Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007170.1 Hibiscus syriacus cultivar Beakdansim tig00018807_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: 75130
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7226 original size:20 final size:21
Alignment explanation
Indices: 7201--7246 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
7191 TTAAATTTTG
7201 TTATTTACATA-AATTTT-ATT
1 TTATTT-CATATAATTTTAATT
*
7221 TTATTTTATATAATTTTAATT
1 TTATTTCATATAATTTTAATT
7242 TTATT
1 TTATT
7247 ATCCAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 12 0.52
21 8 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTTCATATAATTTTAATT
Found at i:7233 original size:21 final size:21
Alignment explanation
Indices: 7204--7246 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
7194 AATTTTGTTA
7204 TTTACATAAATTTT-ATTTTAT
1 TTTACAT-AATTTTAATTTTAT
*
7225 TTTATATAATTTTAATTTTAT
1 TTTACATAATTTTAATTTTAT
7246 T
1 T
7247 ATCCAATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTACATAATTTTAATTTTAT
Found at i:9507 original size:13 final size:13
Alignment explanation
Indices: 9489--9518 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
9479 AAATTCCTAA
9489 TAAATAACGATTT
1 TAAATAACGATTT
9502 TAAATAACGATTT
1 TAAATAACGATTT
9515 TAAA
1 TAAA
9519 AAATCATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
TAAATAACGATTT
Found at i:15342 original size:19 final size:19
Alignment explanation
Indices: 15315--15396 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
15305 ATAGTACCTA
*
15315 TATAGTATATACTTATAAG
1 TATAATATATACTTATAAG
15334 TATAATATATACTTAT-A-
1 TATAATATATACTTATAAG
15351 T-T-ATA-A-ACTTATAAG
1 TATAATATATACTTATAAG
*
15366 TATAATATATACTTATAAT
1 TATAATATATACTTATAAG
15385 TATATATATATA
1 TATA-ATATATA
15397 TATATATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
13 6 0.11
14 2 0.04
15 4 0.07
16 2 0.04
17 4 0.07
18 2 0.04
19 27 0.50
20 7 0.13
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (19 bp):
TATAATATATACTTATAAG
Found at i:15361 original size:32 final size:32
Alignment explanation
Indices: 15315--15388 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
15305 ATAGTACCTA
* *
15315 TATAGTATATACTTATAAGTATAATATATACT
1 TATATTATAAACTTATAAGTATAATATATACT
15347 TATATTATAAACTTATAAGTATAATATATACT
1 TATATTATAAACTTATAAGTATAATATATACT
15379 TATAATTATA
1 TAT-ATTATA
15389 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 33 0.85
33 6 0.15
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATTATAAACTTATAAGTATAATATATACT
Found at i:15405 original size:19 final size:19
Alignment explanation
Indices: 15313--15405 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 19
15303 TTATAGTACC
*
15313 TATATAGTATATACTTATAA
1 TATATACTATATA-TTATAA
*
15333 GTATA-A-TATATACTTATAT
1 -TATATACTATATA-TTATAA
* *
15352 TATAAACT-TATAAGTATAA
1 TATATACTATAT-ATTATAA
15371 TATATACT-TATAATTATATA
1 TATATACTATAT-ATTATA-A
15391 TATATA-TATATATTA
1 TATATACTATATATTA
15406 AAATTGTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
18 4 0.06
19 41 0.66
20 13 0.21
21 4 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (19 bp):
TATATACTATATATTATAA
Found at i:20246 original size:33 final size:33
Alignment explanation
Indices: 20199--20267 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
20189 CAGTAGTTGC
*
20199 ATATTAACTGAGATATAGTATTTATTTGTAATT
1 ATATTAACTAAGATATAGTATTTATTTGTAATT
20232 ATATTAACTAAGATATAGTATTTATTTGTAATT
1 ATATTAACTAAGATATAGTATTTATTTGTAATT
20265 ATA
1 ATA
20268 GATAAGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (33 bp):
ATATTAACTAAGATATAGTATTTATTTGTAATT
Found at i:21337 original size:23 final size:23
Alignment explanation
Indices: 21311--21358 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
21301 ATAAAGTACA
*
21311 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
21334 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
21357 AT
1 AT
21359 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:21764 original size:21 final size:20
Alignment explanation
Indices: 21734--21787 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
21724 GATAGACACT
*
21734 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
21755 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
21778 TTACATTATA
1 TTACATTATA
21788 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:21775 original size:23 final size:23
Alignment explanation
Indices: 21749--21811 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
21739 ATATAACCAT
21749 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
21772 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
21795 TACCTATTACATCATAT
1 TACCTATTACATTATAT
21812 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:22152 original size:20 final size:20
Alignment explanation
Indices: 22127--22165 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22117 TCCACAGTGA
* *
22127 AAAAAGTATGGACACTTTAT
1 AAAAAGGATAGACACTTTAT
22147 AAAAAGGATAGACACTTTA
1 AAAAAGGATAGACACTTTA
22166 CAATATAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAAGGATAGACACTTTAT
Found at i:22153 original size:429 final size:429
Alignment explanation
Indices: 21470--22338 Score: 1722
Period size: 429 Copynumber: 2.0 Consensus size: 429
21460 GGATCGATAC
21470 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
21535 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATATATATACCG
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATATATATACCG
21600 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
131 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
21665 AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
196 AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
21730 CACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGC
261 CACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGC
21795 TACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCG
326 TACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCG
21860 ATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
391 ATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
21899 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
21964 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAAT-ATATATACC
22029 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
130 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
22094 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACAC-TTTATAAAAAGGATAG
195 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
22158 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
260 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
22223 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
325 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
22288 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
390 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
22328 TTTAACAGTGT
1 TTTAACAGTGT
22339 ACTGCGAATT
Statistics
Matches: 439, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
429 317 0.72
430 122 0.28
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (429 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATATATATACCG
TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
CACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGC
TACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCG
ATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
Found at i:22193 original size:21 final size:20
Alignment explanation
Indices: 22163--22216 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
22153 GATAGACACT
*
22163 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
22184 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
22207 TTACATTATA
1 TTACATTATA
22217 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:22204 original size:23 final size:23
Alignment explanation
Indices: 22178--22240 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
22168 ATATAACCAT
22178 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
22201 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
22224 TACCTATTACATCATAT
1 TACCTATTACATTATAT
22241 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:25149 original size:184 final size:184
Alignment explanation
Indices: 24797--25336 Score: 1030
Period size: 184 Copynumber: 2.9 Consensus size: 184
24787 TTTTAAATGG
*
24797 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
24862 TAAAACCGGTATA-TTATACCGGTTATATTAC-AAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
24925 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
24979 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
25044 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
25109 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
25163 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
25228 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
25293 GATGTGTAAAATGTCGACACTTTTTGAAATCGTATCGACACATT
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATT
25337 CAATGCTGCA
Statistics
Matches: 352, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
182 76 0.22
183 18 0.05
184 258 0.73
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:26365 original size:24 final size:24
Alignment explanation
Indices: 26328--26380 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
26318 CCGTTCTATC
26328 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
26352 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
26376 TATTT
1 TATTT
26381 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:26571 original size:20 final size:19
Alignment explanation
Indices: 26525--26571 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
26515 TCCGGTATCA
*
26525 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
26544 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
26565 TTTTACC
1 TTTTACC
26572 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:26735 original size:20 final size:20
Alignment explanation
Indices: 26687--26736 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
26677 TCGACACTTT
26687 TAATTTTACCGGTTTTATCA
1 TAATTTTACCGGTTTTATCA
*
26707 T-TTTGTTACCGGTTTTATCA
1 TAATT-TTACCGGTTTTATCA
26727 TAATTTTACC
1 TAATTTTACC
26737 TGGTATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (20 bp):
TAATTTTACCGGTTTTATCA
Found at i:27218 original size:228 final size:227
Alignment explanation
Indices: 26802--27249 Score: 781
Period size: 228 Copynumber: 2.0 Consensus size: 227
26792 TTAAAACTGC
*
26802 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
26867 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
26932 TTAGAATTTAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TTAGAATTTAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
26997 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
*
27029 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
27094 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
27159 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATA
130 TTTAGAATTT-AATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATA
27223 AGTATGGACACTTTTATAAAAAGGATA
194 AGTATGGACACTTTTATAAAAAGGATA
27250 GATAATTTAC
Statistics
Matches: 209, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
227 4 0.02
228 166 0.79
229 39 0.19
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:37314 original size:16 final size:17
Alignment explanation
Indices: 37293--37344 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
37283 TCATATTCAT
37293 AAATTAAATAATAAC-A
1 AAATTAAATAATAACTA
* *
37309 AAATTAATTAATGACTA
1 AAATTAAATAATAACTA
*
37326 AAATAAAATAA-AA-TA
1 AAATTAAATAATAACTA
37341 AAAT
1 AAAT
37345 AAAAATTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 6 0.20
16 14 0.47
17 10 0.33
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATTAAATAATAACTA
Found at i:37334 original size:5 final size:5
Alignment explanation
Indices: 37324--37348 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
37314 AATTAATGAC
37324 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
37349 ATTAACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:43333 original size:27 final size:27
Alignment explanation
Indices: 43296--43352 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
43286 AAAATGAAAC
*
43296 AAAAATTAAATTTTAGGTATAGTTTTA
1 AAAAATTAAATTCTAGGTATAGTTTTA
43323 AAAAATTAAATTCTAGGTATAGTTTTA
1 AAAAATTAAATTCTAGGTATAGTTTTA
43350 AAA
1 AAA
43353 CAGACCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (27 bp):
AAAAATTAAATTCTAGGTATAGTTTTA
Found at i:44095 original size:15 final size:15
Alignment explanation
Indices: 44071--44106 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
44061 ATTGATTTTT
44071 TTTAAAATTTTTTAA
1 TTTAAAATTTTTTAA
*
44086 TTTAATATTTTTTAA
1 TTTAAAATTTTTTAA
44101 -TTAAAA
1 TTTAAAA
44107 AAACAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAAATTTTTTAA
Found at i:44644 original size:27 final size:28
Alignment explanation
Indices: 44614--44674 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
44604 ACTGTTAATC
*
44614 AACCGAAA-TAATTCAGTTCGATCGATT
1 AACCGAAACTAATTCAATTCGATCGATT
44641 AACC-AAACTAATTCAATTCGATCGATT
1 AACCGAAACTAATTCAATTCGATCGATT
*
44668 AATCGAA
1 AACCGAA
44675 TTAGTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 3 0.10
27 25 0.83
28 2 0.07
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (28 bp):
AACCGAAACTAATTCAATTCGATCGATT
Found at i:59998 original size:18 final size:17
Alignment explanation
Indices: 59975--60010 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
59965 GACCTATCGC
59975 TCTTTTCTTCTTTACCTT
1 TCTTTTCTT-TTTACCTT
*
59993 TCTTTTCTTTTTCCCTT
1 TCTTTTCTTTTTACCTT
60010 T
1 T
60011 GCTCCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTTTCTTTTTACCTT
Done.