Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000585.1 Hibiscus syriacus cultivar Beakdansim tig00001141_pilon, 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: 75485
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:2294 original size:19 final size:19
Alignment explanation
Indices: 2243--2387 Score: 148
Period size: 19 Copynumber: 8.1 Consensus size: 19
2233 GTCTTTTGGT
*
2243 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2262 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2282 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2299 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2315 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2334 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2351 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2367 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2386 GA
1 GA
2388 TTTTGGTTTC
Statistics
Matches: 105, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
14 19 0.18
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 57 0.54
20 17 0.16
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2310 original size:33 final size:33
Alignment explanation
Indices: 2268--2332 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
2258 ACGAGATAAT
**
2268 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
2301 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
2333 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:2327 original size:52 final size:52
Alignment explanation
Indices: 2251--2387 Score: 220
Period size: 52 Copynumber: 2.6 Consensus size: 52
2241 GTGAAATGAA
* * **
2251 AATCGCAACGAGATAATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
2304 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
2356 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
2388 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 67 0.85
53 12 0.15
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2405 original size:19 final size:18
Alignment explanation
Indices: 2383--2449 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
2373 AAAATCGCAA
*
2383 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
2402 TGCGTTTTTTATTTCGCGT
1 TGCG-ATTTTATTTCGCGT
*
2421 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
2441 TGCGATTTT
1 TGCGATTTT
2450 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 24 0.60
20 15 0.38
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.49
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:2995 original size:20 final size:20
Alignment explanation
Indices: 2973--3100 Score: 141
Period size: 20 Copynumber: 6.3 Consensus size: 20
2963 GTAAATTGCG
* * *
2973 TTGCGAAAGTCAGAATCGCG
1 TTGCGATAGTCAGTATCGCA
* * * *
2993 TTGCGAAAGTTAGTATCTCG
1 TTGCGATAGTCAGTATCGCA
* *
3013 TTGCGATTTTGT-ATTATCGCA
1 TTGCGA--TAGTCAGTATCGCA
*
3034 TTGCGATAGTAAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
3054 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
3074 TTGCGATAGTCAGTATCGCA
1 TTGCGATAGTCAGTATCGCA
3094 TTGCGAT
1 TTGCGAT
3101 TTTCACAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 77 0.82
21 12 0.13
22 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGTATCGCA
Found at i:3119 original size:81 final size:81
Alignment explanation
Indices: 2973--3121 Score: 183
Period size: 81 Copynumber: 1.8 Consensus size: 81
2963 GTAAATTGCG
* * * * ** *
2973 TTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGTATCTCGTTGCGATTTTGTATTATCGCATTGC
1 TTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTACAATATCGCATTGC
3038 GATAGTAAGTATCGCA
66 GATAGTAAGTATCGCA
* * * *
3054 TTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCACAAT-TCGCGTTG
1 TTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-ACAATATCGCATTG
3118 CGAT
65 CGAT
3122 TTACTTATTC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 54 0.96
82 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (81 bp):
TTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTACAATATCGCATTGC
GATAGTAAGTATCGCA
Found at i:3211 original size:21 final size:21
Alignment explanation
Indices: 3171--3211 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3161 ACTGTAGACC
**
3171 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
3192 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
3212 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:3373 original size:16 final size:15
Alignment explanation
Indices: 3352--3381 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3342 TTTTCTCTAA
3352 ACATAATCATATACAG
1 ACATAATCAT-TACAG
3368 ACATAATCATTACA
1 ACATAATCATTACA
3382 TGTTCATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.27
Consensus pattern (15 bp):
ACATAATCATTACAG
Found at i:3943 original size:15 final size:16
Alignment explanation
Indices: 3917--3947 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3907 ATAAAAAACT
3917 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
3933 AATAA-TTAAATTTAA
1 AATAATTTAAATTTAA
3948 TGTATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:4621 original size:2 final size:2
Alignment explanation
Indices: 4614--4648 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4604 AAAAATGAAT
4614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4649 CACTTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6565 original size:20 final size:20
Alignment explanation
Indices: 6540--6588 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
6530 ATCGATCGAT
6540 GGAATTGGCCAAGAGGCGGG
1 GGAATTGGCCAAGAGGCGGG
6560 GGAATTGGCCAAGAGGCGGG
1 GGAATTGGCCAAGAGGCGGG
*
6580 TGAATTGGC
1 GGAATTGGC
6589 AATAAATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.47, T:0.14
Consensus pattern (20 bp):
GGAATTGGCCAAGAGGCGGG
Found at i:7254 original size:20 final size:20
Alignment explanation
Indices: 7229--7270 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
7219 CCGTTAAACA
7229 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
* *
7249 GGGGGAATCTGTACCCTCTG
1 GGGGGAATCGGTACCCCCTG
7269 GG
1 GG
7271 CATTCTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.19
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:7338 original size:18 final size:20
Alignment explanation
Indices: 7303--7343 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
7293 AAAACAAGCA
*
7303 GGGGGTATCTGTTCCCCT-T
1 GGGGGTATCTGTTACCCTCT
7322 GGGGGTATCTG-TACCCTCT
1 GGGGGTATCTGTTACCCTCT
7341 GGG
1 GGG
7344 CAATCTGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.07, C:0.24, G:0.37, T:0.32
Consensus pattern (20 bp):
GGGGGTATCTGTTACCCTCT
Found at i:30147 original size:64 final size:64
Alignment explanation
Indices: 30046--30195 Score: 266
Period size: 64 Copynumber: 2.4 Consensus size: 64
30036 TCCTAATTTT
* * *
30046 GGTGGCCAAAACGTGAAAATACGGAAAACTAGGGAAGACCTATTGGTGATTTTCGCCTGGAAAA
1 GGTGGCTAAAGCGTGAGAATACGGAAAACTAGGGAAGACCTATTGGTGATTTTCGCCTGGAAAA
30110 GGTGGCTAAAGCGTGAGAATACGGAAAACTAGGGAAGACCTATTGGTGATTTTCGCCTGGAAAA
1 GGTGGCTAAAGCGTGAGAATACGGAAAACTAGGGAAGACCTATTGGTGATTTTCGCCTGGAAAA
30174 GGTGGCTAAAGCGTGAG-ATACG
1 GGTGGCTAAAGCGTGAGAATACG
30196 CTGAAATATC
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
63 5 0.06
64 78 0.94
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (64 bp):
GGTGGCTAAAGCGTGAGAATACGGAAAACTAGGGAAGACCTATTGGTGATTTTCGCCTGGAAAA
Found at i:34540 original size:28 final size:27
Alignment explanation
Indices: 34501--34575 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
34491 GTTTGTTATT
* * *
34501 TATATGATTAAATATATATTATACATGA
1 TATATTATTAAATATATATTAAAAAT-A
* *
34529 TATATTATTAAAAATATTTTTAAAAATA
1 TATATTATTAAATATA-TATTAAAAATA
34557 TATATTA-TAAATAATATAT
1 TATATTATTAAAT-ATATAT
34576 AATGTATCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 6 0.16
28 25 0.66
29 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (27 bp):
TATATTATTAAATATATATTAAAAATA
Found at i:34545 original size:12 final size:12
Alignment explanation
Indices: 34530--34569 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
34520 TATACATGAT
34530 ATATTATTAAAA
1 ATATTATTAAAA
*
34542 ATATTTTTAAAA
1 ATATTATTAAAA
*
34554 ATATATATTATAA
1 ATAT-TATTAAAA
34567 ATA
1 ATA
34570 ATATATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATTATTAAAA
Found at i:34545 original size:14 final size:14
Alignment explanation
Indices: 34501--34569 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
34491 GTTTGTTATT
* *
34501 TATATGATTAAATA
1 TATATTATTAAAAA
**
34515 TATATTA-TACATGA
1 TATATTATTA-AAAA
34529 TATATTATTAAAAA
1 TATATTATTAAAAA
34543 TAT-TT-TTAAAAA
1 TATATTATTAAAAA
*
34555 TATA-TATTATAAA
1 TATATTATTAAAAA
34568 TA
1 TA
34570 ATATATAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
12 11 0.24
13 12 0.27
14 20 0.44
15 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (14 bp):
TATATTATTAAAAA
Found at i:34573 original size:14 final size:14
Alignment explanation
Indices: 34509--34575 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
34499 TTTATATGAT
34509 TAAAT-ATATATTA
1 TAAATAATATATTA
* *
34522 TACATGATATATTA
1 TAAATAATATATTA
*
34536 TTAAA-AATAT-TTT
1 -TAAATAATATATTA
*
34549 TAAAAATATATATTA
1 TAAATA-ATATATTA
34564 TAAATAATATAT
1 TAAATAATATAT
34576 AATGTATCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
14 22 0.51
15 10 0.23
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (14 bp):
TAAATAATATATTA
Found at i:36564 original size:87 final size:87
Alignment explanation
Indices: 36437--36612 Score: 352
Period size: 87 Copynumber: 2.0 Consensus size: 87
36427 CAATAACCAA
36437 CGGGTGTTGGTTCAAGTGGTAAATTGTTTAATATTGTTAACTGAATTAACCGATAACCGAAGTTT
1 CGGGTGTTGGTTCAAGTGGTAAATTGTTTAATATTGTTAACTGAATTAACCGATAACCGAAGTTT
36502 GAAAAAATCATTAACCGTTAAC
66 GAAAAAATCATTAACCGTTAAC
36524 CGGGTGTTGGTTCAAGTGGTAAATTGTTTAATATTGTTAACTGAATTAACCGATAACCGAAGTTT
1 CGGGTGTTGGTTCAAGTGGTAAATTGTTTAATATTGTTAACTGAATTAACCGATAACCGAAGTTT
36589 GAAAAAATCATTAACCGTTAAC
66 GAAAAAATCATTAACCGTTAAC
36611 CG
1 CG
36613 ATCAAACCCA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (87 bp):
CGGGTGTTGGTTCAAGTGGTAAATTGTTTAATATTGTTAACTGAATTAACCGATAACCGAAGTTT
GAAAAAATCATTAACCGTTAAC
Found at i:42163 original size:6 final size:6
Alignment explanation
Indices: 42152--42189 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
42142 ACTAAAATAT
42152 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TC
1 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TC
42190 AAAAGGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTAAA
Found at i:42247 original size:15 final size:14
Alignment explanation
Indices: 42227--42268 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
42217 CTAAGACTAG
42227 ATTAAAGAAATTGAA
1 ATTAAAGAAATT-AA
*
42242 ATTAAAGACA-TAA
1 ATTAAAGAAATTAA
*
42255 ATTAAAAAAATTAA
1 ATTAAAGAAATTAA
42269 CACATATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 10 0.43
14 4 0.17
15 9 0.39
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (14 bp):
ATTAAAGAAATTAA
Found at i:43846 original size:65 final size:64
Alignment explanation
Indices: 43727--43852 Score: 166
Period size: 65 Copynumber: 2.0 Consensus size: 64
43717 TTTCAAATGC
* *
43727 ATTTTGTGTACCGATGCACAACCATGCATCGATACACTCAGGATTTTATTGAAACATCGAATTG
1 ATTTTGTGTACCGATGCACAACCATGCATCGATACACTCAAGATATTATTGAAACATCGAATTG
* * *
43791 ATTTTGTGTACCGATGTACACACCATGCATTGATGCACAC-CAAGCTATT-TTGAAACATCGAA
1 ATTTTGTGTACCGATGCACA-ACCATGCATCGAT--ACACTCAAGATATTATTGAAACATCGAA
43853 GCAAATTTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
64 19 0.35
65 25 0.46
66 6 0.11
67 4 0.07
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (64 bp):
ATTTTGTGTACCGATGCACAACCATGCATCGATACACTCAAGATATTATTGAAACATCGAATTG
Found at i:43862 original size:65 final size:64
Alignment explanation
Indices: 43729--43875 Score: 154
Period size: 65 Copynumber: 2.3 Consensus size: 64
43719 TCAAATGCAT
* * *** *
43729 TTTGTGTACCGATGCACAACCATGCATCGATACACTCAGGATTTTATTGAAACATCGAATTGAT
1 TTTGTGTACCGATGCACAACCATGCATCGATACACTCAAGATATTATTGAAACATCGAAGCAAA
* * *
43793 TTTGTGTACCGATGTACACACCATGCATTGATGCACAC-CAAGCTATT-TTGAAACATCGAAGCA
1 TTTGTGTACCGATGCACA-ACCATGCATCGAT--ACACTCAAGATATTATTGAAACATCGAAGCA
43856 AA
63 AA
* *
43858 TTTGTGCATCGATGCACA
1 TTTGTGTACCGATGCACA
43876 CCTTAGTGTA
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
64 17 0.25
65 41 0.60
66 6 0.09
67 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (64 bp):
TTTGTGTACCGATGCACAACCATGCATCGATACACTCAAGATATTATTGAAACATCGAAGCAAA
Found at i:46423 original size:45 final size:46
Alignment explanation
Indices: 46369--46456 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
46359 AATCGAATGT
* * *
46369 ATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGTGC
1 ATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAGTGC
46414 ATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
1 ATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAG
46457 GCTTTTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 17 0.44
46 22 0.56
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (46 bp):
ATTTGATGCATCAATGCACAAGACCATGCATCGATGCACTCAGTGC
Found at i:50695 original size:19 final size:19
Alignment explanation
Indices: 50671--50716 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
50661 TAGTGAGAAA
50671 CAAGGCTAGACTTGTTGCT
1 CAAGGCTAGACTTGTTGCT
50690 CAAGGCTAGACTTGTTGCT
1 CAAGGCTAGACTTGTTGCT
*
50709 TAAGGCTA
1 CAAGGCTA
50717 TACTCAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (19 bp):
CAAGGCTAGACTTGTTGCT
Found at i:54359 original size:26 final size:23
Alignment explanation
Indices: 54308--54361 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 23
54298 TGTTAAAACT
*
54308 TTTG-ATGTTTTTGGATTGGATG
1 TTTGAATGTTTTTGGATTGAATG
54330 TTTGAATGTTTTATGGATGTTGAATG
1 TTTGAATGTTTT-TGGA--TTGAATG
54356 TTTGAA
1 TTTGAA
54362 CTTGACTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 4 0.15
26 12 0.44
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (23 bp):
TTTGAATGTTTTTGGATTGAATG
Found at i:55175 original size:65 final size:64
Alignment explanation
Indices: 55042--55176 Score: 146
Period size: 65 Copynumber: 2.1 Consensus size: 64
55032 TCGAATGCAT
* * * * * *** *
55042 TTTGTGTACCAATGCACAGCCATGCATCGATGCACTCAGGATTTTATTAAAACATCGAATTGAT
1 TTTGTGTACCAATGCACAACCATGCATCAATGCACCCAGGATATTATTAAAACATCAAAGAAAA
* *
55106 TTTGTGTACCAATGCACACACCATGCATCAATGCACACCAGGCTATT-TTCAAACATCAAAGAAA
1 TTTGTGTACCAATGCACA-ACCATGCATCAATGCAC-CCAGGATATTATTAAAACATCAAAGAAA
55170 A
64 A
55171 TTTGTG
1 TTTGTG
55177 CACCGATACA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
64 18 0.31
65 33 0.57
66 7 0.12
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (64 bp):
TTTGTGTACCAATGCACAACCATGCATCAATGCACCCAGGATATTATTAAAACATCAAAGAAAA
Found at i:73433 original size:19 final size:18
Alignment explanation
Indices: 73393--73436 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
73383 AATTTTTATC
* *
73393 AAAACATTATTTTTCAAA
1 AAAAAATTAATTTTCAAA
*
73411 AAAAAATTAATTTTGAAA
1 AAAAAATTAATTTTCAAA
73429 TAAAAAAT
1 -AAAAAAT
73437 GTTTTGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAAATTAATTTTCAAA
Found at i:73527 original size:12 final size:13
Alignment explanation
Indices: 73500--73532 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
73490 ATATTATAAT
*
73500 TTTTCAAACTTAG
1 TTTTCAAACATAG
73513 TTTTCAAA-ATAG
1 TTTTCAAACATAG
73525 TTTTCAAA
1 TTTTCAAA
73533 TTTTCCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Done.