Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000454.1 Hibiscus syriacus cultivar Beakdansim tig00000841_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: 66083
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1848 original size:5 final size:5
Alignment explanation
Indices: 1838--1864 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1828 CCAAGGTACC
1838 TTGCA TTGCA TTGCA TTGCA TTGCA TT
1 TTGCA TTGCA TTGCA TTGCA TTGCA TT
1865 CATAGCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTGCA
Found at i:2407 original size:15 final size:16
Alignment explanation
Indices: 2387--2416 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2377 CCCTTTCATC
2387 TAGAGT-ATGGGATGG
1 TAGAGTGATGGGATGG
2402 TAGAGTGATGGGATG
1 TAGAGTGATGGGATG
2417 ACTCTCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27
Consensus pattern (16 bp):
TAGAGTGATGGGATGG
Found at i:8913 original size:20 final size:20
Alignment explanation
Indices: 8873--8914 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
8863 ATTCCACCTC
* *
8873 ATGCAACTATATGCTCTTAA
1 ATGCAACTATATGATCCTAA
*
8893 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
8913 AT
1 AT
8915 CGGTTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:10144 original size:30 final size:32
Alignment explanation
Indices: 10086--10145 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
10076 TATATGATTT
* *
10086 ATATGAATATATGATTATGTGATAATATGAGA
1 ATATGAATATAAGATTATGTAATAATATGAGA
*
10118 ATAT-AATATAAGA-TATGTAATTATATGA
1 ATATGAATATAAGATTATGTAATAATATGA
10146 TCATAGATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.52
31 8 0.32
32 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (32 bp):
ATATGAATATAAGATTATGTAATAATATGAGA
Found at i:10782 original size:19 final size:21
Alignment explanation
Indices: 10746--10784 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
10736 AAATGACTTA
10746 TATGATGATATAAGAATATGT
1 TATGATGATATAAGAATATGT
10767 TATGA-GATAT-AGAATATG
1 TATGATGATATAAGAATATG
10785 AATGTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
TATGATGATATAAGAATATGT
Found at i:14067 original size:31 final size:31
Alignment explanation
Indices: 14024--14095 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
14014 ATCAACTAAG
* *
14024 AGTATCTGAACTATTATTTTTATTTCGTTTT
1 AGTATCTAAACTATTACTTTTATTTCGTTTT
*
14055 AGTATCTAAACTATTACTTTTGTTTCGTTTT
1 AGTATCTAAACTATTACTTTTATTTCGTTTT
*
14086 ATTATCTAAA
1 AGTATCTAAA
14096 TTTTCATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.54
Consensus pattern (31 bp):
AGTATCTAAACTATTACTTTTATTTCGTTTT
Found at i:15440 original size:12 final size:14
Alignment explanation
Indices: 15409--15440 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15399 TCTTTTCTTC
15409 AATATTAATAAATA
1 AATATTAATAAATA
15423 AATATTAA-AAAT-
1 AATATTAATAAATA
15435 AATATT
1 AATATT
15441 TTTCCTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 4 0.22
14 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAATAAATA
Found at i:17262 original size:3 final size:3
Alignment explanation
Indices: 17254--17329 Score: 88
Period size: 3 Copynumber: 25.7 Consensus size: 3
17244 TATTTATTTA
*
17254 AAT AAT AAT AAT -AT ATAT AAT AAT -AT AAGT AAT AAT AAT -AT ATT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
17298 AAT AAT AAAT AAT AAT AAT AAT AA- AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
17330 AATGAAAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.12
3 47 0.73
4 9 0.14
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:17266 original size:21 final size:21
Alignment explanation
Indices: 17241--17329 Score: 72
Period size: 24 Copynumber: 4.0 Consensus size: 21
17231 TCTGGGCTTG
*
17241 TAATATTTATTTAAATAATAA
1 TAATATATATTTAAATAATAA
*
17262 TAATATATATAATAATATAAGTAA
1 TAATATATAT-TTAA-ATAA-TAA
*
17286 TAATAATATATTAATAATAAATAA
1 TAAT-ATATATTTA-AAT-AATAA
* *
17310 TAATA-ATAATAAAATAATAA
1 TAATATATATTTAAATAATAA
17330 AATGAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
20 5 0.09
21 12 0.21
22 9 0.16
23 5 0.09
24 17 0.30
25 9 0.16
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (21 bp):
TAATATATATTTAAATAATAA
Found at i:17287 original size:27 final size:25
Alignment explanation
Indices: 17252--17330 Score: 117
Period size: 24 Copynumber: 3.2 Consensus size: 25
17242 AATATTTATT
17252 TAAATAATAATAATATATATAATAA
1 TAAATAATAATAATATATATAATAA
17277 TATAAGTAATAATAATATAT-TAATAA
1 TA-AA-TAATAATAATATATATAATAA
*
17303 TAAATAATAATAATA-ATAAAATAA
1 TAAATAATAATAATATATATAATAA
17327 TAAA
1 TAAA
17331 ATGAAAAAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
23 2 0.04
24 20 0.40
25 4 0.08
26 10 0.20
27 14 0.28
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
TAAATAATAATAATATATATAATAA
Found at i:17337 original size:14 final size:14
Alignment explanation
Indices: 17254--17329 Score: 82
Period size: 14 Copynumber: 5.4 Consensus size: 14
17244 TATTTATTTA
*
17254 AATAATAATAATAT
1 AATAATAATAAAAT
*
17268 ATATAATAATATAAGT
1 A-ATAATAATA-AAAT
* *
17284 AATAATAATATATT
1 AATAATAATAAAAT
*
17298 AATAATAA-ATAAT
1 AATAATAATAAAAT
17311 AATAATAATAAAAT
1 AATAATAATAAAAT
17325 AATAA
1 AATAA
17330 AATGAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.23
14 20 0.38
15 18 0.34
16 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:17582 original size:73 final size:73
Alignment explanation
Indices: 17471--17840 Score: 591
Period size: 73 Copynumber: 5.1 Consensus size: 73
17461 CGAGTGATGG
* *
17471 AAATTTCTATTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTAAAGAAAAACAATCTCA
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
17536 AGTGAGAT
66 AGTGAGAT
* *
17544 AAATTTCTGTTTCGAGTGAAATTGTCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
17609 AGTGAGAT
66 AGTGAGAT
* *
17617 AAATTTCTGTTTCGAGTGAAACTGTCTCATGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCG
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
17682 AGTGAGAT
66 AGTGAGAT
* * * *
17690 AAATCGT-TGTTTCGAGGGAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTA
1 AAAT-TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTC
17754 AAGTGAGAT
65 AAGTGAGAT
* * *
17763 AAATTAT-TGTTTCGAGGGAAACTGTCTCAAGCGATACAAAGTTTGTTTTAAGAAAAACAATCTC
1 AAATT-TCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTC
17827 AAGTGAGAT
65 AAGTGAGAT
17836 AAATT
1 AAATT
17841 GCTATTTGAA
Statistics
Matches: 278, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
73 277 1.00
74 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (73 bp):
AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
AGTGAGAT
Found at i:18154 original size:165 final size:164
Alignment explanation
Indices: 17882--18370 Score: 816
Period size: 164 Copynumber: 3.0 Consensus size: 164
17872 TATGGATGTG
* * * * *
17882 GGAAATAGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT-
** *
17947 AGAAAAGATTGAATGAGAAACTATAGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGAT
65 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGAT
18012 TGGGTAACATGCCCCAATCTCATGATAATGCTGTT
130 TGGGTAACATGCCCCAATCTCATGATAATGCTGTT
18047 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
18112 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGAT
65 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGAT
18177 TGGGTAACATGCCCCAATCTCATGATAATGCTGTT
130 TGGGTAACATGCCCCAATCTCATGATAATGCTGTT
*
18212 GGAAATATTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTA
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTA
* * * *
18277 GAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGATT
66 GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATT
* * *
18342 GGATAACATGACCCAATCTCAAGATAATG
131 GGGTAACATGCCCCAATCTCATGATAATG
18371 TTCATTATTG
Statistics
Matches: 307, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
164 134 0.44
165 132 0.43
166 41 0.13
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (164 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTA
GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATT
GGGTAACATGCCCCAATCTCATGATAATGCTGTT
Found at i:18940 original size:22 final size:22
Alignment explanation
Indices: 18888--18941 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
18878 AAAGTTTTCC
*
18888 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
*
18910 TCTTTGAAGAGATAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
18932 TCTTTGAAGA
1 TCTTTGAAGA
18942 ATGTAGATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCTTTGAAGAGAGAATCTATCA
Found at i:23604 original size:7 final size:7
Alignment explanation
Indices: 23587--23658 Score: 56
Period size: 7 Copynumber: 9.4 Consensus size: 7
23577 ATGTTTCCTT
23587 TTTTTTC
1 TTTTTTC
23594 -TTTTTC
1 TTTTTTC
23600 TTTTTTC
1 TTTTTTC
23607 TTATTTTTTC
1 ---TTTTTTC
23617 TTTTTCATC
1 TTTTT--TC
23626 TTTTTTC
1 TTTTTTC
*
23633 TTTTCTTT
1 TTTT-TTC
23641 TTTTCTTC
1 TTTT-TTC
*
23649 TTCTTTC
1 TTTTTTC
23656 TTT
1 TTT
23659 GCTGGATGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
6 6 0.11
7 22 0.41
8 12 0.22
9 7 0.13
10 7 0.13
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:23604 original size:16 final size:16
Alignment explanation
Indices: 23584--23658 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
23574 TCCATGTTTC
*
23584 CTTTTT-TTTCTTTTT
1 CTTTTTCTTTTTTTTT
*
23599 CTTTTTTCTTATTTTTT
1 C-TTTTTCTTTTTTTTT
* *
23616 CTTTTTCATCTTTTTT
1 CTTTTTCTTTTTTTTT
23632 C-TTTTCTTTTTTTCTT
1 CTTTTTCTTTTTTT-TT
23648 CTTCTTTCTTT
1 CTT-TTTCTTT
23659 GCTGGATGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
15 11 0.22
16 22 0.45
17 9 0.18
18 7 0.14
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
CTTTTTCTTTTTTTTT
Found at i:23613 original size:23 final size:22
Alignment explanation
Indices: 23584--23658 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 22
23574 TCCATGTTTC
23584 CTTTTTTTTCTTTTTCTTTTTT
1 CTTTTTTTTCTTTTTCTTTTTT
23606 CTTATTTTTTCTTTTTCATCTTTTTT
1 CTT-TTTTTTC-TTTT--TCTTTTTT
*
23632 CTTTTCTTTT-TTTCTTCTTCTTT
1 CTTTT-TTTTCTTT-TTCTTTTTT
23655 CTTT
1 CTTT
23659 GCTGGATGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
22 3 0.07
23 18 0.39
24 7 0.15
25 3 0.07
26 15 0.33
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (22 bp):
CTTTTTTTTCTTTTTCTTTTTT
Found at i:23614 original size:26 final size:25
Alignment explanation
Indices: 23585--23654 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 25
23575 CCATGTTTCC
*
23585 TTTTTTTTCTTTTTCTTTTTTCTTAT
1 TTTTTTTTCTTCTTCTTTTTTCTT-T
*
23611 TTTTTCTTT-TTCATCTTTTTTCTTT
1 TTTTT-TTTCTTCTTCTTTTTTCTTT
23636 TCTTTTTTTCTTCTTCTTT
1 T-TTTTTTTCTTCTTCTTT
23655 CTTTGCTGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 5 0.13
26 30 0.79
27 3 0.08
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTTTTCTTCTTCTTTTTTCTTT
Found at i:23631 original size:11 final size:11
Alignment explanation
Indices: 23586--23650 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
23576 CATGTTTCCT
23586 TTTTTTTCTT-
1 TTTTTTTCTTC
23596 TTTCTTTT-TTC
1 TTT-TTTTCTTC
*
23607 TTATTTT-TTC
1 TTTTTTTCTTC
*
23617 --TTTTTCATC
1 TTTTTTTCTTC
*
23626 TTTTTTCTTTTC
1 TTTTTT-TCTTC
23638 TTTTTTTCTTC
1 TTTTTTTCTTC
23649 TT
1 TT
23651 CTTTCTTTGC
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
8 4 0.09
9 2 0.05
10 12 0.28
11 16 0.37
12 9 0.21
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:26671 original size:14 final size:14
Alignment explanation
Indices: 26652--26727 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
26642 AAATGTAATT
*
26652 ATGCAAAAATGCAA
1 ATGCAAAAATGAAA
** *
26666 ATGCAAATGTAAAA
1 ATGCAAAAATGAAA
*
26680 ATG--AAAATGTAA
1 ATGCAAAAATGAAA
* * *
26692 ATACAAACATAAAA
1 ATGCAAAAATGAAA
26706 ATGCAAAAATGCAAA
1 ATGCAAAAATG-AAA
26721 ATGCAAA
1 ATGCAAA
26728 TGTAAATATA
Statistics
Matches: 44, Mismatches: 15, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
12 7 0.16
14 27 0.61
15 10 0.23
ACGTcount: A:0.61, C:0.11, G:0.12, T:0.17
Consensus pattern (14 bp):
ATGCAAAAATGAAA
Found at i:26681 original size:20 final size:20
Alignment explanation
Indices: 26656--26712 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
26646 GTAATTATGC
*
26656 AAAAATGCAAATGCAAATGT
1 AAAAATGAAAATGCAAATGT
* **
26676 AAAAATGAAAATGTAAATAC
1 AAAAATGAAAATGCAAATGT
* *
26696 AAACATAAAAATGCAAA
1 AAAAATGAAAATGCAAA
26713 AATGCAAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAAATGAAAATGCAAATGT
Found at i:29193 original size:26 final size:21
Alignment explanation
Indices: 29140--29189 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
29130 GATAATAAAT
29140 AATAAAATTTAATACTTGAAA
1 AATAAAATTTAATACTTGAAA
29161 AATAAAATTTAATACTTGAAA
1 AATAAAATTTAATACTTGAAA
29182 AATAAAAT
1 AATAAAAT
29190 AAAACATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (21 bp):
AATAAAATTTAATACTTGAAA
Found at i:30466 original size:14 final size:13
Alignment explanation
Indices: 30449--30490 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
30439 AAAGGAATAA
*
30449 ATAATATATTTAT
1 ATAATATATATAT
30462 CATAATATATATAT
1 -ATAATATATATAT
*
30476 AT-ATATATACAT
1 ATAATATATATAT
30488 ATA
1 ATA
30491 CGAGATAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 12 0.48
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:31680 original size:3 final size:3
Alignment explanation
Indices: 31672--31748 Score: 90
Period size: 3 Copynumber: 26.0 Consensus size: 3
31662 ATATTTATTT
*
31672 TAA TAA TAA TAA T-A TATA TAA TAA T-A TAA GTAA TAA TAA T-A TAT
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA
31716 TAA TAA TAAA TAA TAA TAA TAA TAA -AA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
31749 AATGAAAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
2 8 0.12
3 48 0.74
4 9 0.14
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31685 original size:21 final size:21
Alignment explanation
Indices: 31660--31747 Score: 78
Period size: 21 Copynumber: 4.2 Consensus size: 21
31650 TCTGGGCTTG
* *
31660 TAATATTTATTTTAATAATAA
1 TAATATATATATTAATAATAA
*
31681 TAATATATATAATAAT-ATAA
1 TAATATATATATTAATAATAA
31701 GTAATAATAATATATTAATAATAAA
1 -TAAT-AT-ATATATTAATAAT-AA
31726 TAATA-ATA-A-TAATAA-AA
1 TAATATATATATTAATAATAA
31743 TAATA
1 TAATA
31748 AAATGAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
17 7 0.12
19 6 0.10
20 5 0.09
21 20 0.34
22 2 0.03
23 10 0.17
24 6 0.10
25 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (21 bp):
TAATATATATATTAATAATAA
Found at i:31706 original size:27 final size:25
Alignment explanation
Indices: 31673--31749 Score: 113
Period size: 24 Copynumber: 3.1 Consensus size: 25
31663 TATTTATTTT
31673 AATAATAATAATATATATAATAATA
1 AATAATAATAATATATATAATAATA
31698 TAAGTAATAATAATATAT-TAATAATA
1 -AA-TAATAATAATATATATAATAATA
*
31724 AATAATAATAATA-ATAAAATAATA
1 AATAATAATAATATATATAATAATA
31748 AA
1 AA
31750 ATGAAAAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
23 2 0.04
24 20 0.42
25 2 0.04
26 10 0.21
27 14 0.29
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
AATAATAATAATATATATAATAATA
Found at i:31756 original size:14 final size:14
Alignment explanation
Indices: 31672--31748 Score: 84
Period size: 14 Copynumber: 5.4 Consensus size: 14
31662 ATATTTATTT
*
31672 TAATAATAATAATA
1 TAATAATAATAAAA
*
31686 TATATAATAATATAAG
1 TA-ATAATAATA-AAA
* *
31702 TAATAATAATATAT
1 TAATAATAATAAAA
*
31716 TAATAATAA-ATAA
1 TAATAATAATAAAA
31729 TAATAATAATAAAA
1 TAATAATAATAAAA
31743 TAATAA
1 TAATAA
31749 AATGAAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.22
14 21 0.39
15 18 0.33
16 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:34011 original size:93 final size:94
Alignment explanation
Indices: 33908--34079 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 94
33898 AAGATTGCAT
* * * *
33908 GTGTGTTTGTTTCTTTATTTTTAAAGGTATTCATGTTCAATTTGTGTTCTTGTTC-GTTTATTTA
1 GTGTGTTTGTTTCTTTATTTTTAAAGGCATTCATGTTCAATTCGTGGTCGTGTTCAGTTTATTTA
33972 TTTTTGAAGGTGTTCGCGAACATGATTGC
66 TTTTTGAAGGTGTTCGCGAACATGATTGC
* * *
34001 GTGTGTTTGTTTTTTTATTTTTAAAGGCATTCATGTTCAATTCGTGGTCGTGTTCATTTTTTTTA
1 GTGTGTTTGTTTCTTTATTTTTAAAGGCATTCATGTTCAATTCGTGGTCGTGTTCAGTTTATTTA
34066 TTTTTGAAGGTGTT
66 TTTTTGAAGGTGTT
34080 TATGAACATG
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 50 0.70
94 21 0.30
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (94 bp):
GTGTGTTTGTTTCTTTATTTTTAAAGGCATTCATGTTCAATTCGTGGTCGTGTTCAGTTTATTTA
TTTTTGAAGGTGTTCGCGAACATGATTGC
Found at i:38296 original size:21 final size:21
Alignment explanation
Indices: 38254--38299 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
38244 TTTTTTTCTC
*
38254 TTTTTCTTTCAAACAACTTTT
1 TTTTTCTTTCAAACAACATTT
***
38275 TTTTTCTTTCATTTAACATTT
1 TTTTTCTTTCAAACAACATTT
38296 TTTT
1 TTTT
38300 GATGGGGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTCTTTCAAACAACATTT
Found at i:39163 original size:6 final size:5
Alignment explanation
Indices: 39152--39181 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
39142 TGATTTCTGC
39152 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
39182 CATGCTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:39208 original size:6 final size:6
Alignment explanation
Indices: 39193--39234 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
39183 ATGCTCGATC
39193 AAAATGA AAAATA AAACA-A AAAATA AAAATA AAAATA AAAAT
1 AAAAT-A AAAATA AAA-ATA AAAATA AAAATA AAAATA AAAAT
39235 GTAATGGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 1 0.03
6 26 0.79
7 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:44765 original size:18 final size:19
Alignment explanation
Indices: 44744--44790 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
44734 GTAAAAAGAT
*
44744 ATTAAAAT-AATAAAAGTG
1 ATTAAAATAAATAAAAGTA
44762 ATT-AAATAAATAAAAGTA
1 ATTAAAATAAATAAAAGTA
*
44780 ATTAAAGTAAA
1 ATTAAAATAAA
44791 AATAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGTA
Found at i:54961 original size:19 final size:20
Alignment explanation
Indices: 54937--54983 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
54927 GAAAAAACTG
*
54937 AAGAAAAAGAGA-GAACTTT
1 AAGAAAAAGACATGAACTTT
54956 AAGAAAAA-ACATGAACTTT
1 AAGAAAAAGACATGAACTTT
*
54975 AAGCAAAAG
1 AAGAAAAAG
54984 GGCAAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.60, C:0.09, G:0.17, T:0.15
Consensus pattern (20 bp):
AAGAAAAAGACATGAACTTT
Found at i:59578 original size:33 final size:33
Alignment explanation
Indices: 59542--59604 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
59532 GCTAAATCTA
59542 AAAAAATA-AAAAATAGTT-TAGGGACTAAAATG
1 AAAAAATATAAAAA-AGTTATAGGGACTAAAATG
**
59574 AAAAAATATGCAAAAGTTATAGGGACTAAAA
1 AAAAAATATAAAAAAGTTATAGGGACTAAAA
59605 GCTAATTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.21
Consensus pattern (33 bp):
AAAAAATATAAAAAAGTTATAGGGACTAAAATG
Found at i:60906 original size:24 final size:23
Alignment explanation
Indices: 60844--60907 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
60834 GGCTAGGGTA
*
60844 GGCTCCAGGTCAGGTTTGGTTTG
1 GGCTCCAGGTCAGGTTTAGTTTG
* * *
60867 GGCTCCGGGTCGGGTTCTATTTTG
1 GGCTCCAGGTCAGGTT-TAGTTTG
*
60891 GGCTCCAGGTAAGGTTT
1 GGCTCCAGGTCAGGTTT
60908 TGGTTGGGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.09, C:0.19, G:0.38, T:0.34
Consensus pattern (23 bp):
GGCTCCAGGTCAGGTTTAGTTTG
Found at i:61577 original size:137 final size:138
Alignment explanation
Indices: 61136--61726 Score: 722
Period size: 140 Copynumber: 4.3 Consensus size: 138
61126 CAAGCTACGG
* * * * ** * *
61136 GTTCTTCTCATCATGAACTCTCTACTGGAAATATCGATCCCTCGAGTGAGGCGTCCCTGATTCAA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCACTGATTCAA
* * * *
61201 CTCCAAATACGATGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTC
66 CTCCATATACGATGAATCGAGAAAAGGTTGAACAAG-T-TTCTCATTATGAACTTCTTCTCCCTC
*
61266 TATCGGATGA
129 TATCAGATGA
* * * *
61276 GTTCTTCTTATTATAAACTCTCTATTGGAAAT-TTAATCCCTCAAGTGAGGCGTTGA-TGATTCA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCG-TCACTGATTCA
** * *
61339 ACTCCATATGTGATGAATTGAGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCT
65 ACTCCATATACGATGAATCGAGAAAAGGTTGAACAAG-T-TTCTCATTATGAACTTCTTCTCCCT
61404 CTATCAGATGA
128 CTATCAGATGA
* *
61415 GTTATTCTCATTATGAACT-TCCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCACTGATTTA
1 GTTCTTCTCATTATGAACTCT-CCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCACTGATTCA
* *
61479 ACTCCATATACAATGAGTCGAGAAAAGGTTGAACAAG-TTCTCATTATGAACTTCTTCTCCCTCT
65 ACTCCATATACGATGAATCGAGAAAAGGTTGAACAAGTTTCTCATTATGAACTTCTTCTCCCTCT
61543 ATCAGATGA
130 ATCAGATGA
* *
61552 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATAACTGATTCAA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCACTGATTCAA
* ** * * *
61617 CTCAATATGTGATGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATTAACTTCTTCTCCCCC
66 CTCCATATACGATGAATCGAGAAAAGGTTGAACAAG-T-TTCTCATTATGAACTTCTTCTCCCTC
* *
61682 TATCGGACGA
129 TATCAGATGA
* * * * *
61692 GTTCTTATCGTTGTGAACTTTCCACTGGAAATGTT
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTT
61727 GATTGGTTTA
Statistics
Matches: 394, Mismatches: 49, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
137 124 0.31
138 2 0.01
139 119 0.30
140 149 0.38
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.34
Consensus pattern (138 bp):
GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTCACTGATTCAA
CTCCATATACGATGAATCGAGAAAAGGTTGAACAAGTTTCTCATTATGAACTTCTTCTCCCTCTA
TCAGATGA
Found at i:61659 original size:277 final size:277
Alignment explanation
Indices: 61172--61726 Score: 799
Period size: 277 Copynumber: 2.0 Consensus size: 277
61162 GGAAATATCG
* * * *
61172 ATCCCTCGAGTGAGGCGTCCCTGATTCAACTCCAAATACGATGAATCGAGCAAAGGTTGAACAAG
1 ATCCCTCAAGTGAGGCGTCACTGATTCAACTCCAAATACAATGAATCGAGAAAAGGTTGAACAAG
* * * * *
61237 TTCTTCTCATTATGAATTTCTTCTTCCTCTATCGGATGAGTTCTTCTTATTATAAACTCTCTATT
66 -T-TTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATAAACTCTCCATT
* * * *
61302 GGAAATTTAATCCCTCAAGTGAGGCGTTGATGATTCAACTCCATATGTGATGAATTGAGAAAAGG
129 GGAAATTTAATCCCTCAAGTGAGGCGATAATGATTCAACTCAATATGTGATGAATCGAGAAAAGG
* * *
61367 TTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCTATCAGATGAGTTATTCTCATTATGAA
194 TTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCCCTATCAGACGAGTTATTATCATTATGAA
*
61432 CTTCCCATTGGAAATGTTA
259 CTTCCCACTGGAAATGTTA
* * *
61451 ATCCCTCAAGTGAGGCGTCACTGATTTAACTCCATATACAATGAGTCGAGAAAAGGTTGAACAAG
1 ATCCCTCAAGTGAGGCGTCACTGATTCAACTCCAAATACAATGAATCGAGAAAAGGTTGAACAAG
*
61516 -TTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGG
66 TTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATAAACTCTCCATTGG
*
61580 AAATGTTAATCCCTCAAGTGAGGC-ATAACTGATTCAACTCAATATGTGATGAATCGAGCAAAGG
131 AAAT-TTAATCCCTCAAGTGAGGCGATAA-TGATTCAACTCAATATGTGATGAATCGAGAAAAGG
* * * * * *
61644 TTGAACAAGTTCTTCTCATTATTAACTTCTTCTCCCCCTATCGGACGAGTTCTTATCGTTGTGAA
194 TTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCCCTATCAGACGAGTTATTATCATTATGAA
*
61709 CTTTCCACTGGAAATGTT
259 CTTCCCACTGGAAATGTT
61727 GATTGGTTTA
Statistics
Matches: 245, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
276 64 0.26
277 123 0.50
279 58 0.24
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (277 bp):
ATCCCTCAAGTGAGGCGTCACTGATTCAACTCCAAATACAATGAATCGAGAAAAGGTTGAACAAG
TTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATAAACTCTCCATTGG
AAATTTAATCCCTCAAGTGAGGCGATAATGATTCAACTCAATATGTGATGAATCGAGAAAAGGTT
GAACAAGTTCTTCTCATTATGAACTTATTCTCCCCCTATCAGACGAGTTATTATCATTATGAACT
TCCCACTGGAAATGTTA
Found at i:62445 original size:9 final size:9
Alignment explanation
Indices: 62431--62465 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
62421 GTTTCCAGAC
62431 TCATCTTCT
1 TCATCTTCT
62440 TCATCTTCT
1 TCATCTTCT
62449 TCATCTTCT
1 TCATCTTCT
62458 TC-TCTTCT
1 TCATCTTCT
62466 CCAACATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.09, C:0.34, G:0.00, T:0.57
Consensus pattern (9 bp):
TCATCTTCT
Found at i:65824 original size:14 final size:15
Alignment explanation
Indices: 65800--65828 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
65790 CCTTGAACCC
65800 TTTTCTCTTTTCTTT
1 TTTTCTCTTTTCTTT
65815 TTTTCT-TTTTCTTT
1 TTTTCTCTTTTCTTT
65829 CTTAGGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTCTTTTCTTT
Done.