Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001555.1 Hibiscus syriacus cultivar Beakdansim tig00003074_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: 55889
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:12804 original size:16 final size:16
Alignment explanation
Indices: 12783--12817 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12773 ACTTAGCAGT
*
12783 TTTAAAAAAATAAAAA
1 TTTAAAAAAAGAAAAA
*
12799 TTTAAACAAAGAAAAA
1 TTTAAAAAAAGAAAAA
12815 TTT
1 TTT
12818 TGGAAAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
TTTAAAAAAAGAAAAA
Found at i:12845 original size:21 final size:21
Alignment explanation
Indices: 12806--12845 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12796 AAATTTAAAC
*
12806 AAAGAAAAATTTTGGAAAAGA
1 AAAGAAAAATTTTAGAAAAGA
* *
12827 AAAGAAAACTTTTATAAAA
1 AAAGAAAAATTTTAGAAAA
12846 CCAGAGGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (21 bp):
AAAGAAAAATTTTAGAAAAGA
Found at i:14916 original size:17 final size:18
Alignment explanation
Indices: 14890--14923 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14880 AGAAGAAGAT
14890 TAAACCTCAA-AAGCCAA
1 TAAACCTCAAGAAGCCAA
*
14907 TAAACTTCAAGAAGCCA
1 TAAACCTCAAGAAGCCA
14924 TGAAAAGACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.26, G:0.09, T:0.15
Consensus pattern (18 bp):
TAAACCTCAAGAAGCCAA
Found at i:16271 original size:44 final size:44
Alignment explanation
Indices: 16177--16272 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
16167 AGAAACATGT
* *
16177 TTAAAATTTTTATTTATTTTAAAAGTGTTTTAAATAAATAATAA
1 TTAAAATTATTATTTATTTTAAAAGAGTTTTAAATAAATAATAA
* *
16221 TT-AAATTATTATTTAATTTT-AAGGAGTTTTAAAGTAAGT-ATAA
1 TTAAAATTATTATTT-ATTTTAAAAGAGTTTTAAA-TAAATAATAA
16264 TTAAAATTA
1 TTAAAATTA
16273 ATTAAAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
43 28 0.62
44 17 0.38
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (44 bp):
TTAAAATTATTATTTATTTTAAAAGAGTTTTAAATAAATAATAA
Found at i:27891 original size:22 final size:22
Alignment explanation
Indices: 27849--27892 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
27839 ACTTATTCCG
* *
27849 ATTGTATTATCTCAACTTATGA
1 ATTGTAATATCTCAACATATGA
27871 ATTGTAATAGTCTCAA-ATATGA
1 ATTGTAATA-TCTCAACATATGA
27893 CCAACGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (22 bp):
ATTGTAATATCTCAACATATGA
Found at i:33571 original size:15 final size:15
Alignment explanation
Indices: 33551--33580 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33541 TGATTTACTT
*
33551 ATTAAATTATTAAAC
1 ATTAAATCATTAAAC
33566 ATTAAATCATTAAAC
1 ATTAAATCATTAAAC
33581 TGAGATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTAAATCATTAAAC
Found at i:34073 original size:14 final size:14
Alignment explanation
Indices: 34056--34107 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
34046 AAGTCAAAGG
*
34056 GTTGAATCGGATGA
1 GTTGACTCGGATGA
* *
34070 GTTGATTCAGACTGA
1 GTTGACTCGGA-TGA
*
34085 -TTGACTCGGACGA
1 GTTGACTCGGATGA
34098 GTTGACTCGG
1 GTTGACTCGG
34108 TTAGGTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 2 0.06
14 26 0.84
15 3 0.10
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (14 bp):
GTTGACTCGGATGA
Found at i:38200 original size:200 final size:200
Alignment explanation
Indices: 37850--38226 Score: 619
Period size: 200 Copynumber: 1.9 Consensus size: 200
37840 TTCTTAGTGA
* *
37850 ACTTGGATGACTTCTTTAATGTTTAGGGATGTTTTTTAATTTGTTACTTGTTTATTTCTTTTGTT
1 ACTTGGATGACTTCTTTAATGTTTAAGGATGATTTTTAATTTGTTACTTGTTTATTTCTTTTGTT
* * * *
37915 TTACTCAATTTAAGTTTATAATACAAATTTCACTAAGTCAATGACAATTGTTTAGTGAAACTTAG
66 TTACTCAATTGAAGTTTACAATACAAATTGCACTAAGTCAATGACAATCGTTTAGTGAAACTTAG
*
37980 GTTCATCTCAACATTGAAAGGGTTAGGGAGGCTCAATCAAAATTGGGATTTTTAATTTGAACTTG
131 GTTCATCTCAACACTGAAAGGGTTAGGGAGGCTCAATCAAAATTGGGATTTTTAATTTGAACTTG
38045 GGATT
196 GGATT
* *
38050 ACTTGGATGATTTCTTTCATGTTTAAGGATGATTTTTAATTTGTTACTTGTTTATTTCTTTTGTT
1 ACTTGGATGACTTCTTTAATGTTTAAGGATGATTTTTAATTTGTTACTTGTTTATTTCTTTTGTT
* ** * *
38115 TTATTCAATTGAAGTTTACAATGTAAATTGCACTAAGTCTATGCCAATCGTTTAGTGAAACTTAG
66 TTACTCAATTGAAGTTTACAATACAAATTGCACTAAGTCAATGACAATCGTTTAGTGAAACTTAG
*
38180 GTTCATCTCAACACTGAAAGGGTTAGGGAGGCTCGATCAAAATTGGG
131 GTTCATCTCAACACTGAAAGGGTTAGGGAGGCTCAATCAAAATTGGG
38227 TATCGGTACC
Statistics
Matches: 162, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
200 162 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.42
Consensus pattern (200 bp):
ACTTGGATGACTTCTTTAATGTTTAAGGATGATTTTTAATTTGTTACTTGTTTATTTCTTTTGTT
TTACTCAATTGAAGTTTACAATACAAATTGCACTAAGTCAATGACAATCGTTTAGTGAAACTTAG
GTTCATCTCAACACTGAAAGGGTTAGGGAGGCTCAATCAAAATTGGGATTTTTAATTTGAACTTG
GGATT
Found at i:38340 original size:3 final size:3
Alignment explanation
Indices: 38327--38368 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
38317 GGACCTGTCT
* *
38327 TTA TT- TTA TTA TTA TTA TTA TTA TT- TAA TTA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38369 TTGTTTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.09
3 30 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38352 original size:20 final size:20
Alignment explanation
Indices: 38327--38368 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
38317 GGACCTGTCT
* *
38327 TTATTTTATTATTATTATTA
1 TTATTTAATTAATATTATTA
38347 TTATTTAATTAATATTATTA
1 TTATTTAATTAATATTATTA
38367 TT
1 TT
38369 TTGTTTTTAG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTAATTAATATTATTA
Found at i:38357 original size:17 final size:17
Alignment explanation
Indices: 38337--38369 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38327 TTATTTTATT
*
38337 ATTATTATTATTATTTA
1 ATTAATATTATTATTTA
38354 ATTAATATTATTATTT
1 ATTAATATTATTATTT
38370 TGTTTTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTAATATTATTATTTA
Found at i:45261 original size:22 final size:21
Alignment explanation
Indices: 45230--45314 Score: 59
Period size: 22 Copynumber: 4.0 Consensus size: 21
45220 GACAAGAGGA
*
45230 AAAAGGGAAAAGGTAGAAAAAG
1 AAAAGAGAAAA-GTAGAAAAAG
*
45252 AAAAGAGAAAAATAGTAAAGAAG
1 AAAAGAGAAAAGTAG-AAA-AAG
* *
45275 AAGAAGAAAAAAAGAAGAAAAAG
1 AA-AAG-AGAAAAGTAGAAAAAG
*
45298 AGAA-A-AAAA-TAGAAAAA
1 AAAAGAGAAAAGTAGAAAAA
45315 AGTAATCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
18 7 0.13
19 4 0.08
20 1 0.02
21 3 0.06
22 15 0.29
23 9 0.17
24 6 0.12
25 7 0.13
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (21 bp):
AAAAGAGAAAAGTAGAAAAAG
Found at i:45273 original size:20 final size:19
Alignment explanation
Indices: 45248--45306 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
45238 AAAGGTAGAA
*
45248 AAAGAAAAGAGAAAAATAG
1 AAAGAAAAGAGAAAAAAAG
45267 TAAAGAAGAAGAAGAAAAAAAG
1 -AAAGAA-AAG-AGAAAAAAAG
45289 -AAGAAAAAGAGAAAAAAA
1 AAAG-AAAAGAGAAAAAAA
45307 TAGAAAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
19 9 0.26
20 12 0.34
21 5 0.14
22 9 0.26
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (19 bp):
AAAGAAAAGAGAAAAAAAG
Found at i:45290 original size:17 final size:18
Alignment explanation
Indices: 45268--45314 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
45258 GAAAAATAGT
*
45268 AAAGAAGAAGAAGA-AAA
1 AAAGAAGAAAAAGAGAAA
45285 AAAGAAGAAAAAGAGAAA
1 AAAGAAGAAAAAGAGAAA
45303 AAA-ATAGAAAAA
1 AAAGA-AGAAAAA
45315 AGTAATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAGAAGAAAAAGAGAAA
Found at i:45291 original size:11 final size:10
Alignment explanation
Indices: 45244--45315 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 10
45234 GGGAAAAGGT
45244 AGAAAAAGAAA
1 AGAAAAA-AAA
* *
45255 AGAGAAAAAT
1 AGAAAAAAAA
* *
45265 AGTAAAGAAGA
1 AG-AAAAAAAA
45276 AGAAGAAAAAA
1 AGAA-AAAAAA
*
45287 AGAAGAAAAAG
1 AGAA-AAAAAA
*
45298 AGAAAAAAAT
1 AGAAAAAAAA
45308 AGAAAAAA
1 AGAAAAAA
45316 GTAATCAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
10 19 0.39
11 30 0.61
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:45301 original size:8 final size:8
Alignment explanation
Indices: 45201--45304 Score: 56
Period size: 8 Copynumber: 13.0 Consensus size: 8
45191 AGATAAAGAT
45201 GAGAGAAAA
1 GAGA-AAAA
45210 GA-AAAAA
1 GAGAAAAA
* *
45217 GAGGACAA
1 GAGAAAAA
45225 GAGGAAAAA
1 GA-GAAAAA
* *
45234 GGGAAAAG
1 GAGAAAAA
45242 GTAG-AAAA
1 G-AGAAAAA
45250 -AG-AAAA
1 GAGAAAAA
45256 GAGAAAAA
1 GAGAAAAA
* *
45264 TAG-TAAA
1 GAGAAAAA
*
45271 GAAGAAGAA
1 G-AGAAAAA
*
45280 GAAAAAAA
1 GAGAAAAA
45288 GAAGAAAAA
1 G-AGAAAAA
45297 GAGAAAAA
1 GAGAAAAA
45305 AATAGAAAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 17
0.68 0.15 0.16
Matches are distributed among these distances:
6 6 0.08
7 11 0.15
8 36 0.51
9 18 0.25
ACGTcount: A:0.69, C:0.01, G:0.27, T:0.03
Consensus pattern (8 bp):
GAGAAAAA
Found at i:47197 original size:38 final size:38
Alignment explanation
Indices: 47155--47886 Score: 851
Period size: 38 Copynumber: 19.2 Consensus size: 38
47145 AACTCATTCT
* * *
47155 ATCTTTGTTATTCTTGGCTTCCCCATGAAGAGAAGTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* * * * * *
47193 ATCTTTATTATTCCTAACTCCCTCGCGAAGAGAATTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* *
47231 ATCTTTGTTATTCTTGACTTTCTCATGAAGAGAAGTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* * *
47269 ATATTTGTTATTCTTGACTTCCTAGTGAAGAGAAGGCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* *
47307 ATCTTTTTTATTATTGACTTCCTCGT-ATAGAGAAGTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGA-AGAGAAGTCA
* * * * * *
47345 ATCTTTGTTATTTTTGACTTCCTCATTAAGAAAAATCG
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* *
47383 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAATCG
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
*
47421 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCG
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* *
47459 ATCTTTGTTATTCTTGACTTCCTCGTGAAGATAAGTCG
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
*
47497 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCG
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* * *
47535 ATCTTTGCTATTCTTGACTTCCTCGTGAAGATAAGTCG
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
*
47573 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTTA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* *
47611 ATGTTTGTTATTCTTGACTTCCCCGTGAAGAGAAG-CTA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC-A
* *
47649 ATCTTTGTCATTCTTGACTTCCTTGTGAAGAGAAGTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* * * * *
47687 ATCTTTGTTATTCCTGACTCCCTTGCGAAGAGGAGTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* * ** *
47725 ATCGTCCAATGTCATTCTTGACTTCCTTATGAAGAGGAGTCA
1 ATC-T---TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* * *
47767 ATCTTTATCATTAC-TGA-TTCCCTCGTGGAGAGAAGTCA
1 ATCTTTGTTATT-CTTGACTT-CCTCGTGAAGAGAAGTCA
* *
47805 TTCTTTGTTATTCTTGACTTCCTCGAGAAGAGAAGTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
* * * * * *
47843 ATATCTGTTATTCCTGAATTTCTTGTGAAGAGAAGTCA
1 ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
47881 ATCTTT
1 ATCTTT
47887 CAGTGTTATA
Statistics
Matches: 597, Mismatches: 85, Indels: 24
0.85 0.12 0.03
Matches are distributed among these distances:
37 4 0.01
38 555 0.93
39 6 0.01
41 1 0.00
42 31 0.05
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (38 bp):
ATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA
Found at i:47987 original size:45 final size:45
Alignment explanation
Indices: 47852--48118 Score: 251
Period size: 45 Copynumber: 6.1 Consensus size: 45
47842 AATATCTGTT
* * * * *
47852 ATTCCTGAATTTCTTGTGAAGAGAAGTCAATCTTTCAG---TGTT
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * * ** *
47894 ATACTAGACTTTCTCGTGATGATAAGTCAATC--TCTGTATTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * * * * *
47937 ATTCTTGATTTTCTCGTAAAGAGGAGTTAATATTTTAGTGTTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * * *
47982 CTTCTTGACTTTCTCGCGAAGAGCAGTCAATCTTTCAATATTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
*
48027 A-ACTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * *
48071 ATTCTTGATTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGA-TGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGT-ATTGTC
48116 ATT
1 ATT
48119 TTCAACTTGA
Statistics
Matches: 178, Mismatches: 40, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
40 3 0.02
42 25 0.14
43 26 0.15
44 40 0.22
45 83 0.47
46 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (45 bp):
ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
Found at i:48049 original size:89 final size:90
Alignment explanation
Indices: 47930--48105 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 90
47920 TCAATCTCTG
* * * * * *
47930 TATTGTCATTCTTGATTTTCTCGTAAAGAGGAGTTAATATTTTAGTGTTGTCCTTCTTGACTTTC
1 TATTGTCATACTTGACTTTCTCGTAAAGAGGAGTCAATATTTCAGTATTGTCATTCTTGACTTTC
*
47995 TCGCGAAGAGCAGTCAATCTTTCAA
66 TCGCGAAGAGCAGTCAACCTTTCAA
* * *
48020 TATTGTCA-ACTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTCATTCTTGATTTTC
1 TATTGTCATACTTGACTTTCTCGTAAAGAGGAGTCAATATTTCAGTATTGTCATTCTTGACTTTC
* *
48084 TCGTGAAGAGGAGTCAACCTTT
66 TCGCGAAGAGCAGTCAACCTTT
48106 TAGTGATGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 66 0.89
90 8 0.11
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (90 bp):
TATTGTCATACTTGACTTTCTCGTAAAGAGGAGTCAATATTTCAGTATTGTCATTCTTGACTTTC
TCGCGAAGAGCAGTCAACCTTTCAA
Found at i:48097 original size:134 final size:130
Alignment explanation
Indices: 47869--48115 Score: 332
Period size: 134 Copynumber: 1.9 Consensus size: 130
47859 AATTTCTTGT
* * * * *
47869 GAAGAGAAGTCAATCTTTCAGTGTTATACTAGACTTTCTCGTGATGATAAGTCAATCTCTGTATT
1 GAAGAGAAGTCAATCTTTCAATATTATACTAGACTTTCTCGTGAAGAGAAGTCAATCTCAGTATT
* * *
47934 GTCATTCTTGATTTTCTCGTAAAGAGGAGTTAATATTTTAGTGTTGTCCTTCTTGACTTTCTCGC
66 GTCATTCTTGATTTTCTCGTAAAGAGGAGTCAACATTTTAGTGATGTCCTTCTTGACTTTCTCGC
* * * *
47999 GAAGAGCAGTCAATCTTTCAATATTGTCAACTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAG
1 GAAGAGAAGTCAATCTTTCAATATTAT--ACTAGACTTTCTCGTGAAGAGAAGTCAATC--TCAG
* *
48064 TATTGTCATTCTTGATTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTC
62 TATTGTCATTCTTGATTTTCTCGTAAAGAGGAGTCAACATTTTAGTGATGTC
48116 ATTTTCAACT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
130 23 0.23
132 26 0.26
134 50 0.51
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (130 bp):
GAAGAGAAGTCAATCTTTCAATATTATACTAGACTTTCTCGTGAAGAGAAGTCAATCTCAGTATT
GTCATTCTTGATTTTCTCGTAAAGAGGAGTCAACATTTTAGTGATGTCCTTCTTGACTTTCTCGC
Found at i:48199 original size:50 final size:48
Alignment explanation
Indices: 47985--48205 Score: 203
Period size: 50 Copynumber: 4.7 Consensus size: 48
47975 TGTTGTCCTT
* *
47985 CTTGACTTTCTCGCGAAGAGCAGTCAATCTTTCA---A--T-ATTGTCAA
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGATGTCATT-TCAA
* *
48029 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGT-ATTGTCA-TT---
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGA-TGTCATTTCAA
* *
48074 CTTGATTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTTTCAA
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGATGTCA-TTTCAA
* * *
48124 CTTGACTTTCTCACAAAGAGAAGTCAAGCTTTTAGTGATGTCATTCTCAA
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGATGTCATT-TCAA
*
48174 CTTGACTTTCTCGCGGAGAGGAGTCAACTTTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACTTTT
48206 CAGTAGTATT
Statistics
Matches: 149, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
44 32 0.21
45 38 0.26
46 2 0.01
47 2 0.01
48 1 0.01
49 9 0.06
50 65 0.44
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (48 bp):
CTTGACTTTCTCGCGAAGAGGAGTCAACTTTTAGTGATGTCATTTCAA
Found at i:49004 original size:134 final size:134
Alignment explanation
Indices: 48762--49362 Score: 773
Period size: 134 Copynumber: 4.5 Consensus size: 134
48752 AATGTTTGAT
* * * * *
48762 TTTCAGATTTGGTCTTCTTGAAGA-CAAGAGAAGCAAACCAAATTC-AATTCAATCTTCCCTGAA
1 TTTCAGATTTGGTCTTCCTGAAGAGC-AGTGAAGCAAATC-GATTCTGATTCAATCTTCCCTGAA
* *
48825 GAGC-ACTGAAGTGGATCAAAGTTTACTCGAGTCTGATCTCTCCTAAAGAGTAGAT-GAGTAGAT
64 GAGCAAC-GAAGTGGATCAAAGTTTACTCGAGTCTGATCTCCCCTAAAGAGTAG-TGGAGCAGAT
48888 TCTTCTTC
127 TCTTCTTC
* *
48896 TTTCAGATTTGGTATTCCTTAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
** * * *
48961 GCAACGAAGTATATCAAAG-TTATCTCGAGTCTGATATCCCCTAAAGAGTAGTAGAGCATATTCT
66 GCAACGAAGTGGATCAAAGTTTA-CTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCT
*
49025 TCTTA
130 TCTTC
* *
49030 TTTTAGATTTGGTCTTCCTGAAGAGCAGTGAAGTAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* * * *
49095 GAAACGAAGTGGATCAAAATTTCCTCGAGTCTGATCTCCCATAAAGAGTAGTGGAGCAGATTCTT
66 GCAACGAAGTGGATCAAAGTTTACTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTT
49160 CTTC
131 CTTC
* *
49164 TATCAGATTTGGTCTTCTTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* *** * *
49229 GTAGTAAAGTGGATAAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTT
66 GCAACGAAGTGGATCAAAGTTTACTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTT
*
49294 CCTC
131 CTTC
* * * * * * *
49298 TTTTAGATTTGGTCTTCCTGATA-AGTAATAAAGCAAATCGATTCCGATTCAATCTTTCCTAAAG
1 TTTCAGATTTGGTCTTCCTGA-AGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAG
49362 A
65 A
49363 ATAATTGAAT
Statistics
Matches: 410, Mismatches: 50, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
133 8 0.02
134 396 0.97
135 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (134 bp):
TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
GCAACGAAGTGGATCAAAGTTTACTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTT
CTTC
Found at i:49584 original size:16 final size:15
Alignment explanation
Indices: 49556--49587 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
49546 CGGAACTGTC
49556 TTTATTTATTATTAT
1 TTTATTTATTATTAT
49571 TTTATTTAATTATTAT
1 TTTATTT-ATTATTAT
49587 T
1 T
49588 AATATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTATTATTAT
Found at i:54152 original size:87 final size:88
Alignment explanation
Indices: 54039--54212 Score: 233
Period size: 87 Copynumber: 2.0 Consensus size: 88
54029 GCTCTATTCC
* * * * *
54039 ACATGATCTAGCTAAAACTAAAAATGATTAATTATCATCCAATGGACCGAACAGTAATGAGGAAA
1 ACATGATATAACTAAAACGAAAAATGATTAACTATCATCCAAAGGACCGAACAGTAATGAGGAAA
54104 GAATACAAACAAAAAGATGCTTA
66 GAATACAAACAAAAAGATGCTTA
** **
54127 ACATGATATAACTAAAA-GAAAAATGATTAACTATCATCCAAAGGATTGAGTAGTAATGAGGAAA
1 ACATGATATAACTAAAACGAAAAATGATTAACTATCATCCAAAGGACCGAACAGTAATGAGGAAA
* * *
54191 GAATACATATAAAAAGGTGCTT
66 GAATACAAACAAAAAGATGCTT
54213 GTCAATCAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
87 59 0.80
88 15 0.20
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (88 bp):
ACATGATATAACTAAAACGAAAAATGATTAACTATCATCCAAAGGACCGAACAGTAATGAGGAAA
GAATACAAACAAAAAGATGCTTA
Done.