGATTCAAGTGTCTATTAAAAGATAATTTCATGATCTACAACT
129 TGTTCTATTTGTCTGATTAAGGTGATTCAAGTGTATATTATGAGGTAATTTCATGATCTACAACT
*
49981 TCCATGAAGGACTCAAAAGTCAATTTTAATGTTTTGATTCAAAAAAATGCTTCTGAAATTTTGTG
194 TCCATGAAGGACTTAAAAGTCAATTTTAATGTTTTGATTCAAAAAAATGCTTCTGAAATTTTGTG
* *
50046 GTCTCGATTGCCGGTCTATTTGATATCGTATAAATTTTGGTCCACTTGTCCGATTGAGGTTGTTC
259 GTCTCGATTGCCGGTCTATTTGATATCGTATAAATTTCGGTCCACTTATCCGATTGAGGTTGTTC
*
50111 AAGTGTCGGTTAAAAGGTTATTGTGTAATCTATGACTTTCATTAAGGGCCTGAAAGCTGAATTTG
324 AAGTGTCGGTTAAAAGGTTATTGTATAATCTATGACTTTCATTAAGGGCCTGAAAGCTGAATTTG
* * * *
50176 ATTGATGAGTTTCGTGAAGGGTTTAAGAGTGAATTTTTATGTTTGGTCTCC
389 ATTGATGAGTTTCATGAAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
50227 ATAAACAAATAATTTTTTTTGCTGGATTATTTATCAAATGATCCCTATACTTTTATGCTTTATGC
1 ATAAACAAAT-ATTTTTTTTGCTGGATTATTTATCAAATGATCCCTATACTTTTATGCTTTATGC
* *
50292 TATTTAGTCCCTCACAATTTTTGGGTTGGATGATTGAACGTTTCGTCTTTAATTCTTTTATTTTC
65 TATTTAGTCCCTCA-AATTTTTGGGTTGGACGATTGAACGTTTCGACTTTAATTCTTTTATTTTC
50357 TGTTCTATTTGTCTGATTAAGGTGATTCAAGTGTATATTATGAGGTAATTTCATGATCTACAACT
129 TGTTCTATTTGTCTGATTAAGGTGATTCAAGTGTATATTATGAGGTAATTTCATGATCTACAACT
50422 TCCATGAAGGACTTAAAAGTCAATTTTAATGTTTTGATTCAAAAAAATGCTTCTGAAATTTTGTG
194 TCCATGAAGGACTTAAAAGTCAATTTTAATGTTTTGATTCAAAAAAATGCTTCTGAAATTTTGTG
50487 GTCTCGATTGCCGGTCTATTTGATATCGTATAAATTTCGGTCCACTTATCCGATTGAGGTTGTTC
259 GTCTCGATTGCCGGTCTATTTGATATCGTATAAATTTCGGTCCACTTATCCGATTGAGGTTGTTC
* *
50552 AAGTGTTGGTTAAAAGGTTATTGTATAATCTATGACTTTCGTTAAGGGCCTGAAAGCTGAATTTG
324 AAGTGTCGGTTAAAAGGTTATTGTATAATCTATGACTTTCATTAAGGGCCTGAAAGCTGAATTTG
*
50617 ATTGATGAGTTTCATGGAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
389 ATTGATGAGTTTCATGAAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
* *
50668 ATAAACAAATATTTTTTTTGCTGGATTATCTATCAAATGAT-CCTCATA-TTTCTATGTTTTATG
1 ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCCT-ATACTTT-TATGCTTTATG
* * * * * * *
50731 CTATTTAATCCTTTAAAATTATGGGTTGGACGATTTAACGCTTT-GACTTT--TTTTTTGTATTT
64 CTATTTAGTCCCTCAAATTTTTGGGTTGGACGATTGAACG-TTTCGACTTTAATTCTTT-TATTT
*
50793 TCTGTTCTATTTGTCTGATTAAGGTGATTCAAGTGTATATTATGAGGTAATTTCATGATCTATAA
127 TCTGTTCTATTTGTCTGATTAAGGTGATTCAAGTGTATATTATGAGGTAATTTCATGATCTACAA
* * * * * * * ** * * *
50858 CTTTCATAAAGGACTTAGAAGCCAA--ATAAT-TTTTCAATTCTAAAAAATTATTTTTAAATTTC
192 CTTCCATGAAGGACTTAAAAGTCAATTTTAATGTTTT-GATTCAAAAAAATGCTTCTGAAATTTT
* * * *
50920 GTGGTTTTGATTGCCGGTCTATTTAATATTGTATAA
256 GTGGTCTCGATTGCCGGTCTATTTGATATCGTATAA
50956 TTAATGATTA
Statistics
Matches: 664, Mismatches: 58, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
435 4 0.01
436 56 0.08
437 5 0.01
438 90 0.14
439 32 0.05
440 68 0.10
441 307 0.46
442 102 0.15
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (439 bp):
ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCCTATACTTTTATGCTTTATGCT
ATTTAGTCCCTCAAATTTTTGGGTTGGACGATTGAACGTTTCGACTTTAATTCTTTTATTTTCTG
TTCTATTTGTCTGATTAAGGTGATTCAAGTGTATATTATGAGGTAATTTCATGATCTACAACTTC
CATGAAGGACTTAAAAGTCAATTTTAATGTTTTGATTCAAAAAAATGCTTCTGAAATTTTGTGGT
CTCGATTGCCGGTCTATTTGATATCGTATAAATTTCGGTCCACTTATCCGATTGAGGTTGTTCAA
GTGTCGGTTAAAAGGTTATTGTATAATCTATGACTTTCATTAAGGGCCTGAAAGCTGAATTTGAT
TGATGAGTTTCATGAAGGGTTCAAGAGGGAAATTTTATGTTTGGTCTCC
Found at i:51179 original size:27 final size:27
Alignment explanation
Indices: 51146--51198 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
51136 GATGTAAGTG
* *
51146 ATTGGAATTAGCTATTAATTAGGGTTC
1 ATTGGAATTAGCAAATAATTAGGGTTC
*
51173 ATTGGAATTAGCAAATAATTTGGGTT
1 ATTGGAATTAGCAAATAATTAGGGTT
51199 ATTTGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.40
Consensus pattern (27 bp):
ATTGGAATTAGCAAATAATTAGGGTTC
Found at i:51515 original size:15 final size:14
Alignment explanation
Indices: 51490--51517 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
51480 GTGAATCAAA
51490 ATGTATTTTTTTTT
1 ATGTATTTTTTTTT
51504 ATGTATTTTTTTTT
1 ATGTATTTTTTTTT
51518 GTCTTACCAA
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:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
ATGTATTTTTTTTT
Found at i:52552 original size:11 final size:11
Alignment explanation
Indices: 52538--52567 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
52528 AAGGTCACTT
52538 GAAAAAAAAAA
1 GAAAAAAAAAA
52549 GAAAAAAAAAA
1 GAAAAAAAAAA
52560 GAAGAAAA
1 GAA-AAAA
52568 GAGGCCCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:52636 original size:11 final size:10
Alignment explanation
Indices: 52611--52635 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52601 AAAAAGAAAG
52611 GAAAATAAAA
1 GAAAATAAAA
52621 GAAAATAAAA
1 GAAAATAAAA
52631 GAAAA
1 GAAAA
52636 AGGAAAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (10 bp):
GAAAATAAAA
Found at i:53031 original size:17 final size:17
Alignment explanation
Indices: 53009--53042 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
52999 AACAACTATG
53009 ACACGTAAAATGTCACC
1 ACACGTAAAATGTCACC
53026 ACACGTAAAATGTCACC
1 ACACGTAAAATGTCACC
53043 GTACTTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (17 bp):
ACACGTAAAATGTCACC
Done.