Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008690.1 Hibiscus syriacus cultivar Beakdansim tig00111718_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: 531595
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:499899 original size:19 final size:19
Alignment explanation
Indices: 499874--499959 Score: 120
Period size: 19 Copynumber: 4.5 Consensus size: 19
499864 CGAAACTTAA
499874 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
*
499893 TATCGCAACGCAGAAATGAC
1 AATCGCAACGC-GAAATGAC
* * *
499913 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
499932 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
499950 AATCGCAACG
1 AATCGCAACG
499960 ACAAAATCGC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
18 10 0.16
19 33 0.54
20 18 0.30
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:499899 original size:39 final size:38
Alignment explanation
Indices: 499856--499959 Score: 111
Period size: 39 Copynumber: 2.7 Consensus size: 38
499846 TAGTTTACTT
* **
499856 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACGCGAAA-TTAAAATCGCAACGCGAAATGAAAA
* ** *
499895 TCGCAACGCAGAAATGACTATCGCAATGCGAAATGAAAA
1 TCGCAACGC-GAAATTAAAATCGCAACGCGAAATGAAAA
*
499934 TCGCAACGCGAAA-TGAAATCGCAACG
1 TCGCAACGCGAAATTAAAATCGCAACG
499960 ACAAAATCGC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 8 0.15
38 4 0.08
39 36 0.69
40 4 0.08
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.14
Consensus pattern (38 bp):
TCGCAACGCGAAATTAAAATCGCAACGCGAAATGAAAA
Found at i:499966 original size:19 final size:18
Alignment explanation
Indices: 499873--499978 Score: 112
Period size: 19 Copynumber: 5.9 Consensus size: 18
499863 ACGAAACTTA
499873 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
499891 ACTATCGCAACGCAGAAATG
1 A-AATCGCAACGC-GAAATG
* *
499911 ACTATCGCAATGCGAAATG
1 A-AATCGCAACGCGAAATG
499930 AAAATCGCAACGCGAAATG
1 -AAATCGCAACGCGAAATG
*
499949 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
499963 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
499979 CACAAATCGC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
14 9 0.12
16 8 0.10
18 10 0.13
19 31 0.40
20 19 0.25
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:500026 original size:14 final size:14
Alignment explanation
Indices: 500007--500064 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
499997 TTTCATTTCG
500007 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
500021 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
500037 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
500053 CGTTGCAATTTT
1 CGTTGCGATTTT
500065 CATTTCGCAT
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:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:500071 original size:33 final size:33
Alignment explanation
Indices: 499990--500080 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
499980 ACAAATCGCA
*
499990 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
500023 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
500055 TTGCAATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
500081 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:500099 original size:20 final size:19
Alignment explanation
Indices: 500065--500119 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
500055 TTGCAATTTT
*
500065 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
500084 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
500104 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
500120 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:500627 original size:18 final size:18
Alignment explanation
Indices: 500601--500645 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
500591 GTCGATCAGA
*
500601 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
500619 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
500637 TGATGGCTC
1 TGATGGCTC
500646 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:501988 original size:20 final size:20
Alignment explanation
Indices: 501963--502005 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
501953 AATAGTTTCT
501963 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
501983 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
502003 GAA
1 GAA
502006 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:502310 original size:22 final size:22
Alignment explanation
Indices: 502283--502326 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
502273 AGATGGAGAT
502283 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
502305 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
502327 GTGAGAGAGT
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:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:502541 original size:20 final size:20
Alignment explanation
Indices: 502515--502587 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
502505 GATTATGTAT
502515 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
502535 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
502555 TATCGCGGTT-CGAAAGTAAG
1 TATCGC-GTTGCGAAAGTCAG
*
502575 TATCTCGTTGCGA
1 TATCGCGTTGCGA
502588 TTTTTTATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.06
20 41 0.87
21 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:502606 original size:21 final size:19
Alignment explanation
Indices: 502582--502669 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 19
502572 AAGTATCTCG
502582 TTGCGATTTTTTATTATCGCA
1 TTGCGATTTTTTA-T-TCGCA
*
502603 TTGCGATTTACTTATTCGCA
1 TTGCGATTT-TTTATTCGCA
** *
502623 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTT--TTATTCGCA
*
502644 TTGCGATTTACTTATTCGCA
1 TTGCGATTT-TTTATTCGCA
502664 TTGCGA
1 TTGCGA
502670 ATTGGGAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
20 26 0.48
21 25 0.46
22 3 0.06
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTTTATTCGCA
Found at i:502623 original size:20 final size:20
Alignment explanation
Indices: 502598--502669 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
502588 TTTTTTATTA
502598 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
502618 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
502639 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
502659 TCGCATTGCGA
1 TCGCATTGCGA
502670 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:508290 original size:20 final size:20
Alignment explanation
Indices: 508265--508307 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
508255 TAGTTGAAAA
508265 TCGCGTTACGATTTTCCATT
1 TCGCGTTACGATTTTCCATT
508285 TCGCGTTACGATTTTCCATT
1 TCGCGTTACGATTTTCCATT
508305 TCG
1 TCG
508308 AGTTGCGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.26, G:0.16, T:0.44
Consensus pattern (20 bp):
TCGCGTTACGATTTTCCATT
Found at i:508316 original size:20 final size:20
Alignment explanation
Indices: 508269--508316 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
508259 TGAAAATCGC
*
508269 GTTACGATTTTCCATTTCGC
1 GTTACGATTTTCCATTTCGA
508289 GTTACGATTTTCCATTTCGA
1 GTTACGATTTTCCATTTCGA
*
508309 GTTGCGAT
1 GTTACGAT
508317 AGTCCAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (20 bp):
GTTACGATTTTCCATTTCGA
Found at i:508322 original size:20 final size:20
Alignment explanation
Indices: 508269--508322 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
508259 TGAAAATCGC
** *
508269 GTTACGATTTTCCATTTCGC
1 GTTACGATAGTCCATTTCGA
**
508289 GTTACGATTTTCCATTTCGA
1 GTTACGATAGTCCATTTCGA
*
508309 GTTGCGATAGTCCA
1 GTTACGATAGTCCA
508323 AGTTGTCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (20 bp):
GTTACGATAGTCCATTTCGA
Found at i:509493 original size:43 final size:41
Alignment explanation
Indices: 509429--509537 Score: 164
Period size: 43 Copynumber: 2.6 Consensus size: 41
509419 TTAACAATCA
509429 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
* * * *
509470 CAATGAATTTGTAAACTATCGCAACAACAATTGTAGACTATCG
1 CAACGAATTTGGAAA--ATCGCAACGACAACTGTAGACTATCG
509513 CAACGAATTTGGAAAATCGCAACGA
1 CAACGAATTTGGAAAATCGCAACGA
509538 ATTTGGAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 22 0.37
43 37 0.63
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.22
Consensus pattern (41 bp):
CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
Found at i:509531 original size:19 final size:19
Alignment explanation
Indices: 509509--509556 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
509499 ATTGTAGACT
509509 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
509528 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
509547 ATCGCAACGA
1 ATCGCAACGA
509557 CAACTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:509566 original size:60 final size:62
Alignment explanation
Indices: 509466--509597 Score: 178
Period size: 60 Copynumber: 2.1 Consensus size: 62
509456 ACTGTAGACT
* * * ** *
509466 ATCGCAATGAATTTGTAAACTATCGCAACAACAATTGTAGACTATCGCAACG-AATTTGGAAA
1 ATCGCAACGAATTTGGAAAC-ATCGCAACAACAACTGTAGACTATCGCAACGCAAAATAGAAA
*
509528 ATCGCAACGAATTTGGAAA-ATCGCAACGACAACTGTAGACTATCGCAACGCAAAATAGAAA
1 ATCGCAACGAATTTGGAAACATCGCAACAACAACTGTAGACTATCGCAACGCAAAATAGAAA
509589 ATCGCAACG
1 ATCGCAACG
509598 CGATTTTCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
60 29 0.47
61 16 0.26
62 17 0.27
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (62 bp):
ATCGCAACGAATTTGGAAACATCGCAACAACAACTGTAGACTATCGCAACGCAAAATAGAAA
Found at i:509592 original size:20 final size:20
Alignment explanation
Indices: 509509--509598 Score: 76
Period size: 19 Copynumber: 4.5 Consensus size: 20
509499 ATTGTAGACT
* *
509509 ATCGCAACG-AATTTGGAAA
1 ATCGCAACGCAATATAGAAA
* *
509528 ATCGCAACG-AATTTGGAAA
1 ATCGCAACGCAATATAGAAA
* **
509547 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG-CAA-TATAGAAA
*
509569 ATCGCAACGCAAAATAGAAA
1 ATCGCAACGCAATATAGAAA
509589 ATCGCAACGC
1 ATCGCAACGC
509599 GATTTTCAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
19 28 0.47
20 14 0.23
21 5 0.08
22 13 0.22
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCAATATAGAAA
Found at i:509611 original size:41 final size:41
Alignment explanation
Indices: 509566--509682 Score: 207
Period size: 41 Copynumber: 2.9 Consensus size: 41
509556 ACAACTGTAG
* *
509566 ACTATCGCAACGCAAAATAGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
509607 ACTATCGCAACGTGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
509648 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
509683 ATTTGCGATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:509615 original size:21 final size:21
Alignment explanation
Indices: 509589--509662 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
509579 AAAATAGAAA
509589 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
509610 ATCGCAACGTGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
509630 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
509651 ATCGCAACGCGA
1 ATCGCAACGCGA
509663 AATGGAAAAT
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:509635 original size:20 final size:20
Alignment explanation
Indices: 509522--509683 Score: 96
Period size: 20 Copynumber: 8.0 Consensus size: 20
509512 GCAACGAATT
*
509522 TGGAAAATCGCAA--CGAATT
1 TGGAAAATCGCAACGCGAA-A
*
509541 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAA
** *
509561 TGTAGACTATCGCAACGCAAAA
1 TG--GAAAATCGCAACGCGAAA
* **
509583 TAGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** * *
509603 TTCAACTATCGCAACGTGAAA
1 TGGAA-AATCGCAACGCGAAA
**
509624 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
** *
509644 TTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAA
509665 TGGAAAATCGCAACGCGAA
1 TGGAAAATCGCAACGCGAA
509684 TTTGCGATAG
Statistics
Matches: 105, Mismatches: 30, Indels: 15
0.70 0.20 0.10
Matches are distributed among these distances:
19 13 0.12
20 45 0.43
21 32 0.30
22 15 0.14
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:510263 original size:3 final size:3
Alignment explanation
Indices: 510255--510285 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
510245 AAAATCAAAG
510255 AGA AGA AGA AGA AGA AGA AGA AGA ATGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
510286 TTTACCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:512665 original size:32 final size:32
Alignment explanation
Indices: 512624--512718 Score: 129
Period size: 32 Copynumber: 3.0 Consensus size: 32
512614 TGAAAAAAAC
*
512624 TTTTT-AGTGATATATCACTTAATTTTAGAAA
1 TTTTTCAGTGATATATCACTTCATTTTAGAAA
* * *
512655 TTTTTCAGTGATATATAATTTCATTTCAGAAA
1 TTTTTCAGTGATATATCACTTCATTTTAGAAA
* *
512687 CTTTTCAGTGATATATCACGTCATTTTAGAAA
1 TTTTTCAGTGATATATCACTTCATTTTAGAAA
512719 AATATTCTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 5 0.09
32 49 0.91
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (32 bp):
TTTTTCAGTGATATATCACTTCATTTTAGAAA
Found at i:512847 original size:32 final size:32
Alignment explanation
Indices: 512778--512858 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
512768 GAGCCCAATT
* * *
512778 ACTTCATTTCAGAAACTTTTTGAGTGATATACA
1 ACTTCATTTTAGAAA-ATTTTCAGTGATATACA
*
512811 ACTTCTTTTTAGAAAATTTTCAGTGATATATC-
1 ACTTCATTTTAGAAAATTTTCAGTGATATA-CA
512843 ACTTCATTTTAGAAAA
1 ACTTCATTTTAGAAAA
512859 AAAAAATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 28 0.67
33 14 0.33
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (32 bp):
ACTTCATTTTAGAAAATTTTCAGTGATATACA
Found at i:512947 original size:142 final size:139
Alignment explanation
Indices: 512656--513102 Score: 510
Period size: 142 Copynumber: 3.2 Consensus size: 139
512646 TTTTAGAAAT
* * *
512656 TTTTCAGTGATATATAATTTCATTTCAGAAACTTTTCAGTGATATATCACGTCATTTTAGAAAAA
1 TTTTCAGTGATATATAACTTCATTTCAGAAAATTTTCAGTGATATATCACTTCATTTTAGAAAAA
* * * * * * * *
512721 TATTCTTTTCTCATATACCATTTAATTCACAATGATAGAAAC-TTTCAGA-GCCCAATTACTTCA
66 AAATCTTTTCTCATACATCATTTAATACACAATGACAAAAACTTTTCA-ATGCCCAATCACTTCA
* *
512784 TTTCAGAAAC
130 CTTCAAAAAC
* * * *
512794 TTTTTGAGTGATATACAACTTCTTTTTAGAAAATTTTCAGTGATATATCACTTCATTTTAGAAAA
1 -TTTTCAGTGATATATAACTTCATTTCAGAAAATTTTCAGTGATATATCACTTCATTTTAG--AA
*
512859 AAAAAATCATTTTCTTATACATCATTTAATACACAATGACAAAAACTTTTCAATGCCCAATCACT
63 AAAAAATC-TTTTCTCATACATCATTTAATACACAATGACAAAAACTTTTCAATGCCCAATCACT
*
512924 TTACTTCAAAAAC
127 TCACTTCAAAAAC
* *
512937 TTTTCAGTGATATATAACTTAATTTCATAAACATTTT-AGTGATATATCACTTCATTTTAG-AAA
1 TTTTCAGTGATATATAACTTCATTTCAGAAA-ATTTTCAGTGATATATCACTTCATTTTAGAAAA
** * * * *
513000 AATGTCCCTTTTCTCATACATAATTTAATACACAATGACAAACA-TTTTTAGTG-CCAATCACTT
65 AAAAT--CTTTTCTCATACATCATTTAATACACAATGACAAAAACTTTTCAATGCCCAATCACTT
* *
513063 CACTTTATAAAC
128 CACTTCAAAAAC
*
513075 TTTTCAGTGATATATCACTTCATTTCAG
1 TTTTCAGTGATATATAACTTCATTTCAG
513103 TGTTATATCA
Statistics
Matches: 262, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
138 44 0.17
139 66 0.25
140 33 0.13
141 9 0.03
142 80 0.31
143 30 0.11
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (139 bp):
TTTTCAGTGATATATAACTTCATTTCAGAAAATTTTCAGTGATATATCACTTCATTTTAGAAAAA
AAATCTTTTCTCATACATCATTTAATACACAATGACAAAAACTTTTCAATGCCCAATCACTTCAC
TTCAAAAAC
Found at i:512983 original size:32 final size:32
Alignment explanation
Indices: 512928--512993 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
512918 ATCACTTTAC
512928 TTCAAAAACTTTTCAGTGATATATAACTTAAT
1 TTCAAAAACTTTTCAGTGATATATAACTTAAT
* * *
512960 TTCATAAACATTTT-AGTGATATATCACTTCAT
1 TTCAAAAAC-TTTTCAGTGATATATAACTTAAT
512992 TT
1 TT
512994 TAGAAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (32 bp):
TTCAAAAACTTTTCAGTGATATATAACTTAAT
Found at i:520695 original size:19 final size:19
Alignment explanation
Indices: 520671--520707 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
520661 CAATCCTAAC
520671 AATTAGGCTATAATTTAGT
1 AATTAGGCTATAATTTAGT
520690 AATTAGGCTATAATTTAG
1 AATTAGGCTATAATTTAG
520708 GCAACTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (19 bp):
AATTAGGCTATAATTTAGT
Found at i:523429 original size:17 final size:17
Alignment explanation
Indices: 523404--523443 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
523394 ATGGTTTTCA
* *
523404 GAACTGGATCGGTCAGC
1 GAACCGGATCGGTCAAC
*
523421 GAACCGGATCGGTGAAC
1 GAACCGGATCGGTCAAC
523438 GAACCG
1 GAACCG
523444 CCGTGCTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.25, G:0.35, T:0.12
Consensus pattern (17 bp):
GAACCGGATCGGTCAAC
Found at i:524440 original size:62 final size:62
Alignment explanation
Indices: 524338--524464 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
524328 GCTTTCTCCA
*
524338 ACCAACCATGCATACTCTGTATAGTATAATGGAGGTCGCATTTATAAGGCCAAAAAAATAGC
1 ACCAACCATGCATACTCTGTATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGC
524400 ACCAACCATGCATACTCTGTATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGC
1 ACCAACCATGCATACTCTGTATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGC
524462 ACC
1 ACC
524465 CTACATACAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (62 bp):
ACCAACCATGCATACTCTGTATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGC
Found at i:524601 original size:237 final size:226
Alignment explanation
Indices: 524173--524638 Score: 797
Period size: 237 Copynumber: 2.0 Consensus size: 226
524163 GCTTTCTTCA
524173 ACCAACCATGCATACTCTATATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGCACC
1 ACCAACCATGCATACTCTATATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGCACC
*
524238 CTACATGCAGGGAAAAATGTATTAATACCCCATTTCTTCTTCTTCTTCTTCTCTTTTTTGTTTTC
66 CTACATACAGGGAAAAATGTATTAATACCCCATTTCTTCTTCTTCTTCTTCTCTTTTTTGTTTTC
*
524303 CCTTTGAATTTCAGCCTTTTTCATGGCTTTCTCCAACCAACCATGCATACTCTGTATAGTATAAT
131 CCTTTGAATTTCAGCCTTTTTCATGGATTTCTCCAACCAACCATGCATACTCTGTATAGTATAAT
*
524368 GGAGGTCGCATTTATAAGGCCAAAAAAATAGC
196 GGAGGCCGCATTTATAAGGCC-AAAAAATAGC
*
524400 ACCAACCATGCATACTCTGTATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGCACC
1 ACCAACCATGCATACTCTATATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGCACC
524465 CTACATACAGGGAAAAATGTATTAATACCCTCATTTCTTCTTTTTCTTCTTGTTCTTCTTCTCTT
66 CTACATACAGGGAAAAATGTATTAATACCC-CA--T-TTC---TTCTTC---TTCTTCTTCTCTT
524530 TTTTGTTTTCCCTTTGAATTTCAGCCTTTTTCATGGATTTCTCCAACCAACCATGCATACTCTGT
121 TTTTGTTTTCCCTTTGAATTTCAGCCTTTTTCATGGATTTCTCCAACCAACCATGCATACTCTGT
524595 ATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAATAGC
186 ATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAATAGC
524636 ACC
1 ACC
524639 CTACATGTAA
Statistics
Matches: 225, Mismatches: 4, Indels: 11
0.94 0.02 0.05
Matches are distributed among these distances:
227 93 0.41
228 2 0.01
230 1 0.00
231 3 0.01
234 6 0.03
236 13 0.06
237 107 0.48
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (226 bp):
ACCAACCATGCATACTCTATATAGTATAATGGAGGCCGCATTTATAAGGCCAAAAAAATAGCACC
CTACATACAGGGAAAAATGTATTAATACCCCATTTCTTCTTCTTCTTCTTCTCTTTTTTGTTTTC
CCTTTGAATTTCAGCCTTTTTCATGGATTTCTCCAACCAACCATGCATACTCTGTATAGTATAAT
GGAGGCCGCATTTATAAGGCCAAAAAATAGC
Found at i:525284 original size:31 final size:31
Alignment explanation
Indices: 525246--525401 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
525236 CCCGAAGGAC
* * *
525246 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
525277 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
525308 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
525339 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
525370 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
525401 C
1 C
525402 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:529579 original size:31 final size:31
Alignment explanation
Indices: 529494--529603 Score: 161
Period size: 31 Copynumber: 3.6 Consensus size: 31
529484 TCCATAGATT
* *
529494 CCGAAGAACCTAGGTAATC-ATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
* *
529524 CCGAATAACATA-GTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
529554 CCGAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
529585 CCGAAGAACATAGATAAAC
1 CCGAAGAACATAGGTAAAC
529604 CCTCGACCCT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
29 5 0.07
30 31 0.44
31 35 0.49
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:531316 original size:3 final size:3
Alignment explanation
Indices: 531297--531350 Score: 85
Period size: 3 Copynumber: 18.3 Consensus size: 3
531287 GGGAAAATAC
531297 CTT C-T CTT CTT -TCT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
531341 CTT CTT CTT C
1 CTT CTT CTT C
531351 CAATAATGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 3 0.06
3 44 0.92
4 1 0.02
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:531456 original size:3 final size:3
Alignment explanation
Indices: 531448--531520 Score: 105
Period size: 3 Copynumber: 24.3 Consensus size: 3
531438 AGGAAAATAC
*
531448 CTT CTT CTT CTT -TT TTT CTT CTT CTT -TT CTT CTTT CTTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT C-TT CTT CTT
531493 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
531521 CAATAAGCAC
Statistics
Matches: 66, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
2 4 0.06
3 55 0.83
4 7 0.11
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
CTT
Found at i:531484 original size:12 final size:11
Alignment explanation
Indices: 531452--531519 Score: 93
Period size: 11 Copynumber: 6.0 Consensus size: 11
531442 AAATACCTTC
*
531452 TTCTTCTTTTT
1 TTCTTCTTCTT
531463 TTCTTCTTCTT
1 TTCTTCTTCTT
531474 TTCTTCTT-TCT
1 TTCTTCTTCT-T
531485 TTCTTCTTCTT
1 TTCTTCTTCTT
531496 CTTCTTCTTCTT
1 -TTCTTCTTCTT
531508 CTTCTTCTTCTT
1 -TTCTTCTTCTT
531520 CCAATAAGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
10 1 0.02
11 28 0.53
12 24 0.45
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCTTCTTCTT
Done.