Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014171.1 Corchorus olitorius cultivar O-4 contig14204, 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: 65337
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:408 original size:18 final size:17
Alignment explanation
Indices: 365--419 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
355 GATCTTGATT
*
365 TTTCAGGGCTTTTCTGC
1 TTTCAGAGCTTTTCTGC
382 -TTCAGAGCTTTTCTGC
1 TTTCAGAGCTTTTCTGC
*
398 TTTGTAGAGCTTCTT-TGC
1 TTT-CAGAGCTT-TTCTGC
416 TTTC
1 TTTC
420 TGAATTGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 15 0.47
17 2 0.06
18 13 0.41
19 2 0.06
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (17 bp):
TTTCAGAGCTTTTCTGC
Found at i:4103 original size:25 final size:25
Alignment explanation
Indices: 4073--4120 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
4063 ATGCAATGTC
4073 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
*
4098 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGATTTGAGCTACATGAA
4121 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:4622 original size:50 final size:50
Alignment explanation
Indices: 4554--4828 Score: 437
Period size: 50 Copynumber: 5.5 Consensus size: 50
4544 AAGAGATCCT
*
4554 CGAGTTTGCCTTGTGGAAAAGCCTATGTTGATAATTGACCTGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCTGTATGGAAA
* *
4604 CGAGCTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCAGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCTGTATGGAAA
* **
4654 TGAGTTTGGCTTGTGGAAAAGCCTACATTGATAATTGA-CTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCT-GTATGGAAA
* *
4704 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCCGTTTGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCTGTATGGAAA
4754 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGA-CTCGTATGGAAA
1 CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCT-GTATGGAAA
*
4804 CGAATTTGGCTTGTGGAAAAGCCTA
1 CGAGTTTGGCTTGTGGAAAAGCCTA
4829 AAGCATTCGG
Statistics
Matches: 206, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
49 2 0.01
50 203 0.99
51 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.31
Consensus pattern (50 bp):
CGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACCTGTATGGAAA
Found at i:6445 original size:6 final size:6
Alignment explanation
Indices: 6431--6498 Score: 64
Period size: 6 Copynumber: 10.7 Consensus size: 6
6421 TCAATTCCCT
* ** *
6431 TTTTTA TTTTGA TTTTGA TTTTGA TTTTTT TTTTAA TTTTTGA TTTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA -TTTTGA -TTTTGA
6481 TTTTTGA TTTTTGA TTTT
1 -TTTTGA -TTTTGA TTTT
6499 TTTGTTTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
6 29 0.53
7 26 0.47
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (6 bp):
TTTTGA
Found at i:6506 original size:14 final size:13
Alignment explanation
Indices: 6430--6511 Score: 60
Period size: 14 Copynumber: 6.2 Consensus size: 13
6420 ATCAATTCCC
*
6430 TTTTTTATTTTGA
1 TTTTTTTTTTTGA
**
6443 -TTTTGATTTTGA
1 TTTTTTTTTTTGA
*
6455 -TTTTTTTTTTAA
1 TTTTTTTTTTTGA
*
6467 TTTTTGATTTTTGA
1 TTTTT-TTTTTTGA
*
6481 TTTTTGATTTTTGA
1 TTTTT-TTTTTTGA
6495 TTTTTTTGTTTTTGA
1 -TTTTTT-TTTTTGA
6510 TT
1 TT
6512 GAATTTCTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
12 20 0.34
13 4 0.07
14 22 0.38
15 12 0.21
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTTTGA
Found at i:6508 original size:6 final size:7
Alignment explanation
Indices: 6437--6499 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
6427 CCCTTTTTTA
6437 TTTTGA-
1 TTTTGAT
6443 TTTTGA-
1 TTTTGAT
6449 TTTTGAT
1 TTTTGAT
6456 TTTT--T
1 TTTTGAT
*
6461 TTTTAAT
1 TTTTGAT
6468 TTTTGAT
1 TTTTGAT
6475 TTTTGAT
1 TTTTGAT
6482 TTTTGAT
1 TTTTGAT
6489 TTTTGAT
1 TTTTGAT
6496 TTTT
1 TTTT
6500 TTGTTTTTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
5 5 0.09
6 12 0.23
7 36 0.68
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (7 bp):
TTTTGAT
Found at i:6924 original size:9 final size:10
Alignment explanation
Indices: 6900--6945 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
6890 TTCATTTTTT
*
6900 ATTTTTCGTC
1 ATTTTTCATC
6910 ATTTTTCATC
1 ATTTTTCATC
6920 ATTTTTTCATTC
1 A-TTTTTCA-TC
6932 ATTTTT--TC
1 ATTTTTCATC
6940 ATTTTT
1 ATTTTT
6946 TATTTTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.24
10 10 0.30
11 12 0.36
12 3 0.09
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTTTCATC
Found at i:6925 original size:11 final size:11
Alignment explanation
Indices: 6901--6941 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
6891 TCATTTTTTA
*
6901 TTTTTCGTCA-
1 TTTTTCATCAT
6911 TTTTTCATCAT
1 TTTTTCATCAT
6922 TTTTTCATTCAT
1 TTTTTCA-TCAT
6934 TTTTTCAT
1 TTTTTCAT
6942 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 9 0.32
11 8 0.29
12 11 0.39
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (11 bp):
TTTTTCATCAT
Found at i:6950 original size:7 final size:8
Alignment explanation
Indices: 6888--6952 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 8
6878 AGTGCCTTTA
6888 TTTTCATT
1 TTTTCATT
6896 TTTT-ATT
1 TTTTCATT
6903 TTTCGTCATT
1 TTT--TCATT
6913 TTTCATCATT
1 TTT--TCATT
6923 TTTTCA--
1 TTTTCATT
6929 --TTCATT
1 TTTTCATT
6935 TTTTCATT
1 TTTTCATT
6943 TTTT-ATT
1 TTTTCATT
6950 TTT
1 TTT
6953 ATGGGAAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
4 4 0.08
7 12 0.24
8 17 0.35
9 1 0.02
10 15 0.31
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTTCATT
Found at i:10678 original size:40 final size:40
Alignment explanation
Indices: 10622--11196 Score: 656
Period size: 40 Copynumber: 14.3 Consensus size: 40
10612 CTCCTAATTA
* * * * * *
10622 GGAAGGGGAAATTGAGAATTTATACAACTCTTTTCGGTGG
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
* * *
10662 GGAAAGGCAAACTGAGAATTTAGACAACACTTTCCGGTAGG
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGT-GG
* * *
10703 GGAA-GGCAAACAGGGAATTTAGACAACACCTTCCGGTGG
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
* * *
10742 GGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGA
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
* * * * *
10782 GGAAGGGCAAACTGCGTATTTACACAACAGCTTGCGGTGG
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
* * *
10822 GGAAGGGCAAACTCG-GTATTTAGACAACACCTTCTGGTGG
1 GGAAGGGCAAACT-GAGAATTTAAACAACACCTTCCGGTGG
* * *
10862 GGAAGGGCAAACCGAGTATTTAAACAACACCTTCCGGTGC
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
* * * *
10902 AGAAGGGCAAACTGGGTATTTAAACAACACCTTCTGGTGG
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
* * *
10942 GGCAAGGGCAAATTGGGTATTTAAACAACACCTTCCGGTGG
1 GG-AAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
* *
10983 GGAAGGGCAAA-TGGCGTATTTAAACAACACCTTCCGGTGG
1 GGAAGGGCAAACT-GAGAATTTAAACAACACCTTCCGGTGG
* * *
11023 GGAAAGGCAAACCGGGAATTTAAACAACACCTTCCGGTGG
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
*
11063 GGAAGGGCAAACTGAGTAA-TTAAACAACACCTTCCGGTAG
1 GGAAGGGCAAACTGAG-AATTTAAACAACACCTTCCGGTGG
* * *
11103 GGAAGGGCAAACTAAGAATTTAAACAGCACCTTCTGGTGG
1 GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
**
11143 GGAAGGGCAAACTG-GATATTTTGACAACACCTTCCGGTGG
1 GGAAGGGCAAACTGAGA-ATTTAAACAACACCTTCCGGTGG
*
11183 GGAAGAGCAAACTG
1 GGAAGGGCAAACTG
11197 GGTATTTGGA
Statistics
Matches: 472, Mismatches: 53, Indels: 20
0.87 0.10 0.04
Matches are distributed among these distances:
39 12 0.03
40 413 0.88
41 47 0.10
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (40 bp):
GGAAGGGCAAACTGAGAATTTAAACAACACCTTCCGGTGG
Found at i:10809 original size:120 final size:120
Alignment explanation
Indices: 10622--11203 Score: 727
Period size: 120 Copynumber: 4.8 Consensus size: 120
10612 CTCCTAATTA
* * * * * * * * * * *
10622 GGAAGGGGAAATTGAGAATTTATACAACTCTTTTCGGTGGGGAAAGGCAAACTGAGAATTTAGAC
1 GGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* * * *
10687 AACACTTTCCGGTAGGGGAA-GGCAAACAGGGAATTTAGACAACACCTTCCGGTGG
66 AACACCTTCCGGT-GGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGG
* * * *
10742 GGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGAGGAAGGGCAAACTGCGTATTTACAC
1 GGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* * * * *
10807 AACAGCTTGCGGTGGGGAAGGGCAAACTCGGTATTTAGACAACACCTTCTGGTGG
66 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGG
* **
10862 GGAAGGGCAAACCGAGTATTTAAACAACACCTTCCGGTGCAGAAGGGCAAACTGGGTATTTAAAC
1 GGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
* *
10927 AACACCTTCTGGTGGGGCAAGGGCAAATTGGGTATTTAAACAACACCTTCCGGTGG
66 AACACCTTCCGGTGGGG-AAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGG
* * * *
10983 GGAAGGGCAAA-TGGCGTATTTAAACAACACCTTCCGGTGGGGAAAGGCAAACCGGGAATTTAAA
1 GGAAGGGCAAACT-GAGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAA
* * *
11047 CAACACCTTCCGGTGGGGAAGGGCAAACTGAGTAATTAAACAACACCTTCCGGTAG
65 CAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGG
* * * * * **
11103 GGAAGGGCAAACTAAGAATTTAAACAGCACCTTCTGGTGGGGAAGGGCAAACTGGATATTTTGAC
1 GGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
*
11168 AACACCTTCCGGTGGGGAAGAGCAAACTGGGTATTT
66 AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT
11204 GGACTAAACA
Statistics
Matches: 399, Mismatches: 59, Indels: 8
0.86 0.13 0.02
Matches are distributed among these distances:
119 6 0.02
120 285 0.71
121 108 0.27
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (120 bp):
GGAAGGGCAAACTGAGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAC
AACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGG
Found at i:16837 original size:19 final size:18
Alignment explanation
Indices: 16813--16848 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
16803 TGAAGACTTA
*
16813 TTGAAGACTATTTGAAGAT
1 TTGAAGACCA-TTGAAGAT
16832 TTGAAGACCATTGAAGA
1 TTGAAGACCATTGAAGA
16849 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGACCATTGAAGAT
Found at i:17944 original size:24 final size:24
Alignment explanation
Indices: 17917--17991 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 24
17907 GATCAAGAGG
17917 TAATTATTTAAAGAATAAAAAGGA
1 TAATTATTTAAAGAATAAAAAGGA
* ** * * *
17941 TAATTCA--CACTGGATCAAGAGG-
1 TAATT-ATTTAAAGAATAAAAAGGA
17963 TAATTATTTAAAGAATAAAAAGGA
1 TAATTATTTAAAGAATAAAAAGGA
17987 TAATT
1 TAATT
17992 CACACTGGAT
Statistics
Matches: 35, Mismatches: 12, Indels: 8
0.64 0.22 0.15
Matches are distributed among these distances:
21 1 0.03
22 5 0.14
23 18 0.51
24 10 0.29
25 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (24 bp):
TAATTATTTAAAGAATAAAAAGGA
Found at i:17962 original size:46 final size:46
Alignment explanation
Indices: 17899--18007 Score: 218
Period size: 46 Copynumber: 2.4 Consensus size: 46
17889 TGAGTAATTA
17899 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAAGGATAAT
1 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAAGGATAAT
17945 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAAGGATAAT
1 TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAAGGATAAT
17991 TCACACTGGATCAAGAG
1 TCACACTGGATCAAGAG
18008 CTTTATCTAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (46 bp):
TCACACTGGATCAAGAGGTAATTATTTAAAGAATAAAAAGGATAAT
Found at i:23928 original size:54 final size:54
Alignment explanation
Indices: 23865--24233 Score: 544
Period size: 54 Copynumber: 6.8 Consensus size: 54
23855 TTTTGTAGAA
* * * * *
23865 AGTTGATCCTCAAATGATCAAGTGCGGTTATTCCAAGAAGTTTTTAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
* * * * *
23919 AGTTGATCCTCAGATGATCCAATGCGATCAATCCAAGAAGTTTTCAATGGTCAG
1 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
*
23973 AGTTGATCCTCAAATGATCCAGTGTGGTCATTCCAAGAAGTTTAT-AATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTT-TCAATGATCAG
24027 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
24081 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
1 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
* ** *
24135 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCGAAGAAGTTTTTGATGATTAG
1 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
* * *
24189 AGTTGAT-CTCCAGATGATCCAGTGCGGTCCTTACAAGAAGTTTTC
1 AGTTGATCCT-CAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTC
24234 GAGTGCGGTT
Statistics
Matches: 288, Mismatches: 24, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
53 3 0.01
54 284 0.99
55 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (54 bp):
AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAG
Found at i:24253 original size:26 final size:26
Alignment explanation
Indices: 24209--24259 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
24199 CAGATGATCC
24209 AGTGCGGTCCTTACAAGAAGTTTTCG
1 AGTGCGGTCCTTACAAGAAGTTTTCG
* * *
24235 AGTGCGGTTCTTCCGAGAAGTTTTC
1 AGTGCGGTCCTTACAAGAAGTTTTC
24260 AAAGTTGATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (26 bp):
AGTGCGGTCCTTACAAGAAGTTTTCG
Found at i:24385 original size:181 final size:180
Alignment explanation
Indices: 24081--24415 Score: 487
Period size: 181 Copynumber: 1.9 Consensus size: 180
24071 CAATGATCAG
* *
24081 AGTTGATCCTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTC
1 AGTTGATCCTCAAATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAAAGTTGATCCTC
* * *
24146 AGATGATCCAGTGTGGTCATTCGAAGAAGTTTTTGATGATTAGAGTTGATCTCCAGATGATCCAG
66 AGATGATCCAGTGTGGTCATTCGAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATGATCCAG
24211 TGCGGTCCTTACAAGAAGTTTTCGAGTGCGGTTCTTCCGAGAAGTTTTCAA
131 TGCGGTCCTT-CAAGAAGTTTTCGAGTGCGGTTCTTCCGAGAAGTTTTCAA
* * * * *
24262 AGTTGAT-CTCCAAATGATCCAGTGTGGTCGTTTCATGAAGTTTTCGAA-GATTAAAGTTGATCT
1 AGTTGATCCT-CAAATGATCCAGTGTGGTCATTCCAAGAAGTTTTC-AATGATCAAAGTTGATCC
* *
24325 TCAGATGATCCGGTGTGGTCGTTTC-AAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATGATC
64 TCAGATGATCCAGTGTGGTC-ATTCGAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATGATC
* *
24389 CAGTGTGGTCGTTCAAGAAGTTTTCGA
128 CAGTGCGGTCCTTCAAGAAGTTTTCGA
24416 TGATCAGAGT
Statistics
Matches: 137, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
180 16 0.12
181 116 0.85
182 5 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (180 bp):
AGTTGATCCTCAAATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAAAGTTGATCCTC
AGATGATCCAGTGTGGTCATTCGAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGATGATCCAG
TGCGGTCCTTCAAGAAGTTTTCGAGTGCGGTTCTTCCGAGAAGTTTTCAA
Found at i:24427 original size:53 final size:54
Alignment explanation
Indices: 24262--24452 Score: 278
Period size: 54 Copynumber: 3.5 Consensus size: 54
24252 AAGTTTTCAA
* * * *
24262 AGTTGATCTCCAAATGATCCAGTGTGGTCGTTTCATGAAGTTTTCGAAGATTAA
1 AGTTGATCTCCAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
* *
24316 AGTTGATCTTCAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
1 AGTTGATCTCCAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
*
24370 AGTTGATCTCCAGATGATCCAGTGTGGTCG-TTCAAGAAGTTTTCGATGATCAG
1 AGTTGATCTCCAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
*
24423 AGTTGATCTCCA-ATTTGATCCAGTATGGTC
1 AGTTGATCTCCAGA--TGATCCAGTGTGGTC
24453 ACTCCAAGAA
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
52 1 0.01
53 34 0.27
54 90 0.72
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (54 bp):
AGTTGATCTCCAGATGATCCAGTGTGGTCGTTTCAAGAAGTTTTCGAAGATCAG
Found at i:24518 original size:289 final size:289
Alignment explanation
Indices: 23973--24519 Score: 704
Period size: 289 Copynumber: 1.9 Consensus size: 289
23963 CAATGGTCAG
*
23973 AGTTGATCCTCAAATGATCCAGTGTGGTCATTCCAAGAAGTTTATAATGATCAGAGTTGATCCTC
1 AGTTGATCCTCAAATGATCCAGTGTGGTCATTCCAAGAAGTTTATAATGATCAAAGTTGATCCTC
24038 AGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAG
66 AGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAG
* *
24103 TGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTGTGGTCATTC
131 TGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTATGGTCACTC
* ** * * *
24168 GAAGAAGTTTTTGATGATTAGAGTTGATCTCCAGATGATCCAGTGCGGTCCTTACAAGAAGTTTT
196 CAAGAAGTTTTCCATGATGAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTACAAGAAGTTTT
24233 CGAGTGCGGTTCTTCCGAGAAGTTTTCAA
261 CGAGTGCGGTTCTTCCGAGAAGTTTTCAA
* * * *
24262 AGTTGAT-CTCCAAATGATCCAGTGTGGTCGTTTCATGAAGTTT-TCGAA-GATTAAAGTTGATC
1 AGTTGATCCT-CAAATGATCCAGTGTGGTCATTCCAAGAAGTTTAT--AATGATCAAAGTTGATC
* * * *
24324 TTCAGATGATCCGGTGTGGTCGTTTCAAGAAGTTTTCGAA-GATCAGAGTTGAT-CTCCAGATGA
63 CTCAGATGATCCAGTGTGGTCATTCCAAGAAGTTTTC-AATGATCAGAGTTGATCCT-CAGATGA
* *
24387 TCCAGTGTGGTCGTT-CAAGAAGTTTTCGATGATCAGAGTTGAT-CTCCA-ATTTGATCCAGTAT
126 TCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCT-CAGA--TGATCCAGTAT
* *
24449 GGTCACTCCAAGAAAAG-TTTCCATGATCGAG-GTTGCATCT-TAAATGATCCAGTGCGGTTATT
188 GGTCACTCCAAG--AAGTTTTCCATGAT-GAGAGTTG-ATCTCCAAATGATCCAGTGCGGTCATT
*
24511 -TAAGAAGTT
249 ACAAGAAGTT
24520 CAACTTTGAA
Statistics
Matches: 224, Mismatches: 22, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
287 3 0.01
288 34 0.15
289 144 0.64
290 34 0.15
291 9 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (289 bp):
AGTTGATCCTCAAATGATCCAGTGTGGTCATTCCAAGAAGTTTATAATGATCAAAGTTGATCCTC
AGATGATCCAGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAG
TGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCTCAGATGATCCAGTATGGTCACTC
CAAGAAGTTTTCCATGATGAGAGTTGATCTCCAAATGATCCAGTGCGGTCATTACAAGAAGTTTT
CGAGTGCGGTTCTTCCGAGAAGTTTTCAA
Found at i:26054 original size:19 final size:19
Alignment explanation
Indices: 26030--26147 Score: 52
Period size: 19 Copynumber: 6.4 Consensus size: 19
26020 TTTTTATAGC
26030 TATTTATCTATTATCTATT
1 TATTTATCTATTATCTATT
* * *
26049 TATTTA-CTTTTTTTCTTTT
1 TATTTATC-TATTATCTATT
* **
26068 TATTTAT-TA--ATTTAAC
1 TATTTATCTATTATCTATT
* *
26084 TA-TTATCTATTTATTTA-C
1 TATTTATCTA-TTATCTATT
*
26102 TATTTATCTATTTATTTATT
1 TATTTATCTA-TTATCTATT
* *
26122 AATTTAGCTATTATCTTATT
1 TATTTATCTATTATC-TATT
26142 T-TTTAT
1 TATTTAT
26148 TTTTTTTCCT
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
15 4 0.05
16 6 0.08
18 5 0.07
19 48 0.64
20 12 0.16
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.65
Consensus pattern (19 bp):
TATTTATCTATTATCTATT
Found at i:26087 original size:46 final size:46
Alignment explanation
Indices: 26031--26155 Score: 180
Period size: 46 Copynumber: 2.7 Consensus size: 46
26021 TTTTATAGCT
* *
26031 ATTTATCTATTATCTATTTATTTACTTTTTTTCTTTTTATTTATTA
1 ATTTAACTATTATCTATTTATTTACTTTTTTTCTATTTATTTATTA
* *
26077 ATTTAACTATTATCTATTTATTTACTATTTATCTATTTATTTATTA
1 ATTTAACTATTATCTATTTATTTACTTTTTTTCTATTTATTTATTA
* *
26123 ATTTAGCTATTATCTTATTT-TTTATTTTTTTTC
1 ATTTAACTATTATC-TATTTATTTACTTTTTTTC
26156 CTACCTATCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
46 65 0.93
47 5 0.07
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.66
Consensus pattern (46 bp):
ATTTAACTATTATCTATTTATTTACTTTTTTTCTATTTATTTATTA
Found at i:26096 original size:27 final size:27
Alignment explanation
Indices: 26066--26148 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 27
26056 TTTTTTTCTT
26066 TTTATTTATTAATTTAACTATTATCTA
1 TTTATTTATTAATTTAACTATTATCTA
*
26093 TTTA--T-TT-A-CT-A-T-TTATCTA
1 TTTATTTATTAATTTAACTATTATCTA
*
26112 TTTATTTATTAATTTAGCTATTATCTTA
1 TTTATTTATTAATTTAACTATTATC-TA
26140 TTT-TTTATT
1 TTTATTTATT
26149 TTTTTTCCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 18
0.68 0.05 0.28
Matches are distributed among these distances:
19 11 0.25
20 1 0.02
21 2 0.05
22 3 0.07
23 2 0.05
24 3 0.07
25 1 0.02
26 1 0.02
27 15 0.34
28 5 0.11
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTATTTATTAATTTAACTATTATCTA
Found at i:26105 original size:7 final size:8
Alignment explanation
Indices: 26029--26121 Score: 52
Period size: 8 Copynumber: 11.6 Consensus size: 8
26019 TTTTTTATAG
26029 CTATTTAT
1 CTATTTAT
26037 CTA-TTAT
1 CTATTTAT
26044 CTATTTAT
1 CTATTTAT
* *
26052 TTACTTTTT
1 CTA-TTTAT
* *
26061 TTCTTT-T
1 CTATTTAT
26068 -TATTTAT
1 CTATTTAT
*
26075 -TAATTTAA
1 CT-ATTTAT
26083 CTA-TTAT
1 CTATTTAT
26090 CTATTTATTT
1 CTATTTA--T
26100 ACTATTTAT
1 -CTATTTAT
26109 CTATTTAT
1 CTATTTAT
*
26117 TTATT
1 CTATT
26122 AATTTAGCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
6 4 0.06
7 16 0.23
8 33 0.48
9 8 0.12
10 1 0.01
11 7 0.10
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.66
Consensus pattern (8 bp):
CTATTTAT
Found at i:26197 original size:8 final size:8
Alignment explanation
Indices: 26184--26236 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
26174 TTCACTGTAC
26184 CTATTTAT
1 CTATTTAT
26192 CTATTTAT
1 CTATTTAT
* * *
26200 CTCTATAC
1 CTATTTAT
26208 CTATTTAT
1 CTATTTAT
*
26216 CTTTTTAT
1 CTATTTAT
*
26224 TTATTTAT
1 CTATTTAT
*
26232 TTATT
1 CTATT
26237 ATTATTATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (8 bp):
CTATTTAT
Found at i:26208 original size:24 final size:24
Alignment explanation
Indices: 26157--26223 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
26147 TTTTTTTTCC
* *
26157 TACCTATCTATCTA-TTATTCACTG
1 TACCTATTTATCTATTTA-TCACTA
*
26181 TACCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCACTA
*
26205 TACCTATTTATCTTTTTAT
1 TACCTATTTATCTATTTAT
26224 TTATTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.01, T:0.54
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCACTA
Found at i:37084 original size:42 final size:42
Alignment explanation
Indices: 37028--37146 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 42
37018 ATATCCATTG
* *
37028 ATATATG-TCATACATCCTTCATGCATTATCCATGT-CTTTGT
1 ATATATGTTCATACATCCATCATGCATTATCCAT-TCCTTTGC
37069 ATATATGTTCATACATCCATCATGCATTATCCATTCCTTTGC
1 ATATATGTTCATACATCCATCATGCATTATCCATTCCTTTGC
* *** *
37111 ATATATGTTCATGCATAGGTCATGAATTATCCATTC
1 ATATATGTTCATACATCCATCATGCATTATCCATTC
37147 ATTACTACAT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 8 0.12
42 61 0.88
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (42 bp):
ATATATGTTCATACATCCATCATGCATTATCCATTCCTTTGC
Found at i:38309 original size:16 final size:14
Alignment explanation
Indices: 38283--38333 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
38273 CAAGAGACGT
*
38283 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-GG
38298 TTTTCAAGGAAAAGG
1 TTTTCAA-GAAAAGG
*
38313 TTTTCAA-AAATGAG
1 TTTTCAAGAAAAG-G
38327 TTTTCAA
1 TTTTCAA
38334 AATTTTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.12
14 8 0.25
15 15 0.47
16 5 0.16
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:40670 original size:67 final size:67
Alignment explanation
Indices: 40560--40773 Score: 297
Period size: 67 Copynumber: 3.2 Consensus size: 67
40550 TTTTAGAAGT
* *
40560 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCAGAA-GATGATTGGAAGACAATCTCATCAA-G
1 ACACCGAAAGACGGTTTGCTAGAAAGAATTTTCA-AATGTTGATTGGAAGACAATCTCATCAAGG
40623 AAGC
65 AA-C
* *
40627 ACATCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGA
1 ACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATCAAGGA
*
40692 AT
66 AC
* * *
40694 ACACCGGAAGACGGTTTGCTAGAAAGAATTTTCGAATGTTGATTGGAAGACAATCTCATTAAGGA
1 ACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATCAAGGA
*
40759 AT
66 AC
* *
40761 ACATCGGAAGACG
1 ACACCGAAAGACG
40774 ATCTCAACAA
Statistics
Matches: 136, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
66 2 0.01
67 131 0.96
68 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.24
Consensus pattern (67 bp):
ACACCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATCAAGGA
AC
Found at i:40864 original size:64 final size:64
Alignment explanation
Indices: 40763--40951 Score: 297
Period size: 64 Copynumber: 3.0 Consensus size: 64
40753 TAAGGAATAC
*** *
40763 ATCGGAAGACGATCTCAACAAGAAGTACACCAGAAGATGATTTCTCAAAAATTTTCAGAAGTTG
1 ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTG
* *
40827 ATCGGAAGACGATTTTGTCAAGAATTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTG
1 ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTG
* * *
40891 ATCGGGAGACGATCTTGTCCAGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAAG
1 ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAG
40952 ATCTCGTCAA
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 114 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (64 bp):
ATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTG
Found at i:40965 original size:50 final size:50
Alignment explanation
Indices: 40901--41001 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
40891 ATCGGGAGAC
* *
40901 GATCTTGTCCAGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAA
1 GATCTCGTCAAGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAA
* *
40951 GATCTCGTCAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAGAA
1 GATCTCGTCAAGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAA
41001 G
1 G
41002 TCGATCGGAA
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:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (50 bp):
GATCTCGTCAAGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAA
Found at i:41027 original size:64 final size:64
Alignment explanation
Indices: 40951--41363 Score: 630
Period size: 64 Copynumber: 6.5 Consensus size: 64
40941 ATTTTCAGAA
* * *
40951 GATCTCGTCAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAGAAGTCGATCGGAAGAC
1 GATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
41015 GATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
1 GATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
* *
41079 GATCTTGTCAAGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAAGTTGATCGGCAGAC
1 GATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
* * * *
41143 GATCTCGTCAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAAAAGTCGATCGGAAGAC
1 GATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
* *
41207 GATCTTGTCAAGAAGTACACTAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTAATCGGAAGAC
1 GATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
* * * * **
41271 GATCTT-CCTAAAAAGTACACCAGAAGATAGTTTCTCGAAAGGTTTCAGAAGTTGATCGGAAGAC
1 GATCTTGTC-AAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
* * *
41335 GATCTTGTTAAGAAATACACCGGAAGATG
1 GATCTTGTCAAGAAGTACACCAGAAGATG
41364 ATTTTTTAGA
Statistics
Matches: 316, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
63 1 0.00
64 315 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (64 bp):
GATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGAC
Found at i:41081 original size:178 final size:178
Alignment explanation
Indices: 40781--41321 Score: 789
Period size: 178 Copynumber: 3.0 Consensus size: 178
40771 ACGATCTCAA
* * *
40781 CAAGAAGTACACCAGAAGATGATTTCTCAAAAATTTTCAGAAGTTGATCGGAAGACGATTTTGTC
1 CAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAGAAGTCGATCGGAAGACGATCTTGTC
* *
40846 AAGAATTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGGAGACGATCTTGTCC
66 AAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCC
40911 AGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAAGATCTCGT
131 AGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAAGATCTCGT
40959 CAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAGAAGTCGATCGGAAGACGATCTTGTC
1 CAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAGAAGTCGATCGGAAGACGATCTTGTC
*
41024 AAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCA
66 AAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCC
41089 AGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAAGTTGATCGGCAGACGATCTCGT
131 AGAAGTACACCAGAAGATGGTATCTCAAAAATTTTC--------A---G-A-A-GATCTCGT
*
41151 CAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAAAAGTCGATCGGAAGACGATCTTGTC
1 CAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAGAAGTCGATCGGAAGACGATCTTGTC
* *
41216 AAGAAGTACACTAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTAATCGGAAGACGATC-T-TCC
66 AAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCC
* * * * **
41279 TAAAAAGTACACCAGAAGATAGTTTCTCGAAAGGTTTCAGAAG
131 --AGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAAG
41322 TTGATCGGAA
Statistics
Matches: 331, Mismatches: 16, Indels: 32
0.87 0.04 0.08
Matches are distributed among these distances:
178 161 0.49
179 1 0.00
180 1 0.00
181 1 0.00
184 1 0.00
186 1 0.00
189 1 0.00
190 3 0.01
191 2 0.01
192 159 0.48
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (178 bp):
CAAGAAGTACACCAGAAGATGTTTTCTCAAAAATTTTCAGAAGTCGATCGGAAGACGATCTTGTC
AAGAAGTACACCAGAAGATGGTTTCTCAAAAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCC
AGAAGTACACCAGAAGATGGTATCTCAAAAATTTTCAGAAGATCTCGT
Found at i:41616 original size:50 final size:50
Alignment explanation
Indices: 41432--41598 Score: 255
Period size: 50 Copynumber: 3.3 Consensus size: 50
41422 TCCAGAAGCC
*
41432 AATTGGAAGATAGTTCAAAGGATAAGCGGAAGAC-ATTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGA-TCCTTTTAAGATTG
*
41482 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCATTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATTG
* * * * *
41532 AATTGGAAGACAGTTTAAAGGATGAGCGGGAGACGGTCCTTTTAAGATTA
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATTG
41582 AATTGGAAGACAGTTCA
1 AATTGGAAGACAGTTCA
41599 GAGGTTTATC
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
50 106 0.99
51 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (50 bp):
AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATTG
Found at i:41616 original size:100 final size:101
Alignment explanation
Indices: 41432--41624 Score: 271
Period size: 100 Copynumber: 1.9 Consensus size: 101
41422 TCCAGAAGCC
* * *
41432 AATTGGAAGATAGTTCAAAGGATAAGCGGAAGACATTCCTTTTAAGATTGAATTGGAAGACAGTT
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATTAAATTGGAAGACAGTT
41497 CAAAGGATAAGCGGAAGACGAT-CATTTTAAGATTG
66 CAAAGGATAAGCGGAAGACGATCCATTTTAAGATTG
* * * *
41532 AATTGGAAGACAGTTTAAAGGATGAGCGGGAGACGGTCCTTTTAAGATTAAATTGGAAGACAGTT
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATTAAATTGGAAGACAGTT
* * * * *
41597 CAGAGGTTTATCGGGAGACGATCCATTT
66 CAAAGGATAAGCGGAAGACGATCCATTT
41625 CGAAGTAAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
100 75 0.94
101 5 0.06
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (101 bp):
AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATTAAATTGGAAGACAGTT
CAAAGGATAAGCGGAAGACGATCCATTTTAAGATTG
Found at i:42831 original size:104 final size:102
Alignment explanation
Indices: 42643--42832 Score: 242
Period size: 102 Copynumber: 1.8 Consensus size: 102
42633 CAGGTATGTA
* * * * *
42643 TAGCAATTTGTTTGGAAAAATTAAGGTTGGGATGAGTTTAAGGGGCCGAGGAGAAAAGCTGGAGA
1 TAGCAATTTGTTTGGAAAAATTAAGGTTGGAATGAGTTTAAGGGACCGAGAAAAAAAGATGGAGA
42708 TTTCTGGTTTGTTTGAAGGTGTTGGGTTCTTTAGATC
66 TTTCTGGTTTGTTTGAAGGTGTTGGGTTCTTTAGATC
* * *
42745 TAGCAATTTGTTTGGAACAAA-TATGGTTGGAATCGAGTTTAA-GGACTGAGAAAAAACAATATG
1 TAGCAATTTGTTTGGAA-AAATTAAGGTTGGAAT-GAGTTTAAGGGACCGAG-AAAAA-AAGATG
42808 GAGATTT-TGAGTTTGTTTGAAGGTG
62 GAGATTTCTG-GTTTGTTTGAAGGTG
42833 GATGTCGATG
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
102 33 0.44
103 16 0.21
104 26 0.35
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.34
Consensus pattern (102 bp):
TAGCAATTTGTTTGGAAAAATTAAGGTTGGAATGAGTTTAAGGGACCGAGAAAAAAAGATGGAGA
TTTCTGGTTTGTTTGAAGGTGTTGGGTTCTTTAGATC
Found at i:45056 original size:25 final size:25
Alignment explanation
Indices: 45009--45056 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
44999 AAAAATTTTT
* *
45009 GTTAGCAAAAGAGAAGGAGGAATCA
1 GTTAACAAAAGAGAAGGAAGAATCA
45034 GTTAACAAAA-AGAAGGGAAGAAT
1 GTTAACAAAAGAGAA-GGAAGAAT
45057 ACTCATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.52, C:0.06, G:0.29, T:0.12
Consensus pattern (25 bp):
GTTAACAAAAGAGAAGGAAGAATCA
Found at i:57564 original size:24 final size:24
Alignment explanation
Indices: 57537--57602 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
57527 CATAATAATT
57537 ATATATAATTAATTATAAAACAAA
1 ATATATAATTAATTATAAAACAAA
*
57561 ATATATAATT-ATATATATAACAAA
1 ATATATAATTAAT-TATAAAACAAA
*
57585 ATATATATTATAATTATA
1 ATATATAAT-TAATTATA
57603 TTATATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
23 2 0.05
24 28 0.76
25 5 0.14
26 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATATAATTAATTATAAAACAAA
Found at i:57592 original size:68 final size:67
Alignment explanation
Indices: 57520--57647 Score: 197
Period size: 67 Copynumber: 1.9 Consensus size: 67
57510 AATTTAAATT
*
57520 TATATATCATAA-TA-ATTATATATAATTAATTATAAAACAAAATATATAATTATATATATAACA
1 TATATATTATAATTATATTATATATAATTAATTATAAAAC-AAATATATAATTATATATATAACA
57583 AAA
65 AAA
* * *
57586 TATATATTATAATTATATTATATATAATTAATTGTGAAACAAATATGTAATTATATATATAA
1 TATATATTATAATTATATTATATATAATTAATTATAAAACAAATATATAATTATATATATAA
57648 ATATTAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
66 11 0.20
67 23 0.41
68 22 0.39
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (67 bp):
TATATATTATAATTATATTATATATAATTAATTATAAAACAAATATATAATTATATATATAACAA
AA
Found at i:59863 original size:14 final size:15
Alignment explanation
Indices: 59844--59876 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
59834 TTTTGTTTTA
59844 TTTCGTATTT-TGTT
1 TTTCGTATTTGTGTT
*
59858 TTTCGTTTTTGTGTT
1 TTTCGTATTTGTGTT
59873 TTTC
1 TTTC
59877 TTAACATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.03, C:0.09, G:0.15, T:0.73
Consensus pattern (15 bp):
TTTCGTATTTGTGTT
Found at i:63601 original size:17 final size:17
Alignment explanation
Indices: 63575--63607 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
63565 GAAATTGCGT
63575 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
63591 TTTATTTTTTCTATTTT
1 TTTA-TTTTTCTATTTT
63608 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Done.