Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001427.1 Hibiscus syriacus cultivar Beakdansim tig00002772_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: 88772
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:262 original size:21 final size:21
Alignment explanation
Indices: 224--264 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
214 TTAAAAGTGT
*
224 TTAATGTGATGATTTATGATG
1 TTAATGTGATGATCTATGATG
245 TTAATGTGAT-AGTCTATGAT
1 TTAATGTGATGA-TCTATGAT
265 AATGACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.46
Consensus pattern (21 bp):
TTAATGTGATGATCTATGATG
Found at i:13435 original size:77 final size:78
Alignment explanation
Indices: 13345--13497 Score: 181
Period size: 77 Copynumber: 2.0 Consensus size: 78
13335 TTCGAATTAA
**
13345 AAAAACTTATTTAATTAATT-C-AACTTAAATAT-ACATT-AAAGACTTATAATCGGAATTACA-
1 AAAAACTTATTTAATT-ATTCCGAA-TTAAATATCA-ATTAAAAGACTTATAATCAAAATTACAT
13405 ATCTTTAATGTTTATTT
63 AT-TTTAATGTTTATTT
* * *
13422 AAAATCTTATTTAATTATTCCGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTAT
1 AAAAACTTATTTAATTATTCCGAATTAAATATCAATTAAAAGACTTATAATCAAAATTACA-TAT
13487 TTTAATGTTTA
65 TTTAATGTTTA
13498 CTTACTATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
76 3 0.05
77 27 0.42
78 22 0.34
79 11 0.17
80 2 0.03
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (78 bp):
AAAAACTTATTTAATTATTCCGAATTAAATATCAATTAAAAGACTTATAATCAAAATTACATATT
TTAATGTTTATTT
Found at i:14741 original size:3 final size:3
Alignment explanation
Indices: 14735--14782 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
14725 TTTTATTTTT
*
14735 TTA TTA TTA TTA TTA TCA TTA TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
14781 TT
1 TT
14783 TTGTTTGCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:14764 original size:22 final size:22
Alignment explanation
Indices: 14738--14783 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
14728 TATTTTTTTA
14738 TTATTATTATTATCATTATTAT
1 TTATTATTATTATCATTATTAT
*
14760 TTATTATTATTATTATTATTAT
1 TTATTATTATTATCATTATTAT
14782 TT
1 TT
14784 TGTTTGCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATCATTATTAT
Found at i:20533 original size:22 final size:23
Alignment explanation
Indices: 20507--20559 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
20497 AAGTGTTTAA
*
20507 ATGATTTTT-TTAATATTAAAAT
1 ATGATTTTTATTAATATAAAAAT
20529 ATGATTTTTAATTAATATAAAAAT
1 ATGATTTTT-ATTAATATAAAAAT
20553 AT-ATTTT
1 ATGATTTT
20560 ATGGAGTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.32
23 5 0.18
24 14 0.50
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATGATTTTTATTAATATAAAAAT
Found at i:23659 original size:21 final size:21
Alignment explanation
Indices: 23635--23699 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
23625 CGATCTCTTA
23635 TGAAAAAGGATCCATCCCTTT
1 TGAAAAAGGATCCATCCCTTT
*
23656 TGAAAATA-GATCAATCCC--T
1 TGAAAA-AGGATCCATCCCTTT
* *
23675 TAAAAAAGGGATACATCCCTTT
1 TGAAAAA-GGATCCATCCCTTT
23697 TGA
1 TGA
23700 GTGTTTAGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
18 1 0.03
19 6 0.18
20 8 0.24
21 15 0.44
22 4 0.12
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (21 bp):
TGAAAAAGGATCCATCCCTTT
Found at i:26997 original size:13 final size:13
Alignment explanation
Indices: 26976--27009 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
26966 TATCTTATTT
*
26976 TTATTTTTAGGAA
1 TTATCTTTAGGAA
*
26989 TTATCTTTATGAA
1 TTATCTTTAGGAA
27002 TTATCTTT
1 TTATCTTT
27010 TGTTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (13 bp):
TTATCTTTAGGAA
Found at i:27223 original size:21 final size:22
Alignment explanation
Indices: 27199--27239 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27189 TCTTTCAAAA
*
27199 ATGCTAAG-TATGTTTTCTACC
1 ATGCTAAGCTAAGTTTTCTACC
*
27220 ATGCTTAGCTAAGTTTTCTA
1 ATGCTAAGCTAAGTTTTCTA
27240 TTGCCAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (22 bp):
ATGCTAAGCTAAGTTTTCTACC
Found at i:32269 original size:43 final size:44
Alignment explanation
Indices: 32209--32292 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
32199 ATAGCAGCTT
* *
32209 TTAACAAACGCCGCAATAGGTACTGATATTTAGCGTCGTTTGTC
1 TTAACAAACGCCGCAATAGGTACTGAGATTTAGCGACGTTTGTC
* **
32253 TTAA-AAATGCCGCAATAGGTGTTGAGATTTAGCGACGTTT
1 TTAACAAACGCCGCAATAGGTACTGAGATTTAGCGACGTTT
32293 TTATCACAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 31 0.89
44 4 0.11
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (44 bp):
TTAACAAACGCCGCAATAGGTACTGAGATTTAGCGACGTTTGTC
Found at i:37792 original size:13 final size:13
Alignment explanation
Indices: 37774--37799 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37764 GATGCTGGGC
37774 GCAGTGAAGGAGA
1 GCAGTGAAGGAGA
37787 GCAGTGAAGGAGA
1 GCAGTGAAGGAGA
37800 TGGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.46, T:0.08
Consensus pattern (13 bp):
GCAGTGAAGGAGA
Found at i:48287 original size:39 final size:38
Alignment explanation
Indices: 48233--48384 Score: 135
Period size: 39 Copynumber: 3.9 Consensus size: 38
48223 GTACACCCAA
* * *
48233 TAAGGGCTTACCATGTGCACAAAGCAGAAGAGCATGCGG
1 TAAGGTCTTACCATGTGCACAAAGC-GAAGAGCCTACGG
* *
48272 TAAGGTCTTATCATGTGCACAAAGCGAATGAGCCTACAG
1 TAAGGTCTTACCATGTGCACAAAGCGAA-GAGCCTACGG
* * ** * *
48311 TAAGGACTTACCCTAAGCACAAATTCGAGGAGCCTACGG
1 TAAGGTCTTACCATGTGCACAAA-GCGAAGAGCCTACGG
* *
48350 TAAGGTCTTATCC-TGTGCATAAAGCAGAGGAGCCT
1 TAAGGTCTTA-CCATGTGCACAAAGC-GAAGAGCCT
48385 GCGGAAAGCG
Statistics
Matches: 91, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
38 4 0.04
39 82 0.90
40 5 0.05
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (38 bp):
TAAGGTCTTACCATGTGCACAAAGCGAAGAGCCTACGG
Found at i:50737 original size:20 final size:20
Alignment explanation
Indices: 50690--50746 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
50680 CTCCCTTGTA
*
50690 CCTAGTTTCAAAACCCCTTG
1 CCTAGTTTCAAACCCCCTTG
* *
50710 ACTGGTTTCTAAACCCCCTT-
1 CCTAGTTTC-AAACCCCCTTG
50730 CCTAGTTTCAAAACCCC
1 CCTAGTTTC-AAACCCC
50747 ATGTTATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.25, C:0.37, G:0.09, T:0.30
Consensus pattern (20 bp):
CCTAGTTTCAAACCCCCTTG
Found at i:51803 original size:483 final size:481
Alignment explanation
Indices: 50886--51843 Score: 1555
Period size: 483 Copynumber: 2.0 Consensus size: 481
50876 CACAATCTCA
*
50886 TTCCATCATATAAAAACAACCCAATGACACTTGAAGAAGGTAACTACACTTATCCAAACGTAGAG
1 TTCCATCATATAAAAACAACCCAATGACACTTGAAGAAGGTAACTACACTTATCCAAACATAGAG
* *
50951 ATCAAGAGAAAAGAGTTTTTATTCTTATTTCATTCATTTTCTCTTGTACATAAGTGCATTGAGCT
66 ATCAAGAGAAAAGAATTTTTATTCTTATTTCATTCATTTTATCTTGTACATAAGTGCATTGAGCT
* * *
51016 TATTGTATATCTTTTTAATTCATTCTTTGTGAGCTTAATTCTTGTAAATACCTACCTATAGAGGT
131 TACTGTATATCTTTTTAATTCATTCTTTGTGAGCTTAATTCTTGTAAACACCTACCTAGAGAGGT
* *
51081 ATTCTTATTTACCCAAATCAAACCTTGTAAAGGGGGGGAAAGGTTCTATTTTAGCCCTTGAAAAA
196 ATTCTTATTTACCCAAATCAAACCTTGTAAAGGAGGGGAAAGGTTCTAGTTTAGCCCTTGAAAAA
*
51146 ACTAGAGAATTGTAAAGGTTACACCTTATCCATGAAAGGTAAGAACAAATTAGTGAATTTGTTAG
261 ACTAGAGAATTGTAAAGGTTACACCTTATCCATAAAAGGTAAGAACAAATTAGTGAATTTGTTAG
51211 AAAATCCTTGTGTGGAGCTAAGGTAGTAGATGTAGACTTGGTTGAGAAGTCGATCCACTATATAT
326 AAAATCCTTGTGTGGAGCTAAGGTAGTAGATGTAGACTTGGTTGAGAAGTCGATCCACTATATAT
* *
51276 AGTTGTGCCAAATTTTCTATCTTTTATTACTTCCACACCAAAGATTTTTAAAGGCCAATTCAGCC
391 AGTTGTACCAAATTTTCTATCTTTTATTACTTCCACACCAAAGATTTTTAAAGGCCAATTCACCC
51341 CCTCTTGGTGGTTTTCGGTTGATTGT
456 CCTCTTGGTGGTTTTCGGTTGATTGT
* *
51367 TTCCATCATATAAAAACAACCCAA-GAATACTTGAAGAAGGTAACTACACTTATCCAAGCATAGA
1 TTCCATCATATAAAAACAACCCAATG-ACACTTGAAGAAGGTAACTACACTTATCCAAACATAGA
* * *
51431 GATCAAGAGAAAAGAATATTTTTCATTTTTATTTCATTTATTTTATCTTGTACATAAGTGTATTG
65 GATCAAGAGAAAAG-A-ATTTTT-ATTCTTATTTCATTCATTTTATCTTGTACATAAGTGCATTG
* * *
51496 AGCTTACTGTATATCTTTTTAATTCTTTCTTTGTGTGCTTAATTCTTGTAAACACTTACCTAGAG
127 AGCTTACTGTATATCTTTTTAATTCATTCTTTGTGAGCTTAATTCTTGTAAACACCTACCTAGAG
*
51561 AGGTATTCTTGTTTACCCAAATCAAACCTTGTAAA-GAGGGGAAAGGTTCTAGTTTAGCCCTTG-
192 AGGTATTCTTATTTACCCAAATCAAACCTTGTAAAGGAGGGGAAAGGTTCTAGTTTAGCCCTTGA
* * * *
51624 AAAAACTAGAGAATTTTAAAGGTTACACCTTATCCTTAAAATGTAAGAACAAATTAGTGATTTTG
257 AAAAACTAGAGAATTGTAAAGGTTACACCTTATCCATAAAAGGTAAGAACAAATTAGTGAATTTG
* * *
51689 TTAGAAAATCCTTATTGTTGAGCTAAGGTAGTAGATGTAGGCTTGGTTGAGAAGTCGAAT-CACT
322 TTAGAAAATCCTT-GTGTGGAGCTAAGGTAGTAGATGTAGACTTGGTTGAGAAGTCG-ATCCACT
* *
51753 ATATATCGTTGTACCAAATTTTCTATCTTTTATTGCTTCCACACCAAAGATTTTTAAAGGCCAAT
385 ATATATAGTTGTACCAAATTTTCTATCTTTTATTACTTCCACACCAAAGATTTTTAAAGGCCAAT
* *
51818 TCACCCCCTCTTTGTGTTTTTCGGTT
450 TCACCCCCTCTTGGTGGTTTTCGGTT
51844 AATCATTTCA
Statistics
Matches: 440, Mismatches: 31, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
480 1 0.00
481 73 0.17
482 74 0.17
483 160 0.36
484 132 0.30
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (481 bp):
TTCCATCATATAAAAACAACCCAATGACACTTGAAGAAGGTAACTACACTTATCCAAACATAGAG
ATCAAGAGAAAAGAATTTTTATTCTTATTTCATTCATTTTATCTTGTACATAAGTGCATTGAGCT
TACTGTATATCTTTTTAATTCATTCTTTGTGAGCTTAATTCTTGTAAACACCTACCTAGAGAGGT
ATTCTTATTTACCCAAATCAAACCTTGTAAAGGAGGGGAAAGGTTCTAGTTTAGCCCTTGAAAAA
ACTAGAGAATTGTAAAGGTTACACCTTATCCATAAAAGGTAAGAACAAATTAGTGAATTTGTTAG
AAAATCCTTGTGTGGAGCTAAGGTAGTAGATGTAGACTTGGTTGAGAAGTCGATCCACTATATAT
AGTTGTACCAAATTTTCTATCTTTTATTACTTCCACACCAAAGATTTTTAAAGGCCAATTCACCC
CCTCTTGGTGGTTTTCGGTTGATTGT
Found at i:55044 original size:2 final size:2
Alignment explanation
Indices: 55032--55085 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
55022 AAATTGGAAA
*
55032 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55074 AT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT
55086 TTAAATTACC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:55784 original size:2 final size:2
Alignment explanation
Indices: 55777--55801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55767 TTTCAAAAGG
55777 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
55802 GAATGTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56369 original size:2 final size:2
Alignment explanation
Indices: 56362--56400 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
56352 ACAAGCATAC
56362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56401 GGATTAGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62199 original size:24 final size:24
Alignment explanation
Indices: 62172--62227 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
62162 ATTTTGGAAT
62172 GAAACTTAAAGATTTAAAAGTTTA
1 GAAACTTAAAGATTTAAAAGTTTA
* *
62196 GAAACTTACAGGTTTAAAAGTTTA
1 GAAACTTAAAGATTTAAAAGTTTA
62220 GAAACTTA
1 GAAACTTA
62228 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (24 bp):
GAAACTTAAAGATTTAAAAGTTTA
Found at i:63068 original size:41 final size:40
Alignment explanation
Indices: 63023--63132 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 40
63013 ATTCACGTTG
* * *
63023 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGTGTTTTTC
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
*
63064 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATTTTC
63105 CATTTCGCGTTGCGATAGTTGAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAATCGC
63133 AACGCGATCT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
40 7 0.11
41 55 0.87
42 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:63114 original size:20 final size:20
Alignment explanation
Indices: 63048--63120 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
63038 TAGTTGAAAA
* *
63048 TCGCGTTGTGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
63068 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
63089 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
63109 TCGCGTTGCGAT
1 TCGCGTTGCGAT
63121 AGTTGAAATC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.11, C:0.21, G:0.27, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:63132 original size:20 final size:21
Alignment explanation
Indices: 63068--63132 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 21
63058 TTTTTCCATT
* *
63068 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
63089 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
63109 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
63129 TCGC
1 TCGC
63133 AACGCGATCT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:63193 original size:41 final size:39
Alignment explanation
Indices: 63165--63388 Score: 297
Period size: 41 Copynumber: 5.5 Consensus size: 39
63155 ATTCGCGTTG
63165 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTG--TTTC
*
63206 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTG--TTTC
*
63247 CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGTGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTG--TTTC
63288 CATTTCGCGTTGCGATAGTTGAAAATCGCGTT-TCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGT-G--TTTC
*
63329 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTG--TTTC
* *
63370 CGTTTCGCGTTGCAATAGT
1 CATTTCGCGTTGCGATAGT
63389 CTACAGTTGT
Statistics
Matches: 174, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
40 1 0.01
41 173 0.99
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (39 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGTTTC
Found at i:63243 original size:142 final size:142
Alignment explanation
Indices: 62994--63270 Score: 493
Period size: 142 Copynumber: 2.0 Consensus size: 142
62984 AATTCGCATT
*
62994 GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGTGT
1 GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGTGA
* *
63059 TTTTCCATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
66 TTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
63124 TGAAATCGCAAC
131 TGAAATCGCAAC
* *
63136 GCGATCTCCA-TCATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTG
1 GCGATCTCCACT-ATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGTG
63200 ATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG
65 ATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG
63265 TTGAAA
130 TTGAAA
63271 ATCGTGTTGT
Statistics
Matches: 129, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 1 0.01
142 128 0.99
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (142 bp):
GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGTGA
TTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
TGAAATCGCAAC
Found at i:63254 original size:82 final size:82
Alignment explanation
Indices: 63165--63436 Score: 420
Period size: 82 Copynumber: 3.3 Consensus size: 82
63155 ATTCGCGTTG
63165 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAA
63230 ATCGCGTTGCGATTTTC
66 ATCGCGTTGCGATTTTC
*
63247 CATTTCGCGTTGCGATAGTTGAAAATCGTGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAA
*
63312 ATCGCGTTTCGATTTTC
66 ATCGCGTTGCGATTTTC
* * * *
63329 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCGTTTCGCGTTGCAATAGTCT-AC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGT-TGAA
* *
63393 AGTTGTCGTTGCGATTTTC
65 AATCG-CGTTGCGATTTTC
* * *
63412 CGTTTTGCGTTGCGATAGTTAAAAA
1 CATTTCGCGTTGCGATAGTTGAAAA
63437 AAAGATTTTG
Statistics
Matches: 175, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
82 140 0.80
83 35 0.20
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (82 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGTGATTTTCCATTTCGCGTTGCGATAGTTGAAA
ATCGCGTTGCGATTTTC
Found at i:63312 original size:123 final size:124
Alignment explanation
Indices: 63165--63436 Score: 424
Period size: 123 Copynumber: 2.2 Consensus size: 124
63155 ATTCGCGTTG
63165 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGT-GATTTTCCATTTCGCGTTGCGATAGTTGAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTT-TCGATTTTCCATTTCGCGTTGCGATAGTTGAA
* *
63229 AATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGT-GTTGTGATTTTC
65 AATCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCT-AAAATCGTCGTTGCGATTTTC
63288 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTTCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTTCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
* * * *
63353 ATCGCGTTGCGATTTTCCGTTTCGCGTTGCAATAGTCTACAGTTGTCGTTGCGATTTTC
66 ATCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCTAAAATCGTCGTTGCGATTTTC
* * *
63412 CGTTTTGCGTTGCGATAGTTAAAAA
1 CATTTCGCGTTGCGATAGTTGAAAA
63437 AAAGATTTTG
Statistics
Matches: 137, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
122 1 0.01
123 102 0.74
124 34 0.25
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (124 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTTCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
ATCGCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCTAAAATCGTCGTTGCGATTTTC
Found at i:63517 original size:6 final size:6
Alignment explanation
Indices: 63506--63559 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
63496 AGACACGTAT
63506 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GA-CAC GA-CAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
63552 GA-CAC GAC
1 GACCAC GAC
63560 ACGGACGGCG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 15 0.32
6 32 0.68
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:64060 original size:10 final size:10
Alignment explanation
Indices: 64045--64121 Score: 93
Period size: 10 Copynumber: 7.2 Consensus size: 10
64035 CCGTCTCGTC
64045 TCGGGTCGGG
1 TCGGGTCGGG
64055 TCGGGTCGGG
1 TCGGGTCGGG
64065 TCGGGTCGGG
1 TCGGGTCGGG
64075 TCGGGTC-GG
1 TCGGGTCGGG
64084 TCGTGGTCGTGG
1 TCG-GGTCG-GG
64096 TCGTGGTCGTGG
1 TCG-GGTCG-GG
64108 TCGTGGTCGTGG
1 TCG-GGTCG-GG
64120 TC
1 TC
64122 ATACGTGTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
9 5 0.08
10 31 0.48
12 28 0.44
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.27
Consensus pattern (10 bp):
TCGGGTCGGG
Found at i:64065 original size:15 final size:16
Alignment explanation
Indices: 64045--64121 Score: 97
Period size: 15 Copynumber: 4.8 Consensus size: 16
64035 CCGTCTCGTC
64045 TCGGGTCGGGTCG-GG
1 TCGGGTCGGGTCGTGG
64060 TCGGGTCGGGTCG-GG
1 TCGGGTCGGGTCGTGG
64075 TCGGGTC-GGTCGTGG
1 TCGGGTCGGGTCGTGG
64090 TCGTGGTCGTGGTCGTGG
1 TCG-GGTCG-GGTCGTGG
64108 TCGTGGTCGTGGTC
1 TCG-GGTCG-GGTC
64122 ATACGTGTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
14 5 0.09
15 27 0.47
16 4 0.07
18 22 0.38
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.27
Consensus pattern (16 bp):
TCGGGTCGGGTCGTGG
Found at i:64093 original size:6 final size:5
Alignment explanation
Indices: 64045--64121 Score: 93
Period size: 6 Copynumber: 14.4 Consensus size: 5
64035 CCGTCTCGTC
64045 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC-GG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG
64096 TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCG-GG TCG-GG TCG-GG TCG-GG TC
64122 ATACGTGTCT
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.06
5 32 0.46
6 34 0.49
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:64260 original size:21 final size:21
Alignment explanation
Indices: 64196--64260 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
64186 TCTTTTTTTT
*
64196 AACTATCGCAACGCGAAATGG
1 AACTATCGCAACGCGAAATGC
* ** *
64217 AA-AATCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGC
64237 AACTATCGCAACGCGAAATGC
1 AACTATCGCAACGCGAAATGC
64258 AAC
1 AAC
64261 GCGAATTTGC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (21 bp):
AACTATCGCAACGCGAAATGC
Found at i:69656 original size:23 final size:23
Alignment explanation
Indices: 69626--69672 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
69616 TATATTTAAA
69626 AAATAAATCACAAAAATGAAGTG
1 AAATAAATCACAAAAATGAAGTG
*
69649 AAATAAATTACAAAAATGAAGTG
1 AAATAAATCACAAAAATGAAGTG
69672 A
1 A
69673 CTTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.19
Consensus pattern (23 bp):
AAATAAATCACAAAAATGAAGTG
Found at i:72841 original size:20 final size:20
Alignment explanation
Indices: 72797--72848 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
72787 TTTAATTTTG
*
72797 GTATCGATACTAAGTGTTGAA
1 GTATCGATACTAAG-CTTGAA
72818 -TATCGATACTAA-CTTGAGA
1 GTATCGATACTAAGCTTGA-A
72837 GTATCGATACTA
1 GTATCGATACTA
72849 CCCTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.14
19 1 0.04
20 23 0.82
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACTAAGCTTGAA
Found at i:76358 original size:19 final size:19
Alignment explanation
Indices: 76334--76371 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
76324 CTTTGTATTT
*
76334 TATTTTAAATATGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
76353 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
76372 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:77113 original size:25 final size:25
Alignment explanation
Indices: 77067--77114 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
77057 ATAAGTTTTC
*
77067 TTTATCTCAATTTATTTATTTAATT
1 TTTATCTCAATTTACTTATTTAATT
*
77092 TTTATCTC-ATTATACTTCTTTAA
1 TTTATCTCAATT-TACTTATTTAA
77115 ATAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATCTCAATTTACTTATTTAATT
Found at i:82035 original size:24 final size:24
Alignment explanation
Indices: 81999--82051 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
81989 AAATATTATT
* *
81999 TTTTAGGTATTTTAGTTTAA-ATAG
1 TTTTAAGTATTTTAATTTAAGAT-G
*
82023 TTTTAAGTGTTTTAATTTAAGATG
1 TTTTAAGTATTTTAATTTAAGATG
82047 TTTTA
1 TTTTA
82052 GCTTGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (24 bp):
TTTTAAGTATTTTAATTTAAGATG
Found at i:85215 original size:2 final size:2
Alignment explanation
Indices: 85208--85244 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
85198 TATGTACATA
85208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
85245 AAGGTAGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:88560 original size:20 final size:20
Alignment explanation
Indices: 88535--88594 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
88525 GATATGAGAT
88535 TGATTGTAAATGTTTGGAAA
1 TGATTGTAAATGTTTGGAAA
*
88555 TGA---T---TGTTTGG-AT
1 TGATTGTAAATGTTTGGAAA
88568 TGATTGTAAATGTTTGGAAA
1 TGATTGTAAATGTTTGGAAA
88588 TGATTGT
1 TGATTGT
88595 TTGGAAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
16 1 0.03
17 1 0.03
19 7 0.23
20 11 0.35
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (20 bp):
TGATTGTAAATGTTTGGAAA
Found at i:88569 original size:33 final size:33
Alignment explanation
Indices: 88532--88599 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
88522 TTTGATATGA
88532 GATTGATTGTAAATGTTTGGAAATGATTGTTTG
1 GATTGATTGTAAATGTTTGGAAATGATTGTTTG
88565 GATTGATTGTAAATGTTTGGAAATGATTGTTTG
1 GATTGATTGTAAATGTTTGGAAATGATTGTTTG
88598 GA
1 GA
88600 AGCTAAATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (33 bp):
GATTGATTGTAAATGTTTGGAAATGATTGTTTG
Done.