Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016162.1 Corchorus olitorius cultivar O-4 contig16195, 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: 36154
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9351 original size:13 final size:13
Alignment explanation
Indices: 9333--9357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9323 CACAATTATT
9333 TATACTATATATC
1 TATACTATATATC
9346 TATACTATATAT
1 TATACTATATAT
9358 AAAAGTACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
TATACTATATATC
Found at i:10423 original size:20 final size:20
Alignment explanation
Indices: 10386--10424 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10376 TACTATTATT
10386 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
10406 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
10425 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:10618 original size:22 final size:22
Alignment explanation
Indices: 10590--10740 Score: 69
Period size: 22 Copynumber: 6.9 Consensus size: 22
10580 TGTCTCGGTG
10590 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
10612 TGGTTATTATAATTCCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
10635 -GGATATGAAAATTCCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* * *
10654 TGTGATTACCAAACTTTCATATGGA
1 TG-G-TTATCAAAATTTCATA-AGA
* * **
10679 -AGTTATTAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
10700 AGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
10722 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
10741 GCAAGTTATT
Statistics
Matches: 94, Mismatches: 25, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
20 2 0.02
21 5 0.05
22 82 0.87
23 4 0.04
24 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:10741 original size:22 final size:22
Alignment explanation
Indices: 10642--10741 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
10632 GGAGGATATG
* *
10642 AAAATTCCATAGTGTGATTACC
1 AAAATTTCATAGTGTGGTTACC
* **
10664 AAACTTTCATA-TG-GAAGTTATT
1 AAAATTTCATAGTGTG--GTTACC
* * *
10686 AAAATTTCAT-GGGAAGGTTATC
1 AAAATTTCATAGTG-TGGTTACC
10708 AAAATTTCATAGTGTGGTTACC
1 AAAATTTCATAGTGTGGTTACC
10730 AAAATTTCATAG
1 AAAATTTCATAG
10742 CAAGTTATTA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
20 1 0.02
21 2 0.03
22 55 0.90
23 2 0.03
24 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGTGTGGTTACC
Found at i:10779 original size:65 final size:66
Alignment explanation
Indices: 10587--10785 Score: 188
Period size: 66 Copynumber: 3.0 Consensus size: 66
10577 TTTTGTCTCG
* * * * * * * * *
10587 GTGTGGTTATCAAAATTTCATAAG-ATGGTTATTATAATTCCATGAGG-AGGATATGAAAATTCC
1 GTGTGATTACCAAAATTTCATATGCA-AGTTATTAAAATTTCAT-AGGAAGGTTATCAAAATTTC
10650 ATA
64 ATA
* * *
10653 GTGTGATTACCAAACTTTCATATGGAAGTTATTAAAATTTCATGGGAAGGTTATCAAAATTTCAT
1 GTGTGATTACCAAAATTTCATATGCAAGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCAT
10718 A
66 A
* * ** * **
10719 GTGTGGTTACCAAAATTTCATA-GCAAGTTATTAAATTTTTTTATGAAGGTTATTGAAATTTCAT
1 GTGTGATTACCAAAATTTCATATGCAAGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCAT
10783 A
66 A
10784 GT
1 GT
10786 ACTATCACAA
Statistics
Matches: 110, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
65 39 0.35
66 70 0.64
67 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (66 bp):
GTGTGATTACCAAAATTTCATATGCAAGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTCAT
A
Found at i:10846 original size:22 final size:22
Alignment explanation
Indices: 10816--11212 Score: 209
Period size: 22 Copynumber: 17.9 Consensus size: 22
10806 AGGTTATCAA
* *
10816 AGAGATTATCAAAATGTCATAG
1 AGAGGTTATCAAAATTTCATAG
*
10838 CGAGGTTAT-AAGAATTTCATAG
1 AGAGGTTATCAA-AATTTCATAG
* *
10860 TGTGGTTAAT-AAAATTTCATA-
1 AGAGGTT-ATCAAAATTTCATAG
*
10881 AGGAGGTTA-CTAATATTTCAT-G
1 A-GAGGTTATC-AAAATTTCATAG
*
10903 GGAAGGTTATCAAAATTTCATAG
1 AG-AGGTTATCAAAATTTCATAG
* * *
10926 TGTGGTTATCAAAATCTT-TTAG
1 AGAGGTTATCAAAAT-TTCATAG
* *
10948 TGTGGTTATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATA-G
*
10971 A-AGGTTATAAAAGTCTCAATTTCATA-
1 AGAGGTTAT-CAA-----AATTTCATAG
*
10997 AG-GAG-TACCAAAA-TTCGATAG
1 AGAG-GTTATCAAAATTTC-ATAG
*
11018 A-AGGTTATC-AAATCTCATAG
1 AGAGGTTATCAAAATTTCATAG
* *
11038 AGTGATTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
*
11060 AGATCGGATTATC-AAATTTTATAG
1 AGA--GG-TTATCAAAATTTCATAG
*
11084 -GAAGATTATCAAAATTTCA-ATG
1 AG-AGGTTATCAAAATTTCATA-G
* *
11106 CGAGGTTATCAAAATTACATA-
1 AGAGGTTATCAAAATTTCATAG
* *
11127 ATGTGATTATCAAAATTTCATAG
1 A-GAGGTTATCAAAATTTCATAG
* * * *
11150 AGGGGTCAACAAAATAGT-ATAG
1 AGAGGTTATCAAAAT-TTCATAG
*
11172 AGAGGTTATCAAAATTTCATAA
1 AGAGGTTATCAAAATTTCATAG
*
11194 AGAGGTTATCAAATTTTCA
1 AGAGGTTATCAAAATTTCA
11213 AAATGTGATT
Statistics
Matches: 290, Mismatches: 46, Indels: 78
0.70 0.11 0.19
Matches are distributed among these distances:
19 3 0.01
20 14 0.05
21 26 0.09
22 197 0.68
23 17 0.06
24 12 0.04
25 7 0.02
26 4 0.01
27 1 0.00
28 9 0.03
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:11074 original size:46 final size:42
Alignment explanation
Indices: 11005--11237 Score: 165
Period size: 44 Copynumber: 5.3 Consensus size: 42
10995 TAAGGAGTAC
11005 CAAAA-TTCGATAGA-AGGTTATCAAATCTCATAGAGTGATTAT
1 CAAAATTTC-ATAGAGAGGTTATCAAAT-TCATAGAGTGATTAT
* *
11047 CAAAATTTCATAGAGATCGGATTATCAAATTTTATAG-GAAGATTAT
1 CAAAATTTCATAGAGA--GG-TTATCAAA-TTCATAGAG-TGATTAT
*
11093 CAAAATTTCA-ATGCGAGGTTATCAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATA-GAGAGGTTATC-AAATT-CATAGA-GTGATTAT
* * * * *
11137 CAAAATTTCATAGAGGGGTCAACAAAATAGT-ATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTATC-AAAT--TCATAGAGTGATTAT
* * *
11181 CAAAATTTCATAAAGAGGTTATCAAATTTTCA-AAATGTGATTAC
1 CAAAATTTCATAGAGAGGTTATCAAA--TTCATAGA-GTGATTAT
11225 CAAAATTTCATAG
1 CAAAATTTCATAG
11238 TGGTATTTTT
Statistics
Matches: 151, Mismatches: 20, Indels: 38
0.72 0.10 0.18
Matches are distributed among these distances:
42 10 0.07
43 17 0.11
44 82 0.54
45 8 0.05
46 33 0.22
47 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (42 bp):
CAAAATTTCATAGAGAGGTTATCAAATTCATAGAGTGATTAT
Found at i:11722 original size:22 final size:22
Alignment explanation
Indices: 11440--11811 Score: 144
Period size: 22 Copynumber: 16.8 Consensus size: 22
11430 AATTTGTTGC
* *
11440 TATCAAGATTTCATAGGGAGGTT
1 TATCAAAATTTCATAAGGAGG-T
* *
11463 TATCAAAATTTTAT-TGGAAGGTT
1 TATCAAAATTTCATAAGG-AGG-T
11486 TATCAAAATTTCAT-AGCGAGGT
1 TATCAAAATTTCATAAG-GAGGT
* * *
11508 TATCACAATTTCAT-AGTGTGAT
1 TATCAAAATTTCATAAG-GAGGT
11530 TATCAAAATTT--T-A-GAGTGT
1 TATCAAAATTTCATAAGGAG-GT
* *
11549 AATTACTAACAA-TTCATATGGAGGT
1 TA-T-C-AA-AATTTCATAAGGAGGT
* * * *
11574 T-TTAAATTTTCATAACGTGGT
1 TATCAAAATTTCATAAGGAGGT
* * *
11595 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAAGGAGGT
* * *
11617 TATCAACATCTCAT-AGTGTTGGT
1 TATCAAAATTTCATAAG-G-AGGT
** **
11640 TATCAAAATTTCATTGGGAAAT
1 TATCAAAATTTCATAAGGAGGT
11662 TATCAAAATTTCAT-AGTGAGGT
1 TATCAAAATTTCATAAG-GAGGT
* *
11684 CT-TCAAAATTCCTTAAGGAGGT
1 -TATCAAAATTTCATAAGGAGGT
* *
11706 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAAGGAGGT
**
11728 TA-CAAAAAAATTT-ATAAAAAGGT
1 TATC---AAAATTTCATAAGGAGGT
* * * *
11751 TCTCAAAATTCCAT-AGTAACGT
1 TATCAAAATTTCATAAG-GAGGT
** **
11773 TATTGAAATTTCATAATAAGGT
1 TATCAAAATTTCATAAGGAGGT
11795 TATCAAAATTTCATAAG
1 TATCAAAATTTCATAAG
11812 AAGATCATAA
Statistics
Matches: 262, Mismatches: 60, Indels: 55
0.69 0.16 0.15
Matches are distributed among these distances:
18 2 0.01
19 2 0.01
20 4 0.02
21 25 0.10
22 146 0.56
23 67 0.26
24 11 0.04
25 2 0.01
26 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAAGGAGGT
Found at i:11824 original size:22 final size:22
Alignment explanation
Indices: 11778--11824 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
11768 AACGTTATTG
* * * *
11778 AAATTTCATAATAAGGTTATCA
1 AAATTTCATAAGAAGATCATAA
11800 AAATTTCATAAGAAGATCATAA
1 AAATTTCATAAGAAGATCATAA
11822 AAA
1 AAA
11825 ATAGTGTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
AAATTTCATAAGAAGATCATAA
Found at i:13196 original size:22 final size:22
Alignment explanation
Indices: 13168--13401 Score: 127
Period size: 22 Copynumber: 10.5 Consensus size: 22
13158 TGTCTCTGTG
13168 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
13190 TGGTTATTATAATTTCATGAGG
1 TGGTTATCAAAATTTCATAAGA
* *
13212 GGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * *
13234 TGGTTACCAAAACTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
13257 -AGTTATCAAAATTTTCATGGGA
1 TGGTTATCAAAA-TTTCATAAGA
* *
13279 AGGTTATCAAAATTTCA-AAGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
13301 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
** * *
13323 TCAGGTTATTGAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* **
13347 AGGTTATTGAAATTTCAT-AGTA
1 TGGTTATCAAAATTTCATAAG-A
* *
13369 TGGTTATCACAATTTTAT-AGAA
1 TGGTTATCAAAATTTCATAAG-A
*
13391 AGGTTATCAAA
1 TGGTTATCAAA
13402 GAGATTATCA
Statistics
Matches: 163, Mismatches: 39, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.02
22 124 0.76
23 17 0.10
24 18 0.11
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:13431 original size:22 final size:21
Alignment explanation
Indices: 13406--13819 Score: 133
Period size: 22 Copynumber: 18.7 Consensus size: 21
13396 ATCAAAGAGA
*
13406 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
13428 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
13450 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
13472 TTA-CTAATATTTGATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* *
13494 TTATCAAAATTTTATAGTATGG
1 TTATCAAAATTTCATAGGA-GG
* * *
13516 TTGTCAAAATATT-TTAGTGTGG
1 TTATCAAAAT-TTCATAG-GAGG
* *
13538 TTAACAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
13560 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * * *
13585 AATACCAACATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
* ** *
13607 TTATC-AAATCTCATAAAATGA
1 TTATCAAAATTTCATAGGA-GG
*
13628 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAG-GA--GG
* **
13652 ATTATGAAAATTT-ATAGGAATA
1 -TTATCAAAATTTCATAGG-AGG
**
13674 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
13696 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
13718 TTATCAAAATTACATAATGTA-A
1 TTATCAAAATTTCAT-A-GGAGG
* *
13740 TTATCAAAATTTTATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
13762 TCAACAAAATTTTATGAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
13784 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
13806 TTATCAAATTTTCA
1 TTATCAAAATTTCA
13820 AAATGTGATT
Statistics
Matches: 290, Mismatches: 70, Indels: 64
0.68 0.17 0.15
Matches are distributed among these distances:
20 17 0.06
21 28 0.10
22 196 0.68
23 16 0.06
24 7 0.02
25 15 0.05
26 2 0.01
28 9 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:13728 original size:44 final size:43
Alignment explanation
Indices: 13674--13841 Score: 142
Period size: 44 Copynumber: 3.8 Consensus size: 43
13664 TATAGGAATA
* *
13674 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATG-TGTTATCAAAATTTCAAAGAGAGG
* * * * *
13718 TTATCAAAATTACATAATGTAATTATCAAAATTTTATAGAGGGG
1 TTATCAAAATTTCATAATGT-GTTATCAAAATTTCAAAGAGAGG
* * * *
13762 TCAACAAAATTTTATGAA-GAGGTTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCAT-AATG-TGTTATCAAAATTTCA-AAGAGAGG
* * *
13806 TTATCAAATTTTCAAAATGTGATTACCAAAATTTCA
1 TTATCAAAATTTCATAATGTG-TTATCAAAATTTCA
13842 TAGCGGTATT
Statistics
Matches: 95, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
43 4 0.04
44 88 0.93
45 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (43 bp):
TTATCAAAATTTCATAATGTGTTATCAAAATTTCAAAGAGAGG
Found at i:13770 original size:66 final size:65
Alignment explanation
Indices: 13673--13800 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 65
13663 TTATAGGAAT
* ** * *
13673 ATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATG
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAA--GAGGTTATCAAAATTACATAATG
13737 TA
64 TA
* * *
13739 ATTATCAAAATTTTATAGAGGGGTCAACAAAATTTTATGAAGAGGTTATCAAAATTTCATAA
1 ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCA-GAAGAGGTTATCAAAATTACATAA
13801 AGAGGTTATC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
66 50 0.96
68 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (65 bp):
ATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAGAAGAGGTTATCAAAATTACATAATGTA
Found at i:13770 original size:88 final size:87
Alignment explanation
Indices: 13678--13844 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 87
13668 GGAATATTAT
* * *
13678 CAAAATTTCAT-AGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTAAT
1 CAAAATTTCATAAGAG--GTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTAAT
* *
13741 TATCAAAATTTTATAGAGGGGTCAA
63 TACCAAAATTTCATAGAGGGGTCAA
* * * *
13766 CAAAATTTTATGAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCAT-AAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTAATTA
13831 CCAAAATTTCATAG
65 CCAAAATTTCATAG
13845 CGGTATTTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
88 62 0.93
89 2 0.03
90 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
CAAAATTTCATAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTAATTAC
CAAAATTTCATAGAGGGGTCAA
Found at i:13816 original size:21 final size:22
Alignment explanation
Indices: 13674--13843 Score: 121
Period size: 22 Copynumber: 7.7 Consensus size: 22
13664 TATAGGAATA
** **
13674 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAAAGAGG
*
13696 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * *
13718 TTATCAAAATTACATAATGTA-A
1 TTATCAAAATTTCATAAAG-AGG
* * *
13740 TTATCAAAATTTTATAGAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
13762 TCAACAAAATTTTATGAAGAGG
1 TTATCAAAATTTCATAAAGAGG
13784 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
* * *
13806 TTATCAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAAA-GAGG
*
13828 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
13844 GCGGTATTTC
Statistics
Matches: 115, Mismatches: 27, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
21 4 0.03
22 107 0.93
23 4 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:14202 original size:23 final size:23
Alignment explanation
Indices: 14134--14237 Score: 108
Period size: 23 Copynumber: 4.6 Consensus size: 23
14124 CATAAGGAGA
*
14134 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGTAGGT
*
14157 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGTAGGT
*
14180 TTATCAAAATTTCT-TAGCTAGG-
1 TTATCAAAATTT-TATAGGTAGGT
* * *
14202 TTATCACAATTTCATA-GT-GTGA
1 TTATCAAAATTTTATAGGTAG-GT
14224 TTATCAAAATTTTA
1 TTATCAAAATTTTA
14238 AAGTGTGATT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
20 1 0.01
21 2 0.03
22 25 0.36
23 40 0.58
24 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGTAGGT
Found at i:14349 original size:23 final size:22
Alignment explanation
Indices: 13925--14349 Score: 199
Period size: 22 Copynumber: 19.6 Consensus size: 22
13915 TTATGGAGTA
* *
13925 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGTGAGGTT
*
13945 ATCAAAATTTCATA-TGAATGTT
1 ATCAAAATTTCATAGTG-AGGTT
*
13967 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-TGAGGTT
* *
13989 TTCAAAATTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGTGA-GGTT
* *
14011 ATCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAGTGAGGT-T
* *
14033 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGTT
* * *
14055 AACAAAATTTTATAATGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* **
14077 AT-ATAAA-GTCATAGAAAGGTT
1 ATCA-AAATTTCATAGTGAGGTT
*
14098 ATCAAAA-TT--T-GT-A-GCT
1 ATCAAAATTTCATAGTGAGGTT
* *
14114 ATCAAGATTTCATAAG-GAGATT
1 ATCAAAATTTCAT-AGTGAGGTT
* *
14136 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGTGAGG-TT
*
14159 ATCAAAATTTTATAG-GAAGGTTT
1 ATCAAAATTTCATAGTG-AGG-TT
*
14182 ATCAAAATTTCTTAGCT-AGGTT
1 ATCAAAATTTCATAG-TGAGGTT
* * *
14204 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* * * *
14226 ATCAAAATTTTAAAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
14248 A-CTAACAA-TTCATA-TGGAGGTT
1 ATC-AA-AATTTCATAGT-GAGGTT
* * * ** *
14270 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
* *
14292 ATCAATATATCAT-GTGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
* * *
14314 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGGTT
14337 ATCAAAATTTCAT
1 ATCAAAATTTCAT
14350 TGGGAGGTGA
Statistics
Matches: 305, Mismatches: 66, Indels: 65
0.70 0.15 0.15
Matches are distributed among these distances:
16 8 0.03
17 3 0.01
18 1 0.00
19 2 0.01
20 12 0.04
21 27 0.09
22 190 0.62
23 61 0.20
24 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:15884 original size:19 final size:18
Alignment explanation
Indices: 15851--15886 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15841 TGGAAATAAT
15851 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
15869 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
15887 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:18523 original size:22 final size:22
Alignment explanation
Indices: 18498--18541 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18488 TAAGTCGATT
*
18498 ATTTGGCTCCTTTAAA-CGACAA
1 ATTT-GCTCCTTGAAATCGACAA
*
18520 ATTTTCTCCTTGAAATCGACAA
1 ATTTGCTCCTTGAAATCGACAA
18542 GTCCTTTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (22 bp):
ATTTGCTCCTTGAAATCGACAA
Found at i:26228 original size:22 final size:22
Alignment explanation
Indices: 26180--26229 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
26170 GGCTCGATCA
*
26180 GGAGGTCTTCAAAATTTCATAG
1 GGAGGTCTTCAAAATTCCATAG
* *
26202 TGAGGTCTTCAAAATTCCTTAG
1 GGAGGTCTTCAAAATTCCATAG
26224 GGAGGT
1 GGAGGT
26230 TAACAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (22 bp):
GGAGGTCTTCAAAATTCCATAG
Found at i:26251 original size:22 final size:22
Alignment explanation
Indices: 26226--26272 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
26216 TTCCTTAGGG
* * *
26226 AGGTTAACAAAATTTTATAAGA
1 AGGTTAAAAAAAATTTATAAAA
26248 AGGTTAAAAAAAATTTATAAAA
1 AGGTTAAAAAAAATTTATAAAA
26270 AGG
1 AGG
26273 CTCTCAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.15, T:0.28
Consensus pattern (22 bp):
AGGTTAAAAAAAATTTATAAAA
Found at i:26346 original size:22 final size:22
Alignment explanation
Indices: 26299--26346 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
26289 TATCGTTATT
* *
26299 AAAATTTCATAGGAAAGTTATC
1 AAAATTTCATAGGAAAGTCATA
*
26321 AAAATTTCATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAAGTCATA
26343 AAAA
1 AAAA
26347 ATCGTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAAGTCATA
Found at i:27944 original size:26 final size:26
Alignment explanation
Indices: 27895--27945 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
27885 ATTATTAAAA
27895 TATTTTATTTAGAAAAATTAAATTTT
1 TATTTTATTTAGAAAAATTAAATTTT
*
27921 TATTTTATTTAGAAAAATTCAATTT
1 TATTTTATTTAGAAAAATTAAATTT
27946 GTACAGTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
TATTTTATTTAGAAAAATTAAATTTT
Done.