Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014441.1 Corchorus olitorius cultivar O-4 contig14474, 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: 38373
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:2355 original size:34 final size:35
Alignment explanation
Indices: 2309--2374 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
2299 TTCAATAACC
* *
2309 TTACATCTTTTGTGATATTGGTTATCATATTTTTA
1 TTACATCTTTTGTAATATTGATTATCATATTTTTA
*
2344 TTACAT-TTTTGTAATTTTGATTATCATATTT
1 TTACATCTTTTGTAATATTGATTATCATATTT
2375 CTCCAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.24, C:0.08, G:0.09, T:0.59
Consensus pattern (35 bp):
TTACATCTTTTGTAATATTGATTATCATATTTTTA
Found at i:3240 original size:203 final size:201
Alignment explanation
Indices: 2891--3300 Score: 723
Period size: 203 Copynumber: 2.0 Consensus size: 201
2881 GCTTAATAAC
*
2891 TTTATCAATGGTGAATGTTATTATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
2956 GATACAAAACATTATTATTATATATAAAACTATACCAAAAAAAAAATAGTTGAACATTAGTGGTT
66 GATACAAAACATTACTATTATATATAAAACTATACC-AAAAAAAAATAGTTGAACATTAGTGGTT
3021 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
130 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGAT
*
3086 CTGATTTA
194 CCGATTTA
3094 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * *
3159 GATACAACACATTACTATTATATATATAGAACTATACC-AAAAAAATTAGTTGAACATTAGTTGT
66 GATACAAAACATTACTATTATATATA-A-AACTATACCAAAAAAAAATAGTTGAACATTAGTGGT
3223 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
3288 CCGATTTA
194 CCGATTTA
3296 TTTAT
1 TTTAT
3301 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
202 17 0.09
203 172 0.86
204 1 0.01
205 9 0.05
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAAAACATTACTATTATATATAAAACTATACCAAAAAAAAATAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:3719 original size:2 final size:2
Alignment explanation
Indices: 3707--3749 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
3697 AGTTTAGACT
3707 TA TA TA GTA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3749 T
1 T
3750 TATTTTAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3731 original size:19 final size:17
Alignment explanation
Indices: 3707--3749 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
3697 AGTTTAGACT
3707 TATATAGTAT-ATATATA
1 TATATA-TATAATATATA
3724 TATATATATAATATATA
1 TATATATATAATATATA
3741 TATATATAT
1 TATATATAT
3750 TATTTTAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATATATAATATATA
Found at i:4615 original size:45 final size:47
Alignment explanation
Indices: 4566--4675 Score: 161
Period size: 49 Copynumber: 2.3 Consensus size: 47
4556 AGCAACAATT
* *
4566 AATATTAGCTTTATTTTGATGAATTATCT-AG-AGATGGAGGAGTAG
1 AATATCAGCTTTATTTTGATGAATTACCTAAGAAGATGGAGGAGTAG
*
4611 AATATCAACTTTATTTTGATGAATTACCTAGAGATAGATGGAGGAGTAG
1 AATATCAGCTTTATTTTGATGAATTACCTA-AGA-AGATGGAGGAGTAG
4660 AATATCAGCTTTATTT
1 AATATCAGCTTTATTT
4676 AGATAATGCA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
45 26 0.46
47 2 0.04
49 29 0.51
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (47 bp):
AATATCAGCTTTATTTTGATGAATTACCTAAGAAGATGGAGGAGTAG
Found at i:4831 original size:31 final size:31
Alignment explanation
Indices: 4796--4858 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
4786 AACAACTACG
* *
4796 AAAAATATAGCCCTAATAAGAAGATGACTGC
1 AAAAATATAACCATAATAAGAAGATGACTGC
4827 AAAAATATAACCATAATAAGAAGATGACTGC
1 AAAAATATAACCATAATAAGAAGATGACTGC
4858 A
1 A
4859 GCGCACGCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (31 bp):
AAAAATATAACCATAATAAGAAGATGACTGC
Found at i:4920 original size:15 final size:17
Alignment explanation
Indices: 4886--4930 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
4876 CCTGCTTGTA
4886 ATAATTATT-TTTAGATT
1 ATAA-TATTATTTAGATT
4903 ATAATA-TATTTA-ATT
1 ATAATATTATTTAGATT
4918 ATAATATTATTTA
1 ATAATATTATTTA
4931 TAGTCATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATAATATTATTTAGATT
Found at i:6261 original size:332 final size:330
Alignment explanation
Indices: 5313--7085 Score: 1425
Period size: 333 Copynumber: 5.4 Consensus size: 330
5303 TCAAAAGCGT
*
5313 AAAACGCCCTCCAATATTTTTGGCGTTGATTTATATA-TTTTTATGAGTATTTTAGTCAAAAATT
1 AAAA-GCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTA-TCAAAAATT
* * * *
5377 GAGGAGAAATCTTTTCGTGTCAATTTTTGCAAAATTTTAACCGAAATCATCTACTAACAAAACCA
64 GAGGAAAAATCTTTT-G-GTCAATTTTTGCAAAATTTTAACCGAAATC--GT-GT-A-ATAACCA
* * * * * * *
5442 TCACGGTTTTTTGCTAAAAACGCCTTCCAGGGACCCGACTCAATTTTGTATGATTTTTGGCTCCG
122 TCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGTATGATTTTTGGCACCG
*
5507 AGACTACTTGAAATATCTATATTCATT-TAATCAAATCTGT-GTCACATTGGATTTAAGGATTTG
187 AGACTCCTTGAAATATCTATATTCATTCTAATCAAATCT-TAGTCACATTGGATTTAAGGATTTG
* * * *
5570 TTTTTACAAGCATATGAATCTTATTTCGATTTAATTAGAAATTAATTT-GGAAAAAATAGGAAAA
251 TTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT-ATTTCAGAAAAAATATGAAAA
* *
5634 ATGATATTAGAAATGTC
315 ATGATATTA-AAGTGTG
* * * *
5651 AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTGTGAGTATTTTAGCCAAAAATTG
1 AAAAGCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTA-TCAAAAATTG
* * * * * *
5716 AGGAAATATCTTTTGGAT-AAGTTTTTACAAAATCTTAACTGAAATCGTGTAATAATCATCGCAG
65 AGGAAAAATCTTTTGG-TCAA-TTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCAC-G
* *** * *** * * ** *
5780 TTTTTTAAATAAAAAAGCG-TTCTGGGGCTTTGGCTCAAATTTATATGATTTTTGGTGCCAAGAC
127 GTTTTTGGCTAAAAACGCGTTTC-GGGGCCCCGGCTCAATTTTGTATGATTTTTGGCACCGAGAC
* * * * * *
5844 TCCTTGAAATATCCATATTCA-TCTAATCAAATCTCAGCCACATTGGGTTTAAGAATTTGTTTTC
191 TCCTTGAAATATCTATATTCATTCTAATCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTT
* * * *
5908 ACAAGCATCTGAATGTTGTTTCGATTTAGTTAGAAATTATTTCAG-AAAAATATGAAGAATGATG
256 ACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTATTTCAGAAAAAATATGAAAAATGATA
*
5972 TTAACAGCGTG
321 TTAA-AGTGTG
* ** *
5983 AAAAGTCCTCCAATATTTTTGATGTTAAATTATATAATTTTTTATGAGTATTTTATCCAAAAATT
1 AAAAGCCCTCCAATATTTTTGGCGTTGAATTATAT-ATTTTTTATGAGTATTTTAT-CAAAAATT
* * * * *
6048 GACGAAAAAT-TTTTAAGGTCATTTTTTGCAATATTTTAACCAAAATCGTGTACTAACCATCACG
64 GAGGAAAAATCTTTT--GGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACG
* *
6112 GTTTTTGGCTAAAAACTCGTTTCGGGGCCCCGGCTCAATTTTGTATGATTTTTGGCACCGACACT
127 GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGTATGATTTTTGGCACCGAGACT
* * * *
6177 CCTTGAAATATCTATATT-ATTCTAATAAAATCTTAGTCGCATTGCATTTAAGGATTTCTTTTTA
192 CCTTGAAATATCTATATTCATTCTAATCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTA
* * * * *
6241 CGAGCATCTTAATCTTGTTTCGATTTAATTATAAATTAATTCAGAAAAAATATGGAAAAACGATA
257 CAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTATTTCAGAAAAAATAT-GAAAAATGATA
6306 TTAAAAGTGTG
321 TT-AAAGTGTG
* * * *
6317 AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAAGAGTATTATGGAT-AAAAATT
1 AAAAGCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATT-T-TATCAAAAATT
* * * *
6381 GAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGG
64 GAGGAAAAATCTTT-TGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACGG
* * * * * * * *
6446 GTTTTGGCTAAAAACGCATTTCGAGG-CCAGGTTCAGTTTTGAATGATTTTTGGCGA-TGAGACT
128 TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGTATGATTTTTGGC-ACCGAGACT
** *
6509 CCTTGAAATATCTATATTCA-TCTAGAT-AAATC-----C-CA---G------CCA-TTGTTTCT
192 CCTTGAAATATCTATATTCATTCTA-ATCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTT
* * * * * * * *
6556 ACAAGCATCTTAATCATATTTCGTTTTTAATTAGAAATTAATTCGGAAAAAAAATAGGAAAAACG
256 ACAAGCATCTGAATCTTGTTTCG-ATTTAATTAGAAATTATTTC--AGAAAAAATATGAAAAATG
*
6621 ATATTCAAAGCGTG
318 ATATT-AAAGTGTG
* * * *** * * * **
6635 AAACGCCCTTCAATCTTTTTTATGCTAAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTG
1 AAAAGCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTATC-AAAAATTG
* * *
6700 AGGAAAAATATTTTGGATCATTTTTTGCAAAATATTAACCGAAATCGTG---TAA-CATCA-GGT
65 AGGAAAAATCTTTTGG-TCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACGGT
* * * * * *
6760 TTTT---T--TAATGCGTTCCGGAGCCCCAGG--------T-TA-G--TTTTGGCACCTAAACTC
129 TTTTGGCTAAAAACGCGTTTCGGGGCCCC-GGCTCAATTTTGTATGATTTTTGGCACCGAGACTC
* * * *
6808 CTAGAAATATCTATATTCA-TCTAATAAAATCTCAGCCACATTGGATTTAAGGA------TTTAC
193 CTTGAAATATCTATATTCATTCTAATCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTAC
* * * * * * * *
6866 AAGTATTTAAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAGTAGGGAAAACGATAT
258 AAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTATTTCAGAAAAAA-TATGAAAAATGATAT
* *
6931 TAGAAGCGTA
322 TA-AAGTGTG
* * * * * **
6941 AAAAACCCTTCAATATTTTTTTGCATTGAATTATATATTTTTTATGAGTGTTTTGGCCAAAAATT
1 AAAAGCCCTCCAATA-TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTT-ATCAAAAATT
* * * * * *
7006 GAAGAAATACCTTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCACGA
64 GAGGAAAAATCTTTT-GGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACGG
7071 TTTTTGGCTAAAAAC
128 TTTTTGGCTAAAAAC
7086 ACGCTCCAGG
Statistics
Matches: 1159, Mismatches: 210, Indels: 153
0.76 0.14 0.10
Matches are distributed among these distances:
297 3 0.00
298 39 0.03
300 1 0.00
301 1 0.00
302 1 0.00
303 1 0.00
304 2 0.00
305 7 0.01
306 33 0.03
307 98 0.08
308 33 0.03
309 2 0.00
310 6 0.01
311 5 0.00
312 6 0.01
313 7 0.01
314 5 0.00
315 4 0.00
316 26 0.02
317 23 0.02
318 112 0.10
319 9 0.01
326 2 0.00
327 1 0.00
331 2 0.00
332 263 0.23
333 312 0.27
334 52 0.04
335 5 0.00
336 3 0.00
337 53 0.05
338 42 0.04
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (330 bp):
AAAAGCCCTCCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTATCAAAAATTGA
GGAAAAATCTTTTGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACGGTTT
TTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAATTTTGTATGATTTTTGGCACCGAGACTCCTT
GAAATATCTATATTCATTCTAATCAAATCTTAGTCACATTGGATTTAAGGATTTGTTTTTACAAG
CATCTGAATCTTGTTTCGATTTAATTAGAAATTATTTCAGAAAAAATATGAAAAATGATATTAAA
GTGTG
Found at i:7291 original size:172 final size:173
Alignment explanation
Indices: 6999--7343 Score: 534
Period size: 172 Copynumber: 2.0 Consensus size: 173
6989 TGTTTTGGCC
6999 AAAAATTGAAGAAATACCTTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC
1 AAAAATTGAAGAAATACCTTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC
* *
7064 ATCACGATTTTTGGCTAAAAACACGCTCCAGGGCCCTAGGTTAGTTTTGCATGATTTTTTGCGCT
66 ATCACGATTTTTGGCTAAAAACACGCTCCAGGGCCCGAGGTTAGTTTTACATGATTTTTTGCGCT
7129 AAAACTCCTTGAG-ATACCCATACTCATCTAATCAAATCTCAT
131 AAAACTCCTTGAGAATACCCATACTCATCTAATCAAATCTCAT
* * *
7171 AAAAATTGAGGAAATA-TTTTTCCGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAAT
1 AAAAATTGAAGAAATACCTTTT-CGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAT
* * * * *
7235 CATCACGGTTTTTGGCTAAAAACGCGTTTCAGGGTCCCGA-GTTAGTTTTACATGATTTTTTGTG
65 CATCACGATTTTTGGCTAAAAACACGCTCCAGGG-CCCGAGGTTAGTTTTACATGATTTTTTGCG
* *
7299 CTAAGACTCCTTGAGATATACCCATATTCATCTAATCAAATCTCA
129 CTAAAACTCCTTGAGA-ATACCCATACTCATCTAATCAAATCTCA
7344 ACCATATAGC
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
171 4 0.03
172 122 0.78
173 4 0.03
174 27 0.17
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (173 bp):
AAAAATTGAAGAAATACCTTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATC
ATCACGATTTTTGGCTAAAAACACGCTCCAGGGCCCGAGGTTAGTTTTACATGATTTTTTGCGCT
AAAACTCCTTGAGAATACCCATACTCATCTAATCAAATCTCAT
Found at i:7795 original size:331 final size:326
Alignment explanation
Indices: 7170--9569 Score: 2140
Period size: 331 Copynumber: 7.3 Consensus size: 326
7160 TCAAATCTCA
* * *
7170 TAAAAATTGAGG-AAATATTTTTCCGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAA
1 TAAAAATT-AGGAAAATA-TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT--CAA
* * * * *
7234 TCATCACGGTTTTTGGCTAAAAACGCGTTTC-AGGGTCCCGAG-TTAGTTTTACATGATTTTTTG
62 --ATCACGATTTTTGGCTAAAAACGCGTTTCGA-GGCCCCG-GCTCAGTTTTGCATGATTTTTGG
* * * * * * * * * *
7297 TGCTAAGACTCCTTGAGATATACCCATATTCATCTAATCAAATCTCAACCATATAGCATTTAAGG
123 CGCCAAGACTCCTT-A-AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGG
* * * *
7362 ATTTGTTTTTACGAGCATCTGAAT-ATTGTTTCAATTTAATTAGAAATTAATTCATAAAAATTAT
186 ATTTGTTTTTACGAGCATCTGAATCA-TGTTTCGATTTAATTAGAAATTAATTTA-AAAAAATAG
* * * * * * * *
7426 GAAAAACAATATGAAAAGCTTGAAAAGTCCTCCAATCTTTTTGACATTAAATTATATATATTTCA
249 GAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATATTTTA
7491 TGAGTATTTTAGC
314 TGAGTATTTTAGC
* * * *
7504 GAAAAATTAGGAAAATATTTTACTGGTCATTTTTTGTAAAATTTTAGCCGAAATCGTTAGTCGAA
1 TAAAAATTAGGAAAATATTTT-CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG-T-GTC-AA
* * * * * * *
7569 ATCACAATTTTTGGCTAATAACGCGTTAT-GAGGCCCCGGTTCAATGTTGCATAATTTTTGGCAC
62 ATCACGATTTTTGGCTAAAAACGCGTT-TCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
* * *
7633 CGAGACTCCATAAAATATCTATATTCATCTAAACAAATCTCAGCCACATTGGATTTAAGGATTTG
126 CAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG
*** * * *
7698 -TAAAACAAACATCTGAATCATGTTTCGATTTAATTAGAAATTAATTGTAAAAATAATAAGAAAA
191 TTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATT-TAAAAA-AATAGGAAAA
* * * *
7762 ACGATATTATAAGCATGGAAAGCCCTTCAATCTTTTTGGCATTGAATTATATA-ATTTTTATGAG
254 ACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATA-TTTTATGAG
* *
7826 TATTGTGGC
318 TATTTTAGC
* * * * * * *
7835 TAAAAATT-GAGTAAATAACTTTCGAGTCAATTTTTGCAAACTTCTAGCCGAAATTGTGTAATAG
1 TAAAAATTAG-GAAAAT-ATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTCA-A-
* * * *
7899 TCATCACGATTTTTGGCTAAAAACGCGTTTCG-GAGTCCCGACTAAGTTTTGCATGA-TTTTGAC
62 --ATCACGATTTTTGGCTAAAAACGCGTTTCGAG-GCCCCGGCTCAGTTTTGCATGATTTTTG-G
* * * * * ** **
7962 CCCCAAGACTCTTTAAGATATCCATATTCATCTAATCAAATCTCAGCTTCATTGGATTTAATAAT
123 CGCCAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT
* * *
8027 TTGTTTTTACGAGCATCTGAAT-ATTGTTTCGATTTAATTAGAAATTAA-TTCAGAAAATATGAA
188 TTGTTTTTACGAGCATCTGAATCA-TGTTTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAA
* * * * *
8090 AAACAATATTAAAAGCGTGAAAAGTCCTCCAATATTTTTGGCATTAAATTATATATATTTTATGA
252 AAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATATTTTATGA
8155 GTATTTTAGAC
317 GTATTTTAG-C
* * *
8166 -AAAAATTGATGGAAAA-ATTTTTCGGGTCATTTTTTGCAAAATTTTAACTGAAATCGTGTACTA
1 TAAAAATT-A-GGAAAATA-TTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-C-A
* * * * *
8229 ACCATCACGGTTTTTGGCAAAAAAGGTGTTTCGGGGCCCCGGCGT-AGTTTTGCATGATTTTTGG
61 A--ATCACGATTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGC-TCAGTTTTGCATGATTTTTGG
* * * *
8293 AGCCGAA-ACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAACGA
123 CGCC-AAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGA
* * * * * *
8357 TTTGTTTTTATGTGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATATGAA
187 TTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAA
* * * * *
8422 AAACGATATTTA-TAGCGTGAAAAGTCC-TCTAAT-TTTTTGGCACTT-AATTATGTATATTCTA
252 AAACAATA-TTAGAAGCGTGAAAAGCCCTTC-AATCTTTTTGGCA-TTGAATTATATATATTTTA
* * * *
8483 TGAGCATTGTGGT
314 TGAGTATTTTAGC
* * * * * *
8496 TAAAAAATGAGTCAAAATATTTT-GCGTTAATTTTTGCAAAATTTTAGCCAAAATCGTGT-ACCA
1 T-AAAAATTAG-GAAAATATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTCA-AA
* * * * *
8559 TCATGA-TTTT---T------GCGTTTCGAGGTCCCGGATCAGTTTTGCATGATTTTTGGTGGCA
63 TCACGATTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCA
* * *
8614 AAACTCCTTAAAGTATCTATATTCATCTAACCAAATCAT-AGCCACATTGGATTTAAGGATTTTT
128 AGACTCCTTAAAATATCTATATTCATCTAACCAAATC-TCAGCCACATTGGATTTAAGGA-TTTG
* * *
8678 TTTTTACAAGCATTTGAATCATATTTCGATTTAATTAGAAATTAATTTGAAAAAAAGTAGGAAAA
191 TTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTT-AAAAAAA-TAGGAAAA
* *
8743 ACAATATTAGAAGCGTGAGAAGCCCTT-AATCTTTTTGGCTTTGAATTATATAT-TTTTAATGAG
254 ACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATATTTT-ATGAG
* *
8806 TATTGTGGC
318 TATTTTAGC
* * *
8815 TAAAAATTTAGAAAAATA-TTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGT-ACTAT
1 TAAAAA-TTAGGAAAATATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTCA-AAT
* * * * * *
8878 CATGGTTCTTTGGCTAAAAACGTGTTTCGGGGCCCTGGGTCAGTTTTGCATGATTTTTGGCGCCA
64 CACGATT-TTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCA
* * *
8943 AGACTCTCTAAAATATATCTATATTCATCTAACCAAATCTCGGCCACATTGTATTTAAGGATTTG
128 AGACTC-CTTAAA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTG
* * * * * * *
9008 TTTTTTAAGAG-TTTTAAATCTTGTTTCGATTTAATCAGAAATTTATTTGGAAATAAAATAGGAA
191 -TTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTT--AAA-AAAATAGGAA
** * * * *
9072 AAATGATATTAGAAGCGTGAAAAATG-CTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTAT
252 AAACAATATTAGAAGCGTG-AAAA-GCCCTTCAATCTTTTTGGCATTGAATTATATATATTTTAT
*
9136 GAGTATTATT-GT
315 GAGTATT-TTAGC
* *
9148 TAGAAATCAAGGAAAA-ATCTTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAA
1 TAAAAAT-TAGGAAAATAT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-C-AA
* * * * *
9211 CCATCACGGTTTTTTTCGGCTAAAAATGTGTTCCGAGG-CCCGGCTCAGTTTTGCATGATTTTTT
62 --ATCAC-G-ATTTTT-GGCTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTG
* * * * *
9275 GTGCTAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCGCATTAGATTTAAGGA
122 GCGCCAAGACTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGA
* * * * *
9340 TTTGTTTTTATGAGCATCTAAATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAAAAAATAGG
187 TTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATT--TAAAAAAATAGG
* * *
9405 AAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTT--TATGTCGAATTATATATTTTTT
250 AAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCAT-T-GAATTATATATATTTT
9468 ATGAGTATTTTAGC
313 ATGAGTATTTTAGC
* *
9482 CAAAAATT-GAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACAT
1 TAAAAATTAG-GAAAATAT-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTCAAAT
* *
9545 CACGGTTTTTGGGTAAAAACGCGTT
64 CACGATTTTTGGCTAAAAACGCGTT
9570 ACAGGGCCAT
Statistics
Matches: 1703, Mismatches: 262, Indels: 209
0.78 0.12 0.10
Matches are distributed among these distances:
315 3 0.00
316 86 0.05
317 50 0.03
318 68 0.04
319 58 0.03
320 4 0.00
323 1 0.00
325 4 0.00
326 5 0.00
327 13 0.01
328 6 0.00
329 46 0.03
330 198 0.12
331 458 0.27
332 180 0.11
333 175 0.10
334 144 0.08
335 55 0.03
336 84 0.05
337 8 0.00
338 37 0.02
339 20 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (326 bp):
TAAAAATTAGGAAAATATTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTCAAATCA
CGATTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
CTCCTTAAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
ACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTTAAAAAAATAGGAAAAACAATAT
TAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATATTTTATGAGTATTTTAG
C
Found at i:13553 original size:25 final size:26
Alignment explanation
Indices: 13508--13556 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
13498 TATCTAACTT
13508 TTTACTCAACCTTTGACAATTAAACA
1 TTTACTCAACCTTTGACAATTAAACA
*
13534 TTTACTCAACTTTTGA-AATTAAA
1 TTTACTCAACCTTTGACAATTAAA
13557 ATGCCCCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (26 bp):
TTTACTCAACCTTTGACAATTAAACA
Found at i:29114 original size:15 final size:16
Alignment explanation
Indices: 29089--29118 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29079 CTATGTTAAA
29089 AAATCAAATATATAAT
1 AAATCAAATATATAAT
29105 AAAT-AAATATATAA
1 AAATCAAATATATAA
29119 CAAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATCAAATATATAAT
Found at i:29125 original size:17 final size:15
Alignment explanation
Indices: 29085--29128 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
29075 TCAACTATGT
29085 TAAAAAATCAAATATA
1 TAAAAAAT-AAATATA
*
29101 TAATAAATAAATATA
1 TAAAAAATAAATATA
29116 TAACAAAAATAAA
1 T-A-AAAAATAAA
29129 ACGAATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAAAATAAATATA
Found at i:29924 original size:31 final size:32
Alignment explanation
Indices: 29883--29965 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 32
29873 TAAAAGTACA
*
29883 AAATTAGTCCCTGAAGTGGAGTGAAAATA-GC
1 AAATTAGTCCCTGAAGTGGAGTAAAAATATGC
* * *
29914 AAATTGGTCCCTCAAGT-GA-AAAAAATATGC
1 AAATTAGTCCCTGAAGTGGAGTAAAAATATGC
*
29944 AATTTAGTCCCTGAAGTGGAGT
1 AAATTAGTCCCTGAAGTGGAGT
29966 TAACTGAGCA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
29 6 0.15
30 18 0.44
31 17 0.41
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.25
Consensus pattern (32 bp):
AAATTAGTCCCTGAAGTGGAGTAAAAATATGC
Found at i:30168 original size:30 final size:31
Alignment explanation
Indices: 30107--30181 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
30097 AAAAATAGTT
*
30107 AGGGACCCAATTGCTCAATTAACTCCACTTC
1 AGGGACCCAATTGCTCAACTAACTCCACTTC
* * *
30138 AGGGACTCAATTGCTC-ACTAAGTTCACTTC
1 AGGGACCCAATTGCTCAACTAACTCCACTTC
*
30168 AGGGACCCATTTGC
1 AGGGACCCAATTGC
30182 ATATTTGCCC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 23 0.61
31 15 0.39
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (31 bp):
AGGGACCCAATTGCTCAACTAACTCCACTTC
Found at i:30256 original size:18 final size:17
Alignment explanation
Indices: 30233--30277 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
30223 AAAAATATCA
*
30233 TTTTTCTTCTTTTCTTTT
1 TTTTTCTT-TTTTATTTT
30251 TTTTTCTTTTTTATTTT
1 TTTTTCTTTTTTATTTT
30268 TATTTT-TTTT
1 T-TTTTCTTTT
30278 AAATATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTTCTTTTTTATTTT
Found at i:30267 original size:15 final size:16
Alignment explanation
Indices: 30232--30278 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
30222 AAAAAATATC
*
30232 ATTTTTCTTCTTTTCTT
1 ATTTTTATTCTTTT-TT
30249 -TTTTT-TTCTTTTTT
1 ATTTTTATTCTTTTTT
30263 ATTTTTATT-TTTTTT
1 ATTTTTATTCTTTTTT
30278 A
1 A
30279 AATATCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (16 bp):
ATTTTTATTCTTTTTT
Found at i:37032 original size:74 final size:74
Alignment explanation
Indices: 36911--37063 Score: 288
Period size: 74 Copynumber: 2.1 Consensus size: 74
36901 TGCGAAACCC
*
36911 TATTTATCCCTTTCAATCTGACCTAATCTAGCCTATTTCTTGTGAGTGAATCCTTTTCTATCCTT
1 TATTTATCCCTTTCAATCTAACCTAATCTAGCCTATTTCTTGTGAGTGAATCCTTTTCTATCCTT
36976 CCGCTACGT
66 CCGCTACGT
36985 TATTTATCCCTTTCAATCTAACCTAATCTAGCCTATTTCTTGTGAGTGAATCCTTTTCTATCCTT
1 TATTTATCCCTTTCAATCTAACCTAATCTAGCCTATTTCTTGTGAGTGAATCCTTTTCTATCCTT
*
37050 CTGCTACGT
66 CCGCTACGT
37059 TATTT
1 TATTT
37064 TTCATGTTCA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (74 bp):
TATTTATCCCTTTCAATCTAACCTAATCTAGCCTATTTCTTGTGAGTGAATCCTTTTCTATCCTT
CCGCTACGT
Done.