Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019033.1 Corchorus olitorius cultivar O-4 contig19066, 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: 48433
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:675 original size:25 final size:25
Alignment explanation
Indices: 634--683 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
624 CAAGCCGAGC
634 TAAGGTCTTCCGAATAAAAACAAGG
1 TAAGGTCTTCCGAATAAAAACAAGG
* *
659 TAAGGTCTTTCGGATAAAAACAAGG
1 TAAGGTCTTCCGAATAAAAACAAGG
684 GGCGTTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (25 bp):
TAAGGTCTTCCGAATAAAAACAAGG
Found at i:1502 original size:30 final size:30
Alignment explanation
Indices: 1463--1532 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
1453 ACATGTCTCT
*
1463 CTACTTACAAAAAGGGATCAATTTGGTCCCC
1 CTACTTACAAAAA-CGATCAATTTGGTCCCC
* *
1494 CTAC-TACAAAAACTATCAATTTGGTCCCT
1 CTACTTACAAAAACGATCAATTTGGTCCCC
1523 CTACTTACAA
1 CTACTTACAA
1533 TTTGGTGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 18 0.51
30 13 0.37
31 4 0.11
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (30 bp):
CTACTTACAAAAACGATCAATTTGGTCCCC
Found at i:1817 original size:31 final size:29
Alignment explanation
Indices: 1780--1901 Score: 113
Period size: 31 Copynumber: 4.0 Consensus size: 29
1770 AATATATAAT
1780 CAATTGACAGATTTTGTTAAGTAGAGGGAC
1 CAATTGACAGATTTTG-TAAGTAGAGGGAC
* **
1810 TCAATTGACACCAAATTGTAAGTAGAGGGAC
1 -CAATTGACA-GATTTTGTAAGTAGAGGGAC
1841 CAGATTGACAG-TTTT-TATAGTAGAGGGAC
1 CA-ATTGACAGATTTTGTA-AGTAGAGGGAC
***
1870 CAAATTGATCCTTTTTTGTAAGTAGAGGGAC
1 C-AATTGA-CAGATTTTGTAAGTAGAGGGAC
1901 C
1 C
1902 TGTACGGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.03
29 19 0.25
30 4 0.05
31 45 0.59
32 6 0.08
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (29 bp):
CAATTGACAGATTTTGTAAGTAGAGGGAC
Found at i:1871 original size:29 final size:31
Alignment explanation
Indices: 1828--1901 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
1818 CACCAAATTG
*
1828 TAAGTAGAGGGACCAGATTGA-CAGTTTTTA
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
** *
1858 T-AGTAGAGGGACCAAATTGATCCTTTTTTG
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
1888 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
1902 TGTACGGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 18 0.47
30 8 0.21
31 12 0.32
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCAGTTTTTA
Found at i:2052 original size:42 final size:44
Alignment explanation
Indices: 2001--2094 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
1991 AGTGCATTAC
* * *
2001 CTAA-ATTCTACT-T-CATCTCTAGGTTATTTATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
2042 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
2087 CTAATATT
1 CTAATATT
2095 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 33 0.72
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:4128 original size:22 final size:23
Alignment explanation
Indices: 4103--4148 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
4093 TAATATCCAC
4103 ACACAATTAAT-ATGTAAT-TAAA
1 ACACAATTAATCATG-AATATAAA
*
4125 ACACACTTAATCATGAATATAAA
1 ACACAATTAATCATGAATATAAA
4148 A
1 A
4149 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATGAATATAAA
Found at i:4774 original size:24 final size:24
Alignment explanation
Indices: 4742--4789 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4732 AATGTTGGAG
*
4742 TCCCTATCGATATGATAAAGATAT
1 TCCCGATCGATATGATAAAGATAT
*
4766 TCCCGATCGATATGATAAGGATAT
1 TCCCGATCGATATGATAAAGATAT
4790 CGGATCGAAT
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:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (24 bp):
TCCCGATCGATATGATAAAGATAT
Found at i:6350 original size:2 final size:2
Alignment explanation
Indices: 6339--6384 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
6329 TAACATTTAG
*
6339 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
6381 TA TA
1 TA TA
6385 AAAGTACGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7415 original size:19 final size:19
Alignment explanation
Indices: 7400--7438 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
7390 TACTATTATT
7400 TTTTGAATTTAATATTTTA
1 TTTTGAATTTAATATTTTA
* *
7419 TTTTTAATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
7439 AATGTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTGAATTTAATATTTTA
Found at i:7437 original size:20 final size:20
Alignment explanation
Indices: 7399--7438 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7389 TTACTATTAT
7399 TTTTTGAATTTAATATTTTA
1 TTTTTGAATTTAATATTTTA
*
7419 TTTTT-AATTTCAATTTTTTA
1 TTTTTGAATTT-AATATTTTA
7439 AATGTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTGAATTTAATATTTTA
Found at i:7661 original size:22 final size:22
Alignment explanation
Indices: 7603--8233 Score: 219
Period size: 22 Copynumber: 28.8 Consensus size: 22
7593 TTGTCTCTAT
*
7603 GAGGTTATCAAAATTTCAT-AA
1 GAGGTTATCAAAATTTCATGAG
*
7624 GATGGTTAAT-ATAATTTCATGAG
1 GA-GGTT-ATCAAAATTTCATGAG
* * * *
7647 GAGGTTATCGAAATTCCATAAT
1 GAGGTTATCAAAATTTCATGAG
* * *
7669 GTGGTTACCAAAATTTCGT-ATG
1 GAGGTTATCAAAATTTCATGA-G
*
7691 GAAGTTATCAAAATTTCATG-G
1 GAGGTTATCAAAATTTCATGAG
* *
7712 GAAGGTTATCAAAATTTCATAAT
1 G-AGGTTATCAAAATTTCATGAG
* * *
7735 GTGGTTACCAAAATTTCATAGTAT
1 GAGGTTATCAAAATTTCAT-G-AG
* * *
7759 CAGGTTATTAAAATTTC-TTAG
1 GAGGTTATCAAAATTTCATGAG
*
7780 GAAGGTTATTGAAAA-TTCAT-AG
1 G-AGGTTA-TCAAAATTTCATGAG
* * *
7802 TGTGGTTAACAAAATTTCATAAG
1 -GAGGTTATCAAAATTTCATGAG
* * *
7825 GAGGTTATTAATATTTCATGTG
1 GAGGTTATCAAAATTTCATGAG
* *
7847 GAGGTTATCAAAATTTTAT-ACT
1 GAGGTTATCAAAATTTCATGA-G
*
7869 GTGGTTATCAAAATTTCAT-ATG
1 GAGGTTATCAAAATTTCATGA-G
* * * *
7891 AAGATTATAAAAGTCTCAATTTCATAAG
1 GAGGTTAT-CAA-----AATTTCATGAG
* *
7919 GA-G-TACCAAAATTTGAT-AG
1 GAGGTTATCAAAATTTCATGAG
* * *
7938 AAGGTTAT-AAAATCTCATAAG
1 GAGGTTATCAAAATTTCATGAG
* *
7959 GA-G-TACCAAAAATTTCATAAG
1 GAGGTTATC-AAAATTTCATGAG
* *
7980 GA-G-TACCAAAATTTCATAAG
1 GAGGTTATCAAAATTTCATGAG
* *
8000 GA-G-TACCAAAATTTGAT-AG
1 GAGGTTATCAAAATTTCATGAG
* *
8019 AAGGTTATC-AAATCTCAT-A-
1 GAGGTTATCAAAATTTCATGAG
* *
8038 GAGTTTTTATCGAAATTTCAT-AG
1 GAG--GTTATCAAAATTTCATGAG
8061 AGATCGGTTTATCAAAATTT-AT-AG
1 -GA--GG-TTATCAAAATTTCATGAG
*
8085 GAAGATTATCAAAATTTCAT-AG
1 G-AGGTTATCAAAATTTCATGAG
** *
8107 TGTTGTTATCAAAATTTCA-AAG
1 -GAGGTTATCAAAATTTCATGAG
* * *
8129 CAAGGTTATCAAAATTAT-ATAAT
1 -GAGGTTATCAAAATT-TCATGAG
* *
8152 GTGATTATCAAAATTTCATAGAG
1 GAGGTTATCAAAATTTCAT-GAG
* * *
8175 G-GGTCAACAAAATTTTAT-A-
1 GAGGTTATCAAAATTTCATGAG
* *
8194 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCATGAG
*
8216 GAGGTTATCAAATTTTCA
1 GAGGTTATCAAAATTTCA
8234 AAATGTGATT
Statistics
Matches: 463, Mismatches: 97, Indels: 99
0.70 0.15 0.15
Matches are distributed among these distances:
19 11 0.02
20 70 0.15
21 58 0.13
22 250 0.54
23 25 0.05
24 22 0.05
25 13 0.03
26 3 0.01
28 10 0.02
29 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATGAG
Found at i:7718 original size:66 final size:65
Alignment explanation
Indices: 7605--7902 Score: 282
Period size: 66 Copynumber: 4.5 Consensus size: 65
7595 GTCTCTATGA
* * * * * * *
7605 GGTTATCAAAATTTCATAAGATGGTTAATATAATTTCATGAGGAGGTTATCGAAATTCCATAATG
1 GGTTACCAAAATTTCATATGA-AGTTATTAAAATTTCATGAGGAGGTTATCAAAATTTCATAATG
7670 T
65 T
* *
7671 GGTTACCAAAATTTCGTATGGAAGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTCATAAT
1 GGTTACCAAAATTTCATAT-GAAGTTATTAAAATTTCATGAGG-AGGTTATCAAAATTTCATAAT
7735 GT
64 GT
* *
7737 GGTTACCAAAATTTCATA-GTATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAAA-TTCA
1 GGTTACCAAAATTTCATATG-A--A-GTTATTAAAATTTCATGAGG-AGGTTA-TCAAAATTTCA
*
7799 TAGTGT
60 TAATGT
* * * * * * *
7805 GGTTAACAAAATTTCATAAGGAGGTTATTAATATTTCATGTGGAGGTTATCAAAATTTTATACTG
1 GGTTACCAAAATTTCAT-ATGAAGTTATTAAAATTTCATGAGGAGGTTATCAAAATTTCATAATG
7870 T
65 T
*
7871 GGTTATCAAAATTTCATATGAAGATTA-TAAAA
1 GGTTACCAAAATTTCATATGAAG-TTATTAAAA
7903 GTCTCAATTT
Statistics
Matches: 193, Mismatches: 26, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
64 1 0.01
65 16 0.08
66 114 0.59
67 7 0.04
68 47 0.24
69 7 0.04
70 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (65 bp):
GGTTACCAAAATTTCATATGAAGTTATTAAAATTTCATGAGGAGGTTATCAAAATTTCATAATGT
Found at i:7967 original size:40 final size:40
Alignment explanation
Indices: 7912--8037 Score: 166
Period size: 40 Copynumber: 3.1 Consensus size: 40
7902 AGTCTCAATT
7912 TCATAAGGAGTACCAAAATTTGATAGAAGGTTATAAAATC
1 TCATAAGGAGTACCAAAATTTGATAGAAGGTTATAAAATC
* * * *
7952 TCATAAGGAGTACCAAAAATTTCAT--AAGGAGTACCAAAATT
1 TCATAAGGAGTACC-AAAATTTGATAGAAGG-TTA-TAAAATC
*
7993 TCATAAGGAGTACCAAAATTTGATAGAAGGTTATCAAATC
1 TCATAAGGAGTACCAAAATTTGATAGAAGGTTATAAAATC
8033 TCATA
1 TCATA
8038 GAGTTTTTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
39 4 0.06
40 34 0.47
41 30 0.42
42 4 0.06
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (40 bp):
TCATAAGGAGTACCAAAATTTGATAGAAGGTTATAAAATC
Found at i:7969 original size:20 final size:20
Alignment explanation
Indices: 7908--8013 Score: 135
Period size: 20 Copynumber: 5.2 Consensus size: 20
7898 TAAAAGTCTC
7908 AATTTCATAAGGAGTACCAA
1 AATTTCATAAGGAGTACCAA
* * *
7928 AATTTGATAGAAGG-TTA-TAA
1 AATTTCAT--AAGGAGTACCAA
*
7948 AATCTCATAAGGAGTACCAAA
1 AATTTCATAAGGAGTACC-AA
7969 AATTTCATAAGGAGTACCAA
1 AATTTCATAAGGAGTACCAA
7989 AATTTCATAAGGAGTACCAA
1 AATTTCATAAGGAGTACCAA
8009 AATTT
1 AATTT
8014 GATAGAAGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.05
19 2 0.03
20 42 0.58
21 21 0.29
22 4 0.05
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (20 bp):
AATTTCATAAGGAGTACCAA
Found at i:8300 original size:22 final size:21
Alignment explanation
Indices: 8273--8595 Score: 130
Period size: 22 Copynumber: 15.0 Consensus size: 21
8263 ATTTCTGGGG
8273 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
* *
8294 ATGGTTATC-AAA-TT-A-GGA
1 A-GGTTATCAAAATTTCATAGT
* * *
8312 AGGTTATTAAACTTTTATTA-T
1 AGGTTATCAAAATTTCA-TAGT
* * *
8333 GGAGTAATCAAAATTTCATATGA
1 AG-GTTATCAAAATTTCATA-GT
*
8356 AGGTTATCAAAATTTCACAGTTT
1 AGGTTATCAAAATTTCATAG--T
*
8379 A-GTTTTCAAAATTTCATAAG-
1 AGGTTATCAAAATTTCAT-AGT
8399 AGGGTTATCAAAATTTCATAATATGT
1 A-GGTTATCAAAATTTC---ATA-GT
* * * *
8425 AGATTAACAAAATTACATAAT
1 AGGTTATCAAAATTTCATAGT
** * *
8446 GAGGTTATCAAAAAATCATGGGG
1 -AGGTTATCAAAATTTCAT-AGT
8469 AGGTTATCAAAA-TT--T-GT
1 AGGTTATCAAAATTTCATAGT
* **
8486 A-GTTATCAAGATTTCATAAAC
1 AGGTTATCAAAATTTCAT-AGT
* *
8507 AGGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATA-GT
* *
8529 AGGTTTATCAAAATTTTATAGGG
1 AGG-TTATCAAAATTTCATA-GT
* *
8552 AGGTTTATCAAAATTTTATAGGA
1 AGG-TTATCAAAATTTCATA-GT
8575 AGGTTTATCAAAATTTCATAG
1 AGG-TTATCAAAATTTCATAG
8596 CGAGATTGTA
Statistics
Matches: 231, Mismatches: 42, Indels: 57
0.70 0.13 0.17
Matches are distributed among these distances:
16 9 0.04
17 10 0.04
18 4 0.02
19 5 0.02
20 4 0.02
21 12 0.05
22 106 0.46
23 64 0.28
24 1 0.00
25 15 0.06
26 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGT
Found at i:8540 original size:23 final size:23
Alignment explanation
Indices: 8510--8595 Score: 154
Period size: 23 Copynumber: 3.7 Consensus size: 23
8500 CATAAACAGG
8510 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
8533 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
8556 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
8579 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
8596 CGAGATTGTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:8631 original size:21 final size:21
Alignment explanation
Indices: 8579--8634 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
8569 ATAGGAAGGT
8579 TTATCAAAATTTCATAGCGAGA
1 TTATC-AAATTTCATAGCGAGA
* * *
8601 TTGT-ACAATTTCATAGTGTGA
1 TTATCA-AATTTCATAGCGAGA
8622 TTATCAAATTTCA
1 TTATCAAATTTCA
8635 GAATGTGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
TTATCAAATTTCATAGCGAGA
Found at i:8816 original size:22 final size:22
Alignment explanation
Indices: 8791--8837 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
8781 CAAAATTCCT
* * *
8791 TAAGGAGGTTAACAAAATTTTA
1 TAAGAAGGTTAAAAAAAATTTA
8813 TAAGAAGGTTAAAAAAAATTTA
1 TAAGAAGGTTAAAAAAAATTTA
8835 TAA
1 TAA
8838 AAATGTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.30
Consensus pattern (22 bp):
TAAGAAGGTTAAAAAAAATTTA
Found at i:9008 original size:2 final size:2
Alignment explanation
Indices: 9001--9025 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8991 ATAAAACTAG
9001 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 T
9026 TCTTCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10935 original size:14 final size:14
Alignment explanation
Indices: 10904--10934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
10894 TTCTCTGAGA
10904 TTTATTATTTTATT
1 TTTATTATTTTATT
10918 TTTACTTATTTTATT
1 TTTA-TTATTTTATT
10933 TT
1 TT
10935 ATTTTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTATTTTATT
Found at i:11016 original size:15 final size:14
Alignment explanation
Indices: 10992--11034 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
10982 TTCTCTGAGA
10992 TTTATTATTTTATT
1 TTTATTATTTTATT
11006 TTTACTTATTTTA-T
1 TTTA-TTATTTTATT
*
11020 TTTATT-TTTCATT
1 TTTATTATTTTATT
11033 TT
1 TT
11035 ATTGCCCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.15
13 5 0.19
14 9 0.35
15 8 0.31
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTATTTTATT
Found at i:22589 original size:8 final size:8
Alignment explanation
Indices: 22557--22606 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
22547 ATTAATATGC
22557 TATTTATAA
1 TATTTAT-A
22566 TATTT-TA
1 TATTTATA
22573 -ATTCT-TA
1 TATT-TATA
22580 TATTTATA
1 TATTTATA
22588 TATTTATA
1 TATTTATA
*
22596 TATATATA
1 TATTTATA
22604 TAT
1 TAT
22607 AGAGGCCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
6 3 0.08
7 5 0.14
8 24 0.65
9 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:26310 original size:42 final size:42
Alignment explanation
Indices: 26263--26346 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
26253 AAAATTAAGT
*
26263 CAAATTGCCCCTTACCGTCAATGCCGTTAGTCACGTGACGGC
1 CAAATTACCCCTTACCGTCAATGCCGTTAGTCACGTGACGGC
26305 CAAATTACCCCTTACCGTCAATGCCGTTAGTCACGTGACGGC
1 CAAATTACCCCTTACCGTCAATGCCGTTAGTCACGTGACGGC
26347 ACGTGACTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (42 bp):
CAAATTACCCCTTACCGTCAATGCCGTTAGTCACGTGACGGC
Found at i:27383 original size:15 final size:16
Alignment explanation
Indices: 27358--27387 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27348 TTGACCGGAT
27358 TTTTCTTATTTATTTA
1 TTTTCTTATTTATTTA
27374 TTTT-TTATTTATTT
1 TTTTCTTATTTATTT
27388 TTGTTTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTATTTATTTA
Found at i:28277 original size:58 final size:58
Alignment explanation
Indices: 28212--28327 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
28202 AGACATCATC
* *
28212 GTTGTTCTTCTTTTATATAACATCGATTGTATATTTGACATGTTGAAGTTATTTTTTT
1 GTTGTTCTTCTTTCATATAACATCGATTGTATATTTGACATGTTGAAGTCATTTTTTT
28270 GTTGTTCTTCTTTCATATAACATCGATTGTATATTTGACATGTTGAAGTCATTTTTTT
1 GTTGTTCTTCTTTCATATAACATCGATTGTATATTTGACATGTTGAAGTCATTTTTTT
28328 CAATTGTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.53
Consensus pattern (58 bp):
GTTGTTCTTCTTTCATATAACATCGATTGTATATTTGACATGTTGAAGTCATTTTTTT
Found at i:28605 original size:11 final size:11
Alignment explanation
Indices: 28589--28613 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28579 AAAAATTTAA
28589 ATTTAAAAAAT
1 ATTTAAAAAAT
28600 ATTTAAAAAAT
1 ATTTAAAAAAT
28611 ATT
1 ATT
28614 ATTTTATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAAAAAAT
Found at i:29608 original size:22 final size:22
Alignment explanation
Indices: 29562--29620 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
29552 AAACCATAAA
*
29562 ATGAAAATTTGATAATCTCCAT
1 ATGAAATTTTGATAATCTCCAT
*
29584 ATGAAATTTTGATAATCT-TATT
1 ATGAAATTTTGATAATCTCCA-T
*
29606 ATGGAATTTTGATAA
1 ATGAAATTTTGATAA
29621 CCACACAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
ATGAAATTTTGATAATCTCCAT
Found at i:37582 original size:40 final size:40
Alignment explanation
Indices: 37533--37614 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
37523 CCAAGAAAAT
*
37533 AACATTCTCTTGTCATTAACCAAGAAAAATGCAAGAATCA
1 AACAATCTCTTGTCATTAACCAAGAAAAATGCAAGAATCA
37573 AACAATCTCTTGTCATTAACCAAGAAAAATGCAAGAATCA
1 AACAATCTCTTGTCATTAACCAAGAAAAATGCAAGAATCA
37613 AA
1 AA
37615 TTAACAATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.23
Consensus pattern (40 bp):
AACAATCTCTTGTCATTAACCAAGAAAAATGCAAGAATCA
Found at i:41640 original size:49 final size:48
Alignment explanation
Indices: 41559--41703 Score: 179
Period size: 49 Copynumber: 3.0 Consensus size: 48
41549 CACTCAAAGC
* *
41559 AATCTTTTACATTTCC-TGCACTTTTTCTCAATTTTTACAACAAAATTG
1 AATCATTTACTTTTCCTTGCACTTTTTCTCAATTTTTA-AACAAAATTG
*
41607 AAT-ATTTATTTTTCCTTGCACATTTTTCTCAATTTTTAAGACAAAATTG
1 AATCATTTACTTTTCCTTGCAC-TTTTTCTCAATTTTTAA-ACAAAATTG
* * * *
41656 -ATCATTTACTTTTCATTGTACTTTTTATCAATTTTTATACAAAATTG
1 AATCATTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAACAAAATTG
41703 A
1 A
41704 TTGGCACGCT
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
47 18 0.21
48 26 0.31
49 40 0.48
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (48 bp):
AATCATTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAACAAAATTG
Found at i:43411 original size:91 final size:86
Alignment explanation
Indices: 43195--43501 Score: 383
Period size: 91 Copynumber: 3.6 Consensus size: 86
43185 TTCTTTGTGT
* * * * *
43195 TCTAACTATTAGCAACTAACCATTTTGATTTATGATTTAGTTTGT-GTATTCTTTCATTGA-TAT
1 TCTAACCATTACCTACTAACCATTTTAATTTATGATTTAGTTTGTGGTATTCTCTCATTGATTAT
43258 ATTTAGATATAAA-TTTATGC
66 ATTTAGATATAAAGTTTATGC
* **
43278 TCTAACCATTACCTACTAACCATTTTGATTTATGAGCTAGTTTGTGGTATTCTCTCATTGATATA
1 TCTAACCATTACCTACTAACCATTTTAATTTATGATTTAGTTTGTGGTATTCTCTCATTG----A
43343 TTAAATATTTAGATATAAAGTTTATGC
62 TT--ATATTTAGATATAAAGTTTATGC
* * *
43370 TCTAACCATTACCTA-TGACCATTCTT-CTTTATGATTTAGTTTGTGGTATTCTCTCATTGGTT-
1 TCTAACCATTACCTACTAACCATT-TTAATTTATGATTTAGTTTGTGGTATTCTCTCATTGATTA
* *
43432 TATTTAGTTATAAAGTTTATCC
65 TATTTAGATATAAAGTTTATGC
*
43454 TCTAACCATTACCTACTAACCATTTTAATTTATGATTTAGCTTGTGGT
1 TCTAACCATTACCTACTAACCATTTTAATTTATGATTTAGTTTGTGGT
43502 TTGAATTGTG
Statistics
Matches: 196, Mismatches: 16, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
83 40 0.20
84 50 0.26
85 26 0.13
87 2 0.01
88 1 0.01
89 1 0.01
91 52 0.27
92 24 0.12
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (86 bp):
TCTAACCATTACCTACTAACCATTTTAATTTATGATTTAGTTTGTGGTATTCTCTCATTGATTAT
ATTTAGATATAAAGTTTATGC
Found at i:46969 original size:43 final size:42
Alignment explanation
Indices: 46904--46990 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 42
46894 TGTGTGGCGA
46904 AACTCTTACATGTATTCCCAAGCTCTAATTTGAAGCTCCTAAG
1 AACTCTTACATGTATTCCCAAGCTCTAATTTGAAGCTCC-AAG
*
46947 AACTCTTACATGTATTCTCAAGCTCTAATTTGAAGCTCCAAG
1 AACTCTTACATGTATTCCCAAGCTCTAATTTGAAGCTCCAAG
46989 AA
1 AA
46991 GTCATTGACC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (42 bp):
AACTCTTACATGTATTCCCAAGCTCTAATTTGAAGCTCCAAG
Found at i:46988 original size:20 final size:20
Alignment explanation
Indices: 46921--46988 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
46911 ACATGTATTC
46921 CCAAGCTCTAATTTGAAGCT
1 CCAAGCTCTAATTTGAAGCT
* **
46941 CCTAAGAACTCTTACATGT-ATTCT
1 CC-AAG--CTC-TA-ATTTGAAGCT
46965 -CAAGCTCTAATTTGAAGCT
1 CCAAGCTCTAATTTGAAGCT
46984 CCAAG
1 CCAAG
46989 AAGTCATTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
18 3 0.09
19 5 0.14
20 9 0.26
21 3 0.09
22 3 0.09
23 4 0.11
24 5 0.14
25 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (20 bp):
CCAAGCTCTAATTTGAAGCT
Found at i:47906 original size:15 final size:15
Alignment explanation
Indices: 47886--47934 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
47876 GTTGTTATTC
*
47886 TTCTTCTCCTTTTCG
1 TTCTTCTCCTTCTCG
*
47901 TTCTTCTTCTTCTCG
1 TTCTTCTCCTTCTCG
* * *
47916 TTATTCTCTTTCTCC
1 TTCTTCTCCTTCTCG
47931 TTCT
1 TTCT
47935 CTAGGTGGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.02, C:0.33, G:0.04, T:0.61
Consensus pattern (15 bp):
TTCTTCTCCTTCTCG
Done.