Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015900.1 Corchorus olitorius cultivar O-4 contig15933, 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: 10811
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:246 original size:22 final size:22
Alignment explanation
Indices: 218--279 Score: 108
Period size: 22 Copynumber: 2.8 Consensus size: 22
208 TGCAGAACAC
218 GTCCTGTCCAGATCTTGGCCAA
1 GTCCTGTCCAGATCTTGGCCAA
240 GTCCTGTCCAGATCTTGGCCAA
1 GTCCTGTCCAGATCTTGGCCAA
262 GTCCTGTCCAAGA-CTTGG
1 GTCCTGTCC-AGATCTTGG
280 GCTGTTGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 36 0.92
23 3 0.08
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (22 bp):
GTCCTGTCCAGATCTTGGCCAA
Found at i:403 original size:69 final size:70
Alignment explanation
Indices: 258--418 Score: 252
Period size: 69 Copynumber: 2.3 Consensus size: 70
248 CAGATCTTGG
* * *
258 CCAAGTCCTGTCCAAGACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
323 GTTAC
66 GTTAC
* * *
328 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGC-AAATTACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
392 GTTAC
66 GTTAC
*
397 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
419 TGCGGGAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
69 51 0.61
70 32 0.39
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (70 bp):
CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
GTTAC
Found at i:1409 original size:43 final size:43
Alignment explanation
Indices: 1344--2599 Score: 1189
Period size: 43 Copynumber: 28.6 Consensus size: 43
1334 TATTATGATC
* * **
1344 AGGGGCA-TTTTGGAAAGAGAAAACAGGGACCTTCCAACTGGGA
1 AGGGGCATTTTTGGAAA-TGAAAACAGGGACCTTCCGACCAGGA
* * *
1387 AGGGGTATTTTTGGAAATGAAAACAAGGACCTTCCGACTAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* * * * ** *
1430 AGTGGCA-TTTTCGAAAAGAAAATAAAGACC-TCGCAACCAGG-
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTC-CGACCAGGA
* *
1471 AGGGGCA-TTTTGGAAAGAGAAAACAGGGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAA-TGAAAACAGGGACCTTCCGACCAGGA
* * * * ** *
1514 AGGGACATTTTT-GAAAAGACAATAAAGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* *
1556 AGGGGCA-TTTTGGAAATGAAAACAAGGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* * **
1598 AGGGGTATTTTTGGAAATGAAAACAAGGACCTTCCGACTGGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
**
1641 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCTAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
1684 AGGGGCATTTTTGGAAA-GACAATA-AGCTGTGACCTTCCGACCAGGA
1 AGGGGCATTTTTGGAAATGA-AA-ACAG--G-GACCTTCCGACCAGGA
* * *
1730 AAGGGCA-TTTTGGAAATGAAAACAAGGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* **
1772 AGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACTGGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
*
1815 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
1858 AGGGGCATTTTTGGAAA-GACAATA-AGCTGTGACCTTCCGACC-GGA
1 AGGGGCATTTTTGGAAATGA-AA-ACAG--G-GACCTTCCGACCAGGA
*
1903 AGGGGCATTTTTGGAAATGACAGAA-AGTTGTGACCTTCCGACCGGGA
1 AGGGGCATTTTTGGAAATGA-A-AACAG--G-GACCTTCCGACCAGGA
* *
1950 AGGGGCATTTTTGGAATAGGAGAA-AGTTGTGACCTTCCGACC-GGA
1 AGGGGCATTTTTGGAA-ATGAAAACAG--G-GACCTTCCGACCAGGA
* *
1995 A-GGGCATTTTTGGAATTAAGAGACAATAAGCTGTAGACCTTCCGACCAGGA
1 AGGGGCATTTTTGGAA--ATGA-A-AA-CAG--G--GACCTTCCGACCAGGA
*
2046 AGGGGCATTTTTGGAAATGACAGAA-AGCTGTGACCTTCCGACCGGGA
1 AGGGGCATTTTTGGAAATGA-A-AACAG--G-GACCTTCCGACCAGGA
* *
2093 AGGGGCATTTTTGGAATAAGAGAA-AGTTGTGACCTTCCGACCAGGA
1 AGGGGCATTTTTGGAA-ATGAAAACAG--G-GACCTTCCGACCAGGA
* * *
2139 AGGGGCATTTTTGGAAA-GACAATGAGCTGTGACCTTCCGACCGGGA
1 AGGGGCATTTTTGGAAATGA-AA--A-CAGGGACCTTCCGACCAGGA
* *
2185 AGGGGCA-TTTTGGAAATGAAAACAAGGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* **
2227 AGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACTGGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
*
2270 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
*
2313 AGGGGCATTTTTGGAAA-GACAATA-AGCTGTGACCTTCCGACCGGGA
1 AGGGGCATTTTTGGAAATGA-AA-ACAG--G-GACCTTCCGACCAGGA
* * *
2359 AGGGGCATCTTTGGAAATGAAAACAAGGACCTTCCAACCAGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* * **
2402 AAGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACTGGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* **
2445 AGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACTGGGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
* *
2488 AGGGGCATTTTTGGAAATGAAAACAGGGAACTTCCAACC-GAGA
1 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAG-GA
* * **
2531 AGGGGCATGTTTTGGAAA-GAAAGAAAAAAGGACCTTCCGACTGGGA
1 AGGGGCAT-TTTTGGAAATG--A-AAACAGGGACCTTCCGACCAGGA
2577 AGGGGCATTTTTGG-AAT-AAAACA
1 AGGGGCATTTTTGGAAATGAAAACA
2600 ATGAAAACAG
Statistics
Matches: 1052, Mismatches: 106, Indels: 112
0.83 0.08 0.09
Matches are distributed among these distances:
41 24 0.02
42 155 0.15
43 461 0.44
44 45 0.04
45 64 0.06
46 194 0.18
47 57 0.05
48 11 0.01
49 5 0.00
50 18 0.02
51 4 0.00
52 14 0.01
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (43 bp):
AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCGACCAGGA
Found at i:1773 original size:174 final size:173
Alignment explanation
Indices: 1344--2592 Score: 1322
Period size: 174 Copynumber: 7.1 Consensus size: 173
1334 TATTATGATC
* * * * *
1344 AGGGGCA-TTTTGGAAAGAGAA-AACAGGGACCTTCCAACTGGGAAGGGGTATTTTTGGAAATGA
1 AGGGGCATTTTTGGAAAGACAATAAC-GTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATGA
* * * * * * * *
1407 AAACAAGGACCTTCCGACTAGGAAGTGGCA-TTTTCGAAAAGAAAATAAAGACC-TCGCAACCAG
65 AAACAAGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAAGGACCTTC-CGACCGG
*
1470 G-AGGGGCA-TTTTGGAAAGAGAAAACAGGGACCTTCCAACCAGGA
129 GAAGGGGCATTTTTGGAAA-TGAAAACAGGGACCTTCCAACCAGGA
* * * * *
1514 AGGGACATTTTTGAAAAGACAATAA--AGACCTTCCAACCAGGAAGGGGCA-TTTTGGAAATGAA
1 AGGGGCATTTTTGGAAAGACAATAACGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATGAA
* * *
1576 AACAAGGACCTTCCAACCAGGAAGGGGTATTTTTGGAAATGAAAACAAGGACCTTCCGACTGGGA
66 AACAAGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACCGGGA
*
1641 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCTAACCAGGA
131 AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
* *
1684 AGGGGCATTTTTGGAAAGACAATAAGCTGTGACCTTCCGACCAGGAAAGGGCA-TTTTGGAAATG
1 AGGGGCATTTTTGGAAAGACAATAA-C-GTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATG
* *
1748 AAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACTGG
64 AAAACAAGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACCGG
1813 GAAGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
129 GAAGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
1858 AGGGGCATTTTTGGAAAGACAATAAGCTGTGACCTTCCGACC-GGAAGGGGCATTTTTGGAAATG
1 AGGGGCATTTTTGGAAAGACAATAA-C-GTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATG
* * * ***
1922 ACAGAA-AGTTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAGGAGAAAGTTGTGACCTT
64 A-A-AACA--AG-GACCTTCCGACCAGGAAGGGGCATTTTTGGAA-ATGA-AAACAAG-GACCTT
* * *
1986 CCGACC-GGAA-GGGCATTTTTGGAATTAAGAGACAATAAGCTGTAGACCTTCCGACCAGGA
121 CCGACCGGGAAGGGGCATTTTTGGAA--ATGA-A-AA-CAG--G--GACCTTCCAACCAGGA
2046 AGGGGCATTTTTGGAAATGACAGA-AAGCTGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAT
1 AGGGGCATTTTTGGAAA-GACA-ATAA-C-GTGACCTTCCGACCGGGAAGGGGCATTTTTGGAA-
* *** *
2110 AAGAGAAAGTTGTGACCTTCCGACCAGGAAGGGGCATTTTTGGAAA-GACAATGAGC-TGTGACC
61 ATGA-AAACAAG-GACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGA-AA--A-CAAG-GACC
*
2173 TTCCGACCGGGAAGGGGCA-TTTTGGAAATGAAAACAAGGACCTTCCAACCAGGA
119 TTCCGACCGGGAAGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
* * *
2227 AGGGGCATTTTTGGAAATGAAAACAA-G-GACCTTCCGACTGGGAAGGGGCATTTTTGGAAATGA
1 AGGGGCATTTTTGGAAA-GACAATAACGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATGA
* * * *
2290 AAACAGGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAA-GACAATAAGCTGTGACCTTCCGAC
65 AAACAAGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAA---G-GACCTTCCGAC
* *
2354 CGGGAAGGGGCATCTTTGGAAATGAAAACAAGGACCTTCCAACCAGGA
126 CGGGAAGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
* * * *
2402 AAGGGCATTTTTGGAAATGAAAACAA-G-GACCTTCCGACTGGGAAGGGGCATTTTTGGAAATGA
1 AGGGGCATTTTTGGAAA-GACAATAACGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATGA
** * * * *
2465 AAACAAGGACCTTCCGACTGGGAAGGGGCATTTTTGGAAATGAAAACAGGGAACTTCCAACCGAG
65 AAACAAGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACCGGG
* * * **
2530 AAGGGGCATGTTTTGGAAA-GAAAGAAAAAAGGACCTTCCGACTGGGA
130 AAGGGGCAT-TTTTGGAAATG--A-AAACAGGGACCTTCCAACCAGGA
2577 AGGGGCATTTTTGGAA
1 AGGGGCATTTTTGGAA
2593 TAAAACAATG
Statistics
Matches: 953, Mismatches: 77, Indels: 93
0.85 0.07 0.08
Matches are distributed among these distances:
168 38 0.04
169 44 0.05
170 62 0.07
171 22 0.02
172 24 0.03
173 19 0.02
174 254 0.27
175 172 0.18
176 10 0.01
177 32 0.03
178 31 0.03
179 17 0.02
180 9 0.01
181 52 0.05
182 1 0.00
183 3 0.00
184 2 0.00
185 1 0.00
186 3 0.00
187 5 0.01
188 36 0.04
189 73 0.08
190 34 0.04
191 9 0.01
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (173 bp):
AGGGGCATTTTTGGAAAGACAATAACGTGACCTTCCGACCGGGAAGGGGCATTTTTGGAAATGAA
AACAAGGACCTTCCGACCAGGAAGGGGCATTTTTGGAAATGAAAACAAGGACCTTCCGACCGGGA
AGGGGCATTTTTGGAAATGAAAACAGGGACCTTCCAACCAGGA
Found at i:3354 original size:20 final size:20
Alignment explanation
Indices: 3331--3373 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3321 TTCTTAAGAG
3331 TTCAACCTTTTAATTA-AAAT
1 TTCAACC-TTTAATTACAAAT
*
3351 TTCAACCTTTATTTACAAAT
1 TTCAACCTTTAATTACAAAT
3371 TTC
1 TTC
3374 TTAAAAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (20 bp):
TTCAACCTTTAATTACAAAT
Found at i:3355 original size:50 final size:50
Alignment explanation
Indices: 3204--3725 Score: 419
Period size: 50 Copynumber: 10.4 Consensus size: 50
3194 AAAATTTCGT
** * ** * *
3204 CTTTATTTACAAATTAGTTTAAAGTTCAATATTTTAACTTAAAGATTTC-AT
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAA-TTAAA-AGTTCAAC
*
3255 CTTTATTTACAAATTGCTTAAAAGGTTTCAA-CTTTTCAATTAAAAGTTCAAC
1 CTTTATTTACAAATTTCTTAAAA-G-TTCAACCTTTT-AATTAAAAGTTCAAC
* ** * *
3307 CTTCACATACAAATTTCTTAAGAGTTCAACCTTTTAATTAAAATTTCAAC
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAAGTTCAAC
** * *
3357 CTTTATTTACAAATTTCTTAAAAGTTTGACCTTTTAATCT-AAAGTCCAAT
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAAT-TAAAAGTTCAAC
* * * * * *
3407 CATTATTTACAAACTACTTACAAGCTTCAATCTTTTAATTAAAAGTCCAAC
1 CTTTATTTACAAATTTCTTAAAAG-TTCAACCTTTTAATTAAAAGTTCAAC
* * ** * * *
3458 TTTTATTCACCCATTTCTCAAAAGTTCAATCTTTTAATTAAAAGTTCCAC
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAAGTTCAAC
* * * * * *
3508 TTTTATTTACCAATTTCTCAAAAGTTCAATCTTTTAATTAAAGGTTCCAC
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAAGTTCAAC
* * * * * *
3558 TTTTATTTACAAATTGCTTAAAGGTTC-CCTCTTTTAACTAAAAGTTCAAA
1 CTTTATTTACAAATTTCTTAAAAGTTCAAC-CTTTTAATTAAAAGTTCAAC
* * * *
3608 CTTCACTTACAAATTTCTTAAAAGTTC-ACTCTTTTAATT-AAAGATCCAAT
1 CTTTATTTACAAATTTCTTAAAAGTTCAAC-CTTTTAATTAAAAG-TTCAAC
* * * * * *
3658 CTTTATTCACAAATTGCTTAAAAGTTCCAATC-TTTGATTAAAAATCCAAC
1 CTTTATTTACAAATTTCTTAAAAGTT-CAACCTTTTAATTAAAAGTTCAAC
*
3708 CTTTATTCACAAATTTCT
1 CTTTATTTACAAATTTCT
3726 CAAAGTTTCA
Statistics
Matches: 387, Mismatches: 71, Indels: 27
0.80 0.15 0.06
Matches are distributed among these distances:
49 4 0.01
50 275 0.71
51 71 0.18
52 30 0.08
53 7 0.02
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.41
Consensus pattern (50 bp):
CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAAGTTCAAC
Found at i:3492 original size:151 final size:149
Alignment explanation
Indices: 3204--3684 Score: 434
Period size: 151 Copynumber: 3.2 Consensus size: 149
3194 AAAATTTCGT
** * ** * * *
3204 CTTTATTTACAAATTAGTTTAAAGTTCAATATTTTAACTTAAAGATTTC-ATCTTTATTTACAAA
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAA-TTAAAGGTTCCAAT-ATTATTTACAAA
* * * * * * *
3268 TTGCTTAAAAGGTTTCAA-CTTTTCAATTAAAAGTTCAACCTTCACATACAAATTTCTTAAGAGT
64 CTACTT-AAA-GCTTCAATCTTTT-AACTAAAAGTTCAAACTTCACTTACAAATTTCTTAAAAGT
*
3332 TCAACCTTTTAATTAAAATTTCAAC
126 TCAATCTTTTAATTAAAA-TTCAAC
**
3357 CTTTATTTACAAATTTCTTAAAAGTTTGACCTTTTAATCTAAA-G-TCCAATCATTATTTACAAA
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAAT-TAAAGGTTCCAAT-ATTATTTACAAA
* * * ** *
3420 CTACTTACAAGCTTCAATCTTTTAATTAAAAG-TCCAACTTTTA-TTCACCCATTTCTCAAAAGT
64 CTACTTA-AAGCTTCAATCTTTTAACTAAAAGTTCAAAC-TTCACTT-ACAAATTTCTTAAAAGT
*
3483 TCAATCTTTTAATTAAAAGTTCCAC
126 TCAATCTTTTAATTAAAA-TTCAAC
* * * * * * *
3508 TTTTATTTACCAATTTCTCAAAAGTTCAATCTTTTAATTAAAGGTTCCACTTTTATTTACAAATT
1 CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAGGTTCCAATATTATTTACAAACT
* * ** *
3573 GCTTAAAGGTTCCCTCTTTTAACTAAAAGTTCAAACTTCACTTACAAATTTCTTAAAAGTTCACT
66 ACTTAAAGCTTCAATCTTTTAACTAAAAGTTCAAACTTCACTTACAAATTTCTTAAAAGTTCAAT
* *
3638 CTTTTAATTAAAGATCCAAT
131 CTTTTAATTAAA-ATTCAAC
* *
3658 CTTTATTCACAAATTGCTTAAAAGTTC
1 CTTTATTTACAAATTTCTTAAAAGTTC
3685 CAATCTTTGA
Statistics
Matches: 265, Mismatches: 52, Indels: 25
0.77 0.15 0.07
Matches are distributed among these distances:
150 87 0.33
151 113 0.43
152 31 0.12
153 34 0.13
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (149 bp):
CTTTATTTACAAATTTCTTAAAAGTTCAACCTTTTAATTAAAGGTTCCAATATTATTTACAAACT
ACTTAAAGCTTCAATCTTTTAACTAAAAGTTCAAACTTCACTTACAAATTTCTTAAAAGTTCAAT
CTTTTAATTAAAATTCAAC
Found at i:3799 original size:49 final size:49
Alignment explanation
Indices: 3256--3809 Score: 325
Period size: 50 Copynumber: 11.1 Consensus size: 49
3246 AGATTTCATC
* * * * *
3256 TTTATTTACAAATTGCTTAAAAGGTTTCAACTTTTCAATTAAAAGTTCAACC
1 TTTATTCACAAATTTCTTAAAA-GTTTCAACTTTT-AATTAAAAATCCAA-T
* * * * * *
3308 TTCACAT-ACAAATTTCTTAAGAG-TTCAACCTTTTAATTAAAATTTCAACC
1 TTTA-TTCACAAATTTCTTAAAAGTTTCAA-CTTTTAATTAAAAATCCAA-T
* * * *
3358 TTTATTTACAAATTTCTTAAAAGTTTGACCTTTTAATCT-AAAGTCCAAT
1 TTTATTCACAAATTTCTTAAAAGTTTCAACTTTTAAT-TAAAAATCCAAT
* * * * * * *
3407 CATTATTTACAAACTACTTACAAGCTTCAATCTTTTAATTAAAAGTCCAACT
1 -TTTATTCACAAATTTCTTAAAAGTTTCAA-CTTTTAATTAAAAATCCAA-T
** * * *
3459 TTTATTCACCCATTTCTCAAAAG-TTCAATCTTTTAATTAAAAGTTCCACT
1 TTTATTCACAAATTTCTTAAAAGTTTCAA-CTTTTAATTAAAA-ATCCAAT
* * * ** *
3509 TTTATTTACCAATTTCTCAAAAG-TTCAATCTTTTAATTAAAGGTTCCACT
1 TTTATTCACAAATTTCTTAAAAGTTTCAA-CTTTTAATTAAA-AATCCAAT
* * * * ** * * * *
3559 TTTATTTACAAATTGCTTAAAGGTTCCCTCTTTTAACTAAAAGTTCAAAC
1 TTTATTCACAAATTTCTTAAAAGTTTCAACTTTTAATTAAAA-ATCCAAT
* * *
3609 TTCACTT-ACAAATTTCTTAAAAG-TTCACTCTTTTAATTAAAGATCCAAT
1 TTTA-TTCACAAATTTCTTAAAAGTTTCA-ACTTTTAATTAAAAATCCAAT
* * * *
3658 CTTTATTCACAAATTGCTTAAAAGTTCCAA-TCTTTGATTAAAAATCCAACC
1 -TTTATTCACAAATTTCTTAAAAGTTTCAACT-TTTAATTAAAAATCCAA-T
* * * ** *
3709 TTTATTCACAAATTTC-TCAAAGTTTCAAATTTCCACCTAAAAATTCAAT
1 TTTATTCACAAATTTCTTAAAAGTTTCAACTTT-TAATTAAAAATCCAAT
** *
3758 TTTATTCTTAAATTTCTTAAAAGTTTGAACTTTTAATTAAAAATCCAAT
1 TTTATTCACAAATTTCTTAAAAGTTTCAACTTTTAATTAAAAATCCAAT
3807 TTT
1 TTT
3810 TAACTCAAAG
Statistics
Matches: 399, Mismatches: 80, Indels: 49
0.76 0.15 0.09
Matches are distributed among these distances:
49 51 0.13
50 277 0.69
51 53 0.13
52 17 0.04
53 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (49 bp):
TTTATTCACAAATTTCTTAAAAGTTTCAACTTTTAATTAAAAATCCAAT
Found at i:6162 original size:23 final size:24
Alignment explanation
Indices: 6136--6187 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
6126 TCCAAAAATC
*
6136 CAAA-CACCCCTATAAAGAAAAAG
1 CAAATCACCCATATAAAGAAAAAG
***
6159 CAAATTGGCCATATAAAGAAAAAG
1 CAAATCACCCATATAAAGAAAAAG
6183 CAAAT
1 CAAAT
6188 TGGAGCCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.13
Consensus pattern (24 bp):
CAAATCACCCATATAAAGAAAAAG
Done.