Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007121.1 Corchorus capsularis cultivar CVL-1 contig07142, 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: 19738
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Found at i:214 original size:32 final size:32
Alignment explanation
Indices: 178--255 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
168 GGCGGCTCCA
178 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
210 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
*
242 CCCACTAGGGCGGC
1 CCCACTAGGACGGC
256 AAAACTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (32 bp):
CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
Found at i:335 original size:33 final size:33
Alignment explanation
Indices: 293--355 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
283 TAGTACCGGT
* *
293 GCCGCCCTAGGAGGG-CGGCTTGGCCATGGCTCA
1 GCCGCCCTAGG-GGGACGGCCTAGCCATGGCTCA
326 GCCGCCCTAGGGGGACGGCCTAGCCATGGC
1 GCCGCCCTAGGGGGACGGCCTAGCCATGGC
356 ATGCCGTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.13, C:0.35, G:0.40, T:0.13
Consensus pattern (33 bp):
GCCGCCCTAGGGGGACGGCCTAGCCATGGCTCA
Found at i:402 original size:33 final size:31
Alignment explanation
Indices: 358--448 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 31
348 GCCATGGCAT
358 GCCGTCCCCCTGGTGCGGCATTAGCATGGC-CA
1 GCCG-CCCCCTGG-GCGGCATTAGCATGGCTCA
** *
390 GGCCGCTCCCCTGGGGCGGCCCTACCATGGCTCA
1 -GCCGC-CCCCT-GGGCGGCATTAGCATGGCTCA
*
424 GCCGCCCCCTAGGGCGGCATGAGCA
1 GCCGCCCCCT-GGGCGGCATTAGCA
449 ATTTTAGTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
32 16 0.34
33 27 0.57
34 4 0.09
ACGTcount: A:0.12, C:0.41, G:0.33, T:0.14
Consensus pattern (31 bp):
GCCGCCCCCTGGGCGGCATTAGCATGGCTCA
Found at i:3529 original size:43 final size:43
Alignment explanation
Indices: 3476--3562 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
3466 AAATTTGATA
*
3476 TGAATTAAGTTTTCTCACAGATGTGTAACTTGATCATTTGGAC
1 TGAATTAAGTTTTCTCACAGATGAGTAACTTGATCATTTGGAC
* *
3519 TGAATTAAGTTTTCTCAGAGATGAGTAGCTTGATCATTTGGAC
1 TGAATTAAGTTTTCTCACAGATGAGTAACTTGATCATTTGGAC
3562 T
1 T
3563 TTTTTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.39
Consensus pattern (43 bp):
TGAATTAAGTTTTCTCACAGATGAGTAACTTGATCATTTGGAC
Found at i:8817 original size:27 final size:27
Alignment explanation
Indices: 8787--8841 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
8777 TTCCAGGTTA
* * *
8787 GATTTTAATTTTAATTTTTGTTTGTTT
1 GATTTTAATGTTAACTTTTGTTTCTTT
*
8814 GATTTTGATGTTAACTTTTGTTTCTTT
1 GATTTTAATGTTAACTTTTGTTTCTTT
8841 G
1 G
8842 TATGGCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.16, C:0.04, G:0.15, T:0.65
Consensus pattern (27 bp):
GATTTTAATGTTAACTTTTGTTTCTTT
Found at i:9146 original size:14 final size:13
Alignment explanation
Indices: 9106--9206 Score: 54
Period size: 13 Copynumber: 7.6 Consensus size: 13
9096 GCTAGCCAGA
9106 TGACACTCCACACG
1 TGAC-CTCCACACG
9120 TGACCTCCA-ACG
1 TGACCTCCACACG
9132 TACGACC-CCACACG
1 T--GACCTCCACACG
*
9146 TGATCCTCGA-A-G
1 TGA-CCTCCACACG
9158 T-ACAACTCCACACG
1 TGAC--CTCCACACG
9172 TGACCTCCA-ACG
1 TGACCTCCACACG
*
9184 -GACACCTTCAACACG
1 TG--ACC-TCCACACG
9199 TGACCTCC
1 TGACCTCC
9207 GAAGTACAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 31
0.66 0.04 0.30
Matches are distributed among these distances:
10 1 0.01
11 2 0.03
12 15 0.22
13 22 0.32
14 22 0.32
15 5 0.07
16 1 0.01
ACGTcount: A:0.28, C:0.42, G:0.15, T:0.16
Consensus pattern (13 bp):
TGACCTCCACACG
Found at i:9200 original size:27 final size:26
Alignment explanation
Indices: 9111--9227 Score: 132
Period size: 26 Copynumber: 4.5 Consensus size: 26
9101 CCAGATGACA
9111 CTCCACACGTGACCTCCAACGTACGAC
1 CTCCACACGTGACCTCCAACGTAC-AC
* *
9138 C-CCACACGTGATCCTCGAA-GTACAA
1 CTCCACACGTGA-CCTCCAACGTACAC
*
9163 CTCCACACGTGACCTCCAACGGACAC
1 CTCCACACGTGACCTCCAACGTACAC
* *
9189 CTTCAACACGTGACCTCCGAA-GTACAA
1 C-TCCACACGTGACCTCC-AACGTACAC
9216 CTCCACACGTGA
1 CTCCACACGTGA
9228 TCTCGCTCGT
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
25 8 0.11
26 39 0.51
27 27 0.36
28 2 0.03
ACGTcount: A:0.29, C:0.40, G:0.15, T:0.15
Consensus pattern (26 bp):
CTCCACACGTGACCTCCAACGTACAC
Found at i:9219 original size:53 final size:52
Alignment explanation
Indices: 9110--9227 Score: 177
Period size: 53 Copynumber: 2.2 Consensus size: 52
9100 GCCAGATGAC
* *
9110 ACTCCACACGTGACCTCCAACGTACGACCCCACACGTGATCCTCGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGATCCTCGAAGTACA
9162 ACTCCACACGTGACCTCCAACGGAC-ACCTTCAACACGTGA-CCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACC--CAACACGTGATCCT-CGAAGTACA
9215 ACTCCACACGTGA
1 ACTCCACACGTGA
9228 TCTCGCTCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
51 3 0.05
52 27 0.44
53 31 0.51
ACGTcount: A:0.30, C:0.40, G:0.15, T:0.15
Consensus pattern (52 bp):
ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGATCCTCGAAGTACA
Found at i:12857 original size:50 final size:51
Alignment explanation
Indices: 12770--12909 Score: 210
Period size: 50 Copynumber: 2.8 Consensus size: 51
12760 CAAACATGGG
* *
12770 ATGGGCGCTCGACCCACCATCTTCATGTGTGGGCGAGCGCCAACCCCATAT
1 ATGGGCGCTCGACCCACCATCTTCATGTGTGGTCGAGCGCCAACCCCATAC
* * *
12821 TTGGGTGCTCGACCCA-CATCTTCACGTGTGGTCGAGCGCCAACCCCATAC
1 ATGGGCGCTCGACCCACCATCTTCATGTGTGGTCGAGCGCCAACCCCATAC
* *
12871 ATGGGCGCTCGACCCACCATCTCCATATGTGGTCGAGCG
1 ATGGGCGCTCGACCCACCATCTTCATGTGTGGTCGAGCG
12910 ACCACGCTCG
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 45 0.58
51 33 0.42
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.21
Consensus pattern (51 bp):
ATGGGCGCTCGACCCACCATCTTCATGTGTGGTCGAGCGCCAACCCCATAC
Found at i:13313 original size:14 final size:13
Alignment explanation
Indices: 13278--13347 Score: 51
Period size: 13 Copynumber: 5.4 Consensus size: 13
13268 CCAGATGGCA
13278 CTCCACACGTGAC
1 CTCCACACGTGAC
13291 CTCCA-ACGTACGAC
1 CTCCACACGT--GAC
13305 C-CCACACGTGATC
1 CTCCACACGTGA-C
*
13318 CTCGA-A-GT-AC
1 CTCCACACGTGAC
13328 AACTCCACACGTGAC
1 --CTCCACACGTGAC
13343 CTCCA
1 CTCCA
13348 ACGGACACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
10 1 0.02
11 1 0.02
12 12 0.27
13 17 0.38
14 12 0.27
15 2 0.04
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (13 bp):
CTCCACACGTGAC
Found at i:13367 original size:27 final size:26
Alignment explanation
Indices: 13278--13394 Score: 114
Period size: 26 Copynumber: 4.5 Consensus size: 26
13268 CCAGATGGCA
13278 CTCCACACGTGACCTCCAACGTACGAC
1 CTCCACACGTGACCTCCAACGTAC-AC
* *
13305 C-CCACACGTGATCCTCGAA-GTACAA
1 CTCCACACGTGA-CCTCCAACGTACAC
*
13330 CTCCACACGTGACCTCCAACGGACAC
1 CTCCACACGTGACCTCCAACGTACAC
* ** *
13356 CTTCAACACGTGACCTTTGAA-GTACAA
1 C-TCCACACGTGACC-TCCAACGTACAC
13383 CTCCACACGTGA
1 CTCCACACGTGA
13395 TCTCGCGCGT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
25 8 0.11
26 39 0.53
27 24 0.32
28 3 0.04
ACGTcount: A:0.29, C:0.38, G:0.15, T:0.17
Consensus pattern (26 bp):
CTCCACACGTGACCTCCAACGTACAC
Found at i:13387 original size:53 final size:52
Alignment explanation
Indices: 13277--13394 Score: 168
Period size: 53 Copynumber: 2.2 Consensus size: 52
13267 GCCAGATGGC
* *
13277 ACTCCACACGTGACCTCCAACGTACGACCCCACACGTGATCCTCGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGATCCTCGAAGTACA
*
13329 ACTCCACACGTGACCTCCAACGGAC-ACCTTCAACACGTGA-CCTTTGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACC--CAACACGTGATCC-TCGAAGTACA
13382 ACTCCACACGTGA
1 ACTCCACACGTGA
13395 TCTCGCGCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
51 3 0.05
52 26 0.43
53 31 0.52
ACGTcount: A:0.30, C:0.38, G:0.15, T:0.17
Consensus pattern (52 bp):
ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGATCCTCGAAGTACA
Found at i:16349 original size:110 final size:110
Alignment explanation
Indices: 16139--16375 Score: 343
Period size: 110 Copynumber: 2.2 Consensus size: 110
16129 CGTAGCCAAA
* *
16139 AGTGCCTTTCCTT-TTGTTGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATTTTAACTTG
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATTTTAACTTG
* * *
16203 GAGTGAGTGCACCCATAGGAGTGCTGCATTGGTTGCACCTCCAGG
66 GAGAGAGTGCACCCATAGGAGTGCTGCACTGATTGCACCTCCAGG
* * *
16248 AGTGCCCTTCATTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATTTATATTTTGACTTG
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATTTTAACTTG
* * *
16313 GAGCAG-GTGCACCCTTAGGGGTGTTGCACTGATTGCACCTCCAGG
66 GAG-AGAGTGCACCCATAGGAGTGCTGCACTGATTGCACCTCCAGG
*
16358 AGTGCCCCTCCTTGTTGA
1 AGTGCCCTTCCTTGTTGA
16376 CACTTCTAGC
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
109 11 0.10
110 101 0.89
111 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (110 bp):
AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAAATCTATATTTTAACTTG
GAGAGAGTGCACCCATAGGAGTGCTGCACTGATTGCACCTCCAGG
Found at i:16531 original size:29 final size:29
Alignment explanation
Indices: 16488--16595 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
16478 AAAGAAAGCT
16488 TACTATCAGCCTATGCAGCTTTACAACGCC
1 TACTA-CAGCCTATGCAGCTTTACAACGCC
* * * * *
16518 TACTACAGTCTATGCAGCTTAAAAAAGGCT
1 TACTACAGCCTATGCAGCTT-TACAACGCC
*
16548 TACTAC-GCCTA--CAGCTTTGCAACGCC
1 TACTACAGCCTATGCAGCTTTACAACGCC
*
16574 TACTATAGCCTATGCAGCTTTA
1 TACTACAGCCTATGCAGCTTTA
16596 AAAAGGGCTT
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
26 9 0.15
27 11 0.18
29 25 0.41
30 16 0.26
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (29 bp):
TACTACAGCCTATGCAGCTTTACAACGCC
Found at i:16575 original size:56 final size:60
Alignment explanation
Indices: 16485--16607 Score: 173
Period size: 56 Copynumber: 2.1 Consensus size: 60
16475 AAGAAAGAAA
*
16485 GCTTACTATCAGCCTATGCAGCTTTACAACGCCTACTACAGTCTATGCAGC-TTAAAAAAG
1 GCTTACTATCAGCCTA-GCAGCTTTACAACGCCTACTACAGCCTATGCAGCTTTAAAAAAG
* * *
16545 GCTTACTA-C-GCCTA-CAGCTTTGCAACGCCTACTATAGCCTATGCAGCTTTAAAAAGG
1 GCTTACTATCAGCCTAGCAGCTTTACAACGCCTACTACAGCCTATGCAGCTTTAAAAAAG
16602 GCTTAC
1 GCTTAC
16608 AATACCTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
56 30 0.52
57 14 0.24
58 5 0.09
59 1 0.02
60 8 0.14
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (60 bp):
GCTTACTATCAGCCTAGCAGCTTTACAACGCCTACTACAGCCTATGCAGCTTTAAAAAAG
Found at i:17015 original size:50 final size:49
Alignment explanation
Indices: 16931--17032 Score: 141
Period size: 50 Copynumber: 2.1 Consensus size: 49
16921 CACTTTCTCT
* *
16931 TATGGTGTTGGAAGATTGTCGTCGCTGCTTCATATAGTTGGAAGCTCCA
1 TATGGTGTTGGAAGATTATCGTCGCTGCTTCATATAGCTGGAAGCTCCA
* * * *
16980 TATGGTGTTGGAAAGATTATCGTTGTTGTTTCATATAGCTGGAAGTTCCA
1 TATGGTGTTGG-AAGATTATCGTCGCTGCTTCATATAGCTGGAAGCTCCA
17030 TAT
1 TAT
17033 CCCGTTGGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 11 0.24
50 35 0.76
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (49 bp):
TATGGTGTTGGAAGATTATCGTCGCTGCTTCATATAGCTGGAAGCTCCA
Found at i:17040 original size:50 final size:50
Alignment explanation
Indices: 16937--17043 Score: 126
Period size: 50 Copynumber: 2.2 Consensus size: 50
16927 CTCTTATGGT
* * ***
16937 GTTGG-AAGATTGTCGTCGCTGCTTCATATAGTTGGAAGCTCCATATGGT
1 GTTGGAAAGATTATCGTCGCTGCTTCATATAGCTGGAAGCTCCATATCCC
* * * *
16986 GTTGGAAAGATTATCGTTGTTGTTTCATATAGCTGGAAGTTCCATATCCC
1 GTTGGAAAGATTATCGTCGCTGCTTCATATAGCTGGAAGCTCCATATCCC
17036 GTTGGAAA
1 GTTGGAAA
17044 TTTAACATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
49 5 0.10
50 43 0.90
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (50 bp):
GTTGGAAAGATTATCGTCGCTGCTTCATATAGCTGGAAGCTCCATATCCC
Found at i:17166 original size:45 final size:45
Alignment explanation
Indices: 17111--17379 Score: 161
Period size: 45 Copynumber: 5.9 Consensus size: 45
17101 CCTTCCTCCA
*
17111 ACAAAAATTATACCCTCTTCCAACATGGTGGTGGCGCTTCCAATG
1 ACAAAATTTATACCCTCTTCCAACATGGTGGTGGCGCTTCCAATG
* * ** * ** *
17156 ACAAAAATTATACCATCTT-C--CATGGTGGCTTCCAACGACAATATTG
1 ACAAAATTTATACCCTCTTCCAACATGGTGG-TGGC-GCTTCCA-A-TG
* * * * * * *
17202 TCAAGATTTATGCACGCTTCCAGCATGGTGGTGGTGCTTCCAACAT-
1 ACAAAATTTATACCCTCTTCCAACATGGTGGTGGCGCTTCC-A-ATG
* * * * *
17248 ACAAAATTTATATCCTCTTCCAACATGATTGTGGCGCCTCCAATC
1 ACAAAATTTATACCCTCTTCCAACATGGTGGTGGCGCTTCCAATG
* * * **
17293 ACAAAATTTGTACGCTCTTCCAACATGAG-GGTGGCTCTTCCAGCG
1 ACAAAATTTATACCCTCTTCCAACATG-GTGGTGGCGCTTCCAATG
* ** * *
17338 ATAAAATTTATATGCGCTTCCAACATGGTGGTTGCGCTTCCA
1 ACAAAATTTATACCCTCTTCCAACATGGTGGTGGCGCTTCCA
17380 TCATGATGCT
Statistics
Matches: 164, Mismatches: 49, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
42 8 0.05
43 2 0.01
44 7 0.04
45 88 0.54
46 44 0.27
47 4 0.02
48 3 0.02
49 8 0.05
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (45 bp):
ACAAAATTTATACCCTCTTCCAACATGGTGGTGGCGCTTCCAATG
Found at i:17375 original size:20 final size:19
Alignment explanation
Indices: 17350--17402 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
17340 AAAATTTATA
* *
17350 TGCGCTTCCAACATGGTGGT
1 TGCGCTTCCAACATGAT-GC
*
17370 TGCGCTTCCATCATGATGC
1 TGCGCTTCCAACATGATGC
17389 TGACGCTTCCAACA
1 TG-CGCTTCCAACA
17403 GAGAGCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (19 bp):
TGCGCTTCCAACATGATGC
Found at i:17579 original size:45 final size:45
Alignment explanation
Indices: 17511--17620 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 45
17501 TATGGTGATT
** * *
17511 CTTCCAAACATGGTGACGACGCTTCCAATGA-CAAAATTTATACCCA
1 CTTCC-AACATGGTGGTGTCGCTTCCAATGATCAAAA-TTACACCCA
* ** *
17557 CTTCCAACATGGTGGTGTCGCTTCCAATGATCAGAATTACATGCT
1 CTTCCAACATGGTGGTGTCGCTTCCAATGATCAAAATTACACCCA
17602 CTTCCAACATGGTGGTGTC
1 CTTCCAACATGGTGGTGTC
17621 AAATATCTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 46 0.84
46 9 0.16
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (45 bp):
CTTCCAACATGGTGGTGTCGCTTCCAATGATCAAAATTACACCCA
Found at i:17660 original size:54 final size:55
Alignment explanation
Indices: 17576--17760 Score: 203
Period size: 54 Copynumber: 3.3 Consensus size: 55
17566 TGGTGGTGTC
**
17576 GCTTCCAATGATC-AGAATTACATGCTCTTCCAACATGGTGGTGTCAAATAT-CTT
1 GCTTCCAATGA-CAAGAATTACACCCTCTTCCAACATGGTGGTGTCAAATATACTT
* * *
17630 GTTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGGTGTCGAATATCACTT
1 GCTTCCAATGACAAGAATTACACCCTCTTCCAACATGGTGGTGTCAAATAT-ACTT
* * * * * * *
17686 GCTTCCAATGACAAGAATTATACTCTCTTCTCAACATGATGGTGTCGATTAGCACTC
1 GCTTCCAATGACAAGAATTACACCCTCTTC-CAACATGGTGGTGTCAAATA-TACTT
*
17743 GCTTCCAATGATAAGAAT
1 GCTTCCAATGACAAGAAT
17761 CATACTCTCT
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 44 0.39
56 30 0.27
57 37 0.33
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (55 bp):
GCTTCCAATGACAAGAATTACACCCTCTTCCAACATGGTGGTGTCAAATATACTT
Found at i:17759 original size:57 final size:55
Alignment explanation
Indices: 17574--17771 Score: 213
Period size: 57 Copynumber: 3.6 Consensus size: 55
17564 CATGGTGGTG
* *
17574 TCGCTTCCAATGATC-AGAATTACA-TGCTCTTCCAACATGGTGGTGTCAAATA-TC
1 TCGCTTCCAATGA-CAAGAATTACACT-CTCTTCCAACATGGTGGTGTCGAATACAC
* * * *
17628 TTGTTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGGTGTCGAATATCAC
1 TCGCTTCCAATGACAAGAATTACACTCTCTTCCAACATGGTGGTGTCGAATA-CAC
* * * *
17684 TTGCTTCCAATGACAAGAATTATACTCTCTTCTCAACATGATGGTGTCGATTAGCAC
1 TCGCTTCCAATGACAAGAATTACACTCTCTTC-CAACATGGTGGTGTCGAATA-CAC
* * *
17741 TCGCTTCCAATGATAAGAATCATACTCTCTT
1 TCGCTTCCAATGACAAGAATTACACTCTCTT
17772 TTCCAGCAGT
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 44 0.36
56 30 0.24
57 48 0.39
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (55 bp):
TCGCTTCCAATGACAAGAATTACACTCTCTTCCAACATGGTGGTGTCGAATACAC
Found at i:18303 original size:36 final size:36
Alignment explanation
Indices: 18263--18382 Score: 152
Period size: 36 Copynumber: 3.3 Consensus size: 36
18253 GCTCTGTTTC
* *
18263 TGGCTATAATGCTGATGGCCTAAGTCGCCTAATACT
1 TGGCTATAATGCTGATGGCCTAAGTCGCCCAATAAT
* *
18299 TGGCTATAATGCCGATGGCCTAAGTCGCCCAAAAAT
1 TGGCTATAATGCTGATGGCCTAAGTCGCCCAATAAT
* * * *
18335 TGGCTATAAAGCTGCTGACC-ATAGTCGCCCAATATT
1 TGGCTATAATGCTGATGGCCTA-AGTCGCCCAATAAT
18371 TGGCTATAATGC
1 TGGCTATAATGC
18383 CACTGGCCTT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 1 0.01
36 71 0.99
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (36 bp):
TGGCTATAATGCTGATGGCCTAAGTCGCCCAATAAT
Found at i:18616 original size:46 final size:46
Alignment explanation
Indices: 18544--18728 Score: 228
Period size: 46 Copynumber: 4.0 Consensus size: 46
18534 AGGAGATGCA
* * **
18544 TCTTATGTGAGCACACTTCTGCAGAAAGAATACTCTATACAATAGC
1 TCTTATGTGAGCACACATCTTCAGAAAGAATACTCTATACGGTAGC
* * * * *
18590 TTTTATGTGAGCACACTTCTTAAGAAAGAATACTTTATACGGTAAC
1 TCTTATGTGAGCACACATCTTCAGAAAGAATACTCTATACGGTAGC
* *
18636 TCTTATGTGAGCAGC-CATCTTCAGAAGGAATTCTCTATACGGTAGC
1 TCTTATGTGAGCA-CACATCTTCAGAAAGAATACTCTATACGGTAGC
* * *
18682 TCTTATGTGAGCACCCATCTTCAGAAGGAATTCTCTATACGGTAGC
1 TCTTATGTGAGCACACATCTTCAGAAAGAATACTCTATACGGTAGC
18728 T
1 T
18729 TCTTGCAAAG
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 121 0.98
47 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (46 bp):
TCTTATGTGAGCACACATCTTCAGAAAGAATACTCTATACGGTAGC
Done.