Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020175.1 Corchorus olitorius cultivar O-4 contig20208, 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: 55771
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:199 original size:22 final size:22
Alignment explanation
Indices: 154--202 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
144 CACGCGCGGA
*
154 TCGCGACCCGCCATGGTCCGGG
1 TCGCGACCCGCCATGGTCCAGG
176 TCGCGACCCGCCATGG-CTCAGG
1 TCGCGACCCGCCATGGTC-CAGG
198 TCGCG
1 TCGCG
203 CGTGACCCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.10, C:0.41, G:0.35, T:0.14
Consensus pattern (22 bp):
TCGCGACCCGCCATGGTCCAGG
Found at i:249 original size:13 final size:14
Alignment explanation
Indices: 231--259 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
221 CCGCCATCTA
231 TTTCTG-GTTTTTT
1 TTTCTGTGTTTTTT
244 TTTCTGTGTTTTTT
1 TTTCTGTGTTTTTT
258 TT
1 TT
260 AATCTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.00, C:0.07, G:0.14, T:0.79
Consensus pattern (14 bp):
TTTCTGTGTTTTTT
Found at i:1930 original size:24 final size:23
Alignment explanation
Indices: 1764--1938 Score: 113
Period size: 22 Copynumber: 7.9 Consensus size: 23
1754 GTCTCTGTGT
*
1764 GGTTATCAAAATTTCATA--AGA
1 GGTTATCAAAATTTCATAGGTGA
* *
1785 TGGTTATTATAATTTCAT-GAGT-A
1 -GGTTATCAAAATTTCATAG-GTGA
*
1808 GGTTATCAAAATTCCATAGTGTGA
1 GGTTATCAAAATTTCATAG-GTGA
* *
1832 --TTA-GAAAATTTCATATG-GA
1 GGTTATCAAAATTTCATAGGTGA
* *
1851 AGTTATCAAAATTTCAT-GGGGA
1 GGTTATCAAAATTTCATAGGTGA
*
1873 GGTTATCAAAATTTTATAGTGTGA
1 GGTTATCAAAATTTCATAG-GTGA
*
1897 --TTACCAAAATTTCATAGGATCG-
1 GGTTATCAAAATTTCATAGG-T-GA
*
1919 GGTTATCAAAATTTCTTAGG
1 GGTTATCAAAATTTCATAGG
1939 AAGATTATTG
Statistics
Matches: 119, Mismatches: 19, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
19 2 0.02
20 1 0.01
21 15 0.13
22 75 0.63
23 6 0.05
24 20 0.17
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (23 bp):
GGTTATCAAAATTTCATAGGTGA
Found at i:1945 original size:46 final size:45
Alignment explanation
Indices: 1836--1959 Score: 114
Period size: 46 Copynumber: 2.8 Consensus size: 45
1826 GTGTGATTAG
* *
1836 AAAATTTCATATGGAAG-TTATCAAAATTTCAT-GGGGAGGTTATC
1 AAAATTTCTTA-GGAAGATTATCAAAATTTCATAGGCGAGGTTATC
* *
1880 AAAATTT-TATAGTG-TGATTACCAAAATTTCATAGGATCG-GGTTATC
1 AAAATTTCT-TAG-GAAGATTATCAAAATTTCATAGG--CGAGGTTATC
**
1926 AAAATTTCTTAGGAAGATTATTGAAATTTCATAG
1 AAAATTTCTTAGGAAGATTATCAAAATTTCATAG
1960 TATTATCACA
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
43 2 0.03
44 24 0.38
45 3 0.05
46 33 0.52
47 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (45 bp):
AAAATTTCTTAGGAAGATTATCAAAATTTCATAGGCGAGGTTATC
Found at i:1953 original size:68 final size:65
Alignment explanation
Indices: 1810--1960 Score: 169
Period size: 68 Copynumber: 2.3 Consensus size: 65
1800 CATGAGTAGG
* * * * *
1810 TTATCAAAATTCCATAGTGTGATTAGAAAATTTCATATGGAAGTTATCAAAATTTCATGGGGAGG
1 TTATCAAAATTTCATAGTGTGATTACAAAATTTCATATGGAAGTTATCAAAATTTCATAGGAAGA
* * *
1875 TTATCAAAATTTTATAGTGTGATTACCAAAATTTCATA-GGATCGGGTTATCAAAATTTCTTAGG
1 TTATCAAAATTTCATAGTGTGATTA-CAAAATTTCATATGGA---AGTTATCAAAATTTCATAGG
1939 AAGA
62 AAGA
**
1943 TTATTGAAATTTCATAGT
1 TTATCAAAATTTCATAGT
1961 ATTATCACAA
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
65 26 0.37
66 11 0.15
68 34 0.48
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (65 bp):
TTATCAAAATTTCATAGTGTGATTACAAAATTTCATATGGAAGTTATCAAAATTTCATAGGAAGA
Found at i:2022 original size:22 final size:21
Alignment explanation
Indices: 1997--2388 Score: 125
Period size: 22 Copynumber: 17.7 Consensus size: 21
1987 ATCAAAGAGA
*
1997 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
2019 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
* * *
2041 TTAACAAAATTGCATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
*
2063 TTA-CTAATATTTCATGAGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
*
2085 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
*
2107 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
**
2129 TTTTAAAAGTCTCAATTTCATA--AGG
1 --TT---A-TCAAAATTTCATAGGAGG
* * * *
2154 AGTACCAAAATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
*
2176 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
* * * *
2196 ATATCGAAATTTTATCGAGATCGG
1 TTATCAAAATTTCATAG-GA--GG
* *
2220 ATTATCGAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATAGG-AGG
* **
2242 TTGTCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
2264 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* *** *
2286 TTATCAAAATTACATAATCTGA
1 TTATCAAAATTTCAT-AGGAGG
*
2308 TTATCAAAATTTCATAGAGGGGG
1 TTATCAAAATTTCAT--AGGAGG
* * *
2331 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
2353 TTA-CAAAAAATTCATAAAGAGA
1 TTATC-AAAATTTCAT-AGGAGG
*
2375 TTATCAAATTTTCA
1 TTATCAAAATTTCA
2389 AAATGTGATT
Statistics
Matches: 271, Mismatches: 68, Indels: 62
0.68 0.17 0.15
Matches are distributed among these distances:
19 2 0.01
20 22 0.08
21 29 0.11
22 156 0.58
23 27 0.10
24 8 0.03
25 15 0.06
27 1 0.00
28 11 0.04
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:2119 original size:44 final size:43
Alignment explanation
Indices: 1997--2969 Score: 271
Period size: 44 Copynumber: 22.6 Consensus size: 43
1987 ATCAAAGAGA
* *
1997 TTATCAAAATGTCATAGCGAGGTTAT-AAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTATCAA-AATTTCATAGTGAGG
* * * *
2041 TTAACAAAATTGCATAAGAAGGTTA-CTAATATTTCATGAG-GAGG
1 TTATCAAAATTTCAT-AGGAGGTTATC-AAAATTTCAT-AGTGAGG
*
2085 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGTG-AGG
** * * *
2129 TTTTAAAAGTCTCAATTTCATAAGGA-G-TACCAAAATTTGATAG-AAGG
1 --TT---A-TCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGTGAGG
* * * * * *
2176 TTATC-AAATCTCATA-GAGTGATATCGAAATTTTATCGAGATCGG
1 TTATCAAAATTTCATAGGAG-GTTATCAAAATTTCATAGTGA--GG
* * * **
2220 ATTATCGAAATTT-ATAGGAAGATTGTCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGG-AGGTTATCAAAATTTCATAGTGAGG
* * * ** *
2264 TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATCTGA
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGTGAGG
* * * * *
2308 TTATCAAAATTTCATAGAGGGGGTCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCAT--AGGAGGTTATCAAAATTTCATAGTGAGG
* * * * * * * *
2353 TTA-CAAAAAATTCATAAAGAGATTATCAAATTTTCAAAATGTGA
1 TTATC-AAAATTTCAT-AGGAGGTTATCAAAATTTCATAGTGAGG
* * *
2397 TTACCAAAATTTCATA-GTGG---T----ATTTC-TAGGGAGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGTGAGG
* *
2431 TTATCAAAATTTCATAGTATGGTTA-CCAAA--T--TAG-GAAGG
1 TTATCAAAATTTCATAGGA-GGTTATCAAAATTTCATAGTG-AGG
* * * * * *
2470 TTATTAAACTTTTATTATGGA-GTAATCAAAGTTTCATA-TGATAG
1 TTATCAAAATTTCA-TA-GGAGGTTATCAAAATTTCATAGTGA-GG
* * *
2514 TTATCAAAATTTCATAGTTTA-GTTTTCAAATTTTCATA---A-G
1 TTATCAAAATTTCATAG--GAGGTTATCAAAATTTCATAGTGAGG
* * * *
2554 --AGCAAAATTTCATAGTAGGTAGATCAAAATTTCATA-TAGAGA
1 TTATCAAAATTTCATAGGAGGT-TATCAAAATTTCATAGT-GAGG
* * * *** *
2596 TTAACAAAATTTCATAATGAGATTATCAAAAAACCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGTGAGG
* *
2640 TTATCAAAA-TT--T-GTA-GTTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTCAT-AGTGAGG
* *
2678 TTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAG-GAAGG
1 TTATCAAAATTTCATA-GGAGG-TTATCAAAATTTCATAGTG-AGG
* * * *
2723 TTTATCAAAATTTCATAGCGAGGTTATCACAACTTCATAGTGTGA
1 -TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGTGAGG
* *
2768 TTATCAAAATTTC--A-GAGTGTGATCACTAACAATTCATA-TGGAGG
1 TTATCAAAATTTCATAGGAG-GTTATCA--AA-ATTTCATAGT-GAGG
* * * * * * *
2812 TTTTTAAATTTTCATAACGTGGTTATCAATATATCATA-TGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATAGT-GAGG
* * * * * * *
2856 TTATCAACATCTCATAGTGTTGGTCATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCATAG-G-AGGTTATCAAAATTTCATAGTGAGG
* * *
2901 TTATCAAAATTTCATAGCGAGGTCT-TCAAAATTCCTTAGGGAGG
1 TTATCAAAATTTCATAG-GAGGT-TATCAAAATTTCATAGTGAGG
* *
2945 TTAACAAAATTTCATAAGAAGGTTA
1 TTATCAAAATTTCAT-AGGAGGTTA
2970 AAAAAATTAT
Statistics
Matches: 676, Mismatches: 163, Indels: 180
0.66 0.16 0.18
Matches are distributed among these distances:
34 18 0.03
35 4 0.01
36 4 0.01
37 2 0.00
38 53 0.08
39 27 0.04
40 18 0.03
41 25 0.04
42 9 0.01
43 27 0.04
44 284 0.42
45 120 0.18
46 43 0.06
47 12 0.02
48 15 0.02
49 2 0.00
50 11 0.02
51 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGTGAGG
Found at i:2362 original size:23 final size:23
Alignment explanation
Indices: 2312--2373 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
2302 ATCTGATTAT
*
2312 CAAAATTTCATAGAGGGGGTCAA
1 CAAAATTTCATAGAGAGGGTCAA
* *
2335 CAAAATTTTATAGAGAGGTTACAA
1 CAAAATTTCATAGAGAGGGT-CAA
*
2359 -AAAA-TTCATAAAGAG
1 CAAAATTTCATAGAGAG
2374 ATTATCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 9 0.27
23 21 0.64
24 3 0.09
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (23 bp):
CAAAATTTCATAGAGAGGGTCAA
Found at i:2519 original size:22 final size:22
Alignment explanation
Indices: 2494--2611 Score: 67
Period size: 22 Copynumber: 5.6 Consensus size: 22
2484 TTATGGAGTA
*
2494 ATCAAAGTTTCATA-TGATAGTT
1 ATCAAAATTTCATAGT-ATAGTT
*
2516 ATCAAAATTTCATAGTTTAGTT
1 ATCAAAATTTCATAGTATAGTT
* *
2538 TTCAAATTTTC--A-TA-AG--
1 ATCAAAATTTCATAGTATAGTT
*
2554 AGCAAAATTTCATAGTAGGTAG--
1 ATCAAAATTTCATAGTA--TAGTT
*
2576 ATCAAAATTTCATA-TAGAGATT
1 ATCAAAATTTCATAGTATAG-TT
*
2598 AACAAAATTTCATA
1 ATCAAAATTTCATA
2612 ATGAGATTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
16 8 0.11
18 3 0.04
19 5 0.07
20 1 0.01
21 2 0.03
22 55 0.73
23 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGTATAGTT
Found at i:2683 original size:22 final size:21
Alignment explanation
Indices: 2556--3061 Score: 208
Period size: 22 Copynumber: 23.2 Consensus size: 21
2546 TTCATAAGAG
* *
2556 CAAAATTTCATAGTAGGTAGAT
1 CAAAATTTCATAGGAGGT-TAT
* * *
2578 CAAAATTTCATATAGAGATTAA
1 CAAAATTTCATA-GGAGGTTAT
* *
2600 CAAAATTTCATAATGAGATTAT
1 CAAAATTTCAT-AGGAGGTTAT
***
2622 CAAAAAACCATAGGGAGGTTAT
1 CAAAATTTCATA-GGAGGTTAT
*
2644 CAAAA-TT--T-GTA-GTTAT
1 CAAAATTTCATAGGAGGTTAT
*
2660 CAAGATTTCATAAGGAGGTTAT
1 CAAAATTTCAT-AGGAGGTTAT
*
2682 CAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATA-GGAGG-TTAT
*
2705 CAAAATTTTATAGGAAGGTTTAT
1 CAAAATTTCATAGG-AGG-TTAT
2728 CAAAATTTCATAGCGAGGTTAT
1 CAAAATTTCATAG-GAGGTTAT
* * * *
2750 CACAACTTCATAGTGTGATTAT
1 CAAAATTTCATAG-GAGGTTAT
*
2772 CAAAATTTC--A-GAGTGTGAT
1 CAAAATTTCATAGGAG-GTTAT
* *
2791 CACTAACAATTCATATGGAGGTTTT
1 CA--AA-ATTTCATA-GGAGGTTAT
* * * *
2816 TAAATTTTCATAACGTGGTTAT
1 CAAAATTTCAT-AGGAGGTTAT
* *
2838 CAATATATCATATGGAGGTTAT
1 CAAAATTTCATA-GGAGGTTAT
* * * *
2860 CAACATCTCATAGTGTTGGTCAT
1 CAAAATTTCATAG-G-AGGTTAT
* *
2883 CAAAATTTCATTGGGAAGTTAT
1 CAAAATTTCA-TAGGAGGTTAT
2905 CAAAATTTCATAGCGAGGTCT-T
1 CAAAATTTCATAG-GAGGT-TAT
* * *
2927 CAAAATTCCTTAGGGAGGTTAA
1 CAAAATTTCATA-GGAGGTTAT
*
2949 CAAAATTTCATAAGAAGGTTA-
1 CAAAATTTCAT-AGGAGGTTAT
* * ** *
2970 AAAAAATT-ATAAAAAGGTTCT
1 CAAAATTTCAT-AGGAGGTTAT
* ** *
2991 CGAAATTTCATAATATCGTTATT
1 CAAAATTTCATAGGA-GGTTA-T
* *
3014 GAAAA-TTCATAGGAATGTTAT
1 CAAAATTTCATAGG-AGGTTAT
* *
3035 CAAAATTTCATAAGGAGATCAT
1 CAAAATTTCAT-AGGAGGTTAT
3057 CAAAA
1 CAAAA
3062 ATACTGTAAT
Statistics
Matches: 364, Mismatches: 82, Indels: 76
0.70 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
18 2 0.01
19 7 0.02
20 11 0.03
21 30 0.08
22 219 0.60
23 71 0.20
24 4 0.01
25 4 0.01
26 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (21 bp):
CAAAATTTCATAGGAGGTTAT
Found at i:2708 original size:23 final size:22
Alignment explanation
Indices: 2556--2969 Score: 227
Period size: 22 Copynumber: 19.0 Consensus size: 22
2546 TTCATAAGAG
* *
2556 CAAAATTTCATA-GTAGGTAGAT
1 CAAAATTTCATAGGGAGGT-TAT
** * *
2578 CAAAATTTCATATAGAGATTAA
1 CAAAATTTCATAGGGAGGTTAT
** *
2600 CAAAATTTCATAATGAGATTAT
1 CAAAATTTCATAGGGAGGTTAT
***
2622 CAAAAAACCATAGGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*
2644 CAAAA-TT--T--GTA-GTTAT
1 CAAAATTTCATAGGGAGGTTAT
* *
2660 CAAGATTTCATAAGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*
2682 CAAAATTTTATAGGGAGGTTTAT
1 CAAAATTTCATAGGGAGG-TTAT
* *
2705 CAAAATTTTATAGGAAGGTTTAT
1 CAAAATTTCATAGGGAGG-TTAT
*
2728 CAAAATTTCATAGCGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * * * *
2750 CACAACTTCATAGTGTGATTAT
1 CAAAATTTCATAGGGAGGTTAT
* * * * *
2772 CAAAATTTCAGAGTGTGATCA-
1 CAAAATTTCATAGGGAGGTTAT
* *
2793 CTAACAA-TTCATATGGAGGTTTT
1 C-AA-AATTTCATAGGGAGGTTAT
* * ** *
2816 TAAATTTTCATAACGTGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * *
2838 CAATATATCATATGGAGGTTAT
1 CAAAATTTCATAGGGAGGTTAT
* * ** *
2860 CAACATCTCATAGTGTTGGTCAT
1 CAAAATTTCATAG-GGAGGTTAT
* *
2883 CAAAATTTCATTGGGAAGTTAT
1 CAAAATTTCATAGGGAGGTTAT
*
2905 CAAAATTTCATAGCGAGGTCT-T
1 CAAAATTTCATAGGGAGGT-TAT
* * *
2927 CAAAATTCCTTAGGGAGGTTAA
1 CAAAATTTCATAGGGAGGTTAT
* *
2949 CAAAATTTCATAAGAAGGTTA
1 CAAAATTTCATAGGGAGGTTA
2970 AAAAAATTAT
Statistics
Matches: 298, Mismatches: 79, Indels: 30
0.73 0.19 0.07
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
21 5 0.02
22 215 0.72
23 63 0.21
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAT
Found at i:2981 original size:20 final size:22
Alignment explanation
Indices: 2942--2988 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
2932 TTCCTTAGGG
* *
2942 AGGTTAACAAAATTTCATAAGA
1 AGGTTAACAAAAATTCATAAAA
2964 AGGTTAA-AAAAATT-ATAAAA
1 AGGTTAACAAAAATTCATAAAA
2984 AGGTT
1 AGGTT
2989 CTCGAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (22 bp):
AGGTTAACAAAAATTCATAAAA
Found at i:5302 original size:15 final size:15
Alignment explanation
Indices: 5257--5316 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
5247 CTGATCAACC
5257 AACCCAACCCATCCC-
1 AACCC-ACCCATCCCA
* * *
5272 AGCCAACCCAAACCCA
1 AACCCACCC-ATCCCA
*
5288 AACCCACCTATCCCA
1 AACCCACCCATCCCA
*
5303 AATCCACCCATCCC
1 AACCCACCCATCCC
5317 TACCATTCAA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
14 4 0.12
15 24 0.71
16 6 0.18
ACGTcount: A:0.35, C:0.55, G:0.02, T:0.08
Consensus pattern (15 bp):
AACCCACCCATCCCA
Found at i:6386 original size:8 final size:8
Alignment explanation
Indices: 6346--6538 Score: 75
Period size: 8 Copynumber: 24.5 Consensus size: 8
6336 AAATAATAAT
6346 AATA-ATA
1 AATAGATA
*
6353 AAAAGATA
1 AATAGATA
*
6361 AATAGGTA
1 AATAGATA
* *
6369 TAGAGATA
1 AATAGATA
*
6377 AATTGATA
1 AATAGATA
6385 AATAGATA
1 AATAGATA
* *
6393 CAGAGA-A
1 AATAGATA
6400 TAATAGATA
1 -AATAGATA
*
6409 AATAGGTA
1 AATAGATA
* *
6417 AGTA-AAA
1 AATAGATA
**
6424 AAGGGATAA
1 AATAGAT-A
*
6433 TAATAAATA
1 -AATAGATA
*
6442 AATGGAT-
1 AATAGATA
*
6449 AATAGCTA
1 AATAGATA
6457 AATTA-ATA
1 AA-TAGATA
*
6465 AAAAGATA
1 AATAGATA
6473 AATAGTAAATA
1 AATAG---ATA
6484 AATAGAT-
1 AATAGATA
*
6491 AATAGTTA
1 AATAGATA
6499 AATTA-ATA
1 AA-TAGATA
6507 AATA-A-A
1 AATAGATA
6513 AA-AGATA
1 AATAGATA
6520 AATAG-TA
1 AATAGATA
*
6527 AATAAATA
1 AATAGATA
6535 AATA
1 AATA
6539 ATAGTTAAAT
Statistics
Matches: 133, Mismatches: 35, Indels: 35
0.66 0.17 0.17
Matches are distributed among these distances:
5 1 0.01
6 4 0.03
7 30 0.23
8 79 0.59
9 7 0.05
10 4 0.03
11 8 0.06
ACGTcount: A:0.61, C:0.01, G:0.13, T:0.25
Consensus pattern (8 bp):
AATAGATA
Found at i:6487 original size:4 final size:4
Alignment explanation
Indices: 6455--6539 Score: 52
Period size: 4 Copynumber: 21.8 Consensus size: 4
6445 GGATAATAGC
* * * **
6455 TAAA TTAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGA T-AA TAGT TAAA
1 TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
6501 TTAA TAAA TAAA AAAGA TAAA T-AG TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAA
6540 TAGTTAAATT
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
3 8 0.14
4 46 0.78
5 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:6506 original size:19 final size:18
Alignment explanation
Indices: 6428--6553 Score: 63
Period size: 19 Copynumber: 7.0 Consensus size: 18
6418 GTAAAAAAGG
* *
6428 GATAATAATAAATAAATG
1 GATAATAGTAAATAAATA
*
6446 GATAATAGCTAAATTAATAAAAA
1 GATAATAG-T--A--AATAAATA
6469 GATAAATAGTAAATAAATA
1 GAT-AATAGTAAATAAATA
6488 GATAATAGT---TAAATTA
1 GATAATAGTAAATAAA-TA
6504 -ATAA-A-T-AA-AAA-A
1 GATAATAGTAAATAAATA
6516 GATAAATAGTAAATAAATA
1 GAT-AATAGTAAATAAATA
* *
6535 AATAATAGTTAAATTAATA
1 GATAATAG-TAAATAAATA
6554 AAAAAAATCT
Statistics
Matches: 85, Mismatches: 6, Indels: 33
0.69 0.05 0.27
Matches are distributed among these distances:
12 1 0.01
13 3 0.04
14 6 0.07
15 9 0.11
16 3 0.04
17 2 0.02
18 21 0.25
19 23 0.27
21 2 0.02
23 10 0.12
24 5 0.06
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.29
Consensus pattern (18 bp):
GATAATAGTAAATAAATA
Found at i:6526 original size:47 final size:47
Alignment explanation
Indices: 6431--6560 Score: 182
Period size: 47 Copynumber: 2.9 Consensus size: 47
6421 AAAAAGGGAT
* * *
6431 AATAATAAATAAATGGATAATAGCTAAA-T--T-AAT-AAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAAGATA
6473 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAAGATA
*
6520 AATAGTAAATAAATAAATAATAGTTAAATTAATAAA-AAAAA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAA
6561 TCTTTTTAGT
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
42 25 0.32
43 1 0.01
45 1 0.01
46 8 0.10
47 44 0.56
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.27
Consensus pattern (47 bp):
AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAAGATA
Found at i:6528 original size:28 final size:28
Alignment explanation
Indices: 6478--6539 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
6468 AGATAAATAG
* *
6478 TAAAT-AAATAGATAATAGTTAAATTAA
1 TAAATAAAAAAGATAATAGTTAAATAAA
6505 TAAATAAAAAAGATAAATAG-TAAATAAA
1 TAAATAAAAAAGAT-AATAGTTAAATAAA
6533 TAAATAA
1 TAAATAA
6540 TAGTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 5 0.16
28 21 0.68
29 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.27
Consensus pattern (28 bp):
TAAATAAAAAAGATAATAGTTAAATAAA
Found at i:6548 original size:15 final size:15
Alignment explanation
Indices: 6429--6541 Score: 70
Period size: 15 Copynumber: 7.4 Consensus size: 15
6419 TAAAAAAGGG
6429 ATAAT-AATAAATAA
1 ATAATAAATAAATAA
* **
6443 ATGGAT-AATAGCTAA
1 AT-AATAAATAAATAA
6458 ATTAATAAA-AAGATAA
1 A-TAATAAATAA-ATAA
* *
6474 ATAGTAAATAAATAG
1 ATAATAAATAAATAA
** *
6489 ATAATAGTTAAATTA
1 ATAATAAATAAATAA
*
6504 ATAAATAAAAAAGATAA
1 AT-AATAAATAA-ATAA
*
6521 ATAGTAAATAAATAA
1 ATAATAAATAAATAA
6536 ATAATA
1 ATAATA
6542 GTTAAATTAA
Statistics
Matches: 72, Mismatches: 20, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
14 2 0.03
15 43 0.60
16 22 0.31
17 5 0.07
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (15 bp):
ATAATAAATAAATAA
Found at i:6554 original size:19 final size:18
Alignment explanation
Indices: 6473--6555 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 18
6463 TAAAAAGATA
*
6473 AATAGTAAATAAATAGAT
1 AATAGTAAATAAATAAAT
*
6491 AATAGT---TAAATTAAT
1 AATAGTAAATAAATAAAT
* *
6506 AA-A-TAAA-AAAGATA-
1 AATAGTAAATAAATAAAT
6520 AATAGTAAATAAATAAAT
1 AATAGTAAATAAATAAAT
*
6538 AATAGTTAAATTAATAAA
1 AATAG-TAAATAAATAAA
6556 AAAAATCTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
13 1 0.02
14 3 0.06
15 14 0.29
16 4 0.08
17 5 0.10
18 11 0.22
19 11 0.22
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (18 bp):
AATAGTAAATAAATAAAT
Found at i:7822 original size:24 final size:25
Alignment explanation
Indices: 7777--7823 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
7767 CCACCACTAA
**
7777 ACCCTAGACTTCATTAGTTTTTTAT
1 ACCCTAGACTTCATTACCTTTTTAT
*
7802 ACCCTAGAC-TCATTCCCTTTTT
1 ACCCTAGACTTCATTACCTTTTT
7824 GGGTTTGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.21, C:0.28, G:0.06, T:0.45
Consensus pattern (25 bp):
ACCCTAGACTTCATTACCTTTTTAT
Found at i:8256 original size:54 final size:53
Alignment explanation
Indices: 8121--9148 Score: 913
Period size: 54 Copynumber: 19.0 Consensus size: 53
8111 TTCTTAATCA
* * *
8121 ACCGCACTGGATCTTTTAAGATTCAAC-CTTGATCA-CGAAAACCTTCCTTGGAATG
1 ACCGCACTGGATCATTGAGGA-TCAACTC-TGATCATCGAAAA-CTT-CTTGGAATG
* * ** * * *
8176 ATCGCATTGGATCCAATTGAAAATCAACTCTGATCATCAAAAACGTCTTTGAATG
1 ACCGCACTGGAT-C-ATTGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * * * * * *
8231 ACTGCACTGTATCAATTGAAGATCAACTATGATCATTGAAAATTTCTTGGAAAG
1 ACCGCACTGGATC-ATTGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * * **
8285 ACCGCACTAGATCATCTG-GGATCAACTTTGATCTTTAAAAACTTCTTGGAATG
1 ACCGCACTGGATCAT-TGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * *
8338 ACCGCACTGGATCATTTGGGGATCAACTCTGATCATTGAAAACTTCTTGGATTG
1 ACCGCACTGGATCA-TTGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * * * *
8392 ACCGCAAAT-GTTCAATT-AGAGATCAACTCTAATCATCAAAAACTTCTTAGAATG
1 ACCGC-ACTGGATC-ATTGAG-GATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * * * * *
8446 ATCGCACCGAATCATTTAGGAGCAACTCTGATCATTGAAAACTTCTTGGAATG
1 ACCGCACTGGATCATTGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * *
8499 ACCACACTGGATCAATCTG-GGATTAACTCTAATCATCGAAAACTTCTTGGAATG
1 ACCGCACTGGATC-AT-TGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * * *
8553 ACCACACTAGATCAATCTGA-GATCAACTTTGATCATCAAAAACTTCTTGGAACT-
1 ACCGCACTGGATC-AT-TGAGGATCAACTCTGATCATCGAAAACTTCTTGGAA-TG
* * * * * *
8607 TCCTCACTAGATC-TTCTAGAGATCAACTCTGATCATCGAAAATTTTTTGGAATG
1 ACCGCACTGGATCATT-GAG-GATCAACTCTGATCATCGAAAACTTCTTGGAATG
*
8661 ACCGCACTGGATCATCT-AGGGATCAACTTTGATCA-CTGAAAACTTCTTTGGAATG
1 ACCGCACTGGATCAT-TGA-GGATCAACTCTGATCATC-GAAAACTTC-TTGGAATG
**
8716 ACCGCACTGGATCATCT-AGGGATCAACTCTGATCAAAGAAAACTTCTTGGAATG
1 ACCGCACTGGATCAT-TGA-GGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * *
8770 ACCACACTGGATCAATTG-GATATCAACTCTGATCATCGAAAACTTTTTGGAATG
1 ACCGCACTGGATC-ATTGAG-GATCAACTCTGATCATCGAAAACTTCTTGGAATG
*
8824 ACCGCACTGGATCATTTAGGGATCAACTCTGATCA-CTGAAAACTTCTTTGGAATG
1 ACCGCACTGGATCATTGA-GGATCAACTCTGATCATC-GAAAACTTC-TTGGAATG
* ** * *
8879 ACCGCACTAGATCATCT-AGGGATCAACTCTGATCAAAGAAAACTTATTAGAATG
1 ACCGCACTGGATCAT-TGA-GGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * *
8933 ACCGCACTGGATCTTTG-GCGATCAACTCTGACCATTGAAAACTTCTTGGAATG
1 ACCGCACTGGATCATTGAG-GATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * * *
8986 ACCGCACTGGATCTTTTGGGGATCAACTCTGACCATTGAAAACTTCTTGGAATG
1 ACCGCACTGGATC-ATTGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
* * * **
9040 ATCGCACTGGATCTTTTG-GCGATCAACATCTGACCATAAAAAACTTCTTGGAATG
1 ACCGCACTGGATC-ATTGAG-GATCAAC-TCTGATCATCGAAAACTTCTTGGAATG
* *
9095 ACCGCACTGGATCTTTG-GCGATCAACTCTGATCATTGAAAACTTCTTGGAATG
1 ACCGCACTGGATCATTGAG-GATCAACTCTGATCATCGAAAACTTCTTGGAATG
9148 A
1 A
9149 GATCAACTCT
Statistics
Matches: 824, Mismatches: 108, Indels: 84
0.81 0.11 0.08
Matches are distributed among these distances:
51 1 0.00
52 3 0.00
53 165 0.20
54 455 0.55
55 173 0.21
56 16 0.02
57 11 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (53 bp):
ACCGCACTGGATCATTGAGGATCAACTCTGATCATCGAAAACTTCTTGGAATG
Found at i:9245 original size:37 final size:37
Alignment explanation
Indices: 9114--9747 Score: 845
Period size: 37 Copynumber: 17.4 Consensus size: 37
9104 GATCTTTGGC
** * *
9114 GATCAACTCTGATCAT--TGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
9149 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-AAAAAAAACTTCTTGAAACGA
9187 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-AAAAAAAACTTCTTGAAACGA
* *
9225 GATCAACTTTGATCATAAAAAAAA-TTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
*
9261 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAAAACTTCTTGAAACGA
** *
9299 GATCAACTCTGATC--AACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
9334 GATCAACTCTGATCAT---AAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
*
9368 GATCAACTCTGATCATAAAAAACAA-TTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAA-AACTTCTTGAAACGA
*
9405 GATCAACTCTGATCATAAAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT--AAAAAAAACTTCTTGAAACGA
** *
9444 GATCAACTCTGATC--AACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
9479 GATCAACTCTGATCAT--AAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
9514 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
9551 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-AAAAAAAACTTCTTGAAACGA
*
9589 GATCAACTCTGATCATAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
* *
9626 GAACAACTCTGATCAT---AAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
* * *
9660 GATCAACTTTGATCATAAAAAAAACTTATTGAAATGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
* ** * *
9697 GAACAACTCTGATCAT--CGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
9732 GATCAACTCTGATCAT
1 GATCAACTCTGATCAT
9748 CGAAAACTTC
Statistics
Matches: 542, Mismatches: 35, Indels: 44
0.87 0.06 0.07
Matches are distributed among these distances:
34 63 0.12
35 142 0.26
36 26 0.05
37 146 0.27
38 134 0.25
39 31 0.06
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (37 bp):
GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
Found at i:9763 original size:35 final size:36
Alignment explanation
Indices: 9114--9760 Score: 819
Period size: 35 Copynumber: 17.8 Consensus size: 36
9104 GATCTTTGGC
** * *
9114 GATCAACTCTGATCAT-TGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
9149 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT--AAAAAAACTTCTTGAAACGA
9187 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT--AAAAAAACTTCTTGAAACGA
* * *
9225 GATCAACTTTGATCATAAAAAAAATTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
*
9261 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT--AAAAAAACTTCTTGAAACGA
** *
9299 GATCAACTCTGATCA-ACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
9334 GATCAACTCTGATCAT--AAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
* *
9368 GATCAACTCTGATCATAAAAAACAATTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAA-ACTTCTTGAAACGA
*
9405 GATCAACTCTGATCATAAAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT---AAAAAAACTTCTTGAAACGA
** *
9444 GATCAACTCTGATCA-ACGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
9479 GATCAACTCTGATCAT-AAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
9514 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-AAAAAAACTTCTTGAAACGA
9551 GATCAACTCTGATCATAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT--AAAAAAACTTCTTGAAACGA
*
9589 GATCAACTCTGATCATAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAAACTTCTTGAAACGA
* *
9626 GAACAACTCTGATCAT--AAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
* * *
9660 GATCAACTTTGATCATAAAAAAAACTTATTGAAATGA
1 GATCAACTCTGATCAT-AAAAAAACTTCTTGAAACGA
* ** * *
9697 GAACAACTCTGATCAT-CGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
**
9732 GATCAACTCTGATCAT-CGAAAACTTCTTG
1 GATCAACTCTGATCATAAAAAAACTTCTTG
9761 GAACAACCGC
Statistics
Matches: 554, Mismatches: 39, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
34 63 0.11
35 155 0.28
36 37 0.07
37 128 0.23
38 138 0.25
39 27 0.05
40 6 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.26
Consensus pattern (36 bp):
GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
Found at i:9824 original size:54 final size:54
Alignment explanation
Indices: 9731--9984 Score: 180
Period size: 54 Copynumber: 4.7 Consensus size: 54
9721 TCTTGGAATG
* * * *
9731 AGATCAACTCTGATCATC-GAAAACTTCTTGGAACA-ACCGCACCGGATTATCTGG
1 AGATCAACTCTAATC-TCTGAAAACTTCTTTGAA-AGACCGCACCGGATCATCTGA
* * * *
9785 GGATCAACTCTAATCTCTAAAAACTTCTTTGAAAGACCGCACGGGGTCATCTGA
1 AGATCAACTCTAATCTCTGAAAACTTCTTTGAAAGACCGCACCGGATCATCTGA
* * ** * *
9839 AGATCAACT-TAGATTTCTGAAAACTTCTATGAAAGACCATATC-GAGTCATCTTA
1 AGATCAACTCTA-ATCTCTGAAAACTTCTTTGAAAGACCGCACCGGA-TCATCTGA
** * * * * *
9893 AGATC-TGTTTAGATCTCTGAAAACTTCTATGAAAGACCACACTAGG-TCATCTTA
1 AGATCAACTCTA-ATCTCTGAAAACTTCTTTGAAAGACCGCAC-CGGATCATCTGA
** *
9947 AGATCTGCT-TAGATCTCTGAAAACTTCTATGAAAGACC
1 AGATCAACTCTA-ATCTCTGAAAACTTCTTTGAAAGACC
9985 ACACTAAGTC
Statistics
Matches: 166, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
53 7 0.04
54 157 0.95
55 1 0.01
56 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (54 bp):
AGATCAACTCTAATCTCTGAAAACTTCTTTGAAAGACCGCACCGGATCATCTGA
Found at i:9985 original size:54 final size:54
Alignment explanation
Indices: 9797--10001 Score: 268
Period size: 54 Copynumber: 3.8 Consensus size: 54
9787 ATCAACTCTA
* * * ** * **
9797 ATCTCTAAAAACTTCTTTGAAAGACCGCACGGGGTCATCTGAAGATCAACTTAG
1 ATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCTGCTTAG
* * * *
9851 ATTTCTGAAAACTTCTATGAAAGACCATA-TCGAGTCATCTTAAGATCTGTTTAG
1 ATCTCTGAAAACTTCTATGAAAGACCACACTAG-GTCATCTTAAGATCTGCTTAG
9905 ATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCTGCTTAG
1 ATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCTGCTTAG
* *
9959 ATCTCTGAAAACTTCTATGAAAGACCACACTAAGTCATTTTAA
1 ATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATCTTAA
10002 ACACTTGTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 129 0.98
55 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (54 bp):
ATCTCTGAAAACTTCTATGAAAGACCACACTAGGTCATCTTAAGATCTGCTTAG
Found at i:11004 original size:11 final size:11
Alignment explanation
Indices: 10988--11021 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
10978 TATCATTTCC
10988 TTCTTTTTTTT
1 TTCTTTTTTTT
10999 TTC-TTTTTTT
1 TTCTTTTTTTT
*
11009 TCCTTTTTTTT
1 TTCTTTTTTTT
11020 TT
1 TT
11022 GCCACACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:11157 original size:40 final size:39
Alignment explanation
Indices: 11078--11159 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
11068 ATCTTTTTGA
** * *
11078 AAAACATTTTTTCTCTTTTAAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTAAAAAGATCACACCTAGAGG
* *
11117 AAAACATTTTTTTTCTTTTGAAAAAGATCACGCCTAGAGG
1 AAAACATTTTTTCTCTTTT-AAAAAGATCACACCTAGAGG
11157 AAA
1 AAA
11160 GTTTCATTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 18 0.50
40 18 0.50
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTAAAAAGATCACACCTAGAGG
Found at i:11370 original size:20 final size:22
Alignment explanation
Indices: 11338--11383 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
11328 CTTTCCTCCG
11338 TCTTTTGCTTTTTCAACT-TTT
1 TCTTTTGCTTTTTCAACTCTTT
*
11359 TCTTTT-CTTTTTCAATTCTTT
1 TCTTTTGCTTTTTCAACTCTTT
11380 TCTT
1 TCTT
11384 CATTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (22 bp):
TCTTTTGCTTTTTCAACTCTTT
Found at i:11822 original size:55 final size:55
Alignment explanation
Indices: 11753--11859 Score: 214
Period size: 55 Copynumber: 1.9 Consensus size: 55
11743 CTTTTCTGAA
11753 AACACTTTCTTGAAAAGCATTTTTGACTTTTGAAAAACTCTTTGATCAAAATGAC
1 AACACTTTCTTGAAAAGCATTTTTGACTTTTGAAAAACTCTTTGATCAAAATGAC
11808 AACACTTTCTTGAAAAGCATTTTTGACTTTTGAAAAACTCTTTGATCAAAAT
1 AACACTTTCTTGAAAAGCATTTTTGACTTTTGAAAAACTCTTTGATCAAAAT
11860 CCAAAAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (55 bp):
AACACTTTCTTGAAAAGCATTTTTGACTTTTGAAAAACTCTTTGATCAAAATGAC
Found at i:14499 original size:8 final size:8
Alignment explanation
Indices: 14469--14669 Score: 67
Period size: 8 Copynumber: 25.1 Consensus size: 8
14459 TAAAAAAAAA
14469 AGATAAAT
1 AGATAAAT
* * *
14477 AGGTATAG
1 AGATAAAT
14485 AGATAAAT
1 AGATAAAT
*
14493 TGATAAAT
1 AGATAAAT
14501 AGATACAGAT
1 AGATA-A-AT
14511 A-AT-AAT
1 AGATAAAT
14517 AGATAAAT
1 AGATAAAT
*
14525 AAGAGAATAAT
1 -AGA-TA-AAT
14536 AGATAAAT
1 AGATAAAT
* *
14544 AGGTAAGT
1 AGATAAAT
* *
14552 A-AAAAAG
1 AGATAAAT
*
14559 GGATAATAAT
1 AGAT-A-AAT
*
14569 AAATAAAT
1 AGATAAAT
*
14577 GGAT-AAT
1 AGATAAAT
*
14584 AGCTAAATT
1 AGATAAA-T
*
14593 A-ATAAAA
1 AGATAAAT
14600 AGATAAAT
1 AGATAAAT
14608 AG-TAAAT
1 AGATAAAT
* *
14615 AAATAGAT
1 AGATAAAT
**
14623 A-ATAGTT
1 AGATAAAT
* *
14630 AAATTAAT
1 AGATAAAT
* *
14638 AAATAAAA
1 AGATAAAT
14646 AGATAAAT
1 AGATAAAT
14654 AG-TAAAT
1 AGATAAAT
*
14661 AAATAAAT
1 AGATAAAT
14669 A
1 A
14670 ATAGTTAAAT
Statistics
Matches: 138, Mismatches: 39, Indels: 32
0.66 0.19 0.15
Matches are distributed among these distances:
6 3 0.02
7 29 0.21
8 81 0.59
9 11 0.08
10 11 0.08
11 3 0.02
ACGTcount: A:0.60, C:0.01, G:0.13, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Found at i:14617 original size:27 final size:27
Alignment explanation
Indices: 14610--14670 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
14600 AGATAAATAG
* *
14610 TAAATAAATAGAT-AATAGTTAAATTAA
1 TAAATAAAAAGATAAATAG-TAAATAAA
14637 TAAATAAAAAGATAAATAGTAAATAAA
1 TAAATAAAAAGATAAATAGTAAATAAA
14664 TAAATAA
1 TAAATAA
14671 TAGTTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (27 bp):
TAAATAAAAAGATAAATAGTAAATAAA
Found at i:14638 original size:19 final size:18
Alignment explanation
Indices: 14507--14669 Score: 65
Period size: 19 Copynumber: 9.1 Consensus size: 18
14497 AAATAGATAC
* *
14507 AGATAATAATAGATAAAT
1 AGATAATAGTAAATAAAT
* * *
14525 AAGAGAATAATAGATAAAT
1 -AGATAATAGTAAATAAAT
* *
14544 AGGT-A-AGTAAA-AAAG
1 AGATAATAGTAAATAAAT
* *
14559 GGATAATAATAAATAAAT
1 AGATAATAGTAAATAAAT
* *
14577 GGATAATAGCTAAATTAATAAAA
1 AGATAATAG-T--A--AATAAAT
14600 AGATAAATAGTAAATAAAT
1 AGAT-AATAGTAAATAAAT
*
14619 AGATAATAGTTAAATTAAT
1 AGATAATAG-TAAATAAAT
*
14638 AAATAA-A--AAGATAAAT
1 AGATAATAGTAA-ATAAAT
14654 AG-TAA-A-TAAATAAAT
1 AGATAATAGTAAATAAAT
14669 A
1 A
14670 ATAGTTAAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 28
0.71 0.11 0.17
Matches are distributed among these distances:
15 18 0.16
16 13 0.11
17 6 0.05
18 19 0.17
19 41 0.36
21 2 0.02
23 10 0.09
24 5 0.04
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (18 bp):
AGATAATAGTAAATAAAT
Found at i:14643 original size:46 final size:46
Alignment explanation
Indices: 14563--14691 Score: 187
Period size: 46 Copynumber: 2.9 Consensus size: 46
14553 AAAAAGGGAT
* * *
14563 AATAATAAATAAATGGATAATAGCTAAA-T--T-AATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
14605 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
*
14651 AATAGTAAATAAATAAATAATAGTTAAATTAATAAA-AAAAA
1 AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAA
14692 TCTTTTTGGT
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
42 25 0.32
43 1 0.01
45 6 0.08
46 47 0.59
ACGTcount: A:0.64, C:0.01, G:0.08, T:0.27
Consensus pattern (46 bp):
AATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAAAGATA
Found at i:14684 original size:19 final size:18
Alignment explanation
Indices: 14561--14686 Score: 59
Period size: 19 Copynumber: 7.1 Consensus size: 18
14551 TAAAAAAGGG
* **
14561 ATAATAATAAATAAATGG
1 ATAATAGTAAATAAATAA
*
14579 ATAATAGCTAAATTAATAA
1 ATAATAG-TAAATAAATAA
* *
14598 A-AAGA-TAAAT-AGTAA
1 ATAATAGTAAATAAATAA
**
14613 ATAAATAG-ATAATAGTTAA
1 AT-AATAGTA-AATAAATAA
*
14632 AT--TAATAAATAAA-AA
1 ATAATAGTAAATAAATAA
14647 GATAAATAGTAAATAAATAA
1 -AT-AATAGTAAATAAATAA
*
14667 ATAATAGTTAAATTAATAA
1 ATAATAG-TAAATAAATAA
14686 A
1 A
14687 AAAAATCTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 25
0.68 0.12 0.21
Matches are distributed among these distances:
15 7 0.09
16 13 0.16
17 5 0.06
18 17 0.21
19 37 0.46
20 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.29
Consensus pattern (18 bp):
ATAATAGTAAATAAATAA
Found at i:22097 original size:46 final size:46
Alignment explanation
Indices: 22022--22119 Score: 180
Period size: 46 Copynumber: 2.2 Consensus size: 46
22012 CTCGTGACAC
*
22022 CATA-ACTTTTCTAGATTTGTTGTGTATGGATTCGTATTAAGCCCA
1 CATATACTTTTCTAGATTTGTTGTGCATGGATTCGTATTAAGCCCA
22067 CATATACTTTTCTAGATTTGTTGTGCATGGATTCGTATTAAGCCCA
1 CATATACTTTTCTAGATTTGTTGTGCATGGATTCGTATTAAGCCCA
22113 CATATAC
1 CATATAC
22120 ATGAAGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 4 0.08
46 47 0.92
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (46 bp):
CATATACTTTTCTAGATTTGTTGTGCATGGATTCGTATTAAGCCCA
Found at i:25210 original size:3 final size:3
Alignment explanation
Indices: 25204--25238 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
25194 TAATTATTCC
25204 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
25239 CAAGTCAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25377 original size:22 final size:22
Alignment explanation
Indices: 25352--25404 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
25342 AAACATGAGA
25352 TGCCATGTCTAACTTAGATATG
1 TGCCATGTCTAACTTAGATATG
25374 TGCCATGTCTAACTTAGATATG
1 TGCCATGTCTAACTTAGATATG
25396 TGCCATGTC
1 TGCCATGTC
25405 AAACATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (22 bp):
TGCCATGTCTAACTTAGATATG
Found at i:34220 original size:20 final size:19
Alignment explanation
Indices: 34181--34217 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34171 ACATAGTCCA
34181 TCAACATAATTTATTTTTG
1 TCAACATAATTTATTTTTG
*
34200 TCAACTTAATTTATTTTT
1 TCAACATAATTTATTTTT
34218 TGTAAAGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.57
Consensus pattern (19 bp):
TCAACATAATTTATTTTTG
Found at i:34468 original size:17 final size:16
Alignment explanation
Indices: 34440--34473 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
34430 TTTGCTAGTG
34440 TGTGTATATAATTATA
1 TGTGTATATAATTATA
34456 TGTGTATTATAATTATA
1 TGTGTA-TATAATTATA
34473 T
1 T
34474 ACATAACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TGTGTATATAATTATA
Found at i:37109 original size:16 final size:17
Alignment explanation
Indices: 37066--37116 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
37056 TTATTTATAT
37066 CATTTAAAAAAACTACC
1 CATTTAAAAAAACTACC
* *
37083 TATCTAAAAAAA-TACC
1 CATTTAAAAAAACTACC
*
37099 CATTTAGAAAAAATTACC
1 CATTTA-AAAAAACTACC
37117 ACAAACTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 8 0.29
17 16 0.57
18 4 0.14
ACGTcount: A:0.53, C:0.20, G:0.02, T:0.25
Consensus pattern (17 bp):
CATTTAAAAAAACTACC
Found at i:52873 original size:11 final size:11
Alignment explanation
Indices: 52857--52906 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
52847 CTCCAATTTA
52857 TCTTCAAATGG
1 TCTTCAAATGG
52868 TCTTC-AA--G
1 TCTTCAAATGG
* *
52876 TCTCCAAATAG
1 TCTTCAAATGG
*
52887 TCTTCGAATGG
1 TCTTCAAATGG
52898 TCTTCAAAT
1 TCTTCAAAT
52907 ACGAACTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
10 2 0.06
11 22 0.71
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (11 bp):
TCTTCAAATGG
Found at i:52873 original size:30 final size:28
Alignment explanation
Indices: 52827--52904 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 28
52817 CTTGAAATAA
* *
52827 ATCTTCAATAGTCTTCAAGTCTCCAATTT
1 ATCTTCAATGGTCTTCAAGTCTCCAA-AT
52856 ATCTTCAAATGGTCTTCAAGTCTCCAAAT
1 ATCTTC-AATGGTCTTCAAGTCTCCAAAT
52885 AGTCTTCGAATGGTCTTCAA
1 A-TCTTC-AATGGTCTTCAA
52905 ATACGAACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.18
30 36 0.82
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (28 bp):
ATCTTCAATGGTCTTCAAGTCTCCAAAT
Found at i:54350 original size:14 final size:15
Alignment explanation
Indices: 54331--54360 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54321 CAATCAAAGC
54331 AATAAT-CAAGGAAA
1 AATAATGCAAGGAAA
54345 AATAATGCAAGGAAA
1 AATAATGCAAGGAAA
54360 A
1 A
54361 TTAAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13
Consensus pattern (15 bp):
AATAATGCAAGGAAA
Found at i:54748 original size:21 final size:21
Alignment explanation
Indices: 54718--54767 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
54708 GGAATGGCGA
**
54718 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
* *
54739 TGGCATGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
54760 TGGTACGG
1 TGGCACGG
54768 TGAATGGTCG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.12, C:0.20, G:0.48, T:0.20
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Done.