Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009571.1 Hibiscus syriacus cultivar Beakdansim tig00116934_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: 592744
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:533631 original size:40 final size:40
Alignment explanation
Indices: 533587--533682 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
533577 ACAGTCAGAA
533587 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
* * *
533627 TCGCATTGCTAT-TTACATATTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGT-CATAATCGCATTGCGATTTACATAT
533667 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
533683 GGAAAATCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.02
40 47 0.96
41 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:535721 original size:26 final size:25
Alignment explanation
Indices: 535690--535757 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 25
535680 ATTATATTTT
535690 TATTTACTTTATTTTGTTAAATATTAA
1 TATTTACTTTATTTTGTT-AAT-TTAA
*
535717 T-TTTA--TTATTATT-TCTCATTTAA
1 TATTTACTTTATT-TTGT-TAATTTAA
535740 TATTTACTTTATTTTGTT
1 TATTTACTTTATTTTGTT
535758 TTTTAATGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 14
0.69 0.02 0.29
Matches are distributed among these distances:
23 5 0.15
24 12 0.35
25 6 0.18
26 10 0.29
27 1 0.03
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (25 bp):
TATTTACTTTATTTTGTTAATTTAA
Found at i:541535 original size:50 final size:50
Alignment explanation
Indices: 541476--541600 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 50
541466 CCCTACGCGG
* *** **
541476 CGTATAGCGCGCTGCAGGGGCTGCGCTATA-CCCACGTGGTGCCAGTTCAC
1 CGTATAGCGCGGTGCAGGGGC-GCGCTATACCCCACGTGACACCAAATCAC
*
541526 CGTATAGCGCGGTGCAAGGGGCGCGCTATACCCCACGTGACACCAAATCAT
1 CGTATAGCGCGGTGC-AGGGGCGCGCTATACCCCACGTGACACCAAATCAC
541577 CGTATAGCGCGGTGCAGGGG-GCGC
1 CGTATAGCGCGGTGCAGGGGCGCGC
541601 ACTTTACTGC
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 4 0.06
50 27 0.41
51 35 0.53
ACGTcount: A:0.19, C:0.30, G:0.34, T:0.17
Consensus pattern (50 bp):
CGTATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGACACCAAATCAC
Found at i:543184 original size:37 final size:36
Alignment explanation
Indices: 543108--543184 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
543098 TTTTTATATT
*
543108 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAA-TATATAAATATTATCAA
* *
543145 TTTAATTTTTTAAAGAAAAA-ATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAAATATATAAATATTAT-CAA
543182 TTT
1 TTT
543185 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 12 0.34
37 18 0.51
38 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAAATATATAAATATTATCAA
Found at i:543366 original size:20 final size:20
Alignment explanation
Indices: 543330--543367 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
543320 ATCCTATTCC
**
543330 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
543350 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
543368 GTGAACCAAA
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:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:543565 original size:19 final size:19
Alignment explanation
Indices: 543541--543577 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
543531 ATTATTACTC
543541 TGGTGGAGTTTTTTTAAGA
1 TGGTGGAGTTTTTTTAAGA
543560 TGGTGGAGTTTTTTTAAG
1 TGGTGGAGTTTTTTTAAG
543578 TAGACGGGAG
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:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (19 bp):
TGGTGGAGTTTTTTTAAGA
Found at i:551567 original size:125 final size:125
Alignment explanation
Indices: 551389--551661 Score: 361
Period size: 125 Copynumber: 2.2 Consensus size: 125
551379 GGTTCAACCA
* * ** *
551389 TAGTGGTGTTTTTTAAACAAACGCCGCTAAAGACTCGTACTTTAGTGGTGTTTTTTTAAACAAAC
1 TAGTGGCG-TTTTTATACAAACGAAGCTAAAGACTCGTACTTTAGTGGCG--TTTTTAAACAAAC
* ***
551454 ACCGCTAAAGACTCATACTTTAGTGGCGTTT-T-TATACAAACGTTGCTAAAGACTCGTACTT
63 ACCGCTAAACACTCATACTTTAGTGGCGTTTGTGTATACAAACGCCACTAAAGACTCGTACTT
*
551515 TAGTGGCGTTTTTATACAAACGAAGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACACC
1 TAGTGGCGTTTTTATACAAACGAAGCTAAAGACTCGTACTTTAGTGGCGTTTTTAAACAAACACC
* ** * *
551580 GCTATACACTTGTACTTTAGTGGCGTTTGTGTTTAGAAACGCCACTAAAGACTCGTACTT
66 GCTAAACACTCATACTTTAGTGGCGTTTGTGTATACAAACGCCACTAAAGACTCGTACTT
*
551640 TAGTGGCGTTTATATACAAACG
1 TAGTGGCGTTTTTATACAAACG
551662 TCGCTATACA
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
123 39 0.30
124 1 0.01
125 82 0.64
126 7 0.05
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (125 bp):
TAGTGGCGTTTTTATACAAACGAAGCTAAAGACTCGTACTTTAGTGGCGTTTTTAAACAAACACC
GCTAAACACTCATACTTTAGTGGCGTTTGTGTATACAAACGCCACTAAAGACTCGTACTT
Found at i:551668 original size:84 final size:82
Alignment explanation
Indices: 551389--551708 Score: 354
Period size: 84 Copynumber: 3.8 Consensus size: 82
551379 GGTTCAACCA
* * * *
551389 TAGTGGTGTTTTTTAAACAAACGCCGCTAAAGACTCGTACTTTAGTGGTGTTTTTTTAAACAAAC
1 TAGTGGCG-TTTTTATACAAACGCCGCTAAACACTCGTACTTTAGTGGCGTTTTTTT--ACAAAC
* * *
551454 ACCGCTAAAGACTCATACTT
63 GCCACTAAAGACTCGTACTT
** * * *
551474 TAGTGGCGTTTTTATACAAACGTTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACG-A
1 TAGTGGCGTTTTTATACAAACGCCGCTAAACACTCGTACTTTAGTGGCGTTTTTTTACAAACGCC
551538 AGCTAAAGACTCGTACTT
66 A-CTAAAGACTCGTACTT
* * * *
551556 TAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTTTAGTGGCGTTTGTGTTTAGAAACG
1 TAGTGGCGTTTTTATACAAACGCCGCTAAACACTCGTACTTTAGTGGCGTTT-T-TTTACAAACG
551621 CCACTAAAGACTCGTACTT
64 CCACTAAAGACTCGTACTT
* * * ** * * * *
551640 TAGTGGCGTTTATATACAAACGTCGCTATACACTTATACTTTAATGGCATTTTTATACAAACGTC
1 TAGTGGCGTTTTTATACAAACGCCGCTAAACACTCGTACTTTAGTGGCGTTTTTTTACAAACGCC
551705 ACTA
66 ACTA
551709 TACACACTAC
Statistics
Matches: 203, Mismatches: 28, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
82 80 0.39
83 2 0.01
84 113 0.56
85 8 0.04
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (82 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAACACTCGTACTTTAGTGGCGTTTTTTTACAAACGCC
ACTAAAGACTCGTACTT
Found at i:551680 original size:125 final size:123
Alignment explanation
Indices: 551405--551701 Score: 342
Period size: 125 Copynumber: 2.4 Consensus size: 123
551395 TGTTTTTTAA
** * * * * *
551405 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGTGTTTTTTTAAACAAACACCGCTAAAGACTCAT
1 ACAAACGAAGCTAAACACTCATACTTTAGTGGCG--TTTTTATACAAACACCGCTAAACACTCAT
*** *
551470 ACTTTAGTGGCGTTTTTATACAAACGTTGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
64 ACTTTAGTGGCGTTTTTATACAAACGCCACTAAAGACTCGTACTTTAGTGGCGTTTATAT
* * * **
551530 ACAAACGAAGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACACCGCTATACACTTGTAC
1 ACAAACGAAGCTAAACACTCATACTTTAGTGGCGTTTTTATACAAACACCGCTAAACACTCATAC
* *
551595 TTTAGTGGCGTTTGTGTTTAGAAACGCCACTAAAGACTCGTACTTTAGTGGCGTTTATAT
66 TTTAGTGGCGTTT-T-TATACAAACGCCACTAAAGACTCGTACTTTAGTGGCGTTTATAT
** * * * *
551655 ACAAACGTCGCTATACACTTATACTTTAATGGCATTTTTATACAAAC
1 ACAAACGAAGCTAAACACTCATACTTTAGTGGCGTTTTTATACAAAC
551702 GTCACTATAC
Statistics
Matches: 148, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
123 39 0.26
124 1 0.01
125 108 0.73
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (123 bp):
ACAAACGAAGCTAAACACTCATACTTTAGTGGCGTTTTTATACAAACACCGCTAAACACTCATAC
TTTAGTGGCGTTTTTATACAAACGCCACTAAAGACTCGTACTTTAGTGGCGTTTATAT
Found at i:551704 original size:41 final size:41
Alignment explanation
Indices: 551389--551702 Score: 358
Period size: 41 Copynumber: 7.5 Consensus size: 41
551379 GGTTCAACCA
* *
551389 TAGTGGTGTTTTTTAAACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
551431 TAGTGGTGTTTTTTTAAACAAACACCGCTAAAGACTCATACTT
1 TAGTGGCG--TTTTTATACAAACGCCGCTAAAGACTCGTACTT
**
551474 TAGTGGCGTTTTTATACAAACGTTGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
**
551515 TAGTGGCGTTTTTATACAAACGAAGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
551556 TAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * *
551597 TAGTGGCGTTTGTGTTTAGAAACGCCACTAAAGACTCGTACTT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
* * * * **
551640 TAGTGGCGTTTATATACAAACGTCGCTATACACTTATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
551681 TAATGGCATTTTTATACAAACG
1 TAGTGGCGTTTTTATACAAACG
551703 TCACTATACA
Statistics
Matches: 234, Mismatches: 35, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
41 153 0.65
42 9 0.04
43 72 0.31
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:551928 original size:41 final size:40
Alignment explanation
Indices: 551883--552018 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 40
551873 CGTTTGTTTC
*
551883 ACAAACGCCACAACATATAA-GTACTTTAGTGGCATTT-TAAA
1 ACAAACGCCACAACA-A-AACCTACTTTAGTGGCATTTCT-AA
*
551924 ACAAACGCCACAACAAAATCCTACTTTAGTGGCGTTTCTAA
1 ACAAACGCCACAACAAAA-CCTACTTTAGTGGCATTTCTAA
* * * * * *
551965 ACAAATGCCACAA-AAGAATCATTCTTTAGTTGCGTTTATAA
1 ACAAACGCCACAACAA-AA-CCTACTTTAGTGGCATTTCTAA
552006 ACAAACGCCACAA
1 ACAAACGCCACAA
552019 TAAAGTACAT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.02
40 3 0.04
41 77 0.93
42 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (40 bp):
ACAAACGCCACAACAAAACCTACTTTAGTGGCATTTCTAA
Found at i:562026 original size:44 final size:41
Alignment explanation
Indices: 561944--562056 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 41
561934 ATTCTGTGTT
* ** * *
561944 ATTTAGCGGCGTTTGTAACAAAAATGCC-GTAATATACCATAC
1 ATTTAGCAGCGTTTGTATTAAAAACGCCACT-ATATACCA-AC
*
561986 ATTTAGCAGCGTTTGTATCATAAAAACGCCACTATATACCAAT
1 ATTTAGCAGCGTTTGTAT--TAAAAACGCCACTATATACCAAC
*
562029 TTTTAGCAGCGTTTGTATTAAAAACGCC
1 ATTTAGCAGCGTTTGTATTAAAAACGCC
562057 GTTAAACCTC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
41 10 0.16
42 16 0.26
43 18 0.30
44 16 0.26
45 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (41 bp):
ATTTAGCAGCGTTTGTATTAAAAACGCCACTATATACCAAC
Found at i:562111 original size:43 final size:43
Alignment explanation
Indices: 562047--562156 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 43
562037 GCGTTTGTAT
* * ** * * *
562047 TAAAAACGCCGTTAAACCTCAATGCCTATTGTGGCATTTTAGC
1 TAAAAACGCCGCTAAATCTCAACACATATTGCGACATTTTAGC
* *
562090 TAAAAACGTCGCTAAATCTCAACACATATTGCGACATTTTCGC
1 TAAAAACGCCGCTAAATCTCAACACATATTGCGACATTTTAGC
* *
562133 TAAAAACGCCACTAAATATCAACA
1 TAAAAACGCCGCTAAATCTCAACA
562157 ACTTTTGCTG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (43 bp):
TAAAAACGCCGCTAAATCTCAACACATATTGCGACATTTTAGC
Found at i:582292 original size:20 final size:20
Alignment explanation
Indices: 582267--582359 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
582257 TTTTCCCAAT
582267 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
582287 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
582307 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
582328 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
582349 TCGCAATGCGA
1 TCGCAATGCGA
582360 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:582309 original size:41 final size:41
Alignment explanation
Indices: 582264--582359 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
582254 CGATTTTCCC
582264 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
582305 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
582346 AAATCGCAATGCGA
1 AATTCGCAATGCGA
582360 TACTGACTAT
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:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:582313 original size:21 final size:20
Alignment explanation
Indices: 582267--582359 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
582257 TTTTCCCAAT
*
582267 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
582287 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
582307 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
582328 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
582349 TCGCAATGCGA
1 TCGCAATGCGA
582360 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:582373 original size:20 final size:20
Alignment explanation
Indices: 582348--582441 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
582338 AATTGGGAAA
*
582348 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
582368 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
582389 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
582409 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
582429 TTCGCAACGCGAT
1 ATCGCAACGCGAT
582442 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:582422 original size:41 final size:41
Alignment explanation
Indices: 582345--582422 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
582335 GCGAATTGGG
* * **
582345 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
582386 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
582423 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:583010 original size:19 final size:19
Alignment explanation
Indices: 582986--583030 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
582976 GCAACGAGAT
*
582986 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
583005 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
583024 AATCGCA
1 AATCGCA
583031 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:583048 original size:19 final size:19
Alignment explanation
Indices: 583026--583210 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
583016 GAAACCAAAA
*
583026 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
583045 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
583064 TCGCGTTGCAATTTTAATT
1 TCGCGTTGCGATTTTCATT
583083 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
583103 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
583119 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
583136 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
583150 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
583169 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
583189 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
583209 TC
1 TC
583211 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 48 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:583100 original size:39 final size:38
Alignment explanation
Indices: 583026--583111 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 38
583016 GAAACCAAAA
* * *
583026 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCAATTTTAATTTCGCGTTGCGATTTTCATT
583064 TCGCGTTGCAATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCAATTTTAATTTCGC-GTTGCGATTTTCATT
583103 TCGCGTTGC
1 TCGCGTTGC
583112 GATTGTCTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 20 0.45
39 24 0.55
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCAATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:583135 original size:33 final size:33
Alignment explanation
Indices: 583098--583185 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
583088 GTTGCGATTT
* *
583098 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
583131 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
583164 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
583186 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:583187 original size:20 final size:20
Alignment explanation
Indices: 583153--583210 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
583143 GCGATTCTCT
**
583153 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
583173 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
583193 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
583211 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:585266 original size:42 final size:42
Alignment explanation
Indices: 585206--585328 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
585196 GCTCGACTCG
* * *
585206 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
585248 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
585290 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
585329 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:585286 original size:21 final size:21
Alignment explanation
Indices: 585262--585328 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
585252 TCATTCCTCG
585262 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
585283 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
585304 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
585325 AGAG
1 AGAG
585329 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:586703 original size:14 final size:14
Alignment explanation
Indices: 586684--586719 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
586674 ATTGTTTAAT
586684 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
586698 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
586712 TGATTTGT
1 TGATTTGT
586720 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:586920 original size:19 final size:19
Alignment explanation
Indices: 586898--586981 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
586888 CGAAATTAAA
*
586898 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
586917 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
586933 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
586950 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
586969 TTCGCATTGCGAT
1 TTCGCATTGCGAT
586982 AGTAATTTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.11
16 6 0.11
17 6 0.11
19 37 0.67
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:586989 original size:19 final size:19
Alignment explanation
Indices: 586948--587001 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
586938 TGCGATTTTC
** *
586948 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATAGTA
586967 ATTTCGCATTGCGATAGTA
1 ATTTCGCATTGCGATAGTA
*
586986 ATTTCCGCGTTGCGAT
1 ATTT-CGCATTGCGAT
587002 GGACATTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGTA
Found at i:589286 original size:11 final size:11
Alignment explanation
Indices: 589270--589303 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
589260 TCTTCGGGGA
589270 CTTTTCTTCTT
1 CTTTTCTTCTT
589281 CTTTTCTTCTT
1 CTTTTCTTCTT
589292 CTTTTCTTCTT
1 CTTTTCTTCTT
589303 C
1 C
589304 AGGATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
CTTTTCTTCTT
Found at i:590658 original size:14 final size:15
Alignment explanation
Indices: 590638--590710 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
590628 TGAAAATCGC
590638 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
590653 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
590670 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
590688 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
590704 -TTGCGAT
1 ATTGCGAT
590711 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:590675 original size:19 final size:19
Alignment explanation
Indices: 590634--590700 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
590624 GAAATGAAAA
590634 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
590650 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
590667 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
590685 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
590701 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:590836 original size:14 final size:14
Alignment explanation
Indices: 590817--590853 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
590807 CATCAATTAA
590817 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
590831 ACAAATCATCTTTT
1 ACAAATCAACATTT
590845 ACAAATCAA
1 ACAAATCAA
590854 TTAACAATCA
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:591311 original size:17 final size:17
Alignment explanation
Indices: 591291--591326 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
591281 CGTTGCGATT
591291 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
591308 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
591325 TT
1 TT
591327 TCTCGTTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:591459 original size:14 final size:14
Alignment explanation
Indices: 591442--591478 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
591432 CATCAATTAA
591442 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
591456 ACAAATCATCTTTT
1 ACAAATCAACATTT
591470 ACAAATCAA
1 ACAAATCAA
591479 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
Done.