Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003267.1 Hibiscus syriacus cultivar Beakdansim tig00006866_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: 204893
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
File 2 of 2
Found at i:159716 original size:2 final size:2
Alignment explanation
Indices: 159709--160030 Score: 158
Period size: 2 Copynumber: 170.5 Consensus size: 2
159699 CTAATTCGTA
159709 AT AT AT AT -T AT A- AT AT ACT A- AT AT AT AT ACT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
*
159749 A- AT AT GA- AT AT AT AT AT AT AC AT ACT AT A- AT AT AT A- AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
159789 AT AT ACT ACT AT A- AT AT AT A- AT AT A- AT AT AT AT A- AT AT AT
1 AT AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
159829 ACT AT AT AC A- AT AT AC A- AT AT AT A- AT AT AT ACT A- AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
159869 A- AT AT A- AT AT AT A- AT CT A- AT -T CAT A- AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
159905 A- AT ACT AT A- AT A- AT AT ACT AT AT A- ACT AT AT A- AT GAT AT
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT -AT AT
* * * *
159944 AT ACT AT AT AA AT AT -T AT A- AT AT AC AT AA AT AT CAT ACC AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT
*
159985 AT A- AT AT AT AT -T AT AT A- AA AT A- AT AT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
160021 AT AT GAT AT A
1 AT AT -AT AT A
160031 ATTCAAAGGT
Statistics
Matches: 253, Mismatches: 15, Indels: 104
0.68 0.04 0.28
Matches are distributed among these distances:
1 36 0.14
2 186 0.74
3 31 0.12
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:159784 original size:59 final size:56
Alignment explanation
Indices: 159709--160020 Score: 244
Period size: 59 Copynumber: 5.5 Consensus size: 56
159699 CTAATTCGTA
*
159709 ATATATATTATAATATACTA-ATATATATACTATAATATATAATATGAATATATATAT
1 ATATATACTATAATATA-TATATATATATACTATAATATATAATAT-AATATATATAT
*
159766 ATACATACTATAATATATAATATATATACTACTATAATATATAATATAATATATATA-
1 ATATATACTATAATATAT-ATATATATA-TACTATAATATATAATATAATATATATAT
*
159823 ATATATACTATATACAATATACAATATATAATATA-TACTAATATATAATAT-A-ATATATA-
1 ATATATAC--TAT--AATATA-TATATAT-ATATACTA-TAATATATAATATAATATATATAT
* *
159882 ATCTA-ATTCATAATATATAT-TATA-ATACTATAATAATATACTATATAACTATATA-AT
1 ATATATACT-ATAATATATATATATATATACTATAAT-ATATA--ATATAA-TATATATAT
*
159939 GATATATACTAT-ATAAATAT-TATAATATAC-ATAAATATCATACCATATAATATATAT-T
1 -ATATATACTATAATATATATATAT-ATATACTAT-AATAT-ATA--ATATAATATATATAT
*
159997 ATATA-A-AATAATATATA-ATATATA
1 ATATATACTATAATATATATATATATA
160021 ATATGATATA
Statistics
Matches: 214, Mismatches: 13, Indels: 58
0.75 0.05 0.20
Matches are distributed among these distances:
51 7 0.03
52 8 0.04
53 3 0.01
54 6 0.03
55 12 0.06
56 13 0.06
57 45 0.21
58 36 0.17
59 51 0.24
60 3 0.01
61 27 0.13
62 3 0.01
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (56 bp):
ATATATACTATAATATATATATATATATACTATAATATATAATATAATATATATAT
Found at i:159999 original size:7 final size:7
Alignment explanation
Indices: 159707--160024 Score: 232
Period size: 7 Copynumber: 43.9 Consensus size: 7
159697 AACTAATTCG
159707 TAATATA
1 TAATATA
159714 T-AT-TA
1 TAATATA
159719 TAATATA
1 TAATATA
159726 CTAATATA
1 -TAATATA
159734 T-ATACTA
1 TAATA-TA
159741 TAATATA
1 TAATATA
159748 TAATAT-
1 TAATATA
*
159754 GAATATA
1 TAATATA
159761 T-ATATA
1 TAATATA
159767 TACATACTA
1 TA-ATA-TA
159776 TAATATA
1 TAATATA
159783 TAATATA
1 TAATATA
159790 TATACTACTA
1 TA-A-TA-TA
159800 TAATATA
1 TAATATA
159807 TAATATA
1 TAATATA
159814 -ATATATA
1 TA-ATATA
159821 TAATATA
1 TAATATA
159828 TACTATATA
1 TA--ATATA
*
159837 CAATATA
1 TAATATA
*
159844 CAATATA
1 TAATATA
159851 TAATATA
1 TAATATA
*
159858 TACTA-A
1 TAATATA
159864 TATATAATA
1 TA-AT-ATA
159873 TAATATA
1 TAATATA
*
159880 T-A-ATC
1 TAATATA
159885 TAAT-TCA
1 TAATAT-A
159892 TAATATA
1 TAATATA
159899 T-AT-TA
1 TAATATA
159904 TAATACTA
1 TAATA-TA
159912 TAATAATA
1 TAAT-ATA
*
159920 TACTATA
1 TAATATA
159927 TAACTATA
1 TAA-TATA
159935 TAATGATA
1 TAAT-ATA
159943 TATACTATA
1 TA-A-TATA
159952 TAAATATTA
1 T-AATA-TA
159961 TAATATACA
1 TAATAT--A
159970 TAAATATCA
1 T-AATAT-A
**
159979 TACCATA
1 TAATATA
159986 TAATATA
1 TAATATA
*
159993 TATTATA
1 TAATATA
160000 TAA-A-A
1 TAATATA
160005 TAATATA
1 TAATATA
160012 TAATATA
1 TAATATA
160019 TAATAT
1 TAATAT
160025 GATATAATTC
Statistics
Matches: 257, Mismatches: 16, Indels: 76
0.74 0.05 0.22
Matches are distributed among these distances:
5 13 0.05
6 31 0.12
7 115 0.45
8 56 0.22
9 31 0.12
10 11 0.04
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (7 bp):
TAATATA
Found at i:160356 original size:58 final size:59
Alignment explanation
Indices: 160241--160368 Score: 143
Period size: 58 Copynumber: 2.2 Consensus size: 59
160231 TAGAATGTTC
** * * *
160241 AAAAAGTTTAGGGATCAATTTAAAATGAATGTCATAGTTTGGGGATAAAATAAAAATACT
1 AAAAAGTTTAGGGATCAATTTAAAA-GAAAATCATAATTTAGGAATAAAATAAAAATACT
* * *
160301 AAAAAGTTT-GAGGATTAATTTAAAA-AAAATCATAATTTAGGAATAAAATTAAAATATT
1 AAAAAGTTTAG-GGATCAATTTAAAAGAAAATCATAATTTAGGAATAAAATAAAAATACT
*
160359 TAAAAGTTTA
1 AAAAAGTTTA
160369 AATACTAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
58 34 0.60
59 1 0.02
60 22 0.39
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (59 bp):
AAAAAGTTTAGGGATCAATTTAAAAGAAAATCATAATTTAGGAATAAAATAAAAATACT
Found at i:161841 original size:2 final size:2
Alignment explanation
Indices: 161799--161825 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
161789 CATTAAACGT
161799 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
161826 TTAAATGGAG
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:163650 original size:23 final size:23
Alignment explanation
Indices: 163624--163668 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
163614 CACCACAGCT
*
163624 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
163647 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
163669 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:163906 original size:149 final size:149
Alignment explanation
Indices: 163636--163950 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
163626 TATAATTGCA
*
163636 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
* *
163700 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAGGACTTCACACCTGTT
65 TTCCTTAAGAATCATATACATATACCAGGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTT
163765 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
163785 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
163850 TCCTTAAGAATCATATACATATACCAGGGATCAAGTATGTGTCTTTCAAGACTTCACACTTGTTC
66 TCCTTAAGAATCATATACATATACCAGGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTTC
163915 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
163934 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
163951 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACCAGGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTTC
CAAAGAATATACATATGTC
Found at i:165387 original size:21 final size:21
Alignment explanation
Indices: 165363--165407 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
165353 TGTTGTTCGT
* *
165363 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
165384 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
165405 TTG
1 TTG
165408 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:168548 original size:23 final size:23
Alignment explanation
Indices: 168522--168566 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
168512 CACCATAGCT
*
168522 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
168545 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
168567 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:168812 original size:149 final size:149
Alignment explanation
Indices: 168542--168848 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
168532 CACCGAAGTG
*
168542 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
*
168607 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTTCCAAAGAAT
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTTCCAAAGAAT
168672 ATACATATGTCCCAAAGGA
131 ATACATATGTCCCAAAGGA
168691 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
168756 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTTCCAAAGAAT
66 AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTTCCAAAGAAT
*
168821 ATACATATGTCCCGAAGGA
131 ATACATATGTCCCAAAGGA
168840 CCGCGTAGA
1 CCGCGTAGA
168849 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACCTGTTCCAAAGAAT
ATACATATGTCCCAAAGGA
Found at i:170286 original size:21 final size:21
Alignment explanation
Indices: 170262--170306 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
170252 TGTTGTTCGT
* *
170262 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
170283 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
170304 TTG
1 TTG
170307 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:172834 original size:37 final size:37
Alignment explanation
Indices: 172740--172844 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
172730 CATTTTCGTC
*
172740 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* ** * * *
172777 TTGTTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
172814 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
172845 CCACAAGTAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:177992 original size:183 final size:183
Alignment explanation
Indices: 177678--178214 Score: 923
Period size: 183 Copynumber: 2.9 Consensus size: 183
177668 ATTAAATCCG
* *
177678 TAAAGCTGAGCTAGTCCACTAAGGCAATAGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
177743 ATATATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* * *
177808 TTTTCAGGCCAAAGACTTTGTGATGAGATGAACCCTACAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTA
*
177861 TAAAGATGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
177926 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
177991 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTA
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTA
178044 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * * *
178109 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACCGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
178173 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
178215 TAAACTGATA
Statistics
Matches: 335, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 334 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTA
Found at i:179434 original size:36 final size:36
Alignment explanation
Indices: 179394--179510 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
179384 ATACTTTGTC
179394 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
** * * ** * * *
179430 TCACTCAAGATTATTTTTCTTAAAAAAAGATTTGTC
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
* * *
179466 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGACTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
179506 TCACT
1 TCACT
179511 CAAGGTTGTT
Statistics
Matches: 55, Mismatches: 22, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
36 38 0.69
37 7 0.13
38 1 0.02
39 4 0.07
40 5 0.09
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (36 bp):
TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
Found at i:179453 original size:72 final size:75
Alignment explanation
Indices: 179353--179527 Score: 200
Period size: 72 Copynumber: 2.4 Consensus size: 75
179343 ATGCAGATGA
* * * * * *
179353 TTATCTCACTCAA-ATTTTTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTATTTTTCTTAAAA-AAAGATTTGTCTCACTTGAGACCGTTTTCACTC
179415 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
179425 TTATTTCACTCAAGATTATTTTTCTTAAAAAAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTATTTTTCTTAAAAAAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
179490 AAGAAGGCAT
66 AAGAAGGCAT
* *
179500 TTCATTTCACTCAAGGTTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTATTTTTCTTAA
179528 GAAGATTTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
71 2 0.02
72 47 0.53
73 11 0.12
74 1 0.01
75 8 0.09
76 19 0.22
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (75 bp):
TTATTTCACTCAAGATTATTTTTCTTAAAAAAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:179562 original size:73 final size:72
Alignment explanation
Indices: 179353--179564 Score: 182
Period size: 72 Copynumber: 2.9 Consensus size: 72
179343 ATGCAGATGA
* * * * * * * *
179353 TTATCTCACTCAA-ATTTTTTTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTT-TCTCG
1 TTATTTCACTCAAGA-TTATTTTTCTTAAAAAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCG
179416 AAAGAAGAT
64 AAAGAAGAT
* *
179425 TTATTTCACTCAAGATTATTTTTCTTAAAAAAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTATTTTTCTT-AAAAAAGATTTATCTCGCTTGAGACAGTTTTCACTCGA
179490 AAGAAGGCAT
65 AAGAA-G-AT
* * * * * *
179500 TTCATTTCACTCAAGGTTGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCG
1 TT-ATTTCACTCAAGATTATTTTTCTTAAAAAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCG
179562 AAA
64 AAA
179565 CAGAAAATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
72 43 0.36
73 34 0.29
74 16 0.14
75 6 0.05
76 19 0.16
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (72 bp):
TTATTTCACTCAAGATTATTTTTCTTAAAAAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAA
AGAAGAT
Found at i:179586 original size:39 final size:39
Alignment explanation
Indices: 179543--179695 Score: 117
Period size: 39 Copynumber: 3.6 Consensus size: 39
179533 TTTTATCTTG
*
179543 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * * *
179582 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCT
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTCC
* *
179633 CATGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
179672 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
179696 TAAACATTGA
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
39 46 0.53
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 25 0.29
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:179707 original size:104 final size:104
Alignment explanation
Indices: 179598--179917 Score: 511
Period size: 106 Copynumber: 3.1 Consensus size: 104
179588 ACAGTTTCTC
* *
179598 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCATGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
179663 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
179702 TTGAAAACATTTCCCTTGAAATGATTTTTTTCTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTT-TCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
179767 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
64 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
179808 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
* ** *
179870 TTTGTCTCTCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
179909 TTGAAAACA
1 TTGAAAACA
179918 ATTTAACGAA
Statistics
Matches: 203, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 49 0.24
105 9 0.04
106 97 0.48
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:179864 original size:36 final size:36
Alignment explanation
Indices: 179817--179892 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
179807 ATTGAAAACA
* *
179817 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCGCTTGAGACAG
* *
179853 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCGCTTGAGACAG
179889 TTTC
1 TTTC
179893 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCGCTTGAGACAG
Found at i:180246 original size:105 final size:104
Alignment explanation
Indices: 180092--180720 Score: 901
Period size: 105 Copynumber: 6.0 Consensus size: 104
180082 ATATCGTGAC
* * * * *
180092 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCC
* *
180156 CAATTTAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
64 CAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
180197 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
180262 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 A-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
180302 ACTTCAGA-AACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
180366 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
180406 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
180471 ATCTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
180511 ACTCCAGACAATGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
180572 ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * ** * * * *
180611 ACTCGAGACAACACAAGTTCAACTTCAAAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * *
180676 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
180717 ACTC
1 ACTC
180721 GGAATAATGC
Statistics
Matches: 481, Mismatches: 33, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
100 78 0.16
101 4 0.01
102 3 0.01
103 5 0.01
104 115 0.24
105 238 0.49
106 38 0.08
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:180377 original size:209 final size:209
Alignment explanation
Indices: 180092--180720 Score: 919
Period size: 209 Copynumber: 3.0 Consensus size: 209
180082 ATATCGTGAC
* * * *
180092 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT
* *
180156 CAATTTAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
64 CAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
180221 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
129 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
180286 CAACGAAGGATATTGG
194 CAACGAAGGATATTGG
* * *
180302 ACTTCAGA-AACGCAAGTTCAACTTCACGATGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
180366 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* *
180431 CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAAAGCCAATTTCAACTTCAC
130 CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCAC
180496 AACGAAGGATATTGG
195 AACGAAGGATATTGG
* *
180511 ACTCCAGACAATGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* * * *
180572 ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTC
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
** * * * * ** *
180637 AAAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCAC
131 ACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCAC
* *
180702 GACGGAGGATATTGG
195 AACGAAGGATATTGG
180717 ACTC
1 ACTC
180721 GGAATAATGC
Statistics
Matches: 381, Mismatches: 34, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
205 81 0.21
206 50 0.13
207 1 0.00
208 15 0.04
209 183 0.48
210 51 0.13
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (209 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
ACGAAGGATATTGG
Found at i:181316 original size:37 final size:37
Alignment explanation
Indices: 181263--181367 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
181253 CATTTTCGTC
181263 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
181300 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
181337 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
181368 CCACAAGAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:182258 original size:2 final size:2
Alignment explanation
Indices: 182251--182286 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
182241 TAATACTTTG
* *
182251 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
182287 TTTTTTCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:188221 original size:13 final size:13
Alignment explanation
Indices: 188203--188250 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
188193 TGATAAATAA
188203 AAAAAATTACAAT
1 AAAAAATTACAAT
* *
188216 AAAAAAGTCCAAT
1 AAAAAATTACAAT
* *
188229 AAACAACTACAAT
1 AAAAAATTACAAT
188242 -AAAAATTAC
1 AAAAAATTAC
188251 TAAATACAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.65, C:0.15, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAAAATTACAAT
Found at i:189878 original size:107 final size:107
Alignment explanation
Indices: 189692--189906 Score: 403
Period size: 107 Copynumber: 2.0 Consensus size: 107
189682 ATGCCCAAGA
189692 CTGCAGCAACAGGAGACATCCGCCGATAGCATTTCTCCTATAGTCAATGGCTCGACACATCTCCC
1 CTGCAGCAACAGGAGACATCCGCCGATAGCATTTCTCCTATAGTCAATGGCTCGACACATCTCCC
189757 TATACAAGAAAGCCAAAACTGGTGAGCCCCGACTGAGTGATC
66 TATACAAGAAAGCCAAAACTGGTGAGCCCCGACTGAGTGATC
* * *
189799 CTGCAGCAGCAGGAGACATCCGCCGATAGCATTTCTCTTGTAGTCAATGGCTCGACACATCTCCC
1 CTGCAGCAACAGGAGACATCCGCCGATAGCATTTCTCCTATAGTCAATGGCTCGACACATCTCCC
189864 TATACAAGAAAGCCAAAACTGGTGAGCCCCGACTGAGTGATC
66 TATACAAGAAAGCCAAAACTGGTGAGCCCCGACTGAGTGATC
189906 C
1 C
189907 AGCCAGATGA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (107 bp):
CTGCAGCAACAGGAGACATCCGCCGATAGCATTTCTCCTATAGTCAATGGCTCGACACATCTCCC
TATACAAGAAAGCCAAAACTGGTGAGCCCCGACTGAGTGATC
Found at i:190641 original size:9 final size:9
Alignment explanation
Indices: 190627--190660 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
190617 TAAGTAAAAT
190627 ATTAAATAA
1 ATTAAATAA
190636 ATTAAAT-A
1 ATTAAATAA
*
190644 CTTAAATAA
1 ATTAAATAA
190653 ATTAAATA
1 ATTAAATA
190661 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:190659 original size:17 final size:17
Alignment explanation
Indices: 190623--190661 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
190613 TATATAAGTA
190623 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
190639 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
190656 AAATAC
1 AAATAC
190662 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:190722 original size:20 final size:19
Alignment explanation
Indices: 190697--190744 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
190687 TACCTTAAAC
* *
190697 AGAGAATATAAGAGTATTTG
1 AGAGAAT-TAAGAGAAATTG
190717 AGAGAAGTTAAGAGAAATTG
1 AGAGAA-TTAAGAGAAATTG
190737 AGAGAATT
1 AGAGAATT
190745 TGGTGTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 22 0.88
21 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (19 bp):
AGAGAATTAAGAGAAATTG
Found at i:193300 original size:89 final size:89
Alignment explanation
Indices: 193145--193363 Score: 393
Period size: 90 Copynumber: 2.4 Consensus size: 89
193135 GAAGGATATA
193145 AAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACATCCTGCACTGAAG
1 AAAATCAAGAAACCCCCGAAGGCTTAGTTTC-TAAAATCTCATTTGAAAACATCCTGCACTGAAG
* *
193210 GTCTTATGGATGGCCCGAAGGACTT
65 GTCTTATGGATGACACGAAGGACTT
*
193235 AAAATCAAGAAACCCCCGAAGGCTTAGTTTCTATAATCTCATTTGAAAACATCCTGCACTGAAGG
1 AAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGG
193300 TCTTATGGATGACACGAAGGACTT
66 TCTTATGGATGACACGAAGGACTT
193324 ACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCT
1 A-AAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCT
193364 TTTGTTTTGA
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
89 56 0.45
90 68 0.55
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (89 bp):
AAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGG
TCTTATGGATGACACGAAGGACTT
Found at i:193401 original size:39 final size:39
Alignment explanation
Indices: 193356--193785 Score: 555
Period size: 39 Copynumber: 11.2 Consensus size: 39
193346 GCTTAGTTTC
* * * *
193356 TAAAATCTTTTGTTTTGAGAGAAACTATTTCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * * *
193395 CAAAATCTTGTATTTCGAGGGAAACTATCTCAAGCGAAA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
193434 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* *
193473 TAAAATCTTCTATTTCGAGGGAAACTATCTCAAGAGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * *
193512 CAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGTGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* *
193551 TAAAATCTTCTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* *
193590 TAAAATTTTCTGTTTCGAGAGAAACTATCTCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * *
193629 TAAAATCTTTTGTTTCAAGGGAAACTACCTCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * * *
193668 T-AAATATTCTGTTTCAAGTGAAAATATCTCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * *
193706 T-AAATCTTCTGTTTCAAGGGAAGCTACCTCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
* * *
193744 TAAAA--TT-TGTTTCAAGGAAAACTACCTCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
193780 TAAAAT
1 TAAAAT
193786 TCGTTTCAAG
Statistics
Matches: 347, Mismatches: 42, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
36 32 0.09
37 2 0.01
38 66 0.19
39 247 0.71
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (39 bp):
TAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGA
Found at i:193885 original size:30 final size:31
Alignment explanation
Indices: 193788--193885 Score: 94
Period size: 34 Copynumber: 3.1 Consensus size: 31
193778 GATAAAATTC
* *
193788 GTTTCAAGGG-AATGA-CTCAAAGATGGTATT
1 GTTTCAAGGGAAACGATCTCAAAGATAGT-TT
* * *
193818 GTTTCAAGGGAAACAATATCAAAGAAAATAATTT
1 GTTTCAAGGGAAACGATCTCAAAG---ATAGTTT
193852 GTTTCAAGGGAAACGATCTCAAAGAT-GTTT
1 GTTTCAAGGGAAACGATCTCAAAGATAGTTT
193882 GTTT
1 GTTT
193886 TGTTTCAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 17 0.31
31 5 0.09
32 6 0.11
34 24 0.44
35 3 0.05
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (31 bp):
GTTTCAAGGGAAACGATCTCAAAGATAGTTT
Found at i:193932 original size:33 final size:31
Alignment explanation
Indices: 193783--193984 Score: 122
Period size: 33 Copynumber: 6.1 Consensus size: 31
193773 AGCGAGATAA
** *
193783 AATTCGTTTCAAGGG-AATGACTCAAAGATGGT
1 AATT-GTTTCAAGGGAAACAACTCAAAGAT-TT
* **
193815 -ATTGTTTCAAGGGAAACAATATCAAAGAAAAT
1 AATTGTTTCAAGGGAAACAA-CTCAAAG-ATTT
*
193847 AATTTGTTTCAAGGGAAACGATCTCAAAGATGTTT
1 AA-TTGTTTCAAGGGAAAC-AACTCAAAGA--TTT
** * *
193882 GTTTTGTTTCAAAGGAAATAGACTCAAAGATTT
1 -AATTGTTTCAAGGGAAACA-ACTCAAAGATTT
* * *
193915 AATTCGTTTCGAGGGAAACAATTTCAAATATGGTT
1 AATT-GTTTCAAGGGAAACAA-CTCAAAGAT--TT
193950 -ATTGTTTCAAGGGAAACAAACTCAAAGATTT
1 AATTGTTTCAAGGGAAAC-AACTCAAAGATTT
193981 AATT
1 AATT
193985 TCTTTTTTTC
Statistics
Matches: 130, Mismatches: 24, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
30 10 0.08
31 8 0.06
32 13 0.10
33 45 0.35
34 28 0.22
35 26 0.20
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (31 bp):
AATTGTTTCAAGGGAAACAACTCAAAGATTT
Found at i:193978 original size:66 final size:66
Alignment explanation
Indices: 193783--193984 Score: 216
Period size: 66 Copynumber: 3.1 Consensus size: 66
193773 AGCGAGATAA
**
193783 AATTCGTTTCAAGGG-AATGA-CTCAAAGATGG-TATTGTTTCAAGGGAAACAATA-TCAAAGAA
1 AATTCGTTTCAAGGGAAACAATCTCAAAGATGGTTATTGTTTCAAGGGAAACAA-ACTCAAAG-A
**
193844 AAT
64 TTT
* * * * *
193847 AATTTGTTTCAAGGGAAACGATCTCAAAGATGTTTGTT-TTGTTTCAAAGGAAATAGACTCAAAG
1 AATTCGTTTCAAGGGAAACAATCTCAAAGATG---GTTATTGTTTCAAGGGAAACAAACTCAAAG
193911 ATTT
63 ATTT
* * *
193915 AATTCGTTTCGAGGGAAACAATTTCAAATATGGTTATTGTTTCAAGGGAAACAAACTCAAAGATT
1 AATTCGTTTCAAGGGAAACAATCTCAAAGATGGTTATTGTTTCAAGGGAAACAAACTCAAAGATT
193980 T
66 T
193981 AATT
1 AATT
193985 TCTTTTTTTC
Statistics
Matches: 115, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
64 14 0.12
65 7 0.06
66 41 0.36
68 30 0.26
69 22 0.19
70 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (66 bp):
AATTCGTTTCAAGGGAAACAATCTCAAAGATGGTTATTGTTTCAAGGGAAACAAACTCAAAGATT
T
Found at i:194005 original size:15 final size:15
Alignment explanation
Indices: 193985--194057 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 15
193975 AGATTTAATT
193985 TCTTTTTTTCTTTTC
1 TCTTTTTTTCTTTTC
194000 TCTTTTTTTTCTTTTC
1 TC-TTTTTTTCTTTTC
** *
194016 T-TTTTGCTATGTTTC
1 TCTTTTTTTCT-TTTC
*
194031 T-TTTTCTTTTTTTTC
1 TCTTTT-TTTCTTTTC
194046 TCTTTTTGTTCT
1 TCTTTTT-TTCT
194058 GATTGGATCT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
14 6 0.13
15 17 0.37
16 23 0.50
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (15 bp):
TCTTTTTTTCTTTTC
Found at i:194011 original size:11 final size:11
Alignment explanation
Indices: 193990--194057 Score: 59
Period size: 11 Copynumber: 5.9 Consensus size: 11
193980 TAATTTCTTT
193990 TTTTCTTTTCTC
1 TTTT-TTTTCTC
194002 TTTTTTTTCT-
1 TTTTTTTTCTC
*
194012 TTTCTTTTTGCTA
1 TTT-TTTTT-CTC
194025 TGTTTCTTTT-TC
1 T-TTT-TTTTCTC
194037 TTTTTTTTCTC
1 TTTTTTTTCTC
*
194048 TTTTTGTTCT
1 TTTTTTTTCT
194058 GATTGGATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 7 0.15
11 25 0.52
12 8 0.17
13 2 0.04
14 6 0.12
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:194661 original size:7 final size:7
Alignment explanation
Indices: 194649--194780 Score: 78
Period size: 7 Copynumber: 18.9 Consensus size: 7
194639 TATGTGATAG
194649 GGTTTAT
1 GGTTTAT
194656 GGTTTA-
1 GGTTTAT
*
194662 GGTTTTAG
1 GG-TTTAT
194670 GGTTTAT
1 GGTTTAT
*
194677 GATTTA-
1 GGTTTAT
194683 GGATTTA-
1 GG-TTTAT
*
194690 GGATTTAA
1 GG-TTTAT
194698 GGTTTAT
1 GGTTTAT
*
194705 GGTTTAG
1 GGTTTAT
194712 GGTTTAT
1 GGTTTAT
194719 AGG-TTA-
1 -GGTTTAT
*
194725 GGATTCAT
1 GG-TTTAT
*
194733 GGTTTAG
1 GGTTTAT
194740 GGTTTAT
1 GGTTTAT
*
194747 AGTTTA-
1 GGTTTAT
* *
194753 GAGCTTAG
1 G-GTTTAT
194761 GGTTTAT
1 GGTTTAT
*
194768 GATTTAT
1 GGTTTAT
194775 GGTTTA
1 GGTTTA
194781 ATTTATGCAC
Statistics
Matches: 98, Mismatches: 17, Indels: 20
0.73 0.13 0.15
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 84 0.86
8 9 0.09
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.48
Consensus pattern (7 bp):
GGTTTAT
Found at i:194663 original size:14 final size:14
Alignment explanation
Indices: 194649--194780 Score: 108
Period size: 14 Copynumber: 9.4 Consensus size: 14
194639 TATGTGATAG
*
194649 GGTTTATGGTTTA-
1 GGTTTAGGGTTTAT
194662 GGTTTTAGGGTTTAT
1 GG-TTTAGGGTTTAT
* *
194677 GATTTAGGATTTA-
1 GGTTTAGGGTTTAT
*
194690 GGATTTAAGGTTTAT
1 GG-TTTAGGGTTTAT
194705 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAT
* *
194719 AGG-TTAGGATTCAT
1 -GGTTTAGGGTTTAT
194733 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAT
* * * *
194747 AGTTTAGAGCTTAG
1 GGTTTAGGGTTTAT
* *
194761 GGTTTATGATTTAT
1 GGTTTAGGGTTTAT
194775 GGTTTA
1 GGTTTA
194781 ATTTATGCAC
Statistics
Matches: 92, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
13 5 0.05
14 82 0.89
15 5 0.05
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.48
Consensus pattern (14 bp):
GGTTTAGGGTTTAT
Found at i:197366 original size:11 final size:11
Alignment explanation
Indices: 197350--197376 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
197340 GTTCGAGTTT
197350 GAGCTTGAACC
1 GAGCTTGAACC
197361 GAGCTTGAACC
1 GAGCTTGAACC
197372 GAGCT
1 GAGCT
197377 CAAATTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.19
Consensus pattern (11 bp):
GAGCTTGAACC
Found at i:197429 original size:23 final size:23
Alignment explanation
Indices: 197394--197481 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
197384 GAGTTTGAGT
* * ***
197394 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGTTTCAATCGAGCTCAGTC
197417 TCGAGTTTCAATCGAG-TCGAGTC
1 TCGAGTTTCAATCGAGCTC-AGTC
*
197440 TCGAGTTTCAATCGAGCTTGAGTC
1 TCGAGTTTCAATCGAGC-TCAGTC
197464 TCGAGTTTCAATCGAGCT
1 TCGAGTTTCAATCGAGCT
197482 TTTGATTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.04
23 32 0.57
24 21 0.38
25 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (23 bp):
TCGAGTTTCAATCGAGCTCAGTC
Found at i:197467 original size:24 final size:24
Alignment explanation
Indices: 197417--197482 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
197407 GAGCTCAAAA
*
197417 TCGAGTTTCAATCGAG-TCGAGTC
1 TCGAGTTTCAATCGAGCTTGAGTC
197440 TCGAGTTTCAATCGAGCTTGAGTC
1 TCGAGTTTCAATCGAGCTTGAGTC
197464 TCGAGTTTCAATCGAGCTT
1 TCGAGTTTCAATCGAGCTT
197483 TTGATTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 16 0.39
24 25 0.61
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (24 bp):
TCGAGTTTCAATCGAGCTTGAGTC
Found at i:197595 original size:30 final size:31
Alignment explanation
Indices: 197505--197580 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
197495 ATTTGAGCCT
197505 TTTCGAGTTCGAGTCAAGTTTCAATATTTTC
1 TTTCGAGTTCGAGTCAAGTTTCAATATTTTC
197536 TTTCGAGTTCGAGTCAAGTTTCAATATTTTC
1 TTTCGAGTTCGAGTCAAGTTTCAATATTTTC
197567 TTT-GAGTTCGAGTC
1 TTTCGAGTTCGAGTC
197581 GAGCTTGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 11 0.24
31 34 0.76
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCAAGTTTCAATATTTTC
Found at i:201665 original size:3 final size:3
Alignment explanation
Indices: 201657--201713 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
201647 CATCTGAGCG
201657 TAT TAT TAT TAT TAT TA- TAT TA- TAT TA- TAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
201700 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
201714 CAAGACCGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 41 0.82
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:204829 original size:21 final size:20
Alignment explanation
Indices: 204791--204829 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
204781 GTTGAGTTTT
204791 TATTTAAATTTAATTGTAAA
1 TATTTAAATTTAATTGTAAA
204811 TATTTATAATATT-ATTGTA
1 TATTTA-AAT-TTAATTGTA
204830 CTGTTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 9 0.53
22 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TATTTAAATTTAATTGTAAA
Done.