Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013068.1 Corchorus capsularis cultivar CVL-1 contig13089, 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: 176052
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:37014 original size:12 final size:12
Alignment explanation
Indices: 36997--37051 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
36987 TTAATACAGG
36997 TATCGACGGATA
1 TATCGACGGATA
37009 TATCGAACGGATA
1 TATCG-ACGGATA
37022 TATCGACGGATA
1 TATCGACGGATA
*
37034 TATCAACGGATA
1 TATCGACGGATA
37046 TATCGA
1 TATCGA
37052 GGTATCGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
12 28 0.70
13 12 0.30
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:37031 original size:25 final size:24
Alignment explanation
Indices: 36997--37051 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
36987 TTAATACAGG
36997 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATC-AACGGATA
37022 TATCGACGGATATATCAACGGATA
1 TATCGACGGATATATCAACGGATA
37046 TATCGA
1 TATCGA
37052 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (24 bp):
TATCGACGGATATATCAACGGATA
Found at i:38102 original size:3 final size:3
Alignment explanation
Indices: 38094--38143 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
38084 TCATTTCCCC
38094 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
38142 CA
1 CA
38144 CATATTCCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:38498 original size:10 final size:10
Alignment explanation
Indices: 38483--38508 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38473 AATTTAATAT
38483 GGATATTTAC
1 GGATATTTAC
38493 GGATATTTAC
1 GGATATTTAC
38503 GGATAT
1 GGATAT
38509 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:38547 original size:20 final size:19
Alignment explanation
Indices: 38524--38569 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
38514 GATTTATCGA
38524 GATATCGGTAAATATCGACG
1 GATATCGG-AAATATCGACG
* *
38544 GATACACGGATATATCGACG
1 GATA-TCGGAAATATCGACG
38564 GATATC
1 GATATC
38570 CCGTGACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (19 bp):
GATATCGGAAATATCGACG
Found at i:44135 original size:18 final size:18
Alignment explanation
Indices: 44112--44149 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
44102 CATTTCATCA
44112 TATCATCATCCAAATCCC
1 TATCATCATCCAAATCCC
44130 TATCATCATCCAAATCCC
1 TATCATCATCCAAATCCC
44148 TA
1 TA
44150 CAAGTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
TATCATCATCCAAATCCC
Found at i:45714 original size:30 final size:32
Alignment explanation
Indices: 45660--45725 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
45650 AACTTTATAT
* *
45660 TTTCCGATTGTACCCTTATTTTT-AAAACATA
1 TTTCCAATTGTACCATTATTTTTAAAAACATA
45691 TTTCCAATTGTACCATT-TTTTTAAAAACATA
1 TTTCCAATTGTACCATTATTTTTAAAAACATA
45722 TTTC
1 TTTC
45726 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTCCAATTGTACCATTATTTTTAAAAACATA
Found at i:45737 original size:30 final size:29
Alignment explanation
Indices: 45678--45737 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
45668 TGTACCCTTA
*
45678 TTTTTAAAACATATTTCCAATTGTACCATT
1 TTTTTAAAACATATTTCAAATTG-ACCATT
45708 TTTTTAAAAACATATTTCTAAATTG-CCATT
1 TTTTT-AAAACATATTTC-AAATTGACCATT
45738 ACTAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 10 0.37
31 12 0.44
32 5 0.19
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTTTAAAACATATTTCAAATTGACCATT
Found at i:45935 original size:19 final size:20
Alignment explanation
Indices: 45908--45945 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
45898 TACTATTAGT
45908 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
45928 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
45946 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:46139 original size:22 final size:22
Alignment explanation
Indices: 46111--47223 Score: 214
Period size: 22 Copynumber: 49.9 Consensus size: 22
46101 TGTCTCTATG
*
46111 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
46133 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
46156 -GGTTATCAAAATTCCATAGCG-
1 TGGTTATCAAAATTTCATAG-GA
*
46177 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
46200 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
46221 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
46243 TCAGGTTATTAAATTTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
46267 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
* * ** *
46289 TGATTAATTTTCACAATTTTGTAGAA
1 TGGTT-A---TCAAAATTTCATAGGA
* **
46315 AGGTTATCAAATATCAAAATGTCATAGTG
1 TGGTTATCAAA-AT-----T-TCATAGGA
*
46344 TGGTTAACAAAATTTCATTAGGA
1 TGGTTATCAAAATTTCA-TAGGA
* *
46367 -GGTTA-CTAATATTTCATGGGGA
1 TGGTTATC-AAAATTTCAT-AGGA
* *
46389 -GGTTATC-AAATTTTATAGCA
1 TGGTTATCAAAATTTCATAGGA
* *
46409 TGGTTATTAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAGGA
* *
46431 AGGTTATAAAAGTCTCAATTTCATA--A
1 TGGTTAT-CAA-----AATTTCATAGGA
* * *
46457 GGAGTT-CCAAAATTTGATA-GA
1 TG-GTTATCAAAATTTCATAGGA
* *
46478 AGGTTATC-AAATCTCATA-GA
1 TGGTTATCAAAATTTCATAGGA
* * *
46498 GTGATTATCGAAATTTCATAGAAA
1 -TGGTTATCAAAATTTCATAG-GA
*
46522 TCAGATTATCAAAATTT-ATAGGA
1 T--GGTTATCAAAATTTCATAGGA
* *
46545 AGATTATCAAAATTTCATA--A
1 TGGTTATCAAAATTTCATAGGA
* *
46565 T-GTTATCAAAATTCCAGAGCGA
1 TGGTTATCAAAATTTCATAG-GA
*
46587 -GGTTATCAAAATTACATA--A
1 TGGTTATCAAAATTTCATAGGA
*
46606 TGTGATTATCATAATTTCATA-GA
1 TG-G-TTATCAAAATTTCATAGGA
* * * * *
46629 GGGGTCAACAAAATTTTATAAAGA
1 -TGGTTATCAAAATTTCAT-AGGA
* *
46653 -GGTTATCAAAATTTCAGAAAGA
1 TGGTTATCAAAATTTCA-TAGGA
* *
46675 -GGTTATCAAATTTTC--AGAA
1 TGGTTATCAAAATTTCATAGGA
46694 TGTGATTA-CAAAAATTTCATA-G-
1 TG-G-TTATC-AAAATTTCATAGGA
* ** *
46716 TGGTATTTCTGGGAAGCTTATCA-A-AA
1 TGGT-TATC----AAAATT-TCATAGGA
*
46742 T--TTCAT-AGTATAATTACCAAATTAGGA
1 TGGTT-ATCA--A-AATT-TC--A-TAGGA
* * * *
46769 AGGTTATTAAACTTTTATTATGGA
1 TGGTTATCAAAATTTCA-TA-GGA
*
46793 -GGATATCAAAATTTCAT-GGA
1 TGGTTATCAAAATTTCATAGGA
** **
46813 -GAATATCAAAATTTCATAGTT
1 TGGTTATCAAAATTTCATAGGA
* * *
46834 TAGTTTTCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
*
46856 TGGTTATCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGGA
***
46878 TGCAGATCAAAATTTCATAGGGA
1 TGGTTATCAAAATTTCATA-GGA
* * *
46901 -GATTAACAAAATTTCATAATGA
1 TGGTTATCAAAATTTCAT-AGGA
**
46923 -GGTTATCAAAAAATCATAGGGA
1 TGGTTATCAAAATTTCATA-GGA
46945 -GGTTATCAAAA-TT--T--G-
1 TGGTTATCAAAATTTCATAGGA
* * *
46960 TAGTTATCAAGATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
** **
46982 AAGTTATCAAAATTTTTTAAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
47005 -GGTTTATCAAAATTTTATAGGAA
1 TGG-TTATCAAAATTTCATAGG-A
**
47028 TATTTATCAAAATTTCATAGCGA
1 TGGTTATCAAAATTTCATAG-GA
47051 -GGTTATCAAAATTTCATA--A
1 TGGTTATCAAAATTTCATAGGA
* *
47070 TGTGATTATCAAAATTTCAGAGTA
1 TG-G-TTATCAAAATTTCATAGGA
* *
47094 TGATTA-CTAACAA-TTAATATGGA
1 TGGTTATC-AA-AATTTCATA-GGA
* * * *
47117 -GGTTTTTAAATTTTCATAACG-
1 TGGTTATCAAAATTTCAT-AGGA
* *
47138 TGGTTATCAATATATCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* * * *
47161 -GGTTATCAACATCTCATATTGT
1 TGGTTATCAAAATTTCATA-GGA
* *
47183 TAGTTATCAAAATTTCATTGGGA
1 TGGTTATCAAAATTTCA-TAGGA
*
47206 -AGTTATCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
47224 CTGAGATCTT
Statistics
Matches: 799, Mismatches: 178, Indels: 229
0.66 0.15 0.19
Matches are distributed among these distances:
16 10 0.01
17 2 0.00
19 21 0.03
20 47 0.06
21 57 0.07
22 454 0.57
23 93 0.12
24 37 0.05
25 21 0.03
26 22 0.03
27 5 0.01
28 14 0.02
29 16 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:46489 original size:20 final size:23
Alignment explanation
Indices: 46466--46563 Score: 75
Period size: 21 Copynumber: 4.4 Consensus size: 23
46456 AGGAGTTCCA
*
46466 AAATTTGATAGAAG-G-TTATC-
1 AAATTTCATAGAAGTGATTATCG
*
46486 AAATCTCATAG-AGTGATTATCG
1 AAATTTCATAGAAGTGATTATCG
* *
46508 AAATTTCATAGAAATCAGATTATCA
1 AAATTTCATAGAAGT--GATTATCG
*
46533 AAATTT-ATAGGAA--GATTATCA
1 AAATTTCATA-GAAGTGATTATCG
46554 AAATTTCATA
1 AAATTTCATA
46564 ATGTTATCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
19 2 0.03
20 10 0.15
21 19 0.29
22 13 0.20
23 2 0.03
24 3 0.05
25 16 0.25
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (23 bp):
AAATTTCATAGAAGTGATTATCG
Found at i:46813 original size:20 final size:20
Alignment explanation
Indices: 46788--46829 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
46778 AACTTTTATT
*
46788 ATGGAGGATATCAAAATTTC
1 ATGGAGAATATCAAAATTTC
46808 ATGGAGAATATCAAAATTTC
1 ATGGAGAATATCAAAATTTC
46828 AT
1 AT
46830 AGTTTAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (20 bp):
ATGGAGAATATCAAAATTTC
Found at i:46931 original size:44 final size:44
Alignment explanation
Indices: 46791--47276 Score: 224
Period size: 44 Copynumber: 11.2 Consensus size: 44
46781 TTTTATTATG
* * *
46791 GAGGATATCAAAATTTCAT--GGAGAATATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATA-AT
* * * *
46834 TA-GTTTTCAAAATTTCATA-AGATGGTTATCAAAATTTCATAGTAT
1 GAGGTTATCAAAATTTCATAGGGA-GATTATCAAAATTTCATA--AT
*
46879 GCA-G--ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
1 G-AGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
** * *
46921 GAGGTTATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
* * * ** *
46961 -A-GTTATCAAGATTTCATA-AGAAAGTTATCAAAATTTTTTAAG
1 GAGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAAT
* * * **
47003 GAGGTTTATCAAAATTTTATAGGAATATTTATCAAAATTTCATAGC
1 GAGG-TTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAAT
** * *
47049 GAGGTTATCAAAATTTCATAATGTGATTATCAAAATTTCAGAGTAT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATA--AT
* * * * * * *
47095 GA--TTA-CTAACAA-TTAATATGGAGGTTTTTAAATTTTCATAAC
1 GAGGTTATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAAT
* * * * * * * *
47137 GTGGTTATCAATATATCATATGGAGGTTATCAACATCTCATATT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
* *
47181 GTTA-GTTATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATACT
1 G--AGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAAT
* * * * *
47226 GAGATCT-TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATAA-
1 GAGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
47269 GAAGGTTA
1 G-AGGTTA
47277 AAAAAAATTT
Statistics
Matches: 327, Mismatches: 83, Indels: 65
0.69 0.17 0.14
Matches are distributed among these distances:
37 2 0.01
38 23 0.07
39 3 0.01
40 1 0.00
41 3 0.01
42 20 0.06
43 11 0.03
44 170 0.52
45 70 0.21
46 24 0.07
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
Found at i:47015 original size:23 final size:22
Alignment explanation
Indices: 46985--47064 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 22
46975 CATAAGAAAG
*
46985 TTATCAAAATTTTTTAAGGAGGT
1 TTATCAAAATTTTAT-AGGAGGT
**
47008 TTATCAAAATTTTATAGGAATAT
1 TTATCAAAATTTTATAGG-AGGT
*
47031 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAG-GAGGT
47053 TTATCAAAATTT
1 TTATCAAAATTT
47065 CATAATGTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
22 15 0.31
23 33 0.67
24 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAGGT
Found at i:47274 original size:22 final size:22
Alignment explanation
Indices: 47249--47290 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
47239 TTCCTTAGGG
*
47249 AGGTT-AACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTT-ATAAGA
47271 AGGTTAAAAAAAATTTATAA
1 AGGTTAAAAAAAATTTATAA
47291 AAAAGTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAAATTTATAAGA
Found at i:47836 original size:22 final size:22
Alignment explanation
Indices: 47809--47871 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
47799 TACAGCTCTG
47809 TATATTGTAATATTAATATTAA
1 TATATTGTAATATTAATATTAA
*
47831 TATATTGTAATAATAATA-TAA
1 TATATTGTAATATTAATATTAA
**
47852 TATATAATAATATATAATAT
1 TATATTGTAATAT-TAATAT
47872 AGTAATACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.37
22 22 0.63
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (22 bp):
TATATTGTAATATTAATATTAA
Found at i:47860 original size:15 final size:15
Alignment explanation
Indices: 47840--47878 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
47830 ATATATTGTA
47840 ATAATAATATA-ATAT
1 ATAATAATATATA-AT
47855 ATAATAATATATAAT
1 ATAATAATATATAAT
*
47870 ATAGTAATA
1 ATAATAATA
47879 CTTGAAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
ATAATAATATATAAT
Found at i:47861 original size:10 final size:10
Alignment explanation
Indices: 47838--47870 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
47828 TAATATATTG
47838 TAATAATA-A
1 TAATAATATA
47847 T-ATAATATA
1 TAATAATATA
47856 TAATAATATA
1 TAATAATATA
47866 TAATA
1 TAATA
47871 TAGTAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.27
9 3 0.14
10 13 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATAATATA
Found at i:47869 original size:28 final size:28
Alignment explanation
Indices: 47816--47870 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
47806 CTGTATATTG
*
47816 TAATATTAATATTAATATATTGTAATAA
1 TAATATTAATATTAATATATTATAATAA
47844 TAATA-TAATATATAATA-ATATATAATA
1 TAATATTAATAT-TAATATAT-TATAATA
47871 TAGTAATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
TAATATTAATATTAATATATTATAATAA
Found at i:50183 original size:18 final size:19
Alignment explanation
Indices: 50156--50196 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
50146 GGATTTGTAT
*
50156 TATATCTATCTAT-CTATC
1 TATATCTATCTATACTATA
*
50174 TATATTTATCTATACTATA
1 TATATCTATCTATACTATA
50193 TATA
1 TATA
50197 AAAGTACGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATCTATCTATACTATA
Found at i:50585 original size:20 final size:20
Alignment explanation
Indices: 50560--50604 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
50550 CCCTAACGTG
50560 TAATT-ATTTTATTTGACTT-A
1 TAATTAATTTT-TTTG-CTTGA
50580 TAATTAATTTTTTTGCTTGA
1 TAATTAATTTTTTTGCTTGA
50600 TAATT
1 TAATT
50605 GTAACTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.13
20 15 0.65
21 5 0.22
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (20 bp):
TAATTAATTTTTTTGCTTGA
Found at i:51972 original size:135 final size:135
Alignment explanation
Indices: 51749--52092 Score: 411
Period size: 135 Copynumber: 2.5 Consensus size: 135
51739 TGACCGGAAC
* * *
51749 ATACCAAGGGCCTTCCTTTAAGATGATTCTCAATTTTAAAACAGGGAAGATTTTAAGGGATTCCT
1 ATACCAAGGGCCTCCCTTTAAGATGATTCTCAATTTTAAAACAGGGGAGATTTCAAGGGATTCCT
* * * *
51814 CTTTGAAAGCCTTCACCATCAAAGAAGATTTAAAATGATGGAAGAAAACACTGAAATAACGATTT
66 CTTTGAAAGCCTTCACCATCAAAGAAGATTGAAAATGATGAAAGAAAACACTGAAACAACGATTG
51879 AACAA
131 AACAA
* * *
51884 ATACCAAGGGCCTCCCTTTATGATGATTTTCAATTTTAAAACAGGGGAGAGTTCAAGGGATTCCT
1 ATACCAAGGGCCTCCCTTTAAGATGATTCTCAATTTTAAAACAGGGGAGATTTCAAGGGATTCCT
* * *** ** * *
51949 CTTTGAAAGCGTTCACCTTCAAAGAAGATTGATGCTTCTGAAAGAAAACATTGGAACAACGATTG
66 CTTTGAAAGCCTTCACCATCAAAGAAGATTGAAAATGATGAAAGAAAACACTGAAACAACGATTG
52014 AACAA
131 AACAA
*** * * * * * *
52019 ATACCACCAGCCTCCCTTT-GGAATGATTCTCAAGTTTAAAATAGGGGATATTTCATGGTATTCC
1 ATACCAAGGGCCTCCCTTTAAG-ATGATTCTCAATTTTAAAACAGGGGAGATTTCAAGGGATTCC
*
52083 ACTTTGAAAG
65 TCTTTGAAAG
52093 TGTTAAACTT
Statistics
Matches: 177, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
134 1 0.01
135 176 0.99
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (135 bp):
ATACCAAGGGCCTCCCTTTAAGATGATTCTCAATTTTAAAACAGGGGAGATTTCAAGGGATTCCT
CTTTGAAAGCCTTCACCATCAAAGAAGATTGAAAATGATGAAAGAAAACACTGAAACAACGATTG
AACAA
Found at i:53745 original size:31 final size:31
Alignment explanation
Indices: 53709--53782 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
53699 ATACTTGGTA
*
53709 GGTCCCTATACTTAAAAGAAAAAG-TCAATTT
1 GGTCCCTCTACTTAAAA-AAAAAGATCAATTT
*
53740 GGTCCCTCTAC-T-AAAAAAATGATCAATTT
1 GGTCCCTCTACTTAAAAAAAAAGATCAATTT
*
53769 AGTCCCTCTACTTA
1 GGTCCCTCTACTTA
53783 CAGGTTTAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.14
29 20 0.54
30 2 0.05
31 10 0.27
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (31 bp):
GGTCCCTCTACTTAAAAAAAAAGATCAATTT
Found at i:55246 original size:16 final size:16
Alignment explanation
Indices: 55225--55258 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
55215 ACAATTCAGA
55225 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
55241 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
55257 AA
1 AA
55259 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:57585 original size:66 final size:65
Alignment explanation
Indices: 57489--57628 Score: 226
Period size: 66 Copynumber: 2.1 Consensus size: 65
57479 TTCAGTCAAC
* * *
57489 CAAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAG
1 CAAAAAAAAAAAAAAGCTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGACAAAACTTAGAG
*
57554 CAAAAAAAAAAAAAAGGCTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGACAACACTTAGA
1 CAAAAAAAAAAAAAA-GCTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGACAAAACTTAGA
57619 G
65 G
*
57620 CACAAAAAA
1 CAAAAAAAA
57629 TTGAACTACG
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 15 0.22
66 54 0.78
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.14
Consensus pattern (65 bp):
CAAAAAAAAAAAAAAGCTCACTAAGTTGAAAATCCTGCAAAGGACGGCTTAGACAAAACTTAGAG
Found at i:58393 original size:16 final size:16
Alignment explanation
Indices: 58372--58405 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
58362 ACAATTCAGA
58372 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
58388 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
58404 AA
1 AA
58406 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:62940 original size:12 final size:13
Alignment explanation
Indices: 62925--62969 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
62915 AATCTAAATC
62925 TAAAGCAGATT-A
1 TAAAGCAGATTAA
*
62937 TAAAGCAAATTAA
1 TAAAGCAGATTAA
*
62950 TAAAGTAGATTAA
1 TAAAGCAGATTAA
62963 TAAAGCA
1 TAAAGCA
62970 AGCAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (13 bp):
TAAAGCAGATTAA
Found at i:62976 original size:25 final size:25
Alignment explanation
Indices: 62925--62977 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
62915 AATCTAAATC
**
62925 TAAAGCAGATTATAAAGCAAATTAA
1 TAAAGCAGATTATAAAGCAAAGCAA
*
62950 TAAAGTAGATTAATAAAGC-AAGCAA
1 TAAAGCAGATT-ATAAAGCAAAGCAA
62975 TAA
1 TAA
62978 TTAAAAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.23
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAAGCAA
Found at i:66866 original size:11 final size:12
Alignment explanation
Indices: 66838--66869 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
66828 AATGAATTTT
66838 TTTTTATTTTGAA
1 TTTTT-TTTTGAA
66851 TTTTTTTTTGAA
1 TTTTTTTTTGAA
66863 TTTTTTT
1 TTTTTTT
66870 GAAAACCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:66867 original size:13 final size:13
Alignment explanation
Indices: 66837--66869 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
66827 AAATGAATTT
66837 TTTTTTATTTTGAA
1 TTTTTT-TTTTGAA
66851 -TTTTTTTTTGAA
1 TTTTTTTTTTGAA
66863 TTTTTTT
1 TTTTTTT
66870 GAAAACCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:70335 original size:27 final size:27
Alignment explanation
Indices: 70279--70352 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
70269 AAGTGAACTT
*
70279 AAAATGACCAAAAT-ACCCTAAATGCA
1 AAAATGACCAAAATGCCCCTAAATGCA
* **
70305 AAAATGACCAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTAAATGCA
70332 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
70353 TGTGACCCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 14 0.33
27 28 0.67
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATGCA
Found at i:74378 original size:5 final size:6
Alignment explanation
Indices: 74361--74386 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
74351 AATGCGGCTT
74361 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
74387 CAAGACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:77979 original size:5 final size:5
Alignment explanation
Indices: 77969--77994 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
77959 GTTGTTTAAA
77969 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
77995 TTGCAAGGTT
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:83017 original size:24 final size:24
Alignment explanation
Indices: 82990--83041 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
82980 TTTTTGATTT
82990 AATTTCTCATAATTTAATTAATTA
1 AATTTCTCATAATTTAATTAATTA
83014 AATTTCTCATAATTTAATTAATTA
1 AATTTCTCATAATTTAATTAATTA
83038 AATT
1 AATT
83042 ATGAAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTTCTCATAATTTAATTAATTA
Found at i:96412 original size:30 final size:30
Alignment explanation
Indices: 96356--96412 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
96346 CAAGTCTATA
*
96356 ATAAGTCCTTGGCGCATAATTCCTTCCATG
1 ATAAGTCCTTGGCGCATAATTACTTCCATG
96386 ATAAG-CCTTGGGCGCATCAA-TACTTCC
1 ATAAGTCCTT-GGCGCAT-AATTACTTCC
96413 TATTTTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 4 0.17
30 18 0.75
31 2 0.08
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (30 bp):
ATAAGTCCTTGGCGCATAATTACTTCCATG
Found at i:108857 original size:19 final size:18
Alignment explanation
Indices: 108833--108868 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
108823 TGAAGATTTC
108833 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
108852 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
108869 ATTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:114275 original size:87 final size:84
Alignment explanation
Indices: 114082--114289 Score: 206
Period size: 87 Copynumber: 2.4 Consensus size: 84
114072 CAGGCACTAA
* * * *
114082 ATCCTCCACCAAATCAGTTTCCAAAGATTTTGCATCACTACTAACTAAAACTCCTAGGAAGATCA
1 ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACCACTACCAACCAAAACTCCTAGGAAGATCA
*
114147 CTGAAATTTGAATTCAAAAT
66 C-GAAAATTGAATTCAAAAT
* * * *
114167 ATCCTCTACCATAAT-ATTTTCCAAAGATTTTGCACCA-TAACCACCCATAACTCCATTAGGAAG
1 ATCCTCCACCAT-ATCAGTTTCCAAAGATTTTGCACCACT-ACCAACCAAAACTCC--TAGGAAG
*
114230 ATCAC-AATCAATTGAATTCAAATT
62 ATCACGAA--AATTGAATTCAAAAT
* * * *
114254 ATTCTCCACCCTATCAGTTTCCACAGAATTTGCACC
1 ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACC
114290 TAAAAATCCT
Statistics
Matches: 100, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
84 1 0.01
85 43 0.43
86 4 0.04
87 52 0.52
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.29
Consensus pattern (84 bp):
ATCCTCCACCATATCAGTTTCCAAAGATTTTGCACCACTACCAACCAAAACTCCTAGGAAGATCA
CGAAAATTGAATTCAAAAT
Found at i:115936 original size:125 final size:125
Alignment explanation
Indices: 115714--115955 Score: 466
Period size: 125 Copynumber: 1.9 Consensus size: 125
115704 ATATTTATGT
*
115714 TATAATGGGTAGTTTTTATCTAAAATGAGTAGTTTTTATTTTATTTTGAATTTTTAAAAAACTGA
1 TATAATGGGTAGTTTTTATCTAAAATGAGTAGCTTTTATTTTATTTTGAATTTTTAAAAAACTGA
115779 GTTTGTCTCCGAATCAACTCGTGAGACAAACTCAGGTTTTGGCATTATAATTAGTATAGA
66 GTTTGTCTCCGAATCAACTCGTGAGACAAACTCAGGTTTTGGCATTATAATTAGTATAGA
*
115839 TATAATGGGTAGTTTTTATCTAAAATGGGTAGCTTTTATTTTATTTTGAATTTTTAAAAAACTGA
1 TATAATGGGTAGTTTTTATCTAAAATGAGTAGCTTTTATTTTATTTTGAATTTTTAAAAAACTGA
115904 GTTTGTCTCCGAATCAACTCGTGAGACAAACTCAGGTTTTGGCATTATAATT
66 GTTTGTCTCCGAATCAACTCGTGAGACAAACTCAGGTTTTGGCATTATAATT
115956 TGTCTCCGAA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 115 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (125 bp):
TATAATGGGTAGTTTTTATCTAAAATGAGTAGCTTTTATTTTATTTTGAATTTTTAAAAAACTGA
GTTTGTCTCCGAATCAACTCGTGAGACAAACTCAGGTTTTGGCATTATAATTAGTATAGA
Found at i:115980 original size:49 final size:49
Alignment explanation
Indices: 115905--116004 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
115895 AAAAACTGAG
* *
115905 TTTGTCTCCGAATCAACTCGTGAGACAAACTCAGGTTTTGGCATTATAA
1 TTTGTCTCCGAATCAACTCGTAAGACAAACTCAGGTTTTGACATTATAA
115954 TTTGTCTCCGAATCAACTCGTAAGACAAACTCAGGTTTTGACATTATAA
1 TTTGTCTCCGAATCAACTCGTAAGACAAACTCAGGTTTTGACATTATAA
116003 TT
1 TT
116005 AATATAGATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (49 bp):
TTTGTCTCCGAATCAACTCGTAAGACAAACTCAGGTTTTGACATTATAA
Found at i:116918 original size:32 final size:32
Alignment explanation
Indices: 116859--116947 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 32
116849 GAACCCGTCC
* *
116859 GACCTGAGACCCGAATGACCCGCAACCTAGAT
1 GACCCGAGACCCGAATGACCCGTAACCTAGAT
* *
116891 GACCCGAGATCCGAGTGACCCGTAACCTAGAT
1 GACCCGAGACCCGAATGACCCGTAACCTAGAT
*
116923 GACCCGAAACCCGAATGACCCGTAA
1 GACCCGAGACCCGAATGACCCGTAA
116948 TCCGAGTGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.31, C:0.34, G:0.22, T:0.12
Consensus pattern (32 bp):
GACCCGAGACCCGAATGACCCGTAACCTAGAT
Found at i:116940 original size:16 final size:16
Alignment explanation
Indices: 116867--116993 Score: 89
Period size: 16 Copynumber: 7.9 Consensus size: 16
116857 CCGACCTGAG
*
116867 ACCCGAATGACCCGCA
1 ACCCGAATGACCCGAA
* *
116883 A-CCTAGATGACCCGAG
1 ACCCGA-ATGACCCGAA
* * *
116899 ATCCGAGTGACCCGTA
1 ACCCGAATGACCCGAA
*
116915 A-CCTAGATGACCCGAA
1 ACCCGA-ATGACCCGAA
*
116931 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGAA
* *
116947 ATCCGAGTGA-CCGAA
1 ACCCGAATGACCCGAA
* *
116962 ACCCATAATGACCCAAA
1 ACCC-GAATGACCCGAA
*
116979 ACCCGAATAACCCGA
1 ACCCGAATGACCCGA
116994 GAAGTTAACC
Statistics
Matches: 83, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
15 13 0.16
16 56 0.67
17 14 0.17
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.12
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:116958 original size:32 final size:32
Alignment explanation
Indices: 116867--116975 Score: 132
Period size: 32 Copynumber: 3.4 Consensus size: 32
116857 CCGACCTGAG
* *
116867 ACCCGAATGACCCGCAACCTAGATGACCCGAG
1 ACCCGAATGACCCGTAACCTAGATGACCCGAA
* *
116899 ATCCGAGTGACCCGTAACCTAGATGACCCGAA
1 ACCCGAATGACCCGTAACCTAGATGACCCGAA
*
116931 ACCCGAATGACCCGTAATCCGAG-TGA-CCGAA
1 ACCCGAATGACCCGTAA-CCTAGATGACCCGAA
*
116962 ACCCATAATGACCC
1 ACCC-GAATGACCC
116976 AAAACCCGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
31 9 0.13
32 54 0.81
33 4 0.06
ACGTcount: A:0.32, C:0.35, G:0.20, T:0.13
Consensus pattern (32 bp):
ACCCGAATGACCCGTAACCTAGATGACCCGAA
Found at i:116973 original size:48 final size:47
Alignment explanation
Indices: 116872--116995 Score: 137
Period size: 48 Copynumber: 2.6 Consensus size: 47
116862 CTGAGACCCG
* * *
116872 AATGACCCGCAA-CCTAGATGACCCGAGATCCGAGTGACCCGTAACCT
1 AATGACCCGAAACCCGA-ATGACCCGAGATCCGAGTGACCCGAAACCT
116919 AGATGACCCGAAACCCGAATGACCCGTA-ATCCGAGTGA-CCGAAACCCAT
1 A-ATGACCCGAAACCCGAATGACCCG-AGATCCGAGTGACCCGAAA-CC-T
* *
116968 AATGACCCAAAACCCGAATAACCCGAGA
1 AATGACCCGAAACCCGAATGACCCGAGA
116996 AGTTAACCCG
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
47 7 0.11
48 53 0.80
49 6 0.09
ACGTcount: A:0.35, C:0.33, G:0.19, T:0.12
Consensus pattern (47 bp):
AATGACCCGAAACCCGAATGACCCGAGATCCGAGTGACCCGAAACCT
Found at i:118227 original size:12 final size:12
Alignment explanation
Indices: 118210--118237 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
118200 ACACGTTTAT
118210 ACGACACGAAAC
1 ACGACACGAAAC
118222 ACGACACGAAAC
1 ACGACACGAAAC
118234 ACGA
1 ACGA
118238 ATTGCCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:124168 original size:2 final size:2
Alignment explanation
Indices: 124161--124189 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
124151 AATAATAATA
124161 AT 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 AT A
124190 AGCAAGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128683 original size:35 final size:35
Alignment explanation
Indices: 128643--128717 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
128633 CGAACCCATG
*
128643 ACCACACTTGCAACAAACCTTACACTCGACTTCCT
1 ACCACACTTACAACAAACCTTACACTCGACTTCCT
128678 ACCACACTTACAACAAACCTTACACTCGACTTCCT
1 ACCACACTTACAACAAACCTTACACTCGACTTCCT
128713 ACCAC
1 ACCAC
128718 TAAGCCACCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.33, C:0.41, G:0.04, T:0.21
Consensus pattern (35 bp):
ACCACACTTACAACAAACCTTACACTCGACTTCCT
Found at i:129927 original size:33 final size:33
Alignment explanation
Indices: 129884--129948 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
129874 CCATGGAAAC
129884 TAAACAATGGAAAAGT-TTTCTTACA-AAAAAAGT
1 TAAACAATGGAAAAGTATTT-TTA-AGAAAAAAGT
*
129917 TAAACCATGGAAAAGTATTTTTAAGAAAAAAG
1 TAAACAATGGAAAAGTATTTTTAAGAAAAAAG
129949 AAAAGTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.03
33 25 0.86
34 3 0.10
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (33 bp):
TAAACAATGGAAAAGTATTTTTAAGAAAAAAGT
Found at i:134389 original size:53 final size:53
Alignment explanation
Indices: 134331--134431 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
134321 CACGTGTCAT
** *
134331 TTTTTGGTACACGTGACGTGACATGTGTCACTTTTTGGTACATGTGGCACGAC
1 TTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCACGAC
* * *
134384 TTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGC
1 TTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGC
134432 GTGCCACGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.37
Consensus pattern (53 bp):
TTTTTGGTACACGTGACGTGACACATGTCACTTTTTGGTACACGTGGCACGAC
Found at i:135813 original size:16 final size:16
Alignment explanation
Indices: 135792--135824 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
135782 CCATCTAAGC
135792 AACTGATAAGAGTAGG
1 AACTGATAAGAGTAGG
135808 AACTGATAAGAGTAGG
1 AACTGATAAGAGTAGG
135824 A
1 A
135825 TAAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.18
Consensus pattern (16 bp):
AACTGATAAGAGTAGG
Found at i:153239 original size:67 final size:67
Alignment explanation
Indices: 153111--153240 Score: 190
Period size: 67 Copynumber: 1.9 Consensus size: 67
153101 GAAGGGGTAA
*
153111 ATTACTTAACATTAATTAAGAGGGAAAAACCTAATATCACATGTAACTGAGTCAAATCCCCAACT
1 ATTACTTAACATTAATTAAGAGGGAAAAACCTAATATCACACGTAACTGAGTCAAATCCCCAACT
153176 AT
66 AT
* * * * *
153178 ATTATTTAACATTAATTAAGAGGGAAAAAAGCTAATTTTACACGTAACTGAGTTAAA-CCCCAA
1 ATTACTTAACATTAATTAAGAGGG-AAAAACCTAATATCACACGTAACTGAGTCAAATCCCCAA
153241 AGTATACTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 29 0.52
68 27 0.48
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.28
Consensus pattern (67 bp):
ATTACTTAACATTAATTAAGAGGGAAAAACCTAATATCACACGTAACTGAGTCAAATCCCCAACT
AT
Found at i:158021 original size:124 final size:124
Alignment explanation
Indices: 157763--158021 Score: 263
Period size: 125 Copynumber: 2.1 Consensus size: 124
157753 ATTTGAAATT
* ** * *
157763 GAAAGGAAAATTAAGTGATCAACACCACAATCCCTGTACCAAATGAGCTATAATCCAATTTTCAT
1 GAAAGAAAAATTAAGTGATCAACACCACAATCCCCATACCAAATGAGCTATAATCAAATTTTAAT
* * * * * * * **
157828 TGTCTTAATCAACAACAATATCTATCTAAACATTAAGTAAAATAAAATAATGTGAAATT
66 AGCCTTAATCAACAACAATATCTATCTAAACACTAAGCAAAAAAAAATAATCTCAAAGA
* * * *
157887 GAAAGGAAAATTAAGTGATCAAGACCACAATCCCCATA-TAAATTATTGCTATAATCAAATTTTA
1 GAAAGAAAAATTAAGTGATCAACACCACAATCCCCATACCAAATGA--GCTATAATCAAATTTTA
** * * *
157951 ATAGCCTTCGTCAACAACAATATCTCTCTAAACACTAAGCAAAAAAAAAT-GTCTCAAGGA
64 ATAGCCTTAATCAACAACAATATCTATCTAAACACTAAGCAAAAAAAAATAATCTCAAAGA
158011 GACAA-AAAAAT
1 GA-AAGAAAAAT
158022 GACCTAACAT
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
123 5 0.05
124 46 0.42
125 59 0.54
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (124 bp):
GAAAGAAAAATTAAGTGATCAACACCACAATCCCCATACCAAATGAGCTATAATCAAATTTTAAT
AGCCTTAATCAACAACAATATCTATCTAAACACTAAGCAAAAAAAAATAATCTCAAAGA
Found at i:158113 original size:43 final size:42
Alignment explanation
Indices: 158066--158146 Score: 112
Period size: 41 Copynumber: 1.9 Consensus size: 42
158056 ATAAAATCTA
158066 AACCCT-AAACATAACATATAAACCCTAGGTGAGAT-AAAGGCAT
1 AACCCTAAAAC-T-ACAT-TAAACCCTAGGTGAGATGAAAGGCAT
*
158109 AACCCTAAAACTATATTAAACCCTAGGTGAGATGAAAG
1 AACCCTAAAACTACATTAAACCCTAGGTGAGATGAAAG
158147 AAAAGACATG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
41 17 0.49
42 7 0.20
43 7 0.20
44 4 0.11
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (42 bp):
AACCCTAAAACTACATTAAACCCTAGGTGAGATGAAAGGCAT
Found at i:160985 original size:11 final size:11
Alignment explanation
Indices: 160948--160985 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
160938 CGATACTATA
*
160948 AAATAAATTAT
1 AAATTAATTAT
160959 CAAA-TAATTAT
1 -AAATTAATTAT
160970 AAATTAATTAT
1 AAATTAATTAT
160981 AAATT
1 AAATT
160986 TCATTTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:163005 original size:19 final size:20
Alignment explanation
Indices: 162966--163005 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
162956 ATCACATTTA
162966 ATATTTATCTTTTAGTAAATT
1 ATATTTATCTTTTA-TAAATT
*
162987 ATATTTCTCTTTT-TAAATT
1 ATATTTATCTTTTATAAATT
163006 TCCTCCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (20 bp):
ATATTTATCTTTTATAAATT
Found at i:163816 original size:11 final size:12
Alignment explanation
Indices: 163795--163819 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
163785 AGTATGATTC
163795 TTTCTTTTTTTT
1 TTTCTTTTTTTT
163807 TTTCTTTTTTTT
1 TTTCTTTTTTTT
163819 T
1 T
163820 AAAGAAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Done.