Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024666.1 Corchorus olitorius cultivar O-4 contig24699, 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: 13786
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Found at i:59 original size:39 final size:39
Alignment explanation
Indices: 5--86 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
1 TCTT
*
5 CATAGTCGACTAATCTCACCAAAATGATTGTAGTTAGGC
1 CATAGTCGACTAATCTCACCAAAATGATTATAGTTAGGC
44 CATAGTCGACTAATCTCACCAAAATGATTATAGTTAGGC
1 CATAGTCGACTAATCTCACCAAAATGATTATAGTTAGGC
83 CATA
1 CATA
87 AACAATGGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (39 bp):
CATAGTCGACTAATCTCACCAAAATGATTATAGTTAGGC
Found at i:327 original size:154 final size:154
Alignment explanation
Indices: 47--394 Score: 608
Period size: 154 Copynumber: 2.3 Consensus size: 154
37 GTTAGGCCAT
*
47 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAG
*
112 TTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATTAGCCCAAAATAACAAGTG
177 TTCCAAATGAGCTAAAAACATCAC
131 TTCCAAATGAGCTAAAAACATCAC
*
201 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAAG
1 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAG
* *
266 TTTGCCAAATCGAAGACGATTCCAAACGGAACTAATGGGCCCCGA-TAGCTCCAAAATAACAAGT
66 TTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATTAGC-CCAAAATAACAAGT
*
330 GTTCCAAATGAGCTAAAAACTTCAC
130 GTTCCAAATGAGCTAAAAACATCAC
* *
355 AGTGGACTAATCTCACCAAAATGATTGTAGTTAGGCCATA
1 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
395 GTCGACTAAT
Statistics
Matches: 185, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
153 3 0.02
154 182 0.98
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (154 bp):
AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAG
TTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATTAGCCCAAAATAACAAGTG
TTCCAAATGAGCTAAAAACATCAC
Found at i:403 original size:39 final size:39
Alignment explanation
Indices: 359--433 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
349 CTTCACAGTG
* *
359 GACTAATCTCACCAAAATGATTGTAGTTAGGCCATAGTC
1 GACTAATCTCACCAAAATGATTATAGTAAGGCCATAGTC
398 GACTAATCTCACCAAAATGATTATAGTAAGGCCATA
1 GACTAATCTCACCAAAATGATTATAGTAAGGCCATA
434 AACAATGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (39 bp):
GACTAATCTCACCAAAATGATTATAGTAAGGCCATAGTC
Found at i:409 original size:193 final size:192
Alignment explanation
Indices: 201--586 Score: 684
Period size: 193 Copynumber: 2.0 Consensus size: 192
191 AAAACATCAC
* *
201 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAAG
1 AGTCGACTAATCTCACCAAAATGATTATAGTAAGGCCATAAACAATGGAAAGAAAAGCATTGAAG
*
266 TTTGCCAAATCGAAGACGATTCCAAACGGAACTAATGGGCCCCGA-TAGCTCCAAAATAACAAGT
66 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTAGC-CCAAAATAACAAGT
* *
330 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGGCCAT
130 GTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCT-ACCAAAATGATTATAGTTAGGCCAT
*
394 AGTCGACTAATCTCACCAAAATGATTATAGTAAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTCGACTAATCTCACCAAAATGATTATAGTAAGGCCATAAACAATGGAAAGAAAAGCATTGAAG
*
459 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTAGCCCAAAATAACAAGTG
524 TTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTACCAAAATGATTATAGTTAGGCCAT
131 TTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTACCAAAATGATTATAGTTAGGCCAT
586 A
1 A
587 AACAATGGAA
Statistics
Matches: 185, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
192 25 0.14
193 157 0.85
194 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (192 bp):
AGTCGACTAATCTCACCAAAATGATTATAGTAAGGCCATAAACAATGGAAAGAAAAGCATTGAAG
TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTAGCCCAAAATAACAAGTG
TTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTACCAAAATGATTATAGTTAGGCCAT
Found at i:951 original size:154 final size:154
Alignment explanation
Indices: 394--1134 Score: 1147
Period size: 153 Copynumber: 4.9 Consensus size: 154
384 GTTAGGCCAT
*
394 AGTCGACTAATCTCACCAAAATGATTATAGTAAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
459 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
524 TTCCAAATGAGCTAAAAACTTCAC
131 TTCCAAATGAGCTAAAAACTTCAC
548 AGTCGACTAATCT-ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* *** *** * *
612 TTTGCCAAATCGAAGATGATTCAAAACTTCACTAATAATCCCCAATAGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
677 TTCCAAATGAGCTAAAAACTTCAC
131 TTCCAAATGAGCTAAAAACTTCAC
* * *
701 AGTGGACTAATC-CACCAAAATGATTATA-TGTAGGCCATAAACAATGGAAAGAAAGGCATCGAA
1 AGTCGACTAATCTCACCAAAATGATTATAGT-TAGGCCATAAACAATGGAAAGAAAAGCATTG-A
* *
764 GG-TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGGCCCAAAATAACAAG
64 GGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAG
*
828 TTTTCCAAATGAGCTAAAAACTTCAC
129 TGTTCCAAATGAGCTAAAAACTTCAC
854 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
1 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
*
919 TTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
984 TTCCAAATGAGCTAAAAACTTCAC
131 TTCCAAATGAGCTAAAAACTTCAC
* *
1008 AGTCGACTAATCTCACCTAAATGATTATAG-T------T-----A-GGAAAGAAAAGCATTGAGT
1 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * *
1060 TTTACCAAATCGAAGACGATTCAAAAGGGAACTAATGGGCCCCGATTGGCCCAAAATTACAAGTG
66 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
1125 TTCCAAATGA
131 TTCCAAATGA
1135 ACAATTATTA
Statistics
Matches: 547, Mismatches: 34, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
141 89 0.16
142 1 0.00
147 1 0.00
152 1 0.00
153 280 0.51
154 174 0.32
155 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (154 bp):
AGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTG
TTCCAAATGAGCTAAAAACTTCAC
Found at i:1396 original size:29 final size:29
Alignment explanation
Indices: 1354--1551 Score: 231
Period size: 29 Copynumber: 6.9 Consensus size: 29
1344 TTAATTGACC
*
1354 TTTTTGCATATCCAGGGGCATTTTGGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* * * *
1383 TTTTTACCCATCCAAGGGCA--TTAGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* * * *
1410 TCTTTGCATATTCAGGGGCATTTTGGTTA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* * *
1439 TTTTTGCACATTCTGGGGCATTTT-GACA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* *
1467 TTTTTGCATATCCGGGGGCATTTTGGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
* *
1496 TTTTTGCACATCTAGGGGCATTTTAGTCA
1 TTTTTGCACATCCAGGGGCATTTTGGTCA
1525 TTTTTGCACATCCAGGGGCATTTTGGT
1 TTTTTGCACATCCAGGGGCATTTTGGT
1552 TTTATTCTTA
Statistics
Matches: 138, Mismatches: 28, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
27 20 0.14
28 23 0.17
29 95 0.69
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (29 bp):
TTTTTGCACATCCAGGGGCATTTTGGTCA
Found at i:1442 original size:56 final size:57
Alignment explanation
Indices: 1354--1551 Score: 263
Period size: 57 Copynumber: 3.5 Consensus size: 57
1344 TTAATTGACC
* * *
1354 TTTTTGCATATCCAGGGGCATTTTGGTCATTTTTACCCATCCAAGGGCA-TTAGTCA
1 TTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTAGTCA
* * * * * * *
1410 TCTTTGCATATTCAGGGGCATTTTGGTTATTTTTGCACATTCTGGGGCATTTTGACA
1 TTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTAGTCA
* *
1467 TTTTTGCATATCCGGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTAGTCA
1 TTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCA-TTTAGTCA
*
1525 TTTTTGCACATCCAGGGGCATTTTGGT
1 TTTTTGCATATCCAGGGGCATTTTGGT
1552 TTTATTCTTA
Statistics
Matches: 119, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
56 41 0.34
57 47 0.39
58 31 0.26
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (57 bp):
TTTTTGCATATCCAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTAGTCA
Found at i:5921 original size:17 final size:18
Alignment explanation
Indices: 5899--5936 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5889 TTAGAAATGG
*
5899 AAAAAGGATAAAATCA-A
1 AAAAAGGAAAAAATCAGA
*
5916 AAAAAGTAAAAAATCAGA
1 AAAAAGGAAAAAATCAGA
5934 AAA
1 AAA
5937 TCTAAAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.74, C:0.05, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAAGGAAAAAATCAGA
Found at i:6910 original size:154 final size:154
Alignment explanation
Indices: 6629--8203 Score: 2534
Period size: 154 Copynumber: 10.2 Consensus size: 154
6619 CGTTTCGACA
* *
6629 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAATGCATTAAGGTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * *
6694 GATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGGGCTAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
*
6759 ACTTCACAGTGGACTAATCTCACC
131 ACTTCACAGTCGACTAATCTCACC
* *
6783 AAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
6848 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
*
6913 ACTTCACAGTCGACAAATCTCACC
131 ACTTCACAGTCGACTAATCTCACC
* * * *
6937 TAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGCATTGAGTTTTGCAAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
** * * *
7002 GATTCAAAACAAAACTAATGGGCTCCGATGGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
* * *
7067 ACTTCACAATCAATTAATCTCACC
131 ACTTCACAGTCGACTAATCTCACC
*
7091 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
7156 GATTCAAAACGGAACTAAAT-GGCCCCGATAGGCCCAAAATAACAAGTT-TTCCAAATGAGCTAA
66 GATTCAAAACGGAACT-AATGGGCCCCGATAGGCCCAAAATAACAA-TTGTTCCAAATGAGCTAA
* *
7219 ACACTTCACAATCGACTAATCTCACC
129 AAACTTCACAGTCGACTAATCTCACC
* *
7245 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGAA
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * * *
7310 TATTGAAAACGGAACTAATGGGCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
7375 ACTTCACAGTCGACTAATCTCACC
131 ACTTCACAGTCGACTAATCTCACC
*
7399 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAA
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
*
7464 TATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
7529 ACTTCACAGTCGACTAATCTCACC
131 ACTTCACAGTCGACTAATCTCACC
* * * *
7553 TAGATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTTGCAAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
** * *
7618 GATTCAAAACAAAACTAATGGGCCCCGATTGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
* * *
7683 ACTTCACAGTGGACTAACCTGACC
131 ACTTCACAGTCGACTAATCTCACC
*
7707 AAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * * * * *
7772 AATTCAAAACGGAACAAATGGGCCCCGATTGGCCCTATATTACAAGTT-TTCCAAATGAGCTAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA-TTGTTCCAAATGAGCTAAA
*
7836 AACTTCACAATC-ACTTAATCTCACC
130 AACTTCACAGTCGAC-TAATCTCACC
*
7861 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
*
7926 GATTCAAAACGGAACTAAAT-GGTCCCGATAGGCCCAAAATAACAAGTT-TTCCAAATGAGCTAA
66 GATTCAAAACGGAACT-AATGGGCCCCGATAGGCCCAAAATAACAA-TTGTTCCAAATGAGCTAA
*
7989 AAACTTCACAATCGACTAATCTCACC
129 AAACTTCACAGTCGACTAATCTCACC
* *
8015 AAAATGATTATAGTTATGCCATAAACAATGCAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
8080 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTT-TTCCAAATGAGCTAAA
66 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA-TTGTTCCAAATGAGCTAAA
8144 AACTTCACAGTCGACTAATCTCACC
130 AACTTCACAGTCGACTAATCTCACC
8169 AAAATGATTATAGTTAGGCCATAAACAATGGAAAG
1 AAAATGATTATAGTTAGGCCATAAACAATGGAAAG
8204 TGATACGAAT
Statistics
Matches: 1316, Mismatches: 96, Indels: 18
0.92 0.07 0.01
Matches are distributed among these distances:
153 9 0.01
154 1297 0.99
155 10 0.01
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (154 bp):
AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAA
ACTTCACAGTCGACTAATCTCACC
Found at i:12096 original size:69 final size:68
Alignment explanation
Indices: 11968--12108 Score: 246
Period size: 69 Copynumber: 2.1 Consensus size: 68
11958 ATTATAATTA
* *
11968 GGCCATAAACAATGGAAAGAAAAGCTTTGAGTTTGCCAAATCGAAGACGATTTAAAACGGAACTA
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
12033 ATG
66 ATG
*
12036 GGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGA-GTTTGCCAAATCGAAGACGATTCAAAACGGAACT
12101 AATG
65 AATG
12105 GGCC
1 GGCC
12109 CCGATAGGCC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
68 28 0.41
69 41 0.59
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (68 bp):
GGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
ATG
Found at i:12222 original size:222 final size:222
Alignment explanation
Indices: 11829--12261 Score: 749
Period size: 222 Copynumber: 2.0 Consensus size: 222
11819 CATAAAATGC
* *
11829 AAAGAAAAACATTGAGGTTTGCCAAATTGAAGACGATTCAAAACAGAACTAATCGGCCTCGATAG
1 AAAGAAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATCGGCCCCGATAG
* *
11894 GTCCAAAATAAAAAGTGTTCCAAATGAGCTGAAAACTTCACAGTCGACTAATCTCACCAAAATGA
66 GCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGA
* *
11959 TTATAATTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGTTTGCCAAATCGAAGACGATTTAAA
131 TTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATCGAAGACGATTCAAA
12024 ACGGAACTAATGGGCCATAAACAATTG
196 ACGGAACTAATGGGCCATAAACAATTG
* * *
12051 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG
1 AAAGAAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATCGGCCCCGATAG
* *
12116 GCCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGA
66 GCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGA
*
12181 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATCGAAGACGATTCAAA
131 TTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATCGAAGACGATTCAAA
*
12246 ACGTAACTAATGGGCC
196 ACGGAACTAATGGGCC
12262 CAGATAGGCC
Statistics
Matches: 198, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
222 198 1.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (222 bp):
AAAGAAAAACATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATCGGCCCCGATAG
GCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGA
TTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCCAAATCGAAGACGATTCAAA
ACGGAACTAATGGGCCATAAACAATTG
Found at i:12472 original size:154 final size:154
Alignment explanation
Indices: 12036--13786 Score: 2546
Period size: 154 Copynumber: 11.3 Consensus size: 154
12026 GGAACTAATG
*
12036 GGCCATAAACAATTGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* *
12101 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
12166 ATCTCACCAAAATGATTATAGTTA
131 ATCTCACCAAAATGATTATAGTTA
*
12190 GGCCATAAACAATGGAAAGAAAAGCATTGA-GTTTGCCAAATCGAAGACGATTCAAAACGTAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* * *
12254 AATGGGCCCAGATAGGCCCAAAATAACTAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
12319 ATCTCACCAAAATGATTATAGTTA
131 ATCTCACCAAAATGATTATAGTTA
*
12343 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* * *
12408 AATGGGTCTCGATAGG-CCACAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACT
66 AATGGGCCCCGATAGGCCCA-AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* *
12472 AATC-AATCCAAAATGATTATAGCTA
130 AATCTCA-CCAAAATGATTATAGTTA
* * * * * *
12497 CGCCATAAAGAATGAAAAGAAATGCATTAAGGTTTGCCAAATCGAAGACGATTCAATACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* ** * * *
12562 AATGGGACCAAATAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTGACAGTCGACTA
66 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
12627 ATCTCACCAAAATGATTATAGTTA
131 ATCTCACCAAAATGATTATAGTTA
**
12651 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAATATTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* * * *
12716 AATGGGCCCCGATAGGCACAAAATAACAATTATTCCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
12781 ATCTCACCTAAAATGATTATAGTTA
131 ATCTCACC-AAAATGATTATAGTTA
* * ***
12806 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATTGTAGAATCTTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* * *
12871 AATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAAACTTCACAGTCGACAA
66 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
12936 ATCTCACCTAAATGATTATAGTTA
131 ATCTCACCAAAATGATTATAGTTA
* **
12960 GGCCATAAACAATGGAAAGAAAAGCATTGA-GTTTGGCAAAATCGAAGACGATTCAAAACAAAAC
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-GCCAAATCGAAGACGATTCAAAACGGAAC
*
13024 TAATGGGCCCCGATGGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
65 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
**
13089 AATCTGTCCAAAATGATTATAGTTA
130 AATCTCACCAAAATGATTATAGTTA
* * *
13114 GGCCATAAACAATTGAAAGAAAAGCATTGAGG-TTGCCAAATCGAAGACAATTCAAAACGGAACA
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* * *
13178 AATGGGCCCCGATAGGCCCAAAATAACAAGTTTTCCATATGAGCTAAAAACTTCACTGTGGACTA
66 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
13243 ATCTCACCAAAATGATTATAGTTA
131 ATCTCACCAAAATGATTATAGTTA
* * * ***
13267 GGCCATACACAATGTAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACTTCACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
*** *
13332 AATAATCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACTGTGGACTA
66 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
13397 ATCTCAACC-AAATGATTATAGGTA
131 ATCTC-ACCAAAATGATTATAGTTA
* ** **
13421 GGCCATAAACAATGGAAAGAAAGGCATCAAAGG-TTGCCAAATCGAAGACGATTCAAAACGTCAC
1 GGCCATAAACAATGGAAAGAAAAGCAT-TGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAAC
*
13485 TAATGGTCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
65 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* *
13550 AATCTGACTAAAATGATTATAGTTA
130 AATCTCACCAAAATGATTATAGTTA
* * * * ***
13575 GGCCATACACAATGGAAAGATCGAAGAATTGAGGTTTGCCAAATCGAAGATGATTCAAAACTTCA
1 GGCCATAAACAATGGAAAGA--AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAA
*** * *
13640 CTAATAATCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGGTAAAAACTTCACAGTTGGA
64 CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG-TGGA
13705 CTAATCTACACCGAAAATGATTATAGTTA
128 CTAATCT-CACC-AAAATGATTATAGTTA
* * * * *
13734 GGCCATACACAACGTAAAG-AAAGCATTGAGGTTTGGCAAATCCGAAGATGATT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT-CGAAGACGATT
Statistics
Matches: 1449, Mismatches: 129, Indels: 35
0.90 0.08 0.02
Matches are distributed among these distances:
153 296 0.20
154 827 0.57
155 162 0.11
156 107 0.07
157 22 0.02
158 2 0.00
159 33 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
ATCTCACCAAAATGATTATAGTTA
Done.