Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024433.1 Corchorus olitorius cultivar O-4 contig24466, 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: 31258
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2611 original size:27 final size:27
Alignment explanation
Indices: 2570--2667 Score: 81
Period size: 27 Copynumber: 3.7 Consensus size: 27
2560 AGTGGACTTA
* *
2570 AAATGACCCACATGCCCCTGAATATGC
1 AAATGACCAAAATGCCCCTGAATATGC
* * * **
2597 AAATGACCAAAATG-CCCTTATTGTAA
1 AAATGACCAAAATGCCCCTGAATATGC
* *
2623 AAATGACCAAAATGACCCTGAACATGC
1 AAATGACCAAAATGCCCCTGAATATGC
* * *
2650 GAATGATCAAAACGCCCC
1 AAATGACCAAAATGCCCC
2668 CTGGGTGACC
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
26 21 0.40
27 32 0.60
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAATATGC
Found at i:3493 original size:50 final size:50
Alignment explanation
Indices: 3435--3535 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
3425 TAATATGCCA
* *
3435 TTTGAAAAGTAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGTAAATTTTGATCTTAGACTCACAAATGGAAAGCAATCTTAT
* *
3485 TTTGAAAAGTGAATTTTGATTTTAGACTCACAAATGGAAAGCAATCTTAT
1 TTTGAAAAGTAAATTTTGATCTTAGACTCACAAATGGAAAGCAATCTTAT
3535 T
1 T
3536 ATAAAATTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (50 bp):
TTTGAAAAGTAAATTTTGATCTTAGACTCACAAATGGAAAGCAATCTTAT
Found at i:3832 original size:14 final size:13
Alignment explanation
Indices: 3813--3848 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
3803 AATTCTTTTC
3813 TTCATTTTTCCATT
1 TTCATTTTTCCA-T
*
3827 TTCATTTTTTCAT
1 TTCATTTTTCCAT
3840 TTCATTTTT
1 TTCATTTTT
3849 TTTTTGCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCATTTTTCCAT
Found at i:3850 original size:14 final size:14
Alignment explanation
Indices: 3813--3849 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
3803 AATTCTTTTC
*
3813 TTCATTTTTCCATT
1 TTCATTTTTTCATT
3827 TTCATTTTTTCA-T
1 TTCATTTTTTCATT
3840 TTCATTTTTT
1 TTCATTTTTT
3850 TTTTGCATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCATTTTTTCATT
Found at i:7033 original size:75 final size:75
Alignment explanation
Indices: 6939--7084 Score: 231
Period size: 75 Copynumber: 1.9 Consensus size: 75
6929 TTTAATCCTC
* **
6939 TCGAAATCATTGTTTTGACTAAAACTGACTT-TGAAACATCTTTTGATTAAAACTCATCATTTCT
1 TCGAAATCATTGCTTTGACTAAAACTGA-TTCTGAAACATCTTTTGATTAAAACTCATCATCCCT
7003 TTGCTCACAGT
65 TTGCTCACAGT
* *
7014 TCGAAATCATTGCTTTGACTAAAACTTATTCTGAAACATCTTTTGATTAAAACTTATCATCCCTT
1 TCGAAATCATTGCTTTGACTAAAACTGATTCTGAAACATCTTTTGATTAAAACTCATCATCCCTT
7079 TGCTCA
66 TGCTCA
7085 TAGTCTAGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 2 0.03
75 63 0.97
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (75 bp):
TCGAAATCATTGCTTTGACTAAAACTGATTCTGAAACATCTTTTGATTAAAACTCATCATCCCTT
TGCTCACAGT
Found at i:11835 original size:35 final size:36
Alignment explanation
Indices: 11780--11883 Score: 131
Period size: 35 Copynumber: 2.9 Consensus size: 36
11770 AACTAAAACC
*
11780 GAAAA-TGATAGGAACTTTTCCTAAATTGAAAACT-T
1 GAAAACTGATAGGAAC-TTTCCTAATTTGAAAACTCT
* *
11815 GAAAACTGATAAGAACTTTCCTAATTTTAAAACTCT
1 GAAAACTGATAGGAACTTTCCTAATTTGAAAACTCT
* *
11851 GAAAACTGGATGGGAACTTTCCCAATTTGAAAA
1 GAAAACT-GATAGGAACTTTCCTAATTTGAAAA
11884 GAACTTAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 21 0.36
36 17 0.29
37 21 0.36
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (36 bp):
GAAAACTGATAGGAACTTTCCTAATTTGAAAACTCT
Found at i:12493 original size:31 final size:31
Alignment explanation
Indices: 12458--12518 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
12448 ATTATTCCAT
12458 CTTAAAAGCCTTATATTGAATTGGAATTAAA
1 CTTAAAAGCCTTATATTGAATTGGAATTAAA
12489 CTTAAAAGCCTTATATTGAATTGGAATTAA
1 CTTAAAAGCCTTATATTGAATTGGAATTAA
12519 GCTTTAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (31 bp):
CTTAAAAGCCTTATATTGAATTGGAATTAAA
Found at i:13005 original size:45 final size:45
Alignment explanation
Indices: 12954--13045 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
12944 TAGAGTATTA
12954 ATTTCTAGGCTCATTTAGCCTTGATTCCAAATTAATTTATTCGAT
1 ATTTCTAGGCTCATTTAGCCTTGATTCCAAATTAATTTATTCGAT
12999 ATTTCTAGGCTCATTTAGCCTTGATTCCAAATTAATTTATTCGAT
1 ATTTCTAGGCTCATTTAGCCTTGATTCCAAATTAATTTATTCGAT
13044 AT
1 AT
13046 ATATATAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (45 bp):
ATTTCTAGGCTCATTTAGCCTTGATTCCAAATTAATTTATTCGAT
Found at i:18808 original size:54 final size:54
Alignment explanation
Indices: 18750--18977 Score: 260
Period size: 54 Copynumber: 4.2 Consensus size: 54
18740 TATTACTACT
* *
18750 TTTTACTTTTTAGCCTAATTACTCTA-AATTAAACTAATTACTGTTTACTCTTTC
1 TTTTACTTTTTAGCTTAATTAC-CCAGAATTAAACTAATTACTGTTTACTCTTTC
* * *
18804 TTTTACTCTTTAGCTTAATTACCCAGAATTAAACTAATTACTATTTACTCTTGC
1 TTTTACTTTTTAGCTTAATTACCCAGAATTAAACTAATTACTGTTTACTCTTTC
* * * ** *
18858 TTTTACTCTTTAGCTTAATTACCCAGAATTAAACTAACTATTGACTACTCCTTC
1 TTTTACTTTTTAGCTTAATTACCCAGAATTAAACTAATTACTGTTTACTCTTTC
* * * * * *
18912 TTTTACTTTTTAGTTTAATTGCTCCTGAATTAAACTAATCTTCTGGTTACTCTTTA
1 TTTTACTTTTTAGCTTAATTAC-CCAGAATTAAACTAAT-TACTGTTTACTCTTTC
*
18968 TTCTACTTTT
1 TTTTACTTTT
18978 GATTACTCTT
Statistics
Matches: 147, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
53 2 0.01
54 112 0.76
55 14 0.10
56 19 0.13
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.48
Consensus pattern (54 bp):
TTTTACTTTTTAGCTTAATTACCCAGAATTAAACTAATTACTGTTTACTCTTTC
Found at i:18986 original size:22 final size:22
Alignment explanation
Indices: 18951--19109 Score: 174
Period size: 22 Copynumber: 7.2 Consensus size: 22
18941 TTAAACTAAT
* *
18951 CTTCTGGTTACTCTTTATTCTA
1 CTTCTGATTACTCTTTCTTCTA
*
18973 CTTTTGATTACTCTTTCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
* ** * *
18995 CTTTTGAAAACTTTTTCTCCTA
1 CTTCTGATTACTCTTTCTTCTA
* * *
19017 CTCCTTATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTCTA
*
19039 CTTCTAATTACTCTTTCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
* *
19061 CTTCTGATTACTTTTTCTTTTA
1 CTTCTGATTACTCTTTCTTCTA
* *
19083 CTTCTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTCTA
19105 CTTCT
1 CTTCT
19110 TTTTAGTTTA
Statistics
Matches: 114, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 114 1.00
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.57
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTCTA
Found at i:19041 original size:66 final size:66
Alignment explanation
Indices: 18958--19109 Score: 196
Period size: 66 Copynumber: 2.3 Consensus size: 66
18948 AATCTTCTGG
* * * * * *
18958 TTACTCTTTATTCTACTTTTGATTACTCTTTCTTCTACTTTTGAAAACTTTTTCTCCTACTCCTT
1 TTACTCTTTCTTTTACTTCTAATTACTCTTTCTTCTACTTCTGAAAACTTTTTCTCCTACTCCTG
19023 A
66 A
** ** *
19024 TTACTCTTTCTTTTACTTCTAATTACTCTTTCTTCTACTTCTGATTACTTTTTCTTTTACTTCTG
1 TTACTCTTTCTTTTACTTCTAATTACTCTTTCTTCTACTTCTGAAAACTTTTTCTCCTACTCCTG
19089 A
66 A
*
19090 TTACTCTTCCTTTTACTTCT
1 TTACTCTTTCTTTTACTTCT
19110 TTTTAGTTTA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (66 bp):
TTACTCTTTCTTTTACTTCTAATTACTCTTTCTTCTACTTCTGAAAACTTTTTCTCCTACTCCTG
A
Found at i:19190 original size:57 final size:57
Alignment explanation
Indices: 19083--19728 Score: 533
Period size: 58 Copynumber: 11.0 Consensus size: 57
19073 TTTTCTTTTA
* ***
19083 CTTCTGATTACTCTTCCTTTTACTTCTTTTTAGTTTAATT-CAGAGTAATTAAACTAAT
1 CTTCTGATTACTCTTTCTTTTAC-TCTTTTTAGTTTAATTACTCTG-AATTAAACTAAT
** *
19141 CTTCCAATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAAATAAT
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAACTAAT
** *
19198 CTTCCAATTGCTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAAT
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTAC-TCTGAATTAAACTAAT
* *
19256 CTTCTGATTACTC---CTTTTACTCTTTTTAGCTTAATTACTCTCGAATTAGACTAAT
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCT-GAATTAAACTAAT
* * * *
19311 CTTCTGATTACCCCTTCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTGAACTAAT
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTC-TGAATTAAACTAAT
* *** * ** ** ***
19369 CTTCTGATTACTCTTTCATTTACTTCGGATTACTCTTCCTTTTACTTCT-TTTTAGTTTAATT
1 CTTCTGATTACTCTTTCTTTTAC-TCTTTTTAGT-TT--AATTAC-TCTGAATTAAACTAA-T
* * *
19431 ACTT-TGAATTAAACTAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGCTTAATTTCTCTAA
1 -CTTCTG-ATT--AC---TC-T----TT-CT------TTTACTCTTTTTAGTTTAATTACTCTGA
**
19495 ATTAAACTTTT
47 ATTAAACTAAT
*
19506 TTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAAT
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTAC-TCTGAATTAAACTAAT
* * * *
19564 CTTCTAATTACTCCTTCTTTTACTGTTTTTAGATTAATTACTCTGAATTAAACTAAT
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAACTAAT
19621 CTTCTGATTACTCTTTCTTTTACTCTTTTTAG--TAATTACTTCTGAATTAAACTAA-
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTAC-TCTGAATTAAACTAAT
* * * **
19676 CTACTGATTACTTTTTC-TTTA--CTTCTTAGCCTAATTACTCTGAATTAAACTAA
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAACTAA
19729 ATATTGATCC
Statistics
Matches: 484, Mismatches: 66, Indels: 81
0.77 0.10 0.13
Matches are distributed among these distances:
52 7 0.01
53 15 0.03
54 14 0.03
55 70 0.14
56 15 0.03
57 133 0.27
58 154 0.32
59 6 0.01
60 2 0.00
61 5 0.01
62 8 0.02
63 10 0.02
64 2 0.00
65 2 0.00
68 3 0.01
69 3 0.01
72 2 0.00
73 2 0.00
74 6 0.01
75 6 0.01
76 7 0.01
78 2 0.00
79 5 0.01
80 5 0.01
ACGTcount: A:0.25, C:0.19, G:0.05, T:0.51
Consensus pattern (57 bp):
CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTGAATTAAACTAAT
Found at i:19399 original size:22 final size:22
Alignment explanation
Indices: 19369--19416 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
19359 TTGAACTAAT
* *
19369 CTTCTGATTACTCTTTCATTTA
1 CTTCGGATTACTCTTCCATTTA
*
19391 CTTCGGATTACTCTTCCTTTTA
1 CTTCGGATTACTCTTCCATTTA
19413 CTTC
1 CTTC
19417 TTTTTAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.15, C:0.27, G:0.06, T:0.52
Consensus pattern (22 bp):
CTTCGGATTACTCTTCCATTTA
Found at i:19417 original size:308 final size:305
Alignment explanation
Indices: 19060--19700 Score: 966
Period size: 308 Copynumber: 2.1 Consensus size: 305
19050 TCTTTCTTCT
*
19060 ACTTCTGATTACTTTTTCTTTTACTTCTGATTACTCTTCCTTTTACTTCTTTTTAGTTTAATT-C
1 ACTTCTGATTACTTTTTC-TTTACTTCGGATTACTCTTCCTTTTACTTCTTTTTAGTTTAATTAC
* * *
19124 AGAGTAATTAAACTAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTCTGAAT
65 AGTG-AATTAAACTAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTAAAT
*
19189 TAAAATAATCTTCCAATTGCTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTA
129 TAAAATAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTA
* * *
19254 ATCTTCTGATTACT-C-CTTTTACTCTTTTTAGCTTAATTACTCTCGAATTAGACTAATCTTCTG
194 ATCTTCTAATTACTCCTCTTTTACTCTTTTTAGATTAATTACTCT-GAATTAAACTAATCTTCTG
*
19317 ATTACCCCTTCTTTTACTCTTTTTAGCTTAATTAC-TCTTGAATTGAACTA
258 ATTACCCCTTCTTTTACTCTTTTTAG--TAATTACTTC-TGAATTAAACTA
*
19367 ATCTTCTGATTACTCTTTCATTTACTTCGGATTACTCTTCCTTTTACTTCTTTTTAGTTTAATTA
1 A-CTTCTGATTACTTTTTC-TTTACTTCGGATTACTCTTCCTTTTACTTCTTTTTAGTTTAATTA
** *
19432 CTTTGAATTAAACTAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGCTTAATTTCTCTAAAT
64 CAGTGAATTAAACTAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTAAAT
* ** * **
19497 TAAACTTTTTTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTA
129 TAAAATAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTA
*
19562 ATCTTCTAATTACTCCTTCTTTTACTGTTTTTAGATTAATTACTCTGAATTAAACTAATCTTCTG
194 ATCTTCTAATTACTCC-TCTTTTACTCTTTTTAGATTAATTACTCTGAATTAAACTAATCTTCTG
* *
19627 ATTACTCTTTCTTTTACTCTTTTTAGTAATTACTTCTGAATTAAACTA
258 ATTACCCCTTCTTTTACTCTTTTTAGTAATTACTTCTGAATTAAACTA
*
19675 ACTACTGATTACTTTTTCTTTACTTC
1 ACTTCTGATTACTTTTTCTTTACTTC
19701 TTAGCCTAAT
Statistics
Matches: 303, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
306 8 0.03
307 16 0.05
308 206 0.68
309 5 0.02
310 42 0.14
311 26 0.09
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (305 bp):
ACTTCTGATTACTTTTTCTTTACTTCGGATTACTCTTCCTTTTACTTCTTTTTAGTTTAATTACA
GTGAATTAAACTAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTAAATTA
AAATAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAAT
CTTCTAATTACTCCTCTTTTACTCTTTTTAGATTAATTACTCTGAATTAAACTAATCTTCTGATT
ACCCCTTCTTTTACTCTTTTTAGTAATTACTTCTGAATTAAACTA
Found at i:19447 original size:138 final size:137
Alignment explanation
Indices: 19267--19529 Score: 375
Period size: 138 Copynumber: 1.9 Consensus size: 137
19257 TTCTGATTAC
* **
19267 TCCTTTTACTCTTTTTAGCTTAATTACTCTCGAATTAGACTAATCTTCTGATTACCCCTTCTTTT
1 TCCTTTTACTCTTTTTAGCTTAATTACTCTCGAATTAAACTAATCTTCCAATTACCCCTTCTTTT
* *
19332 ACTCTTTTTAGCTTAATTACTCTTGAATTGAACTAATCTTCTGATTACTCTTTCATTTACTTCGG
66 ACTCTTTTTAGCTTAATTACTC-TAAATTAAACTAATCTTCTGATTACTCTTTCATTTACTTCGG
19397 ATTACTCT
130 ATTACTCT
* * * *
19405 TCCTTTTACTTCTTTTTAGTTTAATTACT-TTGAATTAAACTAATCTTCCAATTACTCTTTCTTT
1 TCCTTTTAC-TCTTTTTAGCTTAATTACTCTCGAATTAAACTAATCTTCCAATTACCCCTTCTTT
* ** * *
19469 TACTCTTTTTAGCTTAATTTCTCTAAATTAAACTTTTTTTCTGATTACTCTTTCTTTTACT
65 TACTCTTTTTAGCTTAATTACTCTAAATTAAACTAATCTTCTGATTACTCTTTCATTTACT
19530 CTTTTTAGTT
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 32 0.29
138 60 0.55
139 18 0.16
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.52
Consensus pattern (137 bp):
TCCTTTTACTCTTTTTAGCTTAATTACTCTCGAATTAAACTAATCTTCCAATTACCCCTTCTTTT
ACTCTTTTTAGCTTAATTACTCTAAATTAAACTAATCTTCTGATTACTCTTTCATTTACTTCGGA
TTACTCT
Found at i:19545 original size:195 final size:193
Alignment explanation
Indices: 19208--19587 Score: 550
Period size: 195 Copynumber: 2.0 Consensus size: 193
19198 CTTCCAATTG
* **
19208 CTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCTGATTACTCCTTT
1 CTCTTCCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCCAATTACTCCTTT
* *
19273 TACTCTTTTTAGCTTAATTACTCTCGAATTAGACTAATCTTCTGATTACCCCTTCTTTTACTCTT
66 TACTCTTTTTAGCTTAATTACTCTCAAATTAAACTAATCTTCTGATTACCCCTTCTTTTACTCTT
* * *
19338 TTTAGCTTAATTAC-TCTTGAATTGAACTAATCTTCTGATTACTCTTTCATTTACTTCGGATTA
131 TTTAGCTTAATTACTTC-TGAATTAAACTAATCTTCTAATTACTCCTTCATTTACTTCGGATTA
19401 CTCTTCCTTTTACTTCTTTTTAGTTTAATTACTT-TGAATTAAACTAATCTTCCAATTACTCTTT
1 CTCTTCCTTTTAC-TCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCCAATTACTC---
* ** * * *
19465 CTTTTACTCTTTTTAGCTTAATTTCTCT-AAATTAAACTTTTTTTCTGATTACTCTTTCTTTTAC
62 CTTTTACTCTTTTTAGCTTAATTACTCTCAAATTAAACTAATCTTCTGATTACCCCTTCTTTTAC
* *
19529 TCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCTAATTACTCCTTCTTTTACT
127 TCTTTTTAGCTTAATTACTTCTGAATTAAACTAATCTTCTAATTACTCCTTCATTTACT
19588 GTTTTTAGAT
Statistics
Matches: 166, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
193 37 0.22
194 20 0.12
195 80 0.48
196 29 0.17
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (193 bp):
CTCTTCCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCCAATTACTCCTTT
TACTCTTTTTAGCTTAATTACTCTCAAATTAAACTAATCTTCTGATTACCCCTTCTTTTACTCTT
TTTAGCTTAATTACTTCTGAATTAAACTAATCTTCTAATTACTCCTTCATTTACTTCGGATTA
Found at i:19547 original size:30 final size:30
Alignment explanation
Indices: 19454--19547 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
19444 CTAATCTTCC
*
19454 AATTACTCTTTCTTTTACTCTTTTTAGCTT
1 AATTACTCTTTCTTTTACTCTTTTTAGTTT
* *** ** *
19484 AATTTCTCTAAATTAAACT-TTTTT--TCT
1 AATTACTCTTTCTTTTACTCTTTTTAGTTT
*
19511 GATTACTCTTTCTTTTACTCTTTTTAGTTT
1 AATTACTCTTTCTTTTACTCTTTTTAGTTT
19541 AATTACT
1 AATTACT
19548 TCTGAATTAA
Statistics
Matches: 44, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
27 13 0.30
28 5 0.11
29 5 0.11
30 21 0.48
ACGTcount: A:0.21, C:0.17, G:0.03, T:0.59
Consensus pattern (30 bp):
AATTACTCTTTCTTTTACTCTTTTTAGTTT
Found at i:19554 original size:115 final size:115
Alignment explanation
Indices: 19391--19728 Score: 474
Period size: 115 Copynumber: 3.0 Consensus size: 115
19381 CTTTCATTTA
* * *
19391 CTTCGGATTACTCTTCCTTTTACTTCTTTTTAGTTTAATTACTT-TGAATTAAACTAATCTTCCA
1 CTTCTGATTACTCTTTCTTTTAC-TCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCTA
* * **
19455 ATTACTCTTTCTTTTACTCTTTTTAGCTTAATTTCTCTAAATTAAACTTTT
65 ATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTGAATTAAACTAAT
*
19506 TTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCTAA
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCTAA
* * *
19571 TTACTCCTTCTTTTACTGTTTTTAGATTAATTACTCTGAATTAAACTAAT
66 TTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTGAATTAAACTAAT
* *
19621 CTTCTGATTACTCTTTCTTTTACTCTTTTTAG--TAATTACTTCTGAATTAAACTAA-CTACTGA
1 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCTAA
* * *
19683 TTACTTTTTC-TTTA--CTTCTTAGCCTAATTACTCTGAATTAAACTAA
66 TTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTGAATTAAACTAA
19729 ATATTGATCC
Statistics
Matches: 202, Mismatches: 20, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
109 28 0.14
111 4 0.02
112 13 0.06
113 23 0.11
114 20 0.10
115 114 0.56
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.51
Consensus pattern (115 bp):
CTTCTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTACTTCTGAATTAAACTAATCTTCTAA
TTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTGAATTAAACTAAT
Found at i:19757 original size:54 final size:53
Alignment explanation
Indices: 19426--19789 Score: 214
Period size: 57 Copynumber: 6.5 Consensus size: 53
19416 CTTTTTAGTT
* * * ** * *
19426 TAATTACTTTGAATTAAACTAATCTTCCAATTACTCTTTCTTTTACTCTTTTTAGCT
1 TAATTACTCTGAATTAAACTAA-ATACTGATTACTCTTTC-TTTA--CTTCTTAGCC
* * *** * * **
19483 TAATTTCTCTAAATTAAACTTTTTTTCTGATTACTCTTTCTTTTACTCTTTTTAGTT
1 TAATTACTCTGAATTAAAC-TAAATACTGATTACTCTTTC-TTTA--CTTCTTAGCC
* * * * * **
19540 TAATTACTTCTGAATTAAACTAATCTTCTAATTACTCCTTCTTTTACTGTTTTTAGAT
1 TAATTAC-TCTGAATTAAACTAA-ATACTGATTACTCTTTC-TTTAC--TTCTTAGCC
* * *
19598 TAATTACTCTGAATTAAACTAATCTTCTGATTACTCTTTCTTTTACTCTTTTTAG--
1 TAATTACTCTGAATTAAACTAA-ATACTGATTACTCTTTC-TTTA--CTTCTTAGCC
* *
19653 TAATTACTTCTGAATTAAACTAACTACTGATTACTTTTTCTTTACTTCTTAGCC
1 TAATTAC-TCTGAATTAAACTAAATACTGATTACTCTTTCTTTACTTCTTAGCC
* * *
19707 TAATTACTCTGAATTAAACTAAATATTGATCCT-CATCTTT-TTTGCTTCTTAGCT
1 TAATTACTCTGAATTAAACTAAATACTGAT--TAC-TCTTTCTTTACTTCTTAGCC
* *
19761 TAATTGCTCTGAATTAAACTAACTACTGA
1 TAATTACTCTGAATTAAACTAAATACTGA
19790 CTTTACTTAT
Statistics
Matches: 264, Mismatches: 30, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
52 7 0.03
53 21 0.08
54 50 0.19
55 27 0.10
56 16 0.06
57 96 0.36
58 46 0.17
59 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.49
Consensus pattern (53 bp):
TAATTACTCTGAATTAAACTAAATACTGATTACTCTTTCTTTACTTCTTAGCC
Found at i:25473 original size:45 final size:45
Alignment explanation
Indices: 25404--25517 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
25394 AAAGGTTTCA
*
25404 AGTTGAAAACCCGCAAAGGACGGCCTGAATCCAACGGGGGTTCTGG
1 AGTTGAAAACCCG-AAAGGGCGGCCTGAATCCAACGGGGGTTCTGG
* *
25450 AGTTGAAAGCCCGAAAGGGCGGCCTGAATCCAACGGGGGTTCTTG
1 AGTTGAAAACCCGAAAGGGCGGCCTGAATCCAACGGGGGTTCTGG
*
25495 AGTTGAAAACTCGAAAGGGCGGC
1 AGTTGAAAACCCGAAAGGGCGGC
25518 TCGAGTGAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
45 51 0.81
46 12 0.19
ACGTcount: A:0.28, C:0.22, G:0.34, T:0.16
Consensus pattern (45 bp):
AGTTGAAAACCCGAAAGGGCGGCCTGAATCCAACGGGGGTTCTGG
Found at i:26402 original size:64 final size:63
Alignment explanation
Indices: 26300--26761 Score: 590
Period size: 64 Copynumber: 7.3 Consensus size: 63
26290 AGTTTTTATT
* * *
26300 AGAGTTTCTGTTTCAACTCAAAATCTTGCTTCATTTTAAAATCCTGTTTGAGGTCTCTGG-CAG
1 AGAGTTTCTGTTTTAATTCAAAATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGTC-G
** * *
26363 AGAGTTTCTGTTTTAATTCGCCAATCTTGTTTCCTTTTAAAATCTTGTTTGAGGTCTCTGGTCG
1 AGAGTTTCTGTTTTAATTC-AAAATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGTCG
* * *
26427 AGAGTTTCTGTTTTAATTCAAAAATCTTGTTTCATTTGAAAATCTTGTTCGAGGTCTCTGGTCG
1 AGAGTTTCTGTTTTAATTC-AAAATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGTCG
** * *
26491 AGAGTTTCTGTTCAAATCCAAAAGTCTTGTTTCATTTTAAAATCCTG-TTCAGGTCTCTGG-CAG
1 AGAGTTTCTGTTTTAATTCAAAA-TCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGTC-G
** * * * * *
26554 AGAGTTTCTGTTTTAATTCGCCAATCTTGTCTCATTTTAAAATCCAGTTCGAGGTCTTTAGTCG
1 AGAGTTTCTGTTTTAATTC-AAAATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGTCG
* * *
26618 AGAGTTTCTGTTTTAATTCAAACATCTTGTTTCATTTTAAAATCATGTTCGATGTCTCTGGTCG
1 AGAGTTTCTGTTTTAATTCAAA-ATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGTCG
*
26682 AGAGTTTCTGTTTTAATTCAAAAATCTTGTTTCATTTGAAAATCC-GATTTGAGGTCTCTGGTCG
1 AGAGTTTCTGTTTTAATTC-AAAATCTTGTTTCATTTTAAAATCCTG-TTTGAGGTCTCTGGTCG
26746 AGAGTTTCTGTTTTAA
1 AGAGTTTCTGTTTTAA
26762 AATCATGTTC
Statistics
Matches: 346, Mismatches: 43, Indels: 19
0.85 0.11 0.05
Matches are distributed among these distances:
62 1 0.00
63 72 0.21
64 268 0.77
65 5 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (63 bp):
AGAGTTTCTGTTTTAATTCAAAATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGTCG
Found at i:26624 original size:191 final size:190
Alignment explanation
Indices: 26300--26761 Score: 687
Period size: 191 Copynumber: 2.4 Consensus size: 190
26290 AGTTTTTATT
* *
26300 AGAGTTTCTGTTTCAACTCAAAATCTTGCTTCATTTTAAAATCCTGTTTGAGGTCTCTGGCAGAG
1 AGAGTTTCTG-TTCAAATCAAAATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGCAGAG
* * ** * *
26365 AGTTTCTGTTTTAATTCGCCAATCTTGTTTCCTTTTAAAATCTTGTTTGAGGTCTCTGGTCGAGA
65 AGTTTCTGTTTTAATTCGCCAATCTTGTCTCATTTTAAAATCCAGTTCGAGGTCTCTAGTCGAGA
*
26430 GTTTCTGTTTTAATTCAAAAATCTTGTTTCATTTGAAAATCTTGTTCGAGGTCTCTGGTCG
130 GTTTCTGTTTTAATTCAAAAATCTTGTTTCATTTGAAAATCATGTTCGAGGTCTCTGGTCG
*
26491 AGAGTTTCTGTTCAAATCCAAAAGTCTTGTTTCATTTTAAAATCCTG-TTCAGGTCTCTGGCAGA
1 AGAGTTTCTGTTCAAAT-CAAAA-TCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGCAGA
*
26555 GAGTTTCTGTTTTAATTCGCCAATCTTGTCTCATTTTAAAATCCAGTTCGAGGTCTTTAGTCGAG
64 GAGTTTCTGTTTTAATTCGCCAATCTTGTCTCATTTTAAAATCCAGTTCGAGGTCTCTAGTCGAG
* * *
26620 AGTTTCTGTTTTAATTCAAACATCTTGTTTCATTTTAAAATCATGTTCGATGTCTCTGGTCG
129 AGTTTCTGTTTTAATTCAAAAATCTTGTTTCATTTGAAAATCATGTTCGAGGTCTCTGGTCG
* * *
26682 AGAGTTTCTGTTTTAATTCAAAAATCTTGTTTCATTTGAAAATCC-GATTTGAGGTCTCTGGTC-
1 AGAGTTTCTG-TTCAAATC-AAAATCTTGTTTCATTTTAAAATCCTG-TTTGAGGTCTCTGG-CA
26745 GAGAGTTTCTGTTTTAA
62 GAGAGTTTCTGTTTTAA
26762 AATCATGTTC
Statistics
Matches: 246, Mismatches: 18, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
190 7 0.03
191 178 0.72
192 60 0.24
193 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (190 bp):
AGAGTTTCTGTTCAAATCAAAATCTTGTTTCATTTTAAAATCCTGTTTGAGGTCTCTGGCAGAGA
GTTTCTGTTTTAATTCGCCAATCTTGTCTCATTTTAAAATCCAGTTCGAGGTCTCTAGTCGAGAG
TTTCTGTTTTAATTCAAAAATCTTGTTTCATTTGAAAATCATGTTCGAGGTCTCTGGTCG
Done.