Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007779.1 Hibiscus syriacus cultivar Beakdansim tig00110062_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: 298930
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:237470 original size:64 final size:64
Alignment explanation
Indices: 237372--237495 Score: 155
Period size: 64 Copynumber: 1.9 Consensus size: 64
237362 GTGCATGGTC
* * * *
237372 TGTGTATCGGTACATAAAATGCATTCGGTGTTCAAA-ATATTC-AGGAGTGCATTGATGCATGCC
1 TGTGCATCGGTACACAAAATGCATTCGATGTTCAAATA-ATTCAAGG-GTGCATCGATGCATGCC
237435 T
64 T
*
237436 TGTGCATCGGTACACAAAATGCATTCGAAT-TTCAATTAATTCAAGGGTGCATCGATGCAT
1 TGTGCATCGGTACACAAAATGCATTCG-ATGTTCAAATAATTCAAGGGTGCATCGATGCAT
237496 TGTACACTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
64 47 0.90
65 5 0.10
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (64 bp):
TGTGCATCGGTACACAAAATGCATTCGATGTTCAAATAATTCAAGGGTGCATCGATGCATGCCT
Found at i:238868 original size:12 final size:12
Alignment explanation
Indices: 238851--238880 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
238841 CATTGTTTTG
238851 TCTTTAATATTT
1 TCTTTAATATTT
238863 TCTTTAATATTT
1 TCTTTAATATTT
238875 T-TTTAA
1 TCTTTAA
238881 ATCTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTTAATATTT
Found at i:239772 original size:14 final size:13
Alignment explanation
Indices: 239748--239815 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
239738 GCGAGAACAC
*
239748 AAAGCAAAAAGAA
1 AAAGAAAAAAGAA
239761 AAGAGAAAAAAGAA
1 AA-AGAAAAAAGAA
239775 AAAGAAATGATAA-AA
1 AAAGAAA--A-AAGAA
* *
239790 AAATAAAAGAGAA
1 AAAGAAAAAAGAA
*
239803 AAAGAAGAAAGAA
1 AAAGAAAAAAGAA
239816 GAAAAAAGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 1 0.02
13 20 0.45
14 12 0.27
15 9 0.20
16 2 0.05
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:242628 original size:136 final size:135
Alignment explanation
Indices: 242372--242653 Score: 408
Period size: 136 Copynumber: 2.1 Consensus size: 135
242362 TGTCACCTTG
* *
242372 GAGATTGTTTCTCTAGAAACAAAGTTTCATCTCGCTTGAGAAAGCTTCCTTTGAAGCCCAAATTT
1 GAGATAGTTTCTCTAGAAACAAAGTTTCATCTCGCTTGAGAAAGCTTCCCTTGAAGCCCAAATTT
* *
242437 CAGAGTTGTTTCACTTGAAAAAAAGTTGATCTCACTTGAGATTGTTTTCCTAAAAAACTTTTGTC
66 CAGAGTTGTTTCACTTGAAAAAAAGTTGATCTCACTTGAGATTGTTTTCCTAAAAAA-ATTCGTC
*
242502 TCTCTC
130 TCGCTC
* * *
242508 GAGATAGTTTCTCTCA-AAACAAAGTTTCGTCTCGCTTGAGACAGTTTCCCTTGAAGCCCAAATT
1 GAGATAGTTTCTCT-AGAAACAAAGTTTCATCTCGCTTGAGAAAGCTTCCCTTGAAGCCCAAATT
* *
242572 T-TGAATTTGTTTCACTTGAAAAAAA-TTGATCTCACTTGAGATTGTTTTCCTAAAAAAAATTCG
65 TCAG-AGTTGTTTCACTTGAAAAAAAGTTGATCTCACTTGAGATTGTTTTCCT-AAAAAAATTCG
*
242635 TCTCGCTT
128 TCTCGCTC
242643 GAGATAGTTTC
1 GAGATAGTTTC
242654 CCTTGAAATG
Statistics
Matches: 132, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
135 47 0.36
136 84 0.64
137 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (135 bp):
GAGATAGTTTCTCTAGAAACAAAGTTTCATCTCGCTTGAGAAAGCTTCCCTTGAAGCCCAAATTT
CAGAGTTGTTTCACTTGAAAAAAAGTTGATCTCACTTGAGATTGTTTTCCTAAAAAAATTCGTCT
CGCTC
Found at i:243552 original size:104 final size:103
Alignment explanation
Indices: 243378--243692 Score: 323
Period size: 104 Copynumber: 3.0 Consensus size: 103
243368 AATGAGAATG
* * * * * * *
243378 AACAACTTCATATGAAAGTGGCCATAACTCTCCAACTTGGATGAGTAA-TGTCATCTTTAAAACC
1 AACAACATCATCTGAAAGTGGACATAACTTTTCAACATGGATGA--AAGTGTCATCTTCAAAACC
* *
243442 ATATTATCTCCAAATTAACTCAACTTCCTCAACAAGAA-A
64 AAATTATCTCTAAATTAACTCAACTTCCTCAACAAGAAGA
*
243481 AACCAACATCATCTGAAAGTGGACATAACTTTTCAACATGGATGAACAGTGTCATCTTCAACACC
1 AA-CAACATCATCTGAAAGTGGACATAACTTTTCAACATGGATGAA-AGTGTCATCTTCAAAACC
* * * *
243546 AGATTATCTCTAGATTGACTCAACTTCCTCAACAAGAAGG
64 AAATTATCTCTAAATTAACTCAACTTCCTCAACAAGAAGA
* * * * * *
243586 AACAACGTCATCTGAAAG-CGACCAAAACTTTTCAACATGGATCAGAAGTGTCGTCTTCAATACC
1 AACAACATCATCTGAAAGTGGA-CATAACTTTTCAACATGGATGA-AAGTGTCATCTTCAAAACC
* * * * *
243650 AAATTATCTCTAAATTGAC-CGACTTCTTCAACGAGAAGG
64 AAATTATCTCTAAATTAACTCAACTTCCTCAACAAGAAGA
243689 AACA
1 AACA
243693 TTGTCATCTT
Statistics
Matches: 182, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
102 1 0.01
103 26 0.14
104 152 0.84
105 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AACAACATCATCTGAAAGTGGACATAACTTTTCAACATGGATGAAAGTGTCATCTTCAAAACCAA
ATTATCTCTAAATTAACTCAACTTCCTCAACAAGAAGA
Found at i:248530 original size:19 final size:19
Alignment explanation
Indices: 248470--248533 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
248460 GGTTCCACTA
* *
248470 GACCTGAACTGTTTGACCC
1 GACCCGAACTGTTTGATCC
**
248489 GACTTGAACTGTTTGGCAT--
1 GACCCGAACTGTTT-G-ATCC
248508 GACCCGAACTGTTTGATCC
1 GACCCGAACTGTTTGATCC
248527 GACCCGA
1 GACCCGA
248534 CCCGTTGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 2 0.05
18 1 0.03
19 32 0.86
20 1 0.03
21 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (19 bp):
GACCCGAACTGTTTGATCC
Found at i:248736 original size:16 final size:17
Alignment explanation
Indices: 248704--248736 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
248694 TGACTTTGAC
248704 CAAAAAGTCAAATTTTT
1 CAAAAAGTCAAATTTTT
*
248721 CAAAAAGTCATATTTT
1 CAAAAAGTCAAATTTT
248737 ATGCTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
CAAAAAGTCAAATTTTT
Found at i:252588 original size:71 final size:72
Alignment explanation
Indices: 252513--252694 Score: 267
Period size: 71 Copynumber: 2.5 Consensus size: 72
252503 AAATAATCGT
* * * *
252513 TACCTATTACGTTAAAATAGATACCGGTTTCTTTAACGGATAATAATAATGTAAACGA-AAAAAA
1 TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAGGATAATAATAATGTAAACGATAAAAAA
252577 TAGGCTC
66 TAGGCTC
* * * *
252584 TACCTATTACGTTAAACTAGCTAACGATTTGTTTAAAGGTTAATAATAATGTAAACGATTTAAAA
1 TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAGGATAATAATAATGTAAACGA-TAAAAA
252649 ATAGGCTC
65 ATAGGCTC
*
252657 TACCTATTACGTTAAACTACCTACCGATTTCTTTAAAG
1 TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAG
252695 ATATATTTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
71 51 0.52
73 47 0.48
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (72 bp):
TACCTATTACGTTAAACTAGCTACCGATTTCTTTAAAGGATAATAATAATGTAAACGATAAAAAA
TAGGCTC
Found at i:252790 original size:12 final size:12
Alignment explanation
Indices: 252775--252799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
252765 TTAATACTTA
252775 AATTTCAATTTG
1 AATTTCAATTTG
252787 AATTTCAATTTG
1 AATTTCAATTTG
252799 A
1 A
252800 GCTCCACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (12 bp):
AATTTCAATTTG
Found at i:254020 original size:75 final size:72
Alignment explanation
Indices: 253875--254035 Score: 216
Period size: 75 Copynumber: 2.2 Consensus size: 72
253865 CTTAAGCGGT
* * *
253875 TAAAATAAAATAGGCGCTACCTTTACGTTAATCATCTACCGGTTTGTTTAAAGGTTACTAATAAT
1 TAAAATAAAATAGGCGCTACCTTTACGTTAATCATATA-CGGTTTGTTTAAAGATGACTAATAAT
253940 ATAAACGG
65 ATAAACGG
*
253948 TAAAATAAAATAGGTGCTACCTATTACGTTAAAATACATATA-GGTTTGTTTAAAGATGACTAAT
1 TAAAATAAAATAGGCGCTACCT-TTACGTT--AAT-CATATACGGTTTGTTTAAAGATGACTAAT
* *
254012 TATGTAAACGG
62 AATATAAACGG
254023 TAAAATAAAATAG
1 TAAAATAAAATAG
254036 ACGTAAATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
73 21 0.27
74 7 0.09
75 42 0.54
76 3 0.04
77 5 0.06
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (72 bp):
TAAAATAAAATAGGCGCTACCTTTACGTTAATCATATACGGTTTGTTTAAAGATGACTAATAATA
TAAACGG
Found at i:254425 original size:199 final size:198
Alignment explanation
Indices: 254077--254682 Score: 793
Period size: 199 Copynumber: 3.0 Consensus size: 198
254067 GCTCGTACCA
* * ** *
254077 ATACTTTTATTTCAGTATGCTTCTCAAACAATTTGCACCCAAAATATATCGATACACATATA-AT
1 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATA-
*
254141 AAGTATCGGTACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAA
65 AAGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAA
* * * *
254206 CGGTAAAAGTTTATCGGTATATTGATAATAGGTGTAAATACCAAATATCGATATTTTTATATATG
130 CGGTAAAAATCTATCGGTATATTGATAATAGGCGTAAATACCAAGTATCGATATTTTTATATA-G
254271 TATCG
194 TATCG
254276 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
1 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
* * * *
254341 ATTATTGTTACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTTAATTAACAATGTAAAC
66 AGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* * * * * *
254406 GGTAAAAATCTACCGGTATATTGATAATAGACGTAAATATCAAGTATCAACACTTTTATATAGAT
131 GGTAAAAATCTATCGGTATATTGATAATAGGCGTAAATACCAAGTATCGATATTTTTATATAG-T
*
254471 ATGG
195 ATCG
* *
254475 ATACTTTTATTCCAATATGTTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATACATAA
1 ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
* * * * * *
254540 AGTATCAATACTAATAATTTCGAAACCTATTACTTTAAAGTAATATGTAAATTAACAATGTACAC
66 AGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* ** * * * * *
254605 GATAAACGTTTCTATCGGTATCATT-AAAATAGGGGTAAATGTCCAAGTATCGATATTGTCATAT
131 GGTAAA--AATCTATCGGTAT-ATTGATAATAGGCGTAAAT-ACCAAGTATCGATATTTTTATAT
254669 AAGTATCG
192 -AGTATCG
254677 ATACTT
1 ATACTT
254683 ATAATTTCAA
Statistics
Matches: 353, Mismatches: 47, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
198 1 0.00
199 298 0.84
200 1 0.00
201 22 0.06
202 29 0.08
203 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (198 bp):
ATACTTTTATTCCAATATGCTTCTCAAACAATTTGCATGCAAAATGTATCGATACACATATATAA
AGTATCGATACTTAGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
GGTAAAAATCTATCGGTATATTGATAATAGGCGTAAATACCAAGTATCGATATTTTTATATAGTA
TCG
Found at i:255160 original size:226 final size:226
Alignment explanation
Indices: 254743--255342 Score: 660
Period size: 226 Copynumber: 2.7 Consensus size: 226
254733 ACGGTAATAT
* * * ** *
254743 AACAATTTAAGTAATTAACATATTTTGCTATCGTCGGATTTCTAAAAC-CCTATCAGTTTTGAAC
1 AACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAGGCACC-ATCA-TTTTAAAC
** **** *
254807 AGATACTACCTATTACATTAAATAAACACTA-TTTGTTATGTTATTATGGTTGATAATGTTTTCA
64 AGACGCTACCTATTACATTAAATAAGTGTTACTTTGTTATGTTATTATGGTTGATAATATTTTCA
** * ** ** *
254871 GTAATT-ATGTCATTTTGTTATCGTTGGATTTCTAAGGCTTTATCAGCTTAAACTTTGGTAACAT
129 GTAATTAACCT-ATTTTGTTATCATCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACAT
*
254935 TTTAGGCGTTACCAAATATGTTGATAATATTGAA
193 TTTAGACGTTACCAAATATGTTGATAATATTGAA
* * *
254969 AACAAATTAAGTAATTAACATATTTTGTTATCGTCTGATTTTTAAGGCATCATCGATTTTAAACA
1 AACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAGGCACCATC-ATTTTAAACA
* * * * *
255034 GGCGCTACCTATTACATTAAATAAGTGTTACTTTATTATGTTAATATGGTTGATACTATTTTCAA
65 GACGCTACCTATTACATTAAATAAGTGTTACTTTGTTATGTTATTATGGTTGATAATATTTTCAG
* *
255099 TAATTAACCTATTTTGTTATTATCAGATTTTTAAGGCTCAATCAGCTTAAA-TTTAGTAACATTT
130 TAATTAACCTATTTTGTTATCATCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACATTT
* *
255163 TAGACGTTACCTAATATGTTGATAATATTGAT
195 TAGACGTTACCAAATATGTTGATAATATTGAA
* * * * *
255195 AACTAATTAAGTAATTAACTTATTTTGTTAAT-ATCAGATTTCTAAGG-ACCCAACAACTTTAAA
1 AACAAATTAAGTAATTAACATATTTTGTT-ATCGTCAGATTTCTAAGGCA-CCATC-ATTTTAAA
* * * * *
255258 AAGACGCAACCTATTACATTAAATAAGTGTTAC-ATGTTATATTATTATGATTGATAATA-TTTC
63 CAGACGCTACCTATTACATTAAATAAGTGTTACTTTGTTATGTTATTATGGTTGATAATATTTTC
255321 TAGTAATTAACC-ATTTATGTTA
128 -AGTAATTAACCTATTT-TGTTA
255343 AAGTCAAAAA
Statistics
Matches: 314, Mismatches: 52, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
224 8 0.03
225 36 0.11
226 196 0.62
227 72 0.23
228 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (226 bp):
AACAAATTAAGTAATTAACATATTTTGTTATCGTCAGATTTCTAAGGCACCATCATTTTAAACAG
ACGCTACCTATTACATTAAATAAGTGTTACTTTGTTATGTTATTATGGTTGATAATATTTTCAGT
AATTAACCTATTTTGTTATCATCAGATTTCTAAGGCTCAATCAGCTTAAACTTTAGTAACATTTT
AGACGTTACCAAATATGTTGATAATATTGAA
Found at i:256061 original size:32 final size:33
Alignment explanation
Indices: 256025--256102 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
256015 TTTAAATAGT
* *
256025 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
256057 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
256090 TATTATTTATTTA
1 TATTATTT-TTTA
256103 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:259960 original size:34 final size:33
Alignment explanation
Indices: 259884--259990 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
259874 GTGGTAAGAA
* *
259884 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
259918 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
259953 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
259987 ATTT
1 ATTT
259991 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:259972 original size:36 final size:34
Alignment explanation
Indices: 259917--259995 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
259907 TTTAAATAGT
*
259917 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
259949 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
259983 TATTATTTATTTA
1 TATTATTTTTTTA
259996 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:260157 original size:17 final size:17
Alignment explanation
Indices: 260135--260188 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
260125 AATGTTAATA
260135 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
260152 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
260169 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
260186 TTT
1 TTT
260189 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:261119 original size:17 final size:17
Alignment explanation
Indices: 261090--261122 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
261080 AGGTATGTTT
261090 TTAAATTTGTTTAATTA
1 TTAAATTTGTTTAATTA
261107 TTAATATTT-TTTAATT
1 TTAA-ATTTGTTTAATT
261123 TAAAATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTAAATTTGTTTAATTA
Found at i:261749 original size:21 final size:21
Alignment explanation
Indices: 261719--261766 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
261709 GCAGGGGTAC
* *
261719 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
261740 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
261761 ATGCCA
1 ATGCCA
261767 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:261796 original size:21 final size:21
Alignment explanation
Indices: 261770--261863 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
261760 TATGCCATCT
* *
261770 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
261791 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
261812 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
261833 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
261854 CCGCAGGGTT
1 CCGCAGGGTT
261864 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:262418 original size:40 final size:39
Alignment explanation
Indices: 262374--262457 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
262364 AAATGTTTTT
* *
262374 AAAATACAAATTATATTATTCGAAATTTAAATTTAAAATA
1 AAAATAAAAATAATATTATTC-AAATTTAAATTTAAAATA
262414 AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
1 AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
*
262453 TAAAT
1 AAAAT
262458 TATAGTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 22 0.54
40 19 0.46
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
Found at i:262443 original size:33 final size:34
Alignment explanation
Indices: 262402--262476 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
262392 TTCGAAATTT
*
262402 AAATTTAAAATAAAAATAAAAATAATATTATTC-
1 AAATTTAAAATAAAAATAAAAATAATAGTATTCA
* * * *
262435 AAATTTAAATTTAAAATATAAATTATAGTATTCA
1 AAATTTAAAATAAAAATAAAAATAATAGTATTCA
262469 AAATTTAA
1 AAATTTAA
262477 CATTAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 28 0.78
34 8 0.22
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (34 bp):
AAATTTAAAATAAAAATAAAAATAATAGTATTCA
Found at i:263102 original size:128 final size:128
Alignment explanation
Indices: 262874--263883 Score: 1832
Period size: 128 Copynumber: 7.9 Consensus size: 128
262864 TTACCTGATT
262874 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
262939 TGATGAAATAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
263002 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
** *** *
263067 TGACGAAATAATGGAAGTTGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
263130 TACTGATATATCTAGTGTCCCCGATGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
263195 TGACGAAATAATGGAA-GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
263257 TACTG--ATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
263320 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
263383 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
263448 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
263511 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
263576 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
263639 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
263704 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
263767 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
263832 TGACGAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
263884 ACTCCGATTA
Statistics
Matches: 848, Mismatches: 27, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
125 73 0.09
126 46 0.05
127 45 0.05
128 683 0.81
129 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:263967 original size:8 final size:8
Alignment explanation
Indices: 263954--263994 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
263944 TCACAATCTT
263954 TCAAATTC
1 TCAAATTC
263962 TCAAATTC
1 TCAAATTC
* *
263970 CCAAACTC
1 TCAAATTC
263978 T-AAATTC
1 TCAAATTC
263985 TCAAATTC
1 TCAAATTC
263993 TC
1 TC
263995 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:268153 original size:56 final size:56
Alignment explanation
Indices: 268067--268175 Score: 209
Period size: 56 Copynumber: 1.9 Consensus size: 56
268057 TTGGAAAGAA
*
268067 CAAATATTTCTAAATTATATGGATGTGTATATGAACAACTAAAATTAATATAATAC
1 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAATAC
268123 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAA
1 CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAA
268176 CACAGAGACA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (56 bp):
CAAATATTTCTAAATTATATCGATGTGTATATGAACAACTAAAATTAATATAATAC
Found at i:271071 original size:32 final size:32
Alignment explanation
Indices: 271004--271082 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
270994 TCATTTTGTT
* *
271004 AAAATAAAATCGAAGTTGAAACTAAATATTAAA
1 AAAATAAAA-CGAAATTGAAAATAAATATTAAA
*
271037 AAAATAAAACGAAATT-AAAATAGATAATTAAA
1 AAAATAAAACGAAATTGAAAATAAAT-ATTAAA
*
271069 AAAATCAAA-GAAAT
1 AAAATAAAACGAAAT
271083 CAGATAAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.29
32 20 0.49
33 9 0.22
ACGTcount: A:0.66, C:0.05, G:0.08, T:0.22
Consensus pattern (32 bp):
AAAATAAAACGAAATTGAAAATAAATATTAAA
Found at i:272668 original size:2 final size:2
Alignment explanation
Indices: 272661--272699 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
272651 TAAGACAGGA
*
272661 AG AG AG AG ACG -G AG TG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
272700 CCTTTCTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.49, T:0.03
Consensus pattern (2 bp):
AG
Found at i:277811 original size:16 final size:18
Alignment explanation
Indices: 277779--277811 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
277769 TATTAATGTA
277779 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
277797 TGAAT-ATTT-TATTTT
1 TGAATCATTTATATTTT
277812 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:278049 original size:23 final size:25
Alignment explanation
Indices: 278001--278063 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
277991 ACAATTTATC
*
278001 AAATATAATATTTTTTATTGTAAAA
1 AAATATAATATTTTCTATTGTAAAA
278026 AAATAT-ATATTTTCTATTGT-AAA
1 AAATATAATATTTTCTATTGTAAAA
278049 AAATATAATATTTTC
1 AAATATAATATTTTC
278064 CCATCATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 9 0.25
24 21 0.58
25 6 0.17
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
AAATATAATATTTTCTATTGTAAAA
Found at i:278505 original size:130 final size:130
Alignment explanation
Indices: 278301--278548 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
278291 AATTTTATTC
* *
278301 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
278366 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
278431 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
278496 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
278549 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:278993 original size:35 final size:35
Alignment explanation
Indices: 278943--279018 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
278933 AATTGAATTT
* *
278943 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
278978 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
279013 AATTGA
1 AATTGA
279019 GGTATGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:290383 original size:21 final size:21
Alignment explanation
Indices: 290359--290493 Score: 85
Period size: 21 Copynumber: 6.3 Consensus size: 21
290349 TATCCCGAAT
*
290359 GACCACATATATGTCCCATCG
1 GACCACATATATGTCCCATAG
* * *
290380 GACCCCATAGAATTGTCCCGTAG
1 GACCACATA-TA-TGTCCCATAG
* * *
290403 GACCACATATATGTTCCAAAT
1 GACCACATATATGTCCCATAG
* * * *
290424 GACCAAATATATGTCCAAAAAA
1 GACCACATATATGTCC-CATAG
* *
290446 GACCGA-ATATATGTTCCAAAG
1 GACC-ACATATATGTCCCATAG
*
290467 GATCACATATATGTCCCGA-AG
1 GACCACATATATGTCCC-ATAG
290488 GACCAC
1 GACCAC
290494 GTAGAACCCT
Statistics
Matches: 88, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 51 0.58
22 19 0.22
23 17 0.19
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (21 bp):
GACCACATATATGTCCCATAG
Found at i:291782 original size:50 final size:52
Alignment explanation
Indices: 291713--291814 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
291703 GTTTCTATAA
*
291713 ACTTTTCTAATGCTTCATCAATC-AAA-CACTCATGAATTGCAAGAATAAAC
1 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
291763 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
1 ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
291815 CAGCTGTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 22 0.45
51 3 0.06
52 24 0.49
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (52 bp):
ACTTTCCTAATGCTTCATCAATCAAAAGCACTCATGAATTGCAAGAATAAAC
Found at i:296970 original size:27 final size:26
Alignment explanation
Indices: 296940--296994 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
296930 TACAGTCGCT
**
296940 TACTCCAAGCCTAGGGTATTCCCTAAA
1 TACTCCAAG-CTAGGAAATTCCCTAAA
*
296967 TACTCCAAGCTTGGAAATTCCCTAAA
1 TACTCCAAGCTAGGAAATTCCCTAAA
296993 TA
1 TA
296995 ATCTTATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (26 bp):
TACTCCAAGCTAGGAAATTCCCTAAA
Done.