Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 50 of 50
Found at i:11668512 original size:14 final size:15
Alignment explanation
Indices: 11668486--11668515 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11668476 TACCCTTTGT
11668486 TTTAAATAATTTAAC
1 TTTAAATAATTTAAC
11668501 TTTAAA-AATTTAAC
1 TTTAAATAATTTAAC
11668515 T
1 T
11668516 ATTTTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAATAATTTAAC
Found at i:11668697 original size:24 final size:24
Alignment explanation
Indices: 11668648--11668699 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11668638 AATAACAAAA
**
11668648 AAAAAACAATTAGTTTATTACCTT
1 AAAAAACAATTAGTTTATTAAATT
*
11668672 AAAAAACCATTAGTTTATTAAATT
1 AAAAAACAATTAGTTTATTAAATT
11668696 AAAA
1 AAAA
11668700 TTCCACTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (24 bp):
AAAAAACAATTAGTTTATTAAATT
Found at i:11676376 original size:20 final size:20
Alignment explanation
Indices: 11676351--11676443 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
11676341 TTTTCCCAAT
11676351 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
11676371 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
*
11676391 TTTGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
11676412 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
11676433 TCGCAATGCGA
1 TCGCAATGCGA
11676444 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:11676398 original size:41 final size:41
Alignment explanation
Indices: 11676348--11676443 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
11676338 CGATTTTCCC
11676348 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
11676389 AATTTGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
11676430 AAATCGCAATGCGA
1 AATTCGCAATGCGA
11676444 TACTGACTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:11676457 original size:20 final size:20
Alignment explanation
Indices: 11676432--11676525 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
11676422 AATTGGGAAA
*
11676432 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
11676452 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
11676473 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
11676493 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
11676513 TTCGCAACGCGAT
1 ATCGCAACGCGAT
11676526 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:11676506 original size:41 final size:41
Alignment explanation
Indices: 11676429--11676506 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
11676419 GCGAATTGGG
* * **
11676429 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
11676470 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
11676507 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:11677132 original size:19 final size:19
Alignment explanation
Indices: 11677110--11677270 Score: 117
Period size: 20 Copynumber: 8.8 Consensus size: 19
11677100 CAAAATCGTA
11677110 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
11677129 TTGCGATTTTAATTTCGCGG
1 TTGCGATTTTCATTTCGC-G
11677149 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
11677168 TTGTGATTGTC---T-G-G
1 TTGCGATTTTCATTTCGCG
* **
11677182 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
11677201 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
11677215 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* * *
11677235 TTGTGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
11677255 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
11677271 AACCAAAAGA
Statistics
Matches: 111, Mismatches: 18, Indels: 26
0.72 0.12 0.17
Matches are distributed among these distances:
14 19 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 36 0.32
20 47 0.42
21 1 0.01
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:11677195 original size:33 final size:33
Alignment explanation
Indices: 11677158--11677245 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
11677148 GTTGCGATTT
* *
11677158 TCATTTCGCGTTGTGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGTGATTCTCTCGTCGCGATAG
* *
11677191 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGTGATTCTCTCGTCGCGATAG
11677224 TCATTTCCGCGTTGTGATTCTC
1 TCATTT-CGCGTTGTGATTCTC
11677246 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGTGATTCTCTCGTCGCGATAG
Found at i:11679331 original size:42 final size:42
Alignment explanation
Indices: 11679271--11679393 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
11679261 GCTCGACTCG
* * *
11679271 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
11679313 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
11679355 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
11679394 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:11679351 original size:21 final size:21
Alignment explanation
Indices: 11679327--11679393 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
11679317 TCATTCCTCG
11679327 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
11679348 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
11679369 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
11679390 AGAG
1 AGAG
11679394 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:11680770 original size:14 final size:14
Alignment explanation
Indices: 11680751--11680786 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11680741 ATTGTTTAAT
11680751 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
11680765 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
11680779 TGATTTGT
1 TGATTTGT
11680787 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:11680917 original size:19 final size:19
Alignment explanation
Indices: 11680893--11680959 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
11680883 AAAAAGTACT
*
11680893 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
11680912 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
11680926 ATCGCAACGCGAAAATG-AA
1 ATCGCAACGCG-AAATGAAA
11680945 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
11680960 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 4 0.10
19 20 0.50
20 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:11680986 original size:19 final size:19
Alignment explanation
Indices: 11680964--11681081 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
11680954 CGAAATTAAA
11680964 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
11680983 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
11680998 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
11681016 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
11681031 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * ** *
11681049 TTCGCATTGCAATAGTAAT
1 TTCGCGTTGCGATTTTCAT
11681068 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
11681082 GGACATTAAG
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
14 17 0.24
16 6 0.08
17 6 0.08
19 33 0.46
20 9 0.13
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:11681010 original size:33 final size:33
Alignment explanation
Indices: 11680968--11681058 Score: 173
Period size: 33 Copynumber: 2.8 Consensus size: 33
11680958 ATTAAATTCG
11680968 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
11681001 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
11681034 CGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGC
11681059 AATAGTAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:11683369 original size:12 final size:12
Alignment explanation
Indices: 11683352--11683376 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11683342 TTCTTCGGGA
11683352 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11683364 CTTTTTCTTCTT
1 CTTTTTCTTCTT
11683376 C
1 C
11683377 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:11684864 original size:14 final size:14
Alignment explanation
Indices: 11684845--11684881 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11684835 CATCAATTAA
11684845 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
11684859 ACAAATCATCTTTT
1 ACAAATCAACATTT
11684873 ACAAATCAA
1 ACAAATCAA
11684882 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:11685271 original size:20 final size:20
Alignment explanation
Indices: 11685246--11685296 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
11685236 ATTCATTTGA
*
11685246 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
11685266 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
11685286 TTATCGCAACG
1 CTATCGCAACG
11685297 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:11685346 original size:14 final size:14
Alignment explanation
Indices: 11685327--11685380 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
11685317 GAAAATCGCA
11685327 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
11685341 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
11685358 CATTGCAATTTTCTCG
1 --TTGCGATTTTCTCG
11685374 TTGCGAT
1 TTGCGAT
11685381 AGCCATTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:11685388 original size:33 final size:33
Alignment explanation
Indices: 11685322--11685396 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
11685312 GAAATGAAAA
* ***
11685322 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCAATTTTCTCGTTGCGATAGCCATT
11685355 TCGCATTGCAATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCAATTTTCTCGTTGCGATAGCCATT
*
11685388 TCGCGTTGC
1 TCGCATTGC
11685397 GATAGTCTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
TCGCATTGCAATTTTCTCGTTGCGATAGCCATT
Found at i:11685506 original size:14 final size:14
Alignment explanation
Indices: 11685487--11685523 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11685477 CATCAATTAA
11685487 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
11685501 ACAAATCATCTTTT
1 ACAAATCAACATTT
11685515 ACAAATCAA
1 ACAAATCAA
11685524 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:11687425 original size:20 final size:19
Alignment explanation
Indices: 11687390--11687445 Score: 94
Period size: 20 Copynumber: 2.9 Consensus size: 19
11687380 GAAACTTAAA
11687390 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
11687409 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
11687429 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
11687446 AAATCACAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:11687464 original size:14 final size:14
Alignment explanation
Indices: 11687445--11687502 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
11687435 ATGCGAAATG
*
11687445 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
11687459 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
11687475 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
11687491 AAAATCGCAACG
1 AAAATCGCAACG
11687503 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:11687488 original size:32 final size:33
Alignment explanation
Indices: 11687429--11687507 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
11687419 GGAAATGACT
*
11687429 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
*
11687462 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGACAAA
11687494 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
11687508 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGACAAA
Found at i:11687536 original size:19 final size:17
Alignment explanation
Indices: 11687514--11687608 Score: 69
Period size: 18 Copynumber: 5.6 Consensus size: 17
11687504 GAAACACAAA
11687514 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
11687533 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
11687549 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
11687565 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
11687581 TCG-TTGCGATTTTCA-T
1 TCGCTTGCGA-TTTCATT
11687597 TCGCATTGCGAT
1 TCGC-TTGCGAT
11687609 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 15 0.24
17 1 0.02
18 18 0.29
19 10 0.16
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:11687555 original size:14 final size:14
Alignment explanation
Indices: 11687536--11687593 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
11687526 TTTCATTTCG
11687536 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
11687550 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
11687566 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
11687582 CGTTGCGATTTT
1 CGTTGCGATTTT
11687594 CATTCGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:11687566 original size:32 final size:33
Alignment explanation
Indices: 11687519--11687608 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
11687509 ACAAATCGCA
11687519 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
11687552 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
11687584 TTGCGATTTTCA-TTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
11687609 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 44 0.80
33 11 0.20
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:11687627 original size:20 final size:20
Alignment explanation
Indices: 11687602--11687647 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11687592 TTCATTCGCA
11687602 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
11687622 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
11687642 TTGCGA
1 TTGCGA
11687648 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:11688145 original size:18 final size:18
Alignment explanation
Indices: 11688119--11688163 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
11688109 GTCGATCAGA
*
11688119 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
11688137 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
11688155 TGATGGCTC
1 TGATGGCTC
11688164 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:11689503 original size:20 final size:20
Alignment explanation
Indices: 11689478--11689515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11689468 AATAGTTTCT
11689478 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
11689498 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
11689516 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:11689802 original size:22 final size:22
Alignment explanation
Indices: 11689777--11689820 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11689767 GATTTAGATA
11689777 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
11689799 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
11689821 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:11690019 original size:21 final size:22
Alignment explanation
Indices: 11689989--11690084 Score: 69
Period size: 20 Copynumber: 4.6 Consensus size: 22
11689979 CGCTTTGAAA
*
11689989 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGATTATGTAAGT
* *
11690010 ATCGCGTTGCGA--AAGTAAGT
1 ATCGCATTGCGATTATGTAAGT
* * * * *
11690030 ATCTCGTTGCGATT-TTTTATT
1 ATCGCATTGCGATTATGTAAGT
*
11690051 ATCGCATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGTAAGT
11690071 ATCGCATTGCGATT
1 ATCGCATTGCGATT
11690085 TTCCCAATTC
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
19 3 0.05
20 29 0.51
21 25 0.44
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (22 bp):
ATCGCATTGCGATTATGTAAGT
Found at i:11690052 original size:41 final size:41
Alignment explanation
Indices: 11689989--11690086 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
11689979 CGCTTTGAAA
* *
11689989 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
* * * * *
11690030 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
11690071 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
11690087 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGT
Found at i:11690102 original size:41 final size:41
Alignment explanation
Indices: 11690011--11690145 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
11690001 TTATGTATTA
* * * ** *
11690011 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
11690051 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
11690093 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
11690134 TCGCGTTGCGAT
1 TCGCGTTGCGAT
11690146 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:11690116 original size:20 final size:20
Alignment explanation
Indices: 11690072--11690164 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
11690062 ATAGTCAGTA
* **
11690072 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
11690093 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
11690113 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
11690134 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
11690154 TCGCATTGCGA
1 TCGCATTGCGA
11690165 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:11690146 original size:41 final size:41
Alignment explanation
Indices: 11690072--11690167 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
11690062 ATAGTCAGTA
*
11690072 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
11690113 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
11690154 TCGCATTGCGAATT
1 TCGCATTGCGAATT
11690168 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:11690751 original size:2 final size:2
Alignment explanation
Indices: 11690744--11690774 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11690734 ATACCCAATT
11690744 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 T
11690775 TAAAAAGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11691493 original size:18 final size:18
Alignment explanation
Indices: 11691467--11691503 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11691457 GTGTCTAACA
* *
11691467 TATCCACTTTTCAACTTG
1 TATCAACTTGTCAACTTG
11691485 TATCAACTTGTCAACTTG
1 TATCAACTTGTCAACTTG
11691503 T
1 T
11691504 GGTAGCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.43
Consensus pattern (18 bp):
TATCAACTTGTCAACTTG
Found at i:11700728 original size:14 final size:14
Alignment explanation
Indices: 11700709--11700735 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11700699 TTATATCTTT
11700709 ATAATTTGGGTCAC
1 ATAATTTGGGTCAC
11700723 ATAATTTGGGTCA
1 ATAATTTGGGTCA
11700736 ACCTTTCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (14 bp):
ATAATTTGGGTCAC
Done.