Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005866.1 Hibiscus syriacus cultivar Beakdansim tig00013789_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: 84908
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:735 original size:10 final size:10
Alignment explanation
Indices: 706--751 Score: 65
Period size: 10 Copynumber: 4.4 Consensus size: 10
696 AAAAGTGATG
706 AGAAAGAAAGA
1 AGAAA-AAAGA
717 AGAAAAAAAGA
1 AG-AAAAAAGA
728 AGAAAAAAGA
1 AGAAAAAAGA
*
738 AGAAAAATGA
1 AGAAAAAAGA
748 AGAA
1 AGAA
752 GAAGATGTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 21 0.64
11 9 0.27
12 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AGAAAAAAGA
Found at i:4971 original size:34 final size:34
Alignment explanation
Indices: 4933--5010 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
4923 ACATTCGTGC
*
4933 ATTTGATGATTATACCTGGAATGCATATTTCTGT
1 ATTTGATGATTACACCTGGAATGCATATTTCTGT
* * *
4967 ATTTGGTGATTGCACCTGGAGTGCATATTTCTGT
1 ATTTGATGATTACACCTGGAATGCATATTTCTGT
5001 -TTCTGATGAT
1 ATT-TGATGAT
5011 AGCACATGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 2 0.05
34 36 0.95
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (34 bp):
ATTTGATGATTACACCTGGAATGCATATTTCTGT
Found at i:5021 original size:34 final size:34
Alignment explanation
Indices: 4949--5029 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
4939 TGATTATACC
* * * *
4949 TGGAATGCATATTTCTGTATTTGGTGATTGCACC
1 TGGAGTGCATATTTCTGTATTTGATGATAGCACA
4983 TGGAGTGCATATTTCTGT-TTCTGATGATAGCACA
1 TGGAGTGCATATTTCTGTATT-TGATGATAGCACA
*
5017 TGGAGTGCTTATT
1 TGGAGTGCATATT
5030 GCGCACACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 2 0.05
34 39 0.95
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.41
Consensus pattern (34 bp):
TGGAGTGCATATTTCTGTATTTGATGATAGCACA
Found at i:8625 original size:17 final size:15
Alignment explanation
Indices: 8582--8629 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
8572 GTAAAACATC
8582 TTATATCTGTAAATA
1 TTATATCTGTAAATA
* * *
8597 TGATAACTGTAATTATT
1 TTATATCTGTAA--ATA
8614 TTATATCTGTAAATA
1 TTATATCTGTAAATA
8629 T
1 T
8630 CTAATAACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 13 0.52
17 12 0.48
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (15 bp):
TTATATCTGTAAATA
Found at i:8643 original size:17 final size:17
Alignment explanation
Indices: 8623--8681 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
8613 TTTATATCTG
8623 TAAATATCTAATAACTA
1 TAAATATCTAATAACTA
* *
8640 TAAATATATGATAACTA
1 TAAATATCTAATAACTA
* * * * *
8657 AAAACATCTTATAATTG
1 TAAATATCTAATAACTA
8674 TAAATATC
1 TAAATATC
8682 CGATAAAGGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAATATCTAATAACTA
Found at i:12289 original size:34 final size:34
Alignment explanation
Indices: 12223--12296 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
12213 CCATTTGCTT
* **
12223 TTATTATTATTAATATTATTATATTATTATATTA
1 TTATTATTATTAATATTATTATATAAAAATATTA
*
12257 TTATTATTATTATTATTATTA-ATAAAAAATATTA
1 TTATTATTATTAATATTATTATAT-AAAAATATTA
12291 TTATTA
1 TTATTA
12297 AATTTCAGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TTATTATTATTAATATTATTATATAAAAATATTA
Found at i:12296 original size:3 final size:3
Alignment explanation
Indices: 12223--12277 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
12213 CCATTTGCTT
*
12223 TTA TTA TTA TTA ATA TTA TTA -TA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12269 TTA TTA TTA
1 TTA TTA TTA
12278 ATAAAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:13648 original size:41 final size:41
Alignment explanation
Indices: 13568--13648 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
13558 ACTTTTTATA
* *
13568 TTTTAATATTATAGTTTTAATTTCATTTATTTTAGTTATTG
1 TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
* *
13609 TTTTAATTTTATA-TGTTTATTTTCA-ATATATTTAATTATT
1 TTTTAATATTATAGT-TTTAATTTCATATAT-TTTAATTATT
13649 ATTATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.64
Consensus pattern (41 bp):
TTTTAATATTATAGTTTTAATTTCATATATTTTAATTATTG
Found at i:14574 original size:27 final size:27
Alignment explanation
Indices: 14511--14568 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
14501 AATTCTTTCC
* *
14511 TTTCAAAATTTTTATATATACTTATTTT
1 TTTCATAATATTTATATATA-TTATTTT
14539 TTTCATAATATTTATATATATTATTTT
1 TTTCATAATATTTATATATATTATTTT
14566 TTT
1 TTT
14569 ATTAATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTCATAATATTTATATATATTATTTT
Found at i:23657 original size:15 final size:14
Alignment explanation
Indices: 23626--23709 Score: 66
Period size: 15 Copynumber: 5.7 Consensus size: 14
23616 TATTATGCTT
23626 AAAGAAGAAGAAA-GA
1 AAAGAA-AA-AAATGA
23641 AAAGAACAAAAATGA
1 AAAGAA-AAAAATGA
23656 AAATGAAAAAAAT-A
1 AAA-GAAAAAAATGA
**
23670 AAA-AATAAAAAAAA
1 AAAGAA-AAAAATGA
23684 TAAAGAAAAAAATGA
1 -AAAGAAAAAAATGA
23699 AAATGAAAAAA
1 AAA-GAAAAAA
23710 TAAAATAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
12 2 0.03
13 5 0.09
14 11 0.19
15 35 0.60
16 5 0.09
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.08
Consensus pattern (14 bp):
AAAGAAAAAAATGA
Found at i:23691 original size:28 final size:28
Alignment explanation
Indices: 23660--23739 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
23650 AAATGAAAAT
23660 GAAAAAAATAAAAAATAAAAAAAATAAA
1 GAAAAAAATAAAAAATAAAAAAAATAAA
* *
23688 GAAAAAAAT-GAAAAT-GAAAAAAT-AA
1 GAAAAAAATAAAAAATAAAAAAAATAAA
* *
23713 -AATAAAATAAAAAGAGAGAAAAAAATA
1 GAAAAAAATAAAAA-ATA-AAAAAAATA
23740 GAAAAATAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
24 7 0.17
25 5 0.12
26 8 0.20
27 5 0.12
28 16 0.39
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (28 bp):
GAAAAAAATAAAAAATAAAAAAAATAAA
Found at i:23709 original size:42 final size:43
Alignment explanation
Indices: 23636--23744 Score: 141
Period size: 42 Copynumber: 2.5 Consensus size: 43
23626 AAAGAAGAAG
23636 AAAGAAAAGAACAAAAATGAAAATGAAAAAAATAAAA-AATAAAAA
1 AAAG-AAAGAA-AAAAATGAAAATGAAAAAAATAAAATAA-AAAAA
* *
23681 AAATAAAGAAAAAAATGAAAATG-AAAAAATAAAATAAAATAA
1 AAAGAAAGAAAAAAATGAAAATGAAAAAAATAAAATAAAAAAA
*
23723 AAAGAGAGAAAAAAATAGAAAA
1 AAAGAAAGAAAAAAAT-GAAAA
23745 ATAGAGTCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 29 0.50
43 20 0.34
44 6 0.10
45 3 0.05
ACGTcount: A:0.79, C:0.01, G:0.10, T:0.10
Consensus pattern (43 bp):
AAAGAAAGAAAAAAATGAAAATGAAAAAAATAAAATAAAAAAA
Found at i:24776 original size:22 final size:22
Alignment explanation
Indices: 24751--24798 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
24741 ACATTCTTCG
24751 AAGATGATAGATTCTCTTTTCA
1 AAGATGATAGATTCTCTTTTCA
24773 AAGATGATAGATTCTCTTTTCA
1 AAGATGATAGATTCTCTTTTCA
24795 AAGA
1 AAGA
24799 AGAAAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
AAGATGATAGATTCTCTTTTCA
Found at i:25348 original size:112 final size:112
Alignment explanation
Indices: 25144--25480 Score: 532
Period size: 112 Copynumber: 3.0 Consensus size: 112
25134 TAGCAAAGAT
* * * *
25144 TCGAATCCATCACTCAATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTCAATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
*
25208 AGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* ** *
25256 TCGGATTCATCACTTGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCGAATTCATCACTCAATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
* *
25321 AGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
25368 TTGAATTCATCACTCAATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTCAATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
25433 AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
25480 T
1 T
25481 TAACTCTATC
Statistics
Matches: 204, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
112 169 0.83
113 35 0.17
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (112 bp):
TCGAATTCATCACTCAATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:25987 original size:28 final size:28
Alignment explanation
Indices: 25927--25993 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
25917 TCCATTTGCT
* *
25927 TTTATTATTATTAATATTATTAATATTA
1 TTTATTATTATTAATATTATTAAAAATA
*
25955 TTTATTATTATTATTATTATTAAAAA-A
1 TTTATTATTATTAATATTATTAAAAATA
25982 TATTATTATTAT
1 T-TTATTATTAT
25994 ATTTCAGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 2 0.06
28 33 0.94
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTATTATTATTAATATTATTAAAAATA
Found at i:25993 original size:3 final size:3
Alignment explanation
Indices: 25928--25976 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
25918 CCATTTGCTT
* *
25928 TTA TTA TTA TTA ATA TTA TTA ATA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
25974 TTA
1 TTA
25977 AAAAATATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28271 original size:9 final size:10
Alignment explanation
Indices: 28250--28280 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28240 GGACCGGCTG
*
28250 AAAACCGGAA
1 AAAATCGGAA
28260 AAAATCGGAA
1 AAAATCGGAA
28270 AAAATCGGAA
1 AAAATCGGAA
28280 A
1 A
28281 TTTTGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.61, C:0.13, G:0.19, T:0.06
Consensus pattern (10 bp):
AAAATCGGAA
Found at i:43573 original size:18 final size:18
Alignment explanation
Indices: 43550--43586 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43540 AACCTTACAA
43550 CTCCCTCAAGAATTATAC
1 CTCCCTCAAGAATTATAC
43568 CTCCCTCAAGAATTATAC
1 CTCCCTCAAGAATTATAC
43586 C
1 C
43587 CCAAATTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.27
Consensus pattern (18 bp):
CTCCCTCAAGAATTATAC
Found at i:44518 original size:3 final size:3
Alignment explanation
Indices: 44506--44541 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
44496 AATAAAATTG
44506 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44542 ATAAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:46617 original size:21 final size:21
Alignment explanation
Indices: 46587--46634 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
46577 AGTGTCAAAC
* *
46587 AATAACAAAATCGATAGAAAA-
1 AATAATAAAATCAATA-AAAAT
46608 AATAATAAAATCAATAAAAAT
1 AATAATAAAATCAATAAAAAT
46629 AATAAT
1 AATAAT
46635 TTTTTCGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (21 bp):
AATAATAAAATCAATAAAAAT
Found at i:53859 original size:15 final size:15
Alignment explanation
Indices: 53839--53869 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53829 GGAGAAAACT
53839 AGTTCTCATCCCATA
1 AGTTCTCATCCCATA
53854 AGTTCTCATCCCATA
1 AGTTCTCATCCCATA
53869 A
1 A
53870 AGTGAGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.06, T:0.32
Consensus pattern (15 bp):
AGTTCTCATCCCATA
Found at i:60353 original size:21 final size:21
Alignment explanation
Indices: 60317--60372 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
60307 TCACACGTTA
* *
60317 AATTCAATGGACCATGCATTG
1 AATTAAATGGAGCATGCATTG
*
60338 AATTAAATTGAGCATGCATTG
1 AATTAAATGGAGCATGCATTG
*
60359 AATTCAATGGAGCA
1 AATTAAATGGAGCA
60373 CCACGCGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (21 bp):
AATTAAATGGAGCATGCATTG
Found at i:60925 original size:15 final size:15
Alignment explanation
Indices: 60905--60938 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
60895 GTGATGTAAC
60905 ATGCGCAGGTAGAGT
1 ATGCGCAGGTAGAGT
* *
60920 ATGCGCTGGTGGAGT
1 ATGCGCAGGTAGAGT
60935 ATGC
1 ATGC
60939 ACTGGTGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.41, T:0.24
Consensus pattern (15 bp):
ATGCGCAGGTAGAGT
Found at i:60943 original size:15 final size:15
Alignment explanation
Indices: 60916--60948 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
60906 TGCGCAGGTA
*
60916 GAGTATGCGCTGGTG
1 GAGTATGCACTGGTG
60931 GAGTATGCACTGGTG
1 GAGTATGCACTGGTG
60946 GAG
1 GAG
60949 CACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.45, T:0.24
Consensus pattern (15 bp):
GAGTATGCACTGGTG
Found at i:70624 original size:6 final size:6
Alignment explanation
Indices: 70613--70671 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
70603 AGAAGAAAGA
70613 ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT
1 ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT ATCCCT
70661 ATCCCT ATCCC
1 ATCCCT ATCCC
70672 ATAGACGGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.17, C:0.51, G:0.00, T:0.32
Consensus pattern (6 bp):
ATCCCT
Found at i:73184 original size:20 final size:20
Alignment explanation
Indices: 73134--73189 Score: 94
Period size: 22 Copynumber: 2.7 Consensus size: 20
73124 AAAGTTGAAG
73134 GTGCATCGATGCATTAAGGA
1 GTGCATCGATGCATTAAGGA
73154 GTGCACATCGATGCATTAAGGA
1 GTG--CATCGATGCATTAAGGA
73176 GTGCATCGATGCAT
1 GTGCATCGATGCAT
73190 GGGAATTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.41
22 20 0.59
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (20 bp):
GTGCATCGATGCATTAAGGA
Found at i:73958 original size:63 final size:62
Alignment explanation
Indices: 73879--73999 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 62
73869 GAGGGTTTAT
* *
73879 CTATGTTCTACGGAACATATGGACTGAA-TTACCTATG-TCTTTCGGGACATATAGACAGTATAC
1 CTATGTTCTAAGGAACATATGGAC--AATTTACCTAGGTTC-TTCGGGACATATAGACAGTATAC
* *
73942 CTATGTTCTAAGGAACATATGGACAATTTACCTAGGTTCTTCGGGACCTATGGACAGT
1 CTATGTTCTAAGGAACATATGGACAATTTACCTAGGTTCTTCGGGACATATAGACAGT
74000 TGCCGAGGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 2 0.04
62 25 0.48
63 25 0.48
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (62 bp):
CTATGTTCTAAGGAACATATGGACAATTTACCTAGGTTCTTCGGGACATATAGACAGTATAC
Found at i:73960 original size:31 final size:31
Alignment explanation
Indices: 73879--73999 Score: 109
Period size: 31 Copynumber: 3.9 Consensus size: 31
73869 GAGGGTTTAT
* *
73879 CTATGTTCTACGGAACATATGGACTGAATTAC
1 CTATGTTCTACGGAACATATGGACAGTA-TAC
* * *
73911 CTATG-TCTTTCGGGACATATAGACAGTATAC
1 CTATGTTC-TACGGAACATATGGACAGTATAC
* * *
73942 CTATGTTCTAAGGAACATATGGACAATTTAC
1 CTATGTTCTACGGAACATATGGACAGTATAC
* * * *
73973 CTAGGTTCTTCGGGACCTATGGACAGT
1 CTATGTTCTACGGAACATATGGACAGT
74000 TGCCGAGGTT
Statistics
Matches: 70, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
31 48 0.69
32 22 0.31
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (31 bp):
CTATGTTCTACGGAACATATGGACAGTATAC
Found at i:74162 original size:18 final size:19
Alignment explanation
Indices: 74127--74163 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
74117 CACGGAATGT
74127 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
74147 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
74164 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:74387 original size:36 final size:38
Alignment explanation
Indices: 74314--74388 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 38
74304 GTTGGAAAAT
*
74314 ATTTATATATTTTCTTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTTAAAAAAATTAAAATCATAAA
*
74352 ATTTATATATTTT-TTTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTTAAAAAAATT-AAAATCATAAA
74388 A
1 A
74389 AGGTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 13 0.38
37 8 0.24
38 13 0.38
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (38 bp):
ATTTATATATTTTCTTTTAAAAAAATTAAAATCATAAA
Found at i:75332 original size:21 final size:22
Alignment explanation
Indices: 75297--75338 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
75287 GAAATTTTTC
75297 ACTGTTCACGGTATTGTTCATT
1 ACTGTTCACGGTATTGTTCATT
75319 ACTGTTCA-GGTATTGTTCAT
1 ACTGTTCACGGTATTGTTCAT
75339 ATCATATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (22 bp):
ACTGTTCACGGTATTGTTCATT
Done.