Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005205.1 Hibiscus syriacus cultivar Beakdansim tig00011773_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: 40306
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:420 original size:64 final size:65
Alignment explanation
Indices: 93--421 Score: 482
Period size: 65 Copynumber: 5.1 Consensus size: 65
83 AAGTTTTTTT
* *
93 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCTCTTGAAATGAATTTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * * *
158 TCTTGAGACAATTTCTCTTGAAACATCATCTGTGAGATCATTTCCCTCAAAATGAATTTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * **
223 ACTTGATACAGTTTCTCTTGAAACATCATCTTTGAGATTATTTCCCTTAAAATGAATTTTGTCTC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * *
288 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAAATCGTTTCCCTT-AAATGAATCTTGTCTA
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
* * * * *
352 TCTTGAGACAATTTCTCTTGAAAAATCATCTTTGAGATCGTTTCCCTTTAAACGAA-TTTGTCCC
1 TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
416 TCTTGA
1 TCTTGA
422 AACATAATCT
Statistics
Matches: 237, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
64 70 0.30
65 167 0.70
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (65 bp):
TCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTAAAATGAATTTTGTCTC
Found at i:726 original size:134 final size:131
Alignment explanation
Indices: 474--808 Score: 379
Period size: 134 Copynumber: 2.5 Consensus size: 131
464 GATGGCCAGT
* **
474 CATCCTCATCGCGTAGGAATCATGTCATCCACGACCAGATCTCCTCATCACGTAGGAGTTGCGTC
1 CATCCTCATCACGTAGGAAT-ATGTCATCCACGACCAGATCTCCTCATCACGTAGGAGCCGCGTC
* * *
539 ACCTTAGATAACCAGCCGTCCTCATCACATAGGAACAGTGTTATCATCATCCCTTAAA-ATGGCT
65 ACCTTAGATAACCAGCCATCCTCATCACATAGAAACAGTGTTATCATCATCCC-TAAAGAT-GAT
603 AA-C
128 AAGC
** * *
606 CATTTTCATCACGTAGGAACTGTGTCATCCACCAACCAGATCTCCTCATCACGTAGGAGCCGCGT
1 CATCCTCATCACGTAGGAA-TATGTCATCCA-CGACCAGATCTCCTCATCACGTAGGAGCCGCGT
*** * **
671 CAACCTTAGATAACCATTTATCCTTATCGTATAGAAATC-GTGTTATCATCATCCCTAAAGATGA
64 C-ACCTTAGATAACCAGCCATCCTCATCACATAGAAA-CAGTGTTATCATCATCCCTAAAGATGA
735 TAAGC
127 TAAGC
* * * * *
740 CATCCTCATCATGTAGGAAATATGTTATCCATCGACCAGATCTCCTCATCACATAGGAGACGTGT
1 CATCCTCATCACGTAGG-AATATGTCATCCA-CGACCAGATCTCCTCATCACGTAGGAGCCGCGT
805 CACC
64 CACC
809 CGTAGACGAC
Statistics
Matches: 170, Mismatches: 26, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
132 25 0.15
133 43 0.25
134 99 0.58
135 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (131 bp):
CATCCTCATCACGTAGGAATATGTCATCCACGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
CCTTAGATAACCAGCCATCCTCATCACATAGAAACAGTGTTATCATCATCCCTAAAGATGATAAG
C
Found at i:1006 original size:3 final size:3
Alignment explanation
Indices: 998--1025 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
988 TCTTAAAAAA
998 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1026 TACATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5565 original size:3 final size:3
Alignment explanation
Indices: 5542--5594 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
5532 GTCCCTTTTA
* * *
5542 TAT TTT TAT TAT T-T TAA TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5587 TAT TAT TA
1 TAT TAT TA
5595 AATAATTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 36 0.88
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5713 original size:14 final size:14
Alignment explanation
Indices: 5673--5713 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5663 AAACTTGATG
5673 CAGACCCGGTCCAA
1 CAGACCCGGTCCAA
* *
5687 GAGATCCGGTCCAA
1 CAGACCCGGTCCAA
*
5701 CAGACCCGATCCA
1 CAGACCCGGTCCA
5714 GTAGAACCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.29, C:0.39, G:0.22, T:0.10
Consensus pattern (14 bp):
CAGACCCGGTCCAA
Found at i:12755 original size:12 final size:13
Alignment explanation
Indices: 12738--12769 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
12728 CAGAAAAAAA
12738 GAAAAAAGAAA-T
1 GAAAAAAGAAATT
12750 GAAAAAAGAAATT
1 GAAAAAAGAAATT
12763 GAAAAAA
1 GAAAAAA
12770 AAAGAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (13 bp):
GAAAAAAGAAATT
Found at i:12772 original size:16 final size:16
Alignment explanation
Indices: 12751--12781 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12741 AAAAGAAATG
12751 AAAAAAGAAATTGAAA
1 AAAAAAGAAATTGAAA
12767 AAAAAAGAAATTGAA
1 AAAAAAGAAATTGAA
12782 TCAAGACGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAAAAGAAATTGAAA
Found at i:17731 original size:29 final size:29
Alignment explanation
Indices: 17687--17751 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
17677 TCTCTATTAT
*
17687 AATTTATAAAAGGTTTTA-TCCTTAATTTA
1 AATTTATAAAAGG-TTTAGTCATTAATTTA
* *
17716 AATTTATAAAATGTTTAGTCATTAATTTT
1 AATTTATAAAAGGTTTAGTCATTAATTTA
17745 AATTTAT
1 AATTTAT
17752 GTAAAGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (29 bp):
AATTTATAAAAGGTTTAGTCATTAATTTA
Found at i:20820 original size:41 final size:42
Alignment explanation
Indices: 20719--20820 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 42
20709 ATTTGTAAGT
* * * * *
20719 CCTTCGGGCCATCTGTAAGTCTTTCGACCATGATGCTTAAAT
1 CCTTCGGGTCATCTATAAGTCTTTCGACCAAGATGCATAAAG
*
20761 CCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-ATAAAG
1 CCTTCGGGTCATCTATAAGTCTTTCGACCAAGATGCATAAAG
*
20802 CCTTCGGGTCATCCATAAG
1 CCTTCGGGTCATCTATAAG
20821 ACCTTCAGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 22 0.42
42 31 0.58
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (42 bp):
CCTTCGGGTCATCTATAAGTCTTTCGACCAAGATGCATAAAG
Found at i:21107 original size:177 final size:175
Alignment explanation
Indices: 20797--21179 Score: 561
Period size: 177 Copynumber: 2.2 Consensus size: 175
20787 AGCAAGATGA
* * * *
20797 TAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
1 TAAATCCTACGGGTCATCCATAAGACCTTCAGTACAGGATGTTTTCAAATGAGATTTTAGAAACC
* * *
20862 ATGCCTTCGAGGGTTTACTAATTATCTCAAAAGTGTTGTTAAAGGAAGCTAAGCCTAACAAAGGG
66 AAGCCTTCGAGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
* * *
20927 GTTCCTTGACAACTAAGAAACTAAGCCTTCG-GGCGTTTCTTGATTT
131 GTTCATTGACAACTAAGAAACCAAGCCTTCGTGG-GTTTCTT-AATT
* * *
20973 GTAAGTCCTACGGGCCATCCATAAGACCTTCAGTACATGATGTTTTCAAATGAGATTTTAGAAAC
1 -TAAATCCTACGGGTCATCCATAAGACCTTCAGTACAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
21038 CAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAATAAAGG
65 CAAGCCTTCGAGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGG
*
21103 GGTTCATTGACAACTAATAAACCAAGCCTTCGTGGGTTTCTTAATT
130 GGTTCATTGACAACTAAGAAACCAAGCCTTCGTGGGTTTCTTAATT
* **
21149 TAAATCCTTCGGGTCATCTGTAAGACCTTCA
1 TAAATCCTACGGGTCATCCATAAGACCTTCA
21180 ATGCAAGATG
Statistics
Matches: 184, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
175 26 0.14
176 3 0.02
177 153 0.83
178 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (175 bp):
TAAATCCTACGGGTCATCCATAAGACCTTCAGTACAGGATGTTTTCAAATGAGATTTTAGAAACC
AAGCCTTCGAGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACAAAGGG
GTTCATTGACAACTAAGAAACCAAGCCTTCGTGGGTTTCTTAATT
Found at i:21439 original size:3 final size:3
Alignment explanation
Indices: 21419--21453 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
21409 GTCCCATTTT
*
21419 TTA TTT TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21454 AATAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:21439 original size:17 final size:16
Alignment explanation
Indices: 21414--21449 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
21404 TTTTTGTCCC
*
21414 ATTTTTTATTTTTATT
1 ATTTTTTATTATTATT
21430 ATTTTATTATTATTATT
1 ATTTT-TTATTATTATT
21447 ATT
1 ATT
21450 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTTTATTATTATT
Found at i:21620 original size:42 final size:41
Alignment explanation
Indices: 21573--21666 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 41
21563 TTGTAAGTCA
* * * *
21573 TTCGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAAGCC
1 TTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-ATAAAGCC
* *
21615 TTCGGGTTATCTATAAGTCTTTCGAGTAAGATGATAAAGCC
1 TTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAAGCC
21656 TTCGGGTCATC
1 TTCGGGTCATC
21667 CATGAGACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 17 0.38
42 28 0.62
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
TTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAAGCC
Found at i:21959 original size:177 final size:175
Alignment explanation
Indices: 21649--22031 Score: 559
Period size: 177 Copynumber: 2.2 Consensus size: 175
21639 AGTAAGATGA
* * * * *
21649 TAAAGCCTTCGGGTCATCCATGAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAACT
1 TAAATCCTACGGGTCATCCATAAGACCTTCAGTACATGATGTTTTCAAATGAGATTTTAGAAACC
* **** *
21714 ATGCCTTCGGGGGTTTACTAATTATCTCAAAAGTGTTGTTAAAGGAAGCTAAGCCTAACAAAGGG
66 AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAACAGTTAAAGGAAACTAAGCCTAACAAAGGG
* * * *
21779 GTTCATTGATAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTT
131 GTTCATTGACAACTAAGAAACCAAGCCTTCGCGGGTTTCTT-AATT
* *
21825 GTAAGTCCTACGGGCCATCCATAAGACCTTCAGTACATGATGTTTTCAAATGAGATTTTAGAAAC
1 -TAAATCCTACGGGTCATCCATAAGACCTTCAGTACATGATGTTTTCAAATGAGATTTTAGAAAC
21890 CAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAACAGTTAAAGGAAACTAAGCCTAACAAAGG
65 CAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAACAGTTAAAGGAAACTAAGCCTAACAAAGG
*
21955 GGTTCCTTGACAACTAAGAAACCAAGCCTTCGCGGGTTTCTTAATT
130 GGTTCATTGACAACTAAGAAACCAAGCCTTCGCGGGTTTCTTAATT
* **
22001 TAAATCCTTCGGGTCATCTGTAAGACCTTCA
1 TAAATCCTACGGGTCATCCATAAGACCTTCA
22032 ATGCAAGATG
Statistics
Matches: 183, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
175 26 0.14
176 3 0.02
177 154 0.84
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (175 bp):
TAAATCCTACGGGTCATCCATAAGACCTTCAGTACATGATGTTTTCAAATGAGATTTTAGAAACC
AAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAACAGTTAAAGGAAACTAAGCCTAACAAAGGG
GTTCATTGACAACTAAGAAACCAAGCCTTCGCGGGTTTCTTAATT
Found at i:22057 original size:42 final size:42
Alignment explanation
Indices: 22000--22085 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
21990 GTTTCTTAAT
* *
22000 TTAAATCCTTCGGGTCATCTGTAAGACCTTCAATGCAAGATG
1 TTAAAACCTTCGGGTCATCTATAAGACCTTCAATGCAAGATG
* * *
22042 TTAAAACCTTTGGGTCATCTATAAGACCTTCAGTGCAGGATG
1 TTAAAACCTTCGGGTCATCTATAAGACCTTCAATGCAAGATG
22084 TT
1 TT
22086 TTCCAATGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (42 bp):
TTAAAACCTTCGGGTCATCTATAAGACCTTCAATGCAAGATG
Found at i:25495 original size:632 final size:632
Alignment explanation
Indices: 23605--25961 Score: 4547
Period size: 632 Copynumber: 3.7 Consensus size: 632
23595 TTTTACCTTT
23605 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
1 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
*
23670 TTATATATTTATTTATTTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCATTTTTT
66 TTATATATTTATTTATTTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCCTTTTTT
23735 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
131 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
23800 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
196 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
23865 CTAATGTCATTTTCTGATATTTTTAAATAAATAAATAAATAAT-CTATTTATAAAACCCTAAAAT
261 CTAATGTCATTTTCTGATATTTTTAAATAAATAAATAAAT-ATCCTATTTATAAAACCCTAAAAT
23929 GTATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGATTG
325 GTATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGATTG
23994 AATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAGAGA
390 AATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAGAGA
* *
24059 CAATTTATAATCAACGAGTACAAATTTTGGGCGTTGTGGGGGTGCTAATCATTCCCCAAACGTAA
455 CAATTTATAATCAACGAGTACCAATTTTGGGCGTTGTGGGGGTGCTAATTATTCCCCAAACGTAA
*
24124 CCGACCACGAAT-CCCTTTTTATAACTAAAAAGAATGAATTTTTGGTTATACGCAAACTAATTTA
520 CCGACCACGAATCCCCTTTTTATAACTAAAAAGAATGAATTTTTGGTTATACGCAGACTAATTTA
24188 TCTTTTAAATAATTTTTTCTTAAAAACTCTCTTAAAAAATGATTTTTA
585 TCTTTTAAATAATTTTTTCTTAAAAACTCTCTTAAAAAATGATTTTTA
24236 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
1 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
*
24301 TTATATATTTATTTAATTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCCTTTTTT
66 TTATATATTTATTTATTTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCCTTTTTT
24366 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
131 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
24431 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
196 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
24496 CTAATGTCATTTTCTGATATTTTTAAATAAATAAATAAATAAATATCCTATTTATAAAACCCTAA
261 CTAATGTCATTTTCTGATA-TTTT---TAAATAAATAAATAAATATCCTATTTATAAAACCCTAA
24561 AATGTATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGA
322 AATGTATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGA
24626 TTGAATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAG
387 TTGAATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAG
24691 AGACAATTTATAATCAACGAGTACCAATTTTGGGCGTTGTGGGGGTGCTAATTATTCCCCAAACG
452 AGACAATTTATAATCAACGAGTACCAATTTTGGGCGTTGTGGGGGTGCTAATTATTCCCCAAACG
24756 TAACCGACCACGAATCCCCTTTTTATAACTAAAAAGAATGAATTTTTGGTTATACGCAGACTAAT
517 TAACCGACCACGAATCCCCTTTTTATAACTAAAAAGAATGAATTTTTGGTTATACGCAGACTAAT
24821 TTATCTTTTAAATAATTTTTTCTTAAAAACTCTCTTAAAAAATGATTTTTA
582 TTATCTTTTAAATAATTTTTTCTTAAAAACTCTCTTAAAAAATGATTTTTA
24872 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
1 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
24937 TTATATATTTATTTATTTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCCTTTTTT
66 TTATATATTTATTTATTTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCCTTTTTT
25002 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
131 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
25067 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
196 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
25132 CTAATGTCATTTTCTGATATTTTTAAATAAATAAATAAATATCCTATTTATAAAACCCTAAAATG
261 CTAATGTCATTTTCTGATATTTTTAAATAAATAAATAAATATCCTATTTATAAAACCCTAAAATG
25197 TATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGATTGA
326 TATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGATTGA
25262 ATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAGAGAC
391 ATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAGAGAC
*
25327 AATTTATAATCAACGAGTACCAACTTTGGGCGTTGTGGGGGTGCTAATTATTCCCCAAACGTAAC
456 AATTTATAATCAACGAGTACCAATTTTGGGCGTTGTGGGGGTGCTAATTATTCCCCAAACGTAAC
25392 CGACCACGAATCCCCTTTTTATAACTAAAAAGAATGAATTTTTGGTTATACGCAGACTAATTTAT
521 CGACCACGAATCCCCTTTTTATAACTAAAAAGAATGAATTTTTGGTTATACGCAGACTAATTTAT
25457 CTTTTAAATAATTTTTTCTTAAAAACTCTCTTAAAAAATGATTTTTA
586 CTTTTAAATAATTTTTTCTTAAAAACTCTCTTAAAAAATGATTTTTA
25504 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
1 TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
** *
25569 TTATATATTTATTTATTTTTTATATATTAAATGGATTATCTTAAAGCAATTAGATGTCCTTTTTT
66 TTATATATTTATTTATTTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCCTTTTTT
*
25634 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGGAAAA
131 GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
*
25699 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAACTAA
196 ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
25764 CTAGATGTCATTTTCTGATATTTTTAAATAAATAAATAAATATCCTATTTATAAAACCCTAAAAT
261 CTA-ATGTCATTTTCTGATATTTTTAAATAAATAAATAAATATCCTATTTATAAAACCCTAAAAT
25829 GTATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGATTG
325 GTATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGATTG
25894 AATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAGAGA
390 AATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAGAGA
25959 CAA
455 CAA
25962 CCCTTTTTAT
Statistics
Matches: 1707, Mismatches: 12, Indels: 12
0.99 0.01 0.01
Matches are distributed among these distances:
631 277 0.16
632 610 0.36
633 194 0.11
634 2 0.00
635 247 0.14
636 377 0.22
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (632 bp):
TATGTTTCAATATTTTAAATATAATACTTAATTATTATTTTATTTCATAATTTAATTAAATATTT
TTATATATTTATTTATTTTTTATATATTAAATGGGCTATCTTAAAGCAACTAGATGTCCTTTTTT
GATATTTTTAAATAAATAAAATACTATATTTAATTTAGTTTTATTTAAATTATTTTTTAGAAAAA
ATTAACATATTCTTACTAATATTTATTTATTTTTTATATTAAAGAAAGGGGTTGTCTTAAAGTAA
CTAATGTCATTTTCTGATATTTTTAAATAAATAAATAAATATCCTATTTATAAAACCCTAAAATG
TATATTTTTACATTAGTTTTATAAAAATTATTTTTATATATTTTTCCTTAGAATTATCCGATTGA
ATCTGAAATAACAAGATTGTAAATTAAATTTATATTAGAATTCTTATATTTCCACTAATAGAGAC
AATTTATAATCAACGAGTACCAATTTTGGGCGTTGTGGGGGTGCTAATTATTCCCCAAACGTAAC
CGACCACGAATCCCCTTTTTATAACTAAAAAGAATGAATTTTTGGTTATACGCAGACTAATTTAT
CTTTTAAATAATTTTTTCTTAAAAACTCTCTTAAAAAATGATTTTTA
Found at i:27423 original size:11 final size:11
Alignment explanation
Indices: 27381--27428 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
27371 TAATTTTTGG
*
27381 TTTTTGTTTT-
1 TTTTTATTTTC
*
27391 TTTTTACTTTC
1 TTTTTATTTTC
27402 TTTGGTTATTTTC
1 TTT--TTATTTTC
27415 TTTTTATTTTC
1 TTTTTATTTTC
27426 TTT
1 TTT
27429 GTTACATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
13 10 0.31
ACGTcount: A:0.06, C:0.08, G:0.06, T:0.79
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:27441 original size:23 final size:24
Alignment explanation
Indices: 27391--27442 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
27381 TTTTTGTTTT
** *
27391 TTTTTACTTTCTTTGGTTATTTTC
1 TTTTTACTTTCTTTGGTTACATTA
*
27415 TTTTTATTTTCTTT-GTTACATTA
1 TTTTTACTTTCTTTGGTTACATTA
27438 TTTTT
1 TTTTT
27443 TCTTATTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.73
Consensus pattern (24 bp):
TTTTTACTTTCTTTGGTTACATTA
Found at i:28543 original size:22 final size:22
Alignment explanation
Indices: 28518--28560 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28508 GTTCACCATA
28518 ATTTTTGCCTTCTTTTTCTTAC
1 ATTTTTGCCTTCTTTTTCTTAC
*
28540 ATTTTTGCCTTGTTTTTCTTA
1 ATTTTTGCCTTCTTTTTCTTA
28561 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.07, T:0.65
Consensus pattern (22 bp):
ATTTTTGCCTTCTTTTTCTTAC
Found at i:28722 original size:43 final size:43
Alignment explanation
Indices: 28661--28744 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
28651 TCTAAACTTC
* **
28661 AAAGTAACAATTCACAAATGTACCAAACTAACATATTACAACT
1 AAAGTAACAACTCACAAATACACCAAACTAACATATTACAACT
*
28704 AAAGTAACAACTCACAAATACATCAAACTAACATATTACAA
1 AAAGTAACAACTCACAAATACACCAAACTAACATATTACAA
28745 TCATTCTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.54, C:0.21, G:0.04, T:0.21
Consensus pattern (43 bp):
AAAGTAACAACTCACAAATACACCAAACTAACATATTACAACT
Found at i:31863 original size:2 final size:2
Alignment explanation
Indices: 31858--31882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31848 ATATATATAT
31858 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
31883 TGAATGTAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35710 original size:20 final size:21
Alignment explanation
Indices: 35685--35726 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
35675 CCAACTTACA
35685 ATGCATTATG-AACCATTATT
1 ATGCATTATGCAACCATTATT
*
35705 ATGCATTATGCAACTATTATT
1 ATGCATTATGCAACCATTATT
35726 A
1 A
35727 GTTGTATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGCATTATGCAACCATTATT
Done.