Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011217.1 Corchorus capsularis cultivar CVL-1 contig11238, 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: 28816
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:12934 original size:2 final size:2
Alignment explanation
Indices: 12922--12957 Score: 54
Period size: 2 Copynumber: 17.0 Consensus size: 2
12912 TTGCAAGATC
12922 AT AT AT CAT AT AT CAT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
12958 TGTATCCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 28 0.88
3 4 0.12
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12938 original size:14 final size:13
Alignment explanation
Indices: 12919--12957 Score: 62
Period size: 12 Copynumber: 3.0 Consensus size: 13
12909 GTATTGCAAG
12919 ATCATATATCATAT
1 ATCATATAT-ATAT
12933 ATCATATATATAT
1 ATCATATATATAT
12946 AT-ATATATATAT
1 ATCATATATATAT
12958 TGTATCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 10 0.40
13 6 0.24
14 9 0.36
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATCATATATATAT
Found at i:14322 original size:33 final size:33
Alignment explanation
Indices: 14278--14343 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
14268 TCTGACTTCA
* *
14278 ATTAATAGTGTTTCCACCTTTTTAAATTGCATG
1 ATTAATAGTGTTCCCACCTTTTCAAATTGCATG
*
14311 ATTAATGGTGTTCCCACCTTTTCAAATTGCATG
1 ATTAATAGTGTTCCCACCTTTTCAAATTGCATG
14344 CCCTTTATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (33 bp):
ATTAATAGTGTTCCCACCTTTTCAAATTGCATG
Found at i:15964 original size:32 final size:32
Alignment explanation
Indices: 15927--16124 Score: 220
Period size: 32 Copynumber: 5.9 Consensus size: 32
15917 TATTGACTCC
* *
15927 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCCTGAATTAAGTCCTTTATTCT
*
15959 ACTTAATTACCATGAATTAAG-CCTTTTATTGACT
1 ACTTAATTACCCTGAATTAAGTCC-TTTATT--CT
* *
15993 CCACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 --ACTTAATTACCCTGAATTAAGTCCTTTATTCT
16027 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACT
1 ACTTAATTACCCTGAATTAAGTCC-TTTATT--CT
* *
16061 CCACTTAATTACCCTGAATTAAATTCTTTATTCT
1 --ACTTAATTACCCTGAATTAAGTCCTTTATTCT
*
16095 ACTTAATTACCCTGAATTAAGCCCTTTATT
1 ACTTAATTACCCTGAATTAAGTCCTTTATT
16125 GACTCTACTT
Statistics
Matches: 143, Mismatches: 11, Indels: 24
0.80 0.06 0.13
Matches are distributed among these distances:
31 2 0.01
32 79 0.55
34 8 0.06
36 52 0.36
37 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTCCTTTATTCT
Found at i:15995 original size:68 final size:68
Alignment explanation
Indices: 15905--16138 Score: 414
Period size: 68 Copynumber: 3.4 Consensus size: 68
15895 ATCTTTTTAG
15905 ATTAAGCCCTTTTATTGACTCCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACC
1 ATTAAG-CCTTTTATTGACTCCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACC
*
15970 ATGA
65 CTGA
15974 ATTAAGCCTTTTATTGACTCCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACCC
1 ATTAAGCCTTTTATTGACTCCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACCC
16039 TGA
66 TGA
* *
16042 ATTAAGCCTTTTATTGACTCCACTTAATTACCCTGAATTAAATTCTTTATTCTACTTAATTACCC
1 ATTAAGCCTTTTATTGACTCCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACCC
16107 TGA
66 TGA
* *
16110 ATTAAGCCCTTTATTGACTCTACTTAATT
1 ATTAAGCCTTTTATTGACTCCACTTAATT
16139 TGCTTCCCTG
Statistics
Matches: 160, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 154 0.96
69 6 0.04
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.44
Consensus pattern (68 bp):
ATTAAGCCTTTTATTGACTCCACTTAATTACCTTGAATTAAGTTCTTTATTCTACTTAATTACCC
TGA
Found at i:16179 original size:41 final size:40
Alignment explanation
Indices: 16134--16425 Score: 356
Period size: 41 Copynumber: 7.1 Consensus size: 40
16124 TGACTCTACT
* * *
16134 TAATTTGCTTCCCTGAAATTAAGTCTATGCCTGT-CTTTACC
1 TAATTT-CTTCCTTGAAATTAAGTCTGTG-CTTTACTTTACC
*
16175 TAATTTCTTTCGTTGAAATTAAGTCTGTGCTTTACTTTACC
1 TAATTTC-TTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
*
16216 TAATTTCTTTGCTTGAAATTAAGTCTGTGCTTTACTTTACC
1 TAATTTC-TTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
* *
16257 TAATTTCATTCCTTGAAATGAAGTAC-ATGCTTTACTTTACC
1 TAATTTC-TTCCTTGAAATTAAGT-CTGTGCTTTACTTTACC
* *
16298 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTATC
1 TAATTT-CTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
* *
16339 TAATTTCCATCCTTGAAATTAAGTTTGTGCTTTACTTTACC
1 TAATTT-CTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
* *
16380 TAATTTCCTTCCTTGAAATAAAGTATGTGC-TTATCTTTACC
1 TAATTT-CTTCCTTGAAATTAAGTCTGTGCTTTA-CTTTACC
16421 TAATT
1 TAATT
16426 ACCATGACTT
Statistics
Matches: 226, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
40 7 0.03
41 217 0.96
42 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (40 bp):
TAATTTCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
Found at i:16300 original size:123 final size:123
Alignment explanation
Indices: 16167--16425 Score: 394
Period size: 123 Copynumber: 2.1 Consensus size: 123
16157 TCTATGCCTG
* * ** *
16167 TCTTTACCTAATTTCTTTCGTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCTTTGCTTGA
1 TCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCATCCTTGA
*
16232 AATTAAGTCTGTGCTTTACTTTACCTAATTTCATTCCTTGAAATGAAGTACATGCTT-
66 AATTAAGTCTGTGCTTTACTTTACCTAATTTCATTCCTTGAAATAAAGTACATGCTTA
* *
16289 TACTTTACCTAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTTATCTAATTTCCATCCTTG
1 T-CTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCATCCTTG
* * **
16354 AAATTAAGTTTGTGCTTTACTTTACCTAATTTCCTTCCTTGAAATAAAGTATGTGCTTA
65 AAATTAAGTCTGTGCTTTACTTTACCTAATTTCATTCCTTGAAATAAAGTACATGCTTA
16413 TCTTTACCTAATT
1 TCTTTACCTAATT
16426 ACCATGACTT
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
122 1 0.01
123 121 0.98
124 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.47
Consensus pattern (123 bp):
TCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCATCCTTGA
AATTAAGTCTGTGCTTTACTTTACCTAATTTCATTCCTTGAAATAAAGTACATGCTTA
Found at i:16475 original size:37 final size:37
Alignment explanation
Indices: 16415--16531 Score: 155
Period size: 37 Copynumber: 3.2 Consensus size: 37
16405 TGTGCTTATC
* *
16415 TTTACCTAATTACCATGACTTAAGTCCTTTAACTGCT
1 TTTACTTAATTACCATGAATTAAGTCCTTTAACTGCT
* * *
16452 TTTACTTAATTTCCTTGAATTAAG-CCATTTGACTGCT
1 TTTACTTAATTACCATGAATTAAGTCC-TTTAACTGCT
* *
16489 TTTACTTAATTGCCATGAATTAAGTCCTTTAACTACT
1 TTTACTTAATTACCATGAATTAAGTCCTTTAACTGCT
16526 TTTACT
1 TTTACT
16532 CCCTCCGTCC
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.03
37 65 0.94
38 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (37 bp):
TTTACTTAATTACCATGAATTAAGTCCTTTAACTGCT
Found at i:16899 original size:41 final size:41
Alignment explanation
Indices: 16839--16976 Score: 115
Period size: 39 Copynumber: 3.7 Consensus size: 41
16829 AAGACTTTGT
*
16839 TTTTCTTAATTGCCC--AATTAAGACTTTAATTATGCTTAC
1 TTTTCTTAATTACCCTGAATTAAGACTTTAATTATGCTTAC
* *
16878 TTTTCGTAATTACCCTGAATTAA-A----ACTT-TG--T--
1 TTTTCTTAATTACCCTGAATTAAGACTTTAATTATGCTTAC
* * * *
16909 TTTTCTTAATTA-CC-AAATTAAGACCTTGATTATGCTCAC
1 TTTTCTTAATTACCCTGAATTAAGACTTTAATTATGCTTAC
16948 TTTTCTTAATTACCCTGAATTAAGACTTT
1 TTTTCTTAATTACCCTGAATTAAGACTTT
16977 GCTTTTCTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
29 6 0.08
30 3 0.04
31 11 0.15
33 1 0.01
34 2 0.03
35 4 0.05
36 3 0.04
39 25 0.33
40 3 0.04
41 17 0.23
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (41 bp):
TTTTCTTAATTACCCTGAATTAAGACTTTAATTATGCTTAC
Found at i:17319 original size:70 final size:70
Alignment explanation
Indices: 16784--17308 Score: 773
Period size: 70 Copynumber: 7.5 Consensus size: 70
16774 AATTTCCTTG
* * * * *
16784 AATTAAGCCCCTGACTGTGTTTACTCTTCTTAATTACCCTGAATTAAGACTTTGTTTTTCTTAAT
1 AATTAAGACCTTGACTGTGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
* *
16849 TGCCC
66 TACCA
* * * * * * *
16854 AATTAAGACTTTAATTATGCTTACTTTTCGTAATTACCCTGAATTAAAACTTTGTTTTTCTTAAT
1 AATTAAGACCTTGACTGTGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
16919 TACCA
66 TACCA
* * *
16924 AATTAAGACCTTGATTATGCTCACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
1 AATTAAGACCTTGACTGTGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
16989 TACCA
66 TACCA
* * *
16994 AATTGAGACCTTGACTGTGATTACTTTTCTTAATTACCATGAATTAAGACTTTGCTTTTCTTAAT
1 AATTAAGACCTTGACTGTGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
17059 TACCA
66 TACCA
* * * *
17064 AATTAGGACCTCGACTGTGTTTACTTTTCTTAATTACCCTGAATTAAGACTTTGTTTTTCTTAAT
1 AATTAAGACCTTGACTGTGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
17129 TACCA
66 TACCA
*
17134 AATTAAGACCTTGACTGTG-TTCACTTTTCTTAATTACTCTGAATTAAGACTTTGCTTTTCTTAA
1 AATTAAGACCTTGACTGTGCTT-ACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAA
17198 TTACCA
65 TTACCA
* *
17204 AATTAAGACCTTGATTATGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
1 AATTAAGACCTTGACTGTGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
17269 TACCA
66 TACCA
* *
17274 AATTAGGACCTTGACTGTGGTTACTTTTCTTAATT
1 AATTAAGACCTTGACTGTGCTTACTTTTCTTAATT
17309 TTTCTTAATT
Statistics
Matches: 412, Mismatches: 41, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
69 2 0.00
70 408 0.99
71 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.10, T:0.44
Consensus pattern (70 bp):
AATTAAGACCTTGACTGTGCTTACTTTTCTTAATTACCCTGAATTAAGACTTTGCTTTTCTTAAT
TACCA
Found at i:21787 original size:64 final size:64
Alignment explanation
Indices: 21710--21839 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
21700 TGATGCAGCG
21710 TGTTTTTATTAAGTCTTTAGTTTAATTTTTATTTCTGTCCTTATTTTTAGATTTAGGTTAGTAA
1 TGTTTTTATTAAGTCTTTAGTTTAATTTTTATTTCTGTCCTTATTTTTAGATTTAGGTTAGTAA
21774 TGTTTTTATTAAGTCTTTAGTTTAATTTTTATTTCTGTCCTTATTTTTAGATTTAGGTTAGTAA
1 TGTTTTTATTAAGTCTTTAGTTTAATTTTTATTTCTGTCCTTATTTTTAGATTTAGGTTAGTAA
21838 TG
1 TG
21840 GGCTTTATAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.22, C:0.06, G:0.13, T:0.59
Consensus pattern (64 bp):
TGTTTTTATTAAGTCTTTAGTTTAATTTTTATTTCTGTCCTTATTTTTAGATTTAGGTTAGTAA
Found at i:23792 original size:18 final size:18
Alignment explanation
Indices: 23735--23794 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
23725 TTTCCTTTGA
*
23735 TAAATTAAACAAAATCTT
1 TAAAATAAACAAAATCTT
* * *
23753 TAAAAGAAATAAAAT-TAC
1 TAAAATAAACAAAATCT-T
*
23771 TAAACTAAACAAAATCTT
1 TAAAATAAACAAAATCTT
23789 TAAAAT
1 TAAAAT
23795 TATTATGTAT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAAATAAACAAAATCTT
Found at i:25631 original size:27 final size:27
Alignment explanation
Indices: 25600--25663 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
25590 ATTTCTGGAA
25600 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
*
25627 AACAAGAGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
25654 AACAGAGGGA
1 AACA-AGGGA
25664 GTATATTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 30 0.88
28 4 0.12
ACGTcount: A:0.56, C:0.08, G:0.27, T:0.09
Consensus pattern (27 bp):
AACAAGGGAAATGGACAATTAAAAAGG
Found at i:27170 original size:51 final size:51
Alignment explanation
Indices: 27049--27502 Score: 550
Period size: 51 Copynumber: 8.8 Consensus size: 51
27039 GCCCACCCCC
*
27049 AAACCCATTATGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATTATGATT
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGG---ATTATGATT
* *
27103 AAACCCATTGTGATTTTCAACCACTGCTCCTCCAACTAATGGATTATGATT
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATGATT
*
27154 GAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATGATT
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATGATT
* * * * *
27205 GAACCCATAGTAATTTTCAACCATTGCTCCTCCAACAAATGGATTATGATT
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATGATT
* * *
27256 AAACTCATTGTGATTTTCAAGCATTTCTCCTGCAACTAATGGATTATTATGATT
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGG---ATTATGATT
*
27310 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAAAGGATTATGATT
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATGATT
* * * ***
27361 AAACCCATTGTGATTTTCAACCATTGCTCCTCCAGCTAATTGG-TTCTGCCC
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAA-TGGATTATGATT
* * * * * * ***
27412 AAACCCATTATGATTTTCAAACATGGCTTCTCCAGCTAATTGATTATGCCC
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATGATT
* * * *
27463 AAACCCAATATGATTTCCAAGCATTGCTCCTCCAGCTAAT
1 AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAAT
27503 TGCAATTGGT
Statistics
Matches: 355, Mismatches: 40, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
50 2 0.01
51 265 0.75
52 2 0.01
54 86 0.24
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
AAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATGATT
Found at i:27334 original size:156 final size:154
Alignment explanation
Indices: 27061--27501 Score: 521
Period size: 156 Copynumber: 2.8 Consensus size: 154
27051 ACCCATTATG
* *
27061 ATTTTCAAGCATTGCTCCTCCAACTAATGGATTATTATGATTAAACCCATTGTGATTTTCAACCA
1 ATTTTCAACCATTGCTCCTCCAACAAATGG--TATTATGATTAAACCCATTGTGATTTTCAACCA
*
27126 CTGCTCCTCCAACTAATGGATTATGATTGAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACT
64 CTGCTCCTCCAACTAATGGATTATGATTAAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACT
* *
27191 AATGGATTATGATTGAACCCATAGTA
129 AAAGGATTATGATTAAACCCATAGTA
* * *
27217 ATTTTCAACCATTGCTCCTCCAACAAATGG-ATTATGATTAAACTCATTGTGATTTTCAAGCATT
1 ATTTTCAACCATTGCTCCTCCAACAAATGGTATTATGATTAAACCCATTGTGATTTTCAACCACT
* *
27281 TCTCCTGCAACTAATGGATTATTATGATTAAACCCATTGTGATTTTCAAGCATTGCTCCTCCAAC
66 GCTCCTCCAACTAATGG---ATTATGATTAAACCCATTGTGATTTTCAAGCATTGCTCCTCCAAC
* *
27346 TAAAGGATTATGATTAAACCCATTGTG
128 TAAAGGATTATGATTAAACCCATAGTA
* * * *** * *
27373 ATTTTCAACCATTGCTCCTCCAGCTAATTGG--TTCTGCCCAAACCCATTATGATTTTCAAACA-
1 ATTTTCAACCATTGCTCCTCCAAC-AAATGGTATTATGATTAAACCCATTGTGATTTTCAACCAC
* * * *** * * * *
27435 TGGCTTCTCCAGCTAATTGATTATGCCCAAACCCAATATGATTTCCAAGCATTGCTCCTCCAGCT
65 T-GCTCCTCCAACTAATGGATTATGATTAAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACT
27500 AA
129 AA
27502 TTGCAATTGG
Statistics
Matches: 247, Mismatches: 33, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
153 87 0.35
155 1 0.00
156 154 0.62
157 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (154 bp):
ATTTTCAACCATTGCTCCTCCAACAAATGGTATTATGATTAAACCCATTGTGATTTTCAACCACT
GCTCCTCCAACTAATGGATTATGATTAAACCCATTGTGATTTTCAAGCATTGCTCCTCCAACTAA
AGGATTATGATTAAACCCATAGTA
Found at i:27419 original size:207 final size:207
Alignment explanation
Indices: 27049--27502 Score: 624
Period size: 207 Copynumber: 2.2 Consensus size: 207
27039 GCCCACCCCC
27049 AAACCCATTATGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATTATGATTAAACCCATTGT
1 AAACCCATTATGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATTATGATTAAACCCATTGT
* * *
27114 GATTTTCAACCACTGCTCCTCCAACTAATGGATTATGATTGAACCCATTGTGATTTTCAAGCATT
66 GATTTTCAACCACTGCTCCTCCAACTAAAGGATTATGATTAAACCCATTGTGATTTTCAACCATT
*** * *
27179 GCTCCTCCAACTAATGGATTATGATTGAACCCA-TAGTAATTTTCAACCATTGCTCCTCCAACAA
131 GCTCCTCCAACTAATGGATTATGACCAAACCCATTA-TAATTTTCAAACATGGCTCCTCCAACAA
27243 ATGGATTATGATT
195 ATGGATTATGATT
* * * *
27256 AAACTCATTGTGATTTTCAAGCATTTCTCCTGCAACTAATGGATTATTATGATTAAACCCATTGT
1 AAACCCATTATGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATTATGATTAAACCCATTGT
* *
27321 GATTTTCAAGCATTGCTCCTCCAACTAAAGGATTATGATTAAACCCATTGTGATTTTCAACCATT
66 GATTTTCAACCACTGCTCCTCCAACTAAAGGATTATGATTAAACCCATTGTGATTTTCAACCATT
* * * * * * *
27386 GCTCCTCCAGCTAATTGG-TTCTGCCCAAACCCATTATGATTTTCAAACATGGCTTCTCCAGCTA
131 GCTCCTCCAACTAA-TGGATTATGACCAAACCCATTATAATTTTCAAACATGGCTCCTCCAACAA
* ***
27450 ATTGATTATGCCC
195 ATGGATTATGATT
* * *
27463 AAACCCAATATGATTTCCAAGCATTGCTCCTCCAGCTAAT
1 AAACCCATTATGATTTTCAAGCATTGCTCCTCCAACTAAT
27503 TGCAATTGGT
Statistics
Matches: 213, Mismatches: 32, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
207 208 0.98
208 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (207 bp):
AAACCCATTATGATTTTCAAGCATTGCTCCTCCAACTAATGGATTATTATGATTAAACCCATTGT
GATTTTCAACCACTGCTCCTCCAACTAAAGGATTATGATTAAACCCATTGTGATTTTCAACCATT
GCTCCTCCAACTAATGGATTATGACCAAACCCATTATAATTTTCAAACATGGCTCCTCCAACAAA
TGGATTATGATT
Found at i:27524 original size:57 final size:56
Alignment explanation
Indices: 27398--27527 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 56
27388 TCCTCCAGCT
* * *
27398 AATTGGTTCTGCCCAAACCCATTATGATTTTCAAACATGGCTTCTCCAGCTAATTG
1 AATTGGTTCTGCCCAAACCCAATATGATTTCCAAACATGGCTCCTCCAGCTAATTG
* * *
27454 -A----TTATGCCCAAACCCAATATGATTTCCAAGCATTGCTCCTCCAGCTAATTG
1 AATTGGTTCTGCCCAAACCCAATATGATTTCCAAACATGGCTCCTCCAGCTAATTG
*
27505 CAATTGGTTCTCCCCAAACCCAA
1 -AATTGGTTCTGCCCAAACCCAA
27528 ACCCATTATG
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
51 44 0.73
53 1 0.02
55 1 0.02
57 14 0.23
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.30
Consensus pattern (56 bp):
AATTGGTTCTGCCCAAACCCAATATGATTTCCAAACATGGCTCCTCCAGCTAATTG
Found at i:27680 original size:72 final size:72
Alignment explanation
Indices: 27558--27692 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
27548 ATTGCTACTT
* *
27558 CATGATTTGATGATATTGATATATTAACACTTGGGTGATCCTCAATAGCCTTATTACCACTTGTT
1 CATGATTTGATGATATTGATATATTAACACTTGGGTGATCCTCAACAGCCTTATCACCACTTGTT
27623 CCTCCTC
66 CCTCCTC
* * *
27630 CATGCTTTGATGGTATTGATATATTAACACTTGGGTGATCTTCAACAGCCTTATCACCACTTG
1 CATGATTTGATGATATTGATATATTAACACTTGGGTGATCCTCAACAGCCTTATCACCACTTG
27693 ACGTCCCTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (72 bp):
CATGATTTGATGATATTGATATATTAACACTTGGGTGATCCTCAACAGCCTTATCACCACTTGTT
CCTCCTC
Done.