Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011648.1 Corchorus capsularis cultivar CVL-1 contig11669, 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: 40849
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:51 original size:10 final size:11
Alignment explanation
Indices: 23--53 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13 CTTCTTTCTT
23 TTTTTTTTAAA
1 TTTTTTTTAAA
*
34 TTTTTTTTAAT
1 TTTTTTTTAAA
45 TTTTTTTTA
1 TTTTTTTTA
54 CATCAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:222 original size:21 final size:22
Alignment explanation
Indices: 187--232 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
177 AAAAATTATA
**
187 AAAAGGAGAGGCGGTATTTAGC
1 AAAAGGAGAGGCGGTAAATAGC
*
209 AAAAGG-GGGGCGGTAAATAGC
1 AAAAGGAGAGGCGGTAAATAGC
230 AAA
1 AAA
233 TCCCATCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.37, T:0.13
Consensus pattern (22 bp):
AAAAGGAGAGGCGGTAAATAGC
Found at i:556 original size:2 final size:2
Alignment explanation
Indices: 551--580 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
541 CCCGTGTGTG
551 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
581 TTCAATTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1880 original size:2 final size:2
Alignment explanation
Indices: 1873--1905 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1863 AAATGCTTTC
*
1873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1906 ACTAAGAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3095 original size:2 final size:2
Alignment explanation
Indices: 3088--3112 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3078 AAAATGGTAC
3088 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3113 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4167 original size:34 final size:34
Alignment explanation
Indices: 4124--4189 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 34
4114 GAGAGAGCTG
4124 TCACATGTGAACGAGG-GAGTTTGTTGGAGTTCTA
1 TCACATGTGAACG-GGAGAGTTTGTTGGAGTTCTA
4158 TCACATGTGAACGGGAGAGTTTGTTGGAGTTC
1 TCACATGTGAACGGGAGAGTTTGTTGGAGTTC
4190 ACATGTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 2 0.06
34 29 0.94
ACGTcount: A:0.23, C:0.12, G:0.33, T:0.32
Consensus pattern (34 bp):
TCACATGTGAACGGGAGAGTTTGTTGGAGTTCTA
Found at i:4192 original size:30 final size:32
Alignment explanation
Indices: 4124--4197 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 32
4114 GAGAGAGCTG
4124 TCACATGTGAACGAGGGAGTTTGTTGGAGTTCTA
1 TCACATGTGAACGAGGGAGTTTGTTGGAG-T-TA
4158 TCACATGTGAACG-GGAGAGTTTGTTGGAG-T-
1 TCACATGTGAACGAGG-GAGTTTGTTGGAGTTA
4188 TCACATGTGA
1 TCACATGTGA
4198 GTGTCACATC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
30 10 0.26
31 1 0.03
33 2 0.05
34 26 0.67
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.31
Consensus pattern (32 bp):
TCACATGTGAACGAGGGAGTTTGTTGGAGTTA
Found at i:8186 original size:45 final size:42
Alignment explanation
Indices: 8122--8215 Score: 145
Period size: 45 Copynumber: 2.2 Consensus size: 42
8112 AACAATAATT
*
8122 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT--A-GAGTAG
8167 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
8209 AAT-TTAG
1 AATATTAG
8216 GTAATGCACT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 9 0.19
43 1 0.02
45 34 0.71
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATAGAGTAG
Found at i:8706 original size:48 final size:48
Alignment explanation
Indices: 8576--8710 Score: 171
Period size: 48 Copynumber: 2.8 Consensus size: 48
8566 ATTAACAAAA
* * * * *
8576 CTGTCCGGATCGGATAAGCCTCCGATACCCAATTTAACCGGTACACAG
1 CTGTCCGGACCGGATAGGCCTCCAATACCCAGTTTAACCAGTACACAG
* * *
8624 CTGTCCAGACCTGATAGGCCTCCAATACCCAGTTTAACTAGTACACAG
1 CTGTCCGGACCGGATAGGCCTCCAATACCCAGTTTAACCAGTACACAG
* **
8672 CTGTCCGGACCGGATAGGCCTCCCATACTTAGTTTAACC
1 CTGTCCGGACCGGATAGGCCTCCAATACCCAGTTTAACC
8711 TGTTGGATCG
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (48 bp):
CTGTCCGGACCGGATAGGCCTCCAATACCCAGTTTAACCAGTACACAG
Found at i:8788 original size:31 final size:29
Alignment explanation
Indices: 8753--8816 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
8743 AATCATAAAA
*
8753 AATCCATAATGTTTTTCTTTTGGGACAAATT
1 AATCCATAATGTTTTT-TTTT-GAACAAATT
* *
8784 AATCCTTTATGTTTTTTTTTGAACAAATT
1 AATCCATAATGTTTTTTTTTGAACAAATT
8813 AATC
1 AATC
8817 TCTTATGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 12 0.40
30 4 0.13
31 14 0.47
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (29 bp):
AATCCATAATGTTTTTTTTTGAACAAATT
Found at i:8812 original size:29 final size:31
Alignment explanation
Indices: 8761--8826 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
8751 AAAATCCATA
*
8761 ATGTTTTTCTTTTGGGACAAATTAATC-CTTT
1 ATGTTTTTCTTTTGGAACAAATTAATCTC-TT
8792 ATGTTTTT-TTTT-GAACAAATTAATCTCTT
1 ATGTTTTTCTTTTGGAACAAATTAATCTCTT
8821 ATGTTT
1 ATGTTT
8827 CAAAATTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 20 0.61
30 5 0.15
31 8 0.24
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.55
Consensus pattern (31 bp):
ATGTTTTTCTTTTGGAACAAATTAATCTCTT
Found at i:15089 original size:23 final size:23
Alignment explanation
Indices: 15054--15099 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
15044 ACCCAAAAAA
15054 AAGAAAAAGAAACATATACTGAAT
1 AAGAAAAAGAAACAT-TACTGAAT
*
15078 AAGAAAAA-AAACATTATTGAAT
1 AAGAAAAAGAAACATTACTGAAT
15100 TGCTCATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.20
Consensus pattern (23 bp):
AAGAAAAAGAAACATTACTGAAT
Found at i:15588 original size:16 final size:16
Alignment explanation
Indices: 15569--15603 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
15559 ACAATTCAGA
15569 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
*
15585 AAGCAGAAAAGCTGTG
1 AAGCAGAAAAGCTCTG
15601 AAG
1 AAG
15604 TATTTCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.29, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:15801 original size:90 final size:91
Alignment explanation
Indices: 15648--15870 Score: 340
Period size: 90 Copynumber: 2.5 Consensus size: 91
15638 GCTTAAGAAG
* * * *
15648 ATTGAAAGAAGATCCACGAATGTGGAAAATTCTTCTTTCAAAGAAGATTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
* * *
15713 ACTGAAGA-CCAGTTATTGGGGAGTT
66 ACTGAAGACCCAGTTATTGAGAAATT
* *
15738 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
15803 ACTGAAGACCCAGTTATTGAGAAATT
66 ACTGAAGACCCAGTTATTGAGAAATT
* *
15829 ATTGAAAGAAGATCAACGTATGTGGAGGATTCTTCTTTCAAA
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
15871 TTATCAAAGA
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 67 0.56
91 53 0.44
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (91 bp):
ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
ACTGAAGACCCAGTTATTGAGAAATT
Found at i:15809 original size:26 final size:26
Alignment explanation
Indices: 15780--15834 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
15770 TTCTTTCAAA
*
15780 GAAGATCCAATTATTGCAG-AATTACT
1 GAAGACCCAATTATTG-AGAAATTACT
* *
15806 GAAGACCCAGTTATTGAGAAATTATT
1 GAAGACCCAATTATTGAGAAATTACT
15832 GAA
1 GAA
15835 AGAAGATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (26 bp):
GAAGACCCAATTATTGAGAAATTACT
Found at i:18629 original size:16 final size:16
Alignment explanation
Indices: 18610--18644 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
18600 ATAATTCGGA
*
18610 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTATG
18626 AAGCAGAAAAGCTATG
1 AAGCAGAAAAGCTATG
18642 AAG
1 AAG
18645 TATTTCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.14, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTATG
Found at i:18842 original size:90 final size:91
Alignment explanation
Indices: 18689--18911 Score: 349
Period size: 90 Copynumber: 2.5 Consensus size: 91
18679 GCTTAAGAAG
* * *
18689 ATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAAGATTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
** *
18754 ACTGAAGACC-AGTTATTGGGGAGTT
66 ACTGAAGACCTAGTTATTGGAAAATT
* *
18779 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
18844 ACTGAAGACCTAGTTATTGGAAAATT
66 ACTGAAGACCTAGTTATTGGAAAATT
* *
18870 ATTGAAAGAAGATCCACGTATGTGGAGGATTTTTCTTTCAAA
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
18912 TTATCAAAGA
Statistics
Matches: 121, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 70 0.58
91 51 0.42
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (91 bp):
ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGATCCAATTATTGCAGAATT
ACTGAAGACCTAGTTATTGGAAAATT
Found at i:19720 original size:30 final size:31
Alignment explanation
Indices: 19662--19726 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
19652 GAACTGGTGG
*
19662 GTATAAGTTGGTGGATAGACTATATTTTTCAT
1 GTATAAGTTGGAGGATA-ACTATATTTTTCAT
* *
19694 GTATAAGTTGGAGGAT-ACTGTATTTTTCTT
1 GTATAAGTTGGAGGATAACTATATTTTTCAT
19724 GTA
1 GTA
19727 GTGACGTGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 15 0.50
32 15 0.50
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (31 bp):
GTATAAGTTGGAGGATAACTATATTTTTCAT
Found at i:20499 original size:32 final size:31
Alignment explanation
Indices: 20449--20526 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 31
20439 GCAATTAAAG
20449 GTTTGTTTTGCATCAATTATCAAAAAATAAAAA
1 GTTTGTTTTGCATCAATTATC-AAAAA-AAAAA
*
20482 GTTTG-TTTGCATTAATTATCAAAAAAAAAA
1 GTTTGTTTTGCATCAATTATCAAAAAAAAAA
20512 GTTTGTTTTGCATCA
1 GTTTGTTTTGCATCA
20527 CTGAGTAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 10 0.24
31 13 0.31
32 14 0.33
33 5 0.12
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (31 bp):
GTTTGTTTTGCATCAATTATCAAAAAAAAAA
Found at i:21434 original size:15 final size:15
Alignment explanation
Indices: 21405--21466 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
21395 AGTTAGGCCG
*
21405 GGTTGAATTTAGGTTA
1 GGTT-AATTTGGGTTA
* *
21421 GGTTAATTCGGGTTCG
1 GGTTAATTTGGGTT-A
*
21437 GGTTGAATTTGGGTCA
1 GGTT-AATTTGGGTTA
*
21453 AGTTAATTTGGGTT
1 GGTTAATTTGGGTT
21467 CGAGTTCAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 17 0.47
16 11 0.31
17 8 0.22
ACGTcount: A:0.19, C:0.05, G:0.34, T:0.42
Consensus pattern (15 bp):
GGTTAATTTGGGTTA
Found at i:21439 original size:32 final size:32
Alignment explanation
Indices: 21403--21468 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
21393 TGAGTTAGGC
* *
21403 CGGGTTGAATTTAGGTTAGGTTAATTCGGGTT
1 CGGGTTGAATTTAGGTCAAGTTAATTCGGGTT
* *
21435 CGGGTTGAATTTGGGTCAAGTTAATTTGGGTT
1 CGGGTTGAATTTAGGTCAAGTTAATTCGGGTT
21467 CG
1 CG
21469 AGTTCAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.08, G:0.35, T:0.39
Consensus pattern (32 bp):
CGGGTTGAATTTAGGTCAAGTTAATTCGGGTT
Found at i:21440 original size:16 final size:16
Alignment explanation
Indices: 21403--21483 Score: 58
Period size: 16 Copynumber: 5.0 Consensus size: 16
21393 TGAGTTAGGC
*
21403 CGGGTTGAATTTAGGTT
1 CGGGTT-AATTTGGGTT
* *
21420 -AGGTTAATTCGGGTT
1 CGGGTTAATTTGGGTT
21435 CGGGTTGAATTTGGG-T
1 CGGGTT-AATTTGGGTT
**
21451 CAAGTTAATTTGGGTT
1 CGGGTTAATTTGGGTT
* *
21467 CGAGTTCAATATGGGTT
1 CGGGTT-AATTTGGGTT
21484 TTAGCTAGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
15 16 0.31
16 19 0.37
17 16 0.31
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (16 bp):
CGGGTTAATTTGGGTT
Found at i:21482 original size:32 final size:32
Alignment explanation
Indices: 21422--21482 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
21412 TTTAGGTTAG
* * *
21422 GTTAATTCGGGTTCGGGTTGAATTTGGGTCAA
1 GTTAATTCGGGTTCGAGTTCAATATGGGTCAA
*
21454 GTTAATTTGGGTTCGAGTTCAATATGGGT
1 GTTAATTCGGGTTCGAGTTCAATATGGGT
21483 TTTAGCTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39
Consensus pattern (32 bp):
GTTAATTCGGGTTCGAGTTCAATATGGGTCAA
Found at i:22553 original size:222 final size:222
Alignment explanation
Indices: 22167--22606 Score: 853
Period size: 222 Copynumber: 2.0 Consensus size: 222
22157 CCTAATAATT
22167 AAGGTAACAAATTAAATTTAGGTTTAGACCCTATTTATAAATATGAAAAGAATTAAATTCAGATT
1 AAGGTAACAAATTAAATTTAGGTTTAGACCCTATTTATAAATATGAAAAGAATTAAATTCAGATT
* * *
22232 TAGCCCCTAGTTATTAATATGGAGAATTTAAACCCCTTGATTTTAGGTTATTATTGAATAAGGTT
66 TAGCCCCTAATTATTAATATGGAGAATTTAAACCCCTTGATCTTAGGTTATTATTGAATAAGATT
22297 TTAGAAATTATAGTAAGTTTTCTAATGACAAATCAGGAGGATCAAATAGCAAAACTCATTTGTTA
131 TTAGAAATTATAGTAAGTTTTCTAATGACAAATCAGGAGGATCAAATAGCAAAACTCATTTGTTA
22362 AACCATTCTAAAAAATTATTATTTATA
196 AACCATTCTAAAAAATTATTATTTATA
22389 AAGGTAACAAATTAAATTTAGGTTTAGACCCTATTTATAAATATGAAAAGAATTAAATTCAGATT
1 AAGGTAACAAATTAAATTTAGGTTTAGACCCTATTTATAAATATGAAAAGAATTAAATTCAGATT
22454 TAGCCCCTAATTATTAATATGGAGAATTTAAACCCCTTGATCTTAGGTTATTATTGAATAAGATT
66 TAGCCCCTAATTATTAATATGGAGAATTTAAACCCCTTGATCTTAGGTTATTATTGAATAAGATT
22519 TTAGAAATTATAGTAAGTTTTCTAATGACAAATCAGGAGGATCAAATAGCAAAACTCATTTGTTA
131 TTAGAAATTATAGTAAGTTTTCTAATGACAAATCAGGAGGATCAAATAGCAAAACTCATTTGTTA
22584 AACCATTCTAAAAAATTATTATT
196 AACCATTCTAAAAAATTATTATT
22607 ATTTAATATT
Statistics
Matches: 215, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
222 215 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (222 bp):
AAGGTAACAAATTAAATTTAGGTTTAGACCCTATTTATAAATATGAAAAGAATTAAATTCAGATT
TAGCCCCTAATTATTAATATGGAGAATTTAAACCCCTTGATCTTAGGTTATTATTGAATAAGATT
TTAGAAATTATAGTAAGTTTTCTAATGACAAATCAGGAGGATCAAATAGCAAAACTCATTTGTTA
AACCATTCTAAAAAATTATTATTTATA
Found at i:25701 original size:52 final size:51
Alignment explanation
Indices: 25621--25724 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 51
25611 CTTCTTCTAC
25621 AGTCTTGCGTTTTTTGCAACTCAAGAATATTGGAGTT-TTCATACATTATCA
1 AGTCTTGCGTTTTTTGCAACTCAAGAATATTGGA-TTATTCATACATTATCA
*
25672 AGTCTTGCGTTTTTTTGCAACTCAGGAATATTGGATTATTCATACATTATCA
1 AGTCTTGCG-TTTTTTGCAACTCAAGAATATTGGATTATTCATACATTATCA
25724 A
1 A
25725 TTCATCTAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
51 11 0.22
52 39 0.78
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (51 bp):
AGTCTTGCGTTTTTTGCAACTCAAGAATATTGGATTATTCATACATTATCA
Found at i:34167 original size:10 final size:10
Alignment explanation
Indices: 34152--34176 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34142 GAGGACTCTA
34152 GAATTTTCTG
1 GAATTTTCTG
34162 GAATTTTCTG
1 GAATTTTCTG
34172 GAATT
1 GAATT
34177 ATGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:37213 original size:34 final size:34
Alignment explanation
Indices: 37172--37240 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
37162 ACCAAAGAAA
*
37172 AAAAAACCACCAAATAAGTACAGATCGAAGAGAG
1 AAAAAACCACCAAATAAATACAGATCGAAGAGAG
* *
37206 AAAAAACCACCAAATAAATACATATCGTAGAGAG
1 AAAAAACCACCAAATAAATACAGATCGAAGAGAG
37240 A
1 A
37241 TACTCATTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.57, C:0.17, G:0.14, T:0.12
Consensus pattern (34 bp):
AAAAAACCACCAAATAAATACAGATCGAAGAGAG
Done.