Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014978.1 Corchorus olitorius cultivar O-4 contig15011, 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: 100436
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1787 original size:51 final size:52
Alignment explanation
Indices: 1708--1812 Score: 185
Period size: 51 Copynumber: 2.0 Consensus size: 52
1698 TTTATCATAT
*
1708 GATGCCAAGCAACGGGATTATTTGCACTTTCAAGTAAAAATATCAATGTTAG
1 GATGCCAAGCAACGGGATTATTTGCACTTTCAAGTAAAAACATCAATGTTAG
*
1760 GATGCCAAGCAAC-GGATTATTTGCACTTTCAAGTAAATACATCAATGTTAG
1 GATGCCAAGCAACGGGATTATTTGCACTTTCAAGTAAAAACATCAATGTTAG
1811 GA
1 GA
1813 GAAGAATCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 38 0.75
52 13 0.25
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
GATGCCAAGCAACGGGATTATTTGCACTTTCAAGTAAAAACATCAATGTTAG
Found at i:11996 original size:33 final size:33
Alignment explanation
Indices: 11958--12118 Score: 251
Period size: 33 Copynumber: 5.0 Consensus size: 33
11948 GGCCACGGCG
11958 CCGCCCTCGCCCTGGACAACGGGCACGCCGCCC
1 CCGCCCTCGCCCTGGACAACGGGCACGCCGCCC
11991 CCGCCCTCGCCCTGGACAACGGGCACGCCGCCC
1 CCGCCCTCGCCCTGGACAACGGGCACGCCGCCC
*
12024 CCGCCCTCGCCATGGACAACGGGCACGCCGCCC
1 CCGCCCTCGCCCTGGACAACGGGCACGCCGCCC
12057 CCGCACC-CGCCCTGGACAACGGGCACGCCG---
1 CCGC-CCTCGCCCTGGACAACGGGCACGCCGCCC
*
12087 CCGCACC-CGGCCTGGACAACGGGCACGCCGCC
1 CCGC-CCTCGCCCTGGACAACGGGCACGCCGCC
12119 GTACCCGGCC
Statistics
Matches: 122, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
30 29 0.24
33 91 0.75
34 2 0.02
ACGTcount: A:0.14, C:0.52, G:0.29, T:0.05
Consensus pattern (33 bp):
CCGCCCTCGCCCTGGACAACGGGCACGCCGCCC
Found at i:12034 original size:66 final size:63
Alignment explanation
Indices: 11945--12138 Score: 254
Period size: 66 Copynumber: 3.1 Consensus size: 63
11935 GCTGAACCAG
* *
11945 AACGGCCACGGCGCCGCCCTCGCCCTGGACAACGGGCACGCCGCCCCCGC-CCTCGCCCTGGAC
1 AACGGGCACGCCGCCGCCCTCGCCCTGGACAACGGGCACGCCGCCCCCGCACC-CGCCCTGGAC
*
12008 AACGGGCACGCCGCCCCCGCCCTCGCCATGGACAACGGGCACGCCGCCCCCGCACCCGCCCTGGA
1 AACGGGCACGCCG---CCGCCCTCGCCCTGGACAACGGGCACGCCGCCCCCGCACCCGCCCTGGA
12073 C
63 C
* * *
12074 AACGGGCACGCCGCCGCACC-CGGCCTGGACAACGGGCACGCCG---CCGTACCCGGCCTGGAC
1 AACGGGCACGCCGCCGC-CCTCGCCCTGGACAACGGGCACGCCGCCCCCGCACCCGCCCTGGAC
12134 AACGG
1 AACGG
12139 TCACCAACCA
Statistics
Matches: 119, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
60 20 0.17
63 36 0.30
64 2 0.02
66 59 0.50
67 2 0.02
ACGTcount: A:0.15, C:0.49, G:0.30, T:0.05
Consensus pattern (63 bp):
AACGGGCACGCCGCCGCCCTCGCCCTGGACAACGGGCACGCCGCCCCCGCACCCGCCCTGGAC
Found at i:12119 original size:33 final size:33
Alignment explanation
Indices: 11968--12138 Score: 225
Period size: 33 Copynumber: 5.4 Consensus size: 33
11958 CCGCCCTCGC
*
11968 CCTGGACAACGGGCACGCCGCCCCCGC-CCTCGC
1 CCTGGACAACGGGCACGCCGCCCCCGCACC-CGG
12001 CCTGGACAACGGGCACGCCGCCCCCGC-CCTC-G
1 CCTGGACAACGGGCACGCCGCCCCCGCACC-CGG
*
12033 CCATGGACAACGGGCACGCCGCCCCCGCACCCGC
1 CC-TGGACAACGGGCACGCCGCCCCCGCACCCGG
12067 CCTGGACAACGGGCACGCCG---CCGCACCCGG
1 CCTGGACAACGGGCACGCCGCCCCCGCACCCGG
*
12097 CCTGGACAACGGGCACGCCG---CCGTACCCGG
1 CCTGGACAACGGGCACGCCGCCCCCGCACCCGG
12127 CCTGGACAACGG
1 CCTGGACAACGG
12139 TCACCAACCA
Statistics
Matches: 131, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
30 50 0.38
32 2 0.02
33 75 0.57
34 4 0.03
ACGTcount: A:0.16, C:0.49, G:0.30, T:0.05
Consensus pattern (33 bp):
CCTGGACAACGGGCACGCCGCCCCCGCACCCGG
Found at i:12236 original size:25 final size:25
Alignment explanation
Indices: 12203--12252 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12193 GTTTGATAGA
*
12203 AAAGTTGGATAAATTTCAGTTTGTT
1 AAAGATGGATAAATTTCAGTTTGTT
*
12228 AAAGATGGATAAATTTGAGTTTGTT
1 AAAGATGGATAAATTTCAGTTTGTT
12253 TAATAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (25 bp):
AAAGATGGATAAATTTCAGTTTGTT
Found at i:18800 original size:26 final size:26
Alignment explanation
Indices: 18764--18847 Score: 70
Period size: 26 Copynumber: 3.4 Consensus size: 26
18754 GGTGAGTGTA
18764 AGTTTCTACTATTCGAATTATGAGACG
1 AGTTT-TACTATTCGAATTATGAGACG
* * *
18791 AGTTTTACTA--C--ATGATCAGA-A
1 AGTTTTACTATTCGAATTATGAGACG
** *
18812 AAATTGACTATTCGAATTATGAGACG
1 AGTTTTACTATTCGAATTATGAGACG
18838 AGTTTTACTA
1 AGTTTTACTA
18848 CATGATCAGA
Statistics
Matches: 40, Mismatches: 12, Indels: 11
0.63 0.19 0.17
Matches are distributed among these distances:
21 7 0.17
22 7 0.17
23 1 0.03
24 1 0.03
25 7 0.17
26 12 0.30
27 5 0.12
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (26 bp):
AGTTTTACTATTCGAATTATGAGACG
Found at i:18840 original size:47 final size:47
Alignment explanation
Indices: 18771--18865 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
18761 GTAAGTTTCT
18771 ACTATTCGAATTATGAGACGAGTTTTACTACATGATCAGAAAAATTG
1 ACTATTCGAATTATGAGACGAGTTTTACTACATGATCAGAAAAATTG
18818 ACTATTCGAATTATGAGACGAGTTTTACTACATGATCAGAAAAATTG
1 ACTATTCGAATTATGAGACGAGTTTTACTACATGATCAGAAAAATTG
18865 A
1 A
18866 TTCGTGTGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (47 bp):
ACTATTCGAATTATGAGACGAGTTTTACTACATGATCAGAAAAATTG
Found at i:19049 original size:19 final size:19
Alignment explanation
Indices: 19025--19062 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19015 ATGAGACTAA
19025 TGTATTATGTAATTTATAT
1 TGTATTATGTAATTTATAT
19044 TGTATTATGTAATTTATAT
1 TGTATTATGTAATTTATAT
19063 AGGTTATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
TGTATTATGTAATTTATAT
Found at i:23945 original size:22 final size:22
Alignment explanation
Indices: 23920--24037 Score: 94
Period size: 22 Copynumber: 5.3 Consensus size: 22
23910 TAGAAATATC
*
23920 GATAACCACACTGTGAAAATTT
1 GATAACCACACTATGAAAATTT
* * *
23942 GATAACCTCATTATG-ATATTT
1 GATAACCACACTATGAAAATTT
*** *
23963 CGATAACCTTTCTATAAAAATTT
1 -GATAACCACACTATGAAAATTT
* * *
23986 GATAATCACACTGTGAAATTTT
1 GATAACCACACTATGAAAATTT
* *
24008 GATAACCATACTAATGAAATTTT
1 GATAACCACACT-ATGAAAATTT
24031 GATAACC
1 GATAACC
24038 TGAGTGTATG
Statistics
Matches: 74, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
21 5 0.07
22 48 0.65
23 21 0.28
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
GATAACCACACTATGAAAATTT
Found at i:24029 original size:23 final size:24
Alignment explanation
Indices: 23999--24059 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
23989 AATCACACTG
23999 TGAAATTTTGATAACCAT-ACT-AA
1 TGAAATTTTGATAACC-TGACTGAA
* *
24022 TGAAATTTTGATAACCTGAGTGTA
1 TGAAATTTTGATAACCTGACTGAA
24046 TGAAATTTTGATAA
1 TGAAATTTTGATAA
24060 TCACACTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 1 0.03
23 18 0.53
24 15 0.44
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (24 bp):
TGAAATTTTGATAACCTGACTGAA
Found at i:24237 original size:22 final size:22
Alignment explanation
Indices: 24186--24462 Score: 103
Period size: 22 Copynumber: 12.6 Consensus size: 22
24176 ATATCCTCTT
*
24186 TATGTAATTTTGATAATCTCTT-C
1 TATGAAATTTTGATAA-C-CTTAC
* * *
24209 -ATAAAATTTTCATAACCTTCC
1 TATGAAATTTTGATAACCTTAC
* *
24230 TATGAAATTTTGTTAACCTTAT
1 TATGAAATTTTGATAACCTTAC
* ** *
24252 TGTGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCTTAC
* *
24274 TCTAAAATTTCT-ATAACCTTTA-
1 TATGAAATTT-TGATAACC-TTAC
24296 TATGAAATTTT-ATTAACCCCTTA-
1 TATGAAATTTTGA-TAA--CCTTAC
* * *
24319 -A-GAAACTTTAATAACCTTAT
1 TATGAAATTTTGATAACCTTAC
* * *
24339 TATGAGATTTTGGTAATCTCTA-
1 TATGAAATTTTGATAACCT-TAC
24361 TATGAAATTTTGATAA-C-TAC
1 TATGAAATTTTGATAACCTTAC
* *
24381 ATTAT-AAATTTTTGATAATC-TCC
1 --TATGAAA-TTTTGATAACCTTAC
* ****
24404 ATATGAAATTTTGTTAATAACAC
1 -TATGAAATTTTGATAACCTTAC
* *
24427 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTAC
*
24449 TATGTAATTTTGAT
1 TATGAAATTTTGAT
24463 TTGCTATCAA
Statistics
Matches: 197, Mismatches: 38, Indels: 39
0.72 0.14 0.14
Matches are distributed among these distances:
19 7 0.04
20 3 0.02
21 19 0.10
22 152 0.77
23 14 0.07
24 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTAC
Found at i:24385 original size:44 final size:44
Alignment explanation
Indices: 24337--24462 Score: 141
Period size: 44 Copynumber: 2.9 Consensus size: 44
24327 TAATAACCTT
* *
24337 ATTATGAGATTTTGGTAATCTCTATATGAAATTTTGATAACT-AC
1 ATTATGAAATTTTGATAATCTCTATATGAAATTTTGATAA-TAAC
* *
24381 ATTAT-AAATTTTTGATAATCTCCATATGAAATTTTGTTAATAAC
1 ATTATGAAA-TTTTGATAATCTCTATATGAAATTTTGATAATAAC
* * *
24425 ACTATGAAATTTTGATAATCT-TCCTATGTAATTTTGAT
1 ATTATGAAATTTTGATAATCTCT-ATATGAAATTTTGAT
24463 TTGCTATCAA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
43 3 0.04
44 63 0.91
45 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (44 bp):
ATTATGAAATTTTGATAATCTCTATATGAAATTTTGATAATAAC
Found at i:28338 original size:55 final size:57
Alignment explanation
Indices: 28236--28353 Score: 186
Period size: 55 Copynumber: 2.1 Consensus size: 57
28226 TAGAATCAGG
* *
28236 TGAACGAATCTAGTAACATAATAATCAGGTGAAAGAATCTAGTAAAACAATTACAAAAT
1 TGAACGAATCTAGTAAC--AATAATCAGGTGAAAGAATCTAGAAAAACAATTACAAAAC
28295 TGAACGAATCTAGTAAC-AT-ATCAGGTGAAAGAATCTAGAAAAACAATTACAAAAC
1 TGAACGAATCTAGTAACAATAATCAGGTGAAAGAATCTAGAAAAACAATTACAAAAC
28350 TGAA
1 TGAA
28354 ACTTTCAAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
55 38 0.67
56 2 0.04
59 17 0.30
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22
Consensus pattern (57 bp):
TGAACGAATCTAGTAACAATAATCAGGTGAAAGAATCTAGAAAAACAATTACAAAAC
Found at i:28354 original size:30 final size:29
Alignment explanation
Indices: 28265--28354 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 29
28255 AATAATCAGG
*
28265 TGAAAGAATCTAGTAAAACAATTACAAAAT
1 TGAAAGAATCTAG-AAAACAATTACAAAAC
* * **
28295 TGAACGAATCTAG-TAAC-A-TATC--AGG
1 TGAAAGAATCTAGAAAACAATTA-CAAAAC
28320 TGAAAGAATCTAGAAAAACAATTACAAAAC
1 TGAAAGAATCTAG-AAAACAATTACAAAAC
28350 TGAAA
1 TGAAA
28355 CTTTCAAGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 13 0.29
26 2 0.04
27 5 0.11
28 5 0.11
29 2 0.04
30 18 0.40
ACGTcount: A:0.53, C:0.12, G:0.13, T:0.21
Consensus pattern (29 bp):
TGAAAGAATCTAGAAAACAATTACAAAAC
Found at i:30422 original size:15 final size:15
Alignment explanation
Indices: 30402--30431 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30392 TGTCACATTA
*
30402 GGGTTGGTATTGCGT
1 GGGTTGGCATTGCGT
30417 GGGTTGGCATTGCGT
1 GGGTTGGCATTGCGT
30432 TTGAAGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.10, G:0.47, T:0.37
Consensus pattern (15 bp):
GGGTTGGCATTGCGT
Found at i:33256 original size:31 final size:31
Alignment explanation
Indices: 33220--33349 Score: 163
Period size: 31 Copynumber: 4.2 Consensus size: 31
33210 ACACATGGCA
*
33220 TGCCACATGTCACTTTTTAGTACACGTGGCG
1 TGCCACATGTCACTTTTTAGTACACGTGACG
*
33251 AGCCACATGTCACTTTTTTA-TACACGTGACG
1 TGCCACATGTCAC-TTTTTAGTACACGTGACG
* *
33282 TGCCACATGTCGCTTTTTGGTACACGTGACG
1 TGCCACATGTCACTTTTTAGTACACGTGACG
* * * * *
33313 TGCCGCATGTCGCTTTTTGGTACACGTGGCA
1 TGCCACATGTCACTTTTTAGTACACGTGACG
33344 TGCCAC
1 TGCCAC
33350 GTCGGACACC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 5 0.06
31 77 0.88
32 6 0.07
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (31 bp):
TGCCACATGTCACTTTTTAGTACACGTGACG
Found at i:33329 original size:62 final size:62
Alignment explanation
Indices: 33190--33349 Score: 185
Period size: 62 Copynumber: 2.6 Consensus size: 62
33180 CACGTGGCAT
* * * * * *
33190 GCCACGTGTCACTTTGTGAAACACATGGCATGCCACATGTCACTTTTTAGTACACGTGGCGA
1 GCCACATGTCACTTTTTGATACACGTGACATGCCACATGTCACTTTTTAGTACACGTGACGA
* * * * *
33252 GCCACATGTCACTTTTTTATACACGTGACGTGCCACATGTCGCTTTTTGGTACACGTGACGT
1 GCCACATGTCACTTTTTGATACACGTGACATGCCACATGTCACTTTTTAGTACACGTGACGA
* * * *
33314 GCCGCATGTCGCTTTTTGGTACACGTGGCATGCCAC
1 GCCACATGTCACTTTTTGATACACGTGACATGCCAC
33350 GTCGGACACC
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 81 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (62 bp):
GCCACATGTCACTTTTTGATACACGTGACATGCCACATGTCACTTTTTAGTACACGTGACGA
Found at i:67579 original size:16 final size:16
Alignment explanation
Indices: 67558--67592 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
67548 AGCTCAGCTC
67558 GTTTATAAAATACAAT
1 GTTTATAAAATACAAT
67574 GTTTATAAAATACAAT
1 GTTTATAAAATACAAT
67590 GTT
1 GTT
67593 CATGTTCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (16 bp):
GTTTATAAAATACAAT
Found at i:77926 original size:15 final size:15
Alignment explanation
Indices: 77902--77936 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
77892 AGAGAGTGAA
* *
77902 GATGGGGAAGCTCTT
1 GATGGAGAAGCACTT
77917 GATGGAGAAGCACTT
1 GATGGAGAAGCACTT
77932 GATGG
1 GATGG
77937 GGTCAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.40, T:0.23
Consensus pattern (15 bp):
GATGGAGAAGCACTT
Found at i:80518 original size:11 final size:11
Alignment explanation
Indices: 80498--80532 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
80488 TTGACAGCGC
80498 AACAAAAACAA
1 AACAAAAACAA
*
80509 AACGAAAACAA
1 AACAAAAACAA
80520 AACAAAAACAA
1 AACAAAAACAA
80531 AA
1 AA
80533 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:80927 original size:20 final size:22
Alignment explanation
Indices: 80901--80951 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 22
80891 TTACACTAAT
80901 TTTATATA-AGATTAATTATAA
1 TTTATATATAGATTAATTATAA
80922 TTATATATATAGATTAATTATAA
1 TT-TATATATAGATTAATTATAA
80945 TTTATAT
1 TTTATAT
80952 TATATTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.07
22 11 0.39
23 15 0.54
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTATATATAGATTAATTATAA
Found at i:80955 original size:23 final size:23
Alignment explanation
Indices: 80901--80963 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
80891 TTACACTAAT
80901 TTTATA-TA-AGATTAATTATAA
1 TTTATATTATAGATTAATTATAA
80922 -TTATATATATAGATTAATTATAA
1 TTTATAT-TATAGATTAATTATAA
*
80945 TTTATATTATA-TTTAATTA
1 TTTATATTATAGATTAATTA
80964 GTCCAAAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 5 0.14
22 9 0.24
23 17 0.46
24 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTATATTATAGATTAATTATAA
Found at i:87658 original size:2 final size:2
Alignment explanation
Indices: 87646--87678 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
87636 AGGATGCATA
*
87646 AT AT A- AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87679 CAAGAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90195 original size:26 final size:26
Alignment explanation
Indices: 90159--90211 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
90149 AGATGCAATC
90159 TCTCATAGAAAGACAC-CTTTTCATGT
1 TCTCATAGAAAGACACAC-TTTCATGT
90185 TCTCATAGAAAGACACACTTTCATGT
1 TCTCATAGAAAGACACACTTTCATGT
90211 T
1 T
90212 TTTGCAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (26 bp):
TCTCATAGAAAGACACACTTTCATGT
Found at i:92438 original size:31 final size:31
Alignment explanation
Indices: 92403--92465 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
92393 TCACTTATTG
*
92403 TGAATCAAACTCAACTTTGAAACCATGATCA
1 TGAATCAAACTCAACTTTGAAACCAAGATCA
92434 TGAATCAAACTCAACTTTGAAACCAAGATCA
1 TGAATCAAACTCAACTTTGAAACCAAGATCA
92465 T
1 T
92466 CAAGTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (31 bp):
TGAATCAAACTCAACTTTGAAACCAAGATCA
Found at i:96154 original size:31 final size:31
Alignment explanation
Indices: 96091--96237 Score: 161
Period size: 31 Copynumber: 4.7 Consensus size: 31
96081 GCATGCCATG
** * * *
96091 TGTCACTTTTTGAAACACTTGGCATGCCACA
1 TGTCACTTTTTGGTACACGTGGCGTGCTACA
* * *
96122 TGTCACTTTTGGGTACACATGGCGTGATACA
1 TGTCACTTTTTGGTACACGTGGCGTGCTACA
*
96153 TGTCACTTTTTGGTACATGTGGCGTGCCT-CA
1 TGTCACTTTTTGGTACACGTGGCGTG-CTACA
*
96184 TGTCGCTTTTTGGTACACGTGGCGTGCTACA
1 TGTCACTTTTTGGTACACGTGGCGTGCTACA
** *
96215 TGTTGCTTTTTGGTACATGTGGC
1 TGTCACTTTTTGGTACACGTGGC
96238 AAGCCACGTC
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
30 2 0.02
31 96 0.97
32 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (31 bp):
TGTCACTTTTTGGTACACGTGGCGTGCTACA
Done.