Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017096.1 Corchorus olitorius cultivar O-4 contig17129, 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: 32996
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:803 original size:164 final size:166
Alignment explanation
Indices: 486--811 Score: 376
Period size: 164 Copynumber: 2.0 Consensus size: 166
476 TCCATGTTAA
** * **
486 TTTAACTCTGAAACCCTAATTCCCAAATTACTTTATGAACAAACCCTAAAATTTGCAGAAACTTC
1 TTTAACTCAAAAACACTAATTCCCAAATTACTTTATGAACAAACCCTAAAATTCCCAGAAACTTC
** * * *
551 CCAAATACCCAGAAACAATTCATAGTAATAACTCATAATACAACACTTTTTTTCCAATACCCATA
66 CCAAATACCCAGAAACAATTCATACAAAAAAATCATAATACAACACTTTTTTTCCAAAACCCATA
* *
616 ACAGATAATCTATTCTAACCCAAAAT-CACAATCAT
131 ACAGAAAATCGATTCTAACCCAAAATCCACAATCAT
*
651 TTTAACTCAAAAACACTAATTCCC-AATT-CATCTTATGAACAAATCCTAAAATTCCCA-AAA-T
1 TTTAACTCAAAAACACTAATTCCCAAATTAC-T-TTATGAACAAACCCTAAAATTCCCAGAAACT
* * * * *
712 ATCGC-AATAACTCAGAAACAATTCATACAAAAAAATTATAATATAACATTTTTTTTCCAAAACC
64 -TCCCAAAT-ACCCAGAAACAATTCATACAAAAAAATCATAATACAACACTTTTTTTCCAAAACC
* * * *
776 CATAACCGAAAATCGGTTTTTACCCAAAATCCACAA
127 CATAACAGAAAATCGATTCTAACCCAAAATCCACAA
812 AAAGAAAAAC
Statistics
Matches: 134, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
163 5 0.04
164 81 0.60
165 48 0.36
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (166 bp):
TTTAACTCAAAAACACTAATTCCCAAATTACTTTATGAACAAACCCTAAAATTCCCAGAAACTTC
CCAAATACCCAGAAACAATTCATACAAAAAAATCATAATACAACACTTTTTTTCCAAAACCCATA
ACAGAAAATCGATTCTAACCCAAAATCCACAATCAT
Found at i:1191 original size:16 final size:16
Alignment explanation
Indices: 1157--1189 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1147 TCTTTTTTGG
*
1157 TTAAATGAATTTAAAT
1 TTAAATGAAATTAAAT
1173 TTAAAT-AAATTAAAT
1 TTAAATGAAATTAAAT
1188 TT
1 TT
1190 TATTTCGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTAAATGAAATTAAAT
Found at i:2691 original size:47 final size:47
Alignment explanation
Indices: 2622--2920 Score: 517
Period size: 47 Copynumber: 6.3 Consensus size: 47
2612 AGTAAGTAGA
* *
2622 AGGTAAATAAACTAAGTAGTAAAAGAATAAGAGATTAGTTTAATTCT
1 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
*
2669 AGGTAATTAAACTAAGTAGTAAAAAAAGAAGAGATTAGTTTAATTCT
1 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
2716 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
1 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
2763 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
1 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
2810 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
1 AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
* * *
2857 AGGTAATTAAACTAAGTAAATTAAAAGAAGAAGAGCTTAGTTTAATTTT
1 AGGTAATTAAACTAAGT--AGTAAAAGAAGAAGAGATTAGTTTAATTCT
*
2906 GGGTAATTAAACTAA
1 AGGTAATTAAACTAA
2921 AGAAGAGGTT
Statistics
Matches: 242, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
47 201 0.83
49 41 0.17
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.30
Consensus pattern (47 bp):
AGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCT
Found at i:2950 original size:36 final size:36
Alignment explanation
Indices: 2884--2956 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
2874 AAATTAAAAG
* * **
2884 AAGAAGAGCTTAGTTTAATTTTGGGTAATTAAACTA
1 AAGAAGAGCTTAGTTTAATTCTAGAAAATTAAACTA
*
2920 AAGAAGAGGTTAGTTTAATTCTAGAAAATTAAACTA
1 AAGAAGAGCTTAGTTTAATTCTAGAAAATTAAACTA
2956 A
1 A
2957 GTAGCGAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (36 bp):
AAGAAGAGCTTAGTTTAATTCTAGAAAATTAAACTA
Found at i:5810 original size:33 final size:36
Alignment explanation
Indices: 5765--5891 Score: 134
Period size: 38 Copynumber: 3.5 Consensus size: 36
5755 AACACCAGGA
*
5765 CAAGCGATTAATGAAATT-T-ATTA-GTCTTGGTCC
1 CAAGCGAATAATGAAATTATCATTAGGTCTTGGTCC
* *
5798 TAAGCGAATAATGAAATTGATCGCTTAGGTCTTGGTCC
1 CAAGCGAATAATGAAATT-ATC-ATTAGGTCTTGGTCC
* * *
5836 CAAGCGAATAATGAAATTCATCGCTTGGGTCTTGATCC
1 CAAGCGAATAATGAAATT-ATC-ATTAGGTCTTGGTCC
*
5874 CAAGCGAATGATGAAATT
1 CAAGCGAATAATGAAATT
5892 GATCGCTTGG
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
33 16 0.20
35 1 0.01
37 3 0.04
38 61 0.75
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (36 bp):
CAAGCGAATAATGAAATTATCATTAGGTCTTGGTCC
Found at i:5841 original size:38 final size:38
Alignment explanation
Indices: 5788--5907 Score: 195
Period size: 38 Copynumber: 3.2 Consensus size: 38
5778 AAATTTATTA
* *
5788 GTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTAG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
*
5826 GTCTTGGTCCCAAGCGAATAATGAAATTCATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
* *
5864 GTCTTGATCCCAAGCGAATGATGAAATTGATCGCTTGG
1 GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
5902 GTCTTG
1 GTCTTG
5908 ATCAAAAGTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (38 bp):
GTCTTGGTCCCAAGCGAATAATGAAATTGATCGCTTGG
Found at i:5908 original size:38 final size:38
Alignment explanation
Indices: 5788--5937 Score: 194
Period size: 38 Copynumber: 3.9 Consensus size: 38
5778 AAATTTATTA
* * *
5788 GTCTTGGTCCTAAGCGAATAATGAAATTGATCGCTTAG
1 GTCTTGATCCCAAGCGAATAATGAAATTGATCGCTTGG
* *
5826 GTCTTGGTCCCAAGCGAATAATGAAATTCATCGCTTGG
1 GTCTTGATCCCAAGCGAATAATGAAATTGATCGCTTGG
*
5864 GTCTTGATCCCAAGCGAATGATGAAATTGATCGCTTGG
1 GTCTTGATCCCAAGCGAATAATGAAATTGATCGCTTGG
** * *
5902 GTCTTGATCAAAAGTGAATAAT-AAATTTGGTCGCTT
1 GTCTTGATCCCAAGCGAATAATGAAA-TTGATCGCTT
5938 TGTTGCAAGT
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 3 0.03
38 97 0.97
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (38 bp):
GTCTTGATCCCAAGCGAATAATGAAATTGATCGCTTGG
Found at i:21596 original size:20 final size:21
Alignment explanation
Indices: 21554--21598 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
21544 ACAAAAATTA
* *
21554 AATTAAAGCAAAATCAACTAT
1 AATTAAAGCAAAATAAACCAT
*
21575 AATT-AAGCAAACTAAACCAT
1 AATTAAAGCAAAATAAACCAT
21595 AATT
1 AATT
21599 TCAACTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.56, C:0.16, G:0.04, T:0.24
Consensus pattern (21 bp):
AATTAAAGCAAAATAAACCAT
Found at i:23556 original size:34 final size:34
Alignment explanation
Indices: 23513--23580 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
23503 CAGCCACATG
*
23513 TTGAACTTTGTACCTTGGAAGCCGTTGGCCTCAA
1 TTGAACTTTGTACCTTGGAAGCCGTCGGCCTCAA
* * *
23547 TTGAACTTTGTGCCTTGTAGGCCGTCGGCCTCAA
1 TTGAACTTTGTACCTTGGAAGCCGTCGGCCTCAA
23581 CCTTGATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (34 bp):
TTGAACTTTGTACCTTGGAAGCCGTCGGCCTCAA
Found at i:23798 original size:209 final size:211
Alignment explanation
Indices: 23405--23806 Score: 612
Period size: 209 Copynumber: 1.9 Consensus size: 211
23395 GGGAAGCCGA
* * * * *
23405 CCTCAACCAATTTGAATACTTGGGAGGCTGTCGACCTCCATCTATCTTCACCTCTTGGAAGACCG
1 CCTCAACCAATTTAAATACTCGGGAGACTGTCGACCTCCATCAATCTTCACCTCTTGGAAGACCA
** * *
23470 TCTGCCTCAATTGAGTTTTAACCTAGAGGGTGTCAGCCACATGTTGAACTTTGTACCTTGGAAGC
66 TCTGCCTCAATTGAGTTTTAACCTAGAGGCCGTCAGCCACATATTGAACTTTGTACCTTGGAAAC
* * * *
23535 CGTTGGCCTCAATTGAACTTTGTGCCTTGTAGGCCGTCGGCCTCAACCTTGATTTTCCTTGGGTG
131 CGTCGGCCTCAATTGAACTTTGTACCTTGGAGGCCGTCAGCCTCAACCTTGATTTTCCTTGGGTG
23600 CTTGGAAAGTCGTTGG
196 CTTGGAAAGTCGTTGG
23616 CCTCAACCAATTTAAATACTCGGGATGAC-GTCGACCTCCATCAATCTTCACCTCTTGG-AGACC
1 CCTCAACCAATTTAAATACTCGGGA-GACTGTCGACCTCCATCAATCTTCACCTCTTGGAAGACC
*
23679 ATCTGCCTCAATTGAGTTTTAACCTAGAGGCCGTCAGCCAGA-ATTGAACTTTGTACCTTGGAAA
65 ATCTGCCTCAATTGAGTTTTAACCTAGAGGCCGTCAGCCACATATTGAACTTTGTACCTTGGAAA
* * * *
23743 CCGTCGGCCTCAATTGAACTTTGTACCTTGGAGGTCGTCAGCCTTAGCTTTGATTTTCCTTGGG
130 CCGTCGGCCTCAATTGAACTTTGTACCTTGGAGGCCGTCAGCCTCAACCTTGATTTTCCTTGGG
23807 AGGCCATCGG
Statistics
Matches: 172, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
209 76 0.44
210 43 0.25
211 51 0.30
212 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (211 bp):
CCTCAACCAATTTAAATACTCGGGAGACTGTCGACCTCCATCAATCTTCACCTCTTGGAAGACCA
TCTGCCTCAATTGAGTTTTAACCTAGAGGCCGTCAGCCACATATTGAACTTTGTACCTTGGAAAC
CGTCGGCCTCAATTGAACTTTGTACCTTGGAGGCCGTCAGCCTCAACCTTGATTTTCCTTGGGTG
CTTGGAAAGTCGTTGG
Found at i:24889 original size:8 final size:8
Alignment explanation
Indices: 24876--24919 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
24866 AGCCCAATTG
24876 TAAAAAAA
1 TAAAAAAA
24884 T-AAAAAA
1 TAAAAAAA
24891 TAAAAAAA
1 TAAAAAAA
*
24899 TTAAATAAA
1 -TAAAAAAA
*
24908 TAATAAAA
1 TAAAAAAA
24916 TAAA
1 TAAA
24920 GGAAGAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
7 7 0.23
8 16 0.53
9 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
TAAAAAAA
Found at i:25058 original size:3 final size:3
Alignment explanation
Indices: 25052--25189 Score: 233
Period size: 3 Copynumber: 46.0 Consensus size: 3
25042 TTAGGAGGAA
25052 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
25100 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
25148 AAT AAT AAT AAT AAT AGT AAT AAT AGT AAT AA- AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
25190 TTTGGAATAA
Statistics
Matches: 127, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
2 2 0.02
3 122 0.96
4 3 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25698 original size:28 final size:28
Alignment explanation
Indices: 25636--25710 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
25626 TATAGGCATA
* *
25636 AAATTACCGTTTTACCCTAAGAATGAGT
1 AAATTACCGTTTTACCCTTAGAATAAGT
*
25664 AAATTACCGTTTTACCCTTAGAA-AATT
1 AAATTACCGTTTTACCCTTAGAATAAGT
* *
25691 AAATTTACAGTTTTTCCCTT
1 AAA-TTACCGTTTTACCCTT
25711 TTAACCTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 5 0.12
28 36 0.88
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (28 bp):
AAATTACCGTTTTACCCTTAGAATAAGT
Found at i:27455 original size:34 final size:34
Alignment explanation
Indices: 27414--27480 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
27404 TTAACCTAAG
27414 GCCGTCGGCCACAATTGAACTTTGTACCTTGGAA
1 GCCGTCGGCCACAATTGAACTTTGTACCTTGGAA
*
27448 GCCGTCGGCCTCAATTGAACTTTGTACCTTGGA
1 GCCGTCGGCCACAATTGAACTTTGTACCTTGGA
27481 GGTCGTTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (34 bp):
GCCGTCGGCCACAATTGAACTTTGTACCTTGGAA
Found at i:27494 original size:34 final size:34
Alignment explanation
Indices: 27414--27495 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
27404 TTAACCTAAG
* *
27414 GCCGTCGGCCACAATTGAACTTTGTACCTTGGAA
1 GCCGTCGACCTCAATTGAACTTTGTACCTTGGAA
* *
27448 GCCGTCGGCCTCAATTGAACTTTGTACCTTGGAG
1 GCCGTCGACCTCAATTGAACTTTGTACCTTGGAA
* *
27482 GTCGTTGACCTCAA
1 GCCGTCGACCTCAA
27496 CCTTAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (34 bp):
GCCGTCGACCTCAATTGAACTTTGTACCTTGGAA
Found at i:27580 original size:102 final size:102
Alignment explanation
Indices: 27465--27649 Score: 289
Period size: 102 Copynumber: 1.8 Consensus size: 102
27455 GCCTCAATTG
* * *
27465 AACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTTCTTAGGAGGCTATCGTCCTCGTC
1 AACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTCCTTAGGAGGCCATCGGCCTCGTC
27530 TTGCTTAATTGCTTGGGAAGCCGTTGATCTCAACCTT
66 TTGCTTAATTGCTTGGGAAGCCGTTGATCTCAACCTT
* * * * * *
27567 AACTTTGTACCTTGGAGGTCGTTGGCCTTAACTTTGATTTTCCTTGGGAGGCCATCGGCTTCGTC
1 AACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTCCTTAGGAGGCCATCGGCCTCGTC
27632 TTGCTTAATTGCTTGGGA
66 TTGCTTAATTGCTTGGGA
27650 GGCTGTTGGC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 74 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (102 bp):
AACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTCCTTAGGAGGCCATCGGCCTCGTC
TTGCTTAATTGCTTGGGAAGCCGTTGATCTCAACCTT
Found at i:27664 original size:102 final size:102
Alignment explanation
Indices: 27444--27666 Score: 288
Period size: 102 Copynumber: 2.2 Consensus size: 102
27434 TTTGTACCTT
* * *
27444 GGAAGCCGTCGGCCTCAA--TTGAACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTT
1 GGAAGCCGTTGACCTCAACCTT-AACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTC
* *
27507 CTTAGGAGGCTATCGTCCTCGTCTTGCTTAATTGCTTG
65 CTTAGGAGGCCATCGGCCTCGTCTTGCTTAATTGCTTG
* * * * *
27545 GGAAGCCGTTGATCTCAACCTTAACTTTGTACCTTGGAGGTCGTTGGCCTTAACTTTGATTTTCC
1 GGAAGCCGTTGACCTCAACCTTAACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTCC
* *
27610 TTGGGAGGCCATCGGCTTCGTCTTGCTTAATTGCTTG
66 TTAGGAGGCCATCGGCCTCGTCTTGCTTAATTGCTTG
* * *
27647 GGAGGCTGTTGGCCTCAACC
1 GGAAGCCGTTGACCTCAACC
27667 AATTTGAATA
Statistics
Matches: 104, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
101 15 0.14
102 87 0.84
103 2 0.02
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.35
Consensus pattern (102 bp):
GGAAGCCGTTGACCTCAACCTTAACTTTGTACCTTGGAGGTCGTTGACCTCAACCTTAATTTTCC
TTAGGAGGCCATCGGCCTCGTCTTGCTTAATTGCTTG
Found at i:27800 original size:34 final size:34
Alignment explanation
Indices: 27755--27832 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
27745 CTAGAGGCCG
*
27755 TCGACCACAATTGAACTTTGTACCTTGGAAGCCA
1 TCGACCTCAATTGAACTTTGTACCTTGGAAGCCA
* *
27789 TCGACCTCAATTGAACTTTGTACCTTGGAGGCCG
1 TCGACCTCAATTGAACTTTGTACCTTGGAAGCCA
*
27823 TTGACCTCAA
1 TCGACCTCAA
27833 CCTTAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (34 bp):
TCGACCTCAATTGAACTTTGTACCTTGGAAGCCA
Found at i:27901 original size:337 final size:336
Alignment explanation
Indices: 27287--27901 Score: 1079
Period size: 337 Copynumber: 1.8 Consensus size: 336
27277 GGGCGTGACA
* *
27287 GGCTTCGTCTTGCTTAATTGCTTGGGAAGTCGTTGGCCTCAATCGATTTGAATACTTGGGATGTC
1 GGCTTCGTCTTGCTTAATTGCTTGGGAAGTCGTTGGCCTCAACCAATTTGAATACTTGGGATGTC
27352 GTCGACCTTCATCAATCTTCACATCTTAGAGATCACCTGCCTCAATTGAATTTTAACCTAAGGCC
66 GTCGACCTTCATCAATCTTCACATCTTAGAGATCACCTGCCTCAATTGAATTTTAACCTAAGGCC
* * *
27417 GTCGGCCACAATTGAACTTTGTACCTTGGAAGCCGTCGGCCTCAATTGAACTTTGTACCTTGGAG
131 GTCGACCACAATTGAACTTTGTACCTTGGAAGCCATCGACCTCAATTGAACTTTGTACCTTGGAG
* *
27482 GTCGTTGACCTCAACCTTAATTTTTCTTAGGAGGCTATCGTCCTCGTCTTGCTTAATTGCTTGGG
196 GCCGTTGACCTCAACCTTAATTTTTCTTAGGAGGCTATCGACCTCGTCTTGCTTAATTGCTTGGG
*
27547 AAGCCGTTGATCTCAACCTTAACTTTGTACCTTGGAGGTCGTTGGCCTTAACTTTGATTTTCCTT
261 AAGCCGTTGACCTCAACCTTAACTTTGTACCTTGGAGGTCGTTGGCCTTAACTTTGATTTTCCTT
27612 GGGAGGCCATC
326 GGGAGGCCATC
*
27623 GGCTTCGTCTTGCTTAATTGCTTGGG-AGGCTGTTGGCCTCAACCAATTTGAATACTTGGGATGT
1 GGCTTCGTCTTGCTTAATTGCTTGGGAAGTC-GTTGGCCTCAACCAATTTGAATACTTGGGATGT
* * ** *
27687 TGTCGACCTTCATCAATCTTCACGTCTTAGAGATCATTTGCCTCAATTGACTTTTAACCTAGAGG
65 CGTCGACCTTCATCAATCTTCACATCTTAGAGATCACCTGCCTCAATTGAATTTTAACCTA-AGG
27752 CCGTCGACCACAATTGAACTTTGTACCTTGGAAGCCATCGACCTCAATTGAACTTTGTACCTTGG
129 CCGTCGACCACAATTGAACTTTGTACCTTGGAAGCCATCGACCTCAATTGAACTTTGTACCTTGG
27817 AGGCCGTTGACCTCAACCTTAATTTTTCTTAGGAGGCTATCGACCTCGTCTTGCTTAATTGCTTG
194 AGGCCGTTGACCTCAACCTTAATTTTTCTTAGGAGGCTATCGACCTCGTCTTGCTTAATTGCTTG
27882 GGAAGCCGTTGACCTCAACC
259 GGAAGCCGTTGACCTCAACC
27902 AATTTGAATA
Statistics
Matches: 263, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
335 3 0.01
336 113 0.43
337 147 0.56
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (336 bp):
GGCTTCGTCTTGCTTAATTGCTTGGGAAGTCGTTGGCCTCAACCAATTTGAATACTTGGGATGTC
GTCGACCTTCATCAATCTTCACATCTTAGAGATCACCTGCCTCAATTGAATTTTAACCTAAGGCC
GTCGACCACAATTGAACTTTGTACCTTGGAAGCCATCGACCTCAATTGAACTTTGTACCTTGGAG
GCCGTTGACCTCAACCTTAATTTTTCTTAGGAGGCTATCGACCTCGTCTTGCTTAATTGCTTGGG
AAGCCGTTGACCTCAACCTTAACTTTGTACCTTGGAGGTCGTTGGCCTTAACTTTGATTTTCCTT
GGGAGGCCATC
Found at i:28072 original size:25 final size:25
Alignment explanation
Indices: 28041--28108 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
28031 GAAAACAAAA
*
28041 CCATCGGCCTAAAATTGATATTTAG
1 CCATCGGCCTAGAATTGATATTTAG
*
28066 CCATCGGCCTAGAATTGATATTTGG
1 CCATCGGCCTAGAATTGATATTTAG
28091 CCATCGGCCTAGAATTGA
1 CCATCGGCCTAGAATTGA
28109 GAGACAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (25 bp):
CCATCGGCCTAGAATTGATATTTAG
Done.