Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024228.1 Corchorus olitorius cultivar O-4 contig24261, 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: 56109
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1271 original size:2 final size:2
Alignment explanation
Indices: 1251--1298 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1241 TATCTTATCT
*
1251 TA TA T- TA TA -A TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1291 TA TA TA TA
1 TA TA TA TA
1299 GATAGCCTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3601 original size:17 final size:17
Alignment explanation
Indices: 3579--3612 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3569 ATTGCCTGTT
3579 TAACTCATGTTTATGTG
1 TAACTCATGTTTATGTG
3596 TAACTCATGTTTATGTG
1 TAACTCATGTTTATGTG
3613 GTTTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
TAACTCATGTTTATGTG
Found at i:7647 original size:18 final size:18
Alignment explanation
Indices: 7626--7663 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7616 ACGCCGGCGT
7626 TCTCTGTCACGGTCACGG
1 TCTCTGTCACGGTCACGG
* *
7644 TCTCTGTCTCGGTCTCGG
1 TCTCTGTCACGGTCACGG
7662 TC
1 TC
7664 GCGTTCTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.34, G:0.26, T:0.34
Consensus pattern (18 bp):
TCTCTGTCACGGTCACGG
Found at i:7652 original size:6 final size:6
Alignment explanation
Indices: 7635--7683 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
7625 TTCTCTGTCA
* * * * *
7635 CGGTCA CGGTCT CTGTCT CGGTCT CGGTCG CGTTCT CTGTCT CGGTCT
1 CGGTCT CGGTCT CGGTCT CGGTCT CGGTCT CGGTCT CGGTCT CGGTCT
7683 C
1 C
7684 TATCGCGTGC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.02, C:0.35, G:0.29, T:0.35
Consensus pattern (6 bp):
CGGTCT
Found at i:7658 original size:12 final size:12
Alignment explanation
Indices: 7641--7684 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
7631 GTCACGGTCA
7641 CGGTCTCTGTCT
1 CGGTCTCTGTCT
* *
7653 CGGTCTCGGTCG
1 CGGTCTCTGTCT
*
7665 CGTTCTCTGTCT
1 CGGTCTCTGTCT
7677 CGGTCTCT
1 CGGTCTCT
7685 ATCGCGTGCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.27, T:0.39
Consensus pattern (12 bp):
CGGTCTCTGTCT
Found at i:7682 original size:24 final size:24
Alignment explanation
Indices: 7626--7683 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
7616 ACGCCGGCGT
* *
7626 TCTCTGTCACGGTCACGGTCTCTG
1 TCTCGGTCTCGGTCACGGTCTCTG
* *
7650 TCTCGGTCTCGGTCGCGTTCTCTG
1 TCTCGGTCTCGGTCACGGTCTCTG
7674 TCTCGGTCTC
1 TCTCGGTCTC
7684 TATCGCGTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.26, T:0.36
Consensus pattern (24 bp):
TCTCGGTCTCGGTCACGGTCTCTG
Found at i:7689 original size:24 final size:24
Alignment explanation
Indices: 7644--7691 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
7634 ACGGTCACGG
*
7644 TCTCTGTCTCGGTCTCGGTCGCGT
1 TCTCTGTCTCGGTCTCGATCGCGT
*
7668 TCTCTGTCTCGGTCTCTATCGCGT
1 TCTCTGTCTCGGTCTCGATCGCGT
7692 GCCCTATCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.02, C:0.33, G:0.25, T:0.40
Consensus pattern (24 bp):
TCTCTGTCTCGGTCTCGATCGCGT
Found at i:8263 original size:15 final size:15
Alignment explanation
Indices: 8224--8252 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8214 AAGTTTATTG
8224 ATAAT-ATATAATAT
1 ATAATAATATAATAT
8238 ATAATAATATAATAT
1 ATAATAATATAATAT
8253 TTATCAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAATATAATAT
Found at i:8579 original size:31 final size:31
Alignment explanation
Indices: 8544--8615 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
8534 TAAATTACTG
*
8544 CAAATTAAAACAAAT-TAAGCATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGCATTAAATTAAA
* *
8575 CAAA-TAATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGCATTAAATTAAA
8606 CAAATTAAAA
1 CAAATTAAAA
8616 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 7 0.21
31 24 0.71
32 3 0.09
ACGTcount: A:0.61, C:0.10, G:0.04, T:0.25
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGCATTAAATTAAA
Found at i:8878 original size:2 final size:2
Alignment explanation
Indices: 8873--8901 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8863 GTCAAAATGT
8873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8902 TTTTAGTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9811 original size:19 final size:19
Alignment explanation
Indices: 9789--9840 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
9779 TATACAATTA
9789 AATATATATTATATATAAT
1 AATATATATTATATATAAT
*
9808 AATAT-TAGATATATATAAT
1 AATATATA-TTATATATAAT
* *
9827 TATATATATAATAT
1 AATATATATTATAT
9841 TTTATATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 23 0.85
20 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AATATATATTATATATAAT
Found at i:9833 original size:12 final size:12
Alignment explanation
Indices: 9775--9853 Score: 63
Period size: 12 Copynumber: 6.2 Consensus size: 12
9765 CGAATATTAA
*
9775 TATATATACAAT
1 TATATATATAAT
*
9787 TAAATATAT-AT
1 TATATATATAAT
9798 TATATATAATAATAT
1 TATATAT-AT-A-AT
9813 TAGATATATATAAT
1 T--ATATATATAAT
9827 TATATATATAA-
1 TATATATATAAT
*
9838 TATTTTATATAAT
1 TA-TATATATAAT
9851 TAT
1 TAT
9854 TAAACGGTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
11 10 0.18
12 28 0.51
13 2 0.04
14 3 0.05
15 4 0.07
16 2 0.04
17 6 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (12 bp):
TATATATATAAT
Found at i:9846 original size:14 final size:15
Alignment explanation
Indices: 9789--9850 Score: 67
Period size: 14 Copynumber: 4.2 Consensus size: 15
9779 TATACAATTA
9789 AATATATATTATATAT
1 AATA-ATATTATATAT
*
9805 AATAATATTAGATAT
1 AATAATATTATATAT
9820 -AT-ATAATTATATAT
1 AATAAT-ATTATATAT
*
9834 -ATAATATTTTATAT
1 AATAATATTATATAT
9848 AAT
1 AAT
9851 TATTAAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.05
14 20 0.50
15 14 0.35
16 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATAATATTATATAT
Found at i:10663 original size:28 final size:32
Alignment explanation
Indices: 10631--10707 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 32
10621 GATGAAAATC
10631 TCAATTTG-GTCCC-CTACCTAA-AA-AATTG
1 TCAATTTGAGTCCCTCTACCTAATAATAATTG
* *
10659 TCAA-TTGAGTCCCTTTACTTAATAATAATTG
1 TCAATTTGAGTCCCTCTACCTAATAATAATTG
10690 TCAA-TTGAGTCCCTCTAC
1 TCAATTTGAGTCCCTCTAC
10708 TTGCAAGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 3 0.07
28 9 0.21
29 6 0.14
30 2 0.05
31 22 0.52
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (32 bp):
TCAATTTGAGTCCCTCTACCTAATAATAATTG
Found at i:17989 original size:14 final size:14
Alignment explanation
Indices: 17970--18000 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17960 TAGGTATAAT
*
17970 TGAAGTTTGTGGTA
1 TGAAGTTTGTGATA
17984 TGAAGTTTGTGATA
1 TGAAGTTTGTGATA
17998 TGA
1 TGA
18001 TCTTATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (14 bp):
TGAAGTTTGTGATA
Found at i:19943 original size:41 final size:42
Alignment explanation
Indices: 19888--20007 Score: 120
Period size: 41 Copynumber: 2.9 Consensus size: 42
19878 ACCGAAACTC
19888 TACTTGAATACTGAAAAGCCAGCTCGGGGCTGCTGGAAA-TT
1 TACTTGAATACTGAAAAGCCAGCTCGGGGCTGCTGGAAAGTT
* * * * *
19929 TACTTAAATACTGAAGAGCCTA-CTTGGGGC-GTTGAAAAGTT
1 TACTTGAATACTGAAAAGCC-AGCTCGGGGCTGCTGGAAAGTT
* *** *
19970 TACTCGAATACTGAAAAGATTGCTCGGGGCTACTGGAA
1 TACTTGAATACTGAAAAGCCAGCTCGGGGCTGCTGGAA
20008 TGCCTCCTTT
Statistics
Matches: 60, Mismatches: 15, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
40 6 0.10
41 49 0.82
42 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (42 bp):
TACTTGAATACTGAAAAGCCAGCTCGGGGCTGCTGGAAAGTT
Found at i:20163 original size:38 final size:38
Alignment explanation
Indices: 20093--20979 Score: 785
Period size: 38 Copynumber: 23.9 Consensus size: 38
20083 AATTGAAAAG
* *
20093 TGCTGGAAGATGACCTGTTTCTAGTCAACTTTGATATC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATATC
* * * *
20131 TGTTGAAAGACGACCTGTTTCCAGTTACCTTTGATAAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
* *
20169 TGCTGAAAGATGACCTGTTTCCAGTCGACTTTGATAAC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATATC
* * *
20207 TGCTGAAAGAGGACCTGTTTCCAGTTAACTCTTGATAAC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATATC
* *
20246 TGCTGAAAGAGGACCTGTTTCCAGTCAACTTTGATAAC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATATC
* * *
20284 CGCTGAAAGATGACTTGTTTCCAGTCAACTTTGATAACC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
*
20323 T-CTGAAAGATGACCTGTTTCCAGTCACCTTTGATTAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGA-TATC
* * * *
20360 TTCTTAAAGATAACCTGTTTCCAATCAACTTTGATGAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
* *
20398 TGCTGAAAGATGACCTGTTTCCAATCAATTTTGATGAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
20436 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
*
20474 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATATC
* *
20512 --C--------G--CTGTTTCCAGTCGATC-TTGAGGA-C
1 TGCTGAAAGATGACCTGTTTCCAGTC-AACTTTGA-TATC
* * *
20538 TGCTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
*
20577 T-CTGAAAGATGACCTGTTTCCAGTCAACTTTGATAATT
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
* *
20615 TG-TAAAAGATGACCTGTTTCCAGTCAGCTTTGATGAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
20652 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGA-C
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
* *
20690 TGCTAAAAGATGACCTATTTCCAGT---C---G--ATC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATATC
** * * *
20720 T--TGATAA-CCG--CTGTTTCCAATCAACTTTGATGTT
1 TGCTGA-AAGATGACCTGTTTCCAGTCAACTTTGATATC
*
20754 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTAATGAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
* *
20792 AGCTGAAAGATGACCTGTTTCCGGTCAACTTTGATAAT-
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGAT-ATC
* * ** * * *
20830 TGTTGAAAGATGACCAGTTTCCAGTCGTCCTTAATAAC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATATC
* * * * * *
20868 TTCTGAAAGATGACCTGTTTCTAGTCGA-TCCTGAGAAC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATATC
* * * *
20906 TGCTGAAAGATAACCTGTTTCCAGTCGA-TCTTGAAAAC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATATC
*
20944 TGCTGAAAGATGACCCGTTTCCAGTCAACTTTGATA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATA
20980 ACTTCTTTGA
Statistics
Matches: 708, Mismatches: 94, Indels: 94
0.79 0.10 0.10
Matches are distributed among these distances:
26 26 0.04
27 3 0.00
28 5 0.01
29 4 0.01
30 2 0.00
32 2 0.00
34 2 0.00
35 3 0.00
36 6 0.01
37 9 0.01
38 600 0.85
39 46 0.06
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (38 bp):
TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATATC
Found at i:20222 original size:76 final size:76
Alignment explanation
Indices: 20093--20980 Score: 886
Period size: 76 Copynumber: 12.0 Consensus size: 76
20083 AATTGAAAAG
* * * * * *
20093 TGCTGGAAGATGACCTGTTTCTAGTCAACTTTGATATCTGTTGAAAGACGACCTGTTTCCAGTTA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
*
20158 CCTTTGATAAT
66 ACTTTGATAAT
* * *
20169 TGCTGAAAGATGACCTGTTTCCAGTCGACTTTGATAACTGCTGAAAGAGGACCTGTTTCCAGTTA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
*
20234 ACTCTTGATAAC
66 ACT-TTGATAAT
* * *
20246 TGCTGAAAGAGGACCTGTTTCCAGTCAACTTTGATAACCGCTGAAAGATGACTTGTTTCCAGTCA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
*
20311 ACTTTGATAACC
66 ACTTTGATAA-T
* * * * * * *
20323 T-CTGAAAGATGACCTGTTTCCAGTCACCTTTGATTATTTCTTAAAGATAACCTGTTTCCAATCA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
*
20387 ACTTTGATGAT
66 ACTTTGATAAT
* * * *
20398 TGCTGAAAGATGACCTGTTTCCAATCAATTTTGATGATTGCTGAAAGATGACCTGTTTCCAGTCA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
*
20463 ACTTTGATGAT
66 ACTTTGATAAT
20474 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAAC--C--------G--CTGTTTCCAGTCG
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTC-
* ** *
20527 ATC-TTGAGGAC
65 AACTTTGATAAT
* *
20538 TGCTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACCT-CTGAAAGATGACCTGTTTCCAGTC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAA-CTGCTGAAAGATGACCTGTTTCCAGTC
20602 AACTTTGATAATT
65 AACTTTGATAA-T
* * * *
20615 TG-TAAAAGATGACCTGTTTCCAGTCAGCTTTGATGATTGCTGAAAGATGACCTGTTTCCAGTCA
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
* *
20679 ACTTTGATGAC
66 ACTTTGATAAT
* * * *
20690 TGCTAAAAGATGACCTATTTCCAGTCGA-TCTTGATAAC--C--------G--CTGTTTCCAATC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATAACTGCTGAAAGATGACCTGTTTCCAGTC
**
20742 AACTTTGATGTT
65 AACTTTGATAAT
* * *
20754 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTAATGA-TAGCTGAAAGATGACCTGTTTCCGGTC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACT-GCTGAAAGATGACCTGTTTCCAGTC
20818 AACTTTGATAAT
65 AACTTTGATAAT
* * ** * * * * *
20830 TGTTGAAAGATGACCAGTTTCCAGTCGTCCTTAATAACTTCTGAAAGATGACCTGTTTCTAGTCG
1 TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
* * *
20895 A-TCCTGAGAAC
66 ACT-TTGATAAT
* * * *
20906 TGCTGAAAGATAACCTGTTTCCAGTCGA-TCTTGAAAACTGCTGAAAGATGACCCGTTTCCAGTC
1 TGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATAACTGCTGAAAGATGACCTGTTTCCAGTC
20970 AACTTTGATAA
65 AACTTTGATAA
20981 CTTCTTTGAG
Statistics
Matches: 675, Mismatches: 98, Indels: 78
0.79 0.12 0.09
Matches are distributed among these distances:
64 104 0.15
65 4 0.01
66 4 0.01
74 4 0.01
75 8 0.01
76 476 0.71
77 75 0.11
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (76 bp):
TGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTGAAAGATGACCTGTTTCCAGTCA
ACTTTGATAAT
Found at i:20551 original size:64 final size:64
Alignment explanation
Indices: 20450--20576 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 64
20440 GAAAGATGAC
* * * *
20450 CTGTTTCCAGTCAACTTTGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACCG
1 CTGTTTCCAGTCAACTTTGAGGACTGCTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACCG
*
20514 CTGTTTCCAGTCGA-TCTTGAGGACTGCTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACC
1 CTGTTTCCAGTCAACT-TTGAGGACTGCTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACC
20577 TCTGAAAGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 1 0.02
64 56 0.98
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (64 bp):
CTGTTTCCAGTCAACTTTGAGGACTGCTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACCG
Found at i:20673 original size:216 final size:216
Alignment explanation
Indices: 20299--20948 Score: 785
Period size: 216 Copynumber: 3.0 Consensus size: 216
20289 AAAGATGACT
* ** * * *
20299 TGTTTCCAGTCAACTTTGATAACCT-CTGAAAGATGACCTGTTTCCAGTCACCTTTGATTATTTC
1 TGTTTCCAATCAACTTTGAGGA-CTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAATATC
* * * * * **
20363 TTAAAGATAACCTGTTTCCAATCAACTTTGATGATTGCTGAAAGATGACCTGTTTCCAATCAATT
65 TGAAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCAGCT
*
20428 TTGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGATTGCTGAAAGATGACCTGTT
130 TTGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGACTGCTGAAAGATGACCTGTT
20493 TCCAGTCAA-CTTTGATAACCGC
195 TCCAGTCAATC-TTGATAACCGC
* * * * **
20515 TGTTTCCAGTCGA-TCTTGAGGACTGCTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACCTC
1 TGTTTCCAATCAACT-TTGAGGACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAATATC
*
20579 TGAAAGATGACCTGTTTCCAGTCAACTTTGATAATTTG-TAAAAGATGACCTGTTTCCAGTCAGC
65 TGAAAGATGACCTGTTTCCAGTCAACTTTGATAA-TTGCTGAAAGATGACCTGTTTCCAGTCAGC
* *
20643 TTTGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGACTGCTAAAAGATGACCTAT
129 TTTGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGACTGCTGAAAGATGACCTGT
*
20708 TTCCAGTCGATCTTGATAACCGC
194 TTCCAGTCAATCTTGATAACCGC
* ** * * *
20731 TGTTTCCAATCAACTTTGATGTTTGCTGAAAGATGACCTGTTTCCAGTCAACTTTAATGATAGCT
1 TGTTTCCAATCAACTTTGAGGACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAATATCT
* * * *
20796 GAAAGATGACCTGTTTCCGGTCAACTTTGATAATTGTTGAAAGATGACCAGTTTCCAGTC-GTCC
66 GAAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCAG-CT
* * * * * *
20860 TTAATAACTT-CTGAAAGATGACCTGTTTCTAGTCGA-TCCTGA-GAACTGCTGAAAGATAACCT
130 TTGATGA-TTGCTGAAAGATGACCTGTTTCCAGTCAACT-TTGATG-ACTGCTGAAAGATGACCT
* * *
20922 GTTTCCAGTCGATCTTGAAAACTGC
192 GTTTCCAGTCAATCTTGATAACCGC
20947 TG
1 TG
20949 AAAGATGACC
Statistics
Matches: 377, Mismatches: 47, Indels: 20
0.85 0.11 0.05
Matches are distributed among these distances:
215 9 0.02
216 361 0.96
217 7 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (216 bp):
TGTTTCCAATCAACTTTGAGGACTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATAATATCT
GAAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTGAAAGATGACCTGTTTCCAGTCAGCTT
TGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGACTGCTGAAAGATGACCTGTTT
CCAGTCAATCTTGATAACCGC
Found at i:20734 original size:140 final size:140
Alignment explanation
Indices: 20590--20856 Score: 403
Period size: 140 Copynumber: 1.9 Consensus size: 140
20580 GAAAGATGAC
* * * *
20590 CTGTTTCCAGTCAACTTTGATAATTTG-TAAAAGATGACCTGTTTCCAGTCAGCTTTGATGATTG
1 CTGTTTCCAATCAACTTTGAT-ATTTGCTAAAAGATGACCTGTTTCCAGTCAACTTTAATGATAG
*
20654 CTGAAAGATGACCTGTTTCCAGTCAACTTTGATGACTGCTAAAAGATGACCTA-TTTCCAGTCGA
65 CTGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTAAAAGATGACC-AGTTTCCAGTCGA
20718 TCTTGATAACCG
129 TCTTGATAACCG
* *
20730 CTGTTTCCAATCAACTTTGATGTTTGCTGAAAGATGACCTGTTTCCAGTCAACTTTAATGATAGC
1 CTGTTTCCAATCAACTTTGATATTTGCTAAAAGATGACCTGTTTCCAGTCAACTTTAATGATAGC
* * * *
20795 TGAAAGATGACCTGTTTCCGGTCAACTTTGATAATTGTTGAAAGATGACCAGTTTCCAGTCG
66 TGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTAAAAGATGACCAGTTTCCAGTCG
20857 TCCTTAATAA
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
139 5 0.04
140 109 0.96
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (140 bp):
CTGTTTCCAATCAACTTTGATATTTGCTAAAAGATGACCTGTTTCCAGTCAACTTTAATGATAGC
TGAAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTAAAAGATGACCAGTTTCCAGTCGATC
TTGATAACCG
Found at i:20738 original size:178 final size:179
Alignment explanation
Indices: 20540--20901 Score: 419
Period size: 178 Copynumber: 2.0 Consensus size: 179
20530 TTGAGGACTG
* * * *
20540 CTGAAAAATGACCAGTTTCCAGTCAACTTTGATAACCT-CTGAAAGATGACCTGTTTCCAGTCAA
1 CTGAAAAACGA-CTGTTTCCAATCAACTTTGAT-A-TTGCTGAAAGATGACCTGTTTCCAGTCAA
* * *
20604 CTTTGATAATTTG-TAAAAGATGACCTGTTTCCAGTCAGCTTTGATGATTGCTGAAAGATGACCT
63 CTTTGATGA-TTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGATTGCTGAAAGATGACCT
*
20668 GTTTCCAGTCAACTTTGATGACTGCTAAAAGATGACCTATTTCCAGTCGATCT
127 GTTTCCAGTCAACTTTGATAACTGCTAAAAGATGACCTATTTCCAGTCGATCT
* * *
20721 -TGATAACCG-CTGTTTCCAATCAACTTTGATGTTTGCTGAAAGATGACCTGTTTCCAGTCAACT
1 CTGAAAAACGACTGTTTCCAATCAACTTTGAT-ATTGCTGAAAGATGACCTGTTTCCAGTCAACT
* * * * * *
20784 TTAATGATAGCTGAAAGATGACCTGTTTCCGGTCAACTTTGATAATTGTTGAAAGATGACCAGTT
65 TTGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGATTGCTGAAAGATGACCTGTT
** * * * * * *
20849 TCCAGTCGTCCTTAATAACTTCTGAAAGATGACCTGTTTCTAGTCGATC-
130 TCCAGTCAACTTTGATAACTGCTAAAAGATGACCTATTTCCAGTCGATCT
20898 CTGA
1 CTGA
20902 GAACTGCTGA
Statistics
Matches: 152, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
177 3 0.02
178 143 0.94
180 6 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (179 bp):
CTGAAAAACGACTGTTTCCAATCAACTTTGATATTGCTGAAAGATGACCTGTTTCCAGTCAACTT
TGATGATTGCTGAAAGATGACCTGTTTCCAGTCAACTTTGATGATTGCTGAAAGATGACCTGTTT
CCAGTCAACTTTGATAACTGCTAAAAGATGACCTATTTCCAGTCGATCT
Found at i:22678 original size:16 final size:15
Alignment explanation
Indices: 22638--22680 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 15
22628 ACAGAGGTTG
22638 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
22653 ACAGAAAAACAATTAA
1 ACAG-AAAACAATTAA
22669 ACTAGAAAACAA
1 AC-AGAAAACAA
22681 AGCAGAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.15
16 20 0.77
17 2 0.08
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:26450 original size:28 final size:28
Alignment explanation
Indices: 26409--26507 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 28
26399 GCCATCCAGG
* * *
26409 GGGCACTTTGGTCATTTTGCACGTCCAA
1 GGGCATTTTGGTCATTTCGCACATCCAA
* * *
26437 GGGCATTTTAGTCA-TTCGCACATTCAG
1 GGGCATTTTGGTCATTTCGCACATCCAA
* * *
26464 GGGCATTTTGGTCA-TTGGCATATTCAA
1 GGGCATTTTGGTCATTTCGCACATCCAA
**
26491 GGGCACGTTGGTCATTT
1 GGGCATTTTGGTCATTT
26508 TAAGTTCACT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
27 44 0.76
28 14 0.24
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.34
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTCGCACATCCAA
Found at i:26467 original size:27 final size:27
Alignment explanation
Indices: 26434--26495 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
26424 TTTGCACGTC
26434 CAAGGGCATTTTAGTCATTCGCACATT
1 CAAGGGCATTTTAGTCATTCGCACATT
* * * *
26461 CAGGGGCATTTTGGTCATTGGCATATT
1 CAAGGGCATTTTAGTCATTCGCACATT
26488 CAAGGGCA
1 CAAGGGCA
26496 CGTTGGTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (27 bp):
CAAGGGCATTTTAGTCATTCGCACATT
Found at i:30032 original size:13 final size:13
Alignment explanation
Indices: 30014--30038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30004 AAAGGAAGAG
30014 GAAGAAGAAGTTA
1 GAAGAAGAAGTTA
30027 GAAGAAGAAGTT
1 GAAGAAGAAGTT
30039 CGACTAAGTA
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (13 bp):
GAAGAAGAAGTTA
Found at i:37903 original size:21 final size:21
Alignment explanation
Indices: 37877--37932 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
37867 ACTCACAAAG
37877 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
37898 AAGTTTCAAGCTCATTGGAGA
1 AAGTTTCAAGCTCATTGGAGA
*
37919 AGGTTTCAAGCTCA
1 AAGTTTCAAGCTCA
37933 ATTGAGTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (21 bp):
AAGTTTCAAGCTCATTGGAGA
Found at i:39905 original size:2 final size:2
Alignment explanation
Indices: 39898--39937 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39888 AAAACATTCA
39898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39938 TGAGTGTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40601 original size:24 final size:25
Alignment explanation
Indices: 40568--40619 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
40558 AAGAAGGAAA
*
40568 AAAAACCTTGCACTAGGGCAAGACT
1 AAAAACCTTGCACTAGGACAAGACT
* *
40593 AAAAA-CTTGTATTAGGACAAGACT
1 AAAAACCTTGCACTAGGACAAGACT
40617 AAA
1 AAA
40620 TCTCTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.19
Consensus pattern (25 bp):
AAAAACCTTGCACTAGGACAAGACT
Found at i:42609 original size:21 final size:22
Alignment explanation
Indices: 42572--42615 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
42562 TCACGGGTAA
*
42572 TTCGGGTTTCGGGTCATATGGG
1 TTCGGGTTTCGGGTCATACGGG
*
42594 TTCGGGTTT-TGGTCATACGGG
1 TTCGGGTTTCGGGTCATACGGG
42615 T
1 T
42616 CCCGGGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.09, C:0.14, G:0.39, T:0.39
Consensus pattern (22 bp):
TTCGGGTTTCGGGTCATACGGG
Found at i:42621 original size:22 final size:22
Alignment explanation
Indices: 42574--42632 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
42564 ACGGGTAATT
* *
42574 CGGGTTTCGGGTCATATGGGTT
1 CGGGTTTCGGGTCATACGGGTC
*
42596 CGGGTTT-TGGTCATACGGGTCC
1 CGGGTTTCGGGTCATACGGGT-C
42618 CGGGTCATTCGGGTC
1 CGGGT--TTCGGGTC
42633 TCAGGTTGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 11 0.38
22 12 0.41
24 2 0.07
25 4 0.14
ACGTcount: A:0.08, C:0.20, G:0.39, T:0.32
Consensus pattern (22 bp):
CGGGTTTCGGGTCATACGGGTC
Found at i:43320 original size:21 final size:20
Alignment explanation
Indices: 43299--43368 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 20
43289 TCATAATATA
43299 AATTTTATTGAATAAATGAT
1 AATTTTATTGAATAAATGAT
** * *
43319 AATGTAGAAT-AAGTAAAATTAT
1 AAT-TTTATTGAA-T-AAATGAT
*
43341 AAATTTTATTGAATAAAAGAT
1 -AATTTTATTGAATAAATGAT
43362 AATTTTA
1 AATTTTA
43369 ATCTATAATA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
20 12 0.33
21 9 0.25
22 10 0.28
23 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
AATTTTATTGAATAAATGAT
Found at i:46924 original size:46 final size:46
Alignment explanation
Indices: 46863--46952 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
46853 GTGCAGAAAA
* * *
46863 TCTCAAACAAGATGATTTTCCCCTTTTTGCCTTCAATTCTTATGGC
1 TCTCAAACAAAATGATTTTCCCCTTTCTGCCTTCAACTCTTATGGC
* **
46909 TCTCGAACAAAATGATTTTCTGCTTTCTGCCTTCAACTCTTATG
1 TCTCAAACAAAATGATTTTCCCCTTTCTGCCTTCAACTCTTATG
46953 CCTTCTCTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (46 bp):
TCTCAAACAAAATGATTTTCCCCTTTCTGCCTTCAACTCTTATGGC
Found at i:48241 original size:22 final size:23
Alignment explanation
Indices: 48205--48310 Score: 196
Period size: 23 Copynumber: 4.6 Consensus size: 23
48195 ATTATGTACT
48205 AAAAAGATCATTTTTTTTGTGAA
1 AAAAAGATCATTTTTTTTGTGAA
48228 AAAAAGATCATTTTTTTTGTGAA
1 AAAAAGATCATTTTTTTTGTGAA
48251 AAAAAGATCATTTTTTTTTGTGAA
1 AAAAAGATCA-TTTTTTTTGTGAA
48275 AAAAAGATCA-TTTTTTTGTGAA
1 AAAAAGATCATTTTTTTTGTGAA
48297 AAAAAGATCATTTT
1 AAAAAGATCATTTT
48311 CACATTGTAA
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
22 22 0.27
23 36 0.44
24 23 0.28
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (23 bp):
AAAAAGATCATTTTTTTTGTGAA
Found at i:49100 original size:41 final size:38
Alignment explanation
Indices: 49017--49105 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 38
49007 AGTGAGCTTC
*
49017 ATAATTTAATTCAAGGGTCTTGACTTGATCTTGAATCA
1 ATAATTTGATTCAAGGGTCTTGACTTGATCTTGAATCA
**
49055 ATAATTTGATTCAAGGGTCTTGATGACTTGATCTTGAATTG
1 ATAATTTGATTCAAGGGTC-T--TGACTTGATCTTGAATCA
49096 ATAATTTGAT
1 ATAATTTGAT
49106 GGCTTGAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 18 0.40
39 1 0.02
41 26 0.58
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (38 bp):
ATAATTTGATTCAAGGGTCTTGACTTGATCTTGAATCA
Found at i:49234 original size:31 final size:32
Alignment explanation
Indices: 49179--49240 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
49169 TTCAAATAAG
49179 TTGATGAAGATCAAAATAATAATTTTCTTGAATA
1 TTGATGAAGATC-AAATAATAA-TTTCTTGAATA
49213 TTGATGAAGATC-AA-AATAATTTCTTGAA
1 TTGATGAAGATCAAATAATAATTTCTTGAA
49241 AGCTTCAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 9 0.32
31 5 0.18
32 2 0.07
34 12 0.43
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (32 bp):
TTGATGAAGATCAAATAATAATTTCTTGAATA
Found at i:49369 original size:28 final size:28
Alignment explanation
Indices: 49334--49389 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
49324 ATTCTTCAAG
*
49334 AATAATTCTAC-AATAATTTTGGATCTTC
1 AATAATTCT-CTAATAACTTTGGATCTTC
49362 AATAATTCTCTAATAACTTTGGATCTTC
1 AATAATTCTCTAATAACTTTGGATCTTC
49390 TTTGATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (28 bp):
AATAATTCTCTAATAACTTTGGATCTTC
Done.