Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007127.1 Hibiscus syriacus cultivar Beakdansim tig00018622_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: 53932
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2471 original size:13 final size:13
Alignment explanation
Indices: 2453--2479 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2443 AGCAATTTAA
2453 AATGAATCTATTG
1 AATGAATCTATTG
2466 AATGAATCTATTG
1 AATGAATCTATTG
2479 A
1 A
2480 CTGTTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AATGAATCTATTG
Found at i:4188 original size:44 final size:43
Alignment explanation
Indices: 4141--4271 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 43
4131 TTTGTTCTAA
* *
4141 AAAAACACCA-CTAAATGACCTAACAGTTTGCAGCTTTTGTTAC
1 AAAAACA-CAGCTAAAAGACCTAACAGTTTGCAGCGTTTGTTAC
*
4184 AAAAACACAGCTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
1 AAAAACACAGCTAAAAGACCTAACAGTTTGCAGCGTTTGTTAC
* ** * * ** *
4227 TAAAATGC-GCTAAAAGACGTAACATTTTGTGGCGTTTGTTCC
1 AAAAACACAGCTAAAAGACCTAACAGTTTGCAGCGTTTGTTAC
4269 AAA
1 AAA
4272 TCGTTGCTAA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
42 34 0.45
43 42 0.55
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (43 bp):
AAAAACACAGCTAAAAGACCTAACAGTTTGCAGCGTTTGTTAC
Found at i:4251 original size:42 final size:43
Alignment explanation
Indices: 4141--4338 Score: 165
Period size: 42 Copynumber: 4.7 Consensus size: 43
4131 TTTGTTCTAA
* * *
4141 AAAAACACCA-CTAAATGACCTAACAGTTTGCAGCTTTTGTTAC
1 AAAAACA-CAGCTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
4184 AAAAACACAGCTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
1 AAAAACACAGCTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
* ** * **
4227 TAAAATGC-GCTAAAAGACGTAACATTTTGTGGCGTTTGTT-C
1 AAAAACACAGCTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
* * *** * * *
4268 CAAATCGTTGCT-AAA-ACCTTAACATTTTGCGGTGTTTGTT-T
1 AAAAACACAGCTAAAAGACC-TAACATTTTGCAGCGTTTGTTAC
* *
4309 AAAAACACCGCTAAAAGACCCAACATTTTG
1 AAAAACACAGCTAAAAGACCTAACATTTTG
4339 AAAAAACACT
Statistics
Matches: 127, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
40 2 0.02
41 34 0.27
42 46 0.36
43 45 0.35
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (43 bp):
AAAAACACAGCTAAAAGACCTAACATTTTGCAGCGTTTGTTAC
Found at i:4346 original size:31 final size:31
Alignment explanation
Indices: 4309--4369 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
4299 GTGTTTGTTT
*
4309 AAAAACACCGCTAAAAGACCCAACATTTTGA
1 AAAAACACCGATAAAAGACCCAACATTTTGA
* * *
4340 AAAAACACTGATAAAAGACCTAACCTTTTG
1 AAAAACACCGATAAAAGACCCAACATTTTG
4370 CGGCATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.20
Consensus pattern (31 bp):
AAAAACACCGATAAAAGACCCAACATTTTGA
Found at i:13078 original size:11 final size:11
Alignment explanation
Indices: 13062--13089 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
13052 GAGAGTTTAA
13062 ATTGATGCATG
1 ATTGATGCATG
13073 ATTGATGCATG
1 ATTGATGCATG
13084 ATTGAT
1 ATTGAT
13090 ACAATATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (11 bp):
ATTGATGCATG
Found at i:13703 original size:16 final size:16
Alignment explanation
Indices: 13684--13715 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13674 GGAAACAAGG
13684 GAAATAATTCATGCAC
1 GAAATAATTCATGCAC
13700 GAAATAATTCATGCAC
1 GAAATAATTCATGCAC
13716 TTACACAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
GAAATAATTCATGCAC
Found at i:14755 original size:11 final size:11
Alignment explanation
Indices: 14739--14781 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
14729 TGCAATCTCT
14739 TTGTCAAGTTA
1 TTGTCAAGTTA
14750 TTGTCAAGTTA
1 TTGTCAAGTTA
*
14761 TTGTTAAGTTA
1 TTGTCAAGTTA
*
14772 TTGTAAAGTT
1 TTGTCAAGTT
14782 GATATGGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (11 bp):
TTGTCAAGTTA
Found at i:20773 original size:16 final size:16
Alignment explanation
Indices: 20739--20772 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20729 AAAATATTAT
20739 AAAGTTTGATTGCAGA
1 AAAGTTTGATTGCAGA
*
20755 AAAGTTTGGTTG-AGA
1 AAAGTTTGATTGCAGA
20770 AAA
1 AAA
20773 ATAAATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.29
Consensus pattern (16 bp):
AAAGTTTGATTGCAGA
Found at i:33333 original size:54 final size:54
Alignment explanation
Indices: 33274--34337 Score: 1457
Period size: 54 Copynumber: 19.7 Consensus size: 54
33264 TTACCGAATA
33274 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
33328 GGCACTAAGTGTACATTTCACGGAATTCTTCTTATGTGGATGAATAACGGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * ** *
33382 GGCATTAAGTGTGCATTTCACTGAATTCATCCTATGTGGATGAATAGTCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
33436 GGCACTAAGTGTGCATTTCACGGAATTTATCCCATGTGGATAAATAATCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * ** *
33490 GGCACTAAGTGTGCTTTTCACGAAATTCATCATATGTGGATGAATATTCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
33544 GGCACTAACTGTGCATTTCACGGAATTCATCCTATGTGGATGAATGACTGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * *
33598 GGCACTAAGTATGCATTCCATGGAATTCATCTTATATGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
33652 AGCACTAAGTGCGTATTTCACGGAATTCATCTTATGCGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
33706 AGCACTAAGTGCGAATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
33760 GGCACTAAGTGTTCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
33814 GGCAATAAGTGGGCATTTCATGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * *
33868 AACACTAAGTGGGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
** * ** *
33922 AACACTAAGTGTGCATTT-ATCAGAATTCATCCTATGTGGATGAATAATTGTTTT
1 GGCACTAAGTGTGCATTTCA-CGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
33976 GGCACTAAGTGTGTATTTCACAGAATTCAACCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
34030 GGCACTAAGTGTGCATTTCAGGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
34084 GGCACTAAGTGTGCATTTCAGGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
34138 GGCAAC-AAGTGTGCATTTCACGAAATTTATCCTACGTGGATGAATAACCGTTTC
1 GGC-ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
34192 GACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * **
34246 AGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAGTAATTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
34300 GCCACTAAGTGTGAATTTCACAGAATTTATCCTATGTG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTG
34338 CATTTCACGG
Statistics
Matches: 896, Mismatches: 110, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
53 3 0.00
54 890 0.99
55 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:34337 original size:25 final size:25
Alignment explanation
Indices: 34309--34362 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
34299 CGCCACTAAG
*
34309 TGTGAATTTCACAGAATTTATCCTA
1 TGTGAATTTCACAGAATTCATCCTA
* * *
34334 TGTGCATTTCACGGAATTCATTCTA
1 TGTGAATTTCACAGAATTCATCCTA
34359 TGTG
1 TGTG
34363 GATGAGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (25 bp):
TGTGAATTTCACAGAATTCATCCTA
Found at i:34671 original size:17 final size:19
Alignment explanation
Indices: 34649--34691 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
34639 GAAACAACGA
*
34649 ATGCACT-TCA-TGCATCG
1 ATGCACTCTCAGTGCACCG
*
34666 ATGCACTCTTAGTGCACCG
1 ATGCACTCTCAGTGCACCG
34685 ATGCACT
1 ATGCACT
34692 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (19 bp):
ATGCACTCTCAGTGCACCG
Found at i:34671 original size:64 final size:65
Alignment explanation
Indices: 34510--34671 Score: 213
Period size: 66 Copynumber: 2.5 Consensus size: 65
34500 TGAAAAAATT
* * *
34510 AAACATCGAATGCATTTTATGCATCAATGCACATACCATGCATCGATGCACTCAGGTTTTTATAA
1 AAACATCGAATGCATTTTATGCATCGATGCACATAACATGCATCGATGCACTCAGGTATTTAT-A
34575 A
65 A
34576 AAACATCGAATGCATTTTATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-T
1 AAACATCGAATGCATTTTATGCATCGATGCACATA-ACATGCATCGATGCACTCAGG-TATTTAT
*
34639 -G
64 AA
* * *
34640 AAACAACGAATGCACTTCATGCATCGATGCAC
1 AAACATCGAATGCATTTTATGCATCGATGCAC
34672 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
64 29 0.33
65 1 0.01
66 53 0.61
67 4 0.05
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTTATGCATCGATGCACATAACATGCATCGATGCACTCAGGTATTTATAA
Found at i:42410 original size:21 final size:22
Alignment explanation
Indices: 42372--42414 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
42362 TTGAATGCTT
* *
42372 TTGGATTGTTTTACTTTGTTTG
1 TTGGATTGTTTGAATTTGTTTG
42394 TTGGA-TGTTTGAATTTGTTTG
1 TTGGATTGTTTGAATTTGTTTG
42415 GATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.12, C:0.02, G:0.26, T:0.60
Consensus pattern (22 bp):
TTGGATTGTTTGAATTTGTTTG
Found at i:43236 original size:64 final size:65
Alignment explanation
Indices: 43121--43245 Score: 164
Period size: 64 Copynumber: 1.9 Consensus size: 65
43111 AATGCATTTT
* * * ** *
43121 ATGTATCGATGCACTCAAGTTTTTATGAAAAACATTGAATGCGTTTTATGCATCGATGCACAAGA
1 ATGTATCGATGCACTCAACTATTTATG-AAAACATCGAATGCACTTCATGCATCGATGCACAAGA
43186 C
65 C
43187 ATGTATCGATGCACTCAGACTATTT-TG-AAACATCGAATGCACTTCATGCATCGATGCAC
1 ATGTATCGATGCACTCA-ACTATTTATGAAAACATCGAATGCACTTCATGCATCGATGCAC
43246 TCTTAGTACC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 28 0.54
66 19 0.37
67 5 0.10
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (65 bp):
ATGTATCGATGCACTCAACTATTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGAC
Found at i:45208 original size:22 final size:22
Alignment explanation
Indices: 45172--45233 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
45162 TGATTTTTGC
*
45172 ATATGA-TGTTATCATGAACAT
1 ATATGATTTTTATCATGAACAT
45193 ATATGATTTTTATCATGAACAT
1 ATATGATTTTTATCATGAACAT
45215 ATATGATTTTTATCATGAA
1 ATATGATTTTTATCATGAA
45234 TGTTATTTCG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 6 0.15
22 33 0.85
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (22 bp):
ATATGATTTTTATCATGAACAT
Found at i:45644 original size:36 final size:36
Alignment explanation
Indices: 45604--45676 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
45594 ATATGGTTAT
* *
45604 GGAATAATGGCAAGTGTATTGGTAAAATAAGCTTAC
1 GGAATAATGGCAAATATATTGGTAAAATAAGCTTAC
*
45640 GGAATAATGGTAAATATATTGGTAAAATAAGCTTAC
1 GGAATAATGGCAAATATATTGGTAAAATAAGCTTAC
45676 G
1 G
45677 AGCTTATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (36 bp):
GGAATAATGGCAAATATATTGGTAAAATAAGCTTAC
Found at i:45705 original size:45 final size:44
Alignment explanation
Indices: 45632--45742 Score: 152
Period size: 45 Copynumber: 2.5 Consensus size: 44
45622 TTGGTAAAAT
* *
45632 AAGCTTACGGAAT-AATGGTAAATATATTGGTAAAATAAGCTTAC
1 AAGCTTATGGGATAAATGGT-AATATATTGGTAAAATAAGCTTAC
* * *
45676 GAGCTTATGGTATTAAATGGTAGTATATTGGTAAAATAAGCTTAC
1 AAGCTTATGGGA-TAAATGGTAATATATTGGTAAAATAAGCTTAC
45721 AAGCTTATGGGATAAATGGTAA
1 AAGCTTATGGGATAAATGGTAA
45743 AAGATTTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 18 0.31
45 34 0.59
46 6 0.10
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (44 bp):
AAGCTTATGGGATAAATGGTAATATATTGGTAAAATAAGCTTAC
Found at i:50714 original size:15 final size:16
Alignment explanation
Indices: 50694--50725 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
50684 CAAAGTTATA
50694 ATTATATA-AAAATAT
1 ATTATATATAAAATAT
50709 ATTATATATAAAATAT
1 ATTATATATAAAATAT
50725 A
1 A
50726 ATAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTATATATAAAATAT
Found at i:50840 original size:27 final size:24
Alignment explanation
Indices: 50810--50863 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 24
50800 AAAAAAATAT
50810 AATTAAAATATTAATATATGATTTAAA
1 AATTAAAATATT--TAT-TGATTTAAA
*
50837 AATTAAAATATTTATTTATTTAAA
1 AATTAAAATATTTATTGATTTAAA
50861 AAT
1 AAT
50864 ATCAGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 11 0.42
25 3 0.12
27 12 0.46
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AATTAAAATATTTATTGATTTAAA
Found at i:52515 original size:3 final size:3
Alignment explanation
Indices: 52497--52547 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
52487 TTATTTTATT
* * *
52497 TAA T-A TAA TAA CAA TAA TAA TAT TTA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
52542 TAA TAA
1 TAA TAA
52548 AAGTAACTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52521 original size:24 final size:25
Alignment explanation
Indices: 52493--52543 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
52483 ATATTTATTT
52493 TATTTA-ATATAATAACAAT-AATAA
1 TATTTATA-ATAATAACAATAAATAA
*
52517 TATTTATAATAATAATAATAAATAA
1 TATTTATAATAATAACAATAAATAA
52542 TA
1 TA
52544 ATAAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TATTTATAATAATAACAATAAATAA
Found at i:52930 original size:117 final size:117
Alignment explanation
Indices: 52724--52950 Score: 386
Period size: 117 Copynumber: 1.9 Consensus size: 117
52714 CCCAAAGGCT
* *
52724 TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGC
52789 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGACCGAATG
66 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGACCGAATG
* *
52841 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC-GAAGGCTTTTGAAAACATC-AAAA
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTG-AGG-GTTTGAAAACATCAAAAA
52904 GCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
64 GCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
52951 TGACCCGAAG
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
116 1 0.01
117 91 0.88
118 12 0.12
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (117 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGGTTTGAAAACATCAAAAAGC
TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGACCGAATG
Found at i:52980 original size:76 final size:77
Alignment explanation
Indices: 52841--53052 Score: 358
Period size: 76 Copynumber: 2.8 Consensus size: 77
52831 AGACCGAATG
*
52841 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTTGAAAACATC-AAAAG
1 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAG
52905 CTCCCGAAGGC-T
65 CTCCCGAAGGCTT
*
52917 TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
52982 TCCCGAAGGCTT
66 TCCCGAAGGCTT
*
52994 TTTTGGAAACATCATGCACCTGAAGGGCTTACAGATGACCCGAAGGTTTTG-AAACATCA
1 TTTTGGAAACATCATGCA-CTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
53053 TGCACTGAAG
Statistics
Matches: 129, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
75 12 0.09
76 60 0.47
77 27 0.21
78 30 0.23
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (77 bp):
TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCTT
Found at i:53068 original size:121 final size:116
Alignment explanation
Indices: 52907--53166 Score: 391
Period size: 121 Copynumber: 2.2 Consensus size: 116
52897 ATCAAAAGCT
52907 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAA
1 CCCGAAGG--TTTT-GAAACATCATGCACTGAAGGACTTACAGATGACCCGAA-GCTTTTGAAAA
*
52971 CATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACCTGAAGGGCTTACAGATGA
62 CATCAAAAAGCTCCCGAAGGC-TTTTT--AAAAATCATGCA-CTGAAGGGC-TA-AGATGA
53032 CCCGAAGGTTTTGAAACATCATGCACTGAAGG-CTTACAGATGACCCGAAGCTTTTGAAAACATC
1 CCCGAAGGTTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGCTTTTGAAAACATC
*
53096 AAAAAGCTCCCGAAGGCTTTTTAAAAATCATGCAGTGAAGGGCTAAGATGA
66 AAAAAGCTCCCGAAGGCTTTTTAAAAATCATGCACTGAAGGGCTAAGATGA
53147 CCCGAA-GTTTTGAAACATCA
1 CCCGAAGGTTTTGAAACATCA
53167 AAAAGCTCCC
Statistics
Matches: 132, Mismatches: 2, Indels: 13
0.90 0.01 0.09
Matches are distributed among these distances:
114 14 0.11
115 12 0.09
116 2 0.02
117 8 0.06
118 11 0.08
120 7 0.05
121 46 0.35
122 20 0.15
123 4 0.03
125 8 0.06
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (116 bp):
CCCGAAGGTTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGCTTTTGAAAACATC
AAAAAGCTCCCGAAGGCTTTTTAAAAATCATGCACTGAAGGGCTAAGATGA
Found at i:53093 original size:44 final size:45
Alignment explanation
Indices: 52994--53096 Score: 165
Period size: 43 Copynumber: 2.3 Consensus size: 45
52984 CCGAAGGCTT
*
52994 TTTTGGAAACATCATGCACCTGAAGGGCTTACAGATGACCCGAAGG
1 TTTT-GAAACATCATGCACCTGAAGGGCTTACAGATGACCCGAAGC
53040 TTTTGAAACATCATGCA-CTGAA-GGCTTACAGATGACCCGAAGC
1 TTTTGAAACATCATGCACCTGAAGGGCTTACAGATGACCCGAAGC
53083 TTTTGAAAACATCA
1 TTTTG-AAACATCA
53097 AAAAGCTCCC
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
43 25 0.45
44 13 0.24
45 13 0.24
46 4 0.07
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (45 bp):
TTTTGAAACATCATGCACCTGAAGGGCTTACAGATGACCCGAAGC
Found at i:53147 original size:193 final size:197
Alignment explanation
Indices: 52698--53241 Score: 848
Period size: 193 Copynumber: 2.8 Consensus size: 197
52688 AGAGGTCTTA
* *
52698 AAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTT-GAAACATCATGCACTGAAGGACTTACAGATGACC
*
52763 CTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
65 C-GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
*
52827 TTAC--A-GA-CCGAATGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
129 TTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
52888 TTTG
194 TTTG
52892 AAAACATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACC
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTT-GAAACATCATGCACTGAAGGACTTACAGATGACC
*
52956 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACCTGAAGGG
65 CGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCA-CTGAAGGA
53021 CTTACAGATGACCCGAAGGTTTTG-AAACATCATGCACTGAA-GGCTTACAGATGACCCGAA-GC
128 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
53083 TTTTG
193 TTTTG
* * *
53088 AAAACATCAAAAAGCTCCCGAAGGCTTTTT-AAAAATCATGCAGTGAAGGGC-TA-AGATGACCC
1 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAACATCATGCACTGAAGGACTTACAGATGACCC
*
53150 GAA-GTTTTG-AAACATCAAAAAGCTCCCGAAGGCTTTTT-GAAACATCATGCACTGAAGGACTT
66 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
*
53212 ACAGATGACCCGAAGGCTTTGAAAACATCA
131 ACAGATGACCCGAAGGTTTTGAAAACATCA
53242 AAAGCTCTCG
Statistics
Matches: 330, Mismatches: 11, Indels: 23
0.91 0.03 0.06
Matches are distributed among these distances:
188 30 0.09
189 21 0.06
190 5 0.02
191 24 0.07
192 6 0.02
193 99 0.30
194 29 0.09
195 30 0.09
196 15 0.05
197 41 0.12
198 19 0.06
199 11 0.03
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (197 bp):
AAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAACATCATGCACTGAAGGACTTACAGATGACCC
GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTT
ACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
TG
Found at i:53364 original size:75 final size:74
Alignment explanation
Indices: 53032--53493 Score: 712
Period size: 74 Copynumber: 6.3 Consensus size: 74
53022 TTACAGATGA
*
53032 CCCGAAGG--TTTTGAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGCTTTTGAAAACAT
1 CCCGAAGGCTTTTTGAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
53095 CAAAAAGCT
66 CAAAAAGCT
* *
53104 CCCGAAGGCTTTTT-AAAAATCATGCAGTGAAGGGC-TA-AGATGACCCGAA-GTTTTG-AAACA
1 CCCGAAGGCTTTTTGAAACATCATGCACTGAA-GGCTTACAGATGACCCGAAGGTTTTGAAAACA
53164 TCAAAAAGCT
65 TCAAAAAGCT
*
53174 CCCGAAGGCTTTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
1 CCCGAAGGCTTTTTGAAACATCATGCACTGAAGG-CTTACAGATGACCCGAAGGTTTTGAAAACA
53239 TC-AAAAGCT
65 TCAAAAAGCT
* *
53248 CTCGAAGGCTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTTGAAACATCATGCACTGAA-GGCTTACAGATGACCCGAAGGTTTTGAAAACA
53313 TCAAAAAGCT
65 TCAAAAAGCT
*
53323 CTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTTG-AAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGTTTTGAAAACA
53388 TCAAAAAGCT
65 TCAAAAAGCT
* *
53398 CCCGAAGGC-TTTTGAAA-ACTCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAACA-TCATGCACTGAAGG-CTTACAGATGACCCGAAGGTTTTGAAAAC
53461 ATC-AAAAGCT
64 ATCAAAAAGCT
53471 CCCGAAGGCTTTTTGAAACATCA
1 CCCGAAGGCTTTTTGAAACATCA
53494 AAAAGCTCCC
Statistics
Matches: 361, Mismatches: 13, Indels: 30
0.89 0.03 0.07
Matches are distributed among these distances:
70 31 0.09
71 21 0.06
72 23 0.06
73 61 0.17
74 127 0.35
75 81 0.22
76 17 0.05
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (74 bp):
CCCGAAGGCTTTTTGAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGTTTTGAAAACAT
CAAAAAGCT
Found at i:53371 original size:149 final size:149
Alignment explanation
Indices: 53032--53493 Score: 739
Period size: 149 Copynumber: 3.2 Consensus size: 149
53022 TTACAGATGA
53032 CCCGAAGG--TTTTGAAACATCATGCACTGAAGGCTTACAGATGACCCGAA-GCTTTTGAAAACA
1 CCCGAAGGCTTTTTGAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGC-TTTGAAAACA
* *
53094 TCAAAAAGCTCCCGAAGGCTTTTTAAAA-ATCATGCAGTGAAGGGC-TA-AGATGACCCGAA-GT
65 TCAAAAAGCTCCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
53155 TTTG-AAACATCAAAAAGCT
130 TTTGAAAACATCAAAAAGCT
53174 CCCGAAGGCTTTTTGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACA
1 CCCGAAGGCTTTTTGAAACATCATGCACTGAAGG-CTTACAGATGACCCGAAGGCTTTGAAAACA
* *
53239 TC-AAAAGCTCTCGAAGGCTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
65 TCAAAAAGCTCCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
53303 TTTGAAAACATCAAAAAGCT
130 TTTGAAAACATCAAAAAGCT
* *
53323 CTCGAAGGCTTTTTGAAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGGCTTTTTG-AAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGCTTTGAAAACA
* * *
53388 TCAAAAAGCTCCCGAAGGCTTTTGAAAAC-TCATGCACTAAAGGACTTACAGATGACCCGAAGGC
65 TCAAAAAGCTCCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
53452 TTTGAAAACATC-AAAAGCT
130 TTTGAAAACATCAAAAAGCT
53471 CCCGAAGGCTTTTTGAAACATCA
1 CCCGAAGGCTTTTTGAAACATCA
53494 AAAAGCTCCC
Statistics
Matches: 297, Mismatches: 12, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
142 8 0.03
144 46 0.15
145 45 0.15
146 4 0.01
147 20 0.07
148 27 0.09
149 104 0.35
150 43 0.14
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (149 bp):
CCCGAAGGCTTTTTGAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTCCCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
TTGAAAACATCAAAAAGCT
Found at i:53513 original size:29 final size:29
Alignment explanation
Indices: 53443--53523 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 29
53433 TTACAGATGA
53443 CCCGAAGGC-TTTGAAAACATC-AAAAGCT
1 CCCGAAGGCTTTTG-AAACATCAAAAAGCT
53471 CCCGAAGGCTTTTTGAAACATCAAAAAGCT
1 CCCGAAGGC-TTTTGAAACATCAAAAAGCT
53501 CCCGAAGGCTTTTGGAAACATCA
1 CCCGAAGGCTTTT-GAAACATCA
53524 TGCACTACAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
28 9 0.18
29 11 0.22
30 29 0.59
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (29 bp):
CCCGAAGGCTTTTGAAACATCAAAAAGCT
Done.