Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003531.1 Hibiscus syriacus cultivar Beakdansim tig00007454_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: 90993
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2131 original size:130 final size:130
Alignment explanation
Indices: 1969--2279 Score: 342
Period size: 131 Copynumber: 2.4 Consensus size: 130
1959 ATAATTTTAA
* * *
1969 GAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTGAAA-C
1 GAGTGAAAAAGATAATATCTAA-TATTTCCAATCGAGAATAAATGACCTCTCGTACATT-AAAGC
* * * * * * *
2033 ATTCATTTATTACCCCAAT-TAAATAAAAAGATATTACTATTTCGTCTTAA-AATTCAATATCGA
64 AGTAATTTATTACCCCAATCAAAATAAAAAGATATCACTATTTCATCCTAAGAA-TCAATATCAA
2096 TTC
128 TTC
*
2099 GAGTGAAAAAGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCTTACATTAAAGCA
1 GAGTGAAAAAGATAATATCTAAT-ATTTCCAATCGAGAATAAATGACCTCTCGTACATTAAAGCA
* * * * *
2164 GTAATTTATTGCTCCAATCAAAATGAAGAGATATCACTATTTCATCCTAAGAATCAATATTAATT
65 GTAATTTATTACCCCAATCAAAATAAAAAGATATCACTATTTCATCCTAAGAATCAATATCAATT
2229 C
130 C
* * * * * *
2230 GAGAGATAACA-ACAATATCAAACTAATTCCAATTGAGAATAAATGACCTC
1 GAGTGA-AAAAGATAATATCTAA-TATTTCCAATCGAGAATAAATGACCTC
2280 AAATACCTTA
Statistics
Matches: 153, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
129 4 0.03
130 69 0.45
131 74 0.48
132 6 0.04
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (130 bp):
GAGTGAAAAAGATAATATCTAATATTTCCAATCGAGAATAAATGACCTCTCGTACATTAAAGCAG
TAATTTATTACCCCAATCAAAATAAAAAGATATCACTATTTCATCCTAAGAATCAATATCAATTC
Found at i:3822 original size:2 final size:2
Alignment explanation
Indices: 3815--3847 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3805 TATGATTCTT
3815 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 T
3848 GTTCTTTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5351 original size:22 final size:22
Alignment explanation
Indices: 5321--5381 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
5311 ACCGATACCA
*
5321 AAGGGAGGTATCGATACCAACC
1 AAGGAAGGTATCGATACCAACC
5343 AAGGAAGGTATCGATACCAACC
1 AAGGAAGGTATCGATACCAACC
*
5365 AAGGGAA-GTATCAATAC
1 AA-GGAAGGTATCGATAC
5382 TGTTGAAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 32 0.89
23 4 0.11
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.15
Consensus pattern (22 bp):
AAGGAAGGTATCGATACCAACC
Found at i:5986 original size:24 final size:24
Alignment explanation
Indices: 5959--6014 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
5949 CGGGATACTC
*
5959 CTACGTGGTCTTTAGGGACAAATT
1 CTACGTGGTCCTTAGGGACAAATT
* *
5983 CTACGCGGTCCTTCGGGACAAATT
1 CTACGTGGTCCTTAGGGACAAATT
*
6007 CTATGTGG
1 CTACGTGG
6015 CACTTCGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (24 bp):
CTACGTGGTCCTTAGGGACAAATT
Found at i:6022 original size:24 final size:24
Alignment explanation
Indices: 5912--6011 Score: 71
Period size: 24 Copynumber: 4.3 Consensus size: 24
5902 GAGTCGAGGG
* *
5912 TTCTATGCGGTCCTTTGGGGC-AA
1 TTCTATGCGGTCCTTCGGGACAAA
* * * *
5935 -TCTATGTGATCCTTCGGGA-TAC
1 TTCTATGCGGTCCTTCGGGACAAA
* * * * *
5957 TCCTACGTGGTCTTTAGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
*
5981 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
6005 TTCTATG
1 TTCTATG
6012 TGGCACTTCG
Statistics
Matches: 57, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
22 16 0.28
23 14 0.25
24 27 0.47
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (24 bp):
TTCTATGCGGTCCTTCGGGACAAA
Found at i:8507 original size:17 final size:18
Alignment explanation
Indices: 8485--8521 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
8475 ACCAATTTTT
*
8485 AAAAAAATTGA-AATTAA
1 AAAAAAATTAAGAATTAA
8502 AAAAAAATTAAGAATTAA
1 AAAAAAATTAAGAATTAA
8520 AA
1 AA
8522 TAACCAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAAAAATTAAGAATTAA
Found at i:10312 original size:2 final size:2
Alignment explanation
Indices: 10305--10345 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
10295 AGTAGGCTGC
10305 TA TA TA 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 TA TA TA T
10346 TTGGTGTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10819 original size:36 final size:36
Alignment explanation
Indices: 10774--10843 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
10764 ATCTTAATAA
10774 AAAAAAATATTATGTATATTTTTATTGAGTTATTAT
1 AAAAAAATATTATGTATATTTTTATTGAGTTATTAT
10810 AAAAAAATATTATGTATATTTTTATTGAGTTATT
1 AAAAAAATATTATGTATATTTTTATTGAGTTATT
10844 TCTTAAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (36 bp):
AAAAAAATATTATGTATATTTTTATTGAGTTATTAT
Found at i:18972 original size:13 final size:13
Alignment explanation
Indices: 18952--18982 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
18942 ACCCAACCTA
18952 TTGA-CCGACTCG
1 TTGACCCGACTCG
18964 TTGACCCGACTCG
1 TTGACCCGACTCG
18977 TTGACC
1 TTGACC
18983 GTTGACCGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (13 bp):
TTGACCCGACTCG
Found at i:21471 original size:24 final size:25
Alignment explanation
Indices: 21444--21551 Score: 107
Period size: 24 Copynumber: 4.5 Consensus size: 25
21434 AAATATTTTA
*
21444 TCTGATTTCTGACT-TGAATTATGT
1 TCTGATTTCTGACTCTGAATTCTGT
* * *
21468 TCTGATATATGAC-CTGAATTTTGT
1 TCTGATTTCTGACTCTGAATTCTGT
*
21492 TCTGATTTCTGA-TCTGGATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
* * *
21516 TATGATATCTG-TTCTGAATTCTGT
1 TCTGATTTCTGACTCTGAATTCTGT
*
21540 TATGATTTCTGA
1 TCTGATTTCTGA
21552 TATCTCCGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (25 bp):
TCTGATTTCTGACTCTGAATTCTGT
Found at i:21496 original size:12 final size:11
Alignment explanation
Indices: 21489--21546 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
21479 ACCTGAATTT
21489 TGTTCTGATTTC
1 TGTTCTGA-TTC
*
21501 TGATCTGGATTC
1 TGTTCT-GATTC
*
21513 TGTTATGATATC
1 TGTTCTGAT-TC
21525 TGTTCTGAATTC
1 TGTTCTG-ATTC
*
21537 TGTTATGATT
1 TGTTCTGATT
21547 TCTGATATCT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 6 0.16
12 28 0.74
13 4 0.11
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (11 bp):
TGTTCTGATTC
Found at i:21501 original size:48 final size:48
Alignment explanation
Indices: 21444--21552 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
21434 AAATATTTTA
* *
21444 TCTGATTTCTGA-CTTGAATTATGTTCTGATATATGACCTGAATTTTGT
1 TCTGATTTCTGATC-TGAATTATGTTATGATATATGACCTGAATTCTGT
* * * **
21492 TCTGATTTCTGATCTGGATTCTGTTATGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTATGTTATGATATATGACCTGAATTCTGT
*
21540 TATGATTTCTGAT
1 TCTGATTTCTGAT
21553 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 51 0.98
49 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTATGTTATGATATATGACCTGAATTCTGT
Found at i:21549 original size:12 final size:12
Alignment explanation
Indices: 21510--21550 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
21500 CTGATCTGGA
21510 TTCTGTTATGAT
1 TTCTGTTATGAT
* * *
21522 ATCTGTTCTGAA
1 TTCTGTTATGAT
21534 TTCTGTTATGAT
1 TTCTGTTATGAT
21546 TTCTG
1 TTCTG
21551 ATATCTCCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (12 bp):
TTCTGTTATGAT
Found at i:25819 original size:24 final size:24
Alignment explanation
Indices: 25786--25857 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
25776 TATATGACCA
* *
25786 GAATTCTGTTCTGATTTTTGATAT
1 GAATTATGTTATGATTTTTGATAT
* * * * *
25810 GGATTATGTTATGATATCTGTTCT
1 GAATTATGTTATGATTTTTGATAT
* *
25834 GAATTATGTTTTGATTTTTTATAT
1 GAATTATGTTATGATTTTTGATAT
25858 CTCCGTTTAA
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (24 bp):
GAATTATGTTATGATTTTTGATAT
Found at i:27236 original size:22 final size:22
Alignment explanation
Indices: 27211--27265 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
27201 TCAGGAGTTA
* *
27211 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
27233 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
27255 CGGGAGTTATA
1 CAGGAGTTATA
27266 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:31214 original size:2 final size:2
Alignment explanation
Indices: 31207--31241 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31197 GTACAAAATA
31207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31242 GGTTAAAGTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32887 original size:24 final size:23
Alignment explanation
Indices: 32852--32913 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
32842 TTTTAATAAT
*
32852 AAAAAATCTTTAATATTCA-ATCCA
1 AAAAAATATTTAATATT-ATAT-CA
* *
32876 AAAAAATATTTAA-AATATATTA
1 AAAAAATATTTAATATTATATCA
32898 AAAAAATATTTAATAT
1 AAAAAATATTTAATAT
32914 ATGTTAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 15 0.47
23 5 0.16
24 12 0.38
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAAAATATTTAATATTATATCA
Found at i:32895 original size:11 final size:11
Alignment explanation
Indices: 32876--32910 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
32866 ATTCAATCCA
32876 AAAAAATATTT
1 AAAAAATATTT
* *
32887 AAAATATATTA
1 AAAAAATATTT
32898 AAAAAATATTT
1 AAAAAATATTT
32909 AA
1 AA
32911 TATATGTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAAAATATTT
Found at i:32900 original size:22 final size:22
Alignment explanation
Indices: 32875--32922 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
32865 TATTCAATCC
32875 AAAAAAATATTTAAAATATATT
1 AAAAAAATATTTAAAATATATT
* *
32897 AAAAAAATATTTAATATATGTT
1 AAAAAAATATTTAAAATATATT
32919 AAAA
1 AAAA
32923 GACATTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAAAATATTTAAAATATATT
Found at i:34376 original size:15 final size:14
Alignment explanation
Indices: 34356--34386 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
34346 TTTTATAGTT
34356 TTATTATTTTTATAA
1 TTATTATTTTT-TAA
34371 TTATTATTTTTTAA
1 TTATTATTTTTTAA
34385 TT
1 TT
34387 CAAATTGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATTTTTTAA
Found at i:34382 original size:17 final size:17
Alignment explanation
Indices: 34346--34386 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
34336 ATAATTTTGC
*
34346 TTTTATAGTTTTATTAT
1 TTTTATAATTTTATTAT
34363 TTTTATAA--TTATTAT
1 TTTTATAATTTTATTAT
34378 TTTT-TAATT
1 TTTTATAATT
34387 CAAATTGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
17 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTATAATTTTATTAT
Found at i:35095 original size:2 final size:2
Alignment explanation
Indices: 35088--35116 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35078 TAAATAGAAT
35088 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 T
35117 TAAGTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36312 original size:19 final size:18
Alignment explanation
Indices: 36273--36317 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
36263 ACTTTTGATA
* *
36273 TTTATTATAAAGTTTATT
1 TTTATTTTAAAGTTAATT
36291 TTTATTTTAAAGTCTAATT
1 TTTATTTTAAAGT-TAATT
36310 TTTATTTT
1 TTTATTTT
36318 TGAAATCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTTAAAGTTAATT
Found at i:36368 original size:35 final size:35
Alignment explanation
Indices: 36322--36392 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
36312 TATTTTTGAA
*
36322 ATCATATAGTGCAAGGATGATGAATAACCAAATAC
1 ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
36357 ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
1 ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
36392 A
1 A
36393 AAAGTAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.21
Consensus pattern (35 bp):
ATCATATAGTGCAAGGATGATGAAGAACCAAATAC
Found at i:36509 original size:35 final size:35
Alignment explanation
Indices: 36463--36530 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
36453 TTACTTTTGG
*
36463 ATTTGGTTCTTCATCATCCTTACGCTATATGATGT
1 ATTTGGTTCTTCATCATCCTTACACTATATGATGT
* *
36498 ATTTGGTTCTTCATCATCTTTGCACTATATGAT
1 ATTTGGTTCTTCATCATCCTTACACTATATGAT
36531 TTCAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (35 bp):
ATTTGGTTCTTCATCATCCTTACACTATATGATGT
Found at i:36570 original size:18 final size:19
Alignment explanation
Indices: 36535--36579 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
36525 TATGATTTCA
*
36535 AAAATAAAAATTAGACTTT
1 AAAATAAAAATTAAACTTT
36554 AAAATAAAAA-TAAACTTT
1 AAAATAAAAATTAAACTTT
*
36572 ATAATAAA
1 AAAATAAA
36580 TATCAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAAAATTAAACTTT
Found at i:38953 original size:20 final size:20
Alignment explanation
Indices: 38928--38965 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38918 AAATATAGAA
*
38928 AATTTAGATAAATTAAAAAT
1 AATTTAAATAAATTAAAAAT
*
38948 AATTTAAATAATTTAAAA
1 AATTTAAATAAATTAAAA
38966 TAGTAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AATTTAAATAAATTAAAAAT
Found at i:40133 original size:22 final size:21
Alignment explanation
Indices: 40064--40133 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
40054 AGAATATGTC
* *
40064 TTTTAACATATATTAAATATTT
1 TTTTAATATATATTAAAGA-TT
*
40086 TTTTAATATATTTTAAAGATT
1 TTTTAATATATATTAAAGATT
40107 TTTTAAT-TGAATATTAAAGATT
1 TTTTAATAT--ATATTAAAGATT
40129 TTTTA
1 TTTTA
40134 TTATTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 9 0.21
22 32 0.76
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTAATATATATTAAAGATT
Found at i:41901 original size:20 final size:20
Alignment explanation
Indices: 41876--41931 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
41866 AGTGGCTGAA
*
41876 AATCGGTTTGACCGGTTTTG
1 AATCGGTTTGACCGGTTTCG
41896 AATCGGTTTTGACCGG-TTCG
1 AATCGG-TTTGACCGGTTTCG
*
41916 AATCAGTTTGACCGGT
1 AATCGGTTTGACCGGT
41932 CTGACCCGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 9 0.28
20 14 0.44
21 9 0.28
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.36
Consensus pattern (20 bp):
AATCGGTTTGACCGGTTTCG
Found at i:41949 original size:5 final size:5
Alignment explanation
Indices: 41934--41982 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
41924 TGACCGGTCT
* *
41934 GACCC GA-CC GACCC GACTC GACCC GACCGTT GACCC GACCC GACCC GAC
1 GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GAC
41983 TGTTGACCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
4 4 0.11
5 29 0.78
7 4 0.11
ACGTcount: A:0.20, C:0.51, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:41971 original size:22 final size:22
Alignment explanation
Indices: 41943--41990 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
41933 TGACCCGACC
*
41943 GACCCGACTCGACCCGACCGTT
1 GACCCGACCCGACCCGACCGTT
*
41965 GACCCGACCCGACCCGACTGTT
1 GACCCGACCCGACCCGACCGTT
41987 GACC
1 GACC
41991 GTTGACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCCGACCGTT
Found at i:49231 original size:9 final size:9
Alignment explanation
Indices: 49179--49239 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
49169 GTGGCTGAAA
*
49179 ACCGATTTG
1 ACCGGTTTG
49188 ACCGGTTTTG
1 ACCGG-TTTG
49198 AACCGGTTTCG
1 -ACCGGTTT-G
* *
49209 ATCGGTTCG
1 ACCGGTTTG
49218 AACCGGTTTG
1 -ACCGGTTTG
*
49228 ACCGGTCTG
1 ACCGGTTTG
49237 ACC
1 ACC
49240 CGACCCGACT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 16 0.38
10 20 0.48
11 6 0.14
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:53710 original size:10 final size:10
Alignment explanation
Indices: 53681--53768 Score: 85
Period size: 10 Copynumber: 9.1 Consensus size: 10
53671 GCTGCTGGAA
53681 AACCGGTTTG
1 AACCGGTTTG
*
53691 -ACCAGTTTTG
1 AACC-GGTTTG
53701 AACCGGTTTG
1 AACCGGTTTG
*
53711 -ACCGGTTCG
1 AACCGGTTTG
53720 AACCGGTTTG
1 AACCGGTTTG
*
53730 -ACCGGTCTG
1 AACCGGTTTG
53739 AACCGGTTTG
1 AACCGGTTTG
* *
53749 -ACCGATCTG
1 AACCGGTTTG
*
53758 AACCGGGTTG
1 AACCGGTTTG
53768 A
1 A
53769 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 26 0.42
10 33 0.53
11 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:53724 original size:19 final size:20
Alignment explanation
Indices: 53681--53770 Score: 123
Period size: 19 Copynumber: 4.7 Consensus size: 20
53671 GCTGCTGGAA
* *
53681 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACCGGTTCTG
53701 AACCGGTTTGACCGGTTC-G
1 AACCGGTTTGACCGGTTCTG
53720 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
53739 AACCGGTTTGACC-GATCTG
1 AACCGGTTTGACCGGTTCTG
*
53758 AACCGGGTTGACC
1 AACCGGTTTGACC
53771 CGACCCGACT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
18 3 0.05
19 46 0.71
20 16 0.25
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:53786 original size:17 final size:17
Alignment explanation
Indices: 53764--53804 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
53754 TCTGAACCGG
*
53764 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
53781 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
53798 GTTGACC
1 GTTGACC
53805 GTGACCGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:60998 original size:9 final size:9
Alignment explanation
Indices: 60984--61034 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
60974 CTGCTGGAAA
60984 ACCGGTTTG
1 ACCGGTTTG
*
60993 ACCGGTTCG
1 ACCGGTTTG
*
61002 AACCGTTTTG
1 -ACCGGTTTG
*
61012 ACCGGTCTG
1 ACCGGTTTG
61021 AACCGGTTTG
1 -ACCGGTTTG
61031 ACCG
1 ACCG
61035 ATCTGAACCG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:61011 original size:19 final size:19
Alignment explanation
Indices: 60983--61052 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
60973 GCTGCTGGAA
60983 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
*
61002 AACCGTTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
61021 AACCGGTTTGACCGATCTG
1 AACCGGTTTGACCGGTCTG
*
61040 AACCGGGTTGACC
1 AACCGGTTTGACC
61053 CGACCCGACT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 45 0.98
20 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:61068 original size:17 final size:17
Alignment explanation
Indices: 61046--61103 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
61036 TCTGAACCGG
61046 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
61063 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
* *
61080 GTTGACCCAACCCGACC
1 GTTGACCCGACCCGACT
61097 GTTGACC
1 GTTGACC
61104 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.19, C:0.41, G:0.22, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:61105 original size:7 final size:7
Alignment explanation
Indices: 61093--61123 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
61083 GACCCAACCC
61093 GACCGTT
1 GACCGTT
61100 GACCGTT
1 GACCGTT
61107 GACCGTT
1 GACCGTT
61114 GACCGTT
1 GACCGTT
61121 GAC
1 GAC
61124 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:66763 original size:2 final size:2
Alignment explanation
Indices: 66756--66780 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66746 TTAAAATTAA
66756 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
66781 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:76109 original size:24 final size:24
Alignment explanation
Indices: 76068--76140 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
76058 ATAAATGGAG
*
76068 ATATCAGAAATAAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
76092 ATATCAGATATCATAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
* * *
76116 AGATCAAAAATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
76140 A
1 A
76141 GGTAATGTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:80842 original size:24 final size:24
Alignment explanation
Indices: 80808--80862 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
80798 AAACGAAGAT
* *
80808 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
*
80832 ATCAGATATCAAAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
*
80856 AACAGAA
1 ATCAGAA
80863 TTCAGGTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:83370 original size:17 final size:18
Alignment explanation
Indices: 83348--83389 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
83338 GGTCAACTGT
83348 GGTCAACACCA-GTCAAC
1 GGTCAACACCAGGTCAAC
**
83365 GGTCAAC-GTAGGTCAAC
1 GGTCAACACCAGGTCAAC
83382 GGTCAACA
1 GGTCAACA
83390 GTCGACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.14
Consensus pattern (18 bp):
GGTCAACACCAGGTCAAC
Found at i:85564 original size:24 final size:24
Alignment explanation
Indices: 85537--85608 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
85527 AAACGAAGAT
*
85537 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
85561 ATCAGATATCAAAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
85585 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
85609 GTAATGTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:85608 original size:12 final size:12
Alignment explanation
Indices: 85549--85608 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
85539 CATAAATCAA
85549 AACAGAATTCAG
1 AACAGAATTCAG
* *
85561 ATCAG-ATATCAA
1 AACAGAAT-TCAG
*
85573 AACAGAATCCAG
1 AACAGAATTCAG
* *
85585 ATCAGAAATCAG
1 AACAGAATTCAG
85597 AACAGAATTCAG
1 AACAGAATTCAG
85609 GTAATGTATA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Done.