Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019776.1 Corchorus olitorius cultivar O-4 contig19809, 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: 64611
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:1324 original size:307 final size:305
Alignment explanation
Indices: 731--1344 Score: 1156
Period size: 307 Copynumber: 2.0 Consensus size: 305
721 TTCATCAGAG
731 ATCGATAACCTTCTTAATTGATTAATATTTAACTTTCGTTCTTATTAGCCCTGTAGTTTTTTAGT
1 ATCGATAACCTTCTTAATTGATTAATATTTAACTTTCGTTCTTATTAGCCCTGTAGTTTTTTAGT
796 AAATTCAAATAAGAAAATTGATAACCTTCCTTAATTATTGAAGATAACCATAATTGTATAATAAT
66 AAATTCAAATAAGAAAATTGATAACCTTCCTTAATTATTGAAGATAACCATAATTGTATAATAAT
861 TTAAGTTTTTTTTGTTCGTTCAATGAGATTAATTATTTCAAATCTCTGCAAATTAAATGACCAGA
131 TTAAGTTTTTTTTGTTCGTTCAATGAGATTAATTATTTCAAATCTCTGCAAATTAAATGACCAGA
*
926 TTTTGATGATTAATTAATCAAAATTTATGAAAATGAAAAGTACGCATGTGTGGAATATATGATTT
196 TTTTGATGATTAATTAATCAAAATTTATGAAAATGAAAAGTACACATGTGTGGAATATATGATTT
*
991 ATCAATTATTAACATACGTGCAGCGCACGTGCTTTAACTAGTATA
261 ATCAATTATTAACATACGTACAGCGCACGTGCTTTAACTAGTATA
*
1036 ATCGATAACCTTCTTAATTGATTAATGTTTAACTTTCGTTCTTATTAGCCCTGTAGTTTTTTAGT
1 ATCGATAACCTTCTTAATTGATTAATATTTAACTTTCGTTCTTATTAGCCCTGTAGTTTTTTAGT
1101 AAATTCAAATAAGAAAATTGATAACCTTCCTTAATTATTGAAGATAACCATAATTGTATAATAAT
66 AAATTCAAATAAGAAAATTGATAACCTTCCTTAATTATTGAAGATAACCATAATTGTATAATAAT
* *
1166 TTAAGTTTTTTTTTTTTTCGTTCAATGAGATTAATTATTTTAAATCTCTGCAAATTAAATGACCA
131 TTAAG--TTTTTTTTGTTCGTTCAATGAGATTAATTATTTCAAATCTCTGCAAATTAAATGACCA
*
1231 GATTTTGATGATTAATTAATCAAAATTTATGAAAATGAAAAGTACATATGTGTGGAATATATGAT
194 GATTTTGATGATTAATTAATCAAAATTTATGAAAATGAAAAGTACACATGTGTGGAATATATGAT
1296 TTATCAATTATTAACATACGTACAGCGCACGTGCTTTAACTAGTATA
259 TTATCAATTATTAACATACGTACAGCGCACGTGCTTTAACTAGTATA
1343 AT
1 AT
1345 TATATATACT
Statistics
Matches: 301, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
305 134 0.45
307 167 0.55
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (305 bp):
ATCGATAACCTTCTTAATTGATTAATATTTAACTTTCGTTCTTATTAGCCCTGTAGTTTTTTAGT
AAATTCAAATAAGAAAATTGATAACCTTCCTTAATTATTGAAGATAACCATAATTGTATAATAAT
TTAAGTTTTTTTTGTTCGTTCAATGAGATTAATTATTTCAAATCTCTGCAAATTAAATGACCAGA
TTTTGATGATTAATTAATCAAAATTTATGAAAATGAAAAGTACACATGTGTGGAATATATGATTT
ATCAATTATTAACATACGTACAGCGCACGTGCTTTAACTAGTATA
Found at i:1907 original size:16 final size:16
Alignment explanation
Indices: 1886--1927 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1876 AAGAAAAAAT
1886 AAAAAT-AATAATAAAG
1 AAAAATAAAT-ATAAAG
*
1902 AAAAATAAATTTAAAG
1 AAAAATAAATATAAAG
1918 AAAAATAAAT
1 AAAAATAAAT
1928 CAGAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAAATAAATATAAAG
Found at i:1922 original size:17 final size:16
Alignment explanation
Indices: 1897--1927 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1887 AAAATAATAA
1897 TAAAGAAAAATAAATT
1 TAAAGAAAAATAAATT
1913 TAAAGAAAAATAAAT
1 TAAAGAAAAATAAAT
1928 CAGAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
TAAAGAAAAATAAATT
Found at i:3050 original size:31 final size:30
Alignment explanation
Indices: 3015--3091 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
3005 ATACCGTACA
3015 GGTCCCTCTACTTACAAAAAAGGATCAATTT
1 GGTCCCTCTACTTACAAAAAAGG-TCAATTT
* * **
3046 GGTCCCTTTAC-TATAAAAACTGTCAATTT
1 GGTCCCTCTACTTACAAAAAAGGTCAATTT
3075 GGTCCCTCTACTTACAA
1 GGTCCCTCTACTTACAA
3092 TTTGGTGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.44
30 12 0.31
31 10 0.26
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (30 bp):
GGTCCCTCTACTTACAAAAAAGGTCAATTT
Found at i:3286 original size:12 final size:12
Alignment explanation
Indices: 3262--3294 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3252 CTGGAAGCTC
3262 ACAACAAAC-TCA
1 ACAA-AAACATCA
3274 ACAAAAACATCA
1 ACAAAAACATCA
3286 ACAAAAACA
1 ACAAAAACA
3295 GAAGTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.06
Consensus pattern (12 bp):
ACAAAAACATCA
Found at i:6807 original size:26 final size:26
Alignment explanation
Indices: 6778--6846 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
6768 CTTAAGTCTA
6778 AGTTTATGAAATCTACACAGACTTGC
1 AGTTTATGAAATCTACACAGACTTGC
* *
6804 AGTTTATGAAATCTACACATACTTGT
1 AGTTTATGAAATCTACACAGACTTGC
6830 AGTTTATGAAATCTACA
1 AGTTTATGAAATCTACA
6847 TAGAAATTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (26 bp):
AGTTTATGAAATCTACACAGACTTGC
Found at i:13909 original size:42 final size:42
Alignment explanation
Indices: 13850--13933 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
13840 AAGTCTTTTT
13850 TTATAAACCTTGAGGTATCTAGTACAGTCTCATTGGATCCTA
1 TTATAAACCTTGAGGTATCTAGTACAGTCTCATTGGATCCTA
13892 TTATAAACCTTGAGGTATCTAGTACAGTCTCATTGGATCCTA
1 TTATAAACCTTGAGGTATCTAGTACAGTCTCATTGGATCCTA
13934 ATTAGTCATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (42 bp):
TTATAAACCTTGAGGTATCTAGTACAGTCTCATTGGATCCTA
Found at i:13992 original size:13 final size:13
Alignment explanation
Indices: 13974--14000 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13964 CCATATAGAG
13974 AGAAGTTCTTCCA
1 AGAAGTTCTTCCA
13987 AGAAGTTCTTCCA
1 AGAAGTTCTTCCA
14000 A
1 A
14001 CTTCTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (13 bp):
AGAAGTTCTTCCA
Found at i:22184 original size:38 final size:38
Alignment explanation
Indices: 22133--22440 Score: 426
Period size: 38 Copynumber: 8.1 Consensus size: 38
22123 GCGGGAATTC
** *
22133 TAAC-GAAACTTCTAAACGAA-GACCTACTCAGGTTTACT
1 TAACGGAAA-TTCTAAAC-AAGGACCTAAGCAGGTTTGCT
* * * *
22171 TAACGGGAGTTCT-AACAAGGACCTAAGCAAGTTTGAT
1 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
*
22208 TAAAC-GAAACTTCTAAGCAAGGACCTAAGCAGGTTTGCT
1 T-AACGGAAA-TTCTAAACAAGGACCTAAGCAGGTTTGCT
*
22247 TAACGGGAATTCTAAACAAGGACCTAAGCAGGTTTGCT
1 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
22285 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
1 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
* *
22323 TAACGAAAATTTTAAACAGAGGACCTAAGCAGGTTTGCT
1 TAACGGAAATTCTAAACA-AGGACCTAAGCAGGTTTGCT
* *
22362 TAACAGAAATTCTAAACAATGACCTAAGCAGGTTTGCT
1 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
22400 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
1 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
22438 TAA
1 TAA
22441 ACAAAGCTCT
Statistics
Matches: 240, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
36 2 0.01
37 19 0.08
38 157 0.65
39 62 0.26
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (38 bp):
TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
Found at i:22184 original size:50 final size:50
Alignment explanation
Indices: 22084--22186 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 50
22074 GGTTTGATTG
*
22084 AACGAAACTCTAAGCATAGACCTAAGCAGGTTCACTTAAGCGGGAATTCT
1 AACGAAACTCTAAACATAGACCTAAGCAGGTTCACTTAAGCGGGAATTCT
** * *
22134 AACGAAACTTCTAAACGA-AGACCTACTCAGGTTTACTTAA-CGGGAGTTCT
1 AACGAAAC-TCTAAAC-ATAGACCTAAGCAGGTTCACTTAAGCGGGAATTCT
22184 AAC
1 AAC
22187 AAGGACCTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 20 0.43
51 25 0.54
52 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (50 bp):
AACGAAACTCTAAACATAGACCTAAGCAGGTTCACTTAAGCGGGAATTCT
Found at i:22365 original size:115 final size:113
Alignment explanation
Indices: 22133--22596 Score: 447
Period size: 115 Copynumber: 4.0 Consensus size: 113
22123 GCGGGAATTC
** * * *
22133 TAAC-GAAACTTCTAAACGAAGACCTACTCAGGTTTACTTAACGGGAGTTCT-AACAAGGACCTA
1 TAACAGAAA-TTCTAAAC-AAGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTA
* * * *
22196 AGCAAGTTTGATTAAACGAAACTTCTAAGCAAGGACCTAAGCAGGTTTGCT
64 AGCAGGTTTGCTT-AACGAAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
* *
22247 TAACGGGAATTCTAAACAAGGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAA
1 TAACAGAAATTCTAAACAA-GACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAA
*
22312 GCAGGTTTGCTTAACGAAAATTTTAAACAGAGGACCTAAGCAGGTTTGCT
65 GCAGGTTTGCTTAACGAAAATTCTAAACA-AGGACCTAAGCAGGTTTGCT
22362 TAACAGAAATTCTAAACAATGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAA
1 TAACAGAAATTCTAAACAA-GACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAA
** ***
22427 GCAGGTTTGCTTAAAC-AAAGCTCTCCGC-AGAGATCCTAAGCAGGTTTGCT
65 GCAGGTTTGCTT-AACGAAAATTCTAAACAAG-GA-CCTAAGCAGGTTTGCT
** * * ** * * * *
22477 TAAACA-AAGCTCTCAGCAGAGATCCTAAGCAGGTTCACCTAAACGGGAATTTCTAAATAAAGAC
1 T-AACAGAAATTCTAAACA-AGA-CCTAAGCAGGTT-TGCTTAAC-GGAAATTCTAAACAAGGAC
* * * * *
22541 CTAAGCAGGTTTTCTTAAATG-AGATTCTAAACATA-GACCTAAGTAGGTTTACT
61 CTAAGCAGGTTTGCTT-AACGAAAATTCTAAACA-AGGACCTAAGCAGGTTTGCT
22594 TAA
1 TAA
22597 ATGGCCACTC
Statistics
Matches: 295, Mismatches: 40, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
113 4 0.01
114 54 0.18
115 153 0.52
116 22 0.07
117 20 0.07
118 41 0.14
120 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (113 bp):
TAACAGAAATTCTAAACAAGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAAG
CAGGTTTGCTTAACGAAAATTCTAAACAAGGACCTAAGCAGGTTTGCT
Found at i:22465 original size:77 final size:75
Alignment explanation
Indices: 22133--22479 Score: 414
Period size: 77 Copynumber: 4.5 Consensus size: 75
22123 GCGGGAATTC
** * * *
22133 TAACGAAACTTCTAAACGAA-GACCTACTCAGGTTTACTTAACGGGAGTTCT-AACAAGGACCTA
1 TAACGAAAC-TCTAAAC-AAGGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTA
* *
22196 AGCAAGTTTGAT
64 AGCAGGTTTGCT
* *
22208 TAAACGAAACTTCTAAGCAAGGACCTAAGCAGGTTTGCTTAACGGGAATTCTAAACAAGGACCTA
1 T-AACGAAAC-TCTAAACAAGGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTA
22273 AGCAGGTTTGCT
64 AGCAGGTTTGCT
* * *
22285 TAACGGAAATTCTAAACAAGGACCTAAGCAGGTTTGCTTAACGAAAATTTTAAACAGAGGACCTA
1 TAAC-GAAACTCTAAACAAGGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACA-AGGACCTA
22350 AGCAGGTTTGCT
64 AGCAGGTTTGCT
* *
22362 TAACAGAAATTCTAAACAATGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAA
1 TAAC-GAAACTCTAAACAAGGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAA
22427 GCAGGTTTGCT
65 GCAGGTTTGCT
***
22438 TAAAC-AAAGCTCTCCGC-AGAGATCCTAAGCAGGTTTGCTTAA
1 T-AACGAAA-CTCTAAACAAG-GA-CCTAAGCAGGTTTGCTTAA
22480 ACAAAGCTCT
Statistics
Matches: 242, Mismatches: 21, Indels: 16
0.87 0.08 0.06
Matches are distributed among these distances:
75 7 0.03
76 114 0.47
77 121 0.50
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (75 bp):
TAACGAAACTCTAAACAAGGACCTAAGCAGGTTTGCTTAACGGAAATTCTAAACAAGGACCTAAG
CAGGTTTGCT
Found at i:22520 original size:39 final size:39
Alignment explanation
Indices: 22422--22511 Score: 171
Period size: 39 Copynumber: 2.3 Consensus size: 39
22412 TAAACAAGGA
*
22422 CCTAAGCAGGTTTGCTTAAACAAAGCTCTCCGCAGAGAT
1 CCTAAGCAGGTTTGCTTAAACAAAGCTCTCAGCAGAGAT
22461 CCTAAGCAGGTTTGCTTAAACAAAGCTCTCAGCAGAGAT
1 CCTAAGCAGGTTTGCTTAAACAAAGCTCTCAGCAGAGAT
22500 CCTAAGCAGGTT
1 CCTAAGCAGGTT
22512 CACCTAAACG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTAAGCAGGTTTGCTTAAACAAAGCTCTCAGCAGAGAT
Found at i:22599 original size:38 final size:37
Alignment explanation
Indices: 22180--22597 Score: 376
Period size: 38 Copynumber: 10.9 Consensus size: 37
22170 TTAACGGGAG
* *
22180 TTCT-AACAAGGACCTAAGCAAGTTTGATTAAACGAAA
1 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAAA-GAAA
* * *
22217 CTTCTAAGCAAGGACCTAAGCAGGTTTGCTTAACGGGAA
1 -TTCTAAACAAGGACCTAAGCAGGTTTGCTTAA-AGAAA
*
22256 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAACGGAAA
1 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAA-AGAAA
*
22294 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAACGAAAA
1 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAAAG-AAA
*
22332 TTTTAAACAGAGGACCTAAGCAGGTTTGCTTAACAGAAA
1 TTCTAAACA-AGGACCTAAGCAGGTTTGCTTAA-AGAAA
* *
22371 TTCTAAACAATGACCTAAGCAGGTTTGCTTAACGGAAA
1 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAA-AGAAA
*
22409 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAAACAAA
1 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAAAGAAA
* *** *
22446 GCTCTCCGC-AGAGATCCTAAGCAGGTTTGCTTAAACAAA
1 -TTCTAAACAAG-GA-CCTAAGCAGGTTTGCTTAAAGAAA
* * * ** * *
22485 GCTCTCAGC-AGAGATCCTAAGCAGGTTCACCTAAACGGGAAT
1 -TTCTAAACAAG-GA-CCTAAGCAGGTTTGCTTAAA---GAAA
* * * *
22527 TTCTAAATAAAGACCTAAGCAGGTTTTCTTAAATGAGA
1 TTCTAAACAAGGACCTAAGCAGGTTTGCTTAAA-GAAA
* *
22565 TTCTAAACATA-GACCTAAGTAGGTTTACTTAAA
1 TTCTAAACA-AGGACCTAAGCAGGTTTGCTTAAA
22598 TGGCCACTCT
Statistics
Matches: 327, Mismatches: 40, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
37 6 0.02
38 177 0.54
39 117 0.36
40 18 0.06
41 6 0.02
42 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (37 bp):
TTCTAAACAAGGACCTAAGCAGGTTTGCTTAAAGAAA
Found at i:42252 original size:15 final size:16
Alignment explanation
Indices: 42219--42258 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
42209 TTTGTTTGTT
42219 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
42235 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
42250 TTGCTTTCT
1 TTGTTTTCT
42259 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:46795 original size:12 final size:11
Alignment explanation
Indices: 46777--46806 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
46767 TCCCTCTAGA
46777 AAAAAAAAAAT
1 AAAAAAAAAAT
46788 ATAAAAAAAAAT
1 A-AAAAAAAAAT
46800 AAAAAAA
1 AAAAAAA
46807 GATTGCTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:49008 original size:15 final size:16
Alignment explanation
Indices: 48975--49014 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
48965 TTTGTTTGTT
48975 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
48991 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTATAA
*
49006 TTGCTTTCT
1 TTGTTTTCT
49015 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:56492 original size:13 final size:13
Alignment explanation
Indices: 56474--56498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56464 CTTGGCATGA
56474 GTGATGATTTTTG
1 GTGATGATTTTTG
56487 GTGATGATTTTT
1 GTGATGATTTTT
56499 CTTGTTACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:56831 original size:19 final size:19
Alignment explanation
Indices: 56809--56859 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
56799 GGGCTGAAAT
56809 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
56828 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
56847 TAATT-ATTATTAA
1 TAATTAATTATTAA
56860 AAATCCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:60541 original size:13 final size:13
Alignment explanation
Indices: 60523--60548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60513 AACGTAACAA
60523 CAAAAATCATCAC
1 CAAAAATCATCAC
60536 CAAAAATCATCAC
1 CAAAAATCATCAC
60549 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Done.