Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019746.1 Corchorus olitorius cultivar O-4 contig19779, 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: 10961
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Found at i:535 original size:2 final size:2
Alignment explanation
Indices: 523--570 Score: 60
Period size: 2 Copynumber: 23.0 Consensus size: 2
513 AGTTTAGACT
* *
523 TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
567 TA TA
1 TA TA
571 AAAGTACGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 36 0.90
3 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1622 original size:19 final size:19
Alignment explanation
Indices: 1607--1645 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1597 TACTATTATT
1607 TTTTGAATTTAATATTTTA
1 TTTTGAATTTAATATTTTA
* *
1626 TTTTTAATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
1646 AATGTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTGAATTTAATATTTTA
Found at i:1644 original size:20 final size:20
Alignment explanation
Indices: 1606--1645 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1596 TTACTATTAT
1606 TTTTTGAATTTAATATTTTA
1 TTTTTGAATTTAATATTTTA
*
1626 TTTTT-AATTTCAATTTTTTA
1 TTTTTGAATTT-AATATTTTA
1646 AATGTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTGAATTTAATATTTTA
Found at i:1836 original size:22 final size:22
Alignment explanation
Indices: 1811--2043 Score: 172
Period size: 22 Copynumber: 10.5 Consensus size: 22
1801 TGTCTCTGTG
* *
1811 TGGTTATTAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
1833 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
1856 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
1877 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
1900 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAGGA
* *
1921 AGGTTATCAAAATTGCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
1943 TGGTTACCAAAATTCCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
1965 TCAGGTTATTAAAATTTCTTAGGGA
1 T--GGTTATCAAAATTTCATA-GGA
**
1990 -GGTTATTGAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* * *
2011 TGGTTATCACAATTTTATAGAA
1 TGGTTATCAAAATTTCATAGGA
*
2033 AGGTTATCAAA
1 TGGTTATCAAA
2044 GAGATTATCA
Statistics
Matches: 168, Mismatches: 29, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
21 7 0.04
22 139 0.83
23 5 0.03
24 14 0.08
25 3 0.02
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:1881 original size:44 final size:44
Alignment explanation
Indices: 1812--3084 Score: 200
Period size: 44 Copynumber: 29.4 Consensus size: 44
1802 GTCTCTGTGT
* * * * *
1812 GGTTATTAAAATTTCATA-AGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCAT-AGGA
*
1856 GGTTATCAAAATTCCATAGTG-TGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATA-GGA
* * * * * *
1900 AGTTATCAAAATTTCAT-GGGAAGGTTATCAAAATTGCATAGTGT
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAG-GA
* * *
1944 GGTTACCAAAATTCCATAG-GATCAGGTTATTAAAATTTCTTAGGGA
1 GGTTATCAAAATTCCATAGTGAT--GGTTATCAAAATTTCATA-GGA
** * * * *
1990 GGTTATTGAAATTTCATAGTG-TGGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAG-GA
* *
2034 GGTTATC---A----A-A--GA-GATTATCAAAATGTCATAGCGA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAG-GA
* * *
2068 GGTTAT-AAGAATTTCATAGTG-TGGTTAACAAAATTTTATAAGGA
1 GGTTATCAA-AATTCCATAGTGATGGTTATCAAAATTTCAT-AGGA
* * * * *
2112 GGTTA-CTAATATTTCATGGGGA-GGTTATCAAAATTTCATAGTGT
1 GGTTATC-AAAATTCCATAGTGATGGTTATCAAAATTTCATAG-GA
* * * *
2156 GGTTATCAAAA-TCTCTTA-CGAAGGTTATAAAAGTCTCAATTTCATAAGGA
1 GGTTATCAAAATTC-CATAGTGATGGTTAT-CAA-----AATTTCAT-AGGA
* ** * *
2206 -G-TACCAAAATTTGATA--GAAGGTTATC-AAATCTCATA-GA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAGGA
* * * * *
2244 GTGATTATCGAAATTTCATAGAGATCGAATTATCAAAATTT-ATAAGAA
1 G-G-TTATCAAAATTCCATAGTGAT-G-GTTATCAAAATTTCAT-AGGA
* * * * * *
2292 GATTATCAAAATTTCAAAGCGA-GGTTATCAAAATTAT-ATAATGT
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATT-TCAT-AGGA
* * * * * * * *
2336 GATTATCAAAATTTCATAGAG-GGGTCAACAAAATTTTATAGAAA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAG-GA
* ** * * * * *
2380 GGTTATCAAAATTTCATA-AAAAGGTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTC-ATAGGA
* * * * *
2424 GATTACCGAAATTTCATA--G-TGG---T----ATTTC-TGGGGA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCAT-AGGA
* ** * *
2458 GGTTATCAAAATTTCATAGT-ATAATTTTACCAAA--T--TAGGAA
1 GGTTATCAAAATTCCATAGTGATGGTTAT-CAAAATTTCATAGG-A
* * * * * *
2499 GGTTATTAAACTT--TTA-TTATGGAGTAATCAAAATTTCAGA-GA
1 GGTTATCAAAATTCCATAGTGAT-G-GTTATCAAAATTTCATAGGA
* * * *
2541 GGATATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATAGTTTA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAG--GA
* * *
2586 -GTTTTCAAAATTTCATAGT-AT-GTAGATCAAAATTTCATAGGGA
1 GGTTATCAAAATTCCATAGTGATGGT-TATCAAAATTTCATA-GGA
* * * * **
2629 GATTA-AAAAATTTTCATAATGA-GGTTATCAAAAAAATCATAGTGA
1 GGTTATCAAAA-TTCCATAGTGATGGTTATC-AAAATTTCATAG-GA
* * *
2674 AGTTATCAAAATT---T-GT-A--GTTATCAAGATTTTATAAGGA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCAT-AGGA
** * *
2712 GGTTATCAAAATTTTATAGGGA-GGTTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTCCATAGTGATGG-TTATCAAAATTTCATAGG-A
* * * *
2757 GGTTTATCAAAATTTCATAGCGA-GGTTATCACAATTTCATAGTGT
1 GG-TTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAG-GA
* * * * * *
2802 GATTATCAAAATTTCAGAGTG-TGATTA-CTAACTATTCATATGGA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAAT-TTCATA-GGA
* * * * ** * *
2846 GGTTTTTAAATTTTCATAACG-TGGTTATCAATATATCATATGGA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATA-GGA
* * *
2890 GGTTATCAACA-TCTCATAGTGTTGGTTATCAAAATTTCATTGGAA
1 GGTTATCAAAATTC-CATAGTGATGGTTATCAAAATTTCATAGG-A
* * * *
2935 AGTTATCAAAATTTCATAGTGA-GGTCT-TCAAAATTCCTTAGAGA
1 GGTTATCAAAATTCCATAGTGATGGT-TATCAAAATTTCATAG-GA
* * * * ** * **
2979 GGTTAAT-AAAATTTCATA-AGAAGGCTAAAAAAAATTT-GTAAAAA
1 GGTT-ATCAAAATTCCATAGTGATGG-TTATCAAAATTTCAT-AGGA
* * * *
3023 GGTTCTCGAAATTCCATAGTG-TCGTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAGG-A
* *
3067 GGTTATCAGAATTTCATA
1 GGTTATCAAAATTCCATA
3085 AGGAGATCAT
Statistics
Matches: 891, Mismatches: 217, Indels: 242
0.66 0.16 0.18
Matches are distributed among these distances:
34 39 0.04
35 4 0.00
36 2 0.00
37 2 0.00
38 23 0.03
39 15 0.02
40 15 0.02
41 19 0.02
42 45 0.05
43 51 0.06
44 435 0.49
45 118 0.13
46 82 0.09
47 17 0.02
48 11 0.01
49 2 0.00
50 9 0.01
51 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTCCATAGTGATGGTTATCAAAATTTCATAGGA
Found at i:1889 original size:66 final size:66
Alignment explanation
Indices: 1808--2039 Score: 245
Period size: 66 Copynumber: 3.5 Consensus size: 66
1798 TCTTGTCTCT
** * *
1808 GTGTGGTTATTAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCAT
1 GTGTGGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCATGAGGAGGTTATCAAAATTCCAT
1873 A
66 A
* * *
1874 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTGC
1 GTGTGGTTACCAAAATTTCATA-GGATGGTTATTAAAATTTCATGAGG-AGGTTATCAAAATTCC
1937 ATA
64 ATA
* * ** *
1940 GTGTGGTTACCAAAATTCCATAGGATCAGGTTATTAAAATTTC-TTAGGGAGGTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATAGGAT--GGTTATTAAAATTTCATGA-GGAGGTTATCAAAATTC
2004 CATA
63 CATA
* * * * *
2008 GTGTGGTTATCACAATTTTATAGAAAGGTTAT
1 GTGTGGTTACCAAAATTTCATAGGATGGTTAT
2040 CAAAGAGATT
Statistics
Matches: 139, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
65 5 0.04
66 80 0.58
67 3 0.02
68 49 0.35
69 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAGGATGGTTATTAAAATTTCATGAGGAGGTTATCAAAATTCCAT
A
Found at i:2073 original size:22 final size:22
Alignment explanation
Indices: 2048--2444 Score: 141
Period size: 22 Copynumber: 17.9 Consensus size: 22
2038 ATCAAAGAGA
* *
2048 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
2070 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
2092 TTAACAAAATTTTATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
2114 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
2136 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
2158 TTATCAAAATCTCTTACG-AAGG
1 TTATCAAAATTTCATA-GTGAGG
* *
2180 TTAT-AAAAGTCTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
2205 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
2227 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
2248 TTATCGAAATTTCATAGAGATCGAA
1 TTATCAAAATTTCATAGTGA--G-G
* *
2273 TTATCAAAATTT-ATAAG-AAGA
1 TTATCAAAATTTCAT-AGTGAGG
* *
2294 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
2316 TTATCAAAATTAT-ATAATGTGA
1 TTATCAAAATT-TCATAGTGAGG
* *
2338 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * **
2360 TCAACAAAATTTTATAGAAAGG
1 TTATCAAAATTTCATAGTGAGG
***
2382 TTATCAAAATTTCATAAAAAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
2404 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
2426 TTACCGAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
2445 GTATTTCTGG
Statistics
Matches: 284, Mismatches: 65, Indels: 52
0.71 0.16 0.13
Matches are distributed among these distances:
20 9 0.03
21 33 0.12
22 201 0.71
23 8 0.03
24 4 0.01
25 20 0.07
26 5 0.02
27 4 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:2180 original size:144 final size:144
Alignment explanation
Indices: 1902--2188 Score: 341
Period size: 144 Copynumber: 2.0 Consensus size: 144
1892 CATATGGAAG
* * *
1902 TTATCAAAATTTCATGGGAAGGTTATCAAAATTGCATAGTGTGGTTACCAAAATTCCATAGGATC
1 TTATCAAAATGTCATGCGAAGGTTATCAAAATTGCATAGTGTGGTTAACAAAATTCCATAGGA--
* * ** *
1967 AGGTTATTAAAATTTCTTAGGGAGGTTATTGAAATTTCATAGTGTGGTTATCACAATTTTATAGA
64 AGGTTACTAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAGA
*
2032 AAGGTTATCAAAGAGA
129 AAGGTTATAAAAGAGA
* **
2048 TTATCAAAATGTCATAGCG-AGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTTATAAGG
1 TTATCAAAATGTCAT-GCGAAGGTTATCAA-AATTGCATAGTGTGGTTAACAAAATTCCAT-AGG
* *
2111 -AGGTTACTAATATTTCATGGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATCTCTTA-
63 AAGGTTACTAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAAT-T-TTAT
*
2174 CG-AAGGTTATAAAAG
126 AGAAAGGTTATAAAAG
2189 TCTCAATTTC
Statistics
Matches: 121, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
144 62 0.51
145 4 0.03
146 50 0.41
147 5 0.04
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (144 bp):
TTATCAAAATGTCATGCGAAGGTTATCAAAATTGCATAGTGTGGTTAACAAAATTCCATAGGAAG
GTTACTAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAGAAA
GGTTATAAAAGAGA
Found at i:2572 original size:22 final size:22
Alignment explanation
Indices: 2525--3084 Score: 180
Period size: 22 Copynumber: 25.6 Consensus size: 22
2515 TTATGGAGTA
* *
2525 ATCAAAATTTCAGA-G-AGGAT
1 ATCAAAATTTCATATGAAGGTT
2545 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
2567 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * * *
2589 TTCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* * *
2611 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGAAGGTT
*
2633 A-AAAAATTTTCATAATG-AGGTT
1 ATCAAAA-TTTCAT-ATGAAGGTT
**
2655 ATCAAAAAAATCATAGTGAA-GTT
1 ATC-AAAATTTCATA-TGAAGGTT
*
2678 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGAAGGTT
* * * *
2694 ATCAAGATTTTATAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
2716 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* *
2739 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
*
2762 ATCAAAATTTCATA-GCGAGGTT
1 ATCAAAATTTCATATG-AAGGTT
* * *
2784 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
2806 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
2828 A-CTAACTATTCATATGGAGGTT
1 ATCAAAAT-TTCATATGAAGGTT
* * * * *
2850 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
* * *
2872 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * **
2894 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
*
2917 ATCAAAATTTCAT-TGGAAAGTT
1 ATCAAAATTTCATAT-GAAGGTT
2939 ATCAAAATTTCATAGTG-AGGTCT
1 ATCAAAATTTCATA-TGAAGGT-T
* *
2962 -TCAAAATTCCTTA-GAGAGGTT
1 ATCAAAATTTCATATGA-AGGTT
* *
2983 AAT-AAAATTTCATAAGAAGGCTA
1 -ATCAAAATTTCATATGAAGG-TT
** * **
3006 AAAAAAATTT-GTAAAAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * * **
3027 CTCGAAATTCCATAGTG-TCGTT
1 ATCAAAATTTCATA-TGAAGGTT
* *
3049 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
*
3071 ATCAGAATTTCATA
1 ATCAAAATTTCATA
3085 AGGAGATCAT
Statistics
Matches: 410, Mismatches: 88, Indels: 82
0.71 0.15 0.14
Matches are distributed among these distances:
16 12 0.03
18 2 0.00
20 18 0.04
21 26 0.06
22 251 0.61
23 94 0.23
24 7 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:2929 original size:23 final size:22
Alignment explanation
Indices: 2525--2996 Score: 273
Period size: 22 Copynumber: 21.6 Consensus size: 22
2515 TTATGGAGTA
* *
2525 ATCAAAATTTC--AGAGAGGAT
1 ATCAAAATTTCATAGTGAGGTT
2545 ATCAAAATTTCATA-TGAAGGTT
1 ATCAAAATTTCATAGTG-AGGTT
*
2567 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-TGAGGTT
* * *
2589 TTCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAGTGAGGT-T
* *
2611 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGTT
* *
2633 A-AAAAATTTTCATAATGAGGTT
1 ATCAAAA-TTTCATAGTGAGGTT
** *
2655 ATCAAAAAAATCATAGTGAAGTT
1 ATC-AAAATTTCATAGTGAGGTT
2678 ATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGTGAGGTT
* *
2694 ATCAAGATTTTATAAG-GAGGTT
1 ATCAAAATTTCAT-AGTGAGGTT
* *
2716 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGTGAGG-TT
*
2739 ATCAAAATTTTATAG-GAAGGTTT
1 ATCAAAATTTCATAGTG-AGG-TT
*
2762 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
2784 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* * *
2806 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* *
2828 A-CTAACTATTCATA-TGGAGGTT
1 ATCAAAAT-TTCATAGT-GAGGTT
* * * ** *
2850 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
* *
2872 ATCAATATATCATA-TGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
* * *
2894 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* *
2917 ATCAAAATTTCATTG-GAAAGTT
1 ATCAAAATTTCATAGTG-AGGTT
2939 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGTGAGGT-T
* * *
2962 -TCAAAATTCCTTAGAGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
2983 AAT-AAAATTTCATA
1 -ATCAAAATTTCATA
2997 AGAAGGCTAA
Statistics
Matches: 356, Mismatches: 63, Indels: 64
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 2 0.01
19 2 0.01
20 12 0.03
21 19 0.05
22 223 0.63
23 80 0.22
24 6 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:3096 original size:22 final size:22
Alignment explanation
Indices: 3054--3096 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3044 TCGTTATTAA
* *
3054 AATTTCATAGGAAGGTTATCAG
1 AATTTCATAGGAAGATCATCAG
3076 AATTTCATAAGG-AGATCATCA
1 AATTTCAT-AGGAAGATCATCA
3097 AAAATAGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (22 bp):
AATTTCATAGGAAGATCATCAG
Found at i:5528 original size:15 final size:15
Alignment explanation
Indices: 5490--5528 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5480 ATCTTTAATG
*
5490 TAAACATAT-ATAAA
1 TAAACAAATAATAAA
5504 TAAA-AAATAATAAA
1 TAAACAAATAATAAA
5518 TAAACAAATAA
1 TAAACAAATAA
5529 ATAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 13 0.59
15 6 0.27
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACAAATAATAAA
Found at i:6002 original size:49 final size:49
Alignment explanation
Indices: 5925--6025 Score: 166
Period size: 49 Copynumber: 2.1 Consensus size: 49
5915 ATATCCTTCG
* *
5925 TTATTTTTAACTTTTAAGGTTTAATATGTAATTTTATTAATCAATTAAA
1 TTATCTTTAACTTTTAAAGTTTAATATGTAATTTTATTAATCAATTAAA
* *
5974 TTATCTTTAACTTTTAAAGTTTCATATGTAATTTTATTTATCAATTAAA
1 TTATCTTTAACTTTTAAAGTTTAATATGTAATTTTATTAATCAATTAAA
6023 TTA
1 TTA
6026 AATATATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (49 bp):
TTATCTTTAACTTTTAAAGTTTAATATGTAATTTTATTAATCAATTAAA
Found at i:8962 original size:13 final size:12
Alignment explanation
Indices: 8920--8964 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
8910 TCATGCACCC
8920 AAAACAATTTATTT
1 AAAACAATTTA--T
*
8934 AAAACCATTTAT
1 AAAACAATTTAT
8946 AAAACAATTTGAT
1 AAAACAATTT-AT
8959 AAAACA
1 AAAACA
8965 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 8 0.29
14 10 0.36
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (12 bp):
AAAACAATTTAT
Found at i:10405 original size:6 final size:6
Alignment explanation
Indices: 10394--10442 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
10384 AGCCCATTCA
*
10394 TTCTTT TTCTTT TTCTTTCT TTCTCT TTCTTT TT-TTT TT-TTT TT-TTT
1 TTCTTT TTCTTT TTC-TT-T TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
10441 TT
1 TT
10443 TTTAAAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 15 0.38
6 17 0.44
7 3 0.08
8 4 0.10
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTCTTT
Found at i:10414 original size:10 final size:9
Alignment explanation
Indices: 10397--10445 Score: 57
Period size: 8 Copynumber: 5.4 Consensus size: 9
10387 CCATTCATTC
10397 TTTTTCTTT
1 TTTTTCTTT
10406 TTCTTTCTTT
1 TT-TTTCTTT
*
10416 CTCTTTCTTT
1 -TTTTTCTTT
10426 TTTTT-TTT
1 TTTTTCTTT
10434 TTTTT-TTT
1 TTTTTCTTT
10442 TTTT
1 TTTT
10446 AAAGTTTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 15 0.42
9 6 0.17
10 14 0.39
11 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Done.