Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008913.1 Hibiscus syriacus cultivar Beakdansim tig00112216_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: 629305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:554029 original size:18 final size:18
Alignment explanation
Indices: 554003--554037 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
553993 TCGAAAGGAC
*
554003 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
554021 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
554038 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:555228 original size:12 final size:12
Alignment explanation
Indices: 555193--555253 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
555183 CTGATACTTA
555193 ACATGGATTCTG
1 ACATGGATTCTG
*
555205 ATAT-GATATCTG
1 ACATGGAT-TCTG
555217 ACATGGATTCTG
1 ACATGGATTCTG
* *
555229 ATAT-GATACTTG
1 ACATGGATTC-TG
*
555241 ACTTGGATTCTG
1 ACATGGATTCTG
555253 A
1 A
555254 TCTGTTACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
11 7 0.18
12 24 0.63
13 7 0.18
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (12 bp):
ACATGGATTCTG
Found at i:555297 original size:24 final size:24
Alignment explanation
Indices: 555175--555290 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
555165 TTCGATTTGA
* *
555175 ATTCTGATCTGATACTTAACATGG
1 ATTCTGATATGATACTTGACATGG
555199 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
555223 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
555247 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATATGATACTTGACATGG
555270 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
555291 CTGATTTATG
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:555307 original size:24 final size:24
Alignment explanation
Indices: 555227--555300 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
555217 ACATGGATTC
* *
555227 TGATATGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
555251 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
555275 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
555299 TG
1 TG
555301 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:558738 original size:18 final size:18
Alignment explanation
Indices: 558712--558746 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
558702 TCGAAAGGGC
*
558712 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
558730 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
558747 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:559938 original size:12 final size:12
Alignment explanation
Indices: 559901--559939 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
559891 ATATGATACT
559901 TGACATGGATTC
1 TGACATGGATTC
*
559913 TGATAT-GATATC
1 TGACATGGAT-TC
559925 TGACATGGATTC
1 TGACATGGATTC
559937 TGA
1 TGA
559940 TCTGATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:560007 original size:24 final size:24
Alignment explanation
Indices: 559885--560000 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
559875 TTCGATTTGA
559885 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
559909 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* * *
559933 ATTCTGATCTGATAATTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
559957 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATATGATACTTGACATGG
559980 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
560001 CTGATTTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 78 0.95
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:577064 original size:23 final size:23
Alignment explanation
Indices: 577030--577098 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
577020 CACCACAGCT
*
577030 CGTATAAA-TGCATCAAAGTGCCA
1 CGTA-AAATTGCACCAAAGTGCCA
* * *
577053 CGTAGAATTGCACCGAAGTGCCG
1 CGTAAAATTGCACCAAAGTGCCA
**
577076 CGTAAAATTGCACCGTAGTGCCA
1 CGTAAAATTGCACCAAAGTGCCA
577099 TATAAGATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.05
23 36 0.95
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAAAATTGCACCAAAGTGCCA
Found at i:579189 original size:12 final size:12
Alignment explanation
Indices: 579164--579233 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
579154 ACAGAGATAT
* *
579164 CAGAAATCAAAA
1 CAGAATTCAGAA
579176 CAGAATTCAGAA
1 CAGAATTCAGAA
579188 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
579200 CAGAATCCAGAT
1 CAGAATTCAGAA
*
579212 CAGAAATCAGAA
1 CAGAATTCAGAA
*
579224 CATAATTCAG
1 CAGAATTCAG
579234 GTCATATATC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:579196 original size:24 final size:24
Alignment explanation
Indices: 579162--579256 Score: 109
Period size: 24 Copynumber: 4.0 Consensus size: 24
579152 AAACAGAGAT
*
579162 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
579186 AACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
579210 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
579234 GTCATATATCAGAACAAAATTCA
1 ATCAGAAATCAGAACAGAATTCA
579257 AGTCGAAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:579267 original size:48 final size:48
Alignment explanation
Indices: 579162--579270 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
579152 AAACAGAGAT
* * *
579162 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
* ** *
579210 ATCAGAAATCAGAACATAATTCAGGTCATATATCAGAACAAAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAA-TCAAG
579259 -TC-GAAAATCAGA
1 ATCAG-AAATCAGA
579271 TAAAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 47 0.90
49 4 0.08
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.18
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAAAATCAAG
Found at i:579268 original size:24 final size:24
Alignment explanation
Indices: 579193--579270 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
579183 CAGAACAGAT
* * *
579193 ATCAGAACAGAA-TCCAGATCAGAA
1 ATCAGAACAAAATTCAAG-TCATAA
* * *
579217 ATCAGAACATAATTCAGGTCATAT
1 ATCAGAACAAAATTCAAGTCATAA
579241 ATCAGAACAAAATTCAAGTCGA-AA
1 ATCAGAACAAAATTCAAGTC-ATAA
579265 ATCAGA
1 ATCAGA
579271 TAAAATATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 40 0.91
25 4 0.09
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAACAAAATTCAAGTCATAA
Found at i:583551 original size:2 final size:2
Alignment explanation
Indices: 583544--583572 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
583534 CTTTTAAAAC
583544 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 A
583573 CCCCCATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:583763 original size:12 final size:12
Alignment explanation
Indices: 583746--583828 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
583736 CATAAATCAA
583746 AACAGAATTCAG
1 AACAGAATTCAG
583758 AACAG-ATATCAG
1 AACAGAAT-TCAG
*
583770 AACAGAATCCAG
1 AACAGAATTCAG
* *
583782 ATCAGAAATCAG
1 AACAGAATTCAG
*
583794 AACATAATTCAG
1 AACAGAATTCAG
** *
583806 GTCA-TATATCAG
1 AACAGAAT-TCAG
583818 AACAGAATTCA
1 AACAGAATTCA
583829 AGTCAAAAAT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
11 4 0.07
12 46 0.85
13 4 0.07
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.19
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:583768 original size:24 final size:24
Alignment explanation
Indices: 583741--583828 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
583731 GATATCATAA
* *
583741 ATCAAAACAGAATTCAGAACAGAT
1 ATCAGAACAGAATTCAGATCAGAT
* *
583765 ATCAGAACAGAATCCAGATCAGAA
1 ATCAGAACAGAATTCAGATCAGAT
* * *
583789 ATCAGAACATAATTCAGGTCATAT
1 ATCAGAACAGAATTCAGATCAGAT
583813 ATCAGAACAGAATTCA
1 ATCAGAACAGAATTCA
583829 AGTCAAAAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCAGAT
Found at i:583815 original size:48 final size:47
Alignment explanation
Indices: 583734--583842 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 47
583724 AAACGGAGAT
* *
583734 ATCATAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAAAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
* * ** * *
583781 GATCAGAAATCAGAACATAATTCAGGTCATATATCAGAACAGAATTCA
1 -ATCAAAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
583829 AGTCAAAAATCAGA
1 A-TCAAAAATCAGA
583843 TAAAATATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.19
Consensus pattern (47 bp):
ATCAAAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:583833 original size:24 final size:25
Alignment explanation
Indices: 583734--583842 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 25
583724 AAACGGAGAT
* *
583734 ATCATAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
583758 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
583782 ATCAGAAATCAGAACATAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
583806 GTCATATATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
583831 -TCAAAAATCAGA
1 ATCAGAAATCAGA
583843 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.19
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:591526 original size:2 final size:2
Alignment explanation
Indices: 591521--591547 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
591511 TTTTTTGAAG
591521 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
591548 GGACTTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:592665 original size:5 final size:5
Alignment explanation
Indices: 592637--592686 Score: 64
Period size: 5 Copynumber: 10.0 Consensus size: 5
592627 GTCCGTCCGT
* * * *
592637 CTCGT CTCGG CTCGG CTCGA CACGG CACGG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
592687 GTCGTGGTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.06, C:0.40, G:0.36, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:592697 original size:6 final size:6
Alignment explanation
Indices: 592686--592736 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
592676 GCTCGGCTCG
592686 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
592734 GGT
1 GGT
592737 AATACGTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:597469 original size:5 final size:5
Alignment explanation
Indices: 597455--597493 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
597445 TCCGTCCCGT
* * *
597455 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
597494 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.05, C:0.41, G:0.36, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:597502 original size:6 final size:6
Alignment explanation
Indices: 597491--597599 Score: 182
Period size: 6 Copynumber: 18.2 Consensus size: 6
597481 TCGGCTCGGC
*
597491 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * *
597539 TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
597587 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
597600 AATACGTGTC
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 101 1.00
ACGTcount: A:0.04, C:0.17, G:0.50, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:599164 original size:30 final size:30
Alignment explanation
Indices: 599130--599204 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
599120 TTTTAATGAA
599130 TATTTAATTTGGAATAATTAAATAAGATTT
1 TATTTAATTTGGAATAATTAAATAAGATTT
* * *
599160 TATTTAATGTGGGATAATTAAATTAGATTT
1 TATTTAATTTGGAATAATTAAATAAGATTT
*
599190 TAATTAATTTGGAAT
1 TATTTAATTTGGAAT
599205 TACAAACCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (30 bp):
TATTTAATTTGGAATAATTAAATAAGATTT
Found at i:600083 original size:19 final size:20
Alignment explanation
Indices: 600045--600095 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
600035 GAAACCCCTT
*
600045 TGAAAATGCATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
600065 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
600084 TGAAGATACATG
1 TGAAAATACATG
600096 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:609185 original size:64 final size:63
Alignment explanation
Indices: 609116--609339 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 63
609106 TTATATGAAT
*
609116 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATTGGTAGTGCATCGATGCACCCA--TTAATAATAAA-ACATCGAATGCAA-T
609179 C-
62 CG
* ** * *
609180 GTGCATTGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
** ** * * *
609244 GTGCATCGATGCATTAGG-AGTGCATCGATGCATCCCAACAATAATACTACATCGAATAC-CTTG
1 GTGCATCGATGCATT-GGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
* **
609307 GATGCACCGATGCATCAGTAGTGCATCGATGCA
1 G-TGCATCGATGCATTGGTAGTGCATCGATGCA
609340 TACCTTCATT
Statistics
Matches: 132, Mismatches: 21, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
63 6 0.05
64 119 0.90
65 5 0.04
66 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATTGGTAGTGCATCGATGCACCCATTAATAATAAAACATCGAATGCAATCG
Found at i:609668 original size:12 final size:12
Alignment explanation
Indices: 609650--609697 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
609640 TATATATGTT
609650 CATGTGATATG-
1 CATGTGATATGA
609661 CTATGTGATATGA
1 C-ATGTGATATGA
609674 CATGTGATATGA
1 CATGTGATATGA
609686 CATGTGATATGA
1 CATGTGATATGA
609698 GAACATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.03
12 33 0.94
13 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:609748 original size:29 final size:29
Alignment explanation
Indices: 609713--609786 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
609703 TGATATGAAG
609713 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
609742 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
609771 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
609787 ACATATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:609888 original size:15 final size:15
Alignment explanation
Indices: 609871--609948 Score: 111
Period size: 15 Copynumber: 5.2 Consensus size: 15
609861 GAGGGTATAA
* *
609871 TAGTCCTTCAGGATA
1 TAGTCCTTCGGGATG
**
609886 TAGTCCTTCGGGGCG
1 TAGTCCTTCGGGATG
609901 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
609916 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
609931 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
609946 TAG
1 TAG
609949 GAGTCCTACG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.31
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:609945 original size:30 final size:30
Alignment explanation
Indices: 609871--609948 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
609861 GAGGGTATAA
* * *
609871 TAGTCCTTCAGGATATAGTCCTTCGGGGCG
1 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
609901 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
1 TAGTCCTTCGGGATGTAGTCCTTCGGGACG
609931 TAGTCCTTCGGGATGTAG
1 TAGTCCTTCGGGATGTAG
609949 GAGTCCTACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.31
Consensus pattern (30 bp):
TAGTCCTTCGGGATGTAGTCCTTCGGGACG
Found at i:616199 original size:64 final size:63
Alignment explanation
Indices: 616130--616353 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 63
616120 TTATATGAAT
*
616130 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTATTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATTGGTAGTGCATCGATGCACCCA--TTAATAATAAA-ACATCGAATGCAA-T
616193 C-
62 CG
** * *
616194 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
** * ** * * *
616258 GTGCATCGATGCATTAGG-AGTGCATCGATGCATCCCAACAATGATACTACATCGAATAC-CTTG
1 GTGCATCGATGCATT-GGTAGTGCATCGATGCA-CCCATTAATAATAAAACATCGAATGCAATCG
* **
616321 GATGCACCGATGCATCAGTAGTGCATCGATGCA
1 G-TGCATCGATGCATTGGTAGTGCATCGATGCA
616354 TACCTTCATT
Statistics
Matches: 133, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
63 6 0.05
64 120 0.90
65 5 0.04
66 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATTGGTAGTGCATCGATGCACCCATTAATAATAAAACATCGAATGCAATCG
Found at i:616680 original size:12 final size:12
Alignment explanation
Indices: 616663--616709 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
616653 ATATATGTTC
*
616663 ATGTGATATGCT
1 ATGTGATATGAT
616675 ATGTGATATGAT
1 ATGTGATATGAT
*
616687 ATGTGATATGAC
1 ATGTGATATGAT
*
616699 CTGTGATATGA
1 ATGTGATATGA
616710 GAACATGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.26, T:0.38
Consensus pattern (12 bp):
ATGTGATATGAT
Found at i:616767 original size:29 final size:29
Alignment explanation
Indices: 616725--616798 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
616715 TGATATGAAG
616725 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
616754 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
616783 TGACATGAG-TACATGA
1 TGACATGAGCTACATGA
616799 ACATATGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Found at i:616901 original size:15 final size:15
Alignment explanation
Indices: 616883--616960 Score: 147
Period size: 15 Copynumber: 5.2 Consensus size: 15
616873 GAGGGTATAA
616883 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
616898 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
616913 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
*
616928 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGATG
616943 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
616958 TAG
1 TAG
616961 GAGTCCTACG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:623275 original size:63 final size:65
Alignment explanation
Indices: 623126--623289 Score: 198
Period size: 63 Copynumber: 2.6 Consensus size: 65
623116 TTATATGAAT
*
623126 GTGCATCGATGCATT-GGTAGTGCATCGATGCA--CTATTTTAAAATAAAGACATCGAATGCAAT
1 GTGCATCGATGCATTAGG-AGTGCATCGATGCATCCCA-TTTAAAATAAAGACATCGAATGCAAT
623188 TC
64 TC
* * * *
623190 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCA-TTAATAGTGAA-A-ATCGAATGCAA-T
1 GTGCATCGATGCATTAGGAGTGCATCGATGCATCCCATTTAA-AATAAAGACATCGAATGCAATT
623251 C
65 C
623252 GGTGCATCGATGCATTAGGAGTGCATCGATGCATCCCA
1 -GTGCATCGATGCATTAGGAGTGCATCGATGCATCCCA
623290 ACATGATACT
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
62 2 0.02
63 46 0.52
64 33 0.38
65 5 0.06
66 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (65 bp):
GTGCATCGATGCATTAGGAGTGCATCGATGCATCCCATTTAAAATAAAGACATCGAATGCAATTC
Found at i:623306 original size:63 final size:62
Alignment explanation
Indices: 623174--623348 Score: 185
Period size: 63 Copynumber: 2.8 Consensus size: 62
623164 TAAAATAAAG
* *
623174 ACATCGAATGCAATTC-GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGA
1 ACATCGAATGCAA-TCGGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAATAATACT-A
* * * *
623237 AAATCGAATGCAATCGGTGCATCGATGCATTAGGAGTGCATCGATGCATCCCAACATGATACT-
1 ACATCGAATGCAATCGGTGCATCGATGCATAAGTAGTGCATCGATGCATCCC-A-ATAATACTA
* * * * *
623300 ACATCGAATAC-CTTGGATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 ACATCGAATGCAATCGG-TGCATCGATGCATAAGTAGTGCATCGATGCAT
623349 ACCTTCATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
62 5 0.05
63 84 0.88
64 1 0.01
65 5 0.05
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (62 bp):
ACATCGAATGCAATCGGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAATAATACTA
Found at i:623703 original size:12 final size:13
Alignment explanation
Indices: 623657--623703 Score: 73
Period size: 12 Copynumber: 3.8 Consensus size: 13
623647 ATATATGTTC
623657 ATGTGATATG-CT
1 ATGTGATATGACT
623669 ATGTGATATGA-T
1 ATGTGATATGACT
623681 ATGTGATATGACT
1 ATGTGATATGACT
623694 -TGTGATATGA
1 ATGTGATATGA
623704 GAACATGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 32 0.97
13 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.40
Consensus pattern (13 bp):
ATGTGATATGACT
Found at i:623763 original size:29 final size:29
Alignment explanation
Indices: 623721--623790 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
623711 ATATGAAGTG
623721 ATGAGCTACATGATCACAAGAGAAATAAC
1 ATGAGCTACATGATCACAAGAGAAATAAC
*
623750 ATGAGCTACATGATCACAAGAGAAATGAC
1 ATGAGCTACATGATCACAAGAGAAATAAC
623779 ATGAG-TACATGA
1 ATGAGCTACATGA
623791 ACATATGAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.17
29 33 0.82
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (29 bp):
ATGAGCTACATGATCACAAGAGAAATAAC
Found at i:623891 original size:15 final size:15
Alignment explanation
Indices: 623873--623935 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
623863 GAGGGTATAA
623873 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
623888 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
* *
623903 TAGTCCTTCAGGACG
1 TAGTCCTTCGGGATG
623918 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
623933 TAG
1 TAG
623936 GAGTCCTACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.16, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Done.