Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013998.1 Corchorus capsularis cultivar CVL-1 contig14019, 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: 114900
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:351 original size:30 final size:32
Alignment explanation
Indices: 306--371 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
296 TGGCAATATA
* *
306 GAAATATGTTTTTAAAAA-AAGCATACAATTG
1 GAAATATGATTTTAAAAATAAGCATACAATCG
**
337 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
1 GAAATATGATTTTAAAAATAAGCATACAATCG
368 GAAA
1 GAAA
372 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (32 bp):
GAAATATGATTTTAAAAATAAGCATACAATCG
Found at i:407 original size:2 final size:2
Alignment explanation
Indices: 400--540 Score: 88
Period size: 2 Copynumber: 70.0 Consensus size: 2
390 TTCGTACTTT
* * * * *
400 TA TA TA TA GTA TA GA TG TA GA TA TA TC TA TA TA TC TA TA CTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * * * * * *
444 GA TA TA TC TA TA TA TC TA TA TG TC TA -A CA TA AA GA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
528 TA TA CA -A TA TA TA
1 TA TA TA TA TA TA TA
541 AAAGTACGAG
Statistics
Matches: 104, Mismatches: 30, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
1 2 0.02
2 96 0.92
3 6 0.06
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3208 original size:96 final size:96
Alignment explanation
Indices: 3051--3244 Score: 361
Period size: 96 Copynumber: 2.0 Consensus size: 96
3041 TATATAGAGT
* *
3051 ATATTTGATTGGAATGGGTTTGTATTCGGATTACCAAGTGTTTGATGTTATTACCCTCTCAAATT
1 ATATTTGATTGGAATGGATTTATATTCGGATTACCAAGTGTTTGATGTTATTACCCTCTCAAATT
3116 CATCTCCCTTTTCTCAGCAAGTACATAGAAA
66 CATCTCCCTTTTCTCAGCAAGTACATAGAAA
3147 ATATTTGATTGGAATGGATTTATATTCGGATTACCAAGTGTTTGATGTTATTACCCTCTCAAATT
1 ATATTTGATTGGAATGGATTTATATTCGGATTACCAAGTGTTTGATGTTATTACCCTCTCAAATT
*
3212 CATCTCCCTTTTCTCAGCAATTACATAGAAA
66 CATCTCCCTTTTCTCAGCAAGTACATAGAAA
3243 AT
1 AT
3245 TTTAACATAT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (96 bp):
ATATTTGATTGGAATGGATTTATATTCGGATTACCAAGTGTTTGATGTTATTACCCTCTCAAATT
CATCTCCCTTTTCTCAGCAAGTACATAGAAA
Found at i:9934 original size:12 final size:12
Alignment explanation
Indices: 9917--9943 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9907 AATCTATTGG
9917 AATAAGTTGAAA
1 AATAAGTTGAAA
9929 AATAAGTTGAAA
1 AATAAGTTGAAA
9941 AAT
1 AAT
9944 TATTAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (12 bp):
AATAAGTTGAAA
Found at i:12116 original size:72 final size:72
Alignment explanation
Indices: 11999--12466 Score: 313
Period size: 72 Copynumber: 6.5 Consensus size: 72
11989 TATAGCAATT
*
11999 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAA-ATGAGT-TT
1 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAGA-GAGTGCT
12062 TCTCAAATC
65 TC-CAAATC
* * *
12071 ACCAATTTCAGGTGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGTGAAGAGAGTGCTT
1 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAGAGAGTGCTT
12136 CCAAATC
66 CCAAATC
* * * * * * **
12143 ACCAATTTGAGGCGGAATAGATTCAATCAACTGATTTTGGGAGAGAT-TCAATGAAGTA-AGTGC
1 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCT-AGCGAAG-AGAGTGC
* *
12206 -CCCAAGAAC
64 TTCCAA-ATC
* * * * * ** * * * ** *** *
12215 ACCAATTTGATGCGGAATTGGTCCACTCAATTGGTTCTTTGATAAGTTTATTGACTTGAGTGCTG
1 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAGAGAGTGCTT
12280 CCAAATC
66 CCAAATC
* * * * * * * * **
12287 ACCAATTTGATGCGGAATCGGTCCACTCAATTGGTTTTGAGAGAGATCCAATGAAGTA-AGTGC-
1 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAG-AGAGTGCT
*
12350 TCCAAGAAC
65 TCCAA-ATC
* * * * * * * * *
12359 ACCAATTTGATGCGGAATAGGTCCACTCAGCTGATTTTGGGAGAGGTCCAGTGAAGTGAGTGCTC
1 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAGAGAGTGCTT
12424 CCAAA-C
66 CCAAATC
** * * *
12430 TACCAATTTGAGTTGGAATAGGTCCATTCAATTGGTT
1 -ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTT
12467 ACTCGAGAGG
Statistics
Matches: 318, Mismatches: 65, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
71 10 0.03
72 294 0.92
73 14 0.04
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (72 bp):
ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAGAGAGTGCTT
CCAAATC
Found at i:12475 original size:144 final size:144
Alignment explanation
Indices: 12070--12466 Score: 458
Period size: 144 Copynumber: 2.8 Consensus size: 144
12060 TTTCTCAAAT
* * * * * *
12070 CACCAATTTCAGGTGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGTGAAGAGAGTGCT
1 CACCAATTTGATGCGGAATAGGTCCACTCAACTGGTTTTGGGAGAGGTCTAGTGAAGTGAGTGCT
* * * * * * * *
12135 TCCAAATCACCAATTTGAGGCGGAATAGATTCAATCAACTGATTTTGGGAGAGATTCAATGAAGT
66 CCCAAATCACCAATTTGAGTCGGAATAGGTCCAATCAATTGGTTTTGAGAGAGATCCAATGAAGT
12200 AAGTGCCCCAAGAA
131 AAGTGCCCCAAGAA
* * * * * * * **
12214 CACCAATTTGATGCGGAATTGGTCCACTCAATTGGTTCTT-TGATAAGTTTATTGACTTGAGTGC
1 CACCAATTTGATGCGGAATAGGTCCACTCAACTGGTT-TTGGGAGAGGTCTAGTGAAGTGAGTGC
* * *
12278 TGCCAAATCACCAATTTGA-TGCGGAATCGGTCCACTCAATTGGTTTTGAGAGAGATCCAATGAA
65 TCCCAAATCACCAATTTGAGT-CGGAATAGGTCCAATCAATTGGTTTTGAGAGAGATCCAATGAA
*
12342 GTAAGTGCTCCAAGAA
129 GTAAGTGCCCCAAGAA
* * *
12358 CACCAATTTGATGCGGAATAGGTCCACTCAGCTGATTTTGGGAGAGGTCCAGTGAAGTGAGTGCT
1 CACCAATTTGATGCGGAATAGGTCCACTCAACTGGTTTTGGGAGAGGTCTAGTGAAGTGAGTGCT
* *
12423 CCCAAA-CTACCAATTTGAGTTGGAATAGGTCCATTCAATTGGTT
66 CCCAAATC-ACCAATTTGAGTCGGAATAGGTCCAATCAATTGGTT
12467 ACTCGAGAGG
Statistics
Matches: 206, Mismatches: 42, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
143 3 0.01
144 201 0.98
145 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (144 bp):
CACCAATTTGATGCGGAATAGGTCCACTCAACTGGTTTTGGGAGAGGTCTAGTGAAGTGAGTGCT
CCCAAATCACCAATTTGAGTCGGAATAGGTCCAATCAATTGGTTTTGAGAGAGATCCAATGAAGT
AAGTGCCCCAAGAA
Found at i:12493 original size:216 final size:216
Alignment explanation
Indices: 11999--12513 Score: 515
Period size: 216 Copynumber: 2.4 Consensus size: 216
11989 TATAGCAATT
* * * * ** * * * ** **
11999 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAATGAGTTTTC
1 ACCAATTTGATGCGGAATAGGTCCACTCAATTGGTTCTTCGAGAAGTTTAGTGACGTGAGTGCTC
* * * * * *
12064 TCAAATCACCAATTTCAGGTGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGTGAAGAG
66 TCAAATCACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGAGAGAGATCCAATGAAGAG
* * *
12129 AGTGCTTCCAAATCACCAATTTGAGGCGGAATAGATTCAATCAACTGATTTTGGGAGAGATTCAA
131 AGTGCTTCCAAAACACCAATTTGAGGCGGAATAGATCCAATCAACTGATTTTGGGAGAGATCCAA
12194 TGAAGTAAGTGCCCCAAGAAC
196 TGAAGTAAGTGCCCCAAGAAC
* * * * *
12215 ACCAATTTGATGCGGAATTGGTCCACTCAATTGGTTCTTTGATAAGTTTATTGACTTGAGTGCTG
1 ACCAATTTGATGCGGAATAGGTCCACTCAATTGGTTCTTCGAGAAGTTTAGTGACGTGAGTGCT-
* * * * *
12280 C-CAAATCACCAATTTGATGCGGAATCGGTCCACTCAATTGGTTTTGAGAGAGATCCAATGAAGT
65 CTCAAATCACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGAGAGAGATCCAATGAAG-
* * * * *
12344 A-AGTGC-TCCAAGAACACCAATTTGATGCGGAATAGGTCCACTCAGCTGATTTTGGGAGAGGTC
129 AGAGTGCTTCCAA-AACACCAATTTGAGGCGGAATAGATCCAATCAACTGATTTTGGGAGAGATC
* *
12407 CAGTGAAGTGAGTGCTCCC-A-AAC
193 CAATGAAGTAAGTGC-CCCAAGAAC
* * *
12430 TACCAATTTGA-GTTGGAATAGGTCCATTCAATTGGTTAC-TCGAGAGGTTTAGTGTA-GTGAGT
1 -ACCAATTTGATG-CGGAATAGGTCCACTCAATTGGTT-CTTCGAGAAGTTTAGTG-ACGTGAGT
*
12492 GCTCTCAAATTACCAATTTGAG
62 GCTCTCAAATCACCAATTTGAG
12514 ATGGAATGCA
Statistics
Matches: 243, Mismatches: 47, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
215 10 0.04
216 226 0.93
217 7 0.03
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (216 bp):
ACCAATTTGATGCGGAATAGGTCCACTCAATTGGTTCTTCGAGAAGTTTAGTGACGTGAGTGCTC
TCAAATCACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGAGAGAGATCCAATGAAGAG
AGTGCTTCCAAAACACCAATTTGAGGCGGAATAGATCCAATCAACTGATTTTGGGAGAGATCCAA
TGAAGTAAGTGCCCCAAGAAC
Found at i:15616 original size:42 final size:45
Alignment explanation
Indices: 15550--15635 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 45
15540 TTTTTTTATT
**
15550 AATTATGGAAAGATTTTGTAAATCTA-AT-ATT-TAATTTTTTGA
1 AATTATGGAAAGATTTAATAAATCTACATAATTGTAATTTTTTGA
15592 AATTATGGAAAGATATTAAT-AATCTACTATAATTGTAATTTTTT
1 AATTATGGAAAGAT-TTAATAAATCTAC-ATAATTGTAATTTTTT
15636 TGTTGGCCAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
42 20 0.54
43 3 0.08
44 2 0.05
45 3 0.08
46 9 0.24
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (45 bp):
AATTATGGAAAGATTTAATAAATCTACATAATTGTAATTTTTTGA
Found at i:20139 original size:72 final size:72
Alignment explanation
Indices: 19951--20158 Score: 263
Period size: 72 Copynumber: 2.9 Consensus size: 72
19941 TATAGCACTT
* * **
19951 ACCAATTTGAGGCGGAATAGCTCCACTCAACTGGTTGTGGGAGAGGTCTAGCGAAATGAGTTTTC
1 ACCAATTTGAGGCGGAATAGCTCCACTCAATTGGTTGTGGGAGAGGTCTAACGAAATGAGTGCTC
*
20016 TCAAATC
66 CCAAATC
* * * *
20023 ACCAATTTCAGGTGGAATAGCTCCACTCAATTGGTTGCGAGAGAGGTCTAACGAAATGAGTGCTC
1 ACCAATTTGAGGCGGAATAGCTCCACTCAATTGGTTGTGGGAGAGGTCTAACGAAATGAGTGCTC
20088 CCAAATC
66 CCAAATC
* * * * * * * *
20095 ACCAATTTGACGCGGAATAGATTCACTCAATTGATTTTGGGAGAGATCCAATGAAATGAGTGCT
1 ACCAATTTGAGGCGGAATAGCTCCACTCAATTGGTTGTGGGAGAGGTCTAACGAAATGAGTGCT
20159 TGCCTTATTA
Statistics
Matches: 115, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 115 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (72 bp):
ACCAATTTGAGGCGGAATAGCTCCACTCAATTGGTTGTGGGAGAGGTCTAACGAAATGAGTGCTC
CCAAATC
Found at i:20337 original size:72 final size:72
Alignment explanation
Indices: 20259--20572 Score: 275
Period size: 72 Copynumber: 4.4 Consensus size: 72
20249 TTTATAGACT
* *
20259 TGAGTGCTGCCAAATCACCAATTTGATGCGGAATCGGTCCACTCAATTGGTTTTGAGAGAGGTCC
1 TGAGTGCTCCCAAATCACCAATTTGATGCGGAATAGGTCCACTCAATTGGTTTTGAGAGAGGTCC
20324 AATGAAG
66 AATGAAG
* * ** * *
20331 TAAGTGC-CCCAAGAACACCAATTTGATGCGGAATAGGTCCACTCAGCTGATTTTGGGAGAGGTC
1 TGAGTGCTCCCAA-ATCACCAATTTGATGCGGAATAGGTCCACTCAATTGGTTTTGAGAGAGGTC
*
20395 CAGTGAAG
65 CAATGAAG
** * * * * *
20403 TGAGTGCTGTCAAATTACCAATTTGACT-TGGAATAGTTCCAATCAACTT-GTTTAGATG-GAGG
1 TGAGTGCTCCCAAATCACCAATTTGA-TGCGGAATAGGTCCACTCAA-TTGGTTTTGA-GAGAGG
*
20465 TCTAATGAAG
63 TCCAATGAAG
* * * *
20475 TGAGTGCTCCCAAAAT-ACCAATTTGA-GTTGGAATAGGTCCATTCAATTGGTTACT-CGAGAGG
1 TGAGTGCTCCC-AAATCACCAATTTGATG-CGGAATAGGTCCACTCAATTGGTT-TTGAGAGAGG
* * *
20537 -CTTAGTGTAG
63 TC-CAATGAAG
*
20547 TGAGTGCTCTCAAATCACCAATTTGA
1 TGAGTGCTCCCAAATCACCAATTTGA
20573 GATGGAATGC
Statistics
Matches: 195, Mismatches: 34, Indels: 26
0.76 0.13 0.10
Matches are distributed among these distances:
71 12 0.06
72 173 0.89
73 10 0.05
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (72 bp):
TGAGTGCTCCCAAATCACCAATTTGATGCGGAATAGGTCCACTCAATTGGTTTTGAGAGAGGTCC
AATGAAG
Found at i:20535 original size:144 final size:144
Alignment explanation
Indices: 20259--20572 Score: 336
Period size: 144 Copynumber: 2.2 Consensus size: 144
20249 TTTATAGACT
* * * *
20259 TGAGTGCTGCCAAATCACCAATTTGATGCGGAATCGGTCCACTCAATTGGTTTTGAGAGAGGTCC
1 TGAGTGCTGTCAAATCACCAATTTGATGCGGAATAGGTCCAATCAATTGGTTTAGAGAGAGGTCC
* * *
20324 AATGAAGTAAGTGCCCCAAGAACACCAATTTGATGCGGAATAGGTCCACTCAGCTGATTTTGGGA
66 AATGAAGTAAGTGCCCCAAGAACACCAATTTGATGCGGAATAGGTCCACTCAACTGATTCTGCGA
20389 GAGG-TCCAGTGAAG
131 GAGGCT-CAGTGAAG
* * *
20403 TGAGTGCTGTCAAATTACCAATTTGACT-TGGAATAGTTCCAATCAACTT-GTTTAGATG-GAGG
1 TGAGTGCTGTCAAATCACCAATTTGA-TGCGGAATAGGTCCAATCAA-TTGGTTTAGA-GAGAGG
* * * * * * *
20465 TCTAATGAAGTGAGTGCTCCCAA-AATACCAATTTGA-GTTGGAATAGGTCCATTCAATTGGTTA
63 TCCAATGAAGTAAGTGC-CCCAAGAACACCAATTTGATG-CGGAATAGGTCCACTCAACTGATT-
* *
20528 CT-CGAGAGGCTTAGTGTAG
125 CTGCGAGAGGCTCAGTGAAG
*
20547 TGAGTGCTCTCAAATCACCAATTTGA
1 TGAGTGCTGTCAAATCACCAATTTGA
20573 GATGGAATGC
Statistics
Matches: 142, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
143 1 0.01
144 130 0.92
145 11 0.08
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (144 bp):
TGAGTGCTGTCAAATCACCAATTTGATGCGGAATAGGTCCAATCAATTGGTTTAGAGAGAGGTCC
AATGAAGTAAGTGCCCCAAGAACACCAATTTGATGCGGAATAGGTCCACTCAACTGATTCTGCGA
GAGGCTCAGTGAAG
Found at i:22208 original size:17 final size:17
Alignment explanation
Indices: 22186--22235 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
22176 ATATCATATG
22186 ATACCATCCATAGAATC
1 ATACCATCCATAGAATC
22203 ATACCATCCATAGAATC
1 ATACCATCCATAGAATC
*
22220 ATACCATCCATGGAAT
1 ATACCATCCATAGAAT
22236 TCGAAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (17 bp):
ATACCATCCATAGAATC
Found at i:22756 original size:31 final size:32
Alignment explanation
Indices: 22682--22747 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
22672 TCATACTAAC
*
22682 AATAAACAACACAATTTTCATAATAATTAAATA
1 AATAAACAACACAA-TTTCATAATAATAAAATA
*
22715 AATAAACAACACAA-TTCATAATCATAAAATA
1 AATAAACAACACAATTTCATAATAATAAAATA
22746 AA
1 AA
22748 ACCACAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 17 0.55
33 14 0.45
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.26
Consensus pattern (32 bp):
AATAAACAACACAATTTCATAATAATAAAATA
Found at i:24176 original size:1 final size:1
Alignment explanation
Indices: 24172--24198 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
24162 AAAAAAATTT
24172 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
24199 GACCTAAGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40481 original size:13 final size:13
Alignment explanation
Indices: 40463--40487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40453 TGTATCATGC
40463 TTTTGAATCCGGT
1 TTTTGAATCCGGT
40476 TTTTGAATCCGG
1 TTTTGAATCCGG
40488 ATAAAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (13 bp):
TTTTGAATCCGGT
Found at i:41659 original size:19 final size:19
Alignment explanation
Indices: 41635--41674 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
41625 ATGTGATTCA
41635 ATTTGAAACTAATTAGACT
1 ATTTGAAACTAATTAGACT
41654 ATTTGAAACTAATTAGACT
1 ATTTGAAACTAATTAGACT
41673 AT
1 AT
41675 AATAACGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTTGAAACTAATTAGACT
Found at i:43338 original size:2 final size:2
Alignment explanation
Indices: 43331--43365 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
43321 GCCTAATTGA
*
43331 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43366 AAGAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:45101 original size:33 final size:33
Alignment explanation
Indices: 45059--45124 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
45049 CAACATCTGT
45059 TTGGTTGAGTGGAAGGAACTTCCAATGAAATTA
1 TTGGTTGAGTGGAAGGAACTTCCAATGAAATTA
45092 TTGGTTGAGTGGAAGGAACTTCCAATGAAATTA
1 TTGGTTGAGTGGAAGGAACTTCCAATGAAATTA
45125 AGTAAGGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (33 bp):
TTGGTTGAGTGGAAGGAACTTCCAATGAAATTA
Found at i:46747 original size:5 final size:5
Alignment explanation
Indices: 46731--46761 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
46721 TCATAACCAA
*
46731 AAACT AAGCT AAACT AAACT AAACT AAACT A
1 AAACT AAACT AAACT AAACT AAACT AAACT A
46762 CTCATTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.19, G:0.03, T:0.19
Consensus pattern (5 bp):
AAACT
Found at i:58412 original size:11 final size:11
Alignment explanation
Indices: 58396--58438 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
58386 TATACTATAT
58396 CTAATTAATAG
1 CTAATTAATAG
*
58407 CTAATTAATAT
1 CTAATTAATAG
58418 CTAATTAATAG
1 CTAATTAATAG
*
58429 TTAATTAATA
1 CTAATTAATA
58439 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:58420 original size:22 final size:22
Alignment explanation
Indices: 58392--58438 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
58382 CCATTATACT
58392 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
58414 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
58436 ATA
1 ATA
58439 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:83941 original size:2 final size:2
Alignment explanation
Indices: 83934--83959 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
83924 CAAGAACATC
83934 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
83960 TTTGAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90988 original size:2 final size:2
Alignment explanation
Indices: 90983--91021 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
90973 TGTGCGTAAT
90983 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
91022 TCTAACCTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:93021 original size:22 final size:22
Alignment explanation
Indices: 92995--93041 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
92985 CTAGTAAATT
** *
92995 ATAGTGTGGTCATCGAAATTTC
1 ATAGTGTAATCATCAAAATTTC
*
93017 ATAGTGTAATTATCAAAATTTC
1 ATAGTGTAATCATCAAAATTTC
93039 ATA
1 ATA
93042 AGAAGTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
ATAGTGTAATCATCAAAATTTC
Found at i:93051 original size:22 final size:22
Alignment explanation
Indices: 93026--93147 Score: 81
Period size: 22 Copynumber: 5.5 Consensus size: 22
93016 CATAGTGTAA
93026 TTATCAAAATTTCATAAGA-AG
1 TTATCAAAATTTCATAAGATAG
*
93047 TTTATCAAAATTTCATAATATAG
1 -TTATCAAAATTTCATAAGATAG
* ** * *
93070 TTACCAAAATTTTGT-TGTATTG
1 TTATCAAAATTTCATAAG-ATAG
* * * **
93092 TTATTAAAATTTTATATGGCAG
1 TTATCAAAATTTCATAAGATAG
93114 TTATCAAAATTAT-ATAAGA-ATG
1 TTATCAAAATT-TCATAAGATA-G
93136 TTATCAAAATTT
1 TTATCAAAATTT
93148 TGGTTTGTGG
Statistics
Matches: 79, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
21 2 0.03
22 72 0.91
23 5 0.06
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGATAG
Found at i:93101 original size:66 final size:66
Alignment explanation
Indices: 93026--93173 Score: 160
Period size: 66 Copynumber: 2.2 Consensus size: 66
93016 CATAGTGTAA
* *
93026 TTATCAAAATTTCATA-AGAAGTTTATCAAAATT-TCATAA-TATAGTTACCAAAATTTT-GTTG
1 TTATTAAAATTTCATATAGAAG-TTATCAAAATTAT-ATAAGAAT-GTTACCAAAATTTTGGTT-
*
93087 TATTG
62 TATGG
* * * * *
93092 TTATTAAAATTTTATATGGCAGTTATCAAAATTATATAAGAATGTTATCAAAATTTTGGTTTGTG
1 TTATTAAAATTTCATATAGAAGTTATCAAAATTATATAAGAATGTTACCAAAATTTTGGTTTATG
93157 G
66 G
93158 TTATTAAAATTTCATA
1 TTATTAAAATTTCATA
93174 GGAATATTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
66 60 0.87
67 9 0.13
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (66 bp):
TTATTAAAATTTCATATAGAAGTTATCAAAATTATATAAGAATGTTACCAAAATTTTGGTTTATG
G
Found at i:94625 original size:17 final size:17
Alignment explanation
Indices: 94588--94625 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
94578 TCATAGTACC
*
94588 TAGGTAGTATGAGATGC
1 TAGGTAGTATGAGATGA
*
94605 TAGGTAGTATGAGGTGA
1 TAGGTAGTATGAGATGA
94622 TAGG
1 TAGG
94626 CTGCATTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.39, T:0.29
Consensus pattern (17 bp):
TAGGTAGTATGAGATGA
Found at i:113939 original size:57 final size:57
Alignment explanation
Indices: 113848--113963 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
113838 AAAATATAAT
* * *
113848 AATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGAGTAA
1 AATAGTAATAAAGATATTAGATTTAATTAAATAAAAATAGACTTTTTAGTTGAGTAA
* *
113905 AATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGACTTTTTAGTTGAGTAA
1 AATAGTAATAAAGATATTAGATTTAATTAAATAAAAATAGACTTTTTAGTTGAGTAA
113962 AA
1 AA
113964 CTATAAAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.47, C:0.01, G:0.13, T:0.39
Consensus pattern (57 bp):
AATAGTAATAAAGATATTAGATTTAATTAAATAAAAATAGACTTTTTAGTTGAGTAA
Done.